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= 012794
(456 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 155 bits (393), Expect = 4e-38, Method: Compositional matrix adjust.
Identities = 114/289 (39%), Positives = 168/289 (58%), Gaps = 17/289 (5%)
Query: 29 AISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQH 87
A+ + +LSDL+ V A + +VFT+TK + +E++ L + ++ALHGD+SQ
Sbjct: 7 AVPAPVRGRLEVLSDLLYV-ASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQG 65
Query: 88 QRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE 147
+RER + FRQG+ VLVATDVAARGLDIP VDL++HY +P+ E + HRSGRTGRAG+
Sbjct: 66 ERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRG 125
Query: 148 GTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFF 207
G +L++ +RR V +LER VG +F+ V+PP E+VLE+ ++A L V + +
Sbjct: 126 GRVVLLYGPRERRDVEALERAVGRRFKRVNPPTPEEVLEAKWRHLLARLARVPEKDYRLY 185
Query: 208 TPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVT-------LQLTRDSAF 260
A RL E + +AA LA L G + + RSL+ E+GW T L L R A
Sbjct: 186 QDFAGRLFAEGRVEVVAALLALLLGGAP--AERSLLTGEEGWRTYKATGPRLSLPRLVAL 243
Query: 261 SRG-----FMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLP 304
+G A + GF D+ P A E+ + + RV+G + ++P
Sbjct: 244 LKGQGLEVGKVAEAEGGFYVDLRPEARPEVAGLRLEPARRVEG-LLEIP 291
>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 = 142 bits (358), Expect = 4e-34, Method: Compositional matrix adjust.
Identities = 87/190 (45%), Positives = 123/190 (64%), Gaps = 2/190 (1%)
Query: 29 AISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQH 87
A+ + +LSDL+ V A + +VFT+TK + +E++ L + ++ALHGD+SQ
Sbjct: 10 AVPAPVRGRLEVLSDLLYV-ASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQG 68
Query: 88 QRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE 147
+RER L FRQG+ VLVATDVAARGLDIP VDL++HY LP+ E + HRSGRTGRAG+
Sbjct: 69 ERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRG 128
Query: 148 GTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFF 207
G +L++ +RR V +LER VG +F+ V+PP E+VLE+ ++A L V + +
Sbjct: 129 GRVVLLYGPRERRDVEALERAVGRRFKRVNPPTPEEVLEAKWRHLLARLARVPEKDYRLY 188
Query: 208 TPTAQRLIEE 217
A RL E
Sbjct: 189 QDFAGRLFAE 198
>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 = 115 bits (289), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 51/114 (44%), Positives = 80/114 (70%), Gaps = 1/114 (0%)
Query: 55 IVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARG 113
+VF +TKRD E++ L I + A+HGD+SQ QRE+ + F+Q K +L+ATDV +RG
Sbjct: 242 LVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVXSRG 301
Query: 114 LDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER 167
+D+ +++ +I+Y LP +PE++ HR GRTGRAGK+G AI + + + +R +ER
Sbjct: 302 IDVNDLNCVINYHLPQNPESYXHRIGRTGRAGKKGKAISIINRREYKKLRYIER 355
>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 = 108 bits (269), Expect = 8e-24, Method: Compositional matrix adjust.
Identities = 60/145 (41%), Positives = 80/145 (55%), Gaps = 1/145 (0%)
Query: 22 AEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVS-LALTSIIASEAL 80
+E I + + KR+ L DL+ K T+VF +TK+ AD + A ++
Sbjct: 17 SENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSI 76
Query: 81 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 140
HGD SQ RE L+ FR GK +LVAT VAARGLDI NV +I+++LP+D E +VHR GR
Sbjct: 77 HGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGR 136
Query: 141 TGRAGKEGTAILMFTSSQRRTVRSL 165
TGR G G A F + L
Sbjct: 137 TGRVGNLGLATSFFNERNINITKDL 161
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 107 bits (267), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 61/150 (40%), Positives = 85/150 (56%), Gaps = 5/150 (3%)
Query: 7 MFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE 66
+F +VG+ E + + + + + KR+ L DL+ K T+VF +TK+ AD
Sbjct: 236 IFLAVGRVGSTSENITQKV----VWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADS 291
Query: 67 VS-LALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHY 125
+ A ++HGD SQ RE L+ FR GK +LVAT VAARGLDI NV +I++
Sbjct: 292 LEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINF 351
Query: 126 ELPNDPETFVHRSGRTGRAGKEGTAILMFT 155
+LP+D E +VHR GRTGR G G A F
Sbjct: 352 DLPSDIEEYVHRIGRTGRVGNLGLATSFFN 381
>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 = 105 bits (261), Expect = 8e-23, Method: Compositional matrix adjust.
Identities = 60/173 (34%), Positives = 95/173 (54%), Gaps = 3/173 (1%)
Query: 16 NQDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI 74
+DE EGIK + ++ K L DL + ++F TKR D ++ +
Sbjct: 220 KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT-QAVIFCNTKRKVDWLTEKMREA 278
Query: 75 -IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
++HGD+ Q +RE + FR G VL++TDV ARGLD+P V LII+Y+LPN+ E
Sbjct: 279 NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL 338
Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLE 186
++HR GR+GR G++G AI + R +R +E+ + + + V + +LE
Sbjct: 339 YIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLILE 391
>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 = 104 bits (260), Expect = 8e-23, Method: Compositional matrix adjust.
Identities = 60/173 (34%), Positives = 95/173 (54%), Gaps = 3/173 (1%)
Query: 16 NQDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI 74
+DE EGIK + ++ K L DL + ++F TKR D ++ +
Sbjct: 242 KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT-QAVIFCNTKRKVDWLTEKMREA 300
Query: 75 -IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
++HGD+ Q +RE + FR G VL++TDV ARGLD+P V LII+Y+LPN+ E
Sbjct: 301 NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL 360
Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLE 186
++HR GR+GR G++G AI + R +R +E+ + + + V + +LE
Sbjct: 361 YIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLILE 413
>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 = 103 bits (257), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 57/154 (37%), Positives = 87/154 (56%), Gaps = 3/154 (1%)
Query: 16 NQDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI 74
+DE EGIK + ++ K L DL + ++F TKR D ++ +
Sbjct: 242 KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT-QAVIFCNTKRKVDWLTEKMREA 300
Query: 75 -IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
++HGD+ Q +RE + FR G VL++TDV ARGLD+P V LII+Y+LPN+ E
Sbjct: 301 NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL 360
Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER 167
++HR GR+GR G++G AI + R +R +E+
Sbjct: 361 YIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQ 394
>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 = 103 bits (257), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 57/154 (37%), Positives = 87/154 (56%), Gaps = 3/154 (1%)
Query: 16 NQDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI 74
+DE EGIK + ++ K L DL + ++F TKR D ++ +
Sbjct: 241 KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT-QAVIFCNTKRKVDWLTEKMREA 299
Query: 75 -IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
++HGD+ Q +RE + FR G VL++TDV ARGLD+P V LII+Y+LPN+ E
Sbjct: 300 NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL 359
Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER 167
++HR GR+GR G++G AI + R +R +E+
Sbjct: 360 YIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQ 393
>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 = 103 bits (257), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 52/143 (36%), Positives = 88/143 (61%), Gaps = 2/143 (1%)
Query: 29 AISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQH 87
I +K ++L D++ I+F +TK ++++ L + + +HG + Q
Sbjct: 14 VIQVREENKFSLLKDVLMT-ENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQE 72
Query: 88 QRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE 147
R +N F++G++ LVATDVAARG+DI N+ L+I+Y+LP + E++VHR+GRTGRAG +
Sbjct: 73 DRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNK 132
Query: 148 GTAILMFTSSQRRTVRSLERDVG 170
G AI T+ ++R + +E +G
Sbjct: 133 GKAISFVTAFEKRFLADIEEYIG 155
