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= 043080
(458 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2FC7|A Chain A, Solution Structure Of The Zz Domain Of Zzz3 Protein
Length = 82
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 22/36 (61%)
Query: 319 HFGVGCDYCGMSPIIGERYKCKDCVESIGFDLCEAC 354
H G CD CG+ PI G R+ C+DC + D C++C
Sbjct: 19 HVGFKCDNCGIEPIQGVRWHCQDCPPEMSLDFCDSC 54
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 14 EAFSDEFKCCVCLELLYKPVVLACGHISCFWCVY----NAMNSWHESNCPVCRNPY 65
E +E C +CLELL +PV C H C C+ + N+ + NCPVCR PY
Sbjct: 14 EMIKEEVTCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPY 69
Score = 35.4 bits (80), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 6/55 (10%)
Query: 207 DDLSCAACKKMLFKPVVLNCGHVFCELCLFV------PEDGNFKCPNCQSLQPYG 255
++++C C ++L +PV +C H FC C+ + DG CP C+ P+G
Sbjct: 18 EEVTCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG 72
>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 = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 16 FSDEFKCCVCLELLYKPVVLACGHISCFWCVY----NAMNSWHESNCPVCRNPY 65
+E C +CLELL +P+ L CGH C C+ +M ES+CPVCR Y
Sbjct: 16 VKEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISY 69
Score = 36.6 bits (83), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 7/57 (12%)
Query: 207 DDLSCAACKKMLFKPVVLNCGHVFCELCLF------VPEDGNFKCPNCQ-SLQPYGL 256
++++C C ++L +P+ L+CGH FC+ CL + + G CP C+ S QP +
Sbjct: 18 EEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENI 74
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 15 AFSDEFKCCVCLELLYKPVVLACGHISCFWCVYNAMNSWH-ESNCPVCRN 63
A +C +CLEL+ +PV C HI C +C+ +N S CP+C+N
Sbjct: 17 AMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKN 66
Score = 32.0 bits (71), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 209 LSCAACKKMLFKPVVLNCGHVFCELC---LFVPEDGNFKCPNCQS 250
L C C +++ +PV C H+FC+ C L + G +CP C++
Sbjct: 22 LECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKN 66
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 6/64 (9%)
Query: 1 MEAEEHEIELADKEAFSDEFKCCVCLELLYKPVVLACGHISCFWCVYNAMNSWHESN--C 58
M+A++ E+ + +E +C +C E + V L C H C +C+ N W + C
Sbjct: 35 MQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAHSFCSYCI----NEWMKRKIEC 90
Query: 59 PVCR 62
P+CR
Sbjct: 91 PICR 94
Score = 38.1 bits (87), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 2/79 (2%)
Query: 202 NWVSVDDLSCAACKKMLFKPVVLNCGHVFCELCLFVPEDGNFKCPNCQSLQPYGLPSVCL 261
N V ++L C C + + V LNC H FC C+ +CP C+ + + L
Sbjct: 47 NDVLENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICR--KDIKSKTYSL 104
Query: 262 IIEHFLEERFSDLYAERKE 280
++++ + + ++L +E KE
Sbjct: 105 VLDNXINKMVNNLSSEVKE 123
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 6/64 (9%)
Query: 1 MEAEEHEIELADKEAFSDEFKCCVCLELLYKPVVLACGHISCFWCVYNAMNSWHESN--C 58
M+A++ E+ + +E +C +C E + V L C H C +C+ N W + C
Sbjct: 35 MQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAHSFCSYCI----NEWMKRKIEC 90
Query: 59 PVCR 62
P+CR
Sbjct: 91 PICR 94
Score = 37.0 bits (84), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 2/79 (2%)
Query: 202 NWVSVDDLSCAACKKMLFKPVVLNCGHVFCELCLFVPEDGNFKCPNCQSLQPYGLPSVCL 261
N V ++L C C + + V LNC H FC C+ +CP C+ + + L
Sbjct: 47 NDVLENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICR--KDIKSKTYSL 104
Query: 262 IIEHFLEERFSDLYAERKE 280
++++ + + ++L +E KE
Sbjct: 105 VLDNCINKMVNNLSSEVKE 123
>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 = 0.003, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 6/64 (9%)
Query: 1 MEAEEHEIELADKEAFSDEFKCCVCLELLYKPVVLACGHISCFWCVYNAMNSWHESN--C 58
M+A++ E+ + +E +C +C E + V L C H C +C+ N W + C
Sbjct: 46 MQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAHSFCSYCI----NEWMKRKIEC 101
Query: 59 PVCR 62
P+CR
Sbjct: 102 PICR 105
Score = 37.4 bits (85), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 207 DDLSCAACKKMLFKPVVLNCGHVFCELCLFVPEDGNFKCPNCQSLQPYGLPSVCLIIEHF 266
++L C C + + V LNC H FC C+ +CP C+ + + L++++
