Psyllid ID: psy17123

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-----
Protein Sequence
MAAVNTTTDAGAETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHKEYEDSNLY
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccHHHHcccEEEEEEcccEEEEEEEEEEcccccEEEccEEEEEEccccccEEEEEEEEEEEcccEEEEEccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccHHHHHHHHHHHcccEEEEEccccEEEEEEccccHHHHHHHHHHHHHHcccccccEEEEEEEEEEEcccEEcccccccccccccccc
Coil and Loop (DISEMBL)
maavntttdagaetkdrkrKESILDLSKFLDKVIRVKfaggrecsgilkgfdpllnlvldNTTEYLRVTYQSVQVRSWCSIVRRqesrrnvhrrdhkeyedsnly
Flexible Loop (DISEMBL)
maavntttdagaetkdrkrkesildlskfLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYqsvqvrswcsivrrqesrrnvhrrdhkeyedsnly
Low Complexity Region (SEG)
MAAVNTTTDAGAETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHKEYEDSNLY
Disordered region (IsUnstruct)
**********************ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVR**********************
Disordered Region (DISOPRED)
***************************KFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHKE*****L*
Disordered Region (DISEMBL)
********************ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQE*******************
Disordered Region (DISPRO)
*****************KRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHKEYE*****
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAAVNTTTDAGAETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHKEYEDSNLY
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	105	2.2.26 [Sep-21-2011]
Q9CQQ8	103	U6 snRNA-associated Sm-li	yes	N/A	0.504	0.514	0.792	1e-18
Q9UK45	103	U6 snRNA-associated Sm-li	yes	N/A	0.504	0.514	0.792	1e-18
O74499	113	U6 snRNA-associated Sm-li	yes	N/A	0.533	0.495	0.571	3e-12
Q54HF6	97	Probable U6 snRNA-associa	yes	N/A	0.476	0.515	0.64	2e-11
P53905	115	U6 snRNA-associated Sm-li	yes	N/A	0.457	0.417	0.562	6e-10
P62309	76	Small nuclear ribonucleop	no	N/A	0.390	0.539	0.512	2e-06
P62308	76	Small nuclear ribonucleop	no	N/A	0.390	0.539	0.512	2e-06
Q3ZBL0	76	Small nuclear ribonucleop	no	N/A	0.390	0.539	0.512	2e-06
Q9VXE0	76	Probable small nuclear ri	no	N/A	0.380	0.526	0.5	2e-06
Q9N4G9	77	Probable small nuclear ri	no	N/A	0.390	0.532	0.487	2e-06

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

 Score = 91.7 bits (226), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 42/53 (79%), Positives = 48/53 (90%)

Query: 15 KDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          K++K+KESILDLSK++DK IRVKF GGRE SGILKGFDPLLNLVLD T EY+R
Sbjct: 4  KEKKKKESILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTMEYMR 56

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

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

 Score = 91.7 bits (226), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 42/53 (79%), Positives = 48/53 (90%)

Query: 15 KDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          K++K+KESILDLSK++DK IRVKF GGRE SGILKGFDPLLNLVLD T EY+R
Sbjct: 4  KEKKKKESILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMR 56

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

Homo sapiens (taxid: 9606)

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

 Score = 70.5 bits (171), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 32/56 (57%), Positives = 43/56 (76%)

Query: 12 AETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          ++  +R RKESILDLS++ D+ I+  F GGR+ +GILKGFD L+NLVLD+  E LR
Sbjct: 14 SQPTERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLR 69

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner.

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

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

 Score = 67.4 bits (163), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/50 (64%), Positives = 38/50 (76%)

Query: 18 KRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
           +KESILDL KFL K I VKF GGRE  GILKG+D L+N+ LD T E++R
Sbjct: 7  PKKESILDLQKFLGKEICVKFTGGREVQGILKGYDQLVNITLDQTQEFIR 56

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

Dictyostelium discoideum (taxid: 44689)

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

 Score = 62.8 bits (151), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 27/48 (56%), Positives = 38/48 (79%)

Query: 19 RKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYL 66
          ++E+ILDL+K+ D  IRVK  GG+   G+LKG+D L+NLVLD+T EY+
Sbjct: 23 KREAILDLAKYKDSKIRVKLMGGKLVIGVLKGYDQLMNLVLDDTVEYM 70

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

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

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

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/41 (51%), Positives = 28/41 (68%)

Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          +L KF+DK + +K  GGR   GIL+GFDP +NLV+D   E 
Sbjct: 8  ELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEM 48

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

Mus musculus (taxid: 10090)

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

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/41 (51%), Positives = 28/41 (68%)

Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          +L KF+DK + +K  GGR   GIL+GFDP +NLV+D   E 
Sbjct: 8  ELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEM 48

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

Homo sapiens (taxid: 9606)

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

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/41 (51%), Positives = 28/41 (68%)

Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          +L KF+DK + +K  GGR   GIL+GFDP +NLV+D   E 
Sbjct: 8  ELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEM 48

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

Bos taurus (taxid: 9913)

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

 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 20/40 (50%), Positives = 31/40 (77%)

Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTE 64
          ++ K++DK + +K  GGR  +GIL+GFDP +N+VLD+T E
Sbjct: 8  EVKKYMDKRMMLKLNGGRAVTGILRGFDPFMNVVLDDTVE 47

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

Drosophila melanogaster (taxid: 7227)

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

 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 29/41 (70%)

Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          +L K++DK + +K  G R  SGIL+GFDP +N+V+D   EY
Sbjct: 8  ELKKYMDKEMDLKLNGNRRVSGILRGFDPFMNMVIDEAVEY 48

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

Caenorhabditis elegans (taxid: 6239)

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	105
328791249	113	PREDICTED: U6 snRNA-associated Sm-like p	0.638	0.592	0.731	2e-20
383847376	115	PREDICTED: U6 snRNA-associated Sm-like p	0.561	0.513	0.813	1e-19
340721932	113	PREDICTED: u6 snRNA-associated Sm-like p	0.638	0.592	0.701	2e-19
328791247	109	PREDICTED: U6 snRNA-associated Sm-like p	0.590	0.568	0.758	3e-19
156544990	115	PREDICTED: U6 snRNA-associated Sm-like p	0.533	0.486	0.821	7e-19
357613355	116	U6 snRNA-associated Sm-like protein [Dan	0.580	0.525	0.721	1e-18
307194533	107	U6 snRNA-associated Sm-like protein LSm7	0.533	0.523	0.821	1e-18
242009022	109	conserved hypothetical protein [Pediculu	0.533	0.513	0.803	2e-18
91089491	113	PREDICTED: similar to U6 snRNA-associate	0.533	0.495	0.803	2e-18
332374862	116	unknown [Dendroctonus ponderosae]	0.523	0.474	0.818	3e-18

>gi|328791249|ref|XP_003251537.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7 isoform 2 [Apis mellifera] gi|350407868|ref|XP_003488222.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like [Bombus impatiens] gi|380018582|ref|XP_003693206.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like isoform 2 [Apis florea]

 Score =  103 bits (256), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 49/67 (73%), Positives = 57/67 (85%)

Query: 1  MAAVNTTTDAGAETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLD 60
          M+A     +A  E K+RK+KESILDLSK+L+K IRVKFAGGRE +GILKG+DPLLNLVLD
Sbjct: 1  MSAAKQQQNAHGEPKERKKKESILDLSKYLEKNIRVKFAGGREAAGILKGYDPLLNLVLD 60

Query: 61 NTTEYLR 67
          NTTEYLR
Sbjct: 61 NTTEYLR 67

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383847376|ref|XP_003699330.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like [Megachile rotundata]

 Score =  100 bits (249), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 48/59 (81%), Positives = 54/59 (91%)

Query: 9  DAGAETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          +A  E K+RKRKESILDLSK+L+K IRVKFAGGRE +GILKG+DPLLNLVLDNTTEYLR
Sbjct: 11 NAHGEPKERKRKESILDLSKYLEKNIRVKFAGGREAAGILKGYDPLLNLVLDNTTEYLR 69

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340721932|ref|XP_003399367.1| PREDICTED: u6 snRNA-associated Sm-like protein LSm7-like [Bombus terrestris]

 Score = 99.4 bits (246), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/67 (70%), Positives = 55/67 (82%)

Query: 1  MAAVNTTTDAGAETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLD 60
          M+      +   E K+RK+KESILDLSK+L+K IRVKFAGGRE +GILKG+DPLLNLVLD
Sbjct: 1  MSTAKQQQNTHGEPKERKKKESILDLSKYLEKNIRVKFAGGREAAGILKGYDPLLNLVLD 60

Query: 61 NTTEYLR 67
          NTTEYLR
Sbjct: 61 NTTEYLR 67

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328791247|ref|XP_001121212.2| PREDICTED: U6 snRNA-associated Sm-like protein LSm7 isoform 1 [Apis mellifera] gi|380018580|ref|XP_003693205.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7-like isoform 1 [Apis florea]

 Score = 99.4 bits (246), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 47/62 (75%), Positives = 55/62 (88%)

Query: 6  TTTDAGAETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          +  +A  E K+RK+KESILDLSK+L+K IRVKFAGGRE +GILKG+DPLLNLVLDNTTEY
Sbjct: 2  SQQNAHGEPKERKKKESILDLSKYLEKNIRVKFAGGREAAGILKGYDPLLNLVLDNTTEY 61

Query: 66 LR 67
          LR
Sbjct: 62 LR 63

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156544990|ref|XP_001608041.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm7 [Nasonia vitripennis]

 Score = 97.8 bits (242), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 46/56 (82%), Positives = 53/56 (94%)

Query: 12 AETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          ++ K++KRKESILDLSK+L+K IRVKFAGGRE SGILKG+DPLLNLVLDNTTEYLR
Sbjct: 14 SDQKEKKRKESILDLSKYLEKNIRVKFAGGREASGILKGYDPLLNLVLDNTTEYLR 69

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357613355|gb|EHJ68454.1| U6 snRNA-associated Sm-like protein [Danaus plexippus]

 Score = 97.4 bits (241), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 44/61 (72%), Positives = 55/61 (90%)

Query: 7  TTDAGAETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYL 66
          ++  G + K+++RKESILDLSK+L+K IRVKFAGGRE +GILKG+DPLLNLVLDNTTE+L
Sbjct: 11 SSQGGGDNKEKRRKESILDLSKYLEKCIRVKFAGGREAAGILKGYDPLLNLVLDNTTEFL 70

Query: 67 R 67
          R
Sbjct: 71 R 71

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307194533|gb|EFN76825.1| U6 snRNA-associated Sm-like protein LSm7 [Harpegnathos saltator]

 Score = 96.7 bits (239), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 46/56 (82%), Positives = 52/56 (92%)

Query: 12 AETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
           E K++KRKESILDLSK+L+K IRVKFAGGRE +GILKG+DPLLNLVLDNTTEYLR
Sbjct: 6  VEHKEKKRKESILDLSKYLEKNIRVKFAGGREAAGILKGYDPLLNLVLDNTTEYLR 61

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242009022|ref|XP_002425292.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212509057|gb|EEB12554.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score = 96.3 bits (238), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/56 (80%), Positives = 52/56 (92%)

Query: 12 AETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
           + K++KRKESILDLSK+L+K IRVKFAGGRE +GILKGFDPLLNLVLDNTTE+LR
Sbjct: 8  GDQKEKKRKESILDLSKYLEKSIRVKFAGGREAAGILKGFDPLLNLVLDNTTEFLR 63

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91089491|ref|XP_969723.1| PREDICTED: similar to U6 snRNA-associated Sm-like protein [Tribolium castaneum]

 Score = 96.3 bits (238), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/56 (80%), Positives = 51/56 (91%)

Query: 12 AETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
           + K++KRKESILDLSK+L+K IRVKFAGGRE SGILKG+DPLLNLVLDNT EYLR
Sbjct: 13 GDQKEKKRKESILDLSKYLEKTIRVKFAGGREASGILKGYDPLLNLVLDNTIEYLR 68

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332374862|gb|AEE62572.1| unknown [Dendroctonus ponderosae]

 Score = 95.9 bits (237), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 45/55 (81%), Positives = 51/55 (92%)

Query: 13 ETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          + K++KRKESILDLSK+L+K IRVKFAGGRE SGILKG+DPLLNLVLDNT EYLR
Sbjct: 17 DQKEKKRKESILDLSKYLEKTIRVKFAGGREASGILKGYDPLLNLVLDNTIEYLR 71

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	105
UNIPROTKB|Q9UK45	103	LSM7 "U6 snRNA-associated Sm-l	0.504	0.514	0.792	2.8e-18
FB|FBgn0261068	110	LSm7 [Drosophila melanogaster	0.504	0.481	0.811	3.6e-18
ZFIN|ZDB-GENE-030131-8284	103	lsm7 "LSM7 homolog, U6 small n	0.504	0.514	0.773	7.5e-18
WB|WBGene00003081	104	lsm-7 [Caenorhabditis elegans	0.514	0.519	0.642	8.8e-15
UNIPROTKB|Q23543	104	lsm-7 "Protein LSM-7" [Caenorh	0.514	0.519	0.642	8.8e-15
ASPGD|ASPL0000056132	136	AN0767 [Emericella nidulans (t	0.714	0.551	0.493	1.3e-13
DICTYBASE|DDB_G0289499	97	lsm7 "putative U6 small nuclea	0.466	0.505	0.653	3.9e-12
POMBASE|SPCC285.12	113	lsm7 "U6 snRNP-associated prot	0.533	0.495	0.571	3.9e-12
UNIPROTKB|G4NLE3	146	MGG_02938 "Uncharacterized pro	0.504	0.363	0.566	5e-12
TAIR|locus:2056825	99	EMB2816 "AT2G03870" [Arabidops	0.466	0.494	0.591	8.2e-12

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

 Score = 221 (82.9 bits), Expect = 2.8e-18, P = 2.8e-18
 Identities = 42/53 (79%), Positives = 48/53 (90%)

Query:    15 KDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
             K++K+KESILDLSK++DK IRVKF GGRE SGILKGFDPLLNLVLD T EY+R
Sbjct:     4 KEKKKKESILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMR 56

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0017070 "U6 snRNA binding" evidence=NAS

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

GO:0005634 "nucleus" evidence=NAS

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

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

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

GO:0005515 "protein binding" evidence=IPI

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

 Score = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 43/53 (81%), Positives = 49/53 (92%)

Query:    15 KDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
             K+++RKESILDLSK+L+K IRVKFAGGRE SGILKG+D LLNLVLDNT EYLR
Sbjct:    13 KEKRRKESILDLSKYLEKQIRVKFAGGREASGILKGYDALLNLVLDNTVEYLR 65

GO:0005688 "U6 snRNP" evidence=ISS

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

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

GO:0022008 "neurogenesis" evidence=IMP

ZFIN|ZDB-GENE-030131-8284 lsm7 "LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 217 (81.4 bits), Expect = 7.5e-18, P = 7.5e-18
 Identities = 41/53 (77%), Positives = 47/53 (88%)

Query:    15 KDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
             KD+K+KESI DLSK++DK IRVKF GGRE SG+LKGFDPLLNLVLD T EY+R
Sbjct:     4 KDKKKKESIFDLSKYIDKHIRVKFQGGREASGVLKGFDPLLNLVLDGTIEYMR 56

GO:0003674 "molecular_function" evidence=ND

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

 Score = 188 (71.2 bits), Expect = 8.8e-15, P = 8.8e-15
 Identities = 36/56 (64%), Positives = 48/56 (85%)

Query:    14 TKD--RKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
             +KD  +++KES++DL++FLDK IRVKF GGRE SG+L+GFD LLN+VLD+  EYLR
Sbjct:     2 SKDEGKRKKESVVDLTRFLDKEIRVKFQGGREASGVLRGFDQLLNMVLDDCREYLR 57

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

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

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

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

GO:0040020 "regulation of meiosis" evidence=IMP

GO:0008406 "gonad development" evidence=IMP

GO:0016477 "cell migration" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

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

 Score = 188 (71.2 bits), Expect = 8.8e-15, P = 8.8e-15
 Identities = 36/56 (64%), Positives = 48/56 (85%)

Query:    14 TKD--RKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
             +KD  +++KES++DL++FLDK IRVKF GGRE SG+L+GFD LLN+VLD+  EYLR
Sbjct:     2 SKDEGKRKKESVVDLTRFLDKEIRVKFQGGREASGVLRGFDQLLNMVLDDCREYLR 57

GO:0005515 "protein binding" evidence=IPI

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

 Score = 177 (67.4 bits), Expect = 1.3e-13, P = 1.3e-13
 Identities = 37/75 (49%), Positives = 53/75 (70%)

Query:    10 AGAETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVT 69
             A  + +++ +KE+ILDL+K++DK +RVKF GGRE SGILKG+D L+NLVLD+  E +R  
Sbjct:    37 AQQQQQEKPKKENILDLTKYMDKEVRVKFNGGREVSGILKGYDQLMNLVLDDVKESMRDD 96

Query:    70 YQSVQVRSWCSIVRR 84
               +   R+   IV R
Sbjct:    97 EGNETTRALGLIVAR 111

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

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

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

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

GO:0005688 "U6 snRNP" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

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

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

 Score = 163 (62.4 bits), Expect = 3.9e-12, P = 3.9e-12
 Identities = 32/49 (65%), Positives = 38/49 (77%)

Query:    19 RKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
             +KESILDL KFL K I VKF GGRE  GILKG+D L+N+ LD T E++R
Sbjct:     8 KKESILDLQKFLGKEICVKFTGGREVQGILKGYDQLVNITLDQTQEFIR 56

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

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

GO:0006402 "mRNA catabolic process" evidence=ISS

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

GO:0005730 "nucleolus" evidence=ISS

GO:0005688 "U6 snRNP" evidence=ISS

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

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

 Score = 163 (62.4 bits), Expect = 3.9e-12, P = 3.9e-12
 Identities = 32/56 (57%), Positives = 43/56 (76%)

Query:    12 AETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
             ++  +R RKESILDLS++ D+ I+  F GGR+ +GILKGFD L+NLVLD+  E LR
Sbjct:    14 SQPTERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLR 69

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=IDA

GO:0005681 "spliceosomal complex" evidence=NAS

GO:0005688 "U6 snRNP" evidence=ISO

GO:0005829 "cytosol" evidence=IDA

GO:0006402 "mRNA catabolic process" evidence=ISS

GO:0008033 "tRNA processing" evidence=IEA

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

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

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

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

 Score = 162 (62.1 bits), Expect = 5.0e-12, P = 5.0e-12
 Identities = 30/53 (56%), Positives = 42/53 (79%)

Query:    15 KDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
             ++R +KE+ILDL+K++DK ++VKF GGRE  G LKG+D L+NLVLD   E +R
Sbjct:    50 RERPKKENILDLAKYMDKEVQVKFNGGREVIGTLKGYDALMNLVLDEVKETMR 102

GO:0003674 "molecular_function" evidence=ND

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

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 29/49 (59%), Positives = 40/49 (81%)

Query:    19 RKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
             RKE++LDL+KF+DK ++VK  GGR+ +G LKG+D LLNLVLD   E++R
Sbjct:     4 RKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFVR 52

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM;ISS

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

---

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)
Q54HF6	LSM7_DICDI	No assigned EC number	0.64	0.4761	0.5154	yes	N/A
Q9UK45	LSM7_HUMAN	No assigned EC number	0.7924	0.5047	0.5145	yes	N/A
P53905	LSM7_YEAST	No assigned EC number	0.5625	0.4571	0.4173	yes	N/A
Q9CQQ8	LSM7_MOUSE	No assigned EC number	0.7924	0.5047	0.5145	yes	N/A
O74499	LSM7_SCHPO	No assigned EC number	0.5714	0.5333	0.4955	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	105
cd01729	89	cd01729, LSm7, Like-Sm protein 7	2e-28
cd01719	70	cd01719, Sm_G, Sm protein G	2e-14
smart00651	67	smart00651, Sm, snRNP Sm proteins	3e-11
pfam01423	66	pfam01423, LSM, LSM domain	3e-10
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	5e-08
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	5e-08
cd00600	63	cd00600, Sm_like, Sm and related proteins	1e-07
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	3e-07
cd01727	91	cd01727, LSm8, Like-Sm protein 8	7e-06
cd06168	73	cd06168, LSMD1, LSM domain containing 1	1e-05
cd11679	65	cd11679, archaeal_Sm_like, archaeal Sm-related pro	5e-05
cd01722	69	cd01722, Sm_F, Sm protein F	8e-05
cd01730	82	cd01730, LSm3, Like-Sm protein 3	1e-04
cd01732	76	cd01732, LSm5, Like-Sm protein 5	1e-04
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	3e-04
cd01726	68	cd01726, LSm6, Like-Sm protein 6	7e-04

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

 Score = 98.0 bits (245), Expect = 2e-28
 Identities = 38/48 (79%), Positives = 43/48 (89%)

Query: 20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          KESILDLSK++DK IRVKF GGRE +GILKG+D LLNLVLD+T EYLR
Sbjct: 1  KESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLR 48

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

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

 Score = 62.1 bits (152), Expect = 2e-14
 Identities = 20/41 (48%), Positives = 30/41 (73%)

Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          +L K++DK + +K  G R+ SG+L+GFDP +NLVLD+  E 
Sbjct: 4  ELKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEE 44

