Psyllid ID: psy5557

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210---
Protein Sequence
MKISIAPKGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVNVKVIKGGDSGKKWLRGVKQGVDQLSLAKER
Secondary Structure (PSIPRED)
cccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHcEEcccccEEEEEHHHHHHHHHHHHHHHHHHEEEcccccccccEEEEEEEccEEEEccccccHHHHHHccccccHHHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEEcHHHHHHHHHHHHHHHHEEcccccccccEEEEEEccEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mkisiapkgaisprigkrkkkKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNrqqglypnqkrTLIGYLRSVDQFANLVLHKTIErihvgnqygdiprgifiiRGENVVLMGEVVTVVNVKVIkggdsgkkWLRGVKQGVDQLSLAKER
Flexible Loop (DISEMBL)
mkisiapkgaisprigkrkkkkkeeenkkkqkkkeekkqkkkeekkqkkkekkeekeekkekkkeekkqkkeeekdkkkeekkqkkkeekkqkkkeekkqkkkkeekknkkaeeqnrqqglypnqkRTLIGYLRSVDQFANLVLHKTIERihvgnqygdiprGIFIIRGENVVLMGEVVTVVNVKVikggdsgkkwlrgvkqgvdqlslaker
Low Complexity Region (SEG)
MKISIAPKGAISPRIGKRkkkkkeeenkkkqkkkeekkqkkkeekkqkkkekkeekeekkekkkeekkqkkeeekdkkkeekkqkkkeekkqkkkeekkqkkkkeekknkkaeeqNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEvvtvvnvkvIKGGDSGKKWLRGVKQGVDQLSLAKER
Disordered region (IsUnstruct)
*****************************************************************************************************************************KRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVNVKVIKGGDSGKKWLRGVK************
Disordered Region (DISOPRED)
***********************************************************************************************************************GLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVNVKV**************KQGVDQLSLA***
Disordered Region (DISEMBL)
MKISIAPKGAISP*********************************************************************************************************QGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVNVKVIKGGDSGKKWLRGVKQGVDQLSLAKER
Disordered Region (DISPRO)
********GAIS*RIG*RKKKKKE********************************************************************KK*EEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVNVKVIKGGDSGKKWLRGVKQGVDQLSL****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKISIAPKGAISPRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVNVKVIKGGDSGKKWLRGVKQGVDQLSLAKER
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	213	2.2.26 [Sep-21-2011]
Q5E9Z8	133	U6 snRNA-associated Sm-li	yes	N/A	0.244	0.390	0.807	4e-23
O15116	133	U6 snRNA-associated Sm-li	yes	N/A	0.244	0.390	0.807	4e-23
Q8VC85	133	U6 snRNA-associated Sm-li	yes	N/A	0.244	0.390	0.807	5e-23
P87173	140	U6 snRNA-associated Sm-li	yes	N/A	0.234	0.357	0.7	9e-16

>sp|Q5E9Z8|LSM1_BOVIN U6 snRNA-associated Sm-like protein LSm1 OS=Bos taurus GN=LSM1 PE=2 SV=1

 Score =  107 bits (268), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 42/52 (80%), Positives = 51/52 (98%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
           RTLIG+LRS+DQFANLVLH+T+ERIHVG +YGDIPRGIF++RGENVVL+GE+
Sbjct: 26  RTLIGFLRSIDQFANLVLHQTVERIHVGKKYGDIPRGIFVVRGENVVLLGEI 77

Plays a role in replication-dependent histone mRNA degradation. Binds specifically to the 3'-terminal U-tract of U6 snRNA.
Bos taurus (taxid: 9913)

>sp|O15116|LSM1_HUMAN U6 snRNA-associated Sm-like protein LSm1 OS=Homo sapiens GN=LSM1 PE=1 SV=1

 Score =  107 bits (268), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 42/52 (80%), Positives = 51/52 (98%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
           RTLIG+LRS+DQFANLVLH+T+ERIHVG +YGDIPRGIF++RGENVVL+GE+
Sbjct: 26  RTLIGFLRSIDQFANLVLHQTVERIHVGKKYGDIPRGIFVVRGENVVLLGEI 77

Plays a role in replication-dependent histone mRNA degradation. Binds specifically to the 3'-terminal U-tract of U6 snRNA.

Homo sapiens (taxid: 9606)

>sp|Q8VC85|LSM1_MOUSE U6 snRNA-associated Sm-like protein LSm1 OS=Mus musculus GN=Lsm1 PE=2 SV=1

 Score =  107 bits (268), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 42/52 (80%), Positives = 51/52 (98%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
           RTLIG+LRS+DQFANLVLH+T+ERIHVG +YGDIPRGIF++RGENVVL+GE+
Sbjct: 26  RTLIGFLRSIDQFANLVLHQTVERIHVGKKYGDIPRGIFVVRGENVVLLGEI 77

Plays a role in replication-dependent histone mRNA degradation. Binds specifically to the 3'-terminal U-tract of U6 snRNA.

Mus musculus (taxid: 10090)

>sp|P87173|LSM1_SCHPO U6 snRNA-associated Sm-like protein LSm1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=lsm1 PE=3 SV=1

 Score = 83.6 bits (205), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 35/50 (70%), Positives = 43/50 (86%)

Query: 129 LIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
           LIG LRS DQFANL+L  TIERI+V + YGDI RG++I+RGENVVL+GE+
Sbjct: 34  LIGILRSFDQFANLMLQYTIERIYVDDMYGDIDRGVYIVRGENVVLLGEL 83

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

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

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	213
125811580	137	GA18077 [Drosophila pseudoobscura pseudo	0.244	0.379	0.903	6e-23
195382173	137	GJ21790 [Drosophila virilis] gi|19414460	0.244	0.379	0.903	6e-23
198437342	133	PREDICTED: similar to U6 snRNA-associate	0.309	0.496	0.727	1e-22
427786347	135	Putative der and-387 small nuclear ribon	0.272	0.429	0.775	1e-22
148298867	138	LSM1-like protein [Bombyx mori] gi|95102	0.244	0.376	0.884	1e-22
357609556	138	LSM1-like protein [Danaus plexippus]	0.244	0.376	0.884	1e-22
346471247	135	hypothetical protein [Amblyomma maculatu	0.272	0.429	0.775	2e-22
66770685	137	IP04948p [Drosophila melanogaster]	0.244	0.379	0.884	2e-22
194881822	137	GG20797 [Drosophila erecta] gi|190658207	0.244	0.379	0.884	2e-22
195025615	137	GH21171 [Drosophila grimshawi] gi|193902	0.244	0.379	0.884	2e-22

>gi|125811580|ref|XP_001361929.1| GA18077 [Drosophila pseudoobscura pseudoobscura] gi|195170162|ref|XP_002025882.1| GL10169 [Drosophila persimilis] gi|54637105|gb|EAL26508.1| GA18077 [Drosophila pseudoobscura pseudoobscura] gi|194110746|gb|EDW32789.1| GL10169 [Drosophila persimilis]

 Score =  113 bits (282), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 47/52 (90%), Positives = 51/52 (98%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
           RTLIGYLRSVDQFANLVL +TIERIHVGNQYGDIPRG+FIIRGENVVL+GE+
Sbjct: 29  RTLIGYLRSVDQFANLVLQRTIERIHVGNQYGDIPRGVFIIRGENVVLLGEI 80

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195382173|ref|XP_002049805.1| GJ21790 [Drosophila virilis] gi|194144602|gb|EDW60998.1| GJ21790 [Drosophila virilis]

 Score =  113 bits (282), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 47/52 (90%), Positives = 51/52 (98%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
           RTLIGYLRSVDQFANLVL +TIERIHVGNQYGDIPRG+FIIRGENVVL+GE+
Sbjct: 29  RTLIGYLRSVDQFANLVLQRTIERIHVGNQYGDIPRGVFIIRGENVVLLGEI 80

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198437342|ref|XP_002124367.1| PREDICTED: similar to U6 snRNA-associated Sm-like protein LSm1 (Cancer-associated Sm-like) (Small nuclear ribonuclear CaSm) [Ciona intestinalis]

 Score =  112 bits (280), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 48/66 (72%), Positives = 57/66 (86%)

Query: 113 EEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENV 172
           EE +++Q +     R LIGYLRSVDQFANLVLHKT+ER+HVG+ YGDIPRGIF+IRGENV
Sbjct: 12  EEIDKKQLVMLRDGRILIGYLRSVDQFANLVLHKTVERVHVGSMYGDIPRGIFVIRGENV 71

Query: 173 VLMGEV 178
           VL+GEV
Sbjct: 72  VLLGEV 77

Source: Ciona intestinalis

Species: Ciona intestinalis

Genus: Ciona

Family: Cionidae

Order: Enterogona

Class: Ascidiacea

Phylum: Chordata

Superkingdom: Eukaryota

>gi|427786347|gb|JAA58625.1| Putative der and-387 small nuclear ribonucleoprotein splicing factor [Rhipicephalus pulchellus]

 Score =  112 bits (280), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 45/58 (77%), Positives = 53/58 (91%)

Query: 121 LYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
           ++    RTLIGYLRS+DQFANLVLH+TIERIHVG QYGDIPRGIF+IRG+NVVL+GE+
Sbjct: 22  VFLRDGRTLIGYLRSIDQFANLVLHQTIERIHVGRQYGDIPRGIFVIRGDNVVLLGEI 79

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|148298867|ref|NP_001091827.1| LSM1-like protein [Bombyx mori] gi|95102704|gb|ABF51290.1| LSM1-like protein [Bombyx mori]

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 46/52 (88%), Positives = 50/52 (96%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
           RTLIGYLR VDQFANLVLHKTIERIHVG +YGDIPRGIFI+RGENVVL+GE+
Sbjct: 30  RTLIGYLRCVDQFANLVLHKTIERIHVGKEYGDIPRGIFIVRGENVVLLGEI 81

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357609556|gb|EHJ66513.1| LSM1-like protein [Danaus plexippus]

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 46/52 (88%), Positives = 50/52 (96%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
           RTLIGYLR VDQFANLVLHKTIERIHVG +YGDIPRGIFI+RGENVVL+GE+
Sbjct: 30  RTLIGYLRCVDQFANLVLHKTIERIHVGREYGDIPRGIFIVRGENVVLLGEI 81

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|346471247|gb|AEO35468.1| hypothetical protein [Amblyomma maculatum]

 Score =  111 bits (278), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 45/58 (77%), Positives = 53/58 (91%)

Query: 121 LYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
           ++    RTLIGYLRS+DQFANLVLH+TIERIHVG QYGDIPRGIF+IRG+NVVL+GE+
Sbjct: 22  VFLRDGRTLIGYLRSIDQFANLVLHQTIERIHVGKQYGDIPRGIFVIRGDNVVLLGEI 79

Source: Amblyomma maculatum

Species: Amblyomma maculatum

Genus: Amblyomma

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66770685|gb|AAY54654.1| IP04948p [Drosophila melanogaster]

 Score =  111 bits (278), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 46/52 (88%), Positives = 51/52 (98%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
           RTLIGYLRSVDQFANLVL +TIERIHVGN+YGDIPRG+FIIRGENVVL+GE+
Sbjct: 29  RTLIGYLRSVDQFANLVLQRTIERIHVGNEYGDIPRGVFIIRGENVVLLGEI 80

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194881822|ref|XP_001975020.1| GG20797 [Drosophila erecta] gi|190658207|gb|EDV55420.1| GG20797 [Drosophila erecta]

 Score =  111 bits (278), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 46/52 (88%), Positives = 51/52 (98%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
           RTLIGYLRSVDQFANLVL +TIERIHVGN+YGDIPRG+FIIRGENVVL+GE+
Sbjct: 29  RTLIGYLRSVDQFANLVLQRTIERIHVGNEYGDIPRGVFIIRGENVVLLGEI 80

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195025615|ref|XP_001986091.1| GH21171 [Drosophila grimshawi] gi|193902091|gb|EDW00958.1| GH21171 [Drosophila grimshawi]

 Score =  111 bits (278), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 46/52 (88%), Positives = 51/52 (98%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
           RTLIGYLRSVDQFANLVL +TIERIHVGN+YGDIPRG+FIIRGENVVL+GE+
Sbjct: 29  RTLIGYLRSVDQFANLVLQRTIERIHVGNEYGDIPRGVFIIRGENVVLLGEI 80

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	213
FB|FBgn0261067	137	LSm1 [Drosophila melanogaster	0.239	0.372	0.901	1.3e-20
UNIPROTKB|Q5E9Z8	133	LSM1 "U6 snRNA-associated Sm-l	0.239	0.383	0.823	7.2e-20
UNIPROTKB|E2R7S6	133	LSM1 "Uncharacterized protein"	0.239	0.383	0.823	7.2e-20
UNIPROTKB|O15116	133	LSM1 "U6 snRNA-associated Sm-l	0.239	0.383	0.823	7.2e-20
UNIPROTKB|I3LCU8	133	LSM1 "Uncharacterized protein"	0.239	0.383	0.823	7.2e-20
MGI|MGI:1914457	133	Lsm1 "LSM1 homolog, U6 small n	0.239	0.383	0.823	7.2e-20
RGD|1304967	133	Lsm1 "LSM1 homolog, U6 small n	0.239	0.383	0.823	7.2e-20
ZFIN|ZDB-GENE-040801-68	133	lsm1 "LSM1 homolog, U6 small n	0.239	0.383	0.803	5.1e-19
POMBASE|SPBC3D6.08c	140	lsm1 "mRNA decapping complex s	0.239	0.364	0.686	3.8e-14
UNIPROTKB|E1C962	133	E1C962 "Uncharacterized protei	0.178	0.285	0.815	1.6e-13

FB|FBgn0261067 LSm1 [Drosophila melanogaster (taxid:7227)]

 Score = 243 (90.6 bits), Expect = 1.3e-20, P = 1.3e-20
 Identities = 46/51 (90%), Positives = 50/51 (98%)

Query:   127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177
             RTLIGYLRSVDQFANLVL +TIERIHVGN+YGDIPRG+FIIRGENVVL+GE
Sbjct:    29 RTLIGYLRSVDQFANLVLQRTIERIHVGNEYGDIPRGVFIIRGENVVLLGE 79

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

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0006396 "RNA processing" evidence=ISS

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

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

UNIPROTKB|Q5E9Z8 LSM1 "U6 snRNA-associated Sm-like protein LSm1" [Bos taurus (taxid:9913)]

 Score = 236 (88.1 bits), Expect = 7.2e-20, P = 7.2e-20
 Identities = 42/51 (82%), Positives = 50/51 (98%)

Query:   127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177
             RTLIG+LRS+DQFANLVLH+T+ERIHVG +YGDIPRGIF++RGENVVL+GE
Sbjct:    26 RTLIGFLRSIDQFANLVLHQTVERIHVGKKYGDIPRGIFVVRGENVVLLGE 76

GO:0071044 "histone mRNA catabolic process" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|E2R7S6 LSM1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 236 (88.1 bits), Expect = 7.2e-20, P = 7.2e-20
 Identities = 42/51 (82%), Positives = 50/51 (98%)

Query:   127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177
             RTLIG+LRS+DQFANLVLH+T+ERIHVG +YGDIPRGIF++RGENVVL+GE
Sbjct:    26 RTLIGFLRSIDQFANLVLHQTVERIHVGKKYGDIPRGIFVVRGENVVLLGE 76

GO:0071044 "histone mRNA catabolic process" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|O15116 LSM1 "U6 snRNA-associated Sm-like protein LSm1" [Homo sapiens (taxid:9606)]

 Score = 236 (88.1 bits), Expect = 7.2e-20, P = 7.2e-20
 Identities = 42/51 (82%), Positives = 50/51 (98%)

Query:   127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177
             RTLIG+LRS+DQFANLVLH+T+ERIHVG +YGDIPRGIF++RGENVVL+GE
Sbjct:    26 RTLIGFLRSIDQFANLVLHQTVERIHVGKKYGDIPRGIFVVRGENVVLLGE 76

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0000375 "RNA splicing, via transesterification reactions" evidence=TAS

GO:0071044 "histone mRNA catabolic process" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0008380 "RNA splicing" evidence=TAS

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

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

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

UNIPROTKB|I3LCU8 LSM1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 236 (88.1 bits), Expect = 7.2e-20, P = 7.2e-20
 Identities = 42/51 (82%), Positives = 50/51 (98%)

Query:   127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177
             RTLIG+LRS+DQFANLVLH+T+ERIHVG +YGDIPRGIF++RGENVVL+GE
Sbjct:    26 RTLIGFLRSIDQFANLVLHQTVERIHVGKKYGDIPRGIFVVRGENVVLLGE 76

GO:0071044 "histone mRNA catabolic process" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

MGI|MGI:1914457 Lsm1 "LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 236 (88.1 bits), Expect = 7.2e-20, P = 7.2e-20
 Identities = 42/51 (82%), Positives = 50/51 (98%)

Query:   127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177
             RTLIG+LRS+DQFANLVLH+T+ERIHVG +YGDIPRGIF++RGENVVL+GE
Sbjct:    26 RTLIGFLRSIDQFANLVLHQTVERIHVGKKYGDIPRGIFVVRGENVVLLGE 76

GO:0003674 "molecular_function" evidence=ND

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0071044 "histone mRNA catabolic process" evidence=ISO

RGD|1304967 Lsm1 "LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]

 Score = 236 (88.1 bits), Expect = 7.2e-20, P = 7.2e-20
 Identities = 42/51 (82%), Positives = 50/51 (98%)

Query:   127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177
             RTLIG+LRS+DQFANLVLH+T+ERIHVG +YGDIPRGIF++RGENVVL+GE
Sbjct:    26 RTLIGFLRSIDQFANLVLHQTVERIHVGRKYGDIPRGIFVVRGENVVLLGE 76

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0071044 "histone mRNA catabolic process" evidence=IEA;ISO

ZFIN|ZDB-GENE-040801-68 lsm1 "LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 228 (85.3 bits), Expect = 5.1e-19, P = 5.1e-19
 Identities = 41/51 (80%), Positives = 49/51 (96%)

Query:   127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177
             RTLIG LRS+DQFANLVLH+T+ERIHVG ++GDIPRGIF++RGENVVL+GE
Sbjct:    26 RTLIGILRSIDQFANLVLHQTVERIHVGKKFGDIPRGIFVVRGENVVLLGE 76

GO:0003674 "molecular_function" evidence=ND

POMBASE|SPBC3D6.08c lsm1 "mRNA decapping complex subunit (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 182 (69.1 bits), Expect = 3.8e-14, P = 3.8e-14
 Identities = 35/51 (68%), Positives = 43/51 (84%)

Query:   127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177
             + LIG LRS DQFANL+L  TIERI+V + YGDI RG++I+RGENVVL+GE
Sbjct:    32 KKLIGILRSFDQFANLMLQYTIERIYVDDMYGDIDRGVYIVRGENVVLLGE 82

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

GO:0000290 "deadenylation-dependent decapping of nuclear-transcribed mRNA" evidence=ISO

GO:0000339 "RNA cap binding" evidence=ISO

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

GO:0003723 "RNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0005845 "mRNA cap binding complex" evidence=ISO

GO:0008380 "RNA splicing" evidence=IEA

UNIPROTKB|E1C962 E1C962 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 31/38 (81%), Positives = 37/38 (97%)

Query:   140 ANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177
             ANLVLH+T+ERIHVG +YGDIPRGIF++RGENVVL+GE
Sbjct:    39 ANLVLHQTVERIHVGKKYGDIPRGIFVVRGENVVLLGE 76

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0071044 "histone mRNA catabolic process" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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	213
cd01728	74	cd01728, LSm1, Like-Sm protein 1	4e-34
cd01727	91	cd01727, LSm8, Like-Sm protein 8	3e-10
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	6e-10
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	7e-10
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	7e-10
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	1e-09
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-09
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-09
smart00651	67	smart00651, Sm, snRNP Sm proteins	4e-09
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	6e-09
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	1e-08
pfam01423	66	pfam01423, LSM, LSM domain	1e-08
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	1e-08
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-08
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	3e-07
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	3e-07
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	4e-07
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	4e-07
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	5e-07
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	9e-07
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	1e-06
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	1e-06
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	1e-06
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	1e-06
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	1e-06
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	2e-06
PTZ00053	470	PTZ00053, PTZ00053, methionine aminopeptidase 2; P	2e-06
TIGR02794	346	TIGR02794, tolA_full, TolA protein	2e-06
PRK13735	942	PRK13735, PRK13735, conjugal transfer mating pair	2e-06
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	2e-06
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	3e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-06
CHL00204	1832	CHL00204, ycf1, Ycf1; Provisional	5e-06
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	5e-06
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	6e-06
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	6e-06
pfam05087	887	pfam05087, Rota_VP2, Rotavirus VP2 protein	6e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	8e-06
TIGR02794	346	TIGR02794, tolA_full, TolA protein	8e-06
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	8e-06
CHL00204	1832	CHL00204, ycf1, Ycf1; Provisional	9e-06
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	1e-05
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	1e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-05
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	1e-05
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	2e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-05
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	2e-05
pfam05087	887	pfam05087, Rota_VP2, Rotavirus VP2 protein	2e-05
PTZ00399	651	PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Pro	2e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-05
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	3e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	3e-05
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	3e-05
pfam08496	154	pfam08496, Peptidase_S49_N, Peptidase family S49 N	3e-05
TIGR02794	346	TIGR02794, tolA_full, TolA protein	4e-05
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	4e-05
cd01719	70	cd01719, Sm_G, Sm protein G	4e-05
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	5e-05
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	5e-05
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	5e-05
PTZ00053	470	PTZ00053, PTZ00053, methionine aminopeptidase 2; P	6e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	6e-05
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	6e-05
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	6e-05
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	6e-05
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	6e-05
PRK11778	330	PRK11778, PRK11778, putative inner membrane peptid	7e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	8e-05
PRK13735	942	PRK13735, PRK13735, conjugal transfer mating pair	8e-05
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	9e-05
TIGR02794	346	TIGR02794, tolA_full, TolA protein	1e-04
TIGR02794	346	TIGR02794, tolA_full, TolA protein	1e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-04
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	1e-04
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-04
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	1e-04
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	1e-04
pfam05758	832	pfam05758, Ycf1, Ycf1	1e-04
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	2e-04
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	2e-04
PRK13735	942	PRK13735, PRK13735, conjugal transfer mating pair	2e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	2e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-04
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	2e-04
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	2e-04
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	2e-04
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	2e-04
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	2e-04
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-04
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	2e-04
pfam05758	832	pfam05758, Ycf1, Ycf1	2e-04
pfam05758	832	pfam05758, Ycf1, Ycf1	2e-04
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	2e-04
COG0810	244	COG0810, TonB, Periplasmic protein TonB, links inn	2e-04
CHL00189	742	CHL00189, infB, translation initiation factor 2; P	2e-04
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	2e-04
COG5116	926	COG5116, RPN2, 26S proteasome regulatory complex c	2e-04
PRK05035	695	PRK05035, PRK05035, electron transport complex pro	2e-04
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	2e-04
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	3e-04
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	3e-04
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	3e-04
pfam08496	154	pfam08496, Peptidase_S49_N, Peptidase family S49 N	3e-04
COG5116	926	COG5116, RPN2, 26S proteasome regulatory complex c	3e-04
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	3e-04
PLN02967	581	PLN02967, PLN02967, kinase	3e-04
TIGR02794	346	TIGR02794, tolA_full, TolA protein	4e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-04
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	4e-04
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	4e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	5e-04
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	5e-04
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	5e-04
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	5e-04
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	6e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	6e-04
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	6e-04
pfam05758	832	pfam05758, Ycf1, Ycf1	6e-04
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	6e-04
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	7e-04
PRK00448	1437	PRK00448, polC, DNA polymerase III PolC; Validated	7e-04
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	8e-04
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	8e-04
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	8e-04
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	8e-04
PRK11778	330	PRK11778, PRK11778, putative inner membrane peptid	9e-04
PRK11778	330	PRK11778, PRK11778, putative inner membrane peptid	9e-04
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	9e-04
COG5116	926	COG5116, RPN2, 26S proteasome regulatory complex c	9e-04
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	9e-04
pfam09468	287	pfam09468, RNase_H2-Ydr279, Ydr279p protein family	9e-04
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	0.001
PRK13735	942	PRK13735, PRK13735, conjugal transfer mating pair	0.001
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	0.001
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.001
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.001
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.001
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.001
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	0.001
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	0.001
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	0.001
pfam05758	832	pfam05758, Ycf1, Ycf1	0.001
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	0.001
PRK05035	695	PRK05035, PRK05035, electron transport complex pro	0.001
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	0.001
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	0.001
PRK00448	1437	PRK00448, polC, DNA polymerase III PolC; Validated	0.001
PRK00448	1437	PRK00448, polC, DNA polymerase III PolC; Validated	0.001
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	0.001
pfam09468	287	pfam09468, RNase_H2-Ydr279, Ydr279p protein family	0.001
PRK12903	925	PRK12903, secA, preprotein translocase subunit Sec	0.001
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	0.001
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	0.001
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	0.001
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	0.001
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	0.001
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	0.002
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	0.002
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.002
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.002
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.002
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	0.002
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	0.002
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	0.002
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	0.002
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	0.002
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	0.002
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	0.002
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	0.002
COG0810	244	COG0810, TonB, Periplasmic protein TonB, links inn	0.002
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	0.002
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	0.002
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	0.002
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	0.002
pfam00183	529	pfam00183, HSP90, Hsp90 protein	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
smart00786	196	smart00786, SHR3_chaperone, ER membrane protein SH	0.002
PRK04950	213	PRK04950, PRK04950, ProP expression regulator; Pro	0.002
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	0.003
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	0.003
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	0.003
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	0.003
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.003
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	0.003
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	0.003
pfam08496	154	pfam08496, Peptidase_S49_N, Peptidase family S49 N	0.003
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	0.003
pfam05758	832	pfam05758, Ycf1, Ycf1	0.003
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	0.003
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	0.003
PRK12705	508	PRK12705, PRK12705, hypothetical protein; Provisio	0.003
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	0.003
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	0.003
PRK08451	535	PRK08451, PRK08451, DNA polymerase III subunits ga	0.003
PTZ00053	470	PTZ00053, PTZ00053, methionine aminopeptidase 2; P	0.004
TIGR02794	346	TIGR02794, tolA_full, TolA protein	0.004
TIGR02794	346	TIGR02794, tolA_full, TolA protein	0.004
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	0.004
pfam05758	832	pfam05758, Ycf1, Ycf1	0.004
COG0810	244	COG0810, TonB, Periplasmic protein TonB, links inn	0.004
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	0.004
pfam00183	529	pfam00183, HSP90, Hsp90 protein	0.004
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	0.004
PRK12585	197	PRK12585, PRK12585, putative monovalent cation/H+	0.004
COG4942	420	COG4942, COG4942, Membrane-bound metallopeptidase	0.004
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	0.004
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	0.004
pfam06375	561	pfam06375, BLVR, Bovine leukaemia virus receptor (	0.004
pfam08229	196	pfam08229, SHR3_chaperone, ER membrane protein SH3	0.004
COG5354	561	COG5354, COG5354, Uncharacterized protein, contain	0.004
pfam09731	493	pfam09731, Mitofilin, Mitochondrial inner membrane	0.004
pfam10310	436	pfam10310, DUF2413, Protein of unknown function (D	0.004

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

 Score =  116 bits (292), Expect = 4e-34
 Identities = 42/52 (80%), Positives = 46/52 (88%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
           R LIG LRS DQFANLVL  T+ERI VGNQYGDIPRG+FIIRGENVVL+GE+
Sbjct: 23  RKLIGILRSFDQFANLVLEDTVERIIVGNQYGDIPRGLFIIRGENVVLLGEI 74

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

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

 Score = 54.5 bits (132), Expect = 3e-10
 Identities = 19/53 (35%), Positives = 33/53 (62%), Gaps = 1/53 (1%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERI-HVGNQYGDIPRGIFIIRGENVVLMGEV 178
           R ++G L+  DQ  NL+L    ER+        ++P G++++RG+NV ++GEV
Sbjct: 20  RVIVGTLKGFDQTTNLILSNCHERVYSSDEGVEEVPLGLYLLRGDNVAVIGEV 72

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

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 57.6 bits (140), Expect = 6e-10
 Identities = 26/74 (35%), Positives = 60/74 (81%)

Query: 28  KKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKK 87
             K+  K+ KK  +K EKK+++++K+++K+    KKKEE++++++E+K+++KEE++++ +
Sbjct: 404 GSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAE 463

Query: 88  EEKKQKKKEEKKQK 101
           EEK+++++++KKQ 
Sbjct: 464 EEKEEEEEKKKKQA 477

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 57.6 bits (140), Expect = 7e-10
 Identities = 32/73 (43%), Positives = 59/73 (80%)

Query: 15  IGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEE 74
            G +K  KK ++  +K +KK E+++K+K++K    K+K+EE+EE+KEKK+EEK++++EE 
Sbjct: 403 TGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEA 462

Query: 75  KDKKKEEKKQKKK 87
           +++K+EE+++KKK
Sbjct: 463 EEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 57.2 bits (139), Expect = 7e-10
 Identities = 32/80 (40%), Positives = 62/80 (77%)

Query: 23  KEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEK 82
           +EE       KK  KK KK  EK +KK+E+++++++KK    ++K++++EEEK+KK+EEK
Sbjct: 396 EEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455

Query: 83  KQKKKEEKKQKKKEEKKQKK 102
           +++++E +++K++EE+K+KK
Sbjct: 456 EEEEEEAEEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 56.5 bits (137), Expect = 1e-09
 Identities = 26/75 (34%), Positives = 59/75 (78%)

Query: 11  ISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQK 70
              +   +K KK  E+ +KK+++++++K+KK    K+K++E++EEKE+K+E+K+EE+++ 
Sbjct: 403 TGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEA 462

Query: 71  KEEEKDKKKEEKKQK 85
           +EE++++++++KKQ 
Sbjct: 463 EEEKEEEEEKKKKQA 477

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 56.1 bits (136), Expect = 2e-09
 Identities = 30/76 (39%), Positives = 60/76 (78%), Gaps = 1/76 (1%)

Query: 18  RKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDK 77
              KK  ++ KK  +K E+K++++K+EKK KK    ++KEE++E++KE+K+++KEEE+++
Sbjct: 403 TGSKKATKKIKKIVEKAEKKREEEKKEKK-KKAFAGKKKEEEEEEEKEKKEEEKEEEEEE 461

Query: 78  KKEEKKQKKKEEKKQK 93
            +EEK+++++++KKQ 
Sbjct: 462 AEEEKEEEEEKKKKQA 477

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 55.7 bits (135), Expect = 3e-09
 Identities = 29/68 (42%), Positives = 56/68 (82%)

Query: 37  KKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKE 96
           KK  KK +K  +K EKK E+E+K++KKK    +KKEEE++++KE+K+++K+EE+++ ++E
Sbjct: 406 KKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEE 465

Query: 97  EKKQKKKK 104
           ++++++KK
Sbjct: 466 KEEEEEKK 473

Length = 482

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

 Score = 51.0 bits (123), Expect = 4e-09
 Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 2/51 (3%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177
           R   G L+  DQF NLVL    E +  G +      G+  IRG N+V +  
Sbjct: 19  REYRGTLKGFDQFMNLVLEDVEETVKDGEK--KRKLGLVFIRGNNIVYIIL 67

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

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 54.9 bits (133), Expect = 6e-09
 Identities = 31/73 (42%), Positives = 59/73 (80%)

Query: 40  KKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKK 99
            KK  KK KK  +K EK+ ++EKK+++KK    ++K++++EE+K+KK+EEK+++++E ++
Sbjct: 405 SKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEE 464

Query: 100 QKKKKEEKKNKKA 112
           +K+++EEKK K+A
Sbjct: 465 EKEEEEEKKKKQA 477

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 53.8 bits (130), Expect = 1e-08
 Identities = 25/71 (35%), Positives = 58/71 (81%)

Query: 45  KKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKK 104
           KK  KK KK  ++ +K++++E+K++KK+    KKKEE+++++KE+K+++K+EE+++ +++
Sbjct: 406 KKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEE 465

Query: 105 EEKKNKKAEEQ 115
           +E++ +K ++Q
Sbjct: 466 KEEEEEKKKKQ 476

Length = 482

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

 Score = 49.9 bits (120), Expect = 1e-08
 Identities = 21/51 (41%), Positives = 26/51 (50%), Gaps = 3/51 (5%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177
           R L G L+  DQF NLVL    E I  G        G+ +IRG N+VL+  
Sbjct: 19  RELRGTLKGFDQFMNLVLDDVEETIKDGKVN---KLGLVLIRGNNIVLISP 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|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 53.6 bits (130), Expect = 1e-08
 Identities = 33/105 (31%), Positives = 67/105 (63%), Gaps = 3/105 (2%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKE-KKKEEKKQKKEEEK 75
           + K+  +E + + +  KKE   + K+E  K + + +KE +E + E +K E++  +KEE  
Sbjct: 39  EAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQKEENL 98

Query: 76  DKKKEEKKQKKKEEKKQKKKEEKKQK--KKKEEKKNKKAEEQNRQ 118
           D+K E  +++++E +K++K+ E+KQ+  +KKEE+  +  EEQ ++
Sbjct: 99  DRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQE 143

Length = 520

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 53.0 bits (128), Expect = 2e-08
 Identities = 26/79 (32%), Positives = 60/79 (75%)

Query: 33  KKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQ 92
           ++E +     ++  +K K+  E+ E+K+E++K+EKK+K    K K++EE+++K+K+E+++
Sbjct: 396 EEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455

Query: 93  KKKEEKKQKKKKEEKKNKK 111
           +++EE+ +++K+EE++ KK
Sbjct: 456 EEEEEEAEEEKEEEEEKKK 474

Length = 482

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 49.6 bits (119), Expect = 3e-07
 Identities = 25/70 (35%), Positives = 47/70 (67%), Gaps = 1/70 (1%)

Query: 29  KKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKE 88
             +  ++  K +++EE+K  K  ++E +EE +EKK+E+KK+++E +  K   E+ Q+K E
Sbjct: 254 SPEVLRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEE-QRKLE 312

Query: 89  EKKQKKKEEK 98
           EK++KK+  K
Sbjct: 313 EKERKKQARK 322

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 49.5 bits (119), Expect = 3e-07
 Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 41  KKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQ 100
           K    + +++E +       E+KK  KKQ+K E+K +K+E +K   K++ +   K  K +
Sbjct: 390 KPLLAEGEEEEGENGNLSPAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAK--KAK 447

Query: 101 KKKKEEKK 108
               E KK
Sbjct: 448 GPDGETKK 455

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 49.5 bits (119), Expect = 4e-07
 Identities = 20/74 (27%), Positives = 55/74 (74%)

Query: 5   IAPKGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKK 64
           +      + +I K  +K +++  ++K++KK++    KK+E++++++++K+E+E+++E+++
Sbjct: 402 LTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEE 461

Query: 65  EEKKQKKEEEKDKK 78
            E+++++EEEK KK
Sbjct: 462 AEEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 49.1 bits (118), Expect = 4e-07
 Identities = 18/70 (25%), Positives = 55/70 (78%)

Query: 45  KKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKK 104
             +K  +K ++  EK EKK+EE+K++K+++    K++++++++E++K+++++E+++++ +
Sbjct: 404 GSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAE 463

Query: 105 EEKKNKKAEE 114
           EEK+ ++ ++
Sbjct: 464 EEKEEEEEKK 473

Length = 482

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 49.0 bits (118), Expect = 5e-07
 Identities = 31/102 (30%), Positives = 66/102 (64%), Gaps = 6/102 (5%)

Query: 19  KKKKKEEENKKKQK----KKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEE 74
           ++ KKE E  KK+     K+E  K + + EK+ +++  + +K EK+  +KEE   +K E 
Sbjct: 45  EEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQKEENLDRKLEL 104

Query: 75  KDKKKEE-KKQKKKEEKKQKKKEEKKQK-KKKEEKKNKKAEE 114
            +K++EE +K++K+ E+KQ++ E+K+++ ++  E++ ++ E 
Sbjct: 105 LEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQELER 146

Length = 520

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 48.3 bits (115), Expect = 9e-07
 Identities = 21/125 (16%), Positives = 51/125 (40%), Gaps = 17/125 (13%)

Query: 17  KRKKKKKEEENKKKQKKKEEKK----------------QKKKEEKKQKKKEKKEEKEEKK 60
           +++ + +E++ +KK      ++                 +  E KK +  EK E K  KK
Sbjct: 289 EQRAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAENAEIKKTRTAEKNEAKARKK 348

Query: 61  EKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQG 120
           E   ++++  + E   + ++E+       + ++   + K+K   +   N+    +N +  
Sbjct: 349 E-IAQKRRAAEREINREARQERAAAMARARARRAAVKAKKKGLIDASPNEDTPSENEESK 407

Query: 121 LYPNQ 125
             P Q
Sbjct: 408 GSPPQ 412

Length = 429

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 47.9 bits (115), Expect = 1e-06
 Identities = 29/101 (28%), Positives = 60/101 (59%)

Query: 18  RKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDK 77
           RKK  + +  + +++ K   ++ KKE +  KK+   E KEE  + + E +K+ +E   + 
Sbjct: 25  RKKIAEAKIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNEL 84

Query: 78  KKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQ 118
           +K EK+  +KEE   +K E  ++++++ EKK K+ E++ ++
Sbjct: 85  QKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQE 125

Length = 520

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 47.9 bits (115), Expect = 1e-06
 Identities = 32/118 (27%), Positives = 69/118 (58%), Gaps = 2/118 (1%)

Query: 14  RIGKRKKKKKEEENKK--KQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKK 71
           +I + K K+ EEE K+  ++ KKE +  KK+   + K++  K   E +KE ++   + +K
Sbjct: 27  KIAEAKIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQK 86

Query: 72  EEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKRTL 129
            E++  +KEE   +K E  +++++E +K++K+ E+K+ +  +++   + L   Q + L
Sbjct: 87  LEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQEL 144

Length = 520

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 47.6 bits (114), Expect = 1e-06
 Identities = 30/76 (39%), Positives = 50/76 (65%), Gaps = 3/76 (3%)

Query: 8   KGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEK 67
              +SP + ++  K +EEE +K  K  EE++Q   EE ++KK+EKK+E+ E K  K   +
Sbjct: 250 NLKLSPEVLRKVDKTREEEEEKILKAAEEERQ---EEAQEKKEEKKKEEREAKLAKLSPE 306

Query: 68  KQKKEEEKDKKKEEKK 83
           +Q+K EEK++KK+ +K
Sbjct: 307 EQRKLEEKERKKQARK 322

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 48.0 bits (115), Expect = 1e-06
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 2/71 (2%)

Query: 19  KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK 78
           K    E E ++ +       ++KK  KKQ+K EKK EKEE   +K   KK+ +   K  K
Sbjct: 390 KPLLAEGEEEEGENGNLSPAERKKLRKKQRKAEKKAEKEE--AEKAAAKKKAEAAAKKAK 447

Query: 79  KEEKKQKKKEE 89
             + + KK + 
Sbjct: 448 GPDGETKKVDP 458

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 47.9 bits (115), Expect = 1e-06
 Identities = 15/104 (14%), Positives = 43/104 (41%)

Query: 24  EEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKK 83
           EEE  +K++ K E +++ K E ++    + EE+ + +       ++  E     +   + 
Sbjct: 39  EEEEARKEEAKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAPAEEAAEAAAAAEAAARP 98

Query: 84  QKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKR 127
            + +  +  +    + + KK  +KK     ++ + +       +
Sbjct: 99  AEDEAARPAEAAARRPKAKKAAKKKKGPKPKKKKPKRKAARGGK 142

Length = 746

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 47.2 bits (113), Expect = 2e-06
 Identities = 19/65 (29%), Positives = 45/65 (69%), Gaps = 6/65 (9%)

Query: 45  KKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEE------KKQKKKEEK 98
            +  +K  K  +EE+++  K  +++++EE ++KK+E+KK++++ +      ++Q+K EEK
Sbjct: 255 PEVLRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEEK 314

