Citrus Sinensis ID: 034180

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100--
Protein Sequence
MQAFVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVCFLLVCF
Secondary Structure (PSIPRED)
cccEEEEEEEEEEEEEEcccccccccccccccccccccccccHHHHcccEEEEEEcccEEEEEEEEEccccccEEEEcEEEEEEccEEccEEEEEEcEEEEc
Secondary Structure Prediction (SSPRO)
ccEEEEEEEEEEEEEEccccccccHHHHHHHccccccHHHHHHHHHHcccEEEEEccccEEEEEEEEEcccccEEEEEEEEEEccEEEEEEEEEEEEEEEEc
Coil and Loop (DISEMBL)
MQAFVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVqvkltggrqvtgtlKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVCFLLVCF
Flexible Loop (DISEMBL)
MQAFVEINAVSFFIVCRSARVSFNLGflkslkmsgrKETVLDLAkfvdkgvqvkltggrqvtgtlkGYDQLLNLVLDEAVEFLRGNLYNGIFVIVCFLLVCF
Low Complexity Region (SEG)
MQAFVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVCFLLVCF
Disordered region (IsUnstruct)
***FVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVCFLLVC*
Disordered Region (DISOPRED)
**AFVEINAVSFFI******************************KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVCFLLVCF
Disordered Region (DISEMBL)
MQAFVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVCFLLVCF
Disordered Region (DISPRO)
MQAFVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVCFLLVCF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHi
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MQAFVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVCFLLVCF
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	102	2.2.26 [Sep-21-2011]
O74499	113	U6 snRNA-associated Sm-li	yes	no	0.529	0.477	0.563	1e-11
Q9UK45	103	U6 snRNA-associated Sm-li	yes	no	0.519	0.514	0.528	4e-11
Q9CQQ8	103	U6 snRNA-associated Sm-li	yes	no	0.519	0.514	0.528	9e-11
Q54HF6	97	Probable U6 snRNA-associa	yes	no	0.5	0.525	0.568	1e-10
P53905	115	U6 snRNA-associated Sm-li	yes	no	0.470	0.417	0.583	2e-10
O82221	80	Probable small nuclear ri	no	no	0.578	0.737	0.466	2e-07
P62309	76	Small nuclear ribonucleop	no	no	0.578	0.776	0.440	2e-07
P62308	76	Small nuclear ribonucleop	no	no	0.578	0.776	0.440	2e-07
Q3ZBL0	76	Small nuclear ribonucleop	no	no	0.578	0.776	0.440	2e-07
Q9VXE0	76	Probable small nuclear ri	no	no	0.578	0.776	0.423	2e-07

>sp|O74499|LSM7_SCHPO U6 snRNA-associated Sm-like protein LSm7 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=lsm7 PE=1 SV=1

 Score = 68.2 bits (165), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 31/55 (56%), Positives = 43/55 (78%), Gaps = 1/55 (1%)

Query: 36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNG 90
          RKE++LDL+++ D+ +Q   TGGRQ+TG LKG+DQL+NLVLD+  E LR N  +G
Sbjct: 21 RKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLR-NPEDG 74

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner.
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q9UK45|LSM7_HUMAN U6 snRNA-associated Sm-like protein LSm7 OS=Homo sapiens GN=LSM7 PE=1 SV=1

 Score = 66.6 bits (161), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 42/53 (79%)

Query: 32 KMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
          K   +KE++LDL+K++DK ++VK  GGR+ +G LKG+D LLNLVLD  +E++R
Sbjct: 4  KEKKKKESILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMR 56

Binds specifically to the 3'-terminal U-tract of U6 snRNA.

Homo sapiens (taxid: 9606)

>sp|Q9CQQ8|LSM7_MOUSE U6 snRNA-associated Sm-like protein LSm7 OS=Mus musculus GN=Lsm7 PE=3 SV=1

 Score = 65.5 bits (158), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 42/53 (79%)

Query: 32 KMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
          K   +KE++LDL+K++DK ++VK  GGR+ +G LKG+D LLNLVLD  +E++R
Sbjct: 4  KEKKKKESILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTMEYMR 56

Binds specifically to the 3'-terminal U-tract of U6 snRNA.

Mus musculus (taxid: 10090)

>sp|Q54HF6|LSM7_DICDI Probable U6 snRNA-associated Sm-like protein LSm7 OS=Dictyostelium discoideum GN=lsm7 PE=3 SV=1

 Score = 64.7 bits (156), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 29/51 (56%), Positives = 40/51 (78%)

Query: 34 SGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
          + +KE++LDL KF+ K + VK TGGR+V G LKGYDQL+N+ LD+  EF+R
Sbjct: 6  NPKKESILDLQKFLGKEICVKFTGGREVQGILKGYDQLVNITLDQTQEFIR 56

Binds specifically to the 3'-terminal U-tract of U6 snRNA.

Dictyostelium discoideum (taxid: 44689)

>sp|P53905|LSM7_YEAST U6 snRNA-associated Sm-like protein LSm7 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=LSM7 PE=1 SV=2

 Score = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 28/48 (58%), Positives = 39/48 (81%)

Query: 36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFL 83
          ++E +LDLAK+ D  ++VKL GG+ V G LKGYDQL+NLVLD+ VE++
Sbjct: 23 KREAILDLAKYKDSKIRVKLMGGKLVIGVLKGYDQLMNLVLDDTVEYM 70

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM7 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM7, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|O82221|RUXG_ARATH Probable small nuclear ribonucleoprotein G OS=Arabidopsis thaliana GN=At2g23930 PE=2 SV=1

 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/60 (46%), Positives = 39/60 (65%), Gaps = 1/60 (1%)

Query: 36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV 95
          R     DL K++DK +Q+KL   R VTGTL+G+DQ +NLV+D  VE + GN    I ++V
Sbjct: 3  RSGQPPDLKKYMDKKLQIKLNANRMVTGTLRGFDQFMNLVVDNTVE-VNGNDKTDIGMVV 61

Probable common Sm protein, is found in U1 and U2 snRNPs.

Arabidopsis thaliana (taxid: 3702)

>sp|P62309|RUXG_MOUSE Small nuclear ribonucleoprotein G OS=Mus musculus GN=Snrpg PE=1 SV=1

 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 36/59 (61%)

Query: 37 KETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV 95
          K    +L KF+DK + +KL GGR V G L+G+D  +NLV+DE VE       N I ++V
Sbjct: 3  KAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVV 61

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5.

Mus musculus (taxid: 10090)

>sp|P62308|RUXG_HUMAN Small nuclear ribonucleoprotein G OS=Homo sapiens GN=SNRPG PE=1 SV=1

 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 36/59 (61%)

Query: 37 KETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV 95
          K    +L KF+DK + +KL GGR V G L+G+D  +NLV+DE VE       N I ++V
Sbjct: 3  KAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVV 61

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5.

Homo sapiens (taxid: 9606)

>sp|Q3ZBL0|RUXG_BOVIN Small nuclear ribonucleoprotein G OS=Bos taurus GN=SNRPG PE=3 SV=1

 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 36/59 (61%)

Query: 37 KETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV 95
          K    +L KF+DK + +KL GGR V G L+G+D  +NLV+DE VE       N I ++V
Sbjct: 3  KAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVV 61

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5.

Bos taurus (taxid: 9913)

>sp|Q9VXE0|RUXG_DROME Probable small nuclear ribonucleoprotein G OS=Drosophila melanogaster GN=SmG PE=3 SV=1

 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/59 (42%), Positives = 39/59 (66%)

Query: 37 KETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV 95
          K    ++ K++DK + +KL GGR VTG L+G+D  +N+VLD+ VE  + N  N I ++V
Sbjct: 3  KAHPPEVKKYMDKRMMLKLNGGRAVTGILRGFDPFMNVVLDDTVEECKDNTKNNIGMVV 61

Associated with snRNP U1, U2, U4/U6 and U5.

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	102
449463763	99	PREDICTED: U6 snRNA-associated Sm-like p	0.509	0.525	1.0	4e-21
388499482	99	unknown [Lotus japonicus]	0.509	0.525	1.0	4e-21
356512406	99	PREDICTED: U6 snRNA-associated Sm-like p	0.509	0.525	1.0	4e-21
388507056	99	unknown [Medicago truncatula]	0.509	0.525	1.0	4e-21
351720779	99	uncharacterized protein LOC100306498 [Gl	0.509	0.525	1.0	4e-21
359487263	99	PREDICTED: U6 snRNA-associated Sm-like p	0.509	0.525	1.0	4e-21
224059650	99	predicted protein [Populus trichocarpa]	0.509	0.525	1.0	5e-21
294463208	98	unknown [Picea sitchensis]	0.509	0.530	0.961	7e-21
15227722	99	U6 snRNA-associated Sm-like protein LSm7	0.529	0.545	0.944	8e-21
297814702	99	hypothetical protein ARALYDRAFT_484298 [	0.529	0.545	0.944	8e-21

>gi|449463763|ref|XP_004149601.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like isoform 1 [Cucumis sativus] gi|449463765|ref|XP_004149602.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like isoform 2 [Cucumis sativus] gi|449530742|ref|XP_004172352.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like isoform 1 [Cucumis sativus] gi|449530744|ref|XP_004172353.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like isoform 2 [Cucumis sativus]

 Score =  105 bits (262), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 52/52 (100%), Positives = 52/52 (100%)

Query: 33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
          MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR
Sbjct: 1  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 52

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388499482|gb|AFK37807.1| unknown [Lotus japonicus]

 Score =  105 bits (261), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 52/52 (100%), Positives = 52/52 (100%)

Query: 33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
          MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR
Sbjct: 1  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 52

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356512406|ref|XP_003524910.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like [Glycine max]

 Score =  105 bits (261), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 52/52 (100%), Positives = 52/52 (100%)

Query: 33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
          MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR
Sbjct: 1  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 52

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388507056|gb|AFK41594.1| unknown [Medicago truncatula]

 Score =  105 bits (261), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 52/52 (100%), Positives = 52/52 (100%)

Query: 33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
          MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR
Sbjct: 1  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 52

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351720779|ref|NP_001235908.1| uncharacterized protein LOC100306498 [Glycine max] gi|255628715|gb|ACU14702.1| unknown [Glycine max]

 Score =  105 bits (261), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 52/52 (100%), Positives = 52/52 (100%)

Query: 33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
          MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR
Sbjct: 1  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 52

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487263|ref|XP_003633551.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like isoform 1 [Vitis vinifera] gi|359487265|ref|XP_003633552.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like isoform 2 [Vitis vinifera] gi|359487267|ref|XP_003633553.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like isoform 3 [Vitis vinifera] gi|359487269|ref|XP_003633554.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like isoform 4 [Vitis vinifera]

 Score =  105 bits (261), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 52/52 (100%), Positives = 52/52 (100%)

Query: 33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
          MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR
Sbjct: 1  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 52

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224059650|ref|XP_002299952.1| predicted protein [Populus trichocarpa] gi|224104033|ref|XP_002313290.1| predicted protein [Populus trichocarpa] gi|118483640|gb|ABK93714.1| unknown [Populus trichocarpa] gi|222847210|gb|EEE84757.1| predicted protein [Populus trichocarpa] gi|222849698|gb|EEE87245.1| predicted protein [Populus trichocarpa]

 Score =  104 bits (260), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 52/52 (100%), Positives = 52/52 (100%)

Query: 33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
          MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR
Sbjct: 1  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 52

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|294463208|gb|ADE77140.1| unknown [Picea sitchensis]

 Score =  104 bits (259), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 50/52 (96%), Positives = 52/52 (100%)

Query: 33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
          MSGRKETVLDLAKF+DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA+EFLR
Sbjct: 1  MSGRKETVLDLAKFIDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAIEFLR 52

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15227722|ref|NP_178480.1| U6 snRNA-associated Sm-like protein LSm7 [Arabidopsis thaliana] gi|30678085|ref|NP_849931.1| U6 snRNA-associated Sm-like protein LSm7 [Arabidopsis thaliana] gi|4582434|gb|AAD24820.1| putative snRNP splicing factor [Arabidopsis thaliana] gi|27765062|gb|AAO23652.1| At2g03870 [Arabidopsis thaliana] gi|110742944|dbj|BAE99367.1| putative snRNP splicing factor [Arabidopsis thaliana] gi|330250666|gb|AEC05760.1| U6 snRNA-associated Sm-like protein LSm7 [Arabidopsis thaliana] gi|330250667|gb|AEC05761.1| U6 snRNA-associated Sm-like protein LSm7 [Arabidopsis thaliana]

 Score =  104 bits (259), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 51/54 (94%), Positives = 53/54 (98%)

Query: 33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86
          MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEF+R +
Sbjct: 1  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFVRDH 54

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297814702|ref|XP_002875234.1| hypothetical protein ARALYDRAFT_484298 [Arabidopsis lyrata subsp. lyrata] gi|297321072|gb|EFH51493.1| hypothetical protein ARALYDRAFT_484298 [Arabidopsis lyrata subsp. lyrata]

 Score =  104 bits (259), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 51/54 (94%), Positives = 53/54 (98%)

Query: 33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86
          MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEF+R +
Sbjct: 1  MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFVRDH 54

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	102
TAIR|locus:2056825	99	EMB2816 "AT2G03870" [Arabidops	0.509	0.525	0.980	1.1e-21
UNIPROTKB|G4NLE3	146	MGG_02938 "Uncharacterized pro	0.480	0.335	0.673	4.4e-13
FB|FBgn0261068	110	LSm7 [Drosophila melanogaster	0.519	0.481	0.584	1.5e-12
ASPGD|ASPL0000056132	136	AN0767 [Emericella nidulans (t	0.480	0.360	0.612	3.9e-12
UNIPROTKB|Q9UK45	103	LSM7 "U6 snRNA-associated Sm-l	0.519	0.514	0.528	8.2e-12
POMBASE|SPCC285.12	113	lsm7 "U6 snRNP-associated prot	0.480	0.433	0.591	1e-11
DICTYBASE|DDB_G0289499	97	lsm7 "putative U6 small nuclea	0.480	0.505	0.591	1.3e-11
SGD|S000005091	115	LSM7 "Lsm (Like Sm) protein" [	0.509	0.452	0.566	1.3e-11
WB|WBGene00003081	104	lsm-7 [Caenorhabditis elegans	0.480	0.471	0.551	2.2e-11
UNIPROTKB|Q23543	104	lsm-7 "Protein LSM-7" [Caenorh	0.480	0.471	0.551	2.2e-11

TAIR|locus:2056825 EMB2816 "AT2G03870" [Arabidopsis thaliana (taxid:3702)]

 Score = 253 (94.1 bits), Expect = 1.1e-21, P = 1.1e-21
 Identities = 51/52 (98%), Positives = 52/52 (100%)

Query:    33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
             MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEF+R
Sbjct:     1 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFVR 52

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM;ISS

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

UNIPROTKB|G4NLE3 MGG_02938 "Uncharacterized protein" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 172 (65.6 bits), Expect = 4.4e-13, P = 4.4e-13
 Identities = 33/49 (67%), Positives = 40/49 (81%)

Query:    36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
             +KE +LDLAK++DK VQVK  GGR+V GTLKGYD L+NLVLDE  E +R
Sbjct:    54 KKENILDLAKYMDKEVQVKFNGGREVIGTLKGYDALMNLVLDEVKETMR 102

GO:0003674 "molecular_function" evidence=ND

FB|FBgn0261068 LSm7 [Drosophila melanogaster (taxid:7227)]

 Score = 167 (63.8 bits), Expect = 1.5e-12, P = 1.5e-12
 Identities = 31/53 (58%), Positives = 42/53 (79%)

Query:    32 KMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
             K   RKE++LDL+K+++K ++VK  GGR+ +G LKGYD LLNLVLD  VE+LR
Sbjct:    13 KEKRRKESILDLSKYLEKQIRVKFAGGREASGILKGYDALLNLVLDNTVEYLR 65

GO:0005688 "U6 snRNP" evidence=ISS

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

GO:0071011 "precatalytic spliceosome" evidence=IDA

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0022008 "neurogenesis" evidence=IMP

ASPGD|ASPL0000056132 AN0767 [Emericella nidulans (taxid:162425)]

 Score = 163 (62.4 bits), Expect = 3.9e-12, P = 3.9e-12
 Identities = 30/49 (61%), Positives = 40/49 (81%)

Query:    36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
             +KE +LDL K++DK V+VK  GGR+V+G LKGYDQL+NLVLD+  E +R
Sbjct:    46 KKENILDLTKYMDKEVRVKFNGGREVSGILKGYDQLMNLVLDDVKESMR 94

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

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

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

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

GO:0005688 "U6 snRNP" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

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

UNIPROTKB|Q9UK45 LSM7 "U6 snRNA-associated Sm-like protein LSm7" [Homo sapiens (taxid:9606)]

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 28/53 (52%), Positives = 42/53 (79%)

Query:    32 KMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
             K   +KE++LDL+K++DK ++VK  GGR+ +G LKG+D LLNLVLD  +E++R
Sbjct:     4 KEKKKKESILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMR 56

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0017070 "U6 snRNA binding" evidence=NAS

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

GO:0005634 "nucleus" evidence=NAS

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

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

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

GO:0005515 "protein binding" evidence=IPI

POMBASE|SPCC285.12 lsm7 "U6 snRNP-associated protein Lsm7 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 159 (61.0 bits), Expect = 1.0e-11, P = 1.0e-11
 Identities = 29/49 (59%), Positives = 40/49 (81%)

Query:    36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
             RKE++LDL+++ D+ +Q   TGGRQ+TG LKG+DQL+NLVLD+  E LR
Sbjct:    21 RKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLR 69

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=IDA

GO:0005681 "spliceosomal complex" evidence=NAS

GO:0005688 "U6 snRNP" evidence=ISO

GO:0005829 "cytosol" evidence=IDA

GO:0006402 "mRNA catabolic process" evidence=ISS

GO:0008033 "tRNA processing" evidence=IEA

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

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

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

DICTYBASE|DDB_G0289499 lsm7 "putative U6 small nuclear ribonucleoparticle-associated protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 158 (60.7 bits), Expect = 1.3e-11, P = 1.3e-11
 Identities = 29/49 (59%), Positives = 39/49 (79%)

