Citrus Sinensis ID: 030131

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180--
Protein Sequence
MEGQVGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKTLPVRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQARGSSQG
Secondary Structure (PSIPRED)
cccccccccccEEcccEEEEEEccccEEEEEEEEEEccccEEEEEEcccccccccEEEEEcccEEEEEEEcccccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHccccEEEEccEEEEEEEEEEcccccccccccccHHHHHHHHHHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEEEEEEEEEEccccEEEEEEEEEcccccEEEEEEcccccccccEEEEEccEEEEEEEEcccccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccEEEccccEEEEcEEEEcccccccccccccHHHHHHHHHHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
megqvggsgeeFAVGCLLSIKttlgdefdgqvmafDRFTNMLVIQEglksgprrniRLLNANYikdfsflgqaddpldpkkcfldlSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSktlpvrwdKTVIVVMNEvrvsspylpesvsggtAAANERVKKVLEFERKRLQARGSSQG
Flexible Loop (DISEMBL)
megqvggsgeeFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEglksgprrnIRLLNANYIKDFSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQaeadaqrigvgVTTEAQNIFdalsktlpvrwDKTVIVVMNEVrvsspylpesvsggtaaaNERVKKVLEFERkrlqargssqg
Low Complexity Region (SEG)
MEGQVGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKTLPVRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQARGSSQG
Disordered region (IsUnstruct)
**********EFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKTLPVRWDKTVIVVMNEVRVSSPY***********************************
Disordered Region (DISOPRED)
***********FAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQ*******RRNIRLLNANYIKDF*******************************************VTTEAQNIFDALSKTLPVRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFER***********
Disordered Region (DISEMBL)
********GEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKTLPVRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKR*********
Disordered Region (DISPRO)
********GEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKTLPVRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQA******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEGQVGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKTLPVRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQARGSSQG
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	182	2.2.26 [Sep-21-2011]
Q6GP89	194	Protein LSM12 homolog OS=	N/A	no	0.895	0.840	0.311	3e-16
Q6P833	194	Protein LSM12 homolog OS=	yes	no	0.895	0.840	0.311	2e-15
Q6PBA2	196	Protein LSM12 homolog A O	yes	no	0.950	0.882	0.284	2e-15
Q6NSN1	196	Protein LSM12 homolog B O	no	no	0.950	0.882	0.284	2e-14
Q5RAT5	195	Protein LSM12 homolog OS=	yes	no	0.868	0.810	0.304	3e-14
Q9D0R8	195	Protein LSM12 homolog OS=	yes	no	0.868	0.810	0.304	3e-14
Q3MHD2	195	Protein LSM12 homolog OS=	yes	no	0.868	0.810	0.304	3e-14
Q0VCF9	195	Protein LSM12 homolog OS=	yes	no	0.868	0.810	0.304	3e-14
Q5ZML5	194	Protein LSM12 homolog OS=	yes	no	0.961	0.902	0.284	6e-14
Q9VYR0	217	Protein LSM12 homolog A O	yes	no	0.851	0.714	0.25	3e-08

>sp|Q6GP89|LSM12_XENLA Protein LSM12 homolog OS=Xenopus laevis GN=lsm12 PE=2 SV=1

 Score = 84.7 bits (208), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 52/167 (31%), Positives = 85/167 (50%), Gaps = 4/167 (2%)

Query: 5   VGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGP--RRNIRLLNAN 62
           + G GE FA+G  +S +T       G+V+AFD  + ML ++    SG     +I LLN +
Sbjct: 1   MAGPGEYFAIGAYVSCRTCQETRLQGEVVAFDYPSKMLALKCPSSSGKANHADILLLNLD 60

Query: 63  YIKDFSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDAL 122
           Y+ D   + +      P    L++++L +R  L   +  + A  I  GV+ + Q +F  +
Sbjct: 61  YVSDVEVINERTQ-TPPPLASLNITKLASRARLEKEEKLSQAYAISAGVSLDGQQLFQTI 119

Query: 123 SKTLP-VRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLE 168
            KT+   +W +  IVVM+EV +S PY  E+  G    A   V K++E
Sbjct: 120 HKTIKDCKWQEKNIVVMDEVVISPPYQVENCKGKEGRALTHVCKIVE 166

Xenopus laevis (taxid: 8355)

>sp|Q6P833|LSM12_XENTR Protein LSM12 homolog OS=Xenopus tropicalis GN=lsm12 PE=2 SV=2

 Score = 82.0 bits (201), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 52/167 (31%), Positives = 84/167 (50%), Gaps = 4/167 (2%)

Query: 5   VGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSG-PRR-NIRLLNAN 62
           + G GE FA+G  +S +T       G+V+AFD  + ML ++    SG P   +I LLN +
Sbjct: 1   MAGPGEYFAIGAYVSCRTCQETRLQGEVVAFDYPSKMLALKCPSSSGKPNHADILLLNLD 60

Query: 63  YIKDFSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDAL 122
           Y+ D   + +      P    L++++L +R  L   +  + A  I  GV+ + Q +F  +
Sbjct: 61  YVSDVEVINERTQ-TPPPLASLNITKLASRARLEKEEKLSQAYAISAGVSLDGQQLFQTI 119

Query: 123 SKTLP-VRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLE 168
            KT+   +W +  IVVM E  +S PY  E+  G    A   V K++E
Sbjct: 120 HKTIKDCKWQEKNIVVMEEAVISPPYQVENCKGKEGRALCHVCKIVE 166

Xenopus tropicalis (taxid: 8364)

>sp|Q6PBA2|LS12A_DANRE Protein LSM12 homolog A OS=Danio rerio GN=lsm12a PE=2 SV=1

 Score = 81.6 bits (200), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 51/179 (28%), Positives = 92/179 (51%), Gaps = 6/179 (3%)

Query: 7   GSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRR--NIRLLNANYI 64
           G GE F+VG  +S  T LG    G+V+AFD  + ML ++    SG     ++ L+N  Y+
Sbjct: 5   GPGEYFSVGSHVSCLTCLGQRLQGEVVAFDYPSKMLTLKCPSSSGKPNLSDVILINLAYV 64

Query: 65  KDFSFLG-QADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALS 123
            +   +  + + P  P    L++S+L  R         + A  I  GV+ E Q +F  + 
Sbjct: 65  SEVDIINDRTETP--PPLASLNISKLANRARTEKEDKLSQAYAISAGVSIEGQQLFQTIH 122

Query: 124 KTLP-VRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQARGSSQ 181
           KT+   +W +  I+VM++V +S PY  E+  G   +A   ++K++E   + ++++ + Q
Sbjct: 123 KTIKDCKWQEKNIIVMDDVVISPPYQVENCKGKEGSALSHIRKIVEKHFRDVESQKTMQ 181

Danio rerio (taxid: 7955)

>sp|Q6NSN1|LS12B_DANRE Protein LSM12 homolog B OS=Danio rerio GN=lsm12b PE=2 SV=1

 Score = 79.0 bits (193), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 51/179 (28%), Positives = 92/179 (51%), Gaps = 6/179 (3%)

Query: 7   GSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRR--NIRLLNANYI 64
           G GE F+VG  +S  T LG    G+V+AFD  + ML ++    SG     ++ L+N  Y+
Sbjct: 5   GPGEYFSVGSHVSCLTCLGQRLQGEVVAFDYPSKMLTLKCAPSSGKPNLSDVMLVNLAYV 64

Query: 65  KDFSFL-GQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALS 123
            +   +  +A+ P  P    L+ ++L  R         + A  +  GV+ E Q +F  + 
Sbjct: 65  SEVDIITDRAETP--PPLASLNFNKLVNRARAEKEDKLSLAYAVSAGVSVEGQQLFQTIH 122

Query: 124 KTLP-VRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQARGSSQ 181
           KT+   +W +  I+VM++V +S PY  ++  G   +A   V+K++E   + ++++ S Q
Sbjct: 123 KTIKECKWQEKNIIVMDDVVISPPYQVDNCKGKEGSALSHVRKIVEKHFRDVESQISVQ 181

Danio rerio (taxid: 7955)

>sp|Q5RAT5|LSM12_PONAB Protein LSM12 homolog OS=Pongo abelii GN=LSM12 PE=2 SV=1

 Score = 78.2 bits (191), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 50/164 (30%), Positives = 85/164 (51%), Gaps = 6/164 (3%)

Query: 9   GEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSG-PRR-NIRLLNANYIKD 66
           GE F+VG  +S +T       G+V+AFD  + ML ++    SG P   +I L+N  Y+ +
Sbjct: 6   GEYFSVGSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPSSSGKPNHADILLINLQYVSE 65

Query: 67  FSFLG-QADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKT 125
              +  + + P  P    L++S+L ++      +  + A  I  GV+ E Q +F  + KT
Sbjct: 66  VEIINDRTETP--PPLASLNVSKLASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKT 123

Query: 126 LP-VRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLE 168
           +   +W +  IVVM EV ++ PY  E+  G   +A   V+K++E
Sbjct: 124 IKDCKWQEKNIVVMEEVVITPPYQVENCKGKEGSALSHVRKIVE 167

Pongo abelii (taxid: 9601)

>sp|Q9D0R8|LSM12_MOUSE Protein LSM12 homolog OS=Mus musculus GN=Lsm12 PE=1 SV=1

 Score = 78.2 bits (191), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 50/164 (30%), Positives = 85/164 (51%), Gaps = 6/164 (3%)

Query: 9   GEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSG-PRR-NIRLLNANYIKD 66
           GE F+VG  +S +T       G+V+AFD  + ML ++    SG P   +I L+N  Y+ +
Sbjct: 6   GEYFSVGSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPSSSGKPNHADILLINLQYVSE 65

Query: 67  FSFLG-QADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKT 125
              +  + + P  P    L++S+L ++      +  + A  I  GV+ E Q +F  + KT
Sbjct: 66  VEIINDRTETP--PPLASLNVSKLASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKT 123

Query: 126 LP-VRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLE 168
           +   +W +  IVVM EV ++ PY  E+  G   +A   V+K++E
Sbjct: 124 IKDCKWQEKNIVVMEEVVITPPYQVENCKGKEGSALSHVRKIVE 167

Mus musculus (taxid: 10090)

>sp|Q3MHD2|LSM12_HUMAN Protein LSM12 homolog OS=Homo sapiens GN=LSM12 PE=1 SV=2

 Score = 78.2 bits (191), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 50/164 (30%), Positives = 85/164 (51%), Gaps = 6/164 (3%)

Query: 9   GEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSG-PRR-NIRLLNANYIKD 66
           GE F+VG  +S +T       G+V+AFD  + ML ++    SG P   +I L+N  Y+ +
Sbjct: 6   GEYFSVGSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPSSSGKPNHADILLINLQYVSE 65

Query: 67  FSFLG-QADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKT 125
              +  + + P  P    L++S+L ++      +  + A  I  GV+ E Q +F  + KT
Sbjct: 66  VEIINDRTETP--PPLASLNVSKLASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKT 123

Query: 126 LP-VRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLE 168
           +   +W +  IVVM EV ++ PY  E+  G   +A   V+K++E
Sbjct: 124 IKDCKWQEKNIVVMEEVVITPPYQVENCKGKEGSALSHVRKIVE 167

Homo sapiens (taxid: 9606)

>sp|Q0VCF9|LSM12_BOVIN Protein LSM12 homolog OS=Bos taurus GN=LSM12 PE=2 SV=2

 Score = 78.2 bits (191), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 50/164 (30%), Positives = 85/164 (51%), Gaps = 6/164 (3%)

Query: 9   GEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSG-PRR-NIRLLNANYIKD 66
           GE F+VG  +S +T       G+V+AFD  + ML ++    SG P   +I L+N  Y+ +
Sbjct: 6   GEYFSVGSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPSSSGKPNHADILLINLQYVSE 65

Query: 67  FSFLG-QADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKT 125
              +  + + P  P    L++S+L ++      +  + A  I  GV+ E Q +F  + KT
Sbjct: 66  VEIINDRTETP--PPLASLNVSKLASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKT 123

Query: 126 LP-VRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLE 168
           +   +W +  IVVM EV ++ PY  E+  G   +A   V+K++E
Sbjct: 124 IKDCKWQEKNIVVMEEVVITPPYQVENCKGKEGSALSHVRKIVE 167

Bos taurus (taxid: 9913)

>sp|Q5ZML5|LSM12_CHICK Protein LSM12 homolog OS=Gallus gallus GN=LSM12 PE=2 SV=1

 Score = 77.0 bits (188), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 53/186 (28%), Positives = 93/186 (50%), Gaps = 11/186 (5%)

Query: 5   VGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSG-PRR-NIRLLNAN 62
           +   GE F+VG  +S +T       G+V+AFD  + ML ++    SG P   +I L+N  
Sbjct: 1   MAAPGECFSVGSQVSCRTCQEQRLQGEVVAFDYPSKMLALKCPSSSGKPNHADILLVNLQ 60

Query: 63  YIKDFSFLG-QADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDA 121
           Y+ +   +  + + P  P    L++S+L  +  +   +  + A  I  GV+ E Q +F  
Sbjct: 61  YVSEVEIINDRTETP--PPLASLNVSKLANKARMEKEEKLSQAYAISAGVSLEGQQLFQT 118

Query: 122 LSKTLP-VRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLE-----FERKRLQ 175
           + KT+   +W +  IVVM EV ++ PY  E+  G   +A   V+K++E      E +++ 
Sbjct: 119 IHKTIKDCKWQEKNIVVMEEVVIAPPYQVENCKGKEGSALGHVRKIVEKHFRDVESQKVM 178

Query: 176 ARGSSQ 181
            R  +Q
Sbjct: 179 QRSQAQ 184

Gallus gallus (taxid: 9031)

>sp|Q9VYR0|LS12A_DROME Protein LSM12 homolog A OS=Drosophila melanogaster GN=CG15735 PE=2 SV=2

 Score = 58.2 bits (139), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 41/164 (25%), Positives = 83/164 (50%), Gaps = 9/164 (5%)

Query: 12  FAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPR-RNIRLLNANYIKDFSFL 70
           F++G  +   T   +E +G+V+AFD  T ML+++   KS     +I  +N +   +   +
Sbjct: 16  FSIGSTVVCTTCFNEEVEGEVLAFDHNTKMLILKCRSKSTEELSDIYAMNLSLCSNVQVI 75

Query: 71  GQADDPL-DPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKTL--- 126
            + +    DP+K  L+  +++ R+ +  RQ    ++     V+ EAQ ++ A++K     
Sbjct: 76  KECNGNFDDPQKLNLEQVKMRLRKTVERRQDYLKSK--NADVSPEAQELYRAIAKQYGYN 133

Query: 127 PVRWDKTVIVVMNEVRVSSPYLPESV--SGGTAAANERVKKVLE 168
            V W    I ++NEV +S PY  ++V  S     +   +K++++
Sbjct: 134 EVSWQGLNIQILNEVTISPPYRVDNVVSSSNNETSCNYIKRIIK 177

Drosophila melanogaster (taxid: 7227)

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	182
225424772	178	PREDICTED: uncharacterized protein LOC10	0.967	0.988	0.806	9e-80
224099701	189	predicted protein [Populus trichocarpa]	0.945	0.910	0.808	1e-76
255581182	177	conserved hypothetical protein [Ricinus	0.972	1.0	0.773	9e-76
449434891	181	PREDICTED: uncharacterized protein LOC10	0.961	0.966	0.782	3e-75
224111310	184	predicted protein [Populus trichocarpa]	0.994	0.983	0.763	3e-75
357516753	188	LSM12-like protein [Medicago truncatula]	0.934	0.904	0.794	4e-74
388514745	181	unknown [Lotus japonicus]	0.967	0.972	0.761	6e-74
356526846	186	PREDICTED: uncharacterized protein LOC10	0.983	0.962	0.754	2e-73
388495968	181	unknown [Lotus japonicus]	0.967	0.972	0.755	2e-73
388518615	181	unknown [Lotus japonicus]	0.967	0.972	0.75	7e-73

>gi|225424772|ref|XP_002269008.1| PREDICTED: uncharacterized protein LOC100267269 [Vitis vinifera]

 Score =  301 bits (770), Expect = 9e-80,   Method: Compositional matrix adjust.
 Identities = 142/176 (80%), Positives = 161/176 (91%)

Query: 6   GGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIK 65
             SG+EFAVGC+LSIKT+LGDEF+GQ++ +DR +N+LV+QEG  SGPRRNIRLL ANYIK
Sbjct: 3   ASSGDEFAVGCILSIKTSLGDEFEGQIITYDRPSNILVLQEGSDSGPRRNIRLLKANYIK 62

Query: 66  DFSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKT 125
           +FS+LGQA+DPLDPKKC +DL+ LQARE +A+RQAEADA+RIGVGVT EAQNIFDALSKT
Sbjct: 63  EFSYLGQAEDPLDPKKCCIDLNALQAREEVAIRQAEADAERIGVGVTVEAQNIFDALSKT 122

Query: 126 LPVRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQARGSSQ 181
           LPVRWDKT IVVMNEVRVSSPYLPESVSGGT AANERVKKVLEFERKRLQAR + Q
Sbjct: 123 LPVRWDKTAIVVMNEVRVSSPYLPESVSGGTPAANERVKKVLEFERKRLQARVAGQ 178

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224099701|ref|XP_002311583.1| predicted protein [Populus trichocarpa] gi|222851403|gb|EEE88950.1| predicted protein [Populus trichocarpa]

 Score =  290 bits (743), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 139/172 (80%), Positives = 156/172 (90%)

Query: 10  EEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSF 69
           E+FAVGCLLSIKTTLG+EFDGQVM FDR +N+LV+QEG K GP+RNIR L ANYIK+FSF
Sbjct: 18  EDFAVGCLLSIKTTLGEEFDGQVMTFDRPSNILVLQEGSKHGPKRNIRFLKANYIKEFSF 77

