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= psy10478
(451 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 195 bits (496), Expect = 3e-50, Method: Compositional matrix adjust.
Identities = 110/277 (39%), Positives = 150/277 (54%), Gaps = 17/277 (6%)
Query: 133 VLIAIDEAHCVSQWGHDFRPSYRCLSELRLPLPDVPILAVTATATPVVIDDICTSLMLRD 192
VL+A+DEAHC+SQWGHDFRP Y L +LR P +P +A+TATA DI L L D
Sbjct: 141 VLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLND 200
Query: 193 PNIINTGFDRPNLYLAASVKQDDIMADLRKLTNFENQFEG-STIIYCPTKVICEKVCDVL 251
P I + FDRPN+ K L +L + + G S IIYC ++ E L
Sbjct: 201 PLIQISSFDRPNIRYMLMEK----FKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARL 256
Query: 252 SRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPKD 311
GI YHA + R ++ F +D +++VVAT AFGMGI+KP+VR V+H+ P++
Sbjct: 257 QSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRN 316
Query: 312 LSAYYQEIGRAGRDGLSSVCYTFYKTAD--FTKNNMIFQPNLNDSEIQEHSKTMMKRVEK 369
+ +YYQE GRAGRDGL + FY AD + + + +P +I+ H M
Sbjct: 317 IESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPQGQLQDIERHKLNAMG---A 373
Query: 370 YLELRTCRRKYLLNHFKGSSVTVAESQVPPDKCCDNC 406
+ E +TCRR LLN+F E + P CD C
Sbjct: 374 FAEAQTCRRLVLLNYF-------GEGRQEPCGNCDIC 403
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 190 bits (483), Expect = 1e-48, Method: Compositional matrix adjust.
Identities = 108/277 (38%), Positives = 148/277 (53%), Gaps = 17/277 (6%)
Query: 133 VLIAIDEAHCVSQWGHDFRPSYRCLSELRLPLPDVPILAVTATATPVVIDDICTSLMLRD 192
VL+A+DEAHC+SQWGHDFRP Y L +LR P +P A+TATA DI L L D
Sbjct: 141 VLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFXALTATADDTTRQDIVRLLGLND 200
Query: 193 PNIINTGFDRPNLYLAASVKQDDIMADLRKLTNFENQFEG-STIIYCPTKVICEKVCDVL 251
P I + FDRPN+ K L +L + + G S IIYC ++ E L
Sbjct: 201 PLIQISSFDRPNIRYXLXEK----FKPLDQLXRYVQEQRGKSGIIYCNSRAKVEDTAARL 256
Query: 252 SRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPKD 311
GI YHA + R ++ F +D +++VVAT AFG GI+KP+VR V+H+ P++
Sbjct: 257 QSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXGINKPNVRFVVHFDIPRN 316
Query: 312 LSAYYQEIGRAGRDGLSSVCYTFYKTAD--FTKNNMIFQPNLNDSEIQEHSKTMMKRVEK 369
+ +YYQE GRAGRDGL + FY AD + + + +P +I+ H +
Sbjct: 317 IESYYQETGRAGRDGLPAEAXLFYDPADXAWLRRCLEEKPQGQLQDIERHK---LNAXGA 373
Query: 370 YLELRTCRRKYLLNHFKGSSVTVAESQVPPDKCCDNC 406
+ E +TCRR LLN+F E + P CD C
Sbjct: 374 FAEAQTCRRLVLLNYF-------GEGRQEPCGNCDIC 403
>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 = 182 bits (463), Expect = 3e-46, Method: Compositional matrix adjust.
