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= 028419
(209 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3FL2|A Chain A, Crystal Structure Of The Ring Domain Of The E3 Ubiquitin-
Protein Ligase Uhrf1
Length = 124
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 19/74 (25%)
Query: 1 MAQPVTTPCAHNFCKSCLEEAFSGKSFVRERSRGGRALRSQKTIMKCPSCTTDISDFLKD 60
+ +P+TT C HN CK CL+ +F + F CP+C D+
Sbjct: 62 VFRPITTVCQHNVCKDCLDRSFRAQVF------------------SCPACRYDLGRSYAM 103
Query: 61 PQVNRELMEVIESL 74
QVN+ L V+ L
Sbjct: 104 -QVNQPLQTVLNQL 116
>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 = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 18/54 (33%)
Query: 1 MAQPVTTPCAHNFCKSCLEEAFSGKSFVRERSRGGRALRSQKTIMKCPSCTTDI 54
+ QPVTT C HN CK CL+ +F + F CP+C D+
Sbjct: 88 VYQPVTTECFHNVCKDCLQRSFKAQVF------------------SCPACRHDL 123
>pdb|4DQ1|A Chain A, Thymidylate Synthase From Staphylococcus Aureus.
pdb|4DQ1|B Chain B, Thymidylate Synthase From Staphylococcus Aureus
Length = 321
Score = 35.4 bits (80), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 6/78 (7%)
Query: 53 DISDF----LKDPQVNRELMEVIESLKQKTEEDDELAEESNDEGTDASEGISDLVPXXXX 108
D++DF L DP+ N + E ++ KQ+ EDD A++ D G + D V
Sbjct: 106 DMTDFGHRALSDPEFNEQYKEQMKQFKQRILEDDTFAKQFGDLGNVYGKQWRDWV--DKD 163
Query: 109 XXXXXXXXTIVTGCSHNP 126
T++ HNP
Sbjct: 164 GNHFDQLKTVIEQIKHNP 181
>pdb|3L11|A Chain A, Crystal Structure Of The Ring Domain Of Rnf168
Length = 115
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 23/99 (23%), Positives = 40/99 (40%), Gaps = 30/99 (30%)
Query: 1 MAQPVTTPCAHNFCKSCLEEAFSGKSFVRERSRGGRALRSQKTIMKCPSCTTDISDFL-- 58
+ +PVT PC H CK C + +K + CP C +S +
Sbjct: 25 LVEPVTLPCNHTLCKPCFQSTV------------------EKASLCCPFCRRRVSSWTRY 66
Query: 59 ---KDPQVNRELMEVIE-------SLKQKTEEDDELAEE 87
++ VN EL +I+ L+ +E +E+A++
Sbjct: 67 HTRRNSLVNVELWTIIQKHYPRECKLRASGQESEEVADD 105
>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 = 30.8 bits (68), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 21/80 (26%)
Query: 9 CAHNFCKSCLEEAFSGKSFVRERSRGGRALRSQKTIMKCPSCTTDISDFLKDPQVNRELM 68
C+HN+C C+ + S K+ +CP+C +++ D + NR L
Sbjct: 41 CSHNYCSLCIRKFLSYKT-------------------QCPTCCVTVTE--PDLKNNRILD 79
Query: 69 EVIESLKQKTEEDDELAEES 88
E+++SL + A ES
Sbjct: 80 ELVKSLNFARNHLLQFALES 99
>pdb|2EGP|A Chain A, Solution Structure Of The Ring-Finger Domain From Human
Tripartite Motif Protein 34
Length = 79
Score = 30.4 bits (67), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 14/72 (19%)
Query: 1 MAQPVTTPCAHNFCKSCLEEAFSGKSFVRERSRGGRALRSQKTIMKCPSCTTDISDFLKD 60
+ +P++ C H+ C++C+ S K V S GG++ CP C IS +
Sbjct: 22 LTEPLSLDCGHSLCRACI--TVSNKEAV--TSMGGKS--------SCPVC--GISYSFEH 67
Query: 61 PQVNRELMEVIE 72
Q N+ L ++E
Sbjct: 68 LQANQHLANIVE 79
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 30.0 bits (66), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 20/54 (37%), Gaps = 19/54 (35%)
Query: 1 MAQPVTTPCAHNFCKSCLEEAFSGKSFVRERSRGGRALRSQKTIMKCPSCTTDI 54
+ VT CAH+FC C+ E K ++CP C DI
Sbjct: 63 FIEAVTLNCAHSFCSYCINEWMKRK-------------------IECPICRKDI 97
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 20/54 (37%), Gaps = 19/54 (35%)
Query: 1 MAQPVTTPCAHNFCKSCLEEAFSGKSFVRERSRGGRALRSQKTIMKCPSCTTDI 54
+ VT CAH+FC C+ E K ++CP C DI
Sbjct: 63 FIEAVTLNCAHSFCSYCINEWMKRK-------------------IECPICRKDI 97
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 16/54 (29%)
Query: 1 MAQPVTTPCAHNFCKSCLEEAFSGKSFVRERSRGGRALRSQKTIMKCPSCTTDI 54
+ +PVT C HNFC C+ + + E S G KCP C T +
Sbjct: 30 LQKPVTIDCGHNFCLKCITQ-------IGETSCG---------FFKCPLCKTSV 67
