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= psy9277
(178 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 275 bits (704), Expect = 7e-75, Method: Compositional matrix adjust.
Identities = 130/166 (78%), Positives = 147/166 (88%)
Query: 1 MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
MA GS + + ED++ VEFETSE+V+V TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct: 6 MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 65
Query: 61 RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
R+IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +
Sbjct: 66 RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 125
Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct: 126 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 171
>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 = 275 bits (704), Expect = 8e-75, Method: Compositional matrix adjust.
Identities = 130/166 (78%), Positives = 147/166 (88%)
Query: 1 MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
MA GS + + ED++ VEFETSE+V+V TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct: 7 MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 66
Query: 61 RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
R+IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +
Sbjct: 67 RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 126
Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct: 127 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 172
>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 = 275 bits (704), Expect = 8e-75, Method: Compositional matrix adjust.
Identities = 130/166 (78%), Positives = 147/166 (88%)
Query: 1 MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
MA GS + + ED++ VEFETSE+V+V TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct: 7 MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 66
Query: 61 RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
R+IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +
Sbjct: 67 RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 126
Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct: 127 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 172
>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 = 266 bits (681), Expect = 4e-72, Method: Compositional matrix adjust.
Identities = 125/155 (80%), Positives = 140/155 (90%)
Query: 17 LSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQA 76
++ VEFETSE+V+V TFD MGLREDLLRGIYAYGFEKPSAIQQR+IK I+KGRDVIAQ+
Sbjct: 1 MTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQS 60
Query: 77 QSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIG 136
QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +LALGD+MNVQCHACIG
Sbjct: 61 QSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIG 120
Query: 137 GTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR 171
GTN+ ED+RKLDYGQHVV+GTPGRVFDMIR R
Sbjct: 121 GTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLR 155
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 246 bits (629), Expect = 4e-66, Method: Compositional matrix adjust.
Identities = 114/139 (82%), Positives = 127/139 (91%)
Query: 33 TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQ 92
TFD MGLREDLLRGIYAYGFEKPSAIQQR+IK I+KGRDVIAQ+QSGTGKTATFS+S+LQ
Sbjct: 2 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 93 SLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQH 152
LD Q+RETQ L L+PTRELAVQ+QK +LALGD+MNVQCHACIGGTN+ ED+RKLDYGQH
Sbjct: 62 CLDIQVRETQALILAPTRELAVQVQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQH 121
Query: 153 VVSGTPGRVFDMIRSSQGR 171
VV+GTPGRVFDMIR R
Sbjct: 122 VVAGTPGRVFDMIRRRSLR 140
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 242 bits (618), Expect = 6e-65, Method: Compositional matrix adjust.
Identities = 112/134 (83%), Positives = 125/134 (93%)
Query: 33 TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQ 92
TFD MGLREDLLRGIYAYGFEKPSAIQQR+IK I+KGRDVIAQ+QSGTGKTATFS+S+LQ
Sbjct: 2 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 93 SLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQH 152
LD Q+RETQ L L+PTRELAVQ+QK +LALGD+MNVQ HACIGGTN+ ED+RKLDYGQH
Sbjct: 62 CLDIQVRETQALILAPTRELAVQVQKGLLALGDYMNVQSHACIGGTNVGEDIRKLDYGQH 121
Query: 153 VVSGTPGRVFDMIR 166
VV+GTPGRVFDMIR
Sbjct: 122 VVAGTPGRVFDMIR 135
>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation
Initiation Factor 4a-2
Length = 237
Score = 206 bits (524), Expect = 6e-54, Method: Compositional matrix adjust.
Identities = 96/138 (69%), Positives = 114/138 (82%), Gaps = 1/138 (0%)
Query: 29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
E+V FD+M L+E LLRGIYAYGFEKPSAIQQR+I P +KG DVIAQAQSGTGKTATF+I
Sbjct: 27 EIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAI 86
Query: 89 SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD 148
SILQ L+ + +ETQ L L+PTRELA QIQKV+LALGD+M CHACIGGTN+ +++KL
Sbjct: 87 SILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQ 146
Query: 149 Y-GQHVVSGTPGRVFDMI 165
H+V GTPGRVFDM+
Sbjct: 147 AEAPHIVVGTPGRVFDML 164
>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 = 202 bits (513), Expect = 1e-52, Method: Compositional matrix adjust.
Identities = 94/138 (68%), Positives = 113/138 (81%), Gaps = 1/138 (0%)
Query: 29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
E+V +FD+M L E LLRGIYAYGFEKPSAIQQR+I P +KG DVIAQAQSGTGKTATF+I
Sbjct: 11 EIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAI 70
Query: 89 SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD 148
SILQ ++ L+ TQ L L+PTRELA QIQKVV+ALGD+M CHACIGGTN+ +++KL
Sbjct: 71 SILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQ 130
Query: 149 Y-GQHVVSGTPGRVFDMI 165
H++ GTPGRVFDM+
Sbjct: 131 MEAPHIIVGTPGRVFDML 148
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 201 bits (512), Expect = 1e-52, Method: Compositional matrix adjust.