Sbjct: 63 NELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICR--KDIKSKTYSLVLDNC 120
Query: 267 LEERFSDLYAERKE 280
+ + ++L +E KE
Sbjct: 121 INKMVNNLSSEVKE 134
>pdb|2EGP|A Chain A, Solution Structure Of The Ring-Finger Domain From Human
Tripartite Motif Protein 34
Length = 79
Score = 38.1 bits (87), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 5/54 (9%)
Query: 18 DEFKCCVCLELLYKPVVLACGHISCFWCVY----NAMNSW-HESNCPVCRNPYN 66
+E C +CLELL +P+ L CGH C C+ A+ S +S+CPVC Y+
Sbjct: 11 EEVTCPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYS 64
Score = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 7/49 (14%)
Query: 207 DDLSCAACKKMLFKPVVLNCGHVFCELCLFVPE-------DGNFKCPNC 248
++++C C ++L +P+ L+CGH C C+ V G CP C
Sbjct: 11 EEVTCPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVC 59
>pdb|2DIP|A Chain A, Solution Structure Of The Zz Domain Of Zinc Finger Swim
Domain Containing Protein 2
Length = 98
Score = 38.1 bits (87), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 319 HFGVGCDYCGMSPIIGERYKCKDCVESIGFDLCEACHNNPAKVPGRFNQQHKPEHKFEIM 378
H G+ C+ C PI G+ YKC +C+E + LC+ C ++ + F + K K+ +
Sbjct: 29 HLGIPCNNCKQFPIEGKCYKCTECIE---YHLCQECFDSYCHLSHTFTFREKRNQKWRSL 85
Query: 379 Q 379
+
Sbjct: 86 E 86
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 37.4 bits (85), Expect = 0.018, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 3/47 (6%)
Query: 207 DDLSCAACKKMLFKPVVLNCGHVFCELCLFVPED---GNFKCPNCQS 250
+++ C C +L KPV ++CGH FC C+ + G FKCP C++
Sbjct: 19 EEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKT 65
Score = 36.2 bits (82), Expect = 0.041, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 16 FSDEFKCCVCLELLYKPVVLACGHISCFWCVYN-AMNSWHESNCPVCR 62
+E C +CL++L KPV + CGH C C+ S CP+C+
Sbjct: 17 LQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCK 64
>pdb|2D8T|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 146
Length = 71
Score = 36.6 bits (83), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 21 KCCVCLELLYKPVVLACGHISCFWCVYNAMNSWHESNCPVCRN 63
+C +CL+ PV L C H+ C+ CV A SW C +CR
Sbjct: 17 ECAICLQTCVHPVSLPCKHVFCYLCVKGA--SWLGKRCALCRQ 57
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 15/25 (60%)
Query: 211 CAACKKMLFKPVVLNCGHVFCELCL 235
CA C + PV L C HVFC LC+
Sbjct: 18 CAICLQTCVHPVSLPCKHVFCYLCV 42
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 35.4 bits (80), Expect = 0.062, Method: Composition-based stats.
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 207 DDLSCAACKKMLFKPVVLNCGHVFCELCLFVPED---GNFKCPNC 248
+++ C C +L KPV ++CGH FC C+ + G FKCP C
Sbjct: 19 EEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC 63
Score = 34.7 bits (78), Expect = 0.12, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 16 FSDEFKCCVCLELLYKPVVLACGHISCFWCVYN-AMNSWHESNCPVC 61
+E C +CL++L KPV + CGH C C+ S CP+C
Sbjct: 17 LQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC 63
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 34.7 bits (78), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 27/44 (61%), Gaps = 3/44 (6%)
Query: 208 DLSCAACKKMLFKPVVLNCGHVFCELCL---FVPEDGNFKCPNC 248
+ SC+ C + L +PV++ CGH FC+ C+ + + +F CP C
Sbjct: 15 EASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPCPVC 58
Score = 32.0 bits (71), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 25/53 (47%), Gaps = 9/53 (16%)
Query: 14 EAFSDEFKCCVCLELLYKPVVLACGHISCFWCVYNAMNSWHES-----NCPVC 61
E E C VCLE L +PV++ CGH C C+ W E CPVC
Sbjct: 10 ENLQVEASCSVCLEYLKEPVIIECGHNFCKACI----TRWWEDLERDFPCPVC 58
>pdb|1RMD|A Chain A, Rag1 Dimerization Domain
Length = 116
Score = 33.5 bits (75), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 28/46 (60%), Gaps = 3/46 (6%)
Query: 206 VDDLSCAACKKMLFKPVVLNCGHVFCELCLF--VPEDGNFKCPNCQ 249
V +SC C+ +L PV +C H+FC +C+ + G++ CP+C+
Sbjct: 21 VKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSY-CPSCR 65
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 16 FSDEFKCCVCLELLYKPVVLACGHISCFWCVYNAMNSWHESNCPVCRNP 64
F C +C +L PV +C H+ C C+ + S CP CR P