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 103 bits (257), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 56/154 (36%), Positives = 87/154 (56%), Gaps = 3/154 (1%)
Query: 16 NQDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI 74
+DE EGIK + ++ K L DL + ++F TKR D ++ +
Sbjct: 205 KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT-QAVIFCNTKRKVDWLTEKMREA 263
Query: 75 -IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
++HGD+ Q +RE + FR G VL++TDV ARGLD+P V LII+Y+LPN+ E
Sbjct: 264 NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL 323
Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER 167
++HR GR+GR G++G A+ + R +R +E+
Sbjct: 324 YIHRIGRSGRYGRKGVAVNFVKNDDIRVLRDIEQ 357
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 103 bits (256), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 56/154 (36%), Positives = 87/154 (56%), Gaps = 3/154 (1%)
Query: 16 NQDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI 74
+DE EGIK + ++ K L DL + ++F TKR D ++ +
Sbjct: 205 KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT-QAVIFCNTKRKVDWLTEKMREA 263
Query: 75 -IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
++HGD+ Q +RE + FR G VL++TDV ARGLD+P V LII+Y+LPN+ E
Sbjct: 264 NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL 323
Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER 167
++HR GR+GR G++G A+ + R +R +E+
Sbjct: 324 YIHRIGRSGRYGRKGVAVNFVKNDDIRVLRDIEQ 357
>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 = 99.0 bits (245), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 55/137 (40%), Positives = 84/137 (61%), Gaps = 5/137 (3%)
Query: 27 LYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDIS 85
+Y ++ A KR+ L ++++ A G TIVF +TKR AD ++ L+ + ++HGD
Sbjct: 280 IYEVNKYA--KRSKLIEILSEQADG--TIVFVETKRGADFLASFLSEKEFPTTSIHGDRL 335
Query: 86 QHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG 145
Q QRE+ L F+ G VL+AT VA+RGLDI N+ +I+Y++P+ + +VHR GRTGR G
Sbjct: 336 QSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVG 395
Query: 146 KEGTAILMFTSSQRRTV 162
G A F + R +
Sbjct: 396 NNGRATSFFDPEKDRAI 412
>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 = 96.7 bits (239), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 52/137 (37%), Positives = 80/137 (58%), Gaps = 16/137 (11%)
Query: 26 KLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEA-----L 80
+LY K +L++L V G +I+F TK+ A+ L + SE L
Sbjct: 219 QLYMDCKNEADKFDVLTELYGVMTIGS-SIIFVATKKTAN----VLYGKLKSEGHEVSIL 273
Query: 81 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETF 134
HGD+ +R+R ++ FR+G+ VL+ T+V ARG+DIP V ++++Y+LP DP T+
Sbjct: 274 HGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATY 333
Query: 135 VHRSGRTGRAGKEGTAI 151
+HR GRTGR G++G AI
Sbjct: 334 IHRIGRTGRFGRKGVAI 350
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 95.5 bits (236), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 47/119 (39%), Positives = 73/119 (61%), Gaps = 16/119 (13%)
Query: 39 TILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQ 98
TI S +I V K +++ + K + EVS+ LHGD+ +R+R ++ FR+
Sbjct: 242 TIGSSIIFVATKKTANVLYGKLKSEGHEVSI----------LHGDLQTQERDRLIDDFRE 291
Query: 99 GKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETFVHRSGRTGRAGKEGTAI 151
G+ VL+ T+V ARG+DIP V ++++Y+LP DP T++HR GRTGR G++G AI
Sbjct: 292 GRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAI 350
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 94.4 bits (233), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 47/119 (39%), Positives = 73/119 (61%), Gaps = 16/119 (13%)
Query: 39 TILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQ 98
TI S +I V K +++ + K + EVS+ LHGD+ +R+R ++ FR+
Sbjct: 34 TIGSSIIFVATKKTANVLYGKLKSEGHEVSI----------LHGDLQTQERDRLIDDFRE 83
Query: 99 GKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETFVHRSGRTGRAGKEGTAI 151
G+ VL+ T+V ARG+DIP V ++++Y+LP DP T++HR GRTGR G++G AI
Sbjct: 84 GRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAI 142
>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 = 93.2 bits (230), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 52/137 (37%), Positives = 79/137 (57%), Gaps = 16/137 (11%)
Query: 26 KLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEA-----L 80
+LY K +L++L V G +I+F TK+ A+ L + SE L
Sbjct: 12 QLYXDCKNEADKFDVLTELYGVXTIGS-SIIFVATKKTAN----VLYGKLKSEGHEVSIL 66
Query: 81 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETF 134
HGD+ +R+R ++ FR+G+ VL+ T+V ARG+DIP V +++Y+LP DP T+
Sbjct: 67 HGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATY 126
Query: 135 VHRSGRTGRAGKEGTAI 151
+HR GRTGR G++G AI
Sbjct: 127 IHRIGRTGRFGRKGVAI 143
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 92.4 bits (228), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 50/142 (35%), Positives = 80/142 (56%), Gaps = 23/142 (16%)
Query: 16 NQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSII 75
N+ +K +LY + T +S +I V K +++ + K + EVS+
Sbjct: 20 NEADKFDVLTELYGLXTIGSS-------IIFVATKKTANVLYGKLKSEGHEVSI------ 66
Query: 76 ASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN------ 129
LHGD+ +R+R ++ FR+G+ VL+ T+V ARG+DIP V +++Y+LP
Sbjct: 67 ----LHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQA 122
Query: 130 DPETFVHRSGRTGRAGKEGTAI 151
DP T++HR GRTGR G++G AI
Sbjct: 123 DPATYIHRIGRTGRFGRKGVAI 144
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 89.0 bits (219), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 45/99 (45%), Positives = 66/99 (66%), Gaps = 5/99 (5%)
Query: 54 TIVFTQTK-RDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAAR 112
IVF +T+ R A V L +I L GD+ Q R R ++ FR+G++ +L+ TDVA+R
Sbjct: 223 VIVFVRTRNRVAKLVRLFDNAI----ELRGDLPQSVRNRNIDAFREGEYDMLITTDVASR 278
Query: 113 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 151
GLDIP V+ +I+++ P D T++HR GRTGR G++G AI
Sbjct: 279 GLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAI 317
>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 = 86.7 bits (213), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 40/98 (40%), Positives = 61/98 (62%), Gaps = 1/98 (1%)
Query: 54 TIVFTQTKRDADEV-SLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAAR 112
++F + K D D + L + + A+HG Q +R + + FR+GK VLVATDVA++
Sbjct: 57 VLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASK 116
Query: 113 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTA 150
GLD P + +I+Y++P + E +VHR GRTG +G G A
Sbjct: 117 GLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIA 154
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 85.1 bits (209), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 51/142 (35%), Positives = 85/142 (59%), Gaps = 9/142 (6%)
Query: 18 DEKLAEGIK-LYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIA 76
+E EGIK LY + K +L +L + G ++I+F + K A+E++ +T+
Sbjct: 324 EELSVEGIKQLYMDCQSEEHKYNVLVELYGLLTIG-QSIIFCKKKDTAEEIARRMTADGH 382
Query: 77 SEA-LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP------N 129
+ A L G++ QR+ ++ FR G VLV T+V ARG+D+ V+L+++Y++P
Sbjct: 383 TVACLTGNLEGAQRDAIMDSFRVGTSKVLVTTNVIARGIDVSQVNLVVNYDMPLDQAGRP 442
Query: 130 DPETFVHRSGRTGRAGKEGTAI 151
DP+T++HR GRTGR G+ G +I
Sbjct: 443 DPQTYLHRIGRTGRFGRVGVSI 464
>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 = 81.3 bits (199), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 40/100 (40%), Positives = 65/100 (65%), Gaps = 1/100 (1%)
Query: 53 KTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA 111
++IVF + + E++ L I + L G++ Q +R + +G+ VLVATDVAA
Sbjct: 32 RSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAA 91
Query: 112 RGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 151
RG+DIP+V + ++++P +T++HR GRT RAG++GTAI
Sbjct: 92 RGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAI 131
>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 = 80.9 bits (198), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 44/159 (27%), Positives = 83/159 (52%), Gaps = 2/159 (1%)
Query: 13 QVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT 72
