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= psy3978
(243 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 69 VKWEYIQQIRGFGNEDIKCPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPIC 128
++ E +Q + + ++CPICL+L + P T+C H FC C+L L K +CP+C
Sbjct: 6 LRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLN-QKKGPSQCPLC 64
>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 = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 83 EDIKCPICLDLPRAPQMTRCGHCFCWPCIL--HYLALSDKSWRKCPICYEAVHLGDLKSF 140
E++ CPICL+L P CGH FC C+ H ++ DK CP+C + +++
Sbjct: 18 EEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRPN 77
Query: 141 RSV 143
R V
Sbjct: 78 RHV 80
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 45.1 bits (105), Expect = 4e-05, Method: Composition-based stats.
Identities = 20/50 (40%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 83 EDIKCPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPICYEAV 132
E++ CPICLD+ + P CGH FC CI + + + KCP+C +V
Sbjct: 19 EEVICPICLDILQKPVTIDCGHNFCLKCITQ-IGETSCGFFKCPLCKTSV 67
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 43.5 bits (101), Expect = 1e-04, Method: Composition-based stats.
Identities = 19/46 (41%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 83 EDIKCPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPIC 128
E++ CPICLD+ + P CGH FC CI + + + KCP+C
Sbjct: 19 EEVICPICLDILQKPVTIDCGHNFCLKCITQ-IGETSCGFFKCPLC 63
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 83 EDIKCPICLDLPRAPQMTRCGHCFCWPCI-LHYLALSDKSWR-KCPICYEAVHLGDLK 138
E++ CPICL+L + P C H FC CI L+Y + + + CP+C G+LK
Sbjct: 18 EEVTCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLK 75
>pdb|2EGP|A Chain A, Solution Structure Of The Ring-Finger Domain From Human
Tripartite Motif Protein 34
Length = 79
Score = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 83 EDIKCPICLDLPRAPQMTRCGHCFCWPCIL-----HYLALSDKSWRKCPIC 128
E++ CPICL+L P CGH C CI ++ KS CP+C
Sbjct: 11 EEVTCPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKS--SCPVC 59
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 36.2 bits (82), Expect = 0.019, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 87 CPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPIC 128
C +CL+ + P + CGH FC CI + ++ + CP+C
Sbjct: 18 CSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDF-PCPVC 58
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 35.4 bits (80), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 84 DIKCPICLDLPRAPQMTR-CGHCFCWPCILHYLALSDKSWRKCPICYEAV 132
++ CPICLD+ + T+ C H FC CI+ L +K +CP C + +
Sbjct: 54 ELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNK---ECPTCRKKL 100
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 33.9 bits (76), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 72 EYIQQIRGFGNEDIKCPICLDLPRAPQMTR-CGHCFCWPCILHYLALSDKSWRKCPICYE 130
E + R +E + CPICLD+ + T+ C H FC CI+ L +K +CP C +
Sbjct: 42 EIVVSPRSLHSE-LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNK---ECPTCRK 97
Query: 131 AV 132
+
Sbjct: 98 KL 99
>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf
Receptor-Associated Factor 6 Protein
Length = 86
Score = 33.9 bits (76), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 86 KCPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPI 127
+CPICL R T CGH FC CI+ + + KCP+
Sbjct: 27 ECPICLMALREAVQTPCGHRFCKACIIKSIR---DAGHKCPV 65
>pdb|2ECY|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger)" Domain Of Tnf Receptor-Associated Factor 3
Length = 66
