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= psy14082
(233 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 89.0 bits (219), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 41/63 (65%), Positives = 51/63 (80%), Gaps = 2/63 (3%)
Query: 25 YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSA--LRNICIFGGTPK 82
Y+LPA VHI+HQ +++GDGPI LVLAPTRELAQQ+Q VA E+ A L++ CI+GG PK
Sbjct: 83 YLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPK 142
Query: 83 GPQ 85
GPQ
Sbjct: 143 GPQ 145
>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human
Dead-Box Rna Helicase Ddx5 (P68)
Length = 253
Score = 88.6 bits (218), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 41/63 (65%), Positives = 51/63 (80%), Gaps = 2/63 (3%)
Query: 25 YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSA--LRNICIFGGTPK 82
Y+LPA VHI+HQ +++GDGPI LVLAPTRELAQQ+Q VA E+ A L++ CI+GG PK
Sbjct: 97 YLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPK 156
Query: 83 GPQ 85
GPQ
Sbjct: 157 GPQ 159
>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 = 76.3 bits (186), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 36/70 (51%), Positives = 49/70 (70%)
Query: 109 VIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAAR 168
+VFVETKK + + L E ++ IHGD++Q+DR+ L+ FR GK+PILVAT VAAR
Sbjct: 49 TLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAAR 108
Query: 169 GLDVEDVNTV 178
GLD+ +V V
Sbjct: 109 GLDISNVKHV 118
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 75.9 bits (185), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 36/69 (52%), Positives = 49/69 (71%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
+VFVETKK + + L E ++ IHGD++Q+DR+ L+ FR GK+PILVAT VAARG
Sbjct: 280 LVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARG 339
Query: 170 LDVEDVNTV 178
LD+ +V V
Sbjct: 340 LDISNVKHV 348
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/43 (53%), Positives = 29/43 (67%), Gaps = 2/43 (4%)
Query: 45 PIALVLAPTRELAQQIQTVAKEFS--SALRNICIFGGTPKGPQ 85
PI+LVLAPTRELA QI A++FS S +R ++GG G Q
Sbjct: 102 PISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQ 144
>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 = 72.0 bits (175), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 34/71 (47%), Positives = 48/71 (67%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ +VF TK + E+I + L R H A +HGD +Q +R+ V+ FRQG+ +LVATDVAA
Sbjct: 30 RAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAA 89
Query: 168 RGLDVEDVNTV 178
RGLD+ V+ V
Sbjct: 90 RGLDIPQVDLV 100
>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 = 71.2 bits (173), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 35/71 (49%), Positives = 48/71 (67%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ +VF TK + E+I + L R H A +HGD +Q +R+ VL FRQG+ +LVATDVAA
Sbjct: 33 RAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAA 92
Query: 168 RGLDVEDVNTV 178
RGLD+ V+ V
Sbjct: 93 RGLDIPQVDLV 103
>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 = 67.4 bits (163), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 50/71 (70%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ ++F T++KVE++T LR ++ + I+ D QQ+RD ++ +FR G + IL++TD+ A
Sbjct: 262 QAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLA 321
Query: 168 RGLDVEDVNTV 178
RG+DV+ V+ V
Sbjct: 322 RGIDVQQVSLV 332
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 29/70 (41%), Gaps = 20/70 (28%)
Query: 44 GPIALVLAPTRELAQQIQTVAK--------------------EFSSALRNICIFGGTPKG 83
P AL+LAPTRELA QIQ V E + LR+ I GTP
Sbjct: 90 APQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGR 149
Query: 84 PQDCLPLHRF 93
D + RF
Sbjct: 150 VFDNIQRRRF 159
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 67.4 bits (163), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 50/71 (70%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ ++F T++KVE++T LR ++ + I+ D QQ+RD ++ +FR G + IL++TD+ A
Sbjct: 32 QAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLA 91
Query: 168 RGLDVEDVNTV 178
RG+DV+ V+ V
Sbjct: 92 RGIDVQQVSLV 102
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 65.5 bits (158), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 49/71 (69%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ ++F T++KVE++T LR ++ + I+ D QQ+RD + +FR G + IL++TD+ A
Sbjct: 261 QAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSGSSRILISTDLLA 320
Query: 168 RGLDVEDVNTV 178
RG+DV+ V+ V
Sbjct: 321 RGIDVQQVSLV 331
Score = 32.3 bits (72), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 20/39 (51%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 44 GPIALVLAPTRELAQQIQTV--AKEFSSALRNICIFGGT 80
P AL LAPTRELA QIQ V A F ++ GGT
Sbjct: 89 APQALXLAPTRELALQIQKVVXALAFHXDIKVHACIGGT 127
>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 = 65.5 bits (158), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 36/88 (40%), Positives = 52/88 (59%), Gaps = 2/88 (2%)
Query: 91 HRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLN 150
RF C+ + KN F +VF +TK+ +++ LR A IHGD +Q R+ V+
Sbjct: 225 ERFEALCR--LLKNKEFYGLVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIR 282
Query: 151 DFRQGKAPILVATDVAARGLDVEDVNTV 178
F+Q K IL+ATDV +RG+DV D+N V
Sbjct: 283 LFKQKKIRILIATDVXSRGIDVNDLNCV 310
