Psyllid ID: psy3154

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-
Protein Sequence
MEDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNRTPAL
Secondary Structure (PSIPRED)
ccccccccccccccHHHHHHHcccEEEEEEcccEEEEEEEEEEcccccEEEccEEEEEEEEEccccHHHHHHccccEEccEEEEEccEEEEEccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccHHHHHHccccEEEEEEEccccEEEEEEEEEcccccEEEEEEEEEEEEEEcccccccEEEccEEEEEcEEEEEccEEEEEccccccccc
Coil and Loop (DISEMBL)
medeqiptisvkeplDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKrsipmlfvrgdgvilvsppnrtpal
Flexible Loop (DISEMBL)
medeqiptisvkepldlirlsldervhvkmrnervlrgklhayDQHLNMVLGDVEETVTTVEIDEETYEEIYKttkrsipmlfvrgdgvilvsppnrtpal
Low Complexity Region (SEG)
MEDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGdveetvttveideetyeeiykttkRSIPMLFVRGDGVILVSPPNRTPAL
Disordered region (IsUnstruct)
*************PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV*********
Disordered Region (DISOPRED)
****************LIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTV*************TKRSIPMLFVRGDGVILVS*PN*****
Disordered Region (DISEMBL)
MEDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNRTPAL
Disordered Region (DISPRO)
**********VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPN*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNRTPAL
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	101	2.2.26 [Sep-21-2011]
P62311	102	U6 snRNA-associated Sm-li	yes	N/A	0.940	0.931	0.810	6e-40
P62310	102	U6 snRNA-associated Sm-li	yes	N/A	0.940	0.931	0.810	6e-40
Q32PE9	102	U6 snRNA-associated Sm-li	yes	N/A	0.940	0.931	0.810	6e-40
Q1ZXK3	97	Probable U6 snRNA-associa	yes	N/A	0.881	0.917	0.752	4e-32
Q9Y7M4	93	Probable U6 snRNA-associa	yes	N/A	0.851	0.924	0.593	3e-23
P57743	89	U6 snRNA-associated Sm-li	yes	N/A	0.762	0.865	0.457	1e-13
O26745	81	Putative snRNP Sm-like pr	yes	N/A	0.801	1.0	0.329	2e-06
Q54NC5	112	Probable small nuclear ri	no	N/A	0.782	0.705	0.365	1e-05
Q9YEQ5	77	Putative snRNP Sm-like pr	yes	N/A	0.584	0.766	0.356	1e-05
Q0W8R9	72	Putative snRNP Sm-like pr	yes	N/A	0.693	0.972	0.325	1e-05

>sp|P62311|LSM3_MOUSE U6 snRNA-associated Sm-like protein LSm3 OS=Mus musculus GN=Lsm3 PE=3 SV=2

 Score =  162 bits (410), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 77/95 (81%), Positives = 90/95 (94%)

Query: 3   DEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVE 62
           D+Q  T +V+EPLDLIRLSLDER++VKMRN+R LRG+LHAYDQHLNM+LGDVEETVTT+E
Sbjct: 6   DQQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIE 65

Query: 63  IDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNR 97
           IDEETYEEIYK+TKR+IPMLFVRGDGV+LV+PP R
Sbjct: 66  IDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 100

Binds specifically to the 3'-terminal U-tract of U6 snRNA.
Mus musculus (taxid: 10090)

>sp|P62310|LSM3_HUMAN U6 snRNA-associated Sm-like protein LSm3 OS=Homo sapiens GN=LSM3 PE=1 SV=2

 Score =  162 bits (410), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 77/95 (81%), Positives = 90/95 (94%)

Query: 3   DEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVE 62
           D+Q  T +V+EPLDLIRLSLDER++VKMRN+R LRG+LHAYDQHLNM+LGDVEETVTT+E
Sbjct: 6   DQQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIE 65

Query: 63  IDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNR 97
           IDEETYEEIYK+TKR+IPMLFVRGDGV+LV+PP R
Sbjct: 66  IDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 100

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

Homo sapiens (taxid: 9606)

>sp|Q32PE9|LSM3_BOVIN U6 snRNA-associated Sm-like protein LSm3 OS=Bos taurus GN=LSM3 PE=3 SV=3

 Score =  162 bits (410), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 77/95 (81%), Positives = 90/95 (94%)

Query: 3   DEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVE 62
           D+Q  T +V+EPLDLIRLSLDER++VKMRN+R LRG+LHAYDQHLNM+LGDVEETVTT+E
Sbjct: 6   DQQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIE 65

Query: 63  IDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNR 97
           IDEETYEEIYK+TKR+IPMLFVRGDGV+LV+PP R
Sbjct: 66  IDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 100

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

Bos taurus (taxid: 9913)

>sp|Q1ZXK3|LSM3_DICDI Probable U6 snRNA-associated Sm-like protein LSm3 OS=Dictyostelium discoideum GN=lsm3 PE=3 SV=1

 Score =  136 bits (342), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 67/89 (75%), Positives = 76/89 (85%)

Query: 10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYE 69
          +V+EPLDLIRLSLDER+ VKMR +R LRGKLHAYDQHLNM+L DVEET+  VE DEET E
Sbjct: 8  TVEEPLDLIRLSLDERIFVKMRQDRELRGKLHAYDQHLNMILSDVEETIKVVEKDEETDE 67

Query: 70 EIYKTTKRSIPMLFVRGDGVILVSPPNRT 98
          EI +  KR+I MLFVRGDGVIL+SPP RT
Sbjct: 68 EIIRNIKRNIKMLFVRGDGVILISPPLRT 96

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

Dictyostelium discoideum (taxid: 44689)

>sp|Q9Y7M4|LSM3_SCHPO Probable U6 snRNA-associated Sm-like protein LSm3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=lsm3 PE=1 SV=2

 Score =  106 bits (265), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 51/86 (59%), Positives = 66/86 (76%)

Query: 10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYE 69
          +V EPLDL+RLSLDE V+VK+R +R L G+LHAYD+HLNMVLGD EE VT  + +E   +
Sbjct: 6  AVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKD 65

Query: 70 EIYKTTKRSIPMLFVRGDGVILVSPP 95
          +  KT ++   MLFVRGD VIL++PP
Sbjct: 66 KALKTIRKHYEMLFVRGDSVILIAPP 91

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

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

>sp|P57743|LSM3_YEAST U6 snRNA-associated Sm-like protein LSm3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=LSM3 PE=1 SV=1

 Score = 75.1 bits (183), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 38/83 (45%), Positives = 55/83 (66%), Gaps = 6/83 (7%)

Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYK 73
          PLDL++L+LDERV++K+R  R L G L A+D H N+VL D  ET+  +  +EE  E    
Sbjct: 4  PLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLN-NEELSE---- 58

Query: 74 TTKRSIPMLFVRGDGVILVSPPN 96
           ++R   M+F+RGD V L+S P+
Sbjct: 59 -SERRCEMVFIRGDTVTLISTPS 80

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM3 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM3, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM3 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

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

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

 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 51/94 (54%), Gaps = 13/94 (13%)

Query: 1  MEDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTT 60
          M D     ++V+ PLD +  SL+  V +K++ +R  RG L ++D H+N+VL D EE    
Sbjct: 1  MIDVSSQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEE---- 56

Query: 61 VEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP 94
          +E  E T         R +  + +RGD ++ +SP
Sbjct: 57 LEDGEVT---------RRLGTVLIRGDNIVYISP 81

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

>sp|Q54NC5|SMD2_DICDI Probable small nuclear ribonucleoprotein Sm D2 OS=Dictyostelium discoideum GN=snrpd2 PE=3 SV=1

 Score = 48.9 bits (115), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 49/82 (59%), Gaps = 3/82 (3%)

Query: 14  PLDLIRLSLDE--RVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEI 71
           PL ++  S++   +V + +RN + L G++ A+D+H NMVL +V+E  T V    +  ++ 
Sbjct: 19  PLSILMDSVNNNTQVLINVRNNKKLLGRVRAFDRHCNMVLENVKEIWTEVPKTAKGKKKA 78

Query: 72  YKTTK-RSIPMLFVRGDGVILV 92
               K R I  +F+RGD VILV
Sbjct: 79  KPINKDRFISKMFLRGDSVILV 100

Required for pre-mRNA splicing. Required for snRNP biogenesis.

Dictyostelium discoideum (taxid: 44689)

>sp|Q9YEQ5|RUXX_AERPE Putative snRNP Sm-like protein OS=Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) GN=APE_0525a PE=3 SV=1

 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 14/73 (19%)

Query: 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPM 81
          +D  V VK+++   ++G L  YDQHLN++LGD               EEI +T+ R + +
Sbjct: 17 VDTPVLVKLKSGLRIKGVLKTYDQHLNIILGDA--------------EEIGETSIRRLGL 62

Query: 82 LFVRGDGVILVSP 94
            VRGD V++++P
Sbjct: 63 TLVRGDSVVVITP 75

Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) (taxid: 272557)

>sp|Q0W8R9|RUXX_UNCMA Putative snRNP Sm-like protein OS=Uncultured methanogenic archaeon RC-I GN=UNCMA_29510 PE=3 SV=1

 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 42/83 (50%), Gaps = 13/83 (15%)

Query: 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEI 71
          + PLD++  +L+  V V+++  R  RG+L  YD H+N+VL + EE               
Sbjct: 3  QRPLDVLNEALNSPVIVRLKGGREFRGELQGYDMHMNLVLDNAEELKEN----------- 51

Query: 72 YKTTKRSIPMLFVRGDGVILVSP 94
               R +  + VRGD V+ VSP
Sbjct: 52 --EASRKLGTIIVRGDTVVYVSP 72

Uncultured methanogenic archaeon RC-I (taxid: 351160)

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	101
110671432	101	putative U6 snRNA-associated Sm-like pro	1.0	1.0	1.0	1e-50
156544005	103	PREDICTED: U6 snRNA-associated Sm-like p	0.970	0.951	0.826	7e-41
242009034	102	snrnp sm protein, putative [Pediculus hu	0.940	0.931	0.873	8e-41
157123813	101	snrnp sm protein [Aedes aegypti] gi|1088	0.950	0.950	0.854	8e-41
170029969	101	snrnp sm protein [Culex quinquefasciatus	0.950	0.950	0.843	2e-40
442761385	148	Putative u6 small nuclear rna associated	0.950	0.648	0.822	4e-40
383857174	103	PREDICTED: U6 snRNA-associated Sm-like p	0.970	0.951	0.828	4e-40
110755468	103	PREDICTED: u6 snRNA-associated Sm-like p	0.970	0.951	0.828	4e-40
241171152	102	snrnp sm protein, putative [Ixodes scapu	0.930	0.921	0.840	5e-40
347966098	101	AGAP013519-PA [Anopheles gambiae str. PE	0.950	0.950	0.843	8e-40

>gi|110671432|gb|ABG81967.1| putative U6 snRNA-associated Sm-like protein LSm3 [Diaphorina citri]

 Score =  202 bits (515), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 101/101 (100%), Positives = 101/101 (100%)

Query: 1   MEDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTT 60
           MEDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTT
Sbjct: 1   MEDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTT 60

Query: 61  VEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNRTPAL 101
           VEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNRTPAL
Sbjct: 61  VEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNRTPAL 101

Source: Diaphorina citri

Species: Diaphorina citri

Genus: Diaphorina

Family: Psyllidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156544005|ref|XP_001607844.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm3-like [Nasonia vitripennis]

 Score =  171 bits (432), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 81/98 (82%), Positives = 92/98 (93%)

Query: 4   EQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEI 63
           EQ P I+VKEPLDLIRLSLDER++VKMRNER LRG+LHAYDQHLNMVLG+VEETVTT+EI
Sbjct: 6   EQAPAINVKEPLDLIRLSLDERIYVKMRNERELRGRLHAYDQHLNMVLGEVEETVTTIEI 65

Query: 64  DEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNRTPAL 101
           DEETYEE+Y+TTKR+IPMLFVRGDGVILVSPP+   A+
Sbjct: 66  DEETYEEVYRTTKRTIPMLFVRGDGVILVSPPSMRAAI 103

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242009034|ref|XP_002425298.1| snrnp sm protein, putative [Pediculus humanus corporis] gi|212509063|gb|EEB12560.1| snrnp sm protein, putative [Pediculus humanus corporis]

 Score =  170 bits (431), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 83/95 (87%), Positives = 89/95 (93%)

Query: 4   EQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEI 63
           E IP I+VKEPLDLIRLSLDER++VKMRNER LRG+LHAYDQHLNMVLGD EETVTTVEI
Sbjct: 6   ENIPAITVKEPLDLIRLSLDERIYVKMRNERELRGRLHAYDQHLNMVLGDAEETVTTVEI 65

Query: 64  DEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNRT 98
           DEETYEE+YKTTKR+IPMLFVRGDGVILVSPP R 
Sbjct: 66  DEETYEEVYKTTKRTIPMLFVRGDGVILVSPPLRA 100

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157123813|ref|XP_001653925.1| snrnp sm protein [Aedes aegypti] gi|108874209|gb|EAT38434.1| AAEL009671-PA [Aedes aegypti]

 Score =  170 bits (431), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 82/96 (85%), Positives = 91/96 (94%)

Query: 2  EDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTV 61
          E+EQ+P I VKEPLDLIRLSLDE+++VKMRNER LRG+LHA+DQHLNMVLGD EETVTTV
Sbjct: 3  EEEQLPIIPVKEPLDLIRLSLDEKIYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTV 62

Query: 62 EIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNR 97
          EIDEETYEE+YKTTKR+IPMLFVRGDGVILVSPP R
Sbjct: 63 EIDEETYEEVYKTTKRTIPMLFVRGDGVILVSPPMR 98

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170029969|ref|XP_001842863.1| snrnp sm protein [Culex quinquefasciatus] gi|167865323|gb|EDS28706.1| snrnp sm protein [Culex quinquefasciatus]

 Score =  169 bits (429), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 81/96 (84%), Positives = 91/96 (94%)

Query: 2  EDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTV 61
          E+EQ+P I VKEPLDLIRLSLDE+++VKMRNER LRG+LHA+DQHLNMVLGD EETVTTV
Sbjct: 3  EEEQMPIIPVKEPLDLIRLSLDEKIYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTV 62

Query: 62 EIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNR 97
          EIDEETYEE+YKT+KR+IPMLFVRGDGVILVSPP R
Sbjct: 63 EIDEETYEEVYKTSKRTIPMLFVRGDGVILVSPPMR 98

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|442761385|gb|JAA72851.1| Putative u6 small nuclear rna associated, partial [Ixodes ricinus]

 Score =  168 bits (426), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 79/96 (82%), Positives = 91/96 (94%)

Query: 2   EDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTV 61
           + EQ PT +V+EPLDL+RLSLDE+++VKMRNER LRG+LHAYDQHLNM+LGDVEETVT+V
Sbjct: 50  DGEQAPTTAVEEPLDLVRLSLDEKIYVKMRNERELRGRLHAYDQHLNMILGDVEETVTSV 109

Query: 62  EIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNR 97
           EIDEETYEE+YK+TKRSIPMLFVRGDGVILVSPP R
Sbjct: 110 EIDEETYEEVYKSTKRSIPMLFVRGDGVILVSPPVR 145

Source: Ixodes ricinus

Species: Ixodes ricinus

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383857174|ref|XP_003704080.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm3-like [Megachile rotundata]

 Score =  168 bits (426), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 82/99 (82%), Positives = 92/99 (92%), Gaps = 1/99 (1%)

Query: 2   EDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTV 61
           E EQ+P I+VKEPLDLIRLSLDER++VKMRNER LRG+LHAYDQHLNMVLG+ EETVTTV
Sbjct: 4   EAEQVPAINVKEPLDLIRLSLDERIYVKMRNERELRGRLHAYDQHLNMVLGEAEETVTTV 63

Query: 62  EIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPN-RTP 99
           EIDEETYEE+Y+TTKR+I MLFVRGDGVILVSPP+ R P
Sbjct: 64  EIDEETYEEVYRTTKRNISMLFVRGDGVILVSPPSMRAP 102

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|110755468|ref|XP_001121255.1| PREDICTED: u6 snRNA-associated Sm-like protein LSm3-like [Apis mellifera] gi|340729056|ref|XP_003402825.1| PREDICTED: u6 snRNA-associated Sm-like protein LSm3-like isoform 1 [Bombus terrestris] gi|340729058|ref|XP_003402826.1| PREDICTED: u6 snRNA-associated Sm-like protein LSm3-like isoform 2 [Bombus terrestris] gi|350401475|ref|XP_003486164.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm3-like [Bombus impatiens] gi|380013750|ref|XP_003690912.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm3-like [Apis florea]

 Score =  168 bits (425), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 82/99 (82%), Positives = 92/99 (92%), Gaps = 1/99 (1%)

Query: 2   EDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTV 61
           E EQ+P I+VKEPLDLIRLSLDER++VKMRNER LRG+LHAYDQHLNMVLG+ EETVTTV
Sbjct: 4   ETEQVPAINVKEPLDLIRLSLDERIYVKMRNERELRGRLHAYDQHLNMVLGEAEETVTTV 63

Query: 62  EIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPN-RTP 99
           EIDEETYEE+Y+TTKR+I MLFVRGDGVILVSPP+ R P
Sbjct: 64  EIDEETYEEVYRTTKRNISMLFVRGDGVILVSPPSMRAP 102

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|241171152|ref|XP_002410602.1| snrnp sm protein, putative [Ixodes scapularis] gi|215494871|gb|EEC04512.1| snrnp sm protein, putative [Ixodes scapularis]

 Score =  168 bits (425), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 79/94 (84%), Positives = 90/94 (95%)

Query: 4  EQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEI 63
          EQ PT +V+EPLDL+RLSLDE+++VKMRNER LRG+LHAYDQHLNM+LGDVEETVT+VEI
Sbjct: 6  EQAPTTAVEEPLDLVRLSLDEKIYVKMRNERELRGRLHAYDQHLNMILGDVEETVTSVEI 65

Query: 64 DEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNR 97
          DEETYEE+YK+TKRSIPMLFVRGDGVILVSPP R
Sbjct: 66 DEETYEEVYKSTKRSIPMLFVRGDGVILVSPPVR 99

Source: Ixodes scapularis

Species: Ixodes scapularis

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347966098|ref|XP_003435864.1| AGAP013519-PA [Anopheles gambiae str. PEST] gi|333470212|gb|EGK97549.1| AGAP013519-PA [Anopheles gambiae str. PEST]

 Score =  167 bits (423), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 81/96 (84%), Positives = 90/96 (93%)

Query: 2  EDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTV 61
          E+EQ+P I VKEPLDLIRLSLDE+++VKMR ER LRG+LHA+DQHLNMVLGD EETVTTV
Sbjct: 3  EEEQMPIIPVKEPLDLIRLSLDEKIYVKMRYERELRGRLHAFDQHLNMVLGDAEETVTTV 62

Query: 62 EIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNR 97
          EIDEETYEE+YKTTKR+IPMLFVRGDGVILVSPP R
Sbjct: 63 EIDEETYEEVYKTTKRTIPMLFVRGDGVILVSPPMR 98

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	101
FB|FBgn0051184	103	LSm3 [Drosophila melanogaster	0.950	0.932	0.602	4.2e-24
UNIPROTKB|Q32PE9	102	LSM3 "U6 snRNA-associated Sm-l	0.940	0.931	0.578	5.3e-24
UNIPROTKB|P62310	102	LSM3 "U6 snRNA-associated Sm-l	0.940	0.931	0.578	5.3e-24
UNIPROTKB|F2Z5S4	102	LSM3 "Uncharacterized protein"	0.940	0.931	0.578	5.3e-24
MGI|MGI:1914928	102	Lsm3 "LSM3 homolog, U6 small n	0.940	0.931	0.578	5.3e-24
RGD|1305971	102	Lsm3 "LSM3 homolog, U6 small n	0.940	0.931	0.578	5.3e-24
UNIPROTKB|F1P280	96	LSM3 "Uncharacterized protein"	0.930	0.979	0.574	2.3e-23
TAIR|locus:2036257	98	LSM3B "AT1G76860" [Arabidopsis	0.900	0.928	0.571	7e-22
TAIR|locus:2014922	97	LSM3A "AT1G21190" [Arabidopsis	0.881	0.917	0.550	1.5e-21
DICTYBASE|DDB_G0277107	97	lsm3 "putative U6 small nuclea	0.881	0.917	0.584	3.9e-21

FB|FBgn0051184 LSm3 [Drosophila melanogaster (taxid:7227)]

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 59/98 (60%), Positives = 66/98 (67%)

Query:     2 EDEQIPTI--SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGXXXXXXX 59
             E EQ+  +   VKEPLDLIRLSLDE+V+VKMRNER LRG+LHA+DQHLNMVLG       
Sbjct:     4 ETEQLSQVILPVKEPLDLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVT 63

Query:    60 XXXXXXXXXXXXXXXXXRSIPMLFVRGDGVILVSPPNR 97
                              R+IPMLFVRGDGVILVSPP R
Sbjct:    64 TVEIDEETYEEVYKTAKRTIPMLFVRGDGVILVSPPMR 101

GO:0005688 "U6 snRNP" evidence=ISS

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

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

GO:0003729 "mRNA binding" evidence=ISS

GO:0033962 "cytoplasmic mRNA processing body assembly" evidence=IMP

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

GO:0071011 "precatalytic spliceosome" evidence=IDA

UNIPROTKB|Q32PE9 LSM3 "U6 snRNA-associated Sm-like protein LSm3" [Bos taurus (taxid:9913)]

 Score = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 55/95 (57%), Positives = 66/95 (69%)

Query:     3 DEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGXXXXXXXXXX 62
             D+Q  T +V+EPLDLIRLSLDER++VKMRN+R LRG+LHAYDQHLNM+LG          
Sbjct:     6 DQQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIE 65

Query:    63 XXXXXXXXXXXXXXRSIPMLFVRGDGVILVSPPNR 97
                           R+IPMLFVRGDGV+LV+PP R
Sbjct:    66 IDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 100

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

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|P62310 LSM3 "U6 snRNA-associated Sm-like protein LSm3" [Homo sapiens (taxid:9606)]

 Score = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 55/95 (57%), Positives = 66/95 (69%)

Query:     3 DEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGXXXXXXXXXX 62
             D+Q  T +V+EPLDLIRLSLDER++VKMRN+R LRG+LHAYDQHLNM+LG          
Sbjct:     6 DQQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIE 65

Query:    63 XXXXXXXXXXXXXXRSIPMLFVRGDGVILVSPPNR 97
                           R+IPMLFVRGDGV+LV+PP R
Sbjct:    66 IDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 100

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=TAS

GO:0006397 "mRNA processing" evidence=TAS

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

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

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

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

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

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|F2Z5S4 LSM3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 55/95 (57%), Positives = 66/95 (69%)

Query:     3 DEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGXXXXXXXXXX 62
             D+Q  T +V+EPLDLIRLSLDER++VKMRN+R LRG+LHAYDQHLNM+LG          
Sbjct:     6 DQQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIE 65

Query:    63 XXXXXXXXXXXXXXRSIPMLFVRGDGVILVSPPNR 97
                           R+IPMLFVRGDGV+LV+PP R
Sbjct:    66 IDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 100

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

MGI|MGI:1914928 Lsm3 "LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 55/95 (57%), Positives = 66/95 (69%)

Query:     3 DEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGXXXXXXXXXX 62
             D+Q  T +V+EPLDLIRLSLDER++VKMRN+R LRG+LHAYDQHLNM+LG          
Sbjct:     6 DQQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIE 65

Query:    63 XXXXXXXXXXXXXXRSIPMLFVRGDGVILVSPPNR 97
                           R+IPMLFVRGDGV+LV+PP R
Sbjct:    66 IDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 100

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0030629 "U6 snRNA 3'-end binding" evidence=ISO

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

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

RGD|1305971 Lsm3 "LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]

 Score = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 55/95 (57%), Positives = 66/95 (69%)

Query:     3 DEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGXXXXXXXXXX 62
             D+Q  T +V+EPLDLIRLSLDER++VKMRN+R LRG+LHAYDQHLNM+LG          
Sbjct:     6 DQQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIE 65

Query:    63 XXXXXXXXXXXXXXRSIPMLFVRGDGVILVSPPNR 97
                           R+IPMLFVRGDGV+LV+PP R
Sbjct:    66 IDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 100

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

UNIPROTKB|F1P280 LSM3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 269 (99.8 bits), Expect = 2.3e-23, P = 2.3e-23
 Identities = 54/94 (57%), Positives = 65/94 (69%)

Query:     4 EQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGXXXXXXXXXXX 63
             +Q  T +V+EPLDLIRLSLDER++VKMRN+R LRG+LHAYDQHLNM+LG           
Sbjct:     1 QQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIEI 60

Query:    64 XXXXXXXXXXXXXRSIPMLFVRGDGVILVSPPNR 97
                          R+IPMLFVRGDGV+LV+PP R
Sbjct:    61 DEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 94

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

TAIR|locus:2036257 LSM3B "AT1G76860" [Arabidopsis thaliana (taxid:3702)]

 Score = 255 (94.8 bits), Expect = 7.0e-22, P = 7.0e-22
 Identities = 52/91 (57%), Positives = 62/91 (68%)

Query:    10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGXXXXXXXXXXXXXXXXX 69
             +V+EPLDLIRLSLDER++VK+R++R LRGKLHA+DQHLNM+LG                 
Sbjct:     8 TVREPLDLIRLSLDERIYVKLRSDRELRGKLHAFDQHLNMILGDVEETITTVEIDDETYE 67

Query:    70 XXXXXXXRSIPMLFVRGDGVILVSPPNRTPA 100
                    R+I  LFVRGDGVILVSPP RT A
Sbjct:    68 EIVRTTKRTIEFLFVRGDGVILVSPPLRTAA 98

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2014922 LSM3A "AT1G21190" [Arabidopsis thaliana (taxid:3702)]

 Score = 252 (93.8 bits), Expect = 1.5e-21, P = 1.5e-21
 Identities = 49/89 (55%), Positives = 62/89 (69%)

