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= psy3604
         (496 letters)

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

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



>pdb|1VS3|A Chain A, Crystal Structure Of The Trna Pseudouridine Synthase Trua
           From Thermus Thermophilus Hb8
 pdb|1VS3|B Chain B, Crystal Structure Of The Trna Pseudouridine Synthase Trua
           From Thermus Thermophilus Hb8
          Length = 249

 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/81 (33%), Positives = 37/81 (45%), Gaps = 18/81 (22%)

Query: 223 LNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKY-----------------WFPQAGLDI 265
           LN  LP D+KVV    V   + AR D L+R Y+Y                 W  +  LD+
Sbjct: 79  LNRLLPEDLKVVGAREVAPDFHARKDALWRAYRYRILVRPHPSPLLRHRALWVRRP-LDL 137

Query: 266 DAMHKAAQYLVGTHDFRNLCK 286
           +AM +A   L+G H+F    K
Sbjct: 138 EAMEEALSLLLGRHNFLGFAK 158


>pdb|2NQP|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
           Complex With Leucyl Trna
 pdb|2NQP|B Chain B, Crystal Structure Of Pseudoudirinde Synthase Trua In
           Complex With Leucyl Trna
 pdb|2NQP|C Chain C, Crystal Structure Of Pseudoudirinde Synthase Trua In
           Complex With Leucyl Trna
 pdb|2NQP|D Chain D, Crystal Structure Of Pseudoudirinde Synthase Trua In
           Complex With Leucyl Trna
 pdb|2NR0|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
           Complex With Leucyl Trna
 pdb|2NR0|B Chain B, Crystal Structure Of Pseudoudirinde Synthase Trua In
           Complex With Leucyl Trna
 pdb|2NR0|C Chain C, Crystal Structure Of Pseudoudirinde Synthase Trua In
           Complex With Leucyl Trna
 pdb|2NR0|D Chain D, Crystal Structure Of Pseudoudirinde Synthase Trua In
           Complex With Leucyl Trna
 pdb|2NRE|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
           Complex With Leucyl Trna
          Length = 270

 Score = 40.8 bits (94), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 34/75 (45%), Gaps = 16/75 (21%)

Query: 223 LNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQ----------------AGLDID 266
           +N NLP DI V     VP+ + ARF    R Y+Y                      LD +
Sbjct: 87  VNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAE 146

Query: 267 AMHKAAQYLVGTHDF 281
            MH+AAQ L+G +DF
Sbjct: 147 RMHRAAQCLLGENDF 161


>pdb|1DJ0|A Chain A, The Crystal Structure Of E. Coli Pseudouridine Synthase I
           At 1.5 Angstrom Resolution
 pdb|1DJ0|B Chain B, The Crystal Structure Of E. Coli Pseudouridine Synthase I
           At 1.5 Angstrom Resolution
          Length = 264

 Score = 40.8 bits (94), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 34/75 (45%), Gaps = 16/75 (21%)

Query: 223 LNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQ----------------AGLDID 266
           +N NLP DI V     VP+ + ARF    R Y+Y                      LD +
Sbjct: 81  VNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAE 140

Query: 267 AMHKAAQYLVGTHDF 281
            MH+AAQ L+G +DF
Sbjct: 141 RMHRAAQCLLGENDF 155


>pdb|2BTQ|B Chain B, Structure Of Btubab Heterodimer From Prosthecobacter
           Dejongeii
          Length = 426

 Score = 32.3 bits (72), Expect = 0.66,   Method: Compositional matrix adjust.
 Identities = 15/37 (40%), Positives = 22/37 (59%), Gaps = 2/37 (5%)

Query: 237 SPVPEKYSARFDCLFRNYKY--WFPQAGLDIDAMHKA 271
           + V E+  A+FD +F N+ Y  W+  AG+  D M KA
Sbjct: 375 AAVFERLIAQFDIMFDNHAYTHWYENAGVSRDMMAKA 411


>pdb|3N89|A Chain A, Kh Domains
 pdb|3N89|B Chain B, Kh Domains
          Length = 376

 Score = 32.0 bits (71), Expect = 0.79,   Method: Compositional matrix adjust.
 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 2/55 (3%)

Query: 355 QFPWSSTGATTPNELFRRVFLLSFLAWVDQYR--IRQTAHCNIFTNLCTFYVPTY 407
           Q P  S G TTP+   ++V +  +   VD+ R  +R+  H  +F  L    +P +
Sbjct: 66  QLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRNCHFTVFMALSKMKMPLH 120


  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    0.134    0.406 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,804,345
Number of Sequences: 62578
Number of extensions: 563581
Number of successful extensions: 1036
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1030
Number of HSP's gapped (non-prelim): 5
length of query: 496
length of database: 14,973,337
effective HSP length: 103
effective length of query: 393
effective length of database: 8,527,803
effective search space: 3351426579
effective search space used: 3351426579
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)