Citrus Sinensis ID: 034895

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80
Protein Sequence
MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALEPVSKSQ
Secondary Structure (PSIPRED)
cccccccccHHHHcccEEEEEEcccEEEEEEEEEEcccccEEEccEEEEEccEEEEEEEEEEEcccEEEEEEcccccccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHHccEEEEEEccccEEEEEEccccHHHHHHHHHHEEEcccccccEEEEEEEccEEEEEEccccccccc
Coil and Loop (DISEMBL)
msrsgqppdlkkYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTvevngnekndiGMVVIRGNSVVTVEALEPVSKSQ
Flexible Loop (DISEMBL)
msrsgqppdlkkYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVngnekndigmvVIRGNSVVTvealepvsksq
Low Complexity Region (SEG)
MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALEPVSKSQ
Disordered region (IsUnstruct)
****************KLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEA********
Disordered Region (DISOPRED)
***********KYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVE**EP*****
Disordered Region (DISEMBL)
**********KKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEA********
Disordered Region (DISPRO)
*****QPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALEPV****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALEPVSKSQ
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	80	2.2.26 [Sep-21-2011]
O82221	80	Probable small nuclear ri	yes	no	0.987	0.987	0.898	3e-36
P24715	81	Probable small nuclear ri	N/A	no	0.95	0.938	0.921	5e-34
P62309	76	Small nuclear ribonucleop	yes	no	0.937	0.986	0.610	2e-19
P62308	76	Small nuclear ribonucleop	yes	no	0.937	0.986	0.610	2e-19
Q3ZBL0	76	Small nuclear ribonucleop	yes	no	0.937	0.986	0.610	2e-19
Q9VXE0	76	Probable small nuclear ri	yes	no	0.937	0.986	0.610	2e-19
A8MWD9	76	Small nuclear ribonucleop	no	no	0.925	0.973	0.589	3e-17
Q54RX0	85	Probable small nuclear ri	yes	no	0.875	0.823	0.577	2e-16
Q9N4G9	77	Probable small nuclear ri	yes	no	0.95	0.987	0.551	4e-16
O74966	77	Small nuclear ribonucleop	yes	no	0.937	0.974	0.468	9e-14

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

 Score =  150 bits (378), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 71/79 (89%), Positives = 76/79 (96%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMV 60
          MSRSGQPPDLKKYMDKKLQIKLNANRM+ GTLRGFDQFMNLV+DNTVEVNGN+K DIGMV
Sbjct: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMVTGTLRGFDQFMNLVVDNTVEVNGNDKTDIGMV 60

Query: 61 VIRGNSVVTVEALEPVSKS 79
          VIRGNS+VTVEALEPV +S
Sbjct: 61 VIRGNSIVTVEALEPVGRS 79

Probable common Sm protein, is found in U1 and U2 snRNPs.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  142 bits (358), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 70/76 (92%), Positives = 72/76 (94%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMV 60
          MS SGQPP LKKYMDK+LQI L ANRMIVGTLRGFDQFMNLV+DNTVEVNGNEKNDIGMV
Sbjct: 1  MSTSGQPPALKKYMDKQLQINLKANRMIVGTLRGFDQFMNLVVDNTVEVNGNEKNDIGMV 60

Query: 61 VIRGNSVVTVEALEPV 76
          VIRGNSVVTVEALEPV
Sbjct: 61 VIRGNSVVTVEALEPV 76

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

Medicago sativa (taxid: 3879)

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

 Score = 94.4 bits (233), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/77 (61%), Positives = 60/77 (77%), Gaps = 2/77 (2%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV-NGNEKNDIGM 59
          MS++  PP+LKK+MDKKL +KLN  R + G LRGFD FMNLVID  VE+    ++N+IGM
Sbjct: 1  MSKA-HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGM 59

Query: 60 VVIRGNSVVTVEALEPV 76
          VVIRGNS++ +EALE V
Sbjct: 60 VVIRGNSIIMLEALERV 76

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 = 94.4 bits (233), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/77 (61%), Positives = 60/77 (77%), Gaps = 2/77 (2%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV-NGNEKNDIGM 59
          MS++  PP+LKK+MDKKL +KLN  R + G LRGFD FMNLVID  VE+    ++N+IGM
Sbjct: 1  MSKA-HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGM 59

Query: 60 VVIRGNSVVTVEALEPV 76
          VVIRGNS++ +EALE V
Sbjct: 60 VVIRGNSIIMLEALERV 76

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 = 94.4 bits (233), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/77 (61%), Positives = 60/77 (77%), Gaps = 2/77 (2%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV-NGNEKNDIGM 59
          MS++  PP+LKK+MDKKL +KLN  R + G LRGFD FMNLVID  VE+    ++N+IGM
Sbjct: 1  MSKA-HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGM 59

Query: 60 VVIRGNSVVTVEALEPV 76
          VVIRGNS++ +EALE V
Sbjct: 60 VVIRGNSIIMLEALERV 76

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 = 94.0 bits (232), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/77 (61%), Positives = 61/77 (79%), Gaps = 2/77 (2%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTV-EVNGNEKNDIGM 59
          MS++  PP++KKYMDK++ +KLN  R + G LRGFD FMN+V+D+TV E   N KN+IGM
Sbjct: 1  MSKA-HPPEVKKYMDKRMMLKLNGGRAVTGILRGFDPFMNVVLDDTVEECKDNTKNNIGM 59

Query: 60 VVIRGNSVVTVEALEPV 76
          VVIRGNS+V VEAL+ V
Sbjct: 60 VVIRGNSIVMVEALDRV 76

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

Drosophila melanogaster (taxid: 7227)

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

 Score = 87.0 bits (214), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 46/78 (58%), Positives = 58/78 (74%), Gaps = 4/78 (5%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV--NGNEKNDIG 58
          MS++  PP+LKK+ DKK  +KLN  R + G LRGFD FMNLVID  VE+  +G +KN IG
Sbjct: 1  MSKA-HPPELKKFTDKKFSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQKN-IG 58

Query: 59 MVVIRGNSVVTVEALEPV 76
          MV IRGNS++ +EALE V
Sbjct: 59 MVEIRGNSIIMLEALERV 76

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

Homo sapiens (taxid: 9606)

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

 Score = 84.3 bits (207), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/71 (57%), Positives = 54/71 (76%), Gaps = 1/71 (1%)

Query: 8  PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIGMVVIRGNS 66
          PDL K +DKKL IKLN NR + G LRGFD FMN+ + +TVE V+  EK +IGMV+IRGNS
Sbjct: 9  PDLTKLLDKKLAIKLNGNRTVHGILRGFDTFMNIALKDTVEVVSPTEKYEIGMVIIRGNS 68

Query: 67 VVTVEALEPVS 77
          ++ +E LE ++
Sbjct: 69 ILLMEPLESMA 79

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

Dictyostelium discoideum (taxid: 44689)

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

 Score = 83.2 bits (204), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 43/78 (55%), Positives = 57/78 (73%), Gaps = 2/78 (2%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKN-DIGM 59
          MS++  PP+LKKYMDK++ +KLN NR + G LRGFD FMN+VID  VE   +  + ++GM
Sbjct: 1  MSKT-HPPELKKYMDKEMDLKLNGNRRVSGILRGFDPFMNMVIDEAVEYQKDGGSVNLGM 59

Query: 60 VVIRGNSVVTVEALEPVS 77
           VIRGNSVV +E  E +S
Sbjct: 60 TVIRGNSVVIMEPKERIS 77

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

Caenorhabditis elegans (taxid: 6239)

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

 Score = 75.5 bits (184), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 37/79 (46%), Positives = 61/79 (77%), Gaps = 4/79 (5%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE--VNGNEKNDIG 58
          MS++G  PDLKKY+D+++ ++LN +R + G LRG+D F+N+V+++++E  V+G EK  IG
Sbjct: 1  MSKAG-APDLKKYLDRQVFVQLNGSRKVYGVLRGYDIFLNIVLEDSIEEKVDG-EKVKIG 58

Query: 59 MVVIRGNSVVTVEALEPVS 77
           V IRGNSV+ +E L+ ++
Sbjct: 59 SVAIRGNSVIMIETLDKMT 77

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

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

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	80
282848218	80	putative small nuclear ribonucleoprotein	1.0	1.0	0.937	2e-36
225440849	80	PREDICTED: probable small nuclear ribonu	1.0	1.0	0.937	4e-36
357511115	80	hypothetical protein MTR_7g104930 [Medic	0.987	0.987	0.949	5e-36
356505386	79	PREDICTED: probable small nuclear ribonu	0.987	1.0	0.936	6e-36
242050850	80	hypothetical protein SORBIDRAFT_02g03900	1.0	1.0	0.912	9e-36
224088536	80	predicted protein [Populus trichocarpa]	1.0	1.0	0.912	1e-35
356538387	79	PREDICTED: probable small nuclear ribonu	0.987	1.0	0.936	2e-35
224138462	80	predicted protein [Populus trichocarpa]	1.0	1.0	0.9	2e-35
118483312	80	unknown [Populus trichocarpa]	1.0	1.0	0.9	3e-35
388492630	80	unknown [Lotus japonicus]	0.987	0.987	0.911	3e-35

>gi|282848218|gb|ADB02890.1| putative small nuclear ribonucleoprotein polypeptide G/SNRNP-G [Jatropha curcas]

 Score =  155 bits (393), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 75/80 (93%), Positives = 80/80 (100%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMV 60
          MSRSGQPPDLKKYMDKKLQIKLNANRM+VGTLRGFDQFMNLV+DNTVEVNG+EKNDIGMV
Sbjct: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEVNGDEKNDIGMV 60

Query: 61 VIRGNSVVTVEALEPVSKSQ 80
          VIRGNSVVTVEALEPV+K+Q
Sbjct: 61 VIRGNSVVTVEALEPVNKTQ 80

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225440849|ref|XP_002282193.1| PREDICTED: probable small nuclear ribonucleoprotein G [Vitis vinifera] gi|297740131|emb|CBI30313.3| unnamed protein product [Vitis vinifera]

 Score =  155 bits (391), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 75/80 (93%), Positives = 78/80 (97%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMV 60
          MSRSGQPPDLKKYMDKKLQIKLNANRM+VGTLRGFDQFMNLV+DNTVEVNGNEK DIGMV
Sbjct: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEVNGNEKTDIGMV 60

Query: 61 VIRGNSVVTVEALEPVSKSQ 80
          VIRGNSVVTVEALEPVS+ Q
Sbjct: 61 VIRGNSVVTVEALEPVSRMQ 80

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357511115|ref|XP_003625846.1| hypothetical protein MTR_7g104930 [Medicago truncatula] gi|87240819|gb|ABD32677.1| Like-Sm ribonucleoprotein-related, core [Medicago truncatula] gi|355500861|gb|AES82064.1| hypothetical protein MTR_7g104930 [Medicago truncatula]

 Score =  154 bits (390), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 75/79 (94%), Positives = 79/79 (100%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMV 60
          MSRSGQPPDLKKYMDK+LQIKLNANRMIVGTLRGFDQFMNLV+DNTVEVNGNEKNDIGMV
Sbjct: 1  MSRSGQPPDLKKYMDKQLQIKLNANRMIVGTLRGFDQFMNLVVDNTVEVNGNEKNDIGMV 60

Query: 61 VIRGNSVVTVEALEPVSKS 79
          VIRGNSVVTVEALEPV++S
Sbjct: 61 VIRGNSVVTVEALEPVNRS 79

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356505386|ref|XP_003521472.1| PREDICTED: probable small nuclear ribonucleoprotein G [Glycine max] gi|356572580|ref|XP_003554446.1| PREDICTED: probable small nuclear ribonucleoprotein G-like [Glycine max] gi|255625815|gb|ACU13252.1| unknown [Glycine max]

 Score =  154 bits (389), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 74/79 (93%), Positives = 79/79 (100%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMV 60
          MSRSGQPPDLKKYMDKKLQIKLNANRM+VGTLRGFDQFMNLV+DNTVEVNGNEKNDIGMV
Sbjct: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEVNGNEKNDIGMV 60

Query: 61 VIRGNSVVTVEALEPVSKS 79
          VIRGNSVVTVEALEPV+++
Sbjct: 61 VIRGNSVVTVEALEPVNRT 79

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242050850|ref|XP_002463169.1| hypothetical protein SORBIDRAFT_02g039000 [Sorghum bicolor] gi|241926546|gb|EER99690.1| hypothetical protein SORBIDRAFT_02g039000 [Sorghum bicolor]

 Score =  154 bits (388), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 73/80 (91%), Positives = 79/80 (98%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMV 60
          MSRSGQPPDLKKYMDKKLQIKLNANR+++GTLRGFDQFMNLVIDNTVEVNGNEKNDIGMV
Sbjct: 1  MSRSGQPPDLKKYMDKKLQIKLNANRVVIGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMV 60

Query: 61 VIRGNSVVTVEALEPVSKSQ 80
          VIRGNSVV +EALEPV+K+Q
Sbjct: 61 VIRGNSVVMIEALEPVAKAQ 80

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224088536|ref|XP_002308466.1| predicted protein [Populus trichocarpa] gi|222854442|gb|EEE91989.1| predicted protein [Populus trichocarpa]

 Score =  153 bits (386), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 73/80 (91%), Positives = 79/80 (98%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMV 60
          MSRSGQPPDLKKYMDKKLQIKLNANRM+VGTLRGFDQFMNLV+DNTVEVNG+EK DIGMV
Sbjct: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEVNGDEKTDIGMV 60

Query: 61 VIRGNSVVTVEALEPVSKSQ 80
          VIRGNSVVTVEALEPV+++Q
Sbjct: 61 VIRGNSVVTVEALEPVNRAQ 80

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538387|ref|XP_003537685.1| PREDICTED: probable small nuclear ribonucleoprotein G [Glycine max] gi|255630063|gb|ACU15385.1| unknown [Glycine max]

 Score =  153 bits (386), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 74/79 (93%), Positives = 78/79 (98%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMV 60
          MSRSGQPPDLKKYMDKKLQIKLN NRMIVGTLRGFDQFMNLV+DNTVEVNGNEKNDIGMV
Sbjct: 1  MSRSGQPPDLKKYMDKKLQIKLNGNRMIVGTLRGFDQFMNLVVDNTVEVNGNEKNDIGMV 60

Query: 61 VIRGNSVVTVEALEPVSKS 79
          VIRGNSVVTVEALEPV+++
Sbjct: 61 VIRGNSVVTVEALEPVNRA 79

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224138462|ref|XP_002322820.1| predicted protein [Populus trichocarpa] gi|222867450|gb|EEF04581.1| predicted protein [Populus trichocarpa]

 Score =  152 bits (384), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 72/80 (90%), Positives = 79/80 (98%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMV 60
          MSRSGQPPDLKKYMDKKLQIKLNANRM+VGTLRGFDQFMNLV+DNTV+VNG+EK DIGMV
Sbjct: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVDVNGDEKTDIGMV 60

Query: 61 VIRGNSVVTVEALEPVSKSQ 80
          VIRGNSVVTVEALEPV+++Q
Sbjct: 61 VIRGNSVVTVEALEPVTRTQ 80

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118483312|gb|ABK93558.1| unknown [Populus trichocarpa]

 Score =  152 bits (384), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 72/80 (90%), Positives = 79/80 (98%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMV 60
          MSRSGQPPDLKKYMDKKLQIKLNANRM+VGTLRGFDQFMNLV+DNTVEVNG+EK DIGMV
Sbjct: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEVNGDEKTDIGMV 60

Query: 61 VIRGNSVVTVEALEPVSKSQ 80
          V+RGNSVVTVEALEPV+++Q
Sbjct: 61 VLRGNSVVTVEALEPVNRAQ 80

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388492630|gb|AFK34381.1| unknown [Lotus japonicus]

 Score =  152 bits (383), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 72/79 (91%), Positives = 78/79 (98%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMV 60
          MSRSGQPPDLKKYMDK LQIKLNANRMIVGTLRG+DQFMN+V+DNTVEVNGNEKNDIGMV
Sbjct: 1  MSRSGQPPDLKKYMDKNLQIKLNANRMIVGTLRGYDQFMNMVVDNTVEVNGNEKNDIGMV 60

Query: 61 VIRGNSVVTVEALEPVSKS 79
          VIRGNSVVTVEALEPV+++
Sbjct: 61 VIRGNSVVTVEALEPVTRT 79

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	80
TAIR|locus:2061446	80	SNRNP-G "AT2G23930" [Arabidops	0.987	0.987	0.898	2.2e-34
TAIR|locus:2080777	79	AT3G11500 "AT3G11500" [Arabido	0.987	1.0	0.898	2.8e-34
FB|FBgn0261791	76	SmG "Small ribonucleoprotein p	0.937	0.986	0.610	4.4e-20
ZFIN|ZDB-GENE-040912-105	76	zgc:103688 "zgc:103688" [Danio	0.937	0.986	0.610	9.2e-20
UNIPROTKB|Q3ZBL0	76	SNRPG "Small nuclear ribonucle	0.937	0.986	0.610	1.9e-19
UNIPROTKB|P62308	76	SNRPG "Small nuclear ribonucle	0.937	0.986	0.610	1.9e-19
UNIPROTKB|F2Z5V2	76	LOC100525867 "Uncharacterized	0.937	0.986	0.610	1.9e-19
RGD|1584713	76	Snrpg "small nuclear ribonucle	0.937	0.986	0.610	1.9e-19
GENEDB_PFALCIPARUM|MAL8P1.48	83	MAL8P1.48 "small nuclear ribon	0.962	0.927	0.532	3.6e-18
UNIPROTKB|A8MWD9	76	A8MWD9 "Small nuclear ribonucl	0.925	0.973	0.589	1.2e-17

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

 Score = 373 (136.4 bits), Expect = 2.2e-34, P = 2.2e-34
 Identities = 71/79 (89%), Positives = 76/79 (96%)

Query:     1 MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMV 60
             MSRSGQPPDLKKYMDKKLQIKLNANRM+ GTLRGFDQFMNLV+DNTVEVNGN+K DIGMV
Sbjct:     1 MSRSGQPPDLKKYMDKKLQIKLNANRMVTGTLRGFDQFMNLVVDNTVEVNGNDKTDIGMV 60

Query:    61 VIRGNSVVTVEALEPVSKS 79
             VIRGNS+VTVEALEPV +S
Sbjct:    61 VIRGNSIVTVEALEPVGRS 79

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0005829 "cytosol" evidence=IDA

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

 Score = 372 (136.0 bits), Expect = 2.8e-34, P = 2.8e-34
 Identities = 71/79 (89%), Positives = 77/79 (97%)

Query:     1 MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMV 60
             MSRSGQPPDLKKYMDKKLQIKLNANRM+VGTLRGFDQFMNLV+DNTVEVNG++K DIGMV
Sbjct:     1 MSRSGQPPDLKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEVNGDDKTDIGMV 60

Query:    61 VIRGNSVVTVEALEPVSKS 79
             VIRGNS+VTVEALEPV +S
Sbjct:    61 VIRGNSIVTVEALEPVGRS 79

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0005730 "nucleolus" evidence=IDA

GO:0005829 "cytosol" evidence=RCA

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

 Score = 238 (88.8 bits), Expect = 4.4e-20, P = 4.4e-20
 Identities = 47/77 (61%), Positives = 61/77 (79%)

Query:     1 MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIGM 59
             MS++  PP++KKYMDK++ +KLN  R + G LRGFD FMN+V+D+TVE    N KN+IGM
Sbjct:     1 MSKA-HPPEVKKYMDKRMMLKLNGGRAVTGILRGFDPFMNVVLDDTVEECKDNTKNNIGM 59

Query:    60 VVIRGNSVVTVEALEPV 76
             VVIRGNS+V VEAL+ V
Sbjct:    60 VVIRGNSIVMVEALDRV 76

GO:0005634 "nucleus" evidence=IDA

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

GO:0005681 "spliceosomal complex" evidence=ISS

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

GO:0000245 "spliceosomal complex assembly" evidence=ISS

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

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

 Score = 235 (87.8 bits), Expect = 9.2e-20, P = 9.2e-20
 Identities = 47/77 (61%), Positives = 60/77 (77%)

Query:     1 MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGM 59
             MS +  PP+LKK+MDKKL +KLN  R + G LRGFD FMNLV+D+T+E+  G + N IGM
Sbjct:     1 MSEA-HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVVDDTIEMAPGGQMNTIGM 59

Query:    60 VVIRGNSVVTVEALEPV 76
             VVIRGNS++ +EALE V
Sbjct:    60 VVIRGNSIIMLEALERV 76

GO:0003674 "molecular_function" evidence=ND

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

 Score = 232 (86.7 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 47/77 (61%), Positives = 60/77 (77%)

Query:     1 MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV-NGNEKNDIGM 59
             MS++  PP+LKK+MDKKL +KLN  R + G LRGFD FMNLVID  VE+    ++N+IGM
Sbjct:     1 MSKA-HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGM 59

Query:    60 VVIRGNSVVTVEALEPV 76
             VVIRGNS++ +EALE V
Sbjct:    60 VVIRGNSIIMLEALERV 76

GO:0005683 "U7 snRNP" evidence=ISS

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

 Score = 232 (86.7 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 47/77 (61%), Positives = 60/77 (77%)

Query:     1 MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV-NGNEKNDIGM 59
             MS++  PP+LKK+MDKKL +KLN  R + G LRGFD FMNLVID  VE+    ++N+IGM
Sbjct:     1 MSKA-HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGM 59

Query:    60 VVIRGNSVVTVEALEPV 76
             VVIRGNS++ +EALE V
Sbjct:    60 VVIRGNSIIMLEALERV 76

GO:0003723 "RNA binding" evidence=IEA

GO:0000245 "spliceosomal complex assembly" evidence=NAS

GO:0005681 "spliceosomal complex" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

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

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

GO:0005683 "U7 snRNP" evidence=IDA

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

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

GO:0000387 "spliceosomal snRNP assembly" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

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

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

GO:0006397 "mRNA processing" evidence=TAS

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

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0034660 "ncRNA metabolic process" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

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

 Score = 232 (86.7 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 47/77 (61%), Positives = 60/77 (77%)

Query:     1 MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV-NGNEKNDIGM 59
             MS++  PP+LKK+MDKKL +KLN  R + G LRGFD FMNLVID  VE+    ++N+IGM
Sbjct:     1 MSKA-HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGM 59

Query:    60 VVIRGNSVVTVEALEPV 76
             VVIRGNS++ +EALE V
Sbjct:    60 VVIRGNSIIMLEALERV 76

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

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

GO:0005683 "U7 snRNP" evidence=IEA

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

 Score = 232 (86.7 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 47/77 (61%), Positives = 60/77 (77%)

Query:     1 MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV-NGNEKNDIGM 59
             MS++  PP+LKK+MDKKL +KLN  R + G LRGFD FMNLVID  VE+    ++N+IGM
Sbjct:     1 MSKA-HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGM 59

Query:    60 VVIRGNSVVTVEALEPV 76
             VVIRGNS++ +EALE V
Sbjct:    60 VVIRGNSIIMLEALERV 76

GO:0005683 "U7 snRNP" evidence=ISO

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

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

GENEDB_PFALCIPARUM|MAL8P1.48 MAL8P1.48 "small nuclear ribonucleoprotein, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 41/77 (53%), Positives = 59/77 (76%)

Query:     1 MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMV 60
             + ++G   D +K+M+K+LQI LN NR +VG LRG+D FMNLV+DNT+E+  +E+ DIG+V
Sbjct:     5 VGKAGPASDFRKFMEKRLQIYLNGNRQVVGILRGYDTFMNLVLDNTMEIKKDEQIDIGVV 64

Query:    61 VIRGNSVVTVEALEPVS 77
             VIRGNS+   E L+ V+
Sbjct:    65 VIRGNSISYWECLDKVN 81

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

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

 Score = 215 (80.7 bits), Expect = 1.2e-17, P = 1.2e-17
 Identities = 46/78 (58%), Positives = 58/78 (74%)

Query:     1 MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV--NGNEKNDIG 58
             MS++  PP+LKK+ DKK  +KLN  R + G LRGFD FMNLVID  VE+  +G +KN IG
Sbjct:     1 MSKA-HPPELKKFTDKKFSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQKN-IG 58