Query:    36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
             +KE++LDL KF+ K + VK TGGR+V G LKGYDQL+N+ LD+  EF+R
Sbjct:     8 KKESILDLQKFLGKEICVKFTGGREVQGILKGYDQLVNITLDQTQEFIR 56

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

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

GO:0006402 "mRNA catabolic process" evidence=ISS

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

GO:0005730 "nucleolus" evidence=ISS

GO:0005688 "U6 snRNP" evidence=ISS

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

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

SGD|S000005091 LSM7 "Lsm (Like Sm) protein" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 158 (60.7 bits), Expect = 1.3e-11, P = 1.3e-11
 Identities = 30/53 (56%), Positives = 41/53 (77%)

Query:    32 KMSG-RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFL 83
             K  G ++E +LDLAK+ D  ++VKL GG+ V G LKGYDQL+NLVLD+ VE++
Sbjct:    18 KFEGPKREAILDLAKYKDSKIRVKLMGGKLVIGVLKGYDQLMNLVLDDTVEYM 70

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

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=IMP;IPI

GO:0046540 "U4/U6 x U5 tri-snRNP complex" evidence=NAS;IDA

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0005737 "cytoplasm" evidence=IEA;IDA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0008033 "tRNA processing" evidence=IEA

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

GO:0006364 "rRNA processing" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA;TAS;IPI

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

GO:0005688 "U6 snRNP" evidence=IDA

WB|WBGene00003081 lsm-7 [Caenorhabditis elegans (taxid:6239)]

 Score = 156 (60.0 bits), Expect = 2.2e-11, P = 2.2e-11
 Identities = 27/49 (55%), Positives = 41/49 (83%)

Query:    36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
             +KE+V+DL +F+DK ++VK  GGR+ +G L+G+DQLLN+VLD+  E+LR
Sbjct:     9 KKESVVDLTRFLDKEIRVKFQGGREASGVLRGFDQLLNMVLDDCREYLR 57

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

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0008340 "determination of adult lifespan" evidence=IMP

GO:0042127 "regulation of cell proliferation" evidence=IMP

GO:0040020 "regulation of meiosis" evidence=IMP

GO:0008406 "gonad development" evidence=IMP

GO:0016477 "cell migration" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

UNIPROTKB|Q23543 lsm-7 "Protein LSM-7" [Caenorhabditis elegans (taxid:6239)]

 Score = 156 (60.0 bits), Expect = 2.2e-11, P = 2.2e-11
 Identities = 27/49 (55%), Positives = 41/49 (83%)

Query:    36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
             +KE+V+DL +F+DK ++VK  GGR+ +G L+G+DQLLN+VLD+  E+LR
Sbjct:     9 KKESVVDLTRFLDKEIRVKFQGGREASGVLRGFDQLLNMVLDDCREYLR 57

GO:0005515 "protein binding" evidence=IPI

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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

Your Input:
	GSVIVG00008837001	SubName- Full=Chromosome chr13 scaffold_210, whole genome shotgun sequence; (113 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00023663001	SubName- Full=Chromosome chr7 scaffold_31, whole genome shotgun sequence; (97 aa)				•	•	•	•		0.977
	GSVIVG00020489001	SubName- Full=Chromosome chr5 scaffold_2, whole genome shotgun sequence; (87 aa)				•	•	•	•		0.973
	GSVIVG00031776001	hypothetical protein LOC100253870 (172 aa)			•	•	•	•	•		0.966
	GSVIVG00017697001	SubName- Full=Chromosome chr17 scaffold_16, whole genome shotgun sequence; (86 aa)				•	•	•	•		0.888
	GSVIVG00034053001	SubName- Full=Putative uncharacterized protein (Chromosome chr9 scaffold_7, whole genome shotgu [...] (128 aa)				•	•	•	•		0.830
	GSVIVG00013856001	SubName- Full=Chromosome chr16 scaffold_10, whole genome shotgun sequence; (98 aa)				•	•	•	•	•	0.764
	GSVIVG00002878001	SubName- Full=Chromosome chr18 scaffold_137, whole genome shotgun sequence; (132 aa)				•	•	•	•		0.734
	GSVIVG00030614001	SubName- Full=Chromosome chr1 scaffold_5, whole genome shotgun sequence; (104 aa)				•	•	•	•		0.728
	GSVIVG00033465001	SubName- Full=Chromosome chr19 scaffold_66, whole genome shotgun sequence; (107 aa)				•	•	•	•		0.716
	GSVIVG00027979001	SubName- Full=Chromosome chr7 scaffold_42, whole genome shotgun sequence; (115 aa)				•	•	•	•		0.672

---

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	102
cd01729	89	cd01729, LSm7, Like-Sm protein 7	1e-27
cd01719	70	cd01719, Sm_G, Sm protein G	7e-16
pfam01423	66	pfam01423, LSM, LSM domain	3e-11
smart00651	67	smart00651, Sm, snRNP Sm proteins	3e-11
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	2e-10
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	4e-09
cd01727	91	cd01727, LSm8, Like-Sm protein 8	8e-09
cd00600	63	cd00600, Sm_like, Sm and related proteins	2e-08
cd01730	82	cd01730, LSm3, Like-Sm protein 3	2e-08
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	4e-07
cd01726	68	cd01726, LSm6, Like-Sm protein 6	6e-07
cd01728	74	cd01728, LSm1, Like-Sm protein 1	2e-06
cd01717	80	cd01717, Sm_B, Sm protein B	4e-06
cd06168	73	cd06168, LSMD1, LSM domain containing 1	5e-06
cd11679	65	cd11679, archaeal_Sm_like, archaeal Sm-related pro	2e-05
cd01722	69	cd01722, Sm_F, Sm protein F	3e-04
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	9e-04

>gnl|CDD|212476 cd01729, LSm7, Like-Sm protein 7

 Score = 96.1 bits (240), Expect = 1e-27
 Identities = 34/48 (70%), Positives = 43/48 (89%)

Query: 37 KETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
          KE++LDL+K+VDK ++VK  GGR+VTG LKGYDQLLNLVLD+ VE+LR
Sbjct: 1  KESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLR 48

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 89

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

 Score = 65.6 bits (161), Expect = 7e-16
 Identities = 23/54 (42%), Positives = 37/54 (68%)

Query: 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV 95
          +L K++DK + +KL G R+V+G L+G+D  +NLVLD+AVE +       I ++V
Sbjct: 4  ELKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVGDGEKTPIGMVV 57

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

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

 Score = 53.7 bits (130), Expect = 3e-11
 Identities = 21/45 (46%), Positives = 30/45 (66%)

Query: 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86
           L K + K V V+L  GR++ GTLKG+DQ +NLVLD+  E ++  
Sbjct: 2  FLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDG 46

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

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

 Score = 53.7 bits (130), Expect = 3e-11
 Identities = 20/45 (44%), Positives = 29/45 (64%)

Query: 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG 85
            L K + K V V+L  GR+  GTLKG+DQ +NLVL++  E ++ 
Sbjct: 1  KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKD 45

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

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

 Score = 51.9 bits (125), Expect = 2e-10
 Identities = 21/39 (53%), Positives = 27/39 (69%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81
          L K ++K V VKL  GR+  GTL G+DQ +NLVLD+  E
Sbjct: 12 LKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEE 50

Length = 79

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

 Score = 48.3 bits (116), Expect = 4e-09
 Identities = 23/44 (52%), Positives = 31/44 (70%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86
          L + ++K V VKL GG++V G LKG+DQ LNLVL+ A E + G 
Sbjct: 6  LNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGE 49

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

>gnl|CDD|212474 cd01727, LSm8, Like-Sm protein 8

 Score = 48.3 bits (116), Expect = 8e-09
 Identities = 18/39 (46%), Positives = 24/39 (61%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81
          L  +++K V V  T GR + GTLKG+DQ  NL+L    E
Sbjct: 4  LEDYLNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHE 42

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 91

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

 Score = 46.5 bits (111), Expect = 2e-08
 Identities = 21/44 (47%), Positives = 28/44 (63%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86
          L  F+ K V V+L  GR +TGTL  +D+ +NLVLD+ VE  R  
Sbjct: 1  LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDG 44

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

>gnl|CDD|212477 cd01730, LSm3, Like-Sm protein 3

 Score = 47.2 bits (113), Expect = 2e-08
 Identities = 19/42 (45%), Positives = 27/42 (64%), Gaps = 1/42 (2%)

Query: 41 LDLAKF-VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81
          LDL +  +D+ V VKL G R++ G L  YDQ LN++L +  E
Sbjct: 3  LDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEE 44

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 82

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

 Score = 43.4 bits (103), Expect = 4e-07
 Identities = 20/43 (46%), Positives = 26/43 (60%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG 85
          L   ++  V V+L GGR+  G L+GYD  +NLVLD A E   G
Sbjct: 9  LNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDG 51

Length = 72

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

 Score = 42.9 bits (102), Expect = 6e-07
 Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 3/54 (5%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNL---YNGIFV 93
          L K + K V VKL  G +  G L   D  +NLVL++  E++ G L   Y   F+
Sbjct: 6  LKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYGDAFI 59

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

>gnl|CDD|212475 cd01728, LSm1, Like-Sm protein 1

 Score = 41.7 bits (99), Expect = 2e-06
 Identities = 23/58 (39%), Positives = 35/58 (60%), Gaps = 5/58 (8%)

Query: 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE-FLRGNLYN----GIFVI 94
           L + +DK + V L  GR++ G L+ +DQ  NLVL++ VE  + GN Y     G+F+I
Sbjct: 6  SLEEELDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERIIVGNQYGDIPRGLFII 63

The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. Accumulation of uridylated RNAs in an lsm1 mutant suggests an involvement of the LSm1-7 complex in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm1-7, together with Pat1, are also called the decapping activator. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 74

>gnl|CDD|212464 cd01717, Sm_B, Sm protein B

 Score = 41.0 bits (97), Expect = 4e-06
 Identities = 14/40 (35%), Positives = 25/40 (62%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEF 82
          + ++++  ++V L  GRQ  GT   +D+ +NLVL +  EF
Sbjct: 5  MLQYINYRMRVTLQDGRQFVGTFLAFDKHMNLVLSDCEEF 44

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 80

>gnl|CDD|212486 cd06168, LSMD1, LSM domain containing 1

 Score = 40.6 bits (96), Expect = 5e-06
 Identities = 15/51 (29%), Positives = 26/51 (50%)

Query: 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNG 90
           L L K + + ++V LT GR + GT    D+  N++L  A E+ + +    
Sbjct: 1  RLKLRKLLGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSDLGA 51

The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSMD1 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes, forming heptameric and hexameric ring structures similar to those found in eukaryotes. Length = 73

>gnl|CDD|212490 cd11679, archaeal_Sm_like, archaeal Sm-related protein

 Score = 38.4 bits (90), Expect = 2e-05
 Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 2/54 (3%)

Query: 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQL-LNLVLDEAVEFLRGNLYNGIFVI 94
          +L   +DK V V L+ G+  TG L G+D   LN+VL  A +   GN +  + + 
Sbjct: 4  ELNSLLDKEVIVTLSNGKTYTGQLVGFDPSSLNIVLTNAKD-SSGNKFPKVIIN 56

Archaeal Sm-related proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain. Length = 65

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

 Score = 35.7 bits (83), Expect = 3e-04
 Identities = 16/45 (35%), Positives = 20/45 (44%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNL 87
          L     K V VKL  G +  GTL   D  +NL L    E++ G  
Sbjct: 6  LNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKF 50

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

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

 Score = 34.8 bits (80), Expect = 9e-04
 Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 45 KFVDKGVQVKLTG-GRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86
            V   ++V++ G   Q+ G L   D  +NL L + +E +   
Sbjct: 7  SLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVGEE 49

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	102
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.77
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.74
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.71
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.69
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.69
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.68
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.66
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.65
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.65
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.65
KOG1780	77	consensus Small Nuclear ribonucleoprotein G [RNA p	99.64
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.64
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.64
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.6
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.58
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.58
KOG1781	108	consensus Small Nuclear ribonucleoprotein splicing	99.58
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.56
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.55
KOG3482	79	consensus Small nuclear ribonucleoprotein (snRNP)	99.54
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.53
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.44
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.4
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.39
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.37
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.36
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.24
KOG1783	77	consensus Small nuclear ribonucleoprotein F [RNA p	99.18
KOG1775	84	consensus U6 snRNA-associated Sm-like protein [RNA	99.03
KOG1774	88	consensus Small nuclear ribonucleoprotein E [RNA p	98.98
KOG3460	91	consensus Small nuclear ribonucleoprotein (snRNP)	98.96
KOG1784	96	consensus Small Nuclear ribonucleoprotein splicing	98.83
KOG3168	177	consensus U1 snRNP component [Transcription]	98.7
KOG1782	129	consensus Small Nuclear ribonucleoprotein splicing	98.6
KOG3448	96	consensus Predicted snRNP core protein [RNA proces	98.58
KOG3293	134	consensus Small nuclear ribonucleoprotein (snRNP)	97.79
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	97.78
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	97.14
KOG3428	109	consensus Small nuclear ribonucleoprotein SMD1 and	97.07
KOG3459	114	consensus Small nuclear ribonucleoprotein (snRNP)	96.64
KOG3172	119	consensus Small nuclear ribonucleoprotein Sm D3 [R	96.13
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	95.7
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	95.66
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	95.5
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	95.27
PRK14638	150	hypothetical protein; Provisional	94.84
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	94.8
PRK14639	140	hypothetical protein; Provisional	94.29
PRK02001	152	hypothetical protein; Validated	94.03
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	93.86
COG1923	77	Hfq Uncharacterized host factor I protein [General	93.51
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	93.39
PRK14091	165	RNA-binding protein Hfq; Provisional	92.83
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	92.33
PRK14644	136	hypothetical protein; Provisional	92.17
PRK14640	152	hypothetical protein; Provisional	91.5
PRK14633	150	hypothetical protein; Provisional	91.43
PRK14642	197	hypothetical protein; Provisional	90.56
PRK14645	154	hypothetical protein; Provisional	90.36
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	90.28
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	90.17
PRK00092	154	ribosome maturation protein RimP; Reviewed	89.86
PRK14636	176	hypothetical protein; Provisional	89.74
PRK14643	164	hypothetical protein; Provisional	89.63
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	89.61
PRK14634	155	hypothetical protein; Provisional	89.53
COG0779	153	Uncharacterized protein conserved in bacteria [Fun	89.46
PRK14646	155	hypothetical protein; Provisional	89.13
PRK14632	172	hypothetical protein; Provisional	88.69
PRK14091	165	RNA-binding protein Hfq; Provisional	88.39
PRK14647	159	hypothetical protein; Provisional	87.54
PRK14631	174	hypothetical protein; Provisional	86.81
PRK14637	151	hypothetical protein; Provisional	86.51
PRK14641	173	hypothetical protein; Provisional	83.5
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	81.49

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

Probab=99.77  E-value=1.9e-18  Score=114.61  Aligned_cols=60  Identities=60%  Similarity=1.006  Sum_probs=53.7

Q ss_pred             cCCcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc--------eeecEEEEEE
Q 034180           37 KETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN--------LYNGIFVIVC   96 (102)
Q Consensus        37 ~~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~--------~~~~iG~iv~   96 (102)
                      +.++++|.++++|+|.|+|+|||+++|+|.|||+||||+|++|+|+..++        ..+.+|.++.
T Consensus         1 ~~~~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~i   68 (81)
T cd01729           1 KESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVC   68 (81)
T ss_pred             CcchhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEE
Confidence            35688999999999999999999999999999999999999999998652        4577898876

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.

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

Probab=99.74  E-value=8e-18  Score=109.47  Aligned_cols=57  Identities=44%  Similarity=0.721  Sum_probs=52.7

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC   96 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~   96 (102)
                      .++|+++++|+|.|+|+||++++|+|.|||+||||+|+||+|+.++.+.+.+|.++.
T Consensus         2 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~I   58 (72)
T cd01719           2 PPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVI   58 (72)
T ss_pred             chhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEE
Confidence            468999999999999999999999999999999999999999987777888888764

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.

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.71  E-value=4.2e-17  Score=105.61  Aligned_cols=57  Identities=37%  Similarity=0.550  Sum_probs=51.3

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC   96 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~   96 (102)
                      ...|.++++++|.|+|+||++|+|+|.|||+|||++|+||.|..+++..+.+|.++.
T Consensus         6 ~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~i   62 (72)
T PRK00737          6 LDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVI   62 (72)
T ss_pred             HHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEE
Confidence            456899999999999999999999999999999999999999987777778887754

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

Probab=99.69  E-value=1.1e-16  Score=105.36  Aligned_cols=56  Identities=21%  Similarity=0.421  Sum_probs=49.9

Q ss_pred             chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEE---eCceeecEEEEEE
Q 034180           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFL---RGNLYNGIFVIVC   96 (102)
Q Consensus        41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~---~~~~~~~iG~iv~   96 (102)
                      ..|+++++++|.|+++|||+++|+|.|||+|||++|+||+|++   +++..+.+|.++.
T Consensus         6 ~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~i   64 (76)
T cd01732           6 ELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILL   64 (76)
T ss_pred             HHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEE
Confidence            4478999999999999999999999999999999999999998   4455677888765

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.

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

Probab=99.69  E-value=1.1e-16  Score=102.20  Aligned_cols=56  Identities=41%  Similarity=0.510  Sum_probs=51.2

Q ss_pred             chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC   96 (102)
Q Consensus        41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~   96 (102)
                      ..|+++++|+|.|+|+||++|+|+|.|||+|||++|+||+|+.+++..+.+|.++-
T Consensus         3 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~i   58 (68)
T cd01731           3 DVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVI   58 (68)
T ss_pred             HHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEE
Confidence            45889999999999999999999999999999999999999988877788887754

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.

