Citrus Sinensis ID: 042488

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------
Protein Sequence
MSGEEEENAAELKIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHccccccHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccEcccccHHHHHHHHHHHHHccccHHHHHHHHccccccHHHHHHHcHcHccccccccHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
msgeeeenAAELKIGDVFRILSRYQLAEFElcvlgnlcpETVEEAIAMVpsiktrgrahdDEAIEKMLNDLSLIKKFE
Flexible Loop (DISEMBL)
msgeeeenaaelkigdvFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSiktrgrahddeAIEKMlndlslikkfe
Low Complexity Region (SEG)
MSGEEEENAAELKIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE
Disordered region (IsUnstruct)
***********LKIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSI**************************
Disordered Region (DISOPRED)
***************DVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRG***DDEAIEKMLNDLSLIK***
Disordered Region (DISEMBL)
**********ELKIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE
Disordered Region (DISPRO)
*******NAAELKIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSGEEEENAAELKIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE
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	78	2.2.26 [Sep-21-2011]
Q9D7M8	142	DNA-directed RNA polymera	yes	no	0.794	0.436	0.384	1e-06
O15514	142	DNA-directed RNA polymera	yes	no	0.794	0.436	0.384	1e-06
Q54S04	155	DNA-directed RNA polymera	yes	no	0.769	0.387	0.421	7e-06
Q9VEA5	139	DNA-directed RNA polymera	yes	no	0.628	0.352	0.442	2e-05

>sp|Q9D7M8|RPB4_MOUSE DNA-directed RNA polymerase II subunit RPB4 OS=Mus musculus GN=Polr2d PE=2 SV=2

 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 43/65 (66%), Gaps = 3/65 (4%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           I  V  +L + +L +FEL  L NLCPET EE+ A++PS++ R    +DE ++++L+D+  
Sbjct: 80  IASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR---FEDEELQQILDDIQT 136

Query: 74  IKKFE 78
            + F+
Sbjct: 137 KRSFQ 141

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA.
Mus musculus (taxid: 10090)

>sp|O15514|RPB4_HUMAN DNA-directed RNA polymerase II subunit RPB4 OS=Homo sapiens GN=POLR2D PE=1 SV=1

 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 43/65 (66%), Gaps = 3/65 (4%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           I  V  +L + +L +FEL  L NLCPET EE+ A++PS++ R    +DE ++++L+D+  
Sbjct: 80  IASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR---FEDEELQQILDDIQT 136

Query: 74  IKKFE 78
            + F+
Sbjct: 137 KRSFQ 141

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA.

Homo sapiens (taxid: 9606)

>sp|Q54S04|RPB4_DICDI DNA-directed RNA polymerase II subunit rpb4 OS=Dictyostelium discoideum GN=polr2d PE=3 SV=1

 Score = 49.3 bits (116), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 27/64 (42%), Positives = 42/64 (65%), Gaps = 4/64 (6%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           I  V   LS+  L EFE+  L NLCPE  +EA +++PS+K   +  DDE ++ +L++LS 
Sbjct: 95  IKQVRTALSKQNLEEFEIASLANLCPEISDEAKSLIPSLK---KMEDDE-LQAILDELSN 150

Query: 74  IKKF 77
           ++KF
Sbjct: 151 LRKF 154

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA.

Dictyostelium discoideum (taxid: 44689)

>sp|Q9VEA5|RPB4_DROME DNA-directed RNA polymerase II 16 kDa polypeptide OS=Drosophila melanogaster GN=Rpb4 PE=2 SV=5

 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/52 (44%), Positives = 37/52 (71%), Gaps = 3/52 (5%)

Query: 20  ILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDL 71
           +L + +L +FEL  LGNLCPE  EEA A++PS++ R    +DE + ++L+D+
Sbjct: 83  LLMQKKLHKFELAALGNLCPEAPEEAKALIPSLEGR---FEDEELRQILDDI 131

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Associates with POLR2G.

Drosophila melanogaster (taxid: 7227)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

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	78
225446712	138	PREDICTED: DNA-directed RNA polymerase I	0.833	0.471	0.907	2e-26
224083811	138	predicted protein [Populus trichocarpa]	0.833	0.471	0.907	2e-26
357513239	114	DNA-directed RNA polymerase II subunit R	0.833	0.570	0.892	9e-26
357513237	138	DNA-directed RNA polymerase II subunit R	0.833	0.471	0.892	1e-25
388495724	138	unknown [Lotus japonicus]	0.833	0.471	0.892	1e-25
255562011	138	DNA-directed RNA polymerase II, putative	0.833	0.471	0.876	2e-25
351727683	138	uncharacterized protein LOC100499661 [Gl	0.833	0.471	0.876	4e-25
449441240	138	PREDICTED: DNA-directed RNA polymerase I	0.833	0.471	0.846	4e-25
146403790	138	putative 15.9 kDa subunit of RNA polymer	0.833	0.471	0.846	1e-24
351724197	138	uncharacterized protein LOC100527316 [Gl	0.833	0.471	0.861	1e-24

>gi|225446712|ref|XP_002282413.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB4 [Vitis vinifera] gi|147856183|emb|CAN80281.1| hypothetical protein VITISV_017448 [Vitis vinifera] gi|302143481|emb|CBI22042.3| unnamed protein product [Vitis vinifera]

 Score =  122 bits (307), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 59/65 (90%), Positives = 61/65 (93%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           +  V  ILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKT+GRAHDDEAIEKMLNDLSL
Sbjct: 74  VRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTKGRAHDDEAIEKMLNDLSL 133

Query: 74  IKKFE 78
           IKKFE
Sbjct: 134 IKKFE 138

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224083811|ref|XP_002307132.1| predicted protein [Populus trichocarpa] gi|224096326|ref|XP_002310604.1| predicted protein [Populus trichocarpa] gi|222853507|gb|EEE91054.1| predicted protein [Populus trichocarpa] gi|222856581|gb|EEE94128.1| predicted protein [Populus trichocarpa]

 Score =  122 bits (306), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 59/65 (90%), Positives = 61/65 (93%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           +  V  ILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKT+GRAHDDEAIEKMLNDLSL
Sbjct: 74  VRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTKGRAHDDEAIEKMLNDLSL 133

Query: 74  IKKFE 78
           IKKFE
Sbjct: 134 IKKFE 138

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357513239|ref|XP_003626908.1| DNA-directed RNA polymerase II subunit RPB4 [Medicago truncatula] gi|355520930|gb|AET01384.1| DNA-directed RNA polymerase II subunit RPB4 [Medicago truncatula]

 Score =  120 bits (301), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 58/65 (89%), Positives = 60/65 (92%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           +  V  IL+RYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRA DDEAIEKMLNDLSL
Sbjct: 50  VRQVREILARYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAQDDEAIEKMLNDLSL 109

Query: 74  IKKFE 78
           IKKFE
Sbjct: 110 IKKFE 114

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357513237|ref|XP_003626907.1| DNA-directed RNA polymerase II subunit RPB4 [Medicago truncatula] gi|355520929|gb|AET01383.1| DNA-directed RNA polymerase II subunit RPB4 [Medicago truncatula] gi|388497296|gb|AFK36714.1| unknown [Medicago truncatula]

 Score =  120 bits (301), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 58/65 (89%), Positives = 60/65 (92%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           +  V  IL+RYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRA DDEAIEKMLNDLSL
Sbjct: 74  VRQVREILARYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAQDDEAIEKMLNDLSL 133

Query: 74  IKKFE 78
           IKKFE
Sbjct: 134 IKKFE 138

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388495724|gb|AFK35928.1| unknown [Lotus japonicus]

 Score =  120 bits (300), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 58/65 (89%), Positives = 60/65 (92%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           +  V  IL+RYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRA DDEAIEKMLNDLSL
Sbjct: 74  VRQVREILARYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAQDDEAIEKMLNDLSL 133

Query: 74  IKKFE 78
           IKKFE
Sbjct: 134 IKKFE 138

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255562011|ref|XP_002522014.1| DNA-directed RNA polymerase II, putative [Ricinus communis] gi|223538818|gb|EEF40418.1| DNA-directed RNA polymerase II, putative [Ricinus communis]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 57/65 (87%), Positives = 60/65 (92%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           +  V  ILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKT+GRAHDDEAIEKML DLS+
Sbjct: 74  VRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTKGRAHDDEAIEKMLTDLSM 133

Query: 74  IKKFE 78
           IKKFE
Sbjct: 134 IKKFE 138

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351727683|ref|NP_001237937.1| uncharacterized protein LOC100499661 [Glycine max] gi|255625623|gb|ACU13156.1| unknown [Glycine max]

 Score =  118 bits (296), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 57/65 (87%), Positives = 60/65 (92%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           +  V  IL+RYQLAEFELCVLGNLCPETVEEAIAMVPSIK+RGRA DDEAIEKMLNDLSL
Sbjct: 74  VRQVREILARYQLAEFELCVLGNLCPETVEEAIAMVPSIKSRGRAQDDEAIEKMLNDLSL 133

Query: 74  IKKFE 78
           IKKFE
Sbjct: 134 IKKFE 138

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449441240|ref|XP_004138390.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB4-like [Cucumis sativus] gi|449526195|ref|XP_004170099.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB4-like [Cucumis sativus]

 Score =  118 bits (296), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 55/65 (84%), Positives = 60/65 (92%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           +  V  +LSRYQLAEFELCVLGNLCPETVEEAIAMVPS+KT+GR HDDEAIEKMLNDLSL
Sbjct: 74  VRQVREVLSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSL 133

Query: 74  IKKFE 78
           IK+FE
Sbjct: 134 IKRFE 138

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|146403790|gb|ABQ32301.1| putative 15.9 kDa subunit of RNA polymerase II [Artemisia annua]

 Score =  117 bits (292), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 55/65 (84%), Positives = 60/65 (92%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           +  V  +LSR+QLAEFELCVLGNLCPETVEEAIAMVPSIK+RGR HDDEAIEKMLND+SL
Sbjct: 74  VRQVRELLSRHQLAEFELCVLGNLCPETVEEAIAMVPSIKSRGRGHDDEAIEKMLNDMSL 133

Query: 74  IKKFE 78
           IKKFE
Sbjct: 134 IKKFE 138

Source: Artemisia annua

Species: Artemisia annua

Genus: Artemisia

Family: Asteraceae

Order: Asterales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351724197|ref|NP_001238073.1| uncharacterized protein LOC100527316 [Glycine max] gi|255632071|gb|ACU16388.1| unknown [Glycine max]

 Score =  116 bits (291), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 56/65 (86%), Positives = 60/65 (92%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           +  V  IL+RYQLAEFELCVLGNLCPETVEEAIA+VPSIK+RGRA DDEAIEKMLNDLSL
Sbjct: 74  VRQVREILARYQLAEFELCVLGNLCPETVEEAIAVVPSIKSRGRAQDDEAIEKMLNDLSL 133

Query: 74  IKKFE 78
           IKKFE
Sbjct: 134 IKKFE 138

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	78
TAIR|locus:2178158	138	NRPB4 [Arabidopsis thaliana (t	0.833	0.471	0.815	1.1e-31
UNIPROTKB|Q1JQ91	142	POLR2D "Polymerase (RNA) II (D	0.794	0.436	0.4	5.3e-10
FB|FBgn0263757	139	Rpb4 [Drosophila melanogaster	0.628	0.352	0.461	3.6e-09
UNIPROTKB|F1P2S1	147	POLR2D "Uncharacterized protei	0.794	0.421	0.415	3.3e-08
UNIPROTKB|E2RPH1	142	POLR2D "Uncharacterized protei	0.794	0.436	0.4	6.8e-08
UNIPROTKB|E9PB93	104	POLR2D "DNA-directed RNA polym	0.794	0.596	0.4	6.8e-08
UNIPROTKB|O15514	142	POLR2D "DNA-directed RNA polym	0.794	0.436	0.4	6.8e-08
MGI|MGI:1916491	142	Polr2d "polymerase (RNA) II (D	0.794	0.436	0.4	6.8e-08
RGD|1308565	142	Polr2d "polymerase (RNA) II (D	0.794	0.436	0.4	6.8e-08
DICTYBASE|DDB_G0282739	155	rpb4 "DNA-directed RNA polymer	0.769	0.387	0.421	1.4e-07

TAIR|locus:2178158 NRPB4 [Arabidopsis thaliana (taxid:3702)]

 Score = 280 (103.6 bits), Expect = 1.1e-31, Sum P(2) = 1.1e-31
 Identities = 53/65 (81%), Positives = 60/65 (92%)

Query:    14 IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
             +  V  ILSR+QL EFELCVLGNLCPETVEEA+AMVPS+KT+GRAHDDEAIEKMLNDLSL
Sbjct:    74 VRQVREILSRHQLTEFELCVLGNLCPETVEEAVAMVPSLKTKGRAHDDEAIEKMLNDLSL 133

Query:    74 IKKFE 78
             +K+FE
Sbjct:   134 VKRFE 138

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;IDA

GO:0005634 "nucleus" evidence=ISM

GO:0008152 "metabolic process" evidence=IEA

GO:0032774 "RNA biosynthetic process" evidence=IEA

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IDA;IPI

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

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

UNIPROTKB|Q1JQ91 POLR2D "Polymerase (RNA) II (DNA directed) polypeptide D" [Bos taurus (taxid:9913)]

