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= psy4494
(234 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 191 bits (484), Expect = 4e-49, Method: Compositional matrix adjust.
Identities = 89/192 (46%), Positives = 124/192 (64%), Gaps = 18/192 (9%)
Query: 49 FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
+Y+VR KP+ +D ++++ L++ R++ QSGIIY S K+ E + L+N G+ AYHA
Sbjct: 240 YYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHA 299
Query: 109 KLESN------------------VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
LE ++AFG+GIDKP+VRFVIHH +SKSMEN+YQESGRAG
Sbjct: 300 NLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAG 359
Query: 151 RDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAW 210
RD A CILYY D+F++SSMV + G LY +VSYC + ++CRR ++A +FDE W
Sbjct: 360 RDDMKADCILYYGFGDIFRISSMVVMENVGQQKLYEMVSYCQNISKCRRVLMAQHFDEVW 419
Query: 211 SDTECRGMCDHC 222
+ C MCD+C
Sbjct: 420 NSEACNKMCDNC 431
Score = 60.5 bits (145), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 26/41 (63%), Positives = 33/41 (80%), Gaps = 3/41 (7%)
Query: 14 WRTSFYQV---SIAFGLGIDKPNVRFVIHHCLSKSMENFYQ 51
W + QV ++AFG+GIDKP+VRFVIHH +SKSMEN+YQ
Sbjct: 313 WSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQ 353
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 112 bits (279), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 74/216 (34%), Positives = 116/216 (53%), Gaps = 44/216 (20%)
Query: 30 DKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKEC 89
D+PN+R+++ ME F KP LD+L + + R +SGIIY S +
Sbjct: 209 DRPNIRYML-------MEKF-----KP------LDQLMRYVQEQ-RGKSGIIYCNSRAKV 249
Query: 90 EDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVI 131
ED L+++G+ +AYHA LE+NV ++AFG+GI+KPNVRFV+
Sbjct: 250 EDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVV 309
Query: 132 HHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTG-LANL----YN 186
H + +++E++YQE+GRAGRDG A +L+Y D+ L + ++ G L ++ N
Sbjct: 310 HFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPQGQLQDIERHKLN 369
Query: 187 IVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHC 222
+ + CRR ++ +YF E + C G CD C
Sbjct: 370 AMGAFAEAQTCRRLVLLNYFGEGRQEP-C-GNCDIC 403
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 16/30 (53%), Positives = 27/30 (90%)
Query: 22 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQ 51
++AFG+GI+KPNVRFV+H + +++E++YQ
Sbjct: 293 TVAFGMGINKPNVRFVVHFDIPRNIESYYQ 322
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 105 bits (263), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 72/218 (33%), Positives = 110/218 (50%), Gaps = 48/218 (22%)
Query: 30 DKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKEC 89
D+PN+R+ + + KP LD+L + + R +SGIIY S +
Sbjct: 209 DRPNIRYXLXE------------KFKP------LDQLXRYVQEQ-RGKSGIIYCNSRAKV 249
Query: 90 EDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVI 131
ED L+++G+ +AYHA LE+NV ++AFG GI+KPNVRFV+
Sbjct: 250 EDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXGINKPNVRFVV 309
Query: 132 HHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYC 191
H + +++E++YQE+GRAGRDG A L+Y D L + ++ G L +I +
Sbjct: 310 HFDIPRNIESYYQETGRAGRDGLPAEAXLFYDPADXAWLRRCLEEKPQG--QLQDIERHK 367
Query: 192 L-------DQTRCRRAIIASYFDEAWSDTECRGMCDHC 222
L + CRR ++ +YF E + C G CD C
Sbjct: 368 LNAXGAFAEAQTCRRLVLLNYFGEGRQEP-C-GNCDIC 403
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 26/31 (83%)
Query: 21 VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQ 51
++AFG GI+KPNVRFV+H + +++E++YQ
Sbjct: 292 ATVAFGXGINKPNVRFVVHFDIPRNIESYYQ 322
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 36.2 bits (82), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 29/121 (23%), Positives = 53/121 (43%), Gaps = 24/121 (19%)
Query: 64 DELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLES----------- 112
D + ++ R RN+ ++ T + K EDL + L+ G++V+ H+++++
Sbjct: 432 DLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLR 491
Query: 113 ----NVSIAFGL---GIDKPNVRFVI-----HHCLSKSMENFYQESGRAGRDGQIAHCIL 160
+V + L G+D P V V +S + Q GRA R+ H I+
Sbjct: 492 LGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAN-GHVIM 550
Query: 161 Y 161
Y
Sbjct: 551 Y 551
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 29/121 (23%), Positives = 53/121 (43%), Gaps = 24/121 (19%)
Query: 64 DELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLES----------- 112
D + ++ R RN+ ++ T + K EDL + L+ G++V+ H+++++
Sbjct: 433 DLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLR 492
Query: 113 ----NVSIAFGL---GIDKPNVRFVI-----HHCLSKSMENFYQESGRAGRDGQIAHCIL 160
+V + L G+D P V V +S + Q GRA R+ H I+
Sbjct: 493 LGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAN-GHVIM 551
Query: 161 Y 161
Y
Sbjct: 552 Y 552
