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= 032568
(138 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 = 104 bits (260), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 53/137 (38%), Positives = 92/137 (67%), Gaps = 5/137 (3%)
Query: 2 SGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQY 61
+G+ EE+A++L EF A+ L+N EV ++L+H+ +Q + D+ ++S+VF K+L Y
Sbjct: 20 AGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDE--QELSEVFMKTLNY 77
Query: 62 VKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDD 121
RFSR+KN + + VR +L + +L +FEL L NLCPET EE+ A++PS++ R +D
Sbjct: 78 TARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR---FED 134
Query: 122 EAIEKMLNDLSLIKKFE 138
E ++++L+D+ + F+
Sbjct: 135 EELQQILDDIQTKRSFQ 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 = 65.1 bits (157), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 43/135 (31%), Positives = 74/135 (54%), Gaps = 9/135 (6%)
Query: 6 EENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDD--PMNQVSQVFEKSLQYVK 63
EE+AA+LK+G EF L E I+++ Q + ++ PM + V +K++ Y
Sbjct: 7 EEDAAQLKLGPEFENEDMLTVSEAKILIETVLAQRARETNGEIPM---TDVMKKTVAYFN 63
Query: 64 RFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEA 123
F+R+K +A IL + +FE LG LC E EEA ++PS+ + DD+
Sbjct: 64 VFARFKTAEATYACERILGN-RFHKFERAQLGTLCCEDAEEARTLIPSLANK---IDDQN 119
Query: 124 IEKMLNDLSLIKKFE 138
++ +L++LS ++KF+
Sbjct: 120 LQGILDELSTLRKFQ 134
>pdb|1WCM|D Chain D, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
Length = 177
Score = 50.4 bits (119), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 43/159 (27%), Positives = 77/159 (48%), Gaps = 33/159 (20%)
Query: 4 EEEENAAELKIGDEF------------------LKAKCLMNCEVAIILDHKYEQLQQ-TS 44
EEEENAA L++G EF L L+ E + +++ Q+ T
Sbjct: 16 EEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKTR 75
Query: 45 DDPMNQVSQVFEKS-----------LQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCV 93
+ + + + E++ +QY+ FSR+++ + V V ++L L FE+
Sbjct: 76 EKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQ 135
Query: 94 LGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLS 132
LG+L +T +EA ++PS+ + DDE +E++L +LS
Sbjct: 136 LGSLACDTADEAKTLIPSLN--NKISDDE-LERILKELS 171
>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 = 49.7 bits (117), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 48/78 (61%), Gaps = 3/78 (3%)
Query: 55 FEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKT 114
+ ++QY+ FSR+++ + V V ++L L FE+ LG+L +T +EA ++PS+
Sbjct: 107 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLN- 165
Query: 115 RGRAHDDEAIEKMLNDLS 132
+ DDE +E++L +LS
Sbjct: 166 -NKISDDE-LERILKELS 181
>pdb|3QT1|D Chain D, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
Length = 219
Score = 49.7 bits (117), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 48/78 (61%), Gaps = 3/78 (3%)
Query: 55 FEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKT 114
+ ++QY+ FSR+++ + V V ++L L FE+ LG+L +T +EA ++PS+
Sbjct: 139 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLN- 197
Query: 115 RGRAHDDEAIEKMLNDLS 132
+ DDE +E++L +LS
Sbjct: 198 -NKISDDE-LERILKELS 213
Score = 25.8 bits (55), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 4 EEEENAAELKIGDEF 18
EEEENAA L++G EF
Sbjct: 17 EEEENAATLQLGQEF 31
>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 = 49.7 bits (117), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 48/78 (61%), Gaps = 3/78 (3%)
Query: 55 FEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKT 114
+ ++QY+ FSR+++ + V V ++L L FE+ LG+L +T +EA ++PS+
Sbjct: 141 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLN- 199
Query: 115 RGRAHDDEAIEKMLNDLS 132
+ DDE +E++L +LS
Sbjct: 200 -NKISDDE-LERILKELS 215
Score = 25.8 bits (55), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 4 EEEENAAELKIGDEF 18
EEEENAA L++G EF
Sbjct: 19 EEEENAATLQLGQEF 33
>pdb|1PQV|D Chain D, Rna Polymerase Ii-Tfiis Complex
Length = 221
Score = 49.3 bits (116), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 48/78 (61%), Gaps = 3/78 (3%)
Query: 55 FEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKT 114
+ ++QY+ FSR+++ + V V ++L L FE+ LG+L +T +EA ++PS+
Sbjct: 141 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLN- 199
Query: 115 RGRAHDDEAIEKMLNDLS 132
+ DDE +E++L +LS
Sbjct: 200 -NKISDDE-LERILKELS 215
Score = 25.8 bits (55), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 4 EEEENAAELKIGDEF 18
EEEENAA L++G EF
Sbjct: 19 EEEENAATLQLGQEF 33
>pdb|3RIS|A Chain A, Crystal Structure Of The Catalytic Domain Of Uchl5, A
Proteasome- Associated Human Deubiquitinating Enzyme,
Reveals An Unproductive Form Of The Enzyme
pdb|3RIS|B Chain B, Crystal Structure Of The Catalytic Domain Of Uchl5, A
Proteasome- Associated Human Deubiquitinating Enzyme,
Reveals An Unproductive Form Of The Enzyme
pdb|3RIS|C Chain C, Crystal Structure Of The Catalytic Domain Of Uchl5, A
Proteasome- Associated Human Deubiquitinating Enzyme,
Reveals An Unproductive Form Of The Enzyme
pdb|3RIS|D Chain D, Crystal Structure Of The Catalytic Domain Of Uchl5, A
Proteasome- Associated Human Deubiquitinating Enzyme,
Reveals An Unproductive Form Of The Enzyme
Length = 245
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 25/112 (22%), Positives = 49/112 (43%), Gaps = 12/112 (10%)
Query: 23 CLMNCEVAIILD--HKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREI 80
C V+++L+ H+ L +T + + SQ F+ +++ + N D +RQV
Sbjct: 93 CATQAIVSVLLNCTHQDVHLGETLSE-FKEFSQSFDAAMKGLA----LSNSDVIRQVHNS 147
Query: 81 LSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLS 132
+R Q+ EF+ E+A V + GR ++ + + + DL
Sbjct: 148 FARQQMFEFD-----TKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLG 194
>pdb|3PDK|A Chain A, Crystal Structure Of Phosphoglucosamine Mutase From B.
