Citrus Sinensis ID: 032568

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------14
Protein Sequence
MSGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE
Secondary Structure (PSIPRED)
cccHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHccccHHHHHHHHccccccHHHHHHHccccccccccccHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccHHHHHHHHccccccHHHHHHHcHHHccccccccHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MSGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEqlqqtsddpmnqVSQVFEKSLQYVKRFsryknpdaVRQVREILSRYQLAEFElcvlgnlcpETVEEAIAMVpsiktrgrahdDEAIEKMLNDLSLIKKFE
Flexible Loop (DISEMBL)
msgeeeenaaelkiGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQyvkrfsryknpdavrqVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSiktrgrahddeAIEKMlndlslikkfe
Low Complexity Region (SEG)
MSGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE
Disordered region (IsUnstruct)
************KIGDEFLKAKCLMNCEVAIILDHKYEQL************QVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSI**************************
Disordered Region (DISOPRED)
****EEENAAELKIGDEFLKAKCLMNCEVAIIL********************VFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK**
Disordered Region (DISEMBL)
**********ELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE
Disordered Region (DISPRO)
******ENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE
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	138	2.2.26 [Sep-21-2011]
Q9D7M8	142	DNA-directed RNA polymera	yes	no	0.956	0.929	0.386	1e-22
O15514	142	DNA-directed RNA polymera	yes	no	0.956	0.929	0.386	1e-22
Q54S04	155	DNA-directed RNA polymera	yes	no	0.942	0.838	0.380	4e-20
Q9VEA5	139	DNA-directed RNA polymera	yes	no	0.884	0.877	0.377	3e-18
O74825	135	DNA-directed RNA polymera	yes	no	0.913	0.933	0.318	1e-10
P20433	221	DNA-directed RNA polymera	yes	no	0.543	0.339	0.333	6e-06

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

 Score =  104 bits (260), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 53/137 (38%), Positives = 92/137 (67%), Gaps = 5/137 (3%)

Query: 2   SGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQY 61
           +G+ EE+A++L    EF  A+ L+N EV ++L+H+ +Q +   D+   ++S+VF K+L Y
Sbjct: 10  AGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDE--QELSEVFMKTLNY 67

Query: 62  VKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDD 121
             RFSR+KN + +  VR +L + +L +FEL  L NLCPET EE+ A++PS++ R    +D
Sbjct: 68  TARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR---FED 124

Query: 122 EAIEKMLNDLSLIKKFE 138
           E ++++L+D+   + F+
Sbjct: 125 EELQQILDDIQTKRSFQ 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 =  104 bits (260), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 53/137 (38%), Positives = 92/137 (67%), Gaps = 5/137 (3%)

Query: 2   SGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQY 61
           +G+ EE+A++L    EF  A+ L+N EV ++L+H+ +Q +   D+   ++S+VF K+L Y
Sbjct: 10  AGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDE--QELSEVFMKTLNY 67

Query: 62  VKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDD 121
             RFSR+KN + +  VR +L + +L +FEL  L NLCPET EE+ A++PS++ R    +D
Sbjct: 68  TARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR---FED 124

Query: 122 EAIEKMLNDLSLIKKFE 138
           E ++++L+D+   + F+
Sbjct: 125 EELQQILDDIQTKRSFQ 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 = 96.7 bits (239), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 56/147 (38%), Positives = 89/147 (60%), Gaps = 17/147 (11%)

Query: 4   EEEENAAELKIGDEFLKAKCLMNCEVAIILDHK----------YEQ---LQQTSDDPMNQ 50
           +EEE+   LK   +   AK L+N EVAI+L+H+          + Q   L     + +N 
Sbjct: 12  QEEEDLTTLKFPRDLKDAKFLLNSEVAILLEHRKGISESEGTEFPQNTLLIHLYYNSIND 71

Query: 51  VSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVP 110
           + + F K+L Y ++FSRYKN  +++QVR  LS+  L EFE+  L NLCPE  +EA +++P
Sbjct: 72  IIRTFHKTLAYAEKFSRYKNKTSIKQVRTALSKQNLEEFEIASLANLCPEISDEAKSLIP 131

Query: 111 SIKTRGRAHDDEAIEKMLNDLSLIKKF 137
           S+K   +  DDE ++ +L++LS ++KF
Sbjct: 132 SLK---KMEDDE-LQAILDELSNLRKF 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 = 90.5 bits (223), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 48/127 (37%), Positives = 79/127 (62%), Gaps = 5/127 (3%)

Query: 6   EENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRF 65
           +E+AA+L+   EF  A+ L+  EV ++LDH+  + Q  S D   + S+VF K+  Y   F
Sbjct: 11  DEDAADLQFPKEFENAETLLISEVHMLLDHR--KRQNESADEEQEFSEVFMKTYAYTDSF 68

Query: 66  SRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIE 125
            ++KN + +   R +L + +L +FEL  LGNLCPE  EEA A++PS++ R    +DE + 
Sbjct: 69  RKFKNKETIMSARSLLMQKKLHKFELAALGNLCPEAPEEAKALIPSLEGR---FEDEELR 125

Query: 126 KMLNDLS 132
           ++L+D+ 
Sbjct: 126 QILDDIG 132

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

>sp|O74825|RPB4_SCHPO DNA-directed RNA polymerase II subunit rpb4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb4 PE=1 SV=1

 Score = 65.1 bits (157), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 43/135 (31%), Positives = 74/135 (54%), Gaps = 9/135 (6%)

Query: 6   EENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDD--PMNQVSQVFEKSLQYVK 63
           EE+AA+LK+G EF     L   E  I+++    Q  + ++   PM   + V +K++ Y  
Sbjct: 7   EEDAAQLKLGPEFENEDMLTVSEAKILIETVLAQRARETNGEIPM---TDVMKKTVAYFN 63

Query: 64  RFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEA 123
            F+R+K  +A      IL   +  +FE   LG LC E  EEA  ++PS+  +    DD+ 
Sbjct: 64  VFARFKTAEATYACERILGN-RFHKFERAQLGTLCCEDAEEARTLIPSLANK---IDDQN 119

Query: 124 IEKMLNDLSLIKKFE 138
           ++ +L++LS ++KF+
Sbjct: 120 LQGILDELSTLRKFQ 134

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.

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

>sp|P20433|RPB4_YEAST DNA-directed RNA polymerase II subunit RPB4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPB4 PE=1 SV=1

 Score = 49.7 bits (117), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 48/78 (61%), Gaps = 3/78 (3%)

Query: 55  FEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKT 114
            + ++QY+  FSR+++ + V  V ++L    L  FE+  LG+L  +T +EA  ++PS+  
Sbjct: 141 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLN- 199

Query: 115 RGRAHDDEAIEKMLNDLS 132
             +  DDE +E++L +LS
Sbjct: 200 -NKISDDE-LERILKELS 215

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. The RPB4-RPB7 subcomplex is necessary for promoter-directed transcription initiation but is not required for recruitment of Pol II to active preinitiation complexes and seems to be dispensable for transcription elongation and termination. The RPB4-RPB7 subcomplex recruits FCP1 to Pol II. Involved in DNA repair of damage in the transcribed strand. RPB4 is dispensable under optimal growth conditions, but becomes essential during heat or cold shock and under nutrient depletion. Suppresses the RBP9-mediated transcription-coupled repair (TCR) subpathway of nucleotide excision repair (NER) but facilitates the RAD26-mediated TCR subpathway. Under stress conditions only, involved in mRNA export to the cytoplasm. Involved in mRNA decay. Promotes or enhances the deadenylation process of specific mRNAs and may recruit PAT1 and the LSM1-7 complex to these mRNAs, thus stimulating their decapping and further decay.

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

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	138
225446712	138	PREDICTED: DNA-directed RNA polymerase I	1.0	1.0	0.963	2e-72
224083811	138	predicted protein [Populus trichocarpa]	1.0	1.0	0.963	2e-72
388495724	138	unknown [Lotus japonicus]	1.0	1.0	0.956	6e-72
351727683	138	uncharacterized protein LOC100499661 [Gl	1.0	1.0	0.949	1e-71
351724197	138	uncharacterized protein LOC100527316 [Gl	1.0	1.0	0.949	2e-71
255562011	138	DNA-directed RNA polymerase II, putative	1.0	1.0	0.942	4e-71
357513237	138	DNA-directed RNA polymerase II subunit R	1.0	1.0	0.949	5e-71
449441240	138	PREDICTED: DNA-directed RNA polymerase I	1.0	1.0	0.920	6e-70
351722549	195	uncharacterized protein LOC100527704 [Gl	0.978	0.692	0.955	1e-69
297807017	138	RPB15.9 [Arabidopsis lyrata subsp. lyrat	1.0	1.0	0.905	1e-69

>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 =  276 bits (707), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 133/138 (96%), Positives = 137/138 (99%)

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEVA+IL+HKYEQLQQ SDDP+NQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVAVILEHKYEQLQQMSDDPLNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHD 120
           YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKT+GRAHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKKFE 138
           DEAIEKMLNDLSLIKKFE
Sbjct: 121 DEAIEKMLNDLSLIKKFE 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 =  276 bits (706), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 133/138 (96%), Positives = 137/138 (99%)

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGD+FLKAKCLMNCEVA+IL+HKYEQLQQ SDDPMNQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDDFLKAKCLMNCEVALILEHKYEQLQQMSDDPMNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHD 120
           YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKT+GRAHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKKFE 138
           DEAIEKMLNDLSLIKKFE
Sbjct: 121 DEAIEKMLNDLSLIKKFE 138

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  275 bits (702), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 132/138 (95%), Positives = 137/138 (99%)

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEV++IL+HKYEQLQQ+SDDPMNQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQSSDDPMNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHD 120
           YVKRFSRYKNPDAVRQVREIL+RYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRA D
Sbjct: 61  YVKRFSRYKNPDAVRQVREILARYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAQD 120

Query: 121 DEAIEKMLNDLSLIKKFE 138
           DEAIEKMLNDLSLIKKFE
Sbjct: 121 DEAIEKMLNDLSLIKKFE 138

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  274 bits (700), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 131/138 (94%), Positives = 137/138 (99%)

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEV++IL+HKYEQLQQTSDDPMNQ+SQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQTSDDPMNQISQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHD 120
           YVKRFSRYKNPDAVRQVREIL+RYQLAEFELCVLGNLCPETVEEAIAMVPSIK+RGRA D
Sbjct: 61  YVKRFSRYKNPDAVRQVREILARYQLAEFELCVLGNLCPETVEEAIAMVPSIKSRGRAQD 120

