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= psy1621
(224 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 263 bits (671), Expect = 8e-71, Method: Compositional matrix adjust.
Identities = 129/174 (74%), Positives = 142/174 (81%), Gaps = 2/174 (1%)
Query: 53 RVLIVGDSMT--RIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESM 110
R+L+ + +T IRQFYI +ERE+WK DTLCDLY TL+ITQAVIF NTRRKVDWLTE M
Sbjct: 241 RILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKM 300
Query: 111 LKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSN 170
++FTVSAMHGDMDQ RDVIMR+FRSGSSRVLITTDLLARGIDVQQVSLVINYDLP+N
Sbjct: 301 HARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTN 360
Query: 171 RENYIHXXXXXXXXXXXXVAINFVTAEDKRTLKDTEQFYNTRIEEMPMNVADLI 224
RENYIH VAIN VT EDKRTL+D E FYNT IEEMP+NVADLI
Sbjct: 361 RENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI 414
>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 = 262 bits (670), Expect = 1e-70, Method: Compositional matrix adjust.
Identities = 129/174 (74%), Positives = 142/174 (81%), Gaps = 2/174 (1%)
Query: 53 RVLIVGDSMTR--IRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESM 110
R+L+ + +T IRQFYI +ERE+WK DTLCDLY TL+ITQAVIF NTRRKVDWLTE M
Sbjct: 215 RILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKM 274
Query: 111 LKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSN 170
++FTVSAMHGDMDQ RDVIMR+FRSGSSRVLITTDLLARGIDVQQVSLVINYDLP+N
Sbjct: 275 HARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTN 334
Query: 171 RENYIHXXXXXXXXXXXXVAINFVTAEDKRTLKDTEQFYNTRIEEMPMNVADLI 224
RENYIH VAIN VT EDKRTL+D E FYNT IEEMP+NVADLI
Sbjct: 335 RENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI 388
>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 = 234 bits (596), Expect = 3e-62, Method: Compositional matrix adjust.
Identities = 111/174 (63%), Positives = 138/174 (79%), Gaps = 2/174 (1%)
Query: 53 RVLIVGDSMT--RIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESM 110
R+L+ D +T I+QF++ +ERE+WKFDTLCDLY TL+ITQAVIFCNT+RKVDWLTE M
Sbjct: 238 RILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKM 297
Query: 111 LKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSN 170
+ FTVS+MHGDM Q R+ IM++FRSG+SRVLI+TD+ ARG+DV QVSL+INYDLP+N
Sbjct: 298 REANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNN 357
Query: 171 RENYIHXXXXXXXXXXXXVAINFVTAEDKRTLKDTEQFYNTRIEEMPMNVADLI 224
RE YIH VAINFV +D R L+D EQ+Y+T+I+EMPMNVADLI
Sbjct: 358 RELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI 411
>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 = 234 bits (596), Expect = 4e-62, Method: Compositional matrix adjust.
Identities = 111/174 (63%), Positives = 138/174 (79%), Gaps = 2/174 (1%)
Query: 53 RVLIVGDSMT--RIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESM 110
R+L+ D +T I+QF++ +ERE+WKFDTLCDLY TL+ITQAVIFCNT+RKVDWLTE M
Sbjct: 237 RILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKM 296
Query: 111 LKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSN 170
+ FTVS+MHGDM Q R+ IM++FRSG+SRVLI+TD+ ARG+DV QVSL+INYDLP+N
Sbjct: 297 REANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNN 356
Query: 171 RENYIHXXXXXXXXXXXXVAINFVTAEDKRTLKDTEQFYNTRIEEMPMNVADLI 224
RE YIH VAINFV +D R L+D EQ+Y+T+I+EMPMNVADLI
Sbjct: 357 RELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI 410
>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 = 234 bits (596), Expect = 4e-62, Method: Compositional matrix adjust.
Identities = 111/174 (63%), Positives = 138/174 (79%), Gaps = 2/174 (1%)
Query: 53 RVLIVGDSMT--RIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESM 110
R+L+ D +T I+QF++ +ERE+WKFDTLCDLY TL+ITQAVIFCNT+RKVDWLTE M
Sbjct: 238 RILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKM 297
Query: 111 LKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSN 170
+ FTVS+MHGDM Q R+ IM++FRSG+SRVLI+TD+ ARG+DV QVSL+INYDLP+N
Sbjct: 298 REANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNN 357
Query: 171 RENYIHXXXXXXXXXXXXVAINFVTAEDKRTLKDTEQFYNTRIEEMPMNVADLI 224
RE YIH VAINFV +D R L+D EQ+Y+T+I+EMPMNVADLI
Sbjct: 358 RELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI 411
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 233 bits (594), Expect = 6e-62, Method: Compositional matrix adjust.
Identities = 110/174 (63%), Positives = 138/174 (79%), Gaps = 2/174 (1%)
Query: 53 RVLIVGDSMT--RIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESM 110
R+L+ D +T I+QF++ +ERE+WKFDTLCDLY TL+ITQAVIFCNT+RKVDWLTE M
Sbjct: 201 RILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKM 260
Query: 111 LKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSN 170
+ FTVS+MHGDM Q R+ IM++FRSG+SRVLI+TD+ ARG+DV QVSL+INYDLP+N
Sbjct: 261 REANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNN 320
Query: 171 RENYIHXXXXXXXXXXXXVAINFVTAEDKRTLKDTEQFYNTRIEEMPMNVADLI 224
RE YIH VA+NFV +D R L+D EQ+Y+T+I+EMPMNVADLI
Sbjct: 321 RELYIHRIGRSGRYGRKGVAVNFVKNDDIRVLRDIEQYYSTQIDEMPMNVADLI 374
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 233 bits (594), Expect = 7e-62, Method: Compositional matrix adjust.
Identities = 110/174 (63%), Positives = 138/174 (79%), Gaps = 2/174 (1%)
Query: 53 RVLIVGDSMT--RIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESM 110
R+L+ D +T I+QF++ +ERE+WKFDTLCDLY TL+ITQAVIFCNT+RKVDWLTE M
Sbjct: 201 RILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKM 260
Query: 111 LKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSN 170
+ FTVS+MHGDM Q R+ IM++FRSG+SRVLI+TD+ ARG+DV QVSL+INYDLP+N
Sbjct: 261 REANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNN 320
Query: 171 RENYIHXXXXXXXXXXXXVAINFVTAEDKRTLKDTEQFYNTRIEEMPMNVADLI 224
RE YIH VA+NFV +D R L+D EQ+Y+T+I+EMPMNVADLI
Sbjct: 321 RELYIHRIGRSGRYGRKGVAVNFVKNDDIRVLRDIEQYYSTQIDEMPMNVADLI 374
>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 = 233 bits (594), Expect = 7e-62, Method: Compositional matrix adjust.
