Citrus Sinensis ID: 034564

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-
Protein Sequence
MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKRTLADGA
Secondary Structure (PSIPRED)
cccccccccccccccHHHHHHcccccEEEEEcccEEEEEEEEEEccEEcEEEEcEEEEEccEEEcccccEEEEcccEEEEEcccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccHHHHHHHccccEEEEEcccEEEEEEEEEEccHHHHEHHccHHHHcccccccccEEEEEcccEEEEEcccccccccc
Coil and Loop (DISEMBL)
mstggekgsattktpadflksirgrpvvvklnsgvdyRGILACLDGYMNIAMEQTEEYVNGQLknkygdafirgnnvlyistskrtladga
Flexible Loop (DISEMBL)
mstggekgsattktpadflksirgrpvvvklnsgvdyRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNnvlyistskrtladga
Low Complexity Region (SEG)
MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKRTLADGA
Disordered region (IsUnstruct)
*****************FLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIS**********
Disordered Region (DISOPRED)
*******************KSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIST*********
Disordered Region (DISEMBL)
*************TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTS********
Disordered Region (DISPRO)
***********TKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTS********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKRTLADGA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	91	2.2.26 [Sep-21-2011]
P62313	80	U6 snRNA-associated Sm-li	yes	no	0.868	0.987	0.848	2e-34
P62312	80	U6 snRNA-associated Sm-li	yes	no	0.868	0.987	0.848	2e-34
B0DWN3	99	U6 snRNA-associated Sm-li	N/A	no	0.802	0.737	0.698	5e-26
Q4PG71	85	U6 snRNA-associated Sm-li	N/A	no	0.934	1.0	0.6	5e-25
Q552U1	88	Probable U6 snRNA-associa	yes	no	0.758	0.784	0.724	3e-23
A6R363	80	U6 snRNA-associated Sm-li	N/A	no	0.835	0.95	0.662	1e-22
Q9UUI1	75	U6 snRNA-associated Sm-li	yes	no	0.747	0.906	0.661	1e-22
A8NHT8	95	U6 snRNA-associated Sm-li	N/A	no	0.802	0.768	0.739	9e-22
Q2HAN0	82	U6 snRNA-associated Sm-li	N/A	no	0.846	0.939	0.625	2e-21
Q1DRN0	80	U6 snRNA-associated Sm-li	N/A	no	0.824	0.937	0.6	3e-21

>sp|P62313|LSM6_MOUSE U6 snRNA-associated Sm-like protein LSm6 OS=Mus musculus GN=Lsm6 PE=3 SV=1

 Score =  144 bits (362), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 67/79 (84%), Positives = 72/79 (91%)

Query: 9  SATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYG 68
          S   +TP+DFLK I GRPVVVKLNSGVDYRG+LACLDGYMNIA+EQTEEYVNGQLKNKYG
Sbjct: 2  SLRKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKYG 61

Query: 69 DAFIRGNNVLYISTSKRTL 87
          DAFIRGNNVLYIST KR +
Sbjct: 62 DAFIRGNNVLYISTQKRRM 80

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.
Mus musculus (taxid: 10090)

>sp|P62312|LSM6_HUMAN U6 snRNA-associated Sm-like protein LSm6 OS=Homo sapiens GN=LSM6 PE=1 SV=1

 Score =  144 bits (362), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 67/79 (84%), Positives = 72/79 (91%)

Query: 9  SATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYG 68
          S   +TP+DFLK I GRPVVVKLNSGVDYRG+LACLDGYMNIA+EQTEEYVNGQLKNKYG
Sbjct: 2  SLRKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKYG 61

Query: 69 DAFIRGNNVLYISTSKRTL 87
          DAFIRGNNVLYIST KR +
Sbjct: 62 DAFIRGNNVLYISTQKRRM 80

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

Homo sapiens (taxid: 9606)

>sp|B0DWN3|LSM6_LACBS U6 snRNA-associated Sm-like protein LSm6 OS=Laccaria bicolor (strain S238N-H82 / ATCC MYA-4686) GN=LSM6 PE=3 SV=1

 Score =  116 bits (290), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 51/73 (69%), Positives = 64/73 (87%)

Query: 12 TKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAF 71
          T +P DFLK + G+ V+V+L SGVDYRG+L+CLDGYMNIA+EQTEE+VNG + N+YGDAF
Sbjct: 25 TGSPTDFLKGVVGKRVIVRLTSGVDYRGLLSCLDGYMNIALEQTEEHVNGVVTNRYGDAF 84

Query: 72 IRGNNVLYISTSK 84
          IRGNNVLYIS ++
Sbjct: 85 IRGNNVLYISAAE 97

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

Laccaria bicolor (strain S238N-H82 / ATCC MYA-4686) (taxid: 486041)

>sp|Q4PG71|LSM6_USTMA U6 snRNA-associated Sm-like protein LSm6 OS=Ustilago maydis (strain 521 / FGSC 9021) GN=LSM6 PE=3 SV=2

 Score =  112 bits (281), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 51/85 (60%), Positives = 67/85 (78%)

Query: 1  MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60
          MS   ++ +A   +P DFLK + G+ V V+LNSG+DYRG+L+CLDGYMNIA+EQT EYV+
Sbjct: 1  MSAAAQQPNAKAGSPNDFLKGVIGKNVNVRLNSGIDYRGVLSCLDGYMNIALEQTVEYVD 60

Query: 61 GQLKNKYGDAFIRGNNVLYISTSKR 85
          G  KN YGDAFIRGNNV+YI+  ++
Sbjct: 61 GIKKNSYGDAFIRGNNVMYITALEK 85

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

Ustilago maydis (strain 521 / FGSC 9021) (taxid: 237631)

>sp|Q552U1|LSM6_DICDI Probable U6 snRNA-associated Sm-like protein LSm6 OS=Dictyostelium discoideum GN=lsm6 PE=3 SV=1

 Score =  106 bits (265), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 50/69 (72%), Positives = 56/69 (81%)

Query: 17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNN 76
          +F K   GRPVVVKLN+GV+YRGIL  +DG MNI MEQTEEY+NGQLK KYGD F+RGNN
Sbjct: 19 NFFKMCIGRPVVVKLNNGVEYRGILEVVDGNMNIVMEQTEEYLNGQLKTKYGDCFLRGNN 78

Query: 77 VLYISTSKR 85
          VLYIS   R
Sbjct: 79 VLYISAQPR 87

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

Dictyostelium discoideum (taxid: 44689)

>sp|A6R363|LSM6_AJECN U6 snRNA-associated Sm-like protein LSm6 OS=Ajellomyces capsulata (strain NAm1 / WU24) GN=LSM6 PE=3 SV=1

 Score =  104 bits (260), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 51/77 (66%), Positives = 61/77 (79%), Gaps = 1/77 (1%)

Query: 6  EKGSATT-KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLK 64
          E GSA+  K P+ FL  I G PV VKLNSGV Y+G L  +DGYMNIA+E+TEEYV+G+L+
Sbjct: 2  ENGSASEGKDPSAFLSEITGAPVTVKLNSGVVYKGELQSVDGYMNIALEKTEEYVDGKLR 61

Query: 65 NKYGDAFIRGNNVLYIS 81
            YGDAF+RGNNVLYIS
Sbjct: 62 RSYGDAFVRGNNVLYIS 78

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

Ajellomyces capsulata (strain NAm1 / WU24) (taxid: 339724)

>sp|Q9UUI1|LSM6_SCHPO U6 snRNA-associated Sm-like protein LSm6 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=lsm6 PE=1 SV=1

 Score =  104 bits (260), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 45/68 (66%), Positives = 60/68 (88%)

Query: 14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIR 73
          +P +FL  + G+ V+++L+SGVDY+GIL+CLDGYMN+A+E+TEEYVNG+  N YGDAFIR
Sbjct: 4  SPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIR 63

Query: 74 GNNVLYIS 81
          GNNVLY+S
Sbjct: 64 GNNVLYVS 71

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|A8NHT8|LSM6_COPC7 U6 snRNA-associated Sm-like protein LSm6 OS=Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003) GN=LSM6 PE=3 SV=2

 Score =  102 bits (253), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 54/73 (73%), Positives = 63/73 (86%)

Query: 12 TKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAF 71
          T +P DFLK + G+ VVV+L SGVDYRGIL+CLDGYMNIAMEQTEE VNG++ N+YGDAF
Sbjct: 21 TGSPTDFLKGVVGKRVVVRLLSGVDYRGILSCLDGYMNIAMEQTEESVNGKVVNRYGDAF 80

Query: 72 IRGNNVLYISTSK 84
          IRGNNVLYIS  +
Sbjct: 81 IRGNNVLYISADE 93

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003) (taxid: 240176)

>sp|Q2HAN0|LSM6_CHAGB U6 snRNA-associated Sm-like protein LSm6 OS=Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970) GN=LSM6 PE=3 SV=2

 Score =  100 bits (250), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 50/80 (62%), Positives = 59/80 (73%), Gaps = 3/80 (3%)

Query: 6  EKGSATT---KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQ 62
          E G+AT    K P+ FL  I G PV VKLNSGV Y+G L  +DGYMNIA+E+TEEYVNG 
Sbjct: 2  ENGAATQGEGKDPSGFLSEIIGNPVTVKLNSGVVYKGELQSVDGYMNIALEKTEEYVNGA 61

Query: 63 LKNKYGDAFIRGNNVLYIST 82
           +  YGDAF+RGNNV+YIS 
Sbjct: 62 KRRSYGDAFVRGNNVMYISA 81

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970) (taxid: 306901)

>sp|Q1DRN0|LSM6_COCIM U6 snRNA-associated Sm-like protein LSm6 OS=Coccidioides immitis (strain RS) GN=LSM6 PE=3 SV=1

 Score =  100 bits (248), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 45/75 (60%), Positives = 59/75 (78%)

Query: 7  KGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNK 66
          +G+A ++ P+ FL  I G  V VKLNSGV Y+G L  +DGYMNIA+E+T+E+VNG+L+  
Sbjct: 4  RGAADSQDPSAFLSGITGASVTVKLNSGVVYKGELQSIDGYMNIALEKTQEFVNGKLRKS 63

Query: 67 YGDAFIRGNNVLYIS 81
          YGD F+RGNNVLYIS
Sbjct: 64 YGDVFVRGNNVLYIS 78

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

Coccidioides immitis (strain RS) (taxid: 246410)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	91
224098796	91	predicted protein [Populus trichocarpa]	1.0	1.0	1.0	8e-46
225434160	91	PREDICTED: U6 snRNA-associated Sm-like p	1.0	1.0	0.989	2e-45
224112373	91	predicted protein [Populus trichocarpa]	1.0	1.0	0.978	6e-45
255587821	91	small nuclear ribonucleoprotein f, putat	1.0	1.0	0.978	1e-44
449445280	92	PREDICTED: U6 snRNA-associated Sm-like p	1.0	0.989	0.956	4e-44
388506496	90	unknown [Lotus japonicus]	0.978	0.988	0.955	1e-42
351721500	91	uncharacterized protein LOC100306112 [Gl	1.0	1.0	0.934	6e-42
357474665	91	U6 snRNA-associated Sm-like protein LSm6	1.0	1.0	0.923	4e-41
356568356	91	PREDICTED: U6 snRNA-associated Sm-like p	1.0	1.0	0.923	4e-41
297817284	91	hypothetical protein ARALYDRAFT_486445 [	1.0	1.0	0.912	4e-40

>gi|224098796|ref|XP_002311269.1| predicted protein [Populus trichocarpa] gi|118483023|gb|ABK93423.1| unknown [Populus trichocarpa] gi|222851089|gb|EEE88636.1| predicted protein [Populus trichocarpa]

 Score =  187 bits (475), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 91/91 (100%), Positives = 91/91 (100%)

Query: 1  MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60
          MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN
Sbjct: 1  MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60

Query: 61 GQLKNKYGDAFIRGNNVLYISTSKRTLADGA 91
          GQLKNKYGDAFIRGNNVLYISTSKRTLADGA
Sbjct: 61 GQLKNKYGDAFIRGNNVLYISTSKRTLADGA 91

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225434160|ref|XP_002278412.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm6 [Vitis vinifera] gi|296084324|emb|CBI24712.3| unnamed protein product [Vitis vinifera]

 Score =  186 bits (471), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 90/91 (98%), Positives = 91/91 (100%)

Query: 1  MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60
          MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN
Sbjct: 1  MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60

Query: 61 GQLKNKYGDAFIRGNNVLYISTSKRTLADGA 91
          GQLKNKYGDAFIRGNNVLYISTSKRTLA+GA
Sbjct: 61 GQLKNKYGDAFIRGNNVLYISTSKRTLAEGA 91

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224112373|ref|XP_002316168.1| predicted protein [Populus trichocarpa] gi|118482915|gb|ABK93371.1| unknown [Populus trichocarpa] gi|222865208|gb|EEF02339.1| predicted protein [Populus trichocarpa]

 Score =  184 bits (467), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 89/91 (97%), Positives = 90/91 (98%)

Query: 1  MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60
          MS+GGEKGS TTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN
Sbjct: 1  MSSGGEKGSTTTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60

Query: 61 GQLKNKYGDAFIRGNNVLYISTSKRTLADGA 91
          GQLKNKYGDAFIRGNNVLYISTSKRTLADGA
Sbjct: 61 GQLKNKYGDAFIRGNNVLYISTSKRTLADGA 91

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255587821|ref|XP_002534408.1| small nuclear ribonucleoprotein f, putative [Ricinus communis] gi|223525355|gb|EEF27977.1| small nuclear ribonucleoprotein f, putative [Ricinus communis]

 Score =  183 bits (464), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 89/91 (97%), Positives = 90/91 (98%)

Query: 1  MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60
          MS GGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN
Sbjct: 1  MSGGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60

Query: 61 GQLKNKYGDAFIRGNNVLYISTSKRTLADGA 91
          GQLKNKYGDAFIRGNNVLYIST+KRTLADGA
Sbjct: 61 GQLKNKYGDAFIRGNNVLYISTTKRTLADGA 91

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449445280|ref|XP_004140401.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm6-like [Cucumis sativus] gi|449498381|ref|XP_004160523.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm6-like [Cucumis sativus]

 Score =  181 bits (459), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 87/91 (95%), Positives = 90/91 (98%)

Query: 1  MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60
          MS GGEKGSA+TKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN
Sbjct: 1  MSIGGEKGSASTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60

Query: 61 GQLKNKYGDAFIRGNNVLYISTSKRTLADGA 91
          GQLKNKYGDAFIRGNNVLYISTSKRTLA+G+
Sbjct: 61 GQLKNKYGDAFIRGNNVLYISTSKRTLAEGS 91

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388506496|gb|AFK41314.1| unknown [Lotus japonicus]

 Score =  177 bits (448), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 85/89 (95%), Positives = 87/89 (97%)

Query: 3  TGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQ 62
          +G EKGS TTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQ
Sbjct: 2  SGAEKGSGTTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQ 61

Query: 63 LKNKYGDAFIRGNNVLYISTSKRTLADGA 91
          LKNKYGDAFIRGNNVLYISTSKRTLA+GA
Sbjct: 62 LKNKYGDAFIRGNNVLYISTSKRTLAEGA 90

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351721500|ref|NP_001237723.1| uncharacterized protein LOC100306112 [Glycine max] gi|255627589|gb|ACU14139.1| unknown [Glycine max]

 Score =  174 bits (441), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 87/91 (95%)

Query: 1  MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60
          MS  G+ GS TTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN
Sbjct: 1  MSGTGKAGSGTTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60

Query: 61 GQLKNKYGDAFIRGNNVLYISTSKRTLADGA 91
          GQLKNKYGDAFIRGNNVLYISTSKRTLA+GA
Sbjct: 61 GQLKNKYGDAFIRGNNVLYISTSKRTLAEGA 91

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357474665|ref|XP_003607617.1| U6 snRNA-associated Sm-like protein LSm6 [Medicago truncatula] gi|355508672|gb|AES89814.1| U6 snRNA-associated Sm-like protein LSm6 [Medicago truncatula] gi|388502230|gb|AFK39181.1| unknown [Medicago truncatula]

 Score =  171 bits (434), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 84/91 (92%), Positives = 86/91 (94%)

Query: 1  MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60
          MS   + GS TTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN
Sbjct: 1  MSGTEKSGSGTTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60

Query: 61 GQLKNKYGDAFIRGNNVLYISTSKRTLADGA 91
          GQLKNKYGDAFIRGNNVLYISTSKRTLA+GA
Sbjct: 61 GQLKNKYGDAFIRGNNVLYISTSKRTLAEGA 91

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356568356|ref|XP_003552377.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm6-like [Glycine max]

 Score =  171 bits (434), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 84/91 (92%), Positives = 86/91 (94%)

Query: 1  MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60
          MS   + GS TTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN
Sbjct: 1  MSGTEKAGSGTTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60

Query: 61 GQLKNKYGDAFIRGNNVLYISTSKRTLADGA 91
          GQLKNKYGDAFIRGNNVLYISTSKRTLA+GA
Sbjct: 61 GQLKNKYGDAFIRGNNVLYISTSKRTLAEGA 91

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297817284|ref|XP_002876525.1| hypothetical protein ARALYDRAFT_486445 [Arabidopsis lyrata subsp. lyrata] gi|297322363|gb|EFH52784.1| hypothetical protein ARALYDRAFT_486445 [Arabidopsis lyrata subsp. lyrata]

 Score =  168 bits (425), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 83/91 (91%), Positives = 84/91 (92%)

Query: 1  MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60
          MS  GEK S TTKTPADFLKSIRGRPVVVKLNSGVDYRGIL CLDGYMNIAMEQTEEYVN
Sbjct: 1  MSGVGEKVSGTTKTPADFLKSIRGRPVVVKLNSGVDYRGILTCLDGYMNIAMEQTEEYVN 60

Query: 61 GQLKNKYGDAFIRGNNVLYISTSKRTLADGA 91
          GQLKNKYGDAFIRGNNVLYIST K T+ADGA
Sbjct: 61 GQLKNKYGDAFIRGNNVLYISTVKMTVADGA 91

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	91
TAIR|locus:2043969	91	LSM6B "AT2G43810" [Arabidopsis	1.0	1.0	0.879	1.3e-38
TAIR|locus:2080487	91	LSM6A "AT3G59810" [Arabidopsis	1.0	1.0	0.879	3e-37
UNIPROTKB|P62312	80	LSM6 "U6 snRNA-associated Sm-l	0.868	0.987	0.848	3.7e-32
MGI|MGI:1925901	80	Lsm6 "LSM6 homolog, U6 small n	0.868	0.987	0.848	3.7e-32
ZFIN|ZDB-GENE-040625-50	80	lsm6 "LSM6 homolog, U6 small n	0.868	0.987	0.835	7.7e-32
WB|WBGene00003080	77	lsm-6 [Caenorhabditis elegans	0.802	0.948	0.835	2.1e-29
FB|FBgn0034564	79	CG9344 [Drosophila melanogaste	0.769	0.886	0.828	2.4e-28
DICTYBASE|DDB_G0275719	88	lsm6 "putative U6 small nuclea	0.758	0.784	0.724	1.6e-22
POMBASE|SPAC2F3.17c	75	lsm6 "U6 snRNP-associated prot	0.747	0.906	0.661	2.6e-22
GENEDB_PFALCIPARUM|PF13_0142	77	PF13_0142 "u6 snRNA-associated	0.769	0.909	0.642	4.3e-22

TAIR|locus:2043969 LSM6B "AT2G43810" [Arabidopsis thaliana (taxid:3702)]

 Score = 413 (150.4 bits), Expect = 1.3e-38, P = 1.3e-38
 Identities = 80/91 (87%), Positives = 84/91 (92%)

Query:     1 MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60
             MS  GEK S TTKTPADFLKSIRG+PVVVKLNSGVDYRGIL CLDGYMNIAMEQTEEYVN
Sbjct:     1 MSGVGEKASGTTKTPADFLKSIRGKPVVVKLNSGVDYRGILTCLDGYMNIAMEQTEEYVN 60

Query:    61 GQLKNKYGDAFIRGNNVLYISTSKRTLADGA 91
             GQLKN YGDAF+RGNNVLYIST+K TL+DGA
Sbjct:    61 GQLKNTYGDAFVRGNNVLYISTTKGTLSDGA 91

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISS

GO:0005732 "small nucleolar ribonucleoprotein complex" evidence=ISS

TAIR|locus:2080487 LSM6A "AT3G59810" [Arabidopsis thaliana (taxid:3702)]

 Score = 400 (145.9 bits), Expect = 3.0e-37, P = 3.0e-37
 Identities = 80/91 (87%), Positives = 81/91 (89%)

Query:     1 MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60
             MS   EK S TTKTPADFLKSIRGRPVVVKLNSGVDYRG L CLDGYMNIAMEQTEEYVN
Sbjct:     1 MSGVEEKVSGTTKTPADFLKSIRGRPVVVKLNSGVDYRGTLTCLDGYMNIAMEQTEEYVN 60

Query:    61 GQLKNKYGDAFIRGNNVLYISTSKRTLADGA 91
             GQLKNKYGDAFIRGNNVLYIST   T+ADGA
Sbjct:    61 GQLKNKYGDAFIRGNNVLYISTVNMTVADGA 91

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISS

GO:0005732 "small nucleolar ribonucleoprotein complex" evidence=ISS

UNIPROTKB|P62312 LSM6 "U6 snRNA-associated Sm-like protein LSm6" [Homo sapiens (taxid:9606)]

 Score = 352 (129.0 bits), Expect = 3.7e-32, P = 3.7e-32
 Identities = 67/79 (84%), Positives = 72/79 (91%)

Query:     9 SATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYG 68
             S   +TP+DFLK I GRPVVVKLNSGVDYRG+LACLDGYMNIA+EQTEEYVNGQLKNKYG
Sbjct:     2 SLRKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKYG 61

Query:    69 DAFIRGNNVLYISTSKRTL 87
             DAFIRGNNVLYIST KR +
Sbjct:    62 DAFIRGNNVLYISTQKRRM 80

GO:0003723 "RNA binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008033 "tRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=TAS

GO:0030532 "small nuclear ribonucleoprotein complex" evidence=TAS

GO:0000288 "nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0043928 "exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

MGI|MGI:1925901 Lsm6 "LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 352 (129.0 bits), Expect = 3.7e-32, P = 3.7e-32
 Identities = 67/79 (84%), Positives = 72/79 (91%)

Query:     9 SATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYG 68
             S   +TP+DFLK I GRPVVVKLNSGVDYRG+LACLDGYMNIA+EQTEEYVNGQLKNKYG
Sbjct:     2 SLRKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKYG 61

Query:    69 DAFIRGNNVLYISTSKRTL 87
             DAFIRGNNVLYIST KR +
Sbjct:    62 DAFIRGNNVLYISTQKRRM 80

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISO

GO:0006364 "rRNA processing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006402 "mRNA catabolic process" evidence=ISO

GO:0008033 "tRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=ISO

ZFIN|ZDB-GENE-040625-50 lsm6 "LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 349 (127.9 bits), Expect = 7.7e-32, P = 7.7e-32
 Identities = 66/79 (83%), Positives = 72/79 (91%)

Query:     9 SATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYG 68
             S   +TP+DFLK I GRPVVVKLNSGVDYRG+LACLDGYMNIA+EQTEEYVNGQLKNKYG
Sbjct:     2 SLRKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIAVEQTEEYVNGQLKNKYG 61

Query:    69 DAFIRGNNVLYISTSKRTL 87
             DAF+RGNNVLYIST KR +
Sbjct:    62 DAFLRGNNVLYISTQKRKM 80

GO:0003674 "molecular_function" evidence=ND

WB|WBGene00003080 lsm-6 [Caenorhabditis elegans (taxid:6239)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 61/73 (83%), Positives = 68/73 (93%)

Query:    13 KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFI 72
             + PA+FLK + G+PVVVKLNSGVDYRGILACLDGYMNIA+EQTEEY NGQL+NKYGDAFI
Sbjct:     5 QNPAEFLKKVIGKPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYSNGQLQNKYGDAFI 64

Query:    73 RGNNVLYISTSKR 85
             RGNNVLYISTS +
Sbjct:    65 RGNNVLYISTSTK 77

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0010171 "body morphogenesis" evidence=IMP

GO:0040002 "collagen and cuticulin-based cuticle development" evidence=IMP

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

FB|FBgn0034564 CG9344 [Drosophila melanogaster (taxid:7227)]

 Score = 316 (116.3 bits), Expect = 2.4e-28, P = 2.4e-28
 Identities = 58/70 (82%), Positives = 63/70 (90%)

Query:    16 ADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGN 75
             + F+  I GRPV VKLN+GVDYRG+LACLDGYMNI +EQTEEYVNGQLKNKYGDAFIRGN
Sbjct:     8 SQFINQIHGRPVAVKLNNGVDYRGVLACLDGYMNICLEQTEEYVNGQLKNKYGDAFIRGN 67

Query:    76 NVLYISTSKR 85
             NVLYIST KR
Sbjct:    68 NVLYISTQKR 77

GO:0030532 "small nuclear ribonucleoprotein complex" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0000398 "mRNA splicing, via spliceosome" evidence=ISS

GO:0005688 "U6 snRNP" evidence=NAS

DICTYBASE|DDB_G0275719 lsm6 "putative U6 small nuclear ribonucleoparticle-associated protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 261 (96.9 bits), Expect = 1.6e-22, P = 1.6e-22
 Identities = 50/69 (72%), Positives = 56/69 (81%)

