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= psy2696
(180 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 3/67 (4%)
Query: 35 KNPLLCHVCDDYYTEPCLLSCYHSFCARCLRGRTVDGKLSCPICGQHTLLKEGSTLPPPD 94
+N L C +C +Y+ E L+C HSFC+ C+ + K+ CPIC + +K + D
Sbjct: 51 ENELQCIICSEYFIEAVTLNCAHSFCSYCI-NEWMKRKIECPICRKD--IKSKTYSLVLD 107
Query: 95 NVLKQLI 101
N + +++
Sbjct: 108 NXINKMV 114
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 35 KNPLLCHVCDDYYTEPCLLSCYHSFCARCLRGRTVDGKLSCPICGQ 80
+N L C +C +Y+ E L+C HSFC+ C+ + K+ CPIC +
Sbjct: 51 ENELQCIICSEYFIEAVTLNCAHSFCSYCI-NEWMKRKIECPICRK 95
>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 = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 35 KNPLLCHVCDDYYTEPCLLSCYHSFCARCLRGRTVDGKLSCPIC 78
+N L C +C +Y+ E L+C HSFC+ C+ + K+ CPIC
Sbjct: 62 ENELQCIICSEYFIEAVTLNCAHSFCSYCI-NEWMKRKIECPIC 104
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 33/76 (43%), Gaps = 15/76 (19%)
Query: 35 KNPLLCHVCDDYYTEPCLLSCYHSFCARCL-----RGRTVDGKLSCPICGQHTLLKEGST 89
K + C +C + EP C HSFC C+ R DGK +CP+C
Sbjct: 17 KEEVTCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVC----------R 66
Query: 90 LPPPDNVLKQLIEVAN 105
+P P LK + VAN
Sbjct: 67 VPYPFGNLKPNLHVAN 82
>pdb|2EGP|A Chain A, Solution Structure Of The Ring-Finger Domain From Human
Tripartite Motif Protein 34
Length = 79
Score = 35.4 bits (80), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 6/51 (11%)
Query: 35 KNPLLCHVCDDYYTEPCLLSCYHSFCARCLRGR------TVDGKLSCPICG 79
+ + C +C + TEP L C HS C C+ ++ GK SCP+CG
Sbjct: 10 QEEVTCPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCG 60
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 34.3 bits (77), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 38 LLCHVCDDYYTEPCLLSCYHSFCARCLR--GRTVDGKLSCPIC 78
++C +C D +P + C H+FC +C+ G T G CP+C
Sbjct: 21 VICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC 63
>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 = 33.9 bits (76), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 35 KNPLLCHVCDDYYTEPCLLSCYHSFCARCL-----RGRTVDGKLSCPIC 78
K + C +C + T+P L C HSFC CL + G+ SCP+C
Sbjct: 17 KEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVC 65
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 33.5 bits (75), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 35 KNPLLCHVCDDYYTEPCLLSCYHSFCARCLR--GRTVDGKLSCPIC 78
+ ++C +C D +P + C H+FC +C+ G T G CP+C
Sbjct: 18 QEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC 63
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 32.7 bits (73), Expect = 0.12, Method: Composition-based stats.
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 40 CHVCDDYYTEPCLLSCYHSFCARCLRG--RTVDGKLSCPIC 78
C VC +Y EP ++ C H+FC C+ ++ CP+C
Sbjct: 18 CSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPCPVC 58
>pdb|3KNV|A Chain A, Crystal Structure Of The Ring And First Zinc Finger
Domains Of Traf2
Length = 141
Score = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 29/69 (42%), Gaps = 5/69 (7%)
Query: 39 LCHVCDDYYTEPCLLSCYHSFCARCLRGRTVDGKLSCPICGQHTLLKEG-----STLPPP 93
LC C + P C H +C+ CL G +C C + +EG S+ P
Sbjct: 33 LCSACRNVLRRPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIYEEGISILESSSAFP 92
Query: 94 DNVLKQLIE 102
DN ++ +E
Sbjct: 93 DNAARREVE 101
>pdb|3L11|A Chain A, Crystal Structure Of The Ring Domain Of Rnf168
Length = 115
Score = 31.6 bits (70), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 17/39 (43%)
Query: 40 CHVCDDYYTEPCLLSCYHSFCARCLRGRTVDGKLSCPIC 78
C +C + EP L C H+ C C + L CP C
Sbjct: 18 CGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFC 56
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 30.8 bits (68), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 36 NP-LLCHVCDDYYTEPC-LLSCYHSFCARCLRGRTVDGKLSCPIC 78
NP L+C +C Y+ + ++ C HSFC C+ R ++ CPIC
Sbjct: 13 NPHLMCVLCGGYFIDATTIIECLHSFCKTCI-VRYLETSKYCPIC 56
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 30.8 bits (68), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 36 NP-LLCHVCDDYYTEPC-LLSCYHSFCARCLRGRTVDGKLSCPIC 78
NP L+C +C Y+ + ++ C HSFC C+ R ++ CPIC
Sbjct: 13 NPHLMCVLCGGYFIDATTIIECLHSFCKTCI-VRYLETSKYCPIC 56
>pdb|2CT2|A Chain A, Solution Structure Of The Ring Domain Of The Tripartite
Motif Protein 32
Length = 88
Score = 30.4 bits (67), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 8/71 (11%)
Query: 35 KNPLLCHVCDDYYTE----PCLLSCYHSFCARCLR---GRTVDGKLSCPICGQHTLLKEG 87
+ L C +C + +TE P LL C H+ C +CL +++G + CP C + T +
Sbjct: 13 REVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSING-VRCPFCSKITRITSL 71
