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= 035975
(685 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3ZTG|A Chain A, Solution Structure Of The Ring Finger-Like Domain Of
Retinoblastoma Binding Protein-6 (Rbbp6)
pdb|3ZTG|B Chain B, Solution Structure Of The Ring Finger-Like Domain Of
Retinoblastoma Binding Protein-6 (Rbbp6)
Length = 92
Score = 60.5 bits (145), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 45/74 (60%), Gaps = 2/74 (2%)
Query: 130 ENGNFPSELKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVE--KARCPKCFSSKCRLED 187
E+ P EL C +C + +AV+IPCC +S+C++CIR L+E + CP C + +
Sbjct: 6 EDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA 65
Query: 188 LLPNVSLRQAIEHF 201
L+ N LRQA+ +F
Sbjct: 66 LIANKFLRQAVNNF 79
>pdb|2YUR|A Chain A, Solution Structure Of The Ring Finger Of Human
Retinoblastoma-Binding Protein 6
Length = 74
Score = 52.8 bits (125), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 37/57 (64%), Gaps = 2/57 (3%)
Query: 124 TNASAMENGNFPSELKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVE--KARCPKC 178
++ S+ E+ P EL C +C + +AV+IPCC +S+C++CIR L+E + CP C
Sbjct: 2 SSGSSGEDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTC 58
>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 = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 18/41 (43%), Positives = 25/41 (60%)
Query: 138 LKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEKARCPKC 178
L+C +C F A++IP C H++C CIR L K +CP C
Sbjct: 23 LRCGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTC 63
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 131 NGNFPSELKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEKARCPKC 178
N +EL+C +C+ F EAV + C HSFC CI + K CP C
Sbjct: 47 NDVLENELQCIICSEYFIEAVTLNC-AHSFCSYCINEWMKRKIECPIC 93
>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 = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 131 NGNFPSELKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEKARCPKC 178
N +EL+C +C+ F EAV + C HSFC CI + K CP C
Sbjct: 58 NDVLENELQCIICSEYFIEAVTLNC-AHSFCSYCINEWMKRKIECPIC 104
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 131 NGNFPSELKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEKARCPKC 178
N +EL+C +C+ F EAV + C HSFC CI + K CP C
Sbjct: 47 NDVLENELQCIICSEYFIEAVTLNC-AHSFCSYCINEWMKRKIECPIC 93
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 39.3 bits (90), Expect = 0.007, Method: Composition-based stats.
Identities = 16/39 (41%), Positives = 20/39 (51%)
Query: 140 CSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEKARCPKC 178
CS+C +A I C H+FC+ CI RCPKC
Sbjct: 18 CSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKC 56
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 39.3 bits (90), Expect = 0.008, Method: Composition-based stats.
Identities = 18/41 (43%), Positives = 20/41 (48%)
Query: 138 LKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEKARCPKC 178
L C LC F +A I C HSFC+ CI L CP C
Sbjct: 12 LMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPIC 52
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 38.9 bits (89), Expect = 0.011, Method: Composition-based stats.
Identities = 18/41 (43%), Positives = 20/41 (48%)
Query: 138 LKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEKARCPKC 178
L C LC F +A I C HSFC+ CI L CP C
Sbjct: 16 LMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPIC 56
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 38.9 bits (89), Expect = 0.011, Method: Composition-based stats.
