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= 008882
(550 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4F3T|A Chain A, Human Argonaute-2 - Mir-20a Complex
Length = 861
Score = 340 bits (873), Expect = 1e-93, Method: Compositional matrix adjust.
Identities = 178/314 (56%), Positives = 212/314 (67%), Gaps = 19/314 (6%)
Query: 197 PDVSGSYGRIKRVCETELGIVSQCCQPRQASRLNIPYFENVALKINVKVGGRNTVLVDAV 256
P + Y +KRV +T LG+ +QC Q + R N+ LKINVK+GG N +L+
Sbjct: 525 PGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLP-- 582
Query: 257 QKRIPLVTDRPTIIFGSDVTHPQPGEDSSPSIAAVVASMDWPEVTKYRGLVSAQAHNQEI 316
Q R P V +P I G+DVTHP G+ PSIAAVV SMD +Y V Q H QEI
Sbjct: 583 QGRPP-VFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMD-AHPNRYCATVRVQQHRQEI 640
Query: 317 IQDLYKSTQDPFGGSVHGGMIRELLIAFRRSTNLKPHRIIFYRDGVGEGQFSQVLLHEMS 376
IQDL M+RELLI F +ST KP RIIFYRDGV EGQF QVL HE+
Sbjct: 641 IQDL-------------AAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELL 687
Query: 377 AIRQACASLEEGYAPPVTFVVVQKRHHTRLFPAEHNNRDLTDRSGNILPGTVVDTQICHP 436
AIR+AC LE+ Y P +TF+VVQKRHHTRLF + N R +SGNI GT VDT+I HP
Sbjct: 688 AIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNER--VGKSGNIPAGTTVDTKITHP 745
Query: 437 TQFDFYLNSHAGIRGTSRPIHYHVLYDENRFSADDLQVLTNNLCYTYARCTRSVSIVPPA 496
T+FDFYL SHAGI+GTSRP HYHVL+D+NRFS+D+LQ+LT LC+TY RCTRSVSI PA
Sbjct: 746 TEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPA 805
Query: 497 YYAHLAAFRARYYI 510
YYAHL AFRARY++
Sbjct: 806 YYAHLVAFRARYHL 819
Score = 35.8 bits (81), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 23/34 (67%)
Query: 121 PVRPGFGTVGRKCVVRANHFMVQLAERDIHHYDV 154
P RP FGT GR ++AN F + + + DI+HY++
Sbjct: 28 PPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYEL 61
>pdb|4EI1|A Chain A, Crystal Structure Of Human Argonaute2
pdb|4EI3|A Chain A, Crystal Structure Of Human Argonaute2
Length = 859
Score = 340 bits (872), Expect = 1e-93, Method: Compositional matrix adjust.
Identities = 178/314 (56%), Positives = 212/314 (67%), Gaps = 19/314 (6%)
Query: 197 PDVSGSYGRIKRVCETELGIVSQCCQPRQASRLNIPYFENVALKINVKVGGRNTVLVDAV 256
P + Y +KRV +T LG+ +QC Q + R N+ LKINVK+GG N +L+
Sbjct: 523 PGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLP-- 580
Query: 257 QKRIPLVTDRPTIIFGSDVTHPQPGEDSSPSIAAVVASMDWPEVTKYRGLVSAQAHNQEI 316
Q R P V +P I G+DVTHP G+ PSIAAVV SMD +Y V Q H QEI
Sbjct: 581 QGRPP-VFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMD-AHPNRYCATVRVQQHRQEI 638
Query: 317 IQDLYKSTQDPFGGSVHGGMIRELLIAFRRSTNLKPHRIIFYRDGVGEGQFSQVLLHEMS 376
IQDL M+RELLI F +ST KP RIIFYRDGV EGQF QVL HE+
Sbjct: 639 IQDL-------------AAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELL 685
Query: 377 AIRQACASLEEGYAPPVTFVVVQKRHHTRLFPAEHNNRDLTDRSGNILPGTVVDTQICHP 436
AIR+AC LE+ Y P +TF+VVQKRHHTRLF + N R +SGNI GT VDT+I HP
Sbjct: 686 AIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNER--VGKSGNIPAGTTVDTKITHP 743
Query: 437 TQFDFYLNSHAGIRGTSRPIHYHVLYDENRFSADDLQVLTNNLCYTYARCTRSVSIVPPA 496
T+FDFYL SHAGI+GTSRP HYHVL+D+NRFS+D+LQ+LT LC+TY RCTRSVSI PA
Sbjct: 744 TEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPA 803
Query: 497 YYAHLAAFRARYYI 510
YYAHL AFRARY++
Sbjct: 804 YYAHLVAFRARYHL 817
Score = 35.8 bits (81), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 23/34 (67%)
Query: 121 PVRPGFGTVGRKCVVRANHFMVQLAERDIHHYDV 154
P RP FGT GR ++AN F + + + DI+HY++
Sbjct: 26 PPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYEL 59
>pdb|4F1N|A Chain A, Crystal Structure Of Kluyveromyces Polysporus Argonaute With
A Guide Rna
pdb|4F1N|B Chain B, Crystal Structure Of Kluyveromyces Polysporus Argonaute With
A Guide Rna
Length = 1046
Score = 177 bits (450), Expect = 1e-44, Method: Compositional matrix adjust.
