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= 029808
(187 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2KK0|A Chain A, Solution Structure Of Dead Ringer-Like Protein 1 (At-Rich
Interactive Domain-Containing Protein 3a) From Homo
Sapiens, Northeast Structural Genomics Consortium (Nesg)
Target Hr4394c
Length = 145
Score = 65.9 bits (159), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 29/66 (43%), Positives = 43/66 (65%)
Query: 65 KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLS 124
++P + + LDL L+V VT +GGL +VI + W+E+ N PT+ITSA+F LR Y+
Sbjct: 55 RIPIMAKQVLDLFMLYVLVTEKGGLVEVINKKLWREITKGLNLPTSITSAAFTLRTQYMK 114
Query: 125 LLYHFE 130
LY +E
Sbjct: 115 YLYPYE 120
>pdb|1C20|A Chain A, Solution Structure Of The Dna-Binding Domain From The Dead
Ringer Protein
Length = 128
Score = 60.1 bits (144), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 42/66 (63%)
Query: 65 KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLS 124
++P + LDL+ L+ V +RGGL VI + W+E++ + P++ITSA+F LR Y+
Sbjct: 43 RLPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGLHLPSSITSAAFTLRTQYMK 102
Query: 125 LLYHFE 130
LY +E
Sbjct: 103 YLYPYE 108
>pdb|1KQQ|A Chain A, Solution Structure Of The Dead Ringer Arid-Dna Complex
Length = 139
Score = 57.8 bits (138), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 41/66 (62%)
Query: 65 KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLS 124
++P + LDL+ L+ V +RGGL VI + W+E++ + P++ITSA+ LR Y+
Sbjct: 45 RLPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGLHLPSSITSAALTLRTQYMK 104
Query: 125 LLYHFE 130
LY +E
Sbjct: 105 YLYPYE 110
>pdb|1RYU|A Chain A, Solution Structure Of The Swi1 Arid
Length = 120
Score = 53.9 bits (128), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 28/65 (43%), Positives = 42/65 (64%), Gaps = 1/65 (1%)
Query: 66 VPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSL 125
+P VG K LDL+RL+V V GGL +V ++++W+E+ N T +SA+ L+K Y+
Sbjct: 42 LPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKKWRELATNLNV-GTSSSAASSLKKQYIQC 100
Query: 126 LYHFE 130
LY FE
Sbjct: 101 LYAFE 105
>pdb|2CXY|A Chain A, Crystal Structure Of The Hbaf250b At-Rich Interaction
Domain (Arid)
pdb|2EH9|A Chain A, Crystal Structure Of The Hbaf250b At-Rich Interaction
Domain (Arid)
Length = 125
Score = 50.4 bits (119), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 66 VPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSL 125
+P VG K LDL RL+V V GGL +V ++++W+E+ N T +SA+ L+K Y+
Sbjct: 43 LPAVGKKPLDLFRLYVCVKEIGGLAQVNKNKKWRELATNLNV-GTSSSAASSLKKQYIQY 101
Query: 126 LYHFEQVYYFRKEAP 140
L+ FE +E P
Sbjct: 102 LFAFECKIERGEEPP 116
>pdb|2LM1|A Chain A, Solution Nmr Structure Of Lysine-Specific Demethylase Lid
From Drosophila Melanogaster, Northeast Structural
Genomics Consortium Target Fr824d
Length = 107
Score = 47.8 bits (112), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 42/82 (51%), Gaps = 1/82 (1%)
Query: 49 FWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFP 108
F + F + G K+P V KALDL+ L V GG+ + +DR+W +V +P
Sbjct: 19 FLDQIAKFWELQGSSLKIPMVERKALDLYTLHRIVQEEGGMEQTTKDRKWAKVANRMQYP 78
Query: 109 TTITSASFVLRKYYLSLLYHFE 130
++ S L+ +Y +L+ FE
Sbjct: 79 SS-KSVGATLKAHYERILHPFE 99
>pdb|2JRZ|A Chain A, Solution Structure Of The BrightARID DOMAIN FROM THE HUMAN
Jarid1c Protein
Length = 117
Score = 47.0 bits (110), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 56 FHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSAS 115
F + G K+P V + LDL+ L V GG + +DRRW V N+P S
Sbjct: 22 FWEIQGSSLKIPNVERRILDLYSLSKIVVEEGGYEAICKDRRWARVAQRLNYPPGKNIGS 81
Query: 116 FVLRKYYLSLLYHFE 130
LR +Y ++Y +E
Sbjct: 82 L-LRSHYERIVYPYE 95
>pdb|2YQE|A Chain A, Solution Structure Of The Arid Domain Of Jarid1d Protein
Length = 100
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 53 LEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTIT 112
+ F + G K+P V K LDL+ L V GG + +DRRW V ++P
Sbjct: 18 IAKFWEIQGSSLKIPNVERKILDLYSLSKIVIEEGGYEAICKDRRWARVAQRLHYPPGKN 77
Query: 113 SASFVLRKYYLSLLYHFE 130
