RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy800
(204 letters)
>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 = 101 bits (252), Expect = 2e-28
Identities = 40/85 (47%), Positives = 57/85 (67%), Gaps = 2/85 (2%)
Query: 102 YTMTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEY 161
+ S T+LPLEL+DKCIGS + +IMK+++E GTL GFDD+VN++L+DVTEY
Sbjct: 5 HHHHHHSQDPMSMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEY 64
Query: 162 ESTPEGRRITKLDQILLNGNNITML 186
++ K ++LLNGN + ML
Sbjct: 65 DTVTGVTE--KHSEMLLNGNGMCML 87
Score = 69.9 bits (171), Expect = 3e-16
Identities = 30/57 (52%), Positives = 42/57 (73%)
Query: 3 APSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH 59
S T+LPLEL+DKCIGS + +IMK+++E GTL GFDD+VN++L+DVT+
Sbjct: 9 HHSQDPMSMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYD 65
>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 = 92.9 bits (231), Expect = 4e-25
Identities = 22/75 (29%), Positives = 46/75 (61%), Gaps = 6/75 (8%)
Query: 116 LLPLELVDKCIGSR----IHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRIT 171
+ P+ L+ + + +R + + + + I G + GFD+++N++L+D E S + R+
Sbjct: 15 VQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRK-- 72
Query: 172 KLDQILLNGNNITML 186
+L +I+L G+NIT+L
Sbjct: 73 QLGRIMLKGDNITLL 87
Score = 58.7 bits (142), Expect = 6e-12
Identities = 12/53 (22%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 13 LLPLELVDKCIGSR----IHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS 61
+ P+ L+ + + +R + + + + I G + GFD+++N++L+D + H
Sbjct: 15 VQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSK 67
>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 = 92.4 bits (229), Expect = 2e-24
Identities = 39/94 (41%), Positives = 56/94 (59%), Gaps = 12/94 (12%)
Query: 105 TAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYEST 164
S + +LPL L+DKCIG+RI+++MK DKE G L GFD++VNM+L+DV EY
Sbjct: 16 QGGSNQKGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFK 75
Query: 165 PEGR------------RITKLDQILLNGNNITML 186
+ + +L+ ILL+GNN+ ML
Sbjct: 76 ADEEDISGGNKKLKRVMVNRLETILLSGNNVAML 109
Score = 72.7 bits (178), Expect = 5e-17
Identities = 28/59 (47%), Positives = 40/59 (67%)
Query: 2 TAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD 60
S + +LPL L+DKCIG+RI+++MK DKE G L GFD++VNM+L+DV +
Sbjct: 16 QGGSNQKGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGF 74
>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 = 90.8 bits (226), Expect = 2e-24
Identities = 22/74 (29%), Positives = 44/74 (59%), Gaps = 4/74 (5%)
Query: 114 STLLPLELVDKCIGSRIHIIMKNDK-EIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITK 172
+ +LP ++V +G I + MK ++ ++VG L G DD++N+ L + E + ++
Sbjct: 2 AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECK---GEEKVRS 58
Query: 173 LDQILLNGNNITML 186
L +I+L GNN+ ++
Sbjct: 59 LGEIVLRGNNVVLI 72
Score = 64.3 bits (157), Expect = 3e-14
Identities = 16/51 (31%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 11 STLLPLELVDKCIGSRIHIIMKNDK-EIVGTLNGFDDFVNMLLEDVTDCHD 60
+ +LP ++V +G I + MK ++ ++VG L G DD++N+ L + +C
Sbjct: 2 AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKG 52
>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 = 84.7 bits (210), Expect = 5e-22
Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 110 ATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRR 169
+ + PL+ + + S + I +K D+E G L FD +N++L D E E +G
Sbjct: 8 SQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELE---DGEV 64
Query: 170 ITKLDQILLNGNNITML 186
+L +L+ G+NI +
Sbjct: 65 TRRLGTVLIRGDNIVYI 81