++ +E +G+ Y T K L+ L + + ++I+F + + + ++ ++
Sbjct: 7 EINLMEELTLKGVTQYYAYVTERQKVHCLNTLFSR-LQINQSIIFCNSSQRVELLAKKIS 65
Query: 73 SI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDP 131
+ + +H + Q R R + FR G LV TD+ RG+DI V+++I+++ P
Sbjct: 66 QLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLA 125
Query: 132 ETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVG 170
ET++HR GR+GR G G AI + T R ++S+E +G
Sbjct: 126 ETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLG 164
>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 = 79.7 bits (195), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/110 (37%), Positives = 67/110 (60%), Gaps = 7/110 (6%)
Query: 52 GKTIVFTQTKRDADEVSLALTSIIASEAL-HGDISQHQRERTLNGFRQGKFTVLVATDVA 110
G+ I+F QT+R+A +++ + +L G+++ QR + FR GK VL+ T+V
Sbjct: 35 GQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVC 94
Query: 111 ARGLDIPNVDLIIHYELPN------DPETFVHRSGRTGRAGKEGTAILMF 154
ARG+D+ V ++++++LP D ET++HR GRTGR GK+G A M
Sbjct: 95 ARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMI 144
>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 = 79.3 bits (194), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 34/87 (39%), Positives = 55/87 (63%)
Query: 80 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 139
HG I+Q++R + F++ + +LV TDV ARG+D PNV ++ +P++ ++HR G
Sbjct: 66 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 140 RTGRAGKEGTAILMFTSSQRRTVRSLE 166
RT R+GKEG+++L + VR LE
Sbjct: 126 RTARSGKEGSSVLFICKDELPFVRELE 152
>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 = 79.3 bits (194), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 34/87 (39%), Positives = 55/87 (63%)
Query: 80 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 139
HG I+Q++R + F++ + +LV TDV ARG+D PNV ++ +P++ ++HR G
Sbjct: 66 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 140 RTGRAGKEGTAILMFTSSQRRTVRSLE 166
RT R+GKEG+++L + VR LE
Sbjct: 126 RTARSGKEGSSVLFICKDELPFVRELE 152
>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 = 79.3 bits (194), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 34/87 (39%), Positives = 55/87 (63%)
Query: 80 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 139
HG I+Q++R + F++ + +LV TDV ARG+D PNV ++ +P++ ++HR G
Sbjct: 66 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 140 RTGRAGKEGTAILMFTSSQRRTVRSLE 166
RT R+GKEG+++L + VR LE
Sbjct: 126 RTARSGKEGSSVLFICKDELPFVRELE 152
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 79.0 bits (193), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 53/152 (34%), Positives = 86/152 (56%), Gaps = 3/152 (1%)
Query: 17 QDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI- 74
++E EGI+ + I+ K L DL + ++F T+R D ++ + +
Sbjct: 246 KEELTLEGIRQFYINVEREEWKLDTLCDLYETLTIT-QAVIFINTRRKVDWLTEKMHARD 304
Query: 75 IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF 134
A+HGD+ Q +R+ + FR G VL+ TD+ ARG+D+ V L+I+Y+LP + E +
Sbjct: 305 FTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENY 364
Query: 135 VHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 166
+HR GR GR G++G AI M T +RT+R +E
Sbjct: 365 IHRIGRGGRFGRKGVAINMVTEEDKRTLRDIE 396
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 79.0 bits (193), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 34/87 (39%), Positives = 55/87 (63%)
Query: 80 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 139
HG I+Q++R + F++ + +LV TDV ARG+D PNV ++ +P++ ++HR G
Sbjct: 321 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 380
Query: 140 RTGRAGKEGTAILMFTSSQRRTVRSLE 166
RT R+GKEG+++L + VR LE
Sbjct: 381 RTARSGKEGSSVLFICKDELPFVRELE 407
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 79.0 bits (193), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 42/122 (34%), Positives = 68/122 (55%), Gaps = 12/122 (9%)
Query: 53 KTIVFTQTKRDADEVSLALTSIIASE--------ALHGDISQHQRERTLNGFRQGKFTVL 104
K I+F T + + L SI+ +E HG I+Q++R + F++ + +L
Sbjct: 290 KAIIFAPTVK----FTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGIL 345
Query: 105 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 164
V TDV ARG+D PNV ++ +P++ ++HR GRT R+GKEG+++L + VR
Sbjct: 346 VCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRE 405
Query: 165 LE 166
LE
Sbjct: 406 LE 407
>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 = 78.6 bits (192), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 42/122 (34%), Positives = 68/122 (55%), Gaps = 12/122 (9%)
Query: 53 KTIVFTQTKRDADEVSLALTSIIASE--------ALHGDISQHQRERTLNGFRQGKFTVL 104
K I+F T + + L SI+ +E HG I+Q++R + F++ + +L
Sbjct: 341 KAIIFAPTVK----FTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGIL 396
Query: 105 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 164
V TDV ARG+D PNV ++ +P++ ++HR GRT R+GKEG+++L + VR
Sbjct: 397 VCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRE 456
Query: 165 LE 166
LE
Sbjct: 457 LE 458
>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 = 78.6 bits (192), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 53/152 (34%), Positives = 86/152 (56%), Gaps = 3/152 (1%)
Query: 17 QDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI- 74
++E EGI+ + I+ K L DL + ++F T+R D ++ + +
Sbjct: 220 KEELTLEGIRQFYINVEREEWKLDTLCDLYETLTIT-QAVIFINTRRKVDWLTEKMHARD 278
Query: 75 IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF 134
A+HGD+ Q +R+ + FR G VL+ TD+ ARG+D+ V L+I+Y+LP + E +
Sbjct: 279 FTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENY 338
Query: 135 VHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 166
+HR GR GR G++G AI M T +RT+R +E
Sbjct: 339 IHRIGRGGRFGRKGVAINMVTEEDKRTLRDIE 370
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 78.6 bits (192), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 41/137 (29%), Positives = 77/137 (56%), Gaps = 3/137 (2%)
Query: 37 KRTILSDLITVYAKG--GKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTL 93
+R L L T+++K + I+F + + ++ +T + + H + Q +R +
Sbjct: 242 ERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVF 301
Query: 94 NGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM 153
+ FRQGK LV +D+ RG+DI V+++I+++ P ET++HR GR+GR G G AI +
Sbjct: 302 HEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINL 361
Query: 154 FTSSQRRTVRSLERDVG 170
+ R + +E+++G
Sbjct: 362 INWNDRFNLYKIEQELG 378
>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 = 77.8 bits (190), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 50/165 (30%), Positives = 81/165 (49%), Gaps = 29/165 (17%)
Query: 4 YFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRD 63
Y+V+ S ++DEK LY T A + +I + + + + + ++
Sbjct: 310 YYVLCS------SRDEKFQALCNLYGAITIAQA-------MIFCHTRKTASWLAAELSKE 356
Query: 64 ADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII 123
+V+L L G++ QR + FR+GK VLV T+V ARG+D+ V ++I
Sbjct: 357 GHQVAL----------LSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVI 406
Query: 124 HYELPNDP------ETFVHRSGRTGRAGKEGTAILMFTSSQRRTV 162
+++LP D ET++HR GRTGR GK G A+ M S +
Sbjct: 407 NFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNI 451
>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 = 77.8 bits (190), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 50/160 (31%), Positives = 84/160 (52%), Gaps = 14/160 (8%)
Query: 13 QVGNQDEKLAEGIKLYAISTTATSKRTILSDL---ITVYAKGGKTIVFTQTKRDADEVSL 69
++ ++E L + Y + ++ K L +L IT+ + ++F T++ A ++
Sbjct: 266 KLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITI----AQAMIFCHTRKTASWLAA 321
Query: 70 ALTSIIASEAL-HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP 128
L+ AL G++ QR + FR+GK VLV T+V ARG+D+ V ++I+++LP
Sbjct: 322 ELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLP 381
Query: 129 NDP------ETFVHRSGRTGRAGKEGTAILMFTSSQRRTV 162
D ET++HR GRTGR GK G A+ M S +
Sbjct: 382 VDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNI 421
>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 = 77.8 bits (190), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 50/160 (31%), Positives = 84/160 (52%), Gaps = 14/160 (8%)
