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= 039929
         (113 letters)

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

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



>pdb|1ZXU|A Chain A, X-Ray Structure Of Protein From Arabidopsis Thaliana
           At5g01750
 pdb|2Q4M|A Chain A, Ensemble Refinement Of The Crystal Structure Of Protein
           From Arabidopsis Thaliana At5g01750
          Length = 217

 Score =  165 bits (417), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 71/110 (64%), Positives = 90/110 (81%)

Query: 1   QVFRGESTEPQDLIFSAKMSSMWNVRTKLDVFLANNTKEDVCDFRVKGSWFERSCTIYAG 60
           QVFRG ST+ +DL+++ K SS   ++TKLDVFL +N  E  CDFRVKGSW ERSC +YAG
Sbjct: 103 QVFRGGSTDQRDLLYTVKRSSXLQLKTKLDVFLGHNKDEKRCDFRVKGSWLERSCVVYAG 162

Query: 61  ESSTIIAQMHKKHTVQSILIGKDNFAVTVYPNIDYAFIVALIVILDEINH 110
           ES  I+AQ H+KHTVQS+ +GKDNF+VTVYPN+DYAFI +L+VILD++N 
Sbjct: 163 ESDAIVAQXHRKHTVQSVFLGKDNFSVTVYPNVDYAFIASLVVILDDVNR 212


>pdb|3ZVK|A Chain A, Crystal Structure Of Vapbc2 From Rickettsia Felis Bound To
           A Dna Fragment From Their Promoter
 pdb|3ZVK|B Chain B, Crystal Structure Of Vapbc2 From Rickettsia Felis Bound To
           A Dna Fragment From Their Promoter
 pdb|3ZVK|C Chain C, Crystal Structure Of Vapbc2 From Rickettsia Felis Bound To
           A Dna Fragment From Their Promoter
 pdb|3ZVK|D Chain D, Crystal Structure Of Vapbc2 From Rickettsia Felis Bound To
           A Dna Fragment From Their Promoter
          Length = 134

 Score = 26.9 bits (58), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 17/62 (27%)

Query: 26  RTKLDVFLANNTKEDVCDFRVKGSWFERSCTIYAGESSTIIAQMHKKHTVQSILIGKDNF 85
           ++KLD+FL   ++ ++ DF  K       CT Y GE  T + Q       + ++IG ++ 
Sbjct: 58  QSKLDIFL---SRLEIIDFSAK-------CTFYYGELRTELEQ-------KGLIIGNNDL 100

Query: 86  AV 87
            +
Sbjct: 101 LI 102


>pdb|2O05|A Chain A, Human Spermidine Synthase
 pdb|2O05|B Chain B, Human Spermidine Synthase
 pdb|2O06|A Chain A, Human Spermidine Synthase
 pdb|2O06|B Chain B, Human Spermidine Synthase
 pdb|2O07|A Chain A, Human Spermidine Synthase
 pdb|2O07|B Chain B, Human Spermidine Synthase
 pdb|2O0L|A Chain A, Human Spermidine Synthase
 pdb|2O0L|B Chain B, Human Spermidine Synthase
          Length = 304

 Score = 26.9 bits (58), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 12/51 (23%), Positives = 28/51 (54%), Gaps = 7/51 (13%)

Query: 46 VKGSWFERSCTIYAGESSTI-IAQM--HKKHTVQSILIGKDNFAVTVYPNI 93
          ++  WF  +C+++ G++ ++ + Q+  H++   Q IL+    F    Y N+
Sbjct: 18 IREGWFRETCSLWPGQALSLQVEQLLHHRRSRYQDILV----FRSKTYGNV 64


>pdb|3RW9|A Chain A, Crystal Structure Of Human Spermidine Synthase In
          Complex With Decarboxylated S-Adenosylhomocysteine
 pdb|3RW9|B Chain B, Crystal Structure Of Human Spermidine Synthase In
          Complex With Decarboxylated S-Adenosylhomocysteine
          Length = 304

 Score = 26.6 bits (57), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 12/51 (23%), Positives = 28/51 (54%), Gaps = 7/51 (13%)

Query: 46 VKGSWFERSCTIYAGESSTI-IAQM--HKKHTVQSILIGKDNFAVTVYPNI 93
          ++  WF  +C+++ G++ ++ + Q+  H++   Q IL+    F    Y N+
Sbjct: 18 IREGWFRETCSLWPGQALSLQVEQLLHHRRSRYQDILV----FRSKTYGNV 64


  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    0.133    0.391 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,111,523
Number of Sequences: 62578
Number of extensions: 102175
Number of successful extensions: 280
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 279
Number of HSP's gapped (non-prelim): 4
length of query: 113
length of database: 14,973,337
effective HSP length: 77
effective length of query: 36
effective length of database: 10,154,831
effective search space: 365573916
effective search space used: 365573916
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: 45 (21.9 bits)