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= psy17942
         (90 letters)

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

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



>pdb|2Y69|H Chain H, Bovine Heart Cytochrome C Oxidase Re-Refined With
          Molecular Oxygen
 pdb|2Y69|U Chain U, Bovine Heart Cytochrome C Oxidase Re-Refined With
          Molecular Oxygen
          Length = 86

 Score = 32.3 bits (72), Expect = 0.070,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 4/68 (5%)

Query: 2  SFLPKEERTK-CWSARDKYWEC---LDSHEGNADSCKEFRTSYEQFCPGQWVKHFDRRYH 57
          S  P + +T+ CW     +  C   + +  G+   C+ +R  Y+  CP  WV  +D R  
Sbjct: 19 SRFPNQNQTRNCWQNYLDFHRCEKAMTAKGGDVSVCEWYRRVYKSLCPISWVSTWDDRRA 78

Query: 58 FLKFKNKI 65
             F  KI
Sbjct: 79 EGTFPGKI 86


>pdb|1OCC|H Chain H, Structure Of Bovine Heart Cytochrome C Oxidase At The
          Fully Oxidized State
 pdb|1OCC|U Chain U, Structure Of Bovine Heart Cytochrome C Oxidase At The
          Fully Oxidized State
 pdb|2OCC|H Chain H, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
          State
 pdb|2OCC|U Chain U, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
          State
 pdb|1OCO|H Chain H, Bovine Heart Cytochrome C Oxidase In Carbon
          Monoxide-bound State
 pdb|1OCO|U Chain U, Bovine Heart Cytochrome C Oxidase In Carbon
          Monoxide-bound State
 pdb|1OCR|H Chain H, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
          State
 pdb|1OCR|U Chain U, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
          State
 pdb|1OCZ|H Chain H, Bovine Heart Cytochrome C Oxidase In Azide-Bound State
 pdb|1OCZ|U Chain U, Bovine Heart Cytochrome C Oxidase In Azide-Bound State
 pdb|1V54|H Chain H, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
          State
 pdb|1V54|U Chain U, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
          State
 pdb|1V55|H Chain H, Bovine Heart Cytochrome C Oxidase At The Fully Reduced
          State
 pdb|1V55|U Chain U, Bovine Heart Cytochrome C Oxidase At The Fully Reduced
          State
 pdb|2DYR|H Chain H, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
          State
 pdb|2DYR|U Chain U, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
          State
 pdb|2DYS|H Chain H, Bovine Heart Cytochrome C Oxidase Modified By Dccd
 pdb|2DYS|U Chain U, Bovine Heart Cytochrome C Oxidase Modified By Dccd
 pdb|2EIJ|H Chain H, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
          State
 pdb|2EIJ|U Chain U, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
          State
 pdb|2EIK|H Chain H, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome
          C Oxidase In The Fully Reduced State
 pdb|2EIK|U Chain U, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome
          C Oxidase In The Fully Reduced State
 pdb|2EIL|H Chain H, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome
          C Oxidase In The Fully Oxidized State
 pdb|2EIL|U Chain U, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome
          C Oxidase In The Fully Oxidized State
 pdb|2EIM|H Chain H, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
          Oxidase In The Fully Reduced State
 pdb|2EIM|U Chain U, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
          Oxidase In The Fully Reduced State
 pdb|2EIN|H Chain H, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
          Oxidase In The Fully Oxidized State
 pdb|2EIN|U Chain U, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
          Oxidase In The Fully Oxidized State
 pdb|2ZXW|H Chain H, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
          State (1-S X-Ray Exposure Dataset)
 pdb|2ZXW|U Chain U, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
          State (1-S X-Ray Exposure Dataset)
 pdb|3ABL|H Chain H, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
          State (15-S X-Ray Exposure Dataset)
 pdb|3ABL|U Chain U, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
          State (15-S X-Ray Exposure Dataset)
 pdb|3ABM|H Chain H, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
          State (200-S X-Ray Exposure Dataset)
 pdb|3ABM|U Chain U, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
          State (200-S X-Ray Exposure Dataset)
 pdb|3ABK|H Chain H, Bovine Heart Cytochrome C Oxidase At The No-Bound Fully
          Reduced State (50k)
 pdb|3ABK|U Chain U, Bovine Heart Cytochrome C Oxidase At The No-Bound Fully
          Reduced State (50k)
 pdb|3AG1|H Chain H, Bovine Heart Cytochrome C Oxidase In The Carbon
          Monoxide-Bou Reduced State At 280 K
 pdb|3AG1|U Chain U, Bovine Heart Cytochrome C Oxidase In The Carbon
          Monoxide-Bou Reduced State At 280 K
 pdb|3AG2|H Chain H, Bovine Heart Cytochrome C Oxidase In The Carbon
          Monoxide-Bou Reduced State At 100 K
 pdb|3AG2|U Chain U, Bovine Heart Cytochrome C Oxidase In The Carbon
          Monoxide-Bou Reduced State At 100 K
 pdb|3AG3|H Chain H, Bovine Heart Cytochrome C Oxidase In The Nitric
          Oxide-Bound Reduced State At 100 K
 pdb|3AG3|U Chain U, Bovine Heart Cytochrome C Oxidase In The Nitric
          Oxide-Bound Reduced State At 100 K
 pdb|3AG4|H Chain H, Bovine Heart Cytochrome C Oxidase In The Cyanide
          Ion-Bound F Reduced State At 100 K
 pdb|3AG4|U Chain U, Bovine Heart Cytochrome C Oxidase In The Cyanide
          Ion-Bound F Reduced State At 100 K
 pdb|3ASN|H Chain H, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
          State Measured At 1.7470 Angstrom Wavelength
 pdb|3ASN|U Chain U, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
          State Measured At 1.7470 Angstrom Wavelength
 pdb|3ASO|H Chain H, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
          State Measured At 0.9 Angstrom Wavelength
 pdb|3ASO|U Chain U, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
          State Measured At 0.9 Angstrom Wavelength
 pdb|2YBB|S Chain S, Fitted Model For Bovine  Mitochondrial Supercomplex
          I1iii2iv1 By Single Particle Cryo-Em (Emd-1876)
          Length = 85

