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= 000915
(1225 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 43.1 bits (100), Expect = 0.001, Method: Composition-based stats.
Identities = 16/39 (41%), Positives = 21/39 (53%)
Query: 145 IACDSCDLWYHAFCVGFDPEGTCEDTWLCPRCVAEVPQN 183
I CD CD WYH CVG E W CP+C ++ ++
Sbjct: 34 IGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKKD 72
>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 = 40.0 bits (92), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 145 IACDSCDLWYHAFCVGFDP-EGTCEDTWLCPRCV 177
I CDSC WYH C G + E + + CP+CV
Sbjct: 59 IGCDSCQTWYHFLCSGLEQFEYYLYEKFFCPKCV 92
>pdb|1CHC|A Chain A, Structure Of The C3hc4 Domain By 1h-Nuclear Magnetic
Resonance Spectroscopy; A New Structural Class Of Zinc-
Finger
Length = 68
Score = 39.3 bits (90), Expect = 0.015, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 5/66 (7%)
Query: 26 RCGICMDVVIDRGVLDCCQHWFCFACIDNWSTITNLCPLCQGEFQLITCVPVYDTIGSNN 85
RC IC++ + + C H FC+ CI W CPLC+ + V TI S++
Sbjct: 7 RCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCK-----VPVESVVHTIESDS 61
Query: 86 IDGDSL 91
GD L
Sbjct: 62 EFGDQL 67
>pdb|3QZV|A Chain A, Crystal Structure Of Bptf Phd-Linker-Bromo In Complex With
Histone H4k12ac Peptide
Length = 174
Score = 38.1 bits (87), Expect = 0.029, Method: Composition-based stats.
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 145 IACDSCDLWYHAFCVG-FDPEGTCEDTWLCPRC 176
I CD C WYH CVG E D ++CP+C
Sbjct: 24 IGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 56
>pdb|2KU3|A Chain A, Solution Structure Of Brd1 Phd1 Finger
Length = 71
Score = 38.1 bits (87), Expect = 0.029, Method: Composition-based stats.
Identities = 26/69 (37%), Positives = 33/69 (47%), Gaps = 21/69 (30%)
Query: 113 IDENAV--ICLDGDGCKIRSGSMVAEESSNLDTSIACDSCDLWYHAFCVG--FDPEGTCE 168
IDE+AV IC+DG ES N + + CD C+L H C G + PEG
Sbjct: 13 IDEDAVCSICMDG-------------ESQNSNVILFCDMCNLAVHQECYGVPYIPEG--- 56
Query: 169 DTWLCPRCV 177
WLC C+
Sbjct: 57 -QWLCRHCL 64
>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 = 38.1 bits (87), Expect = 0.034, Method: Composition-based stats.
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 145 IACDSCDLWYHAFCVG-FDPEGTCEDTWLCPRC 176
I CD C WYH CVG E D ++CP+C
Sbjct: 24 IGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 56
>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 = 37.4 bits (85), Expect = 0.046, Method: Composition-based stats.
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 145 IACDSCDLWYHAFCVG-FDPEGTCEDTWLCPRC 176
I CD C WYH CVG E D ++CP+C
Sbjct: 24 IGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 56
>pdb|2L43|A Chain A, Structural Basis For Histone Code Recognition By
Brpf2-Phd1 Finger
Length = 88
Score = 37.0 bits (84), Expect = 0.062, Method: Composition-based stats.
