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= 003516
(813 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 = 439 bits (1130), Expect = e-123, Method: Compositional matrix adjust.
Identities = 249/673 (36%), Positives = 376/673 (55%), Gaps = 40/673 (5%)
Query: 132 PRPGYGQVGTKCIVKANHFFAELPDKDLNQYDVTITPEVASRTVNRAIMAELVRLYKESD 191
PRP +G G ++AN F ++P D+ Y++ I PE R VNR I+ +V+ +K
Sbjct: 29 PRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQI 88
Query: 192 LGMRLPAYDGRKSLYTAGELPFVWKEFKIKLVDELDGINGPKRVREYKVVIKFAARANMH 251
G R P +DGRK+LYTA LP + ++++ + G + R +KV IK+ + ++
Sbjct: 89 FGDRKPVFDGRKNLYTAMPLPIGRDKVELEVT-----LPGEGKDRIFKVSIKWVSCVSLQ 143
Query: 252 HLGQFLAGKRADAPQEALQILDIVLRELSTKRYCPIGRSFFSPSIRTPQRLGDGLESWCG 311
L L+G+ P E +Q LD+V+R L + RY P+GRSFF+ S LG G E W G
Sbjct: 144 ALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFG 203
Query: 312 FYQSIRPTQMGLSLNIDMASAAFIEPLPVIEFVAQLLGKDVLS---RTLSDSDRVKIKKA 368
F+QS+RP+ + LNID+++ AF + PVIEFV ++L + + L+DS RVK K
Sbjct: 204 FHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKE 263
Query: 369 LRGVKVEVTHRGTVRRKYRVSGLTSQPTRELVFPVDDNSTMK---SVVEYFQEMYGFTIQ 425
++G+KVE+TH G ++RKYRV +T +P FP+ S +V +YF++ + ++
Sbjct: 264 IKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLR 323
Query: 426 HTHLPCLQVGNQKKANYLPMEACKIVEGQRYTKRLNERQITALLKVTCQRPRDRENDILQ 485
+ HLPCLQVG ++K YLP+E C IV GQR K+L + Q + +++ T + DR+ +I +
Sbjct: 324 YPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISK 383
Query: 486 TVQQNAYDQDLYAKEFGIKISEKLASVEARILPAPWLKYHENGKEKD-CLPQVGQWNMMN 544
++ +++ D Y +EFGI + +++ V R+L P + Y G+ K P G W+M N
Sbjct: 384 LMRSASFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILY--GGRNKAIATPVQGVWDMRN 441
Query: 545 KKMINGMTVSRW--ACINFSRSVQESVARGFCNELAQMCQVSGMEFNPEPVIPIHNARPD 602
K+ G+ + W AC R E + F +L ++ + +GM +P + D
Sbjct: 442 KQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGAD 501
Query: 603 QVEKALKHVYHSSMSKTKGKELELLLAILPDNNGSLYGDLKRICETDLGIISQCCLTKHV 662
VE +H+ K L+L++ ILP +Y ++KR+ +T LG+ +QC K+V
Sbjct: 502 SVEPMFRHL------KNTYAGLQLVVVILPGKT-PVYAEVKRVGDTVLGMATQCVQMKNV 554
Query: 663 FKISKQYLANVSLKINVKMGGRNTVLLDAISCRIPLVSDIPTIIFGADVTHPENGEDSSP 722
+ + Q L+N+ LKINVK+GG N +LL P V P I GADVTHP G+ P
Sbjct: 555 QRTTPQTLSNLCLKINVKLGGVNNILLPQGR---PPVFQQPVIFLGADVTHPPAGDGKKP 611
Query: 723 SIAAVVASQDWPEVTKYAGLVCAQAHRQELIQDLYKTWHDPVRGTVSGGMIRDLLISFRK 782
SIAAVV S D +Y V Q HRQE+IQDL M+R+LLI F K
Sbjct: 612 SIAAVVGSMD-AHPNRYCATVRVQQHRQEIIQDL-------------AAMVRELLIQFYK 657
Query: 783 ATGQKPLRIIFYR 795
+T KP RIIFYR
Sbjct: 658 STRFKPTRIIFYR 670
>pdb|4EI1|A Chain A, Crystal Structure Of Human Argonaute2
pdb|4EI3|A Chain A, Crystal Structure Of Human Argonaute2
Length = 859
Score = 439 bits (1128), Expect = e-123, Method: Compositional matrix adjust.