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

Probab=99.68  E-value=2.3e-16  Score=103.50  Aligned_cols=58  Identities=31%  Similarity=0.361  Sum_probs=51.1

Q ss_pred             CcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc---eeecEEEEEE
Q 034180           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN---LYNGIFVIVC   96 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~---~~~~iG~iv~   96 (102)
                      +.++|.++++|+|.|+++|||++.|+|.|||+|||++|+||.|+...+   ..+.+|.++-
T Consensus         3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~vi   63 (74)
T cd01728           3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFII   63 (74)
T ss_pred             chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEE
Confidence            567899999999999999999999999999999999999999987542   3467788765

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.

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

Probab=99.66  E-value=3.5e-16  Score=101.65  Aligned_cols=56  Identities=32%  Similarity=0.440  Sum_probs=49.2

Q ss_pred             chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC----ceeecEEEEEE
Q 034180           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG----NLYNGIFVIVC   96 (102)
Q Consensus        41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~----~~~~~iG~iv~   96 (102)
                      ++|++++|++|.|+++|||.+.|+|.|||+|||++|++|+|+...    ...+.+|.++.
T Consensus         2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~i   61 (74)
T cd01727           2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYII   61 (74)
T ss_pred             hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEE
Confidence            579999999999999999999999999999999999999999742    24566787764

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.

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

Probab=99.65  E-value=5.7e-16  Score=98.85  Aligned_cols=56  Identities=27%  Similarity=0.351  Sum_probs=50.4

Q ss_pred             chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC   96 (102)
Q Consensus        41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~   96 (102)
                      ..|++++|++|.|+|++|++|+|+|.|||+|||++|+||+|..+++....+|.++-
T Consensus         3 ~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~I   58 (67)
T cd01726           3 EFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFI   58 (67)
T ss_pred             HHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEE
Confidence            45789999999999999999999999999999999999999887777777887653

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.

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

Probab=99.65  E-value=6.1e-16  Score=102.35  Aligned_cols=55  Identities=31%  Similarity=0.443  Sum_probs=47.2

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc-------------eeecEEEEEE
Q 034180           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN-------------LYNGIFVIVC   96 (102)
Q Consensus        42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~-------------~~~~iG~iv~   96 (102)
                      .|++.++|+|.|+++|||+++|+|.|||+||||+|+||+|++.++             ..+.+|.++.
T Consensus         5 ~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~i   72 (82)
T cd01730           5 LIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFV   72 (82)
T ss_pred             HHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEE
Confidence            357789999999999999999999999999999999999998542             3456777654

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.

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

Probab=99.65  E-value=6.3e-16  Score=101.40  Aligned_cols=56  Identities=23%  Similarity=0.433  Sum_probs=49.0

Q ss_pred             chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc----------eeecEEEEEE
Q 034180           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN----------LYNGIFVIVC   96 (102)
Q Consensus        41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~----------~~~~iG~iv~   96 (102)
                      ..|.+|++++|.|+++|||++.|+|.|||+||||+|+||+|++.++          +.+.+|+++.
T Consensus         3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~i   68 (79)
T cd01717           3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLL   68 (79)
T ss_pred             chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEE
Confidence            4689999999999999999999999999999999999999987432          3467888764

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.

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

Probab=99.64  E-value=1.9e-16  Score=104.87  Aligned_cols=57  Identities=46%  Similarity=0.690  Sum_probs=53.5

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC   96 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~   96 (102)
                      .|+|++|++|++.+++++||...|+|.|||.|||+||+++.|...++....+|.++-
T Consensus         6 ~PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vI   62 (77)
T KOG1780|consen    6 HPELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVI   62 (77)
T ss_pred             CchHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEE
Confidence            459999999999999999999999999999999999999999998888999998764

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

Probab=99.64  E-value=9.2e-16  Score=100.82  Aligned_cols=56  Identities=18%  Similarity=0.299  Sum_probs=50.9

Q ss_pred             chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC------ceeecEEEEEE
Q 034180           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG------NLYNGIFVIVC   96 (102)
Q Consensus        41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~------~~~~~iG~iv~   96 (102)
                      ..|+++++++|+|+++|||.+.|+|.|||++||++|+||.|+..+      .+.+.+|+++.
T Consensus         3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~I   64 (75)
T cd06168           3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMI   64 (75)
T ss_pred             hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEE
Confidence            468999999999999999999999999999999999999999854      45788998875

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.

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

Probab=99.64  E-value=5.6e-16  Score=99.24  Aligned_cols=56  Identities=29%  Similarity=0.342  Sum_probs=50.5

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV   95 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv   95 (102)
                      ...|+++++++|.|+|+||++|+|+|.|||+|||++|+||+|+.+++....+|.++
T Consensus         3 ~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~   58 (68)
T cd01722           3 KPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVL   58 (68)
T ss_pred             HHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEE
Confidence            45689999999999999999999999999999999999999998777677777765

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.

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

Probab=99.60  E-value=9.2e-15  Score=91.70  Aligned_cols=55  Identities=33%  Similarity=0.525  Sum_probs=50.7

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc-eeecEEEEEE
Q 034180           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN-LYNGIFVIVC   96 (102)
Q Consensus        42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~-~~~~iG~iv~   96 (102)
                      .|++++|++|+|.++||++++|+|.+||+|||++|+||.|..+++ ..+.+|.++-
T Consensus         2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~i   57 (67)
T PF01423_consen    2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFI   57 (67)
T ss_dssp             HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEE
T ss_pred             hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEE
Confidence            588999999999999999999999999999999999999999887 8888887653

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

>smart00651 Sm snRNP Sm proteins

Probab=99.58  E-value=7e-15  Score=92.09  Aligned_cols=54  Identities=37%  Similarity=0.592  Sum_probs=48.7

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC-ceeecEEEEE
Q 034180           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG-NLYNGIFVIV   95 (102)
Q Consensus        42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~-~~~~~iG~iv   95 (102)
                      .|+++++++|.|.|+||+++.|+|.|||+|||++|+||.|+.++ ++.+.+|.++
T Consensus         2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~   56 (67)
T smart00651        2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVF   56 (67)
T ss_pred             hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEE
Confidence            58899999999999999999999999999999999999999877 5666677654

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

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

Probab=99.58  E-value=8.4e-15  Score=95.81  Aligned_cols=47  Identities=45%  Similarity=0.660  Sum_probs=43.7

Q ss_pred             cCCcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEE
Q 034180           37 KETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFL   83 (102)
Q Consensus        37 ~~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~   83 (102)
                      +.+...|+++++++|.|+|++|++|.|+|.|||+|||++|+||+|+.
T Consensus         6 ~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~   52 (79)
T COG1958           6 PLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEII   52 (79)
T ss_pred             CCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEe
Confidence            34566789999999999999999999999999999999999999998

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

Probab=99.58  E-value=1e-16  Score=111.33  Aligned_cols=66  Identities=52%  Similarity=0.857  Sum_probs=59.9

Q ss_pred             ccCCCcCCcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc--------eeecEEEEEEE
Q 034180           32 KMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN--------LYNGIFVIVCF   97 (102)
Q Consensus        32 ~ms~~~~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~--------~~~~iG~iv~~   97 (102)
                      .+.+++++.++|.+|++|+|+|++.+||+..|+|.|||+.||+||++++|+..++        +.+.+|++||+
T Consensus        11 ~e~~kkEsilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~R   84 (108)
T KOG1781|consen   11 FEKPKKESILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCR   84 (108)
T ss_pred             ccccchhHHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEc
Confidence            3668889999999999999999999999999999999999999999999987442        34899999996

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

Probab=99.56  E-value=1.7e-14  Score=96.09  Aligned_cols=57  Identities=26%  Similarity=0.374  Sum_probs=48.7

Q ss_pred             cchHHhhcCC--eEEEEEc--CCeEEEEEEEEecCccceEEcceEEEEe-CceeecEEEEEE
Q 034180           40 VLDLAKFVDK--GVQVKLT--GGRQVTGTLKGYDQLLNLVLDEAVEFLR-GNLYNGIFVIVC   96 (102)
Q Consensus        40 ~~~L~~~i~K--~V~V~Lk--~Gr~i~G~L~gfD~~mNLVL~da~E~~~-~~~~~~iG~iv~   96 (102)
                      ...+.+++++  +|.|+++  +|++++|+|.|||+|||++|+||+|+.. ++..+.+|.++.
T Consensus         8 ~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~ili   69 (79)
T cd01718           8 INLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILL   69 (79)
T ss_pred             HHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEE
Confidence            4458899998  6777776  8999999999999999999999999986 566778898765

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

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

Probab=99.55  E-value=2.2e-14  Score=88.55  Aligned_cols=53  Identities=32%  Similarity=0.534  Sum_probs=47.8

Q ss_pred             HHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV   95 (102)
Q Consensus        43 L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv   95 (102)
                      |++++|++|.|.++||+.+.|+|.|||+|||++|+||.|..++...+.+|.++
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~~~~~~~~~   53 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGKKRVLGLVL   53 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCcEEECCeEE
Confidence            56789999999999999999999999999999999999998877667677664

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.

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

Probab=99.54  E-value=9e-15  Score=96.94  Aligned_cols=58  Identities=31%  Similarity=0.318  Sum_probs=54.2

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVCF   97 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~~   97 (102)
                      .+.|+.+.+|+|.|+||+|.+|+|+|.+.|.|||+.|.+|+|++++.....+|.|+-+
T Consensus        10 KpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEilIR   67 (79)
T KOG3482|consen   10 KPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEILIR   67 (79)
T ss_pred             hHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEEEE
Confidence            4569999999999999999999999999999999999999999999999999998743

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

Probab=99.53  E-value=2.7e-14  Score=96.40  Aligned_cols=43  Identities=23%  Similarity=0.445  Sum_probs=39.6

Q ss_pred             HHhhc--CCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC
Q 034180           43 LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG   85 (102)
Q Consensus        43 L~~~i--~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~   85 (102)
                      |.+.+  +++|.|+|++|+++.|+|.|||+|||++|+||+|.+.+
T Consensus         7 L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~   51 (87)
T cd01720           7 LTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTE   51 (87)
T ss_pred             HHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeec
Confidence            56666  89999999999999999999999999999999998765

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.

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

Probab=99.44  E-value=3.8e-13  Score=86.75  Aligned_cols=53  Identities=19%  Similarity=0.139  Sum_probs=45.5

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEE
Q 034180           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVI   94 (102)
Q Consensus        42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~i   94 (102)
                      .|.+..|++|.|+||||.+|+|+|.++|+|||++|+||.+...++....+|.+
T Consensus         4 ~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v   56 (70)
T cd01721           4 LLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQV   56 (70)
T ss_pred             HHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcE
Confidence            47788999999999999999999999999999999999987655544555554

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.

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

Probab=99.40  E-value=8.9e-13  Score=86.11  Aligned_cols=45  Identities=22%  Similarity=0.295  Sum_probs=41.3

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc
Q 034180           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN   86 (102)
Q Consensus        42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~   86 (102)
                      .|++..|++|.|.|++|++++|+|.++|+|||++|+||.|...++
T Consensus         5 ~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g   49 (76)
T cd01723           5 LLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDG   49 (76)
T ss_pred             HHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCC
Confidence            478899999999999999999999999999999999999985444

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

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

Probab=99.39  E-value=1.3e-12  Score=88.40  Aligned_cols=55  Identities=25%  Similarity=0.303  Sum_probs=49.2

Q ss_pred             chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV   95 (102)
Q Consensus        41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv   95 (102)
                      -.|++..|++|.|.|+||.+|+|+|.++|+|||++|+||.|..+++....+|.++
T Consensus         4 ~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~   58 (90)
T cd01724           4 RFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLS   58 (90)
T ss_pred             HHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEE
Confidence            3578899999999999999999999999999999999999998877777777664

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.

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.37  E-value=2.2e-12  Score=87.67  Aligned_cols=54  Identities=28%  Similarity=0.465  Sum_probs=44.5

Q ss_pred             HHhhcCC--eEEEEEcC--CeEEEEEEEEecCccceEEcceEEEEeC-ceeecEEEEEE
Q 034180           43 LAKFVDK--GVQVKLTG--GRQVTGTLKGYDQLLNLVLDEAVEFLRG-NLYNGIFVIVC   96 (102)
Q Consensus        43 L~~~i~K--~V~V~Lk~--Gr~i~G~L~gfD~~mNLVL~da~E~~~~-~~~~~iG~iv~   96 (102)
                      +.+++++  +|.|.+.+  +++++|+|.|||+|||++|+||+|+..+ +..+.+|.++-
T Consensus        19 ~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilI   77 (89)
T PTZ00138         19 IFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILL   77 (89)
T ss_pred             HHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEE
Confidence            6678774  67777766  5999999999999999999999999754 46678888764

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

Probab=99.36  E-value=2.3e-12  Score=85.09  Aligned_cols=54  Identities=24%  Similarity=0.242  Sum_probs=47.2

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV   95 (102)
Q Consensus        42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv   95 (102)
                      .|+...|++|.|.||||.+|+|+|.++|+|||++|+||++..+++....+|.++
T Consensus        13 ~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~   66 (78)
T cd01733          13 LLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIM   66 (78)
T ss_pred             HHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEE
Confidence            367889999999999999999999999999999999999887676665666653

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.

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

Probab=99.24  E-value=2.9e-11  Score=80.10  Aligned_cols=45  Identities=29%  Similarity=0.291  Sum_probs=41.0

Q ss_pred             chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC
Q 034180           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG   85 (102)
Q Consensus        41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~   85 (102)
                      ..|++..|++|.|.||+|.+++|+|.++|+|||++|+||++..++
T Consensus         4 ~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~   48 (81)
T cd01725           4 SFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPE   48 (81)
T ss_pred             HHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCC
Confidence            357889999999999999999999999999999999999887543

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.

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

Probab=99.18  E-value=2e-12  Score=85.69  Aligned_cols=61  Identities=30%  Similarity=0.335  Sum_probs=53.4

Q ss_pred             cCCCcCCcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEE
Q 034180           33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFV   93 (102)
Q Consensus        33 ms~~~~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~   93 (102)
                      |+.+..+...|++.+||+|.|+|.+|-.|+|+|.+.|.|||+.|+.|+|+.+++..+..|.
T Consensus         1 ~s~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygd   61 (77)
T KOG1783|consen    1 MSEGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGD   61 (77)
T ss_pred             CCcccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccc
Confidence            4444444556999999999999999999999999999999999999999999988888773

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

Probab=99.03  E-value=1.3e-10  Score=77.80  Aligned_cols=50  Identities=24%  Similarity=0.458  Sum_probs=43.6

Q ss_pred             CCcchHH-hhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCce
Q 034180           38 ETVLDLA-KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNL   87 (102)
Q Consensus        38 ~~~~~L~-~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~   87 (102)
                      ..|++|- +.+++++.|.+|+.|++.|+|.|||.|.|++|+|+.|+..+.+
T Consensus         6 llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~e   56 (84)
T KOG1775|consen    6 LLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPE   56 (84)
T ss_pred             cccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCC
Confidence            3456644 7899999999999999999999999999999999999975543

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

Probab=98.98  E-value=3e-10  Score=76.80  Aligned_cols=53  Identities=30%  Similarity=0.498  Sum_probs=43.3

Q ss_pred             HHhhcCC--eEEEEEc--CCeEEEEEEEEecCccceEEcceEEEE-eCceeecEEEEE
Q 034180           43 LAKFVDK--GVQVKLT--GGRQVTGTLKGYDQLLNLVLDEAVEFL-RGNLYNGIFVIV   95 (102)
Q Consensus        43 L~~~i~K--~V~V~Lk--~Gr~i~G~L~gfD~~mNLVL~da~E~~-~~~~~~~iG~iv   95 (102)
                      +-+|++.  +|.|.|.  -|..++|.++|||+|||+||++|+|.. +.+.++++|+|+
T Consensus        17 Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRil   74 (88)
T KOG1774|consen   17 IFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRIL   74 (88)
T ss_pred             HHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEE
Confidence            4478775  5666665  488999999999999999999999986 456667999886

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

Probab=98.96  E-value=1.1e-10  Score=79.20  Aligned_cols=47  Identities=40%  Similarity=0.619  Sum_probs=41.9

Q ss_pred             CCcchHHh-hcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEe
Q 034180           38 ETVLDLAK-FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR   84 (102)
Q Consensus        38 ~~~~~L~~-~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~   84 (102)
                      ..|++|.+ +++.+|.|+++++|++.|+|.|||+|+|++|.|++|.+.
T Consensus         4 ~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit   51 (91)
T KOG3460|consen    4 EEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETIT   51 (91)
T ss_pred             cccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEE
Confidence            35667665 499999999999999999999999999999999999873

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

Probab=98.83  E-value=3.4e-09  Score=72.89  Aligned_cols=46  Identities=35%  Similarity=0.603  Sum_probs=42.9

Q ss_pred             chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc
Q 034180           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN   86 (102)
Q Consensus        41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~   86 (102)
                      +.|..|++++|.|...|||.+.|.|.|||+-.||+|+++.|++...
T Consensus         3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~   48 (96)
T KOG1784|consen    3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSE   48 (96)
T ss_pred             hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhh
Confidence            4689999999999999999999999999999999999999998543

>KOG3168 consensus U1 snRNP component [Transcription]

Probab=98.70  E-value=1.4e-09  Score=81.58  Aligned_cols=44  Identities=30%  Similarity=0.584  Sum_probs=41.0

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFL   83 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~   83 (102)
                      +..+.+++|.+++|.++|||.+.|.+.+||.|||++|.||+|..
T Consensus         6 sskml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r   49 (177)
T KOG3168|consen    6 SSKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFR   49 (177)
T ss_pred             hhHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHh
Confidence            44678899999999999999999999999999999999999975

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

Probab=98.60  E-value=5e-09  Score=75.29  Aligned_cols=50  Identities=38%  Similarity=0.647  Sum_probs=44.4