Query: 70  LGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKTLPVR 129
           +GQA+DPLD KKC++DL  LQARE LA+RQAEADA+RIGVGVT EAQ+IFDALSKTLPVR
Sbjct: 78  VGQAEDPLDIKKCYIDLHSLQAREELALRQAEADAERIGVGVTAEAQSIFDALSKTLPVR 137

Query: 130 WDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQARGSSQ 181
           WDKTVIVVMNEVRV SPYL E VSGGT AAN+RVKKVLE ERKRLQARG+S+
Sbjct: 138 WDKTVIVVMNEVRVGSPYLAECVSGGTPAANDRVKKVLELERKRLQARGASR 189

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255581182|ref|XP_002531404.1| conserved hypothetical protein [Ricinus communis] gi|223528997|gb|EEF30988.1| conserved hypothetical protein [Ricinus communis]

 Score =  288 bits (736), Expect = 9e-76,   Method: Compositional matrix adjust.
 Identities = 140/181 (77%), Positives = 156/181 (86%), Gaps = 4/181 (2%)

Query: 1   MEGQVGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLN 60
           MEG    + EEFAVGC LSIKT LGDEF+GQV+ FDR +N+L    G K GPRRNIR L 
Sbjct: 1   MEGSNNNNSEEFAVGCFLSIKTILGDEFEGQVITFDRPSNIL----GSKHGPRRNIRFLK 56

Query: 61  ANYIKDFSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFD 120
           ANYIK+FSFLGQA+DPLD KKC++DL  LQARE LA+RQAEA+A+R+GVGVT EAQNIFD
Sbjct: 57  ANYIKEFSFLGQAEDPLDVKKCYIDLHSLQAREELALRQAEAEAERLGVGVTAEAQNIFD 116

Query: 121 ALSKTLPVRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQARGSS 180
           ALSKTLPVRWDKTVIVVMNEVRV++PYLPE VSGGT AANERVKKVLEFERKRLQARG+ 
Sbjct: 117 ALSKTLPVRWDKTVIVVMNEVRVNNPYLPECVSGGTPAANERVKKVLEFERKRLQARGTG 176

Query: 181 Q 181
           Q
Sbjct: 177 Q 177

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434891|ref|XP_004135229.1| PREDICTED: uncharacterized protein LOC101211481 [Cucumis sativus] gi|449478540|ref|XP_004155346.1| PREDICTED: uncharacterized LOC101211481 [Cucumis sativus]

 Score =  286 bits (731), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 137/175 (78%), Positives = 156/175 (89%)

Query: 7   GSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKD 66
           G+G++F+VG   SIKTTLGDEF GQV+ FDR +N+LV+QEG K GPRRNIRLL ANYIK+
Sbjct: 7   GNGDDFSVGSFFSIKTTLGDEFQGQVITFDRPSNILVLQEGSKPGPRRNIRLLKANYIKE 66

Query: 67  FSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKTL 126
           FSFLG  +DPLD K C+LDL+ L+ARE LA+RQAEA+A+RIGVGVT+EAQ+IFDALSKTL
Sbjct: 67  FSFLGHGEDPLDLKNCYLDLNTLRAREELAIRQAEAEAERIGVGVTSEAQSIFDALSKTL 126

Query: 127 PVRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQARGSSQ 181
           PVRWDKTVIVVMNEVRVSSPYLPESVSGGT AANERVKKVLE+ERKRLQ RG  Q
Sbjct: 127 PVRWDKTVIVVMNEVRVSSPYLPESVSGGTPAANERVKKVLEWERKRLQVRGGGQ 181

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224111310|ref|XP_002315810.1| predicted protein [Populus trichocarpa] gi|222864850|gb|EEF01981.1| predicted protein [Populus trichocarpa]

 Score =  286 bits (731), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 139/182 (76%), Positives = 157/182 (86%), Gaps = 1/182 (0%)

Query: 1   MEG-QVGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLL 59
           MEG  +  + E+F VGCLLSIKTTLG+EF GQV+ FDR +N+LV+QEG K GP++NIR L
Sbjct: 3   MEGSNINSNREDFTVGCLLSIKTTLGEEFHGQVITFDRPSNILVLQEGSKPGPKKNIRFL 62

Query: 60  NANYIKDFSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIF 119
            ANYIK+FSFLGQA+DPLD KKC++DL  LQARE LA+RQAEADA+RIGVGVT EAQ IF
Sbjct: 63  KANYIKEFSFLGQAEDPLDIKKCYIDLHSLQAREELALRQAEADAERIGVGVTAEAQGIF 122

Query: 120 DALSKTLPVRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQARGS 179
            ALSKTLPVRWDKT IVVMNEV VSSPYLPE VSGGT AAN+RVKKVLE ERKRLQARG+
Sbjct: 123 YALSKTLPVRWDKTSIVVMNEVHVSSPYLPECVSGGTPAANDRVKKVLELERKRLQARGA 182

Query: 180 SQ 181
           SQ
Sbjct: 183 SQ 184

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357516753|ref|XP_003628665.1| LSM12-like protein [Medicago truncatula] gi|355522687|gb|AET03141.1| LSM12-like protein [Medicago truncatula] gi|388519341|gb|AFK47732.1| unknown [Medicago truncatula]

 Score =  282 bits (721), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 135/170 (79%), Positives = 150/170 (88%)

Query: 10  EEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSF 69
           +EFAVGC LSI+TTLGDEF+GQV+ FDR +N LV+QEG K GPRRNIRLL A+YIKDF+F
Sbjct: 16  DEFAVGCFLSIRTTLGDEFEGQVVTFDRDSNYLVLQEGSKHGPRRNIRLLKADYIKDFTF 75

Query: 70  LGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKTLPVR 129
           LGQ  DPLDP  C LD++ LQ+RE LA+RQAEADA+RIGVGVT+EAQNIFDALSKTLPVR
Sbjct: 76  LGQGQDPLDPNHCLLDINALQSREELAIRQAEADAERIGVGVTSEAQNIFDALSKTLPVR 135

Query: 130 WDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQARGS 179
           WDKTVIVVMNEVRVSSPY  E V GGT AAN+RVKKVLEFERKRLQ RGS
Sbjct: 136 WDKTVIVVMNEVRVSSPYHSECVIGGTPAANDRVKKVLEFERKRLQLRGS 185

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388514745|gb|AFK45434.1| unknown [Lotus japonicus]

 Score =  281 bits (720), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 134/176 (76%), Positives = 155/176 (88%)

Query: 4   QVGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANY 63
           +V  S EE A+GC+LSI+TTLGDEF+GQV+ FDR +N+L++Q+G K GP RN RLL ANY
Sbjct: 3   EVSNSVEELAIGCILSIRTTLGDEFEGQVVTFDRPSNILILQQGSKHGPHRNFRLLKANY 62

Query: 64  IKDFSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALS 123
           IKDF+FLGQA+DPLDP  CFLDL+ LQARE +A+RQAEADA+RIGVGVT+EAQ+IFDALS
Sbjct: 63  IKDFTFLGQAEDPLDPTNCFLDLTALQAREVVAIRQAEADAERIGVGVTSEAQSIFDALS 122

Query: 124 KTLPVRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQARGS 179
           KTLPVRWDKTVIVVMNEVRV SPY  +SV GGT AAN+RVKKVLEFERKRLQ RGS
Sbjct: 123 KTLPVRWDKTVIVVMNEVRVGSPYNSDSVIGGTPAANDRVKKVLEFERKRLQLRGS 178

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356526846|ref|XP_003532027.1| PREDICTED: uncharacterized protein LOC100499950 [Glycine max]

 Score =  280 bits (716), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 138/183 (75%), Positives = 154/183 (84%), Gaps = 4/183 (2%)

Query: 1   MEG----QVGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNI 56
           MEG     +  + EE AVGCLLSI+TTLGDEF+GQV+ FDR +N+LV+QE  K  PRRN+
Sbjct: 1   MEGGNNSSINSNPEELAVGCLLSIRTTLGDEFEGQVVTFDRPSNILVLQEPSKPSPRRNL 60

Query: 57  RLLNANYIKDFSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQ 116
           RLL ANYIKDF+FLG A DPLDP  CFLDL+ LQ RE +AVRQAEADA+RIGVGVT+EAQ
Sbjct: 61  RLLKANYIKDFTFLGHAQDPLDPNTCFLDLTALQQREDVAVRQAEADAERIGVGVTSEAQ 120

Query: 117 NIFDALSKTLPVRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQA 176
           +IFDALSKTLPVRWDKTVIVVMNEVRVSSPY  ESV GGT AAN+RVKKVLEFERKRLQ 
Sbjct: 121 SIFDALSKTLPVRWDKTVIVVMNEVRVSSPYHSESVVGGTPAANDRVKKVLEFERKRLQL 180

Query: 177 RGS 179
           R S
Sbjct: 181 RSS 183

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388495968|gb|AFK36050.1| unknown [Lotus japonicus]

 Score =  280 bits (716), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 133/176 (75%), Positives = 154/176 (87%)

Query: 4   QVGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANY 63
           +V  S EE A+GC+LSI+TTLGDEF+GQV+ FDR +N+L++Q+G K GP RN RLL ANY
Sbjct: 3   EVSNSVEELAIGCILSIRTTLGDEFEGQVVTFDRPSNILILQQGSKHGPHRNFRLLKANY 62

Query: 64  IKDFSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALS 123
           IKDF+FLGQA+DPLDP  CFLDL+ LQARE +A+RQAEADA+RIGVGVT+EAQ+IFDALS
Sbjct: 63  IKDFTFLGQAEDPLDPTNCFLDLTALQAREVVAIRQAEADAERIGVGVTSEAQSIFDALS 122

Query: 124 KTLPVRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQARGS 179
           KTLPVRWDKTVIV MNEVRV SPY  +SV GGT AAN+RVKKVLEFERKRLQ RGS
Sbjct: 123 KTLPVRWDKTVIVAMNEVRVGSPYNSDSVIGGTPAANDRVKKVLEFERKRLQLRGS 178

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388518615|gb|AFK47369.1| unknown [Lotus japonicus]

 Score =  278 bits (711), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 132/176 (75%), Positives = 154/176 (87%)

Query: 4   QVGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANY 63
           +V  S EE A+GC+LSI+TTLGDEF+GQV+ FDR +N+L++Q+G K GP RN R L ANY
Sbjct: 3   EVSNSVEELAIGCILSIRTTLGDEFEGQVVTFDRPSNILILQQGSKHGPHRNFRSLKANY 62

Query: 64  IKDFSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALS 123
           IKDF+FLGQA+DPLDP  CFLDL+ LQARE +A+RQAEADA+RIGVGVT+EAQ+IFDALS
Sbjct: 63  IKDFTFLGQAEDPLDPTNCFLDLTALQAREVVAIRQAEADAERIGVGVTSEAQSIFDALS 122

Query: 124 KTLPVRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQARGS 179
           KTLPVRWDKTVIVVMNEVRV SPY  +SV GGT AAN+RVK+VLEFERKRLQ RGS
Sbjct: 123 KTLPVRWDKTVIVVMNEVRVGSPYNSDSVIGGTPAANDRVKRVLEFERKRLQLRGS 178

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	182
TAIR|locus:2199882	188	AT1G24050 "AT1G24050" [Arabido	0.961	0.930	0.576	1.8e-48
DICTYBASE|DDB_G0270402	218	DDB_G0270402 "unknown" [Dictyo	0.505	0.422	0.462	2.9e-22
TAIR|locus:2020648	224	AT1G70220 "AT1G70220" [Arabido	0.714	0.580	0.423	5.5e-22
ZFIN|ZDB-GENE-040426-2164	196	lsm12b "LSM12 homolog b (S. ce	0.956	0.887	0.286	8.6e-17
ZFIN|ZDB-GENE-040516-12	196	lsm12a "LSM12 homolog a (S. ce	0.950	0.882	0.290	4.7e-16
MGI|MGI:1919592	195	Lsm12 "LSM12 homolog (S. cerev	0.873	0.815	0.300	6e-16
ASPGD|ASPL0000014693	247	AN3955 [Emericella nidulans (t	0.901	0.663	0.333	2.3e-14
SGD|S000001163	187	LSM12 "Protein of unknown func	0.945	0.919	0.215	4e-08
FB|FBgn0036057	186	CG14164 [Drosophila melanogast	0.774	0.758	0.233	4.1e-05

TAIR|locus:2199882 AT1G24050 "AT1G24050" [Arabidopsis thaliana (taxid:3702)]

 Score = 506 (183.2 bits), Expect = 1.8e-48, P = 1.8e-48
 Identities = 102/177 (57%), Positives = 132/177 (74%)

Query:     5 VGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPR--RNIRLLNAN 62
             +GG GE+FAVG + S+K   GDEF G VMA+D   N +  +EG K  P   +N R++NA+
Sbjct:    12 IGGEGEKFAVGNIYSVKVITGDEFRGIVMAYDPIPNFVFFEEGTKPRPGHLKNTRMVNAS 71

Query:    63 YIKDFSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDAL 122
             +I   S+LG+ +DPLD     +DL+ L+A+E LA+RQAEADA+R+GVGVT EAQ+IFDAL
Sbjct:    72 FITGLSYLGKTEDPLDSDNFSVDLNGLRAKEALAIRQAEADAERMGVGVTAEAQSIFDAL 131

Query:   123 SKTLPVRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQARGS 179
             SKTLPV+W+ + I+VM EVRV SPYL + V GGT AAN RVKKVLE ER+RLQ  G+
Sbjct:   132 SKTLPVQWENSDILVMKEVRVRSPYLSDCVFGGTDAANNRVKKVLELERRRLQLFGT 188

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

DICTYBASE|DDB_G0270402 DDB_G0270402 "unknown" [Dictyostelium discoideum (taxid:44689)]

 Score = 201 (75.8 bits), Expect = 2.9e-22, Sum P(2) = 2.9e-22
 Identities = 43/93 (46%), Positives = 64/93 (68%)

Query:    84 LDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKTLPVRWDKTVIVVMNEVRV 143
             L++  +  ++   +++A   A +IGVGVT EAQ IF++LS+TLP  W    I+V+NEV++
Sbjct:   125 LNVQLIIKKQDEVIKKAAQKAMKIGVGVTPEAQEIFNSLSRTLPCDWSGENIIVLNEVKI 184

Query:   144 SSPYLPESVSGGTAAAN-ERVKKVLEFERKRLQ 175
             SSPY  E+ +G     + ERVKKVLE ERK+L+
Sbjct:   185 SSPYNIENCTGPENCKSIERVKKVLEAERKKLK 217

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

TAIR|locus:2020648 AT1G70220 "AT1G70220" [Arabidopsis thaliana (taxid:3702)]

 Score = 256 (95.2 bits), Expect = 5.5e-22, P = 5.5e-22
 Identities = 58/137 (42%), Positives = 84/137 (61%)

Query:    41 MLVIQEGLKSGP--RRNIRLLNANYIKDFSFLGQADDPLDPKKCFLDLSRLQAREHLAVR 98
             ++++QEG K  P   +++R++N NYI +   LG+  + L  K   ++L  L  +E+ A+ 
Sbjct:    89 LVILQEGTKPKPLDSKSLRMVNVNYITEMKNLGRVKERL-AKNTLVNLDGLIEKENHAIS 147

Query:    99 QAEADAQRIGVGVTTEAQNIFDALSKTLPVRWDKTVIVVMNEVRVSSPYLPESVSGGTAA 158
               E    +IG GVT E Q IFDA+SKTLP+RW    ++VM +V + SPY  + V GG   
Sbjct:   148 NVE----KIGFGVTAEGQMIFDAISKTLPIRWVNKEMLVMGDVFIRSPYHSDCVYGGPRM 203

Query:   159 ANERVKKVLEFERKRLQ 175
              NERVK VL  ERK+LQ
Sbjct:   204 VNERVKHVLGQERKKLQ 220

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

ZFIN|ZDB-GENE-040426-2164 lsm12b "LSM12 homolog b (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 207 (77.9 bits), Expect = 8.6e-17, P = 8.6e-17
 Identities = 51/178 (28%), Positives = 91/178 (51%)

Query:     7 GSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSG-PR-RNIRLLNANYI 64
             G GE F+VG  +S  T LG    G+V+AFD  + ML ++    SG P   ++ L+N  Y+
Sbjct:     5 GPGEYFSVGSHVSCLTCLGQRLQGEVVAFDYPSKMLTLKCPSSSGKPNLSDVILINLAYV 64

Query:    65 KDFSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSK 124
              +   +    +   P    L++S+L  R         + A  I  GV+ E Q +F  + K
Sbjct:    65 SEVDIINDRTET-PPPLASLNISKLANRARTEKEDKLSQAYAISAGVSIEGQQLFQTIHK 123

Query:   125 TLP-VRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQARGSSQ 181
             T+   +W +  I+VM++V +S PY  E+  G   +A   ++K++E   + ++++ + Q
Sbjct:   124 TIKDCKWQEKNIIVMDDVVISPPYQVENCKGKEGSALSHIRKIVEKHFRDVESQKTMQ 181

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

ZFIN|ZDB-GENE-040516-12 lsm12a "LSM12 homolog a (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 200 (75.5 bits), Expect = 4.7e-16, P = 4.7e-16
 Identities = 52/179 (29%), Positives = 93/179 (51%)

Query:     7 GSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSG-PR-RNIRLLNANYI 64
             G GE F+VG  +S  T LG    G+V+AFD  + ML ++    SG P   ++ L+N  Y+
Sbjct:     5 GPGEYFSVGSHVSCLTCLGQRLQGEVVAFDYPSKMLTLKCAPSSGKPNLSDVMLVNLAYV 64

Query:    65 KDFSFL-GQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALS 123
              +   +  +A+ P  P    L+ ++L  R         + A  +  GV+ E Q +F  + 
Sbjct:    65 SEVDIITDRAETP--PPLASLNFNKLVNRARAEKEDKLSLAYAVSAGVSVEGQQLFQTIH 122