Identities = 249/673 (36%), Positives = 375/673 (55%), Gaps = 40/673 (5%)
Query: 132 PRPGYGQVGTKCIVKANHFFAELPDKDLNQYDVTITPEVASRTVNRAIMAELVRLYKESD 191
PRP +G G ++AN F ++P D+ Y++ I PE R VNR I+ +V+ +K
Sbjct: 27 PRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQI 86
Query: 192 LGMRLPAYDGRKSLYTAGELPFVWKEFKIKLVDELDGINGPKRVREYKVVIKFAARANMH 251
G R P +DGRK+LYTA LP + ++++ + G + R +KV IK+ + ++
Sbjct: 87 FGDRKPVFDGRKNLYTAMPLPIGRDKVELEVT-----LPGEGKDRIFKVSIKWVSCVSLQ 141
Query: 252 HLGQFLAGKRADAPQEALQILDIVLRELSTKRYCPIGRSFFSPSIRTPQRLGDGLESWCG 311
L L+G+ P E +Q LD+V+R L + RY P+GRSFF+ S LG G E W G
Sbjct: 142 ALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFG 201
Query: 312 FYQSIRPTQMGLSLNIDMASAAFIEPLPVIEFVAQLLGKDVLS---RTLSDSDRVKIKKA 368
F+QS+RP+ + LNID+++ AF + PVIEFV ++L + + L+DS RVK K
Sbjct: 202 FHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKE 261
Query: 369 LRGVKVEVTHRGTVRRKYRVSGLTSQPTRELVFPVDDNSTMK---SVVEYFQEMYGFTIQ 425
++G+KVE+TH G ++RKYRV +T +P FP+ S +V +YF++ + ++
Sbjct: 262 IKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLR 321
Query: 426 HTHLPCLQVGNQKKANYLPMEACKIVEGQRYTKRLNERQITALLKVTCQRPRDRENDILQ 485
+ HLPCLQVG ++K YLP+E C IV GQR K+L + Q + +++ T + DR+ +I +
Sbjct: 322 YPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISK 381
Query: 486 TVQQNAYDQDLYAKEFGIKISEKLASVEARILPAPWLKYHENGKEKD-CLPQVGQWNMMN 544
++ ++ D Y +EFGI + +++ V R+L P + Y G+ K P G W+M N
Sbjct: 382 LMRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILY--GGRNKAIATPVQGVWDMRN 439
Query: 545 KKMINGMTVSRW--ACINFSRSVQESVARGFCNELAQMCQVSGMEFNPEPVIPIHNARPD 602
K+ G+ + W AC R E + F +L ++ + +GM +P + D
Sbjct: 440 KQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGAD 499
Query: 603 QVEKALKHVYHSSMSKTKGKELELLLAILPDNNGSLYGDLKRICETDLGIISQCCLTKHV 662
VE +H+ K L+L++ ILP +Y ++KR+ +T LG+ +QC K+V
Sbjct: 500 SVEPMFRHL------KNTYAGLQLVVVILPGKT-PVYAEVKRVGDTVLGMATQCVQMKNV 552
Query: 663 FKISKQYLANVSLKINVKMGGRNTVLLDAISCRIPLVSDIPTIIFGADVTHPENGEDSSP 722
+ + Q L+N+ LKINVK+GG N +LL P V P I GADVTHP G+ P
Sbjct: 553 QRTTPQTLSNLCLKINVKLGGVNNILLPQGR---PPVFQQPVIFLGADVTHPPAGDGKKP 609
Query: 723 SIAAVVASQDWPEVTKYAGLVCAQAHRQELIQDLYKTWHDPVRGTVSGGMIRDLLISFRK 782
SIAAVV S D +Y V Q HRQE+IQDL M+R+LLI F K
Sbjct: 610 SIAAVVGSMD-AHPNRYCATVRVQQHRQEIIQDL-------------AAMVRELLIQFYK 655
Query: 783 ATGQKPLRIIFYR 795
+T KP RIIFYR
Sbjct: 656 STRFKPTRIIFYR 668
>pdb|3VNA|A Chain A, Structural Insights Into Small Rna Sorting And Mrna
Binding By Arabidopsis Ago Mid Domains
Length = 154
Score = 237 bits (605), Expect = 2e-62, Method: Compositional matrix adjust.
