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= 027332
(225 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2WP7|A Chain A, Crystal Structure Of Desumoylase(Duf862)
Length = 168
Score = 47.4 bits (111), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 37/124 (29%), Positives = 56/124 (45%), Gaps = 11/124 (8%)
Query: 46 GIFHSGIEAHGLEYGFGAHEYRTSGVFEVEPKSCPGFIFRRSVLLGTTNLSRAEFRSFME 105
GI+H+ I H E+ FG+ SG+ P V +G T ++ F ++
Sbjct: 35 GIWHTSIVVHKDEFFFGS-----SGISSCTPGGTLLGPPDSVVDVGNTEVTEEIFLEYLS 89
Query: 106 HLSGK-YHGDTYHLIAKNCNHFTEEVCMQLTGKCIPGWVNRMAR---LGSFCNCLLP--E 159
L + G+ Y+L NCN F+ EV LTG+ IP ++ + F L P +
Sbjct: 90 SLGESLFRGEAYNLFEHNCNTFSNEVAQFLTGRKIPSYITDLPSEVLSTPFGQALRPFLD 149
Query: 160 SIQI 163
SIQI
Sbjct: 150 SIQI 153
>pdb|3EBQ|A Chain A, Crystal Structure Of Human Pppde1
Length = 170
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 37/127 (29%), Positives = 57/127 (44%), Gaps = 17/127 (13%)
Query: 46 GIFHSGIEAHGLEYGFGAHEYRT---SGVFEVEPKSCPGFIFRRSVLLGTTNLSRAEFRS 102
GI+H+ I H E+ FG+ + G P S V +G+T ++ F
Sbjct: 37 GIWHTSIVVHKDEFFFGSGGISSCPPGGTLLGPPDSV--------VDVGSTEVTEEIFLE 88
Query: 103 FMEHLSGK-YHGDTYHLIAKNCNHFTEEVCMQLTGKCIPGWVNRMAR---LGSFCNCLLP 158
++ L + G+ Y+L NCN F+ EV LTG+ IP ++ + F L P
Sbjct: 89 YLSSLGESLFRGEAYNLFEHNCNTFSNEVAQFLTGRKIPSYITDLPSEVLSTPFGQALRP 148
Query: 159 --ESIQI 163
+SIQI
Sbjct: 149 LLDSIQI 155
>pdb|4F5N|A Chain A, Open Ternary Complex Of R283k Dna Polymerase Beta With A
Metal Free Dctp Analog
pdb|4F5O|A Chain A, Open Ternary Complex Of R283k Dna Polymerase Beta With A
One Metal Bound Dctp Analog
pdb|4F5P|A Chain A, Open Ternary Mismatch Complex Of R283k Dna Polymerase Beta
With A Datp Analog
pdb|4F5Q|A Chain A, Closed Ternary Complex Of R283k Dna Polymerase Beta
pdb|4F5R|A Chain A, Open And Closed Ternary Complex Of R283k Dna Polymerase
Beta With A Dctp Analog In The Same Asymmetric Unit
pdb|4F5R|B Chain B, Open And Closed Ternary Complex Of R283k Dna Polymerase
Beta With A Dctp Analog In The Same Asymmetric Unit
pdb|4GXI|A Chain A, R283k Dna Polymerase Beta Binary Complex With A Templating
8og
pdb|4GXJ|A Chain A, R283k Dna Polymerase Beta Ternary Complex With A
Templating 8og And Incoming Dctp Analog
pdb|4GXK|A Chain A, R283k Dna Polymerase Beta Ternary Complex With A
Templating 8og And Incoming Datp Analog
Length = 335
Score = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 6/54 (11%)
Query: 33 LTPLNNY----LYWFGLGIFHSGIEAHGLEYGFGAHEY--RTSGVFEVEPKSCP 80
L P + Y LY+ G IF+ ++AH LE GF +EY R GV V + P
Sbjct: 259 LIPKDQYYCGVLYFTGSDIFNKNMKAHALEKGFTINEYTIRPLGVTGVAGEPLP 312
>pdb|3UXO|A Chain A, Crystal Structure Of Rat Dna Polymerase Beta Mutator I260q
Apoenzyme
pdb|3UXO|B Chain B, Crystal Structure Of Rat Dna Polymerase Beta Mutator I260q
Apoenzyme
pdb|3UXP|A Chain A, Co-Crystal Structure Of Rat Dna Polymerase Beta Mutator
I260q: Enzyme- Dna-Ddttp
pdb|3UXP|B Chain B, Co-Crystal Structure Of Rat Dna Polymerase Beta Mutator
I260q: Enzyme- Dna-Ddttp
Length = 335
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 33 LTPLNNY----LYWFGLGIFHSGIEAHGLEYGFGAHEY--RTSGVFEVEPKSCP 80
L P + Y LY+ G IF+ + AH LE GF +EY R GV V + P
Sbjct: 259 LQPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLP 312
>pdb|1JN3|A Chain A, Fidelity Properties And Structure Of M282l Mutator Mutant
Of Dna Polymerase: Subtle Structural Changes Influence
The Mechanism Of Nucleotide Discrimination
Length = 251
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 33 LTPLNNY----LYWFGLGIFHSGIEAHGLEYGFGAHEY--RTSGVFEVEPKSCP 80
L P + Y LY+ G IF+ + AH LE GF +EY R GV V + P
Sbjct: 175 LIPKDQYYCGVLYFTGSDIFNKNLRAHALEKGFTINEYTIRPLGVTGVAGEPLP 228
>pdb|2BPF|A Chain A, Structures Of Ternary Complexes Of Rat Dna Polymerase
Beta, A Dna Template-Primer, And Ddctp
pdb|2BPG|A Chain A, Structures Of Ternary Complexes Of Rat Dna Polymerase
Beta, A Dna Template-Primer, And Ddctp
pdb|2BPG|B Chain B, Structures Of Ternary Complexes Of Rat Dna Polymerase
Beta, A Dna Template-Primer, And Ddctp
pdb|1HUO|A Chain A, Crystal Structure Of Dna Polymerase Beta Complexed With
Dna And Cr-Tmppcp
pdb|1HUO|B Chain B, Crystal Structure Of Dna Polymerase Beta Complexed With
Dna And Cr-Tmppcp
pdb|1HUZ|A Chain A, Crystal Structure Of Dna Polymerase Complexed With Dna And
Cr-Pcp
pdb|1HUZ|B Chain B, Crystal Structure Of Dna Polymerase Complexed With Dna And
Cr-Pcp
pdb|1BPD|A Chain A, Crystal Structure Of Rat Dna Polymerase Beta: Evidence For
A Common Polymerase Mechanism
pdb|3UXN|A Chain A, Crystal Structure Of Rat Dna Polymerase Beta, Wild Type
Apoenzyme
pdb|3UXN|B Chain B, Crystal Structure Of Rat Dna Polymerase Beta, Wild Type
Apoenzyme
Length = 335
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 33 LTPLNNY----LYWFGLGIFHSGIEAHGLEYGFGAHEY--RTSGVFEVEPKSCP 80
L P + Y LY+ G IF+ + AH LE GF +EY R GV V + P
Sbjct: 259 LIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLP 312