Query: 13 QVGNQDEKLAEGIKLYAISTTATSKRTILSDL---ITVYAKGGKTIVFTQTKRDADEVSL 69
++ ++E L + Y + ++ K L +L IT+ + ++F T++ A ++
Sbjct: 229 KLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITI----AQAMIFCHTRKTASWLAA 284
Query: 70 ALTSIIASEAL-HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP 128
L+ AL G++ QR + FR+GK VLV T+V ARG+D+ V ++I+++LP
Sbjct: 285 ELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLP 344
Query: 129 NDP------ETFVHRSGRTGRAGKEGTAILMFTSSQRRTV 162
D ET++HR GRTGR GK G A+ M S +
Sbjct: 345 VDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNI 384
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 50/154 (32%), Positives = 83/154 (53%), Gaps = 14/154 (9%)
Query: 13 QVGNQDEKLAEGIKLYAISTTATSKRTILSDL---ITVYAKGGKTIVFTQTKRDADEVSL 69
++ ++E L + Y + ++ K L +L IT+ + ++F T++ A ++
Sbjct: 245 KLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITI----AQAMIFCHTRKTASWLAA 300
Query: 70 ALTSIIASEAL-HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP 128
L+ AL G++ QR + FR+GK VLV T+V ARG+D+ V ++I+++LP
Sbjct: 301 ELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLP 360
Query: 129 NDP------ETFVHRSGRTGRAGKEGTAILMFTS 156
D ET++HR GRTGR GK G A+ M S
Sbjct: 361 VDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDS 394
>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 = 73.9 bits (180), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 52/163 (31%), Positives = 89/163 (54%), Gaps = 9/163 (5%)
Query: 17 QDEKLAEGIKLYAISTTATSKR----TILSDLITVYAKGGKTIVFTQTKRDADEVSLAL- 71
+DE EGIK + ++ + T L D I+V + ++F T+R +E++ L
Sbjct: 226 KDELTLEGIKQFYVNVEEEEYKYECLTDLYDSISV----TQAVIFCNTRRKVEELTTKLR 281
Query: 72 TSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDP 131
A++ D+ Q +R+ + FR G +L++TD+ ARG+D+ V L+I+Y+LP +
Sbjct: 282 NDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANK 341
Query: 132 ETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFE 174
E ++HR GR GR G++G AI T+ +R LE+ + E
Sbjct: 342 ENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIE 384
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 72.0 bits (175), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 50/157 (31%), Positives = 86/157 (54%), Gaps = 9/157 (5%)
Query: 23 EGIKLYAISTTATSKR----TILSDLITVYAKGGKTIVFTQTKRDADEVSLAL-TSIIAS 77
EGIK + ++ + T L D I+V + ++F T+R +E++ L
Sbjct: 2 EGIKQFYVNVEEEEYKYECLTDLYDSISV----TQAVIFCNTRRKVEELTTKLRNDKFTV 57
Query: 78 EALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHR 137
A++ D+ Q +R+ + FR G +L++TD+ ARG+D+ V L+I+Y+LP + E ++HR
Sbjct: 58 SAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHR 117
Query: 138 SGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFE 174
GR GR G++G AI T+ +R LE+ + E
Sbjct: 118 IGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIE 154
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 71.6 bits (174), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 52/163 (31%), Positives = 87/163 (53%), Gaps = 9/163 (5%)
Query: 17 QDEKLAEGIKLYAISTTATSKR----TILSDLITVYAKGGKTIVFTQTKRDADEVSLAL- 71
+DE EGIK + ++ + T L D I+V + ++F T+R +E++ L
Sbjct: 225 KDELTLEGIKQFYVNVEEEEYKYECLTDLYDSISV----TQAVIFCNTRRKVEELTTKLR 280
Query: 72 TSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDP 131
A++ D+ Q +R+ FR G +L++TD+ ARG+D+ V L+I+Y+LP +
Sbjct: 281 NDKFTVSAIYSDLPQQERDTIXKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANK 340
Query: 132 ETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFE 174
E ++HR GR GR G++G AI T+ R LE+ + E
Sbjct: 341 ENYIHRIGRGGRFGRKGVAINFVTNEDVGAXRELEKFYSTQIE 383
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 69.3 bits (168), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 37/128 (28%), Positives = 62/128 (48%)
Query: 24 GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 83
G++ Y + K L DL+ V I +R L + + A+H
Sbjct: 224 GLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRG 283
Query: 84 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 143
+ Q +R F+ + +LVAT++ RG+DI V++ +Y++P D +T++HR R GR
Sbjct: 284 MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR 343
Query: 144 AGKEGTAI 151
G +G AI
Sbjct: 344 FGTKGLAI 351
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 68.9 bits (167), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 37/128 (28%), Positives = 62/128 (48%)
Query: 24 GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 83
G++ Y + K L DL+ V I +R L + + A+H
Sbjct: 224 GLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRG 283
Query: 84 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 143
+ Q +R F+ + +LVAT++ RG+DI V++ +Y++P D +T++HR R GR
Sbjct: 284 MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR 343
Query: 144 AGKEGTAI 151
G +G AI
Sbjct: 344 FGTKGLAI 351
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 68.9 bits (167), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 37/128 (28%), Positives = 62/128 (48%)
Query: 24 GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 83
G++ Y + K L DL+ V I +R L + + A+H
Sbjct: 223 GLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRG 282
Query: 84 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 143
+ Q +R F+ + +LVAT++ RG+DI V++ +Y++P D +T++HR R GR
Sbjct: 283 MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR 342
Query: 144 AGKEGTAI 151
G +G AI
Sbjct: 343 FGTKGLAI 350
>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56
Length = 172
Score = 68.6 bits (166), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 37/128 (28%), Positives = 62/128 (48%)
Query: 24 GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 83
G++ Y + K L DL+ V I +R L + + A+H
Sbjct: 5 GLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRG 64
Query: 84 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 143
+ Q +R F+ + +LVAT++ RG+DI V++ +Y++P D +T++HR R GR
Sbjct: 65 MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR 124
Query: 144 AGKEGTAI 151
G +G AI
Sbjct: 125 FGTKGLAI 132
>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 = 59.3 bits (142), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 38/113 (33%), Positives = 55/113 (48%), Gaps = 9/113 (7%)
Query: 50 KGGKTIVFTQTKRDADEVSLALTS-------IIASEALHGD--ISQHQRERTLNGFRQGK 100
+ K IVFT + A ++ L + + D +SQ +++ L+ F +G+
Sbjct: 360 QNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGE 419
Query: 101 FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM 153
F VLVAT V GLD+P VDL++ YE + R GRTGR ILM
Sbjct: 420 FNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMPGRVIILM 472
>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 = 56.6 bits (135), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 29/112 (25%), Positives = 57/112 (50%), Gaps = 1/112 (0%)
Query: 44 LITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFT 102
LI KG I++ +++D+++V+++L ++ I + A H ++ + + +
Sbjct: 260 LINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQ 319
Query: 103 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF 154
V+VAT G+D P+V +IH+ + E + SGR GR + IL +
Sbjct: 320 VVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYY 371
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/106 (24%), Positives = 55/106 (51%), Gaps = 1/106 (0%)
Query: 50 KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
+G I++ ++ ++ + L S I++ A H + + R F++ ++VAT
Sbjct: 235 RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV 294
Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF 154
G++ PNV ++H+++P + E++ +GR GR G A+L +
Sbjct: 295 AFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFY 340
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 55.1 bits (131), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 26/106 (24%), Positives = 54/106 (50%), Gaps = 1/106 (0%)
Query: 50 KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
+G I++ ++ ++ + L S I++ A H + + R F++ ++VAT
Sbjct: 235 RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV 294
Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF 154
G++ PNV ++H+++P + E++ +GR GR G A L +
Sbjct: 295 AFGXGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAXLFY 340
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 47/79 (59%), Gaps = 9/79 (11%)
Query: 80 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF----V 135
+HG +SQ +++R + F +G++ +LV+T V G+D+P ++++ +PE F +
Sbjct: 619 MHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMV----IENPERFGLAQL 674
Query: 136 HR-SGRTGRAGKEGTAILM 153
H+ GR GR G+E L+
Sbjct: 675 HQLRGRVGRGGQEAYCFLV 693
>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 = 49.3 bits (116), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 41/147 (27%), Positives = 71/147 (48%), Gaps = 21/147 (14%)
Query: 35 TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT-----SIIASEALH-------- 81
T R + + T + + I+FT+T++ A +S +T + + +A H
Sbjct: 384 TKLRNTIMEQYTRTEESARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSS 443
Query: 82 --GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 139
++Q++++ ++ FR GK +L+AT VA GLDI +++I Y L + V G
Sbjct: 444 EFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARG 503
Query: 140 RTGRAGKEGTAILMFTSS----QRRTV 162
R RA E T +L+ S +R TV
Sbjct: 504 R-ARAD-ESTYVLVAHSGSGVIERETV 528
>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 = 48.9 bits (115), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 36/112 (32%), Positives = 54/112 (48%), Gaps = 21/112 (18%)
Query: 81 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII-----HYELPNDPETFV 135
HG + + + ER +N F +F VLV T + G+DIP + II H+ L +
Sbjct: 845 HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQ-----L 899
Query: 136 HR-SGRTGRAGKEGTAIL-------MFTSSQRR--TVRSLERDVGCKFEFVS 177
H+ GR GR+ + A L M T +Q+R + SLE D+G F +
Sbjct: 900 HQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLE-DLGAGFALAT 950
>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 = 48.5 bits (114), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 35/158 (22%), Positives = 72/158 (45%), Gaps = 9/158 (5%)
Query: 8 FSHSTQVGNQDEKLAEGIKLYA----ISTTATSKRTILSDLITVYAKGGKTIVFTQTKRD 63
F+ DE+ E ++ + I+ + +K L +++ + K K I+FT+
Sbjct: 303 FNKIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKD-KIIIFTRH--- 358
Query: 64 ADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII 123
+E+ ++ + A+ S+ +RE L GFR G+F +V++ V G+D+P+ ++ +
Sbjct: 359 -NELVYRISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGV 417
Query: 124 HYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRT 161
++ R GR R K +++ R T
Sbjct: 418 IMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRGT 455
>pdb|2FZL|A Chain A, Structure Of C-Terminal Domain Of Archaeoglobus Fulgidus
Xpb
Length = 219
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 33/143 (23%), Positives = 67/143 (46%), Gaps = 9/143 (6%)
Query: 8 FSHSTQVGNQDEKLAEGIKLYA----ISTTATSKRTILSDLITVYAKGGKTIVFTQTKRD 63
F+ DE+ E ++ + I+ + +K L +++ + K K I+FT+
Sbjct: 68 FNKIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKD-KIIIFTRH--- 123
Query: 64 ADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII 123
+E+ ++ + A+ S+ +RE L GFR G+F +V++ V G+D+P+ ++ +
Sbjct: 124 -NELVYRISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGV 182
Query: 124 HYELPNDPETFVHRSGRTGRAGK 146
++ R GR R K
Sbjct: 183 IMSGSGSAREYIQRLGRILRPSK 205
>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 = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 37/111 (33%), Positives = 57/111 (51%), Gaps = 11/111 (9%)
Query: 50 KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
+ + +V T TK+ +++++ L I I LH +I +R + R GK+ VLV +
Sbjct: 450 RNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 509
Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK--EGTAIL 152
+ GLDIP V L+ L D E F+ RS R+ GRA + EG I+
Sbjct: 510 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNAEGRVIM 557
>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 = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 37/111 (33%), Positives = 57/111 (51%), Gaps = 11/111 (9%)
Query: 50 KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
+ + +V T TK+ +++++ L I I LH +I +R + R GK+ VLV +
Sbjct: 444 RNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK--EGTAIL 152
+ GLDIP V L+ L D E F+ RS R+ GRA + EG I+
Sbjct: 504 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNAEGRVIM 551
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 45.1 bits (105), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 50 KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
+ +T+V T TK+ A++++ L I LH +I +R + R GK+ VLV +
Sbjct: 443 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 502
Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 157
+ GLDIP V L+ L D E F+ RS R+ GRA + ++M+ +
Sbjct: 503 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNANGHVIMYADT 554
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 45.1 bits (105), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 50 KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
+ +T+V T TK+ A++++ L I LH +I +R + R GK+ VLV +
Sbjct: 444 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 157
+ GLDIP V L+ L D E F+ RS R+ GRA + ++M+ +
Sbjct: 504 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNANGHVIMYADT 555
>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 = 45.1 bits (105), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 50 KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
+ +T+V T TK+ A++++ L I LH +I +R + R GK+ VLV +
Sbjct: 444 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 157
+ GLDIP V L+ L D E F+ RS R+ GRA + ++M+ +
Sbjct: 504 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNANGHVIMYADT 555
>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 = 45.1 bits (105), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 50 KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
+ +T+V T TK+ A++++ L I LH +I +R + R GK+ VLV +
Sbjct: 444 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 157
+ GLDIP V L+ L D E F+ RS R+ GRA + ++M+ +
Sbjct: 504 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNANGHVIMYADT 555
>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex
Length = 683
Score = 45.1 bits (105), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 50 KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
+ +T+V T TK+ A++++ L I LH +I +R + R GK+ VLV +
Sbjct: 469 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 528
Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 157
+ GLDIP V L+ L D E F+ RS R+ GRA + ++M+ +
Sbjct: 529 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNANGHVIMYADT 580
>pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleotide
Excision Repair Enzyme
Length = 665
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 34/104 (32%), Positives = 53/104 (50%), Gaps = 9/104 (8%)
Query: 49 AKGGKTIVFTQTKRDADEV-SLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVAT 107
A+G +T+V T R A+E+ S + I + LH ++ +R+ + R G + LV
Sbjct: 438 ARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGI 497
Query: 108 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK 146
++ GLDIP V L+ L D E F+ RS R+ GRA +
Sbjct: 498 NLLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAAR 538
>pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide Excision Repair
Enzyme Uvrb From Thermus Thermophilus
Length = 664
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 34/104 (32%), Positives = 53/104 (50%), Gaps = 9/104 (8%)
Query: 49 AKGGKTIVFTQTKRDADEV-SLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVAT 107
A+G +T+V T R A+E+ S + I + LH ++ +R+ + R G + LV
Sbjct: 437 ARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGI 496
Query: 108 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK 146
++ GLDIP V L+ L D E F+ RS R+ GRA +
Sbjct: 497 NLLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAAR 537
>pdb|4I1S|A Chain A, Melanoma Differentiation Associated Protein-5 Helicase