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. 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|197820 smart00651, Sm, snRNP Sm proteins

 Score = 53.7 bits (130), Expect = 3e-11
 Identities = 18/52 (34%), Positives = 29/52 (55%)

Query: 24 LDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQV 75
            L K + K + V+   GRE  G LKGFD  +NLVL++  E ++   +  ++
Sbjct: 1  KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKL 52

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

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

 Score = 51.4 bits (124), Expect = 3e-10
 Identities = 20/49 (40%), Positives = 27/49 (55%)

Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSV 73
           L K L K + V+   GRE  G LKGFD  +NLVLD+  E ++    + 
Sbjct: 2  FLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNK 50

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 = 45.8 bits (109), Expect = 5e-08
 Identities = 20/40 (50%), Positives = 24/40 (60%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          L K L+K + VK   GRE  G L GFD  +NLVLD+  E 
Sbjct: 12 LKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEI 51

Length = 79

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

 Score = 45.6 bits (109), Expect = 5e-08
 Identities = 21/39 (53%), Positives = 28/39 (71%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTE 64
          L++ L+K + VK  GG+E  G+LKGFD  LNLVL+N  E
Sbjct: 6  LNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEE 44

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|212462 cd00600, Sm_like, Sm and related proteins

 Score = 44.5 bits (106), Expect = 1e-07
 Identities = 17/42 (40%), Positives = 23/42 (54%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          L  F+ K + V+   GR  +G L  FD  +NLVLD+  E  R
Sbjct: 1  LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGR 42

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|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional

 Score = 43.4 bits (103), Expect = 3e-07
 Identities = 20/42 (47%), Positives = 27/42 (64%), Gaps = 1/42 (2%)

Query: 24 LD-LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTE 64
          LD L+  L+  + V+  GGRE  G L+G+D  +NLVLDN  E
Sbjct: 6  LDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEE 47

Length = 72

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

 Score = 40.6 bits (96), Expect = 7e-06
 Identities = 20/50 (40%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQV 75
          L  +L+K + V    GR   G LKGFD   NL+L N  E  RV      V
Sbjct: 4  LEDYLNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHE--RVYSSDEGV 51

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

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

 Score = 39.8 bits (94), Expect = 1e-05
 Identities = 15/45 (33%), Positives = 20/45 (44%)

Query: 23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
           L L K L + +RV    GR   G     D   N++L N  EY +
Sbjct: 1  RLKLRKLLGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRK 45

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

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

 Score = 38.0 bits (89), Expect = 5e-05
 Identities = 17/40 (42%), Positives = 24/40 (60%), Gaps = 1/40 (2%)

Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPL-LNLVLDNTT 63
          +L+  LDK + V  + G+  +G L GFDP  LN+VL N  
Sbjct: 4  ELNSLLDKEVIVTLSNGKTYTGQLVGFDPSSLNIVLTNAK 43

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

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

 Score = 37.6 bits (88), Expect = 8e-05
 Identities = 16/40 (40%), Positives = 19/40 (47%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          L+    K + VK   G E  G L   D  +NL L NT EY
Sbjct: 6  LNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEY 45

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

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

 Score = 37.2 bits (87), Expect = 1e-04
 Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 24 LDLSKF-LDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          LDL +  LD+ + VK  G RE  G L  +D  LN++L +  E 
Sbjct: 3  LDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEET 45

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

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

 Score = 36.8 bits (86), Expect = 1e-04
 Identities = 13/32 (40%), Positives = 19/32 (59%)

Query: 34 IRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          I +     +E  G L GFD  +N+VL++ TEY
Sbjct: 16 IWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEY 47

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

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

 Score = 35.9 bits (83), Expect = 3e-04
 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 5/58 (8%)

Query: 28 KFLDKVIRVKFAG-GRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRR 84
            +   IRV+  G   +  G L   D  +NL L +T E +       +VRS  ++V R
Sbjct: 7  SLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVG----EEKVRSLGTVVLR 60

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

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

 Score = 34.8 bits (81), Expect = 7e-04
 Identities = 17/40 (42%), Positives = 23/40 (57%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          L K + K + VK   G E  G+L   D  +NLVL++T EY
Sbjct: 6  LKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEY 45

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	105
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.92
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.91
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.9
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.9
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.89
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.89
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.89
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.88
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.88
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.87
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.87
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.86
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.86
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.86
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.83
KOG1781|consensus	108		99.83
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.83
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.83
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.81
KOG1780|consensus	77		99.81
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.8
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.78
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.77
KOG3482|consensus	79		99.7
KOG1784|consensus	96		99.68
KOG1782|consensus	129		99.58
KOG1783|consensus	77		99.57
KOG3460|consensus	91		99.55
KOG3168|consensus	177		99.55
KOG1775|consensus	84		99.48
KOG1774|consensus	88		99.45
KOG3293|consensus	134		99.38
KOG3448|consensus	96		99.36
KOG3172|consensus	119		99.03
KOG3428|consensus	109		98.86
KOG3459|consensus	114		98.34
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	98.14
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	97.94
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	97.29
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	96.8
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	96.74
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	96.64
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	96.42
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	96.29
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	95.89
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	95.64
PRK14638	150	hypothetical protein; Provisional	95.35
COG1923	77	Hfq Uncharacterized host factor I protein [General	95.12
PRK14639	140	hypothetical protein; Provisional	94.79
PRK02001	152	hypothetical protein; Validated	94.72
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	94.51
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	94.15
PRK14644	136	hypothetical protein; Provisional	93.68
PRK14091	165	RNA-binding protein Hfq; Provisional	93.19
PRK14091	165	RNA-binding protein Hfq; Provisional	93.11
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	93.01
PRK14640	152	hypothetical protein; Provisional	92.85
PRK14633	150	hypothetical protein; Provisional	92.28
KOG1073|consensus	361		91.95
PRK14645	154	hypothetical protein; Provisional	91.51
PRK14642	197	hypothetical protein; Provisional	91.32
PRK14636	176	hypothetical protein; Provisional	91.09
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	91.02
PRK00092	154	ribosome maturation protein RimP; Reviewed	90.83
PRK14632	172	hypothetical protein; Provisional	90.54
PRK14634	155	hypothetical protein; Provisional	90.49
PRK14643	164	hypothetical protein; Provisional	90.47
COG0779	153	Uncharacterized protein conserved in bacteria [Fun	90.15
PRK14647	159	hypothetical protein; Provisional	89.82
PRK14646	155	hypothetical protein; Provisional	89.32
PRK14631	174	hypothetical protein; Provisional	88.49
PRK06955	300	biotin--protein ligase; Provisional	87.69
PRK14637	151	hypothetical protein; Provisional	87.44
PRK14641	173	hypothetical protein; Provisional	87.35
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	84.28
PRK13325	592	bifunctional biotin--[acetyl-CoA-carboxylase] liga	82.09
TIGR00121	237	birA_ligase birA, biotin-[acetyl-CoA-carboxylase]	81.92

>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=6.3e-25  Score=142.81  Aligned_cols=77  Identities=56%  Similarity=0.770  Sum_probs=67.5

Q ss_pred             ccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCce----eeeeeEEeeEEEcCCcEEEEEecC
Q psy17123         20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQ----SVQVRSWCSIVRRQESRRNVHRRD   95 (105)
Q Consensus        20 ~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~----~~~~~~lg~vlIRG~~I~~i~~~d   95 (105)
                      ++++..|.++++|+|+|+|+|||.|+|+|.|||+||||+|++|+|+...++.    ....+.+|.++|||++|++|++.|
T Consensus         1 ~~~~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~   80 (81)
T cd01729           1 KESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD   80 (81)
T ss_pred             CcchhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence            3578899999999999999999999999999999999999999999764321    124688999999999999999876


Q ss_pred             C
Q psy17123         96 H   96 (105)
Q Consensus        96 ~   96 (105)
                      +
T Consensus        81 ~   81 (81)
T cd01729          81 G   81 (81)
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. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

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

Probab=99.91  E-value=1.1e-23  Score=134.19  Aligned_cols=70  Identities=34%  Similarity=0.535  Sum_probs=63.8

Q ss_pred             hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123         23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH   96 (105)
Q Consensus        23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~   96 (105)
                      .++|+++++|+|+|+|++||.++|+|.|||+||||+|++|.|+..+.    ..+.+|.++|||++|++|++.|.
T Consensus         2 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~----~~~~lg~v~IRG~~I~~i~~~~~   71 (72)
T cd01719           2 PPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGG----EKNNIGMVVIRGNSIVMLEALER   71 (72)
T ss_pred             chhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCC----ceeEeceEEECCCEEEEEEcccc
Confidence            46899999999999999999999999999999999999999986432    36889999999999999998875

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.

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

Probab=99.90  E-value=1.5e-23  Score=133.89  Aligned_cols=73  Identities=29%  Similarity=0.380  Sum_probs=64.9

Q ss_pred             hhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123         24 LDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH   96 (105)
Q Consensus        24 ~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~   96 (105)
                      +.|+++++++|+|+++|||.|.|+|+|||+||||+|++|.|+....++....+.+|.++|||++|++|+++|.
T Consensus         2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d~   74 (74)
T cd01727           2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEIDE   74 (74)
T ss_pred             hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccCC
Confidence            5799999999999999999999999999999999999999987643323346789999999999999999874

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=99.90  E-value=3.3e-23  Score=132.87  Aligned_cols=73  Identities=29%  Similarity=0.289  Sum_probs=65.2

Q ss_pred             cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEec
Q psy17123         21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRR   94 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~   94 (105)
                      .+++.|+++++|+|.|.++|||.|.|+|.|||+||||+|+||.|+...++ ++..+.+|.++|||++|++|+++
T Consensus         2 ~~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~-~~~~~~lG~~viRG~~V~~ig~~   74 (74)
T cd01728           2 PGTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGD-KYGDIPRGIFIIRGENVVLLGEI   74 (74)
T ss_pred             CchHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCC-ccceeEeeEEEEECCEEEEEEcC
Confidence            46889999999999999999999999999999999999999999876542 23468899999999999999853

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.

>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=99.89  E-value=4.3e-23  Score=129.62  Aligned_cols=68  Identities=31%  Similarity=0.433  Sum_probs=61.6

Q ss_pred             chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123         22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR   93 (105)
Q Consensus        22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~   93 (105)
                      |...|+++++++|+|+|++|+.|.|+|.|||+||||+|++|.|...++    ..+.+|.++|||++|++|++
T Consensus         1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~----~~~~lg~~~iRG~~I~~i~~   68 (68)
T cd01731           1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGE----PVRKYGRVVIRGDNVLFISP   68 (68)
T ss_pred             ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCC----eEeEcCcEEEeCCEEEEEcC
Confidence            356789999999999999999999999999999999999999987654    36789999999999999974

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.

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.89  E-value=7.1e-23  Score=130.25  Aligned_cols=69  Identities=33%  Similarity=0.433  Sum_probs=61.8

Q ss_pred             cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123         21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR   93 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~   93 (105)
                      .|...|+++++++|+|+|+||+.|+|+|.|||+||||+|+||.|...+ +   ..+.+|.++|||++|++|.+
T Consensus         4 ~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-~---~~~~lg~v~iRG~~V~~i~~   72 (72)
T PRK00737          4 RPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDG-E---VVRKLGKVVIRGDNVVYVSP   72 (72)
T ss_pred             chHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCC-C---eEeEcCcEEEeCCEEEEEcC
Confidence            467789999999999999999999999999999999999999997533 2   36789999999999999863

>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=99.89  E-value=1.7e-22  Score=130.10  Aligned_cols=72  Identities=21%  Similarity=0.275  Sum_probs=62.6

Q ss_pred             chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEec
Q psy17123         22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRR   94 (105)
Q Consensus        22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~   94 (105)
                      |...|+++++++|+|++++||++.|+|.|||+|||++|+||.|++..+++ ...+.+|.++|||++|++|++.
T Consensus         4 P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~-~~~~~lg~v~iRG~nV~~i~p~   75 (76)
T cd01732           4 PLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEG-RKITKLDQILLNGNNICMLVPG   75 (76)
T ss_pred             hHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCC-ceeeEcCeEEEeCCeEEEEECC
Confidence            45568999999999999999999999999999999999999999743321 1467899999999999999863

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.

>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=99.88  E-value=1.5e-22  Score=131.65  Aligned_cols=72  Identities=25%  Similarity=0.289  Sum_probs=61.7

Q ss_pred             chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCce---------eeeeeEEeeEEEcCCcEEEEE
Q psy17123         22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQ---------SVQVRSWCSIVRRQESRRNVH   92 (105)
Q Consensus        22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~---------~~~~~~lg~vlIRG~~I~~i~   92 (105)
                      |...|+.+++++|.|+|+|||.|.|+|+|||+||||+|+||.|++.....         ....+.+|.++|||++|++|+
T Consensus         2 pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~   81 (82)
T cd01730           2 PLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVS   81 (82)
T ss_pred             chHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEEC
Confidence            44567888999999999999999999999999999999999999864211         124689999999999999986


Q ss_pred             e
Q psy17123         93 R   93 (105)
Q Consensus        93 ~   93 (105)
                      +
T Consensus        82 ~   82 (82)
T cd01730          82 P   82 (82)
T ss_pred             C
Confidence            3

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

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

Probab=99.88  E-value=4.2e-22  Score=128.52  Aligned_cols=69  Identities=23%  Similarity=0.399  Sum_probs=60.8

Q ss_pred             hhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCc------eeeeeeEEeeEEEcCCcEEEEE
Q psy17123         24 LDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTY------QSVQVRSWCSIVRRQESRRNVH   92 (105)
Q Consensus        24 ~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~------~~~~~~~lg~vlIRG~~I~~i~   92 (105)
                      ..|.+|++++|+|.|+|||.|.|+|.|||+||||+|+||.|++....      ...+.+.+|+++|||++|++|+
T Consensus         3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~   77 (79)
T cd01717           3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMT   77 (79)
T ss_pred             chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEE
Confidence            46899999999999999999999999999999999999999875321      1234688999999999999997

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.

>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=99.87  E-value=4.8e-22  Score=124.69  Aligned_cols=67  Identities=21%  Similarity=0.312  Sum_probs=59.5

Q ss_pred             chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEE
Q psy17123         22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVH   92 (105)
Q Consensus        22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~   92 (105)
                      |...|+++++++|+|+|++|++|+|+|.|||+||||+|++|.|....+    ..+.+|.++|||++|++|+
T Consensus         1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~----~~~~~~~v~IRG~~I~~I~   67 (67)
T cd01726           1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQ----LKNKYGDAFIRGNNVLYIS   67 (67)
T ss_pred             CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCc----eeeEeCCEEEECCEEEEEC
Confidence            356789999999999999999999999999999999999999865332    3678999999999999884

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.

>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=126.22  Aligned_cols=70  Identities=17%  Similarity=0.258  Sum_probs=62.5

Q ss_pred             hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCc--eeeeeeEEeeEEEcCCcEEEEE
Q psy17123         23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTY--QSVQVRSWCSIVRRQESRRNVH   92 (105)
Q Consensus        23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~--~~~~~~~lg~vlIRG~~I~~i~   92 (105)
                      ...|++|++++|+|+|+|||.|.|+|.|||++|||+|++|.|+...+.  ...+.|.+|+++|||++|++|+
T Consensus         2 ~~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~   73 (75)
T cd06168           2 RQKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIE   73 (75)
T ss_pred             HhHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEE
Confidence            356899999999999999999999999999999999999999986432  2235799999999999999997

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

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

Probab=99.86  E-value=7.8e-22  Score=124.13  Aligned_cols=67  Identities=25%  Similarity=0.290  Sum_probs=59.8

Q ss_pred             chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEE
Q psy17123         22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVH   92 (105)
Q Consensus        22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~   92 (105)
                      |...|+++++++|+|+|+||++|+|+|.|||+||||+|+||.|+....    ....+|.++|||++|++|.
T Consensus         2 p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~----~~~~lg~~~IRG~~I~~i~   68 (68)
T cd01722           2 PKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGK----STGNLGEVLIRCNNVLYIR   68 (68)
T ss_pred             HHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCc----cccCcCcEEEECCEEEEEC
Confidence            567899999999999999999999999999999999999999985332    2577999999999999983

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.

>smart00651 Sm snRNP Sm proteins

Probab=99.86  E-value=3.9e-21  Score=119.15  Aligned_cols=66  Identities=30%  Similarity=0.431  Sum_probs=60.5

Q ss_pred             hHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123         25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR   93 (105)
Q Consensus        25 ~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~   93 (105)
                      .|+++++++|+|.|+||+.+.|+|.+||+||||+|++|.|+..++.   +.+.+|.++|||++|++|++
T Consensus         2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~---~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651        2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGE---KKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCc---EEeEeCCEEEcCCEEEEEeC
Confidence            5889999999999999999999999999999999999999876532   47899999999999999974

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

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

Probab=99.86  E-value=3.8e-21  Score=119.35  Aligned_cols=66  Identities=32%  Similarity=0.452  Sum_probs=61.0

Q ss_pred             hHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123         25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR   93 (105)
Q Consensus        25 ~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~   93 (105)
                      .|++++|++|+|+|+||+.++|+|.+||+||||+|++|.|....+.   +.+.+|.++|||++|++|++
T Consensus         2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~---~~~~~~~~~irG~~I~~I~~   67 (67)
T PF01423_consen    2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP---EKRSLGLVFIRGSNIRYISL   67 (67)
T ss_dssp             HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES---EEEEEEEEEEEGGGEEEEEE
T ss_pred             hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC---cEeECcEEEEECCEEEEEEC
Confidence            5899999999999999999999999999999999999999976542   47889999999999999985

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 ....

>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=99.85  E-value=5.9e-21  Score=123.93  Aligned_cols=74  Identities=20%  Similarity=0.301  Sum_probs=63.2

Q ss_pred             cccccchhhHHhhcCC--EEEEEEc--CCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEE
Q psy17123         17 RKRKESILDLSKFLDK--VIRVKFA--GGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVH   92 (105)
Q Consensus        17 ~~~~~~~~~L~~~i~k--~V~V~Lk--dGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~   92 (105)
                      |..-.|...|.+++++  +|.|.++  +|+.++|+|.|||+||||+|+||+|+...++   ..+.+|.++|||++|++|+
T Consensus         2 ~~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~---~~~~lG~iliRGnnV~~I~   78 (79)
T cd01718           2 KVMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTK---TRKPLGRILLKGDNITLIQ   78 (79)
T ss_pred             ccccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCc---eEeEcCcEEEeCCEEEEEc
Confidence            4456788889999998  6777766  9999999999999999999999999975332   3678999999999999997


Q ss_pred             e
Q psy17123         93 R   93 (105)
Q Consensus        93 ~   93 (105)
                      +
T Consensus        79 p   79 (79)
T cd01718          79 N   79 (79)
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 E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

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

Probab=99.85  E-value=1.1e-20  Score=124.67  Aligned_cols=72  Identities=21%  Similarity=0.229  Sum_probs=61.2

Q ss_pred             chhhHHhhc--CCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCce---------eeeeeEEeeEEEcCCcEEE
Q psy17123         22 SILDLSKFL--DKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQ---------SVQVRSWCSIVRRQESRRN   90 (105)
Q Consensus        22 ~~~~L~~~i--~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~---------~~~~~~lg~vlIRG~~I~~   90 (105)
                      |...|.+.+  +++|.|+|++|+.+.|+|.|||+||||+|+||.|++.....         ....+.+|.+||||++|++
T Consensus         3 Pl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~   82 (87)
T cd01720           3 PLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVIL   82 (87)
T ss_pred             hHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEE
Confidence            455678886  89999999999999999999999999999999998764221         1346789999999999999


Q ss_pred             EEe
Q psy17123         91 VHR   93 (105)
Q Consensus        91 i~~   93 (105)
                      |.+
T Consensus        83 Is~   85 (87)
T cd01720          83 VLR   85 (87)
T ss_pred             Eec
Confidence            974

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

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

Probab=99.84  E-value=1.2e-20  Score=119.54  Aligned_cols=69  Identities=20%  Similarity=0.124  Sum_probs=61.7

Q ss_pred             hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecC
Q psy17123         23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRD   95 (105)
Q Consensus        23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d   95 (105)
                      ...|++..|++|+|+||||.+|+|+|.++|+|||++|++|.+...+++    ...+|.++|||++|.+|+.+|
T Consensus         2 ~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~----~~~~~~v~IRG~nI~~v~lPd   70 (70)
T cd01721           2 IKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGR----VSQLEQVYIRGSKIRFFILPD   70 (70)
T ss_pred             hHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCc----EeEcCcEEEeCCEEEEEEeCC
Confidence            456899999999999999999999999999999999999988655543    466899999999999999775

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.

