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= 025186
(256 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DKT|A Chain A, Solution Structure Of The Chy Zinc Finger Domain Of The
Ring Finger And Chy Zinc Finger Domain-Containing
Protein 1 From Mus Musculus
Length = 143
Score = 105 bits (262), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 52/124 (41%), Positives = 77/124 (62%), Gaps = 5/124 (4%)
Query: 17 GCKHYRRRCRIRAPCCNEIFDCRHCH--NEAASMLRNPYDRHELVR-QDVKQVAQVCTNC 73
GC+HY R C ++APCC++++ CR CH NE + R + + + ++ Q C +C
Sbjct: 18 GCEHYDRACLLKAPCCDKLYTCRLCHDTNEDHQLDRFKVKEVQCINCEKLQHAQQTCEDC 77
Query: 74 GVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLC 133
GEY+C IC +D D K Q+HC+ CGICRIG +E++FHC +C C +T+LR H C
Sbjct: 78 STLFGEYYCSICHLFDKD--KRQYHCESCGICRIGPKEDFFHCLKCNLCLTTNLRGKHKC 135
Query: 134 IENS 137
IE+
Sbjct: 136 IESG 139
>pdb|2K2C|A Chain A, Solution Nmr Structure Of N-Terminal Domain Of Human
Pirh2. Northeast Structural Genomics Consortium (Nesg)
Target Ht2a
Length = 137
Score = 102 bits (253), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 54/139 (38%), Positives = 81/139 (58%), Gaps = 7/139 (5%)
Query: 1 MEGSANERITFG--KMGYGCKHYRRRCRIRAPCCNEIFDCRHCH--NEAASMLRNPYDRH 56
M +A E G + GC+HY R C ++APCC++++ CR CH NE + R
Sbjct: 1 MAATAREDGATGEERGQRGCEHYDRGCLLKAPCCDKLYTCRLCHDNNEDHQLDRFKVKEV 60
Query: 57 ELVR-QDVKQVAQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFH 115
+ + + ++ Q C C GEY+CDIC +D D K Q+HC++CGICRIG +E++FH
Sbjct: 61 QCINCEKIQHAQQTCEECSTLFGEYYCDICHLFDKD--KKQYHCENCGICRIGPKEDFFH 118
Query: 116 CKRCGSCYSTSLRNNHLCI 134
C +C C + +L+ H CI
Sbjct: 119 CLKCNLCLAMNLQGRHKCI 137
>pdb|2K2D|A Chain A, Solution Nmr Structure Of C-Terminal Domain Of Human
Pirh2. Northeast Structural Genomics Consortium (Nesg)
Target Ht2c
Length = 79
Score = 74.3 bits (181), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 31/60 (51%), Positives = 44/60 (73%)
Query: 187 SVIDMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNT 246
S +DM+R W+++D+E+ T MP +Y++ V ILCNDCN + V FHI+G KC C+SYNT
Sbjct: 7 SALDMTRYWRQLDDEVAQTPMPSEYQNMTVDILCNDCNGRSTVQFHILGMKCKICESYNT 66
>pdb|2JRJ|A Chain A, Solution Structure Of The Human Pirh2 Ring-H2 Domain.
Northeast Structural Genomics Consortium Target Ht2b
Length = 52
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 135 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKS 187
EN +CPIC E + S V+ CGH +H CY EM+K + Y CP+C S
Sbjct: 1 ENVSQQNCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLK-EGYRCPLCMHS 52
>pdb|2ECM|A Chain A, Solution Structure Of The Ring Domain Of The Ring Finger
And Chy Zinc Finger Domain-Containing Protein 1 From Mus
Musculus
Length = 55
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/44 (47%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 142 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 185
CPIC E + S V+ CGH +H CY EM+K + Y CP+CS
Sbjct: 8 CPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLK-EGYRCPLCS 50
>pdb|3L11|A Chain A, Crystal Structure Of The Ring Domain Of Rnf168
Length = 115
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 4/53 (7%)
Query: 141 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSR 193
C IC E L + + + C HT+ C+ +++ CCP C + V +R
Sbjct: 17 QCGICMEILVEPV----TLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSSWTR 65
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 30.8 bits (68), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 7/56 (12%)
Query: 133 CIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 188
+EN + C IC EY +++ + C H+ C +E +KR K CPIC K +
Sbjct: 49 VLENELQ--CIICSEYFIEAV----TLNCAHSFCSYCINEWMKR-KIECPICRKDI 97
>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 = 30.8 bits (68), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 7/56 (12%)
Query: 133 CIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 188
+EN + C IC EY +++ + C H+ C +E +KR K CPIC K +
Sbjct: 60 VLENELQ--CIICSEYFIEAV----TLNCAHSFCSYCINEWMKR-KIECPICRKDI 108
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 30.8 bits (68), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 7/55 (12%)
Query: 134 IENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 188
+EN + C IC EY +++ + C H+ C +E +KR K CPIC K +
Sbjct: 50 LENELQ--CIICSEYFIEAV----TLNCAHSFCSYCINEWMKR-KIECPICRKDI 97
>pdb|2CT2|A Chain A, Solution Structure Of The Ring Domain Of The Tripartite
Motif Protein 32
Length = 88
Score = 30.4 bits (67), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 141 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR--DKYCCPICSK 186
CPIC E + ++ CGHT+ +C +++ + CP CSK
Sbjct: 17 ECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSK 64
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 27.7 bits (60), Expect = 6.2, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 142 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189
C +C L D + +CGH H EC +M CP+C +V+
Sbjct: 8 CAVCLAELEDGEEARFLPRCGHGFHAECV-DMWLGSHSTCPLCRLTVV 54
>pdb|3CNF|T Chain T, 3.88 Angstrom Structure Of Cytoplasmic Polyhedrosis Virus By
Cryo-Electron Microscopy
Length = 1057
Score = 27.7 bits (60), Expect = 6.7, Method: Composition-based stats.