Query: 121 DEAIEKMLNDLSLIKKFE 138
           DEAIEKMLNDLSLIKKFE
Sbjct: 121 DEAIEKMLNDLSLIKKFE 138

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  273 bits (697), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 131/138 (94%), Positives = 137/138 (99%)

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEV++IL+HKYEQLQQTSDDPMNQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQTSDDPMNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHD 120
           YVKRFSRYKNPDAVRQVREIL+RYQLAEFELCVLGNLCPETVEEAIA+VPSIK+RGRA D
Sbjct: 61  YVKRFSRYKNPDAVRQVREILARYQLAEFELCVLGNLCPETVEEAIAVVPSIKSRGRAQD 120

Query: 121 DEAIEKMLNDLSLIKKFE 138
           DEAIEKMLNDLSLIKKFE
Sbjct: 121 DEAIEKMLNDLSLIKKFE 138

Source: Glycine max

Species: Glycine max

Genus: Glycine

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 =  272 bits (695), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 130/138 (94%), Positives = 136/138 (98%)

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQ 60
           MSGEEEENA+ELKIGDEFLKAKCLMNCEVA+IL+HKYEQLQQ S+DPMNQVSQVFEKSLQ
Sbjct: 1   MSGEEEENASELKIGDEFLKAKCLMNCEVALILEHKYEQLQQMSNDPMNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHD 120
           YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKT+GRAHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKKFE 138
           DEAIEKML DLS+IKKFE
Sbjct: 121 DEAIEKMLTDLSMIKKFE 138

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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 =  271 bits (694), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 131/138 (94%), Positives = 136/138 (98%)

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEV++IL+HKYEQLQQ+SDD MNQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQSSDDAMNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHD 120
           YVKRFSRYKNPDAVRQVREIL+RYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRA D
Sbjct: 61  YVKRFSRYKNPDAVRQVREILARYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAQD 120

Query: 121 DEAIEKMLNDLSLIKKFE 138
           DEAIEKMLNDLSLIKKFE
Sbjct: 121 DEAIEKMLNDLSLIKKFE 138

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

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 =  268 bits (685), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 127/138 (92%), Positives = 135/138 (97%)

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEV++IL+HKYEQLQQ S+DP NQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHD 120
           YVKRFSRYKNPDAVRQVRE+LSRYQLAEFELCVLGNLCPETVEEAIAMVPS+KT+GR HD
Sbjct: 61  YVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120

Query: 121 DEAIEKMLNDLSLIKKFE 138
           DEAIEKMLNDLSLIK+FE
Sbjct: 121 DEAIEKMLNDLSLIKRFE 138

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351722549|ref|NP_001236224.1| uncharacterized protein LOC100527704 [Glycine max] gi|255632992|gb|ACU16850.1| unknown [Glycine max]

 Score =  267 bits (683), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 129/135 (95%), Positives = 134/135 (99%)

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEVA+IL+HKYEQLQQTSDDPMNQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVALILEHKYEQLQQTSDDPMNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHD 120
           YVKRFSRYKNPDAVRQVREIL+RY+LAEFELCVLGNLCPETVEEAIAMVPSIK+RGRA D
Sbjct: 61  YVKRFSRYKNPDAVRQVREILARYELAEFELCVLGNLCPETVEEAIAMVPSIKSRGRAQD 120

Query: 121 DEAIEKMLNDLSLIK 135
           DEAIEKMLNDLSLIK
Sbjct: 121 DEAIEKMLNDLSLIK 135

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297807017|ref|XP_002871392.1| RPB15.9 [Arabidopsis lyrata subsp. lyrata] gi|297317229|gb|EFH47651.1| RPB15.9 [Arabidopsis lyrata subsp. lyrata]

 Score =  267 bits (682), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 125/138 (90%), Positives = 136/138 (98%)

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEV++IL+HK+EQLQQ S+DPMNQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKFEQLQQVSEDPMNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHD 120
           YVKRFSRYKNPDAVRQVREILSR+QL EFELCVLGNLCPETVEEA+AMVPS+KT+GRAHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRHQLTEFELCVLGNLCPETVEEAVAMVPSLKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKKFE 138
           DEAIEKMLNDLSL+K+FE
Sbjct: 121 DEAIEKMLNDLSLVKRFE 138

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	138
TAIR|locus:2178158	138	NRPB4 [Arabidopsis thaliana (t	1.0	1.0	0.905	8.5e-65
UNIPROTKB|Q1JQ91	142	POLR2D "Polymerase (RNA) II (D	0.956	0.929	0.401	1.1e-23
UNIPROTKB|E2RPH1	142	POLR2D "Uncharacterized protei	0.956	0.929	0.394	2.3e-23
UNIPROTKB|O15514	142	POLR2D "DNA-directed RNA polym	0.956	0.929	0.394	2.3e-23
MGI|MGI:1916491	142	Polr2d "polymerase (RNA) II (D	0.956	0.929	0.394	2.3e-23
RGD|1308565	142	Polr2d "polymerase (RNA) II (D	0.956	0.929	0.394	2.3e-23
ZFIN|ZDB-GENE-040714-2	145	polr2d "polymerase (RNA) II (D	0.949	0.903	0.397	2.9e-23
UNIPROTKB|F1P2S1	147	POLR2D "Uncharacterized protei	0.956	0.897	0.394	3.8e-23
WB|WBGene00018391	144	rpb-4 [Caenorhabditis elegans	0.949	0.909	0.384	4.9e-21
DICTYBASE|DDB_G0282739	155	rpb4 "DNA-directed RNA polymer	0.956	0.851	0.393	4.4e-20

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

 Score = 660 (237.4 bits), Expect = 8.5e-65, P = 8.5e-65
 Identities = 125/138 (90%), Positives = 136/138 (98%)

Query:     1 MSGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQ 60
             MSGEEEENAAELKIGDEFLKAKCLMNCEV++IL+HK+EQLQQ S+DPMNQVSQVFEKSLQ
Sbjct:     1 MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKFEQLQQISEDPMNQVSQVFEKSLQ 60

Query:    61 YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHD 120
             YVKRFSRYKNPDAVRQVREILSR+QL EFELCVLGNLCPETVEEA+AMVPS+KT+GRAHD
Sbjct:    61 YVKRFSRYKNPDAVRQVREILSRHQLTEFELCVLGNLCPETVEEAVAMVPSLKTKGRAHD 120

Query:   121 DEAIEKMLNDLSLIKKFE 138
             DEAIEKMLNDLSL+K+FE
Sbjct:   121 DEAIEKMLNDLSLVKRFE 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 = 272 (100.8 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 55/137 (40%), Positives = 93/137 (67%)

Query:     2 SGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQY 61
             SG+ EE+A++L    EF  A+ L+N EV ++L+H+ +Q +   D+   ++S+VF K+L Y
Sbjct:    10 SGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDE--QELSEVFMKTLNY 67

Query:    62 VKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDD 121
               RFSR+KN + +  VR +L + +L +FEL  L NLCPET EE+ A++PS++  GR  D+
Sbjct:    68 TARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLE--GRFEDE 125

Query:   122 EAIEKMLNDLSLIKKFE 138
             E ++++L+D+   + F+
Sbjct:   126 E-LQQILDDIQTKRSFQ 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|E2RPH1 POLR2D "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 269 (99.8 bits), Expect = 2.3e-23, P = 2.3e-23
 Identities = 54/137 (39%), Positives = 93/137 (67%)

Query:     2 SGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQY 61
             +G+ EE+A++L    EF  A+ L+N EV ++L+H+ +Q +   D+   ++S+VF K+L Y
Sbjct:    10 AGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDE--QELSEVFMKTLNY 67

Query:    62 VKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDD 121
               RFSR+KN + +  VR +L + +L +FEL  L NLCPET EE+ A++PS++  GR  D+
Sbjct:    68 TARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLE--GRFEDE 125

Query:   122 EAIEKMLNDLSLIKKFE 138
             E ++++L+D+   + F+
Sbjct:   126 E-LQQILDDIQTKRSFQ 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|O15514 POLR2D "DNA-directed RNA polymerase II subunit RPB4" [Homo sapiens (taxid:9606)]

 Score = 269 (99.8 bits), Expect = 2.3e-23, P = 2.3e-23
 Identities = 54/137 (39%), Positives = 93/137 (67%)

Query:     2 SGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQY 61
             +G+ EE+A++L    EF  A+ L+N EV ++L+H+ +Q +   D+   ++S+VF K+L Y
Sbjct:    10 AGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDE--QELSEVFMKTLNY 67

Query:    62 VKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDD 121
               RFSR+KN + +  VR +L + +L +FEL  L NLCPET EE+ A++PS++  GR  D+
Sbjct:    68 TARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLE--GRFEDE 125

Query:   122 EAIEKMLNDLSLIKKFE 138
             E ++++L+D+   + F+
Sbjct:   126 E-LQQILDDIQTKRSFQ 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 = 269 (99.8 bits), Expect = 2.3e-23, P = 2.3e-23
 Identities = 54/137 (39%), Positives = 93/137 (67%)

Query:     2 SGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQY 61
             +G+ EE+A++L    EF  A+ L+N EV ++L+H+ +Q +   D+   ++S+VF K+L Y
Sbjct:    10 AGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDE--QELSEVFMKTLNY 67

Query:    62 VKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDD 121
               RFSR+KN + +  VR +L + +L +FEL  L NLCPET EE+ A++PS++  GR  D+
Sbjct:    68 TARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLE--GRFEDE 125

Query:   122 EAIEKMLNDLSLIKKFE 138
             E ++++L+D+   + F+
Sbjct:   126 E-LQQILDDIQTKRSFQ 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 = 269 (99.8 bits), Expect = 2.3e-23, P = 2.3e-23
 Identities = 54/137 (39%), Positives = 93/137 (67%)

Query:     2 SGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQY 61
             +G+ EE+A++L    EF  A+ L+N EV ++L+H+ +Q +   D+   ++S+VF K+L Y
Sbjct:    10 AGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDE--QELSEVFMKTLNY 67

Query:    62 VKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDD 121
               RFSR+KN + +  VR +L + +L +FEL  L NLCPET EE+ A++PS++  GR  D+
Sbjct:    68 TARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLE--GRFEDE 125

Query:   122 EAIEKMLNDLSLIKKFE 138
             E ++++L+D+   + F+
Sbjct:   126 E-LQQILDDIQTKRSFQ 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

