Psyllid ID: psy11512

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--
Protein Sequence
MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVEE
Secondary Structure (PSIPRED)
cccccccHHHHHcccEEEEEEccccEEEEEEEEEccccEEEEEcEEEEEccccEEEEEEEEc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHHcEEEEEEccccEEEEEEccccHHHHHHHHHHHHHcccccccccccccc
Coil and Loop (DISEMBL)
mskshppelkkFMDKKVTLKLNANRNVTGILRGFDPFMNLVLdegveyrkdntvhnigmvee
Flexible Loop (DISEMBL)
mskshppelkKFMDKKVTLKLNANrnvtgilrgfdpFMNLVLDEGveyrkdntvhnigmvee
Low Complexity Region (SEG)
MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVEE
Disordered region (IsUnstruct)
***************KVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHN******
Disordered Region (DISOPRED)
****HPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV**
Disordered Region (DISEMBL)
MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVEE
Disordered Region (DISPRO)
****HPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRK************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVEE
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	62	2.2.26 [Sep-21-2011]
Q9N4G9	77	Probable small nuclear ri	yes	N/A	0.951	0.766	0.711	3e-19
Q9VXE0	76	Probable small nuclear ri	yes	N/A	0.967	0.789	0.733	4e-19
P62309	76	Small nuclear ribonucleop	yes	N/A	0.967	0.789	0.716	1e-18
P62308	76	Small nuclear ribonucleop	yes	N/A	0.967	0.789	0.716	1e-18
Q3ZBL0	76	Small nuclear ribonucleop	yes	N/A	0.967	0.789	0.716	1e-18
A8MWD9	76	Small nuclear ribonucleop	no	N/A	0.983	0.802	0.704	3e-18
O82221	80	Probable small nuclear ri	yes	N/A	0.951	0.737	0.639	1e-12
P24715	81	Probable small nuclear ri	N/A	N/A	0.935	0.716	0.525	5e-10
O74966	77	Small nuclear ribonucleop	yes	N/A	0.967	0.779	0.45	6e-10
Q54RX0	85	Probable small nuclear ri	yes	N/A	0.935	0.682	0.517	2e-09

>sp|Q9N4G9|RUXG_CAEEL Probable small nuclear ribonucleoprotein G OS=Caenorhabditis elegans GN=snr-7 PE=3 SV=1

 Score = 94.0 bits (232), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 42/59 (71%), Positives = 51/59 (86%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGM 59
          MSK+HPPELKK+MDK++ LKLN NR V+GILRGFDPFMN+V+DE VEY+KD    N+GM
Sbjct: 1  MSKTHPPELKKYMDKEMDLKLNGNRRVSGILRGFDPFMNMVIDEAVEYQKDGGSVNLGM 59

Associated with snRNP U1, U2, U4/U6 and U5.
Caenorhabditis elegans (taxid: 6239)

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

 Score = 93.6 bits (231), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 44/60 (73%), Positives = 52/60 (86%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          MSK+HPPE+KK+MDK++ LKLN  R VTGILRGFDPFMN+VLD+ VE  KDNT +NIGMV
Sbjct: 1  MSKAHPPEVKKYMDKRMMLKLNGGRAVTGILRGFDPFMNVVLDDTVEECKDNTKNNIGMV 60

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

Drosophila melanogaster (taxid: 7227)

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

 Score = 91.7 bits (226), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 43/60 (71%), Positives = 49/60 (81%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          MSK+HPPELKKFMDKK++LKLN  R+V GILRGFDPFMNLV+DE VE       +NIGMV
Sbjct: 1  MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMV 60

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

Mus musculus (taxid: 10090)

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

 Score = 91.7 bits (226), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 43/60 (71%), Positives = 49/60 (81%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          MSK+HPPELKKFMDKK++LKLN  R+V GILRGFDPFMNLV+DE VE       +NIGMV
Sbjct: 1  MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMV 60

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

Homo sapiens (taxid: 9606)

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

 Score = 91.7 bits (226), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 43/60 (71%), Positives = 49/60 (81%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          MSK+HPPELKKFMDKK++LKLN  R+V GILRGFDPFMNLV+DE VE       +NIGMV
Sbjct: 1  MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMV 60

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

Bos taurus (taxid: 9913)

>sp|A8MWD9|RUXGL_HUMAN Small nuclear ribonucleoprotein G-like protein OS=Homo sapiens PE=2 SV=2

 Score = 90.1 bits (222), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 43/61 (70%), Positives = 47/61 (77%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          MSK+HPPELKKF DKK +LKLN  R+V GILRGFDPFMNLV+DE VE        NIGMV
Sbjct: 1  MSKAHPPELKKFTDKKFSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQKNIGMV 60

Query: 61 E 61
          E
Sbjct: 61 E 61

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

Homo sapiens (taxid: 9606)

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

 Score = 72.0 bits (175), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 39/61 (63%), Positives = 46/61 (75%), Gaps = 2/61 (3%)

Query: 1  MSKS-HPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGM 59
          MS+S  PP+LKK+MDKK+ +KLNANR VTG LRGFD FMNLV+D  VE    N   +IGM
Sbjct: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMVTGTLRGFDQFMNLVVDNTVEV-NGNDKTDIGM 59

Query: 60 V 60
          V
Sbjct: 60 V 60

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

Arabidopsis thaliana (taxid: 3702)

>sp|P24715|RUXG_MEDSA Probable small nuclear ribonucleoprotein G OS=Medicago sativa GN=C29 PE=3 SV=1

 Score = 63.2 bits (152), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 31/59 (52%), Positives = 40/59 (67%), Gaps = 1/59 (1%)

Query: 2  SKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          +   PP LKK+MDK++ + L ANR + G LRGFD FMNLV+D  VE    N  ++IGMV
Sbjct: 3  TSGQPPALKKYMDKQLQINLKANRMIVGTLRGFDQFMNLVVDNTVEV-NGNEKNDIGMV 60

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

Medicago sativa (taxid: 3879)

>sp|O74966|RUXG_SCHPO Small nuclear ribonucleoprotein G OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=smg1 PE=1 SV=1

 Score = 62.8 bits (151), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 27/60 (45%), Positives = 44/60 (73%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          MSK+  P+LKK++D++V ++LN +R V G+LRG+D F+N+VL++ +E + D     IG V
Sbjct: 1  MSKAGAPDLKKYLDRQVFVQLNGSRKVYGVLRGYDIFLNIVLEDSIEEKVDGEKVKIGSV 60

Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site.

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

>sp|Q54RX0|RUXG_DICDI Probable small nuclear ribonucleoprotein G OS=Dictyostelium discoideum GN=snrpG PE=3 SV=1

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 30/58 (51%), Positives = 37/58 (63%)

Query: 3  KSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          K   P+L K +DKK+ +KLN NR V GILRGFD FMN+ L + VE       + IGMV
Sbjct: 5  KQADPDLTKLLDKKLAIKLNGNRTVHGILRGFDTFMNIALKDTVEVVSPTEKYEIGMV 62

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

Dictyostelium discoideum (taxid: 44689)

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	62
307214549	76	Probable small nuclear ribonucleoprotein	0.967	0.789	0.766	8e-19
357619057	76	small nuclear ribonucleoprotein G [Danau	0.967	0.789	0.766	9e-19
332376801	76	unknown [Dendroctonus ponderosae]	0.967	0.789	0.75	1e-18
313217530	76	unnamed protein product [Oikopleura dioi	0.967	0.789	0.666	1e-18
193713710	79	PREDICTED: probable small nuclear ribonu	0.967	0.759	0.733	2e-18
114050793	76	small nuclear ribonucleoprotein G [Bomby	0.967	0.789	0.75	3e-18
198427430	89	PREDICTED: similar to small nuclear ribo	0.967	0.674	0.716	3e-18
156541626	76	PREDICTED: probable small nuclear ribonu	0.967	0.789	0.733	5e-18
194763519	101	GF21254 [Drosophila ananassae] gi|190618	0.967	0.594	0.75	5e-18
427784695	77	Putative small ribonucleoprotein particl	0.967	0.779	0.75	5e-18

>gi|307214549|gb|EFN89534.1| Probable small nuclear ribonucleoprotein G [Harpegnathos saltator]

 Score = 97.8 bits (242), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 46/60 (76%), Positives = 54/60 (90%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          MSK+HPPELKK+MDKK++LKLNA R+VTGILRGFDPFMN+V+DE VE  KD T +NIGMV
Sbjct: 1  MSKAHPPELKKYMDKKLSLKLNAGRHVTGILRGFDPFMNMVIDETVEECKDGTKNNIGMV 60

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357619057|gb|EHJ71789.1| small nuclear ribonucleoprotein G [Danaus plexippus]

 Score = 97.4 bits (241), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 46/60 (76%), Positives = 52/60 (86%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          MSK+HPPELKKFMDKK+++KLNA R VTG+LRGFDPFMNLVLDE VE  KD   +NIGMV
Sbjct: 1  MSKAHPPELKKFMDKKLSIKLNAGRAVTGVLRGFDPFMNLVLDESVEECKDGQRNNIGMV 60

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332376801|gb|AEE63540.1| unknown [Dendroctonus ponderosae]

 Score = 97.1 bits (240), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 45/60 (75%), Positives = 51/60 (85%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          MSK+HPPELKKFMDKK+ LKLN  R VTGILRGFDPFMNLV+DE +E  +D T +NIGMV
Sbjct: 1  MSKAHPPELKKFMDKKLCLKLNGGRQVTGILRGFDPFMNLVVDESIEECRDGTKNNIGMV 60

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|313217530|emb|CBY38609.1| unnamed protein product [Oikopleura dioica] gi|313236587|emb|CBY19879.1| unnamed protein product [Oikopleura dioica]

 Score = 97.1 bits (240), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 40/60 (66%), Positives = 52/60 (86%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          MSK+HPPELKKFMD+K+++K+N  R V G+LRGFDPFMNLV+D+ +EYRKDN+ H +GM 
Sbjct: 1  MSKAHPPELKKFMDRKMSVKVNGGRKVEGVLRGFDPFMNLVIDDAIEYRKDNSSHTMGMC 60

Source: Oikopleura dioica

Species: Oikopleura dioica

Genus: Oikopleura

Family: Oikopleuridae

Class: Appendicularia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|193713710|ref|XP_001949387.1| PREDICTED: probable small nuclear ribonucleoprotein G-like [Acyrthosiphon pisum]

 Score = 96.7 bits (239), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 44/60 (73%), Positives = 53/60 (88%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          MSK+HPPELK+++DKK++LKLNANR V G+LRGFDPFMNLVLDE VE  KD  V++IGMV
Sbjct: 1  MSKAHPPELKRYLDKKLSLKLNANRQVAGVLRGFDPFMNLVLDETVEKIKDGVVNSIGMV 60

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|114050793|ref|NP_001040405.1| small nuclear ribonucleoprotein G [Bombyx mori] gi|95102770|gb|ABF51326.1| small nuclear ribonucleoprotein G [Bombyx mori]

 Score = 95.9 bits (237), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 45/60 (75%), Positives = 51/60 (85%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          MSK+HPPELKKFMDKK ++KLNA R VTG+LRGFDPFMNLVLDE VE  KD   +N+GMV
Sbjct: 1  MSKAHPPELKKFMDKKWSIKLNAGRAVTGVLRGFDPFMNLVLDESVEECKDGQRNNVGMV 60

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198427430|ref|XP_002130422.1| PREDICTED: similar to small nuclear ribonucleoprotein G [Ciona intestinalis]

 Score = 95.5 bits (236), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 43/60 (71%), Positives = 51/60 (85%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          MSK+HPPELKKFMDKK+ LKLN  R++ GILRGFDPFMNLV+D+G+  RKD +V  IGMV
Sbjct: 14 MSKAHPPELKKFMDKKLDLKLNGGRSIQGILRGFDPFMNLVIDDGIGKRKDGSVEKIGMV 73

Source: Ciona intestinalis

Species: Ciona intestinalis

Genus: Ciona

Family: Cionidae

Order: Enterogona

Class: Ascidiacea

Phylum: Chordata

Superkingdom: Eukaryota

>gi|156541626|ref|XP_001601035.1| PREDICTED: probable small nuclear ribonucleoprotein G-like [Nasonia vitripennis]

 Score = 95.1 bits (235), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 44/60 (73%), Positives = 52/60 (86%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          MSK+HPPELKKFMDKK++LKLN  R+V GILRGFDPFMN+V+DE +E  KD T +NIGMV
Sbjct: 1  MSKAHPPELKKFMDKKLSLKLNGGRHVIGILRGFDPFMNMVIDESIEECKDGTKNNIGMV 60

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194763519|ref|XP_001963880.1| GF21254 [Drosophila ananassae] gi|190618805|gb|EDV34329.1| GF21254 [Drosophila ananassae]

 Score = 95.1 bits (235), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/60 (75%), Positives = 52/60 (86%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          MSK+HPPELKK+MDK++ LKLN  R VTGILRGFDPFMN+VLD+ VE  KDNT +NIGMV
Sbjct: 26 MSKAHPPELKKYMDKRMMLKLNGGRAVTGILRGFDPFMNVVLDDTVEECKDNTKNNIGMV 85

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427784695|gb|JAA57799.1| Putative small ribonucleoprotein particle protein smg [Rhipicephalus pulchellus]

 Score = 94.7 bits (234), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/60 (75%), Positives = 51/60 (85%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          MSK+HPPELKK+MDKK++L+LN +R VTGILRGFDPFMNLVLDE VE  K    HNIGMV
Sbjct: 1  MSKAHPPELKKYMDKKLSLRLNGSRVVTGILRGFDPFMNLVLDETVEETKGGEKHNIGMV 60

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	62
FB|FBgn0261791	76	SmG "Small ribonucleoprotein p	0.967	0.789	0.733	2.5e-19
WB|WBGene00004920	77	snr-7 [Caenorhabditis elegans	0.951	0.766	0.711	2.5e-19
UNIPROTKB|Q3ZBL0	76	SNRPG "Small nuclear ribonucle	0.967	0.789	0.716	2.8e-18
UNIPROTKB|P62308	76	SNRPG "Small nuclear ribonucle	0.967	0.789	0.716	2.8e-18
UNIPROTKB|F2Z5V2	76	LOC100525867 "Uncharacterized	0.967	0.789	0.716	2.8e-18
RGD|1584713	76	Snrpg "small nuclear ribonucle	0.967	0.789	0.716	2.8e-18
UNIPROTKB|A8MWD9	76	A8MWD9 "Small nuclear ribonucl	0.983	0.802	0.704	9.5e-18
ZFIN|ZDB-GENE-040912-105	76	zgc:103688 "zgc:103688" [Danio	0.967	0.789	0.65	5.3e-17
TAIR|locus:2061446	80	SNRNP-G "AT2G23930" [Arabidops	0.951	0.737	0.639	7.9e-14
TAIR|locus:2080777	79	AT3G11500 "AT3G11500" [Arabido	0.951	0.746	0.622	1e-13

FB|FBgn0261791 SmG "Small ribonucleoprotein particle protein SmG" [Drosophila melanogaster (taxid:7227)]

 Score = 231 (86.4 bits), Expect = 2.5e-19, P = 2.5e-19
 Identities = 44/60 (73%), Positives = 52/60 (86%)

Query:     1 MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
             MSK+HPPE+KK+MDK++ LKLN  R VTGILRGFDPFMN+VLD+ VE  KDNT +NIGMV
Sbjct:     1 MSKAHPPEVKKYMDKRMMLKLNGGRAVTGILRGFDPFMNVVLDDTVEECKDNTKNNIGMV 60

GO:0005634 "nucleus" evidence=IDA

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

GO:0005681 "spliceosomal complex" evidence=ISS

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

GO:0000245 "spliceosomal complex assembly" evidence=ISS

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

WB|WBGene00004920 snr-7 [Caenorhabditis elegans (taxid:6239)]

 Score = 231 (86.4 bits), Expect = 2.5e-19, P = 2.5e-19
 Identities = 42/59 (71%), Positives = 51/59 (86%)

Query:     1 MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGM 59
             MSK+HPPELKK+MDK++ LKLN NR V+GILRGFDPFMN+V+DE VEY+KD    N+GM
Sbjct:     1 MSKTHPPELKKYMDKEMDLKLNGNRRVSGILRGFDPFMNMVIDEAVEYQKDGGSVNLGM 59

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

GO:0040011 "locomotion" evidence=IMP

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

GO:0002119 "nematode larval development" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0016246 "RNA interference" evidence=IMP

GO:0006898 "receptor-mediated endocytosis" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0040027 "negative regulation of vulval development" evidence=IMP

GO:0006915 "apoptotic process" evidence=IMP

GO:0043186 "P granule" evidence=IDA

UNIPROTKB|Q3ZBL0 SNRPG "Small nuclear ribonucleoprotein G" [Bos taurus (taxid:9913)]

 Score = 221 (82.9 bits), Expect = 2.8e-18, P = 2.8e-18
 Identities = 43/60 (71%), Positives = 49/60 (81%)

Query:     1 MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
             MSK+HPPELKKFMDKK++LKLN  R+V GILRGFDPFMNLV+DE VE       +NIGMV
Sbjct:     1 MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMV 60

GO:0005683 "U7 snRNP" evidence=ISS

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|P62308 SNRPG "Small nuclear ribonucleoprotein G" [Homo sapiens (taxid:9606)]

 Score = 221 (82.9 bits), Expect = 2.8e-18, P = 2.8e-18
 Identities = 43/60 (71%), Positives = 49/60 (81%)

Query:     1 MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
             MSK+HPPELKKFMDKK++LKLN  R+V GILRGFDPFMNLV+DE VE       +NIGMV
Sbjct:     1 MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMV 60

GO:0003723 "RNA binding" evidence=IEA

GO:0000245 "spliceosomal complex assembly" evidence=NAS

GO:0005681 "spliceosomal complex" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

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

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

GO:0005683 "U7 snRNP" evidence=IDA

GO:0005689 "U12-type spliceosomal complex" evidence=IDA

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

GO:0000387 "spliceosomal snRNP assembly" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006369 "termination of RNA polymerase II transcription" evidence=TAS

GO:0006397 "mRNA processing" evidence=TAS

GO:0008334 "histone mRNA metabolic process" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0034660 "ncRNA metabolic process" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|F2Z5V2 LOC100525867 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 221 (82.9 bits), Expect = 2.8e-18, P = 2.8e-18
 Identities = 43/60 (71%), Positives = 49/60 (81%)

Query:     1 MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
             MSK+HPPELKKFMDKK++LKLN  R+V GILRGFDPFMNLV+DE VE       +NIGMV
Sbjct:     1 MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMV 60

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

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

GO:0005683 "U7 snRNP" evidence=IEA

RGD|1584713 Snrpg "small nuclear ribonucleoprotein polypeptide G" [Rattus norvegicus (taxid:10116)]

 Score = 221 (82.9 bits), Expect = 2.8e-18, P = 2.8e-18
 Identities = 43/60 (71%), Positives = 49/60 (81%)

