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= 043965
(342 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 64.3 bits (155), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 23/48 (47%), Positives = 32/48 (66%)
Query: 210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCR 257
+ L+C VC E++ +G +++PC H FH CI+PWLE SCPVCR
Sbjct: 12 VGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCR 59
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 61.6 bits (148), Expect = 6e-10, Method: Composition-based stats.
Identities = 26/52 (50%), Positives = 34/52 (65%), Gaps = 1/52 (1%)
Query: 210 IDKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPVCRFQV 260
+D ++CAVCL E E G EA+ +P C H FH EC+ WL S+CP+CR V
Sbjct: 2 MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53
>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 = 60.5 bits (145), Expect = 1e-09, Method: Composition-based stats.
Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 7/74 (9%)
Query: 195 PAANKAVLKALPTVTIDKN-------LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWL 247
P A+K + ALP + + ++ + C +C E+ G+ A E+PC H FH C+ WL
Sbjct: 15 PPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWL 74
Query: 248 EVRSSCPVCRFQVP 261
+ +CPVCR P
Sbjct: 75 QKSGTCPVCRCMFP 88
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 60.1 bits (144), Expect = 2e-09, Method: Composition-based stats.
Identities = 24/45 (53%), Positives = 31/45 (68%)
Query: 216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV 260
CAVCLE+F+ +E PCKH FH +C++ WLEVR CP+C V
Sbjct: 18 CAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPV 62
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 52.0 bits (123), Expect = 5e-07, Method: Composition-based stats.
Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRF----QVPSD 263
+C +CL E G + + +PC H FH C+ WL CP+CR Q+PS+
Sbjct: 16 KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQLPSE 68
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 27/42 (64%)
Query: 216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCR 257
C VC+ +FE + +PC H+FH +C+ WL+ +CP+CR
Sbjct: 26 CVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICR 67
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 195 PAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCP 254
A + VL + V ++ LQC +C E F EA + C H F CI W++ + CP
Sbjct: 36 QAQKEEVLSHMNDV-LENELQCIICSEYF---IEAVTLNCAHSFCSYCINEWMKRKIECP 91
Query: 255 VCRFQVPSDDFKIQGNGSGNR 275
+CR + S + + + N+
Sbjct: 92 ICRKDIKSKTYSLVLDNXINK 112
Score = 28.5 bits (62), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 20/41 (48%)
Query: 12 ICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIH 52
CS +N M+ I+CP C I + S + + IN ++
Sbjct: 75 FCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNXINKMVN 115
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 195 PAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCP 254
A + VL + V ++ LQC +C E F EA + C H F CI W++ + CP
Sbjct: 36 QAQKEEVLSHMNDV-LENELQCIICSEYF---IEAVTLNCAHSFCSYCINEWMKRKIECP 91
Query: 255 VCRFQVPSDDFKIQGNGSGNR 275
+CR + S + + + N+
Sbjct: 92 ICRKDIKSKTYSLVLDNCINK 112
Score = 28.1 bits (61), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 20/41 (48%)
Query: 12 ICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIH 52
CS +N M+ I+CP C I + S + + IN ++
Sbjct: 75 FCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMVN 115
>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 = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 196 AANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPV 255
A + VL + V ++ LQC +C E F EA + C H F CI W++ + CP+
Sbjct: 48 AQKEEVLSHMNDV-LENELQCIICSEYF---IEAVTLNCAHSFCSYCINEWMKRKIECPI 103
Query: 256 CRFQVPSDDFKIQGNGSGNR 275
CR + S + + + N+
Sbjct: 104 CRKDIKSKTYSLVLDNCINK 123
Score = 28.5 bits (62), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 20/41 (48%)