Identities = 94/138 (68%), Positives = 113/138 (81%), Gaps = 1/138 (0%)
Query: 29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
E+V +FD+M L E LLRGIYAYGFEKPSAIQQR+I P +KG DVIAQAQSGTGKTATF+I
Sbjct: 37 EIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAI 96
Query: 89 SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD 148
SILQ ++ L+ TQ L L+PTRELA QIQKVV+ALGD+M CHACIGGTN+ +++KL
Sbjct: 97 SILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQ 156
Query: 149 Y-GQHVVSGTPGRVFDMI 165
H++ GTPGRVFDM+
Sbjct: 157 MEAPHIIVGTPGRVFDML 174
>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 = 188 bits (478), Expect = 1e-48, Method: Compositional matrix adjust.
Identities = 89/138 (64%), Positives = 107/138 (77%), Gaps = 1/138 (0%)
Query: 29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
E+V +FD+M L E LLRGIYAYGFE PSAIQQR+I P + G DVIAQAQSGTG TATF+I
Sbjct: 12 EIVDSFDDMNLSESLLRGIYAYGFEXPSAIQQRAILPCIXGYDVIAQAQSGTGXTATFAI 71
Query: 89 SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD 148
SILQ ++ L TQ L L+PTRELA QIQ VV+ALGD+M CHACIGGTN+ +++ L
Sbjct: 72 SILQQIELDLXATQALVLAPTRELAQQIQXVVMALGDYMGASCHACIGGTNVRAEVQXLQ 131
Query: 149 Y-GQHVVSGTPGRVFDMI 165
H++ GTPGRVFDM+
Sbjct: 132 MEAPHIIVGTPGRVFDML 149
>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex
pdb|2VSO|B Chain B, Crystal Structure Of A Translation Initiation Complex
pdb|2VSX|A Chain A, Crystal Structure Of A Translation Initiation Complex
pdb|2VSX|B Chain B, Crystal Structure Of A Translation Initiation Complex
Length = 395
Score = 179 bits (454), Expect = 8e-46, Method: Compositional matrix adjust.
Identities = 89/156 (57%), Positives = 117/156 (75%), Gaps = 2/156 (1%)
Query: 16 DLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQ 75
D+ + +T+ D +VV FD+M L E+LLRG++ YGFE+PSAIQQR+I PI++G DV+AQ
Sbjct: 7 DIEESQIQTNYD-KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQ 65
Query: 76 AQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACI 135
AQSGTGKT TFSI+ LQ +DT ++ Q L L+PTRELA+QIQKVV+AL M+++ HACI
Sbjct: 66 AQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACI 125
Query: 136 GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR 171
GGT+ ED L Q +V GTPGRVFD I+ + R
Sbjct: 126 GGTSFVEDAEGLRDAQ-IVVGTPGRVFDNIQRRRFR 160
>pdb|1QDE|A Chain A, Crystal Structure Of The Atpase Domain Of Translation
Initiation Factor 4a From Saccharomyces Cerevisiae-The
Prototype Of The Dead Box Protein Family
Length = 224
Score = 177 bits (448), Expect = 3e-45, Method: Compositional matrix adjust.
Identities = 86/143 (60%), Positives = 110/143 (76%), Gaps = 1/143 (0%)
Query: 29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
+VV FD+M L E+LLRG++ YGFE+PSAIQQR+I PI++G DV+AQAQSGTGKT TFSI
Sbjct: 11 KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSI 70
Query: 89 SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD 148
+ LQ +DT ++ Q L L+PTRELA+QIQKVV+AL M+++ HACIGGT+ ED L
Sbjct: 71 AALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR 130
Query: 149 YGQHVVSGTPGRVFDMIRSSQGR 171
Q +V GTPGRVFD I+ + R
Sbjct: 131 DAQ-IVVGTPGRVFDNIQRRRFR 152
>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain
Length = 223
Score = 176 bits (446), Expect = 7e-45, Method: Compositional matrix adjust.
Identities = 86/143 (60%), Positives = 109/143 (76%), Gaps = 1/143 (0%)
Query: 29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
+VV FD+M L E LLRG++ YGFE+PSAIQQR+I PI++G DV+AQAQSGTGKT TFSI
Sbjct: 18 KVVYKFDDMELDEQLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSI 77
Query: 89 SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD 148
+ LQ +DT ++ Q L L+PTRELA+QIQKVV+AL M+++ HACIGGT+ ED L
Sbjct: 78 AALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR 137
Query: 149 YGQHVVSGTPGRVFDMIRSSQGR 171
Q +V GTPGRVFD I+ + R
Sbjct: 138 DAQ-IVVGTPGRVFDNIQRRRFR 159
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 172 bits (435), Expect = 1e-43, Method: Compositional matrix adjust.