ZFIN|ZDB-GENE-040714-2 polr2d "polymerase (RNA) II (DNA directed) polypeptide D" [Danio rerio (taxid:7955)]

 Score = 268 (99.4 bits), Expect = 2.9e-23, P = 2.9e-23
 Identities = 54/136 (39%), Positives = 91/136 (66%)

Query:     3 GEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYV 62
             G+ EE+A++L    EF  A+ L+N EV ++L+H+ +Q +   D+   ++S+VF K+L Y 
Sbjct:    14 GDVEEDASQLMFPKEFENAETLLNSEVHMLLEHRKQQNESAEDE--QELSEVFMKTLNYT 71

Query:    63 KRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDE 122
              RFSR+KN + +  VR +L + +L +FEL  L NLCPE  EEA A++PS++  GR  D+E
Sbjct:    72 ARFSRFKNRETIASVRSLLLQKKLHKFELASLANLCPEAAEEAKALIPSLE--GRFEDEE 129

Query:   123 AIEKMLNDLSLIKKFE 138
              ++++L+D+   + F+
Sbjct:   130 -LQQILDDIQTKRSFQ 144

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0044237 "cellular metabolic process" evidence=IEA

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

GO:0003824 "catalytic activity" evidence=IEA

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

 Score = 267 (99.0 bits), Expect = 3.8e-23, P = 3.8e-23
 Identities = 54/137 (39%), Positives = 92/137 (67%)

Query:     2 SGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQY 61
             + + EE+A++L    EF  A+ L+N EV ++L+H+ +Q +   D+   ++S+VF K+L Y
Sbjct:    15 TADVEEDASQLVFPKEFETAETLLNSEVHMLLEHRKQQNESAEDE--QELSEVFMKTLNY 72

Query:    62 VKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDD 121
               RFSR+KN + +  VR +L + +L +FEL  L NLCPET EEA A++PS++  GR  D+
Sbjct:    73 TARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEEAKALIPSLE--GRFEDE 130

Query:   122 EAIEKMLNDLSLIKKFE 138
             E ++++L+D+   + F+
Sbjct:   131 E-LQQILDDIQTKRSFQ 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

WB|WBGene00018391 rpb-4 [Caenorhabditis elegans (taxid:6239)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 53/138 (38%), Positives = 85/138 (61%)

Query:     3 GEEEENAAELKIGDEFLKAKC--LMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQ 60
             G+ EE+AAE K   EF    C  L+  EV ++L+H+ +  +  S D + ++S+VF K+L 
Sbjct:    12 GQVEEDAAECKFPKEFETTTCDALLTAEVYLLLEHRRQSSE--SKDEIEEMSEVFIKTLN 69

Query:    61 YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHD 120
             Y +R SR+KN + +R VR I S   L +FE+  + NLCPE  EEA A+VPS++ +    +
Sbjct:    70 YARRMSRFKNRETIRAVRAIFSEKHLHKFEVAQIANLCPENAEEAKALVPSLENK---IE 126

Query:   121 DEAIEKMLNDLSLIKKFE 138
             +  +E++L DL   + F+
Sbjct:   127 ESELEEVLKDLQSKRTFQ 144

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

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

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

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

 Score = 238 (88.8 bits), Expect = 4.4e-20, P = 4.4e-20
 Identities = 59/150 (39%), Positives = 91/150 (60%)

Query:     2 SG-EEEENAAELKIGDEFLKAKCLMNCEVAIILDHKY--------EQLQQTS-----DDP 47
             SG +EEE+   LK   +   AK L+N EVAI+L+H+         E  Q T       + 
Sbjct:     9 SGIQEEEDLTTLKFPRDLKDAKFLLNSEVAILLEHRKGISESEGTEFPQNTLLIHLYYNS 68

Query:    48 MNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIA 107
             +N + + F K+L Y ++FSRYKN  +++QVR  LS+  L EFE+  L NLCPE  +EA +
Sbjct:    69 INDIIRTFHKTLAYAEKFSRYKNKTSIKQVRTALSKQNLEEFEIASLANLCPEISDEAKS 128

Query:   108 MVPSIKTRGRAHDDEAIEKMLNDLSLIKKF 137
             ++PS+K   +  DDE ++ +L++LS ++KF
Sbjct:   129 LIPSLK---KMEDDE-LQAILDELSNLRKF 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q54S04	RPB4_DICDI	No assigned EC number	0.3809	0.9420	0.8387	yes	no
O15514	RPB4_HUMAN	No assigned EC number	0.3868	0.9565	0.9295	yes	no
Q9D7M8	RPB4_MOUSE	No assigned EC number	0.3868	0.9565	0.9295	yes	no
Q9VEA5	RPB4_DROME	2, ., 7, ., 7, ., 6	0.3779	0.8840	0.8776	yes	no
O74825	RPB4_SCHPO	No assigned EC number	0.3185	0.9130	0.9333	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00018813001	SubName- Full=Putative uncharacterized protein (Chromosome chr12 scaffold_18, whole genome shotgun sequence); (138 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00024229001	SubName- Full=Putative uncharacterized protein (Chromosome chr6 scaffold_3, whole genome shotgu [...] (176 aa)				•	•	•	•		0.963
	GSVIVG00002744001	SubName- Full=Chromosome chr1 scaffold_135, whole genome shotgun sequence; (78 aa)				•	•	•	•		0.927
	GSVIVG00028076001	SubName- Full=Chromosome chr7 scaffold_42, whole genome shotgun sequence; (533 aa)				•		•			0.905
	GSVIVG00002140001	SubName- Full=Chromosome chr19 scaffold_126, whole genome shotgun sequence; (528 aa)				•		•			0.905
	GSVIVG00020457001	SubName- Full=Chromosome chr5 scaffold_2, whole genome shotgun sequence; (208 aa)				•		•			0.903
	GSVIVG00038611001	RecName- Full=Pyruvate kinase; EC=2.7.1.40; (573 aa)						•			0.899
	GSVIVG00036953001	SubName- Full=Chromosome chr1 scaffold_84, whole genome shotgun sequence; (417 aa)						•			0.899
	GSVIVG00034786001	SubName- Full=Chromosome chr5 scaffold_72, whole genome shotgun sequence; (471 aa)						•			0.899
	GSVIVG00034055001	RecName- Full=Nucleoside diphosphate kinase; EC=2.7.4.6; (159 aa)						•			0.899
	26N20_30	RecName- Full=Pyruvate kinase; EC=2.7.1.40; (493 aa)						•			0.899

---

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	138
smart00657	118	smart00657, RPOL4c, DNA-directed RNA-polymerase II	4e-36
pfam03874	110	pfam03874, RNA_pol_Rpb4, RNA polymerase Rpb4	5e-29
COG5250	138	COG5250, RPB4, RNA polymerase II, fourth largest s	1e-21

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

 Score =  120 bits (302), Expect = 4e-36
 Identities = 49/123 (39%), Positives = 79/123 (64%), Gaps = 5/123 (4%)

Query: 16  DEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVR 75
            EF  A CL N EV ++L+ K +  +  S++    +S V +K+L+Y+ +F+R+KN + VR
Sbjct: 1   PEFKNATCLTNSEVQLLLELKRQSKE--SEEEQQPLSTVMKKTLKYLSKFARFKNREIVR 58

Query: 76  QVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIK 135
            VR +L   +L +FE+  LGNL PET EEA  ++PS++ R    D+E +E++L+DLS + 
Sbjct: 59  AVRTLLKSKKLHKFEIAQLGNLRPETAEEAQLLIPSLEER---IDEEELEELLDDLSSLL 115

Query: 136 KFE 138
            F 
Sbjct: 116 PFY 118

Length = 118

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

 Score =  101 bits (254), Expect = 5e-29
 Identities = 37/110 (33%), Positives = 67/110 (60%), Gaps = 3/110 (2%)

Query: 23  CLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILS 82
            L N EV  IL  + E+ ++ S      ++ +  K+L+Y+ +FSR KNP++ R++ E L 
Sbjct: 1   YLTNSEVLEILKKELEERRRESRYVEENLNTILRKTLEYLNKFSRLKNPESARELVEELK 60

Query: 83  RYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLS 132
            ++L +FE   + NL PET +E  A++ S+++R     +E +E++L+ LS
Sbjct: 61  EFELTKFEALQIVNLLPETADELRAIIESLESR---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 = 83.5 bits (206), Expect = 1e-21
 Identities = 44/138 (31%), Positives = 79/138 (57%), Gaps = 7/138 (5%)

Query: 4   EEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTS---DDPMNQVSQVFEKSLQ 60
             EE+AA+LK+G EF     LM  E   +++ + E+ ++ +   +   N V +VF+ +L 
Sbjct: 5   IFEEDAAQLKLGPEFENEDMLMLSEARYLIEGQLERRRRETNGAEFRSNDV-KVFKSTLG 63

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHD 120
           Y+  F R+K+ +    +R  LS     EFE+  LG+L  ++ EEA  ++PS+  +    D
Sbjct: 64  YLDDFCRFKDKEVAEALRTTLSGLGFHEFEIAQLGSLFCQSAEEAKTLIPSLGNK---ID 120

Query: 121 DEAIEKMLNDLSLIKKFE 138
           D  ++ +L +LSL++KF+
Sbjct: 121 DAILQAILKELSLLRKFQ 138

Length = 138

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	138
KOG2351	134	consensus RNA polymerase II, fourth largest subuni	100.0
COG5250	138	RPB4 RNA polymerase II, fourth largest subunit [Tr	100.0
smart00657	118	RPOL4c DNA-directed RNA-polymerase II subunit.	99.98
PRK14981	112	DNA-directed RNA polymerase subunit F; Provisional	99.97
PF03874	117	RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR00	99.95
COG1460	114	Uncharacterized protein conserved in archaea [Func	99.82
KOG4168	149	consensus Predicted RNA polymerase III subunit C17	98.88

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

Probab=100.00  E-value=1.7e-44  Score=258.65  Aligned_cols=134  Identities=51%  Similarity=0.844  Sum_probs=127.4

