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= 047248
(439 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1M9O|A Chain A, Nmr Structure Of The First Zinc Binding Domain Of
Nup475TTPTIS11
Length = 77
Score = 33.1 bits (74), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 8/66 (12%)
Query: 100 CQYYLKTGTCKFGATCKFHHPRDKAGIAGRVSLNVLGYPLRPNEIECAYYLRTGQCKFGS 159
C+ Y ++G C++GA C+F H + A R +P E+ C + G+C +GS
Sbjct: 15 CRTYSESGRCRYGAKCQFAHGLGELRQANR-------HPKYKTEL-CHKFKLQGRCPYGS 66
Query: 160 TCKFHH 165
C F H
Sbjct: 67 RCHFIH 72
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 7/65 (10%)
Query: 55 CSYYIRTGLCRFGATCRFNHPPNRKLAIATARIKGDYPERVGQPECQYYLKTGTCKFGAT 114
C Y +G CR+GA C+F H + R +P + C + G C +G+
Sbjct: 15 CRTYSESGRCRYGAKCQFAH------GLGELRQANRHP-KYKTELCHKFKLQGRCPYGSR 67
Query: 115 CKFHH 119
C F H
Sbjct: 68 CHFIH 72
Score = 28.9 bits (63), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 347 RPGEPLCIFYSRYGICKFGPSCKFDHPMG 375
R LC YS G C++G C+F H +G
Sbjct: 9 RYKTELCRTYSESGRCRYGAKCQFAHGLG 37
>pdb|2CQE|A Chain A, Solution Structure Of The Zinc-Finger Domain In Kiaa1064
Protein
Length = 98
Score = 32.3 bits (72), Expect = 0.55, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 30/77 (38%), Gaps = 24/77 (31%)
Query: 43 SGSLPERPGEPDCSYYIRTGLCRFGATCRFNHPPNRKLAIATARIKGDYPERVGQPECQY 102
SG LP++ C +YI TG C C + H GD+P C+
Sbjct: 6 SGELPKK--RELCKFYI-TGFCARAENCPYMH--------------GDFP-------CKL 41
Query: 103 YLKTGTCKFGATCKFHH 119
Y TG C G C F H
Sbjct: 42 YHTTGNCINGDDCMFSH 58
>pdb|2RHK|C Chain C, Crystal Structure Of Influenza A Ns1a Protein In Complex
With F2f3 Fragment Of Human Cellular Factor Cpsf30,
Northeast Structural Genomics Targets Or8c And Hr6309a
pdb|2RHK|D Chain D, Crystal Structure Of Influenza A Ns1a Protein In Complex
With F2f3 Fragment Of Human Cellular Factor Cpsf30,
Northeast Structural Genomics Targets Or8c And Hr6309a
Length = 72
Score = 32.0 bits (71), Expect = 0.77, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 19/71 (26%)
Query: 100 CQYYLKTGTCKFGATCKFHHPRDKAGIAGRVSLNVLGYPLRPNEIECAYYLRTGQCKFGS 159
C+++L+ G CK G C+F H D ++ EC +Y + G+C
Sbjct: 19 CKHWLR-GLCKKGDQCEFLHEYDMTKMS-----------------ECYFYSKFGECS-NK 59
Query: 160 TCKFHHPQPNN 170
C F H P +
Sbjct: 60 ECPFLHIDPES 70
>pdb|1BXK|A Chain A, Dtdp-Glucose 4,6-Dehydratase From E. Coli
pdb|1BXK|B Chain B, Dtdp-Glucose 4,6-Dehydratase From E. Coli
Length = 355
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 34/151 (22%), Positives = 60/151 (39%), Gaps = 19/151 (12%)
Query: 97 QPECQYYLKTGTCKFGATCKFHHPRDKAGIAGRVSLNVLG-YPLRPNEIECAYYLRTGQC 155
QP+C +L + H R G A + N++G Y L E AY+ +
Sbjct: 74 QPDCVMHLAAES---------HVDRSIDGPAAFIETNIVGTYTLL--EAARAYWNALTED 122
Query: 156 KFGSTCKFHHPQPNNMMVSLRGSPVYPTVQSPTTPS------QQSYAGGITNWSRASFIP 209
K S +FHH + + L + + T +P PS + S + W R +P
Sbjct: 123 K-KSAFRFHHISTDEVYGDLHSTDDFFTETTPYAPSSPYSASKASSDHLVRAWLRTYGLP 181
Query: 210 SPRWQGPSSYAPMLLPQGMVSVPGWNTYSGQ 240
+ ++Y P P+ ++ + N +G+
Sbjct: 182 TLITNCSNNYGPYHFPEKLIPLMILNALAGK 212
>pdb|2ZWY|A Chain A, Alpha-L-Fucosidase
pdb|2ZWY|B Chain B, Alpha-L-Fucosidase
pdb|2ZWZ|A Chain A, Alpha-L-Fucosidase Complexed With Inhibitor, Core1
pdb|2ZWZ|B Chain B, Alpha-L-Fucosidase Complexed With Inhibitor, Core1
pdb|2ZX5|A Chain A, Alpha-L-Fucosidase Complexed With Inhibitor, F10
pdb|2ZX5|B Chain B, Alpha-L-Fucosidase Complexed With Inhibitor, F10