Identities = 111/305 (36%), Positives = 160/305 (52%), Gaps = 25/305 (8%)
Query: 124 LFLSRIP------RIVLIAIDEAHCVSQWGHDFRPSYRCLSELRLPLPDVPILAVTATAT 177
+F+SR+ R IA+DE HC SQWGHDFRP Y+ L L+ P+ ++ +TATAT
Sbjct: 152 MFMSRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATAT 211
Query: 178 PVVIDDICTSLMLRDPNIINTGFDRPNLYLAASVK---QDDIMADLRKLTNFENQFEG-S 233
V+ D L + F+RPNLY K +D + D+ KL N +++G S
Sbjct: 212 NHVLTDAQKILCIEKCFTFTASFNRPNLYYEVRQKPSNTEDFIEDIVKLIN--GRYKGQS 269
Query: 234 TIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGM 293
IIYC ++ E+V L GI YHA++ + + +H + + I+VVVAT AFGM
Sbjct: 270 GIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGM 329
Query: 294 GIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFYKTAD-FTKNNMIFQPNLN 352
GIDKPDVR VIH+ K + YYQE GRAGRD + + C +Y D F ++M+ N+
Sbjct: 330 GIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSMVVMENVG 389
Query: 353 DSEIQEHSKTMMKRVEKYLELRTCRRKYLLNHFKGSSVTVAESQVPPDKCCDNCRHNEML 412
++ E V + CRR + HF V +E+ +K CDNC +
Sbjct: 390 QQKLYE-------MVSYCQNISKCRRVLMAQHF--DEVWNSEA---CNKMCDNCCKDSAF 437
Query: 413 ELEQV 417
E + +
Sbjct: 438 ERKNI 442
>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 = 61.6 bits (148), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 31/108 (28%), Positives = 55/108 (50%)
Query: 235 IIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMG 294
+++C TK +++ L G + H +S QR+++ LF + I++++AT G
Sbjct: 242 LVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVXSRG 301
Query: 295 IDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFYKTADFTK 342
ID D+ CVI+Y P++ +Y IGR GR G + ++ K
Sbjct: 302 IDVNDLNCVINYHLPQNPESYXHRIGRTGRAGKKGKAISIINRREYKK 349
>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 = 55.5 bits (132), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 29/106 (27%), Positives = 48/106 (45%)
Query: 235 IIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMG 294
+I+C TK + + + + H + K+R+ I F +V+++T + G
Sbjct: 281 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 340
Query: 295 IDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFYKTADF 340
+D P V +I+Y P + Y IGR+GR G V F K D
Sbjct: 341 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI 386
>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 = 55.1 bits (131), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 29/106 (27%), Positives = 48/106 (45%)
Query: 235 IIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMG 294
+I+C TK + + + + H + K+R+ I F +V+++T + G
Sbjct: 259 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 318
Query: 295 IDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFYKTADF 340
+D P V +I+Y P + Y IGR+GR G V F K D
Sbjct: 319 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI 364
>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 = 55.1 bits (131), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 29/106 (27%), Positives = 48/106 (45%)
Query: 235 IIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMG 294
+I+C TK + + + + H + K+R+ I F +V+++T + G
Sbjct: 281 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 340
Query: 295 IDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFYKTADF 340
+D P V +I+Y P + Y IGR+GR G V F K D
Sbjct: 341 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI 386
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 55.1 bits (131), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 29/107 (27%), Positives = 48/107 (44%)
Query: 234 TIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGM 293
+I+C TK + + + + H + K+R+ I F +V+++T +
Sbjct: 243 AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWAR 302
Query: 294 GIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFYKTADF 340
G+D P V +I+Y P + Y IGR+GR G V F K D
Sbjct: 303 GLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDI 349
>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 = 55.1 bits (131), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 29/106 (27%), Positives = 48/106 (45%)
Query: 235 IIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMG 294
+I+C TK + + + + H + K+R+ I F +V+++T + G
Sbjct: 280 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 339
