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= 023002
(289 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 = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 22/31 (70%), Positives = 27/31 (87%)
Query: 258 LPFACFICRKPFVDPVVTKCKHYFCEHCALK 288
+PF CFICR+ F +PVVTKC+HYFCE CAL+
Sbjct: 14 IPFRCFICRQAFQNPVVTKCRHYFCESCALE 44
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 35.8 bits (81), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 244 EEGVGQSDDDDEDSLPFACFICRKPFVDPVVTKCKHYFCEHC 285
EE + +D E+ L C IC + F++ V C H FC +C
Sbjct: 40 EEVLSHMNDVLENELQ--CIICSEYFIEAVTLNCAHSFCSYC 79
>pdb|1M9O|A Chain A, Nmr Structure Of The First Zinc Binding Domain Of
Nup475TTPTIS11
Length = 77
Score = 35.4 bits (80), Expect = 0.033, 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 = 1.9, 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|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 35.4 bits (80), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 244 EEGVGQSDDDDEDSLPFACFICRKPFVDPVVTKCKHYFCEHC 285
EE + +D E+ L C IC + F++ V C H FC +C
Sbjct: 40 EEVLSHMNDVLENELQ--CIICSEYFIEAVTLNCAHSFCSYC 79
>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 = 35.0 bits (79), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 244 EEGVGQSDDDDEDSLPFACFICRKPFVDPVVTKCKHYFCEHC 285
EE + +D E+ L C IC + F++ V C H FC +C
Sbjct: 51 EEVLSHMNDVLENELQ--CIICSEYFIEAVTLNCAHSFCSYC 90
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 34.3 bits (77), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 18/28 (64%)
Query: 262 CFICRKPFVDPVVTKCKHYFCEHCALKV 289
C IC + +PV TKC H FC+ C LK+
Sbjct: 24 CPICLELIKEPVSTKCDHIFCKFCMLKL 51
>pdb|1RMD|A Chain A, Rag1 Dimerization Domain
Length = 116
Score = 32.3 bits (72), Expect = 0.29, 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|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 = 0.32, 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 = 0.54, 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|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 29.6 bits (65), Expect = 1.8, Method: Composition-based stats.
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 261 ACFICRKPFVDPVVTKCKHYFCEHC 285
+C +C + +PV+ +C H FC+ C
Sbjct: 17 SCSVCLEYLKEPVIIECGHNFCKAC 41
>pdb|2D8T|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 146
Length = 71
Score = 29.6 bits (65), Expect = 2.1, Method: Composition-based stats.
Identities = 12/24 (50%), Positives = 13/24 (54%)
Query: 262 CFICRKPFVDPVVTKCKHYFCEHC 285
C IC + V PV CKH FC C
Sbjct: 18 CAICLQTCVHPVSLPCKHVFCYLC 41
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 28.5 bits (62), Expect = 4.5, Method: Composition-based stats.
Identities = 10/28 (35%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 262 CFICRKPFVDPV-VTKCKHYFCEHCALK 288
C IC+ +D +T+C H FC+ C ++
Sbjct: 18 CSICKGYLIDATTITECLHTFCKSCIVR 45
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 28.5 bits (62), Expect = 4.6, Method: Composition-based stats.
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 262 CFICRKPFVDPVVTKCKHYFCEHC 285
C IC + +PV C H FC C
Sbjct: 22 CPICLELLKEPVSADCNHSFCRAC 45
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 28.1 bits (61), Expect = 5.2, Method: Composition-based stats.
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 260 FACFICRKPFVDPVVTKCKHYFCEHCALK 288
+ C IC + V T C H FC+ C +K
Sbjct: 7 YECPICLMALREAVQTPCGHRFCKACIIK 35
>pdb|3FL2|A Chain A, Crystal Structure Of The Ring Domain Of The E3 Ubiquitin-
Protein Ligase Uhrf1
Length = 124
Score = 27.7 bits (60), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 260 FACFICRKPFVDPVVTKCKHYFCEHC 285
F C C++ P+ T C+H C+ C
Sbjct: 53 FQCICCQELVFRPITTVCQHNVCKDC 78
>pdb|2CQE|A Chain A, Solution Structure Of The Zinc-Finger Domain In Kiaa1064
Protein
Length = 98
Score = 27.3 bits (59), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 12/21 (57%), Positives = 12/21 (57%)
Query: 190 CKDYKETGYCGYGDSCKFMHD 210
CK Y TG C GD C F HD
Sbjct: 39 CKLYHTTGNCINGDDCMFSHD 59
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 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,343,552
Number of Sequences: 62578
Number of extensions: 312689
Number of successful extensions: 703
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 679
Number of HSP's gapped (non-prelim): 27
length of query: 289
length of database: 14,973,337
effective HSP length: 98
effective length of query: 191
effective length of database: 8,840,693
effective search space: 1688572363
effective search space used: 1688572363
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)