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= psy8987
(173 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 87.4 bits (215), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 38/87 (43%), Positives = 60/87 (68%), Gaps = 19/87 (21%)
Query: 18 RSDKLLVRDVNPHLLCVLCRGYFVEATSIVECLHSCDFVSYFSHFCKLLFGFVSVCKSCI 77
R+ ++ + ++NPHL+CVLC GYF++AT+I+ECLH S CK+CI
Sbjct: 3 RTTRIKITELNPHLMCVLCGGYFIDATTIIECLH-------------------SFCKTCI 43
Query: 78 VKYIKTSRYCPICDVQLNRQDPFLSLK 104
V+Y++TS+YCPICDVQ+++ P L+++
Sbjct: 44 VRYLETSKYCPICDVQVHKTRPLLNIR 70
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 87.4 bits (215), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 38/87 (43%), Positives = 60/87 (68%), Gaps = 19/87 (21%)
Query: 18 RSDKLLVRDVNPHLLCVLCRGYFVEATSIVECLHSCDFVSYFSHFCKLLFGFVSVCKSCI 77
R+ ++ + ++NPHL+CVLC GYF++AT+I+ECLH S CK+CI
Sbjct: 3 RTTRIKITELNPHLMCVLCGGYFIDATTIIECLH-------------------SFCKTCI 43
Query: 78 VKYIKTSRYCPICDVQLNRQDPFLSLK 104
V+Y++TS+YCPICDVQ+++ P L+++
Sbjct: 44 VRYLETSKYCPICDVQVHKTRPLLNIR 70
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 84.7 bits (208), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 37/84 (44%), Positives = 58/84 (69%), Gaps = 19/84 (22%)
Query: 21 KLLVRDVNPHLLCVLCRGYFVEATSIVECLHSCDFVSYFSHFCKLLFGFVSVCKSCIVKY 80
++ + ++NPHL+CVLC GYF++AT+I+ECLH S CK+CIV+Y
Sbjct: 2 RIKITELNPHLMCVLCGGYFIDATTIIECLH-------------------SFCKTCIVRY 42
Query: 81 IKTSRYCPICDVQLNRQDPFLSLK 104
++TS+YCPICDVQ+++ P L+++
Sbjct: 43 LETSKYCPICDVQVHKTRPLLNIR 66
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 19/77 (24%)
Query: 24 VRDVNPHLLCVLCRGYFVEATSIVECLHSCDFVSYFSHFCKLLFGFVSVCKSCIVKYIKT 83
+ ++ P++LC +C+GY ++AT+I ECLH + CKSCIV++
Sbjct: 9 LSELTPYILCSICKGYLIDATTITECLH-------------------TFCKSCIVRHFYY 49
Query: 84 SRYCPICDVQLNRQDPF 100
S CP C++ +++ P
Sbjct: 50 SNRCPKCNIVVHQTQPL 66
>pdb|3TXM|A Chain A, Crystal Structure Of Rpn6 From Drosophila Melanogaster,
Gd(3+) Complex
pdb|3TXN|A Chain A, Crystal Structure Of Rpn6 From Drosophila Melanogaster,
Native Data
Length = 394
Score = 32.0 bits (71), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 25/96 (26%), Positives = 42/96 (43%), Gaps = 4/96 (4%)
Query: 4 NSITYNAIEMRPTSRSDKLLVRDVNPHLLCV-LCRGYFVEATSIVECLHSCDFVSYFSHF 62
S TY+A+ P +R+ R + C +G + I+ DF + FS+F
Sbjct: 145 ESKTYHALSNLPKARAALTSARTTANAIYCPPKVQGALDLQSGILHAADERDFKTAFSYF 204
Query: 63 CKLLFGFVSVCKSCIVKYIKTSRYCPICDVQLNRQD 98
+ GF SV VK + + +Y +C + L + D
Sbjct: 205 YEAFEGFDSVDS---VKALTSLKYMLLCKIMLGQSD 237
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 31.6 bits (70), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 20/61 (32%)
Query: 30 HLLCVLCRGYFVEATSIVECLHSCDFVSYFSHFCKLLFGFVSVCKSCIVKYIKTSRYCPI 89
L C++C YF+EA ++ C HS F SY CI +++K CPI
Sbjct: 53 ELQCIICSEYFIEAVTL-NCAHS--FCSY-----------------CINEWMKRKIECPI 92
Query: 90 C 90
C
Sbjct: 93 C 93
>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 = 31.2 bits (69), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 20/61 (32%)
Query: 30 HLLCVLCRGYFVEATSIVECLHSCDFVSYFSHFCKLLFGFVSVCKSCIVKYIKTSRYCPI 89
L C++C YF+EA ++ C HS F SY CI +++K CPI
Sbjct: 64 ELQCIICSEYFIEAVTL-NCAHS--FCSY-----------------CINEWMKRKIECPI 103
Query: 90 C 90
C
Sbjct: 104 C 104
