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= 019980
(333 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 32/48 (66%)
Query: 283 CVICRLDYEDGETLTVLSCKHSYHSECINNWLKINKVCPVCSAEVSTS 330
CV+C D+E + L VL C H +H++C++ WLK N+ CP+C A+ S
Sbjct: 26 CVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGPS 73
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 52.0 bits (123), Expect = 5e-07, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 30/45 (66%)
Query: 283 CVICRLDYEDGETLTVLSCKHSYHSECINNWLKINKVCPVCSAEV 327
C +C D++ + L + CKH++H +C+ WL++ KVCP+C+ V
Sbjct: 18 CAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPV 62
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 49.3 bits (116), Expect = 3e-06, Method: Composition-based stats.
Identities = 18/45 (40%), Positives = 26/45 (57%)
Query: 283 CVICRLDYEDGETLTVLSCKHSYHSECINNWLKINKVCPVCSAEV 327
C IC E+GE + L C H +H C++ WL NK CP+C ++
Sbjct: 17 CTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDI 61
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 48.1 bits (113), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 28/49 (57%)
Query: 280 GFSCVICRLDYEDGETLTVLSCKHSYHSECINNWLKINKVCPVCSAEVS 328
G C +C+ DY GE++ L C H +H CI WL+ + CPVC ++
Sbjct: 15 GLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLT 63
>pdb|2L0B|A Chain A, Solution Nmr Structure Of Zinc Finger Domain Of E3
Ubiquitin-Protein Ligase Praja-1 From Homo Sapiens,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4710b
Length = 91
Score = 45.8 bits (107), Expect = 3e-05, Method: Composition-based stats.
Identities = 17/41 (41%), Positives = 24/41 (58%)
Query: 283 CVICRLDYEDGETLTVLSCKHSYHSECINNWLKINKVCPVC 323
C IC +Y G+ T L C H +H C++ WL+ + CPVC
Sbjct: 43 CPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVC 83
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 280 GFSCVICRLDYEDGETLTVLS-CKHSYHSECINNWLKINKVCPVCSAEV 327
G C +C + EDGE L C H +H+EC++ WL + CP+C V
Sbjct: 5 GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 281 FSCVICRLDYEDGETLTVLSCKHSYHSECINNWLKINKVCPVCSAEVSTSGHS 333
C+IC + + TL +C HS+ S CIN W+K CP+C ++ + +S
Sbjct: 54 LQCIICSEYFIEAVTL---NCAHSFCSYCINEWMKRKIECPICRKDIKSKTYS 103
>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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 281 FSCVICRLDYEDGETLTVLSCKHSYHSECINNWLKINKVCPVCSAEVSTSGHS 333
C+IC + + TL +C HS+ S CIN W+K CP+C ++ + +S
Sbjct: 65 LQCIICSEYFIEAVTL---NCAHSFCSYCINEWMKRKIECPICRKDIKSKTYS 114
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 281 FSCVICRLDYEDGETLTVLSCKHSYHSECINNWLKINKVCPVCSAEVSTSGHS 333
C+IC + + TL +C HS+ S CIN W+K CP+C ++ + +S
Sbjct: 54 LQCIICSEYFIEAVTL---NCAHSFCSYCINEWMKRKIECPICRKDIKSKTYS 103
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 283 CVICRLDYEDGETLTVLSCKHSYHSECINNWLKINKVCPVCSAEV 327
CV+C + D T ++ C HS+ CI +L+ +K CP+C +V
Sbjct: 18 CVLCGGYFIDATT--IIECLHSFCKTCIVRYLETSKYCPICDVQV 60
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 283 CVICRLDYEDGETLTVLSCKHSYHSECINNWLKINKVCPVCSAEV 327
CV+C + D T ++ C HS+ CI +L+ +K CP+C +V
Sbjct: 14 CVLCGGYFIDATT--IIECLHSFCKTCIVRYLETSKYCPICDVQV 56
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 283 CVICRLDYEDGETLTVLSCKHSYHSECINNWLKINKVCPVCSAEV 327
CV+C + D T ++ C HS+ CI +L+ +K CP+C +V
Sbjct: 18 CVLCGGYFIDATT--IIECLHSFCKTCIVRYLETSKYCPICDVQV 60
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 283 CVICRLDYEDGETLTVLSCKHSYHSECINNWLKINKVCPVCSAEVSTSGHS 333
C IC DG +L C HS+ +CI+ W ++ CP+C +++ + S
Sbjct: 18 CCICM----DGRADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANES 64
>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 = 36.2 bits (82), Expect = 0.027, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 283 CVICRLDYEDGETLTV-LSCKHSYHSECINNWLKINKVCPVCSAEVSTSGHS 333
C IC ED ++ L C H++ CI W++ N CP+C V + H+
Sbjct: 8 CPIC---LEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVESVVHT 56
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 36.2 bits (82), Expect = 0.027, Method: Composition-based stats.