>pdb|1BPE|A Chain A, Crystal Structure Of Rat Dna Polymerase Beta; Evidence For
A Common Polymerase Mechanism
Length = 335
Score = 32.7 bits (73), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 33 LTPLNNY----LYWFGLGIFHSGIEAHGLEYGFGAHEY--RTSGVFEVEPKSCP 80
L P + Y LY+ G IF+ + AH LE GF +EY R GV V + P
Sbjct: 259 LIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLP 312
>pdb|3V7J|A Chain A, Co-crystal Structure Of Wild Type Rat Polymerase Beta:
Enzyme-dna Binary Complex
Length = 340
Score = 32.7 bits (73), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 33 LTPLNNY----LYWFGLGIFHSGIEAHGLEYGFGAHEY--RTSGVFEVEPKSCP 80
L P + Y LY+ G IF+ + AH LE GF +EY R GV V + P
Sbjct: 264 LIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLP 317
>pdb|3OGU|A Chain A, Dna Polymerase Beta Mutant 5p20 Complexed With 6bp Of Dna
Length = 335
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 33 LTPLNNY----LYWFGLGIFHSGIEAHGLEYGFGAHEY--RTSGVFEVEPKSCP 80
L P + Y LY+ G IF+ + AH LE GF +EY R GV V + P
Sbjct: 259 LIPKDQYYCGMLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLP 312
>pdb|1RPL|A Chain A, 2.3 Angstroms Crystal Structure Of The Catalytic Domain Of
Dna Polymerase Beta
Length = 251
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 33 LTPLNNY----LYWFGLGIFHSGIEAHGLEYGFGAHEY--RTSGVFEVEPKSCP 80
L P + Y LY+ G IF+ + AH LE GF +EY R GV V + P
Sbjct: 175 LIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLP 228
>pdb|3V7K|A Chain A, Co-crystal Structure Of K72e Variant Of Rat Polymerase
Beta: Enzyme- Dna Binary Complex
pdb|3V7L|A Chain A, Apo Structure Of Rat Dna Polymerase Beta K72e Variant
Length = 340
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 33 LTPLNNY----LYWFGLGIFHSGIEAHGLEYGFGAHEY--RTSGVFEVEPKSCP 80
L P + Y LY+ G IF+ + AH LE GF +EY R GV V + P
Sbjct: 264 LIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLP 317
>pdb|9ICG|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dctp
(1 Millimolar) And Zncl2 (1 Millimolar)
pdb|9ICH|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dgtp
(1 Millimolar) And Zncl2 (1 Millimolar)
pdb|9ICI|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dttp
(1 Millimolar) And Zncl2 (1 Millimolar)
pdb|9ICJ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna
pdb|9ICK|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Artificial Mother Liquor
pdb|9ICL|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Pyrophosphate And Mncl2
pdb|9ICM|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Double Stranded Dna (No 5'-Phosphate)
pdb|9ICN|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2',3'-
Dideoxycytidine-5'-Triphosphate, Soaked In The Presence
Of Ddctp And Mgcl2
pdb|9ICO|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Dttp And Mgcl2
pdb|9ICP|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of
Pyrophosphate (1 Millimolar) And Mgcl2 (5 Millimolar)
pdb|9ICQ|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Datp (1
Millimolar) And Mncl2 (5 Millimolar)
pdb|9ICR|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2'-
Deoxycytidine-5'-Triphosphate, Soaked In The Presence Of
Dctp And Mncl2
pdb|9ICS|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2',3'-
Dideoxycytidine-5'-Triphosphate, Soaked In The Presence
Of Ddctp And Mncl2
pdb|9ICT|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2'-
Deoxyguanosine-5'-Triphosphate, Soaked In The Presence
Of Dgtp And Mncl2
pdb|9ICU|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Dttp (1
Millimolar) And Mncl2 (5 Millimolar)
pdb|9ICV|A Chain A, Dna Polymerase Beta (e.c.2.7.7.7)/dna Complex + 2'-
Deoxyadenosine-5'-triphosphate, Soaked In The Presence
Of Datp And Zncl2
pdb|9ICW|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Native Structure
pdb|9ICX|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Six Base Pairs Of Dna (non Gapped Dna Only)
pdb|9ICY|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7) Complexed With Seven
Base Pairs Of Dna (Non Gapped Dna Only)
pdb|8ICB|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of
Artificial Mother Liquor
pdb|8ICC|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna (no 5'-phosphate)
pdb|8ICE|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Cdcl2 (1 Millimolar)
pdb|8ICF|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(10 Millimolar) And Mgcl2 (50 Millimolar)
pdb|8ICG|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Mgcl2 (5 Millimolar)
pdb|8ICH|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dctp
(1 Millimolar) And Mgcl2 (5 Millimolar)
pdb|8ICI|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dgtp
(1 Millimolar) And Mgcl2 (5 Millimolar)
pdb|8ICJ|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + THYMIDINE-
5'-Triphosphate, Soaked In The Presence Of Dttp And
Mgcl2
pdb|8ICK|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar), Mgcl2 (5 Millimolar), And Mncl2 (5
Millimolar)
