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= 017858
(365 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2PLA|A Chain A, Crystal Structure Of Human Glycerol-3-Phosphate
Dehydrogenase 1-Like Protein
pdb|2PLA|B Chain B, Crystal Structure Of Human Glycerol-3-Phosphate
Dehydrogenase 1-Like Protein
Length = 349
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 15/89 (16%)
Query: 271 YRSSVNGKNKCKISYLQDPGFAEVKYLHWYGYPLKSLPSNLSAKKLVLVEVPDSDIERLW 330
+ +VNG+ K++ + + VKYL P LP N+ A + V D+D+ L
Sbjct: 43 FEETVNGR---KLTDIINNDHENVKYL-----PGHKLPENVVAMSNLSEAVQDADL--LV 92
Query: 331 HCVKHYSKLNQIIHAACNMLTAKIPNPTL 359
+ H Q IH C+ +T ++P L
Sbjct: 93 FVIPH-----QFIHRICDEITGRVPKKAL 116
>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 = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 42/95 (44%), Gaps = 12/95 (12%)
Query: 45 WGVRKIYEMKALEYHHAIRLFSRHAFKQNHPDVGYEELSCKVMKYAQGVPLALKVLGCFL 104
W V + +E+ + + R+ N PD EL+ + YA G ++
Sbjct: 342 WDVSRSSTGNLVEWFLLRKAYERNDVAPNKPDE--RELARRTESYA----------GGYV 389
Query: 105 HKREKEVWESATDKLQRILYPSILEVLKISYDSLD 139
+ EK +WE+ + LYPSI+ +S D+L+
Sbjct: 390 KEPEKGLWENIVYLDYKSLYPSIIITHNVSPDTLN 424
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok
Length = 773
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 42/95 (44%), Gaps = 12/95 (12%)
Query: 45 WGVRKIYEMKALEYHHAIRLFSRHAFKQNHPDVGYEELSCKVMKYAQGVPLALKVLGCFL 104
W V + +E+ + + R+ N PD EL+ + YA G ++
Sbjct: 342 WDVSRSSTGNLVEWFLLRKAYERNDVAPNKPDE--RELARRTESYA----------GGYV 389
Query: 105 HKREKEVWESATDKLQRILYPSILEVLKISYDSLD 139
+ EK +WE+ + LYPSI+ +S D+L+
Sbjct: 390 KEPEKGLWENIVYLDYKSLYPSIIITHNVSPDTLN 424
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 29.3 bits (64), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 42/95 (44%), Gaps = 12/95 (12%)
Query: 45 WGVRKIYEMKALEYHHAIRLFSRHAFKQNHPDVGYEELSCKVMKYAQGVPLALKVLGCFL 104
W V + +E+ + + R+ N PD EL+ + YA G ++
Sbjct: 342 WDVSRSSTGNLVEWFLLRKAYERNELAPNKPDE--RELARRRESYA----------GGYV 389
Query: 105 HKREKEVWESATDKLQRILYPSILEVLKISYDSLD 139
+ E+ +WE+ R LYPSI+ +S D+L+
Sbjct: 390 KEPERGLWENIVYLDFRSLYPSIIITHNVSPDTLN 424
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 29.3 bits (64), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 42/95 (44%), Gaps = 12/95 (12%)
Query: 45 WGVRKIYEMKALEYHHAIRLFSRHAFKQNHPDVGYEELSCKVMKYAQGVPLALKVLGCFL 104
W V + +E+ + + R+ N PD EL+ + YA G ++
Sbjct: 342 WDVSRSSTGNLVEWFLLRKAYERNELAPNKPDE--RELARRRESYA----------GGYV 389
Query: 105 HKREKEVWESATDKLQRILYPSILEVLKISYDSLD 139
+ E+ +WE+ R LYPSI+ +S D+L+
Sbjct: 390 KEPERGLWENIVYLDFRSLYPSIIITHNVSPDTLN 424
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 42/95 (44%), Gaps = 12/95 (12%)
Query: 45 WGVRKIYEMKALEYHHAIRLFSRHAFKQNHPDVGYEELSCKVMKYAQGVPLALKVLGCFL 104
W V + +E+ + + R+ N PD EL+ + YA G ++
Sbjct: 342 WDVSRSSTGNLVEWFLLRKAYERNELAPNKPDE--RELARRRESYA----------GGYV 389
Query: 105 HKREKEVWESATDKLQRILYPSILEVLKISYDSLD 139
+ E+ +WE+ R LYPSI+ +S D+L+
Sbjct: 390 KEPERGLWENIVYLDFRSLYPSIIITHNVSPDTLN 424
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 42/95 (44%), Gaps = 12/95 (12%)
Query: 45 WGVRKIYEMKALEYHHAIRLFSRHAFKQNHPDVGYEELSCKVMKYAQGVPLALKVLGCFL 104
W V + +E+ + + R+ N PD EL+ + YA G ++
Sbjct: 342 WDVSRSSTGNLVEWFLLRKAYERNELAPNKPDE--RELARRRESYA----------GGYV 389