Identities = 26/69 (37%), Positives = 33/69 (47%), Gaps = 21/69 (30%)
Query: 113 IDENAV--ICLDGDGCKIRSGSMVAEESSNLDTSIACDSCDLWYHAFCVG--FDPEGTCE 168
IDE+AV IC+DG ES N + + CD C+L H C G + PEG
Sbjct: 22 IDEDAVCSICMDG-------------ESQNSNVILFCDMCNLAVHQECYGVPYIPEG--- 65
Query: 169 DTWLCPRCV 177
WLC C+
Sbjct: 66 -QWLCRHCL 73
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 37.0 bits (84), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 5 LEEQTFQVDNTENDLLNFECGRCGICMDVVIDRGVLDCCQHWFCFACIDNWSTITNLCPL 64
++ Q +V + ND+L E +C IC + I+ L+C H FC CI+ W CP+
Sbjct: 35 MQAQKEEVLSHMNDVLENE-LQCIICSEYFIEAVTLNC-AHSFCSYCINEWMKRKIECPI 92
Query: 65 CQGEFQLITCVPVYD 79
C+ + + T V D
Sbjct: 93 CRKDIKSKTYSLVLD 107
>pdb|2LV9|A Chain A, Solution Nmr Structure Of The Phd Domain Of Human Mll5,
Northeast Structural Genomics Consortium Target Hr6512a
Length = 98
Score = 36.6 bits (83), Expect = 0.081, Method: Composition-based stats.
Identities = 15/32 (46%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 145 IACDSCDLWYHAFCVGFDPEGTCEDTWLCPRC 176
I CD C +W H C+G D + DT+LC RC
Sbjct: 43 ICCDKCSVWQHIDCMGIDRQHI-PDTYLCERC 73
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 36.6 bits (83), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 5 LEEQTFQVDNTENDLLNFECGRCGICMDVVIDRGVLDCCQHWFCFACIDNWSTITNLCPL 64
++ Q +V + ND+L E +C IC + I+ L+C H FC CI+ W CP+
Sbjct: 35 MQAQKEEVLSHMNDVLENE-LQCIICSEYFIEAVTLNC-AHSFCSYCINEWMKRKIECPI 92
Query: 65 CQGEFQLITCVPVYD 79
C+ + + T V D
Sbjct: 93 CRKDIKSKTYSLVLD 107
>pdb|4EPO|C Chain C, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|G Chain G, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|H Chain H, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|K Chain K, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|L Chain L, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
Length = 149
Score = 36.2 bits (82), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 5 LEEQTFQVDNTENDLLNFECGRCGICMDVVIDRGVLDCCQHWFCFACIDNWSTITNLCPL 64
++ Q +V + ND+L E +C IC + I+ L+C H FC CI+ W CP+
Sbjct: 46 MQAQKEEVLSHMNDVLENE-LQCIICSEYFIEAVTLNC-AHSFCSYCINEWMKRKIECPI 103
Query: 65 CQGEFQLITCVPVYD 79
C+ + + T V D
Sbjct: 104 CRKDIKSKTYSLVLD 118
>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 = 35.8 bits (81), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 145 IACDSCDLWYHAFCVG-FDPEGTCEDTWLCPRC 176
I CD C WYH CVG E D ++CP+C
Sbjct: 24 IGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 56
>pdb|3ZVZ|B Chain B, Phd Finger Of Human Uhrf1
Length = 57
Score = 35.8 bits (81), Expect = 0.14, Method: Composition-based stats.
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 5/38 (13%)
Query: 142 DTSIACDSCDLWYHAFCVGFDPEGT---CEDTWLCPRC 176
D + CD CD+ +H +C+ DP + ED W CP C
Sbjct: 18 DKQLMCDECDMAFHIYCL--DPPLSSVPSEDEWYCPEC 53
>pdb|3KQI|A Chain A, Crystal Structure Of Phf2 Phd Domain Complexed With
H3k4me3 Peptide
Length = 75
Score = 35.4 bits (80), Expect = 0.19, Method: Composition-based stats.
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 145 IACDSCDLWYHAFCVGFDPEGTCE-DTWLCPRC 176
I CD+C W+H CVG + E + D + CP C
Sbjct: 26 IECDACKDWFHGSCVGVEEEEAPDIDIYHCPNC 58
>pdb|2L5U|A Chain A, Structure Of The First Phd Finger (Phd1) From Chd4 (Mi2b)
Length = 61
Score = 35.0 bits (79), Expect = 0.28, Method: Composition-based stats.
