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= 015426
(407 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2UZG|A Chain A, Zf-Ubp Domain Of Vdu1
Length = 97
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/47 (46%), Positives = 30/47 (63%), Gaps = 2/47 (4%)
Query: 156 NLWMCV--ICGFVGCGRYKGGHAIIHWKETEHCYSLELETQRVWDYA 200
NLW C+ C +VGCG + H+ IH +ET+H ++ L T RVW YA
Sbjct: 37 NLWACLENRCSYVGCGESQVDHSTIHSQETKHYLTVNLTTLRVWCYA 83
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 42.4 bits (98), Expect = 5e-04, Method: Composition-based stats.
Identities = 28/65 (43%), Positives = 33/65 (50%), Gaps = 10/65 (15%)
Query: 75 TGYTGSLEHVQPAPASSTEQPSCPVCLERLDQDTSGILTTICNHSFHCSCISKWTDS--S 132
+G +G+ EHV S E CPVC E S + CNH FH SCI W + S
Sbjct: 3 SGSSGTEEHV----GSGLE---CPVCKEDYALGES-VRQLPCNHLFHDSCIVPWLEQHDS 54
Query: 133 CPVCR 137
CPVCR
Sbjct: 55 CPVCR 59
>pdb|3C5K|A Chain A, Crystal Structure Of Human Hdac6 Zinc Finger Domain
Length = 109
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 26/59 (44%)
Query: 148 CFVCQTSENLWMCVICGFVGCGRYKGGHAIIHWKETEHCYSLELETQRVWDYAGDNYVH 206
C C T + W+C+ C V CGRY GH + H + H L W Y YVH
Sbjct: 27 CGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVH 85
>pdb|3GV4|A Chain A, Crystal Structure Of Human Hdac6 Zinc Finger Domain And
Ubiquitin C-Terminal Peptide Rlrgg
pdb|3PHD|A Chain A, Crystal Structure Of Human Hdac6 In Complex With Ubiquitin
pdb|3PHD|B Chain B, Crystal Structure Of Human Hdac6 In Complex With Ubiquitin
pdb|3PHD|C Chain C, Crystal Structure Of Human Hdac6 In Complex With Ubiquitin
pdb|3PHD|D Chain D, Crystal Structure Of Human Hdac6 In Complex With Ubiquitin
Length = 107
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 26/59 (44%)
Query: 148 CFVCQTSENLWMCVICGFVGCGRYKGGHAIIHWKETEHCYSLELETQRVWDYAGDNYVH 206
C C T + W+C+ C V CGRY GH + H + H L W Y YVH
Sbjct: 25 CGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVH 83
>pdb|2I50|A Chain A, Solution Structure Of Ubp-M Znf-Ubp Domain
Length = 126
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 156 NLWMCVICGFVGCGR-YKGGHAIIHW---KETEHCYSLELETQRVWDYAGDNYV 205
++W+C+ CG GCGR + HA+ H+ + HC L L+ VW Y DN V
Sbjct: 53 SVWLCLKCGHQGCGRNSQEQHALKHYLTPRSEPHCLVLSLDNWSVWCYVCDNEV 106
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 97 CPVCLERLDQDTSGILTTICNHSFHCSCISKW--TDSSCPVCR 137
C VCL L+ C H FH C+ W + S+CP+CR
Sbjct: 8 CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 50
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 148 CFVCQTSENLWMCVICGFVGCGRY----KGG--HAIIHWKETEHCYSLELET 193
C C ENLW+ + G + CGR GG HA+ H++ET + +++L T
Sbjct: 218 CSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLGT 269
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 37.4 bits (85), Expect = 0.017, Method: Composition-based stats.
