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= psy12660
(294 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 61.6 bits (148), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 44/143 (30%), Positives = 70/143 (48%), Gaps = 9/143 (6%)
Query: 31 GVGESEPNPYFYQNLAEAEYCVALFMYMRLLGYPAHKITILSTYNGQKHLIRDVINTRCA 90
G E N + N EA C + + G +I +++ Y GQ+ I + +
Sbjct: 641 GREEISANGTSFLNRIEAMNCERIITKLFRDGVKPEQIGVITPYEGQRAYILQYMQMNGS 700
Query: 91 DNPLIGRPHKVTTVDKYQGQQNDYILLSLVRT---ASVGHLRDVRRLIVAMSRARLGLYV 147
+ + +V +VD +QG++ DYI+LS VR ++G LRD RRL V ++RA+ GL +
Sbjct: 701 LDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRLNVGLTRAKYGLVI 760
Query: 148 FARV-SLFRNCFELTPAFNQLMI 169
SL RN +N L+I
Sbjct: 761 LGNPRSLARNTL-----WNHLLI 778
>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|B Chain B, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK7|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
Length = 624
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 32/111 (28%), Positives = 57/111 (51%), Gaps = 3/111 (2%)
Query: 42 YQNLAEAEYCVALFMYMRLLGYPAHKITILSTYNGQKHLIRDVINTRCADNPLIGRPHKV 101
Y N EA + + G +I I++ Y GQ+ + + + + + + ++
Sbjct: 474 YLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEI 533
Query: 102 TTVDKYQGQQNDYILLSLVRT---ASVGHLRDVRRLIVAMSRARLGLYVFA 149
+VD +QG++ D+I+LS VR +G L D RRL VA++RAR G+ +
Sbjct: 534 ASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVG 584
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 32/111 (28%), Positives = 57/111 (51%), Gaps = 3/111 (2%)
Query: 42 YQNLAEAEYCVALFMYMRLLGYPAHKITILSTYNGQKHLIRDVINTRCADNPLIGRPHKV 101
Y N EA + + G +I I++ Y GQ+ + + + + + + ++
Sbjct: 473 YLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEI 532
Query: 102 TTVDKYQGQQNDYILLSLVRT---ASVGHLRDVRRLIVAMSRARLGLYVFA 149
+VD +QG++ D+I+LS VR +G L D RRL VA++RAR G+ +
Sbjct: 533 ASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVG 583
>pdb|2WJV|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJV|B Chain B, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJY|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2 Orthorhombic Form
Length = 800
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 32/111 (28%), Positives = 57/111 (51%), Gaps = 3/111 (2%)
Query: 42 YQNLAEAEYCVALFMYMRLLGYPAHKITILSTYNGQKHLIRDVINTRCADNPLIGRPHKV 101
Y N EA + + G +I I++ Y GQ+ + + + + + + ++
Sbjct: 650 YLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEI 709
Query: 102 TTVDKYQGQQNDYILLSLVRT---ASVGHLRDVRRLIVAMSRARLGLYVFA 149
+VD +QG++ D+I+LS VR +G L D RRL VA++RAR G+ +
Sbjct: 710 ASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVG 760
>pdb|4B3G|A Chain A, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
pdb|4B3G|B Chain B, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
Length = 646
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 50/84 (59%), Gaps = 10/84 (11%)
Query: 62 GYPAHKITILSTYNGQKHLIRDVINTRCADNPLIGRPHKVTTVDKYQGQQNDYILLSLVR 121
G PA I ++S YN Q L+R + R +P + ++ +VD +QG++ + ++LS VR