pdb|2ZX6|A Chain A, Alpha-L-Fucosidase Complexed With Inhibitor, F10-1c
pdb|2ZX6|B Chain B, Alpha-L-Fucosidase Complexed With Inhibitor, F10-1c
pdb|2ZX7|A Chain A, Alpha-L-Fucosidase Complexed With Inhibitor, F10-2c
pdb|2ZX7|B Chain B, Alpha-L-Fucosidase Complexed With Inhibitor, F10-2c
pdb|2ZX8|A Chain A, Alpha-L-Fucosidase Complexed With Inhibitor, F10-2c-O
pdb|2ZX8|B Chain B, Alpha-L-Fucosidase Complexed With Inhibitor, F10-2c-O
pdb|2ZX9|A Chain A, Alpha-L-Fucosidase Complexed With Inhibitor, B4
pdb|2ZX9|B Chain B, Alpha-L-Fucosidase Complexed With Inhibitor, B4
pdb|2ZXA|A Chain A, Alpha-L-Fucosidase Complexed With Inhibitor, Fnj-Acetyl
pdb|2ZXA|B Chain B, Alpha-L-Fucosidase Complexed With Inhibitor, Fnj-Acetyl
pdb|2ZXB|A Chain A, Alpha-L-Fucosidase Complexed With Inhibitor, Ph-6fnj
pdb|2ZXB|B Chain B, Alpha-L-Fucosidase Complexed With Inhibitor, Ph-6fnj
pdb|2ZXD|A Chain A, Alpha-L-Fucosidase Complexed With Inhibitor, Iso-6fnj
pdb|2ZXD|B Chain B, Alpha-L-Fucosidase Complexed With Inhibitor, Iso-6fnj
Length = 455
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 201 NWSRASFIPSPRWQGPSSYAPMLLPQGMVSVPGWNTYSGQLGSV 244
+W P+W + + + + G+ SVPGW T +G+LG V
Sbjct: 11 DWESLREHTVPKWFDKAKFG-IFIHWGIYSVPGWATPTGELGKV 53
>pdb|1ODU|A Chain A, Crystal Structure Of Thermotoga Maritima Alpha-Fucosidase
In Complex With Fucose
pdb|1ODU|B Chain B, Crystal Structure Of Thermotoga Maritima Alpha-Fucosidase
In Complex With Fucose
Length = 449
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 201 NWSRASFIPSPRWQGPSSYAPMLLPQGMVSVPGWNTYSGQLGSV 244
+W P+W + + + + G+ SVPGW T +G+LG V
Sbjct: 11 DWESLREHTVPKWFDKAKFG-IFIHWGIYSVPGWATPTGELGKV 53
>pdb|2WSP|A Chain A, Thermotoga Maritima Alpha-L-Fucosynthase, Tmd224g, In
Complex With Alpha-L-Fuc-(1-2)-Beta-L-Fuc-N3
pdb|2WSP|B Chain B, Thermotoga Maritima Alpha-L-Fucosynthase, Tmd224g, In
Complex With Alpha-L-Fuc-(1-2)-Beta-L-Fuc-N3
Length = 449
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 201 NWSRASFIPSPRWQGPSSYAPMLLPQGMVSVPGWNTYSGQLGSV 244
+W P+W + + + + G+ SVPGW T +G+LG V
Sbjct: 11 DWESLREHTVPKWFDKAKFG-IFIHWGIYSVPGWATPTGELGKV 53
>pdb|1HL8|A Chain A, Crystal Structure Of Thermotoga Maritima Alpha-Fucosidase
pdb|1HL8|B Chain B, Crystal Structure Of Thermotoga Maritima Alpha-Fucosidase
pdb|1HL9|A Chain A, Crystal Structure Of Thermotoga Maritima Alpha-Fucosidase
In Complex With A Mechanism Based Inhibitor
pdb|1HL9|B Chain B, Crystal Structure Of Thermotoga Maritima Alpha-Fucosidase
In Complex With A Mechanism Based Inhibitor
Length = 449
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 211 PRWQGPSSYAPMLLPQGMVSVPGWNTYSGQLGSV 244
P+W + + + + G+ SVPGW T +G+LG V
Sbjct: 21 PKWFDKAKFG-IFIHWGIYSVPGWATPTGELGKV 53
>pdb|3EUE|A Chain A, Crystal Structure Of Ligand-Free Human Uridine
Phosphorylase 1 (Hupp1)
pdb|3EUF|A Chain A, Crystal Structure Of Bau-Bound Human Uridine Phosphorylase
1
pdb|3EUF|B Chain B, Crystal Structure Of Bau-Bound Human Uridine Phosphorylase
1
pdb|3EUF|C Chain C, Crystal Structure Of Bau-Bound Human Uridine Phosphorylase
1
pdb|3EUF|D Chain D, Crystal Structure Of Bau-Bound Human Uridine Phosphorylase
1
pdb|3NBQ|A Chain A, Human Uridine Phosphorylase 1 (Hupp1) With 5-Fluorouracil
pdb|3NBQ|B Chain B, Human Uridine Phosphorylase 1 (Hupp1) With 5-Fluorouracil
pdb|3NBQ|C Chain C, Human Uridine Phosphorylase 1 (Hupp1) With 5-Fluorouracil
