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= psy2047
(233 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MWY|W Chain W, Crystal Structure Of The Chromodomain-atpase Portion Of
The Yeast Chd1 Chromatin Remodeler
Length = 800
Score = 94.0 bits (232), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 71/233 (30%), Positives = 105/233 (45%), Gaps = 52/233 (22%)
Query: 4 DSEDDARYEDKRKEQATFEVEQVDQAKRIISPFMLRRLKKDVLTELPKKTALVIKVPMIP 63
D E D +D+ +E E + R I PF+LRRLKKDV LP KT +++V +
Sbjct: 428 DQEIDFENQDEEQE------EYIHDLHRRIQPFILRRLKKDVEKSLPSKTERILRVELSD 481
Query: 64 SQAEKYRGLMEDFKKTANPEGSNRSNEISHMSMFMMLRKMANHPLGLRYYF---QENTLR 120
Q E Y+ ++ K + + S +++ L+K +NHP Y F +E L+
Sbjct: 482 VQTEYYKNILT--KNYSALTAGAKGGHFSLLNIMNELKKASNHP----YLFDNAEERVLQ 535
Query: 121 EIADCLVEDPTYKGTNPQYILEDISWLSDYDIHQLSLKHKTLDCAKYKVPDDLVVESGKL 180
+ D + V L++ SGK+
Sbjct: 536 KFGDG-------------------------------------KMTRENVLRGLIMSSGKM 558
Query: 181 KKLDEILPDLKKNGHRVLIFSQFIFVLDILGHYMDIRGWRHLRLDGATQVSSR 233
LD++L LKK+GHRVLIFSQ + +LDILG Y+ I+G RLDG + R
Sbjct: 559 VLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQR 611
>pdb|1Z63|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COMPLEX
With Dsdna
pdb|1Z63|B Chain B, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COMPLEX
With Dsdna
Length = 500
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 47/88 (53%), Gaps = 5/88 (5%)
Query: 27 DQAKRIISPFMLRRLKKD--VLTELPKKTALVIKVPMIPSQAEKYRGLMED-FKKTANPE 83
++ K IISPF+LRR K D ++ +LP K + + P QA Y+ +E+ F +
Sbjct: 230 EELKAIISPFILRRTKYDKAIINDLPDKIETNVYCNLTPEQAAXYKAEVENLFNNIDSVT 289
Query: 84 GSNRSNEISHMSMFMMLRKMANHPLGLR 111
G R I +S + L+++ +HP L+
Sbjct: 290 GIKRKGXI--LSTLLKLKQIVDHPALLK 315
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 47/88 (53%), Gaps = 5/88 (5%)
Query: 27 DQAKRIISPFMLRRLKKD--VLTELPKKTALVIKVPMIPSQAEKYRGLMED-FKKTANPE 83
++ K IISPF+LRR K D ++ +LP K + + P QA Y+ +E+ F +
Sbjct: 230 EELKAIISPFILRRTKYDKAIINDLPDKIETNVYCNLTPEQAAMYKAEVENLFNNIDSVT 289
Query: 84 GSNRSNEISHMSMFMMLRKMANHPLGLR 111
G R I +S + L+++ +HP L+
Sbjct: 290 GIKRKGMI--LSTLLKLKQIVDHPALLK 315
>pdb|2WZQ|A Chain A, Insertion Mutant E173gp174 Of The Ns3 Protease-Helicase
From Dengue Virus
Length = 619
Score = 31.2 bits (69), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 28 QAKRIISPFMLRRLKKDVLTELPKKTALVIKVPMIPSQAEKYRG 71
+A R+I P R LK +LT+ P++ L +P+ P+ A + RG
Sbjct: 419 RAGRVIDP--RRCLKPVILTDGPERVILAGPIPVTPASAAQRRG 460
>pdb|2WHX|A Chain A, A Second Conformation Of The Ns3 Protease-Helicase From
Dengue Virus
Length = 618
Score = 31.2 bits (69), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 28 QAKRIISPFMLRRLKKDVLTELPKKTALVIKVPMIPSQAEKYRG 71
+A R+I P R LK +LT+ P++ L +P+ P+ A + RG
Sbjct: 418 RAGRVIDP--RRCLKPVILTDGPERVILAGPIPVTPASAAQRRG 459
>pdb|2VBC|A Chain A, Crystal Structure Of The Ns3 Protease-Helicase From Dengue
Virus
Length = 618
Score = 31.2 bits (69), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 28 QAKRIISPFMLRRLKKDVLTELPKKTALVIKVPMIPSQAEKYRG 71
+A R+I P R LK +LT+ P++ L +P+ P+ A + RG
Sbjct: 418 RAGRVIDP--RRCLKPVILTDGPERVILAGPIPVTPASAAQRRG 459
>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 = 31.2 bits (69), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 28 QAKRIISPFMLRRLKKDVLTELPKKTALVIKVPMIPSQAEKYRG 71
+A R+I P R LK +LT+ P++ L +P+ P+ A + RG
Sbjct: 251 RAGRVIDP--RRCLKPVILTDGPERVILAGPIPVTPASAAQRRG 292
