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= 028543
         (207 letters)

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

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



>pdb|3BF0|A Chain A, Crystal Structure Of Escherichia Coli Signal Peptide
           Peptidase (Sppa), Native Crystals
 pdb|3BF0|B Chain B, Crystal Structure Of Escherichia Coli Signal Peptide
           Peptidase (Sppa), Native Crystals
 pdb|3BF0|C Chain C, Crystal Structure Of Escherichia Coli Signal Peptide
           Peptidase (Sppa), Native Crystals
 pdb|3BF0|D Chain D, Crystal Structure Of Escherichia Coli Signal Peptide
           Peptidase (Sppa), Native Crystals
          Length = 593

 Score = 30.4 bits (67), Expect = 0.67,   Method: Compositional matrix adjust.
 Identities = 28/117 (23%), Positives = 50/117 (42%), Gaps = 11/117 (9%)

Query: 60  LFDIMDTIVRDPFYHDVPAFFGMSMKELIECKHPNAWIEFEMGMISEMELARKFFTDGRP 119
           LFDI++TI +     ++     M +K       P+      M  I +    ++F   G+P
Sbjct: 72  LFDIVNTIRQAKDDRNITGIV-MDLKNFAGGDQPS------MQYIGKA--LKEFRDSGKP 122

Query: 120 FDLEGLKICMKKGYAYLDGVEELLHELKQSNYEMHAFTNYPIWYEIIEDKLKISTYL 176
               G      +G  YL      +    Q   ++H F    ++Y+ + DKLK+ST++
Sbjct: 123 VYAVGENYS--QGQYYLASFANKIWLSPQGVVDLHGFATNGLYYKSLLDKLKVSTHV 177


>pdb|2RC7|A Chain A, Crystal Structure Of The Nr3a Ligand Binding Core Complex
           With Glycine At 1.58 Angstrom Resolution
 pdb|2RC8|A Chain A, Crystal Structure Of The Nr3a Ligand Binding Core Complex
           With D- Serine At 1.45 Angstrom Resolution
 pdb|2RC8|B Chain B, Crystal Structure Of The Nr3a Ligand Binding Core Complex
           With D- Serine At 1.45 Angstrom Resolution
 pdb|2RC9|A Chain A, Crystal Structure Of The Nr3a Ligand Binding Core Complex
           With Acpc At 1.96 Angstrom Resolution
 pdb|2RC9|B Chain B, Crystal Structure Of The Nr3a Ligand Binding Core Complex
           With Acpc At 1.96 Angstrom Resolution
 pdb|2RC7|B Chain B, Crystal Structure Of The Nr3a Ligand Binding Core Complex
           With Glycine At 1.58 Angstrom Resolution
          Length = 294

 Score = 29.6 bits (65), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 11/74 (14%)

Query: 95  AWIEFEMGMISEMELARKFFTDGRPFDLEGLKICMKKGYAYLDGVEELLHELKQSNYEMH 154
           A +++E+ + ++     K  T G+PF +EG  I +         + EL+     S Y+ H
Sbjct: 226 ALLDYEVSIDADC----KLLTVGKPFAIEGYGIGLPPNSPLTSNISELI-----SQYKSH 276

Query: 155 AFTN--YPIWYEII 166
            F +  +  WY+++
Sbjct: 277 GFMDVLHDKWYKVV 290


>pdb|3BEZ|A Chain A, Crystal Structure Of Escherichia Coli Signal Peptide
           Peptidase (Sppa), Semet Crystals
 pdb|3BEZ|B Chain B, Crystal Structure Of Escherichia Coli Signal Peptide
           Peptidase (Sppa), Semet Crystals
 pdb|3BEZ|C Chain C, Crystal Structure Of Escherichia Coli Signal Peptide
           Peptidase (Sppa), Semet Crystals
 pdb|3BEZ|D Chain D, Crystal Structure Of Escherichia Coli Signal Peptide
           Peptidase (Sppa), Semet Crystals
          Length = 593

 Score = 27.7 bits (60), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 2/66 (3%)

Query: 111 RKFFTDGRPFDLEGLKICMKKGYAYLDGVEELLHELKQSNYEMHAFTNYPIWYEIIEDKL 170
           ++F   G+P    G      +G  YL      +    Q   ++H F    ++Y+ + DKL
Sbjct: 114 KEFRDSGKPVYAVGENYS--QGQYYLASFANKIWLSPQGVVDLHGFATNGLYYKSLLDKL 171

Query: 171 KISTYL 176
           K+ST++
Sbjct: 172 KVSTHV 177


  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
   0.325    0.139    0.426 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,831,309
Number of Sequences: 62578
Number of extensions: 227391
Number of successful extensions: 574
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: 570
Number of HSP's gapped (non-prelim): 6
length of query: 207
length of database: 14,973,337
effective HSP length: 94
effective length of query: 113
effective length of database: 9,091,005
effective search space: 1027283565
effective search space used: 1027283565
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)