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= 033982
(107 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IYD|A Chain A, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
pdb|3IYD|B Chain B, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
pdb|3LU0|A Chain A, Molecular Model Of Escherichia Coli Core Rna Polymerase
pdb|3LU0|B Chain B, Molecular Model Of Escherichia Coli Core Rna Polymerase
pdb|4IGC|A Chain A, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|B Chain B, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|F Chain F, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|G Chain G, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 329
Score = 26.9 bits (58), Expect = 3.2, Method: Composition-based stats.
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 80 LQKVKDILSSQGVKAEMIVEVWDP 103
L ++KD+L+S+G+ M +E W P
Sbjct: 300 LTEIKDVLASRGLSLGMRLENWPP 323
>pdb|1XS9|D Chain D, A Model Of The Ternary Complex Formed Between Mara, The
Alpha-Ctd Of Rna Polymerase And Dna
Length = 84
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 80 LQKVKDILSSQGVKAEMIVEVWDP 103
L ++KD+L+S+G+ M +E W P
Sbjct: 55 LTEIKDVLASRGLSLGMRLENWPP 78
>pdb|1LB2|B Chain B, Structure Of The E. Coli Alpha C-Terminal Domain Of Rna
Polymerase In Complex With Cap And Dna
pdb|1LB2|E Chain E, Structure Of The E. Coli Alpha C-Terminal Domain Of Rna
Polymerase In Complex With Cap And Dna
pdb|3N4M|B Chain B, E. Coli Rna Polymerase Alpha Subunit C-Terminal Domain In
Complex With Cap And Dna
pdb|3N4M|C Chain C, E. Coli Rna Polymerase Alpha Subunit C-Terminal Domain In
Complex With Cap And Dna
pdb|3N97|B Chain B, Rna Polymerase Alpha C-Terminal Domain (E. Coli) And Sigma
Region 4 (T. Aq. Mutant) Bound To (Up,-35 Element) Dna
pdb|3N97|C Chain C, Rna Polymerase Alpha C-Terminal Domain (E. Coli) And Sigma
Region 4 (T. Aq. Mutant) Bound To (Up,-35 Element) Dna
Length = 84
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 80 LQKVKDILSSQGVKAEMIVEVWDP 103
L ++KD+L+S+G+ M +E W P
Sbjct: 55 LTEIKDVLASRGLSLGMRLENWPP 78
>pdb|1COO|A Chain A, The Cooh-Terminal Domain Of Rna Polymerase Alpha Subunit
Length = 98
Score = 26.2 bits (56), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 80 LQKVKDILSSQGVKAEMIVEVWDP 103
L ++KD+L+S+G+ M +E W P
Sbjct: 69 LTEIKDVLASRGLSLGMRLENWPP 92
>pdb|2JZB|A Chain A, Solution Structure Of The Complex Between E.Coli Nusa-Ar2
And Rnap-Actd
Length = 99
Score = 26.2 bits (56), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 80 LQKVKDILSSQGVKAEMIVEVWDP 103
L ++KD+L+S+G+ M +E W P
Sbjct: 70 LTEIKDVLASRGLSLGMRLENWPP 93
>pdb|3ARC|D Chain D, Crystal Structure Of Oxygen-Evolving Photosystem Ii At 1.9
Angstrom Resolution
pdb|3ARC|DD Chain d, Crystal Structure Of Oxygen-Evolving Photosystem Ii At 1.9
Angstrom Resolution
Length = 342
Score = 25.8 bits (55), Expect = 5.9, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 32 IFMAQPPTKSEFVFTAPFGYARLYSSALTTQGFVN 66
+F+ P +S + F FG A ++ L QGF N
Sbjct: 146 VFLIYPLGQSSWFFAPSFGVAAIFRFLLFFQGFHN 180
>pdb|3A0B|D Chain D, Crystal Structure Of Br-Substituted Photosystem Ii Complex
pdb|3A0B|DD Chain d, Crystal Structure Of Br-Substituted Photosystem Ii Complex
pdb|3A0H|D Chain D, Crystal Structure Of I-Substituted Photosystem Ii Complex
pdb|3A0H|DD Chain d, Crystal Structure Of I-Substituted Photosystem Ii Complex
Length = 340
Score = 25.8 bits (55), Expect = 6.1, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 32 IFMAQPPTKSEFVFTAPFGYARLYSSALTTQGFVN 66
+F+ P +S + F FG A ++ L QGF N
Sbjct: 144 VFLIYPLGQSSWFFAPSFGVAAIFRFLLFFQGFHN 178
>pdb|1IZL|D Chain D, Crystal Structure Of Photosystem Ii
pdb|1IZL|N Chain N, Crystal Structure Of Photosystem Ii
pdb|1S5L|D Chain D, Architecture Of The Photosynthetic Oxygen Evolving Center
pdb|1S5L|DD Chain d, Architecture Of The Photosynthetic Oxygen Evolving Center
pdb|1W5C|D Chain D, Photosystem Ii From Thermosynechococcus Elongatus
pdb|1W5C|J Chain J, Photosystem Ii From Thermosynechococcus Elongatus
pdb|2AXT|D Chain D, Crystal Structure Of Photosystem Ii From
Thermosynechococcus Elongatus
pdb|2AXT|DD Chain d, Crystal Structure Of Photosystem Ii From
Thermosynechococcus Elongatus
pdb|3BZ1|D Chain D, Crystal Structure Of Cyanobacterial Photosystem Ii (Part 1
Of 2). This File Contains First Monomer Of Psii Dimer
pdb|3BZ2|D Chain D, Crystal Structure Of Cyanobacterial Photosystem Ii (Part 2
Of 2). This File Contains Second Monomer Of Psii Dimer
pdb|3KZI|D Chain D, Crystal Structure Of Monomeric Form Of Cyanobacterial
Photosystem Ii
pdb|3PRQ|D Chain D, Crystal Structure Of Cyanobacterial Photosystem Ii In
Complex With Terbutryn (Part 1 Of 2). This File Contains
First Monomer Of Psii Dimer
pdb|3PRR|D Chain D, Crystal Structure Of Cyanobacterial Photosystem Ii In
Complex With Terbutryn (Part 2 Of 2). This File Contains
Second Monomer Of Psii Dimer
pdb|4FBY|D Chain D, Fs X-Ray Diffraction Of Photosystem Ii
pdb|4FBY|Q Chain Q, Fs X-Ray Diffraction Of Photosystem Ii
pdb|4IXQ|D Chain D, Rt Fs X-ray Diffraction Of Photosystem Ii, Dark State
pdb|4IXQ|DD Chain d, Rt Fs X-ray Diffraction Of Photosystem Ii, Dark State
pdb|4IXR|D Chain D, Rt Fs X-ray Diffraction Of Photosystem Ii, First
Illuminated State
pdb|4IXR|DD Chain d, Rt Fs X-ray Diffraction Of Photosystem Ii, First
Illuminated State
Length = 352
Score = 25.8 bits (55), Expect = 6.1, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 32 IFMAQPPTKSEFVFTAPFGYARLYSSALTTQGFVN 66
+F+ P +S + F FG A ++ L QGF N
Sbjct: 156 VFLIYPLGQSSWFFAPSFGVAAIFRFLLFFQGFHN 190
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
0.321 0.132 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,780,356
Number of Sequences: 62578
Number of extensions: 88342
Number of successful extensions: 265
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 257
Number of HSP's gapped (non-prelim): 8
length of query: 107
length of database: 14,973,337
effective HSP length: 72
effective length of query: 35
effective length of database: 10,467,721
effective search space: 366370235
effective search space used: 366370235
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: 45 (21.9 bits)