Query:   124 KTLP-VRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQARGSSQ 181
             KT+   +W +  I+VM++V +S PY  ++  G   +A   V+K++E   + ++++ S Q
Sbjct:   123 KTIKECKWQEKNIIVMDDVVISPPYQVDNCKGKEGSALSHVRKIVEKHFRDVESQISVQ 181

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

MGI|MGI:1919592 Lsm12 "LSM12 homolog (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 199 (75.1 bits), Expect = 6.0e-16, P = 6.0e-16
 Identities = 49/163 (30%), Positives = 83/163 (50%)

Query:     9 GEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSG-PRR-NIRLLNANYIKD 66
             GE F+VG  +S +T       G+V+AFD  + ML ++    SG P   +I L+N  Y+ +
Sbjct:     6 GEYFSVGSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPSSSGKPNHADILLINLQYVSE 65

Query:    67 FSFLGQADDPLDPKKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKTL 126
                +    +   P    L++S+L ++      +  + A  I  GV+ E Q +F  + KT+
Sbjct:    66 VEIINDRTET-PPPLASLNVSKLASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKTI 124

Query:   127 P-VRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLE 168
                +W +  IVVM EV ++ PY  E+  G   +A   V+K++E
Sbjct:   125 KDCKWQEKNIVVMEEVVITPPYQVENCKGKEGSALSHVRKIVE 167

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

ASPGD|ASPL0000014693 AN3955 [Emericella nidulans (taxid:162425)]

 Score = 184 (69.8 bits), Expect = 2.3e-14, P = 2.3e-14
 Identities = 62/186 (33%), Positives = 98/186 (52%)

Query:    14 VGCLLSIKTTLGDE-FDGQVMAFDRFTNMLVIQ--EGLKSGPRRNIRLLNANYIKDFSFL 70
             VG  + I T       +G V   D  TN++ +   +G ++G   N  ++  + I+ F  L
Sbjct:    39 VGARVRITTNPATSTIEGIVFTADPITNLVAVNTADGKQTGAG-NYHVIPISRIQSFELL 97

Query:    71 --------GQADDPLD--PKKCFLDLSRLQAREHLAVRQAE-ADAQRIGVGVTTEAQNIF 119
                     G A    D  P    LD+  L+ RE  AV + + A+A+R G GVT EAQ++F
Sbjct:    98 SLPPSAQSGGATSFSDAQPSLHALDIRALKKREADAVVEMQNAEARR-GKGVTREAQDLF 156

Query:   120 DALSKTLPV-RWDKTVIVVMNEVRVSSPYLPES----VSGGTAAANERVKKVLEFERKRL 174
             +A  +T+P  RWD   I+V + V ++ PY  +     V+G TAA   R++KVLE ER+++
Sbjct:   157 NAFIRTMPTTRWDGANIIVADAVSIAPPYRVDDCRPLVAGDTAAL-ARIRKVLEMERQKI 215

Query:   175 QARGSS 180
             + R +S
Sbjct:   216 EFRNAS 221

GO:0016070 "RNA metabolic process" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

SGD|S000001163 LSM12 "Protein of unknown function that may function in RNA processing" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 129 (50.5 bits), Expect = 4.0e-08, P = 4.0e-08
 Identities = 39/181 (21%), Positives = 85/181 (46%)

Query:    11 EFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFL 70
             E  +G  + +   L    +G++ +F+   N L IQ   K+   +N +++   +IK    +
Sbjct:     6 EQTLGFRIKVTNVLDVVTEGRLYSFNSSNNTLTIQTTKKNQSPQNFKVIKCTFIKHLEVI 65

Query:    71 GQADDPLDPKK-----CFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKT 125
             G        KK      ++++ R++     +V  ++      G GV+ E Q IFD + KT
Sbjct:    66 GDKPSFNSFKKQQIKPSYVNVERVEKLLKESVIASKKKELLRGKGVSAEGQFIFDQIFKT 125

Query:   126 L-PVRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERV---KKVLEFERKRLQARGSSQ 181
             +   +W    I+++++V+V  PY  E +      +N+ +   ++++E   ++L+     +
Sbjct:   126 IGDTKWVAKDIIILDDVKVQPPYKVEDIKVLHEGSNQSITLIQRIVERSWEQLEQDDGRK 185

Query:   182 G 182
             G
Sbjct:   186 G 186

GO:0010494 "cytoplasmic stress granule" evidence=IDA

GO:0005737 "cytoplasm" evidence=IEA;IDA

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0005840 "ribosome" evidence=IDA

GO:0016070 "RNA metabolic process" evidence=ISS;IPI

GO:0003723 "RNA binding" evidence=ISS

FB|FBgn0036057 CG14164 [Drosophila melanogaster (taxid:7227)]

 Score = 111 (44.1 bits), Expect = 4.1e-05, P = 4.1e-05
 Identities = 36/154 (23%), Positives = 68/154 (44%)

Query:    12 FAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSG-----PRRNIRLLNANYIKD 66
             F VG ++  KT  GD   G+V+AFD    ML+++    +G        N+ ++N +   D
Sbjct:     8 FTVGSIVRCKTCFGDNISGEVVAFDLGVKMLIMKCPSSNGGGDEQTTCNVTIVNLSLCMD 67

Query:    67 FSFLGQADDPLDPKKCF-LDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKT 125
                + +A  P + ++   +DL  ++ R   A        +      +   Q +F  L K 
Sbjct:    68 IEIVKEAIPPAEVQQPEPIDLPMIRERYRYATEHRTLSCRSYHPNASPFGQALFRLLVKR 127

Query:   126 L--P-VRW----DKTVIVVMNEVRVSSPYLPESV 152
                P + W    D+  I ++ +V + +PY  E++
Sbjct:   128 FGDPAIIWQNKGDQVAINILRQVVIDAPYATENI 161


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.318   0.135   0.380    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      182       182   0.00098  109 3  11 22  0.44    32
                                                     31  0.40    35


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  9
  No. of states in DFA:  573 (61 KB)
  Total size of DFA:  133 KB (2084 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  16.11u 0.10s 16.21t   Elapsed:  00:00:01
  Total cpu time:  16.11u 0.10s 16.21t   Elapsed:  00:00:01
  Start:  Fri May 10 09:53:20 2013   End:  Fri May 10 09:53:21 2013

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

---

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)
Q6P833	LSM12_XENTR	No assigned EC number	0.3113	0.8956	0.8402	yes	no
Q9D0R8	LSM12_MOUSE	No assigned EC number	0.3048	0.8681	0.8102	yes	no
Q0VCF9	LSM12_BOVIN	No assigned EC number	0.3048	0.8681	0.8102	yes	no
Q3MHD2	LSM12_HUMAN	No assigned EC number	0.3048	0.8681	0.8102	yes	no
Q5RAT5	LSM12_PONAB	No assigned EC number	0.3048	0.8681	0.8102	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	182
pfam09793	90	pfam09793, AD, Anticodon-binding domain	6e-31
smart00995	90	smart00995, AD, Anticodon-binding domain	9e-28
cd01735	61	cd01735, LSm12_N, Like-Sm protein 12, N-terminal d	1e-06

>gnl|CDD|220406 pfam09793, AD, Anticodon-binding domain

 Score =  107 bits (269), Expect = 6e-31
 Identities = 38/87 (43%), Positives = 56/87 (64%), Gaps = 3/87 (3%)

Query: 83  FLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKTLP-VRWDKTVIVVMNEV 141
            ++L R++ R   A+ +A+    RIG GV+ E Q +FDAL+KT+P  RWD   IVV++EV
Sbjct: 4   PVNLERIEKRLRKAIEEAKEKEARIGKGVSPEGQELFDALAKTIPDCRWDGKNIVVLDEV 63

Query: 142 RVSSPYLPESVS--GGTAAANERVKKV 166
            +S PY  ++V   G  + A ERV+KV
Sbjct: 64  TISPPYKVDNVKSLGDNSKALERVQKV 90

This domain of approximately 100 residues is conserved from plants to humans. It is frequently found in association with Lsm domain-containing proteins. It is an anticodon-binding domain of a prolyl-tRNA synthetase, whose PDB structure is available under the identifier 1h4q. Length = 90

>gnl|CDD|214962 smart00995, AD, Anticodon-binding domain

 Score = 99.3 bits (248), Expect = 9e-28
 Identities = 37/87 (42%), Positives = 54/87 (62%), Gaps = 3/87 (3%)

Query: 83  FLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKTLP-VRWDKTVIVVMNEV 141
            ++L R++ R   A+ QA+  A   G GV+ E Q IFDA++KT+P  RW    IVV++EV
Sbjct: 4   PVNLERVKKRLRKAIEQAKRKADSKGKGVSPEGQEIFDAIAKTIPDCRWQGKNIVVLDEV 63

Query: 142 RVSSPYLPESV--SGGTAAANERVKKV 166
            +S PY  E+V    G + A ERV+K+
Sbjct: 64  TISPPYTVENVKKLSGNSKALERVQKI 90

This domain of approximately 100 residues is conserved from plants to humans. It is frequently found in association with Lsm domain-containing proteins. Length = 90

>gnl|CDD|212482 cd01735, LSm12_N, Like-Sm protein 12, N-terminal domain

 Score = 43.5 bits (103), Expect = 1e-06
 Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 2/59 (3%)

Query: 10 EEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRR--NIRLLNANYIKD 66
          E F+VG  +S KT  G    G+V+AFD  + ML ++    SG     +I ++N +Y+ D
Sbjct: 1  EYFSVGSQVSCKTCFGQRIQGEVVAFDHPSKMLALKCPSSSGKPNLADISIVNLDYVSD 59

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. 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. Length = 61

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	182
KOG4401	184	consensus Uncharacterized conserved protein [Funct	100.0
PF09793	91	AD: Anticodon-binding domain; InterPro: IPR019181	99.97
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	99.9
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	99.72
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	97.79
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	96.72
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	96.39
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	96.23
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	95.98
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	95.88
PRK00737	72	small nuclear ribonucleoprotein; Provisional	95.77
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	95.76
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	95.55
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	95.35
PF03614	165	Flag1_repress: Repressor of phase-1 flagellin; Int	95.27
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	95.26
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	95.19
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	95.1
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	95.04
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	94.21
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	94.08
KOG1073	361	consensus Uncharacterized mRNA-associated protein	93.78
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	93.74
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	93.59
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	92.68
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	92.58
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	92.44
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	92.04
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	91.83
cd01737	62	LSm16_N LSm16 belongs to a family of Sm-like prote	91.73
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	90.54
KOG1783	77	consensus Small nuclear ribonucleoprotein F [RNA p	89.9
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	89.58
PF01245	113	Ribosomal_L19: Ribosomal protein L19; InterPro: IP	88.15
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	88.1
TIGR01024	113	rplS_bact ribosomal protein L19, bacterial type. T	85.5
CHL00084	117	rpl19 ribosomal protein L19	84.75
PF08863	92	YolD: YolD-like protein; InterPro: IPR014962 These	84.08
KOG1784	96	consensus Small Nuclear ribonucleoprotein splicing	83.09
PRK05338	116	rplS 50S ribosomal protein L19; Provisional	82.89

>KOG4401 consensus Uncharacterized conserved protein [Function unknown]

Probab=100.00  E-value=2.7e-34  Score=225.50  Aligned_cols=173  Identities=28%  Similarity=0.381  Sum_probs=144.7

Q ss_pred             CCCCCCceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEE---EEecCCeeEEEEecCCCC--CCC-
Q 030131            5 VGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIR---LLNANYIKDFSFLGQADD--PLD-   78 (182)
Q Consensus         5 m~~~~~~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~---iIn~~~Ik~i~vl~~~~~--~~~-   78 (182)
                      |++...++++|+.|+|+|++|...+|+||+||..+++|+|.++++++.+....   ++|.+|++.++++.+...  ++. 
T Consensus         1 m~p~s~~vavg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~~s~~~P~~~~~~~~~~~~~~~~~e~~~~k~~fp~~~~   80 (184)
T KOG4401|consen    1 MKPASATVAVGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTPSSNGKPNHAKFDIVINNNYSQLVESYLDKEAFPPAKS   80 (184)
T ss_pred             CCCCcceeEEEEEEEecccccceeeeEEEEEEcccCeeEecccccCCCCccchhhHHHHHHHHHHHHHhcccccCCchhh
Confidence            78889999999999999999999999999999999999999996655444444   799999999988876541  111 


Q ss_pred             CCCCCCCHHHHH-HHHHHHHHHH-HHHHHHcCCCCCHHHHHHHHHHhhhcc-eEEcCCcEEEeeeEEEcCCCCCCCccCC
Q 030131           79 PKKCFLDLSRLQ-AREHLAVRQA-EADAQRIGVGVTTEAQNIFDALSKTLP-VRWDKTVIVVMNEVRVSSPYLPESVSGG  155 (182)
Q Consensus        79 ~~l~~v~~~~l~-~r~~~ai~~~-~~~~~~~g~gvs~egQ~lFd~L~Kt~p-v~W~~~~IvV~d~V~I~pPY~~~n~~~~  155 (182)
                      ..+-++|++.+. .++..+.+.+ ....+..|+|||+|||+||+.|.||+| ++|.+++|+||++|.|.|||..+||.+.
T Consensus        81 qq~~~~~lnglr~~k~~~~~~~~~t~s~r~~~~gvS~egQ~lf~~l~Kti~D~~W~nkdI~Il~eV~v~~PY~ve~i~g~  160 (184)
T KOG4401|consen   81 QQCFPVDLNGLRIEKELTKTEPALTKSLRMSNPGVSAEGQQLFRQLEKTIGDTKWVNKDILILKEVVVISPYVVEDIFGL  160 (184)
T ss_pred             cccccccCchhHHHhhhhcccccccHhHhhcCCCcCHHHHHHHHHHHhhcCCceEeecCcEEEeeeeecCCceeeeeecc
Confidence            123356666555 4555555554 455556679999999999999999999 9999999999999999999999999999


Q ss_pred             ChhHHHHHHHHHHHHHHHHhhh
Q 030131          156 TAAANERVKKVLEFERKRLQAR  177 (182)
Q Consensus       156 ~~~~l~rV~kIl~~~~~~~~~~  177 (182)
                      +..+..+||||+++..+.++++
T Consensus       161 ~~aan~~v~kI~~~~~r~~~~~  182 (184)
T KOG4401|consen  161 TKAANGQVQKILEKVSRTYESR  182 (184)
T ss_pred             chhhhhHHHHHHHHHHhhhhhc
Confidence            8889999999999999998865

>PF09793 AD: Anticodon-binding domain; InterPro: IPR019181 Sm and Sm-like proteins of the Lsm (like Sm) domain family are generally involved in essential RNA-processing tasks []

Probab=99.97  E-value=3.3e-32  Score=195.31  Aligned_cols=87  Identities=51%  Similarity=0.777  Sum_probs=83.8

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhhcc-eEEcCCcEEEeeeEEEcCCCCCCCcc---CC
Q 030131           80 KKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKTLP-VRWDKTVIVVMNEVRVSSPYLPESVS---GG  155 (182)
Q Consensus        80 ~l~~v~~~~l~~r~~~ai~~~~~~~~~~g~gvs~egQ~lFd~L~Kt~p-v~W~~~~IvV~d~V~I~pPY~~~n~~---~~  155 (182)
                      +|++||+++|++|+++++++++..++++|+|||++||+||++|+||+| |+|+|++|+|||+|+|+|||+++||+   ++
T Consensus         1 ~~~~l~i~~l~~r~~~ai~~~~~~~~~~~~~vs~egQ~lF~~l~Kt~~dv~W~g~~IiV~d~V~I~pPY~~~nv~~~~~~   80 (91)
T PF09793_consen    1 PPPPLDIERLQKRLRKAIEEAKRKLSSIGPGVSPEGQKLFDALSKTIPDVRWDGKNIIVLDEVKISPPYKVENVSSLGGG   80 (91)
T ss_pred             CCCcCCHHHHHHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHHHHhhCCCCEECCCeEEEeCceEEcCCCCccceeeCCCC
Confidence            478999999999999999999999999999999999999999999999 99999999999999999999999998   67


Q ss_pred             ChhHHHHHHHH
Q 030131          156 TAAANERVKKV  166 (182)
Q Consensus       156 ~~~~l~rV~kI  166 (182)
                      +..+++|||||
T Consensus        81 ~~~al~~VkKI   91 (91)
T PF09793_consen   81 DSKALERVKKI   91 (91)
T ss_pred             ChHHHhheecC
Confidence            88999999986

All the LSM proteins are evolutionarily conserved in eukaryotes with an N-terminal Lsm domain to bind nucleic acids, followed by an as yet uncharacterised C-terminal region, some of which have a C-terminal methyltransferase domain. This entry represents the central region of approximately 100 residues, which is conserved from plants to humans and is frequently found in association with Lsm domain-containing proteins.

