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= 043807
(242 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 = 67.4 bits (163), Expect = 7e-12, Method: Composition-based stats.
Identities = 27/50 (54%), Positives = 32/50 (64%)
Query: 65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV 114
D EC +CL ELEDGE R LP C H FH +C+ WL H+ CP+CR V
Sbjct: 4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 68 ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTS 122
+C ICL LE+GE VR LP C H FH C+ WL+ + CP+CR + Q S S
Sbjct: 16 KCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQLPSES 69
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 33/48 (68%), Gaps = 1/48 (2%)
Query: 65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRS 112
+Q+ CV+C+ + E +++R+LP C H FH +C+ WL + CP+CR+
Sbjct: 22 EQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRA 68
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 50.8 bits (120), Expect = 6e-07, Method: Composition-based stats.
Identities = 25/55 (45%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 68 ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTS 122
EC +C + GE VR LP C H FH CI WL H CPVCR + Q +T+
Sbjct: 17 ECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATN 70
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 69 CVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV 114
C +CL + + + + + P C+HAFH +C+ WL +CP+C PV
Sbjct: 18 CAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPV 62
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCR 111
D+ EC IC+ DG +LP C H+F +CI W H CP+CR
Sbjct: 13 TDEEECCICM----DGRADLILP-CAHSFCQKCIDKWSDRHRNCPICR 55
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 69 CVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCR 111
C IC E G++ LP C H FH C+ WL CPVCR
Sbjct: 43 CPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCR 84
>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 = 35.0 bits (79), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 69 CVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV 114
C ICL + + M LP C HAF CI W+ + CP+C+ PV
Sbjct: 8 CPICLEDPSNYSMA--LP-CLHAFCYVCITRWIRQNPTCPLCKVPV 50
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 33.9 bits (76), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 16/76 (21%), Positives = 37/76 (48%), Gaps = 14/76 (18%)
Query: 87 SCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTSGEAANLPNYKIMITSCLD--VVSL 144
+C H+F CI W+ CP+CR + + Y +++ +C++ V +L
Sbjct: 70 NCAHSFCSYCINEWMKRKIECPICRKDIKSKT------------YSLVLDNCINKMVNNL 117
Query: 145 ATSIEDKQQLLATTLK 160
++ +++++ +L K
Sbjct: 118 SSEVKERRIVLIRERK 133
>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 = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/76 (21%), Positives = 37/76 (48%), Gaps = 14/76 (18%)
Query: 87 SCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTSGEAANLPNYKIMITSCLD--VVSL 144
+C H+F CI W+ CP+CR + + Y +++ +C++ V +L
Sbjct: 81 NCAHSFCSYCINEWMKRKIECPICRKDIKSKT------------YSLVLDNCINKMVNNL 128
Query: 145 ATSIEDKQQLLATTLK 160
++ +++++ +L K
Sbjct: 129 SSEVKERRIVLIRERK 144
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 87 SCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKS 120
+C H+F CI W+ CP+CR + + S
Sbjct: 70 NCAHSFCSYCINEWMKRKIECPICRKDIKSKTYS 103
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 88 CRHAFHVQCIGNWLLGHTICPV 109
C HAFH CI WL +CP+
Sbjct: 67 CNHAFHFHCISRWLKTRQVCPL 88
>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 = 32.0 bits (71), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 88 CRHAFHVQCIGNWLLGHTICPV 109
C HAFH CI WL +CP+
Sbjct: 75 CNHAFHFHCISRWLKTRQVCPL 96
>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 = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 88 CRHAFHVQCIGNWLLGHTICPV 109
C HAFH CI WL +CP+
Sbjct: 73 CNHAFHFHCISRWLKTRQVCPL 94
>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 = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 88 CRHAFHVQCIGNWLLGHTICPV 109
C HAFH CI WL +CP+
Sbjct: 57 CNHAFHFHCISRWLKTRQVCPL 78
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 32.0 bits (71), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 88 CRHAFHVQCIGNWLLGHTICPV 109
C HAFH CI WL +CP+
Sbjct: 84 CNHAFHFHCISRWLKTRQVCPL 105
>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 = 31.6 bits (70), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 88 CRHAFHVQCIGNWLLGHTICPV 109
C HAFH CI WL +CP+
Sbjct: 73 CNHAFHFHCISRWLKTRQVCPL 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 = 31.6 bits (70), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 88 CRHAFHVQCIGNWLLGHTICPV 109
C HAFH CI WL +CP+
Sbjct: 65 CNHAFHFHCISRWLKTRQVCPL 86
>pdb|3LRQ|A Chain A, Crystal Structure Of The U-Box Domain Of Human Ubiquitin-
Protein Ligase (E3), Northeast Structural Genomics
Consortium Target Hr4604d.