Identities = 22/53 (41%), Positives = 30/53 (56%), Gaps = 12/53 (22%)
Query: 93 EQPSCPVCLERLDQDTSGILTTICNHSFHCSCIS------KWTD--SSCPVCR 137
E+ +CP+CLE L + S CNHSF +CI+ + TD +CPVCR
Sbjct: 18 EEVTCPICLELLKEPVSA----DCNHSFCRACITLNYESNRNTDGKGNCPVCR 66
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 37.4 bits (85), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 6/67 (8%)
Query: 75 TGYTGSLEHVQPAPAS-STEQPSCPVCLERLDQDTSGILTTI-CNHSFHCSCISKW--TD 130
+G +G L + P + +EQ C VC+ D ++ +L + CNH FH C+ KW +
Sbjct: 3 SGSSGQLPSYRFNPNNHQSEQTLCVVCM--CDFESRQLLRVLPCNHEFHAKCVDKWLKAN 60
Query: 131 SSCPVCR 137
+CP+CR
Sbjct: 61 RTCPICR 67
>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 = 35.4 bits (80), Expect = 0.051, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 93 EQPSCPVCL-ERLDQDTSGILTTICNHSFHCSCISKWTDSS--CPVCR 137
++ CP+C E + D + L C+H FH C+S W S CPVCR
Sbjct: 39 QEMCCPICCSEYVKGDVATELP--CHHYFHKPCVSIWLQKSGTCPVCR 84
>pdb|2G43|A Chain A, Structure Of The Znf Ubp Domain From Deubiquitinating
Enzyme Isopeptidase T (Isot)
pdb|2G43|B Chain B, Structure Of The Znf Ubp Domain From Deubiquitinating
Enzyme Isopeptidase T (Isot)
pdb|2G45|A Chain A, Co-Crystal Structure Of Znf Ubp Domain From The
Deubiquitinating Enzyme Isopeptidase T (Isot) In Complex
With Ubiquitin
pdb|2G45|D Chain D, Co-Crystal Structure Of Znf Ubp Domain From The
Deubiquitinating Enzyme Isopeptidase T (Isot) In Complex
With Ubiquitin
Length = 129
Score = 35.4 bits (80), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 148 CFVCQTSENLWMCVICGFVGCGRY----KGG--HAIIHWKETEHCYSLELET 193
C C ENLW+ + G + CGR GG HA+ H++ET + +++L T
Sbjct: 37 CSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLGT 88
>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 = 35.0 bits (79), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 32/60 (53%), Gaps = 13/60 (21%)
Query: 93 EQPSCPVCLERLDQDTSGILTTICNHSFHCSCISK--------WTDSSCPVCRYCQQQPE 144
E+ +CP+CLE L Q L+ C HSF +C++ +SSCPVCR QPE
Sbjct: 18 EEVTCPICLELLTQP----LSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRI-SYQPE 72
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 16/67 (23%)
Query: 75 TGYTGSLEHVQPAPASSTEQPSCPVCLERLDQDTSGILTTICNHSFHCSCISKW-----T 129
+G +G+LE++Q + SC VCLE L + + C H+F +CI++W
Sbjct: 3 SGSSGALENLQ-------VEASCSVCLEYLKEP----VIIECGHNFCKACITRWWEDLER 51
Query: 130 DSSCPVC 136
D CPVC
Sbjct: 52 DFPCPVC 58
>pdb|2L80|A Chain A, Solution Structure Of The Zinc Finger Domain Of Usp13
Length = 116
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 125 ISKWTDSSCPVCRYCQQQPEKSICFVCQTSENLWMCVICGFVGCGRY------KGGHAII 178
+SK+ ++ + + P C C ENLW+ + G V CG++ GHA+
Sbjct: 3 VSKYANNLTQLDNGVRIPPSGWKCARCDLRENLWLNLTDGSVLCGKWFFDSSGGNGHALE 62
Query: 179 HWKETEHCYSLELET 193
H+++ + +++L T
Sbjct: 63 HYRDMGYPLAVKLGT 77
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 33.5 bits (75), Expect = 0.25, Method: Composition-based stats.
Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 5/43 (11%)
Query: 97 CPVCLERLD-QDTSGILTTICNHSFHCSCISKWTD--SSCPVC 136
C VCLE +D GI C H+FH C+ KW + CP+C
Sbjct: 18 CAVCLEDFKPRDELGICP--CKHAFHRKCLIKWLEVRKVCPLC 58
>pdb|2EGP|A Chain A, Solution Structure Of The Ring-Finger Domain From Human
Tripartite Motif Protein 34
Length = 79
Score = 32.0 bits (71), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 33/70 (47%), Gaps = 20/70 (28%)
Query: 76 GYTGSLEHVQPAPASSTEQPSCPVCLERLDQDTSGILTTICNHSFHCSCI---------S 126
G +GS +VQ E+ +CP+CLE L + L+ C HS +CI S
Sbjct: 1 GSSGSSGNVQ-------EEVTCPICLELLTEP----LSLDCGHSLCRACITVSNKEAVTS 49
Query: 127 KWTDSSCPVC 136
SSCPVC
Sbjct: 50 MGGKSSCPVC 59
>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 = 32.0 bits (71), Expect = 0.73, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 96 SCPVCLE---RLDQDTSGILTTICNHSFHCSCI--SKWTDSSCPVCR 137
