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= 008670
(557 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 = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 29/44 (65%)
Query: 501 VKCSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPICK 544
++C +C+E+Y +GE V +L C H +H CI WL + CP+C+
Sbjct: 16 LECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCR 59
>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 = 47.0 bits (110), Expect = 3e-05, Method: Composition-based stats.
Identities = 17/42 (40%), Positives = 24/42 (57%)
Query: 503 CSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPICK 544
C IC EYV G+ L C H +H C+ WL+ + CP+C+
Sbjct: 43 CPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCR 84
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 20/43 (46%), Positives = 26/43 (60%)
Query: 502 KCSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPICK 544
KC+IC GE+V RL C H +H +C+ QWL CPIC+
Sbjct: 16 KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICR 58
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 42.4 bits (98), Expect = 6e-04, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 498 NDDVKCSICQEEYVVGEEVGRL-HCQHRYHVLCIQQWLRLTNWCPICK 544
+D V+C++C E GEE L C H +H C+ WL + CP+C+
Sbjct: 3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 50
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 42.4 bits (98), Expect = 7e-04, Method: Composition-based stats.
Identities = 14/41 (34%), Positives = 26/41 (63%)
Query: 503 CSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPIC 543
C++C E++ +E+G C+H +H C+ +WL + CP+C
Sbjct: 18 CAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLC 58
>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 = 0.011, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 3/46 (6%)
Query: 499 DDVKCSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPICK 544
++++C IC E ++ E L+C H + CI +W++ CPIC+
Sbjct: 63 NELQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIECPICR 105
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 37.7 bits (86), Expect = 0.016, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 3/46 (6%)
Query: 499 DDVKCSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPICK 544
++++C IC E ++ E L+C H + CI +W++ CPIC+
Sbjct: 52 NELQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIECPICR 94
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 37.7 bits (86), Expect = 0.017, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 3/46 (6%)
Query: 499 DDVKCSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPICK 544
++++C IC E ++ E L+C H + CI +W++ CPIC+
Sbjct: 52 NELQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIECPICR 94
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 37.7 bits (86), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 503 CSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPICK 544
C +C ++ + + L C H +H C+ +WL+ CPIC+
Sbjct: 26 CVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICR 67
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 37.0 bits (84), Expect = 0.025, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 11/70 (15%)
Query: 475 LKCLKTSIYQPAPLDVALSCSGNNDDVKCSICQEEYVVGEEVGRLHCQHRYHVLCIQQWL 534
++C +I + +D L C N C + V GE C H +H C+ W+
Sbjct: 13 VECDTCAICRVQVMDACLRCQAENKQEDCVV-----VWGE------CNHSFHNCCMSLWV 61
Query: 535 RLTNWCPICK 544
+ N CP+C+
Sbjct: 62 KQNNRCPLCQ 71
>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 = 34.7 bits (78), Expect = 0.13, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 498 NDDVKCSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPIC 543
+D ++C IC E + + + + C H Y LCI+++L CP C
Sbjct: 20 DDLLRCGICFEYFNIAMIIPQ--CSHNYCSLCIRKFLSYKTQCPTC 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 = 34.7 bits (78), Expect = 0.15, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 8/55 (14%)
Query: 488 LDVALSCSGNNDDVKCSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPI 542
+D+ + C N + S EE V V C H +H CI +WL+ CP+
Sbjct: 32 MDLCIECQAN----QASATSEECTVAWGV----CNHAFHFHCISRWLKTRQVCPL 78
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 34.3 bits (77), Expect = 0.17, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 8/55 (14%)
Query: 488 LDVALSCSGNNDDVKCSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPI 542
+D+ + C N + S EE V V C H +H CI +WL+ CP+
Sbjct: 59 MDLCIECQAN----QASATSEECTVAWGV----CNHAFHFHCISRWLKTRQVCPL 105
>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 = 34.3 bits (77), Expect = 0.17, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 8/55 (14%)
Query: 488 LDVALSCSGNNDDVKCSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPI 542
+D+ + C N + S EE V V C H +H CI +WL+ CP+
Sbjct: 40 MDLCIECQAN----QASATSEECTVAWGV----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 = 34.3 bits (77), Expect = 0.21, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 8/55 (14%)
Query: 488 LDVALSCSGNNDDVKCSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPI 542
+D+ + C N + S EE V V C H +H CI +WL+ CP+
Sbjct: 50 MDLCIECQAN----QASATSEECTVAWGV----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 = 33.9 bits (76), Expect = 0.27, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 8/55 (14%)
Query: 488 LDVALSCSGNNDDVKCSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPI 542
+D+ + C N + S EE V V C H +H CI +WL+ CP+
Sbjct: 48 MDLCIECQAN----QASATSEECTVAWGV----CNHAFHFHCISRWLKTRQVCPL 94
>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 = 33.5 bits (75), Expect = 0.33, Method: Composition-based stats.