Identities = 119/367 (32%), Positives = 184/367 (50%), Gaps = 32/367 (8%)
Query: 200 SGSYGRIKRVCETELGIVSQCCQPRQASRLNIPYFENVALKINVKVGGRNTVL-VDAVQK 258
S Y R+K + + + G ++ C + +I Y NV +K+N+K+ G N L ++ +
Sbjct: 694 SAVYDRLKYITDLKFGALNSCVVWDNFKKNSIQYNSNVVMKMNLKLLGSNHSLSIENNKL 753
Query: 259 RIPLVTDRPTIIFGSDVTHPQPGEDSSPSIAAVVASMDWPEVTKYRGLVSAQ-AHNQEII 317
I ++ P ++ GSDVTH P +D + SIA++V S D + T++ G Q +EII
Sbjct: 754 LIDKESNLPILVLGSDVTH-YPEKDQN-SIASLVGSYD-DKFTQFPGDYMLQDGPGEEII 810
Query: 318 QDLYKSTQDPFGGSVHGGMIRELLIAFRRSTNLKPHRIIFYRDGVGEGQFSQVLLHEMSA 377
++ GS+ M+ L I + + P +I+++RDGV QFSQV+ E+ +
Sbjct: 811 TNV---------GSL---MLNRLKIYQKHNNGKLPTKIMYFRDGVSVDQFSQVVKIEVKS 858
Query: 378 IRQAC----ASLEEG--YAPPVTFVVVQKRHHTRLFPAEHNNRDLTDRS------GNILP 425
I+++ L G Y PPVT + KR+ R P + N ++ GN++P
Sbjct: 859 IKESVRKFGPQLNGGNKYDPPVTCIATVKRNQVRFIPIQENAKNEKGEEVAVQSMGNVMP 918
Query: 426 GTVVDTQICHPTQFDFYLNSHAGIRGTSRPIHYHVLYDENRFSADDLQVLTNNLCYTYAR 485
GTVVD I FDF++ SH ++GT P HY LYDEN+ ++D LQ + NNLCY + R
Sbjct: 919 GTVVDRGITSVAHFDFFIQSHQALKGTGVPCHYWCLYDENQSTSDYLQEICNNLCYIFGR 978
Query: 486 CTRSVSIVPPAYYAHLAAFRARYYIXXXXXXXXXXXXXXXXXXXNLAIRP---LPVIKDN 542
T SV + P YYA L RA + + LP + DN
Sbjct: 979 STTSVKVPAPVYYADLLCTRATCFFKAGFELNMAQAPKEKGSKDQPTVSKNVLLPQVNDN 1038
Query: 543 VKDVMFY 549
+K VM+Y
Sbjct: 1039 IKSVMYY 1045
>pdb|2YHB|A Chain A, Crystal Structure Of The N. Crassa Qde-2 Ago Mid-Piwi
Domains
Length = 437
Score = 177 bits (448), Expect = 2e-44, Method: Compositional matrix adjust.