Query: 12 ICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIH 52
CS +N M+ I+CP C I + S + + IN ++
Sbjct: 86 FCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMVN 126
>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 = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 22/59 (37%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 209 TIDKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFK 266
TID L+C +C E F I A +P C H + CI +L ++ CP C V D K
Sbjct: 18 TIDDLLRCGICFEYFNI---AMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLK 73
>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 = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQGNG 271
+C +CLE+ N + +PC H F CI W+ +CP+C+ V S I+ +
Sbjct: 7 RCPICLED--PSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVESVVHTIESDS 61
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV 260
+C +C++ G +PC H F +CI W + +CP+CR Q+
Sbjct: 17 ECCICMD----GRADLILPCAHSFCQKCIDKWSDRHRNCPICRLQM 58
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 34.3 bits (77), Expect = 0.092, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV 260
++ +L C +C F E C H F CI+ +LE CP+C QV
Sbjct: 12 LNPHLMCVLCGGYFIDATTIIE--CLHSFCKTCIVRYLETSKYCPICDVQV 60
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 34.3 bits (77), Expect = 0.092, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV 260
++ +L C +C F E C H F CI+ +LE CP+C QV
Sbjct: 8 LNPHLMCVLCGGYFIDATTIIE--CLHSFCKTCIVRYLETSKYCPICDVQV 56
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV 260
++ +L C +C F E C H F CI+ +LE CP+C QV
Sbjct: 12 LNPHLMCVLCGGYFIDATTIIE--CLHSFCKTCIVRYLETSKYCPICDVQV 60
>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 = 33.1 bits (74), Expect = 0.21, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 234 CKHKFHGECIMPWLEVRSSCPV 255
C H FH CI WL+ R CP+
Sbjct: 57 CNHAFHFHCISRWLKTRQVCPL 78
>pdb|2D8T|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 146
Length = 71
Score = 33.1 bits (74), Expect = 0.23, Method: Composition-based stats.
Identities = 24/70 (34%), Positives = 36/70 (51%), Gaps = 11/70 (15%)
Query: 206 PTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECI--MPWLEVRSSCPVCRFQVPSD 263
P++T+ +CA+CL+ +PCKH F C+ WL R C +CR ++P +
Sbjct: 11 PSLTVP---ECAICLQTCV---HPVSLPCKHVFCYLCVKGASWLGKR--CALCRQEIP-E 61
Query: 264 DFKIQGNGSG 273
DF G SG
Sbjct: 62 DFLDSGPSSG 71
>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 = 32.7 bits (73), Expect = 0.26, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 234 CKHKFHGECIMPWLEVRSSCPV 255
C H FH CI WL+ R CP+
Sbjct: 65 CNHAFHFHCISRWLKTRQVCPL 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 = 32.7 bits (73), Expect = 0.27, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 234 CKHKFHGECIMPWLEVRSSCPV 255
C H FH CI WL+ R CP+
Sbjct: 75 CNHAFHFHCISRWLKTRQVCPL 96
>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 = 32.7 bits (73), Expect = 0.29, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 234 CKHKFHGECIMPWLEVRSSCPV 255
C H FH CI WL+ R CP+
Sbjct: 73 CNHAFHFHCISRWLKTRQVCPL 94
>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 = 32.7 bits (73), Expect = 0.30, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 234 CKHKFHGECIMPWLEVRSSCPV 255
C H FH CI WL+ R CP+
Sbjct: 73 CNHAFHFHCISRWLKTRQVCPL 94
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 32.7 bits (73), Expect = 0.30, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 234 CKHKFHGECIMPWLEVRSSCPV 255
C H FH CI WL+ R CP+
Sbjct: 67 CNHAFHFHCISRWLKTRQVCPL 88
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 32.0 bits (71), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 234 CKHKFHGECIMPWLEVRSSCPV 255
C H FH CI WL+ R CP+
Sbjct: 84 CNHAFHFHCISRWLKTRQVCPL 105
>pdb|2JRJ|A Chain A, Solution Structure Of The Human Pirh2 Ring-H2 Domain.