 Score = 123 (48.4 bits), Expect = 5.3e-10, Sum P(2) = 5.3e-10
 Identities = 26/65 (40%), Positives = 44/65 (67%)

Query:    14 IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
             I  V  +L + +L +FEL  L NLCPET EE+ A++PS++  GR  D+E ++++L+D+  
Sbjct:    80 IASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLE--GRFEDEE-LQQILDDIQT 136

Query:    74 IKKFE 78
              + F+
Sbjct:   137 KRSFQ 141

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

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IEA

GO:0004672 "protein kinase activity" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

FB|FBgn0263757 Rpb4 [Drosophila melanogaster (taxid:7227)]

 Score = 115 (45.5 bits), Expect = 3.6e-09, Sum P(2) = 3.6e-09
 Identities = 24/52 (46%), Positives = 38/52 (73%)

Query:    20 ILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDL 71
             +L + +L +FEL  LGNLCPE  EEA A++PS++  GR  D+E + ++L+D+
Sbjct:    83 LLMQKKLHKFELAALGNLCPEAPEEAKALIPSLE--GRFEDEE-LRQILDDI 131

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS;IDA

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=ISS;IDA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISS;IDA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=ISS

GO:0005700 "polytene chromosome" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008283 "cell proliferation" evidence=IDA

GO:0043966 "histone H3 acetylation" evidence=IDA

GO:0043967 "histone H4 acetylation" evidence=IDA

GO:0003682 "chromatin binding" evidence=IDA

GO:0005671 "Ada2/Gcn5/Ada3 transcription activator complex" evidence=IDA

GO:0007095 "mitotic G2 DNA damage checkpoint" evidence=IGI

GO:0022008 "neurogenesis" evidence=IMP

UNIPROTKB|F1P2S1 POLR2D "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 126 (49.4 bits), Expect = 3.3e-08, P = 3.3e-08
 Identities = 27/65 (41%), Positives = 44/65 (67%)

Query:    14 IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
             I  V  +L + +L +FEL  L NLCPET EEA A++PS++  GR  D+E ++++L+D+  
Sbjct:    85 IASVRSLLLQKKLHKFELACLANLCPETAEEAKALIPSLE--GRFEDEE-LQQILDDIQT 141

Query:    74 IKKFE 78
              + F+
Sbjct:   142 KRSFQ 146

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0004672 "protein kinase activity" evidence=IEA

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IEA

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

UNIPROTKB|E2RPH1 POLR2D "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 123 (48.4 bits), Expect = 6.8e-08, P = 6.8e-08
 Identities = 26/65 (40%), Positives = 44/65 (67%)

Query:    14 IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
             I  V  +L + +L +FEL  L NLCPET EE+ A++PS++  GR  D+E ++++L+D+  
Sbjct:    80 IASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLE--GRFEDEE-LQQILDDIQT 136

Query:    74 IKKFE 78
              + F+
Sbjct:   137 KRSFQ 141

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

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IEA

GO:0004672 "protein kinase activity" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E9PB93 POLR2D "DNA-directed RNA polymerase II subunit RPB4" [Homo sapiens (taxid:9606)]

 Score = 123 (48.4 bits), Expect = 6.8e-08, P = 6.8e-08
 Identities = 26/65 (40%), Positives = 44/65 (67%)

Query:    14 IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
             I  V  +L + +L +FEL  L NLCPET EE+ A++PS++  GR  D+E ++++L+D+  
Sbjct:    42 IASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLE--GRFEDEE-LQQILDDIQT 98

Query:    74 IKKFE 78
              + F+
Sbjct:    99 KRSFQ 103

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

UNIPROTKB|O15514 POLR2D "DNA-directed RNA polymerase II subunit RPB4" [Homo sapiens (taxid:9606)]

 Score = 123 (48.4 bits), Expect = 6.8e-08, P = 6.8e-08
 Identities = 26/65 (40%), Positives = 44/65 (67%)

Query:    14 IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
             I  V  +L + +L +FEL  L NLCPET EE+ A++PS++  GR  D+E ++++L+D+  
Sbjct:    80 IASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLE--GRFEDEE-LQQILDDIQT 136

Query:    74 IKKFE 78
              + F+
Sbjct:   137 KRSFQ 141

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IMP

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IDA

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

GO:0004672 "protein kinase activity" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=TAS

GO:0006289 "nucleotide-excision repair" evidence=TAS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=TAS

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=TAS

GO:0006370 "7-methylguanosine mRNA capping" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0050434 "positive regulation of viral transcription" evidence=TAS

GO:0006468 "protein phosphorylation" evidence=IDA

MGI|MGI:1916491 Polr2d "polymerase (RNA) II (DNA directed) polypeptide D" [Mus musculus (taxid:10090)]

 Score = 123 (48.4 bits), Expect = 6.8e-08, P = 6.8e-08
 Identities = 26/65 (40%), Positives = 44/65 (67%)

Query:    14 IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
             I  V  +L + +L +FEL  L NLCPET EE+ A++PS++  GR  D+E ++++L+D+  
Sbjct:    80 IASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLE--GRFEDEE-LQQILDDIQT 136

Query:    74 IKKFE 78
              + F+
Sbjct:   137 KRSFQ 141

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=ISO

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0006468 "protein phosphorylation" evidence=ISO

GO:0044237 "cellular metabolic process" evidence=IEA

RGD|1308565 Polr2d "polymerase (RNA) II (DNA directed) polypeptide D" [Rattus norvegicus (taxid:10116)]

 Score = 123 (48.4 bits), Expect = 6.8e-08, P = 6.8e-08
 Identities = 26/65 (40%), Positives = 44/65 (67%)

Query:    14 IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
             I  V  +L + +L +FEL  L NLCPET EE+ A++PS++  GR  D+E ++++L+D+  
Sbjct:    80 IASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLE--GRFEDEE-LQQILDDIQT 136

Query:    74 IKKFE 78
              + F+
Sbjct:   137 KRSFQ 141

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;ISO

GO:0004672 "protein kinase activity" evidence=IEA;ISO

GO:0005634 "nucleus" evidence=ISO

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IEA;ISO

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IEA;ISO

GO:0006468 "protein phosphorylation" evidence=ISO

DICTYBASE|DDB_G0282739 rpb4 "DNA-directed RNA polymerase II subunit 4" [Dictyostelium discoideum (taxid:44689)]

 Score = 120 (47.3 bits), Expect = 1.4e-07, P = 1.4e-07
 Identities = 27/64 (42%), Positives = 42/64 (65%)