Identities = 110/319 (34%), Positives = 169/319 (52%), Gaps = 30/319 (9%)
Query: 203 YGRIKRVCETELGIVSQCCQPRQ--ASRLNIPYFENVALKINVKVGGRNTVLVDAVQKRI 260
Y +KR + G+ + CC + +++ + YF NV LK+N+K GG N ++ I
Sbjct: 94 YNMVKRAADITFGVHTVCCVAEKFLSTKGQLGYFANVGLKVNLKFGGTN----HNIKTPI 149
Query: 261 PLVTDRPTIIFGSDVTHPQ---PGED--SSPSIAAVVASMDWPEVTKYRGLVSAQAHNQE 315
PL+ T++ G DVTHP G+ S+PSI +V+++D + ++ +V H QE
Sbjct: 150 PLLAKGKTMVVGYDVTHPTNLAAGQSPASAPSIVGLVSTID-QHLGQWPAMVWNNPHGQE 208
Query: 316 IIQDLYKSTQDPFGGSVHGGMIRELLIAFRRSTNLKPHRIIFYRDGVGEGQFSQVLLHEM 375
+ + + D F + EL + + P I+ +RDGV EGQF V+ E+
Sbjct: 209 SMTEQF---TDKFKTRL------ELWRSNPANNRSLPENILIFRDGVSEGQFQMVIKDEL 259
Query: 376 SAIRQACASL-EEGYAPPVTFVVVQKRHHTRLFPAEHNNRDLTDRSGNILPGTVVDTQIC 434
+R AC + G P +T +V KRH TR FP + + +S GTVVD +
Sbjct: 260 PLVRAACKLVYPAGKLPRITLIVSVKRHQTRFFPTDPKHIHFKSKSPK--EGTVVDRGVT 317
Query: 435 HPTQFDFYLNSHAGIRGTSRPIHYHVLYDE------NRFSADDLQVLTNNLCYTYARCTR 488
+ +DF+L +HA ++GT+R HY VL DE +AD L+ LT+++CY + R T+
Sbjct: 318 NVRYWDFFLQAHASLQGTARSAHYTVLVDEIFRADYGNKAADTLEQLTHDMCYLFGRATK 377
Query: 489 SVSIVPPAYYAHLAAFRAR 507
+VSI PPAYYA L RAR
Sbjct: 378 AVSICPPAYYADLVCDRAR 396
>pdb|4G0O|A Chain A, Crystal Structure Of Arabidopsis Thaliana Ago5 Mid Domain
pdb|4G0O|B Chain B, Crystal Structure Of Arabidopsis Thaliana Ago5 Mid Domain
Length = 139
Score = 125 bits (315), Expect = 4e-29, Method: Composition-based stats.
Identities = 60/98 (61%), Positives = 69/98 (70%), Gaps = 4/98 (4%)
Query: 155 FNPRPVIPISSSNPNQIEKALVDVHNRTTXXXXXXXXXXXXXPDVSGSYGRIKRVCETEL 214
F P+P IP S P IE+AL+D+H R PDV+GSYG+IKR+CETEL
Sbjct: 46 FKPQPAIPFISCPPEHIEEALLDIHKRAPGLQLLIVIL----PDVTGSYGKIKRICETEL 101
Query: 215 GIVSQCCQPRQASRLNIPYFENVALKINVKVGGRNTVL 252
GIVSQCCQPRQ ++LN Y ENVALKINVK GGRNTVL
Sbjct: 102 GIVSQCCQPRQVNKLNKQYMENVALKINVKTGGRNTVL 139
>pdb|2YHA|A Chain A, Crystal Structure Of The N. Crassa Qde-2 Ago Mid-Piwi
Domains
Length = 388
Score = 117 bits (292), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 91/319 (28%), Positives = 141/319 (44%), Gaps = 79/319 (24%)
Query: 203 YGRIKRVCETELGIVSQCCQPRQ--ASRLNIPYFENVALKINVKVGGRNTVLVDAVQKRI 260
Y +KR + G+ + CC + +++ + YF NV LK+N+K GG N ++ I
Sbjct: 94 YNMVKRAADITFGVHTVCCVAEKFLSTKGQLGYFANVGLKVNLKFGGTN----HNIKTPI 149
Query: 261 PLVTDRPTIIFGSDVTHP---QPGED--SSPSIAAVVASMDWPEVTKYRGLVSAQAHNQE 315
PL+ T++ G DVTHP G+ S+PSI +V+++D + ++ +V H QE