Q ss_pred             CChhhhhhhhccccCccccccccccHHHHHHHHHHHHHHhhhcCCCCCcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHH
Q 032568            1 MSGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREI   80 (138)
Q Consensus         1 ~~~~~~e~~~~l~lG~~f~~~~~Ls~~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~l   80 (138)
                      |++++||||++|+||++|..+.||++|||+.+|+++..++++ +.|+..+++.||.+|+.|+++||+|++++++.+||.+
T Consensus         1 ~~g~~EEdAa~lk~g~EFe~~~~L~~sEa~lllE~~~~q~~r-s~d~~~~~s~Vf~kTl~Y~~~FsRfKn~etv~avr~i   79 (134)
T KOG2351|consen    1 PRGEEEEDAAELKLGKEFETADALMLSEARLLLEHRLEQRRR-SEDDESEMSDVFKKTLQYLDRFSRFKNRETVRAVRTI   79 (134)
T ss_pred             CcchhhccHHhccccHHHHHHHHHHHHHHHHHHHHHHHHHhh-cccccchHHHHHHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence            578999999999999999999999999999999999987754 5677889999999999999999999999999999999


Q ss_pred             HHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhhcC
Q 032568           81 LSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE  138 (138)
Q Consensus        81 l~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~f~  138 (138)
                      |+..|||+||+|||+||||+|++|||+|||||++|  + +|+.|++||+.|+..|+|+
T Consensus        80 Ls~~~lhkFE~A~lgnLcpetaEEAkaLvPSL~nk--i-dD~~le~iL~dls~lr~fq  134 (134)
T KOG2351|consen   80 LSGKGLHKFEVAQLGNLCPETAEEAKALVPSLENK--I-DDDELEQILKDLSTLRTFQ  134 (134)
T ss_pred             HhhCCcchhhHHHHhccCcccHHHHHHhccccccc--c-CHHHHHHHHHHHHHHHhcC
Confidence            99999999999999999999999999999999964  5 9999999999999999996

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

Probab=100.00  E-value=1.1e-34  Score=206.79  Aligned_cols=133  Identities=32%  Similarity=0.563  Sum_probs=119.0

Q ss_pred             hhhhhhhhccccCccccccccccHHHHHHHHHHHHHHhhhcCCCCCc--chhHHHHHHHHHHHhhcCCCCHHHHHHHHHH
Q 032568            3 GEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMN--QVSQVFEKSLQYVKRFSRYKNPDAVRQVREI   80 (138)
Q Consensus         3 ~~~~e~~~~l~lG~~f~~~~~Ls~~EV~~iL~~~~~~~~~~~~~~~~--~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~l   80 (138)
                      ++.||||++||+|++|+|..+|++||++.+++....++++.....+.  +...++++|+.|++.||+|++.+.+.+++.+
T Consensus         4 ~~~ee~aa~lklg~efe~ed~l~lsEAr~lie~~l~~rrretn~~e~~s~dvk~~k~T~~Yl~~F~Rfkd~e~~~a~~~~   83 (138)
T COG5250           4 AIFEEDAAQLKLGPEFENEDMLMLSEARYLIEGQLERRRRETNGAEFRSNDVKVFKSTLGYLDDFCRFKDKEVAEALRTT   83 (138)
T ss_pred             hHhhhhHHHhhcCccccchHHHHHHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence            57899999999999999999999999999999988776432222122  3344699999999999999999999999999


Q ss_pred             HHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhhcC
Q 032568           81 LSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE  138 (138)
Q Consensus        81 l~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~f~  138 (138)
                      |+..|+|+||+||+++|||+|++|||+|||||.+|  + +|..+|.||++++.+|+|+
T Consensus        84 L~~~gfh~fEiAqlGsL~c~saeEAktLiPSL~nk--i-dD~~lq~ilkels~l~~~~  138 (138)
T COG5250          84 LSGLGFHEFEIAQLGSLFCQSAEEAKTLIPSLGNK--I-DDAILQAILKELSLLRKFQ  138 (138)
T ss_pred             HccCCcchhhHHHhhccccccHHHHHhhccccccc--c-cHHHHHHHHHHHHHHHhhC
Confidence            99999999999999999999999999999999964  6 9999999999999999996

>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit

Probab=99.98  E-value=5e-32  Score=194.79  Aligned_cols=118  Identities=42%  Similarity=0.715  Sum_probs=106.2

Q ss_pred             ccccccccccHHHHHHHHHHHHHHhhhcCCCCCcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHHHh
Q 032568           16 DEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLG   95 (138)
Q Consensus        16 ~~f~~~~~Ls~~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~l~   95 (138)
                      ++|.|++||||+||+.||+.++...  .+.++..+++.++++|++|+++|+++++++++.++++.|+.++|++||++||+
T Consensus         1 ~~f~~a~~L~n~Ev~~ll~~k~~~~--~~~~~~~~l~~v~~~tl~Yl~~~~~~~~~e~i~~~~~~L~~~~L~k~E~~~i~   78 (118)
T smart00657        1 PEFKNATCLTNSEVQLLLELKRQSK--ESEEEQQPLSTVMKKTLKYLSKFARFKNREIVRAVRTLLKSKKLHKFEIAQLG   78 (118)
T ss_pred             CCccchhHhHHHHHHHHHHHHHHhh--ccccccchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCCHHHHHHHh
Confidence            3699999999999999999754322  23344557899999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhhcC
Q 032568           96 NLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE  138 (138)
Q Consensus        96 NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~f~  138 (138)
                      ||||+|++||++||||++.  |+ +++++++||++|+++|.|+
T Consensus        79 Nl~P~s~~E~~~lI~sl~~--r~-~ee~l~~iL~~i~~~~~~~  118 (118)
T smart00657       79 NLRPETAEEAQLLIPSLEE--RI-DEEELEELLDDLSSLLPFY  118 (118)
T ss_pred             CCCCCCHHHHHHHhhhhhc--cC-CHHHHHHHHHHHHHhcCCC
Confidence            9999999999999999984  56 9999999999999999985

>PRK14981 DNA-directed RNA polymerase subunit F; Provisional

Probab=99.97  E-value=1.6e-30  Score=185.74  Aligned_cols=111  Identities=23%  Similarity=0.369  Sum_probs=101.5

Q ss_pred             cCccccccccccHHHHHHHHHHHHHHhhhcCCCCCcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHH
Q 032568           14 IGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCV   93 (138)
Q Consensus        14 lG~~f~~~~~Ls~~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~   93 (138)
                      +|++..+.+|||++||+.||+++..++         ++++++++|++|+++|+++++.++.+.+++++...+|++|++++
T Consensus         2 i~k~i~~e~~lt~sEa~~iL~~~~~~~---------els~~~~ktl~y~~kFsk~~~e~a~elve~L~~~~~l~e~~a~~   72 (112)
T PRK14981          2 IGKKILEEEYITIAEAKEILSEIEEER---------ELSYELRRTLDYLNRFSKLDPEDAEELVEELLELEKMKEKTAVK   72 (112)
T ss_pred             chhhhhhcccccHHHHHHHHHHHHhcc---------chhHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHccCCCHHHHHH
Confidence            477788999999999999999987532         78999999999999999999888999999999988899999999


Q ss_pred             HhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhh
Q 032568           94 LGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK  136 (138)
Q Consensus        94 l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~  136 (138)
                      |+||||+|+||||+||||++.  ++ ++++|++||++|++||.
T Consensus        73 I~nL~P~~~dElrai~~~~~~--~~-~~e~l~~ILd~l~k~~~  112 (112)
T PRK14981         73 IADILPETRDELRAIFAKERY--TL-SPEELDEILDIVKKYRE  112 (112)
T ss_pred             HHhcCCCCHHHHHHHHHHhcc--CC-CHHHHHHHHHHHHHhhC
Confidence            999999999999999999952  44 99999999999999973

>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=99.95  E-value=2.7e-27  Score=168.70  Aligned_cols=110  Identities=33%  Similarity=0.600  Sum_probs=93.4

Q ss_pred             cccHHHHHHHHHHHHHHhhhcC-------CCCCcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHHHh
Q 032568           23 CLMNCEVAIILDHKYEQLQQTS-------DDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLG   95 (138)
Q Consensus        23 ~Ls~~EV~~iL~~~~~~~~~~~-------~~~~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~l~   95 (138)
                      ||||+||..+|+++.+..+..+       .++..+.+.++++|++|+++|+++++++++..+++.|..+||+++|++||+
T Consensus         1 ~Lsn~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Yl~~~~~~~~~e~~~~l~~~L~~~~L~~~E~~qi~   80 (117)
T PF03874_consen    1 LLSNYEVLQILEKRREEQKNKSKKKQKNKEDPPENLNTIQYKTLEYLEKFSKFQNPESIKELREELKKFGLTEFEILQII   80 (117)
T ss_dssp             EE-HHHHHHHHHHHHHHHHCHCHHHHHHHHHCSSCHCHHHHHHHHHHHHH-SSSSHHHHHHHHHHHTTSTS-HHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHHHHhhhccccccccccccchHHHHHHHHHHHHccccCCCHHHHHHHHHHHhcccCCHHHHHHHh
Confidence            7999999999997665443221       134568899999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhh
Q 032568           96 NLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIK  135 (138)
Q Consensus        96 NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r  135 (138)
                      |+||+|++|+++|||+++.  |+ ++++|++||++|++||
T Consensus        81 Nl~P~~~~El~~ii~~~~~--r~-~ee~l~~iL~~v~~~~  117 (117)
T PF03874_consen   81 NLRPTTAVELRAIIESLES--RF-SEEDLEEILDLVSKYR  117 (117)
T ss_dssp             HH--SSHHHHHHHSTTGTT--TS-THHHHHHHHHHHHHHT
T ss_pred             cCCCCCHHHHHHHHHHhcc--CC-CHHHHHHHHHHHHHhC
Confidence            9999999999999999984  66 9999999999999997

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=99.82  E-value=9.5e-20  Score=129.59  Aligned_cols=111  Identities=21%  Similarity=0.347  Sum_probs=98.7

Q ss_pred             cCccccccccccHHHHHHHHHHHHHHhhhcCCCCCcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHH
Q 032568           14 IGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCV   93 (138)
Q Consensus        14 lG~~f~~~~~Ls~~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~   93 (138)
                      +|+..-+.+++|++||+.||.++..         +.++++.++.||+|+++|+++.+.++.+.+.++++-.++.+.-++.
T Consensus         3 i~k~~le~~yiti~Eak~il~~~~~---------~~eL~y~~~~al~y~~kFakldpe~a~e~veEL~~i~~~~e~~avk   73 (114)
T COG1460           3 IGKKILEEKYITISEAKKILSKVER---------EEELTYEQREALEYAEKFAKLDPEKARELVEELLSIVKMSEKIAVK   73 (114)
T ss_pred             hHHHHhhccCccHHHHHHHHHHhcc---------cccchHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhccccHHHHHH
Confidence            4566668899999999999999721         4478999999999999999999888888999999988899999999