Query:     1 MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
             MSK+HPPELKKFMDKK++LKLN  R+V GILRGFDPFMNLV+DE VE       +NIGMV
Sbjct:     1 MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMV 60

GO:0005683 "U7 snRNP" evidence=ISO

GO:0005689 "U12-type spliceosomal complex" evidence=ISO

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

UNIPROTKB|A8MWD9 A8MWD9 "Small nuclear ribonucleoprotein G-like protein" [Homo sapiens (taxid:9606)]

 Score = 216 (81.1 bits), Expect = 9.5e-18, P = 9.5e-18
 Identities = 43/61 (70%), Positives = 47/61 (77%)

Query:     1 MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
             MSK+HPPELKKF DKK +LKLN  R+V GILRGFDPFMNLV+DE VE        NIGMV
Sbjct:     1 MSKAHPPELKKFTDKKFSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQKNIGMV 60

Query:    61 E 61
             E
Sbjct:    61 E 61

GO:0003723 "RNA binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

ZFIN|ZDB-GENE-040912-105 zgc:103688 "zgc:103688" [Danio rerio (taxid:7955)]

 Score = 209 (78.6 bits), Expect = 5.3e-17, P = 5.3e-17
 Identities = 39/60 (65%), Positives = 49/60 (81%)

Query:     1 MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
             MS++HPPELKKFMDKK++LKLN  R+V GILRGFDPFMNLV+D+ +E      ++ IGMV
Sbjct:     1 MSEAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVVDDTIEMAPGGQMNTIGMV 60

GO:0003674 "molecular_function" evidence=ND

TAIR|locus:2061446 SNRNP-G "AT2G23930" [Arabidopsis thaliana (taxid:3702)]

 Score = 179 (68.1 bits), Expect = 7.9e-14, P = 7.9e-14
 Identities = 39/61 (63%), Positives = 46/61 (75%)

Query:     1 MSKS-HPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGM 59
             MS+S  PP+LKK+MDKK+ +KLNANR VTG LRGFD FMNLV+D  VE    N   +IGM
Sbjct:     1 MSRSGQPPDLKKYMDKKLQIKLNANRMVTGTLRGFDQFMNLVVDNTVEVN-GNDKTDIGM 59

Query:    60 V 60
             V
Sbjct:    60 V 60

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0005829 "cytosol" evidence=IDA

TAIR|locus:2080777 AT3G11500 "AT3G11500" [Arabidopsis thaliana (taxid:3702)]

 Score = 178 (67.7 bits), Expect = 1.0e-13, P = 1.0e-13
 Identities = 38/61 (62%), Positives = 46/61 (75%)

Query:     1 MSKS-HPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGM 59
             MS+S  PP+LKK+MDKK+ +KLNANR V G LRGFD FMNLV+D  VE   D+   +IGM
Sbjct:     1 MSRSGQPPDLKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEVNGDDKT-DIGM 59

Query:    60 V 60
             V
Sbjct:    60 V 60

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0005730 "nucleolus" evidence=IDA

GO:0005829 "cytosol" evidence=RCA

---

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)
P62309	RUXG_MOUSE	No assigned EC number	0.7166	0.9677	0.7894	yes	N/A
P62308	RUXG_HUMAN	No assigned EC number	0.7166	0.9677	0.7894	yes	N/A
O74966	RUXG_SCHPO	No assigned EC number	0.45	0.9677	0.7792	yes	N/A
Q3ZBL0	RUXG_BOVIN	No assigned EC number	0.7166	0.9677	0.7894	yes	N/A
O82221	RUXG_ARATH	No assigned EC number	0.6393	0.9516	0.7375	yes	N/A
P40204	RUXG_YEAST	No assigned EC number	0.52	0.8064	0.6493	yes	N/A
Q54RX0	RUXG_DICDI	No assigned EC number	0.5172	0.9354	0.6823	yes	N/A
A8MWD9	RUXGL_HUMAN	No assigned EC number	0.7049	0.9838	0.8026	no	N/A
Q9VXE0	RUXG_DROME	No assigned EC number	0.7333	0.9677	0.7894	yes	N/A
Q9N4G9	RUXG_CAEEL	No assigned EC number	0.7118	0.9516	0.7662	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	62
cd01719	70	cd01719, Sm_G, Sm protein G	2e-30
cd01729	89	cd01729, LSm7, Like-Sm protein 7	5e-16
pfam01423	66	pfam01423, LSM, LSM domain	7e-16
smart00651	67	smart00651, Sm, snRNP Sm proteins	3e-13
cd00600	63	cd00600, Sm_like, Sm and related proteins	1e-10
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	4e-10
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	4e-09
cd01727	91	cd01727, LSm8, Like-Sm protein 8	5e-09
cd01726	68	cd01726, LSm6, Like-Sm protein 6	2e-08
cd06168	73	cd06168, LSMD1, LSM domain containing 1	1e-06
cd01718	79	cd01718, Sm_E, Sm protein E	1e-05
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	1e-05
cd01728	74	cd01728, LSm1, Like-Sm protein 1	8e-05
PTZ00138	89	PTZ00138, PTZ00138, small nuclear ribonucleoprotei	8e-05
cd01730	82	cd01730, LSm3, Like-Sm protein 3	5e-04
cd01722	69	cd01722, Sm_F, Sm protein F	5e-04
cd01717	80	cd01717, Sm_B, Sm protein B	6e-04
cd01732	76	cd01732, LSm5, Like-Sm protein 5	0.002

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

 Score =  100 bits (252), Expect = 2e-30
 Identities = 38/56 (67%), Positives = 45/56 (80%)

Query: 5  HPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          HPPELKK+MDK+++LKLN NR V+G+LRGFDPFMNLVLD+ VE   D     IGMV
Sbjct: 1  HPPELKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVGDGEKTPIGMV 56

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|212476 cd01729, LSm7, Like-Sm protein 7

 Score = 64.9 bits (159), Expect = 5e-16
 Identities = 23/44 (52%), Positives = 33/44 (75%)

Query: 8  ELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKD 51
          +L K++DKK+ +K    R VTGIL+G+D  +NLVLD+ VEY +D
Sbjct: 6  DLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRD 49

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|201787 pfam01423, LSM, LSM domain

 Score = 63.7 bits (156), Expect = 7e-16
 Identities = 25/54 (46%), Positives = 36/54 (66%)

Query: 7  PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
            L+K + K+VT++L   R + G L+GFD FMNLVLD+  E  KD  V+ +G+V
Sbjct: 1  KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLGLV 54

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

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

 Score = 57.1 bits (139), Expect = 3e-13
 Identities = 23/55 (41%), Positives = 32/55 (58%), Gaps = 1/55 (1%)

Query: 7  PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKD-NTVHNIGMV 60
            LKK + K+V ++L   R   G L+GFD FMNLVL++  E  KD      +G+V
Sbjct: 1  KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLV 55

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

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

 Score = 50.3 bits (121), Expect = 1e-10
 Identities = 24/52 (46%), Positives = 34/52 (65%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          LK F+ K V+++L   R +TG L  FD +MNLVLD+ VE  +D  V  +G+V
Sbjct: 1  LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRVLGLV 52

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

 Score = 49.6 bits (119), Expect = 4e-10
 Identities = 21/48 (43%), Positives = 28/48 (58%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHN 56
          LKK ++K+V +KL   R   G L GFD +MNLVLD+  E    +   N
Sbjct: 12 LKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKN 59

Length = 79

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

 Score = 46.8 bits (112), Expect = 4e-09
 Identities = 19/52 (36%), Positives = 31/52 (59%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          L + ++K V +KL   + V G+L+GFD  +NLVL+   E  +  +V  +G V
Sbjct: 6  LNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGTV 57

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

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

 Score = 47.1 bits (113), Expect = 5e-09
 Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 2/53 (3%)

Query: 7  PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVE--YRKDNTVHNI 57
            L+ +++K+V +     R + G L+GFD   NL+L    E  Y  D  V  +
Sbjct: 2  SLLEDYLNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHERVYSSDEGVEEV 54

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|212473 cd01726, LSm6, Like-Sm protein 6

 Score = 45.2 bits (108), Expect = 2e-08
 Identities = 19/50 (38%), Positives = 25/50 (50%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIG 58
          LKK + K V +KL       G+L   D +MNLVL++  EY     V   G
Sbjct: 6  LKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYG 55

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|212486 cd06168, LSMD1, LSM domain containing 1

 Score = 41.0 bits (97), Expect = 1e-06
 Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 5/58 (8%)

Query: 8  ELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHN-----IGMV 60
          +L+K + + + + L   R + G     D   N++L    EYRK + +       +G+V
Sbjct: 3  KLRKLLGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSDLGAEEPRSLGLV 60

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

>gnl|CDD|212465 cd01718, Sm_E, Sm protein E

 Score = 38.3 bits (90), Expect = 1e-05
 Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 17 VTLKLNANRNVTGILRGFDPFMNLVLDEGVE-YRKDNTVHNIG 58
          + L    +  + G + GFD +MNLVLD+  E + K NT   +G
Sbjct: 23 IWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVHLKTNTRKPLG 65

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|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional

 Score = 38.1 bits (89), Expect = 1e-05
 Identities = 18/52 (34%), Positives = 26/52 (50%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          L   ++  V ++L   R   G L+G+D  MNLVLD   E +    V  +G V
Sbjct: 9  LNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKV 60

Length = 72

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

 Score = 36.0 bits (84), Expect = 8e-05
 Identities = 18/35 (51%), Positives = 23/35 (65%)

Query: 14 DKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEY 48
          DKK+ + L   R + GILR FD F NLVL++ VE 
Sbjct: 12 DKKILVVLRDGRKLIGILRSFDQFANLVLEDTVER 46

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|185472 PTZ00138, PTZ00138, small nuclear ribonucleoprotein; Provisional

 Score = 36.2 bits (84), Expect = 8e-05
 Identities = 16/38 (42%), Positives = 24/38 (63%), Gaps = 1/38 (2%)

Query: 22 NANRNVTGILRGFDPFMNLVLDEGVE-YRKDNTVHNIG 58
          + N  + G + GFD +MN+VLD+  E Y K NT  ++G
Sbjct: 36 HPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLG 73

Length = 89

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

 Score = 34.1 bits (79), Expect = 5e-04
 Identities = 11/36 (30%), Positives = 22/36 (61%)

Query: 13 MDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEY 48
          +D++V +KL  +R + G L  +D  +N++L +  E 
Sbjct: 10 LDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEET 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|212469 cd01722, Sm_F, Sm protein F

 Score = 33.7 bits (78), Expect = 5e-04
 Identities = 15/42 (35%), Positives = 17/42 (40%)

Query: 7  PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEY 48
          P L     K V +KL       G L   D +MNL L    EY
Sbjct: 4  PFLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEY 45

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|212464 cd01717, Sm_B, Sm protein B

 Score = 34.1 bits (79), Expect = 6e-04
 Identities = 13/42 (30%), Positives = 23/42 (54%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRK 50
          + ++++ ++ + L   R   G    FD  MNLVL +  E+RK
Sbjct: 5  MLQYINYRMRVTLQDGRQFVGTFLAFDKHMNLVLSDCEEFRK 46

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

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

 Score = 32.6 bits (75), Expect = 0.002
 Identities = 10/25 (40%), Positives = 17/25 (68%)

Query: 24 NRNVTGILRGFDPFMNLVLDEGVEY 48
          ++   G L GFD ++N+VL++  EY
Sbjct: 23 DKEFVGTLLGFDDYVNMVLEDVTEY 47

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	62
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.86
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.82
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.81
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.81
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.8
KOG1780|consensus	77		99.8
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.79
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.78
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.78
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.77
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.77
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.75
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.75
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.74
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.72
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.72
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.71
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.71
KOG3482|consensus	79		99.7
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.68
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.66
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.65
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.57
KOG1781|consensus	108		99.56
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.56
KOG1783|consensus	77		99.49
KOG1775|consensus	84		99.45
KOG1774|consensus	88		99.33
KOG3460|consensus	91		99.21
KOG3168|consensus	177		99.17
KOG1784|consensus	96		98.99
KOG3448|consensus	96		98.93
KOG1782|consensus	129		98.84
KOG3293|consensus	134		98.82
KOG3172|consensus	119		98.5
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	98.36
KOG3428|consensus	109		98.13
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	97.93
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	97.16
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	96.83
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	96.8
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	96.74
PRK14638	150	hypothetical protein; Provisional	96.73
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	96.68
PRK14639	140	hypothetical protein; Provisional	96.44
PRK02001	152	hypothetical protein; Validated	96.41
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	96.41
KOG3459|consensus	114		96.37
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	96.31
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	96.03
COG1923	77	Hfq Uncharacterized host factor I protein [General	95.94
PRK14640	152	hypothetical protein; Provisional	95.8
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	95.69
PRK14633	150	hypothetical protein; Provisional	95.51
PRK14642	197	hypothetical protein; Provisional	95.22
PRK14645	154	hypothetical protein; Provisional	95.09
PRK00092	154	ribosome maturation protein RimP; Reviewed	94.97
PRK14632	172	hypothetical protein; Provisional	94.95
PRK14636	176	hypothetical protein; Provisional	94.86
PRK14644	136	hypothetical protein; Provisional	94.74
PRK14634	155	hypothetical protein; Provisional	94.73
PRK14643	164	hypothetical protein; Provisional	94.61
PRK14646	155	hypothetical protein; Provisional	94.59
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	94.48
PRK14647	159	hypothetical protein; Provisional	94.39
COG0779	153	Uncharacterized protein conserved in bacteria [Fun	94.13
PRK14091	165	RNA-binding protein Hfq; Provisional	93.91
PRK14631	174	hypothetical protein; Provisional	93.85
PRK14637	151	hypothetical protein; Provisional	93.79
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	93.63
PRK14091	165	RNA-binding protein Hfq; Provisional	93.61
PRK14641	173	hypothetical protein; Provisional	93.27
PRK14630	143	hypothetical protein; Provisional	91.14
PRK14635	162	hypothetical protein; Provisional	90.18
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	89.53
PRK06955	300	biotin--protein ligase; Provisional	86.87
PF03614	165	Flag1_repress: Repressor of phase-1 flagellin; Int	85.88
PRK10898	353	serine endoprotease; Provisional	83.02
TIGR02038	351	protease_degS periplasmic serine pepetdase DegS. T	82.45
PF11607	101	DUF3247: Protein of unknown function (DUF3247); In	81.64
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	81.62
PF14563	42	DUF4444: Domain of unknown function (DUF4444); PDB	81.58
PRK13325	592	bifunctional biotin--[acetyl-CoA-carboxylase] liga	80.04

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.86  E-value=2.2e-21  Score=109.40  Aligned_cols=61  Identities=31%  Similarity=0.511  Sum_probs=54.1

Q ss_pred             CCCCCchhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          1 MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         1 m~~~~~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      |+..+...|.++++++|.|+++||++|.|+|.|||+|||++|+||.|...++..+.+|.++
T Consensus         1 ~~~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~   61 (72)
T PRK00737          1 MAQRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVV   61 (72)
T ss_pred             CCcchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEE
Confidence            7755555689999999999999999999999999999999999999987766677888764

>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=99.85  E-value=4e-21  Score=108.63  Aligned_cols=57  Identities=70%  Similarity=1.137  Sum_probs=52.8

Q ss_pred             CchhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          5 HPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         5 ~~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      ++++|+++++|+|.|++++|+++.|+|.|||+||||+|++|+|+..+...+.+|.++
T Consensus         1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~   57 (72)
T cd01719           1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVV   57 (72)
T ss_pred             CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEE
Confidence            478999999999999999999999999999999999999999998777788888874

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.

>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=99.84  E-value=1.6e-20  Score=108.14  Aligned_cols=58  Identities=43%  Similarity=0.804  Sum_probs=51.7

Q ss_pred             CCchhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCC--------ceeeeeEee
Q psy11512          4 SHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDN--------TVHNIGMVE   61 (62)
Q Consensus         4 ~~~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~--------~~~~lG~v~   61 (62)
                      -.+++|.++++++|+|+++|||++.|+|.|||+||||+|++|+|+..++        ..+.+|.++
T Consensus         2 ~~~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~   67 (81)
T cd01729           2 ESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVV   67 (81)
T ss_pred             cchhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEE
Confidence            3567899999999999999999999999999999999999999997642        467789875

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.

>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=99.82  E-value=9.7e-20  Score=101.38  Aligned_cols=55  Identities=35%  Similarity=0.537  Sum_probs=50.6

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      .+|+++++++|.|++++|++|.|+|.|||+|||++|+||+|+..++..+.+|.++
T Consensus         3 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~   57 (68)
T cd01731           3 DVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVV   57 (68)
T ss_pred             HHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEE
Confidence            3589999999999999999999999999999999999999998877788888764

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=99.81  E-value=1.1e-19  Score=101.16  Aligned_cols=55  Identities=29%  Similarity=0.440  Sum_probs=50.0

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      .+|+++++++|+|+|++|++|+|+|.|||+|||++|+||+|...++....+|.|+
T Consensus         3 ~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~   57 (67)
T cd01726           3 EFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAF   57 (67)
T ss_pred             HHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEE
Confidence            4589999999999999999999999999999999999999987776777888764

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.

>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=99.81  E-value=1.5e-19  Score=103.20  Aligned_cols=56  Identities=23%  Similarity=0.589  Sum_probs=49.4

Q ss_pred             chh-HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEe---cCCceeeeeEee
Q psy11512          6 PPE-LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYR---KDNTVHNIGMVE   61 (62)
Q Consensus         6 ~~~-L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~---~~~~~~~lG~v~   61 (62)
                      |.+ |+++++++|.|++++|++++|+|.|||+|||++|+||+|+.   .++..+.+|.++
T Consensus         4 P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~   63 (76)
T cd01732           4 PLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQIL   63 (76)
T ss_pred             hHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEE
Confidence            444 79999999999999999999999999999999999999997   344567888864

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.

>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=99.80  E-value=1.8e-19  Score=100.58  Aligned_cols=57  Identities=32%  Similarity=0.423  Sum_probs=50.8

Q ss_pred             CchhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          5 HPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         5 ~~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      +.++|+++++++|+|+|++|++|+|+|.|||+|||++|+||+|+..++....+|.++
T Consensus         2 p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~   58 (68)
T cd01722           2 PKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVL   58 (68)
T ss_pred             HHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEE
Confidence            345689999999999999999999999999999999999999997766677788764

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.

>KOG1780|consensus

Probab=99.80  E-value=9.5e-20  Score=103.66  Aligned_cols=61  Identities=69%  Similarity=1.013  Sum_probs=56.3

Q ss_pred             CCCCCchhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          1 MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         1 m~~~~~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      ||++..|+|++|++|++.+++..||.+.|+|.|||.|||+||+++.|...++....+|.++
T Consensus         1 Msksg~PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~v   61 (77)
T KOG1780|consen    1 MSKSGHPELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVV   61 (77)
T ss_pred             CCcccCchHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEE
Confidence            8999555999999999999999999999999999999999999999998888888888764

>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=99.79  E-value=1.2e-18  Score=99.28  Aligned_cols=55  Identities=20%  Similarity=0.442  Sum_probs=50.3

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecC------CceeeeeEee
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKD------NTVHNIGMVE   61 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~------~~~~~lG~v~   61 (62)
                      +.|.++++++|+|+++|||.|.|+|.|||+||||+|++|.|+...      .+.+.+|.|+
T Consensus         3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~   63 (75)
T cd06168           3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVM   63 (75)
T ss_pred             hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEE
Confidence            458999999999999999999999999999999999999999854      4688999885

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.

