RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17123
(105 letters)
>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 = 74.2 bits (182), Expect = 7e-19
Identities = 32/55 (58%), Positives = 41/55 (74%)
Query: 15 KDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVT 69
+R RKESILDLS++ D+ I+ F GGR+ +GILKGFD L+NLVLD+ E LR
Sbjct: 17 TERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNP 71
>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 = 72.0 bits (177), Expect = 2e-18
Identities = 22/48 (45%), Positives = 29/48 (60%)
Query: 20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
K +L KF+DK + +K GGR GIL+GFDP +NLV+D E
Sbjct: 3 KAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMAT 50
>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 = 68.1 bits (167), Expect = 7e-17
Identities = 14/48 (29%), Positives = 28/48 (58%)
Query: 20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
+ + L++ L+ ++ VK G +E G+L+ +D +NLVL ++ E
Sbjct: 8 ETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQS 55
>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 = 64.2 bits (157), Expect = 2e-15
Identities = 16/42 (38%), Positives = 23/42 (54%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
L++ L + V+ GGRE G L G+D +NLVL + E
Sbjct: 9 LNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQN 50
>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 = 62.4 bits (152), Expect = 1e-14
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 14 TKDRKRKESILD-LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
+ R + LD L L+ + +K G RE G+LK FD +NLVL++ E
Sbjct: 7 SSQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEEL 59
>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 = 62.0 bits (151), Expect = 2e-14
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 15 KDRKRKESILD-LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVT 69
E+ LD L LD+ + +K G R G L+ FD N+VL + E +
Sbjct: 3 HHHHHMETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQL 58
>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 = 60.5 bits (147), Expect = 6e-14
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYL 66
L + K + VK E GIL+ FD +NL+L++ E +
Sbjct: 16 LQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEII 56
>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 = 61.5 bits (149), Expect = 7e-14
Identities = 21/70 (30%), Positives = 30/70 (42%), Gaps = 1/70 (1%)
Query: 1 MAAVNTTTDAGAETKDRKRKESILDL-SKFLDKVIRVKFAGGRECSGILKGFDPLLNLVL 59
M+ G + L L K + I V G +E SG+L+GFD +N+VL
Sbjct: 7 MSETPANKSQGGSNQKGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVL 66
Query: 60 DNTTEYLRVT 69
D+ EY
Sbjct: 67 DDVQEYGFKA 76
>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 = 57.3 bits (139), Expect = 1e-12
Identities = 14/40 (35%), Positives = 20/40 (50%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
+ + LDK + V G E G L G+D LN+VL +
Sbjct: 9 IHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMI 48
>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 = 56.8 bits (137), Expect = 2e-12
Identities = 12/44 (27%), Positives = 22/44 (50%)
Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRV 68
+ + +D +R GR G K FD +NL+L + E+ ++
Sbjct: 8 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKI 51
>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 = 55.6 bits (134), Expect = 6e-12
Identities = 15/42 (35%), Positives = 24/42 (57%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
+ LD+++ VK G RE +G L +D LN+VL + E +
Sbjct: 14 VRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVT 55
>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 = 55.0 bits (133), Expect = 9e-12
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
L+K + K + ++ + G + GIL D +NL L+ T EY
Sbjct: 9 LNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEY 48
>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 = 52.3 bits (126), Expect = 1e-10
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 26 LSKFLDKVIRVKFAGGR-ECSGILKGFDPLLNLVLDNTTEY 65
+ + K+IRV+ G + G L+G D +NL L N E
Sbjct: 10 VKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMEC 50
>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 = 48.6 bits (116), Expect = 4e-09
Identities = 15/40 (37%), Positives = 19/40 (47%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
L+ K + VK G E G L D +N+ L NT EY
Sbjct: 11 LNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEY 50
>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 = 48.7 bits (116), Expect = 4e-09
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
+ K + + V RE +G L GFD +N+VL + TEY
Sbjct: 25 IDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEY 64
>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 = 43.7 bits (103), Expect = 4e-07
Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 1/41 (2%)
Query: 26 LSKFLDKVIRVKF-AGGRECSGILKGFDPLLNLVLDNTTEY 65
L ++ + VK E G L D NL L+ E+
Sbjct: 26 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEF 66
>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 = 40.4 bits (94), Expect = 2e-05
Identities = 12/43 (27%), Positives = 22/43 (51%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRV 68
+ + +D +R GR G K FD +NL+L + E+ ++
Sbjct: 9 MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKI 51
>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 = 37.0 bits (86), Expect = 1e-04
Identities = 11/63 (17%), Positives = 22/63 (34%), Gaps = 7/63 (11%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR-----VTYQSVQVRSWCS 80
L+ + I V+ G +G L+ D +NL L + +R +
