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= psy7062
(148 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2PBI|B Chain B, The Multifunctional Nature Of Gbeta5RGS9 REVEALED FROM ITS
CRYSTAL Structure
pdb|2PBI|D Chain D, The Multifunctional Nature Of Gbeta5RGS9 REVEALED FROM ITS
CRYSTAL Structure
Length = 354
Score = 32.7 bits (73), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 8/73 (10%)
Query: 38 RMYDFGSNNPNPVINCEGVSKNVVEVGFQEDGKWMFTGGEDCRARIWD------LSLCFI 91
R+YD ++ + + E + V F G+ +F G D +WD +S+ F
Sbjct: 265 RLYDLRADREVAIYSKESIIFGASSVDFSLSGRLLFAGYNDYTINVWDVLKGSRVSILFG 324
Query: 92 QQ--VNALRITPD 102
+ V+ LR++PD
Sbjct: 325 HENRVSTLRVSPD 337
>pdb|2YMU|A Chain A, Structure Of A Highly Repetitive Propeller Structure
pdb|2YMU|B Chain B, Structure Of A Highly Repetitive Propeller Structure
Length = 577
Score = 31.6 bits (70), Expect = 0.18, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 55 GVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLCFIQ-------QVNALRITPDKQLLA 107
G S +V V F DG+ + + +D ++W+ + +Q VN + PD Q +A
Sbjct: 219 GHSSSVRGVAFSPDGQTIASASDDKTVKLWNRNGQLLQTLTGHSSSVNGVAFRPDGQTIA 278
Query: 108 SAEE 111
SA +
Sbjct: 279 SASD 282
Score = 30.0 bits (66), Expect = 0.51, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 55 GVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLCFIQ-------QVNALRITPDKQLLA 107
G S +V V F DG+ + + +D ++W+ + +Q V + +PD Q +A
Sbjct: 465 GHSSSVRGVAFSPDGQTIASASDDKTVKLWNRNGQLLQTLTGHSSSVRGVAFSPDGQTIA 524
Query: 108 SAEE 111
SA +
Sbjct: 525 SASD 528
Score = 30.0 bits (66), Expect = 0.56, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 55 GVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLCFIQ-------QVNALRITPDKQLLA 107
G S +V V F DG+ + + +D ++W+ + +Q V + +PD Q +A
Sbjct: 55 GHSSSVWGVAFSPDGQTIASASDDKTVKLWNRNGQLLQTLTGHSSSVRGVAFSPDGQTIA 114
Query: 108 SAEE 111
SA +
Sbjct: 115 SASD 118
Score = 30.0 bits (66), Expect = 0.56, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 55 GVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLCFIQ-------QVNALRITPDKQLLA 107
G S +V V F DG+ + + +D ++W+ + +Q V + +PD Q +A
Sbjct: 178 GHSSSVWGVAFSPDGQTIASASDDKTVKLWNRNGQLLQTLTGHSSSVRGVAFSPDGQTIA 237
Query: 108 SAEE 111
SA +
Sbjct: 238 SASD 241
Score = 30.0 bits (66), Expect = 0.56, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 55 GVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLCFIQ-------QVNALRITPDKQLLA 107
G S +V V F DG+ + + +D ++W+ + +Q V + +PD Q +A
Sbjct: 342 GHSSSVWGVAFSPDGQTIASASDDKTVKLWNRNGQLLQTLTGHSSSVRGVAFSPDGQTIA 401
Query: 108 SAEE 111
SA +
Sbjct: 402 SASD 405
Score = 28.9 bits (63), Expect = 1.0, Method: Composition-based stats.
Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 55 GVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLCFIQQVN-------ALRITPDKQLLA 107
G S +V V F DG+ + + +D ++W+ + +Q + + +PD Q +A
Sbjct: 383 GHSSSVRGVAFSPDGQTIASASDDKTVKLWNRNGQLLQTLTGHSSSVWGVAFSPDDQTIA 442
Query: 108 SAEE 111
SA +
Sbjct: 443 SASD 446
Score = 28.9 bits (63), Expect = 1.0, Method: Composition-based stats.
