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= 007176
(614 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JXJ|A Chain A, Nmr Structure Of The Arid Domain From The Histone H3k4
Demethylase Rbp2
Length = 96
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 31/97 (31%), Positives = 47/97 (48%), Gaps = 14/97 (14%)
Query: 442 EFLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGGFHVGNGINW 501
+FL + +F L+G T +P ++ K LDL+ L + V S+GGF +
Sbjct: 10 DFLDQLAKFWELQGSTLKIP----------VVERKILDLYALSKIVASKGGFEMVT---- 55
Query: 502 KGQVFSKMRNHTLTNRMTGVGNTLKRHYETYLLEYEL 538
K + +SK+ + G G+ LK HYE L YEL
Sbjct: 56 KEKKWSKVGSRLGYLPGKGTGSLLKSHYERILYPYEL 92
>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 = 37.7 bits (86), Expect = 0.017, Method: Composition-based stats.
Identities = 28/96 (29%), Positives = 43/96 (44%), Gaps = 14/96 (14%)
Query: 443 FLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGGFHVGNGINWK 502
FL + +F L+G + +P ++ K LDL+ L+R V GG K
Sbjct: 19 FLDQIAKFWELQGSSLKIP----------MVERKALDLYTLHRIVQEEGGMEQTT----K 64
Query: 503 GQVFSKMRNHTLTNRMTGVGNTLKRHYETYLLEYEL 538
+ ++K+ N VG TLK HYE L +E+
Sbjct: 65 DRKWAKVANRMQYPSSKSVGATLKAHYERILHPFEV 100
>pdb|1C20|A Chain A, Solution Structure Of The Dna-Binding Domain From The Dead
Ringer Protein
Length = 128
Score = 37.7 bits (86), Expect = 0.018, Method: Composition-based stats.
Identities = 35/126 (27%), Positives = 52/126 (41%), Gaps = 28/126 (22%)
Query: 413 QAQQIISLNPLPLKKHGCGRAPIQVCSEEEFLRDVMQFLILRGHTRLVPQGGLAEFPDAI 472
Q +Q+ +N P +K EFL D+ F+ RG + P I
Sbjct: 10 QVRQLYEINDDPKRK--------------EFLDDLFSFMQKRGTP-------INRLP--I 46
Query: 473 LNAKRLDLFNLYREVVSRGGF-HVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLKRHYET 531
+ LDL+ LY V++RGG V N W+ ++ L + +T TL+ Y
Sbjct: 47 MAKSVLDLYELYNLVIARGGLVDVINKKLWQ----EIIKGLHLPSSITSAAFTLRTQYMK 102
Query: 532 YLLEYE 537
YL YE
Sbjct: 103 YLYPYE 108
>pdb|1KQQ|A Chain A, Solution Structure Of The Dead Ringer Arid-Dna Complex
Length = 139
Score = 35.8 bits (81), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 36/126 (28%), Positives = 52/126 (41%), Gaps = 28/126 (22%)
Query: 413 QAQQIISLNPLPLKKHGCGRAPIQVCSEEEFLRDVMQFLILRGHTRLVPQGGLAEFPDAI 472
Q +Q+ +N P +K EFL D+ F+ RG P L I
Sbjct: 12 QVRQLYEINDDPKRK--------------EFLDDLFSFMQKRG----TPINRLP-----I 48
Query: 473 LNAKRLDLFNLYREVVSRGGF-HVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLKRHYET 531
+ LDL+ LY V++RGG V N W+ ++ L + +T TL+ Y
Sbjct: 49 MAKSVLDLYELYNLVIARGGLVDVINKKLWQ----EIIKGLHLPSSITSAALTLRTQYMK 104
Query: 532 YLLEYE 537
YL YE
Sbjct: 105 YLYPYE 110
>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 = 34.3 bits (77), Expect = 0.19, Method: Composition-based stats.
Identities = 30/99 (30%), Positives = 41/99 (41%), Gaps = 16/99 (16%)
Query: 441 EEFLRDVMQFLILRGH-TRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGGF-HVGNG 498
+EFL D+ F+ RG +P I+ + LDLF LY V +GG V N
Sbjct: 36 KEFLDDLFSFMQKRGTPVNRIP----------IMAKQVLDLFMLYVLVTEKGGLVEVINK 85
Query: 499 INWKGQVFSKMRNHTLTNRMTGVGNTLKRHYETYLLEYE 537
W+ + L +T TL+ Y YL YE
Sbjct: 86 KLWR----EITKGLNLPTSITSAAFTLRTQYMKYLYPYE 120
>pdb|3N9L|A Chain A, Cekdm7a From C.Elegans, Complex With H3k4me3 Peptide And
Nog
pdb|3N9M|A Chain A, Cekdm7a From C.Elegans, Alone
pdb|3N9M|C Chain C, Cekdm7a From C.Elegans, Alone
pdb|3N9N|A Chain A, Cekdm7a From C.Elegans, Complex With H3k4me3k9me2 Peptide
And Nog
pdb|3N9O|A Chain A, Cekdm7a From C.Elegans, Complex With H3k4me3 Peptide,
H3k9me2 Peptide And Nog
pdb|3N9P|A Chain A, Cekdm7a From C.Elegans, Complex With H3k4me3k27me2 Peptide
And Nog
pdb|3N9Q|A Chain A, Cekdm7a From C.Elegans, Complex With H3k4me3 Peptide,
H3k27me2 Peptide And Nog
pdb|3PUQ|A Chain A, Cekdm7a From C.Elegans, Complex With Alpha-Kg
pdb|3PUQ|C Chain C, Cekdm7a From C.Elegans, Complex With Alpha-Kg
pdb|3PUR|A Chain A, Cekdm7a From C.Elegans, Complex With D-2-Hg
pdb|3PUR|C Chain C, Cekdm7a From C.Elegans, Complex With D-2-Hg
Length = 528
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 6/40 (15%)
Query: 559 WVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQC 598
W+ C C W HF C GL F+ Y ++ CP+C
Sbjct: 58 WIGCDSCQTWYHFLC---SGLEQFEYYLYE---KFFCPKC 91
>pdb|2EQY|A Chain A, Solution Structure Of The Arid Domain Of Jarid1b Protein
