Psyllid ID: psy6026

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10
Protein Sequence
MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQLLQDATRKEAVNATR
Secondary Structure (PSIPRED)
cccccHHHHHHHccccEEEEEEccccEEEEEEEEEcccccEEEEcEEEEccccccEEccccEEEEEcccEEEEEEccccccHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHccccEEEEEEccEEEEEEEEEcccEEEEEEcEEEEEcccccccEEEccEEEEEccEEEEEEcccccccHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNikltdisvtdpdkyphmlsvkncfirgsvvryvqlpgdevdtQLLQDATRKEAVNATR
Flexible Loop (DISEMBL)
MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPgdevdtqllqdatrkeavnatr
Low Complexity Region (SEG)
MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQLLQDATRKEAVNATR
Disordered region (IsUnstruct)
***LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEV******************
Disordered Region (DISOPRED)
*ERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDT****************
Disordered Region (DISEMBL)
MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQLLQDAT*********
Disordered Region (DISPRO)
*ERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQLLQDATRKE******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQLLQDATRKEAVNATR
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	98	2.2.26 [Sep-21-2011]
O35900	95	U6 snRNA-associated Sm-li	yes	N/A	0.938	0.968	0.923	3e-45
Q9Y333	95	U6 snRNA-associated Sm-li	yes	N/A	0.938	0.968	0.923	3e-45
Q54TF6	117	Probable U6 snRNA-associa	yes	N/A	0.918	0.769	0.688	4e-32
P38203	95	U6 snRNA-associated Sm-li	yes	N/A	0.928	0.957	0.659	1e-28
O94408	96	U6 snRNA-associated Sm-li	yes	N/A	0.969	0.989	0.610	3e-27
A9CTE0	97	Probable U6 snRNA-associa	N/A	N/A	0.877	0.886	0.329	2e-10
Q8SQK1	94	Probable U6 snRNA-associa	yes	N/A	0.795	0.829	0.385	3e-09
Q9QXA5	137	U6 snRNA-associated Sm-li	no	N/A	0.846	0.605	0.337	1e-06
Q9Y4Z0	139	U6 snRNA-associated Sm-li	no	N/A	0.765	0.539	0.35	2e-06
Q3ZBK6	139	U6 snRNA-associated Sm-li	no	N/A	0.765	0.539	0.35	2e-06

>sp|O35900|LSM2_MOUSE U6 snRNA-associated Sm-like protein LSm2 OS=Mus musculus GN=Lsm2 PE=3 SV=1

 Score =  179 bits (455), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 85/92 (92%), Positives = 89/92 (96%)

Query: 4  LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
          +LFYSFFKSLVGKDVVVELKND+SICGTLHSVDQYLNIKLTDISVTDP+KYPHMLSVKNC
Sbjct: 1  MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC 60

Query: 64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEAVN 95
          FIRGSVVRYVQLP DEVDTQLLQDA RKEA+ 
Sbjct: 61 FIRGSVVRYVQLPADEVDTQLLQDAARKEALQ 92

Binds specifically to the 3'-terminal U-tract of U6 snRNA. May be involved in pre-mRNA splicing.
Mus musculus (taxid: 10090)

>sp|Q9Y333|LSM2_HUMAN U6 snRNA-associated Sm-like protein LSm2 OS=Homo sapiens GN=LSM2 PE=1 SV=1

 Score =  179 bits (455), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 85/92 (92%), Positives = 89/92 (96%)

Query: 4  LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
          +LFYSFFKSLVGKDVVVELKND+SICGTLHSVDQYLNIKLTDISVTDP+KYPHMLSVKNC
Sbjct: 1  MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC 60

Query: 64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEAVN 95
          FIRGSVVRYVQLP DEVDTQLLQDA RKEA+ 
Sbjct: 61 FIRGSVVRYVQLPADEVDTQLLQDAARKEALQ 92

Binds specifically to the 3'-terminal U-tract of U6 snRNA. May be involved in pre-mRNA splicing.

Homo sapiens (taxid: 9606)

>sp|Q54TF6|LSM2_DICDI Probable U6 snRNA-associated Sm-like protein LSm2 OS=Dictyostelium discoideum GN=lsm2 PE=3 SV=1

 Score =  136 bits (342), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 62/90 (68%), Positives = 76/90 (84%)

Query: 4  LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
          +LF+SF+KSLVGK++ VELKND+SI G L SVDQ+LNIKL DI V + DKYP+M+SVKNC
Sbjct: 1  MLFFSFYKSLVGKEITVELKNDLSITGLLQSVDQFLNIKLKDIKVNEEDKYPYMISVKNC 60

Query: 64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEA 93
          FIRGSVVRYV LP ++VD + LQD +R EA
Sbjct: 61 FIRGSVVRYVHLPAEDVDVETLQDHSRLEA 90

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

Dictyostelium discoideum (taxid: 44689)

>sp|P38203|LSM2_YEAST U6 snRNA-associated Sm-like protein LSm2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=LSM2 PE=1 SV=1

 Score =  124 bits (312), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 60/91 (65%), Positives = 74/91 (81%)

Query: 4  LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
          +LF+SFFK+LV ++VVVELKND+ I GTL SVDQ+LN+KL +IS TD  KYPH+ SV+N 
Sbjct: 1  MLFFSFFKTLVDQEVVVELKNDIEIKGTLQSVDQFLNLKLDNISCTDEKKYPHLGSVRNI 60

Query: 64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEAV 94
          FIRGS VRYV L  + VDT LLQDATR+E +
Sbjct: 61 FIRGSTVRYVYLNKNMVDTNLLQDATRREVM 91

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

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

>sp|O94408|LSM2_SCHPO U6 snRNA-associated Sm-like protein LSm2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=lsm2 PE=3 SV=1

 Score =  120 bits (300), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 58/95 (61%), Positives = 71/95 (74%)

Query: 4  LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
          +LFYSFFK+L+  +V VELKND+SI G L SVDQ+LN+KL +ISV D  KYPHM +VK+ 
Sbjct: 1  MLFYSFFKTLIDTEVTVELKNDMSIRGILKSVDQFLNVKLENISVVDASKYPHMAAVKDL 60

Query: 64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEAVNATR 98
          FIRGSVVRYV +    VDT LL DA R++  N  R
Sbjct: 61 FIRGSVVRYVHMSSAYVDTILLADACRRDLANNKR 95

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

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

>sp|A9CTE0|LSM2_ENTBH Probable U6 snRNA-associated Sm-like protein LSm2 OS=Enterocytozoon bieneusi (strain H348) GN=LSM2 PE=3 SV=1

 Score = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/91 (32%), Positives = 59/91 (64%), Gaps = 5/91 (5%)

Query: 4  LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKY----PHMLS 59
          +LF+ +FKS +  +++V LKND+SI G L +VD +LNIK+ ++     +++      + +
Sbjct: 1  MLFFEYFKSQLNNEIIVNLKNDISISGILKNVDPFLNIKIENVIAISTNEFIKINKSITN 60

Query: 60 VKNCFIRGSVVRYVQLPGDEVDTQLLQDATR 90
          ++ C IRGS ++ V+L  + ++  +++ ATR
Sbjct: 61 IQLCSIRGSAIKSVELKKNGLEEHMVE-ATR 90

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. LSM2 binds specifically to the 3'-terminal U-tract of U6 snRNA. Required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

Enterocytozoon bieneusi (strain H348) (taxid: 481877)

>sp|Q8SQK1|LSM2_ENCCU Probable U6 snRNA-associated Sm-like protein LSm2 OS=Encephalitozoon cuniculi (strain GB-M1) GN=LSM2 PE=3 SV=1

 Score = 60.5 bits (145), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 32/83 (38%), Positives = 49/83 (59%), Gaps = 5/83 (6%)

Query: 4  LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
          +LFY FF+S +G  V V LK  V + G L  +D YLN+ L D+ +     +P + S+  C
Sbjct: 1  MLFYEFFRSSIGSRVSVMLKAGVYVSGRLGGIDPYLNLSLLDVRIL--SSHPGLSSISVC 58

Query: 64 FIRGSVVRYVQLPGDEVDTQLLQ 86
           IRGS ++Y+ +   + D +LLQ
Sbjct: 59 SIRGSSIKYILV---DKDAKLLQ 78

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. LSM2 binds specifically to the 3'-terminal U-tract of U6 snRNA. Required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.

Encephalitozoon cuniculi (strain GB-M1) (taxid: 284813)

>sp|Q9QXA5|LSM4_MOUSE U6 snRNA-associated Sm-like protein LSm4 OS=Mus musculus GN=Lsm4 PE=2 SV=1

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/89 (33%), Positives = 51/89 (57%), Gaps = 6/89 (6%)

Query: 4  LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVT--DPDKYPHMLSVK 61
          +L  S  K+     ++VELKN  +  G L S D ++NI L ++  T  D DK+  M    
Sbjct: 1  MLPLSLLKTAQNHPMLVELKNGETYNGHLVSCDNWMNINLREVICTSRDGDKFWRM---P 57

Query: 62 NCFIRGSVVRYVQLPGDEVDTQLLQDATR 90
           C+IRGS ++Y+++P DE+   + ++A +
Sbjct: 58 ECYIRGSTIKYLRIP-DEIIDMVREEAAK 85

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

Mus musculus (taxid: 10090)

>sp|Q9Y4Z0|LSM4_HUMAN U6 snRNA-associated Sm-like protein LSm4 OS=Homo sapiens GN=LSM4 PE=1 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 46/80 (57%), Gaps = 5/80 (6%)

Query: 4  LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVT--DPDKYPHMLSVK 61
          +L  S  K+     ++VELKN  +  G L S D ++NI L ++  T  D DK+  M    
Sbjct: 1  MLPLSLLKTAQNHPMLVELKNGETYNGHLVSCDNWMNINLREVICTSRDGDKFWRM---P 57

Query: 62 NCFIRGSVVRYVQLPGDEVD 81
           C+IRGS ++Y+++P + +D
Sbjct: 58 ECYIRGSTIKYLRIPDEIID 77

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

Homo sapiens (taxid: 9606)

>sp|Q3ZBK6|LSM4_BOVIN U6 snRNA-associated Sm-like protein LSm4 OS=Bos taurus GN=LSM4 PE=2 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 46/80 (57%), Gaps = 5/80 (6%)

Query: 4  LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVT--DPDKYPHMLSVK 61
          +L  S  K+     ++VELKN  +  G L S D ++NI L ++  T  D DK+  M    
Sbjct: 1  MLPLSLLKTAQNHPMLVELKNGETYNGHLVSCDNWMNINLREVICTSRDGDKFWRM---P 57

Query: 62 NCFIRGSVVRYVQLPGDEVD 81
           C+IRGS ++Y+++P + +D
Sbjct: 58 ECYIRGSTIKYLRIPDEIID 77

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

Bos taurus (taxid: 9913)

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	98
195012846	104	GH15400 [Drosophila grimshawi] gi|193897	0.979	0.923	0.937	7e-46
350410763	140	PREDICTED: U6 snRNA-associated Sm-like p	0.979	0.685	0.906	1e-45
195440762	106	GK10160 [Drosophila willistoni] gi|19416	0.959	0.886	0.946	2e-45
21358381	95	CG10418 [Drosophila melanogaster] gi|195	0.969	1.0	0.936	2e-45
157118346	95	small nuclear ribonucleoprotein Sm D1, p	0.969	1.0	0.926	3e-45
194869802	112	GG15573 [Drosophila erecta] gi|190654307	0.959	0.839	0.946	3e-45
345488169	95	PREDICTED: U6 snRNA-associated Sm-like p	0.969	1.0	0.926	3e-45
195102462	94	GH23600 [Drosophila grimshawi] gi|193905	0.959	1.0	0.946	4e-45
195126148	95	GI13004 [Drosophila mojavensis] gi|19391	0.969	1.0	0.926	5e-45
125978707	95	GA10305 [Drosophila pseudoobscura pseudo	0.969	1.0	0.926	5e-45

>gi|195012846|ref|XP_001983759.1| GH15400 [Drosophila grimshawi] gi|193897241|gb|EDV96107.1| GH15400 [Drosophila grimshawi]

 Score =  187 bits (475), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 90/96 (93%), Positives = 93/96 (96%)

Query: 3   RLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKN 62
           R LFYSFFKSLVGK+VVVELKND+SICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKN
Sbjct: 9   RTLFYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKN 68

Query: 63  CFIRGSVVRYVQLPGDEVDTQLLQDATRKEAVNATR 98
           CFIRGSVVRYVQLPGDEVDTQLLQDA RKEAV +TR
Sbjct: 69  CFIRGSVVRYVQLPGDEVDTQLLQDAARKEAVVSTR 104

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350410763|ref|XP_003489131.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm2-like [Bombus impatiens]

 Score =  186 bits (473), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 87/96 (90%), Positives = 91/96 (94%)

Query: 3   RLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKN 62
           ++LFYSFFKSL+GKDVVVELKND+SICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKN
Sbjct: 45  KMLFYSFFKSLIGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKN 104

Query: 63  CFIRGSVVRYVQLPGDEVDTQLLQDATRKEAVNATR 98
           CFIRGSVVRYVQLPGDEVDTQLLQDA RKEA    R
Sbjct: 105 CFIRGSVVRYVQLPGDEVDTQLLQDAARKEAAVQAR 140

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195440762|ref|XP_002068209.1| GK10160 [Drosophila willistoni] gi|194164294|gb|EDW79195.1| GK10160 [Drosophila willistoni]

 Score =  186 bits (472), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 89/94 (94%), Positives = 92/94 (97%)

Query: 5   LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCF 64
           LFYSFFKSLVGK+VVVELKND+SICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCF
Sbjct: 13  LFYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCF 72

Query: 65  IRGSVVRYVQLPGDEVDTQLLQDATRKEAVNATR 98
           IRGSVVRYVQLPGDEVDTQLLQDA RKEAV +TR
Sbjct: 73  IRGSVVRYVQLPGDEVDTQLLQDAARKEAVVSTR 106

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|21358381|ref|NP_648570.1| CG10418 [Drosophila melanogaster] gi|195327103|ref|XP_002030261.1| GM25341 [Drosophila sechellia] gi|195376259|ref|XP_002046914.1| GJ13149 [Drosophila virilis] gi|195493810|ref|XP_002094573.1| GE21899 [Drosophila yakuba] gi|195589798|ref|XP_002084636.1| GD14374 [Drosophila simulans] gi|7294589|gb|AAF49929.1| CG10418 [Drosophila melanogaster] gi|194119204|gb|EDW41247.1| GM25341 [Drosophila sechellia] gi|194154072|gb|EDW69256.1| GJ13149 [Drosophila virilis] gi|194180674|gb|EDW94285.1| GE21899 [Drosophila yakuba] gi|194196645|gb|EDX10221.1| GD14374 [Drosophila simulans] gi|220951570|gb|ACL88328.1| CG10418-PA [synthetic construct]

 Score =  186 bits (471), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 89/95 (93%), Positives = 93/95 (97%)

Query: 4  LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
          +LFYSFFKSLVGK+VVVELKND+SICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC
Sbjct: 1  MLFYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 60

Query: 64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEAVNATR 98
          FIRGSVVRYVQLPGDEVDTQLLQDA RKEAV +TR
Sbjct: 61 FIRGSVVRYVQLPGDEVDTQLLQDAARKEAVVSTR 95

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157118346|ref|XP_001653182.1| small nuclear ribonucleoprotein Sm D1, putative [Aedes aegypti] gi|158292631|ref|XP_314020.2| AGAP005136-PA [Anopheles gambiae str. PEST] gi|108883305|gb|EAT47530.1| AAEL001363-PA [Aedes aegypti] gi|157017082|gb|EAA09471.3| AGAP005136-PA [Anopheles gambiae str. PEST]

 Score =  185 bits (470), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 88/95 (92%), Positives = 92/95 (96%)

Query: 4  LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
          +LFYSFFKSLVGKDVVVELKND+SICGTLHSVDQYLNIKLTDISVTDP+KYPHMLSVKNC
Sbjct: 1  MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC 60

Query: 64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEAVNATR 98
          FIRGSVVRYVQLPGDEVDTQLLQDA RKEAV + R
Sbjct: 61 FIRGSVVRYVQLPGDEVDTQLLQDAARKEAVTSVR 95

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194869802|ref|XP_001972524.1| GG15573 [Drosophila erecta] gi|190654307|gb|EDV51550.1| GG15573 [Drosophila erecta]

 Score =  185 bits (469), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 89/94 (94%), Positives = 92/94 (97%)

Query: 5   LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCF 64
           LFYSFFKSLVGK+VVVELKND+SICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCF
Sbjct: 19  LFYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCF 78

Query: 65  IRGSVVRYVQLPGDEVDTQLLQDATRKEAVNATR 98
           IRGSVVRYVQLPGDEVDTQLLQDA RKEAV +TR
Sbjct: 79  IRGSVVRYVQLPGDEVDTQLLQDAARKEAVVSTR 112

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345488169|ref|XP_001605095.2| PREDICTED: U6 snRNA-associated Sm-like protein LSm2-like [Nasonia vitripennis]

 Score =  185 bits (469), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 88/95 (92%), Positives = 91/95 (95%)

Query: 4  LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
          +LFYSFFKSLVGKDVVVELKND+SICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC
Sbjct: 1  MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 60

Query: 64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEAVNATR 98
          FIRGSVVRYVQLPGDEVDTQLLQDA RKEA   +R
Sbjct: 61 FIRGSVVRYVQLPGDEVDTQLLQDAARKEAATQSR 95

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195102462|ref|XP_001998083.1| GH23600 [Drosophila grimshawi] gi|193905529|gb|EDW04396.1| GH23600 [Drosophila grimshawi]

 Score =  184 bits (468), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 89/94 (94%), Positives = 92/94 (97%)

Query: 5  LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCF 64
          LFYSFFKSLVGK+VVVELKND+SICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCF
Sbjct: 1  LFYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCF 60

Query: 65 IRGSVVRYVQLPGDEVDTQLLQDATRKEAVNATR 98
          IRGSVVRYVQLPGDEVDTQLLQDA RKEAV +TR
Sbjct: 61 IRGSVVRYVQLPGDEVDTQLLQDAARKEAVVSTR 94

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195126148|ref|XP_002007536.1| GI13004 [Drosophila mojavensis] gi|193919145|gb|EDW18012.1| GI13004 [Drosophila mojavensis]

 Score =  184 bits (468), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 88/95 (92%), Positives = 93/95 (97%)

Query: 4  LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
          +LFYSFFKSLVGK+VVVELKND+SICGTLHSVDQYLNIKLTDISVTDP+KYPHMLSVKNC
Sbjct: 1  MLFYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC 60

Query: 64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEAVNATR 98
          FIRGSVVRYVQLPGDEVDTQLLQDA RKEAV +TR
Sbjct: 61 FIRGSVVRYVQLPGDEVDTQLLQDAARKEAVVSTR 95

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|125978707|ref|XP_001353386.1| GA10305 [Drosophila pseudoobscura pseudoobscura] gi|195160603|ref|XP_002021164.1| GL25187 [Drosophila persimilis] gi|54642144|gb|EAL30893.1| GA10305 [Drosophila pseudoobscura pseudoobscura] gi|194118277|gb|EDW40320.1| GL25187 [Drosophila persimilis]

 Score =  184 bits (468), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 88/95 (92%), Positives = 93/95 (97%)

Query: 4  LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
          +LFYSFFKSLVGK+VVVELKND+SICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC
Sbjct: 1  MLFYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 60

Query: 64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEAVNATR 98
          FIRGSVVRYVQLPG+EVDTQLLQDA RKEAV +TR
Sbjct: 61 FIRGSVVRYVQLPGEEVDTQLLQDAARKEAVVSTR 95

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	98
UNIPROTKB|A6QQV3	95	LSM2 "LSM2 protein" [Bos tauru	0.928	0.957	0.934	8.4e-42
UNIPROTKB|Q9Y333	95	LSM2 "U6 snRNA-associated Sm-l	0.928	0.957	0.934	8.4e-42
MGI|MGI:90676	95	Lsm2 "LSM2 homolog, U6 small n	0.928	0.957	0.934	8.4e-42
ZFIN|ZDB-GENE-000616-10	95	smx5 "smx5" [Danio rerio (taxi	0.918	0.947	0.944	1.1e-41
WB|WBGene00001808	97	gut-2 [Caenorhabditis elegans	0.948	0.958	0.795	1.5e-37
TAIR|locus:2014480	93	LSM2 "AT1G03330" [Arabidopsis	0.918	0.967	0.733	2.6e-31
UNIPROTKB|I3LGB3	72	LSM2 "Uncharacterized protein"	0.693	0.944	0.941	2.3e-30
DICTYBASE|DDB_G0281779	117	lsm2 "putative U6 small nuclea	0.918	0.769	0.688	7.9e-30
ASPGD|ASPL0000065787	98	AN10963 [Emericella nidulans (	0.938	0.938	0.695	9.1e-29
UNIPROTKB|G4NCP9	97	MGG_00355 "U6 snRNA-associated	0.938	0.948	0.619	7.3e-27

UNIPROTKB|A6QQV3 LSM2 "LSM2 protein" [Bos taurus (taxid:9913)]

 Score = 443 (161.0 bits), Expect = 8.4e-42, P = 8.4e-42
 Identities = 85/91 (93%), Positives = 89/91 (97%)

Query:     4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
             +LFYSFFKSLVGKDVVVELKND+SICGTLHSVDQYLNIKLTDISVTDP+KYPHMLSVKNC
Sbjct:     1 MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC 60

Query:    64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEAV 94
             FIRGSVVRYVQLP DEVDTQLLQDA RKEA+
Sbjct:    61 FIRGSVVRYVQLPADEVDTQLLQDAARKEAL 91

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

GO:0019901 "protein kinase binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

UNIPROTKB|Q9Y333 LSM2 "U6 snRNA-associated Sm-like protein LSm2" [Homo sapiens (taxid:9606)]

 Score = 443 (161.0 bits), Expect = 8.4e-42, P = 8.4e-42
 Identities = 85/91 (93%), Positives = 89/91 (97%)

Query:     4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
             +LFYSFFKSLVGKDVVVELKND+SICGTLHSVDQYLNIKLTDISVTDP+KYPHMLSVKNC
Sbjct:     1 MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC 60

Query:    64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEAV 94
             FIRGSVVRYVQLP DEVDTQLLQDA RKEA+
Sbjct:    61 FIRGSVVRYVQLPADEVDTQLLQDAARKEAL 91

GO:0019901 "protein kinase binding" evidence=IEA

GO:0017070 "U6 snRNA binding" evidence=NAS

GO:0005634 "nucleus" evidence=NAS

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

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

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

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

GO:0005515 "protein binding" evidence=IPI

MGI|MGI:90676 Lsm2 "LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 443 (161.0 bits), Expect = 8.4e-42, P = 8.4e-42
 Identities = 85/91 (93%), Positives = 89/91 (97%)

Query:     4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
             +LFYSFFKSLVGKDVVVELKND+SICGTLHSVDQYLNIKLTDISVTDP+KYPHMLSVKNC
Sbjct:     1 MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC 60

Query:    64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEAV 94
             FIRGSVVRYVQLP DEVDTQLLQDA RKEA+
Sbjct:    61 FIRGSVVRYVQLPADEVDTQLLQDAARKEAL 91

GO:0000244 "assembly of spliceosomal tri-snRNP" evidence=ISO

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0006402 "mRNA catabolic process" evidence=ISO