Q ss_pred             CcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEe-Ccee
Q 034180           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR-GNLY   88 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~-~~~~   88 (102)
                      ....+.++++|++.|.|+|||.+.|.|.+||+|-|++|++|+|++. ++.+
T Consensus        10 ~t~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y   60 (129)
T KOG1782|consen   10 FTTSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKY   60 (129)
T ss_pred             chhHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeeccee
Confidence            4556899999999999999999999999999999999999999973 4433

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

Probab=98.58  E-value=2e-07  Score=64.06  Aligned_cols=58  Identities=29%  Similarity=0.329  Sum_probs=49.5

Q ss_pred             chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEEEE
Q 034180           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVCFL   98 (102)
Q Consensus        41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~~~   98 (102)
                      ...+..+|++|.|.||++-.+.|+|.|.|+|+|+-|.|..-...++..+....-+|||
T Consensus         5 sfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfI   62 (96)
T KOG3448|consen    5 SFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFI   62 (96)
T ss_pred             HHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEE
Confidence            3467789999999999999999999999999999999998877766666666666665

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

Probab=97.79  E-value=2.6e-05  Score=56.40  Aligned_cols=45  Identities=24%  Similarity=0.287  Sum_probs=39.9

Q ss_pred             HHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCce
Q 034180           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNL   87 (102)
Q Consensus        43 L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~   87 (102)
                      |...-+.++.|.||+|.+|.|.|...|.+|||.|.+++++.++..
T Consensus         7 L~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgd   51 (134)
T KOG3293|consen    7 LKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGD   51 (134)
T ss_pred             HHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCC
Confidence            444567899999999999999999999999999999999986643

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

Probab=97.78  E-value=2.4e-05  Score=50.96  Aligned_cols=37  Identities=27%  Similarity=0.410  Sum_probs=30.1

Q ss_pred             CeEEEEEc--CC--eEEEEEEEEecCccceEEcceEEEEeC
Q 034180           49 KGVQVKLT--GG--RQVTGTLKGYDQLLNLVLDEAVEFLRG   85 (102)
Q Consensus        49 K~V~V~Lk--~G--r~i~G~L~gfD~~mNLVL~da~E~~~~   85 (102)
                      ++|+|-++  +|  -.++|.|.+||+|+|++|.|+.|....
T Consensus         9 ~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~   49 (66)
T cd01739           9 IRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK   49 (66)
T ss_pred             cEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence            56666664  33  489999999999999999999998754

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

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

Probab=97.14  E-value=0.0018  Score=41.61  Aligned_cols=43  Identities=21%  Similarity=0.323  Sum_probs=34.1

Q ss_pred             HHhhcCCeEEEEEcCCeEEEEEEEEecC---ccceEEcceEEEEeC
Q 034180           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQ---LLNLVLDEAVEFLRG   85 (102)
Q Consensus        43 L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~---~mNLVL~da~E~~~~   85 (102)
                      +..++|++|.|+++||..|+|.|.+++.   -+.++|..|....++
T Consensus         7 ~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~   52 (77)
T PF14438_consen    7 LTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKS   52 (77)
T ss_dssp             HHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS-
T ss_pred             HHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccc
Confidence            5678999999999999999999999997   789999988876543

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

Probab=97.07  E-value=0.0012  Score=46.63  Aligned_cols=46  Identities=28%  Similarity=0.409  Sum_probs=41.1

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG   85 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~   85 (102)
                      .-.|.+..+.+|.|.|++|....|++.+.|.+||..|.++.=..++
T Consensus         4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~   49 (109)
T KOG3428|consen    4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG   49 (109)
T ss_pred             HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC
Confidence            3457888999999999999999999999999999999998877664

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

Probab=96.64  E-value=0.0002  Score=50.86  Aligned_cols=56  Identities=18%  Similarity=0.265  Sum_probs=44.8

Q ss_pred             cccccCCCcCCcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEe
Q 034180           29 KSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR   84 (102)
Q Consensus        29 ~~~~ms~~~~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~   84 (102)
                      +.-.+.++|.+...-+.--..+|.|.++|++.+.|...|||.|.|++|+++.|.+.
T Consensus        17 e~~ef~~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwt   72 (114)
T KOG3459|consen   17 EEEEFNTGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWT   72 (114)
T ss_pred             cccccCcCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCC
Confidence            34445666655555554556789999999999999999999999999999999763

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

Probab=96.13  E-value=0.019  Score=40.85  Aligned_cols=44  Identities=20%  Similarity=0.169  Sum_probs=38.8

Q ss_pred             HHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc
Q 034180           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN   86 (102)
Q Consensus        43 L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~   86 (102)
                      |.+.-+.-|.+.++.|..|+|.|+--|.+||++|+|..-...+.
T Consensus        10 LhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg   53 (119)
T KOG3172|consen   10 LHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDG   53 (119)
T ss_pred             eecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCC
Confidence            45566788999999999999999999999999999998877654

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

Probab=95.70  E-value=0.017  Score=43.35  Aligned_cols=43  Identities=26%  Similarity=0.363  Sum_probs=32.9

Q ss_pred             CCcchHHhhcCCeEEEEEcCCeEEEEEEEEecC-ccceEEcceEE
Q 034180           38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQ-LLNLVLDEAVE   81 (102)
Q Consensus        38 ~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~-~mNLVL~da~E   81 (102)
                      .+|++..+|++|+|.|.+.| +++.|.+..+|. .-|+||-+-.|
T Consensus         7 ~~p~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e   50 (166)
T PF06372_consen    7 KSPLEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE   50 (166)
T ss_dssp             S-HHHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T
T ss_pred             CCHHHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc
Confidence            46888999999999999999 999999999994 47899886554

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.

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

Probab=95.66  E-value=0.027  Score=36.06  Aligned_cols=29  Identities=24%  Similarity=0.446  Sum_probs=25.1

Q ss_pred             cCCeEEEEEcCCeEEEEEEEEecCccceE
Q 034180           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLV   75 (102)
Q Consensus        47 i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLV   75 (102)
                      -+.+|.|-|.+|-.++|.+.|||+|+=++
T Consensus        10 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll   38 (61)
T cd01716          10 EKIPVTIYLVNGVQLKGQIESFDNFTVLL   38 (61)
T ss_pred             cCCcEEEEEeCCcEEEEEEEEEcceEEEE
Confidence            34689999999999999999999998444

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

>TIGR02383 Hfq RNA chaperone Hfq

Probab=95.50  E-value=0.033  Score=35.71  Aligned_cols=28  Identities=29%  Similarity=0.464  Sum_probs=24.8

Q ss_pred             CCeEEEEEcCCeEEEEEEEEecCccceE
Q 034180           48 DKGVQVKLTGGRQVTGTLKGYDQLLNLV   75 (102)
Q Consensus        48 ~K~V~V~Lk~Gr~i~G~L~gfD~~mNLV   75 (102)
                      +.+|.|-|.+|-.++|.+.|||+|+=++
T Consensus        15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll   42 (61)
T TIGR02383        15 RIPVTVFLVNGVQLKGVIESFDNFTVLL   42 (61)
T ss_pred             CCcEEEEEeCCcEEEEEEEEEeeeEEEE
Confidence            4689999999999999999999998444

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

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

Probab=95.27  E-value=0.059  Score=32.00  Aligned_cols=33  Identities=21%  Similarity=0.355  Sum_probs=28.5

Q ss_pred             hcCCeEEEEEcCCeEEEEEEEEecCccceEEcce
Q 034180           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA   79 (102)
Q Consensus        46 ~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da   79 (102)
                      .+||+|++.. ++..++|+..|+|+.-.|+++..
T Consensus         1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~   33 (48)
T PF02237_consen    1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTE   33 (48)
T ss_dssp             STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEET
T ss_pred             CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEEC
Confidence            3789999999 67777999999999999998654

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 ....

>PRK14638 hypothetical protein; Provisional

Probab=94.84  E-value=0.07  Score=38.92  Aligned_cols=39  Identities=13%  Similarity=0.306  Sum_probs=31.9

Q ss_pred             CCcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEc
Q 034180           38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD   77 (102)
Q Consensus        38 ~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~   77 (102)
                      +.+.+..+++|++|.|++++++.++|+|.++|+- ++.|.
T Consensus        90 ~~~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~  128 (150)
T PRK14638         90 RGPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS  128 (150)
T ss_pred             CCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            3455688999999999999999999999999863 34443

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=94.80  E-value=0.064  Score=36.00  Aligned_cols=30  Identities=20%  Similarity=0.418  Sum_probs=25.6

Q ss_pred             cCCeEEEEEcCCeEEEEEEEEecCccceEE
Q 034180           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVL   76 (102)
Q Consensus        47 i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL   76 (102)
                      -+.+|.|-|.+|-.++|.+.|||+|.=++-
T Consensus        18 ~~~~VtifL~NG~~l~G~I~~fD~ftVll~   47 (79)
T PRK00395         18 ERVPVTIYLVNGIKLQGQIESFDNFVVLLR   47 (79)
T ss_pred             cCCCEEEEEeCCcEEEEEEEEEccEEEEEE
Confidence            346899999999999999999999984443

>PRK14639 hypothetical protein; Provisional

Probab=94.29  E-value=0.11  Score=37.41  Aligned_cols=38  Identities=18%  Similarity=0.296  Sum_probs=31.6

Q ss_pred             CCcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEE
Q 034180           38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVL   76 (102)
Q Consensus        38 ~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL   76 (102)
                      +.+.+..+++|++|.|++.+++.+.|+|.++|+- ++.|
T Consensus        78 ~~~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l  115 (140)
T PRK14639         78 SKIEHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL  115 (140)
T ss_pred             CCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence            3455688999999999999999999999999873 4554

>PRK02001 hypothetical protein; Validated

Probab=94.03  E-value=0.13  Score=37.75  Aligned_cols=37  Identities=22%  Similarity=0.396  Sum_probs=31.0

Q ss_pred             CcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEE
Q 034180           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVL   76 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL   76 (102)
                      .+.+..+++|++|.|++.+++.++|.|.++|+- ++.|
T Consensus        81 ~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l  117 (152)
T PRK02001         81 VPRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL  117 (152)
T ss_pred             CHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence            445688999999999999999999999999864 3444

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

Probab=93.86  E-value=0.17  Score=34.73  Aligned_cols=39  Identities=13%  Similarity=0.224  Sum_probs=34.7

Q ss_pred             HhhcCCeEEEEEcCCeEEEEEEEEecC-ccceEEcceEEE
Q 034180           44 AKFVDKGVQVKLTGGRQVTGTLKGYDQ-LLNLVLDEAVEF   82 (102)
Q Consensus        44 ~~~i~K~V~V~Lk~Gr~i~G~L~gfD~-~mNLVL~da~E~   82 (102)
                      .+|+|++|.+..+++-.|+|+|...|. --.|.|.++.-+
T Consensus         4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~   43 (96)
T PF12701_consen    4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSF   43 (96)
T ss_dssp             CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEET
T ss_pred             ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeec
Confidence            368999999999999999999999995 578999998765

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

Probab=93.51  E-value=0.18  Score=33.74  Aligned_cols=31  Identities=19%  Similarity=0.370  Sum_probs=25.7

Q ss_pred             hHHhh--cCCeEEEEEcCCeEEEEEEEEecCcc
Q 034180           42 DLAKF--VDKGVQVKLTGGRQVTGTLKGYDQLL   72 (102)
Q Consensus        42 ~L~~~--i~K~V~V~Lk~Gr~i~G~L~gfD~~m   72 (102)
                      .|+..  -+.+|.|-|.+|-.+.|.+.|||+|.
T Consensus        11 fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~   43 (77)
T COG1923          11 FLNALRKEKIPVTIFLVNGFKLQGQVESFDNFV   43 (77)
T ss_pred             HHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEE
Confidence            35543  34688999999999999999999997

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

Probab=93.39  E-value=0.34  Score=30.90  Aligned_cols=36  Identities=11%  Similarity=0.170  Sum_probs=29.8

Q ss_pred             hcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEE
Q 034180           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE   81 (102)
Q Consensus        46 ~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E   81 (102)
                      .+|..|++++-.|.+++|.+.+||.-.++++-.+.+
T Consensus         4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s   39 (61)
T cd01735           4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS   39 (61)
T ss_pred             ccccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence            378999999999999999999999877766554433

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.

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=92.83  E-value=0.23  Score=37.42  Aligned_cols=44  Identities=20%  Similarity=0.352  Sum_probs=31.7

Q ss_pred             ccCCCcCCcch--HHhhc--CCeEEEEEcCCeEEEEEEEEecCccceE
Q 034180           32 KMSGRKETVLD--LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLV   75 (102)
Q Consensus        32 ~ms~~~~~~~~--L~~~i--~K~V~V~Lk~Gr~i~G~L~gfD~~mNLV   75 (102)
                      +|++++....+  |+.+.  ..+|.|-|.+|-.++|.+.|||+|.=|+
T Consensus         4 ~m~~~~~nlQD~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL   51 (165)
T PRK14091          4 NMAEKVNNLQDIFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILL   51 (165)
T ss_pred             cccccccchHHHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEE
Confidence            46654444444  55443  3578888999999999999999997443

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

Probab=92.33  E-value=0.44  Score=31.08  Aligned_cols=34  Identities=38%  Similarity=0.496  Sum_probs=28.1

Q ss_pred             CCcchHHhhcCCeEEEEEc---CC-eEEEEEEEEecCc
Q 034180           38 ETVLDLAKFVDKGVQVKLT---GG-RQVTGTLKGYDQL   71 (102)
Q Consensus        38 ~~~~~L~~~i~K~V~V~Lk---~G-r~i~G~L~gfD~~   71 (102)
                      ..+.+..+++|+.|.|+++   +| +.+.|.|.++|+-
T Consensus        15 ~~~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~   52 (83)
T cd01734          15 KKEADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD   52 (83)
T ss_pred             CCHHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC
Confidence            3455688999999999997   55 6999999999863

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

>PRK14644 hypothetical protein; Provisional

Probab=92.17  E-value=0.39  Score=34.64  Aligned_cols=38  Identities=18%  Similarity=0.258  Sum_probs=30.7

Q ss_pred             CcchHHhhcCCeEEEEEcCC----eEEEEEEEEecCccceEEc
Q 034180           39 TVLDLAKFVDKGVQVKLTGG----RQVTGTLKGYDQLLNLVLD   77 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk~G----r~i~G~L~gfD~~mNLVL~   77 (102)
                      ...++.+++|++|.|++++.    ++++|.|.++|+- ++.|.
T Consensus        76 ~~~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~  117 (136)
T PRK14644         76 ETDELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK  117 (136)
T ss_pred             CHHHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            33478899999999999876    8999999999873 35553

>PRK14640 hypothetical protein; Provisional

Probab=91.50  E-value=0.53  Score=34.27  Aligned_cols=37  Identities=24%  Similarity=0.397  Sum_probs=29.7

Q ss_pred             CcchHHhhcCCeEEEEE----cCCeEEEEEEEEecCccceEE
Q 034180           39 TVLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVL   76 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~L----k~Gr~i~G~L~gfD~~mNLVL   76 (102)
                      .+.+..+++|++|.|++    .++++++|.|.++|+- ++.|
T Consensus        88 ~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l  128 (152)
T PRK14640         88 KVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITL  128 (152)
T ss_pred             CHHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence            44568899999999998    5679999999999864 3444

>PRK14633 hypothetical protein; Provisional

Probab=91.43  E-value=0.55  Score=34.17  Aligned_cols=37  Identities=16%  Similarity=0.281  Sum_probs=29.5

Q ss_pred             CcchHHhhcCCeEEEEE----cCCeEEEEEEEEecCccceEE
Q 034180           39 TVLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVL   76 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~L----k~Gr~i~G~L~gfD~~mNLVL   76 (102)
                      .+.+..+++|++|.|++    .+++.++|+|.++|+- ++.|
T Consensus        85 ~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l  125 (150)
T PRK14633         85 NIIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL  125 (150)
T ss_pred             CHHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence            44568899999999998    4669999999999874 3444

>PRK14642 hypothetical protein; Provisional

Probab=90.56  E-value=0.66  Score=35.68  Aligned_cols=38  Identities=16%  Similarity=0.322  Sum_probs=30.7

Q ss_pred             CCcchHHhhcCCeEEEEEc-------------CCeEEEEEEEEecCccceEE
Q 034180           38 ETVLDLAKFVDKGVQVKLT-------------GGRQVTGTLKGYDQLLNLVL   76 (102)
Q Consensus        38 ~~~~~L~~~i~K~V~V~Lk-------------~Gr~i~G~L~gfD~~mNLVL   76 (102)
                      +...+..+++|++|.|+++             +.+.++|+|.++|+- ++.|
T Consensus        90 k~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l  140 (197)
T PRK14642         90 RHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI  140 (197)
T ss_pred             CCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence            3455688999999999997             679999999999864 3444

>PRK14645 hypothetical protein; Provisional

Probab=90.36  E-value=0.68  Score=34.00  Aligned_cols=32  Identities=22%  Similarity=0.302  Sum_probs=27.1

Q ss_pred             CcchHHhhcCCeEEEEEcCCeEEEEEEEEecCc
Q 034180           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQL   71 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~   71 (102)
                      .+.+..+++|++|.|++ +++.++|+|.++|+-
T Consensus        93 ~~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~  124 (154)
T PRK14645         93 TARHFERFAGLKAKVRG-PGENFTGRIKAVSGD  124 (154)
T ss_pred             CHHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC
Confidence            34468889999999986 789999999999864

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

Probab=90.28  E-value=2.2  Score=27.59  Aligned_cols=50  Identities=26%  Similarity=0.325  Sum_probs=35.5

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEec-CccceEEcceEEEEeCceeecEEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEAVEFLRGNLYNGIFVIVC   96 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD-~~mNLVL~da~E~~~~~~~~~iG~iv~   96 (102)
                      ...|++++|++|.|.+..|.. +|+|.+.. .|.  +|+..    .....-++..|+.
T Consensus        13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDhI--vl~~~----~~~~~IR~~~IV~   63 (66)
T PF10842_consen   13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDHI--VLEEN----GTPFFIRIAQIVW   63 (66)
T ss_pred             HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCEE--EEEeC----CcEEEEEeeeEEE
Confidence            345889999999999976665 99999995 444  55433    3445566666664

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

Probab=90.17  E-value=0.55  Score=33.23  Aligned_cols=36  Identities=31%  Similarity=0.553  Sum_probs=26.3

Q ss_pred             cchHHhhcCCeEEEEEc----CCeEEEEEEEEecCccceEE
Q 034180           40 VLDLAKFVDKGVQVKLT----GGRQVTGTLKGYDQLLNLVL   76 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk----~Gr~i~G~L~gfD~~mNLVL   76 (102)
                      +.++.+++|++|.|+++    +.+++.|+|.++|+ -.++|
T Consensus        79 ~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l  118 (141)
T PF02576_consen   79 PRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL  118 (141)
T ss_dssp             HHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred             HHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence            44688999999999994    45799999999987 23444

; PDB: 1IB8_A.

