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= 007001
(622 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2QGQ|A Chain A, Crystal Structure Of Tm_1862 From Thermotoga Maritima.
Northeast Structural Genomics Consortium Target Vr77
pdb|2QGQ|B Chain B, Crystal Structure Of Tm_1862 From Thermotoga Maritima.
Northeast Structural Genomics Consortium Target Vr77
pdb|2QGQ|C Chain C, Crystal Structure Of Tm_1862 From Thermotoga Maritima.
Northeast Structural Genomics Consortium Target Vr77
pdb|2QGQ|D Chain D, Crystal Structure Of Tm_1862 From Thermotoga Maritima.
Northeast Structural Genomics Consortium Target Vr77
pdb|2QGQ|E Chain E, Crystal Structure Of Tm_1862 From Thermotoga Maritima.
Northeast Structural Genomics Consortium Target Vr77
pdb|2QGQ|F Chain F, Crystal Structure Of Tm_1862 From Thermotoga Maritima.
Northeast Structural Genomics Consortium Target Vr77
pdb|2QGQ|G Chain G, Crystal Structure Of Tm_1862 From Thermotoga Maritima.
Northeast Structural Genomics Consortium Target Vr77
pdb|2QGQ|H Chain H, Crystal Structure Of Tm_1862 From Thermotoga Maritima.
Northeast Structural Genomics Consortium Target Vr77
Length = 304
Score = 107 bits (267), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 80/281 (28%), Positives = 132/281 (46%), Gaps = 27/281 (9%)
Query: 189 LPINVGCLGACTYCKTKHARGHLGSYTVESLVGRVRTVIADGVKEVWLSSEDTGAYGRDI 248
+ I+ GC CT+C +G L S ++E + V ++ +G KE+ L ++DT +YG D+
Sbjct: 8 VKISDGCDRGCTFCSIPSFKGSLRSRSIEDITREVEDLLKEGKKEIILVAQDTTSYGIDL 67
Query: 249 GVN--LPILLNAIVAELPPDGSTMLRIGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQ 306
LP LL + + +G +R+ +P + E + I+ L V + VPVQ
Sbjct: 68 YRKQALPDLLRRLNS---LNGEFWIRVXYLHPDHLTEEI--ISAXLELDKVVKYFDVPVQ 122
Query: 307 SGSDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKE 366
GSD +L R + + + + ++ E P + T II GFPGET+EDF + ++E
Sbjct: 123 HGSDKILKLXGRTKSSEELKKXLSSIRERFPDAVLRTSIIVGFPGETEEDFEELKQFVEE 182
Query: 367 YKFPQVHISQFYPRPGTPAARMK-KVPSAVVKKRSREL--------TSVFEAFT----PY 413
+F ++ + GT A +K KV K+R EL S + F +
Sbjct: 183 IQFDKLGAFVYSDEEGTVAFNLKEKVDPEXAKRRQEELLLLQAEISNSRLDRFVGKKLKF 242
Query: 414 L--GMEGR--VERIWITEIAADGIHLV---GHTKGYVQVLV 447
L G EG+ V R W DG+ V G +++V++
Sbjct: 243 LVEGKEGKFLVGRTWTEAPEVDGVVFVRGKGKIGDFLEVVI 283
>pdb|3CIX|A Chain A, X-ray Structure Of The [fefe]-hydrogenase Maturase Hyde
From Thermotoga Maritima In Complex With Thiocyanate
Length = 348
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 59/202 (29%), Positives = 83/202 (41%), Gaps = 27/202 (13%)
Query: 195 CLGACTYCKTKHARGHLGSY--TVESLVGRVRTVIADGVKEVWLSSEDTGAYGRDIGVNL 252
C C YC + +L Y T E +V R R + G K + L S + Y +
Sbjct: 63 CRKNCLYCGLRRDNKNLKRYRMTPEEIVERARLAVQFGAKTIVLQSGEDPYY-------M 115
Query: 253 PILLNAIVAELPPDG-STMLRIGMTNPPFILEHLKEIAE---VLRHPCVYSFLHVPVQSG 308
P +++ IV E+ G + L +G P E KE +LRH LH ++
Sbjct: 116 PDVISDIVKEIKKMGVAVTLSLG-EWPREYYEKWKEAGADRYLLRHETANPVLHRKLRPD 174
Query: 309 SDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKEYK 368
+ S NR L TL EL G + + G PG+T +D + +KE+
Sbjct: 175 T----SFENRLNXLL-------TLKEL--GYETGAGSMVGLPGQTIDDLVDDLLFLKEHD 221
