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= 021517
(311 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 30.0 bits (66), Expect = 1.9, 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 WDVSRSSTGNLVEWFLLRKAYERNDVAPNKPD--ERELARRTESYA----------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 = 2.1, 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 WDVSRSSTGNLVEWFLLRKAYERNDVAPNKPD--ERELARRTESYA----------GGYV 389
Query: 105 HKREKEVWESATDKLQRILYPSILEVLKISYDSLD 139
+ EK +WE+ + LYPSI+ +S D+L+
Sbjct: 390 KEPEKGLWENIVYLDYKSLYPSIIITHNVSPDTLN 424
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 29.6 bits (65), Expect = 2.4, 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 = 29.6 bits (65), Expect = 2.4, 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 = 29.6 bits (65), Expect = 2.5, 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|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 29.6 bits (65), Expect = 2.5, 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|4HOQ|A Chain A, Crystal Structure Of Full-length Human Ifit5
Length = 482
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 51/176 (28%), Positives = 67/176 (38%), Gaps = 36/176 (20%)
Query: 140 DKEKNIFLDVACFFQ----GEDVDLVMKFFNASGFYPEI--GMSVLVDKSLIAIDSHKKI 193
D K I L++ C F ED+DL + + G E S L +L+A H K
Sbjct: 7 DTLKAILLELECHFTWNLLKEDIDL-FEVEDTIGQQLEFLTTKSRLALYNLLAYVKHLKG 65
Query: 194 TMHDLLQ--ELGREIVRQESIDPANRSRLWHHEDIYEVLTYNTFYRSSVNGKNKCKISYL 251
D L+ E EI++QE H D EV RS V N + Y
Sbjct: 66 QNKDALECLEQAEEIIQQE------------HSDKEEV-------RSLVTWGNYAWVYYH 106
Query: 252 QDPGFAEVKYLHWYGYPLKSL--PSNLSAKKLVLVEVPDSDIERLWHCVKVCISYY 305
D KY G K L PSN +E P++D E+ W +K YY
Sbjct: 107 XDQLEEAQKYTGKIGNVCKKLSSPSNYK------LECPETDCEKGWALLKFGGKYY 156
>pdb|3ZGQ|A Chain A, Crystal Structure Of Human Interferon-induced Protein
Ifit5
pdb|4HOR|A Chain A, Crystal Structure Of Full-length Human Ifit5 With
5`-triphosphate Oligocytidine
pdb|4HOS|A Chain A, Crystal Structure Of Full-length Human Ifit5 With
5`-triphosphate Oligouridine
pdb|4HOT|A Chain A, Crystal Structure Of Full-length Human Ifit5 With
5`-triphosphate Oligoadenine
pdb|4J0U|A Chain A, Crystal Structure Of Ifit5/isg58
Length = 482
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 51/176 (28%), Positives = 67/176 (38%), Gaps = 36/176 (20%)
Query: 140 DKEKNIFLDVACFFQ----GEDVDLVMKFFNASGFYPEI--GMSVLVDKSLIAIDSHKKI 193
D K I L++ C F ED+DL + + G E S L +L+A H K
Sbjct: 7 DTLKAILLELECHFTWNLLKEDIDL-FEVEDTIGQQLEFLTTKSRLALYNLLAYVKHLKG 65
Query: 194 TMHDLLQ--ELGREIVRQESIDPANRSRLWHHEDIYEVLTYNTFYRSSVNGKNKCKISYL 251
D L+ E EI++QE H D EV RS V N + Y
Sbjct: 66 QNKDALECLEQAEEIIQQE------------HSDKEEV-------RSLVTWGNYAWVYYH 106
Query: 252 QDPGFAEVKYLHWYGYPLKSL--PSNLSAKKLVLVEVPDSDIERLWHCVKVCISYY 305
D KY G K L PSN +E P++D E+ W +K YY
Sbjct: 107 MDQLEEAQKYTGKIGNVCKKLSSPSNYK------LECPETDCEKGWALLKFGGKYY 156
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase
Mutant
Length = 774
Score = 28.5 bits (62), Expect = 4.6, 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 WDVSRSSTGNLVEWFLLRKAYERNELAPNKPD--EKELARRRQSYE----------GGYV 389
Query: 105 HKREKEVWESATDKLQRILYPSILEVLKISYDSLD 139
+ E+ +WE+ R LYPSI+ +S D+L+
Sbjct: 390 KEPERGLWENIVYLDFRSLYPSIIITHNVSPDTLN 424
>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 28.5 bits (62), Expect = 4.6, 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 WDVSRSSTGNLVEWFLLRKAYERNELAPNKPD--EKELARRRQSYE----------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 = 28.5 bits (62), Expect = 5.2, 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|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
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+ + YA G ++
Sbjct: 342 WDVSRSSTGNLVEWFLLRKAYKRNELAPNKPDE--RELARRRGGYA----------GGYV 389
Query: 105 HKREKEVWESATDKLQRILYPSILEVLKISYDSLD 139
+ E+ +W++ R LYPSI+ +S D+L+
Sbjct: 390 KEPERGLWDNIVYLDFRSLYPSIIITHNVSPDTLN 424
>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 = 7.7, 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
>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 = 8.0, 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
0.323 0.139 0.428
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,590,956
Number of Sequences: 62578
Number of extensions: 389631
Number of successful extensions: 751
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 745
Number of HSP's gapped (non-prelim): 20
length of query: 311
length of database: 14,973,337
effective HSP length: 99
effective length of query: 212
effective length of database: 8,778,115
effective search space: 1860960380
effective search space used: 1860960380
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 bits)