Query:    17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNN 76
             +F K   GRPVVVKLN+GV+YRGIL  +DG MNI MEQTEEY+NGQLK KYGD F+RGNN
Sbjct:    19 NFFKMCIGRPVVVKLNNGVEYRGILEVVDGNMNIVMEQTEEYLNGQLKTKYGDCFLRGNN 78

Query:    77 VLYISTSKR 85
             VLYIS   R
Sbjct:    79 VLYISAQPR 87

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0046540 "U4/U6 x U5 tri-snRNP complex" evidence=ISS

GO:0006402 "mRNA catabolic process" evidence=ISS

GO:0005732 "small nucleolar ribonucleoprotein complex" evidence=ISS

GO:0005730 "nucleolus" evidence=ISS

GO:0005688 "U6 snRNP" evidence=ISS

GO:0000398 "mRNA splicing, via spliceosome" evidence=ISS

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0008033 "tRNA processing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

POMBASE|SPAC2F3.17c lsm6 "U6 snRNP-associated protein Lsm6 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 259 (96.2 bits), Expect = 2.6e-22, P = 2.6e-22
 Identities = 45/68 (66%), Positives = 60/68 (88%)

Query:    14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIR 73
             +P +FL  + G+ V+++L+SGVDY+GIL+CLDGYMN+A+E+TEEYVNG+  N YGDAFIR
Sbjct:     4 SPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIR 63

Query:    74 GNNVLYIS 81
             GNNVLY+S
Sbjct:    64 GNNVLYVS 71

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005688 "U6 snRNP" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0008033 "tRNA processing" evidence=IEA

GO:0030490 "maturation of SSU-rRNA" evidence=ISO

GO:0045292 "mRNA cis splicing, via spliceosome" evidence=ISO

GO:0046540 "U4/U6 x U5 tri-snRNP complex" evidence=ISO

GENEDB_PFALCIPARUM|PF13_0142 PF13_0142 "u6 snRNA-associated sm-like protein, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 257 (95.5 bits), Expect = 4.3e-22, P = 4.3e-22
 Identities = 45/70 (64%), Positives = 60/70 (85%)

Query:    11 TTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDA 70
             +T +P DF++S++GR V+V+LN+G DY+GILACLD  MN+A+EQTEEY +G+L +KY DA
Sbjct:     2 STNSPKDFVESLKGRAVIVRLNNGTDYKGILACLDERMNVALEQTEEYYDGELTDKYNDA 61

Query:    71 FIRGNNVLYI 80
             FIRGNNV YI
Sbjct:    62 FIRGNNVFYI 71

GO:0005681 "spliceosomal complex" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q6BR90	LSM6_DEBHA	No assigned EC number	0.5194	0.8351	0.8941	yes	no
P0CR24	LSM6_CRYNJ	No assigned EC number	0.5652	0.7582	0.7840	yes	no
P54999	RUXF_YEAST	No assigned EC number	0.3827	0.8791	0.9302	yes	no
P57670	RUXX_THEAC	No assigned EC number	0.3974	0.8461	0.9277	yes	no
A4RQ29	LSM6_MAGO7	No assigned EC number	0.5802	0.8571	0.9397	N/A	no
Q552U1	LSM6_DICDI	No assigned EC number	0.7246	0.7582	0.7840	yes	no
A1DM27	LSM6_NEOFI	No assigned EC number	0.6351	0.8131	0.925	N/A	no
Q2HAN0	LSM6_CHAGB	No assigned EC number	0.625	0.8461	0.9390	N/A	no
Q0UWI9	LSM6_PHANO	No assigned EC number	0.5116	0.9010	0.9213	N/A	no
Q4WNI0	LSM6_ASPFU	No assigned EC number	0.6351	0.8131	0.925	yes	no
Q9UUI1	LSM6_SCHPO	No assigned EC number	0.6617	0.7472	0.9066	yes	no
Q97BU5	RUXX_THEVO	No assigned EC number	0.3717	0.8461	0.9277	yes	no
Q75BR7	LSM6_ASHGO	No assigned EC number	0.4177	0.8131	0.8705	yes	no
A7UXE4	LSM6_NEUCR	No assigned EC number	0.5844	0.8461	0.9390	N/A	no
A8NHT8	LSM6_COPC7	No assigned EC number	0.7397	0.8021	0.7684	N/A	no
Q1DRN0	LSM6_COCIM	No assigned EC number	0.6	0.8241	0.9375	N/A	no
A1CE19	LSM6_ASPCL	No assigned EC number	0.5844	0.8461	0.9871	N/A	no
A6R363	LSM6_AJECN	No assigned EC number	0.6623	0.8351	0.95	N/A	no
P62312	LSM6_HUMAN	No assigned EC number	0.8481	0.8681	0.9875	yes	no
P62313	LSM6_MOUSE	No assigned EC number	0.8481	0.8681	0.9875	yes	no
O74016	RUXX_PYRHO	No assigned EC number	0.3287	0.8021	0.9733	yes	no
Q4PG71	LSM6_USTMA	No assigned EC number	0.6	0.9340	1.0	N/A	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	91
cd01726	68	cd01726, LSm6, Like-Sm protein 6	8e-44
cd01722	69	cd01722, Sm_F, Sm protein F	8e-24
smart00651	67	smart00651, Sm, snRNP Sm proteins	2e-20
pfam01423	66	pfam01423, LSM, LSM domain	4e-19
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	1e-15
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	3e-15
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	4e-14
cd00600	63	cd00600, Sm_like, Sm and related proteins	1e-12
cd01723	76	cd01723, LSm4, Like-Sm protein 4	4e-09
cd01733	78	cd01733, LSm10, Like-Sm protein 10	4e-07
cd01719	70	cd01719, Sm_G, Sm protein G	1e-06
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	4e-06
cd01725	89	cd01725, LSm2, Like-Sm protein 2	1e-05
cd01721	70	cd01721, Sm_D3, Sm protein D3	0.003
PTZ00138	89	PTZ00138, PTZ00138, small nuclear ribonucleoprotei	0.004

>gnl|CDD|212473 cd01726, LSm6, Like-Sm protein 6

 Score =  135 bits (343), Expect = 8e-44
 Identities = 52/68 (76%), Positives = 60/68 (88%)

Query: 14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIR 73
          TP+ FLK I G+PVVVKL +GV+YRG+LACLDGYMN+ +E TEEYV+GQL  KYGDAFIR
Sbjct: 1  TPSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYGDAFIR 60

Query: 74 GNNVLYIS 81
          GNNVLYIS
Sbjct: 61 GNNVLYIS 68

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 68

>gnl|CDD|212469 cd01722, Sm_F, Sm protein F

 Score = 85.3 bits (212), Expect = 8e-24
 Identities = 31/66 (46%), Positives = 44/66 (66%)

Query: 15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRG 74
          P  FL  + G+PV+VKL  G++Y+G L  +D YMN+ +  TEEY++G+     G+  IR 
Sbjct: 2  PKPFLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKFTGNLGEVLIRC 61

Query: 75 NNVLYI 80
          NNVLYI
Sbjct: 62 NNVLYI 67

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers. Length = 69

>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins

 Score = 76.4 bits (189), Expect = 2e-20
 Identities = 31/66 (46%), Positives = 43/66 (65%), Gaps = 1/66 (1%)

Query: 17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN-GQLKNKYGDAFIRGN 75
           FLK + G+ V+V+L +G +YRG L   D +MN+ +E  EE V  G+ K K G  FIRGN
Sbjct: 1  KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGN 60

Query: 76 NVLYIS 81
          N++YI 
Sbjct: 61 NIVYII 66

small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing. Length = 67

>gnl|CDD|201787 pfam01423, LSM, LSM domain

 Score = 73.3 bits (181), Expect = 4e-19
 Identities = 25/65 (38%), Positives = 38/65 (58%)

Query: 17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNN 76
           FL+ + G+ V V+L +G + RG L   D +MN+ ++  EE +     NK G   IRGNN
Sbjct: 1  KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLGLVLIRGNN 60

Query: 77 VLYIS 81
          ++ IS
Sbjct: 61 IVLIS 65

The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings. Length = 66

>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional

 Score = 64.6 bits (158), Expect = 1e-15
 Identities = 26/67 (38%), Positives = 41/67 (61%)

Query: 15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRG 74
          P D L +    PV+V+L  G ++RG L   D +MN+ ++  EE  +G++  K G   IRG
Sbjct: 5  PLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRG 64

Query: 75 NNVLYIS 81
          +NV+Y+S
Sbjct: 65 DNVVYVS 71

Length = 72

>gnl|CDD|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1

 Score = 63.4 bits (155), Expect = 3e-15
 Identities = 25/68 (36%), Positives = 39/68 (57%)

Query: 14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIR 73
           P D L     + V+VKL  G + RG+L   D ++N+ +E  EE + G+   K G   +R
Sbjct: 1  RPLDVLNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGTVLVR 60

Query: 74 GNNVLYIS 81
          G+NV++IS
Sbjct: 61 GDNVVFIS 68

The archaeal Sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain. Length = 69

>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]

 Score = 60.8 bits (148), Expect = 4e-14
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 4/77 (5%)

Query: 9  SATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQ---LKN 65
          S     P  FLK +  + V+VKL +G +YRG L   D YMN+ ++  EE ++        
Sbjct: 2  SMLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVR 61

Query: 66 KYG-DAFIRGNNVLYIS 81
          + G +  IRG+N++ IS
Sbjct: 62 RLGGEVLIRGDNIVLIS 78

Length = 79

>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins

 Score = 56.9 bits (138), Expect = 1e-12
 Identities = 18/58 (31%), Positives = 26/58 (44%)

Query: 24 GRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIS 81
          G+ V V+L  G    G L   D YMN+ ++   E          G   IRG+N++ I 
Sbjct: 6  GKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRVLGLVLIRGSNIVSIR 63

The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes. Length = 63

>gnl|CDD|212470 cd01723, LSm4, Like-Sm protein 4

 Score = 48.3 bits (116), Expect = 4e-09
 Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQ-TEEYVNGQLKNKYGDAFIR 73
          P   L++ +G PV+V+L +G  Y G L   D +MNI ++       +G    K  + +IR
Sbjct: 2  PLSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKMPECYIR 61

Query: 74 GNNVLYIS 81
          GN + Y+ 
Sbjct: 62 GNTIKYLR 69

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 76

>gnl|CDD|212480 cd01733, LSm10, Like-Sm protein 10

 Score = 42.9 bits (102), Expect = 4e-07
 Identities = 19/64 (29%), Positives = 36/64 (56%), Gaps = 2/64 (3%)

Query: 18 FLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQ-TEEYVNGQLKNKYGDAFIRGNN 76
           L++++GR   V+L +    RGI+  +DG+MNI +   T     G+    + + F++G N
Sbjct: 13 LLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQH-HFDEFFVQGRN 71

Query: 77 VLYI 80
          + Y+
Sbjct: 72 IRYV 75

The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-membered ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing. Length = 78

>gnl|CDD|212466 cd01719, Sm_G, Sm protein G

 Score = 41.7 bits (99), Expect = 1e-06
 Identities = 19/62 (30%), Positives = 30/62 (48%)

Query: 19 LKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVL 78
          LK    + + +KLN      G+L   D +MN+ ++   E V    K   G   IRGN+++
Sbjct: 5  LKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVGDGEKTPIGMVVIRGNSII 64

Query: 79 YI 80
           I
Sbjct: 65 MI 66

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Length = 70

>gnl|CDD|212489 cd11678, archaeal_LSm, archaeal Like-Sm protein

 Score = 40.6 bits (95), Expect = 4e-06
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 1/68 (1%)

Query: 15 PADFLKSIRGRPVVVKL-NSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIR 73
          P   +KS+ G  + V++       +G L  +D YMN+ +  T E V  +     G   +R
Sbjct: 1  PNKKVKSLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVGEEKVRSLGTVVLR 60

Query: 74 GNNVLYIS 81
          GNN+L I 
Sbjct: 61 GNNILLIQ 68

The archaeal Sm-like (LSm): The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes. Length = 69

>gnl|CDD|212472 cd01725, LSm2, Like-Sm protein 2

 Score = 39.5 bits (93), Expect = 1e-05
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 6/68 (8%)

Query: 17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLK----NKYGDAFI 72
           F K++ G+ V V+L + +   G L  +D Y+NI +      VN   K        + FI
Sbjct: 4  SFFKTLVGKEVTVELKNDLSITGTLHSVDQYLNIKLTNIS--VNDPEKYPHLLSVKNCFI 61

Query: 73 RGNNVLYI 80
          RG+ V Y+
Sbjct: 62 RGSVVRYV 69

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 89

>gnl|CDD|212468 cd01721, Sm_D3, Sm protein D3

 Score = 32.9 bits (76), Expect = 0.003
 Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 27 VVVKLNSGVDYRGILACLDGYMNIAMEQ-TEEYVNGQLKNKYGDAFIRGNNVLYI 80
          V V+L +G  YRG L   +  MN  ++  T    +G+  +K    +IRG+ + +I
Sbjct: 13 VTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGK-VSKLEQVYIRGSQIRFI 66

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Length = 70

>gnl|CDD|185472 PTZ00138, PTZ00138, small nuclear ribonucleoprotein; Provisional

 Score = 33.2 bits (76), Expect = 0.004
 Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 39 GILACLDGYMNIAMEQTEE-YVNGQLKNKYGDAFIRGNNVLYISTSK 84
          G +   D YMN+ ++  EE Y     +   G   ++G+N+  I  +K
Sbjct: 43 GKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMAAK 89

Length = 89

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	91
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.93
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.93
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.92
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.92
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.92
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.91
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.91
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.91
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.91
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.9
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.9
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.89
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.89
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.88
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.88
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.88
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.88
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.87
KOG3482	79	consensus Small nuclear ribonucleoprotein (snRNP)	99.86
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.86
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.86
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.84
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.83
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.82
KOG1780	77	consensus Small Nuclear ribonucleoprotein G [RNA p	99.77
KOG1783	77	consensus Small nuclear ribonucleoprotein F [RNA p	99.76
KOG3293	134	consensus Small nuclear ribonucleoprotein (snRNP)	99.71
KOG3460	91	consensus Small nuclear ribonucleoprotein (snRNP)	99.68
KOG1781	108	consensus Small Nuclear ribonucleoprotein splicing	99.67
KOG3172	119	consensus Small nuclear ribonucleoprotein Sm D3 [R	99.64
KOG3448	96	consensus Predicted snRNP core protein [RNA proces	99.64
KOG1775	84	consensus U6 snRNA-associated Sm-like protein [RNA	99.62
KOG1774	88	consensus Small nuclear ribonucleoprotein E [RNA p	99.54
KOG1782	129	consensus Small Nuclear ribonucleoprotein splicing	99.5
KOG3428	109	consensus Small nuclear ribonucleoprotein SMD1 and	99.45
KOG1784	96	consensus Small Nuclear ribonucleoprotein splicing	99.41
KOG3168	177	consensus U1 snRNP component [Transcription]	99.36
KOG3459	114	consensus Small nuclear ribonucleoprotein (snRNP)	98.66
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	98.18
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	98.16
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	97.64
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	96.94
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	96.85
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	96.47
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	96.46
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	96.35
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	96.07
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	95.76
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	95.66
PRK14638	150	hypothetical protein; Provisional	95.13
PRK14639	140	hypothetical protein; Provisional	94.87
PRK02001	152	hypothetical protein; Validated	94.84
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	94.73
COG1923	77	Hfq Uncharacterized host factor I protein [General	94.04
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	93.01
PRK14091	165	RNA-binding protein Hfq; Provisional	92.59
PRK14640	152	hypothetical protein; Provisional	92.38
PRK14644	136	hypothetical protein; Provisional	92.19
PRK14633	150	hypothetical protein; Provisional	91.78
PRK00092	154	ribosome maturation protein RimP; Reviewed	91.48
PRK14091	165	RNA-binding protein Hfq; Provisional	91.1
PRK14634	155	hypothetical protein; Provisional	91.0
PRK14632	172	hypothetical protein; Provisional	90.84
PRK14645	154	hypothetical protein; Provisional	90.69
PRK14636	176	hypothetical protein; Provisional	90.65
PRK14642	197	hypothetical protein; Provisional	90.63
PRK06955	300	biotin--protein ligase; Provisional	90.22
KOG1073	361	consensus Uncharacterized mRNA-associated protein	90.0
PRK14643	164	hypothetical protein; Provisional	89.77
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	89.7
PRK14646	155	hypothetical protein; Provisional	89.59
COG0779	153	Uncharacterized protein conserved in bacteria [Fun	89.02
PRK14647	159	hypothetical protein; Provisional	88.83
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	88.13
PRK14637	151	hypothetical protein; Provisional	87.88
PRK13325	592	bifunctional biotin--[acetyl-CoA-carboxylase] liga	87.87
PRK14641	173	hypothetical protein; Provisional	86.88
PRK14631	174	hypothetical protein; Provisional	85.7
TIGR00121	237	birA_ligase birA, biotin-[acetyl-CoA-carboxylase]	82.67

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.93  E-value=4.1e-25  Score=133.45  Aligned_cols=70  Identities=37%  Similarity=0.687  Sum_probs=65.8

Q ss_pred             CChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEe
Q 034564           13 KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        13 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~   82 (91)
                      ..|+.+|+++++++|+|+|+||+.|.|+|.+||+|||++|+||.|..+++..++++.++|||++|++|++
T Consensus         3 ~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~V~~i~~   72 (72)
T PRK00737          3 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVSP   72 (72)
T ss_pred             cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeCCEEEEEcC
Confidence            5799999999999999999999999999999999999999999998777667899999999999999963

>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.93  E-value=3.6e-25  Score=131.94  Aligned_cols=67  Identities=93%  Similarity=1.460  Sum_probs=63.4

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEE
Q 034564           15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIS   81 (91)
Q Consensus        15 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~   81 (91)
                      |+++|++++|++|+|+|++|++|+|+|.+||+||||+|+||.+..++.....++.++|||++|++|+
T Consensus         1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~IRG~~I~~I~   67 (67)
T cd01726           1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNVLYIS   67 (67)
T ss_pred             CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEEECCEEEEEC
Confidence            7899999999999999999999999999999999999999999877767789999999999999984

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.92  E-value=6.8e-25  Score=131.91  Aligned_cols=70  Identities=23%  Similarity=0.405  Sum_probs=64.3

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCC
Q 034564           15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSK   84 (91)
Q Consensus        15 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~   84 (91)
                      |+.+|+++.|++|+|+|+||.+|+|+|.++|+|||++|+||.+...+.+..+++.+||||++|+||++||
T Consensus         1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v~IRG~nI~~v~lPd   70 (70)
T cd01721           1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRGSKIRFFILPD   70 (70)
T ss_pred             ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcEEEeCCEEEEEEeCC
Confidence            7899999999999999999999999999999999999999988643334578899999999999999997

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.92  E-value=7.7e-25  Score=130.92  Aligned_cols=68  Identities=46%  Similarity=0.924  Sum_probs=63.9

Q ss_pred             ChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEE
Q 034564           14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIS   81 (91)
Q Consensus        14 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~   81 (91)
                      +|.++|++++|++|+|+|+||++|+|+|.+||+|||++|+||++..++.....+|.++|||++|+||+
T Consensus         1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~IRG~~I~~i~   68 (68)
T cd01722           1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRCNNVLYIR   68 (68)
T ss_pred             CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEECCEEEEEC
Confidence            58999999999999999999999999999999999999999999877766678999999999999984

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.

>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences

Probab=99.92  E-value=1.2e-24  Score=129.88  Aligned_cols=68  Identities=46%  Similarity=0.736  Sum_probs=63.7

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEe
Q 034564           15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        15 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~   82 (91)
                      |+.+|+++++++|+|+|++|+.|.|+|.+||+|||++|+||+|...+...+.++.++|||++|++|++
T Consensus         1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~I~~i~~   68 (68)
T cd01731           1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRGDNVLFISP   68 (68)
T ss_pred             ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeCCEEEEEcC
Confidence            78999999999999999999999999999999999999999998666567889999999999999974

They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.

>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.91  E-value=3.2e-24  Score=130.73  Aligned_cols=73  Identities=29%  Similarity=0.528  Sum_probs=66.9

Q ss_pred             ChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEE-ecCeeeeeeceEEEeCCcEEEEEeCCCc
Q 034564           14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEY-VNGQLKNKYGDAFIRGNNVLYISTSKRT   86 (91)
Q Consensus        14 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~-~~g~~~~~l~~v~IRG~~I~~i~~~~~~   86 (91)
                      .|+.+|+++.|++|.|+|+||++|+|+|.+||+|||++|+||++. .+|++...++.+||||++|+||+.|++.
T Consensus         1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~~   74 (76)
T cd01723           1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDEI   74 (76)
T ss_pred             CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHHH
Confidence            389999999999999999999999999999999999999999987 4565556789999999999999999864

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.91  E-value=4.1e-24  Score=129.27  Aligned_cols=71  Identities=30%  Similarity=0.464  Sum_probs=65.5

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCC
Q 034564           15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKR   85 (91)
Q Consensus        15 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~   85 (91)
                      |.++|.++++|+|.|+|++|++|.|+|.+||+||||+|+||.|+.++...+++|.++|||++|++|++.|.
T Consensus         1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~IRG~~I~~i~~~~~   71 (72)
T cd01719           1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVIRGNSIVMLEALER   71 (72)
T ss_pred             CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEECCCEEEEEEcccc
Confidence            45789999999999999999999999999999999999999998766667899999999999999998764

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.91  E-value=7.1e-24  Score=129.46  Aligned_cols=71  Identities=23%  Similarity=0.484  Sum_probs=65.1

Q ss_pred             CChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe---cCeeeeeeceEEEeCCcEEEEEeC
Q 034564           13 KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV---NGQLKNKYGDAFIRGNNVLYISTS   83 (91)
Q Consensus        13 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~---~g~~~~~l~~v~IRG~~I~~i~~~   83 (91)
                      ..|+.+|+++++++|+|+|++|+++.|+|.|||+|||++|+||.|+.   +++..+++|.++|||++|++|++.
T Consensus         2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p~   75 (76)
T cd01732           2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVPG   75 (76)
T ss_pred             cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEECC
Confidence            46899999999999999999999999999999999999999999975   454567899999999999999853

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.91  E-value=1.6e-23  Score=131.57  Aligned_cols=73  Identities=22%  Similarity=0.326  Sum_probs=68.3

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCCcc
Q 034564           15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKRTL   87 (91)
Q Consensus        15 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~~~   87 (91)
                      +..||+++.|++|+|+|+||.+|+|+|.++|+|||++|+||+++.+++...+++.++|||++|+||++||...
T Consensus         2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lPd~l~   74 (90)
T cd01724           2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILPDSLN   74 (90)
T ss_pred             HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcCCcCC
Confidence            6789999999999999999999999999999999999999999877666778999999999999999998864

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.90  E-value=3.7e-23  Score=126.81  Aligned_cols=73  Identities=21%  Similarity=0.375  Sum_probs=67.0

Q ss_pred             cCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeC
Q 034564           11 TTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTS   83 (91)
Q Consensus        11 ~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~   83 (91)
                      ....+..||+++.|++|.|+|+||.+|+|+|.++|+|||++|+||++..++....+++.+||||++|+||++|
T Consensus         6 ~~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~lP   78 (78)
T cd01733           6 LENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVHIP   78 (78)
T ss_pred             hhchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEEcC
Confidence            4567899999999999999999999999999999999999999999876565556899999999999999987

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.