>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=99.78  E-value=1.1e-18  Score=100.51  Aligned_cols=56  Identities=29%  Similarity=0.481  Sum_probs=48.4

Q ss_pred             chh-HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCC-------------ceeeeeEee
Q psy11512          6 PPE-LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDN-------------TVHNIGMVE   61 (62)
Q Consensus         6 ~~~-L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~-------------~~~~lG~v~   61 (62)
                      |++ |+.+++++|.|++++||++.|+|.|||+||||+|+||+|++...             ..+.+|.++
T Consensus         2 pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~   71 (82)
T cd01730           2 PLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLF   71 (82)
T ss_pred             chHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEE
Confidence            555 68999999999999999999999999999999999999997542             356777764

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

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

Probab=99.78  E-value=1.7e-18  Score=98.87  Aligned_cols=55  Identities=27%  Similarity=0.524  Sum_probs=48.8

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecC----------CceeeeeEee
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKD----------NTVHNIGMVE   61 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~----------~~~~~lG~v~   61 (62)
                      +.|.+|++++|+|+++|||.+.|+|.|||+||||+|+||+|+...          .+.+.+|.++
T Consensus         3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~   67 (79)
T cd01717           3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVL   67 (79)
T ss_pred             chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEE
Confidence            468999999999999999999999999999999999999998643          2457888875

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

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

Probab=99.77  E-value=1.9e-18  Score=97.73  Aligned_cols=55  Identities=27%  Similarity=0.446  Sum_probs=48.6

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecC----CceeeeeEee
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKD----NTVHNIGMVE   61 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~----~~~~~lG~v~   61 (62)
                      |.|.++++++|+|++++||.+.|+|.|||+|||++|++|.|+...    ...+.+|.++
T Consensus         2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~   60 (74)
T cd01727           2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYI   60 (74)
T ss_pred             hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEE
Confidence            679999999999999999999999999999999999999998642    2466788764

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

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

Probab=99.77  E-value=3.5e-18  Score=97.19  Aligned_cols=56  Identities=38%  Similarity=0.462  Sum_probs=49.0

Q ss_pred             chhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCC---ceeeeeEee
Q psy11512          6 PPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDN---TVHNIGMVE   61 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~---~~~~lG~v~   61 (62)
                      .++|.++++++|.|++++||++.|+|.|||+|||++|+||.|+...+   ..+.+|.++
T Consensus         4 ~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~v   62 (74)
T cd01728           4 TASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFI   62 (74)
T ss_pred             hHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEE
Confidence            45699999999999999999999999999999999999999986432   356778765

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.

>smart00651 Sm snRNP Sm proteins

Probab=99.75  E-value=7.6e-18  Score=92.48  Aligned_cols=55  Identities=42%  Similarity=0.656  Sum_probs=49.6

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecC-CceeeeeEee
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKD-NTVHNIGMVE   61 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-~~~~~lG~v~   61 (62)
                      ++|.++++++|+|+++||+.+.|+|.+||+|||++|++|+|+..+ ...+.+|.++
T Consensus         1 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~   56 (67)
T smart00651        1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVF   56 (67)
T ss_pred             ChhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEE
Confidence            368999999999999999999999999999999999999999876 5677777663

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

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

Probab=99.75  E-value=1e-17  Score=92.07  Aligned_cols=54  Identities=37%  Similarity=0.575  Sum_probs=50.4

Q ss_pred             hHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCC-ceeeeeEee
Q psy11512          8 ELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDN-TVHNIGMVE   61 (62)
Q Consensus         8 ~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~-~~~~lG~v~   61 (62)
                      +|+++++++|+|+++||++++|+|.+||+|||++|++|.|....+ +.+.+|.++
T Consensus         2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~   56 (67)
T PF01423_consen    2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVF   56 (67)
T ss_dssp             HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEE
T ss_pred             hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEE
Confidence            589999999999999999999999999999999999999998776 788888764

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 ....

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

Probab=99.74  E-value=1.5e-17  Score=94.78  Aligned_cols=43  Identities=47%  Similarity=0.694  Sum_probs=41.3

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEe
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYR   49 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~   49 (62)
                      ..|+++++++|.|+|++|++|.|+|.|||+|||++|+||.|+.
T Consensus        10 ~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~   52 (79)
T COG1958          10 SFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEII   52 (79)
T ss_pred             HHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEe
Confidence            3489999999999999999999999999999999999999997

>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=99.72  E-value=4.9e-17  Score=88.07  Aligned_cols=53  Identities=38%  Similarity=0.600  Sum_probs=48.4

Q ss_pred             HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          9 LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         9 L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      |+++++++|+|+++||+.|.|+|.+||+|||++|++|.+...+...+.+|.++
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~~~~~~~~~   53 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGKKRVLGLVL   53 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCcEEECCeEE
Confidence            57899999999999999999999999999999999999998777777777764

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.

>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=99.72  E-value=3.5e-17  Score=94.27  Aligned_cols=57  Identities=32%  Similarity=0.591  Sum_probs=47.2

Q ss_pred             Cchh-HHhcCCCE--EEEEEC--CCeEEEEEEEEecCccceEecceEEEec-CCceeeeeEee
Q psy11512          5 HPPE-LKKFMDKK--VTLKLN--ANRNVTGILRGFDPFMNLVLDEGVEYRK-DNTVHNIGMVE   61 (62)
Q Consensus         5 ~~~~-L~~~l~k~--V~V~l~--~g~~~~G~L~~~D~~mNlvL~~~~e~~~-~~~~~~lG~v~   61 (62)
                      +|.. +.+|++++  |.|.++  +|+++.|+|.|||+|||++|+||+|+.. +...+.+|.++
T Consensus         6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~il   68 (79)
T cd01718           6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRIL   68 (79)
T ss_pred             CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEE
Confidence            3555 79999994  555555  8999999999999999999999999975 45677888864

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.

>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=99.71  E-value=3.9e-17  Score=95.44  Aligned_cols=46  Identities=24%  Similarity=0.453  Sum_probs=41.5

Q ss_pred             chh-HHhcC--CCEEEEEECCCeEEEEEEEEecCccceEecceEEEecC
Q psy11512          6 PPE-LKKFM--DKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKD   51 (62)
Q Consensus         6 ~~~-L~~~l--~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~   51 (62)
                      |.+ |.+++  +++|.|++++|+++.|+|.|||+||||+|+||+|...+
T Consensus         3 Pl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~   51 (87)
T cd01720           3 PLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTE   51 (87)
T ss_pred             hHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeec
Confidence            445 68886  89999999999999999999999999999999998754

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

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

Probab=99.71  E-value=8.2e-17  Score=90.34  Aligned_cols=54  Identities=22%  Similarity=0.179  Sum_probs=48.5

Q ss_pred             hHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          8 ELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         8 ~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      .|.++.|++|.|+||||.+|+|+|.++|+|||++|+||++...+++..++|.++
T Consensus         4 ~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v~   57 (70)
T cd01721           4 LLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVY   57 (70)
T ss_pred             HHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcEE
Confidence            479999999999999999999999999999999999999877776667777663

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.

>KOG3482|consensus

Probab=99.70  E-value=3.1e-17  Score=93.29  Aligned_cols=56  Identities=30%  Similarity=0.425  Sum_probs=53.1

Q ss_pred             chhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          6 PPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      .|||+.+.+|+|.|+||+|.+|+|+|++.|.|||+.|.+|+|++.+.....+|+|+
T Consensus        10 KpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEil   65 (79)
T KOG3482|consen   10 KPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEIL   65 (79)
T ss_pred             hHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEE
Confidence            47899999999999999999999999999999999999999999988899999875

>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=99.68  E-value=2.4e-16  Score=89.59  Aligned_cols=55  Identities=24%  Similarity=0.305  Sum_probs=46.4

Q ss_pred             chh-HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCce-eeeeEe
Q psy11512          6 PPE-LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTV-HNIGMV   60 (62)
Q Consensus         6 ~~~-L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~-~~lG~v   60 (62)
                      |.. |+++.|++|.|+|++|++++|+|.+||+|||++|+||++...+++. ..+|.+
T Consensus         2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v   58 (76)
T cd01723           2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPEC   58 (76)
T ss_pred             chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcE
Confidence            444 7999999999999999999999999999999999999998655543 344544

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

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

Probab=99.66  E-value=5.9e-16  Score=90.74  Aligned_cols=55  Identities=25%  Similarity=0.290  Sum_probs=50.5

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      .+|+++.|++|.|+|++|.+|+|+|.++|.|||++|+||++...++....+|.|+
T Consensus         4 ~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~   58 (90)
T cd01724           4 RFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLS   58 (90)
T ss_pred             HHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEE
Confidence            4689999999999999999999999999999999999999998877778888764

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

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

Probab=99.65  E-value=5.6e-16  Score=88.77  Aligned_cols=55  Identities=24%  Similarity=0.312  Sum_probs=49.2

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      .+|++..|++|.|+||||.+|+|+|.++|+|||++|+||++...++...++|.++
T Consensus        12 ~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~   66 (78)
T cd01733          12 ILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIM   66 (78)
T ss_pred             HHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEE
Confidence            4579999999999999999999999999999999999999887777666777763

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.

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.57  E-value=1.2e-14  Score=85.34  Aligned_cols=56  Identities=30%  Similarity=0.589  Sum_probs=45.2

Q ss_pred             chh-HHhcCCCEEEEEE--CC--CeEEEEEEEEecCccceEecceEEEecC-CceeeeeEee
Q psy11512          6 PPE-LKKFMDKKVTLKL--NA--NRNVTGILRGFDPFMNLVLDEGVEYRKD-NTVHNIGMVE   61 (62)
Q Consensus         6 ~~~-L~~~l~k~V~V~l--~~--g~~~~G~L~~~D~~mNlvL~~~~e~~~~-~~~~~lG~v~   61 (62)
                      |.. +.+|+.++.+|.+  .+  +++++|+|.|||+|||++|+||+|+..+ ...+.+|.++
T Consensus        15 P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~il   76 (89)
T PTZ00138         15 PINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRIL   76 (89)
T ss_pred             CHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEE
Confidence            444 7889888766665  35  6999999999999999999999999753 4567888875

>KOG1781|consensus

Probab=99.56  E-value=1.3e-16  Score=95.11  Aligned_cols=55  Identities=42%  Similarity=0.843  Sum_probs=50.1

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCC--------ceeeeeEee
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDN--------TVHNIGMVE   61 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~--------~~~~lG~v~   61 (62)
                      .+|.+|++++|+|++..||+..|+|.|||+.|||||++++|+..+.        +.|++|+||
T Consensus        20 lDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV   82 (108)
T KOG1781|consen   20 LDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVV   82 (108)
T ss_pred             hhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEE
Confidence            5799999999999999999999999999999999999999997542        458999986

>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=99.56  E-value=1.9e-14  Score=82.73  Aligned_cols=45  Identities=22%  Similarity=0.393  Sum_probs=41.3

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecC
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKD   51 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~   51 (62)
                      .+|+++.|++|.|+||+|.+|+|+|.++|+|||++|+||++...+
T Consensus         4 ~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~   48 (81)
T cd01725           4 SFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPE   48 (81)
T ss_pred             HHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCC
Confidence            358999999999999999999999999999999999999877543

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

>KOG1783|consensus

Probab=99.49  E-value=1.9e-15  Score=85.87  Aligned_cols=60  Identities=30%  Similarity=0.473  Sum_probs=53.0

Q ss_pred             CCCCC-c-hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEe
Q psy11512          1 MSKSH-P-PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV   60 (62)
Q Consensus         1 m~~~~-~-~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v   60 (62)
                      ||+.. | .+|++++||+|.|+|.+|-.|+|+|.|+|.|||+.|+.++|+.+++.++.+|.+
T Consensus         1 ~s~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygda   62 (77)
T KOG1783|consen    1 MSEGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGDA   62 (77)
T ss_pred             CCcccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccce
Confidence            56333 3 458999999999999999999999999999999999999999988888888865

>KOG1775|consensus

Probab=99.45  E-value=2.4e-14  Score=82.16  Aligned_cols=50  Identities=32%  Similarity=0.585  Sum_probs=44.9

Q ss_pred             CCchhH-HhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCc
Q psy11512          4 SHPPEL-KKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNT   53 (62)
Q Consensus         4 ~~~~~L-~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~   53 (62)
                      -.|++| .++++.++.|.+|+.+++.|+|.|||.|.|++|+|++|+..+.+
T Consensus         6 llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~e   56 (84)
T KOG1775|consen    6 LLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPE   56 (84)
T ss_pred             cccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCC
Confidence            357774 99999999999999999999999999999999999999965443

>KOG1774|consensus

Probab=99.33  E-value=3.7e-13  Score=77.99  Aligned_cols=58  Identities=24%  Similarity=0.559  Sum_probs=47.0

Q ss_pred             CCchh-HHhcCCCEEEEEE----CCCeEEEEEEEEecCccceEecceEEEec-CCceeeeeEee
Q psy11512          4 SHPPE-LKKFMDKKVTLKL----NANRNVTGILRGFDPFMNLVLDEGVEYRK-DNTVHNIGMVE   61 (62)
Q Consensus         4 ~~~~~-L~~~l~k~V~V~l----~~g~~~~G~L~~~D~~mNlvL~~~~e~~~-~~~~~~lG~v~   61 (62)
                      .+|.+ +.+|+..+.+|.+    +-|..++|.++|||+|||+||++|+|... +...+.+|+++
T Consensus        11 v~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRil   74 (88)
T KOG1774|consen   11 VQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRIL   74 (88)
T ss_pred             cCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEE
Confidence            35666 5888888877775    46899999999999999999999999863 44555888875

>KOG3460|consensus

Probab=99.21  E-value=1.7e-12  Score=75.57  Aligned_cols=47  Identities=32%  Similarity=0.562  Sum_probs=42.7

Q ss_pred             CCchh-HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEec
Q psy11512          4 SHPPE-LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRK   50 (62)
Q Consensus         4 ~~~~~-L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~   50 (62)
                      ..|.+ |+-+++.+|.|+++++|++.|+|.+||+|+|++|.+++|.+.
T Consensus         4 ~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit   51 (91)
T KOG3460|consen    4 EEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETIT   51 (91)
T ss_pred             cccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEE
Confidence            34666 588999999999999999999999999999999999998863

>KOG3168|consensus

Probab=99.17  E-value=2.2e-12  Score=82.99  Aligned_cols=61  Identities=26%  Similarity=0.535  Sum_probs=53.3

Q ss_pred             CCCCCchhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEec----------CCceeeeeEee
Q psy11512          1 MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRK----------DNTVHNIGMVE   61 (62)
Q Consensus         1 m~~~~~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~----------~~~~~~lG~v~   61 (62)
                      |+-+.+.-|-++++.+++|.++|||.+.|++.+||.|||++|.+|+|+..          ..+++-+|+|+
T Consensus         1 M~~a~sskml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvl   71 (177)
T KOG3168|consen    1 MTVAKSSKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVL   71 (177)
T ss_pred             CCccchhHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEE
Confidence            66677788999999999999999999999999999999999999999852          12577788875

>KOG1784|consensus

Probab=98.99  E-value=3e-10  Score=67.04  Aligned_cols=44  Identities=34%  Similarity=0.591  Sum_probs=41.6

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEec
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRK   50 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~   50 (62)
                      ..|.+|++++|.|...|||.+.|.|.|||+-.||+|+++.|+..
T Consensus         3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~   46 (96)
T KOG1784|consen    3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIF   46 (96)
T ss_pred             hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhh
Confidence            36899999999999999999999999999999999999999864

>KOG3448|consensus

Probab=98.93  E-value=2.4e-09  Score=63.00  Aligned_cols=44  Identities=23%  Similarity=0.383  Sum_probs=40.4

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEec
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRK   50 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~   50 (62)
                      .+.+.++|++|.|+||++-.+.|+|.++|+|+|+.|+|......
T Consensus         5 sfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~   48 (96)
T KOG3448|consen    5 SFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDP   48 (96)
T ss_pred             HHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCc
Confidence            46799999999999999999999999999999999999876644

>KOG1782|consensus

Probab=98.84  E-value=1.1e-10  Score=71.92  Aligned_cols=43  Identities=40%  Similarity=0.634  Sum_probs=41.0

Q ss_pred             hHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEec
Q psy11512          8 ELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRK   50 (62)
Q Consensus         8 ~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~   50 (62)
                      .|.+++++++.|.|+|||.+.|.|.+||+|.|++|++|.|++.
T Consensus        13 sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~   55 (129)
T KOG1782|consen   13 SLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIF   55 (129)
T ss_pred             HHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhhee
Confidence            4899999999999999999999999999999999999999874

>KOG3293|consensus

Probab=98.82  E-value=5.1e-09  Score=64.76  Aligned_cols=48  Identities=27%  Similarity=0.362  Sum_probs=43.7

Q ss_pred             chh-HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCc
Q psy11512          6 PPE-LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNT   53 (62)
Q Consensus         6 ~~~-L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~   53 (62)
                      |+. |...-++++.|+||+|.+|.|.|+.+|.+|||.|.++.++..+++
T Consensus         3 PLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgd   51 (134)
T KOG3293|consen    3 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGD   51 (134)
T ss_pred             chhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCC
Confidence            444 689999999999999999999999999999999999999987654

>KOG3172|consensus

Probab=98.50  E-value=5.8e-07  Score=54.62  Aligned_cols=58  Identities=22%  Similarity=0.202  Sum_probs=50.0

Q ss_pred             CCCCCchh-HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeee
Q psy11512          1 MSKSHPPE-LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIG   58 (62)
Q Consensus         1 m~~~~~~~-L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG   58 (62)
                      ||--.|.. |+..-++-|.+++++|..|+|+|.-.|++||++|+|.+-...++...++-
T Consensus         1 ~s~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le   59 (119)
T KOG3172|consen    1 MSVGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLE   59 (119)
T ss_pred             CccccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeee
Confidence            56666776 69999999999999999999999999999999999999887776555544

>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=98.36  E-value=3.7e-07  Score=51.05  Aligned_cols=37  Identities=24%  Similarity=0.390  Sum_probs=29.9

Q ss_pred             CEEEEEECC--C--eEEEEEEEEecCccceEecceEEEecC
Q psy11512         15 KKVTLKLNA--N--RNVTGILRGFDPFMNLVLDEGVEYRKD   51 (62)
Q Consensus        15 k~V~V~l~~--g--~~~~G~L~~~D~~mNlvL~~~~e~~~~   51 (62)
                      ++|+|.++.  |  -.++|.|++||.|+||+|.|+.|....
T Consensus         9 ~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~   49 (66)
T cd01739           9 IRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK   49 (66)
T ss_pred             cEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence            566666633  2  378999999999999999999998654

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.