Identities = 87/156 (55%), Positives = 114/156 (73%), Gaps = 2/156 (1%)
Query: 16 DLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQ 75
D+ + +T+ D +VV FD+ L E+LLRG++ YGFE+PSAIQQR+I PI++G DV+AQ
Sbjct: 6 DIEESQIQTNYD-KVVYKFDDXELDENLLRGVFGYGFEEPSAIQQRAIXPIIEGHDVLAQ 64
Query: 76 AQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACI 135
AQSGTGKT TFSI+ LQ +DT ++ Q L L+PTRELA+QIQKVV AL +++ HACI
Sbjct: 65 AQSGTGKTGTFSIAALQRIDTSVKAPQALXLAPTRELALQIQKVVXALAFHXDIKVHACI 124
Query: 136 GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR 171
GGT+ ED L Q +V GTPGRVFD I+ + R
Sbjct: 125 GGTSFVEDAEGLRDAQ-IVVGTPGRVFDNIQRRRFR 159
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 129 bits (324), Expect = 8e-31, Method: Compositional matrix adjust.
Identities = 60/133 (45%), Positives = 89/133 (66%)
Query: 32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
+TF++ L+ +LL GI+ GFEKPS IQ+ +I + GRD++A+A++GTGKTA F I L
Sbjct: 21 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTL 80
Query: 92 QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQ 151
+ + +L + Q L + PTRELA+Q +VV LG + C GGTNL +D+ +L+
Sbjct: 81 EKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETV 140
Query: 152 HVVSGTPGRVFDM 164
H++ GTPGRV D+
Sbjct: 141 HILVGTPGRVLDL 153
>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 = 117 bits (293), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 55/134 (41%), Positives = 88/134 (65%), Gaps = 1/134 (0%)
Query: 34 FDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQS 93
F++ L+ +LL GI+ G+EKPS IQ+ SI + GRD++A+A++GTGK+ + I +L+
Sbjct: 5 FEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLER 64
Query: 94 LDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYGQH 152
LD + Q + + PTRELA+Q+ ++ + + M + A GGTNL +D+ +LD H
Sbjct: 65 LDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVH 124
Query: 153 VVSGTPGRVFDMIR 166
VV TPGR+ D+I+
Sbjct: 125 VVIATPGRILDLIK 138
>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 = 108 bits (270), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 60/133 (45%), Positives = 85/133 (63%), Gaps = 2/133 (1%)
Query: 34 FDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQS 93
F+++ L +L G+ A GFE+PS +Q ++I G D+I QA+SGTGKT FS L S
Sbjct: 26 FESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDS 85
Query: 94 LDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMN-VQCHACIGGTNLSEDLRKLDYGQH 152
L + TQ+L L+PTRE+AVQI V+ A+G M ++CH IGGT LS+D +L H
Sbjct: 86 LVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKC-H 144
Query: 153 VVSGTPGRVFDMI 165
+ G+PGR+ +I
Sbjct: 145 IAVGSPGRIKQLI 157
>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p
Length = 226
Score = 106 bits (265), Expect = 7e-24, Method: Compositional matrix adjust.
Identities = 55/152 (36%), Positives = 96/152 (63%), Gaps = 6/152 (3%)
Query: 17 LSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDVIA 74
L++++ + + + +FD +GL +LL+GIYA F+KPS IQ+R++ ++ R++IA
Sbjct: 7 LADIQADPNSPLYSAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIA 66
Query: 75 QAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC 134
Q+QSGTGKTA FS+++L ++ + Q +CL+P+RELA Q +VV +G F +
Sbjct: 67 QSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLI 126
Query: 135 IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
+ + E ++++ V+ GTPG V D++R
Sbjct: 127 VPDS--FEKNKQIN--AQVIVGTPGTVLDLMR 154
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 103 bits (257), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 54/139 (38%), Positives = 89/139 (64%), Gaps = 6/139 (4%)
Query: 30 VVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFS 87
+ +FD +GL +LL+GIYA F+KPS IQ+R++ ++ R++IAQ+QSGTGKTA FS
Sbjct: 3 MAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFS 62
Query: 88 ISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL 147
+++L ++ + Q +CL+P+RELA Q +VV +G F + + + E +++
Sbjct: 63 LTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDS--FEKNKQI 120
Query: 148 DYGQHVVSGTPGRVFDMIR 166
+ V+ GTPG V D++R
Sbjct: 121 N--AQVIVGTPGTVLDLMR 137
>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3
pdb|3RRM|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Nup159, Gle1 H337r, Ip6
And Adp
pdb|3RRN|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Gle1 H337r And Ip6
Length = 395
Score = 103 bits (257), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 54/139 (38%), Positives = 89/139 (64%), Gaps = 6/139 (4%)
Query: 30 VVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFS 87
+ +FD +GL +LL+GIYA F+KPS IQ+R++ ++ R++IAQ+QSGTGKTA FS
Sbjct: 3 MAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFS 62
Query: 88 ISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL 147
+++L ++ + Q +CL+P+RELA Q +VV +G F + + + E +++
Sbjct: 63 LTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDS--FEKNKQI 120
Query: 148 DYGQHVVSGTPGRVFDMIR 166
+ V+ GTPG V D++R
Sbjct: 121 N--AQVIVGTPGTVLDLMR 137
>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
Length = 300
Score = 96.7 bits (239), Expect = 7e-21, Method: Compositional matrix adjust.
