Psyllid ID: psy10835

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80
Protein Sequence
MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKRRGV
Secondary Structure (PSIPRED)
ccccccHHHHHHHHccccEEEEEcccEEEEEcEEEEEEEEEEEEccEEEEEccEEEcccccEEEEcccEEEEEEcccccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHHcccEEEEEEccccEEEEEEEEEcccccEEEEEEEEEEccEEEEEEEEEEEcHHHEEEEEEcccccc
Coil and Loop (DISEMBL)
MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLknkygdtfirgnnvlyistqkrrgv
Flexible Loop (DISEMBL)
msrkeslsqfiqqihgrpvvVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNkygdtfirgnnvlyistqkrrgv
Low Complexity Region (SEG)
MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKRRGV
Disordered region (IsUnstruct)
*********FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIS*******
Disordered Region (DISOPRED)
******L***IQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLY**TQ*****
Disordered Region (DISEMBL)
*********FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKRRGV
Disordered Region (DISPRO)
***KESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQK****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKRRGV
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	80	2.2.26 [Sep-21-2011]
P62313	80	U6 snRNA-associated Sm-li	yes	N/A	0.95	0.95	0.855	2e-32
P62312	80	U6 snRNA-associated Sm-li	yes	N/A	0.95	0.95	0.855	2e-32
B0DWN3	99	U6 snRNA-associated Sm-li	N/A	N/A	0.887	0.717	0.661	7e-23
Q552U1	88	Probable U6 snRNA-associa	yes	N/A	0.862	0.784	0.681	1e-21
Q9UUI1	75	U6 snRNA-associated Sm-li	yes	N/A	0.862	0.92	0.623	2e-21
Q4PG71	85	U6 snRNA-associated Sm-li	N/A	N/A	0.95	0.894	0.592	1e-20
A6R363	80	U6 snRNA-associated Sm-li	N/A	N/A	0.925	0.925	0.594	7e-20
A1DM27	80	U6 snRNA-associated Sm-li	N/A	N/A	0.85	0.85	0.647	1e-19
Q4WNI0	80	U6 snRNA-associated Sm-li	yes	N/A	0.85	0.85	0.647	2e-19
A8NHT8	95	U6 snRNA-associated Sm-li	N/A	N/A	0.887	0.747	0.661	2e-19

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

 Score =  137 bits (345), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 65/76 (85%), Positives = 71/76 (93%)

Query: 3  RKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDT 62
          RK++ S F++QI GRPVVVKL SGVDYRGVL+CLDGYMNIALEQTEEY+NGQLKNKYGD 
Sbjct: 4  RKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKYGDA 63

Query: 63 FIRGNNVLYISTQKRR 78
          FIRGNNVLYISTQKRR
Sbjct: 64 FIRGNNVLYISTQKRR 79

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 =  137 bits (345), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 65/76 (85%), Positives = 71/76 (93%)

Query: 3  RKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDT 62
          RK++ S F++QI GRPVVVKL SGVDYRGVL+CLDGYMNIALEQTEEY+NGQLKNKYGD 
Sbjct: 4  RKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKYGDA 63

Query: 63 FIRGNNVLYISTQKRR 78
          FIRGNNVLYISTQKRR
Sbjct: 64 FIRGNNVLYISTQKRR 79

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 =  105 bits (262), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 47/71 (66%), Positives = 60/71 (84%)

Query: 6  SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIR 65
          S + F++ + G+ V+V+L SGVDYRG+LSCLDGYMNIALEQTEE++NG + N+YGD FIR
Sbjct: 27 SPTDFLKGVVGKRVIVRLTSGVDYRGLLSCLDGYMNIALEQTEEHVNGVVTNRYGDAFIR 86

Query: 66 GNNVLYISTQK 76
          GNNVLYIS  +
Sbjct: 87 GNNVLYISAAE 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|Q552U1|LSM6_DICDI Probable U6 snRNA-associated Sm-like protein LSm6 OS=Dictyostelium discoideum GN=lsm6 PE=3 SV=1

 Score =  101 bits (252), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 47/69 (68%), Positives = 56/69 (81%)

Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNV 69
          F +   GRPVVVKL +GV+YRG+L  +DG MNI +EQTEEY+NGQLK KYGD F+RGNNV
Sbjct: 20 FFKMCIGRPVVVKLNNGVEYRGILEVVDGNMNIVMEQTEEYLNGQLKTKYGDCFLRGNNV 79

Query: 70 LYISTQKRR 78
          LYIS Q R+
Sbjct: 80 LYISAQPRK 88

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

 Score =  100 bits (250), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 43/69 (62%), Positives = 59/69 (85%)

Query: 6  SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIR 65
          S ++F+ ++ G+ V+++L SGVDY+G+LSCLDGYMN+ALE+TEEY+NG+  N YGD FIR
Sbjct: 4  SPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIR 63

Query: 66 GNNVLYIST 74
          GNNVLY+S 
Sbjct: 64 GNNVLYVSA 72

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

 Score = 98.2 bits (243), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 45/76 (59%), Positives = 60/76 (78%)

Query: 2  SRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGD 61
          ++  S + F++ + G+ V V+L SG+DYRGVLSCLDGYMNIALEQT EY++G  KN YGD
Sbjct: 10 AKAGSPNDFLKGVIGKNVNVRLNSGIDYRGVLSCLDGYMNIALEQTVEYVDGIKKNSYGD 69

Query: 62 TFIRGNNVLYISTQKR 77
           FIRGNNV+YI+  ++
Sbjct: 70 AFIRGNNVMYITALEK 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|A6R363|LSM6_AJECN U6 snRNA-associated Sm-like protein LSm6 OS=Ajellomyces capsulata (strain NAm1 / WU24) GN=LSM6 PE=3 SV=1

 Score = 95.9 bits (237), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 44/74 (59%), Positives = 55/74 (74%)

Query: 2  SRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGD 61
          S  +  S F+ +I G PV VKL SGV Y+G L  +DGYMNIALE+TEEY++G+L+  YGD
Sbjct: 7  SEGKDPSAFLSEITGAPVTVKLNSGVVYKGELQSVDGYMNIALEKTEEYVDGKLRRSYGD 66

Query: 62 TFIRGNNVLYISTQ 75
           F+RGNNVLYIS  
Sbjct: 67 AFVRGNNVLYISAD 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.

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

>sp|A1DM27|LSM6_NEOFI U6 snRNA-associated Sm-like protein LSm6 OS=Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) GN=lsm6 PE=3 SV=2

 Score = 94.7 bits (234), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 44/68 (64%), Positives = 54/68 (79%)

Query: 8  SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGN 67
          S F+ +I G PV VKL SGV YRG L  +DGYMNIALE++EE+++G+L+  YGD FIRGN
Sbjct: 13 SAFLGEIIGAPVTVKLNSGVVYRGELQSVDGYMNIALERSEEFVDGKLRRSYGDAFIRGN 72

Query: 68 NVLYISTQ 75
          NVLYIS Q
Sbjct: 73 NVLYISAQ 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.

Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) (taxid: 331117)

>sp|Q4WNI0|LSM6_ASPFU U6 snRNA-associated Sm-like protein LSm6 OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) GN=lsm6 PE=3 SV=2

 Score = 94.7 bits (234), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 44/68 (64%), Positives = 54/68 (79%)

Query: 8  SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGN 67
          S F+ +I G PV VKL SGV Y+G L  +DGYMNIALE++EE+++G+LK  YGD FIRGN
Sbjct: 13 SAFLGEIIGAPVTVKLNSGVVYKGELQSVDGYMNIALERSEEFVDGKLKRSYGDAFIRGN 72

Query: 68 NVLYISTQ 75
          NVLYIS Q
Sbjct: 73 NVLYISAQ 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.

Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (taxid: 330879)

>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 = 94.4 bits (233), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/71 (66%), Positives = 61/71 (85%)

Query: 6  SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIR 65
          S + F++ + G+ VVV+L+SGVDYRG+LSCLDGYMNIA+EQTEE +NG++ N+YGD FIR
Sbjct: 23 SPTDFLKGVVGKRVVVRLLSGVDYRGILSCLDGYMNIAMEQTEESVNGKVVNRYGDAFIR 82

Query: 66 GNNVLYISTQK 76
          GNNVLYIS  +
Sbjct: 83 GNNVLYISADE 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)

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	80
242021065	79	membrane-associated protein, putative [P	0.975	0.987	0.935	8e-36
110749924	79	PREDICTED: u6 snRNA-associated Sm-like p	0.975	0.987	0.923	2e-35
156550741	80	PREDICTED: U6 snRNA-associated Sm-like p	0.975	0.975	0.923	2e-35
332023213	608	U6 snRNA-associated Sm-like protein LSm6	0.975	0.128	0.910	2e-35
307195205	79	U6 snRNA-associated Sm-like protein LSm6	0.975	0.987	0.923	2e-35
357625163	79	putative membrane-associated protein [Da	0.975	0.987	0.923	3e-35
328697100	80	PREDICTED: u6 snRNA-associated Sm-like p	1.0	1.0	0.875	3e-35
307184080	79	U6 snRNA-associated Sm-like protein LSm6	0.975	0.987	0.910	5e-35
58387098	79	AGAP005314-PA [Anopheles gambiae str. PE	0.975	0.987	0.910	7e-35
91082305	79	PREDICTED: similar to AGAP005314-PA [Tri	0.975	0.987	0.897	2e-34

>gi|242021065|ref|XP_002430967.1| membrane-associated protein, putative [Pediculus humanus corporis] gi|212516187|gb|EEB18229.1| membrane-associated protein, putative [Pediculus humanus corporis]

 Score =  154 bits (388), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 73/78 (93%), Positives = 76/78 (97%)

Query: 1  MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG 60
          MSRKE+LSQFIQQIHGRPVVVKL SGVDYRGVL+CLDGYMNIALEQTEEY+NGQLKNKYG
Sbjct: 1  MSRKEALSQFIQQIHGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKYG 60

Query: 61 DTFIRGNNVLYISTQKRR 78
          D FIRGNNVLYISTQKRR
Sbjct: 61 DAFIRGNNVLYISTQKRR 78

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|110749924|ref|XP_001121733.1| PREDICTED: u6 snRNA-associated Sm-like protein LSm6-like [Apis mellifera] gi|350419231|ref|XP_003492114.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm6-like [Bombus impatiens] gi|380023576|ref|XP_003695594.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm6-like [Apis florea] gi|383861934|ref|XP_003706439.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm6-like [Megachile rotundata]

 Score =  152 bits (385), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 72/78 (92%), Positives = 76/78 (97%)

Query: 1  MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG 60
          MSRKE+LSQFIQQIHGRPVVVKL SGVDYRGVL+CLDGYMNIALEQTEEY+NGQLK+KYG
Sbjct: 1  MSRKEALSQFIQQIHGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKDKYG 60

Query: 61 DTFIRGNNVLYISTQKRR 78
          D FIRGNNVLYISTQKRR
Sbjct: 61 DAFIRGNNVLYISTQKRR 78

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156550741|ref|XP_001606104.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm6-like [Nasonia vitripennis]

 Score =  152 bits (384), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 72/78 (92%), Positives = 76/78 (97%)

Query: 1  MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG 60
          MSRKE+LSQFIQQIHGRPVVVKL SGVDYRGVL+CLDGYMNIALEQTEEY+NGQLK+KYG
Sbjct: 1  MSRKEALSQFIQQIHGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKDKYG 60

Query: 61 DTFIRGNNVLYISTQKRR 78
          D FIRGNNVLYISTQKRR
Sbjct: 61 DAFIRGNNVLYISTQKRR 78

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332023213|gb|EGI63469.1| U6 snRNA-associated Sm-like protein LSm6 [Acromyrmex echinatior]

 Score =  152 bits (384), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 71/78 (91%), Positives = 76/78 (97%)

Query: 1   MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG 60
           MSRKE+LSQFIQQIHGRPVVVKL SGVDYRGVL+C+DGYMNIALEQTEEY+NGQLK+KYG
Sbjct: 530 MSRKEALSQFIQQIHGRPVVVKLNSGVDYRGVLACIDGYMNIALEQTEEYVNGQLKDKYG 589

Query: 61  DTFIRGNNVLYISTQKRR 78
           D FIRGNNVLYISTQKRR
Sbjct: 590 DAFIRGNNVLYISTQKRR 607

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307195205|gb|EFN77189.1| U6 snRNA-associated Sm-like protein LSm6 [Harpegnathos saltator]

 Score =  152 bits (384), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 72/78 (92%), Positives = 76/78 (97%)

Query: 1  MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG 60
          MSRKE+LSQFIQQIHGRPVVVKL SGVDYRGVL+CLDGYMNIALEQTEEY+NGQLK+KYG
Sbjct: 1  MSRKEALSQFIQQIHGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKDKYG 60

Query: 61 DTFIRGNNVLYISTQKRR 78
          D FIRGNNVLYISTQKRR
Sbjct: 61 DAFIRGNNVLYISTQKRR 78

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357625163|gb|EHJ75691.1| putative membrane-associated protein [Danaus plexippus]

 Score =  152 bits (384), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 72/78 (92%), Positives = 75/78 (96%)

Query: 1  MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG 60
          MSRKE+LS FIQQIHGRPVVVKL SGVDYRGVL+CLDGYMNIALEQTEEY+NGQLKNKYG
Sbjct: 1  MSRKEALSSFIQQIHGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKYG 60

Query: 61 DTFIRGNNVLYISTQKRR 78
          D FIRGNNVLYISTQKRR
Sbjct: 61 DAFIRGNNVLYISTQKRR 78

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328697100|ref|XP_003240231.1| PREDICTED: u6 snRNA-associated Sm-like protein LSm6-like isoform 1 [Acyrthosiphon pisum] gi|328697102|ref|XP_003240232.1| PREDICTED: u6 snRNA-associated Sm-like protein LSm6-like isoform 2 [Acyrthosiphon pisum]

 Score =  152 bits (384), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 70/80 (87%), Positives = 79/80 (98%)

Query: 1  MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG 60
          MSRKE+L+QFIQQIHGRPVVVKL SGVDYRGV++C+DGYMNIALEQTEEYING+LKNK+G
Sbjct: 1  MSRKEALTQFIQQIHGRPVVVKLNSGVDYRGVMACIDGYMNIALEQTEEYINGELKNKFG 60

Query: 61 DTFIRGNNVLYISTQKRRGV 80
          D+FIRGNNVLYISTQKR+GV
Sbjct: 61 DSFIRGNNVLYISTQKRKGV 80

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307184080|gb|EFN70615.1| U6 snRNA-associated Sm-like protein LSm6 [Camponotus floridanus]

 Score =  151 bits (381), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 71/78 (91%), Positives = 76/78 (97%)

Query: 1  MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG 60
          MSRKE+LSQFIQQIHGRPVVVKL SGVDYRGVL+C+DGYMNIALEQTEEY+NGQLK+KYG
Sbjct: 1  MSRKEALSQFIQQIHGRPVVVKLNSGVDYRGVLACIDGYMNIALEQTEEYVNGQLKDKYG 60

Query: 61 DTFIRGNNVLYISTQKRR 78
          D FIRGNNVLYISTQKRR
Sbjct: 61 DAFIRGNNVLYISTQKRR 78

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|58387098|ref|XP_315329.2| AGAP005314-PA [Anopheles gambiae str. PEST] gi|170059581|ref|XP_001865425.1| Lsm6 protein [Culex quinquefasciatus] gi|55238130|gb|EAA11294.2| AGAP005314-PA [Anopheles gambiae str. PEST] gi|167878291|gb|EDS41674.1| Lsm6 protein [Culex quinquefasciatus] gi|312381097|gb|EFR26918.1| hypothetical protein AND_25803 [Anopheles darlingi] gi|403182446|gb|EJY57393.1| AAEL017161-PA [Aedes aegypti]

 Score =  150 bits (380), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 71/78 (91%), Positives = 75/78 (96%)

Query: 1  MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG 60
          MSRKE+LSQFI QIHGRPVVVKL SGVDYRGVL+CLDGYMNIAL+QTEEY+NGQLKNKYG
Sbjct: 1  MSRKEALSQFINQIHGRPVVVKLNSGVDYRGVLACLDGYMNIALDQTEEYVNGQLKNKYG 60

Query: 61 DTFIRGNNVLYISTQKRR 78
          D FIRGNNVLYISTQKRR
Sbjct: 61 DAFIRGNNVLYISTQKRR 78

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91082305|ref|XP_974175.1| PREDICTED: similar to AGAP005314-PA [Tribolium castaneum] gi|270007198|gb|EFA03646.1| hypothetical protein TcasGA2_TC013740 [Tribolium castaneum]

 Score =  149 bits (377), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 70/78 (89%), Positives = 74/78 (94%)

Query: 1  MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG 60
          MSRKE+LS FIQQIH RPVVVKL SGVDYRGVL+CLDGYMNIALEQTEEY+NGQLKNK+G
Sbjct: 1  MSRKEALSSFIQQIHARPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKFG 60

Query: 61 DTFIRGNNVLYISTQKRR 78
          D FIRGNNVLYISTQKRR
Sbjct: 61 DAFIRGNNVLYISTQKRR 78

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

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	80
FB|FBgn0034564	79	CG9344 [Drosophila melanogaste	0.975	0.987	0.884	2e-33
UNIPROTKB|P62312	80	LSM6 "U6 snRNA-associated Sm-l	0.95	0.95	0.855	8.8e-31
MGI|MGI:1925901	80	Lsm6 "LSM6 homolog, U6 small n	0.95	0.95	0.855	8.8e-31
ZFIN|ZDB-GENE-040625-50	80	lsm6 "LSM6 homolog, U6 small n	0.95	0.95	0.815	6.2e-30
WB|WBGene00003080	77	lsm-6 [Caenorhabditis elegans	0.962	1.0	0.714	4.5e-27
TAIR|locus:2080487	91	LSM6A "AT3G59810" [Arabidopsis	0.837	0.736	0.820	1.9e-26
TAIR|locus:2043969	91	LSM6B "AT2G43810" [Arabidopsis	0.862	0.758	0.768	4e-26
DICTYBASE|DDB_G0275719	88	lsm6 "putative U6 small nuclea	0.862	0.784	0.681	1.5e-21
POMBASE|SPAC2F3.17c	75	lsm6 "U6 snRNP-associated prot	0.85	0.906	0.632	2.4e-21
GENEDB_PFALCIPARUM|PF13_0142	77	PF13_0142 "u6 snRNA-associated	0.837	0.870	0.582	3.6e-18

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

 Score = 364 (133.2 bits), Expect = 2.0e-33, P = 2.0e-33
 Identities = 69/78 (88%), Positives = 73/78 (93%)

Query:     1 MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG 60
             MSRKE+LSQFI QIHGRPV VKL +GVDYRGVL+CLDGYMNI LEQTEEY+NGQLKNKYG
Sbjct:     1 MSRKEALSQFINQIHGRPVAVKLNNGVDYRGVLACLDGYMNICLEQTEEYVNGQLKNKYG 60

Query:    61 DTFIRGNNVLYISTQKRR 78
             D FIRGNNVLYISTQKRR
Sbjct:    61 DAFIRGNNVLYISTQKRR 78

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

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

 Score = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 65/76 (85%), Positives = 71/76 (93%)

Query:     3 RKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDT 62
             RK++ S F++QI GRPVVVKL SGVDYRGVL+CLDGYMNIALEQTEEY+NGQLKNKYGD 
Sbjct:     4 RKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKYGDA 63

Query:    63 FIRGNNVLYISTQKRR 78
             FIRGNNVLYISTQKRR
Sbjct:    64 FIRGNNVLYISTQKRR 79

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 = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 65/76 (85%), Positives = 71/76 (93%)

Query:     3 RKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDT 62
             RK++ S F++QI GRPVVVKL SGVDYRGVL+CLDGYMNIALEQTEEY+NGQLKNKYGD 
Sbjct:     4 RKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKYGDA 63

Query:    63 FIRGNNVLYISTQKRR 78
             FIRGNNVLYISTQKRR
Sbjct:    64 FIRGNNVLYISTQKRR 79

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 = 331 (121.6 bits), Expect = 6.2e-30, P = 6.2e-30
 Identities = 62/76 (81%), Positives = 71/76 (93%)

Query:     3 RKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDT 62
             RK++ S F++QI GRPVVVKL SGVDYRGVL+CLDGYMNIA+EQTEEY+NGQLKNKYGD 
Sbjct:     4 RKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIAVEQTEEYVNGQLKNKYGDA 63

Query:    63 FIRGNNVLYISTQKRR 78
             F+RGNNVLYISTQKR+
Sbjct:    64 FLRGNNVLYISTQKRK 79

GO:0003674 "molecular_function" evidence=ND

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

 Score = 304 (112.1 bits), Expect = 4.5e-27, P = 4.5e-27
 Identities = 55/77 (71%), Positives = 70/77 (90%)

Query:     1 MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG 60
             MS++++ ++F++++ G+PVVVKL SGVDYRG+L+CLDGYMNIALEQTEEY NGQL+NKYG
Sbjct:     1 MSKRQNPAEFLKKVIGKPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYSNGQLQNKYG 60

Query:    61 DTFIRGNNVLYISTQKR 77
             D FIRGNNVLYIST  +
Sbjct:    61 DAFIRGNNVLYISTSTK 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

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

 Score = 298 (110.0 bits), Expect = 1.9e-26, P = 1.9e-26
 Identities = 55/67 (82%), Positives = 61/67 (91%)

Query:     8 SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGN 67
             + F++ I GRPVVVKL SGVDYRG L+CLDGYMNIA+EQTEEY+NGQLKNKYGD FIRGN
Sbjct:    16 ADFLKSIRGRPVVVKLNSGVDYRGTLTCLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGN 75

Query:    68 NVLYIST 74
             NVLYIST
Sbjct:    76 NVLYIST 82

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISS

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

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

 Score = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 53/69 (76%), Positives = 62/69 (89%)