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=89.86  E-value=0.92  Score=32.76  Aligned_cols=32  Identities=31%  Similarity=0.577  Sum_probs=27.6

Q ss_pred             CcchHHhhcCCeEEEEE----cCCeEEEEEEEEecC
Q 034180           39 TVLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQ   70 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~L----k~Gr~i~G~L~gfD~   70 (102)
                      .+.++.+++|+.|.|++    .+++.++|.|.++|+
T Consensus        89 ~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~  124 (154)
T PRK00092         89 KARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG  124 (154)
T ss_pred             CHHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence            34568899999999997    567899999999986

>PRK14636 hypothetical protein; Provisional

Probab=89.74  E-value=0.83  Score=34.22  Aligned_cols=37  Identities=27%  Similarity=0.499  Sum_probs=29.2

Q ss_pred             CcchHHhhcCCeEEEEEc---CC-eEEEEEEEEecCccceEE
Q 034180           39 TVLDLAKFVDKGVQVKLT---GG-RQVTGTLKGYDQLLNLVL   76 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk---~G-r~i~G~L~gfD~~mNLVL   76 (102)
                      .+.+..+++|++|.|+++   +| +.++|+|.++|+- ++.|
T Consensus        89 ~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l  129 (176)
T PRK14636         89 RPKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI  129 (176)
T ss_pred             CHHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence            345688999999999997   55 7999999999863 3444

>PRK14643 hypothetical protein; Provisional

Probab=89.63  E-value=0.89  Score=33.72  Aligned_cols=37  Identities=19%  Similarity=0.249  Sum_probs=29.2

Q ss_pred             CcchHHhhcCCeEEEEEcC----CeEEEEEEEEecCc-cceE
Q 034180           39 TVLDLAKFVDKGVQVKLTG----GRQVTGTLKGYDQL-LNLV   75 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk~----Gr~i~G~L~gfD~~-mNLV   75 (102)
                      ...+..+++|++|.|+++.    .+.++|+|.++|.- ..+.
T Consensus        95 ~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~  136 (164)
T PRK14643         95 SQEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFR  136 (164)
T ss_pred             CHHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEE
Confidence            3556889999999999864    58999999999853 3443

>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=89.61  E-value=1.2  Score=29.55  Aligned_cols=40  Identities=10%  Similarity=0.167  Sum_probs=33.6

Q ss_pred             HhhcCCeEEEEEcCCeEEEEEEEEecCc-cceEEcceEEEE
Q 034180           44 AKFVDKGVQVKLTGGRQVTGTLKGYDQL-LNLVLDEAVEFL   83 (102)
Q Consensus        44 ~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~-mNLVL~da~E~~   83 (102)
                      .+|+|+++.+..+.+-.|+|+|..+|.. --+.|.|+..+-
T Consensus         2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fG   42 (74)
T cd01736           2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFG   42 (74)
T ss_pred             ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeec
Confidence            3689999999999999999999999955 457788877653

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.

>PRK14634 hypothetical protein; Provisional

Probab=89.53  E-value=0.96  Score=33.13  Aligned_cols=37  Identities=19%  Similarity=0.224  Sum_probs=28.9

Q ss_pred             CcchHHhhcCCeEEEEEcC----CeEEEEEEEEecCccceEE
Q 034180           39 TVLDLAKFVDKGVQVKLTG----GRQVTGTLKGYDQLLNLVL   76 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk~----Gr~i~G~L~gfD~~mNLVL   76 (102)
                      .+.+..+++|++|.|++++    .+.++|+|.++|+- ++.|
T Consensus        91 ~~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l  131 (155)
T PRK14634         91 SDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI  131 (155)
T ss_pred             CHHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence            4556889999999999863    28999999999863 3444

>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=89.46  E-value=0.97  Score=33.42  Aligned_cols=34  Identities=29%  Similarity=0.487  Sum_probs=29.6

Q ss_pred             CcchHHhhcCCeEEEEE----cCCeEEEEEEEEecCcc
Q 034180           39 TVLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLL   72 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~L----k~Gr~i~G~L~gfD~~m   72 (102)
                      ...+..+++|+.|.|.+    .+++.++|+|.++|+-.
T Consensus        90 ~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~  127 (153)
T COG0779          90 TAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET  127 (153)
T ss_pred             CHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence            34468899999999999    78899999999999765

>PRK14646 hypothetical protein; Provisional

Probab=89.13  E-value=1.1  Score=32.91  Aligned_cols=38  Identities=21%  Similarity=0.225  Sum_probs=29.5

Q ss_pred             CCcchHHhhcCCeEEEEEcC---C-eEEEEEEEEecCccceEE
Q 034180           38 ETVLDLAKFVDKGVQVKLTG---G-RQVTGTLKGYDQLLNLVL   76 (102)
Q Consensus        38 ~~~~~L~~~i~K~V~V~Lk~---G-r~i~G~L~gfD~~mNLVL   76 (102)
                      +.+.+..+++|++|.|++++   | +.++|.|.++|+- ++.|
T Consensus        90 ~~~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l  131 (155)
T PRK14646         90 TSERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI  131 (155)
T ss_pred             CCHHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence            34556889999999999853   3 7899999999864 3555

>PRK14632 hypothetical protein; Provisional

Probab=88.69  E-value=1.1  Score=33.29  Aligned_cols=38  Identities=18%  Similarity=0.368  Sum_probs=29.9

Q ss_pred             CcchHHhhcCCeEEEEEcC-------CeEEEEEEEEecCccceEEc
Q 034180           39 TVLDLAKFVDKGVQVKLTG-------GRQVTGTLKGYDQLLNLVLD   77 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk~-------Gr~i~G~L~gfD~~mNLVL~   77 (102)
                      .+.+..+++|++|.|++++       .+.++|+|.++|+- ++.|+
T Consensus        89 ~~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~  133 (172)
T PRK14632         89 RAEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR  133 (172)
T ss_pred             CHHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence            3456889999999999975       57999999999863 34443

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=88.39  E-value=0.91  Score=34.26  Aligned_cols=33  Identities=21%  Similarity=0.362  Sum_probs=26.6

Q ss_pred             HHhhc--CCeEEEEEcCCeEEEEEEEEecCccceE
Q 034180           43 LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLV   75 (102)
Q Consensus        43 L~~~i--~K~V~V~Lk~Gr~i~G~L~gfD~~mNLV   75 (102)
                      |+...  ..+|.|-|.+|-.++|.+.|||+|.=|.
T Consensus        97 Ln~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL  131 (165)
T PRK14091         97 LSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLL  131 (165)
T ss_pred             HHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEE
Confidence            55443  3588888999999999999999998444

>PRK14647 hypothetical protein; Provisional

Probab=87.54  E-value=1.5  Score=32.05  Aligned_cols=32  Identities=19%  Similarity=0.353  Sum_probs=27.0

Q ss_pred             CcchHHhhcCCeEEEEEc---------CCeEEEEEEEEecC
Q 034180           39 TVLDLAKFVDKGVQVKLT---------GGRQVTGTLKGYDQ   70 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk---------~Gr~i~G~L~gfD~   70 (102)
                      .+.+..+++|++|.|+++         +.+.++|+|.++|+
T Consensus        90 ~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~  130 (159)
T PRK14647         90 KEADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD  130 (159)
T ss_pred             CHHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence            445688999999999995         34899999999986

>PRK14631 hypothetical protein; Provisional

Probab=86.81  E-value=1.8  Score=32.45  Aligned_cols=32  Identities=19%  Similarity=0.323  Sum_probs=27.2

Q ss_pred             CCcchHHhhcCCeEEEEEc----CCeEEEEEEEEec
Q 034180           38 ETVLDLAKFVDKGVQVKLT----GGRQVTGTLKGYD   69 (102)
Q Consensus        38 ~~~~~L~~~i~K~V~V~Lk----~Gr~i~G~L~gfD   69 (102)
                      ..+.+..+++|++|.|+++    +.+.++|+|.++|
T Consensus       107 ~~~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~  142 (174)
T PRK14631        107 FQLEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD  142 (174)
T ss_pred             CCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence            3455688999999999995    4599999999998

>PRK14637 hypothetical protein; Provisional

Probab=86.51  E-value=1.7  Score=31.76  Aligned_cols=38  Identities=29%  Similarity=0.359  Sum_probs=28.5

Q ss_pred             CCcchHHhhcCCeEEEEEcCCeEE-EEEEEEecCccceEE
Q 034180           38 ETVLDLAKFVDKGVQVKLTGGRQV-TGTLKGYDQLLNLVL   76 (102)
Q Consensus        38 ~~~~~L~~~i~K~V~V~Lk~Gr~i-~G~L~gfD~~mNLVL   76 (102)
                      ..+.+..+++|++|.|++.+.+.+ +|+|.++|+- ++.|
T Consensus        88 ~~~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l  126 (151)
T PRK14637         88 KNAAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVL  126 (151)
T ss_pred             CCHHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEE
Confidence            345568899999999999544556 7999999864 3444

>PRK14641 hypothetical protein; Provisional

Probab=83.50  E-value=2.6  Score=31.57  Aligned_cols=31  Identities=19%  Similarity=0.270  Sum_probs=25.8

Q ss_pred             CcchHHhhcCCeEEEEEcC----CeEEEEEEEEec
Q 034180           39 TVLDLAKFVDKGVQVKLTG----GRQVTGTLKGYD   69 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk~----Gr~i~G~L~gfD   69 (102)
                      .+.+..+++|+.|.|++++    .+.++|.|.++|
T Consensus        95 ~~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~  129 (173)
T PRK14641         95 LPRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS  129 (173)
T ss_pred             CHHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence            3445888999999999865    469999999995

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

Probab=81.49  E-value=4.2  Score=27.26  Aligned_cols=39  Identities=21%  Similarity=0.240  Sum_probs=28.9

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCc-cceEEcc
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQL-LNLVLDE   78 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~-mNLVL~d   78 (102)
                      ...|....||+|.+.|.++.+..|.+.|.|.. .|+..++
T Consensus        16 Lr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~   55 (80)
T PF11095_consen   16 LRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSN   55 (80)
T ss_dssp             HHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEE
T ss_pred             HHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhh
Confidence            34567778999999999999999999999954 5655443

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	102
3swn_C	117	Structure Of The Lsm657 Complex: An Assembly Interm		1e-12
4emk_C	113	Crystal Structure Of Splsm567 Length = 113		3e-12
3cw1_G	76	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		1e-08
3bw1_A	96	Crystal Structure Of Homomeric Yeast Lsm3 Exhibitin		2e-04
1i8f_A	81	The Crystal Structure Of A Heptameric Archaeal Sm P		8e-04

>pdb|3SWN|C Chain C, Structure Of The Lsm657 Complex: An Assembly Intermediate Of The Lsm1 7 And Lsm2 8 Rings Length = 117

Iteration: 1
 Score = 68.2 bits (165), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 31/55 (56%), Positives = 43/55 (78%), Gaps = 1/55 (1%)
Query: 36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNG 90
          RKE++LDL+++ D+ +Q   TGGRQ+TG LKG+DQL+NLVLD+  E LR N  +G
Sbjct: 25 RKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLR-NPEDG 78

>pdb|4EMK|C Chain C, Crystal Structure Of Splsm567 Length = 113

Iteration: 1
 Score = 66.6 bits (161), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 31/55 (56%), Positives = 42/55 (76%), Gaps = 1/55 (1%)
Query: 36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNG 90
          RKE++LDL+++ D+ +Q   TGGRQ+TG LKG+DQL NLVLD+  E LR N  +G
Sbjct: 21 RKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLXNLVLDDVEEQLR-NPEDG 74

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 36/59 (61%)
Query: 37 KETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV 95
          K    +L KF+DK + +KL GGR V G L+G+D  +NLV+DE VE       N I ++V
Sbjct: 3  KAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVV 61

>pdb|3BW1|A Chain A, Crystal Structure Of Homomeric Yeast Lsm3 Exhibiting Novel Octameric Ring Organisation Length = 96

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 38 ETVLDLAKF-VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFL 83
          ET LDL K  +D+ V +KL G R + GTL+ +D   N+VL +AVE +
Sbjct: 9  ETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETI 55

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

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 29/46 (63%)
Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLY 88
          L   + K V VKL    ++ G L+ +DQ +NL+L++A E + GN+Y
Sbjct: 16 LQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVY 61

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	102
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	2e-18
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	9e-18
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	2e-17
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	9e-17
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	5e-16
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	2e-14
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	3e-14
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	2e-13
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	4e-13
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	1e-12
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	5e-12
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	4e-11
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	5e-11
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	3e-10
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	1e-09
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-09
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	3e-08
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	2e-06
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	2e-06
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	5e-06
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	2e-05
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	3e-05
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	4e-05
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	4e-04

>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_C Length = 113

 Score = 72.7 bits (178), Expect = 2e-18
 Identities = 29/49 (59%), Positives = 40/49 (81%)

Query: 36 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
          RKE++LDL+++ D+ +Q   TGGRQ+TG LKG+DQL+NLVLD+  E LR
Sbjct: 21 RKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLR 69

>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G Length = 76

 Score = 70.1 bits (172), Expect = 9e-18
 Identities = 29/64 (45%), Positives = 38/64 (59%), Gaps = 4/64 (6%)

Query: 33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYN--G 90
          MS  K    +L KF+DK + +KL GGR V G L+G+D  +NLV+DE VE       N  G
Sbjct: 1  MS--KAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIG 58

Query: 91 IFVI 94
          + VI
Sbjct: 59 MVVI 62

>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1 Length = 81

 Score = 69.2 bits (170), Expect = 2e-17
 Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 33 MSGRKETVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGI 91
          M+   ET    LA+ ++  V VKL G ++V G L+ YDQ +NLVL ++ E         +
Sbjct: 3  MNFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKL 62

Query: 92 FVIVC 96
            IV 
Sbjct: 63 GTIVI 67

>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A* Length = 81

 Score = 67.8 bits (166), Expect = 9e-17
 Identities = 22/67 (32%), Positives = 37/67 (55%), Gaps = 2/67 (2%)

Query: 30 SLKMSGRKETVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLY 88
          +  +S    T+   L   + K V VKL    ++ G L+ +DQ +NL+L++A E + GN+Y
Sbjct: 2  ASDISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVY 61

Query: 89 N-GIFVI 94
            G  V+
Sbjct: 62 KRGTMVV 68

>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A* Length = 77

 Score = 65.8 bits (161), Expect = 5e-16
 Identities = 23/54 (42%), Positives = 30/54 (55%), Gaps = 2/54 (3%)

Query: 33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86
          M  R   VL+  + +   V V+L GGR+  GTL GYD  +NLVL +A E   G 
Sbjct: 1  MPPRPLDVLN--RSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGE 52

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

 Score = 61.6 bits (150), Expect = 2e-14
 Identities = 17/44 (38%), Positives = 25/44 (56%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86
          L   ++  V +KL G R+  G LK +D  +NLVL++A E   G 
Sbjct: 20 LGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGE 63

>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae} Length = 96

 Score = 61.7 bits (150), Expect = 3e-14
 Identities = 21/50 (42%), Positives = 30/50 (60%), Gaps = 1/50 (2%)

Query: 36 RKETVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
            ET LD L   +D+ V +KL G R + GTL+ +D   N+VL +AVE + 
Sbjct: 7  HMETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIY 56

>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A* Length = 75

 Score = 58.8 bits (143), Expect = 2e-13
 Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86
          M+ R   V+   + +DK V V L  G +  G L GYD  LN+VL +A     G 
Sbjct: 1  MAERPLDVIH--RSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGE 52

>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A Length = 91

 Score = 58.7 bits (142), Expect = 4e-13
 Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 2/52 (3%)

Query: 33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
          M+  K +   + + +D  ++  L  GR   GT K +D+ +NL+L +  EF +
Sbjct: 1  MTVGKSS--KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRK 50

>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B Length = 75

 Score = 57.0 bits (138), Expect = 1e-12
 Identities = 15/47 (31%), Positives = 23/47 (48%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYN 89
          L K + K V ++L+ G    G L   D  +NL L+   E++ G   N
Sbjct: 9  LNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTN 55

>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe} Length = 93

 Score = 56.0 bits (135), Expect = 5e-12
 Identities = 17/42 (40%), Positives = 26/42 (61%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
          +   +D+ V VKL G R++ G L  YD+ LN+VL +A E + 
Sbjct: 14 VRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVT 55

>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A Length = 121

 Score = 54.6 bits (131), Expect = 4e-11
 Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 1/59 (1%)

Query: 29 KSLKMSGRKETVLDL-AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86
           S +  G     L L  K +   + V + G ++ +G L+G+D+ +N+VLD+  E+    
Sbjct: 18 GSNQKGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKA 76

>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F Length = 86

 Score = 53.2 bits (128), Expect = 5e-11
 Identities = 15/47 (31%), Positives = 20/47 (42%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYN 89
          L     K V VKL  G +  G L   D  +N+ L    E++ G L  
Sbjct: 11 LNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSG 57

