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= 017653
(368 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 65.5 bits (158), Expect = 5e-11, Method: Composition-based stats.
Identities = 34/89 (38%), Positives = 49/89 (55%), Gaps = 3/89 (3%)
Query: 6 QTLKVNREKLVACMTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDSCPVCNTDL 65
+T ++ +L + C LC F DATTI ECLHSFC+ CI + E CP+C+ +
Sbjct: 3 RTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYL--ETSKYCPICDVQV 60
Query: 66 -GCAPLEKLRADHNLQDLRIKIFPSKRRN 93
PL +R+D LQD+ K+ P +N
Sbjct: 61 HKTRPLLNIRSDKTLQDIVYKLVPGLFKN 89
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 65.1 bits (157), Expect = 6e-11, Method: Composition-based stats.
Identities = 34/89 (38%), Positives = 49/89 (55%), Gaps = 3/89 (3%)
Query: 6 QTLKVNREKLVACMTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDSCPVCNTDL 65
+T ++ +L + C LC F DATTI ECLHSFC+ CI + E CP+C+ +
Sbjct: 3 RTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYL--ETSKYCPICDVQV 60
Query: 66 -GCAPLEKLRADHNLQDLRIKIFPSKRRN 93
PL +R+D LQD+ K+ P +N
Sbjct: 61 HKTRPLLNIRSDKTLQDIVYKLVPGLFKN 89
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 64.3 bits (155), Expect = 1e-10, Method: Composition-based stats.
Identities = 32/76 (42%), Positives = 43/76 (56%), Gaps = 3/76 (3%)
Query: 19 MTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDSCPVCNTDL-GCAPLEKLRADH 77
+ C LC F DATTI ECLHSFC+ CI + E CP+C+ + PL +R+D
Sbjct: 12 LMCVLCGGYFIDATTIIECLHSFCKTCIVRYL--ETSKYCPICDVQVHKTRPLLNIRSDK 69
Query: 78 NLQDLRIKIFPSKRRN 93
LQD+ K+ P +N
Sbjct: 70 TLQDIVYKLVPGLFKN 85
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 3/72 (4%)
Query: 19 MTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDSCPVCNTDLGCAPLEKLRADHN 78
+ CP+C + ++ T ECLH FC CI + + CP C L LR D N
Sbjct: 55 LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKE-CPTCRKKL--VSKRSLRPDPN 111
Query: 79 LQDLRIKIFPSK 90
L KI+PS+
Sbjct: 112 FDALISKIYPSR 123
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 47.4 bits (111), Expect = 1e-05, Method: Composition-based stats.
Identities = 21/52 (40%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 11 NREKLVACMTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDSCPVCN 62
N +L + C +C DATTI+ECLH+FC+ CI + CP CN
Sbjct: 8 NLSELTPYILCSICKGYLIDATTITECLHTFCKSCIVRHFYYS--NRCPKCN 57
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 33/71 (46%), Gaps = 3/71 (4%)
Query: 19 MTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDSCPVCNTDLGCAPLEKLRADHN 78
+ CP+C + ++ T ECLH FC CI + + CP C L LR D N
Sbjct: 54 LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKE-CPTCRKKL--VSKRSLRPDPN 110
Query: 79 LQDLRIKIFPS 89
L KI+PS
Sbjct: 111 FDALISKIYPS 121
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 30/69 (43%), Gaps = 3/69 (4%)
Query: 19 MTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDSCPVCNTDLGCAPLEKLRADHN 78
+ CP+C + ++ T ECLH FC CI + CP C L LR D N
Sbjct: 35 LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGN-KECPTCRKKL--VSKRSLRPDPN 91
Query: 79 LQDLRIKIF 87
L KI+
Sbjct: 92 FDALISKIY 100
>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 = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 3/47 (6%)
Query: 19 MTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDSCPVCNTDL 65
+ C +CS+ F +A T++ C HSFC CI E + + CP+C D+
Sbjct: 65 LQCIICSEYFIEAVTLN-CAHSFCSYCINEWMKRK--IECPICRKDI 108
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 3/47 (6%)
Query: 19 MTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDSCPVCNTDL 65
+ C +CS+ F +A T++ C HSFC CI E + + CP+C D+
Sbjct: 54 LQCIICSEYFIEAVTLN-CAHSFCSYCINEWMKRK--IECPICRKDI 97
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 3/47 (6%)
Query: 19 MTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDSCPVCNTDL 65
+ C +CS+ F +A T++ C HSFC CI E + + CP+C D+
Sbjct: 54 LQCIICSEYFIEAVTLN-CAHSFCSYCINEWMKRK--IECPICRKDI 97
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 37.7 bits (86), Expect = 0.011, Method: Composition-based stats.
