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= psy7929
(259 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WEN|A Chain A, Solution Structure Of Phd Domain In Ing1-Like Protein
Bac25079
Length = 71
Score = 124 bits (311), Expect = 5e-29, Method: Composition-based stats.
Identities = 47/54 (87%), Positives = 51/54 (94%)
Query: 206 DMPVDPNEPTYCVCQQVSYGEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPK 259
DMPVDPNEPTYC+C QVSYGEMIGCDNPDC IEWFHFACV LTTKP+GKW+CP+
Sbjct: 8 DMPVDPNEPTYCLCHQVSYGEMIGCDNPDCSIEWFHFACVGLTTKPRGKWFCPR 61
>pdb|1WEU|A Chain A, Solution Structure Of Phd Domain In Ing1-Like Protein
Bac25009
Length = 91
Score = 122 bits (305), Expect = 3e-28, Method: Compositional matrix adjust.
Identities = 50/57 (87%), Positives = 54/57 (94%)
Query: 203 DVLDMPVDPNEPTYCVCQQVSYGEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPK 259
DVLDMPVDPNEPTYC+C QVSYGEMIGCDNPDC IEWFHFACV LTTKP+GKW+CP+
Sbjct: 25 DVLDMPVDPNEPTYCLCHQVSYGEMIGCDNPDCSIEWFHFACVGLTTKPRGKWFCPR 81
>pdb|2K1J|A Chain A, Plan Homeodomain Finger Of Tumour Supressor Ing4
Length = 63
Score = 117 bits (292), Expect = 9e-27, Method: Compositional matrix adjust.
Identities = 47/55 (85%), Positives = 52/55 (94%)
Query: 205 LDMPVDPNEPTYCVCQQVSYGEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPK 259
+DMPVDPNEPTYC+C QVSYGEMIGCDNPDC IEWFHFACV LTTKP+GKW+CP+
Sbjct: 1 MDMPVDPNEPTYCLCHQVSYGEMIGCDNPDCSIEWFHFACVGLTTKPRGKWFCPR 55
>pdb|2VNF|A Chain A, Molecular Basis Of Histone H3k4me3 Recognition By Ing4
pdb|2VNF|C Chain C, Molecular Basis Of Histone H3k4me3 Recognition By Ing4
Length = 60
Score = 116 bits (291), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 47/55 (85%), Positives = 52/55 (94%)
Query: 205 LDMPVDPNEPTYCVCQQVSYGEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPK 259
+DMPVDPNEPTYC+C QVSYGEMIGCDNPDC IEWFHFACV LTTKP+GKW+CP+
Sbjct: 1 MDMPVDPNEPTYCLCHQVSYGEMIGCDNPDCSIEWFHFACVGLTTKPRGKWFCPR 55
>pdb|2M1R|A Chain A, Phd Domain Of Ing4 N214d Mutant
Length = 63
Score = 114 bits (286), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 46/55 (83%), Positives = 52/55 (94%)
Query: 205 LDMPVDPNEPTYCVCQQVSYGEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPK 259
+DMPVDPNEPTYC+C QVSYGEMIGCD+PDC IEWFHFACV LTTKP+GKW+CP+
Sbjct: 1 MDMPVDPNEPTYCLCHQVSYGEMIGCDDPDCSIEWFHFACVGLTTKPRGKWFCPR 55
>pdb|4AFL|A Chain A, The Crystal Structure Of The Ing4 Dimerization Domain
Reveals The Functional Organization Of The Ing Family Of
Chromatin Binding Proteins.
pdb|4AFL|B Chain B, The Crystal Structure Of The Ing4 Dimerization Domain
Reveals The Functional Organization Of The Ing Family Of
Chromatin Binding Proteins.
pdb|4AFL|C Chain C, The Crystal Structure Of The Ing4 Dimerization Domain
Reveals The Functional Organization Of The Ing Family Of
Chromatin Binding Proteins.
pdb|4AFL|D Chain D, The Crystal Structure Of The Ing4 Dimerization Domain
Reveals The Functional Organization Of The Ing Family Of
Chromatin Binding Proteins.
pdb|4AFL|E Chain E, The Crystal Structure Of The Ing4 Dimerization Domain
Reveals The Functional Organization Of The Ing Family Of
Chromatin Binding Proteins.
pdb|4AFL|F Chain F, The Crystal Structure Of The Ing4 Dimerization Domain
Reveals The Functional Organization Of The Ing Family Of
Chromatin Binding Proteins
Length = 104
Score = 114 bits (285), Expect = 5e-26, Method: Compositional matrix adjust.