Query:    59 MVVIRGNSVVTVEALEPV 76
             MV IRGNS++ +EALE V
Sbjct:    59 MVEIRGNSIIMLEALERV 76

GO:0003723 "RNA binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P40204	RUXG_YEAST	No assigned EC number	0.4520	0.8625	0.8961	yes	no
Q54RX0	RUXG_DICDI	No assigned EC number	0.5774	0.875	0.8235	yes	no
Q465S1	RUXX_METBF	No assigned EC number	0.3913	0.8375	0.9305	yes	no
P62309	RUXG_MOUSE	No assigned EC number	0.6103	0.9375	0.9868	yes	no
P62308	RUXG_HUMAN	No assigned EC number	0.6103	0.9375	0.9868	yes	no
O74966	RUXG_SCHPO	No assigned EC number	0.4683	0.9375	0.9740	yes	no
Q9VXE0	RUXG_DROME	No assigned EC number	0.6103	0.9375	0.9868	yes	no
P24715	RUXG_MEDSA	No assigned EC number	0.9210	0.95	0.9382	N/A	no
Q3ZBL0	RUXG_BOVIN	No assigned EC number	0.6103	0.9375	0.9868	yes	no
Q9N4G9	RUXG_CAEEL	No assigned EC number	0.5512	0.95	0.9870	yes	no
O82221	RUXG_ARATH	No assigned EC number	0.8987	0.9875	0.9875	yes	no
Q0W8R9	RUXX_UNCMA	No assigned EC number	0.3623	0.8375	0.9305	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00021594001	SubName- Full=Chromosome chr8 scaffold_23, whole genome shotgun sequence; (80 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00017697001	SubName- Full=Chromosome chr17 scaffold_16, whole genome shotgun sequence; (86 aa)				•	•	•	•		0.972
	GSVIVG00023663001	SubName- Full=Chromosome chr7 scaffold_31, whole genome shotgun sequence; (97 aa)				•	•	•	•		0.928
	GSVIVG00020489001	SubName- Full=Chromosome chr5 scaffold_2, whole genome shotgun sequence; (87 aa)				•	•	•	•		0.928
	GSVIVG00033465001	SubName- Full=Chromosome chr19 scaffold_66, whole genome shotgun sequence; (107 aa)				•	•	•	•		0.926
	GSVIVG00031776001	hypothetical protein LOC100253870 (172 aa)			•	•	•	•	•		0.916
	GSVIVG00030614001	SubName- Full=Chromosome chr1 scaffold_5, whole genome shotgun sequence; (104 aa)				•	•	•	•		0.898
	GSVIVG00002878001	SubName- Full=Chromosome chr18 scaffold_137, whole genome shotgun sequence; (132 aa)				•	•	•	•		0.838
	GSVIVG00038875001	SubName- Full=Chromosome chr8 scaffold_99, whole genome shotgun sequence; (110 aa)				•		•			0.807
	GSVIVG00002642001	SubName- Full=Putative uncharacterized protein (Chromosome undetermined scaffold_134, whole gen [...] (276 aa)				•	•	•	•		0.799
	GSVIVG00002744001	SubName- Full=Chromosome chr1 scaffold_135, whole genome shotgun sequence; (78 aa)				•		•			0.771

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	80
cd01719	70	cd01719, Sm_G, Sm protein G	1e-38
smart00651	67	smart00651, Sm, snRNP Sm proteins	5e-20
pfam01423	66	pfam01423, LSM, LSM domain	3e-19
cd01729	89	cd01729, LSm7, Like-Sm protein 7	1e-18
cd01727	91	cd01727, LSm8, Like-Sm protein 8	8e-15
cd00600	63	cd00600, Sm_like, Sm and related proteins	2e-14
cd01728	74	cd01728, LSm1, Like-Sm protein 1	5e-14
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	2e-13
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	1e-12
cd01726	68	cd01726, LSm6, Like-Sm protein 6	6e-11
cd06168	73	cd06168, LSMD1, LSM domain containing 1	9e-10
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	5e-09
cd01730	82	cd01730, LSm3, Like-Sm protein 3	5e-09
cd01717	80	cd01717, Sm_B, Sm protein B	2e-08
PTZ00138	89	PTZ00138, PTZ00138, small nuclear ribonucleoprotei	1e-07
cd01722	69	cd01722, Sm_F, Sm protein F	2e-07
cd01718	79	cd01718, Sm_E, Sm protein E	9e-07
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	1e-06
cd01732	76	cd01732, LSm5, Like-Sm protein 5	3e-04

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

 Score =  122 bits (308), Expect = 1e-38
 Identities = 45/70 (64%), Positives = 55/70 (78%), Gaps = 1/70 (1%)

Query: 6  QPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG-NEKNDIGMVVIRG 64
           PP+LKKYMDK+L +KLN NR + G LRGFD FMNLV+D+ VE  G  EK  IGMVVIRG
Sbjct: 1  HPPELKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVGDGEKTPIGMVVIRG 60

Query: 65 NSVVTVEALE 74
          NS++ +EAL+
Sbjct: 61 NSIIMIEALD 70

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 = 75.2 bits (186), Expect = 5e-20
 Identities = 28/67 (41%), Positives = 44/67 (65%), Gaps = 2/67 (2%)

Query: 8  PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV--NGNEKNDIGMVVIRGN 65
            LKK + K++ ++L   R   GTL+GFDQFMNLV+++  E   +G +K  +G+V IRGN
Sbjct: 1  KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGN 60

Query: 66 SVVTVEA 72
          ++V +  
Sbjct: 61 NIVYIIL 67

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

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

 Score = 73.3 bits (181), Expect = 3e-19
 Identities = 27/64 (42%), Positives = 45/64 (70%), Gaps = 1/64 (1%)

Query: 8  PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIGMVVIRGNS 66
            L+K + K++ ++L   R + GTL+GFDQFMNLV+D+  E +   + N +G+V+IRGN+
Sbjct: 1  KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLGLVLIRGNN 60

Query: 67 VVTV 70
          +V +
Sbjct: 61 IVLI 64

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|212476 cd01729, LSm7, Like-Sm protein 7

 Score = 72.2 bits (178), Expect = 1e-18
 Identities = 30/71 (42%), Positives = 44/71 (61%), Gaps = 9/71 (12%)

Query: 9  DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE---------VNGNEKNDIGM 59
          DL KY+DKK+++K    R + G L+G+DQ +NLV+D+TVE            +E   +G+
Sbjct: 6  DLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPEDPYKLTDETRSLGL 65

Query: 60 VVIRGNSVVTV 70
          VV RG SVV +
Sbjct: 66 VVCRGTSVVLI 76

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. 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|212474 cd01727, LSm8, Like-Sm protein 8

 Score = 62.5 bits (153), Expect = 8e-15
 Identities = 23/66 (34%), Positives = 41/66 (62%), Gaps = 5/66 (7%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-----VNGNEKNDIGMVVIRG 64
          L+ Y++K++ +     R+IVGTL+GFDQ  NL++ N  E       G E+  +G+ ++RG
Sbjct: 4  LEDYLNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHERVYSSDEGVEEVPLGLYLLRG 63

Query: 65 NSVVTV 70
          ++V  +
Sbjct: 64 DNVAVI 69

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

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

 Score = 60.7 bits (148), Expect = 2e-14
 Identities = 24/63 (38%), Positives = 44/63 (69%), Gaps = 1/63 (1%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEK-NDIGMVVIRGNSVV 68
          LK ++ K + ++L   R++ GTL  FD++MNLV+D+ VE   + K   +G+V+IRG+++V
Sbjct: 1  LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRVLGLVLIRGSNIV 60

Query: 69 TVE 71
          ++ 
Sbjct: 61 SIR 63

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

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

 Score = 60.2 bits (147), Expect = 5e-14
 Identities = 29/64 (45%), Positives = 44/64 (68%), Gaps = 4/64 (6%)

Query: 9  DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE--VNGNEKNDI--GMVVIRG 64
           L++ +DKK+ + L   R ++G LR FDQF NLV+++TVE  + GN+  DI  G+ +IRG
Sbjct: 6  SLEEELDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERIIVGNQYGDIPRGLFIIRG 65

Query: 65 NSVV 68
           +VV
Sbjct: 66 ENVV 69

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

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

 Score = 58.4 bits (142), Expect = 2e-13
 Identities = 22/62 (35%), Positives = 40/62 (64%), Gaps = 1/62 (1%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV-NGNEKNDIGMVVIRGNSVV 68
          L + ++K + +KL   + + G L+GFDQ +NLV++N  E+  G     +G V++RG++VV
Sbjct: 6  LNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGTVLVRGDNVV 65

Query: 69 TV 70
           +
Sbjct: 66 FI 67

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

 Score = 56.9 bits (138), Expect = 1e-12
 Identities = 27/66 (40%), Positives = 42/66 (63%), Gaps = 5/66 (7%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG-----NEKNDIGMVVIRG 64
          LKK ++K++ +KL   R   GTL GFDQ+MNLV+D+  E+       N +   G V+IRG
Sbjct: 12 LKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRG 71

Query: 65 NSVVTV 70
          +++V +
Sbjct: 72 DNIVLI 77

Length = 79

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

 Score = 52.1 bits (126), Expect = 6e-11
 Identities = 23/59 (38%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIGMVVIRGNSV 67
          LKK + K + +KL       G L   D +MNLV+++T E V+G      G   IRGN+V
Sbjct: 6  LKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYGDAFIRGNNV 64

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

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

 Score = 49.5 bits (119), Expect = 9e-10
 Identities = 18/68 (26%), Positives = 37/68 (54%), Gaps = 6/68 (8%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE------VNGNEKNDIGMVVIR 63
          L+K + + L++ L   R++VGT    D+  N+++ N  E      +   E   +G+V++ 
Sbjct: 4  LRKLLGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSDLGAEEPRSLGLVMVP 63

Query: 64 GNSVVTVE 71
          G  +V++E
Sbjct: 64 GKHIVSIE 71

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|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional

 Score = 47.3 bits (113), Expect = 5e-09
 Identities = 24/62 (38%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV-NGNEKNDIGMVVIRGNSVV 68
          L   ++  + ++L   R   G L+G+D  MNLV+DN  E+ +G     +G VVIRG++VV
Sbjct: 9  LNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVV 68

Query: 69 TV 70
           V
Sbjct: 69 YV 70

Length = 72

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

 Score = 47.6 bits (114), Expect = 5e-09
 Identities = 22/80 (27%), Positives = 44/80 (55%), Gaps = 15/80 (18%)

Query: 6  QPPDLKKY-MDKKLQIKLNANRMIVGTLRGFDQFMNLVIDN------TVEVNGNE----- 53
          +P DL +  +D+++ +KL  +R + G L  +DQ +N+++ +      TVE++        
Sbjct: 1  EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIY 60

Query: 54 ---KNDIGMVVIRGNSVVTV 70
             K +I M+ +RG+ V+ V
Sbjct: 61 KTTKRNIPMLFVRGDGVILV 80

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|212464 cd01717, Sm_B, Sm protein B

 Score = 46.4 bits (111), Expect = 2e-08
 Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 12/76 (15%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV------------NGNEKNDI 57
          + +Y++ ++++ L   R  VGT   FD+ MNLV+ +  E                EK  +
Sbjct: 5  MLQYINYRMRVTLQDGRQFVGTFLAFDKHMNLVLSDCEEFRKIKPKKKKKGEEREEKRVL 64

Query: 58 GMVVIRGNSVVTVEAL 73
          G+V++RG +VV++   
Sbjct: 65 GLVLLRGENVVSMTVE 80

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

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

 Score = 44.7 bits (106), Expect = 1e-07
 Identities = 20/62 (32%), Positives = 40/62 (64%), Gaps = 4/62 (6%)

Query: 17 KLQIKL--NANRMIVGTLRGFDQFMNLVIDNTVEVN--GNEKNDIGMVVIRGNSVVTVEA 72
          ++QI L  + N  I G + GFD++MN+V+D+  EV    N + D+G ++++G+++  + A
Sbjct: 28 RVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMA 87

Query: 73 LE 74
           +
Sbjct: 88 AK 89

Length = 89

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

 Score = 43.4 bits (103), Expect = 2e-07
 Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 8  PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIGMVVIRGNS 66
          P L     K + +KL       GTL   D +MNL + NT E ++G    ++G V+IR N+
Sbjct: 4  PFLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKFTGNLGEVLIRCNN 63

Query: 67 VVTV 70
          V+ +
Sbjct: 64 VLYI 67

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|212465 cd01718, Sm_E, Sm protein E

 Score = 41.8 bits (99), Expect = 9e-07
 Identities = 18/55 (32%), Positives = 36/55 (65%), Gaps = 4/55 (7%)

Query: 17 KLQIKL--NANRMIVGTLRGFDQFMNLVIDNTVEVN--GNEKNDIGMVVIRGNSV 67
          ++QI L    +  I G + GFD++MNLV+D+  EV+   N +  +G ++++G+++
Sbjct: 20 RVQIWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVHLKTNTRKPLGRILLKGDNI 74

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Length = 79

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

 Score = 41.0 bits (96), Expect = 1e-06
 Identities = 18/64 (28%), Positives = 39/64 (60%), Gaps = 2/64 (3%)

Query: 10 LKKYMDKKLQIKLNAN-RMIVGTLRGFDQFMNLVIDNTVEVNGNEK-NDIGMVVIRGNSV 67
          +K  +  ++++++  +   + G L   D +MNL + +T+E  G EK   +G VV+RGN++
Sbjct: 5  VKSLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVGEEKVRSLGTVVLRGNNI 64

Query: 68 VTVE 71
          + ++
Sbjct: 65 LLIQ 68

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|212479 cd01732, LSm5, Like-Sm protein 5

 Score = 34.9 bits (81), Expect = 3e-04
 Identities = 15/55 (27%), Positives = 33/55 (60%), Gaps = 4/55 (7%)

Query: 17 KLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV----NGNEKNDIGMVVIRGNSV 67
          K+ I + +++  VGTL GFD ++N+V+++  E      G +   +  +++ GN++
Sbjct: 15 KIWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNI 69

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	80
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.92
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.92
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.91
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.91
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.9
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.89
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.89
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.89
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.89
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.89
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.88
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.88
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.88
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.88
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.87
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.86
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.86
KOG1780	77	consensus Small Nuclear ribonucleoprotein G [RNA p	99.86
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.86
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.85
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.85
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.83
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.8
KOG1783	77	consensus Small nuclear ribonucleoprotein F [RNA p	99.77
KOG3482	79	consensus Small nuclear ribonucleoprotein (snRNP)	99.72
KOG3460	91	consensus Small nuclear ribonucleoprotein (snRNP)	99.71
KOG1781	108	consensus Small Nuclear ribonucleoprotein splicing	99.68
KOG3293	134	consensus Small nuclear ribonucleoprotein (snRNP)	99.59
KOG1784	96	consensus Small Nuclear ribonucleoprotein splicing	99.58
KOG3168	177	consensus U1 snRNP component [Transcription]	99.57
KOG3448	96	consensus Predicted snRNP core protein [RNA proces	99.51
KOG1775	84	consensus U6 snRNA-associated Sm-like protein [RNA	99.47
KOG1782	129	consensus Small Nuclear ribonucleoprotein splicing	99.42
KOG1774	88	consensus Small nuclear ribonucleoprotein E [RNA p	99.42
KOG3172	119	consensus Small nuclear ribonucleoprotein Sm D3 [R	99.34
KOG3428	109	consensus Small nuclear ribonucleoprotein SMD1 and	99.33
KOG3459	114	consensus Small nuclear ribonucleoprotein (snRNP)	98.78
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	98.66
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	98.24
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	97.88
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	97.39
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	96.97
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	96.82
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	96.79
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	96.6
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	96.53
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	96.37
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	96.29
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	96.24
PRK14638	150	hypothetical protein; Provisional	96.04
PRK14639	140	hypothetical protein; Provisional	95.63
PRK02001	152	hypothetical protein; Validated	95.57
COG1923	77	Hfq Uncharacterized host factor I protein [General	95.18
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	94.57
PRK14640	152	hypothetical protein; Provisional	94.46
PRK14091	165	RNA-binding protein Hfq; Provisional	94.36
PRK14644	136	hypothetical protein; Provisional	94.13
PRK14633	150	hypothetical protein; Provisional	93.84
PRK14642	197	hypothetical protein; Provisional	93.68
PRK00092	154	ribosome maturation protein RimP; Reviewed	93.51
KOG1073	361	consensus Uncharacterized mRNA-associated protein	93.42
PRK14645	154	hypothetical protein; Provisional	93.4
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	93.27
PRK14636	176	hypothetical protein; Provisional	92.99
PRK14632	172	hypothetical protein; Provisional	92.9
COG0779	153	Uncharacterized protein conserved in bacteria [Fun	92.86
PRK14634	155	hypothetical protein; Provisional	92.7
PRK14091	165	RNA-binding protein Hfq; Provisional	92.62
PRK14643	164	hypothetical protein; Provisional	92.27
PRK14647	159	hypothetical protein; Provisional	92.18
PRK14646	155	hypothetical protein; Provisional	91.9
PRK14631	174	hypothetical protein; Provisional	91.43
PRK14637	151	hypothetical protein; Provisional	91.24
PRK06955	300	biotin--protein ligase; Provisional	90.67
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	90.64
PRK14641	173	hypothetical protein; Provisional	90.13
PF03614	165	Flag1_repress: Repressor of phase-1 flagellin; Int	89.33
PF14563	42	DUF4444: Domain of unknown function (DUF4444); PDB	88.01
PRK14635	162	hypothetical protein; Provisional	87.49
PRK13325	592	bifunctional biotin--[acetyl-CoA-carboxylase] liga	87.07
PF03614	165	Flag1_repress: Repressor of phase-1 flagellin; Int	87.03
TIGR00121	237	birA_ligase birA, biotin-[acetyl-CoA-carboxylase]	86.9
PRK08330	236	biotin--protein ligase; Provisional	86.0
PRK14630	143	hypothetical protein; Provisional	83.9
PTZ00275	285	biotin-acetyl-CoA-carboxylase ligase; Provisional	81.96
PRK10139	455	serine endoprotease; Provisional	81.65

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

Probab=99.92  E-value=3.1e-24  Score=126.10  Aligned_cols=69  Identities=74%  Similarity=1.169  Sum_probs=64.1

Q ss_pred             CCchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecCC
Q 034895            7 PPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALEP   75 (80)
Q Consensus         7 p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d~   75 (80)
                      +++|.++++++|.|+|++|++++|+|.+||+|||++|+||.|+. +...+.+|.++|||++|++|++.|+
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 PPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVIRGNSIVMLEALER   71 (72)
T ss_pred             chhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEECCCEEEEEEcccc
Confidence            56799999999999999999999999999999999999999985 4467789999999999999998875

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

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.92  E-value=1.6e-24  Score=127.15  Aligned_cols=69  Identities=39%  Similarity=0.691  Sum_probs=62.8

Q ss_pred             CCCCCCCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEE
Q 034895            1 MSRSGQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVE   71 (80)
Q Consensus         1 M~~~~~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~   71 (80)
                      |+  ..|+. |.++++++|.|+|+||+.|+|+|.+||+|||++|+||.|.. ++..+.+|.++|||++|++|.
T Consensus         1 ~~--~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~V~~i~   71 (72)
T PRK00737          1 MA--QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVS   71 (72)
T ss_pred             CC--cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeCCEEEEEc
Confidence            56  46887 89999999999999999999999999999999999999986 445678999999999999986

>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=99.91  E-value=4.7e-24  Score=127.76  Aligned_cols=70  Identities=41%  Similarity=0.758  Sum_probs=63.3

Q ss_pred             CCCCchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecC---------ceeeeecEEEEcCCcEEEEEecC
Q 034895            5 GQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG---------NEKNDIGMVVIRGNSVVTVEALE   74 (80)
Q Consensus         5 ~~p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~---------~~~~~~g~v~IrG~~I~~I~~~d   74 (80)
                      ..+++|.++++++|+|.|++||+|.|+|.+||+||||+|++|.|+..         ...+.+|.++|||++|++|.+.+
T Consensus         2 ~~~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~   80 (81)
T cd01729           2 ESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD   80 (81)
T ss_pred             cchhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence            35788999999999999999999999999999999999999999752         24678999999999999998765

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

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

Probab=99.91  E-value=5.6e-24  Score=123.32  Aligned_cols=66  Identities=36%  Similarity=0.688  Sum_probs=60.3

Q ss_pred             CCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEe
Q 034895            7 PPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEA   72 (80)
Q Consensus         7 p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~   72 (80)
                      |++ |+++++++|.|+|++|+.|+|+|.+||+|||++|+||.|.+ +...+.+|.++|||++|++|++
T Consensus         1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~I~~i~~   68 (68)
T cd01731           1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRGDNVLFISP   68 (68)
T ss_pred             ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeCCEEEEEcC
Confidence            555 89999999999999999999999999999999999999985 4466789999999999999964

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

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

Probab=99.90  E-value=1e-23  Score=122.04  Aligned_cols=65  Identities=34%  Similarity=0.553  Sum_probs=59.4

Q ss_pred             CCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEE
Q 034895            7 PPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVE   71 (80)
Q Consensus         7 p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~   71 (80)
                      |++ |++++|++|+|+|++|++|+|+|.+||+|||++|+||+|.. ++..+.+|.++|||++|++|+
T Consensus         1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~IRG~~I~~I~   67 (67)
T cd01726           1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNVLYIS   67 (67)
T ss_pred             CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEEECCEEEEEC
Confidence            566 89999999999999999999999999999999999999875 456678999999999999984

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

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

Probab=99.89  E-value=3.4e-23  Score=124.10  Aligned_cols=67  Identities=30%  Similarity=0.614  Sum_probs=59.8

Q ss_pred             CCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCc--------------eeeeecEEEEcCCcEEEE
Q 034895            6 QPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGN--------------EKNDIGMVVIRGNSVVTV   70 (80)
Q Consensus         6 ~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~--------------~~~~~g~v~IrG~~I~~I   70 (80)
                      .|++ |+.+++++|.|++++||.+.|+|.|||+||||+|+||+|.+..              ..|.+|.+||||++|++|
T Consensus         1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i   80 (82)
T cd01730           1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILV   80 (82)
T ss_pred             CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEE
Confidence            4777 6888999999999999999999999999999999999998621              367899999999999998


Q ss_pred             Ee
Q 034895           71 EA   72 (80)
Q Consensus        71 ~~   72 (80)
                      ++
T Consensus        81 ~~   82 (82)
T cd01730          81 SP   82 (82)
T ss_pred             CC
Confidence            63

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.

>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=5.7e-23  Score=121.87  Aligned_cols=67  Identities=24%  Similarity=0.602  Sum_probs=61.1

Q ss_pred             CCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec----CceeeeecEEEEcCCcEEEEEe
Q 034895            6 QPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN----GNEKNDIGMVVIRGNSVVTVEA   72 (80)
Q Consensus         6 ~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~----~~~~~~~g~v~IrG~~I~~I~~   72 (80)
                      .|++ |+++++++|.|++++|+++.|+|.|||+|||++|+||.|.+    +++.+.+|.++|||++|.+|++
T Consensus         3 ~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p   74 (76)
T cd01732           3 LPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVP   74 (76)
T ss_pred             ChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEEC
Confidence            4777 79999999999999999999999999999999999999975    3356789999999999999985

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.

>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=99.89  E-value=7.9e-23  Score=119.39  Aligned_cols=68  Identities=16%  Similarity=0.233  Sum_probs=61.6

Q ss_pred             CCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecC
Q 034895            7 PPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALE   74 (80)
Q Consensus         7 p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d   74 (80)
                      |++ |+++.|++|.|+|+||.+|+|+|.++|+|||++|+||.+.. +++...++.+||||++|.||..||
T Consensus         1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v~IRG~nI~~v~lPd   70 (70)
T cd01721           1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRGSKIRFFILPD   70 (70)
T ss_pred             ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcEEEeCCEEEEEEeCC
Confidence            555 78999999999999999999999999999999999998764 445667899999999999999987

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.

>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=99.89  E-value=1.6e-22  Score=120.35  Aligned_cols=65  Identities=29%  Similarity=0.628  Sum_probs=59.3

Q ss_pred             CchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecC-----------ceeeeecEEEEcCCcEEEEEe
Q 034895            8 PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG-----------NEKNDIGMVVIRGNSVVTVEA   72 (80)
Q Consensus         8 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~-----------~~~~~~g~v~IrG~~I~~I~~   72 (80)
                      ..|.++++++|.|+++|||.+.|+|.|||+||||+|+||.|++.           .+.+.+|+++|||++|++|+.
T Consensus         3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v   78 (79)
T cd01717           3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV   78 (79)
T ss_pred             chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence            56999999999999999999999999999999999999999751           245789999999999999975

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

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

Probab=99.89  E-value=6.3e-23  Score=119.10  Aligned_cols=65  Identities=34%  Similarity=0.490  Sum_probs=59.0

Q ss_pred             CCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEE
Q 034895            7 PPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVE   71 (80)
Q Consensus         7 p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~   71 (80)
                      |.. |++++|++|.|+|+||++|+|+|.+||+|||++|+||+|.. +.....+|.++|||++|++|.
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 PKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRCNNVLYIR   68 (68)
T ss_pred             HHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEECCEEEEEC
Confidence            555 89999999999999999999999999999999999999875 445678999999999999983

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.

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

Probab=99.88  E-value=4.1e-22  Score=117.32  Aligned_cols=68  Identities=35%  Similarity=0.670  Sum_probs=61.6

Q ss_pred             CchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-----CceeeeecEEEEcCCcEEEEEecCC
Q 034895            8 PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-----GNEKNDIGMVVIRGNSVVTVEALEP   75 (80)
Q Consensus         8 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-----~~~~~~~g~v~IrG~~I~~I~~~d~   75 (80)
                      +.|.++++++|+|.+++|+.+.|+|.+||+|||++|++|.|..     +...+.+|.+++||++|++|++.|+
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            5689999999999999999999999999999999999999974     2246689999999999999998774

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.