>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 = 31.2 bits (69), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 28 QAKRIISPFMLRRLKKDVLTELPKKTALVIKVPMIPSQAEKYRG 71
+A R+I P R LK +LT+ P++ L +P+ P+ A + RG
Sbjct: 251 RAGRVIDP--RRCLKPVILTDGPERVILAGPIPVTPASAAQRRG 292
>pdb|2JLS|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Adp
Length = 451
Score = 31.2 bits (69), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 28 QAKRIISPFMLRRLKKDVLTELPKKTALVIKVPMIPSQAEKYRG 71
+A R+I P R LK +LT+ P++ L +P+ P+ A + RG
Sbjct: 251 RAGRVIDP--RRCLKPVILTDGPERVILAGPIPVTPASAAQRRG 292
>pdb|2JLR|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Amppnp
Length = 451
Score = 31.2 bits (69), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 28 QAKRIISPFMLRRLKKDVLTELPKKTALVIKVPMIPSQAEKYRG 71
+A R+I P R LK +LT+ P++ L +P+ P+ A + RG
Sbjct: 251 RAGRVIDP--RRCLKPVILTDGPERVILAGPIPVTPASAAQRRG 292
>pdb|3QHX|A Chain A, Crystal Structure Of Cystathionine Gamma-Synthase Metb
(Cgs) From Mycobacterium Ulcerans Agy99 Bound To Hepes
pdb|3QHX|B Chain B, Crystal Structure Of Cystathionine Gamma-Synthase Metb
(Cgs) From Mycobacterium Ulcerans Agy99 Bound To Hepes
pdb|3QHX|C Chain C, Crystal Structure Of Cystathionine Gamma-Synthase Metb
(Cgs) From Mycobacterium Ulcerans Agy99 Bound To Hepes
pdb|3QHX|D Chain D, Crystal Structure Of Cystathionine Gamma-Synthase Metb
(Cgs) From Mycobacterium Ulcerans Agy99 Bound To Hepes
pdb|3QI6|A Chain A, Crystal Structure Of Cystathionine Gamma-Synthase Metb
(Cgs) From Mycobacterium Ulcerans Agy99
pdb|3QI6|B Chain B, Crystal Structure Of Cystathionine Gamma-Synthase Metb
(Cgs) From Mycobacterium Ulcerans Agy99
pdb|3QI6|C Chain C, Crystal Structure Of Cystathionine Gamma-Synthase Metb
(Cgs) From Mycobacterium Ulcerans Agy99
pdb|3QI6|D Chain D, Crystal Structure Of Cystathionine Gamma-Synthase Metb
(Cgs) From Mycobacterium Ulcerans Agy99
Length = 392
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 31/58 (53%)
Query: 135 TNPQYILEDISWLSDYDIHQLSLKHKTLDCAKYKVPDDLVVESGKLKKLDEILPDLKK 192
TN + E + + H ++ H + ++ +VPDDLV S ++ + ++L DLK+
Sbjct: 332 TNIFILAESLGSVESLIEHPSAMTHASTAGSQLEVPDDLVRLSVGIEDVADLLDDLKQ 389
>pdb|1YBW|A Chain A, Protease Domain Of Hgfa With No Inhibitor
pdb|1YBW|B Chain B, Protease Domain Of Hgfa With No Inhibitor
pdb|1YC0|A Chain A, Short Form Hgfa With First Kunitz Domain From Hai-1
pdb|2R0K|A Chain A, Protease Domain Of Hgfa With Inhibitor Fab58
Length = 283
Score = 28.1 bits (61), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 8/47 (17%)
Query: 184 DEILPDLKKNGHRVLIFSQFIFVLDI--------LGHYMDIRGWRHL 222
D +L LKK G R SQF+ + + GH I GW HL
Sbjct: 125 DLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHL 171
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 28.1 bits (61), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 53/238 (22%), Positives = 90/238 (37%), Gaps = 57/238 (23%)
Query: 2 DSDSEDDARYEDKRKEQATFEVEQVDQAKRIISPFMLRRLKKDVLTE-LPKKTALVIKVP 60
D+D+ D R ++K Q I++ ++RR D+L++ LP K V+
Sbjct: 269 DADASDKDRAAGEQKLQELIS---------IVNRCLIRR-TSDILSKYLPVKIEQVVCCN 318
Query: 61 MIPSQAEKYRGLMEDFKKTANPEGSNRSNEISHMSMFMML--RKMANHPLGL--RYYFQE 116
+ P Q E Y+ F K A P S ++ +IS S+ + +K+ NHP + + E
Sbjct: 319 LTPLQKELYK----LFLKQAKPVESLQTGKISVSSLSSITSLKKLCNHPALIYEKCLTGE 374
Query: 117 NTLREIADCLVEDPTYKGTNPQYILEDISWLSDYDIHQLSLKHKTLDCAKYKVPDDLVVE 176
D ++ + K PQ
