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= 001920
(996 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2Q5X|A Chain A, Crystal Structure Of The C-Terminal Domain Of Hnup98
Length = 155
Score = 117 bits (293), Expect = 3e-26, Method: Composition-based stats.
Identities = 63/150 (42%), Positives = 91/150 (60%), Gaps = 4/150 (2%)
Query: 829 LRRSDYYTEPRIQELAAKERAEPGFCRRVKDFVVGRHGYGSIKFLGETDVRRLDLESLVQ 888
L + YYT P + +LA K E G C V DF +GR GYGSI F G+ ++ L+L+ +V
Sbjct: 4 LTKVGYYTIPSMDDLA-KITNEKGECI-VSDFTIGRKGYGSIYFEGDVNLTNLNLDDIVH 61
Query: 889 FNNREVIVYMDDSKKPPVGQGLNKPAEVTLLNIKCFDKKTGVQYKEGPKIE--KYKEMLK 946
+EV+VY+DD++KPPVG+GLN+ AEVTL + DK + K ++ Y+ L+
Sbjct: 62 IRRKEVVVYLDDNQKPPVGEGLNRKAEVTLDGVWPTDKTSRCLIKSPDRLADINYEGRLE 121
Query: 947 RKAEDQGAEFISYDPIKGEWKFSVNHFSEY 976
+ QGA+F Y P G W F V+HF++Y
Sbjct: 122 AVSRKQGAQFKEYRPETGSWVFKVSHFAKY 151
>pdb|2Q5Y|A Chain A, Crystal Structure Of The C-Terminal Domain Of Hnup98
pdb|2Q5Y|C Chain C, Crystal Structure Of The C-Terminal Domain Of Hnup98
Length = 152
Score = 113 bits (282), Expect = 5e-25, Method: Composition-based stats.
Identities = 62/147 (42%), Positives = 88/147 (59%), Gaps = 4/147 (2%)
Query: 829 LRRSDYYTEPRIQELAAKERAEPGFCRRVKDFVVGRHGYGSIKFLGETDVRRLDLESLVQ 888
L + YYT P + +LA K E G C V DF +GR GYGSI F G+ ++ L+L+ +V
Sbjct: 8 LTKVGYYTIPSMDDLA-KITNEKGECI-VSDFTIGRKGYGSIYFEGDVNLTNLNLDDIVH 65
Query: 889 FNNREVIVYMDDSKKPPVGQGLNKPAEVTLLNIKCFDKKTGVQYKEGPKIE--KYKEMLK 946
+EV+VY+DD++KPPVG+GLN+ AEVTL + DK + K ++ Y+ L+
Sbjct: 66 IRRKEVVVYLDDNQKPPVGEGLNRKAEVTLDGVWPTDKTSRCLIKSPDRLADINYEGRLE 125
Query: 947 RKAEDQGAEFISYDPIKGEWKFSVNHF 973
+ QGA+F Y P G W F V+HF
Sbjct: 126 AVSRKQGAQFKEYRPETGSWVFKVSHF 152
>pdb|1KO6|A Chain A, Crystal Structure Of C-Terminal Autoproteolytic Domain Of
Nucleoporin Nup98
pdb|1KO6|C Chain C, Crystal Structure Of C-Terminal Autoproteolytic Domain Of
Nucleoporin Nup98
Length = 187
Score = 113 bits (282), Expect = 6e-25, Method: Composition-based stats.