Identities = 56/103 (54%), Positives = 76/103 (73%)
Query: 2 STSYLEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKK 61
+ YLE YLDS+++LP ELQRNF L R+LD R +D+ ID++A +Y + + S ++K
Sbjct: 2 AGXYLEHYLDSIENLPFELQRNFQLXRDLDQRTEDLKAEIDKLATEYXSSARSLSSEEKL 61
Query: 62 ETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLA 104
L +IQ+ + K KE+GDDKVQLA QTYE VDK+IR+LDTDLA
Sbjct: 62 ALLKQIQEAYGKCKEFGDDKVQLAXQTYEXVDKHIRRLDTDLA 104
>pdb|1WES|A Chain A, Solution Structure Of Phd Domain In Inhibitor Of Growth
Family, Member 1-Like
Length = 71
Score = 114 bits (284), Expect = 7e-26, Method: Composition-based stats.
Identities = 44/54 (81%), Positives = 48/54 (88%)
Query: 206 DMPVDPNEPTYCVCQQVSYGEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPK 259
+ +DPNEPTYC+C QVSYGEMIGCDN CPIEWFHF+CVSLT KPKGKWYCPK
Sbjct: 8 EFAIDPNEPTYCLCNQVSYGEMIGCDNEQCPIEWFHFSCVSLTYKPKGKWYCPK 61
>pdb|2QIC|A Chain A, Crystal Structure Of The Ing1 Phd Finger In Complex With A
Histone H3k4me3 Peptide
Length = 62
Score = 113 bits (282), Expect = 1e-25, Method: Composition-based stats.
Identities = 44/54 (81%), Positives = 49/54 (90%)
Query: 206 DMPVDPNEPTYCVCQQVSYGEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPK 259
D+P+DPNEPTYC+C QVSYGEMIGCDN +CPIEWFHF+CV L KPKGKWYCPK
Sbjct: 3 DLPIDPNEPTYCLCNQVSYGEMIGCDNDECPIEWFHFSCVGLNHKPKGKWYCPK 56
>pdb|3C6W|A Chain A, Crystal Structure Of The Ing5 Phd Finger In Complex With
H3k4me3 Peptide
pdb|3C6W|C Chain C, Crystal Structure Of The Ing5 Phd Finger In Complex With
H3k4me3 Peptide
Length = 59
Score = 110 bits (274), Expect = 9e-25, Method: Composition-based stats.
Identities = 43/48 (89%), Positives = 46/48 (95%)
Query: 212 NEPTYCVCQQVSYGEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPK 259
NEPTYC+C QVSYGEMIGCDNPDCPIEWFHFACV LTTKPKGKW+CP+
Sbjct: 7 NEPTYCLCHQVSYGEMIGCDNPDCPIEWFHFACVDLTTKPKGKWFCPR 54
>pdb|2PNX|A Chain A, The Phd Finger Of Ing4 In Complex With An H3k4me3 Histone
Peptide
pdb|2PNX|C Chain C, The Phd Finger Of Ing4 In Complex With An H3k4me3 Histone
Peptide
Length = 55
Score = 108 bits (270), Expect = 3e-24, Method: Composition-based stats.