>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 = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 29/121 (23%), Positives = 53/121 (43%), Gaps = 24/121 (19%)
Query: 64 DELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLES----------- 112
D + ++ R RN+ ++ T + K EDL + L+ G++V+ H+++++
Sbjct: 433 DLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLR 492
Query: 113 ----NVSIAFGL---GIDKPNVRFVI-----HHCLSKSMENFYQESGRAGRDGQIAHCIL 160
+V + L G+D P V V +S + Q GRA R+ H I+
Sbjct: 493 LGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAN-GHVIM 551
Query: 161 Y 161
Y
Sbjct: 552 Y 552
>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 = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 29/121 (23%), Positives = 53/121 (43%), Gaps = 24/121 (19%)
Query: 64 DELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLES----------- 112
D + ++ R RN+ ++ T + K EDL + L+ G++V+ H+++++
Sbjct: 433 DLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLR 492
Query: 113 ----NVSIAFGL---GIDKPNVRFVI-----HHCLSKSMENFYQESGRAGRDGQIAHCIL 160
+V + L G+D P V V +S + Q GRA R+ H I+
Sbjct: 493 LGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAN-GHVIM 551
Query: 161 Y 161
Y
Sbjct: 552 Y 552
>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex
Length = 683
Score = 35.8 bits (81), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 29/121 (23%), Positives = 53/121 (43%), Gaps = 24/121 (19%)
Query: 64 DELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLES----------- 112
D + ++ R RN+ ++ T + K EDL + L+ G++V+ H+++++
Sbjct: 458 DLIGEIHERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLR 517
Query: 113 ----NVSIAFGL---GIDKPNVRFVI-----HHCLSKSMENFYQESGRAGRDGQIAHCIL 160
+V + L G+D P V V +S + Q GRA R+ H I+
Sbjct: 518 LGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAN-GHVIM 576
Query: 161 Y 161
Y
Sbjct: 577 Y 577
>pdb|3LJ4|Y Chain Y, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|Z Chain Z, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|AA Chain a, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|BB Chain b, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|CC Chain c, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|DD Chain d, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|EE Chain e, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|FF Chain f, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|GG Chain g, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|HH Chain h, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|II Chain i, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|3LJ4|JJ Chain j, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The First Biological
Assembly
pdb|1VT0|KK Chain k, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|LL Chain l, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|MM Chain m, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|NN Chain n, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|OO Chain o, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|PP Chain p, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|QQ Chain q, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|RR Chain r, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|SS Chain s, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|TT Chain t, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|UU Chain u, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
pdb|1VT0|VV Chain v, Bacteriophage P22 Portal Protein Bound To Middle Tail
Factor Gp4. This File Contain The Second Biological
Assembly
Length = 166
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 30/55 (54%)
Query: 54 IKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
++P + +D +D+L +M+ +++ GII + E+ E + GLR SA A
Sbjct: 28 VEPQSMQDAVDDLEAMMAEWYQDGKGIITGYVFSDDENPPAEGDDHGLRSSAVSA 82
>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 = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 31/141 (21%), Positives = 60/141 (42%), Gaps = 19/141 (13%)
Query: 45 SMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVS 104
++E Q + ++ D L DL Q+ +I+ + ++ + L E++R VS
Sbjct: 225 TLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQA-VIFCNTKRKVDWLTEKMREANFTVS 283
Query: 105 AYHAKLE---------------SNVSIA---FGLGIDKPNVRFVIHHCLSKSMENFYQES 146
+ H + S V I+ + G+D P V +I++ L + E +
Sbjct: 284 SMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRI 343
Query: 147 GRAGRDGQIAHCILYYRLPDV 167
GR+GR G+ I + + D+
Sbjct: 344 GRSGRYGRKGVAINFVKNDDI 364
>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 = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 31/141 (21%), Positives = 60/141 (42%), Gaps = 19/141 (13%)
Query: 45 SMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVS 104