Query: 99  KQKKK 103
           ++KK+
Sbjct: 315 ERKKQ 319

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional

 Score = 47.4 bits (113), Expect = 2e-06
 Identities = 21/92 (22%), Positives = 47/92 (51%)

Query: 25  EENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQ 84
             N+  + + +++KQ+ K++  +KK +K ++  +  +    E   + +E ++K+  +KK+
Sbjct: 1   AMNENGENEVKQQKQQNKQKGTKKKNKKSKKDVDDDDAFLAELISENQEAENKQNNKKKK 60

Query: 85  KKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQN 116
           KKK++KK+K   E              A  Q+
Sbjct: 61  KKKKKKKKKNLGEAYDLAYDLPVVWSSAAFQD 92

Length = 470

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 47.1 bits (112), Expect = 2e-06
 Identities = 31/97 (31%), Positives = 58/97 (59%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           K++  ++  + + +Q+   EK  K+ E+  ++ +EK+++ EE K K+  E K K E E +
Sbjct: 82  KQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAE 141

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAE 113
           KK +E+ +K+ EE+ + K   + +KK  E KK  +AE
Sbjct: 142 KKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAE 178

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|184287 PRK13735, PRK13735, conjugal transfer mating pair stabilization protein TraG; Provisional

 Score = 47.4 bits (113), Expect = 2e-06
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 3/68 (4%)

Query: 15  IGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKK---EKKKEEKKQKK 71
           IG  +   + EEN  K +  E +   K E   Q  K  +E+  +++       EE  ++ 
Sbjct: 874 IGDTQNSIRGEENTVKGQYSELQNHHKTEALSQNNKYNEEKSAQERMPGADSPEELMKRA 933

Query: 72  EEEKDKKK 79
           +E +DK K
Sbjct: 934 KEYQDKHK 941

Length = 942

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 47.2 bits (113), Expect = 2e-06
 Identities = 31/105 (29%), Positives = 57/105 (54%), Gaps = 2/105 (1%)

Query: 17  KRKKKKKEEENKK--KQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEE 74
           +   K+  EE KK  +  KKE   + K+E  K + + ++E KE + E ++ E++  + EE
Sbjct: 31  EELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNELQRLERRLLQREE 90

Query: 75  KDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
              +K E   KK+E  ++K+KE   ++K  +EK+ +  E    Q+
Sbjct: 91  TLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQR 135

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 46.6 bits (111), Expect = 3e-06
 Identities = 29/122 (23%), Positives = 56/122 (45%), Gaps = 2/122 (1%)

Query: 12  SPRIGKRKKKK--KEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQ 69
           S    K K +       N     K+      ++E K      KK++KE+K  + K++ ++
Sbjct: 13  SGTTQKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEK 72

Query: 70  KKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKRTL 129
           KK+++K+KK+ + + + K   K  KK +K +KK  + K N+  +    +      +    
Sbjct: 73  KKKKKKEKKEPKSEGETKLGFKTPKKSKKTKKKPPKPKPNEDVDNAFNKIAELAEKSNVY 132

Query: 130 IG 131
           IG
Sbjct: 133 IG 134

Length = 413

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 46.7 bits (110), Expect = 4e-06
 Identities = 34/98 (34%), Positives = 58/98 (59%)

Query: 20   KKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKK 79
            KKK EE  K  +  K E +    E +  ++K +  EK++++ KKK +  +KK EEK K  
Sbjct: 1335 KKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKAD 1394

Query: 80   EEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNR 117
            E KK+ ++++KK  + ++    KKK ++  KKAEE+ +
Sbjct: 1395 EAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKK 1432

Length = 2084

>gnl|CDD|214395 CHL00204, ycf1, Ycf1; Provisional

 Score = 46.3 bits (110), Expect = 5e-06
 Identities = 22/83 (26%), Positives = 44/83 (53%)

Query: 31   QKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEK 90
            +K  ++KK      +K+  + +   +EEK+   + E +  KE++ + +     Q+K  E+
Sbjct: 1500 KKINQKKKGFIPSNEKKSIEIENRNQEEKEPAGQGELESDKEKKGNLESVLSNQEKNIEE 1559

Query: 91   KQKKKEEKKQKKKKEEKKNKKAE 113
               + + KK+K KK+ K N +AE
Sbjct: 1560 DYAESDIKKRKNKKQYKSNTEAE 1582

Length = 1832

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 46.0 bits (109), Expect = 5e-06
 Identities = 23/69 (33%), Positives = 42/69 (60%)

Query: 24 EEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKK 83
           E  KK   ++E +++KKKEEK ++K+ KK +  +K+ K K + +Q  +     KK EKK
Sbjct: 6  SEAEKKILTEEELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKKSEKK 65

Query: 84 QKKKEEKKQ 92
           +K++ + +
Sbjct: 66 SRKRDVEDE 74

Length = 1066

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 46.0 bits (109), Expect = 6e-06
 Identities = 26/80 (32%), Positives = 44/80 (55%), Gaps = 10/80 (12%)

Query: 31  QKKKEEKKQKKKE-EKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEE 89
           + + E+K   ++E E+K+KK+EK +EKE KK K           +K+ K + + Q+  + 
Sbjct: 5   ESEAEKKILTEEELERKKKKEEKAKEKELKKLKAA---------QKEAKAKLQAQQASDG 55

Query: 90  KKQKKKEEKKQKKKKEEKKN 109
               KK EKK +K+  E +N
Sbjct: 56  TNVPKKSEKKSRKRDVEDEN 75

Length = 1066

>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 46.0 bits (110), Expect = 6e-06
 Identities = 33/96 (34%), Positives = 57/96 (59%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           K  +K KEE  +KK+K +EE+ +  +E +K+ ++  KE K+E  E  KE ++ +K     
Sbjct: 544 KEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEADEIIKELRQLQKGGYAS 603

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKA 112
            K  E  + +K   K  +K+EKK+KK+KE+++  K 
Sbjct: 604 VKAHELIEARKRLNKANEKKEKKKKKQKEKQEELKV 639

Length = 782

>gnl|CDD|191187 pfam05087, Rota_VP2, Rotavirus VP2 protein

 Score = 46.1 bits (109), Expect = 6e-06
 Identities = 24/92 (26%), Positives = 48/92 (52%), Gaps = 5/92 (5%)

Query: 27  NKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKK 86
           N+++       + ++K+++KQ +K + E KE+  +KK+E      +    ++  ++  K 
Sbjct: 5   NRREANINNNDRMQEKDDEKQDQKNRMELKEKVLDKKEEVVTDNVDSPVKEQSSQENLKI 64

Query: 87  KEEKKQKKKEEKKQ-----KKKKEEKKNKKAE 113
            +E K+  KEE KQ     K K+E +K  + E
Sbjct: 65  ADEVKKSTKEESKQLLEVLKTKEEHQKEIQYE 96

Rotavirus particles consist of three concentric proteinaceous capsid layers. The innermost capsid (core) is made of VP2. The genomic RNA and the two minor proteins VP1 and VP3 are encapsidated within this layer. The N-terminus of rotavirus VP2 is necessary for the encapsidation of VP1 and VP3. Length = 887

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 45.3 bits (108), Expect = 8e-06
 Identities = 29/81 (35%), Positives = 57/81 (70%), Gaps = 3/81 (3%)

Query: 42  KEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKK---KEEKKQKKKEEK 98
           +EE +     KK  K+ KK  +K EKK+++E+++ KKK    +KK   +EE+K+KK+EEK
Sbjct: 396 EEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455

Query: 99  KQKKKKEEKKNKKAEEQNRQQ 119
           ++++++ E++ ++ EE+ ++Q
Sbjct: 456 EEEEEEAEEEKEEEEEKKKKQ 476

Length = 482

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 45.2 bits (107), Expect = 8e-06
 Identities = 30/97 (30%), Positives = 59/97 (60%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           +++ ++ E++   +Q +++E +Q+   EK  K+ E+  ++ E+K+K+ EE K K+  E  
Sbjct: 74  EQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAK 133

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAE 113
            K E + +KK +E+ +K+ EE+ + K   E K K AE
Sbjct: 134 AKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAE 170

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 45.6 bits (109), Expect = 8e-06
 Identities = 28/100 (28%), Positives = 57/100 (57%)

Query: 21  KKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKE 80
              +E  K K++ +E+K++ ++EE K  ++ +KE ++  KE KKE  +  KE  + +K  
Sbjct: 541 ALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEADEIIKELRQLQKGG 600

Query: 81  EKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQG 120
               K  E  + +K+  K  +KK+++KK +K +++  + G
Sbjct: 601 YASVKAHELIEARKRLNKANEKKEKKKKKQKEKQEELKVG 640

Length = 782

>gnl|CDD|214395 CHL00204, ycf1, Ycf1; Provisional

 Score = 45.5 bits (108), Expect = 9e-06
 Identities = 22/80 (27%), Positives = 41/80 (51%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
             +KKK     N+KK  + E + Q++KE   Q + E  +EK+   E     +++  EE+  
Sbjct: 1503 NQKKKGFIPSNEKKSIEIENRNQEEKEPAGQGELESDKEKKGNLESVLSNQEKNIEEDYA 1562

Query: 77   KKKEEKKQKKKEEKKQKKKE 96
            +   +K++ KK+ K   + E
Sbjct: 1563 ESDIKKRKNKKQYKSNTEAE 1582

Length = 1832

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 44.9 bits (107), Expect = 1e-05
 Identities = 18/70 (25%), Positives = 36/70 (51%)

Query: 37  KKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKE 96
           K    + E+++ +       E KK +KK+ K +KK E+++ +K   K+K +   K+ K  
Sbjct: 390 KPLLAEGEEEEGENGNLSPAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGP 449

Query: 97  EKKQKKKKEE 106
           + + KK   +
Sbjct: 450 DGETKKVDPD 459

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 44.9 bits (107), Expect = 1e-05
 Identities = 25/101 (24%), Positives = 54/101 (53%)

Query: 18  RKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDK 77
           RK+  +++    ++  K   ++ KKE +  KK+   E KEE  + + E +++ KE   + 
Sbjct: 19  RKRIAEKKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNEL 78

Query: 78  KKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQ 118
           ++ E++  ++EE   +K E   +K++  EKK K+   + + 
Sbjct: 79  QRLERRLLQREETLDRKMESLDKKEENLEKKEKELSNKEKN 119

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 45.0 bits (107), Expect = 1e-05
 Identities = 20/96 (20%), Positives = 41/96 (42%)

Query: 19  KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK 78
           KK   + ++K    K+E K+  + ++K  ++ ++         K  ++  +    +K  K
Sbjct: 21  KKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDATESDIPKKKTK 80

Query: 79  KEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEE 114
              K    K   K+K K+E    KK E+K     ++
Sbjct: 81  TAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDD 116

Length = 509

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 45.0 bits (107), Expect = 1e-05
 Identities = 24/100 (24%), Positives = 45/100 (45%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
             +++ K++  K   K K +    K+E K+  + +KK  ++  +         K  ++  
Sbjct: 11  AAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDAT 70

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQN 116
           +    KK+ K   K    K   K+K K E   +KKAE++N
Sbjct: 71  ESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKN 110

Length = 509

>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family

 Score = 45.0 bits (107), Expect = 1e-05
 Identities = 20/86 (23%), Positives = 42/86 (48%)

Query: 31  QKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEK 90
           ++ +E   +  KE +K  + EK  E EE+K +    K++  + + +  + E+   + E K
Sbjct: 2   KELREALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAK 61

Query: 91  KQKKKEEKKQKKKKEEKKNKKAEEQN 116
                E    ++++EE K + AE + 
Sbjct: 62  PAASGEGGGGEEEEEEAKAEAAEFRA 87

This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease [Mobile and extrachromosomal element functions, Prophage functions]. Length = 384

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 44.8 bits (107), Expect = 2e-05
 Identities = 32/98 (32%), Positives = 55/98 (56%), Gaps = 10/98 (10%)

Query: 32  KKKEEKKQKKKEE--KKQKKKEKKEEKEEKKEK----KKEEKKQKKEEEKDKKKEEKKQK 85
           KK  E K K+ EE  K+  ++ KKE +  KKE     K+E  K + E EK+ ++   + +
Sbjct: 26  KKIAEAKIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQ 85

Query: 86  KKEEKKQKKKEEKKQK----KKKEEKKNKKAEEQNRQQ 119
           K E++  +K+E   +K    +K+EE+  KK +E  ++Q
Sbjct: 86  KLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQ 123

Length = 520

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 44.7 bits (105), Expect = 2e-05
 Identities = 35/117 (29%), Positives = 61/117 (52%)

Query: 2    KISIAPKGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKE 61
            K   A K A   +     KKK EE  KK    K++ ++ KK  +  K + +    E +  
Sbjct: 1303 KADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAA 1362

Query: 62   KKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQ 118
            ++K E  +KK+EE  KK +  K+K +E+KK  + ++K ++ KK+  + KKA    ++
Sbjct: 1363 EEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKK 1419

Length = 2084

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 44.5 bits (105), Expect = 2e-05
 Identities = 22/73 (30%), Positives = 41/73 (56%)

Query: 47  QKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEE 106
           + + EKK   EE+ E+KK+++++ KE+E  K K  +K+ K + + Q+  +     KK E+
Sbjct: 5   ESEAEKKILTEEELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKKSEK 64

Query: 107 KKNKKAEEQNRQQ 119
           K  K+  E    +
Sbjct: 65  KSRKRDVEDENPE 77

Length = 1066

>gnl|CDD|191187 pfam05087, Rota_VP2, Rotavirus VP2 protein

 Score = 44.5 bits (105), Expect = 2e-05
 Identities = 35/124 (28%), Positives = 60/124 (48%), Gaps = 23/124 (18%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEE------KEEKKEKKKEEKKQK 70
            R++      ++ ++K  E++ QK + E K+K  +KKEE          KE+  +E  + 
Sbjct: 5   NRREANINNNDRMQEKDDEKQDQKNRMELKEKVLDKKEEVVTDNVDSPVKEQSSQENLKI 64

Query: 71  KEEEKDKKKEEKKQ-----KKKEEKKQKKKEEKKQK------------KKKEEKKNKKAE 113
            +E K   KEE KQ     K KEE +++ + E  QK            KK E+ K ++A+
Sbjct: 65  ADEVKKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIPSFEPKESILKKLEDIKPEQAK 124

Query: 114 EQNR 117
           +Q +
Sbjct: 125 KQTK 128

Rotavirus particles consist of three concentric proteinaceous capsid layers. The innermost capsid (core) is made of VP2. The genomic RNA and the two minor proteins VP1 and VP3 are encapsidated within this layer. The N-terminus of rotavirus VP2 is necessary for the encapsidation of VP1 and VP3. Length = 887

>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional

 Score = 44.2 bits (105), Expect = 2e-05
 Identities = 34/106 (32%), Positives = 58/106 (54%), Gaps = 11/106 (10%)

Query: 20  KKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQ--KKEEEKDK 77
           K   +EE ++++++KE  K++K+  K +K++EKK+++ EK EK K    +  K++E+K  
Sbjct: 546 KLDDKEELQREKEEKEALKEQKRLRKLKKQEEKKKKELEKLEKAKIPPAEFFKRQEDKYS 605

Query: 78  KKEEK----KQKKKEE--KKQKKKEEK---KQKKKKEEKKNKKAEE 114
             +E          EE  KK++KK  K   KQ K  EE   K  + 
Sbjct: 606 AFDETGLPTHDADGEEISKKERKKLSKEYDKQAKLHEEYLAKGGKS 651

Length = 651

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 43.8 bits (104), Expect = 3e-05
 Identities = 26/77 (33%), Positives = 54/77 (70%), Gaps = 1/77 (1%)

Query: 53  KEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKA 112
             +K  KK KK  EK +KK EE+ KK+++KK    ++K+++++EEK++K++++E++ ++A
Sbjct: 404 GSKKATKKIKKIVEKAEKKREEE-KKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEA 462

Query: 113 EEQNRQQGLYPNQKRTL 129
           EE+  ++     ++ TL
Sbjct: 463 EEEKEEEEEKKKKQATL 479

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 43.8 bits (104), Expect = 3e-05
 Identities = 20/70 (28%), Positives = 53/70 (75%)

Query: 2   KISIAPKGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKE 61
           K +      I  +  K+++++K+E+ KK    K++++++++E++K+++++++EE+E ++E
Sbjct: 406 KKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEE 465

Query: 62  KKKEEKKQKK 71
           K++EE+K+KK
Sbjct: 466 KEEEEEKKKK 475

Length = 482

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 44.0 bits (103), Expect = 3e-05
 Identities = 31/102 (30%), Positives = 61/102 (59%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
              +  K E E    + +  E+K +  E+KK++ K+K +  ++K E+KK+  + KK+ E+D
Sbjct: 1344 AAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEED 1403

Query: 77   KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQ 118
            KKK ++ +K    KK+  + +KK ++KK+  + KK  E+ ++
Sbjct: 1404 KKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKK 1445

Length = 2084

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 44.1 bits (104), Expect = 3e-05
 Identities = 22/63 (34%), Positives = 37/63 (58%), Gaps = 4/63 (6%)

Query: 19 KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK 78
          +KKKKEE    K K+KE KK K  +++ + K + ++  +     KK EKK +K + +D+ 
Sbjct: 20 RKKKKEE----KAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKKSEKKSRKRDVEDEN 75

Query: 79 KEE 81
           E+
Sbjct: 76 PED 78

Length = 1066

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 43.8 bits (104), Expect = 3e-05
 Identities = 21/103 (20%), Positives = 42/103 (40%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
            + K    +E  K+  + ++K  ++ ++         ++ ++  E    +KK K   +  
Sbjct: 27  SKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDATESDIPKKKTKTAAKAA 86

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
             K   K+K K+E    KK EKK    K++  N   +     Q
Sbjct: 87  AAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQ 129

Length = 509

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 44.3 bits (105), Expect = 3e-05
 Identities = 31/149 (20%), Positives = 56/149 (37%)

Query: 19   KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK 78
            K+  KE+  K K K K  K +K K +KK+KKK+K    + KK       K+   +EK K 
Sbjct: 1150 KEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKL 1209

Query: 79   KEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQ 138
             ++   KK       ++++++QK K ++   K+ + +                   S + 
Sbjct: 1210 DDKPDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEG 1269

Query: 139  FANLVLHKTIERIHVGNQYGDIPRGIFII 167
                   +     +        P G    
Sbjct: 1270 KPKNAPKRVSAVQYSPPPPSKRPDGESNG 1298

Length = 1388

>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal

 Score = 42.5 bits (101), Expect = 3e-05
 Identities = 27/64 (42%), Positives = 35/64 (54%)

Query: 28 KKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKK 87
          KKK KK E +     EE K  K+  +    +KKE K  EK +KK E+   K E+KK KK+
Sbjct: 34 KKKGKKGELEITDLNEEYKDLKESLEAALLDKKELKAWEKAEKKAEKAKAKAEKKKAKKE 93

Query: 88 EEKK 91
          E K 
Sbjct: 94 EPKP 97

This domain is found to the N-terminus of bacterial signal peptidases of the S49 family (pfam01343). Length = 154

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 43.3 bits (102), Expect = 4e-05
 Identities = 33/102 (32%), Positives = 58/102 (56%)

Query: 13  PRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKE 72
             + +R   +K  +  ++  K+ E+KQK+ EE K K+  + + K E + +KK +++ KK+
Sbjct: 92  KELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQ 151

Query: 73  EEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEE 114
            E++ K +   + KK+  + KKK E + K K E K   KAEE
Sbjct: 152 AEEEAKAKAAAEAKKKAAEAKKKAEAEAKAKAEAKAKAKAEE 193

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 43.7 bits (104), Expect = 4e-05
 Identities = 25/88 (28%), Positives = 49/88 (55%)

Query: 31  QKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEK 90
            +++ E+K ++ E   ++ ++ KEE EEKKEK +EE+ +  EE + + ++  K+ KKE  
Sbjct: 528 LERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEAD 587

Query: 91  KQKKKEEKKQKKKKEEKKNKKAEEQNRQ 118
           +  K+  + QK      K  +  E  ++
Sbjct: 588 EIIKELRQLQKGGYASVKAHELIEARKR 615

Length = 782

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

 Score = 40.2 bits (95), Expect = 4e-05
 Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 3/52 (5%)

Query: 124 NQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLM 175
           N  R + G LR  D F NLVL   +E +  G +    P G+ +IRG +++++
Sbjct: 18  NGNRKVSGVLRGFDPFMNLVLDDAVEEVGDGEK---TPIGMVVIRGNSIIMI 66

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

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 42.9 bits (101), Expect = 5e-05
 Identities = 17/93 (18%), Positives = 43/93 (46%), Gaps = 1/93 (1%)

Query: 19  KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK 78
           KK +  E+N+ K +KKE   QK++  +++  +E ++E+     + +  +   K ++K   
Sbjct: 333 KKTRTAEKNEAKARKKEIA-QKRRAAEREINREARQERAAAMARARARRAAVKAKKKGLI 391

Query: 79  KEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKK 111
                +    E ++ K    + +     + N++
Sbjct: 392 DASPNEDTPSENEESKGSPPQVEATTTAEPNRE 424

Length = 429

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 43.0 bits (102), Expect = 5e-05
 Identities = 29/118 (24%), Positives = 62/118 (52%), Gaps = 2/118 (1%)

Query: 14  RIGKRKKKKKEEENKK-KQKKKEEKKQKKKEEKKQKKKEKKEEKEE-KKEKKKEEKKQKK 71
           RI ++K    EE  K+  ++ K+E +  KKE   + K+E  + + E ++E K+   + ++
Sbjct: 21  RIAEKKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNELQR 80

Query: 72  EEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKRTL 129
            E +  ++EE   +K E   +K++  +K++K+   K+    E++   + L   Q+  L
Sbjct: 81  LERRLLQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQREEL 138

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 43.3 bits (102), Expect = 5e-05
 Identities = 21/77 (27%), Positives = 43/77 (55%)

Query: 47  QKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEE 106
            + ++K   +EE + KKK+E+K K++E K  K  +K+ K K + +Q        KK +++
Sbjct: 6   SEAEKKILTEEELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKKSEKK 65

Query: 107 KKNKKAEEQNRQQGLYP 123
            + +  E++N +  + P
Sbjct: 66  SRKRDVEDENPEDFIDP 82

Length = 1066

>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional

 Score = 42.8 bits (101), Expect = 6e-05
 Identities = 21/94 (22%), Positives = 41/94 (43%)

Query: 16  GKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEK 75
              +  + E + +K+Q K++  K+K K+ KK    +     E   E ++ E KQ  +++K
Sbjct: 1   AMNENGENEVKQQKQQNKQKGTKKKNKKSKKDVDDDDAFLAELISENQEAENKQNNKKKK 60

Query: 76  DKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKN 109
            KKK++KK+   E                 +  +
Sbjct: 61  KKKKKKKKKNLGEAYDLAYDLPVVWSSAAFQDNS 94

Length = 470

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 43.1 bits (102), Expect = 6e-05
 Identities = 25/96 (26%), Positives = 38/96 (39%), Gaps = 1/96 (1%)

Query: 19  KKKKKEEENKKKQKKKEEKKQKKKEEKKQK-KKEKKEEKEEKKEKKKEEKKQKKEEEKDK 77
              K E   +++ KKK +K   K + K    K+E KE  E KK+  ++  +         
Sbjct: 4   ASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMV 63

Query: 78  KKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAE 113
           K  +   +    KK+ K   K    K   KK  K E
Sbjct: 64  KDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDE 99

Length = 509

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 43.1 bits (102), Expect = 6e-05
 Identities = 23/77 (29%), Positives = 42/77 (54%)

Query: 38   KQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEE 97
            +Q++ EEK+  K+++ + K + K  K  + K KK+E+K KK    K KK       K+ +
Sbjct: 1143 EQEEVEEKEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVD 1202

Query: 98   KKQKKKKEEKKNKKAEE 114
              +K+K ++K + K   
Sbjct: 1203 SDEKRKLDDKPDNKKSN 1219

Length = 1388

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 42.9 bits (101), Expect = 6e-05
 Identities = 21/84 (25%), Positives = 48/84 (57%)

Query: 27  NKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKK 86
              ++ K        K ++  K+  KK +   KK  + +++    EE + K KEEK +++
Sbjct: 351 KLYEEVKSNTDLSGDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQE 410

Query: 87  KEEKKQKKKEEKKQKKKKEEKKNK 110
           + EKKQK++ ++ ++K++++++ K
Sbjct: 411 ENEKKQKEQADEDKEKRQKDERKK 434

Length = 434

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 42.6 bits (101), Expect = 6e-05
 Identities = 18/56 (32%), Positives = 30/56 (53%)

Query: 18  RKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEE 73
           + K   E++  K  KK   K+ +KKE++K+K K KK  ++ K   K+ +     EE
Sbjct: 379 KTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRRKPSGTSEE 434

Length = 434

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 42.6 bits (101), Expect = 6e-05
 Identities = 18/67 (26%), Positives = 36/67 (53%)

Query: 11  ISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQK 70
           +  R+    + K +  ++KK  K  +K   K+ EKK+K+KEK + K+  ++ K   K++K
Sbjct: 368 LKARVIDELRPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRRK 427

Query: 71  KEEEKDK 77
                ++
Sbjct: 428 PSGTSEE 434

Length = 434

>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase; Provisional

 Score = 42.5 bits (101), Expect = 7e-05
 Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 28 KKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKK 87
          +KK +K E +     E+ K+ K+E K    +KKE K   K QKK+E     K+E K  K 
Sbjct: 32 RKKSQKGELEVTNLNEQYKEMKEELKAALLDKKELKAWHKAQKKKE-----KQEAKAAKA 86

Query: 88 EEKK 91
          + K 
Sbjct: 87 KSKP 90

Length = 330

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 42.2 bits (100), Expect = 8e-05
 Identities = 22/64 (34%), Positives = 45/64 (70%)

Query: 51  EKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNK 110
            ++E +     KK  +K +K  E+ +KK+EE+K++KK++    KK+E++++++KE+K+ +
Sbjct: 395 TEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEE 454

Query: 111 KAEE 114
           K EE
Sbjct: 455 KEEE 458

Length = 482

>gnl|CDD|184287 PRK13735, PRK13735, conjugal transfer mating pair stabilization protein TraG; Provisional

 Score = 42.4 bits (100), Expect = 8e-05
 Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 7/98 (7%)

Query: 14  RIGKRKKKKKEEENKKKQ--KKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKK 71
            I +R +      + K Q      E +    + +   + E+   K +  E +   K +  
Sbjct: 845 IIEQRTQDSGIRNDVKHQVDNMVTEYEGNIGDTQNSIRGEENTVKGQYSELQNHHKTEAL 904

Query: 72  EEEKDKKKEEKKQKK-----KEEKKQKKKEEKKQKKKK 104
            +     +E+  Q++       E+  K+ +E + K K 
Sbjct: 905 SQNNKYNEEKSAQERMPGADSPEELMKRAKEYQDKHKG 942

Length = 942

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

 Score = 39.6 bits (93), Expect = 9e-05
 Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGI-FIIRGENVVLMGE 177
           R   G L   DQ+ NLVL    E I    +      G   +IRG+N+VL+  
Sbjct: 28  REYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79

Length = 79

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 33/103 (32%), Positives = 55/103 (53%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
             +K+K+ EE K KQ  + + K + + EKK K++ KK+ +EE K K   E K+K  E K 
Sbjct: 114 AEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKK 173

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
           K + E K K + + K K +E K + +  + K   +A  +   +
Sbjct: 174 KAEAEAKAKAEAKAKAKAEEAKAKAEAAKAKAAAEAAAKAEAE 216

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 34/106 (32%), Positives = 64/106 (60%), Gaps = 2/106 (1%)

Query: 12  SPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKK 71
             +  K+   KKE+E +KK +++ E+ +K++  ++ ++KE ++    +K  K+ E+  K+
Sbjct: 54  RIQQQKKPAAKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQ 113

Query: 72  EEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNR 117
            EEK K+ EE K K+  E   K K E + +KK +E+  K+AEE+ +
Sbjct: 114 AEEKQKQAEEAKAKQAAE--AKAKAEAEAEKKAKEEAKKQAEEEAK 157

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 42.4 bits (99), Expect = 1e-04
 Identities = 31/97 (31%), Positives = 59/97 (60%)

Query: 21   KKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKE 80
            KK EE+ K  + KK+ ++ KK +E K+K +E K++ +  K+K +E KK  +  + + +  
Sbjct: 1296 KKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAA 1355

Query: 81   EKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNR 117
              + +  EEK +  +++K++ KKK +   KKAEE+ +
Sbjct: 1356 ADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKK 1392

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 42.1 bits (98), Expect = 1e-04
 Identities = 34/105 (32%), Positives = 67/105 (63%)

Query: 14   RIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEE 73
            +  +  K K EE  K +++KK+ ++ KKKE +++KK E+ ++ EE+ + K  E+ +K EE
Sbjct: 1613 KKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEE 1672

Query: 74   EKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQ 118
            +K K +E KK ++ E+K  +  +++ ++ KK E+  KK  E+ ++
Sbjct: 1673 DKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKK 1717

Length = 2084

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 22/70 (31%), Positives = 44/70 (62%)

Query: 21  KKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKE 80
            K++E  K+  KK ++  +K  E K +    ++ E + K+EK K+E+ +KK++E+  + +
Sbjct: 365 DKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDK 424

Query: 81  EKKQKKKEEK 90
           EK+QK + +K
Sbjct: 425 EKRQKDERKK 434

Length = 434

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 41.9 bits (99), Expect = 1e-04
 Identities = 13/61 (21%), Positives = 31/61 (50%)

Query: 57  EEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQN 116
           +E + K K   ++K  +   K   ++ +KK++EK++ K +++ +  K   K+ K +    
Sbjct: 374 DELRPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRRKPSGTSE 433

Query: 117 R 117
            
Sbjct: 434 E 434

Length = 434

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 42.3 bits (99), Expect = 1e-04
 Identities = 24/111 (21%), Positives = 62/111 (55%), Gaps = 3/111 (2%)

Query: 15  IGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEE 74
            GK + + + E  +K + + + + Q    E K +  E++   E + E K++EK       
Sbjct: 798 EGKVEHEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAKQDEKGVDGGGG 857

Query: 75  KDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKA---EEQNRQQGLY 122
            D    E++++++EE++++++EE+++++++EE +   +    E  ++Q +Y
Sbjct: 858 SDGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENEEPLSLEWPETRQKQAIY 908

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 26/98 (26%), Positives = 44/98 (44%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           +R   +++++  ++  K+   KQK+ EE   K     + K E + K+     +K   E  
Sbjct: 109 ERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAK 168

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEE 114
           KK E +  KK   + +KK E +   K   E K K   E
Sbjct: 169 KKAEAEAAKKAAAEAKKKAEAEAAAKAAAEAKKKAEAE 206

Length = 387

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 41.9 bits (99), Expect = 1e-04
 Identities = 17/69 (24%), Positives = 38/69 (55%)

Query: 28  KKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKK 87
           K K+  + E+++++ + + +   E K  K+E++   +E+     EE++D  K E   K +
Sbjct: 225 KLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKLE 284

Query: 88  EEKKQKKKE 96
             K++K +E
Sbjct: 285 ILKEKKDEE 293

The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 21/59 (35%), Positives = 33/59 (55%)

Query: 58  EKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQN 116
              E ++EE +       ++KK  KKQ+K E+K +K++ EK   KKK E   KKA+  +
Sbjct: 392 LLAEGEEEEGENGNLSPAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPD 450

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 41.1 bits (97), Expect = 2e-04
 Identities = 17/67 (25%), Positives = 33/67 (49%)

Query: 30  KQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEE 89
           K    E ++++ +       + KK  K+++K +KK EK++ ++    KK E   +K K  
Sbjct: 390 KPLLAEGEEEEGENGNLSPAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGP 449

Query: 90  KKQKKKE 96
             + KK 
Sbjct: 450 DGETKKV 456

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|184287 PRK13735, PRK13735, conjugal transfer mating pair stabilization protein TraG; Provisional

 Score = 41.7 bits (98), Expect = 2e-04
 Identities = 12/88 (13%), Positives = 34/88 (38%)

Query: 7   PKGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEE 66
            +  +  ++     + +      +   + E+   K +  + +   K E   +  +  +E+
Sbjct: 855 IRNDVKHQVDNMVTEYEGNIGDTQNSIRGEENTVKGQYSELQNHHKTEALSQNNKYNEEK 914

Query: 67  KKQKKEEEKDKKKEEKKQKKKEEKKQKK 94
             Q++    D  +E  K+ K+ + K K 
Sbjct: 915 SAQERMPGADSPEELMKRAKEYQDKHKG 942

Length = 942

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 40.9 bits (96), Expect = 2e-04
 Identities = 27/101 (26%), Positives = 46/101 (45%)

Query: 4   SIAPKGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKK 63
            +  K  +S    +  K       K K++ K  + +KK E+KK+KKKEKKE K E + K 
Sbjct: 32  LVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKKKKEKKEPKSEGETKL 91

Query: 64  KEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKK 104
             +  +K ++ K K  + K  +  +    K  E  ++    
Sbjct: 92  GFKTPKKSKKTKKKPPKPKPNEDVDNAFNKIAELAEKSNVY 132

Length = 413

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 41.7 bits (97), Expect = 2e-04
 Identities = 48/144 (33%), Positives = 87/144 (60%), Gaps = 6/144 (4%)

Query: 14   RIGKRKKKKKEEENKKK--QKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQ-- 69
            +I   ++ KK EE+KKK  + KK E+ +KK  E  +K+ E+ ++ EE K+K+ EEKK+  
Sbjct: 1660 KIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAE 1719

Query: 70   --KKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKR 127
              KK EE++K K E+ +K+ EE K+K +E KK +++K++  + K EE+ + + +   ++ 
Sbjct: 1720 ELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEA 1779

Query: 128  TLIGYLRSVDQFANLVLHKTIERI 151
             +   L   D+   + + K I+ I
Sbjct: 1780 VIEEELDEEDEKRRMEVDKKIKDI 1803

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 41.3 bits (96), Expect = 2e-04
 Identities = 30/102 (29%), Positives = 66/102 (64%)

Query: 19   KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK 78
            KK ++E + K  ++ K+ ++ KKK E+ +K +E +++  E  +K+ EE K+ +E +K + 
Sbjct: 1653 KKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEA 1712

Query: 79   KEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQG 120
            +E+KK ++ ++ +++ K + ++ KK+ E+  KKAEE  + + 
Sbjct: 1713 EEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEE 1754

Length = 2084

>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 41.4 bits (98), Expect = 2e-04
 Identities = 21/81 (25%), Positives = 46/81 (56%)

Query: 39  QKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEK 98
            +++ E+K ++ E   ++ EK +++ EEKK+K +EE+DK  EE +++ ++  K+ KKE  
Sbjct: 528 LERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEAD 587

Query: 99  KQKKKKEEKKNKKAEEQNRQQ 119
           +  K+  + +          +
Sbjct: 588 EIIKELRQLQKGGYASVKAHE 608

Length = 782

>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family

 Score = 41.2 bits (97), Expect = 2e-04
 Identities = 15/90 (16%), Positives = 39/90 (43%)

Query: 39  QKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEK 98
           ++ +E   +  KE ++  E++K  + EE+K + +  K++  +   +  + E+   + E K
Sbjct: 2   KELREALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAK 61

Query: 99  KQKKKKEEKKNKKAEEQNRQQGLYPNQKRT 128
                +     ++ EE   +   +    R 
Sbjct: 62  PAASGEGGGGEEEEEEAKAEAAEFRAYLRG 91

This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease [Mobile and extrachromosomal element functions, Prophage functions]. Length = 384

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 41.6 bits (98), Expect = 2e-04
 Identities = 31/97 (31%), Positives = 49/97 (50%)

Query: 22   KKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEE 81
             K EE  ++Q++ EEK+  K++  K K K K  +  + K KKKE+KK+K   +K KK   
Sbjct: 1135 DKFEEALEEQEEVEEKEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASV 1194

Query: 82   KKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQ 118
                K+ +  +K+K + K   KK        E+   Q
Sbjct: 1195 VGNSKRVDSDEKRKLDDKPDNKKSNSSGSDQEDDEEQ 1231

Length = 1388

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 41.2 bits (97), Expect = 2e-04
 Identities = 27/109 (24%), Positives = 58/109 (53%)

Query: 19   KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK 78
            K+K ++   + ++K+KE +K K    K    ++  + +E  +E+++ E+K+  +E++ K 
Sbjct: 1101 KEKVEKLNAELEKKEKELEKLKNTTPKDMWLEDLDKFEEALEEQEEVEEKEIAKEQRLKS 1160

Query: 79   KEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKR 127
            K + K  K  + K KKKE+KK+K   ++ K       +++      +K 
Sbjct: 1161 KTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKL 1209

Length = 1388

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 41.3 bits (97), Expect = 2e-04
 Identities = 19/83 (22%), Positives = 50/83 (60%)

Query: 22  KKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEE 81
           K  EE K       +K+Q+  +E  +K ++  ++  E K++    ++ + + +++K K+E
Sbjct: 351 KLYEEVKSNTDLSGDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQE 410

Query: 82  KKQKKKEEKKQKKKEEKKQKKKK 104
           + +KK++E+  + KE++++ ++K
Sbjct: 411 ENEKKQKEQADEDKEKRQKDERK 433

Length = 434

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 19/61 (31%), Positives = 32/61 (52%)

Query: 54  EEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAE 113
           +E   K +   E+K  K  ++   K+ EKK+K+KE+ K KK+    +   K  K +  +E
Sbjct: 374 DELRPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRRKPSGTSE 433

Query: 114 E 114
           E
Sbjct: 434 E 434

Length = 434

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 41.3 bits (97), Expect = 2e-04
 Identities = 28/97 (28%), Positives = 48/97 (49%)

Query: 18  RKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDK 77
           R K+ ++E    +++KK+ ++  K+   KQK+ E+   K     K K E + K+     K
Sbjct: 102 RLKQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAK 161

Query: 78  KKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEE 114
           K   + +KK E +  KK   + +KK + E   K A E
Sbjct: 162 KAAAEAKKKAEAEAAKKAAAEAKKKAEAEAAAKAAAE 198

Length = 387

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 2/69 (2%)

Query: 37  KKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK--KEEKKQKKKEEKKQKK 94
           KK K+  E +++++E   E E   E K  +++Q+   E+D     EEK+   K E   K 
Sbjct: 224 KKLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKL 283

Query: 95  KEEKKQKKK 103
           +  K++K +
Sbjct: 284 EILKEKKDE 292

The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 16/71 (22%), Positives = 40/71 (56%)

Query: 18  RKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDK 77
            KK K+  E ++++++ + + +   E K  K++++   +E+     +E++   K E+ DK
Sbjct: 223 TKKLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDK 282

Query: 78  KKEEKKQKKKE 88
            +  K++K +E
Sbjct: 283 LEILKEKKDEE 293

The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 30/119 (25%), Positives = 64/119 (53%), Gaps = 8/119 (6%)

Query: 15  IGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEE 74
              +KKKK+  E  +K KK+ E+KQK K +KK+ KK+K ++K++K +KK ++ ++K E+E
Sbjct: 58  TEAKKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKE 117

Query: 75  KDKKKEEKKQKKKEEKKQKKKEEKKQ--------KKKKEEKKNKKAEEQNRQQGLYPNQ 125
            + K E+  +   E      + + ++        + + + K+  +  ++  ++   P  
Sbjct: 118 AEDKLEDLTKSYSETLSTLSELKPRKYALHKDIYQSRLDRKRRAEVAKKEAEELQNPGF 176

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]

 Score = 40.9 bits (96), Expect = 2e-04
 Identities = 21/90 (23%), Positives = 40/90 (44%), Gaps = 1/90 (1%)

Query: 35  EEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKK 94
           E   ++ + E +  +++ K   E +   +    K K++ + +KK ++ K K K + K K 
Sbjct: 50  EAPTEEPQPEPEPPEEQPKPPTEPETPPEPTPPKPKEKPKPEKKPKKPKPKPKPKPKPKP 109

