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= 044807
(105 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 46.6 bits (109), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 27/46 (58%)
Query: 46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
+ C++CL+E E + +P C H FHAEC+D W + CP+C
Sbjct: 4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLC 49
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 32/48 (66%), Gaps = 1/48 (2%)
Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP 97
C +C+ ++ S++ ++ +P C H FHA+C+D+W + N CP+C + P
Sbjct: 26 CVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGP 72
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/42 (45%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
C+ICLS E ++ +P C H FH C+D+W N KCP+C
Sbjct: 17 CTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPIC 57
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSAT 96
C +C +Y E+++ +P C H FH CI W +D CPVC S T
Sbjct: 18 CPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLT 63
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
C++CL ++ ++ + P CKH FH +C+ +W + CP+C
Sbjct: 18 CAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLC 58
>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 = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 27 TIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLND 86
+I + ++++ E G C IC SEY+ + +P C H FH C+ W + +
Sbjct: 21 SIDALPEILVTEDHGAVG-QEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSG 78
Query: 87 KCPVC 91
CPVC
Sbjct: 79 TCPVC 83
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 33.9 bits (76), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 48 SACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
AC C +E ++ + EC H FH C+ W + N++CP+C
Sbjct: 27 DACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLC 70
>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 = 33.1 bits (74), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 22/46 (47%)
Query: 46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
SS C ICL + + + + C H H C +E + +CP+C
Sbjct: 4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLC 49
>pdb|2JRJ|A Chain A, Solution Structure Of The Human Pirh2 Ring-H2 Domain.
Northeast Structural Genomics Consortium Target Ht2b
Length = 52
Score = 30.8 bits (68), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 23/45 (51%)
Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINS 94
C ICL + + + + C H H C +E + +CP+C++S
Sbjct: 8 CPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCMHS 52
>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 = 30.0 bits (66), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
N C IC ++ T+ C H F + CI+EW + +CP+C
Sbjct: 62 ENELQCIICSEYFIEAVTLNCA----HSFCSYCINEWMKRKIECPIC 104
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 29.6 bits (65), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
N C IC ++ T+ C H F + CI+EW + +CP+C
Sbjct: 51 ENELQCIICSEYFIEAVTLNCA----HSFCSYCINEWMKRKIECPIC 93
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 29.6 bits (65), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
N C IC ++ T+ C H F + CI+EW + +CP+C
Sbjct: 51 ENELQCIICSEYFIEAVTLNCA----HSFCSYCINEWMKRKIECPIC 93
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 28.1 bits (61), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 69 CKHCFHAECIDEWPRLNDKCPVC 91
C H F +CID+W + CP+C
Sbjct: 32 CAHSFCQKCIDKWSDRHRNCPIC 54
>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 = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSAT 96
C IC EY + I IP+C H + + CI ++ +CP C + T
Sbjct: 25 CGICF-EYFNIAMI--IPQCSHNYCSLCIRKFLSYKTQCPTCCVTVT 68
>pdb|1WE9|A Chain A, Solution Structure Of Phd Domain In Nucleic Acid Binding
Protein-like Np_197993
Length = 64
Score = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 22/53 (41%), Gaps = 5/53 (9%)
Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLND-----KCPVCINSATP 97
C C Y + E C C+ FH +C+ P + KCP C N + P
Sbjct: 9 CGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKSGP 61
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 7/47 (14%)
Query: 48 SACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDK---CPVC 91
++CS+CL EYL + I EC H F CI W ++ CPVC
Sbjct: 16 ASCSVCL-EYLKEPVI---IECGHNFCKACITRWWEDLERDFPCPVC 58
>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 = 26.6 bits (57), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 14/32 (43%)
Query: 59 SQETIKCIPECKHCFHAECIDEWPRLNDKCPV 90
S+E C H FH CI W + CP+
Sbjct: 65 SEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 96
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 14/32 (43%)
Query: 59 SQETIKCIPECKHCFHAECIDEWPRLNDKCPV 90
S+E C H FH CI W + CP+
Sbjct: 74 SEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 105
>pdb|3DPL|R Chain R, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation.