Query:     8 SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGN 67
             + F++ I G+PVVVKL SGVDYRG+L+CLDGYMNIA+EQTEEY+NGQLKN YGD F+RGN
Sbjct:    16 ADFLKSIRGKPVVVKLNSGVDYRGILTCLDGYMNIAMEQTEEYVNGQLKNTYGDAFVRGN 75

Query:    68 NVLYISTQK 76
             NVLYIST K
Sbjct:    76 NVLYISTTK 84

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISS

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

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

 Score = 252 (93.8 bits), Expect = 1.5e-21, P = 1.5e-21
 Identities = 47/69 (68%), Positives = 56/69 (81%)

Query:    10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNV 69
             F +   GRPVVVKL +GV+YRG+L  +DG MNI +EQTEEY+NGQLK KYGD F+RGNNV
Sbjct:    20 FFKMCIGRPVVVKLNNGVEYRGILEVVDGNMNIVMEQTEEYLNGQLKTKYGDCFLRGNNV 79

Query:    70 LYISTQKRR 78
             LYIS Q R+
Sbjct:    80 LYISAQPRK 88

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 = 250 (93.1 bits), Expect = 2.4e-21, P = 2.4e-21
 Identities = 43/68 (63%), Positives = 59/68 (86%)

Query:     6 SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIR 65
             S ++F+ ++ G+ V+++L SGVDY+G+LSCLDGYMN+ALE+TEEY+NG+  N YGD FIR
Sbjct:     4 SPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIR 63

Query:    66 GNNVLYIS 73
             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 = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 39/67 (58%), Positives = 52/67 (77%)

Query:     6 SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIR 65
             S   F++ + GR V+V+L +G DY+G+L+CLD  MN+ALEQTEEY +G+L +KY D FIR
Sbjct:     5 SPKDFVESLKGRAVIVRLNNGTDYKGILACLDERMNVALEQTEEYYDGELTDKYNDAFIR 64

Query:    66 GNNVLYI 72
             GNNV YI
Sbjct:    65 GNNVFYI 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	0.5138	0.9	0.8470	yes	N/A
P57670	RUXX_THEAC	No assigned EC number	0.3809	0.7875	0.7590	yes	N/A
P0CR24	LSM6_CRYNJ	No assigned EC number	0.5797	0.8625	0.7840	yes	N/A
Q465S1	RUXX_METBF	No assigned EC number	0.4035	0.7125	0.7916	yes	N/A
A5DRQ6	LSM6_LODEL	No assigned EC number	0.5256	0.9125	0.9125	N/A	N/A
O26745	RUXX_METTH	No assigned EC number	0.4035	0.7125	0.7037	yes	N/A
Q06406	LSM6_YEAST	No assigned EC number	0.4109	0.8625	0.8023	yes	N/A
A4RQ29	LSM6_MAGO7	No assigned EC number	0.5671	0.8375	0.8072	N/A	N/A
Q552U1	LSM6_DICDI	No assigned EC number	0.6811	0.8625	0.7840	yes	N/A
A1DM27	LSM6_NEOFI	No assigned EC number	0.6470	0.85	0.85	N/A	N/A
O29386	RUXX_ARCFU	No assigned EC number	0.3898	0.7375	0.7662	yes	N/A
Q2HAN0	LSM6_CHAGB	No assigned EC number	0.6176	0.85	0.8292	N/A	N/A
Q4WNI0	LSM6_ASPFU	No assigned EC number	0.6470	0.85	0.85	yes	N/A
Q9UUI1	LSM6_SCHPO	No assigned EC number	0.6231	0.8625	0.92	yes	N/A
Q97BU5	RUXX_THEVO	No assigned EC number	0.35	0.75	0.7228	yes	N/A
Q75BR7	LSM6_ASHGO	No assigned EC number	0.4444	0.85	0.8	yes	N/A
Q12U30	RUXX_METBU	No assigned EC number	0.4107	0.7	0.7777	yes	N/A
Q8TL47	RUXX_METAC	No assigned EC number	0.3859	0.7125	0.7916	yes	N/A
A7UXE4	LSM6_NEUCR	No assigned EC number	0.5810	0.925	0.9024	N/A	N/A
Q6CPS7	LSM6_KLULA	No assigned EC number	0.3974	0.925	0.925	yes	N/A
Q1DRN0	LSM6_COCIM	No assigned EC number	0.6029	0.85	0.85	N/A	N/A
C6A1T2	RUXX_THESM	No assigned EC number	0.4137	0.725	0.7631	yes	N/A
A1CE19	LSM6_ASPCL	No assigned EC number	0.6119	0.8375	0.8589	N/A	N/A
Q0W8R9	RUXX_UNCMA	No assigned EC number	0.3684	0.7125	0.7916	yes	N/A
Q8PZZ9	RUXX_METMA	No assigned EC number	0.3859	0.7125	0.7916	yes	N/A
A6R363	LSM6_AJECN	No assigned EC number	0.5945	0.925	0.925	N/A	N/A
P62312	LSM6_HUMAN	No assigned EC number	0.8552	0.95	0.95	yes	N/A
P62313	LSM6_MOUSE	No assigned EC number	0.8552	0.95	0.95	yes	N/A
O74016	RUXX_PYRHO	No assigned EC number	0.3833	0.75	0.8	yes	N/A
Q4PG71	LSM6_USTMA	No assigned EC number	0.5921	0.95	0.8941	N/A	N/A
Q6FYB6	LSM6_CANGA	No assigned EC number	0.4675	0.9125	0.9240	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	80
cd01726	68	cd01726, LSm6, Like-Sm protein 6	5e-38
cd01722	69	cd01722, Sm_F, Sm protein F	6e-22
pfam01423	66	pfam01423, LSM, LSM domain	1e-16
smart00651	67	smart00651, Sm, snRNP Sm proteins	2e-16
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	3e-15
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	3e-14
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	6e-12
cd00600	63	cd00600, Sm_like, Sm and related proteins	2e-10
cd01723	76	cd01723, LSm4, Like-Sm protein 4	4e-06
cd01733	78	cd01733, LSm10, Like-Sm protein 10	2e-05
cd01719	70	cd01719, Sm_G, Sm protein G	3e-05
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	5e-05
cd01725	89	cd01725, LSm2, Like-Sm protein 2	0.002
cd01728	74	cd01728, LSm1, Like-Sm protein 1	0.002

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

 Score =  120 bits (304), Expect = 5e-38
 Identities = 48/66 (72%), Positives = 59/66 (89%)

Query: 8  SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGN 67
          S+F+++I G+PVVVKL +GV+YRGVL+CLDGYMN+ LE TEEY++GQL  KYGD FIRGN
Sbjct: 3  SKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYGDAFIRGN 62

Query: 68 NVLYIS 73
          NVLYIS
Sbjct: 63 NVLYIS 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 = 79.9 bits (198), Expect = 6e-22
 Identities = 31/64 (48%), Positives = 43/64 (67%)

Query: 9  QFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNN 68
           F+  + G+PV+VKL  G++Y+G L  +D YMN+ L  TEEYI+G+     G+  IR NN
Sbjct: 4  PFLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKFTGNLGEVLIRCNN 63

Query: 69 VLYI 72
          VLYI
Sbjct: 64 VLYI 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|201787 pfam01423, LSM, LSM domain

 Score = 66.4 bits (163), Expect = 1e-16
 Identities = 27/65 (41%), Positives = 40/65 (61%)

Query: 9  QFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNN 68
          +F+Q++ G+ V V+L +G + RG L   D +MN+ L+  EE I     NK G   IRGNN
Sbjct: 1  KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLGLVLIRGNN 60

Query: 69 VLYIS 73
          ++ 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|197820 smart00651, Sm, snRNP Sm proteins

 Score = 66.0 bits (162), Expect = 2e-16
 Identities = 29/65 (44%), Positives = 44/65 (67%), Gaps = 1/65 (1%)

Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYIN-GQLKNKYGDTFIRGNN 68
          F++++ G+ V+V+L +G +YRG L   D +MN+ LE  EE +  G+ K K G  FIRGNN
Sbjct: 2  FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNN 61

Query: 69 VLYIS 73
          ++YI 
Sbjct: 62 IVYII 66

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

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

 Score = 63.4 bits (155), Expect = 3e-15
 Identities = 25/59 (42%), Positives = 36/59 (61%)

Query: 15 HGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIS 73
            + V+VKL  G + RGVL   D ++N+ LE  EE I G+   K G   +RG+NV++IS
Sbjct: 10 LNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGTVLVRGDNVVFIS 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|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional

 Score = 60.8 bits (148), Expect = 3e-14
 Identities = 24/57 (42%), Positives = 37/57 (64%)

Query: 17 RPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIS 73
           PV+V+L  G ++RG L   D +MN+ L+  EE  +G++  K G   IRG+NV+Y+S
Sbjct: 15 SPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVS 71

Length = 72

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

 Score = 55.0 bits (133), Expect = 6e-12
 Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 4/73 (5%)

Query: 5  ESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQ---LKNKYGD 61
               F++++  + V+VKL +G +YRG L   D YMN+ L+  EE I+        + G 
Sbjct: 6  PLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGG 65

Query: 62 T-FIRGNNVLYIS 73
             IRG+N++ IS
Sbjct: 66 EVLIRGDNIVLIS 78

Length = 79

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

 Score = 50.3 bits (121), Expect = 2e-10
 Identities = 19/58 (32%), Positives = 26/58 (44%)

Query: 16 GRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIS 73
          G+ V V+L  G    G L   D YMN+ L+   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 = 40.3 bits (95), Expect = 4e-06
 Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 15 HGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQ-TEEYINGQLKNKYGDTFIRGNNVLYIS 73
           G PV+V+L +G  Y G L   D +MNI L+       +G    K  + +IRGN + Y+ 
Sbjct: 10 QGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKMPECYIRGNTIKYLR 69

Query: 74 TQKR 77
              
Sbjct: 70 LPDE 73

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 = 38.3 bits (90), Expect = 2e-05
 Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 2/68 (2%)

Query: 6  SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQ-TEEYINGQLKNKYGDTFI 64
          SL   +Q + GR   V+L +    RG++  +DG+MNI L   T     G+    + + F+
Sbjct: 9  SLVCLLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQH-HFDEFFV 67

Query: 65 RGNNVLYI 72
          +G N+ Y+
Sbjct: 68 QGRNIRYV 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 = 37.9 bits (89), Expect = 3e-05
 Identities = 15/42 (35%), Positives = 22/42 (52%)

Query: 31 GVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYI 72
          GVL   D +MN+ L+   E +    K   G   IRGN+++ I
Sbjct: 25 GVLRGFDPFMNLVLDDAVEEVGDGEKTPIGMVVIRGNSIIMI 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 = 37.1 bits (86), Expect = 5e-05
 Identities = 16/43 (37%), Positives = 22/43 (51%)

Query: 31 GVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIS 73
          G L  +D YMN+ L  T E +  +     G   +RGNN+L I 
Sbjct: 26 GRLVAVDDYMNLHLTDTMECVGEEKVRSLGTVVLRGNNILLIQ 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 = 33.7 bits (78), Expect = 0.002
 Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 10/69 (14%)

Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALE-----QTEEYIN-GQLKNKYGDTF 63
          F + + G+ V V+L + +   G L  +D Y+NI L        E+Y +   +KN     F
Sbjct: 5  FFKTLVGKEVTVELKNDLSITGTLHSVDQYLNIKLTNISVNDPEKYPHLLSVKN----CF 60

Query: 64 IRGNNVLYI 72
          IRG+ V Y+
Sbjct: 61 IRGSVVRYV 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|212475 cd01728, LSm1, Like-Sm protein 1

 Score = 33.3 bits (77), Expect = 0.002
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 8/71 (11%)

Query: 7  LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGD----- 61
           +   +++  + ++V L  G    G+L   D + N+ LE T E I   + N+YGD     
Sbjct: 4  TASLEEEL-DKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERII--VGNQYGDIPRGL 60

Query: 62 TFIRGNNVLYI 72
            IRG NV+ +
Sbjct: 61 FIIRGENVVLL 71

The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. Accumulation of uridylated RNAs in an lsm1 mutant suggests an involvement of the LSm1-7 complex in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm1-7, together with Pat1, are also called the decapping activator. 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 = 74

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	80
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.93
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.93
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.92
cd01721	70	Sm_D3 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	99.9
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.9
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.89
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.88
KOG1783|consensus	77		99.88
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.88
KOG3482|consensus	79		99.88
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.88
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.87
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.87
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.87
KOG1780|consensus	77		99.86
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.86
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.83
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.83
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.79
KOG3460|consensus	91		99.73
KOG3293|consensus	134		99.73
KOG1775|consensus	84		99.67
KOG1781|consensus	108		99.63
KOG3448|consensus	96		99.61
KOG3172|consensus	119		99.52
KOG3168|consensus	177		99.47
KOG1782|consensus	129		99.46
KOG1774|consensus	88		99.44
KOG3428|consensus	109		99.41
KOG1784|consensus	96		99.41
KOG3459|consensus	114		98.79
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	98.24
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	98.19
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	97.35
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	97.06
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	96.93
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	96.89
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	96.87
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	96.48
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	96.18
COG1923	77	Hfq Uncharacterized host factor I protein [General	96.12
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	95.66
PRK14091	165	RNA-binding protein Hfq; Provisional	95.64
PRK14638	150	hypothetical protein; Provisional	95.04
PRK14639	140	hypothetical protein; Provisional	94.92
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	94.87
PRK02001	152	hypothetical protein; Validated	94.45
PRK14091	165	RNA-binding protein Hfq; Provisional	94.24
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	93.72
PRK14644	136	hypothetical protein; Provisional	92.55
PRK14642	197	hypothetical protein; Provisional	92.39
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	91.76
PRK14640	152	hypothetical protein; Provisional	91.52
PRK14633	150	hypothetical protein; Provisional	91.41
KOG1073|consensus	361		91.41
PRK14645	154	hypothetical protein; Provisional	91.12
COG0779	153	Uncharacterized protein conserved in bacteria [Fun	90.8
PRK14643	164	hypothetical protein; Provisional	90.75
PRK00092	154	ribosome maturation protein RimP; Reviewed	90.49
PRK14636	176	hypothetical protein; Provisional	90.3
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	90.04
PRK14632	172	hypothetical protein; Provisional	90.02
PRK14634	155	hypothetical protein; Provisional	89.79
PRK14646	155	hypothetical protein; Provisional	89.37
PRK14647	159	hypothetical protein; Provisional	88.71
PRK14637	151	hypothetical protein; Provisional	87.95
PRK06955	300	biotin--protein ligase; Provisional	87.87
PRK14631	174	hypothetical protein; Provisional	87.18
PRK14641	173	hypothetical protein; Provisional	86.04
PRK13325	592	bifunctional biotin--[acetyl-CoA-carboxylase] liga	86.03
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	83.63
PRK14630	143	hypothetical protein; Provisional	81.51

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.93  E-value=1e-26  Score=136.16  Aligned_cols=70  Identities=34%  Similarity=0.610  Sum_probs=65.4

Q ss_pred             CChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEe
Q psy10835          5 ESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus         5 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~   74 (80)
                      ..|+++|+++++++|.|+|+||++|+|+|.+||+|||++|+||.|..+++..+.+|.++|||++|++|.+
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            5899999999999999999999999999999999999999999997666667789999999999999963

>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=2.1e-26  Score=133.13  Aligned_cols=67  Identities=84%  Similarity=1.347  Sum_probs=62.9

Q ss_pred             hHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEE
Q psy10835          7 LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIS   73 (80)
Q Consensus         7 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~   73 (80)
                      |+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||++..+++....++.++|||++|++|+
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            8899999999999999999999999999999999999999998766766778999999999999984

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.

>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=5.6e-26  Score=131.69  Aligned_cols=68  Identities=46%  Similarity=0.873  Sum_probs=63.4

Q ss_pred             ChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEE
Q psy10835          6 SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIS   73 (80)
Q Consensus         6 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~   73 (80)
                      +|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||+|..++.....+|.++|||++|++|+
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            59999999999999999999999999999999999999999998766656678999999999999984

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.

>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=6.1e-26  Score=132.29  Aligned_cols=70  Identities=21%  Similarity=0.345  Sum_probs=63.4

Q ss_pred             hHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeec
Q psy10835          7 LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus         7 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      |+++|+++.|++|+|+|+||.+|+|+|.++|+|||++|+||.+...+.+...++.++|||++|+||++||
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            7899999999999999999999999999999999999999987533323467899999999999999986

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.

>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=1.1e-25  Score=130.29  Aligned_cols=68  Identities=41%  Similarity=0.647  Sum_probs=63.0

Q ss_pred             hHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEe
Q psy10835          7 LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus         7 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~   74 (80)
                      |+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||+|...+.....+|.++|||++|++|++
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            78999999999999999999999999999999999999999997555456789999999999999974

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=3.3e-25  Score=130.90  Aligned_cols=72  Identities=26%  Similarity=0.442  Sum_probs=65.9

Q ss_pred             ChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhh-hccEeeccccCeEEecCcEEEEEeecc
Q psy10835          6 SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEY-INGQLKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         6 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~-~~~~~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      .|+++|+++.|++|.|+|+||++|+|+|.+||+|||++|+||++. .+|+....++.++|||++|+||++|++
T Consensus         1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~   73 (76)
T cd01723           1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDE   73 (76)
T ss_pred             CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHH
Confidence            489999999999999999999999999999999999999999886 456555668999999999999999875

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=2.3e-25  Score=130.59  Aligned_cols=71  Identities=25%  Similarity=0.432  Sum_probs=64.9

Q ss_pred             hHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeecc
Q psy10835          7 LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         7 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      |.++|+++++|+|.|+|++|++|+|+|.|||+||||+|+||.|+.++...+.+|.++|||++|.+|++.++
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            56789999999999999999999999999999999999999997656556789999999999999998764

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=8.3e-25  Score=129.49  Aligned_cols=70  Identities=24%  Similarity=0.430  Sum_probs=64.2

Q ss_pred             CChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhh---ccEeeccccCeEEecCcEEEEEe
Q psy10835          5 ESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI---NGQLKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus         5 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~---~~~~~~~~g~v~irG~~I~~I~~   74 (80)
                      ..|+++|+++++++|+|++++|+++.|+|.|||+|||++|+||.|+.   +++....+|.++|||++|.+|++
T Consensus         2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p   74 (76)
T cd01732           2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVP   74 (76)
T ss_pred             cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEEC
Confidence            46999999999999999999999999999999999999999999864   44455789999999999999986

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=99.90  E-value=2.3e-24  Score=131.09  Aligned_cols=72  Identities=24%  Similarity=0.387  Sum_probs=66.4

Q ss_pred             ChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeecc
Q psy10835          6 SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         6 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      .|..||+++.|++|+|+|+||.+|+|+|.++|+|||++|+||++...++....++.++|||++|+||++|+.
T Consensus         1 ~~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lPd~   72 (90)
T cd01724           1 KLVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILPDS   72 (90)
T ss_pred             CHhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcCCc
Confidence            367899999999999999999999999999999999999999987666566789999999999999999975

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=4.3e-24  Score=126.93  Aligned_cols=72  Identities=21%  Similarity=0.398  Sum_probs=65.2

Q ss_pred             CCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEee
Q psy10835          4 KESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQ   75 (80)
Q Consensus         4 ~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~   75 (80)
                      ...+..+|+++.|++|+|+||||.+|+|+|.++|+|||++|+||++...++....++.++|||++|+||++|
T Consensus         7 ~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~lP   78 (78)
T cd01733           7 ENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVHIP   78 (78)
T ss_pred             hchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEEcC
Confidence            456788999999999999999999999999999999999999999875555555789999999999999987

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=99.89  E-value=7.1e-24  Score=126.78  Aligned_cols=69  Identities=29%  Similarity=0.384  Sum_probs=61.7

Q ss_pred             ChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhcc-------------EeeccccCeEEecCcEEEE
Q psy10835          6 SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYING-------------QLKNKYGDTFIRGNNVLYI   72 (80)
Q Consensus         6 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~-------------~~~~~~g~v~irG~~I~~I   72 (80)
                      .|+++|+..++|+|.|+|+||++|.|+|.|||+||||+|+||.|...+             +..+.+|.++|||++|++|
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            389999999999999999999999999999999999999999996422             1356889999999999998


Q ss_pred             Ee
Q psy10835         73 ST   74 (80)
Q Consensus        73 ~~   74 (80)
                      ++
T Consensus        81 ~~   82 (82)
T cd01730          81 SP   82 (82)
T ss_pred             CC
Confidence            63

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=99.88  E-value=2e-23  Score=123.81  Aligned_cols=72  Identities=36%  Similarity=0.668  Sum_probs=63.7

Q ss_pred             CCCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhh--ccEe-ecccc-CeEEecCcEEEEEe
Q psy10835          3 RKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI--NGQL-KNKYG-DTFIRGNNVLYIST   74 (80)
Q Consensus         3 ~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~--~~~~-~~~~g-~v~irG~~I~~I~~   74 (80)
                      ....|+++|+++++++|.|+|+||++|+|+|.|||+|||++|+||+|..  +++. ...++ .++|||++|.+|.+
T Consensus         4 ~~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~   79 (79)
T COG1958           4 LGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP   79 (79)
T ss_pred             ccCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence            4567999999999999999999999999999999999999999999975  5554 34555 99999999999863

>KOG1783|consensus

Probab=99.88  E-value=4.8e-23  Score=120.03  Aligned_cols=76  Identities=76%  Similarity=1.170  Sum_probs=73.4

Q ss_pred             CCCCCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeec
Q psy10835          1 MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus         1 m~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      ||+...|.+||++.+||+|.|+|.+|..|+|+|.++|.||||-|+.++|+.+|+..+.++..||||++|.||+..+
T Consensus         1 ~s~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygdaFirGnnVlyIs~~~   76 (77)
T KOG1783|consen    1 MSEGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGDAFIRGNNVLYISTQK   76 (77)
T ss_pred             CCcccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccceeeccccEEEEEecc
Confidence            7888999999999999999999999999999999999999999999999999998999999999999999999875

>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=99.88  E-value=3.2e-23  Score=123.90  Aligned_cols=68  Identities=25%  Similarity=0.422  Sum_probs=60.4

Q ss_pred             HHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhcc--------EeeccccCeEEecCcEEEEEeec
Q psy10835          9 QFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYING--------QLKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus         9 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~--------~~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      ..|+++++|+|.|+|+||++|.|+|.|||+||||+|++|.|+..+        +..+.+|.++|||++|.+|++.+
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            359999999999999999999999999999999999999997432        23567899999999999998764

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.