Score = 30.4 bits (67), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 29 AAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSS-----ALRNICIFGGTPKG 83
A+ I E V + +G A++L PTRELA Q VA E S L+ I+GG
Sbjct: 59 ASFAIPLIELVNENNGIEAIILTPTRELAIQ---VADEIESLKGNKNLKIAKIYGGKAIY 115
Query: 84 PQ 85
PQ
Sbjct: 116 PQ 117
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 63.9 bits (154), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 45/69 (65%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
I+FV TKK + L+ E H +HGD Q+RD +++DFR+G++ +L+ T+V ARG
Sbjct: 247 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 306
Query: 170 LDVEDVNTV 178
+D+ V+ V
Sbjct: 307 IDIPTVSMV 315
>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 = 63.5 bits (153), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 45/69 (65%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
I+FV TKK + L+ E H +HGD Q+RD +++DFR+G++ +L+ T+V ARG
Sbjct: 247 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 306
Query: 170 LDVEDVNTV 178
+D+ V+ V
Sbjct: 307 IDIPTVSMV 315
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 62.8 bits (151), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 47/71 (66%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ ++F+ T++KV+ +T + + +HGD Q++RD ++ +FR G + +L+ TD+ A
Sbjct: 282 QAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLA 341
Query: 168 RGLDVEDVNTV 178
RG+DV+ V+ V
Sbjct: 342 RGIDVQQVSLV 352
Score = 35.8 bits (81), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/36 (55%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 47 ALVLAPTRELAQQIQTVAKEFSSALRNIC--IFGGT 80
ALVLAPTRELAQQIQ V + C GGT
Sbjct: 111 ALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGT 146
>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 = 62.8 bits (151), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 47/71 (66%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ ++F+ T++KV+ +T + + +HGD Q++RD ++ +FR G + +L+ TD+ A
Sbjct: 256 QAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLA 315
Query: 168 RGLDVEDVNTV 178
RG+DV+ V+ V
Sbjct: 316 RGIDVQQVSLV 326
Score = 35.8 bits (81), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/36 (55%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 47 ALVLAPTRELAQQIQTVAKEFSSALRNIC--IFGGT 80
ALVLAPTRELAQQIQ V + C GGT
Sbjct: 85 ALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGT 120
>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 = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 47/71 (66%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ ++F TK+KV+ +T +R + +HGD Q++R+ ++ +FR G + +L++TDV A
Sbjct: 279 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA 338
Query: 168 RGLDVEDVNTV 178
RGLDV V+ +
Sbjct: 339 RGLDVPQVSLI 349
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 24/40 (60%), Gaps = 4/40 (10%)
Query: 47 ALVLAPTRELAQQIQT---VAKEFSSALRNICIFGGTPKG 83
AL+LAPTRELA QIQ ++ + + CI GGT G
Sbjct: 109 ALILAPTRELAVQIQKGLLALGDYMNVQCHACI-GGTNVG 147
>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 = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 47/71 (66%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ ++F TK+KV+ +T +R + +HGD Q++R+ ++ +FR G + +L++TDV A
Sbjct: 279 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA 338
Query: 168 RGLDVEDVNTV 178
RGLDV V+ +
Sbjct: 339 RGLDVPQVSLI 349
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 24/40 (60%), Gaps = 4/40 (10%)
Query: 47 ALVLAPTRELAQQIQT---VAKEFSSALRNICIFGGTPKG 83
AL+LAPTRELA QIQ ++ + + CI GGT G
Sbjct: 109 ALILAPTRELAVQIQKGLLALGDYMNVQCHACI-GGTNVG 147
>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 = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 47/71 (66%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ ++F TK+KV+ +T +R + +HGD Q++R+ ++ +FR G + +L++TDV A
Sbjct: 257 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA 316
Query: 168 RGLDVEDVNTV 178
RGLDV V+ +
Sbjct: 317 RGLDVPQVSLI 327
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 24/40 (60%), Gaps = 4/40 (10%)
Query: 47 ALVLAPTRELAQQIQT---VAKEFSSALRNICIFGGTPKG 83
AL+LAPTRELA QIQ ++ + + CI GGT G
Sbjct: 87 ALILAPTRELAVQIQKGLLALGDYMNVQCHACI-GGTNVG 125
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 47/71 (66%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ ++F TK+KV+ +T +R + +HGD Q++R+ ++ +FR G + +L++TDV A
Sbjct: 242 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA 301
Query: 168 RGLDVEDVNTV 178
RGLDV V+ +
Sbjct: 302 RGLDVPQVSLI 312
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 24/40 (60%), Gaps = 4/40 (10%)
Query: 47 ALVLAPTRELAQQIQT---VAKEFSSALRNICIFGGTPKG 83
AL+LAPTRELA Q+Q ++ + + CI GGT G
Sbjct: 72 ALILAPTRELAVQVQKGLLALGDYMNVQCHACI-GGTNVG 110
>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 = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 47/71 (66%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ ++F TK+KV+ +T +R + +HGD Q++R+ ++ +FR G + +L++TDV A
Sbjct: 278 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA 337
Query: 168 RGLDVEDVNTV 178
RGLDV V+ +
Sbjct: 338 RGLDVPQVSLI 348
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 24/40 (60%), Gaps = 4/40 (10%)
Query: 47 ALVLAPTRELAQQIQT---VAKEFSSALRNICIFGGTPKG 83
AL+LAPTRELA QIQ ++ + + CI GGT G
