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= 040083
(635 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WEE|A Chain A, Solution Structure Of Phd Domain In Phd Finger Family
Protein
Length = 72
Score = 72.4 bits (176), Expect = 7e-13, Method: Composition-based stats.
Identities = 30/55 (54%), Positives = 37/55 (67%)
Query: 570 ENGMVNCVVECACGADEDDGERMVSCDICEVWQHTRCARIPNNEEIPHIFLCNRC 624
E G+ N V+C CG +DDGERM++CD C VW HTRC I N + +P FLC RC
Sbjct: 9 ERGVDNWKVDCKCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRC 63
>pdb|2LV9|A Chain A, Solution Nmr Structure Of The Phd Domain Of Human Mll5,
Northeast Structural Genomics Consortium Target Hr6512a
Length = 98
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/69 (42%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 558 NSERGIVYGQIYENGMVNC-VVECACGADEDDGERMVSCDICEVWQHTRCARIPNNEEIP 616
+S R +Y Q E+G V C CG DDG M+ CD C VWQH C I + + IP
Sbjct: 8 SSGRENLYFQGSEDGSYGTDVTRCICGFTHDDG-YMICCDKCSVWQHIDCMGI-DRQHIP 65
Query: 617 HIFLCNRCE 625
+LC RC+
Sbjct: 66 DTYLCERCQ 74
>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 = 37.4 bits (85), Expect = 0.026, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 580 CACGADEDDGERMVSCDICEVWQHTRCARIPNNE-EIPHIFLCNRCE 625
C C D+ + + CD C+ W H RC I +E E+ ++C +C+
Sbjct: 11 CICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQ 57
>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 = 37.0 bits (84), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 580 CACGADEDDGERMVSCDICEVWQHTRCARIPNNE-EIPHIFLCNRCE 625
C C ED+ + + CD C+ W H RC I +E E+ ++C +C+
Sbjct: 11 CICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQ 57
>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 = 36.2 bits (82), Expect = 0.053, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 580 CACGADEDDGERMVSCDICEVWQHTRCARIPNNE-EIPHIFLCNRCE 625
C C D+ + + CD C+ W H RC I +E E+ ++C +C+
Sbjct: 11 CICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQ 57
>pdb|3O70|A Chain A, Phd-Type Zinc Finger Of Human Phd Finger Protein 13
Length = 68
Score = 36.2 bits (82), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 6/57 (10%)
Query: 568 IYENGMVNCVVECACGADEDDGERMVSCDICEVWQHTRCARIPNNEEIPHIFLCNRC 624
+Y G+V C G M+ C+ C W H CA+I +P +F+C +C
Sbjct: 14 LYFQGLVTCFC-----MKPFAGRPMIECNECHTWIHLSCAKI-RKSNVPEVFVCQKC 64
>pdb|1WE9|A Chain A, Solution Structure Of Phd Domain In Nucleic Acid Binding
Protein-like Np_197993
Length = 64
Score = 35.0 bits (79), Expect = 0.12, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 581 ACGADEDDGERMVSCDICEVWQHTRCARI-PNNEEIPHIFLCNRCEQE 627
ACG E + CD+CE+W H +C +I P E + C C +
Sbjct: 11 ACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK 58
>pdb|3KQI|A Chain A, Crystal Structure Of Phf2 Phd Domain Complexed With
H3k4me3 Peptide
Length = 75
Score = 35.0 bits (79), Expect = 0.12, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 24/56 (42%), Gaps = 3/56 (5%)
Query: 573 MVNCVVECACGADEDDGERMVSCDICEVWQHTRCARIPNNEEIP--HIFLCNRCEQ 626
M V C C D M+ CD C+ W H C + EE P I+ C CE+
Sbjct: 6 MATVPVYCVCRLPYDVTRFMIECDACKDWFHGSCVGV-EEEEAPDIDIYHCPNCEK 60
>pdb|3QZV|A Chain A, Crystal Structure Of Bptf Phd-Linker-Bromo In Complex With
Histone H4k12ac Peptide
Length = 174
Score = 34.3 bits (77), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 580 CACGADEDDGERMVSCDICEVWQHTRCARIPNNE-EIPHIFLCNRCE 625
C C D+ + + CD C+ W H RC I +E E+ ++C +C+
Sbjct: 11 CICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQ 57
>pdb|3O7A|A Chain A, Crystal Structure Of Phf13 In Complex With H3k4me3
Length = 52
Score = 33.9 bits (76), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 589 GERMVSCDICEVWQHTRCARIPNNEEIPHIFLCNRC 624
G M+ C+ C W H CA+I +P +F+C +C
Sbjct: 15 GRPMIECNECHTWIHLSCAKI-RKSNVPEVFVCQKC 49
>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 = 33.5 bits (75), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 578 VECACGADEDDGERMVSCDICEVWQHTRCARIPNNEEIP-HIFLCNRCEQEIVHLSSL 634
V C C D M+ CDIC+ W H C + + + ++ C C ++H SSL
Sbjct: 38 VYCVCRQPYDVNRFMIECDICKDWFHGSCVGVEEHHAVDIDLYHCPNC--AVLHGSSL 93
>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 = 32.7 bits (73), Expect = 0.59, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 19/42 (45%)
Query: 587 DDGERMVSCDICEVWQHTRCARIPNNEEIPHIFLCNRCEQEI 628
DDG M+ CD C+ W H C I + C +C +I
Sbjct: 28 DDGSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKI 69
>pdb|2RSD|A Chain A, Solution Structure Of The Plant Homeodomain (Phd) Of The
E3 Sumo Ligase Siz1 From Rice
Length = 68
Score = 32.7 bits (73), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 6/42 (14%)
Query: 589 GERMVSCDI--CEVWQHTRCARIPN----NEEIPHIFLCNRC 624
+ M+ C+ C+VWQH C IP+ + E+P +F C C
Sbjct: 21 NDSMIQCEDQRCQVWQHLNCVLIPDKPGESAEVPPVFYCELC 62
>pdb|1WEW|A Chain A, Solution Structure Of Phd Domain In Dna-Binding Family
Protein Aam98074
Length = 78
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 13/65 (20%)
Query: 578 VECACGADEDDGERMVSCDI--CEVWQHTRCARIPN-----NEEIPHIFLCNRCEQEIVH 630
V C CG + + + M+ C+ C VWQH C +P+ N +P F C EI
Sbjct: 17 VRCVCG-NSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYC-----EICR 70
Query: 631 LSSLP 635
L+S P
Sbjct: 71 LTSGP 75
>pdb|3KV4|A Chain A, Structure Of Phf8 In Complex With Histone H3
Length = 447
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 573 MVNCVVECACGADEDDGERMVSCDICEVWQHTRCARIPNNEEIP-HIFLCNRCE 625
M + V C C D M+ CD+C+ W H C + + ++ C CE
Sbjct: 1 MASVPVYCLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNCE 54
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
0.324 0.140 0.441
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,352,103
Number of Sequences: 62578
Number of extensions: 810319
Number of successful extensions: 2128
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 2110
Number of HSP's gapped (non-prelim): 20
length of query: 635
length of database: 14,973,337
effective HSP length: 105
effective length of query: 530
effective length of database: 8,402,647
effective search space: 4453402910
effective search space used: 4453402910
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 54 (25.4 bits)