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= 039679
(230 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1G38|A Chain A, Adenine-Specific Methyltransferase M. Taq IDNA COMPLEX
pdb|1G38|D Chain D, Adenine-Specific Methyltransferase M. Taq IDNA COMPLEX
Length = 393
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 39/98 (39%), Gaps = 22/98 (22%)
Query: 78 NLPPWRPGL---------KEVFDAIICDPPYGVRASGRK----LLKGVLDPYTVPDDKRV 124
+LPPW G+ E FD I+ +PPYG+ K + K V D Y
Sbjct: 58 DLPPWAEGILADFLLWEPGEAFDLILGNPPYGIVGEASKYPIHVFKAVKDLYKKAFSTWK 117
Query: 125 GHIPSTAPYCLSECVHDLLDLAGRILVMGGRLVYFYPV 162
G Y L L+ A R+L GG LV+ P
Sbjct: 118 GK------YNLYGA---FLEKAVRLLKPGGVLVFVVPA 146
>pdb|2IBS|A Chain A, Crystal Structure Of The Adenine-Specific Dna
Methyltransferase M.Taqi Complexed With The Cofactor
Analog Aeta And A 10 Bp Dna Containing 2-Aminopurine At
The Target Position
pdb|2IBS|D Chain D, Crystal Structure Of The Adenine-Specific Dna
Methyltransferase M.Taqi Complexed With The Cofactor
Analog Aeta And A 10 Bp Dna Containing 2-Aminopurine At
The Target Position
pdb|2IBT|A Chain A, Crystal Structure Of The Adenine-Specific Dna
Methyltransferase M.Taqi Complexed With The Cofactor
Analog Aeta And A 10 Bp Dna Containing 2- Aminopurine At
The Target Position And An Abasic Site Analog At The
Target Base Partner Position
pdb|2IBT|D Chain D, Crystal Structure Of The Adenine-Specific Dna
Methyltransferase M.Taqi Complexed With The Cofactor
Analog Aeta And A 10 Bp Dna Containing 2- Aminopurine At
The Target Position And An Abasic Site Analog At The
Target Base Partner Position
pdb|2JG3|A Chain A, Mtaqi With Baz
pdb|2JG3|D Chain D, Mtaqi With Baz
pdb|2IH2|A Chain A, Crystal Structure Of The Adenine-Specific Dna
Methyltransferase M.Taqi Complexed With The Cofactor
Analog Aeta And A 10 Bp Dna Containing 5-
Methylpyrimidin-2(1h)-One At The Target Base Partner
Position
pdb|2IH2|D Chain D, Crystal Structure Of The Adenine-Specific Dna
Methyltransferase M.Taqi Complexed With The Cofactor
Analog Aeta And A 10 Bp Dna Containing 5-
Methylpyrimidin-2(1h)-One At The Target Base Partner
Position
pdb|2IH4|A Chain A, Crystal Structure Of The Adenine-Specific Dna
Methyltransferase M.Taqi Complexed With The Cofactor
Analog Aeta And A 10 Bp Dna Containing Pyrrolo-Dc At The
Target Base Partner Position
pdb|2IH4|D Chain D, Crystal Structure Of The Adenine-Specific Dna
Methyltransferase M.Taqi Complexed With The Cofactor
Analog Aeta And A 10 Bp Dna Containing Pyrrolo-Dc At The
Target Base Partner Position
pdb|2IH5|A Chain A, Crystal Structure Of The Adenine-Specific Dna
Methyltransferase M.Taqi Complexed With The Cofactor
Analog Aeta And A 10 Bp Dna Containing An Abasic Site
Analog At The Target Base Partner Position
pdb|2NP6|A Chain A, Crystal Structure Of The Adenine-Specific Dna