Identities = 19/47 (40%), Positives = 29/47 (61%), Gaps = 5/47 (10%)
Query: 19 MTCPLCSKLFRDATTISECLHSFCRKCI---YEKITEEE-IDSCPVC 61
+TCP+C +L ++ + ++C HSFCR CI YE + +CPVC
Sbjct: 20 VTCPICLELLKEPVS-ADCNHSFCRACITLNYESNRNTDGKGNCPVC 65
>pdb|2EGP|A Chain A, Solution Structure Of The Ring-Finger Domain From Human
Tripartite Motif Protein 34
Length = 79
Score = 36.6 bits (83), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 9/69 (13%)
Query: 19 MTCPLCSKLFRDATTISECLHSFCRKCIY----EKITE-EEIDSCPVCNTDLGCAPLEKL 73
+TCP+C +L + ++ +C HS CR CI E +T SCPVC E L
Sbjct: 13 VTCPICLELLTEPLSL-DCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISY---SFEHL 68
Query: 74 RADHNLQDL 82
+A+ +L ++
Sbjct: 69 QANQHLANI 77
>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 = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 13 EKLVACMTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDSCPVCNTDLG 66
+KL C C +L T +EC H+ C+ C+ ++ + ++ SCP C DLG
Sbjct: 73 KKLEQSFMCVCCQELVYQPVT-TECFHNVCKDCL-QRSFKAQVFSCPACRHDLG 124
>pdb|3FL2|A Chain A, Crystal Structure Of The Ring Domain Of The E3 Ubiquitin-
Protein Ligase Uhrf1
Length = 124
Score = 36.2 bits (82), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 19 MTCPLCSKL-FRDATTISECLHSFCRKCIYEKITEEEIDSCPVCNTDLGCAPLEKLRADH 77
C C +L FR TT+ C H+ C+ C+ ++ ++ SCP C DLG + ++ +
Sbjct: 53 FQCICCQELVFRPITTV--CQHNVCKDCL-DRSFRAQVFSCPACRYDLGRS--YAMQVNQ 107
Query: 78 NLQDLRIKIFPS 89
LQ + ++FP
Sbjct: 108 PLQTVLNQLFPG 119
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 35.0 bits (79), Expect = 0.062, Method: Composition-based stats.
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 14 KLVACMTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEID--SCPVCNTDL 65
KL + CP+C + + TI +C H+FC KCI +I E CP+C T +
Sbjct: 16 KLQEEVICPICLDILQKPVTI-DCGHNFCLKCI-TQIGETSCGFFKCPLCKTSV 67
>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 = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 24/44 (54%)
Query: 19 MTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDSCPVCN 62
+ C +C + DA I C +S+C +CI + E + +CP C+
Sbjct: 14 LLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCH 57
>pdb|2YUR|A Chain A, Solution Structure Of The Ring Finger Of Human
Retinoblastoma-Binding Protein 6
Length = 74
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 24/44 (54%)
Query: 19 MTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDSCPVCN 62
+ C +C + DA I C +S+C +CI + E + +CP C+
Sbjct: 16 LLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCH 59
>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 = 0.18, Method: Composition-based stats.
Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 14 KLVACMTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEID--SCPVC 61
KL + CP+C + + TI +C H+FC KCI +I E CP+C
Sbjct: 16 KLQEEVICPICLDILQKPVTI-DCGHNFCLKCI-TQIGETSCGFFKCPLC 63
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 33.5 bits (75), Expect = 0.20, Method: Composition-based stats.