Score = 33.5 bits (75), Expect = 0.12, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 86 KCPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPICYEAV 132
KC C + +P+ T CGH FC C+ AL S KC C E++
Sbjct: 17 KCEKCHLVLCSPKQTECGHRFCESCM---AALLSSSSPKCTACQESI 60
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 72 EYIQQIRGFGNEDIKCPICLDLPRAPQMTR-CGHCFCWPCILHYLALSDKSWRKCPICYE 130
E + R +E + CPICLD+ + T+ C H FC CI+ L +K +CP C +
Sbjct: 23 EIVVSPRSLHSE-LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNK---ECPTCRK 78
Query: 131 AV 132
+
Sbjct: 79 KL 80
>pdb|3HCT|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The P1
Space Group
pdb|3HCU|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The C2
Space Group
pdb|3HCU|C Chain C, Crystal Structure Of Traf6 In Complex With Ubc13 In The C2
Space Group
Length = 118
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 10/61 (16%)
Query: 74 IQQIRGFGNE-------DIKCPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCP 126
+++I+G+ E +CPICL R T CGH FC CI+ + + KCP
Sbjct: 1 MEEIQGYDVEFDPPLESKYECPICLMALREAVQTPCGHRFCKACIIKSIR---DAGHKCP 57
Query: 127 I 127
+
Sbjct: 58 V 58
>pdb|3HCS|A Chain A, Crystal Structure Of The N-Terminal Domain Of Traf6
pdb|3HCS|B Chain B, Crystal Structure Of The N-Terminal Domain Of Traf6
Length = 170
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 10/61 (16%)
Query: 74 IQQIRGFGNE-------DIKCPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCP 126
+++I+G+ E +CPICL R T CGH FC CI+ + + KCP
Sbjct: 1 MEEIQGYDVEFDPPLESKYECPICLMALREAVQTPCGHRFCKACIIKSIR---DAGHKCP 57
Query: 127 I 127
+
Sbjct: 58 V 58
>pdb|1JM7|B Chain B, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 117
Score = 32.0 bits (71), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 7/81 (8%)
Query: 64 DPDQLVKWEYIQQIRGFGNEDIKCPICLDLPRAPQ-MTRCGHCFCWPCILHYLALSDKSW 122
+PD W + + + ++C C ++ R P + C H FC C+ SD
Sbjct: 2 EPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCV------SDCIG 55
Query: 123 RKCPICYEAVHLGDLKSFRSV 143
CP+CY + DLK R +
Sbjct: 56 TGCPVCYTPAWIQDLKINRQL 76
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 86 KCPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPI 127
+CPICL R T CGH FC CI+ + + KCP+
Sbjct: 8 ECPICLMALREAVQTPCGHRFCKACIIKSI---RDAGHKCPV 46
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 31.2 bits (69), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 23/100 (23%), Positives = 43/100 (43%), Gaps = 9/100 (9%)
Query: 29 SLASVHKHKYNKEQFLQANCQFVVRLGEDYGIHLGDPDQLVKWEYIQQIRGFGNEDIKCP 88
S+ +++ K + E +QA + + + E+ + Q K E + + +++C
Sbjct: 3 SMEELNRSKKDFEAIIQAKNKELEQTKEE-----KEKMQAQKEEVLSHMNDVLENELQCI 57
Query: 89 ICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPIC 128
IC + C H FC CI ++ K +CPIC
Sbjct: 58 ICSEYFIEAVTLNCAHSFCSYCINEWM----KRKIECPIC 93
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 31.2 bits (69), Expect = 0.49, Method: Composition-based stats.
Identities = 19/50 (38%), Positives = 24/50 (48%), Gaps = 5/50 (10%)
Query: 85 IKCPICLD-LPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPICYEAVH 133
I C IC L A +T C H FC CI+ + S+ +CP C VH
Sbjct: 16 ILCSICKGYLIDATTITECLHTFCKSCIVRHFYYSN----RCPKCNIVVH 61
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 31.2 bits (69), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 11/62 (17%)
Query: 79 GFGNEDIKCPICLDL-------PRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPICYEA 131
G+ + CPIC+D R T CGH FC C+ L K+ CP C +
