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= 010498
         (509 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|2VFK|A Chain A, Akap18 Delta Central Domain - Amp
 pdb|2VFL|A Chain A, Akap18 Delta Central Domain - Cmp
 pdb|2VFY|A Chain A, Akap18 Delta Central Domain
          Length = 205

 Score = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 44/175 (25%), Positives = 81/175 (46%), Gaps = 20/175 (11%)

Query: 336 TFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARIL 395
           +FH+T+L+++L N+D VN  T+ L  +   V + L+ + L +   G+   +G     +  
Sbjct: 43  SFHITLLVMQLLNEDEVNIGTDALLELKPFVEEILEGKHLTLPFHGIGTFQGQVGFVK-- 100

Query: 396 YAPVEEIGDGDR---LLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKR--RK 450
                 + DGD    LL   +     F E G++     ++  K H T M +       +K
Sbjct: 101 ------LADGDHVSALLEIAETAKRTFQEKGIL--AGESRTFKPHLTFMKLSKAPMLWKK 152

Query: 451 GTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDES-GFYHCCASIPFPE 504
           G R+++      +++QF    +GE ++ +  L       +S G+YHC +SI   E
Sbjct: 153 GVRKIE----PGLYEQFIDHRFGEEILYQIDLCSMLKKKQSNGYYHCESSIVIGE 203


>pdb|3N75|A Chain A, X-Ray Crystal Structure Of The Escherichia Coli Inducible
           Lysine Decarboxylase Ldci
 pdb|3N75|B Chain B, X-Ray Crystal Structure Of The Escherichia Coli Inducible
           Lysine Decarboxylase Ldci
 pdb|3N75|C Chain C, X-Ray Crystal Structure Of The Escherichia Coli Inducible
           Lysine Decarboxylase Ldci
 pdb|3N75|D Chain D, X-Ray Crystal Structure Of The Escherichia Coli Inducible
           Lysine Decarboxylase Ldci
 pdb|3N75|E Chain E, X-Ray Crystal Structure Of The Escherichia Coli Inducible
           Lysine Decarboxylase Ldci
 pdb|3Q16|A Chain A, Linkage Between The Bacterial Acid Stress And Stringent
           Responses: The Structure Of The Inducible Lysine
           Decarboxylase
 pdb|3Q16|B Chain B, Linkage Between The Bacterial Acid Stress And Stringent
           Responses: The Structure Of The Inducible Lysine
           Decarboxylase
 pdb|3Q16|C Chain C, Linkage Between The Bacterial Acid Stress And Stringent
           Responses: The Structure Of The Inducible Lysine
           Decarboxylase
 pdb|3Q16|D Chain D, Linkage Between The Bacterial Acid Stress And Stringent
           Responses: The Structure Of The Inducible Lysine
           Decarboxylase
 pdb|3Q16|E Chain E, Linkage Between The Bacterial Acid Stress And Stringent
           Responses: The Structure Of The Inducible Lysine
           Decarboxylase
          Length = 715

 Score = 32.0 bits (71), Expect = 0.77,   Method: Compositional matrix adjust.
 Identities = 29/94 (30%), Positives = 44/94 (46%), Gaps = 9/94 (9%)

Query: 171 QKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLDYSHFVS 230
           ++ F+  + VK +LPS  +ED    E      +A+   K+  I+   +  P L Y  F  
Sbjct: 557 KRAFDLNLRVKNMLPSLYREDPEFYENMRIQELAQNIHKL--IVHHNL--PDLMYRAFEV 612

Query: 231 LPLAVHPELVDKLVNFQNTILGIT-DVCLDENVG 263
           LP  V    +     FQ  + G+T +V LDE VG
Sbjct: 613 LPTMV----MTPYAAFQKELHGMTEEVYLDEMVG 642


>pdb|1K1G|A Chain A, Structural Basis For Recognition Of The Intron Branch Site
           Rna By Splicing Factor 1
          Length = 131

 Score = 31.6 bits (70), Expect = 1.0,   Method: Composition-based stats.
 Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 19/76 (25%)