Query: 295 IDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFYKTADF 340
+D P V +I+Y P + Y IGR+GR G V F K D
Sbjct: 340 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI 385
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 54.7 bits (130), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 29/107 (27%), Positives = 48/107 (44%)
Query: 234 TIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGM 293
+I+C TK + + + + H + K+R+ I F +V+++T +
Sbjct: 243 AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWAR 302
Query: 294 GIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFYKTADF 340
G+D P V +I+Y P + Y IGR+GR G V F K D
Sbjct: 303 GLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDI 349
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 30/104 (28%), Positives = 46/104 (44%), Gaps = 3/104 (2%)
Query: 234 TIIYCPTKVICEKVCDVLSRNGIQNRP---YHAHISLKQRKEIHGLFVKDLIKVVVATCA 290
II+ PT +C +L ++ P +H I+ +R + F KD ++V T
Sbjct: 291 AIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV 350
Query: 291 FGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTF 334
G+D P+V V+ G P +L+ Y IGR R G F
Sbjct: 351 GARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLF 394
>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 = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 32/104 (30%), Positives = 49/104 (47%), Gaps = 5/104 (4%)
Query: 234 TIIYCPTKVICEKVCDVLSRNGIQNRP---YHAHISLKQRKEIHGLFVKDLIKVVVATCA 290
II+ PT +C +L ++ P +H I+ +R + F KD ++V T
Sbjct: 342 AIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV 401
Query: 291 FGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGL--SSVCY 332
G+D P+V V+ G P +L+ Y IGR R G SSV +
Sbjct: 402 GARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLF 445
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 30/104 (28%), Positives = 46/104 (44%), Gaps = 3/104 (2%)
Query: 234 TIIYCPTKVICEKVCDVLSRNGIQNRP---YHAHISLKQRKEIHGLFVKDLIKVVVATCA 290
II+ PT +C +L ++ P +H I+ +R + F KD ++V T
Sbjct: 291 AIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV 350
Query: 291 FGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTF 334
G+D P+V V+ G P +L+ Y IGR R G F
Sbjct: 351 GARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLF 394
>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 = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 37/140 (26%), Positives = 60/140 (42%), Gaps = 13/140 (9%)
Query: 234 TIIYCPTKVICEKVCDVLSRNGIQNRP---YHAHISLKQRKEIHGLFVKDLIKVVVATCA 290
II+ PT +C +L ++ P +H I+ +R + F KD ++V T
Sbjct: 36 AIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV 95
Query: 291 FGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFYKTADFTKNNMIFQPN 350
G+D P+V V+ G P +L+ Y IGR R G F K+ + F
Sbjct: 96 GARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLF-----ICKDELPFVRE 150
Query: 351 LNDSEIQEHSKTMMKRVEKY 370
L D++ ++ + EKY
Sbjct: 151 LEDAK-----NIVIAKQEKY 165
>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 = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 37/140 (26%), Positives = 60/140 (42%), Gaps = 13/140 (9%)
Query: 234 TIIYCPTKVICEKVCDVLSRNGIQNRP---YHAHISLKQRKEIHGLFVKDLIKVVVATCA 290
II+ PT +C +L ++ P +H I+ +R + F KD ++V T
Sbjct: 36 AIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV 95
Query: 291 FGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFYKTADFTKNNMIFQPN 350
G+D P+V V+ G P +L+ Y IGR R G F K+ + F
Sbjct: 96 GARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLF-----ICKDELPFVRE 150
Query: 351 LNDSEIQEHSKTMMKRVEKY 370
L D++ ++ + EKY
Sbjct: 151 LEDAK-----NIVIAKQEKY 165
>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 = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 29/96 (30%), Positives = 45/96 (46%), Gaps = 3/96 (3%)
Query: 234 TIIYCPTKVICEKVCDVLSRNGIQNRP---YHAHISLKQRKEIHGLFVKDLIKVVVATCA 290
II+ PT +C +L ++ P +H I+ +R + F KD ++V T
Sbjct: 36 AIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV 95
Query: 291 FGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDG 326
G+D P+V V+ G P +L+ Y IGR R G
Sbjct: 96 GARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSG 131
