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= 042220
(255 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3ZU7|B Chain B, Crystal Structure Of A Designed Selected Ankyrin Repeat
Protein In Complex With The Map Kinase Erk2
Length = 169
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 30/88 (34%), Positives = 40/88 (45%), Gaps = 16/88 (18%)
Query: 11 NDQKMTALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNLFQLHSRLRN 70
+DQ T L LAA GH +V ++ D + D GW LH A + +L
Sbjct: 44 DDQGSTPLHLAAWIGHPEIVEVLLKHGADVNAR-DTDGWTPLHLAADNGHL--------- 93
Query: 71 RSVEML------INKQDVNGNTPLHVLA 92
VE+L +N QD G TPLH+ A
Sbjct: 94 EIVEVLLKYGADVNAQDAYGLTPLHLAA 121
>pdb|2XEH|A Chain A, Structural Determinants For Improved Thermal Stability Of
Designed Ankyrin Repeat Proteins With A Redesigned C-
Capping Module.
pdb|2XEH|B Chain B, Structural Determinants For Improved Thermal Stability Of
Designed Ankyrin Repeat Proteins With A Redesigned C-
Capping Module.
pdb|2XEH|C Chain C, Structural Determinants For Improved Thermal Stability Of
Designed Ankyrin Repeat Proteins With A Redesigned C-
Capping Module
Length = 157
Score = 35.4 bits (80), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 16 TALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNLFQLHSRLRNRSVEM 75
T L LAA GH+ +V ++ D + D+ G+ LH A +L + L+ +
Sbjct: 37 TPLHLAAREGHLEIVEVLLKAGADVNAK-DKDGYTPLHLAAREGHLEIVEVLLKAGAD-- 93
Query: 76 LINKQDVNGNTPLHVLA 92
+N +D +G TPLH+ A
Sbjct: 94 -VNAKDKDGYTPLHLAA 109
>pdb|4HQD|A Chain A, Crystal Structure Of Engineered Protein. Northeast
Structural Genomics Consortium Target Or265.
pdb|4HQD|B Chain B, Crystal Structure Of Engineered Protein. Northeast
Structural Genomics Consortium Target Or265
Length = 169
Score = 35.4 bits (80), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 32/96 (33%), Positives = 44/96 (45%), Gaps = 17/96 (17%)
Query: 9 SDNDQKMTALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNLFQLHSRL 68
SD+D + T L AA GH +V +IS D + D G LH+A H +
Sbjct: 33 SDSDGR-TPLHYAAKEGHKEIVKLLISKGADVNAK-DSDGRTPLHYAAKEG-----HKEI 85
Query: 69 RNRSVEMLINK------QDVNGNTPLHVLAAVLQKE 98
V++LI+K +D +G TPLH A KE
Sbjct: 86 ----VKLLISKGADVNAKDSDGRTPLHYAAKEGHKE 117
>pdb|1MJ0|A Chain A, Sank E3_5: An Artificial Ankyrin Repeat Protein
Length = 166
Score = 35.4 bits (80), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 43/84 (51%), Gaps = 5/84 (5%)
Query: 9 SDNDQKMTALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNLFQLHSRL 68
+DND T L LAA GH+ +V ++ D D G LH A A+ +L + L
Sbjct: 43 TDND-GYTPLHLAASNGHLEIVEVLLKNGADVNAS-DLTGITPLHLAAATGHLEIVEVLL 100
Query: 69 RNRSVEMLINKQDVNGNTPLHVLA 92
++ + +N D +G+TPLH+ A
Sbjct: 101 KHGAD---VNAYDNDGHTPLHLAA 121
>pdb|2XEE|A Chain A, Structural Determinants For Improved Thermal Stability Of
Designed Ankyrin Repeat Proteins With A Redesigned C-
Capping Module.
pdb|2XEE|B Chain B, Structural Determinants For Improved Thermal Stability Of
Designed Ankyrin Repeat Proteins With A Redesigned C-
Capping Module.
pdb|2XEE|C Chain C, Structural Determinants For Improved Thermal Stability Of
Designed Ankyrin Repeat Proteins With A Redesigned C-
Capping Module.
