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= psy14827
(220 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 67.0 bits (162), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 31/82 (37%), Positives = 45/82 (54%), Gaps = 8/82 (9%)
Query: 144 WTGVATWRWVANDDTCGICRIAFEGCCSDCKL-----PGDDCPLVWGQCSHCFHIHCIMK 198
W VA W W D C ICR C +C+ ++C + WG C+H FH HCI +
Sbjct: 27 WNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISR 86
Query: 199 WLNSQQVHHQCPMCRQEWKFKE 220
WL ++QV CP+ +EW+F++
Sbjct: 87 WLKTRQV---CPLDNREWEFQK 105
>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 = 66.6 bits (161), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 31/82 (37%), Positives = 45/82 (54%), Gaps = 8/82 (9%)
Query: 144 WTGVATWRWVANDDTCGICRIAFEGCCSDCKL-----PGDDCPLVWGQCSHCFHIHCIMK 198
W VA W W D C ICR C +C+ ++C + WG C+H FH HCI +
Sbjct: 25 WNAVALWAWDIVVDNCAICRNHIXDLCIECQANQASATSEECTVAWGVCNHAFHFHCISR 84
Query: 199 WLNSQQVHHQCPMCRQEWKFKE 220
WL ++QV CP+ +EW+F++
Sbjct: 85 WLKTRQV---CPLDNREWEFQK 103
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 66.6 bits (161), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 31/82 (37%), Positives = 45/82 (54%), Gaps = 8/82 (9%)
Query: 144 WTGVATWRWVANDDTCGICRIAFEGCCSDCKL-----PGDDCPLVWGQCSHCFHIHCIMK 198
W VA W W D C ICR C +C+ ++C + WG C+H FH HCI +
Sbjct: 36 WNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISR 95
Query: 199 WLNSQQVHHQCPMCRQEWKFKE 220
WL ++QV CP+ +EW+F++
Sbjct: 96 WLKTRQV---CPLDNREWEFQK 114
>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 = 66.6 bits (161), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 31/82 (37%), Positives = 45/82 (54%), Gaps = 8/82 (9%)
Query: 144 WTGVATWRWVANDDTCGICRIAFEGCCSDCKL-----PGDDCPLVWGQCSHCFHIHCIMK 198
W VA W W D C ICR C +C+ ++C + WG C+H FH HCI +
Sbjct: 25 WNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISR 84
Query: 199 WLNSQQVHHQCPMCRQEWKFKE 220
WL ++QV CP+ +EW+F++
Sbjct: 85 WLKTRQV---CPLDNREWEFQK 103
>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 = 65.9 bits (159), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 31/82 (37%), Positives = 45/82 (54%), Gaps = 8/82 (9%)
Query: 144 WTGVATWRWVANDDTCGICRIAFEGCCSDCKL-----PGDDCPLVWGQCSHCFHIHCIMK 198
W VA W W D C ICR C +C+ ++C + WG C+H FH HCI +
Sbjct: 17 WNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISR 76
Query: 199 WLNSQQVHHQCPMCRQEWKFKE 220
WL ++QV CP+ +EW+F++
Sbjct: 77 WLKTRQV---CPLDNREWEFQK 95
>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 = 65.5 bits (158), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 31/82 (37%), Positives = 45/82 (54%), Gaps = 8/82 (9%)
Query: 144 WTGVATWRWVANDDTCGICRIAFEGCCSDCKL-----PGDDCPLVWGQCSHCFHIHCIMK 198
W VA W W D C ICR C +C+ ++C + WG C+H FH HCI +
Sbjct: 9 WNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISR 68
Query: 199 WLNSQQVHHQCPMCRQEWKFKE 220
WL ++QV CP+ +EW+F++
Sbjct: 69 WLKTRQV---CPLDNREWEFQK 87
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 57.4 bits (137), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 40/69 (57%), Gaps = 8/69 (11%)
Query: 157 DTCGICRIAFEGCCSDCKL-----PGDDCPLVWGQCSHCFHIHCIMKWLNSQQVHHQCPM 211
D C ICR C +C+ ++C + WG C+H FH HCI +WL ++QV CP+
Sbjct: 32 DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQV---CPL 88
Query: 212 CRQEWKFKE 220
+EW+F++
Sbjct: 89 DNREWEFQK 97
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 40/69 (57%), Gaps = 5/69 (7%)
Query: 150 WRWVANDDTCGICRIAFEGCCSDCKLPG--DDCPLVWGQCSHCFHIHCIMKWLNSQQVHH 207
W W DTC ICR+ C C+ +DC +VWG+C+H FH C+ W+ ++
Sbjct: 9 WSWDVECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQ---NN 65
Query: 208 QCPMCRQEW 216
+CP+C+Q+W
Sbjct: 66 RCPLCQQDW 74
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 33.9 bits (76), Expect = 0.074, Method: Composition-based stats.