pdb|8ICL|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Nicl2 (5 Millimolar)
pdb|8ICM|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar), Mncl2 (5 Millimolar), And Ammonium
Sulfate (75 Millimolar)
pdb|8ICN|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Atp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICO|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of
Azt-Tp (1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICP|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICQ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Of
Datp (0.1 Millimolar) And Mncl2 (0.5 Millimolar)
pdb|8ICR|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICS|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dctp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICT|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dctp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICU|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Ddatp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICV|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dgtp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICW|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dttp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICX|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dttp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICY|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + THYMIDINE-
5'-Triphosphate, Soaked In The Presence Of Dttp And
Mncl2
pdb|8ICZ|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Of
Datp (1 Millimolar), Mncl2 (5 Millimolar), And Lithium
Sulfate (75 Millimolar)
pdb|9ICA|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2'-
Deoxyadenosine-5'-O-(1-Thiotriphosphate), Soaked In The
Presence Of Datp(Alpha)s And Mncl2
pdb|9ICB|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2'-
Deoxyadenosine-5'-Triphosphate, Soaked In The Presence
Of Datp And Cocl2
pdb|9ICC|A Chain A, Dna Polymerase Beta (e.c.2.7.7.7)/dna Complex + 2'-
Deoxyadenosine-5'-triphosphate, Soaked In The Presence
Of Datp And Crcl3
pdb|9ICE|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Cucl2 (0.1 Millimolar)
pdb|9ICF|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2'-
Deoxyadenosine-5'-Triphosphate, Soaked In The Presence
Of Datp And Zncl2
pdb|1ZQQ|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(15 Millimolar) And Nacl (15 Millimolar)
pdb|1ZQR|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Nicl2
pdb|1ZQS|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Tlcl
(0.5 Millimolar)
pdb|1ZQT|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(0.01 Millimolar) And Zncl2 (0.02 Millimolar)
pdb|7ICE|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Cacl2
pdb|7ICF|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Cdcl2
(0.1 Millimolar) (Four-Day Soak)
pdb|7ICG|A Chain A, Dna Polymerase Beta (e.c.2.7.7.7)/dna Complex, Soaked In
The Presence Of Cdcl2
pdb|7ICH|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Cocl2
pdb|7ICI|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Crcl3
(0.1 Millimolar)
pdb|7ICJ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Cucl2
(0.1 Millimolar)
pdb|7ICK|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Mgcl2
pdb|7ICL|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(0.1 Millimolar)
pdb|7ICM|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(1.0 Millimolar)
pdb|7ICN|A Chain A, Dna Polymerase Beta (e.c.2.7.7.7)/dna Complex, Soaked In
The Presence Of Nicl2
pdb|7ICO|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Zncl2
pdb|7ICP|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Zncl2
(0.01 Millimolar)
pdb|7ICQ|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Zncl2
pdb|7ICR|A Chain A, Dna Polymerase Beta (e.c.2.7.7.7)/dna Complex, Soaked In
The Presence Of Zncl2
pdb|7ICS|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Zncl2
pdb|7ICT|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Zncl2 And Mgcl2
pdb|7ICU|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Cdcl2
(0.1 Millimolar)
pdb|7ICV|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(0.1 Millimolar) And In The Absence Of Nacl
pdb|8ICA|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Cacl2 (5 Millimolar)
pdb|1ZQA|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Kcl
(150 Millimolar) At Ph 7.5
pdb|1ZQB|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Bacl2
(150 Millimolar)
pdb|1ZQC|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cacl2
(15 Millimolar)
pdb|1ZQD|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cacl2
(150 Millimolar)
pdb|1ZQE|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Crcl3
(saturated Solution)
pdb|1ZQF|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cscl
(150 Millimolar)
pdb|1ZQG|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of A
Sodium-Free Artificial Mother Liquor At Ph 6.5