Identities = 111/148 (75%), Positives = 131/148 (88%), Gaps = 1/148 (0%)
Query: 543 MNKKMINGMTVSRWACINFSRSVQESVARGFCNELAQMCQVSGMEFNPEPVIPIHNARPD 602
MNKKMING TV+ W CINFSR VQ+++AR FC ELAQMC VSGM FNPEPV+P +ARP+
Sbjct: 1 MNKKMINGGTVNNWICINFSRQVQDNLARTFCQELAQMCYVSGMAFNPEPVLPPVSARPE 60
Query: 603 QVEKALKHVYHSSMSK-TKGKELELLLAILPDNNGSLYGDLKRICETDLGIISQCCLTKH 661
QVEK LK YH + SK ++GKE++LL+ ILPDNNGSLYGDLKRICET+LGI+SQCCLTKH
Sbjct: 61 QVEKVLKTRYHDATSKLSQGKEIDLLIVILPDNNGSLYGDLKRICETELGIVSQCCLTKH 120
Query: 662 VFKISKQYLANVSLKINVKMGGRNTVLL 689
VFK+SKQY+ANV+LKINVK+GGRNTVL+
Sbjct: 121 VFKMSKQYMANVALKINVKVGGRNTVLV 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 = 234 bits (598), Expect = 1e-61, Method: Compositional matrix adjust.
Identities = 110/146 (75%), Positives = 129/146 (88%), Gaps = 1/146 (0%)
Query: 544 NKKMINGMTVSRWACINFSRSVQESVARGFCNELAQMCQVSGMEFNPEPVIPIHNARPDQ 603
NKKMING TV+ W CINFSR VQ+++AR FC ELAQMC VSGM FNPEPV+P +ARP+Q
Sbjct: 2 NKKMINGGTVNNWICINFSRQVQDNLARTFCQELAQMCYVSGMAFNPEPVLPPVSARPEQ 61
Query: 604 VEKALKHVYHSSMSK-TKGKELELLLAILPDNNGSLYGDLKRICETDLGIISQCCLTKHV 662
VEK LK YH + SK ++GKE++LL+ ILPDNNGSLYGDLKRICET+LGI+SQCCLTKHV
Sbjct: 62 VEKVLKTRYHDATSKLSQGKEIDLLIVILPDNNGSLYGDLKRICETELGIVSQCCLTKHV 121
Query: 663 FKISKQYLANVSLKINVKMGGRNTVL 688
FK+SKQY+ANV+LKINVK+GGRNTVL
Sbjct: 122 FKMSKQYMANVALKINVKVGGRNTVL 147
>pdb|3VNB|A Chain A, Structural Insights Into Small Rna Sorting And Mrna
Binding By Arabidopsis Ago Domains
Length = 155
Score = 226 bits (576), Expect = 4e-59, Method: Compositional matrix adjust.
Identities = 108/149 (72%), Positives = 128/149 (85%), Gaps = 2/149 (1%)
Query: 543 MNKKMINGMTVSRWACINFSRSVQESVARGFCNELAQMCQVSGMEFNPEPVIPIHNARPD 602
MNKKMING TV+ W CINFSR VQ+++AR FC ELAQMC VSGM FNPEPV+P +ARP+
Sbjct: 1 MNKKMINGGTVNNWICINFSRQVQDNLARTFCQELAQMCYVSGMAFNPEPVLPPVSARPE 60
Query: 603 QVEKALKHVYHSSMSK-TKGKELELLLAILPD-NNGSLYGDLKRICETDLGIISQCCLTK 660
QVEK LK YH + SK ++GKE++LL+ ILPD N LYGDLKRICET+LGI+SQCCLTK
Sbjct: 61 QVEKVLKTRYHDATSKLSQGKEIDLLIVILPDKKNSDLYGDLKRICETELGIVSQCCLTK 120
Query: 661 HVFKISKQYLANVSLKINVKMGGRNTVLL 689
HVFK+SKQY+ANV+LKINVK+GGRNTVL+
Sbjct: 121 HVFKMSKQYMANVALKINVKVGGRNTVLV 149
>pdb|4G0X|A Chain A, Crystal Structure Of Arabidopsis Thaliana Ago1 Mid Domain
Length = 147
Score = 224 bits (572), Expect = 1e-58, Method: Compositional matrix adjust.
Identities = 107/146 (73%), Positives = 124/146 (84%), Gaps = 1/146 (0%)
Query: 544 NKKMINGMTVSRWACINFSRSVQESVARGFCNELAQMCQVSGMEFNPEPVIPIHNARPDQ 603
NKK ING TV+ W CINFSR VQ+++AR FC ELAQ C VSG FNPEPV+P +ARP+Q
Sbjct: 2 NKKXINGGTVNNWICINFSRQVQDNLARTFCQELAQXCYVSGXAFNPEPVLPPVSARPEQ 61
Query: 604 VEKALKHVYHSSMSK-TKGKELELLLAILPDNNGSLYGDLKRICETDLGIISQCCLTKHV 662
VEK LK YH + SK ++GKE++LL+ ILPDNNGSLYGDLKRICET+LGI+SQCCLTKHV
Sbjct: 62 VEKVLKTRYHDATSKLSQGKEIDLLIVILPDNNGSLYGDLKRICETELGIVSQCCLTKHV 121
Query: 663 FKISKQYLANVSLKINVKMGGRNTVL 688
FK SKQY ANV+LKINVK+GGRNTVL
Sbjct: 122 FKXSKQYXANVALKINVKVGGRNTVL 147
>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 = 149 bits (377), Expect = 5e-36, Method: Compositional matrix adjust.
