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= psy10644
         (196 letters)

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

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



>pdb|2ZFU|A Chain A, Structure Of The Methyltransferase-Like Domain Of
           Nucleomethylin
 pdb|2ZFU|B Chain B, Structure Of The Methyltransferase-Like Domain Of
           Nucleomethylin
          Length = 215

 Score =  160 bits (405), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 74/147 (50%), Positives = 104/147 (70%), Gaps = 3/147 (2%)

Query: 50  LLNKLKSARFRYLNEQLYTSKSEESKDFFTEDRESFEAYHEGFKKQVTQWPINPVDIIIK 109
           +  +L  ARFRYLNEQLY+  S  ++  F ED E+F  YH GF+ QV +WP+ PVD I +
Sbjct: 1   MAQRLDGARFRYLNEQLYSGPSSAAQRLFQEDPEAFLLYHRGFQSQVKKWPLQPVDRIAR 60

Query: 110 SIQERESKGRLVIADLGCGEAKLAAELTQHKVHSLDLVALNERVTSCDMTRTPLKPYSVD 169
            +++R +   LV+AD GCG+ +LA+ + ++ VH  DL +L+ RVT CDM + PL+  SVD
Sbjct: 61  DLRQRPAS--LVVADFGCGDCRLASSI-RNPVHCFDLASLDPRVTVCDMAQVPLEDESVD 117

Query: 170 VAVFCLSLMGTDLAACIKEANRILKLG 196
           VAVFCLSLMGT++   ++EANR+LK G
Sbjct: 118 VAVFCLSLMGTNIRDFLEEANRVLKPG 144


>pdb|2EYQ|A Chain A, Crystal Structure Of Escherichia Coli Transcription-Repair
           Coupling Factor
 pdb|2EYQ|B Chain B, Crystal Structure Of Escherichia Coli Transcription-Repair
           Coupling Factor
          Length = 1151

 Score = 30.8 bits (68), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 18/87 (20%), Positives = 42/87 (48%), Gaps = 2/87 (2%)

Query: 47  REKLLNKLKSARFRYLNEQLYTSKSEESKDFFTEDRESFEAYHEGFKKQVTQWPINPVDI 106
           R+K   K++      L+  +Y  ++ +    F  DRE ++ + + F  + T      ++ 
Sbjct: 557 RQKAAEKVRDVAAELLD--IYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINA 614

Query: 107 IIKSIQERESKGRLVIADLGCGEAKLA 133
           ++  + +  +  RLV  D+G G+ ++A
Sbjct: 615 VLSDMCQPLAMDRLVCGDVGFGKTEVA 641


>pdb|4HG2|A Chain A, The Structure Of A Putative Type Ii Methyltransferase From
           Anaeromyxobacter Dehalogenans.
 pdb|4HG2|B Chain B, The Structure Of A Putative Type Ii Methyltransferase From
           Anaeromyxobacter Dehalogenans
          Length = 257

 Score = 29.6 bits (65), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 31/133 (23%), Positives = 53/133 (39%), Gaps = 23/133 (17%)

Query: 75  KDFFTEDRESFEAYHEGFKKQVTQWPINPVDIIIKSIQERESKGRLVIADLGCGEAKLAA 134
           KD FT   +++ A+   + + + +W        +  +    +  R    D GCG  + + 
Sbjct: 8   KDHFTPVADAYRAFRPRYPRALFRW--------LGEV----APARGDALDCGCGSGQASL 55

Query: 135 ELTQ--HKVHSLDL-------VALNERVT--SCDMTRTPLKPYSVDVAVFCLSLMGTDLA 183
            L +   +VH++D           + RVT        T L P SVDVA+   +    DL 
Sbjct: 56  GLAEFFERVHAVDPGEAQIRQALRHPRVTYAVAPAEDTGLPPASVDVAIAAQAXHWFDLD 115

Query: 184 ACIKEANRILKLG 196
               E  R+ + G
Sbjct: 116 RFWAELRRVARPG 128


>pdb|2VDV|E Chain E, Structure Of Trm8, M7g Methylation Enzyme
 pdb|2VDV|F Chain F, Structure Of Trm8, M7g Methylation Enzyme
          Length = 246

 Score = 27.7 bits (60), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 14/58 (24%), Positives = 28/58 (48%), Gaps = 7/58 (12%)

Query: 87  AYHEGFKKQVTQWPINPVDI-------IIKSIQERESKGRLVIADLGCGEAKLAAELT 137
           A+   F     ++P++P D+         K+ +  +   ++ IAD+GCG   L  +L+
Sbjct: 11  AHSNPFSDHQLEYPVSPQDMDWSKLYPYYKNAENGQMTKKVTIADIGCGFGGLMIDLS 68


>pdb|2VDU|E Chain E, Structure Of Trm8-Trm82, The Yeast Trna M7g Methylation
           Complex
 pdb|2VDU|F Chain F, Structure Of Trm8-Trm82, The Yeast Trna M7g Methylation
           Complex
          Length = 254

 Score = 27.3 bits (59), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 14/58 (24%), Positives = 28/58 (48%), Gaps = 7/58 (12%)

Query: 87  AYHEGFKKQVTQWPINPVDI-------IIKSIQERESKGRLVIADLGCGEAKLAAELT 137
           A+   F     ++P++P D+         K+ +  +   ++ IAD+GCG   L  +L+
Sbjct: 19  AHSNPFSDHQLEYPVSPQDMDWSKLYPYYKNAENGQMTKKVTIADIGCGFGGLMIDLS 76


  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
   0.314    0.129    0.364 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,445,174
Number of Sequences: 62578
Number of extensions: 208009
Number of successful extensions: 470
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 466
Number of HSP's gapped (non-prelim): 9
length of query: 196
length of database: 14,973,337
effective HSP length: 94
effective length of query: 102
effective length of database: 9,091,005
effective search space: 927282510
effective search space used: 927282510
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)