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= 012877
(454 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 87.4 bits (215), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 43/124 (34%), Positives = 76/124 (61%), Gaps = 3/124 (2%)
Query: 21 NSKILVFLTSCKQVKYVFEAFK-KLRPGIPLMCLYGRMKQDRRMAIYAQFCEKRS-VLFC 78
N K ++F + K ++ K + + +P++ +G++ Q++R ++ +F + S +L C
Sbjct: 288 NYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVC 347
Query: 79 TDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSVLFLTPTEMKMLEKL 138
TDV +RG+DF V V+Q+ P ++A+YIHR+GRTAR G SVLF+ E+ + +L
Sbjct: 348 TDVGARGMDF-PNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVREL 406
Query: 139 REAK 142
+AK
Sbjct: 407 EDAK 410
>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 = 87.0 bits (214), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 43/124 (34%), Positives = 76/124 (61%), Gaps = 3/124 (2%)
Query: 21 NSKILVFLTSCKQVKYVFEAFK-KLRPGIPLMCLYGRMKQDRRMAIYAQFCEKRS-VLFC 78
N K ++F + K ++ K + + +P++ +G++ Q++R ++ +F + S +L C
Sbjct: 339 NYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVC 398
Query: 79 TDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSVLFLTPTEMKMLEKL 138
TDV +RG+DF V V+Q+ P ++A+YIHR+GRTAR G SVLF+ E+ + +L
Sbjct: 399 TDVGARGMDFPN-VHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVREL 457
Query: 139 REAK 142
+AK
Sbjct: 458 EDAK 461
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 87.0 bits (214), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 43/124 (34%), Positives = 76/124 (61%), Gaps = 3/124 (2%)
Query: 21 NSKILVFLTSCKQVKYVFEAFK-KLRPGIPLMCLYGRMKQDRRMAIYAQFCEKRS-VLFC 78
N K ++F + K ++ K + + +P++ +G++ Q++R ++ +F + S +L C
Sbjct: 288 NYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVC 347
Query: 79 TDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSVLFLTPTEMKMLEKL 138
TDV +RG+DF V V+Q+ P ++A+YIHR+GRTAR G SVLF+ E+ + +L
Sbjct: 348 TDVGARGMDFPN-VHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVREL 406
Query: 139 REAK 142
+AK
Sbjct: 407 EDAK 410
>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric
Rna-Dna Duplex
pdb|4DB4|B Chain B, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric
Rna-Dna Duplex
Length = 256
Score = 85.9 bits (211), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 43/124 (34%), Positives = 76/124 (61%), Gaps = 3/124 (2%)
Query: 21 NSKILVFLTSCKQVKYVFEAFK-KLRPGIPLMCLYGRMKQDRRMAIYAQFCEKRS-VLFC 78
N K ++F + K ++ K + + +P++ +G++ Q++R ++ +F + S +L C
Sbjct: 33 NYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVC 92
Query: 79 TDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSVLFLTPTEMKMLEKL 138
TDV +RG+DF V V+Q+ P ++A+YIHR+GRTAR G SVLF+ E+ + +L
Sbjct: 93 TDVGARGMDFPN-VHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVREL 151
Query: 139 REAK 142
+AK
Sbjct: 152 EDAK 155
>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
pdb|4DB2|D Chain D, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
Length = 257
Score = 85.9 bits (211), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 43/124 (34%), Positives = 76/124 (61%), Gaps = 3/124 (2%)
Query: 21 NSKILVFLTSCKQVKYVFEAFK-KLRPGIPLMCLYGRMKQDRRMAIYAQFCEKRS-VLFC 78
N K ++F + K ++ K + + +P++ +G++ Q++R ++ +F + S +L C
Sbjct: 33 NYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVC 92
Query: 79 TDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSVLFLTPTEMKMLEKL 138
TDV +RG+DF V V+Q+ P ++A+YIHR+GRTAR G SVLF+ E+ + +L
Sbjct: 93 TDVGARGMDFPN-VHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVREL 151
Query: 139 REAK 142
+AK
Sbjct: 152 EDAK 155
>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
pdb|4DB2|B Chain B, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
Length = 257
Score = 85.5 bits (210), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 43/124 (34%), Positives = 76/124 (61%), Gaps = 3/124 (2%)
Query: 21 NSKILVFLTSCKQVKYVFEAFK-KLRPGIPLMCLYGRMKQDRRMAIYAQFCEKRS-VLFC 78
N K ++F + K ++ K + + +P++ +G++ Q++R ++ +F + S +L C
Sbjct: 33 NYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVC 92
Query: 79 TDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSVLFLTPTEMKMLEKL 138
TDV +RG+DF V V+Q+ P ++A+YIHR+GRTAR G SVLF+ E+ + +L
Sbjct: 93 TDVGARGMDFPN-VHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVREL 151
Query: 139 REAK 142
+AK
Sbjct: 152 EDAK 155
>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain
pdb|2P6N|B Chain B, Human Dead-box Rna Helicase Ddx41, Helicase Domain
Length = 191
Score = 62.0 bits (149), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 36/105 (34%), Positives = 56/105 (53%), Gaps = 4/105 (3%)
Query: 24 ILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAIYAQFCE-KRSVLFCTDVA 82
+L+F V + E L G+ + ++G Q+ R F E K+ VL TDVA
Sbjct: 57 VLIFAEKKADVDAIHEYL--LLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVA 114
Query: 83 SRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSVLFL 127
S+GLDF A+ V+ D PE++ +Y+HR+GRT + G + F+
Sbjct: 115 SKGLDF-PAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFI 158
>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 = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 46/166 (27%), Positives = 72/166 (43%), Gaps = 27/166 (16%)
Query: 2 IVPLEQKLDMLWSFIKAHLNSKI------------------------LVFLTSCKQVKYV 37
I+ L +K +SFIKA +N+ I L CK +
Sbjct: 192 ILNLAKKYXGDYSFIKAKINANIEQSYVEVNENERFEALCRLLKNKEFYGLVFCKTKRDT 251
Query: 38 FEAFKKLRP-GIPLMCLYGRMKQDRRMAIYAQFCEKR-SVLFCTDVASRGLDFNKAVDWV 95
E LR G ++G + Q +R + F +K+ +L TDV SRG+D N ++ V
Sbjct: 252 KELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVXSRGIDVND-LNCV 310
Query: 96 VQVDCPEDVASYIHRVGRTARYNSGGRSVLFLTPTEMKMLEKLREA 141
+ P++ SY HR+GRT R G+++ + E K L + A
Sbjct: 311 INYHLPQNPESYXHRIGRTGRAGKKGKAISIINRREYKKLRYIERA 356
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 38/120 (31%), Positives = 65/120 (54%), Gaps = 6/120 (5%)
Query: 7 QKLDMLWS-FIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAI 65
QKL L + F K +N I +F S +V+ + + L G + RMKQ R +
Sbjct: 244 QKLHCLNTLFSKLQINQAI-IFCNSTNRVELLAKKITDL--GYSCYYSHARMKQQERNKV 300
Query: 66 YAQFCE-KRSVLFCTDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSV 124
+ +F + K L C+D+ +RG+D +AV+ V+ D P+ +Y+HR+GR+ R+ G ++
Sbjct: 301 FHEFRQGKVRTLVCSDLLTRGIDI-QAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAI 359
>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The
Bacillus Subtilis Yxin Protein
pdb|2HJV|B Chain B, Structure Of The Second Domain (Residues 207-368) Of The
Bacillus Subtilis Yxin Protein
Length = 163
Score = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 40/138 (28%), Positives = 66/138 (47%), Gaps = 8/138 (5%)
Query: 6 EQKLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAI 65
E K +L + ++F + + V + + L G P ++G M Q+ R +
Sbjct: 20 ENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDL--GYPCDKIHGGMIQEDRFDV 77
Query: 66 YAQFCEKRS---VLFCTDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGR 122
+F KR L TDVA+RG+D + V+ D P + SY+HR GRT R + G+
Sbjct: 78 MNEF--KRGEYRYLVATDVAARGIDIEN-ISLVINYDLPLEKESYVHRTGRTGRAGNKGK 134
Query: 123 SVLFLTPTEMKMLEKLRE 140
++ F+T E + L + E
Sbjct: 135 AISFVTAFEKRFLADIEE 152
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 38/136 (27%), Positives = 69/136 (50%), Gaps = 4/136 (2%)
Query: 6 EQKLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAI 65
E K D L ++ ++F + ++V ++ E ++ + ++G M Q R +I
Sbjct: 225 EWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMRE--ANFTVSSMHGDMPQKERESI 282
Query: 66 YAQFCEKRS-VLFCTDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSV 124
+F S VL TDV +RGLD + V ++ D P + YIHR+GR+ RY G +V
Sbjct: 283 MKEFRSGASRVLISTDVWARGLDVPQ-VSLIINYDLPNNRELYIHRIGRSGRYGRKGVAV 341
Query: 125 LFLTPTEMKMLEKLRE 140
F+ ++++L + +
Sbjct: 342 NFVKNDDIRVLRDIEQ 357
>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 = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 37/136 (27%), Positives = 69/136 (50%), Gaps = 4/136 (2%)
Query: 6 EQKLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAI 65
E K D L ++ ++F + ++V ++ E ++ + ++G M Q R +I
Sbjct: 261 EWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMRE--ANFTVSSMHGDMPQKERESI 318
Query: 66 YAQFCEKRS-VLFCTDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSV 124
+F S VL TDV +RGLD + V ++ D P + YIHR+GR+ RY G ++
