RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9934
(158 letters)
>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 = 119 bits (299), Expect = 5e-36
Identities = 66/88 (75%), Positives = 72/88 (81%), Gaps = 2/88 (2%)
Query: 71 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
MS PL NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG +G
Sbjct: 1 MSLPL--NPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGH 58
Query: 131 LGEVLIRCNNILYIRGAEEGDEEGEMRE 158
LGEVLIRCNN+LYIRG EE +E+GEMRE
Sbjct: 59 LGEVLIRCNNVLYIRGVEEEEEDGEMRE 86
Score = 90.2 bits (224), Expect = 9e-25
Identities = 50/67 (74%), Positives = 53/67 (79%), Gaps = 2/67 (2%)
Query: 1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
MS PL NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG +G
Sbjct: 1 MSLPL--NPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGH 58
Query: 61 LGEVLIR 67
LGEVLIR
Sbjct: 59 LGEVLIR 65
>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 = 113 bits (284), Expect = 1e-33
Identities = 42/83 (50%), Positives = 48/83 (57%), Gaps = 1/83 (1%)
Query: 68 SLTMSTPLPCNPKPFLNLLTGKSVICKLKW-GHEYKGILVSTDGYMNCQLASTEEIIDGH 126
S +S P NPKPFL L V KLK+ EY+G LVSTD Y N QL EE + G
Sbjct: 11 SSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGV 70
Query: 127 CTGKLGEVLIRCNNILYIRGAEE 149
G LGE+ IRCNN+LYIR
Sbjct: 71 SHGTLGEIFIRCNNVLYIRELPN 93
Score = 91.4 bits (227), Expect = 4e-25
Identities = 34/68 (50%), Positives = 39/68 (57%), Gaps = 1/68 (1%)
Query: 1 MSTPLPCNPKPFLNLLTGKSVICKLKW-GHEYKGILVSTDGYMNCQLASTEEIIDGHCTG 59
+S P NPKPFL L V KLK+ EY+G LVSTD Y N QL EE + G G
Sbjct: 14 ISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHG 73
Query: 60 KLGEVLIR 67
LGE+ IR
Sbjct: 74 TLGEIFIR 81
>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 = 108 bits (273), Expect = 3e-32
Identities = 32/74 (43%), Positives = 44/74 (59%)
Query: 76 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVL 135
+P FLN + GK V+ +L G +YKGIL DGYMN L TEE ++G T G+
Sbjct: 2 DSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAF 61
Query: 136 IRCNNILYIRGAEE 149
IR NN+LY+ ++
Sbjct: 62 IRGNNVLYVSALDD 75
Score = 88.5 bits (220), Expect = 3e-24
Identities = 28/62 (45%), Positives = 36/62 (58%)
Query: 6 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVL 65
+P FLN + GK V+ +L G +YKGIL DGYMN L TEE ++G T G+
Sbjct: 2 DSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAF 61
Query: 66 IR 67
IR
Sbjct: 62 IR 63
>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 = 102 bits (256), Expect = 1e-29
Identities = 25/72 (34%), Positives = 39/72 (54%)
Query: 78 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 137
P ++ K V+ LK G E++G L+ D ++N LA E I DG + G+++IR
Sbjct: 4 RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIR 63
Query: 138 CNNILYIRGAEE 149
+N+L I EE
Sbjct: 64 GDNVLAISPTEE 75
Score = 83.5 bits (207), Expect = 3e-22
Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
P ++ K V+ LK G E++G L+ D ++N LA E I DG + G+++IR
Sbjct: 4 RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIR 63
>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 = 101 bits (254), Expect = 3e-29
Identities = 27/75 (36%), Positives = 39/75 (52%)
Query: 76 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVL 135
P P LN VI +LK G E++G L D +MN L EEI +G K+G V+
Sbjct: 2 PPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVV 61
Query: 136 IRCNNILYIRGAEEG 150
IR + ++++ A G
Sbjct: 62 IRGDTVVFVSPAPGG 76
Score = 85.0 bits (211), Expect = 8e-23
Identities = 27/73 (36%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 6 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVL 65
P P LN VI +LK G E++G L D +MN L EEI +G K+G V+
Sbjct: 2 PPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVV 61
Query: 66 IR--SLTMSTPLP 76
IR ++ +P P
Sbjct: 62 IRGDTVVFVSPAP 74
