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= psy9087
(170 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 89.0 bits (219), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 37/50 (74%), Positives = 45/50 (90%)
Query: 118 IPSFKFNASKHQSDQTSCVVCMCDFETSQVLRGLPCSHEFHAKCVDKWLK 167
+PS++FN + HQS+QT CVVCMCDFE+ Q+LR LPC+HEFHAKCVDKWLK
Sbjct: 9 LPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLK 58
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 42.4 bits (98), Expect = 1e-04, Method: Composition-based stats.
Identities = 18/37 (48%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 131 DQTSCVVCMCDFETSQVLRGLP-CSHEFHAKCVDKWL 166
D C VC+ + E + R LP C H FHA+CVD WL
Sbjct: 4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWL 40
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 21/34 (61%)
Query: 135 CVVCMCDFETSQVLRGLPCSHEFHAKCVDKWLKI 168
C VC+ DF+ L PC H FH KC+ KWL++
Sbjct: 18 CAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEV 51
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 20/32 (62%)
Query: 135 CVVCMCDFETSQVLRGLPCSHEFHAKCVDKWL 166
C +C+ E + +R LPC H FH CVD+WL
Sbjct: 17 CTICLSILEEGEDVRRLPCMHLFHQVCVDQWL 48
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 23/48 (47%)
Query: 120 SFKFNASKHQSDQTSCVVCMCDFETSQVLRGLPCSHEFHAKCVDKWLK 167
S +H C VC D+ + +R LPC+H FH C+ WL+
Sbjct: 3 SGSSGTEEHVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLE 50
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 35.4 bits (80), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 127 KHQSDQTSCVVCMCDFETSQVLRGLPCSHEFHAKCVDKW 165
K +D+ C +CM D +L PC+H F KC+DKW
Sbjct: 10 KQLTDEEECCICM-DGRADLIL---PCAHSFCQKCIDKW 44
>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 = 33.5 bits (75), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 1/58 (1%)
Query: 111 NRYEIESIPSFKFNASKHQSDQTSCV-VCMCDFETSQVLRGLPCSHEFHAKCVDKWLK 167
++ I+++P Q C +C ++ V LPC H FH CV WL+
Sbjct: 18 SKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQ 75
>pdb|3KUQ|A Chain A, Crystal Structure Of The Dlc1 Rhogap Domain
Length = 228
Score = 29.6 bits (65), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 58 PGLFHL--LAMFSSAPLSPYSQAELGSPDSTETVENYEALLSLAERLGEAK 106
P LFHL L +S+P + LG PD + EN A LA + E K
Sbjct: 176 PSLFHLNTLKRENSSPRVMQRKQSLGKPDQKDLNENLAATQGLAHMIAECK 226
>pdb|4DYL|A Chain A, F-Bar Domain Of Human Fes Tyrosine Kinase
Length = 406
Score = 27.3 bits (59), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 7/45 (15%)
Query: 41 NSLRRWRGQTLAPSNTYPGLFHLLAMFSS-------APLSPYSQA 78
+R+W Q + Y GL H +++ S +P SP SQ+
Sbjct: 29 EGMRKWMAQRVKSDREYAGLLHHMSLQDSGGQSRAISPDSPISQS 73
>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 = 26.6 bits (57), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 9/74 (12%)
Query: 100 ERLGEAKPRGLN--RYEIESIPSFKFNASKHQSD----QTSCVVCMCDFETSQVLRGLPC 153
E + +AK + L + E E + + K H +D + C++C F + L C
Sbjct: 26 EAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLN---C 82
Query: 154 SHEFHAKCVDKWLK 167
+H F + C+++W+K
Sbjct: 83 AHSFCSYCINEWMK 96
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 26.6 bits (57), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 47/95 (49%), Gaps = 17/95 (17%)
Query: 80 LGSPDS-TETVENYEALLSLAERLGEAKPRGLN--RYEIESIPSFKFNASKHQSD----Q 132
LGS + + +++EA++ +AK + L + E E + + K H +D +
Sbjct: 1 LGSMEELNRSKKDFEAII-------QAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENE 53
Query: 133 TSCVVCMCDFETSQVLRGLPCSHEFHAKCVDKWLK 167
C++C ++ V L C+H F + C+++W+K
Sbjct: 54 LQCIICS-EYFIEAV--TLNCAHSFCSYCINEWMK 85
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 26.6 bits (57), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 47/95 (49%), Gaps = 17/95 (17%)
Query: 80 LGSPDS-TETVENYEALLSLAERLGEAKPRGLN--RYEIESIPSFKFNASKHQSD----Q 132
LGS + + +++EA++ +AK + L + E E + + K H +D +
Sbjct: 1 LGSMEELNRSKKDFEAII-------QAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENE 53
Query: 133 TSCVVCMCDFETSQVLRGLPCSHEFHAKCVDKWLK 167
C++C ++ V L C+H F + C+++W+K
Sbjct: 54 LQCIICS-EYFIEAV--TLNCAHSFCSYCINEWMK 85
>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 = 26.2 bits (56), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 143 ETSQVLRGLPCSHEFHAKCVDKWLK 167
E V G+ C+H FH C+ +WLK
Sbjct: 66 EECTVAWGV-CNHAFHFHCISRWLK 89
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 26.2 bits (56), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 153 CSHEFHAKCVDKWLK 167
C+H FH C+ +WLK
Sbjct: 84 CNHAFHFHCISRWLK 98
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
0.320 0.133 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,085,442
Number of Sequences: 62578
Number of extensions: 183086
Number of successful extensions: 347
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 330
Number of HSP's gapped (non-prelim): 21
length of query: 170
length of database: 14,973,337
effective HSP length: 92
effective length of query: 78
effective length of database: 9,216,161
effective search space: 718860558
effective search space used: 718860558
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)