++E Q + ++ D L DL Q+ +I+ + ++ + L E++R VS
Sbjct: 247 TLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQA-VIFCNTKRKVDWLTEKMREANFTVS 305
Query: 105 AYHAKLE---------------SNVSIA---FGLGIDKPNVRFVIHHCLSKSMENFYQES 146
+ H + S V I+ + G+D P V +I++ L + E +
Sbjct: 306 SMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRI 365
Query: 147 GRAGRDGQIAHCILYYRLPDV 167
GR+GR G+ I + + D+
Sbjct: 366 GRSGRYGRKGVAINFVKNDDI 386
>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 = 32.3 bits (72), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 31/141 (21%), Positives = 60/141 (42%), Gaps = 19/141 (13%)
Query: 45 SMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVS 104
++E Q + ++ D L DL Q+ +I+ + ++ + L E++R VS
Sbjct: 247 TLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQA-VIFCNTKRKVDWLTEKMREANFTVS 305
Query: 105 AYHAKLE---------------SNVSIA---FGLGIDKPNVRFVIHHCLSKSMENFYQES 146
+ H + S V I+ + G+D P V +I++ L + E +
Sbjct: 306 SMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRI 365
Query: 147 GRAGRDGQIAHCILYYRLPDV 167
GR+GR G+ I + + D+
Sbjct: 366 GRSGRYGRKGVAINFVKNDDI 386
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 32.3 bits (72), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 30/141 (21%), Positives = 60/141 (42%), Gaps = 19/141 (13%)
Query: 45 SMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVS 104
++E Q + ++ D L DL Q+ +I+ + ++ + L E++R VS
Sbjct: 210 TLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQA-VIFCNTKRKVDWLTEKMREANFTVS 268
Query: 105 AYHAKLE---------------SNVSIA---FGLGIDKPNVRFVIHHCLSKSMENFYQES 146
+ H + S V I+ + G+D P V +I++ L + E +
Sbjct: 269 SMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRI 328
Query: 147 GRAGRDGQIAHCILYYRLPDV 167
GR+GR G+ + + + D+
Sbjct: 329 GRSGRYGRKGVAVNFVKNDDI 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 = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 31/141 (21%), Positives = 60/141 (42%), Gaps = 19/141 (13%)
Query: 45 SMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVS 104
++E Q + ++ D L DL Q+ +I+ + ++ + L E++R VS
Sbjct: 246 TLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQA-VIFCNTKRKVDWLTEKMREANFTVS 304
Query: 105 AYHAKLE---------------SNVSIA---FGLGIDKPNVRFVIHHCLSKSMENFYQES 146
+ H + S V I+ + G+D P V +I++ L + E +
Sbjct: 305 SMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRI 364
Query: 147 GRAGRDGQIAHCILYYRLPDV 167
GR+GR G+ I + + D+
Sbjct: 365 GRSGRYGRKGVAINFVKNDDI 385
>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 = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 28/121 (23%), Positives = 54/121 (44%), Gaps = 24/121 (19%)
Query: 64 DELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLES----------- 112
D + ++ +R RN+ ++ T + K EDL + L+ G++V+ H+++++
Sbjct: 439 DLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLR 498
Query: 113 ----NVSIAFGL---GIDKPNVRFVI-----HHCLSKSMENFYQESGRAGRDGQIAHCIL 160
+V + L G+D P V V +S + Q GRA R+ + I+
Sbjct: 499 LGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAE-GRVIM 557
Query: 161 Y 161
Y
Sbjct: 558 Y 558
>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 = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 28/121 (23%), Positives = 54/121 (44%), Gaps = 24/121 (19%)
Query: 64 DELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLES----------- 112
D + ++ +R RN+ ++ T + K EDL + L+ G++V+ H+++++
Sbjct: 433 DLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLR 492
Query: 113 ----NVSIAFGL---GIDKPNVRFVI-----HHCLSKSMENFYQESGRAGRDGQIAHCIL 160
+V + L G+D P V V +S + Q GRA R+ + I+
Sbjct: 493 LGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAE-GRVIM 551
Query: 161 Y 161
Y
Sbjct: 552 Y 552
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 32.0 bits (71), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 30/141 (21%), Positives = 60/141 (42%), Gaps = 19/141 (13%)
Query: 45 SMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVS 104
++E Q + ++ D L DL Q+ +I+ + ++ + L E++R VS
Sbjct: 210 TLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQA-VIFCNTKRKVDWLTEKMREANFTVS 268
Query: 105 AYHAKLE---------------SNVSIA---FGLGIDKPNVRFVIHHCLSKSMENFYQES 146
+ H + S V I+ + G+D P V +I++ L + E +
Sbjct: 269 SMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRI 328
Query: 147 GRAGRDGQIAHCILYYRLPDV 167
GR+GR G+ + + + D+
Sbjct: 329 GRSGRYGRKGVAVNFVKNDDI 349
>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 = 31.6 bits (70), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 24/122 (19%), Positives = 46/122 (37%), Gaps = 23/122 (18%)
Query: 62 CLDELADLMSRRFRNQSGIIYTTSIK----ECEDLREELRNRGLRVSAYHAKLESNVSIA 117
++ + + R N II+ ++K C L+ E + + L + +H K+ N +