Query: 88 STLPPPDNVLK 98
+ L VLK
Sbjct: 72 TQLTDNLTVLK 82
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 30.4 bits (67), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 36 NP-LLCHVCDDYYTEPC-LLSCYHSFCARCLRGRTVDGKLSCPIC 78
NP L+C +C Y+ + ++ C HSFC C+ R ++ CPIC
Sbjct: 9 NPHLMCVLCGGYFIDATTIIECLHSFCKTCI-VRYLETSKYCPIC 52
>pdb|1Z6U|A Chain A, Np95-Like Ring Finger Protein Isoform B [homo Sapiens]
pdb|1Z6U|B Chain B, Np95-Like Ring Finger Protein Isoform B [homo Sapiens]
Length = 150
Score = 30.4 bits (67), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 38 LLCHVCDDYYTEPCLLSCYHSFCARCLRGRTVDGKLSCPICGQHTLLKEGSTLPPPDNVL 97
+C C + +P C+H+ C CL+ SCP C +H L + + P+ +L
Sbjct: 79 FMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPAC-RHDLGQNYIMI--PNEIL 135
Query: 98 KQLIEV 103
+ L+++
Sbjct: 136 QTLLDL 141
>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 = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 28/48 (58%), Gaps = 2/48 (4%)
Query: 38 LLCHVCDDYYTEPCLLS-CYHSFCARCLRGRTVDG-KLSCPICGQHTL 83
LLC +C D T+ ++ C +S+C C+R ++ + +CP C Q+ +
Sbjct: 14 LLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV 61
>pdb|2YUR|A Chain A, Solution Structure Of The Ring Finger Of Human
Retinoblastoma-Binding Protein 6
Length = 74
Score = 28.5 bits (62), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 38 LLCHVCDDYYTEPCLLS-CYHSFCARCLRGRTVDG-KLSCPICGQHTLLKEGSTLP 91
LLC +C D T+ ++ C +S+C C+R ++ + +CP C Q+ + + + P
Sbjct: 16 LLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDALSGP 71
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 28.1 bits (61), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 2/58 (3%)
Query: 38 LLCHVCDDYYTEPCLL-SCYHSFCARCLRGRTVDGKLSCPICGQHTLLKEGSTLPPPD 94
L+C +C D C H FCA C+ G CP C + L+ + S P P+
Sbjct: 55 LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTC-RKKLVSKRSLRPDPN 111
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 27.7 bits (60), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 2/58 (3%)
Query: 38 LLCHVCDDYYTEPCLL-SCYHSFCARCLRGRTVDGKLSCPICGQHTLLKEGSTLPPPD 94
L+C +C D C H FCA C+ G CP C + L+ + S P P+
Sbjct: 54 LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTC-RKKLVSKRSLRPDPN 110
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 27.3 bits (59), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 2/58 (3%)
Query: 38 LLCHVCDDYYTEPCLL-SCYHSFCARCLRGRTVDGKLSCPICGQHTLLKEGSTLPPPD 94
L+C +C D C H FCA C+ G CP C + L+ + S P P+
Sbjct: 35 LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKK-LVSKRSLRPDPN 91
>pdb|2D8T|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 146
Length = 71
Score = 27.3 bits (59), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 40 CHVCDDYYTEPCLLSCYHSFCARCLRGRTVDGKLSCPICGQ 80
C +C P L C H FC C++G + GK C +C Q
Sbjct: 18 CAICLQTCVHPVSLPCKHVFCYLCVKGASWLGK-RCALCRQ 57
>pdb|2CSY|A Chain A, Solution Structure Of The Ring Domain Of The Zinc Finger
Protein 183-Like 1
Length = 81
Score = 26.9 bits (58), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 23/64 (35%), Gaps = 5/64 (7%)
Query: 37 PLLCHVCDDYYTEPCLLSCYHSFCARCLRGRTVDGKLSCPICGQHTLLKEGSTLPPPDNV 96
P C +C + P + C H FC C C IC Q T G P +
Sbjct: 15 PFRCFICRQAFQNPVVTKCRHYFCESCAL-EHFRATPRCYICDQPT----GGIFNPAKEL 69
Query: 97 LKQL 100
+ +L
Sbjct: 70 MAKL 73
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 26.9 bits (58), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 52 LLSCYHSFCARCLRGRTVDGKLSCPIC 78
+L C HSFC +C+ + D +CPIC
Sbjct: 29 ILPCAHSFCQKCID-KWSDRHRNCPIC 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 = 26.6 bits (57), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 38 LLCHVCDDYYTEPCLL-SCYHSFCARCLRGRTVDGKLSCPIC 78
L C +C +Y+ ++ C H++C+ C+R + + K CP C
Sbjct: 23 LRCGICFEYFNIAMIIPQCSHNYCSLCIR-KFLSYKTQCPTC 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
0.323 0.135 0.439
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,627,410
Number of Sequences: 62578
Number of extensions: 165737
Number of successful extensions: 540
Number of sequences better than 100.0: 53
Number of HSP's better than 100.0 without gapping: 27
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 506
Number of HSP's gapped (non-prelim): 57
length of query: 180
length of database: 14,973,337
effective HSP length: 93
effective length of query: 87
effective length of database: 9,153,583
effective search space: 796361721
effective search space used: 796361721
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 48 (23.1 bits)