 Score = 32.3 bits (72), Expect = 0.075,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 4/68 (5%)

Query: 2  SFLPKEERTK-CWSARDKYWEC---LDSHEGNADSCKEFRTSYEQFCPGQWVKHFDRRYH 57
          S  P + +T+ CW     +  C   + +  G+   C+ +R  Y+  CP  WV  +D R  
Sbjct: 18 SRFPNQNQTRNCWQNYLDFHRCEKAMTAKGGDVSVCEWYRRVYKSLCPISWVSTWDDRRA 77

Query: 58 FLKFKNKI 65
             F  KI
Sbjct: 78 EGTFPGKI 85


>pdb|3P5B|L Chain L, The Structure Of The LdlrPCSK9 COMPLEX REVEALS THE
          RECEPTOR IN AN Extended Conformation
          Length = 400

 Score = 29.3 bits (64), Expect = 0.66,   Method: Composition-based stats.
 Identities = 10/25 (40%), Positives = 15/25 (60%)

Query: 21 ECLDSHEGNADSCKEFRTSYEQFCP 45
          ECLD++ G +  C + +  YE  CP
Sbjct: 2  ECLDNNGGCSHVCNDLKIGYECLCP 26


>pdb|3P5C|L Chain L, The Structure Of The LdlrPCSK9 COMPLEX REVEALS THE
          RECEPTOR IN AN Extended Conformation
          Length = 440

 Score = 28.5 bits (62), Expect = 0.89,   Method: Composition-based stats.
 Identities = 10/25 (40%), Positives = 15/25 (60%)

