Citrus Sinensis ID: 040944

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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-------19
Protein Sequence
MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEKGVIHKDPALNSKKEGVSEENQQNSEAGRGSEPDRHNASDKVGAIIFCEYFEIDLLVYFCSFREDDDESVNENDAELVKQIEKQRRRAVAAVGDESLLPQEIPARLRVANPPTIPKSKSN
Secondary Structure (PSIPRED)
ccccccccccccccccHHHHHHHHccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccccccccccEEEEEcccccEEEEEEEEEcEEEEEccccccccccccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHccHHHcEEEEEEHcccccccHccHHHHHHHHHHHHHHHcccccccccccccHcccccccccEEccccHccccccccHHccccccccccccccccccccccEEEEEEEEEEEEEEEEEEcccccccccccccHHHHHHHHHHHHHHHHHHHccccccccccccEEEEcccccccccccc
Coil and Loop (DISEMBL)
MKLDVDVLRYLSKDDFKVLTAVETGmrnheivpfrtraSHCFSQAleehgfpvpsavdcnrhcidddekgvihkdpalnskkegvseenqqnseagrgsepdrhnasdkvGAIIFCEYFEIDLLVYFCsfredddesvneNDAELVKQIEKQRRRAVAavgdesllpqeiparlrvanpptipksksn
Flexible Loop (DISEMBL)
MKLDVDVLrylskddfkvLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDddekgvihkdpalnskkegvseenqqnseagrgsepdrhnasDKVGAIIFCEYFEIDLLVYFCSFREDDDESVNENDAELVKQIEKQRRRAVAavgdesllpqeiparlrvanpptipksksn
Low Complexity Region (SEG)
MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEKGVIHKDPALNSKKEGVSEENQQNSEAGRGSEPDRHNASDKVGAIIFCEYFEIDLLVYFCSFREDDDESVNENDAELVKQIEKQRRRAVAAVGDESLLPQEIPARLRVANPPTIPKSKSN
Disordered region (IsUnstruct)
****VDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDD*******************************************VGAIIFCEYFEIDLLVYFCSFR*********************************************************
Disordered Region (DISOPRED)
*KLDVDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRASHCF*********PVPSAVDCNRHCIDDDEKGVIHKDPALNSKKEGVSEENQQNSEAGRGSEPDRHNASDKVGAIIFCEYFEIDLLVYFCSF**********************RRRAVAAVGDESLLPQEIPARLRVA***********
Disordered Region (DISEMBL)
MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEKGVIHKDPALNS************************NASDKVGAIIFCEYFEIDLLVYFCSFRED********DAELVKQIEKQRRRAVAAVGDESLLPQEIPARLRVANPP********
Disordered Region (DISPRO)
*KLDVDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEKGVIHKDPA**S**************************SDKVGAIIFCEYFEIDLLVYFCSFREDDD*SVNENDAELVKQIEKQRRRAVAAVGDESLLPQEIPARLRVANPPTIP*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEKGVIHKDPALNSKKEGVSEENQQNSEAGRGSEPDRHNASDKVGAIIFCEYFEIDLLVYFCSFREDDDESVNENDAELVKQIEKQRRRAVAAVGDESLLPQEIPARLRVANPPTIPKSKSN
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	188	2.2.26 [Sep-21-2011]
Q54T05	522	Serine/threonine-protein	yes	no	0.175	0.063	0.727	3e-07
Q9BVS4	552	Serine/threonine-protein	yes	no	0.202	0.068	0.657	3e-07
Q9CQS5	547	Serine/threonine-protein	yes	no	0.170	0.058	0.718	4e-07
P40160	425	Serine/threonine-protein	yes	no	0.175	0.077	0.636	2e-05
Q9P7W5	344	Serine/threonine-protein	yes	no	0.164	0.090	0.612	5e-05

>sp|Q54T05|RIO2_DICDI Serine/threonine-protein kinase rio2 OS=Dictyostelium discoideum GN=rio2 PE=3 SV=1

 Score = 55.1 bits (131), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 24/33 (72%), Positives = 27/33 (81%)

Query: 1  MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
          MKLD   LRYLSKDDF+ L AVE GM+NHE+VP
Sbjct: 1  MKLDPKALRYLSKDDFRTLVAVEMGMKNHELVP 33

Required for the final endonucleolytic cleavage of 20S pre-rRNA at site D in the cytoplasm, converting it into the mature 18S rRNA. Involved in normal export of the pre-40S particles from the nucleus to the cytoplasm.
Dictyostelium discoideum (taxid: 44689)
EC: 2EC: .EC: 7EC: .EC: 1EC: 1EC: .EC: 1

>sp|Q9BVS4|RIOK2_HUMAN Serine/threonine-protein kinase RIO2 OS=Homo sapiens GN=RIOK2 PE=1 SV=2

 Score = 54.7 bits (130), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 25/38 (65%), Positives = 31/38 (81%)

Query: 2  KLDVDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRAS 39
          K++V  LRY+S+DDF+VLTAVE GM+NHEIVP    AS
Sbjct: 3  KVNVAKLRYMSRDDFRVLTAVEMGMKNHEIVPGSLIAS 40

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 1

EC: .

EC: 1

>sp|Q9CQS5|RIOK2_MOUSE Serine/threonine-protein kinase RIO2 OS=Mus musculus GN=Riok2 PE=1 SV=1

 Score = 54.3 bits (129), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 23/32 (71%), Positives = 29/32 (90%)

Query: 2  KLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
          K++V  LRY+S+DDF+VLTAVE GM+NHEIVP
Sbjct: 3  KVNVAKLRYMSRDDFRVLTAVEMGMKNHEIVP 34

Mus musculus (taxid: 10090)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 1

EC: .

EC: 1

>sp|P40160|RIO2_YEAST Serine/threonine-protein kinase RIO2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RIO2 PE=1 SV=1

 Score = 49.3 bits (116), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/33 (63%), Positives = 26/33 (78%)

Query: 1  MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
          MKLD   +RYL+ DDF+VL AVE G R+HE+VP
Sbjct: 1  MKLDTSHMRYLTTDDFRVLQAVEQGSRSHEVVP 33

Required for the final endonucleolytic cleavage of 20S pre-rRNA at site D in the cytoplasm, converting it into the mature 18S rRNA. Involved in normal export of the pre-40S particles from the nucleus to the cytoplasm.

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

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 1

EC: .

EC: 1

>sp|Q9P7W5|RIO2_SCHPO Serine/threonine-protein kinase rio2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rio2 PE=3 SV=2

 Score = 47.8 bits (112), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 19/31 (61%), Positives = 25/31 (80%)

Query: 3  LDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
          L++  +RYLS +DF+ LTAVE G RNHE+VP
Sbjct: 4  LNIKAMRYLSAEDFRTLTAVEMGSRNHEVVP 34

Required for the final endonucleolytic cleavage of 20S pre-rRNA at site D in the cytoplasm, converting it into the mature 18S rRNA. Involved in normal export of the pre-40S particles from the nucleus to the cytoplasm.

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

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 1

EC: .

EC: 1

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	188
356569679	452	PREDICTED: serine/threonine-protein kina	0.175	0.073	0.939	1e-09
217074510	460	unknown [Medicago truncatula]	0.175	0.071	0.939	1e-09
356569677	460	PREDICTED: serine/threonine-protein kina	0.175	0.071	0.939	1e-09
388494744	460	unknown [Medicago truncatula]	0.175	0.071	0.939	1e-09
356539800	466	PREDICTED: serine/threonine-protein kina	0.175	0.070	0.939	1e-09
356539798	474	PREDICTED: serine/threonine-protein kina	0.175	0.069	0.939	1e-09
296084383	467	unnamed protein product [Vitis vinifera]	0.154	0.062	0.909	3e-09
225434261	490	PREDICTED: serine/threonine-protein kina	0.154	0.059	0.909	3e-09
118487340	467	unknown [Populus trichocarpa]	0.053	0.021	0.909	4e-09
334185881	458	RIO kinase 2 [Arabidopsis thaliana] gi|3	0.175	0.072	0.909	4e-09

>gi|356569679|ref|XP_003553024.1| PREDICTED: serine/threonine-protein kinase rio2-like isoform 2 [Glycine max]

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/33 (93%), Positives = 32/33 (96%)

Query: 1  MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
          MKLDVDVLRYLSKDDF+VLTAVE GMRNHEIVP
Sbjct: 1  MKLDVDVLRYLSKDDFRVLTAVELGMRNHEIVP 33

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217074510|gb|ACJ85615.1| unknown [Medicago truncatula]

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/33 (93%), Positives = 32/33 (96%)

Query: 1  MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
          MKLDVDVLRYLSKDDF+VLTAVE GMRNHEIVP
Sbjct: 1  MKLDVDVLRYLSKDDFRVLTAVELGMRNHEIVP 33

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356569677|ref|XP_003553023.1| PREDICTED: serine/threonine-protein kinase rio2-like isoform 1 [Glycine max]

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/33 (93%), Positives = 32/33 (96%)

Query: 1  MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
          MKLDVDVLRYLSKDDF+VLTAVE GMRNHEIVP
Sbjct: 1  MKLDVDVLRYLSKDDFRVLTAVELGMRNHEIVP 33

