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= 033666
(114 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 10/78 (12%)
Query: 15 SAGSDTKGSNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRT 74
+ G +K HI RM ++DGR F+G+F DK N+IL D E+R +
Sbjct: 2 TVGKSSKMLQHIDY-------RMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPK 54
Query: 75 SPSPM---EQRCLGIILI 89
+ E+R LG++L+
Sbjct: 55 NSKQAEREEKRVLGLVLL 72
>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 = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 10/78 (12%)
Query: 15 SAGSDTKGSNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRT 74
+ G +K HI RM ++DGR F+G+F DK N+IL D E+R +
Sbjct: 2 TVGKSSKMLQHIDY-------RMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPK 54
Query: 75 SPSPM---EQRCLGIILI 89
+ E+R LG++L+
Sbjct: 55 NSKQAEREEKRVLGLVLL 72
>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 = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 3/80 (3%)
Query: 36 RMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPM---EQRCLGIILIPSS 92
RM ++DGR F+G+F DK N+IL D E+R + + E+R LG++L+
Sbjct: 16 RMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGE 75
Query: 93 CRTSCHVDCSIDEQLSLLKV 112
S V+ + + +V
Sbjct: 76 NLVSMTVEGPPPKDTGIARV 95
>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 = 8e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 3/80 (3%)
Query: 36 RMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPM---EQRCLGIILIPSS 92
RM ++DGR F+G+F DK N+IL D E+R + + E+R LG++L+
Sbjct: 16 RMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGE 75
Query: 93 CRTSCHVDCSIDEQLSLLKV 112
S V+ + + +V
Sbjct: 76 NLVSMTVEGPPPKDTGIARV 95
>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 = 32.0 bits (71), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 23/40 (57%)
Query: 26 ISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDA 65
++ + LL R + V + +G + G H +D Q NI+L +A
Sbjct: 2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANA 41
>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 = 29.3 bits (64), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 33 LCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVE 67
L R+ + ++ R +G+ D NI+L DAVE
Sbjct: 19 LDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVE 53
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.321 0.135 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,968,676
Number of Sequences: 62578
Number of extensions: 104367
Number of successful extensions: 387
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 381
Number of HSP's gapped (non-prelim): 6
length of query: 114
length of database: 14,973,337
effective HSP length: 77
effective length of query: 37
effective length of database: 10,154,831
effective search space: 375728747
effective search space used: 375728747
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)