Query: 95  K-EEKKQKKKKEEKKNKKAEEQNRQQGLYP 123
           K + + + KK   K   KA     Q    P
Sbjct: 110 KVKPQPKPKKPPSKTAAKAPAAPNQPARPP 139

Length = 244

>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional

 Score = 41.4 bits (97), Expect = 2e-04
 Identities = 30/114 (26%), Positives = 50/114 (43%), Gaps = 3/114 (2%)

Query: 13  PRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKE 72
             I K+  +K +++NKK  K  + K  KK + K++KK +KK   ++  +   + K   K+
Sbjct: 46  LDINKKLHEKLDKKNKKFNKTDDLKDSKKTKLKQKKKIKKKLHIDDDYDNFFDSKNNSKQ 105

Query: 73  EEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQK 126
                     ++ K + +K KK   K    K   KK KK      +   Y N K
Sbjct: 106 FAGPLAISLMRKPKPKTEKLKK---KITVNKSTNKKKKKVLSSKDELIKYDNNK 156

Length = 742

>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein

 Score = 41.1 bits (96), Expect = 2e-04
 Identities = 24/116 (20%), Positives = 55/116 (47%), Gaps = 7/116 (6%)

Query: 11  ISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQK 70
              +   ++ ++ +EE  KKQ   ++ +QK    +    K++ E +++++E K   K   
Sbjct: 206 RESQEDAKRAQQLKEELDKKQIDADKAQQKADFAQDNADKQRDEVRQKQQEAKNLPKPAD 265

Query: 71  KEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKK-------EEKKNKKAEEQNRQQ 119
               K+ K+  + QK++ EK Q + ++  ++  K       + K+  KA E+  + 
Sbjct: 266 TSSPKEDKQVAENQKREIEKAQIEIKKNDEEALKAKDHKAFDLKQESKASEKEAED 321

This family consists of several Borrelia P83/P100 antigen proteins. Length = 489

>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

 Score = 41.5 bits (97), Expect = 2e-04
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 28  KKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEE 81
             + K+K ++K    +E K +    + E E    K++EEK        + KK++
Sbjct: 794 AARAKQKPKEKGPNDKEIKIESPSVETEGERCTIKQREEKGIDAPAILNVKKKK 847

Length = 926

>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC; Provisional

 Score = 41.1 bits (97), Expect = 2e-04
 Identities = 17/102 (16%), Positives = 42/102 (41%), Gaps = 1/102 (0%)

Query: 18  RKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDK 77
           R+ K +    ++++KK EE K +  E ++ + + +K  +E + +K  E +  K ++    
Sbjct: 432 RQAKAEIRAIEQEKKKAEEAKARF-EARQARLEREKAAREARHKKAAEARAAKDKDAVAA 490

Query: 78  KKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
                K KK    +    +   +         ++A +   + 
Sbjct: 491 ALARVKAKKAAATQPIVIKAGARPDNSAVIAAREARKAQARA 532

Length = 695

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 41.2 bits (96), Expect = 2e-04
 Identities = 19/48 (39%), Positives = 34/48 (70%), Gaps = 1/48 (2%)

Query: 29  KKQKKKEEKKQKKKEEKKQKKKEKKE-EKEEKKEKKKEEKKQKKEEEK 75
           K  KK+EE  +K K E +QK +E++E EKE++KE+++E +++ +   K
Sbjct: 576 KLAKKREEAVEKAKREAEQKAREEREREKEKEKEREREREREAERAAK 623

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 41.0 bits (97), Expect = 3e-04
 Identities = 24/96 (25%), Positives = 57/96 (59%), Gaps = 1/96 (1%)

Query: 18  RKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDK 77
              K+ E+  ++ ++KKE+ ++++ +  ++ +KE ++  +E K++  E  K+ ++ +K  
Sbjct: 541 ALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEADEIIKELRQLQKGG 600

Query: 78  KKEEKKQKKKEEKKQ-KKKEEKKQKKKKEEKKNKKA 112
               K  +  E +K+  K  EKK+KKKK++K+ ++ 
Sbjct: 601 YASVKAHELIEARKRLNKANEKKEKKKKKQKEKQEE 636

Length = 782

>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family

 Score = 40.8 bits (96), Expect = 3e-04
 Identities = 17/86 (19%), Positives = 40/86 (46%)

Query: 24  EEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKK 83
           +E  +   +  +E ++  ++EK  + +E+K E +  KE+  +   +    E+   + E K
Sbjct: 2   KELREALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAK 61

Query: 84  QKKKEEKKQKKKEEKKQKKKKEEKKN 109
                E    ++EE++ K +  E + 
Sbjct: 62  PAASGEGGGGEEEEEEAKAEAAEFRA 87

This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease [Mobile and extrachromosomal element functions, Prophage functions]. Length = 384

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 41.2 bits (97), Expect = 3e-04
 Identities = 26/102 (25%), Positives = 52/102 (50%)

Query: 16   GKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEK 75
             +R K K + +  K +K K +KK+KKK++    K +K       K    +EK++  ++  
Sbjct: 1155 EQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKPD 1214

Query: 76   DKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNR 117
            +KK       ++++++QK K +K   K+ + KKN  ++    
Sbjct: 1215 NKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSED 1256

Length = 1388

>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal

 Score = 39.4 bits (93), Expect = 3e-04
 Identities = 26/68 (38%), Positives = 36/68 (52%), Gaps = 12/68 (17%)

Query: 15 IGKRKKKKKEE-------ENKKKQKKK-----EEKKQKKKEEKKQKKKEKKEEKEEKKEK 62
          + ++KK KK E       E  K  K+       +KK+ K  EK +KK EK + K EKK+ 
Sbjct: 31 LAQKKKGKKGELEITDLNEEYKDLKESLEAALLDKKELKAWEKAEKKAEKAKAKAEKKKA 90

Query: 63 KKEEKKQK 70
          KKEE K +
Sbjct: 91 KKEEPKPR 98

This domain is found to the N-terminus of bacterial signal peptidases of the S49 family (pfam01343). Length = 154

>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

 Score = 41.1 bits (96), Expect = 3e-04
 Identities = 18/59 (30%), Positives = 27/59 (45%)

Query: 32  KKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEK 90
           K     KQK KE+    K+ K E    + E ++   KQ++E+  D       +KKK  K
Sbjct: 792 KAAARAKQKPKEKGPNDKEIKIESPSVETEGERCTIKQREEKGIDAPAILNVKKKKPYK 850

Length = 926

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 40.8 bits (95), Expect = 3e-04
 Identities = 16/50 (32%), Positives = 35/50 (70%)

Query: 13  PRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEK 62
           P    +  KK+EE  +K +++ E+K ++++E +K+K+KE++ E+E + E+
Sbjct: 571 PLASSKLAKKREEAVEKAKREAEQKAREEREREKEKEKEREREREREAER 620

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|215521 PLN02967, PLN02967, kinase

 Score = 40.8 bits (95), Expect = 3e-04
 Identities = 21/99 (21%), Positives = 43/99 (43%)

Query: 16  GKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEK 75
           G   KKK     K+  KK   +  +  EE  +    +    +++ +K     ++K     
Sbjct: 66  GAVSKKKPTRSVKRATKKTVVEISEPLEEGSELVVNEDAALDKESKKTPRRTRRKAAAAS 125

Query: 76  DKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEE 114
              +EEK +KK  ++++ KK ++  + +  E +    EE
Sbjct: 126 SDVEEEKTEKKVRKRRKVKKMDEDVEDQGSESEVSDVEE 164

Length = 581

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 40.2 bits (94), Expect = 4e-04
 Identities = 30/102 (29%), Positives = 50/102 (49%)

Query: 18  RKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDK 77
             + K + E + ++K KEE K++ +EE K K   + ++K  + +KK E + + K E K K
Sbjct: 129 AAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAKAEAKAK 188

Query: 78  KKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
            K E+ + K E  K K   E   K + E      AE + +  
Sbjct: 189 AKAEEAKAKAEAAKAKAAAEAAAKAEAEAAAAAAAEAERKAD 230

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 40.9 bits (95), Expect = 4e-04
 Identities = 39/109 (35%), Positives = 73/109 (66%), Gaps = 1/109 (0%)

Query: 14   RIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEE 73
            ++ + +KK K EE KK ++ K + ++ KK E+++KK E+ ++KE +++KK EE K+ +EE
Sbjct: 1599 KLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEE 1658

Query: 74   EKDKKKEEKKQKKKEEKK-QKKKEEKKQKKKKEEKKNKKAEEQNRQQGL 121
             K K  EE K+ ++++KK ++ K+ ++ +KK  E   K+AEE  + + L
Sbjct: 1659 NKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEEL 1707

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 40.5 bits (94), Expect = 4e-04
 Identities = 29/105 (27%), Positives = 57/105 (54%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
            K  + KK EE KK  + K+ +++KK +E K+K +E K+  E KK+ ++ +KK    ++K 
Sbjct: 1279 KADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKA 1338

Query: 77   KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGL 121
            ++ ++  +  K E +    E +  ++K E  + KK E + +    
Sbjct: 1339 EEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAA 1383

Length = 2084

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 40.3 bits (95), Expect = 4e-04
 Identities = 23/77 (29%), Positives = 38/77 (49%)

Query: 9   GAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKK 68
           G I   I +  K +  +E + K K   EKK  K  +K   K+ +K+EKE++K K K+  +
Sbjct: 358 GKIERYIEEPLKARVIDELRPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHR 417

Query: 69  QKKEEEKDKKKEEKKQK 85
             K   K +K     ++
Sbjct: 418 DTKNIGKRRKPSGTSEE 434

Length = 434

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 40.4 bits (94), Expect = 4e-04
 Identities = 15/45 (33%), Positives = 34/45 (75%)

Query: 54  EEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEK 98
           +++EE  EK K E +QK  EE++++KE++K++++E +++ ++  K
Sbjct: 579 KKREEAVEKAKREAEQKAREEREREKEKEKEREREREREAERAAK 623

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 40.0 bits (94), Expect = 5e-04
 Identities = 22/98 (22%), Positives = 39/98 (39%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           + KKK K+   K K K    K++ K+  + +KK  ++ ++         +      E   
Sbjct: 15  EAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDATESDI 74

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEE 114
            KK+ K   K    K   K++ K +    +K  KK   
Sbjct: 75  PKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNAL 112

Length = 509

>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family

 Score = 40.0 bits (94), Expect = 5e-04
 Identities = 17/84 (20%), Positives = 38/84 (45%)

Query: 19  KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK 78
            ++   E  K+ +K  E++K  + EE+K +    KEE ++   +    ++   E E    
Sbjct: 4   LREALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAKPA 63

Query: 79  KEEKKQKKKEEKKQKKKEEKKQKK 102
              +    +EE+++ K E  + + 
Sbjct: 64  ASGEGGGGEEEEEEAKAEAAEFRA 87

This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease [Mobile and extrachromosomal element functions, Prophage functions]. Length = 384

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 39.8 bits (93), Expect = 5e-04
 Identities = 28/98 (28%), Positives = 46/98 (46%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           K++ ++  ++   KQK+ EE   K     K K + + +      +K   E K+K E E  
Sbjct: 117 KKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAEAA 176

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEE 114
           KK   + +KK E +   K   + +KK + E K K A E
Sbjct: 177 KKAAAEAKKKAEAEAAAKAAAEAKKKAEAEAKKKAAAE 214

Length = 387

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 40.3 bits (94), Expect = 5e-04
 Identities = 34/112 (30%), Positives = 73/112 (65%)

Query: 8   KGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEK 67
           +   S     + K  KE +N+  +++++EK+Q K+E+KK+K+K K+E K+ K +++ +EK
Sbjct: 81  EKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEK 140

Query: 68  KQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
           +  KE+EK+K+K+ ++ + +EE+K++++   K + KK  KK    +++   +
Sbjct: 141 RPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPE 192

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 39.9 bits (94), Expect = 6e-04
 Identities = 15/52 (28%), Positives = 28/52 (53%)

Query: 22  KKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEE 73
             E +  +K+++K EKK +K+E +K   K+K E   +K +    E K+   +
Sbjct: 408 PAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPDGETKKVDPD 459

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 40.1 bits (93), Expect = 6e-04
 Identities = 38/116 (32%), Positives = 67/116 (57%)

Query: 6    APKGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKE 65
            A K A   +     KKK EE  K ++ KK+ ++ KK +E K+K +E K+  E KK+ ++ 
Sbjct: 1436 AKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEA 1495

Query: 66   EKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGL 121
            +KK  + ++  + K++  + KK E+ +K  E KK ++ K+  + KKAEE+ +   L
Sbjct: 1496 KKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADEL 1551

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 40.1 bits (93), Expect = 6e-04
 Identities = 34/100 (34%), Positives = 65/100 (65%)

Query: 18   RKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDK 77
            +KK +++++  + +KK EE K+  + +KK ++ +K EE ++K E+ K+  + KK+ E+ K
Sbjct: 1424 KKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAK 1483

Query: 78   KKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNR 117
            K +E K+K +E KK+  + +K  + KK+  + KKAEE  +
Sbjct: 1484 KADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKK 1523

Length = 2084

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 39.6 bits (93), Expect = 6e-04
 Identities = 20/95 (21%), Positives = 33/95 (34%), Gaps = 6/95 (6%)

Query: 24  EEENKKKQKKKEEKKQKKKEEKK------QKKKEKKEEKEEKKEKKKEEKKQKKEEEKDK 77
                 K +   E++ KKK +K       +    K+E KE  + KKK  ++  +      
Sbjct: 1   MTTASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLS 60

Query: 78  KKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKA 112
              +      E    KKK +   K    +   KK 
Sbjct: 61  GMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKK 95

Length = 509

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 39.8 bits (93), Expect = 6e-04
 Identities = 16/69 (23%), Positives = 47/69 (68%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           KR++  KE   K +   K+  + K + +  ++ + K +E++ K+E+ ++++K++ +E+K+
Sbjct: 366 KRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDKE 425

Query: 77  KKKEEKKQK 85
           K+++++++K
Sbjct: 426 KRQKDERKK 434

Length = 434

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 40.0 bits (94), Expect = 6e-04
 Identities = 21/71 (29%), Positives = 36/71 (50%)

Query: 20  KKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKK 79
           KK KE    ++++++ + + +   E K  K+E++   EE      EEK+   + E   K 
Sbjct: 224 KKLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKL 283

Query: 80  EEKKQKKKEEK 90
           E  K+KK EE 
Sbjct: 284 EILKEKKDEEL 294

The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 39.9 bits (93), Expect = 6e-04
 Identities = 36/112 (32%), Positives = 73/112 (65%)

Query: 4   SIAPKGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKK 63
           S  P     P    + +  KEEE +K+Q K+E+KK+K+K +++ K ++ KEE +EK+  K
Sbjct: 85  SKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPK 144

Query: 64  KEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQ 115
           ++EK+++K+ E+ + +EE+K++++   K + K+  K+K   ++K+  + E+Q
Sbjct: 145 EKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQ 196

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 39.4 bits (92), Expect = 7e-04
 Identities = 17/96 (17%), Positives = 40/96 (41%)

Query: 25  EENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQ 84
           E  K +  +K E K +KKE  ++++  ++E   E ++++     + +      K ++K  
Sbjct: 331 EIKKTRTAEKNEAKARKKEIAQKRRAAEREINREARQERAAAMARARARRAAVKAKKKGL 390

Query: 85  KKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQG 120
                 +    E ++ K    + +     E NR+  
Sbjct: 391 IDASPNEDTPSENEESKGSPPQVEATTTAEPNREPS 426

Length = 429

>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated

 Score = 39.8 bits (94), Expect = 7e-04
 Identities = 24/91 (26%), Positives = 44/91 (48%)

Query: 21  KKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKE 80
           K   E  +   KKK   K  K+ EK      K + + +  +++ E+ + +KEEE +K  +
Sbjct: 129 KVNNEIERDHLKKKHLPKLIKQYEKFGFGILKIDFEIDDSKEELEKFEAQKEEEDEKLAK 188

Query: 81  EKKQKKKEEKKQKKKEEKKQKKKKEEKKNKK 111
           E  +  K+ + +KKK+ K    K+   +  K
Sbjct: 189 EALEAMKKLEAEKKKQSKNFDPKEGPVQIGK 219

Length = 1437

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 39.5 bits (93), Expect = 8e-04
 Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 29  KKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEE 81
             ++KK  KKQ+K  EKK +K+E ++   +KK +   +K +  + E  K   +
Sbjct: 408 PAERKKLRKKQRK-AEKKAEKEEAEKAAAKKKAEAAAKKAKGPDGETKKVDPD 459

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein

 Score = 39.2 bits (91), Expect = 8e-04
 Identities = 28/100 (28%), Positives = 53/100 (53%), Gaps = 3/100 (3%)

Query: 18  RKKKKKEEENKKKQKKKEEKKQK--KKEEKKQKKKEKKEEKEEKKEKKKE-EKKQKKEEE 74
           ++K    ++N  KQ+ +  +KQ+  K   K       KE+K+  + +K+E EK Q + ++
Sbjct: 233 QQKADFAQDNADKQRDEVRQKQQEAKNLPKPADTSSPKEDKQVAENQKREIEKAQIEIKK 292

Query: 75  KDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEE 114
            D++  + K  K  + KQ+ K  +K+ + KE +  KK E 
Sbjct: 293 NDEEALKAKDHKAFDLKQESKASEKEAEDKELEAQKKREP 332

This family consists of several Borrelia P83/P100 antigen proteins. Length = 489

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 39.5 bits (92), Expect = 8e-04
 Identities = 43/162 (26%), Positives = 80/162 (49%)

Query: 3   ISIAPKGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEK 62
              A     S    KR +K   +    K K  +E K +  +E++++K++ KEEK++KKEK
Sbjct: 64  AKCAESKLSSDEAVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEK 123

Query: 63  KKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLY 122
            KEE K +K +E+ K+K   K+K+KE++K+ ++   ++++KK E+   K+  +   +   
Sbjct: 124 PKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKP 183

Query: 123 PNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGI 164
           PN+K+      +        V  K  E      +  +   G 
Sbjct: 184 PNKKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEEDDGK 225

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota)

 Score = 39.3 bits (92), Expect = 8e-04
 Identities = 25/87 (28%), Positives = 48/87 (55%), Gaps = 1/87 (1%)

Query: 32  KKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKK 91
           K  E+  +K +E+ K  K + K  K+     +     ++K + K ++  EK   + +EKK
Sbjct: 273 KTHEKSMEKLQEKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKK 332

Query: 92  QKKKEEKKQKKKKEEKKNKKAEEQNRQ 118
           ++KK+E+K KKK+ E+  ++ E+   Q
Sbjct: 333 KEKKKEEK-KKKQIERLEERIEKLEVQ 358

DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras. Length = 391

>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase; Provisional

 Score = 39.0 bits (92), Expect = 9e-04
 Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 15 IGKRKKKKKEE-ENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEE 73
          + +RKK +K E E     ++ +E K++ K     KK+ K   K +KK++K+E K  K + 
Sbjct: 29 LAQRKKSQKGELEVTNLNEQYKEMKEELKAALLDKKELKAWHKAQKKKEKQEAKAAKAKS 88

Query: 74 EK 75
          + 
Sbjct: 89 KP 90

Length = 330

>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase; Provisional

 Score = 39.0 bits (92), Expect = 9e-04
 Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 7/64 (10%)

Query: 46  KQKKKEKKEEKE-----EKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQ 100
            Q+KK +K E E     E+ ++ KEE K    ++K+ K   K QKKKE  KQ+ K  K +
Sbjct: 30  AQRKKSQKGELEVTNLNEQYKEMKEELKAALLDKKELKAWHKAQKKKE--KQEAKAAKAK 87

Query: 101 KKKK 104
            K +
Sbjct: 88  SKPR 91

Length = 330

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 39.0 bits (91), Expect = 9e-04
 Identities = 23/98 (23%), Positives = 50/98 (51%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           ++K+  ++E  K+ +K++   +++KK+ ++  K+   ++K+ ++   K     K + E +
Sbjct: 93  QQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAE 152

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEE 114
            K+     KK   + +KK E +  KK   E K K   E
Sbjct: 153 AKRAAAAAKKAAAEAKKKAEAEAAKKAAAEAKKKAEAE 190

Length = 387

>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

 Score = 39.5 bits (92), Expect = 9e-04
 Identities = 19/68 (27%), Positives = 25/68 (36%), Gaps = 9/68 (13%)

Query: 40  KKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKK 99
           K     KQK KEK    +E K          +    + + E    K++EEK         
Sbjct: 792 KAAARAKQKPKEKGPNDKEIK---------IESPSVETEGERCTIKQREEKGIDAPAILN 842

Query: 100 QKKKKEEK 107
            KKKK  K
Sbjct: 843 VKKKKPYK 850

Length = 926

>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota)

 Score = 39.3 bits (92), Expect = 9e-04
 Identities = 27/84 (32%), Positives = 48/84 (57%), Gaps = 1/84 (1%)

Query: 26  ENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEE-KKQKKEEEKDKKKEEKKQ 84
           + K K  K + K+ KK     +   + K + + K E+  E+   + KE++K+KKKEEKK+
Sbjct: 283 QEKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKKKEKKKEEKKK 342

Query: 85  KKKEEKKQKKKEEKKQKKKKEEKK 108
           K+ E  +++ ++ + Q   KEE K
Sbjct: 343 KQIERLEERIEKLEVQATDKEENK 366

DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras. Length = 391

>gnl|CDD|220252 pfam09468, RNase_H2-Ydr279, Ydr279p protein family (RNase H2 complex component)

 Score = 38.9 bits (91), Expect = 9e-04
 Identities = 24/67 (35%), Positives = 34/67 (50%)

Query: 28  KKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKK 87
            K     E K   K  ++ +KKK + EE  E  E + E+K++ KEE K KK +E K  K 
Sbjct: 212 LKSLLIPEFKPLDKYLKESKKKKRETEEDVEAAESRAEKKRKSKEEIKKKKPKESKGVKA 271

Query: 88  EEKKQKK 94
            +K   K
Sbjct: 272 LKKVVAK 278

RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organisms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologues of Ydr279p. It is not known whether non yeast proteins in this family fulfil the same function. Length = 287

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 39.1 bits (92), Expect = 0.001
 Identities = 23/113 (20%), Positives = 45/113 (39%), Gaps = 4/113 (3%)

Query: 19  KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEK----KKEEKKQKKEEE 74
            K +  E  K+     +E  +K KE   + K      +EE+  K    ++ E++ K E E
Sbjct: 2   SKVRVYELAKELGVSSKELLEKLKELGIEVKSHSSTVEEEEARKEEAKREAEEEAKAEAE 61

Query: 75  KDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKR 127
           +    E +++ K E       EE  +     E   + AE++  +      ++ 
Sbjct: 62  EAAAAEAEEEAKAEAAAAAPAEEAAEAAAAAEAAARPAEDEAARPAEAAARRP 114

Length = 746

>gnl|CDD|184287 PRK13735, PRK13735, conjugal transfer mating pair stabilization protein TraG; Provisional

 Score = 39.3 bits (92), Expect = 0.001
 Identities = 17/87 (19%), Positives = 32/87 (36%), Gaps = 8/87 (9%)

Query: 42  KEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQ--KKKEEKK 99
           + + K +      E E      +   + ++   K +  E +   K E   Q  K  EEK 
Sbjct: 856 RNDVKHQVDNMVTEYEGNIGDTQNSIRGEENTVKGQYSELQNHHKTEALSQNNKYNEEKS 915

Query: 100 QKK------KKEEKKNKKAEEQNRQQG 120
            ++        EE   +  E Q++ +G
Sbjct: 916 AQERMPGADSPEELMKRAKEYQDKHKG 942

Length = 942

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 38.9 bits (91), Expect = 0.001
 Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 2/92 (2%)

Query: 3   ISIAPKGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEK 62
                K A +     +K+ K  E  KK +KKK++K  K+K+E K + + K   K  KK K
Sbjct: 43  SEEENKVATTSTKKDKKEDKNNESKKKSEKKKKKK--KEKKEPKSEGETKLGFKTPKKSK 100

Query: 63  KKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKK 94
           K ++K  K +  +D      K  +  EK    
Sbjct: 101 KTKKKPPKPKPNEDVDNAFNKIAELAEKSNVY 132

Length = 413

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 39.4 bits (91), Expect = 0.001
 Identities = 41/102 (40%), Positives = 65/102 (63%), Gaps = 4/102 (3%)

Query: 19   KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKK---EKKKEEKKQKKEEEK 75
            KKK +E++   + KKK E+ +KK +E K+    KK+  E KK   EKKK ++ +KK EE 
Sbjct: 1384 KKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEA 1443

Query: 76   DKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNR 117
             KK +E K+K +E KK ++ ++K ++ KK ++  KKAEE  +
Sbjct: 1444 -KKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKK 1484

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 39.0 bits (90), Expect = 0.001
 Identities = 37/107 (34%), Positives = 62/107 (57%), Gaps = 4/107 (3%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEK----KKEEKKQKKE 72
              ++K +  E KK++ KK+    KKK E+K+K  E K++ EE K+K    KK    +KK 
Sbjct: 1361 AAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKA 1420

Query: 73   EEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
            +E  KK EEKK+  + +KK ++ ++  + KKK E+  K  E + + +
Sbjct: 1421 DEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAE 1467

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 39.0 bits (90), Expect = 0.001
 Identities = 38/103 (36%), Positives = 63/103 (61%), Gaps = 3/103 (2%)

Query: 20   KKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKK---EKKKEEKKQKKEEEKD 76
            KKK +E  KK ++KK+  + KKK E+ +K  E K++ EE K   E KK+ ++ KK +E  
Sbjct: 1417 KKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAK 1476

Query: 77   KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
            KK EE K+  + +KK ++ ++K  + KK  +  KKA+E  + +
Sbjct: 1477 KKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAE 1519

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 39.0 bits (90), Expect = 0.001
 Identities = 35/105 (33%), Positives = 68/105 (64%)

Query: 8    KGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEK 67
            K A   +  +  +KK  E  KK+ ++ ++ ++ KK+E ++KKK ++ +K E++ K K E+
Sbjct: 1675 KKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEE 1734

Query: 68   KQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKA 112
             +K+ EE  KK EE K+ ++E+KK    +++++KK +E +K K+A
Sbjct: 1735 AKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEA 1779

Length = 2084

>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 39.0 bits (92), Expect = 0.001
 Identities = 20/84 (23%), Positives = 48/84 (57%)

Query: 44  EKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKK 103
              ++ + + E+K E+ E   +E ++ KEE ++KK++ ++++ K  ++ +K+ ++  K+ 
Sbjct: 523 ASLEELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEA 582

Query: 104 KEEKKNKKAEEQNRQQGLYPNQKR 127
           K+E      E +  Q+G Y + K 
Sbjct: 583 KKEADEIIKELRQLQKGGYASVKA 606

Length = 782

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 38.6 bits (90), Expect = 0.001
 Identities = 16/70 (22%), Positives = 44/70 (62%)

Query: 25  EENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQ 84
           ++ ++  K+  +K Q   ++  + K E    +E + + K+E+ KQ++ E+K K++ ++ +
Sbjct: 365 DKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDK 424

Query: 85  KKKEEKKQKK 94
           +K+++ ++KK
Sbjct: 425 EKRQKDERKK 434

Length = 434

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 39.2 bits (92), Expect = 0.001
 Identities = 15/63 (23%), Positives = 35/63 (55%)

Query: 56  KEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQ 115
           +E  K +  +E + K +   +KK  +  +K   ++ +KK++EK++ K K+  ++ K   +
Sbjct: 365 EEPLKARVIDELRPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGK 424

Query: 116 NRQ 118
            R+
Sbjct: 425 RRK 427

Length = 434

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 39.2 bits (92), Expect = 0.001
 Identities = 17/71 (23%), Positives = 38/71 (53%)

Query: 41  KKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQ 100
           KK ++  + +E++EE + + E   E K  K+E+E   +++     +++E   K ++  K 
Sbjct: 224 KKLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKL 283

Query: 101 KKKKEEKKNKK 111
           +  KE+K  + 
Sbjct: 284 EILKEKKDEEL 294

The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832

>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein

 Score = 39.2 bits (91), Expect = 0.001
 Identities = 20/103 (19%), Positives = 53/103 (51%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
               K +++ +  +    +++ + ++++++ K   K  +    KE K+  + QK+E EK 
Sbjct: 227 IDADKAQQKADFAQDNADKQRDEVRQKQQEAKNLPKPADTSSPKEDKQVAENQKREIEKA 286

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
           + + +K  ++  + K  K  + KQ+ K  EK+ +  E + +++
Sbjct: 287 QIEIKKNDEEALKAKDHKAFDLKQESKASEKEAEDKELEAQKK 329

This family consists of several Borrelia P83/P100 antigen proteins. Length = 489

>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC; Provisional

 Score = 39.2 bits (92), Expect = 0.001
 Identities = 21/117 (17%), Positives = 42/117 (35%), Gaps = 15/117 (12%)

Query: 8   KGAISPRIGKRKKKKKEEENKK----KQKKKEEKKQKKKEEKKQKKKEKKEEK------- 56
           K  I       ++KKK EE K     +Q + E +K  ++   K+  + +  +        
Sbjct: 435 KAEIRAI---EQEKKKAEEAKARFEARQARLEREKAAREARHKKAAEARAAKDKDAVAAA 491

Query: 57  -EEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKA 112
               K KK    +    +   +         +E +K + +  + +K+       KKA
Sbjct: 492 LARVKAKKAAATQPIVIKAGARPDNSAVIAAREARKAQARARQAEKQAAAAADPKKA 548

Length = 695

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 38.9 bits (90), Expect = 0.001
 Identities = 15/45 (33%), Positives = 35/45 (77%)

Query: 69  QKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAE 113
           +K+EE  +K K E +QK +EE++++K++EK++++++E +  + A+
Sbjct: 579 KKREEAVEKAKREAEQKAREEREREKEKEKEREREREREAERAAK 623

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 38.9 bits (90), Expect = 0.001
 Identities = 15/39 (38%), Positives = 30/39 (76%)

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQ 115
           KK+EE  +K K E +QK +EE++++K+KE+++ ++ E +
Sbjct: 579 KKREEAVEKAKREAEQKAREEREREKEKEKERERERERE 617

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated

 Score = 39.4 bits (93), Expect = 0.001
 Identities = 22/92 (23%), Positives = 44/92 (47%), Gaps = 2/92 (2%)

Query: 23  KEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEK 82
           ++   KK   K  ++ +K      +   E  + KEE   +K E +K++++E+  K+  E 
Sbjct: 136 RDHLKKKHLPKLIKQYEKFGFGILKIDFEIDDSKEE--LEKFEAQKEEEDEKLAKEALEA 193

Query: 83  KQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEE 114
            +K + EKK++ K    ++   +  K    EE
Sbjct: 194 MKKLEAEKKKQSKNFDPKEGPVQIGKKIDKEE 225

Length = 1437

>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated

 Score = 38.7 bits (91), Expect = 0.001
 Identities = 28/99 (28%), Positives = 49/99 (49%), Gaps = 1/99 (1%)

Query: 21  KKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEE-KDKKK 79
           KKK      KQ +K      K + +    KE+ E+ E +KE++ E+  ++  E  K  + 
Sbjct: 140 KKKHLPKLIKQYEKFGFGILKIDFEIDDSKEELEKFEAQKEEEDEKLAKEALEAMKKLEA 199

Query: 80  EEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQ 118
           E+KKQ K  + K+   +  K+  K+E    K+  E+ R+
Sbjct: 200 EKKKQSKNFDPKEGPVQIGKKIDKEEITPMKEINEEERR 238

Length = 1437

>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota)

 Score = 39.3 bits (92), Expect = 0.001
 Identities = 25/91 (27%), Positives = 54/91 (59%)

Query: 31  QKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEK 90
           +K +E+ K  K + K+ KK     E     ++K + K ++  E+ D + +EKK++KK+E+
Sbjct: 280 EKLQEKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKKKEKKKEE 339

Query: 91  KQKKKEEKKQKKKKEEKKNKKAEEQNRQQGL 121
           K+KK+ E+ +++ ++ +     +E+N+   L
Sbjct: 340 KKKKQIERLEERIEKLEVQATDKEENKTVAL 370

DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras. Length = 391

>gnl|CDD|220252 pfam09468, RNase_H2-Ydr279, Ydr279p protein family (RNase H2 complex component)

 Score = 38.5 bits (90), Expect = 0.001
 Identities = 22/76 (28%), Positives = 37/76 (48%)

Query: 29  KKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKE 88
               K+  K     E K   K  K+ +K++++ ++  E  + + E+K K KEE K+KK +
Sbjct: 205 PDLYKELLKSLLIPEFKPLDKYLKESKKKKRETEEDVEAAESRAEKKRKSKEEIKKKKPK 264

Query: 89  EKKQKKKEEKKQKKKK 104
           E K  K  +K   K  
Sbjct: 265 ESKGVKALKKVVAKGM 280

RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organisms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologues of Ydr279p. It is not known whether non yeast proteins in this family fulfil the same function. Length = 287

>gnl|CDD|237258 PRK12903, secA, preprotein translocase subunit SecA; Reviewed

 Score = 39.3 bits (92), Expect = 0.001
 Identities = 28/90 (31%), Positives = 42/90 (46%), Gaps = 4/90 (4%)

Query: 19  KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK 78
           +   +E++N K++ K E  + ++ EE+ Q   E K E  E K   K  K  K    KD  
Sbjct: 837 ELINEEQKNLKQEIKLELSEIQEAEEEIQNINENKNEFVEFKNDPK--KLNKLIIAKD-- 892

Query: 79  KEEKKQKKKEEKKQKKKEEKKQKKKKEEKK 108
              K     +E KQ +K  KK+KK  E+  
Sbjct: 893 VLIKLVISSDEIKQDEKTTKKKKKDLEKTD 922

Length = 925

>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score = 39.3 bits (92), Expect = 0.001
 Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 5/83 (6%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKE-----KKEEKEEKKEKKKEEKKQKK 71
             +   K    K K+    +K  K+++  K+   E     + E+K + K  KK+ +K KK
Sbjct: 730 APRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKAKK 789

Query: 72  EEEKDKKKEEKKQKKKEEKKQKK 94
              K +K     + K+  KK+  
Sbjct: 790 PSAKTQKIAAATKAKRAAKKKVA 812

Length = 813

>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score = 39.0 bits (91), Expect = 0.001
 Identities = 24/85 (28%), Positives = 39/85 (45%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           +R  +   +  ++K KK +  K+  K  +  KK   + +   + EKK + K  KK+  K 
Sbjct: 728 ERAPRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKA 787

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQK 101
           KK   K QK     K K+  +KK  
Sbjct: 788 KKPSAKTQKIAAATKAKRAAKKKVA 812

Length = 813

>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score = 39.0 bits (91), Expect = 0.001
 Identities = 19/80 (23%), Positives = 36/80 (45%)

Query: 27  NKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKK 86
           N  K  +++ KK    ++  ++++  K+   E     + EKK K +  K   ++ KK   
Sbjct: 733 NVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKAKKPSA 792

Query: 87  KEEKKQKKKEEKKQKKKKEE 106
           K +K     + K+  KKK  
Sbjct: 793 KTQKIAAATKAKRAAKKKVA 812

Length = 813

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 39.3 bits (92), Expect = 0.001
 Identities = 18/95 (18%), Positives = 56/95 (58%), Gaps = 3/95 (3%)

Query: 16  GKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKE--- 72
            +R+  +     ++ ++ +EE ++ +++ ++Q  + ++ ++ E  EK + + +Q++    
Sbjct: 618 NERRDTRDNRTRREGRENREENRRNRRQAQQQTAETRESQQAEVTEKARTQDEQQQAPRR 677

Query: 73  EEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEK 107
           E + ++ +EK+Q ++E K    +E+  Q+ ++EE+
Sbjct: 678 ERQRRRNDEKRQAQQEAKALNVEEQSVQETEQEER 712

Length = 1068

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 38.9 bits (91), Expect = 0.001
 Identities = 17/100 (17%), Positives = 58/100 (58%)

Query: 20  KKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKK 79
           + K +E+   K + K E++Q +++ ++  ++++ E ++ +  + + E ++ +EE +  ++
Sbjct: 585 ETKPQEQPAPKAEAKPERQQDRRKPRQNNRRDRNERRDTRDNRTRREGRENREENRRNRR 644

Query: 80  EEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
           + ++Q  +  + Q+ +  +K + + E+++  + E Q R+ 
Sbjct: 645 QAQQQTAETRESQQAEVTEKARTQDEQQQAPRRERQRRRN 684

Length = 1068

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 38.0 bits (89), Expect = 0.002
 Identities = 15/57 (26%), Positives = 32/57 (56%)

Query: 23  KEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKK 79
             E  K ++K+++ +K+ +KEE ++   +KK E   KK K  + + +K + +   +K
Sbjct: 408 PAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPDGETKKVDPDPLGEK 464

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 38.3 bits (90), Expect = 0.002
 Identities = 22/119 (18%), Positives = 48/119 (40%), Gaps = 4/119 (3%)

Query: 14  RIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEK----EEKKEKKKEEKKQ 69
           R+ +  K+      +  +K KE   + K      +++E ++E+     E++ K + E+  
Sbjct: 5   RVYELAKELGVSSKELLEKLKELGIEVKSHSSTVEEEEARKEEAKREAEEEAKAEAEEAA 64

Query: 70  KKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKRT 128
             E E++ K E       EE  +     +   +  E++  + AE   R+       K+ 
Sbjct: 65  AAEAEEEAKAEAAAAAPAEEAAEAAAAAEAAARPAEDEAARPAEAAARRPKAKKAAKKK 123

Length = 746

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 38.6 bits (89), Expect = 0.002
 Identities = 40/124 (32%), Positives = 67/124 (54%), Gaps = 2/124 (1%)

Query: 6    APKGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKK--EKK 63
            A K A   +     KKK EE  K  + KK+ ++ KK EE K+K +E K+  E KK  E+ 
Sbjct: 1423 AKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEA 1482

Query: 64   KEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYP 123
            K+  + KK+ E+ KKK ++ +K  E KK+  + +K ++ KK ++  K  E +   +    
Sbjct: 1483 KKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKA 1542

Query: 124  NQKR 127
             +K+
Sbjct: 1543 EEKK 1546

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 38.6 bits (89), Expect = 0.002
 Identities = 41/103 (39%), Positives = 67/103 (65%), Gaps = 5/103 (4%)

Query: 19   KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKK----EKKKEEKKQKKEEE 74
            +KKK+E + K    KK+ +++KK +E K+K +E K++ +E K     KKK ++ +KK EE
Sbjct: 1370 EKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEE 1429

Query: 75   KDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNR 117
            K KK +E K+K +E KK  + ++K ++ KK E+  KKAEE  +
Sbjct: 1430 K-KKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKK 1471

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 38.6 bits (89), Expect = 0.002
 Identities = 40/120 (33%), Positives = 71/120 (59%), Gaps = 2/120 (1%)

Query: 2    KISIAPKGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKE 61
            K   A K A   +     KKK EE+ KK  + K+    KKK ++ +KK E+K++ +E K+
Sbjct: 1379 KADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKK 1438

Query: 62   KKKEEKK--QKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
            K +E KK  + K++ ++ KK E+ +KK EE K+  + +KK ++ K+  + KK  E+ +++
Sbjct: 1439 KAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKK 1498

Length = 2084

>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 38.7 bits (91), Expect = 0.002
 Identities = 31/99 (31%), Positives = 58/99 (58%), Gaps = 2/99 (2%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           ++K+K +EEE+K  ++ ++E +Q  KE KK+  +  KE ++ +K      K  +  E + 
Sbjct: 555 EKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEADEIIKELRQLQKGGYASVKAHELIEARK 614

Query: 77  K--KKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAE 113
           +  K  EKK+KKK+++K+K++E K   + K     +K E
Sbjct: 615 RLNKANEKKEKKKKKQKEKQEELKVGDEVKYLSLGQKGE 653

Length = 782

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 38.5 bits (90), Expect = 0.002
 Identities = 25/124 (20%), Positives = 50/124 (40%)