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388494744|gb|AFK35438.1| unknown [Medicago truncatula]

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/33 (93%), Positives = 32/33 (96%)

Query: 1  MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
          MKLDVDVLRYLSKDDF+VLTAVE GMRNHEIVP
Sbjct: 1  MKLDVDVLRYLSKDDFRVLTAVELGMRNHEIVP 33

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356539800|ref|XP_003538381.1| PREDICTED: serine/threonine-protein kinase rio2-like isoform 2 [Glycine max]

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/33 (93%), Positives = 32/33 (96%)

Query: 1  MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
          MKLDVDVLRYLSKDDF+VLTAVE GMRNHEIVP
Sbjct: 1  MKLDVDVLRYLSKDDFRVLTAVELGMRNHEIVP 33

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356539798|ref|XP_003538380.1| PREDICTED: serine/threonine-protein kinase rio2-like isoform 1 [Glycine max]

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/33 (93%), Positives = 32/33 (96%)

Query: 1  MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
          MKLDVDVLRYLSKDDF+VLTAVE GMRNHEIVP
Sbjct: 1  MKLDVDVLRYLSKDDFRVLTAVELGMRNHEIVP 33

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296084383|emb|CBI24771.3| unnamed protein product [Vitis vinifera]

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 30/33 (90%), Positives = 32/33 (96%)

Query: 1  MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
          MKLDVDVLRYLSKDDF+VLTAVE GMRNHE+VP
Sbjct: 1  MKLDVDVLRYLSKDDFRVLTAVEMGMRNHELVP 33

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225434261|ref|XP_002276325.1| PREDICTED: serine/threonine-protein kinase rio2-like [Vitis vinifera]

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 30/33 (90%), Positives = 32/33 (96%)

Query: 1  MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
          MKLDVDVLRYLSKDDF+VLTAVE GMRNHE+VP
Sbjct: 1  MKLDVDVLRYLSKDDFRVLTAVEMGMRNHELVP 33

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118487340|gb|ABK95498.1| unknown [Populus trichocarpa]

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 30/33 (90%), Positives = 32/33 (96%)

Query: 1  MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
          MKLDV+VLRYLSKDDF+VLTAVE GMRNHEIVP
Sbjct: 1  MKLDVEVLRYLSKDDFRVLTAVEMGMRNHEIVP 33

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334185881|ref|NP_001190051.1| RIO kinase 2 [Arabidopsis thaliana] gi|332645251|gb|AEE78772.1| RIO kinase 2 [Arabidopsis thaliana]

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 30/33 (90%), Positives = 32/33 (96%)

Query: 1  MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
          MKLDV+VLRYLSKDDF+VLTAVE GMRNHEIVP
Sbjct: 1  MKLDVNVLRYLSKDDFRVLTAVEMGMRNHEIVP 33

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

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	188
TAIR|locus:2080848	461	AT3G51270 [Arabidopsis thalian	0.175	0.071	0.909	1.7e-21
DICTYBASE|DDB_G0282099	522	rio2 "RIO2 subfamily protein k	0.175	0.063	0.727	2.8e-13
ZFIN|ZDB-GENE-040426-2913	512	riok2 "RIO kinase 2 (yeast)" [	0.202	0.074	0.710	9.3e-13
FB|FBgn0039306	538	CG11859 [Drosophila melanogast	0.170	0.059	0.718	6.6e-11
UNIPROTKB|E2R8S0	548	RIOK2 "Uncharacterized protein	0.202	0.069	0.684	2.8e-10
POMBASE|SPBC1703.05	344	SPBC1703.05 "protein kinase, R	0.175	0.095	0.575	2.1e-09
RGD|1311588	551	Riok2 "RIO kinase 2" [Rattus n	0.202	0.068	0.657	3.7e-09
MGI|MGI:1914295	547	Riok2 "RIO kinase 2 (yeast)" [	0.202	0.069	0.657	7.3e-09
UNIPROTKB|F1MBN7	551	RIOK2 "Uncharacterized protein	0.202	0.068	0.657	7.5e-09
UNIPROTKB|F1RNT7	552	RIOK2 "Uncharacterized protein	0.202	0.068	0.657	7.5e-09

TAIR|locus:2080848 AT3G51270 [Arabidopsis thaliana (taxid:3702)]

 Score = 153 (58.9 bits), Expect = 1.7e-21, Sum P(3) = 1.7e-21
 Identities = 30/33 (90%), Positives = 32/33 (96%)

Query:     1 MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
             MKLDV+VLRYLSKDDF+VLTAVE GMRNHEIVP
Sbjct:     1 MKLDVNVLRYLSKDDFRVLTAVEMGMRNHEIVP 33

GO:0003824 "catalytic activity" evidence=IEA

GO:0004674 "protein serine/threonine kinase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0006468 "protein phosphorylation" evidence=IEA

GO:0016772 "transferase activity, transferring phosphorus-containing groups" evidence=IEA

DICTYBASE|DDB_G0282099 rio2 "RIO2 subfamily protein kinase" [Dictyostelium discoideum (taxid:44689)]

 Score = 127 (49.8 bits), Expect = 2.8e-13, Sum P(3) = 2.8e-13
 Identities = 24/33 (72%), Positives = 27/33 (81%)

Query:     1 MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
             MKLD   LRYLSKDDF+ L AVE GM+NHE+VP
Sbjct:     1 MKLDPKALRYLSKDDFRTLVAVEMGMKNHELVP 33

GO:0016772 "transferase activity, transferring phosphorus-containing groups" evidence=IEA

GO:0006468 "protein phosphorylation" evidence=IEA;ISS

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0004674 "protein serine/threonine kinase activity" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0004672 "protein kinase activity" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=IEA

GO:0016740 "transferase activity" evidence=IEA

GO:0016310 "phosphorylation" evidence=IEA

GO:0016301 "kinase activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

ZFIN|ZDB-GENE-040426-2913 riok2 "RIO kinase 2 (yeast)" [Danio rerio (taxid:7955)]

 Score = 134 (52.2 bits), Expect = 9.3e-13, Sum P(3) = 9.3e-13
 Identities = 27/38 (71%), Positives = 32/38 (84%)

Query:     2 KLDVDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRAS 39
             KL+V +LRYLS+DDF+VLTAVE GM+NHEIVP    AS
Sbjct:     3 KLNVVILRYLSRDDFRVLTAVEMGMKNHEIVPVSLIAS 40

GO:0003824 "catalytic activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006468 "protein phosphorylation" evidence=IEA

GO:0004674 "protein serine/threonine kinase activity" evidence=IEA

GO:0016772 "transferase activity, transferring phosphorus-containing groups" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0016301 "kinase activity" evidence=IEA

GO:0016310 "phosphorylation" evidence=IEA

FB|FBgn0039306 CG11859 [Drosophila melanogaster (taxid:7227)]

 Score = 128 (50.1 bits), Expect = 6.6e-11, Sum P(2) = 6.6e-11
 Identities = 23/32 (71%), Positives = 30/32 (93%)

Query:     2 KLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
             KL+V VLRYL+K+DF+VLTA+E GM+NHE+VP
Sbjct:     3 KLNVTVLRYLTKEDFRVLTAIEMGMKNHELVP 34

GO:0006468 "protein phosphorylation" evidence=IEA;NAS

GO:0004672 "protein kinase activity" evidence=NAS

GO:0004674 "protein serine/threonine kinase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0022008 "neurogenesis" evidence=IMP

UNIPROTKB|E2R8S0 RIOK2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 126 (49.4 bits), Expect = 2.8e-10, Sum P(3) = 2.8e-10
 Identities = 26/38 (68%), Positives = 31/38 (81%)

Query:     2 KLDVDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRAS 39
             K++V  LRYLS+DDF+VLTAVE GM+NHEIVP    AS
Sbjct:     3 KVNVAKLRYLSRDDFRVLTAVEMGMKNHEIVPCSLVAS 40

GO:0005524 "ATP binding" evidence=IEA

GO:0004674 "protein serine/threonine kinase activity" evidence=IEA

POMBASE|SPBC1703.05 SPBC1703.05 "protein kinase, RIO family (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 109 (43.4 bits), Expect = 2.1e-09, Sum P(2) = 2.1e-09
 Identities = 19/33 (57%), Positives = 26/33 (78%)

Query:     1 MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
             + L++  +RYLS +DF+ LTAVE G RNHE+VP
Sbjct:     2 VNLNIKAMRYLSAEDFRTLTAVEMGSRNHEVVP 34

GO:0004672 "protein kinase activity" evidence=ISO

GO:0004674 "protein serine/threonine kinase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005737 "cytoplasm" evidence=ISO

GO:0005829 "cytosol" evidence=IDA

GO:0006468 "protein phosphorylation" evidence=IEA

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

RGD|1311588 Riok2 "RIO kinase 2" [Rattus norvegicus (taxid:10116)]

 Score = 124 (48.7 bits), Expect = 3.7e-09, Sum P(2) = 3.7e-09
 Identities = 25/38 (65%), Positives = 31/38 (81%)

