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= psy17123
(105 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 70.5 bits (171), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 32/56 (57%), Positives = 43/56 (76%)
Query: 12 AETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
++ +R RKESILDLS++ D+ I+ F GGR+ +GILKGFD L+NLVLD+ E LR
Sbjct: 18 SQPTERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLR 73
>pdb|4EMK|C Chain C, Crystal Structure Of Splsm567
Length = 113
Score = 68.9 bits (167), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 32/56 (57%), Positives = 42/56 (75%)
Query: 12 AETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
++ +R RKESILDLS++ D+ I+ F GGR+ +GILKGFD L NLVLD+ E LR
Sbjct: 14 SQPTERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLXNLVLDDVEEQLR 69
>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 = 51.2 bits (121), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 21/41 (51%), Positives = 28/41 (68%)
Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
+L KF+DK + +K GGR GIL+GFDP +NLV+D E
Sbjct: 8 ELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEM 48
>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 = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 34/64 (53%), Gaps = 5/64 (7%)
Query: 6 TTTDAGAETKDRKRKESILDLSKFLDKVIR----VKFAGGRECSGILKGFDPLLNLVLDN 61
T + ++K IL L+ +DK I V G +E SG+L+GFD +N+VLD+
Sbjct: 10 TPANKSQGGSNQKGGNIILPLA-LIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDD 68
Query: 62 TTEY 65
EY
Sbjct: 69 VQEY 72
>pdb|1LOJ|A Chain A, Crystal Structure Of A Methanobacterial Sm-Like Archaeal
Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump)
pdb|1LOJ|B Chain B, Crystal Structure Of A Methanobacterial Sm-Like Archaeal
Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump)
pdb|1LOJ|C Chain C, Crystal Structure Of A Methanobacterial Sm-Like Archaeal
Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump)
pdb|1LOJ|D Chain D, Crystal Structure Of A Methanobacterial Sm-Like Archaeal
Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump)
pdb|1LOJ|E Chain E, Crystal Structure Of A Methanobacterial Sm-Like Archaeal
Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump)
pdb|1LOJ|F Chain F, Crystal Structure Of A Methanobacterial Sm-Like Archaeal
Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump)
pdb|1LOJ|G Chain G, Crystal Structure Of A Methanobacterial Sm-Like Archaeal
Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump)
pdb|1LOJ|H Chain H, Crystal Structure Of A Methanobacterial Sm-Like Archaeal
Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump)
pdb|1LOJ|I Chain I, Crystal Structure Of A Methanobacterial Sm-Like Archaeal
Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump)
pdb|1LOJ|J Chain J, Crystal Structure Of A Methanobacterial Sm-Like Archaeal
Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump)
pdb|1LOJ|K Chain K, Crystal Structure Of A Methanobacterial Sm-Like Archaeal
Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump)
pdb|1LOJ|L Chain L, Crystal Structure Of A Methanobacterial Sm-Like Archaeal
Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump)
pdb|1LOJ|M Chain M, Crystal Structure Of A Methanobacterial Sm-Like Archaeal
Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump)
pdb|1LOJ|N Chain N, Crystal Structure Of A Methanobacterial Sm-Like Archaeal
Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump)
Length = 87
Score = 32.7 bits (73), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
L L+ + +K G RE G+LK FD +NLVL++ E
Sbjct: 18 LGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEEL 57
>pdb|1JBM|A Chain A, Heptameric Crystal Structure Of Mth649, An Sm-Like
Archaeal Protein From Methanobacterium
Thermautotrophicum
pdb|1JBM|B Chain B, Heptameric Crystal Structure Of Mth649, An Sm-Like
Archaeal Protein From Methanobacterium
Thermautotrophicum
pdb|1JBM|C Chain C, Heptameric Crystal Structure Of Mth649, An Sm-Like
Archaeal Protein From Methanobacterium
Thermautotrophicum
pdb|1JBM|D Chain D, Heptameric Crystal Structure Of Mth649, An Sm-Like
Archaeal Protein From Methanobacterium
Thermautotrophicum
pdb|1JBM|E Chain E, Heptameric Crystal Structure Of Mth649, An Sm-Like
Archaeal Protein From Methanobacterium
Thermautotrophicum
pdb|1JBM|F Chain F, Heptameric Crystal Structure Of Mth649, An Sm-Like
Archaeal Protein From Methanobacterium
Thermautotrophicum
pdb|1JBM|G Chain G, Heptameric Crystal Structure Of Mth649, An Sm-Like
Archaeal Protein From Methanobacterium
Thermautotrophicum
Length = 86
Score = 32.7 bits (73), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
L L+ + +K G RE G+LK FD +NLVL++ E
Sbjct: 18 LGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEEL 57
>pdb|1JRI|A Chain A, The Crystal Structure Of An Sm-Like Archaeal Protein
With Two Heptamers In The Asymmetric Unit.
