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= psy1175
         (155 letters)

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

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



>pdb|4EMH|A Chain A, Crystal Structure Of Splsm4
 pdb|4EMH|B Chain B, Crystal Structure Of Splsm4
 pdb|4EMH|C Chain C, Crystal Structure Of Splsm4
 pdb|4EMH|D Chain D, Crystal Structure Of Splsm4
 pdb|4EMH|E Chain E, Crystal Structure Of Splsm4
 pdb|4EMH|F Chain F, Crystal Structure Of Splsm4
 pdb|4EMH|G Chain G, Crystal Structure Of Splsm4
 pdb|4EMH|H Chain H, Crystal Structure Of Splsm4
 pdb|4EMH|I Chain I, Crystal Structure Of Splsm4
 pdb|4EMH|J Chain J, Crystal Structure Of Splsm4
 pdb|4EMH|K Chain K, Crystal Structure Of Splsm4
 pdb|4EMH|L Chain L, Crystal Structure Of Splsm4
 pdb|4EMH|M Chain M, Crystal Structure Of Splsm4
 pdb|4EMH|N Chain N, Crystal Structure Of Splsm4
 pdb|4EMH|O Chain O, Crystal Structure Of Splsm4
 pdb|4EMH|P Chain P, Crystal Structure Of Splsm4
 pdb|4EMH|Q Chain Q, Crystal Structure Of Splsm4
 pdb|4EMH|R Chain R, Crystal Structure Of Splsm4
 pdb|4EMH|T Chain T, Crystal Structure Of Splsm4
 pdb|4EMH|U Chain U, Crystal Structure Of Splsm4
 pdb|4EMH|V Chain V, Crystal Structure Of Splsm4
 pdb|4EMH|W Chain W, Crystal Structure Of Splsm4
 pdb|4EMH|X Chain X, Crystal Structure Of Splsm4
 pdb|4EMH|Y Chain Y, Crystal Structure Of Splsm4
          Length = 105

 Score =  105 bits (263), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 47/72 (65%), Positives = 59/72 (81%)

Query: 1   MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDE 60
           +LVELKNGET+NGHL NCD++ N+ LREVI T  DGDKF+R+PECYIRG+ IKYLRI DE
Sbjct: 29  ILVELKNGETFNGHLENCDNYXNLTLREVIRTXPDGDKFFRLPECYIRGNNIKYLRIQDE 88

Query: 61  IIDMVKEDQVQR 72
           ++  V + Q Q+
Sbjct: 89  VLSQVAKQQAQQ 100


>pdb|3PGW|Z Chain Z, Crystal Structure Of Human U1 Snrnp
 pdb|3PGW|W Chain W, Crystal Structure Of Human U1 Snrnp
 pdb|2Y9A|D Chain D, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9A|K Chain K, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9A|R Chain R, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9B|D Chain D, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9B|K Chain K, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9B|R Chain R, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9C|D Chain D, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9C|K Chain K, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9C|R Chain R, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9D|D Chain D, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9D|K Chain K, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9D|R Chain R, Structure Of The Spliceosomal U4 Snrnp Core Domain
          Length = 126

 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 4  ELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPD 59
          E   GE Y G L+  +  MN  +  +  T RDG +  ++ + YIRGS I++L +PD
Sbjct: 21 ETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDG-RVAQLEQVYIRGSKIRFLILPD 75


>pdb|3CW1|D Chain D, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3CW1|S Chain S, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3CW1|T Chain T, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3CW1|U Chain U, Crystal Structure Of Human Spliceosomal U1 Snrnp
          Length = 126

 Score = 42.7 bits (99), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 4  ELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPD 59
          E   GE Y G L+  +  MN  +  +  T RDG +  ++ + YIRG  I++L +PD
Sbjct: 21 ETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDG-RVAQLEQVYIRGCKIRFLILPD 75


>pdb|1D3B|A Chain A, Crystal Structure Of The D3b Subcomplex Of The Human
          Core Snrnp Domain At 2.0a Resolution
 pdb|1D3B|C Chain C, Crystal Structure Of The D3b Subcomplex Of The Human
          Core Snrnp Domain At 2.0a Resolution
 pdb|1D3B|E Chain E, Crystal Structure Of The D3b Subcomplex Of The Human
          Core Snrnp Domain At 2.0a Resolution
 pdb|1D3B|G Chain G, Crystal Structure Of The D3b Subcomplex Of The Human
          Core Snrnp Domain At 2.0a Resolution
 pdb|1D3B|I Chain I, Crystal Structure Of The D3b Subcomplex Of The Human
          Core Snrnp Domain At 2.0a Resolution
 pdb|1D3B|K Chain K, Crystal Structure Of The D3b Subcomplex Of The Human
          Core Snrnp Domain At 2.0a Resolution
          Length = 75

