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= psy405
(66 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 = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/55 (45%), Positives = 33/55 (60%), Gaps = 3/55 (5%)
Query: 8 DGDAYFKEKESFLRDLQHFHETRGTPCRHVPKIGGKEIDLYLLYCLVTSNGGWVK 62
DGD KE FL DL F + RGTP +P + + +DL++LY LVT GG V+
Sbjct: 30 DGDPKRKE---FLDDLFSFMQKRGTPVNRIPIMAKQVLDLFMLYVLVTEKGGLVE 81
>pdb|1C20|A Chain A, Solution Structure Of The Dna-Binding Domain From The
Dead Ringer Protein
Length = 128
Score = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 28/47 (59%)
Query: 15 EKESFLRDLQHFHETRGTPCRHVPKIGGKEIDLYLLYCLVTSNGGWV 61
+++ FL DL F + RGTP +P + +DLY LY LV + GG V
Sbjct: 22 KRKEFLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNLVIARGGLV 68
>pdb|1KQQ|A Chain A, Solution Structure Of The Dead Ringer Arid-Dna Complex
Length = 139
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 28/47 (59%)
Query: 15 EKESFLRDLQHFHETRGTPCRHVPKIGGKEIDLYLLYCLVTSNGGWV 61
+++ FL DL F + RGTP +P + +DLY LY LV + GG V
Sbjct: 24 KRKEFLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNLVIARGGLV 70
>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 = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 26 FHETRGTPCRHVPKIGGKEIDLYLLYCLVTSNGG 59
F E RG+P +P +G K +DL+ LY V GG
Sbjct: 32 FXEERGSPVSSLPAVGKKPLDLFRLYVCVKEIGG 65
>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 = 32.3 bits (72), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 27/46 (58%)
Query: 15 EKESFLRDLQHFHETRGTPCRHVPKIGGKEIDLYLLYCLVTSNGGW 60
++++FL L + + R TP +P +G K+I+L+ ++ GG+
Sbjct: 3 DEQAFLVALYKYMKERKTPIERIPYLGFKQINLWTMFQAAQKLGGY 48
>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 = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 10 DAYFKEKESFLRDLQHFHETRGTPCRHVPKIGGKEIDLYLLYCLVTSNGG 59
+A + K +FL + F E +G+ + +P + K +DLY L+ +V GG
Sbjct: 10 EAKTRVKLNFLDQIAKFWELQGSSLK-IPMVERKALDLYTLHRIVQEEGG 58
>pdb|2EQY|A Chain A, Solution Structure Of The Arid Domain Of Jarid1b Protein
Length = 122
Score = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 9 GDAYFKEKESFLRDLQHFHETRGTPCRHVPKIGGKEIDLYLLYCLVTSNGGWVKKC 64
G+A + K +FL + + E +G+ + +P + K +DL+ L LV GG+ C
Sbjct: 7 GEAQTRVKLNFLDQIAKYWELQGSTLK-IPHVERKILDLFQLNKLVAEEGGFAVVC 61
>pdb|2JXJ|A Chain A, Nmr Structure Of The Arid Domain From The Histone H3k4
Demethylase Rbp2
Length = 96
Score = 29.3 bits (64), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 19 FLRDLQHFHETRGTPCRHVPKIGGKEIDLYLLYCLVTSNGGW 60
FL L F E +G+ + +P + K +DLY L +V S GG+
Sbjct: 11 FLDQLAKFWELQGSTLK-IPVVERKILDLYALSKIVASKGGF 51
>pdb|2YQE|A Chain A, Solution Structure Of The Arid Domain Of Jarid1d Protein
Length = 100
Score = 28.9 bits (63), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 8 DGDAYFKEKESFLRDLQHFHETRGTPCRHVPKIGGKEIDLYLLYCLVTSNGGWVKKC 64
G + + K ++L + F E +G+ + +P + K +DLY L +V GG+ C
Sbjct: 3 SGSSGTRVKLNYLDQIAKFWEIQGSSLK-IPNVERKILDLYSLSKIVIEEGGYEAIC 58
>pdb|2JRZ|A Chain A, Solution Structure Of The BrightARID DOMAIN FROM THE
HUMAN Jarid1c Protein
Length = 117
Score = 28.5 bits (62), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 10 DAYFKEKESFLRDLQHFHETRGTPCRHVPKIGGKEIDLYLLYCLVTSNGGWVKKC 64
+A + K ++L + F E +G+ + +P + + +DLY L +V GG+ C
Sbjct: 6 EAQTRVKLNYLDQIAKFWEIQGSSLK-IPNVERRILDLYSLSKIVVEEGGYEAIC 59
>pdb|3TOQ|A Chain A, Acylphosphatase With Mesophilic Surface And Thermophilic
Core
Length = 99
Score = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 18 SFLRDLQHFHETRGTPCRHVPK 39
S +R LQ + ETRG+P H+ K
Sbjct: 57 SKVRHLQEWAETRGSPKSHIDK 78
>pdb|3SPH|A Chain A, Inward Rectifier Potassium Channel Kir2.2 I223l Mutant In
Complex With Pip2
pdb|3SPJ|A Chain A, Apo Inward Rectifier Potassium Channel Kir2.2 I223l Mutant
Length = 343
Score = 26.2 bits (56), Expect = 5.1, Method: Composition-based stats.