>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=99.88  E-value=2.3e-22  Score=119.01  Aligned_cols=70  Identities=20%  Similarity=0.365  Sum_probs=63.0

Q ss_pred             CCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec--CceeeeecEEEEcCCcEEEEEecCCc
Q 034895            7 PPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN--GNEKNDIGMVVIRGNSVVTVEALEPV   76 (80)
Q Consensus         7 p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~--~~~~~~~g~v~IrG~~I~~I~~~d~~   76 (80)
                      |+. |+++.|++|.|+|++|++++|+|.+||+|||++|+||.+..  ++....++.+||||++|.+|+.+|.+
T Consensus         2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~~   74 (76)
T cd01723           2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDEI   74 (76)
T ss_pred             chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHHH
Confidence            677 79999999999999999999999999999999999999874  44456689999999999999998864

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

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

Probab=99.88  E-value=4.6e-22  Score=114.19  Aligned_cols=64  Identities=39%  Similarity=0.655  Sum_probs=59.7

Q ss_pred             chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCc--eeeeecEEEEcCCcEEEEEe
Q 034895            9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGN--EKNDIGMVVIRGNSVVTVEA   72 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~--~~~~~g~v~IrG~~I~~I~~   72 (80)
                      +|++++|++|+|+|+||++++|+|.+||+|||++|+||.+....  +.++++.+||||++|++|++
T Consensus         2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~   67 (67)
T PF01423_consen    2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL   67 (67)
T ss_dssp             HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred             hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence            48899999999999999999999999999999999999998643  78899999999999999975

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

>smart00651 Sm snRNP Sm proteins

Probab=99.88  E-value=6.4e-22  Score=113.47  Aligned_cols=64  Identities=42%  Similarity=0.702  Sum_probs=59.6

Q ss_pred             chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecC--ceeeeecEEEEcCCcEEEEEe
Q 034895            9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG--NEKNDIGMVVIRGNSVVTVEA   72 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~--~~~~~~g~v~IrG~~I~~I~~   72 (80)
                      +|++++|++|+|+|+||+.++|+|.+||+|||++|+||.|.+.  .+.+.++.+||||++|++|++
T Consensus         2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651        2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence            5899999999999999999999999999999999999999863  567899999999999999974

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

>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=99.87  E-value=5.6e-22  Score=120.30  Aligned_cols=68  Identities=25%  Similarity=0.453  Sum_probs=59.5

Q ss_pred             CCCc-hhhhc--CCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCc--------------eeeeecEEEEcCCcEE
Q 034895            6 QPPD-LKKYM--DKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGN--------------EKNDIGMVVIRGNSVV   68 (80)
Q Consensus         6 ~p~~-L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~--------------~~~~~g~v~IrG~~I~   68 (80)
                      .|+. |.+++  +++|.|+|++|+.+.|+|.|||+||||+|+||+|.+..              +.+++|.+||||++|+
T Consensus         2 gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv   81 (87)
T cd01720           2 GPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVI   81 (87)
T ss_pred             ChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEE
Confidence            5777 67886  89999999999999999999999999999999997521              2457899999999999


Q ss_pred             EEEec
Q 034895           69 TVEAL   73 (80)
Q Consensus        69 ~I~~~   73 (80)
                      +|+.-
T Consensus        82 ~Is~~   86 (87)
T cd01720          82 LVLRN   86 (87)
T ss_pred             EEecC
Confidence            99753

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.

>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=99.86  E-value=2.5e-21  Score=118.05  Aligned_cols=69  Identities=23%  Similarity=0.341  Sum_probs=63.4

Q ss_pred             chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecCCcc
Q 034895            9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALEPVS   77 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d~~~   77 (80)
                      .|+++.|++|+|+|++|..|+|+|.++|.|||++|+||++.. ++....++.++|||++|.||+.||.+.
T Consensus         5 fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lPd~l~   74 (90)
T cd01724           5 FLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILPDSLN   74 (90)
T ss_pred             HHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcCCcCC
Confidence            378999999999999999999999999999999999999875 456678999999999999999999864

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.

>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=99.86  E-value=3.5e-21  Score=114.00  Aligned_cols=65  Identities=23%  Similarity=0.492  Sum_probs=59.8

Q ss_pred             CchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecC-------ceeeeecEEEEcCCcEEEEEe
Q 034895            8 PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG-------NEKNDIGMVVIRGNSVVTVEA   72 (80)
Q Consensus         8 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~-------~~~~~~g~v~IrG~~I~~I~~   72 (80)
                      ..|.++++++|+|+|+|||.|.|+|.|||++||++|+||.|+..       .+.|.+|+++|||++|++|+.
T Consensus         3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v   74 (75)
T cd06168           3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV   74 (75)
T ss_pred             hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence            35899999999999999999999999999999999999999851       457899999999999999974

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.

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

Probab=99.86  E-value=1.1e-21  Score=114.97  Aligned_cols=75  Identities=68%  Similarity=1.087  Sum_probs=69.0

Q ss_pred             CCCCCCCCchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecC-ceeeeecEEEEcCCcEEEEEecCCc
Q 034895            1 MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG-NEKNDIGMVVIRGNSVVTVEALEPV   76 (80)
Q Consensus         1 M~~~~~p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~-~~~~~~g~v~IrG~~I~~I~~~d~~   76 (80)
                      |++++.| +|.+|++|++.++|..||.++|.|.+||.|||+||+++.|..+ +.+..+|.++|||++|+.+.+.|.+
T Consensus         1 Msksg~P-eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~eaL~~~   76 (77)
T KOG1780|consen    1 MSKSGHP-ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMVEALERV   76 (77)
T ss_pred             CCcccCc-hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEeccEEEEEeecccc
Confidence            8999998 9999999999999999999999999999999999999999864 3456799999999999999988764

>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=99.86  E-value=3.1e-21  Score=113.96  Aligned_cols=65  Identities=40%  Similarity=0.645  Sum_probs=58.5

Q ss_pred             CchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec--Cc--eeeeecEEEEcCCcEEEEEe
Q 034895            8 PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN--GN--EKNDIGMVVIRGNSVVTVEA   72 (80)
Q Consensus         8 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~--~~--~~~~~g~v~IrG~~I~~I~~   72 (80)
                      +.|.++++++|.|.+++|++|.|+|.+||+|||++|+||.|..  +.  ..+.+|.++|||++|++|+.
T Consensus         5 ~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~   73 (74)
T cd01728           5 ASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE   73 (74)
T ss_pred             HHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence            4599999999999999999999999999999999999998864  21  35789999999999999975

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.

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

Probab=99.85  E-value=6.5e-21  Score=113.25  Aligned_cols=67  Identities=42%  Similarity=0.737  Sum_probs=57.8

Q ss_pred             CCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec---Cce-eeeec-EEEEcCCcEEEEEe
Q 034895            6 QPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN---GNE-KNDIG-MVVIRGNSVVTVEA   72 (80)
Q Consensus         6 ~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~---~~~-~~~~g-~v~IrG~~I~~I~~   72 (80)
                      .|.. |.++++++|.|+|++|++|+|+|.|||+|||++|+||.|..   +.. .+.++ .++|||++|++|..
T Consensus         7 ~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~   79 (79)
T COG1958           7 LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP   79 (79)
T ss_pred             CcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence            3555 89999999999999999999999999999999999999975   333 24455 99999999999863

>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=99.85  E-value=8.9e-21  Score=107.33  Aligned_cols=62  Identities=37%  Similarity=0.668  Sum_probs=57.4

Q ss_pred             hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecC-ceeeeecEEEEcCCcEEEEE
Q 034895           10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG-NEKNDIGMVVIRGNSVVTVE   71 (80)
Q Consensus        10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~-~~~~~~g~v~IrG~~I~~I~   71 (80)
                      |++++|++|+|+|+||+.|.|+|.+||+|||++|+||.+.+. ...+.++.+||||++|++|.
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~~~~~~~~~irG~~I~~I~   63 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGKKRVLGLVLIRGDNVRLVT   63 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCcEEECCeEEEECCEEEEEC
Confidence            678999999999999999999999999999999999999863 56788999999999999984

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

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

Probab=99.85  E-value=5.9e-21  Score=114.02  Aligned_cols=67  Identities=28%  Similarity=0.662  Sum_probs=59.2

Q ss_pred             CCCc-hhhhcCC--EEEEEEc--CCeEEEEEEEEECCCCceEEcceEEec--CceeeeecEEEEcCCcEEEEEe
Q 034895            6 QPPD-LKKYMDK--KLQIKLN--ANRMIVGTLRGFDQFMNLVIDNTVEVN--GNEKNDIGMVVIRGNSVVTVEA   72 (80)
Q Consensus         6 ~p~~-L~~~~~k--~V~V~l~--~g~~~~G~L~~~D~~~NlvL~~~~e~~--~~~~~~~g~v~IrG~~I~~I~~   72 (80)
                      .|.+ |.+++++  +|.|+++  +|++++|+|.|||+|||++|+||+|+.  +.+.+.+|.++|||++|++|++
T Consensus         6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~p   79 (79)
T cd01718           6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQN   79 (79)
T ss_pred             CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEcC
Confidence            4777 8899988  7888877  899999999999999999999999985  3566789999999999999873

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.

>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=99.84  E-value=1.5e-20  Score=111.92  Aligned_cols=64  Identities=16%  Similarity=0.374  Sum_probs=58.9

Q ss_pred             hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEec
Q 034895           10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEAL   73 (80)
Q Consensus        10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~   73 (80)
                      |+++.|++|.|+|+||.+|+|+|.++|++||++|+||++.. ++....++.+||||++|.||+.|
T Consensus        14 L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~lP   78 (78)
T cd01733          14 LQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVHIP   78 (78)
T ss_pred             HHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEEcC
Confidence            78899999999999999999999999999999999999875 44555799999999999999876

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=99.83  E-value=2.5e-20  Score=111.58  Aligned_cols=67  Identities=24%  Similarity=0.358  Sum_probs=59.6

Q ss_pred             hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCc---eeeeecEEEEcCCcEEEEEecCCc
Q 034895           10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGN---EKNDIGMVVIRGNSVVTVEALEPV   76 (80)
Q Consensus        10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~---~~~~~g~v~IrG~~I~~I~~~d~~   76 (80)
                      |+++.|++|.|+|++|..|+|+|.++|+|||++|+||++....   ....++.++|||++|.+|+.||.+
T Consensus         6 L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~   75 (81)
T cd01725           6 FKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADE   75 (81)
T ss_pred             HHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhH
Confidence            7899999999999999999999999999999999999877532   234578999999999999999864

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.

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.80  E-value=5e-19  Score=107.76  Aligned_cols=68  Identities=32%  Similarity=0.664  Sum_probs=57.3

Q ss_pred             CCCc-hhhhcCC--EEEEEEcC--CeEEEEEEEEECCCCceEEcceEEec--CceeeeecEEEEcCCcEEEEEec
Q 034895            6 QPPD-LKKYMDK--KLQIKLNA--NRMIVGTLRGFDQFMNLVIDNTVEVN--GNEKNDIGMVVIRGNSVVTVEAL   73 (80)
Q Consensus         6 ~p~~-L~~~~~k--~V~V~l~~--g~~~~G~L~~~D~~~NlvL~~~~e~~--~~~~~~~g~v~IrG~~I~~I~~~   73 (80)
                      .|.+ +.+++.+  +|.|++.+  +++++|+|.|||+|||++|+||+|..  +...+.+|.++|||++|++|++.
T Consensus        14 ~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~~   88 (89)
T PTZ00138         14 QPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMAA   88 (89)
T ss_pred             CCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEcC
Confidence            4555 6778755  68888877  59999999999999999999999985  34567899999999999999864

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

Probab=99.77  E-value=8.2e-20  Score=106.77  Aligned_cols=73  Identities=34%  Similarity=0.521  Sum_probs=67.0

Q ss_pred             CCCCCCCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEec
Q 034895            1 MSRSGQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEAL   73 (80)
Q Consensus         1 M~~~~~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~   73 (80)
                      ||..+.|.+ |.+++||+|.|+|.+|-.|+|+|.++|.|||+-|+.++|.. |..++++|..||||++|.+|+..
T Consensus         1 ~s~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygdaFirGnnVlyIs~~   75 (77)
T KOG1783|consen    1 MSEGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGDAFIRGNNVLYISTQ   75 (77)
T ss_pred             CCcccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccceeeccccEEEEEec
Confidence            777777877 89999999999999999999999999999999999999975 66788999999999999999865

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

Probab=99.72  E-value=2.5e-17  Score=96.35  Aligned_cols=66  Identities=29%  Similarity=0.423  Sum_probs=60.4

Q ss_pred             chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecC
Q 034895            9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALE   74 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d   74 (80)
                      +|+.+.|++|.|+|+-|.+|+|+|++.|+|||+.|.+|+|.. |.....+|.++||.+||.+|.-.+
T Consensus        12 FL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEilIRCNNvlyi~gv~   78 (79)
T KOG3482|consen   12 FLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEILIRCNNVLYIRGVP   78 (79)
T ss_pred             HHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEEEEeccEEEEecCC
Confidence            488999999999999999999999999999999999999964 666778999999999999997644

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

Probab=99.71  E-value=1.9e-18  Score=103.42  Aligned_cols=73  Identities=29%  Similarity=0.498  Sum_probs=62.7

Q ss_pred             CCCCCCchh-hhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec----C----------ceeeeecEEEEcCCcE
Q 034895            3 RSGQPPDLK-KYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN----G----------NEKNDIGMVVIRGNSV   67 (80)
Q Consensus         3 ~~~~p~~L~-~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~----~----------~~~~~~g~v~IrG~~I   67 (80)
                      +...|++|- =.++.+|.|+++++|+++|+|.|||+|.|++|.|++|..    +          ..+|.+..+|+||++|
T Consensus         2 ~v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~V   81 (91)
T KOG3460|consen    2 TVEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGV   81 (91)
T ss_pred             cccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeE
Confidence            345789854 559999999999999999999999999999999998864    1          2357899999999999


Q ss_pred             EEEEecCC
Q 034895           68 VTVEALEP   75 (80)
Q Consensus        68 ~~I~~~d~   75 (80)
                      .+|++|-.
T Consensus        82 ilvspp~~   89 (91)
T KOG3460|consen   82 ILVSPPLR   89 (91)
T ss_pred             EEEcCccc
Confidence            99998754

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

Probab=99.68  E-value=1.8e-18  Score=106.22  Aligned_cols=70  Identities=40%  Similarity=0.717  Sum_probs=63.4

Q ss_pred             CCCchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec---------CceeeeecEEEEcCCcEEEEEecCC
Q 034895            6 QPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN---------GNEKNDIGMVVIRGNSVVTVEALEP   75 (80)
Q Consensus         6 ~p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~---------~~~~~~~g~v~IrG~~I~~I~~~d~   75 (80)
                      +.++|.+|++++|+|++..||+.+|+|.|||+.||+||+|+.|+-         +.+.|++|++++||..+++|++.|.
T Consensus        18 silDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG   96 (108)
T KOG1781|consen   18 SILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADG   96 (108)
T ss_pred             HHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcc
Confidence            446799999999999999999999999999999999999999863         2345899999999999999999875

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

Probab=99.59  E-value=2.1e-15  Score=95.93  Aligned_cols=71  Identities=20%  Similarity=0.337  Sum_probs=64.4

Q ss_pred             CCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec--CceeeeecEEEEcCCcEEEEEecCCc
Q 034895            6 QPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN--GNEKNDIGMVVIRGNSVVTVEALEPV   76 (80)
Q Consensus         6 ~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~--~~~~~~~g~v~IrG~~I~~I~~~d~~   76 (80)
                      .|+. |....++++.|+|+||..|.|.|+.+|.+|||.|.++.++.  +.+...++.++|||++|.|+.++|++
T Consensus         2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~i   75 (134)
T KOG3293|consen    2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEI   75 (134)
T ss_pred             cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHH
Confidence            4777 67778999999999999999999999999999999999874  56777899999999999999999864

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

Probab=99.58  E-value=2.6e-15  Score=91.16  Aligned_cols=70  Identities=36%  Similarity=0.656  Sum_probs=63.3

Q ss_pred             chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-----CceeeeecEEEEcCCcEEEEEecCCccC
Q 034895            9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-----GNEKNDIGMVVIRGNSVVTVEALEPVSK   78 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-----~~~~~~~g~v~IrG~~I~~I~~~d~~~~   78 (80)
                      .|..|++++|.|.+.|||.+.|.|.|||+..|++|+++.|+.     +.....+|..+|||+||..|...|+.+.
T Consensus         4 ~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d   78 (96)
T KOG1784|consen    4 TLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELD   78 (96)
T ss_pred             hHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhh
Confidence            489999999999999999999999999999999999999874     4455679999999999999999987543

>KOG3168 consensus U1 snRNP component [Transcription]

Probab=99.57  E-value=4.2e-16  Score=103.58  Aligned_cols=73  Identities=26%  Similarity=0.620  Sum_probs=64.7

Q ss_pred             CCCchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-----------CceeeeecEEEEcCCcEEEEEecC
Q 034895            6 QPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-----------GNEKNDIGMVVIRGNSVVTVEALE   74 (80)
Q Consensus         6 ~p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-----------~~~~~~~g~v~IrG~~I~~I~~~d   74 (80)
                      .+..|.++++.+++|.++|||.|.|+|.+||+|||++|.+|+|..           ++++|-+|++++||++|++.+..+
T Consensus         5 ~sskml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVeg   84 (177)
T KOG3168|consen    5 KSSKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEG   84 (177)
T ss_pred             chhHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccC
Confidence            456789999999999999999999999999999999999999864           346788999999999999999877


Q ss_pred             CccC
Q 034895           75 PVSK   78 (80)
Q Consensus        75 ~~~~   78 (80)
                      .-..
T Consensus        85 ppp~   88 (177)
T KOG3168|consen   85 PPPP   88 (177)
T ss_pred             CCCC
Confidence            5443

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

Probab=99.51  E-value=4.5e-14  Score=85.44  Aligned_cols=67  Identities=24%  Similarity=0.381  Sum_probs=58.4

Q ss_pred             hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCcee---eeecEEEEcCCcEEEEEecCCc
Q 034895           10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEK---NDIGMVVIRGNSVVTVEALEPV   76 (80)
Q Consensus        10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~---~~~g~v~IrG~~I~~I~~~d~~   76 (80)
                      +..++|++|.|+|+|+-.+.|+|.++|+|+|+.|.|....+.++.   .....+||||+.|.||..+...
T Consensus         7 Fkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~   76 (96)
T KOG3448|consen    7 FKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDA   76 (96)
T ss_pred             HHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChhH
Confidence            577899999999999999999999999999999999987764332   3567899999999999987653

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

Probab=99.47  E-value=2.8e-14  Score=84.25  Aligned_cols=70  Identities=26%  Similarity=0.572  Sum_probs=60.5

Q ss_pred             CCCCCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec----CceeeeecEEEEcCCcEEEEEe
Q 034895            3 RSGQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN----GNEKNDIGMVVIRGNSVVTVEA   72 (80)
Q Consensus         3 ~~~~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~----~~~~~~~g~v~IrG~~I~~I~~   72 (80)
                      ..-.|++ ..+++|.+|.|.+++.+++.|+|.+||.|.|++|+|+.|+.    +....+++.+++.|++|....+
T Consensus         4 ~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvP   78 (84)
T KOG1775|consen    4 STLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVP   78 (84)
T ss_pred             hhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEec
Confidence            3446778 57899999999999999999999999999999999999974    3344579999999999987755

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

Probab=99.42  E-value=2.1e-14  Score=91.22  Aligned_cols=69  Identities=39%  Similarity=0.676  Sum_probs=61.0

Q ss_pred             hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec--Cce--eeeecEEEEcCCcEEEEEecCCccC
Q 034895           10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN--GNE--KNDIGMVVIRGNSVVTVEALEPVSK   78 (80)
Q Consensus        10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~--~~~--~~~~g~v~IrG~~I~~I~~~d~~~~   78 (80)
                      |.+++++++.|-|+|||.+.|.|.+||+|.|++|.+|.|+.  ++.  ....|..+|||+||+.+...|..+.
T Consensus        14 l~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dkE   86 (129)
T KOG1782|consen   14 LVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDKE   86 (129)
T ss_pred             HHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcchh
Confidence            88999999999999999999999999999999999999874  432  2456899999999999999887654

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

Probab=99.42  E-value=1.5e-13  Score=81.97  Aligned_cols=69  Identities=28%  Similarity=0.639  Sum_probs=55.7

Q ss_pred             CCCc-hhhhcC--CEEEEEEcC--CeEEEEEEEEECCCCceEEcceEEec--CceeeeecEEEEcCCcEEEEEecC
Q 034895            6 QPPD-LKKYMD--KKLQIKLNA--NRMIVGTLRGFDQFMNLVIDNTVEVN--GNEKNDIGMVVIRGNSVVTVEALE   74 (80)
Q Consensus         6 ~p~~-L~~~~~--k~V~V~l~~--g~~~~G~L~~~D~~~NlvL~~~~e~~--~~~~~~~g~v~IrG~~I~~I~~~d   74 (80)
                      .|.+ +-+|+.  .+|.|+|.+  |-.++|+++|||+|||+||++|+|..  ....+.+|.++++|+||..|...+
T Consensus        12 ~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItli~~~~   87 (88)
T KOG1774|consen   12 QPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITLIQSAG   87 (88)
T ss_pred             CcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcEEEEeecC
Confidence            4555 456664  478888866  88999999999999999999999975  223348999999999999998754

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

Probab=99.34  E-value=8.7e-12  Score=77.90  Aligned_cols=74  Identities=15%  Similarity=0.229  Sum_probs=65.7

Q ss_pred             CCCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecCCccC
Q 034895            5 GQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALEPVSK   78 (80)
Q Consensus         5 ~~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d~~~~   78 (80)
                      +-|.+ |.+..|.-|++++..|..|+|+|.-.|.+||+.|+|..-+. ++....+..+||||+.|.++-.||-+|.
T Consensus         4 gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPdmLKn   79 (119)
T KOG3172|consen    4 GVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPDMLKN   79 (119)
T ss_pred             ccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECchHhhc
Confidence            45777 78999999999999999999999999999999999998764 4566678999999999999999997653

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

Probab=99.33  E-value=1.2e-11  Score=77.16  Aligned_cols=68  Identities=22%  Similarity=0.324  Sum_probs=61.7

Q ss_pred             chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcCCcEEEEEecCCc
Q 034895            9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALEPV   76 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~d~~   76 (80)
                      .|+++.+.++.|+|++|...+|++.+.|.+||..|.++.-...+++.++..++|||++|.|+..||..
T Consensus         6 ~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~~pv~l~~lsirgnniRy~~lpD~l   73 (109)
T KOG3428|consen    6 FLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKGEPVRLDTLSIRGNNIRYYILPDSL   73 (109)
T ss_pred             HHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCCCceeEEEEEeecceEEEEEccCCc
Confidence            47889999999999999999999999999999999999877544566788999999999999999974

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

Probab=98.78  E-value=9.9e-10  Score=68.80  Aligned_cols=69  Identities=25%  Similarity=0.408  Sum_probs=56.6

Q ss_pred             CCCCc-hhhhc--CCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecC--------c------eeeeecEEEEcCCcE
Q 034895            5 GQPPD-LKKYM--DKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG--------N------EKNDIGMVVIRGNSV   67 (80)
Q Consensus         5 ~~p~~-L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~--------~------~~~~~g~v~IrG~~I   67 (80)
                      ..|+. +.+..  ..+|.|.++|++.+-|+..|||.|.|++|+|+.|.|.        .      ..|.+|.+||||++|
T Consensus        23 ~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsv  102 (114)
T KOG3459|consen   23 TGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSV  102 (114)
T ss_pred             cCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeE
Confidence            35666 44443  5689999999999999999999999999999999772        1      257899999999999


Q ss_pred             EEEEec
Q 034895           68 VTVEAL   73 (80)
Q Consensus        68 ~~I~~~   73 (80)
                      +.+.-.
T Consensus       103 I~v~r~  108 (114)
T KOG3459|consen  103 ILVLRN  108 (114)
T ss_pred             EEEEec
Confidence            988743

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

Probab=98.66  E-value=2.3e-08  Score=57.62  Aligned_cols=37  Identities=19%  Similarity=0.389  Sum_probs=31.1

Q ss_pred             CCEEEEEEcC----CeEEEEEEEEECCCCceEEcceEEecC
Q 034895           15 DKKLQIKLNA----NRMIVGTLRGFDQFMNLVIDNTVEVNG   51 (80)
Q Consensus        15 ~k~V~V~l~~----g~~~~G~L~~~D~~~NlvL~~~~e~~~   51 (80)
                      +.+|+|.++.    +-.++|.|.|||+|+||+|.|++|.+.
T Consensus         8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~   48 (66)
T cd01739           8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYR   48 (66)
T ss_pred             CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhc
Confidence            3678888865    457899999999999999999999763

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

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

Probab=98.24  E-value=4.9e-06  Score=48.72  Aligned_cols=59  Identities=12%  Similarity=0.252  Sum_probs=39.0

Q ss_pred             hhhhcCCEEEEEEcCCeEEEEEEEEECC---CCceEEcceEEecCc--------eeeeecEEEEcCCcEE
Q 034895           10 LKKYMDKKLQIKLNANRMIVGTLRGFDQ---FMNLVIDNTVEVNGN--------EKNDIGMVVIRGNSVV   68 (80)
Q Consensus        10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~---~~NlvL~~~~e~~~~--------~~~~~g~v~IrG~~I~   68 (80)
                      +..++|++|.|+++||..|+|.|.+++.   .+.++|+-+......        .......++|+++.|+
T Consensus         7 ~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv   76 (77)
T PF14438_consen    7 LTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV   76 (77)
T ss_dssp             HHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred             HHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence            4678999999999999999999999998   899999998876421        1123456777776664

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

Probab=97.88  E-value=9.2e-05  Score=45.62  Aligned_cols=66  Identities=17%  Similarity=0.337  Sum_probs=53.8

Q ss_pred             hhhcCCEEEEEEcCCeEEEEEEEEEC-CCCceEEcceEEecCc----------eeeeecEEEEcCCcEEEEEecCCc
Q 034895           11 KKYMDKKLQIKLNANRMIVGTLRGFD-QFMNLVIDNTVEVNGN----------EKNDIGMVVIRGNSVVTVEALEPV   76 (80)
Q Consensus        11 ~~~~~k~V~V~l~~g~~~~G~L~~~D-~~~NlvL~~~~e~~~~----------~~~~~g~v~IrG~~I~~I~~~d~~   76 (80)
                      .+|+|++|.+..+.+-.|+|+|..+| +...+.|+|+..+..+          ...-+..+..||+.|.-+...+..
T Consensus         4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~   80 (96)
T PF12701_consen    4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPP   80 (96)
T ss_dssp             CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S
T ss_pred             ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCC
Confidence            46899999999999999999999999 5899999999875311          112468999999999999876653

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

Probab=97.39  E-value=0.00044  Score=46.42  Aligned_cols=64  Identities=28%  Similarity=0.416  Sum_probs=47.3

Q ss_pred             CCCchhhhcCCEEEEEEcCCeEEEEEEEEEC-CCCceEEcceEEecCceeeeecEEEEcCCcEEEEEecCC
Q 034895            6 QPPDLKKYMDKKLQIKLNANRMIVGTLRGFD-QFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALEP   75 (80)
Q Consensus         6 ~p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D-~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~d~   75 (80)
                      .|+.+..|++|.|.|.+.| +++.|.|..+| -..|+||-+-.|. +  .  ...-+|-|-+|..|...++
T Consensus         8 ~p~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e~-~--~--~sv~~I~ghaVk~vevl~~   72 (166)
T PF06372_consen    8 SPLEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQED-G--K--RSVKVIMGHAVKSVEVLSE   72 (166)
T ss_dssp             -HHHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-TT-S-----EEEEEE-GGGEEEEEEEE-
T ss_pred             CHHHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEcccC-C--c--eeEEEEEccceEEEEEccC
Confidence            5788999999999999999 99999999999 6789999876552 2  1  2368899999999987664

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.