Sbjct: 527 GVPARDIAVVSPYNLQVDLLRQSLVHR---HPEL----EIKSVDGFQGREKEAVILSFVR 579
Query: 122 T---ASVGHLRDVRRLIVAMSRAR 142
+ VG L + RR+ VA++RAR
Sbjct: 580 SNRKGEVGFLAEDRRINVAVTRAR 603
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 50/84 (59%), Gaps = 10/84 (11%)
Query: 62 GYPAHKITILSTYNGQKHLIRDVINTRCADNPLIGRPHKVTTVDKYQGQQNDYILLSLVR 121
G PA I ++S YN Q L+R + R +P + ++ +VD +QG++ + ++LS VR
Sbjct: 527 GVPARDIAVVSPYNLQVDLLRQSLVHR---HPEL----EIKSVDGFQGREKEAVILSFVR 579
Query: 122 T---ASVGHLRDVRRLIVAMSRAR 142
+ VG L + RR+ VA++RAR
Sbjct: 580 SNRKGEVGFLAEDRRINVAVTRAR 603
>pdb|2WHX|A Chain A, A Second Conformation Of The Ns3 Protease-Helicase From
Dengue Virus
Length = 618
Score = 31.2 bits (69), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 34/116 (29%), Positives = 55/116 (47%), Gaps = 13/116 (11%)
Query: 95 IGRPHKVTTVDKYQGQ-QNDYILLSLVRTASVGHLRDVRRLIVAMSRARLGLYVFARVSL 153
I R ++T +D + G + IL S+VR A R +R LI+A +R V A +
Sbjct: 182 IFRKKRLTIMDLHPGAGKTKRILPSIVREA---LKRRLRTLILAPTRV-----VAAEMEE 233
Query: 154 FRNCFEL---TPAFNQLMIRPQQLHIVPHETFPTSRLNTSRVPN-SVAIQDMVHMT 205
+ TPA + + ++ H TF T L+++RVPN ++ + D H T
Sbjct: 234 ALRGLPIRYQTPAVKSDHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFT 289
>pdb|2VBC|A Chain A, Crystal Structure Of The Ns3 Protease-Helicase From Dengue
Virus
Length = 618
Score = 31.2 bits (69), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 34/116 (29%), Positives = 55/116 (47%), Gaps = 13/116 (11%)
Query: 95 IGRPHKVTTVDKYQGQ-QNDYILLSLVRTASVGHLRDVRRLIVAMSRARLGLYVFARVSL 153
I R ++T +D + G + IL S+VR A R +R LI+A +R V A +
Sbjct: 182 IFRKKRLTIMDLHPGAGKTKRILPSIVREA---LKRRLRTLILAPTRV-----VAAEMEE 233
Query: 154 FRNCFEL---TPAFNQLMIRPQQLHIVPHETFPTSRLNTSRVPN-SVAIQDMVHMT 205
+ TPA + + ++ H TF T L+++RVPN ++ + D H T
Sbjct: 234 ALRGLPIRYQTPAVKSDHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFT 289
>pdb|2WZQ|A Chain A, Insertion Mutant E173gp174 Of The Ns3 Protease-Helicase
From Dengue Virus
Length = 619
Score = 31.2 bits (69), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 34/116 (29%), Positives = 55/116 (47%), Gaps = 13/116 (11%)
Query: 95 IGRPHKVTTVDKYQGQ-QNDYILLSLVRTASVGHLRDVRRLIVAMSRARLGLYVFARVSL 153
I R ++T +D + G + IL S+VR A R +R LI+A +R V A +
Sbjct: 183 IFRKKRLTIMDLHPGAGKTKRILPSIVREA---LKRRLRTLILAPTRV-----VAAEMEE 234
Query: 154 FRNCFEL---TPAFNQLMIRPQQLHIVPHETFPTSRLNTSRVPN-SVAIQDMVHMT 205
+ TPA + + ++ H TF T L+++RVPN ++ + D H T
Sbjct: 235 ALRGLPIRYQTPAVKSDHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFT 290
>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 = 30.8 bits (68), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 33/118 (27%), Positives = 53/118 (44%), Gaps = 17/118 (14%)
Query: 95 IGRPHKVTTVDKYQGQ-QNDYILLSLVRTASVGHLRDV-----RRLIVAMSRARLGLYVF 148
I R ++T +D + G + IL S+VR A LR + R + M A GL +
Sbjct: 15 IFRKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALRGLPIR 74
Query: 149 ARVSLFRNCFELTPAFNQLMIRPQQLHIVPHETFPTSRLNTSRVPN-SVAIQDMVHMT 205
+ TPA + + ++ H TF T L+++RVPN ++ + D H T