Identities = 15/35 (42%), Positives = 17/35 (48%)
Query: 145 IACDSCDLWYHAFCVGFDPEGTCEDTWLCPRCVAE 179
I CD+C YH C+ D E E W CP C E
Sbjct: 24 ILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE 58
>pdb|2Y43|A Chain A, Rad18 Ubiquitin Ligase Ring Domain Structure
pdb|2Y43|B Chain B, Rad18 Ubiquitin Ligase Ring Domain Structure
Length = 99
Score = 35.0 bits (79), Expect = 0.29, Method: Composition-based stats.
Identities = 28/101 (27%), Positives = 43/101 (42%), Gaps = 16/101 (15%)
Query: 1 MESMLEEQ---TFQVDNTENDLLNFECGRCGICMDVVIDRGVLDCCQHWFCFACIDNWST 57
M+S+ E + V T +DLL RCGIC + ++ C H +C CI + +
Sbjct: 1 MDSLAESRWPPGLAVMKTIDDLL-----RCGICFEYFNIAMIIPQCSHNYCSLCIRKFLS 55
Query: 58 ITNLCPLCQGEFQLITCVPVYDTIGSNNIDGDSLSRGEDWS 98
CP C CV V + NN D L + +++
Sbjct: 56 YKTQCPTC--------CVTVTEPDLKNNRILDELVKSLNFA 88
>pdb|3ASK|A Chain A, Structure Of Uhrf1 In Complex With Histone Tail
pdb|3ASK|B Chain B, Structure Of Uhrf1 In Complex With Histone Tail
pdb|3ASK|C Chain C, Structure Of Uhrf1 In Complex With Histone Tail
pdb|3ASK|D Chain D, Structure Of Uhrf1 In Complex With Histone Tail
Length = 226
Score = 34.7 bits (78), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 5/38 (13%)
Query: 142 DTSIACDSCDLWYHAFCVGFDPEGT---CEDTWLCPRC 176
D + CD CD+ +H +C+ DP + ED W CP C
Sbjct: 187 DKQLMCDECDMAFHIYCL--DPPLSSVPSEDEWYCPEC 222
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 34.7 bits (78), Expect = 0.36, Method: Composition-based stats.
Identities = 15/39 (38%), Positives = 19/39 (48%)
Query: 27 CGICMDVVIDRGVLDCCQHWFCFACIDNWSTITNLCPLC 65
C IC +ID + C H FC +CI +N CP C
Sbjct: 18 CSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKC 56
>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 = 34.7 bits (78), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 5/38 (13%)
Query: 142 DTSIACDSCDLWYHAFCVGFDPEGT---CEDTWLCPRC 176
D + CD CD+ +H +C+ DP + ED W CP C
Sbjct: 203 DKQLMCDECDMAFHIYCL--DPPLSSVPSEDEWYCPEC 238
>pdb|3KV4|A Chain A, Structure Of Phf8 In Complex With Histone H3
Length = 447
Score = 34.7 bits (78), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 145 IACDSCDLWYHAFCVGFDPEGTCE-DTWLCPRCVAEVPQNSSI 186
I CD C W+H CVG + E + D + CP C EV SI
Sbjct: 21 IECDMCQDWFHGSCVGVEEEKAADIDLYHCPNC--EVLHGPSI 61
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 34.3 bits (77), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 27 CGICMDVVIDRGVLDCCQHWFCFACIDNWSTITNLCPLCQ 66
C ICMD D ++ C H FC CID WS CP+C+
Sbjct: 18 CCICMDGRAD--LILPCAHSFCQKCIDKWSDRHRNCPICR 55
>pdb|1WEP|A Chain A, Solution Structure Of Phd Domain In Phf8
Length = 79
Score = 34.3 bits (77), Expect = 0.50, Method: Composition-based stats.
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 145 IACDSCDLWYHAFCVGFDPEGTCE-DTWLCPRCVA 178
I C C W+H CVG + E + D + CP C A
Sbjct: 28 IECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEA 62
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 33.5 bits (75), Expect = 0.67, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 26/63 (41%), Gaps = 14/63 (22%)
Query: 21 NFECGRCGICMDVVIDRGVL--------DC------CQHWFCFACIDNWSTITNLCPLCQ 66
+ EC C IC V+D + DC C H F C+ W N CPLCQ
Sbjct: 12 DVECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71
Query: 67 GEF 69
++
Sbjct: 72 QDW 74
>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 = 33.5 bits (75), Expect = 0.74, Method: Composition-based stats.
