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= psy8689
(72 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3QT1|I Chain I, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
Length = 133
Score = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 26/44 (59%), Positives = 31/44 (70%), Gaps = 2/44 (4%)
Query: 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72
++ +CPKC F Q+Q RSADEPMTTFYKC N CG RW+E
Sbjct: 91 SDRECPKCHSRENVFFQLQIRSADEPMTTFYKCVN--CGHRWKE 132
>pdb|1QYP|A Chain A, Thermococcus Celer Rpb9, Nmr, 25 Structures
Length = 57
Score = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/49 (48%), Positives = 32/49 (65%), Gaps = 2/49 (4%)
Query: 24 ENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72
+ + TT+ CPKC + AY+ ++QTR+ DEP T FYKC KCG WR
Sbjct: 9 KTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKC--TKCGHTWRS 55
>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex
Length = 309
Score = 46.6 bits (109), Expect = 4e-06, Method: Composition-based stats.
Identities = 23/52 (44%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 20 AAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71
A E T C KC+ + + Q+QTRSADEP+TTF C CG RW+
Sbjct: 258 GATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTC--EACGNRWK 307
>pdb|1TFI|A Chain A, A Novel Zn Finger Motif In The Basal Transcriptional
Machinery: Three-Dimensional Nmr Studies Of The
Nucleic- Acid Binding Domain Of Transcriptional
Elongation Factor Tfiis
Length = 50
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/39 (53%), Positives = 26/39 (66%), Gaps = 2/39 (5%)
Query: 33 CPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71
C KC+ + Q+QTRSADEPMTTF C +CG RW+
Sbjct: 12 CGKCKKKNCTYTQVQTRSADEPMTTFVVC--NECGNRWK 48
>pdb|1Y1V|S Chain S, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|S Chain S, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
Length = 179
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/39 (51%), Positives = 26/39 (66%), Gaps = 2/39 (5%)
Query: 33 CPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71
C KC+ + + Q+QTRSADEP+TTF C CG RW+
Sbjct: 141 CGKCKEKKVSYYQLQTRSADEPLTTFCTC--EACGNRWK 177
>pdb|3GTM|S Chain S, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
Length = 173
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/39 (48%), Positives = 25/39 (64%), Gaps = 2/39 (5%)
Query: 33 CPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71
C KC+ + + Q+QTRSAD P+TTF C CG RW+
Sbjct: 135 CGKCKEKKVSYYQLQTRSADHPLTTFCTC--EACGNRWK 171
>pdb|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate
Length = 178
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/39 (46%), Positives = 24/39 (61%), Gaps = 2/39 (5%)
Query: 33 CPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71
C KC+ + + Q+QTRSA P+TTF C CG RW+
Sbjct: 140 CGKCKEKKVSYYQLQTRSAAAPLTTFCTC--EACGNRWK 176
>pdb|3H0G|I Chain I, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|U Chain U, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 113
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 16 VMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72
V A+ + ++++CP+C A F Q +R D MT Y C + CGF + E
Sbjct: 58 VSHDASTDPTLPRSDKECPRCHQHEAVFYQTHSRRGDTMMTLIYVC--VHCGFAFEE 112
>pdb|1I3Q|I Chain I, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|I Chain I, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|I Chain I, Rna Polymerase Ii Elongation Complex
pdb|1K83|I Chain I, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|I Chain I, Wild Type Rna Polymerase Ii
pdb|1NT9|I Chain I, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|I Chain I, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|I Chain I, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|I Chain I, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|I Chain I, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|I Chain I, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|I Chain I, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|I Chain I, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|I Chain I, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|I Chain I, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|I Chain I, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|I Chain I, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|I Chain I, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|I Chain I, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|I Chain I, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|I Chain I, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|I Chain I, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|I Chain I, 12-Subunit Rna Polymerase Ii
pdb|2E2H|I Chain I, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|I Chain I, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|I Chain I, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|I Chain I, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|I Chain I, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|I Chain I, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|I Chain I, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|I Chain I, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|U Chain U, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|I Chain I, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|I Chain I, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|I Chain I, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|I Chain I, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|I Chain I, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|I Chain I, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|I Chain I, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|I Chain I, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|I Chain I, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|I Chain I, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|I Chain I, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|I Chain I, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|I Chain I, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|I Chain I, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|I Chain I, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|J Chain J, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|I Chain I, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|U Chain U, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|I Chain I, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|I Chain I, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|I Chain I, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|I Chain I, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|I Chain I, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|I Chain I, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|I Chain I, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|I Chain I, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|I Chain I, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|I Chain I, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|I Chain I, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|I Chain I, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|I Chain I, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3RZD|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|I Chain I, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|I Chain I, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|I Chain I, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|I Chain I, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|I Chain I, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|I Chain I, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|3J0K|I Chain I, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|I Chain I, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|I Chain I, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|I Chain I, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|I Chain I, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 122
Score = 29.6 bits (65), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKC 61
++ +CPKC F Q Q R D M F+ C
Sbjct: 71 SDRECPKCHSRENVFFQSQQRRKDTSMVLFFVC 103
>pdb|3CER|A Chain A, Crystal Structure Of The Exopolyphosphatase-Like Protein
Q8g5j2. Northeast Structural Genomics Consortium Target
Blr13
pdb|3CER|B Chain B, Crystal Structure Of The Exopolyphosphatase-Like Protein
Q8g5j2. Northeast Structural Genomics Consortium Target
Blr13
pdb|3CER|C Chain C, Crystal Structure Of The Exopolyphosphatase-Like Protein
Q8g5j2. Northeast Structural Genomics Consortium Target
Blr13
pdb|3CER|D Chain D, Crystal Structure Of The Exopolyphosphatase-Like Protein
Q8g5j2. Northeast Structural Genomics Consortium Target
Blr13
pdb|3CER|E Chain E, Crystal Structure Of The Exopolyphosphatase-Like Protein
Q8g5j2. Northeast Structural Genomics Consortium Target
Blr13
Length = 343
Score = 26.6 bits (57), Expect = 3.8, Method: Composition-based stats.