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

Probab=99.90  E-value=7.2e-24  Score=166.36  Aligned_cols=145  Identities=19%  Similarity=0.300  Sum_probs=47.6

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEecCCCCCCCCCCCCCCHHHHHHH
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQADDPLDPKKCFLDLSRLQAR   92 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~~~~~~~~~~l~~v~~~~l~~r   92 (182)
                      -+|+.|+|++.+ .++.|+|||+||.|..|||.+....+ ..++++|.+++|++++++.+.+..            ..++
T Consensus        15 yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e~~-~~sv~~I~ghaVk~vevl~~~~~~------------~~e~   80 (166)
T PF06372_consen   15 YVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQEDG-KRSVKVIMGHAVKSVEVLSEGDQE------------VPEK   80 (166)
T ss_dssp             TTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-TTS--EEEEEE-GGGEEEEEEEE---HH------------HHHH
T ss_pred             hhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEcccCC-ceeEEEEEccceEEEEEccCCchh------------hHHH
Confidence            489999999999 99999999999999999998876644 578999999999999999975421            1111


Q ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhh-hcceEEcC---CcEEEeeeEEEcCCCCCCCccCCChhHHHHHHHHHH
Q 030131           93 EHLAVRQAEADAQRIGVGVTTEAQNIFDALSK-TLPVRWDK---TVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLE  168 (182)
Q Consensus        93 ~~~ai~~~~~~~~~~g~gvs~egQ~lFd~L~K-t~pv~W~~---~~IvV~d~V~I~pPY~~~n~~~~~~~~l~rV~kIl~  168 (182)
                      +..-........ ...+........|-.||.+ .+||.-+|   +.++|.|.|+|.|||+++||+++|+..|.|||++|+
T Consensus        81 l~~~~~~~~~~~-~s~edl~~RK~~l~~wL~~N~ipV~E~g~~~~~l~V~gvvtI~pPY~~e~C~ssN~IIL~RVQ~Li~  159 (166)
T PF06372_consen   81 LQHLFMPEESSG-YSPEDLEKRKESLKQWLEKNRIPVTEQGDPDGTLCVAGVVTIEPPYGPENCSSSNEIILSRVQKLIQ  159 (166)
T ss_dssp             HHT-----------------------------------------------------------------------------
T ss_pred             HHhccCCccccc-CCHHHHHHHHHHHHHHHHHCCCceEeecCCCCeEEEeeEEEECCCCChHhcCCccHHHHHHHHHHHH
Confidence            111101000000 0012334445678889998 77999994   469999999999999999999999999999999999


Q ss_pred             HHHH
Q 030131          169 FERK  172 (182)
Q Consensus       169 ~~~~  172 (182)
                      ++..
T Consensus       160 ~~~~  163 (166)
T PF06372_consen  160 NMPD  163 (166)
T ss_dssp             ----
T ss_pred             hCcc
Confidence            8753

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.

>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=99.72  E-value=1.8e-17  Score=110.01  Aligned_cols=59  Identities=32%  Similarity=0.558  Sum_probs=53.5

Q ss_pred             CceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCC--CcceEEEEecCCeeEEE
Q 030131           10 EEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSG--PRRNIRLLNANYIKDFS   68 (182)
Q Consensus        10 ~~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~--~~~~~~iIn~~~Ik~i~   68 (182)
                      ++|++|+.|+|+|++|++++|+|+|||+.+++|+|+++++.+  +.+|++|||+++|++++
T Consensus         1 ~~f~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s~~~~~~~~dv~ivnls~~~dv~   61 (61)
T cd01735           1 ECFSVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPSSSGKPNHADILLVNLSYVSEVE   61 (61)
T ss_pred             CccccccEEEEEecCCceEEEEEEEecCCCcEEEEECccccCCCCcceEEEEEhhhEEecC
Confidence            479999999999999999999999999999999999876433  46899999999999985

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.

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

Probab=97.79  E-value=0.00015  Score=52.41  Aligned_cols=64  Identities=11%  Similarity=0.173  Sum_probs=52.9

Q ss_pred             eeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCC--------------CCcceEEEEecCCeeEEEEecCCCC
Q 030131           12 FAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKS--------------GPRRNIRLLNANYIKDFSFLGQADD   75 (182)
Q Consensus        12 ~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~--------------~~~~~~~iIn~~~Ik~i~vl~~~~~   75 (182)
                      .-+|++|++.+..+-.|+|.++..|+...+|+|..-...              .....+-+++++-||+++|+.....
T Consensus         5 ~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~~   82 (96)
T PF12701_consen    5 PYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPPP   82 (96)
T ss_dssp             CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-S
T ss_pred             cccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCCC
Confidence            458999999999999999999999999999999764221              1246888999999999999987663

>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=96.72  E-value=0.0064  Score=39.69  Aligned_cols=54  Identities=20%  Similarity=0.386  Sum_probs=40.1

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCC-----CCCcceEEEEecCCeeEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLK-----SGPRRNIRLLNANYIKDF   67 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~-----~~~~~~~~iIn~~~Ik~i   67 (182)
                      .+|++|.|++.+|..+.|.+.+||...+ ++|.....     .......-+|+++.|+.+
T Consensus         4 ~~g~~V~V~l~~g~~~~G~L~~~D~~~N-i~L~~~~~~~~~~~~~~~~~~~irG~~I~~I   62 (63)
T cd00600           4 LVGKTVRVELKDGRVLEGVLVAFDKYMN-LVLDDVEETIKEGKKRVLGLVLIRGDNVRLV   62 (63)
T ss_pred             HCCCEEEEEECCCcEEEEEEEEECCCCC-EEECCEEEEecCCcEEECCeEEEECCEEEEE
Confidence            4799999999999999999999998774 45543311     112345678888888765

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.

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

Probab=96.39  E-value=0.013  Score=38.77  Aligned_cols=55  Identities=20%  Similarity=0.440  Sum_probs=39.5

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCC--C----CcceEEEEecCCeeEEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKS--G----PRRNIRLLNANYIKDFS   68 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~--~----~~~~~~iIn~~~Ik~i~   68 (182)
                      .+|++|+|.+.+|.+++|.+.+||.--+ |+|......  .    ..-...+|+++.|..|.
T Consensus         6 ~~g~~V~V~l~~g~~~~G~L~~~D~~~N-l~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~   66 (67)
T PF01423_consen    6 LIGKRVRVELKNGRTYRGTLVSFDQFMN-LVLSDVTETIKNGPEKRSLGLVFIRGSNIRYIS   66 (67)
T ss_dssp             TTTSEEEEEETTSEEEEEEEEEEETTEE-EEEEEEEEEETTESEEEEEEEEEEEGGGEEEEE
T ss_pred             hCCcEEEEEEeCCEEEEEEEEEeechhe-EEeeeEEEEECCCCcEeECcEEEEECCEEEEEE
Confidence            4699999999999999999999997444 555443211  1    11245688888888764

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 ....

>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=96.23  E-value=0.026  Score=38.49  Aligned_cols=57  Identities=23%  Similarity=0.369  Sum_probs=42.3

Q ss_pred             eccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCC--CC---CcceEEEEecCCeeEEEEec
Q 030131           14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLK--SG---PRRNIRLLNANYIKDFSFLG   71 (182)
Q Consensus        14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~--~~---~~~~~~iIn~~~Ik~i~vl~   71 (182)
                      +|++|.|++.+|..+.|.+.+||.-.|++ |.....  .+   ..-..-+|+++.|..+..++
T Consensus         9 i~k~V~V~L~~g~~~~G~L~~~D~~mNlv-L~~~~E~~~~~~~~~lg~v~IRG~~I~~i~~~~   70 (72)
T cd01719           9 MDKKLSLKLNGNRKVSGILRGFDPFMNLV-LDDAVEVNSGGEKNNIGMVVIRGNSIVMLEALE   70 (72)
T ss_pred             CCCeEEEEECCCeEEEEEEEEEcccccEE-eccEEEEccCCceeEeceEEECCCEEEEEEccc
Confidence            89999999999999999999999766654 433211  01   12245689999999887664

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.

>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=95.98  E-value=0.044  Score=36.71  Aligned_cols=55  Identities=13%  Similarity=0.237  Sum_probs=39.4

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCC-CC---CcceEEEEecCCeeEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLK-SG---PRRNIRLLNANYIKDF   67 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~-~~---~~~~~~iIn~~~Ik~i   67 (182)
                      .+|++|.|++.+|..++|++.+||.--+++.-.+... .+   ..-..-+|+++.|..|
T Consensus         8 ~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~I~~i   66 (68)
T cd01731           8 SLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRGDNVLFI   66 (68)
T ss_pred             hcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeCCEEEEE
Confidence            4799999999999999999999998777665544211 11   1223457777777654

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.

>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=95.88  E-value=0.04  Score=37.99  Aligned_cols=57  Identities=16%  Similarity=0.184  Sum_probs=41.7

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC---CC-----CC--cceEEEEecCCeeEEEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL---KS-----GP--RRNIRLLNANYIKDFSF   69 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~---~~-----~~--~~~~~iIn~~~Ik~i~v   69 (182)
                      .+|.+|+|++.+|..+.|...|||...|+|.=.|..   .+     ..  .-..-+|+++.|.++++
T Consensus         8 ~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v   74 (75)
T cd06168           8 LLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV   74 (75)
T ss_pred             hcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence            389999999999999999999999877766433321   00     11  12456888999988875

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.

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=95.77  E-value=0.057  Score=36.70  Aligned_cols=55  Identities=15%  Similarity=0.295  Sum_probs=39.2

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC-CCCC---cceEEEEecCCeeEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL-KSGP---RRNIRLLNANYIKDF   67 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~-~~~~---~~~~~iIn~~~Ik~i   67 (182)
                      .+|++|.|++.+|.+++|.+.+||.--+++.-.+.. .++.   .-..-+|+++.|..|
T Consensus        12 ~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~V~~i   70 (72)
T PRK00737         12 ALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYV   70 (72)
T ss_pred             hCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeCCEEEEE
Confidence            489999999999999999999999866665544421 1111   122347888887765

>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=95.76  E-value=0.051  Score=36.37  Aligned_cols=55  Identities=16%  Similarity=0.300  Sum_probs=39.0

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC-CCCC---cceEEEEecCCeeEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL-KSGP---RRNIRLLNANYIKDF   67 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~-~~~~---~~~~~iIn~~~Ik~i   67 (182)
                      .+|++|.|++.+|.+++|++.+||+--+++.=.+.. ..++   .-..-+|+++.|..|
T Consensus         8 ~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~IRG~~I~~I   66 (67)
T cd01726           8 IIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNVLYI   66 (67)
T ss_pred             hCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEEECCEEEEE
Confidence            489999999999999999999999766655433321 1111   123457888887765

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.

>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=95.55  E-value=0.055  Score=37.38  Aligned_cols=58  Identities=21%  Similarity=0.297  Sum_probs=42.4

Q ss_pred             eeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC---CC--------C---CcceEEEEecCCeeEEEE
Q 030131           12 FAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL---KS--------G---PRRNIRLLNANYIKDFSF   69 (182)
Q Consensus        12 ~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~---~~--------~---~~~~~~iIn~~~Ik~i~v   69 (182)
                      .-+|++|.|++.+|..+.|.+.|||.-.|++.=.+..   ..        .   ..-..-+|+++.|.+|.|
T Consensus         7 ~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v   78 (79)
T cd01717           7 QLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV   78 (79)
T ss_pred             HHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence            3489999999999999999999999888876432210   00        0   112456889999888875

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.

>smart00651 Sm snRNP Sm proteins

Probab=95.35  E-value=0.063  Score=35.40  Aligned_cols=56  Identities=18%  Similarity=0.333  Sum_probs=38.8

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec---CC--CCCcceEEEEecCCeeEEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG---LK--SGPRRNIRLLNANYIKDFS   68 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~---~~--~~~~~~~~iIn~~~Ik~i~   68 (182)
                      .+|++|.|++.+|.++.|.+.+||+--+++.=.+.   ..  .......-+|+++.|.-|.
T Consensus         6 ~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~   66 (67)
T smart00651        6 LIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYII   66 (67)
T ss_pred             hCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEe
Confidence            47999999999999999999999986665543322   11  0112234478888877653

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

>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella

Probab=95.27  E-value=0.026  Score=43.84  Aligned_cols=50  Identities=16%  Similarity=0.050  Sum_probs=40.5

Q ss_pred             cEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEE
Q 030131           16 CLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFS   68 (182)
Q Consensus        16 ~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~   68 (182)
                      ..|++++.+|++|.|.|+.|++..+.| |- +.. ....+--.|.+.+|..++
T Consensus        30 ~pVrvv~~ng~~f~myV~gf~~~~n~i-L~-p~~-~~~~nRi~~plE~I~t~E   79 (165)
T PF03614_consen   30 IPVRVVSENGQVFCMYVSGFMSKENKI-LA-PDP-FKKENRIRLPLERISTIE   79 (165)
T ss_pred             CceEEEecCCcEEEEEEeccCcccCEE-ec-cCC-CCCCceEEEEhHHhhhHh
Confidence            469999999999999999999999999 53 332 234466678899999887

The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent

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

Probab=95.26  E-value=0.091  Score=36.21  Aligned_cols=57  Identities=18%  Similarity=0.294  Sum_probs=40.5

Q ss_pred             ceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCC---CCCc-----ceEEEEecCCeeEE
Q 030131           11 EFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLK---SGPR-----RNIRLLNANYIKDF   67 (182)
Q Consensus        11 ~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~---~~~~-----~~~~iIn~~~Ik~i   67 (182)
                      .-.+|.+|.|++.+|.++.|.+.+||.--|++.-.+..-   .+..     ...-+|+++.|.-|
T Consensus        13 ~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I   77 (79)
T COG1958          13 KKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLI   77 (79)
T ss_pred             HHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEE
Confidence            345889999999999999999999998777665433211   1111     12567888888765

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

Probab=95.19  E-value=0.051  Score=37.19  Aligned_cols=35  Identities=17%  Similarity=0.218  Sum_probs=27.0

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCC--CCeEEEEec
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRF--TNMLVIQEG   47 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~--~~~lvL~~~   47 (182)
                      .+|..|.|+|.+|..|+|..-++++.  .-.++|+.+
T Consensus        10 lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a   46 (77)
T PF14438_consen   10 LVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMA   46 (77)
T ss_dssp             TTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEE
T ss_pred             CcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEee
Confidence            48999999999999999999999996  466788775

>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=95.10  E-value=0.14  Score=35.28  Aligned_cols=56  Identities=13%  Similarity=0.205  Sum_probs=44.0

Q ss_pred             eeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC---C------------CCCcceEEEEecCCeeEE
Q 030131           12 FAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL---K------------SGPRRNIRLLNANYIKDF   67 (182)
Q Consensus        12 ~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~---~------------~~~~~~~~iIn~~~Ik~i   67 (182)
                      ..+|+++.+.+..+-.++|.++.+|+...+|+|+.-.   .            .....++-+.+++-||++
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            3589999999999999999999999999999996521   0            112346667777777765

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.

>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=95.04  E-value=0.15  Score=34.26  Aligned_cols=55  Identities=18%  Similarity=0.287  Sum_probs=37.9

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC-CCC---CcceEEEEecCCeeEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL-KSG---PRRNIRLLNANYIKDF   67 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~-~~~---~~~~~~iIn~~~Ik~i   67 (182)
                      .+|++|.|.+.+|.++.|.+.+||.--+++.=.+.. ..+   .....-+|+++.|.-|
T Consensus         9 ~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~IRG~~I~~i   67 (68)
T cd01722           9 LTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRCNNVLYI   67 (68)
T ss_pred             cCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEECCEEEEE
Confidence            489999999999999999999999766554433321 111   1235567777776644

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.

>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=94.21  E-value=0.47  Score=32.50  Aligned_cols=57  Identities=18%  Similarity=0.275  Sum_probs=43.2

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--CCCCCc---ceEEEEecCCeeEEEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--LKSGPR---RNIRLLNANYIKDFSF   69 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~~~~~~---~~~~iIn~~~Ik~i~v   69 (182)
                      ..|++|.|.+.+|.+++|.+.+||.--++..-.+.  ..++..   -.--+|+++.|..+.+
T Consensus         9 ~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~   70 (76)
T cd01723           9 AQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRV   70 (76)
T ss_pred             cCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEc
Confidence            47999999999999999999999998887765542  122222   1346799999998753

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=94.08  E-value=0.37  Score=34.28  Aligned_cols=58  Identities=17%  Similarity=0.153  Sum_probs=42.7

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC--CCC--CcceEEEEecCCeeEEEEe
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL--KSG--PRRNIRLLNANYIKDFSFL   70 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~--~~~--~~~~~~iIn~~~Ik~i~vl   70 (182)
                      ..|..|.|.+.+|.+++|.+.++|.--|+..-.+..  ..+  ....--+|+++.|+-|.+-
T Consensus         9 l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lP   70 (90)
T cd01724           9 LTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILP   70 (90)
T ss_pred             CCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcC
Confidence            479999999999999999999999877665544321  111  1224458999999988543

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.

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

Probab=93.78  E-value=0.15  Score=44.95  Aligned_cols=62  Identities=15%  Similarity=0.210  Sum_probs=51.8

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec----CC---C--------CCcceEEEEecCCeeEEEEecCCC
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG----LK---S--------GPRRNIRLLNANYIKDFSFLGQAD   74 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~----~~---~--------~~~~~~~iIn~~~Ik~i~vl~~~~   74 (182)
                      -||+.|.+....|=.|||.+|+.|..-.+|.|+.-    .+   .        ...+++-+.+++-||+|.|.+...
T Consensus         7 yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~p~   83 (361)
T KOG1073|consen    7 YIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQETPA   83 (361)
T ss_pred             cccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccCcc
Confidence            48999999999999999999999999999999542    11   0        125689999999999999998543

>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=93.74  E-value=0.46  Score=33.02  Aligned_cols=57  Identities=9%  Similarity=0.123  Sum_probs=41.5

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--CCCCCc----ceEEEEecCCeeEEEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--LKSGPR----RNIRLLNANYIKDFSF   69 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~~~~~~----~~~~iIn~~~Ik~i~v   69 (182)
                      ..|+.|.|.+.+|.+++|.+.++|+--++..-.+.  ...+..    ..--+|+++.|+-|.+
T Consensus         9 l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~l   71 (81)
T cd01725           9 LVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQL   71 (81)
T ss_pred             CCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEe
Confidence            47999999999999999999999987766554432  111111    1235899999998864

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.