Domain Complex With Inhibitor Non-structural Protein V
Length = 243
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 53/108 (49%), Gaps = 15/108 (13%)
Query: 35 TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT-----SIIASEALH-------- 81
T R + + T + + I+FT+T++ A +S +T + + +A H
Sbjct: 134 TKLRNTIXEHFTRTEESARGIIFTKTRQSAYALSQWITDNKKFAEVGVKAHHLIGAGHSS 193
Query: 82 --GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL 127
+Q+++ ++ FR GK +L+AT VA GLDI +++I Y L
Sbjct: 194 EFKPXTQNEQREVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGL 241
>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 = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 40/167 (23%), Positives = 68/167 (40%), Gaps = 41/167 (24%)
Query: 34 ATSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTSIIA----SEAL-------- 80
+TS+R +L+ A+ G +VF T+R A++ ++ L++I A +E L
Sbjct: 224 STSRRVKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEEN 283
Query: 81 -------------------HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL 121
H + QR + FR+G V+VAT A G+++P +
Sbjct: 284 EGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRV 343
Query: 122 IIH-------YELPNDPETFVHRSGRTGRAG--KEGTAILMFTSSQR 159
I+ Y + +GR GR G + G AI++ R
Sbjct: 344 IVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDR 390
>pdb|3TMI|A Chain A, Structural Basis For Rna Recognition And Activation Of
Rig-I
Length = 695
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 93 LNGFR-QGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 151
L+ F+ G +L+AT VA G+DI +L+I YE + + GR GRA G+
Sbjct: 452 LDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRA--RGSKC 508
Query: 152 LMFTSS 157
+ TS+
Sbjct: 509 FLLTSN 514
>pdb|2YKG|A Chain A, Structural Insights Into Rna Recognition By Rig-I
Length = 696
Score = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 93 LNGFR-QGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 151
L+ F+ G +L+AT VA G+DI +L+I YE + + GR GRA G+
Sbjct: 453 LDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRA--RGSKC 509
Query: 152 LMFTSS 157
+ TS+
Sbjct: 510 FLLTSN 515
>pdb|4AY2|A Chain A, Capturing 5' Tri-Phosphorylated Rna Duplex By Rig-I
Length = 687
Score = 37.7 bits (86), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 93 LNGFR-QGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 151
L+ F+ G +L+AT VA G+DI +L+I YE + + GR GRA G+
Sbjct: 444 LDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRA--RGSKC 500
Query: 152 LMFTSS 157
+ TS+
Sbjct: 501 FLLTSN 506
>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 = 35.8 bits (81), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 4/65 (6%)
Query: 93 LNGFRQGKFT-VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 151
L+ F+ K +L+AT VA G+DI +L++ YE + + GR GRA G+
Sbjct: 686 LDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRAA--GSKC 742
Query: 152 LMFTS 156
++ TS
Sbjct: 743 ILVTS 747
>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 = 35.8 bits (81), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 4/65 (6%)
Query: 93 LNGFRQGKFT-VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 151
L+ F+ K +L+AT VA G+DI +L++ YE + + GR GRA G+
Sbjct: 445 LDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRAA--GSKC 501
Query: 152 LMFTS 156
++ TS
Sbjct: 502 ILVTS 506
>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 = 35.8 bits (81), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 4/65 (6%)
Query: 93 LNGFRQGKFT-VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 151
L+ F+ K +L+AT VA G+DI +L++ YE + + GR GRA G+
Sbjct: 686 LDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRAA--GSKC 742
Query: 152 LMFTS 156
++ TS
Sbjct: 743 ILVTS 747
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 35.4 bits (80), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 37/78 (47%), Gaps = 15/78 (19%)
Query: 81 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII------------HY-EL 127
H +S+ R+ GFRQ K V+VAT A G+++P +II +Y E+
Sbjct: 319 HAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEI 378
Query: 128 PNDPETFVHRSGRTGRAG 145
P + SGR GR G
Sbjct: 379 P--IMEYKQMSGRAGRPG 394
>pdb|3TBK|A Chain A, Mouse Rig-I Atpase Domain
Length = 555
Score = 35.4 bits (80), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 93 LNGFR-QGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 151
L FR G +L+AT VA G+DI +L+I YE + + GR GRA +
Sbjct: 444 LEAFRASGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKXIQTRGR-GRA--RDSKC 500
Query: 152 LMFTSS 157
+ TSS
Sbjct: 501 FLLTSS 506
>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
Bound To Amppnp
Length = 997
Score = 33.5 bits (75), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 10/72 (13%)
Query: 96 FRQGKFTVLVATDVAARGLDIPNVDLIIHYELPND--------PETFVHRSGRTGRAGKE 147
F +G VL AT+ A GL++P +I +D P F +GR GR G +
Sbjct: 421 FSKGFIKVLFATETFAMGLNLPTRTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLD 480
Query: 148 --GTAILMFTSS 157
GT I+M +S
Sbjct: 481 STGTVIVMAYNS 492
>pdb|1NCP|N Chain N, Structural Characterization Of A 39 Residue Synthetic
Peptide Containing The Two Zinc Binding Domains From The
Hiv-1 P7 Nucleocapsid Protein By Cd And Nmr Spectroscopy
Length = 17
Score = 30.8 bits (68), Expect = 1.7, Method: Composition-based stats.
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 441 CFNCGKSGHRASEC 454
CFNCGK GH A C
Sbjct: 3 CFNCGKEGHTARNC 16
>pdb|2L4L|A Chain A, Structural Insights Into The Ctar Dna Recognition By The
Hiv-1 Nucleocapsid Protein: Role Of Sugar Deoxyriboses
In The Binding Polarity Of Nc
Length = 45
Score = 30.8 bits (68), Expect = 1.7, Method: Composition-based stats.
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 441 CFNCGKSGHRASEC 454
CFNCGK GH A C
Sbjct: 5 CFNCGKEGHTARNC 18
>pdb|1BJ6|A Chain A, 1h Nmr Of (12-53) Ncp7D(ACGCC) COMPLEX, 10 STRUCTURES
pdb|1ESK|A Chain A, Solution Structure Of Ncp7 From Hiv-1
Length = 42
Score = 30.8 bits (68), Expect = 1.7, Method: Composition-based stats.
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 441 CFNCGKSGHRASEC 454
CFNCGK GH A C
Sbjct: 4 CFNCGKEGHTARNC 17
>pdb|2EXF|A Chain A, Solution Structure Of The Hiv-1 Nucleocapsid (Ncp7(12-55))
Complexed With The Dna (-) Primer Binding Site
pdb|2JZW|A Chain A, How The Hiv-1 Nucleocapsid Protein Binds And Destabilises
The (-)primer Binding Site During Reverse Transcription
Length = 44
Score = 30.8 bits (68), Expect = 1.7, Method: Composition-based stats.
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 441 CFNCGKSGHRASEC 454
CFNCGK GH A C
Sbjct: 4 CFNCGKEGHTARNC 17
>pdb|2BL6|A Chain A, Solution Structure Of The Zn Complex Of Eiav Ncp11(22-58)
Peptide, Including Two Cchc Zn-Binding Motifs
Length = 37
Score = 30.4 bits (67), Expect = 2.1, Method: Composition-based stats.
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 441 CFNCGKSGHRASEC 454
C+NCGK GH +S+C
Sbjct: 3 CYNCGKPGHLSSQC 16
>pdb|2M3Z|A Chain A, Nmr Solution Structure Of Hiv-1 Nucleocapsid Protein In
Complex With An Inhibitor Displaying A 2 Inhibitors:1 Nc
Stoichiometry
Length = 55
Score = 30.0 bits (66), Expect = 2.4, Method: Composition-based stats.
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 441 CFNCGKSGHRASEC 454
CFNCGK GH A C
Sbjct: 15 CFNCGKEGHIAKNC 28
>pdb|1AAF|A Chain A, Nucleocapsid Zinc Fingers Detected In Retroviruses: Exafs
Studies On Intact Viruses And The Solution-State
Structure Of The Nucleocapsid Protein From Hiv-1
Length = 55
Score = 30.0 bits (66), Expect = 2.4, Method: Composition-based stats.
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 441 CFNCGKSGHRASEC 454
CFNCGK GH A C
Sbjct: 15 CFNCGKEGHIAKNC 28
>pdb|1A1T|A Chain A, Structure Of The Hiv-1 Nucleocapsid Protein Bound To The
Sl3 Psi-Rna Recognition Element, Nmr, 25 Structures
pdb|1MFS|A Chain A, Dynamical Behavior Of The Hiv-1 Nucleocapsid Protein; Nmr,
30 Structures
Length = 55
Score = 30.0 bits (66), Expect = 2.4, Method: Composition-based stats.