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 8/46 (17%)
Query: 502 KCSICQEE---YVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPICK 544
+C IC E+ Y + L C H + +CI +W+R CP+CK
Sbjct: 7 RCPICLEDPSNYSMA-----LPCLHAFCYVCITRWIRQNPTCPLCK 47
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 33.1 bits (74), Expect = 0.42, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 8/55 (14%)
Query: 488 LDVALSCSGNNDDVKCSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPI 542
+D+ + C N + S EE V V C H +H CI +WL+ CP+
Sbjct: 42 MDLCIECQAN----QASATSEECTVAWGV----CNHAFHFHCISRWLKTRQVCPL 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 = 32.7 bits (73), Expect = 0.50, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 8/54 (14%)
Query: 489 DVALSCSGNNDDVKCSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPI 542
D+ + C N + S EE V V C H +H CI +WL+ CP+
Sbjct: 49 DLCIECQAN----QASATSEECTVAWGV----CNHAFHFHCISRWLKTRQVCPL 94
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 31.2 bits (69), Expect = 1.4, Method: Composition-based stats.
Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 498 NDDVKCSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPIC 543
N + C +C ++ + + C H + CI ++L + +CPIC
Sbjct: 9 NPHLMCVLCGGYFIDATTI--IECLHSFCKTCIVRYLETSKYCPIC 52
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 31.2 bits (69), Expect = 1.8, Method: Composition-based stats.
Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 498 NDDVKCSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPIC 543
N + C +C ++ + + C H + CI ++L + +CPIC
Sbjct: 13 NPHLMCVLCGGYFIDATTI--IECLHSFCKTCIVRYLETSKYCPIC 56
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 30.8 bits (68), Expect = 1.8, Method: Composition-based stats.
Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 498 NDDVKCSICQEEYVVGEEVGRLHCQHRYHVLCIQQWLRLTNWCPIC 543
N + C +C ++ + + C H + CI ++L + +CPIC
Sbjct: 13 NPHLMCVLCGGYFIDATTI--IECLHSFCKTCIVRYLETSKYCPIC 56
>pdb|3K1L|B Chain B, Crystal Structure Of Fancl
pdb|3K1L|A Chain A, Crystal Structure Of Fancl
Length = 381
Score = 28.9 bits (63), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 15/64 (23%), Positives = 30/64 (46%), Gaps = 16/64 (25%)
Query: 497 NNDDVKCSICQEEYVVGEEVGRLHCQH-----RYHVLCIQQWLRLT-----------NWC 540
+N++++C+IC + G EV + C + + H +C+++W + C
Sbjct: 305 DNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQC 364
Query: 541 PICK 544
P CK
Sbjct: 365 PFCK 368
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
0.313 0.129 0.372
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,197,361
Number of Sequences: 62578
Number of extensions: 336975
Number of successful extensions: 491
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 466
Number of HSP's gapped (non-prelim): 37
length of query: 557
length of database: 14,973,337
effective HSP length: 104
effective length of query: 453
effective length of database: 8,465,225
effective search space: 3834746925
effective search space used: 3834746925
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 54 (25.4 bits)