>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.90  E-value=4.1e-23  Score=127.42  Aligned_cols=69  Identities=28%  Similarity=0.446  Sum_probs=62.2

Q ss_pred             ChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecC-------------eeeeeeceEEEeCCcEEEE
Q 034564           14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNG-------------QLKNKYGDAFIRGNNVLYI   80 (91)
Q Consensus        14 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g-------------~~~~~l~~v~IRG~~I~~i   80 (91)
                      .|+++|+.+++++|.|.|++||+|.|+|.|||+||||+|+||.|...+             ...+.+|.++|||++|++|
T Consensus         1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i   80 (82)
T cd01730           1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILV   80 (82)
T ss_pred             CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEE
Confidence            389999999999999999999999999999999999999999997432             1467899999999999998


Q ss_pred             Ee
Q 034564           81 ST   82 (91)
Q Consensus        81 ~~   82 (91)
                      ++
T Consensus        81 ~~   82 (82)
T cd01730          81 SP   82 (82)
T ss_pred             CC
Confidence            73

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]

Probab=99.89  E-value=1.9e-22  Score=123.47  Aligned_cols=73  Identities=37%  Similarity=0.724  Sum_probs=64.4

Q ss_pred             ccCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe--cCee-eeeec-eEEEeCCcEEEEEe
Q 034564           10 ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV--NGQL-KNKYG-DAFIRGNNVLYIST   82 (91)
Q Consensus        10 ~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~--~g~~-~~~l~-~v~IRG~~I~~i~~   82 (91)
                      +....|..+|+++++++|.|+|++|++|.|+|.+||+||||+|+||.|+.  ++.. .+.++ .++|||++|++|.+
T Consensus         3 ~~~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~   79 (79)
T COG1958           3 MLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP   79 (79)
T ss_pred             cccCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence            34567899999999999999999999999999999999999999999986  5654 34454 99999999999863

>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.89  E-value=1.9e-22  Score=124.42  Aligned_cols=68  Identities=26%  Similarity=0.413  Sum_probs=61.0

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecC--------eeeeeeceEEEeCCcEEEEEeCC
Q 034564           17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNG--------QLKNKYGDAFIRGNNVLYISTSK   84 (91)
Q Consensus        17 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g--------~~~~~l~~v~IRG~~I~~i~~~~   84 (91)
                      .-|.++++++|+|.|++|++|.|+|.+||+||||+|+||.|+..+        ...+.+|.++|||++|++|++.+
T Consensus         5 ~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~   80 (81)
T cd01729           5 LDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD   80 (81)
T ss_pred             hhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence            448999999999999999999999999999999999999997543        24578999999999999998765

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.88  E-value=2.5e-22  Score=123.86  Aligned_cols=74  Identities=26%  Similarity=0.425  Sum_probs=65.2

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCe--eeeeeceEEEeCCcEEEEEeCCCccc
Q 034564           15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQ--LKNKYGDAFIRGNNVLYISTSKRTLA   88 (91)
Q Consensus        15 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~--~~~~l~~v~IRG~~I~~i~~~~~~~~   88 (91)
                      |+.||+++.|++|+|+|++|.+|+|+|.++|+|||++|+||++..++.  ....++.++|||++|+||+.||...+
T Consensus         2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~   77 (81)
T cd01725           2 FFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADEVD   77 (81)
T ss_pred             hhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhHcC
Confidence            689999999999999999999999999999999999999998864321  23467899999999999999987654

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins

Probab=99.88  E-value=4.3e-22  Score=117.70  Aligned_cols=66  Identities=38%  Similarity=0.694  Sum_probs=62.0

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCe-eeeeeceEEEeCCcEEEEEe
Q 034564           17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQ-LKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        17 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~-~~~~l~~v~IRG~~I~~i~~   82 (91)
                      .+|++++|++|+|+|+||++|+|+|.+||+|||++|+||.+...+. +.+.++.+||||++|++|++
T Consensus         1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~   67 (67)
T PF01423_consen    1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL   67 (67)
T ss_dssp             HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred             ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence            3789999999999999999999999999999999999999987766 77899999999999999975

In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....

>smart00651 Sm snRNP Sm proteins

Probab=99.88  E-value=3.4e-22  Score=118.03  Aligned_cols=66  Identities=45%  Similarity=0.796  Sum_probs=60.9

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecC-eeeeeeceEEEeCCcEEEEEe
Q 034564           17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNG-QLKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        17 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g-~~~~~l~~v~IRG~~I~~i~~   82 (91)
                      .+|++++|++|+|+|+||+++.|+|.+||+|||++|+||+++..+ ...++++.+||||++|++|++
T Consensus         1 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651        1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             ChhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence            378999999999999999999999999999999999999998654 567899999999999999974

small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing

>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.88  E-value=4.4e-22  Score=124.34  Aligned_cols=69  Identities=17%  Similarity=0.319  Sum_probs=61.7

Q ss_pred             ChHHHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecC-------------eeeeeeceEEEeCCcEE
Q 034564           14 TPADFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNG-------------QLKNKYGDAFIRGNNVL   78 (91)
Q Consensus        14 ~p~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g-------------~~~~~l~~v~IRG~~I~   78 (91)
                      +|+++|+.++  +++|.|.|++|+.+.|+|.+||+||||+|+||.|...+             ...+.+|.+||||++|+
T Consensus         2 gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv   81 (87)
T cd01720           2 GPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVI   81 (87)
T ss_pred             ChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEE
Confidence            6999999997  89999999999999999999999999999999996432             13557899999999999


Q ss_pred             EEEe
Q 034564           79 YIST   82 (91)
Q Consensus        79 ~i~~   82 (91)
                      +|+.
T Consensus        82 ~Is~   85 (87)
T cd01720          82 LVLR   85 (87)
T ss_pred             EEec
Confidence            9975

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.87  E-value=1.5e-21  Score=119.99  Aligned_cols=71  Identities=20%  Similarity=0.415  Sum_probs=63.7

Q ss_pred             CCChHHHHhhcCCC--eEEEEEc--CCcEEEEEEEEEcCCCceeeeeeEEEec-CeeeeeeceEEEeCCcEEEEEe
Q 034564           12 TKTPADFLKSIRGR--PVVVKLN--SGVDYRGILACLDGYMNIAMEQTEEYVN-GQLKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        12 ~~~p~~~L~~~~~k--~V~V~L~--~g~~~~G~L~~~D~~mNlvL~~~~e~~~-g~~~~~l~~v~IRG~~I~~i~~   82 (91)
                      +..|+..|.+++++  +|.|+++  +|+++.|+|.|||+||||+|+||+|+.. ++..+++|.++|||++|++|++
T Consensus         4 ~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~p   79 (79)
T cd01718           4 MVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQN   79 (79)
T ss_pred             ccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEcC
Confidence            57899999999998  7788877  8999999999999999999999999864 4566789999999999999973

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]

Probab=99.86  E-value=9.5e-22  Score=118.05  Aligned_cols=73  Identities=41%  Similarity=0.800  Sum_probs=69.2

Q ss_pred             ccCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEe
Q 034564           10 ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        10 ~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~   82 (91)
                      +++.+|.+||+.+.+++|.|.|+.|.+|+|+|++.|.|||+.|.+|+|+.+|....++|+++||.+||.||.-
T Consensus         4 ~~PvNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEilIRCNNvlyi~g   76 (79)
T KOG3482|consen    4 KQPVNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEILIRCNNVLYIRG   76 (79)
T ss_pred             cccCCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEEEEeccEEEEec
Confidence            3578999999999999999999999999999999999999999999999999888899999999999999953

>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.86  E-value=5.2e-21  Score=115.98  Aligned_cols=69  Identities=23%  Similarity=0.283  Sum_probs=61.4

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEec----CeeeeeeceEEEeCCcEEEEEeCCC
Q 034564           17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN----GQLKNKYGDAFIRGNNVLYISTSKR   85 (91)
Q Consensus        17 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~----g~~~~~l~~v~IRG~~I~~i~~~~~   85 (91)
                      +.|.++++++|+|.|++|+.|.|+|.+||+|||++|++|.|+..    +...+.+|.++|||++|++|++.|+
T Consensus         2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d~   74 (74)
T cd01727           2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEIDE   74 (74)
T ss_pred             hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccCC
Confidence            46889999999999999999999999999999999999999742    3345689999999999999998763

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.86  E-value=4.2e-21  Score=117.63  Aligned_cols=66  Identities=21%  Similarity=0.395  Sum_probs=58.8

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecC----------eeeeeeceEEEeCCcEEEEEe
Q 034564           17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNG----------QLKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        17 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g----------~~~~~l~~v~IRG~~I~~i~~   82 (91)
                      +-|.++++++|.|.|++||.|.|+|.+||+||||+|+||.|+..+          ...+.+|.++|||++|++|.+
T Consensus         3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v   78 (79)
T cd01717           3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV   78 (79)
T ss_pred             chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence            357899999999999999999999999999999999999996421          245789999999999999975

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.85  E-value=1.5e-20  Score=114.33  Aligned_cols=68  Identities=29%  Similarity=0.385  Sum_probs=60.4

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe-cCe--eeeeeceEEEeCCcEEEEEe
Q 034564           15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV-NGQ--LKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        15 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~g~--~~~~l~~v~IRG~~I~~i~~   82 (91)
                      +...|.++++++|.|.|++|++|.|+|.+||+|||++|+||.|.. .+.  ..+.+|.++|||++|++|+.
T Consensus         3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~   73 (74)
T cd01728           3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE   73 (74)
T ss_pred             chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence            467799999999999999999999999999999999999999863 221  35789999999999999975

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.84  E-value=1.6e-20  Score=109.49  Aligned_cols=63  Identities=35%  Similarity=0.611  Sum_probs=58.1

Q ss_pred             HhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEE
Q 034564           19 LKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIS   81 (91)
Q Consensus        19 L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~   81 (91)
                      |++++|++|+|+|+||+.|.|+|.+||+|||++|+||.+...+...++++.+||||++|++|.
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~~~~~~~~~irG~~I~~I~   63 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGKKRVLGLVLIRGDNVRLVT   63 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCcEEECCeEEEECCEEEEEC
Confidence            467899999999999999999999999999999999999866556789999999999999984

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.83  E-value=4.8e-20  Score=112.30  Aligned_cols=66  Identities=24%  Similarity=0.436  Sum_probs=60.1

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecC------eeeeeeceEEEeCCcEEEEEe
Q 034564           17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNG------QLKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        17 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g------~~~~~l~~v~IRG~~I~~i~~   82 (91)
                      +.|.++++++|+|.|+|||.|.|+|.+||++||++|+||.|+...      ...+.+|.++|||++|+.+..
T Consensus         3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v   74 (75)
T cd06168           3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV   74 (75)
T ss_pred             hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence            568899999999999999999999999999999999999997532      457899999999999999975

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.82  E-value=2.3e-19  Score=112.42  Aligned_cols=77  Identities=19%  Similarity=0.350  Sum_probs=64.5

Q ss_pred             cCCccCCChHHHHhhcCCC--eEEEEEcC--CcEEEEEEEEEcCCCceeeeeeEEEec-CeeeeeeceEEEeCCcEEEEE
Q 034564            7 KGSATTKTPADFLKSIRGR--PVVVKLNS--GVDYRGILACLDGYMNIAMEQTEEYVN-GQLKNKYGDAFIRGNNVLYIS   81 (91)
Q Consensus         7 ~~~~~~~~p~~~L~~~~~k--~V~V~L~~--g~~~~G~L~~~D~~mNlvL~~~~e~~~-g~~~~~l~~v~IRG~~I~~i~   81 (91)
                      +....+..|+..+.+++.+  +|.|++.+  ++++.|+|.|||+|||++|+||+|... ++..+.+|.++|||++|++|+
T Consensus         7 ~~~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~   86 (89)
T PTZ00138          7 KLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIM   86 (89)
T ss_pred             ccceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEE
Confidence            3334578999999999985  57777767  599999999999999999999999754 345678999999999999997


Q ss_pred             eC
Q 034564           82 TS   83 (91)
Q Consensus        82 ~~   83 (91)
                      +.
T Consensus        87 ~~   88 (89)
T PTZ00138         87 AA   88 (89)
T ss_pred             cC
Confidence            64

>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]

Probab=99.77  E-value=7.2e-19  Score=105.89  Aligned_cols=69  Identities=35%  Similarity=0.503  Sum_probs=62.0

Q ss_pred             HHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCCc
Q 034564           18 FLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKRT   86 (91)
Q Consensus        18 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~~   86 (91)
                      .|++|++|++.+.|..||.+.|+|+|||.|||++|++++|.........++.++|||++|+.+...+..
T Consensus         8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~eaL~~~   76 (77)
T KOG1780|consen    8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMVEALERV   76 (77)
T ss_pred             hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEeccEEEEEeecccc
Confidence            789999999999999999999999999999999999999975433457899999999999999877653

>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]

Probab=99.76  E-value=1.2e-19  Score=108.93  Aligned_cols=72  Identities=83%  Similarity=1.303  Sum_probs=68.5

Q ss_pred             CChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCC
Q 034564           13 KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSK   84 (91)
Q Consensus        13 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~   84 (91)
                      ..|.+||.+.+|++|.|+|.+|-.|+|+|.+.|.|||+-|+.++|+.+|+..++++..||||++|.||+...
T Consensus         5 ~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygdaFirGnnVlyIs~~~   76 (77)
T KOG1783|consen    5 SMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGDAFIRGNNVLYISTQK   76 (77)
T ss_pred             cCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccceeeccccEEEEEecc
Confidence            568999999999999999999999999999999999999999999999998999999999999999998754

>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]

Probab=99.71  E-value=1.5e-17  Score=108.68  Aligned_cols=74  Identities=24%  Similarity=0.514  Sum_probs=69.0

Q ss_pred             ChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe-cCeeeeeeceEEEeCCcEEEEEeCCCcc
Q 034564           14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV-NGQLKNKYGDAFIRGNNVLYISTSKRTL   87 (91)
Q Consensus        14 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~g~~~~~l~~v~IRG~~I~~i~~~~~~~   87 (91)
                      .|+.+|....++++.|+|+||.+|.|.|..+|.+|||.|++++++. +|.+...+++++|||++|.|+.+||+..
T Consensus         2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~ii   76 (134)
T KOG3293|consen    2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEII   76 (134)
T ss_pred             cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHHH
Confidence            5899999999999999999999999999999999999999999974 6777788999999999999999998764

>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]

Probab=99.68  E-value=1.2e-17  Score=102.62  Aligned_cols=74  Identities=30%  Similarity=0.453  Sum_probs=65.5

Q ss_pred             CCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe---cC----------eeeeeeceEEEeCCcEE
Q 034564           12 TKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV---NG----------QLKNKYGDAFIRGNNVL   78 (91)
Q Consensus        12 ~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~---~g----------~~~~~l~~v~IRG~~I~   78 (91)
                      ...|+++|+-+++.+|-|+++++|+++|+|.+||+|.|++|.|+.|+.   ++          ...+.+..+|+||++|+
T Consensus         3 v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vi   82 (91)
T KOG3460|consen    3 VEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVI   82 (91)
T ss_pred             ccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEE
Confidence            457999999999999999999999999999999999999999998853   21          13578899999999999


Q ss_pred             EEEeCCC
Q 034564           79 YISTSKR   85 (91)
Q Consensus        79 ~i~~~~~   85 (91)
                      +|++|-.
T Consensus        83 lvspp~~   89 (91)
T KOG3460|consen   83 LVSPPLR   89 (91)
T ss_pred             EEcCccc
Confidence            9998854

>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]

Probab=99.67  E-value=5.9e-18  Score=106.86  Aligned_cols=73  Identities=25%  Similarity=0.360  Sum_probs=64.8

Q ss_pred             HHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEec--------CeeeeeeceEEEeCCcEEEEEeCCCcc
Q 034564           16 ADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN--------GQLKNKYGDAFIRGNNVLYISTSKRTL   87 (91)
Q Consensus        16 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~--------g~~~~~l~~v~IRG~~I~~i~~~~~~~   87 (91)
                      +-.|.+|++++|+|++..||+..|+|.|||+.|||+|+|+.|+..        +...|++|.+++||..++.|++.|..+
T Consensus        19 ilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e   98 (108)
T KOG1781|consen   19 ILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSE   98 (108)
T ss_pred             HhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchh
Confidence            556799999999999999999999999999999999999999631        124589999999999999999988765


Q ss_pred             c
Q 034564           88 A   88 (91)
Q Consensus        88 ~   88 (91)
                      |
T Consensus        99 ~   99 (108)
T KOG1781|consen   99 E   99 (108)
T ss_pred             h
Confidence            4

>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]

Probab=99.64  E-value=7.7e-16  Score=98.70  Aligned_cols=75  Identities=21%  Similarity=0.367  Sum_probs=68.8

Q ss_pred             cCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCC
Q 034564           11 TTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKR   85 (91)
Q Consensus        11 ~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~   85 (91)
                      ...-|+.+|.+..|.-|++++.+|..|+|+|+..|++||++|+|++.+..+....+++.|||||+.|+|+.+||-
T Consensus         2 s~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPdm   76 (119)
T KOG3172|consen    2 SVGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPDM   76 (119)
T ss_pred             ccccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECchH
Confidence            356789999999999999999999999999999999999999999997655567899999999999999999874

>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]

Probab=99.64  E-value=1.4e-15  Score=94.54  Aligned_cols=71  Identities=28%  Similarity=0.461  Sum_probs=62.4

Q ss_pred             HHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCe--eeeeeceEEEeCCcEEEEEeCCCc
Q 034564           16 ADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQ--LKNKYGDAFIRGNNVLYISTSKRT   86 (91)
Q Consensus        16 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~--~~~~l~~v~IRG~~I~~i~~~~~~   86 (91)
                      .+|++.++|++|.|+|+|+-.+.|+|.++|+|+|+.|.|.....+.+  .-..+..+||||+.|+||.+|...
T Consensus         4 ysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~   76 (96)
T KOG3448|consen    4 YSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDA   76 (96)
T ss_pred             HHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChhH
Confidence            57899999999999999999999999999999999999999864322  334578999999999999998654

>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]

Probab=99.62  E-value=4.3e-16  Score=94.46  Aligned_cols=75  Identities=21%  Similarity=0.469  Sum_probs=67.4

Q ss_pred             ccCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe---cCeeeeeeceEEEeCCcEEEEEeCC
Q 034564           10 ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV---NGQLKNKYGDAFIRGNNVLYISTSK   84 (91)
Q Consensus        10 ~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~---~g~~~~~l~~v~IRG~~I~~i~~~~   84 (91)
                      +....|+.++.+++|.+|+|.+++.+++.|+|.|||.|.|++|+|++|+.   +|....+++++++.|++|..+.+..
T Consensus         3 ~~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPGG   80 (84)
T KOG1775|consen    3 PSTLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPGG   80 (84)
T ss_pred             hhhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecCC
Confidence            34578999999999999999999999999999999999999999999973   4556778999999999999887655

>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]

Probab=99.54  E-value=9.4e-15  Score=89.58  Aligned_cols=81  Identities=23%  Similarity=0.413  Sum_probs=64.5

Q ss_pred             CCCCCccCCccCCChHHHHhhcCCC--eEEEEEcC--CcEEEEEEEEEcCCCceeeeeeEEEecCeee-eeeceEEEeCC
Q 034564            1 MSTGGEKGSATTKTPADFLKSIRGR--PVVVKLNS--GVDYRGILACLDGYMNIAMEQTEEYVNGQLK-NKYGDAFIRGN   75 (91)
Q Consensus         1 ms~~~~~~~~~~~~p~~~L~~~~~k--~V~V~L~~--g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~-~~l~~v~IRG~   75 (91)
                      ||.  +|.-..+..|+.++.+|+..  +|.|+|.+  |-.++|.++|||.|||++|++|.|....... ..+|.++++|+
T Consensus         1 ms~--~kv~kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGD   78 (88)
T KOG1774|consen    1 MSR--EKVQKVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGD   78 (88)
T ss_pred             CCc--ccccceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCC
Confidence            566  33233458999999999874  67778876  7899999999999999999999996432223 38999999999


Q ss_pred             cEEEEEeC
Q 034564           76 NVLYISTS   83 (91)
Q Consensus        76 ~I~~i~~~   83 (91)
                      ||.+|...
T Consensus        79 nItli~~~   86 (88)
T KOG1774|consen   79 NITLIQSA   86 (88)
T ss_pred             cEEEEeec
Confidence            99998754

>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]

Probab=99.50  E-value=2.5e-15  Score=98.21  Aligned_cols=72  Identities=22%  Similarity=0.338  Sum_probs=62.9

Q ss_pred             HHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe-cCe--eeeeeceEEEeCCcEEEEEeCCCcccc
Q 034564           18 FLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV-NGQ--LKNKYGDAFIRGNNVLYISTSKRTLAD   89 (91)
Q Consensus        18 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~g~--~~~~l~~v~IRG~~I~~i~~~~~~~~~   89 (91)
                      -|.+++++++.|-|+|||.+.|+|.|||+|.|++|.+|.|.. -|+  .....|.++|||.||+.++..|..+|+
T Consensus        13 sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dkE~   87 (129)
T KOG1782|consen   13 SLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDKEE   87 (129)
T ss_pred             HHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcchhh
Confidence            378899999999999999999999999999999999999952 232  234679999999999999999888885

>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]

Probab=99.45  E-value=9.4e-13  Score=84.53  Aligned_cols=74  Identities=26%  Similarity=0.357  Sum_probs=67.1

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCCcccc
Q 034564           15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKRTLAD   89 (91)
Q Consensus        15 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~~~~~   89 (91)
                      ...||+++.+.+++|+|++|+.+.|++.++|.+||..|.++.-...| ++.++...+|||++|+|+..||+..=|
T Consensus         3 lvr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~-~pv~l~~lsirgnniRy~~lpD~l~ld   76 (109)
T KOG3428|consen    3 LVRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG-EPVRLDTLSIRGNNIRYYILPDSLNLD   76 (109)
T ss_pred             HHHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC-CceeEEEEEeecceEEEEEccCCcCcc
Confidence            46799999999999999999999999999999999999999988777 556899999999999999999986533

>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]

Probab=99.41  E-value=2.1e-13  Score=85.13  Aligned_cols=72  Identities=26%  Similarity=0.312  Sum_probs=63.8

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe----cCeeeeeeceEEEeCCcEEEEEeCCCccc
Q 034564           17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV----NGQLKNKYGDAFIRGNNVLYISTSKRTLA   88 (91)
Q Consensus        17 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~----~g~~~~~l~~v~IRG~~I~~i~~~~~~~~   88 (91)
                      .-|..|++++|.|.+.|||.+.|.|.|||+..||+|+++-|+.    .|..+..+|..+|||+||..|+..|++..
T Consensus         3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d   78 (96)
T KOG1784|consen    3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELD   78 (96)
T ss_pred             hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhh
Confidence            3478999999999999999999999999999999999999853    34456789999999999999999987654

>KOG3168 consensus U1 snRNP component [Transcription]

Probab=99.36  E-value=1.3e-13  Score=94.45  Aligned_cols=69  Identities=22%  Similarity=0.407  Sum_probs=60.2

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe----------cCeeeeeeceEEEeCCcEEEEEeCCC
Q 034564           17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV----------NGQLKNKYGDAFIRGNNVLYISTSKR   85 (91)
Q Consensus        17 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~----------~g~~~~~l~~v~IRG~~I~~i~~~~~   85 (91)
                      +-|-++++.+++|.++|||+|.|.+.+||.||||+|.+|.|..          +++..+-+++|++||++|++..+.+.
T Consensus         7 skml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegp   85 (177)
T KOG3168|consen    7 SKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGP   85 (177)
T ss_pred             hHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCC
Confidence            3456789999999999999999999999999999999999852          24567889999999999999987654

>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]

Probab=98.66  E-value=4.5e-09  Score=67.76  Aligned_cols=69  Identities=20%  Similarity=0.367  Sum_probs=59.1

Q ss_pred             CChHHHHhhcCC--CeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe-------cCe------eeeeeceEEEeCCcE
Q 034564           13 KTPADFLKSIRG--RPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV-------NGQ------LKNKYGDAFIRGNNV   77 (91)
Q Consensus        13 ~~p~~~L~~~~~--k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~-------~g~------~~~~l~~v~IRG~~I   77 (91)
                      .+|++.+.+...  ..|.|-++|++.+.|.+.+||.|.|++|+|+.|.-       +|.      +.+.++.+||||++|
T Consensus        23 ~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsv  102 (114)
T KOG3459|consen   23 TGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSV  102 (114)
T ss_pred             cCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeE
Confidence            389999988875  57999999999999999999999999999999841       232      257899999999999


Q ss_pred             EEEE
Q 034564           78 LYIS   81 (91)
Q Consensus        78 ~~i~   81 (91)
                      +.+.
T Consensus       103 I~v~  106 (114)
T KOG3459|consen  103 ILVL  106 (114)
T ss_pred             EEEE
Confidence            8876

>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1

Probab=98.18  E-value=9e-06  Score=49.02  Aligned_cols=63  Identities=16%  Similarity=0.289  Sum_probs=41.5

Q ss_pred             HHHHhhcCCCeEEEEEcCCcEEEEEEEEEcC---CCceeeeeeEEEecCe-------eeeeeceEEEeCCcEE
Q 034564           16 ADFLKSIRGRPVVVKLNSGVDYRGILACLDG---YMNIAMEQTEEYVNGQ-------LKNKYGDAFIRGNNVL   78 (91)
Q Consensus        16 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~---~mNlvL~~~~e~~~g~-------~~~~l~~v~IRG~~I~   78 (91)
                      .-++..++|++|.|.++||..|+|+|.+++.   -+.++|+-+.....+.       .....+.++|+++.|+
T Consensus         4 ~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv   76 (77)
T PF14438_consen    4 VYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV   76 (77)
T ss_dssp             HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred             HHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence            4467789999999999999999999999998   8999999998753321       1234567777776654

>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=98.16  E-value=2.1e-06  Score=50.88  Aligned_cols=35  Identities=23%  Similarity=0.331  Sum_probs=30.2

Q ss_pred             CCeEEEEEcC----CcEEEEEEEEEcCCCceeeeeeEEE
Q 034564           24 GRPVVVKLNS----GVDYRGILACLDGYMNIAMEQTEEY   58 (91)
Q Consensus        24 ~k~V~V~L~~----g~~~~G~L~~~D~~mNlvL~~~~e~   58 (91)
                      +.+|+|.++.    +-.++|.|++||.|+||+|.|+.|.
T Consensus         8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~   46 (66)
T cd01739           8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDET   46 (66)
T ss_pred             CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhh
Confidence            4788888885    3478899999999999999999995

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.