Query: 369 FPQVHISQFYPRPGTPAARMKK 390
F V I F P P TP A KK
Sbjct: 222 FDMVGIGPFIPHPDTPLANEKK 243
>pdb|3IIZ|A Chain A, X-Ray Structure Of The Fefe-Hydrogenase Maturase Hyde From
T. Maritima In Complex With S-Adenosyl-L-Methionine
Length = 348
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 60/202 (29%), Positives = 83/202 (41%), Gaps = 27/202 (13%)
Query: 195 CLGACTYCKTKHARGHLGSY--TVESLVGRVRTVIADGVKEVWLSSEDTGAYGRDIGVNL 252
C C YC + +L Y T E +V R R + G K + L S G D +
Sbjct: 63 CRKNCLYCGLRRDNKNLKRYRMTPEEIVERARLAVQFGAKTIVLQS------GED-PYXM 115
Query: 253 PILLNAIVAELPPDG-STMLRIGMTNPPFILEHLKEIAE---VLRHPCVYSFLHVPVQSG 308
P +++ IV E+ G + L +G P E KE +LRH LH ++
Sbjct: 116 PDVISDIVKEIKKMGVAVTLSLG-EWPREYYEKWKEAGADRYLLRHETANPVLHRKLRPD 174
Query: 309 SDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKEYK 368
+ S NR L TL EL G + + G PG+T +D + +KE+
Sbjct: 175 T----SFENRLNXLL-------TLKEL--GYETGAGSMVGLPGQTIDDLVDDLLFLKEHD 221
Query: 369 FPQVHISQFYPRPGTPAARMKK 390
F V I F P P TP A KK
Sbjct: 222 FDMVGIGPFIPHPDTPLANEKK 243
>pdb|3CIW|A Chain A, X-Ray Structure Of The [fefe]-Hydrogenase Maturase Hyde
From Thermotoga Maritima
pdb|3IIX|A Chain A, X-Ray Structure Of The Fefe-Hydrogenase Maturase Hyde From
T. Maritima In Complex With Methionine And
5'deoxyadenosine
Length = 348
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 60/202 (29%), Positives = 83/202 (41%), Gaps = 27/202 (13%)
Query: 195 CLGACTYCKTKHARGHLGSY--TVESLVGRVRTVIADGVKEVWLSSEDTGAYGRDIGVNL 252
C C YC + +L Y T E +V R R + G K + L S G D +
Sbjct: 63 CRKNCLYCGLRRDNKNLKRYRMTPEEIVERARLAVQFGAKTIVLQS------GED-PYXM 115
Query: 253 PILLNAIVAELPPDG-STMLRIGMTNPPFILEHLKEIAE---VLRHPCVYSFLHVPVQSG 308
P +++ IV E+ G + L +G P E KE +LRH LH ++
Sbjct: 116 PDVISDIVKEIKKMGVAVTLSLG-EWPREYYEKWKEAGADRYLLRHETANPVLHRKLRPD 174
Query: 309 SDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKEYK 368
+ S NR L TL EL G + + G PG+T +D + +KE+
Sbjct: 175 T----SFENRLNXLL-------TLKEL--GYETGAGSMVGLPGQTIDDLVDDLLFLKEHD 221
Query: 369 FPQVHISQFYPRPGTPAARMKK 390
F V I F P P TP A KK
Sbjct: 222 FDMVGIGPFIPHPDTPLANEKK 243
>pdb|2PQS|A Chain A, Crystal Structure Of The Bovine Lactadherin C2 Domain
pdb|2PQS|B Chain B, Crystal Structure Of The Bovine Lactadherin C2 Domain
pdb|2PQS|C Chain C, Crystal Structure Of The Bovine Lactadherin C2 Domain
pdb|2PQS|D Chain D, Crystal Structure Of The Bovine Lactadherin C2 Domain
Length = 159
Score = 37.0 bits (84), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 38/132 (28%), Positives = 54/132 (40%), Gaps = 20/132 (15%)
Query: 73 SDSEYMAGQLSAFG----YALTDNSEEADIWLINTQSAMDTLIAKCKSAKKPLVVAGCVP 128
+ S Y LSAF YA DN + + W T SA + L S K+ V G +
Sbjct: 20 ASSYYKTWGLSAFSWFPYYARLDNQGKFNAWTAQTNSASEWLQIDLGSQKR---VTGIIT 76
Query: 129 QGSRDLKELEGVSIVGVQQIDRVVEVVEETLKG-HEVRLL--------HRKKLPALDLPK 179
QG+RD ++ V+ V D V E G E ++ H+K + + P
Sbjct: 77 QGARDFGHIQYVAAYRVAYGDDGVTWTEYKDPGASESKIFPGNMDNNSHKKNI--FETPF 134
Query: 180 VRRNKFVEILPI 191
R FV I P+
Sbjct: 135 QAR--FVRIQPV 144
>pdb|2L9L|A Chain A, Nmr Structure Of The Mouse Mfg-e8 C2 Domain
Length = 170