Score = 62.4 bits (152), Expect = 2e-13
Identities = 15/54 (27%), Positives = 27/54 (50%)
Query: 7 ATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD 60
+ + PL+ + + S + I +K D+E G L FD +N++L D + D
Sbjct: 8 SQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELED 61
>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 = 82.7 bits (205), Expect = 2e-21
Identities = 16/69 (23%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
PL+++ + + + +I+K E G L G+D +N++L D + +G + + +I+
Sbjct: 5 PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQ---DGEVVKRYGKIV 61
Query: 178 LNGNNITML 186
+ G+N+ +
Sbjct: 62 IRGDNVLAI 70
Score = 60.0 bits (146), Expect = 1e-12
Identities = 13/46 (28%), Positives = 25/46 (54%)
Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD 60
PL+++ + + + +I+K E G L G+D +N++L D D
Sbjct: 5 PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQD 50
>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 = 82.7 bits (205), Expect = 2e-21
Identities = 17/69 (24%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
PL+++++ + S + + +K +E GTL+G+D +N++L D E + G + K+ ++
Sbjct: 5 PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQ---NGEVVRKVGSVV 61
Query: 178 LNGNNITML 186
+ G+ + +
Sbjct: 62 IRGDTVVFV 70
Score = 60.4 bits (147), Expect = 8e-13
Identities = 13/47 (27%), Positives = 30/47 (63%)
Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS 61
PL+++++ + S + + +K +E GTL+G+D +N++L D + +
Sbjct: 5 PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNG 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 = 77.1 bits (190), Expect = 6e-19
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 2/79 (2%)
Query: 105 TAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYEST 164
+ + +LPL L++ G I + +KN + G L D+++N+ L +V
Sbjct: 4 SHHHHHHSQDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRT--M 61
Query: 165 PEGRRITKLDQILLNGNNI 183
P+G + +L + + GNNI
Sbjct: 62 PDGDKFFRLPECYIRGNNI 80
Score = 56.7 bits (137), Expect = 5e-11
Identities = 14/55 (25%), Positives = 27/55 (49%)
Query: 2 TAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
+ + +LPL L++ G I + +KN + G L D+++N+ L +V
Sbjct: 4 SHHHHHHSQDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVI 58
>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 = 76.7 bits (189), Expect = 8e-19
Identities = 17/74 (22%), Positives = 38/74 (51%), Gaps = 4/74 (5%)
Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRIT----KL 173
PL+L+ + R++I ++ + +VGTL FD N++L D E ++ +
Sbjct: 11 PLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRC 70
Query: 174 DQILLNGNNITMLG 187
+ + + G+ +T++
Sbjct: 71 EMVFIRGDTVTLIS 84
Score = 57.4 bits (139), Expect = 2e-11
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
PL+L+ + R++I ++ + +VGTL FD N++L D
Sbjct: 11 PLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAV 52
>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 = 74.5 bits (183), Expect = 5e-18
Identities = 17/78 (21%), Positives = 38/78 (48%)
Query: 109 VATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGR 168
+ + + PL+LV + +++ ++ D+E+ G L+ +D+ +NM+L D E + +
Sbjct: 1 MESAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDE 60
Query: 169 RITKLDQILLNGNNITML 186
K + + ML
Sbjct: 61 ETDKDKALKTIRKHYEML 78
Score = 60.6 bits (147), Expect = 1e-12
Identities = 13/51 (25%), Positives = 30/51 (58%)
Query: 6 VATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
+ + + PL+LV + +++ ++ D+E+ G L+ +D+ +NM+L D
Sbjct: 1 MESAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAE 51
