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= 039128
(404 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 33/68 (48%), Gaps = 12/68 (17%)
Query: 18 ISHSFRCCICLDLLYKPIVLSCGHISCFWCV----HRSMNGLRESHCPICR--------R 65
+ C ICL+LL +P+ L CGH C C+ +SM ES CP+CR R
Sbjct: 16 VKEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIR 75
Query: 66 PYNHFPSI 73
P H +I
Sbjct: 76 PNRHVANI 83
Score = 33.1 bits (74), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 195 DVLCTACKQLLIHPVVLNCGHVYCETCI 222
+V C C +LL P+ L+CGH +C+ C+
Sbjct: 19 EVTCPICLELLTQPLSLDCGHSFCQACL 46
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 8/58 (13%)
Query: 16 EKISHSFRCCICLDLLYKPIVLSCGHISCFWCV------HRSMNGLRESHCPICRRPY 67
E I C ICL+LL +P+ C H C C+ +R+ +G + +CP+CR PY
Sbjct: 14 EMIKEEVTCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDG--KGNCPVCRVPY 69
Score = 29.6 bits (65), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 29/67 (43%), Gaps = 6/67 (8%)
Query: 195 DVLCTACKQLLIHPVVLNCGHVYCETCII------TPTVQQLKCEVCQCLNPNGFPKVCL 248
+V C C +LL PV +C H +C CI T + C VC+ P G K L
Sbjct: 19 EVTCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLKPNL 78
Query: 249 ELDQFLE 255
+ +E
Sbjct: 79 HVANIVE 85
>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 = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 16 EKISHSFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICR 64
+K+ SF C C +L+Y+P+ C H C C+ RS S CP CR
Sbjct: 73 KKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFS-CPACR 120
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 22 FRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLR-ESHCPICR 64
C ICL+L+ +P+ C HI C +C+ + +N + S CP+C+
Sbjct: 22 LECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCK 65
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 18 ISHSFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICRR 65
+ + +C IC + + + L+C H C +C++ M R+ CPICR+
Sbjct: 50 LENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMK--RKIECPICRK 95
Score = 35.0 bits (79), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 195 DVLCTACKQLLIHPVVLNCGHVYCETCIITPTVQQLKCEVCQ 236
++ C C + I V LNC H +C CI ++++C +C+
Sbjct: 53 ELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICR 94
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 18 ISHSFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICRR 65
+ + +C IC + + + L+C H C +C++ M R+ CPICR+
Sbjct: 50 LENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMK--RKIECPICRK 95
Score = 35.0 bits (79), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 195 DVLCTACKQLLIHPVVLNCGHVYCETCIITPTVQQLKCEVCQ 236
++ C C + I V LNC H +C CI ++++C +C+
Sbjct: 53 ELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICR 94
>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 = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 18 ISHSFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICRR 65
+ + +C IC + + + L+C H C +C++ M R+ CPICR+
Sbjct: 61 LENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMK--RKIECPICRK 106
Score = 35.4 bits (80), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 195 DVLCTACKQLLIHPVVLNCGHVYCETCIITPTVQQLKCEVCQ 236
++ C C + I V LNC H +C CI ++++C +C+
Sbjct: 64 ELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICR 105
>pdb|2EGP|A Chain A, Solution Structure Of The Ring-Finger Domain From Human
Tripartite Motif Protein 34
Length = 79
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 9/65 (13%)
Query: 11 SNAEPEKISHSFRCCICLDLLYKPIVLSCGHISCFWCVH-------RSMNGLRESHCPIC 63
S+ + C ICL+LL +P+ L CGH C C+ SM G +S CP+C
Sbjct: 2 SSGSSGNVQEEVTCPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGG--KSSCPVC 59
Query: 64 RRPYN 68
Y+
Sbjct: 60 GISYS 64
Score = 32.3 bits (72), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 195 DVLCTACKQLLIHPVVLNCGHVYCETCI 222