pdb|3NBQ|D Chain D, Human Uridine Phosphorylase 1 (Hupp1) With 5-Fluorouracil
Length = 328
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 314 GDCKFGAVCRFHHPRERLLPVPDCVLSPIGL--PLRPGEPLCIFYSRYGICKFGPSCKFD 371
GD KF VC P R+ CV + +GL P R +C RY + K GP
Sbjct: 69 GDVKF--VCVGGSP-SRMKAFIRCVGAELGLDCPGRDYPNICAGTDRYAMYKVGPVLSVS 125
Query: 372 HPMGI 376
H MGI
Sbjct: 126 HGMGI 130
>pdb|3CFO|A Chain A, Triple Mutant Apo Structure
pdb|3CFP|A Chain A, Structure Of The Replicating Complex Of A Pol Alpha Family
Dna Polymerase, Ternary Complex 1
pdb|3CFR|A Chain A, Structure Of The Replicating Complex Of A Pol Alpha Family
Dna Polymerase, Ternary Complex 2
Length = 909
Score = 29.3 bits (64), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|3SUQ|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp
Opposite 2ap (At Rich Sequence)
Length = 897
Score = 28.9 bits (63), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|1Q9Y|A Chain A, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With 8-Oxoguanosine Containing Dna
Length = 906
Score = 28.9 bits (63), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 792 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 825
>pdb|3SUO|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite 2ap (Gc Rich Sequence)
Length = 900
Score = 28.9 bits (63), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|3SUN|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite 2ap (At Rich Sequence)
Length = 895
Score = 28.9 bits (63), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|3NE6|A Chain A, Rb69 Dna Polymerase (S565gY567A) TERNARY COMPLEX WITH DCTP
OPPOSITE Dg
pdb|3NHG|A Chain A, Rb69 Dna Polymerase (S565gY567A) TERNARY COMPLEX WITH DTTP
OPPOSITE Dg
Length = 903
Score = 28.9 bits (63), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|2DY4|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2DY4|B Chain B, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2DY4|C Chain C, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2DY4|D Chain D, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2P5O|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5O|B Chain B, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5O|C Chain C, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5O|D Chain D, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5G|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Damp Opposite An Abasic Site Analog In A 21mer Template
pdb|2P5G|B Chain B, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Damp Opposite An Abasic Site Analog In A 21mer Template
pdb|2P5G|C Chain C, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Damp Opposite An Abasic Site Analog In A 21mer Template
pdb|2P5G|D Chain D, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Damp Opposite An Abasic Site Analog In A 21mer Template
Length = 903
Score = 28.9 bits (63), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|4DTJ|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp Opposite An
Abasic Site And DdtDA AS THE PENULTIMATE BASE-Pair
pdb|4DTM|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp Opposite An
Abasic Site And DdgDC AS THE PENULTIMATE BASE-Pair
Length = 901
Score = 28.9 bits (63), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|3SQ2|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp Opposite 2ap