Sbjct: 325 AVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTS 383
Query: 118 F------------------GLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCI 159
G+D PNV V+ + + N+ GR R G+ +
Sbjct: 384 LVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSV 443
Query: 160 LY 161
L+
Sbjct: 444 LF 445
>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 = 31.6 bits (70), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 37/133 (27%), Positives = 51/133 (38%), Gaps = 21/133 (15%)
Query: 66 LADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESN------------ 113
L L SR NQS II+ S + E L +++ G HAK+
Sbjct: 35 LNTLFSRLQINQS-IIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNG 93
Query: 114 ------VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDV 167
+ F GID V VI+ K E + GR+GR G + I D
Sbjct: 94 LCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDR 153
Query: 168 FKLSSMVFDQQTG 180
F L S+ ++Q G
Sbjct: 154 FNLKSI--EEQLG 164
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 31.6 bits (70), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 24/114 (21%), Positives = 43/114 (37%), Gaps = 23/114 (20%)
Query: 70 MSRRFRNQSGIIYTTSIK----ECEDLREELRNRGLRVSAYHAKLESNVSIAF------- 118
+ R N II+ ++K C L+ E + + L + +H K+ N +
Sbjct: 282 IKERDSNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTSLVKRFKKD 340
Query: 119 -----------GLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILY 161
G+D PNV V+ + + N+ GR R G+ +L+
Sbjct: 341 ESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLF 394
>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 = 31.6 bits (70), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 24/122 (19%), Positives = 46/122 (37%), Gaps = 23/122 (18%)
Query: 62 CLDELADLMSRRFRNQSGIIYTTSIK----ECEDLREELRNRGLRVSAYHAKLESNVSIA 117
++ + + R N II+ ++K C L+ E + + L + +H K+ N +
Sbjct: 19 AVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTS 77
Query: 118 F------------------GLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCI 159
G+D PNV V+ + + N+ GR R G+ +
Sbjct: 78 LVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSV 137
Query: 160 LY 161
L+
Sbjct: 138 LF 139
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 31.6 bits (70), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 24/122 (19%), Positives = 46/122 (37%), Gaps = 23/122 (18%)
Query: 62 CLDELADLMSRRFRNQSGIIYTTSIK----ECEDLREELRNRGLRVSAYHAKLESNVSIA 117
++ + + R N II+ ++K C L+ E + + L + +H K+ N +
Sbjct: 274 AVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTS 332
Query: 118 F------------------GLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCI 159
G+D PNV V+ + + N+ GR R G+ +
Sbjct: 333 LVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSV 392
Query: 160 LY 161
L+
Sbjct: 393 LF 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 = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 24/122 (19%), Positives = 46/122 (37%), Gaps = 23/122 (18%)
Query: 62 CLDELADLMSRRFRNQSGIIYTTSIK----ECEDLREELRNRGLRVSAYHAKLESNVSIA 117
++ + + R N II+ ++K C L+ E + + L + +H K+ N +
Sbjct: 19 AVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTS 77
Query: 118 F------------------GLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCI 159
G+D PNV V+ + + N+ GR R G+ +
Sbjct: 78 LVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSV 137
Query: 160 LY 161
L+
Sbjct: 138 LF 139
>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 = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 24/122 (19%), Positives = 46/122 (37%), Gaps = 23/122 (18%)
Query: 62 CLDELADLMSRRFRNQSGIIYTTSIK----ECEDLREELRNRGLRVSAYHAKLESNVSIA 117
++ + + R N II+ ++K C L+ E + + L + +H K+ N +
Sbjct: 19 AVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTS 77
Query: 118 F------------------GLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCI 159
G+D PNV V+ + + N+ GR R G+ +
Sbjct: 78 LVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSV 137
Query: 160 LY 161
L+
Sbjct: 138 LF 139
>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 = 31.2 bits (69), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 26/116 (22%), Positives = 53/116 (45%), Gaps = 20/116 (17%)
Query: 64 DELADLMSRRFRNQS--GIIYTTSIKECEDLREELRNRGLRVSAYHAKLESN-------- 113
+E + + R +N+ G+++ + ++ ++L LR+ G + A H L +
Sbjct: 224 NERFEALCRLLKNKEFYGLVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRL 283
Query: 114 -------VSIAFGL---GIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCI 159
+ IA + GID ++ VI++ L ++ E++ GR GR G+ I
Sbjct: 284 FKQKKIRILIATDVXSRGIDVNDLNCVINYHLPQNPESYXHRIGRTGRAGKKGKAI 339
>pdb|3JUX|A Chain A, Structure Of The Translocation Atpase Seca From Thermotoga
Maritima
Length = 822
Score = 30.8 bits (68), Expect = 0.71, Method: Composition-based stats.