Query:    14 IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
             I  V   LS+  L EFE+  L NLCPE  +EA +++PS+K   +  DDE ++ +L++LS 
Sbjct:    95 IKQVRTALSKQNLEEFEIASLANLCPEISDEAKSLIPSLK---KMEDDE-LQAILDELSN 150

Query:    74 IKKF 77
             ++KF
Sbjct:   151 LRKF 154

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IGI;ISS

GO:0005737 "cytoplasm" evidence=IDA

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;IGI;ISS

GO:0044237 "cellular metabolic process" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=ISS

GO:0044351 "macropinocytosis" evidence=RCA

---

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	78
smart00657	118	smart00657, RPOL4c, DNA-directed RNA-polymerase II	5e-14
pfam03874	110	pfam03874, RNA_pol_Rpb4, RNA polymerase Rpb4	7e-10
COG5250	138	COG5250, RPB4, RNA polymerase II, fourth largest s	2e-08

>gnl|CDD|128904 smart00657, RPOL4c, DNA-directed RNA-polymerase II subunit

 Score = 61.2 bits (149), Expect = 5e-14
 Identities = 26/65 (40%), Positives = 41/65 (63%), Gaps = 3/65 (4%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           +  V  +L   +L +FE+  LGNL PET EEA  ++PS++ R    D+E +E++L+DLS 
Sbjct: 57  VRAVRTLLKSKKLHKFEIAQLGNLRPETAEEAQLLIPSLEER---IDEEELEELLDDLSS 113

Query: 74  IKKFE 78
           +  F 
Sbjct: 114 LLPFY 118

Length = 118

>gnl|CDD|217775 pfam03874, RNA_pol_Rpb4, RNA polymerase Rpb4

 Score = 50.3 bits (121), Expect = 7e-10
 Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 3/60 (5%)

Query: 13  KIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLS 72
              ++   L  ++L +FE   + NL PET +E  A++ S+++R     +E +E++L+ LS
Sbjct: 51  SARELVEELKEFELTKFEALQIVNLLPETADELRAIIESLESR---FSEEQLEEILDILS 107

This family includes the Rpb4 protein. This family also includes C17 (aka CGRP-RCP) is an essential subunit of RNA polymerase III. C17 forms a subcomplex with C25 which is likely to be the counterpart of subcomplex Rpb4/7 in Pol II. Length = 110

>gnl|CDD|227575 COG5250, RPB4, RNA polymerase II, fourth largest subunit [Transcription]

 Score = 47.3 bits (112), Expect = 2e-08
 Identities = 21/65 (32%), Positives = 37/65 (56%), Gaps = 3/65 (4%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
              +   LS     EFE+  LG+L  ++ EEA  ++PS+  +    DD  ++ +L +LSL
Sbjct: 77  AEALRTTLSGLGFHEFEIAQLGSLFCQSAEEAKTLIPSLGNK---IDDAILQAILKELSL 133

Query: 74  IKKFE 78
           ++KF+
Sbjct: 134 LRKFQ 138

Length = 138

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	78
KOG2351	134	consensus RNA polymerase II, fourth largest subuni	99.92
COG5250	138	RPB4 RNA polymerase II, fourth largest subunit [Tr	99.81
smart00657	118	RPOL4c DNA-directed RNA-polymerase II subunit.	99.81
PRK14981	112	DNA-directed RNA polymerase subunit F; Provisional	99.7
PF03874	117	RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR00	99.68
COG1460	114	Uncharacterized protein conserved in archaea [Func	98.16
KOG4168	149	consensus Predicted RNA polymerase III subunit C17	91.43
COG4545	85	Glutaredoxin-related protein [Posttranslational mo	81.6

>KOG2351 consensus RNA polymerase II, fourth largest subunit [Transcription]

Probab=99.92  E-value=2.4e-25  Score=154.62  Aligned_cols=63  Identities=48%  Similarity=0.799  Sum_probs=60.4

Q ss_pred             cHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhhcC
Q 042488           13 KIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE   78 (78)
Q Consensus        13 ~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~f~   78 (78)
                      ++.+||++|++.|||+||+||||||||+|+||||+|||||+.  ++ +|+.|++||++|+++|+||
T Consensus        72 tv~avr~iLs~~~lhkFE~A~lgnLcpetaEEAkaLvPSL~n--ki-dD~~le~iL~dls~lr~fq  134 (134)
T KOG2351|consen   72 TVRAVRTILSGKGLHKFEVAQLGNLCPETAEEAKALVPSLEN--KI-DDDELEQILKDLSTLRTFQ  134 (134)
T ss_pred             HHHHHHHHHhhCCcchhhHHHHhccCcccHHHHHHhcccccc--cc-CHHHHHHHHHHHHHHHhcC
Confidence            588999999999999999999999999999999999999995  46 9999999999999999997

>COG5250 RPB4 RNA polymerase II, fourth largest subunit [Transcription]

Probab=99.81  E-value=3.9e-20  Score=128.52  Aligned_cols=63  Identities=33%  Similarity=0.576  Sum_probs=59.1

Q ss_pred             cHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhhcC
Q 042488           13 KIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE   78 (78)
Q Consensus        13 ~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~f~   78 (78)
                      ...++|++|+..|+|+||+||+++|||+|+||||+|||||+.|  . +|+.+|.||++++.+|+||
T Consensus        76 ~~~a~~~~L~~~gfh~fEiAqlGsL~c~saeEAktLiPSL~nk--i-dD~~lq~ilkels~l~~~~  138 (138)
T COG5250          76 VAEALRTTLSGLGFHEFEIAQLGSLFCQSAEEAKTLIPSLGNK--I-DDAILQAILKELSLLRKFQ  138 (138)
T ss_pred             HHHHHHHHHccCCcchhhHHHhhccccccHHHHHhhccccccc--c-cHHHHHHHHHHHHHHHhhC
Confidence            3578899999999999999999999999999999999999965  5 9999999999999999997

>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit

Probab=99.81  E-value=6.6e-20  Score=122.57  Aligned_cols=64  Identities=41%  Similarity=0.629  Sum_probs=60.1

Q ss_pred             ccHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhhcC
Q 042488           12 LKIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE   78 (78)
Q Consensus        12 ~~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~f~   78 (78)
                      -+|.++++.|++++||+||+|||+||||+|++||++||||+..  || +++++++||++|++++.|+
T Consensus        55 e~i~~~~~~L~~~~L~k~E~~~i~Nl~P~s~~E~~~lI~sl~~--r~-~ee~l~~iL~~i~~~~~~~  118 (118)
T smart00657       55 EIVRAVRTLLKSKKLHKFEIAQLGNLRPETAEEAQLLIPSLEE--RI-DEEELEELLDDLSSLLPFY  118 (118)
T ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCCCCCHHHHHHHhhhhhc--cC-CHHHHHHHHHHHHHhcCCC
Confidence            3688999999999999999999999999999999999999984  67 9999999999999999985