Query:    10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGXXXXXXXXXXXXXXXXX 69
             +V+EPLDLIRLS++ER++VK+R++R LRGKLHA+DQHLNM+LG                 
Sbjct:     8 TVREPLDLIRLSIEERIYVKLRSDRELRGKLHAFDQHLNMILGDVEEVITTIEIDDETYE 67

Query:    70 XXXXXXXRSIPMLFVRGDGVILVSPPNRT 98
                    R++P LFVRGDGVILVSPP RT
Sbjct:    68 EIVRTTKRTVPFLFVRGDGVILVSPPLRT 96

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0008150 "biological_process" evidence=ND

DICTYBASE|DDB_G0277107 lsm3 "putative U6 small nuclear ribonucleoparticle-associated protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 248 (92.4 bits), Expect = 3.9e-21, P = 3.9e-21
 Identities = 52/89 (58%), Positives = 59/89 (66%)

Query:    10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGXXXXXXXXXXXXXXXXX 69
             +V+EPLDLIRLSLDER+ VKMR +R LRGKLHAYDQHLNM+L                  
Sbjct:     8 TVEEPLDLIRLSLDERIFVKMRQDRELRGKLHAYDQHLNMILSDVEETIKVVEKDEETDE 67

Query:    70 XXXXXXXRSIPMLFVRGDGVILVSPPNRT 98
                    R+I MLFVRGDGVIL+SPP RT
Sbjct:    68 EIIRNIKRNIKMLFVRGDGVILISPPLRT 96

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

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

GO:0006402 "mRNA catabolic process" evidence=ISS

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

GO:0005730 "nucleolus" evidence=ISS

GO:0005688 "U6 snRNP" evidence=ISS

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

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

---

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)
Q8U0P4	RUXX_PYRFU	No assigned EC number	0.3703	0.6732	0.8947	yes	N/A
P57743	LSM3_YEAST	No assigned EC number	0.4578	0.7623	0.8651	yes	N/A
Q8TL47	RUXX_METAC	No assigned EC number	0.3456	0.6732	0.9444	yes	N/A
Q465S1	RUXX_METBF	No assigned EC number	0.3456	0.6732	0.9444	yes	N/A
C6A1T2	RUXX_THESM	No assigned EC number	0.3827	0.6732	0.8947	yes	N/A
O26745	RUXX_METTH	No assigned EC number	0.3297	0.8019	1.0	yes	N/A
Q9Y7M4	LSM3_SCHPO	No assigned EC number	0.5930	0.8514	0.9247	yes	N/A
Q32PE9	LSM3_BOVIN	No assigned EC number	0.8105	0.9405	0.9313	yes	N/A
Q12U30	RUXX_METBU	No assigned EC number	0.3580	0.6732	0.9444	yes	N/A
B6YUU5	RUXX_THEON	No assigned EC number	0.3703	0.6732	0.8717	yes	N/A
Q9V0Y8	RUXX_PYRAB	No assigned EC number	0.3580	0.6732	0.9066	yes	N/A
O29386	RUXX_ARCFU	No assigned EC number	0.3580	0.6732	0.8831	yes	N/A
Q0W8R9	RUXX_UNCMA	No assigned EC number	0.3253	0.6930	0.9722	yes	N/A
Q5JIE0	RUXX_PYRKO	No assigned EC number	0.3827	0.6732	0.8947	yes	N/A
P62310	LSM3_HUMAN	No assigned EC number	0.8105	0.9405	0.9313	yes	N/A
P62311	LSM3_MOUSE	No assigned EC number	0.8105	0.9405	0.9313	yes	N/A
O74016	RUXX_PYRHO	No assigned EC number	0.3703	0.6732	0.9066	yes	N/A
Q1ZXK3	LSM3_DICDI	No assigned EC number	0.7528	0.8811	0.9175	yes	N/A
Q8PZZ9	RUXX_METMA	No assigned EC number	0.3456	0.6732	0.9444	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	101
cd01730	82	cd01730, LSm3, Like-Sm protein 3	1e-52
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	6e-18
smart00651	67	smart00651, Sm, snRNP Sm proteins	2e-16
pfam01423	66	pfam01423, LSM, LSM domain	5e-16
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	3e-15
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	3e-12
cd01720	89	cd01720, Sm_D2, Sm protein D2	2e-11
cd00600	63	cd00600, Sm_like, Sm and related proteins	4e-11
cd01717	80	cd01717, Sm_B, Sm protein B	4e-08
cd01729	89	cd01729, LSm7, Like-Sm protein 7	3e-07
cd06168	73	cd06168, LSMD1, LSM domain containing 1	2e-05
cd01719	70	cd01719, Sm_G, Sm protein G	5e-05
cd01726	68	cd01726, LSm6, Like-Sm protein 6	5e-05
cd01739	63	cd01739, LSm11_M, Like-Sm protein 11, middle domai	5e-05
cd01732	76	cd01732, LSm5, Like-Sm protein 5	7e-05
cd01728	74	cd01728, LSm1, Like-Sm protein 1	3e-04
cd01725	89	cd01725, LSm2, Like-Sm protein 2	0.004

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

 Score =  158 bits (403), Expect = 1e-52
 Identities = 73/82 (89%), Positives = 80/82 (97%)

Query: 13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIY 72
          EPLDLIRLSLDERV+VK+R +R LRG+LHAYDQHLNM+LGDVEET+TTVEIDEETYEEIY
Sbjct: 1  EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIY 60

Query: 73 KTTKRSIPMLFVRGDGVILVSP 94
          KTTKR+IPMLFVRGDGVILVSP
Sbjct: 61 KTTKRNIPMLFVRGDGVILVSP 82

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|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1

 Score = 70.7 bits (174), Expect = 6e-18
 Identities = 30/81 (37%), Positives = 46/81 (56%), Gaps = 13/81 (16%)

Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYK 73
          PLD++  SL++ V VK++  + +RG L  +DQHLN+VL + E      EI E        
Sbjct: 2  PLDVLNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAE------EIIEG------- 48

Query: 74 TTKRSIPMLFVRGDGVILVSP 94
           + R +  + VRGD V+ +SP
Sbjct: 49 ESVRKLGTVLVRGDNVVFISP 69

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|197820 smart00651, Sm, snRNP Sm proteins

 Score = 66.7 bits (164), Expect = 2e-16
 Identities = 25/79 (31%), Positives = 43/79 (54%), Gaps = 12/79 (15%)

Query: 16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTT 75
            ++  + +RV V+++N R  RG L  +DQ +N+VL DVEETV   E             
Sbjct: 1  KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGE------------K 48

Query: 76 KRSIPMLFVRGDGVILVSP 94
          KR + ++F+RG+ ++ +  
Sbjct: 49 KRKLGLVFIRGNNIVYIIL 67

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

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

 Score = 66.0 bits (162), Expect = 5e-16
 Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 13/79 (16%)

Query: 16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTT 75
            ++  L +RV V+++N R LRG L  +DQ +N+VL DVEET             I    
Sbjct: 1  KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEET-------------IKDGK 47

Query: 76 KRSIPMLFVRGDGVILVSP 94
             + ++ +RG+ ++L+SP
Sbjct: 48 VNKLGLVLIRGNNIVLISP 66

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

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

 Score = 64.2 bits (157), Expect = 3e-15
 Identities = 31/81 (38%), Positives = 49/81 (60%), Gaps = 9/81 (11%)

Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYK 73
          PL  ++  L++RV VK++N R  RG L  +DQ++N+VL DVEE ++    D E      K
Sbjct: 8  PLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIIS---HDGE------K 58

Query: 74 TTKRSIPMLFVRGDGVILVSP 94
            +R    + +RGD ++L+SP
Sbjct: 59 NVRRLGGEVLIRGDNIVLISP 79

Length = 79

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

 Score = 56.2 bits (136), Expect = 3e-12
 Identities = 28/84 (33%), Positives = 44/84 (52%), Gaps = 13/84 (15%)

Query: 11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEE 70
           + PLD++  +L+  V V+++  R  RG+L  YD H+N+VL + EE       D E    
Sbjct: 2  AQRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEI-----QDGE---- 52

Query: 71 IYKTTKRSIPMLFVRGDGVILVSP 94
                R +  + +RGD V+ VSP
Sbjct: 53 ----VVRKLGKVVIRGDNVVYVSP 72

Length = 72

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

 Score = 54.6 bits (132), Expect = 2e-11
 Identities = 29/84 (34%), Positives = 45/84 (53%), Gaps = 2/84 (2%)

Query: 14 PLDLIRLSL--DERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEI 71
          PL L+  S+  + +V +  RN + L  ++ A+D+H NMVL +V+E  T V    +  +  
Sbjct: 5  PLSLLTQSVKNNTQVLINCRNNKKLLARVKAFDRHCNMVLENVKEMWTEVPKTGKGKKSK 64

Query: 72 YKTTKRSIPMLFVRGDGVILVSPP 95
               R I  +F+RGD VILV   
Sbjct: 65 PVNKDRFISKMFLRGDSVILVLRN 88

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Length = 89

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

 Score = 53.4 bits (129), Expect = 4e-11
 Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 13/73 (17%)

Query: 21 SLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIP 80
           + + V V++++ RVL G L A+D+++N+VL DV ET    +              R + 
Sbjct: 4  FIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGK-------------VRVLG 50

Query: 81 MLFVRGDGVILVS 93
          ++ +RG  ++ + 
Sbjct: 51 LVLIRGSNIVSIR 63

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

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

 Score = 46.0 bits (110), Expect = 4e-08
 Identities = 20/72 (27%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPM 81
          ++ R+ V +++ R   G   A+D+H+N+VL D EE        ++  EE  +  KR + +
Sbjct: 9  INYRMRVTLQDGRQFVGTFLAFDKHMNLVLSDCEEFRKIKPKKKKKGEE--REEKRVLGL 66

Query: 82 LFVRGDGVILVS 93
          + +RG+ V+ ++
Sbjct: 67 VLLRGENVVSMT 78

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|212476 cd01729, LSm7, Like-Sm protein 7

 Score = 43.7 bits (104), Expect = 3e-07
 Identities = 28/80 (35%), Positives = 44/80 (55%), Gaps = 6/80 (7%)

Query: 15 LDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKT 74
          LDL +  +D+++ VK +  R + G L  YDQ LN+VL D  E +   E   +  +E    
Sbjct: 5  LDLSKY-VDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPEDPYKLTDE---- 59

Query: 75 TKRSIPMLFVRGDGVILVSP 94
            RS+ ++  RG  V+L+SP
Sbjct: 60 -TRSLGLVVCRGTSVVLISP 78

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|212486 cd06168, LSMD1, LSM domain containing 1

 Score = 39.1 bits (92), Expect = 2e-05
 Identities = 12/46 (26%), Positives = 21/46 (45%)

Query: 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEET 67
          L   + V + + RVL G     D+  N++L + EE     ++  E 
Sbjct: 8  LGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSDLGAEE 53

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|212466 cd01719, Sm_G, Sm protein G

 Score = 37.9 bits (89), Expect = 5e-05
 Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 13/71 (18%)

Query: 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPM 81
          +D+R+ +K+   R + G L  +D  +N+VL             ++  EE+    K  I M
Sbjct: 9  MDKRLSLKLNGNRKVSGVLRGFDPFMNLVL-------------DDAVEEVGDGEKTPIGM 55

Query: 82 LFVRGDGVILV 92
          + +RG+ +I++
Sbjct: 56 VVIRGNSIIMI 66

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

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

 Score = 37.9 bits (89), Expect = 5e-05
 Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 13/80 (16%)

Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYK 73
          P   ++  + + V VK++N    RG L   D ++N+VL D EE V               
Sbjct: 2  PSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQ------------ 49

Query: 74 TTKRSIPMLFVRGDGVILVS 93
                   F+RG+ V+ +S
Sbjct: 50 -LVAKYGDAFIRGNNVLYIS 68

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

>gnl|CDD|212485 cd01739, LSm11_M, Like-Sm protein 11, middle domain

 Score = 37.6 bits (88), Expect = 5e-05
 Identities = 17/39 (43%), Positives = 24/39 (61%), Gaps = 4/39 (10%)

Query: 25 RVHVKMRNERVLRGK----LHAYDQHLNMVLGDVEETVT 59
          RV V +R  + +RG     L A+D+H N+ L DV+ET T
Sbjct: 10 RVKVYIRKAKGIRGSCEGYLVAFDKHWNLALVDVDETWT 48

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. LSm11 is an SmD2-like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-membered 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. Length = 63

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

 Score = 37.6 bits (88), Expect = 7e-05
 Identities = 18/54 (33%), Positives = 31/54 (57%)

Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEET 67
          PL+LI   +  ++ + M++++   G L  +D ++NMVL DV E   T E  + T
Sbjct: 4  PLELIDKCIGSKIWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKIT 57

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

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

 Score = 36.0 bits (84), Expect = 3e-04
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 10/71 (14%)

Query: 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPM 81
          LD+++ V +R+ R L G L ++DQ  N+VL D  E +       +    ++         
Sbjct: 11 LDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERIIVGNQYGDIPRGLF--------- 61

Query: 82 LFVRGDGVILV 92
            +RG+ V+L+
Sbjct: 62 -IIRGENVVLL 71

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

>gnl|CDD|212472 cd01725, LSm2, Like-Sm protein 2

 Score = 33.3 bits (77), Expect = 0.004
 Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 11/68 (16%)

Query: 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPM 81
          + + V V+++N+  + G LH+ DQ+LN+ L ++         D E Y  +      S+  
Sbjct: 10 VGKEVTVELKNDLSITGTLHSVDQYLNIKLTNISVN------DPEKYPHL-----LSVKN 58

Query: 82 LFVRGDGV 89
           F+RG  V
Sbjct: 59 CFIRGSVV 66

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	101
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.94
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.94
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.92
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.92
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.92
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.92
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.9
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.9
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.9
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.89
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.88
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.88
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.88
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.87
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.87
KOG3460|consensus	91		99.86
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.86
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.85
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.85
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.85
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.85
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.82
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.82
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.81
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.79
KOG1780|consensus	77		99.78
KOG1781|consensus	108		99.76
KOG3482|consensus	79		99.71
KOG1775|consensus	84		99.66
KOG1783|consensus	77		99.66
KOG3168|consensus	177		99.63
KOG3459|consensus	114		99.52
KOG1784|consensus	96		99.51
KOG1774|consensus	88		99.46
KOG1782|consensus	129		99.46
KOG3293|consensus	134		99.34
KOG3448|consensus	96		99.33
KOG3172|consensus	119		99.22
KOG3428|consensus	109		98.97
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	98.81
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	97.96
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	97.39
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	96.69
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	96.6
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	96.57
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	96.47
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	96.29
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	96.25
COG1923	77	Hfq Uncharacterized host factor I protein [General	96.1
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	95.89
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	95.85
PRK14638	150	hypothetical protein; Provisional	94.24
PRK14639	140	hypothetical protein; Provisional	93.29
PRK02001	152	hypothetical protein; Validated	93.09
KOG1073|consensus	361		93.03
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	92.98
PRK14091	165	RNA-binding protein Hfq; Provisional	91.73
PRK14091	165	RNA-binding protein Hfq; Provisional	90.9
PRK14644	136	hypothetical protein; Provisional	90.71
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	90.12
PRK14640	152	hypothetical protein; Provisional	89.92
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	89.58
PF03614	165	Flag1_repress: Repressor of phase-1 flagellin; Int	89.3
PRK14633	150	hypothetical protein; Provisional	89.15
PRK14642	197	hypothetical protein; Provisional	89.14
PRK14636	176	hypothetical protein; Provisional	88.56
PRK14645	154	hypothetical protein; Provisional	87.66
PRK14632	172	hypothetical protein; Provisional	87.59
COG0779	153	Uncharacterized protein conserved in bacteria [Fun	87.4
PRK14643	164	hypothetical protein; Provisional	87.26
PRK14634	155	hypothetical protein; Provisional	86.44
PRK00092	154	ribosome maturation protein RimP; Reviewed	86.37
PRK14646	155	hypothetical protein; Provisional	85.79
PRK14647	159	hypothetical protein; Provisional	85.15
PRK14631	174	hypothetical protein; Provisional	85.08
PRK14641	173	hypothetical protein; Provisional	83.01
PRK14637	151	hypothetical protein; Provisional	82.46
PRK06955	300	biotin--protein ligase; Provisional	82.39
PF14563	42	DUF4444: Domain of unknown function (DUF4444); PDB	82.12

>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=99.94  E-value=2.4e-26  Score=144.93  Aligned_cols=82  Identities=87%  Similarity=1.266  Sum_probs=68.3

Q ss_pred             ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154          13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV   92 (101)
Q Consensus        13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I   92 (101)
                      .|+++|+.+++++|.|+|++||+|.|+|.|||+||||+|+||.|++....+..+..+.......|.+|.+||||++|++|
T Consensus         1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i   80 (82)
T cd01730           1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILV   80 (82)
T ss_pred             CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEE
Confidence            49999999999999999999999999999999999999999999987543221111122234688999999999999999


Q ss_pred             ec
Q psy3154          93 SP   94 (101)
Q Consensus        93 ~~   94 (101)
                      ++
T Consensus        81 ~~   82 (82)
T cd01730          81 SP   82 (82)
T ss_pred             CC
Confidence            74

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

>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=99.94  E-value=3.1e-26  Score=146.07  Aligned_cols=84  Identities=35%  Similarity=0.521  Sum_probs=70.3

Q ss_pred             CChHHHHHHhc--CCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeE
Q psy3154          12 KEPLDLIRLSL--DERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGV   89 (101)
Q Consensus        12 ~~Pl~lL~~~l--~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I   89 (101)
                      .+|+++|+.++  +++|.|+|++|++|.|+|.|||+||||+|+||.|++...++++...+.......+++|.+||||++|
T Consensus         1 ~gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~V   80 (87)
T cd01720           1 TGPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSV   80 (87)
T ss_pred             CChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEE
Confidence            48999999998  7999999999999999999999999999999999987654332211122245688899999999999


Q ss_pred             EEEecC
Q psy3154          90 ILVSPP   95 (101)
Q Consensus        90 v~I~~~   95 (101)
                      ++|+..
T Consensus        81 v~Is~~   86 (87)
T cd01720          81 ILVLRN   86 (87)
T ss_pred             EEEecC
Confidence            999864

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.

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.92  E-value=1e-24  Score=134.51  Aligned_cols=70  Identities=37%  Similarity=0.696  Sum_probs=63.9

Q ss_pred             CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154          12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL   91 (101)
Q Consensus        12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~   91 (101)
                      +.|+++|+++++++|.|+|+||++|.|+|.|||+|||++|+||.|++..             ...+++|.+||||++|++
T Consensus         3 ~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-------------~~~~~lg~v~iRG~~V~~   69 (72)
T PRK00737          3 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDG-------------EVVRKLGKVVIRGDNVVY   69 (72)
T ss_pred             cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCC-------------CeEeEcCcEEEeCCEEEE
Confidence            6899999999999999999999999999999999999999999997531             246789999999999999


Q ss_pred             Eec
Q psy3154          92 VSP   94 (101)
Q Consensus        92 I~~   94 (101)
                      |++
T Consensus        70 i~~   72 (72)
T PRK00737         70 VSP   72 (72)
T ss_pred             EcC
Confidence            974

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

Probab=99.92  E-value=2.3e-24  Score=135.71  Aligned_cols=80  Identities=30%  Similarity=0.493  Sum_probs=65.9

Q ss_pred             CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154          12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL   91 (101)
Q Consensus        12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~   91 (101)
                      +.+++ |.++++++|+|+|+|||+|+|+|.|||+||||+|++|.|+.......     .......+.+|.++|||+||++
T Consensus         2 ~~~~~-L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~-----~~~~~~~~~lG~v~iRG~nV~~   75 (81)
T cd01729           2 ESILD-LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDP-----YKLTDKTRQLGLVVCRGTSVVL   75 (81)
T ss_pred             cchhh-HHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcc-----cccccceeEccEEEEcCCEEEE
Confidence            34555 78889999999999999999999999999999999999987642110     0012357889999999999999


Q ss_pred             EecCCC
Q psy3154          92 VSPPNR   97 (101)
Q Consensus        92 I~~~~~   97 (101)
                      |++.||
T Consensus        76 i~~~~~   81 (81)
T cd01729          76 ISPVDG   81 (81)
T ss_pred             EecCCC
Confidence            999886

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.

>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=99.92  E-value=2.8e-24  Score=133.96  Aligned_cols=74  Identities=26%  Similarity=0.490  Sum_probs=65.4

Q ss_pred             CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154          12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL   91 (101)
Q Consensus        12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~   91 (101)
                      ..|+++|+++++++|+|++++||+|.|+|.|||+|||++|+||.|++..+  ++        ...+++|.+||||++|++
T Consensus         2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~--~~--------~~~~~lg~v~iRG~nV~~   71 (76)
T cd01732           2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITP--EG--------RKITKLDQILLNGNNICM   71 (76)
T ss_pred             cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcC--CC--------ceeeEcCeEEEeCCeEEE
Confidence            36999999999999999999999999999999999999999999998421  11        146789999999999999


Q ss_pred             EecC
Q psy3154          92 VSPP   95 (101)
Q Consensus        92 I~~~   95 (101)
                      |++.
T Consensus        72 i~p~   75 (76)
T cd01732          72 LVPG   75 (76)
T ss_pred             EECC
Confidence            9964

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

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

Probab=99.92  E-value=2e-24  Score=131.63  Aligned_cols=68  Identities=41%  Similarity=0.735  Sum_probs=62.6

Q ss_pred             hHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEe
Q psy3154          14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVS   93 (101)
Q Consensus        14 Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~   93 (101)
                      |+++|+++++++|+|+|++|+.|.|+|.|||+|||++|+||.|++..             ...+.+|.+||||++|++|+
T Consensus         1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-------------~~~~~lg~~~iRG~~I~~i~   67 (68)
T cd01731           1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDG-------------EPVRKYGRVVIRGDNVLFIS   67 (68)
T ss_pred             ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecC-------------CeEeEcCcEEEeCCEEEEEc
Confidence            89999999999999999999999999999999999999999998642             14678999999999999997


Q ss_pred             c
Q psy3154          94 P   94 (101)
Q Consensus        94 ~   94 (101)
                      +
T Consensus        68 ~   68 (68)
T cd01731          68 P   68 (68)
T ss_pred             C
Confidence            5

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=99.90  E-value=1.4e-23  Score=127.63  Aligned_cols=67  Identities=28%  Similarity=0.441  Sum_probs=61.0

Q ss_pred             hHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEe
Q psy3154          14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVS   93 (101)
Q Consensus        14 Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~   93 (101)
                      |+++|+++++++|.|+|++|++|.|+|.|||+|||++|+||.|+...             ...+.+|.+||||++|++|+
T Consensus         1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~-------------~~~~~~~~v~IRG~~I~~I~   67 (67)
T cd01726           1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNG-------------QLKNKYGDAFIRGNNVLYIS   67 (67)
T ss_pred             CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCC-------------ceeeEeCCEEEECCEEEEEC
Confidence            89999999999999999999999999999999999999999886421             24678999999999999985

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.

>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=99.90  E-value=2.7e-23  Score=128.26  Aligned_cols=71  Identities=24%  Similarity=0.497  Sum_probs=63.3

Q ss_pred             hHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEe
Q psy3154          14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVS   93 (101)
Q Consensus        14 Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~   93 (101)
                      |-..|+++++|+|+|+|++|++|.|+|.|||+|||++|+||.|++..             ...+.+|.++|||++|++|+
T Consensus         1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~-------------~~~~~lg~v~IRG~~I~~i~   67 (72)
T cd01719           1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSG-------------GEKNNIGMVVIRGNSIVMLE   67 (72)
T ss_pred             CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccC-------------CceeEeceEEECCCEEEEEE
Confidence            34678999999999999999999999999999999999999998631             24678999999999999999


Q ss_pred             cCCC
Q psy3154          94 PPNR   97 (101)
Q Consensus        94 ~~~~   97 (101)
                      +.|.
T Consensus        68 ~~~~   71 (72)
T cd01719          68 ALER   71 (72)
T ss_pred             cccc
Confidence            8874

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.

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

Probab=99.90  E-value=6.3e-23  Score=128.38  Aligned_cols=76  Identities=22%  Similarity=0.469  Sum_probs=62.8

Q ss_pred             HHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEec
Q psy3154          16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP   94 (101)
Q Consensus        16 ~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~   94 (101)
                      +-|..+++++|+|+|+|||.|.|+|.|||+||||+|+||.|++...+.+.   ........|++|++||||++|++|+.
T Consensus         3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~---~~~~~~~~r~lG~v~iRG~~Vv~i~v   78 (79)
T cd01717           3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKS---KNSEREEKRTLGLVLLRGENIVSMTV   78 (79)
T ss_pred             chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEecccccc---ccccCcceeEeeeEEEcCCEEEEEEE
Confidence            34778899999999999999999999999999999999999987543210   01112467899999999999999985

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.

>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=99.89  E-value=7.6e-23  Score=124.83  Aligned_cols=68  Identities=19%  Similarity=0.331  Sum_probs=61.2

Q ss_pred             ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154          13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV   92 (101)
Q Consensus        13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I   92 (101)
                      .|+++|+++++++|+|+|++|++|.|+|.|||+|||++|+||.|+...             ...+.+|.+||||++|++|
T Consensus         1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~-------------~~~~~lg~~~IRG~~I~~i   67 (68)
T cd01722           1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDG-------------KSTGNLGEVLIRCNNVLYI   67 (68)
T ss_pred             CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCC-------------ccccCcCcEEEECCEEEEE
Confidence            489999999999999999999999999999999999999999987421             1356799999999999998


Q ss_pred             e
Q psy3154          93 S   93 (101)
Q Consensus        93 ~   93 (101)
                      +
T Consensus        68 ~   68 (68)
T cd01722          68 R   68 (68)
T ss_pred             C
Confidence            4

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.