Query: 4    SIAPKGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKK 63
              +     + ++ K K KKKE++ KK    K +K       K+    EK++  ++   KK
Sbjct: 1158 LKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKPDNKK 1217

Query: 64   KEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYP 123
                   +E+++++K + KK   K  K +K    K  +   E   +  ++E   +     
Sbjct: 1218 SNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAPKR 1277

Query: 124  NQKR 127
                
Sbjct: 1278 VSAV 1281

Length = 1388

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 37.9 bits (88), Expect = 0.002
 Identities = 23/86 (26%), Positives = 48/86 (55%), Gaps = 3/86 (3%)

Query: 32  KKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKK 91
           K  EE K        ++++  KE  ++ ++  K+  + K E +  ++ E K    KEEK 
Sbjct: 351 KLYEEVKSNTDLSGDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKA---KEEKL 407

Query: 92  QKKKEEKKQKKKKEEKKNKKAEEQNR 117
           ++++ EKKQK++ +E K K+ +++ +
Sbjct: 408 KQEENEKKQKEQADEDKEKRQKDERK 433

Length = 434

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 23/101 (22%), Positives = 50/101 (49%)

Query: 19  KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK 78
           + K+ E+E    Q++K++ ++  K+   ++K+ ++   +     K + + + K      K
Sbjct: 102 RLKQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAK 161

Query: 79  KEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
           K   + KKK E +  KK   + KKK E +   KA  + +++
Sbjct: 162 KAAAEAKKKAEAEAAKKAAAEAKKKAEAEAAAKAAAEAKKK 202

Length = 387

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 25/108 (23%), Positives = 59/108 (54%), Gaps = 2/108 (1%)

Query: 12  SPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKK 71
           + R  +++KKK++++ ++ Q+K+  ++++ K+ +K++   ++++K+ ++  K+   KQK+
Sbjct: 74  AKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALKQKQ 133

Query: 72  EEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
            EE   K     + K E   + K+     KK   E K K   E  ++ 
Sbjct: 134 AEEAAAKAAAAAKAKAEA--EAKRAAAAAKKAAAEAKKKAEAEAAKKA 179

Length = 387

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 29/104 (27%), Positives = 50/104 (48%), Gaps = 1/104 (0%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKK-EEKKQKKEEEK 75
           ++KK+ +E   +   K+K+ ++   K     K K + E K      KK   + +KK E +
Sbjct: 115 EQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAE 174

Query: 76  DKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
             KK   + KKK E +   K   + KKK E +  KKA  + +++
Sbjct: 175 AAKKAAAEAKKKAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKK 218

Length = 387

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 28/98 (28%), Positives = 44/98 (44%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           K+   K+++  +   K     K K + E K+     K+   E K+K + E  +K   E  
Sbjct: 125 KQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAEAAKKAAAEAK 184

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEE 114
           KK E +   K   + +KK E + +KK   E K K A E
Sbjct: 185 KKAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKKAAAE 222

Length = 387

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 20/99 (20%), Positives = 53/99 (53%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           +++ ++ +++   +Q++ ++ ++++   ++QKK+ ++  K+   ++K+ E+   K     
Sbjct: 86  QQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAA 145

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQ 115
           K K E + K+     +K   E K+K + E  K   AE +
Sbjct: 146 KAKAEAEAKRAAAAAKKAAAEAKKKAEAEAAKKAAAEAK 184

Length = 387

>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 17/84 (20%), Positives = 35/84 (41%)

Query: 21  KKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKE 80
              EE   + +  +E+ K   + E   +    K +++ K EKK ++ K K + +   K +
Sbjct: 51  APTEEPQPEPEPPEEQPKPPTEPETPPEPTPPKPKEKPKPEKKPKKPKPKPKPKPKPKPK 110

Query: 81  EKKQKKKEEKKQKKKEEKKQKKKK 104
            K Q K ++   K   +      +
Sbjct: 111 VKPQPKPKKPPSKTAAKAPAAPNQ 134

Length = 244

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 38.1 bits (88), Expect = 0.002
 Identities = 15/62 (24%), Positives = 42/62 (67%)

Query: 64  KEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYP 123
           K  KK+++  EK K++ E+K +++ E++++K++E+++++++E ++  KA   + +  +  
Sbjct: 576 KLAKKREEAVEKAKREAEQKAREEREREKEKEKEREREREREAERAAKASSSSHESRMSE 635

Query: 124 NQ 125
            Q
Sbjct: 636 PQ 637

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 38.1 bits (88), Expect = 0.002
 Identities = 19/51 (37%), Positives = 35/51 (68%), Gaps = 3/51 (5%)

Query: 15  IGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKE 65
           +   K  KK EE  +K K+  E +QK +EE ++++KEK++E+E ++E++ E
Sbjct: 572 LASSKLAKKREEAVEKAKR--EAEQKAREE-REREKEKEKEREREREREAE 619

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score = 38.6 bits (90), Expect = 0.002
 Identities = 22/76 (28%), Positives = 36/76 (47%)

Query: 33  KKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQ 92
           K   +K KK +  K+  K ++  K+   E     + +KK + K  KK+ +K KK   K Q
Sbjct: 736 KTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKAKKPSAKTQ 795

Query: 93  KKKEEKKQKKKKEEKK 108
           K     K K+  ++K 
Sbjct: 796 KIAAATKAKRAAKKKV 811

Length = 813

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 38.4 bits (90), Expect = 0.002
 Identities = 21/51 (41%), Positives = 38/51 (74%)

Query: 61  EKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKK 111
           ++ KEE  ++ EE K+K  +  K+K++E+K QK+K++KK+KKK +++K K 
Sbjct: 362 DELKEELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKG 412

Length = 414

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 24/64 (37%), Positives = 45/64 (70%)

Query: 49  KKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKK 108
           K+ +KE  +E++E++KEEKK+++E+  DK++E  ++++KEEKK+K K+ K+   + E   
Sbjct: 29  KEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWELLN 88

Query: 109 NKKA 112
             K 
Sbjct: 89  KTKP 92

Length = 529

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 38.5 bits (90), Expect = 0.002
 Identities = 20/102 (19%), Positives = 57/102 (55%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           + ++ +KE E  K + ++  ++ ++ +E+  + KE+ EE E +    +E  ++ + E ++
Sbjct: 261 ELEEAEKEIEELKSELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEE 320

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQ 118
            ++  ++ K+K E  +++ EE++   ++ E+   + EE   +
Sbjct: 321 LEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEE 362

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 38.5 bits (90), Expect = 0.002
 Identities = 18/104 (17%), Positives = 51/104 (49%)

Query: 18  RKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDK 77
             +++  E  ++ ++ + E    ++  ++ + + ++ E+  ++ K+K E  +++ EE++ 
Sbjct: 285 ELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERET 344

Query: 78  KKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGL 121
             EE +Q   E ++ K++ E+K     EE +      +     L
Sbjct: 345 LLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREELAEL 388

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 21/97 (21%), Positives = 56/97 (57%)

Query: 19  KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK 78
           + +++ EE +++  + +E+ ++ + E    ++  +E + E +E ++  ++ K++ E  K+
Sbjct: 278 ELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKE 337

Query: 79  KEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQ 115
           + E+++   EE +Q   E ++ K++ EEK +   EE 
Sbjct: 338 ELEERETLLEELEQLLAELEEAKEELEEKLSALLEEL 374

Length = 1163

>gnl|CDD|129022 smart00786, SHR3_chaperone, ER membrane protein SH3

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 11/39 (28%), Positives = 23/39 (58%)

Query: 55  EKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQK 93
           E+++ K+K++   +++KE      K+    +K E KK+K
Sbjct: 158 ERKDAKQKEEFAAEERKEALAAAAKKSATPQKVETKKKK 196

This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs). Shr3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of Shr3, AAPs are retained in the ER. Length = 196

>gnl|CDD|235322 PRK04950, PRK04950, ProP expression regulator; Provisional

 Score = 37.6 bits (88), Expect = 0.002
 Identities = 12/58 (20%), Positives = 34/58 (58%)

Query: 53  KEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNK 110
           +E K + + ++ E++ +K+E   +K+K  ++++K + K  +KK + + +K + +    
Sbjct: 104 EEAKAKVQAQRAEQQAKKREAAGEKEKAPRRERKPKPKAPRKKRKPRAQKPEPQHTPV 161

Length = 213

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 37.5 bits (88), Expect = 0.003
 Identities = 29/113 (25%), Positives = 67/113 (59%), Gaps = 16/113 (14%)

Query: 18  RKKKKKEEENKKKQK----KKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEE 73
           R+ + ++ E +  QK     ++ +  +K+EE+ +KK+++ E+K+++ EKK+EE ++  EE
Sbjct: 80  RRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEE 139

Query: 74  EKDK-------KKEEKKQKKKEEKKQKKKEE-----KKQKKKKEEKKNKKAEE 114
           +  +         EE K+   E+ +++ + E     K+ +++ +E+ +KKA+E
Sbjct: 140 QLQELERISGLTAEEAKEILLEKVEEEARHEAAVLIKEIEEEAKEEADKKAKE 192

Length = 520

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 37.9 bits (88), Expect = 0.003
 Identities = 14/94 (14%), Positives = 37/94 (39%), Gaps = 1/94 (1%)

Query: 34  KEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQK 93
           K+ +  +K E K  +KKE  +++   + +   E +Q++     + +  +   K ++K   
Sbjct: 333 KKTRTAEKNEAK-ARKKEIAQKRRAAEREINREARQERAAAMARARARRAAVKAKKKGLI 391

Query: 94  KKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKR 127
                +    + E+      +        PN++ 
Sbjct: 392 DASPNEDTPSENEESKGSPPQVEATTTAEPNREP 425

Length = 429

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 37.5 bits (87), Expect = 0.003
 Identities = 17/94 (18%), Positives = 37/94 (39%), Gaps = 1/94 (1%)

Query: 8   KGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEK 67
           K   +    + K +KKE   K++  ++E  ++  ++E+       +  +   K KKK   
Sbjct: 333 KKTRTAEKNEAKARKKEIAQKRRAAEREINRE-ARQERAAAMARARARRAAVKAKKKGLI 391

Query: 68  KQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQK 101
                E+   + EE K    + +     E  ++ 
Sbjct: 392 DASPNEDTPSENEESKGSPPQVEATTTAEPNREP 425

Length = 429

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 37.5 bits (87), Expect = 0.003
 Identities = 24/140 (17%), Positives = 56/140 (40%), Gaps = 15/140 (10%)

Query: 18  RKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEK----------EEKKEKKKEEK 67
            +K    +E K+   ++  + ++K++EKK      +  +           E   +  E K
Sbjct: 274 ERKYPLTDEFKEHHAEQRAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAENAEIK 333

Query: 68  KQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKR 127
           K +  E     K E K +KKE  ++++  E++  ++  +++         ++     +K+
Sbjct: 334 KTRTAE-----KNEAKARKKEIAQKRRAAEREINREARQERAAAMARARARRAAVKAKKK 388

Query: 128 TLIGYLRSVDQFANLVLHKT 147
            LI    + D  +     K 
Sbjct: 389 GLIDASPNEDTPSENEESKG 408

Length = 429

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 37.8 bits (87), Expect = 0.003
 Identities = 37/110 (33%), Positives = 70/110 (63%), Gaps = 2/110 (1%)

Query: 14   RIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEE 73
            +  + +KKK E+  KK+ ++K++ ++ KK E++ K K  +E K+ +++KKK E+ +K EE
Sbjct: 1626 KKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEE 1685

Query: 74   EKDKKKEEKKQKKKEEKK--QKKKEEKKQKKKKEEKKNKKAEEQNRQQGL 121
            ++ K  E  K++ +E KK  + KK+E ++KKK EE K  + E + + +  
Sbjct: 1686 DEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEA 1735

Length = 2084

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 37.7 bits (88), Expect = 0.003
 Identities = 18/105 (17%), Positives = 37/105 (35%), Gaps = 2/105 (1%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           K+K  ++ ++         +      E    KKK K   K      K   KK+ K+E   
Sbjct: 45  KKKTPEQIDQVLIFLSGMVKDTDDATESDIPKKKTKTAAK--AAAAKAPAKKKLKDELDS 102

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGL 121
            KK EKK    ++      ++     + ++  +   ++      +
Sbjct: 103 SKKAEKKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDDLDDDDI 147

Length = 509

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 37.7 bits (88), Expect = 0.003
 Identities = 20/93 (21%), Positives = 33/93 (35%)

Query: 20  KKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKK 79
                +     +++ ++K +K   + K K    KEE +E  E KK+  +Q  +       
Sbjct: 2   TTASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSG 61

Query: 80  EEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKA 112
             K      E    KK+ K   K    K   K 
Sbjct: 62  MVKDTDDATESDIPKKKTKTAAKAAAAKAPAKK 94

Length = 509

>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal

 Score = 36.4 bits (85), Expect = 0.003
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 4/68 (5%)

Query: 46  KQKKKEKKEEKEEKK--EKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKK 103
            QKKK KK E E     E+ K+ K+  +    DKK  E K  +K EKK +K + K +KKK
Sbjct: 32  AQKKKGKKGELEITDLNEEYKDLKESLEAALLDKK--ELKAWEKAEKKAEKAKAKAEKKK 89

Query: 104 KEEKKNKK 111
            ++++ K 
Sbjct: 90  AKKEEPKP 97

This domain is found to the N-terminus of bacterial signal peptidases of the S49 family (pfam01343). Length = 154

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 38.1 bits (88), Expect = 0.003
 Identities = 20/111 (18%), Positives = 51/111 (45%), Gaps = 9/111 (8%)

Query: 19  KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKE---------EKKQ 69
           K    E E+  ++  +E ++  + E +  ++   + E+E + E K E         E+K 
Sbjct: 632 KGDVAEAEHTGERTGEEGERPTEAEGENGEESGGEAEQEGETETKGENESEGEIPAERKG 691

Query: 70  KKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQG 120
           ++E E + + +E   K + E ++ + E + + +  E++   +  E+  +  
Sbjct: 692 EQEGEGEIEAKEADHKGETEAEEVEHEGETEAEGTEDEGEIETGEEGEEVE 742

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 37.7 bits (88), Expect = 0.003
 Identities = 14/71 (19%), Positives = 38/71 (53%)

Query: 34  KEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQK 93
           K+ K+  + EE++++   + E   E K  K+E++   +E+     +E++   K E+  + 
Sbjct: 224 KKLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKL 283

Query: 94  KKEEKKQKKKK 104
           +  ++K+ ++ 
Sbjct: 284 EILKEKKDEEL 294

The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832

>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota)

 Score = 37.7 bits (88), Expect = 0.003
 Identities = 26/84 (30%), Positives = 47/84 (55%), Gaps = 2/84 (2%)

Query: 19  KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK 78
           +K K  +   K+ KK     +   + K++ K + + + E+   + KE+KK+KK+EEK KK
Sbjct: 284 EKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKKKEKKKEEKKKK 343

Query: 79  KEEK--KQKKKEEKKQKKKEEKKQ 100
           + E+  ++ +K E +   KEE K 
Sbjct: 344 QIERLEERIEKLEVQATDKEENKT 367

DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras. Length = 391

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 37.0 bits (86), Expect = 0.003
 Identities = 20/90 (22%), Positives = 46/90 (51%)

Query: 27  NKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKK 86
                 +    +Q+ K+   Q+  E +E KEE+KE    E K+ K + + + +E +++ +
Sbjct: 37  PSSPSDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENE 96

Query: 87  KEEKKQKKKEEKKQKKKKEEKKNKKAEEQN 116
           +E+++   + EK+ ++K E    K+    +
Sbjct: 97  EEDEESSDENEKETEEKTESNVEKEITNPS 126

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional

 Score = 37.8 bits (88), Expect = 0.003
 Identities = 26/144 (18%), Positives = 73/144 (50%), Gaps = 10/144 (6%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           K++++  +E  +  Q+ ++E ++K +    + K+    E+ +++++ + E+++ + EE+ 
Sbjct: 26  KKRQRLAKEAERILQEAQKEAEEKLEAALLEAKELLLRERNQQRQEARREREELQREEER 85

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQ--------QGLYPNQKRT 128
             ++E++   + EK    + + ++++K    +  + EE  +Q         GL P Q R 
Sbjct: 86  LVQKEEQLDARAEKLDNLENQLEEREKALSARELELEELEKQLDNELYRVAGLTPEQARK 145

Query: 129 LIGYLRSVDQFANLVLHKTIERIH 152
           L+  L+ +D        + +++I 
Sbjct: 146 LL--LKLLDAELEEEKAQRVKKIE 167

Length = 508

>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein

 Score = 37.9 bits (88), Expect = 0.003
 Identities = 25/101 (24%), Positives = 59/101 (58%)

Query: 19  KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK 78
            +K+ E++N+  +K  +E+++ KKE +++ ++ K+ E+ +K E +KE ++  K  +K+ +
Sbjct: 523 LEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKERERNKKLELEKEAQEALKALKKEVE 582

Query: 79  KEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
              ++ K+K+  K K+ +  +   K +E K K  ++    Q
Sbjct: 583 SIIRELKEKKIHKAKEIKSIEDLVKLKETKQKIPQKPTNFQ 623

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function [DNA metabolism, Other]. Length = 771

>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein

 Score = 37.5 bits (87), Expect = 0.003
 Identities = 26/94 (27%), Positives = 55/94 (58%)

Query: 23  KEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEK 82
           K    +K+ ++K E  +K  +E+++ KKE ++E EE KE+++ +K + ++E ++  K  K
Sbjct: 519 KLSALEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKERERNKKLELEKEAQEALKALK 578

Query: 83  KQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQN 116
           K+ +   ++ K+K+  K K+ K  +   K +E  
Sbjct: 579 KEVESIIRELKEKKIHKAKEIKSIEDLVKLKETK 612

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function [DNA metabolism, Other]. Length = 771

>gnl|CDD|236267 PRK08451, PRK08451, DNA polymerase III subunits gamma and tau; Validated

 Score = 37.7 bits (88), Expect = 0.003
 Identities = 16/81 (19%), Positives = 38/81 (46%)

Query: 14  RIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEE 73
           +I K  K  +      K+ K   +K+K   E   +  E++ +K++++ ++ + K+  + +
Sbjct: 451 KIQKALKSAENPLQSLKEFKPSNEKKKIDTESTAEMLEEEAKKDDEEVQETQLKEATELQ 510

Query: 74  EKDKKKEEKKQKKKEEKKQKK 94
           E     E+  ++ KE    K 
Sbjct: 511 EFMINNEDLIEEAKELFGIKS 531

Length = 535

>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional

 Score = 37.4 bits (87), Expect = 0.004
 Identities = 19/72 (26%), Positives = 41/72 (56%)

Query: 46  KQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKE 105
           +  + E K++K++ K+K  ++K +K +++ D       +   E ++ + K+  K+KKKK+
Sbjct: 4   ENGENEVKQQKQQNKQKGTKKKNKKSKKDVDDDDAFLAELISENQEAENKQNNKKKKKKK 63

Query: 106 EKKNKKAEEQNR 117
           +KK KK   +  
Sbjct: 64  KKKKKKNLGEAY 75

Length = 470

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 37.1 bits (86), Expect = 0.004
 Identities = 31/116 (26%), Positives = 49/116 (42%)

Query: 6   APKGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKE 65
             K A   +     + +K+ + + K++ +EE K K   E K+K  E K++ E + + K E
Sbjct: 125 KAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAKAE 184

Query: 66  EKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGL 121
            K + K EE   K E  K K   E   K + E       E ++     E     GL
Sbjct: 185 AKAKAKAEEAKAKAEAAKAKAAAEAAAKAEAEAAAAAAAEAERKADEAELGDIFGL 240

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 37.1 bits (86), Expect = 0.004
 Identities = 29/98 (29%), Positives = 54/98 (55%), Gaps = 2/98 (2%)

Query: 18  RKKKKKEEENKKKQKKKEEKKQKKKEEK--KQKKKEKKEEKEEKKEKKKEEKKQKKEEEK 75
            K+ +++++  ++ K K+  + K K E   ++K KE+ +++ E++ K K   + KK+  +
Sbjct: 111 AKQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAE 170

Query: 76  DKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAE 113
            KKK E + K K E K K K E+ + K +  K    AE
Sbjct: 171 AKKKAEAEAKAKAEAKAKAKAEEAKAKAEAAKAKAAAE 208

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family

 Score = 37.3 bits (87), Expect = 0.004
 Identities = 14/96 (14%), Positives = 43/96 (44%), Gaps = 2/96 (2%)

Query: 20  KKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKK 79
           K+ +E   +  ++ ++  + +K  E +++K E    KEE  +   E  + ++  ++ + K
Sbjct: 2   KELREALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAK 61

Query: 80  EEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQ 115
                  +    ++++EE K +  +     +  ++ 
Sbjct: 62  PAA--SGEGGGGEEEEEEAKAEAAEFRAYLRGGDDA 95

This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease [Mobile and extrachromosomal element functions, Prophage functions]. Length = 384

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 37.3 bits (87), Expect = 0.004
 Identities = 19/65 (29%), Positives = 34/65 (52%)

Query: 18  RKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDK 77
            + +++EEE   + +   E K  K+E++   +++     EEK++  K E   K E  K+K
Sbjct: 230 SETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKLEILKEK 289

Query: 78  KKEEK 82
           K EE 
Sbjct: 290 KDEEL 294

The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832

>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]

 Score = 37.1 bits (86), Expect = 0.004
 Identities = 19/78 (24%), Positives = 35/78 (44%)

Query: 38  KQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEE 97
              K  E   ++ + + E  E++ K   E +   E    K KE+ K +KK +K + K + 
Sbjct: 44  LAAKVLEAPTEEPQPEPEPPEEQPKPPTEPETPPEPTPPKPKEKPKPEKKPKKPKPKPKP 103

Query: 98  KKQKKKKEEKKNKKAEEQ 115
           K + K K + + K  +  
Sbjct: 104 KPKPKPKVKPQPKPKKPP 121

Length = 244

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 37.4 bits (86), Expect = 0.004
 Identities = 17/50 (34%), Positives = 35/50 (70%), Gaps = 2/50 (4%)

Query: 37  KKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKK 86
           K  KK+EE  +K K + E+K   +E+++ EK+++KE E+++++E ++  K
Sbjct: 576 KLAKKREEAVEKAKREAEQK--AREEREREKEKEKEREREREREAERAAK 623

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 37.1 bits (86), Expect = 0.004
 Identities = 25/56 (44%), Positives = 41/56 (73%)

Query: 51  EKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEE 106
           EK+ EKE   E+++EEK++KKEEE+    +E++  ++EEK++KKK+ KK K+   E
Sbjct: 28  EKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTE 83

Length = 529

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 36.6 bits (85), Expect = 0.004
 Identities = 19/82 (23%), Positives = 46/82 (56%)

Query: 16  GKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEK 75
              +    E+E KK   ++  + ++ KEE+K+    + +E +   EK+ EE +++ EEE 
Sbjct: 40  PSDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEED 99

Query: 76  DKKKEEKKQKKKEEKKQKKKEE 97
           ++  +E +++ +E+ +   ++E
Sbjct: 100 EESSDENEKETEEKTESNVEKE 121

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter subunit G; Reviewed

 Score = 37.0 bits (85), Expect = 0.004
 Identities = 23/87 (26%), Positives = 56/87 (64%), Gaps = 1/87 (1%)

Query: 29  KKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKE-KKKEEKKQKKEEEKDKKKEEKKQKKK 87
           KK   K++K    ++E+ +K ++++EE EE+ E +++EEK  ++E+++++++E ++Q  +
Sbjct: 111 KKDDIKKKKSLIIRQEQIEKARQEREELEERMEWERREEKIDEREDQEEQEREREEQTIE 170

Query: 88  EEKKQKKKEEKKQKKKKEEKKNKKAEE 114
           E+    + E  +Q + + E  + K E+
Sbjct: 171 EQSDDSEHEIIEQDESETESDDDKTEK 197

Length = 197

>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division and chromosome partitioning]

 Score = 37.4 bits (87), Expect = 0.004
 Identities = 13/96 (13%), Positives = 36/96 (37%)

Query: 19  KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK 78
              + E   ++ +      +Q+ ++ K  +  E++++   +   +    ++K EE +  +
Sbjct: 174 AAVRAEIAAEQAELTTLLSEQRAQQAKLAQLLEERKKTLAQLNSELSADQKKLEELRANE 233

Query: 79  KEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEE 114
              K +    E    K  E     +    + + AE 
Sbjct: 234 SRLKNEIASAEAAAAKAREAAAAAEAAAARARAAEA 269

Length = 420

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 37.2 bits (86), Expect = 0.004
 Identities = 30/111 (27%), Positives = 42/111 (37%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
             KK  K++  K     K+  K   K  KK KK  KK  K+  K  KK  KK  K   K 
Sbjct: 222 AAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKTAKKALKKAAKAVKKAAKKAAKAAAKA 281

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKR 127
            K   K  K K + K+K  ++     K +            ++     +KR
Sbjct: 282 AKGAAKATKGKAKAKKKAGKKAAAGSKAKATAKAPKRGAKGKKAKKVTKKR 332

Length = 333

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 37.2 bits (86), Expect = 0.004
 Identities = 31/111 (27%), Positives = 42/111 (37%)

Query: 2   KISIAPKGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKE 61
           K   A K     +  K     K+      +  K+ KK  KK  KK  K  KK  K+  K 
Sbjct: 218 KAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKTAKKALKKAAKAVKKAAKKAAKA 277

Query: 62  KKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKA 112
             K  K   K  +   K ++K  KK     + K   K  K+  + KK KK 
Sbjct: 278 AAKAAKGAAKATKGKAKAKKKAGKKAAAGSKAKATAKAPKRGAKGKKAKKV 328

Length = 333

>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR)

 Score = 37.4 bits (86), Expect = 0.004
 Identities = 33/122 (27%), Positives = 59/122 (48%), Gaps = 5/122 (4%)

Query: 4   SIAPKGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKK 63
           S +P+    P + K+ KK K++E K+K+K++++ K+K+ E  K       +         
Sbjct: 184 SKSPEKGDVPAVEKKSKKPKKKEKKEKEKERDKDKKKEVEGFKSLLLALDDSPASAASVA 243

Query: 64  KEEKKQ-----KKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQ 118
           + ++              +  E K  + +E KK  K ++KKQ+K+KEEKK KK    +R 
Sbjct: 244 EADEASLANTVSGTAPDSEPDEPKDAEAEETKKSPKHKKKKQRKEKEEKKKKKKHHHHRC 303

Query: 119 QG 120
             
Sbjct: 304 HH 305

This family consists of several bovine specific leukaemia virus receptors which are thought to function as transmembrane proteins, although their exact function is unknown. Length = 561

>gnl|CDD|149343 pfam08229, SHR3_chaperone, ER membrane protein SH3

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 12/39 (30%), Positives = 21/39 (53%)

Query: 66  EKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKK 104
           E K  K  E+   +E +     +E++  + E+K+ KKKK
Sbjct: 158 EWKDAKLLEEFAAEEAEAAAAAKEEESAEGEKKESKKKK 196

This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs). SH3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of SH3, AAPs are retained in the ER. Length = 196

>gnl|CDD|227657 COG5354, COG5354, Uncharacterized protein, contains Trp-Asp (WD) repeat [General function prediction only]

 Score = 37.2 bits (86), Expect = 0.004
 Identities = 21/96 (21%), Positives = 37/96 (38%), Gaps = 2/96 (2%)

Query: 15  IGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQK--KKEKKEEKEEKKEKKKEEKKQKKE 72
           I   KK  K   ++    +K    +     +     KKE  E+  E  ++ K     KK 
Sbjct: 462 IESAKKYVKPSRHRFVPFEKAVIMEADSANRSSAPRKKELVEQWPEYSDEDKIRSLLKKL 521

Query: 73  EEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKK 108
              +  KE  +  ++ E  Q  K E +++   E K+
Sbjct: 522 RAIEALKERMRSGEELEVIQVNKIETEEEVLSELKE 557

Length = 561

>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein

 Score = 37.3 bits (87), Expect = 0.004
 Identities = 27/113 (23%), Positives = 63/113 (55%), Gaps = 6/113 (5%)

Query: 10  AISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQ 69
            +S ++ + K +++EE  +  ++K+EE   K +EE   + + K+   E++   + E +K+
Sbjct: 174 QLSKKLAELKAEEEEELERALKEKREELLSKLEEELLARLESKEAALEKQLRLEFEREKE 233

Query: 70  KKEEEKDKKKEEKKQKKKEEKKQKKKEE------KKQKKKKEEKKNKKAEEQN 116
           +  ++ ++K  ++ +++ E  +QK K E      + Q++  +E K K  EE+N
Sbjct: 234 ELRKKYEEKLRQELERQAEAHEQKLKNELALQAIELQREFNKEIKEKVEEERN 286

Mitofilin controls mitochondrial cristae morphology. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex. The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence rich in positive-charged and hydroxylated residues and a membrane anchor domain. In addition, it has three centrally located coiled coil domains. Length = 493

>gnl|CDD|220684 pfam10310, DUF2413, Protein of unknown function (DUF2413)

 Score = 37.1 bits (86), Expect = 0.004
 Identities = 18/100 (18%), Positives = 40/100 (40%), Gaps = 3/100 (3%)

Query: 19  KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK 78
            KK K+ +  K   + +E   +  +E +Q +K K  +K ++  +    +  KK     K 
Sbjct: 15  TKKPKKGDASKDSTEDDEDILEFLDELEQSEKAKPPKKPKEASRPGTPRNPKK---SSKP 71

Query: 79  KEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQ 118
            E      +E+  + +K  +  +    + K    E +  +
Sbjct: 72  TESSAASSEEKPAKPRKSAESTRSSHPKSKAPSTESEEEE 111

This is a family of proteins conserved in fungi. The function is not known. Length = 436

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	213
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.88
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.87
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.87
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.84
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.83
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.81
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.8
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.8
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.8
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.8
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.79
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.78
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.77
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.74
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.74
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.72
KOG1780|consensus	77		99.72
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.71
KOG1782|consensus	129		99.68
KOG1784|consensus	96		99.68
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.67
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.67
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.66
KOG1781|consensus	108		99.64
KOG3482|consensus	79		99.62
KOG3460|consensus	91		99.52
KOG3168|consensus	177		99.46
KOG1783|consensus	77		99.44
KOG1775|consensus	84		99.4
KOG3293|consensus	134		99.15
KOG1774|consensus	88		99.09
KOG3448|consensus	96		98.88
KOG3428|consensus	109		98.58
KOG3172|consensus	119		98.55
KOG3459|consensus	114		98.02
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	97.84
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	97.44
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	96.87
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	96.47
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	96.29
PF11600	216	CAF-1_p150: Chromatin assembly factor 1 complex p1	96.05
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	95.84
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	95.05
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	94.81
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	94.52
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	94.35
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	93.93
PRK14638	150	hypothetical protein; Provisional	92.68
COG1923	77	Hfq Uncharacterized host factor I protein [General	91.76
PRK14639	140	hypothetical protein; Provisional	91.69
PRK02001	152	hypothetical protein; Validated	90.66
TIGR02794	346	tolA_full TolA protein. TolA couples the inner mem	89.37
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	89.32
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	88.96
PRK14091	165	RNA-binding protein Hfq; Provisional	88.87
PRK14644	136	hypothetical protein; Provisional	88.46
PRK14091	165	RNA-binding protein Hfq; Provisional	88.24
PRK14640	152	hypothetical protein; Provisional	87.88
PRK14633	150	hypothetical protein; Provisional	87.57
PF11600	216	CAF-1_p150: Chromatin assembly factor 1 complex p1	86.99
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	86.5
PRK06955	300	biotin--protein ligase; Provisional	86.23
PRK14636	176	hypothetical protein; Provisional	86.09
PRK14642	197	hypothetical protein; Provisional	85.49
PRK14632	172	hypothetical protein; Provisional	85.06
PF03614	165	Flag1_repress: Repressor of phase-1 flagellin; Int	84.79
PRK14645	154	hypothetical protein; Provisional	84.62
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	84.5
TIGR00121	237	birA_ligase birA, biotin-[acetyl-CoA-carboxylase]	84.15
PRK14647	159	hypothetical protein; Provisional	83.0
PRK14634	155	hypothetical protein; Provisional	82.34
PRK00092	154	ribosome maturation protein RimP; Reviewed	82.07
PRK14646	155	hypothetical protein; Provisional	82.06
KOG2412|consensus	591		81.86
PRK08330	236	biotin--protein ligase; Provisional	81.3
PRK14643	164	hypothetical protein; Provisional	80.89
COG0340	238	BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenz	80.87
COG0779	153	Uncharacterized protein conserved in bacteria [Fun	80.64
PRK14631	174	hypothetical protein; Provisional	80.2

>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=99.88  E-value=1.5e-22  Score=151.38  Aligned_cols=74  Identities=26%  Similarity=0.326  Sum_probs=65.1

Q ss_pred             HHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC-c----cceeccceeeeecCcEEEEEeec
Q psy5557         106 EKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN-Q----YGDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       106 E~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n-~----~~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      |....|.+++|++|+|.|+|||.|.|+|+|||+||||||++|+|+++.++ .    ...+.+|+++|||+||++|+++|
T Consensus         2 ~~~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~   80 (81)
T cd01729           2 ESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD   80 (81)
T ss_pred             cchhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence            45677999999999999999999999999999999999999999986432 1    13567999999999999999775

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.

>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=99.87  E-value=5.9e-22  Score=146.58  Aligned_cols=71  Identities=58%  Similarity=0.949  Sum_probs=64.7

Q ss_pred             HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEee
Q psy5557         108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV  178 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~i  178 (213)
                      ...|.+++|++|+|.|+||+.|.|+|.|||+||||+|+||+|+++.++.+..+++|+++||||||++|+.+
T Consensus         4 ~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~~   74 (74)
T cd01728           4 TASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGEI   74 (74)
T ss_pred             hHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEcC
Confidence            56799999999999999999999999999999999999999998765545578899999999999999863

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.

>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=99.87  E-value=6.5e-22  Score=144.85  Aligned_cols=72  Identities=26%  Similarity=0.504  Sum_probs=64.1

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecC-CccceeccceeeeecCcEEEEEeecc
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVG-NQYGDIPRGIFIIRGENVVLMGEVVT  180 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~-n~~~er~LGlVlIRGnnIV~I~~iD~  180 (213)
                      ..|..|+|++|+|+|+||+.|.|+|.|||+||||||++|+|++... ..+..+.+|+++|||+||++|+++|.
T Consensus         2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d~   74 (74)
T cd01727           2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEIDE   74 (74)
T ss_pred             hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccCC
Confidence            4689999999999999999999999999999999999999987543 23346689999999999999999874

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.

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

Probab=99.85  E-value=2.2e-21  Score=142.24  Aligned_cols=69  Identities=28%  Similarity=0.454  Sum_probs=62.5

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeecc
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVT  180 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~  180 (213)
                      .+|.+++|++|+|.|+||+.|.|+|.|||+||||+|+||.|++. ++  ..+.+|.++|||+||++|+++|.
T Consensus         3 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~-~~--~~~~lg~v~IRG~~I~~i~~~~~   71 (72)
T cd01719           3 PELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNS-GG--EKNNIGMVVIRGNSIVMLEALER   71 (72)
T ss_pred             hhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEcc-CC--ceeEeceEEECCCEEEEEEcccc
Confidence            57999999999999999999999999999999999999999863 22  25678999999999999999874

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.

>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=99.85  E-value=3.8e-21  Score=142.73  Aligned_cols=71  Identities=13%  Similarity=0.156  Sum_probs=62.9

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE  177 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~  177 (213)
                      +.+.|..++|++|+|.|+||+.|.|+|.|||+||||||+||.|++...+....+.+|.+|||||||++|++
T Consensus         4 P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p   74 (76)
T cd01732           4 PLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVP   74 (76)
T ss_pred             hHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEEC
Confidence            46789999999999999999999999999999999999999999854432235679999999999999986

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.

>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=99.85  E-value=3.4e-21  Score=142.39  Aligned_cols=68  Identities=26%  Similarity=0.335  Sum_probs=60.8

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC-------ccceeccceeeeecCcEEEEE
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN-------QYGDIPRGIFIIRGENVVLMG  176 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n-------~~~er~LGlVlIRGnnIV~I~  176 (213)
                      +.|..|+|++|+|.|+|||.|.|+|.|||+||||||+||.|+++...       ....+++|++||||+||++|+
T Consensus         3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~   77 (79)
T cd01717           3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMT   77 (79)
T ss_pred             chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEE
Confidence            67999999999999999999999999999999999999999875432       123578999999999999997

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.

>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=99.85  E-value=3.4e-21  Score=143.64  Aligned_cols=72  Identities=21%  Similarity=0.250  Sum_probs=62.5

Q ss_pred             HHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC----------ccceeccceeeeecCcEEEE
Q psy5557         106 EKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN----------QYGDIPRGIFIIRGENVVLM  175 (213)
Q Consensus       106 E~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n----------~~~er~LGlVlIRGnnIV~I  175 (213)
                      ++...|..+++++|+|.|+|||.|.|+|.|||+||||||+||.|+++...          ....+.+|++||||+||++|
T Consensus         1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i   80 (82)
T cd01730           1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILV   80 (82)
T ss_pred             CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEE
Confidence            35678899999999999999999999999999999999999999985421          11256899999999999999


Q ss_pred             Ee
Q psy5557         176 GE  177 (213)
Q Consensus       176 ~~  177 (213)
                      ++
T Consensus        81 ~~   82 (82)
T cd01730          81 SP   82 (82)
T ss_pred             CC
Confidence            74

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

>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=99.84  E-value=6.2e-21  Score=137.10  Aligned_cols=67  Identities=25%  Similarity=0.261  Sum_probs=60.8

Q ss_pred             HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557         108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE  177 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~  177 (213)
                      ...|..++|++|+|.|+||+.|.|+|.|||+||||+|+||+|++..+   ..+.+|.++|||+||++|++
T Consensus         2 ~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~---~~~~lg~~~iRG~~I~~i~~   68 (68)
T cd01731           2 LDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGE---PVRKYGRVVIRGDNVLFISP   68 (68)
T ss_pred             hHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCC---eEeEcCcEEEeCCEEEEEcC
Confidence            57899999999999999999999999999999999999999986533   25679999999999999974

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

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.83  E-value=2.3e-20  Score=136.19  Aligned_cols=69  Identities=26%  Similarity=0.252  Sum_probs=61.2

Q ss_pred             HHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557         106 EKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE  177 (213)
Q Consensus       106 E~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~  177 (213)
                      -+...|..++|++|.|.|+||+.|.|+|.|||+||||+|+||.|++. +.  ..+.+|.++|||+||++|++
T Consensus         4 ~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~-~~--~~~~lg~v~iRG~~V~~i~~   72 (72)
T PRK00737          4 RPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQD-GE--VVRKLGKVVIRGDNVVYVSP   72 (72)
T ss_pred             chHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcC-CC--eEeEcCcEEEeCCEEEEEcC
Confidence            36789999999999999999999999999999999999999999753 22  24679999999999999964

>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=99.81  E-value=1.2e-19  Score=134.57  Aligned_cols=69  Identities=20%  Similarity=0.247  Sum_probs=61.8

Q ss_pred             HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC---ccceeccceeeeecCcEEEEE
Q psy5557         108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN---QYGDIPRGIFIIRGENVVLMG  176 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n---~~~er~LGlVlIRGnnIV~I~  176 (213)
                      .+.|..|||++|+|.|+|||.|.|+|.|||+||||||+||.|++....   ....+.+|+++|||++|++|.
T Consensus         2 ~~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~   73 (75)
T cd06168           2 RQKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIE   73 (75)
T ss_pred             HhHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEE
Confidence            367999999999999999999999999999999999999999986432   234778999999999999997

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.