GO:0008380 "RNA splicing" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IDA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

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

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

ZFIN|ZDB-GENE-000616-10 smx5 "smx5" [Danio rerio (taxid:7955)]

 Score = 442 (160.7 bits), Expect = 1.1e-41, P = 1.1e-41
 Identities = 85/90 (94%), Positives = 88/90 (97%)

Query:     4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
             +LFYSFFKSLVGKDVVVELKND+SICGTLHSVDQYLNIKLTDISVTDP+KYPHMLSVKNC
Sbjct:     1 MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC 60

Query:    64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEA 93
             FIRGSVVRYVQLP DEVDTQLLQDA RKEA
Sbjct:    61 FIRGSVVRYVQLPADEVDTQLLQDAARKEA 90

GO:0006397 "mRNA processing" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

WB|WBGene00001808 gut-2 [Caenorhabditis elegans (taxid:6239)]

 Score = 403 (146.9 bits), Expect = 1.5e-37, P = 1.5e-37
 Identities = 74/93 (79%), Positives = 89/93 (95%)

Query:     4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
             +LF+SFFKSLVGKDVVVELKND+SICGTLHSVDQYLN+KLTDI+V+DP+++PHM+SVKNC
Sbjct:     1 MLFFSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNMKLTDITVSDPERFPHMVSVKNC 60

Query:    64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEAVNA 96
             FIRGSVVRYVQLP D+VDTQLL D+ RKE +++
Sbjct:    61 FIRGSVVRYVQLPSDQVDTQLLADSCRKELLDS 93

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

GO:0040011 "locomotion" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

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

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

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

GO:0040007 "growth" evidence=IMP

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

GO:0040020 "regulation of meiosis" evidence=IMP

GO:0007281 "germ cell development" evidence=IMP

GO:0008406 "gonad development" evidence=IMP

GO:0016477 "cell migration" evidence=IMP

TAIR|locus:2014480 LSM2 "AT1G03330" [Arabidopsis thaliana (taxid:3702)]

 Score = 344 (126.2 bits), Expect = 2.6e-31, P = 2.6e-31
 Identities = 66/90 (73%), Positives = 76/90 (84%)

Query:     4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
             +LF+S+FK LVG++V VELKND++I GTLHSVDQYLNIKL +  V D DKYPHMLSV+NC
Sbjct:     1 MLFFSYFKDLVGQEVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNC 60

Query:    64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEA 93
             FIRGSVVRYVQLP D VD  LL DA R+EA
Sbjct:    61 FIRGSVVRYVQLPKDGVDVDLLHDAARREA 90

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

UNIPROTKB|I3LGB3 LSM2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 335 (123.0 bits), Expect = 2.3e-30, P = 2.3e-30
 Identities = 64/68 (94%), Positives = 66/68 (97%)

Query:    27 SICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQLLQ 86
             SICGTLHSVDQYLNIKLTDISVTDP+KYPHMLSVKNCFIRGSVVRYVQLP DEVDTQLLQ
Sbjct:     1 SICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADEVDTQLLQ 60

Query:    87 DATRKEAV 94
             DA RKEA+
Sbjct:    61 DAARKEAL 68

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

GO:0019901 "protein kinase binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

DICTYBASE|DDB_G0281779 lsm2 "putative U6 small nuclear ribonucleoparticle-associated protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 330 (121.2 bits), Expect = 7.9e-30, P = 7.9e-30
 Identities = 62/90 (68%), Positives = 76/90 (84%)

Query:     4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
             +LF+SF+KSLVGK++ VELKND+SI G L SVDQ+LNIKL DI V + DKYP+M+SVKNC
Sbjct:     1 MLFFSFYKSLVGKEITVELKNDLSITGLLQSVDQFLNIKLKDIKVNEEDKYPYMISVKNC 60

Query:    64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEA 93
             FIRGSVVRYV LP ++VD + LQD +R EA
Sbjct:    61 FIRGSVVRYVHLPAEDVDVETLQDHSRLEA 90

GO:0006397 "mRNA processing" evidence=IEA

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

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

GO:0006402 "mRNA catabolic process" evidence=ISS

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

GO:0005730 "nucleolus" evidence=ISS

GO:0005688 "U6 snRNP" evidence=ISS

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

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

ASPGD|ASPL0000065787 AN10963 [Emericella nidulans (taxid:162425)]

 Score = 320 (117.7 bits), Expect = 9.1e-29, P = 9.1e-29
 Identities = 64/92 (69%), Positives = 73/92 (79%)

Query:     4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
             +LF+SFFK+L  + V +ELKND+ I GTL SVDQYLNIKL DI V D DKYPH+ SVKN 
Sbjct:     1 MLFFSFFKTLTNQVVTIELKNDIRIRGTLKSVDQYLNIKLDDIDVLDLDKYPHLSSVKNM 60

Query:    64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEAVN 95
             FIRGSVVRYV LP  EVD  LL+DATR+EA N
Sbjct:    61 FIRGSVVRYVVLPRSEVDVGLLEDATRREAAN 92

GO:0005730 "nucleolus" evidence=IEA

GO:0005688 "U6 snRNP" evidence=IEA

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

GO:0005829 "cytosol" evidence=IEA

GO:0000932 "cytoplasmic mRNA processing body" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

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

UNIPROTKB|G4NCP9 MGG_00355 "U6 snRNA-associated Sm-like protein LSm2" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 302 (111.4 bits), Expect = 7.3e-27, P = 7.3e-27
 Identities = 57/92 (61%), Positives = 72/92 (78%)

Query:     4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
             +LF+SFFK+L+  ++ VELKN + I GTL SVDQYLN+KL DISV +  KYPH+ +VKN 
Sbjct:     1 MLFFSFFKTLIDVEITVELKNSIQIRGTLKSVDQYLNLKLDDISVVEDIKYPHLSAVKNV 60

Query:    64 FIRGSVVRYVQLPGDEVDTQLLQDATRKEAVN 95
             FIRGSVVRY+ LP   VD  LL+DATR+EA +
Sbjct:    61 FIRGSVVRYIHLPASHVDVPLLEDATRREAAS 92

GO:0003674 "molecular_function" evidence=ND

---

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)
P38203	LSM2_YEAST	No assigned EC number	0.6593	0.9285	0.9578	yes	N/A
O94408	LSM2_SCHPO	No assigned EC number	0.6105	0.9693	0.9895	yes	N/A
Q54TF6	LSM2_DICDI	No assigned EC number	0.6888	0.9183	0.7692	yes	N/A
Q8SQK1	LSM2_ENCCU	No assigned EC number	0.3855	0.7959	0.8297	yes	N/A
O35900	LSM2_MOUSE	No assigned EC number	0.9239	0.9387	0.9684	yes	N/A
Q9Y333	LSM2_HUMAN	No assigned EC number	0.9239	0.9387	0.9684	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	98
cd01725	89	cd01725, LSm2, Like-Sm protein 2	9e-63
smart00651	67	smart00651, Sm, snRNP Sm proteins	3e-17
cd01733	78	cd01733, LSm10, Like-Sm protein 10	6e-16
pfam01423	66	pfam01423, LSM, LSM domain	3e-15
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	5e-15
cd01723	76	cd01723, LSm4, Like-Sm protein 4	6e-12
cd00600	63	cd00600, Sm_like, Sm and related proteins	9e-12
cd01724	92	cd01724, Sm_D1, Sm protein D1	1e-08
cd01726	68	cd01726, LSm6, Like-Sm protein 6	1e-07
cd01721	70	cd01721, Sm_D3, Sm protein D3	2e-06
cd01722	69	cd01722, Sm_F, Sm protein F	1e-05
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	3e-05
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	2e-04
cd11679	65	cd11679, archaeal_Sm_like, archaeal Sm-related pro	0.002

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

 Score =  184 bits (470), Expect = 9e-63
 Identities = 76/89 (85%), Positives = 85/89 (95%)

Query: 5  LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCF 64
          LF+SFFK+LVGK+V VELKND+SI GTLHSVDQYLNIKLT+ISV DP+KYPH+LSVKNCF
Sbjct: 1  LFFSFFKTLVGKEVTVELKNDLSITGTLHSVDQYLNIKLTNISVNDPEKYPHLLSVKNCF 60

Query: 65 IRGSVVRYVQLPGDEVDTQLLQDATRKEA 93
          IRGSVVRYVQLP DEVDT+LLQDATR+EA
Sbjct: 61 IRGSVVRYVQLPADEVDTELLQDATRREA 89

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

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

 Score = 68.7 bits (169), Expect = 3e-17
 Identities = 27/68 (39%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 8  SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRG 67
           F K L+GK V+VELKN     GTL   DQ++N+ L D+  T  D       +   FIRG
Sbjct: 1  KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGE-KKRKLGLVFIRG 59

Query: 68 SVVRYVQL 75
          + + Y+ L
Sbjct: 60 NNIVYIIL 67

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

>gnl|CDD|212480 cd01733, LSm10, Like-Sm protein 10

 Score = 66.0 bits (162), Expect = 6e-16
 Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 2/68 (2%)

Query: 9  FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
            ++L G+   VEL+N+ S+ G + +VD ++NI L+D + TD     H       F++G 
Sbjct: 13 LLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQHHFD--EFFVQGR 70

Query: 69 VVRYVQLP 76
           +RYV +P
Sbjct: 71 NIRYVHIP 78

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. 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-membered 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. Length = 78

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

 Score = 63.7 bits (156), Expect = 3e-15
 Identities = 24/68 (35%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 8  SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRG 67
           F + L+GK V VELKN   + GTL   DQ++N+ L D+  T  D   + L      IRG
Sbjct: 1  KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLG--LVLIRG 58

Query: 68 SVVRYVQL 75
          + +  +  
Sbjct: 59 NNIVLISP 66

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

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

 Score = 63.5 bits (155), Expect = 5e-15
 Identities = 24/77 (31%), Positives = 32/77 (41%), Gaps = 2/77 (2%)

Query: 1  MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPH--ML 58
          M   L  SF K L+ K V+V+LKN     GTL   DQY+N+ L D+              
Sbjct: 3  MLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRR 62

Query: 59 SVKNCFIRGSVVRYVQL 75
                IRG  +  +  
Sbjct: 63 LGGEVLIRGDNIVLISP 79

Length = 79

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

 Score = 55.7 bits (135), Expect = 6e-12
 Identities = 24/69 (34%), Positives = 41/69 (59%), Gaps = 5/69 (7%)

Query: 15 GKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPD--KYPHMLSVKNCFIRGSVVRY 72
          G  V+VELKN  +  G L + D ++NI L ++  T  D  ++  M     C+IRG+ ++Y
Sbjct: 11 GHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKM---PECYIRGNTIKY 67

Query: 73 VQLPGDEVD 81
          ++LP + +D
Sbjct: 68 LRLPDEVID 76

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

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

 Score = 54.9 bits (133), Expect = 9e-12
 Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 11 KSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVV 70
          K  +GK V VELK+   + GTL + D+Y+N+ L D  V +  +   +  +    IRGS +
Sbjct: 2  KDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDD--VVETGRDGKVRVLGLVLIRGSNI 59

Query: 71 RYVQ 74
            ++
Sbjct: 60 VSIR 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|212471 cd01724, Sm_D1, Sm protein D1

 Score = 47.2 bits (113), Expect = 1e-08
 Identities = 32/85 (37%), Positives = 46/85 (54%), Gaps = 6/85 (7%)

Query: 9  FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
          F   L  + V +ELKN   + GT+  VD  +N  L ++ +T   K P  +S+    IRG+
Sbjct: 5  FLMKLSNETVTIELKNGTVVHGTITGVDVSMNTHLKNVKLTLKGKNP--VSLDTLSIRGN 62

Query: 69 VVRYVQLPGDEV--DTQLLQDATRK 91
           +RY+ LP D +  DT LL D T K
Sbjct: 63 NIRYIILP-DSLNLDT-LLVDDTPK 85

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit 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. Length = 92

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

 Score = 44.0 bits (105), Expect = 1e-07
 Identities = 24/69 (34%), Positives = 34/69 (49%), Gaps = 10/69 (14%)

Query: 9  FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKN----CF 64
          F K ++GK VVV+LKN V   G L  +D Y+N+ L D       +      +       F
Sbjct: 5  FLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQ------LVAKYGDAF 58

Query: 65 IRGSVVRYV 73
          IRG+ V Y+
Sbjct: 59 IRGNNVLYI 67

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|212468 cd01721, Sm_D3, Sm protein D3

 Score = 41.4 bits (98), Expect = 2e-06
 Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 4/60 (6%)

Query: 18 VVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPD-KYPHMLSVKNCFIRGSVVRYVQLP 76
          V VELK      G L   +  +N +L D++VT  D K   +  V   +IRGS +R++ LP
Sbjct: 13 VTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGKVSKLEQV---YIRGSQIRFIILP 69

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 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. Length = 70

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

 Score = 39.1 bits (92), Expect = 1e-05
 Identities = 17/37 (45%), Positives = 24/37 (64%)

Query: 9  FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTD 45
          F   L GK V+V+LK  +   GTL SVD Y+N++L +
Sbjct: 5  FLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLAN 41

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|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1

 Score = 38.3 bits (90), Expect = 3e-05
 Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 2/60 (3%)

Query: 14 VGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYV 73
          + K+V+V+LK    + G L   DQ+LN+ L +       +    L      +RG  V ++
Sbjct: 10 LNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKL--GTVLVRGDNVVFI 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|212489 cd11678, archaeal_LSm, archaeal Like-Sm protein

 Score = 35.9 bits (83), Expect = 2e-04
 Identities = 18/36 (50%), Positives = 25/36 (69%), Gaps = 1/36 (2%)

Query: 11 KSLVGKDVVVELKNDVS-ICGTLHSVDQYLNIKLTD 45
          KSLVG  + VE+K D + + G L +VD Y+N+ LTD
Sbjct: 6  KSLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTD 41

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|212490 cd11679, archaeal_Sm_like, archaeal Sm-related protein

 Score = 33.8 bits (78), Expect = 0.002
 Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 7/63 (11%)

Query: 12 SLVGKDVVVELKNDVSICGTLHSVDQY-LNIKLTDISVTDPDKYPHMLSVKNCFIRGSVV 70
          SL+ K+V+V L N  +  G L   D   LNI LT+   +  +K+P +       I G+ +
Sbjct: 7  SLLDKEVIVTLSNGKTYTGQLVGFDPSSLNIVLTNAKDSSGNKFPKV------IINGNRI 60

Query: 71 RYV 73
            +
Sbjct: 61 SEI 63

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	98
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.95
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.95
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.95
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.95
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.93
KOG3448|consensus	96		99.92
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.92
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.9
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.9
KOG3293|consensus	134		99.89
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.89
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.89
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.86
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.86
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.86
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.86
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
KOG3172|consensus	119		99.83
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.83
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.83
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.81
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.79
KOG3428|consensus	109		99.78
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.78
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.77
KOG3482|consensus	79		99.76
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.75
KOG1783|consensus	77		99.75
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.74
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.7
KOG1780|consensus	77		99.68
KOG3460|consensus	91		99.59
KOG1775|consensus	84		99.57
KOG1784|consensus	96		99.36
KOG1774|consensus	88		99.23
KOG1781|consensus	108		99.11
KOG1782|consensus	129		99.07
KOG3168|consensus	177		98.81
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	98.27
KOG3459|consensus	114		98.25
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	97.87
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	97.45
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	97.38
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	97.27
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	96.73
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	96.71
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	96.64
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	96.42
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	96.16
COG1923	77	Hfq Uncharacterized host factor I protein [General	96.09
KOG1073|consensus	361		95.83
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	95.12
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	94.42
PRK14638	150	hypothetical protein; Provisional	93.92
PRK14091	165	RNA-binding protein Hfq; Provisional	93.77
PRK14091	165	RNA-binding protein Hfq; Provisional	93.14
PRK14639	140	hypothetical protein; Provisional	93.07
PRK02001	152	hypothetical protein; Validated	92.87
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	90.59
PRK14644	136	hypothetical protein; Provisional	90.34
PRK14640	152	hypothetical protein; Provisional	89.67
COG0779	153	Uncharacterized protein conserved in bacteria [Fun	89.59
PRK14642	197	hypothetical protein; Provisional	89.03
PRK14633	150	hypothetical protein; Provisional	88.68
PRK14645	154	hypothetical protein; Provisional	87.44
PRK14636	176	hypothetical protein; Provisional	87.02
PRK14632	172	hypothetical protein; Provisional	86.87
PRK14643	164	hypothetical protein; Provisional	86.53
PRK00092	154	ribosome maturation protein RimP; Reviewed	86.41
PRK14634	155	hypothetical protein; Provisional	86.23
PRK14646	155	hypothetical protein; Provisional	85.33
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	85.32
PRK14647	159	hypothetical protein; Provisional	84.82
PRK06955	300	biotin--protein ligase; Provisional	84.04
PRK14637	151	hypothetical protein; Provisional	83.28
PRK09618	142	flgD flagellar basal body rod modification protein	82.88
PRK14631	174	hypothetical protein; Provisional	82.25
PRK14641	173	hypothetical protein; Provisional	81.45
PRK08330	236	biotin--protein ligase; Provisional	81.26

>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=99.95  E-value=6.1e-28  Score=154.45  Aligned_cols=86  Identities=28%  Similarity=0.490  Sum_probs=76.4

Q ss_pred             chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCc-ccccH
Q psy6026           5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGD-EVDTQ   83 (98)
Q Consensus         5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~-~~d~~   83 (98)
                      .|+.||+++.|++|+|+||||.+|+|+|.++|+|||++|+||+++.+++.  ...++.+||||++|+||++||. ..|..
T Consensus         1 ~~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~--~~~~~~v~IRG~nI~yi~lPd~l~~~~~   78 (90)
T cd01724           1 KLVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRN--PVPLDTLSIRGNNIRYFILPDSLNLDTL   78 (90)
T ss_pred             CHhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCc--eeEcceEEEeCCEEEEEEcCCcCCcchh
Confidence            37899999999999999999999999999999999999999999988765  4589999999999999999998 47777


Q ss_pred             HhHHHHHHH
Q psy6026          84 LLQDATRKE   92 (98)
Q Consensus        84 ~~~~~~r~~   92 (98)
                      ++++++...
T Consensus        79 l~~~~~~~~   87 (90)
T cd01724          79 LVDSTPKPK   87 (90)
T ss_pred             hhhcCCccc
Confidence            777754433

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

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

Probab=99.95  E-value=1.2e-27  Score=150.35  Aligned_cols=80  Identities=88%  Similarity=1.344  Sum_probs=72.4

Q ss_pred             chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCcccccHH
Q psy6026           5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQL   84 (98)
Q Consensus         5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~~~d~~~   84 (98)
                      +|+.||+++.|++|+|+||||.+|+|+|.++|.|||++|+||+++.+++......++++||||++|+||++||+.+|.+.
T Consensus         1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~~~~   80 (81)
T cd01725           1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADEVDTEL   80 (81)
T ss_pred             ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhHcCccc
Confidence            58999999999999999999999999999999999999999999887654334567999999999999999999888764

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.

>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=99.95  E-value=4.6e-27  Score=144.02  Aligned_cols=70  Identities=30%  Similarity=0.468  Sum_probs=66.3

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026           6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus         6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      |+++|+++.|++|+|+||||.+|+|+|.++|+|||++|+||+++.++|+  ...++++||||++|+||++||
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 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGR--VSQLEQVYIRGSKIRFFILPD   70 (70)
T ss_pred             ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCc--EeEcCcEEEeCCEEEEEEeCC
Confidence            8899999999999999999999999999999999999999999888875  357899999999999999996

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.

>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=99.95  E-value=4.7e-27  Score=145.92  Aligned_cols=76  Identities=30%  Similarity=0.604  Sum_probs=69.5

Q ss_pred             chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCcccc
Q psy6026           5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVD   81 (98)
Q Consensus         5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~~~d   81 (98)
                      .|++||+++.|++|+|+||||++|+|+|.+||+|||++|+||+++.++|.. ...++.+||||++|+||++|++.+|
T Consensus         1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~-~~~~~~v~IRG~~I~~i~~p~~~~~   76 (76)
T cd01723           1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDK-FWKMPECYIRGNTIKYLRVPDEIID   76 (76)
T ss_pred             CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcE-eeeCCcEEEeCCEEEEEEcCHHHCC
Confidence            599999999999999999999999999999999999999999999887752 3568999999999999999987543

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.

>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=99.93  E-value=2e-25  Score=139.48  Aligned_cols=70  Identities=31%  Similarity=0.660  Sum_probs=65.9

Q ss_pred             chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecC
Q psy6026           5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLP   76 (98)
Q Consensus         5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p   76 (98)
                      .+.+||+++.|++|+|+||||.+|+|+|.++|+|||++|+||+++++++.+  ..++.+||||++|+||++|
T Consensus         9 tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~--~~~~~v~IRG~nI~yI~lP   78 (78)
T cd01733           9 TLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQ--VQVEEIMVTGRNIRYVHIP   78 (78)
T ss_pred             hHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCce--eECCcEEEECCEEEEEEcC
Confidence            578999999999999999999999999999999999999999999887753  4789999999999999998

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.

>KOG3448|consensus

Probab=99.92  E-value=1.6e-24  Score=136.85  Aligned_cols=92  Identities=89%  Similarity=1.351  Sum_probs=88.1

Q ss_pred             cchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCcccccH
Q psy6026           4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQ   83 (98)
Q Consensus         4 ~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~~~d~~   83 (98)
                      |+.++|+++++|+.|.|+||||..+.|+|.++|+|+|+.|+|..+++++..|+......+||||+.|+||++|.+..|.+
T Consensus         1 mLFysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~vdtq   80 (96)
T KOG3448|consen    1 MLFYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDAVDTQ   80 (96)
T ss_pred             CchHHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChhHHHHH
Confidence            78899999999999999999999999999999999999999999999998888888999999999999999999999999


Q ss_pred             HhHHHHHHHHhh
Q psy6026          84 LLQDATRKEAVN   95 (98)
Q Consensus        84 ~~~~~~r~~~~~   95 (98)
                      .++++.|.|.-.
T Consensus        81 ll~da~R~e~~~   92 (96)
T KOG3448|consen   81 LLQDAARREAIL   92 (96)
T ss_pred             HHHHHHHHHHHh
Confidence            999999998753

>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=99.92  E-value=1.7e-24  Score=131.49  Aligned_cols=67  Identities=31%  Similarity=0.504  Sum_probs=61.9

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026           6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ   74 (98)
Q Consensus         6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~   74 (98)
                      |++||++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..++.  ...++.+||||++|+||+
T Consensus         1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~--~~~~~~v~IRG~~I~~I~   67 (67)
T cd01726           1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQL--KNKYGDAFIRGNNVLYIS   67 (67)
T ss_pred             CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCce--eeEeCCEEEECCEEEEEC
Confidence            8999999999999999999999999999999999999999998776543  458999999999999984

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.

>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=99.90  E-value=1.6e-23  Score=127.56  Aligned_cols=68  Identities=32%  Similarity=0.424  Sum_probs=61.8

Q ss_pred             chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026           5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ   74 (98)
Q Consensus         5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~   74 (98)
                      .|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||++...++.  ...+|.+||||++|+||.
T Consensus         1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~--~~~lg~~~IRG~~I~~i~   68 (68)
T cd01722           1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKS--TGNLGEVLIRCNNVLYIR   68 (68)
T ss_pred             CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCcc--ccCcCcEEEECCEEEEEC
Confidence            48999999999999999999999999999999999999999998765433  357999999999999984

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.