pdb|1JRI|B Chain B, The Crystal Structure Of An Sm-Like Archaeal Protein
With Two Heptamers In The Asymmetric Unit.
pdb|1JRI|C Chain C, The Crystal Structure Of An Sm-Like Archaeal Protein
With Two Heptamers In The Asymmetric Unit.
pdb|1JRI|D Chain D, The Crystal Structure Of An Sm-Like Archaeal Protein
With Two Heptamers In The Asymmetric Unit.
pdb|1JRI|E Chain E, The Crystal Structure Of An Sm-Like Archaeal Protein
With Two Heptamers In The Asymmetric Unit.
pdb|1JRI|F Chain F, The Crystal Structure Of An Sm-Like Archaeal Protein
With Two Heptamers In The Asymmetric Unit.
pdb|1JRI|G Chain G, The Crystal Structure Of An Sm-Like Archaeal Protein
With Two Heptamers In The Asymmetric Unit.
pdb|1JRI|H Chain H, The Crystal Structure Of An Sm-Like Archaeal Protein
With Two Heptamers In The Asymmetric Unit.
pdb|1JRI|I Chain I, The Crystal Structure Of An Sm-Like Archaeal Protein
With Two Heptamers In The Asymmetric Unit.
pdb|1JRI|J Chain J, The Crystal Structure Of An Sm-Like Archaeal Protein
With Two Heptamers In The Asymmetric Unit.
pdb|1JRI|K Chain K, The Crystal Structure Of An Sm-Like Archaeal Protein
With Two Heptamers In The Asymmetric Unit.
pdb|1JRI|L Chain L, The Crystal Structure Of An Sm-Like Archaeal Protein
With Two Heptamers In The Asymmetric Unit.
pdb|1JRI|M Chain M, The Crystal Structure Of An Sm-Like Archaeal Protein
With Two Heptamers In The Asymmetric Unit.
pdb|1JRI|N Chain N, The Crystal Structure Of An Sm-Like Archaeal Protein
With Two Heptamers In The Asymmetric Unit
Length = 85
Score = 32.7 bits (73), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
L L+ + +K G RE G+LK FD +NLVL++ E
Sbjct: 18 LGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEEL 57
>pdb|1I81|A Chain A, Crystal Structure Of A Heptameric Lsm Protein From
Methanobacterium Thermoautotrophicum
pdb|1I81|B Chain B, Crystal Structure Of A Heptameric Lsm Protein From
Methanobacterium Thermoautotrophicum
pdb|1I81|C Chain C, Crystal Structure Of A Heptameric Lsm Protein From
Methanobacterium Thermoautotrophicum
pdb|1I81|D Chain D, Crystal Structure Of A Heptameric Lsm Protein From
Methanobacterium Thermoautotrophicum
pdb|1I81|E Chain E, Crystal Structure Of A Heptameric Lsm Protein From
Methanobacterium Thermoautotrophicum
pdb|1I81|F Chain F, Crystal Structure Of A Heptameric Lsm Protein From
Methanobacterium Thermoautotrophicum
pdb|1I81|G Chain G, Crystal Structure Of A Heptameric Lsm Protein From
Methanobacterium Thermoautotrophicum
pdb|1MGQ|A Chain A, Crystal Structure Of A Heptameric Sm-Like Protein From
Methanobacterium Thermoautotrophicum
pdb|1MGQ|B Chain B, Crystal Structure Of A Heptameric Sm-Like Protein From
Methanobacterium Thermoautotrophicum
pdb|1MGQ|C Chain C, Crystal Structure Of A Heptameric Sm-Like Protein From
Methanobacterium Thermoautotrophicum
pdb|1MGQ|D Chain D, Crystal Structure Of A Heptameric Sm-Like Protein From
Methanobacterium Thermoautotrophicum
pdb|1MGQ|E Chain E, Crystal Structure Of A Heptameric Sm-Like Protein From
Methanobacterium Thermoautotrophicum
pdb|1MGQ|F Chain F, Crystal Structure Of A Heptameric Sm-Like Protein From
Methanobacterium Thermoautotrophicum
pdb|1MGQ|G Chain G, Crystal Structure Of A Heptameric Sm-Like Protein From
Methanobacterium Thermoautotrophicum
Length = 83
Score = 32.3 bits (72), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTE 64
L L+ + +K G RE G+LK FD +NLVL++ E
Sbjct: 20 LGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEE 58
>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 = 32.3 bits (72), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 26/39 (66%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTE 64
L++ L+ ++ VK G +E G+L+ +D +NLVL ++ E
Sbjct: 14 LAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEE 52
>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 = 32.0 bits (71), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 21 ESILDLSKF-LDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYL 66
E+ LDL K LD+ + +K G R G L+ FD N+VL + E +
Sbjct: 9 ETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETI 55
>pdb|4EMK|A Chain A, Crystal Structure Of Splsm567
Length = 94
Score = 30.0 bits (66), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 15/28 (53%), Positives = 19/28 (67%)
Query: 42 RECSGILKGFDPLLNLVLDNTTEYLRVT 69
RE +G L GFD +N+VL + TEY VT
Sbjct: 41 REFAGTLVGFDDYVNIVLKDVTEYDTVT 68
>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 = 30.0 bits (66), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 15/28 (53%), Positives = 19/28 (67%)
Query: 42 RECSGILKGFDPLLNLVLDNTTEYLRVT 69
RE +G L GFD +N+VL + TEY VT
Sbjct: 29 REFAGTLVGFDDYVNIVLKDVTEYDTVT 56
>pdb|1I5L|A Chain A, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus Complexed With Short Poly-U Rna
pdb|1I5L|B Chain B, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus Complexed With Short Poly-U Rna
pdb|1I5L|C Chain C, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus Complexed With Short Poly-U Rna
pdb|1I5L|D Chain D, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus Complexed With Short Poly-U Rna
pdb|1I5L|E Chain E, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus Complexed With Short Poly-U Rna
