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= psy17636
(222 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human
Dead-Box Rna Helicase Ddx5 (P68)
Length = 253
Score = 72.0 bits (175), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 37/83 (44%), Positives = 48/83 (57%)
Query: 17 EVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKC 76
+ EKNFYQ H D+AR T QE + R ITV G + P PV +F F +M + +
Sbjct: 2 KFEKNFYQEHPDLARRTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQ 61
Query: 77 EYTSPTPIQAQAVPAALSGRDII 99
+T PT IQAQ P ALSG D++
Sbjct: 62 NFTEPTAIQAQGWPVALSGLDMV 84
Score = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/46 (52%), Positives = 32/46 (69%)
Query: 99 IEPQVRSICDHVRPNRQTLLFSATFKKRIEKLARDVLTDPIKIVQG 144
EPQ+R I D +RP+RQTL++SAT+ K + +LA D L D I I G
Sbjct: 207 FEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIG 252
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 54.3 bits (129), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 37/96 (38%), Positives = 56/96 (58%), Gaps = 6/96 (6%)
Query: 99 IEPQVRSIC--DHVRPN--RQTLLFSATFKKRIEKLARDVLTDPIKIVQGDIGEANTDIT 154
EPQ+R I D + P R T++FSATF K I+ LARD L + I + G +G + +IT
Sbjct: 192 FEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENIT 251
Query: 155 QVVINLPQTQKLTWLTHNLVEFLSTGSL-LIFVTKK 189
Q V+ + ++ K ++L +L+ SL L+FV K
Sbjct: 252 QKVVWVEESDKRSFLL-DLLNATGKDSLTLVFVETK 286
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 28/56 (50%)
Query: 44 SGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDII 99
S + +G + P + SF E++M + YT PTP+Q A+P RD++
Sbjct: 1 SMVEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLM 56
>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 = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/45 (53%), Positives = 32/45 (71%)
Query: 100 EPQVRSICDHVRPNRQTLLFSATFKKRIEKLARDVLTDPIKIVQG 144
EPQ+R I D +RP+RQTL++SAT+ K + +LA D L D I I G
Sbjct: 194 EPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIG 238
Score = 50.8 bits (120), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 36/67 (53%)
Query: 33 TPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAA 92
T QE + R ITV G + P PV +F F +M + + +T PT IQAQ P A
Sbjct: 4 TAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVA 63
Query: 93 LSGRDII 99
LSG D++
Sbjct: 64 LSGLDMV 70
>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 = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 51/89 (57%), Gaps = 3/89 (3%)
Query: 103 VRSICDHV--RPNRQTLLFSATFKKRIEKLARDVLTDPIKIVQGDIGEANTDITQVVINL 160
+R I HV RP QTL+FSATF + I+++A + L + + + G +G A +D+ Q + +
Sbjct: 224 MRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEV 283
Query: 161 PQTQKLTWLTHNLVEFLSTGSLLIFVTKK 189
+ K + L L E + G+++ TK+
Sbjct: 284 NKYAKRSKLIEILSE-QADGTIVFVETKR 311
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 31/54 (57%)
Query: 46 ITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDII 99
+ V+G+D P P+ F ++++ + K Y PTPIQ ++P SGRD++
Sbjct: 44 VKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLM 97
>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 = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/62 (43%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 100 EPQVRSICDHVRP----NRQTLLFSATFKKRIEKLARDVLTDPIKIVQGDIGEANTDITQ 155
EPQ+R I + NRQTL+FSATF K I+KLA D L + I + G +G + I Q
Sbjct: 192 EPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIKQ 251
Query: 156 VV 157
+
Sbjct: 252 EI 253
Score = 35.0 bits (79), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 45 GITVSGADPPYP----VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDII 99
I VS P Y + +F D + + Y PTPIQ A+PA L RDI+
Sbjct: 6 SIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIM 64
>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In
Complex With Adp
Length = 245
Score = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 40 LRAKSGITVSGADPPYPVSSFGH----FGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG 95