 Score = 42.7 bits (99), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 4  ELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPD 59
          E   GE Y G L+  +  MN  +  +  T RDG +  ++ + YIRG  I++L +PD
Sbjct: 21 ETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDG-RVAQLEQVYIRGCKIRFLILPD 75


>pdb|1B34|A Chain A, Crystal Structure Of The D1d2 Sub-Complex From The Human
          Snrnp Core Domain
 pdb|3CW1|B Chain B, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3CW1|M Chain M, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3CW1|N Chain N, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3CW1|O Chain O, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3PGW|X Chain X, Crystal Structure Of Human U1 Snrnp
 pdb|3PGW|U Chain U, Crystal Structure Of Human U1 Snrnp
 pdb|2Y9A|B Chain B, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9A|I Chain I, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9A|P Chain P, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9B|B Chain B, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9B|I Chain I, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9B|P Chain P, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9C|B Chain B, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9C|I Chain I, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9C|P Chain P, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9D|B Chain B, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9D|I Chain I, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9D|P Chain P, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|3S6N|A Chain A, Crystal Structure Of The Gemin2-Binding Domain Of Smn,
          Gemin2 In Complex With Smd1D2FEG FROM HUMAN
 pdb|4F7U|A Chain A, Macromolecular Machine 6
 pdb|4F7U|C Chain C, Macromolecular Machine 6
 pdb|1VU2|A Chain A, The 8s Snrnp Assembly Intermediate
 pdb|1VU2|I Chain I, The 8s Snrnp Assembly Intermediate
 pdb|1VU2|Q Chain Q, The 8s Snrnp Assembly Intermediate
 pdb|1VU2|Y Chain Y, The 8s Snrnp Assembly Intermediate
 pdb|1VU2|GG Chain g, The 8s Snrnp Assembly Intermediate
 pdb|1VU2|OO Chain o, The 8s Snrnp Assembly Intermediate
 pdb|1VU2|WW Chain w, The 8s Snrnp Assembly Intermediate
 pdb|1VU3|A Chain A, The 8s Snrnp Assembly Intermediate
 pdb|1VU3|I Chain I, The 8s Snrnp Assembly Intermediate
 pdb|1VU3|Q Chain Q, The 8s Snrnp Assembly Intermediate
 pdb|1VU3|Y Chain Y, The 8s Snrnp Assembly Intermediate
 pdb|1VU3|GG Chain g, The 8s Snrnp Assembly Intermediate
 pdb|1VU3|OO Chain o, The 8s Snrnp Assembly Intermediate
 pdb|4F77|I Chain I, The 8s Snrnp Assembly Intermediate
 pdb|4F77|A Chain A, The 8s Snrnp Assembly Intermediate
 pdb|4F77|Q Chain Q, The 8s Snrnp Assembly Intermediate
 pdb|4F77|Y Chain Y, The 8s Snrnp Assembly Intermediate
 pdb|4F77|GG Chain g, The 8s Snrnp Assembly Intermediate
 pdb|4F77|OO Chain o, The 8s Snrnp Assembly Intermediate
 pdb|4F77|WW Chain w, The 8s Snrnp Assembly Intermediate
          Length = 119

 Score = 37.0 bits (84), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 3  VELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDEI 61
          +ELKNG   +G +   D  MN +L+ V  T ++ +   ++    IRG+ I+Y  +PD +
Sbjct: 17 IELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPV-QLETLSIRGNNIRYFILPDSL 74


>pdb|1M5Q|A Chain A, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|B Chain B, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|C Chain C, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|D Chain D, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|E Chain E, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|F Chain F, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|G Chain G, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|H Chain H, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|I Chain I, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|J Chain J, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|K Chain K, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|L Chain L, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|M Chain M, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|N Chain N, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|O Chain O, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|P Chain P, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|Q Chain Q, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|R Chain R, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|S Chain S, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|T Chain T, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|U Chain U, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|V Chain V, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|W Chain W, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|X Chain X, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|Y Chain Y, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|Z Chain Z, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|1 Chain 1, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
 pdb|1M5Q|2 Chain 2, Crystal Structure Of A Novel Sm-Like Archaeal Protein
          From Pyrobaculum Aerophilum
          Length = 130