>KOG3428|consensus

Probab=98.13  E-value=1.1e-05  Score=48.92  Aligned_cols=44  Identities=30%  Similarity=0.325  Sum_probs=40.4

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEec
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRK   50 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~   50 (62)
                      .+|.++.+.++.|+|++|....|++.++|.+||..|.++.-..+
T Consensus         5 r~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~   48 (109)
T KOG3428|consen    5 RFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK   48 (109)
T ss_pred             HHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecC
Confidence            46899999999999999999999999999999999998876654

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

Probab=97.93  E-value=5.8e-05  Score=42.33  Aligned_cols=42  Identities=19%  Similarity=0.313  Sum_probs=34.1

Q ss_pred             HHhcCCCEEEEEECCCeEEEEEEEEecC---ccceEecceEEEec
Q psy11512          9 LKKFMDKKVTLKLNANRNVTGILRGFDP---FMNLVLDEGVEYRK   50 (62)
Q Consensus         9 L~~~l~k~V~V~l~~g~~~~G~L~~~D~---~mNlvL~~~~e~~~   50 (62)
                      +..++|++|.|.++||..|+|.|.+++.   -+.++|.-|.....
T Consensus         7 ~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~   51 (77)
T PF14438_consen    7 LTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPK   51 (77)
T ss_dssp             HHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS
T ss_pred             HHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccc
Confidence            5889999999999999999999999998   89999988876643

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

Probab=97.16  E-value=0.00077  Score=43.49  Aligned_cols=43  Identities=23%  Similarity=0.342  Sum_probs=33.1

Q ss_pred             CCchhHHhcCCCEEEEEECCCeEEEEEEEEec-CccceEecceEE
Q psy11512          4 SHPPELKKFMDKKVTLKLNANRNVTGILRGFD-PFMNLVLDEGVE   47 (62)
Q Consensus         4 ~~~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D-~~mNlvL~~~~e   47 (62)
                      ..|.++..|++|.|+|.+.| +++.|.|.++| ..-|+||-+-.|
T Consensus         7 ~~p~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e   50 (166)
T PF06372_consen    7 KSPLEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE   50 (166)
T ss_dssp             S-HHHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T
T ss_pred             CCHHHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc
Confidence            45888999999999999999 99999999999 678999886443

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.

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

Probab=96.83  E-value=0.004  Score=36.91  Aligned_cols=40  Identities=18%  Similarity=0.309  Sum_probs=36.1

Q ss_pred             HhcCCCEEEEEECCCeEEEEEEEEecC-ccceEecceEEEe
Q psy11512         10 KKFMDKKVTLKLNANRNVTGILRGFDP-FMNLVLDEGVEYR   49 (62)
Q Consensus        10 ~~~l~k~V~V~l~~g~~~~G~L~~~D~-~mNlvL~~~~e~~   49 (62)
                      .+|+|++|.+..+++..|+|+|..+|. --.|.|.++..+-
T Consensus         4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~G   44 (96)
T PF12701_consen    4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFG   44 (96)
T ss_dssp             CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETT
T ss_pred             ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecC
Confidence            479999999999999999999999994 7899999988663

>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=96.80  E-value=0.0033  Score=34.66  Aligned_cols=33  Identities=27%  Similarity=0.415  Sum_probs=27.5

Q ss_pred             CCCEEEEEECCCeEEEEEEEEecCccceEecce
Q psy11512         13 MDKKVTLKLNANRNVTGILRGFDPFMNLVLDEG   45 (62)
Q Consensus        13 l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~   45 (62)
                      -..+|.|-|.||-.+.|.+.|||+|.=+.-.+.
T Consensus        10 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~g   42 (61)
T cd01716          10 EKIPVTIYLVNGVQLKGQIESFDNFTVLLESDG   42 (61)
T ss_pred             cCCcEEEEEeCCcEEEEEEEEEcceEEEEEECC
Confidence            456788999999999999999999987665543

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=96.74  E-value=0.0039  Score=34.38  Aligned_cols=32  Identities=25%  Similarity=0.370  Sum_probs=27.1

Q ss_pred             CCCEEEEEECCCeEEEEEEEEecCccceEecc
Q psy11512         13 MDKKVTLKLNANRNVTGILRGFDPFMNLVLDE   44 (62)
Q Consensus        13 l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~   44 (62)
                      -..+|.|-|.+|-.+.|.+.|||+|.=+.-.+
T Consensus        14 ~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~   45 (61)
T TIGR02383        14 ERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ   45 (61)
T ss_pred             cCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence            45678888999999999999999998766544

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.

>PRK14638 hypothetical protein; Provisional

Probab=96.73  E-value=0.0042  Score=39.17  Aligned_cols=37  Identities=14%  Similarity=0.312  Sum_probs=31.3

Q ss_pred             chhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEec
Q psy11512          6 PPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLD   43 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~   43 (62)
                      |.++.+++|++|+|++++++.++|+|.++|+- ++.|.
T Consensus        92 ~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~  128 (150)
T PRK14638         92 PKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS  128 (150)
T ss_pred             HHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            45689999999999999999999999999963 44443

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

Probab=96.68  E-value=0.0078  Score=31.03  Aligned_cols=34  Identities=18%  Similarity=0.301  Sum_probs=29.1

Q ss_pred             cCCCEEEEEECCCeEEEEEEEEecCccceEecceE
Q psy11512         12 FMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGV   46 (62)
Q Consensus        12 ~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~   46 (62)
                      .+|++|++.. ++..++|+..++|+.-.|+++...
T Consensus         1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~   34 (48)
T PF02237_consen    1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTED   34 (48)
T ss_dssp             STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETT
T ss_pred             CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECC
Confidence            4799999999 567779999999999999987643

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 ....

>PRK14639 hypothetical protein; Provisional

Probab=96.44  E-value=0.0086  Score=37.37  Aligned_cols=36  Identities=19%  Similarity=0.282  Sum_probs=31.2

Q ss_pred             chhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEe
Q psy11512          6 PPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVL   42 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL   42 (62)
                      |.++.+++|+.|.|++.+++.+.|+|.++|+ -++.|
T Consensus        80 ~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~-~~i~l  115 (140)
T PRK14639         80 IEHFAKSIGELVKITTNEKEKFEGKIVSVDD-ENITL  115 (140)
T ss_pred             HHHHHHhCCCEEEEEECCCcEEEEEEEEEeC-CEEEE
Confidence            4568999999999999999999999999997 35554

>PRK02001 hypothetical protein; Validated

Probab=96.41  E-value=0.0091  Score=37.89  Aligned_cols=36  Identities=19%  Similarity=0.413  Sum_probs=30.9

Q ss_pred             chhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEe
Q psy11512          6 PPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVL   42 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL   42 (62)
                      |..+.+++|+.|+|++.+++.+.|+|.++|+- +++|
T Consensus        82 ~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l  117 (152)
T PRK02001         82 PRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL  117 (152)
T ss_pred             HHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence            45689999999999999999999999999964 3444

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=96.41  E-value=0.0079  Score=34.72  Aligned_cols=34  Identities=26%  Similarity=0.380  Sum_probs=28.2

Q ss_pred             cCCCEEEEEECCCeEEEEEEEEecCccceEecce
Q psy11512         12 FMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEG   45 (62)
Q Consensus        12 ~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~   45 (62)
                      --..+|.|-|.+|-.+.|.+.|||+|.=|.-.+.
T Consensus        17 ~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g   50 (79)
T PRK00395         17 KERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG   50 (79)
T ss_pred             HcCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence            3456788899999999999999999987766554

>KOG3459|consensus

Probab=96.37  E-value=0.00029  Score=42.93  Aligned_cols=37  Identities=24%  Similarity=0.405  Sum_probs=33.6

Q ss_pred             CCEEEEEECCCeEEEEEEEEecCccceEecceEEEec
Q psy11512         14 DKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRK   50 (62)
Q Consensus        14 ~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~   50 (62)
                      ..+|.|-++|++.+.|...|||.|.|++|+++.|.+.
T Consensus        36 ~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwt   72 (114)
T KOG3459|consen   36 NTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWT   72 (114)
T ss_pred             CceeEEEecccHHHHhhhhhhhccccchhhcHHHHCC
Confidence            4568889999999999999999999999999998763

>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=96.31  E-value=0.02  Score=31.49  Aligned_cols=36  Identities=11%  Similarity=0.142  Sum_probs=30.2

Q ss_pred             cCCCEEEEEECCCeEEEEEEEEecCccceEecceEE
Q psy11512         12 FMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVE   47 (62)
Q Consensus        12 ~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e   47 (62)
                      ++|..|++++-.|.+++|.+.+||.--++++-.+.+
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            579999999999999999999999877776544433

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.

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

Probab=96.03  E-value=0.036  Score=31.64  Aligned_cols=41  Identities=15%  Similarity=0.263  Sum_probs=35.0

Q ss_pred             HhcCCCEEEEEECCCeEEEEEEEEec-CccceEecceEEEec
Q psy11512         10 KKFMDKKVTLKLNANRNVTGILRGFD-PFMNLVLDEGVEYRK   50 (62)
Q Consensus        10 ~~~l~k~V~V~l~~g~~~~G~L~~~D-~~mNlvL~~~~e~~~   50 (62)
                      .+|+|+++.+.-+.+..|+|+|..+| +---+.|.|+..+-.
T Consensus         2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGT   43 (74)
T cd01736           2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGT   43 (74)
T ss_pred             ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecc
Confidence            36899999999999999999999999 456677888877643

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.

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

Probab=95.94  E-value=0.02  Score=32.88  Aligned_cols=37  Identities=27%  Similarity=0.392  Sum_probs=28.8

Q ss_pred             CchhHHhc--CCCEEEEEECCCeEEEEEEEEecCccceE
Q psy11512          5 HPPELKKF--MDKKVTLKLNANRNVTGILRGFDPFMNLV   41 (62)
Q Consensus         5 ~~~~L~~~--l~k~V~V~l~~g~~~~G~L~~~D~~mNlv   41 (62)
                      ++++|+.+  -+.+|.|-|.||-.+.|.+.|||+|.=+.
T Consensus         8 QD~fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~VlL   46 (77)
T COG1923           8 QDPFLNALRKEKIPVTIFLVNGFKLQGQVESFDNFVVLL   46 (77)
T ss_pred             chHHHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEEEEE
Confidence            35566444  45678888999999999999999996444

>PRK14640 hypothetical protein; Provisional

Probab=95.80  E-value=0.09  Score=33.12  Aligned_cols=32  Identities=16%  Similarity=0.447  Sum_probs=28.1

Q ss_pred             chhHHhcCCCEEEEEE----CCCeEEEEEEEEecCc
Q psy11512          6 PPELKKFMDKKVTLKL----NANRNVTGILRGFDPF   37 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l----~~g~~~~G~L~~~D~~   37 (62)
                      |.++.+++|+.|.|++    .+.+.++|+|.++|+-
T Consensus        89 ~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~  124 (152)
T PRK14640         89 VAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD  124 (152)
T ss_pred             HHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence            4568999999999999    5679999999999973

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

Probab=95.69  E-value=0.036  Score=31.45  Aligned_cols=36  Identities=25%  Similarity=0.405  Sum_probs=29.2

Q ss_pred             chhHHhcCCCEEEEEEC---CC-eEEEEEEEEecCccceEe
Q psy11512          6 PPELKKFMDKKVTLKLN---AN-RNVTGILRGFDPFMNLVL   42 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~---~g-~~~~G~L~~~D~~mNlvL   42 (62)
                      |.++.+++|+.|.|+++   +| +.+.|.|.++|+- +++|
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            45689999999999996   55 6999999999973 3444

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

>PRK14633 hypothetical protein; Provisional

Probab=95.51  E-value=0.043  Score=34.56  Aligned_cols=36  Identities=14%  Similarity=0.222  Sum_probs=29.6

Q ss_pred             chhHHhcCCCEEEEEE----CCCeEEEEEEEEecCccceEe
Q psy11512          6 PPELKKFMDKKVTLKL----NANRNVTGILRGFDPFMNLVL   42 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l----~~g~~~~G~L~~~D~~mNlvL   42 (62)
                      |.++.+++|++|.|++    .+++.++|+|.++++- ++.|
T Consensus        86 ~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l  125 (150)
T PRK14633         86 IIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL  125 (150)
T ss_pred             HHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence            4568999999999998    4679999999999974 4444

>PRK14642 hypothetical protein; Provisional

Probab=95.22  E-value=0.052  Score=35.91  Aligned_cols=36  Identities=11%  Similarity=0.316  Sum_probs=30.2

Q ss_pred             chhHHhcCCCEEEEEEC-------------CCeEEEEEEEEecCccceEe
Q psy11512          6 PPELKKFMDKKVTLKLN-------------ANRNVTGILRGFDPFMNLVL   42 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~-------------~g~~~~G~L~~~D~~mNlvL   42 (62)
                      +.++.+++|+.|.|+++             +.+.++|+|.++|+- ++.|
T Consensus        92 ~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l  140 (197)
T PRK14642         92 EQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI  140 (197)
T ss_pred             HHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence            45689999999999997             679999999999974 4444

>PRK14645 hypothetical protein; Provisional

Probab=95.09  E-value=0.058  Score=34.22  Aligned_cols=31  Identities=16%  Similarity=0.278  Sum_probs=27.1

Q ss_pred             chhHHhcCCCEEEEEECCCeEEEEEEEEecCc
Q psy11512          6 PPELKKFMDKKVTLKLNANRNVTGILRGFDPF   37 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~   37 (62)
                      +.++.+++|++|.|++ +++.+.|+|.++|+-
T Consensus        94 ~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~  124 (154)
T PRK14645         94 ARHFERFAGLKAKVRG-PGENFTGRIKAVSGD  124 (154)
T ss_pred             HHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC
Confidence            4568999999999986 789999999999963

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=94.97  E-value=0.079  Score=33.19  Aligned_cols=31  Identities=26%  Similarity=0.626  Sum_probs=27.7

Q ss_pred             chhHHhcCCCEEEEEE----CCCeEEEEEEEEecC
Q psy11512          6 PPELKKFMDKKVTLKL----NANRNVTGILRGFDP   36 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l----~~g~~~~G~L~~~D~   36 (62)
                      |.++.+++|+.|.|++    .+++.+.|+|..+|+
T Consensus        90 ~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~  124 (154)
T PRK00092         90 ARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG  124 (154)
T ss_pred             HHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence            4569999999999997    577999999999996

>PRK14632 hypothetical protein; Provisional

Probab=94.95  E-value=0.07  Score=34.34  Aligned_cols=37  Identities=19%  Similarity=0.369  Sum_probs=29.8

Q ss_pred             chhHHhcCCCEEEEEECC-------CeEEEEEEEEecCccceEec
Q psy11512          6 PPELKKFMDKKVTLKLNA-------NRNVTGILRGFDPFMNLVLD   43 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~~-------g~~~~G~L~~~D~~mNlvL~   43 (62)
                      +.++.+++|+.|.|++++       .+.+.|+|.++|+- ++.|+
T Consensus        90 ~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~  133 (172)
T PRK14632         90 AEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR  133 (172)
T ss_pred             HHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence            456899999999999965       58999999999963 44443

>PRK14636 hypothetical protein; Provisional

Probab=94.86  E-value=0.072  Score=34.45  Aligned_cols=36  Identities=17%  Similarity=0.456  Sum_probs=29.2

Q ss_pred             chhHHhcCCCEEEEEEC---CC-eEEEEEEEEecCccceEe
Q psy11512          6 PPELKKFMDKKVTLKLN---AN-RNVTGILRGFDPFMNLVL   42 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~---~g-~~~~G~L~~~D~~mNlvL   42 (62)
                      |.++.+++|++|.|+++   +| +.+.|+|.++|+- ++.|
T Consensus        90 ~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l  129 (176)
T PRK14636         90 PKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI  129 (176)
T ss_pred             HHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence            45689999999999996   55 7999999999862 3444

>PRK14644 hypothetical protein; Provisional

Probab=94.74  E-value=0.092  Score=32.70  Aligned_cols=35  Identities=26%  Similarity=0.403  Sum_probs=29.7

Q ss_pred             hHHhcCCCEEEEEECCC----eEEEEEEEEecCccceEec
Q psy11512          8 ELKKFMDKKVTLKLNAN----RNVTGILRGFDPFMNLVLD   43 (62)
Q Consensus         8 ~L~~~l~k~V~V~l~~g----~~~~G~L~~~D~~mNlvL~   43 (62)
                      ++.+++|+.|.|++++.    +.+.|.|.++|+- ++.|.
T Consensus        79 ~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~  117 (136)
T PRK14644         79 ELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK  117 (136)
T ss_pred             HHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            58999999999999876    9999999999973 45553

>PRK14634 hypothetical protein; Provisional

Probab=94.73  E-value=0.22  Score=31.52  Aligned_cols=31  Identities=13%  Similarity=0.247  Sum_probs=26.8

Q ss_pred             chhHHhcCCCEEEEEECC----CeEEEEEEEEecC
Q psy11512          6 PPELKKFMDKKVTLKLNA----NRNVTGILRGFDP   36 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~~----g~~~~G~L~~~D~   36 (62)
                      |.++.+++|++|.|++.+    .+.+.|+|.++|+
T Consensus        92 ~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~  126 (155)
T PRK14634         92 DRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNE  126 (155)
T ss_pred             HHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeC
Confidence            456899999999999853    3899999999996

>PRK14643 hypothetical protein; Provisional

Probab=94.61  E-value=0.093  Score=33.60  Aligned_cols=37  Identities=19%  Similarity=0.297  Sum_probs=29.6

Q ss_pred             chhHHhcCCCEEEEEECC----CeEEEEEEEEecC-ccceEe
Q psy11512          6 PPELKKFMDKKVTLKLNA----NRNVTGILRGFDP-FMNLVL   42 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~~----g~~~~G~L~~~D~-~mNlvL   42 (62)
                      +.++.+++|++|.|+++.    .+.++|+|.++|+ ...+.+
T Consensus        96 ~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l  137 (164)
T PRK14643         96 QEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRF  137 (164)
T ss_pred             HHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEE
Confidence            456899999999999854    6999999999995 444443

>PRK14646 hypothetical protein; Provisional

Probab=94.59  E-value=0.1  Score=33.09  Aligned_cols=36  Identities=22%  Similarity=0.283  Sum_probs=28.7

Q ss_pred             chhHHhcCCCEEEEEECC----CeEEEEEEEEecCccceEe
Q psy11512          6 PPELKKFMDKKVTLKLNA----NRNVTGILRGFDPFMNLVL   42 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~~----g~~~~G~L~~~D~~mNlvL   42 (62)
                      +.++.+++|++|.|++++    -+.+.|+|.++|+- ++.|
T Consensus        92 ~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l  131 (155)
T PRK14646         92 ERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI  131 (155)
T ss_pred             HHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence            456999999999999853    37889999999963 4444

>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=94.48  E-value=0.07  Score=32.81  Aligned_cols=36  Identities=28%  Similarity=0.584  Sum_probs=26.5

Q ss_pred             chhHHhcCCCEEEEEEC----CCeEEEEEEEEecCccceEe
Q psy11512          6 PPELKKFMDKKVTLKLN----ANRNVTGILRGFDPFMNLVL   42 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~----~g~~~~G~L~~~D~~mNlvL   42 (62)
                      +.++.+++|+.|.|+++    +.+.+.|+|.++|+ -.++|
T Consensus        79 ~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l  118 (141)
T PF02576_consen   79 PRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL  118 (141)
T ss_dssp             HHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred             HHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence            35689999999999994    45799999999997 33444

; PDB: 1IB8_A.