>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=99.88  E-value=4.3e-22  Score=123.30  Aligned_cols=73  Identities=25%  Similarity=0.439  Sum_probs=62.9

Q ss_pred             HHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEecC
Q psy3154          16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPP   95 (101)
Q Consensus        16 ~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~   95 (101)
                      +.|+++++++|+|+++|||.|.|+|+|||+|||++|++|.|+....+ .        ....+.+|.+++||++|++|++.
T Consensus         2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~-~--------~~~~~~lG~~~iRG~~I~~i~~~   72 (74)
T cd01727           2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSD-E--------GVEQVVLGLYIIRGDNIAVVGEI   72 (74)
T ss_pred             hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCC-C--------CceeeEeceEEECCCEEEEEEcc
Confidence            45788999999999999999999999999999999999999865321 0        12467899999999999999998


Q ss_pred             CC
Q psy3154          96 NR   97 (101)
Q Consensus        96 ~~   97 (101)
                      |+
T Consensus        73 d~   74 (74)
T cd01727          73 DE   74 (74)
T ss_pred             CC
Confidence            74

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. 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=99.88  E-value=6.7e-22  Score=122.68  Aligned_cols=71  Identities=30%  Similarity=0.433  Sum_probs=61.9

Q ss_pred             hHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEe
Q psy3154          14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVS   93 (101)
Q Consensus        14 Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~   93 (101)
                      ++..|+++++++|.|+|+|||+|.|+|+|||+|||++|+||.|+.....          ....+.+|.++|||++|++|+
T Consensus         3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~----------~~~~~~lG~~viRG~~V~~ig   72 (74)
T cd01728           3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGD----------KYGDIPRGIFIIRGENVVLLG   72 (74)
T ss_pred             chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCC----------ccceeEeeEEEEECCEEEEEE
Confidence            4567889999999999999999999999999999999999999875321          123578999999999999997


Q ss_pred             c
Q psy3154          94 P   94 (101)
Q Consensus        94 ~   94 (101)
                      .
T Consensus        73 ~   73 (74)
T cd01728          73 E   73 (74)
T ss_pred             c
Confidence            5

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.

>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=99.88  E-value=7.6e-22  Score=123.79  Aligned_cols=74  Identities=24%  Similarity=0.483  Sum_probs=64.3

Q ss_pred             cccCChHHHHHHhcCC--EEEEEEc--CCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEE
Q psy3154           9 ISVKEPLDLIRLSLDE--RVHVKMR--NERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFV   84 (101)
Q Consensus         9 ~~~~~Pl~lL~~~l~k--~V~V~l~--~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~I   84 (101)
                      ..+..|++.+.+++++  +|.|+++  +|++++|+|.|||+|||++|+||.|+...            ....+.+|.++|
T Consensus         2 ~~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~------------~~~~~~lG~ili   69 (79)
T cd01718           2 KVMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLK------------TKTRKPLGRILL   69 (79)
T ss_pred             ccccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecC------------CceEeEcCcEEE
Confidence            3477899999999997  7888887  89999999999999999999999998641            024678999999


Q ss_pred             cCCeEEEEec
Q psy3154          85 RGDGVILVSP   94 (101)
Q Consensus        85 RG~~Iv~I~~   94 (101)
                      ||+||++|++
T Consensus        70 RGnnV~~I~p   79 (79)
T cd01718          70 KGDNITLIQN   79 (79)
T ss_pred             eCCEEEEEcC
Confidence            9999999974

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.

>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=99.87  E-value=1e-21  Score=122.16  Aligned_cols=72  Identities=19%  Similarity=0.343  Sum_probs=62.9

Q ss_pred             HHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEec
Q psy3154          16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP   94 (101)
Q Consensus        16 ~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~   94 (101)
                      +-|+++++++|+|+|+|||.|.|+|.|||+|||++|+||.|++..++..       .....|.+|+++|||++|++|+.
T Consensus         3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~-------~~~~~r~lGlv~IrG~~Iv~i~v   74 (75)
T cd06168           3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSF-------SPTEPRVLGLVMIPGHHIVSIEV   74 (75)
T ss_pred             hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCcc-------CCccEEEeeeEEEeCCeEEEEEE
Confidence            4688999999999999999999999999999999999999998753311       12468999999999999999975

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.

>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=99.87  E-value=1.2e-21  Score=120.15  Aligned_cols=70  Identities=26%  Similarity=0.456  Sum_probs=62.7

Q ss_pred             hHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEe
Q psy3154          14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVS   93 (101)
Q Consensus        14 Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~   93 (101)
                      |+++|+++.|++|.|+|++|.+|+|+|.++|.|||++|+||.+...    ++         +..+++.+||||++|.+|.
T Consensus         1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~----~g---------~~~~~~~v~IRG~nI~~v~   67 (70)
T cd01721           1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTAR----DG---------RVSQLEQVYIRGSKIRFFI   67 (70)
T ss_pred             ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECC----CC---------cEeEcCcEEEeCCEEEEEE
Confidence            8899999999999999999999999999999999999999987532    11         2457899999999999999


Q ss_pred             cCC
Q psy3154          94 PPN   96 (101)
Q Consensus        94 ~~~   96 (101)
                      .||
T Consensus        68 lPd   70 (70)
T cd01721          68 LPD   70 (70)
T ss_pred             eCC
Confidence            886

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.

>KOG3460|consensus

Probab=99.86  E-value=9.3e-23  Score=127.57  Aligned_cols=87  Identities=79%  Similarity=1.197  Sum_probs=76.5

Q ss_pred             ccCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeE
Q psy3154          10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGV   89 (101)
Q Consensus        10 ~~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I   89 (101)
                      .+..|+++|+-+++.+|.|+++++|+++|+|.|||+|.|++|.|+.|+++..+.+..+..+..+...|.+..+||||++|
T Consensus         2 ~v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~V   81 (91)
T KOG3460|consen    2 TVEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGV   81 (91)
T ss_pred             cccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeE
Confidence            46789999999999999999999999999999999999999999999998776544343444556789999999999999


Q ss_pred             EEEecCC
Q psy3154          90 ILVSPPN   96 (101)
Q Consensus        90 v~I~~~~   96 (101)
                      ++|+++=
T Consensus        82 ilvspp~   88 (91)
T KOG3460|consen   82 ILVSPPL   88 (91)
T ss_pred             EEEcCcc
Confidence            9999874

>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=99.86  E-value=3.3e-21  Score=119.91  Aligned_cols=73  Identities=23%  Similarity=0.434  Sum_probs=63.7

Q ss_pred             ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154          13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV   92 (101)
Q Consensus        13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I   92 (101)
                      .|+++|+++.|++|.|.|++|++|.|+|.+||.|||++|+||.|...    ++        .....++.+||||++|.+|
T Consensus         1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~----~g--------~~~~~~~~v~IRG~~I~~i   68 (76)
T cd01723           1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSK----DG--------DKFWKMPECYIRGNTIKYL   68 (76)
T ss_pred             CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECC----CC--------cEeeeCCcEEEeCCEEEEE
Confidence            39999999999999999999999999999999999999999988632    11        1245679999999999999


Q ss_pred             ecCCC
Q psy3154          93 SPPNR   97 (101)
Q Consensus        93 ~~~~~   97 (101)
                      ..+|.
T Consensus        69 ~~p~~   73 (76)
T cd01723          69 RVPDE   73 (76)
T ss_pred             EcCHH
Confidence            98864

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.

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

Probab=99.85  E-value=4.2e-21  Score=115.89  Aligned_cols=67  Identities=36%  Similarity=0.674  Sum_probs=60.6

Q ss_pred             HHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEec
Q psy3154          16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP   94 (101)
Q Consensus        16 ~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~   94 (101)
                      .+|+++++++|+|.|++|+.|+|+|.+||+|||++|+||.|++...            ...+++|.+||||++|++|++
T Consensus         1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~------------~~~~~~~~~~irG~~I~~I~~   67 (67)
T PF01423_consen    1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNG------------PEKRSLGLVFIRGSNIRYISL   67 (67)
T ss_dssp             HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTE------------SEEEEEEEEEEEGGGEEEEEE
T ss_pred             ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCC------------CcEeECcEEEEECCEEEEEEC
Confidence            3789999999999999999999999999999999999999987521            157899999999999999975

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

>smart00651 Sm snRNP Sm proteins

Probab=99.85  E-value=7e-21  Score=114.80  Aligned_cols=66  Identities=36%  Similarity=0.684  Sum_probs=59.9

Q ss_pred             HHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEec
Q psy3154          17 LIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP   94 (101)
Q Consensus        17 lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~   94 (101)
                      +|+++++++|+|.|+||+++.|+|.+||+|||++|+||.|++...            ...+++|.+||||++|++|.+
T Consensus         2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~------------~~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651        2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG------------EKKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCC------------cEEeEeCCEEEcCCEEEEEeC
Confidence            688999999999999999999999999999999999999987521            257899999999999999974

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

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.85  E-value=1.3e-20  Score=120.58  Aligned_cols=80  Identities=24%  Similarity=0.458  Sum_probs=68.5

Q ss_pred             ccCCccccCChHHHHHHhcC--CEEEEEEcCC--eEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeee
Q psy3154           4 EQIPTISVKEPLDLIRLSLD--ERVHVKMRNE--RVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSI   79 (101)
Q Consensus         4 ~~~~~~~~~~Pl~lL~~~l~--k~V~V~l~~g--r~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~l   79 (101)
                      ...++..+..|+.++.+++.  .+|.|++.++  ++|.|+|.|||+|||++|+||.|++..    +        ...+.+
T Consensus         5 ~~~~~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~----~--------~~~~~l   72 (89)
T PTZ00138          5 KRKLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTK----K--------NTRKDL   72 (89)
T ss_pred             ccccceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecC----C--------ceeeEc
Confidence            34667779999999999998  4899998774  899999999999999999999997642    1        246789


Q ss_pred             CeEEEcCCeEEEEecC
Q psy3154          80 PMLFVRGDGVILVSPP   95 (101)
Q Consensus        80 g~v~IRG~~Iv~I~~~   95 (101)
                      |.+|||||||++|++.
T Consensus        73 G~ilIRGnnV~~I~~~   88 (89)
T PTZ00138         73 GRILLKGDNITLIMAA   88 (89)
T ss_pred             CeEEEcCCEEEEEEcC
Confidence            9999999999999875

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

Probab=99.85  E-value=8.8e-21  Score=118.55  Aligned_cols=75  Identities=40%  Similarity=0.676  Sum_probs=62.5

Q ss_pred             cCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEE
Q psy3154          11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVI   90 (101)
Q Consensus        11 ~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv   90 (101)
                      ...|+++|+++++++|.|+|++|++|.|+|.|||+|||++|+||.|++..   +++.      ...+..+.++|||++|+
T Consensus         5 ~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~---~~~~------~~~~~~~~~~IRG~~I~   75 (79)
T COG1958           5 GPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH---DGEK------NVRRLGGEVLIRGDNIV   75 (79)
T ss_pred             cCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEecc---CCcc------ccceeccEEEEECCcEE
Confidence            45689999999999999999999999999999999999999999998741   1100      02344459999999999


Q ss_pred             EEec
Q psy3154          91 LVSP   94 (101)
Q Consensus        91 ~I~~   94 (101)
                      +|.+
T Consensus        76 ~I~~   79 (79)
T COG1958          76 LISP   79 (79)
T ss_pred             EEeC
Confidence            9964

>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=99.82  E-value=7e-20  Score=109.01  Aligned_cols=63  Identities=40%  Similarity=0.686  Sum_probs=57.4

Q ss_pred             HHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEe
Q psy3154          18 IRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVS   93 (101)
Q Consensus        18 L~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~   93 (101)
                      |+++++++|+|.|+||+.|.|+|.+||+|||++|+||.|++..             ...+.++.+||||++|++|.
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~-------------~~~~~~~~~~irG~~I~~I~   63 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE-------------GKKRVLGLVLIRGDNVRLVT   63 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecC-------------CcEEECCeEEEECCEEEEEC
Confidence            4678999999999999999999999999999999999998753             24789999999999999984

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.

>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=99.82  E-value=9.7e-20  Score=116.75  Aligned_cols=71  Identities=18%  Similarity=0.352  Sum_probs=64.2

Q ss_pred             hHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEe
Q psy3154          14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVS   93 (101)
Q Consensus        14 Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~   93 (101)
                      ++.+|+++.|++|.|+|++|..|.|+|.++|.|||++|+||.++...             .....++.+||||++|.+|.
T Consensus         2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~-------------~~~~~~~~v~IRG~nI~yi~   68 (90)
T cd01724           2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKG-------------RNPVPLDTLSIRGNNIRYFI   68 (90)
T ss_pred             HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCC-------------CceeEcceEEEeCCEEEEEE
Confidence            67899999999999999999999999999999999999999887431             13568999999999999999


Q ss_pred             cCCC
Q psy3154          94 PPNR   97 (101)
Q Consensus        94 ~~~~   97 (101)
                      .+|.
T Consensus        69 lPd~   72 (90)
T cd01724          69 LPDS   72 (90)
T ss_pred             cCCc
Confidence            9975

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.

>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=99.81  E-value=2.9e-19  Score=112.46  Aligned_cols=74  Identities=27%  Similarity=0.391  Sum_probs=63.2

Q ss_pred             ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154          13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV   92 (101)
Q Consensus        13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I   92 (101)
                      .|+++|+++.|++|.|+|++|..|.|+|.++|.|||++|+||.++...    +       ......++.++|||++|.+|
T Consensus         1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~----~-------~~~~~~~~~v~IRG~~I~~I   69 (81)
T cd01725           1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPE----K-------YPHMLSVKNCFIRGSVVRYV   69 (81)
T ss_pred             ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCC----C-------cccccccCeEEEECCEEEEE
Confidence            489999999999999999999999999999999999999999765321    1       01234579999999999999


Q ss_pred             ecCCC
Q psy3154          93 SPPNR   97 (101)
Q Consensus        93 ~~~~~   97 (101)
                      ..+|.
T Consensus        70 ~lp~~   74 (81)
T cd01725          70 QLPAD   74 (81)
T ss_pred             EeChh
Confidence            99874

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

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

Probab=99.79  E-value=8.6e-19  Score=109.68  Aligned_cols=71  Identities=21%  Similarity=0.324  Sum_probs=61.9

Q ss_pred             CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154          12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL   91 (101)
Q Consensus        12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~   91 (101)
                      -.+..+|+.+.|++|.|+|++|..|.|+|.++|.|||++|+||.+....             ....++|.+||||++|.+
T Consensus         8 ~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~-------------~~~~~~~~v~IRG~nI~y   74 (78)
T cd01733           8 NTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRN-------------GKQVQVEEIMVTGRNIRY   74 (78)
T ss_pred             chHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCC-------------CceeECCcEEEECCEEEE
Confidence            4568899999999999999999999999999999999999999865321             134579999999999999


Q ss_pred             EecC
Q psy3154          92 VSPP   95 (101)
Q Consensus        92 I~~~   95 (101)
                      |..|
T Consensus        75 I~lP   78 (78)
T cd01733          75 VHIP   78 (78)
T ss_pred             EEcC
Confidence            9865

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.

>KOG1780|consensus

Probab=99.78  E-value=7e-19  Score=107.94  Aligned_cols=71  Identities=27%  Similarity=0.541  Sum_probs=62.8

Q ss_pred             CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154          12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL   91 (101)
Q Consensus        12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~   91 (101)
                      ..|  -|++|++|++.++|.+||.+.|+|.|||.|||+||++++|....             ..+..+|.++|||++|+.
T Consensus         5 g~P--eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~-------------~~~~~ig~~vIrgnsiv~   69 (77)
T KOG1780|consen    5 GHP--ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGD-------------GDKNNIGMVVIRGNSIVM   69 (77)
T ss_pred             cCc--hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCc-------------CCcceeeeEEEeccEEEE
Confidence            357  68899999999999999999999999999999999999997542             235679999999999999


Q ss_pred             EecCCC
Q psy3154          92 VSPPNR   97 (101)
Q Consensus        92 I~~~~~   97 (101)
                      +++.|.
T Consensus        70 ~eaL~~   75 (77)
T KOG1780|consen   70 VEALER   75 (77)
T ss_pred             Eeeccc
Confidence            998775

>KOG1781|consensus

Probab=99.76  E-value=9.4e-20  Score=117.17  Aligned_cols=81  Identities=27%  Similarity=0.436  Sum_probs=68.3

Q ss_pred             HHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEec
Q psy3154          15 LDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP   94 (101)
Q Consensus        15 l~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~   94 (101)
                      +=-|.+|++++|+|++.+||+..|+|+|||+.|||||++++|+...++    +.. +....+|++|++++||..+++|++
T Consensus        19 ilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpd----d~~-~~~~~tR~LGLvV~RGTalvlisp   93 (108)
T KOG1781|consen   19 ILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPD----DPY-KLTDETRKLGLVVCRGTALVLISP   93 (108)
T ss_pred             HhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCC----Ccc-chhhhhheeeeEEEcccEEEEEcC
Confidence            344567799999999999999999999999999999999999987543    111 123346999999999999999999


Q ss_pred             CCCCCC
Q psy3154          95 PNRTPA  100 (101)
Q Consensus        95 ~~~~~~  100 (101)
                      .||+++
T Consensus        94 ~dG~e~   99 (108)
T KOG1781|consen   94 ADGSEE   99 (108)
T ss_pred             Ccchhh
Confidence            999875

>KOG3482|consensus

Probab=99.71  E-value=3.6e-17  Score=100.14  Aligned_cols=72  Identities=18%  Similarity=0.306  Sum_probs=65.4

Q ss_pred             CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154          12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL   91 (101)
Q Consensus        12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~   91 (101)
                      .+|-.||+.+.+++|.|+|+.|.+|.|+|.+.|.|||+.|.+|.|++..             ..+..+|.++||++||.+
T Consensus         7 vNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG-------------~~~g~lGEilIRCNNvly   73 (79)
T KOG3482|consen    7 VNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDG-------------VSTGNLGEILIRCNNVLY   73 (79)
T ss_pred             CCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcc-------------cccccceeEEEEeccEEE
Confidence            4899999999999999999999999999999999999999999998752             246789999999999999


Q ss_pred             EecCC
Q psy3154          92 VSPPN   96 (101)
Q Consensus        92 I~~~~   96 (101)
                      |.-.+
T Consensus        74 i~gv~   78 (79)
T KOG3482|consen   74 IRGVP   78 (79)
T ss_pred             EecCC
Confidence            97654

>KOG1775|consensus

Probab=99.66  E-value=1.1e-16  Score=98.76  Aligned_cols=78  Identities=26%  Similarity=0.468  Sum_probs=68.1

Q ss_pred             ccCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeE
Q psy3154          10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGV   89 (101)
Q Consensus        10 ~~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I   89 (101)
                      +.-.|++++.+|+|++++|.+++.|++.|+|.|||.|.|++|+|+.|+-..++-          ....+++++++.|++|
T Consensus         4 ~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~eg----------r~~tk~~~iLLnGNni   73 (84)
T KOG1775|consen    4 STLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEG----------RRMTKLDQILLNGNNI   73 (84)
T ss_pred             hhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCc----------ceeeeeeeeeecCCcE
Confidence            346799999999999999999999999999999999999999999998765431          2467899999999999


Q ss_pred             EEEecCCC
Q psy3154          90 ILVSPPNR   97 (101)
Q Consensus        90 v~I~~~~~   97 (101)
                      ...-+..+
T Consensus        74 ~mLvPGGe   81 (84)
T KOG1775|consen   74 TMLVPGGE   81 (84)
T ss_pred             EEEecCCC
Confidence            98877654

>KOG1783|consensus

Probab=99.66  E-value=2.3e-17  Score=100.98  Aligned_cols=73  Identities=26%  Similarity=0.380  Sum_probs=66.1

Q ss_pred             cCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEE
Q psy3154          11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVI   90 (101)
Q Consensus        11 ~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv   90 (101)
                      .+.|-++|...+|++|.|+|.+|-.|+|+|.|+|.|||+-|+.+.|+...             ...+++|.+||||++|.
T Consensus         4 ~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ng-------------ql~n~ygdaFirGnnVl   70 (77)
T KOG1783|consen    4 GSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNG-------------QLKNKYGDAFIRGNNVL   70 (77)
T ss_pred             ccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcC-------------cccccccceeeccccEE
Confidence            46789999999999999999999999999999999999999999987642             24688999999999999


Q ss_pred             EEecCC
Q psy3154          91 LVSPPN   96 (101)
Q Consensus        91 ~I~~~~   96 (101)
                      +|+...
T Consensus        71 yIs~~~   76 (77)
T KOG1783|consen   71 YISTQK   76 (77)
T ss_pred             EEEecc
Confidence            999764

>KOG3168|consensus

Probab=99.63  E-value=4.9e-17  Score=113.42  Aligned_cols=82  Identities=22%  Similarity=0.472  Sum_probs=68.6

Q ss_pred             cCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEE
Q psy3154          11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVI   90 (101)
Q Consensus        11 ~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv   90 (101)
                      ...+..+|+. ++.+++|.++|||.|+|.+++||+|||++|.+|.|+.....++.   +.......|-+|+|++||++|+
T Consensus         3 ~a~sskml~~-iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~---~~~~~eEkr~lgLvllRgenIv   78 (177)
T KOG3168|consen    3 VAKSSKMLQH-INYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNR---KMTDGEEKRVLGLVLLRGENIV   78 (177)
T ss_pred             ccchhHHHHh-hcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccc---cccccceeeEEEEEEecCCcEE
Confidence            4556677777 99999999999999999999999999999999999887655432   1123457899999999999999


Q ss_pred             EEecCC
Q psy3154          91 LVSPPN   96 (101)
Q Consensus        91 ~I~~~~   96 (101)
                      +.+..+
T Consensus        79 s~tVeg   84 (177)
T KOG3168|consen   79 SMTVEG   84 (177)
T ss_pred             EEeccC
Confidence            998764

>KOG3459|consensus

Probab=99.52  E-value=1.7e-15  Score=99.14  Aligned_cols=83  Identities=35%  Similarity=0.493  Sum_probs=71.0

Q ss_pred             cCChHHHHHHhcC--CEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCe
Q psy3154          11 VKEPLDLIRLSLD--ERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDG   88 (101)
Q Consensus        11 ~~~Pl~lL~~~l~--k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~   88 (101)
                      ..+|++++..++.  .+|.|.++|++.+-|++.|||.|+|++|+++.|.|++.++.+...+.+.....|++|.+|||||+
T Consensus        22 ~~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGds  101 (114)
T KOG3459|consen   22 NTGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDS  101 (114)
T ss_pred             CcCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCe
Confidence            4499999999887  69999999999999999999999999999999999987655332232334568999999999999


Q ss_pred             EEEEe
Q psy3154          89 VILVS   93 (101)
Q Consensus        89 Iv~I~   93 (101)
                      |+.+.
T Consensus       102 vI~v~  106 (114)
T KOG3459|consen  102 VILVL  106 (114)
T ss_pred             EEEEE
Confidence            99886

>KOG1784|consensus

Probab=99.51  E-value=1.4e-14  Score=92.19  Aligned_cols=74  Identities=19%  Similarity=0.396  Sum_probs=63.7

Q ss_pred             HHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEecC
Q psy3154          16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPP   95 (101)
Q Consensus        16 ~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~   95 (101)
                      +-|+.|++++|.|.+.|||.+.|.|+|||+..|++|+++.|++....         .-..+.-+|.-+|||+||..|...
T Consensus         3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~---------~gv~q~~lGlyiirgeNva~ig~i   73 (96)
T KOG1784|consen    3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSET---------EGVEQIVLGLYIIRGENVAVIGEI   73 (96)
T ss_pred             hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhh---------cchhheeeEEEEEecCccceeeec
Confidence            35788999999999999999999999999999999999999876321         113467799999999999999998


Q ss_pred             CCC
Q psy3154          96 NRT   98 (101)
Q Consensus        96 ~~~   98 (101)
                      |+.
T Consensus        74 DEe   76 (96)
T KOG1784|consen   74 DEE   76 (96)
T ss_pred             chh
Confidence            763

>KOG1774|consensus

Probab=99.46  E-value=7.5e-14  Score=87.21  Aligned_cols=75  Identities=23%  Similarity=0.500  Sum_probs=61.6

Q ss_pred             ccCChHHHHHHhcC--CEEEEEEcC--CeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEc
Q psy3154          10 SVKEPLDLIRLSLD--ERVHVKMRN--ERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVR   85 (101)
Q Consensus        10 ~~~~Pl~lL~~~l~--k~V~V~l~~--gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IR   85 (101)
                      -+..|+.++-+++.  .+|.|+|.+  |-.+.|.+.|||+|||+||++|+|.....            ...+.+|.++++
T Consensus         9 vmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~------------~~rk~lGRilLK   76 (88)
T KOG1774|consen    9 VMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKT------------KSRKELGRILLK   76 (88)
T ss_pred             eecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccc------------cCCCccccEEEc
Confidence            35779999998887  589999976  57899999999999999999999865311            123489999999


Q ss_pred             CCeEEEEecCC
Q psy3154          86 GDGVILVSPPN   96 (101)
Q Consensus        86 G~~Iv~I~~~~   96 (101)
                      ||||.+|...+
T Consensus        77 GDnItli~~~~   87 (88)
T KOG1774|consen   77 GDNITLIQSAG   87 (88)
T ss_pred             CCcEEEEeecC
Confidence            99999997653

>KOG1782|consensus

Probab=99.46  E-value=1.2e-14  Score=96.93  Aligned_cols=74  Identities=27%  Similarity=0.382  Sum_probs=62.6

Q ss_pred             ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154          13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV   92 (101)
Q Consensus        13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I   92 (101)
                      ...+ |-.++++++.|.|+|||.+.|.|.+||+|-|++|.+|+|++....          ....+..|..+|||+||+++
T Consensus        10 ~t~s-l~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~----------~Y~di~~glfiIRGENVvll   78 (129)
T KOG1782|consen   10 FTTS-LVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGN----------KYCDIPRGLFIIRGENVVLL   78 (129)
T ss_pred             chhH-HHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecc----------eecccCceEEEEecCcEEEE
Confidence            3344 445599999999999999999999999999999999999887532          24567789999999999999


Q ss_pred             ecCCC
Q psy3154          93 SPPNR   97 (101)
Q Consensus        93 ~~~~~   97 (101)
                      ...|-
T Consensus        79 Geid~   83 (129)
T KOG1782|consen   79 GEIDL   83 (129)
T ss_pred             ecCCc
Confidence            88753

