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= psy4586
         (294 letters)

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

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



>pdb|2LLV|A Chain A, Solution Structure Of The Yeast Sti1 Dp1 Domain
          Length = 71

 Score = 28.5 bits (62), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 11/59 (18%), Positives = 36/59 (61%)

Query: 89  IMSNPQMQDLIERNPEINHMLNNPELLRQTMEMARNPSMLQELMRTQDRALSNLESIPG 147
           + ++P + + +++NP+ + M+ +P+L+ + +   +NP  + + + T  R ++ + ++ G
Sbjct: 9   LFADPNLIENLKKNPKTSEMMKDPQLVAKLIGYKQNPQAIGQDLFTDPRLMTIMATLMG 67


>pdb|4DWR|B Chain B, Rna Ligase RtcbMN2+ COMPLEX
 pdb|4DWR|A Chain A, Rna Ligase RtcbMN2+ COMPLEX
 pdb|4DWR|C Chain C, Rna Ligase RtcbMN2+ COMPLEX
          Length = 487

 Score = 28.1 bits (61), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 13/70 (18%)

Query: 144 SIPGGYSALQRMYRDIQEPMLN-----------AATQQFSRNPYESNSSGGNPGRVKAPF 192
           + P G+ A+ R+YRD+ +P+L            A T+   +  + S   G   GRV +  
Sbjct: 356 AFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHG--AGRVLSRK 413

Query: 193 RRSKRYLGPR 202
             +++Y G R
Sbjct: 414 AATRQYRGDR 423


>pdb|1UC2|A Chain A, Hypothetical Extein Protein Of Ph1602 From Pyrococcus
           Horikoshii
 pdb|1UC2|B Chain B, Hypothetical Extein Protein Of Ph1602 From Pyrococcus
           Horikoshii
 pdb|4DWQ|A Chain A, Rtcb-GmpMN2+ COMPLEX
 pdb|4DWQ|B Chain B, Rtcb-GmpMN2+ COMPLEX
          Length = 481

 Score = 28.1 bits (61), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 13/70 (18%)

Query: 144 SIPGGYSALQRMYRDIQEPMLN-----------AATQQFSRNPYESNSSGGNPGRVKAPF 192
           + P G+ A+ R+YRD+ +P+L            A T+   +  + S   G   GRV +  
Sbjct: 356 AFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHG--AGRVLSRK 413

Query: 193 RRSKRYLGPR 202
             +++Y G R
Sbjct: 414 AATRQYRGDR 423


>pdb|1B6S|A Chain A, Structure Of N5-Carboxyaminoimidazole Ribonucleotide
           Synthetase
 pdb|1B6S|B Chain B, Structure Of N5-Carboxyaminoimidazole Ribonucleotide
           Synthetase
 pdb|1B6S|C Chain C, Structure Of N5-Carboxyaminoimidazole Ribonucleotide
           Synthetase
 pdb|1B6S|D Chain D, Structure Of N5-Carboxyaminoimidazole Ribonucleotide
           Synthetase
          Length = 355

 Score = 27.7 bits (60), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 14/27 (51%), Positives = 19/27 (70%)

Query: 66  LRTILDNPLVQGMLNDPNSMRNLIMSN 92
           LR I D PL Q ++N+P+ M NLI S+
Sbjct: 263 LRAITDLPLPQPVVNNPSVMINLIGSD 289


>pdb|1B6R|A Chain A, N5-Carboxyaminoimidazole Ribonucleotide Synthetase From E.
           Coli
 pdb|3ETH|A Chain A, Crystal Structure Of E. Coli Purk In Complex With Mgatp
 pdb|3ETH|B Chain B, Crystal Structure Of E. Coli Purk In Complex With Mgatp
 pdb|3ETJ|A Chain A, Crystal Structure E. Coli Purk In Complex With Mg, Adp,
           And Pi
 pdb|3ETJ|B Chain B, Crystal Structure E. Coli Purk In Complex With Mg, Adp,
           And Pi
          Length = 355

 Score = 27.7 bits (60), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 14/27 (51%), Positives = 19/27 (70%)

Query: 66  LRTILDNPLVQGMLNDPNSMRNLIMSN 92
           LR I D PL Q ++N+P+ M NLI S+
Sbjct: 263 LRAITDLPLPQPVVNNPSVMINLIGSD 289


  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
   0.318    0.132    0.387 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,970,407
Number of Sequences: 62578
Number of extensions: 219121
Number of successful extensions: 450
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 446
Number of HSP's gapped (non-prelim): 13
length of query: 294
length of database: 14,973,337
effective HSP length: 98
effective length of query: 196
effective length of database: 8,840,693
effective search space: 1732775828
effective search space used: 1732775828
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)