pdb|1ZQH|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of A
Sodium-Free Artificial Mother Liquor At Ph 7.5
pdb|1ZQI|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Kcl
(150 Millimolar)
pdb|1ZQJ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cacl2
(15 Millimolar) And Mgcl2 (15 Millimolar)
pdb|1ZQK|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Kcl
(75 Millimolar) And Mgcl2 (75 Millimolar)
pdb|1ZQL|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(15 Millimolar) And Mgcl2 (15 Millimolar)
pdb|1ZQM|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(15 Millimolar)
pdb|1ZQN|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Bacl2
(15 Millimolar) And Nacl (15 Millimolar)
pdb|1ZQO|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cacl2
(15 Millimolar) And Nacl (15 Millimolar)
pdb|1ZQP|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Kcl
(75 Millimolar) And Nacl (75 Millimolar)
pdb|1BPX|A Chain A, Dna Polymerase BetaDNA COMPLEX
pdb|1BPY|A Chain A, Human Dna Polymerase Beta Complexed With Gapped Dna And
Ddctp
pdb|1BPZ|A Chain A, Human Dna Polymerase Beta Complexed With Nicked Dna
pdb|1MQ2|A Chain A, Human Dna Polymerase Beta Complexed With Gapped Dna
Containing An 8-Oxo-7,8-Dihydro-Guanine And Damp
pdb|1MQ3|A Chain A, Human Dna Polymerase Beta Complexed With Gapped Dna
Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired
With Dctp
pdb|1TV9|A Chain A, Human Dna Polymerase Beta Complexed With Nicked Dna
Containing A Mismatched Template Adenine And Incoming
Cytidine
pdb|1TVA|A Chain A, Human Dna Polymerase Beta Complexed With Nicked Dna
Containing A Mismatched Template Thymidine And Incoming
Cytidine
pdb|1ZJM|A Chain A, Human Dna Polymerase Beta Complexed With Dna Containing An
A-A Mismatched Primer Terminus
pdb|1ZJN|A Chain A, Human Dna Polymerase Beta Complexed With Dna Containing An
A-A Mismatched Primer Terminus With Dgtp
pdb|2FMP|A Chain A, Dna Polymerase Beta With A Terminated Gapped Dna Substrate
And Ddctp With Sodium In The Catalytic Site
pdb|2FMQ|A Chain A, Sodium In Active Site Of Dna Polymerase Beta
pdb|2FMS|A Chain A, Dna Polymerase Beta With A Gapped Dna Substrate And
Dumpnpp With Magnesium In The Catalytic Site
pdb|2I9G|A Chain A, Dna Polymerase Beta With A Benzo[c]phenanthrene Diol
Epoxide Adducted Guanine Base
pdb|2ISO|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta, Gamma-
Difluoromethylene Triphosphate
pdb|2ISP|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta, Gamma-
Methylene Triphosphate
pdb|2P66|A Chain A, Human Dna Polymerase Beta Complexed With Tetrahydrofuran
(abasic Site) Containing Dna
pdb|2PXI|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta, Gamma-
Monofluoromethylene Triphosphate
pdb|3C2K|A Chain A, Dna Polymerase Beta With A Gapped Dna Substrate And
Dumpnpp With Manganese In The Active Site
pdb|3C2L|A Chain A, Ternary Complex Of Dna Polymerase Beta With A C:dapcpp
Mismatch In The Active Site
pdb|3C2M|A Chain A, Ternary Complex Of Dna Polymerase Beta With A G:dapcpp
Mismatch In The Active Site
pdb|3ISB|A Chain A, Binary Complex Of Human Dna Polymerase Beta With A Gapped
Dna
pdb|3ISC|A Chain A, Binary Complex Of Human Dna Polymerase Beta With An Abasic
Site (Thf) In The Gapped Dna
pdb|3ISD|A Chain A, Ternary Complex Of Human Dna Polymerase Beta With An
Abasic Site (Thf): Dapcpp Mismatch
pdb|3JPN|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Dichloro Methyl Triphosphate
pdb|3JPO|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monochloromethy Triphosphate
pdb|3JPP|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monomethyl Meth Triphosphate
pdb|3JPQ|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monobromo Methy Triphosphate
pdb|3JPR|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Dimethyl Methyl Triphosphate
pdb|3JPS|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Fluoro Methyl M Triphosphate
pdb|3JPT|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Fluoro Chloro M Triphosphate
pdb|3MBY|A Chain A, Ternary Complex Of Dna Polymerase Beta With Template Base
A And 8oxodgtp In The Active Site With A Dideoxy
Terminated Primer
pdb|3LK9|A Chain A, Dna Polymerase Beta With A Gapped Dna Substrate And
Dtmp(Cf2)p(Cf2)p
pdb|3RH4|A Chain A, Dna Polymerase Beta With A Dideoxy-Terminated Primer With
An Incoming Ribonucleotide (Rctp)
pdb|3RJE|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Gapped Dna
Containing 8odg At Template Position
pdb|3RJF|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Gapped Dna
Containing (Syn)8odg At Template Position Paired With
Non-Hydrolyzable Datp Analog (Dapcpp)
pdb|3RJG|A Chain A, Binary Complex Of Dna Polymerase Beta With A Gapped Dna
Containing 8odg:da Base-Pair At Primer Terminus
pdb|3RJH|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Gapped Dna
Containing (Syn)8odg:da At Primer Terminus And
Dg:dcmp(Cf2)ppin The Active Site
