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= 036250
(347 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 68.9 bits (167), Expect = 4e-12, Method: Composition-based stats.
Identities = 29/73 (39%), Positives = 42/73 (57%), Gaps = 7/73 (9%)
Query: 196 PAQKEVVKALPTV-------AIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLE 248
PA KE + ALP + A+ Q++ C +C E+V G+ A E+PC H FH C+ WL+
Sbjct: 16 PASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQ 75
Query: 249 LQSSCPICRYQLP 261
+CP+CR P
Sbjct: 76 KSGTCPVCRCMFP 88
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 65.5 bits (158), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 33/51 (64%)
Query: 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL 260
+ L+C VC E++ +G +++PC H FH CI+PWLE SCP+CR L
Sbjct: 12 VGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSL 62
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 58.5 bits (140), Expect = 5e-09, Method: Composition-based stats.
Identities = 25/50 (50%), Positives = 33/50 (66%), Gaps = 1/50 (2%)
Query: 209 AIDQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQSSCPICR 257
A+D ++CAVCL E G EA+ +P C H FH EC+ WL S+CP+CR
Sbjct: 1 AMDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 50
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 55.1 bits (131), Expect = 5e-08, Method: Composition-based stats.
Identities = 21/41 (51%), Positives = 29/41 (70%)
Query: 216 CAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPIC 256
CAVCLE+F +E PCKH FH +C++ WLE++ CP+C
Sbjct: 18 CAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLC 58
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 194 SLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSC 253
+ AQKE V + ++ +LQC +C E F+ EA + C H F CI W++ + C
Sbjct: 34 KMQAQKEEVLSHMNDVLENELQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIEC 90
Query: 254 PICRYQLPS 262
PICR + S
Sbjct: 91 PICRKDIKS 99
Score = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 20/41 (48%)
Query: 13 ICSRMVNPRMEAGIKCPFCETGFVEQMSSSITDDSINNGIH 53
CS +N M+ I+CP C + S + D+ IN ++
Sbjct: 75 FCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNXINKMVN 115
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 194 SLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSC 253
+ AQKE V + ++ +LQC +C E F+ EA + C H F CI W++ + C
Sbjct: 34 KMQAQKEEVLSHMNDVLENELQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIEC 90
Query: 254 PICRYQLPS 262
PICR + S
Sbjct: 91 PICRKDIKS 99
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 20/41 (48%)
Query: 13 ICSRMVNPRMEAGIKCPFCETGFVEQMSSSITDDSINNGIH 53
CS +N M+ I+CP C + S + D+ IN ++
Sbjct: 75 FCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMVN 115
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 50.4 bits (119), Expect = 1e-06, Method: Composition-based stats.
Identities = 21/53 (39%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRY----QLPSD 263
+C +CL G + + +PC H FH C+ WL CPICR QLPS+
Sbjct: 16 KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQLPSE 68
>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 = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 3/82 (3%)
Query: 194 SLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSC 253
+ AQKE V + ++ +LQC +C E F+ EA + C H F CI W++ + C
Sbjct: 45 KMQAQKEEVLSHMNDVLENELQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIEC 101
Query: 254 PICRYQLPSDDLKVQGNGSGNR 275
PICR + S + + N+
Sbjct: 102 PICRKDIKSKTYSLVLDNCINK 123
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 20/41 (48%)
Query: 13 ICSRMVNPRMEAGIKCPFCETGFVEQMSSSITDDSINNGIH 53
CS +N M+ I+CP C + S + D+ IN ++
Sbjct: 86 FCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMVN 126
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 47.8 bits (112), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 26/42 (61%)
Query: 216 CAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICR 257
C VC+ +F + +PC H+FH +C+ WL+ +CPICR
Sbjct: 26 CVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICR 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 = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 210 IDQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQSSCPICRYQLPSDDLK 266
ID L+C +C E F N A +P C H + CI +L ++ CP C + DLK
Sbjct: 19 IDDLLRCGICFEYF---NIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLK 73
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL 260
+C +C++ G +PC H F +CI W + +CPICR Q+
Sbjct: 17 ECCICMD----GRADLILPCAHSFCQKCIDKWSDRHRNCPICRLQM 58
>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 = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICR 257
+C +CLE+ N + +PC H F CI W+ +CP+C+
Sbjct: 7 RCPICLED--PSNYSMALPCLHAFCYVCITRWIRQNPTCPLCK 47
>pdb|2D8T|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 146
Length = 71
Score = 35.4 bits (80), Expect = 0.052, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQGNGSG 273
+CA+CL+ V +PCKH F C+ L C +CR ++P D L G SG
Sbjct: 17 ECAICLQTCV---HPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDFLD-SGPSSG 71
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 35.0 bits (79), Expect = 0.061, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL 260
++ L C +C F+ E C H F CI+ +LE CPIC Q+
Sbjct: 12 LNPHLMCVLCGGYFIDATTIIE--CLHSFCKTCIVRYLETSKYCPICDVQV 60
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 35.0 bits (79), Expect = 0.061, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL 260
++ L C +C F+ E C H F CI+ +LE CPIC Q+
Sbjct: 8 LNPHLMCVLCGGYFIDATTIIE--CLHSFCKTCIVRYLETSKYCPICDVQV 56
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL 260
++ L C +C F+ E C H F CI+ +LE CPIC Q+
Sbjct: 12 LNPHLMCVLCGGYFIDATTIIE--CLHSFCKTCIVRYLETSKYCPICDVQV 60
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 31.6 bits (70), Expect = 0.74, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 28/63 (44%), Gaps = 9/63 (14%)
Query: 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL------QSSCPICRYQLPSD 263
I +++ C +CLE + E C H F CI E + +CP+CR P
Sbjct: 16 IKEEVTCPICLE---LLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG 72
Query: 264 DLK 266
+LK
Sbjct: 73 NLK 75
>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 = 31.2 bits (69), Expect = 0.79, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 234 CKHKFHGECIMPWLELQSSCPI 255
C H FH CI WL+ + CP+
Sbjct: 57 CNHAFHFHCISRWLKTRQVCPL 78
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 31.2 bits (69), Expect = 0.84, Method: Composition-based stats.
