Citrus Sinensis ID: 033845

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110
Protein Sequence
MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVKHL
Secondary Structure (PSIPRED)
ccccccccccccccccEEEEEEcccccccEEEEEEEcccccHHHHHHHHHHccccEEEEEEccccccccEEEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccEEEEcccccEEEEEEccccccccEEEEEEccccHHHHHHHHHHHccccEEEEEEEcccccccEEEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mnapdryerfvvpegtkkvsyERDTKIINAASFTIEREEHTIGNILRMQLhrdenvlfagyklphplqYKIIVRIhttsqsspmqAYNQAINDLDKELDTLKSAFEVKHL
Flexible Loop (DISEMBL)
mnapdryerfvvpegtkkvsyerdtkiinaasftiereeHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVKHL
Low Complexity Region (SEG)
MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVKHL
Disordered region (IsUnstruct)
*********FVV****KKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHT*********************************
Disordered Region (DISOPRED)
**APDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVKHL
Disordered Region (DISEMBL)
MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVKHL
Disordered Region (DISPRO)
****DRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE***L
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPxxxxxxxxxxxxxxxxxxxxxFEVKHL
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	110	2.2.26 [Sep-21-2011]
Q38859	116	DNA-directed RNA polymera	yes	no	0.981	0.931	0.888	2e-53
Q86JJ5	120	DNA-directed RNA polymera	yes	no	0.954	0.875	0.485	9e-29
P52435	117	DNA-directed RNA polymera	yes	no	0.972	0.914	0.523	3e-28
Q32P79	117	DNA-directed RNA polymera	yes	no	0.972	0.914	0.523	3e-28
O08740	117	DNA-directed RNA polymera	yes	no	0.954	0.897	0.523	7e-28
Q9VJE4	117	DNA-directed RNA polymera	yes	no	0.963	0.905	0.528	1e-27
Q7PVQ9	117	DNA-directed RNA polymera	yes	no	0.954	0.897	0.533	3e-27
Q9GZM3	115	DNA-directed RNA polymera	yes	no	0.945	0.904	0.514	2e-26
Q9H1A7	115	DNA-directed RNA polymera	yes	no	0.945	0.904	0.504	6e-26
Q60SM4	122	Probable DNA-directed RNA	N/A	no	0.918	0.827	0.509	4e-24

>sp|Q38859|RPB11_ARATH DNA-directed RNA polymerase II subunit RPB11 OS=Arabidopsis thaliana GN=RPB13.6 PE=2 SV=1

 Score =  207 bits (526), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 96/108 (88%), Positives = 105/108 (97%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAP+RYERFVVPEGTKKVSY+RDTKIINAASFT+ERE+HTIGNI+RMQLHRDENVLFAG
Sbjct: 1   MNAPERYERFVVPEGTKKVSYDRDTKIINAASFTVEREDHTIGNIVRMQLHRDENVLFAG 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVK 108
           Y+LPHPL+YKIIVRIHTTSQSSPMQAYNQAINDLDKELD LK+ FE +
Sbjct: 61  YQLPHPLKYKIIVRIHTTSQSSPMQAYNQAINDLDKELDYLKNQFEAE 108

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. RPB11 is part of the core element with the central large cleft.
Arabidopsis thaliana (taxid: 3702)

>sp|Q86JJ5|RPB11_DICDI DNA-directed RNA polymerase II subunit rpb11 OS=Dictyostelium discoideum GN=polr2j PE=3 SV=1

 Score =  125 bits (313), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 51/105 (48%), Positives = 83/105 (79%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAPDR+E FV+P+G KKV+  RDTKI NA+ FTI +E+HTIGN++RMQL  D++++FAG
Sbjct: 1   MNAPDRFELFVLPDGAKKVTMVRDTKIPNASMFTILKEDHTIGNLIRMQLIADQDIIFAG 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105
           Y++PHPL++ + +RI T + ++P++   +++  L +E  +L+++F
Sbjct: 61  YRMPHPLEHNVNIRIQTNNNTNPLECVQKSMECLSREFTSLENSF 105

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. RPB11 is part of the core element with the central large cleft.

Dictyostelium discoideum (taxid: 44689)

>sp|P52435|RPB11_HUMAN DNA-directed RNA polymerase II subunit RPB11-a OS=Homo sapiens GN=POLR2J PE=1 SV=1

 Score =  123 bits (309), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 56/107 (52%), Positives = 77/107 (71%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct: 1   MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEV 107
           YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F V
Sbjct: 61  YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRV 107

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. RPB11 is part of the core element with the central large cleft.

Homo sapiens (taxid: 9606)

>sp|Q32P79|RPB11_BOVIN DNA-directed RNA polymerase II subunit RPB11 OS=Bos taurus GN=POLR2J PE=3 SV=1

 Score =  123 bits (309), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 56/107 (52%), Positives = 77/107 (71%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct: 1   MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEV 107
           YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F V
Sbjct: 61  YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRV 107

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. RPB11 is part of the core element with the central large cleft.

Bos taurus (taxid: 9913)

>sp|O08740|RPB11_MOUSE DNA-directed RNA polymerase II subunit RPB11 OS=Mus musculus GN=Polr2j PE=2 SV=1

 Score =  122 bits (306), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 55/105 (52%), Positives = 76/105 (72%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct: 1   MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105
           YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F
Sbjct: 61  YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERF 105

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. RPB11 is part of the core element with the central large cleft.

Mus musculus (taxid: 10090)

>sp|Q9VJE4|RPB11_DROME DNA-directed RNA polymerase II subunit RPB11 OS=Drosophila melanogaster GN=Rpb11 PE=3 SV=1

 Score =  121 bits (304), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 56/106 (52%), Positives = 77/106 (72%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAP  +E F++ EG KK+  E DTK+ NAA FTI +E+HT+GN++R QL +D NVLFAG
Sbjct: 1   MNAPPTFESFLLYEGEKKIIKELDTKVTNAAIFTINKEDHTLGNMIRNQLLKDPNVLFAG 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE 106
           YK+PHPL++K ++RI TT+  SP +A+  AI DL  EL   +  F+
Sbjct: 61  YKVPHPLEHKFVIRIQTTADYSPQEAFMNAITDLLAELSLFEERFK 106

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. RPB11 is part of the core element with the central large cleft.

Drosophila melanogaster (taxid: 7227)

>sp|Q7PVQ9|RPB11_ANOGA DNA-directed RNA polymerase II subunit RPB11 OS=Anopheles gambiae GN=Rpb11 PE=2 SV=2

 Score =  120 bits (300), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 56/105 (53%), Positives = 76/105 (72%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAP  +E F++ EG KK+  E D K+ NAA FT+ +E+HT+GN++R QL +D NVLFAG
Sbjct: 1   MNAPPTFESFLLYEGEKKIIKELDMKVPNAAIFTVNKEDHTLGNMIRNQLLKDPNVLFAG 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105
           YKLPHPL++K ++RI TTS+ SP +A+  AI DL  EL   +  F
Sbjct: 61  YKLPHPLEHKFVLRIQTTSEYSPHEAFMNAITDLLSELSLFEERF 105

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. RPB11 is part of the core element with the central large cleft.

Anopheles gambiae (taxid: 7165)

>sp|Q9GZM3|RPB1B_HUMAN DNA-directed RNA polymerase II subunit RPB11-b1 OS=Homo sapiens GN=POLR2J2 PE=1 SV=1

 Score =  117 bits (293), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 54/105 (51%), Positives = 76/105 (72%), Gaps = 1/105 (0%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAP  +E F++ EG +K++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct: 1   MNAPPAFESFLLFEG-EKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 59

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105
           YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F
Sbjct: 60  YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERF 104

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. RPB11 is part of the core element with the central large cleft.

Homo sapiens (taxid: 9606)

>sp|Q9H1A7|RPB1C_HUMAN DNA-directed RNA polymerase II subunit RPB11-b2 OS=Homo sapiens GN=POLR2J3 PE=2 SV=1

 Score =  115 bits (289), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 53/105 (50%), Positives = 76/105 (72%), Gaps = 1/105 (0%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAP  +E F++ EG +K++  +DTK+ NA  FT+ +E+HT+GNI++ QL +D  VLFAG
Sbjct: 1   MNAPPAFESFLLFEG-EKITINKDTKVPNACLFTMNKEDHTLGNIIKSQLLKDPQVLFAG 59

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105
           YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F
Sbjct: 60  YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERF 104

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. RPB11 is part of the core element with the central large cleft.

Homo sapiens (taxid: 9606)

>sp|Q60SM4|RPB11_CAEBR Probable DNA-directed RNA polymerase II subunit RPB11 OS=Caenorhabditis briggsae GN=rpb-11 PE=3 SV=1

 Score =  109 bits (273), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 52/102 (50%), Positives = 75/102 (73%), Gaps = 1/102 (0%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAP  +E F++ +  KK+  E+DTK+ NAA FTI +E+HT+GN+L++QL +D  VLFAG
Sbjct: 1   MNAPAAFESFLLLDD-KKIYIEKDTKVPNAAIFTINKEDHTLGNMLKIQLLKDPEVLFAG 59

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLK 102
           YK PHPL++KI++R+ TT+ ++P  A   AI DL  EL  L+
Sbjct: 60  YKNPHPLEHKILLRVQTTNATTPADALTTAITDLVGELSLLE 101

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. RPB11 is part of the core element with the central large cleft.

Caenorhabditis briggsae (taxid: 6238)

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	110
449464004	116	PREDICTED: DNA-directed RNA polymerase I	0.981	0.931	0.962	4e-55
255553542	156	DNA-directed RNA polymerase II 13.6 kD p	0.963	0.679	0.962	5e-55
225430537	116	PREDICTED: DNA-directed RNA polymerase I	0.981	0.931	0.944	6e-55
356531671	116	PREDICTED: DNA-directed RNA polymerase I	1.0	0.948	0.936	3e-54
358248360	116	uncharacterized protein LOC100784219 [Gl	1.0	0.948	0.927	3e-54
217070988	116	unknown [Medicago truncatula] gi|3885194	1.0	0.948	0.909	1e-53
224103945	116	predicted protein [Populus trichocarpa]	0.981	0.931	0.925	2e-53
388516987	116	unknown [Lotus japonicus]	1.0	0.948	0.918	5e-53
297819918	116	ATRPB13.6 [Arabidopsis lyrata subsp. lyr	0.981	0.931	0.907	1e-52
147832705	129	hypothetical protein VITISV_015574 [Viti	0.981	0.837	0.842	2e-52

>gi|449464004|ref|XP_004149719.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB11-like [Cucumis sativus] gi|449516703|ref|XP_004165386.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB11-like [Cucumis sativus]

 Score =  218 bits (555), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 104/108 (96%), Positives = 106/108 (98%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG
Sbjct: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVK 108
           YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELD LK+AFE +
Sbjct: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDHLKNAFEAE 108

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255553542|ref|XP_002517812.1| DNA-directed RNA polymerase II 13.6 kD polypeptide, putative [Ricinus communis] gi|223543084|gb|EEF44619.1| DNA-directed RNA polymerase II 13.6 kD polypeptide, putative [Ricinus communis]

 Score =  218 bits (554), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 102/106 (96%), Positives = 105/106 (99%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAPDRYERFVVPEGTKKVSYERDTKIINAASFT+ERE+HTIGNILRMQLHRDENVLFAG
Sbjct: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTVEREDHTIGNILRMQLHRDENVLFAG 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE 106
           Y+LPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELD LKSAFE
Sbjct: 61  YRLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDHLKSAFE 106

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225430537|ref|XP_002285578.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB11 [Vitis vinifera] gi|296082163|emb|CBI21168.3| unnamed protein product [Vitis vinifera]

 Score =  217 bits (553), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 102/108 (94%), Positives = 107/108 (99%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAPDRYERFVVPEGTKKVSYERDTKIINAASFT+ERE+HTIGNILRMQLHRDENVLFAG
Sbjct: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTVEREDHTIGNILRMQLHRDENVLFAG 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVK 108
           YKLPHPLQYKII+RIHTTSQSSPMQAYNQAINDLDKELD LK+AFEV+
Sbjct: 61  YKLPHPLQYKIIIRIHTTSQSSPMQAYNQAINDLDKELDYLKNAFEVE 108