Length = 122
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 26/96 (27%), Positives = 41/96 (42%), Gaps = 14/96 (14%)
Query: 443 FLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGGFHVGNGINWK 502
FL + ++ L+G T +P + K LDLF L + V GGF + K
Sbjct: 17 FLDQIAKYWELQGSTLKIPH----------VERKILDLFQLNKLVAEEGGF----AVVCK 62
Query: 503 GQVFSKMRNHTLTNRMTGVGNTLKRHYETYLLEYEL 538
+ ++K+ VG+ ++ HYE L Y L
Sbjct: 63 DRKWTKIATKMGFAPGKAVGSHIRGHYERILNPYNL 98
>pdb|2NYA|A Chain A, Crystal Structure Of The Periplasmic Nitrate Reductase
(Nap) From Escherichia Coli
pdb|2NYA|F Chain F, Crystal Structure Of The Periplasmic Nitrate Reductase
(Nap) From Escherichia Coli
Length = 792
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 33/77 (42%), Gaps = 11/77 (14%)
Query: 537 ELAHDDVDGECCLLCHSSAAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCP 596
ELA D ++ E S G ++ G+ E+A FG L F DY K GL +
Sbjct: 572 ELAEDQLNDE------SRELGFYLQKGLFEEYAWFGRGHGHDLAPFDDYHKARGLRW--- 622
Query: 597 QCSVTNFKKKSQKTSNG 613
V N K+ + S G
Sbjct: 623 --PVVNGKETQWRYSEG 637
>pdb|3QZV|A Chain A, Crystal Structure Of Bptf Phd-Linker-Bromo In Complex With
Histone H4k12ac Peptide
Length = 174
Score = 29.3 bits (64), Expect = 7.2, Method: Composition-based stats.
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 6/43 (13%)
Query: 559 WVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVT 601
++ C C W H C +G + A+ EYVCPQC T
Sbjct: 23 YIGCDRCQNWYHGRC-----VGILQSEAELID-EYVCPQCQST 59
>pdb|2RI7|A Chain A, Crystal Structure Of Phd Finger-Linker-Bromodomain Y17e
Mutant From Human Bptf In The H3(1-9)k4me2 Bound State
Length = 174
Score = 29.3 bits (64), Expect = 7.4, Method: Composition-based stats.
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 6/43 (13%)
Query: 559 WVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVT 601
++ C C W H C +G + A+ EYVCPQC T
Sbjct: 23 YIGCDRCQNWYHGRC-----VGILQSEAELID-EYVCPQCQST 59
>pdb|2F6J|A Chain A, Crystal Structure Of Phd Finger-Linker-Bromodomain
Fragment Of Human Bptf In The H3(1-15)k4me3 Bound State
pdb|2F6J|B Chain B, Crystal Structure Of Phd Finger-Linker-Bromodomain
Fragment Of Human Bptf In The H3(1-15)k4me3 Bound State
pdb|2F6J|C Chain C, Crystal Structure Of Phd Finger-Linker-Bromodomain
Fragment Of Human Bptf In The H3(1-15)k4me3 Bound State
pdb|2F6N|A Chain A, Crystal Structure Of Phd Finger-Linker-Bromodomain
Fragment Of Human Bptf In The Free Form
pdb|2F6N|B Chain B, Crystal Structure Of Phd Finger-Linker-Bromodomain
Fragment Of Human Bptf In The Free Form
pdb|2FSA|A Chain A, Crystal Structure Of Phd Finger-Linker-Bromodomain
Fragment Of Human Bptf In The H3(1-15)k4me2 Bound State
pdb|2FSA|B Chain B, Crystal Structure Of Phd Finger-Linker-Bromodomain
Fragment Of Human Bptf In The H3(1-15)k4me2 Bound State
pdb|2FSA|C Chain C, Crystal Structure Of Phd Finger-Linker-Bromodomain
Fragment Of Human Bptf In The H3(1-15)k4me2 Bound State
Length = 174
Score = 28.9 bits (63), Expect = 7.9, Method: Composition-based stats.
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 6/43 (13%)
Query: 559 WVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVT 601
++ C C W H C +G + A+ EYVCPQC T
Sbjct: 23 YIGCDRCQNWYHGRC-----VGILQSEAELID-EYVCPQCQST 59
>pdb|1LO1|A Chain A, Estrogen Related Receptor 2 Dna Binding Domain In Complex
With Dna
Length = 98
Score = 28.9 bits (63), Expect = 8.1, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 6/52 (11%)
Query: 562 CGICGEWA---HFGCDRRQGLGAFKDYAKTDGLEYVCP---QCSVTNFKKKS 607
C +CG+ A H+G + AF +EY CP +C +T ++KS
Sbjct: 7 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKS 58
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 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,446,005
Number of Sequences: 62578
Number of extensions: 762616
Number of successful extensions: 1838
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 1830
Number of HSP's gapped (non-prelim): 23
length of query: 614
length of database: 14,973,337
effective HSP length: 105
effective length of query: 509
effective length of database: 8,402,647
effective search space: 4276947323
effective search space used: 4276947323
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)