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= psy6056
(153 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 47 RCPICLLVLNNRSYTDTCLHEFCFLCIKQWSQISSESSPALCKMSKQRLL 96
RCPICL +N S CLH FC++CI +W I + LCK+ + ++
Sbjct: 7 RCPICLEDPSNYSMALPCLHAFCYVCITRW--IRQNPTCPLCKVPVESVV 54
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 25/49 (51%), Gaps = 6/49 (12%)
Query: 31 PSEDDSDG-DRPTSPTS-----RCPICLLVLNNRSYTDTCLHEFCFLCI 73
P E +DG + SP S CPICL +L N T CLH FC CI
Sbjct: 34 PQEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCI 82
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 25/50 (50%), Gaps = 6/50 (12%)
Query: 30 NPSEDDSDG-DRPTSPTS-----RCPICLLVLNNRSYTDTCLHEFCFLCI 73
P E +DG + SP S CPICL +L N T CLH FC CI
Sbjct: 32 TPQEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCI 81
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 34.7 bits (78), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 25/50 (50%), Gaps = 6/50 (12%)
Query: 30 NPSEDDSDG-DRPTSPTS-----RCPICLLVLNNRSYTDTCLHEFCFLCI 73
P E +DG + SP S CPICL +L N T CLH FC CI
Sbjct: 13 TPQEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCI 62
>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 = 31.2 bits (69), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 22/52 (42%), Gaps = 1/52 (1%)
Query: 35 DSDGDRPTSPTSRCPICLLVLNNRSYTDTCLHEFCFLCIKQWSQISSESSPA 86
D + D P CPICL+ L T C H FC CI + + + P
Sbjct: 8 DVEFDPPLESKYECPICLMALREAVQT-PCGHRFCKACIIKSIRDAGHKCPV 58
>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf
Receptor-Associated Factor 6 Protein
Length = 86
Score = 30.8 bits (68), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 35 DSDGDRPTSPTSRCPICLLVLNNRSYTDTCLHEFCFLCI 73
D + D P CPICL+ L T C H FC CI
Sbjct: 15 DVEFDPPLESKYECPICLMALREAVQT-PCGHRFCKACI 52
>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 = 30.4 bits (67), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 22/52 (42%), Gaps = 1/52 (1%)
Query: 35 DSDGDRPTSPTSRCPICLLVLNNRSYTDTCLHEFCFLCIKQWSQISSESSPA 86
D + D P CPICL+ L T C H FC CI + + + P
Sbjct: 8 DVEFDPPLESKYECPICLMALREAVQT-PCGHRFCKACIIKSIRDAGHKCPV 58
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 48 CPICLLVLNNRSYTDTCLHEFCFLCIKQWSQISSESSPA-LCKMSKQR 94
CPICL +L + T C H FC CI Q + S LCK S ++
Sbjct: 23 CPICLDILQ-KPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRK 69
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 19/46 (41%), Gaps = 1/46 (2%)
Query: 41 PTSPTSRCPICLLVLNNRSYTDTCLHEFCFLCIKQWSQISSESSPA 86
P CPICL+ L T C H FC CI + + + P
Sbjct: 2 PLGSKYECPICLMALREAVQT-PCGHRFCKACIIKSIRDAGHKCPV 46
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 27.7 bits (60), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 48 CPICLLVLNNRSYTDTCLHEFCFLCIKQWSQISS 81
CPICL +L + T C H FC CI Q + S
Sbjct: 23 CPICLDILQ-KPVTIDCGHNFCLKCITQIGETSC 55
>pdb|2F9I|B Chain B, Crystal Structure Of The Carboxyltransferase Subunit Of
Acc From Staphylococcus Aureus
pdb|2F9I|D Chain D, Crystal Structure Of The Carboxyltransferase Subunit Of
Acc From Staphylococcus Aureus
Length = 285
Score = 26.9 bits (58), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 25/66 (37%), Gaps = 6/66 (9%)
Query: 25 KQKNDNPSEDDSDGDRPTSPTSRCPICLLVLNNRSYTD------TCLHEFCFLCIKQWSQ 78
K+K +D + D P ++CP C ++ + + C H K+
Sbjct: 10 KKKKYLTVQDSKNNDVPAGIMTKCPKCKKIMYTKELAENLNVCFNCDHHIALTAYKRIEA 69
Query: 79 ISSESS 84
IS E S
Sbjct: 70 ISDEGS 75
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 26.2 bits (56), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 43 SPTSRCPICLLVLNNRSYTDTCLHEFCFLCIKQWSQISSESSPALCKMSKQRLLLFASAT 102
+P C +C + + CLH FC CI ++ + S ++ K R LL +
Sbjct: 13 NPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSD 72
Query: 103 ECLQYINVYDIM 114
+ LQ I VY ++
Sbjct: 73 KTLQDI-VYKLV 83
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 26.2 bits (56), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 43 SPTSRCPICLLVLNNRSYTDTCLHEFCFLCIKQWSQISSESSPALCKMSKQRLLLFASAT 102
+P C +C + + CLH FC CI ++ + S ++ K R LL +
Sbjct: 13 NPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSD 72
Query: 103 ECLQYINVYDIM 114
+ LQ I VY ++
Sbjct: 73 KTLQDI-VYKLV 83
>pdb|2D8T|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 146
Length = 71
Score = 25.8 bits (55), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 3/58 (5%)
Query: 32 SEDDSDGDRPTSPTSRCPICLLVLNNRSYTDTCLHEFCFLCIKQWSQISSESSPALCK 89
S S P+ C ICL + + C H FC+LC+K S + ALC+
Sbjct: 2 SSGSSGNTAPSLTVPECAICLQTCVH-PVSLPCKHVFCYLCVKGASWLGKRC--ALCR 56
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
0.322 0.134 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,154,696
Number of Sequences: 62578
Number of extensions: 144250
Number of successful extensions: 274
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 263
Number of HSP's gapped (non-prelim): 21
length of query: 153
length of database: 14,973,337
effective HSP length: 90
effective length of query: 63
effective length of database: 9,341,317
effective search space: 588502971
effective search space used: 588502971
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: 47 (22.7 bits)