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= 041690
         (233 letters)

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

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



>pdb|1VGM|A Chain A, Crystal Structure Of An Isozyme Of Citrate Synthase From
           Sulfolbus Tokodaii Strain7
 pdb|1VGM|B Chain B, Crystal Structure Of An Isozyme Of Citrate Synthase From
           Sulfolbus Tokodaii Strain7
          Length = 378

 Score = 36.2 bits (82), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 4/92 (4%)

Query: 18  VDPITLLSGPPCCGKTSLLFQFAYNCASQSNANVVF----MCNRSRLQSKRPYLSQSIDP 73
           V  +  L GP   G     F+      S  NA+  F    +  +SRL      + ++ DP
Sbjct: 208 VAALAALKGPLHGGAAEEAFKQFVEIGSVENADKWFEEKIIKGKSRLMGFGHRVYKTYDP 267

Query: 74  SSHVFKLIQMKYVEDDEEIKKYFAAFHQHDKI 105
            + +FK +   + E +E +KKY+    + +K+
Sbjct: 268 RAKIFKTLAKSFAEKNENVKKYYEIAERIEKL 299


>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
 pdb|2XZP|A Chain A, Upf1 Helicase
          Length = 623

 Score = 31.6 bits (70), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 13/33 (39%), Positives = 18/33 (54%)

Query: 20  PITLLSGPPCCGKTSLLFQFAYNCASQSNANVV 52
           P++L+ GPP  GKT       Y+ A Q N  V+
Sbjct: 195 PLSLIQGPPGTGKTVTSATIVYHLARQGNGPVL 227


>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1
           Helicase Core
 pdb|2GK6|A Chain A, Structural And Functional Insights Into The Human Upf1
           Helicase Core
 pdb|2GK6|B Chain B, Structural And Functional Insights Into The Human Upf1
           Helicase Core
 pdb|2GK7|A Chain A, Structural And Functional Insights Into The Human Upf1
           Helicase Core
          Length = 624

 Score = 31.2 bits (69), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 13/33 (39%), Positives = 18/33 (54%)

Query: 20  PITLLSGPPCCGKTSLLFQFAYNCASQSNANVV 52
           P++L+ GPP  GKT       Y+ A Q N  V+
Sbjct: 196 PLSLIQGPPGTGKTVTSATIVYHLARQGNGPVL 228


>pdb|2WJV|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
           Mediated Decay Factors Upf1 And Upf2
 pdb|2WJV|B Chain B, Crystal Structure Of The Complex Between Human Nonsense
           Mediated Decay Factors Upf1 And Upf2
 pdb|2WJY|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
           Mediated Decay Factors Upf1 And Upf2 Orthorhombic Form
          Length = 800

 Score = 30.8 bits (68), Expect = 0.75,   Method: Compositional matrix adjust.
 Identities = 13/33 (39%), Positives = 18/33 (54%)

Query: 20  PITLLSGPPCCGKTSLLFQFAYNCASQSNANVV 52
           P++L+ GPP  GKT       Y+ A Q N  V+
Sbjct: 372 PLSLIQGPPGTGKTVTSATIVYHLARQGNGPVL 404


>pdb|1TAZ|A Chain A, Catalytic Domain Of Human Phosphodiesterase 1b
          Length = 365

 Score = 29.6 bits (65), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 20/91 (21%), Positives = 36/91 (39%), Gaps = 6/91 (6%)

Query: 138 VRTLALCYNAITHANKKSPCKLLLSDTHLGNSTRLLYIYKRWISSI---FTVKGDGPGSF 194
           V+T+      +   +K     LLL    + + T+   ++ RW  ++   F  +GD     
Sbjct: 202 VKTMKTALQQLERIDKPKALSLLLHAADISHPTKQWLVHSRWTKALMEEFFRQGDKEAEL 261

Query: 195 LLRNKNYSRSCGLGKTRIAKYSIALKDLVFE 225
            L    +S  C    T +A+  I   D + E
Sbjct: 262 GL---PFSPLCDRTSTLVAQSQIGFIDFIVE 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
   0.321    0.135    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,442,117
Number of Sequences: 62578
Number of extensions: 227311
Number of successful extensions: 549
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 545
Number of HSP's gapped (non-prelim): 6
length of query: 233
length of database: 14,973,337
effective HSP length: 96
effective length of query: 137
effective length of database: 8,965,849
effective search space: 1228321313
effective search space used: 1228321313
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)