Sbjct: 75 YQ----------TPAVKSDHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFT 122
>pdb|2JLS|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Adp
Length = 451
Score = 30.8 bits (68), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 33/118 (27%), Positives = 53/118 (44%), Gaps = 17/118 (14%)
Query: 95 IGRPHKVTTVDKYQGQ-QNDYILLSLVRTASVGHLRDV-----RRLIVAMSRARLGLYVF 148
I R ++T +D + G + IL S+VR A LR + R + M A GL +
Sbjct: 15 IFRKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALRGLPIR 74
Query: 149 ARVSLFRNCFELTPAFNQLMIRPQQLHIVPHETFPTSRLNTSRVPN-SVAIQDMVHMT 205
+ TPA + + ++ H TF T L+++RVPN ++ + D H T
Sbjct: 75 YQ----------TPAVKSDHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFT 122
>pdb|2JLR|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Amppnp
Length = 451
Score = 30.8 bits (68), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 33/118 (27%), Positives = 53/118 (44%), Gaps = 17/118 (14%)
Query: 95 IGRPHKVTTVDKYQGQ-QNDYILLSLVRTASVGHLRDV-----RRLIVAMSRARLGLYVF 148
I R ++T +D + G + IL S+VR A LR + R + M A GL +
Sbjct: 15 IFRKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALRGLPIR 74
Query: 149 ARVSLFRNCFELTPAFNQLMIRPQQLHIVPHETFPTSRLNTSRVPN-SVAIQDMVHMT 205
+ TPA + + ++ H TF T L+++RVPN ++ + D H T
Sbjct: 75 YQ----------TPAVKSDHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFT 122
>pdb|3PX7|A Chain A, Crystal Structure Of Covalent Complex Of Topoisomerase 1a
With Substrate
Length = 595
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 24/38 (63%), Gaps = 7/38 (18%)
Query: 94 LIGRPHKVTTVDKYQGQQNDYILLSLVRTASVGHLRDV 131
++ P K T++KY G +DY++ S SVGH+RD+
Sbjct: 7 IVESPAKAKTINKYLG--SDYVVKS-----SVGHIRDL 37
>pdb|1MW8|X Chain X, Crystal Structure Of A Complex Between H365r Mutant Of 67
Kda N-Terminal Fragment Of E. Coli Dna Topoisomerase I
And 5'-Acttcgggatg-3'
pdb|1MW9|X Chain X, Crystal Structure Of H365r Mutant Of 67 Kda N-Terminal
Fragment Of E. Coli Dna Topoisomerase I
Length = 592
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 24/38 (63%), Gaps = 7/38 (18%)
Query: 94 LIGRPHKVTTVDKYQGQQNDYILLSLVRTASVGHLRDV 131
++ P K T++KY G +DY++ S SVGH+RD+
Sbjct: 7 IVESPAKAKTINKYLG--SDYVVKS-----SVGHIRDL 37
>pdb|1CY1|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'ptptpt
pdb|1CY2|A Chain A, Complex Of E.Coli Dna Topoisomerase I With Tptptp3'
pdb|1CY6|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 3' Thymidine
Monophosphate
pdb|1CY7|A Chain A, Complex Of E.coli Dna Topoisomerase I With 5'-thymidine
Monophosphate
pdb|1CY8|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'-Thymidine
Monophosphate And 3'-Thymidine Monophosphate
pdb|1CY0|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 3'-5'-Adenosine
Diphosphate
pdb|1CY4|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'ptptptp3'
Length = 599
Score = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 24/38 (63%), Gaps = 7/38 (18%)
Query: 94 LIGRPHKVTTVDKYQGQQNDYILLSLVRTASVGHLRDV 131
++ P K T++KY G +DY++ S SVGH+RD+
Sbjct: 9 IVESPAKAKTINKYLG--SDYVVKS-----SVGHIRDL 39
