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= 025377
(253 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WE9|A Chain A, Solution Structure Of Phd Domain In Nucleic Acid Binding
Protein-like Np_197993
Length = 64
Score = 106 bits (265), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 47/50 (94%), Positives = 49/50 (98%)
Query: 200 CGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSNK 249
CGACGE+YAADEFWICCD+CE WFHGKCVKITPARAEHIKQYKCPSCSNK
Sbjct: 9 CGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK 58
>pdb|3QZV|A Chain A, Crystal Structure Of Bptf Phd-Linker-Bromo In Complex With
Histone H4k12ac Peptide
Length = 174
Score = 51.6 bits (122), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 28/46 (60%)
Query: 203 CGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248
C Y +F+I CD C+ W+HG+CV I + AE I +Y CP C +
Sbjct: 13 CKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQS 58
>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 = 51.2 bits (121), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 28/46 (60%)
Query: 203 CGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248
C Y +F+I CD C+ W+HG+CV I + AE I +Y CP C +
Sbjct: 13 CKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQS 58
>pdb|3KV5|D Chain D, Structure Of Kiaa1718, Human Jumonji Demethylase, In
Complex With N-Oxalylglycine
pdb|3KV5|A Chain A, Structure Of Kiaa1718, Human Jumonji Demethylase, In
Complex With N-Oxalylglycine
pdb|3KV6|A Chain A, Structure Of Kiaa1718, Human Jumonji Demethylase, In
Complex With Alpha-Ketoglutarate
pdb|3KV6|D Chain D, Structure Of Kiaa1718, Human Jumonji Demethylase, In
Complex With Alpha-Ketoglutarate
Length = 488
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 26/46 (56%)
Query: 202 ACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCS 247
C + Y + F I CD+C+ WFHG CV + A I Y CP+C+
Sbjct: 41 VCRQPYDVNRFMIECDICKDWFHGSCVGVEEHHAVDIDLYHCPNCA 86
>pdb|2FUI|A Chain A, Nmr Solution Structure Of Phd Finger Fragment Of Human
Bptf In Free State
pdb|2FUU|A Chain A, Nmr Solution Structure Of The Phd Domain From The Human
Bptf In Complex With H3(1-15)k4me3 Peptide
Length = 62
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 28/46 (60%)
Query: 203 CGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248
C Y +F+I CD C+ W+HG+CV I + AE I +Y CP C +
Sbjct: 13 CKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQS 58
>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 = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 26/38 (68%)
Query: 211 EFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248
+F+I CD C+ W+HG+CV I + AE I +Y CP C +
Sbjct: 21 KFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQS 58
>pdb|3KV4|A Chain A, Structure Of Phf8 In Complex With Histone H3
Length = 447
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 24/44 (54%)
Query: 203 CGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSC 246
C Y F I CD+C+ WFHG CV + +A I Y CP+C
Sbjct: 10 CRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNC 53
>pdb|1WEM|A Chain A, Solution Structure Of Phd Domain In Death Inducer-
Obliterator 1(Dio-1)
Length = 76
Score = 48.1 bits (113), Expect = 4e-06, Method: Composition-based stats.
Identities = 20/42 (47%), Positives = 28/42 (66%), Gaps = 4/42 (9%)
Query: 210 DEFWICCDVCEKWFHGKCVKITPARAEHIKQ----YKCPSCS 247
+ F ICCD CE+WFHG CV I+ AR +++ Y CP+C+
Sbjct: 27 NRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCT 68
>pdb|1WEP|A Chain A, Solution Structure Of Phd Domain In Phf8
Length = 79
Score = 47.0 bits (110), Expect = 1e-05, Method: Composition-based stats.
Identities = 19/44 (43%), Positives = 23/44 (52%)
Query: 203 CGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSC 246
C + Y + F I C +C+ WFHG CV I A I Y CP C
Sbjct: 17 CRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDC 60
>pdb|3KQI|A Chain A, Crystal Structure Of Phf2 Phd Domain Complexed With
H3k4me3 Peptide
Length = 75
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 23/51 (45%)
Query: 202 ACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSNKRAR 252
C Y F I CD C+ WFHG CV + A I Y CP+C +
Sbjct: 14 VCRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEKTHGK 64
>pdb|2K16|A Chain A, Solution Structure Of The Free Taf3 Phd Domain
pdb|2K17|A Chain A, Solution Structure Of The Taf3 Phd Domain In Complex With
A H3k4me3 Peptide
Length = 75
Score = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 214 ICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSNK 249
I CD C+ W+H CV I A E + Q+ CP C+NK
Sbjct: 34 IGCDDCDDWYHWPCVGIMAAPPEEM-QWFCPKCANK 68
>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 = 0.48, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 213 WICCDVCEKWFHGKCVKITPARAEHIKQYKCPSC 246
WI CD C+ W+H C + +++ CP C
Sbjct: 58 WIGCDSCQTWYHFLCSGLEQFEYYLYEKFFCPKC 91
>pdb|2KGG|A Chain A, Solution Structure Of Jarid1a C-Terminal Phd Finger
pdb|2KGI|A Chain A, Solution Structure Of Jarid1a C-Terminal Phd Finger In
Complex With H3(1-9)k4me3
pdb|3GL6|A Chain A, Crystal Structure Of Jarid1a-Phd3 Complexed With H3(1-9)
