RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9158
(133 letters)
>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 = 55.5 bits (134), Expect = 2e-11
Identities = 20/101 (19%), Positives = 39/101 (38%), Gaps = 12/101 (11%)
Query: 7 SPKEQFLSFNTLACLA--KSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS-------- 56
S S + + L + G V+L+N + +G LE+ D +MN+ +
Sbjct: 4 SHHHHHHSQDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPD 63
Query: 57 --RELTFESLFIQSRNVMFIHIPRHVSIVNKVEDALQSKPR 95
+ +I+ N+ ++ I V + A Q + R
Sbjct: 64 GDKFFRLPECYIRGNNIKYLRIQDEVLSQVAKQQAQQRENR 104
>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 = 54.6 bits (131), Expect = 8e-11
Identities = 18/101 (17%), Positives = 36/101 (35%), Gaps = 9/101 (8%)
Query: 18 LACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS---------RELTFESLFIQS 68
L L ++L+N + V G + VD MN ++ + E+L I+
Sbjct: 3 LVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRG 62
Query: 69 RNVMFIHIPRHVSIVNKVEDALQSKPRQSSSAGRTLKQKRA 109
N+ + +P + + + D + A + R
Sbjct: 63 NNIRYFILPDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRG 103
>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 = 50.1 bits (119), Expect = 5e-09
Identities = 15/95 (15%), Positives = 29/95 (30%), Gaps = 9/95 (9%)
Query: 23 KSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS---------RELTFESLFIQSRNVMF 73
G I + G+L + MN MS R E ++I+ + F
Sbjct: 11 HEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRF 70
Query: 74 IHIPRHVSIVNKVEDALQSKPRQSSSAGRTLKQKR 108
+ +P + ++ + G+ K
Sbjct: 71 LILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKA 105
>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 = 47.4 bits (113), Expect = 2e-08
Identities = 13/64 (20%), Positives = 22/64 (34%), Gaps = 9/64 (14%)
Query: 23 KSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS---------RELTFESLFIQSRNVMF 73
G I + G+L + MN MS R E ++I+ + F
Sbjct: 11 HEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRF 70
Query: 74 IHIP 77
+ +P
Sbjct: 71 LILP 74
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 34.3 bits (78), Expect = 0.009
Identities = 26/147 (17%), Positives = 58/147 (39%), Gaps = 56/147 (38%)
Query: 7 SPKE---QFLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSRELT-FE 62
+P E +FL + V E S G+ + V ++ LT FE
Sbjct: 56 TPAELVGKFLGY----------------VSSLVEPSKVGQFDQV-------LNLCLTEFE 92
Query: 63 SLFIQSRNVMFIH------IPRHVSIVNKVEDALQS---------KP--RQSSSA-GRTL 104
+ +++ + IH + + + + K ++ +++ +P ++S+SA R +
Sbjct: 93 NCYLEGND---IHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAV 149
Query: 105 KQKRANLM-----Q---QEVLEKIQAL 123
+ A L+ Q + E+++ L
Sbjct: 150 GEGNAQLVAIFGGQGNTDDYFEELRDL 176
Score = 29.2 bits (65), Expect = 0.45
Identities = 25/162 (15%), Positives = 39/162 (24%), Gaps = 56/162 (34%)
Query: 1 MTAVFDSPKEQFLSFNTLA-CLAKSLVGMITCVDL---RNESSVSGRLEHVDGFMNIYMS 56
+T F K + + N A + G + + NE S S G ++
Sbjct: 1672 LTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLS---- 1727
Query: 57 RELT--------------FESL---FIQSRNVMFI-HIPRHVSI-----------VNKVE 87
T FE L + + F H S+ V +E
Sbjct: 1728 --ATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGH-----SLGEYAALASLADVMSIE 1780
Query: 88 DALQSKPRQSSSAGRTLKQKRANLMQQEVLEKIQALKKQKMA 129
+ + R MQ V M
Sbjct: 1781 SLV-----------EVVFY-RGMTMQVAVPRDELGRSNYGMI 1810
>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 = 31.3 bits (71), Expect = 0.022
Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 9/75 (12%)
Query: 23 KSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS---------RELTFESLFIQSRNVMF 73
L G V L+ G L VDG+MN+ ++ + I+ NV++
Sbjct: 12 NGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLY 71
Query: 74 IHIPRHVSIVNKVED 88
I ++ +
Sbjct: 72 IRGVEEEEEDGEMRE 86
