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= 029383
         (194 letters)

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

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



>pdb|1PFF|A Chain A, Crystal Structure Of Homocysteine Alpha-, Gamma-Lyase At
           1.8 Angstroms
 pdb|1PFF|B Chain B, Crystal Structure Of Homocysteine Alpha-, Gamma-Lyase At
           1.8 Angstroms
          Length = 331

 Score = 30.4 bits (67), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 14/31 (45%), Positives = 20/31 (64%)

Query: 79  EEAGDADFLYKASICCEYRPELMSDLRQALD 109
           E AG  D L + S+ CE   +++ DL+QALD
Sbjct: 298 EAAGLTDNLIRLSVGCENVQDIIDDLKQALD 328


>pdb|2ZUL|A Chain A, Crystal Structure Of Thermus Thermophilus 16s Rrna
           Methyltransferase Rsmc (Ttha0533) In Complex With
           Cofactor S-Adenosyl-L-Methionine
 pdb|2ZWV|A Chain A, Crystal Structure Of Thermus Thermophilus 16s Rrna
           Methyltransferase Rsmc (Ttha0533)
          Length = 375

 Score = 27.7 bits (60), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 8/60 (13%)

Query: 105 RQALD--------ALPLKMLKAEISTLGGRLKNVIVFTSCKEGNAEASQTLANDVQQALN 156
           RQ LD         LPL  + AE+  +   L +V+      E NA  +Q L +DV +AL 
Sbjct: 235 RQVLDLGAGYGALTLPLARMGAEVVGVEDDLASVLSLQKGLEANALKAQALHSDVDEALT 294


>pdb|3DMF|A Chain A, T. Thermophilus 16s Rrna N2 G1207 Methyltransferase (Rsmc)
           In Complex With Adomet
 pdb|3DMG|A Chain A, T. Thermophilus 16s Rrna N2 G1207 Methyltransferase (Rsmc)
           In Complex With Adohcy
 pdb|3DMH|A Chain A, T. Thermophilus 16s Rrna N2 G1207 Methyltransferase (Rsmc)
           In Complex With Adomet And Guanosine
          Length = 381

 Score = 27.7 bits (60), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 8/60 (13%)

Query: 105 RQALD--------ALPLKMLKAEISTLGGRLKNVIVFTSCKEGNAEASQTLANDVQQALN 156
           RQ LD         LPL  + AE+  +   L +V+      E NA  +Q L +DV +AL 
Sbjct: 235 RQVLDLGAGYGALTLPLARMGAEVVGVEDDLASVLSLQKGLEANALKAQALHSDVDEALT 294


>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
           Transcriptional Activator Complex
          Length = 387

 Score = 27.3 bits (59), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 23/93 (24%), Positives = 36/93 (38%), Gaps = 26/93 (27%)

Query: 7   HSEAXXXXXXXINAHLDTLRGLVPP----NGKMDKATLLAEVIRQVK------------- 49
           HS+        +N+ +D L  LVP     + K+DK T+L   ++ +K             
Sbjct: 17  HSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYTEAN 76

Query: 50  ---------ELKTNAIEASKGFLIPTDADEVKV 73
                    ELK   + A+ GFL     D  K+
Sbjct: 77  YKPTFLSDDELKHLILRAADGFLFVVGCDRGKI 109


>pdb|4H10|A Chain A, Intermolecular Recognition Revealed By The Complex
          Structure Of Human Clock-bmal1 Basic Helix-loop-helix
          Domains With E-box Dna
          Length = 73

 Score = 26.9 bits (58), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 4/55 (7%)

Query: 7  HSEAXXXXXXXINAHLDTLRGLVPP----NGKMDKATLLAEVIRQVKELKTNAIE 57
          HS+        +N+ +D L  LVP     + K+DK T+L   ++ +K L+   +E
Sbjct: 13 HSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGAWLE 67


  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
   0.313    0.130    0.357 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,791,260
Number of Sequences: 62578
Number of extensions: 172828
Number of successful extensions: 340
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 337
Number of HSP's gapped (non-prelim): 6
length of query: 194
length of database: 14,973,337
effective HSP length: 94
effective length of query: 100
effective length of database: 9,091,005
effective search space: 909100500
effective search space used: 909100500
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 bits)