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 145 IACDS-CDLWYHAFCVGFDPEGTCEDTWLCPRC 176
+ CD CD W+H CVG PE + ++C C
Sbjct: 19 VQCDGGCDEWFHQVCVGVSPEMAENEDYICINC 51
>pdb|1WEE|A Chain A, Solution Structure Of Phd Domain In Phd Finger Family
Protein
Length = 72
Score = 33.5 bits (75), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 145 IACDSCDLWYHAFCVGFDPEGTCEDTWLCPRCV 177
+ACD C +W+H C+G + +LC RC+
Sbjct: 32 LACDGCGVWHHTRCIGINNADALPSKFLCFRCI 64
>pdb|3IZS|P Chain P, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|O Chain O, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|O Chain O, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|N Chain N, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|N Chain N, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|N Chain N, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 204
Score = 33.5 bits (75), Expect = 0.85, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 6/75 (8%)
Query: 559 LFDPKLLAAFRAAIAGPKCEPVKQPAHLAVKVKKSMLEKGKVRESLTK-KIYGNSNGRRR 617
L DP+ A R A C+PV + + + + GK + K + N+ RR
Sbjct: 134 LVDPQHKAIRRDARYNWICDPVHKH-----REARGLTATGKKSRGINKGHKFNNTKAGRR 188
Query: 618 RAWNRDCEVEFWKYR 632
+ W R + W+YR
Sbjct: 189 KTWKRQNTLSLWRYR 203
>pdb|1S1I|L Chain L, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
Yeast Obtained By Docking Atomic Models For Rna And
Protein Components Into A 11.7 A Cryo-Em Map. This File,
1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is
In File 1s1h
Length = 203
Score = 33.1 bits (74), Expect = 0.87, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 6/75 (8%)
Query: 559 LFDPKLLAAFRAAIAGPKCEPVKQPAHLAVKVKKSMLEKGKVRESLTK-KIYGNSNGRRR 617
L DP+ A R A C+PV + + + + GK + K + N+ RR
Sbjct: 133 LVDPQHKAIRRDARYNWICDPVHKH-----REARGLTATGKKSRGINKGHKFNNTKAGRR 187
Query: 618 RAWNRDCEVEFWKYR 632
+ W R + W+YR
Sbjct: 188 KTWKRQNTLSLWRYR 202
>pdb|3LRQ|A Chain A, Crystal Structure Of The U-Box Domain Of Human
Ubiquitin- Protein Ligase (E3), Northeast Structural
Genomics Consortium Target Hr4604d.
pdb|3LRQ|B Chain B, Crystal Structure Of The U-Box Domain Of Human
Ubiquitin- Protein Ligase (E3), Northeast Structural
Genomics Consortium Target Hr4604d.
pdb|3LRQ|C Chain C, Crystal Structure Of The U-Box Domain Of Human
Ubiquitin- Protein Ligase (E3), Northeast Structural
Genomics Consortium Target Hr4604d.
pdb|3LRQ|D Chain D, Crystal Structure Of The U-Box Domain Of Human
Ubiquitin- Protein Ligase (E3), Northeast Structural
Genomics Consortium Target Hr4604d
Length = 100
Score = 33.1 bits (74), Expect = 0.94, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 23 ECGRCGICMDVVIDRGVLDCCQHWFCFACIDNWSTITNL-CPLCQGEFQL 71
E RC IC + + D + C CF+CI W T CP C+ QL
Sbjct: 21 EVFRCFICXEKLRDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQL 70
>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 = 32.7 bits (73), Expect = 1.3, Method: Composition-based stats.