>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 = 30.7 bits (70), Expect = 0.030
Identities = 11/61 (18%), Positives = 20/61 (32%), Gaps = 9/61 (14%)
Query: 23 KSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS---------RELTFESLFIQSRNVMF 73
+ V L+ G L+ D MN+ + S+ I+ V+F
Sbjct: 10 NRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVF 69
Query: 74 I 74
+
Sbjct: 70 V 70
>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 = 30.3 bits (69), Expect = 0.037
Identities = 11/61 (18%), Positives = 21/61 (34%), Gaps = 9/61 (14%)
Query: 23 KSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS---------RELTFESLFIQSRNVMF 73
+ V L+ GRL D +N+ ++ + + I+ NV+
Sbjct: 10 HRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLA 69
Query: 74 I 74
I
Sbjct: 70 I 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 = 30.4 bits (69), Expect = 0.043
Identities = 12/64 (18%), Positives = 26/64 (40%), Gaps = 9/64 (14%)
Query: 23 KSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS---------RELTFESLFIQSRNVMF 73
++G + L + G L +DG+MN+ + + + FI+ NV++
Sbjct: 10 NKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIRGNNVLY 69
Query: 74 IHIP 77
+
Sbjct: 70 VSAL 73
>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 = 30.4 bits (69), Expect = 0.044
Identities = 9/61 (14%), Positives = 24/61 (39%), Gaps = 9/61 (14%)
Query: 23 KSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS---------RELTFESLFIQSRNVMF 73
+ + + L+ + G L+ D MN+ ++ ++ I+ N+++
Sbjct: 21 GNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVY 80
Query: 74 I 74
I
Sbjct: 81 I 81
>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 = 30.0 bits (68), Expect = 0.052
Identities = 14/76 (18%), Positives = 27/76 (35%), Gaps = 9/76 (11%)
Query: 7 SPKEQFLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS--------RE 58
+ A L + +G V LR+ + G L D +N+ +
Sbjct: 2 ASDISKCFATLGATL-QDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNV 60
Query: 59 LTFESLFIQSRNVMFI 74
++ ++ NV+FI
Sbjct: 61 YKRGTMVVRGENVLFI 76
>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 = 31.7 bits (71), Expect = 0.057
Identities = 28/155 (18%), Positives = 58/155 (37%), Gaps = 37/155 (23%)
Query: 5 FDSPKEQFLSFNTLACLAKSLVGMITCVDLRNESSVSGRL--EHVDGFMNIYMSRE---- 58
F++ + Q+ + L+ + V C D+ + L E +D +I MS++
Sbjct: 9 FETGEHQYQYKDILSVFEDAFVDNFDCKDV--QDMPKSILSKEEID---HIIMSKDAVSG 63
Query: 59 --LTFESLFIQSRNV--MFIHIPRHVSIVNK----VEDALQSKPRQSSSAGRTLKQKRAN 110
F +L + + F+ ++ + ++++ RQ S R ++R
Sbjct: 64 TLRLFWTLLSKQEEMVQKFV-----EEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDR 118
Query: 111 LM-------------QQEVLEKIQALKKQKMAQGV 132
L Q L+ QAL + + A+ V
Sbjct: 119 LYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNV 153
Score = 31.0 bits (69), Expect = 0.12
Identities = 28/157 (17%), Positives = 49/157 (31%), Gaps = 46/157 (29%)
Query: 3 AVFDSPKEQFLSFNTLACL----AKSLVGMITCVDLRNESSVSGRL-EHVDGFMNIYMSR 57
+VF P + L+ + KS V ++ L S V + E +IY+
Sbjct: 379 SVF--PPSAHIPTILLSLIWFDVIKSDVMVVVN-KLHKYSLVEKQPKESTISIPSIYLEL 435
Query: 58 ELTFESL------FIQSRNVM-----------------FIHIPRHVSIVNKVEDA----- 89
++ E+ + N+ + HI H+ + E
Sbjct: 436 KVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRM 495
Query: 90 -------LQSKPRQSSSAGRTLKQKRANLMQQEVLEK 119
L+ K R S+A N +QQ L+
Sbjct: 496 VFLDFRFLEQKIRHDSTA-WNASGSILNTLQQ--LKF 529
>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 = 29.2 bits (66), Expect = 0.12
Identities = 13/61 (21%), Positives = 22/61 (36%), Gaps = 9/61 (14%)
Query: 23 KSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS---------RELTFESLFIQSRNVMF 73
+ + V L+ V G L D MN+ +S ++ I+ NV+
Sbjct: 15 AESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVIL 74
Query: 74 I 74
I
Sbjct: 75 I 75