>KOG3293|consensus

Probab=99.34  E-value=2.4e-12  Score=86.02  Aligned_cols=73  Identities=22%  Similarity=0.390  Sum_probs=65.5

Q ss_pred             ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154          13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV   92 (101)
Q Consensus        13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I   92 (101)
                      .|+.||+.+-+.++.|.|++|.+|.|.|+.-|.+|||.|++|.++..+    +        .+--.++.+.|||++|-++
T Consensus         2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~D----g--------dkf~r~pEcYirGttIkyl   69 (134)
T KOG3293|consen    2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSED----G--------DKFFRMPECYIRGTTIKYL   69 (134)
T ss_pred             cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccC----C--------CceeecceeEEecceeEEE
Confidence            699999999999999999999999999999999999999999988652    2        2456788999999999999


Q ss_pred             ecCCC
Q psy3154          93 SPPNR   97 (101)
Q Consensus        93 ~~~~~   97 (101)
                      ..+|.
T Consensus        70 ri~d~   74 (134)
T KOG3293|consen   70 RIPDE   74 (134)
T ss_pred             eccHH
Confidence            98864

>KOG3448|consensus

Probab=99.33  E-value=1.1e-11  Score=78.54  Aligned_cols=72  Identities=28%  Similarity=0.359  Sum_probs=60.5

Q ss_pred             ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154          13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV   92 (101)
Q Consensus        13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I   92 (101)
                      ..+++.+.++|++|.|.|+++-.+.|+|.++|+|.|+.|.|..-...  ++.         ..--.+..+||||+.|.||
T Consensus         2 LFysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~--~ky---------Phm~Sv~ncfIRGSvvrYv   70 (96)
T KOG3448|consen    2 LFYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDP--DKY---------PHMLSVKNCFIRGSVVRYV   70 (96)
T ss_pred             chHHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCc--ccC---------CCeeeeeeEEEeccEEEEE
Confidence            35789999999999999999999999999999999999999875422  111         2355678899999999999


Q ss_pred             ecC
Q psy3154          93 SPP   95 (101)
Q Consensus        93 ~~~   95 (101)
                      ..+
T Consensus        71 ~l~   73 (96)
T KOG3448|consen   71 QLP   73 (96)
T ss_pred             EeC
Confidence            876

>KOG3172|consensus

Probab=99.22  E-value=4.8e-11  Score=78.16  Aligned_cols=75  Identities=25%  Similarity=0.437  Sum_probs=66.3

Q ss_pred             cccCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCe
Q psy3154           9 ISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDG   88 (101)
Q Consensus         9 ~~~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~   88 (101)
                      +++.-|+.+|.++-+.-|.+.+..|..|+|+|.-.+++||+.|+|+.-+...    +         ....+.++||||+.
T Consensus         1 ~s~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~d----g---------~vs~le~V~IRGS~   67 (119)
T KOG3172|consen    1 MSVGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARD----G---------RVSQLEQVFIRGSK   67 (119)
T ss_pred             CccccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccC----C---------cceeeeeEEEecCe
Confidence            3567899999999999999999999999999999999999999999876541    2         35678899999999


Q ss_pred             EEEEecCC
Q psy3154          89 VILVSPPN   96 (101)
Q Consensus        89 Iv~I~~~~   96 (101)
                      |.++.++|
T Consensus        68 IRFlvlPd   75 (119)
T KOG3172|consen   68 IRFLVLPD   75 (119)
T ss_pred             EEEEECch
Confidence            99998886

>KOG3428|consensus

Probab=98.97  E-value=5.6e-09  Score=68.51  Aligned_cols=69  Identities=23%  Similarity=0.443  Sum_probs=60.0

Q ss_pred             HHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEec
Q psy3154          15 LDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP   94 (101)
Q Consensus        15 l~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~   94 (101)
                      +.+|+.+.+.+|.|.|++|+.+.|++.++|.+||..|.++.-+..              ....++..++|||++|.|+-.
T Consensus         4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~--------------~~pv~l~~lsirgnniRy~~l   69 (109)
T KOG3428|consen    4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK--------------GEPVRLDTLSIRGNNIRYYIL   69 (109)
T ss_pred             HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecC--------------CCceeEEEEEeecceEEEEEc
Confidence            468899999999999999999999999999999999999874432              124678899999999999999


Q ss_pred             CCC
Q psy3154          95 PNR   97 (101)
Q Consensus        95 ~~~   97 (101)
                      +|.
T Consensus        70 pD~   72 (109)
T KOG3428|consen   70 PDS   72 (109)
T ss_pred             cCC
Confidence            874

>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=98.81  E-value=2.6e-09  Score=64.41  Aligned_cols=41  Identities=39%  Similarity=0.472  Sum_probs=33.6

Q ss_pred             HhcC--CEEEEEEcCC----eEEEEEEEEEcCCCceEecceEEEEee
Q psy3154          20 LSLD--ERVHVKMRNE----RVLRGKLHAYDQHLNMVLGDVEETVTT   60 (101)
Q Consensus        20 ~~l~--k~V~V~l~~g----r~i~G~L~~~D~~mNlvL~~~~E~~~~   60 (101)
                      +|+.  .+|+|.++.-    -.++|.|.+||+||||+|.|+.|.|..
T Consensus         3 ~~~~er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~   49 (66)
T cd01739           3 RCVQERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK   49 (66)
T ss_pred             hhhhCCcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence            4444  6888888654    368899999999999999999999875

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

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

Probab=97.96  E-value=3.4e-05  Score=47.49  Aligned_cols=69  Identities=16%  Similarity=0.249  Sum_probs=41.3

Q ss_pred             HHHHHhcCCEEEEEEcCCeEEEEEEEEEcC---CCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEE
Q psy3154          16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQ---HLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVI   90 (101)
Q Consensus        16 ~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~---~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv   90 (101)
                      -++..++|++|.|+++||..|.|+|.+++.   -+.++|+-+........      .............++|+++.|+
T Consensus         5 ~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~------~~~~~~~~~~~~tlii~~~dvv   76 (77)
T PF14438_consen    5 YLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQ------SNSDPLSSEIVETLIIPAKDVV   76 (77)
T ss_dssp             HHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------------EEEEEEE-GGGEEE-----
T ss_pred             HHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccccc------ccCCccCCCCCceEEEeccccC
Confidence            456778999999999999999999999998   89999988876432110      0011233445567777777665

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

Probab=97.39  E-value=0.001  Score=43.06  Aligned_cols=76  Identities=11%  Similarity=0.118  Sum_probs=56.0

Q ss_pred             HHhcCCEEEEEEcCCeEEEEEEEEEcC-CCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEecCCC
Q psy3154          19 RLSLDERVHVKMRNERVLRGKLHAYDQ-HLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNR   97 (101)
Q Consensus        19 ~~~l~k~V~V~l~~gr~i~G~L~~~D~-~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~~~   97 (101)
                      ..|+|++|.+..+.+-.|.|+|..+|. ...+.|+||..+-++.+...    ........-+..+..||+.|--+...+.
T Consensus         4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~----~~ipp~~~v~~~I~Fr~sDIkdL~v~e~   79 (96)
T PF12701_consen    4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTD----REIPPSDEVYDYIVFRGSDIKDLKVIEP   79 (96)
T ss_dssp             CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-S----S---C-CSSSSEEEEETTTEEEEEECE-
T ss_pred             ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcC----cccCCCCceeeEEEEEccccceEEEEcC
Confidence            467999999999999999999999995 88899999988765321110    0112234567899999999988877654


Q ss_pred             C
Q psy3154          98 T   98 (101)
Q Consensus        98 ~   98 (101)
                      .
T Consensus        80 ~   80 (96)
T PF12701_consen   80 P   80 (96)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=96.69  E-value=0.011  Score=36.54  Aligned_cols=69  Identities=10%  Similarity=0.114  Sum_probs=50.0

Q ss_pred             HhcCCEEEEEEcCCeEEEEEEEEEc-CCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154          20 LSLDERVHVKMRNERVLRGKLHAYD-QHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL   91 (101)
Q Consensus        20 ~~l~k~V~V~l~~gr~i~G~L~~~D-~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~   91 (101)
                      .++|+++.+.-+.+-.|.|+|..+| +-.-+.|+||..+-++-.+..  .. .......-+..++.||+.|--
T Consensus         3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~--~~-~ipp~~~vyd~IvFrgsDIkD   72 (74)
T cd01736           3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTD--GP-EIPPSDEVYDYIVFRGSDIKD   72 (74)
T ss_pred             cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCC--CC-ccCCCCcceeEEEEcCCcccc
Confidence            5799999999999999999999999 455577999988766532111  01 112245567789999988753

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.

>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=96.60  E-value=0.013  Score=32.85  Aligned_cols=33  Identities=15%  Similarity=0.291  Sum_probs=29.0

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEEcCCCceEecceE
Q psy3154          22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVE   55 (101)
Q Consensus        22 l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~   55 (101)
                      +|++|++.+ ++..+.|+..++|....|+++...
T Consensus         2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~   34 (48)
T PF02237_consen    2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRTED   34 (48)
T ss_dssp             TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETT
T ss_pred             CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECC
Confidence            789999999 667779999999999999997643

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 ....

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

Probab=96.57  E-value=0.0049  Score=43.59  Aligned_cols=66  Identities=24%  Similarity=0.366  Sum_probs=44.2

Q ss_pred             cCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEc-CCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeE
Q psy3154          11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYD-QHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGV   89 (101)
Q Consensus        11 ~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D-~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I   89 (101)
                      ..+|+.+... ++|.|+|.+.| +++.|.|.++| -.-|+||-+..|       +          ..+  ..-+|.|.+|
T Consensus         6 ~~~p~~~~~y-v~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e-------~----------~~~--sv~~I~ghaV   64 (166)
T PF06372_consen    6 KKSPLEWQDY-VGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE-------D----------GKR--SVKVIMGHAV   64 (166)
T ss_dssp             HS-HHHHHCT-TT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T-------T----------S-E--EEEEE-GGGE
T ss_pred             hCCHHHHHHh-hCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc-------C----------Cce--eEEEEEccce
Confidence            3567777665 99999999999 99999999999 677888876433       1          112  2467889999


Q ss_pred             EEEecCCC
Q psy3154          90 ILVSPPNR   97 (101)
Q Consensus        90 v~I~~~~~   97 (101)
                      -.|...+.
T Consensus        65 k~vevl~~   72 (166)
T PF06372_consen   65 KSVEVLSE   72 (166)
T ss_dssp             EEEEEEE-
T ss_pred             EEEEEccC
Confidence            88877654

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.

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

Probab=96.47  E-value=0.022  Score=35.79  Aligned_cols=65  Identities=17%  Similarity=0.215  Sum_probs=48.2

Q ss_pred             ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEc-CCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154          13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYD-QHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL   91 (101)
Q Consensus        13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D-~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~   91 (101)
                      ..+.+|....|++|.+.|-++.++.|++.|.| ...|+..++-.   +     +          -..++..++|.+.|++
T Consensus        14 rfLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~---T-----P----------lGv~~eAlLR~~DVi~   75 (80)
T PF11095_consen   14 RFLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ---T-----P----------LGVQPEALLRCSDVIS   75 (80)
T ss_dssp             HHHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE---T-----T----------TTEEEEEEEEGGGEEE
T ss_pred             HHHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC---C-----C----------cccChhheeecCCEEE
Confidence            45677888889999999999999999999999 66677766532   1     1          1236789999999999


Q ss_pred             EecC
Q psy3154          92 VSPP   95 (101)
Q Consensus        92 I~~~   95 (101)
                      ++..
T Consensus        76 ~~f~   79 (80)
T PF11095_consen   76 ISFD   79 (80)
T ss_dssp             EEE-
T ss_pred             EEec
Confidence            8754

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.

>TIGR02383 Hfq RNA chaperone Hfq

Probab=96.29  E-value=0.015  Score=34.79  Aligned_cols=32  Identities=19%  Similarity=0.238  Sum_probs=27.3

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEEcCCCceEecc
Q psy3154          22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGD   53 (101)
Q Consensus        22 l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~   53 (101)
                      -+.+|.|-|.+|-.+.|.+.+||+|+=++-.+
T Consensus        14 ~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~   45 (61)
T TIGR02383        14 ERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ   45 (61)
T ss_pred             cCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence            45799999999999999999999999555444

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.

>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=96.25  E-value=0.015  Score=34.69  Aligned_cols=32  Identities=19%  Similarity=0.329  Sum_probs=27.1

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEEcCCCceEecc
Q psy3154          22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGD   53 (101)
Q Consensus        22 l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~   53 (101)
                      -..+|.|-|.+|-.+.|.+.+||+|+=++-.+
T Consensus        10 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   41 (61)
T cd01716          10 EKIPVTIYLVNGVQLKGQIESFDNFTVLLESD   41 (61)
T ss_pred             cCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence            34699999999999999999999999555444

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.

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

Probab=96.10  E-value=0.026  Score=35.12  Aligned_cols=43  Identities=21%  Similarity=0.439  Sum_probs=31.6

Q ss_pred             cccCCh-HHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecc
Q psy3154           9 ISVKEP-LDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGD   53 (101)
Q Consensus         9 ~~~~~P-l~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~   53 (101)
                      .+.+.| +.-+++ -+.+|.|-|.||-.+.|.+++||+|. +.|++
T Consensus         5 ~nlQD~fLn~~Rk-~~i~VtIfLvNG~~L~G~V~sfD~f~-VlL~~   48 (77)
T COG1923           5 QNLQDPFLNALRK-EKIPVTIFLVNGFKLQGQVESFDNFV-VLLKN   48 (77)
T ss_pred             cccchHHHHHHHh-cCCeEEEEEEcCEEEEEEEEeeeeEE-EEEEc
Confidence            344444 333333 55799999999999999999999998 44444

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=95.89  E-value=0.026  Score=35.39  Aligned_cols=33  Identities=15%  Similarity=0.257  Sum_probs=28.2

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEEcCCCceEecce
Q psy3154          22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDV   54 (101)
Q Consensus        22 l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~   54 (101)
                      -+.+|.|-|.+|-.+.|.+.|||+|+=++-.+.
T Consensus        18 ~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g   50 (79)
T PRK00395         18 ERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG   50 (79)
T ss_pred             cCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence            457999999999999999999999996665454

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

Probab=95.85  E-value=0.029  Score=33.52  Aligned_cols=36  Identities=22%  Similarity=0.324  Sum_probs=30.6

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEE
Q psy3154          21 SLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEE   56 (101)
Q Consensus        21 ~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E   56 (101)
                      ++|..|++++..|.+|.|.+.+||.-.++++-.|.+
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            478999999999999999999999888877555443

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.

>PRK14638 hypothetical protein; Provisional

Probab=94.24  E-value=0.11  Score=36.06  Aligned_cols=33  Identities=3%  Similarity=0.206  Sum_probs=27.2

Q ss_pred             HHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEec
Q psy3154          19 RLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLG   52 (101)
Q Consensus        19 ~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~   52 (101)
                      .+++|++|.|++.+++.++|+|.++|.- ++.|.
T Consensus        96 ~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~  128 (150)
T PRK14638         96 VRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS  128 (150)
T ss_pred             HHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            3458999999999999999999999964 35443

>PRK14639 hypothetical protein; Provisional

Probab=93.29  E-value=0.2  Score=34.27  Aligned_cols=33  Identities=24%  Similarity=0.423  Sum_probs=27.6

Q ss_pred             HHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEe
Q psy3154          18 IRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVL   51 (101)
Q Consensus        18 L~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL   51 (101)
                      .++++|+.|.|++.+++.+.|+|.++|.- ++.|
T Consensus        83 f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l  115 (140)
T PRK14639         83 FAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL  115 (140)
T ss_pred             HHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence            34558999999999999999999999984 4555

>PRK02001 hypothetical protein; Validated

Probab=93.09  E-value=0.22  Score=34.67  Aligned_cols=31  Identities=19%  Similarity=0.462  Sum_probs=26.5

Q ss_pred             HhcCCEEEEEEcCCeEEEEEEEEEcCCCceEe
Q psy3154          20 LSLDERVHVKMRNERVLRGKLHAYDQHLNMVL   51 (101)
Q Consensus        20 ~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL   51 (101)
                      +++|+.|+|++.+++.+.|+|.++|.. ++.|
T Consensus        87 r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l  117 (152)
T PRK02001         87 KNIGRELEVLTKNGKKIEGELKSADEN-DITL  117 (152)
T ss_pred             HhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence            458999999999999999999999975 3444

>KOG1073|consensus

Probab=93.03  E-value=0.26  Score=38.75  Aligned_cols=76  Identities=13%  Similarity=0.126  Sum_probs=57.2

Q ss_pred             HHHhcCCEEEEEEcCCeEEEEEEEEEc-CCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEecCC
Q psy3154          18 IRLSLDERVHVKMRNERVLRGKLHAYD-QHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPN   96 (101)
Q Consensus        18 L~~~l~k~V~V~l~~gr~i~G~L~~~D-~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~~   96 (101)
                      ...+||++|.++=+..-.|+|+|.-+| +-.-|-|.+|..+-++-+++.  ........+ -+.-++.||+.|--+...|
T Consensus         4 ~t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~--~pq~p~~~k-Vy~YIlFRGSDIKDL~V~~   80 (361)
T KOG1073|consen    4 VTSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTD--GPQVPPDDK-VYDYILFRGSDIKDLIVQE   80 (361)
T ss_pred             ccccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCC--CCcCCCCcc-ceeeEEecCcccceeeecc
Confidence            346799999999999999999999999 788899999987766533221  111111122 6888999999999777766

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

Probab=92.98  E-value=1  Score=27.23  Aligned_cols=58  Identities=24%  Similarity=0.375  Sum_probs=41.5

Q ss_pred             cCCh--HHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCe
Q psy3154          11 VKEP--LDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDG   88 (101)
Q Consensus        11 ~~~P--l~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~   88 (101)
                      .-+|  .+.|++++|++|.|.+..|+. +|+|.+.-.-. ++|+..                        -...|||=..
T Consensus         7 ~vdpyvyq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDh-Ivl~~~------------------------~~~~~IR~~~   60 (66)
T PF10842_consen    7 LVDPYVYQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDH-IVLEEN------------------------GTPFFIRIAQ   60 (66)
T ss_pred             ccCHHHHHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCE-EEEEeC------------------------CcEEEEEeee
Confidence            3455  688999999999999977765 99999876322 233321                        2357888888


Q ss_pred             EEEEec
Q psy3154          89 VILVSP   94 (101)
Q Consensus        89 Iv~I~~   94 (101)
                      |++|.+
T Consensus        61 IV~v~p   66 (66)
T PF10842_consen   61 IVWVMP   66 (66)
T ss_pred             EEEEcC
Confidence            888753

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=91.73  E-value=0.48  Score=33.53  Aligned_cols=33  Identities=24%  Similarity=0.297  Sum_probs=27.9

Q ss_pred             CCEEEEEEcCCeEEEEEEEEEcCCCceEecceE
Q psy3154          23 DERVHVKMRNERVLRGKLHAYDQHLNMVLGDVE   55 (101)
Q Consensus        23 ~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~   55 (101)
                      ..+|.|-|.+|-.+.|.+.+||+|.=|+-.+..
T Consensus       104 k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~gk  136 (165)
T PRK14091        104 GEPVTMFLVNGVMLQGEIAAFDLFCMLLERDGY  136 (165)
T ss_pred             CCcEEEEEecCcEEEEEEEEEcceEEEEEeCCc
Confidence            469999999999999999999999966555543

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=90.90  E-value=0.65  Score=32.86  Aligned_cols=32  Identities=16%  Similarity=0.160  Sum_probs=27.0

Q ss_pred             CCEEEEEEcCCeEEEEEEEEEcCCCceEecce
Q psy3154          23 DERVHVKMRNERVLRGKLHAYDQHLNMVLGDV   54 (101)
Q Consensus        23 ~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~   54 (101)
                      ..+|.|-|.+|-.+.|++.+||+|.=|+-.+.
T Consensus        24 k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g   55 (165)
T PRK14091         24 KTPVTMFLVKGVKLQGIITWFDNFSILLRRDG   55 (165)
T ss_pred             CCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            36899999999999999999999985555454

>PRK14644 hypothetical protein; Provisional

Probab=90.71  E-value=0.72  Score=31.45  Aligned_cols=34  Identities=18%  Similarity=0.372  Sum_probs=27.9

Q ss_pred             HHHhcCCEEEEEEcCC----eEEEEEEEEEcCCCceEec
Q psy3154          18 IRLSLDERVHVKMRNE----RVLRGKLHAYDQHLNMVLG   52 (101)
Q Consensus        18 L~~~l~k~V~V~l~~g----r~i~G~L~~~D~~mNlvL~   52 (101)
                      +.+++|+.|.|+|++.    +.+.|+|.++|.. ++.|.
T Consensus        80 f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~  117 (136)
T PRK14644         80 LENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK  117 (136)
T ss_pred             HHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            5667999999999876    8999999999974 45554

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

Probab=90.12  E-value=0.94  Score=30.59  Aligned_cols=42  Identities=24%  Similarity=0.415  Sum_probs=27.1

Q ss_pred             cccCChH---HHHHHhcCCEEEEEEc----CCeEEEEEEEEEcCCCceEe
Q psy3154           9 ISVKEPL---DLIRLSLDERVHVKMR----NERVLRGKLHAYDQHLNMVL   51 (101)
Q Consensus         9 ~~~~~Pl---~lL~~~l~k~V~V~l~----~gr~i~G~L~~~D~~mNlvL   51 (101)
                      +..+.|+   .-+..++|+.|.|+++    +.+.+.|+|.++|. -.++|
T Consensus        70 PG~~r~L~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l  118 (141)
T PF02576_consen   70 PGIDRPLKSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL  118 (141)
T ss_dssp             -SSSS--SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred             CCCCCcCCCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence            4455665   4456679999999994    45799999999998 33444

; PDB: 1IB8_A.

>PRK14640 hypothetical protein; Provisional

Probab=89.92  E-value=0.82  Score=31.63  Aligned_cols=33  Identities=18%  Similarity=0.318  Sum_probs=26.2

Q ss_pred             HHhcCCEEEEEE----cCCeEEEEEEEEEcCCCceEec
Q psy3154          19 RLSLDERVHVKM----RNERVLRGKLHAYDQHLNMVLG   52 (101)
Q Consensus        19 ~~~l~k~V~V~l----~~gr~i~G~L~~~D~~mNlvL~   52 (101)
                      .+++|+.|.|++    .+++.+.|+|.++|.. ++.|.
T Consensus        93 ~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~  129 (152)
T PRK14640         93 EKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT  129 (152)
T ss_pred             HHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence            355999999999    5669999999999974 35554

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

Probab=89.58  E-value=1.1  Score=27.75  Aligned_cols=32  Identities=25%  Similarity=0.444  Sum_probs=25.2

Q ss_pred             HHhcCCEEEEEEc---CC-eEEEEEEEEEcCCCceEe
Q psy3154          19 RLSLDERVHVKMR---NE-RVLRGKLHAYDQHLNMVL   51 (101)
Q Consensus        19 ~~~l~k~V~V~l~---~g-r~i~G~L~~~D~~mNlvL   51 (101)
                      ..++|+.|.|+++   +| +.+.|+|.++|.. ++.|
T Consensus        21 ~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l   56 (83)
T cd01734          21 ERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL   56 (83)
T ss_pred             HHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence            3458999999997   55 6899999999984 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.