Identities = 111/174 (63%), Positives = 138/174 (79%), Gaps = 2/174 (1%)
Query: 53 RVLIVGDSMT--RIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESM 110
R+L+ D +T I+QF++ +ERE+WKFDTLCDLY TL+ITQAVIFCNT+RKVDWLTE M
Sbjct: 216 RILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKM 275
Query: 111 LKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSN 170
+ FTVS+MHGDM Q R+ IM++FRSG+SRVLI+TD+ ARG+DV QVSL+INYDLP+N
Sbjct: 276 REANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNN 335
Query: 171 RENYIHXXXXXXXXXXXXVAINFVTAEDKRTLKDTEQFYNTRIEEMPMNVADLI 224
RE YIH VAINFV +D R L+D EQ+Y+T+I+EMPMNVADLI
Sbjct: 336 RELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI 389
>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 = 208 bits (529), Expect = 2e-54, Method: Compositional matrix adjust.
Identities = 98/174 (56%), Positives = 133/174 (76%), Gaps = 2/174 (1%)
Query: 53 RVLIVGDSMTR--IRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESM 110
R+L+ D +T I+QFY+ +E E++K++ L DLY ++S+TQAVIFCNTRRKV+ LT +
Sbjct: 221 RILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKL 280
Query: 111 LKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSN 170
+FTVSA++ D+ Q RD IM++FRSGSSR+LI+TDLLARGIDVQQVSLVINYDLP+N
Sbjct: 281 RNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPAN 340
Query: 171 RENYIHXXXXXXXXXXXXVAINFVTAEDKRTLKDTEQFYNTRIEEMPMNVADLI 224
+ENYIH VAINFVT ED +++ E+FY+T+IEE+P ++A L+
Sbjct: 341 KENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL 394
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 204 bits (520), Expect = 2e-53, Method: Compositional matrix adjust.
Identities = 97/174 (55%), Positives = 131/174 (75%), Gaps = 2/174 (1%)
Query: 53 RVLIVGDSMT--RIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESM 110
R+L+ D +T I+QFY+ +E E++K++ L DLY ++S+TQAVIFCNTRRKV+ LT +
Sbjct: 220 RILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKL 279
Query: 111 LKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSN 170
+FTVSA++ D+ Q RD I ++FRSGSSR+LI+TDLLARGIDVQQVSLVINYDLP+N
Sbjct: 280 RNDKFTVSAIYSDLPQQERDTIXKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPAN 339
Query: 171 RENYIHXXXXXXXXXXXXVAINFVTAEDKRTLKDTEQFYNTRIEEMPMNVADLI 224
+ENYIH VAINFVT ED ++ E+FY+T+IEE+P ++A L+
Sbjct: 340 KENYIHRIGRGGRFGRKGVAINFVTNEDVGAXRELEKFYSTQIEELPSDIATLL 393
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 204 bits (518), Expect = 4e-53, Method: Compositional matrix adjust.
Identities = 94/161 (58%), Positives = 126/161 (78%)
Query: 64 IRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGD 123
I+QFY+ +E E++K++ L DLY ++S+TQAVIFCNTRRKV+ LT + +FTVSA++ D
Sbjct: 4 IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSD 63
Query: 124 MDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHXXXXXXX 183
+ Q RD IM++FRSGSSR+LI+TDLLARGIDVQQVSLVINYDLP+N+ENYIH
Sbjct: 64 LPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGR 123
Query: 184 XXXXXVAINFVTAEDKRTLKDTEQFYNTRIEEMPMNVADLI 224
VAINFVT ED +++ E+FY+T+IEE+P ++A L+
Sbjct: 124 FGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL 164
>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 = 122 bits (306), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 62/180 (34%), Positives = 103/180 (57%), Gaps = 11/180 (6%)
Query: 44 DVNAAELRRRVLIVGDSMTRIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKV 103
D N +L+R +++ I+Q+Y+ D KF LC+LYG ++I QA+IFC+TR+
Sbjct: 291 DPNVIKLKRE----EETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTA 346
Query: 104 DWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVI 163
WL + K+ V+ + G+M R ++ +FR G +VL+TT++ ARGIDV+QVS+VI
Sbjct: 347 SWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVI 406
Query: 164 NYDLPSNR------ENYIHXXXXXXXXXXXXVAINFVTAEDK-RTLKDTEQFYNTRIEEM 216
N+DLP ++ E Y+H +A+N V ++ L ++ +N +IE +
Sbjct: 407 NFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERL 466
>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 = 122 bits (306), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 57/163 (34%), Positives = 97/163 (59%), Gaps = 6/163 (3%)
Query: 60 SMTRIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSA 119
++ IRQ+Y+ E K+ LC++YG+++I QA+IFC TRR WLT M++ VS
Sbjct: 4 TLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSL 63
Query: 120 MHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNR------EN 173
+ G++ R I+++FR G +VLITT++ ARGIDV+QV++V+N+DLP + E
Sbjct: 64 LSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYET 123
Query: 174 YIHXXXXXXXXXXXXVAINFVTAEDKRTLKDTEQFYNTRIEEM 216
Y+H +A N + ++ +L + +N+ I+++
Sbjct: 124 YLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSSIKQL 166
>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 = 122 bits (306), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 62/180 (34%), Positives = 103/180 (57%), Gaps = 11/180 (6%)
Query: 44 DVNAAELRRRVLIVGDSMTRIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKV 103
D N +L+R +++ I+Q+Y+ D KF LC+LYG ++I QA+IFC+TR+
Sbjct: 224 DPNVIKLKRE----EETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTA 279
Query: 104 DWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVI 163
WL + K+ V+ + G+M R ++ +FR G +VL+TT++ ARGIDV+QVS+VI
Sbjct: 280 SWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVI 339
Query: 164 NYDLPSNR------ENYIHXXXXXXXXXXXXVAINFVTAEDK-RTLKDTEQFYNTRIEEM 216
N+DLP ++ E Y+H +A+N V ++ L ++ +N +IE +
Sbjct: 340 NFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERL 399
>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 = 122 bits (306), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 62/180 (34%), Positives = 103/180 (57%), Gaps = 11/180 (6%)
Query: 44 DVNAAELRRRVLIVGDSMTRIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKV 103
D N +L+R +++ I+Q+Y+ D KF LC+LYG ++I QA+IFC+TR+
Sbjct: 261 DPNVIKLKRE----EETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTA 316
Query: 104 DWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVI 163
WL + K+ V+ + G+M R ++ +FR G +VL+TT++ ARGIDV+QVS+VI
Sbjct: 317 SWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVI 376
Query: 164 NYDLPSNR------ENYIHXXXXXXXXXXXXVAINFVTAEDK-RTLKDTEQFYNTRIEEM 216
N+DLP ++ E Y+H +A+N V ++ L ++ +N +IE +
Sbjct: 377 NFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERL 436
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 122 bits (305), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 62/180 (34%), Positives = 103/180 (57%), Gaps = 11/180 (6%)
Query: 44 DVNAAELRRRVLIVGDSMTRIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKV 103
D N +L+R +++ I+Q+Y+ D KF LC+LYG ++I QA+IFC+TR+
Sbjct: 240 DPNVIKLKRE----EETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTA 295
Query: 104 DWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVI 163
WL + K+ V+ + G+M R ++ +FR G +VL+TT++ ARGIDV+QVS+VI
Sbjct: 296 SWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVI 355
Query: 164 NYDLPSNR------ENYIHXXXXXXXXXXXXVAINFVTAEDK-RTLKDTEQFYNTRIEEM 216
N+DLP ++ E Y+H +A+N V ++ L ++ +N +IE +
Sbjct: 356 NFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERL 415
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 110 bits (275), Expect = 6e-25, Method: Compositional matrix adjust.
