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= 034299
(98 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 42/65 (64%), Gaps = 4/65 (6%)
Query: 5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYII 64
P L+ +++++S+ N GR++ G+L+GFD N+++DE E S QQ +G+ +I
Sbjct: 7 PELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSG----QQNNIGMVVI 62
Query: 65 RGDNI 69
RG++I
Sbjct: 63 RGNSI 67
>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 = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 7/75 (9%)
Query: 7 LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLV-----LGL 61
L +Q+I GR I G+LKGFDQ N++LD+ E++ + ++G +L LGL
Sbjct: 32 LSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDG--KLTGAIRKLGL 89
Query: 62 YIIRGDNISIVGEVD 76
++RG + ++ +D
Sbjct: 90 VVVRGTTLVLIAPMD 104
>pdb|4EMK|C Chain C, Crystal Structure Of Splsm567
Length = 113
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 7/75 (9%)
Query: 7 LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLV-----LGL 61
L +Q+I GR I G+LKGFDQ N++LD+ E++ + ++G +L LGL
Sbjct: 28 LSRYQDQRIQATFTGGRQITGILKGFDQLXNLVLDDVEEQLRNPEDG--KLTGAIRKLGL 85
Query: 62 YIIRGDNISIVGEVD 76
++RG + ++ D
Sbjct: 86 VVVRGTTLVLIAPXD 100
>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 = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 6/65 (9%)
Query: 11 VEQQISVITNDGRNIVGVLKGFDQATNIILDESHE-RVYSTKEGVQ-----QLVLGLYII 64
++ ++ I DGR +G K FD+ N+IL + E R K Q + VLGL ++
Sbjct: 13 IDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLL 72
Query: 65 RGDNI 69
RG+N+
Sbjct: 73 RGENL 77
>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 = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 6/65 (9%)
Query: 11 VEQQISVITNDGRNIVGVLKGFDQATNIILDESHE-RVYSTKEGVQ-----QLVLGLYII 64
++ ++ I DGR +G K FD+ N+IL + E R K Q + VLGL ++
Sbjct: 13 IDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLL 72
Query: 65 RGDNI 69
RG+N+
Sbjct: 73 RGENL 77
>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 = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 6/65 (9%)
Query: 11 VEQQISVITNDGRNIVGVLKGFDQATNIILDESHE-RVYSTKEGVQ-----QLVLGLYII 64
++ ++ I DGR +G K FD+ N+IL + E R K Q + VLGL ++
Sbjct: 13 IDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLL 72
Query: 65 RGDNI 69
RG+N+
Sbjct: 73 RGENL 77
>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 = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 6/65 (9%)
Query: 11 VEQQISVITNDGRNIVGVLKGFDQATNIILDESHE-RVYSTKEGVQ-----QLVLGLYII 64
++ ++ I DGR +G K FD+ N+IL + E R K Q + VLGL ++
Sbjct: 13 IDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLL 72
Query: 65 RGDNI 69
RG+N+
Sbjct: 73 RGENL 77
>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 = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 13/76 (17%)
Query: 4 GPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHE----RVYSTKEGVQQLVL 59
G L+ + +Q+ V D I G+L+ FDQ N++L+++ E VY
Sbjct: 13 GATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKR--------- 63
Query: 60 GLYIIRGDNISIVGEV 75
G ++RG+N+ + V
Sbjct: 64 GTMVVRGENVLFISPV 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 = 33.9 bits (76), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 42/82 (51%), Gaps = 11/82 (13%)
Query: 11 VEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVY-------STKEGVQQLVLGLYI 63
+++++ + R +VG L+ FD NI+L ++ E +Y S E ++V
Sbjct: 19 LDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVF---- 74
Query: 64 IRGDNISIVGEVDEELDSHLDL 85
IRGD ++++ E+ D +++
Sbjct: 75 IRGDTVTLISTPSEDDDGAVEI 96
>pdb|3CW1|E Chain E, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|W Chain W, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|X Chain X, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|Y Chain Y, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3PGW|E Chain E, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|H Chain H, Crystal Structure Of Human U1 Snrnp
