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= 044932
         (689 letters)

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

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



>pdb|2AVN|A Chain A, Crystal Structure Of A UbiquinoneMENAQUINONE BIOSYNTHESIS
           Methyltransferase-Related Protein (Tm1389) From
           Thermotoga Maritima Msb8 At 2.35 A Resolution
 pdb|2AVN|B Chain B, Crystal Structure Of A UbiquinoneMENAQUINONE BIOSYNTHESIS
           Methyltransferase-Related Protein (Tm1389) From
           Thermotoga Maritima Msb8 At 2.35 A Resolution
          Length = 260

 Score = 40.4 bits (93), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 347 QVALERGFPAVVSPLGNRRLPFPSGVFDAIHCDGCSITWHAHGGKLLLEMNRILRPSGYF 406
           +VA E+G   VV       LPFPSG F+A+   G  +++  +  K   E+ R+L P G  
Sbjct: 90  EVAREKGVKNVVEAKAED-LPFPSGAFEAVLALGDVLSYVENKDKAFSEIRRVLVPDGLL 148

Query: 407 ILSTKH 412
           I +  +
Sbjct: 149 IATVDN 154


>pdb|4A17|B Chain B, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 5s Rrna, 5.8s
           Rrna And Proteins Of Molecule 2.
 pdb|4A1A|B Chain B, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 5s Rrna, 5.8s
           Rrna And Proteins Of Molecule 3.
 pdb|4A1C|B Chain B, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 5s Rrna, 5.8s
           Rrna And Proteins Of Molecule 4.
 pdb|4A1E|B Chain B, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 5s Rrna, 5.8s
           Rrna And Proteins Of Molecule 1
          Length = 391

 Score = 32.0 bits (71), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 2/67 (2%)

Query: 320 LSFVASLLAKEVLTLTVGLKDDLVDLAQVALERGFPAVVSPLGNRRLPFPSGVFDAIHCD 379
           ++F  SLL KEV   ++  +++++D+  V   +GF  V+   G + L             
Sbjct: 190 VAFAKSLLEKEVKVDSIFAENEMLDVLGVTKGKGFAGVIKRFGVKHL--QKKTHRGYRKV 247

Query: 380 GCSITWH 386
           GC   WH
Sbjct: 248 GCIGAWH 254


>pdb|1PHP|A Chain A, Structure Of The Adp Complex Of The 3-Phosphoglycerate
           Kinase From Bacillus Stearothermophilus At 1.65
           Angstroms
          Length = 394

 Score = 31.6 bits (70), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 7/80 (8%)

Query: 7   FDDIAEPVSADTKVISSKPQYTERKRQWHEIGK---EEDKKVKLESDLDKAKEKKINGSA 63
            D++ E V  D  +I     YT  K   H++GK   EEDK    +S ++KAKEK +    
Sbjct: 205 IDNLLEKV--DNLIIGGGLAYTFVKALGHDVGKSLLEEDKIELAKSFMEKAKEKGVRFYM 262

Query: 64  SVTVIKHE--SRKKNEKTVP 81
            V V+  +  +   N K VP
Sbjct: 263 PVDVVVADRFANDANTKVVP 282


>pdb|3IZR|C Chain C, Localization Of The Large Subunit Ribosomal Proteins Into
           A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
           Ribosome
          Length = 389

 Score = 30.4 bits (67), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 2/61 (3%)

Query: 326 LLAKEVLTLTVGLKDDLVDLAQVALERGFPAVVSPLGNRRLPFPSGVFDAIHCDGCSITW 385
              KEV    V  KD++VD+  V   +G+  VV+  G  RLP  +     +    C   W
Sbjct: 201 FFEKEVPVEAVFQKDEMVDIIGVTKGKGYEGVVTRWGVTRLPRKT--HRGLRKVACIGAW 258

Query: 386 H 386
           H
Sbjct: 259 H 259


>pdb|3L8D|A Chain A, Crystal Structure Of Methyltransferase From Bacillus
           Thuringiensis
          Length = 242

 Score = 29.6 bits (65), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 31/127 (24%), Positives = 53/127 (41%), Gaps = 23/127 (18%)

Query: 305 WGKNIRVVLEIGSAD--LSFVASLLAKEVLTLTVGLKDDL--------------VDLAQV 348
           W +N +   + GS    + F    + KE   L VG  D                VD+++V
Sbjct: 27  WNQNSQEXWDSGSRSTIIPFFEQYVKKEAEVLDVGCGDGYGTYKLSRTGYKAVGVDISEV 86

Query: 349 ALERG-----FPAVVSPLGN-RRLPFPSGVFDAIHCDGCSITWHAHGGKLLLEMNRILRP 402
            +++G      P +    G+   LPF +  F+AI     S+ W     + L E+ R+L+ 
Sbjct: 87  XIQKGKERGEGPDLSFIKGDLSSLPFENEQFEAIXAIN-SLEWTEEPLRALNEIKRVLKS 145

Query: 403 SGYFILS 409
            GY  ++
Sbjct: 146 DGYACIA 152


  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
   0.317    0.134    0.416 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,989,750
Number of Sequences: 62578
Number of extensions: 914528
Number of successful extensions: 2003
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1995
Number of HSP's gapped (non-prelim): 19
length of query: 689
length of database: 14,973,337
effective HSP length: 105
effective length of query: 584
effective length of database: 8,402,647
effective search space: 4907145848
effective search space used: 4907145848
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: 55 (25.8 bits)