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= 028342
(210 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 65.5 bits (158), Expect = 2e-11, Method: Composition-based stats.
Identities = 25/44 (56%), Positives = 31/44 (70%)
Query: 124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
EC +CL+E GE R LP+C HGFH C+D WL S+S+CP CR
Sbjct: 7 ECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 50
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 57.0 bits (136), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 23/45 (51%), Positives = 34/45 (75%), Gaps = 1/45 (2%)
Query: 123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
T CV+C+ +F + +R+LP CNH FH +C+DKWL++N +CP CR
Sbjct: 24 TLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICR 67
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/51 (50%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCL 170
G EC +C ++A GE VR LP CNH FH CI WL + SCP CR L
Sbjct: 13 GSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSL 62
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 50.4 bits (119), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 24/44 (54%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
+C ICLS GE VR LP C H FH C+D+WL +N CP CR
Sbjct: 16 KCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICR 58
>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 = 43.5 bits (101), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
G + C IC SE+ G+ LP C+H FH C+ WL+ + +CP CR
Sbjct: 38 GQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCR 84
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 113 STELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKC 166
S ++K L C +CL +F P + + + P C H FH +C+ KWL CP C
Sbjct: 6 SGKVKELNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLC 58
>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 = 0.014, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 5/46 (10%)
Query: 122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
+ EC IC+ R L+ C H F +CIDKW + +CP CR
Sbjct: 15 EEECCICMDG-----RADLILPCAHSFCQKCIDKWSDRHRNCPICR 55
>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 = 35.4 bits (80), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 125 CVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
C ICL + P LP C H F CI +W+R N +CP C+
Sbjct: 8 CPICLED--PSNYSMALP-CLHAFCYVCITRWIRQNPTCPLCK 47
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 35.4 bits (80), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 125 CVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRH 168
C+ C +E + V + +CNH FH C+ W++ N+ CP C+
Sbjct: 29 CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQ 72
>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 = 33.9 bits (76), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 144 CNHGFHVRCIDKWLRSNSSCP 164
CNH FH CI +WL++ CP
Sbjct: 75 CNHAFHFHCISRWLKTRQVCP 95
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 33.9 bits (76), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 144 CNHGFHVRCIDKWLRSNSSCP 164
CNH FH CI +WL++ CP
Sbjct: 67 CNHAFHFHCISRWLKTRQVCP 87
>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 = 33.9 bits (76), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 144 CNHGFHVRCIDKWLRSNSSCP 164
CNH FH CI +WL++ CP
Sbjct: 57 CNHAFHFHCISRWLKTRQVCP 77
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 33.9 bits (76), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 144 CNHGFHVRCIDKWLRSNSSCP 164
CNH FH CI +WL++ CP
Sbjct: 84 CNHAFHFHCISRWLKTRQVCP 104
>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 = 33.9 bits (76), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 144 CNHGFHVRCIDKWLRSNSSCP 164
CNH FH CI +WL++ CP
Sbjct: 65 CNHAFHFHCISRWLKTRQVCP 85
>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 = 33.9 bits (76), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 144 CNHGFHVRCIDKWLRSNSSCP 164
CNH FH CI +WL++ CP
Sbjct: 73 CNHAFHFHCISRWLKTRQVCP 93
>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 = 33.5 bits (75), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 144 CNHGFHVRCIDKWLRSNSSCP 164
CNH FH CI +WL++ CP
Sbjct: 73 CNHAFHFHCISRWLKTRQVCP 93
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
+ +C+IC F + C H F CI++W++ CP CR
Sbjct: 53 ELQCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICR 94
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
+ +C+IC F + C H F CI++W++ CP CR
Sbjct: 53 ELQCIICSEYFIEA----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 = 32.0 bits (71), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
+ +C+IC F + C H F CI++W++ CP CR
Sbjct: 64 ELQCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICR 105
>pdb|3TKA|A Chain A, Crystal Structure And Solution Saxs Of Methyltransferase
Rsmh From E.Coli
Length = 347
Score = 31.2 bits (69), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 2/67 (2%)
Query: 100 KQKALKTFTVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS 159
K A +TF V+ +L ++ L+ APG R+ ++ H R + +++R
Sbjct: 232 KHPATRTFQAVRIWVNSELEEIEQALKSSLNVLAPGGRLSII--SFHSLEDRIVKRFMRE 289
Query: 160 NSSCPKC 166
NS P+
Sbjct: 290 NSRGPQV 296
>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 = 1.1, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 3/42 (7%)
Query: 125 CVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKC 166
C IC F ++P+C+H + CI K+L + CP C
Sbjct: 25 CGICFEYFNIA---MIIPQCSHNYCSLCIRKFLSYKTQCPTC 63
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 3/52 (5%)
Query: 119 PGLDTECVICL---SEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
P C IC+ SE R+ + +C H F +C+ L++ ++CP CR
Sbjct: 12 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 63
>pdb|2JRJ|A Chain A, Solution Structure Of The Human Pirh2 Ring-H2 Domain.