Sbjct: 319 MKEFRSGASRVLISTDVWARGLDVPQ-VSLIINYDLPNNRELYIHRIGRSGRYGRKGVAI 377
Query: 125 LFLTPTEMKMLEKLRE 140
F+ ++++L + +
Sbjct: 378 NFVKNDDIRILRDIEQ 393
>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 = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 37/136 (27%), Positives = 69/136 (50%), Gaps = 4/136 (2%)
Query: 6 EQKLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAI 65
E K D L ++ ++F + ++V ++ E ++ + ++G M Q R +I
Sbjct: 262 EWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMRE--ANFTVSSMHGDMPQKERESI 319
Query: 66 YAQFCEKRS-VLFCTDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSV 124
+F S VL TDV +RGLD + V ++ D P + YIHR+GR+ RY G ++
Sbjct: 320 MKEFRSGASRVLISTDVWARGLDVPQ-VSLIINYDLPNNRELYIHRIGRSGRYGRKGVAI 378
Query: 125 LFLTPTEMKMLEKLRE 140
F+ ++++L + +
Sbjct: 379 NFVKNDDIRILRDIEQ 394
>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 = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 37/136 (27%), Positives = 69/136 (50%), Gaps = 4/136 (2%)
Query: 6 EQKLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAI 65
E K D L ++ ++F + ++V ++ E ++ + ++G M Q R +I
Sbjct: 262 EWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMRE--ANFTVSSMHGDMPQKERESI 319
Query: 66 YAQFCEKRS-VLFCTDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSV 124
+F S VL TDV +RGLD + V ++ D P + YIHR+GR+ RY G ++
Sbjct: 320 MKEFRSGASRVLISTDVWARGLDVPQ-VSLIINYDLPNNRELYIHRIGRSGRYGRKGVAI 378
Query: 125 LFLTPTEMKMLEKLRE 140
F+ ++++L + +
Sbjct: 379 NFVKNDDIRILRDIEQ 394
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 59.7 bits (143), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 38/136 (27%), Positives = 69/136 (50%), Gaps = 4/136 (2%)
Query: 6 EQKLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAI 65
E K D L ++ ++F + ++V ++ E ++ + ++G M Q R +I
Sbjct: 225 EWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMRE--ANFTVSSMHGDMPQKERESI 282
Query: 66 YAQFCEKRS-VLFCTDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSV 124
+F S VL TDV +RGLD + V ++ D P + YIHR+GR+ RY G +V
Sbjct: 283 MKEFRSGASRVLISTDVWARGLDVPQ-VSLIINYDLPNNRELYIHRIGRSGRYGRKGVAV 341
Query: 125 LFLTPTEMKMLEKLRE 140
F+ ++++L + +
Sbjct: 342 NFVKNDDIRVLRDIEQ 357
>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 = 59.7 bits (143), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 37/136 (27%), Positives = 69/136 (50%), Gaps = 4/136 (2%)
Query: 6 EQKLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAI 65
E K D L ++ ++F + ++V ++ E ++ + ++G M Q R +I
Sbjct: 240 EWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMRE--ANFTVSSMHGDMPQKERESI 297
Query: 66 YAQFCEKRS-VLFCTDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSV 124
+F S VL TDV +RGLD + V ++ D P + YIHR+GR+ RY G ++
Sbjct: 298 MKEFRSGASRVLISTDVWARGLDVPQ-VSLIINYDLPNNRELYIHRIGRSGRYGRKGVAI 356
Query: 125 LFLTPTEMKMLEKLRE 140
F+ ++++L + +
Sbjct: 357 NFVKNDDIRILRDIEQ 372
>pdb|2WAX|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
pdb|2WAX|C Chain C, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
pdb|2WAY|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
pdb|2WAY|C Chain C, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
Length = 193
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 38/139 (27%), Positives = 74/139 (53%), Gaps = 12/139 (8%)
Query: 7 QKLDMLWS-FIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAI 65
QK+ L + F + +N I +F S ++V+ + + +L G ++ +M+Q+ R +
Sbjct: 30 QKVHCLNTLFSRLQINQSI-IFCNSSQRVELLAKKISQL--GYSCFYIHAKMRQEHRNRV 86
Query: 66 YAQF----CEKRSVLFCTDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGG 121
+ F C L CTD+ +RG+D +AV+ V+ D P+ +Y+HR+GR+ R+ G
Sbjct: 87 FHDFRNGLCRN---LVCTDLFTRGIDI-QAVNVVINFDFPKLAETYLHRIGRSGRFGHLG 142
Query: 122 RSVLFLTPTEMKMLEKLRE 140
++ +T + L+ + E
Sbjct: 143 LAINLITYDDRFNLKSIEE 161
>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56
Length = 172
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/108 (25%), Positives = 61/108 (56%), Gaps = 4/108 (3%)
Query: 22 SKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAIYAQFCE-KRSVLFCTD 80
+++++F+ S ++ + + + P + ++ M Q+ R++ Y QF + +R +L T+