Identities = 41/48 (85%), Positives = 45/48 (93%)
Query: 212 NEPTYCVCQQVSYGEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPK 259
NEPTYC+C QVSYGEMIGCDNPDC IEWFHFACV LTTKP+GKW+CP+
Sbjct: 3 NEPTYCLCHQVSYGEMIGCDNPDCSIEWFHFACVGLTTKPRGKWFCPR 50
>pdb|2G6Q|A Chain A, Crystal Structure Of Ing2 Phd Domain In Complex With
H3k4me3 Peptide
Length = 62
Score = 106 bits (264), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 44/54 (81%), Positives = 48/54 (88%)
Query: 206 DMPVDPNEPTYCVCQQVSYGEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPK 259
+ +DPNEPTYC+C QVSYGEMIGCDN CPIEWFHF+CVSLT KPKGKWYCPK
Sbjct: 3 EFAIDPNEPTYCLCNQVSYGEMIGCDNEQCPIEWFHFSCVSLTYKPKGKWYCPK 56
>pdb|1X4I|A Chain A, Solution Structure Of Phd Domain In Inhibitor Of Growth
Protein 3 (Ing3)
Length = 70
Score = 97.4 bits (241), Expect = 6e-21, Method: Composition-based stats.
Identities = 34/44 (77%), Positives = 38/44 (86%)
Query: 216 YCVCQQVSYGEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPK 259
YC+C QVSYGEM+GCDN DCPIEWFH+ CV LT PKGKWYCP+
Sbjct: 8 YCICNQVSYGEMVGCDNQDCPIEWFHYGCVGLTEAPKGKWYCPQ 51
>pdb|2JMI|A Chain A, Nmr Solution Structure Of Phd Finger Fragment Of Yeast
Yng1 Protein In Free State
pdb|2JMJ|A Chain A, Nmr Solution Structure Of The Phd Domain From The Yeast
Yng1 Protein In Complex With H3(1-9)k4me3 Peptide
Length = 90
Score = 80.1 bits (196), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 30/47 (63%), Positives = 33/47 (70%)
Query: 213 EPTYCVCQQVSYGEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPK 259
E YC C+ VSYG M+ CDNP CP EWFH+ CV L PKGKWYC K
Sbjct: 25 EEVYCFCRNVSYGPMVACDNPACPFEWFHYGCVGLKQAPKGKWYCSK 71
>pdb|4GND|A Chain A, Crystal Structure Of Nsd3 Tandem Phd5-C5hch Domains
pdb|4GND|C Chain C, Crystal Structure Of Nsd3 Tandem Phd5-C5hch Domains
pdb|4GNE|A Chain A, Crystal Structure Of Nsd3 Tandem Phd5-C5hch Domains
Complexed With H3 Peptide 1-7
pdb|4GNF|A Chain A, Crystal Structure Of Nsd3 Tandem Phd5-C5hch Domains
Complexed With H3 Peptide 1-15
pdb|4GNG|A Chain A, Crystal Structure Of Nsd3 Tandem Phd5-C5hch Domains
Complexed With H3k9me3 Peptide
pdb|4GNG|D Chain D, Crystal Structure Of Nsd3 Tandem Phd5-C5hch Domains
Complexed With H3k9me3 Peptide
Length = 107
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/34 (50%), Positives = 23/34 (67%), Gaps = 1/34 (2%)
Query: 225 GEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCP 258
GE++ CD DCP + +H C++LT P GKW CP
Sbjct: 25 GELVMCDKKDCP-KAYHLLCLNLTQPPYGKWECP 57
>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 = 37.0 bits (84), Expect = 0.012, Method: Composition-based stats.
Identities = 15/35 (42%), Positives = 23/35 (65%), Gaps = 5/35 (14%)
Query: 227 MIGCDNPDCPIEWFHFACVSLTTKP--KGKWYCPK 259
MIGCD+ D +W+H+ CV + P + +W+CPK
Sbjct: 33 MIGCDDCD---DWYHWPCVGIMAAPPEEMQWFCPK 64
>pdb|1WEM|A Chain A, Solution Structure Of Phd Domain In Death Inducer-
Obliterator 1(Dio-1)
Length = 76
Score = 32.3 bits (72), Expect = 0.28, Method: Composition-based stats.
Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 5/40 (12%)
Query: 210 DPNEPTYCVCQQVSYGE-MIGCDNPDCPIEWFHFACVSLT 248
DPN YC+C+Q MI CD + EWFH CV ++
Sbjct: 13 DPN-ALYCICRQPHNNRFMICCDRCE---EWFHGDCVGIS 48
>pdb|2L5U|A Chain A, Structure Of The First Phd Finger (Phd1) From Chd4 (Mi2b)
Length = 61
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/46 (45%), Positives = 26/46 (56%), Gaps = 8/46 (17%)
Query: 216 YC-VCQQVSYGEMIGCDNPDCPIEWFHFACVS--LTTKPKGKWYCP 258
YC VCQQ GE+I CD CP +H C+ + P+GKW CP
Sbjct: 13 YCEVCQQG--GEIILCDT--CP-RAYHMVCLDPDMEKAPEGKWSCP 53
>pdb|1MM2|A Chain A, Solution Structure Of The 2nd Phd Domain From Mi2b
pdb|2L75|A Chain A, Solution Structure Of Chd4-Phd2 In Complex With H3k9me3
Length = 61
Score = 29.6 bits (65), Expect = 1.6, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 5/37 (13%)
Query: 225 GEMIGCDNPDCPIEWFHFACVS--LTTKPKGKWYCPK 259
GE++ CD CP +H C++ L P G+W CP+
Sbjct: 19 GELLCCDT--CPSS-YHIHCLNPPLPEIPNGEWLCPR 52
>pdb|1MM3|A Chain A, Solution Structure Of The 2nd Phd Domain From Mi2b With C-
Terminal Loop Replaced By Corresponding Loop From Wstf
Length = 61
Score = 28.9 bits (63), Expect = 2.9, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 5/37 (13%)
Query: 225 GEMIGCDNPDCPIEWFHFACV--SLTTKPKGKWYCPK 259
GE++ CD CP +H C+ +L P G+W CP+
Sbjct: 19 GELLCCDT--CPSS-YHIHCLRPALYEVPDGEWQCPR 52
>pdb|1EH1|A Chain A, Ribosome Recycling Factor From Thermus Thermophilus
pdb|2V46|Y Chain Y, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
Trna-Fmet (Part 1 Of 4). This File Contains The 30s
Subunit, Mrna, P-Site Asl, E-Site Trna And Rrf For
Molecule 1.
pdb|2V48|Y Chain Y, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
Trna-Fmet (Part 3 Of 4). This File Contains The 30s
Subunit, Mrna, P-Site Asl, E-Site Trna And Rrf For
Molecule 2.
pdb|2QBE|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 50s Subunit Of The
First 70s Ribosome, With Rrf Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2QBG|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 50s Subunit Of The
Second 70s Ribosome, With Rrf Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2QBI|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 50s
Subunit Of The First 70s Ribosome, With Gentamicin And
Rrf Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2QBK|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 50s
Subunit Of The Second 70s Ribosome, With Gentamicin And
Rrf Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2Z4L|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
50s Subunit Of The First 70s Ribosome, With Paromomycin
And Rrf Bound. The Entire Crystal Structure Contains Two
70s Ribosomes And Is Described In Remark 400.
pdb|2Z4N|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
50s Subunit Of The Second 70s Ribosome, With Paromomycin
And Rrf Bound. The Entire Crystal Structure Contains Two
70s Ribosomes And Is Described In Remark 400.
pdb|3J0D|J Chain J, Models For The T. Thermophilus Ribosome Recycling Factor
Bound To The E. Coli Post-Termination Complex
pdb|3J0E|G Chain G, Models For The T. Thermophilus Ribosome Recycling Factor
And The E. Coli Elongation Factor G Bound To The E. Coli
Post-Termination Complex
Length = 185
Score = 27.3 bits (59), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 6/62 (9%)
Query: 17 PIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMK------HYSKDKKKETLAEIQKY 70
P+ +R L+R + A++ I + + LD +K H S+D+ K AEIQK
Sbjct: 105 PLTEERRKDLVRAVRQYAEEGRVAIRNIRREALDKLKKLAKELHLSEDETKRAEAEIQKI 164
Query: 71 FD 72
D
Sbjct: 165 TD 166
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
0.316 0.133 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,430,722
Number of Sequences: 62578
Number of extensions: 192069
Number of successful extensions: 632
Number of sequences better than 100.0: 42
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 24
Number of HSP's that attempted gapping in prelim test: 613
Number of HSP's gapped (non-prelim): 42
length of query: 259
length of database: 14,973,337
effective HSP length: 97
effective length of query: 162
effective length of database: 8,903,271
effective search space: 1442329902
effective search space used: 1442329902
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)