>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 = 27.9 bits (62), Expect = 0.40
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 10/65 (15%)
Query: 23 KSLVGMITCVDLR-NESSVSGRLEHVDGFMNIYMS---------RELTFESLFIQSRNVM 72
K LV V L+ N + G L D + N+ ++ T +FI+ NV+
Sbjct: 27 KGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVL 86
Query: 73 FIHIP 77
+I
Sbjct: 87 YIREL 91
>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 = 27.1 bits (60), Expect = 0.89
Identities = 10/36 (27%), Positives = 18/36 (50%)
Query: 21 LAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS 56
L + + I V LR + ++GRL D +N+ +
Sbjct: 13 LVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLG 48
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 26.7 bits (58), Expect = 2.0
Identities = 5/39 (12%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 92 SKPRQSSSAGRTLKQKRANLMQQEVLEKIQALKKQKMAQ 130
++ + + ++++ R Q++ L+++ A K +
Sbjct: 75 AQADRLTQEPESIRKWREE--QRKRLQELDAASKVMEQE 111
>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 = 25.3 bits (56), Expect = 2.7
Identities = 15/35 (42%), Positives = 26/35 (74%), Gaps = 1/35 (2%)
Query: 23 KSLVGMITCVDLR-NESSVSGRLEHVDGFMNIYMS 56
KS+VG I V+++ E+ + G+LE VD +MN+Y++
Sbjct: 11 KSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLT 45
>1wi9_A Protein C20ORF116 homolog; helix-turn-helix motif, structural
genomics, riken structural genomics/proteomics
initiative, RSGI, unknown function; NMR {Mus musculus}
SCOP: a.4.5.47
Length = 72
Score = 25.2 bits (55), Expect = 3.2
Identities = 7/24 (29%), Positives = 12/24 (50%)
Query: 110 NLMQQEVLEKIQALKKQKMAQGVM 133
L Q+ + +IQ L + GV+
Sbjct: 32 GLRTQDAINRIQDLLTEGTLTGVI 55
>1j3k_A Bifunctional dihydrofolate reductase-thymidylate synthase;
oxidoreductase, transferase; HET: WRA NDP UMP; 2.10A
{Plasmodium falciparum} SCOP: c.71.1.1 PDB: 3dg8_A*
1j3j_A* 1j3i_A* 3dga_A*
Length = 280
Score = 26.0 bits (57), Expect = 4.3
Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 12/44 (27%)
Query: 60 TFESL------------FIQSRNVMFIHIPRHVSIVNKVEDALQ 91
+ES+ I SR + V I+NKVED +
Sbjct: 108 NWESIPKKFKPLSNRINVILSRTLKKEDFDEDVYIINKVEDLIV 151
>3erp_A Putative oxidoreductase; funded by the national institute of
allergy and infectious D of NIH contract number
HHSN272200700058C; 1.55A {Salmonella enterica subsp}
Length = 353
Score = 25.6 bits (57), Expect = 5.4
Identities = 9/39 (23%), Positives = 18/39 (46%), Gaps = 6/39 (15%)
Query: 98 SSAGRTLKQKRANLMQQEVLEKIQALKK------QKMAQ 130
S A + + + + LEK++ L + QK++Q
Sbjct: 262 SRAASGSRFLKPEQITADKLEKVRRLNELAARRGQKLSQ 300
>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 = 24.9 bits (54), Expect = 7.2
Identities = 6/25 (24%), Positives = 13/25 (52%)
Query: 32 VDLRNESSVSGRLEHVDGFMNIYMS 56
V ++ + SG L D ++N+ +
Sbjct: 43 VVMKGDKEFSGVLRGFDEYVNMVLD 67
>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 = 24.4 bits (53), Expect = 9.0
Identities = 8/48 (16%), Positives = 16/48 (33%), Gaps = 2/48 (4%)
Query: 23 KSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSRELTFESLFIQSRN 70
+ L++ G + D MN+ + E I+ +N
Sbjct: 10 LQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCD--CDEFRKIKPKN 55
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
0.321 0.130 0.352
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: 1,788,451
Number of extensions: 89181
Number of successful extensions: 231
Number of sequences better than 10.0: 1
Number of HSP's gapped: 228
Number of HSP's successfully gapped: 30
Length of query: 133
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 50
Effective length of database: 4,384,350
Effective search space: 219217500
Effective search space used: 219217500
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 (21.9 bits)
S2: 52 (23.8 bits)