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= 033708
(113 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1QVB|A Chain A, Crystal Structure Of The Beta-Glycosidase From The
Hyperthermophile Thermosphaera Aggregans
pdb|1QVB|B Chain B, Crystal Structure Of The Beta-Glycosidase From The
Hyperthermophile Thermosphaera Aggregans
Length = 481
Score = 27.7 bits (60), Expect = 1.8, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 54 GVPVAGSLDQRPSRNDAWSTRMREKYGLDTSEFT----YNPSESHRFQQVATQ 102
G+PV G L + N W+ R+K+GL +F Y + F+++AT
Sbjct: 415 GIPVKGYLHWSLTDNYEWAQGFRQKFGLVMVDFKTKKRYLRPSALVFREIATH 467
>pdb|3PWE|A Chain A, Crystal Structure Of The E. Coli Beta Clamp Mutant
R103c, I305c, C260s, C333s At 2.2a Resolution
pdb|3PWE|B Chain B, Crystal Structure Of The E. Coli Beta Clamp Mutant
R103c, I305c, C260s, C333s At 2.2a Resolution
Length = 366
Score = 26.6 bits (57), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 31 DELIAPRQQIRQPLINRPTPPATG 54
+ L+ P QQ+ PL RPT P G
Sbjct: 8 EHLLKPLQQVSGPLGGRPTLPILG 31
>pdb|3F1V|A Chain A, E. Coli Beta Sliding Clamp, 148-153 Ala Mutant
pdb|3F1V|B Chain B, E. Coli Beta Sliding Clamp, 148-153 Ala Mutant
Length = 366
Score = 26.6 bits (57), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 31 DELIAPRQQIRQPLINRPTPPATG 54
+ L+ P QQ+ PL RPT P G
Sbjct: 8 EHLLKPLQQVSGPLGGRPTLPILG 31
>pdb|1JQL|A Chain A, Mechanism Of Processivity Clamp Opening By The Delta
Subunit Wrench Of The Clamp Loader Complex Of E. Coli
Dna Polymerase Iii: Structure Of Beta-Delta (1-140)
pdb|1JQJ|A Chain A, Mechanism Of Processivity Clamp Opening By The Delta
Subunit Wrench Of The Clamp Loader Complex Of E. Coli
Dna Polymerase Iii: Structure Of The Beta-Delta Complex
pdb|1JQJ|B Chain B, Mechanism Of Processivity Clamp Opening By The Delta
Subunit Wrench Of The Clamp Loader Complex Of E. Coli
Dna Polymerase Iii: Structure Of The Beta-Delta Complex
Length = 366
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 31 DELIAPRQQIRQPLINRPTPPATG 54
+ L+ P QQ+ PL RPT P G
Sbjct: 8 EHLLKPLQQVSGPLGGRPTLPILG 31
>pdb|3QSB|B Chain B, Structure Of E. Coli Poliiibeta With
(Z)-5-(1-((4'-Fluorobiphenyl-4-
Yl)methoxyimino)butyl)-2,2-Dimethyl-4,
6-Dioxocyclohexanecarbonitrile
Length = 366
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 31 DELIAPRQQIRQPLINRPTPPATG 54
+ L+ P QQ+ PL RPT P G
Sbjct: 8 EHLLKPLQQVSGPLGGRPTLPILG 31
>pdb|2XUR|A Chain A, The G157c Mutation In The Escherichia Coli Sliding Clamp
Specifically Affects Initiation Of Replication
pdb|2XUR|B Chain B, The G157c Mutation In The Escherichia Coli Sliding Clamp
Specifically Affects Initiation Of Replication
Length = 373
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 31 DELIAPRQQIRQPLINRPTPPATG 54
+ L+ P QQ+ PL RPT P G
Sbjct: 15 EHLLKPLQQVSGPLGGRPTLPILG 38
>pdb|3Q4L|A Chain A, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4L|B Chain B, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
Length = 368
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 31 DELIAPRQQIRQPLINRPTPPATG 54
+ L+ P QQ+ PL RPT P G
Sbjct: 10 EHLLKPLQQVSGPLGGRPTLPILG 33
>pdb|2POL|A Chain A, Three-Dimensional Structure Of The Beta Subunit Of
Escherichia Coli Dna Polymerase Iii Holoenzyme: A
Sliding Dna Clamp
pdb|2POL|B Chain B, Three-Dimensional Structure Of The Beta Subunit Of
Escherichia Coli Dna Polymerase Iii Holoenzyme: A
Sliding Dna Clamp