+V C C +LL P+ L+CGH C CI
Sbjct: 12 EVTCPICLELLTEPLSLDCGHSLCRACI 39
>pdb|3FL2|A Chain A, Crystal Structure Of The Ring Domain Of The E3
Ubiquitin- Protein Ligase Uhrf1
Length = 124
Score = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 17 KISHSFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICR 64
K+ +F+C C +L+++PI C H C C+ RS S CP CR
Sbjct: 48 KVEETFQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFS-CPACR 94
>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 = 0.030, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 11 SNAEPEKISHSFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGL-RESHCPIC 63
S+ E + C +CL+ L +P+++ CGH C C+ R L R+ CP+C
Sbjct: 5 SSGALENLQVEASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPCPVC 58
Score = 33.1 bits (74), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 194 VDVLCTACKQLLIHPVVLNCGHVYCETCI 222
V+ C+ C + L PV++ CGH +C+ CI
Sbjct: 14 VEASCSVCLEYLKEPVIIECGHNFCKACI 42
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 34.7 bits (78), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 17 KISHSFRCCICLDLLYKPIVLSCGHISCFWCVHR-SMNGLRESHCPICR 64
K+ C ICLD+L KP+ + CGH C C+ + CP+C+
Sbjct: 16 KLQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCK 64
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 195 DVLCTACKQLLIHPVVLNCGHVYCETCI 222
+V+C C +L PV ++CGH +C CI
Sbjct: 20 EVICPICLDILQKPVTIDCGHNFCLKCI 47
>pdb|3L11|A Chain A, Crystal Structure Of The Ring Domain Of Rnf168
Length = 115
Score = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 9/78 (11%)
Query: 23 RCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICRRPYNHFPS--------IC 74
+C IC+++L +P+ L C H C C ++ CP CRR + + +
Sbjct: 17 QCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLC-CPFCRRRVSSWTRYHTRRNSLVN 75
Query: 75 VMLHRLLLKMYPIAYKMR 92
V L ++ K YP K+R
Sbjct: 76 VELWTIIQKHYPRECKLR 93
Score = 31.2 bits (69), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 26/119 (21%), Positives = 51/119 (42%), Gaps = 19/119 (15%)
Query: 192 SIVDVLCTACKQLLIHPVVLNCGHVYCETCIITPTVQQLKCEVCQCLNPNGFPKVCLELD 251
S+ + C C ++L+ PV L C H C+ C + TV++ +C
Sbjct: 12 SLSECQCGICMEILVEPVTLPCNHTLCKPCFQS-TVEKA--------------SLCCPFC 56
Query: 252 QFLEEQFSKEYALRRDVILNHEFATMCSMGAGKSGFISSSGAKGEHSSWLADAHSKVHV 310
+ +++ Y RR+ ++N E T+ + + +SG + E +AD + V +
Sbjct: 57 RRRVSSWTR-YHTRRNSLVNVELWTIIQKHYPRECKLRASGQESEE---VADDYQPVRL 111
>pdb|2D8T|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 146
Length = 71
Score = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 23/46 (50%)
Query: 198 CTACKQLLIHPVVLNCGHVYCETCIITPTVQQLKCEVCQCLNPNGF 243
C C Q +HPV L C HV+C C+ + +C +C+ P F
Sbjct: 18 CAICLQTCVHPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDF 63
Score = 28.5 bits (62), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 23 RCCICLDLLYKPIVLSCGHISCFWCVH-RSMNGLRESHCPICRR 65
C ICL P+ L C H+ C+ CV S G R C +CR+
Sbjct: 17 ECAICLQTCVHPVSLPCKHVFCYLCVKGASWLGKR---CALCRQ 57
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 17 KISHSFRCCICLDLLYKPIVLSCGHISCFWCVHR 50
K+ C ICLD+L KP+ + CGH C C+ +
Sbjct: 16 KLQEEVICPICLDILQKPVTIDCGHNFCLKCITQ 49
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 195 DVLCTACKQLLIHPVVLNCGHVYCETCI 222
+V+C C +L PV ++CGH +C CI
Sbjct: 20 EVICPICLDILQKPVTIDCGHNFCLKCI 47
>pdb|2CSY|A Chain A, Solution Structure Of The Ring Domain Of The Zinc Finger
Protein 183-Like 1
Length = 81
Score = 32.7 bits (73), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 194 VDVLCTACKQLLIHPVVLNCGHVYCETCIITPTVQQLKCEVCQCLNPNG 242
+ C C+Q +PVV C H +CE+C + +C +C P G
Sbjct: 14 IPFRCFICRQAFQNPVVTKCRHYFCESCALEHFRATPRCYICD--QPTG 60
>pdb|1JM7|B Chain B, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 117
Score = 32.7 bits (73), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 27/105 (25%), Positives = 47/105 (44%), Gaps = 15/105 (14%)