Anthracis
pdb|3PDK|B Chain B, Crystal Structure Of Phosphoglucosamine Mutase From B.
Anthracis
Length = 469
Score = 27.3 bits (59), Expect = 2.6, Method: Composition-based stats.
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 3/40 (7%)
Query: 28 EVAIILDHKYEQLQQTSDDPMNQVSQVFE---KSLQYVKR 64
E+ +LD + ++L + + + QVS FE K LQY+K+
Sbjct: 147 EIEALLDKEVDELPRPTGTNLGQVSDYFEGGQKYLQYIKQ 186
>pdb|3TB3|A Chain A, Crystal Structure Of The Uch Domain Of Uch-L5 With 6
Residues Deleted
pdb|3TB3|B Chain B, Crystal Structure Of The Uch Domain Of Uch-L5 With 6
Residues Deleted
Length = 229
Score = 27.3 bits (59), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 25/109 (22%), Positives = 46/109 (42%), Gaps = 16/109 (14%)
Query: 24 LMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSR 83
L+NC H+ L +T + + SQ F+ +++ + N D +RQV +R
Sbjct: 99 LLNCT------HQDVHLGETLSE-FKEFSQSFDAAMKGLA----LSNSDVIRQVHNSFAR 147
Query: 84 YQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLS 132
Q+ EF+ E+A V + GR ++ + + + DL
Sbjct: 148 QQMFEFD-----TKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLG 191
>pdb|3A7S|A Chain A, Catalytic Domain Of Uch37
Length = 228
Score = 26.9 bits (58), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 25/109 (22%), Positives = 46/109 (42%), Gaps = 16/109 (14%)
Query: 24 LMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSR 83
L+NC H+ L +T + + SQ F+ +++ + N D +RQV +R
Sbjct: 97 LLNCT------HQDVHLGETLSE-FKEFSQSFDAAMKGLA----LSNSDVIRQVHNSFAR 145
Query: 84 YQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLS 132
Q+ EF+ E+A V + GR ++ + + + DL
Sbjct: 146 QQMFEFD-----TKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLG 189
>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 = 26.9 bits (58), Expect = 4.0, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 85 QLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDD 121
++A + CV N C T EE +V I RG H D
Sbjct: 460 KMAFRKFCVDHNFCEATEEEKHIVVKVIALRGSYHGD 496
>pdb|1F48|A Chain A, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase
pdb|1IHU|A Chain A, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase In Complex With
Mg-Adp-Alf3
pdb|1II0|A Chain A, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase
pdb|1II0|B Chain B, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase
pdb|1II9|A Chain A, Crystal Structure Of The Escherichia Coli Arsenite-
Translocating Atpase In Complex With Amp-Pnp
pdb|1II9|B Chain B, Crystal Structure Of The Escherichia Coli Arsenite-
Translocating Atpase In Complex With Amp-Pnp
Length = 589
Score = 26.2 bits (56), Expect = 6.8, Method: Composition-based stats.
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 21 AKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSL 59
K ++C AI L + +++ S DP + V QVF +++
Sbjct: 20 GKTSISCATAIRLAEQGKRVLLVSTDPASNVGQVFSQTI 58
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
0.317 0.132 0.366
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,665,002
Number of Sequences: 62578
Number of extensions: 124407
Number of successful extensions: 331
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 315
Number of HSP's gapped (non-prelim): 24
length of query: 138
length of database: 14,973,337
effective HSP length: 89
effective length of query: 49
effective length of database: 9,403,895
effective search space: 460790855
effective search space used: 460790855
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: 46 (22.3 bits)