>PRK14981 DNA-directed RNA polymerase subunit F; Provisional

Probab=99.70  E-value=3.7e-17  Score=109.32  Aligned_cols=60  Identities=17%  Similarity=0.199  Sum_probs=53.4

Q ss_pred             cHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhh
Q 042488           13 KIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIK   75 (78)
Q Consensus        13 ~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r   75 (78)
                      +...|+++++..+|++|++|+|+||||+|+||||+++||++.  ++ ++++|++|||.|++|+
T Consensus        52 a~elve~L~~~~~l~e~~a~~I~nL~P~~~dElrai~~~~~~--~~-~~e~l~~ILd~l~k~~  111 (112)
T PRK14981         52 AEELVEELLELEKMKEKTAVKIADILPETRDELRAIFAKERY--TL-SPEELDEILDIVKKYR  111 (112)
T ss_pred             HHHHHHHHHHccCCCHHHHHHHHhcCCCCHHHHHHHHHHhcc--CC-CHHHHHHHHHHHHHhh
Confidence            345677777777899999999999999999999999999953  56 9999999999999997

>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core

Probab=99.68  E-value=1.4e-16  Score=104.25  Aligned_cols=60  Identities=30%  Similarity=0.467  Sum_probs=53.2

Q ss_pred             cHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhh
Q 042488           13 KIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIK   75 (78)
Q Consensus        13 ~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r   75 (78)
                      ++..+++.|..+||++||++||+|+||+|++|++++||++..  || ++++|++||+.|++||
T Consensus        58 ~~~~l~~~L~~~~L~~~E~~qi~Nl~P~~~~El~~ii~~~~~--r~-~ee~l~~iL~~v~~~~  117 (117)
T PF03874_consen   58 SIKELREELKKFGLTEFEILQIINLRPTTAVELRAIIESLES--RF-SEEDLEEILDLVSKYR  117 (117)
T ss_dssp             HHHHHHHHHTTSTS-HHHHHHHHHH--SSHHHHHHHSTTGTT--TS-THHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhcccCCHHHHHHHhcCCCCCHHHHHHHHHHhcc--CC-CHHHHHHHHHHHHHhC
Confidence            478888999999999999999999999999999999999984  68 9999999999999986

Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....

>COG1460 Uncharacterized protein conserved in archaea [Function unknown]

Probab=98.16  E-value=1e-05  Score=55.39  Aligned_cols=58  Identities=19%  Similarity=0.283  Sum_probs=48.0

Q ss_pred             HHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhh
Q 042488           16 DVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK   76 (78)
Q Consensus        16 ~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~   76 (78)
                      .|.++++-.++.+-=++-|+.+||.|.+|.|++.-+-.-  .. +++++++|||.+.+|+.
T Consensus        56 ~veEL~~i~~~~e~~avkIadI~P~t~~ElRsIla~e~~--~~-s~E~l~~Ildiv~Ky~~  113 (114)
T COG1460          56 LVEELLSIVKMSEKIAVKIADIMPRTPDELRSILAKERV--ML-SDEELDKILDIVDKYRE  113 (114)
T ss_pred             HHHHHHhhccccHHHHHHHHHhCCCCHHHHHHHHHHccC--CC-CHHHHHHHHHHHHHHhc
Confidence            344555555666666999999999999999999999873  45 99999999999999974

>KOG4168 consensus Predicted RNA polymerase III subunit C17 [Transcription]

Probab=91.43  E-value=0.34  Score=34.73  Aligned_cols=54  Identities=24%  Similarity=0.410  Sum_probs=45.8

Q ss_pred             HHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhh
Q 042488           19 RILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLI   74 (78)
Q Consensus        19 ~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~   74 (78)
                      .-+..++|++.|+-||.|+.|-++=|-..+|--..+  ||.+.+++.+++..++++
T Consensus        77 ~k~~~fkLtKAE~LqiiN~rPss~vel~~~iE~~ee--Rf~~ee~i~elv~~i~~~  130 (149)
T KOG4168|consen   77 TKLKSFKLTKAEILQIINLRPSSSVELYLIIEEVEE--RFQDEEDIEELVETISKT  130 (149)
T ss_pred             HHhccccchHHHHHHHhccCcchHHHHHHHHHHHHH--hccchhcHHHHHHhcccc
Confidence            334457999999999999999999999999988874  677889999999888754

>COG4545 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]

Probab=81.60  E-value=0.57  Score=30.78  Aligned_cols=36  Identities=22%  Similarity=0.559  Sum_probs=23.2

Q ss_pred             hhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhhc
Q 042488           35 GNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKF   77 (78)
Q Consensus        35 aNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~f   77 (78)
                      +|+||+++ +|++-+-++.-      +-+--+|-..+.++|+|
T Consensus         9 sn~Cpdca-~a~eyl~rl~v------~yd~VeIt~Sm~NlKrF   44 (85)
T COG4545           9 SNLCPDCA-PAVEYLERLNV------DYDFVEITESMANLKRF   44 (85)
T ss_pred             cccCcchH-HHHHHHHHcCC------CceeeehhhhhhhHHHH
Confidence            69999998 46777777762      22334455566666655

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	78
2c35_A	152	Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii L		6e-08
3h0g_D	135	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		3e-04

>pdb|2C35|A Chain A, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii Length = 152

Iteration: 1
 Score = 52.4 bits (124), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 43/65 (66%), Gaps = 3/65 (4%)
Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           I  V  +L + +L +FEL  L NLCPET EE+ A++PS++ R    +DE ++++L+D+  
Sbjct: 90  IASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR---FEDEELQQILDDIQT 146
Query: 74  IKKFE 78
            + F+
Sbjct: 147 KRSFQ 151

>pdb|3H0G|D Chain D, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 135

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 27/94 (28%), Positives = 46/94 (48%), Gaps = 25/94 (26%)
Query: 7   ENAAELKIGDV-------FRILSRYQLAE---------------FELCVLGNLCPETVEE 44
           E   E+ + DV       F + +R++ AE               FE   LG LC E  EE
Sbjct: 44  ETNGEIPMTDVMKKTVAYFNVFARFKTAEATYACERILGNRFHKFERAQLGTLCCEDAEE 103
Query: 45  AIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE 78
           A  ++PS+  +    DD+ ++ +L++LS ++KF+
Sbjct: 104 ARTLIPSLANK---IDDQNLQGILDELSTLRKFQ 134