Identities = 16/64 (25%), Positives = 32/64 (50%), Gaps = 7/64 (10%)
Query: 55 GVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLCFIQQVN-------ALRITPDKQLLA 107
G S +V V F+ DG+ + + +D ++W+ + +Q + + +PD Q +A
Sbjct: 260 GHSSSVNGVAFRPDGQTIASASDDKTVKLWNRNGQLLQTLTGHSSSVWGVAFSPDGQTIA 319
Query: 108 SAEE 111
SA +
Sbjct: 320 SASD 323
Score = 28.5 bits (62), Expect = 1.3, Method: Composition-based stats.
Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 55 GVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLCFIQQVN-------ALRITPDKQLLA 107
G S +V V F DG+ + + +D ++W+ + +Q + + +PD Q +A
Sbjct: 96 GHSSSVRGVAFSPDGQTIASASDDKTVKLWNRNGQLLQTLTGHSSSVWGVAFSPDGQTIA 155
Query: 108 SAEE 111
SA +
Sbjct: 156 SASD 159
Score = 28.5 bits (62), Expect = 1.4, Method: Composition-based stats.
Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 55 GVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLCFIQQVN-------ALRITPDKQLLA 107
G S +V V F DG+ + + +D ++W+ + +Q + + +PD Q +A
Sbjct: 137 GHSSSVWGVAFSPDGQTIASASDDKTVKLWNRNGQLLQTLTGHSSSVWGVAFSPDGQTIA 196
Query: 108 SAEE 111
SA +
Sbjct: 197 SASD 200
Score = 28.5 bits (62), Expect = 1.5, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 7/65 (10%)
Query: 54 EGVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLCFIQQVN-------ALRITPDKQLL 106
E S +V V F DG+ + + +D ++W+ + +Q + + +PD Q +
Sbjct: 13 EAHSSSVRGVAFSPDGQTIASASDDKTVKLWNRNGQLLQTLTGHSSSVWGVAFSPDGQTI 72
Query: 107 ASAEE 111
ASA +
Sbjct: 73 ASASD 77
Score = 28.1 bits (61), Expect = 1.9, Method: Composition-based stats.
Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 7/62 (11%)
Query: 55 GVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLCFIQQVN-------ALRITPDKQLLA 107
G S +V V F DG+ + + +D ++W+ + +Q + + +PD Q +A
Sbjct: 506 GHSSSVRGVAFSPDGQTIASASDDKTVKLWNRNGQLLQTLTGHSSSVWGVAFSPDGQTIA 565
Query: 108 SA 109
SA
Sbjct: 566 SA 567
Score = 27.7 bits (60), Expect = 2.3, Method: Composition-based stats.
Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 55 GVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLCFIQQVN-------ALRITPDKQLLA 107
G S +V V F DG+ + + +D ++W+ + +Q + + +PD Q +A
Sbjct: 301 GHSSSVWGVAFSPDGQTIASASDDKTVKLWNRNGQHLQTLTGHSSSVWGVAFSPDGQTIA 360
Query: 108 SAEE 111
SA +
Sbjct: 361 SASD 364
>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
Length = 1263
Score = 31.2 bits (69), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 8/43 (18%)
Query: 74 TGGEDCRARIWDLS--------LCFIQQVNALRITPDKQLLAS 108
TG DC ++WDL+ VN R +PD +LLAS
Sbjct: 724 TGSSDCFLKLWDLNQKECRNTMFGHTNSVNHCRFSPDDKLLAS 766
>pdb|1ERJ|A Chain A, Crystal Structure Of The C-Terminal Wd40 Domain Of Tup1
pdb|1ERJ|B Chain B, Crystal Structure Of The C-Terminal Wd40 Domain Of Tup1
pdb|1ERJ|C Chain C, Crystal Structure Of The C-Terminal Wd40 Domain Of Tup1
Length = 393
Score = 31.2 bits (69), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 60 VVEVGFQEDGKWMFTGGEDCRARIWDL 86
+ V F DGK++ TG ED RIWD+
Sbjct: 126 IRSVCFSPDGKFLATGAEDRLIRIWDI 152
Score = 26.6 bits (57), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 4/60 (6%)
Query: 33 GYQHIRMYDFGSNNPNPVINCE-GVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLCFI 91
G + +R++D + + ++ E GV+ V G DGK++ G D R+WD F+
Sbjct: 185 GDRTVRIWDLRTGQCSLTLSIEDGVTTVAVSPG---DGKYIAAGSLDRAVRVWDSETGFL 241
>pdb|2XZM|R Chain R, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
In Complex With Initiation Factor 1. This File Contains
The 40s Subunit And Initiation Factor For Molecule 1
pdb|2XZN|R Chain R, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