Query:     2 KLDVDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRAS 39
             K++V  LRY+S+DDF+VLTAVE GM+NHEIVP    AS
Sbjct:     3 KVNVAKLRYMSRDDFRVLTAVEMGMKNHEIVPCSLVAS 40

GO:0004674 "protein serine/threonine kinase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

MGI|MGI:1914295 Riok2 "RIO kinase 2 (yeast)" [Mus musculus (taxid:10090)]

 Score = 124 (48.7 bits), Expect = 7.3e-09, Sum P(2) = 7.3e-09
 Identities = 25/38 (65%), Positives = 31/38 (81%)

Query:     2 KLDVDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRAS 39
             K++V  LRY+S+DDF+VLTAVE GM+NHEIVP    AS
Sbjct:     3 KVNVAKLRYMSRDDFRVLTAVEMGMKNHEIVPCSLIAS 40

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0004674 "protein serine/threonine kinase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0006468 "protein phosphorylation" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0016301 "kinase activity" evidence=IEA

GO:0016310 "phosphorylation" evidence=IEA

GO:0016740 "transferase activity" evidence=IEA

GO:0016772 "transferase activity, transferring phosphorus-containing groups" evidence=IEA

UNIPROTKB|F1MBN7 RIOK2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 124 (48.7 bits), Expect = 7.5e-09, Sum P(2) = 7.5e-09
 Identities = 25/38 (65%), Positives = 31/38 (81%)

Query:     2 KLDVDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRAS 39
             K++V  LRY+S+DDF+VLTAVE GM+NHEIVP    AS
Sbjct:     3 KVNVAKLRYMSRDDFRVLTAVEMGMKNHEIVPCSLVAS 40

GO:0005524 "ATP binding" evidence=IEA

GO:0004674 "protein serine/threonine kinase activity" evidence=IEA

UNIPROTKB|F1RNT7 RIOK2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 124 (48.7 bits), Expect = 7.5e-09, Sum P(2) = 7.5e-09
 Identities = 25/38 (65%), Positives = 31/38 (81%)

Query:     2 KLDVDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRAS 39
             K++V  LRY+S+DDF+VLTAVE GM+NHEIVP    AS
Sbjct:     3 KVNVAKLRYMSRDDFRVLTAVEMGMKNHEIVPCSLVAS 40

GO:0005524 "ATP binding" evidence=IEA

GO:0004674 "protein serine/threonine kinase activity" 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 Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	188
pfam09202	82	pfam09202, Rio2_N, Rio2, N-terminal	7e-13
COG0478	304	COG0478, COG0478, RIO-like serine/threonine protei	6e-09
cd05144	198	cd05144, RIO2_C, RIO kinase family; RIO2, C-termin	7e-05

>gnl|CDD|220140 pfam09202, Rio2_N, Rio2, N-terminal

 Score = 60.6 bits (148), Expect = 7e-13
 Identities = 21/27 (77%), Positives = 24/27 (88%)

Query: 8  LRYLSKDDFKVLTAVETGMRNHEIVPF 34
          +RYLSK+DF+VLTAVE GMRNHE VP 
Sbjct: 1  MRYLSKEDFRVLTAVEMGMRNHEWVPT 27

Members of this family are found in Rio2, and are structurally homologous to the winged helix (wHTH) domain. They adopt a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains. Length = 82

>gnl|CDD|223554 COG0478, COG0478, RIO-like serine/threonine protein kinase fused to N-terminal HTH domain [Signal transduction mechanisms]

 Score = 53.9 bits (130), Expect = 6e-09
 Identities = 18/34 (52%), Positives = 24/34 (70%)

Query: 1  MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVPF 34
          MKL  +    LSK+DF++L A+E GMR+HE VP 
Sbjct: 1  MKLVAEAYPKLSKEDFRLLRAIEGGMRSHEWVPL 34

Length = 304

>gnl|CDD|240167 cd05144, RIO2_C, RIO kinase family; RIO2, C-terminal catalytic domain

 Score = 41.4 bits (98), Expect = 7e-05
 Identities = 12/21 (57%), Positives = 15/21 (71%)

Query: 44  QALEEHGFPVPSAVDCNRHCI 64
           +AL E GFPVP  +D NRH +
Sbjct: 88  KALYEEGFPVPKPIDWNRHAV 108

The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). RIO kinases are atypical protein serine kinases containing a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. RIO2 is present in archaea and eukaryotes. It contains an N-terminal winged helix (wHTH) domain and a C-terminal RIO kinase catalytic domain. The wHTH domain is primarily seen in DNA-binding proteins, although some wHTH domains may be involved in RNA recognition. RIO2 is essential for survival and is necessary for rRNA cleavage during 40S ribosomal subunit maturation. The biological substrates of RIO2 are still unknown. Length = 198

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	188
COG0478	304	RIO-like serine/threonine protein kinase fused to	99.96
KOG2268	465	consensus Serine/threonine protein kinase [Signal	99.91
PF09202	82	Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This	99.83
cd05146	197	RIO3_euk RIO kinase family; eukaryotic RIO3, catal	97.14
PF15013	77	CCSMST1: CCSMST1 family	92.21
KOG2268	465	consensus Serine/threonine protein kinase [Signal	91.26
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	90.64
COG1522	154	Lrp Transcriptional regulators [Transcription]	90.52
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	89.73
cd05147	190	RIO1_euk RIO kinase family; eukaryotic RIO1, catal	88.73
KOG1165	449	consensus Casein kinase (serine/threonine/tyrosine	82.46
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	80.27

>COG0478 RIO-like serine/threonine protein kinase fused to N-terminal HTH domain [Signal transduction mechanisms]

Probab=99.96  E-value=7.4e-30  Score=226.31  Aligned_cols=106  Identities=27%  Similarity=0.347  Sum_probs=97.9

Q ss_pred             CCcchHHhcccCccchhHHHHHHhhccCCcccchhhhhhhhhhhhhhhCCCCCcccccccccchhhhhc-cccccCCCcc
Q 040944            1 MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEK-GVIHKDPALN   79 (188)
Q Consensus         1 MkL~ae~~r~L~~~DfRVL~AIE~GMRnhE~VP~elI~k~s~~~~~~~hgls~ee~vd~~r~~l~rL~k-~LV~R~~~~~   79 (188)
                      |++.++.+++|+++|||||+|||.|||+|||||.++|.+++        +|+.+++.    ++|++|.+ +||.|+   +
T Consensus         1 ~~~~~~~~~~l~~~D~rlLraiE~~mR~~e~VP~~~i~~~a--------r~~~~~~~----~~L~~L~~l~lv~r~---~   65 (304)
T COG0478           1 MKLVAEAYPKLSKEDFRLLRAIEGGMRSHEWVPLELIKKRA--------RMDEEELL----YRLKRLDKLKLVSRR---T   65 (304)
T ss_pred             CcchhhhhhhcCHHHHHHHHHHHhcccccccccHHHHHHHc--------CCCHHHHH----HHHHHHHhcCceecc---C
Confidence            56789999999999999999999999999999999999998        99977777    79999999 699985   8


Q ss_pred             CCccceehh------------------hhcccccCcCCcCceeeccCC---CeeEEeeehhhh
Q 040944           80 SKKEGVSEE------------------NQQNSEAGRGSEPDRHNASDK---VGAIIFCEYFEI  121 (188)
Q Consensus        80 ~~YeGY~Lt------------------~alG~~IGVGKESDVYea~~~---~~aiKFh~~~~~  121 (188)
                      .+|+|||||                  +++|++||||||||||.|.++   ++|+|||...-+
T Consensus        66 ~~y~Gy~lT~~GyD~LAL~~l~~r~~ve~iG~~IGvGKEsdVY~~~~~~g~~~~vKfHR~Grt  128 (304)
T COG0478          66 ISYEGYQLTFSGYDALALHALVKRGIVEAIGTKIGVGKESDVYVAIDPKGRKVAVKFHRLGRT  128 (304)
T ss_pred             CcceeEEEEecchhHHHHHHHHHcChHHhhccccccCccceEEEEECCCCCEEEEEEeecCch
Confidence            999999988                  899999999999999999654   999999998854

>KOG2268 consensus Serine/threonine protein kinase [Signal transduction mechanisms; General function prediction only]

Probab=99.91  E-value=2.8e-25  Score=203.59  Aligned_cols=141  Identities=32%  Similarity=0.363  Sum_probs=103.4

Q ss_pred             CCcchHHhcccCccchhHHHHHHhhccCCcccchhhhhhhhhhhhhhhCCCCCcccccccccchhhhhc-cccccCCCcc
Q 040944            1 MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEK-GVIHKDPALN   79 (188)
Q Consensus         1 MkL~ae~~r~L~~~DfRVL~AIE~GMRnhE~VP~elI~k~s~~~~~~~hgls~ee~vd~~r~~l~rL~k-~LV~R~~~~~   79 (188)
                      |||+++.+|||+.+|||||+||||||||||.||..+|.+++    -++||.-    .    +.|+.|-| .||...  .+
T Consensus         1 mKl~v~~mryLs~ddFRvLtAvEmgmrnHEiVP~~li~~ia----~ik~gg~----~----k~l~dL~KhkLia~~--r~   66 (465)
T KOG2268|consen    1 MKLNVSVMRYLSRDDFRVLTAVEMGMRNHEIVPTPLIASIA----GIKGGGV----T----KVLSDLCKHKLIAYE--RN   66 (465)
T ss_pred             CccchhhhhhhccchhHHHHHHHHhcccCccccHHHHHHHH----hhccCch----H----HHHHHHHHhHHHHhh--cc
Confidence            89999999999999999999999999999999999999986    3444432    2    35566666 587754  26


