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= 043177
(113 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 72.0 bits (175), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 31/48 (64%), Positives = 38/48 (79%), Gaps = 1/48 (2%)
Query: 31 EDGI-CAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPICR 77
+DG+ CAVCL+E E+GEE R LP C H +HA C+DMWL SHS CP+CR
Sbjct: 3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 50
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 62.4 bits (150), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 27/68 (39%), Positives = 43/68 (63%), Gaps = 3/68 (4%)
Query: 16 IPAHKYHKGTGPVGDEDGICAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPI 75
+P+++++ E +C VC+ +FE + LR LP C H +HA C+D WL ++ CPI
Sbjct: 9 LPSYRFNPNNHQ--SEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPI 65
Query: 76 CRSDATPS 83
CR+D+ PS
Sbjct: 66 CRADSGPS 73
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 59.7 bits (143), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 24/45 (53%), Positives = 32/45 (71%), Gaps = 1/45 (2%)
Query: 35 CAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPICRSD 79
C +CLS EEGE++R LP C+H +H C+D WL ++ CPICR D
Sbjct: 17 CTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVD 60
>pdb|2L0B|A Chain A, Solution Nmr Structure Of Zinc Finger Domain Of E3
Ubiquitin-Protein Ligase Praja-1 From Homo Sapiens,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4710b
Length = 91
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 26 GPVGDEDGICAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPICRSDATP 82
G VG E C +C SE+ +G+ LP C H +H PC+ +WL CP+CR P
Sbjct: 35 GAVGQE-MCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRCMFPP 89
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 35 CAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPICRSDAT 81
C VC ++ GE +R LP C H +H CI WL H +CP+CR T
Sbjct: 18 CPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLT 63
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 34 ICAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPICRSDATPSPQILRP 89
+CAVCL +F+ +EL P C H++H C+ WL CP+C Q+ P
Sbjct: 17 LCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLSGP 71
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 30/61 (49%), Gaps = 11/61 (18%)
Query: 35 CAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPICRSDATPSPQILRPRDSAG 94
C +C+ +G LP C HS+ CID W H NCPICR Q+ +S+G
Sbjct: 18 CCICM----DGRADLILP-CAHSFCQKCIDKWSDRHRNCPICR------LQMTGANESSG 66
Query: 95 P 95
P
Sbjct: 67 P 67
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 34 ICAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPICRSDATPSPQILRPRDSA 93
+C +C F + T+ ECLHS+ CI +L + CPIC + +L R
Sbjct: 13 MCVLCGGYFIDAT---TIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDK 69
Query: 94 GPEDMAAGMV 103
+D+ +V
Sbjct: 70 TLQDIVYKLV 79
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 34 ICAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPICRSDATPSPQILRPRDSA 93
+C +C F + T+ ECLHS+ CI +L + CPIC + +L R
Sbjct: 17 MCVLCGGYFIDAT---TIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDK 73
Query: 94 GPEDMAAGMV 103
+D+ +V
Sbjct: 74 TLQDIVYKLV 83
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 34 ICAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPICRSDATPSPQILRPRDSA 93
+C +C F + T+ ECLHS+ CI +L + CPIC + +L R
Sbjct: 17 MCVLCGGYFIDAT---TIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDK 73
Query: 94 GPEDMAAGMV 103
+D+ +V
Sbjct: 74 TLQDIVYKLV 83
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 27/45 (60%)
Query: 35 CAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPICRSD 79
C C +E ++ + + EC HS+H C+ +W+ ++ CP+C+ D
Sbjct: 29 CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQD 73
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 35 CAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPICRSD 79
C +C F E L C HS+ + CI+ W+ CPICR D
Sbjct: 56 CIICSEYFIEAVTLN----CAHSFCSYCINEWMKRKIECPICRKD 96
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 35 CAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPICRSD 79
C +C F E L C HS+ + CI+ W+ CPICR D
Sbjct: 56 CIICSEYFIEAVTLN----CAHSFCSYCINEWMKRKIECPICRKD 96
>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 = 0.005, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 35 CAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPICRSD 79
C +C F E L C HS+ + CI+ W+ CPICR D
Sbjct: 67 CIICSEYFIEAVTLN----CAHSFCSYCINEWMKRKIECPICRKD 107
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 27/57 (47%), Gaps = 5/57 (8%)
Query: 34 ICAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYS-HSNCPICRSDATPSPQILRP 89
+C +CL + T ECLH + A CI L S + CP CR S + LRP