S +LR +Y ++Y +E
Sbjct: 78 IGS-LLRSHYERIIYPYE 94
>pdb|2JXJ|A Chain A, Nmr Structure Of The Arid Domain From The Histone H3k4
Demethylase Rbp2
Length = 96
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 1/82 (1%)
Query: 49 FWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFP 108
F L F + G K+P V K LDL+ L V S+GG V ++++W +V +
Sbjct: 11 FLDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYL 70
Query: 109 TTITSASFVLRKYYLSLLYHFE 130
+ S +L+ +Y +LY +E
Sbjct: 71 PGKGTGS-LLKSHYERILYPYE 91
>pdb|2EQY|A Chain A, Solution Structure Of The Arid Domain Of Jarid1b Protein
Length = 122
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 1/66 (1%)
Query: 61 GDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRK 120
G K+P V K LDL +L V GG V +DR+W ++ F S + R
Sbjct: 29 GSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHI-RG 87
Query: 121 YYLSLL 126
+Y +L
Sbjct: 88 HYERIL 93
>pdb|2RQ5|A Chain A, Solution Structure Of The At-Rich Interaction Domain
(Arid) Of JumonjiJARID2
Length = 121
Score = 35.4 bits (80), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 32/68 (47%)
Query: 65 KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLS 124
++P +GG LDL F + GG+ +V ++W ++ + P T L++ Y
Sbjct: 33 ELPLIGGCELDLACFFRLINEMGGMQQVTDLKKWNKLADMLRIPKTAQDRLAKLQEAYCQ 92
Query: 125 LLYHFEQV 132
L ++ +
Sbjct: 93 YLLSYDSL 100
>pdb|1IG6|A Chain A, Human Mrf-2 Domain, Nmr, 11 Structures
pdb|2OEH|A Chain A, Determination Of The Three-Dimensional Structure Of The
Mrf2-Dna Complex Using Paramagnetic Spin Labeling
Length = 107
Score = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 32/67 (47%)
Query: 65 KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLS 124
++P +G K ++L +F GG + R+WK + TSA+ R++Y
Sbjct: 24 RIPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYDELGGNPGSTSAATCTRRHYER 83
Query: 125 LLYHFEQ 131
L+ +E+
Sbjct: 84 LILPYER 90
>pdb|2LI6|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Yeast
Protein
Length = 116
Score = 31.6 bits (70), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 8/65 (12%)
Query: 45 SSDLFWATLEAFHKSFGDKFK--------VPTVGGKALDLHRLFVEVTSRGGLGKVIRDR 96
S++L E F KS + K +P +G + ++L L++ V GG +V R +
Sbjct: 12 STELNNKQYELFMKSLIENCKKRNMPLQSIPEIGNRKINLFYLYMLVQKFGGADQVTRTQ 71
Query: 97 RWKEV 101
+W V
Sbjct: 72 QWSMV 76
>pdb|1KKX|A Chain A, Solution Structure Of The Dna-Binding Domain Of Adr6
pdb|1KN5|A Chain A, Solution Structure Of Arid Domain Of Adr6 From
Saccharomyces Cerevisiae
Length = 123
Score = 30.4 bits (67), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 8/56 (14%)
Query: 54 EAFHKSFGDKFK--------VPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEV 101
E F KS + K +P +G + ++L L++ V GG +V R ++W V
Sbjct: 20 ELFMKSLIENCKKRNMPLQSIPEIGNRKINLFYLYMLVQKFGGADQVTRTQQWSMV 75
>pdb|3E0R|A Chain A, Crystal Structure Of Cppa Protein From Streptococcus
Pneumoniae Tigr4
pdb|3E0R|B Chain B, Crystal Structure Of Cppa Protein From Streptococcus
Pneumoniae Tigr4
pdb|3E0R|C Chain C, Crystal Structure Of Cppa Protein From Streptococcus
Pneumoniae Tigr4
pdb|3E0R|D Chain D, Crystal Structure Of Cppa Protein From Streptococcus
Pneumoniae Tigr4
Length = 244
Score = 26.9 bits (58), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 24/42 (57%)
Query: 52 TLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVI 93
TL+A ++ + F + T+G KAL F+ + + GL K++
Sbjct: 15 TLKANNRKLNETFYIETLGXKALLEESAFLSLGDQTGLEKLV 56
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 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,238,157
Number of Sequences: 62578
Number of extensions: 193551
Number of successful extensions: 298
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 281
Number of HSP's gapped (non-prelim): 17
length of query: 187
length of database: 14,973,337
effective HSP length: 93
effective length of query: 94
effective length of database: 9,153,583
effective search space: 860436802
effective search space used: 860436802
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: 48 (23.1 bits)