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.90  E-value=2.4e-23  Score=128.08  Aligned_cols=69  Identities=22%  Similarity=0.297  Sum_probs=63.5

Q ss_pred             cchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026           4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ   74 (98)
Q Consensus         4 ~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~   74 (98)
                      ..|+.+|++++|++|.|+|+||++|+|+|.+||+|||++|+||+++..++.  ...++.+||||++|++|.
T Consensus         3 ~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~--~~~lg~v~iRG~~V~~i~   71 (72)
T PRK00737          3 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEV--VRKLGKVVIRGDNVVYVS   71 (72)
T ss_pred             cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCe--EeEcCcEEEeCCEEEEEc
Confidence            589999999999999999999999999999999999999999999865532  458999999999999986

>KOG3293|consensus

Probab=99.89  E-value=1.6e-23  Score=139.22  Aligned_cols=88  Identities=25%  Similarity=0.525  Sum_probs=79.4

Q ss_pred             cchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCcccccH
Q psy6026           4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQ   83 (98)
Q Consensus         4 ~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~~~d~~   83 (98)
                      |+|+++|+...|+++.||||||.+|.|.|.+||.+|||.|.+++++.++|.. +..+++++|||++|+|+.+||+.+|..
T Consensus         1 mlPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdk-f~r~pEcYirGttIkylri~d~iid~v   79 (134)
T KOG3293|consen    1 MLPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDK-FFRMPECYIRGTTIKYLRIPDEIIDKV   79 (134)
T ss_pred             CcchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCc-eeecceeEEecceeEEEeccHHHHHHH
Confidence            7999999999999999999999999999999999999999999999998864 578999999999999999999988777


Q ss_pred             HhHHHHHHH
Q psy6026          84 LLQDATRKE   92 (98)
Q Consensus        84 ~~~~~~r~~   92 (98)
                      .-+.....+
T Consensus        80 kee~~~~~~   88 (134)
T KOG3293|consen   80 KEECVSNNR   88 (134)
T ss_pred             HHHHHHhcc
Confidence            655444433

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

Probab=99.89  E-value=8.2e-23  Score=124.21  Aligned_cols=67  Identities=28%  Similarity=0.377  Sum_probs=62.1

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026           6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ   74 (98)
Q Consensus         6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~   74 (98)
                      |+++|++++|++|.|+|+||+.|.|+|.+||+|||++|+||+++..++.  ...++.+||||++|.||.
T Consensus         1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~--~~~lg~~~iRG~~I~~i~   67 (68)
T cd01731           1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEP--VRKYGRVVIRGDNVLFIS   67 (68)
T ss_pred             ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCe--EeEcCcEEEeCCEEEEEc
Confidence            8899999999999999999999999999999999999999999876543  457999999999999986

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.

>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=8.3e-23  Score=127.07  Aligned_cols=71  Identities=21%  Similarity=0.454  Sum_probs=63.9

Q ss_pred             ccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEEC--CCCCcceeecceEEEEcCeEEEEe
Q psy6026           3 RLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTD--PDKYPHMLSVKNCFIRGSVVRYVQ   74 (98)
Q Consensus         3 ~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~--~~~~~~~~~~~~v~IRG~~I~~I~   74 (98)
                      +|+|+++|+++++++|.|+|++|+.|.|+|.+||+|||++|+||++..  +++. ....++.++|||++|.+|+
T Consensus         1 ~~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~-~~~~lg~v~iRG~nV~~i~   73 (76)
T cd01732           1 QLLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGR-KITKLDQILLNGNNICMLV   73 (76)
T ss_pred             CcChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCc-eeeEcCeEEEeCCeEEEEE
Confidence            589999999999999999999999999999999999999999999864  3322 2357999999999999998

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.

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

Probab=99.86  E-value=3.3e-21  Score=120.14  Aligned_cols=73  Identities=33%  Similarity=0.384  Sum_probs=62.2

Q ss_pred             ccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECC-CCCc-ceeecceEEEEcCeEEEEec
Q psy6026           3 RLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDP-DKYP-HMLSVKNCFIRGSVVRYVQL   75 (98)
Q Consensus         3 ~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~-~~~~-~~~~~~~v~IRG~~I~~I~~   75 (98)
                      .+.|+++|+.++|++|.|+|+||++|.|+|.+||+|||++|+||+++.. ++.. .....+.++|||++|++|..
T Consensus         5 ~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~   79 (79)
T COG1958           5 GPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP   79 (79)
T ss_pred             cCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence            4568999999999999999999999999999999999999999999863 3321 12244599999999999863

>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=99.86  E-value=3.2e-21  Score=118.76  Aligned_cols=70  Identities=17%  Similarity=0.290  Sum_probs=62.6

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026           6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus         6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      |-++|++++||+|.|+|++|+.|.|+|.+||+|||++|+||+++..+..  ...+|.++|||++|.+|..-|
T Consensus         1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~--~~~lg~v~IRG~~I~~i~~~~   70 (72)
T cd01719           1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGE--KNNIGMVVIRGNSIVMLEALE   70 (72)
T ss_pred             CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCc--eeEeceEEECCCEEEEEEccc
Confidence            4578999999999999999999999999999999999999998864433  468999999999999998654

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.

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

Probab=99.86  E-value=3.9e-21  Score=115.71  Aligned_cols=66  Identities=44%  Similarity=0.646  Sum_probs=60.5

Q ss_pred             HHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEec
Q psy6026           9 FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQL   75 (98)
Q Consensus         9 ~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~   75 (98)
                      +|++++|++|+|+|+||++|+|+|.+||+|||++|+||.++..++. ....++.+||||++|++|++
T Consensus         2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~-~~~~~~~~~irG~~I~~I~~   67 (67)
T PF01423_consen    2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP-EKRSLGLVFIRGSNIRYISL   67 (67)
T ss_dssp             HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES-EEEEEEEEEEEGGGEEEEEE
T ss_pred             hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC-cEeECcEEEEECCEEEEEEC
Confidence            7999999999999999999999999999999999999999877642 24689999999999999985

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=99.86  E-value=3.4e-21  Score=115.84  Aligned_cols=67  Identities=40%  Similarity=0.606  Sum_probs=60.4

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEec
Q psy6026           8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQL   75 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~   75 (98)
                      .+|++++|++|+|+|+||+++.|+|.+||+|||++|+||+++..++. +...++.+||||++|+||+.
T Consensus         1 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~-~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651        1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGE-KKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             ChhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCc-EEeEeCCEEEcCCEEEEEeC
Confidence            37899999999999999999999999999999999999999876521 24689999999999999974

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

>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=99.84  E-value=1.6e-20  Score=118.08  Aligned_cols=69  Identities=28%  Similarity=0.357  Sum_probs=60.5

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCC-----------CCcceeecceEEEEcCeEEEEe
Q psy6026           6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPD-----------KYPHMLSVKNCFIRGSVVRYVQ   74 (98)
Q Consensus         6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~-----------~~~~~~~~~~v~IRG~~I~~I~   74 (98)
                      |+++|+..++++|.|.|++|+.|.|+|.+||.|||++|+||.+....           .....+.+|.+||||++|.+|+
T Consensus         2 pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~   81 (82)
T cd01730           2 PLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVS   81 (82)
T ss_pred             chHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEEC
Confidence            89999999999999999999999999999999999999999986421           1112457899999999999986

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.

>KOG3172|consensus

Probab=99.83  E-value=1.4e-20  Score=122.69  Aligned_cols=86  Identities=27%  Similarity=0.389  Sum_probs=80.7

Q ss_pred             CcccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCccc
Q psy6026           1 MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEV   80 (98)
Q Consensus         1 ~~~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~~~   80 (98)
                      |+.-.|+.+|.+..|+-|++|+++|..|+|+|..+|++||+.|+|++.+.++|.  ...++.+||||+.|+|+.+||...
T Consensus         1 ~s~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~--vs~le~V~IRGS~IRFlvlPdmLK   78 (119)
T KOG3172|consen    1 MSVGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGR--VSQLEQVFIRGSKIRFLVLPDMLK   78 (119)
T ss_pred             CccccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCc--ceeeeeEEEecCeEEEEECchHhh
Confidence            567789999999999999999999999999999999999999999999999986  568999999999999999999999


Q ss_pred             ccHHhHHH
Q psy6026          81 DTQLLQDA   88 (98)
Q Consensus        81 d~~~~~~~   88 (98)
                      ++|+++..
T Consensus        79 nAPmFkk~   86 (119)
T KOG3172|consen   79 NAPMFKKG   86 (119)
T ss_pred             cCcccccc
Confidence            99999743

>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.83  E-value=5e-20  Score=109.33  Aligned_cols=63  Identities=38%  Similarity=0.514  Sum_probs=57.7

Q ss_pred             HhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026          10 FKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ   74 (98)
Q Consensus        10 L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~   74 (98)
                      |++++|++|+|+|+||+.|.|+|.+||+|||++|+||.++.+++.  ...++.+||||++|++|+
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~--~~~~~~~~irG~~I~~I~   63 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGK--KRVLGLVLIRGDNVRLVT   63 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCc--EEECCeEEEECCEEEEEC
Confidence            578899999999999999999999999999999999999887643  468999999999999985

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.

>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=99.83  E-value=5e-20  Score=117.21  Aligned_cols=71  Identities=18%  Similarity=0.240  Sum_probs=60.9

Q ss_pred             chHHHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCC-----------cceeecceEEEEcCeEE
Q psy6026           5 LFYSFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKY-----------PHMLSVKNCFIRGSVVR   71 (98)
Q Consensus         5 ~p~~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~-----------~~~~~~~~v~IRG~~I~   71 (98)
                      -|+++|+.++  |++|.|.|++|+.+.|+|.+||.|||++|+||.++.....           .....+|.+||||++|.
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            4899999997  8999999999999999999999999999999998643210           12346899999999999


Q ss_pred             EEec
Q psy6026          72 YVQL   75 (98)
Q Consensus        72 ~I~~   75 (98)
                      +|+.
T Consensus        82 ~Is~   85 (87)
T cd01720          82 LVLR   85 (87)
T ss_pred             EEec
Confidence            9874

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

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

Probab=99.81  E-value=1.9e-19  Score=113.13  Aligned_cols=70  Identities=21%  Similarity=0.219  Sum_probs=59.5

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCC------cceeecceEEEEcCeEEEEecCC
Q psy6026           8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKY------PHMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~------~~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      .-|.+++|++|.|.|++|++|.|+|.+||+|||++|++|++...+..      .....+|.++|||++|.+|...+
T Consensus         5 ~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~   80 (81)
T cd01729           5 LDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD   80 (81)
T ss_pred             hhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence            34899999999999999999999999999999999999998643210      12457999999999999998654

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

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

Probab=99.79  E-value=1e-18  Score=109.40  Aligned_cols=70  Identities=17%  Similarity=0.282  Sum_probs=60.9

Q ss_pred             cchHHHHhhcCCC--eEEEEEc--CCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026           4 LLFYSFFKSLVGK--DVVVELK--NDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ   74 (98)
Q Consensus         4 ~~p~~~L~~l~gk--~V~V~Lk--ng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~   74 (98)
                      ..|+..+.+++++  +|.|.|+  +|+++.|+|.+||+|||++|+||++....+. ....+|.++|||++|.+|+
T Consensus         5 ~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~-~~~~lG~iliRGnnV~~I~   78 (79)
T cd01718           5 VQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTK-TRKPLGRILLKGDNITLIQ   78 (79)
T ss_pred             cCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCc-eEeEcCcEEEeCCEEEEEc
Confidence            5799999999999  7888887  9999999999999999999999998753222 2357999999999999997

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.

>KOG3428|consensus

Probab=99.78  E-value=1.2e-18  Score=113.71  Aligned_cols=90  Identities=33%  Similarity=0.529  Sum_probs=81.6

Q ss_pred             cchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCc-cccc
Q psy6026           4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGD-EVDT   82 (98)
Q Consensus         4 ~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~-~~d~   82 (98)
                      |..+.||+++.+.+|+|+|+||+...|++.++|.+||..|.++..+.++ ++  ..+..++|||++|||+++||+ .+|.
T Consensus         1 mklvr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~-~p--v~l~~lsirgnniRy~~lpD~l~ld~   77 (109)
T KOG3428|consen    1 MKLVRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG-EP--VRLDTLSIRGNNIRYYILPDSLNLDT   77 (109)
T ss_pred             ChHHHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC-Cc--eeEEEEEeecceEEEEEccCCcCcce
Confidence            5678999999999999999999999999999999999999999999885 43  578999999999999999998 8888


Q ss_pred             HHhHHHHHHHHhhc
Q psy6026          83 QLLQDATRKEAVNA   96 (98)
Q Consensus        83 ~~~~~~~r~~~~~~   96 (98)
                      .++.+.++...++.
T Consensus        78 Llvd~~~~~~~~~~   91 (109)
T KOG3428|consen   78 LLVDDAPRLHLRKN   91 (109)
T ss_pred             eeeehhhhhhhhcc
Confidence            88888888777664

>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=99.78  E-value=2.4e-18  Score=106.51  Aligned_cols=70  Identities=24%  Similarity=0.162  Sum_probs=59.4

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCC-CcceeecceEEEEcCeEEEEec
Q psy6026           6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDK-YPHMLSVKNCFIRGSVVRYVQL   75 (98)
Q Consensus         6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~-~~~~~~~~~v~IRG~~I~~I~~   75 (98)
                      +...|.++++++|.|.|++|+.|.|+|.+||+|||++|+||.+....+ ......+|.++|||++|.+|..
T Consensus         3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~   73 (74)
T cd01728           3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE   73 (74)
T ss_pred             chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence            467799999999999999999999999999999999999998753221 1113578999999999999874

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.

>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=99.77  E-value=2.7e-18  Score=107.14  Aligned_cols=68  Identities=18%  Similarity=0.239  Sum_probs=57.9

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCC--------CcceeecceEEEEcCeEEEEec
Q psy6026           8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDK--------YPHMLSVKNCFIRGSVVRYVQL   75 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~--------~~~~~~~~~v~IRG~~I~~I~~   75 (98)
                      +-|.+++|++|.|.|+||+.+.|+|.+||+|||++|+||.++....        ......+|.+||||++|.+|.+
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            3478899999999999999999999999999999999999864211        1123579999999999999975

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.

>KOG3482|consensus

Probab=99.76  E-value=2e-18  Score=105.59  Aligned_cols=72  Identities=29%  Similarity=0.345  Sum_probs=62.9

Q ss_pred             cccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEec
Q psy6026           2 ERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQL   75 (98)
Q Consensus         2 ~~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~   75 (98)
                      +-..|-+||+.+.||+|.|+||-|.+|.|+|.++|.|||+.|.+|++.-.+..  .-.+|+++||.+||.||.-
T Consensus         5 ~PvNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~--~g~lGEilIRCNNvlyi~g   76 (79)
T KOG3482|consen    5 QPVNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVS--TGNLGEILIRCNNVLYIRG   76 (79)
T ss_pred             ccCCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccc--cccceeEEEEeccEEEEec
Confidence            44568999999999999999999999999999999999999999998543321  2479999999999999953

>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=99.75  E-value=1.1e-17  Score=103.30  Aligned_cols=69  Identities=25%  Similarity=0.218  Sum_probs=59.5

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECC---CCCcceeecceEEEEcCeEEEEecCC
Q psy6026           8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDP---DKYPHMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~---~~~~~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      +.|+++++++|.|.|++|+.|.|+|.+||+|||++|++|.+...   ++. ....+|.++|||++|.+|...|
T Consensus         2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~-~~~~lG~~~iRG~~I~~i~~~d   73 (74)
T cd01727           2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGV-EQVVLGLYIIRGDNIAVVGEID   73 (74)
T ss_pred             hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCc-eeeEeceEEECCCEEEEEEccC
Confidence            46889999999999999999999999999999999999997532   232 2357899999999999998654

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.

>KOG1783|consensus

Probab=99.75  E-value=1.7e-19  Score=110.28  Aligned_cols=72  Identities=31%  Similarity=0.461  Sum_probs=65.0

Q ss_pred             cchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026           4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus         4 ~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      ..|.+||++.+|++|.|+|.+|..|+|+|.++|.|||+.|+.+++...+..  ..+++.+||||++|.||+...
T Consensus         5 ~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql--~n~ygdaFirGnnVlyIs~~~   76 (77)
T KOG1783|consen    5 SMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQL--KNKYGDAFIRGNNVLYISTQK   76 (77)
T ss_pred             cCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcc--cccccceeeccccEEEEEecc
Confidence            468999999999999999999999999999999999999999998775443  458999999999999998753

>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=99.74  E-value=2.6e-17  Score=102.15  Aligned_cols=68  Identities=16%  Similarity=0.266  Sum_probs=59.5

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCC----CCcceeecceEEEEcCeEEEEec
Q psy6026           8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPD----KYPHMLSVKNCFIRGSVVRYVQL   75 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~----~~~~~~~~~~v~IRG~~I~~I~~   75 (98)
                      +.|++++|++|.|.|+||+.+.|+|.++|.+||++|+||.+....    .....+.+|.++|||++|..|++
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            468899999999999999999999999999999999999987532    11235689999999999999985

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

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.70  E-value=1.7e-16  Score=101.40  Aligned_cols=72  Identities=15%  Similarity=0.225  Sum_probs=59.2

Q ss_pred             cchHHHHhhcCCC--eEEEEEcC--CcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecC
Q psy6026           4 LLFYSFFKSLVGK--DVVVELKN--DVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLP   76 (98)
Q Consensus         4 ~~p~~~L~~l~gk--~V~V~Lkn--g~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p   76 (98)
                      ..|+..+.+++..  +|.|.+.+  ++++.|+|.+||+|||++|+||++...++. ....+|.++|||++|.+|+..
T Consensus        13 ~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~-~~~~lG~ilIRGnnV~~I~~~   88 (89)
T PTZ00138         13 TQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKN-TRKDLGRILLKGDNITLIMAA   88 (89)
T ss_pred             cCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCc-eeeEcCeEEEcCCEEEEEEcC
Confidence            4688889888876  57777767  489999999999999999999998754322 245899999999999999753

>KOG1780|consensus

Probab=99.68  E-value=9.8e-17  Score=98.44  Aligned_cols=66  Identities=23%  Similarity=0.352  Sum_probs=60.6

Q ss_pred             HHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecC
Q psy6026           9 FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLP   76 (98)
Q Consensus         9 ~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p   76 (98)
                      .|+++++|++.++|..|+.+.|+|++||.|||++|+++++...++.  ....+.++|||++|..+..-
T Consensus         8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~--~~~ig~~vIrgnsiv~~eaL   73 (77)
T KOG1780|consen    8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGD--KNNIGMVVIRGNSIVMVEAL   73 (77)
T ss_pred             hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCC--cceeeeEEEeccEEEEEeec
Confidence            8999999999999999999999999999999999999999887764  35899999999999988644

>KOG3460|consensus

Probab=99.59  E-value=3.7e-16  Score=97.89  Aligned_cols=73  Identities=30%  Similarity=0.393  Sum_probs=62.5

Q ss_pred             chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEE--CC--CCC-------cceeecceEEEEcCeEEEE
Q psy6026           5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVT--DP--DKY-------PHMLSVKNCFIRGSVVRYV   73 (98)
Q Consensus         5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~--~~--~~~-------~~~~~~~~v~IRG~~I~~I   73 (98)
                      -|+++|+-.++.+|.|+|+++++++|+|.+||+|+|++|+|+.++  .-  +..       ...+.++.+||||++|.+|
T Consensus         5 ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilv   84 (91)
T KOG3460|consen    5 EPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILV   84 (91)
T ss_pred             ccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEE
Confidence            599999999999999999999999999999999999999999864  11  110       1135789999999999999


Q ss_pred             ecCC
Q psy6026          74 QLPG   77 (98)
Q Consensus        74 ~~p~   77 (98)
                      +.|-
T Consensus        85 spp~   88 (91)
T KOG3460|consen   85 SPPL   88 (91)
T ss_pred             cCcc
Confidence            9884

>KOG1775|consensus

Probab=99.57  E-value=1.7e-15  Score=93.52  Aligned_cols=73  Identities=21%  Similarity=0.417  Sum_probs=65.0

Q ss_pred             cccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEE--CCCCCcceeecceEEEEcCeEEEEec
Q psy6026           2 ERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVT--DPDKYPHMLSVKNCFIRGSVVRYVQL   75 (98)
Q Consensus         2 ~~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~--~~~~~~~~~~~~~v~IRG~~I~~I~~   75 (98)
                      ++.+|++++.+++|.++.|.+|+++++.|+|.+||+|.|++|+|++++  .++|+ +..+++.+++.|++|..+..
T Consensus         4 ~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr-~~tk~~~iLLnGNni~mLvP   78 (84)
T KOG1775|consen    4 STLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGR-RMTKLDQILLNGNNITMLVP   78 (84)
T ss_pred             hhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcc-eeeeeeeeeecCCcEEEEec
Confidence            357899999999999999999999999999999999999999999964  55664 35689999999999998753

>KOG1784|consensus

Probab=99.36  E-value=5.4e-13  Score=84.88  Aligned_cols=88  Identities=20%  Similarity=0.271  Sum_probs=75.5

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEE--EC-CCCCcceeecceEEEEcCeEEEEecCCcccccHH
Q psy6026           8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISV--TD-PDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQL   84 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~--~~-~~~~~~~~~~~~v~IRG~~I~~I~~p~~~~d~~~   84 (98)
                      .-|..+++++|.|...||+.+.|.|.+||+..|+.|+++-+  +. ..+. ....+|.++|||.||..|..-|+.+|+.+
T Consensus         3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv-~q~~lGlyiirgeNva~ig~iDEe~d~~l   81 (96)
T KOG1784|consen    3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGV-EQIVLGLYIIRGENVAVIGEIDEELDSRL   81 (96)
T ss_pred             hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcch-hheeeEEEEEecCccceeeecchhhhhhh
Confidence            35788999999999999999999999999999999999984  22 2232 23578999999999999999999999999


Q ss_pred             hHHHHHHHHhhc
Q psy6026          85 LQDATRKEAVNA   96 (98)
Q Consensus        85 ~~~~~r~~~~~~   96 (98)
                      .+...|+|+-++
T Consensus        82 d~tkir~epl~~   93 (96)
T KOG1784|consen   82 DLTKIRAEPLHP   93 (96)
T ss_pred             hhhhcccCCCCC
Confidence            999999887544

>KOG1774|consensus

Probab=99.23  E-value=1.2e-11  Score=77.27  Aligned_cols=67  Identities=18%  Similarity=0.356  Sum_probs=52.9

Q ss_pred             HHHHhhcCCCeEEEEEcC--CcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecC
Q psy6026           7 YSFFKSLVGKDVVVELKN--DVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLP   76 (98)
Q Consensus         7 ~~~L~~l~gk~V~V~Lkn--g~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p   76 (98)
                      +.||+.  -.+|.|.|..  |..+.|.+.+||+|||++|++|++.+..... ...+|.++++|++|..|+-.
T Consensus        18 fr~Lq~--~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~-rk~lGRilLKGDnItli~~~   86 (88)
T KOG1774|consen   18 FRFLQN--RTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKS-RKELGRILLKGDNITLIQSA   86 (88)
T ss_pred             HHHHhc--CCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccC-CCccccEEEcCCcEEEEeec
Confidence            455555  4468888876  7899999999999999999999987653221 23799999999999998754