Identities = 17/40 (42%), Positives = 19/40 (47%), Gaps = 9/40 (22%)
Query: 145 IACDSCDL---WYHAFCVGF--DPEGTCEDTWLCPRCVAE 179
I CD+ D W+H CVG P G W CPRC E
Sbjct: 19 IGCDNPDCSIEWFHFACVGLTTKPRGK----WFCPRCSQE 54
>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 = 32.7 bits (73), Expect = 1.4, Method: Composition-based stats.
Identities = 17/40 (42%), Positives = 19/40 (47%), Gaps = 9/40 (22%)
Query: 145 IACDSCDL---WYHAFCVGF--DPEGTCEDTWLCPRCVAE 179
I CD+ D W+H CVG P G W CPRC E
Sbjct: 24 IGCDNPDCSIEWFHFACVGLTTKPRGK----WFCPRCSQE 59
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 32.3 bits (72), Expect = 1.5, Method: Composition-based stats.
Identities = 13/39 (33%), Positives = 18/39 (46%)
Query: 27 CGICMDVVIDRGVLDCCQHWFCFACIDNWSTITNLCPLC 65
C +C ID + C H FC CI + + CP+C
Sbjct: 14 CVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPIC 52
>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 = 32.3 bits (72), Expect = 1.5, Method: Composition-based stats.
Identities = 17/40 (42%), Positives = 20/40 (50%), Gaps = 9/40 (22%)
Query: 145 IACDSCDL---WYHAFCVGF--DPEGTCEDTWLCPRCVAE 179
I CD+ D W+H CV P+G W CPRCV E
Sbjct: 23 IGCDNPDCPIEWFHFACVDLTTKPKGK----WFCPRCVQE 58
>pdb|2E6R|A Chain A, Solution Structure Of The Phd Domain In Smcy Protein
Length = 92
Score = 32.3 bits (72), Expect = 1.5, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 29/64 (45%), Gaps = 4/64 (6%)
Query: 142 DTSIACDSCDLWYHAFCVGFDPEGTCEDTWLCPRCV-AEVPQ-NSSIDLTQSTNDQ--SG 197
D + CD CD YH FC+ W CP+C+ AE Q + Q+T + SG
Sbjct: 29 DKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILAECKQPPEAFGFEQATQEYSLSG 88
Query: 198 PENA 201
P +
Sbjct: 89 PSSG 92
>pdb|1WEU|A Chain A, Solution Structure Of Phd Domain In Ing1-Like Protein
Bac25009
Length = 91
Score = 32.3 bits (72), Expect = 1.6, Method: Composition-based stats.
Identities = 17/40 (42%), Positives = 19/40 (47%), Gaps = 9/40 (22%)
Query: 145 IACDSCDL---WYHAFCVGF--DPEGTCEDTWLCPRCVAE 179
I CD+ D W+H CVG P G W CPRC E
Sbjct: 50 IGCDNPDCSIEWFHFACVGLTTKPRGK----WFCPRCSQE 85
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 32.3 bits (72), Expect = 1.8, Method: Composition-based stats.
Identities = 13/39 (33%), Positives = 18/39 (46%)
Query: 27 CGICMDVVIDRGVLDCCQHWFCFACIDNWSTITNLCPLC 65
C +C ID + C H FC CI + + CP+C
Sbjct: 18 CVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPIC 56
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 32.3 bits (72), Expect = 1.8, Method: Composition-based stats.
Identities = 13/39 (33%), Positives = 18/39 (46%)
Query: 27 CGICMDVVIDRGVLDCCQHWFCFACIDNWSTITNLCPLC 65
C +C ID + C H FC CI + + CP+C
Sbjct: 18 CVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPIC 56
>pdb|2K1J|A Chain A, Plan Homeodomain Finger Of Tumour Supressor Ing4
Length = 63
Score = 32.3 bits (72), Expect = 1.9, Method: Composition-based stats.