>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A

Probab=97.64  E-value=0.00058  Score=43.31  Aligned_cols=68  Identities=18%  Similarity=0.343  Sum_probs=53.7

Q ss_pred             hhcCCCeEEEEEcCCcEEEEEEEEEcC-CCceeeeeeEEE-ecC--------eeeeeeceEEEeCCcEEEEEeCCCcc
Q 034564           20 KSIRGRPVVVKLNSGVDYRGILACLDG-YMNIAMEQTEEY-VNG--------QLKNKYGDAFIRGNNVLYISTSKRTL   87 (91)
Q Consensus        20 ~~~~~k~V~V~L~~g~~~~G~L~~~D~-~mNlvL~~~~e~-~~g--------~~~~~l~~v~IRG~~I~~i~~~~~~~   87 (91)
                      ..|+|++|.+..+.+-.|+|+|..+|. .-.|.|+|+..+ ..|        ......+.+..||+.|.-+.+.+...
T Consensus         4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~   81 (96)
T PF12701_consen    4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPP   81 (96)
T ss_dssp             CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-
T ss_pred             ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCC
Confidence            368999999999999999999999995 799999999874 111        01235789999999999888776544

>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins

Probab=96.94  E-value=0.0056  Score=42.37  Aligned_cols=65  Identities=23%  Similarity=0.417  Sum_probs=45.9

Q ss_pred             CChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcC-CCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCC
Q 034564           13 KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDG-YMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKR   85 (91)
Q Consensus        13 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~-~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~   85 (91)
                      .+|+.+ ..|++|.|.|.+.| +++.|.|..+|+ .-|++|-+..+  +++    ...-+|-|..|..|...++
T Consensus         7 ~~p~~~-~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e--~~~----~sv~~I~ghaVk~vevl~~   72 (166)
T PF06372_consen    7 KSPLEW-QDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE--DGK----RSVKVIMGHAVKSVEVLSE   72 (166)
T ss_dssp             S-HHHH-HCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T--TS-----EEEEEE-GGGEEEEEEEE-
T ss_pred             CCHHHH-HHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc--CCc----eeEEEEEccceEEEEEccC
Confidence            356666 79999999999999 999999999994 68999987765  332    2357899999999877654

The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.

>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown

Probab=96.85  E-value=0.0096  Score=32.79  Aligned_cols=35  Identities=17%  Similarity=0.220  Sum_probs=30.0

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEE
Q 034564           22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEE   57 (91)
Q Consensus        22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e   57 (91)
                      .+|++|++.+ ++..++|+..++|....|+++....
T Consensus         1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g   35 (48)
T PF02237_consen    1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG   35 (48)
T ss_dssp             STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred             CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence            3789999999 6777799999999999999876543

It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....

>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others

Probab=96.47  E-value=0.0085  Score=35.12  Aligned_cols=36  Identities=28%  Similarity=0.541  Sum_probs=29.1

Q ss_pred             HHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCceeee
Q 034564           18 FLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIAME   53 (91)
Q Consensus        18 ~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~   53 (91)
                      ||.++.  ..+|+|-|.||-.+.|.+.+||+|+=++-.
T Consensus         3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~   40 (61)
T cd01716           3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLLES   40 (61)
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEEE
Confidence            455544  468999999999999999999999866643

Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.

>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins

Probab=96.46  E-value=0.023  Score=34.99  Aligned_cols=63  Identities=21%  Similarity=0.281  Sum_probs=47.9

Q ss_pred             HHHHhhcCCCeEEEEEcCCcEEEEEEEEEc-CCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeC
Q 034564           16 ADFLKSIRGRPVVVKLNSGVDYRGILACLD-GYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTS   83 (91)
Q Consensus        16 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~   83 (91)
                      +.+|..+.|++|.+.|.++.++.|++.++| ...|+..+|-.- .-|    ..+.-.+|.+-|+.++..
T Consensus        16 Lr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~T-PlG----v~~eAlLR~~DVi~~~f~   79 (80)
T PF11095_consen   16 LRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQT-PLG----VQPEALLRCSDVISISFD   79 (80)
T ss_dssp             HHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEET-TTT----EEEEEEEEGGGEEEEEE-
T ss_pred             HHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcCC-Ccc----cChhheeecCCEEEEEec
Confidence            567788889999999999999999999999 457887776642 223    357889999999998764

Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.

>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=96.35  E-value=0.03  Score=34.01  Aligned_cols=59  Identities=20%  Similarity=0.371  Sum_probs=45.3

Q ss_pred             hcCCCeEEEEEcCCcEEEEEEEEEcC-CCceeeeeeEEEe-cC-----e----eeeeeceEEEeCCcEEE
Q 034564           21 SIRGRPVVVKLNSGVDYRGILACLDG-YMNIAMEQTEEYV-NG-----Q----LKNKYGDAFIRGNNVLY   79 (91)
Q Consensus        21 ~~~~k~V~V~L~~g~~~~G~L~~~D~-~mNlvL~~~~e~~-~g-----~----~~~~l~~v~IRG~~I~~   79 (91)
                      +++|+++.+..+.+-.|+|+|.++|. -.-+.|+|+..+- .|     .    ...-++.+..||+.|--
T Consensus         3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD   72 (74)
T cd01736           3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD   72 (74)
T ss_pred             cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence            58999999999999999999999994 4778899988652 11     1    12245778888887743

Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.

>TIGR02383 Hfq RNA chaperone Hfq

Probab=96.07  E-value=0.014  Score=34.14  Aligned_cols=36  Identities=31%  Similarity=0.623  Sum_probs=29.3

Q ss_pred             HHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCceee
Q 034564           17 DFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIAM   52 (91)
Q Consensus        17 ~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL   52 (91)
                      .||..+.  ..+|+|-|.||-.+.|.+.+||+|+=++-
T Consensus         6 ~fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~   43 (61)
T TIGR02383         6 QFLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLE   43 (61)
T ss_pred             HHHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEEE
Confidence            3555544  46899999999999999999999986664

This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=95.76  E-value=0.022  Score=35.00  Aligned_cols=39  Identities=23%  Similarity=0.531  Sum_probs=31.2

Q ss_pred             HHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCceeeeee
Q 034564           17 DFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIAMEQT   55 (91)
Q Consensus        17 ~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~   55 (91)
                      .||..+.  ..+|+|-|.||-.+.|.+.+||+|.=|+-.+.
T Consensus        10 ~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g   50 (79)
T PRK00395         10 PFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG   50 (79)
T ss_pred             HHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence            4555554  46899999999999999999999987765443

>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function

Probab=95.66  E-value=0.093  Score=31.17  Aligned_cols=54  Identities=31%  Similarity=0.483  Sum_probs=40.1

Q ss_pred             HHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEe
Q 034564           16 ADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        16 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~   82 (91)
                      ...|++++|++|.|++..|+. +|+|.++... .++|+..     +      ..+|||=..|++|.+
T Consensus        13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~pD-hIvl~~~-----~------~~~~IR~~~IV~v~p   66 (66)
T PF10842_consen   13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKPD-HIVLEEN-----G------TPFFIRIAQIVWVMP   66 (66)
T ss_pred             HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCC-EEEEEeC-----C------cEEEEEeeeEEEEcC
Confidence            567899999999999987766 9999988632 1233222     1      478999999998853

>PRK14638 hypothetical protein; Provisional

Probab=95.13  E-value=0.098  Score=35.43  Aligned_cols=35  Identities=11%  Similarity=0.182  Sum_probs=29.2

Q ss_pred             HHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeee
Q 034564           18 FLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAME   53 (91)
Q Consensus        18 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~   53 (91)
                      -+.+++|++|.|++.+++.+.|+|.++|.- ++.|.
T Consensus        94 ~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~  128 (150)
T PRK14638         94 DYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS  128 (150)
T ss_pred             HHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            347899999999999999999999999863 44443

>PRK14639 hypothetical protein; Provisional

Probab=94.87  E-value=0.13  Score=34.47  Aligned_cols=34  Identities=21%  Similarity=0.347  Sum_probs=29.1

Q ss_pred             HHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceee
Q 034564           18 FLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAM   52 (91)
Q Consensus        18 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL   52 (91)
                      -+++++|+.|.|.+.+++.+.|+|.++|.- ++.|
T Consensus        82 ~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l  115 (140)
T PRK14639         82 HFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL  115 (140)
T ss_pred             HHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence            348899999999999999999999999873 4544

>PRK02001 hypothetical protein; Validated

Probab=94.84  E-value=0.096  Score=35.68  Aligned_cols=37  Identities=27%  Similarity=0.425  Sum_probs=30.1

Q ss_pred             ChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceee
Q 034564           14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAM   52 (91)
Q Consensus        14 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL   52 (91)
                      .|..| .+++|+.|.|.+.+++.+.|+|.++|.- ++.|
T Consensus        81 ~~~~f-~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l  117 (152)
T PRK02001         81 VPRQY-KKNIGRELEVLTKNGKKIEGELKSADEN-DITL  117 (152)
T ss_pred             CHHHH-HHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence            33444 7899999999999999999999999864 3444

>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=94.73  E-value=0.12  Score=30.26  Aligned_cols=33  Identities=12%  Similarity=0.086  Sum_probs=28.3

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEEcCCCceeeee
Q 034564           22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQ   54 (91)
Q Consensus        22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~   54 (91)
                      .+|..|.+++..|.+++|.+.+||.-.+++.-.
T Consensus         4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk   36 (61)
T cd01735           4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILK   36 (61)
T ss_pred             ccccEEEEEecCCceEEEEEEEecCCCcEEEEE
Confidence            478999999999999999999999776666443

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.

>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]

Probab=94.04  E-value=0.18  Score=30.73  Aligned_cols=34  Identities=26%  Similarity=0.583  Sum_probs=27.5

Q ss_pred             HHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCce
Q 034564           17 DFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNI   50 (91)
Q Consensus        17 ~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNl   50 (91)
                      .||.++.  +.+|.|-|.||-.+.|.+.+||+|.=|
T Consensus        10 ~fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~Vl   45 (77)
T COG1923          10 PFLNALRKEKIPVTIFLVNGFKLQGQVESFDNFVVL   45 (77)
T ss_pred             HHHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEEEE
Confidence            3554443  578999999999999999999999644

>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold

Probab=93.01  E-value=0.54  Score=28.46  Aligned_cols=38  Identities=34%  Similarity=0.554  Sum_probs=29.0

Q ss_pred             CChHHHHhhcCCCeEEEEEc---CC-cEEEEEEEEEcCCCceee
Q 034564           13 KTPADFLKSIRGRPVVVKLN---SG-VDYRGILACLDGYMNIAM   52 (91)
Q Consensus        13 ~~p~~~L~~~~~k~V~V~L~---~g-~~~~G~L~~~D~~mNlvL   52 (91)
                      ..|..| .+++|+.|.|+++   +| +.+.|.|.++|.- ++.|
T Consensus        15 ~~~~~~-~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l   56 (83)
T cd01734          15 KKEADF-ERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL   56 (83)
T ss_pred             CCHHHH-HHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence            334444 7899999999997   55 6899999999873 3444

The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=92.59  E-value=0.32  Score=33.69  Aligned_cols=40  Identities=30%  Similarity=0.484  Sum_probs=31.5

Q ss_pred             HHHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCceeeeee
Q 034564           16 ADFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIAMEQT   55 (91)
Q Consensus        16 ~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~   55 (91)
                      -.||..+.  ..+|+|-|.||-.+.|.+.+||+|.=|.-.+.
T Consensus        94 d~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g  135 (165)
T PRK14091         94 DVFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG  135 (165)
T ss_pred             HHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            34666655  45799999999999999999999986665443

>PRK14640 hypothetical protein; Provisional

Probab=92.38  E-value=0.62  Score=31.51  Aligned_cols=37  Identities=22%  Similarity=0.481  Sum_probs=28.9

Q ss_pred             ChHHHHhhcCCCeEEEEEc----CCcEEEEEEEEEcCCCceee
Q 034564           14 TPADFLKSIRGRPVVVKLN----SGVDYRGILACLDGYMNIAM   52 (91)
Q Consensus        14 ~p~~~L~~~~~k~V~V~L~----~g~~~~G~L~~~D~~mNlvL   52 (91)
                      .|..| .+++|+.|.|+|+    +.+.+.|+|.++|.. ++.|
T Consensus        88 ~~~~f-~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l  128 (152)
T PRK14640         88 KVAQF-EKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITL  128 (152)
T ss_pred             CHHHH-HHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence            33444 7899999999994    679999999999873 4444

>PRK14644 hypothetical protein; Provisional

Probab=92.19  E-value=0.4  Score=32.03  Aligned_cols=35  Identities=23%  Similarity=0.118  Sum_probs=29.3

Q ss_pred             HHhhcCCCeEEEEEcCC----cEEEEEEEEEcCCCceeee
Q 034564           18 FLKSIRGRPVVVKLNSG----VDYRGILACLDGYMNIAME   53 (91)
Q Consensus        18 ~L~~~~~k~V~V~L~~g----~~~~G~L~~~D~~mNlvL~   53 (91)
                      -+.+++|+.|.|.|++.    +.+.|.|.++|.. ++.|.
T Consensus        79 ~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~  117 (136)
T PRK14644         79 ELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK  117 (136)
T ss_pred             HHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            46889999999999976    9999999999873 45554

>PRK14633 hypothetical protein; Provisional

Probab=91.78  E-value=0.59  Score=31.59  Aligned_cols=34  Identities=21%  Similarity=0.369  Sum_probs=27.5

Q ss_pred             HHhhcCCCeEEEEEc----CCcEEEEEEEEEcCCCceee
Q 034564           18 FLKSIRGRPVVVKLN----SGVDYRGILACLDGYMNIAM   52 (91)
Q Consensus        18 ~L~~~~~k~V~V~L~----~g~~~~G~L~~~D~~mNlvL   52 (91)
                      -+.+++|++|.|+++    +++.++|+|.+++.. ++.|
T Consensus        88 ~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l  125 (150)
T PRK14633         88 QAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL  125 (150)
T ss_pred             HHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence            347899999999984    569999999999874 4444

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=91.48  E-value=0.89  Score=30.62  Aligned_cols=29  Identities=38%  Similarity=0.641  Sum_probs=25.4

Q ss_pred             HHhhcCCCeEEEEE----cCCcEEEEEEEEEcC
Q 034564           18 FLKSIRGRPVVVKL----NSGVDYRGILACLDG   46 (91)
Q Consensus        18 ~L~~~~~k~V~V~L----~~g~~~~G~L~~~D~   46 (91)
                      -+++++|+.|.|.+    .+++.+.|+|.++|.
T Consensus        92 ~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~  124 (154)
T PRK00092         92 DFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG  124 (154)
T ss_pred             HHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence            34889999999997    467999999999987

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=91.10  E-value=0.42  Score=33.08  Aligned_cols=40  Identities=30%  Similarity=0.504  Sum_probs=31.4

Q ss_pred             HHHHhhcCC--CeEEEEEcCCcEEEEEEEEEcCCCceeeeee
Q 034564           16 ADFLKSIRG--RPVVVKLNSGVDYRGILACLDGYMNIAMEQT   55 (91)
Q Consensus        16 ~~~L~~~~~--k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~   55 (91)
                      -.||..+..  .+|+|-|.+|-.++|.+.+||+|.=|.-.+.
T Consensus        14 D~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g   55 (165)
T PRK14091         14 DIFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRDG   55 (165)
T ss_pred             HHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            446666654  5788999999999999999999976665443

>PRK14634 hypothetical protein; Provisional

Probab=91.00  E-value=0.73  Score=31.34  Aligned_cols=37  Identities=24%  Similarity=0.408  Sum_probs=28.4

Q ss_pred             ChHHHHhhcCCCeEEEEEcC----CcEEEEEEEEEcCCCceee
Q 034564           14 TPADFLKSIRGRPVVVKLNS----GVDYRGILACLDGYMNIAM   52 (91)
Q Consensus        14 ~p~~~L~~~~~k~V~V~L~~----g~~~~G~L~~~D~~mNlvL   52 (91)
                      .|..| .+++|+.|.|+|.+    .+.|.|+|.++|.- ++.|
T Consensus        91 ~~~~f-~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l  131 (155)
T PRK14634         91 SDRDF-QTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI  131 (155)
T ss_pred             CHHHH-HHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence            34444 78999999999974    28999999999863 4444

>PRK14632 hypothetical protein; Provisional

Probab=90.84  E-value=0.76  Score=31.79  Aligned_cols=35  Identities=20%  Similarity=0.416  Sum_probs=28.0

Q ss_pred             HHhhcCCCeEEEEEcC-------CcEEEEEEEEEcCCCceeee
Q 034564           18 FLKSIRGRPVVVKLNS-------GVDYRGILACLDGYMNIAME   53 (91)
Q Consensus        18 ~L~~~~~k~V~V~L~~-------g~~~~G~L~~~D~~mNlvL~   53 (91)
                      -+++++|+.|.|+|++       .+.+.|+|.++|.- ++.|.
T Consensus        92 ~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~  133 (172)
T PRK14632         92 QMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR  133 (172)
T ss_pred             HHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence            3478999999999986       58999999999863 44443

>PRK14645 hypothetical protein; Provisional

Probab=90.69  E-value=0.76  Score=31.28  Aligned_cols=33  Identities=15%  Similarity=0.391  Sum_probs=26.6

Q ss_pred             HHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceee
Q 034564           18 FLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAM   52 (91)
Q Consensus        18 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL   52 (91)
                      -+.+++|+.|.|.+ +++.+.|+|.++|.- .+.|
T Consensus        96 df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l  128 (154)
T PRK14645         96 HFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTF  128 (154)
T ss_pred             HHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence            34789999999986 789999999999874 3444

>PRK14636 hypothetical protein; Provisional

Probab=90.65  E-value=1  Score=31.32  Aligned_cols=37  Identities=30%  Similarity=0.617  Sum_probs=28.6

Q ss_pred             ChHHHHhhcCCCeEEEEEc---CC-cEEEEEEEEEcCCCceee
Q 034564           14 TPADFLKSIRGRPVVVKLN---SG-VDYRGILACLDGYMNIAM   52 (91)
Q Consensus        14 ~p~~~L~~~~~k~V~V~L~---~g-~~~~G~L~~~D~~mNlvL   52 (91)
                      .|..| .+++|++|.|+|+   +| +.+.|+|.++|.- ++.|
T Consensus        89 ~~~df-~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l  129 (176)
T PRK14636         89 RPKDF-ADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI  129 (176)
T ss_pred             CHHHH-HHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence            34444 7899999999997   55 7999999999873 3444

>PRK14642 hypothetical protein; Provisional

Probab=90.63  E-value=0.55  Score=33.34  Aligned_cols=34  Identities=15%  Similarity=0.270  Sum_probs=28.0

Q ss_pred             HHhhcCCCeEEEEEc-------------CCcEEEEEEEEEcCCCceee
Q 034564           18 FLKSIRGRPVVVKLN-------------SGVDYRGILACLDGYMNIAM   52 (91)
Q Consensus        18 ~L~~~~~k~V~V~L~-------------~g~~~~G~L~~~D~~mNlvL   52 (91)
                      -+.+++|+.|.|+|+             +.+.|+|+|.++|.. ++.|
T Consensus        94 df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l  140 (197)
T PRK14642         94 DFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI  140 (197)
T ss_pred             HHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence            347889999999998             679999999999874 4444

>PRK06955 biotin--protein ligase; Provisional

Probab=90.22  E-value=2.2  Score=31.56  Aligned_cols=50  Identities=22%  Similarity=0.290  Sum_probs=35.6

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCC
Q 034564           22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGN   75 (91)
Q Consensus        22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~   75 (91)
                      ++|++|+|...+++.+.|++.++|....|+++..    +|.+.-..|.|.+|..
T Consensus       247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~~----~g~~~~~sGeV~~~~~  296 (300)
T PRK06955        247 YAGREVVLLEDGAELARGVAHGIDETGQLLLDTP----AGRQAIAAGDVSLREA  296 (300)
T ss_pred             cCCCeEEEEECCCcEEEEEEeeECCCceEEEEeC----CCeEEEEEEEEEEecc
Confidence            5689999976677889999999999999998532    2222233456665543

>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]

Probab=90.00  E-value=1  Score=34.71  Aligned_cols=66  Identities=15%  Similarity=0.323  Sum_probs=52.0

Q ss_pred             hhcCCCeEEEEEcCCcEEEEEEEEEc-CCCceeeeeeEEEe------cCe----eeeeeceEEEeCCcEEEEEeCCC
Q 034564           20 KSIRGRPVVVKLNSGVDYRGILACLD-GYMNIAMEQTEEYV------NGQ----LKNKYGDAFIRGNNVLYISTSKR   85 (91)
Q Consensus        20 ~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~e~~------~g~----~~~~l~~v~IRG~~I~~i~~~~~   85 (91)
                      ..|||+.|.+.=+..-.|+|+|.-+| +-.-|-|+++..+-      ++.    ...-+..|+.||+.|.-+.+.+.
T Consensus         5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~   81 (361)
T KOG1073|consen    5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQET   81 (361)
T ss_pred             cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccC
Confidence            46899999999999999999999999 77889999985531      111    11156889999999998877664

>PRK14643 hypothetical protein; Provisional

Probab=89.77  E-value=1.4  Score=30.29  Aligned_cols=30  Identities=20%  Similarity=0.163  Sum_probs=25.9

Q ss_pred             HHhhcCCCeEEEEEcC----CcEEEEEEEEEcCC
Q 034564           18 FLKSIRGRPVVVKLNS----GVDYRGILACLDGY   47 (91)
Q Consensus        18 ~L~~~~~k~V~V~L~~----g~~~~G~L~~~D~~   47 (91)
                      -+.+++|++|.|.|++    .+.+.|+|.++|.-
T Consensus        98 df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T PRK14643         98 ELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN  131 (164)
T ss_pred             HHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence            4478999999999975    59999999999864

>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes []

Probab=89.70  E-value=1.1  Score=29.50  Aligned_cols=35  Identities=29%  Similarity=0.399  Sum_probs=25.5

Q ss_pred             HHHhhcCCCeEEEEEc----CCcEEEEEEEEEcCCCceee
Q 034564           17 DFLKSIRGRPVVVKLN----SGVDYRGILACLDGYMNIAM   52 (91)
Q Consensus        17 ~~L~~~~~k~V~V~L~----~g~~~~G~L~~~D~~mNlvL   52 (91)
                      .-+.+++|++|.|.++    +.+.+.|+|.++|. -.++|
T Consensus        80 ~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l  118 (141)
T PF02576_consen   80 RDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL  118 (141)
T ss_dssp             HHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred             HHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence            4558999999999995    45799999999998 34444

; PDB: 1IB8_A.

