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= psy5557
         (213 letters)

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

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



>pdb|1I8F|A Chain A, The Crystal Structure Of A Heptameric Archaeal Sm Protein:
           Implications For The Eukaryotic Snrnp Core
 pdb|1I8F|B Chain B, The Crystal Structure Of A Heptameric Archaeal Sm Protein:
           Implications For The Eukaryotic Snrnp Core
 pdb|1I8F|C Chain C, The Crystal Structure Of A Heptameric Archaeal Sm Protein:
           Implications For The Eukaryotic Snrnp Core
 pdb|1I8F|D Chain D, The Crystal Structure Of A Heptameric Archaeal Sm Protein:
           Implications For The Eukaryotic Snrnp Core
 pdb|1I8F|E Chain E, The Crystal Structure Of A Heptameric Archaeal Sm Protein:
           Implications For The Eukaryotic Snrnp Core
 pdb|1I8F|F Chain F, The Crystal Structure Of A Heptameric Archaeal Sm Protein:
           Implications For The Eukaryotic Snrnp Core
 pdb|1I8F|G Chain G, The Crystal Structure Of A Heptameric Archaeal Sm Protein:
           Implications For The Eukaryotic Snrnp Core
 pdb|1LNX|A Chain A, Crystal Structure Of The P.Aerophilum Smap1 Heptamer In A
           New Crystal Form (C2221)
 pdb|1LNX|B Chain B, Crystal Structure Of The P.Aerophilum Smap1 Heptamer In A
           New Crystal Form (C2221)
 pdb|1LNX|C Chain C, Crystal Structure Of The P.Aerophilum Smap1 Heptamer In A
           New Crystal Form (C2221)
 pdb|1LNX|D Chain D, Crystal Structure Of The P.Aerophilum Smap1 Heptamer In A
           New Crystal Form (C2221)
 pdb|1LNX|E Chain E, Crystal Structure Of The P.Aerophilum Smap1 Heptamer In A
           New Crystal Form (C2221)
 pdb|1LNX|F Chain F, Crystal Structure Of The P.Aerophilum Smap1 Heptamer In A
           New Crystal Form (C2221)
 pdb|1LNX|G Chain G, Crystal Structure Of The P.Aerophilum Smap1 Heptamer In A
           New Crystal Form (C2221)
          Length = 81

 Score = 35.4 bits (80), Expect = 0.023,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 26/46 (56%), Gaps = 4/46 (8%)

Query: 131 GYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMG 176
           G LRS DQ  NL+L    E I  GN Y    RG  ++RGENV+ + 
Sbjct: 36  GILRSFDQHVNLLLEDA-EEIIDGNVY---KRGTMVVRGENVLFIS 77


>pdb|3CW1|G Chain G, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3CW1|3 Chain 3, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3CW1|4 Chain 4, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3CW1|5 Chain 5, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3PGW|G Chain G, Crystal Structure Of Human U1 Snrnp
 pdb|3PGW|J Chain J, Crystal Structure Of Human U1 Snrnp
 pdb|2Y9A|G Chain G, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9A|N Chain N, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9A|U Chain U, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9B|G Chain G, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9B|N Chain N, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9B|U Chain U, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9C|G Chain G, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9C|N Chain N, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9C|U Chain U, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9D|G Chain G, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9D|N Chain N, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9D|U Chain U, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|3S6N|G Chain G, Crystal Structure Of The Gemin2-Binding Domain Of Smn,
           Gemin2 In Complex With Smd1D2FEG FROM HUMAN
 pdb|4F7U|G Chain G, Macromolecular Machine 6
 pdb|4F7U|J Chain J, Macromolecular Machine 6
 pdb|1VU2|H Chain H, The 8s Snrnp Assembly Intermediate
 pdb|1VU2|P Chain P, The 8s Snrnp Assembly Intermediate
 pdb|1VU2|X Chain X, The 8s Snrnp Assembly Intermediate
 pdb|1VU2|FF Chain f, The 8s Snrnp Assembly Intermediate
 pdb|1VU2|NN Chain n, The 8s Snrnp Assembly Intermediate
 pdb|1VU2|VV Chain v, The 8s Snrnp Assembly Intermediate
 pdb|1VU2|4 Chain 4, The 8s Snrnp Assembly Intermediate
 pdb|1VU3|H Chain H, The 8s Snrnp Assembly Intermediate
 pdb|1VU3|P Chain P, The 8s Snrnp Assembly Intermediate
 pdb|1VU3|X Chain X, The 8s Snrnp Assembly Intermediate
 pdb|1VU3|FF Chain f, The 8s Snrnp Assembly Intermediate
 pdb|1VU3|NN Chain n, The 8s Snrnp Assembly Intermediate
 pdb|1VU3|VV Chain v, The 8s Snrnp Assembly Intermediate
 pdb|4F77|P Chain P, The 8s Snrnp Assembly Intermediate
 pdb|4F77|H Chain H, The 8s Snrnp Assembly Intermediate
 pdb|4F77|X Chain X, The 8s Snrnp Assembly Intermediate
 pdb|4F77|FF Chain f, The 8s Snrnp Assembly Intermediate
 pdb|4F77|NN Chain n, The 8s Snrnp Assembly Intermediate
 pdb|4F77|VV Chain v, The 8s Snrnp Assembly Intermediate
 pdb|4F77|4 Chain 4, The 8s Snrnp Assembly Intermediate
          Length = 76

