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= 045506
(173 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1GBG|A Chain A, Bacillus Licheniformis Beta-Glucanase
Length = 214
Score = 30.8 bits (68), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 30/107 (28%), Positives = 44/107 (41%), Gaps = 14/107 (13%)
Query: 53 GEFSPAQKSIIADFLLSLNPQKNQ--LGSHFTTPQPSVSKRWHTIQTYMKKAGKGQTRVF 110
GE Q + +++ P KN + S FT P+ W I ++ GK T+V
Sbjct: 62 GENRSVQTYGYGLYEVNMKPAKNVGIVSSFFTYTGPTDGTPWDEID--IEFLGKDTTKV- 118
Query: 111 IASQFSDKNCSLGKILKKAQGFCMSNCGFHGSNPQHNSAFIWVGNSV 157
QF+ +G K + N GF +N H AF W NS+
Sbjct: 119 ---QFNYYTNGVGNHEK------IVNLGFDAANSYHTYAFDWQPNSI 156
>pdb|4GD1|Y Chain Y, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
Length = 183
Score = 30.4 bits (67), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 55 FSPA-QKSIIADFLLSLNPQKNQLGSHFTTPQPSVSKRWHTIQTYMKKAGKGQTRVFIAS 113
SPA +K+I+A L LNP N GS P P +++ T + + Q RV + +
Sbjct: 74 MSPAVEKAIMASDL-GLNP--NSAGSDIRVPLPPLTEERRKDLTKIVRGEAEQARVAVRN 130
Query: 114 QFSDKNCSLGKILKKAQ 130
D N + +LK +
Sbjct: 131 VRRDANDKVKALLKDKE 147
>pdb|3VST|A Chain A, The Complex Structure Of Xylc With Tris
pdb|3VST|B Chain B, The Complex Structure Of Xylc With Tris
pdb|3VST|C Chain C, The Complex Structure Of Xylc With Tris
pdb|3VST|D Chain D, The Complex Structure Of Xylc With Tris
pdb|3VSU|A Chain A, The Complex Structure Of Xylc With Xylobiose
pdb|3VSU|B Chain B, The Complex Structure Of Xylc With Xylobiose
pdb|3VSU|C Chain C, The Complex Structure Of Xylc With Xylobiose
pdb|3VSU|D Chain D, The Complex Structure Of Xylc With Xylobiose
pdb|3VSV|A Chain A, The Complex Structure Of Xylc With Xylose
pdb|3VSV|B Chain B, The Complex Structure Of Xylc With Xylose
pdb|3VSV|C Chain C, The Complex Structure Of Xylc With Xylose
pdb|3VSV|D Chain D, The Complex Structure Of Xylc With Xylose
Length = 638
Score = 30.4 bits (67), Expect = 0.60, Method: Composition-based stats.
Identities = 15/40 (37%), Positives = 27/40 (67%), Gaps = 7/40 (17%)
Query: 41 LEGN-----LPVSILWYGEFSPAQKSIIADFLLSLNPQKN 75
+EGN LP S ++GEF+P ++ + D+LL++N +K+
Sbjct: 85 VEGNVWRCQLPNS--FFGEFNPYKEEVFGDWLLTVNEKKH 122
>pdb|1EK8|A Chain A, Crystal Structure Of The Ribosome Recycling Factor (Rrf)
From Escherichia Coli
pdb|1ZN0|A Chain A, Coordinates Of Rrf And Ef-G Fitted Into Cryo-Em Map Of The
50s Subunit Bound With Both Ef-G (Gdpnp) And Rrf
pdb|1ZN1|A Chain A, Coordinates Of Rrf Fitted Into Cryo-Em Map Of The 70s
Post- Termination Complex
pdb|2RDO|8 Chain 8, 50s Subunit With Ef-G(Gdpnp) And Rrf Bound
pdb|4GAS|Y Chain Y, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
Length = 185
Score = 30.0 bits (66), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 55 FSPA-QKSIIADFLLSLNPQKNQLGSHFTTPQPSVSKRWHTIQTYMKKAGKGQTRVFIAS 113
SPA +K+I+A L LNP N GS P P +++ T + + Q RV + +
Sbjct: 74 MSPAVEKAIMASDL-GLNP--NSAGSDIRVPLPPLTEERRKDLTKIVRGEAEQARVAVRN 130
Query: 114 QFSDKNCSLGKILKKAQ 130
D N + +LK +
Sbjct: 131 VRRDANDKVKALLKDKE 147
>pdb|1ISE|A Chain A, Crystal Structure Of A Mutant Of Ribosome Recycling Factor
From Escherichia Coli, Arg132gly
Length = 185
Score = 29.6 bits (65), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 55 FSPA-QKSIIADFLLSLNPQKNQLGSHFTTPQPSVSKRWHTIQTYMKKAGKGQTRVFIAS 113
SPA +K+I+A L LNP N GS P P +++ T + + Q RV + +
Sbjct: 74 MSPAVEKAIMASDL-GLNP--NSAGSDIRVPLPPLTEERRKDLTKIVRGEAEQARVAVRN 130
Query: 114 QFSDKNCSLGKILKKAQ 130
D N + +LK +
Sbjct: 131 VGRDANDKVKALLKDKE 147
>pdb|3D6E|A Chain A, Crystal Structure Of The Engineered 1,3-1,4-Beta-Glucanase
Protein From Bacillus Licheniformis
pdb|3D6E|B Chain B, Crystal Structure Of The Engineered 1,3-1,4-Beta-Glucanase
Protein From Bacillus Licheniformis
Length = 201
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 42/94 (44%), Gaps = 14/94 (14%)
Query: 66 FLLSLNPQKNQ--LGSHFTTPQPSVSKRWHTIQTYMKKAGKGQTRVFIASQFSDKNCSLG 123
+ +++ P KN + + +T+ P+ W I ++ GK T+V QF+ +G
Sbjct: 62 YEVNMKPAKNVGIVSAFYTSTGPTDGTPWDEID--IEFLGKDTTKV----QFNYYTNGVG 115
Query: 124 KILKKAQGFCMSNCGFHGSNPQHNSAFIWVGNSV 157
K + N GF +N H AF W NS+
Sbjct: 116 NHEK------IVNLGFDAANSYHTYAFDWQPNSI 143
>pdb|3O5S|A Chain A, Crystal Structure Of The Endo-Beta-1,3-1,4 Glucanase From
Bacillus Subtilis (Strain 168)
Length = 238
Score = 28.5 bits (62), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 29/107 (27%), Positives = 42/107 (39%), Gaps = 14/107 (13%)
Query: 53 GEFSPAQKSIIADFLLSLNPQKNQ--LGSHFTTPQPSVSKRWHTIQTYMKKAGKGQTRVF 110
GE Q + + + P KN + S FT P+ W I ++ GK T+V
Sbjct: 86 GENRSVQTYGYGLYEVRMKPAKNTGIVSSFFTYTGPTDGTPWDEID--IEFLGKDTTKV- 142
Query: 111 IASQFSDKNCSLGKILKKAQGFCMSNCGFHGSNPQHNSAFIWVGNSV 157
QF+ G K + + GF +N H AF W NS+
Sbjct: 143 ---QFNYYTNGAGNHEK------IVDLGFDAANAYHTYAFDWQPNSI 180
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 0.135 0.440
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,294,192
Number of Sequences: 62578
Number of extensions: 203786
Number of successful extensions: 1104
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1098
Number of HSP's gapped (non-prelim): 15
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: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)