pdb|3LRQ|B Chain B, Crystal Structure Of The U-Box Domain Of Human Ubiquitin-
Protein Ligase (E3), Northeast Structural Genomics
Consortium Target Hr4604d.
pdb|3LRQ|C Chain C, Crystal Structure Of The U-Box Domain Of Human Ubiquitin-
Protein Ligase (E3), Northeast Structural Genomics
Consortium Target Hr4604d.
pdb|3LRQ|D Chain D, Crystal Structure Of The U-Box Domain Of Human Ubiquitin-
Protein Ligase (E3), Northeast Structural Genomics
Consortium Target Hr4604d
Length = 100
Score = 30.8 bits (68), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 69 CVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTI-CPVCRSPV 114
C IC +L D RL P C CI WL CP CR+P+
Sbjct: 25 CFICXEKLRDA---RLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPL 68
>pdb|3QQ5|A Chain A, Crystal Structure Of The [fefe]-Hydrogenase Maturation
Protein Hydf
Length = 423
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 68 ECVICLGELEDGEMVRLLPSCRHAFHVQCIG-----NWLLGHT 105
E V + ELEDG+ V ++ C H + IG WL+ HT
Sbjct: 307 ESVRKIEELEDGDTVVIMEGCTHRPLTEDIGRVKIPRWLVNHT 349
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 59 CKLFRVD-QSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCR 111
C + RV C+ C E + + V + C H+FH C+ W+ + CP+C+
Sbjct: 18 CAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71
>pdb|2QIW|A Chain A, Crystal Structure Of A Putative Phosphoenolpyruvate
Phosphonomutase (ncgl1015, Cgl1060) From Corynebacterium
Glutamicum Atcc 13032 At 1.80 A Resolution
pdb|2QIW|B Chain B, Crystal Structure Of A Putative Phosphoenolpyruvate
Phosphonomutase (ncgl1015, Cgl1060) From Corynebacterium
Glutamicum Atcc 13032 At 1.80 A Resolution
Length = 255
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 22/47 (46%)
Query: 103 GHTICPVCRSPVADQPKSTSGEAANLPNYKIMITSCLDVVSLATSIE 149
G + + PVAD S+ GE N +Y ++ VS+ S++
Sbjct: 40 GFSGLTIGSHPVADATGSSDGENXNFADYXAVVKKITSAVSIPVSVD 86
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 69 CVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVC 110
CV+C G D + C H+F CI +L CP+C
Sbjct: 18 CVLCGGYFIDATTI---IECLHSFCKTCIVRYLETSKYCPIC 56
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 27.7 bits (60), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 69 CVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVC 110
CV+C G D + C H+F CI +L CP+C
Sbjct: 18 CVLCGGYFIDATTI---IECLHSFCKTCIVRYLETSKYCPIC 56
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 27.7 bits (60), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 69 CVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVC 110
CV+C G D + C H+F CI +L CP+C
Sbjct: 14 CVLCGGYFIDATTI---IECLHSFCKTCIVRYLETSKYCPIC 52
>pdb|2JRJ|A Chain A, Solution Structure Of The Human Pirh2 Ring-H2 Domain.
Northeast Structural Genomics Consortium Target Ht2b
Length = 52
Score = 26.9 bits (58), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 20/47 (42%)
Query: 64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVC 110
V Q C ICL ++ +V + C H H C L CP+C
Sbjct: 3 VSQQNCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLC 49
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
0.323 0.135 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,201,970
Number of Sequences: 62578
Number of extensions: 165807
Number of successful extensions: 497
Number of sequences better than 100.0: 36
Number of HSP's better than 100.0 without gapping: 26
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 468
Number of HSP's gapped (non-prelim): 37
length of query: 242
length of database: 14,973,337
effective HSP length: 96
effective length of query: 146
effective length of database: 8,965,849
effective search space: 1309013954
effective search space used: 1309013954
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 bits)