Query: 165 GKEGSTQKKFEKEMGVKII-------------------LPSSKKEDSIIIEGNSTDSVAK 205
           G  G+T K  EKE   KI+                   LP   +    ++  N+ ++V K
Sbjct: 29  GPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKK 88

Query: 206 ASEKIQAIIAEAVESP 221
           A E+I+ I+ + +E+P
Sbjct: 89  AVEQIRNILKQGIETP 104


>pdb|3AGP|A Chain A, Structure Of Viral Polymerase Form I
 pdb|3AGQ|A Chain A, Structure Of Viral Polymerase Form Ii
 pdb|3AVT|A Chain A, Structure Of Viral Rna Polymerase Complex 1
 pdb|3AVU|A Chain A, Structure Of Viral Rna Polymerase Complex 2
 pdb|3AVV|A Chain A, Structure Of Viral Rna Polymerase Complex 3
 pdb|3AVW|A Chain A, Structure Of Viral Rna Polymerase Complex 4
 pdb|3AVX|A Chain A, Structure Of Viral Rna Polymerase Complex 5
 pdb|3AVY|A Chain A, Structure Of Viral Rna Polymerase Complex 6
 pdb|3VNU|A Chain A, Complex Structure Of Viral Rna Polymerase I
 pdb|3VNV|A Chain A, Complex Structure Of Viral Rna Polymerase Ii
 pdb|4FWT|A Chain A, Complex Structure Of Viral Rna Polymerase Form Iii
          Length = 1289

 Score = 30.8 bits (68), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 34/142 (23%), Positives = 62/142 (43%), Gaps = 15/142 (10%)

Query: 154 EVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAI 213
           E+ AS+++ ++ + G+        M  K  L  +  +  + IE        KA++K   +
Sbjct: 3   EITASLVKELRERTGAGM------MDCKKALTEANGDIELAIENMRKSGAIKAAKKAGNV 56

Query: 214 IAEAVESPSLDYSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDS 273
            A+ V    +D ++ + L +    + V K   FQ       D  LD  V  K     +D 
Sbjct: 57  AADGVIKTKIDGNYGIILEVNCQTDFVAKDAGFQ----AFADKVLDAAVAGK----ITDV 108

Query: 274 EEKEQQVDQEHKVAVELNIGDN 295
           E  + Q ++E +VA+   IG+N
Sbjct: 109 EVLKAQFEEE-RVALVAKIGEN 129


>pdb|3MMP|A Chain A, Structure Of The Qb Replicase, An Rna-Dependent Rna
           Polymerase Consisting Of Viral And Host Proteins
 pdb|3MMP|C Chain C, Structure Of The Qb Replicase, An Rna-Dependent Rna
           Polymerase Consisting Of Viral And Host Proteins
          Length = 678

 Score = 28.5 bits (62), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 34/142 (23%), Positives = 62/142 (43%), Gaps = 15/142 (10%)

Query: 154 EVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAI 213
           E+ AS+++ ++ + G+        M  K  L  +  +  + IE        KA++K   +
Sbjct: 3   EITASLVKELRERTGAGM------MDCKKALTEANGDIELAIENMRKSGAIKAAKKAGNV 56

Query: 214 IAEAVESPSLDYSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDS 273
            A+ V    +D ++ + L +    + V K   FQ       D  LD  V  K     +D 
Sbjct: 57  AADGVIKTKIDGNYGIILEVNCQTDFVAKDAGFQ----AFADKVLDAAVAGK----ITDV 108

Query: 274 EEKEQQVDQEHKVAVELNIGDN 295
           E  + Q ++E +VA+   IG+N
Sbjct: 109 EVLKAQFEEE-RVALVAKIGEN 129


  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
   0.315    0.132    0.375 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,096,486
Number of Sequences: 62578
Number of extensions: 572429
Number of successful extensions: 1448
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 1443
Number of HSP's gapped (non-prelim): 23
length of query: 509
length of database: 14,973,337
effective HSP length: 103
effective length of query: 406
effective length of database: 8,527,803
effective search space: 3462288018
effective search space used: 3462288018
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)