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= 048256
         (102 letters)

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

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



>pdb|3VTA|A Chain A, Crystal Structure Of Cucumisin, A Subtilisin-Like
           Endoprotease From Cucumis Melo L
 pdb|3VTA|B Chain B, Crystal Structure Of Cucumisin, A Subtilisin-Like
           Endoprotease From Cucumis Melo L
          Length = 621

 Score = 52.4 bits (124), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 32/104 (30%), Positives = 55/104 (52%), Gaps = 8/104 (7%)

Query: 3   NFNYPSITV---PKLSGSITVTRRVKNVG-SPGTYQARVKTPQGVSVTIAPKSLKFINVG 58
           + NYPS  +   P  + +    R + +V     TY+A +  PQG+++++ P  L F  +G
Sbjct: 521 DLNYPSFGLSVSPSQTFNQYFNRTLTSVAPQASTYRAMISAPQGLTISVNPNVLSFNGLG 580

Query: 59  EEKSFKVIIKAKNASVTKDYVFGELIWSDEKQHQVRSPIVVKAV 102
           + KSF + ++    S+    V   L+WSD   H VRSPI + ++
Sbjct: 581 DRKSFTLTVR---GSIKGFVVSASLVWSD-GVHYVRSPITITSL 620


>pdb|3I6S|A Chain A, Crystal Structure Of The Plant Subtilisin-Like Protease
           Sbt3
 pdb|3I6S|B Chain B, Crystal Structure Of The Plant Subtilisin-Like Protease
           Sbt3
 pdb|3I74|A Chain A, Crystal Structure Of The Plant Subtilisin-Like Protease
           Sbt3 In Complex With A Chloromethylketone Inhibitor
 pdb|3I74|B Chain B, Crystal Structure Of The Plant Subtilisin-Like Protease
           Sbt3 In Complex With A Chloromethylketone Inhibitor
          Length = 649

 Score = 49.3 bits (116), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 34/109 (31%), Positives = 58/109 (53%), Gaps = 9/109 (8%)

Query: 2   VNFNYPS-ITVPKLSGSITVT-----RRVKNVG-SPGTYQARVKTPQGVSVTIAPKSLKF 54
            + NYPS I +  + G+ T+      R V NVG    TY+A++K P+  +++++P+ L F
Sbjct: 538 ADLNYPSFIALYSIEGNFTLLEQKFKRTVTNVGKGAATYKAKLKAPKNSTISVSPQILVF 597

Query: 55  INVGEEKSFKVIIKAKNASVTKDYVFGELIWSDEK-QHQVRSPIVVKAV 102
            N  E++S+ + I+          V G + W ++   H VRSPIV   +
Sbjct: 598 KNKNEKQSYTLTIRYIGDEGQSRNV-GSITWVEQNGNHSVRSPIVTSPI 645


>pdb|1NOU|A Chain A, Native Human Lysosomal Beta-Hexosaminidase Isoform B
 pdb|1NOU|B Chain B, Native Human Lysosomal Beta-Hexosaminidase Isoform B
 pdb|1NOW|A Chain A, Human Lysosomal Beta-Hexosaminidase Isoform B In Complex
           With (2r,3r,
           4s,5r)-2-Acetamido-3,
           4-Dihydroxy-5-Hydroxymethyl-Piperidinium Chloride
           (Galnac-Isofagomine)
 pdb|1NOW|B Chain B, Human Lysosomal Beta-Hexosaminidase Isoform B In Complex
           With (2r,3r,
           4s,5r)-2-Acetamido-3,
           4-Dihydroxy-5-Hydroxymethyl-Piperidinium Chloride
           (Galnac-Isofagomine)
 pdb|1NP0|A Chain A, Human Lysosomal Beta-Hexosaminidase Isoform B In Complex
           With Intermediate Analogue Nag-Thiazoline
 pdb|1NP0|B Chain B, Human Lysosomal Beta-Hexosaminidase Isoform B In Complex
           With Intermediate Analogue Nag-Thiazoline
 pdb|2GJX|B Chain B, Crystallographic Structure Of Human Beta-Hexosaminidase A
 pdb|2GJX|C Chain C, Crystallographic Structure Of Human Beta-Hexosaminidase A
 pdb|2GJX|F Chain F, Crystallographic Structure Of Human Beta-Hexosaminidase A
 pdb|2GJX|G Chain G, Crystallographic Structure Of Human Beta-Hexosaminidase A
          Length = 507