Sbjct: 32 NQVVIFVKSVQRCIALAQLL--VEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN 89
Query: 81 VASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSVLFLT 128
+ RG+D + V+ D PED +Y+HRV R R+ + G ++ F++
Sbjct: 90 LFGRGMDIER-VNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVS 136
>pdb|2YJT|D Chain D, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound
To Regulator Of Ribonuclease Activity A (Rraa)
Length = 170
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 41/135 (30%), Positives = 66/135 (48%), Gaps = 4/135 (2%)
Query: 5 LEQKLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMA 64
LE K +L +K ++ +VF+ ++V + ++ GI L G M Q +R
Sbjct: 14 LEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLRE--AGINNCYLEGEMVQGKRNE 71
Query: 65 IYAQFCEKR-SVLFCTDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRS 123
+ E R +VL TDVA+RG+D V V D P +Y+HR+GRTAR G +
Sbjct: 72 AIKRLTEGRVNVLVATDVAARGIDIPD-VSHVFNFDMPRSGDTYLHRIGRTARAGRKGTA 130
Query: 124 VLFLTPTEMKMLEKL 138
+ + + +L K+
Sbjct: 131 ISLVEAHDHLLLGKV 145
>pdb|2JGN|A Chain A, Ddx3 Helicase Domain
pdb|2JGN|B Chain B, Ddx3 Helicase Domain
pdb|2JGN|C Chain C, Ddx3 Helicase Domain
Length = 185
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 34/101 (33%), Positives = 52/101 (51%), Gaps = 6/101 (5%)
Query: 47 GIPLMCLYG-RMKQDRRMAIYAQFCEKRSVLFCTDVASRGLDFNKAVDWVVQVDCPEDVA 105
G ++G R ++DR A++ K +L T VA+RGLD + V V+ D P D+
Sbjct: 70 GYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISN-VKHVINFDLPSDIE 128
Query: 106 SYIHRVGRTARYNSGGRSVLFLTPTEMK----MLEKLREAK 142
Y+HR+GRT R + G + F + +L+ L EAK
Sbjct: 129 EYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAK 169
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 56.6 bits (135), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 48/82 (58%), Gaps = 2/82 (2%)
Query: 48 IPLMCLYGRMKQDRRMAIYAQFCE-KRSVLFCTDVASRGLDFNKAVDWVVQVDCPEDVAS 106
P + ++ M Q+ R++ Y QF + +R +L T++ RG+D + V+ D PED +
Sbjct: 274 FPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIER-VNIAFNYDMPEDSDT 332
Query: 107 YIHRVGRTARYNSGGRSVLFLT 128
Y+HRV R R+ + G ++ F++
Sbjct: 333 YLHRVARAGRFGTKGLAITFVS 354
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 48/82 (58%), Gaps = 2/82 (2%)
Query: 48 IPLMCLYGRMKQDRRMAIYAQFCE-KRSVLFCTDVASRGLDFNKAVDWVVQVDCPEDVAS 106
P + ++ M Q+ R++ Y QF + +R +L T++ RG+D + V+ D PED +
Sbjct: 275 FPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIER-VNIAFNYDMPEDSDT 333
Query: 107 YIHRVGRTARYNSGGRSVLFLT 128
Y+HRV R R+ + G ++ F++
Sbjct: 334 YLHRVARAGRFGTKGLAITFVS 355
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 48/82 (58%), Gaps = 2/82 (2%)
Query: 48 IPLMCLYGRMKQDRRMAIYAQFCE-KRSVLFCTDVASRGLDFNKAVDWVVQVDCPEDVAS 106
P + ++ M Q+ R++ Y QF + +R +L T++ RG+D + V+ D PED +
Sbjct: 275 FPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIER-VNIAFNYDMPEDSDT 333
Query: 107 YIHRVGRTARYNSGGRSVLFLT 128
Y+HRV R R+ + G ++ F++
Sbjct: 334 YLHRVARAGRFGTKGLAITFVS 355
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 25/53 (47%), Positives = 35/53 (66%), Gaps = 1/53 (1%)
Query: 75 VLFCTDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSVLFL 127
+L TDVASRGLD V+ V+ D P+D+ +YIHR+GRT R G ++ F+
Sbjct: 269 MLITTDVASRGLDI-PLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFI 320
>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 = 55.5 bits (132), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 38/127 (29%), Positives = 59/127 (46%), Gaps = 10/127 (7%)
Query: 8 KLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAIYA 67
K D+L ++F+ + K ++ K G + L+G ++ R +
Sbjct: 230 KFDVLTELYGVMTIGSSIIFVATKKTANVLYGKLKS--EGHEVSILHGDLQTQERDRLID 287
Query: 68 QFCEKRS-VLFCTDVASRGLDFNKAVDWVVQVDCP------EDVASYIHRVGRTARYNSG 120
F E RS VL T+V +RG+D V VV D P D A+YIHR+GRT R+
Sbjct: 288 DFREGRSKVLITTNVLARGIDI-PTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRK 346
Query: 121 GRSVLFL 127
G ++ F+
Sbjct: 347 GVAISFV 353
>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 = 55.1 bits (131), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 49 PLMCLYG-RMKQDRRMAIYAQFCEKRSVLFCTDVASRGLDFNKAVDWVVQVDCPEDVASY 107