>PRK14647 hypothetical protein; Provisional

Probab=94.39  E-value=0.12  Score=32.77  Aligned_cols=31  Identities=13%  Similarity=0.355  Sum_probs=27.0

Q ss_pred             chhHHhcCCCEEEEEEC---------CCeEEEEEEEEecC
Q psy11512          6 PPELKKFMDKKVTLKLN---------ANRNVTGILRGFDP   36 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~---------~g~~~~G~L~~~D~   36 (62)
                      |.++.+++|+.|.|+++         +.+.+.|+|.++|+
T Consensus        91 ~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~  130 (159)
T PRK14647         91 EADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD  130 (159)
T ss_pred             HHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence            45699999999999994         35999999999996

>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.13  E-value=0.16  Score=32.37  Aligned_cols=32  Identities=22%  Similarity=0.422  Sum_probs=29.0

Q ss_pred             hhHHhcCCCEEEEEE----CCCeEEEEEEEEecCcc
Q psy11512          7 PELKKFMDKKVTLKL----NANRNVTGILRGFDPFM   38 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l----~~g~~~~G~L~~~D~~m   38 (62)
                      .++..|+|+.|.|++    .+.+.+.|+|.++|+-.
T Consensus        92 ~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~  127 (153)
T COG0779          92 EHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET  127 (153)
T ss_pred             HHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence            458999999999999    78899999999999764

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=93.91  E-value=0.13  Score=33.35  Aligned_cols=33  Identities=27%  Similarity=0.366  Sum_probs=27.2

Q ss_pred             CCCEEEEEECCCeEEEEEEEEecCccceEecce
Q psy11512         13 MDKKVTLKLNANRNVTGILRGFDPFMNLVLDEG   45 (62)
Q Consensus        13 l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~   45 (62)
                      -..+|.|-|.+|-.+.|.+.+||.|.=|.-.+.
T Consensus       103 ~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g  135 (165)
T PRK14091        103 SGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG  135 (165)
T ss_pred             cCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            345688889999999999999999976665554

>PRK14631 hypothetical protein; Provisional

Probab=93.85  E-value=0.18  Score=32.55  Aligned_cols=30  Identities=23%  Similarity=0.412  Sum_probs=26.6

Q ss_pred             chhHHhcCCCEEEEEEC----CCeEEEEEEEEec
Q psy11512          6 PPELKKFMDKKVTLKLN----ANRNVTGILRGFD   35 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~----~g~~~~G~L~~~D   35 (62)
                      +.++.+|+|+.|.|++.    +.+.+.|+|.++|
T Consensus       109 ~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~  142 (174)
T PRK14631        109 LEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD  142 (174)
T ss_pred             HHHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence            45689999999999995    5599999999998

>PRK14637 hypothetical protein; Provisional

Probab=93.79  E-value=0.17  Score=31.97  Aligned_cols=36  Identities=22%  Similarity=0.314  Sum_probs=27.7

Q ss_pred             chhHHhcCCCEEEEEECCCeEE-EEEEEEecCccceEe
Q psy11512          6 PPELKKFMDKKVTLKLNANRNV-TGILRGFDPFMNLVL   42 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~~g~~~-~G~L~~~D~~mNlvL   42 (62)
                      |.++.+++|+.|.|++.+...+ +|+|.++|+- ++.|
T Consensus        90 ~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l  126 (151)
T PRK14637         90 AAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVL  126 (151)
T ss_pred             HHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEE
Confidence            4569999999999999544455 7999999964 4444

>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=93.63  E-value=0.28  Score=28.31  Aligned_cols=37  Identities=22%  Similarity=0.328  Sum_probs=29.6

Q ss_pred             hHHhcCCCEEEEEECCCeEEEEEEEEec-CccceEecc
Q psy11512          8 ELKKFMDKKVTLKLNANRNVTGILRGFD-PFMNLVLDE   44 (62)
Q Consensus         8 ~L~~~l~k~V~V~l~~g~~~~G~L~~~D-~~mNlvL~~   44 (62)
                      .|.+..|++|.+.|.++.+..|++.|+| +-.|+..++
T Consensus        18 ~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~   55 (80)
T PF11095_consen   18 SLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSN   55 (80)
T ss_dssp             HHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEE
T ss_pred             HHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhh
Confidence            3678899999999999999999999999 557777665

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.

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=93.61  E-value=0.16  Score=32.95  Aligned_cols=37  Identities=30%  Similarity=0.437  Sum_probs=28.6

Q ss_pred             HHhcC--CCEEEEEECCCeEEEEEEEEecCccceEecce
Q psy11512          9 LKKFM--DKKVTLKLNANRNVTGILRGFDPFMNLVLDEG   45 (62)
Q Consensus         9 L~~~l--~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~   45 (62)
                      |+.+.  ..+|.|-|.+|-.++|.+.+||+|.=|.-.+.
T Consensus        17 Ln~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g   55 (165)
T PRK14091         17 LNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRDG   55 (165)
T ss_pred             HHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            54444  44577889999999999999999976665554

>PRK14641 hypothetical protein; Provisional

Probab=93.27  E-value=0.21  Score=32.34  Aligned_cols=38  Identities=16%  Similarity=0.302  Sum_probs=29.9

Q ss_pred             chhHHhcCCCEEEEEECC----CeEEEEEEEEec------CccceEec
Q psy11512          6 PPELKKFMDKKVTLKLNA----NRNVTGILRGFD------PFMNLVLD   43 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~~----g~~~~G~L~~~D------~~mNlvL~   43 (62)
                      +..+.+++|+.|.|++++    .+.+.|+|.++|      ....++..
T Consensus        96 ~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~~~~~~~~~v~~~~~  143 (173)
T PRK14641         96 PRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVSLTEGEGASIVLKPE  143 (173)
T ss_pred             HHHHHHhCCCEEEEEEecccCCeEEEEEEEEeeecccCCCCcEEEEec
Confidence            456899999999999965    578999999995      55555444

>PRK14630 hypothetical protein; Provisional

Probab=91.14  E-value=0.59  Score=29.24  Aligned_cols=30  Identities=27%  Similarity=0.349  Sum_probs=25.3

Q ss_pred             chhHHhcCCCEEEEEECCCeEEEEEEEEecC
Q psy11512          6 PPELKKFMDKKVTLKLNANRNVTGILRGFDP   36 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~   36 (62)
                      +.++.+++|++|.|++... ...|+|.++|+
T Consensus        89 ~~df~r~~G~~v~V~l~~~-~~~G~L~~~~d  118 (143)
T PRK14630         89 DREFKIFEGKKIKLMLDND-FEEGFILEAKA  118 (143)
T ss_pred             HHHHHHhCCCEEEEEEcCc-ceEEEEEEEeC
Confidence            4568999999999999664 45999999996

>PRK14635 hypothetical protein; Provisional

Probab=90.18  E-value=0.82  Score=29.03  Aligned_cols=31  Identities=23%  Similarity=0.282  Sum_probs=26.3

Q ss_pred             chhHHhcCCCEEEEEEC--CCeEEEE---EEEEecC
Q psy11512          6 PPELKKFMDKKVTLKLN--ANRNVTG---ILRGFDP   36 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~--~g~~~~G---~L~~~D~   36 (62)
                      |.++.++.|+.|.|++.  ++..+.|   .|.++|+
T Consensus        91 ~~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~  126 (162)
T PRK14635         91 PEDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDG  126 (162)
T ss_pred             HHHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcC
Confidence            55699999999999985  4678888   9999996

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

Probab=89.53  E-value=2.4  Score=23.59  Aligned_cols=29  Identities=17%  Similarity=0.375  Sum_probs=25.4

Q ss_pred             HHhcCCCEEEEEECCCeEEEEEEEEec-Ccc
Q psy11512          9 LKKFMDKKVTLKLNANRNVTGILRGFD-PFM   38 (62)
Q Consensus         9 L~~~l~k~V~V~l~~g~~~~G~L~~~D-~~m   38 (62)
                      |++++|++|.|.+..|.. +|+|.+.- +|.
T Consensus        16 lq~liG~~vvV~T~~g~v-~G~L~~V~pDhI   45 (66)
T PF10842_consen   16 LQSLIGQRVVVQTTRGSV-RGILVDVKPDHI   45 (66)
T ss_pred             HHHhcCCEEEEEEcCCcE-EEEEEeecCCEE
Confidence            899999999999977665 99999987 665

>PRK06955 biotin--protein ligase; Provisional

Probab=86.87  E-value=2  Score=29.44  Aligned_cols=33  Identities=24%  Similarity=0.411  Sum_probs=28.9

Q ss_pred             hcCCCEEEEEECCCeEEEEEEEEecCccceEec
Q psy11512         11 KFMDKKVTLKLNANRNVTGILRGFDPFMNLVLD   43 (62)
Q Consensus        11 ~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~   43 (62)
                      -+++++|+|...+++.+.|++.|+|+.-.|+++
T Consensus       246 ~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~  278 (300)
T PRK06955        246 AYAGREVVLLEDGAELARGVAHGIDETGQLLLD  278 (300)
T ss_pred             hcCCCeEEEEECCCcEEEEEEeeECCCceEEEE
Confidence            478999999766778899999999999999885

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

Probab=85.88  E-value=1  Score=29.11  Aligned_cols=24  Identities=17%  Similarity=0.385  Sum_probs=21.6

Q ss_pred             CCCEEEEEECCCeEEEEEEEEecC
Q psy11512         13 MDKKVTLKLNANRNVTGILRGFDP   36 (62)
Q Consensus        13 l~k~V~V~l~~g~~~~G~L~~~D~   36 (62)
                      -|+-|+|-+.|||+++|+-.|.|.
T Consensus       119 qg~sIrVyM~DgR~ieG~stGvna  142 (165)
T PF03614_consen  119 QGKSIRVYMADGREIEGKSTGVNA  142 (165)
T ss_pred             CCCeEEEEEcCCcEEEeeecccce
Confidence            467799999999999999999984

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

>PRK10898 serine endoprotease; Provisional

Probab=83.02  E-value=3.6  Score=28.84  Aligned_cols=31  Identities=19%  Similarity=0.320  Sum_probs=26.9

Q ss_pred             CEEEEEECCCeEEEEEEEEecCccceEecce
Q psy11512         15 KKVTLKLNANRNVTGILRGFDPFMNLVLDEG   45 (62)
Q Consensus        15 k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~   45 (62)
                      ..+.|.+.||+.+.++++++|....|-+=..
T Consensus       102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v  132 (353)
T PRK10898        102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKI  132 (353)
T ss_pred             CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEE
Confidence            5789999999999999999999988865544

>TIGR02038 protease_degS periplasmic serine pepetdase DegS

Probab=82.45  E-value=3.8  Score=28.61  Aligned_cols=31  Identities=23%  Similarity=0.377  Sum_probs=27.0

Q ss_pred             CEEEEEECCCeEEEEEEEEecCccceEecce
Q psy11512         15 KKVTLKLNANRNVTGILRGFDPFMNLVLDEG   45 (62)
Q Consensus        15 k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~   45 (62)
                      ..+.|.+.||+.+.++++++|...+|.+=..
T Consensus       102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv  132 (351)
T TIGR02038       102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKI  132 (351)
T ss_pred             CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence            4688999999999999999999998877544

This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).

>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=81.64  E-value=2.8  Score=25.09  Aligned_cols=18  Identities=22%  Similarity=0.527  Sum_probs=14.1

Q ss_pred             CCEEEEEECCCeEEEEEE
Q psy11512         14 DKKVTLKLNANRNVTGIL   31 (62)
Q Consensus        14 ~k~V~V~l~~g~~~~G~L   31 (62)
                      +.+|.+.|+||+.+.|++
T Consensus        28 e~~V~l~L~DGs~l~Gtv   45 (101)
T PF11607_consen   28 EERVELELDDGSMLRGTV   45 (101)
T ss_dssp             T-EEEEEETTS-EEEEEE
T ss_pred             cceEEEEEcCCCeeeeee
Confidence            356888899999999996

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.

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

Probab=81.62  E-value=4.6  Score=27.55  Aligned_cols=32  Identities=31%  Similarity=0.627  Sum_probs=27.5

Q ss_pred             hcCCCEEEEEECCCeEEEEEEEEecCccceEec
Q psy11512         11 KFMDKKVTLKLNANRNVTGILRGFDPFMNLVLD   43 (62)
Q Consensus        11 ~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~   43 (62)
                      -++|++|.+...+ ..++|++.|+|+.-.|++.
T Consensus       269 ~~~g~~v~~~~~~-~~~~G~~~gi~~~G~L~i~  300 (319)
T PRK11886        269 LFLGREVKLIIGD-KEISGIARGIDEQGALLLE  300 (319)
T ss_pred             cccCCeEEEEeCC-cEEEEEEEEECCCceEEEE
Confidence            4689999998744 6799999999999999985

>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A

Probab=81.58  E-value=2  Score=21.99  Aligned_cols=22  Identities=23%  Similarity=0.376  Sum_probs=14.6

Q ss_pred             EEEEEEEecCccceEecceEEE
Q psy11512         27 VTGILRGFDPFMNLVLDEGVEY   48 (62)
Q Consensus        27 ~~G~L~~~D~~mNlvL~~~~e~   48 (62)
                      ..|++.|+|+.+.+.|.+....
T Consensus        10 ~tGtFlGvDE~FGmLLr~~~~T   31 (42)
T PF14563_consen   10 LTGTFLGVDEDFGMLLRDDDTT   31 (42)
T ss_dssp             EEEEEEEE-TT--EEEE-SS-E
T ss_pred             cceeEEeeccccceEEEeCCcc
Confidence            6899999999999999876543

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

Probab=80.04  E-value=5.1  Score=30.21  Aligned_cols=34  Identities=24%  Similarity=0.231  Sum_probs=29.3

Q ss_pred             hcCCCEEEEEECCCeEEEEEEEEecCccceEecc
Q psy11512         11 KFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDE   44 (62)
Q Consensus        11 ~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~   44 (62)
                      -++|++|.+...++..+.|+..|+|+.-.|+|+.
T Consensus       275 ~~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~  308 (592)
T PRK13325        275 RDHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET  308 (592)
T ss_pred             ccCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence            4789999987667778999999999999999863

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	62
3cw1_G	76	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		8e-20
3swn_C	117	Structure Of The Lsm657 Complex: An Assembly Interm		2e-05
4emk_C	113	Crystal Structure Of Splsm567 Length = 113		1e-04

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

Iteration: 1
 Score = 91.7 bits (226), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 43/60 (71%), Positives = 49/60 (81%)
Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          MSK+HPPELKKFMDKK++LKLN  R+V GILRGFDPFMNLV+DE VE       +NIGMV
Sbjct: 1  MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMV 60

>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 = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 16/37 (43%), Positives = 25/37 (67%)
Query: 8  ELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDE 44
          +L ++ D+++       R +TGIL+GFD  MNLVLD+
Sbjct: 31 DLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDD 67

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 8  ELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDE 44
          +L ++ D+++       R +TGIL+GFD   NLVLD+
Sbjct: 27 DLSRYQDQRIQATFTGGRQITGILKGFDQLXNLVLDD 63

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	62
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	3e-24
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	9e-24
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	8e-20
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	4e-19
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	2e-17
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	1e-16
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	3e-16
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	4e-16
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	2e-15
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	4e-14
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	1e-13
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	2e-13
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	3e-11
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	3e-11
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	1e-10
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	3e-10
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	2e-07
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-07
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	3e-06
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	7e-06
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	1e-05
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	2e-05

>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 = 84.7 bits (210), Expect = 3e-24
 Identities = 43/60 (71%), Positives = 49/60 (81%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          MSK+HPPELKKFMDKK++LKLN  R+V GILRGFDPFMNLV+DE VE       +NIGMV
Sbjct: 1  MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMV 60

>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 = 83.5 bits (207), Expect = 9e-24
 Identities = 18/60 (30%), Positives = 34/60 (56%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          ++++    L + ++  V +KL  N+ V G+LR +D  MNLVL +  E + D +   +G +
Sbjct: 6  LAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTI 65

>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 = 73.5 bits (181), Expect = 8e-20
 Identities = 18/60 (30%), Positives = 26/60 (43%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          M       L + +   V ++L   R   G L G+D  MNLVL +  E +    V  +G V
Sbjct: 1  MPPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSV 60

>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 = 72.0 bits (177), Expect = 4e-19
 Identities = 19/60 (31%), Positives = 28/60 (46%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          M  S    L K + KKV ++L++  +  GIL   D +MNL L+   EY      +  G  
Sbjct: 1  MDSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDA 60

>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 = 67.3 bits (165), Expect = 2e-17
 Identities = 14/60 (23%), Positives = 26/60 (43%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          M++     + + +DK V + L       G L G+D  +N+VL +    +    V   G +
Sbjct: 1  MAERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKI 60

>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 = 66.9 bits (163), Expect = 1e-16
 Identities = 18/60 (30%), Positives = 30/60 (50%)

Query: 2  SKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE 61
           K    +L ++ D+++       R +TGIL+GFD  MNLVLD+  E  ++     +    
Sbjct: 21 RKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAI 80

>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 = 64.7 bits (158), Expect = 3e-16
 Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 3  KSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
           +    L+  + K+V +KL  +  + GILR FD  +NL+L++  E   D  V+  G +
Sbjct: 10 ATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-IDGNVYKRGTM 66

>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 = 64.3 bits (157), Expect = 4e-16
 Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 1  MSKSHP-PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGM 59
          ++   P   L   ++  V +KL  +R   G+L+ FD  MNLVL++  E         +G 
Sbjct: 11 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGT 70

Query: 60 V 60
          V
Sbjct: 71 V 71

>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 = 62.9 bits (153), Expect = 2e-15
 Identities = 14/53 (26%), Positives = 25/53 (47%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNT 53
          M+     ++ + +D ++   L   R   G  + FD  MNL+L +  E+RK   
Sbjct: 1  MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP 53

>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 = 59.7 bits (145), Expect = 4e-14
 Identities = 17/53 (32%), Positives = 26/53 (49%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE 61
          LK  +D++V +KL   R + G L+ FD   N+VL + VE         +   E
Sbjct: 15 LKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESE 67

