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= 039647
(290 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 36/64 (56%), Gaps = 2/64 (3%)
Query: 153 IDQDLQCAVWLEEFVMGNEAKQMPYKHKFHGECLMPWLEFHSSCPICRYQLPSDNLKVQG 212
+ L+C V E++ +G +Q+P H FH C++PWLE H SCP+CR L N
Sbjct: 12 VGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTAT-- 69
Query: 213 NGPG 216
N PG
Sbjct: 70 NPPG 73
>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 = 57.4 bits (137), Expect = 1e-08, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 7/72 (9%)
Query: 140 AQKEVVKALPMV-------AIDQDLQCAVWLEEFVMGNEAKQMPYKHKFHGECLMPWLEF 192
A KE + ALP + A+ Q++ C + E+V G+ A ++P H FH C+ WL+
Sbjct: 17 ASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQK 76
Query: 193 HSSCPICRYQLP 204
+CP+CR P
Sbjct: 77 SGTCPVCRCMFP 88
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 53.9 bits (128), Expect = 1e-07, Method: Composition-based stats.
Identities = 24/50 (48%), Positives = 32/50 (64%), Gaps = 1/50 (2%)
Query: 152 AIDQDLQCAVWLEEFVMGNEAKQMPY-KHKFHGECLMPWLEFHSSCPICR 200
A+D ++CAV L E G EA+ +P H FH EC+ WL HS+CP+CR
Sbjct: 1 AMDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 50
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/41 (48%), Positives = 25/41 (60%)
Query: 159 CAVWLEEFVMGNEAKQMPYKHKFHGECLMPWLEFHSSCPIC 199
CAV LE+F +E P KH FH +CL+ WLE CP+C
Sbjct: 18 CAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLC 58
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 158 QCAVWLEEFVMGNEAKQMPYKHKFHGECLMPWLEFHSSCPICRY----QLPSDN 207
+C + L G + +++P H FH C+ WL + CPICR QLPS++
Sbjct: 16 KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQLPSES 69
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 3/81 (3%)
Query: 138 LSAQKEVVKALPMVAIDQDLQCAVWLEEFVMGNEAKQMPYKHKFHGECLMPWLEFHSSCP 197
+ AQKE V + ++ +LQC + E F+ EA + H F C+ W++ CP
Sbjct: 35 MQAQKEEVLSHMNDVLENELQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIECP 91
Query: 198 ICRYQLPSDNLKVQGNGPGNR 218
ICR + S + + N+
Sbjct: 92 ICRKDIKSKTYSLVLDNXINK 112
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 3/81 (3%)
Query: 138 LSAQKEVVKALPMVAIDQDLQCAVWLEEFVMGNEAKQMPYKHKFHGECLMPWLEFHSSCP 197
+ AQKE V + ++ +LQC + E F+ EA + H F C+ W++ CP
Sbjct: 35 MQAQKEEVLSHMNDVLENELQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIECP 91
Query: 198 ICRYQLPSDNLKVQGNGPGNR 218
ICR + S + + N+
Sbjct: 92 ICRKDIKSKTYSLVLDNCINK 112
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 25/42 (59%)
Query: 159 CAVWLEEFVMGNEAKQMPYKHKFHGECLMPWLEFHSSCPICR 200
C V + +F + +P H+FH +C+ WL+ + +CPICR
Sbjct: 26 CVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICR 67
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 3/82 (3%)
Query: 137 SLSAQKEVVKALPMVAIDQDLQCAVWLEEFVMGNEAKQMPYKHKFHGECLMPWLEFHSSC 196
+ AQKE V + ++ +LQC + E F+ EA + H F C+ W++ C
Sbjct: 45 KMQAQKEEVLSHMNDVLENELQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIEC 101
Query: 197 PICRYQLPSDNLKVQGNGPGNR 218
PICR + S + + N+
Sbjct: 102 PICRKDIKSKTYSLVLDNCINK 123
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 36.2 bits (82), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 175 MPYKHKFHGECLMPWLEFHSSCPICRYQLPSDN 207
+P H F +C+ W + H +CPICR Q+ N
Sbjct: 30 LPCAHSFCQKCIDKWSDRHRNCPICRLQMTGAN 62
>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 = 31.6 bits (70), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 150 MVAIDQDLQCAVWLEEFVMGNEAKQMP-YKHKFHGECLMPWLEFHSSCPICRYQLPSDNL 208
M ID L+C + E F N A +P H + C+ +L + + CP C + +L
Sbjct: 16 MKTIDDLLRCGICFEYF---NIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDL 72
Query: 209 K 209
K
Sbjct: 73 K 73
>pdb|1CHC|A Chain A, Structure Of The C3hc4 Domain By 1h-Nuclear Magnetic
Resonance Spectroscopy; A New Structural Class Of Zinc-
Finger
Length = 68
Score = 30.4 bits (67), Expect = 1.1, Method: Composition-based stats.
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 158 QCAVWLEEFVMGNEAKQMPYKHKFHGECLMPWLEFHSSCPICRYQLPS 205
+C + LE+ N + +P H F C+ W+ + +CP+C+ + S
Sbjct: 7 RCPICLED--PSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVES 52
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 28.5 bits (62), Expect = 4.2, Method: Composition-based stats.
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 179 HKFHGECLMPWLEFHSSCPICR 200
H FH C+ W++ ++ CP+C+
Sbjct: 50 HSFHNCCMSLWVKQNNRCPLCQ 71
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 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,329,099
Number of Sequences: 62578
Number of extensions: 334752
Number of successful extensions: 647
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 629
Number of HSP's gapped (non-prelim): 15
length of query: 290
length of database: 14,973,337
effective HSP length: 98
effective length of query: 192
effective length of database: 8,840,693
effective search space: 1697413056
effective search space used: 1697413056
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)