Sbjct: 56 MCPICLDMLKNT---MTTKECLHRFCADCIITALRSGNKECPTCRKKLV-SKRSLRP 108
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 27/57 (47%), Gaps = 5/57 (8%)
Query: 34 ICAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYS-HSNCPICRSDATPSPQILRP 89
+C +CL + T ECLH + A CI L S + CP CR S + LRP
Sbjct: 55 MCPICLDMLKNT---MTTKECLHRFCADCIITALRSGNKECPTCRKKLV-SKRSLRP 107
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 30.4 bits (67), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 27/57 (47%), Gaps = 5/57 (8%)
Query: 34 ICAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYS-HSNCPICRSDATPSPQILRP 89
+C +CL + T ECLH + A CI L S + CP CR S + LRP
Sbjct: 36 MCPICLDMLKNT---MTTKECLHRFCADCIITALRSGNKECPTCRKKLV-SKRSLRP 88
>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 = 29.6 bits (65), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 3/42 (7%)
Query: 35 CAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPIC 76
C +C FE +P+C H+Y + CI +L + CP C
Sbjct: 25 CGIC---FEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTC 63
>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 = 28.5 bits (62), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 35 CAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPICR 77
C +CL E+ CLH++ CI W+ + CP+C+
Sbjct: 8 CPICL---EDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCK 47
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 34 ICAVCLSEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPIC 76
+C++C + T+ ECLH++ CI Y + CP C
Sbjct: 17 LCSICKGYLIDAT---TITECLHTFCKSCIVRHFYYSNRCPKC 56
>pdb|2CT2|A Chain A, Solution Structure Of The Ring Domain Of The Tripartite
Motif Protein 32
Length = 88
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 10/61 (16%)
Query: 25 TGPVGDEDGI-----CAVCLSEFEEGEELR-TLPECLHSYHAPCIDMWLYSHSN---CPI 75
+G G+ D + C +C+ F E E+LR L C H+ C++ L S N CP
Sbjct: 3 SGSSGNLDALREVLECPICMESFTE-EQLRPKLLHCGHTICRQCLEKLLASSINGVRCPF 61
Query: 76 C 76
C
Sbjct: 62 C 62
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 54 CLHSYHAPCIDMWLYSHSNCPI 75
C H++H CI WL + CP+
Sbjct: 84 CNHAFHFHCISRWLKTRQVCPL 105
>pdb|3QZV|A Chain A, Crystal Structure Of Bptf Phd-Linker-Bromo In Complex
With Histone H4k12ac Peptide
Length = 174
Score = 26.9 bits (58), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 7/76 (9%)
Query: 26 GPVGDEDGICAVCLSEFEEGEELRTLPECLHSYHAPCIDMW-----LYSHSNCPICRS-- 78
GP+G + + +C + ++E + C + YH C+ + L CP C+S
Sbjct: 1 GPLGSDTKLYCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTE 60
Query: 79 DATPSPQILRPRDSAG 94
DA L +D G
Sbjct: 61 DAMTVLTPLTEKDYEG 76
>pdb|2HPI|A Chain A, Eubacterial And Eukaryotic Replicative Dna Polymerases Are
Not Homologous: X-Ray Structure Of Dna Polymerase Iii
pdb|2HPM|A Chain A, Eubacterial And Eukaryotic Replicative Dna Polymerases Are
Not Homologous: X-ray Structure Of Dna Polymerase Iii
Length = 1220
Score = 26.9 bits (58), Expect = 2.5, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 7 SIENSMAQLIPAHKYHKGTGPVGDEDGICAVCLSEFEEGEELRTLPECL 55
S E +++ + ++G P ED I + L+E E+GEELR L + +
Sbjct: 1071 SDETGALEVVVFGRAYEGVSPKLKED-IPLLVLAEVEKGEELRVLAQAV 1118
>pdb|3E0D|A Chain A, Insights Into The Replisome From The Crystral Structure Of
The Ternary Complex Of The Eubacterial Dna Polymerase Iii
Alpha-Subunit
pdb|3E0D|B Chain B, Insights Into The Replisome From The Crystral Structure Of
The Ternary Complex Of The Eubacterial Dna Polymerase Iii
Alpha-Subunit
Length = 1220
Score = 26.9 bits (58), Expect = 2.6, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 7 SIENSMAQLIPAHKYHKGTGPVGDEDGICAVCLSEFEEGEELRTLPECL 55
S E +++ + ++G P ED I + L+E E+GEELR L + +
Sbjct: 1071 SDETGALEVVVFGRAYEGVSPKLKED-IPLLVLAEVEKGEELRVLAQAV 1118
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 3/57 (5%)
Query: 26 GPVGDEDGICAVCL---SEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPICRSD 79
G +G C +C+ SE + L EC H + + C+ L + + CP CR
Sbjct: 1 GAMGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKK 57
Score = 26.2 bits (56), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 8/64 (12%)
Query: 19 HKYHKGTGPVGDEDGICAVCL---SEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPI 75
H + G+G V C +C+ SE + L EC H + + C+ L + + CP
Sbjct: 64 HPIYIGSGTVS-----CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPT 118
Query: 76 CRSD 79
CR
Sbjct: 119 CRKK 122
>pdb|1U6G|B Chain B, Crystal Structure Of The Cand1-Cul1-Roc1 Complex
pdb|2HYE|D Chain D, Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Complex
Length = 108
Score = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 54 CLHSYHAPCIDMWLYSHSNCPI 75
C H++H CI WL + CP+
Sbjct: 75 CNHAFHFHCISRWLKTRQVCPL 96
>pdb|3DPL|R Chain R, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation.