>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 = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 47/102 (46%)
Query: 234 TIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGM 293
T+++ TK + + D L G H S + R+E F ++VAT
Sbjct: 49 TLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAAR 108
Query: 294 GIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFY 335
G+D +V+ VI++ P D+ Y IGR GR G + +F+
Sbjct: 109 GLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFF 150
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 47/102 (46%)
Query: 234 TIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGM 293
T+++ TK + + D L G H S + R+E F ++VAT
Sbjct: 279 TLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAAR 338
Query: 294 GIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFY 335
G+D +V+ VI++ P D+ Y IGR GR G + +F+
Sbjct: 339 GLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFF 380
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 35/126 (27%), Positives = 53/126 (42%), Gaps = 11/126 (8%)
Query: 215 DIMADLRKLTNFENQFEGSTIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIH 274
D++ +L L GS+II+ TK + L G + H + ++R +
Sbjct: 232 DVLTELYGLMTI-----GSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLI 286
Query: 275 GLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAP------KDLSAYYQEIGRAGRDGLS 328
F + KV++ T GID P V V++Y P D + Y IGR GR G
Sbjct: 287 DDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRK 346
Query: 329 SVCYTF 334
V +F
Sbjct: 347 GVAISF 352
>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 = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 32/109 (29%), Positives = 47/109 (43%), Gaps = 6/109 (5%)
Query: 232 GSTIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAF 291
GS+II+ TK + L G + H + ++R + F + KV++ T
Sbjct: 244 GSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVL 303
Query: 292 GMGIDKPDVRCVIHYGAP------KDLSAYYQEIGRAGRDGLSSVCYTF 334
GID P V V++Y P D + Y IGR GR G V +F
Sbjct: 304 ARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISF 352
>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 = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 41/82 (50%)
Query: 234 TIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGM 293
+++ TK E++ L R G + H +S +R+ + G F + ++V+VAT
Sbjct: 31 AMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAAR 90
Query: 294 GIDKPDVRCVIHYGAPKDLSAY 315
G+D P V V+HY P AY
Sbjct: 91 GLDIPQVDLVVHYRMPDRAEAY 112
>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera
Form 2, Complete Dimer, Symmetric
pdb|3EAQ|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase Hera
Form 2, Complete Dimer, Symmetric
pdb|3EAR|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Partial Dimer
pdb|3EAR|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Partial Dimer
pdb|3EAS|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Complete Dimer, Asymmetric
pdb|3EAS|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Complete Dimer, Asymmetric
Length = 212
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 41/82 (50%)
Query: 234 TIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGM 293
+++ TK E++ L R G + H +S +R+ + G F + ++V+VAT
Sbjct: 34 AMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAAR 93
Query: 294 GIDKPDVRCVIHYGAPKDLSAY 315
G+D P V V+HY P AY
Sbjct: 94 GLDIPQVDLVVHYRLPDRAEAY 115
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 32/109 (29%), Positives = 47/109 (43%), Gaps = 6/109 (5%)
Query: 232 GSTIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAF 291
GS+II+ TK + L G + H + ++R + F + KV++ T
Sbjct: 36 GSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVL 95
Query: 292 GMGIDKPDVRCVIHYGAP------KDLSAYYQEIGRAGRDGLSSVCYTF 334
GID P V V++Y P D + Y IGR GR G V +F
Sbjct: 96 ARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISF 144
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 49.3 bits (116), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 35/126 (27%), Positives = 53/126 (42%), Gaps = 11/126 (8%)
Query: 215 DIMADLRKLTNFENQFEGSTIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIH 274
D++ +L L GS+II+ TK + L G + H + ++R +