pdb|3RJI|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Gapped Dna
Containing 8odg At Template Position Paired With
Non-Hydrolyzable Dctp Analog (Dcmp(Cf2)pp)
pdb|3RJJ|A Chain A, Ternary Complex Crystal Structure Of Dna Polymerase Beta
With Template 8odg Provides Insight Into Mutagenic
Lesion Bypass
pdb|3RJK|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Gapped Dna
Containing 8odg:dc Base Pair At Primer Terminus And
Dg:dcmp(Cf2)pp In The Active Site
pdb|3TFR|A Chain A, Ternary Complex Structure Of Dna Polymerase Beta With A
Gapped Dna Substrate And A, B Damp(Cf2)pp In The Active
Site
pdb|3TFS|A Chain A, Ternary Complex Structure Of Dna Polymerase Beta With A
Gapped Dna Substrate And A, B Damp(Cfh)pp In The Active
Site: Stereoselective Binding Of (S) Isomer
pdb|4DO9|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monofluoromethylene Triphosphate: Stereoselective
Binding Of R-Isomer
pdb|4DOA|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monofluoromethylene Triphosphate: Non-Interactive
Binding Of S-Isomer
pdb|4DOB|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monochlororomethylene Triphosphate:
Stereoselective Binding Of R-Isomer
pdb|4DOC|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monochlororomethylene Triphosphate:binding Of
S-Isomer
Length = 335
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 33 LTPLNNY----LYWFGLGIFHSGIEAHGLEYGFGAHEY--RTSGVFEVEPKSCP 80
L P + Y LY+ G IF+ + AH LE GF +EY R GV V + P
Sbjct: 259 LIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLP 312
>pdb|2VAN|A Chain A, Nucleotidyl Transfer Mechanism Of Mismatched Dntp
Incorporation By Dna Polymerase B By Structural And
Kinetic Analyses
Length = 245
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 33 LTPLNNY----LYWFGLGIFHSGIEAHGLEYGFGAHEY--RTSGVFEVEPKSCP 80
L P + Y LY+ G IF+ + AH LE GF +EY R GV V + P
Sbjct: 169 LQPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLP 222
>pdb|3K75|D Chain D, X-Ray Crystal Structure Of Reduced Xrcc1 Bound To Dna Pol
Beta Catalytic Domain
pdb|3K75|E Chain E, X-Ray Crystal Structure Of Reduced Xrcc1 Bound To Dna Pol
Beta Catalytic Domain
Length = 252
Score = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 33 LTPLNNY----LYWFGLGIFHSGIEAHGLEYGFGAHEY--RTSGVFEVEPKSCP 80
L P + Y LY+ G IF+ + AH LE GF +EY R GV V + P
Sbjct: 170 LIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLP 223
>pdb|1BPB|A Chain A, Crystal Structure Of Rat Dna Polymerase Beta: Evidence For
A Common Polymerase Mechanism
pdb|1NOM|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7), 31-Kd Domain;
Soaked In The Presence Of Mncl2 (5 Millimolar)
pdb|1ZQU|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7), 31-Kd Domain;
Soaked In The Presence Of Artificial Mother Liquor
pdb|1ZQV|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7), 31-Kd Domain;
Soaked In The Presence Of Cacl2 (150 Millimolar)
pdb|1ZQW|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7), 31-Kd Domain;
Soaked In The Presence Of Cscl (150 Millimolar)
pdb|1ZQX|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7), 31-Kd Domain;
Soaked In The Presence Of Kcl (150 Millimolar)
pdb|1ZQY|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7), 31-Kd Domain;
Soaked In The Presence Of Mgcl2 (50 Millimolar)
pdb|1ZQZ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7), 31-Kd Domain;
Soaked In The Presence Of Mncl2 (50 Millimolar)
pdb|2BPC|A Chain A, Crystal Structure Of Rat Dna Polymerase Beta: Evidence For
A Common Polymerase Mechanism
Length = 248
Score = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 33 LTPLNNY----LYWFGLGIFHSGIEAHGLEYGFGAHEY--RTSGVFEVEPKSCP 80
L P + Y LY+ G IF+ + AH LE GF +EY R GV V + P
Sbjct: 172 LIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLP 225
>pdb|3GDX|A Chain A, Dna Polymerase Beta With A Gapped Dnd Substrate And
Dtmp(Cf2)pp
Length = 326
Score = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 33 LTPLNNY----LYWFGLGIFHSGIEAHGLEYGFGAHEY--RTSGVFEVEPKSCP 80
L P + Y LY+ G IF+ + AH LE GF +EY R GV V + P
Sbjct: 250 LIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLP 303
>pdb|3LQC|B Chain B, X-Ray Crystal Structure Of Oxidized Xrcc1 Bound To Dna Pol
B Thumb Domain
Length = 200
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 33 LTPLNNY----LYWFGLGIFHSGIEAHGLEYGFGAHEY--RTSGVFEVEPKSCP 80
L P + Y LY+ G IF+ + AH LE GF +EY R GV V + P
Sbjct: 118 LIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLP 171
>pdb|3V72|A Chain A, Crystal Structure Of Rat Dna Polymerase Beta Mutator
E295k: Enzyme- Dsdna
Length = 335
Score = 31.2 bits (69), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 33 LTPLNNY----LYWFGLGIFHSGIEAHGLEYGFGAHEY--RTSGVFEVEPKSCP 80
L P + Y LY+ G IF+ + AH LE GF ++Y R GV V + P
Sbjct: 259 LIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINKYTIRPLGVTGVAGEPLP 312
>pdb|3T5O|A Chain A, Crystal Structure Of Human Complement Component C6