>PRK14646 hypothetical protein; Provisional

Probab=89.59  E-value=1.1  Score=30.42  Aligned_cols=34  Identities=29%  Similarity=0.322  Sum_probs=27.3

Q ss_pred             HHhhcCCCeEEEEEcCC----cEEEEEEEEEcCCCceee
Q 034564           18 FLKSIRGRPVVVKLNSG----VDYRGILACLDGYMNIAM   52 (91)
Q Consensus        18 ~L~~~~~k~V~V~L~~g----~~~~G~L~~~D~~mNlvL   52 (91)
                      -+.+++|++|.|+|++.    +.+.|+|.++|.- ++.|
T Consensus        94 df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l  131 (155)
T PRK14646         94 DFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI  131 (155)
T ss_pred             HHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence            44889999999999742    7889999999974 5555

>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=89.02  E-value=2.2  Score=29.11  Aligned_cols=33  Identities=27%  Similarity=0.466  Sum_probs=28.6

Q ss_pred             HHHHhhcCCCeEEEEE----cCCcEEEEEEEEEcCCC
Q 034564           16 ADFLKSIRGRPVVVKL----NSGVDYRGILACLDGYM   48 (91)
Q Consensus        16 ~~~L~~~~~k~V~V~L----~~g~~~~G~L~~~D~~m   48 (91)
                      ..-+..++|+.|.|+|    .+++.+.|+|.++|+-.
T Consensus        91 ~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~  127 (153)
T COG0779          91 AEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET  127 (153)
T ss_pred             HHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence            3445889999999999    68899999999999876

>PRK14647 hypothetical protein; Provisional

Probab=88.83  E-value=1.4  Score=30.02  Aligned_cols=29  Identities=24%  Similarity=0.204  Sum_probs=24.9

Q ss_pred             HHhhcCCCeEEEEEc---------CCcEEEEEEEEEcC
Q 034564           18 FLKSIRGRPVVVKLN---------SGVDYRGILACLDG   46 (91)
Q Consensus        18 ~L~~~~~k~V~V~L~---------~g~~~~G~L~~~D~   46 (91)
                      -+.+++|+.|.|+|+         +.+.+.|+|.++|.
T Consensus        93 ~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~  130 (159)
T PRK14647         93 DYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD  130 (159)
T ss_pred             HHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence            447899999999995         35999999999986

>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional

Probab=88.13  E-value=3.4  Score=30.57  Aligned_cols=48  Identities=19%  Similarity=0.243  Sum_probs=34.3

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeC
Q 034564           22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRG   74 (91)
Q Consensus        22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG   74 (91)
                      ++|++|.+.. ++..+.|++.++|....|+++..    .+.+.-..|.+.+|.
T Consensus       270 ~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~~~----g~~~~~~~gev~~~~  317 (319)
T PRK11886        270 FLGREVKLII-GDKEISGIARGIDEQGALLLEDD----GVEKPFNGGEISLRS  317 (319)
T ss_pred             ccCCeEEEEe-CCcEEEEEEEEECCCceEEEEeC----CcEEEEEEeEEEEec
Confidence            5689999987 45679999999999999999621    122233456666654

>PRK14637 hypothetical protein; Provisional

Probab=87.88  E-value=1.8  Score=29.39  Aligned_cols=35  Identities=17%  Similarity=0.178  Sum_probs=26.1

Q ss_pred             HHhhcCCCeEEEEEcCCcEE-EEEEEEEcCCCceeee
Q 034564           18 FLKSIRGRPVVVKLNSGVDY-RGILACLDGYMNIAME   53 (91)
Q Consensus        18 ~L~~~~~k~V~V~L~~g~~~-~G~L~~~D~~mNlvL~   53 (91)
                      -+.+++|+.|.|.+.+.+.+ .|+|.++|.- ++.|.
T Consensus        92 ~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~  127 (151)
T PRK14637         92 EFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT  127 (151)
T ss_pred             HHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence            34889999999999544555 7999999874 44443

>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed

Probab=87.87  E-value=3.4  Score=33.68  Aligned_cols=33  Identities=18%  Similarity=0.335  Sum_probs=28.6

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEEcCCCceeeee
Q 034564           22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQ   54 (91)
Q Consensus        22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~   54 (91)
                      ++|++|.+...++..+.|+..++|....|+|+.
T Consensus       276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~  308 (592)
T PRK13325        276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET  308 (592)
T ss_pred             cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence            568999987667778999999999999999963

>PRK14641 hypothetical protein; Provisional

Probab=86.88  E-value=1.8  Score=30.11  Aligned_cols=28  Identities=18%  Similarity=0.134  Sum_probs=24.0

Q ss_pred             HHhhcCCCeEEEEEcC----CcEEEEEEEEEc
Q 034564           18 FLKSIRGRPVVVKLNS----GVDYRGILACLD   45 (91)
Q Consensus        18 ~L~~~~~k~V~V~L~~----g~~~~G~L~~~D   45 (91)
                      -+++++|+.|.|.|.+    .+.+.|+|.++|
T Consensus        98 ~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~  129 (173)
T PRK14641         98 QYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS  129 (173)
T ss_pred             HHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence            3488999999999975    468999999995

>PRK14631 hypothetical protein; Provisional

Probab=85.70  E-value=1.7  Score=30.23  Aligned_cols=28  Identities=21%  Similarity=0.364  Sum_probs=24.7

Q ss_pred             HHhhcCCCeEEEEEc----CCcEEEEEEEEEc
Q 034564           18 FLKSIRGRPVVVKLN----SGVDYRGILACLD   45 (91)
Q Consensus        18 ~L~~~~~k~V~V~L~----~g~~~~G~L~~~D   45 (91)
                      -+.+++|+.|.|+|.    +.+.+.|+|.++|
T Consensus       111 df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~  142 (174)
T PRK14631        111 QLQGYIGQQVALRLIAAVENRRKFQAKLLAVD  142 (174)
T ss_pred             HHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence            448899999999996    4599999999998

>TIGR00121 birA_ligase birA, biotin-[acetyl-CoA-carboxylase] ligase region

Probab=82.67  E-value=7.9  Score=27.46  Aligned_cols=31  Identities=23%  Similarity=0.262  Sum_probs=26.8

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEEcCCCceeee
Q 034564           22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAME   53 (91)
Q Consensus        22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~   53 (91)
                      .+|++|.|...+ ..+.|+..++|....|+++
T Consensus       191 ~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~  221 (237)
T TIGR00121       191 HIGREVSLTTGN-GEIEGIARGIDKDGALLLE  221 (237)
T ss_pred             ccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence            458999998754 5799999999999999996

The protein name suggests that this enzyme transfers biotin only to acetyl-CoA-carboxylase but it also transfers the biotin moiety to other proteins. The apparent orthologs among the eukaryotes are larger proteins that contain a single copy of this domain.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	91
3swn_B	77	Structure Of The Lsm657 Complex: An Assembly Interm		1e-23
4emk_B	75	Crystal Structure Of Splsm567 Length = 75		7e-23
3cw1_F	86	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		7e-15
1jbm_A	86	Heptameric Crystal Structure Of Mth649, An Sm-Like		1e-09
1loj_A	87	Crystal Structure Of A Methanobacterial Sm-Like Arc		1e-09
1jri_A	85	The Crystal Structure Of An Sm-Like Archaeal Protei		1e-09
1i81_A	83	Crystal Structure Of A Heptameric Lsm Protein From		2e-09
1n9s_A	93	Crystal Structure Of Yeast Smf In Spacegroup P43212		3e-09
1n9r_A	93	Crystal Structure Of A Heptameric Ring Complex Of Y		6e-09
1i5l_A	77	Crystal Structure Of An Sm-Like Protein (Af-Sm1) Fr		4e-08
1m8v_A	77	Structure Of Pyrococcus Abyssii Sm Protein In Compl		8e-07
1i8f_A	81	The Crystal Structure Of A Heptameric Archaeal Sm P		1e-06
1h64_1	75	Crystal Structure Of The Sm-Related Protein Of P. A		3e-06
4emh_A	105	Crystal Structure Of Splsm4 Length = 105		4e-05
3cw1_G	76	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		2e-04
1th7_A	81	Crystal Structure Of An Archaeal Sm Protein From Su		4e-04

>pdb|3SWN|B Chain B, Structure Of The Lsm657 Complex: An Assembly Intermediate Of The Lsm1 7 And Lsm2 8 Rings Length = 77

Iteration: 1
 Score =  104 bits (260), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 45/68 (66%), Positives = 60/68 (88%)
Query: 14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIR 73
          +P +FL  + G+ V+++L+SGVDY+GIL+CLDGYMN+A+E+TEEYVNG+  N YGDAFIR
Sbjct: 6  SPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIR 65
Query: 74 GNNVLYIS 81
          GNNVLY+S
Sbjct: 66 GNNVLYVS 73

>pdb|4EMK|B Chain B, Crystal Structure Of Splsm567 Length = 75

Iteration: 1
 Score =  102 bits (253), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 44/68 (64%), Positives = 59/68 (86%)
Query: 14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIR 73
          +P +FL  + G+ V+++L+SGVDY+GIL+CLDGY N+A+E+TEEYVNG+  N YGDAFIR
Sbjct: 4  SPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYXNLALERTEEYVNGKKTNVYGDAFIR 63
Query: 74 GNNVLYIS 81
          GNNVLY+S
Sbjct: 64 GNNVLYVS 71

>pdb|3CW1|F Chain F, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 86

Iteration: 1
 Score = 75.5 bits (184), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 33/66 (50%), Positives = 45/66 (68%)
Query: 15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRG 74
          P  FL  + G+PV+VKL  G++Y+G L  +DGYMN+ +  TEEY++G L    G+  IR 
Sbjct: 7  PKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRC 66
Query: 75 NNVLYI 80
          NNVLYI
Sbjct: 67 NNVLYI 72

>pdb|1JBM|A Chain A, Heptameric Crystal Structure Of Mth649, An Sm-Like Archaeal Protein From Methanobacterium Thermautotrophicum Length = 86

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 42/75 (56%)
Query: 10 ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGD 69
             + P D L +    PV++KL    ++RG+L   D +MN+ +   EE  +G++  + G 
Sbjct: 9  VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGT 68
Query: 70 AFIRGNNVLYISTSK 84
            IRG+N++YIS  K
Sbjct: 69 VLIRGDNIVYISRGK 83

>pdb|1LOJ|A Chain A, Crystal Structure Of A Methanobacterial Sm-Like Archaeal Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump) Length = 87

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 42/75 (56%)
Query: 10 ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGD 69
             + P D L +    PV++KL    ++RG+L   D +MN+ +   EE  +G++  + G 
Sbjct: 9  VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGT 68
Query: 70 AFIRGNNVLYISTSK 84
            IRG+N++YIS  K
Sbjct: 69 VLIRGDNIVYISRGK 83

>pdb|1JRI|A Chain A, The Crystal Structure Of An Sm-Like Archaeal Protein With Two Heptamers In The Asymmetric Unit. Length = 85

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 42/75 (56%)
Query: 10 ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGD 69
             + P D L +    PV++KL    ++RG+L   D +MN+ +   EE  +G++  + G 
Sbjct: 9  VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGT 68
Query: 70 AFIRGNNVLYISTSK 84
            IRG+N++YIS  K
Sbjct: 69 VLIRGDNIVYISRGK 83

>pdb|1I81|A Chain A, Crystal Structure Of A Heptameric Lsm Protein From Methanobacterium Thermoautotrophicum Length = 83

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 41/72 (56%)
Query: 10 ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGD 69
             + P D L +    PV++KL    ++RG+L   D +MN+ +   EE  +G++  + G 
Sbjct: 11 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGT 70
Query: 70 AFIRGNNVLYIS 81
            IRG+N++YIS
Sbjct: 71 VLIRGDNIVYIS 82

>pdb|1N9S|A Chain A, Crystal Structure Of Yeast Smf In Spacegroup P43212 Length = 93

Iteration: 1
 Score = 56.6 bits (135), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 31/81 (38%), Positives = 41/81 (50%), Gaps = 1/81 (1%)
Query: 1  MSTGGEKGSATTKTPADFLKSIRGRPVVVKLN-SGVDYRGILACLDGYMNIAMEQTEEYV 59
          MS   +  +     P  FLK +    V VKL  +  +YRG L   D Y N+ + + EE+V
Sbjct: 8  MSESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFV 67
Query: 60 NGQLKNKYGDAFIRGNNVLYI 80
           G      G+ FIR NNVLYI
Sbjct: 68 AGVSHGTLGEIFIRSNNVLYI 88

>pdb|1N9R|A Chain A, Crystal Structure Of A Heptameric Ring Complex Of Yeast Smf In Spacegroup P4122 Length = 93

Iteration: 1
 Score = 55.8 bits (133), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 31/81 (38%), Positives = 41/81 (50%), Gaps = 1/81 (1%)
Query: 1  MSTGGEKGSATTKTPADFLKSIRGRPVVVKLN-SGVDYRGILACLDGYMNIAMEQTEEYV 59
          MS   +  +     P  FLK +    V VKL  +  +YRG L   D Y N+ + + EE+V
Sbjct: 8  MSESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFV 67
Query: 60 NGQLKNKYGDAFIRGNNVLYI 80
           G      G+ FIR NNVLYI
Sbjct: 68 AGVSHGTLGEIFIRCNNVLYI 88

>pdb|1I5L|A Chain A, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From Archaeoglobus Fulgidus Complexed With Short Poly-U Rna Length = 77

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 25/70 (35%), Positives = 39/70 (55%)
Query: 15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRG 74
          P D L      PV+V+L  G ++RG L   D +MN+ +   EE  NG++  K G   IRG
Sbjct: 5  PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRG 64
Query: 75 NNVLYISTSK 84
          + V+++S + 
Sbjct: 65 DTVVFVSPAP 74

>pdb|1M8V|A Chain A, Structure Of Pyrococcus Abyssii Sm Protein In Complex With A Uridine Heptamer Length = 77

Iteration: 1
 Score = 48.9 bits (115), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 41/75 (54%)
Query: 10 ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGD 69
          A  + P D +     + V+V L  G ++RG L   D ++N+ +   E   +G++  +YG 
Sbjct: 2  AMAERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGK 61
Query: 70 AFIRGNNVLYISTSK 84
            IRG+NVL IS ++
Sbjct: 62 IVIRGDNVLAISPTE 76

>pdb|1I8F|A Chain A, The Crystal Structure Of A Heptameric Archaeal Sm Protein: Implications For The Eukaryotic Snrnp Core Length = 81

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 24 GRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIS 81
          G+ V+VKL    + RGIL   D ++N+ +E  EE ++G +  K G   +RG NVL+IS
Sbjct: 21 GKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVY-KRGTMVVRGENVLFIS 77

>pdb|1H64|1 Chain 1, Crystal Structure Of The Sm-Related Protein Of P. Abyssi The Biological Unit Is A Heptamer Length = 75

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 40/73 (54%)
Query: 12 TKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAF 71
           + P D +     + V+V L  G ++RG L   D ++N+ +   E   +G++  +YG   
Sbjct: 2  AERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIV 61
Query: 72 IRGNNVLYISTSK 84
          IRG+NVL IS ++
Sbjct: 62 IRGDNVLAISPTE 74

>pdb|4EMH|A Chain A, Crystal Structure Of Splsm4 Length = 105

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAM-EQTEEYVNGQLKNKYGDAFIR 73
          P   L + +GRP++V+L +G  + G L   D Y N+ + E      +G    +  + +IR
Sbjct: 17 PLTLLNATQGRPILVELKNGETFNGHLENCDNYXNLTLREVIRTXPDGDKFFRLPECYIR 76
Query: 74 GNNVLYISTSKRTLADGA 91
          GNN+ Y+      L+  A
Sbjct: 77 GNNIKYLRIQDEVLSQVA 94

>pdb|3CW1|G Chain G, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 76

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/75 (28%), Positives = 37/75 (49%)
Query: 12 TKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAF 71
          +K     LK    + + +KLN G   +GIL   D +MN+ +++  E      +N  G   
Sbjct: 2  SKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVV 61
Query: 72 IRGNNVLYISTSKRT 86
          IRGN+++ +   +R 
Sbjct: 62 IRGNSIIMLEALERV 76

>pdb|1TH7|A Chain A, Crystal Structure Of An Archaeal Sm Protein From Sulfolobus Solfataricus Length = 81

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/55 (38%), Positives = 31/55 (56%)
Query: 27 VVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIS 81
          V+VKL    + RG+L   D +MN+ +  +EE  +     K G   IRG+NV+ IS
Sbjct: 22 VLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILIS 76

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	91
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	6e-33
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	4e-31
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	5e-31
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	1e-30
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	2e-30
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	8e-30
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	2e-29
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	3e-29
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	1e-26
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	2e-25
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	1e-22
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	4e-21
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	1e-19
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	3e-19
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	4e-19
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	5e-16
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	6e-14
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	2e-12
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	2e-12
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	1e-09
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	2e-08
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	1e-04

>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 =  108 bits (272), Expect = 6e-33
 Identities = 31/82 (37%), Positives = 41/82 (50%), Gaps = 1/82 (1%)

Query: 1  MSTGGEKGSATTKTPADFLKSIRGRPVVVKLN-SGVDYRGILACLDGYMNIAMEQTEEYV 59
          MS   +  +     P  FLK +    V VKL  +  +YRG L   D Y N+ + + EE+V
Sbjct: 8  MSESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFV 67

Query: 60 NGQLKNKYGDAFIRGNNVLYIS 81
           G      G+ FIR NNVLYI 
Sbjct: 68 AGVSHGTLGEIFIRCNNVLYIR 89

>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 =  103 bits (259), Expect = 4e-31
 Identities = 45/71 (63%), Positives = 60/71 (84%)

Query: 12 TKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAF 71
            +P +FL  + G+ V+++L+SGVDY+GIL+CLDGYMN+A+E+TEEYVNG+  N YGDAF
Sbjct: 2  DSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAF 61

Query: 72 IRGNNVLYIST 82
          IRGNNVLY+S 
Sbjct: 62 IRGNNVLYVSA 72

>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 =  103 bits (258), Expect = 5e-31
 Identities = 24/73 (32%), Positives = 41/73 (56%)

Query: 9  SATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYG 68
              + P D L +    PV++KL    ++RG+L   D +MN+ +   EE  +G++  + G
Sbjct: 10 RVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLG 69

Query: 69 DAFIRGNNVLYIS 81
             IRG+N++YIS
Sbjct: 70 TVLIRGDNIVYIS 82

>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 =  101 bits (255), Expect = 1e-30
 Identities = 23/73 (31%), Positives = 40/73 (54%)

Query: 12 TKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAF 71
           + P D +     + V+V L  G ++RG L   D ++N+ +   E   +G++  +YG   
Sbjct: 2  AERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIV 61

Query: 72 IRGNNVLYISTSK 84
          IRG+NVL IS ++
Sbjct: 62 IRGDNVLAISPTE 74

>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 (255), Expect = 2e-30
 Identities = 25/74 (33%), Positives = 39/74 (52%)

Query: 13 KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFI 72
            P D L      PV+V+L  G ++RG L   D +MN+ +   EE  NG++  K G   I
Sbjct: 3  PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVI 62

Query: 73 RGNNVLYISTSKRT 86
          RG+ V+++S +   
Sbjct: 63 RGDTVVFVSPAPGG 76

>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 =  100 bits (251), Expect = 8e-30
 Identities = 35/81 (43%), Positives = 49/81 (60%)

Query: 10 ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGD 69
          +    P  FL  + G+PV+VKL  G++Y+G L  +DGYMN+ +  TEEY++G L    G+
Sbjct: 2  SLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGE 61

Query: 70 AFIRGNNVLYISTSKRTLADG 90
            IR NNVLYI   +    DG
Sbjct: 62 VLIRCNNVLYIRGVEEEEEDG 82

>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 = 98.9 bits (247), Expect = 2e-29
 Identities = 23/78 (29%), Positives = 37/78 (47%)

Query: 9  SATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYG 68
          +   +T    L       V+VKL    + RG+L   D +MN+ +  +EE  +     K G
Sbjct: 4  NFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLG 63

Query: 69 DAFIRGNNVLYISTSKRT 86
             IRG+NV+ IS  + +
Sbjct: 64 TIVIRGDNVILISPLQTS 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 = 99.0 bits (247), Expect = 3e-29
 Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 9  SATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYG 68
          S    T    L+   G+ V+VKL    + RGIL   D ++N+ +E  EE ++G    K G
Sbjct: 6  SKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGN-VYKRG 64

Query: 69 DAFIRGNNVLYIS 81
             +RG NVL+IS
Sbjct: 65 TMVVRGENVLFIS 77

>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 = 93.3 bits (232), Expect = 1e-26
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 9  SATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQ-TEEYVNGQLKNKY 67
          S     P   L + +GRP++V+L +G  + G L   D YMN+ + +      +G    + 
Sbjct: 11 SQDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRL 70

Query: 68 GDAFIRGNNVLYIS 81
           + +IRGNN+ Y+ 
Sbjct: 71 PECYIRGNNIKYLR 84

>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 = 89.3 bits (222), Expect = 2e-25
 Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 10 ATTKTPADFLKSIRGRPVVVKL-NSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYG 68
               P   +KS+ G+ + V++        G L  +D YMN+ +    E    +     G
Sbjct: 1  GAMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLG 60

Query: 69 DAFIRGNNVLYIS 81
          +  +RGNNV+ I 
Sbjct: 61 EIVLRGNNVVLIQ 73

>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 = 82.0 bits (203), Expect = 1e-22
 Identities = 21/74 (28%), Positives = 37/74 (50%)

Query: 12 TKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAF 71
          +K     LK    + + +KLN G   +GIL   D +MN+ +++  E      +N  G   
Sbjct: 2  SKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVV 61

Query: 72 IRGNNVLYISTSKR 85
          IRGN+++ +   +R
Sbjct: 62 IRGNSIIMLEALER 75

>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 = 78.2 bits (193), Expect = 4e-21
 Identities = 16/71 (22%), Positives = 25/71 (35%)

Query: 11 TTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDA 70
          +   P   L    G  V  + N+G  YRG L   +  MN  M             +    
Sbjct: 2  SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQV 61

Query: 71 FIRGNNVLYIS 81
          +IRG  + ++ 
Sbjct: 62 YIRGCKIRFLI 72

>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 = 74.9 bits (184), Expect = 1e-19
 Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 13/89 (14%)

Query: 9  SATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN-------- 60
          +     P D ++      V VKL    +  G L   D ++N+ +   EE V         
Sbjct: 4  AQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETD 63

Query: 61 -----GQLKNKYGDAFIRGNNVLYISTSK 84
                 ++  Y   F+RG++V+ I+  +
Sbjct: 64 KDKALKTIRKHYEMLFVRGDSVILIAPPR 92

>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 = 74.6 bits (183), Expect = 3e-19
 Identities = 15/63 (23%), Positives = 28/63 (44%)

Query: 18 FLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNV 77
          FL  +    V ++L +G    G +  +D  MN  ++  +  +  +   +     IRGNN+
Sbjct: 6  FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNI 65

Query: 78 LYI 80
           Y 
Sbjct: 66 RYF 68

>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 = 74.3 bits (182), Expect = 4e-19
 Identities = 16/71 (22%), Positives = 26/71 (36%)

Query: 11 TTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDA 70
          +   P   L    G  V  + N+G  YRG L   +  MN  M             +    
Sbjct: 2  SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQV 61

Query: 71 FIRGNNVLYIS 81
          +IRG+ + ++ 
Sbjct: 62 YIRGSKIRFLI 72

>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 = 65.6 bits (160), Expect = 5e-16
 Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 1/82 (1%)

Query: 1  MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN 60
               +   + T  P + +    G  + V + S  ++ G L   D Y+NI ++   EY  
Sbjct: 7  HHHHSQDPMSMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDT 66

Query: 61 -GQLKNKYGDAFIRGNNVLYIS 81
             +  K+ +  + GN +  + 
Sbjct: 67 VTGVTEKHSEMLLNGNGMCMLI 88

>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 = 60.5 bits (147), Expect = 6e-14
 Identities = 22/81 (27%), Positives = 31/81 (38%), Gaps = 7/81 (8%)

Query: 9  SATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV-------NG 61
              +TP D LK      V +KL       G L   D + NI +    E +         
Sbjct: 5  HHHMETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELS 64

Query: 62 QLKNKYGDAFIRGNNVLYIST 82
          + + +    FIRG+ V  IST
Sbjct: 65 ESERRCEMVFIRGDTVTLIST 85

>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 = 57.7 bits (139), Expect = 2e-12
 Identities = 16/93 (17%), Positives = 32/93 (34%), Gaps = 15/93 (16%)

Query: 4   GGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNG-- 61
           G  +       P   +    G  + V +    ++ G+L   D Y+N+ ++  +EY     
Sbjct: 18  GSNQKGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKAD 77

Query: 62  -------------QLKNKYGDAFIRGNNVLYIS 81
                         + N+     + GNNV  + 
Sbjct: 78  EEDISGGNKKLKRVMVNRLETILLSGNNVAMLV 110

>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 = 56.9 bits (137), Expect = 2e-12
 Identities = 15/87 (17%), Positives = 30/87 (34%), Gaps = 8/87 (9%)

Query: 2  STGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN- 60
          ++         ++  D  +    + +      G    GIL   D  MN+ ++  EE +  
Sbjct: 12 NSSQPTERPRKESILDLSRYQ-DQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRN 70

Query: 61 ------GQLKNKYGDAFIRGNNVLYIS 81
                     K G   +RG  ++ I+
Sbjct: 71 PEDGKLTGAIRKLGLVVVRGTTLVLIA 97

>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 = 49.5 bits (118), Expect = 1e-09
 Identities = 12/73 (16%), Positives = 26/73 (35%), Gaps = 10/73 (13%)

Query: 19 LKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEY----------VNGQLKNKYG 68
          +       +   L  G  + G     D +MN+ +   +E+             + K   G
Sbjct: 9  MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLG 68

Query: 69 DAFIRGNNVLYIS 81
             +RG N++ ++
Sbjct: 69 LVLLRGENLVSMT 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 = 46.3 bits (110), Expect = 2e-08
 Identities = 12/65 (18%), Positives = 29/65 (44%), Gaps = 1/65 (1%)

Query: 18 FLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEY-VNGQLKNKYGDAFIRGNN 76
          +L++     V +     +   G +   D YMN+ ++  EE     + + + G   ++G+N
Sbjct: 24 YLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDN 83

Query: 77 VLYIS 81
          +  + 
Sbjct: 84 ITLLQ 88

>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 = 37.2 bits (86), Expect = 1e-04
 Identities = 14/85 (16%), Positives = 29/85 (34%), Gaps = 16/85 (18%)

Query: 15  PADFLKSI--RGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDA-- 70
           P   L         V++   +     G +   D + N+ +E  +E      K+  G    
Sbjct: 28  PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKS 87

Query: 71  ------------FIRGNNVLYISTS 83
                       F+RG++V+ +  +
Sbjct: 88  KPVNKDRYISKMFLRGDSVIVVLRN 112

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	91
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.95
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.95
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.94
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.94
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.94
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.94
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.94
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.94
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.94
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.94
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.93
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.93
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.92
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.92
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.92
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.92
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.92
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.91
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.91
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.91
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.9
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.88
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.87
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.84
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	99.15
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	97.03
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	96.94
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	96.88
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	96.81
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	96.76
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	96.68
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	96.67
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	96.64
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	96.54
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	96.45
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	96.32
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	96.23
1ycy_A	71	Conserved hypothetical protein; structural genomic	95.35
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	94.39
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	94.31
3rux_A	270	BIRA bifunctional protein; biotin-protein ligase,	92.28
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	91.47
2rm4_A	103	CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-	90.82
2eay_A	233	Biotin [acetyl-COA-carboxylase] ligase; biotin bio	89.29
1bia_A	321	BIRA bifunctional protein; transcription regulatio	87.84
2ej9_A	237	Putative biotin ligase; biotin biosynthesis, monom	83.02
4hcz_A	58	PHD finger protein 1; protein-peptide complex, tud	82.29

>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

Probab=99.95  E-value=1.3e-27  Score=147.94  Aligned_cols=80  Identities=44%  Similarity=0.840  Sum_probs=70.8