Identities = 61/183 (33%), Positives = 106/183 (57%), Gaps = 13/183 (7%)
Query: 46 NAAELRRRVLIVGDSMTRIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDW 105
NA E+R + + S+ I+Q Y+ + E+ K++ L +LYG L+I Q++IFC + +
Sbjct: 315 NANEIRLKTEEL--SVEGIKQLYMDCQSEEHKYNVLVELYGLLTIGQSIIFCKKKDTAEE 372
Query: 106 LTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINY 165
+ M TV+ + G+++ RD IM FR G+S+VL+TT+++ARGIDV QV+LV+NY
Sbjct: 373 IARRMTADGHTVACLTGNLEGAQRDAIMDSFRVGTSKVLVTTNVIARGIDVSQVNLVVNY 432
Query: 166 DLP------SNRENYIHXXXXXXXXXXXXVAINFVTAEDKRTLKD---TEQFYNTRIEEM 216
D+P + + Y+H V+INFV DK++ ++ ++++ I +
Sbjct: 433 DMPLDQAGRPDPQTYLHRIGRTGRFGRVGVSINFV--HDKKSWEEMNAIQEYFQRPITRV 490
Query: 217 PMN 219
P +
Sbjct: 491 PTD 493
>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 = 108 bits (269), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 54/161 (33%), Positives = 89/161 (55%), Gaps = 1/161 (0%)
Query: 60 SMTRIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSA 119
++ + Q+Y Y+ E K L L+ L I Q++IFCN+ ++V+ L + + + ++
Sbjct: 15 TLKGVTQYYAYVT-ERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFY 73
Query: 120 MHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHXXX 179
+H M Q R+ + FR+G R L+ TDL RGID+Q V++VIN+D P E Y+H
Sbjct: 74 IHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIG 133
Query: 180 XXXXXXXXXVAINFVTAEDKRTLKDTEQFYNTRIEEMPMNV 220
+AIN +T +D+ LK E+ T I+ +P N+
Sbjct: 134 RSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNI 174
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 106 bits (265), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 54/161 (33%), Positives = 83/161 (51%), Gaps = 1/161 (0%)
Query: 60 SMTRIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSA 119
++ I Q+Y ++E E K L L+ L I QA+IFCN+ +V+ L + + ++
Sbjct: 229 TLKGITQYYAFVE-ERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYY 287
Query: 120 MHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHXXX 179
H M Q R+ + +FR G R L+ +DLL RGID+Q V++VIN+D P E Y+H
Sbjct: 288 SHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIG 347
Query: 180 XXXXXXXXXVAINFVTAEDKRTLKDTEQFYNTRIEEMPMNV 220
+AIN + D+ L EQ T I +P +
Sbjct: 348 RSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATI 388
>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 = 106 bits (265), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 55/144 (38%), Positives = 83/144 (57%)
Query: 73 REDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVI 132
RE+ KF L D+ T + +IFC T+ V+ LT+ + + +HG M Q R +
Sbjct: 18 REENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDV 77
Query: 133 MRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHXXXXXXXXXXXXVAIN 192
M +F+ G R L+ TD+ ARGID++ +SLVINYDLP +E+Y+H AI+
Sbjct: 78 MNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAIS 137
Query: 193 FVTAEDKRTLKDTEQFYNTRIEEM 216
FVTA +KR L D E++ I+++
Sbjct: 138 FVTAFEKRFLADIEEYIGFEIQKI 161
>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3
pdb|3RRM|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Nup159, Gle1 H337r, Ip6
And Adp
pdb|3RRN|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Gle1 H337r And Ip6
Length = 395
Score = 103 bits (258), Expect = 6e-23, Method: Compositional matrix adjust.
Identities = 54/137 (39%), Positives = 80/137 (58%), Gaps = 6/137 (4%)
Query: 64 IRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGD 123
I+Q Y+ + E KFD L +LYG ++I ++IF T++ + L + + VS +HGD
Sbjct: 217 IKQLYMDCKNEADKFDVLTELYGVMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGD 276
Query: 124 MDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPS------NRENYIHX 177
+ RD ++ FR G S+VLITT++LARGID+ VS+V+NYDLP+ + YIH
Sbjct: 277 LQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHR 336
Query: 178 XXXXXXXXXXXVAINFV 194
VAI+FV
Sbjct: 337 IGRTGRFGRKGVAISFV 353
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 103 bits (257), Expect = 8e-23, Method: Compositional matrix adjust.