Sbjct: 26 DVLTELYGLXTI-----GSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLI 80
Query: 275 GLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAP------KDLSAYYQEIGRAGRDGLS 328
F + KV++ T GID P V V++Y P D + Y IGR GR G
Sbjct: 81 DDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRK 140
Query: 329 SVCYTF 334
V +F
Sbjct: 141 GVAISF 146
>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 = 48.9 bits (115), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 32/109 (29%), Positives = 47/109 (43%), Gaps = 6/109 (5%)
Query: 232 GSTIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAF 291
GS+II+ TK + L G + H + ++R + F + KV++ T
Sbjct: 37 GSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVL 96
Query: 292 GMGIDKPDVRCVIHYGAP------KDLSAYYQEIGRAGRDGLSSVCYTF 334
GID P V V++Y P D + Y IGR GR G V +F
Sbjct: 97 ARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISF 145
>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|B Chain B, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|C Chain C, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|D Chain D, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
Length = 434
Score = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 31/118 (26%), Positives = 51/118 (43%)
Query: 218 ADLRKLTNFENQFEGSTIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLF 277
A KL ++ TI++ TK + + LS H QR++ F
Sbjct: 287 AKRSKLIEILSEQADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDF 346
Query: 278 VKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFY 335
+KV++AT G+D +++ VI+Y P + Y IGR GR G + +F+
Sbjct: 347 KNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFF 404
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 32/109 (29%), Positives = 45/109 (41%), Gaps = 6/109 (5%)
Query: 232 GSTIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAF 291
G +II+C K E++ ++ +G ++ QR I F KV+V T
Sbjct: 358 GQSIIFCKKKDTAEEIARRMTADGHTVACLTGNLEGAQRDAIMDSFRVGTSKVLVTTNVI 417
Query: 292 GMGIDKPDVRCVIHYGAPKDLSA------YYQEIGRAGRDGLSSVCYTF 334
GID V V++Y P D + Y IGR GR G V F
Sbjct: 418 ARGIDVSQVNLVVNYDMPLDQAGRPDPQTYLHRIGRTGRFGRVGVSINF 466
>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 = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 27/105 (25%), Positives = 48/105 (45%)
Query: 234 TIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGM 293
+I+ K + + + L G++ H ++R + F + V+VAT
Sbjct: 57 VLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASK 116
Query: 294 GIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFYKTA 338
G+D P ++ VI+Y P+++ Y IGR G G + + TF A
Sbjct: 117 GLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKA 161
>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 = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 31/129 (24%), Positives = 52/129 (40%), Gaps = 1/129 (0%)
Query: 212 KQDDIMADLRKLTNFENQFEGS-TIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQR 270
+ DD+ L + Q E + +I++ + ++ + L GI N + +R
Sbjct: 10 RADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKR 69
Query: 271 KEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSV 330
E + + V+VAT GID PDV V ++ P+ Y IGR R G
Sbjct: 70 NEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGT 129
Query: 331 CYTFYKTAD 339
+ + D
Sbjct: 130 AISLVEAHD 138
>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 = 45.1 bits (105), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 43/93 (46%)
Query: 234 TIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGM 293
+II+C + E + +S+ G HA + + R + F L + +V T F
Sbjct: 47 SIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTR 106
Query: 294 GIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDG 326
GID V VI++ PK Y IGR+GR G
Sbjct: 107 GIDIQAVNVVINFDFPKLAETYLHRIGRSGRFG 139
>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 = 45.1 bits (105), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 45/102 (44%)
Query: 233 STIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFG 292
S II+C TK ++ D L G H + + R ++ F + + +VAT
Sbjct: 37 SCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAA 96
Query: 293 MGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTF 334