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 441 CFNCGKSGHRASEC 454
CFNCGK GH A C
Sbjct: 15 CFNCGKEGHIAKNC 28
>pdb|1F6U|A Chain A, Nmr Structure Of The Hiv-1 Nucleocapsid Protein Bound To
Stem-Loop Sl2 Of The Psi-Rna Packaging Signal.
Implications For Genome Recognition
Length = 56
Score = 30.0 bits (66), Expect = 2.4, Method: Composition-based stats.
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 441 CFNCGKSGHRASEC 454
CFNCGK GH A C
Sbjct: 15 CFNCGKEGHIAKNC 28
>pdb|1HVN|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|1HVO|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|2ZNF|A Chain A, High-Resolution Structure Of An Hiv Zinc Fingerlike Domain
Via A New Nmr-Based Distance Geometry Approach
Length = 18
Score = 30.0 bits (66), Expect = 2.9, Method: Composition-based stats.
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 441 CFNCGKSGHRASEC 454
CFNCGK GH A C
Sbjct: 3 CFNCGKEGHIARNC 16
>pdb|2A51|A Chain A, Structure Of The (13-51) Domain Of The Nucleocapsid
Protein Ncp8 From Sivlhoest
Length = 39
Score = 29.6 bits (65), Expect = 3.4, Method: Composition-based stats.
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 441 CFNCGKSGHRASEC 454
CFNCGK GH A C
Sbjct: 3 CFNCGKPGHTARMC 16
>pdb|1RLR|A Chain A, Structure Of Ribonucleotide Reductase Protein R1
Length = 761
Score = 29.6 bits (65), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 38 RTILSDLITVYAKGGKTIVFTQTKRDADEVS 68
+ +L DL+T Y G KT+ + T+ D D++S
Sbjct: 712 QQLLKDLLTAYKFGVKTLYYQNTRDDIDDLS 742
>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 = 29.6 bits (65), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 37/157 (23%), Positives = 61/157 (38%), Gaps = 44/157 (28%)
Query: 50 KGGKTIVFTQTKRDADEVSLALTSIIAS---------------------------EALHG 82
K ++F +R A+ V+L L+ + S +A+ G
Sbjct: 236 KKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRG 295
Query: 83 DISQH-----QRERTL--NGFRQGKFTVLVATDVAARGLDIPNVDLIIH-------YELP 128
++ H + ER L FR+G +VAT + G++ P +II + +
Sbjct: 296 GVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGME 355
Query: 129 NDPETFVHRS-GRTGRAGKE--GTAILMFTSSQRRTV 162
P VH+ GR GR + G I++ TS R V
Sbjct: 356 RIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPREV 392
>pdb|1NC8|A Chain A, High-Resolution Solution Nmr Structure Of The Minimal
Active Domain Of The Human Immunodeficiency Virus Type-2
Nucleocapsid Protein, 15 Structures
Length = 29
Score = 29.6 bits (65), Expect = 3.6, Method: Composition-based stats.
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 441 CFNCGKSGHRASEC 454
C+NCGK GH A +C
Sbjct: 9 CWNCGKEGHSARQC 22
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus Type-2
Nucleocapsid Protein
Length = 49
Score = 29.6 bits (65), Expect = 3.6, Method: Composition-based stats.
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 441 CFNCGKSGHRASEC 454
C+NCGK GH A +C
Sbjct: 9 CWNCGKEGHSARQC 22
>pdb|4ALI|A Chain A, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And Triclosan (P1)
pdb|4ALI|B Chain B, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And Triclosan (P1)
pdb|4ALI|C Chain C, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And Triclosan (P1)
pdb|4ALI|D Chain D, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And Triclosan (P1)
pdb|4ALI|E Chain E, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And Triclosan (P1)
pdb|4ALI|F Chain F, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And Triclosan (P1)
pdb|4ALI|G Chain G, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And Triclosan (P1)
pdb|4ALI|H Chain H, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And Triclosan (P1)
pdb|4ALJ|A Chain A, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And 5-Chloro-2-Phenoxyphenol
pdb|4ALJ|B Chain B, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And 5-Chloro-2-Phenoxyphenol
pdb|4ALJ|C Chain C, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And 5-Chloro-2-Phenoxyphenol
pdb|4ALJ|D Chain D, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And 5-Chloro-2-Phenoxyphenol
pdb|4ALJ|E Chain E, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And 5-Chloro-2-Phenoxyphenol
pdb|4ALJ|F Chain F, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And 5-Chloro-2-Phenoxyphenol
pdb|4ALJ|G Chain G, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And 5-Chloro-2-Phenoxyphenol
pdb|4ALJ|H Chain H, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And 5-Chloro-2-Phenoxyphenol
pdb|4ALK|A Chain A, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And 5-Ethyl-2-Phenoxyphenol
pdb|4ALK|B Chain B, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And 5-Ethyl-2-Phenoxyphenol
pdb|4ALK|C Chain C, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And 5-Ethyl-2-Phenoxyphenol
pdb|4ALK|D Chain D, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And 5-Ethyl-2-Phenoxyphenol
pdb|4ALK|E Chain E, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And 5-Ethyl-2-Phenoxyphenol
pdb|4ALK|F Chain F, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And 5-Ethyl-2-Phenoxyphenol
pdb|4ALK|G Chain G, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And 5-Ethyl-2-Phenoxyphenol
pdb|4ALK|H Chain H, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And 5-Ethyl-2-Phenoxyphenol
pdb|4ALM|A Chain A, Crystal Structure Of S. Aureus Fabi (P43212)
pdb|4ALM|B Chain B, Crystal Structure Of S. Aureus Fabi (P43212)
pdb|4ALM|C Chain C, Crystal Structure Of S. Aureus Fabi (P43212)
pdb|4ALM|D Chain D, Crystal Structure Of S. Aureus Fabi (P43212)
pdb|4ALN|A Chain A, Crystal Structure Of S. Aureus Fabi (P32)
pdb|4ALN|B Chain B, Crystal Structure Of S. Aureus Fabi (P32)
pdb|4ALN|C Chain C, Crystal Structure Of S. Aureus Fabi (P32)
pdb|4ALN|D Chain D, Crystal Structure Of S. Aureus Fabi (P32)
pdb|4ALN|E Chain E, Crystal Structure Of S. Aureus Fabi (P32)
pdb|4ALN|F Chain F, Crystal Structure Of S. Aureus Fabi (P32)
pdb|4ALN|G Chain G, Crystal Structure Of S. Aureus Fabi (P32)
pdb|4ALN|H Chain H, Crystal Structure Of S. Aureus Fabi (P32)
pdb|4ALN|I Chain I, Crystal Structure Of S. Aureus Fabi (P32)
pdb|4ALN|J Chain J, Crystal Structure Of S. Aureus Fabi (P32)
pdb|4ALN|K Chain K, Crystal Structure Of S. Aureus Fabi (P32)
pdb|4ALN|L Chain L, Crystal Structure Of S. Aureus Fabi (P32)
Length = 282
Score = 29.3 bits (64), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 34/121 (28%), Positives = 46/121 (38%), Gaps = 15/121 (12%)
Query: 26 KLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTK-RDADEVSLALTSIIASEALHGDI 84
K Y I A +KR+I + V + G +VFT K R E+ L + EA I
Sbjct: 33 KTYVIMGIA-NKRSIAFGVAKVLDQLGAKLVFTYRKERSRKELEKLLEQLNQPEAHLYQI 91
