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= 036169
(619 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 = 142 bits (357), Expect = 7e-34, Method: Compositional matrix adjust.
Identities = 154/666 (23%), Positives = 265/666 (39%), Gaps = 118/666 (17%)
Query: 3 GSKGEITSLLSNHFKVSITGASGHIFHYS----------GIRRKIIDKVCETNSADL-AE 51
G+ G L +N F++ I I+HY + R+I++ + + + +
Sbjct: 34 GTSGRTIKLQANFFEMDIPKID--IYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGD 91
Query: 52 KDIAYDGEKSLFTIGALPHKKNGVPDLSQTTSNDSPDGHGSNNERDKKRRRVSQSKTFKV 111
+ +DG K+L+T LP ++ V +L T + D + FKV
Sbjct: 92 RKPVFDGRKNLYTAMPLPIGRDKV-ELEVTLPGEGKD------------------RIFKV 132
Query: 112 EISFXXXXXXXXXXXXXHGQESQNSREAFRVLDIILRQHAAKQMN-LGVSLTLEVVFLDL 170
I + G+ E + LD+++R + + +G S
Sbjct: 133 SIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTA----SE 188
Query: 171 GC-----------WGFHSSFQATQGGLSLNIDGSTTSIIKPGPLVDFL--------IANQ 211
GC +GFH S + + + LNID S T+ K P+++F+ I Q
Sbjct: 189 GCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQ 248
Query: 212 N--VHDCYQLHWAKAKRTLKNLRIRVHPFNREYRITGLSDSTCKRQMFSWKSGVKDRNGD 269
+ D ++ + K + LK R+YR+ ++ Q F ++ +G
Sbjct: 249 QKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFP----LQQESG- 303
Query: 270 VKCVDVTVFDYFVNHGRINLCFSGDFPCIDVGKPRKPTYIPIEPCSLLSLQRYTKALTVF 329
+ V+ TV YF + ++ L + PC+ VG+ +K TY+P+E C++++ QR K LT
Sbjct: 304 -QTVECTVAQYFKDRHKLVLRYP-HLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDN 361
Query: 330 QRSALVEKSQQKPQEKMKIITDVMRSNKYDSEPMLRSCAISINSRFAKVEGRILSAPRGA 389
Q S ++ + + ++ + I+ +MRS ++++P +R I + V GR+L P
Sbjct: 362 QTSTMIRATARSAPDRQEEISKLMRSASFNTDPYVREFGIMVKDEMTDVTGRVLQPPSIL 421
Query: 390 Y--------HPKNGRWSFHNKIFVQAAKIDHWAVVNFSAR-----YDIRSLCRDLIRFGE 436
Y P G W NK F +I WA+ F+ + ++S L +
Sbjct: 422 YGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISR 481
Query: 437 MKGIVTPVRADRMFVQMKQKFEKC-PCF------------LLCLLPDKKDSDLYGSWKRK 483
G+ P++ F + Q + P F ++ +LP K + +Y KR
Sbjct: 482 DAGM--PIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGK--TPVYAEVKRV 537
Query: 484 TLSEFGIFNQCLAPTKVNE---HDLMNVLLKINANCQRELTDPXXXXXXXXXXXAIEQSK 540
+ G+ QC+ V L N+ LKIN I +
Sbjct: 538 GDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKL--------------GGVNNILLPQ 583
Query: 541 NLPLVSKVPTIIFGMDVSHGSPGHSNVPSV-ATVGCNSFSRNWPILSRYRASVRSQSAKL 599
P V + P I G DV+H G PS+ A VG N RY A+VR Q +
Sbjct: 584 GRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPN-----RYCATVRVQQHRQ 638
Query: 600 EMTDSL 605
E+ L
Sbjct: 639 EIIQDL 644
>pdb|4EI1|A Chain A, Crystal Structure Of Human Argonaute2
pdb|4EI3|A Chain A, Crystal Structure Of Human Argonaute2
Length = 859
Score = 141 bits (356), Expect = 8e-34, Method: Compositional matrix adjust.