>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1 Length = 77

 Score = 50.8 bits (122), Expect = 3e-10
 Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 43 LAKFVDKGVQVKLTGGR-QVTGTLKGYDQLLNLVLDEAVEFLRGN 86
          +   V K ++V++ G   Q+ G L+G D  +NL L  A+E     
Sbjct: 10 VKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEE 54

>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_A Length = 94

 Score = 49.8 bits (119), Expect = 1e-09
 Identities = 12/40 (30%), Positives = 22/40 (55%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEF 82
          + K +   + V +   R+  GTL G+D  +N+VL +  E+
Sbjct: 25 IDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEY 64

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231

 Score = 49.6 bits (118), Expect = 9e-09
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEF 82
          M+  K +   + + +D  ++  L  GR   GT K +D+ +NL+L +  EF
Sbjct: 1  MTVGKSS--KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEF 48

>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A Length = 93

 Score = 46.4 bits (110), Expect = 3e-08
 Identities = 18/48 (37%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 43 LAKFVDKGVQVKL-TGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYN 89
          L   V+  V VKL     +  GTL   D   NL L+EA EF+ G  + 
Sbjct: 26 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHG 73

>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe} Length = 105

 Score = 41.7 bits (98), Expect = 2e-06
 Identities = 15/67 (22%), Positives = 26/67 (38%), Gaps = 16/67 (23%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE--------------FLRGNLY 88
          L     + + V+L  G    G L+  D  +NL L E +               ++RGN  
Sbjct: 21 LNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIRGN-- 78

Query: 89 NGIFVIV 95
          N  ++ +
Sbjct: 79 NIKYLRI 85

>1m5q_A SMAP3, small nuclear ribonucleoprotein homolog, SM-like P; OB-like fold, B-sheet toroid, 14-MER, cadmium-binding site, translation; 2.00A {Pyrobaculum aerophilum} SCOP: b.38.1.1 Length = 130

 Score = 42.4 bits (99), Expect = 2e-06
 Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFV 93
          V +L   + + VQV L+ G    G L   D  LN+VL  A     G  +N +F+
Sbjct: 2  VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNK-AGEKFNRVFI 54

>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E Length = 92

 Score = 40.6 bits (95), Expect = 5e-06
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 51 VQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86
          V +      ++ G + G+D+ +NLVLD+A E     
Sbjct: 33 VWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X* 3s6n_A Length = 119

 Score = 39.6 bits (92), Expect = 2e-05
 Identities = 14/43 (32%), Positives = 20/43 (46%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG 85
          L K   + V ++L  G QV GT+ G D  +N  L      L+ 
Sbjct: 7  LMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKN 49

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

 Score = 38.9 bits (90), Expect = 3e-05
 Identities = 10/67 (14%), Positives = 20/67 (29%), Gaps = 15/67 (22%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE-------------FLRGNLYN 89
          L +     V  +   G    G L   +  +N  +                  ++RG+   
Sbjct: 10 LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGS--K 67

Query: 90 GIFVIVC 96
            F+I+ 
Sbjct: 68 IRFLILP 74

>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y* 3s6n_B Length = 118

 Score = 38.8 bits (90), Expect = 4e-05
 Identities = 10/43 (23%), Positives = 21/43 (48%)

Query: 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEF 82
          VL  +   +  V +     +++ G +K +D+  N+VL+   E 
Sbjct: 31 VLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEM 73

>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 Length = 75

 Score = 35.1 bits (81), Expect = 4e-04
 Identities = 8/57 (14%), Positives = 15/57 (26%), Gaps = 13/57 (22%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE-------------FLRGN 86
          L +     V  +   G    G L   +  +N  +                  ++RG 
Sbjct: 10 LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGC 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	102
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.74
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.73
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.73
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.72
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.72
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.72
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.71
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.71
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.71
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.7
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.69
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.68
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.68
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.68
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.65
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.64
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.64
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.64
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.6
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.6
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.59
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.56
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.48
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.43
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	98.71
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	96.96
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	96.85
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	96.59
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	96.49
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	96.48
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	96.25
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	95.93
1ycy_A	71	Conserved hypothetical protein; structural genomic	94.65
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	93.71
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	91.41
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	91.4
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	91.4
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	88.31
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	87.91
3rux_A	270	BIRA bifunctional protein; biotin-protein ligase,	87.36
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	86.51

>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G

Probab=99.74  E-value=1.9e-18  Score=111.62  Aligned_cols=58  Identities=43%  Similarity=0.722  Sum_probs=42.5

Q ss_pred             CcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC   96 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~   96 (102)
                      ..+.|++++|++|+|+|+||++|+|+|.|||+|||++|+||+|+.++++.+.+|.++.
T Consensus         5 ~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~v~i   62 (76)
T 3s6n_G            5 HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVI   62 (76)
T ss_dssp             ---------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC----CBSSEEE
T ss_pred             chHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccCCcEeEcCEEEE
Confidence            5789999999999999999999999999999999999999999998888888887754

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

Probab=99.73  E-value=1.3e-17  Score=106.76  Aligned_cols=58  Identities=33%  Similarity=0.375  Sum_probs=53.4

Q ss_pred             CcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC   96 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~   96 (102)
                      +...|.+++|++|+|+|+||++++|+|.|||+|||++|+||+|+..++..+.+|.++-
T Consensus         5 P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~i   62 (75)
T 1h64_1            5 PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVI   62 (75)
T ss_dssp             HHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEE
T ss_pred             HHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeCCceeECCEEEE
Confidence            3566999999999999999999999999999999999999999998888888998753

>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1

Probab=99.73  E-value=1.1e-17  Score=108.93  Aligned_cols=57  Identities=35%  Similarity=0.427  Sum_probs=52.7

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC   96 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~   96 (102)
                      ...|.+++|++|+|+|+||++++|+|.|||+|||++|+||+|+..++..+.+|.++.
T Consensus        11 ~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~i   67 (81)
T 1th7_A           11 HKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVI   67 (81)
T ss_dssp             HHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEE
T ss_pred             HHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecCCceeECCEEEE
Confidence            456899999999999999999999999999999999999999998888888998764

>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B

Probab=99.72  E-value=1.6e-17  Score=106.88  Aligned_cols=57  Identities=26%  Similarity=0.313  Sum_probs=52.6

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC   96 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~   96 (102)
                      ...|++++||+|.|+|+||++|+|+|.|||+|||++|+||+|+.+++..+.+|.++-
T Consensus         6 ~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~i   62 (75)
T 4emk_B            6 NEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFI   62 (75)
T ss_dssp             HHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEETTEEEEEEEEEEE
T ss_pred             HHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEecCCcccEecEEEE
Confidence            456899999999999999999999999999999999999999998888888998754

>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_C

Probab=99.72  E-value=1.3e-17  Score=115.65  Aligned_cols=64  Identities=47%  Similarity=0.770  Sum_probs=44.4

Q ss_pred             cCCCcCCcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC-------ceeecEEEEEE
Q 034180           33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG-------NLYNGIFVIVC   96 (102)
Q Consensus        33 ms~~~~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~-------~~~~~iG~iv~   96 (102)
                      ..++++++++|.+++|++|+|+|+|||+|.|+|.|||+||||||+||+|++.+       ...+.+|+++.
T Consensus        18 ~~~kke~i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~I   88 (113)
T 4emk_C           18 ERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVV   88 (113)
T ss_dssp             --------------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEE
T ss_pred             cCCccchHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEE
Confidence            33567788999999999999999999999999999999999999999999864       35678888764

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

Probab=99.72  E-value=3.9e-17  Score=106.92  Aligned_cols=59  Identities=29%  Similarity=0.467  Sum_probs=53.8

Q ss_pred             CCcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180           38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC   96 (102)
Q Consensus        38 ~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~   96 (102)
                      .+...|.+++|++|+|+|+||++++|+|.|||+|||++|+||+|+..++..+.+|.++-
T Consensus        15 ~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~I   73 (83)
T 1mgq_A           15 RPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLI   73 (83)
T ss_dssp             CTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEE
T ss_pred             ChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecCCcccCCCEEEE
Confidence            34556999999999999999999999999999999999999999998888888998764

>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F

Probab=99.71  E-value=1.3e-17  Score=110.38  Aligned_cols=64  Identities=27%  Similarity=0.272  Sum_probs=53.6

Q ss_pred             cCCCcCCcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180           33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC   96 (102)
Q Consensus        33 ms~~~~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~   96 (102)
                      ||....+...|++++|++|.|+|+||++|+|+|.|||+|||++|+||+|+.+++..+.+|.++-
T Consensus         1 ms~~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~g~~~~~lg~v~I   64 (86)
T 3s6n_F            1 MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLI   64 (86)
T ss_dssp             --CCCCHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEESSEEE
T ss_pred             CCcCcCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcCCceeeEccEEEE
Confidence            4544444456899999999999999999999999999999999999999988777778887653

>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A*

Probab=99.71  E-value=2.9e-17  Score=105.52  Aligned_cols=57  Identities=37%  Similarity=0.525  Sum_probs=52.9

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC   96 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~   96 (102)
                      ...|.+++|++|+|+|+||++++|+|.|||+|||++|+||+|+..++..+.+|.++.
T Consensus         6 ~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~i   62 (77)
T 1i4k_A            6 LDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVI   62 (77)
T ss_dssp             HHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEE
T ss_pred             HHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecCCcEeECCEEEE
Confidence            456899999999999999999999999999999999999999998888888998754

>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_A

Probab=99.71  E-value=2.9e-17  Score=110.99  Aligned_cols=57  Identities=21%  Similarity=0.346  Sum_probs=51.8

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEE-eCceeecEEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFL-RGNLYNGIFVIVC   96 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~-~~~~~~~iG~iv~   96 (102)
                      ..-|.++++++|+|+|+||++|+|+|.|||+|||++|+||+|+. +++..+.+|.++.
T Consensus        22 l~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~I   79 (94)
T 4emk_A           22 LELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKHSEMLL   79 (94)
T ss_dssp             HHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTTCCEEEEEEEEE
T ss_pred             HHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCCCcEeEcCEEEE
Confidence            34478999999999999999999999999999999999999999 6777888998765

>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1

Probab=99.70  E-value=5e-17  Score=104.70  Aligned_cols=58  Identities=28%  Similarity=0.355  Sum_probs=53.5

Q ss_pred             CcchHHhhcCCeEEEEEcCC-eEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180           39 TVLDLAKFVDKGVQVKLTGG-RQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC   96 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk~G-r~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~   96 (102)
                      +...|.++++++|+|+|+|| ++++|+|.|||+|||++|+||+|+.+++..+.+|.++.
T Consensus         6 P~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~i   64 (77)
T 1ljo_A            6 PNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVL   64 (77)
T ss_dssp             HHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEE
T ss_pred             hHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecCCcEeECCeEEE
Confidence            35679999999999999999 99999999999999999999999998888889998764

>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A

Probab=99.69  E-value=6e-17  Score=107.04  Aligned_cols=57  Identities=23%  Similarity=0.362  Sum_probs=49.6

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEE----------eCceeecEEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFL----------RGNLYNGIFVIVC   96 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~----------~~~~~~~iG~iv~   96 (102)
                      .+.|.+++|++|+|+|+|||+|+|+|.|||+|||++|+||+|+.          .+...+.+|.++.
T Consensus         6 ~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~i   72 (91)
T 1d3b_B            6 SSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLL   72 (91)
T ss_dssp             -CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEE
T ss_pred             hHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEE
Confidence            45799999999999999999999999999999999999999975          2345678888764

>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A*

Probab=99.68  E-value=8.2e-17  Score=104.84  Aligned_cols=56  Identities=29%  Similarity=0.357  Sum_probs=51.3

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC   96 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~   96 (102)
                      ...|.++++++|+|+|+||++|+|+|.|||+|||++|+||+|+ +++..+.+|.++.
T Consensus        13 ~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~~~~~~~lg~v~i   68 (81)
T 1i8f_A           13 GATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-IDGNVYKRGTMVV   68 (81)
T ss_dssp             HHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-ETTEEEEEEEEEE
T ss_pred             HHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-cCCcccCCCEEEE
Confidence            4568999999999999999999999999999999999999999 7778888998764

>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae}

Probab=99.68  E-value=8.7e-17  Score=108.14  Aligned_cols=58  Identities=29%  Similarity=0.373  Sum_probs=51.2

Q ss_pred             CcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC-------ceeecEEEEEE
Q 034180           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG-------NLYNGIFVIVC   96 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~-------~~~~~iG~iv~   96 (102)
                      +...|.+++||+|+|+|+|||+++|+|.|||+|||++|+||+|++.+       +..+.+|.++.
T Consensus        11 p~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~I   75 (96)
T 3bw1_A           11 PLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFI   75 (96)
T ss_dssp             HHHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEE
T ss_pred             HHHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEE
Confidence            35579999999999999999999999999999999999999999853       45677888764

>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A

Probab=99.68  E-value=5.7e-17  Score=108.95  Aligned_cols=57  Identities=33%  Similarity=0.314  Sum_probs=50.3

Q ss_pred             cchHHhhcCCeEEEEEcCC-eEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGG-RQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC   96 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~G-r~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~   96 (102)
                      ...|.+++|++|.|+|+|| ++|+|+|.|||+|||++|+||+|+.+++..+.+|.++-
T Consensus        23 ~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~~~~~~~lg~v~I   80 (93)
T 1n9r_A           23 KPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFI   80 (93)
T ss_dssp             ---CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEE
T ss_pred             HHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcCCCeEeEcCEEEE
Confidence            4568899999999999999 99999999999999999999999988888888887653

>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E

Probab=99.65  E-value=1.4e-16  Score=107.07  Aligned_cols=65  Identities=18%  Similarity=0.365  Sum_probs=52.4

Q ss_pred             ccCCCcCCcch-HHhhcCCeEEEEE----cCCeEEEEEEEEecCccceEEcceEEEE-eCceeecEEEEEE
Q 034180           32 KMSGRKETVLD-LAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVLDEAVEFL-RGNLYNGIFVIVC   96 (102)
Q Consensus        32 ~ms~~~~~~~~-L~~~i~K~V~V~L----k~Gr~i~G~L~gfD~~mNLVL~da~E~~-~~~~~~~iG~iv~   96 (102)
                      +|++.+..|.+ |.++++++++|++    +||++|+|+|.|||+|||++|+||+|+. +++..+.+|.++.
T Consensus         9 ~~~~~m~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~i   79 (92)
T 3s6n_E            9 KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIML   79 (92)
T ss_dssp             -----CCCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSCCEEEEEEEEE
T ss_pred             ccceeccCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCCceeEcCeEEE
Confidence            44444555655 7799999999999    9999999999999999999999999998 4566788898764

>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1

Probab=99.64  E-value=6.3e-16  Score=99.73  Aligned_cols=56  Identities=13%  Similarity=0.065  Sum_probs=50.9

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV   95 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv   95 (102)
                      ...|++++|++|.|+|++|++|+|+|.|||+|||++|+||+|+.++++.+.+|.++
T Consensus         7 ~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~~~~~~lg~v~   62 (75)
T 1d3b_A            7 IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVY   62 (75)
T ss_dssp             HHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEE
T ss_pred             HHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCCCcEEEcCeEE
Confidence            34588999999999999999999999999999999999999998777788888874

>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y* 3s6n_B

Probab=99.64  E-value=3.2e-16  Score=108.77  Aligned_cols=67  Identities=18%  Similarity=0.245  Sum_probs=40.9

Q ss_pred             ecCcceeeecccccccccCCCcCCcchHHhhc--CCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEe
Q 034180           16 CRSARVSFNLGFLKSLKMSGRKETVLDLAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR   84 (102)
Q Consensus        16 ~~~~~~~~~~~~~~~~~ms~~~~~~~~L~~~i--~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~   84 (102)
                      -||+++.++....+...+...|  ...|.+++  +++|.|+|+|||+|.|+|.|||+|||++|+||+|++.
T Consensus         7 ~~~~~~~~~~~~~e~~~~~~~P--l~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~   75 (118)
T 1b34_B            7 PKSEMTPEELQKREEEEFNTGP--LSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWT   75 (118)
T ss_dssp             -------------------CCH--HHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC--
T ss_pred             chhhcChhhhhhhhhhhcccCh--HHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEe
Confidence            3799998888888877776543  34477888  5999999999999999999999999999999999873

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

Probab=99.64  E-value=1.1e-15  Score=102.54  Aligned_cols=59  Identities=34%  Similarity=0.477  Sum_probs=48.9

Q ss_pred             CCcchHH-hhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC-------------ceeecEEEEEE
Q 034180           38 ETVLDLA-KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG-------------NLYNGIFVIVC   96 (102)
Q Consensus        38 ~~~~~L~-~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~-------------~~~~~iG~iv~   96 (102)
                      ..|.+|. .++|++|+|+|+||++|+|+|.|||+|||++|+||+|++.+             +..+.+|.++.
T Consensus         8 ~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~i   80 (93)
T 4emg_A            8 AEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFV   80 (93)
T ss_dssp             -CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEE
T ss_pred             CCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEE
Confidence            3466655 55999999999999999999999999999999999999852             24577888764

>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe}

Probab=99.60  E-value=2.1e-15  Score=103.57  Aligned_cols=56  Identities=20%  Similarity=0.269  Sum_probs=44.3

Q ss_pred             chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc-eeecEEEEEE
Q 034180           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN-LYNGIFVIVC   96 (102)
Q Consensus        41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~-~~~~iG~iv~   96 (102)
                      ..|++++|++|.|+|+||++|+|+|.|||+|||++|+||+|...++ ..+.+|.++.
T Consensus        19 ~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg~~~~~lg~v~I   75 (105)
T 4emh_A           19 TLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYI   75 (105)
T ss_dssp             -------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEEE
T ss_pred             HHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCCceeeEcCeEEE
Confidence            3488999999999999999999999999999999999999987554 6778888764

