Citrus Sinensis ID: 041342

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80-------
Protein Sequence
MAHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGSPDPE
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHcccEEEEEEcccEEEEEEEEEEcccccEEEEEEEEEEEccccEEEEEEccEEEEcccEEEEEcccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccHHHHHHHccccEEEEEccccEEEEEEEcccHHHHEEHHccEEEEEcccccEEEcccEEEEccccEEEEEcccccccc
Coil and Loop (DISEMBL)
mahnpsqllpselidrcigSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNgnniailvpggspdpe
Flexible Loop (DISEMBL)
mahnpsqllpselIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLdqillngnniailvpggspdpe
Low Complexity Region (SEG)
MAHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGSPDPE
Disordered region (IsUnstruct)
***********ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILV********
Disordered Region (DISOPRED)
******Q**PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITA***RITKLDQILLNGNNIA****G******
Disordered Region (DISEMBL)
MAHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGSPDPE
Disordered Region (DISPRO)
*****SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGSPDPE
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	87	2.2.26 [Sep-21-2011]
Q5R628	91	U6 snRNA-associated Sm-li	yes	no	0.908	0.868	0.797	3e-31
P62322	91	U6 snRNA-associated Sm-li	yes	no	0.908	0.868	0.797	3e-31
Q9Y4Y9	91	U6 snRNA-associated Sm-li	yes	no	0.908	0.868	0.797	3e-31
Q2HJH0	91	U6 snRNA-associated Sm-li	yes	no	0.908	0.868	0.797	3e-31
Q55EX5	97	Probable U6 snRNA-associa	yes	no	0.885	0.793	0.688	2e-25
O42978	80	U6 snRNA-associated Sm-li	yes	no	0.873	0.95	0.576	3e-18
P40089	93	U6 snRNA-associated Sm-li	yes	no	0.919	0.860	0.458	8e-13
P57670	83	Putative snRNP Sm-like pr	yes	no	0.885	0.927	0.287	4e-06
O26745	81	Putative snRNP Sm-like pr	yes	no	0.781	0.839	0.338	1e-05
Q8PZZ9	72	Putative snRNP Sm-like pr	no	no	0.781	0.944	0.281	2e-05

>sp|Q5R628|LSM5_PONAB U6 snRNA-associated Sm-like protein LSm5 OS=Pongo abelii GN=LSM5 PE=3 SV=3

 Score =  133 bits (335), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 63/79 (79%), Positives = 72/79 (91%)

Query: 4  NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT 63
          NPSQLLP EL+D+CIGS+I ++MK DKE+VGTL GFD +VNMVLEDVTE+EIT EGRRIT
Sbjct: 8  NPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITPEGRRIT 67

Query: 64 KLDQILLNGNNIAILVPGG 82
          KLDQILLNGNNI +LVPGG
Sbjct: 68 KLDQILLNGNNITMLVPGG 86

Plays a role in U6 snRNP assembly and function. Binds to the 3' end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro.
Pongo abelii (taxid: 9601)

>sp|P62322|LSM5_MOUSE U6 snRNA-associated Sm-like protein LSm5 OS=Mus musculus GN=Lsm5 PE=3 SV=2

 Score =  133 bits (335), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 63/79 (79%), Positives = 72/79 (91%)

Query: 4  NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT 63
          NPSQLLP EL+D+CIGS+I ++MK DKE+VGTL GFD +VNMVLEDVTE+EIT EGRRIT
Sbjct: 8  NPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITPEGRRIT 67

Query: 64 KLDQILLNGNNIAILVPGG 82
          KLDQILLNGNNI +LVPGG
Sbjct: 68 KLDQILLNGNNITMLVPGG 86

Plays a role in U6 snRNP assembly and function. Binds to the 3' end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro.

Mus musculus (taxid: 10090)

>sp|Q9Y4Y9|LSM5_HUMAN U6 snRNA-associated Sm-like protein LSm5 OS=Homo sapiens GN=LSM5 PE=1 SV=3

 Score =  133 bits (335), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 63/79 (79%), Positives = 72/79 (91%)

Query: 4  NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT 63
          NPSQLLP EL+D+CIGS+I ++MK DKE+VGTL GFD +VNMVLEDVTE+EIT EGRRIT
Sbjct: 8  NPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITPEGRRIT 67

Query: 64 KLDQILLNGNNIAILVPGG 82
          KLDQILLNGNNI +LVPGG
Sbjct: 68 KLDQILLNGNNITMLVPGG 86

Plays a role in U6 snRNP assembly and function. Binds to the 3' end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro.

Homo sapiens (taxid: 9606)

>sp|Q2HJH0|LSM5_BOVIN U6 snRNA-associated Sm-like protein LSm5 OS=Bos taurus GN=LSM5 PE=3 SV=3

 Score =  133 bits (335), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 63/79 (79%), Positives = 72/79 (91%)

Query: 4  NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT 63
          NPSQLLP EL+D+CIGS+I ++MK DKE+VGTL GFD +VNMVLEDVTE+EIT EGRRIT
Sbjct: 8  NPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITPEGRRIT 67

Query: 64 KLDQILLNGNNIAILVPGG 82
          KLDQILLNGNNI +LVPGG
Sbjct: 68 KLDQILLNGNNITMLVPGG 86

Plays a role in U6 snRNP assembly and function. Binds to the 3' end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro.

Bos taurus (taxid: 9913)

>sp|Q55EX5|LSM5_DICDI Probable U6 snRNA-associated Sm-like protein LSm5 OS=Dictyostelium discoideum GN=lsm5 PE=3 SV=1

 Score =  114 bits (285), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 53/77 (68%), Positives = 63/77 (81%)

Query: 6  SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKL 65
          SQLLP ELI++CIGS+IW+ MK DKE VGTL GFD YVN+ L+DVTEYE T EG +  KL
Sbjct: 14 SQLLPLELIEKCIGSRIWIAMKNDKEFVGTLLGFDAYVNIFLKDVTEYEYTPEGLKTVKL 73

Query: 66 DQILLNGNNIAILVPGG 82
          D ILLNGN++ +LVPGG
Sbjct: 74 DNILLNGNHVCLLVPGG 90

Plays a role in U6 snRNP assembly and function. Binds to the 3' end of U6 snRNA.

Dictyostelium discoideum (taxid: 44689)

>sp|O42978|LSM5_SCHPO U6 snRNA-associated Sm-like protein LSm5 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=lsm5 PE=1 SV=2

 Score = 90.5 bits (223), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 45/78 (57%), Positives = 59/78 (75%), Gaps = 2/78 (2%)

Query: 8  LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQ 67
          +LP ELID+CIGS +WVIMK ++E  GTL GFD YVN+VL+DVTEY+ T  G    K  +
Sbjct: 5  ILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYD-TVTGVT-EKHSE 62

Query: 68 ILLNGNNIAILVPGGSPD 85
          +LLNGN + +L+PGG P+
Sbjct: 63 MLLNGNGMCMLIPGGKPE 80

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. LSm5 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

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

>sp|P40089|LSM5_YEAST U6 snRNA-associated Sm-like protein LSm5 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=LSM5 PE=1 SV=1

 Score = 72.4 bits (176), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 39/85 (45%), Positives = 57/85 (67%), Gaps = 5/85 (5%)

Query: 7  QLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGR-RITKL 65
          ++LP E+ID+ I  K+ ++++ ++E  GTL GFD +VN++LED  E+ I  E   R  K+
Sbjct: 5  EILPLEVIDKTINQKVLIVLQSNREFEGTLVGFDDFVNVILEDAVEWLIDPEDESRNEKV 64

Query: 66 DQ----ILLNGNNIAILVPGGSPDP 86
           Q    +LL+GNNIAILVPGG   P
Sbjct: 65 MQHHGRMLLSGNNIAILVPGGKKTP 89

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. LSM5 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. LSM5, 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. LSM5 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

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

>sp|P57670|RUXX_THEAC Putative snRNP Sm-like protein OS=Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) GN=Ta1240 PE=3 SV=1

 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 49/80 (61%), Gaps = 3/80 (3%)

Query: 1  MAHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGR 60
          M   P+ + P +++   +   + + +KG++E  G L+G+DVY+N+VL++ +E  I  E +
Sbjct: 1  MPKTPANVKPMDVLKSALSRNVLIDVKGNREYSGILEGYDVYMNIVLQNASEI-INGENK 59

Query: 61 RITKLDQILLNGNNIAILVP 80
           +   D++L+ G+N+  + P
Sbjct: 60 GV--YDRVLVRGDNVIFVSP 77

Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) (taxid: 273075)

>sp|O26745|RUXX_METTH Putative snRNP Sm-like protein OS=Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) GN=MTH_649 PE=1 SV=1

 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 3/71 (4%)

Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
          P + +   + S + + +KGD+E  G LK FD+++N+VL D  E E   +G    +L  +L
Sbjct: 14 PLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELE---DGEVTRRLGTVL 70

Query: 70 LNGNNIAILVP 80
          + G+NI  + P
Sbjct: 71 IRGDNIVYISP 81

Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (taxid: 187420)

>sp|Q8PZZ9|RUXX_METMA Putative snRNP Sm-like protein OS=Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88) GN=MM_0339 PE=3 SV=1

 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/71 (28%), Positives = 44/71 (61%), Gaps = 3/71 (4%)

Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
          P ++++  + + + V +KG +E  G LKG+D+++N+VL++  E     EG  ++K   ++
Sbjct: 5  PLDILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEELR---EGEVVSKFSSVV 61

Query: 70 LNGNNIAILVP 80
          + G+N+  + P
Sbjct: 62 IRGDNVVYVSP 72

Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88) (taxid: 192952)

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	87
388498294	87	unknown [Medicago truncatula]	1.0	1.0	0.977	6e-42
388507376	87	unknown [Lotus japonicus]	1.0	1.0	0.977	7e-42
313586491	87	U6 snRNA-associated Sm-like protein LSm5	1.0	1.0	0.965	8e-42
449468622	87	PREDICTED: U6 snRNA-associated Sm-like p	1.0	1.0	0.977	9e-42
225433436	87	PREDICTED: U6 snRNA-associated Sm-like p	1.0	1.0	0.954	5e-41
356524941	87	PREDICTED: uncharacterized protein LOC10	1.0	1.0	0.954	8e-41
224059779	88	predicted protein [Populus trichocarpa]	0.965	0.954	0.988	1e-40
356512167	87	PREDICTED: uncharacterized protein LOC10	1.0	1.0	0.942	2e-40
359477805	88	PREDICTED: U6 snRNA-associated Sm-like p	1.0	0.988	0.943	1e-39
110739170	88	Sm-like protein [Arabidopsis thaliana]	0.977	0.965	0.952	1e-39

>gi|388498294|gb|AFK37213.1| unknown [Medicago truncatula]

 Score =  174 bits (441), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 85/87 (97%), Positives = 87/87 (100%)

Query: 1  MAHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGR 60
          MA+NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTL+GFDVYVNMVLEDVTEYEITAEGR
Sbjct: 1  MANNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLRGFDVYVNMVLEDVTEYEITAEGR 60

Query: 61 RITKLDQILLNGNNIAILVPGGSPDPE 87
          RITKLDQILLNGNNIAILVPGGSPDPE
Sbjct: 61 RITKLDQILLNGNNIAILVPGGSPDPE 87

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388507376|gb|AFK41754.1| unknown [Lotus japonicus]

 Score =  174 bits (440), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 85/87 (97%), Positives = 86/87 (98%)

Query: 1  MAHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGR 60
          MA NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTL+GFDVYVNMVLEDVTEYEITAEGR
Sbjct: 1  MASNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLRGFDVYVNMVLEDVTEYEITAEGR 60

Query: 61 RITKLDQILLNGNNIAILVPGGSPDPE 87
          RITKLDQILLNGNNIAILVPGGSPDPE
Sbjct: 61 RITKLDQILLNGNNIAILVPGGSPDPE 87

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|313586491|gb|ADR71256.1| U6 snRNA-associated Sm-like protein LSm5 [Hevea brasiliensis]

 Score =  174 bits (440), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 84/87 (96%), Positives = 87/87 (100%)

Query: 1  MAHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGR 60
          MA+NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTL+GFDVYVNMVLEDVTEYE+TAEGR
Sbjct: 1  MANNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLRGFDVYVNMVLEDVTEYEVTAEGR 60

Query: 61 RITKLDQILLNGNNIAILVPGGSPDPE 87
          RITKLDQILLNGNNIAILVPGGSPDPE
Sbjct: 61 RITKLDQILLNGNNIAILVPGGSPDPE 87

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449468622|ref|XP_004152020.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm5-like [Cucumis sativus] gi|449522508|ref|XP_004168268.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm5-like [Cucumis sativus]

 Score =  174 bits (440), Expect = 9e-42,   Method: Compositional matrix adjust.
 Identities = 85/87 (97%), Positives = 86/87 (98%)

Query: 1  MAHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGR 60
          MA NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTL+GFDVYVNMVLEDVTEYEITAEGR
Sbjct: 1  MATNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLRGFDVYVNMVLEDVTEYEITAEGR 60

Query: 61 RITKLDQILLNGNNIAILVPGGSPDPE 87
          RITKLDQILLNGNNIAILVPGGSPDPE
Sbjct: 61 RITKLDQILLNGNNIAILVPGGSPDPE 87

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225433436|ref|XP_002285668.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm5 isoform 1 [Vitis vinifera] gi|297741927|emb|CBI33362.3| unnamed protein product [Vitis vinifera]

 Score =  171 bits (433), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 83/87 (95%), Positives = 86/87 (98%)

Query: 1  MAHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGR 60
          M+ NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTL+GFDVYVNMVLEDVTEYEIT+EGR
Sbjct: 1  MSTNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLRGFDVYVNMVLEDVTEYEITSEGR 60

Query: 61 RITKLDQILLNGNNIAILVPGGSPDPE 87
          RITKLDQILLNGNNIAILVPGGSPDPE
Sbjct: 61 RITKLDQILLNGNNIAILVPGGSPDPE 87

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356524941|ref|XP_003531086.1| PREDICTED: uncharacterized protein LOC100306359 [Glycine max] gi|255628297|gb|ACU14493.1| unknown [Glycine max]

 Score =  170 bits (431), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 83/87 (95%), Positives = 86/87 (98%)

Query: 1  MAHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGR 60
          MA+NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTL+GFDVYVNMVLEDVTEYEITAEGR
Sbjct: 1  MANNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLRGFDVYVNMVLEDVTEYEITAEGR 60

Query: 61 RITKLDQILLNGNNIAILVPGGSPDPE 87
          RITKLDQILLNGNNIAILVPGGSP+ E
Sbjct: 61 RITKLDQILLNGNNIAILVPGGSPESE 87

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224059779|ref|XP_002299989.1| predicted protein [Populus trichocarpa] gi|224103927|ref|XP_002313247.1| predicted protein [Populus trichocarpa] gi|118484238|gb|ABK93999.1| unknown [Populus trichocarpa] gi|222847247|gb|EEE84794.1| predicted protein [Populus trichocarpa] gi|222849655|gb|EEE87202.1| predicted protein [Populus trichocarpa]

 Score =  170 bits (430), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 83/84 (98%), Positives = 84/84 (100%)

Query: 4  NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT 63
          NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTL+GFDVYVNMVLEDVTEYEITAEGRRIT
Sbjct: 5  NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLRGFDVYVNMVLEDVTEYEITAEGRRIT 64

Query: 64 KLDQILLNGNNIAILVPGGSPDPE 87
          KLDQILLNGNNIAILVPGGSPDPE
Sbjct: 65 KLDQILLNGNNIAILVPGGSPDPE 88

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356512167|ref|XP_003524792.1| PREDICTED: uncharacterized protein LOC100527929 [Glycine max] gi|255633598|gb|ACU17158.1| unknown [Glycine max]

 Score =  169 bits (428), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 82/87 (94%), Positives = 85/87 (97%)

Query: 1  MAHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGR 60
          MA+NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTL+GFDVY NMVLEDVTEYEITAEGR
Sbjct: 1  MANNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLRGFDVYANMVLEDVTEYEITAEGR 60

Query: 61 RITKLDQILLNGNNIAILVPGGSPDPE 87
          RITKLDQILLNGNNIAILVPGGSP+ E
Sbjct: 61 RITKLDQILLNGNNIAILVPGGSPESE 87

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359477805|ref|XP_003632024.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm5 isoform 2 [Vitis vinifera]

 Score =  167 bits (422), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 83/88 (94%), Positives = 86/88 (97%), Gaps = 1/88 (1%)

Query: 1  MAHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEY-EITAEG 59
          M+ NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTL+GFDVYVNMVLEDVTEY EIT+EG
Sbjct: 1  MSTNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLRGFDVYVNMVLEDVTEYSEITSEG 60

Query: 60 RRITKLDQILLNGNNIAILVPGGSPDPE 87
          RRITKLDQILLNGNNIAILVPGGSPDPE
Sbjct: 61 RRITKLDQILLNGNNIAILVPGGSPDPE 88

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|110739170|dbj|BAF01501.1| Sm-like protein [Arabidopsis thaliana]

 Score =  166 bits (421), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 81/85 (95%), Positives = 84/85 (98%)

Query: 1  MAHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGR 60
          MA+NPSQLLPSELIDRCIGSKIWVIMKGDKELVG LKGFDVYVNMVLEDVTEYEITAEGR
Sbjct: 1  MANNPSQLLPSELIDRCIGSKIWVIMKGDKELVGILKGFDVYVNMVLEDVTEYEITAEGR 60

Query: 61 RITKLDQILLNGNNIAILVPGGSPD 85
          R+TKLDQILLNGNNIAILVPGGSP+
Sbjct: 61 RVTKLDQILLNGNNIAILVPGGSPE 85

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	87
TAIR|locus:2156589	88	SAD1 "SUPERSENSITIVE TO ABA AN	0.977	0.965	0.952	2.9e-39
ZFIN|ZDB-GENE-070822-23	91	zgc:171959 "zgc:171959" [Danio	0.977	0.934	0.755	1.8e-30
UNIPROTKB|Q2HJH0	91	LSM5 "U6 snRNA-associated Sm-l	0.954	0.912	0.773	2.3e-30
UNIPROTKB|Q9Y4Y9	91	LSM5 "U6 snRNA-associated Sm-l	0.954	0.912	0.773	2.3e-30
MGI|MGI:1913623	91	Lsm5 "LSM5 homolog, U6 small n	0.954	0.912	0.773	2.3e-30
WB|WBGene00003079	91	lsm-5 [Caenorhabditis elegans	0.954	0.912	0.761	1.6e-29
UNIPROTKB|O18694	91	lsm-5 "Protein LSM-5" [Caenorh	0.954	0.912	0.761	1.6e-29
FB|FBgn0035675	91	CG6610 [Drosophila melanogaste	0.908	0.868	0.734	4.5e-27
DICTYBASE|DDB_G0268716	97	lsm5 "putative U6 small nuclea	0.885	0.793	0.688	2.9e-25
ASPGD|ASPL0000026389	129	AN5679 [Emericella nidulans (t	0.850	0.573	0.688	1.8e-23

TAIR|locus:2156589 SAD1 "SUPERSENSITIVE TO ABA AND DROUGHT 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 419 (152.6 bits), Expect = 2.9e-39, P = 2.9e-39
 Identities = 81/85 (95%), Positives = 84/85 (98%)

Query:     1 MAHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGR 60
             MA+NPSQLLPSELIDRCIGSKIWVIMKGDKELVG LKGFDVYVNMVLEDVTEYEITAEGR
Sbjct:     1 MANNPSQLLPSELIDRCIGSKIWVIMKGDKELVGILKGFDVYVNMVLEDVTEYEITAEGR 60

Query:    61 RITKLDQILLNGNNIAILVPGGSPD 85
             R+TKLDQILLNGNNIAILVPGGSP+
Sbjct:    61 RVTKLDQILLNGNNIAILVPGGSPE 85

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0003723 "RNA binding" evidence=ISS

GO:0009414 "response to water deprivation" evidence=IMP

GO:0009737 "response to abscisic acid stimulus" evidence=IMP

ZFIN|ZDB-GENE-070822-23 zgc:171959 "zgc:171959" [Danio rerio (taxid:7955)]

 Score = 336 (123.3 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 65/86 (75%), Positives = 75/86 (87%)

Query:     2 AHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRR 61
             A NPSQLLP EL+D+CIGS+I ++MK DKE+VGTL GFD +VNMVLEDVTE+EIT EGRR
Sbjct:     6 ATNPSQLLPLELVDKCIGSRIHIVMKNDKEIVGTLLGFDDFVNMVLEDVTEFEITPEGRR 65

Query:    62 ITKLDQILLNGNNIAILVPGGSPDPE 87
             ITKLDQILLNGNNI +L+PGG   PE
Sbjct:    66 ITKLDQILLNGNNITMLIPGGE-GPE 90

GO:0003674 "molecular_function" evidence=ND

UNIPROTKB|Q2HJH0 LSM5 "U6 snRNA-associated Sm-like protein LSm5" [Bos taurus (taxid:9913)]

 Score = 335 (123.0 bits), Expect = 2.3e-30, P = 2.3e-30
 Identities = 65/84 (77%), Positives = 74/84 (88%)

Query:     4 NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT 63
             NPSQLLP EL+D+CIGS+I ++MK DKE+VGTL GFD +VNMVLEDVTE+EIT EGRRIT
Sbjct:     8 NPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITPEGRRIT 67

Query:    64 KLDQILLNGNNIAILVPGGSPDPE 87
             KLDQILLNGNNI +LVPGG   PE
Sbjct:    68 KLDQILLNGNNITMLVPGGE-GPE 90

GO:0005634 "nucleus" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|Q9Y4Y9 LSM5 "U6 snRNA-associated Sm-like protein LSm5" [Homo sapiens (taxid:9606)]

 Score = 335 (123.0 bits), Expect = 2.3e-30, P = 2.3e-30
 Identities = 65/84 (77%), Positives = 74/84 (88%)

Query:     4 NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT 63
             NPSQLLP EL+D+CIGS+I ++MK DKE+VGTL GFD +VNMVLEDVTE+EIT EGRRIT
Sbjct:     8 NPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITPEGRRIT 67

Query:    64 KLDQILLNGNNIAILVPGGSPDPE 87
             KLDQILLNGNNI +LVPGG   PE
Sbjct:    68 KLDQILLNGNNITMLVPGGE-GPE 90

GO:0003723 "RNA binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005634 "nucleus" evidence=TAS

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

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

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

GO:0005515 "protein binding" evidence=IPI

MGI|MGI:1913623 Lsm5 "LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 335 (123.0 bits), Expect = 2.3e-30, P = 2.3e-30
 Identities = 65/84 (77%), Positives = 74/84 (88%)

Query:     4 NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT 63
             NPSQLLP EL+D+CIGS+I ++MK DKE+VGTL GFD +VNMVLEDVTE+EIT EGRRIT
Sbjct:     8 NPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITPEGRRIT 67

Query:    64 KLDQILLNGNNIAILVPGGSPDPE 87
             KLDQILLNGNNI +LVPGG   PE
Sbjct:    68 KLDQILLNGNNITMLVPGGE-GPE 90

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0006402 "mRNA catabolic process" evidence=ISO

GO:0008380 "RNA splicing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=ISO

WB|WBGene00003079 lsm-5 [Caenorhabditis elegans (taxid:6239)]

 Score = 327 (120.2 bits), Expect = 1.6e-29, P = 1.6e-29
 Identities = 64/84 (76%), Positives = 72/84 (85%)

Query:     4 NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT 63
             NP+ LLP ELID+CIGSKIWVIMK DKE+VGTL GFD YVNMVLEDV EYE TA+G+R+T
Sbjct:     8 NPNTLLPLELIDKCIGSKIWVIMKNDKEIVGTLTGFDDYVNMVLEDVVEYENTADGKRMT 67

Query:    64 KLDQILLNGNNIAILVPGGSPDPE 87
             KLD ILLNGN+I +LVPGG   PE
Sbjct:    68 KLDTILLNGNHITMLVPGGE-GPE 90

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

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

GO:0040020 "regulation of meiosis" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0006915 "apoptotic process" evidence=IMP

UNIPROTKB|O18694 lsm-5 "Protein LSM-5" [Caenorhabditis elegans (taxid:6239)]

 Score = 327 (120.2 bits), Expect = 1.6e-29, P = 1.6e-29
 Identities = 64/84 (76%), Positives = 72/84 (85%)

Query:     4 NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT 63
             NP+ LLP ELID+CIGSKIWVIMK DKE+VGTL GFD YVNMVLEDV EYE TA+G+R+T
Sbjct:     8 NPNTLLPLELIDKCIGSKIWVIMKNDKEIVGTLTGFDDYVNMVLEDVVEYENTADGKRMT 67

Query:    64 KLDQILLNGNNIAILVPGGSPDPE 87
             KLD ILLNGN+I +LVPGG   PE
Sbjct:    68 KLDTILLNGNHITMLVPGGE-GPE 90

GO:0005515 "protein binding" evidence=IPI

FB|FBgn0035675 CG6610 [Drosophila melanogaster (taxid:7227)]

 Score = 304 (112.1 bits), Expect = 4.5e-27, P = 4.5e-27
 Identities = 58/79 (73%), Positives = 69/79 (87%)

Query:     4 NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT 63
             N S L+P EL+D+CIGS+I +IMK DKE+VGTL GFD +VNM+L+DVTEYE T +GRRIT
Sbjct:     9 NISTLMPLELVDKCIGSRIHIIMKNDKEMVGTLLGFDDFVNMLLDDVTEYENTPDGRRIT 68

Query:    64 KLDQILLNGNNIAILVPGG 82
             KLDQILLNGNNI +LVPGG
Sbjct:    69 KLDQILLNGNNITMLVPGG 87

GO:0005688 "U6 snRNP" evidence=NAS

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

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

GO:0005681 "spliceosomal complex" evidence=ISS

DICTYBASE|DDB_G0268716 lsm5 "putative U6 small nuclear ribonucleoparticle-associated protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 287 (106.1 bits), Expect = 2.9e-25, P = 2.9e-25
 Identities = 53/77 (68%), Positives = 63/77 (81%)

Query:     6 SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKL 65
             SQLLP ELI++CIGS+IW+ MK DKE VGTL GFD YVN+ L+DVTEYE T EG +  KL
Sbjct:    14 SQLLPLELIEKCIGSRIWIAMKNDKEFVGTLLGFDAYVNIFLKDVTEYEYTPEGLKTVKL 73

Query:    66 DQILLNGNNIAILVPGG 82
             D ILLNGN++ +LVPGG
Sbjct:    74 DNILLNGNHVCLLVPGG 90

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

ASPGD|ASPL0000026389 AN5679 [Emericella nidulans (taxid:162425)]

 Score = 270 (100.1 bits), Expect = 1.8e-23, P = 1.8e-23
 Identities = 53/77 (68%), Positives = 64/77 (83%)