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356531671|ref|XP_003534400.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB11 [Glycine max]

 Score =  215 bits (548), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 103/110 (93%), Positives = 106/110 (96%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD NVLFAG
Sbjct: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDPNVLFAG 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVKHL 110
           YKLPHPLQYKIIVRIHTTSQSSPMQAYNQ+INDLD+ELD LKSAFE + L
Sbjct: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQSINDLDRELDHLKSAFEAEML 110

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358248360|ref|NP_001240124.1| uncharacterized protein LOC100784219 [Glycine max] gi|255626235|gb|ACU13462.1| unknown [Glycine max]

 Score =  215 bits (547), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 102/110 (92%), Positives = 106/110 (96%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD NVLFAG
Sbjct: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDPNVLFAG 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVKHL 110
           YKLPHPLQYKIIVRIHTTSQSSPMQAYNQ++NDLD+ELD LKSAFE + L
Sbjct: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQSVNDLDRELDHLKSAFEAEML 110

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217070988|gb|ACJ83854.1| unknown [Medicago truncatula] gi|388519401|gb|AFK47762.1| unknown [Medicago truncatula]

 Score =  213 bits (542), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 100/110 (90%), Positives = 106/110 (96%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAPDRYERFVVPEGTKKV+YERDTKIINAASFTIERE+HTIGNILRMQLH+D NVLFAG
Sbjct: 1   MNAPDRYERFVVPEGTKKVAYERDTKIINAASFTIEREDHTIGNILRMQLHKDPNVLFAG 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVKHL 110
           YKLPHPLQYKII+RIHTTSQSSPMQAYNQ+INDLDKELDTLKS FE + L
Sbjct: 61  YKLPHPLQYKIIIRIHTTSQSSPMQAYNQSINDLDKELDTLKSGFEAELL 110

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224103945|ref|XP_002313254.1| predicted protein [Populus trichocarpa] gi|118484276|gb|ABK94017.1| unknown [Populus trichocarpa] gi|222849662|gb|EEE87209.1| predicted protein [Populus trichocarpa]

 Score =  213 bits (541), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 100/108 (92%), Positives = 106/108 (98%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAPDRYERFVVPEGTKKVSYERDTKIINAASFT+ERE+HTIGNILRMQLHRD+NVLFAG
Sbjct: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTVEREDHTIGNILRMQLHRDDNVLFAG 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVK 108
           YKLPHPL+YKIIVRIHTTSQSSPMQAYNQAINDLDKELD LK+AFE +
Sbjct: 61  YKLPHPLKYKIIVRIHTTSQSSPMQAYNQAINDLDKELDHLKNAFEAE 108

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388516987|gb|AFK46555.1| unknown [Lotus japonicus]

 Score =  211 bits (537), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 101/110 (91%), Positives = 104/110 (94%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIERE+HTIGNILRMQLHRD NVLFAG
Sbjct: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREDHTIGNILRMQLHRDPNVLFAG 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVKHL 110
           YKLPHPLQYKIIVRIHT SQSSPMQAYNQ+INDLDKELD LK+AFE   L
Sbjct: 61  YKLPHPLQYKIIVRIHTASQSSPMQAYNQSINDLDKELDHLKNAFEADML 110

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297819918|ref|XP_002877842.1| ATRPB13.6 [Arabidopsis lyrata subsp. lyrata] gi|297323680|gb|EFH54101.1| ATRPB13.6 [Arabidopsis lyrata subsp. lyrata]

 Score =  209 bits (532), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 98/108 (90%), Positives = 105/108 (97%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAPDRYERFVVPEGTKKVSY+RDTKIINAASFTIERE+HTIGNI+RMQLHRDENVLFAG
Sbjct: 1   MNAPDRYERFVVPEGTKKVSYDRDTKIINAASFTIEREDHTIGNIVRMQLHRDENVLFAG 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVK 108
           Y+LPHPL+YKIIVRIHTTSQSSPMQAYNQAINDLDKELD LK+ FE +
Sbjct: 61  YQLPHPLKYKIIVRIHTTSQSSPMQAYNQAINDLDKELDYLKNQFEAE 108

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147832705|emb|CAN70445.1| hypothetical protein VITISV_015574 [Vitis vinifera]

 Score =  209 bits (531), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 102/121 (84%), Positives = 107/121 (88%), Gaps = 13/121 (10%)

Query: 1   MNAPDRYERFVVPEGTKK-------------VSYERDTKIINAASFTIEREEHTIGNILR 47
           MNAPDRYERFVVPEGTKK             VSYERDTKIINAASFT+ERE+HTIGNILR
Sbjct: 1   MNAPDRYERFVVPEGTKKYIVFSLLSQKLSLVSYERDTKIINAASFTVEREDHTIGNILR 60

Query: 48  MQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEV 107
           MQLHRDENVLFAGYKLPHPLQYKII+RIHTTSQSSPMQAYNQAINDLDKELD LK+AFEV
Sbjct: 61  MQLHRDENVLFAGYKLPHPLQYKIIIRIHTTSQSSPMQAYNQAINDLDKELDYLKNAFEV 120

Query: 108 K 108
           +
Sbjct: 121 E 121

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	110
UNIPROTKB|F1PXE5	130	LOC100686835 "Uncharacterized	0.981	0.830	0.518	1.7e-27
UNIPROTKB|Q9H1A6	127	POLR2J1 "DNA-directed RNA poly	0.981	0.850	0.518	1.7e-27
UNIPROTKB|Q32P79	117	POLR2J "DNA-directed RNA polym	0.972	0.914	0.523	2.8e-27
UNIPROTKB|E2RD80	117	LOC100686835 "Uncharacterized	0.972	0.914	0.523	2.8e-27
UNIPROTKB|P52435	117	POLR2J "DNA-directed RNA polym	0.972	0.914	0.523	2.8e-27
RGD|1310198	117	Polr2j "polymerase (RNA) II (D	0.972	0.914	0.523	2.8e-27
ZFIN|ZDB-GENE-050522-120	117	polr2j "polymerase (RNA) II (D	0.972	0.914	0.504	4.5e-27
DICTYBASE|DDB_G0277677	120	rpb11 "RNA polymerase II core	0.954	0.875	0.485	5.7e-27
FB|FBgn0032634	117	Rpb11 "Rpb11" [Drosophila mela	0.963	0.905	0.528	7.3e-27
MGI|MGI:109582	117	Polr2j "polymerase (RNA) II (D	0.954	0.897	0.523	7.3e-27

UNIPROTKB|F1PXE5 LOC100686835 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 308 (113.5 bits), Expect = 1.7e-27, P = 1.7e-27
 Identities = 56/108 (51%), Positives = 78/108 (72%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct:    22 MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 81

Query:    61 YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVK 108
             YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F V+
Sbjct:    82 YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVR 129

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

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q9H1A6 POLR2J1 "DNA-directed RNA polymerase II subunit RPB11-a" [Homo sapiens (taxid:9606)]

 Score = 308 (113.5 bits), Expect = 1.7e-27, P = 1.7e-27
 Identities = 56/108 (51%), Positives = 78/108 (72%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct:     1 MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 60

Query:    61 YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVK 108
             YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F V+
Sbjct:    61 YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVR 108

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

GO:0003677 "DNA binding" evidence=IEA

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

UNIPROTKB|Q32P79 POLR2J "DNA-directed RNA polymerase II subunit RPB11" [Bos taurus (taxid:9913)]

 Score = 306 (112.8 bits), Expect = 2.8e-27, P = 2.8e-27
 Identities = 56/107 (52%), Positives = 77/107 (71%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct:     1 MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 60

Query:    61 YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEV 107
             YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F V
Sbjct:    61 YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRV 107

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

GO:0004672 "protein kinase activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

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

GO:0030275 "LRR domain binding" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2RD80 LOC100686835 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 306 (112.8 bits), Expect = 2.8e-27, P = 2.8e-27
 Identities = 56/107 (52%), Positives = 77/107 (71%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct:     1 MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 60

Query:    61 YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEV 107
             YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F V
Sbjct:    61 YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRV 107

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

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|P52435 POLR2J "DNA-directed RNA polymerase II subunit RPB11-a" [Homo sapiens (taxid:9606)]

 Score = 306 (112.8 bits), Expect = 2.8e-27, P = 2.8e-27
 Identities = 56/107 (52%), Positives = 77/107 (71%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct:     1 MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 60

Query:    61 YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEV 107
             YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F V
Sbjct:    61 YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRV 107

GO:0003677 "DNA binding" evidence=IEA

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

GO:0004672 "protein kinase activity" evidence=IDA

GO:0030275 "LRR domain binding" evidence=IPI

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

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

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

RGD|1310198 Polr2j "polymerase (RNA) II (DNA directed) polypeptide J" [Rattus norvegicus (taxid:10116)]

 Score = 306 (112.8 bits), Expect = 2.8e-27, P = 2.8e-27
 Identities = 56/107 (52%), Positives = 77/107 (71%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct:     1 MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 60

Query:    61 YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEV 107
             YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F V
Sbjct:    61 YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRV 107

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0030275 "LRR domain binding" evidence=IEA;ISO

ZFIN|ZDB-GENE-050522-120 polr2j "polymerase (RNA) II (DNA directed) polypeptide J" [Danio rerio (taxid:7955)]

 Score = 304 (112.1 bits), Expect = 4.5e-27, P = 4.5e-27
 Identities = 54/107 (50%), Positives = 77/107 (71%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAP  +E F++ EG KK++  +DTK+ NA  FT+ +E+HT+GNI+R QL +D  VLFAG
Sbjct:     1 MNAPPAFESFLLFEGEKKITITKDTKVPNACLFTLNKEDHTLGNIIRSQLLKDPQVLFAG 60

Query:    61 YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEV 107
             YK+PHPL++K+++R+ TT   SP +A+  AI DL  EL  L+  F V
Sbjct:    61 YKVPHPLEHKVVIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRV 107

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

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

GO:0003677 "DNA binding" evidence=IEA

DICTYBASE|DDB_G0277677 rpb11 "RNA polymerase II core subunit" [Dictyostelium discoideum (taxid:44689)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 51/105 (48%), Positives = 83/105 (79%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAPDR+E FV+P+G KKV+  RDTKI NA+ FTI +E+HTIGN++RMQL  D++++FAG
Sbjct:     1 MNAPDRFELFVLPDGAKKVTMVRDTKIPNASMFTILKEDHTIGNLIRMQLIADQDIIFAG 60

Query:    61 YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105
             Y++PHPL++ + +RI T + ++P++   +++  L +E  +L+++F
Sbjct:    61 YRMPHPLEHNVNIRIQTNNNTNPLECVQKSMECLSREFTSLENSF 105

GO:0046983 "protein dimerization activity" evidence=IEA

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

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

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

FB|FBgn0032634 Rpb11 "Rpb11" [Drosophila melanogaster (taxid:7227)]

 Score = 302 (111.4 bits), Expect = 7.3e-27, P = 7.3e-27
 Identities = 56/106 (52%), Positives = 77/106 (72%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAP  +E F++ EG KK+  E DTK+ NAA FTI +E+HT+GN++R QL +D NVLFAG
Sbjct:     1 MNAPPTFESFLLYEGEKKIIKELDTKVTNAAIFTINKEDHTLGNMIRNQLLKDPNVLFAG 60

Query:    61 YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE 106
             YK+PHPL++K ++RI TT+  SP +A+  AI DL  EL   +  F+
Sbjct:    61 YKVPHPLEHKFVIRIQTTADYSPQEAFMNAITDLLAELSLFEERFK 106

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

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

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

GO:0005634 "nucleus" evidence=NAS

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

GO:0003677 "DNA binding" evidence=IEA

MGI|MGI:109582 Polr2j "polymerase (RNA) II (DNA directed) polypeptide J" [Mus musculus (taxid:10090)]