Sbjct: 20 FVKSISCQICEHILADPVETSCKHLFCRICILRCLKVM-GSYCPSCRYP 67
>pdb|3L11|A Chain A, Crystal Structure Of The Ring Domain Of Rnf168
Length = 115
Score = 32.7 bits (73), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 205 SVDDLSCAACKKMLFKPVVLNCGHVFCELCL-FVPEDGNFKCPNCQ 249
S+ + C C ++L +PV L C H C+ C E + CP C+
Sbjct: 12 SLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCR 57
Score = 31.6 bits (70), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 18 DEFKCCVCLELLYKPVVLACGHISCFWCVYNAMNSWHESNCPVCRN 63
E +C +C+E+L +PV L C H C C + + CP CR
Sbjct: 14 SECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEK-ASLCCPFCRR 58
>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 = 32.7 bits (73), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 20 FKCCVCLELLYKPVVLACGHISCFWCVYNAMNSWHESNCPVCRN 63
F C C EL+Y+PV C H C C+ + + +CP CR+
Sbjct: 79 FMCVCCQELVYQPVTTECFHNVCKDCLQRSFKA-QVFSCPACRH 121
Score = 28.9 bits (63), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 211 CAACKKMLFKPVVLNCGHVFCELCLFVPEDGN-FKCPNCQ 249
C C++++++PV C H C+ CL F CP C+
Sbjct: 81 CVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACR 120
>pdb|3FL2|A Chain A, Crystal Structure Of The Ring Domain Of The E3
Ubiquitin- Protein Ligase Uhrf1
Length = 124
Score = 32.7 bits (73), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 18 DEFKCCVCLELLYKPVVLACGHISCFWCVYNAMNSWHESNCPVCR 62
+ F+C C EL+++P+ C H C C+ + + +CP CR
Sbjct: 51 ETFQCICCQELVFRPITTVCQHNVCKDCLDRSFRA-QVFSCPACR 94
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 207 DDLSCAACKKMLFKPVVLNCGHVFCELCLFVPEDGN-FKCPNCQ 249
+ C C++++F+P+ C H C+ CL F CP C+
Sbjct: 51 ETFQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACR 94
>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 = 0.53, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 9/45 (20%)
Query: 191 LVGNDLEHKAENWVSVDDLSCAACKKMLFKPVVLNCGHVFCELCL 235
L+G LE K C+AC+ +L +P CGH +C CL
Sbjct: 23 LLGTKLEAK---------YLCSACRNVLRRPFQAQCGHRYCSFCL 58
>pdb|2YUR|A Chain A, Solution Structure Of The Ring Finger Of Human
Retinoblastoma-Binding Protein 6
Length = 74
Score = 32.0 bits (71), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 11 ADKEAFSDEFKCCVCLELLYKPVVL-ACGHISCFWCVYNAMNSWHESNCPVCR 62
+ + DE C +C +++ VV+ CG+ C C+ A+ E CP C
Sbjct: 7 GEDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCH 59
>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 = 32.0 bits (71), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 11 ADKEAFSDEFKCCVCLELLYKPVVL-ACGHISCFWCVYNAMNSWHESNCPVC 61
++ + DE C +C +++ VV+ CG+ C C+ A+ E CP C
Sbjct: 5 SEDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTC 56
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 7/49 (14%)
Query: 16 FSDEFKCCVCLELLYKPVVLACGHISCFWCVYNAMNSWHE--SNCPVCR 62
+DE +CC+C++ ++L C H C C+ + W + NCP+CR
Sbjct: 12 LTDEEECCICMD-GRADLILPCAHSFCQKCI----DKWSDRHRNCPICR 55
>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 = 30.8 bits (68), Expect = 1.8, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 6/49 (12%)
Query: 16 FSDEFKCCVCLELLYKPVVLACGHISCFWCVYNAMNSWHESNCPVCRNP 64
+E C VCL+ V + CGH+ C C CP+CR P
Sbjct: 10 LQEERTCKVCLDRAVSIVFVPCGHLVCAECAPGL------QLCPICRAP 52
>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 = 30.0 bits (66), Expect = 3.0, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 33 VVLACGHISCFWCVYNAMNSWHESNCPVCRNPYNH 67
V CGH+ C C+ +++ + + CP CR NH
Sbjct: 31 VSTECGHVFCSQCLRDSLKN--ANTCPTCRKKINH 63
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 29.6 bits (65), Expect = 3.5, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 33 VVLACGHISCFWCVYNAMNSWHESNCPVCRNPYNH 67
V CGH+ C C+ +++ + + CP CR NH
Sbjct: 28 VSTECGHVFCSQCLRDSLKN--ANTCPTCRKKINH 60
Score = 29.6 bits (65), Expect = 3.5, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 33 VVLACGHISCFWCVYNAMNSWHESNCPVCRNPYNH 67
V CGH+ C C+ +++ + + CP CR NH
Sbjct: 93 VSTECGHVFCSQCLRDSLKN--ANTCPTCRKKINH 125
Score = 29.3 bits (64), Expect = 4.6, Method: Composition-based stats.