>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 = 57.7 bits (140), Expect = 1e-13
 Identities = 14/55 (25%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 7  PELKKFMDKKVTLKLNANRN-VTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
            +K  + K + +++    N + G L G D +MNL L   +E + +  V ++G +
Sbjct: 8  QMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEI 62

>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 = 57.5 bits (139), Expect = 2e-13
 Identities = 16/54 (29%), Positives = 21/54 (38%)

Query: 7  PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          P L     K V +KL       G L   D +MN+ L    EY       ++G V
Sbjct: 9  PFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

>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 = 52.5 bits (126), Expect = 3e-11
 Identities = 12/54 (22%), Positives = 24/54 (44%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVEE 62
          ++  +D+ V +KL  +R + G L  +D  +N+VL +  E             + 
Sbjct: 14 VRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKA 67

>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 = 52.2 bits (125), Expect = 3e-11
 Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 5/65 (7%)

Query: 1  MSKSHP----PELKKFMDKKVTLKLNAN-RNVTGILRGFDPFMNLVLDEGVEYRKDNTVH 55
          +S   P    P LK  ++ +V +KL  N     G L   D + NL L+E  E+    +  
Sbjct: 14 ISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHG 73

Query: 56 NIGMV 60
           +G +
Sbjct: 74 TLGEI 78

>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 = 51.0 bits (122), Expect = 1e-10
 Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 3/63 (4%)

Query: 1  MSKSHPPE--LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYR-KDNTVHNI 57
          MS +  P   + K +   + + + + R   G L GFD ++N+VL +  EY          
Sbjct: 15 MSMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKH 74

Query: 58 GMV 60
            +
Sbjct: 75 SEM 77

>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 = 50.8 bits (121), Expect = 3e-10
 Identities = 14/54 (25%), Positives = 30/54 (55%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVEE 62
          + K +  ++ + +  ++  +G+LRGFD ++N+VLD+  EY       +I    +
Sbjct: 33 IDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNK 86

>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 = 42.5 bits (100), Expect = 2e-07
 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYR-KDNTVHNIGMV 60
          L+     +V L    N  + G + GFD +MNLVLD+  E   K  +   +G +
Sbjct: 25 LQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRI 77

>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 = 43.1 bits (101), Expect = 6e-07
 Identities = 14/50 (28%), Positives = 25/50 (50%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRK 50
          M+     ++ + +D ++   L   R   G  + FD  MNL+L +  E+RK
Sbjct: 1  MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRK 50

>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 = 39.7 bits (93), Expect = 3e-06
 Identities = 11/43 (25%), Positives = 17/43 (39%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKD 51
          L     + + ++L       G L   D +MNL L E +    D
Sbjct: 21 LNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPD 63

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

 Score = 39.2 bits (91), Expect = 7e-06
 Identities = 13/52 (25%), Positives = 20/52 (38%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          L K   + VT++L     V G + G D  MN  L       K+     +  +
Sbjct: 7  LMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETL 58

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

 Score = 38.9 bits (90), Expect = 1e-05
 Identities = 14/61 (22%), Positives = 21/61 (34%), Gaps = 1/61 (1%)

Query: 1  MSKSHPPE-LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGM 59
          MS   P + L +     VT + N      G L   +  MN  +       +D  V  +  
Sbjct: 1  MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ 60

Query: 60 V 60
          V
Sbjct: 61 V 61

>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 = 37.0 bits (86), Expect = 2e-05
 Identities = 11/52 (21%), Positives = 17/52 (32%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          L +     VT + N      G L   +  MN  +       +D  V  +  V
Sbjct: 10 LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQV 61

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	62
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.9
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.87
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.87
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.86
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.85
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.84
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.83
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.83
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.82
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.82
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.82
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.81
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.8
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.8
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.8
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.79
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.79
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.76
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.76
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.76
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.75
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.73
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.69
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.65
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	99.08
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	97.36
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	97.34
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	97.26
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	97.05
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	96.99
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	96.89
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	96.85
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	96.22
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	96.03
1ycy_A	71	Conserved hypothetical protein; structural genomic	95.99
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	95.26
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	95.11
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	94.49
3rux_A	270	BIRA bifunctional protein; biotin-protein ligase,	93.93
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	93.26
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	92.97
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	91.8
2ej9_A	237	Putative biotin ligase; biotin biosynthesis, monom	86.37
1bia_A	321	BIRA bifunctional protein; transcription regulatio	84.12
2dxu_A	235	Biotin--[acetyl-COA-carboxylase] ligase; biotin bi	82.39
2rm4_A	103	CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-	80.74
3bfm_A	235	Biotin protein ligase-like protein of unknown FUN;	80.06

>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=99.90  E-value=5.8e-24  Score=119.91  Aligned_cols=61  Identities=70%  Similarity=1.096  Sum_probs=41.9

Q ss_pred             CCCCCchhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          1 MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         1 m~~~~~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      ||++++++|.++++++|+|+|+||++|+|+|.|||+|||++|+||+|+..+++.+.+|.++
T Consensus         1 ms~~~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~v~   61 (76)
T 3s6n_G            1 MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVV   61 (76)
T ss_dssp             -------------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC----CBSSEE
T ss_pred             CCCcchHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccCCcEeEcCEEE
Confidence            9999999999999999999999999999999999999999999999998877788888764

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

Probab=99.87  E-value=3.6e-22  Score=111.88  Aligned_cols=61  Identities=23%  Similarity=0.360  Sum_probs=55.1

Q ss_pred             CCCCCchhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          1 MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         1 m~~~~~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      ||..+.++|.++++++|+|+++||++|+|+|.|||+|||++|+||+|+..+...+.+|.++
T Consensus         1 m~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~   61 (75)
T 1h64_1            1 MAERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIV   61 (75)
T ss_dssp             --CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             CCchHHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeCCceeECCEEE
Confidence            7777777799999999999999999999999999999999999999998888888999874

>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=99.87  E-value=3e-22  Score=112.52  Aligned_cols=61  Identities=31%  Similarity=0.434  Sum_probs=56.5

Q ss_pred             CCCCCchhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          1 MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         1 m~~~~~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      ||..|.++|+++++++|+|+|+||++|+|+|.|||+|||++|+||+|+..++..+++|.++
T Consensus         1 m~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~   61 (75)
T 4emk_B            1 MDSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAF   61 (75)
T ss_dssp             CCSHHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEETTEEEEEEEEEE
T ss_pred             CCCchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEecCCcccEecEEE
Confidence            7877778899999999999999999999999999999999999999998777788899875

>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=99.86  E-value=1e-21  Score=110.36  Aligned_cols=61  Identities=30%  Similarity=0.465  Sum_probs=55.0

Q ss_pred             CCCCCchhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          1 MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         1 m~~~~~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      ||..+.++|.++++++|+|+|+||++|.|+|.|||+|||++|+||+|+..++..+.+|.++
T Consensus         1 m~~~P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~   61 (77)
T 1i4k_A            1 MPPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVV   61 (77)
T ss_dssp             --CCHHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             CCccHHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecCCcEeECCEEE
Confidence            7776667799999999999999999999999999999999999999999888888999874

>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=99.85  E-value=3.2e-21  Score=109.55  Aligned_cols=55  Identities=33%  Similarity=0.572  Sum_probs=51.8

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      ++|.++++++|+|+|+||++|.|+|.|||+|||++|+||+|+..+...+.+|.++
T Consensus        12 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~   66 (81)
T 1th7_A           12 KVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIV   66 (81)
T ss_dssp             HHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEE
T ss_pred             HHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecCCceeECCEEE
Confidence            4589999999999999999999999999999999999999998888889999875

>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=99.84  E-value=3.3e-21  Score=111.27  Aligned_cols=61  Identities=26%  Similarity=0.458  Sum_probs=49.5

Q ss_pred             CCCCCchhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEec----------CCceeeeeEee
Q psy11512          1 MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRK----------DNTVHNIGMVE   61 (62)
Q Consensus         1 m~~~~~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~----------~~~~~~lG~v~   61 (62)
                      |+-.+.++|.++++++|+|+++|||+|.|+|.|||+||||+|+||+|+..          ....+.+|.|+
T Consensus         1 m~~~~~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~   71 (91)
T 1d3b_B            1 MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVL   71 (91)
T ss_dssp             ------CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEE
T ss_pred             CCCChhHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEE
Confidence            66667788999999999999999999999999999999999999999752          23577889875

>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=99.83  E-value=3.7e-20  Score=104.16  Aligned_cols=61  Identities=23%  Similarity=0.159  Sum_probs=53.3

Q ss_pred             CCCCCchh-HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          1 MSKSHPPE-LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         1 m~~~~~~~-L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      ||-..|.. |++++|++|.|+|++|++|+|+|.|||+|||++|+||+|+..++..+++|.++
T Consensus         1 ~~~~~P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~~~~~~lg~v~   62 (75)
T 1d3b_A            1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVY   62 (75)
T ss_dssp             ---CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEE
T ss_pred             CCccCHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCCCcEEEcCeEE
Confidence            56656655 79999999999999999999999999999999999999998777888999874

>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=99.83  E-value=4.2e-20  Score=108.26  Aligned_cols=56  Identities=25%  Similarity=0.478  Sum_probs=51.5

Q ss_pred             chh-HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEe-cCCceeeeeEee
Q psy11512          6 PPE-LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYR-KDNTVHNIGMVE   61 (62)
Q Consensus         6 ~~~-L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~lG~v~   61 (62)
                      |.. |.++++++|+|++++|++|+|+|.|||+||||+|+||+|+. .++..+.+|.++
T Consensus        21 Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~   78 (94)
T 4emk_A           21 PLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKHSEML   78 (94)
T ss_dssp             HHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTTCCEEEEEEEE
T ss_pred             CHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCCCcEeEcCEEE
Confidence            544 79999999999999999999999999999999999999998 667788999875

>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=99.82  E-value=3e-20  Score=106.99  Aligned_cols=61  Identities=30%  Similarity=0.348  Sum_probs=51.5

Q ss_pred             CCCCCch--hHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          1 MSKSHPP--ELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         1 m~~~~~~--~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      ||....|  +|+++++++|+|+|++|++|+|+|.|||+|||++|+||+|+..+...+.+|.++
T Consensus         1 ms~~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~g~~~~~lg~v~   63 (86)
T 3s6n_F            1 MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVL   63 (86)
T ss_dssp             --CCCCHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEESSEE
T ss_pred             CCcCcCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcCCceeeEccEEE
Confidence            6655433  489999999999999999999999999999999999999997665677888764

>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=99.82  E-value=3.5e-20  Score=104.27  Aligned_cols=55  Identities=24%  Similarity=0.520  Sum_probs=51.5

Q ss_pred             hhHHhcCCCEEEEEECCC-eEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          7 PELKKFMDKKVTLKLNAN-RNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g-~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      ++|.++++++|+|++++| ++|+|+|.|||+|||++|+||+|+..++..+.+|.++
T Consensus         8 ~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~   63 (77)
T 1ljo_A            8 QMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIV   63 (77)
T ss_dssp             HHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             HHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecCCcEeECCeEE
Confidence            458999999999999999 9999999999999999999999999877888999874

>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=99.82  E-value=7.8e-20  Score=104.35  Aligned_cols=55  Identities=31%  Similarity=0.555  Sum_probs=51.7

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      ++|.++++++|+|+|+||++|+|+|.|||+|||++|+||+|+..+...+.+|.++
T Consensus        18 ~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~   72 (83)
T 1mgq_A           18 DALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVL   72 (83)
T ss_dssp             HHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             HHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecCCcccCCCEEE
Confidence            4589999999999999999999999999999999999999999888889999874

>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=99.81  E-value=5.8e-20  Score=104.38  Aligned_cols=54  Identities=33%  Similarity=0.551  Sum_probs=50.1

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      ++|.++++++|+|+|+||++|.|+|.|||+|||++|+||+|+ .+...+.+|.++
T Consensus        14 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~~~~~~~lg~v~   67 (81)
T 1i8f_A           14 ATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-IDGNVYKRGTMV   67 (81)
T ss_dssp             HHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-ETTEEEEEEEEE
T ss_pred             HHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-cCCcccCCCEEE
Confidence            358999999999999999999999999999999999999999 667788999875

>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=99.80  E-value=1.5e-19  Score=108.72  Aligned_cols=56  Identities=34%  Similarity=0.696  Sum_probs=44.2

Q ss_pred             chhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecC-------CceeeeeEee
Q psy11512          6 PPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKD-------NTVHNIGMVE   61 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-------~~~~~lG~v~   61 (62)
                      .++|.+|++++|+|+|+|||+|.|+|.|||+||||+|+||+|+..+       ...+.+|.|+
T Consensus        25 i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~   87 (113)
T 4emk_C           25 ILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVV   87 (113)
T ss_dssp             -------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEE
T ss_pred             HHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEE
Confidence            3569999999999999999999999999999999999999999764       3578899875

>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=99.80  E-value=9.2e-20  Score=106.43  Aligned_cols=56  Identities=29%  Similarity=0.430  Sum_probs=49.7

Q ss_pred             chhHHhcCCCEEEEEECCC-eEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          6 PPELKKFMDKKVTLKLNAN-RNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~~g-~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      .++|.++++++|+|+|++| ++|+|+|.|||+|||++|+||+|+..++..+.+|.++
T Consensus        23 ~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~~~~~~~lg~v~   79 (93)
T 1n9r_A           23 KPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIF   79 (93)
T ss_dssp             ---CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEE
T ss_pred             HHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcCCCeEeEcCEEE
Confidence            3568999999999999999 9999999999999999999999998777788888764

>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=99.80  E-value=1.3e-19  Score=106.07  Aligned_cols=55  Identities=33%  Similarity=0.453  Sum_probs=49.1

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecC-------CceeeeeEee
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKD-------NTVHNIGMVE   61 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-------~~~~~lG~v~   61 (62)
                      .+|.++++++|+|+|+|||+|.|+|.|||+||||+|+||+|+..+       ...+.+|.++
T Consensus        13 ~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~   74 (96)
T 3bw1_A           13 DLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVF   74 (96)
T ss_dssp             HHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEE
T ss_pred             HHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEE
Confidence            348999999999999999999999999999999999999999753       3467899875

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

Probab=99.79  E-value=5.9e-19  Score=102.85  Aligned_cols=57  Identities=25%  Similarity=0.412  Sum_probs=49.6

Q ss_pred             Cchh-HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecC-------------CceeeeeEee
Q psy11512          5 HPPE-LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKD-------------NTVHNIGMVE   61 (62)
Q Consensus         5 ~~~~-L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-------------~~~~~lG~v~   61 (62)
                      .|.+ |+.+++++|+|++++|++|.|+|.|||+||||+|+||+|+...             ...+.+|.++
T Consensus         9 ~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~   79 (93)
T 4emg_A            9 EPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLF   79 (93)
T ss_dssp             CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEE
T ss_pred             CCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEE
Confidence            4666 5777999999999999999999999999999999999999752             2468899875

>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=99.79  E-value=4e-19  Score=117.69  Aligned_cols=61  Identities=26%  Similarity=0.458  Sum_probs=54.1

Q ss_pred             CCCCCchhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEec----------CCceeeeeEee
Q psy11512          1 MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRK----------DNTVHNIGMVE   61 (62)
Q Consensus         1 m~~~~~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~----------~~~~~~lG~v~   61 (62)
                      |+-....+|.+|++++|+|+|+|||+|+|+|.|||+||||+|+||+|+..          ..+.+.+|+|+
T Consensus         1 ~~v~k~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~   71 (231)
T 3pgw_B            1 MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVL   71 (231)
T ss_pred             CCcCchHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEE
Confidence            56666788999999999999999999999999999999999999999863          23678888875

>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=99.76  E-value=4.8e-19  Score=103.31  Aligned_cols=56  Identities=27%  Similarity=0.613  Sum_probs=50.6

Q ss_pred             chh-HHhcCCCEEEEEE----CCCeEEEEEEEEecCccceEecceEEEe-cCCceeeeeEee
Q psy11512          6 PPE-LKKFMDKKVTLKL----NANRNVTGILRGFDPFMNLVLDEGVEYR-KDNTVHNIGMVE   61 (62)
Q Consensus         6 ~~~-L~~~l~k~V~V~l----~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~lG~v~   61 (62)
                      |.+ |.++++++++|++    ++|++|+|+|.|||+||||+|+||+|+. .++..+++|.++
T Consensus        17 Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~   78 (92)
T 3s6n_E           17 PINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIM   78 (92)
T ss_dssp             HHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSCCEEEEEEEE
T ss_pred             CHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCCceeEcCeEE
Confidence            555 7999999999999    9999999999999999999999999997 445678899875

>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=99.76  E-value=2.1e-18  Score=104.21  Aligned_cols=56  Identities=23%  Similarity=0.236  Sum_probs=51.8

Q ss_pred             chhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          6 PPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      .++|.++++++|.|+|++|++|.|+|.+||+||||+|+||+|+..+++..++|.++
T Consensus         4 ~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~~~~~~lg~v~   59 (119)
T 1b34_A            4 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLS   59 (119)
T ss_dssp             HHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEE
T ss_pred             HHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecCCCceeEcceEE
Confidence            45699999999999999999999999999999999999999998777788899874

>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=99.76  E-value=2.7e-18  Score=102.20  Aligned_cols=55  Identities=20%  Similarity=0.284  Sum_probs=44.4

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCC-ceeeeeEee
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDN-TVHNIGMVE   61 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~-~~~~lG~v~   61 (62)
                      .+|.++++++|+|+|++|++|+|+|.|||+||||+|+||+|...++ ..+.+|.|+
T Consensus        19 ~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg~~~~~lg~v~   74 (105)
T 4emh_A           19 TLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECY   74 (105)
T ss_dssp             -------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEE
T ss_pred             HHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCCceeeEcCeEE
Confidence            3489999999999999999999999999999999999999997665 578899875

>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=99.75  E-value=6.3e-18  Score=103.38  Aligned_cols=61  Identities=23%  Similarity=0.159  Sum_probs=52.4

Q ss_pred             CCCCCchh-HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          1 MSKSHPPE-LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         1 m~~~~~~~-L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      ||--.|.. |+++++++|.|+|++|++|+|+|.+||+|||++|+||+|+..+++..++|.|+
T Consensus         1 ~~~~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~~~~l~~v~   62 (126)
T 2y9a_D            1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVY   62 (126)
T ss_dssp             ---CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSCCEEEEEEE
T ss_pred             CCcccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCcEeecccEE
Confidence            66555654 89999999999999999999999999999999999999998777788888874

>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=99.73  E-value=2.6e-18  Score=104.03  Aligned_cols=45  Identities=31%  Similarity=0.715  Sum_probs=42.1

Q ss_pred             chh-HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEec
Q psy11512          6 PPE-LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRK   50 (62)
Q Consensus         6 ~~~-L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~   50 (62)
                      |.. |.++++++|+|++++||+|.|+|.|||+||||+|+||+|+..
T Consensus        29 Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~   74 (121)
T 2fwk_A           29 PLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGF   74 (121)
T ss_dssp             HHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC
T ss_pred             cHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEe
Confidence            444 799999999999999999999999999999999999999984

