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= 016355
(391 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3AXS|A Chain A, Complex Structure Of Trna Methyltransferase Trm1 From
Aquifex Aeolicus With Sinefungin
pdb|3AXT|A Chain A, Complex Structure Of Trna Methyltransferase Trm1 From
Aquifex Aeolicus With S-Adenosyl-L-Methionine
Length = 392
Score = 31.6 bits (70), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 22/97 (22%), Positives = 40/97 (41%), Gaps = 6/97 (6%)
Query: 270 EFCYSCGAEYRDGQQTCQCAFWDEDNSEELTQSVHESEQSAWETFNSLPMIMDAYSDQER 329
E C CG+++ G WDE+ + L + + E+ ET L +I +E
Sbjct: 264 EKCPHCGSKFHIGGPLWIGKLWDEEFTNFLYEEAQKREEIEKETKRILKLI------KEE 317
Query: 330 SQLALIQRFLAGGFSLSDHHPYQSPPRCTDSYGDAMK 366
SQL + ++ + P Q P R + + ++
Sbjct: 318 SQLQTVGFYVLSKLAEKVKLPAQPPIRIAVKFFNGVR 354
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 78 CSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPI 119
C IC E P ++ KC H FC CM ++ K SQ P+
Sbjct: 24 CPICLELIKEP--VSTKCDHIFCKFCMLKLLNQKKGPSQCPL 63
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 78 CSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQ 113
C IC E + +T+ C+H FCS+C+ ++ K++
Sbjct: 56 CIICSE--YFIEAVTLNCAHSFCSYCINEWMKRKIE 89
>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 = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 78 CSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQ 113
C IC E + +T+ C+H FCS+C+ ++ K++
Sbjct: 67 CIICSE--YFIEAVTLNCAHSFCSYCINEWMKRKIE 100
>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 = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 78 CSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQ 113
C IC E M+I +CSH +CS C+R ++ K Q
Sbjct: 25 CGICFEYFNIAMIIP-QCSHNYCSLCIRKFLSYKTQ 59
>pdb|1WIM|A Chain A, Solution Structure Of The Ring Finger Domain Of The Human
Ubcm4-Interacting Protein 4
Length = 94
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 71 GDKSPENCSICCEDKPYPMMITM-KCSHKFCSHCMRTYIDGKVQSS-QVPIRCPQLRC 126
G C +C + P M T+ +C FC+ C++ Y++ ++ + I CP C
Sbjct: 1 GSSGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC 58
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 78 CSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQ 113
C IC E + +T+ C+H FCS+C+ ++ K++
Sbjct: 56 CIICSE--YFIEAVTLNCAHSFCSYCINEWMKRKIE 89
>pdb|3HTK|C Chain C, Crystal Structure Of Mms21 And Smc5 Complex
Length = 267
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 8/63 (12%)
Query: 70 QGDKSPENCSICCEDKPYPM-MITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKY 128
+G K C I C KPY +I+ KC+H F ++ Y+ G CPQ C
Sbjct: 176 EGGKIELTCPITC--KPYEAPLISRKCNHVFDRDGIQNYLQGYTTRD-----CPQAACSQ 228
Query: 129 FIS 131
+S
Sbjct: 229 VVS 231
>pdb|1WD2|A Chain A, Solution Structure Of The C-Terminal Ring From A Ring-Ibr-
Ring (Triad) Motif
Length = 60
Score = 29.3 bits (64), Expect = 3.6, Method: Composition-based stats.
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 245 RRCQQCRRMIELTHGCYHMTCW---CGHEFCYSC 275
+ C +C IE GC HM C C EFC+ C
Sbjct: 7 KECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVC 40
>pdb|4AIE|A Chain A, Structure Of Glucan-1,6-Alpha-Glucosidase From
Lactobacillus Acidophilus Ncfm
Length = 549
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 20/27 (74%)
Query: 312 ETFNSLPMIMDAYSDQERSQLALIQRF 338
ET+N+ P I + YSD +R +L+++ +F
Sbjct: 242 ETWNATPKIAEEYSDPDRHELSMVFQF 268
>pdb|2CT7|A Chain A, Solution Structure Of The Ibr Domain Of The Ring Finger
Protein 31 Protein
Length = 86
Score = 29.3 bits (64), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 16/30 (53%), Gaps = 3/30 (10%)
Query: 196 CPVCERFICVECGVPW---HSSLSCEEYQN 222
CP C + CV C W H SCE++QN
Sbjct: 46 CPQCHQTFCVRCKRQWEEQHRGRSCEDFQN 75
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
0.323 0.135 0.443
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,432,373
Number of Sequences: 62578
Number of extensions: 448912
Number of successful extensions: 1239
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1227
Number of HSP's gapped (non-prelim): 26
length of query: 391
length of database: 14,973,337
effective HSP length: 101
effective length of query: 290
effective length of database: 8,652,959
effective search space: 2509358110
effective search space used: 2509358110
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 52 (24.6 bits)