Identities = 53/138 (38%), Positives = 83/138 (60%), Gaps = 8/138 (5%)
Query: 31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV---KGRDVIAQAQSGTGKTATFS 87
V +F+ + L+ LL+G+YA GF +PS IQ+ ++ P++ +++IAQ+QSGTGKTA F
Sbjct: 91 VKSFEELRLKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAAFV 149
Query: 88 ISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRK 146
+++L ++ + Q LCLSPT ELA+Q KV+ +G F ++ + G L R
Sbjct: 150 LAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLE---RG 206
Query: 147 LDYGQHVVSGTPGRVFDM 164
+ +V GTPG V D
Sbjct: 207 QKISEQIVIGTPGTVLDW 224
>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214
Length = 235
Score = 95.9 bits (237), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 53/138 (38%), Positives = 83/138 (60%), Gaps = 8/138 (5%)
Query: 31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV---KGRDVIAQAQSGTGKTATFS 87
V +F+ + L+ LL+G+YA GF +PS IQ+ ++ P++ +++IAQ+QSGTGKTA F
Sbjct: 24 VKSFEELRLKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAAFV 82
Query: 88 ISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRK 146
+++L ++ + Q LCLSPT ELA+Q KV+ +G F ++ + G L R
Sbjct: 83 LAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLE---RG 139
Query: 147 LDYGQHVVSGTPGRVFDM 164
+ +V GTPG V D
Sbjct: 140 QKISEQIVIGTPGTVLDW 157
>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 = 95.5 bits (236), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 53/138 (38%), Positives = 83/138 (60%), Gaps = 8/138 (5%)
Query: 31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG---RDVIAQAQSGTGKTATFS 87
V +F+ + L+ LL+G+YA GF +PS IQ+ ++ P++ +++IAQ+QSGTGKTA F
Sbjct: 91 VKSFEELRLKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAAFV 149
Query: 88 ISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRK 146
+++L ++ + Q LCLSPT ELA+Q KV+ +G F ++ + G L R
Sbjct: 150 LAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLE---RG 206
Query: 147 LDYGQHVVSGTPGRVFDM 164
+ +V GTPG V D
Sbjct: 207 QKISEQIVIGTPGTVLDW 224
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 95.1 bits (235), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 52/137 (37%), Positives = 82/137 (59%), Gaps = 6/137 (4%)
Query: 31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV--KGRDVIAQAQSGTGKTATFSI 88
V +F+ + L+ LL+G+YA GF +PS IQ+ ++ ++ +++IAQ+QSGTGKTA F +
Sbjct: 40 VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 99
Query: 89 SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKL 147
++L ++ + Q LCLSPT ELA+Q KV+ +G F ++ + G L R
Sbjct: 100 AMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLE---RGQ 156
Query: 148 DYGQHVVSGTPGRVFDM 164
+ +V GTPG V D
Sbjct: 157 KISEQIVIGTPGTVLDW 173
>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 = 95.1 bits (235), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 52/137 (37%), Positives = 82/137 (59%), Gaps = 6/137 (4%)
Query: 31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV--KGRDVIAQAQSGTGKTATFSI 88
V +F+ + L+ LL+G+YA GF +PS IQ+ ++ ++ +++IAQ+QSGTGKTA F +
Sbjct: 24 VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 83
Query: 89 SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKL 147
++L ++ + Q LCLSPT ELA+Q KV+ +G F ++ + G L R
Sbjct: 84 AMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLE---RGQ 140
Query: 148 DYGQHVVSGTPGRVFDM 164
+ +V GTPG V D
Sbjct: 141 KISEQIVIGTPGTVLDW 157
>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 = 95.1 bits (235), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 52/137 (37%), Positives = 82/137 (59%), Gaps = 6/137 (4%)
Query: 31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV--KGRDVIAQAQSGTGKTATFSI 88
V +F+ + L+ LL+G+YA GF +PS IQ+ ++ ++ +++IAQ+QSGTGKTA F +
Sbjct: 61 VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 120
Query: 89 SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKL 147
++L ++ + Q LCLSPT ELA+Q KV+ +G F ++ + G L R
Sbjct: 121 AMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLE---RGQ 177
Query: 148 DYGQHVVSGTPGRVFDM 164
+ +V GTPG V D
Sbjct: 178 KISEQIVIGTPGTVLDW 194
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 92.8 bits (229), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 54/140 (38%), Positives = 76/140 (54%), Gaps = 2/140 (1%)
Query: 31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISI 90
+S F + L+ +LLR I GFE PS +Q I + G DV+ QA+SG GKTA F ++
Sbjct: 6 MSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLAT 65
Query: 91 LQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDY 149
LQ L+ + VL + TRELA QI K +M NV+ GG ++ +D L
Sbjct: 66 LQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKK 125
Query: 150 G-QHVVSGTPGRVFDMIRSS 168
H+V GTPGR+ + R+
Sbjct: 126 NCPHIVVGTPGRILALARNK 145
>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 = 92.8 bits (229), Expect = 9e-20, Method: Compositional matrix adjust.