Identities = 71/145 (48%), Positives = 98/145 (67%), Gaps = 7/145 (4%)
Query: 544 NKKMINGMTVSRWACINFSRSVQESVARGFCNELAQMCQVSGMEFNPEPVIPIHNARPDQ 603
+KKM+NG V+ W C++FS + + + FC +L MC GMEF P+P IP + P+
Sbjct: 2 DKKMVNGAKVTSWTCVSFSTRIDRGLPQEFCKQLIGMCVSKGMEFKPQPAIPFISCPPEH 61
Query: 604 VEKALKHVYHSSMSKTKGKELELLLAILPDNNGSLYGDLKRICETDLGIISQCCLTKHVF 663
+E+AL ++ + L+LL+ ILPD GS YG +KRICET+LGI+SQCC + V
Sbjct: 62 IEEALLDIHK------RAPGLQLLIVILPDVTGS-YGKIKRICETELGIVSQCCQPRQVN 114
Query: 664 KISKQYLANVSLKINVKMGGRNTVL 688
K++KQY+ NV+LKINVK GGRNTVL
Sbjct: 115 KLNKQYMENVALKINVKTGGRNTVL 139
>pdb|1R4K|A Chain A, Solution Structure Of The Drosophila Argonaute 1 Paz
Domain
Length = 169
Score = 124 bits (312), Expect = 1e-28, Method: Compositional matrix adjust.
Identities = 65/168 (38%), Positives = 107/168 (63%), Gaps = 6/168 (3%)
Query: 332 AAFIEPLPVIEFVAQLLG-KDV--LSRTLSDSDRVKIKKALRGVKVEVTHRGTVRRKYRV 388
AF + PVI+F+ ++L +D+ + L+DS RVK K ++G+K+E+TH G +RRKYRV
Sbjct: 2 TAFYKAQPVIDFMCEVLDIRDINEQRKPLTDSQRVKFTKEIKGLKIEITHCGQMRRKYRV 61
Query: 389 SGLTSQPTRELVFPV--DDNSTMK-SVVEYFQEMYGFTIQHTHLPCLQVGNQKKANYLPM 445
+T +P + FP+ ++ T++ +V +YF + Y +++ HLPCLQVG + K YLP+
Sbjct: 62 CNVTRRPAQMQSFPLQLENGQTVECTVAKYFLDKYRMKLRYPHLPCLQVGQEHKHTYLPL 121
Query: 446 EACKIVEGQRYTKRLNERQITALLKVTCQRPRDRENDILQTVQQNAYD 493
E C IV GQR K+L + Q + ++K T + DRE +I V++ ++
Sbjct: 122 EVCNIVAGQRCIKKLTDMQTSTMIKATARSAPDREREINNLVKRADFN 169
>pdb|1SI2|A Chain A, Crystal Structure Of The Paz Domain Of Human Eif2c1 In
Complex With A 9-Mer Sirna-Like Duplex Of
Deoxynucleotide Overhang
Length = 149
Score = 120 bits (300), Expect = 4e-27, Method: Compositional matrix adjust.