 Score = 29.3 bits (64), Expect = 0.55,   Method: Composition-based stats.
 Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 30  PGTYQARVKTPQG-VSVTIAPKSLKFINVGEEKSFKVIIKAKNASVTKDYVFGEL 83
           P  +QA+ +  Q  VS+T+  +   F N+  ++S+ +++K   A +  + V+G L
Sbjct: 66  PAEFQAKTQVQQLLVSITLQSECDAFPNISSDESYTLLVKEPVAVLKANRVWGAL 120


>pdb|2GK1|B Chain B, X-Ray Crystal Structure Of Ngt-Bound Hexa
 pdb|2GK1|D Chain D, X-Ray Crystal Structure Of Ngt-Bound Hexa
 pdb|2GK1|F Chain F, X-Ray Crystal Structure Of Ngt-Bound Hexa
 pdb|2GK1|H Chain H, X-Ray Crystal Structure Of Ngt-Bound Hexa
          Length = 503

 Score = 29.3 bits (64), Expect = 0.56,   Method: Composition-based stats.
 Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 30  PGTYQARVKTPQG-VSVTIAPKSLKFINVGEEKSFKVIIKAKNASVTKDYVFGEL 83
           P  +QA+ +  Q  VS+T+  +   F N+  ++S+ +++K   A +  + V+G L
Sbjct: 66  PAEFQAKTQVQQLLVSITLQSECDAFPNISSDESYTLLVKEPVAVLKANRVWGAL 120


>pdb|1O7A|A Chain A, Human Beta-Hexosaminidase B
 pdb|1O7A|B Chain B, Human Beta-Hexosaminidase B
 pdb|1O7A|C Chain C, Human Beta-Hexosaminidase B
 pdb|1O7A|D Chain D, Human Beta-Hexosaminidase B
 pdb|1O7A|E Chain E, Human Beta-Hexosaminidase B
 pdb|1O7A|F Chain F, Human Beta-Hexosaminidase B
          Length = 515

 Score = 29.3 bits (64), Expect = 0.58,   Method: Composition-based stats.
 Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 30  PGTYQARVKTPQG-VSVTIAPKSLKFINVGEEKSFKVIIKAKNASVTKDYVFGEL 83
           P  +QA+ +  Q  VS+T+  +   F N+  ++S+ +++K   A +  + V+G L
Sbjct: 74  PAEFQAKTQVQQLLVSITLQSECDAFPNISSDESYTLLVKEPVAVLKANRVWGAL 128


>pdb|3LMY|A Chain A, The Crystal Structure Of Beta-Hexosaminidase B In Complex
           With Pyrimethamine
 pdb|3LMY|B Chain B, The Crystal Structure Of Beta-Hexosaminidase B In Complex
           With Pyrimethamine
          Length = 556

 Score = 29.3 bits (64), Expect = 0.59,   Method: Composition-based stats.
 Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 30  PGTYQARVKTPQG-VSVTIAPKSLKFINVGEEKSFKVIIKAKNASVTKDYVFGEL 83
           P  +QA+ +  Q  VS+T+  +   F N+  ++S+ +++K   A +  + V+G L
Sbjct: 115 PAEFQAKTQVQQLLVSITLQSECDAFPNISSDESYTLLVKEPVAVLKANRVWGAL 169