Identities = 54/138 (39%), Positives = 75/138 (54%), Gaps = 2/138 (1%)
Query: 32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
S F + L+ +LLR I GFE PS +Q I + G DV+ QA+SG GKTA F ++ L
Sbjct: 14 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL 73
Query: 92 QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYG 150
Q L+ + VL + TRELA QI K +M NV+ GG ++ +D L
Sbjct: 74 QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKN 133
Query: 151 -QHVVSGTPGRVFDMIRS 167
H+V GTPGR+ + R+
Sbjct: 134 CPHIVVGTPGRILALARN 151
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 92.8 bits (229), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 54/139 (38%), Positives = 75/139 (53%), Gaps = 2/139 (1%)
Query: 32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
S F + L+ +LLR I GFE PS +Q I + G DV+ QA+SG GKTA F ++ L
Sbjct: 8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL 67
Query: 92 QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYG 150
Q L+ + VL + TRELA QI K +M NV+ GG ++ +D L
Sbjct: 68 QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKN 127
Query: 151 -QHVVSGTPGRVFDMIRSS 168
H+V GTPGR+ + R+
Sbjct: 128 CPHIVVGTPGRILALARNK 146
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 92.8 bits (229), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 54/139 (38%), Positives = 75/139 (53%), Gaps = 2/139 (1%)
Query: 32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
S F + L+ +LLR I GFE PS +Q I + G DV+ QA+SG GKTA F ++ L
Sbjct: 8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL 67
Query: 92 QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYG 150
Q L+ + VL + TRELA QI K +M NV+ GG ++ +D L
Sbjct: 68 QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKN 127
Query: 151 -QHVVSGTPGRVFDMIRSS 168
H+V GTPGR+ + R+
Sbjct: 128 CPHIVVGTPGRILALARNK 146
>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In
Complex With Amp
Length = 249
Score = 91.3 bits (225), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 49/142 (34%), Positives = 78/142 (54%)
Query: 29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
E TF ++G+ + L G+ KP+ IQ +I ++GRD+I A++G+GKT F++
Sbjct: 40 EETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFAL 99
Query: 89 SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD 148
IL +L + L L+PTRELA QI + ALG + VQ +GG + L
Sbjct: 100 PILNALLETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALA 159
Query: 149 YGQHVVSGTPGRVFDMIRSSQG 170
H++ TPGR+ D + +++G
Sbjct: 160 KKPHIIIATPGRLIDHLENTKG 181
>pdb|3LY5|A Chain A, Ddx18 Dead-Domain
pdb|3LY5|B Chain B, Ddx18 Dead-Domain
Length = 262
Score = 89.0 bits (219), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 54/145 (37%), Positives = 85/145 (58%), Gaps = 12/145 (8%)
Query: 39 LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL 98
+ E+ L+ I GF + IQ +SI+P+++GRD++A A++G+GKT F I ++ L +L
Sbjct: 61 VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVE-LIVKL 119
Query: 99 R-----ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHA---CIGGTNLSEDLRKLDYG 150
R T VL LSPTRELA+Q V L + M H +GG+N S + +KL G
Sbjct: 120 RFMPRNGTGVLILSPTRELAMQTFGV---LKELMTHHVHTYGLIMGGSNRSAEAQKLGNG 176
Query: 151 QHVVSGTPGRVFDMIRSSQGRRTTN 175
+++ TPGR+ D ++++ G N
Sbjct: 177 INIIVATPGRLLDHMQNTPGFMYKN 201
>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 = 87.0 bits (214), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 47/140 (33%), Positives = 72/140 (51%), Gaps = 4/140 (2%)
Query: 32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
+ F + ++ I F KP+ IQ+R I ++G + Q+Q+GTGKT + + I
Sbjct: 4 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPIX 63
Query: 92 QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM----NVQCHACIGGTNLSEDLRKL 147
+ + + E Q + +PTRELA QI L + F + IGGT+ + L KL
Sbjct: 64 EKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGGTDKQKALEKL 123
Query: 148 DYGQHVVSGTPGRVFDMIRS 167
+ H+V GTPGR+ D IR
Sbjct: 124 NVQPHIVIGTPGRINDFIRE 143
>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 = 84.7 bits (208), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 52/155 (33%), Positives = 81/155 (52%), Gaps = 21/155 (13%)
Query: 30 VVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSIS 89
V+ FD + L + I +++P+ IQ+ +I I++ RD++A AQ+G+GKTA F I
Sbjct: 21 VIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIP 80
Query: 90 ILQSLDTQLRETQ---------VLCLSPTRELAVQI----QKVVLALGDFMNVQCHACI- 135
I+ L Q Q L L+PTRELA+QI QK L N +C+
Sbjct: 81 IINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSL------NTPLRSCVV 134
Query: 136 -GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ 169
GG + +R++ G H++ TPGR+ D I ++
Sbjct: 135 YGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNK 169
>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 = 82.0 bits (201), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 52/148 (35%), Positives = 79/148 (53%), Gaps = 6/148 (4%)
Query: 24 TSEDV-EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGK 82
T DV + + F + LR+ ++ + G++ P+ IQ+ SI I GRD++A AQ+G+GK
Sbjct: 47 TGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGK 106
Query: 83 TATFSISILQSL-----DTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGG 137
TA F + IL L + +L QV+ +SPTRELA+QI ++ GG
