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= psy6026
         (98 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 = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 50/89 (56%), Gaps = 3/89 (3%)

Query: 5   LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCF 64
           L  +   +  G+ ++VELKN  +  G L + D Y N+ L ++  T PD       +  C+
Sbjct: 16  LPLTLLNATQGRPILVELKNGETFNGHLENCDNYXNLTLREVIRTXPDG-DKFFRLPECY 74

Query: 65  IRGSVVRYVQLPGDEVDTQLL-QDATRKE 92
           IRG+ ++Y+++  DEV +Q+  Q A ++E
Sbjct: 75  IRGNNIKYLRIQ-DEVLSQVAKQQAQQRE 102


>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 = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 2/68 (2%)

Query: 9  FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
          F   L  + V +ELKN   + GT+  VD  +N  L  + +T  ++ P  + ++   IRG+
Sbjct: 6  FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREP--VQLETLSIRGN 63

Query: 69 VVRYVQLP 76
           +RY  LP
Sbjct: 64 NIRYFILP 71


>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 = 33.5 bits (75), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 16/37 (43%), Positives = 23/37 (62%)

Query: 9  FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTD 45
          F   L GK V+V+LK  +   G L SVD Y+N++L +
Sbjct: 10 FLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLAN 46


>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 = 33.5 bits (75), Expect = 0.030,   Method: Compositional matrix adjust.
 Identities = 18/53 (33%), Positives = 28/53 (52%)

Query: 6  FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHML 58
          F +   +L+G++V V L N     G LH+VD  LNI L + S    +K+  + 
Sbjct: 1  FVAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRVF 53


>pdb|1LJO|A Chain A, Crystal Structure Of An Sm-Like Protein (Af-Sm2) From
          Archaeoglobus Fulgidus At 1.95a Resolution
          Length = 77

 Score = 32.7 bits (73), Expect = 0.047,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 4/77 (5%)

Query: 4  LLFYSFFKSLVGKDVVVELKNDVS-ICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKN 62
          +L     KS+VGK + VE+K + + + G L  VD Y+N+ LT+      ++   + S+  
Sbjct: 4  VLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEE--KVRSLGE 61

Query: 63 CFIRGSVVRYVQLPGDE 79
            +RG+ V  +Q P +E
Sbjct: 62 IVLRGNNVVLIQ-PQEE 77


>pdb|3SWN|B Chain B, Structure Of The Lsm657 Complex: An Assembly
          Intermediate Of The Lsm1 7 And Lsm2 8 Rings
 pdb|3SWN|E Chain E, Structure Of The Lsm657 Complex: An Assembly
          Intermediate Of The Lsm1 7 And Lsm2 8 Rings
 pdb|3SWN|Q Chain Q, Structure Of The Lsm657 Complex: An Assembly
          Intermediate Of The Lsm1 7 And Lsm2 8 Rings
 pdb|3SWN|T Chain T, Structure Of The Lsm657 Complex: An Assembly
          Intermediate Of The Lsm1 7 And Lsm2 8 Rings
          Length = 77

 Score = 32.0 bits (71), Expect = 0.084,   Method: Compositional matrix adjust.
 Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 2/66 (3%)

Query: 9  FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
          F   ++GK V++ L + V   G L  +D Y+N+ L         K  ++    + FIRG+
Sbjct: 10 FLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYG--DAFIRGN 67

Query: 69 VVRYVQ 74
           V YV 
Sbjct: 68 NVLYVS 73


>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 = 31.6 bits (70), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 6/66 (9%)

Query: 14 VGKDVVVELKNDVSICGTLHSVDQYLNIKLTDI-SVTDPDKYPHMLSVKNCFIRGSVVRY 72
          +GK V+V+L++   I G L S DQ++N+ L D   + D + Y     V    +RG  V +
Sbjct: 20 IGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMV----VRGENVLF 75

Query: 73 VQ-LPG 77
          +  +PG
Sbjct: 76 ISPVPG 81


>pdb|4EMK|B Chain B, Crystal Structure Of Splsm567
          Length = 75

 Score = 30.8 bits (68), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 2/66 (3%)

Query: 9  FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
          F   ++GK V++ L + V   G L  +D Y N+ L         K  ++    + FIRG+
Sbjct: 8  FLNKVIGKKVLIRLSSGVDYKGILSCLDGYXNLALERTEEYVNGKKTNVYG--DAFIRGN 65