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

Probab=89.30  E-value=0.99  Score=31.66  Aligned_cols=39  Identities=21%  Similarity=0.180  Sum_probs=32.5

Q ss_pred             HHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceE
Q psy3154          16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVE   55 (101)
Q Consensus        16 ~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~   55 (101)
                      .+++. -+-+|+|.+.||..|.|.+.+|+..-|.+|..+.
T Consensus        23 ~f~r~-~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~   61 (165)
T PF03614_consen   23 QFWRF-NDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP   61 (165)
T ss_pred             HHHHh-cCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence            34433 4569999999999999999999999999987653

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

>PRK14633 hypothetical protein; Provisional

Probab=89.15  E-value=1  Score=31.12  Aligned_cols=33  Identities=15%  Similarity=0.253  Sum_probs=26.0

Q ss_pred             HHhcCCEEEEEEc----CCeEEEEEEEEEcCCCceEec
Q psy3154          19 RLSLDERVHVKMR----NERVLRGKLHAYDQHLNMVLG   52 (101)
Q Consensus        19 ~~~l~k~V~V~l~----~gr~i~G~L~~~D~~mNlvL~   52 (101)
                      .+++|++|.|+++    +++.+.|+|.++|.. ++.|.
T Consensus        90 ~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~  126 (150)
T PRK14633         90 QALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN  126 (150)
T ss_pred             HHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence            4558999999983    568999999999985 45553

>PRK14642 hypothetical protein; Provisional

Probab=89.14  E-value=0.93  Score=32.91  Aligned_cols=27  Identities=19%  Similarity=0.364  Sum_probs=23.8

Q ss_pred             HhcCCEEEEEEc-------------CCeEEEEEEEEEcCC
Q psy3154          20 LSLDERVHVKMR-------------NERVLRGKLHAYDQH   46 (101)
Q Consensus        20 ~~l~k~V~V~l~-------------~gr~i~G~L~~~D~~   46 (101)
                      +++|+.|.|+|+             +.+.|.|+|.++|..
T Consensus        97 rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~  136 (197)
T PRK14642         97 RFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG  136 (197)
T ss_pred             HhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC
Confidence            448999999998             679999999999974

>PRK14636 hypothetical protein; Provisional

Probab=88.56  E-value=1  Score=31.95  Aligned_cols=33  Identities=12%  Similarity=0.292  Sum_probs=25.8

Q ss_pred             HHhcCCEEEEEEc---CC-eEEEEEEEEEcCCCceEec
Q psy3154          19 RLSLDERVHVKMR---NE-RVLRGKLHAYDQHLNMVLG   52 (101)
Q Consensus        19 ~~~l~k~V~V~l~---~g-r~i~G~L~~~D~~mNlvL~   52 (101)
                      .+++|++|.|+|+   +| +.++|+|.++|.. ++.|.
T Consensus        94 ~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l~  130 (176)
T PRK14636         94 ADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTIA  130 (176)
T ss_pred             HHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEEE
Confidence            3559999999997   55 6999999999874 35543

>PRK14645 hypothetical protein; Provisional

Probab=87.66  E-value=2  Score=29.92  Aligned_cols=32  Identities=9%  Similarity=0.125  Sum_probs=25.3

Q ss_pred             HHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEec
Q psy3154          19 RLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLG   52 (101)
Q Consensus        19 ~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~   52 (101)
                      .+++|++|.|++ +++.+.|+|.++|... +.|.
T Consensus        98 ~r~~G~~v~v~~-~~k~~~G~L~~~~d~~-i~l~  129 (154)
T PRK14645         98 ERFAGLKAKVRG-PGENFTGRIKAVSGDQ-VTFD  129 (154)
T ss_pred             HHhCCCEEEEEc-CCeEEEEEEEEEeCCE-EEEE
Confidence            345899999986 7899999999999753 5443

>PRK14632 hypothetical protein; Provisional

Probab=87.59  E-value=1.4  Score=31.20  Aligned_cols=33  Identities=21%  Similarity=0.398  Sum_probs=25.9

Q ss_pred             HHhcCCEEEEEEcC-------CeEEEEEEEEEcCCCceEec
Q psy3154          19 RLSLDERVHVKMRN-------ERVLRGKLHAYDQHLNMVLG   52 (101)
Q Consensus        19 ~~~l~k~V~V~l~~-------gr~i~G~L~~~D~~mNlvL~   52 (101)
                      ++++|+.|.|++.+       .+.+.|+|.++|.- ++.|.
T Consensus        94 ~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~  133 (172)
T PRK14632         94 SPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR  133 (172)
T ss_pred             HHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence            45589999999975       57999999999864 45443

>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=87.40  E-value=2  Score=29.97  Aligned_cols=43  Identities=26%  Similarity=0.410  Sum_probs=32.3

Q ss_pred             cccCChHH---HHHHhcCCEEEEEE----cCCeEEEEEEEEEcCCCceEec
Q psy3154           9 ISVKEPLD---LIRLSLDERVHVKM----RNERVLRGKLHAYDQHLNMVLG   52 (101)
Q Consensus         9 ~~~~~Pl~---lL~~~l~k~V~V~l----~~gr~i~G~L~~~D~~mNlvL~   52 (101)
                      +..+.|+-   -...++|+.|.|+|    .+++.+.|+|.++|.-+ +++.
T Consensus        82 PGldRpL~~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~~  131 (153)
T COG0779          82 PGLDRPLKTAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTLE  131 (153)
T ss_pred             CCCCCCcCCHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEEE
Confidence            34455543   34456899999999    78899999999999887 4443

>PRK14643 hypothetical protein; Provisional

Probab=87.26  E-value=1.8  Score=30.42  Aligned_cols=30  Identities=20%  Similarity=0.383  Sum_probs=24.8

Q ss_pred             HHHhcCCEEEEEEcC----CeEEEEEEEEEcCCC
Q psy3154          18 IRLSLDERVHVKMRN----ERVLRGKLHAYDQHL   47 (101)
Q Consensus        18 L~~~l~k~V~V~l~~----gr~i~G~L~~~D~~m   47 (101)
                      +..++|++|.|+|+.    .+.+.|+|.++|...
T Consensus        99 f~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~  132 (164)
T PRK14643         99 LVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNT  132 (164)
T ss_pred             HHHhcCCeEEEEEecccCCceEEEEEEEEEeCCc
Confidence            445699999999965    589999999999653

>PRK14634 hypothetical protein; Provisional

Probab=86.44  E-value=1.8  Score=30.06  Aligned_cols=33  Identities=21%  Similarity=0.230  Sum_probs=25.3

Q ss_pred             HHhcCCEEEEEEcC----CeEEEEEEEEEcCCCceEec
Q psy3154          19 RLSLDERVHVKMRN----ERVLRGKLHAYDQHLNMVLG   52 (101)
Q Consensus        19 ~~~l~k~V~V~l~~----gr~i~G~L~~~D~~mNlvL~   52 (101)
                      .+++|++|.|++.+    .+.|.|+|.++|.-. +.|.
T Consensus        96 ~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~~-v~l~  132 (155)
T PRK14634         96 QTFRGFPVEVSHRDDDGSEQRLEGLLLERNEDH-LQIN  132 (155)
T ss_pred             HHhCCCeEEEEEecCCCCeEEEEEEEEEEeCCE-EEEE
Confidence            34589999999963    279999999999743 5443

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=86.37  E-value=1.9  Score=29.70  Aligned_cols=29  Identities=28%  Similarity=0.401  Sum_probs=24.3

Q ss_pred             HHHhcCCEEEEEE----cCCeEEEEEEEEEcCC
Q psy3154          18 IRLSLDERVHVKM----RNERVLRGKLHAYDQH   46 (101)
Q Consensus        18 L~~~l~k~V~V~l----~~gr~i~G~L~~~D~~   46 (101)
                      +.+++|+.|.|++    .+++.+.|+|..+|..
T Consensus        93 f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~  125 (154)
T PRK00092         93 FRRFIGREVKVKLYEPIDGRKKFQGILLAVDGE  125 (154)
T ss_pred             HHHhCCCeEEEEEEcccCCceEEEEEEEEeeCC
Confidence            4455999999997    5678999999999973

>PRK14646 hypothetical protein; Provisional

Probab=85.79  E-value=2  Score=29.81  Aligned_cols=34  Identities=15%  Similarity=0.251  Sum_probs=25.9

Q ss_pred             HHHhcCCEEEEEEcCC----eEEEEEEEEEcCCCceEec
Q psy3154          18 IRLSLDERVHVKMRNE----RVLRGKLHAYDQHLNMVLG   52 (101)
Q Consensus        18 L~~~l~k~V~V~l~~g----r~i~G~L~~~D~~mNlvL~   52 (101)
                      ..+++|++|.|+|++.    +.+.|+|.++|.- ++.|.
T Consensus        95 f~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~  132 (155)
T PRK14646         95 FKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN  132 (155)
T ss_pred             HHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            3455999999999542    6889999999985 45553

>PRK14647 hypothetical protein; Provisional

Probab=85.15  E-value=2.2  Score=29.65  Aligned_cols=28  Identities=14%  Similarity=0.184  Sum_probs=23.2

Q ss_pred             HHhcCCEEEEEEc---------CCeEEEEEEEEEcCC
Q psy3154          19 RLSLDERVHVKMR---------NERVLRGKLHAYDQH   46 (101)
Q Consensus        19 ~~~l~k~V~V~l~---------~gr~i~G~L~~~D~~   46 (101)
                      .+++|+.|.|+++         +.+.+.|+|.++|..
T Consensus        95 ~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~  131 (159)
T PRK14647         95 ERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADG  131 (159)
T ss_pred             HHhCCcEEEEEEeccccccccCCceEEEEEEEeecCC
Confidence            3458999999995         358999999999963

>PRK14631 hypothetical protein; Provisional

Probab=85.08  E-value=2.1  Score=30.34  Aligned_cols=27  Identities=26%  Similarity=0.422  Sum_probs=22.9

Q ss_pred             HHHhcCCEEEEEEc----CCeEEEEEEEEEc
Q psy3154          18 IRLSLDERVHVKMR----NERVLRGKLHAYD   44 (101)
Q Consensus        18 L~~~l~k~V~V~l~----~gr~i~G~L~~~D   44 (101)
                      +.+++|+.|.|++.    +.+.|+|+|.++|
T Consensus       112 f~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~  142 (174)
T PRK14631        112 LQGYIGQQVALRLIAAVENRRKFQAKLLAVD  142 (174)
T ss_pred             HHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence            34559999999995    4589999999998

>PRK14641 hypothetical protein; Provisional

Probab=83.01  E-value=2.6  Score=29.87  Aligned_cols=26  Identities=19%  Similarity=0.322  Sum_probs=21.8

Q ss_pred             HHhcCCEEEEEEcC----CeEEEEEEEEEc
Q psy3154          19 RLSLDERVHVKMRN----ERVLRGKLHAYD   44 (101)
Q Consensus        19 ~~~l~k~V~V~l~~----gr~i~G~L~~~D   44 (101)
                      ++++|+.|.|+|.+    .+.+.|+|.++|
T Consensus       100 ~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~  129 (173)
T PRK14641        100 GRHVGRLLRVTYRDEEGSEHEVTGHLQEVS  129 (173)
T ss_pred             HHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence            34589999999975    468999999995

>PRK14637 hypothetical protein; Provisional

Probab=82.46  E-value=3  Score=28.89  Aligned_cols=33  Identities=21%  Similarity=0.242  Sum_probs=24.6

Q ss_pred             HHhcCCEEEEEEcCCeEE-EEEEEEEcCCCceEec
Q psy3154          19 RLSLDERVHVKMRNERVL-RGKLHAYDQHLNMVLG   52 (101)
Q Consensus        19 ~~~l~k~V~V~l~~gr~i-~G~L~~~D~~mNlvL~   52 (101)
                      .+++|+.|.|++.+.+.+ .|+|.++|.. ++.|.
T Consensus        94 ~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~  127 (151)
T PRK14637         94 SIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT  127 (151)
T ss_pred             HHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence            345899999999545566 7999999975 35444

>PRK06955 biotin--protein ligase; Provisional

Probab=82.39  E-value=3.2  Score=31.50  Aligned_cols=33  Identities=18%  Similarity=0.237  Sum_probs=28.1

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEEcCCCceEecc
Q psy3154          21 SLDERVHVKMRNERVLRGKLHAYDQHLNMVLGD   53 (101)
Q Consensus        21 ~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~   53 (101)
                      ++|++|+|...+++.+.|++.|+|....|+++.
T Consensus       247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~  279 (300)
T PRK06955        247 YAGREVVLLEDGAELARGVAHGIDETGQLLLDT  279 (300)
T ss_pred             cCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence            367899997667788999999999999999863

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

Probab=82.12  E-value=2.2  Score=23.60  Aligned_cols=23  Identities=30%  Similarity=0.482  Sum_probs=15.4

Q ss_pred             EEEEEEEEcCCCceEecceEEEE
Q psy3154          36 LRGKLHAYDQHLNMVLGDVEETV   58 (101)
Q Consensus        36 i~G~L~~~D~~mNlvL~~~~E~~   58 (101)
                      ..|++.|+|+.+.++|++...+.
T Consensus        10 ~tGtFlGvDE~FGmLLr~~~~T~   32 (42)
T PF14563_consen   10 LTGTFLGVDEDFGMLLRDDDTTH   32 (42)
T ss_dssp             EEEEEEEE-TT--EEEE-SS-EE
T ss_pred             cceeEEeeccccceEEEeCCccE
Confidence            67999999999999999876543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	101
4emg_A	93	Crystal Structure Of Splsm3 Length = 93		2e-16
3bw1_A	96	Crystal Structure Of Homomeric Yeast Lsm3 Exhibitin		4e-11
1i81_A	83	Crystal Structure Of A Heptameric Lsm Protein From		2e-04
1th7_A	81	Crystal Structure Of An Archaeal Sm Protein From Su		3e-04
1i5l_A	77	Crystal Structure Of An Sm-Like Protein (Af-Sm1) Fr		4e-04

>pdb|4EMG|A Chain A, Crystal Structure Of Splsm3 Length = 93

Iteration: 1
 Score = 80.9 bits (198), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/86 (47%), Positives = 51/86 (59%)
Query: 10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGXXXXXXXXXXXXXXXXX 69
          +V EPLDL+RLSLDE V+VK+R +R L G+LHAYD+HLN VLG                 
Sbjct: 6  AVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNXVLGDAEEIVTIFDDEETDKD 65
Query: 70 XXXXXXXRSIPMLFVRGDGVILVSPP 95
                 +    LFVRGD VIL++PP
Sbjct: 66 KALKTIRKHYEXLFVRGDSVILIAPP 91

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

Iteration: 1
 Score = 62.8 bits (151), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 32/86 (37%), Positives = 46/86 (53%), Gaps = 6/86 (6%)
Query: 11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGXXXXXXXXXXXXXXXXXX 70
          ++ PLDL++L+LDERV++K+R  R L G L A+D H N+VL                   
Sbjct: 8  METPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLS------DAVETIYQLNNE 61
Query: 71 XXXXXXRSIPMLFVRGDGVILVSPPN 96
                R   M+F+RGD V L+S P+
Sbjct: 62 ELSESERRCEMVFIRGDTVTLISTPS 87

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 13/86 (15%)
Query: 9  ISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGXXXXXXXXXXXXXXXX 68
          ++V+ PLD +  SL+  V +K++ +R  RG L ++D H+N+VL                 
Sbjct: 11 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLN-------------DAE 57
Query: 69 XXXXXXXXRSIPMLFVRGDGVILVSP 94
                  R +  + +RGD ++ +SP
Sbjct: 58 ELEDGEVTRRLGTVLIRGDNIVYISP 83

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 13/74 (17%)
Query: 21 SLDERVHVKMRNERVLRGKLHAYDQHLNMVLGXXXXXXXXXXXXXXXXXXXXXXXXRSIP 80
          SL+  V VK++  + +RG L +YDQH+N+VL                         + + 
Sbjct: 17 SLNNLVLVKLKGNKEVRGMLRSYDQHMNLVL-------------SDSEEIQSDGSGKKLG 63
Query: 81 MLFVRGDGVILVSP 94
           + +RGD VIL+SP
Sbjct: 64 TIVIRGDNVILISP 77

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 13/81 (16%)
Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGXXXXXXXXXXXXXXXXXXXXX 73
          PLD++  SL   V V+++  R  RG L  YD H+N+VL                      
Sbjct: 5  PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVL-------------LDAEEIQNG 51
Query: 74 XXXRSIPMLFVRGDGVILVSP 94
             R +  + +RGD V+ VSP
Sbjct: 52 EVVRKVGSVVIRGDTVVFVSP 72

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	101
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	8e-35
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	4e-30
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	5e-28
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	2e-27
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	7e-27
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	3e-23
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	8e-23
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	2e-22
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	4e-21
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	5e-20
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	2e-19
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	1e-17
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	2e-17
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	4e-17
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	6e-17
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	1e-13
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	7e-13
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	2e-11
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	2e-09
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	6e-09
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-08
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	4e-07
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	3e-06

>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 =  113 bits (285), Expect = 8e-35
 Identities = 51/89 (57%), Positives = 66/89 (74%)

Query: 7  PTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEE 66
             +V EPLDL+RLSLDE V+VK+R +R L G+LHAYD+HLNMVLGD EE VT  + +E 
Sbjct: 3  SAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEET 62

Query: 67 TYEEIYKTTKRSIPMLFVRGDGVILVSPP 95
            ++  KT ++   MLFVRGD VIL++PP
Sbjct: 63 DKDKALKTIRKHYEMLFVRGDSVILIAPP 91

>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 =  102 bits (256), Expect = 4e-30
 Identities = 20/93 (21%), Positives = 48/93 (51%), Gaps = 2/93 (2%)

Query: 10  SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEET-- 67
           ++  PL LI   +  R++V M+ ++   G L  +D+++NMVL DV+E     + ++ +  
Sbjct: 25  NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGG 84

Query: 68  YEEIYKTTKRSIPMLFVRGDGVILVSPPNRTPA 100
            +++ +     +  + + G+ V ++ P     +
Sbjct: 85  NKKLKRVMVNRLETILLSGNNVAMLVPGGDPDS 117

>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 = 96.7 bits (241), Expect = 5e-28
 Identities = 36/89 (40%), Positives = 55/89 (61%), Gaps = 6/89 (6%)

Query: 11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEE 70
          ++ PLDL++L+LDERV++K+R  R L G L A+D H N+VL D  ET+  +  +E +   
Sbjct: 8  METPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSES- 66

Query: 71 IYKTTKRSIPMLFVRGDGVILVSPPNRTP 99
               +R   M+F+RGD V L+S P+   
Sbjct: 67 -----ERRCEMVFIRGDTVTLISTPSEDD 90

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

 Score = 95.8 bits (238), Expect = 2e-27
 Identities = 29/88 (32%), Positives = 48/88 (54%), Gaps = 3/88 (3%)

Query: 11  VKEPLDLIRLSL--DERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETY 68
              PL ++  S+  + +V +  RN + L G++ A+D+H NMVL +V+E  T V    +  
Sbjct: 25  NTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGK 84

Query: 69  EEIYKTTK-RSIPMLFVRGDGVILVSPP 95
           ++     K R I  +F+RGD VI+V   
Sbjct: 85  KKSKPVNKDRYISKMFLRGDSVIVVLRN 112

>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 = 93.2 bits (232), Expect = 7e-27
 Identities = 27/94 (28%), Positives = 47/94 (50%), Gaps = 13/94 (13%)

Query: 1  MEDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTT 60
          + D     ++V+ PLD +  SL+  V +K++ +R  RG L ++D H+N+VL D EE    
Sbjct: 3  VIDVSSQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELED- 61

Query: 61 VEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP 94
                          R +  + +RGD ++ +SP
Sbjct: 62 ------------GEVTRRLGTVLIRGDNIVYISP 83

>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 = 84.3 bits (209), Expect = 3e-23
 Identities = 26/88 (29%), Positives = 44/88 (50%), Gaps = 13/88 (14%)

Query: 11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEE 70
           +    ++  SL+  V VK++  + +RG L +YDQH+N+VL D EE  +           
Sbjct: 7  AETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGS-------- 58

Query: 71 IYKTTKRSIPMLFVRGDGVILVSPPNRT 98
                + +  + +RGD VIL+SP   +
Sbjct: 59 -----GKKLGTIVIRGDNVILISPLQTS 81

>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 = 82.7 bits (205), Expect = 8e-23
 Identities = 28/84 (33%), Positives = 39/84 (46%), Gaps = 13/84 (15%)

Query: 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEI 71
            PLD++  SL   V V+++  R  RG L  YD H+N+VL D EE               
Sbjct: 3  PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNG----------- 51

Query: 72 YKTTKRSIPMLFVRGDGVILVSPP 95
               R +  + +RGD V+ VSP 
Sbjct: 52 --EVVRKVGSVVIRGDTVVFVSPA 73

>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 = 81.6 bits (202), Expect = 2e-22
 Identities = 27/84 (32%), Positives = 39/84 (46%), Gaps = 13/84 (15%)

Query: 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEI 71
          + PLD+I  SLD+ V V ++     RG+L  YD HLN+VL D E                
Sbjct: 3  ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQD------------ 50

Query: 72 YKTTKRSIPMLFVRGDGVILVSPP 95
               +    + +RGD V+ +SP 
Sbjct: 51 -GEVVKRYGKIVIRGDNVLAISPT 73

>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 = 79.1 bits (195), Expect = 4e-21
 Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 12/97 (12%)

Query: 2  EDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTV 61
             Q P      PL+LI   +   + V M++ER   G L  +D ++N+VL DV E  T  
Sbjct: 9  HHSQDPMSMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVT 68

Query: 62 EIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNRT 98
                              + + G+G+ ++ P  + 
Sbjct: 69 G------------VTEKHSEMLLNGNGMCMLIPGGKP 93

>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 = 76.9 bits (189), Expect = 5e-20
 Identities = 26/83 (31%), Positives = 42/83 (50%), Gaps = 7/83 (8%)

Query: 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEI 71
          +  LDL R   D+R+       R + G L  +DQ +N+VL DVEE +   E  + T    
Sbjct: 23 ESILDLSRY-QDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGA-- 79

Query: 72 YKTTKRSIPMLFVRGDGVILVSP 94
               R + ++ VRG  ++L++P
Sbjct: 80 ----IRKLGLVVVRGTTLVLIAP 98

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

 Score = 74.7 bits (184), Expect = 2e-19
 Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 16/94 (17%)

Query: 1  MEDEQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTT 60
          M  +   +         ++ S+ ++V VK+R+   +RG L ++DQH+N++L D EE +  
Sbjct: 1  MASDI--SKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIID- 57

Query: 61 VEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP 94
                               + VRG+ V+ +SP
Sbjct: 58 -------------GNVYKRGTMVVRGENVLFISP 78

>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 = 70.3 bits (172), Expect = 1e-17
 Identities = 20/93 (21%), Positives = 50/93 (53%), Gaps = 8/93 (8%)

Query: 10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYE 69
          +V +   +++  +D R+   +++ R+  G   A+D+H+N++L D +E      I  +  +
Sbjct: 2  TVGKSSKMLQH-IDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRK---IKPKNSK 57

Query: 70 EIYKTTKRSIPMLFVRGDGVILVS----PPNRT 98
          +  +  KR + ++ +RG+ ++ ++    PP  T
Sbjct: 58 QAEREEKRVLGLVLLRGENLVSMTVEGPPPKDT 90

>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 = 68.9 bits (169), Expect = 2e-17
 Identities = 19/86 (22%), Positives = 40/86 (46%), Gaps = 14/86 (16%)

Query: 10 SVKEPLDLIRLSLDERVHVKMRNERV-LRGKLHAYDQHLNMVLGDVEETVTTVEIDEETY 68
          ++  P  +++  + + + V+M+ E   L GKL   D ++N+ L +  E            
Sbjct: 2  AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMEC----------- 50

Query: 69 EEIYKTTKRSIPMLFVRGDGVILVSP 94
              +   RS+  + +RG+ V+L+ P
Sbjct: 51 --KGEEKVRSLGEIVLRGNNVVLIQP 74

>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 = 68.5 bits (168), Expect = 4e-17
 Identities = 18/85 (21%), Positives = 41/85 (48%), Gaps = 14/85 (16%)

Query: 10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYE 69
          S   P +L +  +D+++ +K+   R ++G L  +D  +N+V+             +E  E
Sbjct: 2  SKAHPPELKKF-MDKKLSLKLNGGRHVQGILRGFDPFMNLVI-------------DECVE 47

Query: 70 EIYKTTKRSIPMLFVRGDGVILVSP 94
                + +I M+ +RG+ +I++  
Sbjct: 48 MATSGQQNNIGMVVIRGNSIIMLEA 72

>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 = 67.7 bits (166), Expect = 6e-17
 Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 13/84 (15%)

Query: 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEI 71
            P + +   + ++V +++ +    +G L   D ++N+ L   EE V             
Sbjct: 3  SSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVN------------ 50

Query: 72 YKTTKRSIPMLFVRGDGVILVSPP 95
                     F+RG+ V+ VS  
Sbjct: 51 -GKKTNVYGDAFIRGNNVLYVSAL 73

>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 = 59.8 bits (145), Expect = 1e-13
 Identities = 14/86 (16%), Positives = 30/86 (34%), Gaps = 13/86 (15%)

Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYK 73
          P   +     + V VK++     +G L + D ++NM L + EE +               
Sbjct: 7  PKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDG------------- 53

Query: 74 TTKRSIPMLFVRGDGVILVSPPNRTP 99
               +  + +R + V+ +       
Sbjct: 54 ALSGHLGEVLIRCNNVLYIRGVEEEE 79

>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 = 57.9 bits (140), Expect = 7e-13
 Identities = 17/85 (20%), Positives = 39/85 (45%), Gaps = 16/85 (18%)

Query: 14 PLDLIRLSLDER----VHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYE 69
          P++LI   L  R    V +  +    + G +  +D+++N+VL D EE  +  +       
Sbjct: 17 PINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTK------- 69

Query: 70 EIYKTTKRSIPMLFVRGDGVILVSP 94
               +++ +  + ++GD + L+  
Sbjct: 70 -----SRKQLGRIMLKGDNITLLQS 89

>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 = 54.5 bits (131), Expect = 2e-11
 Identities = 19/95 (20%), Positives = 39/95 (41%), Gaps = 14/95 (14%)

Query: 2  EDEQIPTISVKEPLDLIRLSLDERVHVKMR-NERVLRGKLHAYDQHLNMVLGDVEETVTT 60
          E   I  +    P   ++  ++ RV VK++ N    RG L + D + N+ L + EE    
Sbjct: 10 ESSDISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEF--- 66

Query: 61 VEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPP 95
            +           +  ++  +F+R + V+ +   
Sbjct: 67 --VAGV--------SHGTLGEIFIRCNNVLYIREL 91

>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 = 49.7 bits (119), Expect = 2e-09
 Identities = 15/84 (17%), Positives = 33/84 (39%), Gaps = 12/84 (14%)

Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYK 73
          PL L+  +    + V+++N     G L   D ++N+ L +V  T+               
Sbjct: 17 PLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPD------------G 64

Query: 74 TTKRSIPMLFVRGDGVILVSPPNR 97
               +P  ++RG+ +  +   + 
Sbjct: 65 DKFFRLPECYIRGNNIKYLRIQDE 88

>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 = 48.9 bits (116), Expect = 6e-09
 Identities = 13/87 (14%), Positives = 32/87 (36%), Gaps = 13/87 (14%)

Query: 10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYE 69
          S+  P+ ++  +    V  +     V RGKL   + ++N  + ++  T            
Sbjct: 2  SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGR------- 54

Query: 70 EIYKTTKRSIPMLFVRGDGVILVSPPN 96
                   +  +++RG  +  +  P+
Sbjct: 55 ------VAQLEQVYIRGSKIRFLILPD 75

>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 = 48.9 bits (116), Expect = 2e-08
 Identities = 18/81 (22%), Positives = 41/81 (50%), Gaps = 7/81 (8%)

Query: 22  LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEE--TVTTVEIDEETYEEIYKTTKRSI 79
           +D R+   +++ R+  G   A+D+H+N++L D +E   +      +   EE     KR +
Sbjct: 13  IDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREE-----KRVL 67

Query: 80  PMLFVRGDGVILVSPPNRTPA 100
            ++ +RG+ ++ ++     P 
Sbjct: 68  GLVLLRGENLVSMTVEGPPPK 88

>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 = 42.8 bits (101), Expect = 4e-07
 Identities = 13/87 (14%), Positives = 32/87 (36%), Gaps = 13/87 (14%)

Query: 10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYE 69
          S+  P+ ++  +    V  +     V RGKL   + ++N  + ++  T            
Sbjct: 2  SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGR------- 54