Identities = 29/122 (23%), Positives = 43/122 (35%), Gaps = 23/122 (18%)
Query: 145 SGEGKSSPCMKSLEMTAESGDDAMLKLVTSSECSEATANS-------TAQECGLVGNDLE 197
SG CM ++G +L+ S+EC + A C +
Sbjct: 5 SGTVSCPICMDGYSEIVQNG-----RLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN 59
Query: 198 HKAEN--WVSVDDLSCAACKKMLFKPVVLN--------CGHVFCELCLFVPEDGNFKCPN 247
HK + ++ +SC C + +V N CGHVFC CL CP
Sbjct: 60 HKRYHPIYIGSGTVSCPICMDG-YSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPT 118
Query: 248 CQ 249
C+
Sbjct: 119 CR 120
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 29.6 bits (65), Expect = 3.8, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 33 VVLACGHISCFWCVYNAMNSWHESNCPVCRNPYNH 67
V CGH+ C C+ +++ + + CP CR NH
Sbjct: 24 VSTECGHVFCSQCLRDSLKN--ANTCPTCRKKINH 56
>pdb|1G25|A Chain A, Solution Structure Of The N-Terminal Domain Of The Human
Tfiih Mat1 Subunit
Length = 65
Score = 28.9 bits (63), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 25/53 (47%), Gaps = 10/53 (18%)
Query: 206 VDDLSCAACKKMLF-----KPVVLNCGHVFCELC---LFVPEDGNFKCPNCQS 250
+DD C CK + K +V CGH CE C LFV GN CP C +
Sbjct: 1 MDDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGN--CPECGT 51
>pdb|1BOR|A Chain A, Transcription Factor Pml, A Proto-Oncoprotein, Nmr, 1
Representative Structure At Ph 7.5, 30 C, In The
Presence Of Zinc
Length = 56
Score = 28.5 bits (62), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 3/47 (6%)
Query: 209 LSCAACKKMLFKPVVLNCGHVFCELCLFVPEDGNFKCPNCQSLQPYG 255
L C C+ P +L C H C CL E +CP CQ+ P G
Sbjct: 7 LRCQQCQAEAKCPKLLPCLHTLCSGCL---EASGMQCPICQAPWPLG 50
>pdb|2CT2|A Chain A, Solution Structure Of The Ring Domain Of The Tripartite
Motif Protein 32
Length = 88
Score = 28.5 bits (62), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 5/56 (8%)
Query: 11 ADKEAFSDEFKCCVCLELL----YKPVVLACGHISCFWCVYNAM-NSWHESNCPVC 61
+ +A + +C +C+E +P +L CGH C C+ + +S + CP C
Sbjct: 7 GNLDALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFC 62
>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 = 28.5 bits (62), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 207 DDLSCAACKKMLFKPVVLNCGHVFCELCL-FVPEDGNFKCPNCQ 249
D C C +L P CGH FCE C+ + + KC CQ
Sbjct: 14 DKYKCEKCHLVLCSPKQTECGHRFCESCMAALLSSSSPKCTACQ 57
>pdb|1V87|A Chain A, Solution Structure Of The Ring-H2 Finger Domain Of Mouse
Deltex Protein 2
Length = 114
Score = 28.1 bits (61), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 12/45 (26%)
Query: 223 VLNCGHVFCELCLFVP-----EDGNFKCPNCQSL-------QPYG 255
+ C H F LCL +DG+ +CP+C+++ QP+G
Sbjct: 58 LTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQPWG 102
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
0.317 0.134 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,467,539
Number of Sequences: 62578
Number of extensions: 616833
Number of successful extensions: 1258
Number of sequences better than 100.0: 49
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 28
Number of HSP's that attempted gapping in prelim test: 1186
Number of HSP's gapped (non-prelim): 92
length of query: 458
length of database: 14,973,337
effective HSP length: 102
effective length of query: 356
effective length of database: 8,590,381
effective search space: 3058175636
effective search space used: 3058175636
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)