Northeast Structural Genomics Consortium Target Ht2b
Length = 52
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 19/44 (43%)
Query: 125 CVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRH 168
C ICL + V + C H H C ++ L+ CP C H
Sbjct: 8 CPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCMH 51
>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 = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 3/52 (5%)
Query: 119 PGLDTECVICL---SEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
P C IC+ SE R+ + +C H F +C+ L++ ++CP CR
Sbjct: 7 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 58
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 120 GLDTECVICL---SEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
G C IC+ SE R+ + +C H F +C+ L++ ++CP CR
Sbjct: 1 GAMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 51
>pdb|1V87|A Chain A, Solution Structure Of The Ring-H2 Finger Domain Of Mouse
Deltex Protein 2
Length = 114
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 15/59 (25%)
Query: 109 VVKYSTELKLPGLDTECVICLSEFAPGER--------------VRLLPKCNHGFHVRCI 153
+ KY+ ELK+ + +C+IC+ + A V L KC+H FH+ C+
Sbjct: 13 IRKYTEELKVA-PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCL 70
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 28.1 bits (61), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 125 CVICL---SEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
C IC+ SE R+ + +C H F +C+ L++ ++CP CR
Sbjct: 10 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 55
Score = 28.1 bits (61), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 125 CVICL---SEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
C IC+ SE R+ + +C H F +C+ L++ ++CP CR
Sbjct: 75 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 120
>pdb|3NYB|A Chain A, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 323
Score = 27.3 bits (59), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 112 YSTELKLPGLDTECVIC 128
YST+L LPG D +CV+
Sbjct: 68 YSTDLYLPGSDIDCVVT 84
>pdb|1EXK|A Chain A, Solution Structure Of The Cysteine-Rich Domain Of The
Escherichia Coli Chaperone Protein Dnaj
Length = 79
Score = 26.9 bits (58), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 113 STELKLPGLDTECVICLSEFA-PGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
+ E+++P L+ EC +C A PG + + P C+ V+ + +CP C+
Sbjct: 3 TKEIRIPTLE-ECDVCHGSGAKPGTQPQTCPTCHGSGQVQMRQGFFAVQQTCPHCQ 57
>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 = 26.9 bits (58), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 19/44 (43%)
Query: 123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKC 166
+ C ICL + V + C H H C ++ L+ CP C
Sbjct: 6 SGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLC 49
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
0.323 0.135 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,541,136
Number of Sequences: 62578
Number of extensions: 134215
Number of successful extensions: 327
Number of sequences better than 100.0: 43
Number of HSP's better than 100.0 without gapping: 28
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 294
Number of HSP's gapped (non-prelim): 44
length of query: 210
length of database: 14,973,337
effective HSP length: 95
effective length of query: 115
effective length of database: 9,028,427
effective search space: 1038269105
effective search space used: 1038269105
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)