Query:     6 SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKL 65
             SQLLP ELID+C+GS+IW+IMK DKE  GTL GFD YVNMVLEDVTE++ T  G ++ KL
Sbjct:    49 SQLLPLELIDKCVGSRIWIIMKNDKEFSGTLLGFDDYVNMVLEDVTEFDYT--GAQV-KL 105

Query:    66 DQILLNGNNIAILVPGG 82
              +ILLNGNNI +L+PGG
Sbjct:   106 PKILLNGNNICMLIPGG 122

GO:0005730 "nucleolus" evidence=IEA

GO:0005688 "U6 snRNP" evidence=IEA

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

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

GO:0003723 "RNA binding" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P40089	LSM5_YEAST	No assigned EC number	0.4588	0.9195	0.8602	yes	no
Q55EX5	LSM5_DICDI	No assigned EC number	0.6883	0.8850	0.7938	yes	no
Q2HJH0	LSM5_BOVIN	No assigned EC number	0.7974	0.9080	0.8681	yes	no
Q5R628	LSM5_PONAB	No assigned EC number	0.7974	0.9080	0.8681	yes	no
Q9Y4Y9	LSM5_HUMAN	No assigned EC number	0.7974	0.9080	0.8681	yes	no
P62322	LSM5_MOUSE	No assigned EC number	0.7974	0.9080	0.8681	yes	no
O42978	LSM5_SCHPO	No assigned EC number	0.5769	0.8735	0.95	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00020489001	SubName- Full=Chromosome chr5 scaffold_2, whole genome shotgun sequence; (87 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00023663001	SubName- Full=Chromosome chr7 scaffold_31, whole genome shotgun sequence; (97 aa)				•	•	•	•		0.983
	GSVIVG00031776001	hypothetical protein LOC100253870 (172 aa)				•	•	•	•		0.983
	GSVIVG00008837001	SubName- Full=Chromosome chr13 scaffold_210, whole genome shotgun sequence; (113 aa)				•	•	•	•		0.973
	GSVIVG00021594001	SubName- Full=Chromosome chr8 scaffold_23, whole genome shotgun sequence; (80 aa)				•	•	•	•		0.928
	GSVIVG00013856001	SubName- Full=Chromosome chr16 scaffold_10, whole genome shotgun sequence; (98 aa)				•	•	•	•		0.888
	GSVIVG00034053001	SubName- Full=Putative uncharacterized protein (Chromosome chr9 scaffold_7, whole genome shotgu [...] (128 aa)				•	•	•	•		0.874
	GSVIVG00030614001	SubName- Full=Chromosome chr1 scaffold_5, whole genome shotgun sequence; (104 aa)				•	•		•		0.842
	GSVIVG00017697001	SubName- Full=Chromosome chr17 scaffold_16, whole genome shotgun sequence; (86 aa)			•	•	•		•	•	0.796
	GSVIVG00033465001	SubName- Full=Chromosome chr19 scaffold_66, whole genome shotgun sequence; (107 aa)				•	•		•		0.796
	GSVIVG00002878001	SubName- Full=Chromosome chr18 scaffold_137, whole genome shotgun sequence; (132 aa)				•	•	•	•		0.623

---

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	87
cd01732	76	cd01732, LSm5, Like-Sm protein 5	4e-50
smart00651	67	smart00651, Sm, snRNP Sm proteins	3e-18
pfam01423	66	pfam01423, LSM, LSM domain	7e-18
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	8e-15
cd00600	63	cd00600, Sm_like, Sm and related proteins	2e-14
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	6e-11
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	7e-10
PTZ00138	89	PTZ00138, PTZ00138, small nuclear ribonucleoprotei	1e-09
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	2e-08
cd01730	82	cd01730, LSm3, Like-Sm protein 3	5e-08
cd01718	79	cd01718, Sm_E, Sm protein E	6e-08
cd01726	68	cd01726, LSm6, Like-Sm protein 6	1e-07
cd01728	74	cd01728, LSm1, Like-Sm protein 1	2e-07
cd01729	89	cd01729, LSm7, Like-Sm protein 7	8e-07
cd01722	69	cd01722, Sm_F, Sm protein F	1e-05
cd01719	70	cd01719, Sm_G, Sm protein G	2e-05
cd01727	91	cd01727, LSm8, Like-Sm protein 8	2e-04
cd01720	89	cd01720, Sm_D2, Sm protein D2	0.001
cd01723	76	cd01723, LSm4, Like-Sm protein 4	0.002

>gnl|CDD|212479 cd01732, LSm5, Like-Sm protein 5

 Score =  152 bits (385), Expect = 4e-50
 Identities = 65/76 (85%), Positives = 70/76 (92%)

Query: 7  QLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLD 66
          Q+LP ELID+CIGSKIW+IMK DKE VGTL GFD YVNMVLEDVTEYEIT EGR+ITKLD
Sbjct: 1  QILPLELIDKCIGSKIWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLD 60

Query: 67 QILLNGNNIAILVPGG 82
          QILLNGNNIA+LVPGG
Sbjct: 61 QILLNGNNIAMLVPGG 76

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

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

 Score = 71.0 bits (175), Expect = 3e-18
 Identities = 26/68 (38%), Positives = 41/68 (60%), Gaps = 2/68 (2%)

Query: 13 LIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNG 72
           + + IG ++ V +K  +E  GTLKGFD ++N+VLEDV E     +G +  KL  + + G
Sbjct: 2  FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVK--DGEKKRKLGLVFIRG 59

Query: 73 NNIAILVP 80
          NNI  ++ 
Sbjct: 60 NNIVYIIL 67

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

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

 Score = 69.9 bits (172), Expect = 7e-18
 Identities = 27/69 (39%), Positives = 46/69 (66%), Gaps = 3/69 (4%)

Query: 12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLN 71
          + + + +G ++ V +K  +EL GTLKGFD ++N+VL+DV E   T +  ++ KL  +L+ 
Sbjct: 1  KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEE---TIKDGKVNKLGLVLIR 57

Query: 72 GNNIAILVP 80
          GNNI ++ P
Sbjct: 58 GNNIVLISP 66

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

 Score = 62.7 bits (153), Expect = 8e-15
 Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 9  LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKL-DQ 67
          LP   + + +  ++ V +K  +E  GTL GFD Y+N+VL+DV E       + + +L  +
Sbjct: 7  LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGE 66

Query: 68 ILLNGNNIAILVP 80
          +L+ G+NI ++ P
Sbjct: 67 VLIRGDNIVLISP 79

Length = 79

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

 Score = 61.5 bits (150), Expect = 2e-14
 Identities = 23/62 (37%), Positives = 35/62 (56%), Gaps = 3/62 (4%)

Query: 14 IDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGN 73
          +   IG  + V +K  + L GTL  FD Y+N+VL+DV E   T    ++  L  +L+ G+
Sbjct: 1  LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVE---TGRDGKVRVLGLVLIRGS 57

Query: 74 NI 75
          NI
Sbjct: 58 NI 59

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|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1

 Score = 52.6 bits (127), Expect = 6e-11
 Identities = 24/66 (36%), Positives = 41/66 (62%), Gaps = 3/66 (4%)

Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
          P ++++  +   + V +KG KE+ G LKGFD ++N+VLE+    E   EG  + KL  +L
Sbjct: 2  PLDVLNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENA---EEIIEGESVRKLGTVL 58

Query: 70 LNGNNI 75
          + G+N+
Sbjct: 59 VRGDNV 64

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

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

 Score = 50.0 bits (120), Expect = 7e-10
 Identities = 20/71 (28%), Positives = 45/71 (63%), Gaps = 3/71 (4%)

Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
          P ++++  + S + V +KG +E  G L+G+D+++N+VL++  E     +G  + KL +++
Sbjct: 5  PLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEE---IQDGEVVRKLGKVV 61

Query: 70 LNGNNIAILVP 80
          + G+N+  + P
Sbjct: 62 IRGDNVVYVSP 72

Length = 72

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

 Score = 49.7 bits (119), Expect = 1e-09
 Identities = 21/58 (36%), Positives = 33/58 (56%), Gaps = 2/58 (3%)

Query: 21 KIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAIL 78
          +IW+    +  + G + GFD Y+NMVL+D  E       R+   L +ILL G+NI ++
Sbjct: 30 QIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRK--DLGRILLKGDNITLI 85

Length = 89

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

 Score = 46.3 bits (110), Expect = 2e-08
 Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 4/72 (5%)

Query: 10 PSELIDRCIGSKIWVIMKGD-KELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQI 68
          P++ +   +GS+I V MKGD  +L G L   D Y+N+ L D  E     + R    L  +
Sbjct: 1  PNKKVKSLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVGEEKVR---SLGTV 57

Query: 69 LLNGNNIAILVP 80
          +L GNNI ++ P
Sbjct: 58 VLRGNNILLIQP 69

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

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

 Score = 45.3 bits (108), Expect = 5e-08
 Identities = 17/44 (38%), Positives = 29/44 (65%)

Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEY 53
          P +LI   +  +++V ++GD+EL G L  +D ++NM+L DV E 
Sbjct: 2  PLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEET 45

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|212465 cd01718, Sm_E, Sm protein E

 Score = 44.9 bits (107), Expect = 6e-08
 Identities = 21/54 (38%), Positives = 32/54 (59%), Gaps = 2/54 (3%)

Query: 22 IWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNI 75
          IW+  + D  + G + GFD Y+N+VL+D  E  +    R+   L +ILL G+NI
Sbjct: 23 IWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVHLKTNTRK--PLGRILLKGDNI 74

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 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. Length = 79

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

 Score = 44.0 bits (105), Expect = 1e-07
 Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 3/66 (4%)

Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
          PS+ + + IG  + V +K   E  G L   D Y+N+VLED  EY    +G+ + K     
Sbjct: 2  PSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEY---VDGQLVAKYGDAF 58

Query: 70 LNGNNI 75
          + GNN+
Sbjct: 59 IRGNNV 64

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 = 43.7 bits (104), Expect = 2e-07
 Identities = 15/41 (36%), Positives = 25/41 (60%)

Query: 18 IGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAE 58
          +  KI V+++  ++L+G L+ FD + N+VLED  E  I   
Sbjct: 11 LDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERIIVGN 51

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|212476 cd01729, LSm7, Like-Sm protein 7

 Score = 42.6 bits (101), Expect = 8e-07
 Identities = 16/36 (44%), Positives = 24/36 (66%)

Query: 18 IGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEY 53
          +  KI V  +G +E+ G LKG+D  +N+VL+D  EY
Sbjct: 11 VDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEY 46

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|212469 cd01722, Sm_F, Sm protein F

 Score = 38.7 bits (91), Expect = 1e-05
 Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 8/72 (11%)

Query: 4  NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT 63
          NP   L     +   G  + V +K   E  GTL   D Y+N+ L +  EY    +G+   
Sbjct: 1  NPKPFL-----NGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYI---DGKFTG 52

Query: 64 KLDQILLNGNNI 75
           L ++L+  NN+
Sbjct: 53 NLGEVLIRCNNV 64

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|212466 cd01719, Sm_G, Sm protein G

 Score = 38.7 bits (91), Expect = 2e-05
 Identities = 16/60 (26%), Positives = 38/60 (63%), Gaps = 3/60 (5%)

Query: 21 KIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP 80
          ++ + + G++++ G L+GFD ++N+VL+D    E   +G + T +  +++ GN+I ++  
Sbjct: 12 RLSLKLNGNRKVSGVLRGFDPFMNLVLDDA--VEEVGDGEK-TPIGMVVIRGNSIIMIEA 68

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|212474 cd01727, LSm8, Like-Sm protein 8

 Score = 36.0 bits (84), Expect = 2e-04
 Identities = 19/47 (40%), Positives = 28/47 (59%), Gaps = 1/47 (2%)

Query: 32 LVGTLKGFDVYVNMVLEDVTEYEITA-EGRRITKLDQILLNGNNIAI 77
          +VGTLKGFD   N++L +  E   ++ EG     L   LL G+N+A+
Sbjct: 22 IVGTLKGFDQTTNLILSNCHERVYSSDEGVEEVPLGLYLLRGDNVAV 68

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

>gnl|CDD|212467 cd01720, Sm_D2, Sm protein D2

 Score = 34.6 bits (80), Expect = 0.001
 Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 17/63 (26%)

Query: 30 KELVGTLKGFDVYVNMVLEDV----TEYEITAEG---------RRITKLDQILLNGNNIA 76
          K+L+  +K FD + NMVLE+V    TE   T +G         R I+K+    L G+++ 
Sbjct: 27 KKLLARVKAFDRHCNMVLENVKEMWTEVPKTGKGKKSKPVNKDRFISKM---FLRGDSV- 82

Query: 77 ILV 79
          ILV
Sbjct: 83 ILV 85

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 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. Length = 89

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

 Score = 32.9 bits (76), Expect = 0.002
 Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 2/67 (2%)

Query: 9  LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQI 68
          LP  L+    G  + V +K  +   G L   D ++N+ L++V     + +G R  K+ + 
Sbjct: 1  LPLSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVI--CTSKDGDRFWKMPEC 58

Query: 69 LLNGNNI 75
           + GN I
Sbjct: 59 YIRGNTI 65

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	87
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.95
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.94
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.94
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.93
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.93
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.92
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.92
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.92
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.92
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.91
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.91
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.9
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.9
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.9
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.9
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.9
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.89
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.89
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.88
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.87
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.87
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.86
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.85
KOG1775	84	consensus U6 snRNA-associated Sm-like protein [RNA	99.85
KOG1780	77	consensus Small Nuclear ribonucleoprotein G [RNA p	99.84
KOG3482	79	consensus Small nuclear ribonucleoprotein (snRNP)	99.82
KOG3460	91	consensus Small nuclear ribonucleoprotein (snRNP)	99.77
KOG1783	77	consensus Small nuclear ribonucleoprotein F [RNA p	99.77
KOG1781	108	consensus Small Nuclear ribonucleoprotein splicing	99.72
KOG1774	88	consensus Small nuclear ribonucleoprotein E [RNA p	99.66
KOG3293	134	consensus Small nuclear ribonucleoprotein (snRNP)	99.65
KOG3168	177	consensus U1 snRNP component [Transcription]	99.63
KOG1782	129	consensus Small Nuclear ribonucleoprotein splicing	99.6
KOG1784	96	consensus Small Nuclear ribonucleoprotein splicing	99.58
KOG3448	96	consensus Predicted snRNP core protein [RNA proces	99.46
KOG3172	119	consensus Small nuclear ribonucleoprotein Sm D3 [R	99.45
KOG3428	109	consensus Small nuclear ribonucleoprotein SMD1 and	99.22
KOG3459	114	consensus Small nuclear ribonucleoprotein (snRNP)	99.14
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	98.46
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	98.21
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	97.96
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	97.39
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	97.16
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	96.84
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	96.76
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	96.61
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	96.31
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	95.81
COG1923	77	Hfq Uncharacterized host factor I protein [General	95.8
KOG1073	361	consensus Uncharacterized mRNA-associated protein	95.68
PRK14638	150	hypothetical protein; Provisional	95.47
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	95.41
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	95.18
PRK02001	152	hypothetical protein; Validated	95.13
PRK14639	140	hypothetical protein; Provisional	95.03
PRK14091	165	RNA-binding protein Hfq; Provisional	94.99
PRK14644	136	hypothetical protein; Provisional	94.96
PRK14091	165	RNA-binding protein Hfq; Provisional	94.77
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	94.02
PRK14640	152	hypothetical protein; Provisional	93.51
PRK06955	300	biotin--protein ligase; Provisional	93.33
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	93.07
PRK14633	150	hypothetical protein; Provisional	92.99
PRK14642	197	hypothetical protein; Provisional	92.93
COG0779	153	Uncharacterized protein conserved in bacteria [Fun	92.84
PRK14645	154	hypothetical protein; Provisional	92.65
PRK14636	176	hypothetical protein; Provisional	91.86
PRK14632	172	hypothetical protein; Provisional	91.43
PRK14643	164	hypothetical protein; Provisional	91.32
PRK13325	592	bifunctional biotin--[acetyl-CoA-carboxylase] liga	91.3
PRK00092	154	ribosome maturation protein RimP; Reviewed	91.24
PRK14634	155	hypothetical protein; Provisional	91.12
PRK14646	155	hypothetical protein; Provisional	90.8
PRK14647	159	hypothetical protein; Provisional	90.47
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	90.19
PRK14631	174	hypothetical protein; Provisional	89.75
PRK14641	173	hypothetical protein; Provisional	89.02
PRK14637	151	hypothetical protein; Provisional	88.62
TIGR00121	237	birA_ligase birA, biotin-[acetyl-CoA-carboxylase]	88.21
PRK08330	236	biotin--protein ligase; Provisional	87.7
PRK10898	353	serine endoprotease; Provisional	81.47
COG0340	238	BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenz	81.2
PF11607	101	DUF3247: Protein of unknown function (DUF3247); In	80.83
PRK14630	143	hypothetical protein; Provisional	80.09

>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=99.95  E-value=1.6e-27  Score=143.65  Aligned_cols=75  Identities=83%  Similarity=1.339  Sum_probs=68.9

Q ss_pred             cCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342            8 LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus         8 ~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      .+|+++|.++++++|+|++++||.+.|+|.|||+|||++|+||+|++..+++.+.+.+|.++|||++|++|+|.+
T Consensus         2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p~~   76 (76)
T cd01732           2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVPGG   76 (76)
T ss_pred             cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEECCC
Confidence            589999999999999999999999999999999999999999999986555555789999999999999999764

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.

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.94  E-value=2.2e-26  Score=137.15  Aligned_cols=70  Identities=29%  Similarity=0.688  Sum_probs=64.7

Q ss_pred             cCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342            8 LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP   80 (87)
Q Consensus         8 ~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~   80 (87)
                      ..|+++|+++++++|.|+|+||+.|+|+|.|||+|||++|+||.|++   +++..+.+|.++|||++|++|++
T Consensus         3 ~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~---~~~~~~~lg~v~iRG~~V~~i~~   72 (72)
T PRK00737          3 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQ---DGEVVRKLGKVVIRGDNVVYVSP   72 (72)
T ss_pred             cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEc---CCCeEeEcCcEEEeCCEEEEEcC
Confidence            47999999999999999999999999999999999999999999975   44557899999999999999974

>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=99.94  E-value=3.7e-26  Score=134.58  Aligned_cols=68  Identities=31%  Similarity=0.644  Sum_probs=63.0

Q ss_pred             cHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342           10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP   80 (87)
Q Consensus        10 Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~   80 (87)
                      |+++|+++++++|+|+|+||+.|+|+|.|||+|||++|+||+|++.   +...+.+|.++|||++|++|++
T Consensus         1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~---~~~~~~lg~~~iRG~~I~~i~~   68 (68)
T cd01731           1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDD---GEPVRKYGRVVIRGDNVLFISP   68 (68)
T ss_pred             ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEec---CCeEeEcCcEEEeCCEEEEEcC
Confidence            8999999999999999999999999999999999999999999863   2346899999999999999975

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.

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

Probab=99.93  E-value=9.1e-26  Score=132.72  Aligned_cols=67  Identities=30%  Similarity=0.535  Sum_probs=62.3

Q ss_pred             cHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEE
Q 041342           10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILV   79 (87)
Q Consensus        10 Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~   79 (87)
                      |+++|+++++++|+|+|+||++|+|+|.|||+|||++|+||+|..   ++...+.+|.++|||++|.+|+
T Consensus         1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~---~~~~~~~~~~v~IRG~~I~~I~   67 (67)
T cd01726           1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYV---NGQLKNKYGDAFIRGNNVLYIS   67 (67)
T ss_pred             CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEe---CCceeeEeCCEEEECCEEEEEC
Confidence            899999999999999999999999999999999999999999864   4555789999999999999985

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=99.93  E-value=2e-25  Score=135.88  Aligned_cols=72  Identities=29%  Similarity=0.585  Sum_probs=64.3

Q ss_pred             CcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccC-C---------eeeEeeCeEEEcCCcEEEE
Q 041342            9 LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAE-G---------RRITKLDQILLNGNNIAIL   78 (87)
Q Consensus         9 ~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~-g---------~~~~~~g~v~IRG~~I~~I   78 (87)
                      .|+++|+.+++++|.|+++|||.|.|+|.|||+||||+|+||+|++.... +         ...+.+|.+||||++|++|
T Consensus         1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i   80 (82)
T cd01730           1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILV   80 (82)
T ss_pred             CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEE
Confidence            49999999999999999999999999999999999999999999985321 1         2468999999999999999


Q ss_pred             Ee
Q 041342           79 VP   80 (87)
Q Consensus        79 ~~   80 (87)
                      ++
T Consensus        81 ~~   82 (82)
T cd01730          81 SP   82 (82)
T ss_pred             CC
Confidence            74

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.

>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=99.92  E-value=7.9e-25  Score=130.58  Aligned_cols=69  Identities=25%  Similarity=0.561  Sum_probs=62.8

Q ss_pred             HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342           11 SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus        11 l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      -..|+++++|+|+|+|++|+.|+|+|.|||+||||+|+||+|+.   ++...+.+|.++|||++|++|++.+
T Consensus         2 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~---~~~~~~~lg~v~IRG~~I~~i~~~~   70 (72)
T cd01719           2 PPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVN---SGGEKNNIGMVVIRGNSIVMLEALE   70 (72)
T ss_pred             chhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEc---cCCceeEeceEEECCCEEEEEEccc
Confidence            45789999999999999999999999999999999999999986   3345789999999999999999874

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.

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

Probab=99.92  E-value=6.1e-25  Score=129.59  Aligned_cols=68  Identities=28%  Similarity=0.489  Sum_probs=62.3

Q ss_pred             CcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEE
Q 041342            9 LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILV   79 (87)
Q Consensus         9 ~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~   79 (87)
                      .|+.+|+++++++|+|+|+||+.|+|+|.|||+|||++|+||+|+.   ++.....+|.++|||++|.+|+
T Consensus         1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~---~~~~~~~lg~~~IRG~~I~~i~   68 (68)
T cd01722           1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYI---DGKSTGNLGEVLIRCNNVLYIR   68 (68)
T ss_pred             CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEe---CCccccCcCcEEEECCEEEEEC
Confidence            4899999999999999999999999999999999999999999874   4444678999999999999984

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.

>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=99.92  E-value=1.4e-24  Score=133.75  Aligned_cols=74  Identities=24%  Similarity=0.490  Sum_probs=65.2

Q ss_pred             cCcHHHHhhhc--CCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccC--C--------eeeEeeCeEEEcCCcE
Q 041342            8 LLPSELIDRCI--GSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAE--G--------RRITKLDQILLNGNNI   75 (87)
Q Consensus         8 ~~Pl~~L~~~l--~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~--g--------~~~~~~g~v~IRG~~I   75 (87)
                      ..|+++|.+++  +++|.|+|++|+.+.|+|.|||+|||++|+||+|.+...+  +        ...+.+|.+||||++|
T Consensus         1 ~gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~V   80 (87)
T cd01720           1 TGPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSV   80 (87)
T ss_pred             CChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEE
Confidence            37999999998  8999999999999999999999999999999999875421  1        2356899999999999


Q ss_pred             EEEEeC
Q 041342           76 AILVPG   81 (87)
Q Consensus        76 ~~I~~~   81 (87)
                      ++|++.
T Consensus        81 v~Is~~   86 (87)
T cd01720          81 ILVLRN   86 (87)
T ss_pred             EEEecC
Confidence            999875

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.

>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=99.92  E-value=2.1e-24  Score=131.29  Aligned_cols=73  Identities=26%  Similarity=0.528  Sum_probs=63.5

Q ss_pred             cHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCC-----eeeEeeCeEEEcCCcEEEEEeCC
Q 041342           10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEG-----RRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus        10 Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g-----~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      +...|.++++++|.|+++|||.|.|+|.|||+||||+|++|+|+....+.     ...+.+|.++|||++|++|++.+
T Consensus         3 ~~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~   80 (81)
T cd01729           3 SILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD   80 (81)
T ss_pred             chhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence            34459999999999999999999999999999999999999999753221     24688999999999999998765

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.

>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=99.91  E-value=4.2e-24  Score=129.52  Aligned_cols=74  Identities=31%  Similarity=0.552  Sum_probs=65.0

Q ss_pred             CCCcCcHHHHhhhcCC--EEEEEEc--CCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342            5 PSQLLPSELIDRCIGS--KIWVIMK--GDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP   80 (87)
Q Consensus         5 ~~~~~Pl~~L~~~l~k--~V~V~l~--dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~   80 (87)
                      +.+..|++.|.+++++  +|.|+++  +|+.++|+|.|||+|||++|+||+|+..  .+...+.+|.++|||++|++|++
T Consensus         2 ~~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~--~~~~~~~lG~iliRGnnV~~I~p   79 (79)
T cd01718           2 KVMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHL--KTKTRKPLGRILLKGDNITLIQN   79 (79)
T ss_pred             ccccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEec--CCceEeEcCcEEEeCCEEEEEcC
Confidence            4678999999999999  6777776  9999999999999999999999999863  23456789999999999999984

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.

>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=99.91  E-value=8e-24  Score=126.92  Aligned_cols=71  Identities=21%  Similarity=0.404  Sum_probs=63.1

Q ss_pred             cHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342           10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP   80 (87)
Q Consensus        10 Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~   80 (87)
                      ++..|.++++++|.|.++|||.|.|+|.|||+|||++|+||.|+....+....+.+|.++|||++|++|+.
T Consensus         3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~   73 (74)
T cd01728           3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE   73 (74)
T ss_pred             chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence            56789999999999999999999999999999999999999998754322246889999999999999975

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.

>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=99.90  E-value=1.7e-23  Score=125.81  Aligned_cols=71  Identities=24%  Similarity=0.372  Sum_probs=64.5

Q ss_pred             CcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342            9 LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG   81 (87)
Q Consensus         9 ~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~   81 (87)
                      .|+++|+++.|++|.|+|++|+.++|+|.+||+|||++|+||+++.  .+|+....++.+||||++|.+|+..
T Consensus         1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~--~~g~~~~~~~~v~IRG~~I~~i~~p   71 (76)
T cd01723           1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTS--KDGDKFWKMPECYIRGNTIKYLRVP   71 (76)
T ss_pred             CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEEC--CCCcEeeeCCcEEEeCCEEEEEEcC
Confidence            4999999999999999999999999999999999999999999874  3565556789999999999999854

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.

>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=99.90  E-value=3e-23  Score=124.11  Aligned_cols=71  Identities=30%  Similarity=0.470  Sum_probs=63.3

Q ss_pred             HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcc-CCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342           12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITA-EGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus        12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~-~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      ..|.++++++|+|+++|||.|.|+|.|||+|||++|++|.|+.... ++...+.+|.++|||++|++|++.+
T Consensus         2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d   73 (74)
T cd01727           2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEID   73 (74)
T ss_pred             hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccC
Confidence            4689999999999999999999999999999999999999986532 3445778999999999999999865

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.