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 3/28 (10%)
Query: 186 QCSHCFHIHCIMKWLNSQQVHHQCPMCR 213
+C H FH C+ WL S H CP+CR
Sbjct: 26 RCGHGFHAECVDMWLGS---HSTCPLCR 50
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 187 CSHCFHIHCIMKWLNSQQVHHQCPMCRQ 214
C+H FH CI+ WL + H CP+CR+
Sbjct: 36 CNHLFHDSCIVPWL---EQHDSCPVCRK 60
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 31.6 bits (70), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 183 VWGQCSHCFHIHCIMKWLNSQQVHHQCPMCRQE 215
V +C H F C++K LN ++ QCP+C+ +
Sbjct: 35 VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKND 67
>pdb|1V87|A Chain A, Solution Structure Of The Ring-H2 Finger Domain Of Mouse
Deltex Protein 2
Length = 114
Score = 30.4 bits (67), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 153 VANDDTCGIC--RIAFEGCCSDCKLPGDDCPLVWG---QCSHCFHIHCIMKWL--NSQQV 205
VA ++ C IC ++A SD P+V G +CSH FH+ C++ ++
Sbjct: 22 VAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDG 81
Query: 206 HHQCPMCRQEWKFK 219
QCP C+ + K
Sbjct: 82 SLQCPSCKTIYGEK 95
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 3/26 (11%)
Query: 187 CSHCFHIHCIMKWLNSQQVHHQCPMC 212
C H FH C++KWL ++V CP+C
Sbjct: 36 CKHAFHRKCLIKWLEVRKV---CPLC 58
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 3/29 (10%)
Query: 187 CSHCFHIHCIMKWLNSQQVHHQCPMCRQE 215
C+H FH C+ KWL + + CP+CR +
Sbjct: 44 CNHEFHAKCVDKWLKANRT---CPICRAD 69
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 3/37 (8%)
Query: 183 VWGQCSHCFHIHCIMKWLNSQQVHHQCPMCRQEWKFK 219
V C+H F +CI +W+ + +CP+CR++ K K
Sbjct: 67 VTLNCAHSFCSYCINEWMKRK---IECPICRKDIKSK 100
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 3/37 (8%)
Query: 183 VWGQCSHCFHIHCIMKWLNSQQVHHQCPMCRQEWKFK 219
V C+H F +CI +W+ + +CP+CR++ K K
Sbjct: 67 VTLNCAHSFCSYCINEWMKRK---IECPICRKDIKSK 100
>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 = 28.1 bits (61), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 4/62 (6%)
Query: 156 DDTCGICRIAFEGCCSDCKLPGDDCPLVWGQCSHCFHIHCIMKWLNSQQVHHQ--CPMCR 213
DD +CR+ C + P D L+ +C FHI+C+ L+S + CP CR
Sbjct: 182 DDVNRLCRVCACHLCGGRQDP--DKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECR 239
Query: 214 QE 215
+
Sbjct: 240 ND 241
>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 = 28.1 bits (61), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 3/37 (8%)
Query: 183 VWGQCSHCFHIHCIMKWLNSQQVHHQCPMCRQEWKFK 219
V C+H F +CI +W+ + +CP+CR++ K K
Sbjct: 78 VTLNCAHSFCSYCINEWMKRK---IECPICRKDIKSK 111
>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 = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 4/62 (6%)
Query: 156 DDTCGICRIAFEGCCSDCKLPGDDCPLVWGQCSHCFHIHCIMKWLNSQQVHHQ--CPMCR 213
DD +CR+ C + P D L+ +C FHI+C+ L+S + CP CR
Sbjct: 166 DDVNRLCRVCACHLCGGRQDP--DKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECR 223
Query: 214 QE 215
+
Sbjct: 224 ND 225
>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 = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 15/67 (22%)
Query: 146 GVATWRWVANDDTCGICRIAFEGCCSDCKLPGDDCPLVWGQCSHCFHIHCIMKWLNSQQV 205
G+A + + + CGIC F + ++ QCSH + CI K+L+ +
Sbjct: 12 GLAVMKTIDDLLRCGICFEYF------------NIAMIIPQCSHNYCSLCIRKFLSYKT- 58
Query: 206 HHQCPMC 212
QCP C
Sbjct: 59 --QCPTC 63
>pdb|4FMM|A Chain A, Dimeric Sec14 Family Homolog 3 From Saccharomyces
Cerevisiae Presents Some Novel Features Of Structure
That Lead To A Surprising "dimer- Monomer" State Change
Induced By Substrate Binding
pdb|4FMM|B Chain B, Dimeric Sec14 Family Homolog 3 From Saccharomyces
Cerevisiae Presents Some Novel Features Of Structure
That Lead To A Surprising "dimer- Monomer" State Change
Induced By Substrate Binding
Length = 360
Score = 26.9 bits (58), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 67 WTLRSPFNKILDTALQRRAYGL-----ENEEISSSDMTVGESRSPSETEPGWESNPRPSA 121
W L+ ++I T RR +G+ E+ + ++D+ E+ S + G+E++ RP
Sbjct: 99 WVLKDCIDRITMTLAWRREFGISHLGEEHGDKITADLVAVENESGKQVILGYENDARPIL 158
Query: 122 H 122
+
Sbjct: 159 Y 159
>pdb|1FP0|A Chain A, Solution Structure Of The Phd Domain From The Kap-1
Corepressor
Length = 88
Score = 26.9 bits (58), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 10/45 (22%)
Query: 156 DDTCGICRIAFEGCCSDCKLPGDDCPLVWGQCSHCFHIHCIMKWL 200
DD+ ICR+ C+ PGD ++ QC CFH+ C + L
Sbjct: 22 DDSATICRV--------CQKPGD--LVMCNQCEFCFHLDCHLPAL 56
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 0.130 0.432
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,091,864
Number of Sequences: 62578
Number of extensions: 286500
Number of successful extensions: 703
Number of sequences better than 100.0: 38
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 668
Number of HSP's gapped (non-prelim): 44
length of query: 220
length of database: 14,973,337
effective HSP length: 95
effective length of query: 125
effective length of database: 9,028,427
effective search space: 1128553375
effective search space used: 1128553375
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)