 Score = 302 (111.4 bits), Expect = 7.3e-27, P = 7.3e-27
 Identities = 55/105 (52%), Positives = 76/105 (72%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct:     1 MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 60

Query:    61 YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105
             YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F
Sbjct:    61 YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERF 105

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;IDA

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

GO:0005666 "DNA-directed RNA polymerase III complex" evidence=TAS

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

GO:0030275 "LRR domain binding" evidence=ISO

---

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)
Q86JJ5	RPB11_DICDI	No assigned EC number	0.4857	0.9545	0.875	yes	no
Q9GZM3	RPB1B_HUMAN	No assigned EC number	0.5142	0.9454	0.9043	yes	no
P52435	RPB11_HUMAN	No assigned EC number	0.5233	0.9727	0.9145	yes	no
P87123	RPB11_SCHPO	No assigned EC number	0.4666	0.9454	0.8455	yes	no
Q9VJE4	RPB11_DROME	No assigned EC number	0.5283	0.9636	0.9059	yes	no
P38902	RPB11_YEAST	No assigned EC number	0.4351	0.9818	0.9	yes	no
O08740	RPB11_MOUSE	No assigned EC number	0.5238	0.9545	0.8974	yes	no
Q7PVQ9	RPB11_ANOGA	No assigned EC number	0.5333	0.9545	0.8974	yes	no
Q32P79	RPB11_BOVIN	No assigned EC number	0.5233	0.9727	0.9145	yes	no
Q60SM4	RPB11_CAEBR	No assigned EC number	0.5098	0.9181	0.8278	N/A	no
Q9XVH6	RPB11_CAEEL	No assigned EC number	0.5196	0.9181	0.8278	yes	no
Q38859	RPB11_ARATH	No assigned EC number	0.8888	0.9818	0.9310	yes	no
Q9H1A7	RPB1C_HUMAN	No assigned EC number	0.5047	0.9454	0.9043	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

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.7	0.766
4th Layer	2.7.7.6	0.824

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	110
cd06926	93	cd06926, RNAP_II_RPB11, RPB11 subunit of Eukaryoti	2e-47
pfam13656	77	pfam13656, RNA_pol_L_2, RNA polymerase Rpb3/Rpb11	8e-24
COG1761	99	COG1761, RPB11, DNA-directed RNA polymerase, subun	7e-19
cd07029	85	cd07029, RNAP_I_III_AC19, AC19 subunit of Eukaryot	1e-16
cd07027	83	cd07027, RNAP_RPB11_like, RPB11 subunit of RNA pol	3e-16
PRK01146	85	PRK01146, PRK01146, DNA-directed RNA polymerase su	2e-12
pfam01193	88	pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 di	2e-11
cd06927	83	cd06927, RNAP_L, L subunit of Archaeal RNA polymer	3e-11
cd00460	86	cd00460, RNAP_RPB11_RPB3, RPB11 and RPB3 subunits	1e-08

>gnl|CDD|132902 cd06926, RNAP_II_RPB11, RPB11 subunit of Eukaryotic RNA polymerase II

 Score =  146 bits (371), Expect = 2e-47
 Identities = 53/93 (56%), Positives = 70/93 (75%)

Query: 13  PEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKII 72
           PEG KK++ ++DTK+ NAA+FTI +E+HT+GN+LRMQL +D NVLFAGYK+PHPL++KI 
Sbjct: 1   PEGEKKITEKKDTKVPNAATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIE 60

Query: 73  VRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105
           +RI T    +P +A   AI DL  EL  LK  F
Sbjct: 61  LRIQTDGSITPKEALKNAITDLISELSLLKEEF 93

The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. Length = 93

>gnl|CDD|222292 pfam13656, RNA_pol_L_2, RNA polymerase Rpb3/Rpb11 dimerisation domain

 Score = 86.1 bits (214), Expect = 8e-24
 Identities = 36/77 (46%), Positives = 50/77 (64%)

Query: 29  NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYN 88
           N A+F IE E+HT+GN+LR +L +D +V FAGY +PHPL+ KI +RI T S   P+    
Sbjct: 1   NEATFEIEGEDHTLGNLLREELLKDPDVEFAGYSVPHPLEDKINLRIQTKSGKDPLDVLK 60

Query: 89  QAINDLDKELDTLKSAF 105
           +A+ DL    D L+  F
Sbjct: 61  EALEDLISICDELEKEF 77

The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Many of the members of this family carry only the N-terminal region of Rpb11. Length = 77

>gnl|CDD|224675 COG1761, RPB11, DNA-directed RNA polymerase, subunit L [Transcription]

 Score = 74.3 bits (183), Expect = 7e-19
 Identities = 34/92 (36%), Positives = 50/92 (54%)

Query: 15  GTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVR 74
            T ++      K  N+    IE E+HT+GN+LR +L +DE+V FA Y +PHPL     +R
Sbjct: 1   MTPEMELRIIKKDDNSLELEIEGEDHTLGNLLREELLKDEDVEFAAYSIPHPLIDNPKIR 60

Query: 75  IHTTSQSSPMQAYNQAINDLDKELDTLKSAFE 106
           I T     P +A  +A   + K+L+ L   FE
Sbjct: 61  IKTKGGVDPKEALKRAARKILKDLEELLDQFE 92

Length = 99

>gnl|CDD|132907 cd07029, RNAP_I_III_AC19, AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

 Score = 68.0 bits (167), Expect = 1e-16
 Identities = 26/77 (33%), Positives = 42/77 (54%)

Query: 29  NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYN 88
           + A+F    E+HT+GN LR  + ++  V F GY +PHP + KI +RI T      +    
Sbjct: 9   SCATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSIPHPSENKINLRIQTKGGEPAVDVLK 68

Query: 89  QAINDLDKELDTLKSAF 105
           + + DL++  D + S F
Sbjct: 69  KGLEDLEQICDHILSTF 85

The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to associate with the RPB3 counterpart, AC40, to form a heterodimer, which stabilizes the association of the two largest subunits of RNAP I and RNAP III. Length = 85

>gnl|CDD|132905 cd07027, RNAP_RPB11_like, RPB11 subunit of RNA polymerase

 Score = 67.2 bits (164), Expect = 3e-16
 Identities = 30/75 (40%), Positives = 46/75 (61%)

Query: 29  NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYN 88
           N+ +  +E E+HT+GN+LR +L +D+ V FA Y + HP+  KI +RI T S   P  A  
Sbjct: 9   NSVTVEMENEDHTLGNLLREELLKDDQVDFARYYIKHPVIDKIQIRIQTKSGIKPKDALK 68

Query: 89  QAINDLDKELDTLKS 103
           +A+N L K  + L +
Sbjct: 69  RAVNKLSKLYEHLGT 83

The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts. Length = 83

>gnl|CDD|234909 PRK01146, PRK01146, DNA-directed RNA polymerase subunit L; Provisional

 Score = 57.2 bits (139), Expect = 2e-12
 Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 4/82 (4%)

Query: 26  KII----NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQS 81
           K++    N     IE E+HT+ N+L+ +L  D  V  A Y + HPL    +++I T    
Sbjct: 4   KVLEKEDNELELEIEGEDHTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLKIKTDGGI 63

Query: 82  SPMQAYNQAINDLDKELDTLKS 103
            P++A  +A   +    D    
Sbjct: 64  DPLEALKEAAKRIIDLCDEFLD 85

Length = 85

>gnl|CDD|216354 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimerisation domain

 Score = 54.9 bits (133), Expect = 2e-11
 Identities = 29/88 (32%), Positives = 43/88 (48%), Gaps = 19/88 (21%)

Query: 31 ASFTIEREEHTIGNILRMQLHRD-ENVLFAGYKLPHPLQY------------------KI 71
            F +E E+HT+GN LR  L  D   V  AG K+PHP ++                  K+
Sbjct: 1  IEFLLEGEDHTLGNALRRVLLSDVPGVAIAGVKIPHPAKFSPVKKVNYRVVGVGTDYDKL 60

Query: 72 IVRIHTTSQSSPMQAYNQAINDLDKELD 99
          I+RI T    +P +A  +A+  L ++LD
Sbjct: 61 ILRIETDGSITPEEALKEALKILIEKLD 88

The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Length = 88

>gnl|CDD|132903 cd06927, RNAP_L, L subunit of Archaeal RNA polymerase

 Score = 54.5 bits (132), Expect = 3e-11
 Identities = 22/71 (30%), Positives = 35/71 (49%)

Query: 33  FTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAIN 92
             IE E+HT+ N+L+ +L RD  V  A Y + HPL    +++I T     P++A  +A  
Sbjct: 13  LEIEGEDHTLLNLLKEELLRDPGVKVASYDIEHPLLSNPVLKIKTDGGVDPLEALKEAAK 72

Query: 93  DLDKELDTLKS 103
            L    +    
Sbjct: 73  RLIDLCEEFLD 83

The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer. Length = 83

>gnl|CDD|132901 cd00460, RNAP_RPB11_RPB3, RPB11 and RPB3 subunits of RNA polymerase

 Score = 47.8 bits (114), Expect = 1e-08
 Identities = 29/79 (36%), Positives = 42/79 (53%), Gaps = 7/79 (8%)

Query: 29  NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQY------KIIVRIHTTSQSS 82
           N   F +E E+HT+GN LR  L +   V FA Y + HP++       K I+RI T     
Sbjct: 9   NYVDFVLENEDHTLGNSLRRILLKSP-VEFAAYYVEHPVKLQRTDEDKFILRIETVGSIP 67

Query: 83  PMQAYNQAINDLDKELDTL 101
           P +A  +A+  L K+L+ L
Sbjct: 68  PEEALRRAVEILRKKLEHL 86

The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts. Length = 86

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	110
KOG4392	117	consensus RNA polymerase, subunit L [Transcription	100.0
cd06926	93	RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA poly	100.0
PF13656	77	RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisatio	100.0
cd07029	85	RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA pol	100.0
PRK01146	85	DNA-directed RNA polymerase subunit L; Provisional	100.0
cd06927	83	RNAP_L L subunit of Archaeal RNA polymerase. The a	100.0
cd07027	83	RNAP_RPB11_like RPB11 subunit of RNA polymerase. T	100.0
COG1761	99	RPB11 DNA-directed RNA polymerase, subunit L [Tran	100.0
KOG3438	105	consensus DNA-directed RNA polymerase, subunit L [	99.97
cd00460	86	RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA pol	99.94
PF01193	66	RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation	99.7
PRK14979	195	DNA-directed RNA polymerase subunit D; Provisional	95.97
cd06928	215	RNAP_alpha_NTD N-terminal domain of the Alpha subu	95.67
cd07028	212	RNAP_RPB3_like RPB3 subunit of RNA polymerase. The	95.62
smart00662	224	RPOLD RNA polymerases D. DNA-directed RNA polymera	95.35
TIGR02027	297	rpoA DNA-directed RNA polymerase, alpha subunit, b	95.29
PRK00783	263	DNA-directed RNA polymerase subunit D; Provisional	95.09
PRK05182	310	DNA-directed RNA polymerase subunit alpha; Provisi	94.65
CHL00013	327	rpoA RNA polymerase alpha subunit	94.61
cd07030	259	RNAP_D D subunit of Archaeal RNA polymerase. The D	94.33
CHL00013	327	rpoA RNA polymerase alpha subunit	94.11
PRK05182	310	DNA-directed RNA polymerase subunit alpha; Provisi	94.1
cd06928	215	RNAP_alpha_NTD N-terminal domain of the Alpha subu	93.44
cd07028	212	RNAP_RPB3_like RPB3 subunit of RNA polymerase. The	93.25
cd07031	265	RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polyme	93.19
PRK14979	195	DNA-directed RNA polymerase subunit D; Provisional	92.0
cd07031	265	RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polyme	91.93
COG0202	317	RpoA DNA-directed RNA polymerase, alpha subunit/40	90.94
smart00662	224	RPOLD RNA polymerases D. DNA-directed RNA polymera	90.6
PRK00783	263	DNA-directed RNA polymerase subunit D; Provisional	90.39
cd07030	259	RNAP_D D subunit of Archaeal RNA polymerase. The D	88.04
cd07032	291	RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA poly	85.41
TIGR02027	297	rpoA DNA-directed RNA polymerase, alpha subunit, b	84.69