Identities = 17/40 (42%), Positives = 19/40 (47%), Gaps = 9/40 (22%)
Query: 145 IACDSCDL---WYHAFCVGF--DPEGTCEDTWLCPRCVAE 179
I CD+ D W+H CVG P G W CPRC E
Sbjct: 24 IGCDNPDCSIEWFHFACVGLTTKPRGK----WFCPRCSQE 59
>pdb|2M1R|A Chain A, Phd Domain Of Ing4 N214d Mutant
Length = 63
Score = 31.6 bits (70), Expect = 2.5, Method: Composition-based stats.
Identities = 17/40 (42%), Positives = 18/40 (45%), Gaps = 9/40 (22%)
Query: 145 IACDSCDL---WYHAFCVGF--DPEGTCEDTWLCPRCVAE 179
I CD D W+H CVG P G W CPRC E
Sbjct: 24 IGCDDPDCSIEWFHFACVGLTTKPRGK----WFCPRCSQE 59
>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 = 31.6 bits (70), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 145 IACDSCDLWYHAFCVGFDPEGTCE-DTWLCPRC 176
I CD C W+H CVG + + D + CP C
Sbjct: 53 IECDICKDWFHGSCVGVEEHHAVDIDLYHCPNC 85
>pdb|1WEM|A Chain A, Solution Structure Of Phd Domain In Death Inducer-
Obliterator 1(Dio-1)
Length = 76
Score = 31.6 bits (70), Expect = 3.0, Method: Composition-based stats.
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 7/38 (18%)
Query: 145 IACDSCDLWYHAFCVGFDP------EGTCEDTWLCPRC 176
I CD C+ W+H CVG E ED ++CP C
Sbjct: 31 ICCDRCEEWFHGDCVGISEARGRLLERNGED-YICPNC 67
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 31.6 bits (70), Expect = 3.0, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 8/66 (12%)
Query: 27 CGICMD---VVIDRGVLDC---CQHWFCFACIDNWSTITNLCPLCQGEFQLITCVPVYDT 80
C ICMD ++ G L C H FC C+ + N CP C+ + P+Y
Sbjct: 10 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIY-- 67
Query: 81 IGSNNI 86
IGS +
Sbjct: 68 IGSGTV 73
Score = 30.4 bits (67), Expect = 7.0, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 6/58 (10%)
Query: 27 CGICMD---VVIDRGVLDC---CQHWFCFACIDNWSTITNLCPLCQGEFQLITCVPVY 78
C ICMD ++ G L C H FC C+ + N CP C+ + P+Y
Sbjct: 75 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIY 132
>pdb|1X4I|A Chain A, Solution Structure Of Phd Domain In Inhibitor Of Growth
Protein 3 (Ing3)
Length = 70
Score = 31.6 bits (70), Expect = 3.1, Method: Composition-based stats.
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 9/46 (19%)
Query: 145 IACDSCDL---WYHAFCVGFD--PEGTCEDTWLCPRCVAEVPQNSS 185
+ CD+ D W+H CVG P+G W CP+C A + + S
Sbjct: 20 VGCDNQDCPIEWFHYGCVGLTEAPKGK----WYCPQCTAAMKRRGS 61
>pdb|1F2N|A Chain A, Rice Yellow Mottle Virus
pdb|1F2N|B Chain B, Rice Yellow Mottle Virus
pdb|1F2N|C Chain C, Rice Yellow Mottle Virus
Length = 238
Score = 30.8 bits (68), Expect = 4.6, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 6/59 (10%)
Query: 1080 RSSTTEDGTSKPCIPLESLPCEEGEDLSLAECEELYGPDKEPLVSKFPEVSQKPCGLLD 1138
RSST+ D T+ C+P +LP SLA C ++ P + +V PEVS G ++
Sbjct: 68 RSSTSADATTYDCVPF-NLP----RVWSLARCYSMWKPTRWDVVY-LPEVSATVAGSIE 120
>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 = 30.8 bits (68), Expect = 4.9, Method: Composition-based stats.
Identities = 12/32 (37%), Positives = 15/32 (46%)
Query: 145 IACDSCDLWYHAFCVGFDPEGTCEDTWLCPRC 176
+ CD+C YH C+ WLCPRC
Sbjct: 22 LCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRC 53
>pdb|2PUY|A Chain A, Crystal Structure Of The Bhc80 Phd Finger
pdb|2PUY|B Chain B, Crystal Structure Of The Bhc80 Phd Finger
Length = 60
Score = 30.4 bits (67), Expect = 5.6, Method: Composition-based stats.