LR K I V G D P P+++F + + L++ + + PTPIQ QA+P L G
Sbjct: 7 LRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHG 66
Query: 96 RDII 99
R+++
Sbjct: 67 RELL 70
>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 = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 27/40 (67%)
Query: 100 EPQVRSICDHVRPNRQTLLFSATFKKRIEKLARDVLTDPI 139
EPQ+R I VRP+RQT++ SAT+ + +LA L DP+
Sbjct: 185 EPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPM 224
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 69 LMKALRKCEYTSPTPIQAQAVPAALSGRDII 99
L+K++ + PTPIQ+QA P L G D+I
Sbjct: 31 LLKSIIRVGILKPTPIQSQAWPIILQGIDLI 61
>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In
Complex With Amp
Length = 249
Score = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/41 (46%), Positives = 26/41 (63%)
Query: 59 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDII 99
+F G +VL +A + +T PT IQ +A+P AL GRDII
Sbjct: 44 TFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDII 84
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 26/41 (63%)
Query: 100 EPQVRSICDHVRPNRQTLLFSATFKKRIEKLARDVLTDPIK 140
E +V I + +R+T LFSAT K+++KL R L +P+K
Sbjct: 204 ETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVK 244
>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 = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 25/40 (62%)
Query: 60 FGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDII 99
F F +++AL T+PTPIQA A+P AL G+D+I
Sbjct: 3 FKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLI 42
Score = 33.9 bits (76), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 25/42 (59%)
Query: 100 EPQVRSICDHVRPNRQTLLFSATFKKRIEKLARDVLTDPIKI 141
E +V ++ P+RQTLLFSAT ++LA + +P+ I
Sbjct: 162 EEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLI 203
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 26/42 (61%)
Query: 58 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDII 99
++F F L+ + + + P+PIQ +A+P A++GRDI+
Sbjct: 21 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDIL 62
>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 = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 7/68 (10%)
Query: 60 FGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIEPQVRSICDHVRPNRQTLLF 119
F F +++AL T+PTPI+A A+P AL G+D+I Q R+ +TL F
Sbjct: 3 FKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIG-QARTGTG------KTLAF 55
Query: 120 SATFKKRI 127
+ +R+
Sbjct: 56 ALPIAERL 63
Score = 33.9 bits (76), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 25/42 (59%)
Query: 100 EPQVRSICDHVRPNRQTLLFSATFKKRIEKLARDVLTDPIKI 141
E +V ++ P+RQTLLFSAT ++LA + +P+ I
Sbjct: 162 EEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLI 203
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 35.4 bits (80), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 45/92 (48%), Gaps = 4/92 (4%)
Query: 114 RQTLLFSATFKKRIEKLARDVLTDPIKIVQGDIGEANT-DITQVVINLPQTQKLTWLTHN 172
+Q ++FSAT K I + R + DP++I D + + Q + L +K L +
Sbjct: 185 KQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKL-FD 243
Query: 173 LVEFLSTGSLLIFV--TKKCFELVNLIAKNYW 202
L++ L ++IFV ++C L L+ + +
Sbjct: 244 LLDVLEFNQVVIFVKSVQRCIALAQLLVEQNF 275
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 35.4 bits (80), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 45/92 (48%), Gaps = 4/92 (4%)
Query: 114 RQTLLFSATFKKRIEKLARDVLTDPIKIVQGDIGEANT-DITQVVINLPQTQKLTWLTHN 172
+Q ++FSAT K I + R + DP++I D + + Q + L +K L +
Sbjct: 185 KQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKL-FD 243
Query: 173 LVEFLSTGSLLIFV--TKKCFELVNLIAKNYW 202
L++ L ++IFV ++C L L+ + +
Sbjct: 244 LLDVLEFNQVVIFVKSVQRCIALAQLLVEQNF 275
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 35.0 bits (79), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 45/92 (48%), Gaps = 4/92 (4%)
Query: 114 RQTLLFSATFKKRIEKLARDVLTDPIKIVQGDIGEANT-DITQVVINLPQTQKLTWLTHN 172
+Q ++FSAT K I + R + DP++I D + + Q + L +K L +