Score = 36.2 bits (82), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 33/131 (25%), Positives = 58/131 (44%), Gaps = 18/131 (13%)
Query: 73 SDSEYMAGQLSAFGY----ALTDNSEEADIWLINTQSAMDTLIAKCKSAKKPLVVAGCVP 128
+ S Y L AFG+ DN + + W + SA + L + ++ V G +
Sbjct: 25 ASSSYKTWNLRAFGWYPHLGRLDNQGKINAWTAQSNSAKEWLQVDLGTQRQ---VTGIIT 81
Query: 129 QGSRDLKELEGVSIVGVQQIDRVVE--VVEE-----TLKGHEVRLLHRKKLPALDLPKVR 181
QG+RD ++ V+ V D V+ V EE +G+ H+K + + P +
Sbjct: 82 QGARDFGHIQYVASYKVAHSDDGVQWTVYEEQGSSKVFQGNLDNNSHKKNI--FEKPFMA 139
Query: 182 RNKFVEILPIN 192
R +V +LP++
Sbjct: 140 R--YVRVLPVS 148
>pdb|3BN6|A Chain A, Crystal Structure Of The C2 Domain Of Bovine Lactadherin
At 1.67 Angstrom Resolution
Length = 158
Score = 33.9 bits (76), Expect = 0.25, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 73 SDSEYMAGQLSAFG----YALTDNSEEADIWLINTQSAMDTLIAKCKSAKKPLVVAGCVP 128
+ S Y LSAF YA DN + + W T SA + L S K+ V G +
Sbjct: 19 ASSYYKTWGLSAFSWFPYYARLDNQGKFNAWTAQTNSASEWLQIDLGSQKR---VTGIIT 75
Query: 129 QGSRDLKELEGVS 141
QG+RD ++ V+
Sbjct: 76 QGARDFGHIQYVA 88
>pdb|3ND0|A Chain A, X-Ray Crystal Structure Of A Slow Cyanobacterial Cl-H+
ANTIPORTER
pdb|3ND0|B Chain B, X-Ray Crystal Structure Of A Slow Cyanobacterial Cl-H+
ANTIPORTER
pdb|3Q17|A Chain A, Structure Of A Slow Clc Cl-H+ ANTIPORTER FROM A
CYANOBACTERIUM IN Bromide
pdb|3Q17|B Chain B, Structure Of A Slow Clc Cl-H+ ANTIPORTER FROM A
CYANOBACTERIUM IN Bromide
Length = 466
Score = 33.5 bits (75), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 39/136 (28%), Positives = 51/136 (37%), Gaps = 11/136 (8%)
Query: 80 GQLSAFGYALTDNSEEADIWLINTQSAMDTLI-AKCKSAKKPLVVAGCVPQGSRDLKELE 138
G LS F LTD + A +W N+QS TLI C L+ G G L
Sbjct: 295 GILSLFPLPLTDGGDNAVLWAFNSQSHFSTLILVFCGRFLLTLICYGSGAIGGIFAPMLG 354
Query: 139 GVSIVGVQQI--------DRVVE--VVEETLKGHEVRLLHRKKLPALDLPKVRRNKFVEI 188
SIV V ++ E V+ G V R L A+ L + + I
Sbjct: 355 IASIVSVAMARHFHLLFPSQIPEPAVMAIAGMGALVAATVRAPLTAILLTIEMTDNYFVI 414
Query: 189 LPINVGCLGACTYCKT 204
LP+ V CL A +
Sbjct: 415 LPLLVTCLVASVVAEA 430
>pdb|4I6L|A Chain A, Crystal Structure Of Otub1 In Complex With Ubiquitin
Variant
Length = 229
Score = 33.1 bits (74), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 39/94 (41%), Gaps = 11/94 (11%)
Query: 265 PDGSTMLR-IGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLS 323
PDG++ R G ++ +L+ KE+ F V +S D V E+T+
Sbjct: 45 PDGNSFYRAFGFSHLEALLDDSKELQR---------FKAVSAKSKEDLVSQGFT-EFTIE 94
Query: 324 DFRTVVDTLIELVPGMQIATDIICGFPGETDEDF 357
DF LIE V D++ F ++ D+
Sbjct: 95 DFHNTFMDLIEQVEKQTSVADLLASFNDQSTSDY 128
>pdb|2ZFY|A Chain A, Crystal Structure Of Human Otubain 1
Length = 234
Score = 32.0 bits (71), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 38/94 (40%), Gaps = 11/94 (11%)
Query: 265 PDGSTMLR-IGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLS 323
PDG+ R G ++ +L+ KE+ F V +S D V E+T+
Sbjct: 50 PDGNCFYRAFGFSHLEALLDDSKELQR---------FKAVSAKSKEDLVSQGFT-EFTIE 99
Query: 324 DFRTVVDTLIELVPGMQIATDIICGFPGETDEDF 357
DF LIE V D++ F ++ D+
Sbjct: 100 DFHNTFMDLIEQVEKQTSVADLLASFNDQSTSDY 133
>pdb|3VON|A Chain A, Crystalstructure Of The Ubiquitin Protease