>KOG4392 consensus RNA polymerase, subunit L [Transcription]

Probab=100.00  E-value=7.4e-45  Score=252.44  Aligned_cols=110  Identities=52%  Similarity=0.839  Sum_probs=108.8

Q ss_pred             CCCCccccceecCCCceeeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCC
Q 033845            1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQ   80 (110)
Q Consensus         1 mn~p~~~~~~~l~~~~~Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~   80 (110)
                      ||||+|||+|+|.+|++||+|.+|+|.+|++.|+|++|||||||+||.+|+++|+|.||||++|||++.++.|||||+.+
T Consensus         1 MNaP~~fE~fll~eg~kKvtin~DtKvpNA~~fTiekEDHTLGNii~~qLl~D~~vLFagYkvpHPl~~~~~LRiqtt~d   80 (117)
T KOG4392|consen    1 MNAPPAFESFLLFEGEKKITINKDTKVPNAALFTIEKEDHTLGNIIKSQLLKDPRVLFAGYKVPHPLEHKIILRVQTTED   80 (117)
T ss_pred             CCCchhhhhheeccCCceeEEecCCCCCceEEEEEecccchHHHHHHHHHccCccceEeeecCCCcccccEEEEEecCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHhhhC
Q 033845           81 SSPMQAYNQAINDLDKELDTLKSAFEVKHL  110 (110)
Q Consensus        81 ~~P~~al~~a~~~l~~~~~~l~~~f~~~~~  110 (110)
                      ++|.++|.+|+.++...++.++.+|+.+|.
T Consensus        81 ~~p~~al~~a~~~l~~el~~l~~~f~~~~~  110 (117)
T KOG4392|consen   81 CSPADALTNAITDLIEELSLLENRFKAEAA  110 (117)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999999983

>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II

Probab=100.00  E-value=2.7e-39  Score=219.02  Aligned_cols=93  Identities=57%  Similarity=0.903  Sum_probs=91.1

Q ss_pred             CCCceeeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHH
Q 033845           13 PEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAIN   92 (110)
Q Consensus        13 ~~~~~Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~   92 (110)
                      |||++||++..+++++|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++.+|.+||++|++
T Consensus         1 ~~~~~kv~~~~d~k~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~fagY~vpHPl~~~~~l~i~t~~~~~p~~al~~a~~   80 (93)
T cd06926           1 PEGEKKITEKKDTKVPNAATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIELRIQTDGSITPKEALKNAIT   80 (93)
T ss_pred             CCCccceEEeecCCCCcEEEEEEeCCCchHHHHHHHHHhcCCCeeEEeeccCCCCCCceEEEEEeCCCCCHHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999998999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 033845           93 DLDKELDTLKSAF  105 (110)
Q Consensus        93 ~l~~~~~~l~~~f  105 (110)
                      +|.+.|+++++.|
T Consensus        81 ~l~~~~~~~~~~f   93 (93)
T cd06926          81 DLISELSLLKEEF   93 (93)
T ss_pred             HHHHHHHHHHhhC
Confidence            9999999999876

The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.

>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K

Probab=100.00  E-value=1.8e-36  Score=198.86  Aligned_cols=77  Identities=47%  Similarity=0.788  Sum_probs=72.8

Q ss_pred             ceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 033845           29 NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF  105 (110)
Q Consensus        29 n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~~f  105 (110)
                      |+++|+|.||||||||+||++|+++|+|.||||++||||+++++|||||+++.+|.+||++|+++|+++|++++++|
T Consensus         1 n~~~f~i~~EDHTlgNlLr~~L~~~p~V~fagY~vpHPl~~~i~l~Iqt~~~~~p~~~l~~a~~~l~~~~~~l~~~F   77 (77)
T PF13656_consen    1 NEITFTIYGEDHTLGNLLRYELLKDPDVEFAGYRVPHPLENKINLRIQTKGGITPIEALKKALEDLIKICEELKKEF   77 (77)
T ss_dssp             TEEEEEEES--HHHHHHHHHCCTTSTTEEEEEEEESETTSSEEEEEEEESTTS-HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHHHHHHHHHhhCCCeEEEEeccCCCCCCceEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999987

...

>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

Probab=100.00  E-value=3.6e-36  Score=200.83  Aligned_cols=82  Identities=32%  Similarity=0.575  Sum_probs=79.5

Q ss_pred             cCCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033845           24 DTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS  103 (110)
Q Consensus        24 ~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~  103 (110)
                      .++.+|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++.+|.+||++|+++|++.|+++++
T Consensus         4 ~~~~~n~~~~~i~~EdHTLgNlLr~~L~~~p~V~fagY~vpHPl~~~~~lriqT~~~~~p~~al~~a~~~l~~~~~~~~~   83 (85)
T cd07029           4 EGTDESCATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSIPHPSENKINLRIQTKGGEPAVDVLKKGLEDLEQICDHILS   83 (85)
T ss_pred             ccCCCCeEEEEEeCCCcchHHHHHHHHhhCCCceEEeecccCCCCCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            46899999999999999999999999999999999999999999999999999999899999999999999999999998


Q ss_pred             HH
Q 033845          104 AF  105 (110)
Q Consensus       104 ~f  105 (110)
                      .|
T Consensus        84 ~f   85 (85)
T cd07029          84 TF   85 (85)
T ss_pred             cC
Confidence            76

The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass

>PRK01146 DNA-directed RNA polymerase subunit L; Provisional

Probab=100.00  E-value=2.2e-35  Score=197.09  Aligned_cols=80  Identities=29%  Similarity=0.392  Sum_probs=77.0

Q ss_pred             cCCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033845           24 DTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS  103 (110)
Q Consensus        24 ~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~  103 (110)
                      .++.+|+++|+|.||||||||+||++|+++|+|.||||++|||++++++|||||+++.+|.+||++|+++|++.|++|++
T Consensus         6 i~~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqt~~~~~p~~al~~a~~~L~~~~~~~~~   85 (85)
T PRK01146          6 LEKEDNELELEIEGEDHTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLKIKTDGGIDPLEALKEAAKRIIDLCDEFLD   85 (85)
T ss_pred             EecCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEeecCCCCCCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999999863

>cd06927 RNAP_L L subunit of Archaeal RNA polymerase

Probab=100.00  E-value=5e-35  Score=194.60  Aligned_cols=78  Identities=31%  Similarity=0.446  Sum_probs=75.9

Q ss_pred             CCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q 033845           25 TKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLK  102 (110)
Q Consensus        25 ~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~  102 (110)
                      ++.+|+++|+|.||||||||+||++|+++|+|.||||++|||++++++|||||+++.+|.+||++|+++|++.|++|+
T Consensus         5 ~~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~p~~al~~a~~~l~~~~~~~~   82 (83)
T cd06927           5 EKEDNELELEIEGEDHTLLNLLKEELLRDPGVKVASYDIEHPLLSNPVLKIKTDGGVDPLEALKEAAKRLIDLCEEFL   82 (83)
T ss_pred             EcCCCEEEEEEeCCCchHHHHHHHHHhcCCCeEEEEeecCCCCCCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            468999999999999999999999999999999999999999999999999999989999999999999999999986

The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.

>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase

Probab=100.00  E-value=9.7e-35  Score=193.20  Aligned_cols=78  Identities=40%  Similarity=0.614  Sum_probs=75.5

Q ss_pred             CCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q 033845           25 TKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLK  102 (110)
Q Consensus        25 ~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~  102 (110)
                      ++.+|+++|+|.||||||||+||++|+++|+|.||||++|||++++++|||||+++.+|.+||++|+++|.+.|++++
T Consensus         5 ~~~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrI~T~~~~~P~~al~~a~~~l~~~~~~l~   82 (83)
T cd07027           5 SKEKNSVTVEMENEDHTLGNLLREELLKDDQVDFARYYIKHPVIDKIQIRIQTKSGIKPKDALKRAVNKLSKLYEHLG   82 (83)
T ss_pred             ecCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEEecCCCCCCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHhc
Confidence            467899999999999999999999999999999999999999999999999999989999999999999999999885

The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/

>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]

Probab=100.00  E-value=8.9e-34  Score=194.16  Aligned_cols=93  Identities=35%  Similarity=0.532  Sum_probs=88.6

Q ss_pred             ceeeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHH
Q 033845           16 TKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLD   95 (110)
Q Consensus        16 ~~Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l~   95 (110)
                      .++.++...++.+|+++|++.||||||||+||++|+++++|+||||+||||+.+.+.+||||+++++|++||++|++.++
T Consensus         2 ~~~~~l~ii~~~~n~~~i~i~gEdHTL~NlL~~~L~~d~~V~~a~Y~i~HP~~~~~~i~Ikt~~~~dp~~aL~~A~~~i~   81 (99)
T COG1761           2 TPEMELRIIKKDDNSLELEIEGEDHTLGNLLREELLKDEDVEFAAYSIPHPLIDNPKIRIKTKGGVDPKEALKRAARKIL   81 (99)
T ss_pred             CCceEEEEeccCCCEEEEEEecCCchHHHHHHHHHhCCCCeeEEEEeCCCCCCCCceEEEEECCCCCHHHHHHHHHHHHH
Confidence            46677777789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhh
Q 033845           96 KELDTLKSAFEVKH  109 (110)
Q Consensus        96 ~~~~~l~~~f~~~~  109 (110)
                      +.|++|..+| ++|
T Consensus        82 ~~~~~l~~~~-~~~   94 (99)
T COG1761          82 KDLEELLDQF-EEF   94 (99)
T ss_pred             HHHHHHHHHH-HHH
Confidence            9999999988 776

>KOG3438 consensus DNA-directed RNA polymerase, subunit L [Transcription]

Probab=99.97  E-value=7.5e-32  Score=184.61  Aligned_cols=84  Identities=31%  Similarity=0.594  Sum_probs=80.9

Q ss_pred             CCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 033845           26 KIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF  105 (110)
Q Consensus        26 k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~~f  105 (110)
                      .+.++++|++..|||||||.||+.|+++|.|+||||+||||+++++.|||||.++..+.++|++|+++|+..|+++..+|
T Consensus        13 ~d~~~~Tf~~~eEDHTlgNalR~vI~k~peVefcGYtIPHPse~k~niRIQt~~~~~A~evl~kgl~el~~~c~~v~~kF   92 (105)
T KOG3438|consen   13 TDLSSATFQLREEDHTLGNALRYVIMKNPEVEFCGYTIPHPSEDKINIRIQTRDGDPAVEVLKKGLEELMQLCDHVRSKF   92 (105)
T ss_pred             cCCCceEEEEEecCcchhHHHHHHHhcCCceEEEeccCCCCchhhheEEEEecCCCcchHHHHHHHHHHHHHHHHHHHHH
Confidence            37799999999999999999999999999999999999999999999999999888899999999999999999999999


Q ss_pred             Hhhh
Q 033845          106 EVKH  109 (110)
Q Consensus       106 ~~~~  109 (110)
                      ++++
T Consensus        93 ~~~i   96 (105)
T KOG3438|consen   93 EEEI   96 (105)
T ss_pred             HHHH
Confidence            9875

>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase

Probab=99.94  E-value=1.7e-26  Score=153.68  Aligned_cols=76  Identities=39%  Similarity=0.592  Sum_probs=72.8