>KOG3482|consensus

Probab=99.88  E-value=9.3e-23  Score=118.84  Aligned_cols=74  Identities=41%  Similarity=0.734  Sum_probs=69.9

Q ss_pred             CCCCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEee
Q psy10835          2 SRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQ   75 (80)
Q Consensus         2 ~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~   75 (80)
                      ..|.+|.+||+.+.||+|.|+||.|.+|.|+|.+.|.|||+.|.+|+|+.+|.....+|+++||++||.+|.-.
T Consensus         4 ~~PvNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEilIRCNNvlyi~gv   77 (79)
T KOG3482|consen    4 KQPVNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEILIRCNNVLYIRGV   77 (79)
T ss_pred             cccCCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEEEEeccEEEEecC
Confidence            36889999999999999999999999999999999999999999999999998888999999999999999643

>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=4.3e-23  Score=123.28  Aligned_cols=71  Identities=27%  Similarity=0.428  Sum_probs=62.7

Q ss_pred             hHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccE--eeccccCeEEecCcEEEEEeecc
Q psy10835          7 LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQ--LKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         7 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~--~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      |+.||+++.|++|+|+|+||.+|+|+|.++|+|||++|+||++...+.  ....++.++|||++|+||++|++
T Consensus         2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~   74 (81)
T cd01725           2 FFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPAD   74 (81)
T ss_pred             hhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChh
Confidence            789999999999999999999999999999999999999998753221  23456899999999999999975

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.

>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=99.87  E-value=8.7e-23  Score=123.58  Aligned_cols=70  Identities=17%  Similarity=0.282  Sum_probs=61.7

Q ss_pred             ChHHHHHhhh--CCceEEEecCCcccceeeeeecccchhhhhhhhhhhcc-------------EeeccccCeEEecCcEE
Q psy10835          6 SLSQFIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYING-------------QLKNKYGDTFIRGNNVL   70 (80)
Q Consensus         6 ~p~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~-------------~~~~~~g~v~irG~~I~   70 (80)
                      .|+++|...+  +++|.|+|++|+++.|+|.|||+||||+|+||.|...+             ...+.+|.+||||++|+
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  89999999999999999999999999999999985322             12456899999999999


Q ss_pred             EEEee
Q psy10835         71 YISTQ   75 (80)
Q Consensus        71 ~I~~~   75 (80)
                      +|+..
T Consensus        82 ~Is~~   86 (87)
T cd01720          82 LVLRN   86 (87)
T ss_pred             EEecC
Confidence            99864

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.

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

Probab=99.87  E-value=7.4e-23  Score=117.29  Aligned_cols=66  Identities=41%  Similarity=0.689  Sum_probs=61.0

Q ss_pred             HHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccE-eeccccCeEEecCcEEEEEe
Q psy10835          9 QFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQ-LKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus         9 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~-~~~~~g~v~irG~~I~~I~~   74 (80)
                      .+|++++|++|+|+|+||++|+|+|.+||+|||++|+||.+...+. +.+.++.++|||++|++|++
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            3799999999999999999999999999999999999999976554 67889999999999999985

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=99.87  E-value=9.2e-23  Score=116.77  Aligned_cols=65  Identities=43%  Similarity=0.796  Sum_probs=59.8

Q ss_pred             HHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhcc-EeeccccCeEEecCcEEEEEe
Q psy10835         10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYING-QLKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus        10 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~-~~~~~~g~v~irG~~I~~I~~   74 (80)
                      +|++++|++|+|+|+||+++.|+|.+||+|||++|+||++...+ .....++.++|||++|++|++
T Consensus         2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651        2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence            68999999999999999999999999999999999999997544 456789999999999999974

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

>KOG1780|consensus

Probab=99.86  E-value=3.1e-22  Score=116.91  Aligned_cols=77  Identities=31%  Similarity=0.468  Sum_probs=69.6

Q ss_pred             CCCCCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeecccC
Q psy10835          1 MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKRRG   79 (80)
Q Consensus         1 m~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~~~~   79 (80)
                      ||++.-|  .|++|++|++.++|..|+...|+|.|||.|||++|++++|....+.+..++.++|||++|+.+...++-|
T Consensus         1 Msksg~P--eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~eaL~~~g   77 (77)
T KOG1780|consen    1 MSKSGHP--ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMVEALERVG   77 (77)
T ss_pred             CCcccCc--hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEeccEEEEEeeccccC
Confidence            8999899  7999999999999999999999999999999999999999754444578999999999999999887643

>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=99.86  E-value=2.3e-22  Score=119.80  Aligned_cols=69  Identities=23%  Similarity=0.402  Sum_probs=61.5

Q ss_pred             ChHHHHHhhhCC--ceEEEec--CCcccceeeeeecccchhhhhhhhhhhc-cEeeccccCeEEecCcEEEEEe
Q psy10835          6 SLSQFIQQIHGR--PVVVKLV--SGVDYRGVLSCLDGYMNIALEQTEEYIN-GQLKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus         6 ~p~~~L~~~~~k--~V~V~L~--~g~~~~G~L~~~D~~mNivL~~~~~~~~-~~~~~~~g~v~irG~~I~~I~~   74 (80)
                      .|++.+.+++++  +|.|+++  +|+++.|+|.|||+|||++|+||+|+.. ++....+|.++|||++|.+|++
T Consensus         6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~p   79 (79)
T cd01718           6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQN   79 (79)
T ss_pred             CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEcC
Confidence            689999999999  6778887  8999999999999999999999999754 4456789999999999999974

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.

>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=99.85  E-value=7.3e-22  Score=117.22  Aligned_cols=65  Identities=25%  Similarity=0.403  Sum_probs=57.9

Q ss_pred             HHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhcc----------EeeccccCeEEecCcEEEEEe
Q psy10835         10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYING----------QLKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus        10 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~----------~~~~~~g~v~irG~~I~~I~~   74 (80)
                      -|.++++++|.|.|+||+.+.|+|.|||+||||+|+||.|+...          ...+.+|.++|||++|++|+.
T Consensus         4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v   78 (79)
T cd01717           4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV   78 (79)
T ss_pred             hhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence            48899999999999999999999999999999999999995321          235679999999999999975

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.

>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=99.85  E-value=1.2e-21  Score=115.11  Aligned_cols=68  Identities=24%  Similarity=0.322  Sum_probs=60.4

Q ss_pred             HHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhc----cEeeccccCeEEecCcEEEEEeec
Q psy10835          9 QFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYIN----GQLKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus         9 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~----~~~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      +.|+++++++|.|.|+||+.|.|+|.|||+|||++|++|.|+..    +.....+|.+++||++|.+|++.+
T Consensus         2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d   73 (74)
T cd01727           2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEID   73 (74)
T ss_pred             hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccC
Confidence            46999999999999999999999999999999999999998632    323567899999999999999865

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.

>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=99.84  E-value=1.8e-21  Score=114.68  Aligned_cols=68  Identities=29%  Similarity=0.372  Sum_probs=59.5

Q ss_pred             hHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhh-ccE--eeccccCeEEecCcEEEEEe
Q psy10835          7 LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI-NGQ--LKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus         7 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~-~~~--~~~~~g~v~irG~~I~~I~~   74 (80)
                      +...|+++++|+|.|.|+||++|.|+|.|||+|||++|+||.|.. .++  ..+.+|.++|||++|.+|..
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            456799999999999999999999999999999999999998863 221  24678999999999999975

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=99.83  E-value=1.8e-21  Score=109.95  Aligned_cols=63  Identities=37%  Similarity=0.590  Sum_probs=57.1

Q ss_pred             HHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEE
Q psy10835         11 IQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIS   73 (80)
Q Consensus        11 L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~   73 (80)
                      |++++|++|+|+|+||+.|.|+|.+||+|||++|+||.+...+.....++.++|||++|++|.
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            578899999999999999999999999999999999998754445678999999999999984

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=5.1e-21  Score=113.02  Aligned_cols=66  Identities=26%  Similarity=0.422  Sum_probs=59.6

Q ss_pred             HHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhcc------EeeccccCeEEecCcEEEEEe
Q psy10835          9 QFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYING------QLKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus         9 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~------~~~~~~g~v~irG~~I~~I~~   74 (80)
                      +.|+++++++|+|+|+||+.|.|+|.|||++|||+|+||.|+...      ...+.+|.++|||++|..|+.
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            468999999999999999999999999999999999999997422      346789999999999999985

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=99.79  E-value=8.1e-20  Score=110.98  Aligned_cols=71  Identities=23%  Similarity=0.383  Sum_probs=60.1

Q ss_pred             ChHHHHHhhhCCc--eEEEecC--Ccccceeeeeecccchhhhhhhhhhhc-cEeeccccCeEEecCcEEEEEeec
Q psy10835          6 SLSQFIQQIHGRP--VVVKLVS--GVDYRGVLSCLDGYMNIALEQTEEYIN-GQLKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus         6 ~p~~~L~~~~~k~--V~V~L~~--g~~~~G~L~~~D~~mNivL~~~~~~~~-~~~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      .|+..+.+++.++  |.|++.+  ++++.|+|.|||+|||++|+||+|+.. ++....+|.++|||++|.+|++.+
T Consensus        14 ~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~~~   89 (89)
T PTZ00138         14 QPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMAAK   89 (89)
T ss_pred             CCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEcCC
Confidence            6899999999766  6667767  488999999999999999999999743 344578999999999999998753

>KOG3460|consensus

Probab=99.73  E-value=1.4e-18  Score=103.60  Aligned_cols=76  Identities=29%  Similarity=0.366  Sum_probs=66.1

Q ss_pred             CCCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhh---cc----------EeeccccCeEEecCcE
Q psy10835          3 RKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI---NG----------QLKNKYGDTFIRGNNV   69 (80)
Q Consensus         3 ~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~---~~----------~~~~~~g~v~irG~~I   69 (80)
                      +...|+++|+-+++.+|.|+++++++++|+|.+||+|+|++|.+++|..   ++          +..+.++.+|+||++|
T Consensus         2 ~v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~V   81 (91)
T KOG3460|consen    2 TVEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGV   81 (91)
T ss_pred             cccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeE
Confidence            4467999999999999999999999999999999999999999999852   22          1245678999999999


Q ss_pred             EEEEeeccc
Q psy10835         70 LYISTQKRR   78 (80)
Q Consensus        70 ~~I~~~~~~   78 (80)
                      .+|++|-+.
T Consensus        82 ilvspp~~~   90 (91)
T KOG3460|consen   82 ILVSPPLRL   90 (91)
T ss_pred             EEEcCcccC
Confidence            999998654

>KOG3293|consensus

Probab=99.73  E-value=2.6e-18  Score=108.92  Aligned_cols=72  Identities=22%  Similarity=0.416  Sum_probs=67.1

Q ss_pred             ChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhh-hccEeeccccCeEEecCcEEEEEeecc
Q psy10835          6 SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEY-INGQLKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         6 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~-~~~~~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      .|+.+|....++++.|+||||.+|.|.|+.||.+|||.|+++++. .+|.+...+++++|||++|.|+.+++.
T Consensus         2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~   74 (134)
T KOG3293|consen    2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDE   74 (134)
T ss_pred             cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHH
Confidence            599999999999999999999999999999999999999999986 466778889999999999999998863

>KOG1775|consensus

Probab=99.67  E-value=1.1e-16  Score=94.12  Aligned_cols=73  Identities=22%  Similarity=0.404  Sum_probs=65.6

Q ss_pred             CCCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhh---hccEeeccccCeEEecCcEEEEEee
Q psy10835          3 RKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEY---INGQLKNKYGDTFIRGNNVLYISTQ   75 (80)
Q Consensus         3 ~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~---~~~~~~~~~g~v~irG~~I~~I~~~   75 (80)
                      -...|++++.+.+|++++|.+++.+++.|+|.|||+|.|++|+|++|+   .+|+...+.+++++.|++|..+.+.
T Consensus         4 ~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPG   79 (84)
T KOG1775|consen    4 STLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPG   79 (84)
T ss_pred             hhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecC
Confidence            346799999999999999999999999999999999999999999997   3455677899999999999987653

>KOG1781|consensus

Probab=99.63  E-value=2.7e-16  Score=96.38  Aligned_cols=71  Identities=24%  Similarity=0.393  Sum_probs=62.5

Q ss_pred             HHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhh-c-------cEeeccccCeEEecCcEEEEEeeccc
Q psy10835          8 SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI-N-------GQLKNKYGDTFIRGNNVLYISTQKRR   78 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~-~-------~~~~~~~g~v~irG~~I~~I~~~~~~   78 (80)
                      .=.|.+|++|+|+|++..|++..|+|.|||+.||+||+++.|+. +       +..++++|.+++||..++.|++.+-+
T Consensus        19 ilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~   97 (108)
T KOG1781|consen   19 ILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGS   97 (108)
T ss_pred             HhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcch
Confidence            34799999999999999999999999999999999999999973 2       12458999999999999999987643

>KOG3448|consensus

Probab=99.61  E-value=4.2e-16  Score=93.97  Aligned_cols=71  Identities=27%  Similarity=0.433  Sum_probs=61.9

Q ss_pred             hHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccE--eeccccCeEEecCcEEEEEeecc
Q psy10835          7 LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQ--LKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         7 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~--~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      ..+|++.++|+.|.|+|||+-++.|+|.+.|+|+|+.|.|.......+  ...++..+||||+.|+||.++++
T Consensus         3 FysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd   75 (96)
T KOG3448|consen    3 FYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKD   75 (96)
T ss_pred             hHHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChh
Confidence            468999999999999999999999999999999999999998754322  23456789999999999999875

>KOG3172|consensus

Probab=99.52  E-value=3.7e-15  Score=92.70  Aligned_cols=73  Identities=21%  Similarity=0.309  Sum_probs=65.9

Q ss_pred             CCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeec
Q psy10835          4 KESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus         4 ~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      ...|+.+|++..|.=|++++..|..|+|.|...|++||++|+|.+....+.....++.+||||+.|+|+.+|+
T Consensus         3 ~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPd   75 (119)
T KOG3172|consen    3 VGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPD   75 (119)
T ss_pred             cccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECch
Confidence            3578999999999999999999999999999999999999999998644445678899999999999999886

>KOG3168|consensus

Probab=99.47  E-value=4.6e-14  Score=93.65  Aligned_cols=66  Identities=26%  Similarity=0.463  Sum_probs=58.6

Q ss_pred             HHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhh----------ccEeeccccCeEEecCcEEEEEeec
Q psy10835         11 IQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI----------NGQLKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus        11 L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~----------~~~~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      +-.+++.+.+|.+.||++|.|++.+||.|||++|.+|+|..          ++++.+-++++++||++|++.+..+
T Consensus         9 ml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVeg   84 (177)
T KOG3168|consen    9 MLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEG   84 (177)
T ss_pred             HHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccC
Confidence            66789999999999999999999999999999999999963          2345678999999999999988654

>KOG1782|consensus

Probab=99.46  E-value=6.4e-14  Score=88.80  Aligned_cols=70  Identities=26%  Similarity=0.355  Sum_probs=59.5

Q ss_pred             HHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhh-ccEe--eccccCeEEecCcEEEEEeecc
Q psy10835          8 SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI-NGQL--KNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~-~~~~--~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      ..-|.++++|++.|.|+||+.+.|.|.+||+|-|++|++|.|.. -++.  ....|.++|||+||+.+...+.
T Consensus        11 t~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~   83 (129)
T KOG1782|consen   11 TTSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDL   83 (129)
T ss_pred             hhHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCc
Confidence            34588999999999999999999999999999999999999963 2322  2457899999999999987653

>KOG1774|consensus

Probab=99.44  E-value=1.7e-13  Score=81.62  Aligned_cols=70  Identities=23%  Similarity=0.427  Sum_probs=56.7

Q ss_pred             ChHHHHHhhhCC--ceEEEecC--CcccceeeeeecccchhhhhhhhhhhccEe-eccccCeEEecCcEEEEEee
Q psy10835          6 SLSQFIQQIHGR--PVVVKLVS--GVDYRGVLSCLDGYMNIALEQTEEYINGQL-KNKYGDTFIRGNNVLYISTQ   75 (80)
Q Consensus         6 ~p~~~L~~~~~k--~V~V~L~~--g~~~~G~L~~~D~~mNivL~~~~~~~~~~~-~~~~g~v~irG~~I~~I~~~   75 (80)
                      .|..++-.++..  +|.|+|.+  +..+.|.+.|||+|||+||++|+|...... -..+|.++++|+||-.|...
T Consensus        12 ~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItli~~~   86 (88)
T KOG1774|consen   12 QPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITLIQSA   86 (88)
T ss_pred             CcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcEEEEeec
Confidence            577778888744  57788887  789999999999999999999999632222 24799999999999998753

>KOG3428|consensus

Probab=99.41  E-value=2e-13  Score=85.00  Aligned_cols=70  Identities=24%  Similarity=0.405  Sum_probs=63.7

Q ss_pred             hHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeecc
Q psy10835          7 LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         7 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      ...+|+++.+.+|+|+|+||+...|++.+.|.+||..|.++.....| ...++..+++||++|+|+.+|++
T Consensus         3 lvr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~-~pv~l~~lsirgnniRy~~lpD~   72 (109)
T KOG3428|consen    3 LVRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG-EPVRLDTLSIRGNNIRYYILPDS   72 (109)
T ss_pred             HHHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC-CceeEEEEEeecceEEEEEccCC
Confidence            45789999999999999999999999999999999999999887666 45678899999999999999985

>KOG1784|consensus

Probab=99.41  E-value=1.9e-13  Score=82.84  Aligned_cols=67  Identities=25%  Similarity=0.297  Sum_probs=60.0

Q ss_pred             HHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhh----ccEeeccccCeEEecCcEEEEEeec
Q psy10835         10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI----NGQLKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus        10 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~----~~~~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      -|+.|++|+|.|...||+.+.|.|.|||+..|++|+++-|+.    .|..+..+|..+|||+|+..|.+.+
T Consensus         4 ~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iD   74 (96)
T KOG1784|consen    4 TLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEID   74 (96)
T ss_pred             hHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecc
Confidence            489999999999999999999999999999999999999852    3445567899999999999998765

>KOG3459|consensus

Probab=98.79  E-value=3.6e-09  Score=66.12  Aligned_cols=69  Identities=19%  Similarity=0.326  Sum_probs=57.9

Q ss_pred             CChHHHHHhhh--CCceEEEecCCcccceeeeeecccchhhhhhhhhh-h------ccEe------eccccCeEEecCcE
Q psy10835          5 ESLSQFIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEY-I------NGQL------KNKYGDTFIRGNNV   69 (80)
Q Consensus         5 ~~p~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~-~------~~~~------~~~~g~v~irG~~I   69 (80)
                      ..|++.+....  ..+|.|.++|.+.+.|.+.+||.|+|++|+|+.|. .      +|..      -+.++.+||||++|
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            36888888887  66799999999999999999999999999999983 1      2322      46789999999999


Q ss_pred             EEEE
Q psy10835         70 LYIS   73 (80)
Q Consensus        70 ~~I~   73 (80)
                      +.+.
T Consensus       103 I~v~  106 (114)
T KOG3459|consen  103 ILVL  106 (114)
T ss_pred             EEEE
Confidence            8875

>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=98.24  E-value=8e-07  Score=51.11  Aligned_cols=35  Identities=26%  Similarity=0.262  Sum_probs=29.5

Q ss_pred             CCceEEEecCC----cccceeeeeecccchhhhhhhhhh
Q psy10835         16 GRPVVVKLVSG----VDYRGVLSCLDGYMNIALEQTEEY   50 (80)
Q Consensus        16 ~k~V~V~L~~g----~~~~G~L~~~D~~mNivL~~~~~~   50 (80)
                      +++|.|.++.-    -.++|.|.+||+|+||+|.|+.|.
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            56788888853    467789999999999999999995

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.