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

Probab=99.80  E-value=2.3e-19  Score=126.64  Aligned_cols=67  Identities=31%  Similarity=0.371  Sum_probs=60.6

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE  177 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~  177 (213)
                      ++|..++|++|+|.|+||++|.|+|.|||+||||+|.||.++...+.  ..+++|.+||||++|++|++
T Consensus         1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~--~~~~~~~~~irG~~I~~I~~   67 (67)
T PF01423_consen    1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP--EKRSLGLVFIRGSNIRYISL   67 (67)
T ss_dssp             HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES--EEEEEEEEEEEGGGEEEEEE
T ss_pred             ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC--cEeECcEEEEECCEEEEEEC
Confidence            57999999999999999999999999999999999999999865432  36789999999999999975

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 ....

>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=99.80  E-value=1.7e-19  Score=129.66  Aligned_cols=67  Identities=24%  Similarity=0.258  Sum_probs=59.0

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEE
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMG  176 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~  176 (213)
                      +..+|..++|++|.|.|+||+.|.|+|.|||+||||+|+||.+... +.  ....+|.++|||++|++|+
T Consensus         1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~-~~--~~~~~~~v~IRG~~I~~I~   67 (67)
T cd01726           1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVN-GQ--LKNKYGDAFIRGNNVLYIS   67 (67)
T ss_pred             CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeC-Cc--eeeEeCCEEEECCEEEEEC
Confidence            3578999999999999999999999999999999999999988643 22  2457899999999999984

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=99.80  E-value=2.3e-19  Score=129.50  Aligned_cols=67  Identities=27%  Similarity=0.232  Sum_probs=59.4

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEE
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMG  176 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~  176 (213)
                      +...|..++|++|+|.|+||++|.|+|.|||+||||+|+||.++.. ++  ....+|.++|||+||++|.
T Consensus         2 p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~-~~--~~~~lg~~~IRG~~I~~i~   68 (68)
T cd01722           2 PKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYID-GK--STGNLGEVLIRCNNVLYIR   68 (68)
T ss_pred             HHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeC-Cc--cccCcCcEEEECCEEEEEC
Confidence            4678999999999999999999999999999999999999998753 22  2457899999999999983

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

>smart00651 Sm snRNP Sm proteins

Probab=99.80  E-value=3.2e-19  Score=125.66  Aligned_cols=66  Identities=27%  Similarity=0.316  Sum_probs=59.6

Q ss_pred             HHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557         110 KKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE  177 (213)
Q Consensus       110 ~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~  177 (213)
                      +|.+++|++|+|.|+||+.|.|+|.|||+||||+|+||.++...+  ...+.+|.++|||++|++|++
T Consensus         2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~--~~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651        2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG--EKKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCC--cEEeEeCCEEEcCCEEEEEeC
Confidence            689999999999999999999999999999999999999987542  236789999999999999973

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

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

Probab=99.79  E-value=3.9e-19  Score=135.46  Aligned_cols=71  Identities=20%  Similarity=0.225  Sum_probs=60.7

Q ss_pred             HHHHHHhhc--CCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC----------ccceeccceeeeecCcEEE
Q psy5557         107 KKNKKAEEQ--NRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN----------QYGDIPRGIFIIRGENVVL  174 (213)
Q Consensus       107 ~~~~L~~~L--gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n----------~~~er~LGlVlIRGnnIV~  174 (213)
                      +...|...+  +++|+|.|++|+.|.|+|.|||.||||+|+||.|.+....          ....+++|.||||||||++
T Consensus         3 Pl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~   82 (87)
T cd01720           3 PLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVIL   82 (87)
T ss_pred             hHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEE
Confidence            466788887  8999999999999999999999999999999999875422          0124578999999999999


Q ss_pred             EEe
Q psy5557         175 MGE  177 (213)
Q Consensus       175 I~~  177 (213)
                      |++
T Consensus        83 Is~   85 (87)
T cd01720          83 VLR   85 (87)
T ss_pred             Eec
Confidence            975

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.

>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=99.78  E-value=8.5e-19  Score=131.80  Aligned_cols=70  Identities=19%  Similarity=0.272  Sum_probs=59.3

Q ss_pred             HHHHHHHhhcCC--eEEEEec--CCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557         106 EKKNKKAEEQNR--QQGLYPN--QKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE  177 (213)
Q Consensus       106 E~~~~L~~~LgK--rV~V~Lk--DGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~  177 (213)
                      -+...|.+|+++  +|.|.|.  +|+.|.|+|.|||+||||||+||+|++..+.  ..+.+|.++||||||++|++
T Consensus         6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~--~~~~lG~iliRGnnV~~I~p   79 (79)
T cd01718           6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTK--TRKPLGRILLKGDNITLIQN   79 (79)
T ss_pred             CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCc--eEeEcCcEEEeCCEEEEEcC
Confidence            357789999999  5666665  9999999999999999999999999975332  25678999999999999974

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.

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

Probab=99.77  E-value=1.8e-18  Score=127.56  Aligned_cols=71  Identities=27%  Similarity=0.279  Sum_probs=59.9

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCcc-ceeccceeeeecCcEEEEEe
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQY-GDIPRGIFIIRGENVVLMGE  177 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~-~er~LGlVlIRGnnIV~I~~  177 (213)
                      +...|..++|++|.|.|+||++|.|+|+|||+||||+|+||.|++..+... .....|.++|||+||++|.+
T Consensus         8 ~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~   79 (79)
T COG1958           8 PLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP   79 (79)
T ss_pred             cHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence            468899999999999999999999999999999999999999987412111 13345599999999999963

>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=99.74  E-value=7.4e-18  Score=116.94  Aligned_cols=63  Identities=30%  Similarity=0.415  Sum_probs=56.7

Q ss_pred             HHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEE
Q psy5557         111 KAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMG  176 (213)
Q Consensus       111 L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~  176 (213)
                      |..++|++|+|.|.||+.|.|+|.|||+||||+|++|.++...+   ..+.+|.++|||++|++|.
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~---~~~~~~~~~irG~~I~~I~   63 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEG---KKRVLGLVLIRGDNVRLVT   63 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCC---cEEECCeEEEECCEEEEEC
Confidence            57899999999999999999999999999999999999886542   3568999999999999983

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

>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.74  E-value=1e-17  Score=123.34  Aligned_cols=73  Identities=18%  Similarity=0.126  Sum_probs=62.4

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccc
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTV  181 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~  181 (213)
                      +...|..++|++|.|.|+||+.|.|+|.|||.||||+|.||.+...++..  ...+|.+||||++|.||...|..
T Consensus         2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~--~~~~~~v~IRG~~I~~i~~p~~~   74 (76)
T cd01723           2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDK--FWKMPECYIRGNTIKYLRVPDEI   74 (76)
T ss_pred             chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcE--eeeCCcEEEeCCEEEEEEcCHHH
Confidence            46789999999999999999999999999999999999999876443332  23468999999999999876654

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

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

Probab=99.72  E-value=2.1e-17  Score=120.19  Aligned_cols=69  Identities=13%  Similarity=0.011  Sum_probs=60.2

Q ss_pred             HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeec
Q psy5557         108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      ...|..++|++|+|.|+||.+|.|+|.+||.||||+|.||.+...++.   ...+|.+||||+||.||..+|
T Consensus         2 ~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~---~~~~~~v~IRG~nI~~v~lPd   70 (70)
T cd01721           2 IKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGR---VSQLEQVYIRGSKIRFFILPD   70 (70)
T ss_pred             hHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCc---EeEcCcEEEeCCEEEEEEeCC
Confidence            568999999999999999999999999999999999999976543332   346799999999999998664

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.

>KOG1780|consensus

Probab=99.72  E-value=7.4e-18  Score=126.24  Aligned_cols=69  Identities=28%  Similarity=0.425  Sum_probs=61.7

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeecc
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVT  180 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~  180 (213)
                      ..|..|++++|.|.|++||.++|+|+|||.||||||++|+|...++.   ...+|.++|||++|+++.++|.
T Consensus         7 PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~---~~~ig~~vIrgnsiv~~eaL~~   75 (77)
T KOG1780|consen    7 PELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGD---KNNIGMVVIRGNSIVMVEALER   75 (77)
T ss_pred             chHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCC---cceeeeEEEeccEEEEEeeccc
Confidence            37999999999999999999999999999999999999999854332   3468999999999999998763

>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=99.71  E-value=5.7e-17  Score=123.81  Aligned_cols=73  Identities=16%  Similarity=0.101  Sum_probs=64.0

Q ss_pred             HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccccc
Q psy5557         108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVN  183 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~d  183 (213)
                      ..+|..++|++|+|.|+||.+|.|+|.+||.||||+|+||.++...+.   ...+|.++|||+||.||..+|....
T Consensus         3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~---~~~~~~v~IRG~nI~yi~lPd~l~~   75 (90)
T cd01724           3 VRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRN---PVPLDTLSIRGNNIRYFILPDSLNL   75 (90)
T ss_pred             hHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCc---eeEcceEEEeCCEEEEEEcCCcCCc
Confidence            568999999999999999999999999999999999999987754322   4568999999999999998877633

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.

>KOG1782|consensus

Probab=99.68  E-value=3.4e-18  Score=138.26  Aligned_cols=74  Identities=55%  Similarity=0.807  Sum_probs=71.2

Q ss_pred             HHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccccc
Q psy5557         110 KKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVN  183 (213)
Q Consensus       110 ~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~d  183 (213)
                      .|..++++.|.|.|+|||.+.|+|+|||||.|+||.+|+|+++.++.|..+..|.++|||.||++++.+|.+..
T Consensus        13 sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dkE   86 (129)
T KOG1782|consen   13 SLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDKE   86 (129)
T ss_pred             HHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcchh
Confidence            48899999999999999999999999999999999999999999999999999999999999999999998876

>KOG1784|consensus

Probab=99.68  E-value=2.2e-17  Score=127.96  Aligned_cols=85  Identities=27%  Similarity=0.446  Sum_probs=74.7

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC-ccceeccceeeeecCcEEEEEeeccccccccc
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN-QYGDIPRGIFIIRGENVVLMGEVVTVVNVKVI  187 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n-~~~er~LGlVlIRGnnIV~I~~iD~~~d~s~~  187 (213)
                      +.|.+|+|++|.|++.|||.+.|+|.|||+..||+|++|.|++++.. ...+..+|+.+|||+||.+|+++|+.+|..+.
T Consensus         3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d~~ld   82 (96)
T KOG1784|consen    3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELDSRLD   82 (96)
T ss_pred             hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhhhhhh
Confidence            46899999999999999999999999999999999999999987532 34577899999999999999999999887776


Q ss_pred             cCCCCC
Q psy5557         188 KGGDSG  193 (213)
Q Consensus       188 eg~~~g  193 (213)
                      -.--++
T Consensus        83 ~tkir~   88 (96)
T KOG1784|consen   83 LTKIRA   88 (96)
T ss_pred             hhhccc
Confidence            544444

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.67  E-value=1.9e-16  Score=121.58  Aligned_cols=75  Identities=17%  Similarity=0.238  Sum_probs=59.2

Q ss_pred             hhhHHHHHHHHhhcCCe--EEEEecC--CeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557         102 KKKEEKKNKKAEEQNRQ--QGLYPNQ--KRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE  177 (213)
Q Consensus       102 ~~keE~~~~L~~~LgKr--V~V~LkD--GR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~  177 (213)
                      +.-..++..|..++..+  |.|.+.|  ++.|.|+|.|||+||||||+||.|++..+.  ..+.+|.+|||||||++|++
T Consensus        10 ~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~--~~~~lG~ilIRGnnV~~I~~   87 (89)
T PTZ00138         10 KIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKN--TRKDLGRILLKGDNITLIMA   87 (89)
T ss_pred             eeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCc--eeeEcCeEEEcCCEEEEEEc
Confidence            34455677888888654  5555546  589999999999999999999999865332  25679999999999999986


Q ss_pred             e
Q psy5557         178 V  178 (213)
Q Consensus       178 i  178 (213)
                      .
T Consensus        88 ~   88 (89)
T PTZ00138         88 A   88 (89)
T ss_pred             C
Confidence            4

>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=99.67  E-value=3e-16  Score=116.98  Aligned_cols=75  Identities=16%  Similarity=0.115  Sum_probs=64.1

Q ss_pred             hhhhhHHHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557         100 QKKKKEEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE  177 (213)
Q Consensus       100 ~~~~keE~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~  177 (213)
                      +.+.......+|..+.|++|.|.|+||..|.|+|.+||.||||+|+||.+.. .+.  ....+|.++|||+||.||..
T Consensus         3 ~~~~~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~-~~~--~~~~~~~v~IRG~nI~yI~l   77 (78)
T cd01733           3 RTLLENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIID-RNG--KQVQVEEIMVTGRNIRYVHI   77 (78)
T ss_pred             cchhhchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEc-CCC--ceeECCcEEEECCEEEEEEc
Confidence            4566677888999999999999999999999999999999999999997543 222  13468999999999999974

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

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

Probab=99.66  E-value=4.3e-16  Score=116.43  Aligned_cols=77  Identities=17%  Similarity=0.076  Sum_probs=63.4

Q ss_pred             HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccccccc
Q psy5557         108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVNVK  185 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~d~s  185 (213)
                      .++|.+++|++|.|.|+||.+|.|+|.+||.||||+|+||..... +.......++.++|||++|.||..+|..+|..
T Consensus         3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~-~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~~~   79 (81)
T cd01725           3 FSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDP-EKYPHMLSVKNCFIRGSVVRYVQLPADEVDTE   79 (81)
T ss_pred             hHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcC-CCcccccccCeEEEECCEEEEEEeChhHcCcc
Confidence            468999999999999999999999999999999999999965522 11111235689999999999999888776643

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.

>KOG1781|consensus

Probab=99.64  E-value=2e-17  Score=129.89  Aligned_cols=81  Identities=23%  Similarity=0.271  Sum_probs=71.1

Q ss_pred             hhhHHHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCc-----cceeccceeeeecCcEEEEE
Q psy5557         102 KKKEEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQ-----YGDIPRGIFIIRGENVVLMG  176 (213)
Q Consensus       102 ~~keE~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~-----~~er~LGlVlIRGnnIV~I~  176 (213)
                      +.+.|.+..|..|+++.|+|.+.+||..+|+|.|||+.|||||+||+|++.++..     ...+.+|++++||..|++|+
T Consensus        13 ~~kkEsilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlis   92 (108)
T KOG1781|consen   13 KPKKESILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLIS   92 (108)
T ss_pred             ccchhHHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEc
Confidence            3456789999999999999999999999999999999999999999999865431     12478999999999999999


Q ss_pred             eecccc
Q psy5557         177 EVVTVV  182 (213)
Q Consensus       177 ~iD~~~  182 (213)
                      +.|...
T Consensus        93 p~dG~e   98 (108)
T KOG1781|consen   93 PADGSE   98 (108)
T ss_pred             CCcchh
Confidence            987654

>KOG3482|consensus

Probab=99.62  E-value=6.7e-16  Score=115.72  Aligned_cols=70  Identities=24%  Similarity=0.162  Sum_probs=63.0

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeec
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      +..+|+.+.|++|.|.|.+|..|.|+|++.|.||||.|.+|.|++.. .  ....+|.++||+|||.+|..++
T Consensus         9 PKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG-~--~~g~lGEilIRCNNvlyi~gv~   78 (79)
T KOG3482|consen    9 PKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDG-V--STGNLGEILIRCNNVLYIRGVP   78 (79)
T ss_pred             chHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcc-c--ccccceeEEEEeccEEEEecCC
Confidence            46799999999999999999999999999999999999999998753 2  2567999999999999998654

>KOG3460|consensus

Probab=99.52  E-value=2.8e-15  Score=114.86  Aligned_cols=74  Identities=22%  Similarity=0.259  Sum_probs=64.4

Q ss_pred             HHHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC----c------cceeccceeeeecCcEEE
Q psy5557         105 EEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN----Q------YGDIPRGIFIIRGENVVL  174 (213)
Q Consensus       105 eE~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n----~------~~er~LGlVlIRGnnIV~  174 (213)
                      +++...|.-+|+-+|+|.|+++|.+.|+|.+||+|.||||.|+.|.+..-+    .      ...+.+.++||||++|++
T Consensus         4 ~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vil   83 (91)
T KOG3460|consen    4 EEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVIL   83 (91)
T ss_pred             cccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEE
Confidence            568889999999999999999999999999999999999999998775311    1      235678999999999999


Q ss_pred             EEee
Q psy5557         175 MGEV  178 (213)
Q Consensus       175 I~~i  178 (213)
                      |++.
T Consensus        84 vspp   87 (91)
T KOG3460|consen   84 VSPP   87 (91)
T ss_pred             EcCc
Confidence            9875

>KOG3168|consensus

Probab=99.46  E-value=1.6e-14  Score=122.23  Aligned_cols=74  Identities=26%  Similarity=0.315  Sum_probs=62.7

Q ss_pred             HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecC-------CccceeccceeeeecCcEEEEEeecc
Q psy5557         108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVG-------NQYGDIPRGIFIIRGENVVLMGEVVT  180 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~-------n~~~er~LGlVlIRGnnIV~I~~iD~  180 (213)
                      -+.|.++||.+++|+++|||+|+|+|.+||.||||||.||.|+....       ...+.+-||+|++||.|||+++.-+.
T Consensus         6 sskml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegp   85 (177)
T KOG3168|consen    6 SSKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGP   85 (177)
T ss_pred             hhHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCC
Confidence            36789999999999999999999999999999999999998865321       12346789999999999999987543


Q ss_pred             c
Q psy5557         181 V  181 (213)
Q Consensus       181 ~  181 (213)
                      .
T Consensus        86 p   86 (177)
T KOG3168|consen   86 P   86 (177)
T ss_pred             C
Confidence            3

>KOG1783|consensus

Probab=99.44  E-value=1.6e-14  Score=108.21  Aligned_cols=71  Identities=23%  Similarity=0.205  Sum_probs=62.8

Q ss_pred             HHHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEee
Q psy5557         105 EEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV  178 (213)
Q Consensus       105 eE~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~i  178 (213)
                      +.+-++|..++|++|.|.|.+|-.|.|+|.|+|.||||.|+.|.|+.. +.  ..+++|.+||||+||.+|+..
T Consensus         5 ~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~n-gq--l~n~ygdaFirGnnVlyIs~~   75 (77)
T KOG1783|consen    5 SMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVN-GQ--LKNKYGDAFIRGNNVLYISTQ   75 (77)
T ss_pred             cCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhc-Cc--ccccccceeeccccEEEEEec
Confidence            456789999999999999999999999999999999999999988752 22  356789999999999999864

>KOG1775|consensus

Probab=99.40  E-value=1.8e-13  Score=103.56  Aligned_cols=70  Identities=14%  Similarity=0.171  Sum_probs=60.2

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEee
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV  178 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~i  178 (213)
                      .-+-..||.+|+|++++.+.|.|||+|||.|.|+||.|++||...........++.+++.||||+++-+.
T Consensus        10 EliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPG   79 (84)
T KOG1775|consen   10 ELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPG   79 (84)
T ss_pred             HHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecC
Confidence            3456789999999999999999999999999999999999997665432345789999999999998653

>KOG3293|consensus

Probab=99.15  E-value=5.4e-11  Score=96.95  Aligned_cols=77  Identities=18%  Similarity=0.177  Sum_probs=66.7

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccccccc
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVNVK  185 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~d~s  185 (213)
                      ++.-|...-+.+|.|.|.+|-+|.|+|+.+|.+|||.|.+++.+..++..+  -.+..+.|||++|-||...|.++|..
T Consensus         3 PLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf--~r~pEcYirGttIkylri~d~iid~v   79 (134)
T KOG3293|consen    3 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKF--FRMPECYIRGTTIKYLRIPDEIIDKV   79 (134)
T ss_pred             chhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCce--eecceeEEecceeEEEeccHHHHHHH
Confidence            356788888999999999999999999999999999999999887655543  24688999999999999999887644

>KOG1774|consensus

Probab=99.09  E-value=1.2e-10  Score=89.17  Aligned_cols=71  Identities=18%  Similarity=0.215  Sum_probs=55.0

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeec
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      +-.+|++...-.||..=+-|-.+.|.++|||.||||||++|.|.....+.  ...+|.+++.||||.+|...+
T Consensus        17 Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~--rk~lGRilLKGDnItli~~~~   87 (88)
T KOG1774|consen   17 IFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKS--RKELGRILLKGDNITLIQSAG   87 (88)
T ss_pred             HHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccC--CCccccEEEcCCcEEEEeecC
Confidence            34566666666666666678999999999999999999999886433222  347999999999999998654

>KOG3448|consensus

Probab=98.88  E-value=3e-09  Score=82.63  Aligned_cols=76  Identities=20%  Similarity=0.197  Sum_probs=59.7

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCcc-ceeccceeeeecCcEEEEEeecccccccc
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQY-GDIPRGIFIIRGENVVLMGEVVTVVNVKV  186 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~-~er~LGlVlIRGnnIV~I~~iD~~~d~s~  186 (213)
                      +++..++|+.|.|.|.++-.+.|||.|+|+|+||-|.|..  +.+...| .-..+..+||||+.|-||.......+..+
T Consensus         5 sfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~--v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~vdtql   81 (96)
T KOG3448|consen    5 SFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDIS--VTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDAVDTQL   81 (96)
T ss_pred             HHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeE--eeCcccCCCeeeeeeEEEeccEEEEEEeChhHHHHHH
Confidence            5788999999999999999999999999999999999974  2222222 12346779999999999987654444433

>KOG3428|consensus

Probab=98.58  E-value=3.8e-07  Score=72.90  Aligned_cols=70  Identities=17%  Similarity=0.084  Sum_probs=59.4

Q ss_pred             HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccc
Q psy5557         108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTV  181 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~  181 (213)
                      ..+|..+.+.+|.|.|.+|....|++.+.|.+||..|.++.=. ..+   ....+-.++|||+||=|+-..|..
T Consensus         4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t-~~~---~pv~l~~lsirgnniRy~~lpD~l   73 (109)
T KOG3428|consen    4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMT-VKG---EPVRLDTLSIRGNNIRYYILPDSL   73 (109)
T ss_pred             HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEe-cCC---CceeEEEEEeecceEEEEEccCCc
Confidence            5689999999999999999999999999999999999998522 222   245688999999999999887654

>KOG3172|consensus

Probab=98.55  E-value=3.1e-07  Score=73.74  Aligned_cols=76  Identities=16%  Similarity=0.084  Sum_probs=62.6

Q ss_pred             HHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeecccccccccc
Q psy5557         110 KKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVNVKVIK  188 (213)
Q Consensus       110 ~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~d~s~~e  188 (213)
                      .|...-|.-|.|.+..|..|.|.|.-.|++||++|+|++=...++.   ...+..|||||+.|-++-.+|-...+++..
T Consensus         9 lLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~---vs~le~V~IRGS~IRFlvlPdmLKnAPmFk   84 (119)
T KOG3172|consen    9 LLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGR---VSQLEQVFIRGSKIRFLVLPDMLKNAPMFK   84 (119)
T ss_pred             eeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCc---ceeeeeEEEecCeEEEEECchHhhcCcccc
Confidence            4566778899999999999999999999999999999865433322   335788999999999999988887766554

>KOG3459|consensus

Probab=98.02  E-value=8.7e-07  Score=71.17  Aligned_cols=61  Identities=23%  Similarity=0.273  Sum_probs=52.0

Q ss_pred             CCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecC----Cc-----c-ceeccceeeeecCcEEEEE
Q psy5557         116 NRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVG----NQ-----Y-GDIPRGIFIIRGENVVLMG  176 (213)
Q Consensus       116 gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~----n~-----~-~er~LGlVlIRGnnIV~I~  176 (213)
                      +.+|.|.++|++.+.|.+.|||-|.|++|.++.|.+..-    ..     . ..+++|.+|||||+|+.+.
T Consensus        36 ~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~v~  106 (114)
T KOG3459|consen   36 NTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVILVL  106 (114)
T ss_pred             CceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEEEE
Confidence            678999999999999999999999999999998877431    11     1 2678999999999999886

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

Probab=97.84  E-value=3.6e-05  Score=56.20  Aligned_cols=64  Identities=13%  Similarity=0.075  Sum_probs=39.5

Q ss_pred             HHHhhcCCeEEEEecCCeEEEEEEEEecC---cCceEecceEEEeecC---Cc-cceeccceeeeecCcEE
Q psy5557         110 KKAEEQNRQQGLYPNQKRTLIGYLRSVDQ---FANLVLHKTIERIHVG---NQ-YGDIPRGIFIIRGENVV  173 (213)
Q Consensus       110 ~L~~~LgKrV~V~LkDGR~~~GtL~gFDq---~mNLVLsDavEri~~~---n~-~~er~LGlVlIRGnnIV  173 (213)
                      .+..++|.+|.|++.||..|.|+|.+++.   -+.++|..|.......   .. ........++|.++.|+
T Consensus         6 l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv   76 (77)
T PF14438_consen    6 LLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV   76 (77)
T ss_dssp             HHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred             HHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence            46789999999999999999999999998   8899998875432211   11 11234567888887775

>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=97.44  E-value=0.00011  Score=54.49  Aligned_cols=36  Identities=19%  Similarity=0.217  Sum_probs=29.1

Q ss_pred             CeEEEEec--CC--eEEEEEEEEecCcCceEecceEEEee
Q psy5557         117 RQQGLYPN--QK--RTLIGYLRSVDQFANLVLHKTIERIH  152 (213)
Q Consensus       117 KrV~V~Lk--DG--R~~~GtL~gFDq~mNLVLsDavEri~  152 (213)
                      .+|.|.++  +|  -.++|.|++||.|+||+|.|+.|.+.
T Consensus         9 ~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~   48 (66)
T cd01739           9 IRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYR   48 (66)
T ss_pred             cEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhc
Confidence            56666664  44  38999999999999999999998654

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.

>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=96.87  E-value=0.0047  Score=41.79  Aligned_cols=48  Identities=15%  Similarity=0.184  Sum_probs=36.1

Q ss_pred             hcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeee
Q psy5557         114 EQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIR  168 (213)
Q Consensus       114 ~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIR  168 (213)
                      ++|++|+|.+ ++..+.|++.|+|.+..|+|......+      ...+.|.|++|
T Consensus         1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g~~------~~i~sGdv~~r   48 (48)
T PF02237_consen    1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDGSI------RTISSGDVSLR   48 (48)
T ss_dssp             STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTEEE------EEESSSEEEEE
T ss_pred             CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCCCE------EEEEEEEEEeC
Confidence            4899999999 667779999999999999997653311      12344666665

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

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

Probab=96.47  E-value=0.021  Score=43.66  Aligned_cols=62  Identities=8%  Similarity=0.018  Sum_probs=46.9

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecC-cCceEecceEEEeecCCccceeccceeeeecCcEEEEE
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQ-FANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMG  176 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq-~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~  176 (213)
                      =+..|..+.|++|.+.|-++.+..|+|.|+|. ..|+..++-.    .+-    ..+...+||++.|++++
T Consensus        15 fLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~----TPl----Gv~~eAlLR~~DVi~~~   77 (80)
T PF11095_consen   15 FLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ----TPL----GVQPEALLRCSDVISIS   77 (80)
T ss_dssp             HHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE----TTT----TEEEEEEEEGGGEEEEE
T ss_pred             HHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC----CCc----ccChhheeecCCEEEEE
Confidence            45668888899999999999999999999994 5577776642    221    12467999999999986

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.

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

Probab=96.29  E-value=0.028  Score=43.94  Aligned_cols=71  Identities=14%  Similarity=0.112  Sum_probs=53.3

Q ss_pred             HhhcCCeEEEEecCCeEEEEEEEEecC-cCceEecceEEEeecCC----c--cceeccceeeeecCcEEEEEeecccc
Q psy5557         112 AEEQNRQQGLYPNQKRTLIGYLRSVDQ-FANLVLHKTIERIHVGN----Q--YGDIPRGIFIIRGENVVLMGEVVTVV  182 (213)
Q Consensus       112 ~~~LgKrV~V~LkDGR~~~GtL~gFDq-~mNLVLsDavEri~~~n----~--~~er~LGlVlIRGnnIV~I~~iD~~~  182 (213)
                      ..|||++|.++.+++-.|.|+|..+|. ..+|.|.++.-+=..+-    .  -....+..|++||+.|--+..++...
T Consensus         4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~   81 (96)
T PF12701_consen    4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPP   81 (96)
T ss_dssp             CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-
T ss_pred             ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCC
Confidence            468999999999999999999999995 78999999864322110    0  01124688999999999998776553

>PF11600 CAF-1_p150: Chromatin assembly factor 1 complex p150 subunit, N-terminal; InterPro: IPR021644 P150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesised and acetylated histones H3/H4 into chromatin during DNA replication and repair []

Probab=96.05  E-value=0.11  Score=44.92  Aligned_cols=12  Identities=0%  Similarity=0.027  Sum_probs=8.2

Q ss_pred             HHHHHhhcCCeE
Q psy5557         108 KNKKAEEQNRQQ  119 (213)
Q Consensus       108 ~~~L~~~LgKrV  119 (213)
                      ...|.+|+.++.
T Consensus       179 q~~~~~FF~k~~  190 (216)
T PF11600_consen  179 QARITSFFKKPK  190 (216)
T ss_pred             HHHHHHHhCCCC
Confidence            667788876544

P150 is the HP1 interaction site of CAF-1 and lies within the N-terminal region of the protein [].

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

Probab=95.84  E-value=0.028  Score=48.01  Aligned_cols=63  Identities=16%  Similarity=0.200  Sum_probs=45.2

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecC-cCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccc
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQ-FANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTV  181 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq-~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~  181 (213)
                      ..+..|+++.|.|.+.| ++|.|.|.++|+ ..||||.+..+     +.    ....-+|-|..|-.|..++..
T Consensus        10 ~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e-----~~----~~sv~~I~ghaVk~vevl~~~   73 (166)
T PF06372_consen   10 LEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE-----DG----KRSVKVIMGHAVKSVEVLSEG   73 (166)
T ss_dssp             HHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T-----TS-----EEEEEE-GGGEEEEEEEE--
T ss_pred             HHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc-----CC----ceeEEEEEccceEEEEEccCC
Confidence            56789999999999999 999999999995 67999976432     11    124689999999999988754

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.

>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=95.05  E-value=0.038  Score=40.32  Aligned_cols=31  Identities=23%  Similarity=0.278  Sum_probs=27.9

Q ss_pred             CCeEEEEecCCeEEEEEEEEecCcCceEecc
Q psy5557         116 NRQQGLYPNQKRTLIGYLRSVDQFANLVLHK  146 (213)
Q Consensus       116 gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsD  146 (213)
                      ..+|.|.|.||-.+.|.+.|||+|+=|+-.+
T Consensus        11 ~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   41 (61)
T cd01716          11 KIPVTIYLVNGVQLKGQIESFDNFTVLLESD   41 (61)
T ss_pred             CCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence            6789999999999999999999999777655

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=94.81  E-value=0.047  Score=39.86  Aligned_cols=31  Identities=19%  Similarity=0.250  Sum_probs=27.8

Q ss_pred             CCeEEEEecCCeEEEEEEEEecCcCceEecc
Q psy5557         116 NRQQGLYPNQKRTLIGYLRSVDQFANLVLHK  146 (213)
Q Consensus       116 gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsD  146 (213)
                      ..+|.|.|.+|-.+.|.+.|||.|+=|+-.+
T Consensus        15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~   45 (61)
T TIGR02383        15 RIPVTVFLVNGVQLKGVIESFDNFTVLLESQ   45 (61)
T ss_pred             CCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence            6789999999999999999999999777654

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=94.52  E-value=0.057  Score=41.34  Aligned_cols=33  Identities=21%  Similarity=0.276  Sum_probs=29.2

Q ss_pred             cCCeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557         115 QNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKT  147 (213)
Q Consensus       115 LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa  147 (213)
                      -..+|.|.|.+|-.+.|.+.|||.|+=|+..+-
T Consensus        18 ~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g   50 (79)
T PRK00395         18 ERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG   50 (79)
T ss_pred             cCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence            378899999999999999999999998776554

>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=94.35  E-value=0.19  Score=38.02  Aligned_cols=63  Identities=13%  Similarity=0.117  Sum_probs=44.5

Q ss_pred             HhhcCCeEEEEecCCeEEEEEEEEecC-cCceEecceEEEeecCCc---c----ceeccceeeeecCcEEE
Q psy5557         112 AEEQNRQQGLYPNQKRTLIGYLRSVDQ-FANLVLHKTIERIHVGNQ---Y----GDIPRGIFIIRGENVVL  174 (213)
Q Consensus       112 ~~~LgKrV~V~LkDGR~~~GtL~gFDq-~mNLVLsDavEri~~~n~---~----~er~LGlVlIRGnnIV~  174 (213)
                      ..|||++|.++.+.+-.|.|+|.++|. -.-|.|.|+..+=..+..   .    ....+..++.||+.|--
T Consensus         2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD   72 (74)
T cd01736           2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD   72 (74)
T ss_pred             ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence            468999999999999999999999995 456778887543211110   0    11235678888887753

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.

>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=93.93  E-value=0.13  Score=37.52  Aligned_cols=34  Identities=15%  Similarity=0.117  Sum_probs=30.3

Q ss_pred             hcCCeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557         114 EQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKT  147 (213)
Q Consensus       114 ~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa  147 (213)
                      .+|..|.+.+..|..|.|.+.+||.-.+|++-.|
T Consensus         4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~   37 (61)
T cd01735           4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKC   37 (61)
T ss_pred             ccccEEEEEecCCceEEEEEEEecCCCcEEEEEC
Confidence            5899999999999999999999998888776554

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.

>PRK14638 hypothetical protein; Provisional

Probab=92.68  E-value=0.29  Score=40.69  Aligned_cols=36  Identities=11%  Similarity=0.174  Sum_probs=30.7

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEec
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLH  145 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLs  145 (213)
                      ..+..++|+.|.|+|.+++.|+|+|.++|.- +|+|.
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            4678999999999999999999999999963 45553

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

Probab=91.76  E-value=0.26  Score=37.72  Aligned_cols=32  Identities=19%  Similarity=0.252  Sum_probs=27.1

Q ss_pred             cCCeEEEEecCCeEEEEEEEEecCcCceEecc
Q psy5557         115 QNRQQGLYPNQKRTLIGYLRSVDQFANLVLHK  146 (213)
Q Consensus       115 LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsD  146 (213)
                      -+.+|.|.|.||-.+.|.+.|||+|.=|+=++
T Consensus        18 ~~i~VtIfLvNG~~L~G~V~sfD~f~VlL~~~   49 (77)
T COG1923          18 EKIPVTIFLVNGFKLQGQVESFDNFVVLLKNT   49 (77)
T ss_pred             cCCeEEEEEEcCEEEEEEEEeeeeEEEEEEcC
Confidence            36789999999999999999999997554433

>PRK14639 hypothetical protein; Provisional

Probab=91.69  E-value=0.45  Score=39.11  Aligned_cols=35  Identities=26%  Similarity=0.319  Sum_probs=30.6

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEe
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVL  144 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVL  144 (213)
                      ..+..++|..|.|.|.+++.|.|+|.++|. .+++|
T Consensus        81 ~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~-~~i~l  115 (140)
T PRK14639         81 EHFAKSIGELVKITTNEKEKFEGKIVSVDD-ENITL  115 (140)
T ss_pred             HHHHHhCCCEEEEEECCCcEEEEEEEEEeC-CEEEE
Confidence            467899999999999999999999999998 35555

>PRK02001 hypothetical protein; Validated

Probab=90.66  E-value=0.63  Score=39.00  Aligned_cols=35  Identities=17%  Similarity=0.328  Sum_probs=30.1

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEe
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVL  144 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVL  144 (213)
                      ..+..++|..|.|.|.+++.|.|+|.+||.- +++|
T Consensus        83 ~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l  117 (152)
T PRK02001         83 RQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL  117 (152)
T ss_pred             HHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence            4577899999999999999999999999974 4444

>TIGR02794 tolA_full TolA protein

Probab=89.37  E-value=1.8  Score=40.41  Aligned_cols=14  Identities=21%  Similarity=0.508  Sum_probs=8.7

Q ss_pred             EEecCcCceEecce
Q psy5557         134 RSVDQFANLVLHKT  147 (213)
Q Consensus       134 ~gFDq~mNLVLsDa  147 (213)
                      ..++.|.++|-.-.
T Consensus       259 ~ev~~Y~a~I~~~I  272 (346)
T TIGR02794       259 SEVDKYAAIIQQAI  272 (346)
T ss_pred             chHHHHHHHHHHHH
Confidence            34577887765544

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB.

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

Probab=89.32  E-value=1.1  Score=33.18  Aligned_cols=35  Identities=14%  Similarity=0.095  Sum_probs=28.7

Q ss_pred             HHHHhhcCCeEEEEec---CC-eEEEEEEEEecCcCceEe
Q psy5557         109 NKKAEEQNRQQGLYPN---QK-RTLIGYLRSVDQFANLVL  144 (213)
Q Consensus       109 ~~L~~~LgKrV~V~Lk---DG-R~~~GtL~gFDq~mNLVL  144 (213)
                      ..+..++|..|.|.|.   +| +.|.|+|.++|.- +++|
T Consensus        18 ~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l   56 (83)
T cd01734          18 ADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL   56 (83)
T ss_pred             HHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence            4678899999999996   55 6999999999984 4444

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

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

Probab=88.96  E-value=2.5  Score=31.31  Aligned_cols=53  Identities=17%  Similarity=0.152  Sum_probs=40.0

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE  177 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~  177 (213)
                      +.|++++|++|.|.+..|.. .|+|.+.... .|+|+.+              -..++||=..|++|.+
T Consensus        14 q~lq~liG~~vvV~T~~g~v-~G~L~~V~pD-hIvl~~~--------------~~~~~IR~~~IV~v~p   66 (66)
T PF10842_consen   14 QTLQSLIGQRVVVQTTRGSV-RGILVDVKPD-HIVLEEN--------------GTPFFIRIAQIVWVMP   66 (66)
T ss_pred             HHHHHhcCCEEEEEEcCCcE-EEEEEeecCC-EEEEEeC--------------CcEEEEEeeeEEEEcC
Confidence            57999999999999988776 9999998743 2344332              1457888888888753

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=88.87  E-value=0.58  Score=40.24  Aligned_cols=33  Identities=15%  Similarity=0.198  Sum_probs=29.3

Q ss_pred             cCCeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557         115 QNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKT  147 (213)
Q Consensus       115 LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa  147 (213)
                      -..+|.|.|.+|-.+.|.+.|||.|+=|+..+.
T Consensus       103 ~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g  135 (165)
T PRK14091        103 SGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG  135 (165)
T ss_pred             cCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            377899999999999999999999998777665

>PRK14644 hypothetical protein; Provisional

Probab=88.46  E-value=1.2  Score=36.68  Aligned_cols=35  Identities=11%  Similarity=0.126  Sum_probs=30.3

Q ss_pred             HHHhhcCCeEEEEecCC----eEEEEEEEEecCcCceEec
Q psy5557         110 KKAEEQNRQQGLYPNQK----RTLIGYLRSVDQFANLVLH  145 (213)
Q Consensus       110 ~L~~~LgKrV~V~LkDG----R~~~GtL~gFDq~mNLVLs  145 (213)
                      .+..++|..|.|.|.+.    +.|.|+|.++|. .+|+|.
T Consensus        79 ~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~-~~i~l~  117 (136)
T PRK14644         79 ELENHIGEIIDVSLNKEVNKTDFITGELLENNP-ETITLK  117 (136)
T ss_pred             HHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeC-CEEEEE
Confidence            68899999999999877    899999999997 456664

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=88.24  E-value=0.68  Score=39.84  Aligned_cols=32  Identities=16%  Similarity=0.225  Sum_probs=28.1

Q ss_pred             CCeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557         116 NRQQGLYPNQKRTLIGYLRSVDQFANLVLHKT  147 (213)
Q Consensus       116 gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa  147 (213)
                      ..+|.|.|.+|-.+.|.+.|||+|.=|+..+.
T Consensus        24 k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g   55 (165)
T PRK14091         24 KTPVTMFLVKGVKLQGIITWFDNFSILLRRDG   55 (165)
T ss_pred             CCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            67899999999999999999999987776554

>PRK14640 hypothetical protein; Provisional

Probab=87.88  E-value=1.4  Score=36.56  Aligned_cols=36  Identities=14%  Similarity=0.219  Sum_probs=29.6

Q ss_pred             HHHHhhcCCeEEEEe----cCCeEEEEEEEEecCcCceEec
Q psy5557         109 NKKAEEQNRQQGLYP----NQKRTLIGYLRSVDQFANLVLH  145 (213)
Q Consensus       109 ~~L~~~LgKrV~V~L----kDGR~~~GtL~gFDq~mNLVLs  145 (213)
                      ..+..++|+.|.|+|    .+++.|.|+|.++|.. ++.|.
T Consensus        90 ~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~  129 (152)
T PRK14640         90 AQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT  129 (152)
T ss_pred             HHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence            467899999999999    5669999999999974 45553

>PRK14633 hypothetical protein; Provisional

Probab=87.57  E-value=1.5  Score=36.35  Aligned_cols=37  Identities=14%  Similarity=0.113  Sum_probs=30.0

Q ss_pred             HHHHHhhcCCeEEEEe----cCCeEEEEEEEEecCcCceEec
Q psy5557         108 KNKKAEEQNRQQGLYP----NQKRTLIGYLRSVDQFANLVLH  145 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~L----kDGR~~~GtL~gFDq~mNLVLs  145 (213)
                      ...+..++|+.|.|++    .+++.|+|+|.++|.. +|.|.
T Consensus        86 ~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~  126 (150)
T PRK14633         86 IIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN  126 (150)
T ss_pred             HHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence            3567899999999998    4679999999999874 55553

>PF11600 CAF-1_p150: Chromatin assembly factor 1 complex p150 subunit, N-terminal; InterPro: IPR021644 P150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesised and acetylated histones H3/H4 into chromatin during DNA replication and repair []

Probab=86.99  E-value=19  Score=31.10  Aligned_cols=12  Identities=0%  Similarity=-0.108  Sum_probs=6.2

Q ss_pred             hHHHHHHHHhhc
Q psy5557         104 KEEKKNKKAEEQ  115 (213)
Q Consensus       104 keE~~~~L~~~L  115 (213)
                      .-.+.+|+..-.
T Consensus       179 q~~~~~FF~k~~  190 (216)
T PF11600_consen  179 QARITSFFKKPK  190 (216)
T ss_pred             HHHHHHHhCCCC
Confidence            445556665433

P150 is the HP1 interaction site of CAF-1 and lies within the N-terminal region of the protein [].

