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= 048268
         (244 letters)

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

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



>pdb|3VOX|A Chain A, X-Ray Crystal Structure Of Wild Type Hrtr In The Apo Form
 pdb|3VOX|B Chain B, X-Ray Crystal Structure Of Wild Type Hrtr In The Apo Form
 pdb|3VOX|C Chain C, X-Ray Crystal Structure Of Wild Type Hrtr In The Apo Form
 pdb|3VOX|D Chain D, X-Ray Crystal Structure Of Wild Type Hrtr In The Apo Form
 pdb|3VP5|A Chain A, X-Ray Crystal Structure Of Wild Type Hrtr In The Holo Form
 pdb|3VOK|A Chain A, X-Ray Crystal Structure Of Wild Type Hrtr In The Apo Form
           With The Target Dna
          Length = 189

 Score = 28.1 bits (61), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 13/34 (38%), Positives = 22/34 (64%)

Query: 53  TIELDPDYKPPATASVTSTARENKNEGGTESVVH 86
           T EL+ D+KP ++A+V ++  +N      +SVVH
Sbjct: 116 TYELERDWKPQSSATVPASENDNPISQVLKSVVH 149


>pdb|1I78|A Chain A, Crystal Structure Of Outer Membrane Protease Ompt From
           Escherichia Coli
 pdb|1I78|B Chain B, Crystal Structure Of Outer Membrane Protease Ompt From
           Escherichia Coli
          Length = 297

 Score = 27.3 bits (59), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 29/103 (28%), Positives = 40/103 (38%), Gaps = 9/103 (8%)

Query: 111 KAFDEKHRFTSTATATVASL---DQKIGFTEKISAGTTLVNDKVREMDEKFHVSEKTKSA 167
           +A   K RF         S    D ++G T K S G    +D     D K  ++ ++K  
Sbjct: 168 RAIGYKQRFKMPYIGLTGSYRYEDFELGGTFKYS-GWVESSDNDEHYDPKGRITYRSKVK 226

Query: 168 FSAAEQTVSNAGSAIMKNRYVLTGASWVTGAFNRVTKAAGEVS 210
                    NAG  +  N  V     +V GA+NRVT   G  S
Sbjct: 227 DQNYYSVAVNAGYYVTPNAKV-----YVEGAWNRVTNKKGNTS 264


>pdb|1VPA|A Chain A, Crystal Structure Of 2-C-Methyl-D-Erythritol 4-Phosphate
           Cytidylyltransferase (Tm1393) From Thermotoga Maritima
           At 2.67 A Resolution
 pdb|1VPA|B Chain B, Crystal Structure Of 2-C-Methyl-D-Erythritol 4-Phosphate
           Cytidylyltransferase (Tm1393) From Thermotoga Maritima
           At 2.67 A Resolution
          Length = 234

 Score = 27.3 bits (59), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 34/85 (40%), Gaps = 9/85 (10%)

Query: 92  VSTMLAKGFILGKDAVGKAKAFD--EKHRFTSTATATVASLDQK-------IGFTEKISA 142
           +ST L    I G   V + + F+  EK  F       V   D +       + F EK S 
Sbjct: 48  LSTFLKSEAIDGVVIVTRREWFEVVEKRVFHEKVLGIVEGGDTRSQSVRSALEFLEKFSP 107

Query: 143 GTTLVNDKVREMDEKFHVSEKTKSA 167
              LV+D  R    K HVSE  + A
Sbjct: 108 SYVLVHDSARPFLRKKHVSEVLRRA 132


  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
   0.309    0.123    0.331 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,277,921
Number of Sequences: 62578
Number of extensions: 224507
Number of successful extensions: 542
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 539
Number of HSP's gapped (non-prelim): 16
length of query: 244
length of database: 14,973,337
effective HSP length: 96
effective length of query: 148
effective length of database: 8,965,849
effective search space: 1326945652
effective search space used: 1326945652
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 50 (23.9 bits)