In Complex With Initiation Factor 1. This File Contains
The 40s Subunit And Initiation Factor For Molecule 2
Length = 343
Score = 31.2 bits (69), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 59 NVVEVGFQEDGKWMFTGGEDCRARIWD-LSLCFIQQ-------VNALRITPDKQLLA 107
NV + +GK++ TGG+D + IWD L+L + Q+ +N + P Q +A
Sbjct: 215 NVNHLSISPNGKYIATGGKDKKLLIWDILNLTYPQREFDAGSTINQIAFNPKLQWVA 271
>pdb|2ZKQ|AA Chain a, Structure Of A Mammalian Ribosomal 40s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 317
Score = 29.6 bits (65), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 3/78 (3%)
Query: 13 GQISTVFDSKHLVEMVAALGGYQHIRMYDFGSNNPN---PVINCEGVSKNVVEVGFQEDG 69
G ++ + + +M+ + + I M+ + N P G S V +V DG
Sbjct: 16 GWVTQIATTPQFPDMILSASRDKTIIMWKLTRDETNYGIPQRALRGHSHFVSDVVISSDG 75
Query: 70 KWMFTGGEDCRARIWDLS 87
++ +G D R+WDL+
Sbjct: 76 QFALSGSWDGTLRLWDLT 93
Score = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 25/112 (22%), Positives = 46/112 (41%), Gaps = 35/112 (31%)
Query: 42 FGSNNPNPVI---------------NCEGVSKNVVEVGF------QEDGKWMFTGGEDCR 80
F N+ NP+I NC+ + ++ G+ DG +GG+D +
Sbjct: 156 FSPNSSNPIIVSCGWDKLVKVWNLANCKLKTNHIGHTGYLNTVTVSPDGSLCASGGKDGQ 215
Query: 81 ARIWDL-------SLCFIQQVNALRITPDKQLLASAEELSCCYCGAAVFVYN 125
A +WDL +L +NAL +P++ L C G ++ +++
Sbjct: 216 AMLWDLNEGKHLYTLDGGDIINALCFSPNRYWL-------CAATGPSIKIWD 260
>pdb|4AOW|A Chain A, Crystal Structure Of The Human Rack1 Protein At A
Resolution Of 2.45 Angstrom
pdb|4AOW|B Chain B, Crystal Structure Of The Human Rack1 Protein At A
Resolution Of 2.45 Angstrom
pdb|4AOW|C Chain C, Crystal Structure Of The Human Rack1 Protein At A
Resolution Of 2.45 Angstrom
Length = 340
Score = 29.3 bits (64), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 3/78 (3%)
Query: 13 GQISTVFDSKHLVEMVAALGGYQHIRMYDFGSNNPN---PVINCEGVSKNVVEVGFQEDG 69
G ++ + + +M+ + + I M+ + N P G S V +V DG
Sbjct: 39 GWVTQIATTPQFPDMILSASRDKTIIMWKLTRDETNYGIPQRALRGHSHFVSDVVISSDG 98
Query: 70 KWMFTGGEDCRARIWDLS 87
++ +G D R+WDL+
Sbjct: 99 QFALSGSWDGTLRLWDLT 116
Score = 28.1 bits (61), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 25/112 (22%), Positives = 46/112 (41%), Gaps = 35/112 (31%)
Query: 42 FGSNNPNPVI---------------NCEGVSKNVVEVGF------QEDGKWMFTGGEDCR 80
F N+ NP+I NC+ + ++ G+ DG +GG+D +
Sbjct: 179 FSPNSSNPIIVSCGWDKLVKVWNLANCKLKTNHIGHTGYLNTVTVSPDGSLCASGGKDGQ 238
Query: 81 ARIWDL-------SLCFIQQVNALRITPDKQLLASAEELSCCYCGAAVFVYN 125
A +WDL +L +NAL +P++ L C G ++ +++
Sbjct: 239 AMLWDLNEGKHLYTLDGGDIINALCFSPNRYWL-------CAATGPSIKIWD 283
>pdb|3ZEY|7 Chain 7, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 318
Score = 29.3 bits (64), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 55 GVSKNVVEVGFQEDGKWMFTGGEDCRARIWDL 86
G +K+V+ V F D + + +GG D R+W++
Sbjct: 107 GHTKDVLSVAFSPDNRQIVSGGRDNALRVWNV 138
Score = 26.9 bits (58), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 24/105 (22%), Positives = 47/105 (44%), Gaps = 10/105 (9%)
Query: 15 ISTVFDSKHLVEMVAALGGYQH-IRMYDFGSNNPNPVINCEGVSKNVVEVGFQEDGKWMF 73
+S V S L V GG+ + ++++D + V + +G + V V DG
Sbjct: 155 VSCVRFSPSLDAPVIVSGGWDNLVKVWDLATGRL--VTDLKGHTNYVTSVTVSPDGSLCA 212
Query: 74 TGGEDCRARIWDLS-------LCFIQQVNALRITPDKQLLASAEE 111
+ +D AR+WDL+ + +N + +P++ + +A E
Sbjct: 213 SSDKDGVARLWDLTKGEALSEMAAGAPINQICFSPNRYWMCAATE 257
>pdb|3OW8|A Chain A, Crystal Structure Of The Wd Repeat-Containing Protein 61
pdb|3OW8|B Chain B, Crystal Structure Of The Wd Repeat-Containing Protein 61
pdb|3OW8|C Chain C, Crystal Structure Of The Wd Repeat-Containing Protein 61