>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=93.59  E-value=0.54  Score=31.68  Aligned_cols=57  Identities=14%  Similarity=0.256  Sum_probs=39.9

Q ss_pred             eeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--CCCCC--cceEEEEecCCeeEEE
Q 030131           12 FAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--LKSGP--RRNIRLLNANYIKDFS   68 (182)
Q Consensus        12 ~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~~~~~--~~~~~iIn~~~Ik~i~   68 (182)
                      -..|+.|.|.+.+|.+++|++.++|.--++..-.+.  ...+.  ...--+|+++.|.-+.
T Consensus         7 ~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v~IRG~nI~~v~   67 (70)
T cd01721           7 EAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRGSKIRFFI   67 (70)
T ss_pred             hCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcEEEeCCEEEEEE
Confidence            358999999999999999999999986654433331  11121  1234578888888664

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.

>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=92.68  E-value=0.29  Score=33.37  Aligned_cols=33  Identities=24%  Similarity=0.340  Sum_probs=29.0

Q ss_pred             eccEEEEEecCCCEEEEEEEEEeCCCCeEEEEe
Q 030131           14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQE   46 (182)
Q Consensus        14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~   46 (182)
                      ++++|.|++.+|..+.|++-+||.-.|++.=.+
T Consensus         8 l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~   40 (74)
T cd01727           8 LNKTVSVITVDGRVIVGTLKGFDQATNLILDDS   40 (74)
T ss_pred             cCCEEEEEECCCcEEEEEEEEEccccCEEccce
Confidence            899999999999999999999999877665443

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.

>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=92.58  E-value=0.3  Score=33.97  Aligned_cols=56  Identities=14%  Similarity=0.174  Sum_probs=39.4

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec---CCCC---------CcceEEEEecCCeeEEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG---LKSG---------PRRNIRLLNANYIKDFS   68 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~---~~~~---------~~~~~~iIn~~~Ik~i~   68 (182)
                      .+|++|.|++.+|..+.|++-+||.--|++.=.+-   ..+.         ..-..-+|+++.|..+.
T Consensus        10 ~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~   77 (81)
T cd01729          10 YVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLIS   77 (81)
T ss_pred             hcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEe
Confidence            48999999999999999999999987776543331   1100         11245677887776654

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.

>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=92.44  E-value=1.1  Score=30.94  Aligned_cols=56  Identities=11%  Similarity=0.219  Sum_probs=39.8

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec-CCCCC---cceEEEEecCCeeEEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG-LKSGP---RRNIRLLNANYIKDFS   68 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~-~~~~~---~~~~~iIn~~~Ik~i~   68 (182)
                      .+|+.|.|.+.+|.+++|.+.++|.--++..-.+. ..+++   ...--+|+++.|.-|.
T Consensus        17 l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~   76 (78)
T cd01733          17 LQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVH   76 (78)
T ss_pred             CCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEE
Confidence            47999999999999999999999987765544332 11111   1234478888887664

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.

>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=92.04  E-value=0.38  Score=32.97  Aligned_cols=33  Identities=18%  Similarity=0.351  Sum_probs=28.4

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQ   45 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~   45 (182)
                      .++++|.|++.+|..+.|.+-+||+-.+++.=.
T Consensus        10 ~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d   42 (74)
T cd01728          10 DLDKKVVVLLRDGRKLIGILRSFDQFANLVLQD   42 (74)
T ss_pred             hcCCEEEEEEcCCeEEEEEEEEECCcccEEecc
Confidence            489999999999999999999999876665433

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.

>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=91.83  E-value=0.32  Score=33.81  Aligned_cols=31  Identities=23%  Similarity=0.397  Sum_probs=27.6

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLV   43 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lv   43 (182)
                      ..+++|.|++.+|..+.|.+-+||.-.+++.
T Consensus         9 ~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL   39 (82)
T cd01730           9 SLDERVYVKLRGDRELRGRLHAYDQHLNMIL   39 (82)
T ss_pred             hCCCEEEEEECCCCEEEEEEEEEccceEEec
Confidence            4789999999999999999999998776653

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.

>cd01737 LSm16_N LSm16 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=91.73  E-value=0.55  Score=30.96  Aligned_cols=38  Identities=21%  Similarity=0.363  Sum_probs=32.5

Q ss_pred             eccEEEEEecCC-CEEEEEEEEEeCCCCeEEEEecCCCC
Q 030131           14 VGCLLSIKTTLG-DEFDGQVMAFDRFTNMLVIQEGLKSG   51 (182)
Q Consensus        14 vG~~V~vtt~~~-~~~~G~V~~~D~~~~~lvL~~~~~~~   51 (182)
                      +|+.|+|..-.. .+|+|.|-..|+.+.+|+|..+..++
T Consensus         5 iGs~VSI~C~~~lGVyQG~i~~V~~~~qTI~l~~~~~ng   43 (62)
T cd01737           5 LGSIVSINCGETLGVYQGLVSAVDQESQTISLAFPFHNG   43 (62)
T ss_pred             cceEEEEecCCceEEEEEEEEEeCccceEEEEeecccCC
Confidence            789999986555 69999999999999999998876654

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. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function.

>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=90.54  E-value=0.56  Score=32.30  Aligned_cols=55  Identities=27%  Similarity=0.419  Sum_probs=38.3

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec----CCCC---CcceEEEEecCCeeEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG----LKSG---PRRNIRLLNANYIKDF   67 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~----~~~~---~~~~~~iIn~~~Ik~i   67 (182)
                      .+|++|.|++.+|.++.|.+-+||.--|++.=.+.    ...+   .....-+|+++.|.-|
T Consensus        11 ~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i   72 (76)
T cd01732          11 CIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICML   72 (76)
T ss_pred             hCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEE
Confidence            47999999999999999999999987776532221    0111   1224457788777655

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.

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

Probab=89.90  E-value=0.077  Score=36.28  Aligned_cols=66  Identities=17%  Similarity=0.331  Sum_probs=46.1

Q ss_pred             CCCCCCCCCceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCC--CC---CcceEEEEecCCeeEEE
Q 030131            2 EGQVGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLK--SG---PRRNIRLLNANYIKDFS   68 (182)
Q Consensus         2 ~~~m~~~~~~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~--~~---~~~~~~iIn~~~Ik~i~   68 (182)
                      +++|.++-....+|..|.|+.+.|-.+.|...|.|-=- .|.|.....  ++   +...=-+|+++.|-.|.
T Consensus         3 ~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgym-NiaLe~tee~~ngql~n~ygdaFirGnnVlyIs   73 (77)
T KOG1783|consen    3 EGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYM-NIALESTEEYVNGQLKNKYGDAFIRGNNVLYIS   73 (77)
T ss_pred             cccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHH-HHHHHHHHHHhcCcccccccceeeccccEEEEE
Confidence            57787777788899999999999999999999999532 344533311  12   22334577777766554

>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=89.58  E-value=0.3  Score=34.63  Aligned_cols=31  Identities=29%  Similarity=0.377  Sum_probs=27.1

Q ss_pred             eeeccEEEEEecCCCEEEEEEEEEeCCCCeE
Q 030131           12 FAVGCLLSIKTTLGDEFDGQVMAFDRFTNML   42 (182)
Q Consensus        12 ~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~l   42 (182)
                      ...|++|.|++..|..+.|++-+||.--+++
T Consensus        11 ~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlv   41 (87)
T cd01720          11 VKNNTQVLINCRNNKKLLGRVKAFDRHCNMV   41 (87)
T ss_pred             HcCCCEEEEEEcCCCEEEEEEEEecCccEEE
Confidence            3358999999999999999999999877655

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.

>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=88.15  E-value=1.8  Score=32.16  Aligned_cols=71  Identities=20%  Similarity=0.271  Sum_probs=50.5

Q ss_pred             CCCCCCCceeeccEEEEEecCC-------CEEEEEEEEEeC--CCCeEEEEecCCCCCcceEEEEecCCeeEEEEecCCC
Q 030131            4 QVGGSGEEFAVGCLLSIKTTLG-------DEFDGQVMAFDR--FTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQAD   74 (182)
Q Consensus         4 ~m~~~~~~~~vG~~V~vtt~~~-------~~~~G~V~~~D~--~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~~~~   74 (182)
                      ++...-+.|.+|..|+|++...       +.|+|.|.+..-  ...+++|+.-....+---.--++...|++|+|+....
T Consensus        11 ~~~~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~~~~g~gVE~~f~l~SP~I~~IeV~~~~k   90 (113)
T PF01245_consen   11 QIKKDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRNISQGVGVERVFPLYSPLIKSIEVLRRGK   90 (113)
T ss_dssp             TCSSSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEEEETTEEEEEEEETTSTTEEEEEEEEEBE
T ss_pred             HhhcCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEEEecCccEEEEEEcCCCCeEEEEEEEecc
Confidence            4566778999999999998644       489999999985  4566777664331122223346778999999998653

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....

>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=88.10  E-value=1.5  Score=27.23  Aligned_cols=33  Identities=18%  Similarity=0.292  Sum_probs=26.7

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG   47 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~   47 (182)
                      ++|..|++.+ .++.++|.+..+|+. +.|+|++.
T Consensus         1 ~lG~~V~v~~-~~~~~~G~~~gId~~-G~L~v~~~   33 (48)
T PF02237_consen    1 TLGQEVRVET-GDGEIEGIAEGIDDD-GALLVRTE   33 (48)
T ss_dssp             STTSEEEEEE-TSCEEEEEEEEEETT-SEEEEEET
T ss_pred             CCCCEEEEEE-CCeEEEEEEEEECCC-CEEEEEEC
Confidence            3699999999 888999999999964 55666653

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 ....

>TIGR01024 rplS_bact ribosomal protein L19, bacterial type

Probab=85.50  E-value=6.3  Score=29.31  Aligned_cols=71  Identities=15%  Similarity=0.193  Sum_probs=50.4

Q ss_pred             CCCCCCCceeeccEEEEEecCC-------CEEEEEEEEEeC--CCCeEEEEecCCCCCcceEEEEecCCeeEEEEecCCC
Q 030131            4 QVGGSGEEFAVGCLLSIKTTLG-------DEFDGQVMAFDR--FTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQAD   74 (182)
Q Consensus         4 ~m~~~~~~~~vG~~V~vtt~~~-------~~~~G~V~~~D~--~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~~~~   74 (182)
                      +|...-+.|.+|..|+|+....       +.|+|.|.+..-  .+.+++|+.-...-+---.--++...|++|+|+....
T Consensus        11 ~~~~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i~~gvGVEr~fpl~SP~I~~IeVl~~~k   90 (113)
T TIGR01024        11 QLKKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKISYGVGVERIFPLHSPNIDSIEVVRRGK   90 (113)
T ss_pred             HhhcCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEeccCccEEEEEEcCCCccceEEEEEeCc
Confidence            4555678899999999998653       379999999983  4556788765442233333345678899999997654

This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.

>CHL00084 rpl19 ribosomal protein L19

Probab=84.75  E-value=8.8  Score=28.72  Aligned_cols=71  Identities=13%  Similarity=0.227  Sum_probs=49.9

Q ss_pred             CCCCCCCceeeccEEEEEe--cCCC-----EEEEEEEEEeC--CCCeEEEEecCCCCCcceEEEEecCCeeEEEEecCCC
Q 030131            4 QVGGSGEEFAVGCLLSIKT--TLGD-----EFDGQVMAFDR--FTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQAD   74 (182)
Q Consensus         4 ~m~~~~~~~~vG~~V~vtt--~~~~-----~~~G~V~~~D~--~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~~~~   74 (182)
                      ||...-+.|.+|..|+|+.  ..|.     .|+|.|.+..-  .+.+++|+.-...-+---.--++...|.+|+|+....
T Consensus        15 ~~~~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvRki~~gvGVEr~fpl~SP~I~~IeV~r~gk   94 (117)
T CHL00084         15 FLKKNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVRKVFQGIGVERVFLLHSPKLASIEVLRRSK   94 (117)
T ss_pred             HhhcCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEEEeccCccEEEEEecCCCccceEEEEEeCc
Confidence            4555678899999999998  3443     79999999863  4556777765432223333345778899999998654

>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised

Probab=84.08  E-value=5  Score=27.63  Aligned_cols=50  Identities=12%  Similarity=0.133  Sum_probs=37.7

Q ss_pred             eeccEEEEEecCC---CEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEE
Q 030131           13 AVGCLLSIKTTLG---DEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDF   67 (182)
Q Consensus        13 ~vG~~V~vtt~~~---~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i   67 (182)
                      .-+..|.++.-.+   .+++|.|..+|+..+.|.+....     .....|+.+.|.+|
T Consensus        40 ~~~~~v~ity~~~g~~~~~~G~I~~id~~~~~l~~~~~~-----~~~~~I~~~~I~~I   92 (92)
T PF08863_consen   40 QENQPVTITYYEDGYYQSVTGTIHKIDEINRTLKLKDED-----GETEKIPFDDIIDI   92 (92)
T ss_pred             cCCCEEEEEEEECCeeEEEEEEEEEEcCCCCEEEEEeCC-----CCEEEEEhhhEEEC
Confidence            3467888887554   58889999999999999998632     35566676776653

However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].

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

Probab=83.09  E-value=1.6  Score=31.19  Aligned_cols=61  Identities=13%  Similarity=0.178  Sum_probs=44.4

Q ss_pred             eccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec----CCC----CCcceEEEEecCCeeEEEEecCCC
Q 030131           14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG----LKS----GPRRNIRLLNANYIKDFSFLGQAD   74 (182)
Q Consensus        14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~----~~~----~~~~~~~iIn~~~Ik~i~vl~~~~   74 (182)
                      ++..|.|-|.+|+.+-|.+-+||..++.++=.+.    +..    .-.--+.||++.-+..+--+++..
T Consensus         9 ~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~   77 (96)
T KOG1784|consen    9 MNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEEL   77 (96)
T ss_pred             hhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhh
Confidence            5789999999999999999999998887764432    111    112247788888887776665543

>PRK05338 rplS 50S ribosomal protein L19; Provisional

Probab=82.89  E-value=8.5  Score=28.74  Aligned_cols=71  Identities=15%  Similarity=0.190  Sum_probs=50.3

Q ss_pred             CCCCCCCceeeccEEEEEec--CC-----CEEEEEEEEEeC--CCCeEEEEecCCCCCcceEEEEecCCeeEEEEecCCC
Q 030131            4 QVGGSGEEFAVGCLLSIKTT--LG-----DEFDGQVMAFDR--FTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQAD   74 (182)
Q Consensus         4 ~m~~~~~~~~vG~~V~vtt~--~~-----~~~~G~V~~~D~--~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~~~~   74 (182)
                      +|...-+.|.+|..|+|+..  .|     +.|+|.|.+..-  ...+++|+.-...-+---.--++...|++|+|+....
T Consensus        11 ~~~~~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki~~gvGVEr~fpl~SP~I~~IeV~r~gk   90 (116)
T PRK05338         11 QLRKDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKISYGVGVERTFPLHSPRIDSIEVVRRGK   90 (116)
T ss_pred             HhhcCCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEcccCccEEEEecCCCCcccEEEEEEecc
Confidence            45556788999999999875  34     379999999983  3556778765432233333345678899999997653

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	182
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 40.6 bits (94), Expect = 2e-04
 Identities = 29/189 (15%), Positives = 52/189 (27%), Gaps = 86/189 (45%)

Query: 10  EEFAVGC--LLSIKTT------------------LGDEFDG----QVMA-FDRFTNM--- 41
             F + C  LL   TT                  L          +V +   ++ +    
Sbjct: 260 NAFNLSCKILL---TTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQ 316

Query: 42  -L-------------VIQEGLKSGPRRNIRLLNANYIKDFSFLGQADDPLDP---KKCFL 84
            L             +I E ++ G        + N  K  + +  + + L+P   +K F 
Sbjct: 317 DLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFD 376

Query: 85  DLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIF--DAL--SKTLPVRWDK----TVIV 136
            LS                              +F   A   +  L + W       V+V
Sbjct: 377 RLS------------------------------VFPPSAHIPTILLSLIWFDVIKSDVMV 406

Query: 137 VMNEVRVSS 145
           V+N++   S
Sbjct: 407 VVNKLHKYS 415

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	182
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	99.35
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	97.88
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	97.4
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	97.38
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	97.19
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	96.56
2rm4_A	103	CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-	96.43
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	96.33
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	96.09
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	96.07
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	96.02
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	95.96
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	95.54
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	95.5
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	95.37
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	95.08
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	94.9
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	94.57
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	94.51
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	94.5
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	94.47
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	94.27
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	94.18
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	94.0
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	93.63
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	93.34
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	93.28
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	93.15
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	93.0
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	92.66
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	91.03
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	89.05
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	88.35
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	86.5
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	86.31
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	82.2
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	82.07
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	80.49

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

Probab=99.35  E-value=3.3e-12  Score=89.31  Aligned_cols=61  Identities=10%  Similarity=0.151  Sum_probs=55.9

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEecCCC
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQAD   74 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~~~~   74 (182)
                      -+|++|+|++.+|++++|+||+|||++.+|+|..+ ..+++....+|++++|++|+++++.+
T Consensus        15 li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~-~~~~~~~~~iI~G~aI~eI~v~~~~~   75 (86)
T 1y96_A           15 YIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNF-LEDGSMSVTGIMGHAVQTVETMNEGD   75 (86)
T ss_dssp             TTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEE-CTTSCEEEEEECGGGEEEEEEEECCC
T ss_pred             hcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeec-ccCCeEEEEEEecceEEEEEEecchh
Confidence            38999999999999999999999999999999887 33678899999999999999998865

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

Probab=97.88  E-value=0.0002  Score=49.81  Aligned_cols=73  Identities=15%  Similarity=0.199  Sum_probs=60.8