Sbjct: 150 PLLAKGKTMVVGYDVTHPTNLAAGQSPASAPSIVGLVSTID-QHLGQWPAMVWNNPHGQE 208
Query: 316 IIQDLYKSTQDPFGGSVHGGMIRELLIAFRRSTNLKPHRIIFYRDGVGEGQFSQVLLHEM 375
+ + + D F + EL + + P I+ +RDGV EGQF V+ E+
Sbjct: 209 SMTEQF---TDKFKTRL------ELWRSNPANNRSLPENILIFRDGVSEGQFQMVIKDEL 259
Query: 376 SAIRQACASL-EEGYAPPVTFVVVQKRHHTRLFPAEHNNRDLTDRSGNILPGTVVDTQIC 434
+R AC + G P +T +V
Sbjct: 260 PLVRAACKLVYPAGKLPRITLIV------------------------------------- 282
Query: 435 HPTQFDFYLNSHAGIRGTSRPIHYHVLYDE------NRFSADDLQVLTNNLCYTYARCTR 488
++G S HY VL DE +AD L+ LT+++CY + R T+
Sbjct: 283 -------------SVKG-SGSAHYTVLVDEIFRADYGNKAADTLEQLTHDMCYLFGRATK 328
Query: 489 SVSIVPPAYYAHLAAFRAR 507
+VSI PPAYYA L RAR
Sbjct: 329 AVSICPPAYYADLVCDRAR 347
>pdb|3VNA|A Chain A, Structural Insights Into Small Rna Sorting And Mrna
Binding By Arabidopsis Ago Mid Domains
Length = 154
Score = 99.4 bits (246), Expect = 5e-21, Method: Composition-based stats.
Identities = 53/103 (51%), Positives = 65/103 (63%), Gaps = 4/103 (3%)
Query: 155 FNPRPVIPISSSNPNQIEKAL-VDVHNRTTXXXXXXXXX--XXXXPDVSGS-YGRIKRVC 210
FNP PV+P S+ P Q+EK L H+ T+ PD +GS YG +KR+C
Sbjct: 46 FNPEPVLPPVSARPEQVEKVLKTRYHDATSKLSQGKEIDLLIVILPDNNGSLYGDLKRIC 105
Query: 211 ETELGIVSQCCQPRQASRLNIPYFENVALKINVKVGGRNTVLV 253
ETELGIVSQCC + +++ Y NVALKINVKVGGRNTVLV
Sbjct: 106 ETELGIVSQCCLTKHVFKMSKQYMANVALKINVKVGGRNTVLV 148
>pdb|4G0P|A Chain A, Crystal Structure Of Arabidopsis Thaliana Ago1 Mid Domain
In Complex With Ump
pdb|4G0Q|A Chain A, Crystal Structure Of Arabidopsis Thaliana Ago1 Mid Domain
In Complex With Cmp
pdb|4G0Y|A Chain A, Crystal Structure Of Arabidopsis Ago1 In Complex With Amp
pdb|4G0Z|A Chain A, Crystal Structure Of Arabidopsis Thaliana Ago1 Mid Domain
In Complex With Gmp
Length = 147
Score = 97.4 bits (241), Expect = 2e-20, Method: Composition-based stats.
Identities = 52/102 (50%), Positives = 64/102 (62%), Gaps = 4/102 (3%)
Query: 155 FNPRPVIPISSSNPNQIEKAL-VDVHNRTTXXXXXXXXX--XXXXPDVSGS-YGRIKRVC 210
FNP PV+P S+ P Q+EK L H+ T+ PD +GS YG +KR+C
Sbjct: 46 FNPEPVLPPVSARPEQVEKVLKTRYHDATSKLSQGKEIDLLIVILPDNNGSLYGDLKRIC 105
Query: 211 ETELGIVSQCCQPRQASRLNIPYFENVALKINVKVGGRNTVL 252
ETELGIVSQCC + +++ Y NVALKINVKVGGRNTVL
Sbjct: 106 ETELGIVSQCCLTKHVFKMSKQYMANVALKINVKVGGRNTVL 147
>pdb|3VNB|A Chain A, Structural Insights Into Small Rna Sorting And Mrna
Binding By Arabidopsis Ago Domains
Length = 155
Score = 96.3 bits (238), Expect = 4e-20, Method: Composition-based stats.