pdb|3OW8|D Chain D, Crystal Structure Of The Wd Repeat-Containing Protein 61
Length = 321
Score = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 42 FGSNNPNPVINCEGVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLCFIQQ-------- 93
FG + + + K ++ + + DGK++ +G D I+D++ +
Sbjct: 149 FGVESGKKEYSLDTRGKFILSIAYSPDGKYLASGAIDGIINIFDIATGKLLHTLEGHAMP 208
Query: 94 VNALRITPDKQLLASAEE 111
+ +L +PD QLL +A +
Sbjct: 209 IRSLTFSPDSQLLVTASD 226
>pdb|3PDI|A Chain A, Precursor Bound Nifen
pdb|3PDI|C Chain C, Precursor Bound Nifen
pdb|3PDI|E Chain E, Precursor Bound Nifen
pdb|3PDI|G Chain G, Precursor Bound Nifen
Length = 483
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 102 DKQLLASAEELSCCYCGAAVFVYNSCYPAAV 132
+K+L + + Y AVFVYN+C PA +
Sbjct: 107 EKRLFHAIRQAVESYSPPAVFVYNTCVPALI 137
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length Murine
Apaf-1
Length = 1256
Score = 28.5 bits (62), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 36/89 (40%), Gaps = 17/89 (19%)
Query: 36 HIRMYDFGSNN--------PNPVINCEGV--SKNVVEVGFQEDGKWMFTGGEDCRARIWD 85
H+ FG + PN + GV K V + F DGK + + ED ++W+
Sbjct: 979 HLEYVAFGDEDGAIKIIELPNNRVFSSGVGHKKAVRHIQFTADGKTLISSSEDSVIQVWN 1038
Query: 86 L---SLCFIQ----QVNALRITPDKQLLA 107
F+Q V R+ D +LL+
Sbjct: 1039 WQTGDYVFLQAHQETVKDFRLLQDSRLLS 1067
Score = 27.3 bits (59), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 8/43 (18%)
Query: 74 TGGEDCRARIWDLS--------LCFIQQVNALRITPDKQLLAS 108
TG D ++WDL+ VN R +PD +LLAS
Sbjct: 725 TGSNDFFLKLWDLNQKECRNTMFGHTNSVNHCRFSPDDELLAS 767
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 28.5 bits (62), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 36/89 (40%), Gaps = 17/89 (19%)
Query: 36 HIRMYDFGSNN--------PNPVINCEGV--SKNVVEVGFQEDGKWMFTGGEDCRARIWD 85
H+ FG + PN + GV K V + F DGK + + ED ++W+
Sbjct: 972 HLEYVAFGDEDGAIKIIELPNNRVFSSGVGHKKAVRHIQFTADGKTLISSSEDSVIQVWN 1031
Query: 86 L---SLCFIQ----QVNALRITPDKQLLA 107
F+Q V R+ D +LL+
Sbjct: 1032 WQTGDYVFLQAHQETVKDFRLLQDSRLLS 1060
Score = 27.3 bits (59), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 8/43 (18%)
Query: 74 TGGEDCRARIWDLS--------LCFIQQVNALRITPDKQLLAS 108
TG D ++WDL+ VN R +PD +LLAS
Sbjct: 718 TGSNDFFLKLWDLNQKECRNTMFGHTNSVNHCRFSPDDELLAS 760
>pdb|3MMY|A Chain A, Structural And Functional Analysis Of The Interaction
Between The Nucleoporin Nup98 And The Mrna Export Factor
Rae1
pdb|3MMY|C Chain C, Structural And Functional Analysis Of The Interaction
Between The Nucleoporin Nup98 And The Mrna Export Factor
Rae1
pdb|3MMY|E Chain E, Structural And Functional Analysis Of The Interaction
Between The Nucleoporin Nup98 And The Mrna Export Factor
Rae1
pdb|3MMY|G Chain G, Structural And Functional Analysis Of The Interaction
Between The Nucleoporin Nup98 And The Mrna Export Factor
Rae1
Length = 368
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 60 VVEVGFQEDGKWMFTGGEDCRARIWDLS 87
V++V + +DG +FT D A++WDLS
Sbjct: 89 VLDVCWSDDGSKVFTASCDKTAKMWDLS 116
>pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|B Chain B, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|B Chain B, Rna Polymerase Ii Elongation Complex
pdb|1K83|B Chain B, Crystal Structure Of Yeast Rna Polymerase Ii Complexed With
The Inhibitor Alpha Amanitin
pdb|1NIK|B Chain B, Wild Type Rna Polymerase Ii