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	78
2c35_A	152	Human RPB4, DNA-directed RNA polymerase II 16 kDa	5e-14
3hou_D	221	DNA-directed RNA polymerase II subunit RPB4; RNA p	8e-13
3h0g_D	135	DNA-directed RNA polymerase II subunit RPB4; trans	2e-12
1y14_A	187	B32, RPB4, DNA-directed RNA polymerase II 32 kDa p	6e-12

>2c35_A Human RPB4, DNA-directed RNA polymerase II 16 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: a.60.8.2 Length = 152

 Score = 61.6 bits (149), Expect = 5e-14
 Identities = 25/65 (38%), Positives = 43/65 (66%), Gaps = 3/65 (4%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           I  V  +L + +L +FEL  L NLCPET EE+ A++PS++ R    +DE ++++L+D+  
Sbjct: 90  IASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR---FEDEELQQILDDIQT 146

Query: 74  IKKFE 78
            + F+
Sbjct: 147 KRSFQ 151

>3hou_D DNA-directed RNA polymerase II subunit RPB4; RNA polymerase II, metal-binding, transcription bubble; HET: BRU; 3.20A {Saccharomyces cerevisiae} PDB: 1nt9_D 1y1w_D 1y1y_D 1y77_D* 2b63_D* 2b8k_D 2ja5_D* 2ja6_D* 2ja7_D* 2ja8_D* 2r7z_D 2r92_D 2r93_D 1y1v_D* 3fki_D 3h3v_E 2vum_D* 3hov_D* 3how_D* 3hox_D* ... Length = 221

 Score = 59.6 bits (143), Expect = 8e-13
 Identities = 19/64 (29%), Positives = 37/64 (57%), Gaps = 3/64 (4%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           +G V ++L    L  FE+  LG+L  +T +EA  ++PS+  +     D+ +E++L +LS 
Sbjct: 160 VGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKI---SDDELERILKELSN 216

Query: 74  IKKF 77
           ++  
Sbjct: 217 LETL 220

>3h0g_D DNA-directed RNA polymerase II subunit RPB4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 135

 Score = 56.9 bits (137), Expect = 2e-12
 Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 3/61 (4%)

Query: 18  FRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKF 77
              +   +  +FE   LG LC E  EEA  ++PS+  +    DD+ ++ +L++LS ++KF
Sbjct: 77  CERILGNRFHKFERAQLGTLCCEDAEEARTLIPSLANKI---DDQNLQGILDELSTLRKF 133

Query: 78  E 78
           +
Sbjct: 134 Q 134

>1y14_A B32, RPB4, DNA-directed RNA polymerase II 32 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: a.60.8.2 Length = 187

 Score = 56.9 bits (136), Expect = 6e-12
 Identities = 19/64 (29%), Positives = 37/64 (57%), Gaps = 3/64 (4%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           +G V ++L    L  FE+  LG+L  +T +EA  ++PS+  +     D+ +E++L +LS 
Sbjct: 126 VGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKI---SDDELERILKELSN 182

Query: 74  IKKF 77
           ++  
Sbjct: 183 LETL 186

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	78
3h0g_D	135	DNA-directed RNA polymerase II subunit RPB4; trans	99.9
3hou_D	221	DNA-directed RNA polymerase II subunit RPB4; RNA p	99.85
2c35_A	152	Human RPB4, DNA-directed RNA polymerase II 16 kDa	99.84
1y14_A	187	B32, RPB4, DNA-directed RNA polymerase II 32 kDa p	99.8
1go3_F	107	DNA-directed RNA polymerase subunit F; transferase	99.7
4ayb_F	113	DNA-directed RNA polymerase; transferase, multi-su	99.69
3ayh_A	136	DNA-directed RNA polymerase III subunit RPC9; tran	99.28
2ckz_A	161	DNA-directed RNA polymerase III 18 KD polypeptide;	99.15

>3h0g_D DNA-directed RNA polymerase II subunit RPB4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=99.90  E-value=3.5e-24  Score=146.58  Aligned_cols=63  Identities=35%  Similarity=0.615  Sum_probs=59.5

Q ss_pred             ccHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhhcC
Q 042488           12 LKIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE   78 (78)
Q Consensus        12 ~~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~f~   78 (78)
                      -++.+||++|++ +||+||+|||+||||+|+||||+|||||.+  |+ +|++|++||++|++||+||
T Consensus        72 e~~~~v~~lL~~-~L~~fEia~L~NL~P~t~dEak~LIpsL~~--r~-~de~L~~IL~~l~~~r~f~  134 (135)
T 3h0g_D           72 EATYACERILGN-RFHKFERAQLGTLCCEDAEEARTLIPSLAN--KI-DDQNLQGILDELSTLRKFQ  134 (135)
T ss_dssp             HHHHHHHHHCCC-CSCHHHHHHHHHHCCCCHHHHHHHCGGGTT--TS-CSHHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHh-cCCHHHHHHHccCCCCCHHHHHHHHHHhcc--cC-CHHHHHHHHHHHHHHhccc
Confidence            367899999999 999999999999999999999999999985  46 9999999999999999998

>3hou_D DNA-directed RNA polymerase II subunit RPB4; RNA polymerase II, metal-binding, transcription bubble; HET: BRU; 3.20A {Saccharomyces cerevisiae} PDB: 1nt9_D 1y1w_D 1y1y_D 1y77_D* 2b63_D* 2b8k_D 2ja5_D* 2ja6_D* 2ja7_D* 2ja8_D* 2r7z_D 2r92_D 2r93_D 1y1v_D* 3fki_D 3h3v_E 2vum_D* 3hov_D* 3how_D* 3hox_D* ...

Probab=99.85  E-value=1.1e-21  Score=144.43  Aligned_cols=64  Identities=30%  Similarity=0.603  Sum_probs=60.0

Q ss_pred             hccHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhhc
Q 042488           11 ELKIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKF   77 (78)
Q Consensus        11 ~~~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~f   77 (78)
                      +-++..||++|++.+||+||+|+||||||+|+||||+|||||..  ++ +|++|++||++|++||.|
T Consensus       157 ~EAv~aVrELL~~~gLheFEiAqLANLcPeTaDEARALIPSL~~--k~-sDEeLqeILdeLskyR~~  220 (221)
T 3hou_D          157 QETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN--KI-SDDELERILKELSNLETL  220 (221)
T ss_dssp             HHHHHHHHHHHTTSCCCHHHHHHHHHSCCCSHHHHHHHCTTCTT--SS-CHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHHhcCCChHHhheecccCCCCHHHHHHHHHhhcc--cC-CHHHHHHHHHHHHHhhcc
Confidence            34689999999999999999999999999999999999999985  46 999999999999999987

>2c35_A Human RPB4, DNA-directed RNA polymerase II 16 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: a.60.8.2

