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= 014221
(428 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1JEQ|A Chain A, Crystal Structure Of The Ku Heterodimer
pdb|1JEY|A Chain A, Crystal Structure Of The Ku Heterodimer Bound To Dna
Length = 609
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 13/56 (23%), Positives = 27/56 (48%)
Query: 188 FPVLFVPHQETRVKVPRSETIKKCPDCVGRGNAVCPSCNANQEPEYYKEKQMSQCF 243
F ++F+P + + K+P +E I P+ VG+ A+ + ++ + Q F
Sbjct: 432 FQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFENPVLQQHF 487
>pdb|2CTT|A Chain A, Solution Structure Of Zinc Finger Domain From Human Dnaj
Subfamily A Menber 3
Length = 104
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 17/66 (25%)
Query: 261 CTKCNGKGTIP------CATCGSRGL-----------IKCRKCGGSGSLLTRSFAIVRWK 303
C +CNGKG P C CG G+ CR+CGG GS++ + R
Sbjct: 31 CERCNGKGNEPGTKVQHCHYCGGSGMETINTGPFVMRSTCRRCGGRGSIIISPCVVCRGA 90
Query: 304 TLSTRK 309
+ +K
Sbjct: 91 GQAKQK 96
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 8/48 (16%)
Query: 152 EERETISETEPYLGGNIDGKDNGPALGTWE----LDLRSQFPVLFVPH 195
+ERE E Y GG + P G WE LD RS +P + + H
Sbjct: 373 DERELARRRESYAGGYV----KEPERGLWENIVYLDFRSLYPSIIITH 416
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 8/48 (16%)
Query: 152 EERETISETEPYLGGNIDGKDNGPALGTWE----LDLRSQFPVLFVPH 195
+ERE E Y GG + P G WE LD RS +P + + H
Sbjct: 373 DERELARRRESYAGGYV----KEPERGLWENIVYLDFRSLYPSIIITH 416
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 8/48 (16%)
Query: 152 EERETISETEPYLGGNIDGKDNGPALGTWE----LDLRSQFPVLFVPH 195
+ERE E Y GG + P G WE LD RS +P + + H
Sbjct: 373 DERELARRRESYAGGYV----KEPERGLWENIVYLDFRSLYPSIIITH 416
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 8/48 (16%)
Query: 152 EERETISETEPYLGGNIDGKDNGPALGTWE----LDLRSQFPVLFVPH 195
+ERE E Y GG + P G WE LD RS +P + + H
Sbjct: 373 DERELARRRESYAGGYV----KEPERGLWENIVYLDFRSLYPSIIITH 416
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok
Length = 773
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 8/48 (16%)
Query: 152 EERETISETEPYLGGNIDGKDNGPALGTWE----LDLRSQFPVLFVPH 195
+ERE TE Y GG + P G WE LD +S +P + + H
Sbjct: 373 DERELARRTESYAGGYV----KEPEKGLWENIVYLDYKSLYPSIIITH 416
>pdb|1D5A|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok. Deposition Of Second Native Structure At 2.4
Angstrom
Length = 733
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 8/49 (16%)
Query: 152 EERETISETEPYLGGNIDGKDNGPALGTWE----LDLRSQFPVLFVPHQ 196
+ERE TE Y GG + P G WE LD +S +P + + H
Sbjct: 373 DERELARRTESYAGGYV----KEPEKGLWENIVYLDYKSLYPSIIITHN 417
>pdb|4B7Y|C Chain C, Crystal Structure Of The Msl1-msl2 Complex
pdb|4B7Y|D Chain D, Crystal Structure Of The Msl1-msl2 Complex
pdb|4B86|C Chain C, Crystal Structure Of The Msl1-msl2 Complex (3.5a)
pdb|4B86|D Chain D, Crystal Structure Of The Msl1-msl2 Complex (3.5a)
pdb|4B86|G Chain G, Crystal Structure Of The Msl1-msl2 Complex (3.5a)
pdb|4B86|H Chain H, Crystal Structure Of The Msl1-msl2 Complex (3.5a)
pdb|4B86|K Chain K, Crystal Structure Of The Msl1-msl2 Complex (3.5a)
pdb|4B86|L Chain L, Crystal Structure Of The Msl1-msl2 Complex (3.5a)
Length = 116
Score = 28.5 bits (62), Expect = 7.9, Method: Composition-based stats.
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 211 CPDCVGRGNAVCPSCNANQEPEYYKE-KQMSQCFNCYGR 248
C C G+ + PSC+ ++ E ++E KQ+S NCY +
Sbjct: 67 CKTCKGKKMMMKPSCSWCKDYEQFEENKQLSILVNCYKK 105
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
0.320 0.136 0.434
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,501,526
Number of Sequences: 62578
Number of extensions: 498617
Number of successful extensions: 1033
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1022
Number of HSP's gapped (non-prelim): 17
length of query: 428
length of database: 14,973,337
effective HSP length: 102
effective length of query: 326
effective length of database: 8,590,381
effective search space: 2800464206
effective search space used: 2800464206
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: 53 (25.0 bits)