Q ss_pred             CCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCC------CcceEEEEEeCCCCCHHHHHHHHHHHHHHHH
Q 033845           25 TKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPL------QYKIIVRIHTTSQSSPMQAYNQAINDLDKEL   98 (110)
Q Consensus        25 ~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl------~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~   98 (110)
                      .+.+|+++|+|.||||||||+||++|++ +.|.||||+||||+      .+++.|+|+|+|+.+|.+||.+|++.|.+.|
T Consensus         5 ~~~~~~~~~~~~~edhTl~n~L~~~l~~-~pV~~a~Y~v~hp~~~~~~~~d~~~~~VeT~Gs~~P~~al~~Ai~~L~~~~   83 (86)
T cd00460           5 EKEKNYVDFVLENEDHTLGNSLRRILLK-SPVEFAAYYVEHPVKLQRTDEDKFILRIETVGSIPPEEALRRAVEILRKKL   83 (86)
T ss_pred             cCCCCEEEEEEeCCCchHHHHHHHHHhC-CCceEEEEEeCCCccCCCCCCCeEEEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            5678999999999999999999999999 99999999999999      9999999999999999999999999999998


Q ss_pred             HHH
Q 033845           99 DTL  101 (110)
Q Consensus        99 ~~l  101 (110)
                      +.|
T Consensus        84 ~~~   86 (86)
T cd00460          84 EHL   86 (86)
T ss_pred             hhC
Confidence            764

The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the

>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2

Probab=99.70  E-value=1.6e-17  Score=105.25  Aligned_cols=65  Identities=35%  Similarity=0.556  Sum_probs=61.1

Q ss_pred             eEEEEccCCcchHHHHHHHHhcC-CCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 033845           31 ASFTIEREEHTIGNILRMQLHRD-ENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELD   99 (110)
Q Consensus        31 ~~~~i~~EDHTlgNlLr~~L~~~-~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~   99 (110)
                      ++|.+.|+|||+||+||..|+++ |+|.+++    ||..+++.++|+|+|+.+|.++|.+|++.|++.|+
T Consensus         1 i~~~~~g~~~tl~N~LRr~ll~~vp~~ai~~----~~~~~~~~~~IeT~g~~~p~~~l~~A~~~l~~~~~   66 (66)
T PF01193_consen    1 IEFLLKGEDHTLGNALRRILLSEVPGVAIDG----HPNEDKFVFRIETDGSLTPKEALLKAIKILKEKLN   66 (66)
T ss_dssp             EEEEEESHHHHHHHHHHHHHHSSSEEEEEEE----SSEEEEEEEEEEEBSSS-HHHHHHHHHHHHHHHHC
T ss_pred             CEeEEcCCchHHHHHHHHHHHhcCCCceEEe----cCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHhcC
Confidence            57999999999999999999999 9999999    99999999999999999999999999999998773

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....

>PRK14979 DNA-directed RNA polymerase subunit D; Provisional

Probab=95.97  E-value=0.037  Score=42.06  Aligned_cols=51  Identities=14%  Similarity=0.147  Sum_probs=42.3

Q ss_pred             CCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033845           53 DENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEV  107 (110)
Q Consensus        53 ~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~~f~~  107 (110)
                      .| |. |.|+..-  .++..|.|.|+|+.+|.+||..|++-|.+.++.|.+.+..
T Consensus       138 ~p-vd-a~y~~~~--~dkl~leIeTdGsi~P~~al~~Aa~iL~~~l~~~~~~l~~  188 (195)
T PRK14979        138 QP-CN-AVYKQIS--NDEVEFKVESFGQMDAEDILRSALEILKNKAEKFLQELEG  188 (195)
T ss_pred             cc-ee-eEEecCC--CcEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            45 44 5564322  4899999999999999999999999999999999988764

>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase

Probab=95.67  E-value=0.024  Score=43.25  Aligned_cols=45  Identities=27%  Similarity=0.240  Sum_probs=37.3

Q ss_pred             CeeeeeeeCCC------CCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 033845           55 NVLFAGYKLPH------PLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELD   99 (110)
Q Consensus        55 ~V~fAgY~vpH------Pl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~   99 (110)
                      =|.-+.|.|.-      .-.+++.|-|.|+|+++|.+||..|++.|.+.+.
T Consensus       163 PV~~vny~v~~~~~~~~~~~e~L~leI~TnGsi~P~~Al~~A~~il~~~~~  213 (215)
T cd06928         163 PVRKVNYSVESTRVGQRTDYEKLILEIWTNGSISPEEALAQAAKILINHFS  213 (215)
T ss_pred             CeEEEEEEEEEeecCCCCCceeEEEEEEECCCCCHHHHHHHHHHHHHHHhh
Confidence            36677888643      3357899999999999999999999999988775

The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac

>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase

Probab=95.62  E-value=0.039  Score=42.20  Aligned_cols=52  Identities=17%  Similarity=0.262  Sum_probs=43.9

Q ss_pred             hcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033845           51 HRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS  103 (110)
Q Consensus        51 ~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~  103 (110)
                      -+-.=|.-|+|++. |-.++..|.|-|+|+.+|.+|+.+|++-|++.++.|.+
T Consensus       160 Ak~sPV~~v~y~~~-~~~d~li~~VeT~Gsi~p~~~l~~A~~iL~~~~~~~~~  211 (212)
T cd07028         160 AKFGPVAAIEFRYD-PVADTYIMNVESVGSLPPDQVVVEAIKTLQKKVASILL  211 (212)
T ss_pred             CEeCCceEEEEEEE-ccCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHhh
Confidence            34455677889864 36689999999999999999999999999999998875

The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and

>smart00662 RPOLD RNA polymerases D

Probab=95.35  E-value=0.039  Score=42.21  Aligned_cols=46  Identities=24%  Similarity=0.299  Sum_probs=38.0

Q ss_pred             CeeeeeeeCCCCC----------------CcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Q 033845           55 NVLFAGYKLPHPL----------------QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDT  100 (110)
Q Consensus        55 ~V~fAgY~vpHPl----------------~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~  100 (110)
                      .|..+.|.+.-|-                .+++.|.|.|+|..+|.+||.+|++-|...++.
T Consensus       162 pv~~v~~~~~~~~~~~~~~~~~~c~~~~~~d~l~f~IeT~G~i~p~~al~~A~~iL~~k~~~  223 (224)
T smart00662      162 PVDRVAYQVECPRVVQRTDCCRECDEGEEYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEA  223 (224)
T ss_pred             hhhheeeeccCCccceecccchhhhccCCCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHhh
Confidence            3555667776664                478999999999999999999999999888764

DNA-directed RNA polymerase subunit D and bacterial alpha chain

>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type

Probab=95.29  E-value=0.06  Score=43.06  Aligned_cols=49  Identities=24%  Similarity=0.310  Sum_probs=40.4

Q ss_pred             CeeeeeeeCCC------CCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033845           55 NVLFAGYKLPH------PLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS  103 (110)
Q Consensus        55 ~V~fAgY~vpH------Pl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~  103 (110)
                      -|.-+.|.|..      ...+.+.|.|.|+|+++|.+||.+|++-|.+.|..|.+
T Consensus       154 PV~~Vny~ve~~rv~~~~~~d~li~eIeT~Gsi~P~~al~~A~~iL~~~~~~~~~  208 (297)
T TIGR02027       154 PVLKVNYEVENTRVGQRTDYDKLILEIETNGSITPKDAIAEAAKILIEHLEPFVN  208 (297)
T ss_pred             CeEEEEEEEeeeeccCCccccEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            35667787653      22468999999999999999999999999999988854

This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.

>PRK00783 DNA-directed RNA polymerase subunit D; Provisional

Probab=95.09  E-value=0.029  Score=43.54  Aligned_cols=36  Identities=17%  Similarity=0.172  Sum_probs=29.5

Q ss_pred             eeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcC-CC
Q 033845           18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-EN   55 (110)
Q Consensus        18 Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~-~~   55 (110)
                      ++++.+.  .++.++|.+.|-++|+||+||-.|+.. |.
T Consensus         2 ~~~~~~~--~~~~~~f~~~g~~~t~~NalRRvlls~vp~   38 (263)
T PRK00783          2 EIEILEL--DDRSARFVVEGVTPAFANAIRRAMIADVPT   38 (263)
T ss_pred             ceEEEEc--CCcEEEEEEeCCCHHHHHHHHHHHHHcCCe
Confidence            4566654  558899999999999999999999985 44

>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional

Probab=94.65  E-value=0.1  Score=42.02  Aligned_cols=50  Identities=20%  Similarity=0.228  Sum_probs=40.8

Q ss_pred             CCeeeeeeeCCCC------CCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033845           54 ENVLFAGYKLPHP------LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS  103 (110)
Q Consensus        54 ~~V~fAgY~vpHP------l~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~  103 (110)
                      .-|.-+.|.+.-.      -.+++.|.|.|+|+++|.+||.+|++.|...+..|.+
T Consensus       170 ~PV~~vny~ve~~~~~~~~~~e~L~leI~TnGsi~P~eAl~~A~~iL~~~l~~f~~  225 (310)
T PRK05182        170 SPVKKVNYTVENTRVGQRTDYDKLILEVETDGSITPEEALALAAKILVEQLSVFVD  225 (310)
T ss_pred             CCccceEEEecccccCCCCcceEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence            3366678876542      1468999999999999999999999999999887754

>CHL00013 rpoA RNA polymerase alpha subunit

Probab=94.61  E-value=0.094  Score=42.67  Aligned_cols=50  Identities=18%  Similarity=0.152  Sum_probs=41.2

Q ss_pred             CCeeeeeeeCCCC-----CCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033845           54 ENVLFAGYKLPHP-----LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS  103 (110)
Q Consensus        54 ~~V~fAgY~vpHP-----l~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~  103 (110)
                      .=|.-+.|.|..-     ..+++.|-|.|+|+++|.+||..|++.|.+.+.-|.+
T Consensus       169 sPV~kVny~Ve~~~~~~~~~e~L~lEI~TnGsi~P~~Al~~Aa~il~~~~~~~~~  223 (327)
T CHL00013        169 MPVRNVNYSIHSYGNGNEKQEILFLEIWTNGSITPKEALHEASRNLIDLFIPFLH  223 (327)
T ss_pred             CCeeEEEEEEEEcccCCcccceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            3466777887651     2578999999999999999999999999999887753

>cd07030 RNAP_D D subunit of Archaeal RNA polymerase

Probab=94.33  E-value=0.061  Score=41.69  Aligned_cols=36  Identities=14%  Similarity=0.167  Sum_probs=29.7

Q ss_pred             eeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcC-CC
Q 033845           18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-EN   55 (110)
Q Consensus        18 Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~-~~   55 (110)
                      +|++.+  ..++.++|.+.|-|+|+||+||-.|+.. |.
T Consensus         2 ~~~~~~--~~~~~~~f~~~g~~~s~~NalRRills~vp~   38 (259)
T cd07030           2 EIEVLE--LDDDRARFVLEGVPPAFANAIRRAIISEVPT   38 (259)
T ss_pred             ceEEEe--cCCCEEEEEEeCCCHHHHHHHHHHHHhcCCe
Confidence            456665  3568999999999999999999999985 44

The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w

>CHL00013 rpoA RNA polymerase alpha subunit

Probab=94.11  E-value=0.12  Score=42.16  Aligned_cols=48  Identities=25%  Similarity=0.237  Sum_probs=38.6

Q ss_pred             eeEeeecCCCcceeEEEE----ccCCcchHHHHHHHHhc-CCCeeeeeeeCCC
Q 033845           18 KVSYERDTKIINAASFTI----EREEHTIGNILRMQLHR-DENVLFAGYKLPH   65 (110)
Q Consensus        18 Ki~~~~~~k~~n~~~~~i----~~EDHTlgNlLr~~L~~-~~~V~fAgY~vpH   65 (110)
                      -++........+.+.|.|    .|..|||||+||-.|++ .|+.-+.+-++.+
T Consensus         9 ~ie~~~~~~~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~g   61 (327)
T CHL00013          9 CVESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEG   61 (327)
T ss_pred             ceeEEEecCCCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECC
Confidence            355666677889999999    67889999999999998 4877777767654

>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional

Probab=94.10  E-value=0.13  Score=41.46  Aligned_cols=47  Identities=26%  Similarity=0.311  Sum_probs=35.8