>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=86.50  E-value=1.6  Score=35.15  Aligned_cols=36  Identities=19%  Similarity=0.224  Sum_probs=27.2

Q ss_pred             HHHHHhhcCCeEEEEe----cCCeEEEEEEEEecCcCceEe
Q psy5557         108 KNKKAEEQNRQQGLYP----NQKRTLIGYLRSVDQFANLVL  144 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~L----kDGR~~~GtL~gFDq~mNLVL  144 (213)
                      ...+..++|+.|.|.+    .+.+.|.|+|.++|. .+|+|
T Consensus        79 ~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l  118 (141)
T PF02576_consen   79 PRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL  118 (141)
T ss_dssp             HHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred             HHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence            3578899999999999    345799999999998 45555

; PDB: 1IB8_A.

>PRK06955 biotin--protein ligase; Provisional

Probab=86.23  E-value=2.5  Score=38.22  Aligned_cols=37  Identities=16%  Similarity=0.179  Sum_probs=31.5

Q ss_pred             HHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecc
Q psy5557         110 KKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHK  146 (213)
Q Consensus       110 ~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsD  146 (213)
                      ...-++|+.|.|...++..+.|++.|+|..+.|+|..
T Consensus       243 ~~~~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~  279 (300)
T PRK06955        243 ALHAYAGREVVLLEDGAELARGVAHGIDETGQLLLDT  279 (300)
T ss_pred             HHhhcCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence            3445789999998777788999999999999999953

>PRK14636 hypothetical protein; Provisional

Probab=86.09  E-value=1.8  Score=36.96  Aligned_cols=35  Identities=11%  Similarity=0.191  Sum_probs=28.9

Q ss_pred             HHHHhhcCCeEEEEec---CC-eEEEEEEEEecCcCceEe
Q psy5557         109 NKKAEEQNRQQGLYPN---QK-RTLIGYLRSVDQFANLVL  144 (213)
Q Consensus       109 ~~L~~~LgKrV~V~Lk---DG-R~~~GtL~gFDq~mNLVL  144 (213)
                      ..+..++|+.|.|+|.   +| +.|+|+|.++|.- +++|
T Consensus        91 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l  129 (176)
T PRK14636         91 KDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI  129 (176)
T ss_pred             HHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence            5678999999999997   55 6999999999873 4554

>PRK14642 hypothetical protein; Provisional

Probab=85.49  E-value=2.1  Score=37.56  Aligned_cols=36  Identities=6%  Similarity=0.056  Sum_probs=29.9

Q ss_pred             HHHHHhhcCCeEEEEec-------------CCeEEEEEEEEecCcCceEe
Q psy5557         108 KNKKAEEQNRQQGLYPN-------------QKRTLIGYLRSVDQFANLVL  144 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~Lk-------------DGR~~~GtL~gFDq~mNLVL  144 (213)
                      ...+..++|..|.|+|.             +.+.|.|+|.++|.. +|.|
T Consensus        92 ~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l  140 (197)
T PRK14642         92 EQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI  140 (197)
T ss_pred             HHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence            35678899999999997             679999999999974 4444

>PRK14632 hypothetical protein; Provisional

Probab=85.06  E-value=2.2  Score=36.23  Aligned_cols=36  Identities=25%  Similarity=0.274  Sum_probs=29.4

Q ss_pred             HHHHhhcCCeEEEEecC-------CeEEEEEEEEecCcCceEec
Q psy5557         109 NKKAEEQNRQQGLYPNQ-------KRTLIGYLRSVDQFANLVLH  145 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkD-------GR~~~GtL~gFDq~mNLVLs  145 (213)
                      ..+..++|+.|.|+|.+       .+.|.|+|.++|. .+|+|.
T Consensus        91 ~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~-~~i~l~  133 (172)
T PRK14632         91 EQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEG-DTVVLR  133 (172)
T ss_pred             HHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeC-CEEEEE
Confidence            46789999999999975       5799999999986 355553

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

Probab=84.79  E-value=2  Score=36.85  Aligned_cols=37  Identities=8%  Similarity=-0.006  Sum_probs=32.9

Q ss_pred             HHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557         111 KAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKT  147 (213)
Q Consensus       111 L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa  147 (213)
                      ...+-+-+|+|++.||.+|.|.+.||++--|+||+-+
T Consensus        24 f~r~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~   60 (165)
T PF03614_consen   24 FWRFNDIPVRVVSENGQVFCMYVSGFMSKENKILAPD   60 (165)
T ss_pred             HHHhcCCceEEEecCCcEEEEEEeccCcccCEEeccC
Confidence            3445688999999999999999999999999999776

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

>PRK14645 hypothetical protein; Provisional

Probab=84.62  E-value=2.5  Score=35.43  Aligned_cols=34  Identities=6%  Similarity=0.061  Sum_probs=28.3

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEe
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVL  144 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVL  144 (213)
                      ..+..++|..|.|.+ +++.|.|+|.+||.- +|+|
T Consensus        95 ~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l  128 (154)
T PRK14645         95 RHFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTF  128 (154)
T ss_pred             HHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence            467789999999986 889999999999974 4444

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

Probab=84.50  E-value=2.9  Score=37.54  Aligned_cols=35  Identities=23%  Similarity=0.278  Sum_probs=29.4

Q ss_pred             HHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEec
Q psy5557         110 KKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLH  145 (213)
Q Consensus       110 ~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLs  145 (213)
                      ...-++|+.|.|... +..+.|++.|+|..+.|+|.
T Consensus       266 ~~~~~~g~~v~~~~~-~~~~~G~~~gi~~~G~L~i~  300 (319)
T PRK11886        266 KLDLFLGREVKLIIG-DKEISGIARGIDEQGALLLE  300 (319)
T ss_pred             HhccccCCeEEEEeC-CcEEEEEEEEECCCceEEEE
Confidence            344578999999874 45799999999999999995

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

Probab=84.15  E-value=3.6  Score=35.51  Aligned_cols=37  Identities=22%  Similarity=0.282  Sum_probs=30.5

Q ss_pred             HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEec
Q psy5557         108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLH  145 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLs  145 (213)
                      -.....++|++|.|...+ ..+.|++.|+|..+.|+|.
T Consensus       185 ~~~~~~~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~  221 (237)
T TIGR00121       185 WEKLSAHIGREVSLTTGN-GEIEGIARGIDKDGALLLE  221 (237)
T ss_pred             HHHhhhccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence            344556789999998754 5699999999999999996

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

>PRK14647 hypothetical protein; Provisional

Probab=83.00  E-value=3.3  Score=34.58  Aligned_cols=35  Identities=11%  Similarity=0.209  Sum_probs=28.1

Q ss_pred             HHHHhhcCCeEEEEec---------CCeEEEEEEEEecCcCceEe
Q psy5557         109 NKKAEEQNRQQGLYPN---------QKRTLIGYLRSVDQFANLVL  144 (213)
Q Consensus       109 ~~L~~~LgKrV~V~Lk---------DGR~~~GtL~gFDq~mNLVL  144 (213)
                      ..+..++|..|.|+|.         +.+.|+|+|.++|. .+++|
T Consensus        92 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~-~~v~l  135 (159)
T PRK14647         92 ADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD-GVVTI  135 (159)
T ss_pred             HHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC-CEEEE
Confidence            5678999999999994         35899999999996 34444

>PRK14634 hypothetical protein; Provisional

Probab=82.34  E-value=3.5  Score=34.46  Aligned_cols=36  Identities=11%  Similarity=0.054  Sum_probs=28.6

Q ss_pred             HHHHHhhcCCeEEEEecCC----eEEEEEEEEecCcCceEe
Q psy5557         108 KNKKAEEQNRQQGLYPNQK----RTLIGYLRSVDQFANLVL  144 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~LkDG----R~~~GtL~gFDq~mNLVL  144 (213)
                      ...+..++|+.|.|.|.+.    +.|.|+|.++|.- +|.|
T Consensus        92 ~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l  131 (155)
T PRK14634         92 DRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI  131 (155)
T ss_pred             HHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence            3567899999999998632    7999999999973 4545

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=82.07  E-value=3.8  Score=33.68  Aligned_cols=30  Identities=17%  Similarity=0.177  Sum_probs=26.9

Q ss_pred             HHHHhhcCCeEEEEe----cCCeEEEEEEEEecC
Q psy5557         109 NKKAEEQNRQQGLYP----NQKRTLIGYLRSVDQ  138 (213)
Q Consensus       109 ~~L~~~LgKrV~V~L----kDGR~~~GtL~gFDq  138 (213)
                      ..+..++|+.|.|.|    .+++.|.|+|.++|.
T Consensus        91 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~  124 (154)
T PRK00092         91 RDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG  124 (154)
T ss_pred             HHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence            567899999999997    677899999999998

>PRK14646 hypothetical protein; Provisional

Probab=82.06  E-value=3.6  Score=34.37  Aligned_cols=35  Identities=20%  Similarity=0.088  Sum_probs=28.5

Q ss_pred             HHHHhhcCCeEEEEecCC----eEEEEEEEEecCcCceEe
Q psy5557         109 NKKAEEQNRQQGLYPNQK----RTLIGYLRSVDQFANLVL  144 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDG----R~~~GtL~gFDq~mNLVL  144 (213)
                      ..+..++|..|.|.|.+.    +.|.|+|.+||.- +|.|
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            467899999999999543    7899999999984 5555

>KOG2412|consensus

Probab=81.86  E-value=10  Score=38.33  Aligned_cols=40  Identities=25%  Similarity=0.513  Sum_probs=16.6

Q ss_pred             HHHHHhhHHHHHHHHHHHH-HHHHHHHHhHHHHHHHhhHHH
Q psy5557          35 EEKKQKKKEEKKQKKKEKK-EEKEEKKEKKKEEKKQKKEEE   74 (213)
Q Consensus        35 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~   74 (213)
                      ..+.|+..+++++.+-+++ +..+|+.+.++.++..+++.+
T Consensus       211 qi~~~~~~~e~kr~Eaerk~~~~qEe~Rqk~d~~~~~~eqe  251 (591)
T KOG2412|consen  211 QIRERKERSEEKREEAERKRRAHQEELRQKEDEEAELQEQE  251 (591)
T ss_pred             HHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHhHHH
Confidence            3344444555555554433 223333344443333333333

>PRK08330 biotin--protein ligase; Provisional

Probab=81.30  E-value=6.4  Score=34.04  Aligned_cols=37  Identities=16%  Similarity=0.287  Sum_probs=29.6

Q ss_pred             HHHhhcCCeEEEEecCCeEE-EEEEEEecCcCceEecce
Q psy5557         110 KKAEEQNRQQGLYPNQKRTL-IGYLRSVDQFANLVLHKT  147 (213)
Q Consensus       110 ~L~~~LgKrV~V~LkDGR~~-~GtL~gFDq~mNLVLsDa  147 (213)
                      ....++|++|.|.. ++..+ .|++.|+|..+.|+|...
T Consensus       182 ~~~~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~~  219 (236)
T PRK08330        182 GRSMILGKRVKIIG-DGEILVEGIAEDIDEFGALILRLD  219 (236)
T ss_pred             HHHHhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEEC
Confidence            34467899999986 56665 699999999999999643

>PRK14643 hypothetical protein; Provisional

Probab=80.89  E-value=3.7  Score=34.71  Aligned_cols=31  Identities=13%  Similarity=0.130  Sum_probs=26.9

Q ss_pred             HHHHhhcCCeEEEEecC----CeEEEEEEEEecCc
Q psy5557         109 NKKAEEQNRQQGLYPNQ----KRTLIGYLRSVDQF  139 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkD----GR~~~GtL~gFDq~  139 (213)
                      ..+..++|..|.|.|.+    .+.|.|+|.++|.-
T Consensus        97 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T PRK14643         97 EELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN  131 (164)
T ss_pred             HHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence            56789999999999965    58999999999964

>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]

Probab=80.87  E-value=5.3  Score=35.43  Aligned_cols=41  Identities=12%  Similarity=0.143  Sum_probs=35.5

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKT  147 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa  147 (213)
                      .-..+..++|++|++.+.++..+.|+..++|..+.|+|...
T Consensus       181 ~~~~~~~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~  221 (238)
T COG0340         181 RWRARSLSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD  221 (238)
T ss_pred             HHHHHhccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence            34455667999999999999999999999999999999876

>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=80.64  E-value=4.5  Score=34.14  Aligned_cols=33  Identities=12%  Similarity=0.071  Sum_probs=29.8

Q ss_pred             HHHHHhhcCCeEEEEe----cCCeEEEEEEEEecCcC
Q psy5557         108 KNKKAEEQNRQQGLYP----NQKRTLIGYLRSVDQFA  140 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~L----kDGR~~~GtL~gFDq~m  140 (213)
                      ...+..|+|..|.|.|    .+++.|.|+|.++|.-+
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            3567899999999999    88999999999999877

>PRK14631 hypothetical protein; Provisional

Probab=80.20  E-value=4.8  Score=34.38  Aligned_cols=36  Identities=17%  Similarity=0.147  Sum_probs=29.1

Q ss_pred             HHHHHhhcCCeEEEEec----CCeEEEEEEEEec--CcCceEe
Q psy5557         108 KNKKAEEQNRQQGLYPN----QKRTLIGYLRSVD--QFANLVL  144 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~Lk----DGR~~~GtL~gFD--q~mNLVL  144 (213)
                      ...+..|+|+.|.|+|.    +.+.|+|+|.++|  . .+|.|
T Consensus       109 ~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~-~~v~l  150 (174)
T PRK14631        109 LEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVDLEN-EEIQV  150 (174)
T ss_pred             HHHHHHhCCCeEEEEEecccCCceEEEEEEEEeecCC-CEEEE
Confidence            45788999999999995    5599999999998  4 34444

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	213
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	2e-12
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	9e-12
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	6e-12
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	1e-11
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-10
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	4e-10
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	6e-10
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	7e-10
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	3e-09
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	4e-09
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	4e-09
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	4e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	6e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	7e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	8e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	3e-06
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	3e-05
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	4e-10
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	1e-09
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	1e-09
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	9e-08
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	9e-08
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	1e-06
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	1e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	4e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	5e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	5e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	6e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	6e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	7e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	9e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	9e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	5e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	5e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	6e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	4e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	5e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	7e-04
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	1e-06
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	5e-05
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	6e-06
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	7e-06
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	8e-04
1b6a_A	478	Methionine aminopeptidase; angiogenesis inhibitor;	9e-06
1b6a_A	478	Methionine aminopeptidase; angiogenesis inhibitor;	3e-05
1b6a_A	478	Methionine aminopeptidase; angiogenesis inhibitor;	3e-05
1b6a_A	478	Methionine aminopeptidase; angiogenesis inhibitor;	7e-05
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	3e-05
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	3e-05
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	1e-04
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	6e-05
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	7e-05
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	8e-05
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	1e-04
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	2e-04
1qy5_A	269	Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: N	2e-04
1qy5_A	269	Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: N	5e-04
1qy5_A	269	Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: N	5e-04
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-04
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	3e-04
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	6e-04

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010

 Score = 64.7 bits (158), Expect = 2e-12
 Identities = 7/103 (6%), Positives = 27/103 (26%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
                 +  +     Q K +  +    E +  + +   +      +  +       E  + 
Sbjct: 908  YLGSNETGDSITAVQAKLKNLEAFDGECQSLEGQSNSDLLSILAQLTELNYNGVPELTER 967

Query: 77   KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
            K     +Q    +   +  +     + +  +K +     +   
Sbjct: 968  KDTFFAQQWTGVKSSAETYKNTLLAELERLQKIEDLHHHHHHH 1010

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010

 Score = 62.8 bits (153), Expect = 9e-12
 Identities = 11/99 (11%), Positives = 24/99 (24%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
                K       +        Q K +  +    E +  + +          Q  E   +
Sbjct: 900 NWATTKSVYLGSNETGDSITAVQAKLKNLEAFDGECQSLEGQSNSDLLSILAQLTELNYN 959

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQ 115
              E  ++K     +Q    +   +  K     +    Q
Sbjct: 960 GVPELTERKDTFFAQQWTGVKSSAETYKNTLLAELERLQ 998

>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 = 58.5 bits (142), Expect = 6e-12
 Identities = 22/52 (42%), Positives = 28/52 (53%), Gaps = 4/52 (7%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
             + G LRS DQ  NL+L    E I  GN Y    RG  ++RGENV+ +  V
Sbjct: 32  HEIRGILRSFDQHVNLLLEDAEEIID-GNVY---KRGTMVVRGENVLFISPV 79

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 62.4 bits (152), Expect = 1e-11
 Identities = 26/110 (23%), Positives = 45/110 (40%), Gaps = 4/110 (3%)

Query: 14   RIGKRKKKKKEEENKKK---QKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQK 70
             + + KK     ENK     +K  E+ K+ K   +K    E     E +K +   E+ + 
Sbjct: 915  SVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRM 974

Query: 71   KEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKE-EKKNKKAEEQNRQQ 119
             EEE           ++E  K +K+  + Q +KK  E+   K + +  Q 
Sbjct: 975  SEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQL 1024

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 58.6 bits (142), Expect = 2e-10
 Identities = 22/115 (19%), Positives = 48/115 (41%), Gaps = 4/115 (3%)

Query: 17   KRKKKKKEEENKKKQKKK--EEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEE 74
            +R   K+E +  K + +     KK     E K  + ++K +++ K+ K   EK    E  
Sbjct: 898  RRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEIT 957

Query: 75   KDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKRTL 129
                 E +K +   E+ +  +EE K    +     ++  +  ++      +K+T+
Sbjct: 958  --YSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTI 1010

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 57.8 bits (140), Expect = 4e-10
 Identities = 20/111 (18%), Positives = 49/111 (44%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
            K  K   E+ N  +     E ++ + + ++ +  E++ +    +    +E+  K  +E  
Sbjct: 942  KEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELH 1001

Query: 77   KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKR 127
            + + EKK  ++   K K + E+   + KE+    K E++   + ++   K 
Sbjct: 1002 QTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAKE 1052

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 57.4 bits (139), Expect = 6e-10
 Identities = 19/135 (14%), Positives = 56/135 (41%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
            +RK  ++ +E K   +K    +     E ++ + + +  +  ++E K    +    +E+ 
Sbjct: 934  QRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEI 993

Query: 77   KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSV 136
             K  ++  + + EKK  ++   K K + E+  ++  E+    +       R +    + +
Sbjct: 994  AKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAKEI 1053

Query: 137  DQFANLVLHKTIERI 151
             +     L +  +++
Sbjct: 1054 TETMEKKLVEETKQL 1068

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 57.0 bits (138), Expect = 7e-10
 Identities = 21/109 (19%), Positives = 44/109 (40%), Gaps = 7/109 (6%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKK-----EKKKEEKKQKK 71
            K K + +  E  KK     E K  + + K  ++ ++ +   EK          E +K + 
Sbjct: 908  KLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRS 967

Query: 72   EEEKDKKKEEKKQKKKEEKKQKKKEEKKQKK--KKEEKKNKKAEEQNRQ 118
            + E+ +  EE+ +         ++E  K +K   + + + K  EE   +
Sbjct: 968  DVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADK 1016

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 55.1 bits (133), Expect = 3e-09
 Identities = 16/94 (17%), Positives = 46/94 (48%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
            +    ++E    +K+  + + ++K  EE   K K + E+   + +++    K +KEE   
Sbjct: 985  RVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNR 1044

Query: 77   KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNK 110
            +  ++ K+  +  +K+  +E K+ +    +++ +
Sbjct: 1045 RIHDQAKEITETMEKKLVEETKQLELDLNDERLR 1078

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 54.7 bits (132), Expect = 4e-09
 Identities = 19/110 (17%), Positives = 42/110 (38%), Gaps = 8/110 (7%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKK----EKKKEEKKQKKE 72
            R    +  +     +    +   K+E KK K + +  E+ +K     E K  + ++K +
Sbjct: 879 ARVHYHRTLKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKID 938

Query: 73  EEKDKKKEEKKQKKKEEKKQKKKEEKKQKK----KKEEKKNKKAEEQNRQ 118
           E+  + K   ++    E     + EK +      +  E++ K A  +   
Sbjct: 939 EQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLS 988

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 54.7 bits (132), Expect = 4e-09
 Identities = 17/106 (16%), Positives = 51/106 (48%), Gaps = 3/106 (2%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
              +++ K   N+    ++E  K +K+  + Q +K+  EE  +K + + E+   + +E+  
Sbjct: 974  MSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNT 1033

Query: 77   ---KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
                +KEE  ++  ++ K+  +  +K+  ++ ++      ++  + 
Sbjct: 1034 LLKTEKEELNRRIHDQAKEITETMEKKLVEETKQLELDLNDERLRY 1079

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 51.6 bits (124), Expect = 4e-08
 Identities = 16/120 (13%), Positives = 40/120 (33%), Gaps = 5/120 (4%)

Query: 15  IGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEE 74
           I K  +      +  +  K     Q        K++ KK + E +  ++ ++     E +
Sbjct: 870 IQKHVRGWLARVHYHRTLKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENK 929

Query: 75  KDKKK-----EEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKRTL 129
             + +     + K+ K   EK    +     + +K     ++      +     N+  +L
Sbjct: 930 IMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSL 989

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 51.3 bits (123), Expect = 6e-08
 Identities = 22/106 (20%), Positives = 40/106 (37%), Gaps = 3/106 (2%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEE--- 73
           K +   +E ++   QK       +    +  K     +    +   K+E KK K E    
Sbjct: 857 KYQMMLREHKSIIIQKHVRGWLARVHYHRTLKAIVYLQCCYRRMMAKRELKKLKIEARSV 916

Query: 74  EKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
           E+ KK     + K  + ++K  E+ K+ K   EK N      + + 
Sbjct: 917 ERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTET 962

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 51.3 bits (123), Expect = 7e-08
 Identities = 17/105 (16%), Positives = 35/105 (33%), Gaps = 3/105 (2%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
            R    + +     ++ K    QK       +    +  K     +    +   K E K 
Sbjct: 849 LRGYLVRNKYQMMLREHKSIIIQKHVRGWLARVHYHRTLKAIVYLQCCYRRMMAKRELKK 908

Query: 77  KKKEEK---KQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQ 118
            K E +   + KK     + K  + ++K  ++ K+ K   E+   
Sbjct: 909 LKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNN 953

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 50.9 bits (122), Expect = 8e-08
 Identities = 15/109 (13%), Positives = 41/109 (37%), Gaps = 4/109 (3%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEK- 75
           + K    ++  +    +    +  K     Q    +   K E K+ K E +  ++ ++  
Sbjct: 864 EHKSIIIQKHVRGWLARVHYHRTLKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKKLH 923

Query: 76  ---DKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGL 121
              + K  + ++K  E+ K+ K   +K    +     +  + ++  + L
Sbjct: 924 IGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERL 972

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 46.3 bits (110), Expect = 3e-06
 Identities = 20/89 (22%), Positives = 43/89 (48%), Gaps = 5/89 (5%)

Query: 14   RIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEK-----KEEKEEKKEKKKEEKK 68
             I K +K+  + + +KK  ++   K K + E+   + ++     K EKEE   +  ++ K
Sbjct: 992  EIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAK 1051

Query: 69   QKKEEEKDKKKEEKKQKKKEEKKQKKKEE 97
            +  E  + K  EE KQ + +   ++ + +
Sbjct: 1052 EITETMEKKLVEETKQLELDLNDERLRYQ 1080

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 43.2 bits (102), Expect = 3e-05
 Identities = 17/111 (15%), Positives = 37/111 (33%), Gaps = 1/111 (0%)

Query: 20  KKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKK 79
             +        + K +   ++ K    QK       +       K     +    +   K
Sbjct: 844 ALQALLRGYLVRNKYQMMLREHKSIIIQKHVRGWLARVHYHRTLKAIVYLQCCYRRMMAK 903

Query: 80  EEKKQKKKEEKK-QKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKRTL 129
            E K+ K E +  ++ K+     + K  +  +K +EQN++      +   L
Sbjct: 904 RELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNL 954

>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 = 53.1 bits (128), Expect = 4e-10
 Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 3/52 (5%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
           R + G LR  D F NLV+ + +E    G Q      G+ +IRG +++++  +
Sbjct: 25  RHVQGILRGFDPFMNLVIDECVEMATSGQQ---NNIGMVVIRGNSIIMLEAL 73

>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A Length = 91

 Score = 52.5 bits (126), Expect = 1e-09
 Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 7/56 (12%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPR-------GIFIIRGENVVLM 175
           R  IG  ++ D+  NL+L    E   +  +             G+ ++RGEN+V M
Sbjct: 25  RIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSM 80

>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 = 52.4 bits (126), Expect = 1e-09
 Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 4/56 (7%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYG----DIPRGIFIIRGENVVLMGEV 178
           RTL+G L++ D   N+VL   +E I+  N       +    +  IRG+ V L+   
Sbjct: 31  RTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLISTP 86

>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 = 47.3 bits (113), Expect = 9e-08
 Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 7/54 (12%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVG--NQYGDIPRGIFIIRGENVVLMGEV 178
           + + G LRS DQ  NLVL  + E    G   + G I     +IRG+NV+L+  +
Sbjct: 30  KEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTI-----VIRGDNVILISPL 78

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} Length = 963

 Score = 51.0 bits (121), Expect = 9e-08
 Identities = 19/84 (22%), Positives = 42/84 (50%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           +  ++   +E +K          + K   K+ KKEK   +EEKK++ +E++K+++  +K 
Sbjct: 797 RMYEEASGKEVEKVATAVLSTTARAKARAKKTKKEKGPNEEEKKKEHEEKEKERETNKKG 856

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQ 100
            K+ ++  ++  + K   K  K  
Sbjct: 857 IKETKENDEEFYKNKYSSKPYKVD 880

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} Length = 963

 Score = 47.5 bits (112), Expect = 1e-06
 Identities = 21/90 (23%), Positives = 44/90 (48%)

Query: 40  KKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKK 99
           +  EE   K+ EK          + + + +K ++EK   +EEKK++ +E++K+++  +K 
Sbjct: 797 RMYEEASGKEVEKVATAVLSTTARAKARAKKTKKEKGPNEEEKKKEHEEKEKERETNKKG 856

Query: 100 QKKKKEEKKNKKAEEQNRQQGLYPNQKRTL 129
            K+ KE  +     + + +     N  R L
Sbjct: 857 IKETKENDEEFYKNKYSSKPYKVDNMTRIL 886

>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 = 47.6 bits (113), Expect = 1e-07
 Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 4/56 (7%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGD----IPRGIFIIRGENVVLMGEV 178
           R + G L+  DQ  NLVL    E++               G+ ++RG  +VL+  +
Sbjct: 44  RQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIAPM 99

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 50.2 bits (120), Expect = 1e-07
 Identities = 19/104 (18%), Positives = 51/104 (49%)

Query: 18   RKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDK 77
             + +++EE +++ Q +K++ +Q+  + ++Q ++E+   ++ + EK   + K KK E+   
Sbjct: 934  ARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDIL 993

Query: 78   KKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGL 121
              E++  K  +E+K  ++          E++ K       +   
Sbjct: 994  IMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKH 1037

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 49.8 bits (119), Expect = 2e-07
 Identities = 17/105 (16%), Positives = 57/105 (54%), Gaps = 3/105 (2%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
              + + +    K++ ++   + + + EE++++ ++ + EK++ +++  + ++Q +EEE  
Sbjct: 911  AEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAA 970

Query: 77   KKKEEKKQKKKEEKKQKKKEE---KKQKKKKEEKKNKKAEEQNRQ 118
            ++K + ++   + K +K +++    + +  K  K+ K  EE+   
Sbjct: 971  RQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSD 1015

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 48.7 bits (116), Expect = 4e-07
 Identities = 19/102 (18%), Positives = 50/102 (49%)

Query: 14   RIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEE 73
               +   KK+E E    + +   ++++++ ++ Q +K+K +++    E++ EE++  +++
Sbjct: 914  MRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQK 973

Query: 74   EKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQ 115
             + +K     + KK E      E++  K  KE K  ++    
Sbjct: 974  LQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSD 1015

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 48.7 bits (116), Expect = 5e-07
 Identities = 16/103 (15%), Positives = 56/103 (54%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
              KK++ EE   + + + EE++++ ++ + +KKK +++  + +++ ++EE  ++K + + 
Sbjct: 919  AAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEK 978

Query: 77   KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
               + K +K +++    + +  K  K+++  + + ++      
Sbjct: 979  VTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLA 1021

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 48.7 bits (116), Expect = 5e-07
 Identities = 26/124 (20%), Positives = 68/124 (54%), Gaps = 3/124 (2%)

Query: 18  RKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKE---EKKEKKKEEKKQKKEEE 74
           ++ K+++++ + + K+ E+K  +  EEK   +++ + E E   E +E +     +K+E E
Sbjct: 867 QRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELE 926

Query: 75  KDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKRTLIGYLR 134
           +   + E + +++EE+ Q+ + EKK+ +++     ++ EE+   +     +K T  G ++
Sbjct: 927 EILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIK 986

Query: 135 SVDQ 138
            ++ 
Sbjct: 987 KMED 990

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 48.3 bits (115), Expect = 6e-07
 Identities = 18/103 (17%), Positives = 50/103 (48%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
            K+K +++  + +++ +++E  +QK + EK     + K+ +++    + +  K  KE +  
Sbjct: 950  KKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLL 1009

Query: 77   KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
            +++         E+++K K   K K K E   ++      +++
Sbjct: 1010 EERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEE 1052

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 48.3 bits (115), Expect = 6e-07
 Identities = 22/101 (21%), Positives = 51/101 (50%), Gaps = 2/101 (1%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKE-EKKEKKKEEKKQKKEEEK 75
            + + ++ + E KK Q++  + +++ +EE+  ++K + E+   + K KK E+     E++ 
Sbjct: 940  EERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQN 999

Query: 76   DKKKEEKKQKKKEEKK-QKKKEEKKQKKKKEEKKNKKAEEQ 115
            +K  +E+K  ++          E+++K K   K   K E  
Sbjct: 1000 NKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESM 1040

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 48.3 bits (115), Expect = 7e-07
 Identities = 18/106 (16%), Positives = 57/106 (53%)

Query: 14   RIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEE 73
            R+  +K++ +E  ++ + + +EE+++ ++ + ++KK +++    E++ +++E  +QK + 
Sbjct: 917  RLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQL 976

Query: 74   EKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
            EK     + K+ + +    + +  K  K++K  ++       N  +
Sbjct: 977  EKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAE 1022

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 47.9 bits (114), Expect = 9e-07
 Identities = 22/109 (20%), Positives = 61/109 (55%), Gaps = 4/109 (3%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKE----KKEEKEEKKEKKKEEKKQKKE 72
            K++ ++   E + + +++EE+ Q+ + EKK+ +++    +++ +EE+  ++K + ++   
Sbjct: 922  KQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTA 981

Query: 73   EEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGL 121
            + K KK E+     +++  +  KE K  +++  +     AEE+ + + L
Sbjct: 982  DGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNL 1030

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 47.9 bits (114), Expect = 9e-07
 Identities = 17/104 (16%), Positives = 59/104 (56%), Gaps = 2/104 (1%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           ++K  +  EE    Q+K + + +   E ++ + +   +++E ++   + E + ++EEE+ 
Sbjct: 884 EQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERS 943

Query: 77  KKKEEKKQKKKEE--KKQKKKEEKKQKKKKEEKKNKKAEEQNRQ 118
           ++ + +K+K +++    +++ EE++  ++K + +   A+ + ++
Sbjct: 944 QQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKK 987

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 45.6 bits (108), Expect = 5e-06
 Identities = 22/105 (20%), Positives = 51/105 (48%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
                 ++EE+ K   K K + +    E + + KKE+K  +E +K K+K E +     E+ 
Sbjct: 1017 TTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQI 1076

Query: 77   KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGL 121
             + + +  + K +  +K++E +    + E++ ++K     + + L
Sbjct: 1077 AELQAQIAELKAQLAKKEEELQAALARLEDETSQKNNALKKIREL 1121

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 44.8 bits (106), Expect = 1e-05
 Identities = 19/102 (18%), Positives = 56/102 (54%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           + + K +E +  K++++K E + K+ E+K  +  E+K   +EK + + E   + +E    
Sbjct: 858 EMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVR 917

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQ 118
              ++++ ++   + + + EE++++ ++ + + KK ++Q   
Sbjct: 918 LAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLD 959

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 44.4 bits (105), Expect = 1e-05
 Identities = 23/108 (21%), Positives = 50/108 (46%), Gaps = 4/108 (3%)

Query: 15   IGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQK-KKEKKEEKEEKKEKKKEEKKQKKEE 73
              K + +K   + K K+ + +    + +  K  K +K  +E   +      EE+++ K  
Sbjct: 971  RQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNL 1030

Query: 74   EKDKKKEEKKQ---KKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQ 118
             K K K E      + + +K++K ++E ++ K+K E ++    EQ  +
Sbjct: 1031 TKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAE 1078

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 44.1 bits (104), Expect = 2e-05
 Identities = 17/106 (16%), Positives = 56/106 (52%), Gaps = 4/106 (3%)

Query: 18  RKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDK 77
            ++K   +E  + + +   + ++ +     KK+E +E   E + + +EE+++ ++ + +K
Sbjct: 891 CEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEK 950

Query: 78  KKEEKK----QKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
           KK +++    +++ EE++  +++ + +K   + K  K  ++    +
Sbjct: 951 KKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIME 996

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 43.7 bits (103), Expect = 2e-05
 Identities = 22/111 (19%), Positives = 61/111 (54%), Gaps = 3/111 (2%)

Query: 14  RIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEE 73
           R  +  + K EE  + K+++++ + + K+ E+K  +  +++   ++K + + E   + EE
Sbjct: 854 RQEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEE 913

Query: 74  EKD---KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGL 121
            +     KK+E ++   E + + ++EE++ ++ + EKK  + +  + ++ L
Sbjct: 914 MRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQL 964

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 42.5 bits (100), Expect = 5e-05
 Identities = 19/105 (18%), Positives = 46/105 (43%), Gaps = 4/105 (3%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
            +  ++K + E      K ++ +      + Q  K  KE ++  +E+  +      EEE+ 
Sbjct: 968  EAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKE-RKLLEERVSDLTTNLAEEEEK 1026

Query: 77   KKKEEKKQKKKEEKKQ---KKKEEKKQKKKKEEKKNKKAEEQNRQ 118
             K   K + K E        + +++++ +++ EK  +K E ++  
Sbjct: 1027 AKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSD 1071

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 42.5 bits (100), Expect = 6e-05
 Identities = 25/109 (22%), Positives = 50/109 (45%), Gaps = 3/109 (2%)

Query: 14   RIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKK---EKKKEEKKQK 70
              GK KK + +    + Q  K  K++K  EE+         E+EEK     K K + +  
Sbjct: 981  ADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESM 1040

Query: 71   KEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
              E + + K+E+K +++ EK ++K E +     ++  + +    + + Q
Sbjct: 1041 ISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQ 1089

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 27/121 (22%), Positives = 52/121 (42%), Gaps = 5/121 (4%)

Query: 14   RIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEK-KEEKEEKKEKKKEEKKQKKE 72
            +  K  K++K  E +         ++++K +   K K K +    E + + K+E+K ++E
Sbjct: 998  QNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQE 1057

Query: 73   EEKDKKKEEKKQK----KKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKRT 128
             EK K+K E +      +  E + +  E K Q  KKEE+          +     N  + 
Sbjct: 1058 LEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLEDETSQKNNALKK 1117

Query: 129  L 129
            +
Sbjct: 1118 I 1118

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 41.0 bits (96), Expect = 2e-04
 Identities = 18/102 (17%), Positives = 61/102 (59%), Gaps = 2/102 (1%)

Query: 19  KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK 78
           K  ++EEE + K ++ +  K+++++ + + K+ +++  +  +EK   ++K + E E   +
Sbjct: 851 KVTRQEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAE 910

Query: 79  KEEKKQK--KKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQ 118
            EE + +   K+++ ++   E + + ++EE+++++ + + ++
Sbjct: 911 AEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKK 952

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 41.0 bits (96), Expect = 2e-04
 Identities = 15/110 (13%), Positives = 48/110 (43%), Gaps = 4/110 (3%)

Query: 14   RIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEE 73
            +I + + +  E + +  +K++E +    + E +  +K    +K  + E    + ++  E 
Sbjct: 1075 QIAELQAQIAELKAQLAKKEEELQAALARLEDETSQKNNALKKIRELESHISDLQEDLES 1134

Query: 74   EKDKKKEEKKQKKKEEKK----QKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
            EK  + + +KQK+   ++    + + E+       +++      + +  +
Sbjct: 1135 EKAARNKAEKQKRDLSEELEALKTELEDTLDTTATQQELRGSDYKDDDDK 1184

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 40.6 bits (95), Expect = 2e-04
 Identities = 20/106 (18%), Positives = 50/106 (47%)

Query: 14   RIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEE 73
            R+ K +K ++E E  K++ + E     ++  + Q +  + + +  KKE++ +    + E+
Sbjct: 1047 RLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLED 1106

Query: 74   EKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNRQQ 119
            E  +K    K+ ++ E      +E  + +K    K +K +    ++
Sbjct: 1107 ETSQKNNALKKIRELESHISDLQEDLESEKAARNKAEKQKRDLSEE 1152

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 39.8 bits (93), Expect = 4e-04
 Identities = 20/111 (18%), Positives = 52/111 (46%), Gaps = 9/111 (8%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKK-----EEKKQKK 71
            +      E++N K  K+++  +++  +      +E+++ K   K K K      E + + 
Sbjct: 989  EDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRL 1048