Sbjct: 375 EGFDGALDLFPQNYSTKAVEPQL------------------------------------- 397
Query: 177 SGKLKKLDEILPDLK-KNGHRVLIFSQFIFVLDILGHYMDIRGWRHLRLDGATQVSSR 233
SGK+ LD IL + +V++ S + LD+ R + ++RLDG + R
Sbjct: 398 SGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKR 455
>pdb|3K53|A Chain A, Crystal Structure Of Nfeob From P. Furiosus
pdb|3K53|B Chain B, Crystal Structure Of Nfeob From P. Furiosus
pdb|3K53|C Chain C, Crystal Structure Of Nfeob From P. Furiosus
pdb|3K53|D Chain D, Crystal Structure Of Nfeob From P. Furiosus
Length = 271
Score = 27.7 bits (60), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 38/142 (26%), Positives = 64/142 (45%), Gaps = 30/142 (21%)
Query: 59 VPMIPSQAEKYRG---------LMEDFKKTANP----EGSNRSNEISHMSMFMMLRKMAN 105
VP+IP+ A+K G LM + K T NP + EI H+S +
Sbjct: 140 VPVIPTNAKKGEGVEELKRMIALMAEGKVTTNPIIPRYDEDIEREIKHISELL-----RG 194
Query: 106 HPLGLRYYFQENTLREIADCLVEDPTYKGTNPQYILEDISWLSDYDIHQLSLKHKTLDCA 165
PL +Y +R +A L++ + + I + +L + ++ LKH +
Sbjct: 195 TPLAEKY-----PIRWLALKLLQ------RDEEVIKLVLKYLGQEKMDEI-LKHISELEE 242
Query: 166 KYKVPDDLVVESGKLKKLDEIL 187
KYK P D+V+ S K + L+++L
Sbjct: 243 KYKRPLDIVIASQKYEFLEQLL 264
>pdb|2WUB|A Chain A, Crystal Structure Of Hgfa In Complex With The Allosteric
Non-Inhibitory Antibody Fab40.Deltatrp
pdb|2WUB|C Chain C, Crystal Structure Of Hgfa In Complex With The Allosteric
Non-Inhibitory Antibody Fab40.Deltatrp
pdb|2WUC|A Chain A, Crystal Structure Of Hgfa In Complex With The Allosteric
Non- Inhibitory Antibody Fab40.Deltatrp And
Ac-Kqlr-Chloromethylketone
pdb|3K2U|A Chain A, Crystal Structure Of Hgfa In Complex With The Allosteric
Inhibitory Antibody Fab40
Length = 257
Score = 27.3 bits (59), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 8/47 (17%)
Query: 184 DEILPDLKKNGHRVLIFSQFIFVLDI--------LGHYMDIRGWRHL 222
D +L LKK G R SQF+ + + GH I GW HL
Sbjct: 90 DLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHL 136
>pdb|2R0L|A Chain A, Short Form Hgfa With Inhibitory Fab75
Length = 248
Score = 27.3 bits (59), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 8/47 (17%)
Query: 184 DEILPDLKKNGHRVLIFSQFIFVLDI--------LGHYMDIRGWRHL 222
D +L LKK G R SQF+ + + GH I GW HL
Sbjct: 90 DLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHL 136
>pdb|1XFI|A Chain A, X-Ray Structure Of Gene Product From Arabidopsis Thaliana
At2g17340
pdb|2Q40|A Chain A, Ensemble Refinement Of The Protein Crystal Structure Of
Gene Product From Arabidopsis Thaliana At2g17340
Length = 367
Score = 27.3 bits (59), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 9/64 (14%)
Query: 57 IKVPMIPSQAEK----YRGLMEDFKKTANPEGSNRSNEISHMSMFMMLRKMANHPLGLRY 112
I VP P++AEK Y G++ED KK G + LR+ LG R
Sbjct: 64 ITVPDAPARAEKFAERYAGILEDLKKDPESHGGPPDG-----ILLCRLREQVLRELGFRD 118
Query: 113 YFQE 116
F++
Sbjct: 119 IFKK 122
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
0.319 0.136 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,055,541
Number of Sequences: 62578
Number of extensions: 291096
Number of successful extensions: 811
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 796
Number of HSP's gapped (non-prelim): 27
length of query: 233
length of database: 14,973,337
effective HSP length: 96
effective length of query: 137
effective length of database: 8,965,849
effective search space: 1228321313
effective search space used: 1228321313
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)