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= psy6898
         (111 letters)

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

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



>pdb|3PMQ|A Chain A, Crystal Structure Of The Outer Membrane Decaheme
          Cytochrome Mtrf
          Length = 669

 Score = 30.0 bits (66), Expect = 0.38,   Method: Composition-based stats.
 Identities = 13/22 (59%), Positives = 16/22 (72%)

Query: 23 ISTVISGRIGLDGRDGLPGEPG 44
          I+T++S   G DG DG PGEPG
Sbjct: 17 IATLLSACGGSDGDDGSPGEPG 38


>pdb|1J5T|A Chain A, Crystal Structure Of Indole-3-glycerol Phosphate Synthase
           (tm0140) From Thermotoga Maritima At 3.0 A Resolution
          Length = 242

 Score = 27.3 bits (59), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 12/32 (37%), Positives = 19/32 (59%)

Query: 6   GMLQVLEVHDRRDIGRAISTVISGRIGLDGRD 37
           GM  ++EVH R D+ +  S +    IG++ RD
Sbjct: 141 GMDSLVEVHSREDLEKVFSVIRPKIIGINTRD 172


>pdb|1I4N|A Chain A, Crystal Structure Of Indoleglycerol Phosphate Synthase
           From Thermotoga Maritima
 pdb|1I4N|B Chain B, Crystal Structure Of Indoleglycerol Phosphate Synthase
           From Thermotoga Maritima
          Length = 251

 Score = 27.3 bits (59), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 12/32 (37%), Positives = 19/32 (59%)

Query: 6   GMLQVLEVHDRRDIGRAISTVISGRIGLDGRD 37
           GM  ++EVH R D+ +  S +    IG++ RD
Sbjct: 150 GMDSLVEVHSREDLEKVFSVIRPKIIGINTRD 181


>pdb|1R7O|A Chain A, Crystal Structure Of Apo-mannanase 26a From Psudomonas
           Cellulosa
          Length = 395

 Score = 26.9 bits (58), Expect = 2.9,   Method: Composition-based stats.
 Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 1/32 (3%)

Query: 68  GIPGTNGTKTDHYAMGAD-TKSFSDGVLPSVQ 98
           G+PG NGT+  HY + A+  ++ ++G L   Q
Sbjct: 338 GVPGPNGTQVPHYWVPANRPENINNGTLEDFQ 369


>pdb|1J9Y|A Chain A, Crystal Structure Of Mannanase 26a From Pseudomonas
           Cellulosa
          Length = 385

 Score = 26.9 bits (58), Expect = 3.1,   Method: Composition-based stats.
 Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 1/32 (3%)

Query: 68  GIPGTNGTKTDHYAMGAD-TKSFSDGVLPSVQ 98
           G+PG NGT+  HY + A+  ++ ++G L   Q
Sbjct: 328 GVPGPNGTQVPHYWVPANRPENINNGTLEDFQ 359


>pdb|1GVY|A Chain A, Substrate Distorsion By Beta-Mannanase From Pseudomonas
           Cellulosa
          Length = 383

 Score = 26.6 bits (57), Expect = 3.3,   Method: Composition-based stats.
 Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 1/32 (3%)

Query: 68  GIPGTNGTKTDHYAMGAD-TKSFSDGVLPSVQ 98
           G+PG NGT+  HY + A+  ++ ++G L   Q
Sbjct: 328 GVPGPNGTQVPHYWVPANRPENINNGTLEDFQ 359


>pdb|1ODZ|A Chain A, Expansion Of The Glycosynthase Repertoire To Produce
           Defined Manno-oligosaccharides
 pdb|1ODZ|B Chain B, Expansion Of The Glycosynthase Repertoire To Produce
           Defined Manno-oligosaccharides
          Length = 386

 Score = 26.6 bits (57), Expect = 3.5,   Method: Composition-based stats.
 Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 1/32 (3%)

Query: 68  GIPGTNGTKTDHYAMGAD-TKSFSDGVLPSVQ 98
           G+PG NGT+  HY + A+  ++ ++G L   Q
Sbjct: 329 GVPGPNGTQVPHYWVPANRPENINNGTLEDFQ 360


>pdb|2WHM|A Chain A, Cellvibrio Japonicus Man26a E121a And E320g Double Mutant
           In Complex With Mannobiose
          Length = 385

 Score = 26.6 bits (57), Expect = 3.5,   Method: Composition-based stats.
 Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 1/32 (3%)

Query: 68  GIPGTNGTKTDHYAMGAD-TKSFSDGVLPSVQ 98
           G+PG NGT+  HY + A+  ++ ++G L   Q
Sbjct: 328 GVPGPNGTQVPHYWVPANRPENINNGTLEDFQ 359


>pdb|3HQV|B Chain B, Low Resolution, Molecular Envelope Structure Of Type I
           Collagen In Situ Determined By Fiber Diffraction. Single
           Type I Collagen Molecule, Rigid Body Refinement
 pdb|3HR2|B Chain B, Low Resolution, Molecular Envelope Structure Of Type I
           Collagen In Situ Determined By Fiber Diffraction. Single
           Type I Collagen Molecule, Post Rigid Body Refinement,
           'relaxed'
          Length = 1028

