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= psy3481
         (340 letters)

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

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



>pdb|2R60|A Chain A, Structure Of Apo Sucrose Phosphate Synthase (Sps) Of
           Halothermothrix Orenii
 pdb|2R66|A Chain A, Complex Structure Of Sucrose Phosphate Synthase (Sps)-F6p
           Of Halothermothrix Orenii
 pdb|2R68|A Chain A, Complex Structure Of Sucrose Phosphate Synthase (Sps)-S6p
           Of Halothermothrix Orenii
          Length = 499

 Score = 32.3 bits (72), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 40/144 (27%), Positives = 65/144 (45%), Gaps = 24/144 (16%)

Query: 72  ALKQMIKINFKLSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNM--ELL 129
             ++M K+N   SN+KEM  R+K     I   +T +Y++K I      +STS+    +  
Sbjct: 154 GAQKMEKLNVNTSNFKEMDERFKFHRRIIAERLTMSYADKII------VSTSQERFGQYS 207

Query: 130 QDFYETTLEALKDAKNDRLWFKTNTKLGKLYFDREDFNKL-SRILKQLHQSCQTDDGEDD 188
            D Y   +    D K   +    NT++    FD E  +K+ ++I K L         E D
Sbjct: 208 HDLYRGAVNVEDDDKFSVIPPGVNTRV----FDGEYGDKIKAKITKYL---------ERD 254

Query: 189 LKKGTQLLEIYALEIQMYTAQKNN 212
           L  G++ +E+ A+       QK N
Sbjct: 255 L--GSERMELPAIIASSRLDQKKN 276


>pdb|4IIW|A Chain A, 2.6 Angstrom Crystal Structure Of Putative Yceg-like
           Protein Lmo1499 From Listeria Monocytogenes
 pdb|4IIW|B Chain B, 2.6 Angstrom Crystal Structure Of Putative Yceg-like
           Protein Lmo1499 From Listeria Monocytogenes
          Length = 349

 Score = 32.0 bits (71), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 17/33 (51%), Positives = 22/33 (66%), Gaps = 2/33 (6%)

Query: 139 ALKDAKNDRLWFKTNTKLGKLYFDR--EDFNKL 169
           AL   K+D L+F  NTK GK+YF +  E+ NKL
Sbjct: 308 ALYPEKSDYLYFLANTKTGKVYFSKTLEEHNKL 340


>pdb|3TXM|A Chain A, Crystal Structure Of Rpn6 From Drosophila Melanogaster,
           Gd(3+) Complex
 pdb|3TXN|A Chain A, Crystal Structure Of Rpn6 From Drosophila Melanogaster,
           Native Data
          Length = 394

 Score = 32.0 bits (71), Expect = 0.52,   Method: Compositional matrix adjust.
 Identities = 16/45 (35%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 297 GKMHLR-EGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANM 340
           G +H   E +F+ A + F+EAF+ +D   S +  T LKY++L  +
Sbjct: 187 GILHAADERDFKTAFSYFYEAFEGFDSVDSVKALTSLKYMLLCKI 231


>pdb|2XHE|A Chain A, Crystal Structure Of The Unc18-Syntaxin 1 Complex From
           Monosiga Brevicollis
          Length = 650

 Score = 29.6 bits (65), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 4/57 (7%)

Query: 53  SFQKVLDLESGERGEWGFKALKQMIKINFKLSNYKEMMSRYKQLLLYIKSAVTRNYS 109
           S +++  L   ++GE G  ALKQM+K    L  ++E M +Y  L L + +A+   +S
Sbjct: 307 SARRLQGLRDSQQGEGGAGALKQMLK---DLPQHREQMQKYS-LHLDMSNAINMAFS 359


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

 Score = 29.3 bits (64), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 37/106 (34%), Positives = 53/106 (50%), Gaps = 14/106 (13%)

Query: 66  GEWGFKALKQMIKI--NFKLSNYKEMMSRYKQLLLYI-----KSAVTRNYSEKSINSILD 118
           G+W  KA K+ +K+  NF LS   E MS    L L       K  +T +     INS+  
Sbjct: 89  GKW--KAQKRFLKMSGNFDLS--IEGMSISADLKLGSNPTSGKPTITCSSCSSHINSVHV 144

Query: 119 YISTSKNMELLQDFYETTLEALKDAKNDRLWFK-TNTKLGKL--YF 161
           +IS SK   L+Q F++    AL++  N ++  K TN+   KL  YF
Sbjct: 145 HISKSKVGWLIQLFHKKIESALRNKMNSQVCEKVTNSVSSKLQPYF 190


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

 Score = 28.1 bits (61), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 45/90 (50%), Gaps = 11/90 (12%)

Query: 66  GEWGFKALKQMIKI--NFKLSNYKEMMSRYKQLLLYI-----KSAVTRNYSEKSINSILD 118
           G+W  KA K+ +K+  NF LS   E MS    L L       K  +T +     INS+  
Sbjct: 89  GKW--KAQKRFLKMSGNFDLS--IEGMSISADLKLGSNPTSGKPTITCSSCSSHINSVHV 144

Query: 119 YISTSKNMELLQDFYETTLEALKDAKNDRL 148
           +IS SK   L+Q F++    AL++  N ++
Sbjct: 145 HISKSKVGWLIQLFHKKIESALRNKMNSQV 174


  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    0.391 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,095,444
Number of Sequences: 62578
Number of extensions: 417964
Number of successful extensions: 1138
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1131
Number of HSP's gapped (non-prelim): 16
length of query: 340
length of database: 14,973,337
effective HSP length: 99
effective length of query: 241
effective length of database: 8,778,115
effective search space: 2115525715
effective search space used: 2115525715
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: 52 (24.6 bits)