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= 042488
(78 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2C35|A Chain A, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
pdb|2C35|C Chain C, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
pdb|2C35|E Chain E, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
pdb|2C35|G Chain G, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
Length = 152
Score = 52.4 bits (124), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 43/65 (66%), Gaps = 3/65 (4%)
Query: 14 IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
I V +L + +L +FEL L NLCPET EE+ A++PS++ R +DE ++++L+D+
Sbjct: 90 IASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR---FEDEELQQILDDIQT 146
Query: 74 IKKFE 78
+ F+
Sbjct: 147 KRSFQ 151
>pdb|3H0G|D Chain D, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|P Chain P, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 135
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 46/94 (48%), Gaps = 25/94 (26%)
Query: 7 ENAAELKIGDV-------FRILSRYQLAE---------------FELCVLGNLCPETVEE 44
E E+ + DV F + +R++ AE FE LG LC E EE
Sbjct: 44 ETNGEIPMTDVMKKTVAYFNVFARFKTAEATYACERILGNRFHKFERAQLGTLCCEDAEE 103
Query: 45 AIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE 78
A ++PS+ + DD+ ++ +L++LS ++KF+
Sbjct: 104 ARTLIPSLANK---IDDQNLQGILDELSTLRKFQ 134
>pdb|1NT9|D Chain D, Complete 12-Subunit Rna Polymerase Ii
pdb|1Y1W|D Chain D, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|D Chain D, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|D Chain D, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|D Chain D, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|D Chain D, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|D Chain D, 12-Subunit Rna Polymerase Ii
pdb|2JA5|D Chain D, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|D Chain D, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|D Chain D, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|P Chain P, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|D Chain D, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2R7Z|D Chain D, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|D Chain D, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|D Chain D, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|D Chain D, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3FKI|D Chain D, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3H3V|E Chain E, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|D Chain D, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|P Chain P, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|D Chain D, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|D Chain D, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|D Chain D, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|D Chain D, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|D Chain D, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|D Chain D, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|D Chain D, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|D Chain D, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3PO2|D Chain D, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|D Chain D, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3J0K|D Chain D, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|D Chain D, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|D Chain D, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|D Chain D, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|D Chain D, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 221
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 3/59 (5%)
Query: 14 IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLS 72
+G V ++L L FE+ LG+L +T +EA ++PS+ + DDE +E++L +LS
Sbjct: 160 VGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLN--NKISDDE-LERILKELS 215
>pdb|1WCM|D Chain D, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
Length = 177
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 3/59 (5%)
Query: 14 IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLS 72
+G V ++L L FE+ LG+L +T +EA ++PS+ + DDE +E++L +LS
Sbjct: 116 VGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLN--NKISDDE-LERILKELS 171
>pdb|3QT1|D Chain D, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
Length = 219
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 3/59 (5%)
Query: 14 IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLS 72
+G V ++L L FE+ LG+L +T +EA ++PS+ + DDE +E++L +LS
Sbjct: 158 VGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLN--NKISDDE-LERILKELS 213
>pdb|1PQV|D Chain D, Rna Polymerase Ii-Tfiis Complex
Length = 221
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 3/59 (5%)
Query: 14 IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLS 72
+G V ++L L FE+ LG+L +T +EA ++PS+ + DDE +E++L +LS
Sbjct: 160 VGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLN--NKISDDE-LERILKELS 215
>pdb|1Y14|A Chain A, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7
pdb|1Y14|C Chain C, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7
Length = 187
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 3/59 (5%)
Query: 14 IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLS 72
+G V ++L L FE+ LG+L +T +EA ++PS+ + DDE +E++L +LS
Sbjct: 126 VGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLN--NKISDDE-LERILKELS 181
>pdb|4A0G|A Chain A, Structure Of Bifunctional Dapa Aminotransferase-Dtb
Synthetase From Arabidopsis Thaliana In Its Apo Form.
pdb|4A0G|B Chain B, Structure Of Bifunctional Dapa Aminotransferase-Dtb
Synthetase From Arabidopsis Thaliana In Its Apo Form.
pdb|4A0G|C Chain C, Structure Of Bifunctional Dapa Aminotransferase-Dtb
Synthetase From Arabidopsis Thaliana In Its Apo Form.
pdb|4A0G|D Chain D, Structure Of Bifunctional Dapa Aminotransferase-Dtb
Synthetase From Arabidopsis Thaliana In Its Apo Form.
pdb|4A0H|A Chain A, Structure Of Bifunctional Dapa Aminotransferase-Dtb
Synthetase From Arabidopsis Thaliana Bound To 7-Keto
8-Amino Pelargonic Acid (Kapa)
pdb|4A0H|B Chain B, Structure Of Bifunctional Dapa Aminotransferase-Dtb
Synthetase From Arabidopsis Thaliana Bound To 7-Keto
8-Amino Pelargonic Acid (Kapa)
pdb|4A0R|A Chain A, Structure Of Bifunctional Dapa Aminotransferase-Dtb
Synthetase From Arabidopsis Thaliana Bound To
Dethiobiotin (Dtb).
pdb|4A0R|B Chain B, Structure Of Bifunctional Dapa Aminotransferase-Dtb
Synthetase From Arabidopsis Thaliana Bound To
Dethiobiotin (Dtb)
Length = 831
Score = 26.6 bits (57), Expect = 3.6, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 25 QLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDD 61
++A + CV N C T EE +V I RG H D
Sbjct: 460 KMAFRKFCVDHNFCEATEEEKHIVVKVIALRGSYHGD 496
>pdb|4A0F|A Chain A, Structure Of Selenomethionine Substituted Bifunctional
Dapa Aminotransferase-Dethiobiotin Synthetase From
Arabidopsis Thaliana In Its Apo Form.
pdb|4A0F|B Chain B, Structure Of Selenomethionine Substituted Bifunctional
Dapa Aminotransferase-Dethiobiotin Synthetase From
Arabidopsis Thaliana In Its Apo Form
Length = 831
Score = 26.2 bits (56), Expect = 4.9, Method: Composition-based stats.
Identities = 13/32 (40%), Positives = 15/32 (46%)
Query: 30 ELCVLGNLCPETVEEAIAMVPSIKTRGRAHDD 61
+ CV N C T EE +V I RG H D
Sbjct: 465 KFCVDHNFCEATEEEKHIVVKVIALRGSYHGD 496
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
0.316 0.135 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,048,547
Number of Sequences: 62578
Number of extensions: 62310
Number of successful extensions: 107
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 92
Number of HSP's gapped (non-prelim): 14
length of query: 78
length of database: 14,973,337
effective HSP length: 47
effective length of query: 31
effective length of database: 12,032,171
effective search space: 372997301
effective search space used: 372997301
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)