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A

Probab=99.60  E-value=1.6e-15  Score=116.85  Aligned_cols=57  Identities=23%  Similarity=0.375  Sum_probs=50.4

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEe----------CceeecEEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR----------GNLYNGIFVIVC   96 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~----------~~~~~~iG~iv~   96 (102)
                      ..+|++|+||+|+|+|+|||+|+|+|+|||+||||||+||+|++.          +++.+.+|+++.
T Consensus         6 ~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~I   72 (231)
T 3pgw_B            6 SSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLL   72 (231)
T ss_pred             hHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEE
Confidence            458999999999999999999999999999999999999999873          235678888764

>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X* 3s6n_A

Probab=99.59  E-value=2.5e-15  Score=104.62  Aligned_cols=57  Identities=26%  Similarity=0.280  Sum_probs=51.9

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC   96 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~   96 (102)
                      ...|+++++++|.|+|+||++|+|+|.|||+|||++|+||+|+.+++....+|.++-
T Consensus         4 ~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~~~~~~lg~v~I   60 (119)
T 1b34_A            4 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSI   60 (119)
T ss_dssp             HHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEE
T ss_pred             HHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecCCCceeEcceEEE
Confidence            456899999999999999999999999999999999999999988777788887753

>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A

Probab=99.56  E-value=2.1e-15  Score=105.10  Aligned_cols=54  Identities=26%  Similarity=0.516  Sum_probs=46.9

Q ss_pred             HHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC----------ce-----eecEEEEEE
Q 034180           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG----------NL-----YNGIFVIVC   96 (102)
Q Consensus        43 L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~----------~~-----~~~iG~iv~   96 (102)
                      |.++++++|+|+|+|||+|+|+|.|||+||||+|+||+|++.+          ..     .+.+|.++.
T Consensus        33 L~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~I  101 (121)
T 2fwk_A           33 IDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILL  101 (121)
T ss_dssp             HHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEE
T ss_pred             HHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEE
Confidence            6899999999999999999999999999999999999999842          23     577888764

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

Probab=99.48  E-value=8.1e-14  Score=98.40  Aligned_cols=57  Identities=12%  Similarity=0.064  Sum_probs=50.6

Q ss_pred             CcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV   95 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv   95 (102)
                      +...|+++++++|.|+|++|++|+|+|.+||+|||++|+||+|+.++++...+|.++
T Consensus         6 P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~~~~l~~v~   62 (126)
T 2y9a_D            6 PIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVY   62 (126)
T ss_dssp             SHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSCCEEEEEEE
T ss_pred             HHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCcEeecccEE
Confidence            345688999999999999999999999999999999999999998666677777764

>1m5q_A SMAP3, small nuclear ribonucleoprotein homolog, SM-like P; OB-like fold, B-sheet toroid, 14-MER, cadmium-binding site, translation; 2.00A {Pyrobaculum aerophilum} SCOP: b.38.1.1

Probab=99.43  E-value=1.2e-13  Score=97.88  Aligned_cols=51  Identities=27%  Similarity=0.365  Sum_probs=45.7

Q ss_pred             chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV   95 (102)
Q Consensus        41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv   95 (102)
                      +.|.+++|++|.|+|+||++|+|+|.|||+|||++|+||+|+.    .+.+|.++
T Consensus         3 ~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~----~~~lg~v~   53 (130)
T 1m5q_A            3 AELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA----GEKFNRVF   53 (130)
T ss_dssp             HHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTT----CCEEEEEE
T ss_pred             hHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEc----CCEeceEE
Confidence            5789999999999999999999999999999999999999983    25677764

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

Probab=98.71  E-value=2.4e-08  Score=66.73  Aligned_cols=42  Identities=21%  Similarity=0.237  Sum_probs=40.2

Q ss_pred             CCcchHHhhcCCeEEEEEcCCeEEEEEEEEec-CccceEEcce
Q 034180           38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEA   79 (102)
Q Consensus        38 ~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD-~~mNLVL~da   79 (102)
                      .+|.++++++||+|.|.+.||++|+|.|.+|| ...|++|.|+
T Consensus         7 ~~p~el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~   49 (86)
T 1y96_A            7 KGPLEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNF   49 (86)
T ss_dssp             SCHHHHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEE
T ss_pred             CCHHHHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeec
Confidence            46889999999999999999999999999999 8899999998

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

Probab=96.96  E-value=0.00091  Score=43.84  Aligned_cols=34  Identities=24%  Similarity=0.473  Sum_probs=27.8

Q ss_pred             HHhhc--CCeEEEEEcCCeEEEEEEEEecCccceEEc
Q 034180           43 LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVLD   77 (102)
Q Consensus        43 L~~~i--~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~   77 (102)
                      |+.+.  ..+|.|.|.+|-.++|.+.+||+|+ +.|+
T Consensus        13 Ln~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~-VlL~   48 (79)
T 3sb2_A           13 LNALRKEHVPVSIYLVNGIKLQGHVESFDQYV-VLLR   48 (79)
T ss_dssp             HHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             HHHHHhcCCeEEEEEeCCCEEEEEEEEECCcE-EEEE
Confidence            55554  3579999999999999999999998 4443

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

Probab=96.85  E-value=0.0019  Score=41.73  Aligned_cols=35  Identities=23%  Similarity=0.510  Sum_probs=29.3

Q ss_pred             HHhhc--CCeEEEEEcCCeEEEEEEEEecCccceEEcc
Q 034180           43 LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (102)
Q Consensus        43 L~~~i--~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~d   78 (102)
                      |+.+.  +.+|.|.|.+|..++|.+.+||+|+ +.|++
T Consensus        14 L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~-vlL~~   50 (74)
T 2ylb_A           14 LNALRRERVPVSIYLVNGIKLQGQIESFDQFV-ILLKN   50 (74)
T ss_dssp             HHHHHHHTCCEEEEETTSCEEEEEEEEECSSE-EEEES
T ss_pred             HHHHHhcCCcEEEEEeCCCEEEEEEEEECCcE-EEEEC
Confidence            66665  5799999999999999999999998 55553

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

Probab=96.59  E-value=0.0035  Score=40.92  Aligned_cols=43  Identities=30%  Similarity=0.397  Sum_probs=29.0

Q ss_pred             cCCCcCCcch--HHhhc--CCeEEEEEcCCeEEEEEEEEecCccceE
Q 034180           33 MSGRKETVLD--LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLV   75 (102)
Q Consensus        33 ms~~~~~~~~--L~~~i--~K~V~V~Lk~Gr~i~G~L~gfD~~mNLV   75 (102)
                      |+++.....+  |+..-  +.+|.|-|.+|..++|.+.|||+|+=++
T Consensus         4 ~~~~~~nlQd~fLn~lrk~~~~Vtv~L~nG~~l~G~I~~fD~f~VlL   50 (78)
T 3ahu_A            4 GSMKPINIQDQFLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFTVLL   50 (78)
T ss_dssp             ------CHHHHHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             ccccccChHHHHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEEE
Confidence            4444443433  55443  6799999999999999999999998333

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

Probab=96.49  E-value=0.0063  Score=39.10  Aligned_cols=29  Identities=21%  Similarity=0.298  Sum_probs=25.4

Q ss_pred             cCCeEEEEEcCCeEEEEEEEEecCccceE
Q 034180           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLV   75 (102)
Q Consensus        47 i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLV   75 (102)
                      -+.+|.|-|.+|-.++|.+.|||+|+=++
T Consensus        24 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll   52 (71)
T 2qtx_A           24 NGKKVKIFLRNGEVLDAEVTGVSNYEIMV   52 (71)
T ss_dssp             TTCEEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             cCCcEEEEEeCCeEEEEEEEEEcceEEEE
Confidence            45689999999999999999999998443

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

Probab=96.48  E-value=0.0042  Score=40.97  Aligned_cols=34  Identities=24%  Similarity=0.521  Sum_probs=27.9

Q ss_pred             HHhhc--CCeEEEEEcCCeEEEEEEEEecCccceEEc
Q 034180           43 LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVLD   77 (102)
Q Consensus        43 L~~~i--~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~   77 (102)
                      |+...  +.+|.|.|.+|-.++|.+.|||+|+ +.|+
T Consensus        12 Ln~lrk~~~~Vtv~L~NG~~l~G~I~~fD~ft-VlL~   47 (82)
T 1u1s_A           12 LNTLRKERVPVSIYLVNGIKLQGQIESFDQFV-ILLK   47 (82)
T ss_dssp             HHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             HHHHHHcCCcEEEEEeCCcEEEEEEEEEcceE-EEEe
Confidence            44443  5789999999999999999999998 4444

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

Probab=96.25  E-value=0.0073  Score=39.18  Aligned_cols=33  Identities=27%  Similarity=0.464  Sum_probs=27.7

Q ss_pred             HHhhc--CCeEEEEEcCCeEEEEEEEEecCccceE
Q 034180           43 LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLV   75 (102)
Q Consensus        43 L~~~i--~K~V~V~Lk~Gr~i~G~L~gfD~~mNLV   75 (102)
                      |+.+.  +.+|.|.|.+|-.++|.+.+||+|+=++
T Consensus        12 Ln~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~VlL   46 (77)
T 1kq1_A           12 LENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSL   46 (77)
T ss_dssp             HHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEE
Confidence            55554  6799999999999999999999998333

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

Probab=95.93  E-value=0.011  Score=40.47  Aligned_cols=34  Identities=24%  Similarity=0.516  Sum_probs=28.0

Q ss_pred             HHhhcC--CeEEEEEcCCeEEEEEEEEecCccceEEc
Q 034180           43 LAKFVD--KGVQVKLTGGRQVTGTLKGYDQLLNLVLD   77 (102)
Q Consensus        43 L~~~i~--K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~   77 (102)
                      |+.+..  .+|.|.|.+|-.++|.+.+||+|+ +.|+
T Consensus        14 Ln~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~-VlL~   49 (104)
T 2y90_A           14 LNALRRERVPVSIYLVNGIKLQGQIESFDQFV-ILLK   49 (104)
T ss_dssp             HHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             HHHHHhcCCcEEEEEeCCCEEEEEEEEECCcE-EEEE
Confidence            565544  489999999999999999999998 4444

>1ycy_A Conserved hypothetical protein; structural genomics, southeast collaboratory for structural genomics, secsg, protein structure initiative; 2.80A {Pyrococcus furiosus} SCOP: b.38.1.4

Probab=94.65  E-value=0.032  Score=35.62  Aligned_cols=42  Identities=26%  Similarity=0.548  Sum_probs=34.0

Q ss_pred             HHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC
Q 034180           43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG   85 (102)
Q Consensus        43 L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~   85 (102)
                      |.++-|+||-+...+...++|+|.-||+-. +.|.|+..+...
T Consensus        11 L~~WKg~rvAv~vg~ehSFtGiledFDeEv-iLL~dV~D~~GN   52 (71)
T 1ycy_A           11 LKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIGN   52 (71)
T ss_dssp             HHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTEE
T ss_pred             HHHhCCcEEEEEecCcceeeeehhhcCcce-eehhhHHHHhcc
Confidence            889999999999999999999999999876 788999987643

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

Probab=93.71  E-value=0.1  Score=36.73  Aligned_cols=37  Identities=27%  Similarity=0.453  Sum_probs=31.9

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEE--cce
Q 034180           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVL--DEA   79 (102)
Q Consensus        42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL--~da   79 (102)
                      ...+|+|..|.|.|+||..++|++..+|. -+|+|  .+|
T Consensus         6 ~~sqFlGy~V~v~LkDgs~~qG~I~~vd~-k~LtL~~~~a   44 (125)
T 4a53_A            6 SVADFYGSNVEVLLNNDSKARGVITNFDS-SNSILQLRLA   44 (125)
T ss_dssp             CHHHHTTCEEEEEETTSCEEEEEEEEEET-TTTEEEEEET
T ss_pred             cHHHhcCceEEEEECCCCEeeEEEEeecC-CeeEEecccc
Confidence            57899999999999999999999999984 34666  776

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

Probab=91.41  E-value=0.23  Score=31.64  Aligned_cols=38  Identities=26%  Similarity=0.294  Sum_probs=30.7

Q ss_pred             CcchHHhhcC--CeEEEEEcCCeEEEEEEEEecCccceEEc
Q 034180           39 TVLDLAKFVD--KGVQVKLTGGRQVTGTLKGYDQLLNLVLD   77 (102)
Q Consensus        39 ~~~~L~~~i~--K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~   77 (102)
                      +.-.|++|+.  .+|.|+|.+|..++|.+.-+|.+. +.|.
T Consensus        10 svR~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~c-l~L~   49 (70)
T 3hfo_A           10 SVRQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDG-LGLV   49 (70)
T ss_dssp             HHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             cHHHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCE-EEEE
Confidence            3445777864  689999999999999999999987 4444

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

Probab=91.40  E-value=0.23  Score=31.76  Aligned_cols=40  Identities=20%  Similarity=0.390  Sum_probs=31.6

Q ss_pred             CcchHHhhcC--CeEEEEEcCCeEEEEEEEEecCccceEEcce
Q 034180           39 TVLDLAKFVD--KGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA   79 (102)
Q Consensus        39 ~~~~L~~~i~--K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da   79 (102)
                      +...|++|+.  ++|.|+|.+|..++|.+.-+|.+. +.|.+.
T Consensus        12 svR~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~c-l~L~~~   53 (72)
T 3hfn_A           12 SIRQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTC-VCIADE   53 (72)
T ss_dssp             HHHHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSE-EEEEC-
T ss_pred             cHHHHHHHHhhCceEEEEecCCCEEEEEEEEECCCE-EEEEcC
Confidence            3445788875  589999999999999999999988 555444

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

Probab=91.40  E-value=0.25  Score=35.29  Aligned_cols=32  Identities=25%  Similarity=0.254  Sum_probs=26.7

Q ss_pred             cchHHhhcCCeEEEEE----cCCeEEEEEEEEecCc
Q 034180           40 VLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQL   71 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~L----k~Gr~i~G~L~gfD~~   71 (102)
                      +.+..+++|+.|.|++    .+.+.++|.|.++|+-
T Consensus        96 ~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T 1ib8_A           96 KDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED  131 (164)
T ss_dssp             HHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT
T ss_pred             HHHHHHhCCcEEEEEEecccCCceEEEEEEEEEeCC
Confidence            4457889999999999    4558999999999854

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

Probab=88.31  E-value=0.85  Score=30.05  Aligned_cols=36  Identities=14%  Similarity=0.230  Sum_probs=32.9

Q ss_pred             hhcCCeEEEEEcCCe-EEEEEEEEecCc-cceEEcceE
Q 034180           45 KFVDKGVQVKLTGGR-QVTGTLKGYDQL-LNLVLDEAV   80 (102)
Q Consensus        45 ~~i~K~V~V~Lk~Gr-~i~G~L~gfD~~-mNLVL~da~   80 (102)
                      +|+|+.|.+..+++- .|+|.|...|.. -||.|.++.
T Consensus         6 ~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~f   43 (84)
T 2vc8_A            6 DWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPF   43 (84)
T ss_dssp             TTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEEE
T ss_pred             cccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehhh
Confidence            799999999999998 999999999966 579999994

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

Probab=87.91  E-value=1.2  Score=29.53  Aligned_cols=40  Identities=13%  Similarity=0.096  Sum_probs=34.1

Q ss_pred             HhhcCCeEEEEEcCCeEEEEEEEEecCc-cceEEcceEEEE
Q 034180           44 AKFVDKGVQVKLTGGRQVTGTLKGYDQL-LNLVLDEAVEFL   83 (102)
Q Consensus        44 ~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~-mNLVL~da~E~~   83 (102)
                      ..|+|+++.+..+.+-.|+|+|...|.. --+.|.|+.-+-
T Consensus         9 ~~yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfG   49 (88)
T 2vxe_A            9 LPELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFG   49 (88)
T ss_dssp             SCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECC
T ss_pred             CcccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEec
Confidence            3589999999999999999999999944 568888877654

>3rux_A BIRA bifunctional protein; biotin-protein ligase, ligase-ligase inhibitor complex; HET: BS5; 1.70A {Mycobacterium tuberculosis} PDB: 3l1a_A 3l2z_A 2cgh_A

Probab=87.36  E-value=0.75  Score=34.82  Aligned_cols=33  Identities=33%  Similarity=0.536  Sum_probs=29.2

Q ss_pred             cCCeEEEEEcCCeEEEEEEEEecCccceEEcce
Q 034180           47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA   79 (102)
Q Consensus        47 i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da   79 (102)
                      +|++|.+...+|.+++|+..|.|+.-.|+++..
T Consensus       223 ~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~~  255 (270)
T 3rux_A          223 IGSRVRVELPGGQDVVGIARDIDDQGRLCLDVG  255 (270)
T ss_dssp             TTSEEEEECTTSCEEEEEEEEECTTSCEEEEET
T ss_pred             cCCEEEEEECCCeEEEEEEEEECCCCeEEEEEC
Confidence            589999998889999999999999999988643

>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=86.51  E-value=1  Score=30.18  Aligned_cols=41  Identities=12%  Similarity=0.164  Sum_probs=32.5

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEEecC-ccceEEcceEEE
Q 034180           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQ-LLNLVLDEAVEF   82 (102)
Q Consensus        42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~-~mNLVL~da~E~   82 (102)
                      .-..|+|+++.+..+.+-.|+|+|...|. ---+.|.|+.-+
T Consensus        13 ~~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsf   54 (95)
T 2fb7_A           13 GGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSF   54 (95)
T ss_dssp             ---CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCC
T ss_pred             ccCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEe
Confidence            34578999999999999999999999994 356788876554

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	102
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	3e-13
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	3e-11
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	3e-11
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	5e-11
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	6e-11
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	6e-11
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	1e-10
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	2e-10
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	3e-10
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	2e-09
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	5e-09
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	6e-07
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	2e-06

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

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

 Score = 57.5 bits (139), Expect = 3e-13
 Identities = 14/48 (29%), Positives = 25/48 (52%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNG 90
          + + +D  ++  L  GR   GT K +D+ +NL+L +  EF +    N 
Sbjct: 3  MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNS 50