Sbjct: 21 LNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIR--GN 78
Query: 81 IVR 83
++
Sbjct: 79 NIK 81
>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 = 36.7 bits (85), Expect = 1e-04
Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 4/42 (9%)
Query: 28 KFLDKVIRV----KFAGGRECSGILKGFDPLLNLVLDNTTEY 65
++L R+ G + GFD +NLVLD+ E
Sbjct: 23 RYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEI 64
>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 = 35.5 bits (81), Expect = 7e-04
Identities = 13/52 (25%), Positives = 24/52 (46%)
Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVR 76
+L+ L + ++V + G G+L D LN+VL N + + V +
Sbjct: 4 ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRVFIM 55
>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 = 34.9 bits (80), Expect = 9e-04
Identities = 12/44 (27%), Positives = 21/44 (47%)
Query: 22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
S+L S + + + ++ G +K FD N+VL+N E
Sbjct: 30 SVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEM 73
>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 = 32.4 bits (74), Expect = 0.004
Identities = 11/62 (17%), Positives = 21/62 (33%), Gaps = 6/62 (9%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR----VTYQSVQVRSWCSI 81
L + ++ + G G L + +N + N T R + V +R
Sbjct: 10 LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIR--GCK 67
Query: 82 VR 83
+R
Sbjct: 68 IR 69
>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 = 31.9 bits (72), Expect = 0.014
Identities = 9/42 (21%), Positives = 17/42 (40%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
L K + + ++ G + G + G D +N L L+
Sbjct: 7 LMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLK 48
>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 = 31.6 bits (71), Expect = 0.017
Identities = 8/42 (19%), Positives = 15/42 (35%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
L + ++ + G G L + +N + N T R
Sbjct: 10 LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYR 51
>3rux_A BIRA bifunctional protein; biotin-protein ligase, ligase-ligase
inhibitor complex; HET: BS5; 1.70A {Mycobacterium
tuberculosis} PDB: 3l1a_A 3l2z_A 2cgh_A
Length = 270
Score = 27.3 bits (61), Expect = 0.85
Identities = 11/37 (29%), Positives = 17/37 (45%)
Query: 24 LDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLD 60
S + +RV+ GG++ GI + D L LD
Sbjct: 217 RARSLTIGSRVRVELPGGQDVVGIARDIDDQGRLCLD 253
>3tjo_A Serine protease HTRA1; peptidase, hydrolase; HET: BOG; 2.30A {Homo
sapiens} PDB: 3tjn_A 3nwu_A
Length = 231
Score = 26.1 bits (58), Expect = 1.9
Identities = 5/26 (19%), Positives = 11/26 (42%)
Query: 34 IRVKFAGGRECSGILKGFDPLLNLVL 59
++V+ G +K D ++ L
Sbjct: 89 VKVELKNGATYEAKIKDVDEKADIAL 114
>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 = 26.6 bits (58), Expect = 1.9
Identities = 21/120 (17%), Positives = 37/120 (30%), Gaps = 38/120 (31%)
Query: 16 DRKRKE----SILDLSKFLDKVIRVKFAG--GRE---------CSGILKG---FDPLLNL 57
D K+ SILD+ + + F G G+ I+ G + +
Sbjct: 1650 DNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKE 1709
Query: 58 VLDNTTEY--------LRVTYQSVQVR----SWCSIVRRQESRRNVHRRD----HK--EY 99
+ +++T Y L T Q Q + +S+ + H EY
Sbjct: 1710 INEHSTSYTFRSEKGLLSAT-QFTQPALTLME-KAAFEDLKSKGLIPADATFAGHSLGEY 1767
>1lcy_A HTRA2 serine protease; apoptosis, PDZ domain, caspase activation,
binding, hydrolase; 2.00A {Homo sapiens} SCOP: b.36.1.4
b.47.1.1
Length = 325
Score = 26.1 bits (58), Expect = 2.6
Identities = 5/26 (19%), Positives = 12/26 (46%)
Query: 34 IRVKFAGGRECSGILKGFDPLLNLVL 59
+RV+ G ++ DP+ ++
Sbjct: 73 VRVRLLSGDTYEAVVTAVDPVADIAT 98
>2ej9_A Putative biotin ligase; biotin biosynthesis, monomer, X-RAY
diffraction, structural genomics, NPPSFA; HET: BTN;
2.00A {Methanocaldococcus jannaschii}
Length = 237
Score = 25.7 bits (57), Expect = 3.3
Identities = 6/42 (14%), Positives = 16/42 (38%), Gaps = 3/42 (7%)
Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDP--LLNLVLDNTTE 64
S + K +++ + +G + D ++ L + E
Sbjct: 186 KYSITIGKQVKILLSNNEIITGKVYDIDFDGIV-LGTEKGIE 226
>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex,
RNA binding protein; 2.00A {Homo sapiens}
Length = 86
Score = 25.0 bits (54), Expect = 3.3
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 19 RKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPL-LNLVLDNTTE 64
K+ L+ ++ K +RV + E G + DP+ N+VL N E
Sbjct: 5 MKKGPLEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFLE 51
>3num_A Serine protease HTRA1; DEGP, hydrolase; 2.75A {Homo sapiens} PDB:
3nzi_A 3nwu_A 2ytw_A 2joa_A
Length = 332
Score = 25.7 bits (57), Expect = 3.4
Identities = 5/26 (19%), Positives = 11/26 (42%)
Query: 34 IRVKFAGGRECSGILKGFDPLLNLVL 59
++V+ G +K D ++ L
Sbjct: 72 VKVELKNGATYEAKIKDVDEKADIAL 97
>1l1j_A Heat shock protease HTRA; hydrolase, serine proteinase; 2.80A
{Thermotoga maritima} SCOP: b.47.1.1
Length = 239
Score = 24.9 bits (55), Expect = 6.6
Identities = 6/26 (23%), Positives = 10/26 (38%)
Query: 34 IRVKFAGGRECSGILKGFDPLLNLVL 59
I V G + G D L++ +
Sbjct: 82 ITVTMLDGSKYDAEYIGGDEELDIAV 107
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
0.319 0.133 0.382
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: 1,488,641
Number of extensions: 74859
Number of successful extensions: 149
Number of sequences better than 10.0: 1
Number of HSP's gapped: 148
Number of HSP's successfully gapped: 32
Length of query: 105
Length of database: 6,701,793
Length adjustment: 70
Effective length of query: 35
Effective length of database: 4,747,323
Effective search space: 166156305
Effective search space used: 166156305
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 (23.7 bits)