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= 027217
(226 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 = 115 bits (289), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 58/132 (43%), Positives = 82/132 (62%), Gaps = 10/132 (7%)
Query: 17 GCKHYRRRCRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQP 76
GC+HY R C ++APCC++++ CR CH+ + H+L R VK+V C C+ Q
Sbjct: 18 GCEHYDRACLLKAPCCDKLYTCRLCHDTN--------EDHQLDRFKVKEVQCINCEKLQH 69
Query: 77 VAQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYST 136
Q C +C GEY+C IC +D D K Q+HC+ CGICRIG +E++FHC +C C +T
Sbjct: 70 AQQTCEDCSTLFGEYYCSICHLFDKD--KRQYHCESCGICRIGPKEDFFHCLKCNLCLTT 127
Query: 137 SLRNNHLCIENS 148
+LR H CIE+
Sbjct: 128 NLRGKHKCIESG 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 = 112 bits (279), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 60/147 (40%), Positives = 86/147 (58%), Gaps = 12/147 (8%)
Query: 1 MEGSANERITFG--KMGYGCKHYRRRCRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHEL 58
M +A E G + GC+HY R C ++APCC++++ CR CH+ + H+L
Sbjct: 1 MAATAREDGATGEERGQRGCEHYDRGCLLKAPCCDKLYTCRLCHDNN--------EDHQL 52
Query: 59 VRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRI 118
R VK+V C C+ Q Q C C GEY+CDIC +D D K Q+HC++CGICRI
Sbjct: 53 DRFKVKEVQCINCEKIQHAQQTCEECSTLFGEYYCDICHLFDKD--KKQYHCENCGICRI 110
Query: 119 GGRENYFHCKRCGSCYSTSLRNNHLCI 145
G +E++FHC +C C + +L+ H CI
Sbjct: 111 GPKEDFFHCLKCNLCLAMNLQGRHKCI 137
>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: 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKS 198
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 = 3e-04, Method: Compositional matrix adjust.
Identities = 21/44 (47%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 196
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 = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 4/53 (7%)
Query: 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSR 204
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 = 0.62, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 7/56 (12%)
Query: 144 CIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199
+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 = 0.65, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 7/56 (12%)
Query: 144 CIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199
+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 = 0.65, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 7/56 (12%)
Query: 144 CIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199
+EN + C IC EY +++ + C H+ C +E +KR K CPIC K +
Sbjct: 49 VLENELQ--CIICSEYFIEAV----TLNCAHSFCSYCINEWMKR-KIECPICRKDI 97
>pdb|1PZW|A Chain A, Crystal Structure Of The Zinc Finger Associated Domain
Of The Drosophila Transcription Factor Grauzone
Length = 80
Score = 30.4 bits (67), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 29 APCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTE 74
A C +IFD ++ A +LR + L ++ +VIC+VC T+
Sbjct: 13 AQMCLQIFDVDSGESKVAEVLRQHFWFEVLPNDEISKVICNVCWTQ 58
>pdb|2CT2|A Chain A, Solution Structure Of The Ring Domain Of The Tripartite
Motif Protein 32
Length = 88
Score = 30.0 bits (66), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR--DKYCCPICSK 197
CPIC E + ++ CGHT+ +C +++ + CP CSK
Sbjct: 17 ECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSK 64
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 5/82 (6%)
Query: 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRT 205
E + H C +C Y D+ TT+++C H+ C ++ KY CPIC V
Sbjct: 7 ELNPHLMCVLCGGYFIDA---TTIIECLHSFCKTCIVRYLETSKY-CPICDVQVHKTRPL 62
Query: 206 WK-RIDEELQMNSSIFFPSFFR 226
R D+ LQ P F+
Sbjct: 63 LNIRSDKTLQDIVYKLVPGLFK 84
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 5/82 (6%)
Query: 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRT 205
E + H C +C Y D+ TT+++C H+ C ++ KY CPIC V
Sbjct: 11 ELNPHLMCVLCGGYFIDA---TTIIECLHSFCKTCIVRYLETSKY-CPICDVQVHKTRPL 66
Query: 206 WK-RIDEELQMNSSIFFPSFFR 226