>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 = 99.4 bits (248), Expect = 4e-28
Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 72 STPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLAS-TEEIIDGHCTGK 130
+ P P LN G+ ++ +LK G + G L + D YMN L + DG +
Sbjct: 10 HSQDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFR 69
Query: 131 LGEVLIRCNNILYIRGAEE 149
L E IR NNI Y+R +E
Sbjct: 70 LPECYIRGNNIKYLRIQDE 88
Score = 81.3 bits (201), Expect = 5e-21
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 1/67 (1%)
Query: 2 STPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLAS-TEEIIDGHCTGK 60
+ P P LN G+ ++ +LK G + G L + D YMN L + DG +
Sbjct: 10 HSQDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFR 69
Query: 61 LGEVLIR 67
L E IR
Sbjct: 70 LPECYIR 76
>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 = 98.2 bits (245), Expect = 6e-28
Identities = 30/77 (38%), Positives = 40/77 (51%)
Query: 68 SLTMSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHC 127
++ P L VI KLK E++G+L S D +MN L EE+ DG
Sbjct: 5 DVSSQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEV 64
Query: 128 TGKLGEVLIRCNNILYI 144
T +LG VLIR +NI+YI
Sbjct: 65 TRRLGTVLIRGDNIVYI 81
Score = 83.9 bits (208), Expect = 2e-22
Identities = 26/66 (39%), Positives = 32/66 (48%)
Query: 2 STPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKL 61
P L VI KLK E++G+L S D +MN L EE+ DG T +L
Sbjct: 9 QRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRL 68
Query: 62 GEVLIR 67
G VLIR
Sbjct: 69 GTVLIR 74
>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 = 94.7 bits (236), Expect = 1e-26
Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 1/79 (1%)
Query: 70 TMSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTG 129
M+ L V+ KLK E +G+L S D +MN L+ +EEI
Sbjct: 2 AMNFL-AETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGK 60
Query: 130 KLGEVLIRCNNILYIRGAE 148
KLG ++IR +N++ I +
Sbjct: 61 KLGTIVIRGDNVILISPLQ 79
Score = 80.0 bits (198), Expect = 8e-21
Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 3/77 (3%)
Query: 1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
M+ L V+ KLK E +G+L S D +MN L+ +EEI K
Sbjct: 3 MNFL-AETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKK 61
Query: 61 LGEVLIR--SLTMSTPL 75
LG ++IR ++ + +PL
Sbjct: 62 LGTIVIRGDNVILISPL 78
>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 = 94.7 bits (236), Expect = 1e-26
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 78 NPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLI 136
P + + GK + ++K ++ G L D YMN L + E LGE+++
Sbjct: 5 LPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVL 64
Query: 137 RCNNILYIRGAEE 149
R NN++ I+ EE
Sbjct: 65 RGNNVVLIQPQEE 77
Score = 75.4 bits (186), Expect = 5e-19
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 8 NPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLI 66
P + + GK + ++K ++ G L D YMN L + E LGE+++
Sbjct: 5 LPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVL 64
Query: 67 R 67
R
Sbjct: 65 R 65
>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 = 94.0 bits (234), Expect = 3e-26
Identities = 28/81 (34%), Positives = 41/81 (50%), Gaps = 4/81 (4%)
Query: 71 MST---PLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHC 127
M++ L GK V+ KL+ HE +GIL S D ++N L EEIIDG+
Sbjct: 1 MASDISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNV 60
Query: 128 TGKLGEVLIRCNNILYIRGAE 148
K G +++R N+L+I
Sbjct: 61 Y-KRGTMVVRGENVLFISPVP 80
Score = 78.6 bits (194), Expect = 3e-20
Identities = 25/70 (35%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 1 MST---PLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHC 57
M++ L GK V+ KL+ HE +GIL S D ++N L EEIIDG+
Sbjct: 1 MASDISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNV 60
Query: 58 TGKLGEVLIR 67
K G +++R