pdb|2XEE|D Chain D, Structural Determinants For Improved Thermal Stability Of
Designed Ankyrin Repeat Proteins With A Redesigned C-
Capping Module
Length = 157
Score = 35.4 bits (80), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 16 TALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNLFQLHSRLRNRSVEM 75
T L LAA GH+ +V ++ D + D+ G+ LH A +L + L+ +
Sbjct: 37 TPLHLAAREGHLEIVEVLLKAGADVNAK-DKDGYTPLHLAAREGHLEIVEVLLKAGAD-- 93
Query: 76 LINKQDVNGNTPLHVLA 92
+N +D +G TPLH+ A
Sbjct: 94 -VNAKDKDGYTPLHLAA 109
>pdb|1N0R|A Chain A, 4ank: A Designed Ankyrin Repeat Protein With Four
Identical Consensus Repeats
Length = 126
Score = 35.0 bits (79), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 29/97 (29%), Positives = 46/97 (47%), Gaps = 17/97 (17%)
Query: 3 KSAACISDNDQK-MTALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNL 61
++ A ++ D+ T L LAA GH+ VV ++ D + D+ G LH A + +L
Sbjct: 23 EAGADVNAKDKNGRTPLHLAARNGHLEVVKLLLEAGADVNAK-DKNGRTPLHLAARNGHL 81
Query: 62 FQLHSRLRNRSVEML------INKQDVNGNTPLHVLA 92
V++L +N +D NG TPLH+ A
Sbjct: 82 ---------EVVKLLLEAGADVNAKDKNGRTPLHLAA 109
Score = 34.7 bits (78), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 39/83 (46%), Gaps = 16/83 (19%)
Query: 16 TALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNLFQLHSRLRNRSVEM 75
T L LAA GH+ VV ++ D + D+ G LH A + +L V++
Sbjct: 4 TPLHLAARNGHLEVVKLLLEAGADVNAK-DKNGRTPLHLAARNGHL---------EVVKL 53
Query: 76 L------INKQDVNGNTPLHVLA 92
L +N +D NG TPLH+ A
Sbjct: 54 LLEAGADVNAKDKNGRTPLHLAA 76
>pdb|2QYJ|A Chain A, Crystal Structure Of A Designed Full Consensus Ankyrin
Length = 166
Score = 35.0 bits (79), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 16 TALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNLFQLHSRLRNRSVEM 75
T L LAA GH+ +V ++ D + D+ G+ LH A +L + L+ +
Sbjct: 49 TPLHLAAREGHLEIVEVLLKAGADVNAK-DKDGYTPLHLAAREGHLEIVEVLLKAGAD-- 105
Query: 76 LINKQDVNGNTPLHVLA 92
+N +D +G TPLH+ A
Sbjct: 106 -VNAKDKDGYTPLHLAA 121
>pdb|1N0Q|A Chain A, 3ank: A Designed Ankyrin Repeat Protein With Three
Identical Consensus Repeats
pdb|1N0Q|B Chain B, 3ank: A Designed Ankyrin Repeat Protein With Three
Identical Consensus Repeats
Length = 93
Score = 35.0 bits (79), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 39/83 (46%), Gaps = 16/83 (19%)
Query: 16 TALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNLFQLHSRLRNRSVEM 75
T L LAA GH+ VV ++ D + D+ G LH A + +L V++
Sbjct: 4 TPLHLAARNGHLEVVKLLLEAGADVNAK-DKNGRTPLHLAARNGHL---------EVVKL 53
Query: 76 L------INKQDVNGNTPLHVLA 92
L +N +D NG TPLH+ A
Sbjct: 54 LLEAGADVNAKDKNGRTPLHLAA 76
>pdb|4GMR|A Chain A, Crystal Structure Of Engineered Protein. Northeast
Structural Genomics Consortium Target Or266.
