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= 015404
         (407 letters)

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

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



>pdb|1BP1|A Chain A, Crystal Structure Of Bpi, The Human Bactericidal
           Permeability-Increasing Protein
          Length = 456

 Score = 86.7 bits (213), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 78/338 (23%), Positives = 146/338 (43%), Gaps = 32/338 (9%)

Query: 37  IIISQTGLDFVKDLLITKAISSIIPLALPKIERAVKIPILGNVRMVLSNITIYNIDVLSS 96
           + ISQ GLD+            +  + +P    + KI  LG       ++ I    + SS
Sbjct: 7   VRISQKGLDYASQQGTAALQKELKRIKIPDYSDSFKIKHLGKGHYSFYSMDIREFQLPSS 66

Query: 97  YVK--PGDTGVVFVAYGTTCNLSANWFYEYTTWLLPIEISDHGIASVQVEGMQVG--LTL 152
            +   P + G+ F        +S  W  +     L +     G   + +EGM +   L L
Sbjct: 67  QISMVP-NVGLKFSISNANIKISGKW--KAQKRFLKMS----GNFDLSIEGMSISADLKL 119

Query: 153 GLETQKGTLKLSLVDCGCYVKDISIKLDGGA-SWLYQGMINAFEEQIVSAVENAITKKLK 211
           G     G   ++   C  ++  + + +      WL    I  F ++I SA+ N +  ++ 
Sbjct: 120 GSNPTSGKPTITCSSCSSHINSVHVHISKSKVGWL----IQLFHKKIESALRNKMNSQVC 175

Query: 212 EGI-----SKLDSLLQSLPKEIPVDDHASLNITFVDNPLLTSSSIEFDINGLFTARKKAS 266
           E +     SKL    Q+LP    +D  A +N   V  P  T+ +++  + G F +    +
Sbjct: 176 EKVTNSVSSKLQPYFQTLPVMTKIDSVAGINYGLVAPPATTAETLDVQMKGEFYSENHHN 235

Query: 267 IPNYYNSNLQPPV--FCSDQSKMLGISLDEAVLNSASALYYDAEFMQWTV--DKVPDQS- 321
            P +      PPV  F +   +M+ + L +   N+A  +Y +A  ++ T+  D +P +S 
Sbjct: 236 PPPF-----APPVMEFPAAHDRMVYLGLSDYFFNTAGLVYQEAGVLKMTLRDDMIPKESK 290

Query: 322 -LLNTAGWRFIIPQLYRKYPNDDMNLNISLSSPPVIRV 358
             L T  +   +P++ +K+PN  + +++S S+PP + V
Sbjct: 291 FRLTTKFFGTFLPEVAKKFPNMKIQIHVSASTPPHLSV 328


>pdb|1EWF|A Chain A, The 1.7 Angstrom Crystal Structure Of Bpi
          Length = 456

 Score = 84.7 bits (208), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 77/338 (22%), Positives = 146/338 (43%), Gaps = 32/338 (9%)

Query: 37  IIISQTGLDFVKDLLITKAISSIIPLALPKIERAVKIPILGNVRMVLSNITIYNIDVLSS 96
           + ISQ GLD+            +  + +P    + KI  LG       ++ I    + SS
Sbjct: 7   VRISQKGLDYASQQGTAALQKELKRIKIPDYSDSFKIKHLGKGHYSFYSMDIREFQLPSS 66

Query: 97  YVK--PGDTGVVFVAYGTTCNLSANWFYEYTTWLLPIEISDHGIASVQVEGMQVG--LTL 152
            +   P + G+ F        +S  W  +     L +     G   + +EGM +   L L
Sbjct: 67  QISMVP-NVGLKFSISNANIKISGKW--KAQKRFLKMS----GNFDLSIEGMSISADLKL 119

Query: 153 GLETQKGTLKLSLVDCGCYVKDISIKLDGGA-SWLYQGMINAFEEQIVSAVENAITKKLK 211
           G     G   ++   C  ++  + + +      WL    I  F ++I SA+ N +  ++ 
Sbjct: 120 GSNPTSGKPTITCSSCSSHINSVHVHISKSKVGWL----IQLFHKKIESALRNKMNSQVC 175

Query: 212 EGI-----SKLDSLLQSLPKEIPVDDHASLNITFVDNPLLTSSSIEFDINGLFTARKKAS 266
           E +     S+L    Q+LP    +D  A +N   V  P  T+ +++  + G F +    +
Sbjct: 176 EKVTNSVSSELQPYFQTLPVMTKIDSVAGINYGLVAPPATTAETLDVQMKGEFYSENHHN 235

Query: 267 IPNYYNSNLQPPV--FCSDQSKMLGISLDEAVLNSASALYYDAEFMQWTV--DKVPDQS- 321
            P +      PPV  F +   +M+ + L +   N+A  +Y +A  ++ T+  D +P +S 
Sbjct: 236 PPPF-----APPVMEFPAAHDRMVYLGLSDYFFNTAGLVYQEAGVLKMTLRDDMIPKESK 290

Query: 322 -LLNTAGWRFIIPQLYRKYPNDDMNLNISLSSPPVIRV 358
             L T  +   +P++ +K+PN  + +++S S+PP + V
Sbjct: 291 FRLTTKFFGTFLPEVAKKFPNMKIQIHVSASTPPHLSV 328


>pdb|3H5Q|A Chain A, Crystal Structure Of A Putative Pyrimidine-Nucleoside
           Phosphorylase From Staphylococcus Aureus
          Length = 436

 Score = 28.9 bits (63), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 4/62 (6%)

Query: 242 DNPLLTSSSIEFDINGLFTARKKASIPNYYNSNLQPPVFCSDQSKMLGISLDEAVLNSAS 301
           D   LT+  I F I G      K  IP+Y  S+L   ++  D +    ++L  A +NS  
Sbjct: 15  DGHTLTTEEINFFIGGYV----KGDIPDYQASSLAXAIYFQDXNDDERVALTXAXVNSGD 70

Query: 302 AL 303
            +
Sbjct: 71  XI 72


>pdb|2AYI|A Chain A, Wild-Type Ampt From Thermus Thermophilus
 pdb|2AYI|B Chain B, Wild-Type Ampt From Thermus Thermophilus
 pdb|2AYI|C Chain C, Wild-Type Ampt From Thermus Thermophilus
 pdb|2AYI|D Chain D, Wild-Type Ampt From Thermus Thermophilus
 pdb|2AYI|E Chain E, Wild-Type Ampt From Thermus Thermophilus
          Length = 408

 Score = 28.1 bits (61), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 13/36 (36%), Positives = 17/36 (47%)

Query: 179 LDGGASWLYQGMINAFEEQIVSAVENAITKKLKEGI 214
           LD   +WLY+GM  AF E       +    K  EG+
Sbjct: 77  LDKAPAWLYEGMARAFREGAARLAVSGSDPKALEGL 112


  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    0.135    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,743,646
Number of Sequences: 62578
Number of extensions: 429101
Number of successful extensions: 1027
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1023
Number of HSP's gapped (non-prelim): 5
length of query: 407
length of database: 14,973,337
effective HSP length: 101
effective length of query: 306
effective length of database: 8,652,959
effective search space: 2647805454
effective search space used: 2647805454
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: 53 (25.0 bits)