 Score = 29.3 bits (64), Expect = 0.97,   Method: Compositional matrix adjust.
 Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 2/40 (5%)

Query: 3  VELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRM 42
          V L NGE Y G L   D+ +NI L     +++ G+KF R+
Sbjct: 15 VVLSNGEVYKGVLHAVDNQLNIVLAN--ASNKAGEKFNRV 52


>pdb|3CW1|F Chain F, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3CW1|Z Chain Z, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3CW1|1 Chain 1, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3CW1|2 Chain 2, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3PGW|F Chain F, Crystal Structure Of Human U1 Snrnp
 pdb|3PGW|I Chain I, Crystal Structure Of Human U1 Snrnp
 pdb|2Y9A|F Chain F, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9A|M Chain M, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9A|T Chain T, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9B|F Chain F, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9B|M Chain M, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9B|T Chain T, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9C|F Chain F, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9C|M Chain M, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9C|T Chain T, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9D|F Chain F, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9D|M Chain M, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|2Y9D|T Chain T, Structure Of The Spliceosomal U4 Snrnp Core Domain
 pdb|3S6N|F Chain F, Crystal Structure Of The Gemin2-Binding Domain Of Smn,
          Gemin2 In Complex With Smd1D2FEG FROM HUMAN
 pdb|4F7U|F Chain F, Macromolecular Machine 6
 pdb|4F7U|I Chain I, Macromolecular Machine 6
 pdb|1VU2|D Chain D, The 8s Snrnp Assembly Intermediate
 pdb|1VU2|L Chain L, The 8s Snrnp Assembly Intermediate
 pdb|1VU2|T Chain T, The 8s Snrnp Assembly Intermediate
 pdb|1VU2|BB Chain b, The 8s Snrnp Assembly Intermediate
 pdb|1VU2|JJ Chain j, The 8s Snrnp Assembly Intermediate
 pdb|1VU2|RR Chain r, The 8s Snrnp Assembly Intermediate
 pdb|1VU2|ZZ Chain z, The 8s Snrnp Assembly Intermediate
 pdb|1VU3|D Chain D, The 8s Snrnp Assembly Intermediate
 pdb|1VU3|L Chain L, The 8s Snrnp Assembly Intermediate
 pdb|1VU3|T Chain T, The 8s Snrnp Assembly Intermediate
 pdb|1VU3|BB Chain b, The 8s Snrnp Assembly Intermediate
 pdb|1VU3|JJ Chain j, The 8s Snrnp Assembly Intermediate
 pdb|1VU3|RR Chain r, The 8s Snrnp Assembly Intermediate
 pdb|4F77|L Chain L, The 8s Snrnp Assembly Intermediate
 pdb|4F77|D Chain D, The 8s Snrnp Assembly Intermediate
 pdb|4F77|T Chain T, The 8s Snrnp Assembly Intermediate
 pdb|4F77|BB Chain b, The 8s Snrnp Assembly Intermediate
 pdb|4F77|JJ Chain j, The 8s Snrnp Assembly Intermediate
 pdb|4F77|RR Chain r, The 8s Snrnp Assembly Intermediate
 pdb|4F77|ZZ Chain z, The 8s Snrnp Assembly Intermediate
          Length = 86

 Score = 28.9 bits (63), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 7/59 (11%)

Query: 1  MLVELKNGETYNGHLVNCDHWMNI---NLREVICTSRDGDKFWRMPECYIRGSMIKYLR 56
          ++V+LK G  Y G+LV+ D +MN+   N  E I    DG     + E  IR + + Y+R
Sbjct: 19 VMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYI----DGALSGHLGEVLIRCNNVLYIR 73


  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
   0.328    0.142    0.459 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,800,068
Number of Sequences: 62578
Number of extensions: 116493
Number of successful extensions: 263
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 254
Number of HSP's gapped (non-prelim): 7
length of query: 155
length of database: 14,973,337
effective HSP length: 91
effective length of query: 64
effective length of database: 9,278,739
effective search space: 593839296
effective search space used: 593839296
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 47 (22.7 bits)