P ++G R++ R A+ VL T VASRGLD K + V+ D P + Y
Sbjct: 326 PTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDI-KNIKHVINYDMPSKIDDY 384
Query: 108 IHRVGRTARYNSGGRSVLFLTP 129
+HR+GRT R + GR+ F P
Sbjct: 385 VHRIGRTGRVGNNGRATSFFDP 406
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 55.1 bits (131), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 38/127 (29%), Positives = 59/127 (46%), Gaps = 10/127 (7%)
Query: 8 KLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAIYA 67
K D+L ++F+ + K ++ K G + L+G ++ R +
Sbjct: 230 KFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKS--EGHEVSILHGDLQTQERDRLID 287
Query: 68 QFCEKRS-VLFCTDVASRGLDFNKAVDWVVQVDCP------EDVASYIHRVGRTARYNSG 120
F E RS VL T+V +RG+D V VV D P D A+YIHR+GRT R+
Sbjct: 288 DFREGRSKVLITTNVLARGIDI-PTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRK 346
Query: 121 GRSVLFL 127
G ++ F+
Sbjct: 347 GVAISFV 353
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 55.1 bits (131), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 34/101 (33%), Positives = 52/101 (51%), Gaps = 6/101 (5%)
Query: 47 GIPLMCLYG-RMKQDRRMAIYAQFCEKRSVLFCTDVASRGLDFNKAVDWVVQVDCPEDVA 105
G ++G R ++DR A++ K +L T VA+RGLD + V V+ D P D+
Sbjct: 300 GYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISN-VKHVINFDLPSDIE 358
Query: 106 SYIHRVGRTARYNSGGRSVLFLTPTEMK----MLEKLREAK 142
Y+HR+GRT R + G + F + +L+ L EAK
Sbjct: 359 EYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAK 399
>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1
H337r And Ip6
pdb|3PEV|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1
And Ip6
Length = 188
Score = 54.7 bits (130), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 38/127 (29%), Positives = 59/127 (46%), Gaps = 10/127 (7%)
Query: 8 KLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAIYA 67
K D+L ++F+ + K ++ K G + L+G ++ R +
Sbjct: 23 KFDVLTELYGVXTIGSSIIFVATKKTANVLYGKLKS--EGHEVSILHGDLQTQERDRLID 80
Query: 68 QFCEKRS-VLFCTDVASRGLDFNKAVDWVVQVDCP------EDVASYIHRVGRTARYNSG 120
F E RS VL T+V +RG+D V VV D P D A+YIHR+GRT R+
Sbjct: 81 DFREGRSKVLITTNVLARGIDI-PTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRK 139
Query: 121 GRSVLFL 127
G ++ F+
Sbjct: 140 GVAISFV 146
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 38/127 (29%), Positives = 59/127 (46%), Gaps = 10/127 (7%)
Query: 8 KLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAIYA 67
K D+L ++F+ + K ++ K G + L+G ++ R +
Sbjct: 22 KFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKS--EGHEVSILHGDLQTQERDRLID 79
Query: 68 QFCEKRS-VLFCTDVASRGLDFNKAVDWVVQVDCP------EDVASYIHRVGRTARYNSG 120
F E RS VL T+V +RG+D V VV D P D A+YIHR+GRT R+
Sbjct: 80 DFREGRSKVLITTNVLARGIDI-PTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRK 138
Query: 121 GRSVLFL 127
G ++ F+
Sbjct: 139 GVAISFV 145
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 38/127 (29%), Positives = 59/127 (46%), Gaps = 10/127 (7%)
Query: 8 KLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAIYA 67
K D+L ++F+ + K ++ K G + L+G ++ R +
Sbjct: 24 KFDVLTELYGLXTIGSSIIFVATKKTANVLYGKLKS--EGHEVSILHGDLQTQERDRLID 81
Query: 68 QFCEKRS-VLFCTDVASRGLDFNKAVDWVVQVDCP------EDVASYIHRVGRTARYNSG 120
F E RS VL T+V +RG+D V VV D P D A+YIHR+GRT R+
Sbjct: 82 DFREGRSKVLITTNVLARGIDI-PTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRK 140
Query: 121 GRSVLFL 127
G ++ F+
Sbjct: 141 GVAISFV 147
>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 = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 42/152 (27%), Positives = 73/152 (48%), Gaps = 16/152 (10%)
Query: 6 EQKLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAI 65
++K L + A ++ ++F + K ++ K G + L G M ++R A+
Sbjct: 318 DEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSK--EGHQVALLSGEMMVEQRAAV 375
Query: 66 YAQFCE-KRSVLFCTDVASRGLDFNKAVDWVVQVDCP------EDVASYIHRVGRTARYN 118
+F E K VL T+V +RG+D + V V+ D P D +Y+HR+GRT R+
Sbjct: 376 IERFREGKEKVLVTTNVCARGIDVEQ-VSVVINFDLPVDKDGNPDNETYLHRIGRTGRFG 434
Query: 119 SGGRSVLFL-TPTEMKMLEKLREAKIPIHFTK 149
G +V + + M +L +++E HF K
Sbjct: 435 KRGLAVNMVDSKHSMNILNRIQE-----HFNK 461
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 42/152 (27%), Positives = 73/152 (48%), Gaps = 16/152 (10%)