Identities = 35/135 (25%), Positives = 59/135 (43%), Gaps = 29/135 (21%)
Query: 59 QKDCLDELADLMSRRFRN-QSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESN---- 113
QK+ +++ + + +R++ Q ++ TTSI++ E L L+ +G+ +AK
Sbjct: 456 QKEKYEKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEI 515
Query: 114 ---------VSIAF---GLGID---KPNVRFVIHHCL-------SKSMENFYQESGRAGR 151
V+IA G G D P V + C+ S+ ++N Q GRAGR
Sbjct: 516 VAKAGQKGMVTIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRIDN--QLRGRAGR 573
Query: 152 DGQIAHCILYYRLPD 166
G I + L D
Sbjct: 574 QGDPGESIFFLSLED 588
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 30.4 bits (67), Expect = 0.76, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 110 LESNVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCIL 160
L S I G+ + + NV VI + + +Q GR GR GQ A+C L
Sbjct: 643 LVSTTVIEVGIDVPRANV-MVIENPERFGLAQLHQLRGRVGRGGQEAYCFL 692
>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 = 30.4 bits (67), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 21/41 (51%)
Query: 121 GIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILY 161
GID N+ VI++ L E++ +GR GR G I +
Sbjct: 98 GIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISF 138
>pdb|1K4J|A Chain A, Crystal Structure Of The Acyl-Homoserinelactone Synthase
Esai Complexed With Rhenate
pdb|1KZF|A Chain A, Crystal Structure Of The Acyl-Homoserine Lactone Synthase,
Esai
Length = 230
Score = 30.4 bits (67), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 39/92 (42%), Gaps = 4/92 (4%)
Query: 122 IDKPN-VRFVIHHCLSK-SMENFYQESGRAGRDGQIAHCIL--YYRLPDVFKLSSMVFDQ 177
+D+PN + HC S ++ + ES R D A +L +Y + V L+ + + Q
Sbjct: 92 LDRPNMITHTFQHCFSDVTLPAYGTESSRFFVDKARARALLGEHYPISQVLFLAMVNWAQ 151
Query: 178 QTGLANLYNIVSYCLDQTRCRRAIIASYFDEA 209
N+Y IVS + + R EA
Sbjct: 152 NNAYGNIYTIVSRAMLKILTRSGWQIKVIKEA 183
>pdb|3DIN|A Chain A, Crystal Structure Of The Protein-Translocation Complex
Formed By The Secy Channel And The Seca Atpase
pdb|3DIN|B Chain B, Crystal Structure Of The Protein-Translocation Complex
Formed By The Secy Channel And The Seca Atpase
Length = 871
Score = 30.4 bits (67), Expect = 0.79, Method: Composition-based stats.
Identities = 35/135 (25%), Positives = 59/135 (43%), Gaps = 29/135 (21%)
Query: 59 QKDCLDELADLMSRRFRN-QSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESN---- 113
QK+ +++ + + +R++ Q ++ TTSI++ E L L+ +G+ +AK
Sbjct: 456 QKEKYEKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEI 515
Query: 114 ---------VSIAF---GLGID---KPNVRFVIHHCL-------SKSMENFYQESGRAGR 151
V+IA G G D P V + C+ S+ ++N Q GRAGR
Sbjct: 516 VAKAGQKGMVTIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRIDN--QLRGRAGR 573
Query: 152 DGQIAHCILYYRLPD 166
G I + L D
Sbjct: 574 QGDPGESIFFLSLED 588
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 30.0 bits (66), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 81 IYTTSIKECEDLREELRNRGL---RVSAYHAKLESNVSIAFGLGIDKPNVRFVIHHCLSK 137
++ +I+ DL + +RNR + R Y + ++V+ G+D P V VI+ +
Sbjct: 239 LFDNAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVA---SRGLDIPLVEKVINFDAPQ 295
Query: 138 SMENFYQESGRAGRDGQIAHCILY 161
+ + GR GR G+ I +
Sbjct: 296 DLRTYIHRIGRTGRMGRKGEAITF 319
>pdb|1TYE|B Chain B, Structural Basis For Allostery In Integrins And Binding Of
Ligand- Mimetic Therapeutics To The Platelet Receptor
For Fibrinogen
pdb|1TYE|D Chain D, Structural Basis For Allostery In Integrins And Binding Of
Ligand- Mimetic Therapeutics To The Platelet Receptor
For Fibrinogen
pdb|1TYE|F Chain F, Structural Basis For Allostery In Integrins And Binding Of
Ligand- Mimetic Therapeutics To The Platelet Receptor
For Fibrinogen
Length = 440
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 96 LRNRGLRVSAYHAKLESNVSIAFGLGIDKPNVRFVIHHCLSKSMEN 141
++N G +++ KL SN+ I FG +DKP V ++ +++EN
Sbjct: 131 IQNLGTKLATQMRKLTSNLRIGFGAFVDKP-VSPYMYISPPEALEN 175
>pdb|1JV2|B Chain B, Crystal Structure Of The Extracellular Segment Of Integrin
Alphavbeta3
pdb|1L5G|B Chain B, Crystal Structure Of The Extracellular Segment Of Integrin
Avb3 In Complex With An Arg-Gly-Asp Ligand
pdb|1M1X|B Chain B, Crystal Structure Of The Extracellular Segment Of Integrin
Alpha Vbeta3 Bound To Mn2+
pdb|1U8C|B Chain B, A Novel Adaptation Of The Integrin Psi Domain Revealed
From Its Crystal Structure
Length = 692
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 96 LRNRGLRVSAYHAKLESNVSIAFGLGIDKP 125