Identities = 18/41 (43%), Positives = 20/41 (48%)
Query: 138 LKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEKARCPKC 178
L C LC F +A I C HSFC+ CI L CP C
Sbjct: 16 LMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPIC 56
>pdb|1JM7|B Chain B, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 117
Score = 33.9 bits (76), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 138 LKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEKARCPKCFSSKCRLEDLLPNVSLRQA 197
L+CS C + +E V + C+H FC C+ + CP C++ ++DL N L
Sbjct: 23 LRCSRCTNILREPVCLGGCEHIFCSNCVSDCI--GTGCPVCYTPA-WIQDLKINRQLDSM 79
Query: 198 IE 199
I+
Sbjct: 80 IQ 81
>pdb|2QIZ|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 33.9 bits (76), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 3/71 (4%)
Query: 129 MENGNFPSELKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEKARCPKCFSSK-CRLED 187
+E G+ P E L T+ K+ V++P + + I+ L+ + P F+ +LED
Sbjct: 897 LEYGDVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSDSTDP--FNRMPLKLED 954
Query: 188 LLPNVSLRQAI 198
+ PN LRQ I
Sbjct: 955 VTPNEELRQKI 965
>pdb|3M62|A Chain A, Crystal Structure Of Ufd2 In Complex With The
Ubiquitin-Like (Ubl) Domain Of Rad23
pdb|3M63|A Chain A, Crystal Structure Of Ufd2 In Complex With The
Ubiquitin-Like (Ubl) Domain Of Dsk2
Length = 968
Score = 33.5 bits (75), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 3/71 (4%)
Query: 129 MENGNFPSELKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEKARCPKCFSSK-CRLED 187
+E G+ P E L T+ K+ V++P + + I+ L+ + P F+ +LED
Sbjct: 883 LEYGDVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSDSTDP--FNRMPLKLED 940
Query: 188 LLPNVSLRQAI 198
+ PN LRQ I
Sbjct: 941 VTPNEELRQKI 951
>pdb|2QJ0|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 33.1 bits (74), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 129 MENGNFPSELKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEKARCPKCFSSKCRLEDL 188
+E G+ P E L T+ K+ V++P + + I+ L+ + P +LED+
Sbjct: 897 LEYGDVPDEFLDPLXYTIXKDPVILPASKXNIDRSTIKAHLLSDSTDPFN-RXPLKLEDV 955
Query: 189 LPNVSLRQAI 198
PN LRQ I
Sbjct: 956 TPNEELRQKI 965
>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 = 32.7 bits (73), Expect = 0.70, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 138 LKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVE-KARCPKC 178
+C +C ++A + P C C CIR L E +A+CP C
Sbjct: 23 FRCFICXEKLRDARLCPHCSKLCCFSCIRRWLTEQRAQCPHC 64
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 32.3 bits (72), Expect = 0.87, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 138 LKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEK---ARCPKCFSSKCRLEDLLPNVSL 194
L+C +C L KE V C H FC+ C+ +L +K ++CP C + + L +
Sbjct: 22 LECPICLELIKEPVSTKC-DHIFCKFCMLKLLNQKKGPSQCPLCKNDITK-RSLQESTRF 79
Query: 195 RQAIEHFLE 203
Q +E L+
Sbjct: 80 SQLVEELLK 88
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 32.3 bits (72), Expect = 0.93, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 21/48 (43%), Gaps = 7/48 (14%)
Query: 137 ELKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVE------KARCPKC 178
E+ C +C L KE V C HSFC CI L K CP C
Sbjct: 19 EVTCPICLELLKEPVSADC-NHSFCRACITLNYESNRNTDGKGNCPVC 65
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 136 SELKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEKAR-CPKC 178
SEL C +C + K + C H FC CI L + CP C
Sbjct: 53 SELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTC 96
>pdb|3CH4|B Chain B, The Crystal Structure Of Human Phosphomavelonate Kinase At
1.8 A Resolution
Length = 202
Score = 31.2 bits (69), Expect = 2.0, Method: Composition-based stats.