pdb|3RTR|B Chain B, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|D Chain D, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|F Chain F, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|H Chain H, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|4F52|B Chain B, Structure Of A Glomulin-Rbx1-Cul1 Complex
pdb|4F52|D Chain D, Structure Of A Glomulin-Rbx1-Cul1 Complex
Length = 106
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 14/32 (43%)
Query: 59 SQETIKCIPECKHCFHAECIDEWPRLNDKCPV 90
S+E C H FH CI W + CP+
Sbjct: 63 SEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 94
>pdb|4A0C|D Chain D, Structure Of The Cand1-Cul4b-Rbx1 Complex
pdb|4A0C|F Chain F, Structure Of The Cand1-Cul4b-Rbx1 Complex
pdb|4A0L|F Chain F, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp
Abasic Site Containing Dna-Duplex
pdb|4A0L|I Chain I, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp
Abasic Site Containing Dna-Duplex
Length = 98
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 14/32 (43%)
Query: 59 SQETIKCIPECKHCFHAECIDEWPRLNDKCPV 90
S+E C H FH CI W + CP+
Sbjct: 55 SEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 86
>pdb|2AKJ|A Chain A, Structure Of Spinach Nitrite Reductase
Length = 608
Score = 26.6 bits (57), Expect = 3.9, Method: Composition-based stats.
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 13 APQPPIMIMGLDECTIKSFQKLVLEESK 40
+P+PPI++ GL CT F + E+K
Sbjct: 474 SPEPPILMKGLVACTGSQFCGQAIIETK 501
>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 = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 69 CKHCFHAECIDEWPRLNDKCPVC 91
C H F CI W R N CP+C
Sbjct: 24 CLHAFCYVCITRWIRQNPTCPLC 46
>pdb|3DQV|R Chain R, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation
pdb|3DQV|Y Chain Y, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation
Length = 106
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 14/32 (43%)
Query: 59 SQETIKCIPECKHCFHAECIDEWPRLNDKCPV 90
S+E C H FH CI W + CP+
Sbjct: 63 SEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 94
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 26.2 bits (56), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 69 CKHCFHAECIDEWPRLNDKCPV 90
C H FH CI W + CP+
Sbjct: 67 CNHAFHFHCISRWLKTRQVCPL 88
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 44 GPNSSACSICL---SEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
G + +C IC+ SE + + EC H F ++C+ + + + CP C
Sbjct: 4 GSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTC 54
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 44 GPNSSACSICL---SEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
G + +C IC+ SE + + EC H F ++C+ + + + CP C
Sbjct: 69 GSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTC 119
>pdb|1LDJ|B Chain B, Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiquitin
Ligase Complex
pdb|1LDK|C Chain C, Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin
Ligase Complex
Length = 90
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 14/32 (43%)
Query: 59 SQETIKCIPECKHCFHAECIDEWPRLNDKCPV 90
S+E C H FH CI W + CP+
Sbjct: 47 SEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 78
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 25.4 bits (54), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
CSIC + TI EC H F CI +++CP C
Sbjct: 18 CSICKGYLIDATTIT---ECLHTFCKSCIVRHFYYSNRCPKC 56
>pdb|1JW1|A Chain A, Crystallization And Structure Determination Of Goat
Lactoferrin At 4.0 Resolution: A New Form Of Packing In
Lactoferrins With A High Solvent Content In Crystals
Length = 689
Score = 25.4 bits (54), Expect = 8.7, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 4/37 (10%)
Query: 41 CLPG--PNSSACSICLSEYLSQETIKCIPECKHCFHA 75
C PG P SS C++C + Q KC+P K ++
Sbjct: 491 CAPGADPKSSLCALCAGD--DQGLDKCVPNSKEKYYG 525
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 0.134 0.441
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,233,814
Number of Sequences: 62578
Number of extensions: 111790
Number of successful extensions: 256
Number of sequences better than 100.0: 45
Number of HSP's better than 100.0 without gapping: 34
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 219
Number of HSP's gapped (non-prelim): 49
length of query: 105
length of database: 14,973,337
effective HSP length: 70
effective length of query: 35
effective length of database: 10,592,877
effective search space: 370750695
effective search space used: 370750695
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: 45 (21.9 bits)