GID ++ VI+Y P + +Y GR GR G +F
Sbjct: 97 RGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISF 138
>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56
Length = 172
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 27/52 (51%)
Query: 283 KVVVATCAFGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTF 334
+++VAT FG G+D V +Y P+D Y + RAGR G + TF
Sbjct: 83 RILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITF 134
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/115 (25%), Positives = 48/115 (41%), Gaps = 1/115 (0%)
Query: 221 RKLTNFENQFE-GSTIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVK 279
RKL + + E +I+ + C + +L H + ++R + F
Sbjct: 238 RKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKD 297
Query: 280 DLIKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTF 334
+++VAT FG G+D V +Y P+D Y + RAGR G + TF
Sbjct: 298 FQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITF 352
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/115 (25%), Positives = 48/115 (41%), Gaps = 1/115 (0%)
Query: 221 RKLTNFENQFE-GSTIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVK 279
RKL + + E +I+ + C + +L H + ++R + F
Sbjct: 239 RKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKD 298
Query: 280 DLIKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTF 334
+++VAT FG G+D V +Y P+D Y + RAGR G + TF
Sbjct: 299 FQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITF 353
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/115 (25%), Positives = 48/115 (41%), Gaps = 1/115 (0%)
Query: 221 RKLTNFENQFE-GSTIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVK 279
RKL + + E +I+ + C + +L H + ++R + F
Sbjct: 239 RKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKD 298
Query: 280 DLIKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTF 334
+++VAT FG G+D V +Y P+D Y + RAGR G + TF
Sbjct: 299 FQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITF 353
>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 = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 35/138 (25%), Positives = 59/138 (42%), Gaps = 7/138 (5%)
Query: 232 GSTIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAF 291
G II+C T+ + + + ++G Q ++++QR I F KV++ T
Sbjct: 35 GQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVC 94
Query: 292 GMGIDKPDVRCVIHY------GAPKDLSAYYQEIGRAGRDGLSSVCYTFYKTADFTKNNM 345
GID V V+++ G D Y IGR GR G + + + D + M
Sbjct: 95 ARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIE-VDELPSLM 153
Query: 346 IFQPNLNDSEIQEHSKTM 363
Q + N S Q +++ M
Sbjct: 154 KIQDHFNSSIKQLNAEDM 171
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 41/147 (27%), Positives = 60/147 (40%), Gaps = 15/147 (10%)
Query: 192 DPNIINTGFDRPNLYLAASVKQDDIMADLR--KLTNFENQFEGSTI----IYCPTKVICE 245
DPN+I + L ++KQ ++ R K N + TI I+C T+
Sbjct: 240 DPNVIKLKREEETL---DTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTAS 296
Query: 246 KVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIH 305
+ LS+ G Q + ++QR + F + KV+V T GID V VI+
Sbjct: 297 WLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVIN 356
Query: 306 YGAPKDLSA------YYQEIGRAGRDG 326
+ P D Y IGR GR G
Sbjct: 357 FDLPVDKDGNPDNETYLHRIGRTGRFG 383
>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 = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 41/147 (27%), Positives = 60/147 (40%), Gaps = 15/147 (10%)
Query: 192 DPNIINTGFDRPNLYLAASVKQDDIMADLR--KLTNFENQFEGSTI----IYCPTKVICE 245
DPN+I + L ++KQ ++ R K N + TI I+C T+
Sbjct: 261 DPNVIKLKREEETL---DTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTAS 317
Query: 246 KVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIH 305
+ LS+ G Q + ++QR + F + KV+V T GID V VI+
Sbjct: 318 WLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVIN 377
Query: 306 YGAPKDLSA------YYQEIGRAGRDG 326
+ P D Y IGR GR G
Sbjct: 378 FDLPVDKDGNPDNETYLHRIGRTGRFG 404
>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 = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 41/147 (27%), Positives = 60/147 (40%), Gaps = 15/147 (10%)
Query: 192 DPNIINTGFDRPNLYLAASVKQDDIMADLR--KLTNFENQFEGSTI----IYCPTKVICE 245
DPN+I + L ++KQ ++ R K N + TI I+C T+