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

Probab=99.83  E-value=4.1e-20  Score=119.02  Aligned_cols=72  Identities=31%  Similarity=0.379  Sum_probs=60.6

Q ss_pred             ccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEe-cCceeeeeeEEeeEEEcCCcEEEEE
Q psy17123         20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR-VTYQSVQVRSWCSIVRRQESRRNVH   92 (105)
Q Consensus        20 ~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~-~~~~~~~~~~lg~vlIRG~~I~~i~   92 (105)
                      ..+...|+++++++|.|+|++|++|.|+|+|||+||||+|+||.|+.. ++.. ...+..|.++|||++|++|.
T Consensus         6 ~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~-~~~~~~~~~~IRG~~I~~I~   78 (79)
T COG1958           6 PLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEK-NVRRLGGEVLIRGDNIVLIS   78 (79)
T ss_pred             CCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCcc-ccceeccEEEEECCcEEEEe
Confidence            456788999999999999999999999999999999999999999874 2221 02344459999999999986

>KOG1781|consensus

Probab=99.83  E-value=4.3e-22  Score=133.15  Aligned_cols=87  Identities=52%  Similarity=0.727  Sum_probs=78.6

Q ss_pred             CCccccccccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCcee----eeeeEEeeEEEcCCc
Q psy17123         12 AETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQS----VQVRSWCSIVRRQES   87 (105)
Q Consensus        12 ~~~~~~~~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~----~~~~~lg~vlIRG~~   87 (105)
                      ....+|++++++.+|.+|++|+|+|++.+||...|+|+|||+.|||||++++|+..+++++    .+.|.+|++++||..
T Consensus         8 ~~~~e~~kkEsilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTa   87 (108)
T KOG1781|consen    8 RKKFEKPKKESILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTA   87 (108)
T ss_pred             cccccccchhHHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccE
Confidence            3455789999999999999999999999999999999999999999999999999877642    245999999999999


Q ss_pred             EEEEEecCCcc
Q psy17123         88 RRNVHRRDHKE   98 (105)
Q Consensus        88 I~~i~~~d~~~   98 (105)
                      ++.|++.|+..
T Consensus        88 lvlisp~dG~e   98 (108)
T KOG1781|consen   88 LVLISPADGSE   98 (108)
T ss_pred             EEEEcCCcchh
Confidence            99999998754

>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=99.83  E-value=5.1e-20  Score=112.62  Aligned_cols=63  Identities=32%  Similarity=0.518  Sum_probs=57.9

Q ss_pred             HHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEE
Q psy17123         26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVH   92 (105)
Q Consensus        26 L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~   92 (105)
                      |++++|++|+|+|+||+.|.|+|.+||+|||++|++|.|.....    ..+.+|.++|||++|.+|+
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~----~~~~~~~~~irG~~I~~I~   63 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEG----KKRVLGLVLIRGDNVRLVT   63 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCC----cEEECCeEEEECCEEEEEC
Confidence            57899999999999999999999999999999999999987653    3788999999999999884

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.

>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=99.83  E-value=4.8e-20  Score=118.28  Aligned_cols=72  Identities=14%  Similarity=0.111  Sum_probs=62.7

Q ss_pred             chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123         22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH   96 (105)
Q Consensus        22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~   96 (105)
                      |...|++++|++|.|+|++|+.++|+|.+||+|||++|+||.|...+++   ....++.++|||++|.+|+..|.
T Consensus         2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~---~~~~~~~v~IRG~~I~~i~~p~~   73 (76)
T cd01723           2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGD---KFWKMPECYIRGNTIKYLRVPDE   73 (76)
T ss_pred             chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCc---EeeeCCcEEEeCCEEEEEEcCHH
Confidence            4567899999999999999999999999999999999999998755543   24567899999999999986653

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

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

Probab=99.81  E-value=2.1e-19  Score=119.00  Aligned_cols=73  Identities=19%  Similarity=0.228  Sum_probs=64.9

Q ss_pred             chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCCcc
Q psy17123         22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHKE   98 (105)
Q Consensus        22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~~~   98 (105)
                      ++..|+++.|++|+|+|++|..|+|+|.++|+|||++|+||.+...++.    ...+|.++|||++|.+|+..|...
T Consensus         2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~----~~~~~~v~IRG~nI~yi~lPd~l~   74 (90)
T cd01724           2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRN----PVPLDTLSIRGNNIRYFILPDSLN   74 (90)
T ss_pred             HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCc----eeEcceEEEeCCEEEEEEcCCcCC
Confidence            3567899999999999999999999999999999999999998855443    567999999999999999988753

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.

>KOG1780|consensus

Probab=99.81  E-value=5.7e-20  Score=117.30  Aligned_cols=69  Identities=36%  Similarity=0.541  Sum_probs=62.7

Q ss_pred             hhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123         24 LDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH   96 (105)
Q Consensus        24 ~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~   96 (105)
                      ++|++|++|++.++|..||.+.|+|+|||.||||||++++|...+++    ...+|.++|||++|+.+...|.
T Consensus         7 PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~----~~~ig~~vIrgnsiv~~eaL~~   75 (77)
T KOG1780|consen    7 PELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGD----KNNIGMVVIRGNSIVMVEALER   75 (77)
T ss_pred             chHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCC----cceeeeEEEeccEEEEEeeccc
Confidence            49999999999999999999999999999999999999999866554    5788999999999999987653

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.80  E-value=5.8e-19  Score=116.89  Aligned_cols=76  Identities=16%  Similarity=0.288  Sum_probs=63.6

Q ss_pred             ccccccchhhHHhhcCC--EEEEEEcC--CeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEE
Q psy17123         16 DRKRKESILDLSKFLDK--VIRVKFAG--GRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNV   91 (105)
Q Consensus        16 ~~~~~~~~~~L~~~i~k--~V~V~Lkd--Gr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i   91 (105)
                      .|....|+..+.+++.+  +|.|.+.+  ++.++|+|+|||+||||+|+||.|+..+++   ..+.+|.++|||++|++|
T Consensus         9 ~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~---~~~~lG~ilIRGnnV~~I   85 (89)
T PTZ00138          9 QKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKN---TRKDLGRILLKGDNITLI   85 (89)
T ss_pred             ceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCc---eeeEcCeEEEcCCEEEEE
Confidence            35567888889999875  66777667  589999999999999999999999865433   367899999999999999


Q ss_pred             Eec
Q psy17123         92 HRR   94 (105)
Q Consensus        92 ~~~   94 (105)
                      ++.
T Consensus        86 ~~~   88 (89)
T PTZ00138         86 MAA   88 (89)
T ss_pred             EcC
Confidence            864

>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=99.78  E-value=1.4e-18  Score=112.35  Aligned_cols=70  Identities=21%  Similarity=0.214  Sum_probs=60.6

Q ss_pred             ccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123         20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR   93 (105)
Q Consensus        20 ~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~   93 (105)
                      ......|+.+.|+.|.|+||||..|.|+|.++|+|||++|+||.+...++.    ...+|.++|||++|.+|+.
T Consensus         8 ~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~----~~~~~~v~IRG~nI~yI~l   77 (78)
T cd01733           8 NTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGK----QVQVEEIMVTGRNIRYVHI   77 (78)
T ss_pred             chHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCc----eeECCcEEEECCEEEEEEc
Confidence            344556799999999999999999999999999999999999988754433    4578999999999999985

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.

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

Probab=99.77  E-value=1.9e-18  Score=112.26  Aligned_cols=73  Identities=19%  Similarity=0.179  Sum_probs=61.8

Q ss_pred             hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCCc
Q psy17123         23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHK   97 (105)
Q Consensus        23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~~   97 (105)
                      ...|+++.|++|+|+||+|..|.|+|.++|+|||++|+||.+...++.  .....++.++|||++|.+|+..|..
T Consensus         3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~--~~~~~~~~v~IRG~~I~~I~lp~~~   75 (81)
T cd01725           3 FSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKY--PHMLSVKNCFIRGSVVRYVQLPADE   75 (81)
T ss_pred             hHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCc--ccccccCeEEEECCEEEEEEeChhH
Confidence            456889999999999999999999999999999999999987643322  1245678999999999999987654

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.

>KOG3482|consensus

Probab=99.70  E-value=3.2e-17  Score=104.48  Aligned_cols=71  Identities=24%  Similarity=0.258  Sum_probs=63.5

Q ss_pred             cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecC
Q psy17123         21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRD   95 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d   95 (105)
                      -+.+.|+.+.+|.|.|+||.|.+|+|+|.+.|.||||.|.+|+|++...    ....+|.++||.+||.+|..++
T Consensus         8 NPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~----~~g~lGEilIRCNNvlyi~gv~   78 (79)
T KOG3482|consen    8 NPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGV----STGNLGEILIRCNNVLYIRGVP   78 (79)
T ss_pred             CchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhccc----ccccceeEEEEeccEEEEecCC
Confidence            3567899999999999999999999999999999999999999986543    3678999999999999997654

>KOG1784|consensus

Probab=99.68  E-value=3.5e-17  Score=108.15  Aligned_cols=76  Identities=24%  Similarity=0.314  Sum_probs=69.6

Q ss_pred             hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCCcc
Q psy17123         23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHKE   98 (105)
Q Consensus        23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~~~   98 (105)
                      ...|..|++++|.|.+.|||.+.|.|+||||-.||+|+++.|++.+..+..+...+|+.+|||+||..|+++|++.
T Consensus         2 ts~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~   77 (96)
T KOG1784|consen    2 TSTLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEEL   77 (96)
T ss_pred             chhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhh
Confidence            3568999999999999999999999999999999999999999876655667789999999999999999999864

>KOG1782|consensus

Probab=99.58  E-value=1.6e-16  Score=109.93  Aligned_cols=76  Identities=26%  Similarity=0.296  Sum_probs=67.8

Q ss_pred             hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCCccc
Q psy17123         23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHKEY   99 (105)
Q Consensus        23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~~~~   99 (105)
                      ...|.++++|++.|.|+|||.+.|.|++||||-|++|..|+|++.-++ .+-.+..|..+|||+||+.++.+|....
T Consensus        11 t~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~-~Y~di~~glfiIRGENVvllGeid~dkE   86 (129)
T KOG1782|consen   11 TTSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGN-KYCDIPRGLFIIRGENVVLLGEIDLDKE   86 (129)
T ss_pred             hhHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecc-eecccCceEEEEecCcEEEEecCCcchh
Confidence            445899999999999999999999999999999999999999987654 4566788999999999999999887654

>KOG1783|consensus

Probab=99.57  E-value=4.1e-16  Score=99.40  Aligned_cols=72  Identities=18%  Similarity=0.253  Sum_probs=64.5

Q ss_pred             cccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEec
Q psy17123         19 RKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRR   94 (105)
Q Consensus        19 ~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~   94 (105)
                      .+.+-..|++.+||+|.|+|.+|-.|+|+|.|.|.||||-|+.+.|+....    ..+++|..||||++|.+|+..
T Consensus         4 ~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngq----l~n~ygdaFirGnnVlyIs~~   75 (77)
T KOG1783|consen    4 GSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQ----LKNKYGDAFIRGNNVLYISTQ   75 (77)
T ss_pred             ccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCc----ccccccceeeccccEEEEEec
Confidence            455667899999999999999999999999999999999999999997543    378899999999999999864

>KOG3460|consensus

Probab=99.55  E-value=1.5e-15  Score=99.09  Aligned_cols=75  Identities=27%  Similarity=0.290  Sum_probs=62.2

Q ss_pred             ccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEec--Cc-e------eeeeeEEeeEEEcCCcEEE
Q psy17123         20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRV--TY-Q------SVQVRSWCSIVRRQESRRN   90 (105)
Q Consensus        20 ~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~--~~-~------~~~~~~lg~vlIRG~~I~~   90 (105)
                      .+|...|.=+++.+|.|+++++|.+.|+|.+||+|.|++|+++.|....  .+ +      +...|.+..+|+||++|+.
T Consensus         4 ~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vil   83 (91)
T KOG3460|consen    4 EEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVIL   83 (91)
T ss_pred             cccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEE
Confidence            3445556667999999999999999999999999999999999997752  11 1      1356888999999999999


Q ss_pred             EEec
Q psy17123         91 VHRR   94 (105)
Q Consensus        91 i~~~   94 (105)
                      |++.
T Consensus        84 vspp   87 (91)
T KOG3460|consen   84 VSPP   87 (91)
T ss_pred             EcCc
Confidence            9875

>KOG3168|consensus

Probab=99.55  E-value=7.5e-16  Score=111.60  Aligned_cols=79  Identities=23%  Similarity=0.347  Sum_probs=67.3

Q ss_pred             hhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCc------eeeeeeEEeeEEEcCCcEEEEEecCCc
Q psy17123         24 LDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTY------QSVQVRSWCSIVRRQESRRNVHRRDHK   97 (105)
Q Consensus        24 ~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~------~~~~~~~lg~vlIRG~~I~~i~~~d~~   97 (105)
                      ..|-+++|.+++|.++|||.|.|.|++||+||||+|.+|+|+.+-+.      +..+.|.+|++++||++|++....+..
T Consensus         7 skml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegpp   86 (177)
T KOG3168|consen    7 SKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPP   86 (177)
T ss_pred             hHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCC
Confidence            34678899999999999999999999999999999999999875221      245789999999999999999877666


Q ss_pred             ccccc
Q psy17123         98 EYEDS  102 (105)
Q Consensus        98 ~~~~~  102 (105)
                      .-+|+
T Consensus        87 p~s~s   91 (177)
T KOG3168|consen   87 PPSDS   91 (177)
T ss_pred             CCccc
Confidence            65554

>KOG1775|consensus

Probab=99.48  E-value=3e-14  Score=91.65  Aligned_cols=71  Identities=21%  Similarity=0.277  Sum_probs=62.0

Q ss_pred             hhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecC
Q psy17123         24 LDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRD   95 (105)
Q Consensus        24 ~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d   95 (105)
                      ..+.+.++++|+|.+|+.|+|.|+|.|||.|.|++|+|+.||...++. ....+++.+++.|++|..+.+..
T Consensus        10 EliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~eg-r~~tk~~~iLLnGNni~mLvPGG   80 (84)
T KOG1775|consen   10 ELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEG-RRMTKLDQILLNGNNITMLVPGG   80 (84)
T ss_pred             HHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCc-ceeeeeeeeeecCCcEEEEecCC
Confidence            345778999999999999999999999999999999999999775543 35678999999999999887654

>KOG1774|consensus

Probab=99.45  E-value=8.1e-14  Score=90.61  Aligned_cols=78  Identities=21%  Similarity=0.296  Sum_probs=62.5

Q ss_pred             cccccccchhhHHhhcCC--EEEEEEcC--CeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEE
Q psy17123         15 KDRKRKESILDLSKFLDK--VIRVKFAG--GRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRN   90 (105)
Q Consensus        15 ~~~~~~~~~~~L~~~i~k--~V~V~Lkd--Gr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~   90 (105)
                      -+|..-+|+..+.+|+..  +|.|.|.+  |-.++|.+.|||+|||+||++|+|....++   ..+.+|.++++|++|..
T Consensus         6 v~kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~---~rk~lGRilLKGDnItl   82 (88)
T KOG1774|consen    6 VQKVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTK---SRKELGRILLKGDNITL   82 (88)
T ss_pred             ccceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhcccccc---CCCccccEEEcCCcEEE
Confidence            345567788888888764  56666655  789999999999999999999999865443   24589999999999999


Q ss_pred             EEecC
Q psy17123         91 VHRRD   95 (105)
Q Consensus        91 i~~~d   95 (105)
                      |...+
T Consensus        83 i~~~~   87 (88)
T KOG1774|consen   83 IQSAG   87 (88)
T ss_pred             EeecC
Confidence            98654

>KOG3293|consensus

Probab=99.38  E-value=7e-13  Score=92.04  Aligned_cols=72  Identities=15%  Similarity=0.091  Sum_probs=64.0

Q ss_pred             chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123         22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH   96 (105)
Q Consensus        22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~   96 (105)
                      |...|+...+.++.|+||+|.+|.|.|...|.||||.|.+++++..+++   ....+..++|||++|.++...|.
T Consensus         3 PLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgd---kf~r~pEcYirGttIkylri~d~   74 (134)
T KOG3293|consen    3 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGD---KFFRMPECYIRGTTIKYLRIPDE   74 (134)
T ss_pred             chhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCC---ceeecceeEEecceeEEEeccHH
Confidence            3455777899999999999999999999999999999999999987765   46778899999999999988765

>KOG3448|consensus

Probab=99.36  E-value=4.2e-12  Score=83.76  Aligned_cols=70  Identities=19%  Similarity=0.129  Sum_probs=60.0

Q ss_pred             hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEec
Q psy17123         23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRR   94 (105)
Q Consensus        23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~   94 (105)
                      +...++++|++|.|+||++-.+.|+|.|.|||+|+.|.|....  +++.-++...+..++|||+.|.+|...
T Consensus         4 ysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~--d~~kyPhm~Sv~ncfIRGSvvrYv~l~   73 (96)
T KOG3448|consen    4 YSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVT--DPDKYPHMLSVKNCFIRGSVVRYVQLP   73 (96)
T ss_pred             HHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEee--CcccCCCeeeeeeEEEeccEEEEEEeC
Confidence            4557888999999999999999999999999999999998765  333335677888999999999999853

>KOG3172|consensus

Probab=99.03  E-value=1e-09  Score=74.82  Aligned_cols=72  Identities=19%  Similarity=0.100  Sum_probs=63.7

Q ss_pred             cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123         21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH   96 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~   96 (105)
                      -++-.|++.-+.-|++++..|..|+|.|...+++||++|.|.+-...++.    ...+..|+|||+.|.++...|-
T Consensus         5 vpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~----vs~le~V~IRGS~IRFlvlPdm   76 (119)
T KOG3172|consen    5 VPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGR----VSQLEQVFIRGSKIRFLVLPDM   76 (119)
T ss_pred             cceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCc----ceeeeeEEEecCeEEEEECchH
Confidence            35667899999999999999999999999999999999999998776664    5678899999999999987764

>KOG3428|consensus

Probab=98.86  E-value=2.2e-08  Score=68.23  Aligned_cols=71  Identities=15%  Similarity=0.166  Sum_probs=61.0

Q ss_pred             hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCCcc
Q psy17123         23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHKE   98 (105)
Q Consensus        23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~~~   98 (105)
                      ...|+++.+.+|+|.|++|....|++.+.|.+||..|.++.-..+. +    ...+..+.|||++|.++..+|.-.
T Consensus         4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~-~----pv~l~~lsirgnniRy~~lpD~l~   74 (109)
T KOG3428|consen    4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG-E----PVRLDTLSIRGNNIRYYILPDSLN   74 (109)
T ss_pred             HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC-C----ceeEEEEEeecceEEEEEccCCcC
Confidence            4578899999999999999999999999999999999987765442 2    456788999999999999887643

>KOG3459|consensus

Probab=98.34  E-value=4.8e-08  Score=66.74  Aligned_cols=72  Identities=19%  Similarity=0.176  Sum_probs=56.9

Q ss_pred             cchhhHHhhc--CCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecC----c--e---eeeeeEEeeEEEcCCcEE
Q psy17123         21 ESILDLSKFL--DKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVT----Y--Q---SVQVRSWCSIVRRQESRR   89 (105)
Q Consensus        21 ~~~~~L~~~i--~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~----~--~---~~~~~~lg~vlIRG~~I~   89 (105)
                      .+...|....  ..+|.|.++|++.+.|++.+||.|.|++|+++.|.+..-    +  .   ....|.+|.++|||++|+
T Consensus        24 Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI  103 (114)
T KOG3459|consen   24 GPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVI  103 (114)
T ss_pred             CchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEE
Confidence            4444454554  468999999999999999999999999999999877531    1  1   123688999999999998


Q ss_pred             EEE
Q psy17123         90 NVH   92 (105)
Q Consensus        90 ~i~   92 (105)
                      .+-
T Consensus       104 ~v~  106 (114)
T KOG3459|consen  104 LVL  106 (114)
T ss_pred             EEE
Confidence            875

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

Probab=98.14  E-value=7.8e-06  Score=51.91  Aligned_cols=69  Identities=12%  Similarity=0.201  Sum_probs=42.2

Q ss_pred             cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecC---ccCeEecceEEEEecC---ceeeeeeEEeeEEEcCCcEE
Q psy17123         21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDP---LLNLVLDNTTEYLRVT---YQSVQVRSWCSIVRRQESRR   89 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~---~mNlvL~da~E~~~~~---~~~~~~~~lg~vlIRG~~I~   89 (105)
                      +....+..++|++|.|+++||..|+|+|.+++.   -+.++|..+.......   ...........++|+++.|+
T Consensus         2 Rl~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv   76 (77)
T PF14438_consen    2 RLVYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV   76 (77)
T ss_dssp             --HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred             hHHHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence            345667889999999999999999999999998   8999998887653321   11122344556777776654

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

Probab=97.94  E-value=7.8e-06  Score=51.36  Aligned_cols=38  Identities=34%  Similarity=0.541  Sum_probs=31.4

Q ss_pred             CCEEEEEEcC--C--eEEEEEEEEecCccCeEecceEEEEec
Q psy17123         31 DKVIRVKFAG--G--RECSGILKGFDPLLNLVLDNTTEYLRV   68 (105)
Q Consensus        31 ~k~V~V~Lkd--G--r~i~G~L~~fD~~mNlvL~da~E~~~~   68 (105)
                      .++|+|.++.  |  -.++|.|.+||+|+|++|.|+.|.+..
T Consensus         8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~   49 (66)
T cd01739           8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK   49 (66)
T ss_pred             CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence            3678887764  3  278999999999999999999998764

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.