Q ss_pred             cCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCCccccC
Q 034564           11 TTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKRTLADG   90 (91)
Q Consensus        11 ~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~~~~~~   90 (91)
                      .+..|+++|++++|++|+|+|++|++|.|+|.+||+|||++|+||.++.+|+..++++.++|||++|++|+++|...+.+
T Consensus         3 ~~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~g~~~~~lg~v~IRG~nI~~i~~~d~~~~~~   82 (86)
T 3s6n_F            3 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGVEEEEEDG   82 (86)
T ss_dssp             CCCCHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEESSEEECGGGEEEEEECC------
T ss_pred             cCcCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcCCceeeEccEEEEeCCeEEEEEeCCcccccc
Confidence            36789999999999999999999999999999999999999999999888877889999999999999999999887754

>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*

Probab=99.95  E-value=3e-27  Score=144.47  Aligned_cols=80  Identities=34%  Similarity=0.439  Sum_probs=68.2

Q ss_pred             CCCCCccCCccCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEE
Q 034564            1 MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYI   80 (91)
Q Consensus         1 ms~~~~~~~~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i   80 (91)
                      ||.+..|.   +..|+.+|.++++++|+|+|+||++|.|+|.+||+|||++|+||.|+ ++...+++|.++|||++|++|
T Consensus         1 m~~~~~~~---~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~~~~~~~lg~v~iRG~~I~~i   76 (81)
T 1i8f_A            1 MASDISKC---FATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-IDGNVYKRGTMVVRGENVLFI   76 (81)
T ss_dssp             ------------CCHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-ETTEEEEEEEEEECGGGEEEE
T ss_pred             CCcccCcc---ccchHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-cCCcccCCCEEEECCCEEEEE
Confidence            77765664   78999999999999999999999999999999999999999999998 666778999999999999999


Q ss_pred             EeCC
Q 034564           81 STSK   84 (91)
Q Consensus        81 ~~~~   84 (91)
                      +++|
T Consensus        77 ~~~d   80 (81)
T 1i8f_A           77 SPVP   80 (81)
T ss_dssp             EECC
T ss_pred             EeCC
Confidence            9886

>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

Probab=99.94  E-value=7.1e-27  Score=141.22  Aligned_cols=74  Identities=22%  Similarity=0.332  Sum_probs=68.0

Q ss_pred             cCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCC
Q 034564           11 TTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSK   84 (91)
Q Consensus        11 ~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~   84 (91)
                      ....|..||++++|++|+|+|++|++|+|+|.+||+|||++|+||+++..+.+.++++.++|||++|+||++||
T Consensus         2 ~~~~P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~~~~~~lg~v~IRG~nI~~i~lPd   75 (75)
T 1d3b_A            2 SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLILPD   75 (75)
T ss_dssp             --CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECGGGEEEEEECC
T ss_pred             CccCHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCCCcEEEcCeEEEeCCEEEEEEcCC
Confidence            35789999999999999999999999999999999999999999999865545789999999999999999986

>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

Probab=99.94  E-value=3.8e-27  Score=147.74  Aligned_cols=84  Identities=37%  Similarity=0.616  Sum_probs=63.7

Q ss_pred             CCCCCccCCccCCChHHHHhhcCCCeEEEEEcCC-cEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEE
Q 034564            1 MSTGGEKGSATTKTPADFLKSIRGRPVVVKLNSG-VDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLY   79 (91)
Q Consensus         1 ms~~~~~~~~~~~~p~~~L~~~~~k~V~V~L~~g-~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~   79 (91)
                      ||.+.......+..|.++|.+++|++|+|+|++| ++|+|+|.+||+|||++|+||+|+.++++.+++|.++|||++|++
T Consensus         8 ~~~~~~~~~~~~~~P~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~~~~~~~lg~v~IRG~nI~~   87 (93)
T 1n9r_A            8 MSESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLY   87 (93)
T ss_dssp             ------------------CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECGGGEEE
T ss_pred             cccCccccccccCChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcCCCeEeEcCEEEEcCCeEEE
Confidence            6776666667789999999999999999999999 999999999999999999999998888888899999999999999


Q ss_pred             EEeCC
Q 034564           80 ISTSK   84 (91)
Q Consensus        80 i~~~~   84 (91)
                      |.+++
T Consensus        88 I~~~~   92 (93)
T 1n9r_A           88 IRELP   92 (93)
T ss_dssp             EEECC
T ss_pred             EEeCC
Confidence            99876

>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*

Probab=99.94  E-value=1.6e-26  Score=139.67  Aligned_cols=74  Identities=34%  Similarity=0.583  Sum_probs=69.4

Q ss_pred             CChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCCc
Q 034564           13 KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKRT   86 (91)
Q Consensus        13 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~~   86 (91)
                      ..|.++|++++|++|+|+|+||++|.|+|.+||+|||++|+||.|+..+...+++|.++|||++|++|.++|..
T Consensus         3 ~~P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~d~~   76 (77)
T 1i4k_A            3 PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVFVSPAPGG   76 (77)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEECC--
T ss_pred             ccHHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecCCcEeECCEEEECCCEEEEEEeCCCC
Confidence            57999999999999999999999999999999999999999999988787888999999999999999999875

>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A*

Probab=99.94  E-value=2.3e-26  Score=138.53  Aligned_cols=73  Identities=32%  Similarity=0.572  Sum_probs=68.3

Q ss_pred             CChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCC
Q 034564           13 KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKR   85 (91)
Q Consensus        13 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~   85 (91)
                      ..|.++|.+++|++|+|+|+||++|.|+|.+||+|||++|+||.|+..+...+++|.++|||++|++|.++++
T Consensus         3 ~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~e   75 (75)
T 1h64_1            3 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISPTEE   75 (75)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEEC--
T ss_pred             chHHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeCCceeECCEEEECCCEEEEEEeCCC
Confidence            5799999999999999999999999999999999999999999998877788999999999999999998874

>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

Probab=99.94  E-value=2.8e-26  Score=138.84  Aligned_cols=74  Identities=26%  Similarity=0.446  Sum_probs=69.1

Q ss_pred             CCChHHHHhhcCCCeEEEEEcCC-cEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCC
Q 034564           12 TKTPADFLKSIRGRPVVVKLNSG-VDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKR   85 (91)
Q Consensus        12 ~~~p~~~L~~~~~k~V~V~L~~g-~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~   85 (91)
                      +..|.++|.++++++|+|+|++| ++|.|+|.+||+|||++|+||+|+..++..+++|.++|||++|++|+++|+
T Consensus         3 m~~P~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~nI~~i~~~de   77 (77)
T 1ljo_A            3 MVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQPQEE   77 (77)
T ss_dssp             CCCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEEC--
T ss_pred             ccchHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecCCcEeECCeEEEeCCeEEEEEeCCC
Confidence            46899999999999999999999 999999999999999999999998878788999999999999999999874

>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

Probab=99.94  E-value=3.8e-26  Score=140.23  Aligned_cols=71  Identities=34%  Similarity=0.684  Sum_probs=68.0

Q ss_pred             CCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEe
Q 034564           12 TKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        12 ~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~   82 (91)
                      +..|+.+|.+++|++|+|+|+||++|.|+|.+||+|||++|+||.|+..+...+++|.++|||++|++|++
T Consensus        13 ~~~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~IRG~~I~~i~p   83 (83)
T 1mgq_A           13 VQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP   83 (83)
T ss_dssp             TTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEC
T ss_pred             CcChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecCCcccCCCEEEECCCEEEEEEC
Confidence            68999999999999999999999999999999999999999999998888788999999999999999974

>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

Probab=99.94  E-value=1.4e-26  Score=139.75  Aligned_cols=74  Identities=61%  Similarity=1.130  Sum_probs=68.7

Q ss_pred             CCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCC
Q 034564           12 TKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKR   85 (91)
Q Consensus        12 ~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~   85 (91)
                      +..|+++|++++|++|+|+|+||++|.|+|.+||+|||++|+||.|+.+++..+++|.++|||++|++|++.|+
T Consensus         2 ~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~~   75 (75)
T 4emk_B            2 DSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIRGNNVLYVSALDD   75 (75)
T ss_dssp             CSHHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEETTEEEEEEEEEEEEGGGSSEEEEC--
T ss_pred             CCchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEecCCcccEecEEEEcCCeEEEEEecCC
Confidence            36899999999999999999999999999999999999999999998888778899999999999999998763

>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

Probab=99.94  E-value=2.3e-26  Score=140.46  Aligned_cols=76  Identities=30%  Similarity=0.423  Sum_probs=69.5

Q ss_pred             ccCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCC
Q 034564           10 ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKR   85 (91)
Q Consensus        10 ~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~   85 (91)
                      ..+..|.++|.++++++|+|+|+||++|.|+|.+||+|||++|+||.|+..+...+++|.++|||++|++|.+++.
T Consensus         5 ~~~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~~   80 (81)
T 1th7_A            5 FLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILISPLQT   80 (81)
T ss_dssp             TTCHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECGGGEEEEEEC--
T ss_pred             ccccchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecCCceeECCEEEECCCEEEEEEecCC
Confidence            4467899999999999999999999999999999999999999999998777677899999999999999999875

>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

Probab=99.93  E-value=2.8e-25  Score=139.59  Aligned_cols=77  Identities=21%  Similarity=0.405  Sum_probs=67.4

Q ss_pred             ccCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe-cCeeeeeeceEEEeCCcEEEEEeCCCc
Q 034564           10 ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV-NGQLKNKYGDAFIRGNNVLYISTSKRT   86 (91)
Q Consensus        10 ~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~g~~~~~l~~v~IRG~~I~~i~~~~~~   86 (91)
                      .....|+.+|.++++++|+|+|++|++|.|+|.+||+||||+|+||+|+. +++..+.+|.++|||++|++|.+..+.
T Consensus        16 ~~~~~Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~IRG~nI~~i~p~~~p   93 (94)
T 4emk_A           16 SMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKHSEMLLNGNGMCMLIPGGKP   93 (94)
T ss_dssp             ----CHHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTTCCEEEEEEEEECSTTEEEEEECC--
T ss_pred             cccccCHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCCCcEeEcCEEEEcCCEEEEEEeCCCC
Confidence            34688999999999999999999999999999999999999999999987 666678999999999999999987543

>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}

Probab=99.93  E-value=1.2e-25  Score=143.67  Aligned_cols=80  Identities=29%  Similarity=0.588  Sum_probs=55.9

Q ss_pred             CccCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe-cCeeeeeeceEEEeCCcEEEEEeCCCcc
Q 034564            9 SATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV-NGQLKNKYGDAFIRGNNVLYISTSKRTL   87 (91)
Q Consensus         9 ~~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~g~~~~~l~~v~IRG~~I~~i~~~~~~~   87 (91)
                      +..+..|+.||++++|++|+|+|++|++|.|+|.+||+||||+|+||+|.. +|+..++++.++|||++|+||.+||...
T Consensus        11 ~~~~~~p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg~~~~~lg~v~IRG~nI~~I~~pd~l~   90 (105)
T 4emh_A           11 SQDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIRGNNIKYLRIQDEVL   90 (105)
T ss_dssp             ---------------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEEECGGGEEEEEC-----
T ss_pred             cCCCCcHHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCCceeeEcCeEEEeCCeEEEEecCHHHh
Confidence            445789999999999999999999999999999999999999999999974 5656789999999999999999998765


Q ss_pred             c
Q 034564           88 A   88 (91)
Q Consensus        88 ~   88 (91)
                      +
T Consensus        91 d   91 (105)
T 4emh_A           91 S   91 (105)
T ss_dssp             -
T ss_pred             h
Confidence            3

>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

Probab=99.92  E-value=2.6e-25  Score=134.50  Aligned_cols=73  Identities=29%  Similarity=0.496  Sum_probs=53.3

Q ss_pred             CChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCC
Q 034564           13 KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKR   85 (91)
Q Consensus        13 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~   85 (91)
                      .+|.++|.+++|++|+|+|+||++|.|+|.+||+|||++|+||.|+..++..+++|.++|||++|++|++.|.
T Consensus         3 ~~~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~v~iRG~~I~~i~~~d~   75 (76)
T 3s6n_G            3 KAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIMLEALER   75 (76)
T ss_dssp             -----------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC----CBSSEEECSSSEEEEEC---
T ss_pred             CcchHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccCCcEeEcCEEEECCCeEEEEEeccC
Confidence            3467899999999999999999999999999999999999999998666667899999999999999998875

>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}

Probab=99.92  E-value=1.4e-24  Score=136.53  Aligned_cols=77  Identities=29%  Similarity=0.375  Sum_probs=67.4

Q ss_pred             CCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEec-------CeeeeeeceEEEeCCcEEEEEeCC
Q 034564           12 TKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN-------GQLKNKYGDAFIRGNNVLYISTSK   84 (91)
Q Consensus        12 ~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~-------g~~~~~l~~v~IRG~~I~~i~~~~   84 (91)
                      +.-|..+|.+++|++|+|+|++|++|.|+|.|||+||||+|+||.|+..       +...+.+|.++|||++|++|.+++
T Consensus         8 ~~~p~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nVv~I~~~d   87 (96)
T 3bw1_A            8 METPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLISTPS   87 (96)
T ss_dssp             CCCHHHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEECGGGEEEEECCC
T ss_pred             hhhHHHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEECCCEEEEEEecC
Confidence            4679999999999999999999999999999999999999999999742       355688999999999999999998


Q ss_pred             Cccc
Q 034564           85 RTLA   88 (91)
Q Consensus        85 ~~~~   88 (91)
                      ...+
T Consensus        88 ~~~d   91 (96)
T 3bw1_A           88 EDDD   91 (96)
T ss_dssp             ----
T ss_pred             cccc
Confidence            8754

>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

Probab=99.92  E-value=4.7e-25  Score=137.04  Aligned_cols=79  Identities=18%  Similarity=0.244  Sum_probs=65.4

Q ss_pred             CCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe----------cCeeeeeeceEEEeCCcEEEEE
Q 034564           12 TKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV----------NGQLKNKYGDAFIRGNNVLYIS   81 (91)
Q Consensus        12 ~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~----------~g~~~~~l~~v~IRG~~I~~i~   81 (91)
                      +.+|..+|.++++++|+|+|+||++|.|+|.|||+||||+|+||.|+.          .+...+.+|.++|||++|++|.
T Consensus         2 ~~~~~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~~I~~i~   81 (91)
T 1d3b_B            2 TVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMT   81 (91)
T ss_dssp             -----CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEE
T ss_pred             CCChhHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECCCeEEEEE
Confidence            456788999999999999999999999999999999999999999963          2345789999999999999999


Q ss_pred             eCCCccccC
Q 034564           82 TSKRTLADG   90 (91)
Q Consensus        82 ~~~~~~~~~   90 (91)
                      +++...+|.
T Consensus        82 ~~~~~~~~~   90 (91)
T 1d3b_B           82 VEGPPPKDT   90 (91)
T ss_dssp             EEECCC---
T ss_pred             cCCCCCCCC
Confidence            998776653

>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

Probab=99.92  E-value=1.8e-24  Score=142.10  Aligned_cols=78  Identities=21%  Similarity=0.303  Sum_probs=69.7

Q ss_pred             cCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCCccc
Q 034564           11 TTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKRTLA   88 (91)
Q Consensus        11 ~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~~~~   88 (91)
                      ....|+.||+++++++|+|+|++|++|+|+|.+||+|||++|+||+++..+.+..+++.+||||++|+||++||....
T Consensus         2 ~~~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~~~~l~~v~IRGnnI~~I~lpd~l~~   79 (126)
T 2y9a_D            2 SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRFLILPDMLKN   79 (126)
T ss_dssp             --CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCSSCSS
T ss_pred             CcccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCcEeecccEEEeCCEEEEEEccccccc
Confidence            357899999999999999999999999999999999999999999998644456899999999999999999987543

>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

Probab=99.92  E-value=5.6e-25  Score=137.69  Aligned_cols=78  Identities=15%  Similarity=0.361  Sum_probs=67.5

Q ss_pred             cCCccCCChHHHHhhcCCCeEEEEE----cCCcEEEEEEEEEcCCCceeeeeeEEEe-cCeeeeeeceEEEeCCcEEEEE
Q 034564            7 KGSATTKTPADFLKSIRGRPVVVKL----NSGVDYRGILACLDGYMNIAMEQTEEYV-NGQLKNKYGDAFIRGNNVLYIS   81 (91)
Q Consensus         7 ~~~~~~~~p~~~L~~~~~k~V~V~L----~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~g~~~~~l~~v~IRG~~I~~i~   81 (91)
                      |....+..|+++|.++++++++|++    ++|++|.|+|.|||+||||+|+||+|+. +++..+++|.++|||++|++|+
T Consensus         9 ~~~~~m~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~iRG~nV~~i~   88 (92)
T 3s6n_E            9 KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLLQ   88 (92)
T ss_dssp             -----CCCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSCCEEEEEEEEECGGGEEEEE
T ss_pred             ccceeccCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCCceeEcCeEEEeCCEEEEEE
Confidence            4334578999999999999999999    9999999999999999999999999985 4556789999999999999999


Q ss_pred             eCC
Q 034564           82 TSK   84 (91)
Q Consensus        82 ~~~   84 (91)
                      +.+
T Consensus        89 ~~~   91 (92)
T 3s6n_E           89 SVS   91 (92)
T ss_dssp             EC-
T ss_pred             eCC
Confidence            865

>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

Probab=99.91  E-value=2.5e-24  Score=140.05  Aligned_cols=73  Identities=21%  Similarity=0.323  Sum_probs=68.8

Q ss_pred             ChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCCc
Q 034564           14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKRT   86 (91)
Q Consensus        14 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~~   86 (91)
                      .|+.||+++++++|+|+|++|++|.|+|.+||+||||+|+||+|+..+....+++.+||||++|+||++||..
T Consensus         2 ~p~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~~~~~~lg~v~IRG~nI~~I~~pd~l   74 (119)
T 1b34_A            2 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSL   74 (119)
T ss_dssp             CHHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTTC
T ss_pred             ChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecCCCceeEcceEEEcCCeEEEEEecccc
Confidence            6899999999999999999999999999999999999999999987666678999999999999999999884

>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe}

Probab=99.91  E-value=4.4e-24  Score=133.68  Aligned_cols=74  Identities=26%  Similarity=0.460  Sum_probs=64.4

Q ss_pred             ccCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEec-----C--------eeeeeeceEEEeCCc
Q 034564           10 ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN-----G--------QLKNKYGDAFIRGNN   76 (91)
Q Consensus        10 ~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~-----g--------~~~~~l~~v~IRG~~   76 (91)
                      +....|+.+|+.++|++|+|+|++|++|.|+|.+||+||||+|+||.|+..     |        ...+++|.++|||++
T Consensus         5 ~~~~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG~n   84 (93)
T 4emg_A            5 QAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDS   84 (93)
T ss_dssp             ----CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECGGG
T ss_pred             cccCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECCCe
Confidence            456899999999999999999999999999999999999999999999743     3        246889999999999


Q ss_pred             EEEEEeC
Q 034564           77 VLYISTS   83 (91)
Q Consensus        77 I~~i~~~   83 (91)
                      |++|+++
T Consensus        85 Vv~I~p~   91 (93)
T 4emg_A           85 VILIAPP   91 (93)
T ss_dssp             EEEEECC
T ss_pred             EEEEEec
Confidence            9999975

>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

Probab=99.91  E-value=2.3e-24  Score=140.55  Aligned_cols=78  Identities=19%  Similarity=0.392  Sum_probs=68.5

Q ss_pred             ccCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEec----------Cee-----eeeeceEEEeC
Q 034564           10 ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN----------GQL-----KNKYGDAFIRG   74 (91)
Q Consensus        10 ~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~----------g~~-----~~~l~~v~IRG   74 (91)
                      ..+..|+.+|.++++++|+|+|++|++|.|+|.+||+||||+|+||.|+..          |..     .+.+|.++|||
T Consensus        24 ~~~~~Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG  103 (121)
T 2fwk_A           24 GNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSG  103 (121)
T ss_dssp             CCCCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECG
T ss_pred             ccccCcHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECC
Confidence            467899999999999999999999999999999999999999999999751          333     67899999999


Q ss_pred             CcEEEEEeCCCcc
Q 034564           75 NNVLYISTSKRTL   87 (91)
Q Consensus        75 ~~I~~i~~~~~~~   87 (91)
                      ++|++|.+.+...
T Consensus       104 ~nVv~I~~~~~~~  116 (121)
T 2fwk_A          104 NNVAMLVPGGDPD  116 (121)
T ss_dssp             GGEEEEESSSCC-
T ss_pred             CEEEEEEecCCCC
Confidence            9999999877654

>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

Probab=99.90  E-value=1e-23  Score=136.23  Aligned_cols=76  Identities=21%  Similarity=0.331  Sum_probs=57.2

Q ss_pred             CChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecC-------eeeeeeceEEEeCCcEEEEEeCCC
Q 034564           13 KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNG-------QLKNKYGDAFIRGNNVLYISTSKR   85 (91)
Q Consensus        13 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g-------~~~~~l~~v~IRG~~I~~i~~~~~   85 (91)
                      ..|...|.++++++|+|.|++|++|.|+|.|||+||||+|+||.|+..+       ...+.+|.++|||++|++|+++|.
T Consensus        22 ke~i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~  101 (113)
T 4emk_C           22 KESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIAPMDG  101 (113)
T ss_dssp             ----------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTTEEEEEECC-
T ss_pred             cchHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCeEEEEEecCc
Confidence            4568889999999999999999999999999999999999999997432       356899999999999999999988


Q ss_pred             ccc
Q 034564           86 TLA   88 (91)
Q Consensus        86 ~~~   88 (91)
                      .+|
T Consensus       102 ~ee  104 (113)
T 4emk_C          102 SEE  104 (113)
T ss_dssp             ---
T ss_pred             ccc
Confidence            776

>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

Probab=99.88  E-value=1.9e-22  Score=130.87  Aligned_cols=77  Identities=16%  Similarity=0.255  Sum_probs=65.1

Q ss_pred             cCCChHHHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecC-------e-------eeeeeceEEEeC
Q 034564           11 TTKTPADFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNG-------Q-------LKNKYGDAFIRG   74 (91)
Q Consensus        11 ~~~~p~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g-------~-------~~~~l~~v~IRG   74 (91)
                      ....|+++|..++  +++|+|+|++|+.|.|+|.|||+||||+|+||.|+...       .       ..+++|.+||||
T Consensus        24 ~~~~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG  103 (118)
T 1b34_B           24 FNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRG  103 (118)
T ss_dssp             --CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECG
T ss_pred             cccChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcC
Confidence            3579999999999  59999999999999999999999999999999996311       0       145799999999


Q ss_pred             CcEEEEEeCCCcc
Q 034564           75 NNVLYISTSKRTL   87 (91)
Q Consensus        75 ~~I~~i~~~~~~~   87 (91)
                      ++|++|.+++...
T Consensus       104 ~nVv~I~~~~~~~  116 (118)
T 1b34_B          104 DSVIVVLRNPLIA  116 (118)
T ss_dssp             GGEEEEEECCCCC
T ss_pred             CEEEEEEeCchhh
Confidence            9999999987643

>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

Probab=99.87  E-value=5.2e-22  Score=141.13  Aligned_cols=78  Identities=18%  Similarity=0.252  Sum_probs=68.9

Q ss_pred             CCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEec----------CeeeeeeceEEEeCCcEEEEE
Q 034564           12 TKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN----------GQLKNKYGDAFIRGNNVLYIS   81 (91)
Q Consensus        12 ~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~----------g~~~~~l~~v~IRG~~I~~i~   81 (91)
                      +.++...|.+++|++|+|+|+|||+|.|+|++||+||||+|+||+|+..          +++.++++++||||+||++|.
T Consensus         2 ~v~k~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~Is   81 (231)
T 3pgw_B            2 TVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMT   81 (231)
T ss_pred             CcCchHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEEEE
Confidence            3566789999999999999999999999999999999999999999741          346789999999999999999


Q ss_pred             eCCCcccc
Q 034564           82 TSKRTLAD   89 (91)
Q Consensus        82 ~~~~~~~~   89 (91)
                      +.+..-.|
T Consensus        82 ve~pPp~d   89 (231)
T 3pgw_B           82 VEGPPPKD   89 (231)
T ss_pred             ecCCCCCC
Confidence            88765554

>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

Probab=99.84  E-value=8e-21  Score=125.29  Aligned_cols=67  Identities=28%  Similarity=0.513  Sum_probs=62.5

Q ss_pred             HHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCCc
Q 034564           16 ADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKRT   86 (91)
Q Consensus        16 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~~   86 (91)
                      .++|.+++|++|+|+|++|++|.|+|.+||+||||+|+||+++ .+   +++|.++|||++|++|.+++..
T Consensus         2 ~~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~-~~---~~lg~v~IRG~nI~~I~~~d~~   68 (130)
T 1m5q_A            2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNK-AG---EKFNRVFIMYRYIVHIDSTERR   68 (130)
T ss_dssp             HHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECT-TC---CEEEEEEECGGGEEEEEECCCC
T ss_pred             hhHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEE-cC---CEeceEEEeCCeEEEEEcCCcc
Confidence            4689999999999999999999999999999999999999997 33   6789999999999999999876

>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens}

Probab=99.15  E-value=2.4e-10  Score=70.36  Aligned_cols=69  Identities=19%  Similarity=0.129  Sum_probs=57.8