pdb|4A5W|B Chain B, Crystal Structure Of C5b6
pdb|4E0S|B Chain B, Crystal Structure Of C5b-6
Length = 913
Score = 31.2 bits (69), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 29/97 (29%), Positives = 42/97 (43%), Gaps = 11/97 (11%)
Query: 26 LYLNVYDLTPL--NNYLYW-----FGLGIFHSGI--EAHGLEYGFGAHEYRTSGVFEVEP 76
++L + PL N+ LY FG F SG + L Y F + E + SG+ E E
Sbjct: 316 VFLKALNHLPLEYNSALYSRIFDDFGTHYFTSGSLGGVYDLLYQFSSEELKNSGLTEEEA 375
Query: 77 KSCPGFIFRRSVLLGTTNLSRAEFRSFMEHLSGKYHG 113
K C ++ VL ++ E R LS K+ G
Sbjct: 376 KHCVRIETKKRVLFAKK--TKVEHRCTTNKLSEKHEG 410
>pdb|3BQJ|A Chain A, Va387 Polypeptide
Length = 304
Score = 30.8 bits (68), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 36/70 (51%), Gaps = 6/70 (8%)
Query: 69 SGVFEVEPKSCPGFIFRRSVLLGTTNLSRAEFRSFMEHLSGKYHGDTY--HLIAKNCNHF 126
SG F V+P++ G VLLGTT LS +F ++G Y +L ++N N++
Sbjct: 30 SGAFVVQPQN--GRCTTDGVLLGTTQLSAVNICTFRGDVTGVAGSHDYIMNLASQNWNNY 87
Query: 127 --TEEVCMQL 134
TEE+ L
Sbjct: 88 DPTEEIPAPL 97
>pdb|3RH5|A Chain A, Dna Polymerase Beta Mutant (Y271) With A
Dideoxy-Terminated Primer With An Incoming
Deoxynucleotide (Dctp)
pdb|3RH6|A Chain A, Dna Polymerase Beta Mutant (Y271) With A
Dideoxy-Terminated Primer With An Incoming
Ribonucleotide (Rctp)
Length = 335
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 26/54 (48%), Gaps = 6/54 (11%)
Query: 33 LTPLNNY----LYWFGLGIFHSGIEAHGLEYGFGAHEY--RTSGVFEVEPKSCP 80
L P + Y L + G IF+ + AH LE GF +EY R GV V + P
Sbjct: 259 LIPKDQYYCGVLAFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLP 312
>pdb|3LY8|A Chain A, Crystal Structure Of Mutant D471e Of The Periplasmic
Domain Of Cadc
Length = 372
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 27 YLNVYDLTPLNNYLYWFGLGIFHSGI 52
YL ++L P N LYW GIF + +
Sbjct: 333 YLTAFNLRPGANTLYWIENGIFQTSV 358
>pdb|3LY7|A Chain A, Crystal Structure Of The Periplasmic Domain Of Cadc
pdb|3LYA|A Chain A, Crystal Structure Of The Periplasmic Domain Of Cadc In The
Presence Of K2recl6
Length = 372
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 27 YLNVYDLTPLNNYLYWFGLGIFHSGI 52
YL ++L P N LYW GIF + +
Sbjct: 333 YLTAFNLRPGANTLYWIENGIFQTSV 358
>pdb|3LY9|A Chain A, Crystal Structure Of Mutant D471n Of The Periplasmic
Domain Of Cadc
Length = 372
Score = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 27 YLNVYDLTPLNNYLYWFGLGIFHSGI 52
YL ++L P N LYW GIF + +
Sbjct: 333 YLTAFNLRPGANTLYWIENGIFQTSV 358
>pdb|3O0J|A Chain A, Pde4b In Complex With Ligand An2898
Length = 323
Score = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 61 FGAHEYRTSGVFEVEPKSCPGF-IFRRSVLLGTTNLSRAEFRSFMEHLSGKYHGDT-YH 117
+G + + +G P +C + IF+ LL T +S F ++M L YH D YH
Sbjct: 15 WGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYH 73
>pdb|2QYL|A Chain A, Crystal Structure Of Pde4b2b In Complex With Inhibitor Npv
Length = 337
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 61 FGAHEYRTSGVFEVEPKSCPGF-IFRRSVLLGTTNLSRAEFRSFMEHLSGKYHGDT-YH 117
+G + + +G P +C + IF+ LL T +S F ++M L YH D YH
Sbjct: 26 WGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYH 84
>pdb|3D3P|A Chain A, Crystal Structure Of Pde4b Catalytic Domain In Complex
With A Pyrazolopyridine Inhibitor
pdb|3FRG|A Chain A, Catalytic Domain Of Human Phosphodiesterase 4b2b In
Complex With A Quinoline Inhibitor
pdb|3GWT|A Chain A, Catalytic Domain Of Human Phosphodiesterase 4b2b In
Complex With A Quinoline Inhibitor
pdb|3O56|A Chain A, Catalytic Domain Of Human Phosphodiesterase 4b2b In
Complex With A 5- Heterocycle Pyrazolopyridine Inhibitor
pdb|3O57|A Chain A, Catalytic Domain Of Human Phosphodiesterase 4b2b In
Complex With A 5- Heterocycle Pyrazolopyridine Inhibitor
Length = 353
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 61 FGAHEYRTSGVFEVEPKSCPGF-IFRRSVLLGTTNLSRAEFRSFMEHLSGKYHGDT-YH 117
+G + + +G P +C + IF+ LL T +S F ++M L YH D YH
Sbjct: 26 WGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYH 84
>pdb|3G45|A Chain A, Crystal Structure Of Human Phosphodiesterase 4b With
Regulatory Domain And D155988
pdb|3G45|B Chain B, Crystal Structure Of Human Phosphodiesterase 4b With
Regulatory Domain And D155988
Length = 421
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 37/85 (43%), Gaps = 4/85 (4%)
Query: 37 NNYLYWFGLGIFHSGIEAHGLE--YGFGAHEYRTSGVFEVEPKSCPGF-IFRRSVLLGTT 93
N + FG+ + A LE +G + + +G P +C + IF+ LL T
Sbjct: 78 NTSISRFGVNTENEDHLAKELEDLNKWGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTF 137
Query: 94 NLSRAEFRSFMEHLSGKYHGDT-YH 117
+S F ++M L YH D YH
Sbjct: 138 RISSDTFITYMMTLEDHYHSDVAYH 162
>pdb|3LY2|A Chain A, Catalytic Domain Of Human Phosphodiesterase 4b In Complex
Wi Coumarin-Based Inhibitor
pdb|3LY2|B Chain B, Catalytic Domain Of Human Phosphodiesterase 4b In Complex
Wi Coumarin-Based Inhibitor
pdb|3LY2|C Chain C, Catalytic Domain Of Human Phosphodiesterase 4b In Complex
Wi Coumarin-Based Inhibitor
pdb|3LY2|D Chain D, Catalytic Domain Of Human Phosphodiesterase 4b In Complex
