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= psy11948
(167 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form
1
pdb|2GXS|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form
2
pdb|2GXS|B Chain B, Hera N-Terminal Domain In Complex With Amp, Crystal Form
2
pdb|2GXU|A Chain A, Hera N-Terminal Domain In Complex With Orthophosphate,
Crystal Form 1
Length = 207
Score = 56.2 bits (134), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 28/59 (47%), Positives = 39/59 (66%), Gaps = 1/59 (1%)
Query: 3 EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPI 61
E+ F + I+ AL+ +G TPT IQ+ +P AL KD++G A TG+GKTLAF +PI
Sbjct: 2 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEG-KDLIGQARTGTGKTLAFALPI 59
>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo
Form
pdb|3MWJ|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo
Form
pdb|3MWK|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Complex
With 8-Oxo- Amp
pdb|3MWK|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Complex
With 8-Oxo- Amp
pdb|3MWL|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain In
Complex With 8- Oxoadenosine
pdb|3MWL|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain In
Complex With 8- Oxoadenosine
pdb|3NBF|A Chain A, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|B Chain B, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|C Chain C, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|D Chain D, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NEJ|A Chain A, Q28e Mutant Of Hera Rna Helicase N-Terminal Domain -
Perfectly Twinned Hexagonal Form
pdb|3NEJ|B Chain B, Q28e Mutant Of Hera Rna Helicase N-Terminal Domain -
Perfectly Twinned Hexagonal Form
Length = 207
Score = 54.7 bits (130), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/59 (45%), Positives = 39/59 (66%), Gaps = 1/59 (1%)
Query: 3 EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPI 61
E+ F + I+ AL+ +G TPT I++ +P AL KD++G A TG+GKTLAF +PI
Sbjct: 2 EFKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEG-KDLIGQARTGTGKTLAFALPI 59
>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The
Hyperthermophile Methanococcus Jannaschii
pdb|1HV8|B Chain B, Crystal Structure Of A Dead Box Protein From The
Hyperthermophile Methanococcus Jannaschii
Length = 367
Score = 53.9 bits (128), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 27/63 (42%), Positives = 38/63 (60%), Gaps = 3/63 (4%)
Query: 3 EWVKFN---IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGI 59
E+ FN + + I+ A+ KGF+ PT IQ V+P L +IV A TGSGKT +F I
Sbjct: 4 EYXNFNELNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAI 63
Query: 60 PIL 62
P++
Sbjct: 64 PLI 66
>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In
Complex With Amp
Length = 249
Score = 53.5 bits (127), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 31/66 (46%), Positives = 39/66 (59%), Gaps = 4/66 (6%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
+ + + A Q G+ PTKIQ +P AL R DI+G AETGSGKT AF +PIL +
Sbjct: 48 LGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGR-DIIGLAETGSGKTGAFALPILNAL- 105
Query: 67 NKLENP 72
LE P
Sbjct: 106 --LETP 109
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 37/85 (43%), Gaps = 39/85 (45%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXSANT 142
+DI+G AETGSGKT AF +PIL + LE P
Sbjct: 81 RDIIGLAETGSGKTGAFALPILNAL---LETP---------------------------- 109
Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
+L+AL+L PTRELA Q
Sbjct: 110 --------QRLFALVLTPTRELAFQ 126
>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|B Chain B, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|C Chain C, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|D Chain D, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
Length = 434
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 45/74 (60%), Gaps = 4/74 (5%)