Sbjct: 61 Y-KRGTMVVR 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 = 79.6 bits (196), Expect = 4e-20
Identities = 19/64 (29%), Positives = 30/64 (46%)
Query: 82 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNI 141
FL L+ ++V +LK G + G + D MN L + + + +L + IR NNI
Sbjct: 6 FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNI 65
Query: 142 LYIR 145
Y
Sbjct: 66 RYFI 69
Score = 66.2 bits (161), Expect = 5e-15
Identities = 15/56 (26%), Positives = 26/56 (46%)
Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
FL L+ ++V +LK G + G + D MN L + + + +L + IR
Sbjct: 6 FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIR 61
>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 = 79.3 bits (195), Expect = 5e-20
Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 3/79 (3%)
Query: 71 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
MS +P L+ G V C+ G Y+G L+ + MNCQ+++ +
Sbjct: 1 MSIGVP---IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQ 57
Query: 131 LGEVLIRCNNILYIRGAEE 149
L +V IR + I ++ +
Sbjct: 58 LEQVYIRGSKIRFLILPDM 76
Score = 67.4 bits (164), Expect = 2e-15
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
MS +P L+ G V C+ G Y+G L+ + MNCQ+++ +
Sbjct: 1 MSIGVP---IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQ 57
Query: 61 LGEVLIR 67
L +V IR
Sbjct: 58 LEQVYIR 64
>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 = 77.8 bits (192), Expect = 5e-20
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 3/75 (4%)
Query: 71 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
MS +P L+ G V C+ G Y+G L+ + MNCQ+++ +
Sbjct: 1 MSIGVP---IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQ 57
Query: 131 LGEVLIRCNNILYIR 145
L +V IR I ++
Sbjct: 58 LEQVYIRGCKIRFLI 72
Score = 63.6 bits (155), Expect = 2e-14
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
MS +P L+ G V C+ G Y+G L+ + MNCQ+++ +
Sbjct: 1 MSIGVP---IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQ 57
Query: 61 LGEVLIR 67
L +V IR
Sbjct: 58 LEQVYIR 64
>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 = 71.2 bits (175), Expect = 2e-17
Identities = 23/78 (29%), Positives = 33/78 (42%), Gaps = 4/78 (5%)
Query: 71 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
MS P P L K + KL G +GIL D +MN + E+
Sbjct: 1 MSKAHP----PELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNN 56
Query: 131 LGEVLIRCNNILYIRGAE 148
+G V+IR N+I+ + E
Sbjct: 57 IGMVVIRGNSIIMLEALE 74
Score = 60.0 bits (146), Expect = 3e-13
Identities = 20/67 (29%), Positives = 27/67 (40%), Gaps = 4/67 (5%)
Query: 1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
MS P P L K + KL G +GIL D +MN + E+
Sbjct: 1 MSKAHP----PELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNN 56
Query: 61 LGEVLIR 67
+G V+IR
Sbjct: 57 IGMVVIR 63
>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 = 54.9 bits (132), Expect = 6e-11
Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 3/76 (3%)
Query: 70 TMSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI-IDGHCT 128
MS + P ++ G ++ +K E+ G LV D Y+N L E T
Sbjct: 14 PMSMTIL--PLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVT 71
Query: 129 GKLGEVLIRCNNILYI 144
K E+L+ N + +
Sbjct: 72 EKHSEMLLNGNGMCML 87
Score = 45.2 bits (107), Expect = 2e-07
Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 5/77 (6%)
Query: 1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI-IDGHCTG 59
MS + P ++ G ++ +K E+ G LV D Y+N L E T
Sbjct: 15 MSMTIL--PLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTE 72
Query: 60 KLGEVLIR--SLTMSTP 74
K E+L+ + M P
Sbjct: 73 KHSEMLLNGNGMCMLIP 89
>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 = 55.3 bits (133), Expect = 6e-11
Identities = 20/78 (25%), Positives = 30/78 (38%), Gaps = 8/78 (10%)
Query: 83 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH-------CTGKLGEVL 135
L+ + + G + GIL D MN L EE + KLG V+