Identities = 54/137 (39%), Positives = 80/137 (58%), Gaps = 6/137 (4%)
Query: 64 IRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGD 123
I+Q Y+ + E KFD L +LYG ++I ++IF T++ + L + + VS +HGD
Sbjct: 217 IKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGD 276
Query: 124 MDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPS------NRENYIHX 177
+ RD ++ FR G S+VLITT++LARGID+ VS+V+NYDLP+ + YIH
Sbjct: 277 LQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHR 336
Query: 178 XXXXXXXXXXXVAINFV 194
VAI+FV
Sbjct: 337 IGRTGRFGRKGVAISFV 353
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 102 bits (255), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 58/157 (36%), Positives = 87/157 (55%), Gaps = 6/157 (3%)
Query: 64 IRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGD 123
I+Q Y+ + E KFD L +LYG ++I ++IF T++ + L + + VS +HGD
Sbjct: 9 IKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGD 68
Query: 124 MDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPS------NRENYIHX 177
+ RD ++ FR G S+VLITT++LARGID+ VS+V+NYDLP+ + YIH
Sbjct: 69 LQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHR 128
Query: 178 XXXXXXXXXXXVAINFVTAEDKRTLKDTEQFYNTRIE 214
VAI+FV ++ + Q Y IE
Sbjct: 129 IGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIE 165
>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 = 100 bits (248), Expect = 8e-22, Method: Compositional matrix adjust.
Identities = 58/157 (36%), Positives = 84/157 (53%), Gaps = 6/157 (3%)
Query: 64 IRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGD 123
I+Q Y + E KFD L +LYG +I ++IF T++ + L + + VS +HGD
Sbjct: 10 IKQLYXDCKNEADKFDVLTELYGVXTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGD 69
Query: 124 MDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPS------NRENYIHX 177
+ RD ++ FR G S+VLITT++LARGID+ VS V+NYDLP+ + YIH
Sbjct: 70 LQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHR 129
Query: 178 XXXXXXXXXXXVAINFVTAEDKRTLKDTEQFYNTRIE 214
VAI+FV ++ + Q Y IE
Sbjct: 130 IGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIE 166
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 99.4 bits (246), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 58/157 (36%), Positives = 84/157 (53%), Gaps = 6/157 (3%)
Query: 64 IRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGD 123
I+Q Y + E KFD L +LYG +I ++IF T++ + L + + VS +HGD
Sbjct: 11 IKQLYXDCKNEADKFDVLTELYGLXTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGD 70
Query: 124 MDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPS------NRENYIHX 177
+ RD ++ FR G S+VLITT++LARGID+ VS V+NYDLP+ + YIH
Sbjct: 71 LQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHR 130
Query: 178 XXXXXXXXXXXVAINFVTAEDKRTLKDTEQFYNTRIE 214
VAI+FV ++ + Q Y IE
Sbjct: 131 IGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIE 167
>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56
Length = 172
Score = 87.0 bits (214), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 46/159 (28%), Positives = 85/159 (53%), Gaps = 2/159 (1%)
Query: 60 SMTRIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSA 119
S+ ++Q+Y+ + +++ K L DL L Q VIF + ++ L + ++++ F A
Sbjct: 2 SLHGLQQYYVKL-KDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIA 60
Query: 120 MHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHXXX 179
+H M Q R +QF+ R+L+ T+L RG+D+++V++ NYD+P + + Y+H
Sbjct: 61 IHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVA 120
Query: 180 XXXXXXXXXVAINFVTAE-DKRTLKDTEQFYNTRIEEMP 217
+AI FV+ E D + L D + + I E+P
Sbjct: 121 RAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELP 159
>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 = 86.7 bits (213), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 46/144 (31%), Positives = 74/144 (51%), Gaps = 2/144 (1%)
Query: 64 IRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGD 123
I Q Y+ + E+ +F+ LC L ++FC T+R L + F A+HGD
Sbjct: 214 IEQSYVEVN-ENERFEALCRLLKNKEFY-GLVFCKTKRDTKELASXLRDIGFKAGAIHGD 271
Query: 124 MDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHXXXXXXX 183
+ Q+ R+ ++R F+ R+LI TD+ +RGIDV ++ VINY LP N E+Y H
Sbjct: 272 LSQSQREKVIRLFKQKKIRILIATDVXSRGIDVNDLNCVINYHLPQNPESYXHRIGRTGR 331
Query: 184 XXXXXVAINFVTAEDKRTLKDTEQ 207
AI+ + + + L+ E+
Sbjct: 332 AGKKGKAISIINRREYKKLRYIER 355
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 86.7 bits (213), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 45/155 (29%), Positives = 83/155 (53%), Gaps = 2/155 (1%)
Query: 64 IRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGD 123
++Q+Y+ + +++ K L DL L Q VIF + ++ L + ++++ F A+H
Sbjct: 225 LQQYYVKL-KDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRG 283
Query: 124 MDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHXXXXXXX 183
M Q R +QF+ R+L+ T+L RG+D+++V++ NYD+P + + Y+H
Sbjct: 284 MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR 343
Query: 184 XXXXXVAINFVTAE-DKRTLKDTEQFYNTRIEEMP 217
+AI FV+ E D + L D + + I E+P
Sbjct: 344 FGTKGLAITFVSDENDAKILNDVQDRFEVNISELP 378
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 86.7 bits (213), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 45/155 (29%), Positives = 83/155 (53%), Gaps = 2/155 (1%)
Query: 64 IRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGD 123
++Q+Y+ + +++ K L DL L Q VIF + ++ L + ++++ F A+H
Sbjct: 225 LQQYYVKL-KDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRG 283
Query: 124 MDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHXXXXXXX 183
M Q R +QF+ R+L+ T+L RG+D+++V++ NYD+P + + Y+H
Sbjct: 284 MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR 343
Query: 184 XXXXXVAINFVTAE-DKRTLKDTEQFYNTRIEEMP 217
+AI FV+ E D + L D + + I E+P
Sbjct: 344 FGTKGLAITFVSDENDAKILNDVQDRFEVNISELP 378
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 86.3 bits (212), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 45/155 (29%), Positives = 83/155 (53%), Gaps = 2/155 (1%)
Query: 64 IRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGD 123
++Q+Y+ + +++ K L DL L Q VIF + ++ L + ++++ F A+H