pdb|3RTR|B Chain B, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|D Chain D, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|F Chain F, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|H Chain H, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|4F52|B Chain B, Structure Of A Glomulin-Rbx1-Cul1 Complex
pdb|4F52|D Chain D, Structure Of A Glomulin-Rbx1-Cul1 Complex
Length = 106
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 54 CLHSYHAPCIDMWLYSHSNCPI 75
C H++H CI WL + CP+
Sbjct: 73 CNHAFHFHCISRWLKTRQVCPL 94
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 54 CLHSYHAPCIDMWLYSHSNCPI 75
C H++H CI WL + CP+
Sbjct: 67 CNHAFHFHCISRWLKTRQVCPL 88
>pdb|3DQV|R Chain R, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation
pdb|3DQV|Y Chain Y, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation
Length = 106
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 54 CLHSYHAPCIDMWLYSHSNCPI 75
C H++H CI WL + CP+
Sbjct: 73 CNHAFHFHCISRWLKTRQVCPL 94
>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 = 26.9 bits (58), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 7/76 (9%)
Query: 26 GPVGDEDGICAVCLSEFEEGEELRTLPECLHSYHAPCIDMW-----LYSHSNCPICRS-- 78
GP+G + + +C + ++E + C + YH C+ + L CP C+S
Sbjct: 1 GPLGSDTKLYCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTE 60
Query: 79 DATPSPQILRPRDSAG 94
DA L +D G
Sbjct: 61 DAXTVLTPLTEKDYEG 76
>pdb|4A0C|D Chain D, Structure Of The Cand1-Cul4b-Rbx1 Complex
pdb|4A0C|F Chain F, Structure Of The Cand1-Cul4b-Rbx1 Complex
pdb|4A0L|F Chain F, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp
Abasic Site Containing Dna-Duplex
pdb|4A0L|I Chain I, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp
Abasic Site Containing Dna-Duplex
Length = 98
Score = 26.9 bits (58), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 54 CLHSYHAPCIDMWLYSHSNCPI 75
C H++H CI WL + CP+
Sbjct: 65 CNHAFHFHCISRWLKTRQVCPL 86
>pdb|1LDJ|B Chain B, Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiquitin
Ligase Complex
pdb|1LDK|C Chain C, Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin
Ligase Complex
Length = 90
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 54 CLHSYHAPCIDMWLYSHSNCPI 75
C H++H CI WL + CP+
Sbjct: 57 CNHAFHFHCISRWLKTRQVCPL 78
>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 = 25.8 bits (55), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 35 CAVCL---SEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPICRSD 79
C +C+ SE + L EC H + + C+ L + + CP CR
Sbjct: 13 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKK 60
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 35 CAVCL---SEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPICR 77
C +C+ SE + L EC H + + C+ L + + CP CR
Sbjct: 18 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 63
>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 = 25.4 bits (54), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 26 GPVGDEDGICAVCLSEFEEGEELRTLPECLHSYHAPCIDMW-----LYSHSNCPICRS 78
GP+G + + +C + ++E + C + YH C+ + L CP C+S
Sbjct: 1 GPLGSDTKLYCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQS 58
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 25.4 bits (54), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 35 CAVCL---SEFEEGEELRTLPECLHSYHAPCIDMWLYSHSNCPICRSD 79
C +C+ SE + L EC H + + C+ L + + CP CR
Sbjct: 6 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKK 53
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
0.317 0.132 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,657,790
Number of Sequences: 62578
Number of extensions: 145563
Number of successful extensions: 339
Number of sequences better than 100.0: 52
Number of HSP's better than 100.0 without gapping: 35
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 296
Number of HSP's gapped (non-prelim): 54
length of query: 113
length of database: 14,973,337
effective HSP length: 77
effective length of query: 36
effective length of database: 10,154,831
effective search space: 365573916
effective search space used: 365573916
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: 45 (21.9 bits)