Identities = 154/666 (23%), Positives = 265/666 (39%), Gaps = 118/666 (17%)
Query: 3 GSKGEITSLLSNHFKVSITGASGHIFHYS----------GIRRKIIDKVCETNSADL-AE 51
G+ G L +N F++ I I+HY + R+I++ + + + +
Sbjct: 32 GTSGRTIKLQANFFEMDIPKID--IYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGD 89
Query: 52 KDIAYDGEKSLFTIGALPHKKNGVPDLSQTTSNDSPDGHGSNNERDKKRRRVSQSKTFKV 111
+ +DG K+L+T LP ++ V +L T + D + FKV
Sbjct: 90 RKPVFDGRKNLYTAMPLPIGRDKV-ELEVTLPGEGKD------------------RIFKV 130
Query: 112 EISFXXXXXXXXXXXXXHGQESQNSREAFRVLDIILRQHAAKQMN-LGVSLTLEVVFLDL 170
I + G+ E + LD+++R + + +G S
Sbjct: 131 SIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTA----SE 186
Query: 171 GC-----------WGFHSSFQATQGGLSLNIDGSTTSIIKPGPLVDFL--------IANQ 211
GC +GFH S + + + LNID S T+ K P+++F+ I Q
Sbjct: 187 GCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQ 246
Query: 212 N--VHDCYQLHWAKAKRTLKNLRIRVHPFNREYRITGLSDSTCKRQMFSWKSGVKDRNGD 269
+ D ++ + K + LK R+YR+ ++ Q F ++ +G
Sbjct: 247 QKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFP----LQQESG- 301
Query: 270 VKCVDVTVFDYFVNHGRINLCFSGDFPCIDVGKPRKPTYIPIEPCSLLSLQRYTKALTVF 329
+ V+ TV YF + ++ L + PC+ VG+ +K TY+P+E C++++ QR K LT
Sbjct: 302 -QTVECTVAQYFKDRHKLVLRYP-HLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDN 359
Query: 330 QRSALVEKSQQKPQEKMKIITDVMRSNKYDSEPMLRSCAISINSRFAKVEGRILSAPRGA 389
Q S ++ + + ++ + I+ +MRS ++++P +R I + V GR+L P
Sbjct: 360 QTSTMIRATARSAPDRQEEISKLMRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSIL 419
Query: 390 Y--------HPKNGRWSFHNKIFVQAAKIDHWAVVNFSAR-----YDIRSLCRDLIRFGE 436
Y P G W NK F +I WA+ F+ + ++S L +
Sbjct: 420 YGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISR 479
Query: 437 MKGIVTPVRADRMFVQMKQKFEKC-PCF------------LLCLLPDKKDSDLYGSWKRK 483
G+ P++ F + Q + P F ++ +LP K + +Y KR
Sbjct: 480 DAGM--PIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGK--TPVYAEVKRV 535
Query: 484 TLSEFGIFNQCLAPTKVNE---HDLMNVLLKINANCQRELTDPXXXXXXXXXXXAIEQSK 540
+ G+ QC+ V L N+ LKIN I +
Sbjct: 536 GDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKL--------------GGVNNILLPQ 581
Query: 541 NLPLVSKVPTIIFGMDVSHGSPGHSNVPSV-ATVGCNSFSRNWPILSRYRASVRSQSAKL 599
P V + P I G DV+H G PS+ A VG N RY A+VR Q +
Sbjct: 582 GRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPN-----RYCATVRVQQHRQ 636
Query: 600 EMTDSL 605
E+ L
Sbjct: 637 EIIQDL 642
>pdb|1R4K|A Chain A, Solution Structure Of The Drosophila Argonaute 1 Paz
Domain
Length = 169
Score = 62.8 bits (151), Expect = 5e-10, Method: Composition-based stats.