Q ss_pred             eeEeeecCCCcceeEEEEc----cCCcchHHHHHHHHhcC-CCeeeeeeeCC
Q 033845           18 KVSYERDTKIINAASFTIE----REEHTIGNILRMQLHRD-ENVLFAGYKLP   64 (110)
Q Consensus        18 Ki~~~~~~k~~n~~~~~i~----~EDHTlgNlLr~~L~~~-~~V~fAgY~vp   64 (110)
                      ++++...+..++.+.|.+.    |.++|+||+||-.|+.. |+.-.-+-++.
T Consensus         8 ~i~~~e~~~~~~~~~F~i~Ple~G~g~tlgNaLRRvLLs~ipg~aI~~VkI~   59 (310)
T PRK05182          8 KIEVEEESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKID   59 (310)
T ss_pred             EEEEEeccCCCcEEEEEEeccCCCchhHHHHHHHHHHHhcCCeeEEEEEEEc
Confidence            4555544335799999996    99999999999999984 76666665554

>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase

Probab=93.44  E-value=0.14  Score=39.12  Aligned_cols=40  Identities=28%  Similarity=0.331  Sum_probs=31.6

Q ss_pred             CCCcceeEEEE----ccCCcchHHHHHHHHhcC-CCeeeeeeeCC
Q 033845           25 TKIINAASFTI----EREEHTIGNILRMQLHRD-ENVLFAGYKLP   64 (110)
Q Consensus        25 ~k~~n~~~~~i----~~EDHTlgNlLr~~L~~~-~~V~fAgY~vp   64 (110)
                      +..++.+.|.|    .|.++|+||+||-.|+.. |+.-.-+-++.
T Consensus         5 ~~~~~~~~F~i~pl~~g~~~tlgNaLRRvLLs~ipg~aI~~v~I~   49 (215)
T cd06928           5 NKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIE   49 (215)
T ss_pred             cCCCcEEEEEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEEEEEc
Confidence            44578999999    789999999999999984 66655555543

The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac

>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase

Probab=93.25  E-value=0.11  Score=39.84  Aligned_cols=32  Identities=13%  Similarity=0.208  Sum_probs=28.0

Q ss_pred             CCCcceeEEEEccCCcchHHHHHHHHhcC-CCe
Q 033845           25 TKIINAASFTIEREEHTIGNILRMQLHRD-ENV   56 (110)
Q Consensus        25 ~k~~n~~~~~i~~EDHTlgNlLr~~L~~~-~~V   56 (110)
                      .+.++.++|.+.|-|+|+||+||-.|+.. |..
T Consensus         7 ~~~~~~~~f~l~g~~~t~aNaLRRiLLsevP~~   39 (212)
T cd07028           7 EADKDNVDFILSGVDLAMANALRRVMIAEVPTM   39 (212)
T ss_pred             EcCCCEEEEEEEccChhHHHHHHHHHHHcCcce
Confidence            46889999999999999999999999985 543

The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and

>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II

Probab=93.19  E-value=0.28  Score=38.59  Aligned_cols=40  Identities=20%  Similarity=0.227  Sum_probs=37.0

Q ss_pred             CcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033845           68 QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEV  107 (110)
Q Consensus        68 ~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~~f~~  107 (110)
                      .+.+.|.|-|.|..+|.++|.+|++-|.+.++.+.+.+..
T Consensus       225 ~~~fiF~VES~Gsl~p~~Iv~~Al~iL~~K~~~l~~~l~~  264 (265)
T cd07031         225 PDKFYFNVESTGALPPEQIVLSGLEILKKKLADLQLQLSE  264 (265)
T ss_pred             CCEEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            5779999999999999999999999999999999998764

The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.

>PRK14979 DNA-directed RNA polymerase subunit D; Provisional

Probab=92.00  E-value=0.21  Score=37.97  Aligned_cols=39  Identities=13%  Similarity=0.198  Sum_probs=31.2

Q ss_pred             eeecCCCcceeEEEEccCCcchHHHHHHHHhcC-CCeeeee
Q 033845           21 YERDTKIINAASFTIEREEHTIGNILRMQLHRD-ENVLFAG   60 (110)
Q Consensus        21 ~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~-~~V~fAg   60 (110)
                      +..-+|..+.++|.+. -+.|+||+||-.|+.. |+.-.-+
T Consensus         6 ~~~~~~~~~~~~f~l~-~~~tlgNaLRRvLLssipg~AI~~   45 (195)
T PRK14979          6 EKEKTRIGEEFKFSLK-APISFSSALRRIMISEVPTYAIEN   45 (195)
T ss_pred             eeeeccCCcEEEEEEE-cCccHHHHHHHHHHhcCcceeEEE
Confidence            3344788999999999 9999999999999984 6544444

>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II

Probab=91.93  E-value=0.43  Score=37.57  Aligned_cols=38  Identities=16%  Similarity=0.274  Sum_probs=30.5

Q ss_pred             eeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcC-CCee
Q 033845           18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-ENVL   57 (110)
Q Consensus        18 Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~-~~V~   57 (110)
                      +|++.+  ..++.++|.+.+=|+|+||+||-.|+.. |..-
T Consensus         2 ~i~i~~--~~~~~~~F~l~~~~~s~aNALRRillsevPt~A   40 (265)
T cd07031           2 RVEITE--LTDDKVKFILENTDLSVANSLRRVMIAEVPTLA   40 (265)
T ss_pred             cEEEEE--cCCCEEEEEEEcCcHHHHHHHHHHHHHcCccce
Confidence            456665  4568999999999999999999999984 5433

The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.

>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]

Probab=90.94  E-value=0.54  Score=38.10  Aligned_cols=45  Identities=18%  Similarity=0.049  Sum_probs=32.7

Q ss_pred             eEeeecC--CCcceeEEEEccCCcchHHHHHHHHhcC-CCeeeeeeeC
Q 033845           19 VSYERDT--KIINAASFTIEREEHTIGNILRMQLHRD-ENVLFAGYKL   63 (110)
Q Consensus        19 i~~~~~~--k~~n~~~~~i~~EDHTlgNlLr~~L~~~-~~V~fAgY~v   63 (110)
                      |++...+  ..+-.+++...|-+|||||+||-.|+.. |+.-.-+-+|
T Consensus         7 i~i~~~~~~~~~~~ieplerG~g~tlgNALRRvLLSsiPg~Av~~V~I   54 (317)
T COG0202           7 VKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEI   54 (317)
T ss_pred             eEEEEcccccccEEEEEeeeCCcchhHHHHHHHHHHcCccceEEEEEE
Confidence            4555443  3477889999999999999999999984 6644444333

>smart00662 RPOLD RNA polymerases D

Probab=90.60  E-value=0.38  Score=36.76  Aligned_cols=33  Identities=24%  Similarity=0.299  Sum_probs=26.3

Q ss_pred             eEEEEccCCcchHHHHHHHHhcC-CCeeeeeeeC
Q 033845           31 ASFTIEREEHTIGNILRMQLHRD-ENVLFAGYKL   63 (110)
Q Consensus        31 ~~~~i~~EDHTlgNlLr~~L~~~-~~V~fAgY~v   63 (110)
                      +.|.+.+-++|+||+||-.|+.. |+.-.-+.++
T Consensus         2 ~~f~l~~~~~t~~NaLRRilLs~vp~~aI~~V~I   35 (224)
T smart00662        2 AKFVLEPYGLTLANALRRVLLSSVPGMAVTEVEI   35 (224)
T ss_pred             eEEEEEcCCchHHHHHHHHHHHcCccceEEEEEE
Confidence            67999999999999999999984 6655544444

DNA-directed RNA polymerase subunit D and bacterial alpha chain

>PRK00783 DNA-directed RNA polymerase subunit D; Provisional

Probab=90.39  E-value=0.84  Score=35.39  Aligned_cols=41  Identities=20%  Similarity=0.216  Sum_probs=37.3

Q ss_pred             CCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033845           67 LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEV  107 (110)
Q Consensus        67 l~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~~f~~  107 (110)
                      ..++..+.+.|.|..+|.+++..|++-|.+.++.|.++.+.
T Consensus       221 ~~~~~if~vEs~G~l~p~~iv~~A~~~l~~k~~~~~~~~~~  261 (263)
T PRK00783        221 DENKFIFTVESDGSLPVEEILLEALKILKRKADELIEALEE  261 (263)
T ss_pred             cCCeEEEEeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            35678899999999999999999999999999999998865

>cd07030 RNAP_D D subunit of Archaeal RNA polymerase

Probab=88.04  E-value=1.3  Score=34.26  Aligned_cols=37  Identities=19%  Similarity=0.302  Sum_probs=33.3

Q ss_pred             CcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 033845           68 QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSA  104 (110)
Q Consensus        68 ~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~~  104 (110)
                      .+...+.|.|.|..+|.+++++|++-|.+.++.|.++
T Consensus       222 ~~~~if~vEs~Gsl~p~~il~~A~~~l~~k~~~~~~~  258 (259)
T cd07030         222 EDRFIFEVESDGSLPPKEILLEALRILKEKADELIEA  258 (259)
T ss_pred             CCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            4557888999999999999999999999999999875

The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w

>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

Probab=85.41  E-value=2.3  Score=34.17  Aligned_cols=37  Identities=22%  Similarity=0.266  Sum_probs=33.6

Q ss_pred             CCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033845           67 LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS  103 (110)
Q Consensus        67 l~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~  103 (110)
                      -.+.+.+.|-|.|..+|.+.+.+|++-|.+.|+.+.+
T Consensus       254 ~~d~fiF~VES~G~l~p~~i~~~Ai~iL~~K~~~l~~  290 (291)
T cd07032         254 VRDHFIFSIESTGALPPDVLFLEAIKILKEKCRKLLE  290 (291)
T ss_pred             eCCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHhh
Confidence            3566999999999999999999999999999999875

The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun

>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type

Probab=84.69  E-value=1.3  Score=35.54  Aligned_cols=29  Identities=24%  Similarity=0.236  Sum_probs=23.4

Q ss_pred             ccCCcchHHHHHHHHhcC-CCeeeeeeeCC
Q 033845           36 EREEHTIGNILRMQLHRD-ENVLFAGYKLP   64 (110)
Q Consensus        36 ~~EDHTlgNlLr~~L~~~-~~V~fAgY~vp   64 (110)
                      .|.+|||||+||-.|+.. |++-..+-++.
T Consensus        11 ~g~g~TlGNaLRRvLLs~i~g~aI~~vkI~   40 (297)
T TIGR02027        11 RGFGITLGNALRRVLLSSIPGAAITAVKID   40 (297)
T ss_pred             CCchhHHHHHHHHHHHhcCCceEEEEEEEc
Confidence            588999999999999984 77766666554

This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	110
1i3q_K	120	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		1e-21
3h0g_K	123	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		8e-21
2pa8_L	92	X-Ray Crystal Structure Of The DL SUBCOMPLEX OF THE		3e-08
2waq_L	92	The Complete Structure Of The Archaeal 13-Subunit D		1e-07

>pdb|1I3Q|K Chain K, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 120

Iteration: 1
 Score = 97.8 bits (242), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 47/108 (43%), Positives = 65/108 (60%)
Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAPDR+E F++ EG  K+  + DTK  NA   T E+E+HT+GN++R +L  D  VLFA 
Sbjct: 1   MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAA 60
Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVK 108
           YK+ HP   +  +RI TT    P  A   A N +  +L  LK+ FE +
Sbjct: 61  YKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETE 108

>pdb|3H0G|K Chain K, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 123

Iteration: 1
 Score = 95.1 bits (235), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 49/105 (46%), Positives = 64/105 (60%), Gaps = 1/105 (0%)
Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MN P+RYE  +   G  KV+YE D+K  NAA  T+E+E+HT+ N+L  QL  DE VLFAG
Sbjct: 1   MNQPERYE-LIELMGLPKVTYELDSKSPNAAVVTLEKEDHTLANMLANQLLSDERVLFAG 59
Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105
           YK+PHPL +  I+R+ T    SP Q    A   L   L+ +K  F
Sbjct: 60  YKVPHPLNHNFILRVQTVEDCSPKQVIVDAAKSLITHLEEIKVNF 104

