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= 020671
(323 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CSY|A Chain A, Solution Structure Of The Ring Domain Of The Zinc Finger
Protein 183-Like 1
Length = 81
Score = 84.7 bits (208), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 34/64 (53%), Positives = 48/64 (75%)
Query: 258 LPFACFICRKPFVDPVVTKCKHYFCEHCALKHHSKNKKCFVCNEPTLGIFNTALEIRKRM 317
+PF CFICR+ F +PVVTKC+HYFCE CAL+H +C++C++PT GIFN A E+ ++
Sbjct: 14 IPFRCFICRQAFQNPVVTKCRHYFCESCALEHFRATPRCYICDQPTGGIFNPAKELMAKL 73
Query: 318 AEEG 321
+ G
Sbjct: 74 QKSG 77
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 244 EEGVGQSDDDDEDSLPFACFICRKPFVDPVVTKCKHYFCEHCALKHHSKNKKCFVC 299
EE + +D E+ L C IC + F++ V C H FC +C + + +C +C
Sbjct: 40 EEVLSHMNDVLENELQ--CIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPIC 93
>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 = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 244 EEGVGQSDDDDEDSLPFACFICRKPFVDPVVTKCKHYFCEHCALKHHSKNKKCFVC 299
EE + +D E+ L C IC + F++ V C H FC +C + + +C +C
Sbjct: 51 EEVLSHMNDVLENELQ--CIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPIC 104
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 244 EEGVGQSDDDDEDSLPFACFICRKPFVDPVVTKCKHYFCEHCALKHHSKNKKCFVC 299
EE + +D E+ L C IC + F++ V C H FC +C + + +C +C
Sbjct: 40 EEVLSHMNDVLENELQ--CIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPIC 93
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 37.4 bits (85), Expect = 0.012, Method: Composition-based stats.
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 262 CFICRKPFVDPV-VTKCKHYFCEHCALKHHSKNKKCFVCN 300
C IC+ +D +T+C H FC+ C ++H + +C CN
Sbjct: 18 CSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKCN 57
>pdb|1M9O|A Chain A, Nmr Structure Of The First Zinc Binding Domain Of
Nup475TTPTIS11
Length = 77
Score = 35.4 bits (80), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 26/41 (63%), Gaps = 2/41 (4%)
Query: 175 AHIRVTARFDYQPDICKDYKETGYCGYGDSCKFMHDRGDYK 215
+H+ ++R Y+ ++C+ Y E+G C YG C+F H G+ +
Sbjct: 2 SHMTTSSR--YKTELCRTYSESGRCRYGAKCQFAHGLGELR 40
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 185 YQPDICKDYKETGYCGYGDSCKFMHD 210
Y+ ++C +K G C YG C F+H+
Sbjct: 48 YKTELCHKFKLQGRCPYGSRCHFIHN 73
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 34.3 bits (77), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 20/33 (60%)
Query: 262 CFICRKPFVDPVVTKCKHYFCEHCALKHHSKNK 294
C IC + +PV TKC H FC+ C LK ++ K
Sbjct: 24 CPICLELIKEPVSTKCDHIFCKFCMLKLLNQKK 56
>pdb|2D8T|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 146
Length = 71
Score = 34.3 bits (77), Expect = 0.11, Method: Composition-based stats.
Identities = 15/40 (37%), Positives = 19/40 (47%)
Query: 262 CFICRKPFVDPVVTKCKHYFCEHCALKHHSKNKKCFVCNE 301
C IC + V PV CKH FC C K+C +C +
Sbjct: 18 CAICLQTCVHPVSLPCKHVFCYLCVKGASWLGKRCALCRQ 57
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 33.5 bits (75), Expect = 0.15, Method: Composition-based stats.