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

Probab=99.90  E-value=3.1e-23  Score=125.23  Aligned_cols=74  Identities=34%  Similarity=0.694  Sum_probs=63.7

Q ss_pred             CCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCee-eEee-CeEEEcCCcEEEEEe
Q 041342            6 SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRR-ITKL-DQILLNGNNIAILVP   80 (87)
Q Consensus         6 ~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~-~~~~-g~v~IRG~~I~~I~~   80 (87)
                      ....|+++|+++++++|.|+|+||++|+|+|.|||+|||++|+||+|+.. .++.. .+.+ +.++|||++|++|.+
T Consensus         4 ~~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~-~~~~~~~~~~~~~~~IRG~~I~~I~~   79 (79)
T COG1958           4 LGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIIS-HDGEKNVRRLGGEVLIRGDNIVLISP   79 (79)
T ss_pred             ccCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEec-cCCccccceeccEEEEECCcEEEEeC
Confidence            34578999999999999999999999999999999999999999999974 23433 3444 499999999999863

>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=99.90  E-value=2.7e-23  Score=125.61  Aligned_cols=69  Identities=25%  Similarity=0.432  Sum_probs=61.2

Q ss_pred             HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccC-------CeeeEeeCeEEEcCCcEEEEEe
Q 041342           12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAE-------GRRITKLDQILLNGNNIAILVP   80 (87)
Q Consensus        12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~-------g~~~~~~g~v~IRG~~I~~I~~   80 (87)
                      +.|.++++++|.|.++|||.+.|+|.|||+||||+|+||.|++....       +.+.+.+|+++|||++|++|+.
T Consensus         3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v   78 (79)
T cd01717           3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV   78 (79)
T ss_pred             chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence            46899999999999999999999999999999999999999875321       2356899999999999999974

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.

>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=99.90  E-value=4.8e-23  Score=122.19  Aligned_cols=69  Identities=26%  Similarity=0.422  Sum_probs=63.0

Q ss_pred             cHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342           10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG   81 (87)
Q Consensus        10 Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~   81 (87)
                      |+++|+++.|++|+|+|+||.+|+|+|.++|+|||++|+||.+..  .+|+ ...++.+||||++|.+|...
T Consensus         1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~--~~g~-~~~~~~v~IRG~nI~~v~lP   69 (70)
T cd01721           1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTA--RDGR-VSQLEQVYIRGSKIRFFILP   69 (70)
T ss_pred             ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEEC--CCCc-EeEcCcEEEeCCEEEEEEeC
Confidence            889999999999999999999999999999999999999998864  3554 56789999999999999865

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.

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

Probab=99.89  E-value=1.3e-22  Score=118.39  Aligned_cols=67  Identities=31%  Similarity=0.547  Sum_probs=61.1

Q ss_pred             HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342           12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP   80 (87)
Q Consensus        12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~   80 (87)
                      .+|+++++++|+|+++||+.|+|+|.+||+|||++|++|.|+..  ++.+.+.+|.+||||++|++|++
T Consensus         1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~--~~~~~~~~~~~~irG~~I~~I~~   67 (67)
T PF01423_consen    1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIK--NGPEKRSLGLVFIRGSNIRYISL   67 (67)
T ss_dssp             HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEET--TESEEEEEEEEEEEGGGEEEEEE
T ss_pred             ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEEC--CCCcEeECcEEEEECCEEEEEEC
Confidence            47999999999999999999999999999999999999999973  22268899999999999999975

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=99.89  E-value=1.1e-22  Score=118.52  Aligned_cols=66  Identities=39%  Similarity=0.718  Sum_probs=60.4

Q ss_pred             HHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342           13 LIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP   80 (87)
Q Consensus        13 ~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~   80 (87)
                      +|+++++++|+|+++||+.+.|+|.+||+|||++|+||+|+..  +..+.+.+|.+||||++|++|++
T Consensus         2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~--~~~~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651        2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVK--DGEKKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEec--CCcEEeEeCCEEEcCCEEEEEeC
Confidence            6899999999999999999999999999999999999999874  22457899999999999999974

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

>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=99.88  E-value=6.8e-22  Score=118.82  Aligned_cols=69  Identities=19%  Similarity=0.333  Sum_probs=61.9

Q ss_pred             HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccC---CeeeEeeCeEEEcCCcEEEEEe
Q 041342           12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAE---GRRITKLDQILLNGNNIAILVP   80 (87)
Q Consensus        12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~---g~~~~~~g~v~IRG~~I~~I~~   80 (87)
                      +.|+++++++|+|.++|||.|.|+|.|||++|||+|+||.|+....+   ..+.+.+|+++|||++|++|+.
T Consensus         3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v   74 (75)
T cd06168           3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV   74 (75)
T ss_pred             hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence            46899999999999999999999999999999999999999985422   2357899999999999999974

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

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.87  E-value=1e-21  Score=121.43  Aligned_cols=74  Identities=28%  Similarity=0.482  Sum_probs=64.0

Q ss_pred             CCcCcHHHHhhhcCC--EEEEEEcC--CcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342            6 SQLLPSELIDRCIGS--KIWVIMKG--DKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG   81 (87)
Q Consensus         6 ~~~~Pl~~L~~~l~k--~V~V~l~d--gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~   81 (87)
                      .+..|+..+.+++.+  +|.|.+.|  ++++.|+|.|||+|||++|+||+|+..  ++...+.+|.++|||++|++|++.
T Consensus        11 ~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~--~~~~~~~lG~ilIRGnnV~~I~~~   88 (89)
T PTZ00138         11 IMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYT--KKNTRKDLGRILLKGDNITLIMAA   88 (89)
T ss_pred             eecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEec--CCceeeEcCeEEEcCCEEEEEEcC
Confidence            568999999999996  57777766  589999999999999999999999863  234568999999999999999875

>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=99.87  E-value=1.8e-21  Score=120.50  Aligned_cols=71  Identities=24%  Similarity=0.341  Sum_probs=64.1

Q ss_pred             cHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCCC
Q 041342           10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGS   83 (87)
Q Consensus        10 Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~~   83 (87)
                      ++.+|+++.|++|+|+|+||..|+|+|.++|.|||++|+||+++.   ++.....++.++|||++|.+|...+.
T Consensus         2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~---~~~~~~~~~~v~IRG~nI~yi~lPd~   72 (90)
T cd01724           2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTL---KGRNPVPLDTLSIRGNNIRYFILPDS   72 (90)
T ss_pred             HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEc---CCCceeEcceEEEeCCEEEEEEcCCc
Confidence            688999999999999999999999999999999999999999885   33346789999999999999987653

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.

>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=99.86  E-value=4.1e-21  Score=110.49  Aligned_cols=63  Identities=32%  Similarity=0.566  Sum_probs=57.4

Q ss_pred             HhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEE
Q 041342           14 IDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILV   79 (87)
Q Consensus        14 L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~   79 (87)
                      |++++|++|+|+++||+.|.|+|.+||+|||++|+||.|++.  + ...+.++.+||||++|.+|.
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~--~-~~~~~~~~~~irG~~I~~I~   63 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIK--E-GKKRVLGLVLIRGDNVRLVT   63 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEec--C-CcEEECCeEEEECCEEEEEC
Confidence            578899999999999999999999999999999999999874  2 35789999999999999874

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.

>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=99.85  E-value=6.3e-21  Score=115.95  Aligned_cols=72  Identities=19%  Similarity=0.339  Sum_probs=62.5

Q ss_pred             CcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCe-eeEeeCeEEEcCCcEEEEEeCC
Q 041342            9 LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGR-RITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus         9 ~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~-~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      +|+++|+++.|++|.|+|++|..|+|+|.++|+|||++|+||+++..  ++. ....++.++|||++|.+|+..+
T Consensus         1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~--~~~~~~~~~~~v~IRG~~I~~I~lp~   73 (81)
T cd01725           1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDP--EKYPHMLSVKNCFIRGSVVRYVQLPA   73 (81)
T ss_pred             ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcC--CCcccccccCeEEEECCEEEEEEeCh
Confidence            48899999999999999999999999999999999999999987642  221 2356799999999999998654

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.

>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=99.85  E-value=1e-20  Score=114.38  Aligned_cols=71  Identities=20%  Similarity=0.375  Sum_probs=62.9

Q ss_pred             CcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342            7 QLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP   80 (87)
Q Consensus         7 ~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~   80 (87)
                      ...+..+|+++.|+.|.|+|+||..|+|+|.++|+|||++|+||++..  +++ ....+|.++|||++|.+|+.
T Consensus         7 ~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~--~~~-~~~~~~~v~IRG~nI~yI~l   77 (78)
T cd01733           7 ENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIID--RNG-KQVQVEEIMVTGRNIRYVHI   77 (78)
T ss_pred             hchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEc--CCC-ceeECCcEEEECCEEEEEEc
Confidence            356788999999999999999999999999999999999999998774  233 35579999999999999975

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.

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

Probab=99.85  E-value=1.8e-21  Score=116.23  Aligned_cols=84  Identities=79%  Similarity=1.237  Sum_probs=78.7

Q ss_pred             CCCCCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342            3 HNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus         3 ~~~~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      ++|+..+|++++.++++.++||.+++.|++.|+|.|||.|.|++|+|++|+...++|+...+++++++.|++|.+..+.+
T Consensus         1 ~n~~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPGG   80 (84)
T KOG1775|consen    1 TNPSTLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPGG   80 (84)
T ss_pred             CChhhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecCC
Confidence            47889999999999999999999999999999999999999999999999987778877889999999999999999999


Q ss_pred             CCCC
Q 041342           83 SPDP   86 (87)
Q Consensus        83 ~p~~   86 (87)
                      .|+|
T Consensus        81 e~~E   84 (84)
T KOG1775|consen   81 EGPE   84 (84)
T ss_pred             CCCC
Confidence            8764

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

Probab=99.84  E-value=5e-21  Score=113.66  Aligned_cols=71  Identities=23%  Similarity=0.507  Sum_probs=62.9

Q ss_pred             cCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCCC
Q 041342            8 LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGS   83 (87)
Q Consensus         8 ~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~~   83 (87)
                      ..|  .|.+|++|++.+++..||.+.|+|+|||.|||+||++|+|...  ++ ....+|.++|||++|+.+.+.+.
T Consensus         5 g~P--eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~--~~-~~~~ig~~vIrgnsiv~~eaL~~   75 (77)
T KOG1780|consen    5 GHP--ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNG--DG-DKNNIGMVVIRGNSIVMVEALER   75 (77)
T ss_pred             cCc--hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecC--cC-CcceeeeEEEeccEEEEEeeccc
Confidence            356  7999999999999999999999999999999999999999853  33 35789999999999999987653

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

Probab=99.82  E-value=6.1e-20  Score=108.72  Aligned_cols=77  Identities=26%  Similarity=0.400  Sum_probs=70.2

Q ss_pred             CCCCCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342            3 HNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus         3 ~~~~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      ++.++..|-.+|+.+.+|.|.|+|+.|.+|+|+|.+.|.|||+.|.+|+|+.   +|.....+|.++||.+||.+|...+
T Consensus         2 ~a~~PvNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~i---dG~~~g~lGEilIRCNNvlyi~gv~   78 (79)
T KOG3482|consen    2 SAKQPVNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYI---DGVSTGNLGEILIRCNNVLYIRGVP   78 (79)
T ss_pred             CCcccCCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhh---cccccccceeEEEEeccEEEEecCC
Confidence            4556679999999999999999999999999999999999999999999986   7777889999999999999997543

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

Probab=99.77  E-value=8.9e-20  Score=110.53  Aligned_cols=75  Identities=29%  Similarity=0.507  Sum_probs=66.9

Q ss_pred             CcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCC----------eeeEeeCeEEEcCCcEE
Q 041342            7 QLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEG----------RRITKLDQILLNGNNIA   76 (87)
Q Consensus         7 ~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g----------~~~~~~g~v~IRG~~I~   76 (87)
                      +..|+++|+-+++.+|.|+++++|.++|+|.|||+|.|++|.||+|+.+.-++          ...+.+..+|+||++|+
T Consensus         3 v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vi   82 (91)
T KOG3460|consen    3 VEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVI   82 (91)
T ss_pred             ccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEE
Confidence            56899999999999999999999999999999999999999999999764322          13578899999999999


Q ss_pred             EEEeC
Q 041342           77 ILVPG   81 (87)
Q Consensus        77 ~I~~~   81 (87)
                      +|++.
T Consensus        83 lvspp   87 (91)
T KOG3460|consen   83 LVSPP   87 (91)
T ss_pred             EEcCc
Confidence            99875

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

Probab=99.77  E-value=8.7e-20  Score=108.07  Aligned_cols=74  Identities=27%  Similarity=0.476  Sum_probs=68.7

Q ss_pred             CCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342            6 SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus         6 ~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      ....|-++|.+++|++|.|+|.+|-.|+|+|.++|.||||.|+.++|+.   +|+.++++|.+||||++|.+|+...
T Consensus         3 ~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~---ngql~n~ygdaFirGnnVlyIs~~~   76 (77)
T KOG1783|consen    3 EGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYV---NGQLKNKYGDAFIRGNNVLYISTQK   76 (77)
T ss_pred             cccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHh---cCcccccccceeeccccEEEEEecc
Confidence            3456899999999999999999999999999999999999999999985   7888999999999999999998753

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

Probab=99.72  E-value=9e-19  Score=109.01  Aligned_cols=75  Identities=27%  Similarity=0.486  Sum_probs=66.7

Q ss_pred             CcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCC-----eeeEeeCeEEEcCCcEEEEEeCCC
Q 041342            9 LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEG-----RRITKLDQILLNGNNIAILVPGGS   83 (87)
Q Consensus         9 ~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g-----~~~~~~g~v~IRG~~I~~I~~~~~   83 (87)
                      ..+-.|.+|++++|+|++.+||...|+|.|||+.||+||++++|+..+++.     .+.|++|++++||..+++|++.+.
T Consensus        17 EsilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG   96 (108)
T KOG1781|consen   17 ESILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADG   96 (108)
T ss_pred             hHHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcc
Confidence            346679999999999999999999999999999999999999999876542     246999999999999999998764

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

Probab=99.66  E-value=1.7e-16  Score=95.91  Aligned_cols=75  Identities=29%  Similarity=0.538  Sum_probs=62.4

Q ss_pred             CCcCcHHHHhhhcCC--EEEEEEcC--CcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342            6 SQLLPSELIDRCIGS--KIWVIMKG--DKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG   81 (87)
Q Consensus         6 ~~~~Pl~~L~~~l~k--~V~V~l~d--gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~   81 (87)
                      .+++|++++.+|+..  +|.|.|.+  |-.++|.+.|||+|||+||++|+|...+..  ..+.+|.++++||||..|...
T Consensus         9 vmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~--~rk~lGRilLKGDnItli~~~   86 (88)
T KOG1774|consen    9 VMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTK--SRKELGRILLKGDNITLIQSA   86 (88)
T ss_pred             eecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhcccccc--CCCccccEEEcCCcEEEEeec
Confidence            468999999999985  46666654  889999999999999999999999864322  234899999999999999876


Q ss_pred             C
Q 041342           82 G   82 (87)
Q Consensus        82 ~   82 (87)
                      +
T Consensus        87 ~   87 (88)
T KOG1774|consen   87 G   87 (88)
T ss_pred             C
Confidence            4

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

Probab=99.65  E-value=3.7e-16  Score=100.78  Aligned_cols=73  Identities=21%  Similarity=0.363  Sum_probs=67.7

Q ss_pred             cCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342            8 LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus         8 ~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      ++||++|...-+..+.|+||+|.+|.|.|..+|.+|||.|.+++++.  .||.+...+..++|||++|.++...+
T Consensus         1 mlPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts--~Dgdkf~r~pEcYirGttIkylri~d   73 (134)
T KOG3293|consen    1 MLPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTS--EDGDKFFRMPECYIRGTTIKYLRIPD   73 (134)
T ss_pred             CcchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEec--cCCCceeecceeEEecceeEEEeccH
Confidence            47999999999999999999999999999999999999999999986  47878889999999999999997643

>KOG3168 consensus U1 snRNP component [Transcription]

Probab=99.63  E-value=5.3e-17  Score=109.44  Aligned_cols=76  Identities=28%  Similarity=0.530  Sum_probs=67.2

Q ss_pred             HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEc-------cCCeeeEeeCeEEEcCCcEEEEEeCCCC
Q 041342           12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEIT-------AEGRRITKLDQILLNGNNIAILVPGGSP   84 (87)
Q Consensus        12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~-------~~g~~~~~~g~v~IRG~~I~~I~~~~~p   84 (87)
                      +.|.++++.+++|.++|||.|.|.+.+||.|||++|.+|+|....       .++++.|-+|+|++||++|++.+..+.|
T Consensus         7 skml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegpp   86 (177)
T KOG3168|consen    7 SKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPP   86 (177)
T ss_pred             hHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCC
Confidence            356778999999999999999999999999999999999997542       2456789999999999999999999999


Q ss_pred             CCC
Q 041342           85 DPE   87 (87)
Q Consensus        85 ~~~   87 (87)
                      +++
T Consensus        87 p~s   89 (177)
T KOG3168|consen   87 PPS   89 (177)
T ss_pred             CCc
Confidence            764

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

Probab=99.60  E-value=1.5e-16  Score=102.37  Aligned_cols=74  Identities=20%  Similarity=0.370  Sum_probs=64.2

Q ss_pred             HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCCCCC
Q 041342           12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGSPD   85 (87)
Q Consensus        12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~~p~   85 (87)
                      ..|.+++++++.|.|+|||.+.|.|++||||.|++|++|.|++...+-...+..|..+|||.||+++...+.-+
T Consensus        12 ~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dk   85 (129)
T KOG1782|consen   12 TSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDK   85 (129)
T ss_pred             hHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcch
Confidence            34889999999999999999999999999999999999999987544334577899999999999998766443

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

Probab=99.58  E-value=1.6e-15  Score=93.37  Aligned_cols=72  Identities=24%  Similarity=0.460  Sum_probs=64.5

Q ss_pred             HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcc-CCeeeEeeCeEEEcCCcEEEEEeCCC
Q 041342           12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITA-EGRRITKLDQILLNGNNIAILVPGGS   83 (87)
Q Consensus        12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~-~g~~~~~~g~v~IRG~~I~~I~~~~~   83 (87)
                      +-|..|++++|.|...|||.+.|.|.||||..||+|+++-|+.++. .|.++..+|..+|||+||..|.++..
T Consensus         3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDE   75 (96)
T KOG1784|consen    3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDE   75 (96)
T ss_pred             hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecch
Confidence            3589999999999999999999999999999999999999987642 45667899999999999999987653

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

Probab=99.46  E-value=5.2e-13  Score=81.92  Aligned_cols=71  Identities=18%  Similarity=0.338  Sum_probs=59.8

Q ss_pred             HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342           11 SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus        11 l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      .++++.++|++|.|+|+++-.+.|+|.+.|||.|+.|+|......++ =..--.+..+||||+.|.+|....
T Consensus         4 ysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~k-yPhm~Sv~ncfIRGSvvrYv~l~k   74 (96)
T KOG3448|consen    4 YSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDK-YPHMLSVKNCFIRGSVVRYVQLPK   74 (96)
T ss_pred             HHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCccc-CCCeeeeeeEEEeccEEEEEEeCh
Confidence            57899999999999999999999999999999999999998764211 012356779999999999998653

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

Probab=99.45  E-value=3.3e-13  Score=85.42  Aligned_cols=73  Identities=27%  Similarity=0.393  Sum_probs=65.4

Q ss_pred             CCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342            6 SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG   81 (87)
Q Consensus         6 ~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~   81 (87)
                      ++..|+.+|++.-+.-|+++++.|..|+|.|...|.+||+.|+|.+.+.  .+|. ...+.++||||+.|.++...
T Consensus         2 s~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~--~dg~-vs~le~V~IRGS~IRFlvlP   74 (119)
T KOG3172|consen    2 SVGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTA--RDGR-VSQLEQVFIRGSKIRFLVLP   74 (119)
T ss_pred             ccccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEc--cCCc-ceeeeeEEEecCeEEEEECc
Confidence            4568999999999999999999999999999999999999999999875  3554 66889999999999998754

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

Probab=99.22  E-value=1.5e-10  Score=73.38  Aligned_cols=68  Identities=22%  Similarity=0.384  Sum_probs=61.2

Q ss_pred             HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342           11 SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus        11 l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      +.+|+++.+.+|+|+|++|....|++.+.|.+||..|.++.-+.   .| ++..+..++|||++|.|+....
T Consensus         4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~---~~-~pv~l~~lsirgnniRy~~lpD   71 (109)
T KOG3428|consen    4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTV---KG-EPVRLDTLSIRGNNIRYYILPD   71 (109)
T ss_pred             HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEec---CC-CceeEEEEEeecceEEEEEccC
Confidence            57899999999999999999999999999999999999998764   35 5678999999999999997554

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

Probab=99.14  E-value=5.8e-12  Score=79.89  Aligned_cols=73  Identities=22%  Similarity=0.461  Sum_probs=63.4

Q ss_pred             cCcHHHHhhhcC--CEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcc----CCe------eeEeeCeEEEcCCcE
Q 041342            8 LLPSELIDRCIG--SKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITA----EGR------RITKLDQILLNGNNI   75 (87)
Q Consensus         8 ~~Pl~~L~~~l~--k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~----~g~------~~~~~g~v~IRG~~I   75 (87)
                      .+|++++.....  ..|.|.++|++.+-|++.|||.|.|++|+++.|.|+..    +|.      ..|.+|.+|||||+|
T Consensus        23 ~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsv  102 (114)
T KOG3459|consen   23 TGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSV  102 (114)
T ss_pred             cCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeE
Confidence            479999998887  47899999999999999999999999999999998742    332      268999999999999


Q ss_pred             EEEEe
Q 041342           76 AILVP   80 (87)
Q Consensus        76 ~~I~~   80 (87)
                      +.+..
T Consensus       103 I~v~r  107 (114)
T KOG3459|consen  103 ILVLR  107 (114)
T ss_pred             EEEEe
Confidence            98873

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

Probab=98.46  E-value=1.5e-07  Score=54.98  Aligned_cols=36  Identities=31%  Similarity=0.340  Sum_probs=29.8

Q ss_pred             CEEEEEEcC----CcEEEEEEEEeccccceEEcceEEEEE
Q 041342           20 SKIWVIMKG----DKELVGTLKGFDVYVNMVLEDVTEYEI   55 (87)
Q Consensus        20 k~V~V~l~d----gr~~~G~L~~~D~~mNlvL~~~~e~~~   55 (87)
                      .+|.|.++.    +-.++|.|.+||+|+|++|.|+.|.+.
T Consensus         9 ~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~   48 (66)
T cd01739           9 IRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYR   48 (66)
T ss_pred             cEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhc
Confidence            567776654    226889999999999999999999875

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

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

Probab=98.21  E-value=3.1e-06  Score=50.36  Aligned_cols=65  Identities=11%  Similarity=0.202  Sum_probs=41.5

Q ss_pred             HHHhhhcCCEEEEEEcCCcEEEEEEEEecc---ccceEEcceEEEEEccC--C--eeeEeeCeEEEcCCcEE
Q 041342           12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDV---YVNMVLEDVTEYEITAE--G--RRITKLDQILLNGNNIA   76 (87)
Q Consensus        12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~---~mNlvL~~~~e~~~~~~--g--~~~~~~g~v~IRG~~I~   76 (87)
                      -++..++|++|.|.++||..|+|+|.+++.   -+.++|+.|........  .  .......+++|+++.|+
T Consensus         5 ~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv   76 (77)
T PF14438_consen    5 YLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV   76 (77)
T ss_dssp             HHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred             HHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence            357789999999999999999999999998   89999999887532110  1  12345567777777665

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

Probab=97.96  E-value=7.2e-05  Score=46.81  Aligned_cols=69  Identities=33%  Similarity=0.431  Sum_probs=55.9

Q ss_pred             hhhcCCEEEEEEcCCcEEEEEEEEecc-ccceEEcceEEEEEccCCe--------eeEeeCeEEEcCCcEEEEEeCCCCC
Q 041342           15 DRCIGSKIWVIMKGDKELVGTLKGFDV-YVNMVLEDVTEYEITAEGR--------RITKLDQILLNGNNIAILVPGGSPD   85 (87)
Q Consensus        15 ~~~l~k~V~V~l~dgr~~~G~L~~~D~-~mNlvL~~~~e~~~~~~g~--------~~~~~g~v~IRG~~I~~I~~~~~p~   85 (87)
                      ..|+|++|.+..+++-.|+|+|..+|. ...|.|.++.-+.+  +|.        .......+..||..|..+...+.|+
T Consensus         4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~Gt--E~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~   81 (96)
T PF12701_consen    4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGT--EGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPP   81 (96)
T ss_dssp             CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTE--TTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-
T ss_pred             ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCc--CCCCcCcccCCCCceeeEEEEEccccceEEEEcCCC
Confidence            468999999999999999999999995 89999999986643  221        1346789999999999998877765

>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=97.39  E-value=0.0012  Score=36.02  Aligned_cols=48  Identities=21%  Similarity=0.302  Sum_probs=35.7

Q ss_pred             hcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEc
Q 041342           17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLN   71 (87)
Q Consensus        17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IR   71 (87)
                      .+|++|++.. ++..++|+..++|+...|+++.....      ......|.+++|
T Consensus         1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g~------~~~i~sGdv~~r   48 (48)
T PF02237_consen    1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDGS------IRTISSGDVSLR   48 (48)
T ss_dssp             STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTEE------EEEESSSEEEEE
T ss_pred             CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCCC------EEEEEEEEEEeC
Confidence            3789999999 56777999999999999999765431      123344666654

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 ....

>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=97.16  E-value=0.0028  Score=37.93  Aligned_cols=64  Identities=28%  Similarity=0.386  Sum_probs=49.4

Q ss_pred             hhhcCCEEEEEEcCCcEEEEEEEEec-cccceEEcceEEEEEcc---CCe----eeEeeCeEEEcCCcEEEE
Q 041342           15 DRCIGSKIWVIMKGDKELVGTLKGFD-VYVNMVLEDVTEYEITA---EGR----RITKLDQILLNGNNIAIL   78 (87)
Q Consensus        15 ~~~l~k~V~V~l~dgr~~~G~L~~~D-~~mNlvL~~~~e~~~~~---~g~----~~~~~g~v~IRG~~I~~I   78 (87)
                      .+++|+++.+..+.+-.|+|+|..+| +-.-+.|.|+.-+.++.   ++.    ...-+..++.||+.|..+
T Consensus         2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkDL   73 (74)
T cd01736           2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKDL   73 (74)
T ss_pred             ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccccc
Confidence            36899999999999999999999999 46778899988765421   111    234567899999988654

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.