pdb|4GMR|B Chain B, Crystal Structure Of Engineered Protein. Northeast
Structural Genomics Consortium Target Or266
Length = 169
Score = 33.9 bits (76), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 33/96 (34%), Positives = 45/96 (46%), Gaps = 17/96 (17%)
Query: 9 SDNDQKMTALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNLFQLHSRL 68
SD+D K T L LAA GH VV ++S D + D G LH A + H +
Sbjct: 33 SDSDGK-TPLHLAAENGHKEVVKLLLSQGADPNAK-DSDGKTPLHLAAENG-----HKEV 85
Query: 69 RNRSVEMLI------NKQDVNGNTPLHVLAAVLQKE 98
V++L+ N +D +G TPLH+ A KE
Sbjct: 86 ----VKLLLSQGADPNAKDSDGKTPLHLAAENGHKE 117
>pdb|4F6R|D Chain D, Tubulin:stathmin-Like Domain Complex
Length = 169
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 42/89 (47%), Gaps = 4/89 (4%)
Query: 4 SAACISDNDQKMTALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNLFQ 63
A +++D T L LAA +GH+ +V ++ D D+ G LH A +L
Sbjct: 37 GADVNAEDDSGKTPLHLAAIKGHLEIVEVLLKHGAD-VNAADKMGDTPLHLAALYGHLEI 95
Query: 64 LHSRLRNRSVEMLINKQDVNGNTPLHVLA 92
+ L+N + +N D G TPLH+ A
Sbjct: 96 VEVLLKNGAD---VNATDTYGFTPLHLAA 121
>pdb|3NOC|D Chain D, Designed Ankyrin Repeat Protein (Darpin) Binders To Acrb:
Plasticity Of The Interface
pdb|3NOC|E Chain E, Designed Ankyrin Repeat Protein (Darpin) Binders To Acrb:
Plasticity Of The Interface
Length = 169
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 31/104 (29%), Positives = 47/104 (45%), Gaps = 13/104 (12%)
Query: 3 KSAACISDNDQ-KMTALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNL 61
K+ A ++ D +T L LAA RGH+ +V ++ D D G+ LH A +L
Sbjct: 68 KNGADVNAKDSLGVTPLHLAARRGHLEIVEVLLKNGADVNAS-DSHGFTPLHLAAKRGHL 126
Query: 62 FQLHSRLRNRSVEMLINKQDVNGNTPLHV--------LAAVLQK 97
+ L+N + +N QD G T + LA +LQK
Sbjct: 127 EIVEVLLKNGAD---VNAQDKFGKTAFDISIDNGNEDLAEILQK 167
>pdb|4HB5|A Chain A, Crystal Structure Of Engineered Protein. Northeast
Structural Genomics Consortium Target Or267.
pdb|4HB5|B Chain B, Crystal Structure Of Engineered Protein. Northeast
Structural Genomics Consortium Target Or267
Length = 169
Score = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 30/96 (31%), Positives = 45/96 (46%), Gaps = 17/96 (17%)
Query: 9 SDNDQKMTALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNLFQLHSRL 68
SD+D + T L AA GH +V ++S D + D G LH+A + H +
Sbjct: 33 SDSDGR-TPLHYAAENGHKEIVKLLLSKGADPNAK-DSDGRTPLHYAAENG-----HKEI 85
Query: 69 RNRSVEMLINK------QDVNGNTPLHVLAAVLQKE 98
V++L++K +D +G TPLH A KE
Sbjct: 86 ----VKLLLSKGADPNAKDSDGRTPLHYAAENGHKE 117
>pdb|4GPM|A Chain A, Crystal Structure Of Engineered Protein. Northeast
Structural Genomics Consortium Target Or264.