Identities = 12/40 (30%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 262 CFICRKPFVDPV-VTKCKHYFCEHCALKHHSKNKKCFVCN 300
C +C F+D + +C H FC+ C +++ +K C +C+
Sbjct: 14 CVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICD 53
>pdb|1RMD|A Chain A, Rag1 Dimerization Domain
Length = 116
Score = 32.3 bits (72), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 16/29 (55%)
Query: 260 FACFICRKPFVDPVVTKCKHYFCEHCALK 288
+C IC DPV T CKH FC C L+
Sbjct: 24 ISCQICEHILADPVETSCKHLFCRICILR 52
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 32.3 bits (72), Expect = 0.38, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 6/47 (12%)
Query: 262 CFICRKPFVDPVVTKCKHYFCEHCALKHHSKNK------KCFVCNEP 302
C IC + +PV C H FC C ++ N+ C VC P
Sbjct: 22 CPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVP 68
>pdb|1RGO|A Chain A, Structural Basis For Recognition Of The Mrna Class Ii Au-
Rich Element By The Tandem Zinc Finger Domain Of Tis11d
Length = 70
Score = 32.3 bits (72), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 22/32 (68%)
Query: 185 YQPDICKDYKETGYCGYGDSCKFMHDRGDYKS 216
Y+ ++C+ ++E+G C YG+ C+F H + +S
Sbjct: 4 YKTELCRPFEESGTCKYGEKCQFAHGFHELRS 35
Score = 31.6 bits (70), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 9/26 (34%), Positives = 17/26 (65%)
Query: 185 YQPDICKDYKETGYCGYGDSCKFMHD 210
Y+ ++C+ + G+C YG C F+H+
Sbjct: 42 YKTELCRTFHTIGFCPYGPRCHFIHN 67
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 260 FACFICRKPFVDPV-VTKCKHYFCEHCALKHHSKNKKCFVCN 300
C +C F+D + +C H FC+ C +++ +K C +C+
Sbjct: 16 LMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICD 57
>pdb|2ECV|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Tripartite Motif-Containing Protein 5
Length = 85
Score = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 6/44 (13%)
Query: 262 CFICRKPFVDPVVTKCKHYFCEHCALKHHSKN------KKCFVC 299
C IC + P+ C H FC+ C +H K+ C VC
Sbjct: 22 CPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVC 65
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 11/39 (28%), Positives = 21/39 (53%)
Query: 261 ACFICRKPFVDPVVTKCKHYFCEHCALKHHSKNKKCFVC 299
+C +C + +PV+ +C H FC+ C + ++ F C
Sbjct: 17 SCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPC 55
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 260 FACFICRKPFVDPV-VTKCKHYFCEHCALKHHSKNKKCFVCN 300
C +C F+D + +C H FC+ C +++ +K C +C+
Sbjct: 16 LMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICD 57
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 30.4 bits (67), Expect = 1.5, Method: Composition-based stats.
Identities = 16/43 (37%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 260 FACFICRKPFVDPVVTKCKHYFCEHCALKH-HSKNKKCFVCNE 301
+ C IC + V T C H FC+ C +K KC V NE
Sbjct: 7 YECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNE 49
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 30.0 bits (66), Expect = 1.7, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 26/60 (43%), Gaps = 3/60 (5%)
Query: 248 GQSDDDDEDSLPFACFICR---KPFVDPVVTKCKHYFCEHCALKHHSKNKKCFVCNEPTL 304
G S E +L C +C KP + + CKH F C +K K C +CN P L
Sbjct: 4 GSSGKVKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVL 63
>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 = 28.5 bits (62), Expect = 5.6, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 5/48 (10%)
Query: 262 CFICRKPF-VDPVVTKCKHYFCEHCALKHHSKNKKCFVC----NEPTL 304
C IC + F + ++ +C H +C C K S +C C EP L
Sbjct: 25 CGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDL 72
>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf
Receptor-Associated Factor 6 Protein
Length = 86
Score = 28.1 bits (61), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 260 FACFICRKPFVDPVVTKCKHYFCEHCALKH-HSKNKKCFVCNEPTL 304
+ C IC + V T C H FC+ C +K KC V NE L
Sbjct: 26 YECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILL 71
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 27.7 bits (60), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 262 CFICRKPFVDPVVTKCKHYFCEHCALKHHSKNKKCFVC 299
C IC D ++ C H FC+ C K +++ C +C
Sbjct: 18 CCICMDGRAD-LILPCAHSFCQKCIDKWSDRHRNCPIC 54
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
0.315 0.132 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,428,749
Number of Sequences: 62578
Number of extensions: 359751
Number of successful extensions: 806
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 28
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 775
Number of HSP's gapped (non-prelim): 35
length of query: 323
length of database: 14,973,337
effective HSP length: 99
effective length of query: 224
effective length of database: 8,778,115
effective search space: 1966297760
effective search space used: 1966297760
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: 51 (24.3 bits)