Identities = 15/51 (29%), Positives = 30/51 (58%), Gaps = 8/51 (15%)
Query: 17 ACMTCPLC----SKLFRDATTI--SECLHSFCRKCIYEKITEEEIDSCPVC 61
A ++CP+C S++ ++ I +EC H FC +C+ + + + ++CP C
Sbjct: 2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSL--KNANTCPTC 50
>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 = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 5/47 (10%)
Query: 19 MTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEID----SCPVC 61
+TCP+C +L ++ +C HSFC+ C+ + +D SCPVC
Sbjct: 20 VTCPICLELLTQPLSL-DCGHSFCQACLTANHKKSMLDKGESSCPVC 65
>pdb|1JM7|B Chain B, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 117
Score = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 36/87 (41%), Gaps = 20/87 (22%)
Query: 13 EKLVACMTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDSCPVCNT-----DLG- 66
++L + C C+ + R+ + C H FC C+ + I CPVC T DL
Sbjct: 17 DRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGT----GCPVCYTPAWIQDLKI 72
Query: 67 ----------CAPLEKLRADHNLQDLR 83
C+ L L D+ L DL+
Sbjct: 73 NRQLDSMIQLCSKLRNLLHDNELSDLK 99
>pdb|3HCT|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The
P1 Space Group
pdb|3HCU|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The
C2 Space Group
pdb|3HCU|C Chain C, Crystal Structure Of Traf6 In Complex With Ubc13 In The
C2 Space Group
Length = 118
Score = 32.3 bits (72), Expect = 0.39, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 21 CPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDSCPVCN 62
CP+C R+A + C H FC+ CI + I + CPV N
Sbjct: 21 CPICLMALREAVQ-TPCGHRFCKACIIKSIRDAG-HKCPVDN 60
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 32.3 bits (72), Expect = 0.39, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 21 CPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDSCPVCN 62
CP+C R+A + C H FC+ CI + I + CPV N
Sbjct: 9 CPICLMALREAVQ-TPCGHRFCKACIIKSIRDAG-HKCPVDN 48
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 32.3 bits (72), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 31/48 (64%), Gaps = 2/48 (4%)
Query: 19 MTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDS-CPVCNTDL 65
+ CP+C +L ++ + ++C H FC+ C+ + + +++ S CP+C D+
Sbjct: 22 LECPICLELIKEPVS-TKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDI 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 = 32.0 bits (71), Expect = 0.54, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 29/49 (59%), Gaps = 8/49 (16%)
Query: 19 MTCPLC----SKLFRDATTI--SECLHSFCRKCIYEKITEEEIDSCPVC 61
++CP+C S++ ++ I +EC H FC +C+ + + + ++CP C
Sbjct: 11 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSL--KNANTCPTC 57
>pdb|1PVO|A Chain A, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|B Chain B, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|C Chain C, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|D Chain D, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|E Chain E, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|F Chain F, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1XPR|A Chain A, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|B Chain B, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|C Chain C, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|D Chain D, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|E Chain E, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|F Chain F, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPU|A Chain A, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|B Chain B, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|C Chain C, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|D Chain D, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|E Chain E, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|F Chain F, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPO|A Chain A, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|B Chain B, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|C Chain C, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|D Chain D, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|E Chain E, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|F Chain F, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