>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=96.97  E-value=0.0075  Score=35.61  Aligned_cols=59  Identities=14%  Similarity=0.266  Sum_probs=46.0

Q ss_pred             hhhcCCEEEEEEcCCeEEEEEEEEEC-CCCceEEcceEEecCc-----------eeeeecEEEEcCCcEEE
Q 034895           11 KKYMDKKLQIKLNANRMIVGTLRGFD-QFMNLVIDNTVEVNGN-----------EKNDIGMVVIRGNSVVT   69 (80)
Q Consensus        11 ~~~~~k~V~V~l~~g~~~~G~L~~~D-~~~NlvL~~~~e~~~~-----------~~~~~g~v~IrG~~I~~   69 (80)
                      .+++|+++.+..+.+-.|+|+|..+| +..-+.|.|+..+..+           ...-+..+..||+.|.-
T Consensus         2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD   72 (74)
T cd01736           2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD   72 (74)
T ss_pred             ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence            36899999999999999999999999 6677889998765311           11235678888888753

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

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

Probab=96.82  E-value=0.0049  Score=33.01  Aligned_cols=34  Identities=15%  Similarity=0.276  Sum_probs=29.6

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceE
Q 034895           13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTV   47 (80)
Q Consensus        13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~   47 (80)
                      .+|++|++.+ ++..++|+..++|++..|+++...
T Consensus         1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~   34 (48)
T PF02237_consen    1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTED   34 (48)
T ss_dssp             STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETT
T ss_pred             CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECC
Confidence            3789999999 667779999999999999997653

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 ....

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

Probab=96.79  E-value=0.012  Score=35.28  Aligned_cols=60  Identities=17%  Similarity=0.234  Sum_probs=45.3

Q ss_pred             hhhhcCCEEEEEEcCCeEEEEEEEEEC-CCCceEEcceEEecCceeeeecEEEEcCCcEEEEEec
Q 034895           10 LKKYMDKKLQIKLNANRMIVGTLRGFD-QFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEAL   73 (80)
Q Consensus        10 L~~~~~k~V~V~l~~g~~~~G~L~~~D-~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~   73 (80)
                      |..+.|++|.+.|.++....|++.++| ...|+..+|-.--.|    ..+...+|.+.|++++..
T Consensus        19 l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~TPlG----v~~eAlLR~~DVi~~~f~   79 (80)
T PF11095_consen   19 LLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQTPLG----VQPEALLRCSDVISISFD   79 (80)
T ss_dssp             HHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEETTTT----EEEEEEEEGGGEEEEEE-
T ss_pred             HHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcCCCcc----cChhheeecCCEEEEEec
Confidence            556679999999999999999999999 667777766543223    257899999999998764

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.

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

Probab=96.60  E-value=0.015  Score=33.11  Aligned_cols=36  Identities=11%  Similarity=0.162  Sum_probs=30.9

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEE
Q 034895           13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE   48 (80)
Q Consensus        13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e   48 (80)
                      .+|..|++++..|..++|.+.+||...+++.-.+.+
T Consensus         4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s   39 (61)
T cd01735           4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS   39 (61)
T ss_pred             ccccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence            478999999999999999999999888887665544

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.

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=96.53  E-value=0.0062  Score=36.37  Aligned_cols=31  Identities=23%  Similarity=0.384  Sum_probs=27.4

Q ss_pred             CCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034895           15 DKKLQIKLNANRMIVGTLRGFDQFMNLVIDN   45 (80)
Q Consensus        15 ~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~   45 (80)
                      ..+|.|.|.||-.+.|.+.+||+|.=++-.+
T Consensus        19 ~~~VtifL~NG~~l~G~I~~fD~ftVll~~~   49 (79)
T PRK00395         19 RVPVTIYLVNGIKLQGQIESFDNFVVLLRNT   49 (79)
T ss_pred             CCCEEEEEeCCcEEEEEEEEEccEEEEEEEC
Confidence            5689999999999999999999998666555

>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=96.37  E-value=0.0084  Score=34.17  Aligned_cols=32  Identities=22%  Similarity=0.336  Sum_probs=27.2

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034895           14 MDKKLQIKLNANRMIVGTLRGFDQFMNLVIDN   45 (80)
Q Consensus        14 ~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~   45 (80)
                      -..+|.|.|.||-.++|.+.+||+|.=++-.+
T Consensus        10 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   41 (61)
T cd01716          10 EKIPVTIYLVNGVQLKGQIESFDNFTVLLESD   41 (61)
T ss_pred             cCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence            35689999999999999999999998665444

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=0.0095  Score=33.96  Aligned_cols=31  Identities=19%  Similarity=0.321  Sum_probs=26.9

Q ss_pred             CCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034895           15 DKKLQIKLNANRMIVGTLRGFDQFMNLVIDN   45 (80)
Q Consensus        15 ~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~   45 (80)
                      ..+|.|.|.||-.+.|.+.+||+|.=++-.+
T Consensus        15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~   45 (61)
T TIGR02383        15 RIPVTVFLVNGVQLKGVIESFDNFTVLLESQ   45 (61)
T ss_pred             CCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence            5689999999999999999999998666544

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.

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

Probab=96.24  E-value=0.033  Score=32.19  Aligned_cols=50  Identities=16%  Similarity=0.233  Sum_probs=38.9

Q ss_pred             hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcCCcEEEEE
Q 034895           10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVE   71 (80)
Q Consensus        10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~   71 (80)
                      |++++|++|.|.+..|.. +|+|.+.-.. .++|+..          -...|||=.+|++|.
T Consensus        16 lq~liG~~vvV~T~~g~v-~G~L~~V~pD-hIvl~~~----------~~~~~IR~~~IV~v~   65 (66)
T PF10842_consen   16 LQSLIGQRVVVQTTRGSV-RGILVDVKPD-HIVLEEN----------GTPFFIRIAQIVWVM   65 (66)
T ss_pred             HHHhcCCEEEEEEcCCcE-EEEEEeecCC-EEEEEeC----------CcEEEEEeeeEEEEc
Confidence            889999999999987766 9999998744 3455432          137899999999885

>PRK14638 hypothetical protein; Provisional

Probab=96.04  E-value=0.01  Score=39.02  Aligned_cols=35  Identities=17%  Similarity=0.357  Sum_probs=30.0

Q ss_pred             chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEc
Q 034895            9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVID   44 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~   44 (80)
                      ++.+++|+.|.|++.+++.++|+|.++|.. ++.|.
T Consensus        94 ~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~  128 (150)
T PRK14638         94 DYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS  128 (150)
T ss_pred             HHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            477889999999999999999999999964 45554

>PRK14639 hypothetical protein; Provisional

Probab=95.63  E-value=0.019  Score=37.33  Aligned_cols=35  Identities=17%  Similarity=0.340  Sum_probs=30.2

Q ss_pred             chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEc
Q 034895            9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVID   44 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~   44 (80)
                      ++.+++|+.|.|++.+++.++|+|.++|.. ++.|.
T Consensus        82 ~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l~  116 (140)
T PRK14639         82 HFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITLE  116 (140)
T ss_pred             HHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            477889999999999999999999999984 55553

>PRK02001 hypothetical protein; Validated

Probab=95.57  E-value=0.02  Score=37.80  Aligned_cols=35  Identities=20%  Similarity=0.451  Sum_probs=30.2

Q ss_pred             chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEc
Q 034895            9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVID   44 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~   44 (80)
                      ++.+++|+.|.|++.+++.++|+|.++|.. ++.|.
T Consensus        84 ~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l~  118 (152)
T PRK02001         84 QYKKNIGRELEVLTKNGKKIEGELKSADEN-DITLE  118 (152)
T ss_pred             HHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEEE
Confidence            477889999999999999999999999975 55553

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

Probab=95.18  E-value=0.038  Score=32.77  Aligned_cols=25  Identities=24%  Similarity=0.389  Sum_probs=23.5

Q ss_pred             CCEEEEEEcCCeEEEEEEEEECCCC
Q 034895           15 DKKLQIKLNANRMIVGTLRGFDQFM   39 (80)
Q Consensus        15 ~k~V~V~l~~g~~~~G~L~~~D~~~   39 (80)
                      ..+|.|-|.||-.+.|.+.+||+|.
T Consensus        19 ~i~VtIfLvNG~~L~G~V~sfD~f~   43 (77)
T COG1923          19 KIPVTIFLVNGFKLQGQVESFDNFV   43 (77)
T ss_pred             CCeEEEEEEcCEEEEEEEEeeeeEE
Confidence            6689999999999999999999986

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

Probab=94.57  E-value=0.064  Score=31.65  Aligned_cols=35  Identities=26%  Similarity=0.472  Sum_probs=28.3

Q ss_pred             chhhhcCCEEEEEEc---CC-eEEEEEEEEECCCCceEEc
Q 034895            9 DLKKYMDKKLQIKLN---AN-RMIVGTLRGFDQFMNLVID   44 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~---~g-~~~~G~L~~~D~~~NlvL~   44 (80)
                      ++..++|+.|.|+++   +| +.++|.|.++|.. ++.|.
T Consensus        19 ~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l~   57 (83)
T cd01734          19 DFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTLE   57 (83)
T ss_pred             HHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEEE
Confidence            477889999999997   55 6899999999985 45553

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=94.46  E-value=0.093  Score=34.48  Aligned_cols=35  Identities=17%  Similarity=0.413  Sum_probs=28.9

Q ss_pred             chhhhcCCEEEEEE----cCCeEEEEEEEEECCCCceEEc
Q 034895            9 DLKKYMDKKLQIKL----NANRMIVGTLRGFDQFMNLVID   44 (80)
Q Consensus         9 ~L~~~~~k~V~V~l----~~g~~~~G~L~~~D~~~NlvL~   44 (80)
                      ++.+++|+.|.|++    .+++.++|+|.++|.. ++.|.
T Consensus        91 ~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~  129 (152)
T PRK14640         91 QFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT  129 (152)
T ss_pred             HHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence            47788999999999    5679999999999874 55554

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=94.36  E-value=0.11  Score=34.87  Aligned_cols=32  Identities=19%  Similarity=0.259  Sum_probs=27.1

Q ss_pred             CCEEEEEEcCCeEEEEEEEEECCCCceEEcce
Q 034895           15 DKKLQIKLNANRMIVGTLRGFDQFMNLVIDNT   46 (80)
Q Consensus        15 ~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~   46 (80)
                      ..+|.|.|.+|-.++|++.+||+|.=+.-.+.
T Consensus        24 k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g   55 (165)
T PRK14091         24 KTPVTMFLVKGVKLQGIITWFDNFSILLRRDG   55 (165)
T ss_pred             CCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            45899999999999999999999976665453

>PRK14644 hypothetical protein; Provisional

Probab=94.13  E-value=0.16  Score=32.94  Aligned_cols=35  Identities=17%  Similarity=0.361  Sum_probs=29.6

Q ss_pred             chhhhcCCEEEEEEcCC----eEEEEEEEEECCCCceEEc
Q 034895            9 DLKKYMDKKLQIKLNAN----RMIVGTLRGFDQFMNLVID   44 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~g----~~~~G~L~~~D~~~NlvL~   44 (80)
                      ++.+++|+.|.|++++.    +.++|+|.++|.. ++.|.
T Consensus        79 ~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~  117 (136)
T PRK14644         79 ELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK  117 (136)
T ss_pred             HHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            37788999999999886    9999999999974 56664

>PRK14633 hypothetical protein; Provisional

Probab=93.84  E-value=0.11  Score=34.12  Aligned_cols=35  Identities=9%  Similarity=0.209  Sum_probs=28.6

Q ss_pred             chhhhcCCEEEEEE----cCCeEEEEEEEEECCCCceEEc
Q 034895            9 DLKKYMDKKLQIKL----NANRMIVGTLRGFDQFMNLVID   44 (80)
Q Consensus         9 ~L~~~~~k~V~V~l----~~g~~~~G~L~~~D~~~NlvL~   44 (80)
                      ++.+++|+.|.|++    .+++.++|+|.++|+. ++.|.
T Consensus        88 ~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~  126 (150)
T PRK14633         88 QAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN  126 (150)
T ss_pred             HHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence            47788999999999    4679999999999874 55553

>PRK14642 hypothetical protein; Provisional

Probab=93.68  E-value=0.11  Score=35.77  Aligned_cols=34  Identities=21%  Similarity=0.370  Sum_probs=28.7

Q ss_pred             chhhhcCCEEEEEEc-------------CCeEEEEEEEEECCCCceEE
Q 034895            9 DLKKYMDKKLQIKLN-------------ANRMIVGTLRGFDQFMNLVI   43 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~-------------~g~~~~G~L~~~D~~~NlvL   43 (80)
                      ++.+++|+.|.|+|+             +.+.|+|+|.++|.. ++.|
T Consensus        94 df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l  140 (197)
T PRK14642         94 DFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI  140 (197)
T ss_pred             HHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence            467889999999998             679999999999974 5555

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=93.51  E-value=0.14  Score=33.45  Aligned_cols=35  Identities=17%  Similarity=0.500  Sum_probs=28.3

Q ss_pred             CchhhhcCCEEEEEE----cCCeEEEEEEEEECCCCceEE
Q 034895            8 PDLKKYMDKKLQIKL----NANRMIVGTLRGFDQFMNLVI   43 (80)
Q Consensus         8 ~~L~~~~~k~V~V~l----~~g~~~~G~L~~~D~~~NlvL   43 (80)
                      .++.+++|+.|.|++    .+++.++|+|.++|... +.|
T Consensus        91 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~~-i~l  129 (154)
T PRK00092         91 RDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGET-VTL  129 (154)
T ss_pred             HHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCCE-EEE
Confidence            347888999999997    56799999999999742 444

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

Probab=93.42  E-value=0.35  Score=36.16  Aligned_cols=65  Identities=14%  Similarity=0.212  Sum_probs=52.1

Q ss_pred             hhhcCCEEEEEEcCCeEEEEEEEEEC-CCCceEEcceEEecCc-----------eeeeecEEEEcCCcEEEEEecCC
Q 034895           11 KKYMDKKLQIKLNANRMIVGTLRGFD-QFMNLVIDNTVEVNGN-----------EKNDIGMVVIRGNSVVTVEALEP   75 (80)
Q Consensus        11 ~~~~~k~V~V~l~~g~~~~G~L~~~D-~~~NlvL~~~~e~~~~-----------~~~~~g~v~IrG~~I~~I~~~d~   75 (80)
                      ..|||+.|.+.-+....|+|+|.-+| +..-|-|.++.-+..+           ...-+.-++.||+.|.-+...+.
T Consensus         5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~   81 (361)
T KOG1073|consen    5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQET   81 (361)
T ss_pred             cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccC
Confidence            46899999999999999999999999 8899999998543210           01146789999999997776554

>PRK14645 hypothetical protein; Provisional

Probab=93.40  E-value=0.12  Score=34.13  Aligned_cols=34  Identities=9%  Similarity=0.288  Sum_probs=27.8

Q ss_pred             chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEc
Q 034895            9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVID   44 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~   44 (80)
                      ++.+++|+.|.|++ +++.++|+|.++|.. .+.|.
T Consensus        96 df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l~  129 (154)
T PRK14645         96 HFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTFD  129 (154)
T ss_pred             HHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEEE
Confidence            46788999999986 789999999999874 45553

>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=93.27  E-value=0.12  Score=33.15  Aligned_cols=34  Identities=21%  Similarity=0.558  Sum_probs=25.6

Q ss_pred             chhhhcCCEEEEEEc----CCeEEEEEEEEECCCCceEE
Q 034895            9 DLKKYMDKKLQIKLN----ANRMIVGTLRGFDQFMNLVI   43 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~----~g~~~~G~L~~~D~~~NlvL   43 (80)
                      ++..++|+.|.|+++    +.+.++|+|.++|. -.++|
T Consensus        81 ~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l  118 (141)
T PF02576_consen   81 DFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL  118 (141)
T ss_dssp             HHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred             HHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence            477889999999994    45799999999998 45555

; PDB: 1IB8_A.

>PRK14636 hypothetical protein; Provisional

Probab=92.99  E-value=0.16  Score=34.30  Aligned_cols=35  Identities=23%  Similarity=0.455  Sum_probs=28.3

Q ss_pred             chhhhcCCEEEEEEc---CC-eEEEEEEEEECCCCceEEc
Q 034895            9 DLKKYMDKKLQIKLN---AN-RMIVGTLRGFDQFMNLVID   44 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~---~g-~~~~G~L~~~D~~~NlvL~   44 (80)
                      ++.+++|+.|.|+++   +| +.++|+|.++|.. ++.|.
T Consensus        92 df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l~  130 (176)
T PRK14636         92 DFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTIA  130 (176)
T ss_pred             HHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEEE
Confidence            477889999999997   55 7999999999874 45553

>PRK14632 hypothetical protein; Provisional

Probab=92.90  E-value=0.17  Score=33.93  Aligned_cols=35  Identities=17%  Similarity=0.402  Sum_probs=28.7

Q ss_pred             chhhhcCCEEEEEEcC-------CeEEEEEEEEECCCCceEEc
Q 034895            9 DLKKYMDKKLQIKLNA-------NRMIVGTLRGFDQFMNLVID   44 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~-------g~~~~G~L~~~D~~~NlvL~   44 (80)
                      ++.+++|+.|.|++.+       .+.++|+|.++|.. ++.|.
T Consensus        92 ~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~  133 (172)
T PRK14632         92 QMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR  133 (172)
T ss_pred             HHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence            4778899999999975       58999999999863 55554

>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=92.86  E-value=0.27  Score=32.60  Aligned_cols=34  Identities=15%  Similarity=0.459  Sum_probs=29.3

Q ss_pred             hhhhcCCEEEEEE----cCCeEEEEEEEEECCCCceEEc
Q 034895           10 LKKYMDKKLQIKL----NANRMIVGTLRGFDQFMNLVID   44 (80)
Q Consensus        10 L~~~~~k~V~V~l----~~g~~~~G~L~~~D~~~NlvL~   44 (80)
                      +..++|+.|.|+|    .+++.++|+|.++|+.. +++.
T Consensus        94 f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~~  131 (153)
T COG0779          94 FARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTLE  131 (153)
T ss_pred             HHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEEE
Confidence            6778999999999    78999999999999887 4443

>PRK14634 hypothetical protein; Provisional

Probab=92.70  E-value=0.2  Score=33.08  Aligned_cols=35  Identities=14%  Similarity=0.256  Sum_probs=28.0

Q ss_pred             chhhhcCCEEEEEEcC----CeEEEEEEEEECCCCceEEc
Q 034895            9 DLKKYMDKKLQIKLNA----NRMIVGTLRGFDQFMNLVID   44 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~----g~~~~G~L~~~D~~~NlvL~   44 (80)
                      ++.+++|+.|.|++.+    .+.|+|+|.++|.. ++.|.
T Consensus        94 ~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l~  132 (155)
T PRK14634         94 DFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQIN  132 (155)
T ss_pred             HHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEEE
Confidence            4778899999999964    38999999999974 45553

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=92.62  E-value=0.23  Score=33.36  Aligned_cols=31  Identities=23%  Similarity=0.382  Sum_probs=27.1

Q ss_pred             CCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034895           15 DKKLQIKLNANRMIVGTLRGFDQFMNLVIDN   45 (80)
Q Consensus        15 ~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~   45 (80)
                      ..+|.|.|.||-.++|.+.+||+|.=+.-.+
T Consensus       104 k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~  134 (165)
T PRK14091        104 GEPVTMFLVNGVMLQGEIAAFDLFCMLLERD  134 (165)
T ss_pred             CCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence            5689999999999999999999998666555

>PRK14643 hypothetical protein; Provisional

Probab=92.27  E-value=0.29  Score=32.63  Aligned_cols=30  Identities=17%  Similarity=0.298  Sum_probs=26.1

Q ss_pred             chhhhcCCEEEEEEcC----CeEEEEEEEEECCC
Q 034895            9 DLKKYMDKKLQIKLNA----NRMIVGTLRGFDQF   38 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~----g~~~~G~L~~~D~~   38 (80)
                      ++..++|+.|.|++..    .+.++|+|.++|..
T Consensus        98 df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T PRK14643         98 ELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN  131 (164)
T ss_pred             HHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence            4778899999999965    69999999999965

>PRK14647 hypothetical protein; Provisional

Probab=92.18  E-value=0.25  Score=32.66  Aligned_cols=34  Identities=18%  Similarity=0.436  Sum_probs=27.3

Q ss_pred             chhhhcCCEEEEEEc---------CCeEEEEEEEEECCCCceEE
Q 034895            9 DLKKYMDKKLQIKLN---------ANRMIVGTLRGFDQFMNLVI   43 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~---------~g~~~~G~L~~~D~~~NlvL   43 (80)
                      ++.+++|+.|.|+++         +.+.++|+|.++|.. .+.|
T Consensus        93 ~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~-~v~l  135 (159)
T PRK14647         93 DYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADG-VVTI  135 (159)
T ss_pred             HHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecCC-EEEE
Confidence            477889999999995         359999999999863 4444

>PRK14646 hypothetical protein; Provisional

Probab=91.90  E-value=0.28  Score=32.38  Aligned_cols=35  Identities=23%  Similarity=0.346  Sum_probs=28.1

Q ss_pred             chhhhcCCEEEEEEcC----CeEEEEEEEEECCCCceEEc
Q 034895            9 DLKKYMDKKLQIKLNA----NRMIVGTLRGFDQFMNLVID   44 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~----g~~~~G~L~~~D~~~NlvL~   44 (80)
                      ++..++|+.|.|+|.+    -+.++|+|.++|.. ++.|.
T Consensus        94 df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~  132 (155)
T PRK14646         94 DFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN  132 (155)
T ss_pred             HHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            4778899999999954    37889999999985 55553

>PRK14631 hypothetical protein; Provisional

Probab=91.43  E-value=0.32  Score=32.75  Aligned_cols=34  Identities=18%  Similarity=0.408  Sum_probs=27.6