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 31.2 bits (69), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 20/61 (32%)
Query: 30 HLLCVLCRGYFVEATSIVECLHSCDFVSYFSHFCKLLFGFVSVCKSCIVKYIKTSRYCPI 89
L C++C YF+EA ++ C HS F SY CI +++K CPI
Sbjct: 53 ELQCIICSEYFIEAVTL-NCAHS--FCSY-----------------CINEWMKRKIECPI 92
Query: 90 C 90
C
Sbjct: 93 C 93
>pdb|1OHV|A Chain A, 4-aminobutyrate-aminotransferase From Pig
pdb|1OHV|B Chain B, 4-aminobutyrate-aminotransferase From Pig
pdb|1OHV|C Chain C, 4-aminobutyrate-aminotransferase From Pig
pdb|1OHV|D Chain D, 4-aminobutyrate-aminotransferase From Pig
pdb|1OHW|A Chain A, 4-Aminobutyrate-Aminotransferase Inactivated By
Gamma-Vinyl Gaba
pdb|1OHW|B Chain B, 4-Aminobutyrate-Aminotransferase Inactivated By
Gamma-Vinyl Gaba
pdb|1OHW|C Chain C, 4-Aminobutyrate-Aminotransferase Inactivated By
Gamma-Vinyl Gaba
pdb|1OHW|D Chain D, 4-Aminobutyrate-Aminotransferase Inactivated By
Gamma-Vinyl Gaba
pdb|1OHY|A Chain A, 4-Aminobutyrate-Aminotransferase Inactivated By
Gamma-Ethynyl Gaba
pdb|1OHY|B Chain B, 4-Aminobutyrate-Aminotransferase Inactivated By
Gamma-Ethynyl Gaba
pdb|1OHY|C Chain C, 4-Aminobutyrate-Aminotransferase Inactivated By
Gamma-Ethynyl Gaba
pdb|1OHY|D Chain D, 4-Aminobutyrate-Aminotransferase Inactivated By
Gamma-Ethynyl Gaba
Length = 472
Score = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 22/45 (48%)
Query: 99 PFLSLKYSYIAFASDDYDNDTRIYEQVLQIVLRIYLRKNVLRGTI 143
PF LKY F ++ + R E+V ++++ +K + G I
Sbjct: 219 PFPRLKYPLEEFVKENQQEEARCLEEVEDLIVKYRKKKKTVAGII 263
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 27.7 bits (60), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 22/98 (22%), Positives = 36/98 (36%), Gaps = 25/98 (25%)
Query: 25 RDVNPHLLCVLCRGYFVEATSIVECLHSCDFVSYFSHFCKLLFGFVSVCKSCIVKYIKTS 84
R ++ L+C +C + ECLH C CI+ +++
Sbjct: 49 RSLHSELMCPICLDMLKNTMTTKECLH-------------------RFCADCIITALRSG 89
Query: 85 -RYCPICDVQLN-----RQDPFLSLKYSYIAFASDDYD 116
+ CP C +L R DP S I + D+Y+
Sbjct: 90 NKECPTCRKKLVSKRSLRPDPNFDALISKIYPSRDEYE 127
>pdb|1XG8|A Chain A, Crystal Structure Of Protein Of Unknown Function Sa0789
From Staphylococcus Aureus
Length = 111
Score = 27.3 bits (59), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 4/73 (5%)
Query: 58 YFSHFCKLLFGFVSVCKSCIVKYIKTSRYCPICDVQLNRQDPFLSLKYSYIAFASDD--- 114
YF +++G +C SC+ Y + + L R+ P +S KY+YI D+
Sbjct: 4 YFQSNAVVVYGADVICASCVNAPTSKDIYDWLQPL-LKRKYPNISFKYTYIDITKDNDNL 62
Query: 115 YDNDTRIYEQVLQ 127
D+D + E++ Q
Sbjct: 63 TDHDLQFIERIEQ 75
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 26.6 bits (57), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 71 SVCKSCIVKYIKTSRYCPICDVQL 94
S C+ CI K+ R CPIC +Q+
Sbjct: 35 SFCQKCIDKWSDRHRNCPICRLQM 58
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
0.332 0.143 0.467
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,859,085
Number of Sequences: 62578
Number of extensions: 169104
Number of successful extensions: 353
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 336
Number of HSP's gapped (non-prelim): 24
length of query: 173
length of database: 14,973,337
effective HSP length: 92
effective length of query: 81
effective length of database: 9,216,161
effective search space: 746509041
effective search space used: 746509041
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 48 (23.1 bits)