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

Probab=96.84  E-value=0.0031  Score=36.48  Aligned_cols=37  Identities=14%  Similarity=0.335  Sum_probs=29.1

Q ss_pred             HHhhhcC--CEEEEEEcCCcEEEEEEEEeccccceEEcc
Q 041342           13 LIDRCIG--SKIWVIMKGDKELVGTLKGFDVYVNMVLED   49 (87)
Q Consensus        13 ~L~~~l~--k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~   49 (87)
                      +|+.+..  .+|+|.|.||-.++|.+.+||+|+=++-.+
T Consensus         3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   41 (61)
T cd01716           3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLLESD   41 (61)
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence            3444443  468999999999999999999998666544

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

>TIGR02383 Hfq RNA chaperone Hfq

Probab=96.76  E-value=0.0038  Score=36.08  Aligned_cols=37  Identities=14%  Similarity=0.304  Sum_probs=29.0

Q ss_pred             HHhhhcC--CEEEEEEcCCcEEEEEEEEeccccceEEcc
Q 041342           13 LIDRCIG--SKIWVIMKGDKELVGTLKGFDVYVNMVLED   49 (87)
Q Consensus        13 ~L~~~l~--k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~   49 (87)
                      +|..+..  .+|+|.|.+|-.++|.+.+||+|+=++-.+
T Consensus         7 fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~   45 (61)
T TIGR02383         7 FLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ   45 (61)
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence            3444443  579999999999999999999998666544

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

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=96.61  E-value=0.0068  Score=36.71  Aligned_cols=38  Identities=13%  Similarity=0.281  Sum_probs=30.0

Q ss_pred             HHhhhc--CCEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342           13 LIDRCI--GSKIWVIMKGDKELVGTLKGFDVYVNMVLEDV   50 (87)
Q Consensus        13 ~L~~~l--~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~   50 (87)
                      +|..+.  ...|+|.|.+|-.++|.+.|||+|+=++-.+.
T Consensus        11 fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g   50 (79)
T PRK00395         11 FLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG   50 (79)
T ss_pred             HHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence            444444  35799999999999999999999987765444

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

Probab=96.31  E-value=0.02  Score=39.11  Aligned_cols=64  Identities=19%  Similarity=0.277  Sum_probs=44.2

Q ss_pred             CcHHHHhhhcCCEEEEEEcCCcEEEEEEEEecc-ccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCCC
Q 041342            9 LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDV-YVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGS   83 (87)
Q Consensus         9 ~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~-~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~~   83 (87)
                      .|+ .+..|++|.|.|.+.| +++.|.|..+|. .-|+||-+..|     ++.  .  ..-+|-|-+|..|.....
T Consensus         8 ~p~-~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e-----~~~--~--sv~~I~ghaVk~vevl~~   72 (166)
T PF06372_consen    8 SPL-EWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE-----DGK--R--SVKVIMGHAVKSVEVLSE   72 (166)
T ss_dssp             -HH-HHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T-----TS---E--EEEEE-GGGEEEEEEEE-
T ss_pred             CHH-HHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc-----CCc--e--eEEEEEccceEEEEEccC
Confidence            455 5678999999999999 999999999996 88999986553     332  2  247888999988876543

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

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

Probab=95.81  E-value=0.04  Score=31.81  Aligned_cols=36  Identities=19%  Similarity=0.286  Sum_probs=30.7

Q ss_pred             hcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEE
Q 041342           17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTE   52 (87)
Q Consensus        17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e   52 (87)
                      .+|..|++++..|..++|.+.+||.-.++++-.|.+
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            478999999999999999999999888877655443

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

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

Probab=95.80  E-value=0.044  Score=32.96  Aligned_cols=28  Identities=18%  Similarity=0.389  Sum_probs=24.5

Q ss_pred             CCEEEEEEcCCcEEEEEEEEeccccceE
Q 041342           19 GSKIWVIMKGDKELVGTLKGFDVYVNMV   46 (87)
Q Consensus        19 ~k~V~V~l~dgr~~~G~L~~~D~~mNlv   46 (87)
                      +.+|.|.|.||-.++|.+.+||+|.=++
T Consensus        19 ~i~VtIfLvNG~~L~G~V~sfD~f~VlL   46 (77)
T COG1923          19 KIPVTIFLVNGFKLQGQVESFDNFVVLL   46 (77)
T ss_pred             CCeEEEEEEcCEEEEEEEEeeeeEEEEE
Confidence            4579999999999999999999997443

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

Probab=95.68  E-value=0.042  Score=41.64  Aligned_cols=71  Identities=27%  Similarity=0.361  Sum_probs=57.0

Q ss_pred             hhhcCCEEEEEEcCCcEEEEEEEEec-cccceEEcceEEEEEc---cCCe----eeEeeCeEEEcCCcEEEEEeCCCCC
Q 041342           15 DRCIGSKIWVIMKGDKELVGTLKGFD-VYVNMVLEDVTEYEIT---AEGR----RITKLDQILLNGNNIAILVPGGSPD   85 (87)
Q Consensus        15 ~~~l~k~V~V~l~dgr~~~G~L~~~D-~~mNlvL~~~~e~~~~---~~g~----~~~~~g~v~IRG~~I~~I~~~~~p~   85 (87)
                      ..|||++|.++-+..-.|+|+|.-+| +-.-|-|.++.-+.++   .++.    ....+..++.||+.|..+...+.|.
T Consensus         5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~p~   83 (361)
T KOG1073|consen    5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQETPA   83 (361)
T ss_pred             cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccCcc
Confidence            56899999999999999999999999 7888999998655442   1221    1226789999999999998887664

>PRK14638 hypothetical protein; Provisional

Probab=95.47  E-value=0.056  Score=36.11  Aligned_cols=45  Identities=18%  Similarity=0.278  Sum_probs=34.3

Q ss_pred             CCCCCcCc---HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEc
Q 041342            3 HNPSQLLP---SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLE   48 (87)
Q Consensus         3 ~~~~~~~P---l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~   48 (87)
                      ++|=...|   ...+.+++|++|.|++++++.++|+|.++|.- ++.|.
T Consensus        81 SSPGldRpL~~~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~  128 (150)
T PRK14638         81 SSPGLDRPLRGPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS  128 (150)
T ss_pred             eCCCCCCCCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            34444445   45577889999999999999999999999963 45553

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

Probab=95.41  E-value=0.14  Score=29.93  Aligned_cols=54  Identities=20%  Similarity=0.323  Sum_probs=40.6

Q ss_pred             HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342           11 SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP   80 (87)
Q Consensus        11 l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~   80 (87)
                      ...|++++|++|.|.+..|.. +|+|.+.-.- .++|+..        +      ...|||=..|++|.+
T Consensus        13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~pD-hIvl~~~--------~------~~~~IR~~~IV~v~p   66 (66)
T PF10842_consen   13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKPD-HIVLEEN--------G------TPFFIRIAQIVWVMP   66 (66)
T ss_pred             HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCC-EEEEEeC--------C------cEEEEEeeeEEEEcC
Confidence            567999999999999987665 9999998742 2344433        1      368899888888753

>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=95.18  E-value=0.31  Score=29.55  Aligned_cols=62  Identities=10%  Similarity=0.164  Sum_probs=46.9

Q ss_pred             HHHHhhhcCCEEEEEEcCCcEEEEEEEEecc-ccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342           11 SELIDRCIGSKIWVIMKGDKELVGTLKGFDV-YVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP   80 (87)
Q Consensus        11 l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~-~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~   80 (87)
                      |..|....|++|.+.+.++....|++.++|. ..|+..++-. +   +=|    .....++|..-|++++.
T Consensus        16 Lr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~-T---PlG----v~~eAlLR~~DVi~~~f   78 (80)
T PF11095_consen   16 LRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ-T---PLG----VQPEALLRCSDVISISF   78 (80)
T ss_dssp             HHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE-T---TTT----EEEEEEEEGGGEEEEEE
T ss_pred             HHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC-C---Ccc----cChhheeecCCEEEEEe
Confidence            4567788899999999999999999999994 6677666653 1   234    35789999999999874

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.

>PRK02001 hypothetical protein; Validated

Probab=95.13  E-value=0.084  Score=35.45  Aligned_cols=45  Identities=27%  Similarity=0.375  Sum_probs=35.1

Q ss_pred             CCCCCcCcH---HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEc
Q 041342            3 HNPSQLLPS---ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLE   48 (87)
Q Consensus         3 ~~~~~~~Pl---~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~   48 (87)
                      ++|-...||   ..+.+++|+.|.|++.+++.+.|+|.++|.. ++.|.
T Consensus        71 SSPGldRpL~~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l~  118 (152)
T PRK02001         71 GSAGLTSPLKVPRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITLE  118 (152)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEEE
Confidence            455555554   4577889999999999999999999999964 45553

>PRK14639 hypothetical protein; Provisional

Probab=95.03  E-value=0.094  Score=34.65  Aligned_cols=43  Identities=19%  Similarity=0.287  Sum_probs=33.9

Q ss_pred             CCCCcCc---HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEE
Q 041342            4 NPSQLLP---SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVL   47 (87)
Q Consensus         4 ~~~~~~P---l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL   47 (87)
                      +|=...|   ...+.+++|++|.|++.+++.+.|+|.++|. .++.|
T Consensus        70 SPGl~RpL~~~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~-~~i~l  115 (140)
T PRK14639         70 SPGLERKLSKIEHFAKSIGELVKITTNEKEKFEGKIVSVDD-ENITL  115 (140)
T ss_pred             CCCCCCcCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeC-CEEEE
Confidence            4444444   4567789999999999999999999999997 35555

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=94.99  E-value=0.057  Score=36.83  Aligned_cols=38  Identities=13%  Similarity=0.238  Sum_probs=30.1

Q ss_pred             HHhhhcC--CEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342           13 LIDRCIG--SKIWVIMKGDKELVGTLKGFDVYVNMVLEDV   50 (87)
Q Consensus        13 ~L~~~l~--k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~   50 (87)
                      +|..+..  ..|+|.|.+|-.++|++.+||+|.=+.-.+.
T Consensus        16 fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g   55 (165)
T PRK14091         16 FLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRDG   55 (165)
T ss_pred             HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            4555554  4688999999999999999999986665554

>PRK14644 hypothetical protein; Provisional

Probab=94.96  E-value=0.093  Score=34.58  Aligned_cols=45  Identities=20%  Similarity=0.243  Sum_probs=33.9

Q ss_pred             CCCCCcCcHH--HHhhhcCCEEEEEEcCC----cEEEEEEEEeccccceEEc
Q 041342            3 HNPSQLLPSE--LIDRCIGSKIWVIMKGD----KELVGTLKGFDVYVNMVLE   48 (87)
Q Consensus         3 ~~~~~~~Pl~--~L~~~l~k~V~V~l~dg----r~~~G~L~~~D~~mNlvL~   48 (87)
                      ++|=...||.  .+.+++|+.|.|++++.    +.+.|+|.++|. -++.|.
T Consensus        67 SSPGldRpL~~~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~-~~i~l~  117 (136)
T PRK14644         67 SSPGFDMDYETDELENHIGEIIDVSLNKEVNKTDFITGELLENNP-ETITLK  117 (136)
T ss_pred             ECCCCCCCCCHHHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeC-CEEEEE
Confidence            3444444443  48899999999999887    899999999997 355554

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=94.77  E-value=0.086  Score=35.98  Aligned_cols=38  Identities=13%  Similarity=0.300  Sum_probs=29.8

Q ss_pred             HHhhhcC--CEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342           13 LIDRCIG--SKIWVIMKGDKELVGTLKGFDVYVNMVLEDV   50 (87)
Q Consensus        13 ~L~~~l~--k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~   50 (87)
                      +|..+..  ..|+|.|.+|-.++|.+.+||+|.=+.-.+.
T Consensus        96 fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g  135 (165)
T PRK14091         96 FLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG  135 (165)
T ss_pred             HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            4554444  4689999999999999999999986665443

>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=94.02  E-value=0.16  Score=33.15  Aligned_cols=44  Identities=34%  Similarity=0.448  Sum_probs=29.0

Q ss_pred             CCCCCcCcH---HHHhhhcCCEEEEEEc----CCcEEEEEEEEeccccceEE
Q 041342            3 HNPSQLLPS---ELIDRCIGSKIWVIMK----GDKELVGTLKGFDVYVNMVL   47 (87)
Q Consensus         3 ~~~~~~~Pl---~~L~~~l~k~V~V~l~----dgr~~~G~L~~~D~~mNlvL   47 (87)
                      ++|-...||   ..+.+++|+.|.|+++    +.+.+.|+|.++|. -.++|
T Consensus        68 SSPG~~r~L~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l  118 (141)
T PF02576_consen   68 SSPGIDRPLKSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL  118 (141)
T ss_dssp             E--SSSS--SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred             eCCCCCCcCCCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence            345555665   5788999999999994    45689999999998 44444

; PDB: 1IB8_A.

>PRK14640 hypothetical protein; Provisional

Probab=93.51  E-value=0.42  Score=31.90  Aligned_cols=45  Identities=16%  Similarity=0.307  Sum_probs=33.1

Q ss_pred             CCCCCcCc---HHHHhhhcCCEEEEEE----cCCcEEEEEEEEeccccceEEc
Q 041342            3 HNPSQLLP---SELIDRCIGSKIWVIM----KGDKELVGTLKGFDVYVNMVLE   48 (87)
Q Consensus         3 ~~~~~~~P---l~~L~~~l~k~V~V~l----~dgr~~~G~L~~~D~~mNlvL~   48 (87)
                      ++|=...|   ...+.+++|++|.|++    .+.+.++|+|.++|. -++.|.
T Consensus        78 SSPGl~RpL~~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~-~~v~l~  129 (152)
T PRK14640         78 SSPGLDRPLFKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQG-DMITLT  129 (152)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeC-CEEEEE
Confidence            34444445   4557788999999999    467899999999987 345553

>PRK06955 biotin--protein ligase; Provisional

Probab=93.33  E-value=0.53  Score=34.41  Aligned_cols=50  Identities=18%  Similarity=0.320  Sum_probs=36.2

Q ss_pred             hcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCC
Q 041342           17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGN   73 (87)
Q Consensus        17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~   73 (87)
                      +++++|+|...+++.++|++.|+|+...|+++..       +|.+....|.+.+|..
T Consensus       247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~~-------~g~~~~~sGeV~~~~~  296 (300)
T PRK06955        247 YAGREVVLLEDGAELARGVAHGIDETGQLLLDTP-------AGRQAIAAGDVSLREA  296 (300)
T ss_pred             cCCCeEEEEECCCcEEEEEEeeECCCceEEEEeC-------CCeEEEEEEEEEEecc
Confidence            5688999976677889999999999999998532       2322334566666543

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

Probab=93.07  E-value=0.51  Score=28.18  Aligned_cols=36  Identities=31%  Similarity=0.436  Sum_probs=28.5

Q ss_pred             HHHHhhhcCCEEEEEEc---CC-cEEEEEEEEeccccceEE
Q 041342           11 SELIDRCIGSKIWVIMK---GD-KELVGTLKGFDVYVNMVL   47 (87)
Q Consensus        11 l~~L~~~l~k~V~V~l~---dg-r~~~G~L~~~D~~mNlvL   47 (87)
                      ...+.+++|+.|.|+++   +| +.+.|+|.++|.. ++.|
T Consensus        17 ~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l   56 (83)
T cd01734          17 EADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL   56 (83)
T ss_pred             HHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence            45677889999999997   55 5899999999983 4444

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.

>PRK14633 hypothetical protein; Provisional

Probab=92.99  E-value=0.41  Score=31.91  Aligned_cols=45  Identities=13%  Similarity=0.211  Sum_probs=32.8

Q ss_pred             CCCCCcCc---HHHHhhhcCCEEEEEE----cCCcEEEEEEEEeccccceEEc
Q 041342            3 HNPSQLLP---SELIDRCIGSKIWVIM----KGDKELVGTLKGFDVYVNMVLE   48 (87)
Q Consensus         3 ~~~~~~~P---l~~L~~~l~k~V~V~l----~dgr~~~G~L~~~D~~mNlvL~   48 (87)
                      ++|=...|   ...+.+++|++|.|++    .+++.++|+|.++|+. ++.|.
T Consensus        75 SSPGldRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~  126 (150)
T PRK14633         75 SSPGMNRQIFNIIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN  126 (150)
T ss_pred             eCCCCCCCCCCHHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence            34444445   4567788999999988    3667999999999873 55553

>PRK14642 hypothetical protein; Provisional

Probab=92.93  E-value=0.38  Score=33.69  Aligned_cols=44  Identities=23%  Similarity=0.281  Sum_probs=33.1

Q ss_pred             CCCCCcCcH---HHHhhhcCCEEEEEEc-------------CCcEEEEEEEEeccccceEE
Q 041342            3 HNPSQLLPS---ELIDRCIGSKIWVIMK-------------GDKELVGTLKGFDVYVNMVL   47 (87)
Q Consensus         3 ~~~~~~~Pl---~~L~~~l~k~V~V~l~-------------dgr~~~G~L~~~D~~mNlvL   47 (87)
                      ++|=...||   ..+.+++|+.|.|+++             +.+.|+|+|.++|.. ++.|
T Consensus        81 SSPGldRPLk~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l  140 (197)
T PRK14642         81 SSPGIDRPLRHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI  140 (197)
T ss_pred             eCCCCCCCCCCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence            344444554   4567889999999998             678999999999974 4444

>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=92.84  E-value=0.6  Score=31.46  Aligned_cols=43  Identities=30%  Similarity=0.455  Sum_probs=33.5

Q ss_pred             CCCCcCc---HHHHhhhcCCEEEEEE----cCCcEEEEEEEEeccccceEE
Q 041342            4 NPSQLLP---SELIDRCIGSKIWVIM----KGDKELVGTLKGFDVYVNMVL   47 (87)
Q Consensus         4 ~~~~~~P---l~~L~~~l~k~V~V~l----~dgr~~~G~L~~~D~~mNlvL   47 (87)
                      +|=...|   ...+..++|+.|.|.+    .+++.++|+|.++|.-. +++
T Consensus        81 SPGldRpL~~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~  130 (153)
T COG0779          81 SPGLDRPLKTAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL  130 (153)
T ss_pred             CCCCCCCcCCHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence            4433444   4567788999999999    78899999999999876 444

>PRK14645 hypothetical protein; Provisional

Probab=92.65  E-value=0.43  Score=32.07  Aligned_cols=43  Identities=19%  Similarity=0.265  Sum_probs=31.7

Q ss_pred             CCCCCcCc---HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEE
Q 041342            3 HNPSQLLP---SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVL   47 (87)
Q Consensus         3 ~~~~~~~P---l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL   47 (87)
                      ++|=...|   ...+.+++|++|.|++ +++.++|+|.++|.. .+.|
T Consensus        83 SSPGldRpL~~~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l  128 (154)
T PRK14645         83 ESPGPKRPLFTARHFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTF  128 (154)
T ss_pred             eCCCCCCCCCCHHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence            34444445   3457788999999986 789999999999973 4444

>PRK14636 hypothetical protein; Provisional

Probab=91.86  E-value=0.65  Score=31.82  Aligned_cols=43  Identities=21%  Similarity=0.349  Sum_probs=31.7

Q ss_pred             CCCCcCc---HHHHhhhcCCEEEEEEc---CC-cEEEEEEEEeccccceEE
Q 041342            4 NPSQLLP---SELIDRCIGSKIWVIMK---GD-KELVGTLKGFDVYVNMVL   47 (87)
Q Consensus         4 ~~~~~~P---l~~L~~~l~k~V~V~l~---dg-r~~~G~L~~~D~~mNlvL   47 (87)
                      +|=...|   ...+.+++|++|.|+++   +| +.++|+|.++|.- ++.|
T Consensus        80 SPGldRpL~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l  129 (176)
T PRK14636         80 SPGIDRPLTRPKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI  129 (176)
T ss_pred             CCCCCCCCCCHHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence            4434444   35677899999999997   55 5999999999873 4554

>PRK14632 hypothetical protein; Provisional

Probab=91.43  E-value=0.77  Score=31.31  Aligned_cols=45  Identities=20%  Similarity=0.343  Sum_probs=33.1

Q ss_pred             CCCCCcCc---HHHHhhhcCCEEEEEEcC-------CcEEEEEEEEeccccceEEc
Q 041342            3 HNPSQLLP---SELIDRCIGSKIWVIMKG-------DKELVGTLKGFDVYVNMVLE   48 (87)
Q Consensus         3 ~~~~~~~P---l~~L~~~l~k~V~V~l~d-------gr~~~G~L~~~D~~mNlvL~   48 (87)
                      ++|=...|   ...+.+++|+.|.|++++       .+.+.|+|.++|. -++.|.
T Consensus        79 SSPGldRpL~~~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~-~~i~l~  133 (172)
T PRK14632         79 SSPGLERPFFRAEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEG-DTVVLR  133 (172)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeC-CEEEEE
Confidence            34544455   355778999999999976       5699999999986 355554

>PRK14643 hypothetical protein; Provisional

Probab=91.32  E-value=0.82  Score=31.01  Aligned_cols=40  Identities=15%  Similarity=0.252  Sum_probs=30.6

Q ss_pred             CCCCCcCc---HHHHhhhcCCEEEEEEcC----CcEEEEEEEEeccc
Q 041342            3 HNPSQLLP---SELIDRCIGSKIWVIMKG----DKELVGTLKGFDVY   42 (87)
Q Consensus         3 ~~~~~~~P---l~~L~~~l~k~V~V~l~d----gr~~~G~L~~~D~~   42 (87)
                      ++|=...|   ...+.+++|++|.|++++    .+.++|+|.++|.-
T Consensus        85 SSPGleRpL~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T PRK14643         85 SSSGIEKQIRSQEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN  131 (164)
T ss_pred             cCCCCCCCCCCHHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence            34544445   446778999999999865    57999999999964

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

Probab=91.30  E-value=1.1  Score=35.94  Aligned_cols=32  Identities=28%  Similarity=0.394  Sum_probs=28.1

Q ss_pred             hcCCEEEEEEcCCcEEEEEEEEeccccceEEc
Q 041342           17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLE   48 (87)
Q Consensus        17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~   48 (87)
                      ++|++|.+...+++.+.|+..|+|+...|+|+
T Consensus       276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~  307 (592)
T PRK13325        276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLE  307 (592)
T ss_pred             cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEE
Confidence            56889998766777899999999999999996

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=91.24  E-value=0.85  Score=30.30  Aligned_cols=39  Identities=28%  Similarity=0.407  Sum_probs=30.7

Q ss_pred             CCCCCcCc---HHHHhhhcCCEEEEEE----cCCcEEEEEEEEecc
Q 041342            3 HNPSQLLP---SELIDRCIGSKIWVIM----KGDKELVGTLKGFDV   41 (87)
Q Consensus         3 ~~~~~~~P---l~~L~~~l~k~V~V~l----~dgr~~~G~L~~~D~   41 (87)
                      ++|-...|   ...+.+++|+.|.|++    .+++.+.|+|.++|.
T Consensus        79 SSPGi~RpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~  124 (154)
T PRK00092         79 SSPGLDRPLKKARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG  124 (154)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence            34544455   3567889999999997    567899999999997

>PRK14634 hypothetical protein; Provisional

Probab=91.12  E-value=0.88  Score=30.51  Aligned_cols=44  Identities=14%  Similarity=0.088  Sum_probs=31.7

Q ss_pred             CCCCCcCc---HHHHhhhcCCEEEEEEcC----CcEEEEEEEEeccccceEE
Q 041342            3 HNPSQLLP---SELIDRCIGSKIWVIMKG----DKELVGTLKGFDVYVNMVL   47 (87)
Q Consensus         3 ~~~~~~~P---l~~L~~~l~k~V~V~l~d----gr~~~G~L~~~D~~mNlvL   47 (87)
                      ++|=...|   ...+.+++|++|.|++.+    .+.|.|+|.++|. .++.|
T Consensus        81 SSPGldRpL~~~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~-~~v~l  131 (155)
T PRK14634         81 SSPGIGDQLSSDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNE-DHLQI  131 (155)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeC-CEEEE
Confidence            34544445   345778899999999863    2689999999996 34545

>PRK14646 hypothetical protein; Provisional

Probab=90.80  E-value=1  Score=30.20  Aligned_cols=45  Identities=13%  Similarity=0.000  Sum_probs=32.4

Q ss_pred             CCCCCcCc---HHHHhhhcCCEEEEEEcC---C-cEEEEEEEEeccccceEEc
Q 041342            3 HNPSQLLP---SELIDRCIGSKIWVIMKG---D-KELVGTLKGFDVYVNMVLE   48 (87)
Q Consensus         3 ~~~~~~~P---l~~L~~~l~k~V~V~l~d---g-r~~~G~L~~~D~~mNlvL~   48 (87)
                      ++|=...|   ...+.+++|++|.|++++   | +.++|+|.++|.- ++.|.
T Consensus        81 SSPGldRpL~~~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~  132 (155)
T PRK14646         81 SSQGVSDELTSERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN  132 (155)
T ss_pred             cCCCCCCcCCCHHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            34544445   456778999999999864   3 5789999999974 55553

>PRK14647 hypothetical protein; Provisional

Probab=90.47  E-value=1.1  Score=30.03  Aligned_cols=44  Identities=20%  Similarity=0.249  Sum_probs=31.8

Q ss_pred             CCCCCcCc---HHHHhhhcCCEEEEEEc---------CCcEEEEEEEEeccccceEE
Q 041342            3 HNPSQLLP---SELIDRCIGSKIWVIMK---------GDKELVGTLKGFDVYVNMVL   47 (87)
Q Consensus         3 ~~~~~~~P---l~~L~~~l~k~V~V~l~---------dgr~~~G~L~~~D~~mNlvL   47 (87)
                      ++|=...|   ...+.+++|++|.|+++         +.+.+.|+|.++|. ..+.|
T Consensus        80 SSPG~~RpL~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~-~~v~l  135 (159)
T PRK14647         80 SSPGLDRPLKKEADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD-GVVTI  135 (159)
T ss_pred             cCCCCCCcCCCHHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC-CEEEE
Confidence            34544445   45677899999999995         35799999999996 33444

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

Probab=90.19  E-value=1.9  Score=31.49  Aligned_cols=48  Identities=27%  Similarity=0.385  Sum_probs=35.0

Q ss_pred             hcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcC
Q 041342           17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNG   72 (87)
Q Consensus        17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG   72 (87)
                      ++|++|.+... +..++|++.++|....|++++.       .+.+....|.+.+|.
T Consensus       270 ~~g~~v~~~~~-~~~~~G~~~gi~~~G~L~i~~~-------g~~~~~~~gev~~~~  317 (319)
T PRK11886        270 FLGREVKLIIG-DKEISGIARGIDEQGALLLEDD-------GVEKPFNGGEISLRS  317 (319)
T ss_pred             ccCCeEEEEeC-CcEEEEEEEEECCCceEEEEeC-------CcEEEEEEeEEEEec
Confidence            56889999874 5679999999999999999621       222334557777665

>PRK14631 hypothetical protein; Provisional

Probab=89.75  E-value=1.2  Score=30.42  Aligned_cols=38  Identities=18%  Similarity=0.297  Sum_probs=29.4