Query: 1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
+ + ++ + II + + G+K PT IQ +P + + +D++ A+TGSGKT AF +P
Sbjct: 55 IQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIP-VISSGRDLMACAQTGSGKTAAFLLP 113
Query: 61 ILTGIVNKLENPTE 74
IL+ + LE+P E
Sbjct: 114 ILSKL---LEDPHE 124
Score = 35.4 bits (80), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 26/35 (74%), Gaps = 3/35 (8%)
Query: 80 SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENP 114
S+ +D++ A+TGSGKT AF +PIL+ + LE+P
Sbjct: 91 SSGRDLMACAQTGSGKTAAFLLPILSKL---LEDP 122
>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In
Complex With Adp
Length = 245
Score = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 6 KFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
++ I +++ + GF+ PT IQ +P L R +++ +A TGSGKTLAF IPIL
Sbjct: 33 EYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGR-ELLASAPTGSGKTLAFSIPIL 88
Score = 33.9 bits (76), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 14/22 (63%), Positives = 19/22 (86%)
Query: 83 KDIVGAAETGSGKTLAFGIPIL 104
++++ +A TGSGKTLAF IPIL
Sbjct: 67 RELLASAPTGSGKTLAFSIPIL 88
>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of
Djvlgb, A Pranarian Vasa-Like Rna Helicase
pdb|1WRB|B Chain B, Crystal Structure Of The N-Terminal Reca-Like Domain Of
Djvlgb, A Pranarian Vasa-Like Rna Helicase
Length = 253
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/60 (45%), Positives = 37/60 (61%), Gaps = 5/60 (8%)
Query: 9 IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNK 68
I I+ A YQ+ PT IQ +P A+L +DI+ A+TGSGKT AF IPI+ +V +
Sbjct: 34 IRNNILLASYQR----PTPIQKNAIP-AILEHRDIMACAQTGSGKTAAFLIPIINHLVCQ 88
Score = 43.1 bits (100), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 30/86 (34%), Positives = 37/86 (43%), Gaps = 30/86 (34%)
Query: 82 RKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXSAN 141
+DI+ A+TGSGKT AF IPI+ +V + N
Sbjct: 60 HRDIMACAQTGSGKTAAFLIPIINHLVCQ----------------------------DLN 91
Query: 142 TTEFVKKTRNKLYALILAPTRELAIQ 167
+ K K LILAPTRELAIQ
Sbjct: 92 QQRYSKTAYPK--CLILAPTRELAIQ 115
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 47.0 bits (110), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 29/66 (43%), Positives = 43/66 (65%), Gaps = 2/66 (3%)
Query: 11 ETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT-GIVNKL 69
E I +A+ + GFK T++QS +P +L K++V A+TGSGKT A+ IPIL G+ + +
Sbjct: 3 EKIEQAIREMGFKNFTEVQSKTIP-LMLQGKNVVVRAKTGSGKTAAYAIPILELGMKSLV 61
Query: 70 ENPTEE 75
PT E
Sbjct: 62 VTPTRE 67
Score = 31.6 bits (70), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 14/22 (63%), Positives = 18/22 (81%)
Query: 83 KDIVGAAETGSGKTLAFGIPIL 104
K++V A+TGSGKT A+ IPIL
Sbjct: 32 KNVVVRAKTGSGKTAAYAIPIL 53
>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human
Dead-Box Rna Helicase Ddx5 (P68)
Length = 253
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 8 NIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN 67
N P ++ + ++ F PT IQ+ P AL + D+VG A+TGSGKTL++ +P + I +
Sbjct: 49 NFPANVMDVIARQNFTEPTAIQAQGWPVAL-SGLDMVGVAQTGSGKTLSYLLPAIVHINH 107
Query: 68 K 68
+
Sbjct: 108 Q 108
Score = 34.7 bits (78), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 36/84 (42%), Gaps = 34/84 (40%)
Query: 84 DIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXSANTT 143
D+VG A+TGSGKTL++ +P + I N
Sbjct: 82 DMVGVAQTGSGKTLSYLLPAIVHI---------------------------------NHQ 108
Query: 144 EFVKKTRNKLYALILAPTRELAIQ 167
F+++ + L+LAPTRELA Q
Sbjct: 109 PFLERGDGPI-CLVLAPTRELAQQ 131
>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain
I In Complex With Adp
pdb|3FE2|B Chain B, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain
I In Complex With Adp
Length = 242
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 8 NIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN 67
N P ++ + ++ F PT IQ+ P AL + D+VG A+TGSGKTL++ +P + I +
Sbjct: 35 NFPANVMDVIARQNFTEPTAIQAQGWPVAL-SGLDMVGVAQTGSGKTLSYLLPAIVHINH 93