Q ss_pred             CCccceehh------------------hhcccccCcCCcCceeeccCC---CeeEEeeehhhhhhhhhhccccCcCCcc-
Q 040944           80 SKKEGVSEE------------------NQQNSEAGRGSEPDRHNASDK---VGAIIFCEYFEIDLLVYFCSFREDDDES-  137 (188)
Q Consensus        80 ~~YeGY~Lt------------------~alG~~IGVGKESDVYea~~~---~~aiKFh~~~~~~~~~~~~~~~~~~~~~-  137 (188)
                      ..|+||+||                  .++|.+||||||||||.+.++   +.++|||..-.+       |||.=-+-- 
T Consensus        67 ~k~dGYRLTy~GyDyLAlktL~~R~~v~svGnqIGVGKESDIY~v~d~~G~~~~lK~HRLGRt-------SFR~Vk~kRD  139 (465)
T KOG2268|consen   67 KKYDGYRLTYAGYDYLALKTLSNRGSVESVGNQIGVGKESDIYVVADEEGNPLILKLHRLGRT-------SFRNVKNKRD  139 (465)
T ss_pred             ccccceEeeeccchHHHHHHHHhcchhhhhccccccccccceEEEecCCCCchhHHHHhhhhh-------hHHHhhhhhh
Confidence            789999998                  789999999999999999666   788898876544       343211100 


Q ss_pred             --c--ccchHHHHHHHHHHHHHHHHhhCC
Q 040944          138 --V--NENDAELVKQIEKQRRRAVAAVGD  162 (188)
Q Consensus       138 --~--~e~~~~l~k~l~kqr~~a~aaa~~  162 (188)
                        -  .+--=--.-+|.-+|.=|.-.|+-
T Consensus       140 Y~r~r~~~sWlyLSRlaa~kEfafmkaL~  168 (465)
T KOG2268|consen  140 YLRKRKSGSWLYLSRLAATKEFAFMKALY  168 (465)
T ss_pred             hHhcCCccchhhhHHHHHHHHHHHHHHHH
Confidence              0  000012234677777777777743

>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain

Probab=99.83  E-value=6.7e-22  Score=146.34  Aligned_cols=66  Identities=35%  Similarity=0.539  Sum_probs=51.6

Q ss_pred             hcccCccchhHHHHHHhhccCCcccchhhhhhhhhhhhhhhCCCCCcccccccccchhhhhc-cccccCCCccCCcccee
Q 040944            8 LRYLSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEK-GVIHKDPALNSKKEGVS   86 (188)
Q Consensus         8 ~r~L~~~DfRVL~AIE~GMRnhE~VP~elI~k~s~~~~~~~hgls~ee~vd~~r~~l~rL~k-~LV~R~~~~~~~YeGY~   86 (188)
                      +++|+++|||||+|||+|||||||||.++|.++|        |++.+++.    ++|++|.+ +||.++   +.+|+||+
T Consensus         1 ~r~L~~~d~rvL~aiE~gmk~hE~VP~~~I~~~s--------~l~~~~~~----~~L~~L~~~kLv~~~---~~~Y~GYr   65 (82)
T PF09202_consen    1 LRYLSKEDFRVLRAIEMGMKNHEWVPLELIEKIS--------GLSEGEVE----KRLKRLVKLKLVSRR---NKPYDGYR   65 (82)
T ss_dssp             --T--HHHHHHHHHHHTTTTT-SSEEHHHHHHHH--------T--HHHHH----HHHHHHHHTTSEEEE----SSS-EEE
T ss_pred             CCcCCHHHHHHHHHHHHcccCCccCCHHHHHHHh--------CcCHHHHH----HHHHHHHhcCCcccc---CCCcceEE
Confidence            6899999999999999999999999999999998        99955555    79999999 699996   89999999


Q ss_pred             hh
Q 040944           87 EE   88 (188)
Q Consensus        87 Lt   88 (188)
                      ||
T Consensus        66 LT   67 (82)
T PF09202_consen   66 LT   67 (82)
T ss_dssp             E-
T ss_pred             Ee
Confidence            99

It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.

>cd05146 RIO3_euk RIO kinase family; eukaryotic RIO3, catalytic domain

Probab=97.14  E-value=0.00026  Score=59.52  Aligned_cols=35  Identities=20%  Similarity=0.167  Sum_probs=27.8

Q ss_pred             cccccCcCCcCceeeccC----------CCeeEEeeehhhhhhhhhhccccC
Q 040944           91 QNSEAGRGSEPDRHNASD----------KVGAIIFCEYFEIDLLVYFCSFRE  132 (188)
Q Consensus        91 lG~~IGVGKESDVYea~~----------~~~aiKFh~~~~~~~~~~~~~~~~  132 (188)
                      ++..||+||||+||.|.+          ..+|+|+|+       +-+++|+.
T Consensus         1 ~~g~i~~GKEa~V~~~~~~~~~~~~~~~~~~avKi~r-------~~~~~Fk~   45 (197)
T cd05146           1 INGCISTGKESVVLHANGGSNETEQVIPTECAIKVFK-------TTLNEFKN   45 (197)
T ss_pred             CCCccccCcceEEEEEecCcccccccCCceEEEEEEe-------ccceeEcC
Confidence            356799999999999933          389999998       55677764

The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). RIO kinases are atypical protein serine kinases containing a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. RIO3 is present only in multicellular eukaryotes. Its function is still unknown.

>PF15013 CCSMST1: CCSMST1 family

Probab=92.21  E-value=0.094  Score=39.31  Aligned_cols=25  Identities=40%  Similarity=0.740  Sum_probs=19.3

Q ss_pred             hhhhhhccccCcCCcccccchHHHHHHHHH
Q 040944          122 DLLVYFCSFREDDDESVNENDAELVKQIEK  151 (188)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~e~~~~l~k~l~k  151 (188)
                      =+++|||-+|||+|     .|..|.++|..
T Consensus        42 ~fliyFC~lReEnD-----iD~~L~~~L~e   66 (77)
T PF15013_consen   42 AFLIYFCFLREEND-----IDRWLDKNLYE   66 (77)
T ss_pred             HHHHHHhhcccccc-----HHHHHHhhHHh
Confidence            47899999999865     56677777754

>KOG2268 consensus Serine/threonine protein kinase [Signal transduction mechanisms; General function prediction only]

Probab=91.26  E-value=0.11  Score=49.27  Aligned_cols=37  Identities=41%  Similarity=0.740  Sum_probs=31.7

Q ss_pred             CCcccchhhhh---hhhhhhhhhhCCCCCcccccccccch
Q 040944           28 NHEIVPFRTRA---SHCFSQALEEHGFPVPSAVDCNRHCI   64 (188)
Q Consensus        28 nhE~VP~elI~---k~s~~~~~~~hgls~ee~vd~~r~~l   64 (188)
                      .-.|.-++-|+   .++||+||++||||+|+..|++|||+
T Consensus       146 ~~sWlyLSRlaa~kEfafmkaL~e~gfpVPkpiD~~RH~V  185 (465)
T KOG2268|consen  146 SGSWLYLSRLAATKEFAFMKALYERGFPVPKPIDHNRHCV  185 (465)
T ss_pred             ccchhhhHHHHHHHHHHHHHHHHHcCCCCCCcccccceee
Confidence            34588888765   45699999999999999999999997

>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B

Probab=90.64  E-value=0.16  Score=33.52  Aligned_cols=51  Identities=20%  Similarity=0.321  Sum_probs=41.3

Q ss_pred             cCccchhHHHHHHhhccCCcccchhhhhhhhhhhhhhhCCCCCcccccccccchhhhhc-cccccC
Q 040944           11 LSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEK-GVIHKD   75 (188)
Q Consensus        11 L~~~DfRVL~AIE~GMRnhE~VP~elI~k~s~~~~~~~hgls~ee~vd~~r~~l~rL~k-~LV~R~   75 (188)
                      |+..+|+||.+|...-..  .+....|++..        +++...+.    +.+.+|.+ +||.+.
T Consensus         3 lt~~q~~vL~~l~~~~~~--~~t~~~la~~l--------~~~~~~vs----~~v~~L~~~Glv~r~   54 (62)
T PF12802_consen    3 LTPSQFRVLMALARHPGE--ELTQSELAERL--------GISKSTVS----RIVKRLEKKGLVERE   54 (62)
T ss_dssp             STHHHHHHHHHHHHSTTS--GEEHHHHHHHH--------TS-HHHHH----HHHHHHHHTTSEEEE
T ss_pred             cCHHHHHHHHHHHHCCCC--CcCHHHHHHHH--------CcCHHHHH----HHHHHHHHCCCEEEe
Confidence            678899999999887765  77888888886        88866666    78999998 799885

...