Q ss_pred             CCCCCcCc---HHHHhhhcCCEEEEEEc----CCcEEEEEEEEec
Q 041342            3 HNPSQLLP---SELIDRCIGSKIWVIMK----GDKELVGTLKGFD   40 (87)
Q Consensus         3 ~~~~~~~P---l~~L~~~l~k~V~V~l~----dgr~~~G~L~~~D   40 (87)
                      ++|=...|   ...+.+++|+.|.|++.    +.+.|+|+|.++|
T Consensus        98 SSPGldRpL~~~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~  142 (174)
T PRK14631         98 SSPGWDRPFFQLEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD  142 (174)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence            34444444   45678899999999996    4589999999998

>PRK14641 hypothetical protein; Provisional

Probab=89.02  E-value=1.4  Score=30.18  Aligned_cols=38  Identities=21%  Similarity=0.386  Sum_probs=28.9

Q ss_pred             CCCCCcCc---HHHHhhhcCCEEEEEEcC----CcEEEEEEEEec
Q 041342            3 HNPSQLLP---SELIDRCIGSKIWVIMKG----DKELVGTLKGFD   40 (87)
Q Consensus         3 ~~~~~~~P---l~~L~~~l~k~V~V~l~d----gr~~~G~L~~~D   40 (87)
                      ++|-...|   ...+.+++|+.|.|++.+    .+.++|+|.++|
T Consensus        85 SSPGldRpL~~~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~  129 (173)
T PRK14641         85 SSPGLGEPIILPRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS  129 (173)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence            34444455   355778899999999976    558999999995

>PRK14637 hypothetical protein; Provisional

Probab=88.62  E-value=1.7  Score=29.01  Aligned_cols=44  Identities=20%  Similarity=0.227  Sum_probs=30.7

Q ss_pred             CCCCcCc---HHHHhhhcCCEEEEEEcCCcEE-EEEEEEeccccceEEc
Q 041342            4 NPSQLLP---SELIDRCIGSKIWVIMKGDKEL-VGTLKGFDVYVNMVLE   48 (87)
Q Consensus         4 ~~~~~~P---l~~L~~~l~k~V~V~l~dgr~~-~G~L~~~D~~mNlvL~   48 (87)
                      +|=...|   ...+.+++|++|.|++.+.+.+ +|+|.++|.- ++.|.
T Consensus        80 SPGldRpL~~~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~  127 (151)
T PRK14637         80 SPGIERVIKNAAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT  127 (151)
T ss_pred             CCCCCCCCCCHHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence            4444445   4567788999999999444455 7999999874 44443

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

Probab=88.21  E-value=3.1  Score=29.15  Aligned_cols=31  Identities=26%  Similarity=0.402  Sum_probs=26.8

Q ss_pred             hcCCEEEEEEcCCcEEEEEEEEeccccceEEc
Q 041342           17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLE   48 (87)
Q Consensus        17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~   48 (87)
                      .++++|.+...+ ..+.|+..|+|+...|+++
T Consensus       191 ~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~  221 (237)
T TIGR00121       191 HIGREVSLTTGN-GEIEGIARGIDKDGALLLE  221 (237)
T ss_pred             ccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence            558999998754 5799999999999999996

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

>PRK08330 biotin--protein ligase; Provisional

Probab=87.70  E-value=3.4  Score=28.93  Aligned_cols=34  Identities=18%  Similarity=0.278  Sum_probs=27.5

Q ss_pred             hhcCCEEEEEEcCCcEE-EEEEEEeccccceEEcce
Q 041342           16 RCIGSKIWVIMKGDKEL-VGTLKGFDVYVNMVLEDV   50 (87)
Q Consensus        16 ~~l~k~V~V~l~dgr~~-~G~L~~~D~~mNlvL~~~   50 (87)
                      .+++++|.+.. ++..+ .|+..++|....|+++..
T Consensus       185 ~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~~  219 (236)
T PRK08330        185 MILGKRVKIIG-DGEILVEGIAEDIDEFGALILRLD  219 (236)
T ss_pred             HhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEEC
Confidence            36789999875 56665 799999999999999744

>PRK10898 serine endoprotease; Provisional

Probab=81.47  E-value=3.7  Score=30.67  Aligned_cols=31  Identities=16%  Similarity=0.312  Sum_probs=27.6

Q ss_pred             CEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342           20 SKIWVIMKGDKELVGTLKGFDVYVNMVLEDV   50 (87)
Q Consensus        20 k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~   50 (87)
                      .++.|.+.||+.+.+++.++|....|-|=..
T Consensus       102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v  132 (353)
T PRK10898        102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKI  132 (353)
T ss_pred             CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEE
Confidence            5789999999999999999999999877554

>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]

Probab=81.20  E-value=10  Score=27.01  Aligned_cols=36  Identities=22%  Similarity=0.333  Sum_probs=32.0

Q ss_pred             hhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342           15 DRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDV   50 (87)
Q Consensus        15 ~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~   50 (87)
                      ...++++|++...++....|+..++|....|+++..
T Consensus       186 ~~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~  221 (238)
T COG0340         186 SLSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD  221 (238)
T ss_pred             hccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence            345789999999998999999999999999999876

>PF11607 DUF3247: Protein of unknown function (DUF3247); InterPro: IPR021649 This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris

Probab=80.83  E-value=2.8  Score=26.28  Aligned_cols=17  Identities=18%  Similarity=0.302  Sum_probs=14.4

Q ss_pred             CEEEEEEcCCcEEEEEE
Q 041342           20 SKIWVIMKGDKELVGTL   36 (87)
Q Consensus        20 k~V~V~l~dgr~~~G~L   36 (87)
                      .+|.+.|+||+.+.|++
T Consensus        29 ~~V~l~L~DGs~l~Gtv   45 (101)
T PF11607_consen   29 ERVELELDDGSMLRGTV   45 (101)
T ss_dssp             -EEEEEETTS-EEEEEE
T ss_pred             ceEEEEEcCCCeeeeee
Confidence            58999999999999998

The protein has no known function however its structure has been determined. The protein adopts a Lsm fold however differences with the fold were observed at the N-terminal and internal regions []. ; PDB: 2E12_B.

>PRK14630 hypothetical protein; Provisional

Probab=80.09  E-value=6.7  Score=25.90  Aligned_cols=43  Identities=12%  Similarity=0.094  Sum_probs=30.5

Q ss_pred             CCCCCcCc---HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEE
Q 041342            3 HNPSQLLP---SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVL   47 (87)
Q Consensus         3 ~~~~~~~P---l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL   47 (87)
                      ++|=...|   ...+.+++|++|.|++.. ...+|+|.++|. -++.|
T Consensus        78 SSPGldRpL~~~~df~r~~G~~v~V~l~~-~~~~G~L~~~~d-~~i~l  123 (143)
T PRK14630         78 STPGINRKIKSDREFKIFEGKKIKLMLDN-DFEEGFILEAKA-DSFIF  123 (143)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCEEEEEEcC-cceEEEEEEEeC-CEEEE
Confidence            34444444   456778899999999965 445999999987 44444

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	87
2fwk_A	121	Crystal Structure Of Cryptosporidium Parvum U6 Snrn		1e-21
3swn_A	82	Structure Of The Lsm657 Complex: An Assembly Interm		2e-19
4emk_A	94	Crystal Structure Of Splsm567 Length = 94		1e-17
1i81_A	83	Crystal Structure Of A Heptameric Lsm Protein From		9e-07
1loj_A	87	Crystal Structure Of A Methanobacterial Sm-Like Arc		2e-06
1jbm_A	86	Heptameric Crystal Structure Of Mth649, An Sm-Like		2e-06
1jri_A	85	The Crystal Structure Of An Sm-Like Archaeal Protei		2e-06
1i5l_A	77	Crystal Structure Of An Sm-Like Protein (Af-Sm1) Fr		4e-06
1ljo_A	77	Crystal Structure Of An Sm-Like Protein (Af-Sm2) Fr		9e-06
1m8v_A	77	Structure Of Pyrococcus Abyssii Sm Protein In Compl		8e-05
1h64_1	75	Crystal Structure Of The Sm-Related Protein Of P. A		9e-05
1th7_A	81	Crystal Structure Of An Archaeal Sm Protein From Su		1e-04
3swn_C	117	Structure Of The Lsm657 Complex: An Assembly Interm		4e-04
3cw1_E	92	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		4e-04
4emk_C	113	Crystal Structure Of Splsm567 Length = 113		6e-04
3bw1_A	96	Crystal Structure Of Homomeric Yeast Lsm3 Exhibitin		6e-04

>pdb|2FWK|A Chain A, Crystal Structure Of Cryptosporidium Parvum U6 Snrna- Associated Sm-Like Protein Lsm5 Length = 121

Iteration: 1
 Score = 97.8 bits (242), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 48/90 (53%), Positives = 63/90 (70%), Gaps = 12/90 (13%)
Query: 8   LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT---- 63
           +LP  LID+CIG++I+V+MKGDKE  G L+GFD YVNMVL+DV EY   A+   I+    
Sbjct: 27  ILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNK 86
Query: 64  --------KLDQILLNGNNIAILVPGGSPD 85
                   +L+ ILL+GNN+A+LVPGG PD
Sbjct: 87  KLKRVMVNRLETILLSGNNVAMLVPGGDPD 116

>pdb|3SWN|A Chain A, Structure Of The Lsm657 Complex: An Assembly Intermediate Of The Lsm1 7 And Lsm2 8 Rings Length = 82

Iteration: 1
 Score = 90.5 bits (223), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 45/78 (57%), Positives = 59/78 (75%), Gaps = 2/78 (2%)
Query: 8  LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQ 67
          +LP ELID+CIGS +WVIMK ++E  GTL GFD YVN+VL+DVTEY+ T  G    K  +
Sbjct: 7  ILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYD-TVTGVT-EKHSE 64
Query: 68 ILLNGNNIAILVPGGSPD 85
          +LLNGN + +L+PGG P+
Sbjct: 65 MLLNGNGMCMLIPGGKPE 82

>pdb|4EMK|A Chain A, Crystal Structure Of Splsm567 Length = 94

Iteration: 1
 Score = 84.7 bits (208), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/78 (56%), Positives = 55/78 (70%), Gaps = 2/78 (2%)
Query: 8  LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQ 67
          +LP ELID+CIGS +WVI K ++E  GTL GFD YVN+VL+DVTEY+ T  G    K  +
Sbjct: 19 ILPLELIDKCIGSNLWVIXKSEREFAGTLVGFDDYVNIVLKDVTEYD-TVTGVT-EKHSE 76
Query: 68 ILLNGNNIAILVPGGSPD 85
           LLNGN    L+PGG P+
Sbjct: 77 XLLNGNGXCXLIPGGKPE 94

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 3/71 (4%)
Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
          P + +   + S + + +KGD+E  G LK FD+++N+VL D  E E   +G    +L  +L
Sbjct: 16 PLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELE---DGEVTRRLGTVL 72
Query: 70 LNGNNIAILVP 80
          + G+NI  + P
Sbjct: 73 IRGDNIVYISP 83

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 3/72 (4%)
Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
          P + +   + S + + +KGD+E  G LK FD+++N+VL D  E E   +G    +L  +L
Sbjct: 14 PLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELE---DGEVTRRLGTVL 70
Query: 70 LNGNNIAILVPG 81
          + G+NI  +  G
Sbjct: 71 IRGDNIVYISRG 82

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 3/72 (4%)
Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
          P + +   + S + + +KGD+E  G LK FD+++N+VL D  E E   +G    +L  +L
Sbjct: 14 PLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELE---DGEVTRRLGTVL 70
Query: 70 LNGNNIAILVPG 81
          + G+NI  +  G
Sbjct: 71 IRGDNIVYISRG 82

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 3/72 (4%)
Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
          P + +   + S + + +KGD+E  G LK FD+++N+VL D  E E   +G    +L  +L
Sbjct: 14 PLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELE---DGEVTRRLGTVL 70
Query: 70 LNGNNIAILVPG 81
          + G+NI  +  G
Sbjct: 71 IRGDNIVYISRG 82

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 43/71 (60%), Gaps = 3/71 (4%)
Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
          P ++++R + S + V +KG +E  GTL G+D+++N+VL D  E +    G  + K+  ++
Sbjct: 5  PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQ---NGEVVRKVGSVV 61
Query: 70 LNGNNIAILVP 80
          + G+ +  + P
Sbjct: 62 IRGDTVVFVSP 72

>pdb|1LJO|A Chain A, Crystal Structure Of An Sm-Like Protein (Af-Sm2) From Archaeoglobus Fulgidus At 1.95a Resolution Length = 77

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 46/76 (60%), Gaps = 4/76 (5%)
Query: 6  SQLLPSELIDRCIGSKIWVIMKGDK-ELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITK 64
          + +LP++++   +G  I V MKG++ +LVG L+G D Y+N+ L +  E        ++  
Sbjct: 2  AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAME---CKGEEKVRS 58
Query: 65 LDQILLNGNNIAILVP 80
          L +I+L GNN+ ++ P
Sbjct: 59 LGEIVLRGNNVVLIQP 74

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 41/71 (57%), Gaps = 3/71 (4%)
Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
          P ++I R +   + VI+K   E  G L G+D+++N+VL D    E+  +G  + +  +I+
Sbjct: 7  PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADA---EMIQDGEVVKRYGKIV 63
Query: 70 LNGNNIAILVP 80
          + G+N+  + P
Sbjct: 64 IRGDNVLAISP 74

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 41/71 (57%), Gaps = 3/71 (4%)
Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
          P ++I R +   + VI+K   E  G L G+D+++N+VL D    E+  +G  + +  +I+
Sbjct: 5  PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADA---EMIQDGEVVKRYGKIV 61
Query: 70 LNGNNIAILVP 80
          + G+N+  + P
Sbjct: 62 IRGDNVLAISP 72

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/59 (33%), Positives = 37/59 (62%), Gaps = 3/59 (5%)
Query: 22 IWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP 80
          + V +KG+KE+ G L+ +D ++N+VL D  E +    G+   KL  I++ G+N+ ++ P
Sbjct: 22 VLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGK---KLGTIVIRGDNVILISP 77

>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 = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 14  IDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT----KLDQIL 69
           + R    +I     G +++ G LKGFD  +N+VL+DV E     E  ++T    KL  ++
Sbjct: 32  LSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVV 91
Query: 70  LNGNNIAILVP 80
           + G  + ++ P
Sbjct: 92  VRGTTLVLIAP 102

>pdb|3CW1|E Chain E, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 92

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 10 PSELIDRCIGSK----IWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKL 65
          P  LI R + ++    +W+  + +  + G + GFD Y+N+VL+D  E     + R+  +L
Sbjct: 17 PINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRK--QL 74
Query: 66 DQILLNGNNIAIL 78
           +I+L G+NI +L
Sbjct: 75 GRIMLKGDNITLL 87

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 14 IDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT----KLDQIL 69
          + R    +I     G +++ G LKGFD   N+VL+DV E     E  ++T    KL  ++
Sbjct: 28 LSRYQDQRIQATFTGGRQITGILKGFDQLXNLVLDDVEEQLRNPEDGKLTGAIRKLGLVV 87
Query: 70 LNGNNIAILVP 80
          + G  + ++ P
Sbjct: 88 VRGTTLVLIAP 98

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/82 (24%), Positives = 44/82 (53%), Gaps = 8/82 (9%)
Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTE--YEIT----AEGRRIT 63
          P +L+   +  ++++ ++G + LVGTL+ FD + N+VL D  E  Y++     +E  R  
Sbjct: 11 PLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESER-- 68
Query: 64 KLDQILLNGNNIAILVPGGSPD 85
          + + + + G+ + ++      D
Sbjct: 69 RCEMVFIRGDTVTLISTPSEDD 90

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	87
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	1e-31
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	2e-27
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	4e-26
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	2e-25
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	1e-23
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	4e-23
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	7e-23
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	2e-19
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	2e-19
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	8e-19
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	3e-17
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	2e-16
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	3e-15
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	4e-14
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	6e-14
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	2e-13
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	2e-11
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	3e-11
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	4e-10
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	9e-09
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	1e-08
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	3e-08
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-04

>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 =  104 bits (262), Expect = 1e-31
 Identities = 43/82 (52%), Positives = 57/82 (69%), Gaps = 2/82 (2%)

Query: 4  NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT 63
              +LP ELID+CIGS +WVIMK ++E  GTL GFD YVN+VL+DVTEY+         
Sbjct: 15 MSMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTE-- 72

Query: 64 KLDQILLNGNNIAILVPGGSPD 85
          K  ++LLNGN + +L+PGG P+
Sbjct: 73 KHSEMLLNGNGMCMLIPGGKPE 94

>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 = 95.4 bits (237), Expect = 2e-27
 Identities = 47/95 (49%), Positives = 63/95 (66%), Gaps = 12/95 (12%)

Query: 4   NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGR--- 60
             + +LP  LID+CIG++I+V+MKGDKE  G L+GFD YVNMVL+DV EY   A+     
Sbjct: 23  GGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDIS 82

Query: 61  ---------RITKLDQILLNGNNIAILVPGGSPDP 86
                     + +L+ ILL+GNN+A+LVPGG PD 
Sbjct: 83  GGNKKLKRVMVNRLETILLSGNNVAMLVPGGDPDS 117

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

 Score = 90.8 bits (226), Expect = 4e-26
 Identities = 25/78 (32%), Positives = 47/78 (60%), Gaps = 4/78 (5%)

Query: 6  SQLLPSELIDRCIGSKIWVIMKGDK-ELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITK 64
          + +LP++++   +G  I V MKG++ +LVG L+G D Y+N+ L +  E +      ++  
Sbjct: 2  AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECK---GEEKVRS 58

Query: 65 LDQILLNGNNIAILVPGG 82
          L +I+L GNN+ ++ P  
Sbjct: 59 LGEIVLRGNNVVLIQPQE 76

>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 = 89.5 bits (222), Expect = 2e-25
 Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 6/80 (7%)

Query: 8  LLPSELIDRCIGSK----IWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT 63
          + P  LI R + ++    +W+  + +  + G + GFD Y+N+VL+D  E     + R+  
Sbjct: 15 VQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRK-- 72

Query: 64 KLDQILLNGNNIAILVPGGS 83
          +L +I+L G+NI +L    +
Sbjct: 73 QLGRIMLKGDNITLLQSVSN 92

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

 Score = 84.7 bits (210), Expect = 1e-23
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 3/77 (3%)

Query: 4  NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT 63
            +   P + +   + S + + +KGD+E  G LK FD+++N+VL D  E E   +G    
Sbjct: 10 RVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELE---DGEVTR 66

Query: 64 KLDQILLNGNNIAILVP 80
          +L  +L+ G+NI  + P
Sbjct: 67 RLGTVLIRGDNIVYISP 83

>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 = 83.1 bits (206), Expect = 4e-23
 Identities = 23/78 (29%), Positives = 45/78 (57%), Gaps = 5/78 (6%)

Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
          P ++++R + S + V +KG +E  GTL G+D+++N+VL D  E +    G  + K+  ++
Sbjct: 5  PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQ---NGEVVRKVGSVV 61

Query: 70 LNGNNIAILVPGGSPDPE 87
          + G+ +  + P   P  E
Sbjct: 62 IRGDTVVFVSPA--PGGE 77

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

 Score = 82.3 bits (204), Expect = 7e-23
 Identities = 20/71 (28%), Positives = 40/71 (56%), Gaps = 3/71 (4%)

Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
          P ++I R +   + VI+K   E  G L G+D+++N+VL D    +   +G  + +  +I+
Sbjct: 5  PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQ---DGEVVKRYGKIV 61

Query: 70 LNGNNIAILVP 80
          + G+N+  + P
Sbjct: 62 IRGDNVLAISP 72

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

 Score = 74.5 bits (183), Expect = 2e-19
 Identities = 19/90 (21%), Positives = 40/90 (44%), Gaps = 10/90 (11%)

Query: 1  MAHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGR 60
          M    +   P +L+   +   ++V ++GD+EL G L  +D ++NMVL D  E     +  
Sbjct: 1  MESAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDE 60

Query: 61 RIT----------KLDQILLNGNNIAILVP 80
                         + + + G+++ ++ P
Sbjct: 61 ETDKDKALKTIRKHYEMLFVRGDSVILIAP 90

>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 = 74.4 bits (183), Expect = 2e-19
 Identities = 19/90 (21%), Positives = 44/90 (48%), Gaps = 5/90 (5%)

Query: 1  MAHNPSQL-LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEG 59
          M H+   +  P +L+   +  ++++ ++G + LVGTL+ FD + N+VL D  E       
Sbjct: 1  MHHHHHHMETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNN 60

Query: 60 RRIT----KLDQILLNGNNIAILVPGGSPD 85
            ++    + + + + G+ + ++      D
Sbjct: 61 EELSESERRCEMVFIRGDTVTLISTPSEDD 90

>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 = 72.3 bits (178), Expect = 8e-19
 Identities = 20/71 (28%), Positives = 42/71 (59%), Gaps = 3/71 (4%)

Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
            +++   + + + V +KG+KE+ G L+ +D ++N+VL D  E +    G+   KL  I+
Sbjct: 10 AHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGK---KLGTIV 66

Query: 70 LNGNNIAILVP 80
          + G+N+ ++ P
Sbjct: 67 IRGDNVILISP 77

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

 Score = 68.6 bits (168), Expect = 3e-17
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 3  HNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRI 62
          H+   +LP  L++   G  I V +K  +   G L+  D Y+N+ L +V       +G + 
Sbjct: 10 HSQDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRT--MPDGDKF 67

Query: 63 TKLDQILLNGNNI 75
           +L +  + GNNI
Sbjct: 68 FRLPECYIRGNNI 80

>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 = 66.3 bits (162), Expect = 2e-16
 Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 3/70 (4%)

Query: 6  SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKL 65
            L P   ++   G  + V +K   E  G L   D Y+NM L +  EY    +G     L
Sbjct: 3  LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEY---IDGALSGHL 59

Query: 66 DQILLNGNNI 75
           ++L+  NN+
Sbjct: 60 GEVLIRCNNV 69

>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 = 63.1 bits (154), Expect = 3e-15
 Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 3/71 (4%)

Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
          P+E +++ IG K+ + +    +  G L   D Y+N+ LE   EY     G++        
Sbjct: 5  PNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEY---VNGKKTNVYGDAF 61

Query: 70 LNGNNIAILVP 80
          + GNN+  +  
Sbjct: 62 IRGNNVLYVSA 72

>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 = 60.4 bits (147), Expect = 4e-14
 Identities = 18/75 (24%), Positives = 41/75 (54%), Gaps = 4/75 (5%)

Query: 6  SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKL 65
          S+  P EL  + +  K+ + + G + + G L+GFD ++N+V+++  E   + +      +
Sbjct: 2  SKAHPPEL-KKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQN---NI 57

Query: 66 DQILLNGNNIAILVP 80
            +++ GN+I +L  
Sbjct: 58 GMVVIRGNSIIMLEA 72

>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 = 60.7 bits (147), Expect = 6e-14
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 5/81 (6%)

Query: 4  NPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT 63
           P +    +L  R    +I     G +++ G LKGFD  +N+VL+DV E     E  ++T
Sbjct: 19 RPRKESILDLS-RYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLT 77

Query: 64 ----KLDQILLNGNNIAILVP 80
              KL  +++ G  + ++ P
Sbjct: 78 GAIRKLGLVVVRGTTLVLIAP 98

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

 Score = 58.9 bits (143), Expect = 2e-13
 Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 4/71 (5%)

Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
              +   IG ++ V ++   E+ G L+ FD +VN++LED  E         + K   ++
Sbjct: 12 LGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI----IDGNVYKRGTMV 67

Query: 70 LNGNNIAILVP 80
          + G N+  + P
Sbjct: 68 VRGENVLFISP 78

>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 = 54.7 bits (131), Expect = 2e-11
 Identities = 14/75 (18%), Positives = 32/75 (42%), Gaps = 3/75 (4%)

Query: 6  SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKL 65
          S  +P +++    G  +       +   G L   +  +N  + ++T    T    R+ +L
Sbjct: 2  SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITV---TYRDGRVAQL 58

Query: 66 DQILLNGNNIAILVP 80
          +Q+ + G+ I  L+ 
Sbjct: 59 EQVYIRGSKIRFLIL 73

>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 = 53.3 bits (128), Expect = 3e-11
 Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 4/67 (5%)

Query: 10 PSELIDRCIGSKIWVIMK-GDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQI 68
          P   +   +  ++ V +K    E  GTL   D Y N+ L +  E+     G     L +I
Sbjct: 22 PKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEF---VAGVSHGTLGEI 78

Query: 69 LLNGNNI 75
           +  NN+
Sbjct: 79 FIRCNNV 85

>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 = 50.1 bits (120), Expect = 4e-10
 Identities = 13/70 (18%), Positives = 29/70 (41%), Gaps = 3/70 (4%)

Query: 6  SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKL 65
          S  +P +++    G  +       +   G L   +  +N  + ++T    T    R+ +L
Sbjct: 2  SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITV---TYRDGRVAQL 58

Query: 66 DQILLNGNNI 75
          +Q+ + G  I
Sbjct: 59 EQVYIRGCKI 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 = 47.7 bits (113), Expect = 9e-09
 Identities = 16/67 (23%), Positives = 31/67 (46%), Gaps = 3/67 (4%)

Query: 9  LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQI 68
               + +     + + +K   ++ GT+ G DV +N  L+ V     T + R   +L+ +
Sbjct: 2  KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKM---TLKNREPVQLETL 58

Query: 69 LLNGNNI 75
           + GNNI
Sbjct: 59 SIRGNNI 65

>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 = 46.8 bits (111), Expect = 1e-08
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 7/77 (9%)

Query: 18 IGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEI-------TAEGRRITKLDQILL 70
          I  ++  I++  +  +GT K FD ++N++L D  E+          AE      L  +LL
Sbjct: 13 IDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLL 72

Query: 71 NGNNIAILVPGGSPDPE 87
           G N+  +   G P  +
Sbjct: 73 RGENLVSMTVEGPPPKD 89

>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 = 46.1 bits (109), Expect = 3e-08
 Identities = 17/84 (20%), Positives = 45/84 (53%), Gaps = 13/84 (15%)

Query: 10  PSELIDRCI--GSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEY--------EITAEG 59
           P  ++ + +   +++ +  + +K+L+G +K FD + NMVLE+V E         +   + 
Sbjct: 28  PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKS 87

Query: 60  RRITK---LDQILLNGNNIAILVP 80
           + + K   + ++ L G+++ +++ 
Sbjct: 88  KPVNKDRYISKMFLRGDSVIVVLR 111

>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 = 36.9 bits (85), Expect = 2e-04
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 7/77 (9%)

Query: 18 IGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEIT-----AEGRRITK--LDQILL 70
          I  ++  I++  +  +GT K FD ++N++L D  E+         +  R  K  L  +LL
Sbjct: 13 IDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLL 72