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

Probab=98.19  E-value=1.2e-06  Score=51.31  Aligned_cols=63  Identities=14%  Similarity=0.268  Sum_probs=41.8

Q ss_pred             HHHHHhhhCCceEEEecCCcccceeeeeecc---cchhhhhhhhhhhcc-----E--eeccccCeEEecCcEE
Q psy10835          8 SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDG---YMNIALEQTEEYING-----Q--LKNKYGDTFIRGNNVL   70 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~---~mNivL~~~~~~~~~-----~--~~~~~g~v~irG~~I~   70 (80)
                      .-++..++|++|.|+++||..|.|+|.+++.   -+.++|+.+.....+     .  .....+.++|+++.|+
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            4467889999999999999999999999998   889999888775332     1  1234567888887764

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

Probab=97.35  E-value=0.0002  Score=44.02  Aligned_cols=65  Identities=18%  Similarity=0.362  Sum_probs=52.2

Q ss_pred             hhhCCceEEEecCCcccceeeeeecc-cchhhhhhhhhh-hccE--------eeccccCeEEecCcEEEEEeecc
Q psy10835         13 QIHGRPVVVKLVSGVDYRGVLSCLDG-YMNIALEQTEEY-INGQ--------LKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus        13 ~~~~k~V~V~L~~g~~~~G~L~~~D~-~mNivL~~~~~~-~~~~--------~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      .++|++|.+.-+++-.|.|+|..+|. .-.|.|+|+..+ .+|.        ....++.+..||+.|.-+.+.+-
T Consensus         5 ~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~   79 (96)
T PF12701_consen    5 PYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEP   79 (96)
T ss_dssp             CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-
T ss_pred             cccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcC
Confidence            58999999999999999999999994 788999998764 2221        12357789999999999887653

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=97.06  E-value=0.0012  Score=39.28  Aligned_cols=43  Identities=23%  Similarity=0.611  Sum_probs=32.9

Q ss_pred             CCCCCChHH-HHHhhh--CCceEEEecCCcccceeeeeecccchhh
Q psy10835          1 MSRKESLSQ-FIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIA   43 (80)
Q Consensus         1 m~~~~~p~~-~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNiv   43 (80)
                      |.+..+..+ +|..+.  +.+|+|-|.||..+.|.+.+||+|+=++
T Consensus         1 m~~~~nlQd~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll   46 (79)
T PRK00395          1 MAKGQNLQDPFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLL   46 (79)
T ss_pred             CccccchHHHHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEE
Confidence            555555544 555554  6679999999999999999999999444

>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=96.93  E-value=0.0014  Score=37.28  Aligned_cols=34  Identities=26%  Similarity=0.586  Sum_probs=27.9

Q ss_pred             HHHhhh--CCceEEEecCCcccceeeeeecccchhh
Q psy10835         10 FIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIA   43 (80)
Q Consensus        10 ~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNiv   43 (80)
                      +|+.+-  ..+|+|-|.||..+.|.+.+||+|+=++
T Consensus         3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll   38 (61)
T cd01716           3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLL   38 (61)
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEE
Confidence            455554  5679999999999999999999999443

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.

>TIGR02383 Hfq RNA chaperone Hfq

Probab=96.89  E-value=0.0016  Score=37.01  Aligned_cols=34  Identities=32%  Similarity=0.663  Sum_probs=28.0

Q ss_pred             HHHhhh--CCceEEEecCCcccceeeeeecccchhh
Q psy10835         10 FIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIA   43 (80)
Q Consensus        10 ~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNiv   43 (80)
                      +|+.+-  +.+|+|-|.||..+.|.+.+||+|+=++
T Consensus         7 fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll   42 (61)
T TIGR02383         7 FLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLL   42 (61)
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEE
Confidence            455554  5679999999999999999999999443

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.

>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=96.87  E-value=0.0016  Score=34.87  Aligned_cols=46  Identities=20%  Similarity=0.278  Sum_probs=35.1

Q ss_pred             hCCceEEEecCCcccceeeeeecccchhhhhhhhhhhcc-EeeccccCeEEe
Q psy10835         15 HGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYING-QLKNKYGDTFIR   65 (80)
Q Consensus        15 ~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~-~~~~~~g~v~ir   65 (80)
                      +||+|++.. ++..++|+..++|+...|+++...    | ......|.+++|
T Consensus         2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~----g~~~~i~sGdv~~r   48 (48)
T PF02237_consen    2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRTED----GSIRTISSGDVSLR   48 (48)
T ss_dssp             TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETT----EEEEEESSSEEEEE
T ss_pred             CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECC----CCEEEEEEEEEEeC
Confidence            699999999 567779999999999999997543    3 233445666654

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 ....

>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=96.48  E-value=0.0058  Score=36.49  Aligned_cols=64  Identities=17%  Similarity=0.256  Sum_probs=48.2

Q ss_pred             hHHHHHhhhCCceEEEecCCcccceeeeeec-ccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEee
Q psy10835          7 LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLD-GYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQ   75 (80)
Q Consensus         7 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~   75 (80)
                      .+.+|.++.||+|.+.|.++.+..|++.++| +..|+..+|-.- .=|    ..++-++|.+.|+.++..
T Consensus        15 fLr~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   15 FLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQT-PLG----VQPEALLRCSDVISISFD   79 (80)
T ss_dssp             HHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEET-TTT----EEEEEEEEGGGEEEEEE-
T ss_pred             HHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcCC-Ccc----cChhheeecCCEEEEEec
Confidence            4667888899999999999999999999999 566776665443 123    246889999999998865

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.

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

Probab=96.18  E-value=0.0076  Score=40.40  Aligned_cols=65  Identities=25%  Similarity=0.290  Sum_probs=45.2

Q ss_pred             CChHHHHHhhhCCceEEEecCCcccceeeeeec-ccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeecc
Q psy10835          5 ESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLD-GYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         5 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      .+|+ .+..|++|.|.|.+.| +++.|.|..+| -.-|++|-+..+  +++.    ..-+|-|-+|..|...+.
T Consensus         7 ~~p~-~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e--~~~~----sv~~I~ghaVk~vevl~~   72 (166)
T PF06372_consen    7 KSPL-EWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE--DGKR----SVKVIMGHAVKSVEVLSE   72 (166)
T ss_dssp             S-HH-HHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T--TS-E----EEEEE-GGGEEEEEEEE-
T ss_pred             CCHH-HHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc--CCce----eEEEEEccceEEEEEccC
Confidence            4565 5678999999999999 99999999999 577888886665  2321    247888999999887654

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.

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

Probab=96.12  E-value=0.0097  Score=35.22  Aligned_cols=36  Identities=25%  Similarity=0.619  Sum_probs=29.3

Q ss_pred             HHHhhh--CCceEEEecCCcccceeeeeecccchhhhhh
Q psy10835         10 FIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIALEQ   46 (80)
Q Consensus        10 ~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~   46 (80)
                      ||..+-  +.+|.|-|.||-.+.|.+++||+|. +.|++
T Consensus        11 fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~-VlL~~   48 (77)
T COG1923          11 FLNALRKEKIPVTIFLVNGFKLQGQVESFDNFV-VLLKN   48 (77)
T ss_pred             HHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEE-EEEEc
Confidence            555554  6679999999999999999999998 55553

>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=95.66  E-value=0.0062  Score=35.88  Aligned_cols=60  Identities=20%  Similarity=0.395  Sum_probs=45.1

Q ss_pred             hhhCCceEEEecCCcccceeeeeec-ccchhhhhhhhhh-hccE---------eeccccCeEEecCcEEEE
Q psy10835         13 QIHGRPVVVKLVSGVDYRGVLSCLD-GYMNIALEQTEEY-INGQ---------LKNKYGDTFIRGNNVLYI   72 (80)
Q Consensus        13 ~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNivL~~~~~~-~~~~---------~~~~~g~v~irG~~I~~I   72 (80)
                      .++|+++.+.-+.+-.|.|+|.++| +.--+-|+|+..+ .+|.         ....++.+..||+.|.-+
T Consensus         3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkDL   73 (74)
T cd01736           3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKDL   73 (74)
T ss_pred             cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccccc
Confidence            5899999999999999999999999 4555778888753 1221         123456788999887643

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.

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=95.64  E-value=0.019  Score=38.42  Aligned_cols=34  Identities=26%  Similarity=0.630  Sum_probs=28.1

Q ss_pred             HHHhhh--CCceEEEecCCcccceeeeeecccchhh
Q psy10835         10 FIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIA   43 (80)
Q Consensus        10 ~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNiv   43 (80)
                      +|..+.  ..+|+|-|.||-.++|.+.+||+|.=+.
T Consensus        16 fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL   51 (165)
T PRK14091         16 FLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILL   51 (165)
T ss_pred             HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEE
Confidence            666665  5568899999999999999999998444

>PRK14638 hypothetical protein; Provisional

Probab=95.04  E-value=0.046  Score=35.87  Aligned_cols=37  Identities=11%  Similarity=0.185  Sum_probs=30.8

Q ss_pred             HHHHHhhhCCceEEEecCCcccceeeeeecccchhhhh
Q psy10835          8 SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALE   45 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~   45 (80)
                      ..-+.+++|++|.|++++++.++|+|.++|+- ++.|.
T Consensus        92 ~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~  128 (150)
T PRK14638         92 PKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS  128 (150)
T ss_pred             HHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            34678899999999999999999999999964 35443

>PRK14639 hypothetical protein; Provisional

Probab=94.92  E-value=0.051  Score=35.24  Aligned_cols=37  Identities=22%  Similarity=0.309  Sum_probs=31.1

Q ss_pred             HHHHHhhhCCceEEEecCCcccceeeeeecccchhhhh
Q psy10835          8 SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALE   45 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~   45 (80)
                      ..-++.++|++|.|++.+++.+.|+|.++|+. ++.|.
T Consensus        80 ~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l~  116 (140)
T PRK14639         80 IEHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITLE  116 (140)
T ss_pred             HHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            45678999999999999999999999999973 45443

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

Probab=94.87  E-value=0.091  Score=30.24  Aligned_cols=54  Identities=31%  Similarity=0.477  Sum_probs=40.2

Q ss_pred             HHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEe
Q psy10835          8 SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~   74 (80)
                      .+.|++++|++|.|+...|+. +|+|.+.-.- .++|+..     +      ..+|||=..|++|.+
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            568999999999999987655 9999998732 2354422     2      267899888888753

>PRK02001 hypothetical protein; Validated

Probab=94.45  E-value=0.078  Score=34.96  Aligned_cols=36  Identities=28%  Similarity=0.333  Sum_probs=30.4

Q ss_pred             HHHHhhhCCceEEEecCCcccceeeeeecccchhhhh
Q psy10835          9 QFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALE   45 (80)
Q Consensus         9 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~   45 (80)
                      .-+..++|+.|.|++.+++.+.|+|.++|+. ++.|.
T Consensus        83 ~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l~  118 (152)
T PRK02001         83 RQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITLE  118 (152)
T ss_pred             HHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEEE
Confidence            4677899999999999999999999999964 34443

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=94.24  E-value=0.07  Score=35.78  Aligned_cols=34  Identities=29%  Similarity=0.604  Sum_probs=28.1

Q ss_pred             HHHhhh--CCceEEEecCCcccceeeeeecccchhh
Q psy10835         10 FIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIA   43 (80)
Q Consensus        10 ~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNiv   43 (80)
                      +|..+.  ..+|+|-|.||-.+.|.+.+||.|.=+.
T Consensus        96 fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL  131 (165)
T PRK14091         96 FLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLL  131 (165)
T ss_pred             HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEE
Confidence            566665  5668999999999999999999999444

>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=93.72  E-value=0.058  Score=30.59  Aligned_cols=36  Identities=11%  Similarity=0.088  Sum_probs=30.2

Q ss_pred             hhCCceEEEecCCcccceeeeeecccchhhhhhhhh
Q psy10835         14 IHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEE   49 (80)
Q Consensus        14 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~   49 (80)
                      .+|..|.++...|.+++|.+.+||...+++.-.|..
T Consensus         4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s   39 (61)
T cd01735           4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS   39 (61)
T ss_pred             ccccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence            478999999999999999999999877776555443

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.

>PRK14644 hypothetical protein; Provisional

Probab=92.55  E-value=0.26  Score=31.87  Aligned_cols=36  Identities=19%  Similarity=0.072  Sum_probs=30.2

Q ss_pred             HHHHhhhCCceEEEecCC----cccceeeeeecccchhhhh
Q psy10835          9 QFIQQIHGRPVVVKLVSG----VDYRGVLSCLDGYMNIALE   45 (80)
Q Consensus         9 ~~L~~~~~k~V~V~L~~g----~~~~G~L~~~D~~mNivL~   45 (80)
                      +-+.+++|+.|.|+|++.    +.+.|.|.++|+. ++.|.
T Consensus        78 ~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~  117 (136)
T PRK14644         78 DELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK  117 (136)
T ss_pred             HHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            358899999999999886    9999999999973 45554

>PRK14642 hypothetical protein; Provisional

Probab=92.39  E-value=0.25  Score=34.01  Aligned_cols=36  Identities=17%  Similarity=0.278  Sum_probs=29.9

Q ss_pred             HHHHHhhhCCceEEEec-------------CCcccceeeeeecccchhhh
Q psy10835          8 SQFIQQIHGRPVVVKLV-------------SGVDYRGVLSCLDGYMNIAL   44 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~-------------~g~~~~G~L~~~D~~mNivL   44 (80)
                      ..-+.+++|+.|.|+|+             +.+.++|+|.++|+. ++.|
T Consensus        92 ~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l  140 (197)
T PRK14642         92 EQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI  140 (197)
T ss_pred             HHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence            45678889999999998             679999999999974 4544

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

Probab=91.76  E-value=0.4  Score=28.14  Aligned_cols=32  Identities=28%  Similarity=0.396  Sum_probs=26.9

Q ss_pred             HHHHHhhhCCceEEEec---CC-cccceeeeeeccc
Q psy10835          8 SQFIQQIHGRPVVVKLV---SG-VDYRGVLSCLDGY   39 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~---~g-~~~~G~L~~~D~~   39 (80)
                      ..-+..++|+.|.|+++   +| +.+.|.|.++|+.
T Consensus        17 ~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~   52 (83)
T cd01734          17 EADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD   52 (83)
T ss_pred             HHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC
Confidence            34677889999999997   55 6899999999974

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.

>PRK14640 hypothetical protein; Provisional

Probab=91.52  E-value=0.38  Score=31.53  Aligned_cols=37  Identities=22%  Similarity=0.390  Sum_probs=29.7

Q ss_pred             HHHHHhhhCCceEEEe----cCCcccceeeeeecccchhhhh
Q psy10835          8 SQFIQQIHGRPVVVKL----VSGVDYRGVLSCLDGYMNIALE   45 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L----~~g~~~~G~L~~~D~~mNivL~   45 (80)
                      ..-+.+++|++|.|++    .+.+.++|+|.++|+. ++.|.
T Consensus        89 ~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~  129 (152)
T PRK14640         89 VAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT  129 (152)
T ss_pred             HHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence            3467889999999999    4679999999999974 35553

>PRK14633 hypothetical protein; Provisional

Probab=91.41  E-value=0.4  Score=31.40  Aligned_cols=36  Identities=28%  Similarity=0.377  Sum_probs=29.1

Q ss_pred             HHHHHhhhCCceEEEec----CCcccceeeeeecccchhhh
Q psy10835          8 SQFIQQIHGRPVVVKLV----SGVDYRGVLSCLDGYMNIAL   44 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~----~g~~~~G~L~~~D~~mNivL   44 (80)
                      ..-+.+++|++|.|+++    +++.++|+|.++|+. ++.|
T Consensus        86 ~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l  125 (150)
T PRK14633         86 IIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL  125 (150)
T ss_pred             HHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence            34678899999999984    679999999999974 3444

>KOG1073|consensus

Probab=91.41  E-value=0.22  Score=37.08  Aligned_cols=66  Identities=15%  Similarity=0.337  Sum_probs=51.5

Q ss_pred             HhhhCCceEEEecCCcccceeeeeec-ccchhhhhhhhhh-hcc-----Ee----eccccCeEEecCcEEEEEeecc
Q psy10835         12 QQIHGRPVVVKLVSGVDYRGVLSCLD-GYMNIALEQTEEY-ING-----QL----KNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus        12 ~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNivL~~~~~~-~~~-----~~----~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      ..++|++|.+.=+..-.|+|+|.-+| +-.=|=|++|..+ .++     ..    ...++-++.||+.|.-+.+.+.
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 6677888887432 222     11    1256789999999998887663

>PRK14645 hypothetical protein; Provisional

Probab=91.12  E-value=0.4  Score=31.64  Aligned_cols=35  Identities=14%  Similarity=0.399  Sum_probs=28.5

Q ss_pred             HHHHHhhhCCceEEEecCCcccceeeeeecccchhhh
Q psy10835          8 SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIAL   44 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL   44 (80)
                      ..-+.+++|++|.|++ +++.+.|+|.++|+.. +.|
T Consensus        94 ~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~~-i~l  128 (154)
T PRK14645         94 ARHFERFAGLKAKVRG-PGENFTGRIKAVSGDQ-VTF  128 (154)
T ss_pred             HHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCCE-EEE
Confidence            3467788999999986 7899999999999743 444

>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=90.80  E-value=0.49  Score=31.31  Aligned_cols=36  Identities=25%  Similarity=0.455  Sum_probs=30.8

Q ss_pred             HHHHHhhhCCceEEEe----cCCcccceeeeeecccchhhh
Q psy10835          8 SQFIQQIHGRPVVVKL----VSGVDYRGVLSCLDGYMNIAL   44 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L----~~g~~~~G~L~~~D~~mNivL   44 (80)
                      .+-+..++|+.|.|+|    .+++.+.|+|.++|+-. +.+
T Consensus        91 ~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~  130 (153)
T COG0779          91 AEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL  130 (153)
T ss_pred             HHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence            4578889999999999    68899999999999776 443

>PRK14643 hypothetical protein; Provisional

Probab=90.75  E-value=0.47  Score=31.59  Aligned_cols=32  Identities=13%  Similarity=0.123  Sum_probs=27.5

Q ss_pred             HHHHHhhhCCceEEEecC----Ccccceeeeeeccc
Q psy10835          8 SQFIQQIHGRPVVVKLVS----GVDYRGVLSCLDGY   39 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~~----g~~~~G~L~~~D~~   39 (80)
                      ..-+..++|++|.|+|++    .+.+.|+|.++|+-
T Consensus        96 ~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T PRK14643         96 QEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN  131 (164)
T ss_pred             HHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence            446788999999999975    69999999999954

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=90.49  E-value=0.54  Score=30.67  Aligned_cols=32  Identities=31%  Similarity=0.505  Sum_probs=27.4

Q ss_pred             HHHHHhhhCCceEEEe----cCCcccceeeeeeccc
Q psy10835          8 SQFIQQIHGRPVVVKL----VSGVDYRGVLSCLDGY   39 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L----~~g~~~~G~L~~~D~~   39 (80)
                      ..-+..++|+.|.|++    .+++.+.|.|.++|+.
T Consensus        90 ~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~  125 (154)
T PRK00092         90 ARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGE  125 (154)
T ss_pred             HHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCC
Confidence            4567899999999997    5678999999999973

>PRK14636 hypothetical protein; Provisional

Probab=90.30  E-value=0.51  Score=31.75  Aligned_cols=36  Identities=22%  Similarity=0.447  Sum_probs=28.6

Q ss_pred             HHHHHhhhCCceEEEec---CC-cccceeeeeecccchhhh
Q psy10835          8 SQFIQQIHGRPVVVKLV---SG-VDYRGVLSCLDGYMNIAL   44 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~---~g-~~~~G~L~~~D~~mNivL   44 (80)
                      ..-+..++|++|.|+|+   +| +.++|+|.++|+. ++.|
T Consensus        90 ~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l  129 (176)
T PRK14636         90 PKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI  129 (176)
T ss_pred             HHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence            34678899999999997   45 7999999999863 3444

>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=90.04  E-value=0.44  Score=30.48  Aligned_cols=35  Identities=31%  Similarity=0.413  Sum_probs=26.0

Q ss_pred             HHHHhhhCCceEEEec----CCcccceeeeeecccchhhh
Q psy10835          9 QFIQQIHGRPVVVKLV----SGVDYRGVLSCLDGYMNIAL   44 (80)
Q Consensus         9 ~~L~~~~~k~V~V~L~----~g~~~~G~L~~~D~~mNivL   44 (80)
                      ..+..++|++|.|+++    +.+.+.|+|.++|+ -.+.|
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            5788999999999994    45789999999997 33444

; PDB: 1IB8_A.