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 145 IACDSCDLWYHAFCVGFDPEGTCEDTWLCPRC 176
+ CD+C YH C+ + + W+CPRC
Sbjct: 18 LMCDTCSRVYHLDCLDPPLKTIPKGMWICPRC 49
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 30.4 bits (67), Expect = 6.6, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 6/58 (10%)
Query: 27 CGICMD---VVIDRGVLDC---CQHWFCFACIDNWSTITNLCPLCQGEFQLITCVPVY 78
C ICMD ++ G L C H FC C+ + N CP C+ + P+Y
Sbjct: 6 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIY 63
>pdb|1WE9|A Chain A, Solution Structure Of Phd Domain In Nucleic Acid Binding
Protein-like Np_197993
Length = 64
Score = 30.4 bits (67), Expect = 7.0, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 145 IACDSCDLWYHAFCVGFDPEGTCE-DTWLCPRC 176
I CD C++W+H CV P + CP C
Sbjct: 23 ICCDLCEMWFHGKCVKITPARAEHIKQYKCPSC 55
>pdb|3NG2|A Chain A, Crystal Structure Of The Rnf4 Ring Domain Dimer
pdb|3NG2|B Chain B, Crystal Structure Of The Rnf4 Ring Domain Dimer
Length = 71
Score = 30.0 bits (66), Expect = 7.3, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 6/58 (10%)
Query: 27 CGICMD---VVIDRGVLDC---CQHWFCFACIDNWSTITNLCPLCQGEFQLITCVPVY 78
C ICMD ++ G L C H FC C+ + N CP C+ + P+Y
Sbjct: 13 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIY 70
>pdb|2YQL|A Chain A, Solution Structure Of The Phd Domain In Phd Finger Protein
21a
Length = 56
Score = 30.0 bits (66), Expect = 7.3, Method: Composition-based stats.
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 145 IACDSCDLWYHAFCVGFDPEGTCEDTWLCPRC 176
+ CD+C YH C+ + + W+CPRC
Sbjct: 22 LMCDTCSRVYHLDCLDPPLKTIPKGMWICPRC 53
>pdb|3SHB|A Chain A, Crystal Structure Of Phd Domain Of Uhrf1
Length = 77
Score = 30.0 bits (66), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 5/38 (13%)
Query: 142 DTSIACDSCDLWYHAFCVGFDPEGT---CEDTWLCPRC 176
D + CD CD+ +H +C+ DP + ED W CP C
Sbjct: 39 DKQLMCDECDMAFHIYCL--DPPLSSVPSEDEWYCPEC 74
>pdb|3ZVY|A Chain A, Phd Finger Of Human Uhrf1 In Complex With Unmodified
Histone H3 N-Terminal Tail
pdb|3ZVY|B Chain B, Phd Finger Of Human Uhrf1 In Complex With Unmodified
Histone H3 N-Terminal Tail
Length = 72
Score = 30.0 bits (66), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 5/38 (13%)
Query: 142 DTSIACDSCDLWYHAFCVGFDPEGT---CEDTWLCPRC 176
D + CD CD+ +H +C+ DP + ED W CP C
Sbjct: 33 DKQLMCDECDMAFHIYCL--DPPLSSVPSEDEWYCPEC 68
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
0.311 0.128 0.369
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 34,964,270
Number of Sequences: 62578
Number of extensions: 1440279
Number of successful extensions: 2931
Number of sequences better than 100.0: 83
Number of HSP's better than 100.0 without gapping: 37
Number of HSP's successfully gapped in prelim test: 46
Number of HSP's that attempted gapping in prelim test: 2873
Number of HSP's gapped (non-prelim): 103
length of query: 1225
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1115
effective length of database: 8,089,757
effective search space: 9020079055
effective search space used: 9020079055
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 57 (26.6 bits)