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= psy4512
(101 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4FBK|A Chain A, Crystal Structure Of A Covalently Fused Nbs1-Mre11 Complex
With One Manganese Ion Per Active Site
pdb|4FBK|B Chain B, Crystal Structure Of A Covalently Fused Nbs1-Mre11 Complex
With One Manganese Ion Per Active Site
pdb|4FBQ|A Chain A, Crystal Structure Of A Covalently Fused Nbs1-Mre11 Complex
With Two Manganese Ions Per Active Site
pdb|4FBQ|B Chain B, Crystal Structure Of A Covalently Fused Nbs1-Mre11 Complex
With Two Manganese Ions Per Active Site
Length = 472
Score = 27.7 bits (60), Expect = 1.7, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 6/65 (9%)
Query: 13 DGDVILLATDGVFDNVPDSLLLAELVRA-----QGSKDPMQLQLVANTIALMARTLAFDE 67
D D+ILL D DN P L + +R+ G K P +L+L+++T T +
Sbjct: 115 DVDMILLGGDIFHDNKPSRKALYQALRSLRLNCLGDK-PCELELLSDTSLTTGDTAVCNI 173
Query: 68 TYMSP 72
Y+ P
Sbjct: 174 NYLDP 178
>pdb|4FBW|A Chain A, Crystal Structure Of An Unfused Mre11-Nbs1 Complex With
Two Manganese Ions Per Active Site
pdb|4FBW|B Chain B, Crystal Structure Of An Unfused Mre11-Nbs1 Complex With
Two Manganese Ions Per Active Site
Length = 417
Score = 27.3 bits (59), Expect = 2.0, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 6/65 (9%)
Query: 13 DGDVILLATDGVFDNVPDSLLLAELVRA-----QGSKDPMQLQLVANTIALMARTLAFDE 67
D D+ILL D DN P L + +R+ G K P +L+L+++T T +
Sbjct: 52 DVDMILLGGDIFHDNKPSRKALYQALRSLRLNCLGDK-PCELELLSDTSLTTGDTAVCNI 110
Query: 68 TYMSP 72
Y+ P
Sbjct: 111 NYLDP 115
>pdb|4FCX|B Chain B, S.Pombe Mre11 Apoenzym
pdb|4FCX|A Chain A, S.Pombe Mre11 Apoenzym
Length = 404
Score = 27.3 bits (59), Expect = 2.0, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 6/65 (9%)
Query: 13 DGDVILLATDGVFDNVPDSLLLAELVRA-----QGSKDPMQLQLVANTIALMARTLAFDE 67
D D+ILL D DN P L + +R+ G K P +L+L+++T T +
Sbjct: 47 DVDMILLGGDIFHDNKPSRKALYQALRSLRLNCLGDK-PCELELLSDTSLTTGDTAVCNI 105
Query: 68 TYMSP 72
Y+ P
Sbjct: 106 NYLDP 110
>pdb|3CNL|A Chain A, Crystal Structure Of Gnp-Bound Ylqf From T. Maritima
pdb|3CNN|A Chain A, Gtp-Bound Structure Of Tm Ylqf
pdb|3CNO|A Chain A, Gdp-Bound Structue Of Tm Ylqf
Length = 262
Score = 26.9 bits (58), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 43/86 (50%), Gaps = 6/86 (6%)
Query: 9 FQVEDGDVILLATDGV-FDNVPDSLLLAELVRAQGSKDPMQLQ---LVANTIALMARTLA 64
F +E+G V +L T G+ + N+ L A+L+ GS +++ + + AR++
Sbjct: 140 FSLENG-VKILDTPGILYKNIFSEDLAAKLLLV-GSLPVERIEDQRIFERAFEIFARSIG 197
Query: 65 FDETYMSPFAIQARANGISTQGGKPD 90
+ ++ F AR G+ +GG PD
Sbjct: 198 IESSFSEFFEDFARKRGLLKKGGVPD 223
>pdb|1LVA|A Chain A, Crystal Structure Of A C-Terminal Fragment Of Moorella
Thermoacetica Elongation Factor Selb
Length = 258
Score = 25.8 bits (55), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 48 QLQLVANTIALMARTLAFDET 68
+LQL ANT+AL T +F ET
Sbjct: 118 RLQLAANTVALAGFTPSFSET 138
>pdb|2PLY|A Chain A, Structure Of The Mrna Binding Fragment Of Elongation
Factor Selb In Complex With Secis Rna.
pdb|2PLY|B Chain B, Structure Of The Mrna Binding Fragment Of Elongation
Factor Selb In Complex With Secis Rna
Length = 258
Score = 25.8 bits (55), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 48 QLQLVANTIALMARTLAFDET 68
+LQL ANT+AL T +F ET
Sbjct: 118 RLQLAANTVALAGFTPSFSET 138
>pdb|2UWM|A Chain A, C-Terminal Domain(Wh2-Wh4) Of Elongation Factor Selb In
Complex With Secis Rna
pdb|2UWM|B Chain B, C-Terminal Domain(Wh2-Wh4) Of Elongation Factor Selb In
Complex With Secis Rna
Length = 258
Score = 25.8 bits (55), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 48 QLQLVANTIALMARTLAFDET 68
+LQL ANT+AL T +F ET
Sbjct: 118 RLQLAANTVALAGFTPSFSET 138
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
0.319 0.135 0.371
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,621,210
Number of Sequences: 62578
Number of extensions: 74443
Number of successful extensions: 179
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 173
Number of HSP's gapped (non-prelim): 12
length of query: 101
length of database: 14,973,337
effective HSP length: 67
effective length of query: 34
effective length of database: 10,780,611
effective search space: 366540774
effective search space used: 366540774
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)