Identities = 59/140 (42%), Positives = 88/140 (62%), Gaps = 6/140 (4%)
Query: 339 PVIEFVAQLL---GKDVLSRTLSDSDRVKIKKALRGVKVEVTHRGTVRRKYRVSGLTSQP 395
PVIEF+ ++L D + L+DS RV+ K ++G+KVEVTH G ++RKYRV +T +P
Sbjct: 7 PVIEFMCEVLDIRNIDEQPKPLTDSQRVRFTKEIKGLKVEVTHCGQMKRKYRVCNVTRRP 66
Query: 396 TRELVFPVDDNSTMK---SVVEYFQEMYGFTIQHTHLPCLQVGNQKKANYLPMEACKIVE 452
FP+ S +V +YF++ Y +++ HLPCLQVG ++K YLP+E C IV
Sbjct: 67 ASHQTFPLQLESGQTVECTVAQYFKQKYNLQLKYPHLPCLQVGQEQKHTYLPLEVCNIVA 126
Query: 453 GQRYTKRLNERQITALLKVT 472
GQR K+L + Q + ++K T
Sbjct: 127 GQRCIKKLTDNQTSTMIKAT 146
>pdb|1SI3|A Chain A, Crystal Structure Of The Paz Domain Of Human Eif2c1 In
Complex With A 9-Mer Sirna-Like Duplex
Length = 149
Score = 117 bits (293), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 59/140 (42%), Positives = 85/140 (60%), Gaps = 6/140 (4%)
Query: 339 PVIEFVAQLL---GKDVLSRTLSDSDRVKIKKALRGVKVEVTHRGTVRRKYRVSGLTSQP 395
PVIEF ++L D + L+DS RV+ K ++G+KVEVTH G +RKYRV +T +P
Sbjct: 7 PVIEFXCEVLDIRNIDEQPKPLTDSQRVRFTKEIKGLKVEVTHCGQXKRKYRVCNVTRRP 66
Query: 396 TRELVFPVDDNSTMK---SVVEYFQEMYGFTIQHTHLPCLQVGNQKKANYLPMEACKIVE 452
FP+ S +V +YF++ Y +++ HLPCLQVG ++K YLP+E C IV
Sbjct: 67 ASHQTFPLQLESGQTVECTVAQYFKQKYNLQLKYPHLPCLQVGQEQKHTYLPLEVCNIVA 126
Query: 453 GQRYTKRLNERQITALLKVT 472
GQR K+L + Q + +K T
Sbjct: 127 GQRCIKKLTDNQTSTXIKAT 146
>pdb|2YHB|A Chain A, Crystal Structure Of The N. Crassa Qde-2 Ago Mid-Piwi
Domains
Length = 437
Score = 72.0 bits (175), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 47/149 (31%), Positives = 78/149 (52%), Gaps = 16/149 (10%)
Query: 620 KGKEL----ELLLAILPDNNGSLYGDLKRICETDLGIISQCCLTKHVFKISKQ--YLANV 673
K KEL + ++ +LP + ++Y +KR + G+ + CC+ + Q Y ANV
Sbjct: 71 KVKELMSSHQFVVVLLPRKDVAIYNMVKRAADITFGVHTVCCVAEKFLSTKGQLGYFANV 130
Query: 674 SLKINVKMGGRNTVLLDAISCRIPLVSDIPTIIFGADVTHPEN---GED--SSPSIAAVV 728
LK+N+K GG N I IPL++ T++ G DVTHP N G+ S+PSI +V
Sbjct: 131 GLKVNLKFGGTN----HNIKTPIPLLAKGKTMVVGYDVTHPTNLAAGQSPASAPSIVGLV 186
Query: 729 ASQDWPEVTKYAGLVCAQAHRQELIQDLY 757
++ D + ++ +V H QE + + +
Sbjct: 187 STID-QHLGQWPAMVWNNPHGQESMTEQF 214
>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 = 72.0 bits (175), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 44/144 (30%), Positives = 75/144 (52%), Gaps = 9/144 (6%)
Query: 544 NKKMINGMTVSRWA--CINFSRSVQESVARGFCNELAQMCQVSGMEFNPEPVIPIHNARP 601
NK+ G+ + WA C R E + F +L ++ + +GM +P +
Sbjct: 2 NKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGA 61
Query: 602 DQVEKALKHVYHSSMSKTKGKELELLLAILPDNNGSLYGDLKRICETDLGIISQCCLTKH 661
D VE +H+ ++ L+L++ ILP +Y ++KR+ +T LG+ +QC K+
Sbjct: 62 DSVEPMFRHLKNTYAG------LQLVVVILPGKT-PVYAEVKRVGDTVLGMATQCVQMKN 114
Query: 662 VFKISKQYLANVSLKINVKMGGRN 685
V + + Q L+N+ LKINVK+GG N
Sbjct: 115 VQRTTPQTLSNLCLKINVKLGGVN 138
>pdb|2YHA|A Chain A, Crystal Structure Of The N. Crassa Qde-2 Ago Mid-Piwi
Domains
Length = 388
Score = 71.6 bits (174), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 47/150 (31%), Positives = 78/150 (52%), Gaps = 16/150 (10%)