Sbjct: 108 ALILAPTRELAVQIQKGLLALGDYMNVQCHACI-GGTNVG 146
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 47/71 (66%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ ++F TK+KV+ +T +R + +HGD Q++R+ ++ +FR G + +L++TDV A
Sbjct: 242 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA 301
Query: 168 RGLDVEDVNTV 178
RGLDV V+ +
Sbjct: 302 RGLDVPQVSLI 312
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 24/40 (60%), Gaps = 4/40 (10%)
Query: 47 ALVLAPTRELAQQIQT---VAKEFSSALRNICIFGGTPKG 83
AL+LAPTRELA Q+Q ++ + + CI GGT G
Sbjct: 72 ALILAPTRELAVQVQKGLLALGDYMNVQSHACI-GGTNVG 110
>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 = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 42/128 (32%), Positives = 66/128 (51%), Gaps = 10/128 (7%)
Query: 58 QQIQTVAKEFSSALRN-----ICIFGGTPKG-PQDCLPLHRFVFNCQY-EMAKNPAFKVI 110
++IQ +A EF L+N I I GG Q ++++ + E+ A I
Sbjct: 248 EEIQRMAGEF---LKNYVFVAIGIVGGACSDVKQTIYEVNKYAKRSKLIEILSEQADGTI 304
Query: 111 VFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGL 170
VFVETK+ + + L + IHGD+ Q R+ L DF+ G +L+AT VA+RGL
Sbjct: 305 VFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGL 364
Query: 171 DVEDVNTV 178
D++++ V
Sbjct: 365 DIKNIKHV 372
Score = 30.8 bits (68), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 26/38 (68%), Gaps = 2/38 (5%)
Query: 45 PIALVLAPTRELAQQIQTVAKEFS--SALRNICIFGGT 80
P ++++PTRELA QI A++F+ S L+ ++GGT
Sbjct: 130 PQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGT 167
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 62.0 bits (149), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 45/69 (65%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
I+FV TKK + L+ E H +HGD Q+RD +++DFR+G++ +L+ T+V ARG
Sbjct: 39 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 98
Query: 170 LDVEDVNTV 178
+D+ V+ V
Sbjct: 99 IDIPTVSMV 107
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 62.0 bits (149), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 45/69 (65%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
I+FV TKK + L+ E H +HGD Q+RD +++DFR+G++ +L+ T+V ARG
Sbjct: 41 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 100
Query: 170 LDVEDVNTV 178
+D+ V+ V
Sbjct: 101 IDIPTVSXV 109
>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 = 61.6 bits (148), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 45/69 (65%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
I+FV TKK + L+ E H +HGD Q+RD +++DFR+G++ +L+ T+V ARG
Sbjct: 40 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 99
Query: 170 LDVEDVNTV 178
+D+ V+ V
Sbjct: 100 IDIPTVSXV 108
>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 = 7e-10, Method: Compositional matrix adjust.
Identities = 33/78 (42%), Positives = 49/78 (62%), Gaps = 1/78 (1%)
Query: 101 MAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPIL 160
M +NP I+F TK+ V +T L + IHG Q+DR V+N+F++G+ L
Sbjct: 31 MTENPD-SCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYL 89
Query: 161 VATDVAARGLDVEDVNTV 178
VATDVAARG+D+E+++ V
Sbjct: 90 VATDVAARGIDIENISLV 107
>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 = 58.2 bits (139), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 28/63 (44%), Positives = 40/63 (63%)
Query: 109 VIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAAR 168
V++F E K V+ I L + A+ IHG K Q++R + FR+GK +LVATDVA++
Sbjct: 57 VLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASK 116
Query: 169 GLD 171
GLD
Sbjct: 117 GLD 119
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 57.8 bits (138), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 41/69 (59%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
I+F + K E+I R + + H+ C+ G+ RD +++ FR G + +LV T+V ARG
Sbjct: 361 IIFCKKKDTAEEIARRMTADGHTVACLTGNLEGAQRDAIMDSFRVGTSKVLVTTNVIARG 420
Query: 170 LDVEDVNTV 178
+DV VN V
Sbjct: 421 IDVSQVNLV 429
Score = 31.2 bits (69), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 45 PIALVLAPTRELAQQIQTVAKEFSSALRNICIFG---GTPKGPQ 85
P A+ LAP+RELA+QI V E FG PKG +
Sbjct: 190 PQAICLAPSRELARQIMDVVTEMGKYTEVKTAFGIKDSVPKGAK 233
>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 = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 40/71 (56%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ ++F T+K + L +E H + G+ + R V+ FR+GK +LV T+V A
Sbjct: 268 QAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCA 327
Query: 168 RGLDVEDVNTV 178
RG+DVE V+ V
Sbjct: 328 RGIDVEQVSVV 338
>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 = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 40/71 (56%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ ++F T+K + L +E H + G+ + R V+ FR+GK +LV T+V A
Sbjct: 305 QAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCA 364
Query: 168 RGLDVEDVNTV 178
RG+DVE V+ V
Sbjct: 365 RGIDVEQVSVV 375
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 40/71 (56%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ ++F T+K + L +E H + G+ + R V+ FR+GK +LV T+V A
Sbjct: 284 QAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCA 343
Query: 168 RGLDVEDVNTV 178
RG+DVE V+ V
Sbjct: 344 RGIDVEQVSVV 354
>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 = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 40/71 (56%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ ++F T+K + L +E H + G+ + R V+ FR+GK +LV T+V A