Sbjct: 184 KQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKL-FD 242
Query: 173 LVEFLSTGSLLIFV--TKKCFELVNLIAKNYW 202
L++ L ++IFV ++C L L+ + +
Sbjct: 243 LLDVLEFNQVVIFVKSVQRCIALAQLLVEQNF 274
>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 = 35.0 bits (79), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 58 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDII 99
+ F + L+ + + + P+PIQ +++P ALSGRDI+
Sbjct: 3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDIL 44
Score = 26.9 bits (58), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 113 NRQTLLFSATFKKRIEKLARDVLTDPIKI 141
NRQ LL+SATF ++K L P +I
Sbjct: 177 NRQILLYSATFPLSVQKFMNSHLEKPYEI 205
>pdb|3LY5|A Chain A, Ddx18 Dead-Domain
pdb|3LY5|B Chain B, Ddx18 Dead-Domain
Length = 262
Score = 31.6 bits (70), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 45/95 (47%), Gaps = 8/95 (8%)
Query: 45 GITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTP------IQAQAVPAALSGRDI 98
G+ + G++ G+ G + ++ R ++ TP +Q + A D+
Sbjct: 158 GLIMGGSNRSAEAQKLGN-GINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDV 216
Query: 99 -IEPQVRSICDHVRPNRQTLLFSATFKKRIEKLAR 132
E +++ I + RQT+LFSAT +++E LAR
Sbjct: 217 GFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLAR 251
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 23/34 (67%)
Query: 66 DEVLMKALRKCEYTSPTPIQAQAVPAALSGRDII 99
+E +KA+++ +T+ T IQ +++ L GRD++
Sbjct: 62 NENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLL 95
>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex
With Adp
Length = 236
Score = 31.2 bits (69), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 24/36 (66%)
Query: 103 VRSICDHVRPNRQTLLFSATFKKRIEKLARDVLTDP 138
+ ++ +++ RQTLLFSAT K ++ LAR L +P
Sbjct: 192 MNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNP 227
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At
3.0 A Resolution
Length = 374
Score = 31.2 bits (69), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 59 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDII 99
+F G E L++ + + P+ IQ +A+ + GRD+I
Sbjct: 2 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVI 42
>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 = 31.2 bits (69), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 59 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDII 99
+F G E L++ + + P+ IQ +A+ + GRD+I
Sbjct: 17 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVI 57
Score = 27.3 bits (59), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 26/103 (25%), Positives = 43/103 (41%), Gaps = 28/103 (27%)
Query: 100 EPQVRSICDHVRPNRQTLLFSATFKKRIEKLARDVLTDPIKI--------VQG------- 144
+ Q+ + ++ P Q +L SAT I ++ +TDPI+I ++G
Sbjct: 176 KEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVA 235
Query: 145 ------------DIGEANTDITQVVINLPQTQKLTWLTHNLVE 175
D+ + T ITQ VI +K+ WLT + E
Sbjct: 236 VEREEWKFDTLCDLYDTLT-ITQAVIFCNTKRKVDWLTEKMRE 277
>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 = 31.2 bits (69), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 59 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDII 99
+F G E L++ + + P+ IQ +A+ + GRD+I
Sbjct: 39 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVI 79
Score = 26.9 bits (58), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 26/103 (25%), Positives = 43/103 (41%), Gaps = 28/103 (27%)
Query: 100 EPQVRSICDHVRPNRQTLLFSATFKKRIEKLARDVLTDPIKI--------VQG------- 144
+ Q+ + ++ P Q +L SAT I ++ +TDPI+I ++G
Sbjct: 198 KEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVA 257
Query: 145 ------------DIGEANTDITQVVINLPQTQKLTWLTHNLVE 175
D+ + T ITQ VI +K+ WLT + E
Sbjct: 258 VEREEWKFDTLCDLYDTLT-ITQAVIFCNTKRKVDWLTEKMRE 299
>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 = 31.2 bits (69), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 59 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDII 99
+F G E L++ + + P+ IQ +A+ + GRD+I
Sbjct: 39 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVI 79