Query: 619 TKGKEL----ELLLAILPDNNGSLYGDLKRICETDLGIISQCCLTKHVFKISKQ--YLAN 672
K KEL + ++ +LP + ++Y +KR + G+ + CC+ + Q Y AN
Sbjct: 70 AKVKELMSSHQFVVVLLPRKDVAIYNMVKRAADITFGVHTVCCVAEKFLSTKGQLGYFAN 129
Query: 673 VSLKINVKMGGRNTVLLDAISCRIPLVSDIPTIIFGADVTHPEN---GED--SSPSIAAV 727
V LK+N+K GG N I IPL++ T++ G DVTHP N G+ S+PSI +
Sbjct: 130 VGLKVNLKFGGTN----HNIKTPIPLLAKGKTMVVGYDVTHPTNLAAGQSPASAPSIVGL 185
Query: 728 VASQDWPEVTKYAGLVCAQAHRQELIQDLY 757
V++ D + ++ +V H QE + + +
Sbjct: 186 VSTID-QHLGQWPAMVWNNPHGQESMTEQF 214
>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 = 68.9 bits (167), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 43/144 (29%), Positives = 73/144 (50%), Gaps = 9/144 (6%)
Query: 544 NKKMINGMTVSRWA--CINFSRSVQESVARGFCNELAQMCQVSGMEFNPEPVIPIHNARP 601
NK+ G+ + WA C R E + F +L ++ + +G +P +
Sbjct: 2 NKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGXPIQGQPCFCKYAQGA 61
Query: 602 DQVEKALKHVYHSSMSKTKGKELELLLAILPDNNGSLYGDLKRICETDLGIISQCCLTKH 661
D VE +H+ ++ L+L++ ILP +Y ++KR+ +T LG +QC K+
Sbjct: 62 DSVEPXFRHLKNTYAG------LQLVVVILPGKT-PVYAEVKRVGDTVLGXATQCVQXKN 114
Query: 662 VFKISKQYLANVSLKINVKMGGRN 685
V + + Q L+N+ LKINVK+GG N
Sbjct: 115 VQRTTPQTLSNLCLKINVKLGGVN 138
>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 = 67.8 bits (164), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 99/461 (21%), Positives = 195/461 (42%), Gaps = 78/461 (16%)
Query: 411 SVVEYFQEMYGFTIQHTHLPCLQVGNQKKANYLPMEACKIVEGQRYTKRLNERQITALLK 470
+ ++YF+ Y T+++ + + +G K + +P E IV GQ+ ++ + + +
Sbjct: 423 NTIDYFKRKYDITLKYPDMKLVNLGG--KNDVVPPECLTIVPGQKLKGQIFDTK--TYID 478
Query: 471 VTCQRPRDRENDI----LQTVQQNAYDQDLYAKEFGIKISEKLASVEARILPAPWLKYHE 526
+ RP ++ + I + +++ D + + + V +RIL AP +++ E
Sbjct: 479 FSAIRPTEKFDLISRLSMPAIKRGLTDSEKEESSAPHNSAYQFMRVPSRILDAPVVQFKE 538
Query: 527 NGKE-KDCL------PQVGQWNMMNKKMINGMTVS---RWACINFSRSV----QESVARG 572
+ E KD G WNM + I+ R IN + + ES
Sbjct: 539 STFEYKDKSYGTKHEESKGNWNMKGHQFISTPAKQVNLRAIFINNANTAPPASMESELDI 598
Query: 573 FCNELAQMCQVSGMEFN--PEPVI------PIHN------------------------AR 600
++ A + G++FN +P++ PI +
Sbjct: 599 SMDKFASDVKQLGVDFNVSGKPILINQFGPPIKKFQGGGRGGRGGRGSRGGRGGRGAPSG 658
Query: 601 PDQVEKALKHVYHSSMSKTKGKELELLLAILPDNNGSLYGDLKRICETDLGIISQCCLTK 660
P E + + ++ + +L + N+ ++Y LK I + G ++ C +
Sbjct: 659 PPTFETSPGEISLLNLLENIPSNTYILYVLRRGNDSAVYDRLKYITDLKFGALNSCVVWD 718
Query: 661 HVFKISKQYLANVSLKINVKMGGRNTVL-LDAISCRIPLVSDIPTIIFGADVTH-PENGE 718
+ K S QY +NV +K+N+K+ G N L ++ I S++P ++ G+DVTH PE +
Sbjct: 719 NFKKNSIQYNSNVVMKMNLKLLGSNHSLSIENNKLLIDKESNLPILVLGSDVTHYPEKDQ 778
Query: 719 DSSPSIAAVVASQDWPEVTKYAGLVCAQ-AHRQELIQDLYKTWHDPVRGTVSGGMIRDLL 777
+ SIA++V S D + T++ G Q +E+I + V M+ L
Sbjct: 779 N---SIASLVGSYD-DKFTQFPGDYMLQDGPGEEIITN------------VGSLMLNRLK 822
Query: 778 ISFRKATGQKPLRIIFYR-----SLFLSVLRVKVEIISICV 813
I + G+ P +I+++R F V++++V+ I V
Sbjct: 823 IYQKHNNGKLPTKIMYFRDGVSVDQFSQVVKIEVKSIKESV 863