(At Rich Sequence)
pdb|3SQ4|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp Opposite 2ap
(Gc Rich Sequence)
Length = 902
Score = 28.9 bits (63), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|3SQ1|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dupcpp Opposite
Da
Length = 901
Score = 28.9 bits (63), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|3SPY|A Chain A, Rb69 Dna Polymerase(L415aL561AS565GY567A) TERNARY COMPLEX
WITH Dupcpp Opposite Da
Length = 901
Score = 28.9 bits (63), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|3SPZ|A Chain A, Dna Polymerase(L415aL561AS565GY567A) TERNARY COMPLEX WITH
DUPCPP Opposite Da (Ca2+)
pdb|4FJ5|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp/dt
pdb|4FJ7|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp/dt
pdb|4FJ8|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp/dt
pdb|4FJ9|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp/dt
pdb|4FJG|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp/dc
pdb|4FJH|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp/dc
pdb|4FJI|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp/dc
pdb|4FJJ|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp/dc
pdb|4FJK|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp/da
pdb|4FJL|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp/da
pdb|4FJN|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp/da
pdb|4FJX|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp/dg
pdb|4FK0|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp/dg
pdb|4FK2|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp/dg
pdb|4FK4|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp/dg
Length = 903
Score = 28.9 bits (63), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|3SCX|A Chain A, Rb69 Dna Polymerase Triple Mutant(L561aS565GY567A) TERNARY
COMPLEX With Dupnpp And A Deoxy-Terminated Primer In The
Presence Of Ca2+
pdb|3SI6|A Chain A, Rb69 Dna Polymerase Triple Mutant (L561aS565GY567A)
TERNARY COMPLEX With Dupnpp And A Deoxy-Terminated
Primer In The Presence Of Mg2+
pdb|3SJJ|A Chain A, Rb69 Dna Polymerase Triple Mutant (L561aS565GY567A)
TERNARY COMPLEX With Dupnpp And A Deoxy-Terminated
Primer In The Presence Of Mn2+
pdb|3SNN|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DCTP Opposite Dg In The Presence Of Mg2+
Length = 903
Score = 28.9 bits (63), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|3QEP|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DTTP Opposite Difluorotoluene Nucleoside
pdb|3S9H|A Chain A, Rb69 Dna Polymerase Triple Mutant(L561aS565GY567A) TERNARY
COMPLEX With Dupnpp And A Dideoxy-Terminated Primer In
The Presence Of Ca2+
pdb|3SQ0|A Chain A, Dna Polymerase(L561aS565GY567A) TERNARY COMPLEX WITH
DUPNPP OPPOSITE Da (Mn2+)
pdb|3QEI|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DCTP Opposite Difluorotoluene Nucleoside
pdb|3QER|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DATP Opposite Difluorotoluene Nucleoside
pdb|3QES|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DGTP Opposite Difluorotoluene Nucleoside
pdb|3QET|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DTTP Opposite Dt
pdb|3QEV|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DCTP Opposite Dt
pdb|3QEW|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DDTP Opposite Dt