K4me3 Peptide
Length = 52
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 24/36 (66%), Gaps = 2/36 (5%)
Query: 213 WICCDV-CEKWFHGKCVKITPARAEHIKQYKCPSCS 247
W+ CD C++WFH CV ++P AE+ + Y C +C+
Sbjct: 18 WVQCDGGCDEWFHQVCVGVSPEMAEN-EDYICINCA 52
>pdb|2XB1|A Chain A, Crystal Structure Of The Human Pygo2 Phd Finger In Complex
With The B9l Hd1 Domain
pdb|2XB1|C Chain C, Crystal Structure Of The Human Pygo2 Phd Finger In Complex
With The B9l Hd1 Domain
Length = 105
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 200 CGACGENYAADEFWICCDV-CEKWFHGKCVKITPA 233
CGAC D+ I C+ C+KWFH +C +T +
Sbjct: 6 CGACRSEVNDDQDAILCEASCQKWFHRECTGMTES 40
>pdb|2DX8|A Chain A, Crystal Structure Analysis Of The Phd Domain Of The
Transcription Coactivator Pygophus
pdb|2DX8|B Chain B, Crystal Structure Analysis Of The Phd Domain Of The
Transcription Coactivator Pygophus
Length = 67
Score = 29.6 bits (65), Expect = 1.6, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 6/53 (11%)
Query: 200 CGACGENYAADEFWICCDV-CEKWFHGKCVKITPA-----RAEHIKQYKCPSC 246
CG C D+ I C+ C+KWFH C +T AE + C +C
Sbjct: 12 CGICTNEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTC 64
>pdb|2VPD|A Chain A, Decoding Of Methylated Histone H3 Tail By The Pygo-Bcl9
Wnt Signaling Complex
pdb|2VPD|C Chain C, Decoding Of Methylated Histone H3 Tail By The Pygo-Bcl9
Wnt Signaling Complex
Length = 67
Score = 29.6 bits (65), Expect = 1.6, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 6/53 (11%)
Query: 200 CGACGENYAADEFWICCDV-CEKWFHGKCVKITPA-----RAEHIKQYKCPSC 246
CG C D+ I C+ C+KWFH C +T AE + C +C
Sbjct: 12 CGICTNEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTC 64
>pdb|2VPB|A Chain A, Decoding Of Methylated Histone H3 Tail By The Pygo-Bcl9
Wnt Signaling Complex
Length = 65
Score = 29.6 bits (65), Expect = 1.8, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 6/53 (11%)
Query: 200 CGACGENYAADEFWICCDV-CEKWFHGKCVKITPA-----RAEHIKQYKCPSC 246
CG C D+ I C+ C+KWFH C +T AE + C +C
Sbjct: 11 CGICTNEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTC 63
>pdb|2YYR|A Chain A, Structural Analysis Of Phd Domain Of Pygopus Complexed
With Trimethylated Histone H3 Peptide
pdb|2YYR|B Chain B, Structural Analysis Of Phd Domain Of Pygopus Complexed
With Trimethylated Histone H3 Peptide
Length = 67
Score = 28.5 bits (62), Expect = 3.9, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 6/53 (11%)
Query: 200 CGACGENYAADEFWICCDV-CEKWFHGKCVKITPA-----RAEHIKQYKCPSC 246
CG C D+ I C+ C+KWFH C T AE + C +C
Sbjct: 12 CGICTNEVNDDQDAILCEASCQKWFHRICTGXTETAYGLLTAEASAVWGCDTC 64
>pdb|2LV9|A Chain A, Solution Nmr Structure Of The Phd Domain Of Human Mll5,
Northeast Structural Genomics Consortium Target Hr6512a
Length = 98
Score = 27.7 bits (60), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 210 DEFWICCDVCEKWFHGKCVKITPARAEHI-KQYKCPSC 246
D + ICCD C W H C+ I +HI Y C C
Sbjct: 39 DGYMICCDKCSVWQHIDCMGID---RQHIPDTYLCERC 73
>pdb|3ZVZ|B Chain B, Phd Finger Of Human Uhrf1
Length = 57
Score = 27.3 bits (59), Expect = 8.6, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 200 CGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248
C CG D+ + CD C+ FH C+ + ++ CP C N
Sbjct: 8 CHLCGGRQDPDK-QLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN 55
>pdb|3SHB|A Chain A, Crystal Structure Of Phd Domain Of Uhrf1
Length = 77
Score = 26.9 bits (58), Expect = 9.9, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 200 CGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248
C CG D+ + CD C+ FH C+ + ++ CP C N
Sbjct: 29 CHLCGGRQDPDK-QLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN 76
>pdb|4GY5|A Chain A, Crystal Structure Of The Tandem Tudor Domain And Plant
Homeodomain Of Uhrf1 With Histone H3k9me3
pdb|4GY5|B Chain B, Crystal Structure Of The Tandem Tudor Domain And Plant
Homeodomain Of Uhrf1 With Histone H3k9me3
pdb|4GY5|C Chain C, Crystal Structure Of The Tandem Tudor Domain And Plant
Homeodomain Of Uhrf1 With Histone H3k9me3
pdb|4GY5|D Chain D, Crystal Structure Of The Tandem Tudor Domain And Plant
Homeodomain Of Uhrf1 With Histone H3k9me3
Length = 241
Score = 26.9 bits (58), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 200 CGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248
C CG D+ + CD C+ FH C+ + ++ CP C N
Sbjct: 193 CHLCGGRQDPDK-QLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN 240
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
0.322 0.136 0.446
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,276,022
Number of Sequences: 62578
Number of extensions: 201899
Number of successful extensions: 401
Number of sequences better than 100.0: 38
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 383
Number of HSP's gapped (non-prelim): 38
length of query: 253
length of database: 14,973,337
effective HSP length: 97
effective length of query: 156
effective length of database: 8,903,271
effective search space: 1388910276
effective search space used: 1388910276
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: 50 (23.9 bits)