Q ss_pred             chhhhcCCEEEEEEc----CCeEEEEEEEEEC--CCCceEE
Q 034895            9 DLKKYMDKKLQIKLN----ANRMIVGTLRGFD--QFMNLVI   43 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~----~g~~~~G~L~~~D--~~~NlvL   43 (80)
                      ++.+++|+.|.|++.    +.+.++|+|.++|  . .++.|
T Consensus       111 df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~-~~v~l  150 (174)
T PRK14631        111 QLQGYIGQQVALRLIAAVENRRKFQAKLLAVDLEN-EEIQV  150 (174)
T ss_pred             HHHHhCCCeEEEEEecccCCceEEEEEEEEeecCC-CEEEE
Confidence            477889999999995    4699999999998  4 35554

>PRK14637 hypothetical protein; Provisional

Probab=91.24  E-value=0.33  Score=31.98  Aligned_cols=35  Identities=17%  Similarity=0.363  Sum_probs=27.1

Q ss_pred             chhhhcCCEEEEEEcCCeEE-EEEEEEECCCCceEEc
Q 034895            9 DLKKYMDKKLQIKLNANRMI-VGTLRGFDQFMNLVID   44 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~g~~~-~G~L~~~D~~~NlvL~   44 (80)
                      ++..++|+.|.|++.+...+ +|+|.++|.. ++.|.
T Consensus        92 ~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~  127 (151)
T PRK14637         92 EFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT  127 (151)
T ss_pred             HHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence            47788999999999544555 7999999875 55554

>PRK06955 biotin--protein ligase; Provisional

Probab=90.67  E-value=2.2  Score=30.63  Aligned_cols=33  Identities=18%  Similarity=0.414  Sum_probs=28.8

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034895           13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDN   45 (80)
Q Consensus        13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~   45 (80)
                      ++|++|+|...+++.++|++.++|....|+++.
T Consensus       247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~  279 (300)
T PRK06955        247 YAGREVVLLEDGAELARGVAHGIDETGQLLLDT  279 (300)
T ss_pred             cCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence            478999997667788999999999999999963

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

Probab=90.64  E-value=1.8  Score=31.01  Aligned_cols=47  Identities=19%  Similarity=0.512  Sum_probs=33.8

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCc-eeeeecEEEEcC
Q 034895           13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGN-EKNDIGMVVIRG   64 (80)
Q Consensus        13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~-~~~~~g~v~IrG   64 (80)
                      ++|++|.+... +..++|++.++|....|+++.    .+. +.-..|.+.+|.
T Consensus       270 ~~g~~v~~~~~-~~~~~G~~~gi~~~G~L~i~~----~g~~~~~~~gev~~~~  317 (319)
T PRK11886        270 FLGREVKLIIG-DKEISGIARGIDEQGALLLED----DGVEKPFNGGEISLRS  317 (319)
T ss_pred             ccCCeEEEEeC-CcEEEEEEEEECCCceEEEEe----CCcEEEEEEeEEEEec
Confidence            47999999874 467999999999999999962    122 222346666554

>PRK14641 hypothetical protein; Provisional

Probab=90.13  E-value=0.44  Score=32.13  Aligned_cols=28  Identities=11%  Similarity=0.305  Sum_probs=24.0

Q ss_pred             chhhhcCCEEEEEEcC----CeEEEEEEEEEC
Q 034895            9 DLKKYMDKKLQIKLNA----NRMIVGTLRGFD   36 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~----g~~~~G~L~~~D   36 (80)
                      ++.+++|+.|.|++.+    .+.++|+|.++|
T Consensus        98 ~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~  129 (173)
T PRK14641         98 QYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS  129 (173)
T ss_pred             HHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence            3678899999999965    568999999995

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

Probab=89.33  E-value=0.67  Score=30.95  Aligned_cols=34  Identities=12%  Similarity=0.137  Sum_probs=30.9

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEECCCCceEEcceE
Q 034895           14 MDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTV   47 (80)
Q Consensus        14 ~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~   47 (80)
                      -+-+|+|.+.||..+.|.+.+|+.--|.+|.-+.
T Consensus        28 ~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~   61 (165)
T PF03614_consen   28 NDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP   61 (165)
T ss_pred             cCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence            4668999999999999999999999999998664

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

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

Probab=88.01  E-value=0.6  Score=24.65  Aligned_cols=21  Identities=19%  Similarity=0.455  Sum_probs=14.5

Q ss_pred             EEEEEEEECCCCceEEcceEE
Q 034895           28 IVGTLRGFDQFMNLVIDNTVE   48 (80)
Q Consensus        28 ~~G~L~~~D~~~NlvL~~~~e   48 (80)
                      .+|++.++|+.+.+.|++...
T Consensus        10 ~tGtFlGvDE~FGmLLr~~~~   30 (42)
T PF14563_consen   10 LTGTFLGVDEDFGMLLRDDDT   30 (42)
T ss_dssp             EEEEEEEE-TT--EEEE-SS-
T ss_pred             cceeEEeeccccceEEEeCCc
Confidence            689999999999999998654

>PRK14635 hypothetical protein; Provisional

Probab=87.49  E-value=1.3  Score=29.33  Aligned_cols=36  Identities=11%  Similarity=0.178  Sum_probs=27.9

Q ss_pred             CchhhhcCCEEEEEEc--CCeEEEE---EEEEECCCCceEEc
Q 034895            8 PDLKKYMDKKLQIKLN--ANRMIVG---TLRGFDQFMNLVID   44 (80)
Q Consensus         8 ~~L~~~~~k~V~V~l~--~g~~~~G---~L~~~D~~~NlvL~   44 (80)
                      .++..+.|+.|.|++.  ++..+.|   +|.++|.. ++.|.
T Consensus        92 ~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l~  132 (162)
T PRK14635         92 EDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVELE  132 (162)
T ss_pred             HHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEEE
Confidence            3478889999999885  4678888   99999874 55553

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

Probab=87.07  E-value=4.2  Score=32.13  Aligned_cols=33  Identities=18%  Similarity=0.257  Sum_probs=28.9

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034895           13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDN   45 (80)
Q Consensus        13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~   45 (80)
                      ++|++|.+...+++.++|+..++|....|+|+.
T Consensus       276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~  308 (592)
T PRK13325        276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET  308 (592)
T ss_pred             cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence            479999987677778999999999999999964

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

Probab=87.03  E-value=0.76  Score=30.71  Aligned_cols=32  Identities=22%  Similarity=0.401  Sum_probs=25.4

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEEC-CCCceEEcc
Q 034895           14 MDKKLQIKLNANRMIVGTLRGFD-QFMNLVIDN   45 (80)
Q Consensus        14 ~~k~V~V~l~~g~~~~G~L~~~D-~~~NlvL~~   45 (80)
                      .|+.|+|.+.|||+++|.-.|.| ...-+.+.|
T Consensus       119 qg~sIrVyM~DgR~ieG~stGvnacqVgl~~~~  151 (165)
T PF03614_consen  119 QGKSIRVYMADGREIEGKSTGVNACQVGLILPN  151 (165)
T ss_pred             CCCeEEEEEcCCcEEEeeecccceEEEEEEcCC
Confidence            48899999999999999999988 334444443

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

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

Probab=86.90  E-value=4.6  Score=27.78  Aligned_cols=31  Identities=19%  Similarity=0.360  Sum_probs=27.1

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEECCCCceEEc
Q 034895           13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVID   44 (80)
Q Consensus        13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~   44 (80)
                      ++|++|.+...+ ..++|++.++|....|+++
T Consensus       191 ~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~  221 (237)
T TIGR00121       191 HIGREVSLTTGN-GEIEGIARGIDKDGALLLE  221 (237)
T ss_pred             ccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence            469999998754 5699999999999999997

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

>PRK08330 biotin--protein ligase; Provisional

Probab=86.00  E-value=4.3  Score=27.93  Aligned_cols=33  Identities=18%  Similarity=0.358  Sum_probs=27.2

Q ss_pred             hcCCEEEEEEcCCeEE-EEEEEEECCCCceEEcce
Q 034895           13 YMDKKLQIKLNANRMI-VGTLRGFDQFMNLVIDNT   46 (80)
Q Consensus        13 ~~~k~V~V~l~~g~~~-~G~L~~~D~~~NlvL~~~   46 (80)
                      ++|++|.+.. ++..+ +|++.++|....|+++..
T Consensus       186 ~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~~  219 (236)
T PRK08330        186 ILGKRVKIIG-DGEILVEGIAEDIDEFGALILRLD  219 (236)
T ss_pred             hcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEEC
Confidence            5799999976 55554 799999999999999753

>PRK14630 hypothetical protein; Provisional

Probab=83.90  E-value=1.7  Score=28.30  Aligned_cols=34  Identities=15%  Similarity=0.299  Sum_probs=26.2

Q ss_pred             chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEc
Q 034895            9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVID   44 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~   44 (80)
                      ++.+++|++|.|++.. ...+|+|.++|. -++.|.
T Consensus        91 df~r~~G~~v~V~l~~-~~~~G~L~~~~d-~~i~l~  124 (143)
T PRK14630         91 EFKIFEGKKIKLMLDN-DFEEGFILEAKA-DSFIFK  124 (143)
T ss_pred             HHHHhCCCEEEEEEcC-cceEEEEEEEeC-CEEEEE
Confidence            4678899999999965 445999999987 345553

>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional

Probab=81.96  E-value=4.2  Score=29.08  Aligned_cols=31  Identities=35%  Similarity=0.439  Sum_probs=27.3

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034895           14 MDKKLQIKLNANRMIVGTLRGFDQFMNLVIDN   45 (80)
Q Consensus        14 ~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~   45 (80)
                      +|+.|.|.. ++..+.|++.++|....|+++.
T Consensus       236 ~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~  266 (285)
T PTZ00275        236 KDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR  266 (285)
T ss_pred             CCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence            689999875 5688999999999999999974

>PRK10139 serine endoprotease; Provisional

Probab=81.65  E-value=8.7  Score=29.25  Aligned_cols=59  Identities=20%  Similarity=0.169  Sum_probs=39.4

Q ss_pred             CEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeec--EEEEcCCcEEEEEecC
Q 034895           16 KKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIG--MVVIRGNSVVTVEALE   74 (80)
Q Consensus        16 k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g--~v~IrG~~I~~I~~~d   74 (80)
                      ..+.|++.||+.+.+++.++|....|-+-.......-..-.++  .-+-.|+.|..|..|-
T Consensus       115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~~~~~l~~~~lg~s~~~~~G~~V~aiG~P~  175 (455)
T PRK10139        115 QKISIQLNDGREFDAKLIGSDDQSDIALLQIQNPSKLTQIAIADSDKLRVGDFAVAVGNPF  175 (455)
T ss_pred             CEEEEEECCCCEEEEEEEEEcCCCCEEEEEecCCCCCceeEecCccccCCCCEEEEEecCC
Confidence            5799999999999999999999999988776431111111222  1233466666666553

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	80
3cw1_G	76	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		2e-20
3swn_C	117	Structure Of The Lsm657 Complex: An Assembly Interm		7e-09
4emk_C	113	Crystal Structure Of Splsm567 Length = 113		5e-08
3bw1_A	96	Crystal Structure Of Homomeric Yeast Lsm3 Exhibitin		2e-05
1th7_A	81	Crystal Structure Of An Archaeal Sm Protein From Su		4e-05
1ljo_A	77	Crystal Structure Of An Sm-Like Protein (Af-Sm2) Fr		4e-05
3swn_B	77	Structure Of The Lsm657 Complex: An Assembly Interm		5e-05
1d3b_B	91	Crystal Structure Of The D3b Subcomplex Of The Huma		7e-05
2y9a_A	95	Structure Of The Spliceosomal U4 Snrnp Core Domain		7e-05
3cw1_A	174	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		8e-05
3pgw_B	231	Crystal Structure Of Human U1 Snrnp Length = 231		8e-05
1i5l_A	77	Crystal Structure Of An Sm-Like Protein (Af-Sm1) Fr		1e-04
4emk_B	75	Crystal Structure Of Splsm567 Length = 75		2e-04

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

Iteration: 1
 Score = 94.4 bits (233), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 47/77 (61%), Positives = 60/77 (77%), Gaps = 2/77 (2%)
Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV-NGNEKNDIGM 59
          MS++  PP+LKK+MDKKL +KLN  R + G LRGFD FMNLVID  VE+    ++N+IGM
Sbjct: 1  MSKA-HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGM 59
Query: 60 VVIRGNSVVTVEALEPV 76
          VVIRGNS++ +EALE V
Sbjct: 60 VVIRGNSIIMLEALERV 76

>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 = 55.5 bits (132), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 8/74 (10%)
Query: 9   DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKN--------DIGMV 60
           DL +Y D+++Q      R I G L+GFDQ MNLV+D+  E   N ++         +G+V
Sbjct: 31  DLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLV 90
Query: 61  VIRGNSVVTVEALE 74
           V+RG ++V +  ++
Sbjct: 91  VVRGTTLVLIAPMD 104

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 8/70 (11%)
Query: 9  DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKN--------DIGMV 60
          DL +Y D+++Q      R I G L+GFDQ  NLV+D+  E   N ++         +G+V
Sbjct: 27 DLSRYQDQRIQATFTGGRQITGILKGFDQLXNLVLDDVEEQLRNPEDGKLTGAIRKLGLV 86
Query: 61 VIRGNSVVTV 70
          V+RG ++V +
Sbjct: 87 VVRGTTLVLI 96

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 9/73 (12%)
Query: 7  PPDLKKY-MDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE----VNGNEKND----I 57
          P DL K  +D+++ IKL   R +VGTL+ FD   N+V+ + VE    +N  E ++     
Sbjct: 11 PLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRC 70
Query: 58 GMVVIRGNSVVTV 70
           MV IRG++V  +
Sbjct: 71 EMVFIRGDTVTLI 83

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/66 (31%), Positives = 41/66 (62%), Gaps = 1/66 (1%)
Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGN-EKNDIGMVVIRGNSVV 68
          L + ++  + +KL  N+ + G LR +DQ MNLV+ ++ E+  +     +G +VIRG++V+
Sbjct: 14 LAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVI 73
Query: 69 TVEALE 74
           +  L+
Sbjct: 74 LISPLQ 79

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 28 IVGTLRGFDQFMNLVIDNTVEVNGNEK-NDIGMVVIRGNSVVTVEALE 74
          +VG L G D +MNL + N +E  G EK   +G +V+RGN+VV ++  E
Sbjct: 29 LVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQPQE 76

>pdb|3SWN|B Chain B, Structure Of The Lsm657 Complex: An Assembly Intermediate Of The Lsm1 7 And Lsm2 8 Rings Length = 77

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 27/66 (40%), Positives = 39/66 (59%), Gaps = 1/66 (1%)
Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIGMVVIRGNSVV 68
          L K + KK+ I+L++     G L   D +MNL ++ T E VNG + N  G   IRGN+V+
Sbjct: 11 LNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIRGNNVL 70
Query: 69 TVEALE 74
           V AL+
Sbjct: 71 YVSALD 76

>pdb|1D3B|B Chain B, Crystal Structure Of The D3b Subcomplex Of The Human Core Snrnp Domain At 2.0a Resolution Length = 91

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 23/84 (27%), Positives = 45/84 (53%), Gaps = 13/84 (15%)
Query: 5  GQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVI-----------DNTVEVNGNE 53
          G+   + +++D +++  L   R+ +GT + FD+ MNL++            N+ +    E
Sbjct: 4  GKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREE 63
Query: 54 KNDIGMVVIRGNSVV--TVEALEP 75
          K  +G+V++RG ++V  TVE   P
Sbjct: 64 KRVLGLVLLRGENLVSMTVEGPPP 87

>pdb|2Y9A|A Chain A, Structure Of The Spliceosomal U4 Snrnp Core Domain Length = 95

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 23/84 (27%), Positives = 45/84 (53%), Gaps = 13/84 (15%)
Query: 5  GQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVI-----------DNTVEVNGNE 53
          G+   + +++D +++  L   R+ +GT + FD+ MNL++            N+ +    E
Sbjct: 4  GKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREE 63
Query: 54 KNDIGMVVIRGNSVV--TVEALEP 75
          K  +G+V++RG ++V  TVE   P
Sbjct: 64 KRVLGLVLLRGENLVSMTVEGPPP 87

>pdb|3CW1|A Chain A, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 174

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 13/77 (16%)
Query: 12 KYMDKKLQIKLNANRMIVGTLRGFDQFMNLVI-----------DNTVEVNGNEKNDIGMV 60
          +++D +++  L   R+ +GT + FD+ MNL++            N+ +    EK  +G+V
Sbjct: 11 QHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLV 70
Query: 61 VIRGNSVV--TVEALEP 75
          ++RG ++V  TVE   P
Sbjct: 71 LLRGENLVSMTVEGPPP 87

>pdb|3PGW|B Chain B, Crystal Structure Of Human U1 Snrnp Length = 231

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 13/77 (16%)
Query: 12 KYMDKKLQIKLNANRMIVGTLRGFDQFMNLVI-----------DNTVEVNGNEKNDIGMV 60
          +++D +++  L   R+ +GT + FD+ MNL++            N+ +    EK  +G+V
Sbjct: 11 QHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLV 70
Query: 61 VIRGNSVV--TVEALEP 75
          ++RG ++V  TVE   P
Sbjct: 71 LLRGENLVSMTVEGPPP 87

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/62 (38%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV-NGNEKNDIGMVVIRGNSVV 68
          L + +   + ++L   R   GTL G+D  MNLV+ +  E+ NG     +G VVIRG++VV
Sbjct: 9  LNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVV 68
Query: 69 TV 70
           V
Sbjct: 69 FV 70

>pdb|4EMK|B Chain B, Crystal Structure Of Splsm567 Length = 75

Iteration: 1
 Score = 40.4 bits (93), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/66 (39%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIGMVVIRGNSVV 68
          L K + KK+ I+L++     G L   D + NL ++ T E VNG + N  G   IRGN+V+
Sbjct: 9  LNKVIGKKVLIRLSSGVDYKGILSCLDGYXNLALERTEEYVNGKKTNVYGDAFIRGNNVL 68
Query: 69 TVEALE 74
           V AL+
Sbjct: 69 YVSALD 74

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	80
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	5e-29
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	1e-27
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	1e-23
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	1e-23
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	2e-23
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	3e-22
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	5e-22
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	2e-21
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	4e-21
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	6e-21
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	5e-19
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	6e-19
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	2e-17
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	5e-17
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	5e-15
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	1e-14
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	4e-14
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-09
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	1e-08
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	8e-07
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	4e-06
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	6e-06
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	4e-05
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	1e-04

>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 = 97.8 bits (244), Expect = 5e-29
 Identities = 47/77 (61%), Positives = 58/77 (75%), Gaps = 2/77 (2%)

Query: 1  MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIGM 59
          MS+   PP+LKK+MDKKL +KLN  R + G LRGFD FMNLVID  VE     ++N+IGM
Sbjct: 1  MSK-AHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGM 59

Query: 60 VVIRGNSVVTVEALEPV 76
          VVIRGNS++ +EALE V
Sbjct: 60 VVIRGNSIIMLEALERV 76

>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 = 94.3 bits (235), Expect = 1e-27
 Identities = 21/70 (30%), Positives = 40/70 (57%), Gaps = 1/70 (1%)

Query: 7  PPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIGMVVIRGN 65
             L + ++  + +KL  N+ + G LR +DQ MNLV+ ++ E  +      +G +VIRG+
Sbjct: 11 HKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGD 70

Query: 66 SVVTVEALEP 75
          +V+ +  L+ 
Sbjct: 71 NVILISPLQT 80

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

 Score = 84.4 bits (209), Expect = 1e-23
 Identities = 19/67 (28%), Positives = 37/67 (55%)

Query: 8  PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSV 67
            L+  + K++ +KL  +  I G LR FDQ +NL++++  E+        G +V+RG +V
Sbjct: 14 ATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENV 73

Query: 68 VTVEALE 74
          + +  + 
Sbjct: 74 LFISPVP 80

>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 = 85.0 bits (210), Expect = 1e-23
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 8/80 (10%)

Query: 3   RSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE--------VNGNEK 54
           R     DL +Y D+++Q      R I G L+GFDQ MNLV+D+  E              
Sbjct: 21  RKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAI 80

Query: 55  NDIGMVVIRGNSVVTVEALE 74
             +G+VV+RG ++V +  ++
Sbjct: 81  RKLGLVVVRGTTLVLIAPMD 100

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

 Score = 83.5 bits (207), Expect = 2e-23
 Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 4  SGQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIGMVV 61
            +P D L + +   + ++L   R   GTL G+D  MNLV+ +  E  NG     +G VV
Sbjct: 2  PPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVV 61

Query: 62 IRGNSVVTVEALE 74
          IRG++VV V    
Sbjct: 62 IRGDTVVFVSPAP 74

>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 = 80.8 bits (200), Expect = 3e-22
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 4  SGQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIGMVV 61
          + +P D + + +DK + + L       G L G+D  +N+V+ +     +G      G +V
Sbjct: 2  AERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIV 61

Query: 62 IRGNSVVTVEALE 74
          IRG++V+ +   E
Sbjct: 62 IRGDNVLAISPTE 74

>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 = 80.1 bits (198), Expect = 5e-22
 Identities = 27/69 (39%), Positives = 39/69 (56%), Gaps = 1/69 (1%)

Query: 7  PPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIGMVVIRGN 65
             L K + KK+ I+L++     G L   D +MNL ++ T E VNG + N  G   IRGN
Sbjct: 6  NEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIRGN 65

Query: 66 SVVTVEALE 74
          +V+ V AL+
Sbjct: 66 NVLYVSALD 74

>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 = 79.1 bits (195), Expect = 2e-21
 Identities = 20/82 (24%), Positives = 43/82 (52%), Gaps = 11/82 (13%)

Query: 5  GQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-----------VNGNE 53
          G+   + +++D +++  L   R+ +GT + FD+ MNL++ +  E               E
Sbjct: 4  GKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREE 63

Query: 54 KNDIGMVVIRGNSVVTVEALEP 75
          K  +G+V++RG ++V++    P
Sbjct: 64 KRVLGLVLLRGENLVSMTVEGP 85

>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 = 78.2 bits (193), Expect = 4e-21
 Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 8/69 (11%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV--------NGNEKNDIGMVV 61
          LK  +D+++ IKL   R +VGTL+ FD   N+V+ + VE             +    MV 
Sbjct: 15 LKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVF 74

Query: 62 IRGNSVVTV 70
          IRG++V  +
Sbjct: 75 IRGDTVTLI 83

>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 = 77.4 bits (191), Expect = 6e-21
 Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 8  PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIGMVVIRGNS 66
            L   ++  + IKL  +R   G L+ FD  MNLV+++  E  +G     +G V+IRG++
Sbjct: 18 DALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDN 77

Query: 67 VVTV 70
          +V +
Sbjct: 78 IVYI 81

>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 = 72.3 bits (178), Expect = 5e-19
 Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 2/69 (2%)

Query: 8  PDLKKYMDKKLQIKLNANRM-IVGTLRGFDQFMNLVIDNTVEV-NGNEKNDIGMVVIRGN 65
            +K  + K +++++      +VG L G D +MNL + N +E     +   +G +V+RGN
Sbjct: 8  QMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGN 67

Query: 66 SVVTVEALE 74
          +VV ++  E
Sbjct: 68 NVVLIQPQE 76

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

 Score = 72.5 bits (178), Expect = 6e-19
 Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 2/76 (2%)

Query: 1  MSRSGQP-PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIG 58
          MS    P P L     K + +KL       G L   D +MN+ + NT E ++G     +G
Sbjct: 1  MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLG 60

Query: 59 MVVIRGNSVVTVEALE 74
           V+IR N+V+ +  +E
Sbjct: 61 EVLIRCNNVLYIRGVE 76

>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 = 68.7 bits (168), Expect = 2e-17
 Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 2/69 (2%)

Query: 8  PDLKKYMDKKLQIKLNANRM-IVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIGMVVIRGN 65
          P LK  ++ ++ +KL  N     GTL   D + NL ++   E V G     +G + IR N
Sbjct: 24 PFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCN 83

Query: 66 SVVTVEALE 74
          +V+ +  L 
Sbjct: 84 NVLYIRELP 92

>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 = 67.9 bits (166), Expect = 5e-17
 Identities = 15/75 (20%), Positives = 36/75 (48%), Gaps = 14/75 (18%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV--------------NGNEKN 55
          ++  +D+ + +KL  +R + G L  +D+ +N+V+ +  E+                  + 
Sbjct: 14 VRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRK 73

Query: 56 DIGMVVIRGNSVVTV 70
             M+ +RG+SV+ +
Sbjct: 74 HYEMLFVRGDSVILI 88

>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 = 62.6 bits (152), Expect = 5e-15
 Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 3/71 (4%)

Query: 1  MSRSGQPPDL-KKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN--GNEKNDI 57
          MS +  P +L  K +   L + + + R   GTL GFD ++N+V+ +  E +         
Sbjct: 15 MSMTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKH 74

Query: 58 GMVVIRGNSVV 68
            +++ GN + 
Sbjct: 75 SEMLLNGNGMC 85

>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 = 62.7 bits (152), Expect = 1e-14
 Identities = 15/77 (19%), Positives = 35/77 (45%), Gaps = 16/77 (20%)