Query: 70 EIYKTTKRSIPMLFVRGDGVILVSPPN 96
                   +  +++RG  +  +  P+
Sbjct: 55 ------VAQLEQVYIRGCKIRFLILPD 75

>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 = 41.5 bits (97), Expect = 3e-06
 Identities = 14/83 (16%), Positives = 30/83 (36%), Gaps = 13/83 (15%)

Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYK 73
           +  +     E V ++++N   + G +   D  +N  L  V+ T+   E           
Sbjct: 3  LVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNRE----------- 51

Query: 74 TTKRSIPMLFVRGDGVILVSPPN 96
               +  L +RG+ +     P+
Sbjct: 52 --PVQLETLSIRGNNIRYFILPD 72

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	101
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.94
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.94
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.93
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.93
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.93
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.92
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.92
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.92
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.92
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.92
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.92
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.91
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.91
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.91
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.91
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.91
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.91
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.9
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.9
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.89
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.88
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.88
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.87
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.82
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	98.95
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	97.44
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	97.15
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	97.01
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	96.84
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	96.83
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	96.7
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	96.67
1ycy_A	71	Conserved hypothetical protein; structural genomic	96.66
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	96.52
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	96.49
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	96.08
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	95.29
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	94.88
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	94.11
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	93.67
3rux_A	270	BIRA bifunctional protein; biotin-protein ligase,	90.92
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	88.73
2rm4_A	103	CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-	86.12
2eay_A	233	Biotin [acetyl-COA-carboxylase] ligase; biotin bio	83.11
2e12_A	101	SM-like motif, hypothetical protein XCC3642; novel	82.27

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

Probab=99.94  E-value=2.3e-26  Score=147.21  Aligned_cols=87  Identities=59%  Similarity=0.924  Sum_probs=66.3

Q ss_pred             cccCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCe
Q psy3154           9 ISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDG   88 (101)
Q Consensus         9 ~~~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~   88 (101)
                      +....|+++|+.+++++|+|+|++||+|+|+|.|||+||||+|+||.|++...+++++..+.......+.+|++||||++
T Consensus         5 ~~~~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG~n   84 (93)
T 4emg_A            5 QAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDS   84 (93)
T ss_dssp             ----CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECGGG
T ss_pred             cccCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECCCe
Confidence            45789999999999999999999999999999999999999999999998764432210000112467999999999999


Q ss_pred             EEEEecC
Q psy3154          89 VILVSPP   95 (101)
Q Consensus        89 Iv~I~~~   95 (101)
                      |++|+++
T Consensus        85 Vv~I~p~   91 (93)
T 4emg_A           85 VILIAPP   91 (93)
T ss_dssp             EEEEECC
T ss_pred             EEEEEec
Confidence            9999975

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

Probab=99.94  E-value=3.6e-26  Score=141.15  Aligned_cols=75  Identities=37%  Similarity=0.614  Sum_probs=67.6

Q ss_pred             CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154          12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL   91 (101)
Q Consensus        12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~   91 (101)
                      ..|+++|+++++++|+|+|+||++|.|+|.|||+|||++|+||.|++..             ...+++|.+||||++|++
T Consensus         3 ~~P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-------------~~~~~lg~v~iRG~~I~~   69 (77)
T 1i4k_A            3 PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNG-------------EVVRKVGSVVIRGDTVVF   69 (77)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETT-------------EEEEEEEEEEECGGGEEE
T ss_pred             ccHHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecC-------------CcEeECCEEEECCCEEEE
Confidence            5899999999999999999999999999999999999999999998742             357899999999999999


Q ss_pred             EecCCCCC
Q psy3154          92 VSPPNRTP   99 (101)
Q Consensus        92 I~~~~~~~   99 (101)
                      |.++|+++
T Consensus        70 i~~~d~~~   77 (77)
T 1i4k_A           70 VSPAPGGE   77 (77)
T ss_dssp             EEECC---
T ss_pred             EEeCCCCC
Confidence            99999875

>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=99.93  E-value=1e-25  Score=144.82  Aligned_cols=84  Identities=43%  Similarity=0.749  Sum_probs=71.9

Q ss_pred             ccCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeE
Q psy3154          10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGV   89 (101)
Q Consensus        10 ~~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I   89 (101)
                      .++.|+++|+++++++|+|+|+|||+|+|+|.|||+||||+|+||.|++...++..      .....+.+|.+||||++|
T Consensus         7 ~~~~p~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~------~~~~~r~lG~v~IRG~nV   80 (96)
T 3bw1_A            7 HMETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEE------LSESERRCEMVFIRGDTV   80 (96)
T ss_dssp             CCCCHHHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTC------CCEEEEEEEEEEECGGGE
T ss_pred             hhhhHHHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccc------cCcceeEcCEEEECCCEE
Confidence            57899999999999999999999999999999999999999999999987543210      124578999999999999


Q ss_pred             EEEecCCCCC
Q psy3154          90 ILVSPPNRTP   99 (101)
Q Consensus        90 v~I~~~~~~~   99 (101)
                      ++|++.|+..
T Consensus        81 v~I~~~d~~~   90 (96)
T 3bw1_A           81 TLISTPSEDD   90 (96)
T ss_dssp             EEEECCC---
T ss_pred             EEEEecCccc
Confidence            9999998754

>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=99.93  E-value=8.5e-26  Score=144.94  Aligned_cols=81  Identities=28%  Similarity=0.447  Sum_probs=66.0

Q ss_pred             ccCCccccCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEE
Q psy3154           4 EQIPTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLF   83 (101)
Q Consensus         4 ~~~~~~~~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~   83 (101)
                      .|-|+..+..|+++|.++++++|+|.|++||+|+|+|.|||+||||+|+||.|++..    +        ...+.+|.++
T Consensus        11 ~~~~~~~~~~Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~----~--------~~~~~lg~v~   78 (94)
T 4emk_A           11 SQDPMSMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTV----T--------GVTEKHSEML   78 (94)
T ss_dssp             ---------CHHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETT----T--------CCEEEEEEEE
T ss_pred             ccCCccccccCHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecC----C--------CcEeEcCEEE
Confidence            467888999999999999999999999999999999999999999999999998731    1        2478899999


Q ss_pred             EcCCeEEEEecCC
Q psy3154          84 VRGDGVILVSPPN   96 (101)
Q Consensus        84 IRG~~Iv~I~~~~   96 (101)
                      |||+||++|++..
T Consensus        79 IRG~nI~~i~p~~   91 (94)
T 4emk_A           79 LNGNGMCMLIPGG   91 (94)
T ss_dssp             ECSTTEEEEEECC
T ss_pred             EcCCEEEEEEeCC
Confidence            9999999999874

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

Probab=99.93  E-value=2.3e-25  Score=136.97  Aligned_cols=73  Identities=37%  Similarity=0.600  Sum_probs=66.4

Q ss_pred             CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154          12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL   91 (101)
Q Consensus        12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~   91 (101)
                      ..|+++|+++++++|+|+|+|||+|+|+|.|||+|||++|+||.|++..             ...+.+|.+||||++|++
T Consensus         3 ~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-------------~~~~~lg~v~iRG~~I~~   69 (75)
T 1h64_1            3 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDG-------------EVVKRYGKIVIRGDNVLA   69 (75)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETT-------------EEEEEEEEEEECGGGEEE
T ss_pred             chHHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeC-------------CceeECCEEEECCCEEEE
Confidence            5799999999999999999999999999999999999999999998741             357899999999999999


Q ss_pred             EecCCC
Q psy3154          92 VSPPNR   97 (101)
Q Consensus        92 I~~~~~   97 (101)
                      |.++|+
T Consensus        70 i~~~~e   75 (75)
T 1h64_1           70 ISPTEE   75 (75)
T ss_dssp             EEEC--
T ss_pred             EEeCCC
Confidence            999874

>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=99.92  E-value=4e-25  Score=136.60  Aligned_cols=75  Identities=25%  Similarity=0.462  Sum_probs=67.3

Q ss_pred             ccCChHHHHHHhcCCEEEEEEcCC-eEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCe
Q psy3154          10 SVKEPLDLIRLSLDERVHVKMRNE-RVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDG   88 (101)
Q Consensus        10 ~~~~Pl~lL~~~l~k~V~V~l~~g-r~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~   88 (101)
                      .+-.|+++|.++++++|+|+|++| ++|+|+|.|||+|||++|+||.|++..             ...+.+|.+||||++
T Consensus         2 ~m~~P~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~~-------------~~~~~lg~v~iRG~n   68 (77)
T 1ljo_A            2 AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGE-------------EKVRSLGEIVLRGNN   68 (77)
T ss_dssp             CCCCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETT-------------EEEEEEEEEEECGGG
T ss_pred             CccchHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecC-------------CcEeECCeEEEeCCe
Confidence            346899999999999999999999 999999999999999999999998731             257899999999999


Q ss_pred             EEEEecCCC
Q psy3154          89 VILVSPPNR   97 (101)
Q Consensus        89 Iv~I~~~~~   97 (101)
                      |++|.++|+
T Consensus        69 I~~i~~~de   77 (77)
T 1ljo_A           69 VVLIQPQEE   77 (77)
T ss_dssp             EEEEEEC--
T ss_pred             EEEEEeCCC
Confidence            999999874

>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=99.92  E-value=3.3e-25  Score=138.21  Aligned_cols=74  Identities=35%  Similarity=0.627  Sum_probs=66.3

Q ss_pred             CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154          12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL   91 (101)
Q Consensus        12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~   91 (101)
                      ..|+++|+++++++|+|+|+|||+|.|+|.|||+|||++|+||.|++..             ...+.+|.+||||++|++
T Consensus         8 ~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-------------~~~~~lg~v~iRG~~I~~   74 (81)
T 1th7_A            8 ETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSD-------------GSGKKLGTIVIRGDNVIL   74 (81)
T ss_dssp             HHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSS-------------SCEEEEEEEEECGGGEEE
T ss_pred             cchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecC-------------CceeECCEEEECCCEEEE
Confidence            5799999999999999999999999999999999999999999998742             246899999999999999


Q ss_pred             EecCCCC
Q psy3154          92 VSPPNRT   98 (101)
Q Consensus        92 I~~~~~~   98 (101)
                      |.++|++
T Consensus        75 i~~~~~~   81 (81)
T 1th7_A           75 ISPLQTS   81 (81)
T ss_dssp             EEEC---
T ss_pred             EEecCCC
Confidence            9999874

>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=99.92  E-value=4.7e-25  Score=137.62  Aligned_cols=74  Identities=31%  Similarity=0.500  Sum_probs=66.7

Q ss_pred             ccCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeE
Q psy3154          10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGV   89 (101)
Q Consensus        10 ~~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I   89 (101)
                      ....|+++|.++++++|+|+|+|||+|.|+|.|||+|||++|+||.|+ .    .         ...+.+|.+||||++|
T Consensus         8 ~~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~----~---------~~~~~lg~v~iRG~~I   73 (81)
T 1i8f_A            8 CFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-I----D---------GNVYKRGTMVVRGENV   73 (81)
T ss_dssp             --CCHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-E----T---------TEEEEEEEEEECGGGE
T ss_pred             cccchHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-c----C---------CcccCCCEEEECCCEE
Confidence            367999999999999999999999999999999999999999999998 2    1         2478999999999999


Q ss_pred             EEEecCCC
Q psy3154          90 ILVSPPNR   97 (101)
Q Consensus        90 v~I~~~~~   97 (101)
                      ++|+++||
T Consensus        74 ~~i~~~dg   81 (81)
T 1i8f_A           74 LFISPVPG   81 (81)
T ss_dssp             EEEEECC-
T ss_pred             EEEEeCCC
Confidence            99999986

>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=99.92  E-value=6.9e-25  Score=138.50  Aligned_cols=76  Identities=18%  Similarity=0.248  Sum_probs=67.1

Q ss_pred             cCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEE
Q psy3154          11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVI   90 (101)
Q Consensus        11 ~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv   90 (101)
                      ...|+++|+++++++|+|+|++|++|+|+|.|||+|||++|+||.|+..     +        ...+++|.+||||++|+
T Consensus         4 ~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~-----g--------~~~~~lg~v~IRG~nI~   70 (86)
T 3s6n_F            4 PLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYID-----G--------ALSGHLGEVLIRCNNVL   70 (86)
T ss_dssp             CCCHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEET-----T--------EEEEEESSEEECGGGEE
T ss_pred             CcCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcC-----C--------ceeeEccEEEEeCCeEE
Confidence            4679999999999999999999999999999999999999999998752     1        24688999999999999


Q ss_pred             EEecCCCCC
Q psy3154          91 LVSPPNRTP   99 (101)
Q Consensus        91 ~I~~~~~~~   99 (101)
                      +|.++|+..
T Consensus        71 ~i~~~d~~~   79 (86)
T 3s6n_F           71 YIRGVEEEE   79 (86)
T ss_dssp             EEEECC---
T ss_pred             EEEeCCccc
Confidence            999998865

>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=99.92  E-value=2.5e-25  Score=148.30  Aligned_cols=94  Identities=21%  Similarity=0.393  Sum_probs=71.6

Q ss_pred             CccccCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcc--hhhhhcceeeeeeCeEEE
Q psy3154           7 PTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEE--TYEEIYKTTKRSIPMLFV   84 (101)
Q Consensus         7 ~~~~~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~--~~~~~~~~~~r~lg~v~I   84 (101)
                      .+.....|+++|.++++++|+|.|++||+|+|+|+|||+||||+|+||.|++...+....  ..+.......+.+|++||
T Consensus        22 ~~~~~~~Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~I  101 (121)
T 2fwk_A           22 KGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILL  101 (121)
T ss_dssp             --CCCCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEE
T ss_pred             ccccccCcHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEE
Confidence            445678999999999999999999999999999999999999999999999864211100  011111123789999999


Q ss_pred             cCCeEEEEecCCCCCC
Q psy3154          85 RGDGVILVSPPNRTPA  100 (101)
Q Consensus        85 RG~~Iv~I~~~~~~~~  100 (101)
                      ||++|++|.+.+..++
T Consensus       102 RG~nVv~I~~~~~~~~  117 (121)
T 2fwk_A          102 SGNNVAMLVPGGDPDS  117 (121)
T ss_dssp             CGGGEEEEESSSCC--
T ss_pred             CCCEEEEEEecCCCCC
Confidence            9999999999987764

>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=99.92  E-value=1.2e-24  Score=136.39  Aligned_cols=75  Identities=35%  Similarity=0.682  Sum_probs=67.6

Q ss_pred             CccccCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcC
Q psy3154           7 PTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRG   86 (101)
Q Consensus         7 ~~~~~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG   86 (101)
                      +......|+++|+++++++|+|+|+||++|.|+|.|||+|||++|+||.|++..             ...+.+|.+||||
T Consensus         9 ~~~~~~~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-------------~~~~~lg~v~IRG   75 (83)
T 1mgq_A            9 QRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDG-------------EVTRRLGTVLIRG   75 (83)
T ss_dssp             -CCCTTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETT-------------EEEEEEEEEEECG
T ss_pred             ccccCcChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecC-------------CcccCCCEEEECC
Confidence            444578999999999999999999999999999999999999999999998741             3578999999999


Q ss_pred             CeEEEEec
Q psy3154          87 DGVILVSP   94 (101)
Q Consensus        87 ~~Iv~I~~   94 (101)
                      ++|++|++
T Consensus        76 ~~I~~i~p   83 (83)
T 1mgq_A           76 DNIVYISP   83 (83)
T ss_dssp             GGEEEEEC
T ss_pred             CEEEEEEC
Confidence            99999975

>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=99.91  E-value=4.8e-25  Score=135.78  Aligned_cols=73  Identities=22%  Similarity=0.385  Sum_probs=65.6

Q ss_pred             CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154          12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL   91 (101)
Q Consensus        12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~   91 (101)
                      ..|+++|+++++++|+|+|+||++|+|+|.|||+|||++|+||.|++.     +        ...+++|.+||||++|++
T Consensus         3 ~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~-----~--------~~~~~lg~v~iRG~~I~~   69 (75)
T 4emk_B            3 SSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVN-----G--------KKTNVYGDAFIRGNNVLY   69 (75)
T ss_dssp             SHHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEET-----T--------EEEEEEEEEEEEGGGSSE
T ss_pred             CchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEec-----C--------CcccEecEEEEcCCeEEE
Confidence            679999999999999999999999999999999999999999999863     1        246889999999999999


Q ss_pred             EecCCC
Q psy3154          92 VSPPNR   97 (101)
Q Consensus        92 I~~~~~   97 (101)
                      |++.|.
T Consensus        70 i~~~~~   75 (75)
T 4emk_B           70 VSALDD   75 (75)
T ss_dssp             EEEC--
T ss_pred             EEecCC
Confidence            998763

>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=99.91  E-value=1.5e-24  Score=133.68  Aligned_cols=74  Identities=19%  Similarity=0.362  Sum_probs=66.4

Q ss_pred             ccCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeE
Q psy3154          10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGV   89 (101)
Q Consensus        10 ~~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I   89 (101)
                      +...|+++|++++|++|.|+|++|++|+|+|.|||+|||++|+||.|+..    +         ...+++|.+||||++|
T Consensus         2 ~~~~P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~----~---------~~~~~lg~v~IRG~nI   68 (75)
T 1d3b_A            2 SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYR----D---------GRVAQLEQVYIRGCKI   68 (75)
T ss_dssp             --CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECT----T---------SCEEEEEEEEECGGGE
T ss_pred             CccCHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECC----C---------CcEEEcCeEEEeCCEE
Confidence            45789999999999999999999999999999999999999999999752    1         1368999999999999


Q ss_pred             EEEecCC
Q psy3154          90 ILVSPPN   96 (101)
Q Consensus        90 v~I~~~~   96 (101)
                      .+|..+|
T Consensus        69 ~~i~lPd   75 (75)
T 1d3b_A           69 RFLILPD   75 (75)
T ss_dssp             EEEEECC
T ss_pred             EEEEcCC
Confidence            9999986

>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=99.91  E-value=1.5e-24  Score=143.11  Aligned_cols=87  Identities=26%  Similarity=0.434  Sum_probs=58.2

Q ss_pred             ccccCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCC
Q psy3154           8 TISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGD   87 (101)
Q Consensus         8 ~~~~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~   87 (101)
                      +..+..|+..|.++++++|+|+|+|||+|+|+|.|||+||||+|+||.|++....    + . ......+.+|++||||+
T Consensus        18 ~~~kke~i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~----~-~-~~~~~~r~lG~v~IRG~   91 (113)
T 4emk_C           18 ERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPE----D-G-KLTGAIRKLGLVVVRGT   91 (113)
T ss_dssp             --------------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------------CCEEEEEEEEECTT
T ss_pred             cCCccchHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCC----C-c-ccccceeEccEEEECCC
Confidence            3445678888999999999999999999999999999999999999999986421    0 0 11246899999999999


Q ss_pred             eEEEEecCCCCCC
Q psy3154          88 GVILVSPPNRTPA  100 (101)
Q Consensus        88 ~Iv~I~~~~~~~~  100 (101)
                      +|++|++.|+.+.
T Consensus        92 nIv~I~~~d~~ee  104 (113)
T 4emk_C           92 TLVLIAPMDGSEE  104 (113)
T ss_dssp             TEEEEEECC----
T ss_pred             eEEEEEecCcccc
Confidence            9999999998753

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

Probab=99.91  E-value=1.8e-24  Score=143.52  Aligned_cols=91  Identities=31%  Similarity=0.446  Sum_probs=67.0

Q ss_pred             ccCChHHHHHHhc--CCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhh-hhcceeeeeeCeEEEcC
Q psy3154          10 SVKEPLDLIRLSL--DERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYE-EIYKTTKRSIPMLFVRG   86 (101)
Q Consensus        10 ~~~~Pl~lL~~~l--~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~-~~~~~~~r~lg~v~IRG   86 (101)
                      .+.+|+++|+.++  +++|+|+|++||.|.|+|.|||+||||+|+||.|++...++++...+ .+.....|.+|.+||||
T Consensus        24 ~~~~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG  103 (118)
T 1b34_B           24 FNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRG  103 (118)
T ss_dssp             --CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECG
T ss_pred             cccChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcC
Confidence            3779999999999  59999999999999999999999999999999999865332211000 01123477899999999


Q ss_pred             CeEEEEecCCCCCC
Q psy3154          87 DGVILVSPPNRTPA  100 (101)
Q Consensus        87 ~~Iv~I~~~~~~~~  100 (101)
                      ++|++|++.+..-|
T Consensus       104 ~nVv~I~~~~~~~~  117 (118)
T 1b34_B          104 DSVIVVLRNPLIAG  117 (118)
T ss_dssp             GGEEEEEECCCCCC
T ss_pred             CEEEEEEeCchhhc
Confidence            99999999987543

>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=99.91  E-value=1.1e-24  Score=138.40  Aligned_cols=85  Identities=19%  Similarity=0.422  Sum_probs=68.0

Q ss_pred             ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154          13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV   92 (101)
Q Consensus        13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I   92 (101)
                      +|...|.++++++|+|+|+|||+|+|+|.|||+||||+|+||.|++...+.+.   +.......+.+|++||||++|++|
T Consensus         4 ~~~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~---~~~~~~~~~~lg~v~iRG~~I~~i   80 (91)
T 1d3b_B            4 GKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNS---KQAEREEKRVLGLVLLRGENLVSM   80 (91)
T ss_dssp             ---CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSST---TSCCEEEEEEEEEEEECGGGEEEE
T ss_pred             ChhHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeecccccc---ccccCccEeECCEEEECCCeEEEE
Confidence            57788999999999999999999999999999999999999999875432211   001134689999999999999999


Q ss_pred             ecCCCCCC
Q psy3154          93 SPPNRTPA  100 (101)
Q Consensus        93 ~~~~~~~~  100 (101)
                      ++++..++
T Consensus        81 ~~~~~~~~   88 (91)
T 1d3b_B           81 TVEGPPPK   88 (91)
T ss_dssp             EEEECCC-
T ss_pred             EcCCCCCC
Confidence            99876553

>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=99.91  E-value=1.5e-24  Score=138.86  Aligned_cols=79  Identities=23%  Similarity=0.399  Sum_probs=61.0

Q ss_pred             cCCccccCChHHHHHHhcCCEEEEEEcCC-eEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEE
Q psy3154           5 QIPTISVKEPLDLIRLSLDERVHVKMRNE-RVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLF   83 (101)
Q Consensus         5 ~~~~~~~~~Pl~lL~~~l~k~V~V~l~~g-r~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~   83 (101)
                      ..+......|+++|+++++++|.|+|++| ++|+|+|.|||+|||++|+||.|++.     +        ...+.+|.+|
T Consensus        13 ~~~~~~~~~P~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~-----~--------~~~~~lg~v~   79 (93)
T 1n9r_A           13 DISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVA-----G--------VSHGTLGEIF   79 (93)
T ss_dssp             -------------CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEET-----T--------EEEEECCSEE
T ss_pred             cccccccCChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcC-----C--------CeEeEcCEEE
Confidence            34556678999999999999999999999 99999999999999999999999863     1        2468999999


Q ss_pred             EcCCeEEEEecCC
Q psy3154          84 VRGDGVILVSPPN   96 (101)
Q Consensus        84 IRG~~Iv~I~~~~   96 (101)
                      |||++|++|.+++
T Consensus        80 IRG~nI~~I~~~~   92 (93)
T 1n9r_A           80 IRCNNVLYIRELP   92 (93)
T ss_dssp             ECGGGEEEEEECC
T ss_pred             EcCCeEEEEEeCC
Confidence            9999999999876

>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=5.9e-24  Score=131.23  Aligned_cols=72  Identities=22%  Similarity=0.491  Sum_probs=52.8

Q ss_pred             ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154          13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV   92 (101)
Q Consensus        13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I   92 (101)
                      .|-++|+++++++|+|+|+|||+|+|+|.|||+|||++|+||.|++..             ...+.+|.++|||++|++|
T Consensus         4 ~~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~-------------~~~~~lg~v~iRG~~I~~i   70 (76)
T 3s6n_G            4 AHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATS-------------GQQNNIGMVVIRGNSIIML   70 (76)
T ss_dssp             ----------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC-----------------CBSSEEECSSSEEEE
T ss_pred             cchHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccC-------------CcEeEcCEEEECCCeEEEE
Confidence            367899999999999999999999999999999999999999998642             1367899999999999999


Q ss_pred             ecCCC
Q psy3154          93 SPPNR   97 (101)
Q Consensus        93 ~~~~~   97 (101)
                      ++.|.
T Consensus        71 ~~~d~   75 (76)
T 3s6n_G           71 EALER   75 (76)
T ss_dssp             EC---
T ss_pred             EeccC
Confidence            99874

>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=99.90  E-value=3.4e-24  Score=136.95  Aligned_cols=76  Identities=21%  Similarity=0.462  Sum_probs=66.9

Q ss_pred             cccCChHHHHHHhcCCEEEEEE----cCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEE
Q psy3154           9 ISVKEPLDLIRLSLDERVHVKM----RNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFV   84 (101)
Q Consensus         9 ~~~~~Pl~lL~~~l~k~V~V~l----~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~I   84 (101)
                      ..+..|+++|.++++++|+|++    ++||+|+|+|.|||+|||++|+||.|++..    +        ...+.+|.+||
T Consensus        12 ~~m~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~----~--------~~~~~lg~v~i   79 (92)
T 3s6n_E           12 KVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSK----T--------KSRKQLGRIML   79 (92)
T ss_dssp             --CCCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSS----S--------CCEEEEEEEEE
T ss_pred             eeccCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecC----C--------CceeEcCeEEE
Confidence            3488999999999999999998    999999999999999999999999998742    1        24688999999


Q ss_pred             cCCeEEEEecCC
Q psy3154          85 RGDGVILVSPPN   96 (101)
Q Consensus        85 RG~~Iv~I~~~~   96 (101)
                      ||+||++|++.|
T Consensus        80 RG~nV~~i~~~~   91 (92)
T 3s6n_E           80 KGDNITLLQSVS   91 (92)
T ss_dssp             CGGGEEEEEEC-
T ss_pred             eCCEEEEEEeCC
Confidence            999999999875

>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=99.89  E-value=2.4e-23  Score=135.88  Aligned_cols=75  Identities=21%  Similarity=0.406  Sum_probs=54.7