Query: 71 NGNNIAILVPGGSPDPE 87
           G N+  +   G P  +
Sbjct: 73 RGENLVSMTVEGPPPKD 89

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	87
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.96
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.95
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.94
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.94
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.94
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.94
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.94
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.94
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.94
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.94
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.94
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.94
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.94
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.94
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.93
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.93
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.92
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.92
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.92
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.91
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.91
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.91
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.89
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.85
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	99.19
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	97.89
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	97.56
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	97.24
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	97.2
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	97.15
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	97.14
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	97.11
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	97.05
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	96.98
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	96.75
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	96.68
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	96.28
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	95.9
1ycy_A	71	Conserved hypothetical protein; structural genomic	95.72
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	95.48
2rm4_A	103	CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-	93.16
3rux_A	270	BIRA bifunctional protein; biotin-protein ligase,	92.93
2xk0_A	69	Polycomb protein PCL; transcription, aromatic CAGE	92.9
2eay_A	233	Biotin [acetyl-COA-carboxylase] ligase; biotin bio	92.57
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	92.28
1bia_A	321	BIRA bifunctional protein; transcription regulatio	91.81
2ej9_A	237	Putative biotin ligase; biotin biosynthesis, monom	91.08
2dxu_A	235	Biotin--[acetyl-COA-carboxylase] ligase; biotin bi	88.68
4hcz_A	58	PHD finger protein 1; protein-peptide complex, tud	85.67
2e12_A	101	SM-like motif, hypothetical protein XCC3642; novel	84.43
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	82.93

>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=99.96  E-value=2.2e-28  Score=151.64  Aligned_cols=78  Identities=55%  Similarity=1.029  Sum_probs=68.0

Q ss_pred             CCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCCCCC
Q 041342            6 SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGSPD   85 (87)
Q Consensus         6 ~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~~p~   85 (87)
                      .+..|+++|.++++++|+|+|+|||.|+|+|.|||+|||++|+||+|+..  ++.+.+.+|.++|||++|++|++.++|.
T Consensus        17 ~~~~Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~--~~~~~~~lg~v~IRG~nI~~i~p~~~p~   94 (94)
T 4emk_A           17 MTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDT--VTGVTEKHSEMLLNGNGMCMLIPGGKPE   94 (94)
T ss_dssp             ---CHHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEET--TTCCEEEEEEEEECSTTEEEEEECC---
T ss_pred             ccccCHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEec--CCCcEeEcCEEEEcCCEEEEEEeCCCCC
Confidence            56899999999999999999999999999999999999999999999973  3445789999999999999999998873

>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=99.95  E-value=6.1e-27  Score=139.85  Aligned_cols=74  Identities=34%  Similarity=0.684  Sum_probs=68.3

Q ss_pred             CCcCcHHHHhhhcCCEEEEEEcCC-cEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342            6 SQLLPSELIDRCIGSKIWVIMKGD-KELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus         6 ~~~~Pl~~L~~~l~k~V~V~l~dg-r~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      +++.|+.+|.++++++|+|+|+|| +.|+|+|.|||+|||++|+||+|++   .+...+.+|.++|||++|++|++.+
T Consensus         2 ~m~~P~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~---~~~~~~~lg~v~iRG~nI~~i~~~d   76 (77)
T 1ljo_A            2 AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECK---GEEKVRSLGEIVLRGNNVVLIQPQE   76 (77)
T ss_dssp             CCCCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEE---TTEEEEEEEEEEECGGGEEEEEEC-
T ss_pred             CccchHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEe---cCCcEeECCeEEEeCCeEEEEEeCC
Confidence            457999999999999999999999 9999999999999999999999997   3556889999999999999999864

>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=99.94  E-value=1e-27  Score=154.28  Aligned_cols=81  Identities=58%  Similarity=1.107  Sum_probs=70.1

Q ss_pred             CCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcc-------CCee-----eEeeCeEEEcCC
Q 041342            6 SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITA-------EGRR-----ITKLDQILLNGN   73 (87)
Q Consensus         6 ~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~-------~g~~-----~~~~g~v~IRG~   73 (87)
                      .+..|+++|.++++++|+|+|+|||.|+|+|.|||+||||+|+||+|++...       +|..     .+.+|.++|||+
T Consensus        25 ~~~~Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG~  104 (121)
T 2fwk_A           25 NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGN  104 (121)
T ss_dssp             CCCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGG
T ss_pred             cccCcHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECCC
Confidence            5689999999999999999999999999999999999999999999998531       2333     688999999999


Q ss_pred             cEEEEEeCCCCCC
Q 041342           74 NIAILVPGGSPDP   86 (87)
Q Consensus        74 ~I~~I~~~~~p~~   86 (87)
                      +|++|.+.+.|++
T Consensus       105 nVv~I~~~~~~~~  117 (121)
T 2fwk_A          105 NVAMLVPGGDPDS  117 (121)
T ss_dssp             GEEEEESSSCC--
T ss_pred             EEEEEEecCCCCC
Confidence            9999999999875

>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=99.94  E-value=8.4e-27  Score=140.58  Aligned_cols=78  Identities=27%  Similarity=0.460  Sum_probs=66.6

Q ss_pred             CCCCC--CCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEE
Q 041342            1 MAHNP--SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAIL   78 (87)
Q Consensus         1 ~~~~~--~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I   78 (87)
                      ||+..  ....|+.+|.++++++|+|+|+||+.|+|+|.|||+|||++|+||+|+ .   +...+.+|.++|||++|++|
T Consensus         1 m~~~~~~~~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~---~~~~~~lg~v~iRG~~I~~i   76 (81)
T 1i8f_A            1 MASDISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-I---DGNVYKRGTMVVRGENVLFI   76 (81)
T ss_dssp             ---------CCHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-E---TTEEEEEEEEEECGGGEEEE
T ss_pred             CCcccCccccchHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-c---CCcccCCCEEEECCCEEEEE
Confidence            55543  468999999999999999999999999999999999999999999998 2   34578999999999999999


Q ss_pred             EeCC
Q 041342           79 VPGG   82 (87)
Q Consensus        79 ~~~~   82 (87)
                      ++.+
T Consensus        77 ~~~d   80 (81)
T 1i8f_A           77 SPVP   80 (81)
T ss_dssp             EECC
T ss_pred             EeCC
Confidence            9865

>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=99.94  E-value=2.2e-26  Score=140.41  Aligned_cols=75  Identities=27%  Similarity=0.381  Sum_probs=68.4

Q ss_pred             CcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCCCC
Q 041342            7 QLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGSP   84 (87)
Q Consensus         7 ~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~~p   84 (87)
                      +..|+.+|+++++++|+|+|+||+.|+|+|.|||+|||++|+||+|+.   +|+..+.+|.++|||++|++|++.+.-
T Consensus         4 ~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~---~g~~~~~lg~v~IRG~nI~~i~~~d~~   78 (86)
T 3s6n_F            4 PLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYI---DGALSGHLGEVLIRCNNVLYIRGVEEE   78 (86)
T ss_dssp             CCCHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEE---TTEEEEEESSEEECGGGEEEEEECC--
T ss_pred             CcCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEc---CCceeeEccEEEEeCCeEEEEEeCCcc
Confidence            478999999999999999999999999999999999999999999875   566678999999999999999987643

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

Probab=99.94  E-value=2.1e-26  Score=136.84  Aligned_cols=72  Identities=28%  Similarity=0.565  Sum_probs=66.7

Q ss_pred             cCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342            8 LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus         8 ~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      ..|+.+|.++++++|+|+|+||+.|+|+|.|||+|||++|+||+|++   .+...+.+|.++|||++|++|++.+
T Consensus         3 ~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~---~~~~~~~lg~v~iRG~~I~~i~~~~   74 (75)
T 1h64_1            3 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQ---DGEVVKRYGKIVIRGDNVLAISPTE   74 (75)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEE---TTEEEEEEEEEEECGGGEEEEEEC-
T ss_pred             chHHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEe---eCCceeECCEEEECCCEEEEEEeCC
Confidence            47999999999999999999999999999999999999999999997   3456889999999999999999864

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

Probab=99.94  E-value=1.7e-26  Score=139.81  Aligned_cols=72  Identities=33%  Similarity=0.648  Sum_probs=67.5

Q ss_pred             CCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342            6 SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP   80 (87)
Q Consensus         6 ~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~   80 (87)
                      +...|+.+|.++++++|+|+|+||+.|+|+|.|||+|||++|+||+|++   .+...+.+|.++|||++|++|++
T Consensus        12 ~~~~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~---~~~~~~~lg~v~IRG~~I~~i~p   83 (83)
T 1mgq_A           12 NVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELE---DGEVTRRLGTVLIRGDNIVYISP   83 (83)
T ss_dssp             CTTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEE---TTEEEEEEEEEEECGGGEEEEEC
T ss_pred             cCcChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEe---cCCcccCCCEEEECCCEEEEEEC
Confidence            6689999999999999999999999999999999999999999999997   34568899999999999999975

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

Probab=99.94  E-value=8e-27  Score=138.89  Aligned_cols=72  Identities=25%  Similarity=0.511  Sum_probs=67.0

Q ss_pred             cCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342            8 LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus         8 ~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      ..|+++|+++++++|+|+|+||+.|+|+|.|||+|||++|+||+|+.   ++...+.+|.++|||++|++|++.+
T Consensus         3 ~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~---~~~~~~~lg~v~iRG~~I~~i~~~~   74 (75)
T 4emk_B            3 SSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYV---NGKKTNVYGDAFIRGNNVLYVSALD   74 (75)
T ss_dssp             SHHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEE---TTEEEEEEEEEEEEGGGSSEEEEC-
T ss_pred             CchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEe---cCCcccEecEEEEcCCeEEEEEecC
Confidence            57999999999999999999999999999999999999999999986   5666889999999999999999875

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

Probab=99.94  E-value=1.3e-26  Score=139.70  Aligned_cols=77  Identities=26%  Similarity=0.440  Sum_probs=69.2

Q ss_pred             CCCCCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342            3 HNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus         3 ~~~~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      ++.-...|+.+|.++++++|+|+|+||+.|+|+|.|||+|||++|+||+|++   .+...+.+|.++|||++|++|.+.+
T Consensus         3 m~~~~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~---~~~~~~~lg~v~iRG~~I~~i~~~~   79 (81)
T 1th7_A            3 MNFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQ---SDGSGKKLGTIVIRGDNVILISPLQ   79 (81)
T ss_dssp             CCTTCHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEC---SSSCEEEEEEEEECGGGEEEEEEC-
T ss_pred             ccccccchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEe---cCCceeECCEEEECCCEEEEEEecC
Confidence            3455678999999999999999999999999999999999999999999997   3345789999999999999999865

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

Probab=99.94  E-value=1.4e-26  Score=143.12  Aligned_cols=81  Identities=25%  Similarity=0.467  Sum_probs=65.4

Q ss_pred             CCCCCCCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcc--CC--------eeeEeeCeEEE
Q 041342            1 MAHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITA--EG--------RRITKLDQILL   70 (87)
Q Consensus         1 ~~~~~~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~--~g--------~~~~~~g~v~I   70 (87)
                      |++......|+++|+.+++++|+|+|+|||.|+|+|.|||+|||++|+||+|++...  ++        ...+.+|.++|
T Consensus         1 m~~~~~~~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~i   80 (93)
T 4emg_A            1 MESAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFV   80 (93)
T ss_dssp             --------CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEE
T ss_pred             CCcccccCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEE
Confidence            565567789999999999999999999999999999999999999999999998531  12        24789999999


Q ss_pred             cCCcEEEEEeC
Q 041342           71 NGNNIAILVPG   81 (87)
Q Consensus        71 RG~~I~~I~~~   81 (87)
                      ||++|++|++.
T Consensus        81 RG~nVv~I~p~   91 (93)
T 4emg_A           81 RGDSVILIAPP   91 (93)
T ss_dssp             CGGGEEEEECC
T ss_pred             CCCeEEEEEec
Confidence            99999999974

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

Probab=99.94  E-value=3.6e-26  Score=136.35  Aligned_cols=72  Identities=29%  Similarity=0.629  Sum_probs=67.1

Q ss_pred             cCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342            8 LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus         8 ~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      ..|+++|.++++++|+|+|+||+.|+|+|.|||+|||++|+||+|++   .+...+.+|.++|||++|++|.+.+
T Consensus         3 ~~P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~---~~~~~~~lg~v~iRG~~I~~i~~~d   74 (77)
T 1i4k_A            3 PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQ---NGEVVRKVGSVVIRGDTVVFVSPAP   74 (77)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEE---TTEEEEEEEEEEECGGGEEEEEECC
T ss_pred             ccHHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEe---cCCcEeECCEEEECCCEEEEEEeCC
Confidence            47999999999999999999999999999999999999999999997   3456889999999999999999865

>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=99.94  E-value=3.5e-26  Score=141.91  Aligned_cols=78  Identities=21%  Similarity=0.462  Sum_probs=69.9

Q ss_pred             CCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccC----CeeeEeeCeEEEcCCcEEEEEeC
Q 041342            6 SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAE----GRRITKLDQILLNGNNIAILVPG   81 (87)
Q Consensus         6 ~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~----g~~~~~~g~v~IRG~~I~~I~~~   81 (87)
                      -+..|+.+|.++++++|+|+|+|||.|+|+|.|||+|||++|+||+|++...+    +...+.+|.++|||++|++|++.
T Consensus         7 ~~~~p~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nVv~I~~~   86 (96)
T 3bw1_A            7 HMETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLISTP   86 (96)
T ss_dssp             CCCCHHHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEECGGGEEEEECC
T ss_pred             hhhhHHHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEECCCEEEEEEec
Confidence            46789999999999999999999999999999999999999999999986422    34578999999999999999976


Q ss_pred             CC
Q 041342           82 GS   83 (87)
Q Consensus        82 ~~   83 (87)
                      +.
T Consensus        87 d~   88 (96)
T 3bw1_A           87 SE   88 (96)
T ss_dssp             C-
T ss_pred             Cc
Confidence            54

>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=99.94  E-value=1.3e-26  Score=142.11  Aligned_cols=79  Identities=25%  Similarity=0.427  Sum_probs=67.0

Q ss_pred             CcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcc-------CCeeeEeeCeEEEcCCcEEEEEeC
Q 041342            9 LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITA-------EGRRITKLDQILLNGNNIAILVPG   81 (87)
Q Consensus         9 ~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~-------~g~~~~~~g~v~IRG~~I~~I~~~   81 (87)
                      .|..+|.++++++|+|+|+|||.|+|+|.|||+||||+|+||+|++...       ++...+.+|.++|||++|++|++.
T Consensus         4 ~~~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~~I~~i~~~   83 (91)
T 1d3b_B            4 GKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVE   83 (91)
T ss_dssp             ---CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEE
T ss_pred             ChhHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECCCeEEEEEcC
Confidence            4667889999999999999999999999999999999999999986321       234678999999999999999999


Q ss_pred             CCCCCC
Q 041342           82 GSPDPE   87 (87)
Q Consensus        82 ~~p~~~   87 (87)
                      +.|+++
T Consensus        84 ~~~~~~   89 (91)
T 1d3b_B           84 GPPPKD   89 (91)
T ss_dssp             ECCC--
T ss_pred             CCCCCC
Confidence            988753

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

Probab=99.94  E-value=2.9e-26  Score=141.78  Aligned_cols=76  Identities=22%  Similarity=0.326  Sum_probs=62.2

Q ss_pred             CCCCcCcHHHHhhhcCCEEEEEEcCC-cEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342            4 NPSQLLPSELIDRCIGSKIWVIMKGD-KELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus         4 ~~~~~~Pl~~L~~~l~k~V~V~l~dg-r~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      ..+...|+.+|.++++++|+|+|+|| +.|+|+|.|||+|||++|+||+|++   ++...+.+|.++|||++|++|.+.+
T Consensus        16 ~~~~~~P~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~---~~~~~~~lg~v~IRG~nI~~I~~~~   92 (93)
T 1n9r_A           16 AMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFV---AGVSHGTLGEIFIRCNNVLYIRELP   92 (93)
T ss_dssp             ----------CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEE---TTEEEEECCSEEECGGGEEEEEECC
T ss_pred             ccccCChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEc---CCCeEeEcCEEEEcCCeEEEEEeCC
Confidence            34568899999999999999999999 9999999999999999999999986   4666889999999999999998764

>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=99.93  E-value=1.7e-25  Score=133.34  Aligned_cols=72  Identities=18%  Similarity=0.289  Sum_probs=65.8

Q ss_pred             CcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342            7 QLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG   81 (87)
Q Consensus         7 ~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~   81 (87)
                      ...|+++|++++|++|+|+|++|++|+|+|.|||+|||++|+||+|+.  +++ +.+.+|.++|||++|.+|+..
T Consensus         3 ~~~P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~--~~~-~~~~lg~v~IRG~nI~~i~lP   74 (75)
T 1d3b_A            3 IGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTY--RDG-RVAQLEQVYIRGCKIRFLILP   74 (75)
T ss_dssp             -CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC--TTS-CEEEEEEEEECGGGEEEEEEC
T ss_pred             ccCHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEEC--CCC-cEEEcCeEEEeCCEEEEEEcC
Confidence            467999999999999999999999999999999999999999999985  244 378999999999999999875

>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=99.93  E-value=3e-26  Score=141.48  Aligned_cols=75  Identities=28%  Similarity=0.500  Sum_probs=67.6

Q ss_pred             CCcCcHHHHhhhcCCEEEEEE----cCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342            6 SQLLPSELIDRCIGSKIWVIM----KGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG   81 (87)
Q Consensus         6 ~~~~Pl~~L~~~l~k~V~V~l----~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~   81 (87)
                      .+.+|+++|.++++++++|++    +||++|+|+|.|||+|||++|+||+|+..  ++...+.+|.++|||++|++|++.
T Consensus        13 ~m~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~--~~~~~~~lg~v~iRG~nV~~i~~~   90 (92)
T 3s6n_E           13 VMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHS--KTKSRKQLGRIMLKGDNITLLQSV   90 (92)
T ss_dssp             -CCCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECS--SSCCEEEEEEEEECGGGEEEEEEC
T ss_pred             eccCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEec--CCCceeEcCeEEEeCCEEEEEEeC
Confidence            479999999999999999988    99999999999999999999999999963  344578999999999999999986


Q ss_pred             C
Q 041342           82 G   82 (87)
Q Consensus        82 ~   82 (87)
                      +
T Consensus        91 ~   91 (92)
T 3s6n_E           91 S   91 (92)
T ss_dssp             -
T ss_pred             C
Confidence            4

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

Probab=99.92  E-value=3.1e-25  Score=139.81  Aligned_cols=76  Identities=28%  Similarity=0.473  Sum_probs=56.3

Q ss_pred             CCCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342            5 PSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus         5 ~~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      ..+-.|+.+|.++++++|+|+|+||+.|+|+|.|||+|||++|+||+|+.  .+|+..+.+|.++|||++|++|...+
T Consensus        12 ~~~~~p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~--~dg~~~~~lg~v~IRG~nI~~I~~pd   87 (105)
T 4emh_A           12 QDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTM--PDGDKFFRLPECYIRGNNIKYLRIQD   87 (105)
T ss_dssp             --------------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC--TTSCEEEEEEEEEECGGGEEEEEC--
T ss_pred             CCCCcHHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEc--cCCceeeEcCeEEEeCCeEEEEecCH
Confidence            34578999999999999999999999999999999999999999999985  36666789999999999999998754

>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=99.92  E-value=4.6e-25  Score=140.56  Aligned_cols=77  Identities=27%  Similarity=0.462  Sum_probs=57.3

Q ss_pred             CcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCC----eeeEeeCeEEEcCCcEEEEEeCC
Q 041342            7 QLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEG----RRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus         7 ~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g----~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      ...|+..|.++++++|+|+|+|||.|+|+|.|||+||||||+||+|++...++    ...+.+|.++|||++|++|++.+
T Consensus        21 kke~i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d  100 (113)
T 4emk_C           21 RKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIAPMD  100 (113)
T ss_dssp             -----------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTTEEEEEECC
T ss_pred             ccchHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCeEEEEEecC
Confidence            35678899999999999999999999999999999999999999999754322    35789999999999999999876


Q ss_pred             C
Q 041342           83 S   83 (87)
Q Consensus        83 ~   83 (87)
                      .
T Consensus       101 ~  101 (113)
T 4emk_C          101 G  101 (113)
T ss_dssp             -
T ss_pred             c
Confidence            4

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

Probab=99.92  E-value=2.9e-25  Score=132.47  Aligned_cols=70  Identities=20%  Similarity=0.483  Sum_probs=52.6

Q ss_pred             cHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342           10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus        10 Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      |-.+|.++++++|+|+|+|||.|+|+|.|||+|||++|+||+|+..   +.+.+.+|.++|||++|++|++.+
T Consensus         5 ~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~---~~~~~~lg~v~iRG~~I~~i~~~d   74 (76)
T 3s6n_G            5 HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMAT---SGQQNNIGMVVIRGNSIIMLEALE   74 (76)
T ss_dssp             ---------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCC---C----CBSSEEECSSSEEEEEC--
T ss_pred             chHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEcc---CCcEeEcCEEEECCCeEEEEEecc
Confidence            5578999999999999999999999999999999999999999863   234689999999999999999875

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

Probab=99.91  E-value=2.7e-24  Score=137.95  Aligned_cols=73  Identities=22%  Similarity=0.330  Sum_probs=66.1

Q ss_pred             cCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCCC
Q 041342            8 LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGS   83 (87)
Q Consensus         8 ~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~~   83 (87)
                      +.|+.+|.++++++|+|+|+||++|+|+|.+||+|||++|+||+|+.   .+.+.+.+|.+||||++|++|++.+.
T Consensus         1 M~p~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~---~~~~~~~lg~v~IRG~nI~~I~~pd~   73 (119)
T 1b34_A            1 MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTL---KNREPVQLETLSIRGNNIRYFILPDS   73 (119)
T ss_dssp             -CHHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEEC---TTSCCEEEEEEEECGGGEEEEECCTT
T ss_pred             CChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEec---CCCceeEcceEEEcCCeEEEEEeccc
Confidence            47999999999999999999999999999999999999999999985   23346899999999999999997654

>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=99.91  E-value=5.5e-24  Score=149.13  Aligned_cols=79  Identities=25%  Similarity=0.423  Sum_probs=69.7

Q ss_pred             cCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEc--c-----CCeeeEeeCeEEEcCCcEEEEEe
Q 041342            8 LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEIT--A-----EGRRITKLDQILLNGNNIAILVP   80 (87)
Q Consensus         8 ~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~--~-----~g~~~~~~g~v~IRG~~I~~I~~   80 (87)
                      +.+-..|.++++|+|+|+|+|||+|+|+|++||+||||||+||+|++..  +     ++++.+++|++||||+||++|+.
T Consensus         3 v~k~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~Isv   82 (231)
T 3pgw_B            3 VGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTV   82 (231)
T ss_pred             cCchHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEEEEe
Confidence            4567899999999999999999999999999999999999999999741  1     23468999999999999999998


Q ss_pred             CCCCCC
Q 041342           81 GGSPDP   86 (87)
Q Consensus        81 ~~~p~~   86 (87)
                      .+.|++
T Consensus        83 e~pPp~   88 (231)
T 3pgw_B           83 EGPPPK   88 (231)
T ss_pred             cCCCCC
Confidence            887754

>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=99.91  E-value=4.1e-24  Score=136.83  Aligned_cols=77  Identities=22%  Similarity=0.456  Sum_probs=64.4

Q ss_pred             CcCcHHHHhhhc--CCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcc--C--C-------eeeEeeCeEEEcCC
Q 041342            7 QLLPSELIDRCI--GSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITA--E--G-------RRITKLDQILLNGN   73 (87)
Q Consensus         7 ~~~Pl~~L~~~l--~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~--~--g-------~~~~~~g~v~IRG~   73 (87)
                      +..|+++|.+++  +++|+|+|+|||.|+|+|.|||+|||++|+||+|++...  +  +       ...+.+|.+||||+
T Consensus        25 ~~~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~  104 (118)
T 1b34_B           25 NTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGD  104 (118)
T ss_dssp             -CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGG
T ss_pred             ccChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcCC
Confidence            579999999999  599999999999999999999999999999999987431  1  1       12467999999999


Q ss_pred             cEEEEEeCCC
Q 041342           74 NIAILVPGGS   83 (87)
Q Consensus        74 ~I~~I~~~~~   83 (87)
                      +|++|++.+.
T Consensus       105 nVv~I~~~~~  114 (118)
T 1b34_B          105 SVIVVLRNPL  114 (118)
T ss_dssp             GEEEEEECCC
T ss_pred             EEEEEEeCch
Confidence            9999998765

>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=99.89  E-value=3.5e-23  Score=134.04  Aligned_cols=73  Identities=18%  Similarity=0.297  Sum_probs=66.2

Q ss_pred             CcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342            7 QLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus         7 ~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      ...|+++|+++++++|+|+|++|++|+|+|.+||+|||++|+||+|+.  .+++ ...++.+||||++|.+|+..+
T Consensus         3 ~~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~--~~g~-~~~l~~v~IRGnnI~~I~lpd   75 (126)
T 2y9a_D            3 IGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTY--RDGR-VAQLEQVYIRGSKIRFLILPD   75 (126)
T ss_dssp             -CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEEC--TTSC-CEEEEEEEECGGGEEEEECCS
T ss_pred             cccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEc--CCCc-EeecccEEEeCCEEEEEEccc
Confidence            468999999999999999999999999999999999999999999985  3453 789999999999999999654

>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=99.85  E-value=2.4e-21  Score=125.97  Aligned_cols=67  Identities=16%  Similarity=0.321  Sum_probs=61.8

Q ss_pred             HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCCCC
Q 041342           11 SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGSP   84 (87)
Q Consensus        11 l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~~p   84 (87)
                      ..+|.+++|++|+|+|+||+.|+|+|.|||+|||++|+||+|+    ++   +.+|.++|||++|++|.+.+.|
T Consensus         2 ~~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~----~~---~~lg~v~IRG~nI~~I~~~d~~   68 (130)
T 1m5q_A            2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNK----AG---EKFNRVFIMYRYIVHIDSTERR   68 (130)
T ss_dssp             HHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECT----TC---CEEEEEEECGGGEEEEEECCCC
T ss_pred             hhHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEE----cC---CEeceEEEeCCeEEEEEcCCcc
Confidence            3689999999999999999999999999999999999999996    22   5789999999999999998876

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

Probab=99.19  E-value=1.1e-10  Score=70.94  Aligned_cols=67  Identities=19%  Similarity=0.165  Sum_probs=58.8