Identities = 13/34 (38%), Positives = 15/34 (44%)
Query: 8 IKPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRA 41
I P ID V GGA W V + K +H A
Sbjct: 284 IHPGRIDVVGGGAVVWSRVLARVSEAAKADHGEA 317
>pdb|1NAF|A Chain A, Crystal Structure Of The Human Gga1 Gat Domain
Length = 158
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 2/51 (3%)
Query: 15 HVMGGAAAWENVDTTEEKCPKCEHPRAYFMQI--QTRSADEPMTTFYKCCN 63
H GGAAA + D +E +CE R ++ T DE + + +
Sbjct: 79 HSQGGAAAGSSEDLXKELYQRCERXRPTLFRLASDTEDNDEALAEILQAND 129
>pdb|3IQW|A Chain A, Amppnp Complex Of C. Therm. Get3
pdb|3IQW|B Chain B, Amppnp Complex Of C. Therm. Get3
pdb|3IQX|A Chain A, Adp Complex Of C.Therm. Get3 In Closed Form
pdb|3IQX|B Chain B, Adp Complex Of C.Therm. Get3 In Closed Form
Length = 334
Score = 26.2 bits (56), Expect = 4.7, Method: Composition-based stats.
Identities = 12/50 (24%), Positives = 23/50 (46%)
Query: 13 IDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCC 62
++ ++GG+ N T + K + R ++ + DE +TTF C
Sbjct: 180 LNGILGGSGTLPNGQTLSDVMEKLDSLRVTISEVNAQFKDERLTTFVCVC 229
>pdb|1X79|A Chain A, Crystal Structure Of Human Gga1 Gat Domain Complexed
With The Gat-Binding Domain Of Rabaptin5
Length = 98
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 2/51 (3%)
Query: 13 IDHVMGGAAAWENVDTTEEKCPKCE--HPRAYFMQIQTRSADEPMTTFYKC 61
+ H GGAAA + D +E +CE P + + T DE + +
Sbjct: 29 MSHSQGGAAAGSSEDLMKELYQRCERMRPTLFRLASDTEDNDEALAEILQA 79
>pdb|1NWM|X Chain X, Gat Domain Of Human Gga1
Length = 142
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 2/51 (3%)
Query: 13 IDHVMGGAAAWENVDTTEEKCPKCE--HPRAYFMQIQTRSADEPMTTFYKC 61
+ H GGAAA + D +E +CE P + + T DE + +
Sbjct: 73 MSHSQGGAAAGSSEDLMKELYQRCERMRPTLFRLASDTEDNDEALAEILQA 123
>pdb|1O3X|A Chain A, Crystal Structure Of Human Gga1 Gat Domain
Length = 140
Score = 25.8 bits (55), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 2/51 (3%)
Query: 13 IDHVMGGAAAWENVDTTEEKCPKCE--HPRAYFMQIQTRSADEPMTTFYKC 61
+ H GGAAA + D +E +CE P + + T DE + +
Sbjct: 68 MSHSQGGAAAGSSEDLMKELYQRCERMRPTLFRLASDTEDNDEALAEILQA 118
>pdb|1OXZ|A Chain A, Crystal Structure Of The Human Gga1 Gat Domain
Length = 186
Score = 25.8 bits (55), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 13 IDHVMGGAAAWENVDTTEEKCPKCE--HPRAYFMQIQTRSADEPMTTFYKCCN 63
+ H GGAAA + D +E +CE P + + T DE + + +
Sbjct: 93 MSHSQGGAAAGSSEDLMKELYQRCERMRPTLFRLASDTEDNDEALAEILQAND 145
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
0.324 0.136 0.473
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,328,390
Number of Sequences: 62578
Number of extensions: 66650
Number of successful extensions: 236
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 217
Number of HSP's gapped (non-prelim): 18
length of query: 72
length of database: 14,973,337
effective HSP length: 42
effective length of query: 30
effective length of database: 12,345,061
effective search space: 370351830
effective search space used: 370351830
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)