Query: 6 EQKLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAI 65
++K L + A ++ ++F + K ++ K G + L G M ++R A+
Sbjct: 267 DEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSK--EGHQVALLSGEMMVEQRAAV 324
Query: 66 YAQFCE-KRSVLFCTDVASRGLDFNKAVDWVVQVDCP------EDVASYIHRVGRTARYN 118
+F E K VL T+V +RG+D + V V+ D P D +Y+HR+GRT R+
Sbjct: 325 IERFREGKEKVLVTTNVCARGIDVEQ-VSVVINFDLPVDKDGNPDNETYLHRIGRTGRFG 383
Query: 119 SGGRSVLFL-TPTEMKMLEKLREAKIPIHFTK 149
G +V + + M +L +++E HF K
Sbjct: 384 KRGLAVNMVDSKHSMNILNRIQE-----HFNK 410
>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 = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 42/152 (27%), Positives = 73/152 (48%), Gaps = 16/152 (10%)
Query: 6 EQKLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAI 65
++K L + A ++ ++F + K ++ K G + L G M ++R A+
Sbjct: 251 DEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSK--EGHQVALLSGEMMVEQRAAV 308
Query: 66 YAQFCE-KRSVLFCTDVASRGLDFNKAVDWVVQVDCP------EDVASYIHRVGRTARYN 118
+F E K VL T+V +RG+D + V V+ D P D +Y+HR+GRT R+
Sbjct: 309 IERFREGKEKVLVTTNVCARGIDVEQ-VSVVINFDLPVDKDGNPDNETYLHRIGRTGRFG 367
Query: 119 SGGRSVLFL-TPTEMKMLEKLREAKIPIHFTK 149
G +V + + M +L +++E HF K
Sbjct: 368 KRGLAVNMVDSKHSMNILNRIQE-----HFNK 394
>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 = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 42/152 (27%), Positives = 73/152 (48%), Gaps = 16/152 (10%)
Query: 6 EQKLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAI 65
++K L + A ++ ++F + K ++ K G + L G M ++R A+
Sbjct: 288 DEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSK--EGHQVALLSGEMMVEQRAAV 345
Query: 66 YAQFCE-KRSVLFCTDVASRGLDFNKAVDWVVQVDCP------EDVASYIHRVGRTARYN 118
+F E K VL T+V +RG+D + V V+ D P D +Y+HR+GRT R+
Sbjct: 346 IERFREGKEKVLVTTNVCARGIDVEQ-VSVVINFDLPVDKDGNPDNETYLHRIGRTGRFG 404
Query: 119 SGGRSVLFL-TPTEMKMLEKLREAKIPIHFTK 149
G +V + + M +L +++E HF K
Sbjct: 405 KRGLAVNMVDSKHSMNILNRIQE-----HFNK 431
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 33/88 (37%), Positives = 49/88 (55%), Gaps = 8/88 (9%)
Query: 47 GIPLMCLYGRMKQDRRMAIYAQFCEKRS-VLFCTDVASRGLDFNKAVDWVVQVDCPEDVA 105
G + CL G ++ +R AI F S VL T+V +RG+D ++ V+ VV D P D A
Sbjct: 381 GHTVACLTGNLEGAQRDAIMDSFRVGTSKVLVTTNVIARGIDVSQ-VNLVVNYDMPLDQA 439
Query: 106 ------SYIHRVGRTARYNSGGRSVLFL 127
+Y+HR+GRT R+ G S+ F+
Sbjct: 440 GRPDPQTYLHRIGRTGRFGRVGVSINFV 467
>pdb|3I32|A Chain A, Dimeric Structure Of A Hera Helicase Fragment Including
The C-Terminal Reca Domain, The Dimerization Domain, And
The Rna Binding Domain
Length = 300
Score = 51.6 bits (122), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 47/139 (33%), Positives = 68/139 (48%), Gaps = 4/139 (2%)
Query: 4 PLEQKLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRM 63
P+ +L++L + + +VF + + + + + LR G P L+G M Q R
Sbjct: 11 PVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGL--LRLGHPAQALHGDMSQGERE 68
Query: 64 AIYAQFCEKR-SVLFCTDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGR 122
+ F + VL TDVA+RGLD + VD VV P+ +Y HR GRT R GGR
Sbjct: 69 RVMGAFRQGEVRVLVATDVAARGLDIPQ-VDLVVHYRMPDRAEAYQHRSGRTGRAGRGGR 127
Query: 123 SVLFLTPTEMKMLEKLREA 141
VL P E + +E L A
Sbjct: 128 VVLLYGPRERRDVEALERA 146
>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera
Form 2, Complete Dimer, Symmetric
pdb|3EAQ|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase Hera
Form 2, Complete Dimer, Symmetric
pdb|3EAR|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Partial Dimer
pdb|3EAR|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Partial Dimer
pdb|3EAS|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Complete Dimer, Asymmetric
pdb|3EAS|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Complete Dimer, Asymmetric
Length = 212
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 46/139 (33%), Positives = 68/139 (48%), Gaps = 4/139 (2%)
Query: 4 PLEQKLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRM 63
P+ +L++L + + +VF + + + + + LR G P L+G + Q R
Sbjct: 14 PVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGL--LRLGHPAQALHGDLSQGERE 71
