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= 025608
(250 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CT7|A Chain A, Solution Structure Of The Ibr Domain Of The Ring Finger
Protein 31 Protein
Length = 86
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 150 ESECPNCHRLFCAQCKVAW---HAGIECADFQKLHK 182
E+ CP CH+ FC +CK W H G C DFQ +
Sbjct: 43 EATCPQCHQTFCVRCKRQWEEQHRGRSCEDFQNWKR 78
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 35/123 (28%), Positives = 57/123 (46%), Gaps = 21/123 (17%)
Query: 11 KSLEFNFQELVRF---SMTEN-EMASSTRSETSRSFVCEICVETKLRNESFSIKGCSHMY 66
K+ E + EL R ++T+ E+ S RS S +C IC++ L+N + + K C H +
Sbjct: 21 KTWELSLYELQRTPQEAITDGLEIVVSPRSLHS-ELMCPICLDM-LKN-TMTTKECLHRF 77
Query: 67 CVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGA 126
C DC + + S +E CP C L + R + P+ FD AL + P
Sbjct: 78 CADCIITALRSGNKE------CPT--CRKKLVSK--RSLRPDPNFD----ALISKIYPSR 123
Query: 127 QKF 129
++
Sbjct: 124 DEY 126
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 32/106 (30%), Positives = 51/106 (48%), Gaps = 17/106 (16%)
Query: 11 KSLEFNFQELVRF---SMTEN-EMASSTRSETSRSFVCEICVETKLRNESFSIKGCSHMY 66
K+ E + EL R ++T+ E+ S RS S +C IC++ L+N + + K C H +
Sbjct: 1 KTWELSLYELQRTPQEAITDGLEIVVSPRSLHS-ELMCPICLDM-LKN-TMTTKECLHRF 57
Query: 67 CVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFD 112
C DC + + S +E CP C L + R + P+ FD
Sbjct: 58 CADCIITALRSGNKE------CPT--CRKKLVSK--RSLRPDPNFD 93
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 7/75 (9%)
Query: 11 KSLEFNFQELVRF---SMTEN-EMASSTRSETSRSFVCEICVETKLRNESFSIKGCSHMY 66
K+ E + EL R ++T+ E+ S RS S +C IC++ L+N + + K C H +
Sbjct: 20 KTWELSLYELQRTPQEAITDGLEIVVSPRSLHSE-LMCPICLDM-LKN-TMTTKECLHRF 76
Query: 67 CVDCTVKYVDSKLQE 81
C DC + + S +E
Sbjct: 77 CADCIITALRSGNKE 91
>pdb|1WD2|A Chain A, Solution Structure Of The C-Terminal Ring From A Ring-Ibr-
Ring (Triad) Motif
Length = 60
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 195 LAQNQKWNRCPNCKFYVEKKDGCSYIRCR---CGHAFCYHCGVQLSTVSHGYYCPSCNK 250
+A N K CP C +EK GC+++ CR C FC+ C +Y +CN+
Sbjct: 2 IAANTK--ECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGSAWY--NCNR 56
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 6/46 (13%)
Query: 204 CPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYY-CPSC 248
CP C ++K + CGH FC C Q+ S G++ CP C
Sbjct: 23 CPICLDILQKP-----VTIDCGHNFCLKCITQIGETSCGFFKCPLC 63
>pdb|1ZT2|B Chain B, Heterodimeric Structure Of The Core Primase.
pdb|1ZT2|D Chain D, Heterodimeric Structure Of The Core Primase
Length = 212
Score = 28.1 bits (61), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 29/66 (43%), Gaps = 7/66 (10%)
Query: 166 VAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGCSYIRCRCG 225
+ +A E F+ L E E + + KL + K NRC KFY+EKK R
Sbjct: 83 IRRYAYAEAKQFRSLLHTENEENLLEISKLL-DLKINRCDPIKFYLEKK------RRIIQ 135
Query: 226 HAFCYH 231
FC H
Sbjct: 136 KEFCVH 141
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 28.1 bits (61), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 6/51 (11%)
Query: 199 QKWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYY-CPSC 248
Q+ CP C ++K + CGH FC C Q+ S G++ CP C
Sbjct: 18 QEEVICPICLDILQKP-----VTIDCGHNFCLKCITQIGETSCGFFKCPLC 63
>pdb|1WIM|A Chain A, Solution Structure Of The Ring Finger Domain Of The
Human Ubcm4-Interacting Protein 4
Length = 94
Score = 27.7 bits (60), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 38 TSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENV-TSIGCPVTDC 93
+S S C++C+ + +I C ++C C +YV+ ++E + T+I CP C
Sbjct: 2 SSGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC 58
>pdb|2JMO|A Chain A, Ibr Domain Of Human Parkin
Length = 80
Score = 27.3 bits (59), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 3/69 (4%)
Query: 106 LPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPN---CHRLFCA 162
+ EE ++++ + E + CP C A L+ + + E N C FC
Sbjct: 3 MGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEPDQRKVTCEGGNGLGCGFAFCR 62
Query: 163 QCKVAWHAG 171
+CK A+H G
Sbjct: 63 ECKEAYHEG 71
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
0.324 0.137 0.456
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,394,250
Number of Sequences: 62578
Number of extensions: 293967
Number of successful extensions: 1067
Number of sequences better than 100.0: 41
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 39
Number of HSP's that attempted gapping in prelim test: 1056
Number of HSP's gapped (non-prelim): 53
length of query: 250
length of database: 14,973,337
effective HSP length: 96
effective length of query: 154
effective length of database: 8,965,849
effective search space: 1380740746
effective search space used: 1380740746
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 bits)