Sbjct: 107 TAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGG 166
Query: 138 TNLSEDLRKLDYGQHVVSGTPGRVFDMI 165
T+ + G HVV TPGR+ D +
Sbjct: 167 TSFRHQNECITRGCHVVIATPGRLLDFV 194
>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 = 82.0 bits (201), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 45/136 (33%), Positives = 73/136 (53%), Gaps = 5/136 (3%)
Query: 34 FDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQS 93
F + L+ ++L ++ G P+ IQ ++ ++G+D+I QA++GTGKT F++ I +
Sbjct: 3 FKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 94 LDTQL---RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYG 150
L R+ + L L+PTRELA+Q+ + A+ + V A GGT + L G
Sbjct: 63 LAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVV--AVYGGTGYGKQKEALLRG 120
Query: 151 QHVVSGTPGRVFDMIR 166
V TPGR D +R
Sbjct: 121 ADAVVATPGRALDYLR 136
>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 = 81.6 bits (200), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 44/134 (32%), Positives = 79/134 (58%), Gaps = 3/134 (2%)
Query: 33 TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGR-DVIAQAQSGTGKTATFSISIL 91
F+ + L +++L I GFEKP+ IQ + I + +++AQA++G+GKTA+F+I ++
Sbjct: 7 NFNELNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66
Query: 92 QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQ 151
+ L + + + L+PTRELA+Q+ + +L N++ GG + ++ L
Sbjct: 67 E-LVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NA 124
Query: 152 HVVSGTPGRVFDMI 165
++V GTPGR+ D I
Sbjct: 125 NIVVGTPGRILDHI 138
>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 = 80.9 bits (198), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 44/136 (32%), Positives = 73/136 (53%), Gaps = 5/136 (3%)
Query: 34 FDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQS 93
F + L+ ++L ++ G P+ I+ ++ ++G+D+I QA++GTGKT F++ I +
Sbjct: 3 FKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 94 LDTQL---RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYG 150
L R+ + L L+PTRELA+Q+ + A+ + V A GGT + L G
Sbjct: 63 LAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVV--AVYGGTGYGKQKEALLRG 120
Query: 151 QHVVSGTPGRVFDMIR 166
V TPGR D +R
Sbjct: 121 ADAVVATPGRALDYLR 136
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 75.1 bits (183), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 51/161 (31%), Positives = 92/161 (57%), Gaps = 13/161 (8%)
Query: 23 ETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV--KGRDVIAQAQSGT 80
+ S++V + S + L +++ + I F + +QQ++IKPI+ + DVIA+A++GT
Sbjct: 12 DNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGT 71
Query: 81 GKTATFSISILQSLDTQLRETQVLC----LSPTRELAVQIQKVVLALGDFMN--VQCHAC 134
GKT F I I Q L ++Q + ++PTR+LA+QI+ V + D MN ++ +AC
Sbjct: 72 GKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHD-MNYGLKKYAC 130
Query: 135 ---IGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRSSQGR 171
+GGT+ + K++ ++V TPGR+ D++ +
Sbjct: 131 VSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNK 171
>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 = 75.1 bits (183), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 51/161 (31%), Positives = 92/161 (57%), Gaps = 13/161 (8%)
Query: 23 ETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV--KGRDVIAQAQSGT 80
+ S++V + S + L +++ + I F + +QQ++IKPI+ + DVIA+A++GT
Sbjct: 63 DNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGT 122
Query: 81 GKTATFSISILQSLDTQLRETQVLC----LSPTRELAVQIQKVVLALGDFMN--VQCHAC 134
GKT F I I Q L ++Q + ++PTR+LA+QI+ V + D MN ++ +AC
Sbjct: 123 GKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHD-MNYGLKKYAC 181
Query: 135 ---IGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRSSQGR 171
+GGT+ + K++ ++V TPGR+ D++ +
Sbjct: 182 VSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNK 222
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 73.9 bits (180), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 46/153 (30%), Positives = 80/153 (52%), Gaps = 18/153 (11%)
Query: 31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISI 90
+ +F ++ + E ++ I + +P+ +Q+ +I I + RD++A AQ+G+GKTA F + I
Sbjct: 14 IESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPI 73
Query: 91 LQSLDTQ-----LRETQ-------------VLCLSPTRELAVQIQKVVLALGDFMNVQCH 132
L + + LR + L L+PTRELAVQI + V+
Sbjct: 74 LSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPC 133
Query: 133 ACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMI 165
GG ++ + +R L+ G H++ TPGR+ DM+
Sbjct: 134 VVYGGADIGQQIRDLERGCHLLVATPGRLVDMM 166
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 73.2 bits (178), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 41/114 (35%), Positives = 69/114 (60%), Gaps = 6/114 (5%)
Query: 58 IQQRSIKPIVKG--RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQ 115
IQ++++ ++ R++I Q+QSGTGKTA F++++L +D + + Q +CL+P+RELA Q
Sbjct: 145 IQEKALPLLLSNPPRNMIGQSQSGTGKTAAFALTMLSRVDASVPKPQAICLAPSRELARQ 204
Query: 116 IQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ 169
I VV +G + V+ G + K+D +V GTPG V D+++ Q
Sbjct: 205 IMDVVTEMGKYTEVK--TAFGIKDSVPKGAKID--AQIVIGTPGTVMDLMKRRQ 254
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 72.0 bits (175), Expect = 2e-13, Method: Composition-based stats.