Q ss_pred             HhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhh
Q 032568           94 LGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK  136 (138)
Q Consensus        94 l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~  136 (138)
                      |+++||+|.+|+|+++.+-.-  .+ ++++++.||+.+.+||.
T Consensus        74 IadI~P~t~~ElRsIla~e~~--~~-s~E~l~~Ildiv~Ky~~  113 (114)
T COG1460          74 IADIMPRTPDELRSILAKERV--ML-SDEELDKILDIVDKYRE  113 (114)
T ss_pred             HHHhCCCCHHHHHHHHHHccC--CC-CHHHHHHHHHHHHHHhc
Confidence            999999999999999997762  45 99999999999999984

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

Probab=98.88  E-value=8.1e-09  Score=76.28  Aligned_cols=113  Identities=19%  Similarity=0.278  Sum_probs=88.2

Q ss_pred             ccccccHHHHHHHHHHHHHHhh-----hcCCC----CCcchhHHHHHHHHHHHhhc--CCCCHHHHHHHHHHHHhcCCCH
Q 032568           20 KAKCLMNCEVAIILDHKYEQLQ-----QTSDD----PMNQVSQVFEKSLQYVKRFS--RYKNPDAVRQVREILSRYQLAE   88 (138)
Q Consensus        20 ~~~~Ls~~EV~~iL~~~~~~~~-----~~~~~----~~~~~~~~~~kTl~Yl~~Fs--~~~~~e~~~~v~~ll~~~~l~~   88 (138)
                      ....||++||...|.+..+...     .-+..    +-.+++.+.+.|++|++.-.  .-.+++.+-.+.--+..+||++
T Consensus         7 r~a~LtnyEVl~fL~el~~~n~~~~k~s~r~~~Q~~~~~~l~ti~~et~kYls~~~n~~~qt~E~i~el~~k~~~fkLtK   86 (149)
T KOG4168|consen    7 RNAALTNYEVLQFLNELECMNEEADKSSHRLGAQNILQNDLPTITYETLKYLSDNKNASTQTNESIIELITKLKSFKLTK   86 (149)
T ss_pred             hHHHhhhHHHHHHHHHhhhhhhhhhhhhhhhhcccccccccchhHHHHHHHHhcCcccccccHHHHHHHHHHhccccchH
Confidence            4568999999999988762211     00000    01237889999999999864  3456677777777778899999


Q ss_pred             hHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhh
Q 032568           89 FELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLI  134 (138)
Q Consensus        89 ~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~  134 (138)
                      .|+.+|.|+.|.++-|...+|...++  |+.++++|.+++..++++
T Consensus        87 AE~LqiiN~rPss~vel~~~iE~~ee--Rf~~ee~i~elv~~i~~~  130 (149)
T KOG4168|consen   87 AEILQIINLRPSSSVELYLIIEEVEE--RFQDEEDIEELVETISKT  130 (149)
T ss_pred             HHHHHHhccCcchHHHHHHHHHHHHH--hccchhcHHHHHHhcccc
Confidence            99999999999999999999999984  676999999999988764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	138
2c35_A	152	Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii L		1e-23
3h0g_D	135	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		1e-11
1wcm_D	177	Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang Le		3e-07
1y14_A	187	Crystal Structure Of Yeast Subcomplex Of Rpb4 And R		5e-07
3qt1_D	219	Rna Polymerase Ii Variant Containing A Chimeric Rpb		6e-07
1nt9_D	221	Complete 12-Subunit Rna Polymerase Ii Length = 221		6e-07
1pqv_D	221	Rna Polymerase Ii-Tfiis Complex Length = 221		6e-07

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

Iteration: 1
 Score =  104 bits (260), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 53/137 (38%), Positives = 92/137 (67%), Gaps = 5/137 (3%)
Query: 2   SGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQY 61
           +G+ EE+A++L    EF  A+ L+N EV ++L+H+ +Q +   D+   ++S+VF K+L Y
Sbjct: 20  AGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDE--QELSEVFMKTLNY 77
Query: 62  VKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDD 121
             RFSR+KN + +  VR +L + +L +FEL  L NLCPET EE+ A++PS++ R    +D
Sbjct: 78  TARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR---FED 134
Query: 122 EAIEKMLNDLSLIKKFE 138
           E ++++L+D+   + F+
Sbjct: 135 EELQQILDDIQTKRSFQ 151

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

Iteration: 1
 Score = 65.1 bits (157), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 43/135 (31%), Positives = 74/135 (54%), Gaps = 9/135 (6%)
Query: 6   EENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDD--PMNQVSQVFEKSLQYVK 63
           EE+AA+LK+G EF     L   E  I+++    Q  + ++   PM   + V +K++ Y  
Sbjct: 7   EEDAAQLKLGPEFENEDMLTVSEAKILIETVLAQRARETNGEIPM---TDVMKKTVAYFN 63
Query: 64  RFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEA 123
            F+R+K  +A      IL   +  +FE   LG LC E  EEA  ++PS+  +    DD+ 
Sbjct: 64  VFARFKTAEATYACERILGN-RFHKFERAQLGTLCCEDAEEARTLIPSLANK---IDDQN 119
Query: 124 IEKMLNDLSLIKKFE 138
           ++ +L++LS ++KF+
Sbjct: 120 LQGILDELSTLRKFQ 134

>pdb|1WCM|D Chain D, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang Length = 177

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 43/159 (27%), Positives = 77/159 (48%), Gaps = 33/159 (20%)
Query: 4   EEEENAAELKIGDEF------------------LKAKCLMNCEVAIILDHKYEQLQQ-TS 44
           EEEENAA L++G EF                  L    L+  E  +     +++ Q+ T 
Sbjct: 16  EEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKTR 75
Query: 45  DDPMNQVSQVFEKS-----------LQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCV 93
           +  +  +  + E++           +QY+  FSR+++ + V  V ++L    L  FE+  
Sbjct: 76  EKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQ 135
Query: 94  LGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLS 132
           LG+L  +T +EA  ++PS+    +  DDE +E++L +LS
Sbjct: 136 LGSLACDTADEAKTLIPSLN--NKISDDE-LERILKELS 171

>pdb|1Y14|A Chain A, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7 Length = 187

Iteration: 1
 Score = 49.7 bits (117), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 48/78 (61%), Gaps = 3/78 (3%)
Query: 55  FEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKT 114
            + ++QY+  FSR+++ + V  V ++L    L  FE+  LG+L  +T +EA  ++PS+  
Sbjct: 107 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLN- 165
Query: 115 RGRAHDDEAIEKMLNDLS 132
             +  DDE +E++L +LS
Sbjct: 166 -NKISDDE-LERILKELS 181

>pdb|3QT1|D Chain D, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11 Subunit Length = 219

Iteration: 1
 Score = 49.7 bits (117), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 48/78 (61%), Gaps = 3/78 (3%)
Query: 55  FEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKT 114
            + ++QY+  FSR+++ + V  V ++L    L  FE+  LG+L  +T +EA  ++PS+  
Sbjct: 139 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLN- 197
Query: 115 RGRAHDDEAIEKMLNDLS 132
             +  DDE +E++L +LS
Sbjct: 198 -NKISDDE-LERILKELS 213

>pdb|1NT9|D Chain D, Complete 12-Subunit Rna Polymerase Ii Length = 221

Iteration: 1
 Score = 49.7 bits (117), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 48/78 (61%), Gaps = 3/78 (3%)
Query: 55  FEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKT 114
            + ++QY+  FSR+++ + V  V ++L    L  FE+  LG+L  +T +EA  ++PS+  
Sbjct: 141 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLN- 199
Query: 115 RGRAHDDEAIEKMLNDLS 132
             +  DDE +E++L +LS
Sbjct: 200 -NKISDDE-LERILKELS 215

>pdb|1PQV|D Chain D, Rna Polymerase Ii-Tfiis Complex Length = 221

Iteration: 1
 Score = 49.3 bits (116), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 48/78 (61%), Gaps = 3/78 (3%)
Query: 55  FEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKT 114
            + ++QY+  FSR+++ + V  V ++L    L  FE+  LG+L  +T +EA  ++PS+  
Sbjct: 141 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLN- 199
Query: 115 RGRAHDDEAIEKMLNDLS 132
             +  DDE +E++L +LS
Sbjct: 200 -NKISDDE-LERILKELS 215

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	138
2c35_A	152	Human RPB4, DNA-directed RNA polymerase II 16 kDa	2e-42
3h0g_D	135	DNA-directed RNA polymerase II subunit RPB4; trans	3e-41
3hou_D	221	DNA-directed RNA polymerase II subunit RPB4; RNA p	4e-27
1y14_A	187	B32, RPB4, DNA-directed RNA polymerase II 32 kDa p	1e-25
3ayh_A	136	DNA-directed RNA polymerase III subunit RPC9; tran	1e-04

>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 =  136 bits (343), Expect = 2e-42
 Identities = 53/137 (38%), Positives = 92/137 (67%), Gaps = 5/137 (3%)

Query: 2   SGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQY 61
           +G+ EE+A++L    EF  A+ L+N EV ++L+H+ +Q +   D+   ++S+VF K+L Y
Sbjct: 20  AGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQ--ELSEVFMKTLNY 77

Query: 62  VKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDD 121
             RFSR+KN + +  VR +L + +L +FEL  L NLCPET EE+ A++PS++ R    +D
Sbjct: 78  TARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR---FED 134

Query: 122 EAIEKMLNDLSLIKKFE 138
           E ++++L+D+   + F+
Sbjct: 135 EELQQILDDIQTKRSFQ 151

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

 Score =  132 bits (334), Expect = 3e-41
 Identities = 41/134 (30%), Positives = 73/134 (54%), Gaps = 5/134 (3%)

Query: 5   EEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKR 64
            EE+AA+LK+G EF     L   E  I+++    Q  + ++  +   + V +K++ Y   
Sbjct: 6   FEEDAAQLKLGPEFENEDMLTVSEAKILIETVLAQRARETNGEIPM-TDVMKKTVAYFNV 64

Query: 65  FSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAI 124
           F+R+K  +A      IL   +  +FE   LG LC E  EEA  ++PS+  +    DD+ +
Sbjct: 65  FARFKTAEATYACERILGN-RFHKFERAQLGTLCCEDAEEARTLIPSLANKI---DDQNL 120

Query: 125 EKMLNDLSLIKKFE 138
           + +L++LS ++KF+
Sbjct: 121 QGILDELSTLRKFQ 134

>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 = 99.6 bits (247), Expect = 4e-27
 Identities = 27/141 (19%), Positives = 64/141 (45%), Gaps = 8/141 (5%)