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 13 FKEKESFLRDLQHFHETRGTPCRHVPKIGGKEI 45
F+EK + D HFH+T P P+ K++
Sbjct: 297 FEEKNQYKVDYSHFHKTYEVP--STPRCSAKDL 327
>pdb|3SPG|A Chain A, Inward Rectifier Potassium Channel Kir2.2 R186a Mutant In
Complex With Pip2
Length = 343
Score = 26.2 bits (56), Expect = 5.1, Method: Composition-based stats.
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 13 FKEKESFLRDLQHFHETRGTPCRHVPKIGGKEI 45
F+EK + D HFH+T P P+ K++
Sbjct: 297 FEEKNQYKVDYSHFHKTYEVP--STPRCSAKDL 327
>pdb|3JYC|A Chain A, Crystal Structure Of The Eukaryotic Strong
Inward-Rectifier K+ Channel Kir2.2 At 3.1 Angstrom
Resolution
pdb|3SPC|A Chain A, Inward Rectifier Potassium Channel Kir2.2 In Complex With
Dioctanoylglycerol Pyrophosphate (Dgpp)
pdb|3SPI|A Chain A, Inward Rectifier Potassium Channel Kir2.2 In Complex With
Pip2
Length = 343
Score = 26.2 bits (56), Expect = 5.1, Method: Composition-based stats.
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 13 FKEKESFLRDLQHFHETRGTPCRHVPKIGGKEI 45
F+EK + D HFH+T P P+ K++
Sbjct: 297 FEEKNQYKVDYSHFHKTYEVP--STPRCSAKDL 327
>pdb|1DEQ|C Chain C, The Crystal Structure Of Modified Bovine Fibrinogen (At ~4
Angstrom Resolution)
pdb|1DEQ|F Chain F, The Crystal Structure Of Modified Bovine Fibrinogen (At ~4
Angstrom Resolution)
pdb|1DEQ|P Chain P, The Crystal Structure Of Modified Bovine Fibrinogen (At ~4
Angstrom Resolution)
pdb|1DEQ|S Chain S, The Crystal Structure Of Modified Bovine Fibrinogen (At ~4
Angstrom Resolution)
Length = 411
Score = 25.8 bits (55), Expect = 6.5, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 22/52 (42%), Gaps = 12/52 (23%)
Query: 21 RDLQHFHETRGTPCRHVPKIGGKEIDLY-----------LLYCLVTSNG-GW 60
+D H+ G C+ V G KE LY L+YC + +G GW
Sbjct: 140 QDTVKIHDVTGRDCQDVANKGAKESGLYFIRPLKAKQQFLVYCEIDGSGNGW 191
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
0.321 0.139 0.447
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,236,185
Number of Sequences: 62578
Number of extensions: 76726
Number of successful extensions: 157
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 151
Number of HSP's gapped (non-prelim): 25
length of query: 66
length of database: 14,973,337
effective HSP length: 37
effective length of query: 29
effective length of database: 12,657,951
effective search space: 367080579
effective search space used: 367080579
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: 45 (21.9 bits)