Identities = 69/184 (37%), Positives = 98/184 (53%), Gaps = 17/184 (9%)
Query: 792 DHSNQKDESYVTLNGHRAGEAAIVYEHGANIEALMPKLRRSDYYTEPRIQELAAKERAEP 851
D S Q D + N + A I+ L + YYT P + +LA K E
Sbjct: 19 DESLQDDREEIENNSYHMHPAGII-------------LTKVGYYTIPSMDDLA-KITNEK 64
Query: 852 GFCRRVKDFVVGRHGYGSIKFLGETDVRRLDLESLVQFNNREVIVYMDDSKKPPVGQGLN 911
G C V DF +GR GYGSI F G+ ++ L+L+ +V +EV+VY+DD++KPPVG+GLN
Sbjct: 65 GECI-VSDFTIGRKGYGSIYFEGDVNLTNLNLDDIVHIRRKEVVVYLDDNQKPPVGEGLN 123
Query: 912 KPAEVTLLNIKCFDKKTGVQYKEGPKIE--KYKEMLKRKAEDQGAEFISYDPIKGEWKFS 969
+ AEVTL + DK + K ++ Y+ L+ + QGA+F Y P G W F
Sbjct: 124 RKAEVTLDGVWPTDKTSRCLIKSPDRLADINYEGRLEAVSRKQGAQFKEYRPETGSWVFK 183
Query: 970 VNHF 973
V+HF
Sbjct: 184 VSHF 187
>pdb|3TKN|C Chain C, Structure Of The Nup82-Nup159-Nup98 Heterotrimer
pdb|3TKN|F Chain F, Structure Of The Nup82-Nup159-Nup98 Heterotrimer
pdb|3TKN|I Chain I, Structure Of The Nup82-Nup159-Nup98 Heterotrimer
Length = 152
Score = 112 bits (281), Expect = 7e-25, Method: Composition-based stats.
Identities = 63/147 (42%), Positives = 88/147 (59%), Gaps = 4/147 (2%)
Query: 829 LRRSDYYTEPRIQELAAKERAEPGFCRRVKDFVVGRHGYGSIKFLGETDVRRLDLESLVQ 888
L + YYT P + +LA K E G C V DF +GR GYGSI F G+ ++ L+L+ +V
Sbjct: 8 LTKVGYYTIPSMDDLA-KITNEKGECI-VSDFTIGRKGYGSIYFEGDVNLTNLNLDDIVH 65
Query: 889 FNNREVIVYMDDSKKPPVGQGLNKPAEVTLLNIKCFDKKTGVQYKEGPKIE--KYKEMLK 946
+EVIVY+DD++KPPVG+GLN+ AEVTL + DK + K ++ Y+ L+
Sbjct: 66 IRRKEVIVYVDDNQKPPVGEGLNRKAEVTLDGVWPTDKTSRCLIKSPDRLADINYEGRLE 125
Query: 947 RKAEDQGAEFISYDPIKGEWKFSVNHF 973
+ QGA+F Y P G W F V+HF
Sbjct: 126 AVSRKQGAQFKEYRPETGSWVFKVSHF 152
>pdb|3KEP|A Chain A, Crystal Structure Of The Autoproteolytic Domain From The
Nuclear Pore Complex Component Nup145 From Saccharomyces
Cerevisiae
pdb|3KEP|B Chain B, Crystal Structure Of The Autoproteolytic Domain From The
Nuclear Pore Complex Component Nup145 From Saccharomyces
Cerevisiae
pdb|3KES|A Chain A, Crystal Structure Of The Autoproteolytic Domain From The
Nuclear Pore Complex Component Nup145 From Saccharomyces
Cerevisiae In The Hexagonal, P61 Space Group
pdb|3KES|B Chain B, Crystal Structure Of The Autoproteolytic Domain From The
Nuclear Pore Complex Component Nup145 From Saccharomyces
Cerevisiae In The Hexagonal, P61 Space Group
Length = 174
Score = 69.3 bits (168), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 51/151 (33%), Positives = 79/151 (52%), Gaps = 17/151 (11%)
Query: 834 YYTEP---RIQELAAKERAEPGFCRRVKDFVVGRHGYGSIKFLGETDV-------RRLDL 883
Y+ P +++ L+ K+ A V +FV+GR GYG I F + D+ R
Sbjct: 22 YWCSPSPEQLERLSLKQLAA------VSNFVIGRRGYGCITFQHDVDLTAFTKSFREELF 75
Query: 884 ESLVQF-NNREVIVYMDDSKKPPVGQGLNKPAEVTLLNIKCFDKKTGVQYKEGPKIEKYK 942
+V F +++ V VY D++ KP +G GLN PA +TL N+ DKKT K+ K +++
Sbjct: 76 GKIVIFRSSKTVEVYPDEATKPXIGHGLNVPAIITLENVYPVDKKTKKPXKDTTKFAEFQ 135
Query: 943 EMLKRKAEDQGAEFISYDPIKGEWKFSVNHF 973
++ + +ISY+P G W F VNHF
Sbjct: 136 VFDRKLRSXREXNYISYNPFGGTWTFKVNHF 166
>pdb|3NF5|A Chain A, Crystal Structure Of The C-Terminal Domain Of Nuclear Pore
Complex Component Nup116 From Candida Glabrata
pdb|3NF5|B Chain B, Crystal Structure Of The C-Terminal Domain Of Nuclear Pore
Complex Component Nup116 From Candida Glabrata
Length = 164
Score = 68.6 bits (166), Expect = 2e-11, Method: Composition-based stats.