pdb|3QEX|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DGTP Opposite Dt
pdb|4E3S|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dqtp Opposite Dt
pdb|4DTN|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp Opposite An
Abasic Site And DdaDT AS THE PENULTIMATE BASE-Pair
pdb|4DTO|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp Opposite An
Abasic Site And DdaDT AS THE PENULTIMATE BASE-Pair
pdb|4DTP|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp Opposite An
Abasic Site And DdaDT AS THE PENULTIMATE BASE-Pair
pdb|4DTR|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4DTS|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4DTU|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4DTX|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4FJM|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp/da
Length = 903
Score = 28.9 bits (63), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|1WAF|A Chain A, Dna Polymerase From Bacteriophage Rb69
pdb|1WAF|B Chain B, Dna Polymerase From Bacteriophage Rb69
pdb|1CLQ|A Chain A, Crystal Structure Of A Replication Fork Dna Polymerase
Editing Complex At 2.7 A Resolution
pdb|1IH7|A Chain A, High-Resolution Structure Of Apo Rb69 Dna Polymerase
pdb|1WAJ|A Chain A, Dna Polymerase From Bacteriophage Rb69
pdb|3UIQ|A Chain A, Rb69 Dna Polymerase Ternary Complex Containing Dupnpp
Length = 903
Score = 28.9 bits (63), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|1IG9|A Chain A, Structure Of The Replicating Complex Of A Pol Alpha Family
Dna Polymerase
pdb|1Q9X|A Chain A, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With Tetrahydrofuran Containing Dna
pdb|1Q9X|B Chain B, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With Tetrahydrofuran Containing Dna
pdb|1Q9X|C Chain C, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With Tetrahydrofuran Containing Dna
pdb|1Q9X|D Chain D, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With Tetrahydrofuran Containing Dna
pdb|2ATQ|A Chain A, Rb69 Single-Stranded Dna Binding Protein-Dna Polymerase
Fusion
pdb|2OYQ|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna With 5-
Nimp Opposite An Abasic Site Analog
pdb|2OYQ|B Chain B, Crystal Structure Of Rb69 Gp43 In Complex With Dna With 5-
Nimp Opposite An Abasic Site Analog
pdb|2OYQ|C Chain C, Crystal Structure Of Rb69 Gp43 In Complex With Dna With 5-
Nimp Opposite An Abasic Site Analog
pdb|2OYQ|D Chain D, Crystal Structure Of Rb69 Gp43 In Complex With Dna With 5-
Nimp Opposite An Abasic Site Analog
pdb|2OZM|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna With 5-
Nitp Opposite An Abasic Site Analog
pdb|2OZS|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Datp Opposite Dtmp
pdb|3NCI|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp Opposite Dg
At 1.8 Angstrom Resolution
pdb|4DU1|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp Opposite Dt
pdb|4DU3|A Chain A, Rb69 Dna Polymerase Ternary Complex With Ddtp Opposite Dt
With 3- Deaza-Adenine At The N-1 Position Of Template
Strand
pdb|4DU4|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp Opposite Dt
With 3- Deaza-Adenine At The N-3 Position Of Primer
Strand
Length = 903
Score = 28.9 bits (63), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|3RWU|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Datp
Opposite Difluorotoluene Nucleoside