Identities = 52/104 (50%), Positives = 63/104 (60%), Gaps = 5/104 (4%)
Query: 155 FNPRPVIPISSSNPNQIEKAL-VDVHNRTTXXXXXXXXX--XXXXPDVSGS--YGRIKRV 209
FNP PV+P S+ P Q+EK L H+ T+ PD S YG +KR+
Sbjct: 46 FNPEPVLPPVSARPEQVEKVLKTRYHDATSKLSQGKEIDLLIVILPDKKNSDLYGDLKRI 105
Query: 210 CETELGIVSQCCQPRQASRLNIPYFENVALKINVKVGGRNTVLV 253
CETELGIVSQCC + +++ Y NVALKINVKVGGRNTVLV
Sbjct: 106 CETELGIVSQCCLTKHVFKMSKQYMANVALKINVKVGGRNTVLV 149
>pdb|4G0X|A Chain A, Crystal Structure Of Arabidopsis Thaliana Ago1 Mid Domain
Length = 147
Score = 95.5 bits (236), Expect = 7e-20, Method: Composition-based stats.
Identities = 56/120 (46%), Positives = 69/120 (57%), Gaps = 4/120 (3%)
Query: 137 ANHFMVQLAERDIHHYDVFNPRPVIPISSSNPNQIEKAL-VDVHNRTTXXXXXXXXX--X 193
A F +LA+ FNP PV+P S+ P Q+EK L H+ T+
Sbjct: 28 ARTFCQELAQXCYVSGXAFNPEPVLPPVSARPEQVEKVLKTRYHDATSKLSQGKEIDLLI 87
Query: 194 XXXPDVSGS-YGRIKRVCETELGIVSQCCQPRQASRLNIPYFENVALKINVKVGGRNTVL 252
PD +GS YG +KR+CETELGIVSQCC + + + Y NVALKINVKVGGRNTVL
Sbjct: 88 VILPDNNGSLYGDLKRICETELGIVSQCCLTKHVFKXSKQYXANVALKINVKVGGRNTVL 147
>pdb|3LUC|A Chain A, Crystal Structure Of Mid Domain From Hago2
pdb|3LUC|B Chain B, Crystal Structure Of Mid Domain From Hago2
pdb|3LUC|C Chain C, Crystal Structure Of Mid Domain From Hago2
pdb|3LUD|A Chain A, Crystal Structure Of Mid Domain From Hago2 In Complex With
Amp
pdb|3LUD|B Chain B, Crystal Structure Of Mid Domain From Hago2 In Complex With
Amp
pdb|3LUD|C Chain C, Crystal Structure Of Mid Domain From Hago2 In Complex With
Amp
pdb|3LUG|A Chain A, Crystal Structure Of Mid Domain From Hago2 In Complex With
Cmp
pdb|3LUG|B Chain B, Crystal Structure Of Mid Domain From Hago2 In Complex With
Cmp
pdb|3LUG|C Chain C, Crystal Structure Of Mid Domain From Hago2 In Complex With
Cmp
pdb|3LUH|A Chain A, Crystal Structure Of Mid Domain From Hago2 In Complex With
Gmp
pdb|3LUH|B Chain B, Crystal Structure Of Mid Domain From Hago2 In Complex With
Gmp
pdb|3LUH|C Chain C, Crystal Structure Of Mid Domain From Hago2 In Complex With
Gmp
pdb|3LUJ|A Chain A, Crystal Structure Of Mid Domain From Hago2 In Complex With
Ump
pdb|3LUJ|B Chain B, Crystal Structure Of Mid Domain From Hago2 In Complex With
Ump
pdb|3LUJ|C Chain C, Crystal Structure Of Mid Domain From Hago2 In Complex With
Ump
pdb|3QX8|A Chain A, Crystal Structure Of Mid Domain From Hago2 In Complex With
M7gpppg
pdb|3QX8|B Chain B, Crystal Structure Of Mid Domain From Hago2 In Complex With
M7gpppg
pdb|3QX8|C Chain C, Crystal Structure Of Mid Domain From Hago2 In Complex With
M7gpppg
pdb|3QX9|A Chain A, Crystal Structure Of Mid Domain From Hago2 In Complex With
Atp
pdb|3QX9|B Chain B, Crystal Structure Of Mid Domain From Hago2 In Complex With
Atp
pdb|3QX9|C Chain C, Crystal Structure Of Mid Domain From Hago2 In Complex With
Atp
Length = 138
Score = 46.2 bits (108), Expect = 5e-05, Method: Composition-based stats.