>PRK14632 hypothetical protein; Provisional

Probab=90.02  E-value=0.59  Score=31.31  Aligned_cols=37  Identities=22%  Similarity=0.475  Sum_probs=29.7

Q ss_pred             HHHHHhhhCCceEEEecC-------Ccccceeeeeecccchhhhh
Q psy10835          8 SQFIQQIHGRPVVVKLVS-------GVDYRGVLSCLDGYMNIALE   45 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~~-------g~~~~G~L~~~D~~mNivL~   45 (80)
                      ..-+.+++|+.|.|++.+       .+.+.|+|.++|+. ++.|+
T Consensus        90 ~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~  133 (172)
T PRK14632         90 AEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR  133 (172)
T ss_pred             HHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence            346788999999999986       57999999999963 35554

>PRK14634 hypothetical protein; Provisional

Probab=89.79  E-value=0.64  Score=30.61  Aligned_cols=36  Identities=19%  Similarity=0.219  Sum_probs=28.6

Q ss_pred             HHHHHhhhCCceEEEecC----Ccccceeeeeecccchhhh
Q psy10835          8 SQFIQQIHGRPVVVKLVS----GVDYRGVLSCLDGYMNIAL   44 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~~----g~~~~G~L~~~D~~mNivL   44 (80)
                      ..-+.+++|++|.|++.+    .+.+.|+|.++|+- ++.|
T Consensus        92 ~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l  131 (155)
T PRK14634         92 DRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI  131 (155)
T ss_pred             HHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence            346788999999999974    37999999999964 3545

>PRK14646 hypothetical protein; Provisional

Probab=89.37  E-value=0.71  Score=30.39  Aligned_cols=37  Identities=22%  Similarity=0.205  Sum_probs=29.3

Q ss_pred             HHHHHhhhCCceEEEecCC----cccceeeeeecccchhhhh
Q psy10835          8 SQFIQQIHGRPVVVKLVSG----VDYRGVLSCLDGYMNIALE   45 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~~g----~~~~G~L~~~D~~mNivL~   45 (80)
                      ..-+..++|++|.|+|++.    +.+.|+|.++|+- ++.|.
T Consensus        92 ~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~  132 (155)
T PRK14646         92 ERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN  132 (155)
T ss_pred             HHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            4578889999999999753    7889999999974 45553

>PRK14647 hypothetical protein; Provisional

Probab=88.71  E-value=0.84  Score=30.06  Aligned_cols=31  Identities=23%  Similarity=0.250  Sum_probs=26.5

Q ss_pred             HHHHHhhhCCceEEEec---------CCcccceeeeeecc
Q psy10835          8 SQFIQQIHGRPVVVKLV---------SGVDYRGVLSCLDG   38 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~---------~g~~~~G~L~~~D~   38 (80)
                      ..-+..++|++|.|+++         +.+.+.|+|.++|+
T Consensus        91 ~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~  130 (159)
T PRK14647         91 EADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD  130 (159)
T ss_pred             HHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence            44678899999999995         35899999999996

>PRK14637 hypothetical protein; Provisional

Probab=87.95  E-value=1.2  Score=29.25  Aligned_cols=37  Identities=16%  Similarity=0.147  Sum_probs=28.0

Q ss_pred             HHHHHhhhCCceEEEecCCccc-ceeeeeecccchhhhh
Q psy10835          8 SQFIQQIHGRPVVVKLVSGVDY-RGVLSCLDGYMNIALE   45 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~~g~~~-~G~L~~~D~~mNivL~   45 (80)
                      ..-+..++|++|.|++.+...+ +|+|.++|+. ++.|.
T Consensus        90 ~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~  127 (151)
T PRK14637         90 AAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT  127 (151)
T ss_pred             HHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence            4567889999999999544556 7999999974 34443

>PRK06955 biotin--protein ligase; Provisional

Probab=87.87  E-value=0.65  Score=33.30  Aligned_cols=50  Identities=26%  Similarity=0.268  Sum_probs=35.6

Q ss_pred             hhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecC
Q psy10835         14 IHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGN   67 (80)
Q Consensus        14 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~   67 (80)
                      ++|++|+|...++..+.|+..++|+...|+++..    +|......|++.+|..
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            4699999976667789999999999999988532    2322334566666543

>PRK14631 hypothetical protein; Provisional

Probab=87.18  E-value=1.2  Score=30.00  Aligned_cols=30  Identities=20%  Similarity=0.382  Sum_probs=26.4

Q ss_pred             HHHHHhhhCCceEEEec----CCcccceeeeeec
Q psy10835          8 SQFIQQIHGRPVVVKLV----SGVDYRGVLSCLD   37 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~----~g~~~~G~L~~~D   37 (80)
                      ..-+..++|+.|.|+|.    +.+.++|+|.++|
T Consensus       109 ~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~  142 (174)
T PRK14631        109 LEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD  142 (174)
T ss_pred             HHHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence            45788899999999996    4599999999998

>PRK14641 hypothetical protein; Provisional

Probab=86.04  E-value=1.3  Score=29.82  Aligned_cols=30  Identities=17%  Similarity=0.140  Sum_probs=25.5

Q ss_pred             HHHHHhhhCCceEEEecC----Ccccceeeeeec
Q psy10835          8 SQFIQQIHGRPVVVKLVS----GVDYRGVLSCLD   37 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~~----g~~~~G~L~~~D   37 (80)
                      ..-+.+++|+.|.|++.+    .+.++|+|.++|
T Consensus        96 ~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~  129 (173)
T PRK14641         96 PRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS  129 (173)
T ss_pred             HHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence            346788899999999976    568999999995

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

Probab=86.03  E-value=0.91  Score=35.69  Aligned_cols=50  Identities=22%  Similarity=0.361  Sum_probs=36.5

Q ss_pred             hhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecC
Q psy10835         14 IHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGN   67 (80)
Q Consensus        14 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~   67 (80)
                      ++|++|.+...++..+.|+..++|+...|+|+..    +|......|++.+|..
T Consensus       276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~~----~g~~~~~sGEVslr~~  325 (592)
T PRK13325        276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLETA----EGKQTVVSGEISLRSD  325 (592)
T ss_pred             cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEEC----CCeEEEEEEeEEEeec
Confidence            5699999876666779999999999999999632    2333334566766654

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

Probab=83.63  E-value=1.4  Score=31.45  Aligned_cols=48  Identities=19%  Similarity=0.202  Sum_probs=34.7

Q ss_pred             hhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEec
Q psy10835         14 IHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRG   66 (80)
Q Consensus        14 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG   66 (80)
                      ++|++|.+...+ ..+.|++.++|+...|+++.    ..+.+....|++.++.
T Consensus       270 ~~g~~v~~~~~~-~~~~G~~~gi~~~G~L~i~~----~g~~~~~~~gev~~~~  317 (319)
T PRK11886        270 FLGREVKLIIGD-KEISGIARGIDEQGALLLED----DGVEKPFNGGEISLRS  317 (319)
T ss_pred             ccCCeEEEEeCC-cEEEEEEEEECCCceEEEEe----CCcEEEEEEeEEEEec
Confidence            469999998754 67999999999999999961    1222334456676654

>PRK14630 hypothetical protein; Provisional

Probab=81.51  E-value=3.5  Score=26.78  Aligned_cols=35  Identities=9%  Similarity=0.073  Sum_probs=27.1

Q ss_pred             HHHHHhhhCCceEEEecCCcccceeeeeecccchhhh
Q psy10835          8 SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIAL   44 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL   44 (80)
                      ..-+++++|++|.|++.+ ....|+|.++|+. ++.|
T Consensus        89 ~~df~r~~G~~v~V~l~~-~~~~G~L~~~~d~-~i~l  123 (143)
T PRK14630         89 DREFKIFEGKKIKLMLDN-DFEEGFILEAKAD-SFIF  123 (143)
T ss_pred             HHHHHHhCCCEEEEEEcC-cceEEEEEEEeCC-EEEE
Confidence            456788999999999965 4459999999973 3444

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	80
3swn_B	77	Structure Of The Lsm657 Complex: An Assembly Interm		6e-23
4emk_B	75	Crystal Structure Of Splsm567 Length = 75		1e-21
3cw1_F	86	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		5e-14
1loj_A	87	Crystal Structure Of A Methanobacterial Sm-Like Arc		1e-08
1jbm_A	86	Heptameric Crystal Structure Of Mth649, An Sm-Like		1e-08
1jri_A	85	The Crystal Structure Of An Sm-Like Archaeal Protei		1e-08
1i81_A	83	Crystal Structure Of A Heptameric Lsm Protein From		2e-08
1i5l_A	77	Crystal Structure Of An Sm-Like Protein (Af-Sm1) Fr		3e-07
1n9s_A	93	Crystal Structure Of Yeast Smf In Spacegroup P43212		4e-07
1n9r_A	93	Crystal Structure Of A Heptameric Ring Complex Of Y		8e-07
1i8f_A	81	The Crystal Structure Of A Heptameric Archaeal Sm P		2e-06
1h64_1	75	Crystal Structure Of The Sm-Related Protein Of P. A		6e-05
1m8v_A	77	Structure Of Pyrococcus Abyssii Sm Protein In Compl		6e-05
1th7_A	81	Crystal Structure Of An Archaeal Sm Protein From Su		7e-04
4emh_A	105	Crystal Structure Of Splsm4 Length = 105		8e-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 =  102 bits (254), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 44/74 (59%), Positives = 60/74 (81%)
Query: 1  MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG 60
          M    S ++F+ ++ G+ V+++L SGVDY+G+LSCLDGYMN+ALE+TEEY+NG+  N YG
Sbjct: 1  MGMDSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYG 60
Query: 61 DTFIRGNNVLYIST 74
          D FIRGNNVLY+S 
Sbjct: 61 DAFIRGNNVLYVSA 74

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

Iteration: 1
 Score = 98.2 bits (243), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 42/69 (60%), Positives = 58/69 (84%)
Query: 6  SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIR 65
          S ++F+ ++ G+ V+++L SGVDY+G+LSCLDGY N+ALE+TEEY+NG+  N YGD FIR
Sbjct: 4  SPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYXNLALERTEEYVNGKKTNVYGDAFIR 63
Query: 66 GNNVLYIST 74
          GNNVLY+S 
Sbjct: 64 GNNVLYVSA 72

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

Iteration: 1
 Score = 72.8 bits (177), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 35/72 (48%), Positives = 47/72 (65%)
Query: 1  MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG 60
          MS   +   F+  + G+PV+VKL  G++Y+G L  +DGYMN+ L  TEEYI+G L    G
Sbjct: 1  MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLG 60
Query: 61 DTFIRGNNVLYI 72
          +  IR NNVLYI
Sbjct: 61 EVLIRCNNVLYI 72

>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 = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 37/59 (62%)
Query: 18 PVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQK 76
          PV++KL    ++RGVL   D +MN+ L   EE  +G++  + G   IRG+N++YIS  K
Sbjct: 25 PVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISRGK 83

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 37/59 (62%)
Query: 18 PVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQK 76
          PV++KL    ++RGVL   D +MN+ L   EE  +G++  + G   IRG+N++YIS  K
Sbjct: 25 PVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISRGK 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 = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 37/59 (62%)
Query: 18 PVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQK 76
          PV++KL    ++RGVL   D +MN+ L   EE  +G++  + G   IRG+N++YIS  K
Sbjct: 25 PVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISRGK 83

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 36/57 (63%)
Query: 18 PVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIST 74
          PV++KL    ++RGVL   D +MN+ L   EE  +G++  + G   IRG+N++YIS 
Sbjct: 27 PVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP 83

>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 = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 35/59 (59%)
Query: 18 PVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQK 76
          PV+V+L  G ++RG L   D +MN+ L   EE  NG++  K G   IRG+ V+++S   
Sbjct: 16 PVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVFVSPAP 74

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 41/82 (50%), Gaps = 11/82 (13%)
Query: 1  MSRKESLSQFIQQIHGRPVVVKLVS----------GVDYRGVLSCLDGYMNIALEQTEEY 50
          MS    +S  +Q ++ +P +  LV+            +YRG L   D Y N+ L + EE+
Sbjct: 8  MSESSDISA-MQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEF 66
Query: 51 INGQLKNKYGDTFIRGNNVLYI 72
          + G      G+ FIR NNVLYI
Sbjct: 67 VAGVSHGTLGEIFIRSNNVLYI 88

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 41/82 (50%), Gaps = 11/82 (13%)
Query: 1  MSRKESLSQFIQQIHGRPVVVKLVS----------GVDYRGVLSCLDGYMNIALEQTEEY 50
          MS    +S  +Q ++ +P +  LV+            +YRG L   D Y N+ L + EE+
Sbjct: 8  MSESSDISA-MQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEF 66
Query: 51 INGQLKNKYGDTFIRGNNVLYI 72
          + G      G+ FIR NNVLYI
Sbjct: 67 VAGVSHGTLGEIFIRCNNVLYI 88

>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 = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/68 (39%), Positives = 40/68 (58%), Gaps = 1/68 (1%)
Query: 6  SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIR 65
          +L   +Q   G+ V+VKL    + RG+L   D ++N+ LE  EE I+G +  K G   +R
Sbjct: 11 TLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVY-KRGTMVVR 69
Query: 66 GNNVLYIS 73
          G NVL+IS
Sbjct: 70 GENVLFIS 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 = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 22/60 (36%), Positives = 35/60 (58%)
Query: 17 RPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQK 76
          + V+V L  G ++RG L   D ++N+ L   E   +G++  +YG   IRG+NVL IS  +
Sbjct: 15 KDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISPTE 74

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 22/60 (36%), Positives = 35/60 (58%)
Query: 17 RPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQK 76
          + V+V L  G ++RG L   D ++N+ L   E   +G++  +YG   IRG+NVL IS  +
Sbjct: 17 KDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISPTE 76

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

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 31/55 (56%)
Query: 19 VVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIS 73
          V+VKL    + RG+L   D +MN+ L  +EE  +     K G   IRG+NV+ IS
Sbjct: 22 VLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILIS 76

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

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIAL-EQTEEYINGQLKNKYGDTFIRGNN 68
           +    GRP++V+L +G  + G L   D Y N+ L E      +G    +  + +IRGNN
Sbjct: 20 LLNATQGRPILVELKNGETFNGHLENCDNYXNLTLREVIRTXPDGDKFFRLPECYIRGNN 79
Query: 69 VLYISTQ 75
          + Y+  Q
Sbjct: 80 IKYLRIQ 86

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	80
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	6e-27
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	2e-26
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	2e-26
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	3e-26
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	5e-26
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	2e-25
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	1e-24
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	3e-24
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	8e-22
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	2e-21
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	7e-20
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	5e-17
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	5e-17
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	2e-15
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	2e-15
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	6e-13
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	1e-10
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	2e-10
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	2e-10
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	4e-10
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	5e-08
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	2e-04

>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 = 92.9 bits (231), Expect = 6e-27
 Identities = 35/76 (46%), Positives = 48/76 (63%)

Query: 1  MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG 60
          MS   +   F+  + G+PV+VKL  G++Y+G L  +DGYMN+ L  TEEYI+G L    G
Sbjct: 1  MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLG 60

Query: 61 DTFIRGNNVLYISTQK 76
          +  IR NNVLYI   +
Sbjct: 61 EVLIRCNNVLYIRGVE 76

>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A Length = 83

 Score = 91.6 bits (228), Expect = 2e-26
 Identities = 23/66 (34%), Positives = 37/66 (56%)

Query: 8  SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGN 67
             +      PV++KL    ++RGVL   D +MN+ L   EE  +G++  + G   IRG+
Sbjct: 17 LDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGD 76

Query: 68 NVLYIS 73
          N++YIS
Sbjct: 77 NIVYIS 82

>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 = 91.2 bits (227), Expect = 2e-26
 Identities = 23/67 (34%), Positives = 37/67 (55%)

Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNV 69
           + +    PV+V+L  G ++RG L   D +MN+ L   EE  NG++  K G   IRG+ V
Sbjct: 8  VLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTV 67

Query: 70 LYISTQK 76
          +++S   
Sbjct: 68 VFVSPAP 74

>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 = 90.5 bits (225), Expect = 3e-26
 Identities = 42/67 (62%), Positives = 58/67 (86%)

Query: 8  SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGN 67
          ++F+ ++ G+ V+++L SGVDY+G+LSCLDGYMN+ALE+TEEY+NG+  N YGD FIRGN
Sbjct: 6  NEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIRGN 65

Query: 68 NVLYIST 74
          NVLY+S 
Sbjct: 66 NVLYVSA 72

>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 = 90.0 bits (224), Expect = 5e-26
 Identities = 23/67 (34%), Positives = 37/67 (55%)

Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNV 69
           I +   + V+V L  G ++RG L   D ++N+ L   E   +G++  +YG   IRG+NV
Sbjct: 8  VIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNV 67

Query: 70 LYISTQK 76
          L IS  +
Sbjct: 68 LAISPTE 74

>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 = 89.1 bits (221), Expect = 2e-25
 Identities = 29/82 (35%), Positives = 40/82 (48%), Gaps = 9/82 (10%)

Query: 1  MSRKESLSQ--------FIQQIHGRPVVVKL-VSGVDYRGVLSCLDGYMNIALEQTEEYI 51
          MS    +S         F++ +    V VKL  +  +YRG L   D Y N+ L + EE++
Sbjct: 8  MSESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFV 67

Query: 52 NGQLKNKYGDTFIRGNNVLYIS 73
           G      G+ FIR NNVLYI 
Sbjct: 68 AGVSHGTLGEIFIRCNNVLYIR 89

>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 = 86.7 bits (215), Expect = 1e-24
 Identities = 27/72 (37%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 2  SRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGD 61
              +L   +Q   G+ V+VKL    + RG+L   D ++N+ LE  EE I+G    K G 
Sbjct: 7  KCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGN-VYKRGT 65

Query: 62 TFIRGNNVLYIS 73
            +RG NVL+IS
Sbjct: 66 MVVRGENVLFIS 77

>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 = 85.8 bits (213), Expect = 3e-24
 Identities = 22/64 (34%), Positives = 33/64 (51%)

Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNV 69
           + +     V+VKL    + RG+L   D +MN+ L  +EE  +     K G   IRG+NV
Sbjct: 13 VLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNV 72

Query: 70 LYIS 73
          + IS
Sbjct: 73 ILIS 76

>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 = 80.2 bits (198), Expect = 8e-22
 Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQ-TEEYINGQLKNKYGDTFIRGNN 68
           +    GRP++V+L +G  + G L   D YMN+ L +      +G    +  + +IRGNN
Sbjct: 20 LLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIRGNN 79

Query: 69 VLYIS 73
          + Y+ 
Sbjct: 80 IKYLR 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 = 78.1 bits (193), Expect = 2e-21
 Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 8  SQFIQQIHGRPVVVKLVSG-VDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRG 66
          +Q ++ + G+ + V++        G L  +D YMN+ L    E    +     G+  +RG
Sbjct: 7  NQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRG 66

Query: 67 NNVLYIS 73
          NNV+ I 
Sbjct: 67 NNVVLIQ 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 = 74.3 bits (183), Expect = 7e-20
 Identities = 18/77 (23%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 1  MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG 60
          MS+       +++   + + +KL  G   +G+L   D +MN+ +++  E      +N  G
Sbjct: 1  MSKAHPP--ELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIG 58

Query: 61 DTFIRGNNVLYISTQKR 77
             IRGN+++ +   +R
Sbjct: 59 MVVIRGNSIIMLEALER 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 = 67.4 bits (165), Expect = 5e-17
 Identities = 12/64 (18%), Positives = 23/64 (35%)

Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNV 69
           + +  G  V  +  +G  YRG L   +  MN  +             +    +IRG  +
Sbjct: 9  VLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKI 68

Query: 70 LYIS 73
           ++ 
Sbjct: 69 RFLI 72

>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 = 68.5 bits (167), Expect = 5e-17
 Identities = 16/66 (24%), Positives = 32/66 (48%)

Query: 7  LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRG 66
          L +F+ ++    V ++L +G    G ++ +D  MN  L+  +  +  +   +     IRG
Sbjct: 3  LVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRG 62

Query: 67 NNVLYI 72
          NN+ Y 
Sbjct: 63 NNIRYF 68

>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 = 64.1 bits (156), Expect = 2e-15
 Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 13/80 (16%)

Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYIN-------------GQLK 56
           ++      V VKL    +  G L   D ++N+ L   EE +                ++
Sbjct: 13 LVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIR 72

Query: 57 NKYGDTFIRGNNVLYISTQK 76
            Y   F+RG++V+ I+  +
Sbjct: 73 KHYEMLFVRGDSVILIAPPR 92

>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D Length = 126

 Score = 64.7 bits (157), Expect = 2e-15
 Identities = 12/64 (18%), Positives = 24/64 (37%)

Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNV 69
           + +  G  V  +  +G  YRG L   +  MN  +             +    +IRG+ +
Sbjct: 9  VLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKI 68

Query: 70 LYIS 73
           ++ 
Sbjct: 69 RFLI 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 = 57.5 bits (139), Expect = 6e-13
 Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 9  QFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYIN-GQLKNKYGDTFIRGN 67
          + I +  G  + V + S  ++ G L   D Y+NI L+   EY     +  K+ +  + GN
Sbjct: 23 ELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKHSEMLLNGN 82

Query: 68 NVLYIS 73
           +  + 
Sbjct: 83 GMCMLI 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 = 51.6 bits (124), Expect = 1e-10
 Identities = 19/74 (25%), Positives = 27/74 (36%), Gaps = 7/74 (9%)

Query: 11 IQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI-------NGQLKNKYGDTF 63
          ++      V +KL       G L   D + NI L    E I         + + +    F
Sbjct: 15 LKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVF 74

Query: 64 IRGNNVLYISTQKR 77
          IRG+ V  IST   
Sbjct: 75 IRGDTVTLISTPSE 88

>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 = 51.9 bits (124), Expect = 2e-10
 Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 11/75 (14%)

Query: 6  SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYIN-------GQLKNK 58
           LS++      + +      G    G+L   D  MN+ L+  EE +             K
Sbjct: 27 DLSRYQ----DQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRK 82

Query: 59 YGDTFIRGNNVLYIS 73
           G   +RG  ++ I+
Sbjct: 83 LGLVVVRGTTLVLIA 97

>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 = 51.5 bits (123), Expect = 2e-10
 Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 15/80 (18%)

Query: 9   QFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYING--------------- 53
             I +  G  + V +    ++ GVL   D Y+N+ L+  +EY                  
Sbjct: 31  ALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKR 90

Query: 54  QLKNKYGDTFIRGNNVLYIS 73
            + N+     + GNNV  + 
Sbjct: 91  VMVNRLETILLSGNNVAMLV 110

>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 = 50.2 bits (120), Expect = 4e-10
 Identities = 15/83 (18%), Positives = 30/83 (36%), Gaps = 14/83 (16%)

Query: 1  MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI--------- 51
          + +   + Q I       +   L  G  + G     D +MN+ L   +E+          
Sbjct: 3  VGKSSKMLQHI----DYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQ 58

Query: 52 -NGQLKNKYGDTFIRGNNVLYIS 73
             + K   G   +RG N++ ++
Sbjct: 59 AEREEKRVLGLVLLRGENLVSMT 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 = 44.8 bits (106), Expect = 5e-08
 Identities = 13/70 (18%), Positives = 31/70 (44%), Gaps = 1/70 (1%)

Query: 5  ESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYIN-GQLKNKYGDTF 63
            + +++Q      V +     +   G +   D YMN+ L+  EE  +  + + + G   
Sbjct: 19 NLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIM 78

Query: 64 IRGNNVLYIS 73
          ++G+N+  + 
Sbjct: 79 LKGDNITLLQ 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 = 35.7 bits (82), Expect = 2e-04
 Identities = 13/73 (17%), Positives = 27/73 (36%), Gaps = 14/73 (19%)

Query: 15  HGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDT------------ 62
           +   V++   +     G +   D + N+ LE  +E      K+  G              
Sbjct: 38  NNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYIS 97

Query: 63  --FIRGNNVLYIS 73
             F+RG++V+ + 
Sbjct: 98  KMFLRGDSVIVVL 110