pdb|3QNN|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dgt
Opposite 3tco
pdb|3QNO|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Datp
Opposite 3tco
Length = 901
Score = 28.9 bits (63), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|1RGO|A Chain A, Structural Basis For Recognition Of The Mrna Class Ii Au-
Rich Element By The Tandem Zinc Finger Domain Of Tis11d
Length = 70
Score = 28.9 bits (63), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 8/66 (12%)
Query: 307 CQFYMKTGDCKFGAVCRFHHPRERLLPVPDCVLSPIGLPLRPGEPLCIFYSRYGICKFGP 366
C+ + ++G CK+G C+F H L S P E LC + G C +GP
Sbjct: 9 CRPFEESGTCKYGEKCQFAHGFHEL-------RSLTRHPKYKTE-LCRTFHTIGFCPYGP 60
Query: 367 SCKFDH 372
C F H
Sbjct: 61 RCHFIH 66
>pdb|3LZI|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Datp
Opposite 7,8- Dihydro-8-Oxoguanine
pdb|3LZJ|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp
Opposite 7,8- Dihydro-8-Oxoguanine
pdb|3NAE|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Datp
Opposite Guanidinohydantoin
pdb|3NDK|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp
Opposite Dg
pdb|3NGI|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite Dg
pdb|3SUP|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp
Opposite 2ap (Gc Rich Sequence)
Length = 903
Score = 28.9 bits (63), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|2DTU|A Chain A, Crystal Structure Of The Beta Hairpin Loop Deletion
Variant Of Rb69 Gp43 In Complex With Dna Containing An
Abasic Site Analog
pdb|2DTU|B Chain B, Crystal Structure Of The Beta Hairpin Loop Deletion
Variant Of Rb69 Gp43 In Complex With Dna Containing An
Abasic Site Analog
pdb|2DTU|C Chain C, Crystal Structure Of The Beta Hairpin Loop Deletion
Variant Of Rb69 Gp43 In Complex With Dna Containing An
Abasic Site Analog
pdb|2DTU|D Chain D, Crystal Structure Of The Beta Hairpin Loop Deletion
Variant Of Rb69 Gp43 In Complex With Dna Containing An
Abasic Site Analog
Length = 896
Score = 28.9 bits (63), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 782 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 815
>pdb|3LDS|A Chain A, Crystal Structure Of Rb69 Gp43 With Dna And Datp Opposite
8-
Length = 903
Score = 28.9 bits (63), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|3L8B|A Chain A, Crystal Structure Of A Replicative Dna Polymerase Bound To
The Oxidized Guanine Lesion Guanidinohydantoin
pdb|3L8B|B Chain B, Crystal Structure Of A Replicative Dna Polymerase Bound To
The Oxidized Guanine Lesion Guanidinohydantoin
pdb|3RMA|A Chain A, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMA|B Chain B, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMA|C Chain C, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMA|D Chain D, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMB|A Chain A, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMB|B Chain B, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMB|C Chain C, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMB|D Chain D, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMC|A Chain A, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMC|B Chain B, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMC|C Chain C, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMC|D Chain D, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMD|A Chain A, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMD|B Chain B, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMD|C Chain C, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMD|D Chain D, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3TAB|A Chain A, 5-Hydroxycytosine Paired With Dgmp In Rb69 Gp43