Query: 10  LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV----------------NGNE 53
           + K +  ++ + +  ++   G LRGFD+++N+V+D+  E                     
Sbjct: 33  IDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVM 92

Query: 54  KNDIGMVVIRGNSVVTV 70
            N +  +++ GN+V  +
Sbjct: 93  VNRLETILLSGNNVAML 109

>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 = 60.2 bits (146), Expect = 4e-14
 Identities = 21/91 (23%), Positives = 46/91 (50%), Gaps = 17/91 (18%)

Query: 1  MSRSGQPPDLKKYM-------DKKLQ--------IKLNANRMIVGTLRGFDQFMNLVIDN 45
          M+  GQ   ++K M        + LQ        +    N  I G + GFD++MNLV+D+
Sbjct: 1  MAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDD 60

Query: 46 TVEVN--GNEKNDIGMVVIRGNSVVTVEALE 74
            E++     +  +G ++++G+++  ++++ 
Sbjct: 61 AEEIHSKTKSRKQLGRIMLKGDNITLLQSVS 91

>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 = 51.2 bits (122), Expect = 1e-09
 Identities = 19/77 (24%), Positives = 41/77 (53%), Gaps = 11/77 (14%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-----------VNGNEKNDIG 58
          + +++D +++  L   R+ +GT + FD+ MNL++ +  E               EK  +G
Sbjct: 9  MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLG 68

Query: 59 MVVIRGNSVVTVEALEP 75
          +V++RG ++V++    P
Sbjct: 69 LVLLRGENLVSMTVEGP 85

>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 = 46.7 bits (111), Expect = 1e-08
 Identities = 13/63 (20%), Positives = 27/63 (42%), Gaps = 2/63 (3%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE--VNGNEKNDIGMVVIRGNSV 67
          L     + + ++L       G L   D +MNL +   +    +G++   +    IRGN++
Sbjct: 21 LNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIRGNNI 80

Query: 68 VTV 70
            +
Sbjct: 81 KYL 83

>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 = 42.3 bits (99), Expect = 8e-07
 Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 15/71 (21%)

Query: 15  DKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV---------------NGNEKNDIGM 59
           + ++ I    N+ ++G ++ FD+  N+V++N  E+                 N+   I  
Sbjct: 39  NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISK 98

Query: 60  VVIRGNSVVTV 70
           + +RG+SV+ V
Sbjct: 99  MFLRGDSVIVV 109

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

 Score = 39.3 bits (92), Expect = 4e-06
 Identities = 11/60 (18%), Positives = 21/60 (35%), Gaps = 1/60 (1%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEK-NDIGMVVIRGNSVV 68
          L +     +  + N   +  G L   +  MN  + N      + +   +  V IRG  + 
Sbjct: 10 LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIR 69

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

 Score = 40.0 bits (93), Expect = 6e-06
 Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV-NGNEKNDIGMVVIRGNSV 67
          L K   + + I+L     + GT+ G D  MN  +          E   +  + IRGN++
Sbjct: 7  LMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNI 65

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

 Score = 38.1 bits (88), Expect = 4e-05
 Identities = 11/59 (18%), Positives = 22/59 (37%), Gaps = 1/59 (1%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEK-NDIGMVVIRGNSV 67
          L +     +  + N   +  G L   +  MN  + N      + +   +  V IRG+ +
Sbjct: 10 LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKI 68

>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 = 37.0 bits (85), Expect = 1e-04
 Identities = 15/66 (22%), Positives = 31/66 (46%), Gaps = 3/66 (4%)

Query: 9  DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVV 68
          +L   + +++Q+ L+   +  G L   D  +N+V+ N     G + N    V I    +V
Sbjct: 4  ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFN---RVFIMYRYIV 60

Query: 69 TVEALE 74
           +++ E
Sbjct: 61 HIDSTE 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	80
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.94
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.93
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.93
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.93
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.93
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.92
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.92
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.92
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.92
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.91
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.91
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.91
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.91
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.91
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.91
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.91
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.91
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.89
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.89
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.89
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.88
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.87
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.87
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.84
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	99.34
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	97.5
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	97.3
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	97.27
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	97.21
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	97.2
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	97.11
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	97.11
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	97.05
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	96.9
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	96.85
1ycy_A	71	Conserved hypothetical protein; structural genomic	96.77
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	96.74
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	96.68
2rm4_A	103	CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-	95.52
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	95.4
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	95.25
3rux_A	270	BIRA bifunctional protein; biotin-protein ligase,	93.7
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	93.38
2eay_A	233	Biotin [acetyl-COA-carboxylase] ligase; biotin bio	91.01
1bia_A	321	BIRA bifunctional protein; transcription regulatio	89.16
2ej9_A	237	Putative biotin ligase; biotin biosynthesis, monom	87.33
2dxu_A	235	Biotin--[acetyl-COA-carboxylase] ligase; biotin bi	84.51
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	82.14
3bfm_A	235	Biotin protein ligase-like protein of unknown FUN;	82.01
2e12_A	101	SM-like motif, hypothetical protein XCC3642; novel	81.12

>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=99.94  E-value=9.9e-27  Score=136.69  Aligned_cols=75  Identities=63%  Similarity=1.036  Sum_probs=52.5

Q ss_pred             CCCCCCCCchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecCCc
Q 034895            1 MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALEPV   76 (80)
Q Consensus         1 M~~~~~p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d~~   76 (80)
                      ||++ .+++|.+++|++|+|+|+||++|+|+|.+||+|||++|+||.|+. +++.+.+|.++|||++|++|++.|.+
T Consensus         1 ms~~-~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~v~iRG~~I~~i~~~d~~   76 (76)
T 3s6n_G            1 MSKA-HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIMLEALERV   76 (76)
T ss_dssp             --------------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC----CBSSEEECSSSEEEEEC----
T ss_pred             CCCc-chHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccCCcEeEcCEEEECCCeEEEEEeccCC
Confidence            7777 567899999999999999999999999999999999999999985 45678899999999999999998863

>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=99.93  E-value=6.9e-26  Score=136.02  Aligned_cols=77  Identities=30%  Similarity=0.376  Sum_probs=67.6

Q ss_pred             CCCCCCCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecCCcc
Q 034895            1 MSRSGQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALEPVS   77 (80)
Q Consensus         1 M~~~~~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d~~~   77 (80)
                      ||....|.. |++++|++|+|+|++|++|+|+|.+||+|||++|+||.|.. +...+.+|.++|||++|++|.++|...
T Consensus         1 ms~~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~g~~~~~lg~v~IRG~nI~~i~~~d~~~   79 (86)
T 3s6n_F            1 MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGVEEEE   79 (86)
T ss_dssp             --CCCCHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEESSEEECGGGEEEEEECC---
T ss_pred             CCcCcCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcCCceeeEccEEEEeCCeEEEEEeCCccc
Confidence            888888887 89999999999999999999999999999999999999875 446789999999999999999998754

>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=99.93  E-value=9e-26  Score=133.89  Aligned_cols=74  Identities=27%  Similarity=0.486  Sum_probs=64.5

Q ss_pred             CCCC-----CCCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcCCcEEEEEecC
Q 034895            1 MSRS-----GQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALE   74 (80)
Q Consensus         1 M~~~-----~~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~d   74 (80)
                      ||++     ..|.. |.++++++|+|+|+||++|+|+|.+||+|||++|+||+|+.+...+.+|.++|||++|++|.++|
T Consensus         1 m~~~~~~~~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~lg~v~iRG~~I~~i~~~d   80 (81)
T 1i8f_A            1 MASDISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP   80 (81)
T ss_dssp             ---------CCHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEECGGGEEEEEECC
T ss_pred             CCcccCccccchHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEEcCCcccCCCEEEECCCEEEEEEeCC
Confidence            6665     34555 89999999999999999999999999999999999999986667889999999999999999886

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

Probab=99.93  E-value=9.8e-26  Score=131.79  Aligned_cols=70  Identities=27%  Similarity=0.530  Sum_probs=63.6

Q ss_pred             CCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecCC
Q 034895            6 QPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALEP   75 (80)
Q Consensus         6 ~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d~   75 (80)
                      .|.. |.+++|++|+|+|+||+.|+|+|.+||+|||++|+||.|++ +...+.+|.++|||++|++|.++|+
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 RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISPTEE   75 (75)
T ss_dssp             CHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEEC--
T ss_pred             hHHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeCCceeECCEEEECCCEEEEEEeCCC
Confidence            4766 89999999999999999999999999999999999999985 5667899999999999999999874

>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=99.93  E-value=2.1e-25  Score=130.85  Aligned_cols=70  Identities=36%  Similarity=0.604  Sum_probs=64.4

Q ss_pred             CCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecCC
Q 034895            6 QPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALEP   75 (80)
Q Consensus         6 ~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d~   75 (80)
                      .|.. |.+++|++|+|+|+||+.|+|+|.+||+|||++|+||.|++ +...+++|.++|||++|++|.++|.
T Consensus         4 ~P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~d~   75 (77)
T 1i4k_A            4 RPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVFVSPAPG   75 (77)
T ss_dssp             CHHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEECC-
T ss_pred             cHHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecCCcEeECCEEEECCCEEEEEEeCCC
Confidence            4766 89999999999999999999999999999999999999986 5567889999999999999999885

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

Probab=99.92  E-value=4.1e-25  Score=130.96  Aligned_cols=75  Identities=29%  Similarity=0.573  Sum_probs=65.0

Q ss_pred             CCCCC-CCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecCC
Q 034895            1 MSRSG-QPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALEP   75 (80)
Q Consensus         1 M~~~~-~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d~   75 (80)
                      |+.-. .|.. |.++++++|+|+|+||++|+|+|.+||+|||++|+||+|++ +...+.+|.++|||++|++|.++|+
T Consensus         3 m~~~~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~~   80 (81)
T 1th7_A            3 MNFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILISPLQT   80 (81)
T ss_dssp             CCTTCHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECGGGEEEEEEC--
T ss_pred             ccccccchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecCCceeECCEEEECCCEEEEEEecCC
Confidence            34433 4555 89999999999999999999999999999999999999986 5567899999999999999999874

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

Probab=99.92  E-value=1.1e-24  Score=129.81  Aligned_cols=71  Identities=32%  Similarity=0.607  Sum_probs=64.4

Q ss_pred             CCCCCCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEe
Q 034895            2 SRSGQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEA   72 (80)
Q Consensus         2 ~~~~~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~   72 (80)
                      +....|.. |.++++++|+|+|+||++|+|+|.+||+|||++|+||+|++ ++..+.+|.++|||++|++|++
T Consensus        11 ~~~~~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~IRG~~I~~i~p   83 (83)
T 1mgq_A           11 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP   83 (83)
T ss_dssp             CCTTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEC
T ss_pred             ccCcChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecCCcccCCCEEEECCCEEEEEEC
Confidence            44557777 89999999999999999999999999999999999999985 5567899999999999999974

>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=99.92  E-value=2.2e-25  Score=130.53  Aligned_cols=73  Identities=37%  Similarity=0.555  Sum_probs=64.7

Q ss_pred             CCCCCCCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecCC
Q 034895            1 MSRSGQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALEP   75 (80)
Q Consensus         1 M~~~~~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d~   75 (80)
                      ||.  .|.. |.+++|++|+|+|+||++|+|+|.+||+|||++|+||.|+. +++.+.+|.++|||++|++|++.|.
T Consensus         1 m~~--~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~~   75 (75)
T 4emk_B            1 MDS--SPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIRGNNVLYVSALDD   75 (75)
T ss_dssp             CCS--HHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEETTEEEEEEEEEEEEGGGSSEEEEC--
T ss_pred             CCC--chHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEecCCcccEecEEEEcCCeEEEEEecCC
Confidence            553  4776 89999999999999999999999999999999999999975 5567899999999999999998763

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

Probab=99.92  E-value=8e-25  Score=128.54  Aligned_cols=70  Identities=30%  Similarity=0.623  Sum_probs=63.2

Q ss_pred             CCCc-hhhhcCCEEEEEEcCC-eEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecCC
Q 034895            6 QPPD-LKKYMDKKLQIKLNAN-RMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALEP   75 (80)
Q Consensus         6 ~p~~-L~~~~~k~V~V~l~~g-~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d~   75 (80)
                      .|.. |.++++++|+|+|++| ++|+|+|.+||+|||++|+||+|++ ++..+.+|.++|||++|++|.++|+
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 LPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQPQEE   77 (77)
T ss_dssp             CHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEEC--
T ss_pred             chHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecCCcEeECCeEEEeCCeEEEEEeCCC
Confidence            4555 8999999999999999 9999999999999999999999986 5567899999999999999999874

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

Probab=99.91  E-value=1.8e-24  Score=126.82  Aligned_cols=70  Identities=19%  Similarity=0.207  Sum_probs=64.8

Q ss_pred             CCCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecC
Q 034895            5 GQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALE   74 (80)
Q Consensus         5 ~~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d   74 (80)
                      ..|.. |++++|++|.|+|++|++|+|+|.+||+|||++|+||+|.. +++.+.+|.++|||++|++|..||
T Consensus         4 ~~P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~~~~~~lg~v~IRG~nI~~i~lPd   75 (75)
T 1d3b_A            4 GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLILPD   75 (75)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECGGGEEEEEECC
T ss_pred             cCHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCCCcEEEcCeEEEeCCEEEEEEcCC
Confidence            46777 89999999999999999999999999999999999999985 456789999999999999999986

>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=99.91  E-value=1.1e-24  Score=133.00  Aligned_cols=72  Identities=35%  Similarity=0.566  Sum_probs=63.2

Q ss_pred             CCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec--------CceeeeecEEEEcCCcEEEEEecCCc
Q 034895            6 QPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN--------GNEKNDIGMVVIRGNSVVTVEALEPV   76 (80)
Q Consensus         6 ~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~--------~~~~~~~g~v~IrG~~I~~I~~~d~~   76 (80)
                      .|.. |.++++++|+|+|++|++|+|+|.|||+|||++|+||.|++        +...+++|.++|||++|++|.+++..
T Consensus        10 ~p~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nVv~I~~~d~~   89 (96)
T 3bw1_A           10 TPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLISTPSED   89 (96)
T ss_dssp             CHHHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEECGGGEEEEECCC--
T ss_pred             hHHHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEECCCEEEEEEecCcc
Confidence            5665 89999999999999999999999999999999999999985        23467899999999999999998875


Q ss_pred             c
Q 034895           77 S   77 (80)
Q Consensus        77 ~   77 (80)
                      .
T Consensus        90 ~   90 (96)
T 3bw1_A           90 D   90 (96)
T ss_dssp             -
T ss_pred             c
Confidence            4

>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=2e-24  Score=131.76  Aligned_cols=72  Identities=21%  Similarity=0.407  Sum_probs=63.9

Q ss_pred             CCCCCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec--CceeeeecEEEEcCCcEEEEEecC
Q 034895            3 RSGQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN--GNEKNDIGMVVIRGNSVVTVEALE   74 (80)
Q Consensus         3 ~~~~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~--~~~~~~~g~v~IrG~~I~~I~~~d   74 (80)
                      ....|++ |.++++++|+|+|++|++|+|+|.+||+|||++|+||+|+.  +++.+.+|.++|||++|++|.+..
T Consensus        17 ~~~~Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~IRG~nI~~i~p~~   91 (94)
T 4emk_A           17 MTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKHSEMLLNGNGMCMLIPGG   91 (94)
T ss_dssp             ---CHHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTTCCEEEEEEEEECSTTEEEEEECC
T ss_pred             ccccCHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCCCcEeEcCEEEEcCCEEEEEEeCC
Confidence            3456777 89999999999999999999999999999999999999986  556789999999999999999764

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

Probab=99.91  E-value=3.6e-24  Score=130.14  Aligned_cols=69  Identities=25%  Similarity=0.534  Sum_probs=61.8

Q ss_pred             CCCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecC--------------ceeeeecEEEEcCCcEEE
Q 034895            5 GQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG--------------NEKNDIGMVVIRGNSVVT   69 (80)
Q Consensus         5 ~~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~--------------~~~~~~g~v~IrG~~I~~   69 (80)
                      ..|++ |..+++++|+|+|++|+.|+|+|.|||+|||++|+||+|++.              ...+.+|.++|||++|++
T Consensus         8 ~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG~nVv~   87 (93)
T 4emg_A            8 AEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDSVIL   87 (93)
T ss_dssp             -CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECGGGEEE
T ss_pred             CCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECCCeEEE
Confidence            68898 567799999999999999999999999999999999999862              246889999999999999


Q ss_pred             EEec
Q 034895           70 VEAL   73 (80)
Q Consensus        70 I~~~   73 (80)
                      |+++
T Consensus        88 I~p~   91 (93)
T 4emg_A           88 IAPP   91 (93)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9975

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

Probab=99.91  E-value=2.2e-24  Score=130.02  Aligned_cols=70  Identities=27%  Similarity=0.568  Sum_probs=62.8

Q ss_pred             CCchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-----------CceeeeecEEEEcCCcEEEEEecCC
Q 034895            7 PPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-----------GNEKNDIGMVVIRGNSVVTVEALEP   75 (80)
Q Consensus         7 p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-----------~~~~~~~g~v~IrG~~I~~I~~~d~   75 (80)
                      ..+|.++++++|+|+|+||++|+|+|.|||+|||++|+||+|++           +...+.+|.++|||++|++|.++++
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            45699999999999999999999999999999999999999963           2346889999999999999999875


Q ss_pred             c
Q 034895           76 V   76 (80)
Q Consensus        76 ~   76 (80)
                      -
T Consensus        86 ~   86 (91)
T 1d3b_B           86 P   86 (91)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=99.91  E-value=9e-24  Score=132.46  Aligned_cols=72  Identities=35%  Similarity=0.650  Sum_probs=57.3

Q ss_pred             CCCchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecC--------ceeeeecEEEEcCCcEEEEEecCCcc
Q 034895            6 QPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG--------NEKNDIGMVVIRGNSVVTVEALEPVS   77 (80)
Q Consensus         6 ~p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~--------~~~~~~g~v~IrG~~I~~I~~~d~~~   77 (80)
                      .+++|.++++++|+|+|+|||+|+|+|.|||+||||+|+||+|++.        ...+.+|.++|||++|++|+++|...
T Consensus        24 ~i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~~e  103 (113)
T 4emk_C           24 SILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIAPMDGSE  103 (113)
T ss_dssp             --------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTTEEEEEECC---
T ss_pred             hHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCeEEEEEecCccc
Confidence            3466999999999999999999999999999999999999999863        35789999999999999999988643

>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=99.91  E-value=6.8e-24  Score=131.59  Aligned_cols=73  Identities=21%  Similarity=0.359  Sum_probs=55.0

Q ss_pred             CCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec--CceeeeecEEEEcCCcEEEEEecCCccC
Q 034895            6 QPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN--GNEKNDIGMVVIRGNSVVTVEALEPVSK   78 (80)
Q Consensus         6 ~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~--~~~~~~~g~v~IrG~~I~~I~~~d~~~~   78 (80)
                      .|.. |.+++|++|+|+|++|++|+|+|.+||+|||++|+||+|..  ++..+.+|.++|||++|++|..+|.++.
T Consensus        16 ~p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg~~~~~lg~v~IRG~nI~~I~~pd~l~d   91 (105)
T 4emh_A           16 LPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIRGNNIKYLRIQDEVLS   91 (105)
T ss_dssp             ----------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEEECGGGEEEEEC------
T ss_pred             cHHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCCceeeEcCeEEEeCCeEEEEecCHHHhh
Confidence            4666 89999999999999999999999999999999999999874  4467899999999999999999998653

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

Probab=99.91  E-value=6.6e-24  Score=129.10  Aligned_cols=70  Identities=29%  Similarity=0.475  Sum_probs=62.0

Q ss_pred             CCCc-hhhhcCCEEEEEEcCC-eEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecCC
Q 034895            6 QPPD-LKKYMDKKLQIKLNAN-RMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALEP   75 (80)
Q Consensus         6 ~p~~-L~~~~~k~V~V~l~~g-~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d~   75 (80)
                      .|.. |.+++|++|+|+|++| ++|+|+|.+||+|||++|+||+|+. +++.+.+|.++|||++|++|.+++.
T Consensus        21 ~P~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~~~~~~~lg~v~IRG~nI~~I~~~~~   93 (93)
T 1n9r_A           21 NPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN   93 (93)
T ss_dssp             -----CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECGGGEEEEEECCC
T ss_pred             ChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcCCCeEeEcCEEEEcCCeEEEEEeCCC
Confidence            4555 8999999999999999 9999999999999999999999985 5667899999999999999998874

>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=99.89  E-value=5.2e-23  Score=129.82  Aligned_cols=70  Identities=21%  Similarity=0.268  Sum_probs=64.2

Q ss_pred             CCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecCCc
Q 034895            7 PPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALEPV   76 (80)
Q Consensus         7 p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d~~   76 (80)
                      |+. |+++++++|.|+|++|++|+|+|.+||+|||++|+||+|+. +.+.+.++.+||||++|++|.++|.+
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 LVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSL   74 (119)
T ss_dssp             HHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTTC
T ss_pred             hHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecCCCceeEcceEEEcCCeEEEEEecccc
Confidence            444 89999999999999999999999999999999999999985 44567899999999999999999975

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

Probab=99.89  E-value=8.8e-23  Score=130.07  Aligned_cols=75  Identities=17%  Similarity=0.212  Sum_probs=68.0

Q ss_pred             CCCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecCCccCC
Q 034895            5 GQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALEPVSKS   79 (80)
Q Consensus         5 ~~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d~~~~~   79 (80)
                      ..|.. |.++++++|.|+|++|++|+|+|.+||+|||++|+||+|+. +++...++.+||||++|+||.++|.++..
T Consensus         4 ~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~~~~l~~v~IRGnnI~~I~lpd~l~~~   80 (126)
T 2y9a_D            4 GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRFLILPDMLKNA   80 (126)
T ss_dssp             CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCSSCSSS
T ss_pred             ccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCcEeecccEEEeCCEEEEEEccccccch
Confidence            46777 89999999999999999999999999999999999999985 44577899999999999999999987543

>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=99.89  E-value=2.2e-23  Score=126.66  Aligned_cols=70  Identities=26%  Similarity=0.666  Sum_probs=62.5

Q ss_pred             CCCc-hhhhcCCEEEEEE----cCCeEEEEEEEEECCCCceEEcceEEec--CceeeeecEEEEcCCcEEEEEecCC
Q 034895            6 QPPD-LKKYMDKKLQIKL----NANRMIVGTLRGFDQFMNLVIDNTVEVN--GNEKNDIGMVVIRGNSVVTVEALEP   75 (80)
Q Consensus         6 ~p~~-L~~~~~k~V~V~l----~~g~~~~G~L~~~D~~~NlvL~~~~e~~--~~~~~~~g~v~IrG~~I~~I~~~d~   75 (80)
                      .|++ |.++++++++|++    ++|++|+|+|.|||+|||++|+||+|+.  ++..+.+|.++|||++|++|++.++
T Consensus        16 ~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~iRG~nV~~i~~~~~   92 (92)
T 3s6n_E           16 QPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLLQSVSN   92 (92)
T ss_dssp             CHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSCCEEEEEEEEECGGGEEEEEEC--
T ss_pred             CCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCCceeEcCeEEEeCCEEEEEEeCCC
Confidence            4666 7899999999999    9999999999999999999999999986  4567889999999999999998763

>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=2.5e-23  Score=131.59  Aligned_cols=71  Identities=23%  Similarity=0.507  Sum_probs=62.2

Q ss_pred             CCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-----------Cce-----eeeecEEEEcCCcEE
Q 034895            6 QPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-----------GNE-----KNDIGMVVIRGNSVV   68 (80)
Q Consensus         6 ~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-----------~~~-----~~~~g~v~IrG~~I~   68 (80)
                      .|+. |.++++++|+|+|++|+.|+|+|.|||+||||+|+||+|++           +..     .+.+|.++|||++|+
T Consensus        28 ~Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG~nVv  107 (121)
T 2fwk_A           28 LPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVA  107 (121)
T ss_dssp             CHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGEE
T ss_pred             CcHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECCCEEE
Confidence            4555 78999999999999999999999999999999999999876           213     678999999999999


Q ss_pred             EEEecCCc
Q 034895           69 TVEALEPV   76 (80)
Q Consensus        69 ~I~~~d~~   76 (80)
                      +|...++-
T Consensus       108 ~I~~~~~~  115 (121)
T 2fwk_A          108 MLVPGGDP  115 (121)
T ss_dssp             EEESSSCC
T ss_pred             EEEecCCC
Confidence            99987653

>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=99.87  E-value=2.4e-22  Score=138.50  Aligned_cols=70  Identities=27%  Similarity=0.584  Sum_probs=63.5