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 234 CKHKFHGECIMPWLELQSSCPICR 257
C H FH C+ W++ + CP+C+
Sbjct: 48 CNHSFHNCCMSLWVKQNNRCPLCQ 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 = 31.2 bits (69), Expect = 0.93, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 234 CKHKFHGECIMPWLELQSSCPI 255
C H FH CI WL+ + 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 = 31.2 bits (69), Expect = 1.00, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 234 CKHKFHGECIMPWLELQSSCPI 255
C H FH CI WL+ + CP+
Sbjct: 75 CNHAFHFHCISRWLKTRQVCPL 96
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 30.8 bits (68), Expect = 1.0, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 234 CKHKFHGECIMPWLELQSSCPI 255
C H FH CI WL+ + CP+
Sbjct: 67 CNHAFHFHCISRWLKTRQVCPL 88
>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 = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 234 CKHKFHGECIMPWLELQSSCPI 255
C H FH CI WL+ + 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 = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 234 CKHKFHGECIMPWLELQSSCPI 255
C H FH CI WL+ + CP+
Sbjct: 73 CNHAFHFHCISRWLKTRQVCPL 94
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 234 CKHKFHGECIMPWLELQSSCPI 255
C H FH CI WL+ + CP+
Sbjct: 84 CNHAFHFHCISRWLKTRQVCPL 105
>pdb|1RMD|A Chain A, Rag1 Dimerization Domain
Length = 116
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ-SSCPICRYQLPSDDL 265
+ + C +C E ++ + E CKH F CI+ L++ S CP CRY DL
Sbjct: 22 KSISCQIC--EHILADPV-ETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDL 73
>pdb|1IY8|A Chain A, Crystal Structure Of Levodione Reductase
pdb|1IY8|B Chain B, Crystal Structure Of Levodione Reductase
pdb|1IY8|C Chain C, Crystal Structure Of Levodione Reductase
pdb|1IY8|D Chain D, Crystal Structure Of Levodione Reductase
pdb|1IY8|E Chain E, Crystal Structure Of Levodione Reductase
pdb|1IY8|F Chain F, Crystal Structure Of Levodione Reductase
pdb|1IY8|G Chain G, Crystal Structure Of Levodione Reductase
pdb|1IY8|H Chain H, Crystal Structure Of Levodione Reductase
Length = 267
Score = 28.1 bits (61), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 21/43 (48%)
Query: 51 GIHVGSDRALSLWAPILLRMMTGLAPSRPRITAHEHISSNNSR 93
GI + + ++W P++ M L P PR A E I N S+
Sbjct: 187 GIRINAIAPGAIWTPMVENSMKQLDPENPRKAAEEFIQVNPSK 229
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 28.1 bits (61), Expect = 8.1, Method: Composition-based stats.
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 214 LQCAVCLE---EFVM-GNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL 260
+ C +C++ E V G C H F +C+ L+ ++CP CR ++
Sbjct: 4 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 54
>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 = 27.7 bits (60), Expect = 9.5, Method: Composition-based stats.
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 214 LQCAVCLE---EFVM-GNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL 260
+ C +C++ E V G C H F +C+ L+ ++CP CR ++
Sbjct: 11 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61
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
0.314 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: 9,507,027
Number of Sequences: 62578
Number of extensions: 372060
Number of successful extensions: 513
Number of sequences better than 100.0: 42
Number of HSP's better than 100.0 without gapping: 29
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 475
Number of HSP's gapped (non-prelim): 46
length of query: 347
length of database: 14,973,337
effective HSP length: 100
effective length of query: 247
effective length of database: 8,715,537
effective search space: 2152737639
effective search space used: 2152737639
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (24.6 bits)