Query: 64 AIYAQFCEKR-SVLFCTDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGR 122
+ F + VL TDVA+RGLD + VD VV P+ +Y HR GRT R GGR
Sbjct: 72 RVLGAFRQGEVRVLVATDVAARGLDIPQ-VDLVVHYRLPDRAEAYQHRSGRTGRAGRGGR 130
Query: 123 SVLFLTPTEMKMLEKLREA 141
VL P E + +E L A
Sbjct: 131 VVLLYGPRERRDVEALERA 149
>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25
Rna Helicase
pdb|2RB4|B Chain B, Crystal Structure Of The Helicase Domain Of Human Ddx25
Rna Helicase
Length = 175
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 36/136 (26%), Positives = 67/136 (49%), Gaps = 15/136 (11%)
Query: 22 SKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAIYAQFCE-KRSVLFCTD 80
+ ++F + + K++ + ++ G + L G + ++R +I +F + K VL T+
Sbjct: 35 GQAIIFCQTRRNAKWL--TVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTN 92
Query: 81 VASRGLDFNKAVDWVVQVDCP------EDVASYIHRVGRTARYNSGGRSVLFLTPTEMKM 134
V +RG+D K V VV D P D +Y+HR+GRT R+ G + + E+
Sbjct: 93 VCARGIDV-KQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPS 151
Query: 135 LEKLREAKIPIHFTKA 150
L K+++ HF +
Sbjct: 152 LMKIQD-----HFNSS 162
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 32/108 (29%), Positives = 55/108 (50%), Gaps = 4/108 (3%)
Query: 6 EQKLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAI 65
E KLD L + ++ ++F+ + ++V ++ E K + ++G M Q R I
Sbjct: 265 EWKLDTLCDLYETLTITQAVIFINTRRKVDWLTE--KMHARDFTVSAMHGDMDQKERDVI 322
Query: 66 YAQFCEKRS-VLFCTDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVG 112
+F S VL TD+ +RG+D + V V+ D P + +YIHR+G
Sbjct: 323 MREFRSGSSRVLITTDLLARGIDVQQ-VSLVINYDLPTNRENYIHRIG 369
>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 = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 32/108 (29%), Positives = 55/108 (50%), Gaps = 4/108 (3%)
Query: 6 EQKLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAI 65
E KLD L + ++ ++F+ + ++V ++ E K + ++G M Q R I
Sbjct: 239 EWKLDTLCDLYETLTITQAVIFINTRRKVDWLTE--KMHARDFTVSAMHGDMDQKERDVI 296
Query: 66 YAQFCEKRS-VLFCTDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVG 112
+F S VL TD+ +RG+D + V V+ D P + +YIHR+G
Sbjct: 297 MREFRSGSSRVLITTDLLARGIDVQQ-VSLVINYDLPTNRENYIHRIG 343
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 30/135 (22%), Positives = 57/135 (42%), Gaps = 4/135 (2%)
Query: 9 LDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAIYAQ 68
LD L +++ +++ S +V+ A + GI + ++ + R + +
Sbjct: 224 LDQLMRYVQEQRGKSGIIYCNSRAKVEDT--AARLQSKGISAAAYHAGLENNVRADVQEK 281
Query: 69 FCEKRSVLFCTDVASRGLDFNKA-VDWVVQVDCPEDVASYIHRVGRTARYNSGGRSVLFL 127
F ++ + + G+ NK V +VV D P ++ SY GR R ++LF
Sbjct: 282 F-QRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFY 340
Query: 128 TPTEMKMLEKLREAK 142
P +M L + E K
Sbjct: 341 DPADMAWLRRCLEEK 355
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 37.0 bits (84), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 37/118 (31%), Positives = 58/118 (49%), Gaps = 6/118 (5%)
Query: 31 CKQVKYVFEAFKKLRPG-IPLMCLYGRMKQDRRMAIYAQFCEKRS-VLFCTDVASRGLDF 88
C + V E KLR + +Y + Q R I +F S +L TD+ +RG+D
Sbjct: 37 CNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDV 96
Query: 89 NKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSVLFLTPTE---MKMLEKLREAKI 143
+ V V+ D P + +YIHR+GR R+ G ++ F+T + M+ LEK +I
Sbjct: 97 QQ-VSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQI 153
>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 = 37.0 bits (84), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 37/118 (31%), Positives = 58/118 (49%), Gaps = 6/118 (5%)
Query: 31 CKQVKYVFEAFKKLRPG-IPLMCLYGRMKQDRRMAIYAQFCEKRS-VLFCTDVASRGLDF 88
C + V E KLR + +Y + Q R I +F S +L TD+ +RG+D
Sbjct: 267 CNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDV 326
Query: 89 NKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSVLFLTPTE---MKMLEKLREAKI 143
+ V V+ D P + +YIHR+GR R+ G ++ F+T + M+ LEK +I
Sbjct: 327 QQ-VSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQI 383
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 35.4 bits (80), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 36/118 (30%), Positives = 58/118 (49%), Gaps = 6/118 (5%)
Query: 31 CKQVKYVFEAFKKLRPG-IPLMCLYGRMKQDRRMAIYAQFCEKRS-VLFCTDVASRGLDF 88