Q ss_pred             CChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEc-CCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCCccc
Q 034564           13 KTPADFLKSIRGRPVVVKLNSGVDYRGILACLD-GYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKRTLA   88 (91)
Q Consensus        13 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~~~~   88 (91)
                      .+|. .|.+++||+|.|.|.||++|+|.|.+|| ...|++|.|+.   .+   .+...++|.|..|..|...++..+
T Consensus         7 ~~p~-el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~~---~~---~~~~~~iI~G~aI~eI~v~~~~~~   76 (86)
T 1y96_A            7 KGPL-EWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFL---ED---GSMSVTGIMGHAVQTVETMNEGDH   76 (86)
T ss_dssp             SCHH-HHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEEC---TT---SCEEEEEECGGGEEEEEEEECCCH
T ss_pred             CCHH-HHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeecc---cC---CeEEEEEEecceEEEEEEecchhH
Confidence            4566 5599999999999999999999999999 88999999992   33   245799999999999877665543

>2vxe_A CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA decay, LSM proteins, translational repression, transcription; NMR {Drosophila melanogaster}

Probab=97.03  E-value=0.0081  Score=36.72  Aligned_cols=65  Identities=17%  Similarity=0.287  Sum_probs=52.6

Q ss_pred             hcCCCeEEEEEcCCcEEEEEEEEEc-CCCceeeeeeEEEe-cC--------eeeeeeceEEEeCCcEEEEEeCCC
Q 034564           21 SIRGRPVVVKLNSGVDYRGILACLD-GYMNIAMEQTEEYV-NG--------QLKNKYGDAFIRGNNVLYISTSKR   85 (91)
Q Consensus        21 ~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~e~~-~g--------~~~~~l~~v~IRG~~I~~i~~~~~   85 (91)
                      .++|++|.+..+.+-.|+|+|..+| +..-+.|+|+..+- .|        ....-++.+..||+.|.-+.+.+.
T Consensus        10 ~yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~yIvFrgsDIKdL~V~~~   84 (88)
T 2vxe_A           10 PELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQIAPQSQIYDYILFRGSDIKDIRVVNN   84 (88)
T ss_dssp             CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCTTTCCSSCCCCCCSCEEEEEEETTTEEEEEECCC
T ss_pred             cccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCcCCCCCcccCCCCceeeEEEEccCCccEEEEecc
Confidence            4699999999999999999999999 56889999998752 11        122346889999999999887654

>2ylb_A Protein HFQ; RNA-binding protein, LSM protein, RNA chaperone; 1.15A {Salmonella enterica subsp} PDB: 2yht_A 1hk9_A 2ylc_A* 3gib_A* 3rer_A* 3qo3_A* 3res_A*

Probab=96.94  E-value=0.0012  Score=39.12  Aligned_cols=56  Identities=18%  Similarity=0.386  Sum_probs=42.9

Q ss_pred             HHHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCC
Q 034564           16 ADFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSK   84 (91)
Q Consensus        16 ~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~   84 (91)
                      -.||+.+.  ..+|+|.|.||..++|++.+||+|+=+.- +      +      ...+|--..|.+|.+..
T Consensus        11 d~~L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~vlL~-~------~------~~~LIYKhAIsTI~p~~   68 (74)
T 2ylb_A           11 DPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLK-N------T------VSQMVYKHAISTVVPSR   68 (74)
T ss_dssp             HHHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEE-S------S------SEEEEEGGGEEEEEESS
T ss_pred             HHHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEE-C------C------ceEEEEeeeEEEEeEcc
Confidence            56788877  67999999999999999999999975542 1      1      24566677777777554

>2vc8_A Enhancer of mRNA-decapping protein 3; P-BODY component, cytoplasm, SM-like protein, protein-binding; 1.31A {Homo sapiens}

Probab=96.88  E-value=0.0046  Score=37.46  Aligned_cols=63  Identities=16%  Similarity=0.228  Sum_probs=51.7

Q ss_pred             hhcCCCeEEEEEcCCc-EEEEEEEEEcCC-CceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCC
Q 034564           20 KSIRGRPVVVKLNSGV-DYRGILACLDGY-MNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKR   85 (91)
Q Consensus        20 ~~~~~k~V~V~L~~g~-~~~G~L~~~D~~-mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~   85 (91)
                      .+|+|+.|.++.+++- .|.|.+..+|.. -+|.|.++.  .+|- +.+...|.+++.-|.-+.+.+.
T Consensus         5 ~~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~f--~NG~-~~~s~eVtls~~DI~~L~ii~~   69 (84)
T 2vc8_A            5 TDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPF--HNGV-KCLVPEVTFRAGDITELKILEI   69 (84)
T ss_dssp             CTTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEEE--ETTE-ECSSSEEEEEGGGCSEEEEEEC
T ss_pred             ccccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehhh--hCCC-CCCCcEEEEEecChhheEEEec
Confidence            4689999999999998 999999999976 689999994  4665 3455789999998876665443

>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_A

Probab=96.81  E-value=0.0023  Score=38.35  Aligned_cols=36  Identities=31%  Similarity=0.475  Sum_probs=31.1

Q ss_pred             HHHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCcee
Q 034564           16 ADFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIA   51 (91)
Q Consensus        16 ~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlv   51 (91)
                      -.||..+.  +.+|+|-|.||..+.|.+.+||+|+=+.
T Consensus        13 d~fLn~lrk~~~~Vtv~L~nG~~l~G~I~~fD~f~VlL   50 (78)
T 3ahu_A           13 DQFLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFTVLL   50 (78)
T ss_dssp             HHHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEEE
Confidence            45677766  7899999999999999999999998665

>1kq1_A HFQ, HOST factor for Q beta; hexamer, RNA binding protein, translational regulator, SM motif; 1.55A {Staphylococcus aureus} SCOP: b.38.1.2 PDB: 1kq2_A

Probab=96.76  E-value=0.0029  Score=37.77  Aligned_cols=37  Identities=19%  Similarity=0.313  Sum_probs=31.9

Q ss_pred             HHHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCceee
Q 034564           16 ADFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIAM   52 (91)
Q Consensus        16 ~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL   52 (91)
                      -.||..+.  ..+|.|.|.||-.+.|.+.+||+|+=+.-
T Consensus         9 d~fLn~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~VlL~   47 (77)
T 1kq1_A            9 DKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLN   47 (77)
T ss_dssp             HHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEEE
Confidence            45777777  68999999999999999999999986653

>4a53_A EDC3; RNA binding protein; NMR {Schizosaccharomyces pombe} PDB: 4a54_A

Probab=96.68  E-value=0.0065  Score=39.27  Aligned_cols=55  Identities=18%  Similarity=0.253  Sum_probs=41.2

Q ss_pred             hhcCCCeEEEEEcCCcEEEEEEEEEcCCCceee--eeeEEEecCeeeeeeceEEEeCCcEEEEEeCCC
Q 034564           20 KSIRGRPVVVKLNSGVDYRGILACLDGYMNIAM--EQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKR   85 (91)
Q Consensus        20 ~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL--~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~   85 (91)
                      .+|+|..|.|+|+||..+.|++..+|. -+|.|  ++|...          ..-|+.+.|.-+.+.+.
T Consensus         8 sqFlGy~V~v~LkDgs~~qG~I~~vd~-k~LtL~~~~a~~s----------~~~I~asdI~DLkVl~~   64 (125)
T 4a53_A            8 ADFYGSNVEVLLNNDSKARGVITNFDS-SNSILQLRLANDS----------TKSIVTKDIKDLRILPK   64 (125)
T ss_dssp             HHHTTCEEEEEETTSCEEEEEEEEEET-TTTEEEEEETTTE----------EEEEEGGGEEEEEECCS
T ss_pred             HHhcCceEEEEECCCCEeeEEEEeecC-CeeEEeccccccc----------cceeecccccceeeeec
Confidence            567999999999999999999999983 34555  988531          11677777766655443

>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

Probab=96.67  E-value=0.0069  Score=37.51  Aligned_cols=69  Identities=13%  Similarity=0.263  Sum_probs=53.6

Q ss_pred             HHhhcCCCeEEEEEcCCcEEEEEEEEEc-CCCceeeeeeEEEe-cC--------eeeeeeceEEEeCCcEEEEEeCCCc
Q 034564           18 FLKSIRGRPVVVKLNSGVDYRGILACLD-GYMNIAMEQTEEYV-NG--------QLKNKYGDAFIRGNNVLYISTSKRT   86 (91)
Q Consensus        18 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~e~~-~g--------~~~~~l~~v~IRG~~I~~i~~~~~~   86 (91)
                      --..++|++|.+..+.+-.|+|+|..+| +-.-+.|+|+..+- .|        ....-++.+..||+.|.-+.+.+..
T Consensus        13 ~~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~~ipp~~~vyeyIvFrGsDIKDL~V~e~p   91 (95)
T 2fb7_A           13 GGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCEPP   91 (95)
T ss_dssp             ---CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSSCCCSCCCCSSCEEECSTTEEEEEESCCS
T ss_pred             ccCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCCccCCCCcceeEEEEcCCCcceEEEecCC
Confidence            3467899999999999999999999999 56889999987652 11        1223468999999999999887654

>1u1s_A HFQ protein; SM-like bacterial protein, riken structural genomics/proteomics initiative, RSGI, structural genomics, RNA binding protein; 1.60A {Pseudomonas aeruginosa} SCOP: b.38.1.2 PDB: 1u1t_A 3qui_A* 3m4g_A 3inz_A

Probab=96.64  E-value=0.0032  Score=38.05  Aligned_cols=37  Identities=22%  Similarity=0.521  Sum_probs=31.1

Q ss_pred             HHHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCceee
Q 034564           16 ADFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIAM   52 (91)
Q Consensus        16 ~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL   52 (91)
                      -.||..+.  ..+|+|-|.||..++|.+.+||+|+=+.-
T Consensus         9 d~fLn~lrk~~~~Vtv~L~NG~~l~G~I~~fD~ftVlL~   47 (82)
T 1u1s_A            9 DPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLK   47 (82)
T ss_dssp             HHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEe
Confidence            45677665  67899999999999999999999986653

>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2

Probab=96.54  E-value=0.0036  Score=37.57  Aligned_cols=55  Identities=20%  Similarity=0.417  Sum_probs=39.9

Q ss_pred             HHHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeC
Q 034564           16 ADFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTS   83 (91)
Q Consensus        16 ~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~   83 (91)
                      -.||..+.  ..+|.|.|.||..+.|.+.+||+|+=++ +      +|.      ..+|-=.-|.+|.+.
T Consensus        10 d~fLn~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~VlL-~------~g~------~qLIYKhAISTI~P~   66 (79)
T 3sb2_A           10 DPFLNALRKEHVPVSIYLVNGIKLQGHVESFDQYVVLL-R------NTV------TQMVYKHAISTVVPA   66 (79)
T ss_dssp             HHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEE-E------SSS------EEEEEGGGEEEEEES
T ss_pred             HHHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEE-E------CCc------eEEEEeeeEEEEeec
Confidence            45777766  4579999999999999999999998665 2      231      235555666666654

>2qtx_A Uncharacterized protein MJ1435; HFQ, SM, RNA-binding protein, sRNA, translational regulation, RNA binding protein; 2.50A {Methanocaldococcus jannaschii}

Probab=96.45  E-value=0.006  Score=35.91  Aligned_cols=29  Identities=17%  Similarity=0.274  Sum_probs=26.0

Q ss_pred             CCCeEEEEEcCCcEEEEEEEEEcCCCcee
Q 034564           23 RGRPVVVKLNSGVDYRGILACLDGYMNIA   51 (91)
Q Consensus        23 ~~k~V~V~L~~g~~~~G~L~~~D~~mNlv   51 (91)
                      .+.+|+|-|.||..++|.+.+||+|+=+.
T Consensus        24 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll   52 (71)
T 2qtx_A           24 NGKKVKIFLRNGEVLDAEVTGVSNYEIMV   52 (71)
T ss_dssp             TTCEEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             cCCcEEEEEeCCeEEEEEEEEEcceEEEE
Confidence            35789999999999999999999998665

>1y96_B Gemin7, SIP3, GEM-associated protein 7; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens}

Probab=96.32  E-value=0.02  Score=34.75  Aligned_cols=64  Identities=19%  Similarity=0.246  Sum_probs=51.5

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEEc-CCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeC
Q 034564           15 PADFLKSIRGRPVVVKLNSGVDYRGILACLD-GYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTS   83 (91)
Q Consensus        15 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~   83 (91)
                      -+.+|..+.|++|.+.+.++.++.|++.++| ...|+..++-.- .-|    .++.-.+|+.-|++++..
T Consensus        20 fLr~l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~T-PiG----v~~eAlLR~~Dii~~sF~   84 (85)
T 1y96_B           20 YLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQT-PIG----VQAEALLRCSDIISYTFK   84 (85)
T ss_dssp             HHHHHHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEECC-TTC----CEEEEEEEGGGEEEEEEC
T ss_pred             HHHHHHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhcCC-Ccc----cchhhhhhcCCEEEEEec
Confidence            3567788899999999999999999999999 568887666542 122    367899999999998753

>2y90_A Protein HFQ; RNA-binding protein, SM-like, RNA chaperone; 2.25A {Escherichia coli} PDB: 3qhs_A

Probab=96.23  E-value=0.0051  Score=38.69  Aligned_cols=37  Identities=24%  Similarity=0.534  Sum_probs=31.3

Q ss_pred             HHHHhhcCC--CeEEEEEcCCcEEEEEEEEEcCCCceee
Q 034564           16 ADFLKSIRG--RPVVVKLNSGVDYRGILACLDGYMNIAM   52 (91)
Q Consensus        16 ~~~L~~~~~--k~V~V~L~~g~~~~G~L~~~D~~mNlvL   52 (91)
                      -.||..+..  .+|.|.|.||-.++|++.+||+|+=++-
T Consensus        11 d~fLn~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~VlL~   49 (104)
T 2y90_A           11 DPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLK   49 (104)
T ss_dssp             HHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEE
Confidence            567777775  4899999999999999999999986654

>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

Probab=95.35  E-value=0.13  Score=29.74  Aligned_cols=62  Identities=19%  Similarity=0.330  Sum_probs=44.1

Q ss_pred             HHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEe
Q 034564           16 ADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        16 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~   82 (91)
                      -..|.++.|++|-|-.-....|.|+|..||.- -+.|+|++.+. |.   +-...+++=+.|-.|-+
T Consensus         8 dktL~~WKg~rvAv~vg~ehSFtGiledFDeE-viLL~dV~D~~-GN---k~k~liv~idDinWimL   69 (71)
T 1ycy_A            8 EKVLKEWKGHKVAVSVGGDHSFTGTLEDFDEE-VILLKDVVDVI-GN---RGKQMLIGLEDINWIML   69 (71)
T ss_dssp             HHHHHHHTTSEEEEEEC----CEEEEEEECSS-EEEEEEEEETT-EE---EEEEEEEEGGGEEEEEE
T ss_pred             HHHHHHhCCcEEEEEecCcceeeeehhhcCcc-eeehhhHHHHh-cc---ccceeEEEeccceEEEe
Confidence            34688999999999999999999999999975 47789999863 22   22456677777766654

>3hfo_A SSR3341 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 1.30A {Synechocystis SP}

Probab=94.39  E-value=0.27  Score=28.63  Aligned_cols=60  Identities=18%  Similarity=0.238  Sum_probs=42.9

Q ss_pred             CCCh-HHHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEe
Q 034564           12 TKTP-ADFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        12 ~~~p-~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~   82 (91)
                      +..| ...|+.++  ..+|.|.|.+|..+.|.+.-+|+|.=+.-.+.     +      ..++|.-..|.||.+
T Consensus         6 t~lPsvR~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~cl~L~~~~-----~------~~~LI~r~AI~~I~p   68 (70)
T 3hfo_A            6 SGLPSVRQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDGLGLVDDS-----E------RSTIVRLAAIAYITP   68 (70)
T ss_dssp             CSCHHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEECTT-----C------CEEEEEGGGEEEEEE
T ss_pred             CCCCcHHHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCEEEEEcCC-----C------CeEEEEeeeeEEEee
Confidence            3444 56778887  46899999999999999999999864442211     1      245677777777764

>3hfn_A ASL2047 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 2.31A {Nostoc SP}

Probab=94.31  E-value=0.31  Score=28.54  Aligned_cols=56  Identities=18%  Similarity=0.210  Sum_probs=41.4

Q ss_pred             HHHHhhcCC--CeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEe
Q 034564           16 ADFLKSIRG--RPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        16 ~~~L~~~~~--k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~   82 (91)
                      ...|+.++.  +.|.|.|.+|..+.|++.-+|++.=++- +...          ..++|.-..|.||.+
T Consensus        13 vR~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~cl~L~-~~~~----------~~~LI~R~AI~~Ikp   70 (72)
T 3hfn_A           13 IRQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTCVCIA-DENS----------RQTTIWKQAIAYLQP   70 (72)
T ss_dssp             HHHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSEEEEE-C-------------CEEEEEGGGEEEEEE
T ss_pred             HHHHHHHHhhCceEEEEecCCCEEEEEEEEECCCEEEEE-cCCC----------CeEEEEeeeeEEEEe
Confidence            567888884  5799999999999999999999864432 2211          247777888888865

>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

Probab=92.28  E-value=0.24  Score=35.15  Aligned_cols=34  Identities=26%  Similarity=0.327  Sum_probs=30.3

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeee
Q 034564           22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQT   55 (91)
Q Consensus        22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~   55 (91)
                      .+|++|+|.+.+|..+.|+..++|....|+|+..
T Consensus       222 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~~  255 (270)
T 3rux_A          222 TIGSRVRVELPGGQDVVGIARDIDDQGRLCLDVG  255 (270)
T ss_dssp             STTSEEEEECTTSCEEEEEEEEECTTSCEEEEET
T ss_pred             ccCCEEEEEECCCeEEEEEEEEECCCCeEEEEEC
Confidence            3489999998889999999999999999999754

>1ib8_A Conserved protein SP14.3; nucleic acid binding protein, ribosomal protein, essential gene, structural genomics; NMR {Streptococcus pneumoniae} SCOP: b.38.2.1 d.52.4.1

Probab=91.47  E-value=0.29  Score=32.51  Aligned_cols=29  Identities=17%  Similarity=0.250  Sum_probs=24.9

Q ss_pred             HhhcCCCeEEEEEc----CCcEEEEEEEEEcCC
Q 034564           19 LKSIRGRPVVVKLN----SGVDYRGILACLDGY   47 (91)
Q Consensus        19 L~~~~~k~V~V~L~----~g~~~~G~L~~~D~~   47 (91)
                      +.+++|+.|.|+|.    +.+.+.|+|.++|.-
T Consensus        99 f~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T 1ib8_A           99 VAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED  131 (164)
T ss_dssp             HHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT
T ss_pred             HHHhCCcEEEEEEecccCCceEEEEEEEEEeCC
Confidence            47889999999994    459999999999864

>2rm4_A CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-BODY component, SM-like protein,, protein binding; NMR {Drosophila melanogaster}

Probab=90.82  E-value=1.9  Score=26.68  Aligned_cols=67  Identities=13%  Similarity=0.282  Sum_probs=53.5

Q ss_pred             hhcCCCeEEEEEcCCc-EEEEEEEEEcCCCceeeeeeEEEecCe-eeeeeceEEEeCCcEEEEEeCCCcccc
Q 034564           20 KSIRGRPVVVKLNSGV-DYRGILACLDGYMNIAMEQTEEYVNGQ-LKNKYGDAFIRGNNVLYISTSKRTLAD   89 (91)
Q Consensus        20 ~~~~~k~V~V~L~~g~-~~~G~L~~~D~~mNlvL~~~~e~~~g~-~~~~l~~v~IRG~~I~~i~~~~~~~~~   89 (91)
                      .+|+|+-|.|...+.- .|.|.+..+|+ -++.|.++..  +|- -......|.++..-|..+.+.+..+.|
T Consensus         8 edwiG~~VSI~C~d~LGVyQG~I~~V~~-~~ItL~kaFr--NGiplk~~~~EVtLsa~DI~~L~IIe~~~~~   76 (103)
T 2rm4_A            8 QDWIGCAVSIACDEVLGVFQGLIKQISA-EEITIVRAFR--NGVPLRKQNAEVVLKCTDIRSIDLIEPAKQD   76 (103)
T ss_dssp             GGGTTCEEEEEECTTTCEEEEEEEEEET-TEEEEEEEEE--TTEECSCSSSCEEEETTTEEEEEEEECCCCC
T ss_pred             cceeceEEEEeeCCcceEeeEEEEEccc-ceeEEhhhhh--cCcCcCCCCceEEEEecchhheeeecccccc
Confidence            4789999999999986 99999999995 4599998875  552 123568999999999888877666644

>2eay_A Biotin [acetyl-COA-carboxylase] ligase; biotin biosynthesis, dimer, X-RAY diffraction, structural genomics, NPPSFA; 1.95A {Aquifex aeolicus} PDB: 3efs_A* 3fjp_A 3efr_A*

Probab=89.29  E-value=0.33  Score=33.62  Aligned_cols=47  Identities=19%  Similarity=0.101  Sum_probs=33.6

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeC
Q 034564           22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRG   74 (91)
Q Consensus        22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG   74 (91)
                      .+|++|++...++  +.|+..++|....|+|+...    |......|.|.+|+
T Consensus       186 ~~g~~V~v~~~~~--~~G~~~gId~~G~L~v~~~~----G~~~~~~Gev~~r~  232 (233)
T 2eay_A          186 YLGEEVKLLGEGK--ITGKLVGLSEKGGALILTEE----GIKEILSGEFSLRR  232 (233)
T ss_dssp             TTTSEEEETTEEE--EEEEEEEECTTSCEEEEETT----EEEEECSCCEEEC-
T ss_pred             ccCCEEEEEECCe--EEEEEEEECCCCeEEEEECC----CeEEEEEeEEEEec
Confidence            3689999976654  99999999999999997532    22223446777765

>1bia_A BIRA bifunctional protein; transcription regulation; 2.30A {Escherichia coli} SCOP: a.4.5.1 b.34.1.1 d.104.1.2 PDB: 1bib_A* 1hxd_A* 2ewn_A*

Probab=87.84  E-value=1.4  Score=31.60  Aligned_cols=48  Identities=21%  Similarity=0.178  Sum_probs=34.7

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeC
Q 034564           22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRG   74 (91)
Q Consensus        22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG   74 (91)
                      .+|++|+|... +..+.|+..++|....|+|+...    |......|.|.+|+
T Consensus       271 ~~g~~V~v~~~-~~~~~G~~~gid~~G~L~v~~~~----g~~~~~~Gev~~r~  318 (321)
T 1bia_A          271 FINRPVKLIIG-DKEIFGISRGIDKQGALLLEQDG----IIKPWMGGEISLRS  318 (321)
T ss_dssp             TTTSEEEEEET-TEEEEEEEEEECTTSCEEEEETT----EEEEESSCEEEEC-
T ss_pred             hcCCEEEEEEC-CcEEEEEEEEECCCCeEEEEECC----CEEEEEeeeEEEec
Confidence            46899999875 45899999999999999997532    22223446777664

>2ej9_A Putative biotin ligase; biotin biosynthesis, monomer, X-RAY diffraction, structural genomics, NPPSFA; HET: BTN; 2.00A {Methanocaldococcus jannaschii}

Probab=83.02  E-value=2.2  Score=29.44  Aligned_cols=32  Identities=16%  Similarity=0.040  Sum_probs=28.2

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEEcCCCceeeee
Q 034564           22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQ   54 (91)
Q Consensus        22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~   54 (91)
                      .+|++|+|...++..+.|+..++|....|+ +.
T Consensus       190 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~-~~  221 (237)
T 2ej9_A          190 TIGKQVKILLSNNEIITGKVYDIDFDGIVL-GT  221 (237)
T ss_dssp             STTCEEEEEETTSCEEEEEEEEECSSEEEE-EE
T ss_pred             ccCCEEEEEECCCeEEEEEEEEECCCCeEE-Ec
Confidence            368999999988877999999999999998 64

>4hcz_A PHD finger protein 1; protein-peptide complex, tudor, histone binding, H3K36ME3, N nucleus, transcription; HET: M3L; 1.85A {Homo sapiens}

Probab=82.29  E-value=2.4  Score=23.72  Aligned_cols=25  Identities=24%  Similarity=0.486  Sum_probs=22.8

Q ss_pred             CCCeEEEEEcCCcEEEEEEEEEcCC
Q 034564           23 RGRPVVVKLNSGVDYRGILACLDGY   47 (91)
Q Consensus        23 ~~k~V~V~L~~g~~~~G~L~~~D~~   47 (91)
                      .|..|.+.-.||+.|-|+++.+|..
T Consensus         6 ~GedVLarwsDG~fYlGtI~~V~~~   30 (58)
T 4hcz_A            6 EGQDVLARWTDGLLYLGTIKKVDSA   30 (58)
T ss_dssp             TTCEEEEECTTSCEEEEEEEEEETT
T ss_pred             cCCEEEEEecCCCEEeEEEEEEecC
Confidence            4788999999999999999999876

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	91
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	4e-24
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	4e-24
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	2e-23
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	8e-23
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	5e-21
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	6e-21
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	7e-21
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	2e-20
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	1e-18
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	1e-18
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	1e-16
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	2e-14
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	8e-07