pdb|4GPM|B Chain B, Crystal Structure Of Engineered Protein. Northeast
Structural Genomics Consortium Target Or264
Length = 169
Score = 31.6 bits (70), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 33/96 (34%), Positives = 44/96 (45%), Gaps = 17/96 (17%)
Query: 9 SDNDQKMTALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNLFQLHSRL 68
SD+D + T L AA GH VV +IS D + D G LH A + H +
Sbjct: 33 SDSDGR-TPLHHAAENGHKEVVKLLISKGADVNAK-DSDGRTPLHHAAENG-----HKEV 85
Query: 69 RNRSVEMLINK------QDVNGNTPLHVLAAVLQKE 98
V++LI+K +D +G TPLH A KE
Sbjct: 86 ----VKLLISKGADVNAKDSDGRTPLHHAAENGHKE 117
>pdb|3NOG|D Chain D, Designed Ankyrin Repeat Protein (Darpin) Binders To Acrb:
Plasticity Of The Interface
pdb|3NOG|E Chain E, Designed Ankyrin Repeat Protein (Darpin) Binders To Acrb:
Plasticity Of The Interface
Length = 169
Score = 31.6 bits (70), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 31/104 (29%), Positives = 48/104 (46%), Gaps = 13/104 (12%)
Query: 3 KSAACISDNDQ-KMTALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNL 61
K+ A ++ +D +T L LAA RGH+ VV ++ D D G+ LH A +L
Sbjct: 68 KNGADVNADDSLGVTPLHLAADRGHLEVVEVLLKNGADVNAN-DHNGFTPLHLAANIGHL 126
Query: 62 FQLHSRLRNRSVEMLINKQDVNGNTPLHV--------LAAVLQK 97
+ L++ + +N QD G T + LA +LQK
Sbjct: 127 EIVEVLLKHGAD---VNAQDKFGKTAFDISIDNGNEDLAEILQK 167
>pdb|2Y1L|E Chain E, Caspase-8 In Complex With Darpin-8.4
pdb|2Y1L|F Chain F, Caspase-8 In Complex With Darpin-8.4
Length = 169
Score = 31.6 bits (70), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 4/77 (5%)
Query: 16 TALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNLFQLHSRLRNRSVEM 75
T L LAA GH+ +V ++ D VD G L A +L + L+N +
Sbjct: 49 TPLHLAAFNGHLEIVEVLLKNGADV-NAVDHAGMTPLRLAALFGHLEIVEVLLKNGAD-- 105
Query: 76 LINKQDVNGNTPLHVLA 92
+N D+ G+TPLH+ A
Sbjct: 106 -VNANDMEGHTPLHLAA 121
>pdb|2BKK|B Chain B, Crystal Structure Of Aminoglycoside Phosphotransferase Aph
(3')-Iiia In Complex With The Inhibitor Ar_3a
pdb|2BKK|D Chain D, Crystal Structure Of Aminoglycoside Phosphotransferase Aph
(3')-Iiia In Complex With The Inhibitor Ar_3a
Length = 169
Score = 31.2 bits (69), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 31/104 (29%), Positives = 49/104 (47%), Gaps = 13/104 (12%)
Query: 3 KSAACISDNDQK-MTALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNL 61
K AA ++ +D+ T L LAA RGH+ +V ++ D +D +G+ LH A +L
Sbjct: 68 KYAADVNASDKSGWTPLHLAAYRGHLEIVEVLLKYGAD-VNAMDYQGYTPLHLAAEDGHL 126
Query: 62 FQLHSRLRNRSVEMLINKQDVNGNTPLHV--------LAAVLQK 97
+ L+ + +N QD G T + LA +LQK
Sbjct: 127 EIVEVLLKYGAD---VNAQDKFGKTAFDISIDNGNEDLAEILQK 167
>pdb|4ATZ|D Chain D, Ad5 Knob In Complex With A Designed Ankyrin Repeat
Protein
pdb|4ATZ|E Chain E, Ad5 Knob In Complex With A Designed Ankyrin Repeat
Protein
pdb|4ATZ|F Chain F, Ad5 Knob In Complex With A Designed Ankyrin Repeat
Protein
Length = 154
Score = 31.2 bits (69), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 18 LLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNLFQLHSRLRNRSVEMLI 77
LL AA G V +++ D D G LH A A +L + LRN + +
Sbjct: 6 LLEAARAGQDDEVRILMANGADA-NAYDHYGRTPLHMAAAVGHLEIVEVLLRNGAD---V 61
Query: 78 NKQDVNGNTPLHVLAAV 94
N D NG TPLH+ A++
Sbjct: 62 NAVDTNGTTPLHLAASL 78
>pdb|2V5Q|C Chain C, Crystal Structure Of Wild-type Plk-1 Kinase Domain In
Complex With A Selective Darpin