Q ss_pred             CcHHHHhhhcCCEEEEEEcCCcEEEEEEEEec-cccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCCCCC
Q 041342            9 LPSELIDRCIGSKIWVIMKGDKELVGTLKGFD-VYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGSPD   85 (87)
Q Consensus         9 ~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D-~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~~p~   85 (87)
                      .|+ .|.+++||+|.|.+.||++|+|+|.+|| ...|++|.||.      ++.   ....++|.|..|..|...+.|+
T Consensus         8 ~p~-el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~~------~~~---~~~~~iI~G~aI~eI~v~~~~~   75 (86)
T 1y96_A            8 GPL-EWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFL------EDG---SMSVTGIMGHAVQTVETMNEGD   75 (86)
T ss_dssp             CHH-HHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEEC------TTS---CEEEEEECGGGEEEEEEEECCC
T ss_pred             CHH-HHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeecc------cCC---eEEEEEEecceEEEEEEecchh
Confidence            455 7899999999999999999999999999 89999999992      222   3578999999999999888875

>2fb7_A SM-like protein, LSM-14_N (RAP55); DR.13312, BC055387, AAH55387, stronGly BENT five-stranded antiparallel beta- sheet, structural genomics, PSI; NMR {Danio rerio} SCOP: b.38.1.5 PDB: 2vxf_A

Probab=97.89  E-value=3.4e-05  Score=47.28  Aligned_cols=77  Identities=25%  Similarity=0.321  Sum_probs=58.5

Q ss_pred             cHHHHhhhcCCEEEEEEcCCcEEEEEEEEec-cccceEEcceEEEEEcc---CCe---eeEeeCeEEEcCCcEEEEEeCC
Q 041342           10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFD-VYVNMVLEDVTEYEITA---EGR---RITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus        10 Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D-~~mNlvL~~~~e~~~~~---~g~---~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      |-..-..++|++|.+..+.+-.|+|+|..+| +..-+.|.|+.-+.++.   ++.   ...-+..++.||+.|..+...+
T Consensus        10 ~~~~~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~~ipp~~~vyeyIvFrGsDIKDL~V~e   89 (95)
T 2fb7_A           10 DPSGGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCE   89 (95)
T ss_dssp             ------CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSSCCCSCCCCSSCEEECSTTEEEEEESC
T ss_pred             CCCccCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCCccCCCCcceeEEEEcCCCcceEEEec
Confidence            4445578999999999999999999999999 57888999987654321   110   2345689999999999999999


Q ss_pred             CCCC
Q 041342           83 SPDP   86 (87)
Q Consensus        83 ~p~~   86 (87)
                      .|++
T Consensus        90 ~p~~   93 (95)
T 2fb7_A           90 PPKP   93 (95)
T ss_dssp             CSCS
T ss_pred             CCCC
Confidence            8876

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

Probab=97.56  E-value=0.00065  Score=41.04  Aligned_cols=69  Identities=25%  Similarity=0.303  Sum_probs=55.0

Q ss_pred             hhcCCEEEEEEcCCcEEEEEEEEec-cccceEEcceEEEEEcc-CCe-----eeEeeCeEEEcCCcEEEEEeCCCC
Q 041342           16 RCIGSKIWVIMKGDKELVGTLKGFD-VYVNMVLEDVTEYEITA-EGR-----RITKLDQILLNGNNIAILVPGGSP   84 (87)
Q Consensus        16 ~~l~k~V~V~l~dgr~~~G~L~~~D-~~mNlvL~~~~e~~~~~-~g~-----~~~~~g~v~IRG~~I~~I~~~~~p   84 (87)
                      .|+|++|.+..+.+-.|+|+|..+| +..-+.|.|+.-+.++. ...     ...-+..++.||+.|..+...+..
T Consensus        10 ~yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~yIvFrgsDIKdL~V~~~~   85 (88)
T 2vxe_A           10 PELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQIAPQSQIYDYILFRGSDIKDIRVVNNH   85 (88)
T ss_dssp             CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCTTTCCSSCCCCCCSCEEEEEEETTTEEEEEECCCC
T ss_pred             cccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCcCCCCCcccCCCCceeeEEEEccCCccEEEEeccC
Confidence            4799999999999999999999999 57889999998765421 000     234568999999999999876654

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

Probab=97.24  E-value=0.00047  Score=40.43  Aligned_cols=56  Identities=14%  Similarity=0.303  Sum_probs=40.7

Q ss_pred             HHHHhhhc--CCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342           11 SELIDRCI--GSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus        11 l~~L~~~l--~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      -.+|+.+.  ...|+|.|.+|..++|.+.+||+|+=++-++                ...+|--..|..|.+..
T Consensus        11 d~~L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~vlL~~~----------------~~~LIYKhAIsTI~p~~   68 (74)
T 2ylb_A           11 DPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNT----------------VSQMVYKHAISTVVPSR   68 (74)
T ss_dssp             HHHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEESS----------------SEEEEEGGGEEEEEESS
T ss_pred             HHHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEECC----------------ceEEEEeeeEEEEeEcc
Confidence            34666666  5689999999999999999999998555322                24456666666666554

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

Probab=97.20  E-value=0.00052  Score=40.98  Aligned_cols=36  Identities=14%  Similarity=0.303  Sum_probs=29.6

Q ss_pred             HHHhhhc--CCEEEEEEcCCcEEEEEEEEeccccceEE
Q 041342           12 ELIDRCI--GSKIWVIMKGDKELVGTLKGFDVYVNMVL   47 (87)
Q Consensus        12 ~~L~~~l--~k~V~V~l~dgr~~~G~L~~~D~~mNlvL   47 (87)
                      .+|..+.  ...|+|.|.||..++|.+.+||+|+=++-
T Consensus        10 ~fLn~lrk~~~~Vtv~L~NG~~l~G~I~~fD~ftVlL~   47 (82)
T 1u1s_A           10 PYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLK   47 (82)
T ss_dssp             HHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEe
Confidence            3556555  56899999999999999999999986654

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

Probab=97.15  E-value=0.00044  Score=41.07  Aligned_cols=35  Identities=17%  Similarity=0.376  Sum_probs=29.1

Q ss_pred             HHHhhhcCC--EEEEEEcCCcEEEEEEEEeccccceE
Q 041342           12 ELIDRCIGS--KIWVIMKGDKELVGTLKGFDVYVNMV   46 (87)
Q Consensus        12 ~~L~~~l~k--~V~V~l~dgr~~~G~L~~~D~~mNlv   46 (87)
                      .+|..+..+  .|+|.|.+|..++|.+.+||+|+=++
T Consensus        11 ~fLn~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~VlL   47 (79)
T 3sb2_A           11 PFLNALRKEHVPVSIYLVNGIKLQGHVESFDQYVVLL   47 (79)
T ss_dssp             HHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEE
Confidence            466666654  69999999999999999999998665

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

Probab=97.14  E-value=0.0013  Score=38.78  Aligned_cols=37  Identities=14%  Similarity=0.295  Sum_probs=30.6

Q ss_pred             HHHhhhc--CCEEEEEEcCCcEEEEEEEEeccccceEEc
Q 041342           12 ELIDRCI--GSKIWVIMKGDKELVGTLKGFDVYVNMVLE   48 (87)
Q Consensus        12 ~~L~~~l--~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~   48 (87)
                      .+|+.+.  ...|+|.|.+|..++|.+.+||+|+=++-.
T Consensus        10 ~fLn~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~VlL~~   48 (77)
T 1kq1_A           10 KALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNS   48 (77)
T ss_dssp             HHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEEE
T ss_pred             HHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEEEE
Confidence            3566666  678999999999999999999999866543

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

Probab=97.11  E-value=0.0011  Score=39.29  Aligned_cols=35  Identities=20%  Similarity=0.409  Sum_probs=29.2

Q ss_pred             HHhhhc--CCEEEEEEcCCcEEEEEEEEeccccceEE
Q 041342           13 LIDRCI--GSKIWVIMKGDKELVGTLKGFDVYVNMVL   47 (87)
Q Consensus        13 ~L~~~l--~k~V~V~l~dgr~~~G~L~~~D~~mNlvL   47 (87)
                      +|..+.  ...|+|.|.||..++|.+.+||+|+=++-
T Consensus        15 fLn~lrk~~~~Vtv~L~nG~~l~G~I~~fD~f~VlL~   51 (78)
T 3ahu_A           15 FLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFTVLLE   51 (78)
T ss_dssp             HHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEEEE
Confidence            455555  57899999999999999999999986654

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

Probab=97.05  E-value=0.0023  Score=38.28  Aligned_cols=65  Identities=14%  Similarity=0.125  Sum_probs=53.6

Q ss_pred             hhhcCCEEEEEEcCCc-EEEEEEEEecc-ccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCCCCC
Q 041342           15 DRCIGSKIWVIMKGDK-ELVGTLKGFDV-YVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGSPD   85 (87)
Q Consensus        15 ~~~l~k~V~V~l~dgr-~~~G~L~~~D~-~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~~p~   85 (87)
                      .+|+|+.|.+..+++- .|+|.|..+|+ ..||.|.+|.     .+|- +.....+.+|+.-|..+..++.|+
T Consensus         5 ~~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~f-----~NG~-~~~s~eVtls~~DI~~L~ii~~~~   71 (84)
T 2vc8_A            5 TDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPF-----HNGV-KCLVPEVTFRAGDITELKILEIPG   71 (84)
T ss_dssp             CTTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEEE-----ETTE-ECSSSEEEEEGGGCSEEEEEECCC
T ss_pred             ccccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehhh-----hCCC-CCCCcEEEEEecChhheEEEecCC
Confidence            4799999999999999 99999999996 4689999994     2664 334467999999888887777664

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

Probab=96.98  E-value=0.0017  Score=37.73  Aligned_cols=30  Identities=23%  Similarity=0.380  Sum_probs=26.1

Q ss_pred             CCEEEEEEcCCcEEEEEEEEeccccceEEc
Q 041342           19 GSKIWVIMKGDKELVGTLKGFDVYVNMVLE   48 (87)
Q Consensus        19 ~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~   48 (87)
                      +..|+|.|.||..++|.+.+||+|+=++-.
T Consensus        25 ~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~   54 (71)
T 2qtx_A           25 GKKVKIFLRNGEVLDAEVTGVSNYEIMVKV   54 (71)
T ss_dssp             TCEEEEEETTSCEEEEEEEEECSSEEEEEE
T ss_pred             CCcEEEEEeCCeEEEEEEEEEcceEEEEEe
Confidence            458999999999999999999999866543

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

Probab=96.75  E-value=0.0055  Score=39.07  Aligned_cols=57  Identities=19%  Similarity=0.230  Sum_probs=45.1

Q ss_pred             HhhhcCCEEEEEEcCCcEEEEEEEEeccccceEE--cceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCCCC
Q 041342           14 IDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVL--EDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGSP   84 (87)
Q Consensus        14 L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL--~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~~p   84 (87)
                      ..+|+|..|.|+|+||..++|++..+| --+|.|  ++|..-+             .-|+...|.-+..++.|
T Consensus         7 ~sqFlGy~V~v~LkDgs~~qG~I~~vd-~k~LtL~~~~a~~s~-------------~~I~asdI~DLkVl~~~   65 (125)
T 4a53_A            7 VADFYGSNVEVLLNNDSKARGVITNFD-SSNSILQLRLANDST-------------KSIVTKDIKDLRILPKN   65 (125)
T ss_dssp             HHHHTTCEEEEEETTSCEEEEEEEEEE-TTTTEEEEEETTTEE-------------EEEEGGGEEEEEECCSC
T ss_pred             HHHhcCceEEEEECCCCEeeEEEEeec-CCeeEEecccccccc-------------ceeecccccceeeeecc
Confidence            478999999999999999999999998 456777  8884321             17777778777766655

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

Probab=96.68  E-value=0.0024  Score=39.60  Aligned_cols=39  Identities=13%  Similarity=0.316  Sum_probs=31.6

Q ss_pred             HHHHhhhcCC--EEEEEEcCCcEEEEEEEEeccccceEEcc
Q 041342           11 SELIDRCIGS--KIWVIMKGDKELVGTLKGFDVYVNMVLED   49 (87)
Q Consensus        11 l~~L~~~l~k--~V~V~l~dgr~~~G~L~~~D~~mNlvL~~   49 (87)
                      =.+|..+..+  .|+|.|.+|..++|++.+||+|+=++-++
T Consensus        11 d~fLn~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~VlL~~~   51 (104)
T 2y90_A           11 DPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNT   51 (104)
T ss_dssp             HHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEESS
T ss_pred             HHHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEECC
Confidence            3466766665  79999999999999999999998666543

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

Probab=96.28  E-value=0.03  Score=32.51  Aligned_cols=64  Identities=16%  Similarity=0.156  Sum_probs=44.3

Q ss_pred             CCCCcCc-HHHHhhhcC--CEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342            4 NPSQLLP-SELIDRCIG--SKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP   80 (87)
Q Consensus         4 ~~~~~~P-l~~L~~~l~--k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~   80 (87)
                      .-...+| ...|++++.  ..|.|+|.+|..+.|.+.-+|+++=++-++. .             ..++|.-..|.+|.+
T Consensus         5 ~fdt~lPsvR~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~cl~L~~~~-~-------------~~~LI~R~AI~~Ikp   70 (72)
T 3hfn_A            5 EFDTSLPSIRQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTCVCIADEN-S-------------RQTTIWKQAIAYLQP   70 (72)
T ss_dssp             ----CHHHHHHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSEEEEEC-----------------CEEEEEGGGEEEEEE
T ss_pred             ccCCCCCcHHHHHHHHhhCceEEEEecCCCEEEEEEEEECCCEEEEEcCC-C-------------CeEEEEeeeeEEEEe
Confidence            3366777 788999997  4699999999999999999999875544332 1             145666667777765


Q ss_pred             C
Q 041342           81 G   81 (87)
Q Consensus        81 ~   81 (87)
                      .
T Consensus        71 ~   71 (72)
T 3hfn_A           71 K   71 (72)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=95.90  E-value=0.026  Score=32.62  Aligned_cols=44  Identities=16%  Similarity=0.111  Sum_probs=35.5

Q ss_pred             CCCCcCc-HHHHhhhcC--CEEEEEEcCCcEEEEEEEEeccccceEE
Q 041342            4 NPSQLLP-SELIDRCIG--SKIWVIMKGDKELVGTLKGFDVYVNMVL   47 (87)
Q Consensus         4 ~~~~~~P-l~~L~~~l~--k~V~V~l~dgr~~~G~L~~~D~~mNlvL   47 (87)
                      .-.+.+| ...|++++.  ..|.|+|.+|..+.|.+.-+|+|+=++-
T Consensus         3 ~fdt~lPsvR~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~cl~L~   49 (70)
T 3hfo_A            3 RFDSGLPSVRQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDGLGLV   49 (70)
T ss_dssp             --CCSCHHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             cccCCCCcHHHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCEEEEE
Confidence            4456677 778888885  5799999999999999999999875554

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

Probab=95.72  E-value=0.086  Score=30.01  Aligned_cols=60  Identities=27%  Similarity=0.427  Sum_probs=41.2

Q ss_pred             HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEE
Q 041342           12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILV   79 (87)
Q Consensus        12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~   79 (87)
                      ..|.++.|++|-|-......|+|+|.-||+- -+.|+|++.+..    .   +-..++++=+.|--|-
T Consensus         9 ktL~~WKg~rvAv~vg~ehSFtGiledFDeE-viLL~dV~D~~G----N---k~k~liv~idDinWim   68 (71)
T 1ycy_A            9 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEE-VILLKDVVDVIG----N---RGKQMLIGLEDINWIM   68 (71)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSS-EEEEEEEEETTE----E---EEEEEEEEGGGEEEEE
T ss_pred             HHHHHhCCcEEEEEecCcceeeeehhhcCcc-eeehhhHHHHhc----c---ccceeEEEeccceEEE
Confidence            4688999999999999999999999999975 478899987642    2   1224555555554443

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

Probab=95.48  E-value=0.042  Score=32.83  Aligned_cols=62  Identities=11%  Similarity=0.125  Sum_probs=49.7

Q ss_pred             HHHHhhhcCCEEEEEEcCCcEEEEEEEEec-cccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342           11 SELIDRCIGSKIWVIMKGDKELVGTLKGFD-VYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP   80 (87)
Q Consensus        11 l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D-~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~   80 (87)
                      |.+|....+++|.+.+.++....|++.++| ...|+..++-. +   +=|    .++..++|+.-|++++-
T Consensus        21 Lr~l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-T---PiG----v~~eAlLR~~Dii~~sF   83 (85)
T 1y96_B           21 LRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQ-T---PIG----VQAEALLRCSDIISYTF   83 (85)
T ss_dssp             HHHHHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEC-C---TTC----CEEEEEEEGGGEEEEEE
T ss_pred             HHHHHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhcC-C---Ccc----cchhhhhhcCCEEEEEe
Confidence            556778889999999999999999999999 47777766653 1   123    35789999999998874

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

Probab=93.16  E-value=0.86  Score=27.81  Aligned_cols=65  Identities=11%  Similarity=0.121  Sum_probs=52.3

Q ss_pred             hhhcCCEEEEEEcCCc-EEEEEEEEeccccceEEcceEEEEEccCCe-eeEeeCeEEEcCCcEEEEEeCCCCC
Q 041342           15 DRCIGSKIWVIMKGDK-ELVGTLKGFDVYVNMVLEDVTEYEITAEGR-RITKLDQILLNGNNIAILVPGGSPD   85 (87)
Q Consensus        15 ~~~l~k~V~V~l~dgr-~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~-~~~~~g~v~IRG~~I~~I~~~~~p~   85 (87)
                      .+|+|+-|.|.+.+.- .|+|.+...|+ .+|.|.+|..     +|- -+.....|.++..-|..+..++.++
T Consensus         8 edwiG~~VSI~C~d~LGVyQG~I~~V~~-~~ItL~kaFr-----NGiplk~~~~EVtLsa~DI~~L~IIe~~~   74 (103)
T 2rm4_A            8 QDWIGCAVSIACDEVLGVFQGLIKQISA-EEITIVRAFR-----NGVPLRKQNAEVVLKCTDIRSIDLIEPAK   74 (103)
T ss_dssp             GGGTTCEEEEEECTTTCEEEEEEEEEET-TEEEEEEEEE-----TTEECSCSSSCEEEETTTEEEEEEEECCC
T ss_pred             cceeceEEEEeeCCcceEeeEEEEEccc-ceeEEhhhhh-----cCcCcCCCCceEEEEecchhheeeecccc
Confidence            4899999999999887 99999999995 4599999974     553 1235578889999898888777664

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

Probab=92.93  E-value=0.15  Score=35.69  Aligned_cols=34  Identities=26%  Similarity=0.437  Sum_probs=30.2

Q ss_pred             hcCCEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342           17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDV   50 (87)
Q Consensus        17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~   50 (87)
                      .+|++|+|...+|..+.|+..|+|+...|+|+..
T Consensus       222 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~~  255 (270)
T 3rux_A          222 TIGSRVRVELPGGQDVVGIARDIDDQGRLCLDVG  255 (270)
T ss_dssp             STTSEEEEECTTSCEEEEEEEEECTTSCEEEEET
T ss_pred             ccCCEEEEEECCCeEEEEEEEEECCCCeEEEEEC
Confidence            3589999998889999999999999999999754

>2xk0_A Polycomb protein PCL; transcription, aromatic CAGE; NMR {Drosophila melanogaster}

Probab=92.90  E-value=0.17  Score=29.06  Aligned_cols=53  Identities=13%  Similarity=0.226  Sum_probs=33.3

Q ss_pred             CCCCCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceE-EcceEEEEE
Q 041342            3 HNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMV-LEDVTEYEI   55 (87)
Q Consensus         3 ~~~~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlv-L~~~~e~~~   55 (87)
                      ++|+.-.|.---.=.++..|.++.+||+.|-|+++...+..=+| .+|-.+.|.
T Consensus         3 m~pp~~a~~pa~~~~~geDVL~rw~DG~fYLGtIVd~~~~~ClV~FeD~S~~Wv   56 (69)
T 2xk0_A            3 MAPPVAAPSPAVTYALQEDVFIKCNDGRFYLGTIIDQTSDQYLIRFDDQSEQWC   56 (69)
T ss_dssp             SSCSSSSSCCCCCCCTTCEEEEECTTSCEEEEEEEEECSSCEEEEETTCCEEEE
T ss_pred             CCCCCCCCCcccccccCCeEEEEecCCCEEEEEEEecCCceEEEEecCCcceee
Confidence            44544444322233467899999999999999996665433333 355555553

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

Probab=92.57  E-value=0.11  Score=35.63  Aligned_cols=47  Identities=17%  Similarity=0.282  Sum_probs=33.8

Q ss_pred             hcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcC
Q 041342           17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNG   72 (87)
Q Consensus        17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG   72 (87)
                      .+|++|++...++  +.|+..++|+...|+++..       +|.+....|.|.+|+
T Consensus       186 ~~g~~V~v~~~~~--~~G~~~gId~~G~L~v~~~-------~G~~~~~~Gev~~r~  232 (233)
T 2eay_A          186 YLGEEVKLLGEGK--ITGKLVGLSEKGGALILTE-------EGIKEILSGEFSLRR  232 (233)
T ss_dssp             TTTSEEEETTEEE--EEEEEEEECTTSCEEEEET-------TEEEEECSCCEEEC-
T ss_pred             ccCCEEEEEECCe--EEEEEEEECCCCeEEEEEC-------CCeEEEEEeEEEEec
Confidence            3689999976654  9999999999999999753       222223456777764

>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=92.28  E-value=0.12  Score=33.98  Aligned_cols=44  Identities=23%  Similarity=0.339  Sum_probs=32.1

Q ss_pred             CCCCCcCcHH---HHhhhcCCEEEEEEc----CCcEEEEEEEEeccccceEE
Q 041342            3 HNPSQLLPSE---LIDRCIGSKIWVIMK----GDKELVGTLKGFDVYVNMVL   47 (87)
Q Consensus         3 ~~~~~~~Pl~---~L~~~l~k~V~V~l~----dgr~~~G~L~~~D~~mNlvL   47 (87)
                      ++|=...||.   .+.+++|+.|.|+++    +.+.++|+|.++|.- .+.|
T Consensus        85 SSPGldRpL~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~-~v~l  135 (164)
T 1ib8_A           85 TSPGLERPLKTKDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED-ELTM  135 (164)
T ss_dssp             ECCSSSSCCSSHHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT-EEEE
T ss_pred             eCCCCCCCCCCHHHHHHhCCcEEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence            3555555644   456789999999994    458999999999964 3444

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

Probab=91.81  E-value=0.43  Score=33.89  Aligned_cols=48  Identities=25%  Similarity=0.263  Sum_probs=35.0

Q ss_pred             hcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcC
Q 041342           17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNG   72 (87)
Q Consensus        17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG   72 (87)
                      .+|++|+|... +..+.|+..|+|....|+++..       +|......|.|.+|+
T Consensus       271 ~~g~~V~v~~~-~~~~~G~~~gid~~G~L~v~~~-------~g~~~~~~Gev~~r~  318 (321)
T 1bia_A          271 FINRPVKLIIG-DKEIFGISRGIDKQGALLLEQD-------GIIKPWMGGEISLRS  318 (321)
T ss_dssp             TTTSEEEEEET-TEEEEEEEEEECTTSCEEEEET-------TEEEEESSCEEEEC-
T ss_pred             hcCCEEEEEEC-CcEEEEEEEEECCCCeEEEEEC-------CCEEEEEeeeEEEec
Confidence            46899999876 4589999999999999999743       222233456777764

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

Probab=91.08  E-value=0.59  Score=31.92  Aligned_cols=32  Identities=13%  Similarity=0.314  Sum_probs=28.2

Q ss_pred             hcCCEEEEEEcCCcEEEEEEEEeccccceEEcc
Q 041342           17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLED   49 (87)
Q Consensus        17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~   49 (87)
                      .+|++|+|...++..+.|+..|+|....|+ +.
T Consensus       190 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~-~~  221 (237)
T 2ej9_A          190 TIGKQVKILLSNNEIITGKVYDIDFDGIVL-GT  221 (237)
T ss_dssp             STTCEEEEEETTSCEEEEEEEEECSSEEEE-EE
T ss_pred             ccCCEEEEEECCCeEEEEEEEEECCCCeEE-Ec
Confidence            468999999988777999999999999998 64

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

Probab=88.68  E-value=0.26  Score=33.74  Aligned_cols=31  Identities=13%  Similarity=0.367  Sum_probs=24.3

Q ss_pred             cCCEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342           18 IGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDV   50 (87)
Q Consensus        18 l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~   50 (87)
                      +|++|++...++  +.|+..++|+...|+++..
T Consensus       188 ~g~~V~v~~~~~--~~G~~~gId~~G~L~v~~~  218 (235)
T 2dxu_A          188 LGVRVKILGDGS--FEGIAEDIDDFGRLIIRLD  218 (235)
T ss_dssp             CSSEEEC----C--CEEEEEEECTTSCEEEECT
T ss_pred             cCCeEEEEECCe--EEEEEEEECCCCEEEEEEC
Confidence            689999988766  9999999999999999753

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

Probab=85.67  E-value=1.3  Score=24.45  Aligned_cols=37  Identities=19%  Similarity=0.223  Sum_probs=27.5

Q ss_pred             cCCEEEEEEcCCcEEEEEEEEecccc---ceEEcceEEEE
Q 041342           18 IGSKIWVIMKGDKELVGTLKGFDVYV---NMVLEDVTEYE   54 (87)
Q Consensus        18 l~k~V~V~l~dgr~~~G~L~~~D~~m---NlvL~~~~e~~   54 (87)
                      .|..|.++-+||+.|-|++..+|..-   =+...|-.+.+
T Consensus         6 ~GedVLarwsDG~fYlGtI~~V~~~~~~clV~F~D~s~~W   45 (58)
T 4hcz_A            6 EGQDVLARWTDGLLYLGTIKKVDSAREVCLVQFEDDSQFL   45 (58)
T ss_dssp             TTCEEEEECTTSCEEEEEEEEEETTTTEEEEEETTSCEEE
T ss_pred             cCCEEEEEecCCCEEeEEEEEEecCCCEEEEEEcCCCeEE
Confidence            36789999999999999999998653   33334554444

>2e12_A SM-like motif, hypothetical protein XCC3642; novel SM-like motif, LSM motif, X- RAY crystallography, translation; 1.70A {Xanthomonas campestris PV}

Probab=84.43  E-value=2  Score=25.90  Aligned_cols=26  Identities=12%  Similarity=0.248  Sum_probs=21.0

Q ss_pred             HHHHhhhcC--CEEEEEEcCCcEEEEEE
Q 041342           11 SELIDRCIG--SKIWVIMKGDKELVGTL   36 (87)
Q Consensus        11 l~~L~~~l~--k~V~V~l~dgr~~~G~L   36 (87)
                      |+-|...++  .+|.+++.||+.+.||+
T Consensus        18 Le~~~~~LdGq~~v~i~l~DGs~l~GTv   45 (101)
T 2e12_A           18 LEHWVKLLDGQERVRIELDDGSMIAGTV   45 (101)
T ss_dssp             HHHHHHTSCTTCEEEEEETTSCEEEEEE
T ss_pred             HHHHHHhhCCeeEEEEEEcCCCeEeeee
Confidence            445555565  58999999999999998

