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= 025258
(255 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4H9D|A Chain A, Crystal Structure Of Mn-Dependent Gme Hnh Nicking
Endonuclease From Geobacter Metallireducens Gs-15,
Northeast Structural Genomics Consortium (Nesg) Target
Gmr87
pdb|4H9D|B Chain B, Crystal Structure Of Mn-Dependent Gme Hnh Nicking
Endonuclease From Geobacter Metallireducens Gs-15,
Northeast Structural Genomics Consortium (Nesg) Target
Gmr87
pdb|4H9D|C Chain C, Crystal Structure Of Mn-Dependent Gme Hnh Nicking
Endonuclease From Geobacter Metallireducens Gs-15,
Northeast Structural Genomics Consortium (Nesg) Target
Gmr87
Length = 112
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 38/70 (54%), Gaps = 6/70 (8%)
Query: 157 QVVKRRRIKNNLSRKNLMYRDNFT---CQYCSS---RENLTIDHVVPASRGGEWKWENLV 210
Q VKR + K R++ +++ C YC E LT DH+VP RGG+ N+V
Sbjct: 11 QEVKREKEKARELRRSQWWKNRIARGICHYCGEIFPPEELTXDHLVPVVRGGKSTRGNVV 70
Query: 211 AACFKCNSRK 220
AC +CN+RK
Sbjct: 71 PACKECNNRK 80
>pdb|3ULU|A Chain A, Structure Of Quaternary Complex Of Human Tlr3ecd With
Three Fabs (Form1)
pdb|3ULV|A Chain A, Structure Of Quaternary Complex Of Human Tlr3ecd With
Three Fabs (Form2)
Length = 694
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 25/107 (23%), Positives = 50/107 (46%), Gaps = 17/107 (15%)
Query: 102 VLDISYRPVNVV-----CWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLL 156
+LD+SY +NVV W + F+E ++ + +++ + VR+L
Sbjct: 262 MLDLSYNNLNVVGNDSFAWLPQLEYFFLEYNNIQHLFSHSLH---------GLFNVRYL- 311
Query: 157 QVVKRRRIKNNLSRKNLMYRDNFTCQYCSSRENLTI-DHVVPASRGG 202
+KR K ++S +L D+F+ Q+ E+L + D+ +P +
Sbjct: 312 -NLKRSFTKQSISLASLPKIDDFSFQWLKCLEHLNMEDNDIPGIKSN 357
>pdb|2A0Z|A Chain A, The Molecular Structure Of Toll-like Receptor 3 Ligand
Binding Domain
Length = 705
Score = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 25/107 (23%), Positives = 50/107 (46%), Gaps = 17/107 (15%)
Query: 102 VLDISYRPVNVV-----CWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLL 156
+LD+SY +NVV W + F+E ++ + +++ + VR+L
Sbjct: 257 MLDLSYNNLNVVGNDSFAWLPQLEYFFLEYNNIQHLFSHSLH---------GLFNVRYL- 306
Query: 157 QVVKRRRIKNNLSRKNLMYRDNFTCQYCSSRENLTI-DHVVPASRGG 202
+KR K ++S +L D+F+ Q+ E+L + D+ +P +
Sbjct: 307 -NLKRSFTKQSISLASLPKIDDFSFQWLKCLEHLNMEDNDIPGIKSN 352
>pdb|1ZIW|A Chain A, Human Toll-Like Receptor 3 Extracellular Domain Structure
Length = 680
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 25/107 (23%), Positives = 50/107 (46%), Gaps = 17/107 (15%)
Query: 102 VLDISYRPVNVV-----CWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLL 156
+LD+SY +NVV W + F+E ++ + +++ + VR+L
Sbjct: 252 MLDLSYNNLNVVGNDSFAWLPQLEYFFLEYNNIQHLFSHSLH---------GLFNVRYL- 301
Query: 157 QVVKRRRIKNNLSRKNLMYRDNFTCQYCSSRENLTI-DHVVPASRGG 202
+KR K ++S +L D+F+ Q+ E+L + D+ +P +
Sbjct: 302 -NLKRSFTKQSISLASLPKIDDFSFQWLKCLEHLNMEDNDIPGIKSN 347
>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2
pdb|3LES|B Chain B, 2f5 Epitope Scaffold Es2
pdb|3LEV|A Chain A, Hiv-1 Antibody 2f5 In Complex With Epitope Scaffold Es2
Length = 179
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 223 KTLEEANMQLSRVPKVLVRYLYHAVENHA 251
KT+EE + +L +PK L RYL+ A E A
Sbjct: 77 KTVEEVDGKLKSLPKELKRYLHIAREGEA 105
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 28.1 bits (61), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 216 CNSRKGKKTLEEANMQLSRVPKVLVRYLYHAVENHA 251
+ KT+EE + +L +PK L RYL+ A E A
Sbjct: 162 LKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEA 197
>pdb|1KU2|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
Sigma Subunit Fragment Containing Regions 1.2 To 3.1
pdb|1KU2|B Chain B, Crystal Structure Of Thermus Aquaticus Rna Polymerase
Sigma Subunit Fragment Containing Regions 1.2 To 3.1
Length = 241
Score = 28.1 bits (61), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 223 KTLEEANMQLSRVPKVLVRYLYHAVENHA 251
KT+EE + +L +PK L RYL+ A E A
Sbjct: 78 KTVEEVDGKLKSLPKELKRYLHIAREGEA 106
>pdb|3UGO|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2
Complexed With -10 Promoter Element Ssdna Oligo (Tacaat)
pdb|3UGP|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2
Complexed With -10 Promoter Element Ssdna Oligo (Tataat)
pdb|4GOR|A Chain A, Crystallographic Analysis Of An Rna-Polymerase
Sigma-Subunit Fragment Complexed With -10 Promoter
Element Ssdna: G-Quadruplex Formation And Crystal
Packing
pdb|4GOR|B Chain B, Crystallographic Analysis Of An Rna-Polymerase
Sigma-Subunit Fragment Complexed With -10 Promoter
Element Ssdna: G-Quadruplex Formation And Crystal
Packing
Length = 245
Score = 28.1 bits (61), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 223 KTLEEANMQLSRVPKVLVRYLYHAVENHA 251
KT+EE + +L +PK L RYL+ A E A
Sbjct: 82 KTVEEVDGKLKSLPKELKRYLHIAREGEA 110
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
0.323 0.137 0.424
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,781,148
Number of Sequences: 62578
Number of extensions: 246649
Number of successful extensions: 469
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 464
Number of HSP's gapped (non-prelim): 8
length of query: 255
length of database: 14,973,337
effective HSP length: 97
effective length of query: 158
effective length of database: 8,903,271
effective search space: 1406716818
effective search space used: 1406716818
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: 50 (23.9 bits)