pdb|1NT9|B Chain B, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|B Chain B, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|B Chain B, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|B Chain B, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|B Chain B, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|B Chain B, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|B Chain B, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|B Chain B, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|B Chain B, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|B Chain B, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|B Chain B, Complete Rna Polymerase Ii Elongation Complex With Substrate
Analogue Gmpcpp
pdb|1Y1V|B Chain B, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|B Chain B, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|B Chain B, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|B Chain B, 12-Subunit Rna Polymerase Ii
pdb|2E2H|B Chain B, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|B Chain B, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|B Chain B, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex A
pdb|2JA6|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex B
pdb|2JA7|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex C
pdb|2JA7|N Chain N, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex C
pdb|2JA8|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex D
pdb|2YU9|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With Utp
pdb|2R7Z|B Chain B, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|B Chain B, Elongation Complex Of Rna Polymerase Ii With Artificial Rdrp
Scaffold
pdb|2R93|B Chain B, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|B Chain B, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|B Chain B, Crystal Structure Of 10 Subunit Rna Polymerase Ii In Complex
With The Inhibitor Alpha-Amanitin
pdb|3FKI|B Chain B, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|B Chain B, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|B Chain B, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|B Chain B, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|B Chain B, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|B Chain B, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|B Chain B, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|B Chain B, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|B Chain B, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|C Chain C, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|B Chain B, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|N Chain N, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|B Chain B, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|B Chain B, Complete Rna Polymerase Ii Elongation Complex Iii With A T-U
Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|B Chain B, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|B Chain B, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|B Chain B, Complete Rna Polymerase Ii Elongation Complex Iv With A T-U
Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|B Chain B, 8-oxoguanine Containing Rna Polymerase Ii Elongation Complex
D
pdb|3I4N|B Chain B, 8-oxoguanine Containing Rna Polymerase Ii Elongation Complex
E
pdb|3K1F|B Chain B, Crystal Structure Of Rna Polymerase Ii In Complex With Tfiib