Sbjct: 335 QAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCA 394
Query: 168 RGLDVEDVNTV 178
RG+DVE V+ V
Sbjct: 395 RGIDVEQVSVV 405
>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 = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 40/69 (57%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
I+F + ++VE + + + + +S IH Q+ R+ V +DFR G LV TD+ RG
Sbjct: 48 IIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRG 107
Query: 170 LDVEDVNTV 178
+D++ VN V
Sbjct: 108 IDIQAVNVV 116
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 41/71 (57%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ I+F + +VE + + + +S H QQ+R+ V ++FRQGK LV +D+
Sbjct: 260 QAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLT 319
Query: 168 RGLDVEDVNTV 178
RG+D++ VN V
Sbjct: 320 RGIDIQAVNVV 330
>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 = 50.8 bits (120), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 46/79 (58%), Gaps = 1/79 (1%)
Query: 101 MAKNP-AFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPI 159
+ K P A + IVFV +++V ++ LR + + G+ Q R+ + +G+ +
Sbjct: 24 LLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNV 83
Query: 160 LVATDVAARGLDVEDVNTV 178
LVATDVAARG+D+ DV+ V
Sbjct: 84 LVATDVAARGIDIPDVSHV 102
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 50.8 bits (120), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 38/125 (30%), Positives = 62/125 (49%), Gaps = 24/125 (19%)
Query: 58 QQIQTVAKEFSSALRNICIFGGTPKGPQDCLPL----HRFVFNCQYEMAKNPAFK----- 108
++I+ V K+F + I + C+ L H+FV +K A +
Sbjct: 172 EEIRKVVKDFITNYEEI----------EACIGLANVEHKFVHVKDDWRSKVQALRENKDK 221
Query: 109 -VIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
VIVFV T+ +V + R +AI + GD Q R+ ++ FR+G+ +L+ TDVA+
Sbjct: 222 GVIVFVRTRNRVAKLVRLF----DNAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVAS 277
Query: 168 RGLDV 172
RGLD+
Sbjct: 278 RGLDI 282
>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 = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 42/71 (59%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ I+F +T++ + +T + ++ H + G+ T + R ++ FR GK +L+ T+V A
Sbjct: 36 QAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCA 95
Query: 168 RGLDVEDVNTV 178
RG+DV+ V V
Sbjct: 96 RGIDVKQVTIV 106
>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 = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 38/58 (65%), Gaps = 4/58 (6%)
Query: 25 YMLPAAVHISHQEPV--KQGDGPIALVLAPTRELAQQIQTVAKEFS-SALRNICIFGG 79
Y++P +H+ Q P+ +Q +GP LVL PTRELA ++ ++S L++ICI+GG
Sbjct: 74 YLMPGFIHLDSQ-PISREQRNGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGG 130
>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 = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 30/91 (32%), Positives = 47/91 (51%), Gaps = 4/91 (4%)
Query: 103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICI---HGDKTQQDRDYVLNDFRQGKAPI 159
++ +K I+F T K + L+ E + I HG TQ R ++ F++ ++ I
Sbjct: 30 RDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGI 89
Query: 160 LVATDVAARGLDVEDVNTV-NIGSLQLSANH 189
LV TDV ARG+D +V+ V IG AN+
Sbjct: 90 LVCTDVGARGMDFPNVHEVLQIGVPSELANY 120
>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 = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 30/91 (32%), Positives = 47/91 (51%), Gaps = 4/91 (4%)
Query: 103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICI---HGDKTQQDRDYVLNDFRQGKAPI 159
++ +K I+F T K + L+ E + I HG TQ R ++ F++ ++ I
Sbjct: 30 RDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGI 89
Query: 160 LVATDVAARGLDVEDVNTV-NIGSLQLSANH 189
LV TDV ARG+D +V+ V IG AN+
Sbjct: 90 LVCTDVGARGMDFPNVHEVLQIGVPSELANY 120
>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 = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 30/91 (32%), Positives = 47/91 (51%), Gaps = 4/91 (4%)
Query: 103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICI---HGDKTQQDRDYVLNDFRQGKAPI 159
++ +K I+F T K + L+ E + I HG TQ R ++ F++ ++ I
Sbjct: 30 RDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGI 89
Query: 160 LVATDVAARGLDVEDVNTV-NIGSLQLSANH 189
LV TDV ARG+D +V+ V IG AN+
Sbjct: 90 LVCTDVGARGMDFPNVHEVLQIGVPSELANY 120
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICI---HGDKTQQDRDYVLNDFRQGKAPI 159
++ +K I+F T K + L+ E + I HG TQ R ++ F++ ++ I
Sbjct: 285 RDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGI 344
Query: 160 LVATDVAARGLDVEDVNTV 178
LV TDV ARG+D +V+ V
Sbjct: 345 LVCTDVGARGMDFPNVHEV 363
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICI---HGDKTQQDRDYVLNDFRQGKAPI 159
++ +K I+F T K + L+ E + I HG TQ R ++ F++ ++ I
Sbjct: 336 RDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGI 395
Query: 160 LVATDVAARGLDVEDVNTV 178
LV TDV ARG+D +V+ V
Sbjct: 396 LVCTDVGARGMDFPNVHEV 414
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICI---HGDKTQQDRDYVLNDFRQGKAPI 159
++ +K I+F T K + L+ E + I HG TQ R ++ F++ ++ I
Sbjct: 285 RDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGI 344
Query: 160 LVATDVAARGLDVEDVNTV 178
LV TDV ARG+D +V+ V
Sbjct: 345 LVCTDVGARGMDFPNVHEV 363
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 40/69 (57%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+V++FV++ ++ + + L + AI IH Q++R F+ + ILVAT++