Sbjct: 2 AMGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSL----KNANTCPTCRKK 57
Query: 132 VH 133
++
Sbjct: 58 IN 59
Score = 31.2 bits (69), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 11/61 (18%)
Query: 80 FGNEDIKCPICLDL-------PRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPICYEAV 132
G+ + CPIC+D R T CGH FC C+ L K+ CP C + +
Sbjct: 68 IGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSL----KNANTCPTCRKKI 123
Query: 133 H 133
+
Sbjct: 124 N 124
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 31.2 bits (69), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 23/100 (23%), Positives = 43/100 (43%), Gaps = 9/100 (9%)
Query: 29 SLASVHKHKYNKEQFLQANCQFVVRLGEDYGIHLGDPDQLVKWEYIQQIRGFGNEDIKCP 88
S+ +++ K + E +QA + + + E+ + Q K E + + +++C
Sbjct: 3 SMEELNRSKKDFEAIIQAKNKELEQTKEE-----KEKMQAQKEEVLSHMNDVLENELQCI 57
Query: 89 ICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPIC 128
IC + C H FC CI ++ K +CPIC
Sbjct: 58 ICSEYFIEAVTLNCAHSFCSYCINEWM----KRKIECPIC 93
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 30.8 bits (68), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 36/85 (42%), Gaps = 16/85 (18%)
Query: 96 APQMTRCGHCFCWPCILHYLALSDKSWRKCPICYEAVHLGDLKSFRSVIKRARAVNEEVT 155
A + C H FC CI+ YL S + CPIC VH K+ + R+ +++
Sbjct: 28 ATTIIECLHSFCKTCIVRYLETS----KYCPICDVQVH----KTRPLLNIRSDKTLQDIV 79
Query: 156 FQL--------MKRERGSTVVSPVA 172
++L MKR R P A
Sbjct: 80 YKLVPGLFKNEMKRRRDFYAAHPSA 104
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 30.8 bits (68), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 36/85 (42%), Gaps = 16/85 (18%)
Query: 96 APQMTRCGHCFCWPCILHYLALSDKSWRKCPICYEAVHLGDLKSFRSVIKRARAVNEEVT 155
A + C H FC CI+ YL S + CPIC VH K+ + R+ +++
Sbjct: 28 ATTIIECLHSFCKTCIVRYLETS----KYCPICDVQVH----KTRPLLNIRSDKTLQDIV 79
Query: 156 FQL--------MKRERGSTVVSPVA 172
++L MKR R P A
Sbjct: 80 YKLVPGLFKNEMKRRRDFYAAHPSA 104
>pdb|1RMD|A Chain A, Rag1 Dimerization Domain
Length = 116
Score = 30.8 bits (68), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 36/85 (42%), Gaps = 13/85 (15%)
Query: 83 EDIKCPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPICYEAVHLGDL----K 138
+ I C IC + P T C H FC CIL L + CP C DL K
Sbjct: 22 KSISCQICEHILADPVETSCKHLFCRICILRCLKV---MGSYCPSCRYPCFPTDLESPVK 78
Query: 139 SFRSVIKR------ARAVNEEVTFQ 157
SF +++ A+ NEEV+ +
Sbjct: 79 SFLNILNSLMVKCPAQDCNEEVSLE 103
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 30.4 bits (67), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 4/38 (10%)
Query: 96 APQMTRCGHCFCWPCILHYLALSDKSWRKCPICYEAVH 133
A + C H FC CI+ YL S + CPIC VH
Sbjct: 24 ATTIIECLHSFCKTCIVRYLETS----KYCPICDVQVH 57
>pdb|3IBJ|A Chain A, X-Ray Structure Of Pde2a
pdb|3IBJ|B Chain B, X-Ray Structure Of Pde2a
Length = 691
Score = 30.4 bits (67), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 38 YNKEQFLQANCQFVVRLGEDYGIHLGDPDQLVKWEYIQQIRGFGNEDIKCPICLD 92
+ KEQ L+ CQ ++++ ++ HL D L++ E I + R N +I LD
Sbjct: 170 FQKEQKLKCECQALLQVAKNLFTHLDDVSVLLQ-EIITEARNLSNAEICSVFLLD 223
>pdb|3EB5|A Chain A, Structure Of The Ciap2 Ring Domain
pdb|3EB6|A Chain A, Structure Of The Ciap2 Ring Domain Bound To Ubch5b
Length = 74
Score = 30.0 bits (66), Expect = 1.3, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 11/69 (15%)
Query: 75 QQIRGFGNEDIKCPICLDLPRAPQMTRCGH-CFCWPCILHYLALSDKSWRKCPICYEAVH 133
+Q+R E+ C +C+D + CGH C C S RKCPIC +
Sbjct: 16 EQLRRL-QEERTCKVCMDKEVSIVFIPCGHLVVCKDCA--------PSLRKCPICRSTIK 66
Query: 134 LGDLKSFRS 142
G +++F S
Sbjct: 67 -GTVRTFLS 74