Query: 105 HKREKEVWESATDKLQRILYPSILEVLKISYDSLD 139
+ E+ +WE+ R LYPSI+ +S D+L+
Sbjct: 390 KEPERGLWENIVYLDFRSLYPSIIITHNVSPDTLN 424
>pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna
PolymerasePCNA Monomer Mutant Complex
Length = 775
Score = 28.1 bits (61), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 101 GCFLHKREKEVWESATDKLQRILYPSILEVLKISYDSLD 139
G F+ + EK +WE+ R LYPSI+ +S D+L+
Sbjct: 387 GGFVKEPEKGLWENIVYLDFRALYPSIIITHNVSPDTLN 425
>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 28.1 bits (61), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 42/95 (44%), Gaps = 12/95 (12%)
Query: 45 WGVRKIYEMKALEYHHAIRLFSRHAFKQNHPDVGYEELSCKVMKYAQGVPLALKVLGCFL 104
W V + +E+ + + R+ N PD +EL+ + Y G ++
Sbjct: 342 WDVSRSSTGNLVEWFLLRKAYERNELAPNKPDE--KELARRRQSYE----------GGYV 389
Query: 105 HKREKEVWESATDKLQRILYPSILEVLKISYDSLD 139
+ E+ +WE+ R LYPSI+ +S D+L+
Sbjct: 390 KEPERGLWENIVYLDFRSLYPSIIITHNVSPDTLN 424
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase
Mutant
Length = 774
Score = 28.1 bits (61), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 42/95 (44%), Gaps = 12/95 (12%)
Query: 45 WGVRKIYEMKALEYHHAIRLFSRHAFKQNHPDVGYEELSCKVMKYAQGVPLALKVLGCFL 104
W V + +E+ + + R+ N PD +EL+ + Y G ++
Sbjct: 342 WDVSRSSTGNLVEWFLLRKAYERNELAPNKPDE--KELARRRQSYE----------GGYV 389
Query: 105 HKREKEVWESATDKLQRILYPSILEVLKISYDSLD 139
+ E+ +WE+ R LYPSI+ +S D+L+
Sbjct: 390 KEPERGLWENIVYLDFRSLYPSIIITHNVSPDTLN 424
>pdb|3H3E|A Chain A, Crystal Structure Of Tm1679, A Metal-Dependent Hydrolase
Of The Beta-Lactamase Superfamily
Length = 267
Score = 28.1 bits (61), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 41/99 (41%), Gaps = 24/99 (24%)
Query: 168 SGFYPEIGMSVLVDKSL---------------IAIDSHKKITMH--------DLLQELGR 204
+GF E G SVLVD L + ID K + + LL G+
Sbjct: 25 NGFESEHGFSVLVDSVLFDTGKSDVFLKNARKLGIDLPKDVLISHGHYDHAGGLLYLSGK 84
Query: 205 EI-VRQESIDPANRSRLWHHEDIYEVLTYNTGTEKIEGI 242
+ +R+E++D + D EVL YNTG IE I
Sbjct: 85 RVWLRKEALDQKYSGERYAGADWNEVLYYNTGKFVIERI 123
>pdb|4FM2|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant)
Bound To A Dsdna, In Edition Mode
Length = 793
Score = 27.7 bits (60), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 101 GCFLHKREKEVWESATDKLQRILYPSILEVLKISYDSLD 139
G ++ + EK +WE R LYPSI+ +S D+L+
Sbjct: 409 GGYVKEPEKGLWEGIVSLDFRSLYPSIIITHNVSPDTLN 447
>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 = 27.7 bits (60), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 101 GCFLHKREKEVWESATDKLQRILYPSILEVLKISYDSLD 139
G ++ + EK +WE R LYPSI+ +S D+L+
Sbjct: 409 GGYVKEPEKGLWEGIVSLDFRSLYPSIIITHNVSPDTLN 447
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
0.322 0.138 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,066,350
Number of Sequences: 62578
Number of extensions: 451747
Number of successful extensions: 1031
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1023
Number of HSP's gapped (non-prelim): 20
length of query: 365
length of database: 14,973,337
effective HSP length: 100
effective length of query: 265
effective length of database: 8,715,537
effective search space: 2309617305
effective search space used: 2309617305
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)