Sbjct: 28 LSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVV 87
Query: 136 IRCNNILYIRGAEEGDEE 153
+R ++ I +G EE
Sbjct: 88 VRGTTLVLI-APMDGSEE 104
Score = 41.9 bits (98), Expect = 8e-06
Identities = 16/62 (25%), Positives = 23/62 (37%), Gaps = 7/62 (11%)
Query: 13 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH-------CTGKLGEVL 65
L+ + + G + GIL D MN L EE + KLG V+
Sbjct: 28 LSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVV 87
Query: 66 IR 67
+R
Sbjct: 88 VR 89
>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 = 52.5 bits (126), Expect = 5e-10
Identities = 17/86 (19%), Positives = 30/86 (34%), Gaps = 13/86 (15%)
Query: 72 STPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTG-- 129
S P + L + V KL+ E G L + D ++N L EEI+
Sbjct: 3 SAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEET 62
Query: 130 -----------KLGEVLIRCNNILYI 144
+ +R ++++ I
Sbjct: 63 DKDKALKTIRKHYEMLFVRGDSVILI 88
Score = 44.8 bits (106), Expect = 4e-07
Identities = 15/62 (24%), Positives = 24/62 (38%)
Query: 2 STPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKL 61
S P + L + V KL+ E G L + D ++N L EEI+ +
Sbjct: 3 SAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEET 62
Query: 62 GE 63
+
Sbjct: 63 DK 64
>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 = 49.0 bits (117), Expect = 1e-08
Identities = 18/88 (20%), Positives = 28/88 (31%), Gaps = 10/88 (11%)
Query: 78 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-------DGHCTGK 130
P L L + V KL+ G L + D + N L+ E I +
Sbjct: 10 TPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERR 69
Query: 131 LGEVLIRCNNILYIRGAEEGDEEGEMRE 158
V IR + + I E+ +
Sbjct: 70 CEMVFIRGDTVTLI---STPSEDDDGAV 94
Score = 40.9 bits (96), Expect = 1e-05
Identities = 16/67 (23%), Positives = 22/67 (32%), Gaps = 7/67 (10%)
Query: 8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-------DGHCTGK 60
P L L + V KL+ G L + D + N L+ E I +
Sbjct: 10 TPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERR 69
Query: 61 LGEVLIR 67
V IR
Sbjct: 70 CEMVFIR 76
>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 = 47.9 bits (114), Expect = 3e-08
Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 1/64 (1%)
Query: 82 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI-IDGHCTGKLGEVLIRCNN 140
+L + V + +G ++ D YMN L EEI +LG ++++ +N
Sbjct: 24 YLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDN 83
Query: 141 ILYI 144
I +
Sbjct: 84 ITLL 87
Score = 39.0 bits (91), Expect = 5e-05
Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 3/68 (4%)
Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI-IDGHCTGKLGEVLIR--S 68
+L + V + +G ++ D YMN L EEI +LG ++++ +
Sbjct: 24 YLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDN 83
Query: 69 LTMSTPLP 76
+T+ +
Sbjct: 84 ITLLQSVS 91
>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 = 44.2 bits (104), Expect = 1e-06
Identities = 15/81 (18%), Positives = 28/81 (34%), Gaps = 15/81 (18%)
Query: 79 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTG--------- 129
P ++ G + +K E+ G+L D Y+N L +E
Sbjct: 29 PLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKL 88
Query: 130 ------KLGEVLIRCNNILYI 144
+L +L+ NN+ +
Sbjct: 89 KRVMVNRLETILLSGNNVAML 109
Score = 39.2 bits (91), Expect = 7e-05
Identities = 17/91 (18%), Positives = 31/91 (34%), Gaps = 18/91 (19%)
Query: 9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTG--------- 59
P ++ G + +K E+ G+L D Y+N L +E
Sbjct: 29 PLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKL 88
Query: 60 ------KLGEVLIR--SLTMSTPLPCNPKPF 82
+L +L+ ++ M P +P F
Sbjct: 89 KRVMVNRLETILLSGNNVAMLVP-GGDPDSF 118
>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 = 39.1 bits (91), Expect = 6e-05
Identities = 15/72 (20%), Positives = 27/72 (37%), Gaps = 10/72 (13%)
Query: 83 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----------DGHCTGKLG 132