Query: 85 SQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA 144
E +NGF Q G D+ N+D + H + E R T R
Sbjct: 92 DVQSDEEVINGFEQ-------------IGKDVGNIDGVYHSIAFANMEDLRGRFSETSRE 138
Query: 145 G 145
G
Sbjct: 139 G 139
>pdb|3GNT|A Chain A, Crystal Structure Of The Staphylococcus Aureus Enoyl-Acyl
Carrier Protein Reductase (Fabi) In Apo Form (Two
Molecules In Au)
pdb|3GNT|B Chain B, Crystal Structure Of The Staphylococcus Aureus Enoyl-Acyl
Carrier Protein Reductase (Fabi) In Apo Form (Two
Molecules In Au)
Length = 256
Score = 29.3 bits (64), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 34/121 (28%), Positives = 46/121 (38%), Gaps = 15/121 (12%)
Query: 26 KLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTK-RDADEVSLALTSIIASEALHGDI 84
K Y I A +KR+I + V + G +VFT K R E+ L + EA I
Sbjct: 7 KTYVIMGIA-NKRSIAFGVAKVLDQLGAKLVFTYRKERSRKELEKLLEQLNQPEAHLYQI 65
Query: 85 SQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA 144
E +NGF Q G D+ N+D + H + E R T R
Sbjct: 66 DVQSDEEVINGFEQ-------------IGKDVGNIDGVYHSIAFANMEDLRGRFSETSRE 112
Query: 145 G 145
G
Sbjct: 113 G 113
>pdb|3GNS|A Chain A, Crystal Structure Of The Staphylococcus Aureus Enoyl-Acyl
Carrier Protein Reductase (Fabi) In Apo Form (One
Molecule In Au)
pdb|3GR6|A Chain A, Crystal Structure Of The Staphylococcus Aureus Enoyl-Acyl
Carrier Protein Reductase (Fabi) In Complex With Nadp
And Triclosan
pdb|3GR6|D Chain D, Crystal Structure Of The Staphylococcus Aureus Enoyl-Acyl
Carrier Protein Reductase (Fabi) In Complex With Nadp
And Triclosan
pdb|3GR6|G Chain G, Crystal Structure Of The Staphylococcus Aureus Enoyl-Acyl
Carrier Protein Reductase (Fabi) In Complex With Nadp
And Triclosan
pdb|3GR6|J Chain J, Crystal Structure Of The Staphylococcus Aureus Enoyl-Acyl
Carrier Protein Reductase (Fabi) In Complex With Nadp
And Triclosan
Length = 260
Score = 29.3 bits (64), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 34/121 (28%), Positives = 46/121 (38%), Gaps = 15/121 (12%)
Query: 26 KLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTK-RDADEVSLALTSIIASEALHGDI 84
K Y I A +KR+I + V + G +VFT K R E+ L + EA I
Sbjct: 11 KTYVIMGIA-NKRSIAFGVAKVLDQLGAKLVFTYRKERSRKELEKLLEQLNQPEAHLYQI 69
Query: 85 SQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA 144
E +NGF Q G D+ N+D + H + E R T R
Sbjct: 70 DVQSDEEVINGFEQ-------------IGKDVGNIDGVYHSIAFANMEDLRGRFSETSRE 116
Query: 145 G 145
G
Sbjct: 117 G 117
>pdb|4ALL|A Chain A, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And Triclosan (P212121)
pdb|4ALL|B Chain B, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And Triclosan (P212121)
pdb|4ALL|C Chain C, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And Triclosan (P212121)
pdb|4ALL|D Chain D, Crystal Structure Of S. Aureus Fabi In Complex With Nadp
And Triclosan (P212121)
Length = 277
Score = 28.9 bits (63), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 34/121 (28%), Positives = 46/121 (38%), Gaps = 15/121 (12%)
Query: 26 KLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTK-RDADEVSLALTSIIASEALHGDI 84
K Y I A +KR+I + V + G +VFT K R E+ L + EA I
Sbjct: 28 KTYVIMGIA-NKRSIAFGVAKVLDQLGAKLVFTYRKERSRKELEKLLEQLNQPEAHLYQI 86
Query: 85 SQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA 144
E +NGF Q G D+ N+D + H + E R T R
Sbjct: 87 DVQSDEEVINGFEQ-------------IGKDVGNIDGVYHSIAFANMEDLRGRFSETSRE 133
Query: 145 G 145
G
Sbjct: 134 G 134
>pdb|4FS3|A Chain A, Crystal Structure Of Staphylococcus Aureus Enoyl-Acp
Reductase In Complex With Nadp And Afn-1252
Length = 256
Score = 28.9 bits (63), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 34/121 (28%), Positives = 46/121 (38%), Gaps = 15/121 (12%)
Query: 26 KLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTK-RDADEVSLALTSIIASEALHGDI 84
K Y I A +KR+I + V + G +VFT K R E+ L + EA I
Sbjct: 7 KTYVIMGIA-NKRSIAFGVAKVLDQLGAKLVFTYRKERSRKELEKLLEQLNQPEAHLYQI 65
Query: 85 SQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA 144
E +NGF Q G D+ N+D + H + E R T R
Sbjct: 66 DVQSDEEVINGFEQ-------------IGKDVGNIDGVYHSIAFANMEDLRGRFSETSRE 112
Query: 145 G 145
G
Sbjct: 113 G 113
>pdb|3F1S|A Chain A, Crystal Structure Of Protein Z Complexed With Protein
Z-Dependent Inhibitor
Length = 385
Score = 28.9 bits (63), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 9/23 (39%), Positives = 19/23 (82%)
Query: 215 IEEKGTDALAAALAQLSGFSRPP 237
++E+GT+A+A L++++ +S PP
Sbjct: 331 VDERGTEAVAGILSEITAYSMPP 353
>pdb|3H5C|A Chain A, X-Ray Structure Of Protein Z-Protein Z Inhibitor Complex
Length = 423
Score = 28.9 bits (63), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 9/23 (39%), Positives = 19/23 (82%)
Query: 215 IEEKGTDALAAALAQLSGFSRPP 237
++E+GT+A+A L++++ +S PP
Sbjct: 369 VDERGTEAVAGILSEITAYSMPP 391
>pdb|1KAC|A Chain A, Knob Domain From Adenovirus Serotype 12 In Complex With
Domain 1 Of Its Cellular Receptor Car
pdb|1NOB|A Chain A, Knob Domain From Adenovirus Serotype 12
pdb|1NOB|B Chain B, Knob Domain From Adenovirus Serotype 12
pdb|1NOB|C Chain C, Knob Domain From Adenovirus Serotype 12
pdb|1NOB|D Chain D, Knob Domain From Adenovirus Serotype 12
pdb|1NOB|E Chain E, Knob Domain From Adenovirus Serotype 12
pdb|1NOB|F Chain F, Knob Domain From Adenovirus Serotype 12
Length = 185
Score = 28.5 bits (62), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 236 PPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDR 295
PP + SLI +TL LT++ + G +S V G L ++ T +G +H++ D++
Sbjct: 14 PPPNCSLIQELDAKLTLCLTKNGSIVNGIVSLVGVKGNLLNIQSTTT-TVG-VHLVFDEQ 71
>pdb|1P6A|A Chain A, Structural Basis For Variation In Asdenovirus Affinity For
The Cellular Receptor Car (S489y Mutant)
Length = 185
Score = 28.1 bits (61), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 236 PPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDR 295
PP + SLI +TL LT++ + G +S V G L ++ T +G +H++ D++
Sbjct: 14 PPPNCSLIQELDAKLTLCLTKNGSIVNGIVSLVGVKGNLLNIQSTTT-TVG-VHLVFDEQ 71
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
0.317 0.132 0.378
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,119,273
Number of Sequences: 62578
Number of extensions: 364678
Number of successful extensions: 1171
Number of sequences better than 100.0: 115
Number of HSP's better than 100.0 without gapping: 88
Number of HSP's successfully gapped in prelim test: 27
Number of HSP's that attempted gapping in prelim test: 1045
Number of HSP's gapped (non-prelim): 126
length of query: 456
length of database: 14,973,337
effective HSP length: 102
effective length of query: 354
effective length of database: 8,590,381
effective search space: 3040994874
effective search space used: 3040994874
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)