Query: 11 SNAEPEKISHSFRCCICLDLLYKPIVL-SCGHISCFWCVHRSMNGLRESHCPICRRPYNH 69
S A +++ RC C ++L +P+ L C HI C CV + + CP+C P
Sbjct: 12 SRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIG----TGCPVCYTPAWI 67
Query: 70 FPSICVMLHRLLLKMYPIAYKMREI-------EILEDERRYDFFS 107
+ ++R L M + K+R + ++ ED+ R F+
Sbjct: 68 QD---LKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLFN 109
>pdb|3KNV|A Chain A, Crystal Structure Of The Ring And First Zinc Finger
Domains Of Traf2
Length = 141
Score = 32.3 bits (72), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 197 LCTACKQLLIHPVVLNCGHVYCETCIIT 224
LC+AC+ +L P CGH YC C+ +
Sbjct: 33 LCSACRNVLRRPFQAQCGHRYCSFCLAS 60
>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 = 32.3 bits (72), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 16 EKISHSFRCCICLDLLYKP-IVLSCGHISCFWCVHRSMNGLRESHCPICRRPYN 68
E I+ FRC IC + L + C + CF C+ R + R + CP CR P
Sbjct: 17 ESIAEVFRCFICXEKLRDARLCPHCSKLCCFSCIRRWLTEQR-AQCPHCRAPLQ 69
>pdb|1E4U|A Chain A, N-Terminal Ring Finger Domain Of Human Not-4
Length = 78
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 7/39 (17%)
Query: 38 SCGHISCFWCVHR---SMNGLRESHCPICRRPYNHFPSI 73
+CG+ C +C HR NGL CP CR+PY P++
Sbjct: 32 TCGYQICRFCWHRIRTDENGL----CPACRKPYPEDPAV 66
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 11 SNAEPEKISHSFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICR 64
S+ ++++ CCIC+D ++L C H C C+ + + R +CPICR
Sbjct: 5 SSGRVKQLTDEEECCICMDGRAD-LILPCAHSFCQKCIDKWSD--RHRNCPICR 55
>pdb|2YUR|A Chain A, Solution Structure Of The Ring Finger Of Human
Retinoblastoma-Binding Protein 6
Length = 74
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 11 SNAEPEKISHSFRCCICLDLLYKPIVLS-CGHISCFWCVHRSMNGLRESHCPICRR 65
S+ E + I C IC D++ +V+ CG+ C C+ ++ E CP C +
Sbjct: 5 SSGEDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQ 60
>pdb|4AUQ|B Chain B, Structure Of Birc7-Ubch5b-Ub Complex.
pdb|4AUQ|E Chain E, Structure Of Birc7-Ubch5b-Ub Complex
Length = 62
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 6/57 (10%)
Query: 12 NAEPEKISHSFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICRRPYN 68
A+ ++ C +CLD + + CGH+ C C GL+ CPICR P
Sbjct: 4 EAQLRRLQEERTCKVCLDRAVSIVFVPCGHLVCAECA----PGLQ--LCPICRAPVR 54
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 30.0 bits (66), Expect = 2.4, Method: Composition-based stats.
Identities = 24/103 (23%), Positives = 39/103 (37%), Gaps = 13/103 (12%)
Query: 186 HNCKQISIVDV----LCTACKQLLIHPV-VLNCGHVYCETCIITPTVQQLKCEVCQCLNP 240
H +I I ++ +C C I ++ C H +C+TCI+ C +C
Sbjct: 2 HRTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVH 61
Query: 241 NGFPKVCLELDQFLEE--------QFSKEYALRRDVILNHEFA 275
P + + D+ L++ F E RRD H A
Sbjct: 62 KTRPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSA 104
>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 = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 13 AEPEKISHSFRCCICLDLLYKPIVLSC-GHISCFWCVHRSMNGLRESHCPICRR 65
+E + I C IC D++ +V+ C G+ C C+ ++ E CP C +
Sbjct: 5 SEDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQ 58
Score = 28.1 bits (61), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 195 DVLCTACKQLLIHPVVLNC-GHVYCETCIIT 224
++LC CK ++ VV+ C G+ YC+ CI T
Sbjct: 13 ELLCLICKDIMTDAVVIPCCGNSYCDECIRT 43
>pdb|2CT2|A Chain A, Solution Structure Of The Ring Domain Of The Tripartite
Motif Protein 32
Length = 88
Score = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 11/63 (17%)
Query: 11 SNAEPEKISHSFRCCICLDLL----YKPIVLSCGHISCFWCVHR----SMNGLRESHCPI 62
S+ + + C IC++ +P +L CGH C C+ + S+NG+R CP
Sbjct: 5 SSGNLDALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVR---CPF 61
Query: 63 CRR 65
C +
Sbjct: 62 CSK 64
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 29.3 bits (64), Expect = 4.5, Method: Composition-based stats.
