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= psy1181
         (82 letters)

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

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



>pdb|2JVM|A Chain A, Solution Nmr Structure Of Rhodobacter Sphaeroides
          Protein Rhos4_26430. Northeast Structural Genomics
          Consortium Target Rhr95
          Length = 80

 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 17/39 (43%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 41 VWCDGGSGPTGHPKVYINL-DKPGNHSCGYCGLRFFKED 78
          V CDGG G  GHP+V++++  + G   CGYC  R+  E 
Sbjct: 29 VACDGGEGALGHPRVWLSIPHETGFVECGYCDRRYIHES 67


>pdb|2JRR|A Chain A, Solution Nmr Structure Of Q5lls5 From Silicibacter
          Pomeroyi. Northeast Structural Genomics Consortium
          Target Sir90
          Length = 67

 Score = 33.5 bits (75), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 2/44 (4%)

Query: 37 KERVVWCDGGSGPTGHPKVYINL-DKPGNHSCGYCGLRFFKEDS 79
          K RV  CDGG G  GHP+V++ + +  G   C YC  ++  + S
Sbjct: 13 KSRVA-CDGGEGALGHPRVWLQIPEDTGWVECPYCDCKYVLKGS 55


>pdb|3D5P|A Chain A, Crystal Structure Of A Putative Glucan Synthesis
          Regulator Of Smi1KNR4 FAMILY (BF1740) FROM BACTEROIDES
          FRAGILIS NCTC 9343 AT 1.45 A Resolution
 pdb|3D5P|B Chain B, Crystal Structure Of A Putative Glucan Synthesis
          Regulator Of Smi1KNR4 FAMILY (BF1740) FROM BACTEROIDES
          FRAGILIS NCTC 9343 AT 1.45 A Resolution
          Length = 144

 Score = 31.6 bits (70), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 9/56 (16%)

Query: 2  FEKDDYRPVRFVDKEKHVNTQFAIDLIAEVPPKPCKERVVWCDGGSGPTGHPKVYI 57
          ++KD        D EK +NT           PK  K  ++W +GG G  G   +YI
Sbjct: 10 YKKDGASSASIDDVEKLLNTTL---------PKQYKSFLLWSNGGEGKLGDNYIYI 56


>pdb|2JZ8|A Chain A, Solution Nmr Structure Of Bh09830 From Bartonella
          Henselae Modeled With One Zn+2 Bound. Northeast
          Structural Genomics Consortium Target Bnr55
          Length = 87

 Score = 25.8 bits (55), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 9/33 (27%), Positives = 15/33 (45%)

Query: 42 WCDGGSGPTGHPKVYINLDKPGNHSCGYCGLRF 74
           C G + P  HP ++I++       C YC   +
Sbjct: 26 MCVGATQPFDHPHIFIDMGSTDEKICPYCSTLY 58


  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
   0.321    0.143    0.486 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,172,133
Number of Sequences: 62578
Number of extensions: 121966
Number of successful extensions: 188
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 184
Number of HSP's gapped (non-prelim): 4
length of query: 82
length of database: 14,973,337
effective HSP length: 51
effective length of query: 31
effective length of database: 11,781,859
effective search space: 365237629
effective search space used: 365237629
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: 45 (21.9 bits)