++N G +++ KL SN+ I FG +DKP
Sbjct: 131 IQNLGTKLATQMRKLTSNLRIGFGAFVDKP 160
>pdb|3IJE|B Chain B, Crystal Structure Of The Complete Integrin Alhavbeta3
Ectodomain Plus An Alpha/beta Transmembrane Fragment
Length = 695
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 96 LRNRGLRVSAYHAKLESNVSIAFGLGIDKP 125
++N G +++ KL SN+ I FG +DKP
Sbjct: 131 IQNLGTKLATQMRKLTSNLRIGFGAFVDKP 160
>pdb|3FCS|B Chain B, Structure Of Complete Ectodomain Of Integrin Aiibb3
pdb|3FCS|D Chain D, Structure Of Complete Ectodomain Of Integrin Aiibb3
Length = 690
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 96 LRNRGLRVSAYHAKLESNVSIAFGLGIDKP 125
++N G +++ KL SN+ I FG +DKP
Sbjct: 131 IQNLGTKLATQMRKLTSNLRIGFGAFVDKP 160
>pdb|4G1M|B Chain B, Re-Refinement Of Alpha V Beta 3 Structure
Length = 692
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 96 LRNRGLRVSAYHAKLESNVSIAFGLGIDKP 125
++N G +++ KL SN+ I FG +DKP
Sbjct: 131 IQNLGTKLATQMRKLTSNLRIGFGAFVDKP 160
>pdb|2VC2|B Chain B, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To
Antagonist L-739758
pdb|2VDK|B Chain B, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece
pdb|2VDL|B Chain B, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece
pdb|2VDM|B Chain B, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To
Antagonist Tirofiban
pdb|2VDN|B Chain B, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To
Antagonist Eptifibatide
pdb|2VDO|B Chain B, Integrin Alphaiibbeta3 Headpiece Bound To Fibrinogen Gamma
Chain Peptide, Hhlggakqagdv
pdb|2VDP|B Chain B, Integrin Alphaiibbeta3 Headpiece Bound To Fibrinogen Gamma
Chain Peptide,Lggakqagdv
pdb|2VDQ|B Chain B, Integrin Alphaiibbeta3 Headpiece Bound To A Chimeric
Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv
pdb|2VDR|B Chain B, Integrin Alphaiibbeta3 Headpiece Bound To A Chimeric
Fibrinogen Gamma Chain Peptide, Lggakqrgdv
pdb|3FCU|B Chain B, Structure Of Headpiece Of Integrin Aiibb3 In Open
Conformation
pdb|3FCU|D Chain D, Structure Of Headpiece Of Integrin Aiibb3 In Open
Conformation
pdb|3FCU|F Chain F, Structure Of Headpiece Of Integrin Aiibb3 In Open
Conformation
Length = 461
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 96 LRNRGLRVSAYHAKLESNVSIAFGLGIDKP 125
++N G +++ KL SN+ I FG +DKP
Sbjct: 131 IQNLGTKLATQMRKLTSNLRIGFGAFVDKP 160
>pdb|3T3M|B Chain B, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
pdb|3T3M|D Chain D, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
pdb|3T3P|B Chain B, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
pdb|3T3P|D Chain D, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
Length = 472
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 96 LRNRGLRVSAYHAKLESNVSIAFGLGIDKP 125
++N G +++ KL SN+ I FG +DKP
Sbjct: 131 IQNLGTKLATQMRKLTSNLRIGFGAFVDKP 160
>pdb|3NID|B Chain B, The Closed Headpiece Of Integrin Alphaiib Beta3 And Its
Complex With An Alpahiib Beta3 -Specific Antagonist That
Does Not Induce Opening
pdb|3NID|D Chain D, The Closed Headpiece Of Integrin Alphaiib Beta3 And Its
Complex With An Alpahiib Beta3 -Specific Antagonist That
Does Not Induce Opening
pdb|3NIF|B Chain B, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3NIF|D Chain D, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3NIG|B Chain B, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3NIG|D Chain D, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
Length = 471
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 96 LRNRGLRVSAYHAKLESNVSIAFGLGIDKP 125
++N G +++ KL SN+ I FG +DKP
Sbjct: 131 IQNLGTKLATQMRKLTSNLRIGFGAFVDKP 160
>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 = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 21/42 (50%)
Query: 121 GIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYY 162
G+D NV+ VI+ L +E + GR GR G + ++
Sbjct: 109 GLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFF 150
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 21/42 (50%)
Query: 121 GIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYY 162
G+D NV+ VI+ L +E + GR GR G + ++
Sbjct: 339 GLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFF 380
>pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleotide
Excision Repair Enzyme
Length = 665
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 38/192 (19%), Positives = 73/192 (38%), Gaps = 27/192 (14%)