R D+ LQ P F+
Sbjct: 67 LNIRSDKTLQDIVYKLVPGLFK 88
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 5/82 (6%)
Query: 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRT 205
E + H C +C Y D+ TT+++C H+ C ++ KY CPIC V
Sbjct: 11 ELNPHLMCVLCGGYFIDA---TTIIECLHSFCKTCIVRYLETSKY-CPICDVQVHKTRPL 66
Query: 206 WK-RIDEELQMNSSIFFPSFFR 226
R D+ LQ P F+
Sbjct: 67 LNIRSDKTLQDIVYKLVPGLFK 88
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 31/72 (43%), Gaps = 7/72 (9%)
Query: 153 CPICYEYLFDSLRNT-TVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDE 211
CPIC D L+NT T +C H +C ++ CP C K ++ S+ R D
Sbjct: 57 CPIC----LDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLV--SKRSLRPDP 110
Query: 212 ELQMNSSIFFPS 223
S +PS
Sbjct: 111 NFDALISKIYPS 122
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 27.3 bits (59), Expect = 6.7, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200
C +C L D + +CGH H EC +M CP+C +V+
Sbjct: 8 CAVCLAELEDGEEARFLPRCGHGFHAECV-DMWLGSHSTCPLCRLTVV 54
>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 = 7.0, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 90 EYFCDIC-KFYDDDIEKGQFHCDDCGICRIGG 120
+YFC+ C KF G + C DCG + GG
Sbjct: 36 KYFCEFCGKFAVKRKAVGIWGCKDCGKVKAGG 67
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 27.3 bits (59), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 34/79 (43%), Gaps = 9/79 (11%)
Query: 148 SMHHH--CPICYEYLFDSLRNT-TVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSR 204
S+H CPIC D L+NT T +C H +C ++ CP C K ++ S+
Sbjct: 49 SLHSELMCPIC----LDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLV--SK 102
Query: 205 TWKRIDEELQMNSSIFFPS 223
R D S +PS
Sbjct: 103 RSLRPDPNFDALISKIYPS 121
>pdb|4A0F|A Chain A, Structure Of Selenomethionine Substituted Bifunctional
Dapa Aminotransferase-Dethiobiotin Synthetase From
Arabidopsis Thaliana In Its Apo Form.
pdb|4A0F|B Chain B, Structure Of Selenomethionine Substituted Bifunctional
Dapa Aminotransferase-Dethiobiotin Synthetase From
Arabidopsis Thaliana In Its Apo Form
Length = 831
Score = 26.9 bits (58), Expect = 8.5, Method: Composition-based stats.
Identities = 29/113 (25%), Positives = 41/113 (36%), Gaps = 20/113 (17%)
Query: 52 PYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCD 111
PY +H+LV Q+ VI S C GE F I K D+ QF D
Sbjct: 345 PYTQHKLVHQETVTVIDSRC-----------------GENF-SIYKASDNSSLSQQF--D 384
Query: 112 DCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSL 164
C G + F + T+ R H+ +++ C E L D +
Sbjct: 385 ACASWWTQGPDPTFQAELAREXGYTAARFGHVXFPENVYEPALKCAELLLDGV 437
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 26.9 bits (58), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 161 FDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPIC 195
F+S + V+ C H H +C + +K ++ CPIC
Sbjct: 33 FESRQLLRVLPCNHEFHAKCVDKWLKANRT-CPIC 66
>pdb|1E4U|A Chain A, N-Terminal Ring Finger Domain Of Human Not-4
Length = 78
Score = 26.9 bits (58), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 1/64 (1%)
Query: 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRI-D 210
CP+C E L N CG+ + C+H + + CP C K + +K +
Sbjct: 13 ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAVYKPLSQ 72
Query: 211 EELQ 214
EELQ
Sbjct: 73 EELQ 76
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
0.330 0.141 0.499
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,024,508
Number of Sequences: 62578
Number of extensions: 271814
Number of successful extensions: 924
Number of sequences better than 100.0: 37
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 28
Number of HSP's that attempted gapping in prelim test: 907
Number of HSP's gapped (non-prelim): 38
length of query: 226
length of database: 14,973,337
effective HSP length: 95
effective length of query: 131
effective length of database: 9,028,427
effective search space: 1182723937
effective search space used: 1182723937
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 bits)