Sbjct: 252 QVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFG 311
Query: 168 RGLDVEDVN 176
RG+D+E VN
Sbjct: 312 RGMDIERVN 320
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 40/69 (57%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+V++FV++ ++ + + L + AI IH Q++R F+ + ILVAT++
Sbjct: 252 QVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFG 311
Query: 168 RGLDVEDVN 176
RG+D+E VN
Sbjct: 312 RGMDIERVN 320
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 40/69 (57%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+V++FV++ ++ + + L + AI IH Q++R F+ + ILVAT++
Sbjct: 251 QVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFG 310
Query: 168 RGLDVEDVN 176
RG+D+E VN
Sbjct: 311 RGMDIERVN 319
>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56
Length = 172
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 40/69 (57%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+V++FV++ ++ + + L + AI IH Q++R F+ + ILVAT++
Sbjct: 33 QVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFG 92
Query: 168 RGLDVEDVN 176
RG+D+E VN
Sbjct: 93 RGMDIERVN 101
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 25 YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGP 84
+ LP A ++ + ++G P ALVL PTRELA Q+ + + L+ + ++GGT G
Sbjct: 55 FALPIAERLAPSQ--ERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGK 112
Query: 85 Q 85
Q
Sbjct: 113 Q 113
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 25 YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGP 84
+ LP A ++ + ++G P ALVL PTRELA Q+ + + L+ + ++GGT G
Sbjct: 55 FALPIAERLAPSQ--ERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGK 112
Query: 85 Q 85
Q
Sbjct: 113 Q 113
>pdb|4GL2|A Chain A, Structural Basis For Dsrna Duplex Backbone Recognition By
Mda5
pdb|4GL2|B Chain B, Structural Basis For Dsrna Duplex Backbone Recognition By
Mda5
Length = 699
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 26/38 (68%)
Query: 141 TQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTV 178
TQ ++ V++ FR GK +L+AT VA GLD+++ N V
Sbjct: 449 TQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIV 486
>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex
Length = 683
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 37/73 (50%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ +V TKK ED+T L+ +H + +R ++ D R GK +LV ++
Sbjct: 472 RTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLR 531
Query: 168 RGLDVEDVNTVNI 180
GLD+ +V+ V I
Sbjct: 532 EGLDIPEVSLVAI 544
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 37/73 (50%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ +V TKK ED+T L+ +H + +R ++ D R GK +LV ++
Sbjct: 446 RTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLR 505
Query: 168 RGLDVEDVNTVNI 180
GLD+ +V+ V I
Sbjct: 506 EGLDIPEVSLVAI 518
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 37/73 (50%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ +V TKK ED+T L+ +H + +R ++ D R GK +LV ++
Sbjct: 447 RTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLR 506
Query: 168 RGLDVEDVNTVNI 180
GLD+ +V+ V I
Sbjct: 507 EGLDIPEVSLVAI 519
>pdb|4I1S|A Chain A, Melanoma Differentiation Associated Protein-5 Helicase
Domain Complex With Inhibitor Non-structural Protein V
Length = 243
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 26/38 (68%)
Query: 141 TQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTV 178
TQ ++ V++ FR GK +L+AT VA GLD+++ N V
Sbjct: 199 TQNEQREVISKFRTGKINLLIATTVAEEGLDIKECNIV 236
>pdb|2FDC|A Chain A, Structural Basis Of Dna Damage Recognition And Processing
By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX
pdb|2FDC|B Chain B, Structural Basis Of Dna Damage Recognition And Processing
By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX
Length = 658
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 37/73 (50%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ +V TKK ED+T L+ +H + +R ++ D R GK +LV ++
Sbjct: 447 RTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLR 506
Query: 168 RGLDVEDVNTVNI 180
GLD+ +V+ V I
Sbjct: 507 EGLDIPEVSLVAI 519
>pdb|1T5L|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb Point
Mutant Y96a Revealing A Novel Fold For Domain 2
pdb|1T5L|B Chain B, Crystal Structure Of The Dna Repair Protein Uvrb Point
Mutant Y96a Revealing A Novel Fold For Domain 2
Length = 658
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 37/73 (50%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ +V TKK ED+T L+ +H + +R ++ D R GK +LV ++
Sbjct: 447 RTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLR 506
Query: 168 RGLDVEDVNTVNI 180
GLD+ +V+ V I
Sbjct: 507 EGLDIPEVSLVAI 519
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 29/46 (63%)
Query: 135 CIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNI 180
+HG +Q+++D V+ +F +G+ ILV+T V G+DV N + I
Sbjct: 618 LMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVI 663
>pdb|3V4R|A Chain A, Crystal Structure Of A Uvrb Dimer-Dna Complex
pdb|3V4R|B Chain B, Crystal Structure Of A Uvrb Dimer-Dna Complex
Length = 667
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 38/73 (52%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+V+V TKK ED+T L+ +H + +R ++ D R GK +LV ++
Sbjct: 453 RVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLR 512