Query: 72   EEEKDKKKEEKKQKKKEEKKQK----KKEEKKQKKKKEEKKNKKAEEQNRQ 118
            ++E+  ++E +K K+K E +      +  E + +  + + +  K EE+ + 
Sbjct: 1049 KKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQA 1099

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 39.4 bits (92), Expect = 5e-04
 Identities = 17/101 (16%), Positives = 49/101 (48%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
             + K K E    + + + +++++ ++E +K K+K + E  +  ++  + + +  + + + 
Sbjct: 1031 TKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQL 1090

Query: 77   KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNR 117
             KKEE+ Q      + +  ++    KK  E ++  ++ Q  
Sbjct: 1091 AKKEEELQAALARLEDETSQKNNALKKIRELESHISDLQED 1131

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 39.0 bits (91), Expect = 7e-04
 Identities = 18/101 (17%), Positives = 45/101 (44%)

Query: 17   KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
            ++ K+K E E+    ++  E + +  E K Q  K+++E +      + E  ++    +K 
Sbjct: 1059 EKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLEDETSQKNNALKKI 1118

Query: 77   KKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAEEQNR 117
            ++ E      +E+ + +K    K +K+K +   +    +  
Sbjct: 1119 RELESHISDLQEDLESEKAARNKAEKQKRDLSEELEALKTE 1159

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 46.3 bits (109), Expect = 1e-06
 Identities = 15/73 (20%), Positives = 38/73 (52%)

Query: 30  KQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEE 89
            +  +E +  +K  E+++K+ ++ +   +  E++  EK +K  EE ++++ E+ +K K  
Sbjct: 78  DRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKIN 137

Query: 90  KKQKKKEEKKQKK 102
            +   K   +Q  
Sbjct: 138 NRIADKAFYQQPD 150

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 41.7 bits (97), Expect = 5e-05
 Identities = 15/74 (20%), Positives = 40/74 (54%), Gaps = 7/74 (9%)

Query: 50  KEKKEEKEEKKEKKKEEKK--QKKEEEKDKKKEEKKQKKKEEKKQ--KKKEEKKQKKKKE 105
               +E E  ++ ++E++K  Q+ +      ++E ++K K++ ++  +++ E+ +K K  
Sbjct: 78  DRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKIN 137

Query: 106 EKKNKKAEEQNRQQ 119
              N+ A++   QQ
Sbjct: 138 ---NRIADKAFYQQ 148

>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 = 41.9 bits (99), Expect = 6e-06
 Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 3/52 (5%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
               G L  +D + NL L +T E ++ G +      G   IRG NV+ +  +
Sbjct: 25  VDYKGILSCLDGYMNLALERTEEYVN-GKKTNVY--GDAFIRGNNVLYVSAL 73

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A* 3vkh_C* Length = 3245

 Score = 45.3 bits (107), Expect = 7e-06
 Identities = 18/92 (19%), Positives = 45/92 (48%)

Query: 19   KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK 78
            +K ++ +   ++  +K ++  + ++  + K+K+ +E + +   + KE   QK +   D +
Sbjct: 1945 QKNRELDVKNEQANQKLKQMVQDQQAAEIKQKDARELQVQLDVRNKEIAVQKVKAYADLE 2004

Query: 79   KEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNK 110
            K E     +EE +Q +    + K K++E    
Sbjct: 2005 KAEPTGPLREEVEQLENAANELKLKQDEIVAT 2036

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A* 3vkh_C* Length = 3245

 Score = 39.1 bits (91), Expect = 8e-04
 Identities = 15/116 (12%), Positives = 44/116 (37%), Gaps = 17/116 (14%)

Query: 15   IGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEE 74
            + +  + ++  E K+K  ++ + +   + ++   +K K     EK E     +++ ++ E
Sbjct: 1961 LKQMVQDQQAAEIKQKDARELQVQLDVRNKEIAVQKVKAYADLEKAEPTGPLREEVEQLE 2020

Query: 75   KDKKKEEKKQKKKE-----------------EKKQKKKEEKKQKKKKEEKKNKKAE 113
                + + KQ +                       ++ E+ K +  K + K  ++ 
Sbjct: 2021 NAANELKLKQDEIVATITALEKSIATYKEEYATLIRETEQIKTESSKVKNKVDRSI 2076

>1b6a_A Methionine aminopeptidase; angiogenesis inhibitor; HET: TN4; 1.60A {Homo sapiens} SCOP: a.4.5.25 d.127.1.1 PDB: 1qzy_A* 1boa_A* 1kq0_A 1kq9_A 1bn5_A* 1b59_A* 1yw9_A* 1r5g_A* 1r5h_A* 1r58_A* 1yw8_A* 1yw7_A* 2adu_A* 2ea2_A* 2ea4_A* 2ga2_A* 2oaz_A* Length = 478

 Score = 44.5 bits (105), Expect = 9e-06
 Identities = 21/87 (24%), Positives = 41/87 (47%)

Query: 17  KRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKD 76
           +      EE  KKK++KK++ K      +++  KE     +E   + +    + KE ++D
Sbjct: 25  EGAASTAEEAAKKKRRKKKKSKGPSAAGEQEPDKESGASVDEVARQLERSALEDKERDED 84

Query: 77  KKKEEKKQKKKEEKKQKKKEEKKQKKK 103
            +  +        KK+KKK++K+  K 
Sbjct: 85  DEDGDGDGDGATGKKKKKKKKKRGPKV 111

>1b6a_A Methionine aminopeptidase; angiogenesis inhibitor; HET: TN4; 1.60A {Homo sapiens} SCOP: a.4.5.25 d.127.1.1 PDB: 1qzy_A* 1boa_A* 1kq0_A 1kq9_A 1bn5_A* 1b59_A* 1yw9_A* 1r5g_A* 1r5h_A* 1r58_A* 1yw8_A* 1yw7_A* 2adu_A* 2ea2_A* 2ea4_A* 2ga2_A* 2oaz_A* Length = 478

 Score = 43.4 bits (102), Expect = 3e-05
 Identities = 21/98 (21%), Positives = 46/98 (46%), Gaps = 5/98 (5%)

Query: 9   GAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEK-----KEEKEEKKEKK 63
           G + P   +       EE  KK+++K++K +      +Q+  ++      E   + +   
Sbjct: 16  GDLDPDDREEGAASTAEEAAKKKRRKKKKSKGPSAAGEQEPDKESGASVDEVARQLERSA 75

Query: 64  KEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQK 101
            E+K++ +++E      +    KK++KK+KK+  K Q 
Sbjct: 76  LEDKERDEDDEDGDGDGDGATGKKKKKKKKKRGPKVQT 113

>1b6a_A Methionine aminopeptidase; angiogenesis inhibitor; HET: TN4; 1.60A {Homo sapiens} SCOP: a.4.5.25 d.127.1.1 PDB: 1qzy_A* 1boa_A* 1kq0_A 1kq9_A 1bn5_A* 1b59_A* 1yw9_A* 1r5g_A* 1r5h_A* 1r58_A* 1yw8_A* 1yw7_A* 2adu_A* 2ea2_A* 2ea4_A* 2ga2_A* 2oaz_A* Length = 478

 Score = 43.0 bits (101), Expect = 3e-05
 Identities = 14/89 (15%), Positives = 42/89 (47%)

Query: 20  KKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKK 79
           +++      ++  KK+ +K+KK +      +++ +++      +   + ++   E  ++ 
Sbjct: 23  REEGAASTAEEAAKKKRRKKKKSKGPSAAGEQEPDKESGASVDEVARQLERSALEDKERD 82

Query: 80  EEKKQKKKEEKKQKKKEEKKQKKKKEEKK 108
           E+ +    +      K++KK+KKK+  K 
Sbjct: 83  EDDEDGDGDGDGATGKKKKKKKKKRGPKV 111

>1b6a_A Methionine aminopeptidase; angiogenesis inhibitor; HET: TN4; 1.60A {Homo sapiens} SCOP: a.4.5.25 d.127.1.1 PDB: 1qzy_A* 1boa_A* 1kq0_A 1kq9_A 1bn5_A* 1b59_A* 1yw9_A* 1r5g_A* 1r5h_A* 1r58_A* 1yw8_A* 1yw7_A* 2adu_A* 2ea2_A* 2ea4_A* 2ga2_A* 2oaz_A* Length = 478

 Score = 42.2 bits (99), Expect = 7e-05
 Identities = 15/98 (15%), Positives = 43/98 (43%)

Query: 16  GKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEK 75
           G       + +++++      ++  KK+ +K+KK +      E++  K+      +   +
Sbjct: 11  GSHLNGDLDPDDREEGAASTAEEAAKKKRRKKKKSKGPSAAGEQEPDKESGASVDEVARQ 70

Query: 76  DKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNKKAE 113
            ++   + +++ E+ +    +      KK++KK KK  
Sbjct: 71  LERSALEDKERDEDDEDGDGDGDGATGKKKKKKKKKRG 108

>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 = 40.0 bits (94), Expect = 3e-05
 Identities = 16/51 (31%), Positives = 22/51 (43%), Gaps = 7/51 (13%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIH--VGNQYGDIPRGIFIIRGENVVLM 175
           R   G L   D   NLVL    E  +  V  + G +     +IRG+ VV +
Sbjct: 25  REFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSV-----VIRGDTVVFV 70

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 427

 Score = 42.8 bits (100), Expect = 3e-05
 Identities = 24/111 (21%), Positives = 57/111 (51%), Gaps = 3/111 (2%)

Query: 2   KISIAPKGAISPRIGKRKKKKKEEENKKK---QKKKEEKKQKKKEEKKQKKKEKKEEKEE 58
             S+             + +KKEEE ++    + K++E + K+ E++  +K ++ ++  +
Sbjct: 317 PFSLQETYEAKRNEFLGELQKKEEEMRQMFVQRVKEKEAELKEAEKELHEKFDRLKKLHQ 376

Query: 59  KKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKN 109
            ++KK E+KK+  ++E +  K+ K   +  + +  +    +  K+ +EKKN
Sbjct: 377 DEKKKLEDKKKSLDDEVNAFKQRKTAAELLQSQGSQAGGSQTLKRDKEKKN 427

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 427

 Score = 41.3 bits (96), Expect = 1e-04
 Identities = 28/115 (24%), Positives = 55/115 (47%), Gaps = 4/115 (3%)

Query: 19  KKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKK 78
           +   K+ +   K    +E  + K+ E   + ++K+EE  +   ++ +EK+ + +E + + 
Sbjct: 305 EMGFKDTDPDSKPFSLQETYEAKRNEFLGELQKKEEEMRQMFVQRVKEKEAELKEAEKEL 364

Query: 79  KEEKKQKKKEEKKQKKKEEKKQKKKKEEKKN----KKAEEQNRQQGLYPNQKRTL 129
            E+  + KK  + +KKK E K+K   +E       K A E  + QG      +TL
Sbjct: 365 HEKFDRLKKLHQDEKKKLEDKKKSLDDEVNAFKQRKTAAELLQSQGSQAGGSQTL 419

>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 = 39.2 bits (92), Expect = 6e-05
 Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 7/51 (13%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIH--VGNQYGDIPRGIFIIRGENVVLM 175
           R   G L+S D   NLVL+   E     V  + G +     +IRG+N+V +
Sbjct: 36  REFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTV-----LIRGDNIVYI 81

>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 = 39.4 bits (92), Expect = 7e-05
 Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 10/59 (16%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPR----------GIFIIRGENVVLM 175
           R L G L + D+  N+VL    E + + +                  +  +RG++V+L+
Sbjct: 30  RELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDSVILI 88

>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 = 39.4 bits (92), Expect = 8e-05
 Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 7/54 (12%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIH--VGNQYGDIPRGIFIIRGENVVLMGEV 178
               G L S D + NL L++  E +        G+I      IR  NV+ + E+
Sbjct: 43  TEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEI-----FIRCNNVLYIREL 91

>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 = 38.0 bits (89), Expect = 1e-04
 Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 7/51 (13%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERI--HVGNQYGDIPRGIFIIRGENVVLM 175
               G L   D   N+VL          V  +YG I     +IRG+NV+ +
Sbjct: 25  FEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKI-----VIRGDNVLAI 70

>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 = 38.2 bits (89), Expect = 2e-04
 Identities = 19/52 (36%), Positives = 25/52 (48%), Gaps = 3/52 (5%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
               GYL SVD + N+ L  T E I  G   G +  G  +IR  NV+ +  V
Sbjct: 27  MEYKGYLVSVDGYMNMQLANTEEYID-GALSGHL--GEVLIRCNNVLYIRGV 75

>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A* 1u0y_A* 1yt2_A* Length = 269

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 17/46 (36%), Positives = 28/46 (60%)

Query: 55  EKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQ 100
            K E  E+  EE++  KEE++D   E   ++++EEKK K K+ +K 
Sbjct: 216 SKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKT 261

>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A* 1u0y_A* 1yt2_A* Length = 269

 Score = 39.1 bits (92), Expect = 5e-04
 Identities = 13/47 (27%), Positives = 29/47 (61%)

Query: 50  KEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKE 96
             K E  EE  E+++  K++K++ + +   EE++++KK + K+ +K 
Sbjct: 215 SSKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKT 261

>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A* 1u0y_A* 1yt2_A* Length = 269

 Score = 39.1 bits (92), Expect = 5e-04
 Identities = 14/47 (29%), Positives = 27/47 (57%)

Query: 46  KQKKKEKKEEKEEKKEKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQ 92
             K +  +E  EE++  K+E++    E   ++++EEKK K K+ +K 
Sbjct: 215 SSKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKT 261

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 7/54 (12%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIE-RIHVGNQYGDIPR------GIFIIRGENVV 173
           R  IG  ++ D+  NL+L    E R           R      G+ ++RGEN+V
Sbjct: 25  RIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLV 78

>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 = 37.3 bits (87), Expect = 3e-04
 Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 7/54 (12%)

Query: 124 NQKRTLIGYLRSVDQFANLVLHKTIERIHVG--NQYGDIPRGIFIIRGENVVLM 175
            ++  L+G L  VD + NL L   +E          G+I     ++RG NVVL+
Sbjct: 24  GEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEI-----VLRGNNVVLI 72

>2qag_C Septin-7; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 418

 Score = 39.0 bits (90), Expect = 6e-04
 Identities = 19/110 (17%), Positives = 56/110 (50%)

Query: 1   MKISIAPKGAISPRIGKRKKKKKEEENKKKQKKKEEKKQKKKEEKKQKKKEKKEEKEEKK 60
                  K  ++    +R++   + +  + + ++  + + K++ +K K  E + ++  ++
Sbjct: 307 KNKGQLTKSPLAQMEEERREHVAKMKKMEMEMEQVFEMKVKEKVQKLKDSEAELQRRHEQ 366

Query: 61  EKKKEEKKQKKEEEKDKKKEEKKQKKKEEKKQKKKEEKKQKKKKEEKKNK 110
            KK  E + K+ EEK ++ E++K   + +++  +++   +  +K +KK K
Sbjct: 367 MKKNLEAQHKELEEKRRQFEDEKANWEAQQRILEQQNSSRTLEKNKKKGK 416

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	213
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.88
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.88
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.86
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.85
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.85
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.84
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.84
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.84
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.84
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.84
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.84
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.83
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	99.83
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.83
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.82
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.82
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.82
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.82
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.82
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.8
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.8
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.8
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.76
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.74
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	98.87
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	96.25
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	96.05
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	95.87
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	95.66
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	95.51
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	95.49
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	95.44
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	95.42
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	95.09
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	94.7
1ycy_A	71	Conserved hypothetical protein; structural genomic	94.35
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	94.22
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	94.17
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	91.44
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	91.2
3rux_A	270	BIRA bifunctional protein; biotin-protein ligase,	89.95
2eay_A	233	Biotin [acetyl-COA-carboxylase] ligase; biotin bio	88.82
1bia_A	321	BIRA bifunctional protein; transcription regulatio	88.19
2dxu_A	235	Biotin--[acetyl-COA-carboxylase] ligase; biotin bi	85.87
2ej9_A	237	Putative biotin ligase; biotin biosynthesis, monom	85.55
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	85.47

>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=99.88  E-value=3.9e-23  Score=162.09  Aligned_cols=83  Identities=20%  Similarity=0.280  Sum_probs=57.5

Q ss_pred             hhhhHHHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC----ccceeccceeeeecCcEEEEE
Q psy5557         101 KKKKEEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN----QYGDIPRGIFIIRGENVVLMG  176 (213)
Q Consensus       101 ~~~keE~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n----~~~er~LGlVlIRGnnIV~I~  176 (213)
                      .+.+.+.+..|..|+|++|+|.|+|||.|.|+|+|||+||||||+||+|++..++    ....+++|++||||+||++|+
T Consensus        18 ~~~kke~i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nIv~I~   97 (113)
T 4emk_C           18 ERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIA   97 (113)
T ss_dssp             --------------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTTEEEEE
T ss_pred             cCCccchHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCeEEEEE
Confidence            3556789999999999999999999999999999999999999999999986432    134678999999999999999


Q ss_pred             eeccccc
Q psy5557         177 EVVTVVN  183 (213)
Q Consensus       177 ~iD~~~d  183 (213)
                      ++|....
T Consensus        98 ~~d~~ee  104 (113)
T 4emk_C           98 PMDGSEE  104 (113)
T ss_dssp             ECC----
T ss_pred             ecCcccc
Confidence            9986644

>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=5.1e-23  Score=156.35  Aligned_cols=82  Identities=23%  Similarity=0.257  Sum_probs=68.6

Q ss_pred             HHHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC----ccceeccceeeeecCcEEEEEeecc
Q psy5557         105 EEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN----QYGDIPRGIFIIRGENVVLMGEVVT  180 (213)
Q Consensus       105 eE~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n----~~~er~LGlVlIRGnnIV~I~~iD~  180 (213)
                      +++...|..++|++|+|.|+|||.|.|+|.|||+||||||+||.|++....    ....+++|.+||||+||++|+++|.
T Consensus         9 ~~p~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nVv~I~~~d~   88 (96)
T 3bw1_A            9 ETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLISTPSE   88 (96)
T ss_dssp             CCHHHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEECGGGEEEEECCC-
T ss_pred             hhHHHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEECCCEEEEEEecCc
Confidence            578899999999999999999999999999999999999999999986432    1235789999999999999999988


Q ss_pred             cccccc
Q psy5557         181 VVNVKV  186 (213)
Q Consensus       181 ~~d~s~  186 (213)
                      ..|.++
T Consensus        89 ~~d~~~   94 (96)
T 3bw1_A           89 DDDGAV   94 (96)
T ss_dssp             ----CC
T ss_pred             cccccc
Confidence            877654

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

Probab=99.86  E-value=1.5e-21  Score=141.00  Aligned_cols=71  Identities=17%  Similarity=0.095  Sum_probs=63.4

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeecc
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVT  180 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~  180 (213)
                      +...|..++|++|+|.|+||+.|.|+|.|||+||||+|+||.|++..   ...+.+|.++|||+||++|+++|+
T Consensus         5 P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~---~~~~~lg~v~iRG~~I~~i~~~~e   75 (75)
T 1h64_1            5 PLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDG---EVVKRYGKIVIRGDNVLAISPTEE   75 (75)
T ss_dssp             HHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETT---EEEEEEEEEEECGGGEEEEEEC--
T ss_pred             HHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeC---CceeECCEEEECCCEEEEEEeCCC
Confidence            67899999999999999999999999999999999999999998743   236789999999999999998763

>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=99.85  E-value=9.4e-22  Score=143.18  Aligned_cols=71  Identities=24%  Similarity=0.428  Sum_probs=53.1

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeecc
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVT  180 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~  180 (213)
                      ...+|..++|++|+|.|+||+.|.|+|.|||+||||+|+||.|++..+.   .+.+|.++|||+||++|+++|.
T Consensus         5 ~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~---~~~lg~v~iRG~~I~~i~~~d~   75 (76)
T 3s6n_G            5 HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQ---QNNIGMVVIRGNSIIMLEALER   75 (76)
T ss_dssp             ---------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC-------CBSSEEECSSSEEEEEC---
T ss_pred             chHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccCCc---EeEcCEEEECCCeEEEEEeccC
Confidence            3578999999999999999999999999999999999999999875432   5689999999999999999874

>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=99.85  E-value=3.6e-21  Score=139.35  Aligned_cols=71  Identities=21%  Similarity=0.143  Sum_probs=64.1

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeecc
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVT  180 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~  180 (213)
                      +...|..++|++|+|.|+||+.|.|+|.|||+||||+|+||.|++...   ..+.+|.++|||+||++|+++|.
T Consensus         5 P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~---~~~~lg~v~iRG~~I~~i~~~d~   75 (77)
T 1i4k_A            5 PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGE---VVRKVGSVVIRGDTVVFVSPAPG   75 (77)
T ss_dssp             HHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTE---EEEEEEEEEECGGGEEEEEECC-
T ss_pred             HHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecCC---cEeECCEEEECCCEEEEEEeCCC
Confidence            578999999999999999999999999999999999999999987432   35689999999999999998774

>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=99.84  E-value=5.5e-21  Score=140.20  Aligned_cols=72  Identities=32%  Similarity=0.378  Sum_probs=64.2

Q ss_pred             HHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeecc
Q psy5557         106 EKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVT  180 (213)
Q Consensus       106 E~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~  180 (213)
                      -+...|..++|++|+|.|+||+.|.|+|.|||+||||+|+||.|++...   ..+.+|.++|||+||++|+++|.
T Consensus         9 ~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~---~~~~lg~v~iRG~~I~~i~~~~~   80 (81)
T 1th7_A            9 TAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDG---SGKKLGTIVIRGDNVILISPLQT   80 (81)
T ss_dssp             HHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSS---CEEEEEEEEECGGGEEEEEEC--
T ss_pred             chHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecCC---ceeECCEEEECCCEEEEEEecCC
Confidence            4678999999999999999999999999999999999999999987532   35789999999999999998773

>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=99.84  E-value=2e-21  Score=140.91  Aligned_cols=71  Identities=21%  Similarity=0.257  Sum_probs=63.5

Q ss_pred             HHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeec
Q psy5557         106 EKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       106 E~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      .+...|..++|++|+|.|+||+.|.|+|.|||+||||+|+||.|++. +.  ..+.+|.++|||+||++|+++|
T Consensus         4 ~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~-~~--~~~~lg~v~iRG~~I~~i~~~~   74 (75)
T 4emk_B            4 SPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVN-GK--KTNVYGDAFIRGNNVLYVSALD   74 (75)
T ss_dssp             HHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEET-TE--EEEEEEEEEEEGGGSSEEEEC-
T ss_pred             chHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEec-CC--cccEecEEEEcCCeEEEEEecC
Confidence            46789999999999999999999999999999999999999999863 22  2567999999999999999876

>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=99.84  E-value=4.4e-21  Score=139.29  Aligned_cols=71  Identities=23%  Similarity=0.280  Sum_probs=63.2

Q ss_pred             HHHHHHhhcCCeEEEEecCC-eEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeecc
Q psy5557         107 KKNKKAEEQNRQQGLYPNQK-RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVT  180 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDG-R~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~  180 (213)
                      +...|..++|++|+|.|+|| +.|.|+|.|||+||||+|+||.|++. +.  ..+.+|.++|||+||++|+++|.
T Consensus         6 P~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~-~~--~~~~lg~v~iRG~nI~~i~~~de   77 (77)
T 1ljo_A            6 PNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKG-EE--KVRSLGEIVLRGNNVVLIQPQEE   77 (77)
T ss_dssp             HHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEET-TE--EEEEEEEEEECGGGEEEEEEC--
T ss_pred             hHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEec-CC--cEeECCeEEEeCCeEEEEEeCCC
Confidence            57899999999999999999 99999999999999999999999874 22  25689999999999999998873

>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=99.84  E-value=8e-21  Score=145.02  Aligned_cols=73  Identities=14%  Similarity=0.103  Sum_probs=64.5

Q ss_pred             HHHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeec
Q psy5557         105 EEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       105 eE~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      ..++..|..++|++|+|.|+||+.|.|+|.|||+||||+|+||.|++..+.  ..+.+|.+||||+||++|.+..
T Consensus        19 ~~Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~--~~~~lg~v~IRG~nI~~i~p~~   91 (94)
T 4emk_A           19 ILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTG--VTEKHSEMLLNGNGMCMLIPGG   91 (94)
T ss_dssp             -CHHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTTC--CEEEEEEEEECSTTEEEEEECC
T ss_pred             ccCHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCCC--cEeEcCEEEEcCCEEEEEEeCC
Confidence            346789999999999999999999999999999999999999999973332  2678999999999999999764

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

Probab=99.84  E-value=4.4e-21  Score=142.95  Aligned_cols=74  Identities=22%  Similarity=0.265  Sum_probs=63.4

Q ss_pred             HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeec--C-----CccceeccceeeeecCcEEEEEeecc
Q psy5557         108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHV--G-----NQYGDIPRGIFIIRGENVVLMGEVVT  180 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~--~-----n~~~er~LGlVlIRGnnIV~I~~iD~  180 (213)
                      ..+|..++|++|+|.|+||+.|.|+|+|||+||||||+||.|++..  .     .....+.+|.+||||+||++|.+.+.
T Consensus         6 ~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~~I~~i~~~~~   85 (91)
T 1d3b_B            6 SSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEGP   85 (91)
T ss_dssp             -CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEEEC
T ss_pred             hHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECCCeEEEEEcCCC
Confidence            3578999999999999999999999999999999999999997521  1     12346789999999999999998774


Q ss_pred             c
Q psy5557         181 V  181 (213)
Q Consensus       181 ~  181 (213)
                      .
T Consensus        86 ~   86 (91)
T 1d3b_B           86 P   86 (91)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.84  E-value=9e-21  Score=139.27  Aligned_cols=71  Identities=27%  Similarity=0.356  Sum_probs=64.3

Q ss_pred             HHHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeec
Q psy5557         105 EEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       105 eE~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      ..+...|..++|++|+|.|+||+.|.|+|.|||+||||+|+||.|+ . +.  ..+++|.++|||+||++|+++|
T Consensus        10 ~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~-~~--~~~~lg~v~iRG~~I~~i~~~d   80 (81)
T 1i8f_A           10 ATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-I-DG--NVYKRGTMVVRGENVLFISPVP   80 (81)
T ss_dssp             CCHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-E-TT--EEEEEEEEEECGGGEEEEEECC
T ss_pred             cchHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-c-CC--cccCCCEEEECCCEEEEEEeCC
Confidence            3578899999999999999999999999999999999999999998 3 32  3678999999999999999876

>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=99.83  E-value=5.3e-21  Score=148.54  Aligned_cols=80  Identities=20%  Similarity=0.193  Sum_probs=54.7

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeecccccccc
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVNVKV  186 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~d~s~  186 (213)
                      +..+|..++|++|+|.|+||+.|.|+|.|||+||||+|+||.|...++..  .+.+|.+||||+||+||.++|..+++++
T Consensus        17 p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg~~--~~~lg~v~IRG~nI~~I~~pd~l~d~p~   94 (105)
T 4emh_A           17 PLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDK--FFRLPECYIRGNNIKYLRIQDEVLSQVA   94 (105)
T ss_dssp             ---------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCE--EEEEEEEEECGGGEEEEEC---------
T ss_pred             HHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCCce--eeEcCeEEEeCCeEEEEecCHHHhhhhh
Confidence            56789999999999999999999999999999999999999987544432  4678999999999999999999998887


Q ss_pred             cc
Q psy5557         187 IK  188 (213)
Q Consensus       187 ~e  188 (213)
                      ..
T Consensus        95 ~~   96 (105)
T 4emh_A           95 KQ   96 (105)
T ss_dssp             --
T ss_pred             hh
Confidence            65

>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=99.83  E-value=9.7e-21  Score=141.41  Aligned_cols=73  Identities=26%  Similarity=0.195  Sum_probs=63.8

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeecccc
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVV  182 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~  182 (213)
                      +..+|..++|++|+|.|+||+.|.|+|.|||+||||+|+||.|+.. +.  ..+.+|.++|||+||++|+++|...
T Consensus         7 P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~-g~--~~~~lg~v~IRG~nI~~i~~~d~~~   79 (86)
T 3s6n_F            7 PKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYID-GA--LSGHLGEVLIRCNNVLYIRGVEEEE   79 (86)
T ss_dssp             HHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEET-TE--EEEEESSEEECGGGEEEEEECC---
T ss_pred             cHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcC-Cc--eeeEccEEEEeCCeEEEEEeCCccc
Confidence            6789999999999999999999999999999999999999998753 22  2467999999999999999988664

>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=99.83  E-value=2e-20  Score=162.96  Aligned_cols=72  Identities=22%  Similarity=0.278  Sum_probs=63.2

Q ss_pred             HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeec-C------CccceeccceeeeecCcEEEEEeec
Q psy5557         108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHV-G------NQYGDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~-~------n~~~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      ..+|.+|||++|+|.|+|||.|+|+|+|||+||||||+||+|++.. .      .....+++|+||||||||++|+..+
T Consensus         6 ~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~Isve~   84 (231)
T 3pgw_B            6 SSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEG   84 (231)
T ss_pred             hHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEEEEecC
Confidence            4689999999999999999999999999999999999999998741 1      1234789999999999999999643

>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=99.82  E-value=2.1e-20  Score=147.08  Aligned_cols=72  Identities=13%  Similarity=0.044  Sum_probs=64.6

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccc
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTV  181 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~  181 (213)
                      +..+|..++|++|+|.|+||+.|.|+|.|||+||||+|+||+|+....   ....+|.+||||+||+||.++|..
T Consensus         3 p~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~~---~~~~lg~v~IRG~nI~~I~~pd~l   74 (119)
T 1b34_A            3 LVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNR---EPVQLETLSIRGNNIRYFILPDSL   74 (119)
T ss_dssp             HHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTS---CCEEEEEEEECGGGEEEEECCTTC
T ss_pred             hHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecCCC---ceeEcceEEEcCCeEEEEEecccc
Confidence            467899999999999999999999999999999999999999986432   246899999999999999998773

>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=99.82  E-value=1.4e-20  Score=148.35  Aligned_cols=77  Identities=14%  Similarity=0.082  Sum_probs=65.3

Q ss_pred             HHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecC-------Cccc-----eeccceeeeecCcEE
Q psy5557         106 EKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVG-------NQYG-----DIPRGIFIIRGENVV  173 (213)
Q Consensus       106 E~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~-------n~~~-----er~LGlVlIRGnnIV  173 (213)
                      .++..|..++|++|+|.|+||+.|.|+|+|||+||||||+||.|++...       ....     .+.+|.+||||+||+
T Consensus        28 ~Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG~nVv  107 (121)
T 2fwk_A           28 LPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVA  107 (121)
T ss_dssp             CHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGEE
T ss_pred             CcHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECCCEEE
Confidence            5788999999999999999999999999999999999999999988530       1112     568999999999999


Q ss_pred             EEEeecccc
Q psy5557         174 LMGEVVTVV  182 (213)
Q Consensus       174 ~I~~iD~~~  182 (213)
                      +|++.+...
T Consensus       108 ~I~~~~~~~  116 (121)
T 2fwk_A          108 MLVPGGDPD  116 (121)
T ss_dssp             EEESSSCC-
T ss_pred             EEEecCCCC
Confidence            999877553

>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=99.82  E-value=1.5e-20  Score=142.73  Aligned_cols=74  Identities=18%  Similarity=0.228  Sum_probs=65.7

Q ss_pred             hHHHHHHHHhhcCCeEEEEe----cCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeec
Q psy5557         104 KEEKKNKKAEEQNRQQGLYP----NQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       104 keE~~~~L~~~LgKrV~V~L----kDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      --.+++.|..+++++|+|.+    +||+.|.|+|.|||+||||+|+||.|++..+.  ..+.+|.+||||+||++|+++|
T Consensus        14 m~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~--~~~~lg~v~iRG~nV~~i~~~~   91 (92)
T 3s6n_E           14 MVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTK--SRKQLGRIMLKGDNITLLQSVS   91 (92)
T ss_dssp             CCCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSC--CEEEEEEEEECGGGEEEEEEC-
T ss_pred             ccCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCC--ceeEcCeEEEeCCEEEEEEeCC
Confidence            34588999999999999999    99999999999999999999999999975432  3678999999999999999876

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

Probab=99.82  E-value=3.1e-20  Score=140.60  Aligned_cols=73  Identities=19%  Similarity=0.224  Sum_probs=62.7

Q ss_pred             HHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeec----CC------ccceeccceeeeecCcEEEE
Q psy5557         106 EKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHV----GN------QYGDIPRGIFIIRGENVVLM  175 (213)
Q Consensus       106 E~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~----~n------~~~er~LGlVlIRGnnIV~I  175 (213)
                      .+...|..++|++|+|.|+||+.|.|+|.|||+||||+|+||.|++..    +.      ....+++|++||||+||++|
T Consensus         9 ~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG~nVv~I   88 (93)
T 4emg_A            9 EPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDSVILI   88 (93)
T ss_dssp             CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECGGGEEEE
T ss_pred             CCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECCCeEEEE
Confidence            456788888999999999999999999999999999999999999863    11      01367899999999999999


Q ss_pred             Eee
Q psy5557         176 GEV  178 (213)
Q Consensus       176 ~~i  178 (213)
                      +++
T Consensus        89 ~p~   91 (93)
T 4emg_A           89 APP   91 (93)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            864

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

Probab=99.82  E-value=2.7e-20  Score=137.43  Aligned_cols=70  Identities=24%  Similarity=0.263  Sum_probs=62.9

Q ss_pred             HHHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557         105 EEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE  177 (213)
Q Consensus       105 eE~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~  177 (213)
                      ..+...|..++|++|+|.|+||+.|.|+|.|||+||||+|+||.|++..   ...+.+|.++|||+||++|++
T Consensus        14 ~~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~---~~~~~lg~v~IRG~~I~~i~p   83 (83)
T 1mgq_A           14 QRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDG---EVTRRLGTVLIRGDNIVYISP   83 (83)
T ss_dssp             TCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETT---EEEEEEEEEEECGGGEEEEEC
T ss_pred             cChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecC---CcccCCCEEEECCCEEEEEEC
Confidence            4467899999999999999999999999999999999999999998743   236789999999999999974

>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=99.80  E-value=1.3e-19  Score=131.93  Aligned_cols=70  Identities=13%  Similarity=-0.001  Sum_probs=63.1

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeec
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      +...|..++|++|+|.|++|+.|.|+|.|||+||||+|+||.++..++   ....+|.++|||+||.||..+|
T Consensus         6 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~~---~~~~lg~v~IRG~nI~~i~lPd   75 (75)
T 1d3b_A            6 PIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDG---RVAQLEQVYIRGCKIRFLILPD   75 (75)
T ss_dssp             HHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTS---CEEEEEEEEECGGGEEEEEECC
T ss_pred             HHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCCC---cEEEcCeEEEeCCEEEEEEcCC
Confidence            678999999999999999999999999999999999999999986333   2568999999999999998765

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

Probab=99.80  E-value=5.8e-20  Score=139.44  Aligned_cols=71  Identities=25%  Similarity=0.251  Sum_probs=60.2

Q ss_pred             HHHHHHHhhcCCeEEEEecCC-eEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeec
Q psy5557         106 EKKNKKAEEQNRQQGLYPNQK-RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       106 E~~~~L~~~LgKrV~V~LkDG-R~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      -+..+|..++|++|+|.|+|| +.|.|+|.|||+||||+|+||.|++. +.  ..+.+|.+||||+||++|.+++
T Consensus        21 ~P~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~-~~--~~~~lg~v~IRG~nI~~I~~~~   92 (93)
T 1n9r_A           21 NPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVA-GV--SHGTLGEIFIRCNNVLYIRELP   92 (93)
T ss_dssp             -----CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEET-TE--EEEECCSEEECGGGEEEEEECC
T ss_pred             ChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcC-CC--eEeEcCEEEEcCCeEEEEEeCC
Confidence            467889999999999999999 99999999999999999999999863 22  2568999999999999999876

>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=99.80  E-value=1.4e-19  Score=141.83  Aligned_cols=76  Identities=17%  Similarity=0.193  Sum_probs=62.7

Q ss_pred             HHHHHHHHhhc--CCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCc-----------cceeccceeeeecCc
Q psy5557         105 EEKKNKKAEEQ--NRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQ-----------YGDIPRGIFIIRGEN  171 (213)
Q Consensus       105 eE~~~~L~~~L--gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~-----------~~er~LGlVlIRGnn  171 (213)
                      ..+++.|..++  |++|+|.|+||+.|.|+|+|||+||||||+||.|++.....           ...+++|.+||||+|
T Consensus        26 ~~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~n  105 (118)
T 1b34_B           26 TGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDS  105 (118)
T ss_dssp             CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGG
T ss_pred             cChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcCCE
Confidence            35788999999  59999999999999999999999999999999998743110           124579999999999


Q ss_pred             EEEEEeecc
Q psy5557         172 VVLMGEVVT  180 (213)
Q Consensus       172 IV~I~~iD~  180 (213)
                      |++|++.+.
T Consensus       106 Vv~I~~~~~  114 (118)
T 1b34_B          106 VIVVLRNPL  114 (118)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEeCch
Confidence            999998764

>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=99.76  E-value=1.2e-18  Score=139.17  Aligned_cols=78  Identities=13%  Similarity=0.049  Sum_probs=68.1

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeecccccccc
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVNVKV  186 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~d~s~  186 (213)
                      +..+|..++|++|+|.|+||++|.|+|.|||+||||+|+||+++..++.   ...+|.||||||||.||..+|...+.++
T Consensus         6 P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~---~~~l~~v~IRGnnI~~I~lpd~l~~~~~   82 (126)
T 2y9a_D            6 PIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGR---VAQLEQVYIRGSKIRFLILPDMLKNAPM   82 (126)
T ss_dssp             SHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSC---CEEEEEEEECGGGEEEEECCSSCSSSSH
T ss_pred             HHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCc---EeecccEEEeCCEEEEEEccccccchHH
Confidence            5689999999999999999999999999999999999999998753332   4678999999999999998887765554


Q ss_pred             c
Q psy5557         187 I  187 (213)
Q Consensus       187 ~  187 (213)
                      .
T Consensus        83 l   83 (126)
T 2y9a_D           83 L   83 (126)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=99.74  E-value=2e-18  Score=138.48  Aligned_cols=72  Identities=15%  Similarity=0.172  Sum_probs=64.3

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccccccccc
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVNVKVI  187 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~d~s~~  187 (213)
                      ..|..++|++|+|.|+||+.|.|+|.|||+||||+|+||.|+.  +     ..+|.++|||+||++|.++|..+|..+.
T Consensus         3 ~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~~--~-----~~lg~v~IRG~nI~~I~~~d~~~d~~~f   74 (130)
T 1m5q_A            3 AELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA--G-----EKFNRVFIMYRYIVHIDSTERRIDMREF   74 (130)
T ss_dssp             HHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECTT--C-----CEEEEEEECGGGEEEEEECCCCCCHHHH
T ss_pred             hHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEEc--C-----CEeceEEEeCCeEEEEEcCCcccCHHHH
Confidence            5799999999999999999999999999999999999999862  2     3689999999999999999887665433

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

Probab=98.87  E-value=9.3e-09  Score=77.88  Aligned_cols=66  Identities=15%  Similarity=0.098  Sum_probs=56.8

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEec-CcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccccc
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVD-QFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVN  183 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFD-q~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~d  183 (213)
                      ..|.+|+|+.|.|+|.||++|.|+|.+|| ...||+|.||    ..++.     ...++|.|..|..|..+....+
T Consensus        10 ~el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~----~~~~~-----~~~~iI~G~aI~eI~v~~~~~~   76 (86)
T 1y96_A           10 LEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNF----LEDGS-----MSVTGIMGHAVQTVETMNEGDH   76 (86)
T ss_dssp             HHHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEE----CTTSC-----EEEEEECGGGEEEEEEEECCCH
T ss_pred             HHHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeec----ccCCe-----EEEEEEecceEEEEEEecchhH
Confidence            47999999999999999999999999999 8999999998    12332     4789999999999998765543