Identities = 14/46 (30%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 282 SCVICRLDYEDGETLTVL-SCKHSYHSECINNWLKINKVCPVCSAE 326
+C+ C+ + + + + V C HS+H+ C++ W+K N CP+C +
Sbjct: 28 ACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQD 73
>pdb|1LDJ|B Chain B, Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiquitin
Ligase Complex
pdb|1LDK|C Chain C, Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin
Ligase Complex
Length = 90
Score = 35.8 bits (81), Expect = 0.036, Method: Composition-based stats.
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 301 CKHSYHSECINNWLKINKVCPVCSAE 326
C H++H CI+ WLK +VCP+ + E
Sbjct: 57 CNHAFHFHCISRWLKTRQVCPLDNRE 82
>pdb|4A0C|D Chain D, Structure Of The Cand1-Cul4b-Rbx1 Complex
pdb|4A0C|F Chain F, Structure Of The Cand1-Cul4b-Rbx1 Complex
pdb|4A0L|F Chain F, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
pdb|4A0L|I Chain I, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 98
Score = 35.4 bits (80), Expect = 0.039, Method: Composition-based stats.
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 301 CKHSYHSECINNWLKINKVCPVCSAE 326
C H++H CI+ WLK +VCP+ + E
Sbjct: 65 CNHAFHFHCISRWLKTRQVCPLDNRE 90
>pdb|1U6G|B Chain B, Crystal Structure Of The Cand1-Cul1-Roc1 Complex
pdb|2HYE|D Chain D, Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Complex
Length = 108
Score = 35.4 bits (80), Expect = 0.046, Method: Composition-based stats.
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 301 CKHSYHSECINNWLKINKVCPVCSAE 326
C H++H CI+ WLK +VCP+ + E
Sbjct: 75 CNHAFHFHCISRWLKTRQVCPLDNRE 100
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 35.4 bits (80), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 295 TLTVLSCKHSYHSECINNWLKINKVCPV 322
T+ C H++H CI+ WLK +VCP+
Sbjct: 78 TVAWGVCNHAFHFHCISRWLKTRQVCPL 105
>pdb|3DPL|R Chain R, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation.
pdb|3RTR|B Chain B, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|D Chain D, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|F Chain F, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|H Chain H, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|4F52|B Chain B, Structure Of A Glomulin-Rbx1-Cul1 Complex
pdb|4F52|D Chain D, Structure Of A Glomulin-Rbx1-Cul1 Complex
Length = 106
Score = 35.4 bits (80), Expect = 0.051, Method: Composition-based stats.
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 301 CKHSYHSECINNWLKINKVCPVCSAE 326
C H++H CI+ WLK +VCP+ + E
Sbjct: 73 CNHAFHFHCISRWLKTRQVCPLDNRE 98
>pdb|3DQV|R Chain R, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation
pdb|3DQV|Y Chain Y, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation
Length = 106
Score = 35.0 bits (79), Expect = 0.057, Method: Composition-based stats.
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 301 CKHSYHSECINNWLKINKVCPVCSAE 326
C H++H CI+ WLK +VCP+ + E
Sbjct: 73 CNHAFHFHCISRWLKTRQVCPLDNRE 98
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 35.0 bits (79), Expect = 0.063, Method: Composition-based stats.
