RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1140
(142 letters)
>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3;
RNA-binding protein, SM protein, ring, HOMO octamer,
mRNA processing; 2.50A {Saccharomyces cerevisiae}
Length = 96
Score = 59.7 bits (145), Expect = 6e-13
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSP---TAGVEQVVLGLHIIRGDNI 56
GTL+ FD NI+L D+ E +Y + + IRGD +
Sbjct: 33 LVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTV 80
>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2
complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP
biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens}
PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G
Length = 76
Score = 58.1 bits (141), Expect = 2e-12
Identities = 16/45 (35%), Positives = 28/45 (62%), Gaps = 4/45 (8%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
QG L+GFD +N+++D+ E S +Q +G+ +IRG++I
Sbjct: 27 VQGILRGFDPFMNLVIDECVEMATSG----QQNNIGMVVIRGNSI 67
>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and
PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A
{Schizosaccharomyces pombe} PDB: 3swn_C
Length = 113
Score = 56.9 bits (137), Expect = 1e-11
Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 3/49 (6%)
Query: 11 FFQGTLKGFDQTINIILDDSHERVYSPTAGV---EQVVLGLHIIRGDNI 56
G LKGFDQ +N++LDD E++ +P G LGL ++RG +
Sbjct: 45 QITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTL 93
>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP,
splicing, core snRNP domain, systemic lupus eryth SLE,
RNA binding protein; HET: CIT; 2.00A {Homo sapiens}
SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A
Length = 91
Score = 54.1 bits (130), Expect = 8e-11
Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 11/66 (16%)
Query: 12 FQGTLKGFDQTINIILDDSHERV------YSPTAGVEQVVLGLHIIRGDNIKIPTKISSS 65
F GT K FD+ +N+IL D E E+ VLGL ++RG+N+ +S +
Sbjct: 27 FIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENL-----VSMT 81
Query: 66 TRSPVP 71
P P
Sbjct: 82 VEGPPP 87
>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers
form 35-stranded beta-sheet I heptamer, structural
genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1
PDB: 1lnx_A*
Length = 81
Score = 52.8 bits (127), Expect = 2e-10
Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 5/45 (11%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
+G L+ FDQ +N++L+D+ E + G ++RG+N+
Sbjct: 34 IRGILRSFDQHVNLLLEDAEEIIDG-----NVYKRGTMVVRGENV 73
>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein,
SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus
solfataricus} SCOP: b.38.1.1
Length = 81
Score = 50.4 bits (121), Expect = 2e-09
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
+G L+ +DQ +N++L DS E LG +IRGDN+
Sbjct: 32 VRGMLRSYDQHMNLVLSDSEEIQS----DGSGKKLGTIVIRGDNV 72
>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A
{Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A*
Length = 75
Score = 46.5 bits (111), Expect = 4e-08
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 4/45 (8%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
F+G L G+D +N++L D+ G G +IRGDN+
Sbjct: 27 FRGRLIGYDIHLNVVLADAEMIQ----DGEVVKRYGKIVIRGDNV 67
>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein;
1.70A {Methanothermobacterthermautotrophicus} SCOP:
b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A
Length = 83
Score = 45.4 bits (108), Expect = 1e-07
Identities = 19/45 (42%), Positives = 26/45 (57%), Gaps = 4/45 (8%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
F+G LK FD +N++L+D+ E G LG +IRGDNI
Sbjct: 38 FRGVLKSFDLHMNLVLNDAEELED----GEVTRRLGTVLIRGDNI 78
>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding
protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP:
b.38.1.1 PDB: 1i5l_A*
Length = 77
Score = 45.3 bits (108), Expect = 1e-07
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 4/45 (8%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
F+GTL G+D +N++L D+ E G +G +IRGD +
Sbjct: 27 FRGTLDGYDIHMNLVLLDAEEIQN----GEVVRKVGSVVIRGDTV 67
>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA
binding protein, unknown F; 1.95A {Archaeoglobus
fulgidus} SCOP: b.38.1.1
Length = 77
Score = 45.0 bits (107), Expect = 2e-07
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
G L+G D +N+ L ++ E + LG ++RG+N+
Sbjct: 29 LVGKLEGVDDYMNLYLTNAMECKG----EEKVRSLGEIVLRGNNV 69
>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2
complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP
biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens}
PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F
Length = 86
Score = 43.6 bits (103), Expect = 8e-07
Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIK 57
++G L D +N+ L ++ E + G LG +IR +N+
Sbjct: 29 YKGYLVSVDGYMNMQLANTEEYID----GALSGHLGEVLIRCNNVL 70
>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and
PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A
{Schizosaccharomyces pombe} PDB: 3swn_B
Length = 75
Score = 42.7 bits (101), Expect = 1e-06
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIK 57
++G L D +N+ L+ + E V G + V G IRG+N+
Sbjct: 27 YKGILSCLDGYMNLALERTEEYVN----GKKTNVYGDAFIRGNNVL 68
>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA
decay, LSM proteins, RNA binding protein; 2.70A
{Schizosaccharomyces pombe}
Length = 93
Score = 42.1 bits (99), Expect = 3e-06
Identities = 11/54 (20%), Positives = 22/54 (40%), Gaps = 9/54 (16%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSP---------TAGVEQVVLGLHIIRGDNI 56
G L +D+ +N++L D+ E V + + +RGD++
Sbjct: 32 LNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDSV 85
>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2
complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP
biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens}
PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E
Length = 92
Score = 41.3 bits (97), Expect = 6e-06
Identities = 18/45 (40%), Positives = 31/45 (68%), Gaps = 3/45 (6%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
+G + GFD+ +N++LDD+ E ++S T +Q LG +++GDNI
Sbjct: 43 IEGCIIGFDEYMNLVLDDAEE-IHSKTKSRKQ--LGRIMLKGDNI 84
>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and
PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A
{Schizosaccharomyces pombe} PDB: 3swn_A
Length = 94
Score = 41.4 bits (97), Expect = 6e-06
Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 3/45 (6%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
F GTL GFD +NI+L D E T ++ G+ +
Sbjct: 43 FAGTLVGFDDYVNIVLKDVTEYD---TVTGVTEKHSEMLLNGNGM 84
>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F;
heptamer, translation; 2.80A {Saccharomyces cerevisiae}
SCOP: b.38.1.1 PDB: 1n9s_A
Length = 93
Score = 41.0 bits (96), Expect = 9e-06
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIK 57
++GTL D N+ L+++ E V GV LG IR +N+
Sbjct: 45 YRGTLVSTDNYFNLQLNEAEEFVA----GVSHGTLGEIFIRCNNVL 86
>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics,
structural genomics consortium, SGC, DNA binding
protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1
PDB: 3pgg_A
Length = 121
Score = 41.1 bits (96), Expect = 1e-05
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 11/56 (19%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSP-----------TAGVEQVVLGLHIIRGDNI 56
F G L+GFD+ +N++LDD E + V L ++ G+N+
Sbjct: 51 FSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNV 106
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_A
Length = 231
Score = 35.8 bits (82), Expect = 0.002
Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 6/51 (11%)
Query: 12 FQGTLKGFDQTINIILDDSHE-RVYSPTAG-----VEQVVLGLHIIRGDNI 56
F GT K FD+ +N+IL D E R P E+ VLGL ++RG+N+
Sbjct: 27 FIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENL 77
>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing,
spliceosome, core snRNP domain, systemi erythematosus,
SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP:
b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B
3pgw_X* 3s6n_A
Length = 119
Score = 33.4 bits (76), Expect = 0.007
Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 4/46 (8%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIK 57
GT+ G D ++N L E V L IRG+NI+
Sbjct: 25 VHGTITGVDVSMNTHLKAVKM----TLKNREPVQLETLSIRGNNIR 66
>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing,
spliceosome, core snRNP domain, systemi erythematosus,
SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP:
b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y*
3s6n_B
Length = 118
Score = 33.0 bits (75), Expect = 0.010
Identities = 10/55 (18%), Positives = 21/55 (38%), Gaps = 10/55 (18%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVV----------LGLHIIRGDNI 56
G +K FD+ N++L++ E + + +RGD++
Sbjct: 52 LLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSV 106
>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA
decay, PRE-mRNA splicing, LSM proteins, RNA BI protein;
2.20A {Schizosaccharomyces pombe}
Length = 105
Score = 32.4 bits (74), Expect = 0.016
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIK 57
F G L+ D +N+ L + + G + L IRG+NIK
Sbjct: 39 FNGHLENCDNYMNLTLREVIRTMPD---GDKFFRLPECYIRGNNIK 81