Query: 2   SGEEEENAAELKIGDEFLKAKCLMNCEVA-----IILDHKYEQLQQTSDDPMNQVSQVFE 56
             E   +       ++    +  +N +          + + E +    +      ++  +
Sbjct: 83  KHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLK 142

Query: 57  KSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRG 116
            ++QY+  FSR+++ + V  V ++L    L  FE+  LG+L  +T +EA  ++PS+  + 
Sbjct: 143 NTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKI 202

Query: 117 RAHDDEAIEKMLNDLSLIKKF 137
               D+ +E++L +LS ++  
Sbjct: 203 ---SDDELERILKELSNLETL 220

>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 = 95.0 bits (235), Expect = 1e-25
 Identities = 27/137 (19%), Positives = 63/137 (45%), Gaps = 5/137 (3%)

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQ 60
                 E+  +    D+        +   +   + + E +    +      ++  + ++Q
Sbjct: 55  DETTAVEDEDDDLDEDDV--NADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQ 112

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHD 120
           Y+  FSR+++ + V  V ++L    L  FE+  LG+L  +T +EA  ++PS+  +     
Sbjct: 113 YLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKI---S 169

Query: 121 DEAIEKMLNDLSLIKKF 137
           D+ +E++L +LS ++  
Sbjct: 170 DDELERILKELSNLETL 186

>3ayh_A DNA-directed RNA polymerase III subunit RPC9; transcription; 2.19A {Schizosaccharomyces pombe} Length = 136

 Score = 38.5 bits (89), Expect = 1e-04
 Identities = 22/118 (18%), Positives = 42/118 (35%), Gaps = 12/118 (10%)

Query: 24  LMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRY---------KNPDAV 74
           L N EV   L     +    + +     + V E          +Y            +  
Sbjct: 18  LTNAEVFFHLKEMENEQNARTQERGAAQALVCENLRTIQFEILKYLSSQGNCEGLTKERF 77

Query: 75  RQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLS 132
                I + ++L + E+ V+ N  P +V E  A +  I+ R     +E I K++  ++
Sbjct: 78  LDCIAIFNEFELTKAEILVILNNKPSSVPELYACIEGIEER---FKEEDIFKLVEKIN 132

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	138
3h0g_D	135	DNA-directed RNA polymerase II subunit RPB4; trans	100.0
2c35_A	152	Human RPB4, DNA-directed RNA polymerase II 16 kDa	100.0
3hou_D	221	DNA-directed RNA polymerase II subunit RPB4; RNA p	99.98
1go3_F	107	DNA-directed RNA polymerase subunit F; transferase	99.97
1y14_A	187	B32, RPB4, DNA-directed RNA polymerase II 32 kDa p	99.97
4ayb_F	113	DNA-directed RNA polymerase; transferase, multi-su	99.94
3ayh_A	136	DNA-directed RNA polymerase III subunit RPC9; tran	99.85
2ckz_A	161	DNA-directed RNA polymerase III 18 KD polypeptide;	99.79

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

Probab=100.00  E-value=1.4e-44  Score=264.64  Aligned_cols=131  Identities=31%  Similarity=0.557  Sum_probs=119.9

Q ss_pred             hhhhhhhhccccCccccccccccHHHHHHHHHHHHHHhhhcCCCCCcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHHHH
Q 032568            3 GEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILS   82 (138)
Q Consensus         3 ~~~~e~~~~l~lG~~f~~~~~Ls~~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~   82 (138)
                      +.+||||++|+||++|++++|||||||+.||++..++++.. ..+..+.+.++++|++|+++|++|++++++.+|+++|+
T Consensus         4 ~~~ee~a~~L~lg~eF~~a~~Ls~sEv~~lL~~~~~~r~~~-~~~~~~~~~v~~kTl~Yl~~Fsk~~~~e~~~~v~~lL~   82 (135)
T 3h0g_D            4 AIFEEDAAQLKLGPEFENEDMLTVSEAKILIETVLAQRARE-TNGEIPMTDVMKKTVAYFNVFARFKTAEATYACERILG   82 (135)
T ss_dssp             --CCCCCTTTCSCHHHHHSCBCCHHHHHHHHHHHHHHHHTT-CCSCCCCTTHHHHHHHHHHTTCTTCSHHHHHHHHHHCC
T ss_pred             hHHHHhHHhhCCCHhhcCcccccHHHHHHHHHHHHHHHHhc-ccCCcchhHHHHHHHHHHHHccCCCCHHHHHHHHHHHH
Confidence            57899999999999999999999999999999998776532 13355789999999999999999999999999999999


Q ss_pred             hcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhhcC
Q 032568           83 RYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE  138 (138)
Q Consensus        83 ~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~f~  138 (138)
                      . |||+||+|+|+||||+|++|||+|||||++  |+ ++++|++||++|++||+||
T Consensus        83 ~-~L~~fEia~L~NL~P~t~dEak~LIpsL~~--r~-~de~L~~IL~~l~~~r~f~  134 (135)
T 3h0g_D           83 N-RFHKFERAQLGTLCCEDAEEARTLIPSLAN--KI-DDQNLQGILDELSTLRKFQ  134 (135)
T ss_dssp             C-CSCHHHHHHHHHHCCCCHHHHHHHCGGGTT--TS-CSHHHHHHHHHHHHHTTTC
T ss_pred             h-cCCHHHHHHHccCCCCCHHHHHHHHHHhcc--cC-CHHHHHHHHHHHHHHhccc
Confidence            9 999999999999999999999999999985  45 9999999999999999997

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

Probab=100.00  E-value=3.7e-41  Score=250.76  Aligned_cols=131  Identities=40%  Similarity=0.729  Sum_probs=120.0

Q ss_pred             hhhhhhhhccccCccccccccccHHHHHHHHHHHHHHhhhcCCCCCcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHHHH
Q 032568            3 GEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILS   82 (138)
Q Consensus         3 ~~~~e~~~~l~lG~~f~~~~~Ls~~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~   82 (138)
                      ++++|||++|+||++|.|++|||||||+.||++++.+..  ..++..++++++++|++||++|+++++++++.+++++|.
T Consensus        21 ~~~ee~a~~l~~gkef~~~~~Lt~sEV~~lL~~~~~~~~--~~~~~~els~v~~kTl~Yl~~F~k~k~~e~~~~l~e~L~   98 (152)
T 2c35_A           21 GDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNYTARFSRFKNRETIASVRSLLL   98 (152)
T ss_dssp             ---CCBGGGTBCCSSSSSCEECCHHHHHHHHHHHHHHHH--SSCSSCCCCHHHHHHHHHHHHTCSCCSHHHHHHHHHHHH
T ss_pred             CCccccHHHHhcchhhcccccccHHHHHHHHHHHHHhhc--ccccccchHHHHHHHHHHHHHccCCCCHHHHHHHHHHHH
Confidence            467999999999999999999999999999999987654  234556899999999999999999999999999999999


Q ss_pred             hcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhhcC
Q 032568           83 RYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE  138 (138)
Q Consensus        83 ~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~f~  138 (138)
                      .++||+||+++|+||||+|++|||+||||++.  |+ ++++|++||++|++||+||
T Consensus        99 ~~~L~~~E~a~L~NL~P~t~dEar~lipsl~~--r~-sdEeLe~ILd~l~k~r~f~  151 (152)
T 2c35_A           99 QKKLHKFELACLANLCPETAEESKALIPSLEG--RF-EDEELQQILDDIQTKRSFQ  151 (152)
T ss_dssp             TSSCCHHHHHHHHHHCCSSHHHHHHHCGGGTT--TS-CHHHHHHHHHHHHHHCCCC
T ss_pred             hcCCCHHHHHHhccCCCCCHHHHHHHHHhhcc--CC-CHHHHHHHHHHHHHHHhhc
Confidence            99999999999999999999999999999984  56 9999999999999999996

>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=99.98  E-value=1.5e-32  Score=212.39  Aligned_cols=131  Identities=31%  Similarity=0.553  Sum_probs=110.3

Q ss_pred             hhhhhhhccccCcccccc-----------ccccHHHHHHHHHHHHHHhhhc---C-------------------------
Q 032568            4 EEEENAAELKIGDEFLKA-----------KCLMNCEVAIILDHKYEQLQQT---S-------------------------   44 (138)
Q Consensus         4 ~~~e~~~~l~lG~~f~~~-----------~~Ls~~EV~~iL~~~~~~~~~~---~-------------------------   44 (138)
                      ++||+|+.|+||++|+=.           -.|++||++.|+......+.+.   +                         
T Consensus        19 ~~eenaa~l~lg~efql~q~~~~g~~~~lialnlsearl~i~~al~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (221)
T 3hou_D           19 EEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKHKKKHLKHENANDETTAVEDED   98 (221)
T ss_dssp             CCCCCCSSSCCCGGGCSEEECTTSCEEECCBCCTTHHHHHHHHHHHHHHHHHHHTTCC----------------------
T ss_pred             cchhhhHHhhcCcccceeecccCCchhHhHhhhhHHHHHHHHHHHHHHHHHhhccccccccccccccccccccccccccc
Confidence            578999999999999621           2599999999876533322210   0                         


Q ss_pred             ----------CCC----------------------CcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHH
Q 032568           45 ----------DDP----------------------MNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELC   92 (138)
Q Consensus        45 ----------~~~----------------------~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a   92 (138)
                                .+.                      ..+.+.+|+||++||++|++|++++++.+|+++|..+|||+||+|
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~e~e~~~~~~~~~~~~g~~seVf~KTLdYl~rFSKfkn~EAv~aVrELL~~~gLheFEiA  178 (221)
T 3hou_D           99 DDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVA  178 (221)
T ss_dssp             -------------------CTHHHHHHHHHHHHHHSCSCCHHHHHHHHHHHHSCSCCCHHHHHHHHHHHTTSCCCHHHHH
T ss_pred             ccccccccccccchhhhccchHHHHHHHHHHHhhcCCCccHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHhcCCChHHhh
Confidence                      000                      124578999999999999999999999999999999999999999