Q ss_pred             CCCCCCCCceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec---C-C----------CCCcceEEEEecCCeeEEE
Q 030131            3 GQVGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG---L-K----------SGPRRNIRLLNANYIKDFS   68 (182)
Q Consensus         3 ~~m~~~~~~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~---~-~----------~~~~~~~~iIn~~~Ik~i~   68 (182)
                      |-|+-++...-+|+++.+.+..+=.++|.+|..|+...+|+|+.-   . .          .....++-+.+++-||++.
T Consensus         1 ~~~~~s~~~~yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~yIvFrgsDIKdL~   80 (88)
T 2vxe_A            1 GAMAMSGGLPELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQIAPQSQIYDYILFRGSDIKDIR   80 (88)
T ss_dssp             CCSSSCSSSCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCTTTCCSSCCCCCCSCEEEEEEETTTEEEEE
T ss_pred             CcccccCCCcccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCcCCCCCcccCCCCceeeEEEEccCCccEEE
Confidence            567777778889999999999999999999999999999999652   1 1          1234578899999999999


Q ss_pred             EecCCCC
Q 030131           69 FLGQADD   75 (182)
Q Consensus        69 vl~~~~~   75 (182)
                      |++..+.
T Consensus        81 V~~~~p~   87 (88)
T 2vxe_A           81 VVNNHTL   87 (88)
T ss_dssp             ECCCCCC
T ss_pred             EeccCCC
Confidence            9987653

>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=97.40  E-value=0.0013  Score=48.99  Aligned_cols=104  Identities=17%  Similarity=0.247  Sum_probs=69.0

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEecCCCCCCCCCCCCCCHHHHHHH
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQADDPLDPKKCFLDLSRLQAR   92 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~~~~~~~~~~l~~v~~~~l~~r   92 (182)
                      .+|++|.|.+.+|.++.|.+.+||.--|++.=.+....+..-..-+|+++.|..|...++          .+|...+++.
T Consensus         8 ~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~~~~lg~v~IRG~nI~~I~~~d~----------~~d~~~f~~~   77 (130)
T 1m5q_A            8 LLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRVFIMYRYIVHIDSTER----------RIDMREFAKQ   77 (130)
T ss_dssp             TTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTTCCEEEEEEECGGGEEEEEECCC----------CCCHHHHHHH
T ss_pred             hCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEcCCEeceEEEeCCeEEEEEcCCc----------ccCHHHHHHH
Confidence            479999999999999999999999777665544432223344567999999988764433          1455455543


Q ss_pred             HHHHHHHH---------------HHHHHHcC-CCCCHHHHHHHHHHhhhcc
Q 030131           93 EHLAVRQA---------------EADAQRIG-VGVTTEAQNIFDALSKTLP  127 (182)
Q Consensus        93 ~~~ai~~~---------------~~~~~~~g-~gvs~egQ~lFd~L~Kt~p  127 (182)
                      .++. .--               +.+....| +|..|.||++++.+.+.+.
T Consensus        78 ~~r~-~pg~vk~~~e~~~v~v~~~~~v~~~gveg~g~~a~r~~~~~~~~~~  127 (130)
T 1m5q_A           78 AEKI-FPGMVKYIEETNVVLIGDKVRVSEIGVEGVGPVAERAKRLFEEFLK  127 (130)
T ss_dssp             HHHH-STTCEEEETTTTEEEETTTEEEETTEEECCSHHHHHHHHHHHHHC-
T ss_pred             Hhhc-CCCceeeeeccceEEEeeeEEeeccccccCChHHHHHHHHHHHHHH
Confidence            3332 000               00111234 8899999999999988764

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

Probab=97.38  E-value=0.0013  Score=45.11  Aligned_cols=65  Identities=17%  Similarity=0.229  Sum_probs=53.1

Q ss_pred             eeeccEEEEEecCCC-EEEEEEEEEeCCCCeEEEEecCCCCCcc--eEEEEecCCeeEEEEecCCCCC
Q 030131           12 FAVGCLLSIKTTLGD-EFDGQVMAFDRFTNMLVIQEGLKSGPRR--NIRLLNANYIKDFSFLGQADDP   76 (182)
Q Consensus        12 ~~vG~~V~vtt~~~~-~~~G~V~~~D~~~~~lvL~~~~~~~~~~--~~~iIn~~~Ik~i~vl~~~~~~   76 (182)
                      .-+|+.|++.+.++- +|+|.|+.+|+..++|+|...-.+|-++  .--.+...-|+++++++-+.++
T Consensus         6 ~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~f~NG~~~~s~eVtls~~DI~~L~ii~~~~~~   73 (84)
T 2vc8_A            6 DWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPFHNGVKCLVPEVTFRAGDITELKILEIPGPG   73 (84)
T ss_dssp             TTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEEEETTEECSSSEEEEEGGGCSEEEEEECCCSS
T ss_pred             cccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehhhhCCCCCCCcEEEEEecChhheEEEecCCCC
Confidence            458999999999996 9999999999999999998875554322  3456788999999999875543

>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=97.19  E-value=0.0026  Score=44.70  Aligned_cols=65  Identities=11%  Similarity=0.163  Sum_probs=52.8

Q ss_pred             CceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCC--------------CCCcceEEEEecCCeeEEEEecCCC
Q 030131           10 EEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLK--------------SGPRRNIRLLNANYIKDFSFLGQAD   74 (182)
Q Consensus        10 ~~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~--------------~~~~~~~~iIn~~~Ik~i~vl~~~~   74 (182)
                      ...-+|+++.+.+..+=.|+|.+|..|+...+|+|+.-.+              .....++-+.+++-||++.|+..+.
T Consensus        14 ~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~~ipp~~~vyeyIvFrGsDIKDL~V~e~p~   92 (95)
T 2fb7_A           14 GTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCEPPK   92 (95)
T ss_dssp             --CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSSCCCSCCCCSSCEEECSTTEEEEEESCCSC
T ss_pred             cCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCCccCCCCcceeEEEEcCCCcceEEEecCCC
Confidence            3456999999999999999999999999999999966211              1234578899999999999987543

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

Probab=96.56  E-value=0.0086  Score=43.96  Aligned_cols=66  Identities=20%  Similarity=0.323  Sum_probs=50.6

Q ss_pred             CCCCCCCCceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEecCCC
Q 030131            3 GQVGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQAD   74 (182)
Q Consensus         3 ~~m~~~~~~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~~~~   74 (182)
                      |.|+-+...| +|..|.|++.+|.+++|.|-.+|+.+-+|-|.....     +.--|+.+.|++++|++-+.
T Consensus         1 ~~~~~~~sqF-lGy~V~v~LkDgs~~qG~I~~vd~k~LtL~~~~a~~-----s~~~I~asdI~DLkVl~~~~   66 (125)
T 4a53_A            1 GAMGMSVADF-YGSNVEVLLNNDSKARGVITNFDSSNSILQLRLAND-----STKSIVTKDIKDLRILPKNE   66 (125)
T ss_dssp             CCCCCCHHHH-TTCEEEEEETTSCEEEEEEEEEETTTTEEEEEETTT-----EEEEEEGGGEEEEEECCSCC
T ss_pred             CCccccHHHh-cCceEEEEECCCCEeeEEEEeecCCeeEEecccccc-----ccceeecccccceeeeeccc
Confidence            3444443333 799999999999999999999998776665576532     22289999999999998654

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

Probab=96.43  E-value=0.036  Score=38.91  Aligned_cols=69  Identities=19%  Similarity=0.420  Sum_probs=52.0

Q ss_pred             CCCCCCCCceeeccEEEEEecCC-CEEEEEEEEEeCCCCeEEEEecCCCCC----cceEEEEecCCeeEEEEecCCC
Q 030131            3 GQVGGSGEEFAVGCLLSIKTTLG-DEFDGQVMAFDRFTNMLVIQEGLKSGP----RRNIRLLNANYIKDFSFLGQAD   74 (182)
Q Consensus         3 ~~m~~~~~~~~vG~~V~vtt~~~-~~~~G~V~~~D~~~~~lvL~~~~~~~~----~~~~~iIn~~~Ik~i~vl~~~~   74 (182)
                      |.|+-..++| +|+.|+|...++ ..|+|.|-..|+.+  |+|..+-.||-    ...--.+...-|+++++++...
T Consensus         1 ~~~~~~~edw-iG~~VSI~C~d~LGVyQG~I~~V~~~~--ItL~kaFrNGiplk~~~~EVtLsa~DI~~L~IIe~~~   74 (103)
T 2rm4_A            1 GAMGPTDQDW-IGCAVSIACDEVLGVFQGLIKQISAEE--ITIVRAFRNGVPLRKQNAEVVLKCTDIRSIDLIEPAK   74 (103)
T ss_dssp             CCSSCCSGGG-TTCEEEEEECTTTCEEEEEEEEEETTE--EEEEEEEETTEECSCSSSCEEEETTTEEEEEEEECCC
T ss_pred             CCcCccccce-eceEEEEeeCCcceEeeEEEEEcccce--eEEhhhhhcCcCcCCCCceEEEEecchhheeeecccc
Confidence            5677666654 899999998877 59999999999644  88877655442    2234466778899999998654

>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=96.33  E-value=0.017  Score=38.67  Aligned_cols=63  Identities=21%  Similarity=0.186  Sum_probs=40.6

Q ss_pred             CCceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC--CC--CCcceEEEEecCCeeEEEEec
Q 030131            9 GEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL--KS--GPRRNIRLLNANYIKDFSFLG   71 (182)
Q Consensus         9 ~~~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~--~~--~~~~~~~iIn~~~Ik~i~vl~   71 (182)
                      .....+|++|.|++.+|.++.|.+.+||.--|++.=.+..  ..  ...-..-+|+++.|..+..++
T Consensus         8 ~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~v~iRG~~I~~i~~~d   74 (76)
T 3s6n_G            8 ELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIMLEALE   74 (76)
T ss_dssp             ------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC----CBSSEEECSSSEEEEEC--
T ss_pred             HHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccCCcEeEcCEEEECCCeEEEEEecc
Confidence            3445689999999999999999999999766655433321  11  122345789999998887654

>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=96.09  E-value=0.016  Score=40.03  Aligned_cols=66  Identities=17%  Similarity=0.174  Sum_probs=47.9

Q ss_pred             CCceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC------C-----CCC---cceEEEEecCCeeEEEEecCCC
Q 030131            9 GEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL------K-----SGP---RRNIRLLNANYIKDFSFLGQAD   74 (182)
Q Consensus         9 ~~~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~------~-----~~~---~~~~~iIn~~~Ik~i~vl~~~~   74 (182)
                      .....+|++|.|++.+|..+.|.+.+||.--|++.=.+..      .     .+.   .-..-+|+++.|..|.+.++++
T Consensus         8 ~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~~I~~i~~~~~~~   87 (91)
T 1d3b_B            8 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEGPPP   87 (91)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEEECCC
T ss_pred             HHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECCCeEEEEEcCCCCC
Confidence            3445689999999999999999999999877766443321      0     000   1134589999999998876654

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

Probab=96.07  E-value=0.015  Score=38.67  Aligned_cols=59  Identities=15%  Similarity=0.247  Sum_probs=42.2

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCC-CC---CcceEEEEecCCeeEEEEec
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLK-SG---PRRNIRLLNANYIKDFSFLG   71 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~-~~---~~~~~~iIn~~~Ik~i~vl~   71 (182)
                      .+|++|.|++.+|.++.|.+.+||.--|++.=.+... .+   ..-..-+|+++.|..+...+
T Consensus        12 ~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~   74 (75)
T 1h64_1           12 SLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISPTE   74 (75)
T ss_dssp             TTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEEC-
T ss_pred             HCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeCCceeECCEEEECCCEEEEEEeCC
Confidence            4799999999999999999999997776654443211 11   11234688999998876543

>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=96.02  E-value=0.025  Score=38.23  Aligned_cols=59  Identities=15%  Similarity=0.254  Sum_probs=43.0

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC--CCCC--cceEEEEecCCeeEEEEec
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL--KSGP--RRNIRLLNANYIKDFSFLG   71 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~--~~~~--~~~~~iIn~~~Ik~i~vl~   71 (182)
                      .+|++|.|++.+|.++.|.+.+||.--|++.=.+..  ..+.  .-..-+|+++.|..|...+
T Consensus        17 ~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~   79 (81)
T 1th7_A           17 SLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILISPLQ   79 (81)
T ss_dssp             HTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECGGGEEEEEEC-
T ss_pred             hCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecCCceeECCEEEECCCEEEEEEecC
Confidence            489999999999999999999999877665544321  1111  1234689999998887654

>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=95.96  E-value=0.023  Score=37.89  Aligned_cols=59  Identities=12%  Similarity=0.196  Sum_probs=42.9

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC--CCC--CcceEEEEecCCeeEEEEec
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL--KSG--PRRNIRLLNANYIKDFSFLG   71 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~--~~~--~~~~~~iIn~~~Ik~i~vl~   71 (182)
                      .+|++|.|++.+|.++.|.+.+||.--|++.=.+..  ..+  ..-..-+|+++.|..|...+
T Consensus        12 ~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~d   74 (77)
T 1i4k_A           12 SLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVFVSPAP   74 (77)
T ss_dssp             TTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEECC
T ss_pred             hCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecCCcEeECCEEEECCCEEEEEEeCC
Confidence            479999999999999999999999877665443321  111  11245689999998887654

>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=95.54  E-value=0.033  Score=37.85  Aligned_cols=55  Identities=22%  Similarity=0.282  Sum_probs=38.9

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCC-CC---CcceEEEEecCCeeEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLK-SG---PRRNIRLLNANYIKDF   67 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~-~~---~~~~~~iIn~~~Ik~i   67 (182)
                      .+|++|.|++.+|.++.|.+.+||.--|++.=.+... .+   ..-..-+|+++.|..|
T Consensus        23 ~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~IRG~~I~~i   81 (83)
T 1mgq_A           23 SLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYI   81 (83)
T ss_dssp             TTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEE
T ss_pred             hCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecCCcccCCCEEEECCCEEEEE
Confidence            3799999999999999999999998776654433211 11   1123457888887655

>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=95.50  E-value=0.031  Score=37.21  Aligned_cols=59  Identities=17%  Similarity=0.264  Sum_probs=41.1

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCC-CC---CcceEEEEecCCeeEEEEec
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLK-SG---PRRNIRLLNANYIKDFSFLG   71 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~-~~---~~~~~~iIn~~~Ik~i~vl~   71 (182)
                      .+|++|.|++.+|.++.|++.+||.--|++.=.+... .+   ..-..-+|+++.|..+..++
T Consensus        12 ~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~   74 (75)
T 4emk_B           12 VIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIRGNNVLYVSALD   74 (75)
T ss_dssp             TTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEETTEEEEEEEEEEEEGGGSSEEEEC-
T ss_pred             hCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEecCCcccEecEEEEcCCeEEEEEecC
Confidence            3799999999999999999999998665543333211 11   11235688888888776553

>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=95.37  E-value=0.052  Score=36.20  Aligned_cols=59  Identities=12%  Similarity=0.136  Sum_probs=42.0

Q ss_pred             eeccEEEEEecCC-CEEEEEEEEEeCCCCeEEEEecCC-CCC---cceEEEEecCCeeEEEEec
Q 030131           13 AVGCLLSIKTTLG-DEFDGQVMAFDRFTNMLVIQEGLK-SGP---RRNIRLLNANYIKDFSFLG   71 (182)
Q Consensus        13 ~vG~~V~vtt~~~-~~~~G~V~~~D~~~~~lvL~~~~~-~~~---~~~~~iIn~~~Ik~i~vl~   71 (182)
                      .+|++|.|++.+| .+++|.+.+||.--|++.=.+... .+.   .-..-+|+++.|..+...+
T Consensus        13 ~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~nI~~i~~~d   76 (77)
T 1ljo_A           13 MVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQPQE   76 (77)
T ss_dssp             TTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEEC-
T ss_pred             HCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecCCcEeECCeEEEeCCeEEEEEeCC
Confidence            4789999999999 999999999998776654443211 111   1234588999988876543

>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=95.08  E-value=0.091  Score=35.95  Aligned_cols=61  Identities=18%  Similarity=0.253  Sum_probs=43.3

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCC-CCC---cceEEEEecCCeeEEEEecCC
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLK-SGP---RRNIRLLNANYIKDFSFLGQA   73 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~-~~~---~~~~~iIn~~~Ik~i~vl~~~   73 (182)
                      .+|++|.|++.+|.++.|++.+||.--|++.=.+... .+.   .-..-+|+++.|..+...++.
T Consensus        14 ~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~g~~~~~lg~v~IRG~nI~~i~~~d~~   78 (86)
T 3s6n_F           14 LTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGVEEE   78 (86)
T ss_dssp             HTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEESSEEECGGGEEEEEECC--
T ss_pred             hCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcCCceeeEccEEEEeCCeEEEEEeCCcc
Confidence            3799999999999999999999998776654433211 111   123468999999988776543

>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=94.90  E-value=0.14  Score=36.95  Aligned_cols=62  Identities=10%  Similarity=0.152  Sum_probs=43.3

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec---CCC-C-------CcceEEEEecCCeeEEEEecCCC
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG---LKS-G-------PRRNIRLLNANYIKDFSFLGQAD   74 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~---~~~-~-------~~~~~~iIn~~~Ik~i~vl~~~~   74 (182)
                      .+|++|.|++.+|..+.|.+.+||.-.|++.=.+.   ..+ +       ..-..-+|+++.|..|..++...
T Consensus        31 ~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~~e  103 (113)
T 4emk_C           31 YQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIAPMDGSE  103 (113)
T ss_dssp             -CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTTEEEEEECC---
T ss_pred             HcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCeEEEEEecCccc
Confidence            38999999999999999999999987776543332   110 0       11235689999999988776443

>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=94.57  E-value=0.18  Score=33.47  Aligned_cols=57  Identities=14%  Similarity=0.227  Sum_probs=40.5