pdb|3K7A|B Chain B, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|B Chain B, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|B Chain B, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|B Chain B, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|B Chain B, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|B Chain B, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|B Chain B, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|B Chain B, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|B Chain B, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|B Chain B, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|B Chain B, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|B Chain B, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|3J0K|B Chain B, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|B Chain B, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|B Chain B, Rna Polymerase Ii Elongation Complex Containing A Cpd Lesion
pdb|4BBR|B Chain B, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|B Chain B, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 1224
Score = 28.1 bits (61), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 35/69 (50%), Gaps = 14/69 (20%)
Query: 23 HLVE----MVAALGGYQHIRMYDFGSNNPNPVINCEGVSKNVVEVGFQEDG-KWMFTG-- 75
HL+E VAAL G + G +P I EG+SK + E G+Q G + M+ G
Sbjct: 1025 HLIECLLSKVAALSGNE-------GDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHT 1077
Query: 76 GEDCRARIW 84
G+ A+I+
Sbjct: 1078 GKKLMAQIF 1086
>pdb|3N0E|A Chain A, Crystal Structure Of Wdr5 Mutant (W330y)
Length = 315
Score = 27.7 bits (60), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 23/53 (43%)
Query: 32 GGYQHIRMYDFGSNNPNPVINCEGVSKNVVEVGFQEDGKWMFTGGEDCRARIW 84
GG Q R +F N G +K V V F +G+W+ + D +IW
Sbjct: 1 GGQQMGRGSEFVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIW 53
>pdb|3N0D|A Chain A, Crystal Structure Of Wdr5 Mutant (W330f)
Length = 315
Score = 27.7 bits (60), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 23/53 (43%)
Query: 32 GGYQHIRMYDFGSNNPNPVINCEGVSKNVVEVGFQEDGKWMFTGGEDCRARIW 84
GG Q R +F N G +K V V F +G+W+ + D +IW
Sbjct: 1 GGQQMGRGSEFVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIW 53
>pdb|2LC4|A Chain A, Solution Structure Of Pilp From Pseudomonas Aeruginosa
Length = 111
Score = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/64 (20%), Positives = 29/64 (45%)
Query: 9 LTAFGQISTVFDSKHLVEMVAALGGYQHIRMYDFGSNNPNPVINCEGVSKNVVEVGFQED 68
+ F + T+ +++ +V GG +R+ D+ N V+ +V+E+ +
Sbjct: 28 IETFEMVGTLSNAQGTFALVKGAGGVHRVRVGDYLGRNDGKVVGISEGKIDVIEIVPDGE 87
Query: 69 GKWM 72
G W+
Sbjct: 88 GNWL 91
>pdb|2Y4X|A Chain A, Structure Of A Domain From The Type Iv Pilus Biogenesis
Lipoprotein Pilp, From Pseudomonas Aeruginosa Pa01
pdb|2Y4X|B Chain B, Structure Of A Domain From The Type Iv Pilus Biogenesis
Lipoprotein Pilp, From Pseudomonas Aeruginosa Pa01
pdb|2Y4Y|A Chain A, Structure Of A Domain From The Type Iv Pilus Biogenesis
Lipoprotein Pilp, From Pseudomonas Aeruginosa
pdb|2Y4Y|B Chain B, Structure Of A Domain From The Type Iv Pilus Biogenesis
Lipoprotein Pilp, From Pseudomonas Aeruginosa
pdb|2Y4Y|C Chain C, Structure Of A Domain From The Type Iv Pilus Biogenesis
Lipoprotein Pilp, From Pseudomonas Aeruginosa
pdb|2Y4Y|D Chain D, Structure Of A Domain From The Type Iv Pilus Biogenesis
Lipoprotein Pilp, From Pseudomonas Aeruginosa
Length = 93
Score = 27.3 bits (59), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 13/64 (20%), Positives = 29/64 (45%)
Query: 9 LTAFGQISTVFDSKHLVEMVAALGGYQHIRMYDFGSNNPNPVINCEGVSKNVVEVGFQED 68
+ F + T+ +++ +V GG +R+ D+ N V+ +V+E+ +
Sbjct: 21 IETFEMVGTLSNAQGTFALVKGAGGVHRVRVGDYLGRNDGKVVGISEGKIDVIEIVPDGE 80
Query: 69 GKWM 72
G W+
Sbjct: 81 GNWL 84
>pdb|1GXR|A Chain A, Wd40 Region Of Human Groucho/tle1
pdb|1GXR|B Chain B, Wd40 Region Of Human Groucho/tle1
pdb|2CE8|A Chain A, An Eh1 Peptide Bound To The Groucho-Tle Wd40 Domain.