Q ss_pred             HHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhhc
Q 032568           93 VLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKF  137 (138)
Q Consensus        93 ~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~f  137 (138)
                      +||||||+|++|||+|||||+.  ++ ++++|++||++|++||.|
T Consensus       179 qLANLcPeTaDEARALIPSL~~--k~-sDEeLqeILdeLskyR~~  220 (221)
T 3hou_D          179 QLGSLACDTADEAKTLIPSLNN--KI-SDDELERILKELSNLETL  220 (221)
T ss_dssp             HHHHSCCCSHHHHHHHCTTCTT--SS-CHHHHHHHHHHHHHHSCC
T ss_pred             eecccCCCCHHHHHHHHHhhcc--cC-CHHHHHHHHHHHHHhhcc
Confidence            9999999999999999999985  45 999999999999999987

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

Probab=99.97  E-value=3.8e-31  Score=186.51  Aligned_cols=106  Identities=20%  Similarity=0.284  Sum_probs=93.8

Q ss_pred             cCccccccccccHHHHHHHHHHHHHHhhhcCCCCCcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHH
Q 032568           14 IGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCV   93 (138)
Q Consensus        14 lG~~f~~~~~Ls~~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~   93 (138)
                      +|++|.+++|||+|||+.||+++...         .++++++++|++|+++|+++++.++.+.+ +.|...||++|++++
T Consensus         2 i~kei~~~~~lt~sEa~~iL~~~~~~---------~e~s~~~~ktl~y~~kFsk~~~e~a~~l~-e~L~~~~l~e~~a~~   71 (107)
T 1go3_F            2 IGKKILGERYVTVSEAAEIMYNRAQI---------GELSYEQGCALDYLQKFAKLDKEEAKKLV-EELISLGIDEKTAVK   71 (107)
T ss_dssp             CSSEEEEEEEECHHHHHHHHHHHHHH---------SCCCHHHHHHHHHHHHHCCSCHHHHHHHH-HHHHHTTCCHHHHHH
T ss_pred             chHHHhcccccCHHHHHHHHHHHHhc---------ccccHHHHHHHHHHHHHhCCCHHHHHHHH-HHHHhCCCCHHHHHH
Confidence            68999999999999999999998752         36899999999999999999655555555 445577899999999


Q ss_pred             HhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhh
Q 032568           94 LGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIK  135 (138)
Q Consensus        94 l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r  135 (138)
                      ||||||+|+||||+||||+.     + +++|++||++|++||
T Consensus        72 I~nl~P~t~dElraii~~~~-----~-~eel~~ILd~l~k~~  107 (107)
T 1go3_F           72 IADILPEDLDDLRAIYYKRE-----L-PENAEEILEIVRKYI  107 (107)
T ss_dssp             HHHHCCCSHHHHHHHSTTSC-----C-CTTHHHHHHHHTTCC
T ss_pred             HHHhCCCCHHHHHHHHhccc-----C-cHHHHHHHHHHHHcC
Confidence            99999999999999999996     2 999999999999986

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

Probab=99.97  E-value=3.8e-30  Score=196.09  Aligned_cols=86  Identities=28%  Similarity=0.585  Sum_probs=82.5

Q ss_pred             cchhHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHH
Q 032568           49 NQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKML  128 (138)
Q Consensus        49 ~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL  128 (138)
                      .++++++++|++||++|+++++++++.+|+++|..++|++||+|+|+||||+|++|||+||||++.  |+ ++++|++||
T Consensus       101 ~~ls~v~~KTLeYl~rFsk~kn~Esa~elre~L~~~kL~efE~aqLaNL~PeTadEaraLIpSle~--rl-sdEeLeeIL  177 (187)
T 1y14_A          101 GGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN--KI-SDDELERIL  177 (187)
T ss_dssp             CSCCHHHHHHHHHHHHHCSCCSHHHHHHHHHHHHTTTCCHHHHHHHHHSCCSSHHHHHHHSGGGTT--TS-CHHHHHHHH
T ss_pred             ccccHHHHHHHHHHHHccCCCCHHHHHHHHHHHHhcCCCHHHHHHcCcCCCCCHHHHHHHHHhhcc--CC-CHHHHHHHH
Confidence            478999999999999999999999999999999999999999999999999999999999999984  56 999999999


Q ss_pred             HHHHhhhhc
Q 032568          129 NDLSLIKKF  137 (138)
Q Consensus       129 ~~l~~~r~f  137 (138)
                      ++|++||+|
T Consensus       178 d~L~k~r~~  186 (187)
T 1y14_A          178 KELSNLETL  186 (187)
T ss_dssp             HHHHHHCCC
T ss_pred             HHHHHhhcc
Confidence            999999998

>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=99.94  E-value=6.7e-29  Score=176.54  Aligned_cols=111  Identities=18%  Similarity=0.226  Sum_probs=89.6

Q ss_pred             cCccccccccccHHHHHHHHHHHHHHhhhcCCCCCcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHH
Q 032568           14 IGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCV   93 (138)
Q Consensus        14 lG~~f~~~~~Ls~~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~   93 (138)
                      .|++..+.+++|++||+.||.++.         ...+.++++++|++|+++|+++++.++.+ +++.|...++++|++|+
T Consensus         2 ~~~~ii~e~~it~~eakeiL~~~~---------~~~~~s~~~~ktl~y~~~Fsk~~~e~a~~-l~e~L~~~~l~~~~~a~   71 (113)
T 4ayb_F            2 SSVYIVEEHYIPYSVAKKLLSDVI---------KSGSSSNLLQRTYDYLNSVEKCDAESAQK-VVEELSSIISREDVRAV   71 (113)
T ss_dssp             -CCEEEEEEEECTTGGGGTTTTTS---------SSSCCCTTHHHHHHHTTTTCSSCHHHHHH-HHHHHHTTCCCHHHHHH
T ss_pred             CcceeecccccCHHHHHHHHHHHH---------hcccccHHHHHHHHHHHHHcCCCHHHHHH-HHHHHHHcCCCHHHHHH
Confidence            477788999999999999997752         13467889999999999999996555555 55555567899999999


Q ss_pred             HhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhh
Q 032568           94 LGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK  136 (138)
Q Consensus        94 l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~  136 (138)
                      |+||||+|++|||+||||+++  +.+++++|++||++|++|.+
T Consensus        72 IanL~P~~~dElrali~s~e~--~~~~deeL~~IL~~l~ky~~  112 (113)
T 4ayb_F           72 LASICPITPDEVRSILIMDSN--RTYTSEDIQKIIDIIRKYIK  112 (113)
T ss_dssp             HHHHCCCSSCCCCTTTTTTCC--CCCCCTHHHHHHHHC-----
T ss_pred             HHHcCCCCHHHHHHHHHhhcc--CCCCHHHHHHHHHHHHHHhc
Confidence            999999999999999999984  34699999999999999864

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

Probab=99.85  E-value=6.2e-22  Score=144.53  Aligned_cols=112  Identities=19%  Similarity=0.248  Sum_probs=95.6

Q ss_pred             ccccccHHHHHHHHHHHHHHhhhc--CCC-----CCcchhHHHHHHHHHHHhhc--CCCCHHHHHHHHHHHHhcCCCHhH
Q 032568           20 KAKCLMNCEVAIILDHKYEQLQQT--SDD-----PMNQVSQVFEKSLQYVKRFS--RYKNPDAVRQVREILSRYQLAEFE   90 (138)
Q Consensus        20 ~~~~Ls~~EV~~iL~~~~~~~~~~--~~~-----~~~~~~~~~~kTl~Yl~~Fs--~~~~~e~~~~v~~ll~~~~l~~~E   90 (138)
                      ++.+|||+||..+|.++..+....  ...     ...+++.++++|++|+++|.  .+++++++..+.+.|+.+||+++|
T Consensus        14 ~~a~LsN~EVl~~L~~~~~~~~~~~~~~~~~~~~~~~~l~ti~~e~l~YL~~~p~~~~q~~e~i~~l~~~L~~~~Ltk~E   93 (136)
T 3ayh_A           14 RDAYLTNAEVFFHLKEMENEQNARTQERGAAQALVCENLRTIQFEILKYLSSQGNCEGLTKERFLDCIAIFNEFELTKAE   93 (136)
T ss_dssp             EEEEECHHHHHHHHHHHHHHHHHHHHHHGGGGCCCCHHHHHHHHHHHHHHHTTTCCTTCCHHHHHHHHHTTTTTCCCHHH
T ss_pred             ccccccHHHHHHHHHHHHhhhcccccccCCccccccchHHHHHHHHHHHHHhCCCccccCHHHHHHHHHHHHhcCCCHHH
Confidence            378999999999999987644211  011     12578899999999999994  346899999999999999999999


Q ss_pred             HHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhh
Q 032568           91 LCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLI  134 (138)
Q Consensus        91 ~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~  134 (138)
                      ++||+|+||+|+.|+++||++.+.  |+ +++++++||++|+++
T Consensus        94 ~LqivNl~P~t~vel~~iIEe~e~--Rf-see~ie~IL~~i~~~  134 (136)
T 3ayh_A           94 ILVILNNKPSSVPELYACIEGIEE--RF-KEEDIFKLVEKINTT  134 (136)
T ss_dssp             HHHHHHHCCCSHHHHHHHSTTHHH--HH-TTTTHHHHHHHHHHH
T ss_pred             HHHHhccCCCCHHHHHHHHHhccc--CC-CHHHHHHHHHHHHHh
Confidence            999999999999999999999984  67 999999999999876

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

Probab=99.79  E-value=4e-20  Score=138.47  Aligned_cols=113  Identities=16%  Similarity=0.202  Sum_probs=33.1

Q ss_pred             ccccccHHHHHHHHHHHHHHhhh---------------cCCC--CCcchhHHHHHHHHHHHhhcC---------------
Q 032568           20 KAKCLMNCEVAIILDHKYEQLQQ---------------TSDD--PMNQVSQVFEKSLQYVKRFSR---------------   67 (138)
Q Consensus        20 ~~~~Ls~~EV~~iL~~~~~~~~~---------------~~~~--~~~~~~~~~~kTl~Yl~~Fs~---------------   67 (138)
                      .+.+|||+||..+|.++..++.-               ..+.  +..+++.+++.|++||+++++               
T Consensus         7 ~~a~LSN~EVl~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ti~~e~~~YL~~~p~~~~~~~~~~~~~~~~   86 (161)
T 2ckz_A            7 RNAFLSDYEVLKFLTDLEKKHLWDQKSLAALKKSRSKGKQNRPYNHPELQGITRNVVNYLSINKNFINQEDEGEERESSG   86 (161)
T ss_dssp             EEEEECHHHHHHHHHHHHHHTTCSHHHHHCC----------CCCCCHHHHHHHHHHHHHHTC------------------
T ss_pred             hhhhhhHHHHHHHHHHhhhhccccccchhhhhcccccccccCCCCCccHHHHHHHHHHHHHhCCcccccccccccccccc
Confidence            46789999999999998765320               0011  124688899999999999987               