pdb|3VON|H Chain H, Crystalstructure Of The Ubiquitin Protease
pdb|3VON|O Chain O, Crystalstructure Of The Ubiquitin Protease
pdb|3VON|V Chain V, Crystalstructure Of The Ubiquitin Protease
pdb|3VON|CC Chain c, Crystalstructure Of The Ubiquitin Protease
pdb|3VON|JJ Chain j, Crystalstructure Of The Ubiquitin Protease
Length = 228
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 38/94 (40%), Gaps = 11/94 (11%)
Query: 265 PDGSTMLR-IGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLS 323
PDG+ R G ++ +L+ KE+ F V +S D V E+T+
Sbjct: 44 PDGNCFYRAFGFSHLEALLDDSKELQR---------FKAVSAKSKEDLVSQGFT-EFTIE 93
Query: 324 DFRTVVDTLIELVPGMQIATDIICGFPGETDEDF 357
DF LIE V D++ F ++ D+
Sbjct: 94 DFHNTFMDLIEQVEKQTSVADLLASFNDQSTSDY 127
>pdb|4DDG|A Chain A, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDG|B Chain B, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDG|C Chain C, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDG|J Chain J, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDG|K Chain K, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDG|L Chain L, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDI|A Chain A, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDI|B Chain B, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDI|C Chain C, Crystal Structure Of Human Otub1UBCH5B~UBUB
Length = 399
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 39/94 (41%), Gaps = 11/94 (11%)
Query: 265 PDGSTMLR-IGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLS 323
PDG++ R G ++ +L+ KE+ F V +S D V E+T+
Sbjct: 215 PDGNSFYRAFGFSHLEALLDDSKELQR---------FKAVSAKSKEDLVSQGFT-EFTIE 264
Query: 324 DFRTVVDTLIELVPGMQIATDIICGFPGETDEDF 357
DF LIE V D++ F ++ D+
Sbjct: 265 DFHNTFMDLIEQVEKQTSVADLLASFNDQSTSDY 298
>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 = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 32/140 (22%), Positives = 62/140 (44%), Gaps = 22/140 (15%)
Query: 97 DIWLINTQSAMDTLIAKCKSAKKPLVVAGCVPQGSRDLKE-----LEGVSIVGVQQIDRV 151
D+++I ++ + LI +C+ + + A + LK+ LE +++ GV+ I+RV
Sbjct: 1223 DLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERV 1282
Query: 152 V-------------EVVEE---TLKGHEVRLLHRKKLPALDLPKVRRNKFVEILPI-NVG 194
V E V+E L+ V L +P +D ++ N F++I+ + +
Sbjct: 1283 VMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIE 1342
Query: 195 CLGACTYCKTKHARGHLGSY 214
A Y + + GSY
Sbjct: 1343 AGRAALYKEVYNVIASDGSY 1362
>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 = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 32/140 (22%), Positives = 62/140 (44%), Gaps = 22/140 (15%)
Query: 97 DIWLINTQSAMDTLIAKCKSAKKPLVVAGCVPQGSRDLKE-----LEGVSIVGVQQIDRV 151
D+++I ++ + LI +C+ + + A + LK+ LE +++ GV+ I+RV
Sbjct: 1223 DLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERV 1282
Query: 152 V-------------EVVEE---TLKGHEVRLLHRKKLPALDLPKVRRNKFVEILPI-NVG 194
V E V+E L+ V L +P +D ++ N F++I+ + +
Sbjct: 1283 VMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIE 1342
Query: 195 CLGACTYCKTKHARGHLGSY 214
A Y + + GSY
Sbjct: 1343 AGRAALYKEVYNVIASDGSY 1362