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

Probab=97.29  E-value=0.001  Score=44.56  Aligned_cols=72  Identities=14%  Similarity=0.134  Sum_probs=55.0

Q ss_pred             HhhcCCEEEEEEcCCeEEEEEEEEecC-ccCeEecceEEEEecCce-----eeeeeEEeeEEEcCCcEEEEEecCCcc
Q psy17123         27 SKFLDKVIRVKFAGGRECSGILKGFDP-LLNLVLDNTTEYLRVTYQ-----SVQVRSWCSIVRRQESRRNVHRRDHKE   98 (105)
Q Consensus        27 ~~~i~k~V~V~LkdGr~i~G~L~~fD~-~mNlvL~da~E~~~~~~~-----~~~~~~lg~vlIRG~~I~~i~~~d~~~   98 (105)
                      .+|+|++|.+..+.+-.|+|+|...|. --.|.|.++..+-.++..     ......+..|..||+.|..+...+...
T Consensus         4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~   81 (96)
T PF12701_consen    4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPP   81 (96)
T ss_dssp             CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-
T ss_pred             ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCC
Confidence            368999999999999999999999995 789999998876432210     112335678999999999998766544

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

Probab=96.80  E-value=0.0036  Score=45.79  Aligned_cols=65  Identities=23%  Similarity=0.302  Sum_probs=45.8

Q ss_pred             cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecC-ccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123         21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDP-LLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH   96 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~-~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~   96 (105)
                      -.+....+|++|.|.|.+.| +++.|.+..+|+ .-||||-+..|   ++.     +  ..-+|-|..|..|...+.
T Consensus         7 ~~p~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e---~~~-----~--sv~~I~ghaVk~vevl~~   72 (166)
T PF06372_consen    7 KSPLEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE---DGK-----R--SVKVIMGHAVKSVEVLSE   72 (166)
T ss_dssp             S-HHHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T---TS------E--EEEEE-GGGEEEEEEEE-
T ss_pred             CCHHHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc---CCc-----e--eEEEEEccceEEEEEccC
Confidence            35778899999999999999 999999999995 56999975443   221     2  357899999999987664

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.

>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=96.74  E-value=0.0062  Score=35.41  Aligned_cols=33  Identities=30%  Similarity=0.418  Sum_probs=29.0

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEecCccCeEecce
Q psy17123         29 FLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNT   62 (105)
Q Consensus        29 ~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da   62 (105)
                      .+||+|+|.+ ++..++|+..++|+...|+|...
T Consensus         1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~   33 (48)
T PF02237_consen    1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTE   33 (48)
T ss_dssp             STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEET
T ss_pred             CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEEC
Confidence            4799999999 77777999999999999999653

It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....

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

Probab=96.64  E-value=0.011  Score=38.04  Aligned_cols=65  Identities=14%  Similarity=0.147  Sum_probs=49.5

Q ss_pred             HhhcCCEEEEEEcCCeEEEEEEEEec-CccCeEecceEEEEecCce------eeeeeEEeeEEEcCCcEEEE
Q psy17123         27 SKFLDKVIRVKFAGGRECSGILKGFD-PLLNLVLDNTTEYLRVTYQ------SVQVRSWCSIVRRQESRRNV   91 (105)
Q Consensus        27 ~~~i~k~V~V~LkdGr~i~G~L~~fD-~~mNlvL~da~E~~~~~~~------~~~~~~lg~vlIRG~~I~~i   91 (105)
                      .+++|++|.+..+.+..|+|+|..+| +---|.|.|+..+-.++-.      +.....+..++.||+.|.-+
T Consensus         2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkDL   73 (74)
T cd01736           2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKDL   73 (74)
T ss_pred             ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccccc
Confidence            36899999999999999999999999 4556789998876443221      12345567899999988643

Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.

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

Probab=96.42  E-value=0.0066  Score=37.66  Aligned_cols=32  Identities=16%  Similarity=0.306  Sum_probs=27.8

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEecCccCeEecc
Q psy17123         30 LDKVIRVKFAGGRECSGILKGFDPLLNLVLDN   61 (105)
Q Consensus        30 i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~d   61 (105)
                      -..+|+|.|.||-.++|.+.+||+|+=++-.+
T Consensus        10 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   41 (61)
T cd01716          10 EKIPVTIYLVNGVQLKGQIESFDNFTVLLESD   41 (61)
T ss_pred             cCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence            35689999999999999999999998766544

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

>TIGR02383 Hfq RNA chaperone Hfq

Probab=96.29  E-value=0.0084  Score=37.19  Aligned_cols=32  Identities=19%  Similarity=0.324  Sum_probs=27.8

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEecCccCeEecc
Q psy17123         30 LDKVIRVKFAGGRECSGILKGFDPLLNLVLDN   61 (105)
Q Consensus        30 i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~d   61 (105)
                      -..+|+|.|.+|-.+.|.+.+||+|+=|+-.+
T Consensus        14 ~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~   45 (61)
T TIGR02383        14 ERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ   45 (61)
T ss_pred             cCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence            46799999999999999999999998766544

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

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=95.89  E-value=0.016  Score=37.72  Aligned_cols=34  Identities=15%  Similarity=0.269  Sum_probs=29.1

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEecCccCeEecce
Q psy17123         29 FLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNT   62 (105)
Q Consensus        29 ~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da   62 (105)
                      --...|+|.|.+|-.+.|.+.|||+|.=|+-.+.
T Consensus        17 ~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g   50 (79)
T PRK00395         17 KERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG   50 (79)
T ss_pred             HcCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence            3467999999999999999999999987776553

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

Probab=95.64  E-value=0.075  Score=34.62  Aligned_cols=63  Identities=11%  Similarity=0.090  Sum_probs=46.6

Q ss_pred             cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecC-ccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEE
Q psy17123         21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDP-LLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVH   92 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~-~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~   92 (105)
                      +....|....||+|.+.|.++....|++.++|. ..|+..++-.    .+     .......++|..-|++++
T Consensus        14 rfLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~----TP-----lGv~~eAlLR~~DVi~~~   77 (80)
T PF11095_consen   14 RFLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ----TP-----LGVQPEALLRCSDVISIS   77 (80)
T ss_dssp             HHHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE----TT-----TTEEEEEEEEGGGEEEEE
T ss_pred             HHHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC----CC-----cccChhheeecCCEEEEE
Confidence            445567788899999999999999999999995 4566665522    22     344678999999999886

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.

>PRK14638 hypothetical protein; Provisional

Probab=95.35  E-value=0.046  Score=39.06  Aligned_cols=45  Identities=18%  Similarity=0.286  Sum_probs=35.0

Q ss_pred             CccccccccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEe
Q psy17123         13 ETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVL   59 (105)
Q Consensus        13 ~~~~~~~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL   59 (105)
                      |--|.|-+. +.++.+++|++|.|++++++.++|+|.++|.- ++.|
T Consensus        83 PGldRpL~~-~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l  127 (150)
T PRK14638         83 PGLDRPLRG-PKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITI  127 (150)
T ss_pred             CCCCCCCCC-HHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence            334444444 56788999999999999999999999999963 4545

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

Probab=95.12  E-value=0.036  Score=35.84  Aligned_cols=29  Identities=17%  Similarity=0.330  Sum_probs=25.3

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEecCccCeE
Q psy17123         30 LDKVIRVKFAGGRECSGILKGFDPLLNLV   58 (105)
Q Consensus        30 i~k~V~V~LkdGr~i~G~L~~fD~~mNlv   58 (105)
                      -..+|.|.|.||-.+.|.+.|||+|.=|.
T Consensus        18 ~~i~VtIfLvNG~~L~G~V~sfD~f~VlL   46 (77)
T COG1923          18 EKIPVTIFLVNGFKLQGQVESFDNFVVLL   46 (77)
T ss_pred             cCCeEEEEEEcCEEEEEEEEeeeeEEEEE
Confidence            45799999999999999999999997443

>PRK14639 hypothetical protein; Provisional

Probab=94.79  E-value=0.085  Score=37.30  Aligned_cols=45  Identities=18%  Similarity=0.302  Sum_probs=35.6

Q ss_pred             CccccccccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEe
Q psy17123         13 ETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVL   59 (105)
Q Consensus        13 ~~~~~~~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL   59 (105)
                      |--+.|.+. +.+..+++|+.|.|++.+++.+.|+|.++|. .++.|
T Consensus        71 PGl~RpL~~-~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~-~~i~l  115 (140)
T PRK14639         71 PGLERKLSK-IEHFAKSIGELVKITTNEKEKFEGKIVSVDD-ENITL  115 (140)
T ss_pred             CCCCCcCCC-HHHHHHhCCCEEEEEECCCcEEEEEEEEEeC-CEEEE
Confidence            344444444 6778899999999999999999999999998 35544

>PRK02001 hypothetical protein; Validated

Probab=94.72  E-value=0.091  Score=37.77  Aligned_cols=45  Identities=20%  Similarity=0.197  Sum_probs=35.0

Q ss_pred             CccccccccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEe
Q psy17123         13 ETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVL   59 (105)
Q Consensus        13 ~~~~~~~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL   59 (105)
                      |--+.|.+. +.+..+++|+.|+|++.+++.|+|+|.++|.- ++.|
T Consensus        73 PGldRpL~~-~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l  117 (152)
T PRK02001         73 AGLTSPLKV-PRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL  117 (152)
T ss_pred             CCCCCcCCC-HHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence            333444443 56788999999999999999999999999974 4555

>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=94.51  E-value=0.12  Score=31.93  Aligned_cols=35  Identities=9%  Similarity=0.093  Sum_probs=29.5

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEecCccCeEecceE
Q psy17123         29 FLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTT   63 (105)
Q Consensus        29 ~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~   63 (105)
                      .+|..|++++-.|..|+|.+.+||.-.++++-.|.
T Consensus         4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~   38 (61)
T cd01735           4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCP   38 (61)
T ss_pred             ccccEEEEEecCCceEEEEEEEecCCCcEEEEECc
Confidence            47899999999999999999999988877654433

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.

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

Probab=94.15  E-value=0.59  Score=29.33  Aligned_cols=56  Identities=20%  Similarity=0.221  Sum_probs=40.9

Q ss_pred             cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123         21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR   93 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~   93 (105)
                      -....|++++|++|.|.+..|.. .|+|.+.-.- .|+|+..      +         ...+||=.+|++|.|
T Consensus        11 yvyq~lq~liG~~vvV~T~~g~v-~G~L~~V~pD-hIvl~~~------~---------~~~~IR~~~IV~v~p   66 (66)
T PF10842_consen   11 YVYQTLQSLIGQRVVVQTTRGSV-RGILVDVKPD-HIVLEEN------G---------TPFFIRIAQIVWVMP   66 (66)
T ss_pred             HHHHHHHHhcCCEEEEEEcCCcE-EEEEEeecCC-EEEEEeC------C---------cEEEEEeeeEEEEcC
Confidence            34667999999999999988776 9999997632 1233221      1         258899999998864

>PRK14644 hypothetical protein; Provisional

Probab=93.68  E-value=0.23  Score=35.04  Aligned_cols=47  Identities=17%  Similarity=0.215  Sum_probs=36.6

Q ss_pred             CCCccccccccchhhHHhhcCCEEEEEEcCC----eEEEEEEEEecCccCeEec
Q psy17123         11 GAETKDRKRKESILDLSKFLDKVIRVKFAGG----RECSGILKGFDPLLNLVLD   60 (105)
Q Consensus        11 ~~~~~~~~~~~~~~~L~~~i~k~V~V~LkdG----r~i~G~L~~fD~~mNlvL~   60 (105)
                      ..|--++|.+.  .++.+++|+.|.|+|++.    +.++|.|.++|. -++.|.
T Consensus        67 SSPGldRpL~~--~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~-~~i~l~  117 (136)
T PRK14644         67 SSPGFDMDYET--DELENHIGEIIDVSLNKEVNKTDFITGELLENNP-ETITLK  117 (136)
T ss_pred             ECCCCCCCCCH--HHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeC-CEEEEE
Confidence            34555666664  389999999999999876    899999999997 345553

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=93.19  E-value=0.19  Score=36.76  Aligned_cols=33  Identities=15%  Similarity=0.211  Sum_probs=28.4

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEecCccCeEecce
Q psy17123         30 LDKVIRVKFAGGRECSGILKGFDPLLNLVLDNT   62 (105)
Q Consensus        30 i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da   62 (105)
                      -..+|+|.|.+|-.++|.+.+||+|.=|.-.+.
T Consensus       103 ~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g  135 (165)
T PRK14091        103 SGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG  135 (165)
T ss_pred             cCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            457999999999999999999999987665553

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=93.11  E-value=0.23  Score=36.37  Aligned_cols=33  Identities=18%  Similarity=0.264  Sum_probs=28.2

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEecCccCeEecce
Q psy17123         30 LDKVIRVKFAGGRECSGILKGFDPLLNLVLDNT   62 (105)
Q Consensus        30 i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da   62 (105)
                      -..+|+|.|.+|-.++|.+.+||+|.=|+-.+.
T Consensus        23 ~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g   55 (165)
T PRK14091         23 TKTPVTMFLVKGVKLQGIITWFDNFSILLRRDG   55 (165)
T ss_pred             cCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            356899999999999999999999986666554

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

Probab=93.01  E-value=0.38  Score=30.73  Aligned_cols=43  Identities=30%  Similarity=0.461  Sum_probs=32.6

Q ss_pred             cccccccchhhHHhhcCCEEEEEEc---CC-eEEEEEEEEecCccCeEe
Q psy17123         15 KDRKRKESILDLSKFLDKVIRVKFA---GG-RECSGILKGFDPLLNLVL   59 (105)
Q Consensus        15 ~~~~~~~~~~~L~~~i~k~V~V~Lk---dG-r~i~G~L~~fD~~mNlvL   59 (105)
                      -+.|... +.++.+++|+.|.|+++   +| +.+.|.|.++|.- ++.|
T Consensus        10 l~RpL~~-~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l   56 (83)
T cd01734          10 AERPLKK-EADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL   56 (83)
T ss_pred             CCCcCCC-HHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence            3434443 67788999999999997   56 5999999999983 4444

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

>PRK14640 hypothetical protein; Provisional

Probab=92.85  E-value=0.43  Score=34.06  Aligned_cols=45  Identities=18%  Similarity=0.303  Sum_probs=33.5

Q ss_pred             ccccccccchhhHHhhcCCEEEEEE----cCCeEEEEEEEEecCccCeEec
Q psy17123         14 TKDRKRKESILDLSKFLDKVIRVKF----AGGRECSGILKGFDPLLNLVLD   60 (105)
Q Consensus        14 ~~~~~~~~~~~~L~~~i~k~V~V~L----kdGr~i~G~L~~fD~~mNlvL~   60 (105)
                      --+.|-+. +.+..+++|+.|.|++    .+++.++|+|.++|.. ++.|.
T Consensus        81 Gl~RpL~~-~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~  129 (152)
T PRK14640         81 GLDRPLFK-VAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT  129 (152)
T ss_pred             CCCCcCCC-HHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence            33434433 5678899999999999    5678999999999873 45553

>PRK14633 hypothetical protein; Provisional

Probab=92.28  E-value=0.45  Score=33.95  Aligned_cols=44  Identities=14%  Similarity=0.262  Sum_probs=32.9

Q ss_pred             cccccccchhhHHhhcCCEEEEEEc----CCeEEEEEEEEecCccCeEec
Q psy17123         15 KDRKRKESILDLSKFLDKVIRVKFA----GGRECSGILKGFDPLLNLVLD   60 (105)
Q Consensus        15 ~~~~~~~~~~~L~~~i~k~V~V~Lk----dGr~i~G~L~~fD~~mNlvL~   60 (105)
                      -|.|-+. ..++.+++|++|.|+++    +++.|+|+|.+++.- ++.|.
T Consensus        79 ldRpL~~-~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~  126 (150)
T PRK14633         79 MNRQIFN-IIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN  126 (150)
T ss_pred             CCCCCCC-HHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence            3434433 56778999999999993    668999999999874 55553

>KOG1073|consensus

Probab=91.95  E-value=0.57  Score=38.18  Aligned_cols=71  Identities=13%  Similarity=0.149  Sum_probs=54.4

Q ss_pred             HhhcCCEEEEEEcCCeEEEEEEEEec-CccCeEecceEEEEecCce------eeeeeEEeeEEEcCCcEEEEEecCCc
Q psy17123         27 SKFLDKVIRVKFAGGRECSGILKGFD-PLLNLVLDNTTEYLRVTYQ------SVQVRSWCSIVRRQESRRNVHRRDHK   97 (105)
Q Consensus        27 ~~~i~k~V~V~LkdGr~i~G~L~~fD-~~mNlvL~da~E~~~~~~~------~~~~~~lg~vlIRG~~I~~i~~~d~~   97 (105)
                      ..|||++|.++-|....|+|+|.-.| +--=|-|.++..+-.++..      ..-...+..|+.||+.|+-+...+..
T Consensus         5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~p   82 (361)
T KOG1073|consen    5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQETP   82 (361)
T ss_pred             cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccCc
Confidence            47899999999999999999999999 7778899997554332211      01112678899999999988766644

>PRK14645 hypothetical protein; Provisional

Probab=91.51  E-value=0.53  Score=33.84  Aligned_cols=42  Identities=14%  Similarity=0.183  Sum_probs=31.7

Q ss_pred             cccccccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEe
Q psy17123         15 KDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVL   59 (105)
Q Consensus        15 ~~~~~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL   59 (105)
                      -|.|-+. ..++.+++|++|.|++ +++.++|+|.++|.- .+.|
T Consensus        87 ldRpL~~-~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l  128 (154)
T PRK14645         87 PKRPLFT-ARHFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTF  128 (154)
T ss_pred             CCCCCCC-HHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence            3434433 5667889999999985 889999999999974 3444

>PRK14642 hypothetical protein; Provisional

Probab=91.32  E-value=0.57  Score=35.13  Aligned_cols=42  Identities=19%  Similarity=0.350  Sum_probs=32.8

Q ss_pred             ccccccchhhHHhhcCCEEEEEEc-------------CCeEEEEEEEEecCccCeEe
Q psy17123         16 DRKRKESILDLSKFLDKVIRVKFA-------------GGRECSGILKGFDPLLNLVL   59 (105)
Q Consensus        16 ~~~~~~~~~~L~~~i~k~V~V~Lk-------------dGr~i~G~L~~fD~~mNlvL   59 (105)
                      |.|.+. ..+..+++|+.|.|+|+             +.+.|+|+|.++|.. ++.|
T Consensus        86 dRPLk~-~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l  140 (197)
T PRK14642         86 DRPLRH-EQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI  140 (197)
T ss_pred             CCCCCC-HHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence            334433 56788899999999998             679999999999974 4444

>PRK14636 hypothetical protein; Provisional

Probab=91.09  E-value=0.62  Score=34.18  Aligned_cols=45  Identities=22%  Similarity=0.378  Sum_probs=33.9

Q ss_pred             CccccccccchhhHHhhcCCEEEEEEc---CC-eEEEEEEEEecCccCeEe
Q psy17123         13 ETKDRKRKESILDLSKFLDKVIRVKFA---GG-RECSGILKGFDPLLNLVL   59 (105)
Q Consensus        13 ~~~~~~~~~~~~~L~~~i~k~V~V~Lk---dG-r~i~G~L~~fD~~mNlvL   59 (105)
                      |--+.|... ..+..+++|++|.|+|+   +| +.|+|+|.++|.- ++.|
T Consensus        81 PGldRpL~~-~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l  129 (176)
T PRK14636         81 PGIDRPLTR-PKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI  129 (176)
T ss_pred             CCCCCCCCC-HHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence            444445544 56788999999999997   55 6999999999873 4544

>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=91.02  E-value=0.51  Score=32.84  Aligned_cols=36  Identities=28%  Similarity=0.506  Sum_probs=27.2

Q ss_pred             hhhHHhhcCCEEEEEEc----CCeEEEEEEEEecCccCeEe
Q psy17123         23 ILDLSKFLDKVIRVKFA----GGRECSGILKGFDPLLNLVL   59 (105)
Q Consensus        23 ~~~L~~~i~k~V~V~Lk----dGr~i~G~L~~fD~~mNlvL   59 (105)
                      ..++.+++|+.|.|+++    +.+.+.|+|.++|. -.++|
T Consensus        79 ~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l  118 (141)
T PF02576_consen   79 PRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL  118 (141)
T ss_dssp             HHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred             HHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence            56789999999999994    45799999999998 44444

; PDB: 1IB8_A.