pdb|2CE8|B Chain B, An Eh1 Peptide Bound To The Groucho-Tle Wd40 Domain.
pdb|2CE8|C Chain C, An Eh1 Peptide Bound To The Groucho-Tle Wd40 Domain.
pdb|2CE8|D Chain D, An Eh1 Peptide Bound To The Groucho-Tle Wd40 Domain.
pdb|2CE9|A Chain A, A Wrpw Peptide Bound To The Groucho-Tle Wd40 Domain.
pdb|2CE9|B Chain B, A Wrpw Peptide Bound To The Groucho-Tle Wd40 Domain.
pdb|2CE9|C Chain C, A Wrpw Peptide Bound To The Groucho-Tle Wd40 Domain.
pdb|2CE9|D Chain D, A Wrpw Peptide Bound To The Groucho-Tle Wd40 Domain
Length = 337
Score = 27.3 bits (59), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 35/85 (41%), Gaps = 9/85 (10%)
Query: 36 HIRMYDFGSNNPNPVINCEGVSKNVVEVGFQEDGKWMFTGGEDCRARIWDL-------SL 88
+I ++D +N V +G + + DG ++TGG D R WDL
Sbjct: 164 NIAVWDL--HNQTLVRQFQGHTDGASCIDISNDGTKLWTGGLDNTVRSWDLREGRQLQQH 221
Query: 89 CFIQQVNALRITPDKQLLASAEELS 113
F Q+ +L P + LA E S
Sbjct: 222 DFTSQIFSLGYCPTGEWLAVGMESS 246
Score = 25.8 bits (55), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 24/100 (24%), Positives = 38/100 (38%), Gaps = 18/100 (18%)
Query: 32 GGYQHIRMYDF---GSNNPNPVINCEGVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLS- 87
GG ++++D G+ +P ++C + DG + GGE IWDL+
Sbjct: 69 GGKGCVKVWDISHPGNKSPVSQLDCLNRDNYIRSCKLLPDGCTLIVGGEASTLSIWDLAA 128
Query: 88 ---------LCFIQQVNALRITPDKQLLASAEELSCCYCG 118
AL I+PD ++ SCC G
Sbjct: 129 PTPRIKAELTSSAPACYALAISPDSKVC-----FSCCSDG 163
>pdb|2PM9|A Chain A, Crystal Structure Of Yeast Sec1331 VERTEX ELEMENT OF THE
Copii Vesicular Coat
Length = 416
Score = 26.9 bits (58), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 13/56 (23%), Positives = 26/56 (46%)
Query: 72 MFTGGEDCRARIWDLSLCFIQQVNALRITPDKQLLASAEELSCCYCGAAVFVYNSC 127
+ +GG + IWD++ C N +TP + + + E +S + + V+ S
Sbjct: 129 LASGGNNGEIFIWDMNKCTESPSNYTPLTPGQSMSSVDEVISLAWNQSLAHVFASA 184
>pdb|3MXX|A Chain A, Crystal Structure Of Wdr5 Mutant (S62a)
Length = 315
Score = 26.9 bits (58), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 22/53 (41%)
Query: 32 GGYQHIRMYDFGSNNPNPVINCEGVSKNVVEVGFQEDGKWMFTGGEDCRARIW 84
GG Q R +F N G +K V V F +G+W+ D +IW
Sbjct: 1 GGQQMGRGSEFVKPNYALKFTLAGHTKAVSSVKFSPNGEWLAASSADKLIKIW 53
>pdb|3DM0|A Chain A, Maltose Binding Protein Fusion With Rack1 From A. Thaliana
Length = 694
Score = 26.2 bits (56), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 55 GVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLS 87
G S V +V DG++ +G D R+WDL+
Sbjct: 428 GHSHFVEDVVLSSDGQFALSGSWDGELRLWDLA 460
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
0.322 0.136 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,291,228
Number of Sequences: 62578
Number of extensions: 164292
Number of successful extensions: 635
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 568
Number of HSP's gapped (non-prelim): 80
length of query: 148
length of database: 14,973,337
effective HSP length: 90
effective length of query: 58
effective length of database: 9,341,317
effective search space: 541796386
effective search space used: 541796386
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)