Probab=99.84  E-value=3.2e-21  Score=133.58  Aligned_cols=63  Identities=40%  Similarity=0.735  Sum_probs=59.5

Q ss_pred             cHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhhcC
Q 042488           13 KIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE   78 (78)
Q Consensus        13 ~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~f~   78 (78)
                      ++.+|++.|.+++||+||+|+|+||||+|+|||++||||+..  |+ ++++|++||++|++||+||
T Consensus        89 ~~~~l~e~L~~~~L~~~E~a~L~NL~P~t~dEar~lipsl~~--r~-sdEeLe~ILd~l~k~r~f~  151 (152)
T 2c35_A           89 TIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEG--RF-EDEELQQILDDIQTKRSFQ  151 (152)
T ss_dssp             HHHHHHHHHHTSSCCHHHHHHHHHHCCSSHHHHHHHCGGGTT--TS-CHHHHHHHHHHHHHHCCCC
T ss_pred             HHHHHHHHHHhcCCCHHHHHHhccCCCCCHHHHHHHHHhhcc--CC-CHHHHHHHHHHHHHHHhhc
Confidence            477899999999999999999999999999999999999983  67 9999999999999999997

>1y14_A B32, RPB4, DNA-directed RNA polymerase II 32 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: a.60.8.2

Probab=99.80  E-value=1e-19  Score=131.07  Aligned_cols=62  Identities=31%  Similarity=0.628  Sum_probs=58.5

Q ss_pred             cHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhhc
Q 042488           13 KIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKF   77 (78)
Q Consensus        13 ~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~f   77 (78)
                      ++.+|++.|.+++||+||+|+|+||||+|++|||+||||+..  ++ ++++|++||+.|++||+|
T Consensus       125 sa~elre~L~~~kL~efE~aqLaNL~PeTadEaraLIpSle~--rl-sdEeLeeILd~L~k~r~~  186 (187)
T 1y14_A          125 TVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN--KI-SDDELERILKELSNLETL  186 (187)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHSCCSSHHHHHHHSGGGTT--TS-CHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHHHHHHhcCCCHHHHHHcCcCCCCCHHHHHHHHHhhcc--CC-CHHHHHHHHHHHHHhhcc
Confidence            477899999999999999999999999999999999999984  57 999999999999999998

>1go3_F DNA-directed RNA polymerase subunit F; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: a.60.8.2

Probab=99.70  E-value=1e-17  Score=110.49  Aligned_cols=56  Identities=14%  Similarity=0.152  Sum_probs=49.1

Q ss_pred             HHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhh
Q 042488           14 IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIK   75 (78)
Q Consensus        14 i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r   75 (78)
                      +..+++.|.+.|||+|++++||||||+|+||||+||||+.     + |++|++||+.|++||
T Consensus        52 a~~l~e~L~~~~l~e~~a~~I~nl~P~t~dElraii~~~~-----~-~eel~~ILd~l~k~~  107 (107)
T 1go3_F           52 AKKLVEELISLGIDEKTAVKIADILPEDLDDLRAIYYKRE-----L-PENAEEILEIVRKYI  107 (107)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHCCCSHHHHHHHSTTSC-----C-CTTHHHHHHHHTTCC
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHhCCCCHHHHHHHHhccc-----C-cHHHHHHHHHHHHcC
Confidence            3444555667889999999999999999999999999996     3 999999999999985

>4ayb_F DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_F 2y0s_F 2waq_F 4b1o_F 4b1p_U 2pmz_F 3hkz_F

Probab=99.69  E-value=2.3e-18  Score=114.38  Aligned_cols=61  Identities=25%  Similarity=0.261  Sum_probs=49.2

Q ss_pred             HHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhh
Q 042488           14 IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK   76 (78)
Q Consensus        14 i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~   76 (78)
                      +..+++-|.+.++++||+|+||||||+|+||||+||||+.+  +.++|++|++||+.|++|++
T Consensus        52 a~~l~e~L~~~~l~~~~~a~IanL~P~~~dElrali~s~e~--~~~~deeL~~IL~~l~ky~~  112 (113)
T 4ayb_F           52 AQKVVEELSSIISREDVRAVLASICPITPDEVRSILIMDSN--RTYTSEDIQKIIDIIRKYIK  112 (113)
T ss_dssp             HHHHHHHHHTTCCCHHHHHHHHHHCCCSSCCCCTTTTTTCC--CCCCCTHHHHHHHHC-----
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHcCCCCHHHHHHHHHhhcc--CCCCHHHHHHHHHHHHHHhc
Confidence            45566667778999999999999999999999999999984  33489999999999999974

>3ayh_A DNA-directed RNA polymerase III subunit RPC9; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=99.28  E-value=1.2e-12  Score=88.71  Aligned_cols=59  Identities=25%  Similarity=0.394  Sum_probs=53.4

Q ss_pred             cHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhh
Q 042488           13 KIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLI   74 (78)
Q Consensus        13 ~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~   74 (78)
                      +|..+.+.|+.++|+++|+.||+|+||.|+.|+.++|++..  .|| +|+++++||+.++++
T Consensus        76 ~i~~l~~~L~~~~Ltk~E~LqivNl~P~t~vel~~iIEe~e--~Rf-see~ie~IL~~i~~~  134 (136)
T 3ayh_A           76 RFLDCIAIFNEFELTKAEILVILNNKPSSVPELYACIEGIE--ERF-KEEDIFKLVEKINTT  134 (136)
T ss_dssp             HHHHHHHTTTTTCCCHHHHHHHHHHCCCSHHHHHHHSTTHH--HHH-TTTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHhccCCCCHHHHHHHHHhcc--cCC-CHHHHHHHHHHHHHh
Confidence            46667777778999999999999999999999999999998  378 999999999999875

>2ckz_A DNA-directed RNA polymerase III 18 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=99.15  E-value=3.7e-12  Score=89.09  Aligned_cols=60  Identities=22%  Similarity=0.320  Sum_probs=0.0

Q ss_pred             cHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhh
Q 042488           13 KIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIK   75 (78)
Q Consensus        13 ~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r   75 (78)
                      +|..+.+.|..++|+++|+.||+|+||.|+.|++++|+...  .|| +++++++||+.++.++
T Consensus       102 ~i~~l~~~L~~~~Ltk~E~lqivNl~P~s~vel~~iIEe~e--~Rf-see~ie~IL~ii~~~~  161 (161)
T 2ckz_A          102 SFAELMTKLNSFKLFKAEKLQIVNQLPANMVHLYSIVEECD--ARF-DEKTIEEMLEIISAYA  161 (161)
T ss_dssp             ---------------------------------------------------------------
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHhccCCCCHHHHHHHHHhcc--cCC-CHHHHHHHHHHHHHhC
Confidence            45566666777899999999999999999999999999998  488 9999999999998764