Query: 52 VRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLE 111
VR+KP + LD + + R R + ++ +++ E+L L G+R H +L+
Sbjct: 417 VRVKPT-ENQILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELD 475
Query: 112 SNVSIAF-------------GL-----GIDKPNVRFVI-----HHCLSKSMENFYQESGR 148
+ A G+ G+D P V V +S + Q GR
Sbjct: 476 AFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGR 535
Query: 149 AGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQT---RCRRAIIASY 205
A R+ + + R+ + + + +++ L YN+ +T R I
Sbjct: 536 AARNARGEVWLYADRVSEAMQRAIEETNRRRALQEAYNLEHGITPETVRKEVRAVIRPEG 595
Query: 206 FDEAWSDTECRG 217
++EA + + G
Sbjct: 596 YEEAPLEADLSG 607
>pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide Excision Repair
Enzyme Uvrb From Thermus Thermophilus
Length = 664
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 38/192 (19%), Positives = 73/192 (38%), Gaps = 27/192 (14%)
Query: 52 VRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLE 111
VR+KP + LD + + R R + ++ +++ E+L L G+R H +L+
Sbjct: 416 VRVKPT-ENQILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELD 474
Query: 112 SNVSIAF-------------GL-----GIDKPNVRFVI-----HHCLSKSMENFYQESGR 148
+ A G+ G+D P V V +S + Q GR
Sbjct: 475 AFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGR 534
Query: 149 AGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQT---RCRRAIIASY 205
A R+ + + R+ + + + +++ L YN+ +T R I
Sbjct: 535 AARNARGEVWLYADRVSEAMQRAIEETNRRRALQEAYNLEHGITPETVRKEVRAVIRPEG 594
Query: 206 FDEAWSDTECRG 217
++EA + + G
Sbjct: 595 YEEAPLEADLSG 606
>pdb|2W4B|A Chain A, Epstein-Barr Virus Alkaline Nuclease D203s Mutant
pdb|2W4B|B Chain B, Epstein-Barr Virus Alkaline Nuclease D203s Mutant
Length = 470
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 9/66 (13%)
Query: 86 IKECEDLREELRNRGLRVSAYHAKLESNVSIAFGLGIDKPN----VRFVIHHCLSKSMEN 141
+ E ED EE+ + + L S + AF +D+P +RFV +CL K ++
Sbjct: 4 VDELEDPMEEMTSY-----TFARFLRSPETEAFVRNLDRPPQMPAMRFVYLYCLCKQIQE 58
Query: 142 FYQESG 147
F E+G
Sbjct: 59 FSGETG 64
>pdb|2W45|A Chain A, Epstein-Barr Virus Alkaline Nuclease
pdb|2W45|B Chain B, Epstein-Barr Virus Alkaline Nuclease
Length = 470
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 9/66 (13%)
Query: 86 IKECEDLREELRNRGLRVSAYHAKLESNVSIAFGLGIDKPN----VRFVIHHCLSKSMEN 141
+ E ED EE+ + + L S + AF +D+P +RFV +CL K ++
Sbjct: 4 VDELEDPMEEMTSY-----TFARFLRSPETEAFVRNLDRPPQMPAMRFVYLYCLCKQIQE 58
Query: 142 FYQESG 147
F E+G
Sbjct: 59 FSGETG 64
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 22/50 (44%)
Query: 121 GIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKL 170
GID V VI+ K+ E + GR+GR G + I D F L
Sbjct: 321 GIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNL 370
>pdb|4G1E|B Chain B, Crystal Structure Of Integrin Alpha V Beta 3 With
Coil-Coiled Tag
Length = 738
Score = 28.5 bits (62), Expect = 3.6, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 96 LRNRGLRVSAYHAKLESNVSIAFGLGIDKP 125
++N G +++ KL SN+ I FG +DKP
Sbjct: 131 IQNLGTKLATQMRKLTSNLRIGFGAFVDKP 160
>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 = 28.1 bits (61), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 27/103 (26%), Positives = 45/103 (43%), Gaps = 22/103 (21%)
Query: 61 DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLE--------- 111
+CL +L D +S +I+ + ++ E+L +LRN VSA ++ L
Sbjct: 249 ECLTDLYDSISVT----QAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMK 304
Query: 112 ------SNVSIAFGL---GIDKPNVRFVIHHCLSKSMENFYQE 145
S + I+ L GID V VI++ L + EN+
Sbjct: 305 EFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHR 347
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 28.1 bits (61), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 27/103 (26%), Positives = 45/103 (43%), Gaps = 22/103 (21%)
Query: 61 DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLE--------- 111
+CL +L D +S +I+ + ++ E+L +LRN VSA ++ L
Sbjct: 248 ECLTDLYDSISVT----QAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXK 303
Query: 112 ------SNVSIAFGL---GIDKPNVRFVIHHCLSKSMENFYQE 145
S + I+ L GID V VI++ L + EN+
Sbjct: 304 EFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHR 346
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 28.1 bits (61), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 27/103 (26%), Positives = 45/103 (43%), Gaps = 22/103 (21%)
Query: 61 DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKL---------- 110