Wi Coumarin-Based Inhibitor
pdb|3LY2|E Chain E, Catalytic Domain Of Human Phosphodiesterase 4b In Complex
Wi Coumarin-Based Inhibitor
pdb|3LY2|F Chain F, Catalytic Domain Of Human Phosphodiesterase 4b In Complex
Wi Coumarin-Based Inhibitor
pdb|3LY2|G Chain G, Catalytic Domain Of Human Phosphodiesterase 4b In Complex
Wi Coumarin-Based Inhibitor
pdb|3LY2|H Chain H, Catalytic Domain Of Human Phosphodiesterase 4b In Complex
Wi Coumarin-Based Inhibitor
Length = 357
Score = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 61 FGAHEYRTSGVFEVEPKSCPGF-IFRRSVLLGTTNLSRAEFRSFMEHLSGKYHGDT-YH 117
+G + + +G P +C + IF+ LL T +S F ++M L YH D YH
Sbjct: 46 WGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYH 104
>pdb|1W2X|A Chain A, Crystal Structure Of The Carboxyltransferase Domain Of
Acetyl-Coenzyme A Carboxylase In Complex With Cp-640186
pdb|1W2X|B Chain B, Crystal Structure Of The Carboxyltransferase Domain Of
Acetyl-Coenzyme A Carboxylase In Complex With Cp-640186
pdb|1W2X|C Chain C, Crystal Structure Of The Carboxyltransferase Domain Of
Acetyl-Coenzyme A Carboxylase In Complex With Cp-640186
pdb|3K8X|A Chain A, Crystal Structure Of The Carboxyltransferase Domain Of
Acetyl-Coenzyme A Carboxylase In Complex With
Tepraloxydim
pdb|3K8X|B Chain B, Crystal Structure Of The Carboxyltransferase Domain Of
Acetyl-Coenzyme A Carboxylase In Complex With
Tepraloxydim
pdb|3K8X|C Chain C, Crystal Structure Of The Carboxyltransferase Domain Of
Acetyl-Coenzyme A Carboxylase In Complex With
Tepraloxydim
Length = 758
Score = 28.1 bits (61), Expect = 4.3, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 74 VEPKSCPGFIFRRSVLLGTTNLSRAEFRSFMEHLSGK 110
+EP+ G FRR LL T N ++R LS K
Sbjct: 550 LEPQGMVGIKFRREKLLDTMNRLDDKYRELRSQLSNK 586
>pdb|1UYV|A Chain A, Acetyl-Coa Carboxylase Carboxyltransferase Domain L1705i
V1967i Mutant
pdb|1UYV|B Chain B, Acetyl-Coa Carboxylase Carboxyltransferase Domain L1705i
V1967i Mutant
pdb|1UYV|C Chain C, Acetyl-Coa Carboxylase Carboxyltransferase Domain L1705i
V1967i Mutant
Length = 737
Score = 28.1 bits (61), Expect = 4.3, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 74 VEPKSCPGFIFRRSVLLGTTNLSRAEFRSFMEHLSGK 110
+EP+ G FRR LL T N ++R LS K
Sbjct: 544 LEPQGMVGIKFRREKLLDTMNRLDDKYRELRSQLSNK 580
>pdb|1UYR|A Chain A, Acetyl-Coa Carboxylase Carboxyltransferase Domain In
Complex With Inhibitor Diclofop
pdb|1UYR|B Chain B, Acetyl-Coa Carboxylase Carboxyltransferase Domain In
Complex With Inhibitor Diclofop
pdb|1UYT|A Chain A, Acetyl-Coa Carboxylase Carboxyltransferase Domain
pdb|1UYT|B Chain B, Acetyl-Coa Carboxylase Carboxyltransferase Domain
pdb|1UYT|C Chain C, Acetyl-Coa Carboxylase Carboxyltransferase Domain
Length = 737
Score = 28.1 bits (61), Expect = 4.3, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 74 VEPKSCPGFIFRRSVLLGTTNLSRAEFRSFMEHLSGK 110
+EP+ G FRR LL T N ++R LS K
Sbjct: 544 LEPQGMVGIKFRREKLLDTMNRLDDKYRELRSQLSNK 580
>pdb|3PGQ|A Chain A, Crystal Structure Of The Carboxyltransferase Domain Of S.
Cerevisiae Acetyl Coa Carboxylase In Complex With
Pinoxaden
pdb|3PGQ|B Chain B, Crystal Structure Of The Carboxyltransferase Domain Of S.
Cerevisiae Acetyl Coa Carboxylase In Complex With
Pinoxaden
pdb|3PGQ|C Chain C, Crystal Structure Of The Carboxyltransferase Domain Of S.
Cerevisiae Acetyl Coa Carboxylase In Complex With
Pinoxaden
Length = 764
Score = 28.1 bits (61), Expect = 4.3, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 74 VEPKSCPGFIFRRSVLLGTTNLSRAEFRSFMEHLSGK 110
+EP+ G FRR LL T N ++R LS K
Sbjct: 550 LEPQGMVGIKFRREKLLDTMNRLDDKYRELRSQLSNK 586
>pdb|3H0J|A Chain A, Crystal Structure Of The Carboxyltransferase Domain Of
Acetyl-Coenzyme A Carboxylase In Complex With Compound 2
pdb|3H0J|B Chain B, Crystal Structure Of The Carboxyltransferase Domain Of
Acetyl-Coenzyme A Carboxylase In Complex With Compound 2
pdb|3H0J|C Chain C, Crystal Structure Of The Carboxyltransferase Domain Of
Acetyl-Coenzyme A Carboxylase In Complex With Compound 2
pdb|3H0S|A Chain A, Crystal Structure Of The Carboxyltransferase Domain Of
Acetyl-Coenzyme A Carboxylase In Complex With Compound 7
pdb|3H0S|B Chain B, Crystal Structure Of The Carboxyltransferase Domain Of
Acetyl-Coenzyme A Carboxylase In Complex With Compound 7
pdb|3H0S|C Chain C, Crystal Structure Of The Carboxyltransferase Domain Of
Acetyl-Coenzyme A Carboxylase In Complex With Compound 7
pdb|3H0Q|A Chain A, Crystal Structure Of The Carboxyltransferase Domain Of
Acetyl-Coenzyme A Carboxylase In Complex With Compound 3
pdb|3H0Q|B Chain B, Crystal Structure Of The Carboxyltransferase Domain Of
Acetyl-Coenzyme A Carboxylase In Complex With Compound 3
pdb|3H0Q|C Chain C, Crystal Structure Of The Carboxyltransferase Domain Of
Acetyl-Coenzyme A Carboxylase In Complex With Compound 3
Length = 769
Score = 28.1 bits (61), Expect = 4.3, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 74 VEPKSCPGFIFRRSVLLGTTNLSRAEFRSFMEHLSGK 110