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=90.52  E-value=0.17  Score=38.87  Aligned_cols=52  Identities=21%  Similarity=0.280  Sum_probs=44.9

Q ss_pred             hcccCccchhHHHHHHhhccCCcccchhhhhhhhhhhhhhhCCCCCcccccccccchhhhhc-cccccC
Q 040944            8 LRYLSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEK-GVIHKD   75 (188)
Q Consensus         8 ~r~L~~~DfRVL~AIE~GMRnhE~VP~elI~k~s~~~~~~~hgls~ee~vd~~r~~l~rL~k-~LV~R~   75 (188)
                      ...|++.|.++|..+..+-|    .|...|++..        |+|++.+.    +++.+|.+ |+|++-
T Consensus         3 ~~~lD~~D~~IL~~L~~d~r----~~~~eia~~l--------glS~~~v~----~Ri~~L~~~GiI~~~   55 (154)
T COG1522           3 MMKLDDIDRRILRLLQEDAR----ISNAELAERV--------GLSPSTVL----RRIKRLEEEGVIKGY   55 (154)
T ss_pred             cccccHHHHHHHHHHHHhCC----CCHHHHHHHH--------CCCHHHHH----HHHHHHHHCCceeeE
Confidence            35689999999999999999    8999999997        99977766    79999999 788874

>TIGR00498 lexA SOS regulatory protein LexA

Probab=89.73  E-value=0.26  Score=40.04  Aligned_cols=67  Identities=22%  Similarity=0.359  Sum_probs=50.6

Q ss_pred             hcccCccchhHHHHHHhhccCCcccc-hhhhhhhhhhhhhhhCCCCCcccccccccchhhhhc-cccccCCCccCCccce
Q 040944            8 LRYLSKDDFKVLTAVETGMRNHEIVP-FRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEK-GVIHKDPALNSKKEGV   85 (188)
Q Consensus         8 ~r~L~~~DfRVL~AIE~GMRnhE~VP-~elI~k~s~~~~~~~hgls~ee~vd~~r~~l~rL~k-~LV~R~~~~~~~YeGY   85 (188)
                      |+.|++.+++||..|...++.+.+-| +..|++..        |++....+.   +.|.+|++ ++|.+.   .+.|.|.
T Consensus         1 ~~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~--------~~~s~~tv~---~~l~~L~~~g~i~~~---~~~~~~~   66 (199)
T TIGR00498         1 MKPLTARQQEVLDLIRAHIESTGYPPSIREIARAV--------GLRSPSAAE---EHLKALERKGYIERD---PGKPRAI   66 (199)
T ss_pred             CCccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHh--------CCCChHHHH---HHHHHHHHCCCEecC---CCCCCeE
Confidence            35689999999999998888777756 56777775        887334443   78889999 688886   4666688


Q ss_pred             ehh
Q 040944           86 SEE   88 (188)
Q Consensus        86 ~Lt   88 (188)
                      +++
T Consensus        67 ~~~   69 (199)
T TIGR00498        67 RIL   69 (199)
T ss_pred             EeC
Confidence            775

LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.

>cd05147 RIO1_euk RIO kinase family; eukaryotic RIO1, catalytic domain

Probab=88.73  E-value=0.32  Score=39.47  Aligned_cols=27  Identities=22%  Similarity=0.208  Sum_probs=22.6

Q ss_pred             ccccCcCCcCceeeccC---CCeeEEeeeh
Q 040944           92 NSEAGRGSEPDRHNASD---KVGAIIFCEY  118 (188)
Q Consensus        92 G~~IGVGKESDVYea~~---~~~aiKFh~~  118 (188)
                      ...||.|++|+||.|..   .++|+|..+-
T Consensus         2 ~~~ig~G~~~~Vy~a~~~~g~~vAvKv~~~   31 (190)
T cd05147           2 NGCISTGKEANVYHATTANGEERAIKIYKT   31 (190)
T ss_pred             CCccccccceEEEEEECCCCCEEEEEEEEe
Confidence            46799999999999943   3899999874

The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). RIO kinases are atypical protein serine kinases containing a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. RIO1 is present in archaea, bacteria and eukaryotes. This subfamily is composed of RIO1 proteins from eukaryotes. RIO1 is essential for survival and is required for 18S rRNA processing, proper cell cycle progression and c

>KOG1165 consensus Casein kinase (serine/threonine/tyrosine protein kinase) [Signal transduction mechanisms]

Probab=82.46  E-value=0.77  Score=43.67  Aligned_cols=28  Identities=21%  Similarity=0.068  Sum_probs=24.5

Q ss_pred             hhcccccCcCCcCceeeccCC----CeeEEee
Q 040944           89 NQQNSEAGRGSEPDRHNASDK----VGAIIFC  116 (188)
Q Consensus        89 ~alG~~IGVGKESDVYea~~~----~~aiKFh  116 (188)
                      -.+|.+||.|.++++++|..-    ++||||-
T Consensus        30 yrVGkKIGeGsFG~lf~G~Nl~nne~VAIKfE   61 (449)
T KOG1165|consen   30 YRVGKKIGEGSFGVLFLGKNLYNNEPVAIKFE   61 (449)
T ss_pred             ceeccccccCcceeeecccccccCceEEEEec
Confidence            579999999999999999333    9999995

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=80.27  E-value=1.4  Score=35.95  Aligned_cols=61  Identities=16%  Similarity=0.206  Sum_probs=48.1

Q ss_pred             cCccchhHHHHHHhhccCCcccchhhhhhhhhhhhhhhCCCCCcccccccccchhhhhc-cccccCCCccCCccceehh
Q 040944           11 LSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEK-GVIHKDPALNSKKEGVSEE   88 (188)
Q Consensus        11 L~~~DfRVL~AIE~GMRnhE~VP~elI~k~s~~~~~~~hgls~ee~vd~~r~~l~rL~k-~LV~R~~~~~~~YeGY~Lt   88 (188)
                      +++....-|.+|-.-.++..++.+..|++..        +.+.+++.    ..+.+|.+ +||.+     .+|-|++||
T Consensus         4 ~s~~~edYL~~Iy~l~~~~~~~~~~diA~~L--------~Vsp~sVt----~ml~rL~~~GlV~~-----~~y~gi~LT   65 (154)
T COG1321           4 LSETEEDYLETIYELLEEKGFARTKDIAERL--------KVSPPSVT----EMLKRLERLGLVEY-----EPYGGVTLT   65 (154)
T ss_pred             cchHHHHHHHHHHHHHhccCcccHHHHHHHh--------CCCcHHHH----HHHHHHHHCCCeEE-----ecCCCeEEC
Confidence            4444555566666555588899999999985        99988888    58889999 79998     679999999

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	188
4gyi_A	397	Crystal Structure Of The Rio2 Kinase-AdpMG2+-Phosph		3e-06
4gyg_A	397	Crystal Structure Of The Rio2 Kinase From Chaetomiu		3e-06

>pdb|4GYI|A Chain A, Crystal Structure Of The Rio2 Kinase-AdpMG2+-Phosphoaspartate Complex From Chaetomium Thermophilum Length = 397

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 20/33 (60%), Positives = 27/33 (81%)
Query: 1  MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
          MKLD   +R+L+ +D++VLTAVE G +NHEIVP
Sbjct: 2  MKLDTRAMRHLTAEDWRVLTAVEMGSKNHEIVP 34

>pdb|4GYG|A Chain A, Crystal Structure Of The Rio2 Kinase From Chaetomium Thermophilum Length = 397

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 20/33 (60%), Positives = 27/33 (81%)
Query: 1  MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
          MKLD   +R+L+ +D++VLTAVE G +NHEIVP
Sbjct: 2  MKLDTRAMRHLTAEDWRVLTAVEMGSKNHEIVP 34

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	188
1zar_A	282	RIO2 kinase; serine kinase, winged-helix, RIO doma	3e-10

>1zar_A RIO2 kinase; serine kinase, winged-helix, RIO domain, ADP-Mn complex, rRNA processing, transferase; HET: ADP; 1.75A {Archaeoglobus fulgidus} SCOP: a.4.5.56 d.144.1.9 PDB: 1tqi_A* 1tqp_A* 1tqm_A* 1zao_A* Length = 282

 Score = 56.9 bits (137), Expect = 3e-10
 Identities = 5/29 (17%), Positives = 16/29 (55%)

Query: 5  VDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
           ++   + K  ++++ A+   + ++E VP
Sbjct: 4  AELYGKMGKHSWRIMDAIFKNLWDYEYVP 32

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	188
4gyi_A	397	RIO2 kinase; protein kinase, ADP complex, phosphoa	99.94
1zar_A	282	RIO2 kinase; serine kinase, winged-helix, RIO doma	99.71
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	86.31
1zth_A	258	RIO1 serine protein kinase; ribosome biogenesis, r	81.06

>4gyi_A RIO2 kinase; protein kinase, ADP complex, phosphoaspartate, acyl-phosphat ribosome biogenesis, Ser/Thr protein kinase; HET: PHD ADP; 2.20A {Chaetomium thermophilum} PDB: 4gyg_A

Probab=99.94  E-value=8.8e-28  Score=216.07  Aligned_cols=104  Identities=31%  Similarity=0.399  Sum_probs=90.3