Query: 21 ECLDSHEGNADSCKEFRTSYEQFCP 45
          ECLD++ G +  C + +  YE  CP
Sbjct: 42 ECLDNNGGCSHVCNDLKIGYECLCP 66


>pdb|2W2M|E Chain E, Wt Pcsk9-Deltac Bound To Wt Egf-A Of Ldlr
 pdb|2W2O|E Chain E, Pcsk9-deltac D374y Mutant Bound To Wt Egf-a Of Ldlr
 pdb|2W2P|E Chain E, Pcsk9-Deltac D374a Mutant Bound To Wt Egf-A Of Ldlr
 pdb|2W2Q|E Chain E, Pcsk9-Deltac D374h Mutant Bound To Wt Egf-A Of Ldlr
          Length = 107

 Score = 28.5 bits (62), Expect = 0.95,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 18/35 (51%)

Query: 21 ECLDSHEGNADSCKEFRTSYEQFCPGQWVKHFDRR 55
          ECLD++ G +  C + +  YE  CP  +     RR
Sbjct: 31 ECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRR 65


>pdb|1N7D|A Chain A, Extracellular Domain Of The Ldl Receptor
          Length = 699

 Score = 28.5 bits (62), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 10/25 (40%), Positives = 15/25 (60%)

Query: 21  ECLDSHEGNADSCKEFRTSYEQFCP 45
           ECLD++ G +  C + +  YE  CP
Sbjct: 296 ECLDNNGGCSHVCNDLKIGYECLCP 320


>pdb|1XFE|A Chain A, Solution Structure Of The La7-Egfa Pair From The Ldl
          Receptor
          Length = 83

 Score = 28.5 bits (62), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 10/25 (40%), Positives = 15/25 (60%)

Query: 21 ECLDSHEGNADSCKEFRTSYEQFCP 45
          ECLD++ G +  C + +  YE  CP
Sbjct: 47 ECLDNNGGCSHVCNDLKIGYECLCP 71


>pdb|3BPS|E Chain E, Pcsk9:egf-a Complex
 pdb|3GCX|E Chain E, Pcsk9:egfa (Ph 7.4)
          Length = 83

 Score = 28.1 bits (61), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 18/35 (51%)

Query: 21 ECLDSHEGNADSCKEFRTSYEQFCPGQWVKHFDRR 55
          ECLD++ G +  C + +  YE  CP  +     RR
Sbjct: 7  ECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRR 41


>pdb|1HZ8|A Chain A, Solution Structure And Backbone Dynamics Of A Concatemer
          Of Egf-Homology Modules Of The Human Low Density
          Lipoprotein Receptor
 pdb|1I0U|A Chain A, Solution Structure And Backbone Dynamics Of A Concatemer
          Of Egf-Homology Modules Of The Human Low Density
          Lipoprotein Receptor
          Length = 82

 Score = 28.1 bits (61), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 18/35 (51%)

Query: 21 ECLDSHEGNADSCKEFRTSYEQFCPGQWVKHFDRR 55
          ECLD++ G +  C + +  YE  CP  +     RR
Sbjct: 4  ECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRR 38


>pdb|1HJ7|A Chain A, Nmr Study Of A Pair Of Ldl Receptor Ca2+ Binding
          Epidermal Growth Factor-Like Domains, 20 Structures
          Length = 80

 Score = 28.1 bits (61), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 18/35 (51%)

Query: 21 ECLDSHEGNADSCKEFRTSYEQFCPGQWVKHFDRR 55
          ECLD++ G +  C + +  YE  CP  +     RR
Sbjct: 4  ECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRR 38


>pdb|3M0C|C Chain C, The X-Ray Crystal Structure Of Pcsk9 In Complex With The
           Ldl Receptor
          Length = 791

