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= 032108
(147 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 = 49.7 bits (117), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 30/69 (43%), Positives = 42/69 (60%), Gaps = 4/69 (5%)
Query: 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYV 70
L +L + K++LV LRD ++ G L SFDQ N +LE A E +I G++Y G V
Sbjct: 12 LGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDA-EEIIDGNVY---KRGTMV 67
Query: 71 IRGENVVLI 79
+RGENV+ I
Sbjct: 68 VRGENVLFI 76
>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 = 42.7 bits (99), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 42/83 (50%), Gaps = 9/83 (10%)
Query: 1 MSWAGPDDVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDL 60
MS A P + L ++DKKL + L GR + G L FD F N V++ E G
Sbjct: 1 MSKAHPPE------LKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQ 54
Query: 61 YCDIPLGLYVIRGENVVLIGELD 83
+G+ VIRG +++++ L+
Sbjct: 55 NN---IGMVVIRGNSIIMLEALE 74
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 43/80 (53%), Gaps = 5/80 (6%)
Query: 15 LASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIV---GDLYCDI-PLGLYV 70
L+ Y D+++ GR++ G L FDQ N VL+ E++ G L I LGL V
Sbjct: 32 LSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVV 91
Query: 71 IRGENVVLIGELDLERDELP 90
+RG +VLI +D +E+P
Sbjct: 92 VRGTTLVLIAPMDGS-EEIP 110
>pdb|4EMK|C Chain C, Crystal Structure Of Splsm567
Length = 113
Score = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 38/73 (52%), Gaps = 4/73 (5%)
Query: 15 LASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIV---GDLYCDI-PLGLYV 70
L+ Y D+++ GR++ G L FDQ N VL+ E++ G L I LGL V
Sbjct: 28 LSRYQDQRIQATFTGGRQITGILKGFDQLXNLVLDDVEEQLRNPEDGKLTGAIRKLGLVV 87
Query: 71 IRGENVVLIGELD 83
+RG +VLI D
Sbjct: 88 VRGTTLVLIAPXD 100
>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 = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/68 (41%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 15 LASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGE 74
LA L+ +LV L+ +++ G L S+DQ N VL + E I D LG VIRG+
Sbjct: 14 LAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEE--IQSD-GSGKKLGTIVIRGD 70
Query: 75 NVVLIGEL 82
NV+LI L
Sbjct: 71 NVILISPL 78
>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 = 33.9 bits (76), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 14 SLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRG 73
+L + L+ +++ L+ R+ G L SFD N VL A E + D LG +IRG
Sbjct: 19 ALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEE---LEDGEVTRRLGTVLIRG 75
Query: 74 ENVVLI 79
+N+V I
Sbjct: 76 DNIVYI 81
>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 = 33.9 bits (76), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 14 SLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRG 73
+L + L+ +++ L+ R+ G L SFD N VL A E + D LG +IRG
Sbjct: 17 ALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEE---LEDGEVTRRLGTVLIRG 73
Query: 74 ENVVLI 79
+N+V I
Sbjct: 74 DNIVYI 79
>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 = 33.9 bits (76), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 14 SLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRG 73
+L + L+ +++ L+ R+ G L SFD N VL A E + D LG +IRG
Sbjct: 17 ALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEE---LEDGEVTRRLGTVLIRG 73
Query: 74 ENVVLI 79
+N+V I
Sbjct: 74 DNIVYI 79
>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 = 33.9 bits (76), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 14 SLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRG 73
+L + L+ +++ L+ R+ G L SFD N VL A E + D LG +IRG
Sbjct: 17 ALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEE---LEDGEVTRRLGTVLIRG 73
Query: 74 ENVVLI 79
+N+V I
Sbjct: 74 DNIVYI 79
>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 = 33.5 bits (75), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 23/37 (62%)
Query: 19 LDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERV 55
LD+++ + LR R L+GTL +FD N VL A E +
Sbjct: 19 LDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETI 55
>pdb|1D3B|B Chain B, Crystal Structure Of The D3b Subcomplex Of The Human
Core Snrnp Domain At 2.0a Resolution
pdb|1D3B|D Chain D, Crystal Structure Of The D3b Subcomplex Of The Human
Core Snrnp Domain At 2.0a Resolution
pdb|1D3B|F Chain F, Crystal Structure Of The D3b Subcomplex Of The Human
Core Snrnp Domain At 2.0a Resolution
pdb|1D3B|H Chain H, Crystal Structure Of The D3b Subcomplex Of The Human