Q ss_pred             CCcchHHhcccCccchhHHHHHHhhccCCcccchhhhhhhhhhhhhhhCCCC--Ccccccccccchhhhhc-cccccCCC
Q 040944            1 MKLDVDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFP--VPSAVDCNRHCIDDDEK-GVIHKDPA   77 (188)
Q Consensus         1 MkL~ae~~r~L~~~DfRVL~AIE~GMRnhE~VP~elI~k~s~~~~~~~hgls--~ee~vd~~r~~l~rL~k-~LV~R~~~   77 (188)
                      ||||++.||+|+++|||||+|||+|||||||||+++|.++|        |+.  .+.+.    ++|++|.+ +||.|.  
T Consensus         2 m~l~~~~~r~l~~~d~rvL~ave~g~~~he~vp~~~i~~~~--------~l~~~~~~~~----~~l~~l~~~~lv~~~--   67 (397)
T 4gyi_A            2 MKLDTRAMRHLTAEDWRVLTAVEMGSKNHEIVPTPLIEKIA--------RLRGGSSGVH----KSIATLAKAGLIARM--   67 (397)
T ss_dssp             -CCCCSGGGTCCHHHHHHHHHHHHHTTTCSSEEHHHHHHHH--------CSSSCCCSHH----HHHHHHHHTTSEEEE--
T ss_pred             CcCCHHHHhhcCHHHHHHHHHHHhccCCcccccHHHHHHHh--------CCCCchHhHH----HHHHhhhhcCceeec--
Confidence            89999999999999999999999999999999999999997        774  22343    78999999 699874  


Q ss_pred             ccCCccceehh------------------hhcccccCcCCcCceeeccCC---CeeEEeeeh
Q 040944           78 LNSKKEGVSEE------------------NQQNSEAGRGSEPDRHNASDK---VGAIIFCEY  118 (188)
Q Consensus        78 ~~~~YeGY~Lt------------------~alG~~IGVGKESDVYea~~~---~~aiKFh~~  118 (188)
                      .+.+|+||+||                  .++|.+||+||||+||.|.++   .+|+|+|+.
T Consensus        68 ~~~~y~gy~lt~~gyD~LAL~~L~~rg~iY~I~~~IG~Gk~a~VY~a~d~~G~~vAvKi~r~  129 (397)
T 4gyi_A           68 KEAKYDGYRLTYGGLDYLALHTHAARKDVYSVGSRIGVGKESDIMIVADEKGKQKVLKIHRL  129 (397)
T ss_dssp             ECSSCEEEEECHHHHHHHHHHHHHHTTSCSEEEEEEEECSSEEEEEEECTTCCEEEEEEECT
T ss_pred             cCCCcceeeeccCchHHHHHHHHHHCCCEEEecCEeeeCCceEEEEEECCCCCEEEEEEEec
Confidence            27899999988                  578999999999999999443   899999874

>1zar_A RIO2 kinase; serine kinase, winged-helix, RIO domain, ADP-Mn complex, rRNA processing, transferase; HET: ADP; 1.75A {Archaeoglobus fulgidus} SCOP: a.4.5.56 d.144.1.9 PDB: 1tqi_A* 1tqp_A* 1tqm_A* 1zao_A*

Probab=99.71  E-value=2.3e-18  Score=142.94  Aligned_cols=101  Identities=16%  Similarity=0.217  Sum_probs=85.5

Q ss_pred             cchHHhcccCccchhHHHHHHhhccCCcccchhhhhhhhhhhhhhhCCCCCcccccccccchhhhhc-cccccCCCccCC
Q 040944            3 LDVDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEK-GVIHKDPALNSK   81 (188)
Q Consensus         3 L~ae~~r~L~~~DfRVL~AIE~GMRnhE~VP~elI~k~s~~~~~~~hgls~ee~vd~~r~~l~rL~k-~LV~R~~~~~~~   81 (188)
                      ++++.|++|+++|||||+|+|+||++|+|||+++|.+++        +++.....    .++.+|.+ .++.++   ..+
T Consensus         2 ~~~~~~~~l~~~~~~~l~a~e~g~~~~~~v~~~~i~~~~--------~l~~~~~~----~~l~~l~~~~l~~~~---~~~   66 (282)
T 1zar_A            2 NIAELYGKMGKHSWRIMDAIFKNLWDYEYVPLQLISSHA--------RIGEEKAR----NILKYLSDLRVVQNR---QKD   66 (282)
T ss_dssp             CHHHHHHTCCHHHHHHHHHHHTTTTTCSSEEHHHHHHHH--------TCCHHHHH----HHHHHHHHTTSEEEE---CSS
T ss_pred             chHHHHHhCCHhhhhhhHHHhhCCcCceecCHHHHHHHh--------CCChhhHH----HHHHHHhhCCCcccc---CCC
Confidence            459999999999999999999999999999999999997        88855544    57777777 577764   678


Q ss_pred             ccceehh------------------hhcccccCcCCcCceeeccC---CCeeEEeeeh
Q 040944           82 KEGVSEE------------------NQQNSEAGRGSEPDRHNASD---KVGAIIFCEY  118 (188)
Q Consensus        82 YeGY~Lt------------------~alG~~IGVGKESDVYea~~---~~~aiKFh~~  118 (188)
                      |+||+++                  ..+|..||.|++|.||.|.+   ..+|+|++..
T Consensus        67 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~iG~G~~g~Vy~~~~~~g~~valK~~~~  124 (282)
T 1zar_A           67 YEGSTFTFIGLSLYSLHRLVRSGKVDAIGKLMGEGKESAVFNCYSEKFGECVVKFHKV  124 (282)
T ss_dssp             SCEEEECHHHHHHHHHHHHHHTTSCSEEEEEEEECSSEEEEEEEETTTEEEEEEEECC
T ss_pred             ccceeeecCCccHHHHHHHHhCCeEEEecCEeccCCCceEEEEEeCCCCEEEEEEEEC
Confidence            9999987                  34779999999999999942   3899999863

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=86.31  E-value=0.3  Score=35.34  Aligned_cols=64  Identities=19%  Similarity=0.225  Sum_probs=47.5

Q ss_pred             HhcccCccchhHHHHHHhhccCCcccchhhhhhhhhhhhhhhCCCCCcccccccccchhhhhc-cccccCCCccCCccce
Q 040944            7 VLRYLSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEK-GVIHKDPALNSKKEGV   85 (188)
Q Consensus         7 ~~r~L~~~DfRVL~AIE~GMRnhE~VP~elI~k~s~~~~~~~hgls~ee~vd~~r~~l~rL~k-~LV~R~~~~~~~YeGY   85 (188)
                      .+..|+...+++|.+|....+...-+....|++..        +++...+.    +.+++|++ +||.|.   .   .+|
T Consensus         7 ~~~~lt~~~~~~L~~l~~l~~~~~~~s~~ela~~l--------~is~~tv~----~~l~~Le~~Gli~r~---~---~~~   68 (139)
T 2x4h_A            7 QMSNLSRREFSYLLTIKRYNDSGEGAKINRIAKDL--------KIAPSSVF----EEVSHLEEKGLVKKK---E---DGV   68 (139)
T ss_dssp             ----CCHHHHHHHHHHHHHHTTTSCBCHHHHHHHH--------TCCHHHHH----HHHHHHHHTTSEEEE---T---TEE
T ss_pred             HHhhcCHHHHHHHHHHHHHHhcCCCcCHHHHHHHh--------CCChHHHH----HHHHHHHHCCCEEec---C---CeE
Confidence            35578899999999987665566778888899986        89855555    78999988 799985   2   467


Q ss_pred             ehh
Q 040944           86 SEE   88 (188)
Q Consensus        86 ~Lt   88 (188)
                      .+|
T Consensus        69 ~Lt   71 (139)
T 2x4h_A           69 WIT   71 (139)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            776

>1zth_A RIO1 serine protein kinase; ribosome biogenesis, rRNA, ADP, manganese, transferase; HET: ADP; 1.89A {Archaeoglobus fulgidus} PDB: 1zp9_A* 1ztf_A*

Probab=81.06  E-value=0.51  Score=37.71  Aligned_cols=28  Identities=14%  Similarity=0.089  Sum_probs=23.3

Q ss_pred             hcccccCcCCcCceeeccC---C-C--eeEEeee
Q 040944           90 QQNSEAGRGSEPDRHNASD---K-V--GAIIFCE  117 (188)
Q Consensus        90 alG~~IGVGKESDVYea~~---~-~--~aiKFh~  117 (188)
                      .++.+||.|++|.||.|.+   + .  +|+|.++
T Consensus        50 ~i~~~ig~G~~g~Vy~a~~~~~g~~~~vAvK~~~   83 (258)
T 1zth_A           50 AMGGVISTGKEANVFYADGVFDGKPVAMAVKIYR   83 (258)
T ss_dssp             EEEEEEEECSSEEEEEEEEEETTEEEEEEEEEEC
T ss_pred             hhCCEEeecceEEEEEEEEcCCCcEeeEEEEEEE
Confidence            5778999999999999943   3 6  9999864

---

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	188
d1zara1	89	a.4.5.56 (A:2-90) Rio2 serine protein kinase N-ter	8e-11