+CL +L D +S +I+ + ++ E+L +LRN VSA ++ L
Sbjct: 19 ECLTDLYDSISV----TQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMK 74
Query: 111 -----ESNVSIAFGL---GIDKPNVRFVIHHCLSKSMENFYQE 145
S + I+ L GID V VI++ L + EN+
Sbjct: 75 EFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHR 117
>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 = 28.1 bits (61), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 121 GIDKPNVRFVIHHCLSKSMENFYQESGRAGRDG 153
G+D P ++ VI++ + + +EN+ GR G G
Sbjct: 117 GLDFPAIQHVINYDMPEEIENYVHRIGRTGCSG 149
>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 = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 30/119 (25%), Positives = 49/119 (41%), Gaps = 19/119 (15%)
Query: 45 SMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVS 104
++E Q I ++ LD L DL Q+ +I+ + ++ + L E++ R VS
Sbjct: 224 TLEGIRQFYINVEREEWKLDTLCDLYETLTITQA-VIFINTRRKVDWLTEKMHARDFTVS 282
Query: 105 AYHAKLE---------------SNVSIAFGL---GIDKPNVRFVIHHCLSKSMENFYQE 145
A H ++ S V I L GID V VI++ L + EN+
Sbjct: 283 AMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHR 341
>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 = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 26/111 (23%), Positives = 47/111 (42%), Gaps = 19/111 (17%)
Query: 50 YQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAK 109
Y+ PA + L+ L+DL+ +++ +++T + E E++ + L G A H
Sbjct: 6 YEEEAVPAPVRGRLEVLSDLLYVASPDRA-MVFTRTKAETEEIAQGLLRLGHPAQALHGD 64
Query: 110 L---------------ESNVSIAFGL---GIDKPNVRFVIHHCLSKSMENF 142
L E V +A + G+D P V V+H+ L E +
Sbjct: 65 LSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAY 115
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 27.3 bits (59), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 30/119 (25%), Positives = 49/119 (41%), Gaps = 19/119 (15%)
Query: 45 SMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVS 104
++E Q I ++ LD L DL Q+ +I+ + ++ + L E++ R VS
Sbjct: 250 TLEGIRQFYINVEREEWKLDTLCDLYETLTITQA-VIFINTRRKVDWLTEKMHARDFTVS 308
Query: 105 AYHAKLE---------------SNVSIAFGL---GIDKPNVRFVIHHCLSKSMENFYQE 145
A H ++ S V I L GID V VI++ L + EN+
Sbjct: 309 AMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHR 367
>pdb|1MZH|A Chain A, Qr15, An Aldolase
pdb|1MZH|B Chain B, Qr15, An Aldolase
Length = 225
Score = 26.9 bits (58), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 11/68 (16%)
Query: 72 RRFRNQSGIIYTTSIKECEDL---REELRNRGLRVSAYHAKLESNVS--------IAFGL 120
R++ + + + S KE E+ EEL + V+ YH KL S+++ I F L
Sbjct: 5 RKYIDNAALKPHLSEKEIEEFVLKSEELGIYAVCVNPYHVKLASSIAKKVKVCCVIGFPL 64
Query: 121 GIDKPNVR 128
G++K +V+
Sbjct: 65 GLNKTSVK 72
>pdb|2RC5|A Chain A, Refined Structure Of Fnr From Leptospira Interrogans
pdb|2RC5|B Chain B, Refined Structure Of Fnr From Leptospira Interrogans
pdb|2RC5|C Chain C, Refined Structure Of Fnr From Leptospira Interrogans
pdb|2RC5|D Chain D, Refined Structure Of Fnr From Leptospira Interrogans
pdb|2RC6|A Chain A, Refined Structure Of Fnr From Leptospira Interrogans Bound
To Nadp+
pdb|2RC6|B Chain B, Refined Structure Of Fnr From Leptospira Interrogans Bound
To Nadp+
pdb|2RC6|C Chain C, Refined Structure Of Fnr From Leptospira Interrogans Bound
To Nadp+
pdb|2RC6|D Chain D, Refined Structure Of Fnr From Leptospira Interrogans Bound
To Nadp+
Length = 314
Score = 26.9 bits (58), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 12/72 (16%)
Query: 76 NQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNVSIAFGLGIDKPNVRFVIHHCL 135
QSG + I ED E + +GL Y +L S S ++ G+ + N+ F+I
Sbjct: 67 GQSGGV----IPPGED--PEKKAKGLADVGYTVRLYSIASPSYSFGMKEDNIEFIIKR-- 118
Query: 136 SKSMENFYQESG 147
+N Y E+G
Sbjct: 119 ----DNIYDENG 126
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
0.327 0.139 0.432
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,784,314
Number of Sequences: 62578
Number of extensions: 254395
Number of successful extensions: 839
Number of sequences better than 100.0: 61
Number of HSP's better than 100.0 without gapping: 46
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 772
Number of HSP's gapped (non-prelim): 73
length of query: 234
length of database: 14,973,337
effective HSP length: 96
effective length of query: 138
effective length of database: 8,965,849
effective search space: 1237287162
effective search space used: 1237287162
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 bits)