Query: 69 VVRYVQ 74
           V YV 
Sbjct: 66 NVLYVS 71


>pdb|1N9S|A Chain A, Crystal Structure Of Yeast Smf In Spacegroup P43212
 pdb|1N9S|B Chain B, Crystal Structure Of Yeast Smf In Spacegroup P43212
 pdb|1N9S|C Chain C, Crystal Structure Of Yeast Smf In Spacegroup P43212
 pdb|1N9S|D Chain D, Crystal Structure Of Yeast Smf In Spacegroup P43212
 pdb|1N9S|E Chain E, Crystal Structure Of Yeast Smf In Spacegroup P43212
 pdb|1N9S|F Chain F, Crystal Structure Of Yeast Smf In Spacegroup P43212
 pdb|1N9S|G Chain G, Crystal Structure Of Yeast Smf In Spacegroup P43212
 pdb|1N9S|H Chain H, Crystal Structure Of Yeast Smf In Spacegroup P43212
 pdb|1N9S|I Chain I, Crystal Structure Of Yeast Smf In Spacegroup P43212
 pdb|1N9S|J Chain J, Crystal Structure Of Yeast Smf In Spacegroup P43212
 pdb|1N9S|K Chain K, Crystal Structure Of Yeast Smf In Spacegroup P43212
 pdb|1N9S|L Chain L, Crystal Structure Of Yeast Smf In Spacegroup P43212
 pdb|1N9S|M Chain M, Crystal Structure Of Yeast Smf In Spacegroup P43212
 pdb|1N9S|N Chain N, Crystal Structure Of Yeast Smf In Spacegroup P43212
          Length = 93

 Score = 29.6 bits (65), Expect = 0.42,   Method: Compositional matrix adjust.
 Identities = 17/38 (44%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 9  FFKSLVGKDVVVELK-NDVSICGTLHSVDQYLNIKLTD 45
          F K LV   V V+LK N     GTL S D Y N++L +
Sbjct: 25 FLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNE 62


>pdb|1N9R|A Chain A, Crystal Structure Of A Heptameric Ring Complex Of Yeast
          Smf In Spacegroup P4122
 pdb|1N9R|B Chain B, Crystal Structure Of A Heptameric Ring Complex Of Yeast
          Smf In Spacegroup P4122
 pdb|1N9R|C Chain C, Crystal Structure Of A Heptameric Ring Complex Of Yeast
          Smf In Spacegroup P4122
 pdb|1N9R|D Chain D, Crystal Structure Of A Heptameric Ring Complex Of Yeast
          Smf In Spacegroup P4122
 pdb|1N9R|E Chain E, Crystal Structure Of A Heptameric Ring Complex Of Yeast
          Smf In Spacegroup P4122
 pdb|1N9R|F Chain F, Crystal Structure Of A Heptameric Ring Complex Of Yeast
          Smf In Spacegroup P4122
 pdb|1N9R|G Chain G, Crystal Structure Of A Heptameric Ring Complex Of Yeast
          Smf In Spacegroup P4122
          Length = 93

 Score = 29.3 bits (64), Expect = 0.52,   Method: Compositional matrix adjust.
 Identities = 17/38 (44%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 9  FFKSLVGKDVVVELK-NDVSICGTLHSVDQYLNIKLTD 45
          F K LV   V V+LK N     GTL S D Y N++L +
Sbjct: 25 FLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNE 62


>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 = 28.5 bits (62), Expect = 0.94,   Method: Compositional matrix adjust.
 Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 5/69 (7%)

Query: 18 VVVELKNDVSICGTLHSVDQYLNIKLTDI--SVTDPDKYPHMLSVKNC---FIRGSVVRY 72
          V ++L+   ++ GTL + D + NI L+D   ++   +      S + C   FIRG  V  
Sbjct: 23 VYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTL 82

Query: 73 VQLPGDEVD 81
          +  P ++ D
Sbjct: 83 ISTPSEDDD 91


>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 = 28.5 bits (62), Expect = 0.98,   Method: Compositional matrix adjust.
 Identities = 14/47 (29%), Positives = 28/47 (59%), Gaps = 2/47 (4%)

Query: 30 GTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLP 76
          G L   +  +N ++++I+VT  D    +  ++  +IRGS +R++ LP
Sbjct: 30 GKLIEAEDNMNCQMSNITVTYRD--GRVAQLEQVYIRGSKIRFLILP 74


>pdb|4EMG|A Chain A, Crystal Structure Of Splsm3
 pdb|4EMG|B Chain B, Crystal Structure Of Splsm3
 pdb|4EMG|C Chain C, Crystal Structure Of Splsm3
 pdb|4EMG|D Chain D, Crystal Structure Of Splsm3
 pdb|4EMG|E Chain E, Crystal Structure Of Splsm3
 pdb|4EMG|F Chain F, Crystal Structure Of Splsm3
 pdb|4EMG|G Chain G, Crystal Structure Of Splsm3
 pdb|4EMG|H Chain H, Crystal Structure Of Splsm3
 pdb|4EMG|I Chain I, Crystal Structure Of Splsm3
 pdb|4EMG|J Chain J, Crystal Structure Of Splsm3
 pdb|4EMG|K Chain K, Crystal Structure Of Splsm3
 pdb|4EMG|L Chain L, Crystal Structure Of Splsm3
 pdb|4EMG|M Chain M, Crystal Structure Of Splsm3
 pdb|4EMG|N Chain N, Crystal Structure Of Splsm3
          Length = 93