SCP+C++ + Q+ I++T C H F C+ S ++CP CR
Sbjct: 12 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 58
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 111 ILTTICNHSFHCSCISKW--TDSSCPV 135
+ +CNH+FH CIS+W T CP+
Sbjct: 79 VAWGVCNHAFHFHCISRWLKTRQVCPL 105
>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 = 18/48 (37%), Positives = 25/48 (52%), Gaps = 7/48 (14%)
Query: 92 TEQPSCPVCLERLDQDTSGILTTICNHSFHCSCISKWTD--SSCPVCR 137
T++ C +C+ D L C HSF CI KW+D +CP+CR
Sbjct: 13 TDEEECCICM-----DGRADLILPCAHSFCQKCIDKWSDRHRNCPICR 55
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 97 CPVCLERLDQDTSGILTTICNHSFHCSCISKW--TDSSCPVCR 137
C +CL L++ + C H FH C+ +W T+ CP+CR
Sbjct: 17 CTICLSILEEG-EDVRRLPCMHLFHQVCVDQWLITNKKCPICR 58
>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 = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 111 ILTTICNHSFHCSCISKW--TDSSCPV 135
+ +CNH+FH CIS+W T CP+
Sbjct: 60 VAWGVCNHAFHFHCISRWLKTRQVCPL 86
>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 = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 111 ILTTICNHSFHCSCISKW--TDSSCPV 135
+ +CNH+FH CIS+W T CP+
Sbjct: 70 VAWGVCNHAFHFHCISRWLKTRQVCPL 96
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 96 SCPVCLE---RLDQDTSGILTTICNHSFHCSCI--SKWTDSSCPVCR 137
SCP+C++ + Q+ I++T C H F C+ S ++CP CR
Sbjct: 17 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 63
>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 = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 111 ILTTICNHSFHCSCISKW--TDSSCPV 135
+ +CNH+FH CIS+W T CP+
Sbjct: 52 VAWGVCNHAFHFHCISRWLKTRQVCPL 78
>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 = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 111 ILTTICNHSFHCSCISKW--TDSSCPV 135
+ +CNH+FH CIS+W T CP+
Sbjct: 68 VAWGVCNHAFHFHCISRWLKTRQVCPL 94
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 111 ILTTICNHSFHCSCISKW--TDSSCPV 135
+ +CNH+FH CIS+W T CP+
Sbjct: 62 VAWGVCNHAFHFHCISRWLKTRQVCPL 88
>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 = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 111 ILTTICNHSFHCSCISKW--TDSSCPV 135
+ +CNH+FH CIS+W T CP+
Sbjct: 68 VAWGVCNHAFHFHCISRWLKTRQVCPL 94
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 9/62 (14%)
Query: 81 LEHVQPAPASSTEQPSCPVCLERLDQDTSGILTTICNHSFHCSCISKWTD-----SSCPV 135
+E VQ + + CP+CLE + + S T C+H F C+ K + S CP+
Sbjct: 8 VEEVQNVINAMQKILECPICLELIKEPVS----TKCDHIFCKFCMLKLLNQKKGPSQCPL 63
Query: 136 CR 137
C+
Sbjct: 64 CK 65
>pdb|1JSH|B Chain B, Crystal Structure Of H9 Haemagglutinin Complexed With Lsta
Receptor Analog
pdb|1JSI|B Chain B, Crystal Structure Of H9 Haemagglutinin Bound To Lstc
Receptor Analog
pdb|1JSD|B Chain B, Crystal Structure Of Swine H9 Haemagglutinin
Length = 176
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 40/87 (45%), Gaps = 14/87 (16%)
Query: 288 SEAVKKAIAQKLQKMQAKLDRCVREKKFLDDLNENLLKNQEMWKAKISEIEEREKMALRA 347
S++ +KAI + K+ +D+ ++ +D + SEIE R M
Sbjct: 38 SDSTQKAIDKITSKVNNIVDKMNKQYGIID--------------HEFSEIETRLNMINNK 83
Query: 348 KDDKIQDSEAQLRDLMAYLEAEKTLQQ 374
DD+IQD +L+ LE +KTL +
Sbjct: 84 IDDQIQDIWTYNAELLVLLENQKTLDE 110
>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 = 29.6 bits (65), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 5/43 (11%)
Query: 97 CPVCLERLDQDTSGILTTICNHSFHCSCISKWT--DSSCPVCR 137
CP+CLE ++ + C H+F CI++W + +CP+C+
Sbjct: 8 CPICLE---DPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCK 47
>pdb|1ZRL|A Chain A, Crystal Structure Of Eba-175 Region Ii (Rii)
pdb|1ZRO|A Chain A, Crystal Structure Of Eba-175 Region Ii (Rii) Crystallized
In The Presence Of (Alpha)2,3-Sialyllactose
pdb|1ZRO|B Chain B, Crystal Structure Of Eba-175 Region Ii (Rii) Crystallized