>KOG1781|consensus

Probab=99.11  E-value=9e-12  Score=80.31  Aligned_cols=70  Identities=20%  Similarity=0.262  Sum_probs=59.6

Q ss_pred             HHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECC--CC-C---cceeecceEEEEcCeEEEEecCCc
Q psy6026           9 FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDP--DK-Y---PHMLSVKNCFIRGSVVRYVQLPGD   78 (98)
Q Consensus         9 ~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~--~~-~---~~~~~~~~v~IRG~~I~~I~~p~~   78 (98)
                      -|.++++++|+|++.+|+...|+|.+||+.||++|+|++++-.  +. .   ...+.+|.+.+||..+..|+..|-
T Consensus        21 DLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG   96 (108)
T KOG1781|consen   21 DLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADG   96 (108)
T ss_pred             hHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcc
Confidence            4788999999999999999999999999999999999997532  21 0   124689999999999999997764

>KOG1782|consensus

Probab=99.07  E-value=3.5e-11  Score=80.25  Aligned_cols=70  Identities=23%  Similarity=0.272  Sum_probs=57.7

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEE--ECCCCCcceeecceEEEEcCeEEEEecCCc
Q psy6026           8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISV--TDPDKYPHMLSVKNCFIRGSVVRYVQLPGD   78 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~--~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~   78 (98)
                      .-|-+.+.+++.|-|+||+.+.|.|.+||+|-|++|.+|++  +..+.. .....|.++|||.||..+..-|.
T Consensus        12 ~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y-~di~~glfiIRGENVvllGeid~   83 (129)
T KOG1782|consen   12 TSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKY-CDIPRGLFIIRGENVVLLGEIDL   83 (129)
T ss_pred             hHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeeccee-cccCceEEEEecCcEEEEecCCc
Confidence            34778889999999999999999999999999999999985  222222 13467999999999999986554

>KOG3168|consensus

Probab=98.81  E-value=8.1e-10  Score=77.31  Aligned_cols=76  Identities=16%  Similarity=0.218  Sum_probs=60.3

Q ss_pred             CcccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECC---------CCCcceeecceEEEEcCeEE
Q psy6026           1 MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDP---------DKYPHMLSVKNCFIRGSVVR   71 (98)
Q Consensus         1 ~~~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~---------~~~~~~~~~~~v~IRG~~I~   71 (98)
                      |+..-+..+| .+++.++.|.+.||+++.|.+++||.|||++|.||++...         ++. ..+-++.+++||.+|.
T Consensus         1 M~~a~sskml-~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~e-Ekr~lgLvllRgenIv   78 (177)
T KOG3168|consen    1 MTVAKSSKML-QHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGE-EKRVLGLVLLRGENIV   78 (177)
T ss_pred             CCccchhHHH-HhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccc-eeeEEEEEEecCCcEE
Confidence            4444444444 4679999999999999999999999999999999996421         222 2567999999999999


Q ss_pred             EEecCCc
Q psy6026          72 YVQLPGD   78 (98)
Q Consensus        72 ~I~~p~~   78 (98)
                      .....+-
T Consensus        79 s~tVegp   85 (177)
T KOG3168|consen   79 SMTVEGP   85 (177)
T ss_pred             EEeccCC
Confidence            9987643

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

Probab=98.27  E-value=3.3e-06  Score=51.91  Aligned_cols=46  Identities=24%  Similarity=0.288  Sum_probs=37.2

Q ss_pred             HHHHhhcCCCeEEEEEcCCcEEEEEEEEecc---ccceEEeeEEEECCC
Q psy6026           7 YSFFKSLVGKDVVVELKNDVSICGTLHSVDQ---YLNIKLTDISVTDPD   52 (98)
Q Consensus         7 ~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~---~mNi~L~~~~~~~~~   52 (98)
                      .-++..++|++|.|.++||..|+|++.+++.   -+.++|+-|......
T Consensus         4 ~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~   52 (77)
T PF14438_consen    4 VYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKS   52 (77)
T ss_dssp             HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS-
T ss_pred             HHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccc
Confidence            4567899999999999999999999999998   899999999987653

>KOG3459|consensus

Probab=98.25  E-value=1.5e-07  Score=61.83  Aligned_cols=69  Identities=20%  Similarity=0.286  Sum_probs=55.2

Q ss_pred             hHHHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECC------CCCc-----ceeecceEEEEcCeEEE
Q psy6026           6 FYSFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDP------DKYP-----HMLSVKNCFIRGSVVRY   72 (98)
Q Consensus         6 p~~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~------~~~~-----~~~~~~~v~IRG~~I~~   72 (98)
                      |++.+....  ..+|.|-++|+..+-|++.+||.|+|++|+++.+...      +|..     ..+..+.+||||++|..
T Consensus        25 pls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~  104 (114)
T KOG3459|consen   25 PLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVIL  104 (114)
T ss_pred             chhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEE
Confidence            667776666  5589999999999999999999999999999986421      1211     13568999999999988


Q ss_pred             Ee
Q psy6026          73 VQ   74 (98)
Q Consensus        73 I~   74 (98)
                      +.
T Consensus       105 v~  106 (114)
T KOG3459|consen  105 VL  106 (114)
T ss_pred             EE
Confidence            76

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

Probab=97.87  E-value=0.00015  Score=46.94  Aligned_cols=68  Identities=19%  Similarity=0.271  Sum_probs=55.8

Q ss_pred             hhcCCCeEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEECCCCCc-------ceeecceEEEEcCeEEEEecCCc
Q psy6026          11 KSLVGKDVVVELKNDVSICGTLHSVDQ-YLNIKLTDISVTDPDKYP-------HMLSVKNCFIRGSVVRYVQLPGD   78 (98)
Q Consensus        11 ~~l~gk~V~V~Lkng~~~~G~L~~~D~-~mNi~L~~~~~~~~~~~~-------~~~~~~~v~IRG~~I~~I~~p~~   78 (98)
                      ..++|++|.+..+++..|+|+|..+|. .-.+.|.++..+..++.+       ...-++.+..||+.|.-+.+-+.
T Consensus         4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~   79 (96)
T PF12701_consen    4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEP   79 (96)
T ss_dssp             CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-
T ss_pred             ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcC
Confidence            368999999999999999999999995 789999999987654421       12358899999999999987654

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

Probab=97.45  E-value=0.00012  Score=44.15  Aligned_cols=37  Identities=24%  Similarity=0.284  Sum_probs=30.2

Q ss_pred             CCeEEEEEcCC----cEEEEEEEEeccccceEEeeEEEECC
Q psy6026          15 GKDVVVELKND----VSICGTLHSVDQYLNIKLTDISVTDP   51 (98)
Q Consensus        15 gk~V~V~Lkng----~~~~G~L~~~D~~mNi~L~~~~~~~~   51 (98)
                      +.+|.|.++.-    -.++|.|.+||.|+|+.|.|+.++-.
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            56777777743    37889999999999999999998654

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.

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

Probab=97.38  E-value=0.0016  Score=40.31  Aligned_cols=61  Identities=18%  Similarity=0.283  Sum_probs=48.8

Q ss_pred             hcCCCeEEEEEcCCcEEEEEEEEec-cccceEEeeEEEECCCCCc--------ceeecceEEEEcCeEEE
Q psy6026          12 SLVGKDVVVELKNDVSICGTLHSVD-QYLNIKLTDISVTDPDKYP--------HMLSVKNCFIRGSVVRY   72 (98)
Q Consensus        12 ~l~gk~V~V~Lkng~~~~G~L~~~D-~~mNi~L~~~~~~~~~~~~--------~~~~~~~v~IRG~~I~~   72 (98)
                      +++|+++.+..+.+..|.|+|.++| +---+.|+|+..+..+|..        ...-++.+..||+.|.-
T Consensus         3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD   72 (74)
T cd01736           3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD   72 (74)
T ss_pred             cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence            5789999999999999999999999 4668899999987655432        12247788889988753

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.

>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=97.27  E-value=0.006  Score=38.29  Aligned_cols=65  Identities=18%  Similarity=0.308  Sum_probs=51.4

Q ss_pred             chHHHHhhcCCCeEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecC
Q psy6026           5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQ-YLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLP   76 (98)
Q Consensus         5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~-~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p   76 (98)
                      ..+.+|.++.|++|.+.|.++.++.|+..++|. -.|+..++-.  .|=|     ..+...+|.+-|..+++.
T Consensus        14 rfLr~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   14 RFLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ--TPLG-----VQPEALLRCSDVISISFD   79 (80)
T ss_dssp             HHHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE--TTTT-----EEEEEEEEGGGEEEEEE-
T ss_pred             HHHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC--CCcc-----cChhheeecCCEEEEEec
Confidence            357789999999999999999999999999995 5699888844  3333     358999999999999875

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.

>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=96.73  E-value=0.013  Score=32.89  Aligned_cols=47  Identities=23%  Similarity=0.287  Sum_probs=35.1

Q ss_pred             CCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEE
Q psy6026          14 VGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIR   66 (98)
Q Consensus        14 ~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IR   66 (98)
                      +|++|++.+ ++..++|+..++|+.-.+.++.     ++|..+....+.+++|
T Consensus         2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~-----~~g~~~~i~sGdv~~r   48 (48)
T PF02237_consen    2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRT-----EDGSIRTISSGDVSLR   48 (48)
T ss_dssp             TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEE-----TTEEEEEESSSEEEEE
T ss_pred             CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEE-----CCCCEEEEEEEEEEeC
Confidence            699999999 6677799999999999999976     2332123345666665

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 ....

>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=96.71  E-value=0.0048  Score=36.84  Aligned_cols=37  Identities=24%  Similarity=0.367  Sum_probs=29.6

Q ss_pred             HHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026           9 FFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTD   45 (98)
Q Consensus         9 ~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~   45 (98)
                      ||+.+.  ..+|+|-|.||..++|.+.+||.|+=+.-.+
T Consensus         3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   41 (61)
T cd01716           3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLLESD   41 (61)
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence            455544  5579999999999999999999998665443

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=96.64  E-value=0.0055  Score=36.58  Aligned_cols=37  Identities=27%  Similarity=0.376  Sum_probs=29.7

Q ss_pred             HHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026           9 FFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTD   45 (98)
Q Consensus         9 ~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~   45 (98)
                      ||+.+.  +.+|+|-|.||..+.|.+.+||.|+=+.-.+
T Consensus         7 fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~   45 (61)
T TIGR02383         7 FLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ   45 (61)
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence            455544  5679999999999999999999998665443

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

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=96.42  E-value=0.0084  Score=37.53  Aligned_cols=38  Identities=21%  Similarity=0.393  Sum_probs=30.6

Q ss_pred             HHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026           8 SFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTD   45 (98)
Q Consensus         8 ~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~   45 (98)
                      .||+.+.  +.+|+|-|.||..+.|.+.+||.|+=+.-.+
T Consensus        10 ~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~   49 (79)
T PRK00395         10 PFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNT   49 (79)
T ss_pred             HHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEEC
Confidence            3555554  5679999999999999999999998666544

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

Probab=96.16  E-value=0.056  Score=32.70  Aligned_cols=52  Identities=29%  Similarity=0.443  Sum_probs=40.2

Q ss_pred             HHHHhhcCCCeEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026           7 YSFFKSLVGKDVVVELKNDVSICGTLHSVDQ-YLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ   74 (98)
Q Consensus         7 ~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~-~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~   74 (98)
                      ...|++++|++|.|++-.|+. +|+|.++-. |.  +|+.      .+       ..+|||=..|.+|.
T Consensus        13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDhI--vl~~------~~-------~~~~IR~~~IV~v~   65 (66)
T PF10842_consen   13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDHI--VLEE------NG-------TPFFIRIAQIVWVM   65 (66)
T ss_pred             HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCEE--EEEe------CC-------cEEEEEeeeEEEEc
Confidence            578999999999999988876 999999873 43  3332      12       47889988888874

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

Probab=96.09  E-value=0.011  Score=36.68  Aligned_cols=35  Identities=23%  Similarity=0.382  Sum_probs=29.1

Q ss_pred             HHHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccce
Q psy6026           7 YSFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNI   41 (98)
Q Consensus         7 ~~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi   41 (98)
                      -.||.++.  +.+|+|-|.||...+|.+++||.|.=+
T Consensus         9 D~fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~Vl   45 (77)
T COG1923           9 DPFLNALRKEKIPVTIFLVNGFKLQGQVESFDNFVVL   45 (77)
T ss_pred             hHHHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEEEE
Confidence            35666654  678999999999999999999999743

>KOG1073|consensus

Probab=95.83  E-value=0.027  Score=44.07  Aligned_cols=68  Identities=18%  Similarity=0.220  Sum_probs=55.2

Q ss_pred             hhcCCCeEEEEEcCCcEEEEEEEEec-cccceEEeeEEEECCCCCc-------c-eeecceEEEEcCeEEEEecCCc
Q psy6026          11 KSLVGKDVVVELKNDVSICGTLHSVD-QYLNIKLTDISVTDPDKYP-------H-MLSVKNCFIRGSVVRYVQLPGD   78 (98)
Q Consensus        11 ~~l~gk~V~V~Lkng~~~~G~L~~~D-~~mNi~L~~~~~~~~~~~~-------~-~~~~~~v~IRG~~I~~I~~p~~   78 (98)
                      ..++|+.|.+.-|++..|+|+|.-+| +---|-|.+|..+.+++..       . ..-++.++.||+.|.-+.+-+.
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 7889999999877554321       1 1157889999999997776553

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

Probab=95.12  E-value=0.21  Score=29.71  Aligned_cols=33  Identities=15%  Similarity=0.148  Sum_probs=28.8

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026          13 LVGKDVVVELKNDVSICGTLHSVDQYLNIKLTD   45 (98)
Q Consensus        13 l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~   45 (98)
                      .+|..|.+++..|..++|.+.+||...++.+=.
T Consensus         4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk   36 (61)
T cd01735           4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILK   36 (61)
T ss_pred             ccccEEEEEecCCceEEEEEEEecCCCcEEEEE
Confidence            479999999999999999999999887766444

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.

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

Probab=94.42  E-value=0.22  Score=35.15  Aligned_cols=61  Identities=25%  Similarity=0.319  Sum_probs=43.0

Q ss_pred             HHhhcCCCeEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCc
Q psy6026           9 FFKSLVGKDVVVELKNDVSICGTLHSVDQ-YLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGD   78 (98)
Q Consensus         9 ~L~~l~gk~V~V~Lkng~~~~G~L~~~D~-~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~   78 (98)
                      .+..++||.|.|.+.| +++.|.|..+|. .-|++|-+-.   .++.     ...-+|-|..|..|..-++
T Consensus        11 ~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~---e~~~-----~sv~~I~ghaVk~vevl~~   72 (166)
T PF06372_consen   11 EWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQ---EDGK-----RSVKVIMGHAVKSVEVLSE   72 (166)
T ss_dssp             HHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE----TTS------EEEEEE-GGGEEEEEEEE-
T ss_pred             HHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEcc---cCCc-----eeEEEEEccceEEEEEccC
Confidence            4678999999999999 999999999995 6688887533   2232     2457899999999986653

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.

>PRK14638 hypothetical protein; Provisional

Probab=93.92  E-value=0.12  Score=35.63  Aligned_cols=36  Identities=17%  Similarity=0.232  Sum_probs=29.6

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEe
Q psy6026           8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLT   44 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~   44 (98)
                      .-+..++|+.|.|.+++++.++|+|.++|+. ++.|+
T Consensus        93 ~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~  128 (150)
T PRK14638         93 KDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS  128 (150)
T ss_pred             HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            3467889999999999999999999999963 34443

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=93.77  E-value=0.15  Score=36.04  Aligned_cols=38  Identities=24%  Similarity=0.373  Sum_probs=30.2

Q ss_pred             HHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026           8 SFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTD   45 (98)
Q Consensus         8 ~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~   45 (98)
                      .||+.+.  ..+|+|-|.||-.++|.+.+||.|+=+.-.+
T Consensus        95 ~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~  134 (165)
T PRK14091         95 VFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERD  134 (165)
T ss_pred             HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence            3555555  5579999999999999999999998665444

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=93.14  E-value=0.21  Score=35.25  Aligned_cols=38  Identities=24%  Similarity=0.287  Sum_probs=30.5

Q ss_pred             HHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026           8 SFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTD   45 (98)
Q Consensus         8 ~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~   45 (98)
                      .||+.+.  ..+|+|-|.||..++|++.+||+|.=+.-.+
T Consensus        15 ~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~   54 (165)
T PRK14091         15 IFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRD   54 (165)
T ss_pred             HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence            4566665  4579999999999999999999998665544

>PRK14639 hypothetical protein; Provisional

Probab=93.07  E-value=0.21  Score=34.10  Aligned_cols=35  Identities=29%  Similarity=0.395  Sum_probs=29.6

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEE
Q psy6026           8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKL   43 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L   43 (98)
                      .-++.++|+.|.|.+.+++.+.|+|.++|+. ++.|
T Consensus        81 ~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l  115 (140)
T PRK14639         81 EHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL  115 (140)
T ss_pred             HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence            4467889999999999999999999999983 4444

>PRK02001 hypothetical protein; Validated

Probab=92.87  E-value=0.23  Score=34.48  Aligned_cols=30  Identities=33%  Similarity=0.468  Sum_probs=27.2

Q ss_pred             HHhhcCCCeEEEEEcCCcEEEEEEEEeccc
Q psy6026           9 FFKSLVGKDVVVELKNDVSICGTLHSVDQY   38 (98)
Q Consensus         9 ~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~   38 (98)
                      -+..++|+.|.|.+.++..+.|+|.++|+.
T Consensus        84 ~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~  113 (152)
T PRK02001         84 QYKKNIGRELEVLTKNGKKIEGELKSADEN  113 (152)
T ss_pred             HHHHhCCCEEEEEECCCCEEEEEEEEEeCC
Confidence            456889999999999999999999999974

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

Probab=90.59  E-value=0.66  Score=28.61  Aligned_cols=31  Identities=39%  Similarity=0.413  Sum_probs=26.1

Q ss_pred             HHHhhcCCCeEEEEEc---CC-cEEEEEEEEeccc
Q psy6026           8 SFFKSLVGKDVVVELK---ND-VSICGTLHSVDQY   38 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lk---ng-~~~~G~L~~~D~~   38 (98)
                      .-+..++|+.|.|+++   +| +.+.|.|.++|+.
T Consensus        18 ~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~   52 (83)
T cd01734          18 ADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD   52 (83)
T ss_pred             HHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC
Confidence            3467889999999998   55 6899999999983

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.

>PRK14644 hypothetical protein; Provisional

Probab=90.34  E-value=0.62  Score=31.71  Aligned_cols=35  Identities=23%  Similarity=0.286  Sum_probs=29.0

Q ss_pred             HHhhcCCCeEEEEEcCC----cEEEEEEEEeccccceEEe
Q psy6026           9 FFKSLVGKDVVVELKND----VSICGTLHSVDQYLNIKLT   44 (98)
Q Consensus         9 ~L~~l~gk~V~V~Lkng----~~~~G~L~~~D~~mNi~L~   44 (98)
                      -+..++|+.|.|.|++.    ..+.|+|.++|+. ++.|+
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            47788999999999987    9999999999973 34443

>PRK14640 hypothetical protein; Provisional

Probab=89.67  E-value=0.75  Score=31.72  Aligned_cols=35  Identities=29%  Similarity=0.445  Sum_probs=28.2

Q ss_pred             HHHhhcCCCeEEEEE----cCCcEEEEEEEEeccccceEE
Q psy6026           8 SFFKSLVGKDVVVEL----KNDVSICGTLHSVDQYLNIKL   43 (98)
Q Consensus         8 ~~L~~l~gk~V~V~L----kng~~~~G~L~~~D~~mNi~L   43 (98)
                      .-+..++|+.|.|.|    .+.+.+.|+|.++|+. ++.|
T Consensus        90 ~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l  128 (152)
T PRK14640         90 AQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITL  128 (152)
T ss_pred             HHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence            346788999999999    5779999999999974 3444

>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=89.59  E-value=1.1  Score=31.15  Aligned_cols=33  Identities=24%  Similarity=0.379  Sum_probs=29.3

Q ss_pred             HHHHhhcCCCeEEEEE----cCCcEEEEEEEEecccc
Q psy6026           7 YSFFKSLVGKDVVVEL----KNDVSICGTLHSVDQYL   39 (98)
Q Consensus         7 ~~~L~~l~gk~V~V~L----kng~~~~G~L~~~D~~m   39 (98)
                      ..-+..+.|+.|.|.|    .+.+.+.|+|.++|+.+
T Consensus        91 ~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~  127 (153)
T COG0779          91 AEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET  127 (153)
T ss_pred             HHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence            3557788999999999    79999999999999876

>PRK14642 hypothetical protein; Provisional

Probab=89.03  E-value=0.82  Score=33.10  Aligned_cols=35  Identities=23%  Similarity=0.354  Sum_probs=28.4

Q ss_pred             HHHhhcCCCeEEEEEc-------------CCcEEEEEEEEeccccceEE
Q psy6026           8 SFFKSLVGKDVVVELK-------------NDVSICGTLHSVDQYLNIKL   43 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lk-------------ng~~~~G~L~~~D~~mNi~L   43 (98)
                      .-+..++|+.|.|.|+             +.+.++|+|.++|+. ++.|
T Consensus        93 ~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l  140 (197)
T PRK14642         93 QDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI  140 (197)
T ss_pred             HHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence            3466788999999998             779999999999974 4434

>PRK14633 hypothetical protein; Provisional

Probab=88.68  E-value=0.96  Score=31.14  Aligned_cols=35  Identities=26%  Similarity=0.275  Sum_probs=28.1

Q ss_pred             HHHhhcCCCeEEEEEc----CCcEEEEEEEEeccccceEE
Q psy6026           8 SFFKSLVGKDVVVELK----NDVSICGTLHSVDQYLNIKL   43 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lk----ng~~~~G~L~~~D~~mNi~L   43 (98)
                      .-+..++|+.|.|.++    +++.++|+|.++++. ++.|
T Consensus        87 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l  125 (150)
T PRK14633         87 IQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL  125 (150)
T ss_pred             HHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence            3467889999999994    669999999999874 4444

>PRK14645 hypothetical protein; Provisional

Probab=87.44  E-value=1.1  Score=31.03  Aligned_cols=30  Identities=17%  Similarity=0.249  Sum_probs=25.5

Q ss_pred             HHHhhcCCCeEEEEEcCCcEEEEEEEEeccc
Q psy6026           8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQY   38 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~   38 (98)
                      .-+..++|+.|.|.+ ++..+.|+|.++|+.
T Consensus        95 ~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~  124 (154)
T PRK14645         95 RHFERFAGLKAKVRG-PGENFTGRIKAVSGD  124 (154)
T ss_pred             HHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC
Confidence            345678899999986 889999999999974

>PRK14636 hypothetical protein; Provisional

Probab=87.02  E-value=1.3  Score=31.45  Aligned_cols=30  Identities=20%  Similarity=0.392  Sum_probs=25.8