>pdb|3PWT|A Chain A, Crystal Structure Of Mutant E.Coli Topoisomerase Ia
Length = 596
Score = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 24/38 (63%), Gaps = 7/38 (18%)
Query: 94 LIGRPHKVTTVDKYQGQQNDYILLSLVRTASVGHLRDV 131
++ P K T++KY G +DY++ S SVGH+RD+
Sbjct: 7 IVESPAKAKTINKYLG--SDYVVKS-----SVGHIRDL 37
>pdb|1ECL|A Chain A, Amino Terminal 67kda Domain Of Escherichia Coli Dna
Topoisomerase I (Residues 2-590 Of Mature Protein)
Cloning Artifact Adds Two Residues To The Amino-Terminus
Which Were Not Observed In The Experimental Electron
Density (Gly-2, Ser-1)
Length = 597
Score = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 24/38 (63%), Gaps = 7/38 (18%)
Query: 94 LIGRPHKVTTVDKYQGQQNDYILLSLVRTASVGHLRDV 131
++ P K T++KY G +DY++ S SVGH+RD+
Sbjct: 7 IVESPAKAKTINKYLG--SDYVVKS-----SVGHIRDL 37
>pdb|2A91|A Chain A, Crystal Structure Of Erbb2 Domains 1-3
Length = 517
Score = 28.9 bits (63), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 1/71 (1%)
Query: 127 HLRDVRRLIVAMSRARLGLY-VFARVSLFRNCFELTPAFNQLMIRPQQLHIVPHETFPTS 185
HLR+VR + A + G +F ++ F+ PA N ++P+QL + T
Sbjct: 328 HLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITG 387
Query: 186 RLNTSRVPNSV 196
L S P+S+
Sbjct: 388 YLYISAWPDSL 398
>pdb|1S78|A Chain A, Insights Into Erbb Signaling From The Structure Of The
Erbb2- Pertuzumab Complex
pdb|1S78|B Chain B, Insights Into Erbb Signaling From The Structure Of The
Erbb2- Pertuzumab Complex
pdb|3BE1|A Chain A, Dual Specific Bh1 Fab In Complex With The Extracellular
Domain Of Her2ERBB-2
pdb|3MZW|A Chain A, Her2 Extracelluar Region With Affinity Matured 3-Helix
Affibody Zher2:342
pdb|3N85|A Chain A, Crystallographic Trimer Of Her2 Extracellular Regions In
Complex With Tryptophan-Rich Antibody Fragment
Length = 624
Score = 28.5 bits (62), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 127 HLRDVRRLIVAMSRARLGLY-VFARVSLFRNCFELTPAFNQLMIRPQQLHI 176
HLR+VR + A + G +F ++ F+ PA N ++P+QL +
Sbjct: 327 HLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQV 377
>pdb|1N8Z|C Chain C, Crystal Structure Of Extracellular Domain Of Human Her2
Complexed With Herceptin Fab
Length = 607
Score = 28.1 bits (61), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 127 HLRDVRRLIVAMSRARLGLY-VFARVSLFRNCFELTPAFNQLMIRPQQLHI 176
HLR+VR + A + G +F ++ F+ PA N ++P+QL +
Sbjct: 327 HLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQV 377
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 0.136 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,373,548
Number of Sequences: 62578
Number of extensions: 336131
Number of successful extensions: 599
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 584
Number of HSP's gapped (non-prelim): 24
length of query: 294
length of database: 14,973,337
effective HSP length: 98
effective length of query: 196
effective length of database: 8,840,693
effective search space: 1732775828
effective search space used: 1732775828
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: 51 (24.3 bits)