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= psy12449
(102 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IAY|A Chain A, Ternary Complex Of Dna Polymerase Delta
Length = 919
Score = 67.4 bits (163), Expect = 2e-12, Method: Composition-based stats.
Identities = 41/100 (41%), Positives = 54/100 (54%), Gaps = 5/100 (5%)
Query: 3 KFGTKELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQGS 62
K K+L++ D FK+ VL+GRQLALKISANSVYGFTGA VGKLPC + T G
Sbjct: 609 KRAKKDLRDEK--DPFKRDVLNGRQLALKISANSVYGFTGATVGKLPCLAISSSVTAYGR 666
Query: 63 ---LHEQVICTSRDCPIFYMRKKVQIELISQDQIIQRFGT 99
L + + C + + D ++ +FGT
Sbjct: 667 TMILKTKTAVQEKYCIKNGYKHDAVVVYGDTDSVMVKFGT 706
Score = 28.1 bits (61), Expect = 1.3, Method: Composition-based stats.
Identities = 12/15 (80%), Positives = 13/15 (86%)
Query: 1 MVKFGTKELKEAMTL 15
MVKFGT +LKEAM L
Sbjct: 701 MVKFGTTDLKEAMDL 715
>pdb|2GV9|A Chain A, Crystal Structure Of The Herpes Simplex Virus Type 1 Dna
Polymerase
pdb|2GV9|B Chain B, Crystal Structure Of The Herpes Simplex Virus Type 1 Dna
Polymerase
Length = 1193
Score = 42.7 bits (99), Expect = 5e-05, Method: Composition-based stats.
Identities = 18/29 (62%), Positives = 22/29 (75%)
Query: 22 VLDGRQLALKISANSVYGFTGAQVGKLPC 50
+LD +Q A+K+ NSVYGFTG Q G LPC
Sbjct: 760 LLDKQQAAIKVVCNSVYGFTGVQHGLLPC 788
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 40.0 bits (92), Expect = 3e-04, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 7 KELKEAM--TLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQG 61
+++K+ M T+D +KK+LD RQ A+KI ANS YG+ G + C+ + T G
Sbjct: 461 QKVKKKMKATIDPIEKKLLDYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWG 517
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 40.0 bits (92), Expect = 3e-04, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 7 KELKEAM--TLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQG 61
+++K+ M T+D +KK+LD RQ A+KI ANS YG+ G + C+ + T G
Sbjct: 461 QKVKKKMKATIDPIEKKLLDYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWG 517
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 40.0 bits (92), Expect = 3e-04, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 7 KELKEAM--TLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQG 61
+++K+ M T+D +KK+LD RQ A+KI ANS YG+ G + C+ + T G
Sbjct: 461 QKVKKKMKATIDPIEKKLLDYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWG 517
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 40.0 bits (92), Expect = 3e-04, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 7 KELKEAM--TLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQG 61
+++K+ M T+D +KK+LD RQ A+KI ANS YG+ G + C+ + T G
Sbjct: 461 QKVKKKMKATIDPIEKKLLDYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWG 517
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
Score = 40.0 bits (92), Expect = 3e-04, Method: Composition-based stats.
Identities = 21/52 (40%), Positives = 29/52 (55%)
Query: 10 KEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQG 61
K T+D +KK+LD RQ A+KI ANS YG+ G + C+ + T G
Sbjct: 466 KMKATVDPLEKKLLDYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWG 517
>pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna
PolymerasePCNA Monomer Mutant Complex
Length = 775
Score = 34.7 bits (78), Expect = 0.013, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 31/59 (52%)
Query: 10 KEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQGSLHEQVI 68
K T D +K +LD RQ A+K+ ANS YG+ G + C+ + T G + +++
Sbjct: 467 KXKETQDPIEKILLDYRQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELV 525
>pdb|4AHC|A Chain A, Crystal Structure Of An Evolved Replicating Dna Polymerase
pdb|4AHC|B Chain B, Crystal Structure Of An Evolved Replicating Dna Polymerase
pdb|4AIL|C Chain C, Crystal Structure Of An Evolved Replicating Dna Polymerase
Length = 775
Score = 34.3 bits (77), Expect = 0.018, Method: Composition-based stats.
Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 3 KFGTKELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQGS 62
K TK +KE T D +K +LD RQ A+K+ ANS YG+ G + C+ + T G
Sbjct: 463 KIKTK-MKE--TQDPIEKILLDYRQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGR 519
Query: 63 LHEQVI 68
+ +++
Sbjct: 520 KYIELV 525
>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase
Length = 775
Score = 34.3 bits (77), Expect = 0.018, Method: Composition-based stats.
Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 3 KFGTKELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQGS 62
K TK +KE T D +K +LD RQ A+K+ ANS YG+ G + C+ + T G
Sbjct: 463 KIKTK-MKE--TQDPIEKILLDYRQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGR 519
Query: 63 LHEQVI 68
+ +++
Sbjct: 520 KYIELV 525
>pdb|4FYD|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna And Dgtp
pdb|4FYD|B Chain B, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna And Dgtp
Length = 910
Score = 31.2 bits (69), Expect = 0.17, Method: Composition-based stats.
Identities = 17/38 (44%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 7 KELKEAMTL--DEFKKKVLDGRQLALKISANSVYGFTG 42
+E+K+ M D K+ D RQ ALK++ANS+YG G
Sbjct: 570 REVKKVMKTETDPHKRVQCDIRQQALKLTANSMYGCLG 607
>pdb|4FVM|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha
pdb|4FXD|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna
pdb|4FXD|B Chain B, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna
Length = 910
Score = 31.2 bits (69), Expect = 0.17, Method: Composition-based stats.
Identities = 17/38 (44%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 7 KELKEAMTL--DEFKKKVLDGRQLALKISANSVYGFTG 42
+E+K+ M D K+ D RQ ALK++ANS+YG G
Sbjct: 570 REVKKVMKTETDPHKRVQCDIRQQALKLTANSMYGCLG 607
>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 30.0 bits (66), Expect = 0.36, Method: Composition-based stats.
Identities = 15/32 (46%), Positives = 24/32 (75%), Gaps = 2/32 (6%)
Query: 7 KELKEAM--TLDEFKKKVLDGRQLALKISANS 36
+++K+ M T+D ++K+LD RQ A+KI ANS
Sbjct: 461 QKIKKKMKATIDPIERKLLDYRQRAIKILANS 492
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase
Mutant
Length = 774
Score = 30.0 bits (66), Expect = 0.37, Method: Composition-based stats.
Identities = 15/32 (46%), Positives = 24/32 (75%), Gaps = 2/32 (6%)
Query: 7 KELKEAM--TLDEFKKKVLDGRQLALKISANS 36
+++K+ M T+D ++K+LD RQ A+KI ANS
Sbjct: 461 QKIKKKMKATIDPIERKLLDYRQRAIKILANS 492
>pdb|4FM2|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant)
Bound To A Dsdna, In Edition Mode
Length = 793
Score = 29.3 bits (64), Expect = 0.67, Method: Composition-based stats.
Identities = 16/30 (53%), Positives = 21/30 (70%), Gaps = 2/30 (6%)
Query: 7 KELKEAMTLDEFKKKVLDGRQLALKISANS 36
K +KE+ D +KK+LD RQ A+KI ANS
Sbjct: 488 KRMKESK--DPVEKKLLDYRQRAIKILANS 515
>pdb|4FLT|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLU|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLV|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLW|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLX|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLY|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLZ|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FM0|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FM1|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
Length = 793
Score = 29.3 bits (64), Expect = 0.67, Method: Composition-based stats.
Identities = 16/30 (53%), Positives = 21/30 (70%), Gaps = 2/30 (6%)
Query: 7 KELKEAMTLDEFKKKVLDGRQLALKISANS 36
K +KE+ D +KK+LD RQ A+KI ANS
Sbjct: 488 KRMKESK--DPVEKKLLDYRQRAIKILANS 515
>pdb|4B08|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha,
Selenomethionine Protein
Length = 910
Score = 28.5 bits (62), Expect = 1.0, Method: Composition-based stats.
Identities = 14/27 (51%), Positives = 17/27 (62%)
Query: 16 DEFKKKVLDGRQLALKISANSVYGFTG 42
D K+ D RQ ALK++ANS YG G
Sbjct: 581 DPHKRVQCDIRQQALKLTANSXYGCLG 607
>pdb|2KPI|A Chain A, Solution Nmr Structure Of Streptomyces Coelicolor
Sco3027 Modeled With Zn+2 Bound, Northeast Structural
Genomics Consortium Target Rr58
Length = 56
Score = 26.2 bits (56), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 56 CQTCQGSLHE---QVICTSRDCPIFY-MRKKVQIELISQ 90
C C L E ++ICT +DC + Y +R + + L+ +
Sbjct: 13 CPACHAPLEERDAELICTGQDCGLAYPVRDGIPVLLVDE 51
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
0.324 0.136 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,808,199
Number of Sequences: 62578
Number of extensions: 93743
Number of successful extensions: 262
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 241
Number of HSP's gapped (non-prelim): 22
length of query: 102
length of database: 14,973,337
effective HSP length: 67
effective length of query: 35
effective length of database: 10,780,611
effective search space: 377321385
effective search space used: 377321385
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: 45 (21.9 bits)