Identities = 22/53 (41%), Positives = 30/53 (56%)
Query: 197 PDVSGSYGRIKRVCETELGIVSQCCQPRQASRLNIPYFENVALKINVKVGGRN 249
P + Y +KRV +T LG+ +QC Q + R N+ LKINVK+GG N
Sbjct: 86 PGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVN 138
>pdb|3LUK|A Chain A, Crystal Structure Of Mid Domain From Hago2
pdb|3LUK|B Chain B, Crystal Structure Of Mid Domain From Hago2
pdb|3LUK|C Chain C, Crystal Structure Of Mid Domain From Hago2
Length = 138
Score = 45.4 bits (106), Expect = 8e-05, Method: Composition-based stats.
Identities = 22/53 (41%), Positives = 29/53 (54%)
Query: 197 PDVSGSYGRIKRVCETELGIVSQCCQPRQASRLNIPYFENVALKINVKVGGRN 249
P + Y +KRV +T LG +QC Q + R N+ LKINVK+GG N
Sbjct: 86 PGKTPVYAEVKRVGDTVLGXATQCVQXKNVQRTTPQTLSNLCLKINVKLGGVN 138
>pdb|4G0M|A Chain A, Crystal Structure Of Arabidopsis Thaliana Ago2 Mid Domain
pdb|4G0M|B Chain B, Crystal Structure Of Arabidopsis Thaliana Ago2 Mid Domain
Length = 150
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 22/50 (44%), Positives = 31/50 (62%)
Query: 203 YGRIKRVCETELGIVSQCCQPRQASRLNIPYFENVALKINVKVGGRNTVL 252
Y +K + ET+LG+V+QC A++ Y N+ALK+N KVGG N L
Sbjct: 101 YKTLKWIAETKLGLVTQCFLTGPATKGGDQYRANLALKMNAKVGGSNVEL 150
>pdb|2XDY|A Chain A, Crystal Structure Of The N. Crassa Qde-2 Ago Mid Domain
Length = 145
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 203 YGRIKRVCETELGIVSQCCQPRQ--ASRLNIPYFENVALKINVKVGGRN 249
Y +KR + G+ + CC + +++ + YF NV LK+N+K GG N
Sbjct: 94 YNMVKRAADITFGVHTVCCVAEKFLSTKGQLGYFANVGLKVNLKFGGTN 142
>pdb|3DLB|A Chain A, Crystal Structure Of The Guide-Strand-Containing Argonaute
Protein Silencing Complex
pdb|3DLB|B Chain B, Crystal Structure Of The Guide-Strand-Containing Argonaute
Protein Silencing Complex
pdb|3DLH|A Chain A, Crystal Structure Of The Guide-Strand-Containing Argonaute
Protein Silencing Complex
pdb|3DLH|B Chain B, Crystal Structure Of The Guide-Strand-Containing Argonaute
Protein Silencing Complex
pdb|3F73|A Chain A, Alignment Of Guide-Target Seed Duplex Within An Argonaute
Silencing Complex
pdb|3F73|B Chain B, Alignment Of Guide-Target Seed Duplex Within An Argonaute
Silencing Complex
pdb|3HM9|A Chain A, Crystal Structure Of T. Thermophilus Argonaute Complexed
With Dna Guide Strand And 19-Nt Rna Target Strand
pdb|3HVR|A Chain A, Crystal Structure Of T. Thermophilus Argonaute Complexed
With Dna Guide Strand And 19-Nt Rna Target Strand With
Two Mg2+ At The Cleavage Site
pdb|3HVR|B Chain B, Crystal Structure Of T. Thermophilus Argonaute Complexed
With Dna Guide Strand And 19-Nt Rna Target Strand With
Two Mg2+ At The Cleavage Site
pdb|3HXM|A Chain A, Structure Of An Argonaute Complexed With Guide Dna And
Target Rna Duplex Containing Two Mismatches
Length = 685
Score = 32.3 bits (72), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 34/122 (27%), Positives = 50/122 (40%), Gaps = 27/122 (22%)
Query: 336 MIRELLIAFRRSTNLKPHRIIFYRDG-VGEGQFSQVLLHEMSAIRQACASLEEGYAPPVT 394
++ E L AFRR P R++ RDG V + +F+ L +A A EG A
Sbjct: 522 LLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALAL--------EALA--REGIA--YD 569