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 48 MLRNPYDRHELVRQDVKQVAQVCTNCGVNMG 78
MLR+ HE++R ++ C+N G+ +G
Sbjct: 1005 MLRDIGITHEIIRPSTPELINACSNYGIRLG 1035
>pdb|3J17|A Chain A, Structure Of A Transcribing Cypovirus By Cryo-Electron
Microscopy
Length = 1058
Score = 27.7 bits (60), Expect = 7.3, Method: Composition-based stats.
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 48 MLRNPYDRHELVRQDVKQVAQVCTNCGVNMG 78
MLR+ HE++R ++ C+N G+ +G
Sbjct: 1006 MLRDIGITHEIIRPSTPELIDACSNYGIRLG 1036
>pdb|3IZ3|A Chain A, Cryoem Structure Of Cytoplasmic Polyhedrosis Virus
pdb|3IZX|A Chain A, 3.1 Angstrom Cryoem Structure Of Cytoplasmic Polyhedrosis
Virus
Length = 1058
Score = 27.7 bits (60), Expect = 7.3, Method: Composition-based stats.
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 48 MLRNPYDRHELVRQDVKQVAQVCTNCGVNMG 78
MLR+ HE++R ++ C+N G+ +G
Sbjct: 1006 MLRDIGITHEIIRPSTPELIDACSNYGIRLG 1036
>pdb|3IZR|MM Chain m, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 92
Score = 27.3 bits (59), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 79 EYFCDIC-KFYDDDIEKGQFHCDDCGICRIGG 109
+YFC+ C KF G + C DCG + GG
Sbjct: 36 KYFCEFCGKFAVKRKAVGIWGCKDCGKVKAGG 67
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 27.3 bits (59), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 135 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 188
E + H C +C Y D+ TT+++C H+ C ++ KY CPIC V
Sbjct: 7 ELNPHLMCVLCGGYFIDA---TTIIECLHSFCKTCIVRYLETSKY-CPICDVQV 56
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 27.3 bits (59), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 135 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 188
E + H C +C Y D+ TT+++C H+ C ++ KY CPIC V
Sbjct: 11 ELNPHLMCVLCGGYFIDA---TTIIECLHSFCKTCIVRYLETSKY-CPICDVQV 60
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 27.3 bits (59), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 7/66 (10%)
Query: 142 CPICYEYLFDSLRNT-TVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDE 200
CPIC D L+NT T +C H +C ++ CP C K ++ S+ R D
Sbjct: 57 CPIC----LDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLV--SKRSLRPDP 110
Query: 201 EIEATV 206
+A +
Sbjct: 111 NFDALI 116
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 27.3 bits (59), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 9/73 (12%)
Query: 137 SMHHH--CPICYEYLFDSLRNT-TVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSR 193
S+H CPIC D L+NT T +C H +C ++ CP C K ++ S+
Sbjct: 49 SLHSELMCPIC----LDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLV--SK 102
Query: 194 TWKRIDEEIEATV 206
R D +A +
Sbjct: 103 RSLRPDPNFDALI 115
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
0.328 0.140 0.494
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,180,280
Number of Sequences: 62578
Number of extensions: 320206
Number of successful extensions: 1011
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 991
Number of HSP's gapped (non-prelim): 36
length of query: 256
length of database: 14,973,337
effective HSP length: 97
effective length of query: 159
effective length of database: 8,903,271
effective search space: 1415620089
effective search space used: 1415620089
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 bits)