>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Length = 72

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]

 Score = 84.4 bits (209), Expect = 4e-24
 Identities = 25/69 (36%), Positives = 39/69 (56%)

Query: 15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRG 74
          P D L      PV+V+L  G ++RG L   D +MN+ +   EE  NG++  K G   IRG
Sbjct: 4  PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRG 63

Query: 75 NNVLYISTS 83
          + V+++S +
Sbjct: 64 DTVVFVSPA 72

>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 74

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

 Score = 84.8 bits (210), Expect = 4e-24
 Identities = 24/71 (33%), Positives = 41/71 (57%)

Query: 11 TTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDA 70
            + P D L +    PV++KL    ++RG+L   D +MN+ +   EE  +G++  + G  
Sbjct: 3  NVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTV 62

Query: 71 FIRGNNVLYIS 81
           IRG+N++YIS
Sbjct: 63 LIRGDNIVYIS 73

>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Length = 71

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrococcus abyssi [TaxId: 29292]

 Score = 82.8 bits (205), Expect = 2e-23
 Identities = 23/69 (33%), Positives = 38/69 (55%)

Query: 15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRG 74
          P D +     + V+V L  G ++RG L   D ++N+ +   E   +G++  +YG   IRG
Sbjct: 3  PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRG 62

Query: 75 NNVLYISTS 83
          +NVL IS +
Sbjct: 63 DNVLAISPT 71

>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} Length = 76

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 81.3 bits (201), Expect = 8e-23
 Identities = 23/73 (31%), Positives = 35/73 (47%)

Query: 9  SATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYG 68
          +   +T    L       V+VKL    + RG+L   D +MN+ +  +EE  +     K G
Sbjct: 2  NFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLG 61

Query: 69 DAFIRGNNVLYIS 81
             IRG+NV+ IS
Sbjct: 62 TIVIRGDNVILIS 74

>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D3 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 76.7 bits (189), Expect = 5e-21
 Identities = 16/68 (23%), Positives = 24/68 (35%)

Query: 14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIR 73
           P   L    G  V  + N+G  YRG L   +  MN  M             +    +IR
Sbjct: 2  VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIR 61

Query: 74 GNNVLYIS 81
          G  + ++ 
Sbjct: 62 GCKIRFLI 69

>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 71

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score = 76.3 bits (188), Expect = 6e-21
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIR 73
          T    L+   G+ V+VKL    + RGIL   D ++N+ +E  EE ++G    K G   +R
Sbjct: 2  TLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGN-VYKRGTMVVR 60

Query: 74 GNNVLYIS 81
          G NVL+IS
Sbjct: 61 GENVLFIS 68

>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 68

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Small nuclear ribonucleoprotein F, Smf
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 76.3 bits (188), Expect = 7e-21
 Identities = 27/64 (42%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 19 LKSIRGRPVVVKL-NSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNV 77
          LK +    V VKL  +  +YRG L   D Y N+ + + EE+V G      G+ FIR NNV
Sbjct: 1  LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNV 60

Query: 78 LYIS 81
          LYI 
Sbjct: 61 LYIR 64

>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.5 bits (186), Expect = 2e-20
 Identities = 15/64 (23%), Positives = 28/64 (43%)

Query: 18 FLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNV 77
          FL  +    V ++L +G    G +  +D  MN  ++  +  +  +   +     IRGNN+
Sbjct: 5  FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNI 64

Query: 78 LYIS 81
           Y  
Sbjct: 65 RYFI 68

>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 127

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Sm-Like archaeal protein Smap3
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score = 72.4 bits (178), Expect = 1e-18
 Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 4/65 (6%)

Query: 18 FLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNV 77
           L ++ GR V V L++G  Y+G+L  +D  +NI +             K+   FI    +
Sbjct: 4  ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAG----EKFNRVFIMYRYI 59

Query: 78 LYIST 82
          ++I +
Sbjct: 60 VHIDS 64

>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Length = 75

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]

 Score = 70.5 bits (173), Expect = 1e-18
 Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 1/68 (1%)

Query: 15 PADFLKSIRGRPVVVKLNSG-VDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIR 73
          P   +KS+ G+ + V++        G L  +D YMN+ +    E    +     G+  +R
Sbjct: 6  PNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLR 65

Query: 74 GNNVLYIS 81
          GNNV+ I 
Sbjct: 66 GNNVVLIQ 73

>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]} Length = 92

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: U6 snRNA-associated sm-like protein LSM5
species: Cryptosporidium parvum [TaxId: 5807]

 Score = 66.4 bits (162), Expect = 1e-16
 Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 15/82 (18%)

Query: 15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV--------------- 59
          P   +    G  + V +    ++ G+L   D Y+N+ ++  +EY                
Sbjct: 6  PLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKL 65

Query: 60 NGQLKNKYGDAFIRGNNVLYIS 81
             + N+     + GNNV  + 
Sbjct: 66 KRVMVNRLETILLSGNNVAMLV 87

>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: B core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.2 bits (146), Expect = 2e-14
 Identities = 12/73 (16%), Positives = 26/73 (35%), Gaps = 10/73 (13%)

Query: 19 LKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV----------NGQLKNKYG 68
          +       +   L  G  + G     D +MN+ +   +E+             + K   G
Sbjct: 3  MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLG 62

Query: 69 DAFIRGNNVLYIS 81
             +RG N++ ++
Sbjct: 63 LVLLRGENLVSMT 75

>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D2 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.0 bits (96), Expect = 8e-07
 Identities = 13/83 (15%), Positives = 29/83 (34%), Gaps = 16/83 (19%)

Query: 15 PADFL-KSIR-GRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV------------- 59
          P   L +S++    V++   +     G +   D + N+ +E  +E               
Sbjct: 3  PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKS 62

Query: 60 -NGQLKNKYGDAFIRGNNVLYIS 81
                      F+RG++V+ + 
Sbjct: 63 KPVNKDRYISKMFLRGDSVIVVL 85

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	91
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.94
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.94
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.94
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.93
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.93
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.92
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.92
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.91
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.9
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.9
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.86
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.86
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.82
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	97.27
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	96.91
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	95.83
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	95.66
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	94.86
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	93.77
d2qqra1	59	Jumonji domain-containing protein 2A {Human (Homo	84.11

>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrococcus abyssi [TaxId: 29292]

Probab=99.94  E-value=2.1e-26  Score=136.26  Aligned_cols=70  Identities=33%  Similarity=0.582  Sum_probs=67.0

Q ss_pred             CChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEe
Q 034564           13 KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        13 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~   82 (91)
                      .+|+++|++++|++|+|+|+||++|+|+|.+||+||||+|+||.+..+++..++++.+||||++|++|++
T Consensus         1 ~~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~l~~~~IRG~~I~~Isp   70 (71)
T d1h641_           1 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISP   70 (71)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEE
T ss_pred             CCchHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecCCcEeEcCcEEEECCeEEEEeC
Confidence            3699999999999999999999999999999999999999999999888888999999999999999986

>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=99.94  E-value=2.4e-26  Score=137.06  Aligned_cols=73  Identities=33%  Similarity=0.668  Sum_probs=69.1

Q ss_pred             ccCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEe
Q 034564           10 ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        10 ~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~   82 (91)
                      +....|+++|++++|++|.|+|+||++|.|+|.+||+|||++|+||+++.+++..++++.+||||++|++|++
T Consensus         2 ~~~~~Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~~~~~~~~~~~IRG~~I~~I~p   74 (74)
T d1mgqa_           2 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP   74 (74)
T ss_dssp             CCTTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEC
T ss_pred             CcccCcHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCCCeEeEcceEEEeCCEEEEEeC
Confidence            4578899999999999999999999999999999999999999999999888888999999999999999975

>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]

Probab=99.94  E-value=2e-26  Score=136.76  Aligned_cols=71  Identities=35%  Similarity=0.616  Sum_probs=67.1

Q ss_pred             CCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEe
Q 034564           12 TKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        12 ~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~   82 (91)
                      +..|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||+|+.+++..++++.+||||++|++|++
T Consensus         1 p~~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~IRG~~I~~Isp   71 (72)
T d1i4k1_           1 PPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVFVSP   71 (72)
T ss_dssp             CCCHHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSSSEEEEEEEEEECGGGEEEEEC
T ss_pred             CCChHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecCCeEeEcceEEEeCCeEEEEEc
Confidence            35799999999999999999999999999999999999999999998777778899999999999999974

>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D3 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=6.8e-26  Score=134.57  Aligned_cols=72  Identities=22%  Similarity=0.337  Sum_probs=67.6

Q ss_pred             CChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCC
Q 034564           13 KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSK   84 (91)
Q Consensus        13 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~   84 (91)
                      ..|+.+|++++|++|+|+|+||++|+|+|.+||.|||++|+||+++..+.+..+++.+||||++|+||++||
T Consensus         1 g~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~v~IRG~~I~~i~lpd   72 (72)
T d1d3ba_           1 GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLILPD   72 (72)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECGGGEEEEEECC
T ss_pred             CCchHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCCCcEeEcCeEEEECCEEEEEEcCC
Confidence            369999999999999999999999999999999999999999999876666788999999999999999997

>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]

Probab=99.93  E-value=2.3e-25  Score=133.34  Aligned_cols=72  Identities=26%  Similarity=0.452  Sum_probs=67.6

Q ss_pred             cCCChHHHHhhcCCCeEEEEEcCC-cEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEe
Q 034564           11 TTKTPADFLKSIRGRPVVVKLNSG-VDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        11 ~~~~p~~~L~~~~~k~V~V~L~~g-~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~   82 (91)
                      ++..|+++|+++++++|+|+|++| +.|.|+|.+||+|||++|+||+++..+.+.++++.+||||++|++|.+
T Consensus         2 ~~~~P~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~IRG~~I~~I~p   74 (75)
T d1ljoa_           2 AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQP   74 (75)
T ss_dssp             CCCCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEE
T ss_pred             CccccHHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCCCcEeEcceEEEeCCEEEEEEC
Confidence            457899999999999999999976 799999999999999999999998888888999999999999999986

>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.92  E-value=2.9e-25  Score=132.99  Aligned_cols=72  Identities=32%  Similarity=0.461  Sum_probs=67.2

Q ss_pred             cCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEe
Q 034564           11 TTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIST   82 (91)
Q Consensus        11 ~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~   82 (91)
                      ....|.++|.+++|++|+|+|+||++|.|+|.+||+|||++|+||+++..+.+.++++.+||||++|++|++
T Consensus         4 ~~~~~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~~~v~iRG~~I~~I~~   75 (76)
T d1th7a1           4 LAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILISP   75 (76)
T ss_dssp             TCHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECGGGEEEEEE
T ss_pred             ccccHHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecCCcccCcceEEEECCEEEEEEe
Confidence            455689999999999999999999999999999999999999999998776677899999999999999986

>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=99.92  E-value=1e-24  Score=129.17  Aligned_cols=69  Identities=36%  Similarity=0.583  Sum_probs=63.8

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCC
Q 034564           15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSK   84 (91)
Q Consensus        15 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~   84 (91)
                      +..+|++++|++|+|+|+||++|.|+|.+||+|||++|+||+++.+++ .++++.++|||++|++|++++
T Consensus         3 ~~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~~~-~~~~g~v~iRG~~I~~I~~~P   71 (71)
T d1i8fa_           3 LGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGN-VYKRGTMVVRGENVLFISPVP   71 (71)
T ss_dssp             HHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEETTE-EEEEEEEEECGGGEEEEEECC
T ss_pred             HhHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEECCC-EEEcceEEEeCCeEEEEeCCC
Confidence            567899999999999999999999999999999999999999987764 578999999999999998753

>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Small nuclear ribonucleoprotein F, Smf
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.91  E-value=1.1e-24  Score=128.14  Aligned_cols=66  Identities=41%  Similarity=0.710  Sum_probs=60.7

Q ss_pred             HhhcCCCeEEEEEc-CCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEE-eCC
Q 034564           19 LKSIRGRPVVVKLN-SGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIS-TSK   84 (91)
Q Consensus        19 L~~~~~k~V~V~L~-~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~-~~~   84 (91)
                      |+++++++|.|+|+ +|++|+|+|.+||+|||++|+||++..+++..++++.+||||++|+||+ +||
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~IRG~nI~~I~~~pd   68 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN   68 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECGGGEEEEEECCC
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEecCCcccCcCeEEEECCEEEEEEeCCC
Confidence            57899999999999 5688999999999999999999999988888889999999999999997 543

>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=7.4e-24  Score=128.04  Aligned_cols=72  Identities=21%  Similarity=0.327  Sum_probs=67.1

Q ss_pred             HHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCCcc
Q 034564           16 ADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKRTL   87 (91)
Q Consensus        16 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~~~   87 (91)
                      ..||+++.|++|.|+|+||.+|+|+|.++|+|||++|+||+++..+.+..+++.+||||++|+||++||...
T Consensus         3 v~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~~Ir~i~lPd~l~   74 (80)
T d1b34a_           3 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLP   74 (80)
T ss_dssp             HHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTTCC
T ss_pred             HHHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCCEEEcccEEEcCCEEEEEECCCCcc
Confidence            679999999999999999999999999999999999999999876666788999999999999999998754

>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: U6 snRNA-associated sm-like protein LSM5
species: Cryptosporidium parvum [TaxId: 5807]

Probab=99.90  E-value=5e-24  Score=131.43  Aligned_cols=73  Identities=21%  Similarity=0.443  Sum_probs=65.3

Q ss_pred             cCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEec---------------CeeeeeeceEEEeCC
Q 034564           11 TTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN---------------GQLKNKYGDAFIRGN   75 (91)
Q Consensus        11 ~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~---------------g~~~~~l~~v~IRG~   75 (91)
                      ++..|+.+|+++++++|+|.|+||++|.|+|.+||+||||+|+||.|+..               +...+++|.+||||+
T Consensus         2 ~~~~Pl~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~   81 (92)
T d2fwka1           2 NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGN   81 (92)
T ss_dssp             CCCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGG
T ss_pred             CccChHHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCC
Confidence            46789999999999999999999999999999999999999999999631               124568999999999


Q ss_pred             cEEEEEeC
Q 034564           76 NVLYISTS   83 (91)
Q Consensus        76 ~I~~i~~~   83 (91)
                      +|++|++.
T Consensus        82 ~Vv~I~p~   89 (92)
T d2fwka1          82 NVAMLVPG   89 (92)
T ss_dssp             GEEEEESS
T ss_pred             EEEEEEeC
Confidence            99999864

>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: B core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=3.3e-22  Score=120.75  Aligned_cols=65  Identities=18%  Similarity=0.314  Sum_probs=57.9

Q ss_pred             HhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEec----------CeeeeeeceEEEeCCcEEEEEeC
Q 034564           19 LKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN----------GQLKNKYGDAFIRGNNVLYISTS   83 (91)
Q Consensus        19 L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~----------g~~~~~l~~v~IRG~~I~~i~~~   83 (91)
                      |.++++++|+|.|+|||.|.|+|.|||+||||+|+||.|+..          +...+.+|.++|||++|++|++.
T Consensus         3 L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~~   77 (81)
T d1d3bb_           3 MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVE   77 (81)
T ss_dssp             CGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEE
T ss_pred             hHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEcc
Confidence            578999999999999999999999999999999999999631          12457899999999999999864

>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D2 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=6.9e-22  Score=122.26  Aligned_cols=72  Identities=17%  Similarity=0.290  Sum_probs=62.5

Q ss_pred             ChHHHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEec----C----------eeeeeeceEEEeCCcE
Q 034564           14 TPADFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN----G----------QLKNKYGDAFIRGNNV   77 (91)
Q Consensus        14 ~p~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~----g----------~~~~~l~~v~IRG~~I   77 (91)
                      +|+.+|.+++  +++|+|.|++|+.+.|+|.+||+||||+|+||.|+..    +          ...+++|.++|||++|
T Consensus         2 GPl~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdnV   81 (93)
T d1b34b_           2 GPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSV   81 (93)
T ss_dssp             CHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGE
T ss_pred             CcHHHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCEE
Confidence            6999999998  8999999999999999999999999999999999521    0          1346899999999999


Q ss_pred             EEEEeCCC
Q 034564           78 LYISTSKR   85 (91)
Q Consensus        78 ~~i~~~~~   85 (91)
                      ++|..++.
T Consensus        82 v~I~~~p~   89 (93)
T d1b34b_          82 IVVLRNPL   89 (93)
T ss_dssp             EEEEECCC
T ss_pred             EEEEcChh
Confidence            99977664

>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Sm-Like archaeal protein Smap3
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=99.82  E-value=3.2e-20  Score=120.39  Aligned_cols=68  Identities=28%  Similarity=0.521  Sum_probs=61.2

Q ss_pred             HHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCCcc
Q 034564           16 ADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKRTL   87 (91)
Q Consensus        16 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~~~   87 (91)
                      +++|++++|++|.|+|+||++|.|+|.+||+|||++|+||++.. +   .+++.++|||++|+||..|++..
T Consensus         2 ~~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~-~---~k~~~v~IRG~~I~~I~~~e~~i   69 (127)
T d1m5q1_           2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA-G---EKFNRVFIMYRYIVHIDSTERRI   69 (127)
T ss_dssp             HHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETT-C---CEEEEEEECGGGEEEEEECSCCC
T ss_pred             hhHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECC-C---CcccEEEEeCCeEEEEEcchhhc
Confidence            57899999999999999999999999999999999999999853 3   24688999999999999998754

>d2vxfa1 b.38.1.5 (A:6-85) LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) [TaxId: 7955]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: LSM14 N-terminal domain-like
domain: LSM14 homolog A (Lsm14a)
species: Zebrafish (Danio rerio) [TaxId: 7955]

Probab=97.27  E-value=0.0017  Score=37.60  Aligned_cols=65  Identities=14%  Similarity=0.324  Sum_probs=52.6

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEEcC-CCceeeeeeEEEe-cC--------eeeeeeceEEEeCCcEEEEEeCCCc
Q 034564           22 IRGRPVVVKLNSGVDYRGILACLDG-YMNIAMEQTEEYV-NG--------QLKNKYGDAFIRGNNVLYISTSKRT   86 (91)
Q Consensus        22 ~~~k~V~V~L~~g~~~~G~L~~~D~-~mNlvL~~~~e~~-~g--------~~~~~l~~v~IRG~~I~~i~~~~~~   86 (91)
                      |+|++|.+..+.+-.|+|+|..+|. -.-+.|+|+..+- .|        ....-++.+..||+.|--+...+..
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~~IvFrgsDIKdL~v~e~p   76 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCEPP   76 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSSCCCCCCCCEEEEEEETTTEEEEEESSCC
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCCccCCCCcceeEEEEcCcCcceEEeccCC
Confidence            6899999999999999999999994 4778999998752 11        1233478999999999999887643

>d1biaa2 b.34.1.1 (A:271-317) Biotin repressor/biotin holoenzyme synthetase, C-terminal domain {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: SH3-like barrel
superfamily: C-terminal domain of transcriptional repressors
family: Biotin repressor (BirA)
domain: Biotin repressor/biotin holoenzyme synthetase, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.91  E-value=0.0024  Score=33.20  Aligned_cols=47  Identities=21%  Similarity=0.179  Sum_probs=35.1

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEe
Q 034564           22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIR   73 (91)
Q Consensus        22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IR   73 (91)
                      |+|++|+|.. .++++.|+..++|....|+|+...    |.+...-|.|.||
T Consensus         1 f~gk~V~v~~-g~~~i~G~a~gId~~G~Lll~t~~----g~~~~~sGEVSlR   47 (47)
T d1biaa2           1 FINRPVKLII-GDKEIFGISRGIDKQGALLLEQDG----IIKPWMGGEISLR   47 (47)
T ss_dssp             TTTSEEEEEE-TTEEEEEEEEEECTTSCEEEEETT----EEEEESSCEEEEC
T ss_pred             CCCCEEEEEE-CCeEEEEEEeeECCCCcEEEEECC----CEEEEEEEEEEeC
Confidence            6899999976 457899999999999999997432    2233345666665

>d1u1sa1 b.38.1.2 (A:6-71) Pleiotropic translational regulator Hfq {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Pleiotropic translational regulator Hfq
domain: Pleiotropic translational regulator Hfq
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=95.83  E-value=0.0078  Score=33.55  Aligned_cols=34  Identities=24%  Similarity=0.595  Sum_probs=27.7

Q ss_pred             HHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCce
Q 034564           17 DFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNI   50 (91)
Q Consensus        17 ~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNl   50 (91)
                      .||.++.  ..+|+|-|.||-.+.|.+.+||+|.=|
T Consensus         5 ~fLn~~rk~~~~VtifL~nGvkl~G~I~~fD~ftvL   40 (66)
T d1u1sa1           5 PYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVIL   40 (66)
T ss_dssp             HHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEE
T ss_pred             HHHHHHHHcCCcEEEEEEcCcEEEEEEEEEcceEEE
Confidence            3555544  568999999999999999999999654

>d1kq1a_ b.38.1.2 (A:) Pleiotropic translational regulator Hfq {Staphylococcus aureus [TaxId: 1280]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Pleiotropic translational regulator Hfq
domain: Pleiotropic translational regulator Hfq
species: Staphylococcus aureus [TaxId: 1280]

Probab=95.66  E-value=0.012  Score=32.13  Aligned_cols=37  Identities=22%  Similarity=0.337  Sum_probs=29.7

Q ss_pred             HHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCceeeee
Q 034564           18 FLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIAMEQ   54 (91)
Q Consensus        18 ~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~   54 (91)
                      ||..+.  ..+|+|-|.||-.+.|.+.+||+|.=|.-.+
T Consensus         6 fln~lr~~~~~VtifL~nGvkl~G~I~~fD~ftvlL~~~   44 (60)
T d1kq1a_           6 ALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQ   44 (60)
T ss_dssp             HHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEEET
T ss_pred             HHHHHHHcCCcEEEEEECCcEEEEEEEEEcceEEEEEeC
Confidence            454444  5789999999999999999999998666443

>d1ycya1 b.38.1.4 (A:5-70) Hypothetical protein PF1955 {Pyrococcus furiosus [TaxId: 2261]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: PF1955-like
domain: Hypothetical protein PF1955
species: Pyrococcus furiosus [TaxId: 2261]

Probab=94.86  E-value=0.098  Score=28.43  Aligned_cols=60  Identities=20%  Similarity=0.321  Sum_probs=42.2

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEE
Q 034564           17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIS   81 (91)
Q Consensus        17 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~   81 (91)
                      ..|.++.|++|-|-......|.|+|..||.- -+.|+|++.+. |.+   -..++++=+.|-.|.
T Consensus         5 ktL~~WKg~kvAv~vgsehSFtGiledFDeE-viLL~dV~D~~-GNk---~k~llv~idD~nWim   64 (66)
T d1ycya1           5 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEE-VILLKDVVDVI-GNR---GKQMLIGLEDINWIM   64 (66)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSS-EEEEEEEEETT-EEE---EEEEEEEGGGEEEEE
T ss_pred             HHHHHhCCcEEEEEecCcceeEEEhhhcCcc-eEeehhhHHHh-ccc---cceeEEEeccceeEE
Confidence            4678999999999999999999999999975 47789999863 322   245666666665554

>d1ib8a1 b.38.2.1 (A:91-164) Hypothetical protein SP14.3 (SP0552) {Streptococcus pneumoniae [TaxId: 1313]}

class: All beta proteins
fold: Sm-like fold
superfamily: YhbC-like, C-terminal domain
family: YhbC-like, C-terminal domain
domain: Hypothetical protein SP14.3 (SP0552)
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=93.77  E-value=0.037  Score=30.66  Aligned_cols=30  Identities=17%  Similarity=0.220  Sum_probs=25.7

Q ss_pred             HHhhcCCCeEEEEEc---CC-cEEEEEEEEEcCC
Q 034564           18 FLKSIRGRPVVVKLN---SG-VDYRGILACLDGY   47 (91)
Q Consensus        18 ~L~~~~~k~V~V~L~---~g-~~~~G~L~~~D~~   47 (91)
                      -+..++|+.|.|.|+   +| +.+.|.|.++|+-
T Consensus         8 ~f~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~   41 (74)
T d1ib8a1           8 AVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED   41 (74)
T ss_dssp             HHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT
T ss_pred             HHHHhCCCEEEEEEecccCCceEEEEEEEeecCC
Confidence            348899999999987   34 8999999999975

>d2qqra1 b.34.9.1 (A:897-955) Jumonji domain-containing protein 2A {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Tudor/PWWP/MBT
family: Tudor domain
domain: Jumonji domain-containing protein 2A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.11  E-value=0.79  Score=24.41  Aligned_cols=23  Identities=26%  Similarity=0.346  Sum_probs=20.7

Q ss_pred             CCCeEEEEEcCCcEEEEEEEEEc
Q 034564           23 RGRPVVVKLNSGVDYRGILACLD   45 (91)
Q Consensus        23 ~~k~V~V~L~~g~~~~G~L~~~D   45 (91)
                      +|++|.-+.+|||.|.+++.+.-
T Consensus         5 ~Gq~VI~KhkNgryY~c~V~~~~   27 (59)
T d2qqra1           5 AGQKVISKHKNGRFYQCEVVRLT   27 (59)
T ss_dssp             TTCEEEEECTTSSEEEEEEEEEE
T ss_pred             cccEEEEEccCCcEEEEEEEEee
Confidence            68999999999999999998763