Sbjct: 224 LQQYYVKL-KDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRG 282
Query: 124 MDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHXXXXXXX 183
M Q R +QF+ R+L+ T+L RG+D+++V++ NYD+P + + Y+H
Sbjct: 283 MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR 342
Query: 184 XXXXXVAINFVTAE-DKRTLKDTEQFYNTRIEEMP 217
+AI FV+ E D + L D + + I E+P
Sbjct: 343 FGTKGLAITFVSDENDAKILNDVQDRFEVNISELP 377
>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 = 85.5 bits (210), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 37/100 (37%), Positives = 59/100 (59%)
Query: 77 KFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQF 136
+ + L DL S +A++F T+ + + + + +L+ A+HGDM Q R+ +M F
Sbjct: 15 RLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAF 74
Query: 137 RSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIH 176
R G RVL+ TD+ ARG+D+ QV LV++Y +P E Y H
Sbjct: 75 RQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQH 114
>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 = 84.0 bits (206), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 37/109 (33%), Positives = 64/109 (58%)
Query: 94 VIFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARG 153
++F T+R D+L + +KEF +++HGD Q+ R+ +R F++GS +VLI T + +RG
Sbjct: 304 IVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRG 363
Query: 154 IDVQQVSLVINYDLPSNRENYIHXXXXXXXXXXXXVAINFVTAEDKRTL 202
+D++ + VINYD+PS ++Y+H A +F E R +
Sbjct: 364 LDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAI 412
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 84.0 bits (206), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 47/161 (29%), Positives = 79/161 (49%)
Query: 57 VGDSMTRIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFT 116
VG + I Q +++E D + L L T + ++F T++ D L + + + +
Sbjct: 243 VGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYA 302
Query: 117 VSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIH 176
+++HGD Q R+ + QFRSG S +L+ T + ARG+D+ V VIN+DLPS+ E Y+H
Sbjct: 303 CTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVH 362
Query: 177 XXXXXXXXXXXXVAINFVTAEDKRTLKDTEQFYNTRIEEMP 217
+A +F + KD +E+P
Sbjct: 363 RIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVP 403
>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 = 83.6 bits (205), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 36/100 (36%), Positives = 59/100 (59%)
Query: 77 KFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQF 136
+ + L DL S +A++F T+ + + + + +L+ A+HGD+ Q R+ ++ F
Sbjct: 18 RLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAF 77
Query: 137 RSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIH 176
R G RVL+ TD+ ARG+D+ QV LV++Y LP E Y H
Sbjct: 78 RQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQH 117
>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 = 81.3 bits (199), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 46/160 (28%), Positives = 78/160 (48%)
Query: 58 GDSMTRIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTV 117
G + I Q +++E D + L L T + ++F T++ D L + + + +
Sbjct: 14 GSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYAC 73
Query: 118 SAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHX 177
+++HGD Q R+ + QFRSG S +L+ T + ARG+D+ V VIN+DLPS+ E Y+H
Sbjct: 74 TSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHR 133
Query: 178 XXXXXXXXXXXVAINFVTAEDKRTLKDTEQFYNTRIEEMP 217
+A +F + KD +E+P
Sbjct: 134 IGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVP 173
>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 = 72.4 bits (176), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 39/125 (31%), Positives = 60/125 (48%), Gaps = 1/125 (0%)
Query: 94 VIFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARG 153
+IF + VD + E +L K A+HG DQ R + FR G VL+ TD+ ++G
Sbjct: 58 LIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKG 117
Query: 154 IDVQQVSLVINYDLPSNRENYIHXXXXXXXXXXXXVAINFVT-AEDKRTLKDTEQFYNTR 212
+D + VINYD+P ENY+H +A F+ A D+ L D +
Sbjct: 118 LDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVLMDLKALLLEA 177
Query: 213 IEEMP 217
+++P
Sbjct: 178 KQKVP 182
>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 = 68.2 bits (165), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 40/140 (28%), Positives = 68/140 (48%), Gaps = 8/140 (5%)
Query: 63 RIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKV----DWLTESMLKKEFTVS 118
+I Q+Y + + K L L T++++F R +V +WL E+ + +
Sbjct: 3 KIHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCY--- 59
Query: 119 AMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHXX 178
+ G+M Q R+ +++ G VL+ TD+ ARGID+ VS V N+D+P + + Y+H
Sbjct: 60 -LEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRI 118
Query: 179 XXXXXXXXXXVAINFVTAED 198
AI+ V A D
Sbjct: 119 GRTARAGRKGTAISLVEAHD 138
>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 = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 50/89 (56%), Gaps = 5/89 (5%)
Query: 92 QAVIFCNTRRKVDWLTESMLKKEF----TVSAMHGDMDQNARDVIMRQFRSGSSRVLITT 147
+A+IF T + +L S+LK EF + HG + QN R ++++F+ S +L+ T
Sbjct: 35 KAIIFAPTVKFTSFLC-SILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCT 93
Query: 148 DLLARGIDVQQVSLVINYDLPSNRENYIH 176
D+ ARG+D V V+ +PS NYIH
Sbjct: 94 DVGARGMDFPNVHEVLQIGVPSELANYIH 122
>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 = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 50/89 (56%), Gaps = 5/89 (5%)
Query: 92 QAVIFCNTRRKVDWLTESMLKKEF----TVSAMHGDMDQNARDVIMRQFRSGSSRVLITT 147
+A+IF T + +L S+LK EF + HG + QN R ++++F+ S +L+ T
Sbjct: 35 KAIIFAPTVKFTSFLC-SILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCT 93
Query: 148 DLLARGIDVQQVSLVINYDLPSNRENYIH 176
D+ ARG+D V V+ +PS NYIH
Sbjct: 94 DVGARGMDFPNVHEVLQIGVPSELANYIH 122
>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 = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 50/89 (56%), Gaps = 5/89 (5%)
Query: 92 QAVIFCNTRRKVDWLTESMLKKEF----TVSAMHGDMDQNARDVIMRQFRSGSSRVLITT 147
+A+IF T + +L S+LK EF + HG + QN R ++++F+ S +L+ T
Sbjct: 35 KAIIFAPTVKFTSFLC-SILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCT 93