Length = 419
Score = 31.6 bits (70), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 21/100 (21%), Positives = 40/100 (40%), Gaps = 18/100 (18%)
Query: 168 EPLCRNTQTKRQILSAAESSIQHTPDKGTEDIARPFDGKSDLWKPLNVLVEAAT------ 221
EP R+ Q ++ A+ ++H +D+ D + L + N +V A+
Sbjct: 234 EPASRHVQVAEMVIEKAKRLVEHK-----KDVIILLDSITRLARAYNTVVPASGKVLTGG 288
Query: 222 -------RPRKSLGRPKKAAVSAGLNVSAQAVVDTNQRFD 254
RP++ G + L + A A++DT + D
Sbjct: 289 VDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSKMD 328
>pdb|2HT1|A Chain A, The Closed Ring Structure Of The Rho Transcription
Termination Factor In Complex With Nucleic Acid In The
Motor Domains
pdb|2HT1|B Chain B, The Closed Ring Structure Of The Rho Transcription
Termination Factor In Complex With Nucleic Acid In The
Motor Domains
Length = 433
Score = 31.2 bits (69), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 21/100 (21%), Positives = 40/100 (40%), Gaps = 18/100 (18%)
Query: 168 EPLCRNTQTKRQILSAAESSIQHTPDKGTEDIARPFDGKSDLWKPLNVLVEAAT------ 221
EP R+ Q ++ A+ ++H +D+ D + L + N +V A+
Sbjct: 256 EPASRHVQVAEMVIEKAKRLVEHK-----KDVIILLDSITRLARAYNTVVPASGKVLTGG 310
Query: 222 -------RPRKSLGRPKKAAVSAGLNVSAQAVVDTNQRFD 254
RP++ G + L + A A++DT + D
Sbjct: 311 VDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSKMD 350
>pdb|3M9E|A Chain A, Thyroid Hormone Beta Dna Binding Domain Homodimer With
Inverted Palindrome Tre
pdb|3M9E|B Chain B, Thyroid Hormone Beta Dna Binding Domain Homodimer With
Inverted Palindrome Tre
pdb|3M9E|E Chain E, Thyroid Hormone Beta Dna Binding Domain Homodimer With
Inverted Palindrome Tre
pdb|3M9E|F Chain F, Thyroid Hormone Beta Dna Binding Domain Homodimer With
Inverted Palindrome Tre
Length = 105
Score = 30.0 bits (66), Expect = 2.0, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 7/46 (15%)
Query: 18 CMTCPLCSKLFRDATTISECLHSF--CR---KCIYEKITEEEIDSC 58
C+TC C FR TI + LH C+ KCI +K+T + C
Sbjct: 20 CITCEGCKGFFR--RTIQKSLHPSYSCKYEGKCIIDKVTRNQCQEC 63
>pdb|1PV4|A Chain A, X-Ray Crystal Structure Of The Rho Transcription
Termination Factor In Complex With Single Stranded Dna
pdb|1PV4|B Chain B, X-Ray Crystal Structure Of The Rho Transcription
Termination Factor In Complex With Single Stranded Dna
pdb|1PV4|C Chain C, X-Ray Crystal Structure Of The Rho Transcription
Termination Factor In Complex With Single Stranded Dna
pdb|1PV4|D Chain D, X-Ray Crystal Structure Of The Rho Transcription
Termination Factor In Complex With Single Stranded Dna
pdb|1PV4|E Chain E, X-Ray Crystal Structure Of The Rho Transcription
Termination Factor In Complex With Single Stranded Dna
pdb|1PV4|F Chain F, X-Ray Crystal Structure Of The Rho Transcription
Termination Factor In Complex With Single Stranded Dna
Length = 419
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/100 (21%), Positives = 40/100 (40%), Gaps = 18/100 (18%)
Query: 168 EPLCRNTQTKRQILSAAESSIQHTPDKGTEDIARPFDGKSDLWKPLNVLVEAAT------ 221
EP R+ Q ++ A+ ++H +D+ D + L + N +V A+
Sbjct: 234 EPASRHVQVAEXVIEKAKRLVEHK-----KDVIILLDSITRLARAYNTVVPASGKVLTGG 288
Query: 222 -------RPRKSLGRPKKAAVSAGLNVSAQAVVDTNQRFD 254
RP++ G + L + A A++DT + D
Sbjct: 289 VDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSKXD 328
>pdb|3ICE|A Chain A, Rho Transcription Termination Factor Bound To Rna And
Adp-Bef3
pdb|3ICE|B Chain B, Rho Transcription Termination Factor Bound To Rna And
Adp-Bef3
pdb|3ICE|C Chain C, Rho Transcription Termination Factor Bound To Rna And
Adp-Bef3
pdb|3ICE|D Chain D, Rho Transcription Termination Factor Bound To Rna And
Adp-Bef3
pdb|3ICE|E Chain E, Rho Transcription Termination Factor Bound To Rna And
Adp-Bef3