In The Presence Of (Alpha)2,3-Sialyllactose
Length = 602
Score = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 168 CGRYKGGHAIIHWKETEHCYSLELETQRVWDYAGDNYVHRLIQSKTDGKLVELNSHCLHG 227
C +Y+ II K H S E ETQ+V +NY+ ++ ++K D K+ L ++C
Sbjct: 219 CMKYRDW--IIRSKFEWHTLSKEYETQKVPKENAENYLIKISENKNDAKVSLLLNNC--D 274
Query: 228 KDNCGSCDCVDSGT 241
+ CDC + T
Sbjct: 275 AEYSKYCDCKHTTT 288
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 112 LTTICNHSFHCSCISKWTDSS--CPVCR 137
+T C HSF CI++W CP+CR
Sbjct: 67 VTLNCAHSFCSYCINEWMKRKIECPICR 94
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 29.3 bits (64), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 12/51 (23%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 158 WMCVICGFVGCGRYKGGHAIIHWKETEHCYSLELETQRVWDYAGDNYVHRL 208
+MC+ CGF GC + H + H K+ H + + ++ + ++Y+ +
Sbjct: 58 FMCLQCGFCGC--WNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNI 106
>pdb|3MHH|A Chain A, Structure Of The Saga Ubp8SGF11SUS1SGF73 DUB MODULE
pdb|3MHS|A Chain A, Structure Of The Saga Ubp8SGF11SUS1SGF73 DUB MODULE BOUND
Ubiquitin Aldehyde
pdb|4FJC|A Chain A, Structure Of The Saga Ubp8SGF11(1-72, Delta-Znf)SUS1SGF73
DUB Module
pdb|4FJC|E Chain E, Structure Of The Saga Ubp8SGF11(1-72, Delta-Znf)SUS1SGF73
DUB Module
Length = 476
Score = 29.3 bits (64), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 12/51 (23%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 158 WMCVICGFVGCGRYKGGHAIIHWKETEHCYSLELETQRVWDYAGDNYVHRL 208
+MC+ CGF GC + H + H K+ H + + ++ + ++Y+ +
Sbjct: 63 FMCLQCGFCGC--WNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNI 111
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 29.3 bits (64), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 96 SCPVCLERLDQDTSGILTTICNHSFHCSCISKWT--DSSCPVCR 137
+C C Q+ ++ CNHSFH C+S W ++ CP+C+
Sbjct: 28 ACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71
>pdb|4FIP|A Chain A, Structure Of The Saga Ubp8(S144n)SGF11(1-72,
Delta-Znf)SUS1SGF73 Dub Module
pdb|4FIP|E Chain E, Structure Of The Saga Ubp8(S144n)SGF11(1-72,
Delta-Znf)SUS1SGF73 Dub Module
pdb|4FK5|A Chain A, Structure Of The Saga Ubp8(S144n)SGF11SUS1SGF73 DUB MODULE
Length = 476
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 12/51 (23%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 158 WMCVICGFVGCGRYKGGHAIIHWKETEHCYSLELETQRVWDYAGDNYVHRL 208
+MC+ CGF GC + H + H K+ H + + ++ + ++Y+ +
Sbjct: 63 FMCLQCGFCGC--WNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNI 111
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 112 LTTICNHSFHCSCISKWTDSS--CPVCR 137
+T C HSF CI++W CP+CR
Sbjct: 67 VTLNCAHSFCSYCINEWMKRKIECPICR 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 = 28.9 bits (63), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 112 LTTICNHSFHCSCISKWTDSS--CPVCR 137
+T C HSF CI++W CP+CR
Sbjct: 78 VTLNCAHSFCSYCINEWMKRKIECPICR 105
>pdb|1X3O|A Chain A, Crystal Structure Of The Acyl Carrier Protein From Thermus
Thermophilus Hb8
Length = 80
Score = 28.5 bits (62), Expect = 6.6, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 283 TEKIISEAVKKAIAQKLQKMQAKLDRCVREKKFLDDLNENLLKNQEMWKAKIS----EIE 338
TE+ I E VK IA KLQ + ++ E +F++DL + L E+ EI
Sbjct: 2 TEQEIFEKVKAVIADKLQ---VEPEKVTLEARFIEDLGADSLDTVELIMGLEDEFGLEIS 58
Query: 339 EREKMALRAKDDKIQDSEAQL 359
+ E +R D ++ +A+L
Sbjct: 59 DEEAEKIRTVKDAVEYIKAKL 79
>pdb|4EIW|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|4EIW|B Chain B, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|4EIW|C Chain C, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|4EIW|D Chain D, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|4EIW|E Chain E, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|4EIW|F Chain F, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