Query: 68 K 68
+
Sbjct: 94 Q 94
Score = 34.3 bits (77), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 36/84 (42%), Gaps = 34/84 (40%)
Query: 84 DIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXSANTT 143
D+VG A+TGSGKTL++ +P + I N
Sbjct: 68 DMVGVAQTGSGKTLSYLLPAIVHI---------------------------------NHQ 94
Query: 144 EFVKKTRNKLYALILAPTRELAIQ 167
F+++ + L+LAPTRELA Q
Sbjct: 95 PFLERGDGPI-CLVLAPTRELAQQ 117
>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In
Complex With Adp
Length = 236
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 38/59 (64%), Gaps = 1/59 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
F + + ++ L + ++ T+IQ + AL KD++GAA+TGSGKTLAF +P+L +
Sbjct: 30 FPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQG-KDVLGAAKTGSGKTLAFLVPVLEAL 87
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 16/25 (64%), Positives = 22/25 (88%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGI 107
KD++GAA+TGSGKTLAF +P+L +
Sbjct: 63 KDVLGAAKTGSGKTLAFLVPVLEAL 87
>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|C Chain C, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|D Chain D, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|F Chain F, Crystal Structure Of The Eif4a-Pdcd4 Complex
Length = 388
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSM-VMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
N+ E+++R +Y GF+ P+ IQ ++P + D++ A++G+GKT F I IL I
Sbjct: 19 MNLSESLLRGIYAYGFEKPSAIQQRAILPC--IKGYDVIAQAQSGTGKTATFAISILQQI 76
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSM-VMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
N+ E+++R +Y GF+ P+ IQ ++P + D++ A++G+GKT F I IL I
Sbjct: 45 MNLSESLLRGIYAYGFEKPSAIQQRAILPC--IKGYDVIAQAQSGTGKTATFAISILQQI 102
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
F + ++ +++ GF+ P+ IQ +P A+ R DI+ A+ G+GKT AF IP L +
Sbjct: 26 FYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGR-DILARAKNGTGKTAAFVIPTLEKVK 84
Query: 67 NKL 69
KL
Sbjct: 85 PKL 87
Score = 35.4 bits (80), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 34/85 (40%), Gaps = 39/85 (45%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXSANT 142
+DI+ A+ G+GKT AF IP T
Sbjct: 59 RDILARAKNGTGKTAAFVIP---------------------------------------T 79
Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
E VK NK+ ALI+ PTRELA+Q
Sbjct: 80 LEKVKPKLNKIQALIMVPTRELALQ 104
>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic
Initiation Factor 4a, Eif4a
pdb|2G9N|B Chain B, Structure Of The Dead Domain Of Human Eukaryotic
Initiation Factor 4a, Eif4a
Length = 221
Score = 43.1 bits (100), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 3/61 (4%)
Query: 6 KFNIPETIIRALYQKGFKTPTKIQS-MVMPSALLARKDIVGAAETGSGKTLAFGIPILTG 64
N+ E+++R +Y GF+ P+ IQ ++P + D++ A++G+G T F I IL
Sbjct: 19 DMNLSESLLRGIYAYGFEXPSAIQQRAILPC--IXGYDVIAQAQSGTGXTATFAISILQQ 76
Query: 65 I 65
I
Sbjct: 77 I 77
>pdb|3LY5|A Chain A, Ddx18 Dead-Domain
pdb|3LY5|B Chain B, Ddx18 Dead-Domain
Length = 262
Score = 43.1 bits (100), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 37/58 (63%), Gaps = 1/58 (1%)
Query: 9 IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
+ E ++A+ + GF T+IQ + LL +D++ AA+TGSGKTLAF IP + IV
Sbjct: 61 VNENTLKAIKEMGFTNMTEIQHKSI-RPLLEGRDLLAAAKTGSGKTLAFLIPAVELIV 117
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 36/85 (42%), Gaps = 35/85 (41%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXSANT 142
+D++ AA+TGSGKTLAF IP + IV P
Sbjct: 92 RDLLAAAKTGSGKTLAFLIPAVELIVKLRFMP---------------------------- 123
Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
RN LIL+PTRELA+Q
Sbjct: 124 -------RNGTGVLILSPTRELAMQ 141
>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human
Translation Initiation Factor 4a-2
Length = 237
Score = 42.7 bits (99), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 35/56 (62%), Gaps = 3/56 (5%)