>pdb|2PA8|L Chain L, X-Ray Crystal Structure Of The DL SUBCOMPLEX OF THE SULFOLOBUS Solfataricus Rna Polymerase Length = 92

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 28/66 (42%), Positives = 37/66 (56%)
Query: 29 NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYN 88
          N     IE E+HT+GN++   L R   V FA Y  PHPL  KIIV+I T    +P  A  
Sbjct: 11 NYLELEIEGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVKILTDGSITPKDALL 70
Query: 89 QAINDL 94
          +AI ++
Sbjct: 71 KAIENI 76

>pdb|2WAQ|L Chain L, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 92

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/63 (42%), Positives = 35/63 (55%)
Query: 29 NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYN 88
          N     IE E+HT+GN++   L +   V FA Y  PHPL  KIIV+I T    +P  A  
Sbjct: 11 NYLELEIEGEDHTLGNLIAGTLRKISGVSFASYYQPHPLTDKIIVKILTDGSIAPKDALL 70
Query: 89 QAI 91
          +AI
Sbjct: 71 KAI 73

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	110
1twf_K	120	B13.6, DNA-directed RNA polymerase II 13.6 kDa pol	2e-42
3h0g_K	123	DNA-directed RNA polymerase II subunit RPB11; tran	2e-40
2pa8_L	92	DNA-directed RNA polymerase subunit L; ferredoxin-	2e-27
1xpp_A	115	TA1416, DNA-directed RNA polymerase subunit L; str	9e-25

>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB: 1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K 1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K* 1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ... Length = 120

 Score =  134 bits (338), Expect = 2e-42
 Identities = 47/106 (44%), Positives = 64/106 (60%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAPDR+E F++ EG  K+  + DTK  NA   T E+E+HT+GN++R +L  D  VLFA 
Sbjct: 1   MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAA 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE 106
           YK+ HP   +  +RI TT    P  A   A N +  +L  LK+ FE
Sbjct: 61  YKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFE 106

>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 123

 Score =  129 bits (325), Expect = 2e-40
 Identities = 49/106 (46%), Positives = 63/106 (59%), Gaps = 1/106 (0%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MN P+RYE      G  KV+YE D+K  NAA  T+E+E+HT+ N+L  QL  DE VLFAG
Sbjct: 1   MNQPERYELIE-LMGLPKVTYELDSKSPNAAVVTLEKEDHTLANMLANQLLSDERVLFAG 59

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE 106
           YK+PHPL +  I+R+ T    SP Q    A   L   L+ +K  F 
Sbjct: 60  YKVPHPLNHNFILRVQTVEDCSPKQVIVDAAKSLITHLEEIKVNFM 105

>2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L 2y0s_L Length = 92

 Score = 95.3 bits (237), Expect = 2e-27
 Identities = 28/83 (33%), Positives = 38/83 (45%)

Query: 24  DTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSP 83
                N     IE E+HT+GN++   L R   V FA Y  PHPL  KIIV+I T    +P
Sbjct: 6   LKSESNYLELEIEGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVKILTDGSITP 65

Query: 84  MQAYNQAINDLDKELDTLKSAFE 106
             A  +AI ++           +
Sbjct: 66  KDALLKAIENIRGMTSHYIDEIK 88

>1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural genomics, protein structure initiative, MCSG; 1.60A {Thermoplasma acidophilum} SCOP: d.74.3.2 Length = 115

 Score = 89.2 bits (221), Expect = 9e-25
 Identities = 21/93 (22%), Positives = 42/93 (45%), Gaps = 1/93 (1%)

Query: 14  EGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIV 73
           E T + S    +K  N+ +  +   ++T+   L  ++ +D+ V  A Y + HP+     +
Sbjct: 6   ERTAESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQI 65

Query: 74  RIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE 106
            +   S   P  A  +A+  L K  + L + F+
Sbjct: 66  YVRVKS-GKPQSAIKRAVRKLSKLYEDLGTQFQ 97

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	110
1twf_K	120	B13.6, DNA-directed RNA polymerase II 13.6 kDa pol	100.0
3h0g_K	123	DNA-directed RNA polymerase II subunit RPB11; tran	100.0
1xpp_A	115	TA1416, DNA-directed RNA polymerase subunit L; str	100.0
2pa8_L	92	DNA-directed RNA polymerase subunit L; ferredoxin-	100.0
2pa8_D	265	DNA-directed RNA polymerase subunit D; ferredoxin-	95.49
1twf_C	318	B44.5, DNA-directed RNA polymerase II 45 kDa polyp	94.65
1twf_C	318	B44.5, DNA-directed RNA polymerase II 45 kDa polyp	94.02
1bdf_A	235	RNA polymerase alpha subunit; nucleotidyltransfera	93.75
2a6h_A	315	DNA-directed RNA polymerase alpha chain; RNA polym	93.64
3lu0_A	329	DNA-directed RNA polymerase subunit alpha; E. coli	93.23
1bdf_A	235	RNA polymerase alpha subunit; nucleotidyltransfera	93.22
2a6h_A	315	DNA-directed RNA polymerase alpha chain; RNA polym	92.95
3h0g_C	297	DNA-directed RNA polymerase II subunit RPB3; trans	92.65
2pa8_D	265	DNA-directed RNA polymerase subunit D; ferredoxin-	92.56
3h0g_C	297	DNA-directed RNA polymerase II subunit RPB3; trans	92.29
3lu0_A	329	DNA-directed RNA polymerase subunit alpha; E. coli	91.9

>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB: 1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K 1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K* 1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ...

Probab=100.00  E-value=6.4e-51  Score=286.01  Aligned_cols=109  Identities=43%  Similarity=0.698  Sum_probs=108.0

Q ss_pred             CCCCccccceecCCCceeeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCC
Q 033845            1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQ   80 (110)
Q Consensus         1 mn~p~~~~~~~l~~~~~Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~   80 (110)
                      ||||||||+|+|+||++|+++..+++.+|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++
T Consensus         1 mnap~~~e~f~l~~ge~K~~~~~~~k~~n~~~f~i~~EDHTLgNlLr~~Llk~p~V~fAgY~vpHPl~~~~~lrIqT~~~   80 (120)
T 1twf_K            1 MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG   80 (120)
T ss_dssp             CCSCCSGGGTSCCTTCCSCCEEECSSSTTEEEEEEESCCHHHHHHHHHHHTTCTTEEEEEEECSCTTSCEEEEEEEECTT
T ss_pred             CCCCCccceeecCCCCceEEEEeccCCCCeEEEEEeCCCchHHHHHHHHHhhCCCeeEEeeecCCCCCCccEEEEEECCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033845           81 SSPMQAYNQAINDLDKELDTLKSAFEVKH  109 (110)
Q Consensus        81 ~~P~~al~~a~~~l~~~~~~l~~~f~~~~  109 (110)
                      .+|.+||++|+++|++.|++++++|+++|
T Consensus        81 ~~p~eaL~~a~~~L~~~~~~l~~~f~~e~  109 (120)
T 1twf_K           81 YDPKDALKNACNSIINKLGALKTNFETEW  109 (120)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999977

>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=100.00  E-value=3.6e-51  Score=288.40  Aligned_cols=109  Identities=45%  Similarity=0.676  Sum_probs=107.6

Q ss_pred             CCCCccccceecCCCceeeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCC
Q 033845            1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQ   80 (110)
Q Consensus         1 mn~p~~~~~~~l~~~~~Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~   80 (110)
                      ||||||||+|+| ||++||++.+|++++|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++
T Consensus         1 mnap~~~e~f~l-~ge~Kv~~~~dtk~~n~~~f~i~~EDHTLgNlLr~~Llk~p~V~fAgY~vpHPle~~~~lrIqT~~~   79 (123)
T 3h0g_K            1 MNQPERYELIEL-MGLPKVTYELDSKSPNAAVVTLEKEDHTLANMLANQLLSDERVLFAGYKVPHPLNHNFILRVQTVED   79 (123)
T ss_dssp             CCCCCGGGTSSC-SSCCSCCEEECSSSTTEEEEEEESCCSSHHHHHHHTGGGSTTCSCBCCBCSCTTSCEEEEEEECCSS
T ss_pred             CCCCCccceeEe-CCCcceEEecCCCCCceEEEEEeCCCcchHHHHHHHHhcCCCeeEeeecCCCCCCCceEEEEEECCC
Confidence            999999999999 9999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHhhhC
Q 033845           81 SSPMQAYNQAINDLDKELDTLKSAFEVKHL  110 (110)
Q Consensus        81 ~~P~~al~~a~~~l~~~~~~l~~~f~~~~~  110 (110)
                      .+|++||++|+++|++.|+++++.|++||.
T Consensus        80 ~~p~eaL~~al~~L~~~~~~l~~~F~~~~~  109 (123)
T 3h0g_K           80 CSPKQVIVDAAKSLITHLEEIKVNFMREWE  109 (123)
T ss_dssp             SCSHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999983

>1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural genomics, protein structure initiative, MCSG; 1.60A {Thermoplasma acidophilum} SCOP: d.74.3.2

Probab=100.00  E-value=2.2e-39  Score=225.96  Aligned_cols=97  Identities=22%  Similarity=0.260  Sum_probs=90.2

Q ss_pred             cCCCceeeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHH
Q 033845           12 VPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAI   91 (110)
Q Consensus        12 l~~~~~Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~   91 (110)
                      -++|++|+++..+++.+|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+|+. |.+||++|+
T Consensus         4 ~~~~~~kmeiki~~k~~n~~~f~i~~EDHTLgNlLr~~Llkdp~V~fAgY~vpHPle~~~~lrIqT~~~~-p~eaL~~al   82 (115)
T 1xpp_A            4 QRERTAESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSGK-PQSAIKRAV   82 (115)
T ss_dssp             -----CCCEEEEEEECSSEEEEEEESCCHHHHHHHHHHHTTCTTEEEEEEECSSTTTSCCEEEEEESSSC-HHHHHHHHH
T ss_pred             ccccccceEEEEEcCCCCEEEEEEeCCCchhHHHHHHHHhcCCCeEEEEeecCCCCCCccEEEEEeCCCC-hHHHHHHHH
Confidence            3689999999999999999999999999999999999999999999999999999999999999999987 999999999


Q ss_pred             HHHHHHHHHHHHHHHhhh
Q 033845           92 NDLDKELDTLKSAFEVKH  109 (110)
Q Consensus        92 ~~l~~~~~~l~~~f~~~~  109 (110)
                      ++|++.|+++++.|++++
T Consensus        83 ~~L~~~~~~l~~~f~~a~  100 (115)
T 1xpp_A           83 RKLSKLYEDLGTQFQKEF  100 (115)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            999999999999999875

>2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L 2y0s_L

Probab=100.00  E-value=2.5e-38  Score=212.88  Aligned_cols=89  Identities=31%  Similarity=0.392  Sum_probs=84.6

Q ss_pred             eeecCCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Q 033845           21 YERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDT  100 (110)
Q Consensus        21 ~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~  100 (110)
                      +..+++.+|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++.+|.+||++|+++|++.|++
T Consensus         3 ikvi~k~~n~~~f~i~~EDHTLgN~Lr~~L~~~p~V~fagY~vpHPl~~~~~lrIqT~~~~~p~~al~~a~~~l~~~~~~   82 (92)
T 2pa8_L            3 IRILKSESNYLELEIEGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVKILTDGSITPKDALLKAIENIRGMTSH   82 (92)
T ss_dssp             EEEEEEETTEEEEEEETCCHHHHHHHHHHHHTSTTEEEEEEECSSTTSCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEecCCCeEEEEEecCchhHHHHHHHHHhcCCCeeEEEeecCCCCCCceEEEEEECCCCCHHHHHHHHHHHHHHHHHH
Confidence            34446899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhh
Q 033845          101 LKSAFEVKH  109 (110)
Q Consensus       101 l~~~f~~~~  109 (110)
                      ++++|+++.
T Consensus        83 ~~~~f~~~~   91 (92)
T 2pa8_L           83 YIDEIKGLT   91 (92)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            999999874

>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D 2y0s_D

Probab=95.49  E-value=0.011  Score=44.89  Aligned_cols=34  Identities=9%  Similarity=-0.069  Sum_probs=26.5

Q ss_pred             eeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcC
Q 033845           18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD   53 (110)
Q Consensus        18 Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~   53 (110)
                      +|++...  .++.++|.+.|-|+||||+||-.|+..
T Consensus         2 ~i~i~~~--~~~~~~f~l~g~~~t~~NalRRills~   35 (265)
T 2pa8_D            2 SINLLHK--DDTRIDLVFEGYPLEFVNAIRRASMLY   35 (265)
T ss_dssp             CEEEEEE--CSSEEEEEEESSCHHHHHHHHHHHHHS
T ss_pred             eEEEEEc--CCCEEEEEEeCCCHHHHHHHHHHHHHc
Confidence            3455543  478899999999999999999888874

>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1 d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C 1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C* 1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C 1y77_C* ...