 Score = 31.2 bits (69), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 3/60 (5%)

Query: 116 NRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLM 175
           +++  L  N  R + G LR  D F NLV+ + +E    G Q      G+ +IRG +++++
Sbjct: 14  DKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNN---IGMVVIRGNSIIML 70


>pdb|3BW1|A Chain A, Crystal Structure Of Homomeric Yeast Lsm3 Exhibiting Novel
           Octameric Ring Organisation
 pdb|3BW1|B Chain B, Crystal Structure Of Homomeric Yeast Lsm3 Exhibiting Novel
           Octameric Ring Organisation
          Length = 96

 Score = 30.8 bits (68), Expect = 0.60,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 4/54 (7%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGN--QYGDIPR--GIFIIRGENVVLMG 176
           RTL+G L++ D   N+VL   +E I+  N  +  +  R   +  IRG+ V L+ 
Sbjct: 31  RTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLIS 84


>pdb|1TH7|A Chain A, Crystal Structure Of An Archaeal Sm Protein From
           Sulfolobus Solfataricus
 pdb|1TH7|B Chain B, Crystal Structure Of An Archaeal Sm Protein From
           Sulfolobus Solfataricus
 pdb|1TH7|C Chain C, Crystal Structure Of An Archaeal Sm Protein From
           Sulfolobus Solfataricus
 pdb|1TH7|D Chain D, Crystal Structure Of An Archaeal Sm Protein From
           Sulfolobus Solfataricus
 pdb|1TH7|E Chain E, Crystal Structure Of An Archaeal Sm Protein From
           Sulfolobus Solfataricus
 pdb|1TH7|F Chain F, Crystal Structure Of An Archaeal Sm Protein From
           Sulfolobus Solfataricus
 pdb|1TH7|G Chain G, Crystal Structure Of An Archaeal Sm Protein From
           Sulfolobus Solfataricus
 pdb|1TH7|H Chain H, Crystal Structure Of An Archaeal Sm Protein From
           Sulfolobus Solfataricus
 pdb|1TH7|I Chain I, Crystal Structure Of An Archaeal Sm Protein From
           Sulfolobus Solfataricus
 pdb|1TH7|J Chain J, Crystal Structure Of An Archaeal Sm Protein From
           Sulfolobus Solfataricus
 pdb|1TH7|K Chain K, Crystal Structure Of An Archaeal Sm Protein From
           Sulfolobus Solfataricus
 pdb|1TH7|L Chain L, Crystal Structure Of An Archaeal Sm Protein From
           Sulfolobus Solfataricus
 pdb|1TH7|M Chain M, Crystal Structure Of An Archaeal Sm Protein From
           Sulfolobus Solfataricus
 pdb|1TH7|N Chain N, Crystal Structure Of An Archaeal Sm Protein From
           Sulfolobus Solfataricus
          Length = 81

 Score = 29.3 bits (64), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 20/48 (41%), Positives = 27/48 (56%), Gaps = 7/48 (14%)