Identities = 50/155 (32%), Positives = 87/155 (56%), Gaps = 13/155 (8%)
Query: 23 ETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGR--DVIAQAQSGT 80
+ S++V + S + L +++ + I F + +QQ++IKPI+ DVIA+A++GT
Sbjct: 12 DNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGT 71
Query: 81 GKTATFSISILQSL-----DTQLRETQVLCLSPTRELAVQIQKVVLALGD----FMNVQC 131
GKT F I I Q L D+Q V+ ++PTR+LA+QI+ V + D C
Sbjct: 72 GKTFAFLIPIFQHLINTKFDSQYMVKAVI-VAPTRDLALQIEAEVKKIHDMNYGLKKYAC 130
Query: 132 HACIGGTNLSEDLRKLDYGQ-HVVSGTPGRVFDMI 165
+ +GGT+ + K++ + ++V TPGR+ D++
Sbjct: 131 VSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVL 165
>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex
With Adp
Length = 236
Score = 66.2 bits (160), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 41/141 (29%), Positives = 80/141 (56%), Gaps = 7/141 (4%)
Query: 27 DVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATF 86
+V ++ F + L + L+G+ + + IQ+++I ++G+DV+ A++G+GKT F
Sbjct: 20 NVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAF 79
Query: 87 SISILQSLDTQLRETQ-----VLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLS 141
+ +L++L +L+ T VL +SPTRELA Q +V+ +G + IGG +L
Sbjct: 80 LVPVLEAL-YRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLK 138
Query: 142 EDLRKLDYGQHVVSGTPGRVF 162
+ +++ +++ TPGR+
Sbjct: 139 HEAERIN-NINILVCTPGRLL 158
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 65.9 bits (159), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 35/126 (27%), Positives = 71/126 (56%), Gaps = 7/126 (5%)
Query: 39 LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL 98
+ E + + I GF+ + +Q ++I +++G++V+ +A++G+GKTA ++I IL+
Sbjct: 1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL----- 55
Query: 99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTP 158
+ L ++PTREL Q+ + +G +M+ + GG + ++ VV+ TP
Sbjct: 56 -GMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVRNADIVVA-TP 113
Query: 159 GRVFDM 164
GR+ D+
Sbjct: 114 GRLLDL 119
>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 = 64.7 bits (156), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 42/129 (32%), Positives = 71/129 (55%), Gaps = 7/129 (5%)
Query: 42 DLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL--R 99
DLL+ I G KP+ IQ ++ I++G D+I AQ+GTGKT ++ + LD+Q R
Sbjct: 30 DLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISR 89
Query: 100 ETQ----VLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVS 155
E + +L L+PTRELA+ ++ + + ++ GG N + + + G ++
Sbjct: 90 EQRNGPGMLVLTPTRELALHVEAEC-SKYSYKGLKSICIYGGRNRNGQIEDISKGVDIII 148
Query: 156 GTPGRVFDM 164
TPGR+ D+
Sbjct: 149 ATPGRLNDL 157
>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In
Complex With Adp
Length = 245
Score = 64.7 bits (156), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 40/130 (30%), Positives = 70/130 (53%), Gaps = 10/130 (7%)
Query: 43 LLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRE-T 101
LL+ I GF+ P+ IQ ++I ++ GR+++A A +G+GKT FSI IL L +
Sbjct: 40 LLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGF 99
Query: 102 QVLCLSPTRELAVQIQKVVLALGDFMNVQCH----ACIGGTNL-SEDLRKLDYGQHVVSG 156
+ L +SPTRELA QI + ++ + + + H A + + +K D ++
Sbjct: 100 RALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFD----ILVT 155
Query: 157 TPGRVFDMIR 166
TP R+ +++
Sbjct: 156 TPNRLIYLLK 165
>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human
Dead-Box Rna Helicase Ddx5 (P68)
Length = 253
Score = 62.0 bits (149), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 43/151 (28%), Positives = 72/151 (47%), Gaps = 7/151 (4%)
Query: 31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISI 90
V F +++ I F +P+AIQ + + G D++ AQ+G+GKT ++ +
Sbjct: 42 VLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPA 101
Query: 91 LQSLDTQL---RETQVLCL--SPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR 145
+ ++ Q R +CL +PTRELA Q+Q+V ++ GG +R
Sbjct: 102 IVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIR 161
Query: 146 KLDYGQHVVSGTPGRVFDMIRSSQG--RRTT 174
L+ G + TPGR+ D + + RRTT
Sbjct: 162 DLERGVEICIATPGRLIDFLECGKTNLRRTT 192
>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 = 62.0 bits (149), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 43/151 (28%), Positives = 72/151 (47%), Gaps = 7/151 (4%)
Query: 31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISI 90
V F +++ I F +P+AIQ + + G D++ AQ+G+GKT ++ +
Sbjct: 28 VLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPA 87