Sbjct: 224 DPNVIKLKREEETL---DTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTAS 280
Query: 246 KVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIH 305
+ LS+ G Q + ++QR + F + KV+V T GID V VI+
Sbjct: 281 WLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVIN 340
Query: 306 YGAPKDLSA------YYQEIGRAGRDG 326
+ P D Y IGR GR G
Sbjct: 341 FDLPVDKDGNPDNETYLHRIGRTGRFG 367
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 43/92 (46%)
Query: 235 IIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMG 294
II+C + E + ++ G HA + ++R ++ F + ++ +V + G
Sbjct: 262 IIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRG 321
Query: 295 IDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDG 326
ID V VI++ PK Y IGR+GR G
Sbjct: 322 IDIQAVNVVINFDFPKTAETYLHRIGRSGRFG 353
>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 = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 41/147 (27%), Positives = 60/147 (40%), Gaps = 15/147 (10%)
Query: 192 DPNIINTGFDRPNLYLAASVKQDDIMADLR--KLTNFENQFEGSTI----IYCPTKVICE 245
DPN+I + L ++KQ ++ R K N + TI I+C T+
Sbjct: 291 DPNVIKLKREEETL---DTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTAS 347
Query: 246 KVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIH 305
+ LS+ G Q + ++QR + F + KV+V T GID V VI+
Sbjct: 348 WLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVIN 407
Query: 306 YGAPKDLSA------YYQEIGRAGRDG 326
+ P D Y IGR GR G
Sbjct: 408 FDLPVDKDGNPDNETYLHRIGRTGRFG 434
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 27/51 (52%)
Query: 284 VVVATCAFGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTF 334
+++ T G+D P V VI++ AP+DL Y IGR GR G TF
Sbjct: 269 MLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITF 319
>pdb|2P6R|A Chain A, Crystal Structure Of Superfamily 2 Helicase Hel308 In
Complex With Unwound Dna
pdb|2P6U|A Chain A, Apo Structure Of The Hel308 Superfamily 2 Helicase
Length = 702
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 261 YHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIH-------YGAPKDLS 313
+HA + QR+ + F + IKVVVAT G++ P R ++ Y +S
Sbjct: 302 HHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVS 361
Query: 314 AYYQEIGRAGRDGL 327
Y Q GRAGR G+
Sbjct: 362 EYKQMAGRAGRPGM 375
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 43/99 (43%), Gaps = 11/99 (11%)
Query: 261 YHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIH--YGAPKDLSAYYQE 318
+HA +S R I F + IKV+VAT G++ P +I Y K ++ YY E
Sbjct: 318 HHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDE 377
Query: 319 I---------GRAGRDGLSSVCYTFYKTADFTKNNMIFQ 348
I GRAGR G + + D + +F+
Sbjct: 378 IPIMEYKQMSGRAGRPGFDQIGESIVVVRDKEDVDRVFK 416
>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
Bound To Amppnp
Length = 997
Score = 37.7 bits (86), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 28/66 (42%), Positives = 35/66 (53%), Gaps = 10/66 (15%)
Query: 273 IHGLFVKDLIKVVVATCAFGMGIDKPDVRCVI------HYG-APKDLS--AYYQEIGRAG 323
I LF K IKV+ AT F MG++ P R VI H G ++L+ + Q GRAG
Sbjct: 417 IEILFSKGFIKVLFATETFAMGLNLP-TRTVIFSSIRKHDGNGLRELTPGEFTQMAGRAG 475
Query: 324 RDGLSS 329
R GL S
Sbjct: 476 RRGLDS 481
>pdb|2ZJ2|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 1
pdb|2ZJ5|A Chain A, Archaeal Dna Helicase Hjm Complexed With Adp In Form 1
pdb|2ZJ8|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 2
pdb|2ZJA|A Chain A, Archaeal Dna Helicase Hjm Complexed With Amppcp In Form 2
Length = 720
Score = 36.6 bits (83), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 37/132 (28%), Positives = 58/132 (43%), Gaps = 19/132 (14%)
Query: 201 DRPNLYLAASVKQDDIMADLRKLTNFENQFEGSTIIYCPTKVICEKVCDVLSRNGIQNRP 260
+R L L+ VK ++R L + E + PT EK+ + R G+
Sbjct: 251 ERVALELSKKVKSLLTKPEIRALNELADSLEEN-----PTN---EKLAKAI-RGGVAF-- 299
Query: 261 YHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIH-------YGAPK-DL 312
+HA + +R + F K +IK VVAT GI+ P R +I +G + +
Sbjct: 300 HHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPI 359
Query: 313 SAYYQEIGRAGR 324
+Q +GRAGR
Sbjct: 360 IEVHQMLGRAGR 371
>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 = 35.0 bits (79), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 33/148 (22%), Positives = 61/148 (41%), Gaps = 21/148 (14%)