Q ss_pred             CCCchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-----------CceeeeecEEEEcCCcEEEEEecC
Q 034895            6 QPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-----------GNEKNDIGMVVIRGNSVVTVEALE   74 (80)
Q Consensus         6 ~p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-----------~~~~~~~g~v~IrG~~I~~I~~~d   74 (80)
                      ...+|.++++++|+|+|+|||+|+|+|++||+||||+|+||+|++           +.+.+++|++||||+||++|+..+
T Consensus         5 k~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~Isve~   84 (231)
T 3pgw_B            5 KSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEG   84 (231)
T ss_pred             chHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEEEEecC
Confidence            446799999999999999999999999999999999999999975           235789999999999999999876


Q ss_pred             C
Q 034895           75 P   75 (80)
Q Consensus        75 ~   75 (80)
                      .
T Consensus        85 p   85 (231)
T 3pgw_B           85 P   85 (231)
T ss_pred             C
Confidence            4

>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=99.87  E-value=4.2e-22  Score=125.39  Aligned_cols=73  Identities=23%  Similarity=0.439  Sum_probs=62.2

Q ss_pred             CCCCc-hhhhc--CCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCc---------------eeeeecEEEEcCCc
Q 034895            5 GQPPD-LKKYM--DKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGN---------------EKNDIGMVVIRGNS   66 (80)
Q Consensus         5 ~~p~~-L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~---------------~~~~~g~v~IrG~~   66 (80)
                      ..|+. |.+++  +++|.|+|++|+.|+|+|.|||+|||++|+||+|++..               ..+.+|.+||||++
T Consensus        26 ~~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~n  105 (118)
T 1b34_B           26 TGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDS  105 (118)
T ss_dssp             CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGG
T ss_pred             cChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcCCE
Confidence            36776 78888  59999999999999999999999999999999998511               14579999999999


Q ss_pred             EEEEEecCCcc
Q 034895           67 VVTVEALEPVS   77 (80)
Q Consensus        67 I~~I~~~d~~~   77 (80)
                      |++|.+.+...
T Consensus       106 Vv~I~~~~~~~  116 (118)
T 1b34_B          106 VIVVLRNPLIA  116 (118)
T ss_dssp             EEEEEECCCCC
T ss_pred             EEEEEeCchhh
Confidence            99999987643

>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=99.84  E-value=9.6e-21  Score=121.18  Aligned_cols=65  Identities=22%  Similarity=0.402  Sum_probs=60.7

Q ss_pred             chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcCCcEEEEEecCCc
Q 034895            9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALEPV   76 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~d~~   76 (80)
                      .|.+++|++|.|+|++|+.|+|+|.+||+|||++|+||.|..+   +.+|.++|||++|++|..+|..
T Consensus         4 ~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~~---~~lg~v~IRG~nI~~I~~~d~~   68 (130)
T 1m5q_A            4 ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAG---EKFNRVFIMYRYIVHIDSTERR   68 (130)
T ss_dssp             HHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTTC---CEEEEEEECGGGEEEEEECCCC
T ss_pred             HHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEcC---CEeceEEEeCCeEEEEEcCCcc
Confidence            4889999999999999999999999999999999999999753   5799999999999999999875

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

Probab=99.34  E-value=2.8e-12  Score=76.82  Aligned_cols=66  Identities=23%  Similarity=0.338  Sum_probs=57.9

Q ss_pred             CCCCchhhhcCCEEEEEEcCCeEEEEEEEEEC-CCCceEEcceEEecCceeeeecEEEEcCCcEEEEEecCC
Q 034895            5 GQPPDLKKYMDKKLQIKLNANRMIVGTLRGFD-QFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALEP   75 (80)
Q Consensus         5 ~~p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D-~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~d~   75 (80)
                      ..|.+|.+++||+|.|.|.||+.|+|.|.+|| ..+|++|.|+.+  ++   .+..++|.|..|..|...+.
T Consensus         7 ~~p~el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~~~--~~---~~~~~iI~G~aI~eI~v~~~   73 (86)
T 1y96_A            7 KGPLEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFLE--DG---SMSVTGIMGHAVQTVETMNE   73 (86)
T ss_dssp             SCHHHHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEECT--TS---CEEEEEECGGGEEEEEEEEC
T ss_pred             CCHHHHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeeccc--CC---eEEEEEEecceEEEEEEecc
Confidence            36888999999999999999999999999999 999999999922  22   35799999999999987654

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

Probab=97.50  E-value=0.0017  Score=38.69  Aligned_cols=66  Identities=12%  Similarity=0.197  Sum_probs=54.0

Q ss_pred             hhhcCCEEEEEEcCCeEEEEEEEEEC-CCCceEEcceEEecCc----------eeeeecEEEEcCCcEEEEEecCCc
Q 034895           11 KKYMDKKLQIKLNANRMIVGTLRGFD-QFMNLVIDNTVEVNGN----------EKNDIGMVVIRGNSVVTVEALEPV   76 (80)
Q Consensus        11 ~~~~~k~V~V~l~~g~~~~G~L~~~D-~~~NlvL~~~~e~~~~----------~~~~~g~v~IrG~~I~~I~~~d~~   76 (80)
                      ..++|++|.+..+.+-.|+|+|..+| +..-+.|.|+..+..+          ...-+..+..||+.|.-+...+..
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            45899999999999999999999999 7788999999876411          112367899999999999877653

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

Probab=97.30  E-value=0.00025  Score=41.02  Aligned_cols=55  Identities=25%  Similarity=0.327  Sum_probs=42.7

Q ss_pred             hhhhc--CCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcCCcEEEEEecCCc
Q 034895           10 LKKYM--DKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALEPV   76 (80)
Q Consensus        10 L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~d~~   76 (80)
                      |+.+.  ..+|.|.|.||..++|++.+||+|+=+.- +     +      ...+|--..|.+|.+..++
T Consensus        14 L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~vlL~-~-----~------~~~LIYKhAIsTI~p~~~v   70 (74)
T 2ylb_A           14 LNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLK-N-----T------VSQMVYKHAISTVVPSRPV   70 (74)
T ss_dssp             HHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEE-S-----S------SEEEEEGGGEEEEEESSCC
T ss_pred             HHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEE-C-----C------ceEEEEeeeEEEEeEcccc
Confidence            55554  67999999999999999999999975443 2     1      2567778888888877654

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

Probab=97.27  E-value=0.0016  Score=39.22  Aligned_cols=68  Identities=15%  Similarity=0.271  Sum_probs=53.8

Q ss_pred             hhhhcCCEEEEEEcCCeEEEEEEEEEC-CCCceEEcceEEecCc----------eeeeecEEEEcCCcEEEEEecCCcc
Q 034895           10 LKKYMDKKLQIKLNANRMIVGTLRGFD-QFMNLVIDNTVEVNGN----------EKNDIGMVVIRGNSVVTVEALEPVS   77 (80)
Q Consensus        10 L~~~~~k~V~V~l~~g~~~~G~L~~~D-~~~NlvL~~~~e~~~~----------~~~~~g~v~IrG~~I~~I~~~d~~~   77 (80)
                      -..++|++|.+..+.+-.|+|+|..+| +..-+.|+|+..+..+          ...-+..+..||+.|.-+...+.-+
T Consensus        14 ~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~~ipp~~~vyeyIvFrGsDIKDL~V~e~p~   92 (95)
T 2fb7_A           14 GTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCEPPK   92 (95)
T ss_dssp             --CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSSCCCSCCCCSSCEEECSTTEEEEEESCCSC
T ss_pred             cCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCCccCCCCcceeEEEEcCCCcceEEEecCCC
Confidence            467899999999999999999999999 7888999998755311          1123578999999999998866543

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

Probab=97.21  E-value=0.0003  Score=40.96  Aligned_cols=55  Identities=11%  Similarity=0.255  Sum_probs=37.6

Q ss_pred             hhhhc--CCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcCCcEEEEEecCC
Q 034895           10 LKKYM--DKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALEP   75 (80)
Q Consensus        10 L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~d~   75 (80)
                      |+.+.  ..+|.|.|.||..++|++.+||+|+=+.-.+     +.      ..+|--..|.+|.+..+
T Consensus        12 Ln~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~VlL~~~-----g~------~qLIYKhAISTI~p~~~   68 (77)
T 1kq1_A           12 LENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQ-----GK------QHLIYKHAISTYTVETE   68 (77)
T ss_dssp             HHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEEET-----TE------EEEEEGGGEEEEEC---
T ss_pred             HHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEEEEC-----Ce------eEEEEeeeEEEEeECcc
Confidence            44554  7799999999999999999999997655433     21      34555566666665443

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

Probab=97.20  E-value=0.00036  Score=41.07  Aligned_cols=34  Identities=26%  Similarity=0.374  Sum_probs=28.1

Q ss_pred             hhhhc--CCEEEEEEcCCeEEEEEEEEECCCCceEE
Q 034895           10 LKKYM--DKKLQIKLNANRMIVGTLRGFDQFMNLVI   43 (80)
Q Consensus        10 L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~~NlvL   43 (80)
                      |..+.  ..+|+|.|.||..++|.+.+||+|+=+.-
T Consensus        12 Ln~lrk~~~~Vtv~L~NG~~l~G~I~~fD~ftVlL~   47 (82)
T 1u1s_A           12 LNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLK   47 (82)
T ss_dssp             HHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEe
Confidence            44443  67999999999999999999999985543

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

Probab=97.11  E-value=0.0026  Score=37.02  Aligned_cols=51  Identities=22%  Similarity=0.352  Sum_probs=38.1

Q ss_pred             CCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcCCcEEEEEecCCc
Q 034895           15 DKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALEPV   76 (80)
Q Consensus        15 ~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~d~~   76 (80)
                      ..+|+|.|.||..++|.+.+||+|+=+.-.+     +      ...+|--..|..|.+..++
T Consensus        23 ~~~Vtv~L~nG~~l~G~I~~fD~f~VlL~~~-----g------~qqlIYKhAISTI~p~~~v   73 (78)
T 3ahu_A           23 NTYVTVFLLNGFQLRGQVKGFDNFTVLLESE-----G------KQQLIYKHAISTFAPQKNV   73 (78)
T ss_dssp             TCCEEEEETTSCEEEEEEEEECSSEEEEESS-----S------CEEEEEGGGEEEEEESSCC
T ss_pred             CCcEEEEEeCCeEEEEEEEEEcceEEEEEEC-----C------eeEEEEcceEEEEeecccc
Confidence            7799999999999999999999998655433     2      1345666667777665544

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

Probab=97.11  E-value=0.0012  Score=38.87  Aligned_cols=62  Identities=15%  Similarity=0.251  Sum_probs=50.1

Q ss_pred             hhhcCCEEEEEEcCCe-EEEEEEEEECC-CCceEEcceEEecCceeeeecEEEEcCCcEEEEEecC
Q 034895           11 KKYMDKKLQIKLNANR-MIVGTLRGFDQ-FMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALE   74 (80)
Q Consensus        11 ~~~~~k~V~V~l~~g~-~~~G~L~~~D~-~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~d   74 (80)
                      ++|+|+.|.+..+++- .|.|.|..+|. ..||.|.++..  ++-+.....+.+++.-|..+..++
T Consensus         5 ~~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~f~--NG~~~~s~eVtls~~DI~~L~ii~   68 (84)
T 2vc8_A            5 TDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPFH--NGVKCLVPEVTFRAGDITELKILE   68 (84)
T ss_dssp             CTTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEEEE--TTEECSSSEEEEEGGGCSEEEEEE
T ss_pred             ccccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehhhh--CCCCCCCcEEEEEecChhheEEEe
Confidence            4799999999999998 99999999995 46899999953  333444567999999887776654

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

Probab=97.05  E-value=0.00085  Score=39.21  Aligned_cols=55  Identities=22%  Similarity=0.300  Sum_probs=40.5

Q ss_pred             hhhhc--CCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcCCcEEEEEecCCc
Q 034895           10 LKKYM--DKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALEPV   76 (80)
Q Consensus        10 L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~d~~   76 (80)
                      |..+.  ..+|.|.|.||..++|.+.+||+|+=++ ++     +.      ..+|--..|.+|.+..++
T Consensus        13 Ln~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~VlL-~~-----g~------~qLIYKhAISTI~P~~~v   69 (79)
T 3sb2_A           13 LNALRKEHVPVSIYLVNGIKLQGHVESFDQYVVLL-RN-----TV------TQMVYKHAISTVVPARAV   69 (79)
T ss_dssp             HHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEE-ES-----SS------EEEEEGGGEEEEEESSCC
T ss_pred             HHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEE-EC-----Cc------eEEEEeeeEEEEeecCce
Confidence            44443  5679999999999999999999998654 32     22      346777778888776554

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

Probab=96.90  E-value=0.0074  Score=37.91  Aligned_cols=60  Identities=13%  Similarity=0.247  Sum_probs=47.0

Q ss_pred             CchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEE--cceEEecCceeeeecEEEEcCCcEEEEEecCCcc
Q 034895            8 PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVI--DNTVEVNGNEKNDIGMVVIRGNSVVTVEALEPVS   77 (80)
Q Consensus         8 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL--~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~d~~~   77 (80)
                      ....+|+|..|.|+|+||..++|++..+|. -+|.|  ++|..         +..-|+.+.|.-+...+..+
T Consensus         5 ~~~sqFlGy~V~v~LkDgs~~qG~I~~vd~-k~LtL~~~~a~~---------s~~~I~asdI~DLkVl~~~~   66 (125)
T 4a53_A            5 MSVADFYGSNVEVLLNNDSKARGVITNFDS-SNSILQLRLAND---------STKSIVTKDIKDLRILPKNE   66 (125)
T ss_dssp             CCHHHHTTCEEEEEETTSCEEEEEEEEEET-TTTEEEEEETTT---------EEEEEEGGGEEEEEECCSCC
T ss_pred             ccHHHhcCceEEEEECCCCEeeEEEEeecC-CeeEEecccccc---------ccceeecccccceeeeeccc
Confidence            457899999999999999999999999983 46666  88832         22278888888777766543

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

Probab=96.85  E-value=0.00076  Score=41.30  Aligned_cols=54  Identities=26%  Similarity=0.335  Sum_probs=37.4

Q ss_pred             hhhhc--CCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcCCcEEEEEecCC
Q 034895           10 LKKYM--DKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALEP   75 (80)
Q Consensus        10 L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~d~   75 (80)
                      |+.+.  ..+|.|.|.||..++|++.+||+|+=++- +.           ...+|--..|.+|.+..+
T Consensus        14 Ln~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~VlL~-~~-----------kqqLIYKHAISTI~p~~~   69 (104)
T 2y90_A           14 LNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLK-NT-----------VSQMVYKHAISTVVPSRP   69 (104)
T ss_dssp             HHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEE-SS-----------SEEEEEGGGEEEEEESSC
T ss_pred             HHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEE-CC-----------ceEEEEeeeeEEEeeccc
Confidence            55554  45899999999999999999999985554 21           134455555555555443

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

Probab=96.77  E-value=0.011  Score=33.27  Aligned_cols=60  Identities=23%  Similarity=0.438  Sum_probs=45.1

Q ss_pred             hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcCCcEEEEEec
Q 034895           10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEAL   73 (80)
Q Consensus        10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~   73 (80)
                      |.++-|++|-|.......|+|+|.-||... +.|+|+....|++-   ..++++=+.|-.|-..
T Consensus        11 L~~WKg~rvAv~vg~ehSFtGiledFDeEv-iLL~dV~D~~GNk~---k~liv~idDinWimL~   70 (71)
T 1ycy_A           11 LKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIGNRG---KQMLIGLEDINWIMLL   70 (71)
T ss_dssp             HHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTEEEE---EEEEEEGGGEEEEEEC
T ss_pred             HHHhCCcEEEEEecCcceeeeehhhcCcce-eehhhHHHHhcccc---ceeEEEeccceEEEee
Confidence            788999999999999999999999999874 78999998776542   3567777777766553

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

Probab=96.74  E-value=0.01  Score=34.99  Aligned_cols=59  Identities=10%  Similarity=0.186  Sum_probs=48.1

Q ss_pred             hhhhcCCEEEEEEcCCeEEEEEEEEEC-CCCceEEcceEEecCceeeeecEEEEcCCcEEEEEe
Q 034895           10 LKKYMDKKLQIKLNANRMIVGTLRGFD-QFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEA   72 (80)
Q Consensus        10 L~~~~~k~V~V~l~~g~~~~G~L~~~D-~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~   72 (80)
                      |..+.|++|.+.+.++..+.|++.++| ...|+..++-.--.|    -++...+|++.|.+++.
T Consensus        24 l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPiG----v~~eAlLR~~Dii~~sF   83 (85)
T 1y96_B           24 LLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQTPIG----VQAEALLRCSDIISYTF   83 (85)
T ss_dssp             HHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEECCTTC----CEEEEEEEGGGEEEEEE
T ss_pred             HHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhcCCCcc----cchhhhhhcCCEEEEEe
Confidence            456679999999999999999999999 677777766533223    36789999999999875

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

Probab=96.68  E-value=0.0061  Score=34.86  Aligned_cols=31  Identities=19%  Similarity=0.281  Sum_probs=26.8

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEECCCCceEEc
Q 034895           14 MDKKLQIKLNANRMIVGTLRGFDQFMNLVID   44 (80)
Q Consensus        14 ~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~   44 (80)
                      -+.+|+|.|.||..++|.+.+||+|+=+.-.
T Consensus        24 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~   54 (71)
T 2qtx_A           24 NGKKVKIFLRNGEVLDAEVTGVSNYEIMVKV   54 (71)
T ss_dssp             TTCEEEEEETTSCEEEEEEEEECSSEEEEEE
T ss_pred             cCCcEEEEEeCCeEEEEEEEEEcceEEEEEe
Confidence            4678999999999999999999999865543

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

Probab=95.52  E-value=0.14  Score=30.89  Aligned_cols=64  Identities=11%  Similarity=0.291  Sum_probs=51.7

Q ss_pred             hhhcCCEEEEEEcCCe-EEEEEEEEECCCCceEEcceEEecCce--eeeecEEEEcCCcEEEEEecCCcc
Q 034895           11 KKYMDKKLQIKLNANR-MIVGTLRGFDQFMNLVIDNTVEVNGNE--KNDIGMVVIRGNSVVTVEALEPVS   77 (80)
Q Consensus        11 ~~~~~k~V~V~l~~g~-~~~G~L~~~D~~~NlvL~~~~e~~~~~--~~~~g~v~IrG~~I~~I~~~d~~~   77 (80)
                      ++|+|+-|.|...+.- .|.|.+..+|+ .++.|+++..  ++-  +.....|.++...|..+..++..+
T Consensus         8 edwiG~~VSI~C~d~LGVyQG~I~~V~~-~~ItL~kaFr--NGiplk~~~~EVtLsa~DI~~L~IIe~~~   74 (103)
T 2rm4_A            8 QDWIGCAVSIACDEVLGVFQGLIKQISA-EEITIVRAFR--NGVPLRKQNAEVVLKCTDIRSIDLIEPAK   74 (103)
T ss_dssp             GGGTTCEEEEEECTTTCEEEEEEEEEET-TEEEEEEEEE--TTEECSCSSSCEEEETTTEEEEEEEECCC
T ss_pred             cceeceEEEEeeCCcceEeeEEEEEccc-ceeEEhhhhh--cCcCcCCCCceEEEEecchhheeeecccc
Confidence            5899999999999985 99999999995 4599999876  332  334678999999999888876543

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

Probab=95.40  E-value=0.11  Score=29.70  Aligned_cols=53  Identities=17%  Similarity=0.211  Sum_probs=39.3

Q ss_pred             hhhhc--CCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcCCcEEEEEe
Q 034895           10 LKKYM--DKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEA   72 (80)
Q Consensus        10 L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~   72 (80)
                      |+.++  ..+|.|+|.+|..++|++.-+|++.=.+-.+ .+         ..++|.-..|++|.+
T Consensus        16 lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~cl~L~~~-~~---------~~~LI~R~AI~~Ikp   70 (72)
T 3hfn_A           16 LQNLIKQAAPVEIKLVTGDAITGRVLWQDPTCVCIADE-NS---------RQTTIWKQAIAYLQP   70 (72)
T ss_dssp             HHHHHSSCCEEEEEETTSCEEEEEEEEECSSEEEEEC-------------CEEEEEGGGEEEEEE
T ss_pred             HHHHHhhCceEEEEecCCCEEEEEEEEECCCEEEEEcC-CC---------CeEEEEeeeeEEEEe
Confidence            67776  4589999999999999999999987544433 21         146777777888765

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

Probab=95.25  E-value=0.093  Score=29.81  Aligned_cols=53  Identities=17%  Similarity=0.249  Sum_probs=39.2

Q ss_pred             hhhhc--CCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcCCcEEEEEe
Q 034895           10 LKKYM--DKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEA   72 (80)
Q Consensus        10 L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~   72 (80)
                      |+.++  ..+|.|.|.+|..++|++.-+|++.=++-.+.    +      -..+|.-..|++|.+
T Consensus        14 lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~cl~L~~~~----~------~~~LI~r~AI~~I~p   68 (70)
T 3hfo_A           14 VQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDGLGLVDDS----E------RSTIVRLAAIAYITP   68 (70)
T ss_dssp             HHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEECTT----C------CEEEEEGGGEEEEEE
T ss_pred             HHHHHhhCceEEEEecCCCEEEEEEEEeCCCEEEEEcCC----C------CeEEEEeeeeEEEee
Confidence            67776  57899999999999999999999875554321    1      135666677777754

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

Probab=93.70  E-value=0.12  Score=35.67  Aligned_cols=34  Identities=21%  Similarity=0.381  Sum_probs=30.7

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEECCCCceEEcce
Q 034895           13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNT   46 (80)
Q Consensus        13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~   46 (80)
                      .+|++|+|...+|..++|+..++|....|+++..
T Consensus       222 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~~  255 (270)
T 3rux_A          222 TIGSRVRVELPGGQDVVGIARDIDDQGRLCLDVG  255 (270)
T ss_dssp             STTSEEEEECTTSCEEEEEEEEECTTSCEEEEET
T ss_pred             ccCCEEEEEECCCeEEEEEEEEECCCCeEEEEEC
Confidence            3699999998889999999999999999999754

>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=93.38  E-value=0.052  Score=35.08  Aligned_cols=33  Identities=21%  Similarity=0.430  Sum_probs=26.9

Q ss_pred             hhhhcCCEEEEEE----cCCeEEEEEEEEECCCCceEE
Q 034895           10 LKKYMDKKLQIKL----NANRMIVGTLRGFDQFMNLVI   43 (80)
Q Consensus        10 L~~~~~k~V~V~l----~~g~~~~G~L~~~D~~~NlvL   43 (80)
                      +.+++|+.|.|++    .+.+.++|+|.++|.. .+.|
T Consensus        99 f~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~-~v~l  135 (164)
T 1ib8_A           99 VAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED-ELTM  135 (164)
T ss_dssp             HHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT-EEEE
T ss_pred             HHHhCCcEEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence            6677999999999    4459999999999965 3444

>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=91.01  E-value=0.17  Score=33.94  Aligned_cols=46  Identities=15%  Similarity=0.174  Sum_probs=32.6

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcC
Q 034895           14 MDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRG   64 (80)
Q Consensus        14 ~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG   64 (80)
                      +|++|++...++  ++|+..++|....|+++....   ...-..|.+.+|+
T Consensus       187 ~g~~V~v~~~~~--~~G~~~gId~~G~L~v~~~~G---~~~~~~Gev~~r~  232 (233)
T 2eay_A          187 LGEEVKLLGEGK--ITGKLVGLSEKGGALILTEEG---IKEILSGEFSLRR  232 (233)
T ss_dssp             TTSEEEETTEEE--EEEEEEEECTTSCEEEEETTE---EEEECSCCEEEC-
T ss_pred             cCCEEEEEECCe--EEEEEEEECCCCeEEEEECCC---eEEEEEeEEEEec
Confidence            699999976654  999999999999999975321   1122345666664

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

Probab=89.16  E-value=0.88  Score=31.67  Aligned_cols=48  Identities=17%  Similarity=0.332  Sum_probs=34.0

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcC
Q 034895           13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRG   64 (80)
Q Consensus        13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG   64 (80)
                      ++|++|+|... +..++|+..++|....|+++...   +...-..|.+.+|+
T Consensus       271 ~~g~~V~v~~~-~~~~~G~~~gid~~G~L~v~~~~---g~~~~~~Gev~~r~  318 (321)
T 1bia_A          271 FINRPVKLIIG-DKEIFGISRGIDKQGALLLEQDG---IIKPWMGGEISLRS  318 (321)
T ss_dssp             TTTSEEEEEET-TEEEEEEEEEECTTSCEEEEETT---EEEEESSCEEEEC-
T ss_pred             hcCCEEEEEEC-CcEEEEEEEEECCCCeEEEEECC---CEEEEEeeeEEEec
Confidence            36999999876 45899999999999999997532   11122345666654

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

Probab=87.33  E-value=1  Score=30.22  Aligned_cols=32  Identities=22%  Similarity=0.306  Sum_probs=28.5

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034895           13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDN   45 (80)
Q Consensus        13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~   45 (80)
                      .+|++|++...++..++|+..++|....|+ +.
T Consensus       190 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~-~~  221 (237)
T 2ej9_A          190 TIGKQVKILLSNNEIITGKVYDIDFDGIVL-GT  221 (237)
T ss_dssp             STTCEEEEEETTSCEEEEEEEEECSSEEEE-EE
T ss_pred             ccCCEEEEEECCCeEEEEEEEEECCCCeEE-Ec
Confidence            379999999988877999999999999998 64