Score = 26.9 bits (58), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 26/103 (25%), Positives = 43/103 (41%), Gaps = 28/103 (27%)
Query: 100 EPQVRSICDHVRPNRQTLLFSATFKKRIEKLARDVLTDPIKI--------VQG------- 144
+ Q+ + ++ P Q +L SAT I ++ +TDPI+I ++G
Sbjct: 198 KEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVA 257
Query: 145 ------------DIGEANTDITQVVINLPQTQKLTWLTHNLVE 175
D+ + T ITQ VI +K+ WLT + E
Sbjct: 258 VEREEWKFDTLCDLYDTLT-ITQAVIFCNTKRKVDWLTEKMRE 299
>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 = 31.2 bits (69), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 22/42 (52%)
Query: 58 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDII 99
+ F F F +++A++ + PT IQ + +P AL G +
Sbjct: 4 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESXV 45
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At
3.0 A Resolution
Length = 374
Score = 31.2 bits (69), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 59 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDII 99
+F G E L++ + + P+ IQ +A+ + GRD+I
Sbjct: 2 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVI 42
Score = 27.3 bits (59), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 26/103 (25%), Positives = 43/103 (41%), Gaps = 28/103 (27%)
Query: 100 EPQVRSICDHVRPNRQTLLFSATFKKRIEKLARDVLTDPIKI--------VQG------- 144
+ Q+ + ++ P Q +L SAT I ++ +TDPI+I ++G
Sbjct: 161 KEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVA 220
Query: 145 ------------DIGEANTDITQVVINLPQTQKLTWLTHNLVE 175
D+ + T ITQ VI +K+ WLT + E
Sbjct: 221 VEREEWKFDTLCDLYDTLT-ITQAVIFCNTKRKVDWLTEKMRE 262
>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 = 31.2 bits (69), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 59 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDII 99
+F G E L++ + + P+ IQ +A+ + GRD+I
Sbjct: 38 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVI 78
Score = 26.9 bits (58), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 26/103 (25%), Positives = 43/103 (41%), Gaps = 28/103 (27%)
Query: 100 EPQVRSICDHVRPNRQTLLFSATFKKRIEKLARDVLTDPIKI--------VQG------- 144
+ Q+ + ++ P Q +L SAT I ++ +TDPI+I ++G
Sbjct: 197 KEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVA 256
Query: 145 ------------DIGEANTDITQVVINLPQTQKLTWLTHNLVE 175
D+ + T ITQ VI +K+ WLT + E
Sbjct: 257 VEREEWKFDTLCDLYDTLT-ITQAVIFCNTKRKVDWLTEKMRE 298
>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214
Length = 235
Score = 30.4 bits (67), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 18/26 (69%)
Query: 113 NRQTLLFSATFKKRIEKLARDVLTDP 138
N Q LLFSATF+ + K A+ V+ DP
Sbjct: 200 NCQMLLFSATFEDSVWKFAQKVVPDP 225
>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
Length = 300
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 18/26 (69%)
Query: 113 NRQTLLFSATFKKRIEKLARDVLTDP 138
N Q LLFSATF+ + K A+ V+ DP
Sbjct: 267 NCQMLLFSATFEDSVWKFAQKVVPDP 292
>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 = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 18/26 (69%)
Query: 113 NRQTLLFSATFKKRIEKLARDVLTDP 138
N Q LLFSATF+ + K A+ V+ DP
Sbjct: 200 NCQMLLFSATFEDSVWKFAQKVVPDP 225
>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 = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 18/26 (69%)
Query: 113 NRQTLLFSATFKKRIEKLARDVLTDP 138
N Q LLFSATF+ + K A+ V+ DP
Sbjct: 237 NCQMLLFSATFEDSVWKFAQKVVPDP 262
>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 = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 18/26 (69%)
Query: 113 NRQTLLFSATFKKRIEKLARDVLTDP 138
N Q LLFSATF+ + K A+ V+ DP
Sbjct: 267 NCQMLLFSATFEDSVWKFAQKVVPDP 292
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 18/26 (69%)
Query: 113 NRQTLLFSATFKKRIEKLARDVLTDP 138
N Q LLFSATF+ + K A+ V+ DP
Sbjct: 216 NCQMLLFSATFEDSVWKFAQKVVPDP 241
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 1/82 (1%)
Query: 109 HVRP-NRQTLLFSATFKKRIEKLARDVLTDPIKIVQGDIGEANTDITQVVINLPQTQKLT 167
H+ P N Q +LFSATF +R+EK A + +I + I Q+ ++ +