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	80
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.96
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.94
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.94
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.93
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.93
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.93
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.93
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.93
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.93
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.93
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.92
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.92
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.92
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.91
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.9
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.9
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.9
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.9
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.89
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.89
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.87
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.86
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.85
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.83
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	99.14
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	97.63
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	97.58
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	97.55
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	97.42
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	97.28
1ycy_A	71	Conserved hypothetical protein; structural genomic	97.26
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	96.97
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	96.88
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	96.69
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	96.62
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	96.29
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	96.24
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	96.21
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	96.2
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	95.32
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	91.38
2eay_A	233	Biotin [acetyl-COA-carboxylase] ligase; biotin bio	91.18
3rux_A	270	BIRA bifunctional protein; biotin-protein ligase,	89.7
1bia_A	321	BIRA bifunctional protein; transcription regulatio	87.82
2ej9_A	237	Putative biotin ligase; biotin biosynthesis, monom	87.52
2dxu_A	235	Biotin--[acetyl-COA-carboxylase] ligase; biotin bi	87.08
2rm4_A	103	CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-	86.97

>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=99.96  E-value=2.7e-29  Score=150.65  Aligned_cols=78  Identities=45%  Similarity=0.787  Sum_probs=71.2

Q ss_pred             CCCCCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeeccc
Q psy10835          1 MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKRR   78 (80)
Q Consensus         1 m~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~~~   78 (80)
                      ||++..|+++|++++|++|+|+|+||++|+|+|.|||+|||++|+||+|+.+++..+.+|.++|||++|++|++++..
T Consensus         1 ms~~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~g~~~~~lg~v~IRG~nI~~i~~~d~~   78 (86)
T 3s6n_F            1 MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGVEEE   78 (86)
T ss_dssp             --CCCCHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEESSEEECGGGEEEEEECC--
T ss_pred             CCcCcCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcCCceeeEccEEEEeCCeEEEEEeCCcc
Confidence            899999999999999999999999999999999999999999999999987777778899999999999999998754

>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=4.1e-28  Score=141.94  Aligned_cols=73  Identities=59%  Similarity=1.097  Sum_probs=67.9

Q ss_pred             CChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeecc
Q psy10835          5 ESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         5 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      ..|+++|++++||+|+|+|+||++|+|+|.|||+|||++|+||+|+.+++..+.+|.++|||++|++|++.++
T Consensus         3 ~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~~   75 (75)
T 4emk_B            3 SSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIRGNNVLYVSALDD   75 (75)
T ss_dssp             SHHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEETTEEEEEEEEEEEEGGGSSEEEEC--
T ss_pred             CchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEecCCcccEecEEEEcCCeEEEEEecCC
Confidence            6899999999999999999999999999999999999999999998777777889999999999999998875

>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=2.4e-27  Score=138.84  Aligned_cols=73  Identities=16%  Similarity=0.240  Sum_probs=66.9

Q ss_pred             CCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeec
Q psy10835          4 KESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus         4 ~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      ...|+++|++++|++|+|+|++|++|+|+|.+||+|||++|+||+|+..+++...+|.++|||++|++|++|+
T Consensus         3 ~~~P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~~~~~~lg~v~IRG~nI~~i~lPd   75 (75)
T 1d3b_A            3 IGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLILPD   75 (75)
T ss_dssp             -CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECGGGEEEEEECC
T ss_pred             ccCHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCCCcEEEcCeEEEeCCEEEEEEcCC
Confidence            4689999999999999999999999999999999999999999999754434678999999999999999986

>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=99.93  E-value=3.6e-27  Score=138.18  Aligned_cols=74  Identities=31%  Similarity=0.514  Sum_probs=68.4

Q ss_pred             CChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeeccc
Q psy10835          5 ESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKRR   78 (80)
Q Consensus         5 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~~~   78 (80)
                      ..|+++|++++|++|+|+|+||++|+|+|.|||+|||++|+||.|+..++..+.+|.++|||++|++|++++.+
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            58999999999999999999999999999999999999999999986676778899999999999999998764

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

Probab=99.93  E-value=3.9e-27  Score=137.49  Aligned_cols=72  Identities=33%  Similarity=0.523  Sum_probs=67.4

Q ss_pred             CChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeec
Q psy10835          5 ESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus         5 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      ..|.++|++++|++|+|+|+||++|+|+|.|||+|||++|+||+|+..+...+.+|.++|||++|++|++++
T Consensus         3 ~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~   74 (75)
T 1h64_1            3 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISPTE   74 (75)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEEC-
T ss_pred             chHHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeCCceeECCEEEECCCEEEEEEeCC
Confidence            589999999999999999999999999999999999999999999866667788999999999999999876

>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=99.93  E-value=2.9e-27  Score=139.96  Aligned_cols=78  Identities=31%  Similarity=0.439  Sum_probs=69.0

Q ss_pred             CC-CCCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeeccc
Q psy10835          1 MS-RKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKRR   78 (80)
Q Consensus         1 m~-~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~~~   78 (80)
                      |+ .+..|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||+|+..++..+.+|.++|||++|++|++++.+
T Consensus         3 m~~~~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~~~   81 (81)
T 1th7_A            3 MNFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILISPLQTS   81 (81)
T ss_dssp             CCTTCHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECGGGEEEEEEC---
T ss_pred             ccccccchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecCCceeECCEEEECCCEEEEEEecCCC
Confidence            44 3468999999999999999999999999999999999999999999986666678899999999999999998753

>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=99.93  E-value=3e-27  Score=138.60  Aligned_cols=75  Identities=24%  Similarity=0.469  Sum_probs=53.1

Q ss_pred             CCCCCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeecc
Q psy10835          1 MSRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         1 m~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      ||++  |.++|++++|++|+|+|+||++|+|+|.|||+|||++|+||.|+..++..+.+|.++|||++|++|++.++
T Consensus         1 ms~~--~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~v~iRG~~I~~i~~~d~   75 (76)
T 3s6n_G            1 MSKA--HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIMLEALER   75 (76)
T ss_dssp             ---------------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC----CBSSEEECSSSEEEEEC---
T ss_pred             CCCc--chHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccCCcEeEcCEEEECCCeEEEEEeccC
Confidence            7766  55579999999999999999999999999999999999999997655566889999999999999999875

>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=99.93  E-value=1.3e-26  Score=137.80  Aligned_cols=73  Identities=32%  Similarity=0.578  Sum_probs=68.4

Q ss_pred             CCCCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEe
Q psy10835          2 SRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus         2 ~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~   74 (80)
                      +.+..|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||+|+..++..+.+|.++|||++|++|++
T Consensus        11 ~~~~~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~IRG~~I~~i~p   83 (83)
T 1mgq_A           11 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP   83 (83)
T ss_dssp             CCTTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEC
T ss_pred             ccCcChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecCCcccCCCEEEECCCEEEEEEC
Confidence            4678999999999999999999999999999999999999999999998667677889999999999999975

>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=99.93  E-value=2.2e-26  Score=134.97  Aligned_cols=72  Identities=26%  Similarity=0.419  Sum_probs=67.6

Q ss_pred             CChHHHHHhhhCCceEEEecCC-cccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeec
Q psy10835          5 ESLSQFIQQIHGRPVVVKLVSG-VDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus         5 ~~p~~~L~~~~~k~V~V~L~~g-~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      ..|.++|.++++++|+|+|+|| ++|+|+|.|||+|||++|+||+|+..++..+.+|.++|||++|++|++++
T Consensus         4 ~~P~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~nI~~i~~~d   76 (77)
T 1ljo_A            4 VLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQPQE   76 (77)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEEC-
T ss_pred             cchHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecCCcEeECCeEEEeCCeEEEEEeCC
Confidence            5899999999999999999999 99999999999999999999999866777789999999999999999986

>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=99.93  E-value=1.6e-26  Score=136.91  Aligned_cols=72  Identities=35%  Similarity=0.484  Sum_probs=67.3

Q ss_pred             CCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeec
Q psy10835          4 KESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus         4 ~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      +..|+++|.++++++|+|+|+||++|.|+|.+||+|||++|+||+|+ +++..+.+|.++|||++|++|++++
T Consensus         9 ~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~~~~~~~lg~v~iRG~~I~~i~~~d   80 (81)
T 1i8f_A            9 FATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-IDGNVYKRGTMVVRGENVLFISPVP   80 (81)
T ss_dssp             -CCHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-ETTEEEEEEEEEECGGGEEEEEECC
T ss_pred             ccchHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-cCCcccCCCEEEECCCEEEEEEeCC
Confidence            46899999999999999999999999999999999999999999998 6666788999999999999999876

>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=99.92  E-value=1.6e-26  Score=140.41  Aligned_cols=74  Identities=35%  Similarity=0.599  Sum_probs=63.0

Q ss_pred             CCCChHHHHHhhhCCceEEEecCC-cccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeec
Q psy10835          3 RKESLSQFIQQIHGRPVVVKLVSG-VDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus         3 ~~~~p~~~L~~~~~k~V~V~L~~g-~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      .+..|.++|++++|++|+|+|+|| ++|+|+|.|||+|||++|+||+|+.+++..+.+|.++|||++|++|.+++
T Consensus        18 ~~~~P~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~~~~~~~lg~v~IRG~nI~~I~~~~   92 (93)
T 1n9r_A           18 QPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELP   92 (93)
T ss_dssp             --------CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECGGGEEEEEECC
T ss_pred             ccCChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcCCCeEeEcCEEEEcCCeEEEEEeCC
Confidence            456899999999999999999999 99999999999999999999999867777789999999999999999886

>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=99.92  E-value=5.2e-26  Score=138.46  Aligned_cols=75  Identities=23%  Similarity=0.330  Sum_probs=66.3

Q ss_pred             CCCCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhh-ccEeeccccCeEEecCcEEEEEeec
Q psy10835          2 SRKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI-NGQLKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus         2 ~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~-~~~~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      +....|+++|.++++++|+|+|+||++|+|+|.|||+|||++|+||+|+. +++..+.+|.++|||++|++|.+..
T Consensus        16 ~~~~~Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~IRG~nI~~i~p~~   91 (94)
T 4emk_A           16 SMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKHSEMLLNGNGMCMLIPGG   91 (94)
T ss_dssp             ----CHHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTTCCEEEEEEEEECSTTEEEEEECC
T ss_pred             cccccCHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCCCcEeEcCEEEEcCCEEEEEEeCC
Confidence            34568999999999999999999999999999999999999999999975 5656788999999999999999764

>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=99.92  E-value=5.8e-26  Score=140.61  Aligned_cols=75  Identities=28%  Similarity=0.509  Sum_probs=55.5

Q ss_pred             CCCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhh-hccEeeccccCeEEecCcEEEEEeecc
Q psy10835          3 RKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEY-INGQLKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         3 ~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~-~~~~~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      .|..|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||+|. .+|+....+|.++|||++|++|.+|+.
T Consensus        13 ~~~~p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg~~~~~lg~v~IRG~nI~~I~~pd~   88 (105)
T 4emh_A           13 DPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIRGNNIKYLRIQDE   88 (105)
T ss_dssp             -------------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEEECGGGEEEEEC---
T ss_pred             CCCcHHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCCceeeEcCeEEEeCCeEEEEecCHH
Confidence            356899999999999999999999999999999999999999999985 466567789999999999999999874

>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=2.8e-25  Score=139.98  Aligned_cols=72  Identities=22%  Similarity=0.371  Sum_probs=67.2

Q ss_pred             ChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeecc
Q psy10835          6 SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         6 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      .|+++|+++++++|+|+|+||++|+|+|.+||+|||++|+||+|+..+.....++.++|||++|++|++|+.
T Consensus         2 ~p~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~~~~~~lg~v~IRG~nI~~I~~pd~   73 (119)
T 1b34_A            2 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDS   73 (119)
T ss_dssp             CHHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTT
T ss_pred             ChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecCCCceeEcceEEEcCCeEEEEEeccc
Confidence            699999999999999999999999999999999999999999998655556789999999999999999875

>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=99.90  E-value=3.7e-25  Score=140.76  Aligned_cols=74  Identities=16%  Similarity=0.241  Sum_probs=66.9

Q ss_pred             CCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeecc
Q psy10835          4 KESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         4 ~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      ...|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||+|+..+.....++.+||||++|+||++|+.
T Consensus         3 ~~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~~~~l~~v~IRGnnI~~I~lpd~   76 (126)
T 2y9a_D            3 IGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRFLILPDM   76 (126)
T ss_dssp             -CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCSS
T ss_pred             cccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCcEeecccEEEeCCEEEEEEcccc
Confidence            46899999999999999999999999999999999999999999997433346789999999999999999874

>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=99.90  E-value=8.1e-25  Score=133.31  Aligned_cols=74  Identities=27%  Similarity=0.342  Sum_probs=65.9

Q ss_pred             CChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhc-------cEeeccccCeEEecCcEEEEEeecc
Q psy10835          5 ESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYIN-------GQLKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         5 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~-------~~~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      .-|.++|++++||+|+|+|+||++|.|+|.|||+|||++|+||.|+..       ++..+.+|.++|||++|++|.+++.
T Consensus         9 ~~p~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nVv~I~~~d~   88 (96)
T 3bw1_A            9 ETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLISTPSE   88 (96)
T ss_dssp             CCHHHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEECGGGEEEEECCC-
T ss_pred             hhHHHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEECCCEEEEEEecCc
Confidence            579999999999999999999999999999999999999999999632       3456789999999999999998875


Q ss_pred             c
Q psy10835         78 R   78 (80)
Q Consensus        78 ~   78 (80)
                      .
T Consensus        89 ~   89 (96)
T 3bw1_A           89 D   89 (96)
T ss_dssp             -
T ss_pred             c
Confidence            3

>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=99.90  E-value=3.4e-25  Score=133.37  Aligned_cols=74  Identities=20%  Similarity=0.262  Sum_probs=63.5

Q ss_pred             CChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhh----------ccEeeccccCeEEecCcEEEEEe
Q psy10835          5 ESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI----------NGQLKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus         5 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~----------~~~~~~~~g~v~irG~~I~~I~~   74 (80)
                      .+|.++|.+++|++|+|+|+||++|.|+|.|||+||||+|+||.|+.          .+...+.+|.++|||++|++|++
T Consensus         3 ~~~~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~~I~~i~~   82 (91)
T 1d3b_B            3 VGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTV   82 (91)
T ss_dssp             ----CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEE
T ss_pred             CChhHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECCCeEEEEEc
Confidence            45677899999999999999999999999999999999999999952          24456789999999999999999


Q ss_pred             eccc
Q psy10835         75 QKRR   78 (80)
Q Consensus        75 ~~~~   78 (80)
                      ++..
T Consensus        83 ~~~~   86 (91)
T 1d3b_B           83 EGPP   86 (91)
T ss_dssp             EECC
T ss_pred             CCCC
Confidence            8753

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

Probab=99.90  E-value=7.9e-25  Score=132.81  Aligned_cols=73  Identities=23%  Similarity=0.390  Sum_probs=63.8

Q ss_pred             CCCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhc-----c--------EeeccccCeEEecCcE
Q psy10835          3 RKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYIN-----G--------QLKNKYGDTFIRGNNV   69 (80)
Q Consensus         3 ~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~-----~--------~~~~~~g~v~irG~~I   69 (80)
                      +...|+++|+.++|++|+|+|+||++|+|+|.|||+|||++|+||.|+..     +        +..+.+|.++|||++|
T Consensus         6 ~~~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG~nV   85 (93)
T 4emg_A            6 AVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDSV   85 (93)
T ss_dssp             ---CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECGGGE
T ss_pred             ccCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECCCeE
Confidence            34799999999999999999999999999999999999999999999632     3        1357899999999999


Q ss_pred             EEEEee
Q psy10835         70 LYISTQ   75 (80)
Q Consensus        70 ~~I~~~   75 (80)
                      ++|+++
T Consensus        86 v~I~p~   91 (93)
T 4emg_A           86 ILIAPP   91 (93)
T ss_dssp             EEEECC
T ss_pred             EEEEec
Confidence            999986

>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=99.89  E-value=2.7e-24  Score=135.75  Aligned_cols=74  Identities=23%  Similarity=0.381  Sum_probs=65.1

Q ss_pred             CCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhh----------ccEe-----eccccCeEEecCc
Q psy10835          4 KESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI----------NGQL-----KNKYGDTFIRGNN   68 (80)
Q Consensus         4 ~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~----------~~~~-----~~~~g~v~irG~~   68 (80)
                      ...|+++|.++++++|+|+|+||+.|+|+|.|||+||||+|+||+|+.          +|+.     .+.+|.++|||++
T Consensus        26 ~~~Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG~n  105 (121)
T 2fwk_A           26 IILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNN  105 (121)
T ss_dssp             CCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGG
T ss_pred             ccCcHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECCCE
Confidence            458999999999999999999999999999999999999999999864          1333     6789999999999


Q ss_pred             EEEEEeecc
Q psy10835         69 VLYISTQKR   77 (80)
Q Consensus        69 I~~I~~~~~   77 (80)
                      |++|.+.+.
T Consensus       106 Vv~I~~~~~  114 (121)
T 2fwk_A          106 VAMLVPGGD  114 (121)
T ss_dssp             EEEEESSSC
T ss_pred             EEEEEecCC
Confidence            999998764

>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=99.89  E-value=1.9e-24  Score=131.04  Aligned_cols=73  Identities=16%  Similarity=0.338  Sum_probs=66.0

Q ss_pred             CCChHHHHHhhhCCceEEEe----cCCcccceeeeeecccchhhhhhhhhhh-ccEeeccccCeEEecCcEEEEEeec
Q psy10835          4 KESLSQFIQQIHGRPVVVKL----VSGVDYRGVLSCLDGYMNIALEQTEEYI-NGQLKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus         4 ~~~p~~~L~~~~~k~V~V~L----~~g~~~~G~L~~~D~~mNivL~~~~~~~-~~~~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      ...|+++|.++++++|+|++    +||++|+|+|.|||+|||++|+||+|+. +++..+.+|.++|||++|.+|++.+
T Consensus        14 m~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~iRG~nV~~i~~~~   91 (92)
T 3s6n_E           14 MVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLLQSVS   91 (92)
T ss_dssp             CCCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSCCEEEEEEEEECGGGEEEEEEC-
T ss_pred             ccCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCCceeEcCeEEEeCCEEEEEEeCC
Confidence            34799999999999999999    9999999999999999999999999974 4555678999999999999999875

>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=99.87  E-value=2.1e-23  Score=130.46  Aligned_cols=73  Identities=19%  Similarity=0.347  Sum_probs=56.2

Q ss_pred             CChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhcc-------EeeccccCeEEecCcEEEEEeecc
Q psy10835          5 ESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYING-------QLKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         5 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~-------~~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      ..|...|.++++++|+|+|+||++|.|+|.|||+||||+|+||.|+..+       ...+.+|.++|||++|++|++++.
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            4567799999999999999999999999999999999999999997432       246789999999999999998764

>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=99.86  E-value=9.9e-23  Score=128.02  Aligned_cols=75  Identities=16%  Similarity=0.234  Sum_probs=63.7

Q ss_pred             CCChHHHHHhhh--CCceEEEecCCcccceeeeeecccchhhhhhhhhhhcc-------E-------eeccccCeEEecC
Q psy10835          4 KESLSQFIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYING-------Q-------LKNKYGDTFIRGN   67 (80)
Q Consensus         4 ~~~p~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~-------~-------~~~~~g~v~irG~   67 (80)
                      ...|+++|..++  +++|+|+|+||+.|.|+|.|||+|||++|+||.|+...       +       ..+.+|.++|||+
T Consensus        25 ~~~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~  104 (118)
T 1b34_B           25 NTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGD  104 (118)
T ss_dssp             -CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGG
T ss_pred             ccChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcCC
Confidence            358999999999  59999999999999999999999999999999986311       1       1346999999999


Q ss_pred             cEEEEEeeccc
Q psy10835         68 NVLYISTQKRR   78 (80)
Q Consensus        68 ~I~~I~~~~~~   78 (80)
                      +|++|.+++..
T Consensus       105 nVv~I~~~~~~  115 (118)
T 1b34_B          105 SVIVVLRNPLI  115 (118)
T ss_dssp             GEEEEEECCCC
T ss_pred             EEEEEEeCchh
Confidence            99999998753

>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=99.85  E-value=2.8e-22  Score=137.87  Aligned_cols=71  Identities=21%  Similarity=0.289  Sum_probs=63.7

Q ss_pred             ChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhc----------cEeeccccCeEEecCcEEEEEee
Q psy10835          6 SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYIN----------GQLKNKYGDTFIRGNNVLYISTQ   75 (80)
Q Consensus         6 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~----------~~~~~~~g~v~irG~~I~~I~~~   75 (80)
                      ++...|++++||+|+|+|+||++|+|+|.+||+||||+|+||+|+..          +++.+.+|+++|||+||++|++.
T Consensus         4 ~k~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~Isve   83 (231)
T 3pgw_B            4 GKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVE   83 (231)
T ss_pred             CchHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEEEEec
Confidence            56678999999999999999999999999999999999999999641          23568899999999999999976


Q ss_pred             c
Q psy10835         76 K   76 (80)
Q Consensus        76 ~   76 (80)
                      +
T Consensus        84 ~   84 (231)
T 3pgw_B           84 G   84 (231)
T ss_pred             C
Confidence            5

>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=99.83  E-value=2e-21  Score=124.07  Aligned_cols=66  Identities=30%  Similarity=0.501  Sum_probs=61.0

Q ss_pred             HHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeecc
Q psy10835          8 SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      .++|++++|++|+|+|+||++|+|+|.|||+|||++|+||+|+. +   ..+|.++|||++|++|.+++.
T Consensus         2 ~~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~-~---~~lg~v~IRG~nI~~I~~~d~   67 (130)
T 1m5q_A            2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA-G---EKFNRVFIMYRYIVHIDSTER   67 (130)
T ss_dssp             HHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTT-C---CEEEEEEECGGGEEEEEECCC
T ss_pred             hhHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEc-C---CEeceEEEeCCeEEEEEcCCc
Confidence            46899999999999999999999999999999999999999973 3   578999999999999999875

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

Probab=99.14  E-value=5.9e-11  Score=70.84  Aligned_cols=67  Identities=25%  Similarity=0.179  Sum_probs=57.7