>pdb|3KIO|A Chain A, Mouse Rnase H2 Complex
          Length = 301

 Score = 25.8 bits (55), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 2/40 (5%)

Query: 14  LSGSITVTR-RVKNVGSPGTYQARVKTP-QGVSVTIAPKS 51
           L  ++ VT+  V  VG P TYQAR++    G+ VT+  K+
Sbjct: 130 LDQNVNVTQVFVDTVGXPETYQARLQQHFPGIEVTVKAKA 169


>pdb|3P56|A Chain A, The Structure Of The Human Rnase H2 Complex Defines Key
           Interaction Interfaces Relevant To Enzyme Function And
           Human Disease
 pdb|3P56|D Chain D, The Structure Of The Human Rnase H2 Complex Defines Key
           Interaction Interfaces Relevant To Enzyme Function And
           Human Disease
          Length = 299

 Score = 25.4 bits (54), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 1/29 (3%)

Query: 24  VKNVGSPGTYQARVKTP-QGVSVTIAPKS 51
           V  VG P TYQAR++    G+ VT+  K+
Sbjct: 140 VDTVGMPETYQARLQQSFPGIEVTVKAKA 168


>pdb|3PUF|A Chain A, Crystal Structure Of Human Rnase H2 Complex
 pdb|3PUF|D Chain D, Crystal Structure Of Human Rnase H2 Complex
 pdb|3PUF|G Chain G, Crystal Structure Of Human Rnase H2 Complex
 pdb|3PUF|J Chain J, Crystal Structure Of Human Rnase H2 Complex
 pdb|3PUF|M Chain M, Crystal Structure Of Human Rnase H2 Complex
 pdb|3PUF|P Chain P, Crystal Structure Of Human Rnase H2 Complex
          Length = 302

 Score = 25.4 bits (54), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 1/29 (3%)

Query: 24  VKNVGSPGTYQARVKTP-QGVSVTIAPKS 51
           V  VG P TYQAR++    G+ VT+  K+
Sbjct: 143 VDTVGMPETYQARLQQSFPGIEVTVKAKA 171


>pdb|3P5J|A Chain A, The Structure Of The Human Rnase H2 Complex Defines Key
           Interaction Interfaces Relevant To Enzyme Function And
           Human Disease
          Length = 301

 Score = 25.4 bits (54), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 2/40 (5%)

Query: 14  LSGSITVTR-RVKNVGSPGTYQARVKTP-QGVSVTIAPKS 51
           L  ++ VT+  V  VG P TYQAR++    G+ VT+  K+
Sbjct: 130 LDQNVNVTQVFVDTVGMPETYQARLQQHFPGIEVTVKAKA 169


>pdb|1GZS|B Chain B, Crystal Structure Of The Complex Between The Gef Domain Of
           The Salmonella Typhimurium Sope Toxin And Human Cdc42
 pdb|1GZS|D Chain D, Crystal Structure Of The Complex Between The Gef Domain Of
           The Salmonella Typhimurium Sope Toxin And Human Cdc42
          Length = 165

 Score = 25.4 bits (54), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 10/56 (17%)

Query: 20  VTRRVKNVGSPGTYQARVKTPQG------VSVTIAPKSLK----FINVGEEKSFKV 65
           +    KN G PGT +  V TP G      ++  I+  + K    FIN  ++ SFK+
Sbjct: 69  IGEAAKNAGLPGTTKNDVFTPSGAGANPFITPLISSANSKYPRMFINQHQQASFKI 124


  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
   0.315    0.131    0.365 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,878,326
Number of Sequences: 62578
Number of extensions: 99604
Number of successful extensions: 271
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 268
Number of HSP's gapped (non-prelim): 13
length of query: 102
length of database: 14,973,337
effective HSP length: 67
effective length of query: 35
effective length of database: 10,780,611
effective search space: 377321385
effective search space used: 377321385
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 45 (21.9 bits)