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=90.83  E-value=0.75  Score=32.65  Aligned_cols=31  Identities=29%  Similarity=0.604  Sum_probs=27.8

Q ss_pred             hhhHHhhcCCEEEEEE----cCCeEEEEEEEEecC
Q psy17123         23 ILDLSKFLDKVIRVKF----AGGRECSGILKGFDP   53 (105)
Q Consensus        23 ~~~L~~~i~k~V~V~L----kdGr~i~G~L~~fD~   53 (105)
                      ..++.+++|+.|.|++    .+++.++|+|.++|.
T Consensus        90 ~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~  124 (154)
T PRK00092         90 ARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG  124 (154)
T ss_pred             HHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence            5678899999999997    567899999999997

>PRK14632 hypothetical protein; Provisional

Probab=90.54  E-value=0.79  Score=33.44  Aligned_cols=44  Identities=18%  Similarity=0.251  Sum_probs=32.9

Q ss_pred             cccccccchhhHHhhcCCEEEEEEcC-------CeEEEEEEEEecCccCeEec
Q psy17123         15 KDRKRKESILDLSKFLDKVIRVKFAG-------GRECSGILKGFDPLLNLVLD   60 (105)
Q Consensus        15 ~~~~~~~~~~~L~~~i~k~V~V~Lkd-------Gr~i~G~L~~fD~~mNlvL~   60 (105)
                      -|.|-+. ..+..+++|+.|.|+|++       .+.|+|+|.++|. -++.|.
T Consensus        83 ldRpL~~-~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~-~~i~l~  133 (172)
T PRK14632         83 LERPFFR-AEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEG-DTVVLR  133 (172)
T ss_pred             CCCcCCC-HHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeC-CEEEEE
Confidence            3434433 567889999999999976       5799999999986 355553

>PRK14634 hypothetical protein; Provisional

Probab=90.49  E-value=0.8  Score=32.83  Aligned_cols=45  Identities=13%  Similarity=0.107  Sum_probs=33.2

Q ss_pred             CccccccccchhhHHhhcCCEEEEEEcC----CeEEEEEEEEecCccCeEe
Q psy17123         13 ETKDRKRKESILDLSKFLDKVIRVKFAG----GRECSGILKGFDPLLNLVL   59 (105)
Q Consensus        13 ~~~~~~~~~~~~~L~~~i~k~V~V~Lkd----Gr~i~G~L~~fD~~mNlvL   59 (105)
                      |--|.|.+. ..+..+++|+.|.|++.+    .+.|+|+|.++|.- ++.|
T Consensus        83 PGldRpL~~-~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l  131 (155)
T PRK14634         83 PGIGDQLSS-DRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI  131 (155)
T ss_pred             CCCCCcCCC-HHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence            334444444 667889999999999963    27999999999973 4555

>PRK14643 hypothetical protein; Provisional

Probab=90.47  E-value=0.84  Score=33.13  Aligned_cols=41  Identities=15%  Similarity=0.256  Sum_probs=31.3

Q ss_pred             CccccccccchhhHHhhcCCEEEEEEcC----CeEEEEEEEEecCc
Q psy17123         13 ETKDRKRKESILDLSKFLDKVIRVKFAG----GRECSGILKGFDPL   54 (105)
Q Consensus        13 ~~~~~~~~~~~~~L~~~i~k~V~V~Lkd----Gr~i~G~L~~fD~~   54 (105)
                      |--++|.+. ..++.+++|++|.|+|+.    .+.|+|+|.++|.-
T Consensus        87 PGleRpL~~-~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T PRK14643         87 SGIEKQIRS-QEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN  131 (164)
T ss_pred             CCCCCCCCC-HHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence            333434433 567889999999999965    58999999999964

>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=90.15  E-value=1.3  Score=32.00  Aligned_cols=42  Identities=24%  Similarity=0.445  Sum_probs=33.3

Q ss_pred             ccccccchhhHHhhcCCEEEEEE----cCCeEEEEEEEEecCccCeEe
Q psy17123         16 DRKRKESILDLSKFLDKVIRVKF----AGGRECSGILKGFDPLLNLVL   59 (105)
Q Consensus        16 ~~~~~~~~~~L~~~i~k~V~V~L----kdGr~i~G~L~~fD~~mNlvL   59 (105)
                      |.|... ..+..+++|+.|.|.|    .+++.++|+|.++|.-. +++
T Consensus        85 dRpL~~-~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~  130 (153)
T COG0779          85 DRPLKT-AEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL  130 (153)
T ss_pred             CCCcCC-HHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence            434333 4567889999999999    78899999999999876 444

>PRK14647 hypothetical protein; Provisional

Probab=89.82  E-value=1  Score=32.29  Aligned_cols=40  Identities=20%  Similarity=0.345  Sum_probs=30.9

Q ss_pred             CccccccccchhhHHhhcCCEEEEEEc---------CCeEEEEEEEEecC
Q psy17123         13 ETKDRKRKESILDLSKFLDKVIRVKFA---------GGRECSGILKGFDP   53 (105)
Q Consensus        13 ~~~~~~~~~~~~~L~~~i~k~V~V~Lk---------dGr~i~G~L~~fD~   53 (105)
                      |--+.|.+. ..++.+++|+.|.|+++         +.+.|+|+|.++|.
T Consensus        82 PG~~RpL~~-~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~  130 (159)
T PRK14647         82 PGLDRPLKK-EADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD  130 (159)
T ss_pred             CCCCCcCCC-HHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence            333444444 66788999999999995         35899999999996

>PRK14646 hypothetical protein; Provisional

Probab=89.32  E-value=1.2  Score=31.93  Aligned_cols=45  Identities=13%  Similarity=0.111  Sum_probs=33.0

Q ss_pred             CccccccccchhhHHhhcCCEEEEEEcC---C-eEEEEEEEEecCccCeEe
Q psy17123         13 ETKDRKRKESILDLSKFLDKVIRVKFAG---G-RECSGILKGFDPLLNLVL   59 (105)
Q Consensus        13 ~~~~~~~~~~~~~L~~~i~k~V~V~Lkd---G-r~i~G~L~~fD~~mNlvL   59 (105)
                      |--+.|-+. ..+..+++|+.|.|+|++   | +.++|+|.++|.- ++.|
T Consensus        83 PGldRpL~~-~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l  131 (155)
T PRK14646         83 QGVSDELTS-ERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI  131 (155)
T ss_pred             CCCCCcCCC-HHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence            333444443 567889999999999964   3 6889999999984 5555

>PRK14631 hypothetical protein; Provisional

Probab=88.49  E-value=1.4  Score=32.35  Aligned_cols=39  Identities=15%  Similarity=0.253  Sum_probs=30.7

Q ss_pred             CccccccccchhhHHhhcCCEEEEEEc----CCeEEEEEEEEec
Q psy17123         13 ETKDRKRKESILDLSKFLDKVIRVKFA----GGRECSGILKGFD   52 (105)
Q Consensus        13 ~~~~~~~~~~~~~L~~~i~k~V~V~Lk----dGr~i~G~L~~fD   52 (105)
                      |--+.|-+. ..++.+++|+.|.|+|.    +.+.|+|+|.++|
T Consensus       100 PGldRpL~~-~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~  142 (174)
T PRK14631        100 PGWDRPFFQ-LEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD  142 (174)
T ss_pred             CCCCCcCCC-HHHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence            334444444 66788999999999995    4589999999998

>PRK06955 biotin--protein ligase; Provisional

Probab=87.69  E-value=2.5  Score=32.93  Aligned_cols=32  Identities=22%  Similarity=0.385  Sum_probs=28.4

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEecCccCeEec
Q psy17123         29 FLDKVIRVKFAGGRECSGILKGFDPLLNLVLD   60 (105)
Q Consensus        29 ~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~   60 (105)
                      +++++|+|...+++.++|++.|+|+...|+|.
T Consensus       247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~  278 (300)
T PRK06955        247 YAGREVVLLEDGAELARGVAHGIDETGQLLLD  278 (300)
T ss_pred             cCCCeEEEEECCCcEEEEEEeeECCCceEEEE
Confidence            47899999766778899999999999999985

>PRK14637 hypothetical protein; Provisional

Probab=87.44  E-value=1.6  Score=31.16  Aligned_cols=45  Identities=24%  Similarity=0.318  Sum_probs=32.0

Q ss_pred             CccccccccchhhHHhhcCCEEEEEEcCCeEE-EEEEEEecCccCeEe
Q psy17123         13 ETKDRKRKESILDLSKFLDKVIRVKFAGGREC-SGILKGFDPLLNLVL   59 (105)
Q Consensus        13 ~~~~~~~~~~~~~L~~~i~k~V~V~LkdGr~i-~G~L~~fD~~mNlvL   59 (105)
                      |--|.|-+. ..+..+++|+.|.|++.+.+.+ +|+|.++|.- ++.|
T Consensus        81 PGldRpL~~-~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l  126 (151)
T PRK14637         81 PGIERVIKN-AAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVL  126 (151)
T ss_pred             CCCCCCCCC-HHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEE
Confidence            334444444 6678899999999999544455 7999999874 4444

>PRK14641 hypothetical protein; Provisional

Probab=87.35  E-value=1.6  Score=32.07  Aligned_cols=36  Identities=14%  Similarity=0.264  Sum_probs=28.6

Q ss_pred             ccccccchhhHHhhcCCEEEEEEcC----CeEEEEEEEEec
Q psy17123         16 DRKRKESILDLSKFLDKVIRVKFAG----GRECSGILKGFD   52 (105)
Q Consensus        16 ~~~~~~~~~~L~~~i~k~V~V~Lkd----Gr~i~G~L~~fD   52 (105)
                      +.|.+. ..+..+++|+.|.|+|.+    .+.|+|+|.++|
T Consensus        90 dRpL~~-~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~  129 (173)
T PRK14641         90 GEPIIL-PRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS  129 (173)
T ss_pred             CCcCCC-HHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence            344443 567888999999999975    569999999995

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

Probab=84.28  E-value=5.4  Score=31.02  Aligned_cols=49  Identities=27%  Similarity=0.347  Sum_probs=34.9

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCC
Q psy17123         29 FLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQE   86 (105)
Q Consensus        29 ~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~   86 (105)
                      ++|++|++.. ++..++|++.++|+...|+|..      ++.  .+.-..|.|.+|+.
T Consensus       270 ~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~~------~g~--~~~~~~gev~~~~~  318 (319)
T PRK11886        270 FLGREVKLII-GDKEISGIARGIDEQGALLLED------DGV--EKPFNGGEISLRSW  318 (319)
T ss_pred             ccCCeEEEEe-CCcEEEEEEEEECCCceEEEEe------CCc--EEEEEEeEEEEecC
Confidence            4799999986 4567999999999999999951      121  12334566766653

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

Probab=82.09  E-value=5.8  Score=34.10  Aligned_cols=32  Identities=25%  Similarity=0.195  Sum_probs=28.5

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEecCccCeEec
Q psy17123         29 FLDKVIRVKFAGGRECSGILKGFDPLLNLVLD   60 (105)
Q Consensus        29 ~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~   60 (105)
                      ++|++|++...+++.+.|+..|+|+...|+|+
T Consensus       276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~  307 (592)
T PRK13325        276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLE  307 (592)
T ss_pred             cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEE
Confidence            47999999767778899999999999999995

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

Probab=81.92  E-value=9.3  Score=28.50  Aligned_cols=32  Identities=22%  Similarity=0.376  Sum_probs=27.3

Q ss_pred             hhcCCEEEEEEcCCeEEEEEEEEecCccCeEec
Q psy17123         28 KFLDKVIRVKFAGGRECSGILKGFDPLLNLVLD   60 (105)
Q Consensus        28 ~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~   60 (105)
                      -++|++|+|...+ ..+.|++.|+|+...|+|.
T Consensus       190 ~~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~  221 (237)
T TIGR00121       190 AHIGREVSLTTGN-GEIEGIARGIDKDGALLLE  221 (237)
T ss_pred             hccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence            3479999998644 5699999999999999995

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	105
3swn_C	117	Structure Of The Lsm657 Complex: An Assembly Interm		2e-13
4emk_C	113	Crystal Structure Of Splsm567 Length = 113		7e-13
3cw1_G	76	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		1e-07

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 32/56 (57%), Positives = 43/56 (76%)
Query: 12 AETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          ++  +R RKESILDLS++ D+ I+  F GGR+ +GILKGFD L+NLVLD+  E LR
Sbjct: 18 SQPTERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLR 73

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 32/56 (57%), Positives = 42/56 (75%)
Query: 12 AETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          ++  +R RKESILDLS++ D+ I+  F GGR+ +GILKGFD L NLVLD+  E LR
Sbjct: 14 SQPTERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLXNLVLDDVEEQLR 69

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 21/41 (51%), Positives = 28/41 (68%)
Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          +L KF+DK + +K  GGR   GIL+GFDP +NLV+D   E 
Sbjct: 8  ELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEM 48

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	105
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	7e-19
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	2e-18
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	7e-17
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	2e-15
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	1e-14
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	2e-14
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	6e-14
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	7e-14
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	1e-12
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	2e-12
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	6e-12
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	9e-12
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	1e-10
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	4e-09
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	4e-09
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	4e-07
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-05
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	1e-04
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	1e-04
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	7e-04
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	9e-04

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

 Score = 74.2 bits (182), Expect = 7e-19
 Identities = 32/55 (58%), Positives = 41/55 (74%)

Query: 15 KDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVT 69
           +R RKESILDLS++ D+ I+  F GGR+ +GILKGFD L+NLVLD+  E LR  
Sbjct: 17 TERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNP 71

>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 = 72.0 bits (177), Expect = 2e-18
 Identities = 22/48 (45%), Positives = 29/48 (60%)

Query: 20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          K    +L KF+DK + +K  GGR   GIL+GFDP +NLV+D   E   
Sbjct: 3  KAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMAT 50

>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 = 68.1 bits (167), Expect = 7e-17
 Identities = 14/48 (29%), Positives = 28/48 (58%)

Query: 20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          + +   L++ L+ ++ VK  G +E  G+L+ +D  +NLVL ++ E   
Sbjct: 8  ETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQS 55

>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 = 64.2 bits (157), Expect = 2e-15
 Identities = 16/42 (38%), Positives = 23/42 (54%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          L++ L   + V+  GGRE  G L G+D  +NLVL +  E   
Sbjct: 9  LNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQN 50

>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 = 62.4 bits (152), Expect = 1e-14
 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 14 TKDRKRKESILD-LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          +  R   +  LD L   L+  + +K  G RE  G+LK FD  +NLVL++  E 
Sbjct: 7  SSQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEEL 59

>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 = 62.0 bits (151), Expect = 2e-14
 Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 15 KDRKRKESILD-LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVT 69
                E+ LD L   LD+ + +K  G R   G L+ FD   N+VL +  E +   
Sbjct: 3  HHHHHMETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQL 58

>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 = 60.5 bits (147), Expect = 6e-14
 Identities = 14/41 (34%), Positives = 22/41 (53%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYL 66
          L   + K + VK     E  GIL+ FD  +NL+L++  E +
Sbjct: 16 LQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEII 56

>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 = 61.5 bits (149), Expect = 7e-14
 Identities = 21/70 (30%), Positives = 30/70 (42%), Gaps = 1/70 (1%)

Query: 1  MAAVNTTTDAGAETKDRKRKESILDL-SKFLDKVIRVKFAGGRECSGILKGFDPLLNLVL 59
          M+        G   +        L L  K +   I V   G +E SG+L+GFD  +N+VL
Sbjct: 7  MSETPANKSQGGSNQKGGNIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVL 66

Query: 60 DNTTEYLRVT 69
          D+  EY    
Sbjct: 67 DDVQEYGFKA 76

>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 = 57.3 bits (139), Expect = 1e-12
 Identities = 14/40 (35%), Positives = 20/40 (50%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          + + LDK + V    G E  G L G+D  LN+VL +    
Sbjct: 9  IHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMI 48

>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 = 56.8 bits (137), Expect = 2e-12
 Identities = 12/44 (27%), Positives = 22/44 (50%)

Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRV 68
           + + +D  +R     GR   G  K FD  +NL+L +  E+ ++
Sbjct: 8  KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKI 51

>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 = 55.6 bits (134), Expect = 6e-12
 Identities = 15/42 (35%), Positives = 24/42 (57%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          +   LD+++ VK  G RE +G L  +D  LN+VL +  E + 
Sbjct: 14 VRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVT 55

>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 = 55.0 bits (133), Expect = 9e-12
 Identities = 14/40 (35%), Positives = 23/40 (57%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          L+K + K + ++ + G +  GIL   D  +NL L+ T EY
Sbjct: 9  LNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEY 48

>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 = 52.3 bits (126), Expect = 1e-10
 Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 1/41 (2%)

Query: 26 LSKFLDKVIRVKFAGGR-ECSGILKGFDPLLNLVLDNTTEY 65
          +   + K+IRV+  G   +  G L+G D  +NL L N  E 
Sbjct: 10 VKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMEC 50

>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 = 48.6 bits (116), Expect = 4e-09
 Identities = 15/40 (37%), Positives = 19/40 (47%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          L+    K + VK   G E  G L   D  +N+ L NT EY
Sbjct: 11 LNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEY 50

>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 = 48.7 bits (116), Expect = 4e-09
 Identities = 15/40 (37%), Positives = 22/40 (55%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          + K +   + V     RE +G L GFD  +N+VL + TEY
Sbjct: 25 IDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEY 64

>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 = 43.7 bits (103), Expect = 4e-07
 Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 1/41 (2%)

Query: 26 LSKFLDKVIRVKF-AGGRECSGILKGFDPLLNLVLDNTTEY 65
          L   ++  + VK      E  G L   D   NL L+   E+
Sbjct: 26 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEF 66

>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 = 40.4 bits (94), Expect = 2e-05
 Identities = 12/43 (27%), Positives = 22/43 (51%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRV 68
          + + +D  +R     GR   G  K FD  +NL+L +  E+ ++
Sbjct: 9  MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKI 51

>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 = 37.0 bits (86), Expect = 1e-04
 Identities = 11/63 (17%), Positives = 22/63 (34%), Gaps = 7/63 (11%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR-----VTYQSVQVRSWCS 80
          L+    + I V+   G   +G L+  D  +NL L      +             +R   +
Sbjct: 21 LNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIR--GN 78

Query: 81 IVR 83
           ++
Sbjct: 79 NIK 81

>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 = 36.7 bits (85), Expect = 1e-04
 Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 4/42 (9%)

Query: 28 KFLDKVIRV----KFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          ++L    R+             G + GFD  +NLVLD+  E 
Sbjct: 23 RYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEI 64

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

 Score = 35.5 bits (81), Expect = 7e-04
 Identities = 13/52 (25%), Positives = 24/52 (46%)

Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVR 76
          +L+  L + ++V  + G    G+L   D  LN+VL N +      +  V + 
Sbjct: 4  ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRVFIM 55

>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 = 34.9 bits (80), Expect = 9e-04
 Identities = 12/44 (27%), Positives = 21/44 (47%)

Query: 22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          S+L  S   +  + +     ++  G +K FD   N+VL+N  E 
Sbjct: 30 SVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEM 73

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	105
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.94
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.92
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.91
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.91
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.91
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.91
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.9
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.9
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.9
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.9
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.9
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.9
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.9
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.89
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.88
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.88
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.88
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.88
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.87
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.86
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.86
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.85
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.83
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.8
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	99.15
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	97.11
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	96.88
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	96.8
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	96.7
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	96.61
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	96.49
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	96.44
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	96.32
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	95.83
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	95.57
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	95.3
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	95.15
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	94.84
1ycy_A	71	Conserved hypothetical protein; structural genomic	94.81
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	94.65
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	91.51
3rux_A	270	BIRA bifunctional protein; biotin-protein ligase,	91.06
2eay_A	233	Biotin [acetyl-COA-carboxylase] ligase; biotin bio	82.6
2rm4_A	103	CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-	81.18

>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=99.94  E-value=1.1e-26  Score=158.47  Aligned_cols=88  Identities=42%  Similarity=0.637  Sum_probs=57.8

Q ss_pred             CCCccccccccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCce---eeeeeEEeeEEEcCCc
Q psy17123         11 GAETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQ---SVQVRSWCSIVRRQES   87 (105)
Q Consensus        11 ~~~~~~~~~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~---~~~~~~lg~vlIRG~~   87 (105)
                      ..++.++|+++++..|.++++++|+|+|+|||.|+|+|+|||+||||+|+||+|++.+++.   ....+.+|+++|||++
T Consensus        13 ~~~~~~~~kke~i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~n   92 (113)
T 4emk_C           13 SSQPTERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTT   92 (113)
T ss_dssp             -------------------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTT
T ss_pred             CCCCccCCccchHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCe
Confidence            3456688999999999999999999999999999999999999999999999999865321   1357899999999999


Q ss_pred             EEEEEecCCcc
Q psy17123         88 RRNVHRRDHKE   98 (105)
Q Consensus        88 I~~i~~~d~~~   98 (105)
                      |++|+++|+..
T Consensus        93 Iv~I~~~d~~e  103 (113)
T 4emk_C           93 LVLIAPMDGSE  103 (113)
T ss_dssp             EEEEEECC---
T ss_pred             EEEEEecCccc
Confidence            99999999765

>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=99.92  E-value=1.8e-24  Score=143.35  Aligned_cols=84  Identities=20%  Similarity=0.264  Sum_probs=70.8