>d1zara1 a.4.5.56 (A:2-90) Rio2 serine protein kinase N-terminal domain {Archaeoglobus fulgidus [TaxId: 2234]} Length = 89

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Rio2 serine protein kinase N-terminal domain
domain: Rio2 serine protein kinase N-terminal domain
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 53.9 bits (130), Expect = 8e-11
 Identities = 5/29 (17%), Positives = 16/29 (55%)

Query: 5  VDVLRYLSKDDFKVLTAVETGMRNHEIVP 33
           ++   + K  ++++ A+   + ++E VP
Sbjct: 3  AELYGKMGKHSWRIMDAIFKNLWDYEYVP 31

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	188
d1zara1	89	Rio2 serine protein kinase N-terminal domain {Arch	99.88
d1zara2	191	Rio2 serine protein kinase C-terminal domain {Arch	96.36
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	90.13
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	89.63
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	89.41
d1ckia_	299	Casein kinase-1, CK1 {Rat (Rattus norvegicus) [Tax	88.45
d1byga_	262	Carboxyl-terminal src kinase (csk) {Human (Homo sa	84.82
d1opja_	287	Abelsone tyrosine kinase (abl) {Mouse (Mus musculu	83.89
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	83.58
d1csna_	293	Casein kinase-1, CK1 {Fission yeast (Schizosacchar	83.39
d1fmka3	285	c-src tyrosine kinase {Human (Homo sapiens) [TaxId	82.74
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	80.8

>d1zara1 a.4.5.56 (A:2-90) Rio2 serine protein kinase N-terminal domain {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Rio2 serine protein kinase N-terminal domain
domain: Rio2 serine protein kinase N-terminal domain
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.88  E-value=1.4e-24  Score=161.04  Aligned_cols=70  Identities=16%  Similarity=0.244  Sum_probs=64.9

Q ss_pred             chHHhcccCccchhHHHHHHhhccCCcccchhhhhhhhhhhhhhhCCCCCcccccccccchhhhhc-cccccCCCccCCc
Q 040944            4 DVDVLRYLSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEK-GVIHKDPALNSKK   82 (188)
Q Consensus         4 ~ae~~r~L~~~DfRVL~AIE~GMRnhE~VP~elI~k~s~~~~~~~hgls~ee~vd~~r~~l~rL~k-~LV~R~~~~~~~Y   82 (188)
                      .++.|++|+++|||||+|||+|||||||||+++|.++|        |++.+++.    ++|++|.+ +||+|+   +.+|
T Consensus         2 vae~~~~L~~~dfRvL~aiE~gmrnhE~VP~~lI~~~a--------~l~~~~~~----~~L~~L~k~kLv~~~---~~~Y   66 (89)
T d1zara1           2 IAELYGKMGKHSWRIMDAIFKNLWDYEYVPLQLISSHA--------RIGEEKAR----NILKYLSDLRVVQNR---QKDY   66 (89)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHTTTTTCSSEEHHHHHHHH--------TCCHHHHH----HHHHHHHHTTSEEEE---CSSS
T ss_pred             HHHHHHHcCHHHHHHHHHHHhccccCccccHHHHHHHH--------CCCHHHHH----HHHHHHHHcCCeecc---CCCc
Confidence            48999999999999999999999999999999999998        99966666    79999999 699986   7899


Q ss_pred             cceehh
Q 040944           83 EGVSEE   88 (188)
Q Consensus        83 eGY~Lt   88 (188)
                      +||+||
T Consensus        67 ~GYrLT   72 (89)
T d1zara1          67 EGSTFT   72 (89)
T ss_dssp             CEEEEC
T ss_pred             ceEEee
Confidence            999999

>d1zara2 d.144.1.9 (A:91-281) Rio2 serine protein kinase C-terminal domain {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Protein kinase-like (PK-like)
superfamily: Protein kinase-like (PK-like)
family: RIO1-like kinases
domain: Rio2 serine protein kinase C-terminal domain
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.36  E-value=0.00037  Score=51.83  Aligned_cols=30  Identities=17%  Similarity=0.169  Sum_probs=25.3

Q ss_pred             hhcccccCcCCcCceeeccC--C-CeeEEeeeh
Q 040944           89 NQQNSEAGRGSEPDRHNASD--K-VGAIIFCEY  118 (188)
Q Consensus        89 ~alG~~IGVGKESDVYea~~--~-~~aiKFh~~  118 (188)
                      .++|.+||.|.+|+||.|.+  + .+|+|+++.
T Consensus         2 ~~vg~~IG~G~~g~Vy~a~~~~g~~vAvKi~r~   34 (191)
T d1zara2           2 DAIGKLMGEGKESAVFNCYSEKFGECVVKFHKV   34 (191)
T ss_dssp             SEEEEEEEECSSEEEEEEEETTTEEEEEEEECC
T ss_pred             chhCCEeeeCcceEEEEEECCCCCEEEEEEEec
Confidence            37899999999999999933  3 899998764

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=90.13  E-value=0.058  Score=34.93  Aligned_cols=49  Identities=18%  Similarity=0.327  Sum_probs=40.3

Q ss_pred             ccCccchhHHHHHHhhccCCcccchhhhhhhhhhhhhhhCCCCCcccccccccchhhhhc-ccccc
Q 040944           10 YLSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEK-GVIHK   74 (188)
Q Consensus        10 ~L~~~DfRVL~AIE~GMRnhE~VP~elI~k~s~~~~~~~hgls~ee~vd~~r~~l~rL~k-~LV~R   74 (188)
                      .|+.-|.++|.++..+-|-    |...|++..        |+|++.+.    +++.+|.+ +.|++
T Consensus         2 klD~~D~~IL~~L~~n~r~----s~~~iA~~l--------gis~~tv~----~Ri~~L~~~giI~~   51 (63)
T d2cfxa1           2 KLDQIDLNIIEELKKDSRL----SMRELGRKI--------KLSPPSVT----ERVRQLESFGIIKQ   51 (63)
T ss_dssp             CCCHHHHHHHHHHHHCSCC----CHHHHHHHH--------TCCHHHHH----HHHHHHHHTTSEEE
T ss_pred             CCCHHHHHHHHHHHHcCCC----CHHHHHHHH--------CcCHHHHH----HHHHHHHHCCCeee
Confidence            3788899999999988654    899999987        99965555    79988888 68776

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=89.63  E-value=0.073  Score=34.11  Aligned_cols=49  Identities=22%  Similarity=0.351  Sum_probs=39.8

Q ss_pred             cCccchhHHHHHHhhccCCcccchhhhhhhhhhhhhhhCCCCCcccccccccchhhhhc-cccccC
Q 040944           11 LSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEK-GVIHKD   75 (188)
Q Consensus        11 L~~~DfRVL~AIE~GMRnhE~VP~elI~k~s~~~~~~~hgls~ee~vd~~r~~l~rL~k-~LV~R~   75 (188)
                      |++-|.+||..+...-|-    |...|++..        |+|++.+.    ++|.+|.+ ++|++.
T Consensus         1 lD~~D~kIl~~L~~n~r~----s~~~lA~~~--------gls~~~v~----~Ri~~L~~~giI~~~   50 (60)
T d1i1ga1           1 IDERDKIILEILEKDART----PFTEIAKKL--------GISETAVR----KRVKALEEKGIIEGY   50 (60)
T ss_dssp             CCSHHHHHHHHHHHCTTC----CHHHHHHHH--------TSCHHHHH----HHHHHHHHHTSSCCC
T ss_pred             CCHHHHHHHHHHHHcCCC----CHHHHHHHH--------CcCHHHHH----HHHHHHHHCCCeEeE
Confidence            577899999999987553    889999987        99966665    68988888 688763

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=89.41  E-value=0.072  Score=33.92  Aligned_cols=49  Identities=22%  Similarity=0.304  Sum_probs=39.6

Q ss_pred             cCccchhHHHHHHhhccCCcccchhhhhhhhhhhhhhhCCCCCcccccccccchhhhhc-cccccC
Q 040944           11 LSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEK-GVIHKD   75 (188)
Q Consensus        11 L~~~DfRVL~AIE~GMRnhE~VP~elI~k~s~~~~~~~hgls~ee~vd~~r~~l~rL~k-~LV~R~   75 (188)
                      |++-|.++|..+..+-+-    |...|++..        |+|+..+.    +++.+|.+ +.|++.
T Consensus         1 lD~~D~~Il~~L~~n~r~----s~~eiA~~l--------~ls~~~v~----~Ri~~L~~~giI~~~   50 (60)
T d2cyya1           1 LDEIDKKIIKILQNDGKA----PLREISKIT--------GLAESTIH----ERIRKLRESGVIKKF   50 (60)
T ss_dssp             CCHHHHHHHHHHHHCTTC----CHHHHHHHH--------CSCHHHHH----HHHHHHHHHTSSCCC
T ss_pred             CCHHHHHHHHHHHHcCCC----CHHHHHHHH--------CcCHHHHH----HHHHHHHHCCCeEeE
Confidence            567799999999998554    899999997        99955555    78989888 688763