+ + C L+ G + G + D +MN L +E + LG
Sbjct: 9 MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLG 68
Query: 133 EVLIRCNNILYI 144
VL+R N++ +
Sbjct: 69 LVLLRGENLVSM 80
Score = 32.9 bits (75), Expect = 0.009
Identities = 14/65 (21%), Positives = 23/65 (35%), Gaps = 10/65 (15%)
Query: 13 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----------DGHCTGKLG 62
+ + C L+ G + G + D +MN L +E + LG
Sbjct: 9 MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLG 68
Query: 63 EVLIR 67
VL+R
Sbjct: 69 LVLLR 73
>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 = 31.1 bits (70), Expect = 0.060
Identities = 10/68 (14%), Positives = 25/68 (36%), Gaps = 6/68 (8%)
Query: 85 LLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNI--- 141
+ V+ + + G + + D + N L + +E+ G+ + N
Sbjct: 36 VKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRY 95
Query: 142 ---LYIRG 146
+++RG
Sbjct: 96 ISKMFLRG 103
Score = 29.5 bits (66), Expect = 0.20
Identities = 7/49 (14%), Positives = 18/49 (36%)
Query: 15 LLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGE 63
+ V+ + + G + + D + N L + +E+ G+
Sbjct: 36 VKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGK 84
>2ksk_A Sugarcane defensin 5; csalphabeta motif, antimicrobial protein;
NMR {Saccharum officinarum}
Length = 71
Score = 25.2 bits (54), Expect = 3.5
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 22 ICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
ICK + HEYKG + + +E G C G+
Sbjct: 8 ICKSR-SHEYKGRCIQDMDCNAACVKESESYTGGFCNGR 45
Score = 25.2 bits (54), Expect = 3.5
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 92 ICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 130
ICK + HEYKG + + +E G C G+
Sbjct: 8 ICKSR-SHEYKGRCIQDMDCNAACVKESESYTGGFCNGR 45
>3fvv_A Uncharacterized protein; unknown function, structural genomics,
PSI,MCSG, protein STR initiative, midwest center for
structural genomics; 2.10A {Bordetella pertussis}
Length = 232
Score = 26.2 bits (58), Expect = 4.8
Identities = 8/23 (34%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 46 LASTEEIIDGHCTGKL-GEVLIR 67
+A+ E DG TG++ G R
Sbjct: 135 IATDPEYRDGRYTGRIEGTPSFR 157
Score = 26.2 bits (58), Expect = 4.8
Identities = 8/23 (34%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 116 LASTEEIIDGHCTGKL-GEVLIR 137
+A+ E DG TG++ G R
Sbjct: 135 IATDPEYRDGRYTGRIEGTPSFR 157
>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex,
RNA binding protein; 2.00A {Homo sapiens}
Length = 86
Score = 24.7 bits (53), Expect = 7.1
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTD 39
MS + P + + + K V +EYKG +++TD
Sbjct: 1 MSEWMKKGPLEWQDYI-YKEVRVTASEKNEYKGWVLTTD 38
Score = 24.7 bits (53), Expect = 7.1
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 71 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTD 109
MS + P + + + K V +EYKG +++TD
Sbjct: 1 MSEWMKKGPLEWQDYI-YKEVRVTASEKNEYKGWVLTTD 38
>3aab_A Putative uncharacterized protein ST1653; alpha-crystallin domain,
chaperone; 1.85A {Sulfolobus tokodaii} PDB: 3aac_A
Length = 123
Score = 24.9 bits (55), Expect = 10.0
Identities = 6/25 (24%), Positives = 8/25 (32%)
Query: 133 EVLIRCNNILYIRGAEEGDEEGEMR 157
+ + N L I E E G
Sbjct: 51 KARVSGQNELIIEAEREITEPGVKY 75
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
0.318 0.139 0.438
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: 2,506,943
Number of extensions: 140938
Number of successful extensions: 291
Number of sequences better than 10.0: 1
Number of HSP's gapped: 277
Number of HSP's successfully gapped: 57
Length of query: 158
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 72
Effective length of database: 4,300,587
Effective search space: 309642264
Effective search space used: 309642264
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 (21.7 bits)
S2: 53 (24.5 bits)