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--CCCCCc--ceEEEEecCCeeEEEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--LKSGPR--RNIRLLNANYIKDFSF   69 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~~~~~~--~~~~iIn~~~Ik~i~v   69 (182)
                      .+|++|.|++.+|.+++|++.+||.--|+..=.+.  ...+..  -.--+|+++.|.-+.+
T Consensus        13 ~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~~~~~~lg~v~IRG~nI~~i~l   73 (75)
T 1d3b_A           13 AEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLIL   73 (75)
T ss_dssp             TTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECGGGEEEEEE
T ss_pred             hCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCCCcEEEcCeEEEeCCEEEEEEc
Confidence            47999999999999999999999987765543332  111221  2335888888887753

>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=94.51  E-value=0.17  Score=36.65  Aligned_cols=59  Identities=17%  Similarity=0.165  Sum_probs=43.2

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--CCCCC--cceEEEEecCCeeEEEEec
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--LKSGP--RRNIRLLNANYIKDFSFLG   71 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~~~~~--~~~~~iIn~~~Ik~i~vl~   71 (182)
                      .+|++|.|.+.+|.++.|++.+||.--|++.=.+.  ...+.  .-..-+|+++.|..|.+.+
T Consensus        10 ~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~~~~~~lg~v~IRG~nI~~I~~pd   72 (119)
T 1b34_A           10 LSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPD   72 (119)
T ss_dssp             CTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCT
T ss_pred             hCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecCCCceeEcceEEEcCCeEEEEEecc
Confidence            47899999999999999999999987776544332  11111  2245689999998876443

>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=94.50  E-value=0.18  Score=35.23  Aligned_cols=60  Identities=23%  Similarity=0.321  Sum_probs=42.4

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--C-CCCC--cceEEEEecCCeeEEEEecC
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--L-KSGP--RRNIRLLNANYIKDFSFLGQ   72 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~-~~~~--~~~~~iIn~~~Ik~i~vl~~   72 (182)
                      .+|++|.|++.+|.++.|++.+||.--|++.=.+.  . +.+.  .-..-+|+++.|.-|...++
T Consensus        28 ~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~IRG~nI~~i~p~~~   92 (94)
T 4emk_A           28 CIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKHSEMLLNGNGMCMLIPGGK   92 (94)
T ss_dssp             TTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTTCCEEEEEEEEECSTTEEEEEECC-
T ss_pred             HcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCCCcEeEcCEEEEcCCEEEEEEeCCC
Confidence            37899999999999999999999987665543321  1 1111  22456899999988765533

>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=94.47  E-value=0.11  Score=42.17  Aligned_cols=63  Identities=17%  Similarity=0.217  Sum_probs=45.4

Q ss_pred             eeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--C----CC--------CCcceEEEEecCCeeEEEEecCCC
Q 030131           12 FAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--L----KS--------GPRRNIRLLNANYIKDFSFLGQAD   74 (182)
Q Consensus        12 ~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~----~~--------~~~~~~~iIn~~~Ik~i~vl~~~~   74 (182)
                      ..+|++|+|++.+|.+|.|++.+||.-.|++.=.+.  .    ++        ...-..-+|+++.|..|.+-+...
T Consensus        11 klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~Isve~pPp   87 (231)
T 3pgw_B           11 QHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEGPPP   87 (231)
T ss_pred             HhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEEEEecCCCC
Confidence            358999999999999999999999987765532221  0    00        011245689999999998776543

>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=94.27  E-value=0.1  Score=35.07  Aligned_cols=58  Identities=17%  Similarity=0.230  Sum_probs=41.7

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCC---cceEEEEecCCeeEEEEe
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGP---RRNIRLLNANYIKDFSFL   70 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~---~~~~~iIn~~~Ik~i~vl   70 (182)
                      .+|++|.|++.+|.++.|.+.+||.--|++.=.+....+.   .-..-+|+++.|..|...
T Consensus        19 ~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~lg~v~iRG~~I~~i~~~   79 (81)
T 1i8f_A           19 SIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPV   79 (81)
T ss_dssp             TTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEECGGGEEEEEEC
T ss_pred             HCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEEcCCcccCCCEEEECCCEEEEEEeC
Confidence            4789999999999999999999998776654433211111   123468899988877643

>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=94.18  E-value=0.061  Score=37.59  Aligned_cols=60  Identities=15%  Similarity=0.169  Sum_probs=42.4

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec----CCC----CC---cceEEEEecCCeeEEEEecC
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG----LKS----GP---RRNIRLLNANYIKDFSFLGQ   72 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~----~~~----~~---~~~~~iIn~~~Ik~i~vl~~   72 (182)
                      .+|++|.|++.+|..+.|.+.+||.--|++.=.+.    ..+    +.   .-..-+|+++.|..|...++
T Consensus        18 ~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nVv~I~~~d~   88 (96)
T 3bw1_A           18 NLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLISTPSE   88 (96)
T ss_dssp             GTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEECGGGEEEEECCC-
T ss_pred             HCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEECCCEEEEEEecCc
Confidence            48999999999999999999999987776544332    100    10   11345889999988875543

>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=94.00  E-value=0.33  Score=34.46  Aligned_cols=60  Identities=18%  Similarity=0.308  Sum_probs=41.1

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--CCCCC---cceEEEEecCCeeEEEEecC
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--LKSGP---RRNIRLLNANYIKDFSFLGQ   72 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~~~~~---~~~~~iIn~~~Ik~i~vl~~   72 (182)
                      .+|++|.|++.+|.++.|++.+||.--|++.=.+.  ...+.   .-..-+|+++.|.-|.+.++
T Consensus        24 ~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg~~~~~lg~v~IRG~nI~~I~~pd~   88 (105)
T 4emh_A           24 TQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIRGNNIKYLRIQDE   88 (105)
T ss_dssp             --CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEEECGGGEEEEEC---
T ss_pred             hCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCCceeeEcCeEEEeCCeEEEEecCHH
Confidence            48999999999999999999999987765543332  11121   22456899999988765443

>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=93.63  E-value=0.33  Score=35.64  Aligned_cols=57  Identities=14%  Similarity=0.263  Sum_probs=42.7

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--CCCCC--cceEEEEecCCeeEEEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--LKSGP--RRNIRLLNANYIKDFSF   69 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~~~~~--~~~~~iIn~~~Ik~i~v   69 (182)
                      .+|+.|.|++.+|.++.|++.+||.--|+..=.+.  ...+.  ...--+|+++.|..|.+
T Consensus        13 ~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~~~~l~~v~IRGnnI~~I~l   73 (126)
T 2y9a_D           13 AEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRFLIL   73 (126)
T ss_dssp             CSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEEC
T ss_pred             hCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCcEeecccEEEeCCEEEEEEc
Confidence            58999999999999999999999987665544332  11222  22446899999998874

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

Probab=93.34  E-value=0.1  Score=36.24  Aligned_cols=31  Identities=23%  Similarity=0.455  Sum_probs=27.5

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLV   43 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lv   43 (182)
                      .+|++|.|++.+|..+.|.+.+||.--|++.
T Consensus        17 ~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL   47 (93)
T 4emg_A           17 SLDEIVYVKLRGDRELNGRLHAYDEHLNMVL   47 (93)
T ss_dssp             TTTSEEEEEETTTEEEEEEEEEECTTCCEEE
T ss_pred             hCCCEEEEEECCCcEEEEEEEEECCcccEEe
Confidence            4899999999999999999999998776553

>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=93.28  E-value=0.14  Score=35.65  Aligned_cols=58  Identities=16%  Similarity=0.224  Sum_probs=41.2

Q ss_pred             eeccEEEEEecCC-CEEEEEEEEEeCCCCeEEEEecCC-CCC---cceEEEEecCCeeEEEEe
Q 030131           13 AVGCLLSIKTTLG-DEFDGQVMAFDRFTNMLVIQEGLK-SGP---RRNIRLLNANYIKDFSFL   70 (182)
Q Consensus        13 ~vG~~V~vtt~~~-~~~~G~V~~~D~~~~~lvL~~~~~-~~~---~~~~~iIn~~~Ik~i~vl   70 (182)
                      .+|++|.|++.+| .++.|.+.+||.--+++.=.+... .+.   .-..-+|+++.|.-|...
T Consensus        29 ~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~~~~~~~lg~v~IRG~nI~~I~~~   91 (93)
T 1n9r_A           29 LVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIREL   91 (93)
T ss_dssp             GTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECGGGEEEEEEC
T ss_pred             hCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcCCCeEeEcCEEEEcCCeEEEEEeC
Confidence            4799999999999 999999999998776654433211 111   112468888888877543

>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=93.15  E-value=0.096  Score=38.13  Aligned_cols=61  Identities=23%  Similarity=0.339  Sum_probs=43.1

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec---CC--------CC--------CcceEEEEecCCeeEEEEecCC
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG---LK--------SG--------PRRNIRLLNANYIKDFSFLGQA   73 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~---~~--------~~--------~~~~~~iIn~~~Ik~i~vl~~~   73 (182)
                      .+|++|.|++.+|..+.|.+.+||.--|++.=.+-   ..        .+        ..-..-+|+++.|..|...+++
T Consensus        36 ~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG~nVv~I~~~~~~  115 (121)
T 2fwk_A           36 CIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVAMLVPGGDP  115 (121)
T ss_dssp             TBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGEEEEESSSCC
T ss_pred             HcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECCCEEEEEEecCCC
Confidence            37999999999999999999999977766543221   00        01        1124569999999888765543

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

Probab=93.00  E-value=0.7  Score=30.70  Aligned_cols=49  Identities=18%  Similarity=0.172  Sum_probs=38.4

Q ss_pred             ccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEe
Q 030131           15 GCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFL   70 (182)
Q Consensus        15 G~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl   70 (182)
                      ...|+|...+|+.++|.|.-+||  ++|.|....+     .--+|+-++|.-|..+
T Consensus        23 k~~V~I~L~tGd~l~G~i~WQD~--~cl~L~~~~~-----~~~LI~R~AI~~Ikp~   71 (72)
T 3hfn_A           23 AAPVEIKLVTGDAITGRVLWQDP--TCVCIADENS-----RQTTIWKQAIAYLQPK   71 (72)
T ss_dssp             CCEEEEEETTSCEEEEEEEEECS--SEEEEEC--------CEEEEEGGGEEEEEEC
T ss_pred             CceEEEEecCCCEEEEEEEEECC--CEEEEEcCCC-----CeEEEEeeeeEEEEeC
Confidence            35799999999999999999999  7888885421     2378888998877643

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

Probab=92.66  E-value=0.89  Score=30.02  Aligned_cols=48  Identities=17%  Similarity=0.116  Sum_probs=37.9

Q ss_pred             ccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEE
Q 030131           15 GCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSF   69 (182)
Q Consensus        15 G~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~v   69 (182)
                      ...|+|...+|+.++|.|.-+||  .+|.|+...  +   .--+|+-++|.-|..
T Consensus        21 k~~V~I~L~tG~~l~G~i~WQD~--~cl~L~~~~--~---~~~LI~r~AI~~I~p   68 (70)
T 3hfo_A           21 QTPVEIKLLTGDSLFGTIRWQDT--DGLGLVDDS--E---RSTIVRLAAIAYITP   68 (70)
T ss_dssp             TCEEEEEETTSCEEEEEEEEECS--SEEEEECTT--C---CEEEEEGGGEEEEEE
T ss_pred             CceEEEEecCCCEEEEEEEEeCC--CEEEEEcCC--C---CeEEEEeeeeEEEee
Confidence            35799999999999999999999  788887532  1   124888888887653

>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=91.03  E-value=0.4  Score=34.58  Aligned_cols=57  Identities=23%  Similarity=0.184  Sum_probs=40.3

Q ss_pred             ccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC------CC--CC----------cceEEEEecCCeeEEEEec
Q 030131           15 GCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL------KS--GP----------RRNIRLLNANYIKDFSFLG   71 (182)
Q Consensus        15 G~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~------~~--~~----------~~~~~iIn~~~Ik~i~vl~   71 (182)
                      |++|.|.+.+|..+.|.+.+||.--|++.=.+-.      ..  +.          .-..-+|+++.|..|...+
T Consensus        39 ~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~nVv~I~~~~  113 (118)
T 1b34_B           39 NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLRNP  113 (118)
T ss_dssp             TCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGEEEEEECC
T ss_pred             CcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcCCEEEEEEeCc
Confidence            5999999999999999999999877766543321      10  00          1235688999988776543

>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=89.05  E-value=2  Score=28.54  Aligned_cols=48  Identities=17%  Similarity=0.229  Sum_probs=38.4

Q ss_pred             ccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEec
Q 030131           15 GCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLG   71 (182)
Q Consensus        15 G~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~   71 (182)
                      +..|.|-..+|..++|.|..||+  -+|.|..    +   .-.+|.-++|+-|.-..
T Consensus        21 k~~Vti~L~nG~~l~G~I~~fD~--f~vlL~~----~---~~~LIYKhAIsTI~p~~   68 (74)
T 2ylb_A           21 RVPVSIYLVNGIKLQGQIESFDQ--FVILLKN----T---VSQMVYKHAISTVVPSR   68 (74)
T ss_dssp             TCCEEEEETTSCEEEEEEEEECS--SEEEEES----S---SEEEEEGGGEEEEEESS
T ss_pred             CCcEEEEEeCCCEEEEEEEEECC--cEEEEEC----C---ceEEEEeeeEEEEeEcc
Confidence            56799999999999999999997  5666663    2   22589999999887544

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

Probab=88.35  E-value=2.3  Score=28.61  Aligned_cols=48  Identities=17%  Similarity=0.239  Sum_probs=37.1

Q ss_pred             ccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEec
Q 030131           15 GCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLG   71 (182)
Q Consensus        15 G~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~   71 (182)
                      ...|.|-..+|..++|.|.+||.  -+|.|..    + .  -.+|.-++|+-|.--.
T Consensus        20 k~~VtI~LvnG~~L~G~I~~fD~--f~VlL~~----g-~--~qLIYKhAISTI~P~~   67 (79)
T 3sb2_A           20 HVPVSIYLVNGIKLQGHVESFDQ--YVVLLRN----T-V--TQMVYKHAISTVVPAR   67 (79)
T ss_dssp             TCCEEEEETTSCEEEEEEEEECS--SEEEEES----S-S--EEEEEGGGEEEEEESS
T ss_pred             CCeEEEEEeCCCEEEEEEEEECC--cEEEEEC----C-c--eEEEEeeeEEEEeecC
Confidence            45799999999999999999997  4555541    2 2  2589999999887443

>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=86.50  E-value=5.3  Score=26.66  Aligned_cols=47  Identities=13%  Similarity=0.296  Sum_probs=37.4

Q ss_pred             ccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEE
Q 030131           15 GCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSF   69 (182)
Q Consensus        15 G~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~v   69 (182)
                      +..|.|-..+|..++|.|.+||.  -+|.|...   +   .-.+|.-++|+-|..
T Consensus        19 k~~VtI~L~nG~~l~G~I~~fD~--f~VlL~~~---g---~~qLIYKhAISTI~p   65 (77)
T 1kq1_A           19 QTEVTVFFLNGFQMKGVIEEYDK--YVVSLNSQ---G---KQHLIYKHAISTYTV   65 (77)
T ss_dssp             TCEEEEEETTSCEEEEEEEEECS--SEEEEEET---T---EEEEEEGGGEEEEEC
T ss_pred             CCeEEEEEeCCCEEEEEEEEECC--cEEEEEEC---C---eeEEEEeeeEEEEeE
Confidence            56899999999999999999997  56666642   2   225899999998863

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

Probab=86.31  E-value=4.8  Score=26.53  Aligned_cols=47  Identities=17%  Similarity=0.200  Sum_probs=36.1

Q ss_pred             eccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEE
Q 030131           14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFS   68 (182)
Q Consensus        14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~   68 (182)
                      -+..|.|-..+|..++|.|.+||.  -+|.|...   +   .-.+|.-++|+.|.
T Consensus        24 ~~~~Vtv~L~NG~~l~G~I~~fD~--ftVll~~~---g---~qqliYKhAISTI~   70 (71)
T 2qtx_A           24 NGKKVKIFLRNGEVLDAEVTGVSN--YEIMVKVG---D---RNLLVFKHAIDYIE   70 (71)
T ss_dssp             TTCEEEEEETTSCEEEEEEEEECS--SEEEEEET---T---EEEEEEGGGEEEEE
T ss_pred             cCCcEEEEEeCCeEEEEEEEEEcc--eEEEEEeC---C---ceEEEEeeeeEeec
Confidence            466899999999999999999996  45555542   1   23688999998774

>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=82.20  E-value=2.7  Score=28.86  Aligned_cols=56  Identities=14%  Similarity=0.252  Sum_probs=37.8

Q ss_pred             eccEEEEEe----cCCCEEEEEEEEEeCCCCeEEEEec--C-CCCC--cceEEEEecCCeeEEEE
Q 030131           14 VGCLLSIKT----TLGDEFDGQVMAFDRFTNMLVIQEG--L-KSGP--RRNIRLLNANYIKDFSF   69 (182)
Q Consensus        14 vG~~V~vtt----~~~~~~~G~V~~~D~~~~~lvL~~~--~-~~~~--~~~~~iIn~~~Ik~i~v   69 (182)
                      +|.+|+|+.    .+|.+++|.+-+||.--|++.=.+.  . +...  .-..-+|+++.|..+.-
T Consensus        25 l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~iRG~nV~~i~~   89 (92)
T 3s6n_E           25 LQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLLQS   89 (92)
T ss_dssp             HHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSCCEEEEEEEEECGGGEEEEEE
T ss_pred             hCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCCceeEcCeEEEeCCEEEEEEe
Confidence            677777776    8999999999999986665443332  1 1111  12456888888877653

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

Probab=82.07  E-value=5.9  Score=28.00  Aligned_cols=48  Identities=17%  Similarity=0.229  Sum_probs=37.6