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

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

 Score = 52.4 bits (126), Expect = 3e-11
 Identities = 20/44 (45%), Positives = 26/44 (59%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86
          L + +   V V+L GGR+  GTL GYD  +NLVL +A E   G 
Sbjct: 8  LNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGE 51

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

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

 Score = 52.4 bits (126), Expect = 3e-11
 Identities = 21/55 (38%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 33 MSGRKETVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86
          M+   ET    LA+ ++  V VKL G ++V G L+ YDQ +NLVL ++ E     
Sbjct: 1  MNFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDG 55

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

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

 Score = 52.2 bits (125), Expect = 5e-11
 Identities = 12/42 (28%), Positives = 26/42 (61%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
          + K +   + V + G ++ +G L+G+D+ +N+VLD+  E+  
Sbjct: 10 IDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGF 51

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

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

 Score = 51.2 bits (123), Expect = 6e-11
 Identities = 20/53 (37%), Positives = 32/53 (60%), Gaps = 1/53 (1%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYN-GIFVI 94
          L   + K V VKL    ++ G L+ +DQ +NL+L++A E + GN+Y  G  V+
Sbjct: 7  LQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVV 59

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

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

 Score = 51.2 bits (123), Expect = 6e-11
 Identities = 17/44 (38%), Positives = 25/44 (56%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86
          L   ++  V +KL G R+  G LK +D  +NLVL++A E   G 
Sbjct: 11 LGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGE 54

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

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

 Score = 51.6 bits (124), Expect = 1e-10
 Identities = 15/54 (27%), Positives = 21/54 (38%), Gaps = 9/54 (16%)

Query: 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE---------FLRGN 86
          +L   + + VQV L+ G    G L   D  LN+VL  A           F+   
Sbjct: 4  ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRVFIMYR 57

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

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

 Score = 50.1 bits (120), Expect = 2e-10
 Identities = 17/44 (38%), Positives = 23/44 (52%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86
          + + +DK V V L  G +  G L GYD  LN+VL +A     G 
Sbjct: 7  IHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGE 50

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

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

 Score = 49.7 bits (119), Expect = 3e-10
 Identities = 18/48 (37%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 43 LAKFVDKGVQVKL-TGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYN 89
          L   V+  V VKL     +  GTL   D   NL L+EA EF+ G  + 
Sbjct: 1  LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHG 48

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

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

 Score = 47.4 bits (113), Expect = 2e-09
 Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 43 LAKFVDKGVQVKLT-GGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86
          +   V K ++V++     Q+ G L+G D  +NL L  A+E     
Sbjct: 10 VKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEE 54

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

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

 Score = 47.2 bits (112), Expect = 5e-09
 Identities = 10/45 (22%), Positives = 21/45 (46%)

Query: 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84
          VL  +   +  V +     +++ G +K +D+  N+VL+   E   
Sbjct: 6  VLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWT 50

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

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

 Score = 41.2 bits (97), Expect = 6e-07
 Identities = 14/43 (32%), Positives = 20/43 (46%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG 85
          L K   + V ++L  G QV GT+ G D  +N  L      L+ 
Sbjct: 6  LMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKN 48

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

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

 Score = 39.8 bits (93), Expect = 2e-06
 Identities = 7/44 (15%), Positives = 12/44 (27%)

Query: 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86
          L +     V  +   G    G L   +  +N  +       R  
Sbjct: 7  LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDG 50

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	102
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.69
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.68
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.67
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.66
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.66
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.65
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.62
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.62
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.52
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.51
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.47
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.38
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.21
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	95.54
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	95.24
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	94.52
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	94.5
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	93.61
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	87.48

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

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

Probab=99.69  E-value=2.6e-17  Score=103.86  Aligned_cols=58  Identities=36%  Similarity=0.516  Sum_probs=52.9

Q ss_pred             CcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC   96 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~   96 (102)
                      +...|.+++|++|.|+|+||++|+|+|.|||+|||++|+||.|+.+++..+.+|.++.
T Consensus         4 Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~I   61 (72)
T d1i4k1_           4 PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVI   61 (72)
T ss_dssp             HHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSSSEEEEEEEEEE
T ss_pred             hHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecCCeEeEcceEEE
Confidence            3445889999999999999999999999999999999999999998888888998753

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

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

Probab=99.68  E-value=4.8e-17  Score=104.78  Aligned_cols=55  Identities=24%  Similarity=0.387  Sum_probs=47.5

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC----------ceeecEEEEEE
Q 034180           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG----------NLYNGIFVIVC   96 (102)
Q Consensus        42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~----------~~~~~iG~iv~   96 (102)
                      +|.+|+||+|+|+++|||.+.|+|.|||+||||+|+||+|+...          ...+.+|+++-
T Consensus         2 ~L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~I   66 (81)
T d1d3bb_           2 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLL   66 (81)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEE
T ss_pred             hhHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEE
Confidence            68899999999999999999999999999999999999998631          13467787653

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

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

Probab=99.67  E-value=8.7e-17  Score=102.47  Aligned_cols=56  Identities=36%  Similarity=0.442  Sum_probs=51.9

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV   95 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv   95 (102)
                      ...|.+++|++|.|.|+||++|+|+|.|||+|||++|+||+|+.++++.+.+|.++
T Consensus         9 ~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~~~v~   64 (76)
T d1th7a1           9 HKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIV   64 (76)
T ss_dssp             HHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEE
T ss_pred             HHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecCCcccCcceEE
Confidence            34588999999999999999999999999999999999999999998888999865

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

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

Probab=99.66  E-value=2e-16  Score=100.15  Aligned_cols=57  Identities=30%  Similarity=0.487  Sum_probs=52.7

Q ss_pred             CcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180           39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV   95 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv   95 (102)
                      +...|.+++||+|.|.|+||++|+|+|.|||+|||++|+||.|+.+++..+.+|.++
T Consensus         7 Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~~~~~~~~~~~   63 (74)
T d1mgqa_           7 PLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVL   63 (74)
T ss_dssp             TTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             cHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCCCeEeEcceEE
Confidence            345688999999999999999999999999999999999999999988888898875

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

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

Probab=99.66  E-value=1.4e-16  Score=99.99  Aligned_cols=55  Identities=35%  Similarity=0.391  Sum_probs=50.9

Q ss_pred             chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180           41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV   95 (102)
Q Consensus        41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv   95 (102)
                      ..|++++|++|.|.|+||++|+|+|.|||+|||++|+||.|+.+++..+.+|.++
T Consensus         5 ~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~l~~~~   59 (71)
T d1h641_           5 DVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIV   59 (71)
T ss_dssp             HHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             HHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecCCcEeEcCcEE
Confidence            3488999999999999999999999999999999999999999888888888765

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

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

Probab=99.65  E-value=2.2e-16  Score=99.81  Aligned_cols=55  Identities=31%  Similarity=0.430  Sum_probs=48.8

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV   95 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv   95 (102)
                      .+.|++++||+|.|+|+||++|+|+|.|||+|||++|+||+|+.++ +.+.+|.++
T Consensus         4 ~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~~-~~~~~g~v~   58 (71)
T d1i8fa_           4 GATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDG-NVYKRGTMV   58 (71)
T ss_dssp             HHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEETT-EEEEEEEEE
T ss_pred             hHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEECC-CEEEcceEE
Confidence            4579999999999999999999999999999999999999999765 456678754

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

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

Probab=99.62  E-value=5.1e-16  Score=99.07  Aligned_cols=56  Identities=29%  Similarity=0.376  Sum_probs=51.0

Q ss_pred             cchHHhhcCCeEEEEEcCC-eEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180           40 VLDLAKFVDKGVQVKLTGG-RQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV   95 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~G-r~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv   95 (102)
                      ...|+++++++|.|++++| ++|+|+|.|||+|||++|+||+|+.+++..+.+|.++
T Consensus         7 ~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~   63 (75)
T d1ljoa_           7 NQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIV   63 (75)
T ss_dssp             HHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             HHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCCCcEeEcceEE
Confidence            4458899999999999965 8999999999999999999999999998889999875

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

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

Probab=99.62  E-value=3.2e-16  Score=98.42  Aligned_cols=53  Identities=36%  Similarity=0.433  Sum_probs=48.1

Q ss_pred             HHhhcCCeEEEEEc-CCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180           43 LAKFVDKGVQVKLT-GGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV   95 (102)
Q Consensus        43 L~~~i~K~V~V~Lk-~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv   95 (102)
                      |+++++++|.|+|+ +|++|+|+|.|||+|||++|+||+|..+++..+.+|.++
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~   54 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIF   54 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEE
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEecCCcccCcCeEE
Confidence            56889999999999 568999999999999999999999999888888888764

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

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

Probab=99.52  E-value=4.5e-15  Score=97.09  Aligned_cols=45  Identities=27%  Similarity=0.575  Sum_probs=41.7

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEe
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR   84 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~   84 (102)
                      ...|.++++|+|+|.++||++|.|+|.|||+||||+|+||.|+..
T Consensus         7 l~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~   51 (92)
T d2fwka1           7 LALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGF   51 (92)
T ss_dssp             HHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC
T ss_pred             HHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEe
Confidence            345889999999999999999999999999999999999999863

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

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

Probab=99.51  E-value=2.5e-14  Score=90.11  Aligned_cols=54  Identities=13%  Similarity=0.061  Sum_probs=49.1

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV   95 (102)
Q Consensus        42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv   95 (102)
                      -|.+..|++|.|+|+||++|+|+|.++|+|||++|+||.+...+++...+|.++
T Consensus         6 ~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~v~   59 (72)
T d1d3ba_           6 VLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVY   59 (72)
T ss_dssp             HHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEE
T ss_pred             HHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCCCcEeEcCeEE
Confidence            377899999999999999999999999999999999999998887777777663

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

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

Probab=99.47  E-value=3.8e-14  Score=93.54  Aligned_cols=42  Identities=24%  Similarity=0.458  Sum_probs=37.6

Q ss_pred             HHhhc--CCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEe
Q 034180           43 LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR   84 (102)
Q Consensus        43 L~~~i--~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~   84 (102)
                      |.+++  +++|.|.+++||.++|+|.|||+|||++|+||+|++.
T Consensus         7 l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~   50 (93)
T d1b34b_           7 LTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWT   50 (93)
T ss_dssp             HHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC--
T ss_pred             HHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEE
Confidence            55666  8999999999999999999999999999999999864

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

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

Probab=99.38  E-value=7e-13  Score=85.12  Aligned_cols=54  Identities=26%  Similarity=0.295  Sum_probs=48.6

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV   95 (102)
Q Consensus        42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv   95 (102)
                      .|++..|++|.|.|++|.+|+|+|.++|+|||++|+||.+...+++...+|.+.
T Consensus         5 fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~~~~~~~v~   58 (80)
T d1b34a_           5 FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLS   58 (80)
T ss_dssp             HHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEE
T ss_pred             HHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCCEEEcccEE
Confidence            578899999999999999999999999999999999999998877776666653

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

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

Probab=99.21  E-value=6.4e-12  Score=87.40  Aligned_cols=46  Identities=33%  Similarity=0.453  Sum_probs=42.2

Q ss_pred             cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC
Q 034180           40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG   85 (102)
Q Consensus        40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~   85 (102)
                      .++|++++|++|.|.|+||++|.|+|.++|+|||++|+||.+...+
T Consensus         2 ~~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~~~   47 (127)
T d1m5q1_           2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGE   47 (127)
T ss_dssp             HHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETTCC
T ss_pred             hhHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECCCC
Confidence            4679999999999999999999999999999999999999986443

>d1u1sa1 b.38.1.2 (A:6-71) Pleiotropic translational regulator Hfq {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Pleiotropic translational regulator Hfq
domain: Pleiotropic translational regulator Hfq
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=95.54  E-value=0.011  Score=36.09  Aligned_cols=28  Identities=25%  Similarity=0.581  Sum_probs=24.6

Q ss_pred             CCeEEEEEcCCeEEEEEEEEecCccceEE
Q 034180           48 DKGVQVKLTGGRQVTGTLKGYDQLLNLVL   76 (102)
Q Consensus        48 ~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL   76 (102)
                      ..+|.|-|.+|-.++|.+.|||+|. +.|
T Consensus        14 ~~~VtifL~nGvkl~G~I~~fD~ft-vLL   41 (66)
T d1u1sa1          14 RVPVSIYLVNGIKLQGQIESFDQFV-ILL   41 (66)
T ss_dssp             TCCEEEEETTSCEEEEEEEEECSSE-EEE
T ss_pred             CCcEEEEEEcCcEEEEEEEEEcceE-EEE
Confidence            4689999999999999999999997 344

>d1biaa2 b.34.1.1 (A:271-317) Biotin repressor/biotin holoenzyme synthetase, C-terminal domain {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: SH3-like barrel
superfamily: C-terminal domain of transcriptional repressors
family: Biotin repressor (BirA)
domain: Biotin repressor/biotin holoenzyme synthetase, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.24  E-value=0.023  Score=31.70  Aligned_cols=32  Identities=25%  Similarity=0.619  Sum_probs=28.0

Q ss_pred             hcCCeEEEEEcCCeEEEEEEEEecCccceEEcc
Q 034180           46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE   78 (102)
Q Consensus        46 ~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~d   78 (102)
                      |++|+|+|.. ++++++|+-.|+|+.-.|+|+.
T Consensus         1 f~gk~V~v~~-g~~~i~G~a~gId~~G~Lll~t   32 (47)
T d1biaa2           1 FINRPVKLII-GDKEIFGISRGIDKQGALLLEQ   32 (47)
T ss_dssp             TTTSEEEEEE-TTEEEEEEEEEECTTSCEEEEE
T ss_pred             CCCCEEEEEE-CCeEEEEEEeeECCCCcEEEEE
Confidence            6899999975 5688999999999999998864

>d1ycya1 b.38.1.4 (A:5-70) Hypothetical protein PF1955 {Pyrococcus furiosus [TaxId: 2261]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: PF1955-like
domain: Hypothetical protein PF1955
species: Pyrococcus furiosus [TaxId: 2261]

Probab=94.52  E-value=0.028  Score=33.94  Aligned_cols=43  Identities=26%  Similarity=0.513  Sum_probs=34.2

Q ss_pred             hHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC
Q 034180           42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG   85 (102)
Q Consensus        42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~   85 (102)
                      .|.++-|++|-|...+...+.|+|.-||+-. +.|.|+.++...
T Consensus         6 tL~~WKg~kvAv~vgsehSFtGiledFDeEv-iLL~dV~D~~GN   48 (66)
T d1ycya1           6 VLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIGN   48 (66)
T ss_dssp             HHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTEE
T ss_pred             HHHHhCCcEEEEEecCcceeEEEhhhcCcce-EeehhhHHHhcc
Confidence            3789999999999999999999999999876 788999987543

>d1kq1a_ b.38.1.2 (A:) Pleiotropic translational regulator Hfq {Staphylococcus aureus [TaxId: 1280]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Pleiotropic translational regulator Hfq
domain: Pleiotropic translational regulator Hfq
species: Staphylococcus aureus [TaxId: 1280]

Probab=94.50  E-value=0.036  Score=33.06  Aligned_cols=28  Identities=25%  Similarity=0.426  Sum_probs=24.9

Q ss_pred             CCeEEEEEcCCeEEEEEEEEecCccceE
Q 034180           48 DKGVQVKLTGGRQVTGTLKGYDQLLNLV   75 (102)
Q Consensus        48 ~K~V~V~Lk~Gr~i~G~L~gfD~~mNLV   75 (102)
                      .++|.|-|.+|-.++|.+.|||+|.=++
T Consensus        14 ~~~VtifL~nGvkl~G~I~~fD~ftvlL   41 (60)
T d1kq1a_          14 QTEVTVFFLNGFQMKGVIEEYDKYVVSL   41 (60)
T ss_dssp             TCEEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             CCcEEEEEECCcEEEEEEEEEcceEEEE
Confidence            4689999999999999999999998444

>d1ib8a1 b.38.2.1 (A:91-164) Hypothetical protein SP14.3 (SP0552) {Streptococcus pneumoniae [TaxId: 1313]}

class: All beta proteins
fold: Sm-like fold
superfamily: YhbC-like, C-terminal domain
family: YhbC-like, C-terminal domain
domain: Hypothetical protein SP14.3 (SP0552)
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=93.61  E-value=0.039  Score=32.92  Aligned_cols=33  Identities=27%  Similarity=0.263  Sum_probs=27.9

Q ss_pred             CcchHHhhcCCeEEEEEc---CC-eEEEEEEEEecCc
Q 034180           39 TVLDLAKFVDKGVQVKLT---GG-RQVTGTLKGYDQL   71 (102)
Q Consensus        39 ~~~~L~~~i~K~V~V~Lk---~G-r~i~G~L~gfD~~   71 (102)
                      .+.+..+|+|++|.|+|+   +| +.++|.|.++|+-
T Consensus         5 ~~~~f~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~   41 (74)
T d1ib8a1           5 TKDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED   41 (74)
T ss_dssp             SHHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT
T ss_pred             CHHHHHHhCCCEEEEEEecccCCceEEEEEEEeecCC
Confidence            356789999999999985   34 7999999999865

>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=87.48  E-value=0.61  Score=28.86  Aligned_cols=38  Identities=13%  Similarity=0.177  Sum_probs=33.0

Q ss_pred             hcCCeEEEEEcCCeEEEEEEEEecCc-cceEEcceEEEE
Q 034180           46 FVDKGVQVKLTGGRQVTGTLKGYDQL-LNLVLDEAVEFL   83 (102)
Q Consensus        46 ~i~K~V~V~Lk~Gr~i~G~L~gfD~~-mNLVL~da~E~~   83 (102)
                      |+|+++.+..+.+-.|+|+|...|.. --+.|.|+.-+-
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfG   40 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFG   40 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECC
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEee
Confidence            78999999999999999999999955 458888887664