Q ss_pred             HHHhhcCCCeEEEEEc---CC-cEEEEEEEEecc
Q psy6026           8 SFFKSLVGKDVVVELK---ND-VSICGTLHSVDQ   37 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lk---ng-~~~~G~L~~~D~   37 (98)
                      .-+..++|+.|.|+|+   +| +.+.|+|.++|+
T Consensus        91 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~  124 (176)
T PRK14636         91 KDFADWAGHEARIALSEPLDGRKQFRGELKGIDG  124 (176)
T ss_pred             HHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeC
Confidence            3467889999999997   55 799999999987

>PRK14632 hypothetical protein; Provisional

Probab=86.87  E-value=1.4  Score=31.12  Aligned_cols=36  Identities=19%  Similarity=0.322  Sum_probs=28.5

Q ss_pred             HHHhhcCCCeEEEEEcC-------CcEEEEEEEEeccccceEEe
Q psy6026           8 SFFKSLVGKDVVVELKN-------DVSICGTLHSVDQYLNIKLT   44 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lkn-------g~~~~G~L~~~D~~mNi~L~   44 (98)
                      .-++.++|+.|.|.|++       .+.+.|+|.++|+. ++.|+
T Consensus        91 ~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~  133 (172)
T PRK14632         91 EQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR  133 (172)
T ss_pred             HHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence            34678899999999986       57999999999863 44443

>PRK14643 hypothetical protein; Provisional

Probab=86.53  E-value=1.4  Score=30.83  Aligned_cols=36  Identities=14%  Similarity=0.107  Sum_probs=28.2

Q ss_pred             HHHhhcCCCeEEEEEcC----CcEEEEEEEEeccc-cceEE
Q psy6026           8 SFFKSLVGKDVVVELKN----DVSICGTLHSVDQY-LNIKL   43 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lkn----g~~~~G~L~~~D~~-mNi~L   43 (98)
                      .-+..++|+.|.|.|+.    .+.+.|+|.++|.. ..+.|
T Consensus        97 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l  137 (164)
T PRK14643         97 EELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRF  137 (164)
T ss_pred             HHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEE
Confidence            34668899999999975    69999999999964 34443

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=86.41  E-value=1.6  Score=29.99  Aligned_cols=30  Identities=30%  Similarity=0.513  Sum_probs=26.2

Q ss_pred             HHHhhcCCCeEEEEE----cCCcEEEEEEEEecc
Q psy6026           8 SFFKSLVGKDVVVEL----KNDVSICGTLHSVDQ   37 (98)
Q Consensus         8 ~~L~~l~gk~V~V~L----kng~~~~G~L~~~D~   37 (98)
                      .-+..++|+.|.|.+    .++..+.|+|.++|+
T Consensus        91 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~  124 (154)
T PRK00092         91 RDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG  124 (154)
T ss_pred             HHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence            456788999999997    577899999999997

>PRK14634 hypothetical protein; Provisional

Probab=86.23  E-value=1.6  Score=30.27  Aligned_cols=35  Identities=20%  Similarity=0.323  Sum_probs=27.3

Q ss_pred             HHHhhcCCCeEEEEEcCC----cEEEEEEEEeccccceEE
Q psy6026           8 SFFKSLVGKDVVVELKND----VSICGTLHSVDQYLNIKL   43 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lkng----~~~~G~L~~~D~~mNi~L   43 (98)
                      .-+..++|+.|.|+|.+.    +.+.|+|.++|+. ++.|
T Consensus        93 ~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l  131 (155)
T PRK14634         93 RDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI  131 (155)
T ss_pred             HHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence            346788999999999743    7999999999974 3444

>PRK14646 hypothetical protein; Provisional

Probab=85.33  E-value=1.8  Score=29.93  Aligned_cols=35  Identities=26%  Similarity=0.280  Sum_probs=27.5

Q ss_pred             HHHhhcCCCeEEEEEcCC----cEEEEEEEEeccccceEE
Q psy6026           8 SFFKSLVGKDVVVELKND----VSICGTLHSVDQYLNIKL   43 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lkng----~~~~G~L~~~D~~mNi~L   43 (98)
                      .-+..++|+.|.|+|++.    +.+.|+|.++|+. ++.|
T Consensus        93 ~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l  131 (155)
T PRK14646         93 RDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI  131 (155)
T ss_pred             HHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence            346788999999999643    7889999999974 4444

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

Probab=85.32  E-value=1.3  Score=29.84  Aligned_cols=30  Identities=33%  Similarity=0.524  Sum_probs=23.6

Q ss_pred             HHHhhcCCCeEEEEEc----CCcEEEEEEEEecc
Q psy6026           8 SFFKSLVGKDVVVELK----NDVSICGTLHSVDQ   37 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lk----ng~~~~G~L~~~D~   37 (98)
                      .-+..++|+.|.|.++    +.+.+.|+|.++|+
T Consensus        80 ~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~  113 (141)
T PF02576_consen   80 RDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE  113 (141)
T ss_dssp             HHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET
T ss_pred             HHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC
Confidence            4577889999999994    55799999999998

; PDB: 1IB8_A.

>PRK14647 hypothetical protein; Provisional

Probab=84.82  E-value=2  Score=29.78  Aligned_cols=30  Identities=17%  Similarity=0.252  Sum_probs=25.6

Q ss_pred             HHHhhcCCCeEEEEEc---------CCcEEEEEEEEecc
Q psy6026           8 SFFKSLVGKDVVVELK---------NDVSICGTLHSVDQ   37 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lk---------ng~~~~G~L~~~D~   37 (98)
                      .-+..++|+.|.|.|+         +.+.+.|+|.++|+
T Consensus        92 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~  130 (159)
T PRK14647         92 ADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD  130 (159)
T ss_pred             HHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence            4467889999999996         35999999999996

>PRK06955 biotin--protein ligase; Provisional

Probab=84.04  E-value=6.4  Score=29.72  Aligned_cols=51  Identities=18%  Similarity=0.297  Sum_probs=36.3

Q ss_pred             hcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcC
Q psy6026          12 SLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS   68 (98)
Q Consensus        12 ~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~   68 (98)
                      ...|++|.|...++..+.|+..++|+.-.+.++.     .+|. +....|++.+|..
T Consensus       246 ~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~-----~~g~-~~~~sGeV~~~~~  296 (300)
T PRK06955        246 AYAGREVVLLEDGAELARGVAHGIDETGQLLLDT-----PAGR-QAIAAGDVSLREA  296 (300)
T ss_pred             hcCCCeEEEEECCCcEEEEEEeeECCCceEEEEe-----CCCe-EEEEEEEEEEecc
Confidence            3679999997767788999999999999998853     2231 1234566666543

>PRK14637 hypothetical protein; Provisional

Probab=83.28  E-value=2.4  Score=29.25  Aligned_cols=35  Identities=26%  Similarity=0.308  Sum_probs=26.4

Q ss_pred             HHHhhcCCCeEEEEEcCCcEE-EEEEEEeccccceEE
Q psy6026           8 SFFKSLVGKDVVVELKNDVSI-CGTLHSVDQYLNIKL   43 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lkng~~~-~G~L~~~D~~mNi~L   43 (98)
                      .-+..++|+.|.|.+.+...+ .|+|.++|+. ++.|
T Consensus        91 ~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l  126 (151)
T PRK14637         91 AEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVL  126 (151)
T ss_pred             HHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEE
Confidence            446788999999999544555 7999999974 3444

>PRK09618 flgD flagellar basal body rod modification protein; Provisional

Probab=82.88  E-value=2.3  Score=29.34  Aligned_cols=26  Identities=35%  Similarity=0.484  Sum_probs=24.0

Q ss_pred             hhcCCCeEEEEEcCCcEEEEEEEEec
Q psy6026          11 KSLVGKDVVVELKNDVSICGTLHSVD   36 (98)
Q Consensus        11 ~~l~gk~V~V~Lkng~~~~G~L~~~D   36 (98)
                      .+++||.|.+...+|..+.|++.++.
T Consensus        88 ~slVGk~V~~~~~~g~~~tG~V~~V~  113 (142)
T PRK09618         88 SELIGKEVEWEGEDGEIVSGTVTSVK  113 (142)
T ss_pred             HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence            57899999999999999999999986

>PRK14631 hypothetical protein; Provisional

Probab=82.25  E-value=3  Score=29.53  Aligned_cols=29  Identities=24%  Similarity=0.384  Sum_probs=25.3

Q ss_pred             HHHhhcCCCeEEEEEc----CCcEEEEEEEEec
Q psy6026           8 SFFKSLVGKDVVVELK----NDVSICGTLHSVD   36 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lk----ng~~~~G~L~~~D   36 (98)
                      .-+..++|+.|.|+|+    +.+.++|+|.++|
T Consensus       110 ~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~  142 (174)
T PRK14631        110 EQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD  142 (174)
T ss_pred             HHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence            4467889999999996    5599999999998

>PRK14641 hypothetical protein; Provisional

Probab=81.45  E-value=2.8  Score=29.66  Aligned_cols=29  Identities=21%  Similarity=0.402  Sum_probs=24.6

Q ss_pred             HHHhhcCCCeEEEEEcC----CcEEEEEEEEec
Q psy6026           8 SFFKSLVGKDVVVELKN----DVSICGTLHSVD   36 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lkn----g~~~~G~L~~~D   36 (98)
                      .-++.++|+.|.|.|++    .+.++|+|.++|
T Consensus        97 ~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~  129 (173)
T PRK14641         97 RQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS  129 (173)
T ss_pred             HHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence            44678899999999976    568999999995

>PRK08330 biotin--protein ligase; Provisional

Probab=81.26  E-value=10  Score=27.46  Aligned_cols=33  Identities=18%  Similarity=0.253  Sum_probs=26.8

Q ss_pred             hcCCCeEEEEEcCCcEE-EEEEEEeccccceEEee
Q psy6026          12 SLVGKDVVVELKNDVSI-CGTLHSVDQYLNIKLTD   45 (98)
Q Consensus        12 ~l~gk~V~V~Lkng~~~-~G~L~~~D~~mNi~L~~   45 (98)
                      ...|++|.+.. ++..+ .|+..++|+.-.+.+..
T Consensus       185 ~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~  218 (236)
T PRK08330        185 MILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL  218 (236)
T ss_pred             HhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence            46799999976 55554 79999999999998874

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	98
4emh_A	105	Crystal Structure Of Splsm4 Length = 105		1e-06
1b34_A	119	Crystal Structure Of The D1d2 Sub-Complex From The		3e-04

>pdb|4EMH|A Chain A, Crystal Structure Of Splsm4 Length = 105

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 50/89 (56%), Gaps = 3/89 (3%)
Query: 5   LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCF 64
           L  +   +  G+ ++VELKN  +  G L + D Y N+ L ++  T PD       +  C+
Sbjct: 16  LPLTLLNATQGRPILVELKNGETFNGHLENCDNYXNLTLREVIRTXPDG-DKFFRLPECY 74
Query: 65  IRGSVVRYVQLPGDEVDTQLL-QDATRKE 92
           IRG+ ++Y+++  DEV +Q+  Q A ++E
Sbjct: 75  IRGNNIKYLRIQ-DEVLSQVAKQQAQQRE 102

>pdb|1B34|A Chain A, Crystal Structure Of The D1d2 Sub-Complex From The Human Snrnp Core Domain Length = 119

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 9  FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
          F   L  + V +ELKN   + GT+  VD  +N  L  + +T  ++ P  + ++   IRG+
Sbjct: 6  FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREP--VQLETLSIRGN 63
Query: 69 VVRYVQLP 76
           +RY  LP
Sbjct: 64 NIRYFILP 71

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	98
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	9e-35
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	8e-31
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	6e-28
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	5e-24
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	2e-19
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	8e-16
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	6e-15
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	9e-11
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	1e-09
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	3e-09
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	5e-09
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	3e-08
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	9e-08
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	2e-05
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	8e-05
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	1e-04
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	1e-04
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	1e-04
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	3e-04

>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 =  113 bits (285), Expect = 9e-35
 Identities = 24/90 (26%), Positives = 48/90 (53%), Gaps = 1/90 (1%)

Query: 4   LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNC 63
           +L  +   +  G+ ++VELKN  +  G L + D Y+N+ L ++  T PD       +  C
Sbjct: 15  MLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDG-DKFFRLPEC 73

Query: 64  FIRGSVVRYVQLPGDEVDTQLLQDATRKEA 93
           +IRG+ ++Y+++  + +     Q A ++E 
Sbjct: 74  YIRGNNIKYLRIQDEVLSQVAKQQAQQREN 103

>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 =  104 bits (260), Expect = 8e-31
 Identities = 27/88 (30%), Positives = 39/88 (44%), Gaps = 2/88 (2%)

Query: 5  LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCF 64
              F   L  + V +ELKN   + GT+  VD  +N  L  + +T  ++ P  L  +   
Sbjct: 2  KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQL--ETLS 59

Query: 65 IRGSVVRYVQLPGDEVDTQLLQDATRKE 92
          IRG+ +RY  LP       LL D   K 
Sbjct: 60 IRGNNIRYFILPDSLPLDTLLVDVEPKV 87

>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 = 97.4 bits (242), Expect = 6e-28
 Identities = 21/96 (21%), Positives = 38/96 (39%), Gaps = 2/96 (2%)

Query: 1  MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSV 60
          M   +         G  V  E        G L   +  +N ++++I+VT  D     L  
Sbjct: 1  MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQL-- 58

Query: 61 KNCFIRGSVVRYVQLPGDEVDTQLLQDATRKEAVNA 96
          +  +IRGS +R++ LP    +  +L+    K   + 
Sbjct: 59 EQVYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSG 94

>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 = 85.5 bits (212), Expect = 5e-24
 Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 2/76 (2%)

Query: 1  MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSV 60
          M   +         G  V  E        G L   +  +N ++++I+VT  D     L  
Sbjct: 1  MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQL-- 58

Query: 61 KNCFIRGSVVRYVQLP 76
          +  +IRG  +R++ LP
Sbjct: 59 EQVYIRGCKIRFLILP 74

>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 = 74.4 bits (183), Expect = 2e-19
 Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 2/79 (2%)

Query: 9  FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
          F   L GK V+V+LK  +   G L SVD Y+N++L +            L      IR +
Sbjct: 10 FLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHL--GEVLIRCN 67

Query: 69 VVRYVQLPGDEVDTQLLQD 87
           V Y++   +E +   +++
Sbjct: 68 NVLYIRGVEEEEEDGEMRE 86

>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 = 65.2 bits (159), Expect = 8e-16
 Identities = 23/71 (32%), Positives = 31/71 (43%), Gaps = 3/71 (4%)

Query: 9  FFKSLVGKDVVVELK-NDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRG 67
          F K LV   V V+LK N     GTL S D Y N++L +            L     FIR 
Sbjct: 25 FLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTL--GEIFIRC 82

Query: 68 SVVRYVQLPGD 78
          + V Y++   +
Sbjct: 83 NNVLYIRELPN 93

>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 = 62.7 bits (153), Expect = 6e-15
 Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 2/70 (2%)

Query: 9  FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
          F   ++GK V++ L + V   G L  +D Y+N+ L         K  ++    + FIRG+
Sbjct: 8  FLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYG--DAFIRGN 65

Query: 69 VVRYVQLPGD 78
           V YV    D
Sbjct: 66 NVLYVSALDD 75

>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 = 51.9 bits (125), Expect = 9e-11
 Identities = 19/71 (26%), Positives = 27/71 (38%), Gaps = 3/71 (4%)

Query: 9  FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
               + KDV+V LK      G L   D +LN+ L D  +    +           IRG 
Sbjct: 8  VIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRY--GKIVIRGD 65

Query: 69 VVRYVQLPGDE 79
           V  +  P +E
Sbjct: 66 NVLAIS-PTEE 75

>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 = 49.2 bits (118), Expect = 1e-09
 Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 3/72 (4%)

Query: 9  FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
               +   V+V LK      GTL   D ++N+ L D       +    +   +  IRG 
Sbjct: 8  VLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKV--GSVVIRGD 65

Query: 69 VVRYVQ-LPGDE 79
           V +V   PG E
Sbjct: 66 TVVFVSPAPGGE 77

>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 = 48.1 bits (115), Expect = 3e-09
 Identities = 16/65 (24%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 9  FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
             + +   V+++LK D    G L S D ++N+ L D    +  +    L      IRG 
Sbjct: 19 ALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRL--GTVLIRGD 76

Query: 69 VVRYV 73
           + Y+
Sbjct: 77 NIVYI 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 = 47.7 bits (114), Expect = 5e-09
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 9  FFKSLVGKDVVVELKND-VSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRG 67
            KS+VGK + VE+K +   + G L  VD Y+N+ LT+      ++    L      +RG
Sbjct: 9  MVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSL--GEIVLRG 66

Query: 68 SVVRYVQLPGDE 79
          + V  +Q P +E
Sbjct: 67 NNVVLIQ-PQEE 77

>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 = 45.8 bits (109), Expect = 3e-08
 Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 5/67 (7%)

Query: 8  SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDIS-VTDPDKYPHMLSVKNCFIR 66
          +  +  +GK V+V+L++   I G L S DQ++N+ L D   + D + Y          +R
Sbjct: 14 ATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGT----MVVR 69

Query: 67 GSVVRYV 73
          G  V ++
Sbjct: 70 GENVLFI 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 = 44.6 bits (106), Expect = 9e-08
 Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 9  FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
               +   V+V+LK +  + G L S DQ++N+ L+D      D     L      IRG 
Sbjct: 13 VLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGT--IVIRGD 70

Query: 69 VVRYV 73
           V  +
Sbjct: 71 NVILI 75

>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 = 38.9 bits (91), Expect = 2e-05
 Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 5/76 (6%)

Query: 11 KSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDI--SVTDPDKYPHMLSVKNC---FI 65
          K  + + V ++L+   ++ GTL + D + NI L+D   ++   +      S + C   FI
Sbjct: 16 KLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFI 75

Query: 66 RGSVVRYVQLPGDEVD 81
          RG  V  +  P ++ D
Sbjct: 76 RGDTVTLISTPSEDDD 91

>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 = 37.6 bits (87), Expect = 8e-05
 Identities = 12/66 (18%), Positives = 26/66 (39%), Gaps = 6/66 (9%)

Query: 11 KSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDI--SVTDPDKYPHMLSVKN---CFI 65
               + +         I G L   DQ +N+ L D+   + +P+      +++      +
Sbjct: 29 SRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVV 88

Query: 66 RG-SVV 70
          RG ++V
Sbjct: 89 RGTTLV 94

>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 = 37.1 bits (86), Expect = 1e-04
 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 11/82 (13%)

Query: 8  SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTD-------ISVTDPDKYPHMLSV 60
             +  + + V V+L+ D  + G LH+ D++LN+ L D           + DK   + ++
Sbjct: 12 DLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTI 71

Query: 61 KN----CFIRGSVVRYVQLPGD 78
          +      F+RG  V  +  P +
Sbjct: 72 RKHYEMLFVRGDSVILIAPPRN 93

>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_A Length = 94

 Score = 36.7 bits (85), Expect = 1e-04
 Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 3/72 (4%)

Query: 10 FKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSV 69
           K + G ++ V +K++    GTL   D Y+NI L D++  D              + G+ 
Sbjct: 26 DKCI-GSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVT-GVTEKHSEMLLNGNG 83

Query: 70 VRYVQLPGDEVD 81
          +  +  PG + +
Sbjct: 84 MCMLI-PGGKPE 94

>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A Length = 121

 Score = 36.9 bits (85), Expect = 1e-04
 Identities = 14/60 (23%), Positives = 26/60 (43%)

Query: 14 VGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYV 73
          +G  + V +K D    G L   D+Y+N+ L D+           +S  N  ++  +V  +
Sbjct: 37 IGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRL 96

>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 = 35.4 bits (82), Expect = 3e-04
 Identities = 11/65 (16%), Positives = 26/65 (40%), Gaps = 6/65 (9%)

Query: 11 KSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDIS--VTDPDKYPHMLSVKNCFIRGS 68
          K  + K + ++L     + G L   D ++N+ + +     T   +    +      IRG+
Sbjct: 10 KKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGM----VVIRGN 65

Query: 69 VVRYV 73
           +  +
Sbjct: 66 SIIML 70

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	98
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.96
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.96
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.95
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.95
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.92
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.92
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.92
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.92
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.91
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.91
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.91
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.9
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.9
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.9
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.89
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.88
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.88
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.87
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.85
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.85
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.85
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.84
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.83
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.77
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	99.06
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	97.7
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	97.41
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	97.18
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	97.16
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	97.12
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	97.11
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	97.01
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	96.83
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	96.76
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	96.61
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	96.56
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	96.06
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	94.88
1ycy_A	71	Conserved hypothetical protein; structural genomic	94.65
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	94.14
2rm4_A	103	CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-	92.96
2eay_A	233	Biotin [acetyl-COA-carboxylase] ligase; biotin bio	87.86
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	87.6
3rux_A	270	BIRA bifunctional protein; biotin-protein ligase,	86.08
2dxu_A	235	Biotin--[acetyl-COA-carboxylase] ligase; biotin bi	85.2
1bia_A	321	BIRA bifunctional protein; transcription regulatio	84.74
2ej9_A	237	Putative biotin ligase; biotin biosynthesis, monom	84.66
3by7_A	100	Uncharacterized protein; metagenomics, structural	81.39

>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=99.96  E-value=6.7e-29  Score=166.42  Aligned_cols=90  Identities=22%  Similarity=0.338  Sum_probs=81.4

Q ss_pred             CcccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCccc
Q psy6026           1 MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEV   80 (98)
Q Consensus         1 ~~~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~~~   80 (98)
                      |..+.|++||++++|++|+|+|+||++|+|+|.+||+|||++|+||+++.++++  ...++.+||||++|+||++||...
T Consensus         1 ~~~~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~--~~~l~~v~IRGnnI~~I~lpd~l~   78 (126)
T 2y9a_D            1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGR--VAQLEQVYIRGSKIRFLILPDMLK   78 (126)
T ss_dssp             ---CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSC--CEEEEEEEECGGGEEEEECCSSCS
T ss_pred             CCcccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCc--EeecccEEEeCCEEEEEEcccccc
Confidence            778999999999999999999999999999999999999999999999987765  468999999999999999999988


Q ss_pred             ccHHhHHHHHHH
Q psy6026          81 DTQLLQDATRKE   92 (98)
Q Consensus        81 d~~~~~~~~r~~   92 (98)
                      +.++|++..++.
T Consensus        79 ~~~~l~~~~~k~   90 (126)
T 2y9a_D           79 NAPMLKSMKNKN   90 (126)
T ss_dssp             SSSHHHHHHHHH
T ss_pred             chHHhhhhhhcc
Confidence            889998877764

>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=99.96  E-value=1.5e-28  Score=151.36  Aligned_cols=75  Identities=23%  Similarity=0.362  Sum_probs=68.8

Q ss_pred             CcccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026           1 MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus         1 ~~~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      |..+.|++||++++|++|+|+||||++|+|+|.+||+|||++|+||+++.+++.  ...++.+||||++|+||++||
T Consensus         1 ~~~~~P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~~~--~~~lg~v~IRG~nI~~i~lPd   75 (75)
T 1d3b_A            1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGR--VAQLEQVYIRGCKIRFLILPD   75 (75)
T ss_dssp             ---CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSC--EEEEEEEEECGGGEEEEEECC
T ss_pred             CCccCHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCCCc--EEEcCeEEEeCCEEEEEEcCC
Confidence            778999999999999999999999999999999999999999999999987765  568999999999999999996

>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=99.95  E-value=4.8e-28  Score=160.70  Aligned_cols=89  Identities=27%  Similarity=0.444  Sum_probs=73.9