pdb|2V5Q|D Chain D, Crystal Structure Of Wild-type Plk-1 Kinase Domain In
Complex With A Selective Darpin
Length = 167
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 4/78 (5%)
Query: 15 MTALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNLFQLHSRLRNRSVE 74
+T L LAA GH+ +V ++ D D G+ LH A + +L + L+ +
Sbjct: 48 LTPLHLAAVSGHLEIVEVLLKHGADV-DAADVYGFTPLHLAAMTGHLEIVEVLLKYGAD- 105
Query: 75 MLINKQDVNGNTPLHVLA 92
+N D+ G+TPLH+ A
Sbjct: 106 --VNAFDMTGSTPLHLAA 121
>pdb|1QYM|A Chain A, X-Ray Structure Of Human Gankyrin
Length = 227
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 52 LHFAMASSNLFQLHSRLRNRSVEMLINKQDVNGNTPLHV 90
+H A A NL +H L ++ N QD GNTPLH+
Sbjct: 144 MHRAAAKGNLKMIHILLYYKAS---TNIQDTEGNTPLHL 179
>pdb|1UOH|A Chain A, Human Gankyrin
pdb|1TR4|A Chain A, Solution Structure Of Human Oncogenic Protein Gankyrin
Length = 226
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 52 LHFAMASSNLFQLHSRLRNRSVEMLINKQDVNGNTPLHV 90
+H A A NL +H L ++ N QD GNTPLH+
Sbjct: 143 MHRAAAKGNLKMIHILLYYKAS---TNIQDTEGNTPLHL 178
>pdb|4DUI|A Chain A, Darpin D1 Binding To Tubulin Beta Chain (not In Complex)
Length = 169
Score = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 5/81 (6%)
Query: 15 MTALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNLFQLHSRLRNRSVE 74
+T L LAA GH+ +V ++ D +D G LH A +L + L++ +
Sbjct: 48 LTPLHLAATYGHLEIVEVLLKHGADV-NAIDIXGSTPLHLAALIGHLEIVEVLLKHGAD- 105
Query: 75 MLINKQDVNGNTPLHVLAAVL 95
+N D G+TPLH LAA++
Sbjct: 106 --VNAVDTWGDTPLH-LAAIM 123
>pdb|2AMP|A Chain A, Crystal Structure Of Porcine Transmissible Gastroenteritis
Virus Mpro In Complex With An Inhibitor N1
pdb|2AMP|B Chain B, Crystal Structure Of Porcine Transmissible Gastroenteritis
Virus Mpro In Complex With An Inhibitor N1
Length = 304
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 23/93 (24%), Positives = 41/93 (44%), Gaps = 8/93 (8%)
Query: 51 LLHFAMASSNLFQLHSRLRNRSVEMLINKQDVNGNTPLHVLAAVLQKEK---TAVEEGEI 107
L +F+++ +N+F R + V +++ VN NTP H ++ E A EG
Sbjct: 64 LHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCP 123
Query: 108 K-----ELKPRHTIVATLIATVTFAAGFTLPGG 135
++ + TI + IA + G+ L G
Sbjct: 124 GSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENG 156
>pdb|2O19|A Chain A, Structure Of E. Coli Topoisomersae Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 5.5
pdb|2O19|B Chain B, Structure Of E. Coli Topoisomersae Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 5.5
pdb|2O54|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 7.0
pdb|2O54|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 7.0
pdb|2O59|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol Ph 8.0
pdb|2O59|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol Ph 8.0
pdb|2O5C|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 5.5
pdb|2O5C|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 5.5
pdb|2O5E|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 7.0
pdb|2O5E|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 7.0
Length = 659
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 6/56 (10%)
Query: 78 NKQDVNGNTPLHVLAAVLQKEKTAVEEGEIKELK---PRHTIVATLIATVTFAAGF 130
+ + N TPL V+A + ++ E+GE+ E + PRH ATL++ +T A F
Sbjct: 454 ERDEENDGTPLPVVA---KGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARF 506
>pdb|1I7D|A Chain A, Noncovalent Complex Of E.Coli Dna Topoisomerase Iii With