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

Probab=84.51  E-value=0.91  Score=30.47  Aligned_cols=30  Identities=20%  Similarity=0.345  Sum_probs=24.2

Q ss_pred             cCCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034895           14 MDKKLQIKLNANRMIVGTLRGFDQFMNLVIDN   45 (80)
Q Consensus        14 ~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~   45 (80)
                      +|++|++...++  ++|+..++|....|+++.
T Consensus       188 ~g~~V~v~~~~~--~~G~~~gId~~G~L~v~~  217 (235)
T 2dxu_A          188 LGVRVKILGDGS--FEGIAEDIDDFGRLIIRL  217 (235)
T ss_dssp             CSSEEEC----C--CEEEEEEECTTSCEEEEC
T ss_pred             cCCeEEEEECCe--EEEEEEEECCCCEEEEEE
Confidence            699999988776  999999999999999975

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

Probab=82.14  E-value=1.8  Score=30.26  Aligned_cols=32  Identities=16%  Similarity=0.229  Sum_probs=27.1

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034895           13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDN   45 (80)
Q Consensus        13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~   45 (80)
                      ++|++|+|... +..++|+..++|....|++++
T Consensus       277 ~~g~~V~v~~~-~~~~~G~~~gId~~G~Llv~~  308 (323)
T 3rkx_A          277 IWNRTLLFTEN-DKQFKGQAIDLDYDGYLIVRD  308 (323)
T ss_dssp             CSSSCEEEECC--CEEEEEEEEECTTSCEEEEE
T ss_pred             hcCCEEEEEEC-CeEEEEEEEEECCCCEEEEEE
Confidence            36899999865 567999999999999999974

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

Probab=82.01  E-value=2.4  Score=28.13  Aligned_cols=29  Identities=21%  Similarity=0.282  Sum_probs=25.1

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEECCCCceEEcce
Q 034895           13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNT   46 (80)
Q Consensus        13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~   46 (80)
                      .+|++|+|   +|  ++|+..++|....|+++..
T Consensus       192 ~~g~~V~v---~~--~~G~~~gId~~G~L~v~~~  220 (235)
T 3bfm_A          192 GMGEARTE---AG--RSGTFLGVDEDFGMLLRDE  220 (235)
T ss_dssp             TTTSEEEE---TT--EEEEEEEECTTCCEEEECS
T ss_pred             hcCCEEEE---Ee--EEEEEEEECCCCeEEEEeC
Confidence            36899999   45  9999999999999999753

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

Probab=81.12  E-value=1.9  Score=25.61  Aligned_cols=18  Identities=33%  Similarity=0.717  Sum_probs=16.4

Q ss_pred             CCEEEEEEcCCeEEEEEE
Q 034895           15 DKKLQIKLNANRMIVGTL   32 (80)
Q Consensus        15 ~k~V~V~l~~g~~~~G~L   32 (80)
                      ..+|+++|.||+.+.|++
T Consensus        28 q~~v~i~l~DGs~l~GTv   45 (101)
T 2e12_A           28 QERVRIELDDGSMIAGTV   45 (101)
T ss_dssp             TCEEEEEETTSCEEEEEE
T ss_pred             eeEEEEEEcCCCeEeeee
Confidence            358999999999999997

---

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	80
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	4e-21
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	3e-19
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	4e-19
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	3e-18
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	2e-17
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	2e-17
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	3e-17
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	1e-16
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	7e-16
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	7e-16
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	2e-12
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	1e-10
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	1e-10

>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 = 76.8 bits (189), Expect = 4e-21
 Identities = 19/77 (24%), Positives = 41/77 (53%), Gaps = 11/77 (14%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-----------VNGNEKNDIG 58
          + +++D +++  L   R+ +GT + FD+ MNL++ +  E               EK  +G
Sbjct: 3  MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLG 62

Query: 59 MVVIRGNSVVTVEALEP 75
          +V++RG ++V++    P
Sbjct: 63 LVLLRGENLVSMTVEGP 79

>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 = 71.7 bits (176), Expect = 3e-19
 Identities = 21/65 (32%), Positives = 40/65 (61%), Gaps = 1/65 (1%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV-NGNEKNDIGMVVIRGNSVV 68
          L + ++  + +KL  N+ + G LR +DQ MNLV+ ++ E+ +      +G +VIRG++V+
Sbjct: 12 LAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVI 71

Query: 69 TVEAL 73
           +  L
Sbjct: 72 LISPL 76

>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 = 71.3 bits (175), Expect = 4e-19
 Identities = 19/61 (31%), Positives = 36/61 (59%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVT 69
          L+  + K++ +KL  +  I G LR FDQ +NL++++  E+        G +V+RG +V+ 
Sbjct: 7  LQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLF 66

Query: 70 V 70
          +
Sbjct: 67 I 67

>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 = 69.3 bits (170), Expect = 3e-18
 Identities = 24/62 (38%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIGMVVIRGNSVV 68
          L + +   + ++L   R   GTL G+D  MNLV+ +  E  NG     +G VVIRG++VV
Sbjct: 8  LNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVV 67

Query: 69 TV 70
           V
Sbjct: 68 FV 69

>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 = 67.4 bits (165), Expect = 2e-17
 Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV-NGNEKNDIGMVVIRGNSVV 68
          + + +DK + + L       G L G+D  +N+V+ +   + +G      G +VIRG++V+
Sbjct: 7  IHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVL 66

Query: 69 TV 70
           +
Sbjct: 67 AI 68

>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 = 66.7 bits (163), Expect = 2e-17
 Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 2/67 (2%)

Query: 10 LKKYMDKKLQIKLNAN-RMIVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIGMVVIRGNSV 67
          LK  ++ ++ +KL  N     GTL   D + NL ++   E V G     +G + IR N+V
Sbjct: 1  LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNV 60

Query: 68 VTVEALE 74
          + +  L 
Sbjct: 61 LYIRELP 67

>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 = 66.6 bits (163), Expect = 3e-17
 Identities = 21/62 (33%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV-NGNEKNDIGMVVIRGNSVV 68
          L   ++  + IKL  +R   G L+ FD  MNLV+++  E+ +G     +G V+IRG+++V
Sbjct: 11 LGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIV 70

Query: 69 TV 70
           +
Sbjct: 71 YI 72

>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 = 66.7 bits (163), Expect = 1e-16
 Identities = 14/68 (20%), Positives = 30/68 (44%), Gaps = 3/68 (4%)

Query: 9  DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVV 68
          +L   + +++Q+ L+   +  G L   D  +N+V+ N     G +      V I    +V
Sbjct: 4  ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEK---FNRVFIMYRYIV 60

Query: 69 TVEALEPV 76
           +++ E  
Sbjct: 61 HIDSTERR 68

>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 = 63.7 bits (155), Expect = 7e-16
 Identities = 15/77 (19%), Positives = 36/77 (46%), Gaps = 16/77 (20%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE----------------VNGNE 53
          + K +  ++ + +  ++   G LRGFD+++N+V+D+  E                +    
Sbjct: 10 IDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVM 69

Query: 54 KNDIGMVVIRGNSVVTV 70
           N +  +++ GN+V  +
Sbjct: 70 VNRLETILLSGNNVAML 86

>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 = 63.2 bits (154), Expect = 7e-16
 Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 10 LKKYMDKKLQIKL-NANRMIVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIGMVVIRGNSV 67
          +K  + K +++++      +VG L G D +MNL + N +E     +   +G +V+RGN+V
Sbjct: 10 VKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNV 69

Query: 68 VTV 70
          V +
Sbjct: 70 VLI 72

>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 = 54.9 bits (132), Expect = 2e-12
 Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 15/77 (19%)

Query: 9  DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV---------------NGNE 53
                + ++ I    N+ ++G ++ FD+  N+V++N  E+                 N+
Sbjct: 8  TQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNK 67

Query: 54 KNDIGMVVIRGNSVVTV 70
             I  + +RG+SV+ V
Sbjct: 68 DRYISKMFLRGDSVIVV 84

>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 = 49.8 bits (119), Expect = 1e-10
 Identities = 11/62 (17%), Positives = 20/62 (32%), Gaps = 1/62 (1%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE-VNGNEKNDIGMVVIRGNSVV 68
          L +     +  + N   +  G L   +  MN  + N            +  V IRG  + 
Sbjct: 7  LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIR 66

Query: 69 TV 70
           +
Sbjct: 67 FL 68

>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 = 50.1 bits (120), Expect = 1e-10
 Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV-NGNEKNDIGMVVIRGNSV 67
          L K   + + I+L     + GT+ G D  MN  +          E   +  + IRGN++
Sbjct: 6  LMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNI 64

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	80
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.93
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.92
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.92
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.91
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.91
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.91
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.91
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.9
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.9
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.88
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.88
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.88
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.81
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	97.63
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	97.06
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	96.45
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	96.08
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	96.0
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	94.58

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

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

Probab=99.93  E-value=7.9e-26  Score=130.22  Aligned_cols=67  Identities=28%  Similarity=0.529  Sum_probs=63.0

Q ss_pred             CchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcCCcEEEEEecC
Q 034895            8 PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALE   74 (80)
Q Consensus         8 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~d   74 (80)
                      ..|++++|++|.|+|+||+.|+|+|.+||+|||++|+||.|...++.+++|.+||||++|++|++++
T Consensus         5 ~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~~~~~~~g~v~iRG~~I~~I~~~P   71 (71)
T d1i8fa_           5 ATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP   71 (71)
T ss_dssp             HHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEECGGGEEEEEECC
T ss_pred             HHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEECCCEEEcceEEEeCCeEEEEeCCC
Confidence            4599999999999999999999999999999999999999998778889999999999999998753

>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=99.92  E-value=4.1e-25  Score=126.83  Aligned_cols=67  Identities=27%  Similarity=0.544  Sum_probs=62.2

Q ss_pred             CCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEe
Q 034895            6 QPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEA   72 (80)
Q Consensus         6 ~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~   72 (80)
                      .|++ |++++|++|+|+|+||+.|+|+|.+||+|||++|+||.|.. +++.+++|.+||||++|++|++
T Consensus         2 ~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~l~~~~IRG~~I~~Isp   70 (71)
T d1h641_           2 RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISP   70 (71)
T ss_dssp             CHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEE
T ss_pred             CchHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecCCcEeEcCcEEEECCeEEEEeC
Confidence            5777 89999999999999999999999999999999999999885 5667889999999999999976

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

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

Probab=99.92  E-value=1.2e-24  Score=125.89  Aligned_cols=69  Identities=33%  Similarity=0.627  Sum_probs=63.5

Q ss_pred             CCCCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEe
Q 034895            4 SGQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEA   72 (80)
Q Consensus         4 ~~~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~   72 (80)
                      ...|++ |+++++++|.|+|+||+.|+|+|.+||+|||++|+||.|.+ +++.+++|.+||||++|.+|++
T Consensus         4 ~~~Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~~~~~~~~~~~IRG~~I~~I~p   74 (74)
T d1mgqa_           4 VQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP   74 (74)
T ss_dssp             TTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEC
T ss_pred             ccCcHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCCCeEeEcceEEEeCCEEEEEeC
Confidence            346888 89999999999999999999999999999999999999986 5677889999999999999974

>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=99.91  E-value=6.6e-25  Score=126.39  Aligned_cols=67  Identities=37%  Similarity=0.648  Sum_probs=61.9

Q ss_pred             CCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEe
Q 034895            6 QPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEA   72 (80)
Q Consensus         6 ~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~   72 (80)
                      .|++ |+++++++|+|+|+||++|+|+|.+||+|||++|+||.|+. ++..+++|.+||||++|++|++
T Consensus         3 ~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~IRG~~I~~Isp   71 (72)
T d1i4k1_           3 RPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVFVSP   71 (72)
T ss_dssp             CHHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSSSEEEEEEEEEECGGGEEEEEC
T ss_pred             ChHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecCCeEeEcceEEEeCCeEEEEEc
Confidence            4666 89999999999999999999999999999999999999986 5677899999999999999974

>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=99.91  E-value=1.1e-24  Score=126.58  Aligned_cols=64  Identities=33%  Similarity=0.661  Sum_probs=60.1

Q ss_pred             hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEec
Q 034895           10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEAL   73 (80)
Q Consensus        10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~   73 (80)
                      |.+++|++|+|+|+||+.|+|+|.+||+|||++|+||+|+. +++.+.+|.+||||++|++|++.
T Consensus        12 L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~~~v~iRG~~I~~I~~~   76 (76)
T d1th7a1          12 LAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILISPL   76 (76)
T ss_dssp             HHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECGGGEEEEEEC
T ss_pred             HHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecCCcccCcceEEEECCEEEEEEeC
Confidence            89999999999999999999999999999999999999975 55678999999999999999874

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

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

Probab=99.91  E-value=2.9e-24  Score=123.76  Aligned_cols=69  Identities=17%  Similarity=0.178  Sum_probs=63.9

Q ss_pred             CCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecC
Q 034895            6 QPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALE   74 (80)
Q Consensus         6 ~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d   74 (80)
                      .|+. |.++.|++|+|+|+||++|+|+|.+||.|||++|+||.+.. +++.++++.+||||++|.+|+.||
T Consensus         2 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~v~IRG~~I~~i~lpd   72 (72)
T d1d3ba_           2 VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLILPD   72 (72)
T ss_dssp             CHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECGGGEEEEEECC
T ss_pred             CchHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCCCcEeEcCeEEEECCEEEEEEcCC
Confidence            5777 89999999999999999999999999999999999999875 456778999999999999999987

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

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

Probab=99.91  E-value=2.4e-24  Score=126.50  Aligned_cols=65  Identities=28%  Similarity=0.582  Sum_probs=59.2

Q ss_pred             chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-----------CceeeeecEEEEcCCcEEEEEec
Q 034895            9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-----------GNEKNDIGMVVIRGNSVVTVEAL   73 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-----------~~~~~~~g~v~IrG~~I~~I~~~   73 (80)
                      +|.+|++++|+|.|+|||.|.|+|.|||+||||+|+||.|++           ..+.|.+|+++|||++|++|+..
T Consensus         2 ~L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~~   77 (81)
T d1d3bb_           2 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVE   77 (81)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEE
T ss_pred             hhHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEcc
Confidence            589999999999999999999999999999999999999974           12458899999999999999864

>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=99.90  E-value=6.7e-24  Score=121.18  Aligned_cols=65  Identities=28%  Similarity=0.475  Sum_probs=58.7

Q ss_pred             hhhhcCCEEEEEEc-CCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecC
Q 034895           10 LKKYMDKKLQIKLN-ANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALE   74 (80)
Q Consensus        10 L~~~~~k~V~V~l~-~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d   74 (80)
                      |+++++++|.|+|+ +|++|+|+|.+||+|||++|+||+|.. ++..+.+|.+||||++|.+|+..+
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~IRG~nI~~I~~~p   67 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELP   67 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECGGGEEEEEECC
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEecCCcccCcCeEEEECCEEEEEEeCC
Confidence            67899999999999 568899999999999999999999975 566788999999999999998543

>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=99.90  E-value=8.3e-24  Score=122.80  Aligned_cols=68  Identities=29%  Similarity=0.618  Sum_probs=61.7

Q ss_pred             CCCCc-hhhhcCCEEEEEEcCC-eEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEe
Q 034895            5 GQPPD-LKKYMDKKLQIKLNAN-RMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEA   72 (80)
Q Consensus         5 ~~p~~-L~~~~~k~V~V~l~~g-~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~   72 (80)
                      ..|.. |+++++++|+|+|++| ++|.|+|.+||+|||++|+||.|+. +++.+++|.+||||++|.+|.+
T Consensus         4 ~~P~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~IRG~~I~~I~p   74 (75)
T d1ljoa_           4 VLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQP   74 (75)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEE
T ss_pred             cccHHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCCCcEeEcceEEEeCCEEEEEEC
Confidence            35666 8999999999999976 8999999999999999999999975 5677899999999999999985

>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=99.88  E-value=4.4e-23  Score=123.97  Aligned_cols=72  Identities=25%  Similarity=0.463  Sum_probs=61.5

Q ss_pred             CCCc-hhhhc--CCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecC---------------ceeeeecEEEEcCCcE
Q 034895            6 QPPD-LKKYM--DKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG---------------NEKNDIGMVVIRGNSV   67 (80)
Q Consensus         6 ~p~~-L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~---------------~~~~~~g~v~IrG~~I   67 (80)
                      .|+. |.+++  +++|.|.+++|+.+.|+|.|||+||||+|+||+|++.               ...|.+|.+||||+||
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            4777 77787  8999999999999999999999999999999999751               1347899999999999


Q ss_pred             EEEEecCCcc
Q 034895           68 VTVEALEPVS   77 (80)
Q Consensus        68 ~~I~~~d~~~   77 (80)
                      ++|..++...
T Consensus        82 v~I~~~p~~~   91 (93)
T d1b34b_          82 IVVLRNPLIA   91 (93)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEEcChhhc
Confidence            9998877643

>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=99.88  E-value=8.2e-24  Score=126.62  Aligned_cols=67  Identities=24%  Similarity=0.517  Sum_probs=60.1

Q ss_pred             CCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecC----------------ceeeeecEEEEcCCcEE
Q 034895            6 QPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG----------------NEKNDIGMVVIRGNSVV   68 (80)
Q Consensus         6 ~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~----------------~~~~~~g~v~IrG~~I~   68 (80)
                      .|++ |+++++++|+|.|+||+.|.|+|.|||+||||+|+||.|++.                ...|++|++||||++|+
T Consensus         5 ~Pl~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~~Vv   84 (92)
T d2fwka1           5 LPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVA   84 (92)
T ss_dssp             CHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGEE
T ss_pred             ChHHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCCEEE
Confidence            5666 899999999999999999999999999999999999999741                13467999999999999


Q ss_pred             EEEe
Q 034895           69 TVEA   72 (80)
Q Consensus        69 ~I~~   72 (80)
                      +|++
T Consensus        85 ~I~p   88 (92)
T d2fwka1          85 MLVP   88 (92)
T ss_dssp             EEES
T ss_pred             EEEe
Confidence            9985

>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=99.88  E-value=2.4e-22  Score=117.78  Aligned_cols=69  Identities=22%  Similarity=0.274  Sum_probs=63.7

Q ss_pred             chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecCCcc
Q 034895            9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALEPVS   77 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d~~~   77 (80)
                      .|+++.|++|.|+|+||.+|+|+|.++|.|||+.|+||.+.. +++...++.+||||++|.||+.||.+.
T Consensus         5 fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~~Ir~i~lPd~l~   74 (80)
T d1b34a_           5 FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLP   74 (80)
T ss_dssp             HHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTTCC
T ss_pred             HHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCCEEEcccEEEcCCEEEEEECCCCcc
Confidence            378899999999999999999999999999999999999985 456678999999999999999999865

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

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

Probab=99.81  E-value=9.6e-20  Score=114.66  Aligned_cols=64  Identities=22%  Similarity=0.419  Sum_probs=59.5

Q ss_pred             chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcCCcEEEEEecCC
Q 034895            9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALEP   75 (80)
Q Consensus         9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~d~   75 (80)
                      +|++++|++|.|+|+||+.|+|+|.+||++||++|+||.+..++   .++.++|||++|++|..++.
T Consensus         4 ~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~~~---k~~~v~IRG~~I~~I~~~e~   67 (127)
T d1m5q1_           4 ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGE---KFNRVFIMYRYIVHIDSTER   67 (127)
T ss_dssp             HHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETTCC---EEEEEEECGGGEEEEEECSC
T ss_pred             HHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECCCC---cccEEEEeCCeEEEEEcchh
Confidence            48899999999999999999999999999999999999987655   47889999999999999876

>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=97.63  E-value=0.00047  Score=38.97  Aligned_cols=64  Identities=16%  Similarity=0.316  Sum_probs=52.7

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEEC-CCCceEEcceEEec--Cc--------eeeeecEEEEcCCcEEEEEecCCc
Q 034895           13 YMDKKLQIKLNANRMIVGTLRGFD-QFMNLVIDNTVEVN--GN--------EKNDIGMVVIRGNSVVTVEALEPV   76 (80)
Q Consensus        13 ~~~k~V~V~l~~g~~~~G~L~~~D-~~~NlvL~~~~e~~--~~--------~~~~~g~v~IrG~~I~~I~~~d~~   76 (80)
                      |+|++|.+..+.+-.|+|+|..+| +..-+.|+|+..+.  +.        ...-++.+..||+.|.-+...+.-
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            689999999999999999999999 66778999998763  11        122468999999999999887653

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

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

Probab=97.06  E-value=0.0016  Score=32.97  Aligned_cols=32  Identities=19%  Similarity=0.564  Sum_probs=28.4

Q ss_pred             hcCCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034895           13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDN   45 (80)
Q Consensus        13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~   45 (80)
                      |+|++|+|..- +++++|+..++|....|+|+.
T Consensus         1 f~gk~V~v~~g-~~~i~G~a~gId~~G~Lll~t   32 (47)
T d1biaa2           1 FINRPVKLIIG-DKEIFGISRGIDKQGALLLEQ   32 (47)
T ss_dssp             TTTSEEEEEET-TEEEEEEEEEECTTSCEEEEE
T ss_pred             CCCCEEEEEEC-CeEEEEEEeeECCCCcEEEEE
Confidence            68999999765 578999999999999999974

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

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

Probab=96.45  E-value=0.012  Score=31.39  Aligned_cols=58  Identities=22%  Similarity=0.437  Sum_probs=43.0

Q ss_pred             hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcCCcEEEEE
Q 034895           10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVE   71 (80)
Q Consensus        10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~   71 (80)
                      |.++-|++|-|.......|+|+|.-||... +.|+|+....|++-   ..++++=+.|-.|.
T Consensus         7 L~~WKg~kvAv~vgsehSFtGiledFDeEv-iLL~dV~D~~GNk~---k~llv~idD~nWim   64 (66)
T d1ycya1           7 LKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIGNRG---KQMLIGLEDINWIM   64 (66)
T ss_dssp             HHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTEEEE---EEEEEEGGGEEEEE
T ss_pred             HHHhCCcEEEEEecCcceeEEEhhhcCcce-EeehhhHHHhcccc---ceeEEEeccceeEE
Confidence            788999999999999999999999999874 78999998876543   35666666666554

>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=96.08  E-value=0.0073  Score=32.18  Aligned_cols=31  Identities=6%  Similarity=0.242  Sum_probs=27.2

Q ss_pred             CCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034895           15 DKKLQIKLNANRMIVGTLRGFDQFMNLVIDN   45 (80)
Q Consensus        15 ~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~   45 (80)
                      ..+|.|-|.||-.++|.+.+||+|.=+.-.+
T Consensus        14 ~~~VtifL~nGvkl~G~I~~fD~ftvlL~~~   44 (60)
T d1kq1a_          14 QTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQ   44 (60)
T ss_dssp             TCEEEEEETTSCEEEEEEEEECSSEEEEEET
T ss_pred             CCcEEEEEECCcEEEEEEEEEcceEEEEEeC
Confidence            5789999999999999999999998666544

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

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

Probab=96.00  E-value=0.0051  Score=33.38  Aligned_cols=29  Identities=24%  Similarity=0.417  Sum_probs=25.3

Q ss_pred             CCEEEEEEcCCeEEEEEEEEECCCCceEEc
Q 034895           15 DKKLQIKLNANRMIVGTLRGFDQFMNLVID   44 (80)
Q Consensus        15 ~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~   44 (80)
                      ..+|.|.|.||-.++|.+.+||+|.= .|+
T Consensus        14 ~~~VtifL~nGvkl~G~I~~fD~ftv-LL~   42 (66)
T d1u1sa1          14 RVPVSIYLVNGIKLQGQIESFDQFVI-LLK   42 (66)
T ss_dssp             TCCEEEEETTSCEEEEEEEEECSSEE-EEE
T ss_pred             CCcEEEEEEcCcEEEEEEEEEcceEE-EEE
Confidence            56899999999999999999999965 443

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

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

Probab=94.58  E-value=0.012  Score=31.90  Aligned_cols=35  Identities=20%  Similarity=0.337  Sum_probs=28.1

Q ss_pred             CchhhhcCCEEEEEEc---CC-eEEEEEEEEECCCCceEE
Q 034895            8 PDLKKYMDKKLQIKLN---AN-RMIVGTLRGFDQFMNLVI   43 (80)
Q Consensus         8 ~~L~~~~~k~V~V~l~---~g-~~~~G~L~~~D~~~NlvL   43 (80)
                      .++..++|+.|.|+|+   +| +.++|+|.++|+.. +.|
T Consensus         7 ~~f~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~~-i~l   45 (74)
T d1ib8a1           7 DAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEEDE-LTM   45 (74)
T ss_dssp             HHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETTE-EEE
T ss_pred             HHHHHhCCCEEEEEEecccCCceEEEEEEEeecCCe-EEE
Confidence            3578899999999984   34 89999999999764 444