 Score = 25.4 bits (54), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 27/47 (57%), Gaps = 3/47 (6%)

Query: 28  SGRIGLDGRDGLPGEPGLDGIPG---RNGMDGIPGKDGLPGKDGIPG 71
           SG  G+ G  G PG+ G  G+PG    NG+ G+PG  GL G  G PG
Sbjct: 920 SGPQGIRGDKGEPGDXGARGLPGLKGHNGLQGLPGLAGLHGDQGAPG 966


>pdb|3VNQ|A Chain A, Co-crystal Structure Of Nrps Adenylation Protein Cytc1
           With Atp From Streptomyces
 pdb|3VNR|A Chain A, Co-crystal Structure Of Nrps Adenylation Protein Cytc1
           With Aminobutyric Acid And Amp From Streptomyces
 pdb|3VNS|A Chain A, Co-crystal Structure Of Nrps Adenylation Protein Cytc1
           With D-valine And Amp From Streptomyces
          Length = 544

 Score = 25.4 bits (54), Expect = 8.4,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 1/64 (1%)

Query: 14  HDRRDIGRAISTVISGRIGLDGRDGLPGEPGLDGIPGRNGMDGIPGKDGLPGKDGIPGTN 73
            D   IGRA+ +  +  +G DGRD  PGE G   + G    +G   +  L   +  P   
Sbjct: 348 QDASIIGRALPSFGTRVVGDDGRDVAPGETGELWLSGAQLAEGYLRRPELTA-EKFPEVT 406

Query: 74  GTKT 77
             KT
Sbjct: 407 DEKT 410


>pdb|1PW9|A Chain A, High Resolution Crystal Structure Of An Active
          Recombinant Fragment Of Human Lung Surfactant Protein D
 pdb|1PW9|B Chain B, High Resolution Crystal Structure Of An Active
          Recombinant Fragment Of Human Lung Surfactant Protein D
 pdb|1PW9|C Chain C, High Resolution Crystal Structure Of An Active
          Recombinant Fragment Of Human Lung Surfactant Protein D
 pdb|1PWB|A Chain A, High Resolution Crystal Structure Of An Active
          Recombinant Fragment Of Human Lung Surfactant Protein D
          With Maltose
 pdb|1PWB|B Chain B, High Resolution Crystal Structure Of An Active
          Recombinant Fragment Of Human Lung Surfactant Protein D
          With Maltose
 pdb|1PWB|C Chain C, High Resolution Crystal Structure Of An Active
          Recombinant Fragment Of Human Lung Surfactant Protein D
          With Maltose
 pdb|3IKN|A Chain A, Crystal Structure Of Galactose Bound Trimeric Human Lung
          Surfactant Protein D
 pdb|3IKN|B Chain B, Crystal Structure Of Galactose Bound Trimeric Human Lung
          Surfactant Protein D
 pdb|3IKN|C Chain C, Crystal Structure Of Galactose Bound Trimeric Human Lung
          Surfactant Protein D
 pdb|3IKP|A Chain A, Crystal Structure Of Inositol Phosphate Bound Trimeric
          Human Lung Surfactant Protein D
 pdb|3IKP|B Chain B, Crystal Structure Of Inositol Phosphate Bound Trimeric
          Human Lung Surfactant Protein D
 pdb|3IKP|C Chain C, Crystal Structure Of Inositol Phosphate Bound Trimeric
          Human Lung Surfactant Protein D
 pdb|3IKQ|A Chain A, Crystal Structure Of Alpha 1-2 Mannobiose Bound Trimeric
          Human Lung Surfactant Protein D
 pdb|3IKQ|B Chain B, Crystal Structure Of Alpha 1-2 Mannobiose Bound Trimeric
          Human Lung Surfactant Protein D
 pdb|3IKQ|C Chain C, Crystal Structure Of Alpha 1-2 Mannobiose Bound Trimeric
          Human Lung Surfactant Protein D
 pdb|3IKR|A Chain A, Crystal Structure Of Alpha 1-4 Mannobiose Bound Trimeric
          Human Lung Surfactant Protein D
 pdb|3IKR|B Chain B, Crystal Structure Of Alpha 1-4 Mannobiose Bound Trimeric
          Human Lung Surfactant Protein D
 pdb|3IKR|C Chain C, Crystal Structure Of Alpha 1-4 Mannobiose Bound Trimeric
          Human Lung Surfactant Protein D
          Length = 177

 Score = 25.4 bits (54), Expect = 9.3,   Method: Compositional matrix adjust.
 Identities = 12/24 (50%), Positives = 14/24 (58%)

Query: 47 GIPGRNGMDGIPGKDGLPGKDGIP 70
          G PG  G  GIPG  G  G+ G+P
Sbjct: 1  GSPGLKGDKGIPGDKGAKGESGLP 24


  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    0.144    0.434 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,914,949
Number of Sequences: 62578
Number of extensions: 191804
Number of successful extensions: 486
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 33
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 210
Number of HSP's gapped (non-prelim): 225
length of query: 111
length of database: 14,973,337
effective HSP length: 75
effective length of query: 36
effective length of database: 10,279,987
effective search space: 370079532
effective search space used: 370079532
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)