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= 041805
(215 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok
Length = 773
Score = 33.5 bits (75), Expect = 0.090, Method: Composition-based stats.
Identities = 28/95 (29%), Positives = 45/95 (47%), Gaps = 13/95 (13%)
Query: 4 LEYHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVPLALKVLGCFLYEREKEVWESA 63
+E+ L + + R+ N PD EL+ + YA G ++ E EK +WE+
Sbjct: 353 VEWFLLRKAYERNDVAPNKPD--ERELARRTESYAGG----------YVKEPEKGLWENI 400
Query: 64 INKLQRILHPSILEVLKISYDGLDNKEKNIFLDVA 98
+ + L+PSI+ +S D L N+E DVA
Sbjct: 401 VYLDYKSLYPSIIITHNVSPDTL-NREGCREYDVA 434
>pdb|1D5A|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok. Deposition Of Second Native Structure At 2.4
Angstrom
Length = 733
Score = 33.5 bits (75), Expect = 0.093, Method: Composition-based stats.
Identities = 28/95 (29%), Positives = 45/95 (47%), Gaps = 13/95 (13%)
Query: 4 LEYHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVPLALKVLGCFLYEREKEVWESA 63
+E+ L + + R+ N PD EL+ + YA G ++ E EK +WE+
Sbjct: 353 VEWFLLRKAYERNDVAPNKPD--ERELARRTESYAGG----------YVKEPEKGLWENI 400
Query: 64 INKLQRILHPSILEVLKISYDGLDNKEKNIFLDVA 98
+ + L+PSI+ +S D L N+E DVA
Sbjct: 401 VYLDYKSLYPSIIITHNVSPDTL-NREGCREYDVA 434
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 33.1 bits (74), Expect = 0.11, Method: Composition-based stats.
Identities = 28/95 (29%), Positives = 45/95 (47%), Gaps = 13/95 (13%)
Query: 4 LEYHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVPLALKVLGCFLYEREKEVWESA 63
+E+ L + + R+ N PD EL+ + YA G ++ E E+ +WE+
Sbjct: 353 VEWFLLRKAYERNELAPNKPD--ERELARRRESYAGG----------YVKEPERGLWENI 400
Query: 64 INKLQRILHPSILEVLKISYDGLDNKEKNIFLDVA 98
+ R L+PSI+ +S D L N+E DVA
Sbjct: 401 VYLDFRSLYPSIIITHNVSPDTL-NREGCEEYDVA 434
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 33.1 bits (74), Expect = 0.12, Method: Composition-based stats.
Identities = 28/95 (29%), Positives = 45/95 (47%), Gaps = 13/95 (13%)
Query: 4 LEYHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVPLALKVLGCFLYEREKEVWESA 63
+E+ L + + R+ N PD EL+ + YA G ++ E E+ +WE+
Sbjct: 353 VEWFLLRKAYERNELAPNKPD--ERELARRRESYAGG----------YVKEPERGLWENI 400
Query: 64 INKLQRILHPSILEVLKISYDGLDNKEKNIFLDVA 98
+ R L+PSI+ +S D L N+E DVA
Sbjct: 401 VYLDFRSLYPSIIITHNVSPDTL-NREGCEEYDVA 434
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 33.1 bits (74), Expect = 0.12, Method: Composition-based stats.
Identities = 28/95 (29%), Positives = 45/95 (47%), Gaps = 13/95 (13%)
Query: 4 LEYHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVPLALKVLGCFLYEREKEVWESA 63
+E+ L + + R+ N PD EL+ + YA G ++ E E+ +WE+
Sbjct: 353 VEWFLLRKAYERNELAPNKPD--ERELARRRESYAGG----------YVKEPERGLWENI 400
Query: 64 INKLQRILHPSILEVLKISYDGLDNKEKNIFLDVA 98
+ R L+PSI+ +S D L N+E DVA
Sbjct: 401 VYLDFRSLYPSIIITHNVSPDTL-NREGCEEYDVA 434
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 33.1 bits (74), Expect = 0.12, Method: Composition-based stats.
Identities = 28/95 (29%), Positives = 45/95 (47%), Gaps = 13/95 (13%)
Query: 4 LEYHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVPLALKVLGCFLYEREKEVWESA 63
+E+ L + + R+ N PD EL+ + YA G ++ E E+ +WE+
Sbjct: 353 VEWFLLRKAYERNELAPNKPD--ERELARRRESYAGG----------YVKEPERGLWENI 400
Query: 64 INKLQRILHPSILEVLKISYDGLDNKEKNIFLDVA 98
+ R L+PSI+ +S D L N+E DVA
Sbjct: 401 VYLDFRSLYPSIIITHNVSPDTL-NREGCEEYDVA 434
>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 32.3 bits (72), Expect = 0.19, Method: Composition-based stats.
