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= 041978
(123 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1KI0|A Chain A, The X-Ray Structure Of Human Angiostatin
Length = 253
Score = 26.2 bits (56), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 7 NLRGNVVHTIKGDTCQEGLGQCGASND 33
N RGNV T+ G TCQ Q +++
Sbjct: 183 NYRGNVAVTVSGHTCQHWSAQTPHTHE 209
>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|A Chain A, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|A Chain A, Rna Polymerase Ii Elongation Complex
pdb|1K83|A Chain A, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|A Chain A, Wild Type Rna Polymerase Ii
pdb|1NT9|A Chain A, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|A Chain A, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|A Chain A, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|A Chain A, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|A Chain A, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|A Chain A, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|A Chain A, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|A Chain A, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|A Chain A, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|A Chain A, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|A Chain A, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|A Chain A, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|A Chain A, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|A Chain A, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|A Chain A, 12-Subunit Rna Polymerase Ii
pdb|2E2H|A Chain A, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With
Gtp
pdb|2E2I|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
2'- Dgtp
pdb|2E2J|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
2'- Dutp
pdb|2NVY|A Chain A, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|A Chain A, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation
Complex A
pdb|2JA6|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation
Complex B
pdb|2JA7|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation
Complex C
pdb|2JA7|M Chain M, Cpd Lesion Containing Rna Polymerase Ii Elongation
Complex C
pdb|2JA8|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation
Complex D
pdb|2YU9|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|A Chain A, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|A Chain A, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|A Chain A, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|A Chain A, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|A Chain A, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|A Chain A, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|A Chain A, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|A Chain A, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer With
G<>u Mismatch
pdb|3GTM|A Chain A, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|A Chain A, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|A Chain A, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|A Chain A, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|B Chain B, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|A Chain A, Complete Rna Polymerase Ii Elongation Complex I With A
T-U Mismatch
pdb|3HOU|M Chain M, Complete Rna Polymerase Ii Elongation Complex I With A
T-U Mismatch
pdb|3HOV|A Chain A, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|A Chain A, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|A Chain A, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|A Chain A, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|A Chain A, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|A Chain A, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|A Chain A, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|A Chain A, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|A Chain A, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|A Chain A, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|A Chain A, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|A Chain A, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|A Chain A, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|A Chain A, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt
3'-Deoxy Rna Soaked With Atp
pdb|3S1R|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt
3'-Deoxy Rna Soaked With Gtp
pdb|3S2D|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|4BBR|A Chain A, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|A Chain A, Structure Of An Initially Transcribing Rna Polymerase
Ii- Tfiib Complex
Length = 1733
Score = 26.2 bits (56), Expect = 5.1, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 10 GNVVHTIKGDTCQEGLGQC-GASNDCDLHCKTRHAG 44
G++ +K TCQEG+ +C G DL H G
Sbjct: 59 GSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVG 94
>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A
5nt Dna-Rna Hybrid
pdb|4A3B|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A
4nt Dna-Rna Hybrid
pdb|4A3D|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A
6nt Dna-Rna Hybrid
pdb|4A3E|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A
5nt Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A
6nt Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A
2nt Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A
7nt Dna-Rna Hybrid
pdb|4A3L|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A
7nt Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A
4nt Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A
2nt Dna-Rna Hybrid
pdb|4A3I|A Chain A, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|A Chain A, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
Length = 1732
Score = 26.2 bits (56), Expect = 5.1, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 10 GNVVHTIKGDTCQEGLGQC-GASNDCDLHCKTRHAG 44
G++ +K TCQEG+ +C G DL H G
Sbjct: 59 GSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVG 94
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 26.2 bits (56), Expect = 5.1, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 10 GNVVHTIKGDTCQEGLGQC-GASNDCDLHCKTRHAG 44
G++ +K TCQEG+ +C G DL H G
Sbjct: 59 GSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVG 94
>pdb|2DOH|X Chain X, The X-Ray Crystallographic Structure Of The Angiogenesis
Inhibitor, Angiostatin, Bound A To A Peptide From The
Group A Streptococcal Surface Protein Pam
pdb|2DOI|X Chain X, The X-Ray Crystallographic Structure Of The Angiogenesis
Inhibitor, Angiostatin, Bound To A Peptide From The
Group A Streptococcus Protein Pam
pdb|2DOI|A Chain A, The X-Ray Crystallographic Structure Of The Angiogenesis
Inhibitor, Angiostatin, Bound To A Peptide From The
Group A Streptococcus Protein Pam
Length = 234
Score = 26.2 bits (56), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 7 NLRGNVVHTIKGDTCQEGLGQCGASND 33
N RGNV T+ G TCQ Q +++
Sbjct: 183 NYRGNVAVTVSGHTCQHWSAQTPHTHE 209
>pdb|2L0S|A Chain A, Solution Structure Of Human Plasminogen Kringle 3
Length = 83
Score = 25.8 bits (55), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 7 NLRGNVVHTIKGDTCQEGLGQCGASND 33
N RGNV T+ G TCQ Q +++
Sbjct: 11 NYRGNVAVTVSGHTCQHWSAQTPHTHN 37
>pdb|1LLW|A Chain A, Structural Studies On The Synchronization Of Catalytic
Centers In Glutamate Synthase: Complex With
2-Oxoglutarate
pdb|1LLZ|A Chain A, Structural Studies On The Synchronization Of Catalytic
Centers In Glutamate Synthase: Reduced Enzyme
pdb|1LM1|A Chain A, Structural Studies On The Synchronization Of Catalytic
Centers In Glutamate Synthase: Native Enzyme
pdb|1OFD|A Chain A, Glutamate Synthase From Synechocystis Sp In Complex With
2-Oxoglutarate At 2.0 Angstrom Resolution
pdb|1OFD|B Chain B, Glutamate Synthase From Synechocystis Sp In Complex With
2-Oxoglutarate At 2.0 Angstrom Resolution
pdb|1OFE|A Chain A, Glutamate Synthase From Synechocystis Sp In Complex With
2-Oxoglutarate And L-Don At 2.45 Angstrom Resolution
pdb|1OFE|B Chain B, Glutamate Synthase From Synechocystis Sp In Complex With
2-Oxoglutarate And L-Don At 2.45 Angstrom Resolution
Length = 1520
Score = 25.4 bits (54), Expect = 8.2, Method: Composition-based stats.
Identities = 14/34 (41%), Positives = 16/34 (47%), Gaps = 5/34 (14%)
Query: 5 LINLRGNVVHTI-----KGDTCQEGLGQCGASND 33
+ NLRG HT+ K C E G C A ND
Sbjct: 6 IANLRGKPDHTLVEQALKALGCMEHRGGCSADND 39
>pdb|1AYJ|A Chain A, Determination Of The Three-Dimensional Solution
Structure Of Raphanus Sativus Antifungal Protein 1
(Rs-Afp1) By 1h Nmr, 20 Structures
Length = 51
Score = 25.4 bits (54), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 9/44 (20%)
Query: 26 GQCGASNDCDLHC----KTRHAGQGQGSCDRTIQPPLCTCFYPC 65
G CG +N C C K RH GSC+ C C++PC
Sbjct: 13 GVCGNNNACKNQCINLEKARH-----GSCNYVFPAHKCICYFPC 51
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
0.327 0.144 0.523
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,628,076
Number of Sequences: 62578
Number of extensions: 124335
Number of successful extensions: 264
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 250
Number of HSP's gapped (non-prelim): 30
length of query: 123
length of database: 14,973,337
effective HSP length: 85
effective length of query: 38
effective length of database: 9,654,207
effective search space: 366859866
effective search space used: 366859866
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)