>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=99.69  E-value=5.1e-17  Score=97.90  Aligned_cols=45  Identities=24%  Similarity=0.440  Sum_probs=40.1

Q ss_pred             chh-HHhcC--CCEEEEEECCCeEEEEEEEEecCccceEecceEEEec
Q psy11512          6 PPE-LKKFM--DKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRK   50 (62)
Q Consensus         6 ~~~-L~~~l--~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~   50 (62)
                      |.. |.+++  +++|+|+|++|+.|.|+|.|||+||||+|+||+|+..
T Consensus        28 Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~   75 (118)
T 1b34_B           28 PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWT   75 (118)
T ss_dssp             HHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC--
T ss_pred             hHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEe
Confidence            444 79999  5999999999999999999999999999999999863

>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=99.65  E-value=2.3e-16  Score=96.87  Aligned_cols=51  Identities=22%  Similarity=0.343  Sum_probs=46.1

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      ++|.++++++|.|+|+||++|.|+|.|||+|||++|+||+|+.    .+++|.++
T Consensus         3 ~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~----~~~lg~v~   53 (130)
T 1m5q_A            3 AELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA----GEKFNRVF   53 (130)
T ss_dssp             HHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTT----CCEEEEEE
T ss_pred             hHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEc----CCEeceEE
Confidence            5799999999999999999999999999999999999999973    36777764

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

Probab=99.08  E-value=3.2e-10  Score=65.48  Aligned_cols=42  Identities=21%  Similarity=0.249  Sum_probs=40.4

Q ss_pred             CCchhHHhcCCCEEEEEECCCeEEEEEEEEec-CccceEecce
Q psy11512          4 SHPPELKKFMDKKVTLKLNANRNVTGILRGFD-PFMNLVLDEG   45 (62)
Q Consensus         4 ~~~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D-~~mNlvL~~~   45 (62)
                      ..|.+|.++++|+|.|++.||++|+|+|.+|| ..+|++|.||
T Consensus         7 ~~p~el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~   49 (86)
T 1y96_A            7 KGPLEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNF   49 (86)
T ss_dssp             SCHHHHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEE
T ss_pred             CCHHHHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeec
Confidence            56889999999999999999999999999999 8999999998

>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=97.36  E-value=0.00032  Score=39.42  Aligned_cols=37  Identities=16%  Similarity=0.372  Sum_probs=31.1

Q ss_pred             hHHhcC--CCEEEEEECCCeEEEEEEEEecCccceEecc
Q psy11512          8 ELKKFM--DKKVTLKLNANRNVTGILRGFDPFMNLVLDE   44 (62)
Q Consensus         8 ~L~~~l--~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~   44 (62)
                      +|+.+.  ..+|.|.|.+|-.+.|++.+||+|+=+.-.+
T Consensus        11 fLn~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~VlL~~~   49 (77)
T 1kq1_A           11 ALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQ   49 (77)
T ss_dssp             HHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEEET
T ss_pred             HHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEEEEC
Confidence            466666  7889999999999999999999998666543

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

Probab=97.34  E-value=0.00043  Score=38.42  Aligned_cols=34  Identities=18%  Similarity=0.225  Sum_probs=28.4

Q ss_pred             hcCCCEEEEEECCCeEEEEEEEEecCccceEecc
Q psy11512         11 KFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDE   44 (62)
Q Consensus        11 ~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~   44 (62)
                      +--+.+|+|-|.||-.++|.+.|||+|+=+.-.+
T Consensus        22 r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   55 (71)
T 2qtx_A           22 RLNGKKVKIFLRNGEVLDAEVTGVSNYEIMVKVG   55 (71)
T ss_dssp             GGTTCEEEEEETTSCEEEEEEEEECSSEEEEEET
T ss_pred             HHcCCcEEEEEeCCeEEEEEEEEEcceEEEEEeC
Confidence            3456789999999999999999999998666444

>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=97.26  E-value=0.00037  Score=38.87  Aligned_cols=36  Identities=22%  Similarity=0.348  Sum_probs=30.1

Q ss_pred             hHHhcC--CCEEEEEECCCeEEEEEEEEecCccceEec
Q psy11512          8 ELKKFM--DKKVTLKLNANRNVTGILRGFDPFMNLVLD   43 (62)
Q Consensus         8 ~L~~~l--~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~   43 (62)
                      +|+.+.  ..+|.|.|.+|..++|++.+||+|+=+.-+
T Consensus        13 ~L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~vlL~~   50 (74)
T 2ylb_A           13 FLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKN   50 (74)
T ss_dssp             HHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEES
T ss_pred             HHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEEC
Confidence            366666  778999999999999999999999765543

>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=97.05  E-value=0.00082  Score=38.21  Aligned_cols=35  Identities=23%  Similarity=0.353  Sum_probs=29.0

Q ss_pred             hHHhcC--CCEEEEEECCCeEEEEEEEEecCccceEe
Q psy11512          8 ELKKFM--DKKVTLKLNANRNVTGILRGFDPFMNLVL   42 (62)
Q Consensus         8 ~L~~~l--~k~V~V~l~~g~~~~G~L~~~D~~mNlvL   42 (62)
                      +|+.+.  ..+|+|-|.||-.+.|.+.+||+|+=+.-
T Consensus        11 fLn~lrk~~~~Vtv~L~NG~~l~G~I~~fD~ftVlL~   47 (82)
T 1u1s_A           11 YLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLK   47 (82)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEe
Confidence            355444  77899999999999999999999986654

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

Probab=96.99  E-value=0.0015  Score=36.75  Aligned_cols=36  Identities=31%  Similarity=0.448  Sum_probs=30.0

Q ss_pred             HHhcC--CCEEEEEECCCeEEEEEEEEecCccceEecc
Q psy11512          9 LKKFM--DKKVTLKLNANRNVTGILRGFDPFMNLVLDE   44 (62)
Q Consensus         9 L~~~l--~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~   44 (62)
                      |+.+.  ..+|+|-|.||..+.|.+.+||+|+=+.-.+
T Consensus        16 Ln~lrk~~~~Vtv~L~nG~~l~G~I~~fD~f~VlL~~~   53 (78)
T 3ahu_A           16 LNQIRKENTYVTVFLLNGFQLRGQVKGFDNFTVLLESE   53 (78)
T ss_dssp             HHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEESS
T ss_pred             HHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEEEEEC
Confidence            55555  7889999999999999999999998666543

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

Probab=96.89  E-value=0.0014  Score=36.97  Aligned_cols=34  Identities=21%  Similarity=0.349  Sum_probs=27.6

Q ss_pred             hHHhcCC--CEEEEEECCCeEEEEEEEEecCccceE
Q psy11512          8 ELKKFMD--KKVTLKLNANRNVTGILRGFDPFMNLV   41 (62)
Q Consensus         8 ~L~~~l~--k~V~V~l~~g~~~~G~L~~~D~~mNlv   41 (62)
                      +|+.+..  .+|.|.|.+|..+.|.+.+||+|+=+.
T Consensus        12 fLn~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~VlL   47 (79)
T 3sb2_A           12 FLNALRKEHVPVSIYLVNGIKLQGHVESFDQYVVLL   47 (79)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEE
Confidence            3555544  459999999999999999999997655

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

Probab=96.85  E-value=0.00094  Score=39.46  Aligned_cols=37  Identities=22%  Similarity=0.363  Sum_probs=29.9

Q ss_pred             hHHhcCCC--EEEEEECCCeEEEEEEEEecCccceEecc
Q psy11512          8 ELKKFMDK--KVTLKLNANRNVTGILRGFDPFMNLVLDE   44 (62)
Q Consensus         8 ~L~~~l~k--~V~V~l~~g~~~~G~L~~~D~~mNlvL~~   44 (62)
                      +|+.+..+  +|.|.|.+|-.++|++.+||+|+=+.-+.
T Consensus        13 fLn~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~VlL~~~   51 (104)
T 2y90_A           13 FLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNT   51 (104)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEESS
T ss_pred             HHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEECC
Confidence            46666555  79999999999999999999998666543

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

Probab=96.22  E-value=0.0098  Score=36.07  Aligned_cols=38  Identities=24%  Similarity=0.416  Sum_probs=31.8

Q ss_pred             hHHhcCCCEEEEEECCCeEEEEEEEEecCccceEe--cceE
Q psy11512          8 ELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVL--DEGV   46 (62)
Q Consensus         8 ~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL--~~~~   46 (62)
                      ....|+|..|.|+|+||..+.|++..+| --+|+|  .+|.
T Consensus         6 ~~sqFlGy~V~v~LkDgs~~qG~I~~vd-~k~LtL~~~~a~   45 (125)
T 4a53_A            6 SVADFYGSNVEVLLNNDSKARGVITNFD-SSNSILQLRLAN   45 (125)
T ss_dssp             CHHHHTTCEEEEEETTSCEEEEEEEEEE-TTTTEEEEEETT
T ss_pred             cHHHhcCceEEEEECCCCEeeEEEEeec-CCeeEEeccccc
Confidence            4688999999999999999999999998 334555  7763

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

Probab=96.03  E-value=0.026  Score=32.35  Aligned_cols=42  Identities=17%  Similarity=0.169  Sum_probs=36.3

Q ss_pred             HhcCCCEEEEEECCCeEEEEEEEEec-CccceEecceEEEecC
Q psy11512         10 KKFMDKKVTLKLNANRNVTGILRGFD-PFMNLVLDEGVEYRKD   51 (62)
Q Consensus        10 ~~~l~k~V~V~l~~g~~~~G~L~~~D-~~mNlvL~~~~e~~~~   51 (62)
                      ..|+|++|.+.-+.+..|+|+|..+| +---+.|.|+..+-.+
T Consensus         9 ~~yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTE   51 (88)
T 2vxe_A            9 LPELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTE   51 (88)
T ss_dssp             SCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCT
T ss_pred             CcccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCc
Confidence            35899999999999999999999999 5678899998877433

>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=95.99  E-value=0.01  Score=32.50  Aligned_cols=48  Identities=27%  Similarity=0.433  Sum_probs=33.8

Q ss_pred             CCCCCchh--HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEe
Q psy11512          1 MSKSHPPE--LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYR   49 (62)
Q Consensus         1 m~~~~~~~--L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~   49 (62)
                      |++.+-++  |..+.|++|-+.+.....|.|+|.-||+-. +.|.|++.+.
T Consensus         1 ~~~~~LLdktL~~WKg~rvAv~vg~ehSFtGiledFDeEv-iLL~dV~D~~   50 (71)
T 1ycy_A            1 MGMESLLEKVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVI   50 (71)
T ss_dssp             ----CHHHHHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETT
T ss_pred             CCchhHHHHHHHHhCCcEEEEEecCcceeeeehhhcCcce-eehhhHHHHh
Confidence            44545444  899999999999999999999999999754 6678888774

>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=95.26  E-value=0.024  Score=32.93  Aligned_cols=41  Identities=20%  Similarity=0.246  Sum_probs=34.9

Q ss_pred             HHhcCCCEEEEEECCCeEEEEEEEEec-CccceEecceEEEe
Q psy11512          9 LKKFMDKKVTLKLNANRNVTGILRGFD-PFMNLVLDEGVEYR   49 (62)
Q Consensus         9 L~~~l~k~V~V~l~~g~~~~G~L~~~D-~~mNlvL~~~~e~~   49 (62)
                      -..|+|++|.+.-+.+..|+|+|..+| +---+.|.|+..+-
T Consensus        14 ~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfG   55 (95)
T 2fb7_A           14 GTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFG   55 (95)
T ss_dssp             --CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCS
T ss_pred             cCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEec
Confidence            578999999999999999999999999 56778888877663

>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=95.11  E-value=0.025  Score=35.11  Aligned_cols=32  Identities=16%  Similarity=0.241  Sum_probs=27.2

Q ss_pred             chhHHhcCCCEEEEEE----CCCeEEEEEEEEecCc
Q psy11512          6 PPELKKFMDKKVTLKL----NANRNVTGILRGFDPF   37 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l----~~g~~~~G~L~~~D~~   37 (62)
                      +.++.+++|+.|.|++    .+.+.++|+|.++|+-
T Consensus        96 ~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T 1ib8_A           96 KDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED  131 (164)
T ss_dssp             HHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT
T ss_pred             HHHHHHhCCcEEEEEEecccCCceEEEEEEEEEeCC
Confidence            4458999999999999    4459999999999954

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

Probab=94.49  E-value=0.097  Score=29.71  Aligned_cols=37  Identities=11%  Similarity=0.207  Sum_probs=33.5

Q ss_pred             HhcCCCEEEEEECCCe-EEEEEEEEecCc-cceEecceE
Q psy11512         10 KKFMDKKVTLKLNANR-NVTGILRGFDPF-MNLVLDEGV   46 (62)
Q Consensus        10 ~~~l~k~V~V~l~~g~-~~~G~L~~~D~~-mNlvL~~~~   46 (62)
                      .+|+|+.|.+..+++- .|.|.|..+|.. -||.|.+|.
T Consensus         5 ~~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~f   43 (84)
T 2vc8_A            5 TDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPF   43 (84)
T ss_dssp             CTTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEEE
T ss_pred             ccccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehhh
Confidence            4799999999999998 999999999965 689999984

>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=93.93  E-value=0.28  Score=32.17  Aligned_cols=35  Identities=31%  Similarity=0.470  Sum_probs=30.5

Q ss_pred             hcCCCEEEEEECCCeEEEEEEEEecCccceEecce
Q psy11512         11 KFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEG   45 (62)
Q Consensus        11 ~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~   45 (62)
                      ..+|++|+|...+|..+.|+..|+|+.-.|+++..
T Consensus       221 ~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~~  255 (270)
T 3rux_A          221 LTIGSRVRVELPGGQDVVGIARDIDDQGRLCLDVG  255 (270)
T ss_dssp             SSTTSEEEEECTTSCEEEEEEEEECTTSCEEEEET
T ss_pred             cccCCEEEEEECCCeEEEEEEEEECCCCeEEEEEC
Confidence            35799999998888999999999999999988643

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

Probab=93.26  E-value=0.3  Score=26.74  Aligned_cols=35  Identities=20%  Similarity=0.213  Sum_probs=28.0

Q ss_pred             HHhcC--CCEEEEEECCCeEEEEEEEEecCccceEec
Q psy11512          9 LKKFM--DKKVTLKLNANRNVTGILRGFDPFMNLVLD   43 (62)
Q Consensus         9 L~~~l--~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~   43 (62)
                      |..++  ..+|.|+|.+|..+.|++.-+|.|.=+..+
T Consensus        14 lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~cl~L~~   50 (70)
T 3hfo_A           14 VQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDGLGLVD   50 (70)
T ss_dssp             HHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEEC
T ss_pred             HHHHHhhCceEEEEecCCCEEEEEEEEeCCCEEEEEc
Confidence            45554  467999999999999999999988755543

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

Probab=92.97  E-value=0.24  Score=28.15  Aligned_cols=36  Identities=17%  Similarity=0.293  Sum_probs=32.0

Q ss_pred             HHhcCCCEEEEEECCCeEEEEEEEEec-CccceEecc
Q psy11512          9 LKKFMDKKVTLKLNANRNVTGILRGFD-PFMNLVLDE   44 (62)
Q Consensus         9 L~~~l~k~V~V~l~~g~~~~G~L~~~D-~~mNlvL~~   44 (62)
                      |....+++|.+.+.++.++.|++.++| ...|+..++
T Consensus        24 l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~   60 (85)
T 1y96_B           24 LLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQ   60 (85)
T ss_dssp             HHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEE
T ss_pred             HHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhh
Confidence            677889999999999999999999999 667887665

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

Probab=91.80  E-value=0.57  Score=25.72  Aligned_cols=35  Identities=26%  Similarity=0.351  Sum_probs=28.1

Q ss_pred             HHhcCC--CEEEEEECCCeEEEEEEEEecCccceEec
Q psy11512          9 LKKFMD--KKVTLKLNANRNVTGILRGFDPFMNLVLD   43 (62)
Q Consensus         9 L~~~l~--k~V~V~l~~g~~~~G~L~~~D~~mNlvL~   43 (62)
                      |.+|+.  .+|.|+|.+|..+.|++.-+|.|.=+..+
T Consensus        16 lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~cl~L~~   52 (72)
T 3hfn_A           16 LQNLIKQAAPVEIKLVTGDAITGRVLWQDPTCVCIAD   52 (72)
T ss_dssp             HHHHHSSCCEEEEEETTSCEEEEEEEEECSSEEEEEC
T ss_pred             HHHHHhhCceEEEEecCCCEEEEEEEEECCCEEEEEc
Confidence            566664  45889999999999999999988755544

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

Probab=86.37  E-value=1.5  Score=28.08  Aligned_cols=32  Identities=22%  Similarity=0.212  Sum_probs=28.3

Q ss_pred             cCCCEEEEEECCCeEEEEEEEEecCccceEecc
Q psy11512         12 FMDKKVTLKLNANRNVTGILRGFDPFMNLVLDE   44 (62)
Q Consensus        12 ~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~   44 (62)
                      .+|++|++...++..+.|+..|+|+.-.|+ +.
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            589999999988877999999999998888 53

>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=84.12  E-value=2  Score=28.43  Aligned_cols=33  Identities=30%  Similarity=0.608  Sum_probs=28.1

Q ss_pred             hcCCCEEEEEECCCeEEEEEEEEecCccceEecc
Q psy11512         11 KFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDE   44 (62)
Q Consensus        11 ~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~   44 (62)
                      .++|++|+|...+ ..+.|+..|+|+.-.|+++.
T Consensus       270 ~~~g~~V~v~~~~-~~~~G~~~gid~~G~L~v~~  302 (321)
T 1bia_A          270 NFINRPVKLIIGD-KEIFGISRGIDKQGALLLEQ  302 (321)
T ss_dssp             TTTTSEEEEEETT-EEEEEEEEEECTTSCEEEEE
T ss_pred             hhcCCEEEEEECC-cEEEEEEEEECCCCeEEEEE
Confidence            4579999998765 58999999999999999864

>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=82.39  E-value=1.3  Score=28.43  Aligned_cols=30  Identities=20%  Similarity=0.366  Sum_probs=23.8

Q ss_pred             CCCEEEEEECCCeEEEEEEEEecCccceEecc
Q psy11512         13 MDKKVTLKLNANRNVTGILRGFDPFMNLVLDE   44 (62)
Q Consensus        13 l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~   44 (62)
                      +|++|++...++  +.|+..|+|+.-.|+++.
T Consensus       188 ~g~~V~v~~~~~--~~G~~~gId~~G~L~v~~  217 (235)
T 2dxu_A          188 LGVRVKILGDGS--FEGIAEDIDDFGRLIIRL  217 (235)
T ss_dssp             CSSEEEC----C--CEEEEEEECTTSCEEEEC
T ss_pred             cCCeEEEEECCe--EEEEEEEECCCCEEEEEE
Confidence            799999987776  999999999999999864