>3rkx_A Biotin-[acetyl-COA-carboxylase] ligase; biotin protein ligase, 3 domains, enzyme DNA binding, biotin coupling domains; 2.10A {Staphylococcus aureus} PDB: 3rir_A* 3rkw_A 3rky_A* 3v7c_A* 3v7s_A* 3v8j_A 3v7r_A 3v8k_A* 3v8l_A* 4dq2_A*

Probab=82.93  E-value=2.1  Score=30.57  Aligned_cols=33  Identities=15%  Similarity=0.205  Sum_probs=27.0

Q ss_pred             hcCCEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342           17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDV   50 (87)
Q Consensus        17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~   50 (87)
                      .+|++|+|... +..+.|+..|+|+...|+++..
T Consensus       277 ~~g~~V~v~~~-~~~~~G~~~gId~~G~Llv~~~  309 (323)
T 3rkx_A          277 IWNRTLLFTEN-DKQFKGQAIDLDYDGYLIVRDE  309 (323)
T ss_dssp             CSSSCEEEECC--CEEEEEEEEECTTSCEEEEET
T ss_pred             hcCCEEEEEEC-CeEEEEEEEEECCCCEEEEEEC
Confidence            45789999765 5689999999999999999643

---

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	87
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	3e-22
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	3e-17
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	8e-17
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	1e-16
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	3e-16
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	3e-16
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	2e-14
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	1e-12
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	1e-12
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	1e-12
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	3e-11
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	6e-11
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	6e-10

>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 = 79.9 bits (197), Expect = 3e-22
 Identities = 47/91 (51%), Positives = 63/91 (69%), Gaps = 12/91 (13%)

Query: 6  SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRIT-- 63
          + +LP  LID+CIG++I+V+MKGDKE  G L+GFD YVNMVL+DV EY   A+   I+  
Sbjct: 2  NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGG 61

Query: 64 ----------KLDQILLNGNNIAILVPGGSP 84
                    +L+ ILL+GNN+A+LVPGG P
Sbjct: 62 NKKLKRVMVNRLETILLSGNNVAMLVPGGDP 92

>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 = 67.1 bits (164), Expect = 3e-17
 Identities = 25/76 (32%), Positives = 46/76 (60%), Gaps = 4/76 (5%)

Query: 6  SQLLPSELIDRCIGSKIWVIMKGDK-ELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITK 64
          + +LP++++   +G  I V MKG++ +LVG L+G D Y+N+ L +  E        ++  
Sbjct: 2  AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAME---CKGEEKVRS 58

Query: 65 LDQILLNGNNIAILVP 80
          L +I+L GNN+ ++ P
Sbjct: 59 LGEIVLRGNNVVLIQP 74

>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 = 65.9 bits (161), Expect = 8e-17
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 3/71 (4%)

Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
          P + +   + S + + +KGD+E  G LK FD+++N+VL D  E E   +G    +L  +L
Sbjct: 7  PLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELE---DGEVTRRLGTVL 63

Query: 70 LNGNNIAILVP 80
          + G+NI  + P
Sbjct: 64 IRGDNIVYISP 74

>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 = 65.5 bits (160), Expect = 1e-16
 Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 3/71 (4%)

Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
          P ++I R +   + VI+K   E  G L G+D+++N+VL D        +G  + +  +I+
Sbjct: 3  PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEM---IQDGEVVKRYGKIV 59

Query: 70 LNGNNIAILVP 80
          + G+N+  + P
Sbjct: 60 IRGDNVLAISP 70

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

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

 Score = 64.7 bits (158), Expect = 3e-16
 Identities = 20/71 (28%), Positives = 42/71 (59%), Gaps = 3/71 (4%)

Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
            +++   + + + V +KG+KE+ G L+ +D ++N+VL D  E +    G+   KL  I+
Sbjct: 8  AHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGK---KLGTIV 64

Query: 70 LNGNNIAILVP 80
          + G+N+ ++ P
Sbjct: 65 IRGDNVILISP 75

>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 = 64.3 bits (157), Expect = 3e-16
 Identities = 21/71 (29%), Positives = 43/71 (60%), Gaps = 3/71 (4%)

Query: 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQIL 69
          P ++++R + S + V +KG +E  GTL G+D+++N+VL D  E +    G  + K+  ++
Sbjct: 4  PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQ---NGEVVRKVGSVV 60

Query: 70 LNGNNIAILVP 80
          + G+ +  + P
Sbjct: 61 IRGDTVVFVSP 71

>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 = 59.8 bits (145), Expect = 2e-14
 Identities = 11/67 (16%), Positives = 27/67 (40%), Gaps = 3/67 (4%)

Query: 9  LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQI 68
          +P +++    G  +       +   G L   +  +N  + ++T         R+ +L+Q+
Sbjct: 2  VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTY---RDGRVAQLEQV 58

Query: 69 LLNGNNI 75
           + G  I
Sbjct: 59 YIRGCKI 65

>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 = 55.7 bits (134), Expect = 1e-12
 Identities = 17/84 (20%), Positives = 41/84 (48%), Gaps = 13/84 (15%)

Query: 10 PSELIDRCI--GSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITK--- 64
          P  ++ + +   +++ +  + +K+L+G +K FD + NMVLE+V E           K   
Sbjct: 3  PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKS 62

Query: 65 --------LDQILLNGNNIAILVP 80
                  + ++ L G+++ +++ 
Sbjct: 63 KPVNKDRYISKMFLRGDSVIVVLR 86

>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 = 55.1 bits (133), Expect = 1e-12
 Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 4/67 (5%)

Query: 14 IDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGN 73
          +   IG ++ V ++   E+ G L+ FD +VN++LED  E           K   +++ G 
Sbjct: 7  LQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNV----YKRGTMVVRGE 62

Query: 74 NIAILVP 80
          N+  + P
Sbjct: 63 NVLFISP 69

>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 = 55.2 bits (133), Expect = 1e-12
 Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 7/74 (9%)

Query: 18 IGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEIT-------AEGRRITKLDQILL 70
          I  ++  I++  +  +GT K FD ++N++L D  E+          AE      L  +LL
Sbjct: 7  IDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLL 66

Query: 71 NGNNIAILVPGGSP 84
           G N+  +   G P
Sbjct: 67 RGENLVSMTVEGPP 80

>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 = 51.6 bits (124), Expect = 3e-11
 Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 6/71 (8%)

Query: 16 RCIGSKIWVIMK-GDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNN 74
            +  ++ V +K    E  GTL   D Y N+ L +  E      G     L +I +  NN
Sbjct: 3  GLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEE---FVAGVSHGTLGEIFIRCNN 59

Query: 75 IAILVPGGSPD 85
          +  +     P+
Sbjct: 60 VLYI--RELPN 68

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

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

 Score = 52.4 bits (126), Expect = 6e-11
 Identities = 10/63 (15%), Positives = 26/63 (41%), Gaps = 7/63 (11%)

Query: 13 LIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNG 72
           ++  +G ++ V++   +   G L   D  +N+VL + +            K +++ +  
Sbjct: 4  ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA-------GEKFNRVFIMY 56

Query: 73 NNI 75
            I
Sbjct: 57 RYI 59

>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 = 48.5 bits (116), Expect = 6e-10
 Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 3/63 (4%)

Query: 13 LIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNG 72
           + +     + + +K   ++ GT+ G DV +N  L+ V     T + R   +L+ + + G
Sbjct: 5  FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKM---TLKNREPVQLETLSIRG 61

Query: 73 NNI 75
          NNI
Sbjct: 62 NNI 64

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	87
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.95
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.95
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.95
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.94
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.94
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.93
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.93
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.93
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.92
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.92
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.91
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.86
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.81
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	98.15
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	97.44
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	96.56
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	96.38
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	95.37
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	94.07
d2qqra1	59	Jumonji domain-containing protein 2A {Human (Homo	83.11

>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=99.95  E-value=1.1e-28  Score=150.50  Aligned_cols=79  Identities=58%  Similarity=1.084  Sum_probs=70.1

Q ss_pred             CCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccC------------CeeeEeeCeEEEcCC
Q 041342            6 SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAE------------GRRITKLDQILLNGN   73 (87)
Q Consensus         6 ~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~------------g~~~~~~g~v~IRG~   73 (87)
                      .+.+|+++|+++++++|+|.++|||.|.|+|.|||+|||++|+||.|++...+            +...+.+|++||||+
T Consensus         2 ~~~~Pl~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~   81 (92)
T d2fwka1           2 NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGN   81 (92)
T ss_dssp             CCCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGG
T ss_pred             CccChHHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCC
Confidence            47899999999999999999999999999999999999999999999875311            124578999999999


Q ss_pred             cEEEEEeCCCC
Q 041342           74 NIAILVPGGSP   84 (87)
Q Consensus        74 ~I~~I~~~~~p   84 (87)
                      +|++|++.++|
T Consensus        82 ~Vv~I~p~~~~   92 (92)
T d2fwka1          82 NVAMLVPGGDP   92 (92)
T ss_dssp             GEEEEESSSCC
T ss_pred             EEEEEEeCCCC
Confidence            99999998877

>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=99.95  E-value=2.6e-27  Score=138.31  Aligned_cols=70  Identities=29%  Similarity=0.599  Sum_probs=65.7

Q ss_pred             CcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342            9 LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG   81 (87)
Q Consensus         9 ~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~   81 (87)
                      .|+++|+++++++|+|+++||+.|+|+|.+||+|||++|+||.|+.   ++.+.+.+|.+||||++|++|+|.
T Consensus         2 ~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~---~~~~~~~l~~~~IRG~~I~~Isp~   71 (71)
T d1h641_           2 RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQ---DGEVVKRYGKIVIRGDNVLAISPT   71 (71)
T ss_dssp             CHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEE---TTEEEEEEEEEEECGGGEEEEEEC
T ss_pred             CchHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEe---cCCcEeEcCcEEEECCeEEEEeCC
Confidence            6999999999999999999999999999999999999999999986   455688999999999999999873

>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=99.95  E-value=3.4e-27  Score=139.44  Aligned_cols=73  Identities=34%  Similarity=0.697  Sum_probs=67.0

Q ss_pred             CCcCcHHHHhhhcCCEEEEEEcCC-cEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342            6 SQLLPSELIDRCIGSKIWVIMKGD-KELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG   81 (87)
Q Consensus         6 ~~~~Pl~~L~~~l~k~V~V~l~dg-r~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~   81 (87)
                      +++.|+++|+++++++|+|++++| +.|.|+|.|||+|||++|+||+|+.   ++.+.+.+|.+||||++|.+|+|.
T Consensus         2 ~~~~P~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~---~~~~~~~~g~~~IRG~~I~~I~p~   75 (75)
T d1ljoa_           2 AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECK---GEEKVRSLGEIVLRGNNVVLIQPQ   75 (75)
T ss_dssp             CCCCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEE---TTEEEEEEEEEEECGGGEEEEEEC
T ss_pred             CccccHHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEc---CCCcEeEcceEEEeCCEEEEEECC
Confidence            578999999999999999999965 8999999999999999999999986   445688999999999999999873

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

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

Probab=99.94  E-value=2.1e-27  Score=139.18  Aligned_cols=71  Identities=30%  Similarity=0.645  Sum_probs=65.5

Q ss_pred             cCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342            8 LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG   81 (87)
Q Consensus         8 ~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~   81 (87)
                      ..|+++|+++++++|+|+|+||+.|+|+|.+||+|||++|+||+|+.   ++.+.+.+|.+||||++|.+|+++
T Consensus         2 ~~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~---~~~~~~~~g~~~IRG~~I~~Ispa   72 (72)
T d1i4k1_           2 PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQ---NGEVVRKVGSVVIRGDTVVFVSPA   72 (72)
T ss_dssp             CCHHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEES---SSSEEEEEEEEEECGGGEEEEECC
T ss_pred             CChHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEe---cCCeEeEcceEEEeCCeEEEEEcC
Confidence            46999999999999999999999999999999999999999999985   345678999999999999999853

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

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

Probab=99.94  E-value=7.9e-27  Score=137.31  Aligned_cols=71  Identities=34%  Similarity=0.652  Sum_probs=66.0

Q ss_pred             CcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342            7 QLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP   80 (87)
Q Consensus         7 ~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~   80 (87)
                      ...|+++|+++++++|+|+|+||+.|+|+|.+||+|||++|+||+|+.   ++.+.+.+|.+||||++|.+|+|
T Consensus         4 ~~~Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~---~~~~~~~~~~~~IRG~~I~~I~p   74 (74)
T d1mgqa_           4 VQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELE---DGEVTRRLGTVLIRGDNIVYISP   74 (74)
T ss_dssp             TTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEE---TTEEEEEEEEEEECGGGEEEEEC
T ss_pred             ccCcHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEe---CCCeEeEcceEEEeCCEEEEEeC
Confidence            457999999999999999999999999999999999999999999986   45568899999999999999985

>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=99.93  E-value=1e-25  Score=131.75  Aligned_cols=69  Identities=28%  Similarity=0.531  Sum_probs=62.7

Q ss_pred             cHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342           10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus        10 Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      .-+.|+++++++|+|+|+||+.|+|+|.+||+|||++|+||+|+.   ++ +.+.+|.++|||++|++|++.+
T Consensus         3 ~~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~---~~-~~~~~g~v~iRG~~I~~I~~~P   71 (71)
T d1i8fa_           3 LGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEII---DG-NVYKRGTMVVRGENVLFISPVP   71 (71)
T ss_dssp             HHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEE---TT-EEEEEEEEEECGGGEEEEEECC
T ss_pred             HhHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEE---CC-CEEEcceEEEeCCeEEEEeCCC
Confidence            457899999999999999999999999999999999999999986   33 4688999999999999998653

>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=99.93  E-value=5.2e-26  Score=135.85  Aligned_cols=73  Identities=25%  Similarity=0.445  Sum_probs=63.8

Q ss_pred             HHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccC-------CeeeEeeCeEEEcCCcEEEEEeCCCCC
Q 041342           13 LIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAE-------GRRITKLDQILLNGNNIAILVPGGSPD   85 (87)
Q Consensus        13 ~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~-------g~~~~~~g~v~IRG~~I~~I~~~~~p~   85 (87)
                      .|.+|++++|+|.++|||.|.|+|.|||+||||+|++|.|++....       +...|.+|+++|||++|++|+..+.||
T Consensus         2 ~L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~~~~pp   81 (81)
T d1d3bb_           2 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEGPPP   81 (81)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEEECCC
T ss_pred             hhHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEccCCCC
Confidence            4689999999999999999999999999999999999999865211       134689999999999999999877664

>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=99.93  E-value=1e-25  Score=133.17  Aligned_cols=70  Identities=27%  Similarity=0.518  Sum_probs=64.3

Q ss_pred             CcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342            9 LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG   81 (87)
Q Consensus         9 ~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~   81 (87)
                      .|..+|.++++++|+|+|+||+.|+|+|.+||+|||++|+||+|+.   .+.+.+.+|.+||||++|++|++.
T Consensus         7 ~~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~---~~~~~~~~~~v~iRG~~I~~I~~~   76 (76)
T d1th7a1           7 TAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQ---SDGSGKKLGTIVIRGDNVILISPL   76 (76)
T ss_dssp             HHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEC---SSSCEEEEEEEEECGGGEEEEEEC
T ss_pred             cHHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEe---cCCcccCcceEEEECCEEEEEEeC
Confidence            4889999999999999999999999999999999999999999986   233478999999999999999974

>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=99.92  E-value=3.7e-25  Score=135.31  Aligned_cols=75  Identities=21%  Similarity=0.438  Sum_probs=63.1

Q ss_pred             cCcHHHHhhhc--CCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCC-----------eeeEeeCeEEEcCCc
Q 041342            8 LLPSELIDRCI--GSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEG-----------RRITKLDQILLNGNN   74 (87)
Q Consensus         8 ~~Pl~~L~~~l--~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g-----------~~~~~~g~v~IRG~~   74 (87)
                      .+|+++|.+++  +++|+|.++|||.++|+|.|||+|||++|+||+|++...+.           ...|.+|++||||++
T Consensus         1 tGPl~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdn   80 (93)
T d1b34b_           1 TGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDS   80 (93)
T ss_dssp             CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGG
T ss_pred             CCcHHHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCE
Confidence            47999999999  89999999999999999999999999999999998763211           135789999999999


Q ss_pred             EEEEEeCC
Q 041342           75 IAILVPGG   82 (87)
Q Consensus        75 I~~I~~~~   82 (87)
                      |++|...+
T Consensus        81 Vv~I~~~p   88 (93)
T d1b34b_          81 VIVVLRNP   88 (93)
T ss_dssp             EEEEEECC
T ss_pred             EEEEEcCh
Confidence            99997654

>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=99.92  E-value=7.9e-25  Score=127.02  Aligned_cols=66  Identities=24%  Similarity=0.367  Sum_probs=59.8

Q ss_pred             HhhhcCCEEEEEEc-CCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342           14 IDRCIGSKIWVIMK-GDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus        14 L~~~l~k~V~V~l~-dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      |+++++++|.|+|+ +|+.|+|+|.+||+|||++|+||+|+.   ++...+.+|.+||||++|.+|++.+
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~---~~~~~~~lg~~~IRG~nI~~I~~~p   67 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFV---AGVSHGTLGEIFIRCNNVLYIRELP   67 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEE---TTEEEEECCSEEECGGGEEEEEECC
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEe---cCCcccCcCeEEEECCEEEEEEeCC
Confidence            57899999999999 567899999999999999999999985   5566889999999999999998665

>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=99.91  E-value=1.6e-24  Score=126.80  Aligned_cols=70  Identities=19%  Similarity=0.327  Sum_probs=64.3

Q ss_pred             CcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342            9 LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG   81 (87)
Q Consensus         9 ~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~   81 (87)
                      .|+.+|+++.|++|+|+|+||++|+|+|.+||+|||++|+||+++.  .++ +...++.+||||++|.+|...
T Consensus         2 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~--~~~-~~~~~~~v~IRG~~I~~i~lp   71 (72)
T d1d3ba_           2 VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTY--RDG-RVAQLEQVYIRGCKIRFLILP   71 (72)
T ss_dssp             CHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC--TTS-CEEEEEEEEECGGGEEEEEEC
T ss_pred             CchHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEc--CCC-cEeEcCeEEEECCEEEEEEcC
Confidence            6999999999999999999999999999999999999999999875  234 467899999999999999865

>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=99.86  E-value=1.3e-21  Score=116.44  Aligned_cols=69  Identities=20%  Similarity=0.313  Sum_probs=62.4

Q ss_pred             HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342           11 SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG   82 (87)
Q Consensus        11 l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~   82 (87)
                      +.+|+++.|++|.|+|+||..|+|+|.++|.|||++|+||+++.  .+| +...++.+||||++|.+|+..+
T Consensus         3 v~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~--~~~-~~~~~~~v~IRG~~Ir~i~lPd   71 (80)
T d1b34a_           3 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTL--KNR-EPVQLETLSIRGNNIRYFILPD   71 (80)
T ss_dssp             HHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEEC--TTS-CCEEEEEEEECGGGEEEEECCT
T ss_pred             HHHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEc--CCC-CEEEcccEEEcCCEEEEEECCC
Confidence            57899999999999999999999999999999999999999874  234 4678999999999999998754

>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=99.81  E-value=4.5e-20  Score=118.03  Aligned_cols=67  Identities=16%  Similarity=0.323  Sum_probs=60.5

Q ss_pred             HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCCCC
Q 041342           11 SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGSP   84 (87)
Q Consensus        11 l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~~p   84 (87)
                      ++.|.+++|++|.|+|+||+.|+|+|.+||+|||++|+||++.    +++   .++.++|||++|.+|...+.+
T Consensus         2 ~~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~----~~~---k~~~v~IRG~~I~~I~~~e~~   68 (127)
T d1m5q1_           2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNK----AGE---KFNRVFIMYRYIVHIDSTERR   68 (127)
T ss_dssp             HHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEET----TCC---EEEEEEECGGGEEEEEECSCC
T ss_pred             hhHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEEC----CCC---cccEEEEeCCeEEEEEcchhh
Confidence            5789999999999999999999999999999999999999875    333   578899999999999988765

>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=98.15  E-value=8.8e-06  Score=47.06  Aligned_cols=70  Identities=27%  Similarity=0.409  Sum_probs=57.5

Q ss_pred             hcCCEEEEEEcCCcEEEEEEEEecc-ccceEEcceEEEEEcc---CCe---eeEeeCeEEEcCCcEEEEEeCCCCCC
Q 041342           17 CIGSKIWVIMKGDKELVGTLKGFDV-YVNMVLEDVTEYEITA---EGR---RITKLDQILLNGNNIAILVPGGSPDP   86 (87)
Q Consensus        17 ~l~k~V~V~l~dgr~~~G~L~~~D~-~mNlvL~~~~e~~~~~---~g~---~~~~~g~v~IRG~~I~~I~~~~~p~~   86 (87)
                      |+|+++.+..+.+-.|+|+|..+|. ..-+.|+|+.-+.++.   ++.   ...-++.++.||+.|..+...+.|+|
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~~IvFrgsDIKdL~v~e~p~p   78 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCEPPKP   78 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSSCCCCCCCCEEEEEEETTTEEEEEESSCCCC
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCCccCCCCcceeEEEEcCcCcceEEeccCCCC
Confidence            6899999999999999999999994 6668999998765421   110   23567899999999999999998876

>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=97.44  E-value=0.00033  Score=36.19  Aligned_cols=47  Identities=26%  Similarity=0.266  Sum_probs=35.9

Q ss_pred             hcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEc
Q 041342           17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLN   71 (87)
Q Consensus        17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IR   71 (87)
                      |++++|+|..- ++.+.|+..++|+...|+|+..       +|.+...-|.+.+|
T Consensus         1 f~gk~V~v~~g-~~~i~G~a~gId~~G~Lll~t~-------~g~~~~~sGEVSlR   47 (47)
T d1biaa2           1 FINRPVKLIIG-DKEIFGISRGIDKQGALLLEQD-------GIIKPWMGGEISLR   47 (47)
T ss_dssp             TTTSEEEEEET-TEEEEEEEEEECTTSCEEEEET-------TEEEEESSCEEEEC
T ss_pred             CCCCEEEEEEC-CeEEEEEEeeECCCCcEEEEEC-------CCEEEEEEEEEEeC
Confidence            68999999765 5789999999999999999743       23334455677665

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

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

Probab=96.56  E-value=0.0028  Score=34.35  Aligned_cols=33  Identities=15%  Similarity=0.278  Sum_probs=28.1

Q ss_pred             CCEEEEEEcCCcEEEEEEEEeccccceEEcceE
Q 041342           19 GSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVT   51 (87)
Q Consensus        19 ~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~   51 (87)
                      ...|+|.|.+|-.++|.+.+||+|.=+.-.+..
T Consensus        14 ~~~VtifL~nGvkl~G~I~~fD~ftvlL~~~~~   46 (60)
T d1kq1a_          14 QTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGK   46 (60)
T ss_dssp             TCEEEEEETTSCEEEEEEEEECSSEEEEEETTE
T ss_pred             CCcEEEEEECCcEEEEEEEEEcceEEEEEeCCc
Confidence            468999999999999999999999877655543

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

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

Probab=96.38  E-value=0.002  Score=35.53  Aligned_cols=34  Identities=15%  Similarity=0.346  Sum_probs=27.0

Q ss_pred             HHhhhc--CCEEEEEEcCCcEEEEEEEEeccccceE
Q 041342           13 LIDRCI--GSKIWVIMKGDKELVGTLKGFDVYVNMV   46 (87)
Q Consensus        13 ~L~~~l--~k~V~V~l~dgr~~~G~L~~~D~~mNlv   46 (87)
                      +|..+.  ...|+|.|.+|-.++|.+.+||+|.=+.
T Consensus         6 fLn~~rk~~~~VtifL~nGvkl~G~I~~fD~ftvLL   41 (66)
T d1u1sa1           6 YLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILL   41 (66)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHHHcCCcEEEEEEcCcEEEEEEEEEcceEEEE
Confidence            344443  3579999999999999999999997543

>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=95.37  E-value=0.066  Score=28.73  Aligned_cols=42  Identities=31%  Similarity=0.514  Sum_probs=33.1

Q ss_pred             HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEE
Q 041342           12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYE   54 (87)
Q Consensus        12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~   54 (87)
                      ..|.++.|++|-|-......|.|+|.-||.- -+.|+|++.+.
T Consensus         5 ktL~~WKg~kvAv~vgsehSFtGiledFDeE-viLL~dV~D~~   46 (66)
T d1ycya1           5 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEE-VILLKDVVDVI   46 (66)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSS-EEEEEEEEETT
T ss_pred             HHHHHhCCcEEEEEecCcceeEEEhhhcCcc-eEeehhhHHHh
Confidence            4688999999999999999999999999975 47889998764

>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=94.07  E-value=0.039  Score=30.17  Aligned_cols=36  Identities=22%  Similarity=0.340  Sum_probs=28.5

Q ss_pred             HHHHhhhcCCEEEEEEc---CC-cEEEEEEEEeccccceEE
Q 041342           11 SELIDRCIGSKIWVIMK---GD-KELVGTLKGFDVYVNMVL   47 (87)
Q Consensus        11 l~~L~~~l~k~V~V~l~---dg-r~~~G~L~~~D~~mNlvL   47 (87)
                      .+.+..++|++|.|+|+   +| +.++|+|.++|+-. +.|
T Consensus         6 ~~~f~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~~-i~l   45 (74)
T d1ib8a1           6 KDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEEDE-LTM   45 (74)
T ss_dssp             HHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETTE-EEE
T ss_pred             HHHHHHhCCCEEEEEEecccCCceEEEEEEEeecCCe-EEE
Confidence            45678999999999985   34 59999999999753 444

>d2qqra1 b.34.9.1 (A:897-955) Jumonji domain-containing protein 2A {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Tudor/PWWP/MBT
family: Tudor domain
domain: Jumonji domain-containing protein 2A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.11  E-value=0.93  Score=23.79  Aligned_cols=23  Identities=13%  Similarity=0.091  Sum_probs=20.7

Q ss_pred             cCCEEEEEEcCCcEEEEEEEEec
Q 041342           18 IGSKIWVIMKGDKELVGTLKGFD   40 (87)
Q Consensus        18 l~k~V~V~l~dgr~~~G~L~~~D   40 (87)
                      +|.+|.-+.+|||.|.+++.+.-
T Consensus         5 ~Gq~VI~KhkNgryY~c~V~~~~   27 (59)
T d2qqra1           5 AGQKVISKHKNGRFYQCEVVRLT   27 (59)
T ss_dssp             TTCEEEEECTTSSEEEEEEEEEE
T ss_pred             cccEEEEEccCCcEEEEEEEEee
Confidence            68899999999999999998864