Q ss_pred             cchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCc-cccc
Q psy6026           4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGD-EVDT   82 (98)
Q Consensus         4 ~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~-~~d~   82 (98)
                      |+|++||++++|++|+|+|+||++|.|+|.+||+|||++|+||+++..+++  ...++.+||||++|+||++||. .+|+
T Consensus         1 M~p~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~~~--~~~lg~v~IRG~nI~~I~~pd~l~~d~   78 (119)
T 1b34_A            1 MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNRE--PVQLETLSIRGNNIRYFILPDSLPLDT   78 (119)
T ss_dssp             -CHHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSC--CEEEEEEEECGGGEEEEECCTTCCHHH
T ss_pred             CChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecCCCc--eeEcceEEEcCCeEEEEEeccccccch
Confidence            799999999999999999999999999999999999999999999987665  3689999999999999999998 6777


Q ss_pred             HHhHHHHHHHHh
Q psy6026          83 QLLQDATRKEAV   94 (98)
Q Consensus        83 ~~~~~~~r~~~~   94 (98)
                      .+.+++++++++
T Consensus        79 ~l~~~~pK~k~~   90 (119)
T 1b34_A           79 LLVDVEPKVKSK   90 (119)
T ss_dssp             HTC---------
T ss_pred             hHhhhccccccc
Confidence            888888886554

>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=99.95  E-value=8.4e-28  Score=156.68  Aligned_cols=89  Identities=27%  Similarity=0.573  Sum_probs=56.3

Q ss_pred             cchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCcccccH
Q psy6026           4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQ   83 (98)
Q Consensus         4 ~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~~~d~~   83 (98)
                      ..|++||++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..+|+. ...++.+||||++|+||++||...|++
T Consensus        15 ~~p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg~~-~~~lg~v~IRG~nI~~I~~pd~l~d~p   93 (105)
T 4emh_A           15 MLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDK-FFRLPECYIRGNNIKYLRIQDEVLSQV   93 (105)
T ss_dssp             -----------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCE-EEEEEEEEECGGGEEEEEC--------
T ss_pred             CcHHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCCce-eeEcCeEEEeCCeEEEEecCHHHhhhh
Confidence            5799999999999999999999999999999999999999999999877642 468999999999999999999999999


Q ss_pred             HhHHHHHHHH
Q psy6026          84 LLQDATRKEA   93 (98)
Q Consensus        84 ~~~~~~r~~~   93 (98)
                      +++.....+.
T Consensus        94 ~~~~~~~~~~  103 (105)
T 4emh_A           94 AKQQAQQREN  103 (105)
T ss_dssp             ----------
T ss_pred             hhhhhccccC
Confidence            9987665543

>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=3.3e-25  Score=136.64  Aligned_cols=73  Identities=30%  Similarity=0.458  Sum_probs=66.8

Q ss_pred             cchHHHHhhcCCCeEEEEEcCC-cEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCc
Q psy6026           4 LLFYSFFKSLVGKDVVVELKND-VSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGD   78 (98)
Q Consensus         4 ~~p~~~L~~l~gk~V~V~Lkng-~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~   78 (98)
                      |.|+++|.+++|++|+|+|+|| ++|.|+|.+||+|||++|+||+++..++.  ...++.++|||++|+||+.||+
T Consensus         4 ~~P~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~~~~--~~~lg~v~iRG~nI~~i~~~de   77 (77)
T 1ljo_A            4 VLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEK--VRSLGEIVLRGNNVVLIQPQEE   77 (77)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEE--EEEEEEEEECGGGEEEEEEC--
T ss_pred             cchHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecCCc--EeECCeEEEeCCeEEEEEeCCC
Confidence            7999999999999999999999 99999999999999999999999876543  4689999999999999999974

>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=9.8e-25  Score=135.73  Aligned_cols=76  Identities=25%  Similarity=0.260  Sum_probs=68.3

Q ss_pred             Cccc--chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCc
Q psy6026           1 MERL--LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGD   78 (98)
Q Consensus         1 ~~~~--~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~   78 (98)
                      |+.|  .|+++|++++|++|+|+|+||++|.|+|.+||+|||++|+||+++..++.  ...++.++|||++|++|+.++.
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 MNFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGS--GKKLGTIVIRGDNVILISPLQT   80 (81)
T ss_dssp             CCTTCHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSC--EEEEEEEEECGGGEEEEEEC--
T ss_pred             ccccccchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecCCc--eeECCEEEECCCEEEEEEecCC
Confidence            5566  59999999999999999999999999999999999999999999987654  4689999999999999999874

>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=99.92  E-value=7.6e-25  Score=134.81  Aligned_cols=73  Identities=23%  Similarity=0.270  Sum_probs=67.5

Q ss_pred             cchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCc
Q psy6026           4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGD   78 (98)
Q Consensus         4 ~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~   78 (98)
                      +.|+++|++++|++|+|+|+||++|.|+|.+||+|||++|+||+++..++.  ...++.+||||++|+||+.||.
T Consensus         3 ~~P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~--~~~lg~v~iRG~~I~~i~~~d~   75 (77)
T 1i4k_A            3 PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEV--VRKVGSVVIRGDTVVFVSPAPG   75 (77)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEE--EEEEEEEEECGGGEEEEEECC-
T ss_pred             ccHHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecCCc--EeECCEEEECCCEEEEEEeCCC
Confidence            689999999999999999999999999999999999999999999876643  4689999999999999999975

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

Probab=99.92  E-value=8.7e-25  Score=134.03  Aligned_cols=73  Identities=23%  Similarity=0.248  Sum_probs=66.4

Q ss_pred             cchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCc
Q psy6026           4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGD   78 (98)
Q Consensus         4 ~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~   78 (98)
                      +.|+++|++++|++|+|+|+||+.|.|+|.+||+|||++|+||+++..++.  ...++.++|||++|+||+.+++
T Consensus         3 ~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~--~~~lg~v~iRG~~I~~i~~~~e   75 (75)
T 1h64_1            3 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEV--VKRYGKIVIRGDNVLAISPTEE   75 (75)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEE--EEEEEEEEECGGGEEEEEEC--
T ss_pred             chHHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeCCc--eeECCEEEECCCEEEEEEeCCC
Confidence            579999999999999999999999999999999999999999999876543  4689999999999999999873

>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=99.91  E-value=1.4e-24  Score=136.77  Aligned_cols=76  Identities=29%  Similarity=0.330  Sum_probs=67.2

Q ss_pred             cccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCcc
Q psy6026           2 ERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDE   79 (98)
Q Consensus         2 ~~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~~   79 (98)
                      +...|++||++++|++|+|+|+||+.|+|+|.+||+|||++|+||+++..++.  ...++.+||||++|+||+.||..
T Consensus         3 ~~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~g~~--~~~lg~v~IRG~nI~~i~~~d~~   78 (86)
T 3s6n_F            3 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGAL--SGHLGEVLIRCNNVLYIRGVEEE   78 (86)
T ss_dssp             CCCCHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEE--EEEESSEEECGGGEEEEEECC--
T ss_pred             cCcCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcCCce--eeEccEEEEeCCeEEEEEeCCcc
Confidence            35689999999999999999999999999999999999999999998754322  46899999999999999999863

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

Probab=99.91  E-value=1.3e-24  Score=133.45  Aligned_cols=72  Identities=28%  Similarity=0.396  Sum_probs=65.3

Q ss_pred             cchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026           4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus         4 ~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      +.|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..++.  ...++.++|||++|+||+..|
T Consensus         3 ~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~--~~~lg~v~iRG~~I~~i~~~~   74 (75)
T 4emk_B            3 SSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKK--TNVYGDAFIRGNNVLYVSALD   74 (75)
T ss_dssp             SHHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEETTEE--EEEEEEEEEEGGGSSEEEEC-
T ss_pred             CchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEecCCc--ccEecEEEEcCCeEEEEEecC
Confidence            689999999999999999999999999999999999999999998765432  468999999999999999765

>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=2e-24  Score=137.93  Aligned_cols=74  Identities=28%  Similarity=0.324  Sum_probs=61.2

Q ss_pred             cccchHHHHhhcCCCeEEEEEcCC-cEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026           2 ERLLFYSFFKSLVGKDVVVELKND-VSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus         2 ~~~~p~~~L~~l~gk~V~V~Lkng-~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      +.+.|+++|++++|++|+|+|+|| ++|+|+|.+||+|||++|+||+++..++.  ...+|.+||||++|+||..++
T Consensus        18 ~~~~P~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~~~~--~~~lg~v~IRG~nI~~I~~~~   92 (93)
T 1n9r_A           18 QPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVS--HGTLGEIFIRCNNVLYIRELP   92 (93)
T ss_dssp             --------CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEE--EEECCSEEECGGGEEEEEECC
T ss_pred             ccCChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcCCCe--EeEcCEEEEcCCeEEEEEeCC
Confidence            467899999999999999999999 99999999999999999999999865443  468999999999999999886

>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=99.90  E-value=1.1e-23  Score=141.61  Aligned_cols=80  Identities=25%  Similarity=0.311  Sum_probs=75.4

Q ss_pred             HHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCcccccHHhH
Q psy6026           7 YSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQLLQ   86 (98)
Q Consensus         7 ~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~~~d~~~~~   86 (98)
                      +++|++++|++|+|+|+||+.|.|+|.+||+|||++|+||+++.  +    ..+|.++|||++|++|+.|+..+|+++++
T Consensus         2 ~~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~--~----~~lg~v~IRG~nI~~I~~~d~~~d~~~f~   75 (130)
T 1m5q_A            2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA--G----EKFNRVFIMYRYIVHIDSTERRIDMREFA   75 (130)
T ss_dssp             HHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTT--C----CEEEEEEECGGGEEEEEECCCCCCHHHHH
T ss_pred             hhHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEc--C----CEeceEEEeCCeEEEEEcCCcccCHHHHH
Confidence            57999999999999999999999999999999999999999884  2    36899999999999999999999999999


Q ss_pred             HHHHHH
Q psy6026          87 DATRKE   92 (98)
Q Consensus        87 ~~~r~~   92 (98)
                      ++.+++
T Consensus        76 ~~~~r~   81 (130)
T 1m5q_A           76 KQAEKI   81 (130)
T ss_dssp             HHHHHH
T ss_pred             HHHhhc
Confidence            999887

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

Probab=99.90  E-value=1.9e-23  Score=129.99  Aligned_cols=72  Identities=25%  Similarity=0.326  Sum_probs=65.7

Q ss_pred             ccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026           3 RLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus         3 ~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      ...|+++|.+++|++|+|+|+||++|.|+|.+||+|||++|+||+++ .++.  ...++.+||||++|+||+.+|
T Consensus         9 ~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~~~~--~~~lg~v~iRG~~I~~i~~~d   80 (81)
T 1i8f_A            9 FATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-IDGN--VYKRGTMVVRGENVLFISPVP   80 (81)
T ss_dssp             -CCHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-ETTE--EEEEEEEEECGGGEEEEEECC
T ss_pred             ccchHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-cCCc--ccCCCEEEECCCEEEEEEeCC
Confidence            46899999999999999999999999999999999999999999999 3332  468999999999999999886

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

Probab=99.90  E-value=1.9e-23  Score=130.53  Aligned_cols=72  Identities=21%  Similarity=0.299  Sum_probs=66.1

Q ss_pred             cccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEec
Q psy6026           2 ERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQL   75 (98)
Q Consensus         2 ~~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~   75 (98)
                      +.+.|+++|++++|++|+|+|+||++|.|+|.+||+|||++|+||+++..++.  ...++.+||||++|+||+.
T Consensus        12 ~~~~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~--~~~lg~v~IRG~~I~~i~p   83 (83)
T 1mgq_A           12 NVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEV--TRRLGTVLIRGDNIVYISP   83 (83)
T ss_dssp             CTTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEE--EEEEEEEEECGGGEEEEEC
T ss_pred             cCcChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecCCc--ccCCCEEEECCCEEEEEEC
Confidence            46789999999999999999999999999999999999999999999876543  4689999999999999973

>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=99.89  E-value=6.3e-23  Score=131.27  Aligned_cols=74  Identities=22%  Similarity=0.343  Sum_probs=65.2

Q ss_pred             ccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEEC-CCCCcceeecceEEEEcCeEEEEecCCc
Q psy6026           3 RLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTD-PDKYPHMLSVKNCFIRGSVVRYVQLPGD   78 (98)
Q Consensus         3 ~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~-~~~~~~~~~~~~v~IRG~~I~~I~~p~~   78 (98)
                      ...|+.+|.+++|++|+|+|+||+.|.|+|.+||+|||++|+||+++. .++.  ...++.++|||++|+||....+
T Consensus        18 ~~~Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~--~~~lg~v~IRG~nI~~i~p~~~   92 (94)
T 4emk_A           18 TILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGV--TEKHSEMLLNGNGMCMLIPGGK   92 (94)
T ss_dssp             --CHHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTTCC--EEEEEEEEECSTTEEEEEECC-
T ss_pred             cccCHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCCCc--EeEcCEEEEcCCEEEEEEeCCC
Confidence            468999999999999999999999999999999999999999999987 3333  5689999999999999996643

>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=99.88  E-value=8.7e-23  Score=125.67  Aligned_cols=72  Identities=14%  Similarity=0.236  Sum_probs=53.2

Q ss_pred             chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCc
Q psy6026           5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGD   78 (98)
Q Consensus         5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~   78 (98)
                      .+.++|++++|++|+|+|+||++|.|+|.+||+|||++|+||+++..++.  ...+|.++|||++|+||+..|.
T Consensus         4 ~~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~--~~~lg~v~iRG~~I~~i~~~d~   75 (76)
T 3s6n_G            4 AHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQ--QNNIGMVVIRGNSIIMLEALER   75 (76)
T ss_dssp             ----------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC------CBSSEEECSSSEEEEEC---
T ss_pred             cchHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccCCc--EeEcCEEEECCCeEEEEEeccC
Confidence            47899999999999999999999999999999999999999999876654  4689999999999999998763

>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=99.88  E-value=1.5e-22  Score=129.64  Aligned_cols=79  Identities=24%  Similarity=0.312  Sum_probs=65.2

Q ss_pred             chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCC-----CcceeecceEEEEcCeEEEEecCCcc
Q psy6026           5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDK-----YPHMLSVKNCFIRGSVVRYVQLPGDE   79 (98)
Q Consensus         5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~-----~~~~~~~~~v~IRG~~I~~I~~p~~~   79 (98)
                      -|+.+|++++|++|.|+|+||+.|.|+|.+||+|||++|+||.++....     ......+|.+||||++|.+|..++..
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            5899999999999999999999999999999999999999999864221     12246799999999999999999876


Q ss_pred             cccH
Q psy6026          80 VDTQ   83 (98)
Q Consensus        80 ~d~~   83 (98)
                      .|..
T Consensus        90 ~d~~   93 (96)
T 3bw1_A           90 DDGA   93 (96)
T ss_dssp             ---C
T ss_pred             cccc
Confidence            6543

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

Probab=99.87  E-value=6.4e-22  Score=126.18  Aligned_cols=75  Identities=23%  Similarity=0.276  Sum_probs=63.9

Q ss_pred             cccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECC----CCC-------cceeecceEEEEcCeE
Q psy6026           2 ERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDP----DKY-------PHMLSVKNCFIRGSVV   70 (98)
Q Consensus         2 ~~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~----~~~-------~~~~~~~~v~IRG~~I   70 (98)
                      +...|+++|+.++|++|+|+|+||+.|.|+|.+||+|||++|+||+++..    ++.       .....+|.+||||++|
T Consensus         6 ~~~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG~nV   85 (93)
T 4emg_A            6 AVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDSV   85 (93)
T ss_dssp             ---CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECGGGE
T ss_pred             ccCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECCCeE
Confidence            35689999999999999999999999999999999999999999998753    121       1256899999999999


Q ss_pred             EEEecC
Q psy6026          71 RYVQLP   76 (98)
Q Consensus        71 ~~I~~p   76 (98)
                      .+|+.|
T Consensus        86 v~I~p~   91 (93)
T 4emg_A           86 ILIAPP   91 (93)
T ss_dssp             EEEECC
T ss_pred             EEEEec
Confidence            999976

>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=99.85  E-value=1.3e-21  Score=124.69  Aligned_cols=73  Identities=12%  Similarity=0.234  Sum_probs=65.4

Q ss_pred             cchHHHHhhcCCCeEEEEE----cCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026           4 LLFYSFFKSLVGKDVVVEL----KNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus         4 ~~p~~~L~~l~gk~V~V~L----kng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      ..|+++|.++++++|+|++    +||++|.|+|.+||+|||++|+||+++..++. ....+|.++|||++|.+|+.++
T Consensus        15 ~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~-~~~~lg~v~iRG~nV~~i~~~~   91 (92)
T 3s6n_E           15 VQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTK-SRKQLGRIMLKGDNITLLQSVS   91 (92)
T ss_dssp             CCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSC-CEEEEEEEEECGGGEEEEEEC-
T ss_pred             cCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCC-ceeEcCeEEEeCCEEEEEEeCC
Confidence            5799999999999999999    99999999999999999999999999875433 2468999999999999999765

>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=99.85  E-value=9.4e-22  Score=130.62  Aligned_cols=76  Identities=21%  Similarity=0.367  Sum_probs=65.8

Q ss_pred             ccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCC---------CCc----ceeecceEEEEcCe
Q psy6026           3 RLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPD---------KYP----HMLSVKNCFIRGSV   69 (98)
Q Consensus         3 ~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~---------~~~----~~~~~~~v~IRG~~   69 (98)
                      .+.|+.+|.+++|++|+|+|+||+.|.|+|.+||+|||++|+||+++..+         |..    ....+|.+||||++
T Consensus        26 ~~~Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG~n  105 (121)
T 2fwk_A           26 IILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNN  105 (121)
T ss_dssp             CCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGG
T ss_pred             ccCcHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECCCE
Confidence            47899999999999999999999999999999999999999999986532         211    03579999999999


Q ss_pred             EEEEecCCc
Q psy6026          70 VRYVQLPGD   78 (98)
Q Consensus        70 I~~I~~p~~   78 (98)
                      |++|...+.
T Consensus       106 Vv~I~~~~~  114 (121)
T 2fwk_A          106 VAMLVPGGD  114 (121)
T ss_dssp             EEEEESSSC
T ss_pred             EEEEEecCC
Confidence            999998765

>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=99.85  E-value=1.1e-21  Score=124.13  Aligned_cols=75  Identities=15%  Similarity=0.140  Sum_probs=62.3

Q ss_pred             cchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECC---C-----CCcceeecceEEEEcCeEEEEec
Q psy6026           4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDP---D-----KYPHMLSVKNCFIRGSVVRYVQL   75 (98)
Q Consensus         4 ~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~---~-----~~~~~~~~~~v~IRG~~I~~I~~   75 (98)
                      +.|.++|.+++|++|+|+|+||+.|.|+|.+||+|||++|+||.++..   .     .......+|.++|||++|.+|++
T Consensus         3 ~~~~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~~I~~i~~   82 (91)
T 1d3b_B            3 VGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTV   82 (91)
T ss_dssp             ----CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEE
T ss_pred             CChhHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECCCeEEEEEc
Confidence            568899999999999999999999999999999999999999998531   1     11124689999999999999998


Q ss_pred             CCc
Q psy6026          76 PGD   78 (98)
Q Consensus        76 p~~   78 (98)
                      ++.
T Consensus        83 ~~~   85 (91)
T 1d3b_B           83 EGP   85 (91)
T ss_dssp             EEC
T ss_pred             CCC
Confidence            875

>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=99.84  E-value=8.9e-21  Score=124.78  Aligned_cols=81  Identities=15%  Similarity=0.213  Sum_probs=56.0

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCC-----CcceeecceEEEEcCeEEEEecCCc--
Q psy6026           6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDK-----YPHMLSVKNCFIRGSVVRYVQLPGD--   78 (98)
Q Consensus         6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~-----~~~~~~~~~v~IRG~~I~~I~~p~~--   78 (98)
                      |...|.+++|++|+|+|+||+.|.|+|.+||.||||+|+||.++..+.     ......+|.++|||++|.+|+.+|.  
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            567899999999999999999999999999999999999999976431     1125689999999999999998875  


Q ss_pred             ccccHHhH
Q psy6026          79 EVDTQLLQ   86 (98)
Q Consensus        79 ~~d~~~~~   86 (98)
                      +++.|+.+
T Consensus       104 e~~~p~~~  111 (113)
T 4emk_C          104 EIPNPFVQ  111 (113)
T ss_dssp             --------
T ss_pred             cccCcccc
Confidence            55555443

>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=99.83  E-value=1.9e-20  Score=123.78  Aligned_cols=76  Identities=17%  Similarity=0.185  Sum_probs=63.2

Q ss_pred             ccchHHHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCC------CC------cceeecceEEEEcC
Q psy6026           3 RLLFYSFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPD------KY------PHMLSVKNCFIRGS   68 (98)
Q Consensus         3 ~~~p~~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~------~~------~~~~~~~~v~IRG~   68 (98)
                      .+.|+++|..++  |++|.|+|+||+.|.|+|.+||+|||++|+||+++...      +.      .....+|.+||||+
T Consensus        25 ~~~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~  104 (118)
T 1b34_B           25 NTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGD  104 (118)
T ss_dssp             -CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGG
T ss_pred             ccChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcCC
Confidence            357999999999  59999999999999999999999999999999986421      10      01246999999999


Q ss_pred             eEEEEecCCc
Q psy6026          69 VVRYVQLPGD   78 (98)
Q Consensus        69 ~I~~I~~p~~   78 (98)
                      +|.+|+.++.
T Consensus       105 nVv~I~~~~~  114 (118)
T 1b34_B          105 SVIVVLRNPL  114 (118)
T ss_dssp             GEEEEEECCC
T ss_pred             EEEEEEeCch
Confidence            9999998875

>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=99.77  E-value=1.1e-18  Score=126.42  Aligned_cols=76  Identities=14%  Similarity=0.140  Sum_probs=65.3

Q ss_pred             ccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECC----CC----CcceeecceEEEEcCeEEEEe
Q psy6026           3 RLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDP----DK----YPHMLSVKNCFIRGSVVRYVQ   74 (98)
Q Consensus         3 ~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~----~~----~~~~~~~~~v~IRG~~I~~I~   74 (98)
                      .+.+...|++++|++|+|+|+||++|.|+|.+||+||||+|+||+++..    ++    ......++.+||||++|.+|.
T Consensus         2 ~v~k~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~Is   81 (231)
T 3pgw_B            2 TVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMT   81 (231)
T ss_pred             CcCchHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEEEE
Confidence            3567789999999999999999999999999999999999999998641    10    113578999999999999999


Q ss_pred             cCCc
Q psy6026          75 LPGD   78 (98)
Q Consensus        75 ~p~~   78 (98)
                      +.+-
T Consensus        82 ve~p   85 (231)
T 3pgw_B           82 VEGP   85 (231)
T ss_pred             ecCC
Confidence            8754

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

Probab=99.06  E-value=1.2e-09  Score=68.49  Aligned_cols=65  Identities=22%  Similarity=0.142  Sum_probs=56.7