>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 = 71.2 bits (175), Expect = 6e-17
Identities = 17/69 (24%), Positives = 40/69 (57%), Gaps = 3/69 (4%)
Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
+++ + + + + + +K +KE+ G L +D +N++L D E +S G+ KL I+
Sbjct: 10 AHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGK---KLGTIV 66
Query: 178 LNGNNITML 186
+ G+N+ ++
Sbjct: 67 IRGDNVILI 75
Score = 53.1 bits (128), Expect = 5e-10
Identities = 9/47 (19%), Positives = 25/47 (53%)
Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS 61
+++ + + + + + +K +KE+ G L +D +N++L D +
Sbjct: 10 AHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSD 56
>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 = 67.5 bits (165), Expect = 2e-15
Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 3/75 (4%)
Query: 114 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKL 173
L P ++ G + + +K E G L D ++NM L + EY +G L
Sbjct: 3 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYI---DGALSGHL 59
Query: 174 DQILLNGNNITMLGL 188
++L+ NN+ +
Sbjct: 60 GEVLIRCNNVLYIRG 74
Score = 47.8 bits (114), Expect = 5e-08
Identities = 12/50 (24%), Positives = 21/50 (42%)
Query: 11 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD 60
L P ++ G + + +K E G L D ++NM L + + D
Sbjct: 3 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYID 52
>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 = 65.0 bits (159), Expect = 1e-14
Identities = 18/69 (26%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
P E ++K IG ++ I + + + G L+ D ++N+ LE EY G++
Sbjct: 5 PNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYV---NGKKTNVYGDAF 61
Query: 178 LNGNNITML 186
+ GNN+ +
Sbjct: 62 IRGNNVLYV 70
Score = 46.9 bits (112), Expect = 7e-08
Identities = 12/46 (26%), Positives = 25/46 (54%)
Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD 60
P E ++K IG ++ I + + + G L+ D ++N+ LE + +
Sbjct: 5 PNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVN 50
>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 = 65.4 bits (159), Expect = 3e-14
Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 5/81 (6%)
Query: 111 TNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRI 170
P L+L + RI ++I G L GFD +N++L+DV E PE ++
Sbjct: 18 ERPRKESILDL-SRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKL 76
Query: 171 T----KLDQILLNGNNITMLG 187
T KL +++ G + ++
Sbjct: 77 TGAIRKLGLVVVRGTTLVLIA 97
Score = 47.6 bits (113), Expect = 1e-07
Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 8 TNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSH 62
P L+L + RI ++I G L GFD +N++L+DV + +
Sbjct: 18 ERPRKESILDL-SRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNP 71
>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 = 64.3 bits (156), Expect = 8e-14
Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 3/75 (4%)
Query: 114 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKL 173
S +P++++ + G + + G L +D +N + ++T T R+ +L
Sbjct: 2 SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITV---TYRDGRVAQL 58
Query: 174 DQILLNGNNITMLGL 188
+Q+ + G+ I L L
Sbjct: 59 EQVYIRGSKIRFLIL 73
Score = 49.7 bits (118), Expect = 2e-08
Identities = 8/46 (17%), Positives = 21/46 (45%)
Query: 11 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
S +P++++ + G + + G L +D +N + ++T
Sbjct: 2 SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNIT 47
>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 = 61.2 bits (149), Expect = 3e-13
Identities = 17/70 (24%), Positives = 38/70 (54%), Gaps = 4/70 (5%)
Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
P EL K + ++ + + + + G L GFD F+N+++++ E ++ + + ++
Sbjct: 6 PPEL-KKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQN---NIGMVV 61
Query: 178 LNGNNITMLG 187
+ GN+I ML
Sbjct: 62 IRGNSIIMLE 71
Score = 43.9 bits (104), Expect = 1e-06
Identities = 12/47 (25%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS 61
P EL K + ++ + + + + G L GFD F+N+++++ + S
Sbjct: 6 PPEL-KKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATS 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 = 58.2 bits (141), Expect = 6e-12
Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 4/80 (5%)
Query: 108 SVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEG 167
+ + + IG ++ + +++ EI G L FD VN+LLED E
Sbjct: 2 ASDISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDG--- 58
Query: 168 RRITKLDQILLNGNNITMLG 187
+ K +++ G N+ +
Sbjct: 59 -NVYKRGTMVVRGENVLFIS 77
Score = 45.1 bits (107), Expect = 5e-07
Identities = 15/57 (26%), Positives = 26/57 (45%)
Query: 5 SVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS 61
+ + + IG ++ + +++ EI G L FD VN+LLED + D
Sbjct: 2 ASDISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDG 58
>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 = 57.2 bits (138), Expect = 2e-11
Identities = 20/89 (22%), Positives = 38/89 (42%), Gaps = 4/89 (4%)
Query: 99 HLLYTMTAPSVATNPSTLLPLELVDKCIGSRIHIIMK-NDKEIVGTLNGFDDFVNMLLED 157
H + M+ S + + P + + R+ + +K N E GTL D++ N+ L +
Sbjct: 3 HHHHHMSESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNE 62
Query: 158 VTEYESTPEGRRITKLDQILLNGNNITML 186
E+ G L +I + NN+ +
Sbjct: 63 AEEFV---AGVSHGTLGEIFIRCNNVLYI 88
Score = 40.6 bits (95), Expect = 2e-05
Identities = 13/61 (21%), Positives = 26/61 (42%), Gaps = 1/61 (1%)
Query: 1 MTAPSVATNPSTLLPLELVDKCIGSRIHIIMK-NDKEIVGTLNGFDDFVNMLLEDVTDCH 59
M+ S + + P + + R+ + +K N E GTL D++ N+ L + +
Sbjct: 8 MSESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFV 67
Query: 60 D 60
Sbjct: 68 A 68
>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 = 57.3 bits (138), Expect = 4e-11
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 3/67 (4%)
Query: 117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQI 176
+ + K + I +KN ++ GT+ G D +N L+ V T + R +L+ +
Sbjct: 2 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKM---TLKNREPVQLETL 58
Query: 177 LLNGNNI 183
+ GNNI
Sbjct: 59 SIRGNNI 65
Score = 45.0 bits (106), Expect = 1e-06
Identities = 11/43 (25%), Positives = 20/43 (46%)
Query: 14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
+ + K + I +KN ++ GT+ G D +N L+ V
Sbjct: 2 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVK 44
>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 = 55.5 bits (134), Expect = 6e-11
Identities = 14/70 (20%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 114 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKL 173
S +P++++ + G + + G L +D +N + ++T T R+ +L
Sbjct: 2 SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITV---TYRDGRVAQL 58
Query: 174 DQILLNGNNI 183
+Q+ + G I
Sbjct: 59 EQVYIRGCKI 68
Score = 42.0 bits (99), Expect = 6e-06
Identities = 8/46 (17%), Positives = 21/46 (45%)
Query: 11 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
S +P++++ + G + + G L +D +N + ++T
Sbjct: 2 SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNIT 47
>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 = 49.1 bits (117), Expect = 2e-08
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 7/70 (10%)
Query: 124 KCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEY-------ESTPEGRRITKLDQI 176