>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 = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 20/54 (37%), Gaps = 19/54 (35%)
Query: 1 MAQPVTTPCAHNFCKSCLEEAFSGKSFVRERSRGGRALRSQKTIMKCPSCTTDI 54
+ VT CAH+FC C+ E K ++CP C DI
Sbjct: 74 FIEAVTLNCAHSFCSYCINEWMKRK-------------------IECPICRKDI 108
>pdb|4FGM|A Chain A, Crystal Structure Of The Aminopeptidase N Family Protein
Q5qty1 From Idiomarina Loihiensis. Northeast Structural
Genomics Consortium Target Ilr60
Length = 597
Score = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 53 DISDFLKDPQVNRELMEVIESLK 75
DISDFLKD N+E + ++E L+
Sbjct: 435 DISDFLKDALYNKESLSLVELLQ 457
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 29.3 bits (64), Expect = 1.6, Method: Composition-based stats.
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 1 MAQPVTTPCAHNFCKSCL 18
+ +PV C HNFCK+C+
Sbjct: 25 LKEPVIIECGHNFCKACI 42
>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf
Receptor-Associated Factor 6 Protein
Length = 86
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 1 MAQPVTTPCAHNFCKSCL 18
+ + V TPC H FCK+C+
Sbjct: 35 LREAVQTPCGHRFCKACI 52
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 29.3 bits (64), Expect = 1.9, Method: Composition-based stats.
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 1 MAQPVTTPCAHNFCKSCL 18
+ + V TPC H FCK+C+
Sbjct: 16 LREAVQTPCGHRFCKACI 33
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 28.9 bits (63), Expect = 2.0, Method: Composition-based stats.
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 1 MAQPVTTPCAHNFCKSCLEE 20
+ +PVT C HNFC C+ +
Sbjct: 30 LQKPVTIDCGHNFCLKCITQ 49
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 21/76 (27%)
Query: 1 MAQPVTTPCAHNFCKSCLEEAFSGKSFVRERSRGGRALRSQKTIMKCPSCTTDIS----- 55
+ +PV+T C H FCK C+ + L +K +CP C DI+
Sbjct: 31 IKEPVSTKCDHIFCKFCM----------------LKLLNQKKGPSQCPLCKNDITKRSLQ 74
Query: 56 DFLKDPQVNRELMEVI 71
+ + Q+ EL+++I
Sbjct: 75 ESTRFSQLVEELLKII 90
>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 = 28.5 bits (62), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 1 MAQPVTTPCAHNFCKSCL 18
+ + V TPC H FCK+C+
Sbjct: 28 LREAVQTPCGHRFCKACI 45
>pdb|2CSY|A Chain A, Solution Structure Of The Ring Domain Of The Zinc Finger
Protein 183-Like 1
Length = 81
Score = 28.1 bits (61), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 4 PVTTPCAHNFCKSCLEEAFSG--KSFVRERSRGG 35
PV T C H FC+SC E F + ++ ++ GG
Sbjct: 28 PVVTKCRHYFCESCALEHFRATPRCYICDQPTGG 61
>pdb|3HCS|A Chain A, Crystal Structure Of The N-Terminal Domain Of Traf6
pdb|3HCS|B Chain B, Crystal Structure Of The N-Terminal Domain Of Traf6
Length = 170
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 1 MAQPVTTPCAHNFCKSCL 18
+ + V TPC H FCK+C+
Sbjct: 28 LREAVQTPCGHRFCKACI 45
>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 = 27.3 bits (59), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 8/18 (44%), Positives = 14/18 (77%)
Query: 1 MAQPVTTPCAHNFCKSCL 18
+ QP++ C H+FC++CL
Sbjct: 29 LTQPLSLDCGHSFCQACL 46
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
0.307 0.126 0.353
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,557,574
Number of Sequences: 62578
Number of extensions: 191853
Number of successful extensions: 478
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 454
Number of HSP's gapped (non-prelim): 26
length of query: 209
length of database: 14,973,337
effective HSP length: 94
effective length of query: 115
effective length of database: 9,091,005
effective search space: 1045465575
effective search space used: 1045465575
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 49 (23.5 bits)