Identities = 27/95 (28%), Positives = 45/95 (47%), Gaps = 13/95 (13%)
Query: 4 LEYHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVPLALKVLGCFLYEREKEVWESA 63
+E+ L + + R+ N PD +EL+ + Y G ++ E E+ +WE+
Sbjct: 353 VEWFLLRKAYERNELAPNKPD--EKELARRRQSYEGG----------YVKEPERGLWENI 400
Query: 64 INKLQRILHPSILEVLKISYDGLDNKEKNIFLDVA 98
+ R L+PSI+ +S D L N+E DVA
Sbjct: 401 VYLDFRSLYPSIIITHNVSPDTL-NREGCKEYDVA 434
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase
Mutant
Length = 774
Score = 32.3 bits (72), Expect = 0.19, Method: Composition-based stats.
Identities = 27/95 (28%), Positives = 45/95 (47%), Gaps = 13/95 (13%)
Query: 4 LEYHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVPLALKVLGCFLYEREKEVWESA 63
+E+ L + + R+ N PD +EL+ + Y G ++ E E+ +WE+
Sbjct: 353 VEWFLLRKAYERNELAPNKPD--EKELARRRQSYEGG----------YVKEPERGLWENI 400
Query: 64 INKLQRILHPSILEVLKISYDGLDNKEKNIFLDVA 98
+ R L+PSI+ +S D L N+E DVA
Sbjct: 401 VYLDFRSLYPSIIITHNVSPDTL-NREGCKEYDVA 434
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
Score = 31.2 bits (69), Expect = 0.39, Method: Composition-based stats.
Identities = 27/95 (28%), Positives = 45/95 (47%), Gaps = 13/95 (13%)
Query: 4 LEYHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVPLALKVLGCFLYEREKEVWESA 63
+E+ L + + R+ N PD EL+ + YA G ++ E E+ +W++
Sbjct: 353 VEWFLLRKAYKRNELAPNKPD--ERELARRRGGYAGG----------YVKEPERGLWDNI 400
Query: 64 INKLQRILHPSILEVLKISYDGLDNKEKNIFLDVA 98
+ R L+PSI+ +S D L N+E DVA
Sbjct: 401 VYLDFRSLYPSIIITHNVSPDTL-NREGCKEYDVA 434
>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 = 1.9, Method: Composition-based stats.
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 49 GCFLYEREKEVWESAINKLQRILHPSILEVLKISYDGLDNKEKNIFLDVA 98
G ++ E EK +WE ++ R L+PSI+ +S D L N+E DVA
Sbjct: 409 GGYVKEPEKGLWEGIVSLDFRSLYPSIIITHNVSPDTL-NRENCKEYDVA 457
>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 = 28.9 bits (63), Expect = 2.0, Method: Composition-based stats.
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 49 GCFLYEREKEVWESAINKLQRILHPSILEVLKISYDGLDNKEKNIFLDVA 98
G ++ E EK +WE ++ R L+PSI+ +S D L N+E DVA
Sbjct: 409 GGYVKEPEKGLWEGIVSLDFRSLYPSIIITHNVSPDTL-NRENCKEYDVA 457
>pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna
PolymerasePCNA Monomer Mutant Complex
Length = 775
Score = 28.1 bits (61), Expect = 3.3, Method: Composition-based stats.
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 49 GCFLYEREKEVWESAINKLQRILHPSILEVLKISYDGLD 87
G F+ E EK +WE+ + R L+PSI+ +S D L+
Sbjct: 387 GGFVKEPEKGLWENIVYLDFRALYPSIIITHNVSPDTLN 425
>pdb|3AV4|A Chain A, Crystal Structure Of Mouse Dna Methyltransferase 1
pdb|3AV5|A Chain A, Crystal Structure Of Mouse Dna Methyltransferase 1 With
Adohcy
pdb|3AV6|A Chain A, Crystal Structure Of Mouse Dna Methyltransferase 1 With
Adomet
Length = 1330
Score = 27.7 bits (60), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 33/69 (47%)
Query: 46 KVLGCFLYEREKEVWESAINKLQRILHPSILEVLKISYDGLDNKEKNIFLDVACFFQGED 105
K++ FL V+E INK++ + PS + V + + D L + + V + + +D
Sbjct: 226 KIVVEFLQNNPDAVYEDLINKIETTVPPSTINVNRFTEDSLLRHAQFVVSQVESYDEAKD 285
Query: 106 VNLVMKFLN 114
+ FL+
Sbjct: 286 DDETPIFLS 294
>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase
Length = 775
Score = 27.3 bits (59), Expect = 7.2, Method: Composition-based stats.
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 49 GCFLYEREKEVWESAINKLQRILHPSILEVLKISYDGLD 87
G F+ E EK +WE+ + + L+PSI+ +S D L+
Sbjct: 387 GGFVKEPEKGLWENIVYLDYKSLYPSIIITHNVSPDTLN 425
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
0.318 0.135 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,438,064
Number of Sequences: 62578
Number of extensions: 250593
Number of successful extensions: 699
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 690
Number of HSP's gapped (non-prelim): 32
length of query: 215
length of database: 14,973,337
effective HSP length: 95
effective length of query: 120
effective length of database: 9,028,427
effective search space: 1083411240
effective search space used: 1083411240
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)