>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 = 63.9 bits (154), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 45/149 (30%), Positives = 69/149 (46%), Gaps = 6/149 (4%)
Query: 545 KKMINGMTVSRWACINFSRSVQ-ESVARGFCNELAQMCQVSGMEFNPEPVIPIHN----A 599
K + G V WA ++F+ S + + F + L C GM+ V +
Sbjct: 3 KGVTRGSIVKHWAVLDFTASERFNKMPNDFVDNLIDRCWRLGMQMEAPIVYKTSRMETLS 62
Query: 600 RPDQVEKALKHVYHSSMSKTKGKELELLLAILPDNNGSLYGDLKRICETDLGIISQCCLT 659
+ +E+ L+ V + K G L+L + + Y LK I ET LG+++QC LT
Sbjct: 63 NGNAIEELLRSVIDEASRKHGGARPTLVLCAMSRKDDG-YKTLKWIAETKLGLVTQCFLT 121
Query: 660 KHVFKISKQYLANVSLKINVKMGGRNTVL 688
K QY AN++LK+N K+GG N L
Sbjct: 122 GPATKGGDQYRANLALKMNAKVGGSNVEL 150
>pdb|1VYN|A Chain A, Structure And Nucleic Acid Binding Of The Drosophila
Argonaute2 Paz Domain
Length = 143
Score = 56.6 bits (135), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 39/137 (28%), Positives = 67/137 (48%), Gaps = 7/137 (5%)
Query: 338 LPVIEFVAQLLGKDVLSRTLS-DSDRVKIKKALRGVKVEVTHRGTVR---RKYRVSGLTS 393
+P+IE++ + K ++ T + D R ++ LRG+ V T + + R YRV+GL+
Sbjct: 5 MPMIEYLERFSLKAKINNTTNLDYSRRFLEPFLRGINVVYTPPQSFQSAPRVYRVNGLSR 64
Query: 394 QPTRELVFPVDDNSTMKSVVEYFQEMYGFTIQHTHLPCLQVGNQKKANYLPMEACKIVEG 453
P F D ++ YF + ++ L CL VG+ K+ LP+E C I EG
Sbjct: 65 APASSETFEHDGKKV--TIASYFHSR-NYPLKFPQLHCLNVGSSIKSILLPIELCSIEEG 121
Query: 454 QRYTKRLNERQITALLK 470
Q ++ Q+ ++K
Sbjct: 122 QALNRKDGATQVANMIK 138
>pdb|1R6Z|P Chain P, The Crystal Structure Of The Argonaute2 Paz Domain (as A
Mbp Fusion)
pdb|1R6Z|A Chain A, The Crystal Structure Of The Argonaute2 Paz Domain (as A
Mbp Fusion)
pdb|1R6Z|Z Chain Z, The Crystal Structure Of The Argonaute2 Paz Domain (as A
Mbp Fusion)
Length = 509
Score = 56.2 bits (134), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 39/137 (28%), Positives = 68/137 (49%), Gaps = 7/137 (5%)
Query: 327 IDMASAAFIEPLPVIEFVAQLLGKDVLSRTLS-DSDRVKIKKALRGVKVEVTHRGTVR-- 383
+D++ +F +P+IE++ + K ++ T + D R ++ LRG+ V T + +
Sbjct: 374 VDISHKSFPISMPMIEYLERFSLKAKINNTTNLDYSRRFLEPFLRGINVVYTPPQSFQSA 433
Query: 384 -RKYRVSGLTSQPTRELVFPVDDNSTMKSVVEYFQEMYGFTIQHTHLPCLQVGNQKKANY 442
R YRV+GL+ P F D ++ YF + ++ L CL VG+ K+
Sbjct: 434 PRVYRVNGLSRAPASSETFEHDGKKV--TIASYFHSR-NYPLKFPQLHCLNVGSSIKSIL 490
Query: 443 LPMEACKIVEGQRYTKR 459
LP+E C I EGQ ++
Sbjct: 491 LPIELCSIEEGQALNRK 507
>pdb|1T2R|A Chain A, Structural Basis For 3' End Recognition Of Nucleic Acids
By The Drosophila Argonaute 2 Paz Domain
pdb|1T2S|A Chain A, Structural Basis For 3' End Recognition Of Nucleic Acids
By The Drosophila Argonaute 2 Paz Domain
Length = 123
Score = 53.1 bits (126), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 37/121 (30%), Positives = 60/121 (49%), Gaps = 7/121 (5%)
Query: 338 LPVIEFVAQLLGKDVLSRTLS-DSDRVKIKKALRGVKVEVTHRGTVR---RKYRVSGLTS 393
+P+IE++ + K ++ T + D R ++ LRG+ V T + + R YRV+GL+
Sbjct: 5 MPMIEYLERFSLKAKINNTTNLDYSRRFLEPFLRGINVVYTPPQSFQSAPRVYRVNGLSR 64
Query: 394 QPTRELVFPVDDNSTMKSVVEYFQEMYGFTIQHTHLPCLQVGNQKKANYLPMEACKIVEG 453
P F D ++ YF + ++ L CL VG+ K+ LP+E C I EG
Sbjct: 65 APASSETFEHDGKKV--TIASYFHSR-NYPLKFPQLHCLNVGSSIKSILLPIELCSIEEG 121
