RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14196
(79 letters)
>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 = 79.8 bits (197), Expect = 5e-22
Identities = 39/53 (73%), Positives = 50/53 (94%)
Query: 1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG 53
MSIG+PIK+LHEAEGHI+TCET G+++RGKL+EAEDNMNC M+++TVT+RDG
Sbjct: 1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDG 53
>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 = 80.9 bits (199), Expect = 8e-22
Identities = 39/53 (73%), Positives = 50/53 (94%)
Query: 1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG 53
MSIG+PIK+LHEAEGHI+TCET G+++RGKL+EAEDNMNC M+++TVT+RDG
Sbjct: 1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDG 53
>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 = 70.2 bits (172), Expect = 8e-18
Identities = 17/49 (34%), Positives = 26/49 (53%)
Query: 5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG 53
+P+ LL+ +G I E NG+ F G L ++ MN + +V T DG
Sbjct: 16 LPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDG 64
>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 = 66.9 bits (163), Expect = 2e-16
Identities = 10/48 (20%), Positives = 21/48 (43%)
Query: 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG 53
++ L + +T E NG G + + +MN + V +T ++
Sbjct: 3 LVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNR 50
>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 = 36.5 bits (85), Expect = 6e-05
Identities = 11/47 (23%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVT 47
M+ P+ ++H + + G FRG+L+ + ++N +AD
Sbjct: 1 MA-ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAE 46
>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 = 32.3 bits (74), Expect = 0.002
Identities = 11/49 (22%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGT 54
P + L++ G + ++G ++G L + MN A+ T + +G
Sbjct: 5 PNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALER-TEEYVNGK 52
>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 = 30.6 bits (69), Expect = 0.018
Identities = 12/42 (28%), Positives = 21/42 (50%)
Query: 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVT 47
P++L+ + G + + F G LV +D +N + DVT
Sbjct: 21 PLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVT 62
>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 = 28.8 bits (65), Expect = 0.066
Identities = 9/47 (19%), Positives = 19/47 (40%)
Query: 1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVT 47
+++ P+ L + + + FRG L + +MN + D
Sbjct: 11 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAE 57
>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 = 27.2 bits (61), Expect = 0.20
Identities = 10/49 (20%), Positives = 18/49 (36%)
Query: 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGT 54
P+ +L+ + + G FRG L + +MN + D
Sbjct: 5 PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEV 53
>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 = 27.3 bits (61), Expect = 0.21
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 6 PIKLLHEAEGHIITCETTNGDL-FRGKLVEAEDNMNCAMADVT 47
P +++ G II E + GKL +D MN + +
Sbjct: 6 PNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAM 48
>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 = 25.2 bits (55), Expect = 1.6
Identities = 7/42 (16%), Positives = 18/42 (42%)
Query: 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVT 47
P+ L+ + I+ + G+L ++++N + D
Sbjct: 10 PLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAE 51
>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 = 24.6 bits (54), Expect = 2.0
Identities = 9/56 (16%), Positives = 19/56 (33%)
Query: 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALV 61
L ++ G + + + RG L + ++N + D Y +V
Sbjct: 12 LGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMV 67
>3lq6_A Capsid protein; protruding (P) domain, viral protein; 2.00A {Murine
norovirus 1} PDB: 3lqe_A
Length = 320
Score = 25.3 bits (55), Expect = 2.3
Identities = 7/35 (20%), Positives = 14/35 (40%)
Query: 28 FRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALVP 62
F + + +A T+ +DG+ Y+P
Sbjct: 68 FAAEAAYEFQSGTGEVATFTLIEQDGSAYVPGDRA 102
>1wek_A Hypothetical protein TT1465; rossman fold, structural genomics,
riken structural genomics/proteomics initiative, RSGI,
unknown function; 2.20A {Thermus thermophilus} SCOP:
c.129.1.1
Length = 217
Score = 24.9 bits (55), Expect = 2.6
Identities = 6/15 (40%), Positives = 11/15 (73%)
Query: 2 SIGIPIKLLHEAEGH 16
S+G+ I+L HE + +
Sbjct: 95 SVGLNIELPHEQKPN 109
>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 = 24.3 bits (53), Expect = 3.3
Identities = 8/48 (16%), Positives = 15/48 (31%)
Query: 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG 53
P+ LL + + G L + + N ++D T
Sbjct: 11 PLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQL 58
>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 = 23.8 bits (52), Expect = 4.2
Identities = 11/49 (22%), Positives = 22/49 (44%)
Query: 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGT 54
K+L E+ +++ + RG L + +MN ++D DG+
Sbjct: 10 AHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGS 58
>3h2z_A Mannitol-1-phosphate 5-dehydrogenase; PSI- protein structure
initiative, structural genomics, midwest for structural
genomics (MCSG); 1.90A {Shigella flexneri 2a str}
Length = 382
Score = 24.3 bits (53), Expect = 4.7
Identities = 10/38 (26%), Positives = 14/38 (36%), Gaps = 2/38 (5%)
Query: 17 IITCE--TTNGDLFRGKLVEAEDNMNCAMADVTVTFRD 52
II CE +G ++ A A + V F D
Sbjct: 117 IIACENMVRGTTQLKGHVMNALPEDAKAWVEEHVGFVD 154
>4ak5_A Anhydro-alpha-L-galactosidase; hydrolase, marine glycoside
hydrolase, marine polysaccharide degradation, marine
cazymes, AGAR metabolism; 1.70A {Bacteroides plebeius}
PDB: 4ak7_A* 4ak6_A
Length = 404
Score = 24.0 bits (51), Expect = 8.0
Identities = 7/32 (21%), Positives = 15/32 (46%)
Query: 26 DLFRGKLVEAEDNMNCAMADVTVTFRDGTYYL 57
+ R K+V D + + D + +G +Y+
Sbjct: 228 EDNRFKVVSKGDFDSHKVHDPCIIPYNGKFYM 259
>3b6h_A Prostacyclin synthase; enzyme-inhibitor complex, CYP8A1, cytochrome
P450, endoplasmic reticulum, fatty acid biosynthesis,
heme, iron, isomerase; HET: BOG MXD HEM; 1.62A {Homo
sapiens} PDB: 2iag_A*
Length = 498
Score = 23.6 bits (51), Expect = 8.5
Identities = 12/50 (24%), Positives = 16/50 (32%)
Query: 18 ITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALVPIAGMW 67
T G + E++ ADV TFR LP L +
Sbjct: 165 AGYLTLYGIEALPRTHESQAQDRVHSADVFHTFRQLDRLLPKLARGSLSV 214
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
0.320 0.136 0.428
Gapped
Lambda K H
0.267 0.0718 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,280,814
Number of extensions: 62260
Number of successful extensions: 176
Number of sequences better than 10.0: 1
Number of HSP's gapped: 176
Number of HSP's successfully gapped: 21
Length of query: 79
Length of database: 6,701,793
Length adjustment: 48
Effective length of query: 31
Effective length of database: 5,361,585
Effective search space: 166209135
Effective search space used: 166209135
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (23.4 bits)