An 8-Base Single-Stranded Dna Oligonucleotide
Length = 659
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 6/56 (10%)
Query: 78 NKQDVNGNTPLHVLAAVLQKEKTAVEEGEIKELK---PRHTIVATLIATVTFAAGF 130
+ + N TPL V+A + ++ E+GE+ E + PRH ATL++ +T A F
Sbjct: 454 ERDEENDGTPLPVVA---KGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARF 506
>pdb|1D6M|A Chain A, Crystal Structure Of E. Coli Dna Topoisomerase Iii
Length = 653
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 6/56 (10%)
Query: 78 NKQDVNGNTPLHVLAAVLQKEKTAVEEGEIKELK---PRHTIVATLIATVTFAAGF 130
+ + N TPL V+A + ++ E+GE+ E + PRH ATL++ +T A F
Sbjct: 454 ERDEENDGTPLPVVA---KGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARF 506
>pdb|3Q9U|C Chain C, In Silico And In Vitro Co-Evolution Of A High Affinity
Complementary Protein-Protein Interface
pdb|3Q9U|D Chain D, In Silico And In Vitro Co-Evolution Of A High Affinity
Complementary Protein-Protein Interface
pdb|3Q9N|C Chain C, In Silico And In Vitro Co-Evolution Of A High Affinity
Complementary Protein-Protein Interface
pdb|3Q9N|D Chain D, In Silico And In Vitro Co-Evolution Of A High Affinity
Complementary Protein-Protein Interface
Length = 158
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 41/89 (46%), Gaps = 5/89 (5%)
Query: 3 KSAACISDNDQ-KMTALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNL 61
K+ A ++ +D +T L LAA GH+ +V ++ D D GW LH A S L
Sbjct: 60 KNGADVNASDSAGITPLHLAAYDGHLEIVEVLLKHGADV-NAYDRAGWTPLHLAALSGQL 118
Query: 62 FQLHSRLRNRSVEMLINKQDVNGNTPLHV 90
+ L++ + +N QD G T +
Sbjct: 119 EIVEVLLKHGAD---VNAQDALGLTAFDI 144
>pdb|4F49|A Chain A, 2.25a Resolution Structure Of Transmissible
Gastroenteritis Virus Protease Containing A Covalently
Bound Dipeptidyl Inhibitor
pdb|4F49|B Chain B, 2.25a Resolution Structure Of Transmissible
Gastroenteritis Virus Protease Containing A Covalently
Bound Dipeptidyl Inhibitor
pdb|4F49|C Chain C, 2.25a Resolution Structure Of Transmissible
Gastroenteritis Virus Protease Containing A Covalently
Bound Dipeptidyl Inhibitor
pdb|4F49|D Chain D, 2.25a Resolution Structure Of Transmissible
Gastroenteritis Virus Protease Containing A Covalently
Bound Dipeptidyl Inhibitor
Length = 310
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 23/93 (24%), Positives = 41/93 (44%), Gaps = 8/93 (8%)
Query: 51 LLHFAMASSNLFQLHSRLRNRSVEMLINKQDVNGNTPLHVLAAVLQKEK---TAVEEGEI 107
L +F+++ +N+F R + V +++ VN NTP H ++ E A EG
Sbjct: 69 LHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCP 128
Query: 108 K-----ELKPRHTIVATLIATVTFAAGFTLPGG 135
++ + TI + IA + G+ L G
Sbjct: 129 GSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENG 161
>pdb|4DRX|E Chain E, Gtp-Tubulin In Complex With A Darpin
pdb|4DRX|F Chain F, Gtp-Tubulin In Complex With A Darpin
Length = 169
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 5/81 (6%)
Query: 15 MTALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNLFQLHSRLRNRSVE 74
+T L LAA GH+ +V ++ D +D G LH A +L + L++ +
Sbjct: 48 LTPLHLAATYGHLEIVEVLLKHGADV-NAIDIMGSTPLHLAALIGHLEIVEVLLKHGAD- 105
Query: 75 MLINKQDVNGNTPLHVLAAVL 95
+N D G+TPLH LAA++
Sbjct: 106 --VNAVDTWGDTPLH-LAAIM 123
>pdb|1LVO|A Chain A, Structure Of Coronavirus Main Proteinase Reveals
Combination Of A Chymotrypsin Fold With An Extra Alpha-
Helical Domain
pdb|1LVO|B Chain B, Structure Of Coronavirus Main Proteinase Reveals