---

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	78
d1y14a_	176	a.60.8.2 (A:) RNA polymerase II subunit RBP4 (RpoF	1e-12
d2c35a1	129	a.60.8.2 (A:14-142) RNA polymerase II subunit RBP4	4e-12
d1go3f_	107	a.60.8.2 (F:) RNA polymerase II subunit RBP4 (RpoF	6e-04

>d1y14a_ a.60.8.2 (A:) RNA polymerase II subunit RBP4 (RpoF) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 176

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: RNA polymerase II subunit RBP4 (RpoF)
domain: RNA polymerase II subunit RBP4 (RpoF)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 57.3 bits (138), Expect = 1e-12
 Identities = 19/62 (30%), Positives = 37/62 (59%), Gaps = 3/62 (4%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           +G V ++L    L  FE+  LG+L  +T +EA  ++PS+  +     D+ +E++L +LS 
Sbjct: 115 VGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKI---SDDELERILKELSN 171

Query: 74  IK 75
           ++
Sbjct: 172 LE 173

>d2c35a1 a.60.8.2 (A:14-142) RNA polymerase II subunit RBP4 (RpoF) {Human (Homo sapiens) [TaxId: 9606]} Length = 129

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: RNA polymerase II subunit RBP4 (RpoF)
domain: RNA polymerase II subunit RBP4 (RpoF)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.8 bits (132), Expect = 4e-12
 Identities = 25/65 (38%), Positives = 43/65 (66%), Gaps = 3/65 (4%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           I  V  +L + +L +FEL  L NLCPET EE+ A++PS++ R    +DE ++++L+D+  
Sbjct: 67  IASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR---FEDEELQQILDDIQT 123

Query: 74  IKKFE 78
            + F+
Sbjct: 124 KRSFQ 128

>d1go3f_ a.60.8.2 (F:) RNA polymerase II subunit RBP4 (RpoF) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 107

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: RNA polymerase II subunit RBP4 (RpoF)
domain: RNA polymerase II subunit RBP4 (RpoF)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 33.2 bits (76), Expect = 6e-04
 Identities = 7/58 (12%), Positives = 22/58 (37%), Gaps = 3/58 (5%)

Query: 13  KIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLND 70
           +   +   L    + E     + ++ PE +++  A+    +      + E I +++  
Sbjct: 51  EAKKLVEELISLGIDEKTAVKIADILPEDLDDLRAIYYKREL---PENAEEILEIVRK 105

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	78
d1y14a_	176	RNA polymerase II subunit RBP4 (RpoF) {Baker's yea	99.87
d2c35a1	129	RNA polymerase II subunit RBP4 (RpoF) {Human (Homo	99.82
d1go3f_	107	RNA polymerase II subunit RBP4 (RpoF) {Archaeon Me	99.44

>d1y14a_ a.60.8.2 (A:) RNA polymerase II subunit RBP4 (RpoF) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: RNA polymerase II subunit RBP4 (RpoF)
domain: RNA polymerase II subunit RBP4 (RpoF)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.87  E-value=5.3e-23  Score=145.29  Aligned_cols=62  Identities=31%  Similarity=0.602  Sum_probs=58.5

Q ss_pred             ccHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhh
Q 042488           12 LKIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK   76 (78)
Q Consensus        12 ~~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~   76 (78)
                      -++.+||++|+++|||+||+|+||||||+|+||||+|||||+.  ++ +|++|++||++|++||.
T Consensus       113 es~~~vrelL~~~~L~~fE~a~L~NLcPet~eEAkaLiPSL~~--k~-~de~Lq~IL~~L~~~r~  174 (176)
T d1y14a_         113 ETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN--KI-SDDELERILKELSNLET  174 (176)
T ss_dssp             HHHHHHHHHHHTTTCCHHHHHHHHHSCCSSHHHHHHHSGGGTT--TS-CHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHhcCCCHHHHHHhhccCCCCHHHHHHHhhhhcc--cC-CHHHHHHHHHHHHHhhc
Confidence            3688999999999999999999999999999999999999984  56 99999999999999986

>d2c35a1 a.60.8.2 (A:14-142) RNA polymerase II subunit RBP4 (RpoF) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: RNA polymerase II subunit RBP4 (RpoF)
domain: RNA polymerase II subunit RBP4 (RpoF)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=8e-21  Score=126.20  Aligned_cols=64  Identities=39%  Similarity=0.709  Sum_probs=60.7

Q ss_pred             ccHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhhcC
Q 042488           12 LKIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE   78 (78)
Q Consensus        12 ~~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~f~   78 (78)
                      -++.+|+++|+.++|++||++||+||||+|++||++||||+..  |+ ++++|++||+.|++||+||
T Consensus        65 es~~~~~~ll~~~~L~~~E~~~i~Nl~P~~~~El~~li~~l~~--r~-see~l~~iLd~l~~~r~f~  128 (129)
T d2c35a1          65 ETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEG--RF-EDEELQQILDDIQTKRSFQ  128 (129)
T ss_dssp             HHHHHHHHHHHTSSCCHHHHHHHHHHCCSSHHHHHHHCGGGTT--TS-CHHHHHHHHHHHHHHCCCC
T ss_pred             HHHHHHHHHhcccCCCHHHHHHHhCCCCCCHHHHHHHHHHhcc--CC-CHHHHHHHHHHHHHHhccc
Confidence            4688999999999999999999999999999999999999984  67 9999999999999999997

>d1go3f_ a.60.8.2 (F:) RNA polymerase II subunit RBP4 (RpoF) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: RNA polymerase II subunit RBP4 (RpoF)
domain: RNA polymerase II subunit RBP4 (RpoF)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.44  E-value=6.3e-14  Score=91.03  Aligned_cols=55  Identities=13%  Similarity=0.159  Sum_probs=43.3

Q ss_pred             HHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhh
Q 042488           14 IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLI   74 (78)
Q Consensus        14 i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~   74 (78)
                      +..+++.|.+.|+|+|++|+||||||+|+||+|+++||+..  .+ ++++   |++.|.+|
T Consensus        52 ~~~l~~~L~~~~~~~~~aakIanL~P~~~dElrai~~~~~~--~~-~~ee---Il~il~~y  106 (107)
T d1go3f_          52 AKKLVEELISLGIDEKTAVKIADILPEDLDDLRAIYYKREL--PE-NAEE---ILEIVRKY  106 (107)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHCCCSHHHHHHHSTTSCC--CT-THHH---HHHHHTTC
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHHhCCCCHHHHHHHHHHhcc--CC-CHHH---HHHHHHHh
Confidence            45566667778999999999999999999999999999873  34 5554   55555544