Q ss_pred             cCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEE
Q psy3154          11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVI   90 (101)
Q Consensus        11 ~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv   90 (101)
                      ...|+++|+++++++|.|+|++|++|+|+|.|||+|||++|+||.|++.    ++        ...+.+|.+||||++|+
T Consensus        14 ~~~p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~----dg--------~~~~~lg~v~IRG~nI~   81 (105)
T 4emh_A           14 PMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMP----DG--------DKFFRLPECYIRGNNIK   81 (105)
T ss_dssp             ------------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECT----TS--------CEEEEEEEEEECGGGEE
T ss_pred             CCcHHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEcc----CC--------ceeeEcCeEEEeCCeEE
Confidence            4678999999999999999999999999999999999999999999753    11        24678999999999999


Q ss_pred             EEecCCC
Q psy3154          91 LVSPPNR   97 (101)
Q Consensus        91 ~I~~~~~   97 (101)
                      +|.++|.
T Consensus        82 ~I~~pd~   88 (105)
T 4emh_A           82 YLRIQDE   88 (105)
T ss_dssp             EEEC---
T ss_pred             EEecCHH
Confidence            9999975

>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=99.88  E-value=1.6e-22  Score=146.90  Aligned_cols=84  Identities=18%  Similarity=0.391  Sum_probs=69.5

Q ss_pred             CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154          12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL   91 (101)
Q Consensus        12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~   91 (101)
                      .++-..|.++++++|+|+|+|||+|+|+|+|||+||||+|+||+|++...+++.   +.......|++|++||||+||++
T Consensus         3 v~k~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~---k~~~~~~~R~LGlV~IRGdnIV~   79 (231)
T 3pgw_B            3 VGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNS---KQAEREEKRVLGLVLLRGENLVS   79 (231)
T ss_pred             cCchHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCccc---ccccccceeEeceEEECCCcEEE
Confidence            356778899999999999999999999999999999999999999986432221   11123578999999999999999


Q ss_pred             EecCCCC
Q psy3154          92 VSPPNRT   98 (101)
Q Consensus        92 I~~~~~~   98 (101)
                      |+..+..
T Consensus        80 Isve~pP   86 (231)
T 3pgw_B           80 MTVEGPP   86 (231)
T ss_pred             EEecCCC
Confidence            9987543

>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=99.88  E-value=1e-22  Score=135.29  Aligned_cols=72  Identities=18%  Similarity=0.319  Sum_probs=66.1

Q ss_pred             ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154          13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV   92 (101)
Q Consensus        13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I   92 (101)
                      .|+++|+++++++|.|+|++|++|.|+|.+||+||||+|+||+|+..    +         ...+.+|.+||||+||++|
T Consensus         2 ~p~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~----~---------~~~~~lg~v~IRG~nI~~I   68 (119)
T 1b34_A            2 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLK----N---------REPVQLETLSIRGNNIRYF   68 (119)
T ss_dssp             CHHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECT----T---------SCCEEEEEEEECGGGEEEE
T ss_pred             ChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecC----C---------CceeEcceEEEcCCeEEEE
Confidence            59999999999999999999999999999999999999999999752    1         1357899999999999999


Q ss_pred             ecCCC
Q psy3154          93 SPPNR   97 (101)
Q Consensus        93 ~~~~~   97 (101)
                      .++|.
T Consensus        69 ~~pd~   73 (119)
T 1b34_A           69 ILPDS   73 (119)
T ss_dssp             ECCTT
T ss_pred             Eeccc
Confidence            99987

>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=99.87  E-value=3.1e-22  Score=134.31  Aligned_cols=75  Identities=19%  Similarity=0.367  Sum_probs=66.9

Q ss_pred             ccCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeE
Q psy3154          10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGV   89 (101)
Q Consensus        10 ~~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I   89 (101)
                      +...|+++|+++++++|.|+|++|++|+|+|.+||.|||++|+||.|+..    ++         ...+++.+||||++|
T Consensus         2 ~~~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~----~g---------~~~~l~~v~IRGnnI   68 (126)
T 2y9a_D            2 SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYR----DG---------RVAQLEQVYIRGSKI   68 (126)
T ss_dssp             --CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECT----TS---------CCEEEEEEEECGGGE
T ss_pred             CcccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcC----CC---------cEeecccEEEeCCEE
Confidence            46789999999999999999999999999999999999999999999752    11         367899999999999


Q ss_pred             EEEecCCC
Q psy3154          90 ILVSPPNR   97 (101)
Q Consensus        90 v~I~~~~~   97 (101)
                      .+|.++|.
T Consensus        69 ~~I~lpd~   76 (126)
T 2y9a_D           69 RFLILPDM   76 (126)
T ss_dssp             EEEECCSS
T ss_pred             EEEEcccc
Confidence            99999875

>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=99.82  E-value=2.2e-20  Score=125.83  Aligned_cols=67  Identities=24%  Similarity=0.390  Sum_probs=61.5

Q ss_pred             HHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEec
Q psy3154          15 LDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP   94 (101)
Q Consensus        15 l~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~   94 (101)
                      .++|+++++++|.|+|++|++|.|+|.|||+|||++|+||.|+.                 .+.+|.+||||++|++|.+
T Consensus         2 ~~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~-----------------~~~lg~v~IRG~nI~~I~~   64 (130)
T 1m5q_A            2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA-----------------GEKFNRVFIMYRYIVHIDS   64 (130)
T ss_dssp             HHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTT-----------------CCEEEEEEECGGGEEEEEE
T ss_pred             hhHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEc-----------------CCEeceEEEeCCeEEEEEc
Confidence            57899999999999999999999999999999999999999851                 2578999999999999999


Q ss_pred             CCCC
Q psy3154          95 PNRT   98 (101)
Q Consensus        95 ~~~~   98 (101)
                      +|..
T Consensus        65 ~d~~   68 (130)
T 1m5q_A           65 TERR   68 (130)
T ss_dssp             CCCC
T ss_pred             CCcc
Confidence            9864

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

Probab=98.95  E-value=1.5e-09  Score=68.10  Aligned_cols=68  Identities=24%  Similarity=0.249  Sum_probs=56.5

Q ss_pred             cCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEc-CCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeE
Q psy3154          11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYD-QHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGV   89 (101)
Q Consensus        11 ~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D-~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I   89 (101)
                      ..+|++ |..+++|+|.|+|.||++|.|.|.+|| ...|++|.|+.+                   ......++|.|+.|
T Consensus         6 ~~~p~e-l~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~~~-------------------~~~~~~~iI~G~aI   65 (86)
T 1y96_A            6 KKGPLE-WQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFLE-------------------DGSMSVTGIMGHAV   65 (86)
T ss_dssp             HSCHHH-HHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEECT-------------------TSCEEEEEECGGGE
T ss_pred             hCCHHH-HHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeeccc-------------------CCeEEEEEEecceE
Confidence            456775 566699999999999999999999999 999999999811                   12367899999999


Q ss_pred             EEEecCCCC
Q psy3154          90 ILVSPPNRT   98 (101)
Q Consensus        90 v~I~~~~~~   98 (101)
                      ..|...++.
T Consensus        66 ~eI~v~~~~   74 (86)
T 1y96_A           66 QTVETMNEG   74 (86)
T ss_dssp             EEEEEEECC
T ss_pred             EEEEEecch
Confidence            999876554

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

Probab=97.44  E-value=0.00084  Score=41.95  Aligned_cols=76  Identities=14%  Similarity=0.163  Sum_probs=59.0

Q ss_pred             HhcCCEEEEEEcCCeEEEEEEEEEc-CCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEecCCCC
Q psy3154          20 LSLDERVHVKMRNERVLRGKLHAYD-QHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNRT   98 (101)
Q Consensus        20 ~~l~k~V~V~l~~gr~i~G~L~~~D-~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~~~~   98 (101)
                      .++|+++.+..+.+-.|.|+|..+| +..-+.|+||..+-++-...    .........-+..++.||+.|--+...+.+
T Consensus        10 ~yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~----~~~ipp~~~vy~yIvFrgsDIKdL~V~~~~   85 (88)
T 2vxe_A           10 PELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDT----QFQIAPQSQIYDYILFRGSDIKDIRVVNNH   85 (88)
T ss_dssp             CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCTTTCC----SSCCCCCCSCEEEEEEETTTEEEEEECCCC
T ss_pred             cccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCcCCCC----CcccCCCCceeeEEEEccCCccEEEEeccC
Confidence            3599999999999999999999999 66779999999876642211    111223445578899999999999988776


Q ss_pred             C
Q psy3154          99 P   99 (101)
Q Consensus        99 ~   99 (101)
                      |
T Consensus        86 p   86 (88)
T 2vxe_A           86 T   86 (88)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=97.15  E-value=0.0009  Score=40.57  Aligned_cols=37  Identities=19%  Similarity=0.372  Sum_probs=29.9

Q ss_pred             HHHHHhc--CCEEEEEEcCCeEEEEEEEEEcCCCceEecc
Q psy3154          16 DLIRLSL--DERVHVKMRNERVLRGKLHAYDQHLNMVLGD   53 (101)
Q Consensus        16 ~lL~~~l--~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~   53 (101)
                      .+|+.+.  ..+|.|.|.+|..+.|++.+||+|+ +.|.+
T Consensus        12 ~~L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~-vlL~~   50 (74)
T 2ylb_A           12 PFLNALRRERVPVSIYLVNGIKLQGQIESFDQFV-ILLKN   50 (74)
T ss_dssp             HHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSE-EEEES
T ss_pred             HHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcE-EEEEC
Confidence            3555554  5799999999999999999999999 44443

>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=97.01  E-value=0.0018  Score=39.95  Aligned_cols=29  Identities=21%  Similarity=0.368  Sum_probs=25.7

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEEcCCCceE
Q psy3154          22 LDERVHVKMRNERVLRGKLHAYDQHLNMV   50 (101)
Q Consensus        22 l~k~V~V~l~~gr~i~G~L~~~D~~mNlv   50 (101)
                      -+.+|.|-|.+|-.+.|.+.+||+|+=++
T Consensus        18 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVlL   46 (82)
T 1u1s_A           18 ERVPVSIYLVNGIKLQGQIESFDQFVILL   46 (82)
T ss_dssp             TTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             cCCcEEEEEeCCcEEEEEEEEEcceEEEE
Confidence            45799999999999999999999999444

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

Probab=96.84  E-value=0.0032  Score=38.61  Aligned_cols=29  Identities=21%  Similarity=0.337  Sum_probs=25.5

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEEcCCCceE
Q psy3154          22 LDERVHVKMRNERVLRGKLHAYDQHLNMV   50 (101)
Q Consensus        22 l~k~V~V~l~~gr~i~G~L~~~D~~mNlv   50 (101)
                      -..+|.|.|.+|-.+.|++.+||+|+=++
T Consensus        19 ~k~~VtI~LvnG~~L~G~I~~fD~f~VlL   47 (79)
T 3sb2_A           19 EHVPVSIYLVNGIKLQGHVESFDQYVVLL   47 (79)
T ss_dssp             TTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             cCCeEEEEEeCCCEEEEEEEEECCcEEEE
Confidence            34689999999999999999999999443

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

Probab=96.83  E-value=0.0029  Score=39.97  Aligned_cols=80  Identities=11%  Similarity=0.090  Sum_probs=57.1

Q ss_pred             hHHHHHHhcCCEEEEEEcCCeEEEEEEEEEc-CCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154          14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYD-QHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV   92 (101)
Q Consensus        14 Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D-~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I   92 (101)
                      |-..-..++|+++.+..+.+-.|.|+|..+| +..-+.|+||..+-++-....    ........-+..++.||+.|--+
T Consensus        10 ~~~~~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~----~~ipp~~~vyeyIvFrGsDIKDL   85 (95)
T 2fb7_A           10 DPSGGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTD----RPIAPRDETFEYIIFRGSDIKDL   85 (95)
T ss_dssp             ------CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCS----SCCCSCCCCSSCEEECSTTEEEE
T ss_pred             CCCccCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCC----CccCCCCcceeEEEEcCCCcceE
Confidence            3344456799999999999999999999999 667799999987766422111    11223455678999999999988


Q ss_pred             ecCCC
Q psy3154          93 SPPNR   97 (101)
Q Consensus        93 ~~~~~   97 (101)
                      ...+-
T Consensus        86 ~V~e~   90 (95)
T 2fb7_A           86 TVCEP   90 (95)
T ss_dssp             EESCC
T ss_pred             EEecC
Confidence            87653

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

Probab=96.70  E-value=0.004  Score=39.97  Aligned_cols=35  Identities=17%  Similarity=0.308  Sum_probs=28.1

Q ss_pred             HHHHhc--CCEEEEEEcCCeEEEEEEEEEcCCCceEe
Q psy3154          17 LIRLSL--DERVHVKMRNERVLRGKLHAYDQHLNMVL   51 (101)
Q Consensus        17 lL~~~l--~k~V~V~l~~gr~i~G~L~~~D~~mNlvL   51 (101)
                      +|+.+.  ..+|.|.|.+|-.++|++.+||+|+=++-
T Consensus        13 fLn~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~VlL~   49 (104)
T 2y90_A           13 FLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLK   49 (104)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEE
Confidence            444443  45999999999999999999999994443

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

Probab=96.67  E-value=0.0044  Score=37.74  Aligned_cols=37  Identities=16%  Similarity=0.181  Sum_probs=29.5

Q ss_pred             HHHHhc--CCEEEEEEcCCeEEEEEEEEEcCCCceEecc
Q psy3154          17 LIRLSL--DERVHVKMRNERVLRGKLHAYDQHLNMVLGD   53 (101)
Q Consensus        17 lL~~~l--~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~   53 (101)
                      +|+.+.  ..+|.|.|.+|-.+.|++.+||+|+=++-.+
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            444443  5799999999999999999999999555434

>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=96.66  E-value=0.01  Score=35.01  Aligned_cols=61  Identities=13%  Similarity=0.302  Sum_probs=43.3

Q ss_pred             HHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEec
Q psy3154          16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP   94 (101)
Q Consensus        16 ~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~   94 (101)
                      ..|++|.|++|-+...+...|+|+|.-||... +.|+|+..+.-                 ++-..++++=+.|-.|.+
T Consensus         9 ktL~~WKg~rvAv~vg~ehSFtGiledFDeEv-iLL~dV~D~~G-----------------Nk~k~liv~idDinWimL   69 (71)
T 1ycy_A            9 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIG-----------------NRGKQMLIGLEDINWIML   69 (71)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTE-----------------EEEEEEEEEGGGEEEEEE
T ss_pred             HHHHHhCCcEEEEEecCcceeeeehhhcCcce-eehhhHHHHhc-----------------cccceeEEEeccceEEEe
Confidence            46788999999999999999999999999987 88899987532                 223345666666666554

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

Probab=96.52  E-value=0.0045  Score=37.18  Aligned_cols=32  Identities=22%  Similarity=0.223  Sum_probs=27.2

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEEcCCCceEecc
Q psy3154          22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGD   53 (101)
Q Consensus        22 l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~   53 (101)
                      -+.+|.|-|.+|-.+.|.+.+||+|+=++-.+
T Consensus        24 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   55 (71)
T 2qtx_A           24 NGKKVKIFLRNGEVLDAEVTGVSNYEIMVKVG   55 (71)
T ss_dssp             TTCEEEEEETTSCEEEEEEEEECSSEEEEEET
T ss_pred             cCCcEEEEEeCCeEEEEEEEEEcceEEEEEeC
Confidence            45799999999999999999999999554333

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

Probab=96.49  E-value=0.006  Score=37.26  Aligned_cols=31  Identities=23%  Similarity=0.366  Sum_probs=26.8

Q ss_pred             CCEEEEEEcCCeEEEEEEEEEcCCCceEecc
Q psy3154          23 DERVHVKMRNERVLRGKLHAYDQHLNMVLGD   53 (101)
Q Consensus        23 ~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~   53 (101)
                      +.+|.|-|.+|..+.|.+.+||+|+=++-.+
T Consensus        23 ~~~Vtv~L~nG~~l~G~I~~fD~f~VlL~~~   53 (78)
T 3ahu_A           23 NTYVTVFLLNGFQLRGQVKGFDNFTVLLESE   53 (78)
T ss_dssp             TCCEEEEETTSCEEEEEEEEECSSEEEEESS
T ss_pred             CCcEEEEEeCCeEEEEEEEEEcceEEEEEEC
Confidence            5799999999999999999999999554433

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

Probab=96.08  E-value=0.027  Score=34.84  Aligned_cols=66  Identities=12%  Similarity=0.110  Sum_probs=52.1

Q ss_pred             cCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEc-CCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeE
Q psy3154          11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYD-QHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGV   89 (101)
Q Consensus        11 ~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D-~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I   89 (101)
                      .+..+.+|....+++|.+.+.++-++.|++.++| ...|+..++-.   +     +          --.++..++|+..|
T Consensus        17 ReRfLr~l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~---T-----P----------iGv~~eAlLR~~Di   78 (85)
T 1y96_B           17 RERYLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQ---T-----P----------IGVQAEALLRCSDI   78 (85)
T ss_dssp             HHHHHHHHHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEC---C-----T----------TCCEEEEEEEGGGE
T ss_pred             HHHHHHHHHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhcC---C-----C----------cccchhhhhhcCCE
Confidence            3455777888889999999999999999999999 66777766532   1     1          12377899999999


Q ss_pred             EEEec
Q psy3154          90 ILVSP   94 (101)
Q Consensus        90 v~I~~   94 (101)
                      ++++.
T Consensus        79 i~~sF   83 (85)
T 1y96_B           79 ISYTF   83 (85)
T ss_dssp             EEEEE
T ss_pred             EEEEe
Confidence            99875

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

Probab=95.29  E-value=0.032  Score=36.77  Aligned_cols=39  Identities=21%  Similarity=0.320  Sum_probs=32.1

Q ss_pred             HHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEe--cceEEE
Q psy3154          18 IRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVL--GDVEET   57 (101)
Q Consensus        18 L~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL--~~~~E~   57 (101)
                      ...++|..|.|+|+||..++|++..+|. -+|.|  ++|...
T Consensus         7 ~sqFlGy~V~v~LkDgs~~qG~I~~vd~-k~LtL~~~~a~~s   47 (125)
T 4a53_A            7 VADFYGSNVEVLLNNDSKARGVITNFDS-SNSILQLRLANDS   47 (125)
T ss_dssp             HHHHTTCEEEEEETTSCEEEEEEEEEET-TTTEEEEEETTTE
T ss_pred             HHHhcCceEEEEECCCCEeeEEEEeecC-CeeEEeccccccc
Confidence            3467999999999999999999999984 45777  877543

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

Probab=94.88  E-value=0.073  Score=31.75  Aligned_cols=40  Identities=18%  Similarity=0.186  Sum_probs=33.7

Q ss_pred             cCCh-HHHHHHhcC--CEEEEEEcCCeEEEEEEEEEcCCCceE
Q psy3154          11 VKEP-LDLIRLSLD--ERVHVKMRNERVLRGKLHAYDQHLNMV   50 (101)
Q Consensus        11 ~~~P-l~lL~~~l~--k~V~V~l~~gr~i~G~L~~~D~~mNlv   50 (101)
                      ...| ...|+.++.  ..|.|.|.+|..+.|++.-+|.|+=++
T Consensus         6 t~lPsvR~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~cl~L   48 (70)
T 3hfo_A            6 SGLPSVRQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDGLGL   48 (70)
T ss_dssp             CSCHHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             CCCCcHHHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCEEEE
Confidence            3455 678888875  699999999999999999999998444

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

Probab=94.11  E-value=0.15  Score=30.48  Aligned_cols=41  Identities=15%  Similarity=0.299  Sum_probs=34.2

Q ss_pred             CCh-HHHHHHhcC--CEEEEEEcCCeEEEEEEEEEcCCCceEecc
Q psy3154          12 KEP-LDLIRLSLD--ERVHVKMRNERVLRGKLHAYDQHLNMVLGD   53 (101)
Q Consensus        12 ~~P-l~lL~~~l~--k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~   53 (101)
                      ..| ...|+.++.  ..|.|.|.+|..++|++.-+|.++ +.|.+
T Consensus         9 ~lPsvR~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~c-l~L~~   52 (72)
T 3hfn_A            9 SLPSIRQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTC-VCIAD   52 (72)
T ss_dssp             CHHHHHHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSE-EEEEC
T ss_pred             CCCcHHHHHHHHhhCceEEEEecCCCEEEEEEEEECCCE-EEEEc
Confidence            445 778899886  699999999999999999999998 44443

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

Probab=93.67  E-value=0.13  Score=31.66  Aligned_cols=37  Identities=22%  Similarity=0.178  Sum_probs=33.5

Q ss_pred             HHhcCCEEEEEEcCCe-EEEEEEEEEcCC-CceEecceE
Q psy3154          19 RLSLDERVHVKMRNER-VLRGKLHAYDQH-LNMVLGDVE   55 (101)
Q Consensus        19 ~~~l~k~V~V~l~~gr-~i~G~L~~~D~~-mNlvL~~~~   55 (101)
                      .+|+|+.|.+..+++- .|+|.|..+|.. -|+.|.++.
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            4789999999999998 999999999965 689999994

>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=90.92  E-value=0.33  Score=35.22  Aligned_cols=33  Identities=18%  Similarity=0.230  Sum_probs=29.7

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEEcCCCceEecce
Q psy3154          22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDV   54 (101)
Q Consensus        22 l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~   54 (101)
                      +|++|++.+.++..+.|+..|+|....|+++..
T Consensus       223 ~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~~  255 (270)
T 3rux_A          223 IGSRVRVELPGGQDVVGIARDIDDQGRLCLDVG  255 (270)
T ss_dssp             TTSEEEEECTTSCEEEEEEEEECTTSCEEEEET
T ss_pred             cCCEEEEEECCCeEEEEEEEEECCCCeEEEEEC
Confidence            578999998889999999999999999999753

>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=88.73  E-value=0.45  Score=32.25  Aligned_cols=41  Identities=20%  Similarity=0.478  Sum_probs=29.3

Q ss_pred             ccCChHHHH---HHhcCCEEEEEE----cCCeEEEEEEEEEcCCCceEe
Q psy3154          10 SVKEPLDLI---RLSLDERVHVKM----RNERVLRGKLHAYDQHLNMVL   51 (101)
Q Consensus        10 ~~~~Pl~lL---~~~l~k~V~V~l----~~gr~i~G~L~~~D~~mNlvL   51 (101)
                      ....||.-.   .+++|+.|.|++    .+.+.+.|+|.++|.-. +.|
T Consensus        88 GldRpL~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~-v~l  135 (164)
T 1ib8_A           88 GLERPLKTKDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEEDE-LTM  135 (164)
T ss_dssp             SSSSCCSSHHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETTE-EEE
T ss_pred             CCCCCCCCHHHHHHhCCcEEEEEEecccCCceEEEEEEEEEeCCE-EEE
Confidence            345554333   355999999999    44589999999999753 444

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

Probab=86.12  E-value=2.2  Score=26.89  Aligned_cols=36  Identities=8%  Similarity=0.040  Sum_probs=31.9

Q ss_pred             HhcCCEEEEEEcCCe-EEEEEEEEEcCCCceEecceEE
Q psy3154          20 LSLDERVHVKMRNER-VLRGKLHAYDQHLNMVLGDVEE   56 (101)
Q Consensus        20 ~~l~k~V~V~l~~gr-~i~G~L~~~D~~mNlvL~~~~E   56 (101)
                      +|+|+-|.|.+.+.- .|+|.++.+|+ -++.|.++..
T Consensus         9 dwiG~~VSI~C~d~LGVyQG~I~~V~~-~~ItL~kaFr   45 (103)
T 2rm4_A            9 DWIGCAVSIACDEVLGVFQGLIKQISA-EEITIVRAFR   45 (103)
T ss_dssp             GGTTCEEEEEECTTTCEEEEEEEEEET-TEEEEEEEEE
T ss_pred             ceeceEEEEeeCCcceEeeEEEEEccc-ceeEEhhhhh
Confidence            789999999999986 99999999996 3499988875

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

Probab=83.11  E-value=1  Score=31.75  Aligned_cols=30  Identities=20%  Similarity=0.263  Sum_probs=25.9

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEEcCCCceEecc
Q psy3154          22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGD   53 (101)
Q Consensus        22 l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~   53 (101)
                      +|++|++...++  +.|+..|+|....|+++.
T Consensus       187 ~g~~V~v~~~~~--~~G~~~gId~~G~L~v~~  216 (233)
T 2eay_A          187 LGEEVKLLGEGK--ITGKLVGLSEKGGALILT  216 (233)
T ss_dssp             TTSEEEETTEEE--EEEEEEEECTTSCEEEEE
T ss_pred             cCCEEEEEECCe--EEEEEEEECCCCeEEEEE
Confidence            578999976654  999999999999999975

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

Probab=82.27  E-value=2.6  Score=26.23  Aligned_cols=21  Identities=29%  Similarity=0.589  Sum_probs=17.7

Q ss_pred             HhcC--CEEEEEEcCCeEEEEEE
Q psy3154          20 LSLD--ERVHVKMRNERVLRGKL   40 (101)
Q Consensus        20 ~~l~--k~V~V~l~~gr~i~G~L   40 (101)
                      ..++  .+|++.|.||+.+.|++
T Consensus        23 ~~LdGq~~v~i~l~DGs~l~GTv   45 (101)
T 2e12_A           23 KLLDGQERVRIELDDGSMIAGTV   45 (101)
T ss_dssp             HTSCTTCEEEEEETTSCEEEEEE
T ss_pred             HhhCCeeEEEEEEcCCCeEeeee
Confidence            3354  69999999999999985

---

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	101
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	6e-25
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	1e-23
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	7e-21
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	8e-20
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	1e-19
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	2e-18
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	3e-18
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	8e-17
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	2e-16
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	3e-14
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	4e-11
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	9e-09
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	4e-07

>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 = 87.6 bits (217), Expect = 6e-25
 Identities = 20/87 (22%), Positives = 43/87 (49%), Gaps = 2/87 (2%)

Query: 10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYE 69
          ++  PL LI   +  R++V M+ ++   G L  +D+++NMVL DV+E     + ++ +  
Sbjct: 2  NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGG 61