Query: 454 Q 454
Q
Sbjct: 122 Q 122
>pdb|3MJ0|A Chain A, Crystal Structure Of Drosophia Ago-Paz Domain In Complex
With 3'-End 2'-O-Methylated Rna
Length = 124
Score = 53.1 bits (126), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 37/121 (30%), Positives = 60/121 (49%), Gaps = 7/121 (5%)
Query: 338 LPVIEFVAQLLGKDVLSRTLS-DSDRVKIKKALRGVKVEVTHRGTVR---RKYRVSGLTS 393
+P+IE++ + K ++ T + D R ++ LRG+ V T + + R YRV+GL+
Sbjct: 3 MPMIEYLERFSLKAKINNTTNLDYSRRFLEPFLRGINVVYTPPQSFQSAPRVYRVNGLSR 62
Query: 394 QPTRELVFPVDDNSTMKSVVEYFQEMYGFTIQHTHLPCLQVGNQKKANYLPMEACKIVEG 453
P F D ++ YF + ++ L CL VG+ K+ LP+E C I EG
Sbjct: 63 APASSETFEHDGKKV--TIASYFHSR-NYPLKFPQLHCLNVGSSIKSILLPIELCSIEEG 119
Query: 454 Q 454
Q
Sbjct: 120 Q 120
>pdb|2XDY|A Chain A, Crystal Structure Of The N. Crassa Qde-2 Ago Mid Domain
Length = 145
Score = 46.6 bits (109), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 625 ELLLAILPDNNGSLYGDLKRICETDLGIISQCCLTKHVFKISKQ--YLANVSLKINVKMG 682
+ ++ +LP + ++Y +KR + G+ + CC+ + Q Y ANV LK+N+K G
Sbjct: 80 QFVVVLLPRKDVAIYNMVKRAADITFGVHTVCCVAEKFLSTKGQLGYFANVGLKVNLKFG 139
Query: 683 GRN 685
G N
Sbjct: 140 GTN 142
>pdb|1XDK|B Chain B, Crystal Structure Of The RarbetaRXRALPHA LIGAND BINDING
Domain Heterodimer In Complex With 9-Cis Retinoic Acid
And A Fragment Of The Trap220 Coactivator
pdb|1XDK|F Chain F, Crystal Structure Of The RarbetaRXRALPHA LIGAND BINDING
Domain Heterodimer In Complex With 9-Cis Retinoic Acid
And A Fragment Of The Trap220 Coactivator
Length = 303
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 40/91 (43%), Gaps = 8/91 (8%)
Query: 71 KSDQNDVFMRPSSRPCTVAHKPVNQVCDLXXXXXXXXXXXXRSLCATEMGFPTSSKSLSF 130
++D+N PS + CT +++ ++ DL SLC ++G T++ S
Sbjct: 7 RNDRNKKKKEPSKQECTESYEMTAELDDLTEKIRKAHQETFPSLC--QLGKYTTNSSADH 64
Query: 131 APRPGYG------QVGTKCIVKANHFFAELP 155
R G ++ TKCI+K F LP
Sbjct: 65 RVRLDLGLWDKFSELATKCIIKIVEFAKRLP 95
>pdb|1EZS|A Chain A, Crystal Structure Of Ecotin Mutant M84r, W67a, G68a, Y69a,
D70a Bound To Rat Anionic Trypsin Ii
pdb|1EZS|B Chain B, Crystal Structure Of Ecotin Mutant M84r, W67a, G68a, Y69a,
D70a Bound To Rat Anionic Trypsin Ii
Length = 142
Score = 29.6 bits (65), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 20/41 (48%)
Query: 249 NMHHLGQFLAGKRADAPQEALQILDIVLRELSTKRYCPIGR 289
N+H LG L K + A + D V +ST+ CP G+
Sbjct: 51 NLHRLGGKLENKTLEGAAAAYYVFDKVSSPVSTRMACPDGK 91
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
0.319 0.134 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,921,740
Number of Sequences: 62578
Number of extensions: 929465
Number of successful extensions: 2032
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1978
Number of HSP's gapped (non-prelim): 24
length of query: 813
length of database: 14,973,337
effective HSP length: 107
effective length of query: 706
effective length of database: 8,277,491
effective search space: 5843908646
effective search space used: 5843908646
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)