Query: 395 FVVVQKRHHTRLFPAEHNNRDLTDRSGNILPGTVVDTQICHPTQFDFYLNSHAGIRGTSR 454
V V+K R++P + G + G V + + L H RGT R
Sbjct: 570 LVSVRKSGGGRVYPVQ----------GRLADGLYVPLE----DKTFLLLTVHRDFRGTPR 615
Query: 455 PI 456
P+
Sbjct: 616 PL 617
>pdb|3HK2|A Chain A, Crystal Structure Of T. Thermophilus Argonaute N478 Mutant
Protein Complexed With Dna Guide Strand And 19-Nt Rna
Target Strand
pdb|3HK2|B Chain B, Crystal Structure Of T. Thermophilus Argonaute N478 Mutant
Protein Complexed With Dna Guide Strand And 19-Nt Rna
Target Strand
Length = 685
Score = 32.3 bits (72), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 34/122 (27%), Positives = 50/122 (40%), Gaps = 27/122 (22%)
Query: 336 MIRELLIAFRRSTNLKPHRIIFYRDG-VGEGQFSQVLLHEMSAIRQACASLEEGYAPPVT 394
++ E L AFRR P R++ RDG V + +F+ L +A A EG A
Sbjct: 522 LLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALAL--------EALA--REGIA--YD 569
Query: 395 FVVVQKRHHTRLFPAEHNNRDLTDRSGNILPGTVVDTQICHPTQFDFYLNSHAGIRGTSR 454
V V+K R++P + G + G V + + L H RGT R
Sbjct: 570 LVSVRKSGGGRVYPVQ----------GRLADGLYVPLE----DKTFLLLTVHRDFRGTPR 615
Query: 455 PI 456
P+
Sbjct: 616 PL 617
>pdb|3HJF|A Chain A, Crystal Structure Of T. Thermophilus Argonaute E546 Mutant
Protein Complexed With Dna Guide Strand And 15-Nt Rna
Target Strand
Length = 685
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 33/122 (27%), Positives = 50/122 (40%), Gaps = 27/122 (22%)
Query: 336 MIRELLIAFRRSTNLKPHRIIFYRDG-VGEGQFSQVLLHEMSAIRQACASLEEGYAPPVT 394
++ E L AFRR P R++ R+G V + +F+ L +A A EG A
Sbjct: 522 LLEETLWAFRRKAGRLPSRVLLLREGRVPQDEFALAL--------EALA--REGIA--YD 569
Query: 395 FVVVQKRHHTRLFPAEHNNRDLTDRSGNILPGTVVDTQICHPTQFDFYLNSHAGIRGTSR 454
V V+K R++P + G + G V + + L H RGT R
Sbjct: 570 LVSVRKSGGGRVYPVQ----------GRLADGLYVPLE----DKTFLLLTVHRDFRGTPR 615
Query: 455 PI 456
P+
Sbjct: 616 PL 617
>pdb|3B1B|A Chain A, The Unique Structure Of Wild Type Carbonic Anhydrase
Alpha-Ca1 From Chlamydomonas Reinhardtii
pdb|3B1B|B Chain B, The Unique Structure Of Wild Type Carbonic Anhydrase
Alpha-Ca1 From Chlamydomonas Reinhardtii
Length = 377
Score = 29.3 bits (64), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 6/81 (7%)
Query: 385 LEEGYAPPVTFVVVQKRHHTRLFPAEHNNRDLTDRSGNIL---PGTVVDTQICHPTQFDF 441
+ G+ V + H T PA HN T+R ++L P D PTQF F
Sbjct: 108 INNGHTIQVQWTYNYAGHATIAIPAMHNQ---TNRIVDVLEMRPNDAADRVTAVPTQFHF 164
Query: 442 YLNSHAGIRGTSRPIHYHVLY 462
+ S + G P+ H+++
Sbjct: 165 HSTSEHLLAGKIYPLELHIVH 185
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
0.322 0.137 0.415
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,955,262
Number of Sequences: 62578
Number of extensions: 475351
Number of successful extensions: 881
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 836
Number of HSP's gapped (non-prelim): 21
length of query: 550
length of database: 14,973,337
effective HSP length: 104
effective length of query: 446
effective length of database: 8,465,225
effective search space: 3775490350
effective search space used: 3775490350
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)