Length = 508
Score = 28.5 bits (62), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 32/49 (65%), Gaps = 3/49 (6%)
Query: 281 EETEKIISEAVKKAIAQKLQKMQAKLDRCVREKKFLDDLNENLLKNQEM 329
EET K I EAV++ I ++ Q+++A L + +++ L+ + E LL+ + +
Sbjct: 421 EETAKRIDEAVRRLIEEQYQRVKALL---LEKREVLERVAETLLERETL 466
>pdb|2DHR|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|2DHR|B Chain B, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|2DHR|C Chain C, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|2DHR|D Chain D, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|2DHR|E Chain E, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|2DHR|F Chain F, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
Length = 499
Score = 28.5 bits (62), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 32/49 (65%), Gaps = 3/49 (6%)
Query: 281 EETEKIISEAVKKAIAQKLQKMQAKLDRCVREKKFLDDLNENLLKNQEM 329
EET K I EAV++ I ++ Q+++A L + +++ L+ + E LL+ + +
Sbjct: 412 EETAKRIDEAVRRLIEEQYQRVKALL---LEKREVLERVAETLLERETL 457
>pdb|2D40|A Chain A, Crystal Structure Of Z3393 From Escherichia Coli O157:h7
pdb|2D40|B Chain B, Crystal Structure Of Z3393 From Escherichia Coli O157:h7
pdb|2D40|C Chain C, Crystal Structure Of Z3393 From Escherichia Coli O157:h7
pdb|2D40|D Chain D, Crystal Structure Of Z3393 From Escherichia Coli O157:h7
Length = 354
Score = 28.5 bits (62), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 10/29 (34%), Positives = 20/29 (68%)
Query: 39 DSQDSADKFYQHFNGRQFNSLEEEVCHVL 67
++Q+S ++FYQH +G+ L E + H++
Sbjct: 16 NNQNSREQFYQHISGQNLTPLWESLHHLV 44
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 28.5 bits (62), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 9/50 (18%)
Query: 93 EQPSCPVCLERLDQDTSGILTTICNHSFHCSCISKWTDSS-----CPVCR 137
E+ CP+CL+ L + +T C H+F CI++ ++S CP+C+
Sbjct: 19 EEVICPICLDILQKP----VTIDCGHNFCLKCITQIGETSCGFFKCPLCK 64
>pdb|3VKG|A Chain A, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
Domain
pdb|3VKG|B Chain B, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
Domain
Length = 3245
Score = 28.1 bits (61), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 47/83 (56%), Gaps = 8/83 (9%)
Query: 298 KLQKMQAKLDRCVREKKFLDDLNENLLKNQEMWKAKISEIEEREKMALRAKDDKIQDSEA 357
+L K Q + V + +LD +N+ +L E K ++EE E++ L K++D+EA
Sbjct: 1881 RLLKRQGR-QNYVTPRHYLDFINQVVLLINE----KRDQLEE-EQLHLNIGLKKLRDTEA 1934
Query: 358 QLRDLMAYLEAEKTLQQLSISNE 380
Q++DL L A+K ++L + NE
Sbjct: 1935 QVKDLQVSL-AQKN-RELDVKNE 1955
>pdb|3VKH|A Chain A, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
pdb|3VKH|B Chain B, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
Length = 3367
Score = 28.1 bits (61), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 47/83 (56%), Gaps = 8/83 (9%)
Query: 298 KLQKMQAKLDRCVREKKFLDDLNENLLKNQEMWKAKISEIEEREKMALRAKDDKIQDSEA 357
+L K Q + V + +LD +N+ +L E K ++EE E++ L K++D+EA
Sbjct: 1881 RLLKRQGR-QNYVTPRHYLDFINQVVLLINE----KRDQLEE-EQLHLNIGLKKLRDTEA 1934
Query: 358 QLRDLMAYLEAEKTLQQLSISNE 380
Q++DL L A+K ++L + NE
Sbjct: 1935 QVKDLQVSL-AQKN-RELDVKNE 1955
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
0.319 0.132 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,325,136
Number of Sequences: 62578
Number of extensions: 458011
Number of successful extensions: 1959
Number of sequences better than 100.0: 116
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 96
Number of HSP's that attempted gapping in prelim test: 1923
Number of HSP's gapped (non-prelim): 124
length of query: 407
length of database: 14,973,337
effective HSP length: 101
effective length of query: 306
effective length of database: 8,652,959
effective search space: 2647805454
effective search space used: 2647805454
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)