C + V E KLR + +Y + Q R I +F S +L TD+ +RG+D
Sbjct: 266 CNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSGSSRILISTDLLARGIDV 325
Query: 89 NKAVDWVVQVDCPEDVASYIHRVGRTARYNSGGRSVLFLTPTEM---KMLEKLREAKI 143
+ V V+ D P + +YIHR+GR R+ G ++ F+T ++ + LEK +I
Sbjct: 326 QQ-VSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAXRELEKFYSTQI 382
>pdb|3DMQ|A Chain A, Crystal Structure Of Rapa, A Swi2SNF2 PROTEIN THAT
Recycles Rna Polymerase During Transcription
pdb|3DMQ|B Chain B, Crystal Structure Of Rapa, A Swi2SNF2 PROTEIN THAT
Recycles Rna Polymerase During Transcription
Length = 968
Score = 35.0 bits (79), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 26/112 (23%), Positives = 50/112 (44%), Gaps = 5/112 (4%)
Query: 8 KLDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLY---GRMKQDRRMA 64
+++ L ++ +H + K+LV + + ++ R GI + +++DR A
Sbjct: 490 RVEWLXGYLTSHRSQKVLVICAKAATALQLEQVLRE-REGIRAAVFHEGXSIIERDRAAA 548
Query: 65 IYAQFCEKRSVLFCTDVASRGLDFNKAVDWVVQVDCPEDVASYIHRVGRTAR 116
+A+ VL C+++ S G +F A V D P + R+GR R
Sbjct: 549 WFAEEDTGAQVLLCSEIGSEGRNFQFASH-XVXFDLPFNPDLLEQRIGRLDR 599
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 34.7 bits (78), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 29/135 (21%), Positives = 54/135 (40%), Gaps = 4/135 (2%)
Query: 9 LDMLWSFIKAHLNSKILVFLTSCKQVKYVFEAFKKLRPGIPLMCLYGRMKQDRRMAIYAQ 68
LD L +++ +++ S +V+ A + GI + ++ + R + +
Sbjct: 224 LDQLXRYVQEQRGKSGIIYCNSRAKVEDT--AARLQSKGISAAAYHAGLENNVRADVQEK 281
Query: 69 FCEKRSVLFCTDVASRGLDFNKA-VDWVVQVDCPEDVASYIHRVGRTARYNSGGRSVLFL 127
F ++ + + G NK V +VV D P ++ SY GR R + LF
Sbjct: 282 F-QRDDLQIVVATVAFGXGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAXLFY 340
Query: 128 TPTEMKMLEKLREAK 142
P + L + E K
Sbjct: 341 DPADXAWLRRCLEEK 355
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 33.9 bits (76), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 49/101 (48%), Gaps = 5/101 (4%)
Query: 42 KKLRPGIPLMCLYGRMKQDRRMAIYAQFCEKR-SVLFCTDVASRGLDFNKAVDWVVQVDC 100
K++ P L ++GR+ Q+ + + +F E R +L T V G+D +A V+ ++
Sbjct: 608 KEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRAN--VMVIEN 665
Query: 101 PEDVA-SYIHRV-GRTARYNSGGRSVLFLTPTEMKMLEKLR 139
PE + +H++ GR R L + + +E+LR
Sbjct: 666 PERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAMERLR 706
>pdb|1HJL|A Chain A, Biochemical And Structural Analysis Of The Molybdenum
Cofactor Biosynthesis Protein Moba
Length = 201
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 66 YAQFCEKRSVLFCTDVASRGLDFNKAVDWVVQVDCPEDVASY 107
Y Q E+R ++F +DF+ D V VD PE++A +
Sbjct: 149 YLQAGERRVMVFMRLAGGHAVDFSDHKDAFVNVDTPEELARW 190
>pdb|3V05|A Chain A, 2.4 Angstrom Crystal Structure Of Superantigen-Like
Protein From Staphylococcus Aureus.
pdb|3V05|B Chain B, 2.4 Angstrom Crystal Structure Of Superantigen-Like
Protein From Staphylococcus Aureus.
pdb|3V05|C Chain C, 2.4 Angstrom Crystal Structure Of Superantigen-Like
Protein From Staphylococcus Aureus.
pdb|3V05|D Chain D, 2.4 Angstrom Crystal Structure Of Superantigen-Like
Protein From Staphylococcus Aureus
Length = 218
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 37/88 (42%)
Query: 131 EMKMLEKLREAKIPIHFTKANTKRLQPVSGLLAALLVKYPDMQHRAQKAFITYLRSVHIQ 190
E+K L+ L K+ R GLL + KYP +H Q AF+
Sbjct: 40 ELKNLDGLYRQKVTDKGVYVWKDRKDYFVGLLGKDIEKYPQGEHDKQDAFLVIEEETVNG 99
Query: 191 KDKEVFDVTKLSIDEFSASLGLPMTPKI 218
+ + ++K + EFS + + +T KI
Sbjct: 100 RQYSIGGLSKTNSKEFSKEVDVKVTRKI 127
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.135 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,208,886
Number of Sequences: 62578
Number of extensions: 422901
Number of successful extensions: 1137
Number of sequences better than 100.0: 54
Number of HSP's better than 100.0 without gapping: 48
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1064
Number of HSP's gapped (non-prelim): 55
length of query: 454
length of database: 14,973,337
effective HSP length: 102
effective length of query: 352
effective length of database: 8,590,381
effective search space: 3023814112
effective search space used: 3023814112
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)