Q ss_pred             cccccccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCce---eeeeeEEeeEEEcCCcEEEE
Q psy17123         15 KDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQ---SVQVRSWCSIVRRQESRRNV   91 (105)
Q Consensus        15 ~~~~~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~---~~~~~~lg~vlIRG~~I~~i   91 (105)
                      +---..++...|.+++||+|+|+|+|||.|+|+|+|||+||||+|+||.|++..+++   ....+.+|.++|||++|++|
T Consensus         4 ~~~~~~~p~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nVv~I   83 (96)
T 3bw1_A            4 HHHHMETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLI   83 (96)
T ss_dssp             --CCCCCHHHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEECGGGEEEE
T ss_pred             cchhhhhHHHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEECCCEEEEE
Confidence            334567889999999999999999999999999999999999999999999865321   23578999999999999999


Q ss_pred             EecCCcc
Q psy17123         92 HRRDHKE   98 (105)
Q Consensus        92 ~~~d~~~   98 (105)
                      ++.+...
T Consensus        84 ~~~d~~~   90 (96)
T 3bw1_A           84 STPSEDD   90 (96)
T ss_dssp             ECCC---
T ss_pred             EecCccc
Confidence            9988763

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

Probab=99.91  E-value=4.1e-24  Score=135.28  Aligned_cols=72  Identities=25%  Similarity=0.305  Sum_probs=64.7

Q ss_pred             cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123         21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH   96 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~   96 (105)
                      .|...|.++++++|+|+|+|||.|+|+|.|||+|||++|+||.|+..+.    ..+.+|.++|||++|++|++.|+
T Consensus         4 ~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~----~~~~lg~v~iRG~~I~~i~~~~e   75 (75)
T 1h64_1            4 RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGE----VVKRYGKIVIRGDNVLAISPTEE   75 (75)
T ss_dssp             CHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTE----EEEEEEEEEECGGGEEEEEEC--
T ss_pred             hHHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeCC----ceeECCEEEECCCEEEEEEeCCC
Confidence            4677899999999999999999999999999999999999999997543    47899999999999999998763

>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=99.91  E-value=1.9e-24  Score=137.57  Aligned_cols=71  Identities=34%  Similarity=0.541  Sum_probs=53.4

Q ss_pred             chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123         22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH   96 (105)
Q Consensus        22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~   96 (105)
                      +.+.|++++|++|+|+|+|||.|+|+|.|||+||||+|+||.|+..+++    .+.+|.++|||++|++|++.|.
T Consensus         5 ~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~----~~~lg~v~iRG~~I~~i~~~d~   75 (76)
T 3s6n_G            5 HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQ----QNNIGMVVIRGNSIIMLEALER   75 (76)
T ss_dssp             ---------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC--------CBSSEEECSSSEEEEEC---
T ss_pred             chHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccCCc----EeEcCEEEECCCeEEEEEeccC
Confidence            4678999999999999999999999999999999999999999876543    6889999999999999998874

>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=99.91  E-value=6.1e-24  Score=134.96  Aligned_cols=73  Identities=30%  Similarity=0.358  Sum_probs=65.6

Q ss_pred             cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCCc
Q psy17123         21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHK   97 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~~   97 (105)
                      .|...|+++++++|+|+|+||+.|+|+|.|||+|||++|+||.|+..+.    ..+.+|.++|||++|++|++.|+.
T Consensus         4 ~P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~----~~~~lg~v~iRG~~I~~i~~~d~~   76 (77)
T 1i4k_A            4 RPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGE----VVRKVGSVVIRGDTVVFVSPAPGG   76 (77)
T ss_dssp             CHHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTE----EEEEEEEEEECGGGEEEEEECC--
T ss_pred             cHHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecCC----cEeECCEEEECCCEEEEEEeCCCC
Confidence            4677899999999999999999999999999999999999999997643    378999999999999999998864

>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=99.91  E-value=1.1e-23  Score=139.60  Aligned_cols=78  Identities=22%  Similarity=0.245  Sum_probs=65.6

Q ss_pred             cccccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123         17 RKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH   96 (105)
Q Consensus        17 ~~~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~   96 (105)
                      +....|+..|.++++++|+|+|++||+|+|+|+|||+||||+|+||+|+..+++   ..+.+|.++|||++|++|.+...
T Consensus        16 ~~~~~Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~---~~~~lg~v~IRG~nI~~i~p~~~   92 (94)
T 4emk_A           16 SMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTG---VTEKHSEMLLNGNGMCMLIPGGK   92 (94)
T ss_dssp             ----CHHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTTC---CEEEEEEEEECSTTEEEEEECC-
T ss_pred             cccccCHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCCC---cEeEcCEEEEcCCEEEEEEeCCC
Confidence            344667788999999999999999999999999999999999999999983333   37899999999999999998754


Q ss_pred             c
Q psy17123         97 K   97 (105)
Q Consensus        97 ~   97 (105)
                      +
T Consensus        93 p   93 (94)
T 4emk_A           93 P   93 (94)
T ss_dssp             -
T ss_pred             C
Confidence            3

>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=99.90  E-value=8.4e-24  Score=134.54  Aligned_cols=72  Identities=28%  Similarity=0.365  Sum_probs=64.7

Q ss_pred             cchhhHHhhcCCEEEEEEcCC-eEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123         21 ESILDLSKFLDKVIRVKFAGG-RECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH   96 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdG-r~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~   96 (105)
                      .|...|.++++++|+|+|++| ++|+|+|.|||+|||++|+||.|+..++    ..+.+|.++|||++|++|++.|.
T Consensus         5 ~P~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~~~----~~~~lg~v~iRG~nI~~i~~~de   77 (77)
T 1ljo_A            5 LPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEE----KVRSLGEIVLRGNNVVLIQPQEE   77 (77)
T ss_dssp             CHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTE----EEEEEEEEEECGGGEEEEEEC--
T ss_pred             chHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecCC----cEeECCeEEEeCCeEEEEEeCCC
Confidence            567889999999999999999 9999999999999999999999997532    47899999999999999998873

>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=99.90  E-value=8.9e-24  Score=135.80  Aligned_cols=75  Identities=24%  Similarity=0.245  Sum_probs=65.8

Q ss_pred             cccccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123         17 RKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH   96 (105)
Q Consensus        17 ~~~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~   96 (105)
                      |....|...|.++++++|+|+|+|||.|+|+|.|||+||||+|+||.|+ . +.   ..+.+|.++|||++|++|++.|+
T Consensus         7 ~~~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~-~~---~~~~lg~v~iRG~~I~~i~~~dg   81 (81)
T 1i8f_A            7 KCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-I-DG---NVYKRGTMVVRGENVLFISPVPG   81 (81)
T ss_dssp             ---CCHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-E-TT---EEEEEEEEEECGGGEEEEEECC-
T ss_pred             ccccchHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-c-CC---cccCCCEEEECCCEEEEEEeCCC
Confidence            4456778889999999999999999999999999999999999999998 3 32   47899999999999999998874

>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=99.90  E-value=1.1e-23  Score=136.10  Aligned_cols=74  Identities=24%  Similarity=0.359  Sum_probs=66.3

Q ss_pred             ccccccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123         16 DRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR   93 (105)
Q Consensus        16 ~~~~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~   93 (105)
                      .+....|...|.++++++|+|+|+|||.|+|+|.|||+|||++|+||.|+..+.    ..+.+|.++|||++|++|++
T Consensus        10 ~~~~~~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~----~~~~lg~v~IRG~~I~~i~p   83 (83)
T 1mgq_A           10 RVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGE----VTRRLGTVLIRGDNIVYISP   83 (83)
T ss_dssp             CCCTTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTE----EEEEEEEEEECGGGEEEEEC
T ss_pred             cccCcChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecCC----cccCCCEEEECCCEEEEEEC
Confidence            334567788999999999999999999999999999999999999999997543    47899999999999999975

>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=99.90  E-value=1.2e-23  Score=135.14  Aligned_cols=73  Identities=23%  Similarity=0.350  Sum_probs=65.4

Q ss_pred             ccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123         20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH   96 (105)
Q Consensus        20 ~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~   96 (105)
                      ..|...|.++++++|+|+|+|||.|+|+|.|||+||||+|+||.|++.+.    ..+.+|.++|||++|++|++.|+
T Consensus         8 ~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~----~~~~lg~v~iRG~~I~~i~~~~~   80 (81)
T 1th7_A            8 ETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDG----SGKKLGTIVIRGDNVILISPLQT   80 (81)
T ss_dssp             HHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSS----CEEEEEEEEECGGGEEEEEEC--
T ss_pred             cchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecCC----ceeECCEEEECCCEEEEEEecCC
Confidence            45678899999999999999999999999999999999999999997653    36899999999999999998874

>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=99.90  E-value=5.2e-24  Score=135.11  Aligned_cols=71  Identities=24%  Similarity=0.337  Sum_probs=63.9

Q ss_pred             cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecC
Q psy17123         21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRD   95 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d   95 (105)
                      .|...|++++|++|+|+|+||+.|+|+|.|||+||||+|+||.|+... +   ..+.+|.++|||++|++|++.|
T Consensus         4 ~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-~---~~~~lg~v~iRG~~I~~i~~~~   74 (75)
T 4emk_B            4 SPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNG-K---KTNVYGDAFIRGNNVLYVSALD   74 (75)
T ss_dssp             HHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEETT-E---EEEEEEEEEEEGGGSSEEEEC-
T ss_pred             chHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEecC-C---cccEecEEEEcCCeEEEEEecC
Confidence            467789999999999999999999999999999999999999998643 2   3688999999999999999876

>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=99.90  E-value=2e-23  Score=136.39  Aligned_cols=77  Identities=19%  Similarity=0.275  Sum_probs=65.5

Q ss_pred             hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCc------eeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123         23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTY------QSVQVRSWCSIVRRQESRRNVHRRDH   96 (105)
Q Consensus        23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~------~~~~~~~lg~vlIRG~~I~~i~~~d~   96 (105)
                      ...|.++++++|+|+|+|||.|+|+|+|||+||||+|+||.|++....      .....+.+|.++|||++|++|++.+.
T Consensus         6 ~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~~I~~i~~~~~   85 (91)
T 1d3b_B            6 SSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEGP   85 (91)
T ss_dssp             -CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEEEC
T ss_pred             hHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECCCeEEEEEcCCC
Confidence            457899999999999999999999999999999999999999863210      23467899999999999999998876


Q ss_pred             ccc
Q psy17123         97 KEY   99 (105)
Q Consensus        97 ~~~   99 (105)
                      +.-
T Consensus        86 ~~~   88 (91)
T 1d3b_B           86 PPK   88 (91)
T ss_dssp             CC-
T ss_pred             CCC
Confidence            654

>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=99.90  E-value=2.4e-23  Score=135.56  Aligned_cols=76  Identities=22%  Similarity=0.225  Sum_probs=65.5

Q ss_pred             ccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCCccc
Q psy17123         20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHKEY   99 (105)
Q Consensus        20 ~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~~~~   99 (105)
                      ..|...|++++|++|+|+|+||+.|+|+|.|||+||||+|+||.|+.. ++   ..+.+|.++|||++|++|++.|....
T Consensus         5 ~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~-g~---~~~~lg~v~IRG~nI~~i~~~d~~~~   80 (86)
T 3s6n_F            5 LNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYID-GA---LSGHLGEVLIRCNNVLYIRGVEEEEE   80 (86)
T ss_dssp             CCHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEET-TE---EEEEESSEEECGGGEEEEEECC----
T ss_pred             cCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcC-Cc---eeeEccEEEEeCCeEEEEEeCCcccc
Confidence            356778999999999999999999999999999999999999999853 32   36889999999999999999988664

>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=99.89  E-value=1e-22  Score=129.44  Aligned_cols=71  Identities=18%  Similarity=0.079  Sum_probs=64.6

Q ss_pred             cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecC
Q psy17123         21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRD   95 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d   95 (105)
                      .|...|++++|++|+|+|++|++|+|+|.|||+|||++|+||+|+..+++    .+.+|.++|||++|.+|+..|
T Consensus         5 ~P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~~~----~~~lg~v~IRG~nI~~i~lPd   75 (75)
T 1d3b_A            5 VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGR----VAQLEQVYIRGCKIRFLILPD   75 (75)
T ss_dssp             CHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSC----EEEEEEEEECGGGEEEEEECC
T ss_pred             CHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCCCc----EEEcCeEEEeCCEEEEEEcCC
Confidence            46678999999999999999999999999999999999999999865443    688999999999999999765

>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=99.88  E-value=3.5e-23  Score=136.58  Aligned_cols=77  Identities=19%  Similarity=0.274  Sum_probs=67.2

Q ss_pred             ccccccchhhHHhhcCCEEEEEE----cCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEE
Q psy17123         16 DRKRKESILDLSKFLDKVIRVKF----AGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNV   91 (105)
Q Consensus        16 ~~~~~~~~~~L~~~i~k~V~V~L----kdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i   91 (105)
                      +|....|+..|.++++++|+|++    ++||+|+|+|.|||+||||+|+||+|+..+++   ..+.+|.++|||++|++|
T Consensus        11 ~~~m~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~---~~~~lg~v~iRG~nV~~i   87 (92)
T 3s6n_E           11 QKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTK---SRKQLGRIMLKGDNITLL   87 (92)
T ss_dssp             ---CCCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSC---CEEEEEEEEECGGGEEEE
T ss_pred             ceeccCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCC---ceeEcCeEEEeCCEEEEE
Confidence            45668888999999999999999    99999999999999999999999999975443   368899999999999999


Q ss_pred             EecC
Q psy17123         92 HRRD   95 (105)
Q Consensus        92 ~~~d   95 (105)
                      ++.|
T Consensus        88 ~~~~   91 (92)
T 3s6n_E           88 QSVS   91 (92)
T ss_dssp             EEC-
T ss_pred             EeCC
Confidence            9875

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

Probab=99.88  E-value=2.2e-22  Score=132.70  Aligned_cols=76  Identities=24%  Similarity=0.319  Sum_probs=63.5

Q ss_pred             cccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEec----Cc-----eeeeeeEEeeEEEcCCcEE
Q psy17123         19 RKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRV----TY-----QSVQVRSWCSIVRRQESRR   89 (105)
Q Consensus        19 ~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~----~~-----~~~~~~~lg~vlIRG~~I~   89 (105)
                      ...|...|+.+++++|+|+|++||.|+|+|.|||+||||+|+||+|++..    ++     .....+.+|+++|||++|+
T Consensus         7 ~~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG~nVv   86 (93)
T 4emg_A            7 VAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDSVI   86 (93)
T ss_dssp             --CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECGGGEE
T ss_pred             cCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECCCeEE
Confidence            45667778888999999999999999999999999999999999999863    11     0125789999999999999


Q ss_pred             EEEec
Q psy17123         90 NVHRR   94 (105)
Q Consensus        90 ~i~~~   94 (105)
                      +|++.
T Consensus        87 ~I~p~   91 (93)
T 4emg_A           87 LIAPP   91 (93)
T ss_dssp             EEECC
T ss_pred             EEEec
Confidence            99874

>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=99.88  E-value=9.3e-23  Score=134.67  Aligned_cols=72  Identities=18%  Similarity=0.173  Sum_probs=60.9

Q ss_pred             ccchhhHHhhcCCEEEEEEcCC-eEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecC
Q psy17123         20 KESILDLSKFLDKVIRVKFAGG-RECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRD   95 (105)
Q Consensus        20 ~~~~~~L~~~i~k~V~V~LkdG-r~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d   95 (105)
                      ..|...|.+++|++|+|+|+|| ++|+|+|.|||+||||+|+||.|+..++    ..+.+|.++|||++|++|++.+
T Consensus        20 ~~P~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~~~----~~~~lg~v~IRG~nI~~I~~~~   92 (93)
T 1n9r_A           20 VNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGV----SHGTLGEIFIRCNNVLYIRELP   92 (93)
T ss_dssp             ------CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTE----EEEECCSEEECGGGEEEEEECC
T ss_pred             CChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcCCC----eEeEcCEEEEcCCeEEEEEeCC
Confidence            4566789999999999999999 9999999999999999999999986432    3688999999999999999765

>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=99.88  E-value=4.3e-23  Score=141.77  Aligned_cols=80  Identities=24%  Similarity=0.315  Sum_probs=66.2

Q ss_pred             cccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCc------eeee-----eeEEeeEEEcCCc
Q psy17123         19 RKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTY------QSVQ-----VRSWCSIVRRQES   87 (105)
Q Consensus        19 ~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~------~~~~-----~~~lg~vlIRG~~   87 (105)
                      ...+...|.++++++|+|+|+|||.|+|+|+|||+||||+|+||.|++.+..      +...     .+.+|.++|||++
T Consensus        26 ~~~Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG~n  105 (121)
T 2fwk_A           26 IILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNN  105 (121)
T ss_dssp             CCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGG
T ss_pred             ccCcHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECCCE
Confidence            3566677899999999999999999999999999999999999999985310      0112     6889999999999


Q ss_pred             EEEEEecCCcc
Q psy17123         88 RRNVHRRDHKE   98 (105)
Q Consensus        88 I~~i~~~d~~~   98 (105)
                      |++|++.+.+.
T Consensus       106 Vv~I~~~~~~~  116 (121)
T 2fwk_A          106 VAMLVPGGDPD  116 (121)
T ss_dssp             EEEEESSSCC-
T ss_pred             EEEEEecCCCC
Confidence            99999877654

>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=99.87  E-value=3.1e-22  Score=134.93  Aligned_cols=75  Identities=16%  Similarity=0.135  Sum_probs=56.1

Q ss_pred             cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCCcc
Q psy17123         21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHKE   98 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~~~   98 (105)
                      .+...|++++|++|+|+|++|++|+|+|.|||+||||+|+||+|+..+++   ..+.+|.++|||++|++|++.|...
T Consensus        16 ~p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg~---~~~~lg~v~IRG~nI~~I~~pd~l~   90 (105)
T 4emh_A           16 LPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGD---KFFRLPECYIRGNNIKYLRIQDEVL   90 (105)
T ss_dssp             ----------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSC---EEEEEEEEEECGGGEEEEEC-----
T ss_pred             cHHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCCc---eeeEcCeEEEeCCeEEEEecCHHHh
Confidence            45667899999999999999999999999999999999999999866554   3688999999999999999887653

>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=99.86  E-value=1.4e-21  Score=133.93  Aligned_cols=72  Identities=17%  Similarity=0.176  Sum_probs=65.3

Q ss_pred             chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCCc
Q psy17123         22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHK   97 (105)
Q Consensus        22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~~   97 (105)
                      ++..|+++++++|+|+|++|++|+|+|.+||+||||+|+||+|+..+++    .+.+|.++|||++|++|++.|..
T Consensus         3 p~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~~~----~~~lg~v~IRG~nI~~I~~pd~l   74 (119)
T 1b34_A            3 LVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNRE----PVQLETLSIRGNNIRYFILPDSL   74 (119)
T ss_dssp             HHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSC----CEEEEEEEECGGGEEEEECCTTC
T ss_pred             hHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecCCCc----eeEcceEEEcCCeEEEEEecccc
Confidence            4677999999999999999999999999999999999999999865433    58899999999999999998873

>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=99.86  E-value=2.3e-21  Score=145.79  Aligned_cols=79  Identities=20%  Similarity=0.287  Sum_probs=65.9

Q ss_pred             hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEe-cCc-----eeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123         23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR-VTY-----QSVQVRSWCSIVRRQESRRNVHRRDH   96 (105)
Q Consensus        23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~-~~~-----~~~~~~~lg~vlIRG~~I~~i~~~d~   96 (105)
                      ...|.+|+||+|+|+|+|||+|+|+|+|||+||||+|+||+|++. ..+     +..+.+++|+++|||+||++|+. +.
T Consensus         6 ~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~Isv-e~   84 (231)
T 3pgw_B            6 SSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTV-EG   84 (231)
T ss_pred             hHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEEEEe-cC
Confidence            357999999999999999999999999999999999999999974 111     12368999999999999999984 44


Q ss_pred             cccccc
Q psy17123         97 KEYEDS  102 (105)
Q Consensus        97 ~~~~~~  102 (105)
                      ...+|.
T Consensus        85 pPp~d~   90 (231)
T 3pgw_B           85 PPPKDT   90 (231)
T ss_pred             CCCCCc
Confidence            444543

>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=99.85  E-value=2.5e-21  Score=132.31  Aligned_cols=83  Identities=18%  Similarity=0.193  Sum_probs=64.1

Q ss_pred             cccccccchhhHHhhc--CCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCce----------eeeeeEEeeEE
Q psy17123         15 KDRKRKESILDLSKFL--DKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQ----------SVQVRSWCSIV   82 (105)
Q Consensus        15 ~~~~~~~~~~~L~~~i--~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~----------~~~~~~lg~vl   82 (105)
                      .+.....|...|.+++  +++|+|.|+|||.|.|+|.|||+||||+|+||.|++.....          ....+.+|.++
T Consensus        21 ~~~~~~~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~  100 (118)
T 1b34_B           21 EEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMF  100 (118)
T ss_dssp             -----CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEE
T ss_pred             hhhcccChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEE
Confidence            3445677888899999  59999999999999999999999999999999998743110          01256799999