Identities = 49/149 (32%), Positives = 72/149 (48%), Gaps = 12/149 (8%)
Query: 833 DYYTEPRIQELAAKERAEPGFCRRVKDFVVGRHGYGSIKFLGETDVRRLDLES----LVQ 888
+YY P + LA + E ++V++ VVG YG I+FL D+ + L S LV
Sbjct: 15 NYYISPSLDTLATLSKYE---IQKVENLVVGNKQYGKIEFLDPVDLSDIPLGSICDDLVV 71
Query: 889 FNNREVIVYMDDSKKPPVGQGLNKPAEVTLLNIKCFDKKTGVQYKEGPK--IEKYKEMLK 946
F V++Y + + P G+GLN A ++ N DK T K+ E+Y E LK
Sbjct: 72 FQPXSVLLYNNSTNVPEKGKGLNVRARISCYNCYPLDKSTRKPIKDPNHRIXERYSEKLK 131
Query: 947 RKAEDQGAEFISYDPIKGEWKFSVNHFSE 975
+ F SYDP G + F+V+H E
Sbjct: 132 KIPH---THFESYDPASGTYCFTVDHALE 157
>pdb|3PBP|B Chain B, Structure Of The Yeast Heterotrimeric Nup82-Nup159-Nup116
Nucleoporin Complex
pdb|3PBP|E Chain E, Structure Of The Yeast Heterotrimeric Nup82-Nup159-Nup116
Nucleoporin Complex
pdb|3PBP|H Chain H, Structure Of The Yeast Heterotrimeric Nup82-Nup159-Nup116
Nucleoporin Complex
pdb|3PBP|K Chain K, Structure Of The Yeast Heterotrimeric Nup82-Nup159-Nup116
Nucleoporin Complex
Length = 148
Score = 66.6 bits (161), Expect = 7e-11, Method: Composition-based stats.
Identities = 45/147 (30%), Positives = 72/147 (48%), Gaps = 8/147 (5%)
Query: 833 DYYTEPRIQELAAKERAEPGFCRRVKDFVVGRHGYGSIKFLGETDVRRLDLESL----VQ 888
+YY P + L++ + R+V VVG YG I+FL D+ + L SL +
Sbjct: 4 NYYISPSLDTLSSYSLLQ---LRKVPHLVVGHKSYGKIEFLEPVDLAGIPLTSLGGVIIT 60
Query: 889 FNNREVIVYMDDSKKPPVGQGLNKPAEVTLLNIKCFDKKTGVQYKEGPKIEKYKEMLKRK 948
F + I+Y + +P G+G+N A +T N DK T K+ P + K ++R
Sbjct: 61 FEPKTCIIYANLPNRPKRGEGINVRARITCFNCYPVDKSTRKPIKD-PNHQLVKRHIERL 119
Query: 949 AEDQGAEFISYDPIKGEWKFSVNHFSE 975
++ ++F SYD G + F VNH +E
Sbjct: 120 KKNPNSKFESYDADSGTYVFIVNHAAE 146
>pdb|2AIV|A Chain A, Multiple Conformations In The Ligand-Binding Site Of The
Yeast Nuclear Pore Targeting Domain Of Nup116p
Length = 149
Score = 65.9 bits (159), Expect = 1e-10, Method: Composition-based stats.