Query: 8 NIPETIIRALYQKGFKTPTKIQSM-VMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
N+ E+++R +Y GF+ P+ IQ ++P + D++ A++G+GKT F I IL
Sbjct: 36 NLKESLLRGIYAYGFEKPSAIQQRAIIPC--IKGYDVIAQAQSGTGKTATFAISIL 89
>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain
pdb|1Q0U|B Chain B, Crystal Structure Of The Bstdead N-Terminal Domain
Length = 219
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 3 EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
++ +F II A+ F PT+IQ ++P AL + VG ++TG+GKT A+ +PI
Sbjct: 5 QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRG-ESXVGQSQTGTGKTHAYLLPIX 63
Query: 63 TGI 65
I
Sbjct: 64 EKI 66
Score = 28.5 bits (62), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 32/82 (39%), Gaps = 39/82 (47%)
Query: 86 VGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXSANTTEF 145
VG ++TG+GKT A+ +PI E
Sbjct: 45 VGQSQTGTGKTHAYLLPI---------------------------------------XEK 65
Query: 146 VKKTRNKLYALILAPTRELAIQ 167
+K R ++ A+I APTRELA Q
Sbjct: 66 IKPERAEVQAVITAPTRELATQ 87
>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|I Chain I, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|3EX7|C Chain C, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|H Chain H, The Crystal Structure Of Ejc In Its Transition State
Length = 413
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 9 IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
+ E ++R +Y GF+ P+ IQ + + R D++ +++G+GKT F I +L +
Sbjct: 45 LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGR-DVIAQSQSGTGKTATFSISVLQCL 100
Score = 29.6 bits (65), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 39/85 (45%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXSANT 142
+D++ +++G+GKT F I +L + +
Sbjct: 76 RDVIAQSQSGTGKTATFSISVLQCLDIQ-------------------------------- 103
Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
V++T+ ALILAPTRELA+Q
Sbjct: 104 ---VRETQ----ALILAPTRELAVQ 121
>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|X Chain X, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 411
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 9 IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
+ E ++R +Y GF+ P+ IQ + + R D++ +++G+GKT F I +L +
Sbjct: 45 LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGR-DVIAQSQSGTGKTATFSISVLQCL 100
Score = 29.6 bits (65), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 39/85 (45%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXSANT 142
+D++ +++G+GKT F I +L + +
Sbjct: 76 RDVIAQSQSGTGKTATFSISVLQCLDIQ-------------------------------- 103
Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
V++T+ ALILAPTRELA+Q
Sbjct: 104 ---VRETQ----ALILAPTRELAVQ 121
>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|B Chain B, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|C Chain C, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|D Chain D, Crystal Structure Of Human Apo-Eif4aiii
Length = 391
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 9 IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
+ E ++R +Y GF+ P+ IQ + + R D++ +++G+GKT F I +L +
Sbjct: 23 LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGR-DVIAQSQSGTGKTATFSISVLQCL 78
Score = 29.6 bits (65), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 39/85 (45%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXSANT 142
+D++ +++G+GKT F I +L + +
Sbjct: 54 RDVIAQSQSGTGKTATFSISVLQCLDIQ-------------------------------- 81
Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
V++T+ ALILAPTRELA+Q
Sbjct: 82 ---VRETQ----ALILAPTRELAVQ 99
>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
pdb|2J0Q|B Chain B, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
pdb|2J0S|A Chain A, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 410
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 9 IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
+ E ++R +Y GF+ P+ IQ + + R D++ +++G+GKT F I +L +