pdb|2Y9A|E Chain E, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9A|L Chain L, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9A|S Chain S, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9B|E Chain E, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9B|L Chain L, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9B|S Chain S, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9C|E Chain E, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9C|L Chain L, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9C|S Chain S, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9D|E Chain E, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9D|L Chain L, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9D|S Chain S, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|3S6N|E Chain E, Crystal Structure Of The Gemin2-Binding Domain Of Smn,
Gemin2 In Complex With Smd1D2FEG FROM HUMAN
pdb|4F7U|E Chain E, Macromolecular Machine 6
pdb|4F7U|H Chain H, Macromolecular Machine 6
pdb|1VU2|C Chain C, The 8s Snrnp Assembly Intermediate
pdb|1VU2|K Chain K, The 8s Snrnp Assembly Intermediate
pdb|1VU2|S Chain S, The 8s Snrnp Assembly Intermediate
pdb|1VU2|AA Chain a, The 8s Snrnp Assembly Intermediate
pdb|1VU2|II Chain i, The 8s Snrnp Assembly Intermediate
pdb|1VU2|QQ Chain q, The 8s Snrnp Assembly Intermediate
pdb|1VU2|YY Chain y, The 8s Snrnp Assembly Intermediate
pdb|1VU3|C Chain C, The 8s Snrnp Assembly Intermediate
pdb|1VU3|K Chain K, The 8s Snrnp Assembly Intermediate
pdb|1VU3|S Chain S, The 8s Snrnp Assembly Intermediate
pdb|1VU3|AA Chain a, The 8s Snrnp Assembly Intermediate
pdb|1VU3|II Chain i, The 8s Snrnp Assembly Intermediate
pdb|1VU3|QQ Chain q, The 8s Snrnp Assembly Intermediate
pdb|4F77|K Chain K, The 8s Snrnp Assembly Intermediate
pdb|4F77|C Chain C, The 8s Snrnp Assembly Intermediate
pdb|4F77|S Chain S, The 8s Snrnp Assembly Intermediate
pdb|4F77|AA Chain a, The 8s Snrnp Assembly Intermediate
pdb|4F77|II Chain i, The 8s Snrnp Assembly Intermediate
pdb|4F77|QQ Chain q, The 8s Snrnp Assembly Intermediate
pdb|4F77|YY Chain y, The 8s Snrnp Assembly Intermediate
Length = 92
Score = 33.9 bits (76), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 31/51 (60%), Gaps = 3/51 (5%)
Query: 25 IVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEV 75
I G + GFD+ N++LD++ E TK Q LG +++GDNI+++ V
Sbjct: 43 IEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQ---LGRIMLKGDNITLLQSV 90
>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 = 32.3 bits (72), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 4/47 (8%)
Query: 23 RNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNI 69
R GVLK FD N++L+++ E ++G LG +IRGDNI
Sbjct: 34 REFRGVLKSFDLHMNLVLNDAEE----LEDGEVTRRLGTVLIRGDNI 76
>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 = 32.3 bits (72), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 4/47 (8%)
Query: 23 RNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNI 69
R GVLK FD N++L+++ E ++G LG +IRGDNI
Sbjct: 34 REFRGVLKSFDLHMNLVLNDAEE----LEDGEVTRRLGTVLIRGDNI 76
>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 = 19/47 (40%), Positives = 27/47 (57%), Gaps = 4/47 (8%)
Query: 23 RNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNI 69
R GVLK FD N++L+++ E ++G LG +IRGDNI
Sbjct: 36 REFRGVLKSFDLHMNLVLNDAEE----LEDGEVTRRLGTVLIRGDNI 78
>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 = 32.3 bits (72), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 4/47 (8%)
Query: 23 RNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNI 69