>d1ckia_ d.144.1.7 (A:) Casein kinase-1, CK1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: Protein kinase-like (PK-like)
superfamily: Protein kinase-like (PK-like)
family: Protein kinases, catalytic subunit
domain: Casein kinase-1, CK1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=88.45  E-value=0.063  Score=41.68  Aligned_cols=26  Identities=27%  Similarity=0.124  Sum_probs=21.4

Q ss_pred             cccccCcCCcCceeeccC---C-CeeEEee
Q 040944           91 QNSEAGRGSEPDRHNASD---K-VGAIIFC  116 (188)
Q Consensus        91 lG~~IGVGKESDVYea~~---~-~~aiKFh  116 (188)
                      ++.+||.|.+|.||.|.+   + .+|+|.-
T Consensus        11 l~~~iG~G~fG~Vy~a~~~~~~~~vAvK~~   40 (299)
T d1ckia_          11 LGRKIGSGSFGDIYLGTDIAAGEEVAIKLE   40 (299)
T ss_dssp             EEEEEEECSSSEEEEEEETTTTEEEEEEEE
T ss_pred             EeEEEeeCCCcEEEEEEECCCCCEEEEEEE
Confidence            568899999999999933   2 8999963

>d1byga_ d.144.1.7 (A:) Carboxyl-terminal src kinase (csk) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Protein kinase-like (PK-like)
superfamily: Protein kinase-like (PK-like)
family: Protein kinases, catalytic subunit
domain: Carboxyl-terminal src kinase (csk)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.82  E-value=0.13  Score=40.14  Aligned_cols=28  Identities=14%  Similarity=0.051  Sum_probs=23.0

Q ss_pred             hcccccCcCCcCceeec--cCCCeeEEeee
Q 040944           90 QQNSEAGRGSEPDRHNA--SDKVGAIIFCE  117 (188)
Q Consensus        90 alG~~IGVGKESDVYea--~~~~~aiKFh~  117 (188)
                      .++..||.|.+|.||.|  .+..+|+|..+
T Consensus        10 ~~~~~lG~G~fg~Vy~~~~~~~~vAvK~i~   39 (262)
T d1byga_          10 KLLQTIGKGEFGDVMLGDYRGNKVAVKCIK   39 (262)
T ss_dssp             EEEEEEEECSSCEEEEEEETTEEEEEEECC
T ss_pred             EEeEEEecCCCeEEEEEEECCeEEEEEEEC
Confidence            46788999999999999  33389999764

>d1opja_ d.144.1.7 (A:) Abelsone tyrosine kinase (abl) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Protein kinase-like (PK-like)
superfamily: Protein kinase-like (PK-like)
family: Protein kinases, catalytic subunit
domain: Abelsone tyrosine kinase (abl)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.89  E-value=0.23  Score=38.92  Aligned_cols=39  Identities=10%  Similarity=-0.022  Sum_probs=28.3

Q ss_pred             cCCccceehh---hhcccccCcCCcCceeeccC---C-CeeEEeee
Q 040944           79 NSKKEGVSEE---NQQNSEAGRGSEPDRHNASD---K-VGAIIFCE  117 (188)
Q Consensus        79 ~~~YeGY~Lt---~alG~~IGVGKESDVYea~~---~-~~aiKFh~  117 (188)
                      +..|+-|.+.   -.++..||.|.+|.||.|..   + .+|+|..+
T Consensus         6 ~p~~~~wei~~~~~~~~~~iG~G~fg~Vy~a~~~~~~~~vAvK~i~   51 (287)
T d1opja_           6 SPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLK   51 (287)
T ss_dssp             STTCCTTBCCGGGEEEEEETTTTTTSSEEEEEEGGGTEEEEEEECC
T ss_pred             CCCCcccEecHHHeEEeeEEeeCCCeEEEEEEECCCCeEEEEEEEC
Confidence            3446666554   35678899999999999932   2 79999743

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=83.58  E-value=0.13  Score=33.43  Aligned_cols=51  Identities=10%  Similarity=0.068  Sum_probs=37.1

Q ss_pred             HHHHHhhccCCcccchhhhhhhhhhhhhhhCCCCCcccccccccchhhhhc-cccccCCCccCCcccee
Q 040944           19 LTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEK-GVIHKDPALNSKKEGVS   86 (188)
Q Consensus        19 L~AIE~GMRnhE~VP~elI~k~s~~~~~~~hgls~ee~vd~~r~~l~rL~k-~LV~R~~~~~~~YeGY~   86 (188)
                      |.+|-.-...+.+|....|++..        |++.+++.    ..+.+|.+ +||.+     .+|.|..
T Consensus         9 Lk~I~~l~~~~~~v~~~~iA~~L--------~vs~~SVs----~mikrL~~~GlV~~-----~~Y~~i~   60 (61)
T d2ev0a1           9 IEQIYMLIEEKGYARVSDIAEAL--------AVHPSSVT----KMVQKLDKDEYLIY-----EKYRGLV   60 (61)
T ss_dssp             HHHHHHHHHHHSSCCHHHHHHHH--------TCCHHHHH----HHHHHHHHTTSEEC---------CCE
T ss_pred             HHHHHHHHhcCCCccHHHHHHHh--------CCCchhHH----HHHHHHHHCCCEEE-----ccCCCee
Confidence            45554445566899999999996        99988888    58888888 79998     5676654

>d1csna_ d.144.1.7 (A:) Casein kinase-1, CK1 {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a+b)
fold: Protein kinase-like (PK-like)
superfamily: Protein kinase-like (PK-like)
family: Protein kinases, catalytic subunit
domain: Casein kinase-1, CK1
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=83.39  E-value=0.2  Score=39.05  Aligned_cols=27  Identities=22%  Similarity=0.176  Sum_probs=21.9

Q ss_pred             hcccccCcCCcCceeeccC---C-CeeEEee
Q 040944           90 QQNSEAGRGSEPDRHNASD---K-VGAIIFC  116 (188)
Q Consensus        90 alG~~IGVGKESDVYea~~---~-~~aiKFh  116 (188)
                      .++..||.|.+|.||.|.+   + .+|+|+-
T Consensus         8 ~i~~~iG~G~fG~Vy~a~~~~~~~~vAvK~~   38 (293)
T d1csna_           8 KVGRRIGEGSFGVIFEGTNLLNNQQVAIKFE   38 (293)
T ss_dssp             EEEEEEEECSSCEEEEEEETTTTEEEEEEEE
T ss_pred             EEEEEEecCCCeEEEEEEECCCCCEEEEEEE
Confidence            3678899999999999932   2 7999964

>d1fmka3 d.144.1.7 (A:249-533) c-src tyrosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Protein kinase-like (PK-like)
superfamily: Protein kinase-like (PK-like)
family: Protein kinases, catalytic subunit
domain: c-src tyrosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.74  E-value=0.12  Score=40.82  Aligned_cols=29  Identities=14%  Similarity=-0.021  Sum_probs=23.4

Q ss_pred             hhcccccCcCCcCceeeccCC---CeeEEeee
Q 040944           89 NQQNSEAGRGSEPDRHNASDK---VGAIIFCE  117 (188)
Q Consensus        89 ~alG~~IGVGKESDVYea~~~---~~aiKFh~  117 (188)
                      -.++.+||.|.+|.||.|...   .+|+|..+
T Consensus        19 ~~i~~~iG~G~fg~Vy~~~~~~~~~vAiK~l~   50 (285)
T d1fmka3          19 LRLEVKLGQGCFGEVWMGTWNGTTRVAIKTLK   50 (285)
T ss_dssp             EEEEEEEEECSSCEEEEEEETTTEEEEEEECC
T ss_pred             EEEeeEEeeCCCeEEEEEEECCCCEEEEEEEC
Confidence            357788999999999999332   79999765

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=80.80  E-value=0.32  Score=31.08  Aligned_cols=48  Identities=17%  Similarity=0.255  Sum_probs=38.7

Q ss_pred             cCccchhHHHHHHhhccCCcccchhhhhhhhhhhhhhhCCCCCcccccccccchhhhhc-ccccc
Q 040944           11 LSKDDFKVLTAVETGMRNHEIVPFRTRASHCFSQALEEHGFPVPSAVDCNRHCIDDDEK-GVIHK   74 (188)
Q Consensus        11 L~~~DfRVL~AIE~GMRnhE~VP~elI~k~s~~~~~~~hgls~ee~vd~~r~~l~rL~k-~LV~R   74 (188)
                      |++-|.+||+.+...-+-    |...|++..        |+|...+.    +++.+|.+ +.|.+
T Consensus         3 lD~~D~~IL~~L~~~~r~----s~~eiA~~l--------~ls~~~v~----~Ri~rL~~~GiI~~   51 (63)
T d2cg4a1           3 IDNLDRGILEALMGNART----AYAELAKQF--------GVSPETIH----VRVEKMKQAGIITG   51 (63)
T ss_dssp             CCHHHHHHHHHHHHCTTS----CHHHHHHHH--------TSCHHHHH----HHHHHHHHHTSEEE
T ss_pred             CCHHHHHHHHHHHHcCCC----CHHHHHHHH--------CcCHHHHH----HHHHHHHHCCCeEe
Confidence            678899999999988554    888899887        99955555    78988888 67775