Core Snrnp Domain At 2.0a Resolution
pdb|1D3B|J Chain J, Crystal Structure Of The D3b Subcomplex Of The Human
Core Snrnp Domain At 2.0a Resolution
pdb|1D3B|L Chain L, Crystal Structure Of The D3b Subcomplex Of The Human
Core Snrnp Domain At 2.0a Resolution
Length = 91
Score = 32.3 bits (72), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 7/76 (9%)
Query: 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIP--- 65
V S+ + ++D ++ +L+DGR +GT +FD+ N +L E +
Sbjct: 3 VGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAERE 62
Query: 66 ----LGLYVIRGENVV 77
LGL ++RGEN+V
Sbjct: 63 EKRVLGLVLLRGENLV 78
>pdb|2Y9A|A Chain A, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9A|H Chain H, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9A|O Chain O, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9B|A Chain A, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9B|H Chain H, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9B|O Chain O, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9C|A Chain A, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9C|H Chain H, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9C|O Chain O, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9D|A Chain A, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9D|H Chain H, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9D|O Chain O, Structure Of The Spliceosomal U4 Snrnp Core Domain
Length = 95
Score = 32.3 bits (72), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 7/76 (9%)
Query: 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIP--- 65
V S+ + ++D ++ +L+DGR +GT +FD+ N +L E +
Sbjct: 3 VGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAERE 62
Query: 66 ----LGLYVIRGENVV 77
LGL ++RGEN+V
Sbjct: 63 EKRVLGLVLLRGENLV 78
>pdb|3PGW|B Chain B, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|Q Chain Q, Crystal Structure Of Human U1 Snrnp
Length = 231
Score = 31.2 bits (69), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 27/86 (31%)
Query: 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVL-----------------EGA 51
V S+ + ++D ++ +L+DGR +GT +FD+ N +L E
Sbjct: 3 VGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAERE 62
Query: 52 CERVIVGDLYCDIPLGLYVIRGENVV 77
+RV LGL ++RGEN+V
Sbjct: 63 EKRV----------LGLVLLRGENLV 78
>pdb|3CW1|A Chain A, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|H Chain H, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|I Chain I, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|J Chain J, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 174
Score = 30.8 bits (68), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 27/86 (31%)
Query: 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVL-----------------EGA 51
V S+ + ++D ++ +L+DGR +GT +FD+ N +L E
Sbjct: 3 VGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAERE 62
Query: 52 CERVIVGDLYCDIPLGLYVIRGENVV 77
+RV LGL ++RGEN+V
Sbjct: 63 EKRV----------LGLVLLRGENLV 78
>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 = 30.8 bits (68), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 3/65 (4%)
Query: 15 LASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGE 74
L L ++V L+ GR+ GTL +D N VL A E + G++ + G VIRG+
Sbjct: 9 LNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDA-EEIQNGEVVRKV--GSVVIRGD 65
Query: 75 NVVLI 79
VV +
Sbjct: 66 TVVFV 70
>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 = 30.4 bits (67), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 35/72 (48%), Gaps = 10/72 (13%)
Query: 19 LDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERV-IVGDLYCDIPLGLYVI------ 71
LD+ + V LR R+L G L ++D+ N VL A E V I D D L I
Sbjct: 18 LDEIVYVKLRGDRELNGRLHAYDEHLNXVLGDAEEIVTIFDDEETDKDKALKTIRKHYEX 77
Query: 72 ---RGENVVLIG 80
RG++V+LI
Sbjct: 78 LFVRGDSVILIA 89
>pdb|1B34|B Chain B, Crystal Structure Of The D1d2 Sub-Complex From The Human
Snrnp Core Domain
pdb|3CW1|C Chain C, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|P Chain P, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|Q Chain Q, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|R Chain R, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3PGW|Y Chain Y, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|V Chain V, Crystal Structure Of Human U1 Snrnp