Methyltransferase M.Taqi Complexed With The Cofactor
Analog Aeta And A 10 Bp Dna Containing An Abasic Site
Analog At The Target Position
pdb|2NP6|D Chain D, Crystal Structure Of The Adenine-Specific Dna
Methyltransferase M.Taqi Complexed With The Cofactor
Analog Aeta And A 10 Bp Dna Containing An Abasic Site
Analog At The Target Position
pdb|2NP7|A Chain A, Crystal Structure Of The Adenine-Specific Dna
Methyltransferase M.Taqi Complexed With The Cofactor
Analog Aeta And A 10 Bp Dna Containing An Abasic Site
Analog At The Target Position And Pyrrolo-Dc At The
Target Base Partner Position
Length = 421
Score = 32.7 bits (73), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 39/98 (39%), Gaps = 22/98 (22%)
Query: 78 NLPPWRPGL---------KEVFDAIICDPPYGVRASGRK----LLKGVLDPYTVPDDKRV 124
+LPPW G+ E FD I+ +PPYG+ K + K V D Y
Sbjct: 78 DLPPWAEGILADFLLWEPGEAFDLILGNPPYGIVGEASKYPIHVFKAVKDLYKKAFSTWK 137
Query: 125 GHIPSTAPYCLSECVHDLLDLAGRILVMGGRLVYFYPV 162
G Y L L+ A R+L GG LV+ P
Sbjct: 138 GK------YNLYGA---FLEKAVRLLKPGGVLVFVVPA 166
>pdb|1AQI|A Chain A, Structure Of Adenine-N6-Dna-Methyltransferase Taqi
pdb|1AQI|B Chain B, Structure Of Adenine-N6-Dna-Methyltransferase Taqi
pdb|2ADM|A Chain A, Adenine-N6-Dna-Methyltransferase Taqi
pdb|2ADM|B Chain B, Adenine-N6-Dna-Methyltransferase Taqi
Length = 421
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 39/98 (39%), Gaps = 22/98 (22%)
Query: 78 NLPPWRPGL---------KEVFDAIICDPPYGVRASGRK----LLKGVLDPYTVPDDKRV 124
+LPPW G+ E FD I+ +PPYG+ K + K V D Y
Sbjct: 78 DLPPWAEGILADFLLWEPGEAFDLILGNPPYGIVGEASKYPIHVFKAVKDLYKKAFSTWK 137
Query: 125 GHIPSTAPYCLSECVHDLLDLAGRILVMGGRLVYFYPV 162
G Y L L+ A R+L GG LV+ P
Sbjct: 138 GK------YNLYGA---FLEKAVRLLKPGGVLVFVVPA 166
>pdb|1AQJ|A Chain A, Structure Of Adenine-n6-dna-methyltransferase Taqi
pdb|1AQJ|B Chain B, Structure Of Adenine-n6-dna-methyltransferase Taqi
Length = 421
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 39/98 (39%), Gaps = 22/98 (22%)
Query: 78 NLPPWRPGL---------KEVFDAIICDPPYGVRASGRK----LLKGVLDPYTVPDDKRV 124
+LPPW G+ E FD I+ +PPYG+ K + K V D Y
Sbjct: 78 DLPPWAEGILADFLLWEPGEAFDLILGNPPYGIVGEASKYPIHVFKAVKDLYKKAFSTWK 137
Query: 125 GHIPSTAPYCLSECVHDLLDLAGRILVMGGRLVYFYPV 162
G Y L L+ A R+L GG LV+ P
Sbjct: 138 GK------YNLYGA---FLEKAVRLLKPGGVLVFVVPA 166
>pdb|2WZQ|A Chain A, Insertion Mutant E173gp174 Of The Ns3 Protease-Helicase
From Dengue Virus
Length = 619
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 5/66 (7%)
Query: 45 PFHFVNLPSEDIARSIANRIWITNAYWFAKADNNLPPWRPGLKEVFDAIICDPPYGVRAS 104
PF N P EDI R I R W T W + P +K D C +R S
Sbjct: 325 PFPQSNSPIEDIEREIPERSWNTGFDWITDYQGKTVWFVPSIKAGNDIANC-----LRKS 379
Query: 105 GRKLLK 110
G+++++
Sbjct: 380 GKRVIQ 385
>pdb|2JLQ|A Chain A, Dengue Virus 4 Ns3 Helicase Structure, Apo Enzyme.