Identities = 20/86 (23%), Positives = 33/86 (38%), Gaps = 9/86 (10%)
Query: 196 VLCTACKQLLIHPV-VLNCGHVYCETCIITPTVQQLKCEVCQCLNPNGFPKVCLELDQFL 254
++C C I ++ C H +C+TCI+ C +C P + + D+ L
Sbjct: 12 LMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDKTL 71
Query: 255 EE--------QFSKEYALRRDVILNH 272
++ F E RRD H
Sbjct: 72 QDIVYKLVPGLFKNEMKRRRDFYAAH 97
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 28.9 bits (63), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 24/103 (23%), Positives = 39/103 (37%), Gaps = 13/103 (12%)
Query: 186 HNCKQISIVDV----LCTACKQLLIHPV-VLNCGHVYCETCIITPTVQQLKCEVCQCLNP 240
H +I I ++ +C C I ++ C H +C+TCI+ C +C
Sbjct: 2 HRTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVH 61
Query: 241 NGFPKVCLELDQFLEE--------QFSKEYALRRDVILNHEFA 275
P + + D+ L++ F E RRD H A
Sbjct: 62 KTRPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSA 104
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 28.9 bits (63), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 11/59 (18%)
Query: 19 SHSFRCCICLDLLYKPIV--------LSCGHISCFWCVHRSMNGLRESHCPICRRPYNH 69
S + C IC+D Y IV CGH+ C C+ S+ + CP CR+ NH
Sbjct: 13 SGTVSCPICMDG-YSEIVQNGRLIVSTECGHVFCSQCLRDSLKN--ANTCPTCRKKINH 68
>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 = 28.5 bits (62), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 11/61 (18%)
Query: 17 KISHSFRCCICLDLLYKPIV--------LSCGHISCFWCVHRSMNGLRESHCPICRRPYN 68
+ S + C IC+D Y IV CGH+ C C+ S+ + CP CR+ N
Sbjct: 6 RPSGTVSCPICMDG-YSEIVQNGRLIVSTECGHVFCSQCLRDSLK--NANTCPTCRKKIN 62
Query: 69 H 69
H
Sbjct: 63 H 63
>pdb|1UR6|B Chain B, Nmr Based Structural Model Of The Ubch5b-Cnot4 Complex
Length = 52
Score = 28.1 bits (61), Expect = 8.9, Method: Composition-based stats.
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 7/33 (21%)
Query: 38 SCGHISCFWCVHR---SMNGLRESHCPICRRPY 67
+CG+ C +C HR NGL CP CR+PY
Sbjct: 21 TCGYQICRFCWHRIRTDENGL----CPACRKPY 49
>pdb|1RMD|A Chain A, Rag1 Dimerization Domain
Length = 116
Score = 28.1 bits (61), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 193 IVDVLCTACKQLLIHPVVLNCGHVYCETCII 223
+ + C C+ +L PV +C H++C CI+
Sbjct: 21 VKSISCQICEHILADPVETSCKHLFCRICIL 51
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
0.324 0.137 0.435
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,409,871
Number of Sequences: 62578
Number of extensions: 520503
Number of successful extensions: 1304
Number of sequences better than 100.0: 46
Number of HSP's better than 100.0 without gapping: 26
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 1235
Number of HSP's gapped (non-prelim): 88
length of query: 404
length of database: 14,973,337
effective HSP length: 101
effective length of query: 303
effective length of database: 8,652,959
effective search space: 2621846577
effective search space used: 2621846577
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (25.0 bits)