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= 029185
         (197 letters)

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

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



>pdb|2XF2|A Chain A, Pvc-At
 pdb|2XF2|E Chain E, Pvc-At
          Length = 688

 Score = 29.6 bits (65), Expect = 1.1,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 8/55 (14%)

Query: 95  GEQLAQKQYEILRRKEFANVYLPYGFYAGRFDCSNTMGLMQIMNEEEKKKFGFDM 149
            +Q A K  + +R+  F ++       AGRF     +G+ QIM E+++ KFGFD+
Sbjct: 242 AQQTAGKNADFMRQDLFQSIQ------AGRFP-EWELGV-QIMQEQDQLKFGFDL 288


>pdb|2IUF|A Chain A, The Structures Of Penicillium Vitale Catalase: Resting
           State, Oxidised State (Compound I) And Complex With
           Aminotriazole
 pdb|2IUF|E Chain E, The Structures Of Penicillium Vitale Catalase: Resting
           State, Oxidised State (Compound I) And Complex With
           Aminotriazole
          Length = 688

 Score = 28.5 bits (62), Expect = 2.6,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 30/55 (54%), Gaps = 8/55 (14%)

Query: 95  GEQLAQKQYEILRRKEFANVYLPYGFYAGRFDCSNTMGLMQIMNEEEKKKFGFDM 149
            +Q A K  +  R+  F ++       AGRF     +G+ QIM E+++ KFGFD+
Sbjct: 242 AQQTAGKNADFXRQDLFQSIQ------AGRFP-EWELGV-QIMQEQDQLKFGFDL 288


>pdb|3IIU|M Chain M, Structure Of The Reconstituted Peridinin-Chlorophyll
           A-Protein (Rfpcp) Mutant N89l
          Length = 151

 Score = 27.3 bits (59), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 3/40 (7%)

Query: 10  IAKHGQVVIQKPE---VKVYQIASSVTNPLVTKYLMSLLH 46
           +A  G+V+   PE   + VY   S +T+P V  Y+ SL++
Sbjct: 90  LAALGRVIASVPENMVMDVYDSVSKITDPKVPAYMKSLVN 129


>pdb|3IIS|M Chain M, Structure Of The Reconstituted Peridinin-Chlorophyll
           A-Protein (Rfpcp)
 pdb|2X1Z|M Chain M, Structure Of Peridinin-Chlorophyll-Protein Reconstituted
           With Chl-D
 pdb|2X20|M Chain M, Structure Of Peridinin-Chlorophyll-Protein Reconstituted
           With Chl-B
 pdb|2X21|M Chain M, Structure Of Peridinin-Chlorophyll-Protein Reconstituted
           With Bchl-A
          Length = 151

 Score = 27.3 bits (59), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 9/47 (19%)

Query: 3   VNATLAAIAKHGQVVIQKPE---VKVYQIASSVTNPLVTKYLMSLLH 46
           VNA L      G+V+   PE   + VY   S +T+P V  Y+ SL++
Sbjct: 89  VNAAL------GRVIASVPENMVMDVYDSVSKITDPKVPAYMKSLVN 129


>pdb|1PPR|M Chain M, Peridinin-Chlorophyll-Protein Of Amphidinium Carterae
 pdb|1PPR|N Chain N, Peridinin-Chlorophyll-Protein Of Amphidinium Carterae
 pdb|1PPR|O Chain O, Peridinin-Chlorophyll-Protein Of Amphidinium Carterae
          Length = 312

 Score = 26.6 bits (57), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 9/47 (19%)

Query: 3   VNATLAAIAKHGQVVIQKPE---VKVYQIASSVTNPLVTKYLMSLLH 46
           VNA L      G+V+   PE   + VY   S +T+P V  Y+ SL++
Sbjct: 88  VNAAL------GRVIASVPENMVMDVYDSVSKITDPKVPAYMKSLVN 128


  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
   0.319    0.135    0.390 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,912,459
Number of Sequences: 62578
Number of extensions: 239722
Number of successful extensions: 460
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 459
Number of HSP's gapped (non-prelim): 16
length of query: 197
length of database: 14,973,337
effective HSP length: 94
effective length of query: 103
effective length of database: 9,091,005
effective search space: 936373515
effective search space used: 936373515
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: 49 (23.5 bits)