Sbjct: 44 LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGR-DVIAQSQSGTGKTATFSISVLQCL 99
Score = 29.6 bits (65), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 39/85 (45%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXSANT 142
+D++ +++G+GKT F I +L + +
Sbjct: 75 RDVIAQSQSGTGKTATFSISVLQCLDIQ-------------------------------- 102
Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
V++T+ ALILAPTRELA+Q
Sbjct: 103 ---VRETQ----ALILAPTRELAVQ 120
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At
3.0 A Resolution
Length = 374
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 9 IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
+ E ++R +Y GF+ P+ IQ + + R D++ +++G+GKT F + +L +
Sbjct: 8 LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGR-DVIAQSQSGTGKTATFSVSVLQCL 63
Score = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 39/85 (45%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXSANT 142
+D++ +++G+GKT F + +L + +
Sbjct: 39 RDVIAQSQSGTGKTATFSVSVLQCLDIQ-------------------------------- 66
Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
V++T+ ALILAPTRELA+Q
Sbjct: 67 ---VRETQ----ALILAPTRELAVQ 84
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At
3.0 A Resolution
Length = 374
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 9 IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
+ E ++R +Y GF+ P+ IQ + + R D++ +++G+GKT F + +L +
Sbjct: 8 LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGR-DVIAQSQSGTGKTATFSVSVLQCL 63
Score = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 39/85 (45%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXSANT 142
+D++ +++G+GKT F + +L + +
Sbjct: 39 RDVIAQSQSGTGKTATFSVSVLQCLDIQ-------------------------------- 66
Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
V++T+ ALILAPTRELA+Q
Sbjct: 67 ---VRETQ----ALILAPTRELAVQ 84
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
M+ + F + ++RA+ GF+ P+++Q +P A+L D++ A++G GKT F +
Sbjct: 6 MSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILG-MDVLCQAKSGMGKTAVFVLA 64
Query: 61 ILTGI 65
L +
Sbjct: 65 TLQQL 69
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 29/88 (32%), Positives = 42/88 (47%), Gaps = 25/88 (28%)
Query: 82 RKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXSAN 141
++D++ A+TGSGKT AF +PIL+ I + + P
Sbjct: 52 KRDLMACAQTGSGKTAAFLLPILSQIYS--DGPGEALRA--------------------- 88
Query: 142 TTEFVKKTRNKLY--ALILAPTRELAIQ 167
E + R K Y +L+LAPTRELA+Q
Sbjct: 89 MKENGRYGRRKQYPISLVLAPTRELAVQ 116
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 22 FKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN 67
+ PT +Q +P + ++D++ A+TGSGKT AF +PIL+ I +
Sbjct: 35 YTRPTPVQKHAIP-IIKEKRDLMACAQTGSGKTAAFLLPILSQIYS 79
>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A
Human Dead-Box Protein
pdb|1VEC|B Chain B, Crystal Structure Of The N-Terminal Domain Of RckP54, A
Human Dead-Box Protein
Length = 206
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 52/103 (50%), Gaps = 8/103 (7%)
Query: 3 EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
E+ + + ++ +++ G++ P+ IQ +P AL R DI+ A+ G+GK+ A+ IP+L
Sbjct: 4 EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGR-DILARAKNGTGKSGAYLIPLL 62
Query: 63 TGIVNKLEN-------PTEEDENDSARKDIVGAAETGSGKTLA 98
+ K +N PT E ++ I + G K +A
Sbjct: 63 ERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMA 105
Score = 26.6 bits (57), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 19/85 (22%), Positives = 34/85 (40%), Gaps = 39/85 (45%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXSANT 142
+DI+ A+ G+GK+ A+ IP+L
Sbjct: 41 RDILARAKNGTGKSGAYLIPLL-------------------------------------- 62
Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
E + ++ + A+++ PTRELA+Q
Sbjct: 63 -ERLDLKKDNIQAMVIVPTRELALQ 86
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 34/56 (60%), Gaps = 2/56 (3%)