Q ss_pred             chHHHHhhcCCCeEEEEEcCCcEEEEEEEEec-cccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCc
Q psy6026           5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVD-QYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGD   78 (98)
Q Consensus         5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D-~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~   78 (98)
                      .|. .|++++||+|.|.|.||++|+|+|.++| ...|++|.|+   ..++     .+..++|.|+.|..|.+-++
T Consensus         8 ~p~-el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~---~~~~-----~~~~~iI~G~aI~eI~v~~~   73 (86)
T 1y96_A            8 GPL-EWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNF---LEDG-----SMSVTGIMGHAVQTVETMNE   73 (86)
T ss_dssp             CHH-HHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEE---CTTS-----CEEEEEECGGGEEEEEEEEC
T ss_pred             CHH-HHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeec---ccCC-----eEEEEEEecceEEEEEEecc
Confidence            454 7899999999999999999999999999 8999999999   3332     46899999999999987754

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

Probab=97.70  E-value=0.00054  Score=42.77  Aligned_cols=67  Identities=19%  Similarity=0.283  Sum_probs=55.6

Q ss_pred             hcCCCeEEEEEcCCcEEEEEEEEec-cccceEEeeEEEECCCCCc-------ceeecceEEEEcCeEEEEecCCc
Q psy6026          12 SLVGKDVVVELKNDVSICGTLHSVD-QYLNIKLTDISVTDPDKYP-------HMLSVKNCFIRGSVVRYVQLPGD   78 (98)
Q Consensus        12 ~l~gk~V~V~Lkng~~~~G~L~~~D-~~mNi~L~~~~~~~~~~~~-------~~~~~~~v~IRG~~I~~I~~p~~   78 (98)
                      .++|+++.+..+.+..|+|+|..+| +.--+.|+|+..+..+|.+       ...-++.+..||+.|.-+.+-+.
T Consensus        10 ~yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~yIvFrgsDIKdL~V~~~   84 (88)
T 2vxe_A           10 PELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQIAPQSQIYDYILFRGSDIKDIRVVNN   84 (88)
T ss_dssp             CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCTTTCCSSCCCCCCSCEEEEEEETTTEEEEEECCC
T ss_pred             cccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCcCCCCCcccCCCCceeeEEEEccCCccEEEEecc
Confidence            4689999999999999999999999 5778999999998665432       12247899999999999987653

>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=97.41  E-value=0.00049  Score=43.53  Aligned_cols=71  Identities=15%  Similarity=0.219  Sum_probs=55.4

Q ss_pred             HHHHhhcCCCeEEEEEcCCcEEEEEEEEec-cccceEEeeEEEECCCCCc-------ceeecceEEEEcCeEEEEecCC
Q psy6026           7 YSFFKSLVGKDVVVELKNDVSICGTLHSVD-QYLNIKLTDISVTDPDKYP-------HMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus         7 ~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D-~~mNi~L~~~~~~~~~~~~-------~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      ..--..++|+++.+..|.+..|+|+|..+| +.--+.|+|+..+.++|.+       ...-++.+..||+-|.-+.+-+
T Consensus        11 ~~~~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~~ipp~~~vyeyIvFrGsDIKDL~V~e   89 (95)
T 2fb7_A           11 PSGGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCE   89 (95)
T ss_dssp             -----CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSSCCCSCCCCSSCEEECSTTEEEEEESC
T ss_pred             CCccCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCCccCCCCcceeEEEEcCCCcceEEEec
Confidence            334467899999999999999999999999 5778999999987665432       1234789999999999988754

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

Probab=97.18  E-value=0.00049  Score=42.11  Aligned_cols=56  Identities=14%  Similarity=0.194  Sum_probs=41.8

Q ss_pred             HHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026           8 SFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus         8 ~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      .||+.+.  +.+|+|.|.||..++|++.+||.|+=+.-.       +|.       ..+|-=..|..|....
T Consensus        14 ~fLn~lrk~~~~Vtv~L~nG~~l~G~I~~fD~f~VlL~~-------~g~-------qqlIYKhAISTI~p~~   71 (78)
T 3ahu_A           14 QFLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFTVLLES-------EGK-------QQLIYKHAISTFAPQK   71 (78)
T ss_dssp             HHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEES-------SSC-------EEEEEGGGEEEEEESS
T ss_pred             HHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEEEEE-------CCe-------eEEEEcceEEEEeecc
Confidence            4667666  889999999999999999999999855432       232       3466667777776543

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

Probab=97.16  E-value=0.0046  Score=38.30  Aligned_cols=64  Identities=16%  Similarity=0.285  Sum_probs=53.8

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEec-cccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecC
Q psy6026           6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVD-QYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLP   76 (98)
Q Consensus         6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D-~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p   76 (98)
                      .+.+|.++.|++|.+.|..+..+.|+..++| ...|+..++-.  .+=|     ..++..+|++-|..+++.
T Consensus        20 fLr~l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~--TPiG-----v~~eAlLR~~Dii~~sF~   84 (85)
T 1y96_B           20 YLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQ--TPIG-----VQAEALLRCSDIISYTFK   84 (85)
T ss_dssp             HHHHHHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEC--CTTC-----CEEEEEEEGGGEEEEEEC
T ss_pred             HHHHHHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhcC--CCcc-----cchhhhhhcCCEEEEEec
Confidence            4788999999999999999999999999999 46688888743  2223     468999999999999875

>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=97.12  E-value=0.00061  Score=41.23  Aligned_cols=56  Identities=18%  Similarity=0.255  Sum_probs=42.4

Q ss_pred             HHHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026           7 YSFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus         7 ~~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      -.||+.+.  ..+|+|.|.||..++|++.+||.|+=+.- +      +        ...+|.=..|.+|....
T Consensus        11 d~~L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~vlL~-~------~--------~~~LIYKhAIsTI~p~~   68 (74)
T 2ylb_A           11 DPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLK-N------T--------VSQMVYKHAISTVVPSR   68 (74)
T ss_dssp             HHHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEE-S------S--------SEEEEEGGGEEEEEESS
T ss_pred             HHHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEE-C------C--------ceEEEEeeeEEEEeEcc
Confidence            35677776  78999999999999999999999985443 2      1        24567777788877553

>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=97.11  E-value=0.00062  Score=42.01  Aligned_cols=56  Identities=16%  Similarity=0.246  Sum_probs=40.5

Q ss_pred             HHHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026           7 YSFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus         7 ~~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      -.||+.+.  +.+|+|.|.||..++|++.+||.|+=+.- +      +        ...+|-=..|..|....
T Consensus         9 d~fLn~lrk~~~~Vtv~L~NG~~l~G~I~~fD~ftVlL~-~------~--------~qqLVYKHAISTI~p~~   66 (82)
T 1u1s_A            9 DPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLK-N------T--------VSQMVYKHAISTVVPSR   66 (82)
T ss_dssp             HHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEE-S------S--------SCEEEEGGGEEEEEESS
T ss_pred             HHHHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEe-c------C--------ceEEEEeeeeEEEeecc
Confidence            35666666  77899999999999999999999985543 2      1        13455566677766443

>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=97.01  E-value=0.0014  Score=39.91  Aligned_cols=57  Identities=14%  Similarity=0.180  Sum_probs=42.4

Q ss_pred             HHHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026           7 YSFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus         7 ~~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      -.||+.+.  ..+|+|.|.||..++|++.+||.|+=+.-.+       |       ...+|-=..|.+|....
T Consensus         9 d~fLn~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~VlL~~~-------g-------~~qLIYKhAISTI~p~~   67 (77)
T 1kq1_A            9 DKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQ-------G-------KQHLIYKHAISTYTVET   67 (77)
T ss_dssp             HHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEEET-------T-------EEEEEEGGGEEEEEC--
T ss_pred             HHHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEEEEC-------C-------eeEEEEeeeEEEEeECc
Confidence            35677777  8899999999999999999999998555332       2       23467777788877543

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

Probab=96.83  E-value=0.0015  Score=39.99  Aligned_cols=55  Identities=20%  Similarity=0.299  Sum_probs=41.5

Q ss_pred             HHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026           8 SFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus         8 ~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      .||+.+.  ..+|+|.|.||..+.|++.+||.|+=+. +       +|.       ..+|-=..|.+|....
T Consensus        11 ~fLn~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~VlL-~-------~g~-------~qLIYKhAISTI~P~~   67 (79)
T 3sb2_A           11 PFLNALRKEHVPVSIYLVNGIKLQGHVESFDQYVVLL-R-------NTV-------TQMVYKHAISTVVPAR   67 (79)
T ss_dssp             HHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEE-E-------SSS-------EEEEEGGGEEEEEESS
T ss_pred             HHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEE-E-------CCc-------eEEEEeeeEEEEeecC
Confidence            4666665  4569999999999999999999998654 2       222       3467777888887554

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

Probab=96.76  E-value=0.0012  Score=42.37  Aligned_cols=56  Identities=18%  Similarity=0.262  Sum_probs=40.9

Q ss_pred             HHHHhhcCCC--eEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026           7 YSFFKSLVGK--DVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus         7 ~~~L~~l~gk--~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      -.||+.+..+  +|+|.|.||..++|++.+||.|+=+.-.+               ...+|-=..|.+|....
T Consensus        11 d~fLn~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~VlL~~~---------------kqqLIYKHAISTI~p~~   68 (104)
T 2y90_A           11 DPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNT---------------VSQMVYKHAISTVVPSR   68 (104)
T ss_dssp             HHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEESS---------------SEEEEEGGGEEEEEESS
T ss_pred             HHHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEECC---------------ceEEEEeeeeEEEeecc
Confidence            3567777644  89999999999999999999998554311               23456666777776543

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

Probab=96.61  E-value=0.0043  Score=37.23  Aligned_cols=35  Identities=23%  Similarity=0.232  Sum_probs=28.6

Q ss_pred             HHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEE
Q psy6026           9 FFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKL   43 (98)
Q Consensus         9 ~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L   43 (98)
                      ||+.+.  +.+|+|.|.||..++|.+.+||.|+=+.-
T Consensus        17 fLn~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~   53 (71)
T 2qtx_A           17 FEYARRLNGKKVKIFLRNGEVLDAEVTGVSNYEIMVK   53 (71)
T ss_dssp             CCGGGGGTTCEEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEEEE
Confidence            444433  67899999999999999999999986553

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

Probab=96.56  E-value=0.0039  Score=41.07  Aligned_cols=55  Identities=20%  Similarity=0.182  Sum_probs=40.4

Q ss_pred             HhhcCCCeEEEEEcCCcEEEEEEEEeccccceEE--eeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026          10 FKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKL--TDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus        10 L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L--~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      +..++|..|.|+|+||..++|++..+|. -+|+|  ++|.      .      ...-|+++.|.=+.+-+
T Consensus         7 ~sqFlGy~V~v~LkDgs~~qG~I~~vd~-k~LtL~~~~a~------~------s~~~I~asdI~DLkVl~   63 (125)
T 4a53_A            7 VADFYGSNVEVLLNNDSKARGVITNFDS-SNSILQLRLAN------D------STKSIVTKDIKDLRILP   63 (125)
T ss_dssp             HHHHTTCEEEEEETTSCEEEEEEEEEET-TTTEEEEEETT------T------EEEEEEGGGEEEEEECC
T ss_pred             HHHhcCceEEEEECCCCEeeEEEEeecC-CeeEEeccccc------c------ccceeecccccceeeee
Confidence            3567899999999999999999999983 35555  8872      1      11177777777665443

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

Probab=96.06  E-value=0.025  Score=34.82  Aligned_cols=61  Identities=18%  Similarity=0.190  Sum_probs=48.5

Q ss_pred             hhcCCCeEEEEEcCCc-EEEEEEEEeccc-cceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecC
Q psy6026          11 KSLVGKDVVVELKNDV-SICGTLHSVDQY-LNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLP   76 (98)
Q Consensus        11 ~~l~gk~V~V~Lkng~-~~~G~L~~~D~~-mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p   76 (98)
                      ..++|+.|.++.+++. .|+|.|..+|.. -+|.|.++.   .+|-  ......+.+++.-|.-+.+-
T Consensus         5 ~~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~f---~NG~--~~~s~eVtls~~DI~~L~ii   67 (84)
T 2vc8_A            5 TDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPF---HNGV--KCLVPEVTFRAGDITELKIL   67 (84)
T ss_dssp             CTTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEEE---ETTE--ECSSSEEEEEGGGCSEEEEE
T ss_pred             ccccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehhh---hCCC--CCCCcEEEEEecChhheEEE
Confidence            3678999999999999 999999999964 589999995   3443  22456799999888766543

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

Probab=94.88  E-value=0.2  Score=29.75  Aligned_cols=55  Identities=18%  Similarity=0.224  Sum_probs=39.6

Q ss_pred             HHHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026           7 YSFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ   74 (98)
Q Consensus         7 ~~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~   74 (98)
                      .+.|++++  ..+|.|+|.+|..+.|.+.-+|.++=+.-.+      ++       ...+|.-..|.||.
T Consensus        11 vR~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~cl~L~~~------~~-------~~~LI~r~AI~~I~   67 (70)
T 3hfo_A           11 VRQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDGLGLVDD------SE-------RSTIVRLAAIAYIT   67 (70)
T ss_dssp             HHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEECT------TC-------CEEEEEGGGEEEEE
T ss_pred             HHHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCEEEEEcC------CC-------CeEEEEeeeeEEEe
Confidence            45666666  6789999999999999999999987544322      22       24466666666664

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

Probab=94.65  E-value=0.22  Score=29.20  Aligned_cols=62  Identities=26%  Similarity=0.319  Sum_probs=44.5

Q ss_pred             HHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEec
Q psy6026           7 YSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQL   75 (98)
Q Consensus         7 ~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~   75 (98)
                      -..|..-.|++|-+-.-....++|+|..||+-. +.|.|++....+      +-..++++=+-|.+|.+
T Consensus         8 dktL~~WKg~rvAv~vg~ehSFtGiledFDeEv-iLL~dV~D~~GN------k~k~liv~idDinWimL   69 (71)
T 1ycy_A            8 EKVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIGN------RGKQMLIGLEDINWIML   69 (71)
T ss_dssp             HHHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTEE------EEEEEEEEGGGEEEEEE
T ss_pred             HHHHHHhCCcEEEEEecCcceeeeehhhcCcce-eehhhHHHHhcc------ccceeEEEeccceEEEe
Confidence            457888899999999999999999999999754 678998876543      23466677666666654

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

Probab=94.14  E-value=0.39  Score=28.66  Aligned_cols=55  Identities=16%  Similarity=0.219  Sum_probs=39.4

Q ss_pred             HHHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026           7 YSFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ   74 (98)
Q Consensus         7 ~~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~   74 (98)
                      .+.|++++  ..+|.|+|.+|..+.|++.-.|.++=+.-.+      ++       ...+|.-..|.||.
T Consensus        13 vR~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~cl~L~~~------~~-------~~~LI~R~AI~~Ik   69 (72)
T 3hfn_A           13 IRQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTCVCIADE------NS-------RQTTIWKQAIAYLQ   69 (72)
T ss_dssp             HHHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSEEEEEC----------------CEEEEEGGGEEEEE
T ss_pred             HHHHHHHHhhCceEEEEecCCCEEEEEEEEECCCEEEEEcC------CC-------CeEEEEeeeeEEEE
Confidence            56677776  5679999999999999999999987544432      11       24566666677664

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

Probab=92.96  E-value=0.83  Score=28.80  Aligned_cols=61  Identities=11%  Similarity=0.186  Sum_probs=47.4

Q ss_pred             hcCCCeEEEEEcCCc-EEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecC
Q psy6026          12 SLVGKDVVVELKNDV-SICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLP   76 (98)
Q Consensus        12 ~l~gk~V~V~Lkng~-~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p   76 (98)
                      ..+|+.|.|...+.. .|+|.+..+|. -++.|.+|..   +|-+-.....++-++..-|.-+.+-
T Consensus         9 dwiG~~VSI~C~d~LGVyQG~I~~V~~-~~ItL~kaFr---NGiplk~~~~EVtLsa~DI~~L~II   70 (103)
T 2rm4_A            9 DWIGCAVSIACDEVLGVFQGLIKQISA-EEITIVRAFR---NGVPLRKQNAEVVLKCTDIRSIDLI   70 (103)
T ss_dssp             GGTTCEEEEEECTTTCEEEEEEEEEET-TEEEEEEEEE---TTEECSCSSSCEEEETTTEEEEEEE
T ss_pred             ceeceEEEEeeCCcceEeeEEEEEccc-ceeEEhhhhh---cCcCcCCCCceEEEEecchhheeee
Confidence            678999999999997 99999999995 4488888873   3432123567889999888877643

>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=87.86  E-value=0.45  Score=33.56  Aligned_cols=47  Identities=13%  Similarity=0.152  Sum_probs=34.5

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEc
Q psy6026          13 LVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRG   67 (98)
Q Consensus        13 l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG   67 (98)
                      ..|++|.+...++  +.|+..++|+.-.+.++.     .+|. +....|++.+|+
T Consensus       186 ~~g~~V~v~~~~~--~~G~~~gId~~G~L~v~~-----~~G~-~~~~~Gev~~r~  232 (233)
T 2eay_A          186 YLGEEVKLLGEGK--ITGKLVGLSEKGGALILT-----EEGI-KEILSGEFSLRR  232 (233)
T ss_dssp             TTTSEEEETTEEE--EEEEEEEECTTSCEEEEE-----TTEE-EEECSCCEEEC-
T ss_pred             ccCCEEEEEECCe--EEEEEEEECCCCeEEEEE-----CCCe-EEEEEeEEEEec
Confidence            4699999987665  999999999999999875     2232 233457777765

>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=87.60  E-value=0.52  Score=31.84  Aligned_cols=30  Identities=27%  Similarity=0.293  Sum_probs=25.4

Q ss_pred             HHhhcCCCeEEEEE----cCCcEEEEEEEEeccc
Q psy6026           9 FFKSLVGKDVVVEL----KNDVSICGTLHSVDQY   38 (98)
Q Consensus         9 ~L~~l~gk~V~V~L----kng~~~~G~L~~~D~~   38 (98)
                      -+..++|+.|.|+|    .+.+.++|+|.++|+.
T Consensus        98 df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T 1ib8_A           98 AVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED  131 (164)
T ss_dssp             HHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT
T ss_pred             HHHHhCCcEEEEEEecccCCceEEEEEEEEEeCC
Confidence            35678999999999    4559999999999964

>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=86.08  E-value=1.3  Score=31.85  Aligned_cols=33  Identities=24%  Similarity=0.330  Sum_probs=30.0

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026          13 LVGKDVVVELKNDVSICGTLHSVDQYLNIKLTD   45 (98)
Q Consensus        13 l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~   45 (98)
                      ..|++|+|.+.+|..+.|+..++|+.-.+.++.
T Consensus       222 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~  254 (270)
T 3rux_A          222 TIGSRVRVELPGGQDVVGIARDIDDQGRLCLDV  254 (270)
T ss_dssp             STTSEEEEECTTSCEEEEEEEEECTTSCEEEEE
T ss_pred             ccCCEEEEEECCCeEEEEEEEEECCCCeEEEEE
Confidence            459999999988999999999999999999875

>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=85.20  E-value=0.66  Score=32.80  Aligned_cols=30  Identities=13%  Similarity=0.203  Sum_probs=24.0

Q ss_pred             CCCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026          14 VGKDVVVELKNDVSICGTLHSVDQYLNIKLTD   45 (98)
Q Consensus        14 ~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~   45 (98)
                      .|++|.+...++  +.|+..++|+.-.+.++.
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            799999998877  999999999999999875

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

Probab=84.74  E-value=2.5  Score=30.89  Aligned_cols=49  Identities=12%  Similarity=0.134  Sum_probs=35.7

Q ss_pred             hcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEc
Q psy6026          12 SLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRG   67 (98)
Q Consensus        12 ~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG   67 (98)
                      ...|++|.|...+ ..+.|+..++|+.-.+.++.     .+| .+....|++.+|+
T Consensus       270 ~~~g~~V~v~~~~-~~~~G~~~gid~~G~L~v~~-----~~g-~~~~~~Gev~~r~  318 (321)
T 1bia_A          270 NFINRPVKLIIGD-KEIFGISRGIDKQGALLLEQ-----DGI-IKPWMGGEISLRS  318 (321)
T ss_dssp             TTTTSEEEEEETT-EEEEEEEEEECTTSCEEEEE-----TTE-EEEESSCEEEEC-
T ss_pred             hhcCCEEEEEECC-cEEEEEEEEECCCCeEEEEE-----CCC-EEEEEeeeEEEec
Confidence            3469999998765 47999999999999999875     233 2234557777764

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

Probab=84.66  E-value=2.9  Score=29.35  Aligned_cols=32  Identities=25%  Similarity=0.276  Sum_probs=28.4

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026          13 LVGKDVVVELKNDVSICGTLHSVDQYLNIKLTD   45 (98)
Q Consensus        13 l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~   45 (98)
                      ..|++|.+...++..+.|+..++|+.-.+. +.
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            469999999988877999999999998888 54

>3by7_A Uncharacterized protein; metagenomics, structural genomics, joint center for structur genomics, JCSG, protein structure initiative; 2.60A {Uncultured marine organism}

Probab=81.39  E-value=7.7  Score=24.31  Aligned_cols=58  Identities=22%  Similarity=0.267  Sum_probs=43.9

Q ss_pred             EEEEcCCcEEEEEEEEeccccceEEeeEEEECC----CCCc---------ceeecceEEEEcCeEEEEecCCc
Q psy6026          19 VVELKNDVSICGTLHSVDQYLNIKLTDISVTDP----DKYP---------HMLSVKNCFIRGSVVRYVQLPGD   78 (98)
Q Consensus        19 ~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~----~~~~---------~~~~~~~v~IRG~~I~~I~~p~~   78 (98)
                      .++|++|..+-|.+..-|+.  +.++|+....+    .|+.         ..+.-+.++||.+.|.++.-+..
T Consensus         7 iiRlvSGEEIia~v~et~~~--i~i~nPv~V~~~~~e~gk~~gigF~pW~plsde~~~ii~~~~ViT~~e~~~   77 (100)
T 3by7_A            7 IMRLVTGEDIIGNISESQGL--ITIKKAFVIIPMQATPGKPVQLVLSPWQPYTDDKEIVIDDSKVITITSPKD   77 (100)
T ss_dssp             EEEETTSCEEEEEEEEETTE--EEEEEEEEEEEEC-----CCEEEEEESCTTBCCSEEEEEGGGEEEEECBCH
T ss_pred             EEEecCccceeEEEEecCce--EEEECCEEEEEeecCCCcceeEeeecccccCcCceEEEchhhEEEEEeCCH
Confidence            57999999999999977764  88899886432    1111         14457899999999999998754

---

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	98
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	1e-24
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	8e-20
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	5e-19
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	2e-15
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	5e-15
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	6e-15
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	7e-15
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	6e-14
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	7e-14
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	2e-13
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	6e-09
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	5e-05

>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 = 87.9 bits (218), Expect = 1e-24
 Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 6/82 (7%)

Query: 6  FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFI 65
          F +   +L+G++V V L N     G LH+VD  LNI L + S    +K+  +      FI
Sbjct: 1  FVAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRV------FI 54

Query: 66 RGSVVRYVQLPGDEVDTQLLQD 87
              + ++      +D +    
Sbjct: 55 MYRYIVHIDSTERRIDMREFAK 76

>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 = 74.0 bits (182), Expect = 8e-20
 Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 3/77 (3%)

Query: 9  FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
          F   L  + V +ELKN   + GT+  VD  +N  L  + +T  ++ P  L  +   IRG+
Sbjct: 5  FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQL--ETLSIRGN 62