Query: 148 DLLARGIDVQQVSLVINYDLPSNRENYIH 176
D+ ARG+D V V+ +PS NYIH
Sbjct: 94 DVGARGMDFPNVHEVLQIGVPSELANYIH 122
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 58.9 bits (141), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 50/89 (56%), Gaps = 5/89 (5%)
Query: 92 QAVIFCNTRRKVDWLTESMLKKEF----TVSAMHGDMDQNARDVIMRQFRSGSSRVLITT 147
+A+IF T + +L S+LK EF + HG + QN R ++++F+ S +L+ T
Sbjct: 290 KAIIFAPTVKFTSFLC-SILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCT 348
Query: 148 DLLARGIDVQQVSLVINYDLPSNRENYIH 176
D+ ARG+D V V+ +PS NYIH
Sbjct: 349 DVGARGMDFPNVHEVLQIGVPSELANYIH 377
>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 = 58.5 bits (140), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 50/89 (56%), Gaps = 5/89 (5%)
Query: 92 QAVIFCNTRRKVDWLTESMLKKEF----TVSAMHGDMDQNARDVIMRQFRSGSSRVLITT 147
+A+IF T + +L S+LK EF + HG + QN R ++++F+ S +L+ T
Sbjct: 341 KAIIFAPTVKFTSFLC-SILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCT 399
Query: 148 DLLARGIDVQQVSLVINYDLPSNRENYIH 176
D+ ARG+D V V+ +PS NYIH
Sbjct: 400 DVGARGMDFPNVHEVLQIGVPSELANYIH 428
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 58.2 bits (139), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 50/89 (56%), Gaps = 5/89 (5%)
Query: 92 QAVIFCNTRRKVDWLTESMLKKEF----TVSAMHGDMDQNARDVIMRQFRSGSSRVLITT 147
+A+IF T + +L S+LK EF + HG + QN R ++++F+ S +L+ T
Sbjct: 290 KAIIFAPTVKFTSFLC-SILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCT 348
Query: 148 DLLARGIDVQQVSLVINYDLPSNRENYIH 176
D+ ARG+D V V+ +PS NYIH
Sbjct: 349 DVGARGMDFPNVHEVLQIGVPSELANYIH 377
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 54.7 bits (130), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 34/105 (32%), Positives = 52/105 (49%), Gaps = 6/105 (5%)
Query: 94 VIFCNTRRKVDWLTESMLKKEF-TVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLAR 152
++F TR +V + L + F + GD+ Q+ R+ + FR G +LITTD+ +R
Sbjct: 224 IVFVRTRNRV-----AKLVRLFDNAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASR 278
Query: 153 GIDVQQVSLVINYDLPSNRENYIHXXXXXXXXXXXXVAINFVTAE 197
G+D+ V VIN+D P + YIH AI F+ E
Sbjct: 279 GLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFILNE 323
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 53.9 bits (128), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 41/177 (23%), Positives = 74/177 (41%), Gaps = 9/177 (5%)
Query: 53 RVLIVGDSMTRIRQF----YIYIEREDWK-FDTLCDLYGTLSITQAVIFCNTRRKVDWLT 107
R+L + D + +I F Y+ E +K D L +I+CN+R KV+
Sbjct: 194 RLLGLNDPLIQISSFDRPNIRYMLMEKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTA 253
Query: 108 ESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDL 167
+ K + +A H ++ N R + +F+ ++++ T GI+ V V+++D+
Sbjct: 254 ARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDI 313
Query: 168 PSNRENYIHXXXXXXXXXXXXVAINFVTAED----KRTLKDTEQFYNTRIEEMPMNV 220
P N E+Y A+ F D +R L++ Q IE +N
Sbjct: 314 PRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPQGQLQDIERHKLNA 370
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 41/177 (23%), Positives = 72/177 (40%), Gaps = 9/177 (5%)
Query: 53 RVLIVGDSMTRIRQF----YIYIEREDWK-FDTLCDLYGTLSITQAVIFCNTRRKVDWLT 107
R+L + D + +I F Y E +K D L +I+CN+R KV+
Sbjct: 194 RLLGLNDPLIQISSFDRPNIRYXLXEKFKPLDQLXRYVQEQRGKSGIIYCNSRAKVEDTA 253
Query: 108 ESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDL 167
+ K + +A H ++ N R + +F+ ++++ T GI+ V V+++D+
Sbjct: 254 ARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXGINKPNVRFVVHFDI 313
Query: 168 PSNRENYIHXXXXXXXXXXXXVAINFVTAED----KRTLKDTEQFYNTRIEEMPMNV 220
P N E+Y A F D +R L++ Q IE +N
Sbjct: 314 PRNIESYYQETGRAGRDGLPAEAXLFYDPADXAWLRRCLEEKPQGQLQDIERHKLNA 370
>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 = 46.2 bits (108), Expect = 2e-05, Method: Composition-based stats.
Identities = 27/93 (29%), Positives = 46/93 (49%), Gaps = 14/93 (15%)
Query: 92 QAVIFCNTRRKV----DWLTESMLKKEFTVSAMH----------GDMDQNARDVIMRQFR 137
+ +IF TR+ W+TE+ E V A H M QN + ++ +FR
Sbjct: 402 RGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFR 461
Query: 138 SGSSRVLITTDLLARGIDVQQVSLVINYDLPSN 170
+G +LI T + G+D+++ ++VI Y L +N
Sbjct: 462 TGKINLLIATTVAEEGLDIKECNIVIRYGLVTN 494
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 42.7 bits (99), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/113 (21%), Positives = 57/113 (50%), Gaps = 1/113 (0%)
Query: 51 RRRVLIVGDSMTRIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESM 110
R+ V + M R+ + Y ++ +E + +Y + + + + ++L++ +
Sbjct: 551 RKEVQTMLVPMDRVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEV 610
Query: 111 LKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVI 163
EF + MHG + Q +D +M +F G +L++T ++ GIDV + ++++
Sbjct: 611 FP-EFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMV 662
>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase
pdb|2V1X|B Chain B, Crystal Structure Of Human Recq-Like Dna Helicase
pdb|2WWY|A Chain A, Structure Of Human Recq-Like Helicase In Complex With A
Dna Substrate
pdb|2WWY|B Chain B, Structure Of Human Recq-Like Helicase In Complex With A
Dna Substrate
Length = 591
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/101 (21%), Positives = 48/101 (47%)
Query: 74 EDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIM 133
ED+ D + + G +I+C +++ + +T S+ A H +++ + +
Sbjct: 251 EDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVH 310
Query: 134 RQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENY 174
R++ + +V++ T GID V VI++ + + ENY
Sbjct: 311 RKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENY 351
>pdb|4I1S|A Chain A, Melanoma Differentiation Associated Protein-5 Helicase
Domain Complex With Inhibitor Non-structural Protein V
Length = 243
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 43/90 (47%), Gaps = 14/90 (15%)
Query: 92 QAVIFCNTRRKV----DWLTESMLKKEFTVSAMH----------GDMDQNARDVIMRQFR 137
+ +IF TR+ W+T++ E V A H QN + ++ +FR
Sbjct: 152 RGIIFTKTRQSAYALSQWITDNKKFAEVGVKAHHLIGAGHSSEFKPXTQNEQREVISKFR 211
Query: 138 SGSSRVLITTDLLARGIDVQQVSLVINYDL 167