Q ss_pred             EcCCcEEEEEecCCc
Q psy17123         83 RRQESRRNVHRRDHK   97 (105)
Q Consensus        83 IRG~~I~~i~~~d~~   97 (105)
                      |||++|++|++.+..
T Consensus       101 IRG~nVv~I~~~~~~  115 (118)
T 1b34_B          101 LRGDSVIVVLRNPLI  115 (118)
T ss_dssp             ECGGGEEEEEECCCC
T ss_pred             EcCCEEEEEEeCchh
Confidence            999999999987753

>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=99.83  E-value=1.9e-20  Score=129.74  Aligned_cols=73  Identities=18%  Similarity=0.076  Sum_probs=66.1

Q ss_pred             cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCCc
Q psy17123         21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHK   97 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~~   97 (105)
                      .|...|+++++++|+|+|++|++|.|+|.+||+||||+|+||+|+..+++    ...+|.++|||++|.+|+..|..
T Consensus         5 ~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~----~~~l~~v~IRGnnI~~I~lpd~l   77 (126)
T 2y9a_D            5 VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGR----VAQLEQVYIRGSKIRFLILPDML   77 (126)
T ss_dssp             CSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSC----CEEEEEEEECGGGEEEEECCSSC
T ss_pred             cHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCc----EeecccEEEeCCEEEEEEccccc
Confidence            46778999999999999999999999999999999999999999865543    67899999999999999987754

>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=99.80  E-value=8.4e-20  Score=127.06  Aligned_cols=67  Identities=18%  Similarity=0.359  Sum_probs=61.6

Q ss_pred             hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCCc
Q psy17123         23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHK   97 (105)
Q Consensus        23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~~   97 (105)
                      ...|++++|++|+|+|+||+.|.|+|.|||+||||+|+||.|+  .      .+.+|.++|||++|++|++.|..
T Consensus         2 ~~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~--~------~~~lg~v~IRG~nI~~I~~~d~~   68 (130)
T 1m5q_A            2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNK--A------GEKFNRVFIMYRYIVHIDSTERR   68 (130)
T ss_dssp             HHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECT--T------CCEEEEEEECGGGEEEEEECCCC
T ss_pred             hhHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEE--c------CCEeceEEEeCCeEEEEEcCCcc
Confidence            4679999999999999999999999999999999999999996  2      25789999999999999998875

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

Probab=99.15  E-value=1.6e-10  Score=75.23  Aligned_cols=70  Identities=19%  Similarity=0.142  Sum_probs=59.9

Q ss_pred             cchhhHHhhcCCEEEEEEcCCeEEEEEEEEec-CccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCCccc
Q psy17123         21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFD-PLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHKEY   99 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD-~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~~~~   99 (105)
                      -.+.+|.+++||+|.|+|.||++|+|+|.+|| ...|++|.|+    .++      .....++|.|..|..|...+...+
T Consensus         7 ~~p~el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~----~~~------~~~~~~iI~G~aI~eI~v~~~~~~   76 (86)
T 1y96_A            7 KGPLEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNF----LED------GSMSVTGIMGHAVQTVETMNEGDH   76 (86)
T ss_dssp             SCHHHHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEE----CTT------SCEEEEEECGGGEEEEEEEECCCH
T ss_pred             CCHHHHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeec----ccC------CeEEEEEEecceEEEEEEecchhH
Confidence            35779999999999999999999999999999 9999999998    122      224689999999999988777665


Q ss_pred             c
Q psy17123        100 E  100 (105)
Q Consensus       100 ~  100 (105)
                      .
T Consensus        77 ~   77 (86)
T 1y96_A           77 R   77 (86)
T ss_dssp             H
T ss_pred             H
Confidence            4

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

Probab=97.11  E-value=0.004  Score=40.29  Aligned_cols=71  Identities=13%  Similarity=0.092  Sum_probs=55.8

Q ss_pred             HhhcCCEEEEEEcCCeEEEEEEEEec-CccCeEecceEEEEecCce-----eeeeeEEeeEEEcCCcEEEEEecCCc
Q psy17123         27 SKFLDKVIRVKFAGGRECSGILKGFD-PLLNLVLDNTTEYLRVTYQ-----SVQVRSWCSIVRRQESRRNVHRRDHK   97 (105)
Q Consensus        27 ~~~i~k~V~V~LkdGr~i~G~L~~fD-~~mNlvL~da~E~~~~~~~-----~~~~~~lg~vlIRG~~I~~i~~~d~~   97 (105)
                      ..|+|++|.+..+.+..|+|+|...| +-.-|.|.|+..+-.++..     ......+..++.||+.|..+...+..
T Consensus         9 ~~yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~yIvFrgsDIKdL~V~~~~   85 (88)
T 2vxe_A            9 LPELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQIAPQSQIYDYILFRGSDIKDIRVVNNH   85 (88)
T ss_dssp             SCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCTTTCCSSCCCCCCSCEEEEEEETTTEEEEEECCCC
T ss_pred             CcccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCcCCCCCcccCCCCceeeEEEEccCCccEEEEeccC
Confidence            36899999999999999999999999 5668999998876443221     12344568899999999998876543

>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=96.88  E-value=0.0022  Score=42.04  Aligned_cols=74  Identities=11%  Similarity=0.098  Sum_probs=55.2

Q ss_pred             hhHHhhcCCEEEEEEcCCeEEEEEEEEec-CccCeEecceEEEEecCce-----eeeeeEEeeEEEcCCcEEEEEecCCc
Q psy17123         24 LDLSKFLDKVIRVKFAGGRECSGILKGFD-PLLNLVLDNTTEYLRVTYQ-----SVQVRSWCSIVRRQESRRNVHRRDHK   97 (105)
Q Consensus        24 ~~L~~~i~k~V~V~LkdGr~i~G~L~~fD-~~mNlvL~da~E~~~~~~~-----~~~~~~lg~vlIRG~~I~~i~~~d~~   97 (105)
                      ..-..|+|++|.+..+.+..|+|+|...| +-.-|.|.++..+-.++..     ......+..++.||+-|..+...+.+
T Consensus        12 ~~~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~~ipp~~~vyeyIvFrGsDIKDL~V~e~p   91 (95)
T 2fb7_A           12 SGGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCEPP   91 (95)
T ss_dssp             ----CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSSCCCSCCCCSSCEEECSTTEEEEEESCCS
T ss_pred             CccCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCCccCCCCcceeEEEEcCCCcceEEEecCC
Confidence            34468999999999999999999999999 6667889998765432211     12334567899999999999876654

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

Probab=96.80  E-value=0.0024  Score=39.86  Aligned_cols=34  Identities=12%  Similarity=0.167  Sum_probs=28.6

Q ss_pred             hhcCCEEEEEEcCCeEEEEEEEEecCccCeEecc
Q psy17123         28 KFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDN   61 (105)
Q Consensus        28 ~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~d   61 (105)
                      +--+.+|+|.|.+|-.++|.+.+||+|+=++-.+
T Consensus        22 r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   55 (71)
T 2qtx_A           22 RLNGKKVKIFLRNGEVLDAEVTGVSNYEIMVKVG   55 (71)
T ss_dssp             GGTTCEEEEEETTSCEEEEEEEEECSSEEEEEET
T ss_pred             HHcCCcEEEEEeCCeEEEEEEEEEcceEEEEEeC
Confidence            3356799999999999999999999998666443

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

Probab=96.70  E-value=0.0022  Score=40.21  Aligned_cols=54  Identities=15%  Similarity=0.209  Sum_probs=39.1

Q ss_pred             hHHhhc--CCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecC
Q psy17123         25 DLSKFL--DKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRD   95 (105)
Q Consensus        25 ~L~~~i--~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d   95 (105)
                      .|+.+.  ..+|+|.|.+|..++|.+.+||+|+=++-.+                 ...+|--..|.+|.+..
T Consensus        13 ~L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~vlL~~~-----------------~~~LIYKhAIsTI~p~~   68 (74)
T 2ylb_A           13 FLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNT-----------------VSQMVYKHAISTVVPSR   68 (74)
T ss_dssp             HHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEESS-----------------SEEEEEGGGEEEEEESS
T ss_pred             HHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEECC-----------------ceEEEEeeeEEEEeEcc
Confidence            355664  7899999999999999999999997554321                 12455666666666544

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

Probab=96.61  E-value=0.0023  Score=40.96  Aligned_cols=30  Identities=17%  Similarity=0.326  Sum_probs=26.9

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEecCccCeEe
Q psy17123         30 LDKVIRVKFAGGRECSGILKGFDPLLNLVL   59 (105)
Q Consensus        30 i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL   59 (105)
                      -..+|+|.|.||-.++|.+.+||+|+=|+-
T Consensus        18 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVlL~   47 (82)
T 1u1s_A           18 ERVPVSIYLVNGIKLQGQIESFDQFVILLK   47 (82)
T ss_dssp             TTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             cCCcEEEEEeCCcEEEEEEEEEcceEEEEe
Confidence            377999999999999999999999986654

>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=96.49  E-value=0.0058  Score=38.57  Aligned_cols=35  Identities=20%  Similarity=0.395  Sum_probs=29.5

Q ss_pred             HHhhc--CCEEEEEEcCCeEEEEEEEEecCccCeEec
Q psy17123         26 LSKFL--DKVIRVKFAGGRECSGILKGFDPLLNLVLD   60 (105)
Q Consensus        26 L~~~i--~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~   60 (105)
                      |+.+.  ..+|+|.|.+|-.++|.+.+||+|+=++-.
T Consensus        12 Ln~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~VlL~~   48 (77)
T 1kq1_A           12 LENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNS   48 (77)
T ss_dssp             HHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEEE
T ss_pred             HHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEEEE
Confidence            55554  789999999999999999999999866543

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

Probab=96.44  E-value=0.0041  Score=39.40  Aligned_cols=35  Identities=26%  Similarity=0.406  Sum_probs=29.3

Q ss_pred             HHhh--cCCEEEEEEcCCeEEEEEEEEecCccCeEec
Q psy17123         26 LSKF--LDKVIRVKFAGGRECSGILKGFDPLLNLVLD   60 (105)
Q Consensus        26 L~~~--i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~   60 (105)
                      |+.+  -..+|+|.|.||..++|.+.+||+|+=++-.
T Consensus        16 Ln~lrk~~~~Vtv~L~nG~~l~G~I~~fD~f~VlL~~   52 (78)
T 3ahu_A           16 LNQIRKENTYVTVFLLNGFQLRGQVKGFDNFTVLLES   52 (78)
T ss_dssp             HHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEES
T ss_pred             HHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEEEEE
Confidence            4444  3789999999999999999999999866643

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

Probab=96.32  E-value=0.0052  Score=39.02  Aligned_cols=33  Identities=18%  Similarity=0.369  Sum_probs=27.7

Q ss_pred             HHhhc--CCEEEEEEcCCeEEEEEEEEecCccCeE
Q psy17123         26 LSKFL--DKVIRVKFAGGRECSGILKGFDPLLNLV   58 (105)
Q Consensus        26 L~~~i--~k~V~V~LkdGr~i~G~L~~fD~~mNlv   58 (105)
                      |+.+.  ..+|+|.|.+|..++|.+.+||+|+=++
T Consensus        13 Ln~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~VlL   47 (79)
T 3sb2_A           13 LNALRKEHVPVSIYLVNGIKLQGHVESFDQYVVLL   47 (79)
T ss_dssp             HHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEE
Confidence            45553  5689999999999999999999998654

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

Probab=95.83  E-value=0.0091  Score=39.70  Aligned_cols=34  Identities=18%  Similarity=0.357  Sum_probs=28.5

Q ss_pred             HHhhc--CCEEEEEEcCCeEEEEEEEEecCccCeEe
Q psy17123         26 LSKFL--DKVIRVKFAGGRECSGILKGFDPLLNLVL   59 (105)
Q Consensus        26 L~~~i--~k~V~V~LkdGr~i~G~L~~fD~~mNlvL   59 (105)
                      |+.+.  ..+|+|.|.+|-.++|++.+||+|+=|+-
T Consensus        14 Ln~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~VlL~   49 (104)
T 2y90_A           14 LNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLK   49 (104)
T ss_dssp             HHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEE
Confidence            45554  45999999999999999999999986654

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

Probab=95.57  E-value=0.043  Score=35.22  Aligned_cols=64  Identities=8%  Similarity=0.100  Sum_probs=50.4

Q ss_pred             ccchhhHHhhcCCEEEEEEcCCeEEEEEEEEec-CccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEE
Q psy17123         20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFD-PLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVH   92 (105)
Q Consensus        20 ~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD-~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~   92 (105)
                      ++....|..+.|++|.+.|.++.++.|++.++| ...|+..++-.    .+     ...++..++|+.-|++++
T Consensus        18 eRfLr~l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~----TP-----iGv~~eAlLR~~Dii~~s   82 (85)
T 1y96_B           18 ERYLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQ----TP-----IGVQAEALLRCSDIISYT   82 (85)
T ss_dssp             HHHHHHHHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEC----CT-----TCCEEEEEEEGGGEEEEE
T ss_pred             HHHHHHHHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhcC----CC-----cccchhhhhhcCCEEEEE
Confidence            455666778889999999999999999999999 55577665521    12     345778999999999886

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

Probab=95.30  E-value=0.035  Score=35.57  Aligned_cols=62  Identities=8%  Similarity=0.085  Sum_probs=48.7

Q ss_pred             hhcCCEEEEEEcCCe-EEEEEEEEecCc-cCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123         28 KFLDKVIRVKFAGGR-ECSGILKGFDPL-LNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH   96 (105)
Q Consensus        28 ~~i~k~V~V~LkdGr-~i~G~L~~fD~~-mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~   96 (105)
                      +|+|+.|.+..+++. .|+|.|..+|+. -+|.|.+++   .++-    ......|.+|+.-|..+..++.
T Consensus         6 ~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~f---~NG~----~~~s~eVtls~~DI~~L~ii~~   69 (84)
T 2vc8_A            6 DWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPF---HNGV----KCLVPEVTFRAGDITELKILEI   69 (84)
T ss_dssp             TTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEEE---ETTE----ECSSSEEEEEGGGCSEEEEEEC
T ss_pred             cccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehhh---hCCC----CCCCcEEEEEecChhheEEEec
Confidence            799999999999999 999999999976 589999995   3442    1222458888888877766544

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

Probab=95.15  E-value=0.035  Score=34.41  Aligned_cols=57  Identities=14%  Similarity=0.151  Sum_probs=41.2

Q ss_pred             chhhHHhhc--CCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123         22 SILDLSKFL--DKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR   93 (105)
Q Consensus        22 ~~~~L~~~i--~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~   93 (105)
                      ++..|++|+  ...|.|.|.+|..++|++.-+|+|.=++..+      ++.         .++|.-..|.+|.+
T Consensus        10 svR~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~cl~L~~~------~~~---------~~LI~r~AI~~I~p   68 (70)
T 3hfo_A           10 SVRQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDGLGLVDD------SER---------STIVRLAAIAYITP   68 (70)
T ss_dssp             HHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEECT------TCC---------EEEEEGGGEEEEEE
T ss_pred             cHHHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCEEEEEcC------CCC---------eEEEEeeeeEEEee
Confidence            467788896  4799999999999999999999886443322      111         25666666777654

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

Probab=94.84  E-value=0.038  Score=37.77  Aligned_cols=39  Identities=18%  Similarity=0.404  Sum_probs=33.0

Q ss_pred             hhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEe--cceE
Q psy17123         24 LDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVL--DNTT   63 (105)
Q Consensus        24 ~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL--~da~   63 (105)
                      +...+|+|..|.|+|+||..++|++..+| --+|+|  .+|.
T Consensus         5 ~~~sqFlGy~V~v~LkDgs~~qG~I~~vd-~k~LtL~~~~a~   45 (125)
T 4a53_A            5 MSVADFYGSNVEVLLNNDSKARGVITNFD-SSNSILQLRLAN   45 (125)
T ss_dssp             CCHHHHTTCEEEEEETTSCEEEEEEEEEE-TTTTEEEEEETT
T ss_pred             ccHHHhcCceEEEEECCCCEeeEEEEeec-CCeeEEeccccc
Confidence            35678999999999999999999999998 345666  8774

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

Probab=94.81  E-value=0.17  Score=30.95  Aligned_cols=60  Identities=15%  Similarity=0.236  Sum_probs=41.5

Q ss_pred             hHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123         25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR   93 (105)
Q Consensus        25 ~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~   93 (105)
                      .|++|.|++|-|.......|+|+|.-||.-. |.|.|+..+.-+.        -..++++=+-|-.|..
T Consensus        10 tL~~WKg~rvAv~vg~ehSFtGiledFDeEv-iLL~dV~D~~GNk--------~k~liv~idDinWimL   69 (71)
T 1ycy_A           10 VLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIGNR--------GKQMLIGLEDINWIML   69 (71)
T ss_dssp             HHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTEEE--------EEEEEEEGGGEEEEEE
T ss_pred             HHHHhCCcEEEEEecCcceeeeehhhcCcce-eehhhHHHHhccc--------cceeEEEeccceEEEe
Confidence            4899999999999999999999999999865 6788888764321        1245666666665544

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

Probab=94.65  E-value=0.057  Score=33.61  Aligned_cols=58  Identities=16%  Similarity=0.201  Sum_probs=41.7

Q ss_pred             cchhhHHhhcC--CEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123         21 ESILDLSKFLD--KVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR   93 (105)
Q Consensus        21 ~~~~~L~~~i~--k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~   93 (105)
                      .++..|++|+-  +.|.|+|.+|..++|++.-+|++.=++..+       ..        ..++|....|.+|.+
T Consensus        11 PsvR~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~cl~L~~~-------~~--------~~~LI~R~AI~~Ikp   70 (72)
T 3hfn_A           11 PSIRQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTCVCIADE-------NS--------RQTTIWKQAIAYLQP   70 (72)
T ss_dssp             HHHHHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSEEEEEC------------------CEEEEEGGGEEEEEE
T ss_pred             CcHHHHHHHHhhCceEEEEecCCCEEEEEEEEECCCEEEEEcC-------CC--------CeEEEEeeeeEEEEe
Confidence            35778899974  589999999999999999999875333322       11        136677777777764

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

Probab=91.51  E-value=0.22  Score=34.93  Aligned_cols=42  Identities=21%  Similarity=0.247  Sum_probs=31.2

Q ss_pred             ccccccchhhHHhhcCCEEEEEEc----CCeEEEEEEEEecCccCeEe
Q psy17123         16 DRKRKESILDLSKFLDKVIRVKFA----GGRECSGILKGFDPLLNLVL   59 (105)
Q Consensus        16 ~~~~~~~~~~L~~~i~k~V~V~Lk----dGr~i~G~L~~fD~~mNlvL   59 (105)
                      |.|-+. ..+..+++|+.|.|++.    +.+.|+|+|.++|.- .++|
T Consensus        90 dRpL~~-~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~-~v~l  135 (164)
T 1ib8_A           90 ERPLKT-KDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED-ELTM  135 (164)
T ss_dssp             SSCCSS-HHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT-EEEE
T ss_pred             CCCCCC-HHHHHHhCCcEEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence            444433 55678899999999993    458999999999964 3444

>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=91.06  E-value=0.3  Score=36.46  Aligned_cols=32  Identities=31%  Similarity=0.564  Sum_probs=29.6

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEecCccCeEecc
Q psy17123         30 LDKVIRVKFAGGRECSGILKGFDPLLNLVLDN   61 (105)
Q Consensus        30 i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~d   61 (105)
                      +|++|+|.+.+|+.++|+..|.|+...|+|..
T Consensus       223 ~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~  254 (270)
T 3rux_A          223 IGSRVRVELPGGQDVVGIARDIDDQGRLCLDV  254 (270)
T ss_dssp             TTSEEEEECTTSCEEEEEEEEECTTSCEEEEE
T ss_pred             cCCEEEEEECCCeEEEEEEEEECCCCeEEEEE
Confidence            68999999888999999999999999999964

>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=82.60  E-value=0.83  Score=33.18  Aligned_cols=30  Identities=17%  Similarity=0.211  Sum_probs=26.1

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEecCccCeEecc
Q psy17123         30 LDKVIRVKFAGGRECSGILKGFDPLLNLVLDN   61 (105)
Q Consensus        30 i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~d   61 (105)
                      +|++|+|...++  +.|+..|.|+...|+|..
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            799999976554  999999999999999964

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

Probab=81.18  E-value=9.1  Score=24.97  Aligned_cols=64  Identities=6%  Similarity=0.086  Sum_probs=47.6

Q ss_pred             HhhcCCEEEEEEcCCe-EEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123         27 SKFLDKVIRVKFAGGR-ECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH   96 (105)
Q Consensus        27 ~~~i~k~V~V~LkdGr-~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~   96 (105)
                      .+|+|+-|.|...+-- .|+|.+...|+ -+|.|.+++..   +-  .-......|.+|..-|..+..++.
T Consensus         8 edwiG~~VSI~C~d~LGVyQG~I~~V~~-~~ItL~kaFrN---Gi--plk~~~~EVtLsa~DI~~L~IIe~   72 (103)
T 2rm4_A            8 QDWIGCAVSIACDEVLGVFQGLIKQISA-EEITIVRAFRN---GV--PLRKQNAEVVLKCTDIRSIDLIEP   72 (103)
T ss_dssp             GGGTTCEEEEEECTTTCEEEEEEEEEET-TEEEEEEEEET---TE--ECSCSSSCEEEETTTEEEEEEEEC
T ss_pred             cceeceEEEEeeCCcceEeeEEEEEccc-ceeEEhhhhhc---Cc--CcCCCCceEEEEecchhheeeecc
Confidence            3899999999999987 99999999996 44999988852   21  001234567788887877766543