Query: 69 VVRYVQLPGDEVDTQLL 85
           +RY  LP D +    L
Sbjct: 63 NIRYFILP-DSLPLDTL 78

>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 = 72.1 bits (177), Expect = 5e-19
 Identities = 13/68 (19%), Positives = 28/68 (41%), Gaps = 2/68 (2%)

Query: 9  FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
                G  V  E        G L   +  +N ++++  +T   +   +  ++  +IRG 
Sbjct: 6  VLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSN--ITVTYRDGRVAQLEQVYIRGC 63

Query: 69 VVRYVQLP 76
           +R++ LP
Sbjct: 64 KIRFLILP 71

>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 = 62.4 bits (152), Expect = 2e-15
 Identities = 16/66 (24%), Positives = 25/66 (37%), Gaps = 2/66 (3%)

Query: 8  SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRG 67
                +   V+V LK      GTL   D ++N+ L D       +    +   +  IRG
Sbjct: 6  DVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKV--GSVVIRG 63

Query: 68 SVVRYV 73
            V +V
Sbjct: 64 DTVVFV 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 = 61.6 bits (150), Expect = 5e-15
 Identities = 17/66 (25%), Positives = 24/66 (36%), Gaps = 2/66 (3%)

Query: 8  SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRG 67
                + KDV+V LK      G L   D +LN+ L D  +    +           IRG
Sbjct: 5  DVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRY--GKIVIRG 62

Query: 68 SVVRYV 73
            V  +
Sbjct: 63 DNVLAI 68

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

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

 Score = 61.7 bits (150), Expect = 6e-15
 Identities = 16/65 (24%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 9  FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
               +   V+V+LK +  + G L S DQ++N+ L+D    +         +    IRG 
Sbjct: 11 VLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSD--SEEIQSDGSGKKLGTIVIRGD 68

Query: 69 VVRYV 73
           V  +
Sbjct: 69 NVILI 73

>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 = 61.3 bits (149), Expect = 7e-15
 Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 2/66 (3%)

Query: 8  SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRG 67
              + +   V+++LK D    G L S D ++N+ L D    +  +    L      IRG
Sbjct: 9  DALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRL--GTVLIRG 66

Query: 68 SVVRYV 73
            + Y+
Sbjct: 67 DNIVYI 72

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

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

 Score = 58.9 bits (143), Expect = 6e-14
 Identities = 22/69 (31%), Positives = 30/69 (43%), Gaps = 3/69 (4%)

Query: 11 KSLVGKDVVVELK-NDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSV 69
          K LV   V V+LK N     GTL S D Y N++L +            L     FIR + 
Sbjct: 2  KGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTL--GEIFIRCNN 59

Query: 70 VRYVQLPGD 78
          V Y++   +
Sbjct: 60 VLYIRELPN 68

>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 = 59.0 bits (143), Expect = 7e-14
 Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 3/68 (4%)

Query: 8  SFFKSLVGKDVVVELKND-VSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIR 66
             KS+VGK + VE+K +   + G L  VD Y+N+ LT+    +      + S+    +R
Sbjct: 8  QMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTN--AMECKGEEKVRSLGEIVLR 65

Query: 67 GSVVRYVQ 74
          G+ V  +Q
Sbjct: 66 GNNVVLIQ 73

>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 = 57.8 bits (140), Expect = 2e-13
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)

Query: 8  SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDIS-VTDPDKYPHMLSVKNCFIR 66
          +  +  +GK V+V+L++   I G L S DQ++N+ L D   + D + Y          +R
Sbjct: 5  ATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKR----GTMVVR 60

Query: 67 GSVVRYVQLP 76
          G  V ++   
Sbjct: 61 GENVLFISPV 70

>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 = 46.8 bits (111), Expect = 6e-09
 Identities = 18/88 (20%), Positives = 31/88 (35%), Gaps = 13/88 (14%)

Query: 4  LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDIS--VTDPDKYPHMLSVK 61
          +L  +     +G  + V +K D    G L   D+Y+N+ L D+       D+       K
Sbjct: 4  ILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNK 63

Query: 62 N-----------CFIRGSVVRYVQLPGD 78
                        + G+ V  +   GD
Sbjct: 64 KLKRVMVNRLETILLSGNNVAMLVPGGD 91

>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 = 36.3 bits (84), Expect = 5e-05
 Identities = 7/35 (20%), Positives = 16/35 (45%)

Query: 11 KSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTD 45
             +   +   L++     GT  + D+++N+ L D
Sbjct: 4  LQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCD 38

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	98
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.95
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.94
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.91
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.91
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.91
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.91
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.9
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.9
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.89
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.89
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.84
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.77
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.77
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	97.74
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	96.54
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	96.36
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	95.23
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	95.05
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	91.21
d2qqra1	59	Jumonji domain-containing protein 2A {Human (Homo	80.59

>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=99.95  E-value=1.1e-27  Score=145.14  Aligned_cols=71  Identities=23%  Similarity=0.393  Sum_probs=67.6

Q ss_pred             chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026           5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG   77 (98)
Q Consensus         5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~   77 (98)
                      +|+.+|+++.|++|+|+||||++|+|+|.+||+|||++|+||+++.++++  ...++.+||||++|+||++||
T Consensus         2 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~--~~~~~~v~IRG~~I~~i~lpd   72 (72)
T d1d3ba_           2 VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGR--VAQLEQVYIRGCKIRFLILPD   72 (72)
T ss_dssp             CHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSC--EEEEEEEEECGGGEEEEEECC
T ss_pred             CchHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCCCc--EeEcCeEEEECCEEEEEEcCC
Confidence            69999999999999999999999999999999999999999999988875  467999999999999999997

>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=99.94  E-value=9.4e-27  Score=143.59  Aligned_cols=74  Identities=30%  Similarity=0.519  Sum_probs=68.6

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCccccc
Q psy6026           6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDT   82 (98)
Q Consensus         6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~~~d~   82 (98)
                      ..+||+++.|++|+|+||||.+|+|+|.++|+|||+.|+||+++.++|.+  ..++.+||||++|+||++||+ +|.
T Consensus         2 lv~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~~--~~~~~v~IRG~~Ir~i~lPd~-l~~   75 (80)
T d1b34a_           2 LVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREP--VQLETLSIRGNNIRYFILPDS-LPL   75 (80)
T ss_dssp             HHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCC--EEEEEEEECGGGEEEEECCTT-CCH
T ss_pred             HHHHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCCE--EEcccEEEcCCEEEEEECCCC-ccc
Confidence            57899999999999999999999999999999999999999999988763  589999999999999999986 443

>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=99.91  E-value=8.3e-25  Score=132.74  Aligned_cols=72  Identities=21%  Similarity=0.317  Sum_probs=66.7

Q ss_pred             CcccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026           1 MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ   74 (98)
Q Consensus         1 ~~~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~   74 (98)
                      |....|+++|++++|++|.|+|+||++|.|+|.+||+|||++|+||+++..++.  ...++.+||||++|+||+
T Consensus         2 ~~~~~Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~~~--~~~~~~~~IRG~~I~~I~   73 (74)
T d1mgqa_           2 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEV--TRRLGTVLIRGDNIVYIS   73 (74)
T ss_dssp             CCTTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEE--EEEEEEEEECGGGEEEEE
T ss_pred             CcccCcHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCCCe--EeEcceEEEeCCEEEEEe
Confidence            566789999999999999999999999999999999999999999999887654  468999999999999996

>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=99.91  E-value=1.7e-24  Score=130.29  Aligned_cols=69  Identities=25%  Similarity=0.266  Sum_probs=64.1

Q ss_pred             chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEec
Q psy6026           5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQL   75 (98)
Q Consensus         5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~   75 (98)
                      .|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||+++.+++.  ...++.+||||++|+||+.
T Consensus         2 ~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~--~~~l~~~~IRG~~I~~Isp   70 (71)
T d1h641_           2 RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEV--VKRYGKIVIRGDNVLAISP   70 (71)
T ss_dssp             CHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEE--EEEEEEEEECGGGEEEEEE
T ss_pred             CchHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecCCc--EeEcCcEEEECCeEEEEeC
Confidence            59999999999999999999999999999999999999999999877654  4689999999999999974

>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=2.1e-24  Score=130.32  Aligned_cols=68  Identities=25%  Similarity=0.318  Sum_probs=64.0

Q ss_pred             chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026           5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ   74 (98)
Q Consensus         5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~   74 (98)
                      .|+++|++++|++|+|+|+||++|.|+|.+||+|||++|+||+++..++.  ...++.+||||++|+||+
T Consensus         3 ~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~--~~~~g~~~IRG~~I~~Is   70 (72)
T d1i4k1_           3 RPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEV--VRKVGSVVIRGDTVVFVS   70 (72)
T ss_dssp             CHHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSSSE--EEEEEEEEECGGGEEEEE
T ss_pred             ChHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecCCe--EeEcceEEEeCCeEEEEE
Confidence            59999999999999999999999999999999999999999999987664  468999999999999997

>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]

Probab=99.91  E-value=2.9e-24  Score=130.83  Aligned_cols=71  Identities=31%  Similarity=0.455  Sum_probs=65.0

Q ss_pred             ccchHHHHhhcCCCeEEEEEcCC-cEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEec
Q psy6026           3 RLLFYSFFKSLVGKDVVVELKND-VSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQL   75 (98)
Q Consensus         3 ~~~p~~~L~~l~gk~V~V~Lkng-~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~   75 (98)
                      .++|+++|++++|++|+|+|+|| +.|.|+|.+||+|||++|+||+++..++.  ...++.+||||++|+||..
T Consensus         3 ~~~P~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~--~~~~g~~~IRG~~I~~I~p   74 (75)
T d1ljoa_           3 MVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEK--VRSLGEIVLRGNNVVLIQP   74 (75)
T ss_dssp             CCCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEE--EEEEEEEEECGGGEEEEEE
T ss_pred             ccccHHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCCCc--EeEcceEEEeCCEEEEEEC
Confidence            47899999999999999999976 79999999999999999999999877654  4689999999999999973

>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=99.90  E-value=1e-23  Score=139.66  Aligned_cols=79  Identities=25%  Similarity=0.348  Sum_probs=72.2

Q ss_pred             HHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCcccccHHhH
Q psy6026           7 YSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQLLQ   86 (98)
Q Consensus         7 ~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~~~d~~~~~   86 (98)
                      +++|++++|++|+|+|+||++|.|+|.+||+|||++|+||++...+      .++.+||||++|+||++|++.+|+.+++
T Consensus         2 ~~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~~~------k~~~v~IRG~~I~~I~~~e~~iD~re~a   75 (127)
T d1m5q1_           2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGE------KFNRVFIMYRYIVHIDSTERRIDMREFA   75 (127)
T ss_dssp             HHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETTCC------EEEEEEECGGGEEEEEECSCCCCHHHHH
T ss_pred             hhHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECCCC------cccEEEEeCCeEEEEEcchhhcCHHHHH
Confidence            6899999999999999999999999999999999999999987654      4688999999999999999999999987


Q ss_pred             HHHHH
Q psy6026          87 DATRK   91 (98)
Q Consensus        87 ~~~r~   91 (98)
                      +...+
T Consensus        76 ~~~~k   80 (127)
T d1m5q1_          76 KQAEK   80 (127)
T ss_dssp             HHHHH
T ss_pred             HHHhh
Confidence            76543

>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=6.3e-24  Score=127.19  Aligned_cols=66  Identities=35%  Similarity=0.478  Sum_probs=59.0

Q ss_pred             HhhcCCCeEEEEEc-CCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe-cCC
Q psy6026          10 FKSLVGKDVVVELK-NDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ-LPG   77 (98)
Q Consensus        10 L~~l~gk~V~V~Lk-ng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~-~p~   77 (98)
                      |++++|++|.|+|| +|++|+|+|.+||+|||++|+||+++..++.  ...++.+||||++|+||. +||
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~--~~~lg~~~IRG~nI~~I~~~pd   68 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVS--HGTLGEIFIRCNNVLYIRELPN   68 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEE--EEECCSEEECGGGEEEEEECCC
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEecCCc--ccCcCeEEEECCEEEEEEeCCC
Confidence            67899999999999 6688999999999999999999999876553  468999999999999997 665

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

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

Probab=99.89  E-value=2.4e-23  Score=126.80  Aligned_cols=69  Identities=25%  Similarity=0.273  Sum_probs=64.4

Q ss_pred             chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEec
Q psy6026           5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQL   75 (98)
Q Consensus         5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~   75 (98)
                      .|.++|++++|++|+|+|+||++|.|+|.+||+|||++|+||+++..+++  ...++.+||||++|+||+.
T Consensus         7 ~~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~--~~~~~~v~iRG~~I~~I~~   75 (76)
T d1th7a1           7 TAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGS--GKKLGTIVIRGDNVILISP   75 (76)
T ss_dssp             HHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSC--EEEEEEEEECGGGEEEEEE
T ss_pred             cHHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecCCc--ccCcceEEEECCEEEEEEe
Confidence            48999999999999999999999999999999999999999999988765  4589999999999999974

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

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

Probab=99.89  E-value=1.8e-23  Score=126.09  Aligned_cols=68  Identities=25%  Similarity=0.365  Sum_probs=62.1

Q ss_pred             hHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecC
Q psy6026           6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLP   76 (98)
Q Consensus         6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p   76 (98)
                      +.++|++++|++|+|+|+||+.|.|+|.+||+|||++|+||+++..+.   ...++.+||||++|+||+.+
T Consensus         3 ~~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~~~---~~~~g~v~iRG~~I~~I~~~   70 (71)
T d1i8fa_           3 LGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGN---VYKRGTMVVRGENVLFISPV   70 (71)
T ss_dssp             HHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEETTE---EEEEEEEEECGGGEEEEEEC
T ss_pred             HhHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEECCC---EEEcceEEEeCCeEEEEeCC
Confidence            468999999999999999999999999999999999999999886553   35789999999999999855

>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=99.84  E-value=1.5e-21  Score=122.51  Aligned_cols=74  Identities=20%  Similarity=0.344  Sum_probs=63.3

Q ss_pred             cccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCC-----------C--CcceeecceEEEEcC
Q psy6026           2 ERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPD-----------K--YPHMLSVKNCFIRGS   68 (98)
Q Consensus         2 ~~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~-----------~--~~~~~~~~~v~IRG~   68 (98)
                      +.++|+++|++++|++|.|.|+||+.|.|+|.+||.|||++|+||+++...           +  ......+|.+||||+
T Consensus         2 ~~~~Pl~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~   81 (92)
T d2fwka1           2 NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGN   81 (92)
T ss_dssp             CCCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGG
T ss_pred             CccChHHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCC
Confidence            358999999999999999999999999999999999999999999986321           0  001346899999999


Q ss_pred             eEEEEec
Q psy6026          69 VVRYVQL   75 (98)
Q Consensus        69 ~I~~I~~   75 (98)
                      +|.+|+.
T Consensus        82 ~Vv~I~p   88 (92)
T d2fwka1          82 NVAMLVP   88 (92)
T ss_dssp             GEEEEES
T ss_pred             EEEEEEe
Confidence            9999984

>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=99.77  E-value=7e-19  Score=110.62  Aligned_cols=73  Identities=18%  Similarity=0.227  Sum_probs=61.1

Q ss_pred             hHHHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCC---C---------CcceeecceEEEEcCeEE
Q psy6026           6 FYSFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPD---K---------YPHMLSVKNCFIRGSVVR   71 (98)
Q Consensus         6 p~~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~---~---------~~~~~~~~~v~IRG~~I~   71 (98)
                      |+++|..++  +++|.|.|++|+.+.|+|.+||+|||++|+||.++...   +         ....+.++.+||||++|.
T Consensus         3 Pl~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdnVv   82 (93)
T d1b34b_           3 PLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVI   82 (93)
T ss_dssp             HHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGEE
T ss_pred             cHHHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCEEE
Confidence            889999998  99999999999999999999999999999999986321   0         001356899999999999


Q ss_pred             EEecCCc
Q psy6026          72 YVQLPGD   78 (98)
Q Consensus        72 ~I~~p~~   78 (98)
                      +|..++.
T Consensus        83 ~I~~~p~   89 (93)
T d1b34b_          83 VVLRNPL   89 (93)
T ss_dssp             EEEECCC
T ss_pred             EEEcChh
Confidence            9987764

>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=99.77  E-value=1e-18  Score=107.09  Aligned_cols=67  Identities=15%  Similarity=0.190  Sum_probs=56.9

Q ss_pred             HhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEEC----CC-CC---cceeecceEEEEcCeEEEEecC
Q psy6026          10 FKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTD----PD-KY---PHMLSVKNCFIRGSVVRYVQLP   76 (98)
Q Consensus        10 L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~----~~-~~---~~~~~~~~v~IRG~~I~~I~~p   76 (98)
                      |.+++|++|.|.|+||+.|.|+|.+||.||||+|+||.++.    ++ +.   ...+.+|.++|||++|.+|++.
T Consensus         3 L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~~   77 (81)
T d1d3bb_           3 MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVE   77 (81)
T ss_dssp             CGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEE
T ss_pred             hHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEcc
Confidence            67899999999999999999999999999999999999852    11 11   1235789999999999999864

>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=97.74  E-value=0.00021  Score=42.46  Aligned_cols=66  Identities=15%  Similarity=0.286  Sum_probs=54.5

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEec-cccceEEeeEEEECCCCCc-------ceeecceEEEEcCeEEEEecCCc
Q psy6026          13 LVGKDVVVELKNDVSICGTLHSVD-QYLNIKLTDISVTDPDKYP-------HMLSVKNCFIRGSVVRYVQLPGD   78 (98)
Q Consensus        13 l~gk~V~V~Lkng~~~~G~L~~~D-~~mNi~L~~~~~~~~~~~~-------~~~~~~~v~IRG~~I~~I~~p~~   78 (98)
                      ++|+++.+..|.+..|+|+|..+| +.--+.|+|+..+..+|.+       ...-++.+..||+.|.-+.+-+.
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~~IvFrgsDIKdL~v~e~   75 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCEP   75 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSSCCCCCCCCEEEEEEETTTEEEEEESSC
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCCccCCCCcceeEEEEcCcCcceEEeccC
Confidence            689999999999999999999999 4567999999998655432       12348899999999999987653

>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=96.54  E-value=0.0028  Score=35.46  Aligned_cols=37  Identities=16%  Similarity=0.259  Sum_probs=29.7

Q ss_pred             HHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026           9 FFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTD   45 (98)
Q Consensus         9 ~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~   45 (98)
                      ||+.+.  ..+|+|-|.||-.++|.+.+||.|.=+...+
T Consensus         6 fln~lr~~~~~VtifL~nGvkl~G~I~~fD~ftvlL~~~   44 (60)
T d1kq1a_           6 ALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQ   44 (60)
T ss_dssp             HHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEEET
T ss_pred             HHHHHHHcCCcEEEEEECCcEEEEEEEEEcceEEEEEeC
Confidence            444443  6789999999999999999999998666443

>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=96.36  E-value=0.0024  Score=36.37  Aligned_cols=33  Identities=24%  Similarity=0.476  Sum_probs=27.4

Q ss_pred             HHhhcC--CCeEEEEEcCCcEEEEEEEEeccccce
Q psy6026           9 FFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNI   41 (98)
Q Consensus         9 ~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi   41 (98)
                      ||+.+.  ..+|+|-|.||-.++|.+.+||+|.=+
T Consensus         6 fLn~~rk~~~~VtifL~nGvkl~G~I~~fD~ftvL   40 (66)
T d1u1sa1           6 YLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVIL   40 (66)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEE
T ss_pred             HHHHHHHcCCcEEEEEEcCcEEEEEEEEEcceEEE
Confidence            444444  668999999999999999999999654

>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=95.23  E-value=0.054  Score=28.21  Aligned_cols=47  Identities=15%  Similarity=0.162  Sum_probs=34.8

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEE
Q psy6026          13 LVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIR   66 (98)
Q Consensus        13 l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IR   66 (98)
                      ++|++|.|..- +.++.|+-.++|+.=.+.|+.     .+|. +....|++.||
T Consensus         1 f~gk~V~v~~g-~~~i~G~a~gId~~G~Lll~t-----~~g~-~~~~sGEVSlR   47 (47)
T d1biaa2           1 FINRPVKLIIG-DKEIFGISRGIDKQGALLLEQ-----DGII-KPWMGGEISLR   47 (47)
T ss_dssp             TTTSEEEEEET-TEEEEEEEEEECTTSCEEEEE-----TTEE-EEESSCEEEEC
T ss_pred             CCCCEEEEEEC-CeEEEEEEeeECCCCcEEEEE-----CCCE-EEEEEEEEEeC
Confidence            57999999764 478999999999999999975     2221 23456677665

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

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

Probab=95.05  E-value=0.069  Score=29.60  Aligned_cols=61  Identities=25%  Similarity=0.303  Sum_probs=42.9

Q ss_pred             HHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026           7 YSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ   74 (98)
Q Consensus         7 ~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~   74 (98)
                      -..|..-.|++|-|-......++|+|..||.-. +.|+|++....+      +-..++++=+-|.+|.
T Consensus         4 dktL~~WKg~kvAv~vgsehSFtGiledFDeEv-iLL~dV~D~~GN------k~k~llv~idD~nWim   64 (66)
T d1ycya1           4 EKVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIGN------RGKQMLIGLEDINWIM   64 (66)
T ss_dssp             HHHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTEE------EEEEEEEEGGGEEEEE
T ss_pred             HHHHHHhCCcEEEEEecCcceeEEEhhhcCcce-EeehhhHHHhcc------ccceeEEEeccceeEE
Confidence            356788889999999999999999999999754 678999876643      2345666666665554

>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=91.21  E-value=0.11  Score=29.13  Aligned_cols=31  Identities=26%  Similarity=0.272  Sum_probs=26.0

Q ss_pred             HHHhhcCCCeEEEEEc---CC-cEEEEEEEEeccc
Q psy6026           8 SFFKSLVGKDVVVELK---ND-VSICGTLHSVDQY   38 (98)
Q Consensus         8 ~~L~~l~gk~V~V~Lk---ng-~~~~G~L~~~D~~   38 (98)
                      .-+..++|+.|.|+|+   +| +.++|+|.++|+.
T Consensus         7 ~~f~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~   41 (74)
T d1ib8a1           7 DAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED   41 (74)
T ss_dssp             HHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT
T ss_pred             HHHHHhCCCEEEEEEecccCCceEEEEEEEeecCC
Confidence            3467789999999986   34 8999999999975

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

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

Probab=80.59  E-value=1.3  Score=24.02  Aligned_cols=24  Identities=17%  Similarity=0.151  Sum_probs=21.4

Q ss_pred             cCCCeEEEEEcCCcEEEEEEEEec
Q psy6026          13 LVGKDVVVELKNDVSICGTLHSVD   36 (98)
Q Consensus        13 l~gk~V~V~Lkng~~~~G~L~~~D   36 (98)
                      .+|.+|.-+-|||+.|.+.+.+.-
T Consensus         4 ~~Gq~VI~KhkNgryY~c~V~~~~   27 (59)
T d2qqra1           4 TAGQKVISKHKNGRFYQCEVVRLT   27 (59)
T ss_dssp             CTTCEEEEECTTSSEEEEEEEEEE
T ss_pred             ccccEEEEEccCCcEEEEEEEEee
Confidence            369999999999999999998864