Q ss_pred             CCChHHHHHhhhCCceEEEecCCcccceeeeeec-ccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeecc
Q psy10835          4 KESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLD-GYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         4 ~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      ..+|. .|++++||+|.|.|.||++|+|+|.++| ...|++|.|+.+  ++    .+..++|.|..|..|...+.
T Consensus         6 ~~~p~-el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~~~--~~----~~~~~iI~G~aI~eI~v~~~   73 (86)
T 1y96_A            6 KKGPL-EWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFLE--DG----SMSVTGIMGHAVQTVETMNE   73 (86)
T ss_dssp             HSCHH-HHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEECT--TS----CEEEEEECGGGEEEEEEEEC
T ss_pred             hCCHH-HHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeeccc--CC----eEEEEEEecceEEEEEEecc
Confidence            35676 7999999999999999999999999999 899999999932  22    35689999999999987664

>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=97.63  E-value=7e-05  Score=43.57  Aligned_cols=44  Identities=23%  Similarity=0.488  Sum_probs=32.6

Q ss_pred             CCCCCChHH-HHHhhh--CCceEEEecCCcccceeeeeecccchhhhh
Q psy10835          1 MSRKESLSQ-FIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIALE   45 (80)
Q Consensus         1 m~~~~~p~~-~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNivL~   45 (80)
                      |+++.+..+ +|+.+.  ..+|+|.|.||..++|++.+||+|+ +.|+
T Consensus         1 m~~~~~lQd~fLn~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~-VlL~   47 (77)
T 1kq1_A            1 MIANENIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYV-VSLN   47 (77)
T ss_dssp             -----CHHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             CCcccccHHHHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcE-EEEE
Confidence            666555533 777777  8889999999999999999999999 5554

>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=97.58  E-value=7.9e-05  Score=43.03  Aligned_cols=62  Identities=23%  Similarity=0.484  Sum_probs=41.5

Q ss_pred             CCCCCChH-HHHHhhh--CCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEee
Q psy10835          1 MSRKESLS-QFIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQ   75 (80)
Q Consensus         1 m~~~~~p~-~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~   75 (80)
                      |+++.+.. .+|+.+.  ..+|+|.|.||..++|.+.+||+|+ +.|++.            ...+|.=..|.+|.+.
T Consensus         3 m~~~~~lQd~~L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~-vlL~~~------------~~~LIYKhAIsTI~p~   67 (74)
T 2ylb_A            3 MAKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFV-ILLKNT------------VSQMVYKHAISTVVPS   67 (74)
T ss_dssp             -----CCHHHHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSE-EEEESS------------SEEEEEGGGEEEEEES
T ss_pred             CccccccHHHHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcE-EEEECC------------ceEEEEeeeEEEEeEc
Confidence            55444443 3777777  7889999999999999999999999 555531            1345555566666543

>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=97.55  E-value=8.8e-05  Score=43.63  Aligned_cols=44  Identities=30%  Similarity=0.640  Sum_probs=31.9

Q ss_pred             CCCCCChHH-HHHhhh--CCceEEEecCCcccceeeeeecccchhhhh
Q psy10835          1 MSRKESLSQ-FIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIALE   45 (80)
Q Consensus         1 m~~~~~p~~-~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNivL~   45 (80)
                      |+++.+..+ +|+.+.  +.+|+|.|.||..++|.+.+||+|+ +.|+
T Consensus         1 m~~~~nlQd~fLn~lrk~~~~Vtv~L~NG~~l~G~I~~fD~ft-VlL~   47 (82)
T 1u1s_A            1 MSKGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFV-ILLK   47 (82)
T ss_dssp             -----CCHHHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             CCcccchHHHHHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceE-EEEe
Confidence            555555433 677666  7789999999999999999999999 5555

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

Probab=97.42  E-value=0.00015  Score=42.27  Aligned_cols=35  Identities=34%  Similarity=0.605  Sum_probs=30.3

Q ss_pred             HHHhhh--CCceEEEecCCcccceeeeeecccchhhhh
Q psy10835         10 FIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIALE   45 (80)
Q Consensus        10 ~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNivL~   45 (80)
                      +|+.+.  +.+|+|.|.||..++|.+.+||+|+ +.|+
T Consensus        15 fLn~lrk~~~~Vtv~L~nG~~l~G~I~~fD~f~-VlL~   51 (78)
T 3ahu_A           15 FLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFT-VLLE   51 (78)
T ss_dssp             HHHHHHHHTCCEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             HHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceE-EEEE
Confidence            677776  8889999999999999999999999 4444

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

Probab=97.28  E-value=0.00019  Score=43.90  Aligned_cols=44  Identities=30%  Similarity=0.664  Sum_probs=31.7

Q ss_pred             CCCCCChH-HHHHhhhCC--ceEEEecCCcccceeeeeecccchhhhh
Q psy10835          1 MSRKESLS-QFIQQIHGR--PVVVKLVSGVDYRGVLSCLDGYMNIALE   45 (80)
Q Consensus         1 m~~~~~p~-~~L~~~~~k--~V~V~L~~g~~~~G~L~~~D~~mNivL~   45 (80)
                      |++..+.. .+|+.+..+  +|+|.|.||..++|++.+||+|+ +.|+
T Consensus         3 m~~~~nlQd~fLn~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~-VlL~   49 (104)
T 2y90_A            3 MAKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFV-ILLK   49 (104)
T ss_dssp             -----CCHHHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             CccccccHHHHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcE-EEEE
Confidence            55444443 377887744  79999999999999999999999 5555

>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=97.26  E-value=0.00057  Score=38.48  Aligned_cols=64  Identities=19%  Similarity=0.292  Sum_probs=45.8

Q ss_pred             ChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEe
Q psy10835          6 SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus         6 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~   74 (80)
                      ..-..|+..-|++|-|-......++|+|.-||+-. +.|+|++.+..++.    ..++++=+.|-.|-+
T Consensus         6 LLdktL~~WKg~rvAv~vg~ehSFtGiledFDeEv-iLL~dV~D~~GNk~----k~liv~idDinWimL   69 (71)
T 1ycy_A            6 LLEKVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIGNRG----KQMLIGLEDINWIML   69 (71)
T ss_dssp             HHHHHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTEEEE----EEEEEEGGGEEEEEE
T ss_pred             HHHHHHHHhCCcEEEEEecCcceeeeehhhcCcce-eehhhHHHHhcccc----ceeEEEeccceEEEe
Confidence            33457889999999999999999999999999876 78899998754322    256666666665544

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

Probab=96.97  E-value=0.00088  Score=39.07  Aligned_cols=40  Identities=28%  Similarity=0.609  Sum_probs=31.6

Q ss_pred             CChH-HHHHhhh--CCceEEEecCCcccceeeeeecccchhhhh
Q psy10835          5 ESLS-QFIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIALE   45 (80)
Q Consensus         5 ~~p~-~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNivL~   45 (80)
                      .+.. .+|..+.  ..+|+|.|.||..+.|.+.+||+|+ +.|+
T Consensus         6 ~nlQd~fLn~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~-VlL~   48 (79)
T 3sb2_A            6 QLLQDPFLNALRKEHVPVSIYLVNGIKLQGHVESFDQYV-VLLR   48 (79)
T ss_dssp             CTTHHHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             cchHHHHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcE-EEEE
Confidence            3443 3777776  5559999999999999999999999 4453

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

Probab=96.88  E-value=0.00072  Score=38.71  Aligned_cols=30  Identities=20%  Similarity=0.340  Sum_probs=25.8

Q ss_pred             hCCceEEEecCCcccceeeeeecccchhhhh
Q psy10835         15 HGRPVVVKLVSGVDYRGVLSCLDGYMNIALE   45 (80)
Q Consensus        15 ~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~   45 (80)
                      -+.+|+|.|.||..++|.+.+||+|+ +.|+
T Consensus        24 ~~~~Vtv~L~NG~~l~G~I~~fD~ft-Vll~   53 (71)
T 2qtx_A           24 NGKKVKIFLRNGEVLDAEVTGVSNYE-IMVK   53 (71)
T ss_dssp             TTCEEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             cCCcEEEEEeCCeEEEEEEEEEcceE-EEEE
Confidence            36779999999999999999999999 4443

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

Probab=96.69  E-value=0.0012  Score=39.14  Aligned_cols=66  Identities=18%  Similarity=0.302  Sum_probs=51.7

Q ss_pred             hhhCCceEEEecCCcccceeeeeec-ccchhhhhhhhhh-hccE--------eeccccCeEEecCcEEEEEeeccc
Q psy10835         13 QIHGRPVVVKLVSGVDYRGVLSCLD-GYMNIALEQTEEY-INGQ--------LKNKYGDTFIRGNNVLYISTQKRR   78 (80)
Q Consensus        13 ~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNivL~~~~~~-~~~~--------~~~~~g~v~irG~~I~~I~~~~~~   78 (80)
                      .++|+++.+.-+.+-.|.|+|..+| +..-+-|+||..+ .+|.        ....++.+..||+.|.-+...+..
T Consensus        10 ~yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~yIvFrgsDIKdL~V~~~~   85 (88)
T 2vxe_A           10 PELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQIAPQSQIYDYILFRGSDIKDIRVVNNH   85 (88)
T ss_dssp             CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCTTTCCSSCCCCCCSCEEEEEEETTTEEEEEECCCC
T ss_pred             cccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCcCCCCCcccCCCCceeeEEEEccCCccEEEEeccC
Confidence            3799999999999999999999999 5566889988764 2221        123457799999999999877643

>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=96.62  E-value=0.0012  Score=39.69  Aligned_cols=70  Identities=13%  Similarity=0.245  Sum_probs=51.2

Q ss_pred             hHHHHHhhhCCceEEEecCCcccceeeeeec-ccchhhhhhhhhh-hccE--------eeccccCeEEecCcEEEEEeec
Q psy10835          7 LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLD-GYMNIALEQTEEY-INGQ--------LKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus         7 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNivL~~~~~~-~~~~--------~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      |..--..++|+++.+.-+.+-.|.|+|..+| +..-+-|+||..+ .+|.        ....++.++.||+.|.-+...+
T Consensus        10 ~~~~~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~~ipp~~~vyeyIvFrGsDIKDL~V~e   89 (95)
T 2fb7_A           10 DPSGGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCE   89 (95)
T ss_dssp             ------CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSSCCCSCCCCSSCEEECSTTEEEEEESC
T ss_pred             CCCccCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCCccCCCCcceeEEEEcCCCcceEEEec
Confidence            3334567899999999999999999999999 5666889988764 2221        1234678999999999987754

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

Probab=96.29  E-value=0.0067  Score=35.72  Aligned_cols=64  Identities=16%  Similarity=0.233  Sum_probs=51.2

Q ss_pred             hHHHHHhhhCCceEEEecCCcccceeeeeec-ccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEee
Q psy10835          7 LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLD-GYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQ   75 (80)
Q Consensus         7 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~   75 (80)
                      .+.+|.++.|++|.+.+.++.+..|+..++| ...|+..++-.-- =|    ..++-++|++.|+.++..
T Consensus        20 fLr~l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TP-iG----v~~eAlLR~~Dii~~sF~   84 (85)
T 1y96_B           20 YLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQTP-IG----VQAEALLRCSDIISYTFK   84 (85)
T ss_dssp             HHHHHHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEECCT-TC----CEEEEEEEGGGEEEEEEC
T ss_pred             HHHHHHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhcCCC-cc----cchhhhhhcCCEEEEEec
Confidence            4567888999999999999999999999999 6677776554321 12    356889999999998764

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

Probab=96.24  E-value=0.015  Score=33.09  Aligned_cols=60  Identities=22%  Similarity=0.298  Sum_probs=43.5

Q ss_pred             CCCh-HHHHHhhh--CCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEe
Q psy10835          4 KESL-SQFIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus         4 ~~~p-~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~   74 (80)
                      +..| ...|+.++  .++|.|+|.+|..+.|.+.-+|.++ +.|.+..    +.      .++|.-..|.+|.+
T Consensus         6 t~lPsvR~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~c-l~L~~~~----~~------~~LI~r~AI~~I~p   68 (70)
T 3hfo_A            6 SGLPSVRQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDG-LGLVDDS----ER------STIVRLAAIAYITP   68 (70)
T ss_dssp             CSCHHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSE-EEEECTT----CC------EEEEEGGGEEEEEE
T ss_pred             CCCCcHHHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCE-EEEEcCC----CC------eEEEEeeeeEEEee
Confidence            3445 56788887  6678999999999999999999988 4454331    21      35666677777754

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

Probab=96.21  E-value=0.0029  Score=37.21  Aligned_cols=63  Identities=19%  Similarity=0.227  Sum_probs=51.8

Q ss_pred             HhhhCCceEEEecCCc-ccceeeeeeccc-chhhhhhhhhhhccEeeccccCeEEecCcEEEEEeecc
Q psy10835         12 QQIHGRPVVVKLVSGV-DYRGVLSCLDGY-MNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus        12 ~~~~~k~V~V~L~~g~-~~~G~L~~~D~~-mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      .+++|+.|.+..+++- .|.|.|..+|.. -||.|.++.  .+|- .....++.+++..|.-+.+.+.
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 999999999954 579999993  5664 4455779999999888777654

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

Probab=96.20  E-value=0.0073  Score=37.85  Aligned_cols=38  Identities=26%  Similarity=0.371  Sum_probs=33.2

Q ss_pred             HHhhhCCceEEEecCCcccceeeeeecccchhhh--hhhhh
Q psy10835         11 IQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIAL--EQTEE   49 (80)
Q Consensus        11 L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL--~~~~~   49 (80)
                      ...++|.+|.|+|+||..++|++..+|. -+|.|  ++|..
T Consensus         7 ~sqFlGy~V~v~LkDgs~~qG~I~~vd~-k~LtL~~~~a~~   46 (125)
T 4a53_A            7 VADFYGSNVEVLLNNDSKARGVITNFDS-SNSILQLRLAND   46 (125)
T ss_dssp             HHHHTTCEEEEEETTSCEEEEEEEEEET-TTTEEEEEETTT
T ss_pred             HHHhcCceEEEEECCCCEeeEEEEeecC-CeeEEecccccc
Confidence            4688999999999999999999999994 45777  88864

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

Probab=95.32  E-value=0.036  Score=31.64  Aligned_cols=56  Identities=21%  Similarity=0.334  Sum_probs=41.0

Q ss_pred             HHHHHhhh--CCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEe
Q psy10835          8 SQFIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus         8 ~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~   74 (80)
                      ...|+.++  .++|.|+|.+|..+.|.+.-.|.++ +.|.+..    +      ..++|.-..|.||.+
T Consensus        13 vR~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~c-l~L~~~~----~------~~~LI~R~AI~~Ikp   70 (72)
T 3hfn_A           13 IRQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTC-VCIADEN----S------RQTTIWKQAIAYLQP   70 (72)
T ss_dssp             HHHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSE-EEEEC-------------CEEEEEGGGEEEEEE
T ss_pred             HHHHHHHHhhCceEEEEecCCCEEEEEEEEECCCE-EEEEcCC----C------CeEEEEeeeeEEEEe
Confidence            56889998  4558889999999999999999888 4444332    1      136777777777765

>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=91.38  E-value=0.2  Score=32.24  Aligned_cols=36  Identities=14%  Similarity=0.229  Sum_probs=28.3

Q ss_pred             HHHHHhhhCCceEEEec----CCcccceeeeeecccchhhh
Q psy10835          8 SQFIQQIHGRPVVVKLV----SGVDYRGVLSCLDGYMNIAL   44 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~----~g~~~~G~L~~~D~~mNivL   44 (80)
                      ..-+..++|+.|.|+++    +.+.++|+|.++|+-. +.|
T Consensus        96 ~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~-v~l  135 (164)
T 1ib8_A           96 KDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEEDE-LTM  135 (164)
T ss_dssp             HHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETTE-EEE
T ss_pred             HHHHHHhCCcEEEEEEecccCCceEEEEEEEEEeCCE-EEE
Confidence            34577889999999994    4589999999999643 444

>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=91.18  E-value=0.086  Score=35.40  Aligned_cols=46  Identities=17%  Similarity=0.068  Sum_probs=35.4

Q ss_pred             hCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEec
Q psy10835         15 HGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRG   66 (80)
Q Consensus        15 ~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG   66 (80)
                      +|++|.+...++  +.|+..++|+...|+++..    +|......|++.+|+
T Consensus       187 ~g~~V~v~~~~~--~~G~~~gId~~G~L~v~~~----~G~~~~~~Gev~~r~  232 (233)
T 2eay_A          187 LGEEVKLLGEGK--ITGKLVGLSEKGGALILTE----EGIKEILSGEFSLRR  232 (233)
T ss_dssp             TTSEEEETTEEE--EEEEEEEECTTSCEEEEET----TEEEEECSCCEEEC-
T ss_pred             cCCEEEEEECCe--EEEEEEEECCCCeEEEEEC----CCeEEEEEeEEEEec
Confidence            699999987765  9999999999999998753    243344567888775

>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=89.70  E-value=0.14  Score=35.26  Aligned_cols=33  Identities=27%  Similarity=0.343  Sum_probs=29.8

Q ss_pred             hCCceEEEecCCcccceeeeeecccchhhhhhh
Q psy10835         15 HGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQT   47 (80)
Q Consensus        15 ~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~   47 (80)
                      +|++|+|.+.++..+.|+..++|+...|+++..
T Consensus       223 ~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~~  255 (270)
T 3rux_A          223 IGSRVRVELPGGQDVVGIARDIDDQGRLCLDVG  255 (270)
T ss_dssp             TTSEEEEECTTSCEEEEEEEEECTTSCEEEEET
T ss_pred             cCCEEEEEECCCeEEEEEEEEECCCCeEEEEEC
Confidence            499999998888999999999999999999754

>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=87.82  E-value=0.36  Score=33.59  Aligned_cols=47  Identities=21%  Similarity=0.167  Sum_probs=35.6

Q ss_pred             hCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEec
Q psy10835         15 HGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRG   66 (80)
Q Consensus        15 ~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG   66 (80)
                      +|++|.|...+ ..+.|+..++|+...|+++..    +|......|.+.+|.
T Consensus       272 ~g~~V~v~~~~-~~~~G~~~gid~~G~L~v~~~----~g~~~~~~Gev~~r~  318 (321)
T 1bia_A          272 INRPVKLIIGD-KEIFGISRGIDKQGALLLEQD----GIIKPWMGGEISLRS  318 (321)
T ss_dssp             TTSEEEEEETT-EEEEEEEEEECTTSCEEEEET----TEEEEESSCEEEEC-
T ss_pred             cCCEEEEEECC-cEEEEEEEEECCCCeEEEEEC----CCEEEEEeeeEEEec
Confidence            69999998765 579999999999999998743    233344567777764

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

Probab=87.52  E-value=0.57  Score=31.40  Aligned_cols=46  Identities=15%  Similarity=0.019  Sum_probs=34.2

Q ss_pred             hCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEe
Q psy10835         15 HGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIR   65 (80)
Q Consensus        15 ~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~ir   65 (80)
                      +|++|.+...++..+.|+..++|+...|+ +..    +|......|++.++
T Consensus       191 ~g~~V~v~~~~~~~~~G~~~gId~~G~L~-~~~----~G~~~~~~Gev~~~  236 (237)
T 2ej9_A          191 IGKQVKILLSNNEIITGKVYDIDFDGIVL-GTE----KGIERIPSGICIHV  236 (237)
T ss_dssp             TTCEEEEEETTSCEEEEEEEEECSSEEEE-EET----TEEEEEEGGGEEEE
T ss_pred             cCCEEEEEECCCeEEEEEEEEECCCCeEE-EcC----CCCEEEEEEEEEEe
Confidence            69999999887766999999999999998 643    23333345666554

>2dxu_A Biotin--[acetyl-COA-carboxylase] ligase; biotin biosynthesis, dimer, X-RAY diffraction, structural genomics, NPPSFA; HET: BT5; 1.28A {Pyrococcus horikoshii} PDB: 2dzc_A 2ejg_A* 2e3y_A* 2e41_A* 2e64_A 2ejf_A* 2zgw_A* 1wqw_A* 1wpy_A* 1wq7_A 1wnl_A* 1x01_A* 2dkg_A* 2dth_A* 2dti_A* 2dto_A* 2fyk_A* 2djz_A* 2hni_A 2e10_A ...