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.1 bits (64), Expect = 0.29
Identities = 6/26 (23%), Positives = 10/26 (38%), Gaps = 5/26 (19%)
Query: 55 NIKIPTKISSSTRSPVPD--PQLTDN 78
+K K+ +S + D P L
Sbjct: 21 ALK---KLQASLKLYADDSAPALAIK 43
Score = 28.8 bits (63), Expect = 0.43
Identities = 8/34 (23%), Positives = 16/34 (47%), Gaps = 11/34 (32%)
Query: 89 ERRTL----SFMRFGYRPSVDVLHLSASALKVES 118
E++ L + ++ Y D SA AL +++
Sbjct: 18 EKQALKKLQASLKL-YAD--D----SAPALAIKA 44
Score = 26.1 bits (56), Expect = 4.3
Identities = 8/32 (25%), Positives = 13/32 (40%), Gaps = 9/32 (28%)
Query: 15 TLKGFDQTINIILDDSHERVYSPT----AGVE 42
LK ++ + DDS +P A +E
Sbjct: 21 ALKKLQASLKLYADDS-----APALAIKATME 47
>1chd_A CHEB methylesterase; chemotaxis protein, serine hydrolase, carboxyl
methylesteras; 1.75A {Salmonella typhimurium} SCOP:
c.40.1.1
Length = 203
Score = 27.8 bits (63), Expect = 1.1
Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 99 GYRPSVDVLHLS-ASALKVESMAFIM 123
+RPSVDVL S A ++ I+
Sbjct: 109 RHRPSVDVLFHSVAKHAGRNAVGVIL 134
>3sft_A CHEB, chemotaxis response regulator protein-glutamate
methylesterase; modified doubly-wound/fold,
chemoreceptor; 2.15A {Thermotoga maritima}
Length = 193
Score = 27.8 bits (63), Expect = 1.1
Identities = 8/26 (30%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 99 GYRPSVDVLHLS-ASALKVESMAFIM 123
RP+VD A K +++A I+
Sbjct: 107 NVRPAVDFTLDKAAEIYKSKTIAVIL 132
>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex,
PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM
site, SM fold, heteromeric heptameric ring; 3.60A {Homo
sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D
Length = 126
Score = 27.3 bits (60), Expect = 1.2
Identities = 8/46 (17%), Positives = 15/46 (32%), Gaps = 4/46 (8%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIK 57
++G L + +N + + L IRG I+
Sbjct: 28 YRGKLIEAEDNMNCQMSNITVT----YRDGRVAQLEQVYIRGSKIR 69
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 27.9 bits (62), Expect = 1.5
Identities = 13/40 (32%), Positives = 16/40 (40%), Gaps = 10/40 (25%)
Query: 86 WGIERRTLSFMRFGYRPSVDVLHLSASALKVESMAFIMGL 125
WG RT R+ + S VE MA+IMG
Sbjct: 831 WG-SART----RWEMEAFGE---FSLEGC-VE-MAWIMGF 860
>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing,
core snRNP domain, systemic lupus eryth SLE, RNA
binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP:
b.38.1.1
Length = 75
Score = 26.2 bits (58), Expect = 1.6
Identities = 8/46 (17%), Positives = 16/46 (34%), Gaps = 4/46 (8%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIK 57
++G L + +N + + + L IRG I+
Sbjct: 28 YRGKLIEAEDNMNCQMSN----ITVTYRDGRVAQLEQVYIRGCKIR 69
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 27.5 bits (60), Expect = 1.7
Identities = 20/114 (17%), Positives = 30/114 (26%), Gaps = 36/114 (31%)
Query: 25 IILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISSSTRSPVPDPQLTDNFILLPQ 84
++L + V + N+ KI +TR Q+TD L
Sbjct: 248 LVLLN----VQNAK-----------AWNAFNLS--CKILLTTR----FKQVTD--FLSAA 284
Query: 85 IWGIERRTLSFMRFGYRPS------VDVLHLSASALKVESMAFIMGLTLPCVLS 132
+L P + L L E + T P LS
Sbjct: 285 T--TTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPRE-----VLTTNPRRLS 331
>1a2o_A CHEB methylesterase; bacterial chemotaxis, adaptation, serine
hydrolase; 2.40A {Salmonella typhimurium} SCOP: c.23.1.1
c.40.1.1
Length = 349
Score = 26.7 bits (60), Expect = 3.0
Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 99 GYRPSVDVLHLS-ASALKVESMAFIM 123
+RPSVDVL S A ++ I+
Sbjct: 255 RHRPSVDVLFHSVAKHAGRNAVGVIL 280
>1m5q_A SMAP3, small nuclear ribonucleoprotein homolog, SM-like P;
OB-like fold, B-sheet toroid, 14-MER, cadmium-binding
site, translation; 2.00A {Pyrobaculum aerophilum} SCOP:
b.38.1.1
Length = 130
Score = 25.8 bits (56), Expect = 3.7
Identities = 7/29 (24%), Positives = 14/29 (48%), Gaps = 4/29 (13%)
Query: 11 FFQGTLKGFDQTINIIL----DDSHERVY 35
++G L D +NI+L + + E+
Sbjct: 22 VYKGVLHAVDNQLNIVLANASNKAGEKFN 50
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.325 0.140 0.424
Gapped
Lambda K H
0.267 0.0581 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,123,196
Number of extensions: 115546
Number of successful extensions: 221
Number of sequences better than 10.0: 1
Number of HSP's gapped: 202
Number of HSP's successfully gapped: 33
Length of query: 142
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 58
Effective length of database: 4,356,429
Effective search space: 252672882
Effective search space used: 252672882
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.1 bits)