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= 004369
         (758 letters)

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

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



>pdb|1S4F|A Chain A, Crystal Structure Of Rna-Dependent Rna Polymerase
           Construct 2 From Bovine Viral Diarrhea Virus (Bvdv)
 pdb|1S4F|B Chain B, Crystal Structure Of Rna-Dependent Rna Polymerase
           Construct 2 From Bovine Viral Diarrhea Virus (Bvdv)
 pdb|1S4F|C Chain C, Crystal Structure Of Rna-Dependent Rna Polymerase
           Construct 2 From Bovine Viral Diarrhea Virus (Bvdv)
 pdb|1S4F|D Chain D, Crystal Structure Of Rna-Dependent Rna Polymerase
           Construct 2 From Bovine Viral Diarrhea Virus (Bvdv)
          Length = 601

 Score = 35.4 bits (80), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 26/83 (31%), Positives = 40/83 (48%), Gaps = 20/83 (24%)

Query: 207 EDDTSVGNSLCS----LYSTCGSLNSAIKAFNRIREKNVMSWTTVIGACGENG----EAV 258
           + DTS GNS+ +    +Y+ C S     K+FNR+           I  CG++G    E  
Sbjct: 329 QPDTSAGNSMLNVLTMMYAFCESTGVPYKSFNRV---------ARIHVCGDDGFLITEKG 379

Query: 259 QGLRFFSK---MLSEGIQPNEFT 278
            GL+F +K   +L E  +P + T
Sbjct: 380 LGLKFANKGMQILHEAGKPQKIT 402


>pdb|1S48|A Chain A, Crystal Structure Of Rna-Dependent Rna Polymerase
           Construct 1 (Residues 71-679) From Bvdv
 pdb|1S49|A Chain A, Crystal Structure Of Rna-Dependent Rna Polymerase
           Construct 1 (Residues 71-679) From Bovine Viral Diarrhea
           Virus Complexed With Gtp
          Length = 609

 Score = 34.7 bits (78), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 38/83 (45%), Gaps = 20/83 (24%)

Query: 207 EDDTSVGNS----LCSLYSTCGSLNSAIKAFNRIREKNVMSWTTVIGACGENG----EAV 258
           + DTS GNS    L   Y+ C S     K+FNR+           I  CG++G    E  
Sbjct: 337 QPDTSAGNSXLNVLTXXYAFCESTGVPYKSFNRV---------ARIHVCGDDGFLITEKG 387

Query: 259 QGLRFFSK---MLSEGIQPNEFT 278
            GL+F +K   +L E  +P + T
Sbjct: 388 LGLKFANKGXQILHEAGKPQKIT 410


>pdb|3NMV|B Chain B, Crystal Structure Of Pyrabactin-Bound Abscisic Acid
           Receptor Pyl2 Mutant A93f In Complex With Type 2c
           Protein Phosphatase Abi2
 pdb|3UJK|A Chain A, Crystal Structure Of Protein Phosphatase Abi2
 pdb|3UJL|B Chain B, Crystal Structure Of Abscisic Acid Bound Pyl2 In Complex
           With Type 2c Protein Phosphatase Abi2
          Length = 324

 Score = 32.0 bits (71), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 19/55 (34%), Positives = 24/55 (43%), Gaps = 1/55 (1%)

Query: 110 FVMTFLVNVYGKCGNMEEAQKVFDNLPRINVVSWTSLISGYVQNS-QPELAIHVF 163
           F    L  V   CG   E +     +PR   VS +SL+ G V N   P L+ H F
Sbjct: 8   FKCVPLYGVTSICGRRPEMEDSVSTIPRFLQVSSSSLLDGRVTNGFNPHLSAHFF 62


>pdb|3MMI|A Chain A, Crystal Structure Of The Globular Tail Of Myo4p
 pdb|3MMI|B Chain B, Crystal Structure Of The Globular Tail Of Myo4p
          Length = 386

 Score = 30.8 bits (68), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 32/140 (22%), Positives = 65/140 (46%), Gaps = 6/140 (4%)

Query: 245 TTVIGACGENGEAVQGLRFFSKMLSEGIQPNEFTLTSISSVCGTMLSLRVGAQVHSLGIK 304
           TTV+ +   NG  +Q  +F SK+L   ++    +L    ++ G +  L   +++ +    
Sbjct: 59  TTVVSSLVRNGLLIQSSKFISKVLL-TVESIVMSLPKDETMLGGIFWLSNLSRLPAFAAN 117

Query: 305 ---LGYASNLRVRNSIMYLYLKCGLVDEAQKLFDGMSHVNLVTWNAMIAGHAQMMDLAKD 361
              L  A+    ++ +  +YL   L +E  K+FD +    LV +    + H ++ D+  +
Sbjct: 118 QKTLYEANGGDEKDKLTLIYLN-DLENETLKVFDKIYSTWLVKFMKHASAHIEIFDMVLN 176

Query: 362 DLSAHNGGTEALS-IFSKLN 380
           +    N G E  + +F+ LN
Sbjct: 177 EKLFKNSGDEKFAKLFTFLN 196


  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    0.133    0.391 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,892,386
Number of Sequences: 62578
Number of extensions: 809031
Number of successful extensions: 1770
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1766
Number of HSP's gapped (non-prelim): 9
length of query: 758
length of database: 14,973,337
effective HSP length: 106
effective length of query: 652
effective length of database: 8,340,069
effective search space: 5437724988
effective search space used: 5437724988
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: 55 (25.8 bits)