Query: 185 CTSLMLRDPNIINTGFDRPNLYLAASVKQDDIMADLRKLTNFENQFEGSTIIYCPTKVIC 244
SL+++ I G D P K D + +R+ + + I++ +
Sbjct: 328 AISLLVQAKEI---GLDHP--------KMDKLKEIIRE--QLQRKQNSKIIVFTNYRETA 374
Query: 245 EKVCDVLSRNGIQNRPYHAH--------ISLKQRKEIHGLFVKDLIKVVVATCAFGMGID 296
+K+ + L ++GI+ + + +S +++K I F + V+VAT G+D
Sbjct: 375 KKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLD 434
Query: 297 KPDVRCVIHYGAPKDLSAYYQEIGRAGR 324
P+V V+ Y Q GR GR
Sbjct: 435 VPEVDLVVFYEPVPSAIRSIQRRGRTGR 462
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 32.0 bits (71), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 262 HAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPK-DLSAYYQEIG 320
H +S +++ + F + ++V+T +GID P ++ + L+ +Q G
Sbjct: 620 HGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRG 679
Query: 321 RAGRDGLSSVCY 332
R GR G + C+
Sbjct: 680 RVGRGGQEAYCF 691
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 31.6 bits (70), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 36/81 (44%)
Query: 235 IIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMG 294
+I+C T+ E++ L + ++ + ++R I F +++++T G
Sbjct: 34 VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG 93
Query: 295 IDKPDVRCVIHYGAPKDLSAY 315
ID V VI+Y P + Y
Sbjct: 94 IDVQQVSLVINYDLPANKENY 114
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 36/81 (44%)
Query: 235 IIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMG 294
+I+C T+ E++ L + ++ + ++R I F +++++T G
Sbjct: 263 VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSGSSRILISTDLLARG 322
Query: 295 IDKPDVRCVIHYGAPKDLSAY 315
ID V VI+Y P + Y
Sbjct: 323 IDVQQVSLVINYDLPANKENY 343
>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 = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 36/81 (44%)
Query: 235 IIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMG 294
+I+C T+ E++ L + ++ + ++R I F +++++T G
Sbjct: 264 VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG 323
Query: 295 IDKPDVRCVIHYGAPKDLSAY 315
ID V VI+Y P + Y
Sbjct: 324 IDVQQVSLVINYDLPANKENY 344
>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 = 30.0 bits (66), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 27/57 (47%)
Query: 269 QRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRD 325
++KE+ F I +++AT G+D + VI YG + A Q GRA D
Sbjct: 452 EQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARAD 508
>pdb|1TZ9|A Chain A, Crystal Structure Of The Putative Mannonate Dehydratase
From Enterococcus Faecalis, Northeast Structural
Genomics Target Efr41
pdb|1TZ9|B Chain B, Crystal Structure Of The Putative Mannonate Dehydratase
From Enterococcus Faecalis, Northeast Structural
Genomics Target Efr41
Length = 367
Score = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 11/83 (13%)
Query: 266 SLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRD 325
+LKQ E GL + + V + A G D+ D HY + Y Q + G+
Sbjct: 59 ALKQSVEQEGLALLGIESVAIHD-AIKAGTDQRD-----HY-----IDNYRQTLRNLGKC 107
Query: 326 GLSSVCYTFYKTADFTKNNMIFQ 348
G+S VCY+F + K ++ ++
Sbjct: 108 GISLVCYSFKPIFGWAKTDLAYE 130
>pdb|3L0A|A Chain A, Crystal Structure Of Putative Exonuclease
(Rer070207002219) From Eubacterium Rectale At 2.19 A
Resolution
Length = 266
Score = 28.9 bits (63), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 392 VAESQVPPDKC--CDNCRHNEMLE 413
V +V PD+C CD CRHN +L+
Sbjct: 231 VKNGEVEPDRCELCDCCRHNRVLK 254
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
0.323 0.138 0.425
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,694,728
Number of Sequences: 62578
Number of extensions: 565339
Number of successful extensions: 1178
Number of sequences better than 100.0: 56
Number of HSP's better than 100.0 without gapping: 50
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1107
Number of HSP's gapped (non-prelim): 63
length of query: 451
length of database: 14,973,337
effective HSP length: 102
effective length of query: 349
effective length of database: 8,590,381
effective search space: 2998042969
effective search space used: 2998042969
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)