Combination Of A Chymotrypsin Fold With An Extra Alpha-
Helical Domain
pdb|1LVO|C Chain C, Structure Of Coronavirus Main Proteinase Reveals
Combination Of A Chymotrypsin Fold With An Extra Alpha-
Helical Domain
pdb|1LVO|D Chain D, Structure Of Coronavirus Main Proteinase Reveals
Combination Of A Chymotrypsin Fold With An Extra Alpha-
Helical Domain
pdb|1LVO|E Chain E, Structure Of Coronavirus Main Proteinase Reveals
Combination Of A Chymotrypsin Fold With An Extra Alpha-
Helical Domain
pdb|1LVO|F Chain F, Structure Of Coronavirus Main Proteinase Reveals
Combination Of A Chymotrypsin Fold With An Extra Alpha-
Helical Domain
pdb|1P9U|A Chain A, Coronavirus Main Proteinase (3clpro) Structure: Basis For
Design Of Anti-sars Drugs
pdb|1P9U|B Chain B, Coronavirus Main Proteinase (3clpro) Structure: Basis For
Design Of Anti-sars Drugs
pdb|1P9U|C Chain C, Coronavirus Main Proteinase (3clpro) Structure: Basis For
Design Of Anti-sars Drugs
pdb|1P9U|D Chain D, Coronavirus Main Proteinase (3clpro) Structure: Basis For
Design Of Anti-sars Drugs
pdb|1P9U|E Chain E, Coronavirus Main Proteinase (3clpro) Structure: Basis For
Design Of Anti-sars Drugs
pdb|1P9U|F Chain F, Coronavirus Main Proteinase (3clpro) Structure: Basis For
Design Of Anti-sars Drugs
Length = 302
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 23/93 (24%), Positives = 41/93 (44%), Gaps = 8/93 (8%)
Query: 51 LLHFAMASSNLFQLHSRLRNRSVEMLINKQDVNGNTPLHVLAAVLQKEK---TAVEEGEI 107
L +F+++ +N+F R + V +++ VN NTP H ++ E A EG
Sbjct: 62 LHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCP 121
Query: 108 K-----ELKPRHTIVATLIATVTFAAGFTLPGG 135
++ + TI + IA + G+ L G
Sbjct: 122 GSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENG 154
>pdb|3AJI|A Chain A, Structure Of Gankyrin-S6atpase Photo-Cross-Linked
Site-Specifically, And Incoporated By Genetic Code
Expansion
pdb|3AJI|C Chain C, Structure Of Gankyrin-S6atpase Photo-Cross-Linked
Site-Specifically, And Incoporated By Genetic Code
Expansion
Length = 231
Score = 28.1 bits (61), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 52 LHFAMASSNLFQLHSRLRNRSVEMLINKQDVNGNTPLHV 90
+H A A NL +H L ++ N QD GNTPLH+
Sbjct: 143 MHRAAAKGNLKMVHILLFYKAS---TNIQDTEGNTPLHL 178
>pdb|2DVW|A Chain A, Structure Of The Oncoprotein Gankyrin In Complex With S6
Atpase Of The 26s Proteasome
pdb|2DWZ|A Chain A, Structure Of The Oncoprotein Gankyrin In Complex With S6
Atpase Of The 26s Proteasome
pdb|2DWZ|C Chain C, Structure Of The Oncoprotein Gankyrin In Complex With S6
Atpase Of The 26s Proteasome
Length = 231
Score = 28.1 bits (61), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 52 LHFAMASSNLFQLHSRLRNRSVEMLINKQDVNGNTPLHV 90
+H A A NL +H L ++ N QD GNTPLH+
Sbjct: 143 MHRAAAKGNLKMVHILLFYKAS---TNIQDTEGNTPLHL 178
>pdb|4DYE|A Chain A, Crystal Structure Of An Enolase (Putative Sugar Isomerase,
Target Efi- 502095) From Streptomyces Coelicolor, No Mg,
Ordered Loop
Length = 398
Score = 28.1 bits (61), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 36/92 (39%), Gaps = 1/92 (1%)
Query: 44 VDERGWNLLHFAMASSNLFQLHSRLRNR-SVEMLINKQDVNGNTPLHVLAAVLQKEKTAV 102
VD W+ + A S L +R+ + LI + D G TP + A+ + V
Sbjct: 121 VDVACWDAMGKATGQSVTDLLGGAVRDEVPITALITRADAPGATPADLPKAMAEHAVRVV 180
Query: 103 EEGEIKELKPRHTIVATLIATVTFAAGFTLPG 134
EEG +K + T + A LPG