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

Probab=96.25  E-value=0.022  Score=43.06  Aligned_cols=63  Identities=8%  Similarity=0.017  Sum_probs=50.5

Q ss_pred             HHHHHHHhhcCCeEEEEecCCeEEEEEEEEec-CcCceEecceEEEeecCCccceeccceeeeecCcEEEEE
Q psy5557         106 EKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVD-QFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMG  176 (213)
Q Consensus       106 E~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFD-q~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~  176 (213)
                      --+..|..+.|++|.+.|-++-.+.|++.++| ...|++.++-.    .+    ...+...+||++.|++++
T Consensus        19 RfLr~l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~----TP----iGv~~eAlLR~~Dii~~s   82 (85)
T 1y96_B           19 RYLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQ----TP----IGVQAEALLRCSDIISYT   82 (85)
T ss_dssp             HHHHHHHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEC----CT----TCCEEEEEEEGGGEEEEE
T ss_pred             HHHHHHHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhcC----CC----cccchhhhhhcCCEEEEE
Confidence            35667788889999999999999999999999 56688877641    12    113577999999999986

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

Probab=96.05  E-value=0.03  Score=41.27  Aligned_cols=57  Identities=5%  Similarity=0.029  Sum_probs=41.7

Q ss_pred             HHHHHhhc--CCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeec
Q psy5557         108 KNKKAEEQ--NRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       108 ~~~L~~~L--gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      -.+|+.+.  ..+|.|.|.+|-.+.|.+.+||+|+=|+-++.               ...+|--..|.+|.+..
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 DKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQG---------------KQHLIYKHAISTYTVET   67 (77)
T ss_dssp             HHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEEETT---------------EEEEEEGGGEEEEEC--
T ss_pred             HHHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEEEECC---------------eeEEEEeeeEEEEeECc
Confidence            34566666  89999999999999999999999986665332               23456666677776543

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

Probab=95.87  E-value=0.015  Score=43.13  Aligned_cols=38  Identities=16%  Similarity=0.169  Sum_probs=31.5

Q ss_pred             HHHHhhc--CCeEEEEecCCeEEEEEEEEecCcCceEecc
Q psy5557         109 NKKAEEQ--NRQQGLYPNQKRTLIGYLRSVDQFANLVLHK  146 (213)
Q Consensus       109 ~~L~~~L--gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsD  146 (213)
                      .+|+.+-  ..+|.|.|.||-.+.|.+.|||+|+=|+-.+
T Consensus        14 ~fLn~lrk~~~~Vtv~L~nG~~l~G~I~~fD~f~VlL~~~   53 (78)
T 3ahu_A           14 QFLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFTVLLESE   53 (78)
T ss_dssp             HHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEESS
T ss_pred             HHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEEEEEC
Confidence            4455554  8899999999999999999999999776543

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

Probab=95.66  E-value=0.064  Score=40.74  Aligned_cols=68  Identities=16%  Similarity=0.113  Sum_probs=51.2

Q ss_pred             hhcCCeEEEEecCCeEEEEEEEEec-CcCceEecceEEEeecCCc----c--ceeccceeeeecCcEEEEEeecc
Q psy5557         113 EEQNRQQGLYPNQKRTLIGYLRSVD-QFANLVLHKTIERIHVGNQ----Y--GDIPRGIFIIRGENVVLMGEVVT  180 (213)
Q Consensus       113 ~~LgKrV~V~LkDGR~~~GtL~gFD-q~mNLVLsDavEri~~~n~----~--~er~LGlVlIRGnnIV~I~~iD~  180 (213)
                      .|||++|.++.+.+-.|.|+|..+| +..-|.|.++.-+=..+..    +  ...-+..++.||+.|--+...+.
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            5899999999999999999999999 5668889998543221110    0  11235789999999999886553

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

Probab=95.51  E-value=0.019  Score=41.97  Aligned_cols=32  Identities=9%  Similarity=0.174  Sum_probs=28.3

Q ss_pred             cCCeEEEEecCCeEEEEEEEEecCcCceEecc
Q psy5557         115 QNRQQGLYPNQKRTLIGYLRSVDQFANLVLHK  146 (213)
Q Consensus       115 LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsD  146 (213)
                      -+.+|.|.|.||-.+.|.+.|||+|+=|+-.+
T Consensus        24 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~   55 (71)
T 2qtx_A           24 NGKKVKIFLRNGEVLDAEVTGVSNYEIMVKVG   55 (71)
T ss_dssp             TTCEEEEEETTSCEEEEEEEEECSSEEEEEET
T ss_pred             cCCcEEEEEeCCeEEEEEEEEEcceEEEEEeC
Confidence            36799999999999999999999999777554

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

Probab=95.49  E-value=0.046  Score=42.61  Aligned_cols=55  Identities=15%  Similarity=0.077  Sum_probs=40.3

Q ss_pred             HHHHhhc--CCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeec
Q psy5557         109 NKKAEEQ--NRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       109 ~~L~~~L--gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      .+|+.+.  ..+|.|.|.+|-.+.|.+.+||+|+=|+-++                ...||.-..|.+|.+..
T Consensus        12 ~fLn~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~VlL~~~----------------kqqLIYKHAISTI~p~~   68 (104)
T 2y90_A           12 PFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNT----------------VSQMVYKHAISTVVPSR   68 (104)
T ss_dssp             HHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEESS----------------SEEEEEGGGEEEEEESS
T ss_pred             HHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEECC----------------ceEEEEeeeeEEEeecc
Confidence            4555555  4499999999999999999999998666532                23456666677777654

>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=95.44  E-value=0.028  Score=41.11  Aligned_cols=55  Identities=15%  Similarity=0.077  Sum_probs=42.6

Q ss_pred             HHHHhhc--CCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeec
Q psy5557         109 NKKAEEQ--NRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       109 ~~L~~~L--gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      .+|+.+.  ..+|.|.|.+|-.+.|.+.+||+|+=++-++                ...+|.-..|.+|.+..
T Consensus        12 ~~L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~vlL~~~----------------~~~LIYKhAIsTI~p~~   68 (74)
T 2ylb_A           12 PFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNT----------------VSQMVYKHAISTVVPSR   68 (74)
T ss_dssp             HHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEEESS----------------SEEEEEGGGEEEEEESS
T ss_pred             HHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcEEEEECC----------------ceEEEEeeeEEEEeEcc
Confidence            4566666  8899999999999999999999998655421                23567777788887654

>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=95.42  E-value=0.028  Score=42.16  Aligned_cols=35  Identities=23%  Similarity=0.215  Sum_probs=29.5

Q ss_pred             HHHhhc--CCeEEEEecCCeEEEEEEEEecCcCceEe
Q psy5557         110 KKAEEQ--NRQQGLYPNQKRTLIGYLRSVDQFANLVL  144 (213)
Q Consensus       110 ~L~~~L--gKrV~V~LkDGR~~~GtL~gFDq~mNLVL  144 (213)
                      +|+.+-  ..+|.|.|.||-.+.|.+.|||+|+=|+-
T Consensus        11 fLn~lrk~~~~Vtv~L~NG~~l~G~I~~fD~ftVlL~   47 (82)
T 1u1s_A           11 YLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLK   47 (82)
T ss_dssp             HHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEEE
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEe
Confidence            444444  78999999999999999999999987664

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

Probab=95.09  E-value=0.06  Score=41.42  Aligned_cols=72  Identities=14%  Similarity=0.089  Sum_probs=50.6

Q ss_pred             HHHHHhhcCCeEEEEecCCeEEEEEEEEec-CcCceEecceEEEeecCC----cc--ceeccceeeeecCcEEEEEeec
Q psy5557         108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVD-QFANLVLHKTIERIHVGN----QY--GDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFD-q~mNLVLsDavEri~~~n----~~--~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      ...-..|||++|.++.+.+-.|.|+|..+| +-.-|.|.++.-+=..+.    .+  ....+..++.||+.|-.|...+
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            345678999999999999999999999999 566788998843211111    00  1123588999999999987655

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

Probab=94.70  E-value=0.26  Score=39.56  Aligned_cols=58  Identities=12%  Similarity=0.035  Sum_probs=45.8

Q ss_pred             HHhhcCCeEEEEecCCeEEEEEEEEecCcCceEe--cceEEEeecCCccceeccceeeeecCcEEEEEeecccc
Q psy5557         111 KAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVL--HKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVV  182 (213)
Q Consensus       111 L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVL--sDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~  182 (213)
                      ...|+|+.|.|.|+||..++|++..+| --+|+|  ++|.             +....|+.+.|.-+..+....
T Consensus         7 ~sqFlGy~V~v~LkDgs~~qG~I~~vd-~k~LtL~~~~a~-------------~s~~~I~asdI~DLkVl~~~~   66 (125)
T 4a53_A            7 VADFYGSNVEVLLNNDSKARGVITNFD-SSNSILQLRLAN-------------DSTKSIVTKDIKDLRILPKNE   66 (125)
T ss_dssp             HHHHTTCEEEEEETTSCEEEEEEEEEE-TTTTEEEEEETT-------------TEEEEEEGGGEEEEEECCSCC
T ss_pred             HHHhcCceEEEEECCCCEeeEEEEeec-CCeeEEeccccc-------------cccceeecccccceeeeeccc
Confidence            578999999999999999999999998 345666  8882             122278888888887766553

>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=94.35  E-value=0.11  Score=37.76  Aligned_cols=61  Identities=15%  Similarity=0.195  Sum_probs=43.0

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE  177 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~  177 (213)
                      ..|..+-|++|-|.+....+|+|+|.-||.-. |+|.|++.+..  |.     --.++|+=+.|-.|-.
T Consensus         9 ktL~~WKg~rvAv~vg~ehSFtGiledFDeEv-iLL~dV~D~~G--Nk-----~k~liv~idDinWimL   69 (71)
T 1ycy_A            9 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIG--NR-----GKQMLIGLEDINWIML   69 (71)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTE--EE-----EEEEEEEGGGEEEEEE
T ss_pred             HHHHHhCCcEEEEEecCcceeeeehhhcCcce-eehhhHHHHhc--cc-----cceeEEEeccceEEEe
Confidence            46889999999999999999999999999864 67888887642  22     1346666677666654

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

Probab=94.22  E-value=0.051  Score=40.38  Aligned_cols=55  Identities=13%  Similarity=0.086  Sum_probs=40.7

Q ss_pred             HHHHhhc--CCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeec
Q psy5557         109 NKKAEEQ--NRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       109 ~~L~~~L--gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      .+|+.+.  ..+|.|.|.+|-.+.|.+.+||+|+=|+ .+       +        ...+|.-..|.+|.+..
T Consensus        11 ~fLn~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~VlL-~~-------g--------~~qLIYKhAISTI~P~~   67 (79)
T 3sb2_A           11 PFLNALRKEHVPVSIYLVNGIKLQGHVESFDQYVVLL-RN-------T--------VTQMVYKHAISTVVPAR   67 (79)
T ss_dssp             HHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEEEE-ES-------S--------SEEEEEGGGEEEEEESS
T ss_pred             HHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEE-EC-------C--------ceEEEEeeeEEEEeecC
Confidence            4555554  5679999999999999999999998665 21       1        23467777788887643

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

Probab=94.17  E-value=0.15  Score=38.45  Aligned_cols=64  Identities=13%  Similarity=0.118  Sum_probs=51.0

Q ss_pred             HhhcCCeEEEEecCCe-EEEEEEEEecCc-CceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccc
Q psy5557         112 AEEQNRQQGLYPNQKR-TLIGYLRSVDQF-ANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTV  181 (213)
Q Consensus       112 ~~~LgKrV~V~LkDGR-~~~GtL~gFDq~-mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~  181 (213)
                      .+|||+.|.|.-.++. .|+|.|..+|.. .||.|.+++   .++  + ......|.+++..|..+..+...
T Consensus         5 ~~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~f---~NG--~-~~~s~eVtls~~DI~~L~ii~~~   70 (84)
T 2vc8_A            5 TDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPF---HNG--V-KCLVPEVTFRAGDITELKILEIP   70 (84)
T ss_dssp             CTTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEEE---ETT--E-ECSSSEEEEEGGGCSEEEEEECC
T ss_pred             ccccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehhh---hCC--C-CCCCcEEEEEecChhheEEEecC
Confidence            3799999999999999 999999999976 589999994   333  2 23346688999888888776544

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

Probab=91.44  E-value=1.4  Score=32.05  Aligned_cols=58  Identities=5%  Similarity=-0.047  Sum_probs=43.0

Q ss_pred             HHHHHHhhc--CCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEee
Q psy5557         107 KKNKKAEEQ--NRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV  178 (213)
Q Consensus       107 ~~~~L~~~L--gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~i  178 (213)
                      +...|+.||  ..+|.|.|.+|..++|.+.-+|+|.=.+.++.       .       ..++|....|+||-+.
T Consensus        12 svR~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~cl~L~~~~-------~-------~~~LI~R~AI~~Ikp~   71 (72)
T 3hfn_A           12 SIRQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTCVCIADEN-------S-------RQTTIWKQAIAYLQPK   71 (72)
T ss_dssp             HHHHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSEEEEEC-----------------CEEEEEGGGEEEEEEC
T ss_pred             cHHHHHHHHhhCceEEEEecCCCEEEEEEEEECCCEEEEEcCC-------C-------CeEEEEeeeeEEEEeC
Confidence            456778888  56899999999999999999999864433221       1       2377888889988753

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

Probab=91.20  E-value=1.4  Score=32.03  Aligned_cols=57  Identities=11%  Similarity=0.014  Sum_probs=42.0

Q ss_pred             HHHHHHhhc--CCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557         107 KKNKKAEEQ--NRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE  177 (213)
Q Consensus       107 ~~~~L~~~L--gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~  177 (213)
                      +...|..|+  ..+|.|.|.+|..++|.+..||+|.=++.++       +.       -.++|....|++|-+
T Consensus        10 svR~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~cl~L~~~-------~~-------~~~LI~r~AI~~I~p   68 (70)
T 3hfo_A           10 SVRQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDGLGLVDD-------SE-------RSTIVRLAAIAYITP   68 (70)
T ss_dssp             HHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEECT-------TC-------CEEEEEGGGEEEEEE
T ss_pred             cHHHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCEEEEEcC-------CC-------CeEEEEeeeeEEEee
Confidence            345666776  6789999999999999999999986444322       11       135777788888864

>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=89.95  E-value=0.35  Score=41.79  Aligned_cols=36  Identities=14%  Similarity=0.170  Sum_probs=31.7

Q ss_pred             HhhcCCeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557         112 AEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKT  147 (213)
Q Consensus       112 ~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa  147 (213)
                      ..++|++|.|.+.+|..+.|++.|+|..+.|+|...
T Consensus       220 ~~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~~  255 (270)
T 3rux_A          220 SLTIGSRVRVELPGGQDVVGIARDIDDQGRLCLDVG  255 (270)
T ss_dssp             BSSTTSEEEEECTTSCEEEEEEEEECTTSCEEEEET
T ss_pred             hcccCCEEEEEECCCeEEEEEEEEECCCCeEEEEEC
Confidence            345799999998889999999999999999999754

>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=88.82  E-value=0.31  Score=40.97  Aligned_cols=52  Identities=17%  Similarity=0.174  Sum_probs=36.4

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeec
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRG  169 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRG  169 (213)
                      .....++|++|.|...++  +.|++.|+|..+.|+|......       ...+.|.|.+|+
T Consensus       181 ~~~~~~~g~~V~v~~~~~--~~G~~~gId~~G~L~v~~~~G~-------~~~~~Gev~~r~  232 (233)
T 2eay_A          181 ESKMLYLGEEVKLLGEGK--ITGKLVGLSEKGGALILTEEGI-------KEILSGEFSLRR  232 (233)
T ss_dssp             HHHBTTTTSEEEETTEEE--EEEEEEEECTTSCEEEEETTEE-------EEECSCCEEEC-
T ss_pred             HHhhcccCCEEEEEECCe--EEEEEEEECCCCeEEEEECCCe-------EEEEEeEEEEec
Confidence            344456899999986555  9999999999999999753111       122357777765

>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=88.19  E-value=0.83  Score=39.85  Aligned_cols=53  Identities=21%  Similarity=0.216  Sum_probs=37.7

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeec
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRG  169 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRG  169 (213)
                      .....++|++|.|... +..+.|++.|+|..+.|+|.....       ......|.|.+|+
T Consensus       266 ~~~~~~~g~~V~v~~~-~~~~~G~~~gid~~G~L~v~~~~g-------~~~~~~Gev~~r~  318 (321)
T 1bia_A          266 EKLDNFINRPVKLIIG-DKEIFGISRGIDKQGALLLEQDGI-------IKPWMGGEISLRS  318 (321)
T ss_dssp             HHHBTTTTSEEEEEET-TEEEEEEEEEECTTSCEEEEETTE-------EEEESSCEEEEC-
T ss_pred             HHhhhhcCCEEEEEEC-CcEEEEEEEEECCCCeEEEEECCC-------EEEEEeeeEEEec
Confidence            3445568999999875 458999999999999999965321       1123457777764

>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=85.87  E-value=0.57  Score=39.55  Aligned_cols=31  Identities=13%  Similarity=0.303  Sum_probs=24.7

Q ss_pred             cCCeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557         115 QNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKT  147 (213)
Q Consensus       115 LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa  147 (213)
                      +|++|.|...++  +.|++.|+|..+.|+|.+.
T Consensus       188 ~g~~V~v~~~~~--~~G~~~gId~~G~L~v~~~  218 (235)
T 2dxu_A          188 LGVRVKILGDGS--FEGIAEDIDDFGRLIIRLD  218 (235)
T ss_dssp             CSSEEEC----C--CEEEEEEECTTSCEEEECT
T ss_pred             cCCeEEEEECCe--EEEEEEEECCCCEEEEEEC
Confidence            799999998776  9999999999999999753

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

Probab=85.55  E-value=1.2  Score=37.38  Aligned_cols=34  Identities=9%  Similarity=0.102  Sum_probs=29.7

Q ss_pred             HhhcCCeEEEEecCCeEEEEEEEEecCcCceEecc
Q psy5557         112 AEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHK  146 (213)
Q Consensus       112 ~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsD  146 (213)
                      .-++|++|.|...++..+.|++.|+|..+.|+ .+
T Consensus       188 ~~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~-~~  221 (237)
T 2ej9_A          188 SITIGKQVKILLSNNEIITGKVYDIDFDGIVL-GT  221 (237)
T ss_dssp             BSSTTCEEEEEETTSCEEEEEEEEECSSEEEE-EE
T ss_pred             hCccCCEEEEEECCCeEEEEEEEEECCCCeEE-Ec
Confidence            34689999999988877999999999999999 54

>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=85.47  E-value=1.1  Score=36.26  Aligned_cols=35  Identities=11%  Similarity=0.157  Sum_probs=28.3

Q ss_pred             HHHHhhcCCeEEEEe----cCCeEEEEEEEEecCcCceEe
Q psy5557         109 NKKAEEQNRQQGLYP----NQKRTLIGYLRSVDQFANLVL  144 (213)
Q Consensus       109 ~~L~~~LgKrV~V~L----kDGR~~~GtL~gFDq~mNLVL  144 (213)
                      ..+..++|..|.|.|    .+.+.|.|+|.++|.- +++|
T Consensus        97 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~-~v~l  135 (164)
T 1ib8_A           97 DAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEED-ELTM  135 (164)
T ss_dssp             HHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETT-EEEE
T ss_pred             HHHHHhCCcEEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence            457889999999999    4458999999999964 3444

---

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	213
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	3e-10
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	9e-10
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	5e-09
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	1e-08
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	1e-08
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	1e-08
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	2e-08
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	1e-07
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	2e-07
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	3e-05

>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 = 52.4 bits (126), Expect = 3e-10
 Identities = 19/52 (36%), Positives = 25/52 (48%), Gaps = 4/52 (7%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
             + G LRS DQ  NL+L    E I          RG  ++RGENV+ +  V
Sbjct: 23  HEIRGILRSFDQHVNLLLEDAEEIIDGNV----YKRGTMVVRGENVLFISPV 70

>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 = 51.3 bits (123), Expect = 9e-10
 Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 7/56 (12%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPR-------GIFIIRGENVVLM 175
           R  IG  ++ D+  NL+L    E   +  +             G+ ++RGEN+V M
Sbjct: 19  RIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSM 74

>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 = 48.9 bits (117), Expect = 5e-09
 Identities = 15/49 (30%), Positives = 19/49 (38%), Gaps = 3/49 (6%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLM 175
           R   G L   D   NLVL    E  +          G  +IRG+ VV +
Sbjct: 24  REFRGTLDGYDIHMNLVLLDAEEIQNGEVV---RKVGSVVIRGDTVVFV 69

>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 = 48.2 bits (115), Expect = 1e-08
 Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 3/52 (5%)

Query: 124 NQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLM 175
            ++  L+G L  VD + NL L   +E             G  ++RG NVVL+
Sbjct: 24  GEENQLVGKLEGVDDYMNLYLTNAMECKGEEKV---RSLGEIVLRGNNVVLI 72

>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 = 48.2 bits (115), Expect = 1e-08
 Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 3/52 (5%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
           + + G LRS DQ  NLVL  + E    G+       G  +IRG+NV+L+  +
Sbjct: 28  KEVRGMLRSYDQHMNLVLSDSEEIQSDGSG---KKLGTIVIRGDNVILISPL 76

>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 = 48.7 bits (116), Expect = 1e-08
 Identities = 11/61 (18%), Positives = 21/61 (34%), Gaps = 12/61 (19%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPR------------GIFIIRGENVVL 174
           +   G LR  D++ N+VL    E     ++                     ++ G NV +
Sbjct: 26  KEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVAM 85

Query: 175 M 175
           +
Sbjct: 86  L 86

>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 = 47.4 bits (113), Expect = 2e-08
 Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 3/52 (5%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178
               G L S D + NL L++  E +   +       G   IR  NV+ + E+
Sbjct: 18  TEYRGTLVSTDNYFNLQLNEAEEFVAGVSH---GTLGEIFIRCNNVLYIREL 66

>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 = 45.5 bits (108), Expect = 1e-07
 Identities = 12/49 (24%), Positives = 17/49 (34%), Gaps = 3/49 (6%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLM 175
               G L   D   N+VL                  G  +IRG+NV+ +
Sbjct: 23  FEFRGRLIGYDIHLNVVLADAEMIQDGEVV---KRYGKIVIRGDNVLAI 68

>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 = 45.1 bits (107), Expect = 2e-07
 Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 3/49 (6%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLM 175
           R   G L+S D   NLVL+   E             G  +IRG+N+V +
Sbjct: 27  REFRGVLKSFDLHMNLVLNDAEELEDGEVT---RRLGTVLIRGDNIVYI 72

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

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

 Score = 39.5 bits (92), Expect = 3e-05
 Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 11/59 (18%)

Query: 127 RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPR-----------GIFIIRGENVVL 174
           + L+G +++ D+  N+VL    E      + G   +               +RG++V++
Sbjct: 25  KKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIV 83

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	213
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.85
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.84
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.84
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.84
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.83
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.83
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.82
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.81
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.81
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.8
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.76
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.67
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.64
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	96.72
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	95.54
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	94.49
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	93.48
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	93.24
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	90.61

>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=99.85  E-value=6.1e-22  Score=144.36  Aligned_cols=69  Identities=23%  Similarity=0.295  Sum_probs=60.2

Q ss_pred             HHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC-------ccceeccceeeeecCcEEEEEee
Q psy5557         110 KKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN-------QYGDIPRGIFIIRGENVVLMGEV  178 (213)
Q Consensus       110 ~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n-------~~~er~LGlVlIRGnnIV~I~~i  178 (213)
                      .|.+|||++|+|.|+|||.|.|+|.|||+||||||+||.|++....       ....+.+|++||||+||++|+..
T Consensus         2 ~L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~~   77 (81)
T d1d3bb_           2 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVE   77 (81)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEE
T ss_pred             hhHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEcc
Confidence            4789999999999999999999999999999999999999874322       12357899999999999999743

>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=99.84  E-value=2e-21  Score=139.06  Aligned_cols=67  Identities=31%  Similarity=0.460  Sum_probs=60.9

Q ss_pred             HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEee
Q psy5557         108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV  178 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~i  178 (213)
                      .+.|.+++|++|+|.|+||+.|.|+|.|||+||||+|+||.+++. +   ..+.+|.+||||+||++|+++
T Consensus         4 ~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~-~---~~~~~g~v~iRG~~I~~I~~~   70 (71)
T d1i8fa_           4 GATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIID-G---NVYKRGTMVVRGENVLFISPV   70 (71)
T ss_dssp             HHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEET-T---EEEEEEEEEECGGGEEEEEEC
T ss_pred             hHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEEC-C---CEEEcceEEEeCCeEEEEeCC
Confidence            578999999999999999999999999999999999999998854 2   256789999999999999865

>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=99.84  E-value=2.9e-21  Score=137.81  Aligned_cols=68  Identities=22%  Similarity=0.163  Sum_probs=61.7

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE  177 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~  177 (213)
                      ++..|..++|++|+|.|+||+.|.|+|.|||+||||+|+||.|+...+   ..+.+|.+||||+||++|++
T Consensus         4 Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~---~~~~~g~~~IRG~~I~~Isp   71 (72)
T d1i4k1_           4 PLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGE---VVRKVGSVVIRGDTVVFVSP   71 (72)
T ss_dssp             HHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSSS---EEEEEEEEEECGGGEEEEEC
T ss_pred             hHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecCC---eEeEcceEEEeCCeEEEEEc
Confidence            578899999999999999999999999999999999999999986433   25679999999999999975

>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=99.84  E-value=2.6e-21  Score=137.33  Aligned_cols=69  Identities=17%  Similarity=0.127  Sum_probs=62.1

Q ss_pred             HHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557         106 EKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE  177 (213)
Q Consensus       106 E~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~  177 (213)
                      .++..|..++|++|.|.|+||+.|.|+|.|||+||||+|.||.++... .  ..+.+|.+||||+||++|++
T Consensus         2 ~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-~--~~~~l~~~~IRG~~I~~Isp   70 (71)
T d1h641_           2 RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDG-E--VVKRYGKIVIRGDNVLAISP   70 (71)
T ss_dssp             CHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETT-E--EEEEEEEEEECGGGEEEEEE
T ss_pred             CchHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecC-C--cEeEcCcEEEECCeEEEEeC
Confidence            367889999999999999999999999999999999999999987532 2  25689999999999999986

>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=99.83  E-value=2.1e-21  Score=144.05  Aligned_cols=71  Identities=15%  Similarity=0.160  Sum_probs=62.0

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC------------ccceeccceeeeecCcEEE
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN------------QYGDIPRGIFIIRGENVVL  174 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n------------~~~er~LGlVlIRGnnIV~  174 (213)
                      +...|..++|++|+|.|+||+.|.|+|.|||+||||+|+||.|++....            ....+++|++||||+||++
T Consensus         6 Pl~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~~Vv~   85 (92)
T d2fwka1           6 PLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNVAM   85 (92)
T ss_dssp             HHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGEEE
T ss_pred             hHHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCCEEEE
Confidence            5788999999999999999999999999999999999999999875321            1235689999999999999


Q ss_pred             EEe
Q psy5557         175 MGE  177 (213)
Q Consensus       175 I~~  177 (213)
                      |++
T Consensus        86 I~p   88 (92)
T d2fwka1          86 LVP   88 (92)
T ss_dssp             EES
T ss_pred             EEe
Confidence            986

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

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

Probab=99.83  E-value=7.6e-21  Score=137.02  Aligned_cols=71  Identities=32%  Similarity=0.398  Sum_probs=64.0

Q ss_pred             HHHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEee
Q psy5557         105 EEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV  178 (213)
Q Consensus       105 eE~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~i  178 (213)
                      ..+...|..++|++|+|.|+||+.|.|+|.|||+||||+|.||.++...+.   .+.+|.+||||++|++|+++
T Consensus         6 ~~~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~---~~~~~~v~iRG~~I~~I~~~   76 (76)
T d1th7a1           6 ETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGS---GKKLGTIVIRGDNVILISPL   76 (76)
T ss_dssp             HHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSC---EEEEEEEEECGGGEEEEEEC
T ss_pred             ccHHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecCCc---ccCcceEEEECCEEEEEEeC
Confidence            357789999999999999999999999999999999999999998865432   56899999999999999975

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

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

Probab=99.82  E-value=9.3e-21  Score=135.78  Aligned_cols=69  Identities=25%  Similarity=0.268  Sum_probs=62.0

Q ss_pred             HHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557         106 EKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE  177 (213)
Q Consensus       106 E~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~  177 (213)
                      .++..|..++|++|.|.|+||+.|.|+|.|||+||||+|.||.++...+   ..+.+|.+||||+||++|+|
T Consensus         6 ~Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~~---~~~~~~~~~IRG~~I~~I~p   74 (74)
T d1mgqa_           6 RPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGE---VTRRLGTVLIRGDNIVYISP   74 (74)
T ss_dssp             CTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTE---EEEEEEEEEECGGGEEEEEC
T ss_pred             CcHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCCC---eEeEcceEEEeCCEEEEEeC
Confidence            4678999999999999999999999999999999999999999885432   25678999999999999975

>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=99.81  E-value=2.1e-20  Score=132.87  Aligned_cols=66  Identities=24%  Similarity=0.236  Sum_probs=57.6

Q ss_pred             HHhhcCCeEEEEec-CCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeec
Q psy5557         111 KAEEQNRQQGLYPN-QKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       111 L~~~LgKrV~V~Lk-DGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      |..++|++|.|.|+ +|+.|.|+|.|||+||||+|+||.+++.. .  ....+|.+||||+||++|++++
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~-~--~~~~lg~~~IRG~nI~~I~~~p   67 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAG-V--SHGTLGEIFIRCNNVLYIRELP   67 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETT-E--EEEECCSEEECGGGEEEEEECC
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEecC-C--cccCcCeEEEECCEEEEEEeCC
Confidence            57899999999998 56889999999999999999999997643 2  2567999999999999998654

>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=99.81  E-value=4e-20  Score=133.61  Aligned_cols=68  Identities=24%  Similarity=0.296  Sum_probs=60.6

Q ss_pred             HHHHHHhhcCCeEEEEecCC-eEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557         107 KKNKKAEEQNRQQGLYPNQK-RTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE  177 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDG-R~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~  177 (213)
                      +...|..++|++|+|.|++| +.|.|+|.|||+||||+|+||.|+...+   ..+.+|.+||||+||++|.+
T Consensus         6 P~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~---~~~~~g~~~IRG~~I~~I~p   74 (75)
T d1ljoa_           6 PNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEE---KVRSLGEIVLRGNNVVLIQP   74 (75)
T ss_dssp             HHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTE---EEEEEEEEEECGGGEEEEEE
T ss_pred             cHHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCCC---cEeEcceEEEeCCEEEEEEC
Confidence            57889999999999999865 8999999999999999999999986432   25689999999999999985

>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=99.80  E-value=6.6e-20  Score=137.31  Aligned_cols=73  Identities=18%  Similarity=0.197  Sum_probs=59.0

Q ss_pred             HHHHHHhhc--CCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC-----------ccceeccceeeeecCcEE
Q psy5557         107 KKNKKAEEQ--NRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN-----------QYGDIPRGIFIIRGENVV  173 (213)
Q Consensus       107 ~~~~L~~~L--gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n-----------~~~er~LGlVlIRGnnIV  173 (213)
                      +++.|..++  +++|+|.|+||+.|.|+|.|||+||||||+||.|++....           ....+++|++||||+||+
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            456777787  9999999999999999999999999999999999875321           123568999999999999


Q ss_pred             EEEeec
Q psy5557         174 LMGEVV  179 (213)
Q Consensus       174 ~I~~iD  179 (213)
                      +|....
T Consensus        83 ~I~~~p   88 (93)
T d1b34b_          83 VVLRNP   88 (93)
T ss_dssp             EEEECC
T ss_pred             EEEcCh
Confidence            997543

>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=99.76  E-value=1.6e-18  Score=123.80  Aligned_cols=70  Identities=13%  Similarity=0.005  Sum_probs=62.0

Q ss_pred             HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeec
Q psy5557         107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      +...|..++|++|+|.|+||++|.|+|.+||.||||+|+||.+...++.   ...+|.+||||+||.||..+|
T Consensus         3 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~---~~~~~~v~IRG~~I~~i~lpd   72 (72)
T d1d3ba_           3 PIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGR---VAQLEQVYIRGCKIRFLILPD   72 (72)
T ss_dssp             HHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSC---EEEEEEEEECGGGEEEEEECC
T ss_pred             chHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCCCc---EeEcCeEEEECCEEEEEEcCC
Confidence            5678999999999999999999999999999999999999987653322   457899999999999998765

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

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

Probab=99.67  E-value=8.4e-17  Score=117.18  Aligned_cols=73  Identities=12%  Similarity=0.039  Sum_probs=63.2

Q ss_pred             HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccccc
Q psy5557         108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVN  183 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~d  183 (213)
                      ..+|..++|++|.|.|+||..|.|+|.++|.||||+|+||.+...++.   ...+|.++|||+||.||..+|....
T Consensus         3 v~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~---~~~~~~v~IRG~~Ir~i~lPd~l~~   75 (80)
T d1b34a_           3 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNRE---PVQLETLSIRGNNIRYFILPDSLPL   75 (80)
T ss_dssp             HHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSC---CEEEEEEEECGGGEEEEECCTTCCH
T ss_pred             HHHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCC---EEEcccEEEcCCEEEEEECCCCccc
Confidence            568999999999999999999999999999999999999987643222   4578999999999999998765543

>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=99.64  E-value=2.3e-16  Score=124.70  Aligned_cols=69  Identities=16%  Similarity=0.177  Sum_probs=61.1

Q ss_pred             HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccccc
Q psy5557         108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVN  183 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~d  183 (213)
                      ...|.+++|++|.|.|+||++|.|+|.+||+||||+|+||.+.  .++     .++.++|||++|.+|..++..+|
T Consensus         2 ~~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~--~~~-----k~~~v~IRG~~I~~I~~~e~~iD   70 (127)
T d1m5q1_           2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNK--AGE-----KFNRVFIMYRYIVHIDSTERRID   70 (127)
T ss_dssp             HHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEET--TCC-----EEEEEEECGGGEEEEEECSCCCC
T ss_pred             hhHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEEC--CCC-----cccEEEEeCCeEEEEEcchhhcC
Confidence            3689999999999999999999999999999999999999764  233     36889999999999998887655

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

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

Probab=96.72  E-value=0.0022  Score=41.15  Aligned_cols=47  Identities=21%  Similarity=0.212  Sum_probs=35.3

Q ss_pred             hcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeee
Q psy5557         114 EQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIR  168 (213)
Q Consensus       114 ~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIR  168 (213)
                      |+|++|.|.+ +++.+.|+..|+|...+|+|.....       ....+.|.|.||
T Consensus         1 f~gk~V~v~~-g~~~i~G~a~gId~~G~Lll~t~~g-------~~~~~sGEVSlR   47 (47)
T d1biaa2           1 FINRPVKLII-GDKEIFGISRGIDKQGALLLEQDGI-------IKPWMGGEISLR   47 (47)
T ss_dssp             TTTSEEEEEE-TTEEEEEEEEEECTTSCEEEEETTE-------EEEESSCEEEEC
T ss_pred             CCCCEEEEEE-CCeEEEEEEeeECCCCcEEEEECCC-------EEEEEEEEEEeC
Confidence            7899999986 5578999999999999999975321       112345666665

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

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

Probab=95.54  E-value=0.035  Score=39.77  Aligned_cols=66  Identities=15%  Similarity=0.097  Sum_probs=49.6

Q ss_pred             hcCCeEEEEecCCeEEEEEEEEecC-cCceEecceEEEeecCC----cc--ceeccceeeeecCcEEEEEeec
Q psy5557         114 EQNRQQGLYPNQKRTLIGYLRSVDQ-FANLVLHKTIERIHVGN----QY--GDIPRGIFIIRGENVVLMGEVV  179 (213)
Q Consensus       114 ~LgKrV~V~LkDGR~~~GtL~gFDq-~mNLVLsDavEri~~~n----~~--~er~LGlVlIRGnnIV~I~~iD  179 (213)
                      |||++|.++.+.+-.|.|+|..+|. -.-|.|.|+.-+=..+-    .+  ...-++.++.||+.|--+...+
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~~IvFrgsDIKdL~v~e   74 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCE   74 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSSCCCCCCCCEEEEEEETTTEEEEEESS
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCCccCCCCcceeEEEEcCcCcceEEecc
Confidence            7999999999999999999999995 45688999864421111    00  1223578999999999888655

>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=94.49  E-value=0.027  Score=38.35  Aligned_cols=33  Identities=6%  Similarity=0.089  Sum_probs=29.5

Q ss_pred             CCeEEEEecCCeEEEEEEEEecCcCceEecceE
Q psy5557         116 NRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTI  148 (213)
Q Consensus       116 gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDav  148 (213)
                      ..+|.|.|.+|-.+.|.+.|||+|.=|+..+..
T Consensus        14 ~~~VtifL~nGvkl~G~I~~fD~ftvlL~~~~~   46 (60)
T d1kq1a_          14 QTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGK   46 (60)
T ss_dssp             TCEEEEEETTSCEEEEEEEEECSSEEEEEETTE
T ss_pred             CCcEEEEEECCcEEEEEEEEEcceEEEEEeCCc
Confidence            678999999999999999999999988876653

>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=93.48  E-value=0.06  Score=37.23  Aligned_cols=28  Identities=29%  Similarity=0.363  Sum_probs=25.4

Q ss_pred             CCeEEEEecCCeEEEEEEEEecCcCceE
Q psy5557         116 NRQQGLYPNQKRTLIGYLRSVDQFANLV  143 (213)
Q Consensus       116 gKrV~V~LkDGR~~~GtL~gFDq~mNLV  143 (213)
                      ..+|.|.|.+|-.+.|.+.|||+|.=|+
T Consensus        14 ~~~VtifL~nGvkl~G~I~~fD~ftvLL   41 (66)
T d1u1sa1          14 RVPVSIYLVNGIKLQGQIESFDQFVILL   41 (66)
T ss_dssp             TCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             CCcEEEEEEcCcEEEEEEEEEcceEEEE
Confidence            6789999999999999999999997654

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

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

Probab=93.24  E-value=0.12  Score=35.56  Aligned_cols=60  Identities=15%  Similarity=0.214  Sum_probs=41.8

Q ss_pred             HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEE
Q psy5557         109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMG  176 (213)
Q Consensus       109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~  176 (213)
                      ..|..+-|++|-|.+..-..|+|+|.-||.-. |+|.|++.+..  |.     --.++|+=+.|..|.
T Consensus         5 ktL~~WKg~kvAv~vgsehSFtGiledFDeEv-iLL~dV~D~~G--Nk-----~k~llv~idD~nWim   64 (66)
T d1ycya1           5 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVIG--NR-----GKQMLIGLEDINWIM   64 (66)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETTE--EE-----EEEEEEEGGGEEEEE
T ss_pred             HHHHHhCCcEEEEEecCcceeEEEhhhcCcce-EeehhhHHHhc--cc-----cceeEEEeccceeEE
Confidence            46889999999999999999999999999864 67888877642  22     134666666665553

>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=90.61  E-value=0.2  Score=33.73  Aligned_cols=33  Identities=15%  Similarity=0.096  Sum_probs=27.8

Q ss_pred             HHHHHhhcCCeEEEEec---CC-eEEEEEEEEecCcC
Q psy5557         108 KNKKAEEQNRQQGLYPN---QK-RTLIGYLRSVDQFA  140 (213)
Q Consensus       108 ~~~L~~~LgKrV~V~Lk---DG-R~~~GtL~gFDq~m  140 (213)
                      ...+..|+|..|.|.|.   || +.|.|+|.++|.-.
T Consensus         6 ~~~f~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~~   42 (74)
T d1ib8a1           6 KDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEEDE   42 (74)
T ss_dssp             HHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETTE
T ss_pred             HHHHHHhCCCEEEEEEecccCCceEEEEEEEeecCCe
Confidence            35788999999999984   45 79999999999754