Q ss_pred             ccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEec
Q 030131           15 GCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLG   71 (182)
Q Consensus        15 G~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~   71 (182)
                      ...|.|-+.+|..++|.|..||.  -+|.|..    +   .-.+|.-++|+-|....
T Consensus        21 k~~VtI~LvNG~~L~G~I~~fD~--f~VlL~~----~---kqqLIYKHAISTI~p~~   68 (104)
T 2y90_A           21 RVPVSIYLVNGIKLQGQIESFDQ--FVILLKN----T---VSQMVYKHAISTVVPSR   68 (104)
T ss_dssp             TCCEEEEETTSCEEEEEEEEECS--SEEEEES----S---SEEEEEGGGEEEEEESS
T ss_pred             CCcEEEEEeCCCEEEEEEEEECC--cEEEEEC----C---ceEEEEeeeeEEEeecc
Confidence            34789999999999999999996  5566653    1   23689999999887554

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

Probab=80.49  E-value=9  Score=25.63  Aligned_cols=48  Identities=21%  Similarity=0.350  Sum_probs=36.5

Q ss_pred             ccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEe
Q 030131           15 GCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFL   70 (182)
Q Consensus        15 G~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl   70 (182)
                      +..|.|-..+|..++|.|-+||.  -+|.|...   + .  -.+|.-++|+.|..-
T Consensus        23 ~~~Vtv~L~nG~~l~G~I~~fD~--f~VlL~~~---g-~--qqlIYKhAISTI~p~   70 (78)
T 3ahu_A           23 NTYVTVFLLNGFQLRGQVKGFDN--FTVLLESE---G-K--QQLIYKHAISTFAPQ   70 (78)
T ss_dssp             TCCEEEEETTSCEEEEEEEEECS--SEEEEESS---S-C--EEEEEGGGEEEEEES
T ss_pred             CCcEEEEEeCCeEEEEEEEEEcc--eEEEEEEC---C-e--eEEEEcceEEEEeec
Confidence            45788999999999999999995  45555532   2 2  258999999988643

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	182
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	97.58
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	97.34
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	97.0
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	96.35
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	96.15
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	96.09
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	95.99
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	95.78
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	95.34
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	94.39
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	94.36
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	93.12
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	92.43
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	91.89
d1zq1a1	74	Glutamyl-tRNA(Gln) amidotransferase subunit D, Gat	80.51

>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=97.58  E-value=7.2e-05  Score=53.89  Aligned_cols=104  Identities=17%  Similarity=0.249  Sum_probs=69.6

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEecCCCCCCCCCCCCCCHHHHHHH
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQADDPLDPKKCFLDLSRLQAR   92 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~~~~~~~~~~l~~v~~~~l~~r   92 (182)
                      .+|+.|.|.+.+|.++.|++.+||.--|++.-.+....+++..--+|+++.|+.|.+.++          .+|...+..+
T Consensus         8 ~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~~~k~~~v~IRG~~I~~I~~~e~----------~iD~re~a~~   77 (127)
T d1m5q1_           8 LLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRVFIMYRYIVHIDSTER----------RIDMREFAKQ   77 (127)
T ss_dssp             TTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETTCCEEEEEEECGGGEEEEEECSC----------CCCHHHHHHH
T ss_pred             hCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECCCCcccEEEEeCCeEEEEEcchh----------hcCHHHHHHH
Confidence            479999999999999999999999776665555543334455556899999999965543          2455555444


Q ss_pred             HHHHHHHH-------H-------HHHHHcC-CCCCHHHHHHHHHHhhhc
Q 030131           93 EHLAVRQA-------E-------ADAQRIG-VGVTTEAQNIFDALSKTL  126 (182)
Q Consensus        93 ~~~ai~~~-------~-------~~~~~~g-~gvs~egQ~lFd~L~Kt~  126 (182)
                      +..-....       +       .+....| +|..|.||++++.+...+
T Consensus        78 ~~k~~p~~vkv~eea~~v~i~~~~kvse~gveg~G~~a~r~~~~~~~~~  126 (127)
T d1m5q1_          78 AEKIFPGMVKYIEETNVVLIGDKVRVSEIGVEGVGPVAERAKRLFEEFL  126 (127)
T ss_dssp             HHHHSTTCEEEETTTTEEEETTTEEEETTEEECCSHHHHHHHHHHHHHH
T ss_pred             HhhcCCCcEEeecccceEEeecceeEEEeeeeccChHHHHHHHHHHHhh
Confidence            44210000       0       0011223 899999999999887764

>d2vxfa1 b.38.1.5 (A:6-85) LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) [TaxId: 7955]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: LSM14 N-terminal domain-like
domain: LSM14 homolog A (Lsm14a)
species: Zebrafish (Danio rerio) [TaxId: 7955]

Probab=97.34  E-value=0.0012  Score=43.34  Aligned_cols=61  Identities=11%  Similarity=0.222  Sum_probs=51.3

Q ss_pred             eccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec----CC----------CCCcceEEEEecCCeeEEEEecCCC
Q 030131           14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG----LK----------SGPRRNIRLLNANYIKDFSFLGQAD   74 (182)
Q Consensus        14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~----~~----------~~~~~~~~iIn~~~Ik~i~vl~~~~   74 (182)
                      +|+++.+.+..+=.++|.+|..|+...+|.|+.-    ..          .....++-+.+++-||+++|.+++.
T Consensus         3 IGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~~IvFrgsDIKdL~v~e~p~   77 (80)
T d2vxfa1           3 IGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCEPPK   77 (80)
T ss_dssp             TTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSSCCCCCCCCEEEEEEETTTEEEEEESSCCC
T ss_pred             cCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCCccCCCCcceeEEEEcCcCcceEEeccCCC
Confidence            7999999999999999999999999999999652    11          1234588899999999999987643

>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=97.00  E-value=0.0029  Score=41.47  Aligned_cols=61  Identities=18%  Similarity=0.253  Sum_probs=45.1

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec------CCC-CCc-------ceEEEEecCCeeEEEEecCC
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG------LKS-GPR-------RNIRLLNANYIKDFSFLGQA   73 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~------~~~-~~~-------~~~~iIn~~~Ik~i~vl~~~   73 (182)
                      -+|++|+|++.+|..+.|.+.|||.-.|++.=.+.      ..+ ...       -..-+|+++.|.+|.+.+++
T Consensus         6 ~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~~~~p   80 (81)
T d1d3bb_           6 HIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEGPP   80 (81)
T ss_dssp             GTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEEECC
T ss_pred             HCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEccCCC
Confidence            47999999999999999999999987776543331      111 110       13569999999999877643

>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=96.35  E-value=0.0065  Score=39.16  Aligned_cols=57  Identities=14%  Similarity=0.246  Sum_probs=41.7

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--CCCC--CcceEEEEecCCeeEEEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--LKSG--PRRNIRLLNANYIKDFSF   69 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~~~~--~~~~~~iIn~~~Ik~i~v   69 (182)
                      .+|++|.|.+.+|.++.|.+.+||.--|++.=.+.  ...+  ..-..-+|+++.|..|.-
T Consensus        15 ~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~~~v~iRG~~I~~I~~   75 (76)
T d1th7a1          15 SLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILISP   75 (76)
T ss_dssp             HTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECGGGEEEEEE
T ss_pred             hCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecCCcccCcceEEEECCEEEEEEe
Confidence            48999999999999999999999987766544332  1111  123456888888877653

>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=96.15  E-value=0.0075  Score=38.23  Aligned_cols=55  Identities=15%  Similarity=0.309  Sum_probs=39.7

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC-CCCC---cceEEEEecCCeeEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL-KSGP---RRNIRLLNANYIKDF   67 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~-~~~~---~~~~~iIn~~~Ik~i   67 (182)
                      .+|++|.|.+.+|.++.|++.+||..-|++.=.+.. .+++   ....-+|+++.|..|
T Consensus        10 ~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~l~~~~IRG~~I~~I   68 (71)
T d1h641_          10 SLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAI   68 (71)
T ss_dssp             TTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEE
T ss_pred             hCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecCCcEeEcCcEEEECCeEEEE
Confidence            479999999999999999999999877665544421 1111   123458888888665

>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=96.09  E-value=0.019  Score=36.49  Aligned_cols=57  Identities=14%  Similarity=0.227  Sum_probs=41.7

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--CCCCCc--ceEEEEecCCeeEEEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--LKSGPR--RNIRLLNANYIKDFSF   69 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~~~~~~--~~~~iIn~~~Ik~i~v   69 (182)
                      .+|+.|.|.+.+|.+++|++-+||.--++..-.+.  ...+..  ...-+|+++.|.-|.+
T Consensus        10 ~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~v~IRG~~I~~i~l   70 (72)
T d1d3ba_          10 AEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLIL   70 (72)
T ss_dssp             TTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECGGGEEEEEE
T ss_pred             cCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCCCcEeEcCeEEEECCEEEEEEc
Confidence            47999999999999999999999987666544332  222222  2345889998887754

>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=95.99  E-value=0.0087  Score=38.09  Aligned_cols=55  Identities=11%  Similarity=0.244  Sum_probs=40.8

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--CCCC--CcceEEEEecCCeeEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--LKSG--PRRNIRLLNANYIKDF   67 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~~~~--~~~~~~iIn~~~Ik~i   67 (182)
                      .+|++|.|.+.+|.++.|.+.+||..-|++.=.+.  ...+  .....-+|+++.|..|
T Consensus        11 ~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~IRG~~I~~I   69 (72)
T d1i4k1_          11 SLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVFV   69 (72)
T ss_dssp             TTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSSSEEEEEEEEEECGGGEEEE
T ss_pred             hCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecCCeEeEcceEEEeCCeEEEE
Confidence            47999999999999999999999987777655443  1111  1234568888888655

>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=95.78  E-value=0.01  Score=37.91  Aligned_cols=55  Identities=22%  Similarity=0.302  Sum_probs=39.5

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC-CCC---CcceEEEEecCCeeEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL-KSG---PRRNIRLLNANYIKDF   67 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~-~~~---~~~~~~iIn~~~Ik~i   67 (182)
                      .+|++|.|.+.+|.++.|.+.+||..-|++.=.+.. .++   .....-+|+++.|..|
T Consensus        14 ~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~~~~~~~~~~~IRG~~I~~I   72 (74)
T d1mgqa_          14 SLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYI   72 (74)
T ss_dssp             TTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEE
T ss_pred             hCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCCCeEeEcceEEEeCCEEEEE
Confidence            479999999999999999999999877655444421 111   1224568888888655

>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=95.34  E-value=0.019  Score=36.42  Aligned_cols=56  Identities=20%  Similarity=0.306  Sum_probs=41.0

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCC-CCC--cceEEEEecCCeeEEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLK-SGP--RRNIRLLNANYIKDFS   68 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~-~~~--~~~~~iIn~~~Ik~i~   68 (182)
                      .+|++|.|.+.+|..+.|.+.+||.--|++.=.+... .+.  .-..-+|+++.|.-|.
T Consensus        10 ~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~~~~~~~g~v~iRG~~I~~I~   68 (71)
T d1i8fa_          10 SIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFIS   68 (71)
T ss_dssp             TTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEECGGGEEEEE
T ss_pred             hCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEECCCEEEcceEEEeCCeEEEEe
Confidence            5799999999999999999999998877766555311 111  1234588888886653

>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=94.39  E-value=0.079  Score=33.10  Aligned_cols=59  Identities=15%  Similarity=0.214  Sum_probs=42.3

Q ss_pred             eeccEEEEEecCCC-EEEEEEEEEeCCCCeEEEEecCC-CCC---cceEEEEecCCeeEEEEec
Q 030131           13 AVGCLLSIKTTLGD-EFDGQVMAFDRFTNMLVIQEGLK-SGP---RRNIRLLNANYIKDFSFLG   71 (182)
Q Consensus        13 ~vG~~V~vtt~~~~-~~~G~V~~~D~~~~~lvL~~~~~-~~~---~~~~~iIn~~~Ik~i~vl~   71 (182)
                      .+|++|.|...+|+ .++|.+-+||.--+++.=.+... .+.   .-..-+|+++.|.-|..++
T Consensus         4 ~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~IRG~nI~~I~~~p   67 (68)
T d1n9ra_           4 LVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELP   67 (68)
T ss_dssp             GTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECGGGEEEEEECC
T ss_pred             HCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEecCCcccCcCeEEEECCEEEEEEeCC
Confidence            57999999998665 69999999998777665444311 111   2244589999999887664

>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=94.36  E-value=0.11  Score=33.35  Aligned_cols=57  Identities=18%  Similarity=0.183  Sum_probs=41.8

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--CCCCC--cceEEEEecCCeeEEEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--LKSGP--RRNIRLLNANYIKDFSF   69 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~~~~~--~~~~~iIn~~~Ik~i~v   69 (182)
                      .+|..|.|.+.+|.+++|++-++|.--|+..=.+.  ...+.  ...--+|+++.|.-+.+
T Consensus         9 ~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~~Ir~i~l   69 (80)
T d1b34a_           9 LSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFIL   69 (80)
T ss_dssp             CTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEEC
T ss_pred             cCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCCEEEcccEEEcCCEEEEEEC
Confidence            47999999999999999999999986655443332  11122  23456899999998853

>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=93.12  E-value=0.14  Score=32.54  Aligned_cols=56  Identities=13%  Similarity=0.186  Sum_probs=39.0

Q ss_pred             eeccEEEEEecCC-CEEEEEEEEEeCCCCeEEEEecC--CCC--CcceEEEEecCCeeEEE
Q 030131           13 AVGCLLSIKTTLG-DEFDGQVMAFDRFTNMLVIQEGL--KSG--PRRNIRLLNANYIKDFS   68 (182)
Q Consensus        13 ~vG~~V~vtt~~~-~~~~G~V~~~D~~~~~lvL~~~~--~~~--~~~~~~iIn~~~Ik~i~   68 (182)
                      .+|++|.|.+.+| ..+.|.+-+||.--|++.=.+..  ..+  ..-..-+|+++.|.-|.
T Consensus        13 ~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~IRG~~I~~I~   73 (75)
T d1ljoa_          13 MVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQ   73 (75)
T ss_dssp             TTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEE
T ss_pred             hcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCCCcEeEcceEEEeCCEEEEEE
Confidence            4799999999877 48999999999877665544431  111  12234578888887654

>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=92.43  E-value=0.036  Score=36.67  Aligned_cols=31  Identities=26%  Similarity=0.537  Sum_probs=27.1

Q ss_pred             eeccEEEEEecCCCEEEEEEEEEeCCCCeEE
Q 030131           13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLV   43 (182)
Q Consensus        13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lv   43 (182)
                      .+|++|.|.+.+|..+.|.+.|||.--|++.
T Consensus        13 ~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL   43 (92)
T d2fwka1          13 CIGNRIYVVMKGDKEFSGVLRGFDEYVNMVL   43 (92)
T ss_dssp             TBTSBCEEEETTTEEECCEEEEECTTCCEEE
T ss_pred             HcCCEEEEEEcCCCEEEEEEEEEcCCCCEEE
Confidence            3699999999999999999999998776543

>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=91.89  E-value=0.15  Score=33.76  Aligned_cols=30  Identities=30%  Similarity=0.407  Sum_probs=26.9

Q ss_pred             ccEEEEEecCCCEEEEEEEEEeCCCCeEEE
Q 030131           15 GCLLSIKTTLGDEFDGQVMAFDRFTNMLVI   44 (182)
Q Consensus        15 G~~V~vtt~~~~~~~G~V~~~D~~~~~lvL   44 (182)
                      +.+|.|.|.+|..+.|.+.+||.--|++.=
T Consensus        14 ~~rV~V~lr~~r~~~G~L~afD~~~NlVL~   43 (93)
T d1b34b_          14 NTQVLINCRNNKKLLGRVKAFDRHCNMVLE   43 (93)
T ss_dssp             TCEEEEEETTSCEEEEEEEEECTTCCEEEE
T ss_pred             CcEEEEEECCCCEEEEEEEEeccceeEEee
Confidence            789999999999999999999988777643

>d1zq1a1 b.38.3.1 (A:2-75) Glutamyl-tRNA(Gln) amidotransferase subunit D, GatD {Pyrococcus abyssi [TaxId: 29292]}

class: All beta proteins
fold: Sm-like fold
superfamily: GatD N-terminal domain-like
family: GatD N-terminal domain-like
domain: Glutamyl-tRNA(Gln) amidotransferase subunit D, GatD
species: Pyrococcus abyssi [TaxId: 29292]

Probab=80.51  E-value=2.3  Score=26.65  Aligned_cols=57  Identities=21%  Similarity=0.363  Sum_probs=40.8

Q ss_pred             eeeccEEEEEecCC---CEEEEEEEE-Ee-CCCCeEEEEecCCCCCcceEEEEecCCeeEEEEecCC
Q 030131           12 FAVGCLLSIKTTLG---DEFDGQVMA-FD-RFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQA   73 (182)
Q Consensus        12 ~~vG~~V~vtt~~~---~~~~G~V~~-~D-~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~~~   73 (182)
                      ..+|.+|+|++..+   .+++|.+.- |. +....|+|+-.    +.+|+- ++.+.|+++++++.+
T Consensus        11 ~~~GD~Vri~~~~~~~~~~~eGilmP~~e~s~~~~ivlKL~----nGYNiG-i~~~~i~~ievlek~   72 (74)
T d1zq1a1          11 INVGDFVRITKEEDGEEVTYEGYIMPPYELSAGDTLVLKLE----NGYNIG-IALEKIRRIEVLERA   72 (74)
T ss_dssp             CCTTCEEEEEEESSSSEEECCEEECCCCTTCCCSEEEEEET----TSCEEE-EEGGGEEEEEEEECC
T ss_pred             CCCCCEEEEEEecCCCceEEEEEEcCCcccCCCCEEEEEec----Cceeec-cchhHeeEEEEEeec
Confidence            45899999998665   389999984 22 34578888753    234544 356889999999764