Sbjct: 181 EEGGFDAVKLKGTTDCAGDVAILRAVREALPG 212
>pdb|2BKG|A Chain A, Crystal Structure Of E3_19 An Designed Ankyrin Repeat
Protein
pdb|2BKG|B Chain B, Crystal Structure Of E3_19 An Designed Ankyrin Repeat
Protein
Length = 166
Score = 27.7 bits (60), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 16 TALLLAAGRGHIRVVNEIISTCPDCCKQVDERGWNLLHFAMASSNLFQLHSRLRNRSVEM 75
T L LAA GH+ +V ++ D +D G LH A +L + L+ +
Sbjct: 49 TPLHLAARVGHLEIVEVLLKNGADV-NALDFSGSTPLHLAAKRGHLEIVEVLLKYGAD-- 105
Query: 76 LINKQDVNGNTPLHVLA 92
+N D G+TPLH+ A
Sbjct: 106 -VNADDTIGSTPLHLAA 121
>pdb|2PQI|A Chain A, Crystal Structure Of Active Ribosome Inactivating Protein
From Maize (B-32)
pdb|2PQI|B Chain B, Crystal Structure Of Active Ribosome Inactivating Protein
From Maize (B-32)
pdb|2PQI|C Chain C, Crystal Structure Of Active Ribosome Inactivating Protein
From Maize (B-32)
pdb|2PQJ|A Chain A, Crystal Structure Of Active Ribosome Inactivating Protein
From Maize (B-32), Complex With Adenine
pdb|2PQJ|B Chain B, Crystal Structure Of Active Ribosome Inactivating Protein
From Maize (B-32), Complex With Adenine
pdb|2PQJ|C Chain C, Crystal Structure Of Active Ribosome Inactivating Protein
From Maize (B-32), Complex With Adenine
Length = 243
Score = 27.7 bits (60), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 28/70 (40%), Gaps = 1/70 (1%)
Query: 90 VLAAVLQKEKTAVEEGEIKELKPRHTIVATLIATVT-FAAGFTLPGGYWGKEGPIPGTSI 148
+ VL EK E ELK R + + I + GF PGG W + G T +
Sbjct: 37 IFQPVLPPEKKVPELWLYTELKTRTSSITLAIRMDNLYLVGFRTPGGVWWEFGKDGDTHL 96
Query: 149 LIKNAAFQAF 158
L N + F
Sbjct: 97 LGDNPRWLGF 106
>pdb|2K6H|A Chain A, Nmr Structure Of An Unusually 28 Kda Active Mutant Of
Maize Ribosome-Inactivating Protein (Mod)
Length = 248
Score = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 28/70 (40%), Gaps = 1/70 (1%)
Query: 90 VLAAVLQKEKTAVEEGEIKELKPRHTIVATLIATVT-FAAGFTLPGGYWGKEGPIPGTSI 148
+ VL EK E ELK R + + I + GF PGG W + G T +
Sbjct: 42 IFQPVLPPEKKVPELWLYTELKTRTSSITLAIRMDNLYLVGFRTPGGVWWEFGKDGDTHL 101
Query: 149 LIKNAAFQAF 158
L N + F
Sbjct: 102 LGDNPRWLGF 111
>pdb|2PQG|A Chain A, Crystal Structure Of Inactive Ribosome Inactivating
Protein From Maize (B-32)
pdb|2PQG|B Chain B, Crystal Structure Of Inactive Ribosome Inactivating
Protein From Maize (B-32)
Length = 265
Score = 27.3 bits (59), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 28/70 (40%), Gaps = 1/70 (1%)
Query: 90 VLAAVLQKEKTAVEEGEIKELKPRHTIVATLIATVT-FAAGFTLPGGYWGKEGPIPGTSI 148
+ VL EK E ELK R + + I + GF PGG W + G T +
Sbjct: 36 IFQPVLPPEKKVPELWLYTELKTRTSSITLAIRMDNLYLVGFRTPGGVWWEFGKDGDTHL 95
Query: 149 LIKNAAFQAF 158
L N + F
Sbjct: 96 LGDNPRWLGF 105
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
0.325 0.134 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,218,204
Number of Sequences: 62578
Number of extensions: 213157
Number of successful extensions: 819
Number of sequences better than 100.0: 48
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 48
Number of HSP's that attempted gapping in prelim test: 772
Number of HSP's gapped (non-prelim): 83
length of query: 255
length of database: 14,973,337
effective HSP length: 97
effective length of query: 158
effective length of database: 8,903,271
effective search space: 1406716818
effective search space used: 1406716818
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 bits)