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 11/56 (19%)
Query: 85 IKCPICLDL-------PRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPICYEAVH 133
+ CPIC+D R T CGH FC C+ L K+ CP C + ++
Sbjct: 16 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSL----KNANTCPTCRKKIN 67
>pdb|3T6P|A Chain A, Iap Antagonist-Induced Conformational Change In Ciap1
Promotes E3 Ligase Activation Via Dimerization
Length = 345
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 11/69 (15%)
Query: 75 QQIRGFGNEDIKCPICLDLPRAPQMTRCGH-CFCWPCILHYLALSDKSWRKCPICYEAVH 133
+Q+R E+ C +C+D + CGH C C S RKCPIC +
Sbjct: 287 EQLRRL-QEERTCKVCMDKEVSVVFIPCGHLVVCQECA--------PSLRKCPICRGIIK 337
Query: 134 LGDLKSFRS 142
G +++F S
Sbjct: 338 -GTVRTFLS 345
>pdb|3NG2|A Chain A, Crystal Structure Of The Rnf4 Ring Domain Dimer
pdb|3NG2|B Chain B, Crystal Structure Of The Rnf4 Ring Domain Dimer
Length = 71
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 11/56 (19%)
Query: 85 IKCPICLDL-------PRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPICYEAVH 133
+ CPIC+D R T CGH FC C+ L K+ CP C + ++
Sbjct: 11 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSL----KNANTCPTCRKKIN 62
>pdb|2D8T|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 146
Length = 71
Score = 29.3 bits (64), Expect = 2.0, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 8/49 (16%)
Query: 86 KCPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSW--RKCPICYEAV 132
+C ICL P C H FC YL + SW ++C +C + +
Sbjct: 17 ECAICLQTCVHPVSLPCKHVFC------YLCVKGASWLGKRCALCRQEI 59
>pdb|1MC0|A Chain A, Regulatory Segment Of Mouse 3',5'-Cyclic Nucleotide
Phosphodiesterase 2a, Containing The Gaf A And Gaf B
Domains
Length = 368
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 38 YNKEQFLQANCQFVVRLGEDYGIHLGDPDQLVKWEYIQQIRGFGNEDIKCPICLD 92
+ KEQ L+ CQ ++++ ++ HL D L++ E I + R N +I LD
Sbjct: 170 FQKEQKLKCECQALLQVAKNLFTHLDDVSVLLQ-EIITEARNLSNAEICSVFLLD 223
>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 = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 22/103 (21%), Positives = 44/103 (42%), Gaps = 9/103 (8%)
Query: 30 LASVHKHKYNKEQFLQANCQFVVRLGEDYGIHLGDPDQLVKWEYIQQIRGFGNEDIKCPI 89
+ +++ K + E +QA + + + E+ + Q K E + + +++C I
Sbjct: 15 MEELNRSKKDFEAIIQAKNKELEQTKEE-----KEKMQAQKEEVLSHMNDVLENELQCII 69
Query: 90 CLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPICYEAV 132
C + C H FC CI ++ K +CPIC + +
Sbjct: 70 CSEYFIEAVTLNCAHSFCSYCINEWM----KRKIECPICRKDI 108
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 11/56 (19%)
Query: 85 IKCPICLDL-------PRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPICYEAVH 133
+ CPIC+D R T CGH FC C+ L K+ CP C + ++
Sbjct: 4 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSL----KNANTCPTCRKKIN 55
>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 = 3.9, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 5/68 (7%)
Query: 85 IKCPICLD-LPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPICYEAVHLGDLKSFRSV 143
++C IC + A + +C H +C CI +L+ + CP C V DLK+ R +
Sbjct: 23 LRCGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQ----CPTCCVTVTEPDLKNNRIL 78
Query: 144 IKRARAVN 151
+ +++N
Sbjct: 79 DELVKSLN 86
>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 = 4.1, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 82 NEDIKCPICLDLPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPIC 128
++ +C IC+D RA + C H FC CI + SD+ R CPIC
Sbjct: 13 TDEEECCICMD-GRADLILPCAHSFCQKCIDKW---SDRH-RNCPIC 54