Query: 10 PETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
PE ++RA+ GF+ P+++Q +P A+L D++ A++G GKT F + L +
Sbjct: 17 PE-LLRAIVDCGFEHPSEVQHECIPQAILG-MDVLCQAKSGMGKTAVFVLATLQQL 70
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 34/56 (60%), Gaps = 2/56 (3%)
Query: 10 PETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
PE ++RA+ GF+ P+++Q +P A+L D++ A++G GKT F + L +
Sbjct: 17 PE-LLRAIVDCGFEHPSEVQHECIPQAILG-MDVLCQAKSGMGKTAVFVLATLQQL 70
>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human
Uap56
pdb|1T6N|B Chain B, Crystal Structure Of The N-Terminal Domain Of Human
Uap56
Length = 220
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 31/48 (64%), Gaps = 2/48 (4%)
Query: 10 PETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAF 57
PE ++RA+ GF+ P+++Q +P A+L D++ A++G GKT F
Sbjct: 23 PE-LLRAIVDCGFEHPSEVQHECIPQAILGM-DVLCQAKSGMGKTAVF 68
>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
pdb|3FMP|D Chain D, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
Length = 479
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 36/55 (65%), Gaps = 3/55 (5%)
Query: 13 IIRALYQKGFKTPTKIQSMVMPSALLAR--KDIVGAAETGSGKTLAFGIPILTGI 65
+++ +Y GF P+KIQ +P +LA ++++ +++G+GKT AF + +L+ +
Sbjct: 103 LLQGVYAMGFNRPSKIQENALP-LMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 156
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 36/55 (65%), Gaps = 3/55 (5%)
Query: 13 IIRALYQKGFKTPTKIQSMVMPSALLAR--KDIVGAAETGSGKTLAFGIPILTGI 65
+++ +Y GF P+KIQ +P +LA ++++ +++G+GKT AF + +L+ +
Sbjct: 52 LLQGVYAMGFNRPSKIQENALP-LMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 105
>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp
pdb|3EWS|B Chain B, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp
Length = 445
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 36/55 (65%), Gaps = 3/55 (5%)
Query: 13 IIRALYQKGFKTPTKIQSMVMPSALLAR--KDIVGAAETGSGKTLAFGIPILTGI 65
+++ +Y GF P+KIQ +P +LA ++++ +++G+GKT AF + +L+ +
Sbjct: 73 LLQGVYAMGFNRPSKIQENALP-LMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 126
>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
Length = 300
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 36/55 (65%), Gaps = 3/55 (5%)
Query: 13 IIRALYQKGFKTPTKIQSMVMPSALLAR--KDIVGAAETGSGKTLAFGIPILTGI 65
+++ +Y GF P+KIQ +P +LA ++++ +++G+GKT AF + +L+ +
Sbjct: 103 LLQGVYAMGFNRPSKIQENALP-LMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 156
>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp
And Rna
pdb|3FHT|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Amppnp
And Rna
Length = 412
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 36/55 (65%), Gaps = 3/55 (5%)
Query: 13 IIRALYQKGFKTPTKIQSMVMPSALLAR--KDIVGAAETGSGKTLAFGIPILTGI 65
+++ +Y GF P+KIQ +P +LA ++++ +++G+GKT AF + +L+ +
Sbjct: 36 LLQGVYAMGFNRPSKIQENALP-LMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 89
>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214
Length = 235
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 36/55 (65%), Gaps = 3/55 (5%)
Query: 13 IIRALYQKGFKTPTKIQSMVMPSALLAR--KDIVGAAETGSGKTLAFGIPILTGI 65
+++ +Y GF P+KIQ +P +LA ++++ +++G+GKT AF + +L+ +
Sbjct: 36 LLQGVYAMGFNRPSKIQENALP-LMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 89
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 39/88 (44%), Gaps = 35/88 (39%)
Query: 80 SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXS 139
S D++ A+TG+GKT AF IPI ++N
Sbjct: 58 SEDHDVIARAKTGTGKTFAFLIPIFQHLIN------------------------------ 87
Query: 140 ANTTEFVKKTRNKLYALILAPTRELAIQ 167
T+F ++ + A+I+APTR+LA+Q
Sbjct: 88 ---TKF--DSQYMVKAVIVAPTRDLALQ 110
Score = 35.8 bits (81), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN 67
TP + Q + P D++ A+TG+GKT AF IPI ++N
Sbjct: 45 TPVQ-QKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 87
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 35.4 bits (80), Expect = 0.014, Method: Composition-based stats.