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 301 CKHSYHSECINNWLKINKVCPVCSAE 326
C H++H CI+ WLK +VCP+ + E
Sbjct: 67 CNHAFHFHCISRWLKTRQVCPLDNRE 92
>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 = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 282 SCVICRLDY----EDGETLTVLSCKHSYHSECINNWLKINKVCPVCSAEVS 328
SC IC Y ++G + C H + S+C+ + LK CP C +++
Sbjct: 12 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN 62
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 33.9 bits (76), Expect = 0.13, Method: Composition-based stats.
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 282 SCVICRLDY----EDGETLTVLSCKHSYHSECINNWLKINKVCPVCSAEVS 328
SC IC Y ++G + C H + S+C+ + LK CP C +++
Sbjct: 5 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN 55
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 33.1 bits (74), Expect = 0.21, Method: Composition-based stats.
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 282 SCVICRLDY----EDGETLTVLSCKHSYHSECINNWLKINKVCPVCSAEVS 328
SC IC Y ++G + C H + S+C+ + LK CP C +++
Sbjct: 17 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN 67
>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 = 30.0 bits (66), Expect = 1.7, Method: Composition-based stats.
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 296 LTVLSCKHSYHSECINNWLKINKVCPVCSAEVS 328
+ + C H+Y S CI +L CP C V+
Sbjct: 36 MIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVT 68
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 281 FSCVICRLDY----EDGETLTVLSCKHSYHSECINNWLKINKVCPVCSAEV 327
SC IC Y ++G + C H + S+C+ + LK CP C ++
Sbjct: 8 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 58
Score = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 281 FSCVICRLDY----EDGETLTVLSCKHSYHSECINNWLKINKVCPVCSAEV 327
SC IC Y ++G + C H + S+C+ + LK CP C ++
Sbjct: 73 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 123
>pdb|2ECM|A Chain A, Solution Structure Of The Ring Domain Of The Ring Finger
And Chy Zinc Finger Domain-Containing Protein 1 From Mus
Musculus
Length = 55
Score = 28.5 bits (62), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 19/47 (40%), Gaps = 1/47 (2%)
Query: 283 CVICRLDYEDGETLT-VLSCKHSYHSECINNWLKINKVCPVCSAEVS 328
C IC D + VL C H H C LK CP+CS S
Sbjct: 8 CPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS 54
>pdb|1MM2|A Chain A, Solution Structure Of The 2nd Phd Domain From Mi2b
pdb|2L75|A Chain A, Solution Structure Of Chd4-Phd2 In Complex With H3k9me3
Length = 61
Score = 28.5 bits (62), Expect = 6.0, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 14/48 (29%)
Query: 286 CRLDYEDGETLTVLSCKHSYHSECIN---------NWLKINKVCPVCS 324
CR+ + GE L +C SYH C+N WL CP C+
Sbjct: 12 CRVCKDGGELLCCDTCPSSYHIHCLNPPLPEIPNGEWL-----CPRCT 54
>pdb|2PUY|A Chain A, Crystal Structure Of The Bhc80 Phd Finger
pdb|2PUY|B Chain B, Crystal Structure Of The Bhc80 Phd Finger
Length = 60
Score = 28.1 bits (61), Expect = 7.9, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 7/49 (14%)
Query: 283 CVICRLDYEDGETLTVLSCKHSYHSECINNWLK-INK---VCPVCSAEV 327
C +CR + G+ L +C YH +C++ LK I K +CP C ++
Sbjct: 8 CSVCR---KSGQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQM 53
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
0.310 0.128 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,674,424
Number of Sequences: 62578
Number of extensions: 271248
Number of successful extensions: 440
Number of sequences better than 100.0: 47
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 408
Number of HSP's gapped (non-prelim): 48
length of query: 333
length of database: 14,973,337
effective HSP length: 99
effective length of query: 234
effective length of database: 8,778,115
effective search space: 2054078910
effective search space used: 2054078910
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 52 (24.6 bits)