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= psy2312
         (392 letters)

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

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



>pdb|1L0Q|A Chain A, Tandem Yvtn Beta-Propeller And Pkd Domains From An
           Archaeal Surface Layer Protein
 pdb|1L0Q|B Chain B, Tandem Yvtn Beta-Propeller And Pkd Domains From An
           Archaeal Surface Layer Protein
 pdb|1L0Q|C Chain C, Tandem Yvtn Beta-Propeller And Pkd Domains From An
           Archaeal Surface Layer Protein
 pdb|1L0Q|D Chain D, Tandem Yvtn Beta-Propeller And Pkd Domains From An
           Archaeal Surface Layer Protein
          Length = 391

 Score = 29.6 bits (65), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 35/116 (30%), Positives = 59/116 (50%), Gaps = 17/116 (14%)

Query: 160 VPKGVSMTLNVPKGVSITPNVPKGISMTPNVPRGISMTPNVSKGVSMTPNVSK---GVSM 216
           VP G S     P+GV+++P+  K + +T      +S+    S  V+ T    K   G+++
Sbjct: 70  VPAGSS-----PQGVAVSPD-GKQVYVTNXASSTLSVIDTTSNTVAGTVKTGKSPLGLAL 123

Query: 217 TPNVPKSVSLTPNVPKGVSITPNVPKGVTMTPNVPKGVSITPNVPKGISITPNVSK 272
           +P+  K + +T N  K VS+   V K V  T +V +        PKGI++TP+ +K
Sbjct: 124 SPD-GKKLYVTNNGDKTVSVINTVTKAVINTVSVGRS-------PKGIAVTPDGTK 171



 Score = 28.1 bits (61), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 42/139 (30%), Positives = 67/139 (48%), Gaps = 15/139 (10%)

Query: 68  SPLPKGISITPNVPKGISVTPNVPKGVSMTLNV---PKGVSITPNVPKGISMTPNVPRGI 124
           SP  K + +T N  K +SV   V K V  T++V   PKG+++TP+  K + +       I
Sbjct: 124 SPDGKKLYVTNNGDKTVSVINTVTKAVINTVSVGRSPKGIAVTPDGTK-VYVANFDSXSI 182

Query: 125 SMTPNVSKGVSMTPNVSK---GVSMTPNVPKSVSLTPNVPKGVSMTLNVPKGVS-ITPNV 180
           S+   V+  V  T  V     G+++ P   K  +   NV K  +    +  G + IT  +
Sbjct: 183 SVIDTVTNSVIDTVKVEAAPSGIAVNPEGTK--AYVTNVDKYFNTVSXIDTGTNKITARI 240

Query: 181 PKGISMTPNVPRGISMTPN 199
           P G    P+ P GI++TP+
Sbjct: 241 PVG----PD-PAGIAVTPD 254


>pdb|2O26|A Chain A, Structure Of A Class Iii Rtk Signaling Assembly
 pdb|2O26|B Chain B, Structure Of A Class Iii Rtk Signaling Assembly
 pdb|2O26|E Chain E, Structure Of A Class Iii Rtk Signaling Assembly
 pdb|2O26|F Chain F, Structure Of A Class Iii Rtk Signaling Assembly
 pdb|2O27|A Chain A, Structure Of A Class Iii Rtk Signaling Assembly
 pdb|2O27|B Chain B, Structure Of A Class Iii Rtk Signaling Assembly
          Length = 145

 Score = 28.5 bits (62), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 26/105 (24%), Positives = 46/105 (43%), Gaps = 12/105 (11%)

Query: 146 MTPNVPKSVSLTPNVPKGVSMTLNVPKGVSITPN----VPKGISMTPNVPRGISMTPNVS 201
           +T NV     L  N+P    +TLN   G+ + P+        I ++ ++   +    N+S
Sbjct: 6   VTDNVKDITKLVANLPNDYMITLNYVAGMDVLPSHCWLRDMVIQLSLSLTTLLDKFSNIS 65

Query: 202 KGVSMTPNVSKG--------VSMTPNVPKSVSLTPNVPKGVSITP 238
           +G+S    + K         + M  N PK++  +P  P+  S TP
Sbjct: 66  EGLSNYSIIDKLGKIVDDLVLCMEENAPKNIKESPKRPETRSFTP 110


  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
   0.307    0.126    0.361 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,826,500
Number of Sequences: 62578
Number of extensions: 496404
Number of successful extensions: 940
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 899
Number of HSP's gapped (non-prelim): 54
length of query: 392
length of database: 14,973,337
effective HSP length: 101
effective length of query: 291
effective length of database: 8,652,959
effective search space: 2518011069
effective search space used: 2518011069
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 52 (24.6 bits)