Identities = 30/108 (27%), Positives = 46/108 (42%), Gaps = 39/108 (36%)
Query: 60 PILTGIVNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXX 119
P LT + K P E+ D++ A+TG+GKT AF IPI ++N
Sbjct: 42 PGLTPVQQKTIKPILSSED----HDVIARAKTGTGKTFAFLIPIFQHLIN---------- 87
Query: 120 XXXXXXXXXXXXXXXXXXXSANTTEFVKKTRNKLYALILAPTRELAIQ 167
T+F ++ + A+I+APTR+LA+Q
Sbjct: 88 -----------------------TKF--DSQYMVKAVIVAPTRDLALQ 110
Score = 34.3 bits (77), Expect = 0.035, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 13 IIRALYQKGFKTPTKIQSMVMPSALLARK-DIVGAAETGSGKTLAFGIPILTGIVN 67
I +A+ + F T +Q + L + D++ A+TG+GKT AF IPI ++N
Sbjct: 32 IHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 87
>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp
pdb|3I5Y|A Chain A, Structure Of Mss116p Bound To Ssrna Containing A Single
5-Bru And Amp- Pnp
pdb|3I61|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-beryllium
Fluoride
pdb|3I62|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-aluminum
Fluoride
Length = 563
Score = 35.4 bits (80), Expect = 0.017, Method: Composition-based stats.
Identities = 30/108 (27%), Positives = 46/108 (42%), Gaps = 39/108 (36%)
Query: 60 PILTGIVNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXX 119
P LT + K P E+ D++ A+TG+GKT AF IPI ++N
Sbjct: 93 PGLTPVQQKTIKPILSSED----HDVIARAKTGTGKTFAFLIPIFQHLIN---------- 138
Query: 120 XXXXXXXXXXXXXXXXXXXSANTTEFVKKTRNKLYALILAPTRELAIQ 167
T+F ++ + A+I+APTR+LA+Q
Sbjct: 139 -----------------------TKF--DSQYMVKAVIVAPTRDLALQ 161
Score = 34.3 bits (77), Expect = 0.038, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 13 IIRALYQKGFKTPTKIQSMVMPSALLARK-DIVGAAETGSGKTLAFGIPILTGIVN 67
I +A+ + F T +Q + L + D++ A+TG+GKT AF IPI ++N
Sbjct: 83 IHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 138
>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain
pdb|3IUY|B Chain B, Crystal Structure Of Ddx53 Dead-Box Domain
Length = 228
Score = 35.0 bits (79), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 38/67 (56%), Gaps = 4/67 (5%)
Query: 13 IIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNKLENP 72
+++++ + G PT IQS P +L D++ A+TG+GKTL++ +P G ++ P
Sbjct: 31 LLKSIIRVGILKPTPIQSQAWP-IILQGIDLIVVAQTGTGKTLSYLMP---GFIHLDSQP 86
Query: 73 TEEDEND 79
++ +
Sbjct: 87 ISREQRN 93
>pdb|4F91|B Chain B, Brr2 Helicase Region
Length = 1724
Score = 30.8 bits (68), Expect = 0.33, Method: Composition-based stats.
Identities = 15/35 (42%), Positives = 24/35 (68%)
Query: 20 KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKT 54
+GFKT +IQS + +AL ++++ A TG+GKT
Sbjct: 75 EGFKTLNRIQSKLYRAALETDENLLLCAPTGAGKT 109
Score = 28.1 bits (61), Expect = 2.6, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 26/55 (47%)
Query: 16 ALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNKLE 70
+LYQ F IQ+ V + + ++ A TGSGKT+ IL ++ E
Sbjct: 918 SLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSE 972
>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l
pdb|4F93|B Chain B, Brr2 Helicase Region S1087l, Mg-Atp
Length = 1724
Score = 30.8 bits (68), Expect = 0.33, Method: Composition-based stats.