>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 = 28.1 bits (61), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 5/44 (11%)
Query: 86 KCPICLDLPRAPQMT-RCGHCFCWPCILHYLALSDKSWRKCPIC 128
+CPICL+ P M C H FC+ CI ++ + CP+C
Sbjct: 7 RCPICLEDPSNYSMALPCLHAFCYVCITRWI----RQNPTCPLC 46
>pdb|4IC3|A Chain A, Crystal Structure Of The F495l Mutant Xiap Ring Domain
pdb|4IC3|B Chain B, Crystal Structure Of The F495l Mutant Xiap Ring Domain
Length = 74
Score = 27.7 bits (60), Expect = 5.9, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 10/59 (16%)
Query: 75 QQIRGFGNEDIKCPICLDLPRAPQMTRCGHCF-CWPCILHYLALSDKSWRKCPICYEAV 132
+Q+R E + C IC+D A CGH C C ++ KCP+CY +
Sbjct: 16 EQLRRLQEEKL-CKICMDRNIAIVFVPCGHLVTCKQCA--------EAVDKCPMCYTVI 65
>pdb|4IC2|A Chain A, Crystal Structure Of The Xiap Ring Domain
pdb|4IC2|B Chain B, Crystal Structure Of The Xiap Ring Domain
Length = 74
Score = 27.7 bits (60), Expect = 5.9, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 10/59 (16%)
Query: 75 QQIRGFGNEDIKCPICLDLPRAPQMTRCGHCF-CWPCILHYLALSDKSWRKCPICYEAV 132
+Q+R E + C IC+D A CGH C C ++ KCP+CY +
Sbjct: 16 EQLRRLQEEKL-CKICMDRNIAIVFVPCGHLVTCKQCA--------EAVDKCPMCYTVI 65
>pdb|2Y4T|A Chain A, Crystal Structure Of The Human Co-Chaperone P58(Ipk)
pdb|2Y4T|B Chain B, Crystal Structure Of The Human Co-Chaperone P58(Ipk)
pdb|2Y4T|C Chain C, Crystal Structure Of The Human Co-Chaperone P58(Ipk)
Length = 450
Score = 27.7 bits (60), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 3/59 (5%)
Query: 13 SRGTDYSMGYNNFLMQSLASVHKHKYNKEQFLQANCQFVVRLGEDYGIHLGDPDQLVKW 71
S G D +G N QS+A V KH ++ L A Q L + + GDPD + +
Sbjct: 8 SSGVD--LGTENLYFQSMADVEKHLELGKKLLAAG-QLADALSQFHAAVDGDPDNYIAY 63
>pdb|2YUR|A Chain A, Solution Structure Of The Ring Finger Of Human
Retinoblastoma-Binding Protein 6
Length = 74
Score = 27.3 bits (59), Expect = 7.0, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 83 EDIKCPICLD-LPRAPQMTRCGHCFCWPCILHYLALSDKSWRKCPICYE 130
+++ C IC D + A + CG+ +C CI L SD+ CP C++
Sbjct: 14 DELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDE--HTCPTCHQ 60
>pdb|4B4T|S Chain S, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 523
Score = 27.3 bits (59), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 130 EAVHLGDLKSFRSVI-KRARAVNEEVTFQLMKRERGSTVVSPV 171
+AV LGDLK F S I K + + ++ T+QL R R + + + +
Sbjct: 350 KAVKLGDLKKFTSTITKYKQLLLKDDTYQLCVRLRSNVIKTGI 392
>pdb|2ECG|A Chain A, Solution Structure Of The Ring Domain Of The Baculoviral
Iap Repeat-Containing Protein 4 From Homo Sapiens
Length = 75
Score = 27.3 bits (59), Expect = 8.8, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 10/59 (16%)
Query: 75 QQIRGFGNEDIKCPICLDLPRAPQMTRCGHCF-CWPCILHYLALSDKSWRKCPICYEAV 132
+Q+R E + C IC+D A CGH C C ++ KCP+CY +
Sbjct: 17 EQLRRLQEEKL-CKICMDRNIAIVFVPCGHLVTCKQCA--------EAVDKCPMCYTVI 66
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
0.325 0.139 0.451
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,386,268
Number of Sequences: 62578
Number of extensions: 285976
Number of successful extensions: 865
Number of sequences better than 100.0: 59
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 42
Number of HSP's that attempted gapping in prelim test: 832
Number of HSP's gapped (non-prelim): 60
length of query: 243
length of database: 14,973,337
effective HSP length: 96
effective length of query: 147
effective length of database: 8,965,849
effective search space: 1317979803
effective search space used: 1317979803
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)