Identities = 42/175 (24%), Positives = 88/175 (50%), Gaps = 17/175 (9%)
Query: 195 TSIIKPGPLVDFLIANQNVHDCYQL-------HWAKAKRTLKNLRIRVH---PFNREYRI 244
T+ K P++DF+ ++ D + K + +K L+I + R+YR+
Sbjct: 2 TAFYKAQPVIDFMCEVLDIRDINEQRKPLTDSQRVKFTKEIKGLKIEITHCGQMRRKYRV 61
Query: 245 TGLSDSTCKRQMFSWKSGVKDRNGDVKCVDVTVFDYFVNHGRINLCFSGDFPCIDVGKPR 304
++ + Q F ++ NG + V+ TV YF++ R+ L + PC+ VG+
Sbjct: 62 CNVTRRPAQMQSFP----LQLENG--QTVECTVAKYFLDKYRMKLRYP-HLPCLQVGQEH 114
Query: 305 KPTYIPIEPCSLLSLQRYTKALTVFQRSALVEKSQQKPQEKMKIITDVMRSNKYD 359
K TY+P+E C++++ QR K LT Q S +++ + + ++ + I ++++ ++
Sbjct: 115 KHTYLPLEVCNIVAGQRCIKKLTDMQTSTMIKATARSAPDREREINNLVKRADFN 169
>pdb|3VNB|A Chain A, Structural Insights Into Small Rna Sorting And Mrna
Binding By Arabidopsis Ago Domains
Length = 155
Score = 56.6 bits (135), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 39/138 (28%), Positives = 67/138 (48%), Gaps = 24/138 (17%)
Query: 401 NKIFVQAAKIDHWAVVNFSARYD---IRSLCRDLIRFGEMKG-------IVTPV--RADR 448
NK + +++W +NFS + R+ C++L + + G ++ PV R ++
Sbjct: 2 NKKMINGGTVNNWICINFSRQVQDNLARTFCQELAQMCYVSGMAFNPEPVLPPVSARPEQ 61
Query: 449 MFVQMKQKFEKCPC---------FLLCLLPDKKDSDLYGSWKRKTLSEFGIFNQCLAPT- 498
+ +K ++ L+ +LPDKK+SDLYG KR +E GI +QC
Sbjct: 62 VEKVLKTRYHDATSKLSQGKEIDLLIVILPDKKNSDLYGDLKRICETELGIVSQCCLTKH 121
Query: 499 --KVNEHDLMNVLLKINA 514
K+++ + NV LKIN
Sbjct: 122 VFKMSKQYMANVALKINV 139
>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 = 48.9 bits (115), Expect = 8e-06, Method: Composition-based stats.
Identities = 33/120 (27%), Positives = 60/120 (50%), Gaps = 14/120 (11%)
Query: 226 RTLKNLRIRVH---PFNREYRITGLSDSTCKRQMF--SWKSGVKDRNGDVKCVDVTVFDY 280
+ +K L++ V R+YR+ ++ Q F +SG + V+ TV Y
Sbjct: 38 KEIKGLKVEVTHCGQMKRKYRVCNVTRRPASHQTFPLQLESG--------QTVECTVAQY 89
Query: 281 FVNHGRINLCFSGDFPCIDVGKPRKPTYIPIEPCSLLSLQRYTKALTVFQRSALVEKSQQ 340
F + L + PC+ VG+ +K TY+P+E C++++ QR K LT Q S +++ + +
Sbjct: 90 FKQKYNLQLKYP-HLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIKATAR 148
>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 = 48.9 bits (115), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 39/132 (29%), Positives = 57/132 (43%), Gaps = 21/132 (15%)
Query: 401 NKIFVQAAKIDHWAVVNFSARYD---IRSLCRDLIRFGEMKGI------------VTPVR 445
+K V AK+ W V+FS R D + C+ LI KG+ P
Sbjct: 2 DKKMVNGAKVTSWTCVSFSTRIDRGLPQEFCKQLIGMCVSKGMEFKPQPAIPFISCPPEH 61
Query: 446 ADRMFVQMKQKFEKCPCFLLCLLPDKKDSDLYGSWKRKTLSEFGIFNQCLAP---TKVNE 502
+ + + ++ L+ +LPD S YG KR +E GI +QC P K+N+
Sbjct: 62 IEEALLDIHKRAPGLQ-LLIVILPDVTGS--YGKIKRICETELGIVSQCCQPRQVNKLNK 118
Query: 503 HDLMNVLLKINA 514
+ NV LKIN
Sbjct: 119 QYMENVALKINV 130
>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 = 46.6 bits (109), Expect = 4e-05, Method: Composition-based stats.