+G +LI T + G+D+++ ++VI Y L
Sbjct: 212 TGKINLLIATTVAEEGLDIKECNIVIRYGL 241
>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex
Length = 683
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 43/77 (55%), Gaps = 2/77 (2%)
Query: 99 TRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQ 158
T++ + LT+ + + V+ +H ++ R I+R R G VL+ +LL G+D+ +
Sbjct: 479 TKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPE 538
Query: 159 VSLVINYDLPSNRENYI 175
VSLV D +++E ++
Sbjct: 539 VSLVAILD--ADKEGFL 553
>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 = 22/77 (28%), Positives = 43/77 (55%), Gaps = 2/77 (2%)
Query: 99 TRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQ 158
T++ + LT+ + + V+ +H ++ R I+R R G VL+ +LL G+D+ +
Sbjct: 454 TKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPE 513
Query: 159 VSLVINYDLPSNRENYI 175
VSLV D +++E ++
Sbjct: 514 VSLVAILD--ADKEGFL 528
>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 = 22/77 (28%), Positives = 43/77 (55%), Gaps = 2/77 (2%)
Query: 99 TRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQ 158
T++ + LT+ + + V+ +H ++ R I+R R G VL+ +LL G+D+ +
Sbjct: 453 TKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPE 512
Query: 159 VSLVINYDLPSNRENYI 175
VSLV D +++E ++
Sbjct: 513 VSLVAILD--ADKEGFL 527
>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 = 22/77 (28%), Positives = 43/77 (55%), Gaps = 2/77 (2%)
Query: 99 TRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQ 158
T++ + LT+ + + V+ +H ++ R I+R R G VL+ +LL G+D+ +
Sbjct: 454 TKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPE 513
Query: 159 VSLVINYDLPSNRENYI 175
VSLV D +++E ++
Sbjct: 514 VSLVAILD--ADKEGFL 528
>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 = 22/77 (28%), Positives = 43/77 (55%), Gaps = 2/77 (2%)
Query: 99 TRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQ 158
T++ + LT+ + + V+ +H ++ R I+R R G VL+ +LL G+D+ +
Sbjct: 454 TKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPE 513
Query: 159 VSLVINYDLPSNRENYI 175
VSLV D +++E ++
Sbjct: 514 VSLVAILD--ADKEGFL 528
>pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleotide
Excision Repair Enzyme
Length = 665
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 99 TRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQ 158
T R + LT +++ +H ++D R ++R R G L+ +LL G+D+ +
Sbjct: 449 TVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPE 508
Query: 159 VSLVINYDLPSNRENYI 175
VSLV D +++E ++
Sbjct: 509 VSLVAILD--ADKEGFL 523
>pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide Excision Repair
Enzyme Uvrb From Thermus Thermophilus
Length = 664
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 99 TRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQ 158
T R + LT +++ +H ++D R ++R R G L+ +LL G+D+ +
Sbjct: 448 TVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPE 507
Query: 159 VSLVINYDLPSNRENYI 175
VSLV D +++E ++
Sbjct: 508 VSLVAILD--ADKEGFL 522
>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 = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 33/101 (32%), Positives = 51/101 (50%), Gaps = 13/101 (12%)
Query: 83 DLYGTLSITQAVIFCNTRRKVDWLTESMLK------KEF--TVSAMHGDMDQNARDVIMR 134
DL G + QA I N R V LT+ M + KE V+ +H ++ R I+R
Sbjct: 439 DLIGEI---QARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIR 495
Query: 135 QFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYI 175
R G VL+ +LL G+D+ +VSLV D +++E ++
Sbjct: 496 DLRLGKYDVLVGINLLREGLDIPEVSLVAILD--ADKEGFL 534
>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 = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 33/101 (32%), Positives = 51/101 (50%), Gaps = 13/101 (12%)
Query: 83 DLYGTLSITQAVIFCNTRRKVDWLTESMLK------KEF--TVSAMHGDMDQNARDVIMR 134
DL G + QA I N R V LT+ M + KE V+ +H ++ R I+R
Sbjct: 433 DLIGEI---QARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIR 489
Query: 135 QFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYI 175
R G VL+ +LL G+D+ +VSLV D +++E ++
Sbjct: 490 DLRLGKYDVLVGINLLREGLDIPEVSLVAILD--ADKEGFL 528
>pdb|4AY2|A Chain A, Capturing 5' Tri-Phosphorylated Rna Duplex By Rig-I
Length = 687
Score = 35.8 bits (81), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 35/114 (30%), Positives = 50/114 (43%), Gaps = 17/114 (14%)
Query: 74 EDWKFDTLC----DLYGTLSITQAVIFCNTRRKVDWLT---ESMLKKEFTVSAM---HGD 123
E+ K + LC + Y T ++F TR VD L E K F + G
Sbjct: 369 ENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGK 428
Query: 124 MDQN------ARDVIMRQFR-SGSSRVLITTDLLARGIDVQQVSLVINYDLPSN 170
+QN A+ I+ F+ SG +LI T + GID+ Q +LVI Y+ N
Sbjct: 429 TNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGN 482
>pdb|3TMI|A Chain A, Structural Basis For Rna Recognition And Activation Of
Rig-I
Length = 695
Score = 35.4 bits (80), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 35/114 (30%), Positives = 50/114 (43%), Gaps = 17/114 (14%)
Query: 74 EDWKFDTLC----DLYGTLSITQAVIFCNTRRKVDWLT---ESMLKKEFTVSAM---HGD 123
E+ K + LC + Y T ++F TR VD L E K F + G
Sbjct: 377 ENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGK 436
Query: 124 MDQN------ARDVIMRQFR-SGSSRVLITTDLLARGIDVQQVSLVINYDLPSN 170
+QN A+ I+ F+ SG +LI T + GID+ Q +LVI Y+ N
Sbjct: 437 TNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGN 490
>pdb|2YKG|A Chain A, Structural Insights Into Rna Recognition By Rig-I
Length = 696
Score = 35.4 bits (80), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 35/114 (30%), Positives = 50/114 (43%), Gaps = 17/114 (14%)
Query: 74 EDWKFDTLC----DLYGTLSITQAVIFCNTRRKVDWLT---ESMLKKEFTVSAM---HGD 123
E+ K + LC + Y T ++F TR VD L E K F + G
Sbjct: 378 ENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGK 437
Query: 124 MDQN------ARDVIMRQFR-SGSSRVLITTDLLARGIDVQQVSLVINYDLPSN 170
+QN A+ I+ F+ SG +LI T + GID+ Q +LVI Y+ N
Sbjct: 438 TNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGN 491
>pdb|3TBK|A Chain A, Mouse Rig-I Atpase Domain
Length = 555
Score = 35.4 bits (80), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 30/121 (24%), Positives = 51/121 (42%), Gaps = 23/121 (19%)