>pdb|3K1Q|D Chain D, Backbone Model Of An Aquareovirus Virion By Cryo-Electron
Microscopy And Bioinformatics
pdb|3K1Q|E Chain E, Backbone Model Of An Aquareovirus Virion By Cryo-Electron
Microscopy And Bioinformatics
pdb|3IYL|U Chain U, Atomic Cryoem Structure Of A Nonenveloped Virus Suggests
How Penetration Protein Is Primed For Cell Entry
pdb|3IYL|V Chain V, Atomic Cryoem Structure Of A Nonenveloped Virus Suggests
How Penetration Protein Is Primed For Cell Entry
Length = 412
Score = 30.8 bits (68), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 2/67 (2%)
Query: 267 GSTMLRIGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLSDFR 326
G T G P F L L+E+A P F H+ + +GS V SA R +++
Sbjct: 8 GLTYNFYGQPAPLFDLNDLQELAGCYARPWTSRFSHLAISTGSLPVWSA--RYPSVASRN 65
Query: 327 TVVDTLI 333
VV+TL+
Sbjct: 66 IVVNTLL 72
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 32/140 (22%), Positives = 62/140 (44%), Gaps = 22/140 (15%)
Query: 97 DIWLINTQSAMDTLIAKCKSAKKPLVVAGCVPQGSRDLKE-----LEGVSIVGVQQIDRV 151
D+++I ++ + LI +C+ + + A + LK+ LE +++ GV+ I+RV
Sbjct: 1223 DLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERV 1282
Query: 152 V-------------EVVEE---TLKGHEVRLLHRKKLPALDLPKVRRNKFVEILPI-NVG 194
V E V+E L+ V L +P +D ++ N F++I+ + +
Sbjct: 1283 VMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIE 1342
Query: 195 CLGACTYCKTKHARGHLGSY 214
A Y + + GSY
Sbjct: 1343 AGRAALYKEVYNVIASDGSY 1362
>pdb|1UX8|A Chain A, X-Ray Structure Of Truncated Oxygen-Avid Haemoglobin From
Bacillus Subtilis
Length = 132
Score = 30.0 bits (66), Expect = 3.9, Method: Composition-based stats.
Identities = 23/115 (20%), Positives = 45/115 (39%), Gaps = 8/115 (6%)
Query: 328 VVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKEY-KFPQVHISQFYPRPGTPAA 386
+VDT E V + I FP + E + + +Y P ++ + G P
Sbjct: 20 LVDTFYERVASHPLLKPI---FPSDLTETARKQKQFLTQYLGGPPLYTEEH----GHPML 72
Query: 387 RMKKVPSAVVKKRSRELTSVFEAFTPYLGMEGRVERIWITEIAADGIHLVGHTKG 441
R + +P + +R+ S + ++G+EG + + H+V T+
Sbjct: 73 RARHLPFPITNERADAWLSCMKDAMDHVGLEGEIREFLFGRLELTARHMVNQTEA 127
>pdb|1UJO|A Chain A, Solution Structure Of The Ch Domain From Mouse Trangelin
Length = 144
Score = 30.0 bits (66), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 13/64 (20%), Positives = 32/64 (50%)
Query: 240 DTGAYGRDIGVNLPILLNAIVAELPPDGSTMLRIGMTNPPFILEHLKEIAEVLRHPCVYS 299
D G G + + ++L+ +V L P+GS +++ P + + ++++A+ L+ Y
Sbjct: 30 DRGRLGFQVWLKNGVILSKLVNSLYPEGSKPVKVPENPPSMVFKQMEQVAQFLKAAEDYG 89
Query: 300 FLHV 303
+
Sbjct: 90 VIKT 93
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
0.319 0.137 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,926,799
Number of Sequences: 62578
Number of extensions: 739313
Number of successful extensions: 1683
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1676
Number of HSP's gapped (non-prelim): 18
length of query: 622
length of database: 14,973,337
effective HSP length: 105
effective length of query: 517
effective length of database: 8,402,647
effective search space: 4344168499
effective search space used: 4344168499
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)