Identities = 23/63 (36%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 299 VHGSAQP---VDFKRRPVDLDEFAECHGE-SQPIHVEAEFSNKRKRGLWVDTSGADKSFI 354
V G +QP V RR D+ F E +G +Q + V A ++++RG WV T G D +
Sbjct: 98 VEGISQPIWLVSDTRRVSDIQWFREAYGAVTQTVRVVALEQSRQQRG-WVFTPGVDDAES 156
Query: 355 ESG 357
E G
Sbjct: 157 ECG 159
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 30.4 bits (67), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 136 SELKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEKAR-CPKC 178
SEL C +C + K + C H FC CI L + CP C
Sbjct: 52 SELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTC 95
>pdb|3L11|A Chain A, Crystal Structure Of The Ring Domain Of Rnf168
Length = 115
Score = 30.4 bits (67), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 4/45 (8%)
Query: 136 SELKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEKAR--CPKC 178
SE +C +C + E V +P C H+ C+ C + VEKA CP C
Sbjct: 14 SECQCGICMEILVEPVTLP-CNHTLCKPCFQST-VEKASLCCPFC 56
>pdb|2YSA|A Chain A, Solution Structure Of The Zinc Finger Cchc Domain From The
Human Retinoblastoma-Binding Protein 6 (Retinoblastoma-
Binding Q Protein 1, Rbq-1)
Length = 55
Score = 30.0 bits (66), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 364 TCYMCGSPNHLIRDCPA 380
TC+ CG P H I++CP
Sbjct: 9 TCFRCGKPGHYIKNCPT 25
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 30.0 bits (66), Expect = 4.6, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 8/54 (14%)
Query: 128 AMENGNFPSELKCSLCNTLFK---EAVMIPCCQHSFCEKCIRLVLVEKARCPKC 178
AM++G ++C++C + EA +P C H F +C+ + L + CP C
Sbjct: 1 AMDDG-----VECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLC 49
>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 = 5.7, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 133 NFPSELKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEKAR---CPKC 178
N E CS+C KE V+I C H+FC+ CI + R CP C
Sbjct: 11 NLQVEASCSVCLEYLKEPVIIE-CGHNFCKACITRWWEDLERDFPCPVC 58
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 29.6 bits (65), Expect = 6.1, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 137 ELKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEKA---RCPKCFSS 181
E+ C +C + ++ V I C H+FC KCI + +CP C +S
Sbjct: 20 EVICPICLDILQKPVTIDC-GHNFCLKCITQIGETSCGFFKCPLCKTS 66
>pdb|2YU4|A Chain A, Solution Structure Of The Sp-Ring Domain In Non-Smc
Element 2 Homolog (Mms21, S. Cerevisiae)
Length = 94
Score = 29.6 bits (65), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 8/72 (11%)
Query: 136 SELKCSLCNTLFKEAVMIPCCQHSFCEKCI------RLVLVEKARCPK--CFSSKCRLED 187
S C + K+ V C H++ E I R +KA CP+ C + R D
Sbjct: 6 SGFTCPITKEEMKKPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSD 65
Query: 188 LLPNVSLRQAIE 199
L+ + +LR+AIE
Sbjct: 66 LIQDEALRRAIE 77
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 29.6 bits (65), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 132 GNFPSELKCSLCNTLFKEAVMIPCCQHSFCEKCI 165
G S+ +C +C +EAV P C H FC+ CI
Sbjct: 1 GPLGSKYECPICLMALREAVQTP-CGHRFCKACI 33
>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf
Receptor-Associated Factor 6 Protein
Length = 86
Score = 29.3 bits (64), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 136 SELKCSLCNTLFKEAVMIPCCQHSFCEKCI 165
S+ +C +C +EAV P C H FC+ CI
Sbjct: 24 SKYECPICLMALREAVQTP-CGHRFCKACI 52
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 28.9 bits (63), Expect = 9.8, Method: Composition-based stats.
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 4/45 (8%)
Query: 137 ELKCSLCNTLFKEAVMIPCCQHSFCEKCIRLVLVEKA---RCPKC 178
E+ C +C + ++ V I C H+FC KCI + +CP C
Sbjct: 20 EVICPICLDILQKPVTIDC-GHNFCLKCITQIGETSCGFFKCPLC 63
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
0.314 0.131 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,632,263
Number of Sequences: 62578
Number of extensions: 856994
Number of successful extensions: 1330
Number of sequences better than 100.0: 40
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 1303
Number of HSP's gapped (non-prelim): 40
length of query: 685
length of database: 14,973,337
effective HSP length: 105
effective length of query: 580
effective length of database: 8,402,647
effective search space: 4873535260
effective search space used: 4873535260
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)