+ I R+ I+++ + +GT FD +N++L D E+ E L +
Sbjct: 11 QHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLV 70
Query: 177 LLNGNNITML 186
LL G N+ +
Sbjct: 71 LLRGENLVSM 80
Score = 37.1 bits (86), Expect = 5e-04
Identities = 10/37 (27%), Positives = 21/37 (56%)
Query: 21 KCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTD 57
+ I R+ I+++ + +GT FD +N++L D +
Sbjct: 11 QHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDE 47
>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 = 50.0 bits (119), Expect = 2e-08
Identities = 17/81 (20%), Positives = 43/81 (53%), Gaps = 13/81 (16%)
Query: 118 PLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEY--------ESTPEG 167
PL ++ + + +++ I +N+K+++G + FD NM+LE+V E + +
Sbjct: 28 PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKS 87
Query: 168 RRITK---LDQILLNGNNITM 185
+ + K + ++ L G+++ +
Sbjct: 88 KPVNKDRYISKMFLRGDSVIV 108
Score = 43.0 bits (101), Expect = 6e-06
Identities = 13/44 (29%), Positives = 28/44 (63%), Gaps = 2/44 (4%)
Query: 15 PLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
PL ++ + + +++ I +N+K+++G + FD NM+LE+V
Sbjct: 28 PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVK 71
>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 = 33.1 bits (75), Expect = 0.020
Identities = 7/35 (20%), Positives = 21/35 (60%)
Query: 23 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTD 57
+G + +++ N + G L+ D+ +N++L + ++
Sbjct: 9 LGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASN 43
Score = 32.0 bits (72), Expect = 0.060
Identities = 9/51 (17%), Positives = 22/51 (43%)
Query: 126 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQI 176
+G + +++ N + G L+ D+ +N++L + + R I
Sbjct: 9 LGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRVFIMYRYI 59
>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 = 33.5 bits (76), Expect = 0.029
Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 11/67 (16%)
Query: 126 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEY---------ESTPEGRRITKLDQI 176
I R+ I+++ + +GT FD +N++L D E+ ++ E +R+ L +
Sbjct: 13 IDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGL--V 70
Query: 177 LLNGNNI 183
LL G N+
Sbjct: 71 LLRGENL 77
Score = 30.8 bits (69), Expect = 0.25
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 23 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLED 54
I R+ I+++ + +GT FD +N++L D
Sbjct: 13 IDYRMRCILQDGRIFIGTFKAFDKHMNLILCD 44
>2fb7_A SM-like protein, LSM-14_N (RAP55); DR.13312, BC055387, AAH55387,
stronGly BENT five-stranded antiparallel beta- sheet,
structural genomics, PSI; NMR {Danio rerio} SCOP:
b.38.1.5 PDB: 2vxf_A
Length = 95
Score = 30.2 bits (68), Expect = 0.12
Identities = 20/84 (23%), Positives = 31/84 (36%), Gaps = 7/84 (8%)
Query: 113 PSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNML-LEDVTEY--ESTPEGRR 169
L IGS+I +I K + G L D + + L V + E P R
Sbjct: 5 HHHLEDPSGGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRP 64
Query: 170 I----TKLDQILLNGNNITMLGLH 189
I + I+ G++I L +
Sbjct: 65 IAPRDETFEYIIFRGSDIKDLTVC 88
Score = 25.2 bits (55), Expect = 8.3
Identities = 10/36 (27%), Positives = 13/36 (36%)
Query: 10 PSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFD 45
L IGS+I +I K + G L D
Sbjct: 5 HHHLEDPSGGTPYIGSKISLISKAEIRYEGILYTID 40
>1ycy_A Conserved hypothetical protein; structural genomics, southeast
collaboratory for structural genomics, secsg, protein
structure initiative; 2.80A {Pyrococcus furiosus} SCOP:
b.38.1.4
Length = 71
Score = 28.5 bits (63), Expect = 0.34
Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 121 LVDKCI----GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQI 176
L++K + G ++ + + D GTL FD+ V +LL+DV + + + L+ I
Sbjct: 6 LLEKVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIGNRGKQMLIGLEDI 64
Score = 26.5 bits (58), Expect = 2.0
Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 5/44 (11%)
Query: 18 LVDKCI----GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTD 57
L++K + G ++ + + D GTL FD+ V +LL+DV D
Sbjct: 6 LLEKVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVD 48
>2vxe_A CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA decay, LSM
proteins, translational repression, transcription; NMR
{Drosophila melanogaster}
Length = 88
Score = 28.7 bits (64), Expect = 0.37
Identities = 18/65 (27%), Positives = 26/65 (40%), Gaps = 7/65 (10%)
Query: 126 IGSRIHIIMKNDKEIVGTLNGFDDFVNML-LEDVTEY--ESTPEGRRI----TKLDQILL 178
+GS+I +I K D G L D + L V + E +I D IL
Sbjct: 12 LGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQIAPQSQIYDYILF 71
Query: 179 NGNNI 183
G++I
Sbjct: 72 RGSDI 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 = 30.6 bits (68), Expect = 0.38
Identities = 31/196 (15%), Positives = 60/196 (30%), Gaps = 37/196 (18%)
Query: 8 TNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYF 67
+ + +V+K + + K KE ++ + + LE+ H S + Y
Sbjct: 397 FDVIKSDVMVVVNKLHKYSL--VEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYN 454
Query: 68 ASDLINFIWGLPMITPITCAYSRSH-QYRTLTHLLYTMTAPSVATNPSTLLPLELVDK-- 124
+ L P Y SH + HL + L +++
Sbjct: 455 IPKTFDS-DDLI--PPYLDQYFYSHIGH----HLKNIEHPERMTLFRMVFLDFRFLEQKI 507
Query: 125 --------CIGSRIHI----------IMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPE 166
GS ++ I ND + +N DF+ + E++ +
Sbjct: 508 RHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKY--- 564
Query: 167 GRRITKLDQILLNGNN 182
T L +I L +
Sbjct: 565 ----TDLLRIALMAED 576
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B
2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B
Length = 1131
Score = 29.8 bits (67), Expect = 0.74
Identities = 14/87 (16%), Positives = 31/87 (35%), Gaps = 8/87 (9%)
Query: 79 PMITPITCAYSRSHQYRTLTHLLYTMTAPSVATNPS--TLLPLELVDKCIGSRIHIIMKN 136
IT S + YR + + P+ +P ++ + +G +
Sbjct: 184 SNITHTAKIISSTAGYRVPVTIERLKDGTFHVSFPAVPGKIPFVILMRALG------ILT 237
Query: 137 DKEIVGTLNGFDDFVNMLLEDVTEYES 163
D++IV ++ + N L + + S
Sbjct: 238 DRDIVYAVSLDPEIQNELFPSLEQASS 264
>1v84_A Galactosylgalactosylxylosylprotein 3-beta- glucuronosyltransferase
1; glycoprotein, glycocyltransferase, HNK-1 epitop; HET:
GAL NDG NAG TLA UDP; 1.82A {Homo sapiens} SCOP: c.68.1.7
PDB: 1v83_A* 1v82_A*
Length = 253
Score = 29.2 bits (65), Expect = 0.78
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 77 GLPMITPITCAYSRSHQYRTLTHLLYT-MTAPSV 109
LP I +T YSR Q LT + T + P++
Sbjct: 1 ALPTIHVVTPTYSRPVQKAELTRMANTLLHVPNL 34
>2d0j_A Galactosylgalactosylxylosylprotein 3-beta- glucuronosyltransferase
2; rossmann-like fold, glucuronyltransferase; 2.00A
{Homo sapiens}
Length = 246
Score = 28.8 bits (64), Expect = 1.1
Identities = 13/27 (48%), Positives = 13/27 (48%)
Query: 78 LPMITPITCAYSRSHQYRTLTHLLYTM 104
LP I IT YSR Q LT L T
Sbjct: 2 LPTIYAITPTYSRPVQKAELTRLANTF 28
>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 = 28.4 bits (62), Expect = 1.2
Identities = 8/28 (28%), Positives = 14/28 (50%), Gaps = 4/28 (14%)
Query: 92 HQYRTL-THL-LYTM-TAPSVATNPSTL 116
+ L L LY +AP++A +T+
Sbjct: 20 QALKKLQASLKLYADDSAPALAIK-ATM 46
>3cu0_A Galactosylgalactosylxylosylprotein 3-beta- glucuronosyltransferase
3; glcat-I, glycosyltransferase, heparan sulfate