Identities = 15/35 (42%), Positives = 24/35 (68%)
Query: 20 KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKT 54
+GFKT +IQS + +AL ++++ A TG+GKT
Sbjct: 75 EGFKTLNRIQSKLYRAALETDENLLLCAPTGAGKT 109
Score = 28.1 bits (61), Expect = 2.6, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 26/55 (47%)
Query: 16 ALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNKLE 70
+LYQ F IQ+ V + + ++ A TGSGKT+ IL ++ E
Sbjct: 918 SLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSE 972
>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In
Complex With Adp
pdb|2OXC|B Chain B, Human Dead-Box Rna Helicase Ddx20, Dead Domain In
Complex With Adp
pdb|3B7G|A Chain A, Human Dead-Box Rna Helicase Ddx20, Conserved Domain I
(Dead) In Complex With Amppnp
(Adenosine-(Beta,Gamma)-Imidotriphosphate)
pdb|3B7G|B Chain B, Human Dead-Box Rna Helicase Ddx20, Conserved Domain I
(Dead) In Complex With Amppnp
(Adenosine-(Beta,Gamma)-Imidotriphosphate)
Length = 230
Score = 30.0 bits (66), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 7/72 (9%)
Query: 2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARK--DIVGAAETGSGKTLAFGI 59
A++ + ++ L GF+ P+ +Q +P L R D++ A++G+GKT F
Sbjct: 24 ADFESLLLSRPVLEGLRAAGFERPSPVQLKAIP---LGRCGLDLIVQAKSGTGKTCVFST 80
Query: 60 PILTGIVNKLEN 71
L +V LEN
Sbjct: 81 IALDSLV--LEN 90
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 27.3 bits (59), Expect = 3.8, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 6/75 (8%)
Query: 37 LLARKDIVGAAETGSGKTLAFGIPI-----LTGIVNKLENPTEEDENDSARKDIVGAAET 91
+L+ +D + TG GK+L + IP LT +V+ L + +D+ D + + V AA
Sbjct: 37 VLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLIS-LMKDQVDQLQANGVAAACL 95
Query: 92 GSGKTLAFGIPILTG 106
S +T + ++TG
Sbjct: 96 NSTQTREQQLEVMTG 110
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 26.9 bits (58), Expect = 5.7, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 6/75 (8%)
Query: 37 LLARKDIVGAAETGSGKTLAFGIPI-----LTGIVNKLENPTEEDENDSARKDIVGAAET 91
+L+ +D + TG GK+L + IP LT +V+ L + +D+ D + + V AA
Sbjct: 37 VLSGRDCLVVXPTGGGKSLCYQIPALLLNGLTVVVSPLIS-LXKDQVDQLQANGVAAACL 95
Query: 92 GSGKTLAFGIPILTG 106
S +T + + TG
Sbjct: 96 NSTQTREQQLEVXTG 110
>pdb|1W5D|A Chain A, Crystal Structure Of Pbp4a From Bacillus Subtilis
pdb|2J9P|A Chain A, Crystal Structure Of The Bacillus Subtilis Pbp4a, And Its
Complex With A Peptidoglycan Mimetic Peptide.
pdb|2J9P|B Chain B, Crystal Structure Of The Bacillus Subtilis Pbp4a, And Its
Complex With A Peptidoglycan Mimetic Peptide
Length = 462
Score = 26.6 bits (57), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDE 77
TP + + +L + G AET SGK L F I +L G++++ + ED+
Sbjct: 402 TPAQGKVRAKTGSLSTVSSLSGYAETKSGKKLVFSI-LLNGLIDEEDGKDIEDQ 454
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 26.6 bits (57), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 3/67 (4%)
Query: 3 EWV---KFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGI 59
EW+ +P +I + ++G K Q+ + LL ++ + TGSGKTL +
Sbjct: 6 EWMPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEM 65
Query: 60 PILTGIV 66
I++ ++
Sbjct: 66 GIISFLL 72
>pdb|2IUK|A Chain A, Crystal Structure Of Soybean Lipoxygenase-D
pdb|2IUK|B Chain B, Crystal Structure Of Soybean Lipoxygenase-D
Length = 864
Score = 26.2 bits (56), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 14 IRALYQKGFKTPTKIQSMVMP 34
+R+LY+ G K PT I S + P
Sbjct: 313 VRSLYEGGIKLPTDILSQISP 333
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
0.314 0.132 0.363
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,101,202
Number of Sequences: 62578
Number of extensions: 138823
Number of successful extensions: 380
Number of sequences better than 100.0: 48
Number of HSP's better than 100.0 without gapping: 33
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 275
Number of HSP's gapped (non-prelim): 112
length of query: 167
length of database: 14,973,337
effective HSP length: 92
effective length of query: 75
effective length of database: 9,216,161
effective search space: 691212075
effective search space used: 691212075
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)