Query: 168 RGLDVEDVNTVNI 180
GLD+ +V+ V I
Sbjct: 513 EGLDIPEVSLVAI 525
>pdb|2D7D|A Chain A, Structural Insights Into The Cryptic Dna Dependent Atp-Ase
Activity Of Uvrb
pdb|2NMV|A Chain A, Damage Detection By The Uvrabc Pathway: Crystal Structure
Of Uvrb Bound To Fluorescein-Adducted Dna
Length = 661
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 38/73 (52%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+V+V TKK ED+T L+ +H + +R ++ D R GK +LV ++
Sbjct: 447 RVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLR 506
Query: 168 RGLDVEDVNTVNI 180
GLD+ +V+ V I
Sbjct: 507 EGLDIPEVSLVAI 519
>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 = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 37/61 (60%), Gaps = 6/61 (9%)
Query: 25 YMLPAAVHIS----HQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFS--SALRNICIFG 78
+++P H+ +Q+ + P L+LAPTRELA QI + +++FS + LR+ ++G
Sbjct: 77 FLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYG 136
Query: 79 G 79
G
Sbjct: 137 G 137
>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|B Chain B, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|C Chain C, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|D Chain D, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|E Chain E, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|F Chain F, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
Length = 494
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 8/79 (10%)
Query: 108 KVIVFV---ETKKK-----VEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPI 159
K+IVF ET KK V+D +A R ++ +Q+++ +L++F +G+ +
Sbjct: 363 KIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNV 422
Query: 160 LVATDVAARGLDVEDVNTV 178
LVAT V GLDV +V+ V
Sbjct: 423 LVATSVGEEGLDVPEVDLV 441
>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 = 35.8 bits (81), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 20/36 (55%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 47 ALVLAPTRELAQQIQTVAKEFSSALRNIC--IFGGT 80
ALVLAPTRELAQQIQ V + C GGT
Sbjct: 86 ALVLAPTRELAQQIQXVVMALGDYMGASCHACIGGT 121
>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation
Initiation Factor 4a-2
Length = 237
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 22/37 (59%), Positives = 25/37 (67%), Gaps = 4/37 (10%)
Query: 47 ALVLAPTRELAQQIQTVA---KEFSSALRNICIFGGT 80
ALVLAPTRELAQQIQ V ++ A + CI GGT
Sbjct: 101 ALVLAPTRELAQQIQKVILALGDYMGATCHACI-GGT 136
>pdb|2FWR|A Chain A, Structure Of Archaeoglobus Fulgidis Xpb
pdb|2FWR|B Chain B, Structure Of Archaeoglobus Fulgidis Xpb
pdb|2FWR|C Chain C, Structure Of Archaeoglobus Fulgidis Xpb
pdb|2FWR|D Chain D, Structure Of Archaeoglobus Fulgidis Xpb
Length = 472
Score = 34.7 bits (78), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 141 TQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQVIEVVQ- 199
++++R+ +L FR G+ +V++ V G+DV D N I S SA I ++ +++
Sbjct: 379 SREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRP 438
Query: 200 -DYEKEKRLFSLI 211
+KE L+ LI
Sbjct: 439 SKGKKEAVLYELI 451
>pdb|2FZL|A Chain A, Structure Of C-Terminal Domain Of Archaeoglobus Fulgidus
Xpb
Length = 219
Score = 34.3 bits (77), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 141 TQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSLQLSANHNISQVIEVVQ- 199
++++R+ +L FR G+ +V++ V G+DV D N I S SA I ++ +++
Sbjct: 144 SREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRP 203
Query: 200 -DYEKEKRLFSLI 211
+KE L+ LI
Sbjct: 204 SKGKKEAVLYELI 216
>pdb|2EYQ|A Chain A, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
pdb|2EYQ|B Chain B, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
Length = 1151
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 7/68 (10%)
Query: 119 VEDITRALRR------ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDV 172
VE+I +A R E AI HG +++ + V+NDF + +LV T + G+D+
Sbjct: 822 VENIQKAAERLAELVPEARIAIG-HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDI 880
Query: 173 EDVNTVNI 180
NT+ I
Sbjct: 881 PTANTIII 888
>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 = 32.3 bits (72), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 20/39 (51%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 44 GPIALVLAPTRELAQQIQTV--AKEFSSALRNICIFGGT 80
P AL+LAPTRELA QIQ V A F ++ GGT
Sbjct: 82 APQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGT 120
>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain
Length = 223
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 20/39 (51%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 44 GPIALVLAPTRELAQQIQTV--AKEFSSALRNICIFGGT 80
P AL+LAPTRELA QIQ V A F ++ GGT
Sbjct: 89 APQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGT 127
>pdb|1X18|X Chain X, Contact Sites Of Era Gtpase On The Thermus Thermophilus
30s Subunit
Length = 292
Score = 30.4 bits (67), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 135 CIHGDKTQQDRDYVLNDFRQGKAPILVATD 164
+ G + D + VLN R+GKAP+++A +
Sbjct: 92 VVEGTRWTPDDEMVLNKLREGKAPVILAVN 121
>pdb|1EGA|A Chain A, Crystal Structure Of A Widely Conserved Gtpase Era
pdb|1EGA|B Chain B, Crystal Structure Of A Widely Conserved Gtpase Era
pdb|1X1L|X Chain X, Interaction Of Era,A Gtpase Protein, With The 3'minor
Domain Of The 16s Rrna Within The Thermus Thermophilus
30s Subunit.