Query: 70 EIYKTT--KRSIPMLFVRGDGVILVSP 94
                     +  + + G+ V ++ P
Sbjct: 62 NKKLKRVMVNRLETILLSGNNVAMLVP 88

>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 = 84.2 bits (208), Expect = 1e-23
 Identities = 29/85 (34%), Positives = 48/85 (56%), Gaps = 3/85 (3%)

Query: 14 PLDLIRLSL--DERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEI 71
          PL ++  S+  + +V +  RN + L G++ A+D+H NMVL +V+E  T V    +  ++ 
Sbjct: 3  PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKS 62

Query: 72 YKTTK-RSIPMLFVRGDGVILVSPP 95
              K R I  +F+RGD VI+V   
Sbjct: 63 KPVNKDRYISKMFLRGDSVIVVLRN 87

>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 = 76.7 bits (189), Expect = 7e-21
 Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 13/86 (15%)

Query: 9  ISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETY 68
          ++V+ PLD +  SL+  V +K++ +R  RG L ++D H+N+VL D EE            
Sbjct: 2  VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEV------ 55

Query: 69 EEIYKTTKRSIPMLFVRGDGVILVSP 94
                  R +  + +RGD ++ +SP
Sbjct: 56 -------TRRLGTVLIRGDNIVYISP 74

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

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

 Score = 74.0 bits (182), Expect = 8e-20
 Identities = 27/83 (32%), Positives = 39/83 (46%), Gaps = 13/83 (15%)

Query: 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEI 71
          + PLD+I  SLD+ V V ++     RG+L  YD HLN+VL D E                
Sbjct: 1  ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEV--------- 51

Query: 72 YKTTKRSIPMLFVRGDGVILVSP 94
               +    + +RGD V+ +SP
Sbjct: 52 ----VKRYGKIVIRGDNVLAISP 70

>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 = 73.2 bits (180), Expect = 1e-19
 Identities = 28/81 (34%), Positives = 39/81 (48%), Gaps = 13/81 (16%)

Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYK 73
          PLD++  SL   V V+++  R  RG L  YD H+N+VL D EE                 
Sbjct: 4  PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEV----------- 52

Query: 74 TTKRSIPMLFVRGDGVILVSP 94
             R +  + +RGD V+ VSP
Sbjct: 53 --VRKVGSVVIRGDTVVFVSP 71

>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 = 70.6 bits (173), Expect = 2e-18
 Identities = 16/73 (21%), Positives = 41/73 (56%), Gaps = 3/73 (4%)

Query: 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPM 81
          +D R+   +++ R+  G   A+D+H+N++L D +E      I  +  ++  +  KR + +
Sbjct: 7  IDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRK---IKPKNSKQAEREEKRVLGL 63

Query: 82 LFVRGDGVILVSP 94
          + +RG+ ++ ++ 
Sbjct: 64 VLLRGENLVSMTV 76

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

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

 Score = 70.1 bits (172), Expect = 3e-18
 Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 13/83 (15%)

Query: 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEI 71
          +    ++  SL+  V VK++  + +RG L +YDQH+N+VL D EE  +            
Sbjct: 6  ETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGS--------- 56

Query: 72 YKTTKRSIPMLFVRGDGVILVSP 94
               + +  + +RGD VIL+SP
Sbjct: 57 ----GKKLGTIVIRGDNVILISP 75

>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 = 66.3 bits (162), Expect = 8e-17
 Identities = 19/86 (22%), Positives = 40/86 (46%), Gaps = 14/86 (16%)

Query: 10 SVKEPLDLIRLSLDERVHVKMRN-ERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETY 68
          ++  P  +++  + + + V+M+  E  L GKL   D ++N+ L +  E     +      
Sbjct: 2  AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEK------ 55

Query: 69 EEIYKTTKRSIPMLFVRGDGVILVSP 94
                  RS+  + +RG+ V+L+ P
Sbjct: 56 -------VRSLGEIVLRGNNVVLIQP 74

>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 = 65.5 bits (160), Expect = 2e-16
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 14/75 (18%)

Query: 21 SLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIP 80
          S+ ++V VK+R+   +RG L ++DQH+N++L D EE +                      
Sbjct: 10 SIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEII--------------DGNVYKRG 55

Query: 81 MLFVRGDGVILVSPP 95
           + VRG+ V+ +SP 
Sbjct: 56 TMVVRGENVLFISPV 70

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

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

 Score = 59.8 bits (145), Expect = 3e-14
 Identities = 12/83 (14%), Positives = 30/83 (36%), Gaps = 13/83 (15%)

Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYK 73
          P+ ++  +    V  +     V RGKL   + ++N  + ++  T                
Sbjct: 3  PIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGR----------- 51

Query: 74 TTKRSIPMLFVRGDGVILVSPPN 96
               +  +++RG  +  +  P+
Sbjct: 52 --VAQLEQVYIRGCKIRFLILPD 72

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

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

 Score = 51.6 bits (124), Expect = 4e-11
 Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 14/74 (18%)

Query: 22 LDERVHVKMR-NERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIP 80
          ++ RV VK++ N    RG L + D + N+ L + EE              +   +  ++ 
Sbjct: 5  VNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEF-------------VAGVSHGTLG 51

Query: 81 MLFVRGDGVILVSP 94
           +F+R + V+ +  
Sbjct: 52 EIFIRCNNVLYIRE 65

>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 = 47.0 bits (112), Expect = 9e-09
 Identities = 16/77 (20%), Positives = 25/77 (32%), Gaps = 17/77 (22%)

Query: 21 SLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIP 80
           L   V V + N  V +G LHA D  LN+VL +                           
Sbjct: 8  LLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA-----------------GEKFN 50

Query: 81 MLFVRGDGVILVSPPNR 97
           +F+    ++ +    R
Sbjct: 51 RVFIMYRYIVHIDSTER 67

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

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

 Score = 41.6 bits (98), Expect = 4e-07
 Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 13/76 (17%)

Query: 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPM 81
            E V ++++N   + G +   D  +N  L  V+ T+   E                +  
Sbjct: 10 SHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNRE-------------PVQLET 56

Query: 82 LFVRGDGVILVSPPNR 97
          L +RG+ +     P+ 
Sbjct: 57 LSIRGNNIRYFILPDS 72

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	101
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.94
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.93
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.93
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.92
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.92
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.91
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.91
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.91
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.9
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.89
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.87
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.81
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.75
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	97.1
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	96.48
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	96.33
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	96.26
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	95.78
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	92.69

>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=99.94  E-value=3.4e-27  Score=149.00  Aligned_cols=85  Identities=24%  Similarity=0.463  Sum_probs=68.2

Q ss_pred             ccCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcc--hhhhhcceeeeeeCeEEEcCC
Q psy3154          10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEE--TYEEIYKTTKRSIPMLFVRGD   87 (101)
Q Consensus        10 ~~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~--~~~~~~~~~~r~lg~v~IRG~   87 (101)
                      .+..|+++|+++++++|+|.|+|||.|.|+|.|||+||||+|+||.|++...+++..  ..+.......|++|++||||+
T Consensus         2 ~~~~Pl~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~   81 (92)
T d2fwka1           2 NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGN   81 (92)
T ss_dssp             CCCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGG
T ss_pred             CccChHHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCC
Confidence            577899999999999999999999999999999999999999999999876543221  112223456889999999999


Q ss_pred             eEEEEec
Q psy3154          88 GVILVSP   94 (101)
Q Consensus        88 ~Iv~I~~   94 (101)
                      +|++|++
T Consensus        82 ~Vv~I~p   88 (92)
T d2fwka1          82 NVAMLVP   88 (92)
T ss_dssp             GEEEEES
T ss_pred             EEEEEEe
Confidence            9999996

>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=99.93  E-value=1.4e-26  Score=146.77  Aligned_cols=86  Identities=33%  Similarity=0.490  Sum_probs=64.3

Q ss_pred             CChHHHHHHhc--CCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchh-hhhcceeeeeeCeEEEcCCe
Q psy3154          12 KEPLDLIRLSL--DERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETY-EEIYKTTKRSIPMLFVRGDG   88 (101)
Q Consensus        12 ~~Pl~lL~~~l--~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~-~~~~~~~~r~lg~v~IRG~~   88 (101)
                      .+|+++|.+++  +++|+|+|++||.|.|+|.|||+||||+|+||.|++...++..... ........|++|++||||+|
T Consensus         1 tGPl~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdn   80 (93)
T d1b34b_           1 TGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDS   80 (93)
T ss_dssp             CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGG
T ss_pred             CCcHHHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCE
Confidence            37999999999  7999999999999999999999999999999999998654332111 11234567999999999999


Q ss_pred             EEEEecCCC
Q psy3154          89 VILVSPPNR   97 (101)
Q Consensus        89 Iv~I~~~~~   97 (101)
                      |++|..++.
T Consensus        81 Vv~I~~~p~   89 (93)
T d1b34b_          81 VIVVLRNPL   89 (93)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEcChh
Confidence            999987654

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

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

Probab=99.93  E-value=1e-25  Score=136.06  Aligned_cols=71  Identities=38%  Similarity=0.610  Sum_probs=64.9

Q ss_pred             CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154          12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL   91 (101)
Q Consensus        12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~   91 (101)
                      +.|+++|+++++++|.|+|+||+.|+|+|.+||+|||++|+||.|+...             ...+++|.+||||++|++
T Consensus         1 ~~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-------------~~~~~l~~~~IRG~~I~~   67 (71)
T d1h641_           1 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDG-------------EVVKRYGKIVIRGDNVLA   67 (71)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETT-------------EEEEEEEEEEECGGGEEE
T ss_pred             CCchHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecC-------------CcEeEcCcEEEECCeEEE
Confidence            5799999999999999999999999999999999999999999987531             356889999999999999


Q ss_pred             EecC
Q psy3154          92 VSPP   95 (101)
Q Consensus        92 I~~~   95 (101)
                      |++.
T Consensus        68 Isp~   71 (71)
T d1h641_          68 ISPT   71 (71)
T ss_dssp             EEEC
T ss_pred             EeCC
Confidence            9863

>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=99.92  E-value=1.8e-25  Score=136.04  Aligned_cols=73  Identities=36%  Similarity=0.702  Sum_probs=66.7

Q ss_pred             cccCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCe
Q psy3154           9 ISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDG   88 (101)
Q Consensus         9 ~~~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~   88 (101)
                      ...+.|+++|+++++++|.|+|+||+.|.|+|.|||+|||++|+||.|++..             ...+++|.+||||++
T Consensus         2 ~~~~~Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~-------------~~~~~~~~~~IRG~~   68 (74)
T d1mgqa_           2 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDG-------------EVTRRLGTVLIRGDN   68 (74)
T ss_dssp             CCTTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETT-------------EEEEEEEEEEECGGG
T ss_pred             CcccCcHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCC-------------CeEeEcceEEEeCCE
Confidence            4678999999999999999999999999999999999999999999997531             246889999999999


Q ss_pred             EEEEec
Q psy3154          89 VILVSP   94 (101)
Q Consensus        89 Iv~I~~   94 (101)
                      |++|++
T Consensus        69 I~~I~p   74 (74)
T d1mgqa_          69 IVYISP   74 (74)
T ss_dssp             EEEEEC
T ss_pred             EEEEeC
Confidence            999975

>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=99.92  E-value=2.4e-25  Score=134.80  Aligned_cols=70  Identities=40%  Similarity=0.677  Sum_probs=64.0

Q ss_pred             ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154          13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV   92 (101)
Q Consensus        13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I   92 (101)
                      .|+++|+++++++|.|+|+||++|.|+|.|||+|||++|+||.|+...             ...+++|.+||||++|++|
T Consensus         3 ~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-------------~~~~~~g~~~IRG~~I~~I   69 (72)
T d1i4k1_           3 RPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNG-------------EVVRKVGSVVIRGDTVVFV   69 (72)
T ss_dssp             CHHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSS-------------SEEEEEEEEEECGGGEEEE
T ss_pred             ChHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecC-------------CeEeEcceEEEeCCeEEEE
Confidence            699999999999999999999999999999999999999999997531             2468899999999999999


Q ss_pred             ecC
Q psy3154          93 SPP   95 (101)
Q Consensus        93 ~~~   95 (101)
                      +++
T Consensus        70 spa   72 (72)
T d1i4k1_          70 SPA   72 (72)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            853

>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=99.91  E-value=5.5e-25  Score=135.99  Aligned_cols=75  Identities=20%  Similarity=0.470  Sum_probs=63.1

Q ss_pred             HHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEecC
Q psy3154          18 IRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPP   95 (101)
Q Consensus        18 L~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~   95 (101)
                      |.++++++|+|+|+|||.|.|+|.|||+||||+|++|.|++.....+.   ........|.+|++||||++|++|+..
T Consensus         3 L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~---~~~~~~~~r~lG~v~IRG~~Iv~i~~~   77 (81)
T d1d3bb_           3 MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNS---KQAEREEKRVLGLVLLRGENLVSMTVE   77 (81)
T ss_dssp             CGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSST---TSCCEEEEEEEEEEEECGGGEEEEEEE
T ss_pred             hHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccc---cccccceEEEeeeEEEeCCEEEEEEcc
Confidence            567899999999999999999999999999999999999987543221   112235679999999999999999854

>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=99.91  E-value=1.6e-24  Score=132.35  Aligned_cols=73  Identities=26%  Similarity=0.469  Sum_probs=65.7

Q ss_pred             ccCChHHHHHHhcCCEEEEEEcCC-eEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCe
Q psy3154          10 SVKEPLDLIRLSLDERVHVKMRNE-RVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDG   88 (101)
Q Consensus        10 ~~~~Pl~lL~~~l~k~V~V~l~~g-r~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~   88 (101)
                      ++..|+++|+++++++|+|+|++| +.|.|+|.|||+|||++|+||.|+...             ...+++|.+||||++
T Consensus         2 ~~~~P~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~-------------~~~~~~g~~~IRG~~   68 (75)
T d1ljoa_           2 AMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGE-------------EKVRSLGEIVLRGNN   68 (75)
T ss_dssp             CCCCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETT-------------EEEEEEEEEEECGGG
T ss_pred             CccccHHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCC-------------CcEeEcceEEEeCCE
Confidence            578899999999999999999965 899999999999999999999997531             357899999999999


Q ss_pred             EEEEecC
Q psy3154          89 VILVSPP   95 (101)
Q Consensus        89 Iv~I~~~   95 (101)
                      |++|++.
T Consensus        69 I~~I~p~   75 (75)
T d1ljoa_          69 VVLIQPQ   75 (75)
T ss_dssp             EEEEEEC
T ss_pred             EEEEECC
Confidence            9999863

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

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

Probab=99.91  E-value=2.7e-24  Score=130.04  Aligned_cols=69  Identities=32%  Similarity=0.537  Sum_probs=62.5

Q ss_pred             hHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEe
Q psy3154          14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVS   93 (101)
Q Consensus        14 Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~   93 (101)
                      .-+.|+++++++|.|+|+||+.|+|+|.+||+|||++|+||.|++.              .+.+++|.+||||++|++|+
T Consensus         3 ~~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~--------------~~~~~~g~v~iRG~~I~~I~   68 (71)
T d1i8fa_           3 LGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIID--------------GNVYKRGTMVVRGENVLFIS   68 (71)
T ss_dssp             HHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEET--------------TEEEEEEEEEECGGGEEEEE
T ss_pred             HhHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEEC--------------CCEEEcceEEEeCCeEEEEe
Confidence            4678999999999999999999999999999999999999999863              14678999999999999998


Q ss_pred             cCC
Q psy3154          94 PPN   96 (101)
Q Consensus        94 ~~~   96 (101)
                      +.+
T Consensus        69 ~~P   71 (71)
T d1i8fa_          69 PVP   71 (71)
T ss_dssp             ECC
T ss_pred             CCC
Confidence            753

>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=99.90  E-value=6.3e-24  Score=129.76  Aligned_cols=70  Identities=37%  Similarity=0.665  Sum_probs=64.0

Q ss_pred             CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154          12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL   91 (101)
Q Consensus        12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~   91 (101)
                      +.|..+|+++++++|+|.|+||+.|+|+|.|||+|||++|+||.|+...             ...+.+|.+||||++|++
T Consensus         6 ~~~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-------------~~~~~~~~v~iRG~~I~~   72 (76)
T d1th7a1           6 ETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSD-------------GSGKKLGTIVIRGDNVIL   72 (76)
T ss_dssp             HHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSS-------------SCEEEEEEEEECGGGEEE
T ss_pred             ccHHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecC-------------CcccCcceEEEECCEEEE
Confidence            4589999999999999999999999999999999999999999997542             246789999999999999


Q ss_pred             Eec
Q psy3154          92 VSP   94 (101)
Q Consensus        92 I~~   94 (101)
                      |++
T Consensus        73 I~~   75 (76)
T d1th7a1          73 ISP   75 (76)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            987

>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=99.89  E-value=2.2e-23  Score=126.16  Aligned_cols=72  Identities=17%  Similarity=0.326  Sum_probs=65.3

Q ss_pred             CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154          12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL   91 (101)
Q Consensus        12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~   91 (101)
                      +.|+.+|+++.|++|.|+|+||++|+|+|.+||.|||++|+||.++...             .+.++++.+||||++|.+
T Consensus         1 g~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~-------------~~~~~~~~v~IRG~~I~~   67 (72)
T d1d3ba_           1 GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRD-------------GRVAQLEQVYIRGCKIRF   67 (72)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTT-------------SCEEEEEEEEECGGGEEE
T ss_pred             CCchHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCC-------------CcEeEcCeEEEECCEEEE
Confidence            4699999999999999999999999999999999999999999886431             246789999999999999


Q ss_pred             EecCC
Q psy3154          92 VSPPN   96 (101)
Q Consensus        92 I~~~~   96 (101)
                      |..+|
T Consensus        68 i~lpd   72 (72)
T d1d3ba_          68 LILPD   72 (72)
T ss_dssp             EEECC
T ss_pred             EEcCC
Confidence            99987

>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=99.87  E-value=1.2e-22  Score=121.83  Aligned_cols=65  Identities=26%  Similarity=0.454  Sum_probs=57.0

Q ss_pred             HHHhcCCEEEEEEc-CCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEecC
Q psy3154          18 IRLSLDERVHVKMR-NERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPP   95 (101)
Q Consensus        18 L~~~l~k~V~V~l~-~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~   95 (101)
                      |+++++++|.|+|+ +|++|+|+|.+||+|||++|+||.|+...             ...+++|.+||||++|++|+..
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~-------------~~~~~lg~~~IRG~nI~~I~~~   66 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAG-------------VSHGTLGEIFIRCNNVLYIREL   66 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETT-------------EEEEECCSEEECGGGEEEEEEC
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEecC-------------CcccCcCeEEEECCEEEEEEeC
Confidence            56889999999999 56899999999999999999999997531             2467899999999999999743

>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=99.81  E-value=6.6e-20  Score=112.76  Aligned_cols=70  Identities=19%  Similarity=0.325  Sum_probs=62.6

Q ss_pred             HHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEec
Q psy3154          15 LDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP   94 (101)
Q Consensus        15 l~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~   94 (101)
                      ..+|+++.|++|.|.|++|..|+|+|.++|.|||+.|+||.++...             ....+++.+||||++|.+|..
T Consensus         3 v~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~-------------~~~~~~~~v~IRG~~Ir~i~l   69 (80)
T d1b34a_           3 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKN-------------REPVQLETLSIRGNNIRYFIL   69 (80)
T ss_dssp             HHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTT-------------SCCEEEEEEEECGGGEEEEEC
T ss_pred             HHHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCC-------------CCEEEcccEEEcCCEEEEEEC
Confidence            4689999999999999999999999999999999999999986421             235789999999999999999


Q ss_pred             CCC
Q psy3154          95 PNR   97 (101)
Q Consensus        95 ~~~   97 (101)
                      +|.
T Consensus        70 Pd~   72 (80)
T d1b34a_          70 PDS   72 (80)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            874

>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=99.75  E-value=1.7e-18  Score=114.57  Aligned_cols=66  Identities=24%  Similarity=0.397  Sum_probs=59.5

Q ss_pred             HHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEec
Q psy3154          15 LDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP   94 (101)
Q Consensus        15 l~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~   94 (101)
                      ++.|++++|++|.|.|+||+.|.|+|.+||+|||++|+||.+..                 ..+++.++|||++|.+|..
T Consensus         2 ~~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~-----------------~~k~~~v~IRG~~I~~I~~   64 (127)
T d1m5q1_           2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA-----------------GEKFNRVFIMYRYIVHIDS   64 (127)
T ss_dssp             HHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETT-----------------CCEEEEEEECGGGEEEEEE
T ss_pred             hhHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECC-----------------CCcccEEEEeCCeEEEEEc
Confidence            67899999999999999999999999999999999999998631                 1257889999999999998


Q ss_pred             CCC
Q psy3154          95 PNR   97 (101)
Q Consensus        95 ~~~   97 (101)
                      +|.
T Consensus        65 ~e~   67 (127)
T d1m5q1_          65 TER   67 (127)
T ss_dssp             CSC
T ss_pred             chh
Confidence            875

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

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

Probab=97.10  E-value=0.0016  Score=38.48  Aligned_cols=74  Identities=12%  Similarity=0.148  Sum_probs=56.3

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEEc-CCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEecCCCC
Q psy3154          21 SLDERVHVKMRNERVLRGKLHAYD-QHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNRT   98 (101)
Q Consensus        21 ~l~k~V~V~l~~gr~i~G~L~~~D-~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~~~~   98 (101)
                      ++|+++.+.-+.+-.|.|+|..+| +..-+.|+||..+-++-.+.  +  ........-+..++.||+.|--+...+..
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~--~--~~ipp~~~vy~~IvFrgsDIKdL~v~e~p   76 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPT--D--RPIAPRDETFEYIIFRGSDIKDLTVCEPP   76 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCC--S--SCCCCCCCCEEEEEEETTTEEEEEESSCC
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCC--C--CccCCCCcceeEEEEcCcCcceEEeccCC
Confidence            589999999999999999999999 45558899999876542211  1  11223455678999999999998886643

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

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

Probab=96.48  E-value=0.0082  Score=33.54  Aligned_cols=42  Identities=19%  Similarity=0.459  Sum_probs=33.6

Q ss_pred             HHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEE
Q psy3154          16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETV   58 (101)
Q Consensus        16 ~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~   58 (101)
                      ..|++|.|++|-+...+...|+|+|.-||... +.|+|++.+.
T Consensus         5 ktL~~WKg~kvAv~vgsehSFtGiledFDeEv-iLL~dV~D~~   46 (66)
T d1ycya1           5 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVI   46 (66)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETT
T ss_pred             HHHHHhCCcEEEEEecCcceeEEEhhhcCcce-EeehhhHHHh
Confidence            35788999999999999999999999999987 8889998753

>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=96.33  E-value=0.0057  Score=34.80  Aligned_cols=31  Identities=23%  Similarity=0.369  Sum_probs=26.4

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEEcCCCceEecc
Q psy3154          22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGD   53 (101)
Q Consensus        22 l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~   53 (101)
                      -...|.|-|.+|-.+.|.+.+||+|.= +|++
T Consensus        13 ~~~~VtifL~nGvkl~G~I~~fD~ftv-LL~~   43 (66)
T d1u1sa1          13 ERVPVSIYLVNGIKLQGQIESFDQFVI-LLKN   43 (66)
T ss_dssp             TTCCEEEEETTSCEEEEEEEEECSSEE-EEES
T ss_pred             cCCcEEEEEEcCcEEEEEEEEEcceEE-EEEC
Confidence            457999999999999999999999984 4443

>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=96.26  E-value=0.0064  Score=32.10  Aligned_cols=32  Identities=13%  Similarity=0.268  Sum_probs=28.1

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEEcCCCceEecc
Q psy3154          21 SLDERVHVKMRNERVLRGKLHAYDQHLNMVLGD   53 (101)
Q Consensus        21 ~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~   53 (101)
                      |++++|+|.. +++++.|+..++|....|+|+.
T Consensus         1 f~gk~V~v~~-g~~~i~G~a~gId~~G~Lll~t   32 (47)
T d1biaa2           1 FINRPVKLII-GDKEIFGISRGIDKQGALLLEQ   32 (47)
T ss_dssp             TTTSEEEEEE-TTEEEEEEEEEECTTSCEEEEE
T ss_pred             CCCCEEEEEE-CCeEEEEEEeeECCCCcEEEEE
Confidence            5899999976 5578999999999999999974

>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=95.78  E-value=0.014  Score=32.51  Aligned_cols=34  Identities=18%  Similarity=0.205  Sum_probs=29.0

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEEcCCCceEecceE
Q psy3154          22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVE   55 (101)
Q Consensus        22 l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~   55 (101)
                      -..+|.|-|.+|-.+.|.+.+||+|.=++..+..
T Consensus        13 ~~~~VtifL~nGvkl~G~I~~fD~ftvlL~~~~~   46 (60)
T d1kq1a_          13 NQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGK   46 (60)
T ss_dssp             HTCEEEEEETTSCEEEEEEEEECSSEEEEEETTE
T ss_pred             cCCcEEEEEECCcEEEEEEEEEcceEEEEEeCCc
Confidence            3579999999999999999999999966655544

>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=92.69  E-value=0.067  Score=30.16  Aligned_cols=33  Identities=18%  Similarity=0.498  Sum_probs=26.1

Q ss_pred             HHHhcCCEEEEEEc---C-CeEEEEEEEEEcCCCceEe
Q psy3154          18 IRLSLDERVHVKMR---N-ERVLRGKLHAYDQHLNMVL   51 (101)
Q Consensus        18 L~~~l~k~V~V~l~---~-gr~i~G~L~~~D~~mNlvL   51 (101)
                      ...++|+.|.|+|+   + .+.+.|+|.++|... +.|
T Consensus         9 f~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~~-i~l   45 (74)
T d1ib8a1           9 VAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEEDE-LTM   45 (74)
T ss_dssp             HHHHCSEEEEEECSSCSSSCSEEEEEEEEEETTE-EEE
T ss_pred             HHHhCCCEEEEEEecccCCceEEEEEEEeecCCe-EEE
Confidence            45669999999985   3 479999999999864 444