Query: 91 LQSLDTQL---RETQVLCL--SPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR 145
+ ++ Q R +CL +PTRELA Q+Q+V ++ GG +R
Sbjct: 88 IVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIR 147
Query: 146 KLDYGQHVVSGTPGRVFDMIRSSQG--RRTT 174
L+ G + TPGR+ D + + RRTT
Sbjct: 148 DLERGVEICIATPGRLIDFLECGKTNLRRTT 178
>pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus
Length = 1054
Score = 33.1 bits (74), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 41/100 (41%), Gaps = 7/100 (7%)
Query: 41 EDLLRGIYAYGFEK----PSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDT 96
ED L + F K P AIQ+ K I++ A A +G GKT S + SL
Sbjct: 39 EDFLLKEFVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKT---SFGLAMSLFL 95
Query: 97 QLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIG 136
L+ + + PT L +Q + + + V IG
Sbjct: 96 ALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIG 135
>pdb|1GL9|B Chain B, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
pdb|1GL9|C Chain C, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
Length = 1054
Score = 33.1 bits (74), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 41/100 (41%), Gaps = 7/100 (7%)
Query: 41 EDLLRGIYAYGFEK----PSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDT 96
ED L + F K P AIQ+ K I++ A A +G GKT S + SL
Sbjct: 39 EDFLLKEFVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKT---SFGLAMSLFL 95
Query: 97 QLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIG 136
L+ + + PT L +Q + + + V IG
Sbjct: 96 ALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIG 135
>pdb|2XGJ|A Chain A, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
Processing And Surveillance
pdb|2XGJ|B Chain B, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
Processing And Surveillance
Length = 1010
Score = 33.1 bits (74), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 34/118 (28%), Positives = 48/118 (40%), Gaps = 14/118 (11%)
Query: 58 IQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT-------- 109
Q +I I +G V+ A + GKT +I QSL + R V+ SP
Sbjct: 90 FQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQR---VIYTSPIKALSNQKY 146
Query: 110 RELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDY-GQHVVSGTPGRVFDMIR 166
REL + V L GD C+ T +E LR + Y G V+ +FD +
Sbjct: 147 RELLAEFGDVGLMTGDITINPDAGCLVMT--TEILRSMLYRGSEVMREVAWVIFDEVH 202
>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear
Exosome
Length = 1108
Score = 32.7 bits (73), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 34/118 (28%), Positives = 48/118 (40%), Gaps = 14/118 (11%)
Query: 58 IQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT-------- 109
Q +I I +G V+ A + GKT +I QSL + R V+ SP
Sbjct: 188 FQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQR---VIYTSPIKALSNQKY 244
Query: 110 RELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDY-GQHVVSGTPGRVFDMIR 166
REL + V L GD C+ T +E LR + Y G V+ +FD +
Sbjct: 245 RELLAEFGDVGLMTGDITINPDAGCLVMT--TEILRSMLYRGSEVMREVAWVIFDEVH 300
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 28.5 bits (62), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 73 IAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQ-IQKVVLALGDFMNVQC 131
+ Q G+GKT ++IL + + Q + PT LA+Q ++ V + F N+
Sbjct: 393 LLQGDVGSGKTVVAQLAILDNYEAGF---QTAFMVPTSILAIQHYRRTVESFSKF-NIHV 448
Query: 132 HACIGGTNLSE 142
IG T SE
Sbjct: 449 ALLIGATTPSE 459
>pdb|1TW0|A Chain A, Native Crystal Structure Of Spe16
pdb|1TW0|B Chain B, Native Crystal Structure Of Spe16
pdb|1TXC|A Chain A, Complex Crystal Structure Of Spe16 With Ans
pdb|1TXC|B Chain B, Complex Crystal Structure Of Spe16 With Ans
Length = 157
Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 132 HACIGGTNLSEDLRKLDYGQHVVSGTPG 159
++ +GGT L E L KL + VV+G+ G
Sbjct: 82 YSIVGGTGLPESLEKLSFETKVVAGSGG 109
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
0.317 0.133 0.368
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,875,446
Number of Sequences: 62578
Number of extensions: 183217
Number of successful extensions: 619
Number of sequences better than 100.0: 60
Number of HSP's better than 100.0 without gapping: 55
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 511
Number of HSP's gapped (non-prelim): 62
length of query: 178
length of database: 14,973,337
effective HSP length: 92
effective length of query: 86
effective length of database: 9,216,161
effective search space: 792589846
effective search space used: 792589846
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)