pdb|3IEU|A Chain A, Crystal Structure Of Era In Complex With Gdp
pdb|3IEU|B Chain B, Crystal Structure Of Era In Complex With Gdp
Length = 301
Score = 30.4 bits (67), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 135 CIHGDKTQQDRDYVLNDFRQGKAPILVATD 164
+ G + D + VLN R+GKAP+++A +
Sbjct: 95 VVEGTRWTPDDEMVLNKLREGKAPVILAVN 124
>pdb|3TBK|A Chain A, Mouse Rig-I Atpase Domain
Length = 555
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 40/94 (42%), Gaps = 13/94 (13%)
Query: 98 QYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDR------------ 145
Q E P K I+FV+T+ V+ + + + + G T + R
Sbjct: 381 QEEYHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGXTLPAQ 440
Query: 146 DYVLNDFR-QGKAPILVATDVAARGLDVEDVNTV 178
VL FR G IL+AT VA G+D+ + N V
Sbjct: 441 KCVLEAFRASGDNNILIATSVADEGIDIAECNLV 474
>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 = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 48 LVLAPTRELAQQIQTVAKEFSSALRNI---CIFGGTP 81
L+LAPTRE+A QI +V + + GGTP
Sbjct: 96 LILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTP 132
>pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleotide
Excision Repair Enzyme
Length = 665
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 34/73 (46%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ +V V T + E++T L A +H + R ++ D R G LV ++
Sbjct: 442 RTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLR 501
Query: 168 RGLDVEDVNTVNI 180
GLD+ +V+ V I
Sbjct: 502 EGLDIPEVSLVAI 514
>pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide Excision Repair
Enzyme Uvrb From Thermus Thermophilus
Length = 664
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 34/73 (46%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ +V V T + E++T L A +H + R ++ D R G LV ++
Sbjct: 441 RTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLR 500
Query: 168 RGLDVEDVNTVNI 180
GLD+ +V+ V I
Sbjct: 501 EGLDIPEVSLVAI 513
>pdb|4AY2|A Chain A, Capturing 5' Tri-Phosphorylated Rna Duplex By Rig-I
Length = 687
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 43/102 (42%), Gaps = 13/102 (12%)
Query: 90 LHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHG-----DKTQQD 144
L F Q E NP I+FV+T+ V+ + + + G KT Q+
Sbjct: 373 LEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQN 432
Query: 145 -------RDYVLNDFR-QGKAPILVATDVAARGLDVEDVNTV 178
+ +L+ F+ G IL+AT VA G+D+ N V
Sbjct: 433 TGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLV 474
>pdb|2YKG|A Chain A, Structural Insights Into Rna Recognition By Rig-I
Length = 696
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 43/102 (42%), Gaps = 13/102 (12%)
Query: 90 LHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHG-----DKTQQD 144
L F Q E NP I+FV+T+ V+ + + + G KT Q+
Sbjct: 382 LEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQN 441
Query: 145 -------RDYVLNDFR-QGKAPILVATDVAARGLDVEDVNTV 178
+ +L+ F+ G IL+AT VA G+D+ N V
Sbjct: 442 TGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLV 483
>pdb|3TMI|A Chain A, Structural Basis For Rna Recognition And Activation Of
Rig-I
Length = 695
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 43/102 (42%), Gaps = 13/102 (12%)
Query: 90 LHRFVFNCQYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHG-----DKTQQD 144
L F Q E NP I+FV+T+ V+ + + + G KT Q+
Sbjct: 381 LEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQN 440
Query: 145 -------RDYVLNDFR-QGKAPILVATDVAARGLDVEDVNTV 178
+ +L+ F+ G IL+AT VA G+D+ N V
Sbjct: 441 TGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLV 482
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 28.5 bits (62), Expect = 3.1, Method: Composition-based stats.