biosynthesis, glycoprotein; HET: GAL UDP; 1.90A {Homo
sapiens} SCOP: c.68.1.7 PDB: 1kws_A* 1fgg_A*
Length = 281
Score = 27.3 bits (60), Expect = 3.9
Identities = 9/33 (27%), Positives = 12/33 (36%), Gaps = 1/33 (3%)
Query: 78 LPMITPITCAYSRSHQYRTLTHLLYT-MTAPSV 109
I +T Y+R Q L L T P +
Sbjct: 20 HMTIYVVTPTYARLVQKAELVRLSQTLSLVPRL 52
>2byk_B Chrac-14; nucleosome sliding, histone fold, DNA-binding protein;
2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB:
2bym_B
Length = 128
Score = 26.1 bits (57), Expect = 4.9
Identities = 10/50 (20%), Positives = 17/50 (34%)
Query: 123 DKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITK 172
I D T F+ FV L +D+ Y + ++ +K
Sbjct: 54 ALAHKQNHKTITAKDILQTLTELDFESFVPSLTQDLEVYRKVVKEKKESK 103
>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 = 27.3 bits (60), Expect = 5.0
Identities = 17/71 (23%), Positives = 25/71 (35%), Gaps = 26/71 (36%)
Query: 102 YTMTAPSVATNPSTLLP------LELVDKCIGSRIHIIMKNDKEIV------------GT 143
Y M +A NP + L+ V + +G R ++ EIV G
Sbjct: 1807 YGM----IAINPGRVAASFSQEALQYVVERVGKRTGWLV----EIVNYNVENQQYVAAGD 1858
Query: 144 LNGFDDFVNML 154
L D N+L
Sbjct: 1859 LRALDTVTNVL 1869
>1k6k_A ATP-dependent CLP protease ATP-binding subunit CLPA; chaperone,
ATPase, adaptor binding, X-RAY, structure, N-domain,
hydrolase; 1.80A {Escherichia coli} SCOP: a.174.1.1 PDB:
1r6c_X 1r6o_A* 1r6q_A* 1mg9_B* 1lzw_B* 1mbx_A* 1mbv_A
1mbu_A*
Length = 143
Score = 26.1 bits (57), Expect = 5.2
Identities = 6/19 (31%), Positives = 10/19 (52%)
Query: 87 AYSRSHQYRTLTHLLYTMT 105
A H++ T+ HLL +
Sbjct: 17 AREHRHEFMTVEHLLLALL 35
>2acx_A G protein-coupled receptor kinase 6; GRK, G transferase; HET: ANP;
2.60A {Homo sapiens} PDB: 3nyn_A* 3nyo_A*
Length = 576
Score = 27.1 bits (60), Expect = 5.5
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 154 LLEDVTEYESTPEGRRITKLDQIL 177
L+ V EYE TP+ +R +
Sbjct: 83 FLDGVAEYEVTPDDKRKACGRNLT 106
>1w6s_A Methanol dehydrogenase subunit 1; anisotropic, electron transfer,
oxidoreductase, calcium- binding, methanol utilization,
PQQ; HET: PQQ; 1.2A {Methylobacterium extorquens} SCOP:
b.70.1.1 PDB: 1h4i_A* 1h4j_A* 2d0v_A* 1lrw_A*
Length = 599
Score = 26.8 bits (59), Expect = 6.5
Identities = 6/33 (18%), Positives = 11/33 (33%), Gaps = 2/33 (6%)
Query: 156 EDVTEYESTPEGRRITKLDQILLNGNNITMLGL 188
++ + + L QI N N+ L
Sbjct: 12 DNWVMPGKNYDSNNFSDLKQI--NKGNVKQLRP 42
>1nbw_A Glycerol dehydratase reactivase alpha subunit; molecular chaperone,
actin-like ATPase domain, beta/BETA/alpha swiveling
domain, hydrolase; 2.40A {Klebsiella pneumoniae} SCOP:
c.8.6.1 c.55.1.6 c.55.1.6
Length = 607
Score = 26.4 bits (58), Expect = 7.6
Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 1/64 (1%)
Query: 1 MTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIV-GTLNGFDDFVNMLLEDVTDCH 59
M T P PL ++D GS I+ + +I L G + V++L++
Sbjct: 396 MAIAGALTTPGCAAPLAILDLGAGSTDAAIVNAEGQITAVHLAGAGNMVSLLIKTELGLE 455
Query: 60 DSHL 63
D L
Sbjct: 456 DLSL 459
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
0.322 0.138 0.417
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: 3,129,123
Number of extensions: 184346
Number of successful extensions: 597
Number of sequences better than 10.0: 1
Number of HSP's gapped: 577
Number of HSP's successfully gapped: 76
Length of query: 204
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 115
Effective length of database: 4,216,824
Effective search space: 484934760
Effective search space used: 484934760
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: 55 (25.3 bits)