pdb|2Y9A|C Chain C, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9A|J Chain J, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9A|Q Chain Q, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9B|C Chain C, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9B|J Chain J, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9B|Q Chain Q, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9C|C Chain C, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9C|J Chain J, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9C|Q Chain Q, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9D|C Chain C, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9D|J Chain J, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9D|Q Chain Q, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|3S6N|B Chain B, Crystal Structure Of The Gemin2-Binding Domain Of Smn,
Gemin2 In Complex With Smd1D2FEG FROM HUMAN
pdb|4F7U|B Chain B, Macromolecular Machine 6
pdb|4F7U|D Chain D, Macromolecular Machine 6
pdb|1VU2|B Chain B, The 8s Snrnp Assembly Intermediate
pdb|1VU2|J Chain J, The 8s Snrnp Assembly Intermediate
pdb|1VU2|R Chain R, The 8s Snrnp Assembly Intermediate
pdb|1VU2|Z Chain Z, The 8s Snrnp Assembly Intermediate
pdb|1VU2|HH Chain h, The 8s Snrnp Assembly Intermediate
pdb|1VU2|PP Chain p, The 8s Snrnp Assembly Intermediate
pdb|1VU2|XX Chain x, The 8s Snrnp Assembly Intermediate
pdb|1VU3|B Chain B, The 8s Snrnp Assembly Intermediate
pdb|1VU3|J Chain J, The 8s Snrnp Assembly Intermediate
pdb|1VU3|R Chain R, The 8s Snrnp Assembly Intermediate
pdb|1VU3|Z Chain Z, The 8s Snrnp Assembly Intermediate
pdb|1VU3|HH Chain h, The 8s Snrnp Assembly Intermediate
pdb|1VU3|PP Chain p, The 8s Snrnp Assembly Intermediate
pdb|4F77|J Chain J, The 8s Snrnp Assembly Intermediate
pdb|4F77|B Chain B, The 8s Snrnp Assembly Intermediate
pdb|4F77|R Chain R, The 8s Snrnp Assembly Intermediate
pdb|4F77|Z Chain Z, The 8s Snrnp Assembly Intermediate
pdb|4F77|HH Chain h, The 8s Snrnp Assembly Intermediate
pdb|4F77|PP Chain p, The 8s Snrnp Assembly Intermediate
pdb|4F77|XX Chain x, The 8s Snrnp Assembly Intermediate
Length = 118
Score = 28.5 bits (62), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 30/50 (60%), Gaps = 3/50 (6%)
Query: 4 AGPDDVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACE 53
GP V L+ S+ + + ++L+ R+ +KL+G + +FD+ N VLE E
Sbjct: 26 TGPLSV-LTQSVKN--NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKE 72
>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 = 28.5 bits (62), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 19 LDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACE 53
+ L V+++ R+ GTL FD + N VL+ E
Sbjct: 17 IGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTE 51
>pdb|1TLL|A Chain A, Crystal Structure Of Rat Neuronal Nitric-Oxide Synthase
Reductase Module At 2.3 A Resolution.
pdb|1TLL|B Chain B, Crystal Structure Of Rat Neuronal Nitric-Oxide Synthase
Reductase Module At 2.3 A Resolution
Length = 688
Score = 27.3 bits (59), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 25/46 (54%)
Query: 14 SLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGD 59
+L L + ++ +R+G +L G +F +A V + AC+ VGD
Sbjct: 160 TLLEELGGERILKMREGDELCGQEEAFRTWAKKVFKAACDVFCVGD 205
>pdb|4EMK|A Chain A, Crystal Structure Of Splsm567
Length = 94
Score = 27.3 bits (59), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 19 LDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACE 53
+ L V+ + R+ GTL FD + N VL+ E
Sbjct: 29 IGSNLWVIXKSEREFAGTLVGFDDYVNIVLKDVTE 63
>pdb|1RKI|A Chain A, Structure Of Pag5_736 From P. Aerophilum With Three
Disulphide Bonds
pdb|1RKI|B Chain B, Structure Of Pag5_736 From P. Aerophilum With Three
Disulphide Bonds
Length = 102
Score = 26.6 bits (57), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 10/73 (13%)
Query: 5 GPDDVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDI 64
GP VY+STSL + L+K L L +KL+ + FD+ N+ + C++ ++ ++
Sbjct: 38 GPSKVYVSTSLEN-LEKCL--QLHYFKKLVKNIEIFDEVHNS--KPNCDKCLIVEI---- 88
Query: 65 PLGLYVIRGENVV 77
G+Y +R N V
Sbjct: 89 -GGVYFVRRVNGV 100
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
0.329 0.146 0.445
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,887,495
Number of Sequences: 62578
Number of extensions: 133084
Number of successful extensions: 323
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 301
Number of HSP's gapped (non-prelim): 26
length of query: 147
length of database: 14,973,337
effective HSP length: 90
effective length of query: 57
effective length of database: 9,341,317
effective search space: 532455069
effective search space used: 532455069
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 47 (22.7 bits)