pdb|3ICE|F Chain F, Rho Transcription Termination Factor Bound To Rna And
Adp-Bef3
Length = 422
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 21/100 (21%), Positives = 40/100 (40%), Gaps = 18/100 (18%)
Query: 168 EPLCRNTQTKRQILSAAESSIQHTPDKGTEDIARPFDGKSDLWKPLNVLVEAAT------ 221
EP R+ Q ++ A+ ++H +D+ D + L + N +V A+
Sbjct: 237 EPASRHVQVAEXVIEKAKRLVEHK-----KDVIILLDSITRLARAYNTVVPASGKVLTGG 291
Query: 222 -------RPRKSLGRPKKAAVSAGLNVSAQAVVDTNQRFD 254
RP++ G + L + A A++DT + D
Sbjct: 292 VDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSKXD 331
>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf
Receptor-Associated Factor 6 Protein
Length = 86
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 21 CPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDSCPVCNTDL 65
CP+C R+A + C H FC+ CI + I + CPV N L
Sbjct: 28 CPICLMALREAVQ-TPCGHRFCKACIIKSIRDAG-HKCPVDNEIL 70
>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 = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 19 MTCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDSCPVC 61
+ C +C + F A I +C H++C CI + ++ + CP C
Sbjct: 23 LRCGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYKT--QCPTC 63
>pdb|2PFT|A Chain A, The Crystal Structure Of Mouse Exo70 Reveals Unique
Features Of The Mammalian Exocyst
Length = 571
Score = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 4/45 (8%)
Query: 303 KLNLISEAEVEISLRGQPVLSTLELHNLINWWVQTSSASERIQTV 347
+LNL+S+++V P LS + LHN N+ +++ SE IQ V
Sbjct: 393 QLNLLSKSKV----YEDPALSAIFLHNNYNYILKSLEKSELIQLV 433
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 4/45 (8%)
Query: 21 CPLCSKLF--RDATTISECLHSFCRKCIYEKITEEEIDSCPVCNT 63
C +C + F RD I C H+F RKC+ + + ++ CP+CN
Sbjct: 18 CAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKV--CPLCNM 60
>pdb|2NLL|B Chain B, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding
Domain Heterodimer Bound To Thyroid Response Element
Dna
Length = 103
Score = 28.9 bits (63), Expect = 4.6, Method: Composition-based stats.
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 7/46 (15%)
Query: 18 CMTCPLCSKLFRDATTISECLHSF--CR---KCIYEKITEEEIDSC 58
C+TC C FR TI + LH C+ KC+ +K+T + C
Sbjct: 18 CITCEGCKGFFR--RTIQKNLHPSYSCKYEGKCVIDKVTRNQCQEC 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 = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 12 REKLVACMTCPLCSKLFRDATTISE--CLHSFCRKCIYEKITEEEIDSCPVCNTDL 65
E + + + CP+C + + ++ + C H F CI + E+ DSCPVC L
Sbjct: 9 EEHVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWL--EQHDSCPVCRKSL 62
>pdb|2CT2|A Chain A, Solution Structure Of The Ring Domain Of The Tripartite
Motif Protein 32
Length = 88
Score = 28.9 bits (63), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 6/57 (10%)
Query: 11 NREKLVACMTCPLCSKLFRDAT---TISECLHSFCRKCIYEKITEEEIDS--CPVCN 62
N + L + CP+C + F + + C H+ CR+C+ EK+ I+ CP C+
Sbjct: 8 NLDALREVLECPICMESFTEEQLRPKLLHCGHTICRQCL-EKLLASSINGVRCPFCS 63
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 28.5 bits (62), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 20 TCPLCSKLFRDATTISECLHSFCRKCIYEKITEEEIDS-CPVC 61
+C +C + ++ I EC H+FC+ CI + E D CPVC
Sbjct: 17 SCSVCLEYLKEPVII-ECGHNFCKACITRWWEDLERDFPCPVC 58
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
0.316 0.131 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,383,345
Number of Sequences: 62578
Number of extensions: 344342
Number of successful extensions: 823
Number of sequences better than 100.0: 48
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 36
Number of HSP's that attempted gapping in prelim test: 801
Number of HSP's gapped (non-prelim): 53
length of query: 368
length of database: 14,973,337
effective HSP length: 100
effective length of query: 268
effective length of database: 8,715,537
effective search space: 2335763916
effective search space used: 2335763916
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: 52 (24.6 bits)