Q ss_pred             ----------CCCHHHHHHHHHHHHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhh
Q 032568           68 ----------YKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIK  135 (138)
Q Consensus        68 ----------~~~~e~~~~v~~ll~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r  135 (138)
                                ..+++++..+.+.|+.+||+++|++||+|+||.++.|+++||+..+  +|+ +++++++||++|+.++
T Consensus        87 ~~~~~~~~~~~~~~e~i~~l~~~L~~~~Ltk~E~lqivNl~P~s~vel~~iIEe~e--~Rf-see~ie~IL~ii~~~~  161 (161)
T 2ckz_A           87 AKDAEKSGISKMSDESFAELMTKLNSFKLFKAEKLQIVNQLPANMVHLYSIVEECD--ARF-DEKTIEEMLEIISAYA  161 (161)
T ss_dssp             ------------------------------------------------------------------------------
T ss_pred             ccccccccccccCHHHHHHHHHHHHhcCCCHHHHHHHhccCCCCHHHHHHHHHhcc--cCC-CHHHHHHHHHHHHHhC
Confidence                      3557788888888899999999999999999999999999999998  377 9999999999998874

---

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	138
d2c35a1	129	a.60.8.2 (A:14-142) RNA polymerase II subunit RBP4	1e-40
d1y14a_	176	a.60.8.2 (A:) RNA polymerase II subunit RBP4 (RpoF	3e-30
d1go3f_	107	a.60.8.2 (F:) RNA polymerase II subunit RBP4 (RpoF	2e-16

>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 =  130 bits (328), Expect = 1e-40
 Identities = 52/133 (39%), Positives = 89/133 (66%), Gaps = 5/133 (3%)

Query: 6   EENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRF 65
           EE+A++L    EF  A+ L+N EV ++L+H+ +Q +  S +   ++S+VF K+L Y  RF
Sbjct: 1   EEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNYTARF 58

Query: 66  SRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIE 125
           SR+KN + +  VR +L + +L +FEL  L NLCPET EE+ A++PS++ R    +DE ++
Sbjct: 59  SRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR---FEDEELQ 115

Query: 126 KMLNDLSLIKKFE 138
           ++L+D+   + F+
Sbjct: 116 QILDDIQTKRSFQ 128

>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 =  105 bits (263), Expect = 3e-30
 Identities = 30/140 (21%), Positives = 66/140 (47%), Gaps = 9/140 (6%)

Query: 2   SGEEEENAAELKIGDEFLK-AKCLMNCEVAIIL-----DHKYEQLQQTSDDPMNQVSQVF 55
              E  N     + DE     +  +N +    +     + + E +    +      ++  
Sbjct: 37  LKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDL 96

Query: 56  EKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTR 115
           + ++QY+  FSR+++ + V  V ++L    L  FE+  LG+L  +T +EA  ++PS+  +
Sbjct: 97  KNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNK 156

Query: 116 GRAHDDEAIEKMLNDLSLIK 135
                D+ +E++L +LS ++
Sbjct: 157 I---SDDELERILKELSNLE 173

>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 = 67.5 bits (165), Expect = 2e-16
 Identities = 18/117 (15%), Positives = 51/117 (43%), Gaps = 13/117 (11%)

Query: 14  IGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDA 73
           IG + L  + +   E A I+ ++ +           ++S     +L Y+++F++  + + 
Sbjct: 2   IGKKILGERYVTVSEAAEIMYNRAQI---------GELSYEQGCALDYLQKFAKL-DKEE 51

Query: 74  VRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLND 130
            +++ E L    + E     + ++ PE +++  A+    +      + E I +++  
Sbjct: 52  AKKLVEELISLGIDEKTAVKIADILPEDLDDLRAIYYKREL---PENAEEILEIVRK 105

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	138
d2c35a1	129	RNA polymerase II subunit RBP4 (RpoF) {Human (Homo	100.0
d1y14a_	176	RNA polymerase II subunit RBP4 (RpoF) {Baker's yea	99.96
d1go3f_	107	RNA polymerase II subunit RBP4 (RpoF) {Archaeon Me	99.93

>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=100.00  E-value=3.4e-41  Score=243.02  Aligned_cols=128  Identities=41%  Similarity=0.727  Sum_probs=120.2

Q ss_pred             hhhhhccccCccccccccccHHHHHHHHHHHHHHhhhcCCCCCcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcC
Q 032568            6 EENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQ   85 (138)
Q Consensus         6 ~e~~~~l~lG~~f~~~~~Ls~~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~   85 (138)
                      ||||++|+||++|.|++|||||||+.+|+++++++.  +.++..++++++++|++|+++|+++++++++..+++++..+|
T Consensus         1 ee~a~~l~~~~ef~~~~~Lt~~Ev~~iL~~~~~~~~--~~~~~~~l~~~~~ktl~Yl~~fak~~~~es~~~~~~ll~~~~   78 (129)
T d2c35a1           1 EEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNYTARFSRFKNRETIASVRSLLLQKK   78 (129)
T ss_dssp             CCBGGGTBCCSSSSSCEECCHHHHHHHHHHHHHHHH--SSCSSCCCCHHHHHHHHHHHHTCSCCSHHHHHHHHHHHHTSS
T ss_pred             CcchhhhcccHhhcchhhhhHHHHHHHHHHHHHHHh--cccccccHHHHHHHHHHHHHHhccCCCHHHHHHHHHHhcccC
Confidence            689999999999999999999999999999876653  445667899999999999999999999999999999999999


Q ss_pred             CCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhhcC
Q 032568           86 LAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE  138 (138)
Q Consensus        86 l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~f~  138 (138)
                      |+++|++||+||||+|++||++||||++.  |+ ++++|++||+.|++||+||
T Consensus        79 L~~~E~~~i~Nl~P~~~~El~~li~~l~~--r~-see~l~~iLd~l~~~r~f~  128 (129)
T d2c35a1          79 LHKFELACLANLCPETAEESKALIPSLEG--RF-EDEELQQILDDIQTKRSFQ  128 (129)
T ss_dssp             CCHHHHHHHHHHCCSSHHHHHHHCGGGTT--TS-CHHHHHHHHHHHHHHCCCC
T ss_pred             CCHHHHHHHhCCCCCCHHHHHHHHHHhcc--CC-CHHHHHHHHHHHHHHhccc
Confidence            99999999999999999999999999984  56 9999999999999999997

>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=99.96  E-value=1.7e-29  Score=189.23  Aligned_cols=115  Identities=22%  Similarity=0.428  Sum_probs=84.7

Q ss_pred             ccccccHHHHHHHHHHHHHHhh-----hcCCCCCcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHHH
Q 032568           20 KAKCLMNCEVAIILDHKYEQLQ-----QTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVL   94 (138)
Q Consensus        20 ~~~~Ls~~EV~~iL~~~~~~~~-----~~~~~~~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~l   94 (138)
                      ++.++..++....++....+..     .....+....+.+|++|++||++|++|++++++.+|+++|+.+|||+||+|+|
T Consensus        56 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~~e~~sg~~~~v~~kTldYl~~Fsk~k~~es~~~vrelL~~~~L~~fE~a~L  135 (176)
T d1y14a_          56 LDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQL  135 (176)
T ss_dssp             -----------------CHHHHHHHHHHHHHHHSCSCCHHHHHHHHHHHHHCSCCSHHHHHHHHHHHHTTTCCHHHHHHH
T ss_pred             hhhhhccchhhhhhhhhhhHHHHHhhhhhcccCCCCchHHHHHHHHHHHHhccCCCHHHHHHHHHHHHhcCCCHHHHHHh
Confidence            4556666666655543222211     11223345678999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhhc
Q 032568           95 GNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKF  137 (138)
Q Consensus        95 ~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~f  137 (138)
                      |||||+|+||||+|||||+.  ++ ++++|++||+.|++||..
T Consensus       136 ~NLcPet~eEAkaLiPSL~~--k~-~de~Lq~IL~~L~~~r~~  175 (176)
T d1y14a_         136 GSLACDTADEAKTLIPSLNN--KI-SDDELERILKELSNLETL  175 (176)
T ss_dssp             HHSCCSSHHHHHHHSGGGTT--TS-CHHHHHHHHHHHHHHCCC
T ss_pred             hccCCCCHHHHHHHhhhhcc--cC-CHHHHHHHHHHHHHhhcc
Confidence            99999999999999999984  45 999999999999999963

>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=99.93  E-value=2e-26  Score=160.74  Aligned_cols=105  Identities=17%  Similarity=0.306  Sum_probs=87.2

Q ss_pred             cCccccccccccHHHHHHHHHHHHHHhhhcCCCCCcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHH
Q 032568           14 IGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCV   93 (138)
Q Consensus        14 lG~~f~~~~~Ls~~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~   93 (138)
                      +|+++.+.+++|++||+.||.++.+         ..++++++++|++|+++|+++ +++.+..+.+.|...|++++++|+
T Consensus         2 i~keii~e~~lt~ae~keiL~~~~~---------~~elsye~~~tL~y~~~fak~-~~e~~~~l~~~L~~~~~~~~~aak   71 (107)
T d1go3f_           2 IGKKILGERYVTVSEAAEIMYNRAQ---------IGELSYEQGCALDYLQKFAKL-DKEEAKKLVEELISLGIDEKTAVK   71 (107)
T ss_dssp             CSSEEEEEEEECHHHHHHHHHHHHH---------HSCCCHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHTTCCHHHHHH
T ss_pred             cchhhhhccccCHHHHHHHHHHhhc---------cccccHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHhcCCCHHHHHH
Confidence            5889999999999999999988653         226899999999999999999 556556666666678999999999


Q ss_pred             HhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhh
Q 032568           94 LGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLI  134 (138)
Q Consensus        94 l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~  134 (138)
                      ||||||.|++|+|+++||+..  .. +.   ++|+++|++|
T Consensus        72 IanL~P~~~dElrai~~~~~~--~~-~~---eeIl~il~~y  106 (107)
T d1go3f_          72 IADILPEDLDDLRAIYYKREL--PE-NA---EEILEIVRKY  106 (107)
T ss_dssp             HHHHCCCSHHHHHHHSTTSCC--CT-TH---HHHHHHHTTC
T ss_pred             HHHhCCCCHHHHHHHHHHhcc--CC-CH---HHHHHHHHHh
Confidence            999999999999999998862  22 44   5577777665