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

Probab=80.74  E-value=6.3  Score=22.86  Aligned_cols=37  Identities=5%  Similarity=0.229  Sum_probs=32.0

Q ss_pred             HhcCCCEEEEEECCCe-EEEEEEEEecCccceEecceEE
Q psy11512         10 KKFMDKKVTLKLNANR-NVTGILRGFDPFMNLVLDEGVE   47 (62)
Q Consensus        10 ~~~l~k~V~V~l~~g~-~~~G~L~~~D~~mNlvL~~~~e   47 (62)
                      .+|+|+.|.|...+.- .|.|.+..+|. -+|+|.+|..
T Consensus         8 edwiG~~VSI~C~d~LGVyQG~I~~V~~-~~ItL~kaFr   45 (103)
T 2rm4_A            8 QDWIGCAVSIACDEVLGVFQGLIKQISA-EEITIVRAFR   45 (103)
T ss_dssp             GGGTTCEEEEEECTTTCEEEEEEEEEET-TEEEEEEEEE
T ss_pred             cceeceEEEEeeCCcceEeeEEEEEccc-ceeEEhhhhh
Confidence            5899999999999875 99999999994 5588888763

>3bfm_A Biotin protein ligase-like protein of unknown FUN; structural genomics, joint center for structural genomics, J protein structure initiative; HET: 2PE; 1.70A {Silicibacter SP}

Probab=80.06  E-value=3.3  Score=26.22  Aligned_cols=29  Identities=24%  Similarity=0.298  Sum_probs=25.0

Q ss_pred             hcCCCEEEEEECCCeEEEEEEEEecCccceEecc
Q psy11512         11 KFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDE   44 (62)
Q Consensus        11 ~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~   44 (62)
                      ..+|++|++   +|  +.|+..|+|+.-.|+++.
T Consensus       191 ~~~g~~V~v---~~--~~G~~~gId~~G~L~v~~  219 (235)
T 3bfm_A          191 HGMGEARTE---AG--RSGTFLGVDEDFGMLLRD  219 (235)
T ss_dssp             TTTTSEEEE---TT--EEEEEEEECTTCCEEEEC
T ss_pred             hhcCCEEEE---Ee--EEEEEEEECCCCeEEEEe
Confidence            357899999   45  999999999999999864

---

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	62
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	1e-15
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	1e-13
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	4e-13
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	4e-13
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	5e-13
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	3e-12
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	3e-12
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	8e-12
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	8e-11
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	3e-10
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	9e-10
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	3e-09
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	4e-07

>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 = 61.7 bits (150), Expect = 1e-15
 Identities = 18/60 (30%), Positives = 34/60 (56%)

Query: 1  MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          ++++    L + ++  V +KL  N+ V G+LR +D  MNLVL +  E + D +   +G +
Sbjct: 4  LAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTI 63

>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 = 56.6 bits (137), Expect = 1e-13
 Identities = 17/52 (32%), Positives = 25/52 (48%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          L + +   V ++L   R   G L G+D  MNLVL +  E +    V  +G V
Sbjct: 8  LNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSV 59

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

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

 Score = 55.5 bits (134), Expect = 4e-13
 Identities = 17/52 (32%), Positives = 26/52 (50%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          L   ++  V +KL  +R   G+L+ FD  MNLVL++  E         +G V
Sbjct: 11 LGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTV 62

>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 = 55.6 bits (134), Expect = 4e-13
 Identities = 13/46 (28%), Positives = 23/46 (50%)

Query: 8  ELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNT 53
          ++ + +D ++   L   R   G  + FD  MNL+L +  E+RK   
Sbjct: 2  KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKP 47

>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 = 55.1 bits (133), Expect = 5e-13
 Identities = 13/52 (25%), Positives = 23/52 (44%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          + + +DK V + L       G L G+D  +N+VL +    +    V   G +
Sbjct: 7  IHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKI 58

>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 = 53.2 bits (128), Expect = 3e-12
 Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          L+  + K+V +KL  +  + GILR FD  +NL+L++  E    N     G +
Sbjct: 7  LQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYK-RGTM 57

>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 = 53.2 bits (128), Expect = 3e-12
 Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 9  LKKFMDKKVTLKLNAN-RNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          LK  ++ +V +KL  N     G L   D + NL L+E  E+    +   +G +
Sbjct: 1  LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEI 53

>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 = 52.0 bits (125), Expect = 8e-12
 Identities = 13/55 (23%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 7  PELKKFMDKKVTLKL-NANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
            +K  + K + +++      + G L G D +MNL L   +E + +  V ++G +
Sbjct: 8  QMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEI 62

>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 = 50.2 bits (120), Expect = 8e-11
 Identities = 13/44 (29%), Positives = 27/44 (61%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDN 52
          + K +  ++ + +  ++  +G+LRGFD ++N+VLD+  EY    
Sbjct: 10 IDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKA 53

>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 = 49.3 bits (118), Expect = 3e-10
 Identities = 10/45 (22%), Positives = 19/45 (42%)

Query: 8  ELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDN 52
          EL   + ++V + L+      G+L   D  +N+VL        + 
Sbjct: 4  ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEK 48

>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 = 47.0 bits (112), Expect = 9e-10
 Identities = 13/52 (25%), Positives = 20/52 (38%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          L K   + VT++L     V G + G D  MN  L       K+     +  +
Sbjct: 6  LMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETL 57

>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 = 45.9 bits (109), Expect = 3e-09
 Identities = 11/52 (21%), Positives = 17/52 (32%)

Query: 9  LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
          L +     VT + N      G L   +  MN  +       +D  V  +  V
Sbjct: 7  LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQV 58

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

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

 Score = 40.6 bits (95), Expect = 4e-07
 Identities = 10/46 (21%), Positives = 22/46 (47%), Gaps = 2/46 (4%)

Query: 9  LKKFM--DKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDN 52
          L + +  + +V +    N+ + G ++ FD   N+VL+   E   + 
Sbjct: 7  LTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEV 52

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	62
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.83
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.82
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.82
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.82
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.8
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.79
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.78
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.77
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.75
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.72
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.67
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.67
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.52
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	96.71
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	96.48
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	96.42
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	96.26
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	95.89
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	93.25

>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=99.83  E-value=7.7e-21  Score=105.86  Aligned_cols=61  Identities=30%  Similarity=0.542  Sum_probs=54.9

Q ss_pred             CCCCCchhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          1 MSKSHPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         1 m~~~~~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      |+..+...|.++++++|+|+++||++|+|+|.|||+|||++|++|+|+..+++.+.+|.++
T Consensus         4 ~~~~~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~~~v~   64 (76)
T d1th7a1           4 LAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIV   64 (76)
T ss_dssp             TCHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEE
T ss_pred             ccccHHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecCCcccCcceEE
Confidence            3444445699999999999999999999999999999999999999999998999999875

>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=99.82  E-value=5e-20  Score=101.99  Aligned_cols=60  Identities=30%  Similarity=0.557  Sum_probs=54.1

Q ss_pred             CCCCchh-HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          2 SKSHPPE-LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         2 ~~~~~~~-L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      .-..|.. |+++++++|.|+++||+.|.|+|.|||+|||++|+||+|+..++..+.+|.++
T Consensus         3 ~~~~Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~~~~~~~~~~~   63 (74)
T d1mgqa_           3 NVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVL   63 (74)
T ss_dssp             CTTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             cccCcHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCCCeEeEcceEE
Confidence            3344655 89999999999999999999999999999999999999999888889999874

>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=99.82  E-value=3.3e-20  Score=101.87  Aligned_cols=57  Identities=25%  Similarity=0.433  Sum_probs=52.6

Q ss_pred             Cchh-HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          5 HPPE-LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         5 ~~~~-L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      .|.. |+++++++|.|+++||++|+|+|.|||+|||++|+||.|+..++..+.+|.++
T Consensus         2 ~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~l~~~~   59 (71)
T d1h641_           2 RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIV   59 (71)
T ss_dssp             CHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             CchHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecCCcEeEcCcEE
Confidence            3555 89999999999999999999999999999999999999999888889999874

>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=99.82  E-value=2.8e-20  Score=102.54  Aligned_cols=56  Identities=32%  Similarity=0.566  Sum_probs=52.3

Q ss_pred             chh-HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          6 PPE-LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         6 ~~~-L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      |.. |+++++++|.|+++||++|+|+|.|||+|||++|+||+|+..++..+.+|.++
T Consensus         4 Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~   60 (72)
T d1i4k1_           4 PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVV   60 (72)
T ss_dssp             HHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSSSEEEEEEEEE
T ss_pred             hHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecCCeEeEcceEE
Confidence            444 89999999999999999999999999999999999999998888899999875

>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=99.80  E-value=1.8e-19  Score=100.30  Aligned_cols=57  Identities=25%  Similarity=0.552  Sum_probs=51.9

Q ss_pred             Cchh-HHhcCCCEEEEEECCC-eEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          5 HPPE-LKKFMDKKVTLKLNAN-RNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         5 ~~~~-L~~~l~k~V~V~l~~g-~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      .|.. |+++++++|+|++++| +.|+|+|.|||+|||++|+||+|+..+++.+.+|.++
T Consensus         5 ~P~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~   63 (75)
T d1ljoa_           5 LPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIV   63 (75)
T ss_dssp             CHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             ccHHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCCCcEeEcceEE
Confidence            4554 8999999999999965 8999999999999999999999999888899999874

>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=99.79  E-value=2e-19  Score=99.18  Aligned_cols=55  Identities=31%  Similarity=0.502  Sum_probs=49.6

Q ss_pred             chhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          6 PPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      .+.|+++++++|.|+++||++|+|+|.+||+|||++|++|+|+..+ +.+++|.++
T Consensus         4 ~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~~-~~~~~g~v~   58 (71)
T d1i8fa_           4 GATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDG-NVYKRGTMV   58 (71)
T ss_dssp             HHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEETT-EEEEEEEEE
T ss_pred             hHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEECC-CEEEcceEE
Confidence            3569999999999999999999999999999999999999999654 677888864

>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=99.78  E-value=2.3e-19  Score=100.76  Aligned_cols=54  Identities=28%  Similarity=0.459  Sum_probs=47.4

Q ss_pred             hHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecC----------CceeeeeEee
Q psy11512          8 ELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKD----------NTVHNIGMVE   61 (62)
Q Consensus         8 ~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~----------~~~~~lG~v~   61 (62)
                      .|.+|++++|+|.++|||.|.|+|.|||+||||+|++|+|+...          ...+.+|.++
T Consensus         2 ~L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~   65 (81)
T d1d3bb_           2 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVL   65 (81)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEE
T ss_pred             hhHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEE
Confidence            57899999999999999999999999999999999999998521          1357889875

>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=99.77  E-value=3.4e-19  Score=97.56  Aligned_cols=53  Identities=26%  Similarity=0.429  Sum_probs=48.3

Q ss_pred             HHhcCCCEEEEEEC-CCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          9 LKKFMDKKVTLKLN-ANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         9 L~~~l~k~V~V~l~-~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      |+++++++|.|+|+ +|++|+|+|.+||+|||++|++|+|...++..+++|.++
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~   54 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIF   54 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEE
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEecCCcccCcCeEE
Confidence            57899999999999 568999999999999999999999998888888888764

>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=99.75  E-value=4.8e-18  Score=93.57  Aligned_cols=56  Identities=21%  Similarity=0.157  Sum_probs=51.6

Q ss_pred             chh-HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          6 PPE-LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         6 ~~~-L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      |.. |+++.|++|+|+|+||++|+|+|.+||+|||++|+||++...++....+|.++
T Consensus         3 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~v~   59 (72)
T d1d3ba_           3 PIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVY   59 (72)
T ss_dssp             HHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEE
T ss_pred             chHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCCCcEeEcCeEE
Confidence            544 79999999999999999999999999999999999999998888888888764

>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=99.72  E-value=2.2e-18  Score=98.45  Aligned_cols=46  Identities=30%  Similarity=0.686  Sum_probs=42.5

Q ss_pred             Cchh-HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEec
Q psy11512          5 HPPE-LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRK   50 (62)
Q Consensus         5 ~~~~-L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~   50 (62)
                      .|.+ |.++++++|+|.++||++|.|+|.|||+||||+|+||.|+..
T Consensus         5 ~Pl~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~   51 (92)
T d2fwka1           5 LPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGF   51 (92)
T ss_dssp             CHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC
T ss_pred             ChHHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEe
Confidence            3555 899999999999999999999999999999999999999863

>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=99.67  E-value=6.7e-17  Score=92.83  Aligned_cols=45  Identities=24%  Similarity=0.440  Sum_probs=39.8

Q ss_pred             chh-HHhcC--CCEEEEEECCCeEEEEEEEEecCccceEecceEEEec
Q psy11512          6 PPE-LKKFM--DKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRK   50 (62)
Q Consensus         6 ~~~-L~~~l--~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~   50 (62)
                      |.. |.+++  +++|+|.+++|+.+.|+|.|||+||||+|+||+|+..
T Consensus         3 Pl~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~   50 (93)
T d1b34b_           3 PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWT   50 (93)
T ss_dssp             HHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC--
T ss_pred             cHHHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEE
Confidence            544 67777  8999999999999999999999999999999999863

>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=99.67  E-value=1.9e-16  Score=88.72  Aligned_cols=55  Identities=24%  Similarity=0.251  Sum_probs=50.9

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEecCCceeeeeEee
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMVE   61 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lG~v~   61 (62)
                      -+|+++.|++|.|+|++|.+|+|+|.++|.|||++|+||++...++...+++.+.
T Consensus         4 ~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~~~~~~~v~   58 (80)
T d1b34a_           4 RFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLS   58 (80)
T ss_dssp             HHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEE
T ss_pred             HHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCCEEEcccEE
Confidence            3689999999999999999999999999999999999999998888888888764

>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=99.52  E-value=1.4e-14  Score=87.34  Aligned_cols=43  Identities=23%  Similarity=0.429  Sum_probs=40.7

Q ss_pred             hhHHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEe
Q psy11512          7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYR   49 (62)
Q Consensus         7 ~~L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~   49 (62)
                      ++|++++|++|.|+|+||++|.|+|.+||+|||++|+||++..
T Consensus         3 ~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~   45 (127)
T d1m5q1_           3 AELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA   45 (127)
T ss_dssp             HHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETT
T ss_pred             hHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECC
Confidence            5799999999999999999999999999999999999999763

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

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

Probab=96.71  E-value=0.003  Score=30.74  Aligned_cols=32  Identities=31%  Similarity=0.618  Sum_probs=28.2

Q ss_pred             cCCCEEEEEECCCeEEEEEEEEecCccceEecc
Q psy11512         12 FMDKKVTLKLNANRNVTGILRGFDPFMNLVLDE   44 (62)
Q Consensus        12 ~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~   44 (62)
                      |++++|+|...+ +++.|+..|+|+.-.|+|+.
T Consensus         1 f~gk~V~v~~g~-~~i~G~a~gId~~G~Lll~t   32 (47)
T d1biaa2           1 FINRPVKLIIGD-KEIFGISRGIDKQGALLLEQ   32 (47)
T ss_dssp             TTTSEEEEEETT-EEEEEEEEEECTTSCEEEEE
T ss_pred             CCCCEEEEEECC-eEEEEEEeeECCCCcEEEEE
Confidence            789999997655 78999999999999999874

>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=96.48  E-value=0.0022  Score=33.82  Aligned_cols=29  Identities=24%  Similarity=0.398  Sum_probs=24.7

Q ss_pred             CCCEEEEEECCCeEEEEEEEEecCccceE
Q psy11512         13 MDKKVTLKLNANRNVTGILRGFDPFMNLV   41 (62)
Q Consensus        13 l~k~V~V~l~~g~~~~G~L~~~D~~mNlv   41 (62)
                      -..+|.|-|.+|-.+.|.+.+||+|.=|.
T Consensus        13 ~~~~VtifL~nGvkl~G~I~~fD~ftvLL   41 (66)
T d1u1sa1          13 ERVPVSIYLVNGIKLQGQIESFDQFVILL   41 (66)
T ss_dssp             TTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             cCCcEEEEEEcCcEEEEEEEEEcceEEEE
Confidence            35678999999999999999999996543

>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=96.42  E-value=0.0045  Score=31.97  Aligned_cols=33  Identities=15%  Similarity=0.350  Sum_probs=27.9

Q ss_pred             CCEEEEEECCCeEEEEEEEEecCccceEecceE
Q psy11512         14 DKKVTLKLNANRNVTGILRGFDPFMNLVLDEGV   46 (62)
Q Consensus        14 ~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~   46 (62)
                      ..+|.|-|.+|-.+.|.+.+||+|.=+.-.+..
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            567999999999999999999999766655544

>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=96.26  E-value=0.0028  Score=33.22  Aligned_cols=32  Identities=16%  Similarity=0.206  Sum_probs=27.5

Q ss_pred             chhHHhcCCCEEEEEEC---CC-eEEEEEEEEecCc
Q psy11512          6 PPELKKFMDKKVTLKLN---AN-RNVTGILRGFDPF   37 (62)
Q Consensus         6 ~~~L~~~l~k~V~V~l~---~g-~~~~G~L~~~D~~   37 (62)
                      +.++.+|+|+.|.|+|+   +| +.+.|+|.++|+-
T Consensus         6 ~~~f~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~   41 (74)
T d1ib8a1           6 KDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED   41 (74)
T ss_dssp             HHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT
T ss_pred             HHHHHHhCCCEEEEEEecccCCceEEEEEEEeecCC
Confidence            56699999999999984   34 8999999999965

>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=95.89  E-value=0.014  Score=31.60  Aligned_cols=38  Identities=21%  Similarity=0.308  Sum_probs=33.7

Q ss_pred             cCCCEEEEEECCCeEEEEEEEEec-CccceEecceEEEe
Q psy11512         12 FMDKKVTLKLNANRNVTGILRGFD-PFMNLVLDEGVEYR   49 (62)
Q Consensus        12 ~l~k~V~V~l~~g~~~~G~L~~~D-~~mNlvL~~~~e~~   49 (62)
                      |+|++|.+.-+.+-.|+|+|..+| +---+.|.|+..+-
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfG   40 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFG   40 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECC
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEee
Confidence            799999999999999999999999 44668899988774

>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=93.25  E-value=0.06  Score=27.72  Aligned_cols=40  Identities=28%  Similarity=0.500  Sum_probs=31.6

Q ss_pred             HHhcCCCEEEEEECCCeEEEEEEEEecCccceEecceEEEe
Q psy11512          9 LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYR   49 (62)
Q Consensus         9 L~~~l~k~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~   49 (62)
                      |.++.|++|-|.+.....|.|+|.-||+-. +.|.|++.+.
T Consensus         7 L~~WKg~kvAv~vgsehSFtGiledFDeEv-iLL~dV~D~~   46 (66)
T d1ycya1           7 LKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVI   46 (66)
T ss_dssp             HHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETT
T ss_pred             HHHhCCcEEEEEecCcceeEEEhhhcCcce-EeehhhHHHh
Confidence            889999999999999999999999999754 6778888774