pdb|1MMI|A Chain A, E. Coli Dna Polymerase Beta Subunit
pdb|1MMI|B Chain B, E. Coli Dna Polymerase Beta Subunit
pdb|1UNN|A Chain A, Complex Of Beta-Clamp Processivity Factor And Little
Finger Domain Of Poliv
pdb|1UNN|B Chain B, Complex Of Beta-Clamp Processivity Factor And Little
Finger Domain Of Poliv
pdb|1OK7|A Chain A, A Conserved Protein Binding-site On Bacterial Sliding
Clamps
pdb|1OK7|B Chain B, A Conserved Protein Binding-site On Bacterial Sliding
Clamps
pdb|3BEP|A Chain A, Structure Of A Sliding Clamp On Dna
pdb|3BEP|B Chain B, Structure Of A Sliding Clamp On Dna
pdb|3D1E|A Chain A, Crystal Structure Of E. Coli Sliding Clamp (Beta) Bound
To A Polymerase Ii Peptide
pdb|3D1E|B Chain B, Crystal Structure Of E. Coli Sliding Clamp (Beta) Bound
To A Polymerase Ii Peptide
pdb|3D1F|A Chain A, Crystal Structure Of E. Coli Sliding Clamp (Beta) Bound
To A Polymerase Iii Peptide
pdb|3D1F|B Chain B, Crystal Structure Of E. Coli Sliding Clamp (Beta) Bound
To A Polymerase Iii Peptide
pdb|3D1G|A Chain A, Structure Of A Small Molecule Inhibitor Bound To A Dna
Sliding Clamp
pdb|3D1G|B Chain B, Structure Of A Small Molecule Inhibitor Bound To A Dna
Sliding Clamp
pdb|3QSB|A Chain A, Structure Of E. Coli Poliiibeta With
(Z)-5-(1-((4'-Fluorobiphenyl-4-
Yl)methoxyimino)butyl)-2,2-Dimethyl-4,
6-Dioxocyclohexanecarbonitrile
pdb|3Q4J|A Chain A, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4J|B Chain B, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4J|C Chain C, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4J|D Chain D, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4J|E Chain E, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4J|F Chain F, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4K|A Chain A, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4K|B Chain B, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
Length = 366
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 31 DELIAPRQQIRQPLINRPTPPATG 54
+ L+ P QQ+ PL RPT P G
Sbjct: 8 EHLLKPLQQVSGPLGGRPTLPILG 31
>pdb|2P2W|A Chain A, Crystal Structure Of Citrate Synthase From Thermotoga
Maritima Msb8
Length = 367
Score = 26.2 bits (56), Expect = 5.3, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 21/41 (51%)
Query: 4 PWNLQALIFLLAIIVRAANRPVEYDSDDELIAPRQQIRQPL 44
P N+ +F A +V +EY SD++LI P + P+
Sbjct: 313 PRNMFTALFATARVVGWTAHVIEYVSDNKLIRPTSEYVGPM 353
>pdb|4B1Z|M Chain M, Structure Of The Phactr1 Rpel Domain Bound To G-Actin
pdb|4B1Z|N Chain N, Structure Of The Phactr1 Rpel Domain Bound To G-Actin
Length = 115
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 31/56 (55%), Gaps = 6/56 (10%)
Query: 15 AIIVRAANRPVEYDSDDELIAPRQ------QIRQPLINRPTPPATGVPVAGSLDQR 64
++ ++ +NRP + + +++ I PRQ ++RQ + + T + P A L+QR
Sbjct: 10 SLAIKLSNRPSKRELEEKNILPRQTDEERLELRQQIGTKLTRRLSQRPTAEELEQR 65
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
0.317 0.131 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,356,299
Number of Sequences: 62578
Number of extensions: 125945
Number of successful extensions: 270
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 261
Number of HSP's gapped (non-prelim): 13
length of query: 113
length of database: 14,973,337
effective HSP length: 77
effective length of query: 36
effective length of database: 10,154,831
effective search space: 365573916
effective search space used: 365573916
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)