Sbjct: 286 HLLPRNTQIVLFSATFSERVEKYAERFAPNANEIRLKTEELSVEGIKQLYMDCQSEEHKY 345
Query: 168 WLTHNLVEFLSTGSLLIFVTKK 189
+ L L+ G +IF KK
Sbjct: 346 NVLVELYGLLTIGQSIIFCKKK 367
>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 = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 113 NRQTLLFSATFKKRIEKLARDVLTDPIKI 141
+Q ++FSAT K I + R + DP++I
Sbjct: 190 EKQVMMFSATLSKEIRPVCRKFMQDPMEI 218
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 2/89 (2%)
Query: 102 QVRSICDHVRPNRQTLLFSATFKKRIEKLARDVLTDPIKIVQGDIGEANTDITQVVINLP 161
Q+ I + N Q +L SAT + ++ + + DPI+I+ I Q IN+
Sbjct: 203 QIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVE 262
Query: 162 QTQ-KLTWLTHNLVEFLSTGSLLIFVTKK 189
+ + KL L +L E L+ +IF+ +
Sbjct: 263 REEWKLDTLC-DLYETLTITQAVIFINTR 290
>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p
Length = 226
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 29/75 (38%), Gaps = 5/75 (6%)
Query: 53 PPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIEPQVRSICDHVRP 112
P Y SF G L+K + ++ P+ IQ +A+P L P I
Sbjct: 17 PLYSAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHN-----PPRNMIAQSQSG 71
Query: 113 NRQTLLFSATFKKRI 127
+T FS T R+
Sbjct: 72 TGKTAAFSLTMLTRV 86
>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 = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 5/67 (7%)
Query: 33 TPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAA 92
T Q+ R ++G V A+P + F +++ LR + P+P+Q +A+P
Sbjct: 4 TAQDLSSPRTRTG-DVLLAEP----ADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLG 58
Query: 93 LSGRDII 99
G D+I
Sbjct: 59 RCGLDLI 65
>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 = 28.5 bits (62), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 43/91 (47%), Gaps = 2/91 (2%)
Query: 100 EPQVRSICDHVRPNRQTLLFSATFKKRIEKLARDVLTDPIKIVQGDIGEANTDITQVVIN 159
+ Q+ I + N Q +L SAT + ++ + + DPI+I+ I Q IN
Sbjct: 175 KDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYIN 234
Query: 160 LPQTQ-KLTWLTHNLVEFLSTGSLLIFVTKK 189
+ + + KL L +L E L+ +IF+ +
Sbjct: 235 VEREEWKLDTLC-DLYETLTITQAVIFINTR 264
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 113 NRQTLLFSATFKKRIEKLARDVLTDP----IKIVQGDIGEANTDITQVVI 158
N +TLLFSAT +++KLA +++ + V + EA+ I Q V+
Sbjct: 213 NIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVV 262
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 113 NRQTLLFSATFKKRIEKLARDVLTDP----IKIVQGDIGEANTDITQVVI 158
N +TLLFSAT +++KLA +++ + V + EA+ I Q V+
Sbjct: 213 NIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVV 262
>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 = 28.1 bits (61), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 113 NRQTLLFSATFKKRIEKLARDVLTDP----IKIVQGDIGEANTDITQVVI 158
N +TLLFSAT +++KLA +++ + V + EA+ I Q V+
Sbjct: 264 NIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVV 313
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 26.9 bits (58), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 115 QTLLFSATFKKRIEKLARDVLTDPIKIVQGDIGEANTD-ITQVVINLP-QTQKLTWLTHN 172
Q +LFSATF + + A+ ++ + ++ E N D I Q+ ++ + K LT
Sbjct: 179 QLVLFSATFADAVRQYAKKIVPNA-NTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTE- 236
Query: 173 LVEFLSTGSLLIFVTKK 189
L ++ GS +IFV K
Sbjct: 237 LYGLMTIGSSIIFVATK 253
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
0.320 0.137 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,492,424
Number of Sequences: 62578
Number of extensions: 248749
Number of successful extensions: 750
Number of sequences better than 100.0: 43
Number of HSP's better than 100.0 without gapping: 39
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 674
Number of HSP's gapped (non-prelim): 82
length of query: 222
length of database: 14,973,337
effective HSP length: 95
effective length of query: 127
effective length of database: 9,028,427
effective search space: 1146610229
effective search space used: 1146610229
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: 49 (23.5 bits)