Identities = 45/147 (30%), Positives = 72/147 (48%), Gaps = 8/147 (5%)
Query: 833 DYYTEPRIQELAAKERAEPGFCRRVKDFVVGRHGYGSIKFLGETDVRRLDLESL----VQ 888
+YY P + L++ + R+V VVG YG I+FL D+ + L SL +
Sbjct: 5 NYYISPSLDTLSSYSLLQ---LRKVPHLVVGHKSYGKIEFLEPVDLAGIPLTSLGGVIIT 61
Query: 889 FNNREVIVYMDDSKKPPVGQGLNKPAEVTLLNIKCFDKKTGVQYKEGPKIEKYKEMLKRK 948
F + I+Y + +P G+G+N A +T N DK T K+ P + K ++R
Sbjct: 62 FEPKTCIIYANLPNRPKRGEGINVRARITCFNCYPVDKSTRKPIKD-PNHQLVKRHIERL 120
Query: 949 AEDQGAEFISYDPIKGEWKFSVNHFSE 975
++ ++F SYD G + F VNH +E
Sbjct: 121 KKNPNSKFESYDADSGTYVFIVNHAAE 147
>pdb|3MMY|B Chain B, Structural And Functional Analysis Of The Interaction
Between The Nucleoporin Nup98 And The Mrna Export Factor
Rae1
pdb|3MMY|D Chain D, Structural And Functional Analysis Of The Interaction
Between The Nucleoporin Nup98 And The Mrna Export Factor
Rae1
pdb|3MMY|F Chain F, Structural And Functional Analysis Of The Interaction
Between The Nucleoporin Nup98 And The Mrna Export Factor
Rae1
pdb|3MMY|H Chain H, Structural And Functional Analysis Of The Interaction
Between The Nucleoporin Nup98 And The Mrna Export Factor
Rae1
Length = 56
Score = 35.0 bits (79), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 25/42 (59%)
Query: 344 TEAETGSASQPAGKLESISSMPVYKDKSHEELRWEDYQLGDK 385
T + G ++ + K + I++M Y+ KS EELR EDYQ K
Sbjct: 15 TMVKAGVSTNISTKHQCITAMKEYESKSLEELRLEDYQANRK 56
>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 = 30.4 bits (67), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 6/49 (12%)
Query: 139 AFGSSLFGSST-PFGASSQPAFGATSTPAFGTSNPAFGATSTPAFGATS 186
A+G + +G +T PFGA + A ++P FG S+P F TS P + TS
Sbjct: 1510 AYGGADYGEATSPFGAYGE----APTSPGFGVSSPGFSPTS-PTYSPTS 1553
>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 = 30.4 bits (67), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 6/49 (12%)
Query: 139 AFGSSLFGSST-PFGASSQPAFGATSTPAFGTSNPAFGATSTPAFGATS 186
A+G + +G +T PFGA + A ++P FG S+P F TS P + TS
Sbjct: 1510 AYGGADYGEATSPFGAYGE----APTSPGFGVSSPGFSPTS-PTYSPTS 1553
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
0.311 0.127 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,650,005
Number of Sequences: 62578
Number of extensions: 713071
Number of successful extensions: 1196
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1173
Number of HSP's gapped (non-prelim): 16
length of query: 996
length of database: 14,973,337
effective HSP length: 108
effective length of query: 888
effective length of database: 8,214,913
effective search space: 7294842744
effective search space used: 7294842744
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 56 (26.2 bits)