pdb|3TAB|B Chain B, 5-Hydroxycytosine Paired With Dgmp In Rb69 Gp43
pdb|3TAB|C Chain C, 5-Hydroxycytosine Paired With Dgmp In Rb69 Gp43
pdb|3TAB|D Chain D, 5-Hydroxycytosine Paired With Dgmp In Rb69 Gp43
pdb|3TAE|A Chain A, 5-Hydroxycytosine Paired With Damp In Rb69 Gp43
pdb|3TAE|B Chain B, 5-Hydroxycytosine Paired With Damp In Rb69 Gp43
pdb|3TAE|C Chain C, 5-Hydroxycytosine Paired With Damp In Rb69 Gp43
pdb|3TAE|D Chain D, 5-Hydroxycytosine Paired With Damp In Rb69 Gp43
pdb|3TAF|A Chain A, 5-Fluorocytosine Paired With Ddgmp In Rb69 Gp43
pdb|3TAF|B Chain B, 5-Fluorocytosine Paired With Ddgmp In Rb69 Gp43
pdb|3TAF|C Chain C, 5-Fluorocytosine Paired With Ddgmp In Rb69 Gp43
pdb|3TAF|D Chain D, 5-Fluorocytosine Paired With Ddgmp In Rb69 Gp43
pdb|3TAG|A Chain A, 5-Fluorocytosine Paired With Damp In Rb69 Gp43
pdb|3TAG|B Chain B, 5-Fluorocytosine Paired With Damp In Rb69 Gp43
pdb|3TAG|C Chain C, 5-Fluorocytosine Paired With Damp In Rb69 Gp43
pdb|3TAG|D Chain D, 5-Fluorocytosine Paired With Damp In Rb69 Gp43
Length = 906
Score = 28.9 bits (63), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|3KD1|E Chain E, Closed Binary Complex Of An Rb69 Gp43 Fingers Domain
Mutant Complexed With An Acyclic Gmp Terminated Primer
Template Pair.
pdb|3KD5|E Chain E, Closed Ternary Complex Of An Rb69 Gp43 Fingers Domain
Mutant Complexed With An Acyclic Gmp Terminated Primer
Template Pair And Phosphonoformic Acid
Length = 913
Score = 28.9 bits (63), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|3CQ8|A Chain A, Ternary Complex Of The L415f Mutant Rb69 Exo(-)polymerase
Length = 903
Score = 28.9 bits (63), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 357 SRYGICKF-GPSCKFDHPMGIFTYNLSASSSADAP 390
++Y + F GP C F H GI TYN + + DAP
Sbjct: 789 AKYDVGGFPGPKCPF-HIRGILTYNRAIKGNIDAP 822
>pdb|4II1|A Chain A, Crystal Structure Of The Zinc Finger Of Zgpat
pdb|4II1|B Chain B, Crystal Structure Of The Zinc Finger Of Zgpat
pdb|4II1|C Chain C, Crystal Structure Of The Zinc Finger Of Zgpat
pdb|4II1|D Chain D, Crystal Structure Of The Zinc Finger Of Zgpat
Length = 167
Score = 28.5 bits (62), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 3/66 (4%)
Query: 102 YYLKTGTCKFGATCKFHHPRDKAGIAGRVSLNVLGYPLRPNEIECAYYLRTGQCKFGSTC 161
YY GT ++ + G AG L + YP + C ++L G+C+F C
Sbjct: 37 YYSSWGTLEYHNAMVVGTEEAEDGSAGVRVLYL--YPTHKSLKPCPFFLE-GKCRFKENC 93
Query: 162 KFHHPQ 167
+F H Q
Sbjct: 94 RFSHGQ 99
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.134 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,376,715
Number of Sequences: 62578
Number of extensions: 621729
Number of successful extensions: 1129
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 33
Number of HSP's that attempted gapping in prelim test: 1097
Number of HSP's gapped (non-prelim): 57
length of query: 439
length of database: 14,973,337
effective HSP length: 102
effective length of query: 337
effective length of database: 8,590,381
effective search space: 2894958397
effective search space used: 2894958397
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)