R GVLK FD N++L+++ E ++G LG +IRGDNI
Sbjct: 34 REFRGVLKSFDLHMNLVLNDAEE----LEDGEVTRRLGTVLIRGDNI 76
>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 = 32.3 bits (72), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 25/46 (54%)
Query: 7 LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKE 52
++ + +I V+ + GVL+GFD+ N++LD+ E + E
Sbjct: 33 IDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADE 78
>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 = 32.0 bits (71), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 31/50 (62%), Gaps = 4/50 (8%)
Query: 23 RNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIV 72
+ + G+L+ +DQ N++L +S E + S G + LG +IRGDN+ ++
Sbjct: 30 KEVRGMLRSYDQHMNLVLSDSEE-IQSDGSGKK---LGTIVIRGDNVILI 75
>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 = 29.3 bits (64), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 7 LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQ 56
++ + + VI R G L GFD NI+L + E Y T GV +
Sbjct: 13 IDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTE--YDTVTGVTE 60
>pdb|2GWL|A Chain A, Crystal Structure Of The Salmonella Spvb Atr Domain In
Complex With Nadh
Length = 200
Score = 28.9 bits (63), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 6 GLESLVEQQISVITN----DGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGL 61
GL SL E V+ D + VLK + NII+D++ K + +L +
Sbjct: 66 GLSSLPETDHRVVYRGLKLDKPALSDVLKEYTTIGNIIIDKAFMSTSPDKAWINDTILNI 125
Query: 62 YIIRGDNISIVGEV 75
Y+ +G I+G+V
Sbjct: 126 YLEKGHKGRILGDV 139
>pdb|2GWM|A Chain A, Crystal Structure Of The Salmonella Spvb Atr Domain
Length = 200
Score = 28.9 bits (63), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 6 GLESLVEQQISVITN----DGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGL 61
GL SL E V+ D + VLK + NII+D++ K + +L +
Sbjct: 67 GLSSLPETDHRVVYRGLKLDKPALSDVLKEYTTIGNIIIDKAFMSTSPDKAWINDTILNI 126
Query: 62 YIIRGDNISIVGEV 75
Y+ +G I+G+V
Sbjct: 127 YLEKGHKGRILGDV 140
>pdb|4EMK|A Chain A, Crystal Structure Of Splsm567
Length = 94
Score = 28.5 bits (62), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 7 LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQ 56
++ + + VI R G L GFD NI+L + E Y T GV +
Sbjct: 25 IDKCIGSNLWVIXKSEREFAGTLVGFDDYVNIVLKDVTE--YDTVTGVTE 72
>pdb|3SLG|A Chain A, Crystal Structure Of Pbgp3 Protein From Burkholderia
Pseudomallei
pdb|3SLG|B Chain B, Crystal Structure Of Pbgp3 Protein From Burkholderia
Pseudomallei
pdb|3SLG|C Chain C, Crystal Structure Of Pbgp3 Protein From Burkholderia
Pseudomallei
pdb|3SLG|D Chain D, Crystal Structure Of Pbgp3 Protein From Burkholderia
Pseudomallei
pdb|3SLG|E Chain E, Crystal Structure Of Pbgp3 Protein From Burkholderia
Pseudomallei
pdb|3SLG|F Chain F, Crystal Structure Of Pbgp3 Protein From Burkholderia
Pseudomallei
Length = 372
Score = 26.9 bits (58), Expect = 2.7, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 21/30 (70%), Gaps = 2/30 (6%)
Query: 45 ERVYSTKEGVQQLVLGL--YIIRGDNISIV 72
+ +Y+ KEG ++V +I+RG+NIS+V
Sbjct: 207 DSIYTPKEGSSRVVTQFLGHIVRGENISLV 236
>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 = 25.4 bits (54), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 22 GRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIV 72
GR G L G+D N++L ++ E E V++ +G +IRGD + V
Sbjct: 24 GREFRGTLDGYDIHMNLVLLDAEE--IQNGEVVRK--VGSVVIRGDTVVFV 70
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
0.315 0.138 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,017,244
Number of Sequences: 62578
Number of extensions: 113953
Number of successful extensions: 273
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 249
Number of HSP's gapped (non-prelim): 29
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 45 (21.9 bits)