Identities = 33/120 (27%), Positives = 59/120 (49%), Gaps = 14/120 (11%)
Query: 226 RTLKNLRIRVH---PFNREYRITGLSDSTCKRQMF--SWKSGVKDRNGDVKCVDVTVFDY 280
+ +K L++ V R+YR+ ++ Q F +SG + V+ TV Y
Sbjct: 38 KEIKGLKVEVTHCGQXKRKYRVCNVTRRPASHQTFPLQLESG--------QTVECTVAQY 89
Query: 281 FVNHGRINLCFSGDFPCIDVGKPRKPTYIPIEPCSLLSLQRYTKALTVFQRSALVEKSQQ 340
F + L + PC+ VG+ +K TY+P+E C++++ QR K LT Q S ++ + +
Sbjct: 90 FKQKYNLQLKYP-HLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTXIKATAR 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 = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 36/138 (26%), Positives = 63/138 (45%), Gaps = 25/138 (18%)
Query: 401 NKIFVQAAKIDHWAVVNFSARYD---IRSLCRDLIRFGEMKG-------IVTPV--RADR 448
NK + +++W +NFS + R+ C++L + + G ++ PV R ++
Sbjct: 2 NKKMINGGTVNNWICINFSRQVQDNLARTFCQELAQMCYVSGMAFNPEPVLPPVSARPEQ 61
Query: 449 MFVQMKQKFEKCPC---------FLLCLLPDKKDSDLYGSWKRKTLSEFGIFNQCLAPT- 498
+ +K ++ L+ +LPD S LYG KR +E GI +QC
Sbjct: 62 VEKVLKTRYHDATSKLSQGKEIDLLIVILPDNNGS-LYGDLKRICETELGIVSQCCLTKH 120
Query: 499 --KVNEHDLMNVLLKINA 514
K+++ + NV LKIN
Sbjct: 121 VFKMSKQYMANVALKINV 138
>pdb|3VNA|A Chain A, Structural Insights Into Small Rna Sorting And Mrna
Binding By Arabidopsis Ago Mid Domains
Length = 154
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 36/138 (26%), Positives = 63/138 (45%), Gaps = 25/138 (18%)
Query: 401 NKIFVQAAKIDHWAVVNFSARYD---IRSLCRDLIRFGEMKG-------IVTPV--RADR 448
NK + +++W +NFS + R+ C++L + + G ++ PV R ++
Sbjct: 2 NKKMINGGTVNNWICINFSRQVQDNLARTFCQELAQMCYVSGMAFNPEPVLPPVSARPEQ 61
Query: 449 MFVQMKQKFEKCPC---------FLLCLLPDKKDSDLYGSWKRKTLSEFGIFNQCLAPT- 498
+ +K ++ L+ +LPD S LYG KR +E GI +QC
Sbjct: 62 VEKVLKTRYHDATSKLSQGKEIDLLIVILPDNNGS-LYGDLKRICETELGIVSQCCLTKH 120
Query: 499 --KVNEHDLMNVLLKINA 514
K+++ + NV LKIN
Sbjct: 121 VFKMSKQYMANVALKINV 138
>pdb|4G0X|A Chain A, Crystal Structure Of Arabidopsis Thaliana Ago1 Mid Domain
Length = 147
Score = 42.4 bits (98), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 36/138 (26%), Positives = 61/138 (44%), Gaps = 25/138 (18%)
Query: 401 NKIFVQAAKIDHWAVVNFSARYD---IRSLCRDLIRFGEMKG-------IVTPV--RADR 448
NK + +++W +NFS + R+ C++L + + G ++ PV R ++
Sbjct: 2 NKKXINGGTVNNWICINFSRQVQDNLARTFCQELAQXCYVSGXAFNPEPVLPPVSARPEQ 61
Query: 449 MFVQMKQKFEKCPC---------FLLCLLPDKKDSDLYGSWKRKTLSEFGIFNQCLAPT- 498
+ +K ++ L+ +LPD S LYG KR +E GI +QC
Sbjct: 62 VEKVLKTRYHDATSKLSQGKEIDLLIVILPDNNGS-LYGDLKRICETELGIVSQCCLTKH 120
Query: 499 --KVNEHDLMNVLLKINA 514
K ++ NV LKIN
Sbjct: 121 VFKXSKQYXANVALKINV 138