Query: 131 GYLRSVDQFANLVLHKT--IERIHVGNQYGDIPRGIFIIRGENVVLMG 176
           G LRS DQ  NLVL  +  I+    G + G I     +IRG+NV+L+ 
Sbjct: 34  GMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTI-----VIRGDNVILIS 76


>pdb|3SWN|C Chain C, Structure Of The Lsm657 Complex: An Assembly Intermediate
           Of The Lsm1 7 And Lsm2 8 Rings
 pdb|3SWN|F Chain F, Structure Of The Lsm657 Complex: An Assembly Intermediate
           Of The Lsm1 7 And Lsm2 8 Rings
 pdb|3SWN|O Chain O, Structure Of The Lsm657 Complex: An Assembly Intermediate
           Of The Lsm1 7 And Lsm2 8 Rings
 pdb|3SWN|R Chain R, Structure Of The Lsm657 Complex: An Assembly Intermediate
           Of The Lsm1 7 And Lsm2 8 Rings
          Length = 117

 Score = 28.1 bits (61), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 4/54 (7%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERI---HVGNQYGDIPR-GIFIIRGENVVLMG 176
           R + G L+  DQ  NLVL    E++     G   G I + G+ ++RG  +VL+ 
Sbjct: 48  RQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIA 101


>pdb|4EMK|C Chain C, Crystal Structure Of Splsm567
          Length = 113

 Score = 28.1 bits (61), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 4/54 (7%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERI---HVGNQYGDIPR-GIFIIRGENVVLMG 176
           R + G L+  DQ  NLVL    E++     G   G I + G+ ++RG  +VL+ 
Sbjct: 44  RQITGILKGFDQLXNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIA 97


>pdb|3N9Y|A Chain A, Crystal Structure Of Human Cyp11a1 In Complex With
           Cholesterol
 pdb|3N9Y|B Chain B, Crystal Structure Of Human Cyp11a1 In Complex With
           Cholesterol
 pdb|3N9Z|A Chain A, Crystal Structure Of Human Cyp11a1 In Complex With 22-
           Hydroxycholesterol
 pdb|3N9Z|B Chain B, Crystal Structure Of Human Cyp11a1 In Complex With 22-
           Hydroxycholesterol
 pdb|3NA1|A Chain A, Crystal Structure Of Human Cyp11a1 In Complex With 20-
           Hydroxycholesterol
 pdb|3NA1|B Chain B, Crystal Structure Of Human Cyp11a1 In Complex With 20-
           Hydroxycholesterol
          Length = 487

 Score = 28.1 bits (61), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 2/62 (3%)

Query: 118 QQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENV--VLM 175
           Q+ + P   +  +  L +V +    VLH+ I++   GN  GDI   +F    E++  V+ 
Sbjct: 116 QEVMAPEATKNFLPLLDAVSRDFVSVLHRRIKKAGSGNYSGDISDDLFRFAFESITNVIF 175

Query: 176 GE 177
           GE
Sbjct: 176 GE 177


>pdb|3NA0|A Chain A, Crystal Structure Of Human Cyp11a1 In Complex With 20,22-
           Dihydroxycholesterol
 pdb|3NA0|B Chain B, Crystal Structure Of Human Cyp11a1 In Complex With 20,22-
           Dihydroxycholesterol
          Length = 471

 Score = 28.1 bits (61), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 2/62 (3%)

Query: 118 QQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENV--VLM 175
           Q+ + P   +  +  L +V +    VLH+ I++   GN  GDI   +F    E++  V+ 
Sbjct: 113 QEVMAPEATKNFLPLLDAVSRDFVSVLHRRIKKAGSGNYSGDISDDLFRFAFESITNVIF 172

Query: 176 GE 177
           GE
Sbjct: 173 GE 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
   0.320    0.142    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,086,207
Number of Sequences: 62578
Number of extensions: 92619
Number of successful extensions: 142
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 137
Number of HSP's gapped (non-prelim): 8
length of query: 213
length of database: 14,973,337
effective HSP length: 95
effective length of query: 118
effective length of database: 9,028,427
effective search space: 1065354386
effective search space used: 1065354386
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)