Probab=87.08  E-value=0.25  Score=33.17  Aligned_cols=46  Identities=22%  Similarity=0.317  Sum_probs=31.6

Q ss_pred             hCCceEEEecCCcccceeeeeecccchhhhhhhhhhhcc-EeeccccCeEEec
Q psy10835         15 HGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYING-QLKNKYGDTFIRG   66 (80)
Q Consensus        15 ~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~-~~~~~~g~v~irG   66 (80)
                      +|++|.+...++  +.|+..++|+...|+++..    +| ......|++.+|+
T Consensus       188 ~g~~V~v~~~~~--~~G~~~gId~~G~L~v~~~----~G~~~~~~~Gev~~~~  234 (235)
T 2dxu_A          188 LGVRVKILGDGS--FEGIAEDIDDFGRLIIRLD----SGEVKKVIYGDVSLRF  234 (235)
T ss_dssp             CSSEEEC----C--CEEEEEEECTTSCEEEECT----TSCEEEECCSSCCCEE
T ss_pred             cCCeEEEEECCe--EEEEEEEECCCCEEEEEEC----CCCEEEEEeeEEEEec
Confidence            699999988776  9999999999999999753    23 2334456766653

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

Probab=86.97  E-value=1.3  Score=26.52  Aligned_cols=64  Identities=13%  Similarity=0.210  Sum_probs=51.0

Q ss_pred             HhhhCCceEEEecCCc-ccceeeeeecccchhhhhhhhhhhccEe-eccccCeEEecCcEEEEEeeccc
Q psy10835         12 QQIHGRPVVVKLVSGV-DYRGVLSCLDGYMNIALEQTEEYINGQL-KNKYGDTFIRGNNVLYISTQKRR   78 (80)
Q Consensus        12 ~~~~~k~V~V~L~~g~-~~~G~L~~~D~~mNivL~~~~~~~~~~~-~~~~g~v~irG~~I~~I~~~~~~   78 (80)
                      ++++|+-|.|...+.- .|+|.+...|+ -+|.|.++.  .+|-. .....+|.++...|..+.+.+..
T Consensus         8 edwiG~~VSI~C~d~LGVyQG~I~~V~~-~~ItL~kaF--rNGiplk~~~~EVtLsa~DI~~L~IIe~~   73 (103)
T 2rm4_A            8 QDWIGCAVSIACDEVLGVFQGLIKQISA-EEITIVRAF--RNGVPLRKQNAEVVLKCTDIRSIDLIEPA   73 (103)
T ss_dssp             GGGTTCEEEEEECTTTCEEEEEEEEEET-TEEEEEEEE--ETTEECSCSSSCEEEETTTEEEEEEEECC
T ss_pred             cceeceEEEEeeCCcceEeeEEEEEccc-ceeEEhhhh--hcCcCcCCCCceEEEEecchhheeeeccc
Confidence            4789999999999986 99999999995 448888875  35631 23567999999999988877653

---

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	80
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	1e-20
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	1e-19
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	2e-19
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	2e-19
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	9e-19
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	7e-18
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	2e-17
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	2e-17
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	3e-16
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	5e-16
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	4e-14
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	1e-13
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	1e-06

>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 = 75.1 bits (185), Expect = 1e-20
 Identities = 23/64 (35%), Positives = 37/64 (57%)

Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNV 69
           + +    PV+V+L  G ++RG L   D +MN+ L   EE  NG++  K G   IRG+ V
Sbjct: 7  VLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTV 66

Query: 70 LYIS 73
          +++S
Sbjct: 67 VFVS 70

>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 = 72.8 bits (179), Expect = 1e-19
 Identities = 23/64 (35%), Positives = 37/64 (57%)

Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNV 69
           +      PV++KL    ++RGVL   D +MN+ L   EE  +G++  + G   IRG+N+
Sbjct: 10 ALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNI 69

Query: 70 LYIS 73
          +YIS
Sbjct: 70 VYIS 73

>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 = 72.4 bits (178), Expect = 2e-19
 Identities = 27/68 (39%), Positives = 39/68 (57%), Gaps = 1/68 (1%)

Query: 6  SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIR 65
          +L   +Q   G+ V+VKL    + RG+L   D ++N+ LE  EE I+G    K G   +R
Sbjct: 2  TLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGN-VYKRGTMVVR 60

Query: 66 GNNVLYIS 73
          G NVL+IS
Sbjct: 61 GENVLFIS 68

>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 = 72.0 bits (177), Expect = 2e-19
 Identities = 23/65 (35%), Positives = 36/65 (55%)

Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNV 69
           I +   + V+V L  G ++RG L   D ++N+ L   E   +G++  +YG   IRG+NV
Sbjct: 6  VIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNV 65

Query: 70 LYIST 74
          L IS 
Sbjct: 66 LAISP 70

>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 = 70.5 bits (173), Expect = 9e-19
 Identities = 23/70 (32%), Positives = 36/70 (51%)

Query: 4  KESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTF 63
           E+  + + +     V+VKL    + RG+L   D +MN+ L  +EE  +     K G   
Sbjct: 5  AETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIV 64

Query: 64 IRGNNVLYIS 73
          IRG+NV+ IS
Sbjct: 65 IRGDNVILIS 74

>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 = 68.2 bits (167), Expect = 7e-18
 Identities = 25/63 (39%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 12 QQIHGRPVVVKL-VSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVL 70
          + +    V VKL  +  +YRG L   D Y N+ L + EE++ G      G+ FIR NNVL
Sbjct: 2  KGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVL 61

Query: 71 YIS 73
          YI 
Sbjct: 62 YIR 64

>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 = 67.1 bits (164), Expect = 2e-17
 Identities = 12/64 (18%), Positives = 23/64 (35%)

Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNV 69
           + +  G  V  +  +G  YRG L   +  MN  +             +    +IRG  +
Sbjct: 6  VLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKI 65

Query: 70 LYIS 73
           ++ 
Sbjct: 66 RFLI 69

>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 = 67.0 bits (164), Expect = 2e-17
 Identities = 16/67 (23%), Positives = 32/67 (47%)

Query: 7  LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRG 66
          L +F+ ++    V ++L +G    G ++ +D  MN  L+  +  +  +   +     IRG
Sbjct: 2  LVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRG 61

Query: 67 NNVLYIS 73
          NN+ Y  
Sbjct: 62 NNIRYFI 68

>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 = 64.4 bits (157), Expect = 3e-16
 Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 8  SQFIQQIHGRPVVVKLVSG-VDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRG 66
          +Q ++ + G+ + V++        G L  +D YMN+ L    E    +     G+  +RG
Sbjct: 7  NQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRG 66

Query: 67 NNVLYISTQ 75
          NNV+ I  Q
Sbjct: 67 NNVVLIQPQ 75

>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 = 65.1 bits (159), Expect = 5e-16
 Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 4/69 (5%)

Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNV 69
           +  + GR V V L +G  Y+GVL  +D  +NI L             K+   FI    +
Sbjct: 4  ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAG----EKFNRVFIMYRYI 59

Query: 70 LYISTQKRR 78
          ++I + +RR
Sbjct: 60 VHIDSTERR 68

>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 = 59.5 bits (144), Expect = 4e-14
 Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 15/80 (18%)

Query: 9  QFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI---------------NG 53
            I +  G  + V +    ++ GVL   D Y+N+ L+  +EY                  
Sbjct: 8  ALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKR 67

Query: 54 QLKNKYGDTFIRGNNVLYIS 73
           + N+     + GNNV  + 
Sbjct: 68 VMVNRLETILLSGNNVAMLV 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 = 57.9 bits (140), Expect = 1e-13
 Identities = 15/78 (19%), Positives = 28/78 (35%), Gaps = 14/78 (17%)

Query: 6  SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI----------NGQL 55
           + Q I       +   L  G  + G     D +MN+ L   +E+             + 
Sbjct: 2  KMLQHI----DYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREE 57

Query: 56 KNKYGDTFIRGNNVLYIS 73
          K   G   +RG N++ ++
Sbjct: 58 KRVLGLVLLRGENLVSMT 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 = 40.3 bits (94), Expect = 1e-06
 Identities = 11/73 (15%), Positives = 24/73 (32%), Gaps = 14/73 (19%)

Query: 15 HGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI--------------NGQLKNKYG 60
          +   V++   +     G +   D + N+ LE  +E                         
Sbjct: 13 NNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYIS 72

Query: 61 DTFIRGNNVLYIS 73
            F+RG++V+ + 
Sbjct: 73 KMFLRGDSVIVVL 85

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	80
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.94
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.93
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.93
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.93
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.92
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.92
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.91
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.91
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.89
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.89
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.85
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.85
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.82
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	96.9
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	96.9
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	96.89
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	96.56
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	96.51
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	93.75
d2qqra1	59	Jumonji domain-containing protein 2A {Human (Homo	84.78

>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=7.4e-28  Score=138.64  Aligned_cols=71  Identities=32%  Similarity=0.546  Sum_probs=66.9

Q ss_pred             CCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEe
Q psy10835          4 KESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus         4 ~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~   74 (80)
                      |..|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||+|+..++..+.+|.++|||++|++|++
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            57899999999999999999999999999999999999999999998777677889999999999999975

>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=99.93  E-value=2.5e-27  Score=135.92  Aligned_cols=70  Identities=34%  Similarity=0.532  Sum_probs=66.2

Q ss_pred             CChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEe
Q psy10835          5 ESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus         5 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~   74 (80)
                      ..|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||.+..+++..+.+|.++|||++|++|++
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            3799999999999999999999999999999999999999999998777777889999999999999986

>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=99.93  E-value=6.7e-27  Score=135.21  Aligned_cols=71  Identities=32%  Similarity=0.598  Sum_probs=66.8

Q ss_pred             CCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEe
Q psy10835          4 KESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus         4 ~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~   74 (80)
                      ...|+++|++++||+|+|+|+||++|+|+|.+||+|||++|+||+|+.+++....+|.++|||++|++|++
T Consensus         4 ~~~Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~~~~~~~~~~~IRG~~I~~I~p   74 (74)
T d1mgqa_           4 VQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP   74 (74)
T ss_dssp             TTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEC
T ss_pred             ccCcHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCCCeEeEcceEEEeCCEEEEEeC
Confidence            46799999999999999999999999999999999999999999998777777889999999999999975

>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=7.2e-27  Score=134.58  Aligned_cols=72  Identities=17%  Similarity=0.253  Sum_probs=66.2

Q ss_pred             CChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeec
Q psy10835          5 ESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus         5 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      ..|+.+|+++.|++|+|+|+||++|+|+|.+||+|||++|+||++...+.+...++.++|||++|+||++|+
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            369999999999999999999999999999999999999999998755545567999999999999999986

>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=1.6e-26  Score=134.30  Aligned_cols=72  Identities=32%  Similarity=0.453  Sum_probs=66.1

Q ss_pred             CCCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEe
Q psy10835          3 RKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus         3 ~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~   74 (80)
                      .+..|.++|++++|++|+|+|+||++|+|+|.+||+|||++|+||+|+..+++.+.+|.++|||++|++|++
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            345689999999999999999999999999999999999999999997666566789999999999999986

>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=99.92  E-value=5.2e-26  Score=131.95  Aligned_cols=72  Identities=25%  Similarity=0.392  Sum_probs=66.1

Q ss_pred             CCCChHHHHHhhhCCceEEEecCC-cccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEe
Q psy10835          3 RKESLSQFIQQIHGRPVVVKLVSG-VDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIST   74 (80)
Q Consensus         3 ~~~~p~~~L~~~~~k~V~V~L~~g-~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~   74 (80)
                      +-..|+++|++++|++|+|+|++| +.|.|+|.+||+|||++|+||+|+..++..+.++.++|||++|++|.+
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            346799999999999999999976 789999999999999999999998666677899999999999999986

>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=99.91  E-value=8.1e-26  Score=129.91  Aligned_cols=69  Identities=39%  Similarity=0.611  Sum_probs=63.1

Q ss_pred             hHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeec
Q psy10835          7 LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus         7 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      +-++|++++||+|+|+|+||++|+|+|.+||+|||++|+||.|+.+++ .+++|.++|||++|++|++++
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            457899999999999999999999999999999999999999976664 467999999999999999764

>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=9.6e-26  Score=128.69  Aligned_cols=66  Identities=38%  Similarity=0.667  Sum_probs=60.3

Q ss_pred             HHhhhCCceEEEec-CCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeec
Q psy10835         11 IQQIHGRPVVVKLV-SGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus        11 L~~~~~k~V~V~L~-~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      |++++||+|.|+|+ +|++|+|+|.+||+|||++|+||+|+.+++....+|.++|||++|++|+..|
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~IRG~nI~~I~~~p   67 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELP   67 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECGGGEEEEEECC
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEecCCcccCcCeEEEECCEEEEEEeCC
Confidence            57899999999999 5678999999999999999999999877777788999999999999998554

>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=99.89  E-value=1.4e-24  Score=127.26  Aligned_cols=70  Identities=21%  Similarity=0.362  Sum_probs=64.5

Q ss_pred             HHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeecc
Q psy10835          8 SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      ..||+++.|++|+|+|+||.+|+|+|.++|+|||+.|+||++...+++...++.++|||++|+||++|+.
T Consensus         3 v~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~~Ir~i~lPd~   72 (80)
T d1b34a_           3 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDS   72 (80)
T ss_dssp             HHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTT
T ss_pred             HHHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCCEEEcccEEEcCCEEEEEECCCC
Confidence            5799999999999999999999999999999999999999987555556789999999999999999874

>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=99.89  E-value=3.9e-24  Score=127.77  Aligned_cols=72  Identities=24%  Similarity=0.385  Sum_probs=63.7

Q ss_pred             CCChHHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhc---------------cEeeccccCeEEecCc
Q psy10835          4 KESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYIN---------------GQLKNKYGDTFIRGNN   68 (80)
Q Consensus         4 ~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~---------------~~~~~~~g~v~irG~~   68 (80)
                      -..|+++|+++++|+|+|.|+||+.|.|+|.+||+||||+|+||.|+..               ....+.+|++||||++
T Consensus         3 ~~~Pl~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~~   82 (92)
T d2fwka1           3 IILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNN   82 (92)
T ss_dssp             CCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGG
T ss_pred             ccChHHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCCE
Confidence            3579999999999999999999999999999999999999999998521               1234678999999999


Q ss_pred             EEEEEee
Q psy10835         69 VLYISTQ   75 (80)
Q Consensus        69 I~~I~~~   75 (80)
                      |++|++.
T Consensus        83 Vv~I~p~   89 (92)
T d2fwka1          83 VAMLVPG   89 (92)
T ss_dssp             EEEEESS
T ss_pred             EEEEEeC
Confidence            9999874

>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=99.85  E-value=7.7e-23  Score=119.72  Aligned_cols=65  Identities=22%  Similarity=0.335  Sum_probs=57.9

Q ss_pred             HHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhc----------cEeeccccCeEEecCcEEEEEee
Q psy10835         11 IQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYIN----------GQLKNKYGDTFIRGNNVLYISTQ   75 (80)
Q Consensus        11 L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~----------~~~~~~~g~v~irG~~I~~I~~~   75 (80)
                      |.++++++|+|.|+||+.|.|+|.|||+||||+|+||.|+..          ....+.+|.++|||++|++|++.
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            678999999999999999999999999999999999998521          12357799999999999999874

>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=99.85  E-value=1.4e-22  Score=121.49  Aligned_cols=71  Identities=17%  Similarity=0.267  Sum_probs=61.2

Q ss_pred             ChHHHHHhhh--CCceEEEecCCcccceeeeeecccchhhhhhhhhhhc----c----------EeeccccCeEEecCcE
Q psy10835          6 SLSQFIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYIN----G----------QLKNKYGDTFIRGNNV   69 (80)
Q Consensus         6 ~p~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~----~----------~~~~~~g~v~irG~~I   69 (80)
                      .|+++|.+++  +++|+|.|++|+.+.|+|.|||+||||+|+||.|+..    +          ...+.+|.++|||++|
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            5999999998  9999999999999999999999999999999999521    0          1235789999999999


Q ss_pred             EEEEeec
Q psy10835         70 LYISTQK   76 (80)
Q Consensus        70 ~~I~~~~   76 (80)
                      ++|..++
T Consensus        82 v~I~~~p   88 (93)
T d1b34b_          82 IVVLRNP   88 (93)
T ss_dssp             EEEEECC
T ss_pred             EEEEcCh
Confidence            9997665

>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-21  Score=121.22  Aligned_cols=66  Identities=29%  Similarity=0.461  Sum_probs=60.2

Q ss_pred             HHHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEEeecc
Q psy10835          8 SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYISTQKR   77 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~~~~~   77 (80)
                      +++|++++|++|+|+|+||++|.|+|.+||+|||++|+||++...+    .++.++|||++|++|.+|+.
T Consensus         2 ~~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~~~----k~~~v~IRG~~I~~I~~~e~   67 (127)
T d1m5q1_           2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGE----KFNRVFIMYRYIVHIDSTER   67 (127)
T ss_dssp             HHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETTCC----EEEEEEECGGGEEEEEECSC
T ss_pred             hhHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECCCC----cccEEEEeCCeEEEEEcchh
Confidence            5789999999999999999999999999999999999999986433    46789999999999999875

>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=96.90  E-value=0.00035  Score=39.44  Aligned_cols=63  Identities=14%  Similarity=0.342  Sum_probs=49.6

Q ss_pred             hhCCceEEEecCCcccceeeeeec-ccchhhhhhhhhh-hccE--------eeccccCeEEecCcEEEEEeec
Q psy10835         14 IHGRPVVVKLVSGVDYRGVLSCLD-GYMNIALEQTEEY-INGQ--------LKNKYGDTFIRGNNVLYISTQK   76 (80)
Q Consensus        14 ~~~k~V~V~L~~g~~~~G~L~~~D-~~mNivL~~~~~~-~~~~--------~~~~~g~v~irG~~I~~I~~~~   76 (80)
                      ++|+++.+.-+.+-.|.|+|..+| +.--+.|+||..+ .+|.        ....++.+..||+.|.-+...+
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~~IvFrgsDIKdL~v~e   74 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCE   74 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSSCCCCCCCCEEEEEEETTTEEEEEESS
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCCccCCCCcceeEEEEcCcCcceEEecc
Confidence            689999999999999999999999 4445888988764 2221        1234678999999999988754

>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=96.90  E-value=0.0011  Score=35.48  Aligned_cols=60  Identities=18%  Similarity=0.307  Sum_probs=42.8

Q ss_pred             HHHHhhhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEecCcEEEEE
Q psy10835          9 QFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIS   73 (80)
Q Consensus         9 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~irG~~I~~I~   73 (80)
                      ..|++.-|++|-|-......++|+|+-||+-. |.|+|++.+..++.    ..++++=+.|-.|-
T Consensus         5 ktL~~WKg~kvAv~vgsehSFtGiledFDeEv-iLL~dV~D~~GNk~----k~llv~idD~nWim   64 (66)
T d1ycya1           5 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIGNRG----KQMLIGLEDINWIM   64 (66)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTEEEE----EEEEEEGGGEEEEE
T ss_pred             HHHHHhCCcEEEEEecCcceeEEEhhhcCcce-EeehhhHHHhcccc----ceeEEEeccceeEE
Confidence            46888999999999999999999999999876 78899998754322    25566666555543

>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=96.89  E-value=0.00039  Score=35.28  Aligned_cols=47  Identities=21%  Similarity=0.171  Sum_probs=36.4

Q ss_pred             hhCCceEEEecCCcccceeeeeecccchhhhhhhhhhhccEeeccccCeEEe
Q psy10835         14 IHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIR   65 (80)
Q Consensus        14 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNivL~~~~~~~~~~~~~~~g~v~ir   65 (80)
                      |+||+|+|..-+ +++.|+-.++|+...|+|+..    ++.+....|++.+|
T Consensus         1 f~gk~V~v~~g~-~~i~G~a~gId~~G~Lll~t~----~g~~~~~sGEVSlR   47 (47)
T d1biaa2           1 FINRPVKLIIGD-KEIFGISRGIDKQGALLLEQD----GIIKPWMGGEISLR   47 (47)
T ss_dssp             TTTSEEEEEETT-EEEEEEEEEECTTSCEEEEET----TEEEEESSCEEEEC
T ss_pred             CCCCEEEEEECC-eEEEEEEeeECCCCcEEEEEC----CCEEEEEEEEEEeC
Confidence            689999997655 779999999999999999732    34344556777765

>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=96.56  E-value=0.0014  Score=35.05  Aligned_cols=34  Identities=21%  Similarity=0.383  Sum_probs=28.2

Q ss_pred             HHHhhh--CCceEEEecCCcccceeeeeecccchhh
Q psy10835         10 FIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIA   43 (80)
Q Consensus        10 ~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNiv   43 (80)
                      +|+.+.  ..+|+|-|.||-.+.|.+.+||+|.=+.
T Consensus         6 fln~lr~~~~~VtifL~nGvkl~G~I~~fD~ftvlL   41 (60)
T d1kq1a_           6 ALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSL   41 (60)
T ss_dssp             HHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHHHcCCcEEEEEECCcEEEEEEEEEcceEEEE
Confidence            455554  6779999999999999999999998444

>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=96.51  E-value=0.0016  Score=35.44  Aligned_cols=35  Identities=23%  Similarity=0.589  Sum_probs=28.9

Q ss_pred             HHHhhh--CCceEEEecCCcccceeeeeecccchhhhh
Q psy10835         10 FIQQIH--GRPVVVKLVSGVDYRGVLSCLDGYMNIALE   45 (80)
Q Consensus        10 ~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNivL~   45 (80)
                      +|..+.  ..+|+|-|.||-.+.|.+.+||+|.= .|+
T Consensus         6 fLn~~rk~~~~VtifL~nGvkl~G~I~~fD~ftv-LL~   42 (66)
T d1u1sa1           6 YLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVI-LLK   42 (66)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEE-EEE
T ss_pred             HHHHHHHcCCcEEEEEEcCcEEEEEEEEEcceEE-EEE
Confidence            566665  66799999999999999999999984 454

>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=93.75  E-value=0.032  Score=29.97  Aligned_cols=36  Identities=14%  Similarity=0.230  Sum_probs=28.7

Q ss_pred             HHHHHhhhCCceEEEecC----Ccccceeeeeecccchhhh
Q psy10835          8 SQFIQQIHGRPVVVKLVS----GVDYRGVLSCLDGYMNIAL   44 (80)
Q Consensus         8 ~~~L~~~~~k~V~V~L~~----g~~~~G~L~~~D~~mNivL   44 (80)
                      .+-+..++|+.|.|+|+.    -+.++|.|.++|+-. +.|
T Consensus         6 ~~~f~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~~-i~l   45 (74)
T d1ib8a1           6 KDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEEDE-LTM   45 (74)
T ss_dssp             HHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETTE-EEE
T ss_pred             HHHHHHhCCCEEEEEEecccCCceEEEEEEEeecCCe-EEE
Confidence            356788999999999873    479999999999753 444

>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=84.78  E-value=0.34  Score=25.15  Aligned_cols=23  Identities=26%  Similarity=0.303  Sum_probs=21.2

Q ss_pred             hCCceEEEecCCcccceeeeeec
Q psy10835         15 HGRPVVVKLVSGVDYRGVLSCLD   37 (80)
Q Consensus        15 ~~k~V~V~L~~g~~~~G~L~~~D   37 (80)
                      +|++|.-+-+||+.|.+.+.+.-
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            69999999999999999998865