>pdb|2YHB|A Chain A, Crystal Structure Of The N. Crassa Qde-2 Ago Mid-Piwi
Domains
Length = 437
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 38/156 (24%), Positives = 58/156 (37%), Gaps = 31/156 (19%)
Query: 433 RFGEMKGIVTPVRADRMFVQMKQKFEKCPCFLLCLLPDKKDSDLYGSWKRKTLSEFGIFN 492
RF + P F ++K+ F++ LLP +KD +Y KR FG+
Sbjct: 52 RFSPGMSMSVPGSEKEFFAKVKELMSSHQ-FVVVLLP-RKDVAIYNMVKRAADITFGVHT 109
Query: 493 QC-----LAPTKVNEHDLMNVLLKIN---ANCQRELTDPXXXXXXXXXXXAIEQSKNLPL 544
C TK NV LK+N + P +PL
Sbjct: 110 VCCVAEKFLSTKGQLGYFANVGLKVNLKFGGTNHNIKTP------------------IPL 151
Query: 545 VSKVPTIIFGMDVSHGS---PGHSNVPSVATVGCNS 577
++K T++ G DV+H + G S + + VG S
Sbjct: 152 LAKGKTMVVGYDVTHPTNLAAGQSPASAPSIVGLVS 187
>pdb|2YHA|A Chain A, Crystal Structure Of The N. Crassa Qde-2 Ago Mid-Piwi
Domains
Length = 388
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 33/135 (24%), Positives = 50/135 (37%), Gaps = 28/135 (20%)
Query: 433 RFGEMKGIVTPVRADRMFVQMKQKFEKCPCFLLCLLPDKKDSDLYGSWKRKTLSEFGIFN 492
RF + P F ++K+ F++ LLP +KD +Y KR FG+
Sbjct: 52 RFSPGMSMSVPGSEKEFFAKVKELMSSHQ-FVVVLLP-RKDVAIYNMVKRAADITFGVHT 109
Query: 493 QC-----LAPTKVNEHDLMNVLLKIN---ANCQRELTDPXXXXXXXXXXXAIEQSKNLPL 544
C TK NV LK+N + P +PL
Sbjct: 110 VCCVAEKFLSTKGQLGYFANVGLKVNLKFGGTNHNIKTP------------------IPL 151
Query: 545 VSKVPTIIFGMDVSH 559
++K T++ G DV+H
Sbjct: 152 LAKGKTMVVGYDVTH 166
>pdb|1VYN|A Chain A, Structure And Nucleic Acid Binding Of The Drosophila
Argonaute2 Paz Domain
Length = 143
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 36/80 (45%), Gaps = 19/80 (23%)
Query: 240 REYRITGLSDSTCKRQMFSWKSGVKDRNGDVKCVDVTVFDYFVNHGRINLCFSGDFP--- 296
R YR+ GLS + + F + +G VT+ YF H R + FP
Sbjct: 55 RVYRVNGLSRAPASSETF-------EHDGK----KVTIASYF--HSR---NYPLKFPQLH 98
Query: 297 CIDVGKPRKPTYIPIEPCSL 316
C++VG K +PIE CS+
Sbjct: 99 CLNVGSSIKSILLPIELCSI 118
>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 = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 36/80 (45%), Gaps = 19/80 (23%)
Query: 240 REYRITGLSDSTCKRQMFSWKSGVKDRNGDVKCVDVTVFDYFVNHGRINLCFSGDFP--- 296
R YR+ GLS + + F + +G VT+ YF H R + FP
Sbjct: 435 RVYRVNGLSRAPASSETF-------EHDGK----KVTIASYF--HSR---NYPLKFPQLH 478
Query: 297 CIDVGKPRKPTYIPIEPCSL 316
C++VG K +PIE CS+
Sbjct: 479 CLNVGSSIKSILLPIELCSI 498
>pdb|3MJ0|A Chain A, Crystal Structure Of Drosophia Ago-Paz Domain In Complex
With 3'-End 2'-O-Methylated Rna
Length = 124
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 36/80 (45%), Gaps = 19/80 (23%)