pdb|2JLY|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna And Adp-
Phosphate
pdb|2JLY|B Chain B, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna And Adp-
Phosphate
Length = 451
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 5/66 (7%)
Query: 45 PFHFVNLPSEDIARSIANRIWITNAYWFAKADNNLPPWRPGLKEVFDAIICDPPYGVRAS 104
PF N P EDI R I R W T W + P +K D C +R S
Sbjct: 157 PFPQSNSPIEDIEREIPERSWNTGFDWITDYQGKTVWFVPSIKAGNDIANC-----LRKS 211
Query: 105 GRKLLK 110
G+++++
Sbjct: 212 GKRVIQ 217
>pdb|2VBC|A Chain A, Crystal Structure Of The Ns3 Protease-Helicase From Dengue
Virus
Length = 618
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 5/66 (7%)
Query: 45 PFHFVNLPSEDIARSIANRIWITNAYWFAKADNNLPPWRPGLKEVFDAIICDPPYGVRAS 104
PF N P EDI R I R W T W + P +K D C +R S
Sbjct: 324 PFPQSNSPIEDIEREIPERSWNTGFDWITDYQGKTVWFVPSIKAGNDIANC-----LRKS 378
Query: 105 GRKLLK 110
G+++++
Sbjct: 379 GKRVIQ 384
>pdb|2WHX|A Chain A, A Second Conformation Of The Ns3 Protease-Helicase From
Dengue Virus
Length = 618
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 5/66 (7%)
Query: 45 PFHFVNLPSEDIARSIANRIWITNAYWFAKADNNLPPWRPGLKEVFDAIICDPPYGVRAS 104
PF N P EDI R I R W T W + P +K D C +R S
Sbjct: 324 PFPQSNSPIEDIEREIPERSWNTGFDWITDYQGKTVWFVPSIKAGNDIANC-----LRKS 378
Query: 105 GRKLLK 110
G+++++
Sbjct: 379 GKRVIQ 384
>pdb|2JLS|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Adp
Length = 451
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 5/66 (7%)
Query: 45 PFHFVNLPSEDIARSIANRIWITNAYWFAKADNNLPPWRPGLKEVFDAIICDPPYGVRAS 104
PF N P EDI R I R W T W + P +K D C +R S
Sbjct: 157 PFPQSNSPIEDIEREIPERSWNTGFDWITDYQGKTVWFVPSIKAGNDIANC-----LRKS 211
Query: 105 GRKLLK 110
G+++++
Sbjct: 212 GKRVIQ 217
>pdb|2JLR|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Amppnp
Length = 451
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 5/66 (7%)
Query: 45 PFHFVNLPSEDIARSIANRIWITNAYWFAKADNNLPPWRPGLKEVFDAIICDPPYGVRAS 104
PF N P EDI R I R W T W + P +K D C +R S
Sbjct: 157 PFPQSNSPIEDIEREIPERSWNTGFDWITDYQGKTVWFVPSIKAGNDIANC-----LRKS 211
Query: 105 GRKLLK 110
G+++++
Sbjct: 212 GKRVIQ 217
>pdb|2JLU|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna
pdb|2JLU|B Chain B, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna
pdb|2JLV|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna And
Amppnp
pdb|2JLV|B Chain B, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna And
Amppnp
pdb|2JLW|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna2
pdb|2JLW|B Chain B, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna2
pdb|2JLX|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna And Adp-
Vanadate
pdb|2JLX|B Chain B, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna And Adp-
Vanadate
pdb|2JLZ|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna And Adp
pdb|2JLZ|B Chain B, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna And Adp
Length = 451
Score = 32.0 bits (71), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 5/66 (7%)
Query: 45 PFHFVNLPSEDIARSIANRIWITNAYWFAKADNNLPPWRPGLKEVFDAIICDPPYGVRAS 104
PF N P EDI R I R W T W + P +K D C +R S
Sbjct: 157 PFPQSNSPIEDIEREIPERSWNTGFDWITDYQGKTVWFVPSIKAGNDIANC-----LRKS 211
Query: 105 GRKLLK 110
G+++++
Sbjct: 212 GKRVIQ 217
>pdb|1ODF|A Chain A, Structure Of Ygr205w Protein
Length = 290
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 3/39 (7%)
Query: 6 VFFHRLLDYRKPEVESLAYLF---GVNDALEWKLPKHHH 41
+FF+ L +R PE++SL +F +N+ W+L + H
Sbjct: 189 LFFYSDLLWRNPEIKSLGIVFTTDNINNVYGWRLQQEHE 227
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 0.141 0.462
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,704,032
Number of Sequences: 62578
Number of extensions: 310502
Number of successful extensions: 582
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 574
Number of HSP's gapped (non-prelim): 17
length of query: 230
length of database: 14,973,337
effective HSP length: 96
effective length of query: 134
effective length of database: 8,965,849
effective search space: 1201423766
effective search space used: 1201423766
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)