---

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	105
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	7e-12
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	2e-11
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	1e-10
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	1e-10
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	2e-10
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	8e-10
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	1e-09
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	1e-09
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	1e-09
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	5e-09
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	2e-08
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	1e-06
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	3e-06

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

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

 Score = 54.4 bits (131), Expect = 7e-12
 Identities = 12/43 (27%), Positives = 22/43 (51%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRV 68
          + + +D  +R     GR   G  K FD  +NL+L +  E+ ++
Sbjct: 3  MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKI 45

>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 = 53.3 bits (128), Expect = 2e-11
 Identities = 17/43 (39%), Positives = 25/43 (58%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRV 68
          + K +   I V   G +E SG+L+GFD  +N+VLD+  EY   
Sbjct: 10 IDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFK 52

>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 = 50.9 bits (122), Expect = 1e-10
 Identities = 14/42 (33%), Positives = 26/42 (61%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          L++ L+ ++ VK  G +E  G+L+ +D  +NLVL ++ E   
Sbjct: 12 LAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQS 53

>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 = 50.9 bits (122), Expect = 1e-10
 Identities = 16/42 (38%), Positives = 23/42 (54%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          L++ L   + V+  GGRE  G L G+D  +NLVL +  E   
Sbjct: 8  LNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQN 49

>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 = 50.1 bits (120), Expect = 2e-10
 Identities = 16/42 (38%), Positives = 23/42 (54%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          L   L+  + +K  G RE  G+LK FD  +NLVL++  E   
Sbjct: 11 LGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELED 52

>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 = 48.6 bits (116), Expect = 8e-10
 Identities = 14/40 (35%), Positives = 21/40 (52%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          L   + K + VK     E  GIL+ FD  +NL+L++  E 
Sbjct: 7  LQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI 46

>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 = 48.5 bits (116), Expect = 1e-09
 Identities = 14/42 (33%), Positives = 20/42 (47%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          + + LDK + V    G E  G L G+D  LN+VL +      
Sbjct: 7  IHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQD 48

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

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

 Score = 49.7 bits (119), Expect = 1e-09
 Identities = 13/52 (25%), Positives = 24/52 (46%)

Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVR 76
          +L+  L + ++V  + G    G+L   D  LN+VL N +      +  V + 
Sbjct: 4  ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRVFIM 55

>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 = 48.2 bits (115), Expect = 1e-09
 Identities = 11/43 (25%), Positives = 17/43 (39%), Gaps = 1/43 (2%)

Query: 26 LSKFLDKVIRVKF-AGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          L   ++  + VK      E  G L   D   NL L+   E++ 
Sbjct: 1  LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVA 43

>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 = 46.7 bits (111), Expect = 5e-09
 Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 26 LSKFLDKVIRVKFA-GGRECSGILKGFDPLLNLVLDNTTEYLR 67
          +   + K+IRV+      +  G L+G D  +NL L N  E   
Sbjct: 10 VKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKG 52

>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 = 45.6 bits (108), Expect = 2e-08
 Identities = 12/48 (25%), Positives = 21/48 (43%)

Query: 22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVT 69
          S+L  S   +  + +     ++  G +K FD   N+VL+N  E     
Sbjct: 5  SVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEV 52

>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 = 40.5 bits (95), Expect = 1e-06
 Identities = 8/42 (19%), Positives = 15/42 (35%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          L +    ++  +   G    G L   +  +N  + N T   R
Sbjct: 7  LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYR 48

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

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

 Score = 39.7 bits (93), Expect = 3e-06
 Identities = 11/55 (20%), Positives = 23/55 (41%), Gaps = 4/55 (7%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR----VTYQSVQVR 76
          L K   + + ++   G +  G + G D  +N  L      L+    V  +++ +R
Sbjct: 6  LMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIR 60

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	105
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.9
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.9
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.9
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.9
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.89
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.89
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.89
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.87
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.87
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.86
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.84
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.81
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.73
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	97.3
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	96.81
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	96.02
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	95.81
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	93.64
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	93.6

>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=99.90  E-value=5.7e-24  Score=132.17  Aligned_cols=69  Identities=26%  Similarity=0.304  Sum_probs=62.9

Q ss_pred             cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123         21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR   93 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~   93 (105)
                      .|...|++++|++|+|+|+||+.|+|+|.+||+||||+|++|.|+..+.    +.+.+|.++|||++|++|+|
T Consensus         2 ~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~----~~~~l~~~~IRG~~I~~Isp   70 (71)
T d1h641_           2 RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGE----VVKRYGKIVIRGDNVLAISP   70 (71)
T ss_dssp             CHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTE----EEEEEEEEEECGGGEEEEEE
T ss_pred             CchHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecCC----cEeEcCcEEEECCeEEEEeC
Confidence            4677899999999999999999999999999999999999999986433    36889999999999999986

>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=99.90  E-value=4.6e-24  Score=133.12  Aligned_cols=69  Identities=32%  Similarity=0.397  Sum_probs=62.9

Q ss_pred             cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123         21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR   93 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~   93 (105)
                      .|...|+++++++|+|+|+||+.|+|+|.+||+||||+|+||.|+..++    ..+.+|.++|||++|.+|++
T Consensus         3 ~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~----~~~~~g~~~IRG~~I~~Isp   71 (72)
T d1i4k1_           3 RPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGE----VVRKVGSVVIRGDTVVFVSP   71 (72)
T ss_dssp             CHHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSSS----EEEEEEEEEECGGGEEEEEC
T ss_pred             ChHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecCC----eEeEcceEEEeCCeEEEEEc
Confidence            4577899999999999999999999999999999999999999986543    36889999999999999975

>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=99.90  E-value=6.6e-24  Score=135.16  Aligned_cols=71  Identities=21%  Similarity=0.336  Sum_probs=61.8

Q ss_pred             hHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCc------eeeeeeEEeeEEEcCCcEEEEEecC
Q psy17123         25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTY------QSVQVRSWCSIVRRQESRRNVHRRD   95 (105)
Q Consensus        25 ~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~------~~~~~~~lg~vlIRG~~I~~i~~~d   95 (105)
                      .|.+|+|++|+|.|+|||.|.|+|.|||+||||+|++|.|++....      +....|.+|+++|||++|++|+..+
T Consensus         2 ~L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~~~   78 (81)
T d1d3bb_           2 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEG   78 (81)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEEE
T ss_pred             hhHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEccC
Confidence            5789999999999999999999999999999999999999874211      2345789999999999999998543

>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=99.90  E-value=1.2e-23  Score=131.89  Aligned_cols=70  Identities=26%  Similarity=0.396  Sum_probs=64.0

Q ss_pred             ccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123         20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR   93 (105)
Q Consensus        20 ~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~   93 (105)
                      ..|+..|+++++++|+|+|+||+.|.|+|.|||+||||+|+||.|+..++    ..+.+|.++|||++|.+|+|
T Consensus         5 ~~Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~~----~~~~~~~~~IRG~~I~~I~p   74 (74)
T d1mgqa_           5 QRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGE----VTRRLGTVLIRGDNIVYISP   74 (74)
T ss_dssp             TCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTE----EEEEEEEEEECGGGEEEEEC
T ss_pred             cCcHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCCC----eEeEcceEEEeCCEEEEEeC
Confidence            56788999999999999999999999999999999999999999986543    36889999999999999975

>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=99.89  E-value=1.4e-23  Score=130.98  Aligned_cols=67  Identities=27%  Similarity=0.342  Sum_probs=61.0

Q ss_pred             hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEec
Q psy17123         23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRR   94 (105)
Q Consensus        23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~   94 (105)
                      ...|++++||+|+|+|+||+.|+|+|.+||+||||+|++|.|+..+     +.+.+|.++|||++|++|+++
T Consensus         4 ~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~~-----~~~~~g~v~iRG~~I~~I~~~   70 (71)
T d1i8fa_           4 GATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDG-----NVYKRGTMVVRGENVLFISPV   70 (71)
T ss_dssp             HHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEETT-----EEEEEEEEEECGGGEEEEEEC
T ss_pred             hHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEECC-----CEEEcceEEEeCCeEEEEeCC
Confidence            4679999999999999999999999999999999999999998543     257899999999999999864

>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=99.89  E-value=2.5e-23  Score=131.01  Aligned_cols=70  Identities=24%  Similarity=0.347  Sum_probs=63.7

Q ss_pred             cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEec
Q psy17123         21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRR   94 (105)
Q Consensus        21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~   94 (105)
                      .+...|.+++|++|+|+|+||+.|+|+|.|||+||||+|++|.|+..+++    .+.+|.++|||++|++|+++
T Consensus         7 ~~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~----~~~~~~v~iRG~~I~~I~~~   76 (76)
T d1th7a1           7 TAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGS----GKKLGTIVIRGDNVILISPL   76 (76)
T ss_dssp             HHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSC----EEEEEEEEECGGGEEEEEEC
T ss_pred             cHHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecCCc----ccCcceEEEECCEEEEEEeC
Confidence            35678999999999999999999999999999999999999999876554    67899999999999999874

>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=99.89  E-value=3.4e-23  Score=130.41  Aligned_cols=72  Identities=28%  Similarity=0.335  Sum_probs=64.1

Q ss_pred             cccchhhHHhhcCCEEEEEEcCC-eEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEec
Q psy17123         19 RKESILDLSKFLDKVIRVKFAGG-RECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRR   94 (105)
Q Consensus        19 ~~~~~~~L~~~i~k~V~V~LkdG-r~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~   94 (105)
                      ...|...|+++++++|+|+|++| |.|.|+|.|||+||||+|+||.|+..++    +.+.+|.++|||++|.+|.|.
T Consensus         3 ~~~P~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~----~~~~~g~~~IRG~~I~~I~p~   75 (75)
T d1ljoa_           3 MVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEE----KVRSLGEIVLRGNNVVLIQPQ   75 (75)
T ss_dssp             CCCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTE----EEEEEEEEEECGGGEEEEEEC
T ss_pred             ccccHHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCCC----cEeEcceEEEeCCEEEEEECC
Confidence            45578889999999999999965 8999999999999999999999986544    378999999999999999863

>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=125.76  Aligned_cols=65  Identities=20%  Similarity=0.271  Sum_probs=58.0

Q ss_pred             HHhhcCCEEEEEEc-CCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEec
Q psy17123         26 LSKFLDKVIRVKFA-GGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRR   94 (105)
Q Consensus        26 L~~~i~k~V~V~Lk-dGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~   94 (105)
                      |+++++++|.|+|+ +|+.|+|+|.+||+||||+|++|.|...++    ..+.+|.++|||++|.+|+.+
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~----~~~~lg~~~IRG~nI~~I~~~   66 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGV----SHGTLGEIFIRCNNVLYIREL   66 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTE----EEEECCSEEECGGGEEEEEEC
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEecCC----cccCcCeEEEECCEEEEEEeC
Confidence            57899999999999 668999999999999999999999986543    367899999999999999854

>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=99.87  E-value=6.4e-23  Score=133.07  Aligned_cols=75  Identities=27%  Similarity=0.353  Sum_probs=63.9

Q ss_pred             ccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCc-----------eeeeeeEEeeEEEcCCcE
Q psy17123         20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTY-----------QSVQVRSWCSIVRRQESR   88 (105)
Q Consensus        20 ~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~-----------~~~~~~~lg~vlIRG~~I   88 (105)
                      -.|...|+++++|+|+|.|+|||.|.|+|.|||+||||+|+||.|++....           .....|.+|++||||++|
T Consensus         4 ~~Pl~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~~V   83 (92)
T d2fwka1           4 ILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNV   83 (92)
T ss_dssp             CCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGE
T ss_pred             cChHHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCCEE
Confidence            356778999999999999999999999999999999999999999875321           123467899999999999


Q ss_pred             EEEEec
Q psy17123         89 RNVHRR   94 (105)
Q Consensus        89 ~~i~~~   94 (105)
                      ++|+|.
T Consensus        84 v~I~p~   89 (92)
T d2fwka1          84 AMLVPG   89 (92)
T ss_dssp             EEEESS
T ss_pred             EEEEeC
Confidence            999973

>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=99.86  E-value=7.6e-22  Score=123.08  Aligned_cols=70  Identities=19%  Similarity=0.089  Sum_probs=63.4

Q ss_pred             chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecC
Q psy17123         22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRD   95 (105)
Q Consensus        22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d   95 (105)
                      |...|+++.|++|+|+|+||++|+|+|.+||.|||++|+||.++..++.    .+.+|.++|||++|.+|+..|
T Consensus         3 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~----~~~~~~v~IRG~~I~~i~lpd   72 (72)
T d1d3ba_           3 PIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGR----VAQLEQVYIRGCKIRFLILPD   72 (72)
T ss_dssp             HHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSC----EEEEEEEEECGGGEEEEEECC
T ss_pred             chHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCCCc----EeEcCeEEEECCEEEEEEcCC
Confidence            4567899999999999999999999999999999999999999865543    577999999999999999876

>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=99.84  E-value=3.1e-21  Score=125.78  Aligned_cols=74  Identities=20%  Similarity=0.231  Sum_probs=59.3

Q ss_pred             cchhhHHhhc--CCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCce----------eeeeeEEeeEEEcCCcE
Q psy17123         21 ESILDLSKFL--DKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQ----------SVQVRSWCSIVRRQESR   88 (105)
Q Consensus        21 ~~~~~L~~~i--~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~----------~~~~~~lg~vlIRG~~I   88 (105)
                      .|+..|.+++  +++|+|.|++||.|.|+|.|||+||||+|+||.|++.....          ....|.+|.++|||++|
T Consensus         2 GPl~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdnV   81 (93)
T d1b34b_           2 GPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSV   81 (93)
T ss_dssp             CHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGE
T ss_pred             CcHHHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCEE
Confidence            3566788887  89999999999999999999999999999999998753211          12457899999999999


Q ss_pred             EEEEec
Q psy17123         89 RNVHRR   94 (105)
Q Consensus        89 ~~i~~~   94 (105)
                      ++|...
T Consensus        82 v~I~~~   87 (93)
T d1b34b_          82 IVVLRN   87 (93)
T ss_dssp             EEEEEC
T ss_pred             EEEEcC
Confidence            999754

>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=5.2e-20  Score=116.89  Aligned_cols=74  Identities=16%  Similarity=0.191  Sum_probs=66.0

Q ss_pred             hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCCcccc
Q psy17123         23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHKEYE  100 (105)
Q Consensus        23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~~~~~  100 (105)
                      +..|+++.|++|+|+|++|..|+|+|.++|.|||++|+||.+...+++    ...++.++|||++|.+|+..|.-..+
T Consensus         3 v~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~----~~~~~~v~IRG~~Ir~i~lPd~l~~~   76 (80)
T d1b34a_           3 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNRE----PVQLETLSIRGNNIRYFILPDSLPLD   76 (80)
T ss_dssp             HHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSC----CEEEEEEEECGGGEEEEECCTTCCHH
T ss_pred             HHHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCC----EEEcccEEEcCCEEEEEECCCCcccc
Confidence            567899999999999999999999999999999999999999765543    57899999999999999998876543

>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=99.73  E-value=5.1e-18  Score=116.10  Aligned_cols=66  Identities=18%  Similarity=0.362  Sum_probs=58.8

Q ss_pred             hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123         23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH   96 (105)
Q Consensus        23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~   96 (105)
                      ...|++++|++|.|.|+||+.|.|+|.+||+||||+|+||.+.  ++      ..++.++|||++|.+|+..+.
T Consensus         2 ~~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~--~~------~k~~~v~IRG~~I~~I~~~e~   67 (127)
T d1m5q1_           2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNK--AG------EKFNRVFIMYRYIVHIDSTER   67 (127)
T ss_dssp             HHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEET--TC------CEEEEEEECGGGEEEEEECSC
T ss_pred             hhHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEEC--CC------CcccEEEEeCCeEEEEEcchh
Confidence            5689999999999999999999999999999999999999874  22      246789999999999998765

>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=97.30  E-value=0.00093  Score=41.07  Aligned_cols=69  Identities=12%  Similarity=0.134  Sum_probs=54.5

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEecC-ccCeEecceEEEEecCce-----eeeeeEEeeEEEcCCcEEEEEecCCc
Q psy17123         29 FLDKVIRVKFAGGRECSGILKGFDP-LLNLVLDNTTEYLRVTYQ-----SVQVRSWCSIVRRQESRRNVHRRDHK   97 (105)
Q Consensus        29 ~i~k~V~V~LkdGr~i~G~L~~fD~-~mNlvL~da~E~~~~~~~-----~~~~~~lg~vlIRG~~I~~i~~~d~~   97 (105)
                      |+|++|.+..+.+-.|+|+|...|. -.-|.|.|+..+-.++-.     ......++.++.||+.|..+...+.+
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~~IvFrgsDIKdL~v~e~p   76 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCEPP   76 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSSCCCCCCCCEEEEEEETTTEEEEEESSCC
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCCccCCCCcceeEEEEcCcCcceEEeccCC
Confidence            7899999999999999999999994 456889998876433211     12345678899999999999876643

>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=96.81  E-value=0.002  Score=35.41  Aligned_cols=32  Identities=28%  Similarity=0.608  Sum_probs=28.3

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEecCccCeEecc
Q psy17123         29 FLDKVIRVKFAGGRECSGILKGFDPLLNLVLDN   61 (105)
Q Consensus        29 ~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~d   61 (105)
                      |++|+|+|.. +++++.|+..++|....|+|..
T Consensus         1 f~gk~V~v~~-g~~~i~G~a~gId~~G~Lll~t   32 (47)
T d1biaa2           1 FINRPVKLII-GDKEIFGISRGIDKQGALLLEQ   32 (47)
T ss_dssp             TTTSEEEEEE-TTEEEEEEEEEECTTSCEEEEE
T ss_pred             CCCCEEEEEE-CCeEEEEEEeeECCCCcEEEEE
Confidence            6899999975 5578999999999999999964

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

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

Probab=96.02  E-value=0.0064  Score=35.30  Aligned_cols=34  Identities=15%  Similarity=0.278  Sum_probs=28.9

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEecCccCeEecceE
Q psy17123         30 LDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTT   63 (105)
Q Consensus        30 i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~   63 (105)
                      -..+|+|.|.+|-.++|.+.+||+|.=+.-.+..
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            3679999999999999999999999877655433

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

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

Probab=95.81  E-value=0.0058  Score=36.12  Aligned_cols=29  Identities=17%  Similarity=0.361  Sum_probs=25.5

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEecCccCeE
Q psy17123         30 LDKVIRVKFAGGRECSGILKGFDPLLNLV   58 (105)
Q Consensus        30 i~k~V~V~LkdGr~i~G~L~~fD~~mNlv   58 (105)
                      -...|+|.|.+|-.++|.+.+||+|.=|.
T Consensus        13 ~~~~VtifL~nGvkl~G~I~~fD~ftvLL   41 (66)
T d1u1sa1          13 ERVPVSIYLVNGIKLQGQIESFDQFVILL   41 (66)
T ss_dssp             TTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             cCCcEEEEEEcCcEEEEEEEEEcceEEEE
Confidence            35799999999999999999999996543

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

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

Probab=93.64  E-value=0.21  Score=28.73  Aligned_cols=58  Identities=16%  Similarity=0.264  Sum_probs=39.6

Q ss_pred             hHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEE
Q psy17123         25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNV   91 (105)
Q Consensus        25 ~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i   91 (105)
                      .|++|.+++|-|.......|.|+|.-||.-. |.|.|++.+.-+.        -..++++=+-|-.|
T Consensus         6 tL~~WKg~kvAv~vgsehSFtGiledFDeEv-iLL~dV~D~~GNk--------~k~llv~idD~nWi   63 (66)
T d1ycya1           6 VLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIGNR--------GKQMLIGLEDINWI   63 (66)
T ss_dssp             HHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTEEE--------EEEEEEEGGGEEEE
T ss_pred             HHHHhCCcEEEEEecCcceeEEEhhhcCcce-EeehhhHHHhccc--------cceeEEEeccceeE
Confidence            5889999999999999999999999999865 6778888763221        12355555555544

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

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

Probab=93.60  E-value=0.04  Score=32.19  Aligned_cols=33  Identities=18%  Similarity=0.141  Sum_probs=27.8

Q ss_pred             hhhHHhhcCCEEEEEEc---CC-eEEEEEEEEecCcc
Q psy17123         23 ILDLSKFLDKVIRVKFA---GG-RECSGILKGFDPLL   55 (105)
Q Consensus        23 ~~~L~~~i~k~V~V~Lk---dG-r~i~G~L~~fD~~m   55 (105)
                      ..++.+++|+.|.|+|+   +| +.|+|.|.++|.-.
T Consensus         6 ~~~f~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~~   42 (74)
T d1ib8a1           6 KDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEEDE   42 (74)
T ss_dssp             HHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETTE
T ss_pred             HHHHHHhCCCEEEEEEecccCCceEEEEEEEeecCCe
Confidence            45688999999999985   45 69999999999753