 Score = 28.1 bits (61), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 31/70 (44%), Gaps = 11/70 (15%)

Query: 18 VVVELKNDVSICGTLHSVDQYLNIKLTDI---------SVTDPDKYPHML--SVKNCFIR 66
          V V+L+ D  + G LH+ D++LN  L D            TD DK    +    +  F+R
Sbjct: 22 VYVKLRGDRELNGRLHAYDEHLNXVLGDAEEIVTIFDDEETDKDKALKTIRKHYEXLFVR 81

Query: 67 GSVVRYVQLP 76
          G  V  +  P
Sbjct: 82 GDSVILIAPP 91


>pdb|3VKG|A Chain A, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
            Domain
 pdb|3VKG|B Chain B, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
            Domain
          Length = 3245

 Score = 28.1 bits (61), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 4/62 (6%)

Query: 24   NDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQ 83
            ND  + G L S+D ++++     S  DPDK P  ++V+   I GS + Y     +E D +
Sbjct: 2814 NDADLRGALDSIDYWVDLYSKGRSNIDPDKIP-WIAVRT--ILGSTI-YGGRIDNEFDMR 2869

Query: 84   LL 85
            LL
Sbjct: 2870 LL 2871


>pdb|3VKH|A Chain A, X-Ray Structure Of A Functional Full-Length Dynein Motor
            Domain
 pdb|3VKH|B Chain B, X-Ray Structure Of A Functional Full-Length Dynein Motor
            Domain
          Length = 3367

 Score = 28.1 bits (61), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 4/62 (6%)

Query: 24   NDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQ 83
            ND  + G L S+D ++++     S  DPDK P  ++V+   I GS + Y     +E D +
Sbjct: 2936 NDADLRGALDSIDYWVDLYSKGRSNIDPDKIP-WIAVRT--ILGSTI-YGGRIDNEFDMR 2991

Query: 84   LL 85
            LL
Sbjct: 2992 LL 2993


>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 = 27.7 bits (60), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 2/50 (4%)

Query: 18 VVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRG 67
          V+V+LK +  + G L S DQ++N+ L+D      D     L      IRG
Sbjct: 22 VLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGT--IVIRG 69


>pdb|3SWN|A Chain A, Structure Of The Lsm657 Complex: An Assembly
          Intermediate Of The Lsm1 7 And Lsm2 8 Rings
 pdb|3SWN|D Chain D, Structure Of The Lsm657 Complex: An Assembly
          Intermediate Of The Lsm1 7 And Lsm2 8 Rings
 pdb|3SWN|P Chain P, Structure Of The Lsm657 Complex: An Assembly
          Intermediate Of The Lsm1 7 And Lsm2 8 Rings
 pdb|3SWN|S Chain S, Structure Of The Lsm657 Complex: An Assembly
          Intermediate Of The Lsm1 7 And Lsm2 8 Rings
          Length = 82

 Score = 26.9 bits (58), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 13/37 (35%), Positives = 22/37 (59%)

Query: 14 VGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTD 50
          +G ++ V +K++    GTL   D Y+NI L D++  D
Sbjct: 17 IGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYD 53


>pdb|2FWK|A Chain A, Crystal Structure Of Cryptosporidium Parvum U6 Snrna-
          Associated Sm-Like Protein Lsm5
 pdb|2FWK|B Chain B, Crystal Structure Of Cryptosporidium Parvum U6 Snrna-
          Associated Sm-Like Protein Lsm5
 pdb|3PGG|A Chain A, Crystal Structure Of Cryptosporidium Parvum U6
          Snrna-Associated Sm- Like Protein Lsm5
 pdb|3PGG|B Chain B, Crystal Structure Of Cryptosporidium Parvum U6
          Snrna-Associated Sm- Like Protein Lsm5
          Length = 121

 Score = 26.9 bits (58), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 11/33 (33%), Positives = 18/33 (54%)

Query: 14 VGKDVVVELKNDVSICGTLHSVDQYLNIKLTDI 46
          +G  + V +K D    G L   D+Y+N+ L D+
Sbjct: 37 IGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDV 69


>pdb|4EMK|A Chain A, Crystal Structure Of Splsm567
          Length = 94

 Score = 25.8 bits (55), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 14/47 (29%), Positives = 23/47 (48%)

Query: 4  LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTD 50
          +L        +G ++ V  K++    GTL   D Y+NI L D++  D
Sbjct: 19 ILPLELIDKCIGSNLWVIXKSEREFAGTLVGFDDYVNIVLKDVTEYD 65


  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
   0.321    0.137    0.391 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,720,243
Number of Sequences: 62578
Number of extensions: 95863
Number of successful extensions: 273
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 258
Number of HSP's gapped (non-prelim): 24
length of query: 98
length of database: 14,973,337
effective HSP length: 64
effective length of query: 34
effective length of database: 10,968,345
effective search space: 372923730
effective search space used: 372923730
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)