Query: 63 RIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVD----WLTESMLKKEFTVS 118
++R Y+ ++ E Y T+ ++F TR VD W+ E+
Sbjct: 372 KLRDLYLVLQEE----------YHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPG 421
Query: 119 AMHGDMDQN--------ARDVIMRQFR-SGSSRVLITTDLLARGIDVQQVSLVINYDLPS 169
+ G N A+ ++ FR SG + +LI T + GID+ + +LVI Y+
Sbjct: 422 ILTGRGRTNRATGXTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLVILYEYVG 481
Query: 170 N 170
N
Sbjct: 482 N 482
>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 = 34.7 bits (78), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 43/88 (48%), Gaps = 9/88 (10%)
Query: 91 TQAVIFCNTRRKVDWLTESMLK-----KEFTVSAMHGD---MDQNARDVIMRQFRSGSSR 142
++ ++F N R + ++K K F A + + Q + +I+ +F G
Sbjct: 362 SKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFN 421
Query: 143 VLITTDLLARGIDVQQVSLVINYD-LPS 169
VL+ T + G+DV +V LV+ Y+ +PS
Sbjct: 422 VLVATSVGEEGLDVPEVDLVVFYEPVPS 449
>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 = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 26/46 (56%)
Query: 111 LKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDV 156
+ K F + A+ + R+ I+ FR+G R ++++ +L GIDV
Sbjct: 365 ISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDV 410
>pdb|2FZL|A Chain A, Structure Of C-Terminal Domain Of Archaeoglobus Fulgidus
Xpb
Length = 219
Score = 30.8 bits (68), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 26/46 (56%)
Query: 111 LKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDV 156
+ K F + A+ + R+ I+ FR+G R ++++ +L GIDV
Sbjct: 130 ISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDV 175
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 29.6 bits (65), Expect = 1.2, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 106 LTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVI 163
L +S++ K V+ H + + RD+I FR +V++ T LA G+++ +++I
Sbjct: 306 LLKSLISK--GVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVII 361
>pdb|4A2W|A Chain A, Structure Of Full-Length Duck Rig-I
pdb|4A2W|B Chain B, Structure Of Full-Length Duck Rig-I
Length = 936
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 45/103 (43%), Gaps = 13/103 (12%)
Query: 81 LCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFT------VSAMHGDMDQN------A 128
L D Y T+ ++F TR V L + M + V G DQ +
Sbjct: 622 LDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPS 681
Query: 129 RDVIMRQFR-SGSSRVLITTDLLARGIDVQQVSLVINYDLPSN 170
+ ++ F+ S +R+LI T + GID+ Q +LV+ Y+ N
Sbjct: 682 QKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGN 724
>pdb|4A2Q|A Chain A, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|B Chain B, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|D Chain D, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|E Chain E, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
Length = 797
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 45/103 (43%), Gaps = 13/103 (12%)
Query: 81 LCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFT------VSAMHGDMDQN------A 128
L D Y T+ ++F TR V L + M + V G DQ +
Sbjct: 622 LDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPS 681
Query: 129 RDVIMRQFR-SGSSRVLITTDLLARGIDVQQVSLVINYDLPSN 170
+ ++ F+ S +R+LI T + GID+ Q +LV+ Y+ N
Sbjct: 682 QKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGN 724
>pdb|4A2P|A Chain A, Structure Of Duck Rig-I Helicase Domain
pdb|4A36|A Chain A, Structure Of Duck Rig-I Helicase Domain Bound To 19-Mer
Dsrna And Atp Transition State Analogue
pdb|4A36|B Chain B, Structure Of Duck Rig-I Helicase Domain Bound To 19-Mer
Dsrna And Atp Transition State Analogue
Length = 556
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 45/103 (43%), Gaps = 13/103 (12%)
Query: 81 LCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFT------VSAMHGDMDQN------A 128
L D Y T+ ++F TR V L + M + V G DQ +
Sbjct: 381 LDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPS 440
Query: 129 RDVIMRQFR-SGSSRVLITTDLLARGIDVQQVSLVINYDLPSN 170
+ ++ F+ S +R+LI T + GID+ Q +LV+ Y+ N
Sbjct: 441 QKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGN 483
>pdb|1EI3|B Chain B, Crystal Structure Of Native Chicken Fibrinogen
pdb|1EI3|E Chain E, Crystal Structure Of Native Chicken Fibrinogen
pdb|1M1J|B Chain B, Crystal Structure Of Native Chicken Fibrinogen With Two
Different Bound Ligands
pdb|1M1J|E Chain E, Crystal Structure Of Native Chicken Fibrinogen With Two
Different Bound Ligands
Length = 464
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 61 MTRIRQFYIYIEREDWKFDTLCDLYGTLSI 90
+T+I + IE EDW D + LYG +I
Sbjct: 306 LTKIGPTKVLIEMEDWNGDKVSALYGGFTI 335
>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 = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 98 NTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQ 157
N ++ + L E L E ++ HG M + + +M F VL+ T ++ GID+
Sbjct: 824 NIQKAAERLAE--LVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIP 881
Query: 158 QVSLVI 163
+ +I
Sbjct: 882 TANTII 887
>pdb|3DFG|A Chain A, Crystal Structure Of Recx: A Potent Inhibitor Protein Of
Reca From Xanthomonas Campestris
Length = 162
Score = 27.3 bits (59), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 5/57 (8%)
Query: 116 TVSAMHGDMDQNARDVIMRQFRSGSSRVLI----TTDLLA-RGIDVQQVSLVINYDL 167
++ GD +NA D+I R+F L DLLA RG D + L +DL
Sbjct: 104 AMATFEGDWTENALDLIRRRFGEDGPVDLAQRRKAADLLARRGFDGNSIRLATRFDL 160
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
0.324 0.137 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,711,146
Number of Sequences: 62578
Number of extensions: 191538
Number of successful extensions: 665
Number of sequences better than 100.0: 74
Number of HSP's better than 100.0 without gapping: 72
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 592
Number of HSP's gapped (non-prelim): 75
length of query: 224
length of database: 14,973,337
effective HSP length: 95
effective length of query: 129
effective length of database: 9,028,427
effective search space: 1164667083
effective search space used: 1164667083
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 49 (23.5 bits)