Identities = 27/110 (24%), Positives = 47/110 (42%), Gaps = 20/110 (18%)
Query: 93 FVFNCQYEMAKNPAFKVIVFV-----------ETKKKVEDITRALRRERHSAICI----- 136
VF +MA++ A K+ ++ E K+++DI E+ +
Sbjct: 256 LVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGV 315
Query: 137 ---HGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNIGSL 183
H ++ RD + FRQ K ++VAT A G+++ TV IG +
Sbjct: 316 AYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLP-ARTVIIGDI 364
>pdb|1I58|A Chain A, Structure Of The Histidine Kinase Chea Atp-Binding Domain
In Complex With Atp Analog Adpcp And Magnesium
pdb|1I58|B Chain B, Structure Of The Histidine Kinase Chea Atp-Binding Domain
In Complex With Atp Analog Adpcp And Magnesium
pdb|1I59|A Chain A, Structure Of The Histidine Kinase Chea Atp-Binding Domain
In Complex With Adpnp And Magensium
pdb|1I59|B Chain B, Structure Of The Histidine Kinase Chea Atp-Binding Domain
In Complex With Adpnp And Magensium
pdb|1I5A|A Chain A, Structure Of Chea Domain P4 In Complex With Adpcp And
Manganese
pdb|1I5A|B Chain B, Structure Of Chea Domain P4 In Complex With Adpcp And
Manganese
pdb|1I5B|A Chain A, Structure Of Chea Domain P4 In Complex With Adpnp And
Manganese
pdb|1I5B|B Chain B, Structure Of Chea Domain P4 In Complex With Adpnp And
Manganese
pdb|1I5C|A Chain A, Structure Of Chea Domain P4 In Complex With Adp
pdb|1I5C|B Chain B, Structure Of Chea Domain P4 In Complex With Adp
Length = 189
Score = 27.3 bits (59), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 33/129 (25%), Positives = 63/129 (48%), Gaps = 19/129 (14%)
Query: 111 VFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPIL-VATDVAARG 169
VF + V D+ + + +E + + G+ T+ DR +V + P+L + + G
Sbjct: 10 VFNRFPRMVRDLAKKMNKEVN--FIMRGEDTELDRTFV----EEIGEPLLHLLRNAIDHG 63
Query: 170 LDVEDVNTVN----IGSLQLSANHNISQVIEVVQD----YEKEKRLFSLIRELGKYTLIT 221
++ ++ IG+L LSA H + V+ V+D +KEK +IR+ + LI
Sbjct: 64 IEPKEERIAKGKPPIGTLILSARHEGNNVVIEVEDDGRGIDKEK----IIRKAIEKGLID 119
Query: 222 QESSSTLSE 230
+ ++TLS+
Sbjct: 120 ESKAATLSD 128
>pdb|1I5D|A Chain A, Structure Of Chea Domain P4 In Complex With Tnp-Atp
Length = 191
Score = 27.3 bits (59), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 33/129 (25%), Positives = 63/129 (48%), Gaps = 19/129 (14%)
Query: 111 VFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPIL-VATDVAARG 169
VF + V D+ + + +E + + G+ T+ DR +V + P+L + + G
Sbjct: 12 VFNRFPRMVRDLAKKMNKEVN--FIMRGEDTELDRTFV----EEIGEPLLHLLRNAIDHG 65
Query: 170 LDVEDVNTVN----IGSLQLSANHNISQVIEVVQD----YEKEKRLFSLIRELGKYTLIT 221
++ ++ IG+L LSA H + V+ V+D +KEK +IR+ + LI
Sbjct: 66 IEPKEERIAKGKPPIGTLILSARHEGNNVVIEVEDDGRGIDKEK----IIRKAIEKGLID 121
Query: 222 QESSSTLSE 230
+ ++TLS+
Sbjct: 122 ESKAATLSD 130
>pdb|2NYN|A Chain A, Crystal Structure Of Phenylalanine Ammonia-Lyase From
Anabaena Variabilis
pdb|2NYN|B Chain B, Crystal Structure Of Phenylalanine Ammonia-Lyase From
Anabaena Variabilis
pdb|2NYN|C Chain C, Crystal Structure Of Phenylalanine Ammonia-Lyase From
Anabaena Variabilis
pdb|2NYN|D Chain D, Crystal Structure Of Phenylalanine Ammonia-Lyase From
Anabaena Variabilis
Length = 565
Score = 27.3 bits (59), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 138 GDKTQQDRDYVLNDFRQGKAPIL--VATDVAARGLDVEDVNTV 178
G K DR Y+ ND QG + ++ D+AA G+ V+ V +
Sbjct: 518 GQKPTSDRPYIWNDNEQGLDEHIARISADIAAGGVIVQAVQDI 560
>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 = 26.9 bits (58), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 32/64 (50%), Gaps = 11/64 (17%)
Query: 25 YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQI--QTVA-KEFSSALRNI---CIFG 78
Y+LP I + Q A++ APTRELA QI +T+ +F R I C+ G
Sbjct: 58 YLLPIXEKIKPERAEVQ-----AVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIG 112
Query: 79 GTPK 82
GT K
Sbjct: 113 GTDK 116
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 0.134 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,274,812
Number of Sequences: 62578
Number of extensions: 236555
Number of successful extensions: 719
Number of sequences better than 100.0: 93
Number of HSP's better than 100.0 without gapping: 79
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 611
Number of HSP's gapped (non-prelim): 119
length of query: 233
length of database: 14,973,337
effective HSP length: 96
effective length of query: 137
effective length of database: 8,965,849
effective search space: 1228321313
effective search space used: 1228321313
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)