Query: 240 REYRITGLSDSTCKRQMFSWKSGVKDRNGDVKCVDVTVFDYFVNHGRINLCFSGDFP--- 296
R YR+ GLS + + F + +G VT+ YF H R + FP
Sbjct: 53 RVYRVNGLSRAPASSETF-------EHDGK----KVTIASYF--HSR---NYPLKFPQLH 96
Query: 297 CIDVGKPRKPTYIPIEPCSL 316
C++VG K +PIE CS+
Sbjct: 97 CLNVGSSIKSILLPIELCSI 116
>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 = 30.8 bits (68), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 36/80 (45%), Gaps = 19/80 (23%)
Query: 240 REYRITGLSDSTCKRQMFSWKSGVKDRNGDVKCVDVTVFDYFVNHGRINLCFSGDFP--- 296
R YR+ GLS + + F + +G VT+ YF H R + FP
Sbjct: 55 RVYRVNGLSRAPASSETF-------EHDGK----KVTIASYF--HSR---NYPLKFPQLH 98
Query: 297 CIDVGKPRKPTYIPIEPCSL 316
C++VG K +PIE CS+
Sbjct: 99 CLNVGSSIKSILLPIELCSI 118
>pdb|1X6I|A Chain A, Crystal Structure Of Ygfy From Escherichia Coli
pdb|1X6I|B Chain B, Crystal Structure Of Ygfy From Escherichia Coli
pdb|1X6J|A Chain A, Crystal Structure Of Ygfy From Escherichia Coli
Length = 91
Score = 30.4 bits (67), Expect = 3.4, Method: Composition-based stats.
Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 13/78 (16%)
Query: 209 ANQNVHDCYQLHWAKAKRTLKNLRIRVHPFNREYRITGLSDSTCKRQMFSWKSGVKDRNG 268
++ ++++ ++HWA +R ++ L I + PF E+ LSD KR
Sbjct: 2 SHMDINNKARIHWA-CRRGMRELDISIMPF-FEHEYDSLSDDE-KRIFIRL--------- 49
Query: 269 DVKCVDVTVFDYFVNHGR 286
++C D +F++ +NHG+
Sbjct: 50 -LECDDPDLFNWLMNHGK 66
>pdb|3DZD|A Chain A, Crystal Structure Of Sigma54 Activator Ntrc4 In The
Inactive State
pdb|3DZD|B Chain B, Crystal Structure Of Sigma54 Activator Ntrc4 In The
Inactive State
Length = 368
Score = 30.0 bits (66), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 34/73 (46%), Gaps = 10/73 (13%)
Query: 18 VSITGASGH--------IFHYSGIRRKIIDKVCETNSADLAEKDIAYDGEKSLFTIGALP 69
V ITG SG I YSG + +D C + +LAE ++ + EK FT GAL
Sbjct: 155 VLITGESGTGKEIVARLIHRYSGRKGAFVDLNCASIPQELAESEL-FGHEKGAFT-GALT 212
Query: 70 HKKNGVPDLSQTT 82
KK + Q T
Sbjct: 213 RKKGKLELADQGT 225
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
0.320 0.135 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,182,706
Number of Sequences: 62578
Number of extensions: 675213
Number of successful extensions: 1261
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1244
Number of HSP's gapped (non-prelim): 19
length of query: 619
length of database: 14,973,337
effective HSP length: 105
effective length of query: 514
effective length of database: 8,402,647
effective search space: 4318960558
effective search space used: 4318960558
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: 54 (25.4 bits)