Northeast Structural Genomics Consortium Target Ht2b
Length = 52
Score = 30.8 bits (68), Expect = 0.99, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 216 CAVCLEEFEIGNE-AKEMPCKHKFHGECIMPWLEVRSSCPVC 256
C +CLE+ A +PC H H C L+ CP+C
Sbjct: 8 CPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLC 49
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 234 CKHKFHGECIMPWLEVRSSCPVCR 257
C H FH C+ W++ + CP+C+
Sbjct: 48 CNHSFHNCCMSLWVKQNNRCPLCQ 71
>pdb|4FA8|A Chain A, Multi-Pronged Modulation Of Cytokine Signaling
pdb|4FA8|B Chain B, Multi-Pronged Modulation Of Cytokine Signaling
pdb|4FA8|D Chain D, Multi-Pronged Modulation Of Cytokine Signaling
Length = 203
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 275 RDESLGNEDAQNNLRLGNGEDRVGNGRRYW--IPIPWPFDSLFSMSGS 320
R SLG E + +LG GE++V GR + I I WPF F + S
Sbjct: 18 RRVSLGPEIEVSWFKLGPGEEQVLIGRMHHDVIFIEWPFRGFFDIHRS 65
>pdb|3UEZ|A Chain A, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|3UEZ|B Chain B, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|3UEZ|C Chain C, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|3UEZ|D Chain D, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|A Chain A, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|B Chain B, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|C Chain C, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|D Chain D, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|E Chain E, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|F Chain F, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|M Chain M, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|N Chain N, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|O Chain O, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|P Chain P, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|Q Chain Q, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|R Chain R, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADQ|A Chain A, Crystal Structure Of The Mouse Colony-Stimulating Factor 1
(Mcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADQ|B Chain B, Crystal Structure Of The Mouse Colony-Stimulating Factor 1
(Mcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADQ|C Chain C, Crystal Structure Of The Mouse Colony-Stimulating Factor 1
(Mcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADQ|D Chain D, Crystal Structure Of The Mouse Colony-Stimulating Factor 1
(Mcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
Length = 208
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 275 RDESLGNEDAQNNLRLGNGEDRVGNGRRYW--IPIPWPFDSLFSMSGS 320
R SLG E + +LG GE++V GR + I I WPF F + S
Sbjct: 16 RRVSLGPEIEVSWFKLGPGEEQVLIGRMHHDVIFIEWPFRGFFDIHRS 63
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 30.4 bits (67), Expect = 1.5, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 26/63 (41%), Gaps = 9/63 (14%)
Query: 210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV------RSSCPVCRFQVPSD 263
I + + C +CLE + E C H F CI E + +CPVCR P
Sbjct: 16 IKEEVTCPICLELLK---EPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG 72
Query: 264 DFK 266
+ K
Sbjct: 73 NLK 75
>pdb|2CH8|A Chain A, Structure Of The Epstein-barr Virus Oncogene Barf1
pdb|2CH8|B Chain B, Structure Of The Epstein-barr Virus Oncogene Barf1
pdb|2CH8|C Chain C, Structure Of The Epstein-barr Virus Oncogene Barf1
pdb|2CH8|D Chain D, Structure Of The Epstein-barr Virus Oncogene Barf1
Length = 201
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 275 RDESLGNEDAQNNLRLGNGEDRVGNGRRYW--IPIPWPFDSLFSMSGS 320
R SLG E + +LG GE++V GR + I I WPF F + S
Sbjct: 16 RRVSLGPEIEVSWFKLGPGEEQVLIGRMHHDVIFIEWPFRGFFDIHRS 63
>pdb|3CXL|A Chain A, Crystal Structure Of Human Chimerin 1 (Chn1)
Length = 463
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 5/74 (6%)
Query: 8 YWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIHVRSDRALSLWASILL 67
+WC C+ + + G+KC C + +Q S + D D HV+ +++ L
Sbjct: 221 HWCEYCANFMWGLIAQGVKCADCGLNVHKQCSKMVPNDCKPDLKHVK-----KVYSCDLT 275
Query: 68 RMMTGLSPSRPRIA 81
++ + RP +
Sbjct: 276 TLVKAHTTKRPMVV 289
>pdb|2K4D|A Chain A, E2-C-Cbl Recognition Is Necessary But Not Sufficient For
Ubiquitination Activity
Length = 83
Score = 29.3 bits (64), Expect = 2.9, Method: Composition-based stats.
Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 4/46 (8%)
Query: 216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR-SSCPVCRFQV 260
C +C E + K PC H C+ W E CP CR ++
Sbjct: 27 CKICAEN---DKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEI 69
>pdb|3L11|A Chain A, Crystal Structure Of The Ring Domain Of Rnf168
Length = 115
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 7/60 (11%)
Query: 204 ALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS-SCPVCRFQVPS 262
A+P+++ QC +C+E I E +PC H C +E S CP CR +V S
Sbjct: 9 AIPSLS---ECQCGICME---ILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS 62
>pdb|4A49|A Chain A, Structure Of Phosphotyr371-C-Cbl-Ubch5b Complex
Length = 84
Score = 28.9 bits (63), Expect = 3.9, Method: Composition-based stats.
Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 4/46 (8%)
Query: 216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR-SSCPVCRFQV 260
C +C E + K PC H C+ W E CP CR ++
Sbjct: 30 CKICAEN---DKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEI 72
>pdb|2LDR|A Chain A, Solution Structure Of Helix-Ring Domain Of Cbl-B In The
Tyr363 Phosphorylated Form
Length = 82
Score = 28.9 bits (63), Expect = 4.5, Method: Composition-based stats.
Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 4/46 (8%)
Query: 216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR-SSCPVCRFQV 260
C +C E + K PC H C+ W E CP CR ++
Sbjct: 29 CKICAEN---DKDVKIEPCGHLMCTSCLTAWQESDGQGCPFCRCEI 71
>pdb|1RMD|A Chain A, Rag1 Dimerization Domain
Length = 116
Score = 28.5 bits (62), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 5/54 (9%)
Query: 212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR-SSCPVCRFQV-PSD 263
K++ C +C I + E CKH F CI+ L+V S CP CR+ P+D
Sbjct: 22 KSISCQICEH---ILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTD 72
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 28.5 bits (62), Expect = 6.0, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWL-EVRSSCPV 255
+C +CL EA + PC H+F CI+ + + CPV
Sbjct: 8 ECPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPV 46
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 28.5 bits (62), Expect = 6.2, Method: Composition-based stats.
Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 214 LQCAVCLEEF----EIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV 260
+ C +C++ + + G C H F +C+ L+ ++CP CR ++
Sbjct: 4 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 54
>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 = 28.1 bits (61), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 216 CAVCLEEFEIGNE-AKEMPCKHKFHGECIMPWLEVRSSCPVC 256
C +CLE+ A +PC H H C L+ CP+C
Sbjct: 8 CPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLC 49
>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 = 28.1 bits (61), Expect = 7.4, Method: Composition-based stats.
Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 214 LQCAVCLEEF----EIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV 260
+ C +C++ + + G C H F +C+ L+ ++CP CR ++
Sbjct: 11 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61
>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 = 28.1 bits (61), Expect = 7.9, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 28/65 (43%), Gaps = 9/65 (13%)
Query: 208 VTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMP------WLEVRSSCPVCRFQVP 261
V + + + C +CLE + + + C H F C+ + SSCPVCR
Sbjct: 14 VNVKEEVTCPICLE---LLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQ 70
Query: 262 SDDFK 266
++ +
Sbjct: 71 PENIR 75
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 27.7 bits (60), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 6/73 (8%)
Query: 194 CPAANKAV--LKALPTVTIDKNLQCAVCLEEF-EI---GNEAKEMPCKHKFHGECIMPWL 247
CP K + + P + C +C++ + EI G C H F +C+ L
Sbjct: 51 CPTCRKKINHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSL 110
Query: 248 EVRSSCPVCRFQV 260
+ ++CP CR ++
Sbjct: 111 KNANTCPTCRKKI 123
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 27.7 bits (60), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 25/52 (48%), Gaps = 10/52 (19%)
Query: 212 KNLQ----CAVCLEEFEIGNEAKEMPCKHKFHGECIMPW---LEVRSSCPVC 256
+NLQ C+VCLE + E + C H F CI W LE CPVC
Sbjct: 10 ENLQVEASCSVCLEYLK---EPVIIECGHNFCKACITRWWEDLERDFPCPVC 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
0.317 0.133 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,597,246
Number of Sequences: 62578
Number of extensions: 373014
Number of successful extensions: 595
Number of sequences better than 100.0: 51
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 564
Number of HSP's gapped (non-prelim): 55
length of query: 342
length of database: 14,973,337
effective HSP length: 100
effective length of query: 242
effective length of database: 8,715,537
effective search space: 2109159954
effective search space used: 2109159954
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)