+EP+ G FRR LL T N ++R LS K
Sbjct: 553 LEPQGMVGIKFRREKLLDTMNRLDDKYRELRSQLSNK 589
>pdb|3HMV|A Chain A, Catalytic Domain Of Human Phosphodiesterase 4b2b In
Complex Tetrahydrobenzothiophene Inhibitor
pdb|3HMV|B Chain B, Catalytic Domain Of Human Phosphodiesterase 4b2b In
Complex Tetrahydrobenzothiophene Inhibitor
Length = 378
Score = 28.1 bits (61), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 61 FGAHEYRTSGVFEVEPKSCPGF-IFRRSVLLGTTNLSRAEFRSFMEHLSGKYHGDT-YH 117
+G + + +G P +C + IF+ LL T +S F ++M L YH D YH
Sbjct: 26 WGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYH 84
>pdb|1RO6|A Chain A, Crystal Structure Of Pde4b2b Complexed With Rolipram (r &
S)
pdb|1RO6|B Chain B, Crystal Structure Of Pde4b2b Complexed With Rolipram (r &
S)
pdb|1RO9|A Chain A, Crystal Structures Of The Catalytic Domain Of
Phosphodiesterase 4b2b Complexed With 8-Br-Amp
pdb|1RO9|B Chain B, Crystal Structures Of The Catalytic Domain Of
Phosphodiesterase 4b2b Complexed With 8-Br-Amp
pdb|1ROR|A Chain A, Crystal Structures Of The Catalytic Domain Of
Phosphodiesterase 4b2b Complexed With Amp
pdb|1ROR|B Chain B, Crystal Structures Of The Catalytic Domain Of
Phosphodiesterase 4b2b Complexed With Amp
Length = 378
Score = 27.7 bits (60), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 61 FGAHEYRTSGVFEVEPKSCPGF-IFRRSVLLGTTNLSRAEFRSFMEHLSGKYHGDT-YH 117
+G + + +G P +C + IF+ LL T +S F ++M L YH D YH
Sbjct: 26 WGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYH 84
>pdb|1F0J|A Chain A, Catalytic Domain Of Human Phosphodiesterase 4b2b
pdb|1F0J|B Chain B, Catalytic Domain Of Human Phosphodiesterase 4b2b
Length = 377
Score = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 61 FGAHEYRTSGVFEVEPKSCPGF-IFRRSVLLGTTNLSRAEFRSFMEHLSGKYHGDT-YH 117
+G + + +G P +C + IF+ LL T +S F ++M L YH D YH
Sbjct: 25 WGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYH 83
>pdb|1UYS|A Chain A, Acetyl-Coa Carboxylase Carboxyltransferase Domain In
Complex With Inhibitor Haloxyfop
pdb|1UYS|B Chain B, Acetyl-Coa Carboxylase Carboxyltransferase Domain In
Complex With Inhibitor Haloxyfop
pdb|1UYS|C Chain C, Acetyl-Coa Carboxylase Carboxyltransferase Domain In
Complex With Inhibitor Haloxyfop
Length = 737
Score = 27.7 bits (60), Expect = 5.0, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 74 VEPKSCPGFIFRRSVLLGTTNLSRAEFRSFMEHLSGK 110
+EP+ G FRR LL T N ++R LS K
Sbjct: 544 LEPQGXVGIKFRREKLLDTXNRLDDKYRELRSQLSNK 580
>pdb|1OD2|A Chain A, Acetyl-Coa Carboxylase Carboxyltransferase Domain
pdb|1OD2|B Chain B, Acetyl-Coa Carboxylase Carboxyltransferase Domain
pdb|1OD4|A Chain A, Acetyl-Coa Carboxylase Carboxyltransferase Domain
pdb|1OD4|B Chain B, Acetyl-Coa Carboxylase Carboxyltransferase Domain
pdb|1OD4|C Chain C, Acetyl-Coa Carboxylase Carboxyltransferase Domain
Length = 805
Score = 27.7 bits (60), Expect = 5.0, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 74 VEPKSCPGFIFRRSVLLGTTNLSRAEFRSFMEHLSGK 110
+EP+ G FRR LL T N ++R LS K
Sbjct: 597 LEPQGXVGIKFRREKLLDTXNRLDDKYRELRSQLSNK 633
>pdb|1TB5|A Chain A, Catalytic Domain Of Human Phosphodiesterase 4b In Complex
With Amp
pdb|1TB5|B Chain B, Catalytic Domain Of Human Phosphodiesterase 4b In Complex
With Amp
Length = 381
Score = 27.7 bits (60), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 61 FGAHEYRTSGVFEVEPKSCPGF-IFRRSVLLGTTNLSRAEFRSFMEHLSGKYHGDT-YH 117
+G + + +G P +C + IF+ LL T +S F ++M L YH D YH
Sbjct: 29 WGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYH 87
>pdb|3KKT|A Chain A, Crystal Structure Of Human Pde4b With 5-[3-[(1s,2s,4r)-
Bicyclo[2.2.1]hept-2-Yloxy]-4-Methoxyp
Henyl]tetrahydro-2(1h)- Pyrimidinone Reveals Ordering Of
The C-Terminal Helix Residues 502- 509.
pdb|3KKT|B Chain B, Crystal Structure Of Human Pde4b With 5-[3-[(1s,2s,4r)-
Bicyclo[2.2.1]hept-2-Yloxy]-4-Methoxyp
Henyl]tetrahydro-2(1h)- Pyrimidinone Reveals Ordering Of
The C-Terminal Helix Residues 502- 509
Length = 398
Score = 27.7 bits (60), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 61 FGAHEYRTSGVFEVEPKSCPGF-IFRRSVLLGTTNLSRAEFRSFMEHLSGKYHGDT-YH 117
+G + + +G P +C + IF+ LL T +S F ++M L YH D YH
Sbjct: 46 WGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYH 104
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
0.323 0.139 0.440
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,412,946
Number of Sequences: 62578
Number of extensions: 248720
Number of successful extensions: 522
Number of sequences better than 100.0: 41
Number of HSP's better than 100.0 without gapping: 28
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 492
Number of HSP's gapped (non-prelim): 41
length of query: 225
length of database: 14,973,337
effective HSP length: 95
effective length of query: 130
effective length of database: 9,028,427
effective search space: 1173695510
effective search space used: 1173695510
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)