pdb|1I5L|F Chain F, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus Complexed With Short Poly-U Rna
pdb|1I5L|G Chain G, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus Complexed With Short Poly-U Rna
pdb|1I5L|H Chain H, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus Complexed With Short Poly-U Rna
pdb|1I5L|I Chain I, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus Complexed With Short Poly-U Rna
pdb|1I5L|J Chain J, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus Complexed With Short Poly-U Rna
pdb|1I5L|K Chain K, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus Complexed With Short Poly-U Rna
pdb|1I5L|L Chain L, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus Complexed With Short Poly-U Rna
pdb|1I5L|M Chain M, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus Complexed With Short Poly-U Rna
pdb|1I5L|N Chain N, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus Complexed With Short Poly-U Rna
pdb|1I4K|A Chain A, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|B Chain B, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|C Chain C, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|D Chain D, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|E Chain E, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|F Chain F, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|G Chain G, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|H Chain H, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|I Chain I, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|J Chain J, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|K Chain K, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|L Chain L, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|M Chain M, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|N Chain N, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|O Chain O, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|P Chain P, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|Q Chain Q, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|R Chain R, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|S Chain S, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|T Chain T, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|U Chain U, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|V Chain V, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|W Chain W, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|X Chain X, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|Y Chain Y, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|Z Chain Z, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|1 Chain 1, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
pdb|1I4K|2 Chain 2, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From
Archaeoglobus Fulgidus At 2.5a Resolution
Length = 77
Score = 29.6 bits (65), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTE 64
L++ L + V+ GGRE G L G+D +NLVL + E
Sbjct: 9 LNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEE 47
>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 = 29.6 bits (65), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 24/41 (58%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYL 66
L+K + K + ++ + G + GIL D +NL L+ T EY+
Sbjct: 11 LNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYV 51
>pdb|4EMK|B Chain B, Crystal Structure Of Splsm567
Length = 75
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 23/41 (56%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYL 66
L+K + K + ++ + G + GIL D NL L+ T EY+
Sbjct: 9 LNKVIGKKVLIRLSSGVDYKGILSCLDGYXNLALERTEEYV 49
>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 = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTT 63
+ +L+ L + ++V + G G+L D LN+VL N +
Sbjct: 2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANAS 42
>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 = 26.2 bits (56), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYL 66
L + K + VK E GIL+ FD +NL+L++ E +
Sbjct: 16 LQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEII 56
>pdb|1LJO|A Chain A, Crystal Structure Of An Sm-Like Protein (Af-Sm2) From
Archaeoglobus Fulgidus At 1.95a Resolution
Length = 77
Score = 25.4 bits (54), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 27/57 (47%), Gaps = 5/57 (8%)
Query: 29 FLDKVIRVKFAGGR-ECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRR 84
+ K+IRV+ G + G L+G D +NL L N E +VRS IV R
Sbjct: 13 MVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAME----CKGEEKVRSLGEIVLR 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
0.319 0.133 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,893,963
Number of Sequences: 62578
Number of extensions: 103230
Number of successful extensions: 189
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 172
Number of HSP's gapped (non-prelim): 19
length of query: 105
length of database: 14,973,337
effective HSP length: 70
effective length of query: 35
effective length of database: 10,592,877
effective search space: 370750695
effective search space used: 370750695
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: 45 (21.9 bits)