 Score = 27.7 bits (60), Expect = 1.6,   Method: Composition-based stats.
 Identities = 10/25 (40%), Positives = 15/25 (60%)

Query: 21  ECLDSHEGNADSCKEFRTSYEQFCP 45
           ECLD++ G +  C + +  YE  CP
Sbjct: 314 ECLDNNGGCSHVCNDLKIGYECLCP 338


>pdb|2W2N|E Chain E, Wt Pcsk9-Deltac Bound To Egf-A H306y Mutant Of Ldlr
          Length = 107

 Score = 27.7 bits (60), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 18/35 (51%)

Query: 21 ECLDSHEGNADSCKEFRTSYEQFCPGQWVKHFDRR 55
          ECLD++ G +  C + +  YE  CP  +     RR
Sbjct: 31 ECLDNNGGCSYVCNDLKIGYECLCPDGFQLVAQRR 65


>pdb|3GCW|E Chain E, Pcsk9:egfa(H306y)
          Length = 83

 Score = 27.3 bits (59), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 18/35 (51%)

Query: 21 ECLDSHEGNADSCKEFRTSYEQFCPGQWVKHFDRR 55
          ECLD++ G +  C + +  YE  CP  +     RR
Sbjct: 7  ECLDNNGGCSYVCNDLKIGYECLCPDGFQLVAQRR 41


>pdb|1C4K|A Chain A, Ornithine Decarboxylase Mutant (Gly121tyr)
          Length = 730

 Score = 25.8 bits (55), Expect = 7.2,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 29/63 (46%)

Query: 3   FLPKEERTKCWSARDKYWECLDSHEGNADSCKEFRTSYEQFCPGQWVKHFDRRYHFLKFK 62
           +   EER   ++ R+   E  D ++ N     + R    +F P Q +  ++ R  F++  
Sbjct: 580 YAANEERYNGYTIRELCQELHDFYKNNNTFTYQKRLFLREFFPEQGMLPYEARQEFIRNH 639

Query: 63  NKI 65
           NK+
Sbjct: 640 NKL 642


>pdb|1ORD|A Chain A, Crystallographic Structure Of A Plp-Dependent Ornithine
           Decarboxylase From Lactobacillus 30a To 3.1 Angstroms
           Resolution
 pdb|1ORD|B Chain B, Crystallographic Structure Of A Plp-Dependent Ornithine
           Decarboxylase From Lactobacillus 30a To 3.1 Angstroms
           Resolution
          Length = 730

 Score = 25.8 bits (55), Expect = 7.3,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 29/63 (46%)

Query: 3   FLPKEERTKCWSARDKYWECLDSHEGNADSCKEFRTSYEQFCPGQWVKHFDRRYHFLKFK 62
           +   EER   ++ R+   E  D ++ N     + R    +F P Q +  ++ R  F++  
Sbjct: 580 YAANEERYNGYTIRELCQELHDFYKNNNTFTYQKRLFLREFFPEQGMLPYEARQEFIRNH 639

Query: 63  NKI 65
           NK+
Sbjct: 640 NKL 642


>pdb|3M9Z|A Chain A, Crystal Structure Of Extracellular Domain Of Mouse
          Nkr-P1a
          Length = 139

 Score = 25.8 bits (55), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 1/33 (3%)

Query: 44 CPGQWVKHFDRRYHFLKFKNKIETEGFEKFDSK 76
          CP  W+ H D+ +H  +  N  E EG    D K
Sbjct: 6  CPQDWLSHRDKCFHVSQVSNTWE-EGLVDCDGK 37


  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
   0.318    0.133    0.436 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,060,776
Number of Sequences: 62578
Number of extensions: 114216
Number of successful extensions: 272
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 255
Number of HSP's gapped (non-prelim): 18
length of query: 90
length of database: 14,973,337
effective HSP length: 57
effective length of query: 33
effective length of database: 11,406,391
effective search space: 376410903
effective search space used: 376410903
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)