Probab=94.65  E-value=0.078  Score=41.76  Aligned_cols=54  Identities=13%  Similarity=0.150  Sum_probs=43.5

Q ss_pred             CCeeeeeeeCCC---------CCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033845           54 ENVLFAGYKLPH---------PLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEV  107 (110)
Q Consensus        54 ~~V~fAgY~vpH---------Pl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~~f~~  107 (110)
                      +-|.-+.|.++-         .-.+++.|.|-|+|+.+|.+||.+|++-|.+.|+.|.+.+..
T Consensus       202 ~pv~~v~~~ve~~~~~rv~~~~d~dkfif~VET~Gsi~Peeav~~A~kIL~~kl~~f~~~l~~  264 (318)
T 1twf_C          202 PQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQ  264 (318)
T ss_dssp             CCCGGGTTSCCCCSSSCCCTTCCCCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcceeEEecccccccccccccCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            444555666642         123689999999999999999999999999999999988764

>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1 d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C 1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C* 1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C 1y77_C* ...

Probab=94.02  E-value=0.024  Score=44.68  Aligned_cols=38  Identities=13%  Similarity=0.212  Sum_probs=30.1

Q ss_pred             ceeeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcC-CC
Q 033845           16 TKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-EN   55 (110)
Q Consensus        16 ~~Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~-~~   55 (110)
                      ..+|++..  ..++.++|.+.|-|+||||+||-.|+.. |.
T Consensus         5 ~p~I~i~~--~~~~~~kF~leG~~~tlaNALRRiLLSevPg   43 (318)
T 1twf_C            5 GPQVKIRE--ASKDNVDFILSNVDLAMANSLRRVMIAEIPT   43 (318)
T ss_dssp             SSBCCCSC--CCSSEECCEEBSSCHHHHHHHHHHHHHCCCE
T ss_pred             CCeEEEEE--ecCCEEEEEEEccChhHHHHHHHHHHHcCcc
Confidence            34455554  4688999999999999999999999874 44

>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1

Probab=93.75  E-value=0.038  Score=41.72  Aligned_cols=41  Identities=29%  Similarity=0.281  Sum_probs=31.0

Q ss_pred             eeEeeecCCCcceeEEEEc----cCCcchHHHHHHHHhcC-CCeeeee
Q 033845           18 KVSYERDTKIINAASFTIE----REEHTIGNILRMQLHRD-ENVLFAG   60 (110)
Q Consensus        18 Ki~~~~~~k~~n~~~~~i~----~EDHTlgNlLr~~L~~~-~~V~fAg   60 (110)
                      +|++..  ..++.++|.+.    |-++|+||+||-.|+.. |+.-.-+
T Consensus        13 ~i~i~~--~~~~~~~F~l~Ple~G~~~tlgNaLRRiLLsevpg~AI~~   58 (235)
T 1bdf_A           13 LVDIEQ--VSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVTE   58 (235)
T ss_dssp             EEEEEE--SSSSEEEEEEEEEETTHHHHHHHHHHHHHTTSCCCEEEEE
T ss_pred             eEEEEE--ccCCEEEEEEEecCCCCchHHHHHHHHHHHhcCCceEEEE
Confidence            366655  35788999995    99999999999999884 6544433

>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3aoh_A* 3aoi_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* ...

Probab=93.64  E-value=0.053  Score=42.66  Aligned_cols=38  Identities=18%  Similarity=0.132  Sum_probs=29.8

Q ss_pred             eeeEeeecCCCcceeEEEE----ccCCcchHHHHHHHHhcC-CCe
Q 033845           17 KKVSYERDTKIINAASFTI----EREEHTIGNILRMQLHRD-ENV   56 (110)
Q Consensus        17 ~Ki~~~~~~k~~n~~~~~i----~~EDHTlgNlLr~~L~~~-~~V   56 (110)
                      ++|++...  .++.++|.+    .|-++|+||+||-.|+.. |+.
T Consensus         9 p~i~i~~~--~~~~~~F~l~Ple~G~~~TlgNaLRRiLLsevpg~   51 (315)
T 2a6h_A            9 PVFTVRTQ--GREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGT   51 (315)
T ss_dssp             CEEEEEEE--TTTEEEEEEEEECTTCHHHHHHHHHHHHHHTCEEE
T ss_pred             CeEEEEEc--cCCEEEEEEEccCCCchhHHHHHHHHHHHhcCCce
Confidence            34565543  588999999    499999999999999985 543

>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A

Probab=93.23  E-value=0.07  Score=42.33  Aligned_cols=48  Identities=19%  Similarity=0.304  Sum_probs=38.4

Q ss_pred             CCeeeeeeeCC-----CCC-CcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Q 033845           54 ENVLFAGYKLP-----HPL-QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTL  101 (110)
Q Consensus        54 ~~V~fAgY~vp-----HPl-~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l  101 (110)
                      .=|.-+.|.|.     ... .++..|-|.|+|+++|.+||..|++-|++.+.-|
T Consensus       178 sPV~~Vny~Ve~~rvgq~td~dkL~leI~TdGsi~P~eAl~~Aa~iL~~~l~~f  231 (329)
T 3lu0_A          178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAF  231 (329)
T ss_dssp             CCEEEEEEEEEEECCSSCSCEEEEEEEEEECSSSCHHHHHHHHHHHHHHHTTTS
T ss_pred             CceeeEEEEEeccccCCCcccceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Confidence            44666778664     333 4899999999999999999999999998876544

>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1

Probab=93.22  E-value=0.1  Score=39.32  Aligned_cols=47  Identities=19%  Similarity=0.278  Sum_probs=38.0

Q ss_pred             eeeeeeeCCCC------CCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q 033845           56 VLFAGYKLPHP------LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLK  102 (110)
Q Consensus        56 V~fAgY~vpHP------l~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~  102 (110)
                      |.-+.|+++-.      -.++..|.|-|+|+.+|.+||.+|++-|.+.|+.|.
T Consensus       180 v~~v~y~ve~~~v~~~~~~d~li~eIeT~Gsi~P~eal~~A~~iL~~~~~~f~  232 (235)
T 1bdf_A          180 VERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFV  232 (235)
T ss_dssp             EEEEEEECCBCCCSSCSSEEEEEEEEEECSSSCHHHHHHHHHHHHHHHGGGGC
T ss_pred             EEEEEEEccCccccccccCcEEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            45577776422      236899999999999999999999999999887664

>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3aoh_A* 3aoi_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* ...

Probab=92.95  E-value=0.14  Score=40.19  Aligned_cols=47  Identities=26%  Similarity=0.352  Sum_probs=38.2

Q ss_pred             CeeeeeeeCCC------CCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Q 033845           55 NVLFAGYKLPH------PLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTL  101 (110)
Q Consensus        55 ~V~fAgY~vpH------Pl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l  101 (110)
                      .|.-+.|.+.-      .-.+++.|.|-|+|+.+|.+||.+|++-|.+.|..|
T Consensus       173 pv~~v~y~ve~~rv~~~~~~dkli~eIeT~Gsi~P~eal~~A~~iL~~~l~~f  225 (315)
T 2a6h_A          173 PVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYF  225 (315)
T ss_dssp             CEEEEEEEEEECCBTTBCCCEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHTT
T ss_pred             CceeEEEEeeeeeecccccccEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHH
Confidence            35556776531      234789999999999999999999999999998877

>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=92.65  E-value=0.076  Score=41.55  Aligned_cols=36  Identities=14%  Similarity=0.248  Sum_probs=29.4

Q ss_pred             ceeeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcC
Q 033845           16 TKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD   53 (110)
Q Consensus        16 ~~Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~   53 (110)
                      .++|++..  ..++.++|.+.|-|.||||+||-.|+..
T Consensus         4 ~p~I~i~~--~~~~~~~F~l~g~~~tiaNALRRiLLSe   39 (297)
T 3h0g_C            4 ETHITIRN--ISKNSVDFVLTNTSLAVANSLRRVVLAE   39 (297)
T ss_dssp             CCSBCCCC--BCSSEEEEEECSCCHHHHHHHHHHHHSS
T ss_pred             CCeEEEEE--ccCCEEEEEEECCChhHHHHHHHHHHHc
Confidence            45566665  4668999999999999999999999884

>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D 2y0s_D

Probab=92.56  E-value=0.29  Score=36.96  Aligned_cols=41  Identities=15%  Similarity=0.213  Sum_probs=37.0

Q ss_pred             CcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033845           68 QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVK  108 (110)
Q Consensus        68 ~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~~f~~~  108 (110)
                      .++..+.|.|+|..+|.+++.+|++-|.+.++.|.+.+...
T Consensus       223 ~d~~i~~VEt~Gsl~Pee~v~~A~~iL~~~~~~~~~~l~~~  263 (265)
T 2pa8_D          223 EDKYILEIESVGSLKPERILLEAGKSIIRKIEELEKKLVEV  263 (265)
T ss_dssp             EEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            35678999999999999999999999999999999988764

>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=92.29  E-value=0.11  Score=40.65  Aligned_cols=40  Identities=13%  Similarity=0.239  Sum_probs=37.3

Q ss_pred             CcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033845           68 QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEV  107 (110)
Q Consensus        68 ~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~~f~~  107 (110)
                      .+++.|.|.|+|+.+|.+++.+|++-|.+.++.|.+.++.
T Consensus       226 ~dkfif~VET~Gsl~p~eiv~~A~~iL~~kl~~f~~~L~~  265 (297)
T 3h0g_C          226 PRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLVRDLDE  265 (297)
T ss_dssp             CCCEEEEEEBCSSSCTTTTTHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5789999999999999999999999999999999988764

>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A

Probab=91.90  E-value=0.12  Score=41.02  Aligned_cols=34  Identities=29%  Similarity=0.285  Sum_probs=28.3

Q ss_pred             CcceeEEEEc----cCCcchHHHHHHHHhcC-CCeeeee
Q 033845           27 IINAASFTIE----REEHTIGNILRMQLHRD-ENVLFAG   60 (110)
Q Consensus        27 ~~n~~~~~i~----~EDHTlgNlLr~~L~~~-~~V~fAg   60 (110)
                      .++.+.|.+.    |-++|+||+||-.|+.. |+.-.-+
T Consensus        20 ~~~~~kF~l~PlerG~g~TlgNaLRRvLLssvpg~AIt~   58 (329)
T 3lu0_A           20 SSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTE   58 (329)
T ss_dssp             TTSEEEEEECCCCTTCHHHHHHHHHHHTTTSSCEEEEEE
T ss_pred             CCCEEEEEEEecCCCChhHHHHHHHHHHHhcCCceEEEE
Confidence            6889999998    99999999999999984 6543333

---

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	110
d1twfk_	114	d.74.3.2 (K:) RPB11 {Baker's yeast (Saccharomyces	8e-43
d1xppa_	99	d.74.3.2 (A:) DNA-directed RNA polymerase subunit	7e-23

>d1twfk_ d.74.3.2 (K:) RPB11 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 114

class: Alpha and beta proteins (a+b)
fold: DCoH-like
superfamily: RBP11-like subunits of RNA polymerase
family: RBP11/RpoL
domain: RPB11
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  133 bits (337), Expect = 8e-43
 Identities = 47/106 (44%), Positives = 64/106 (60%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAPDR+E F++ EG  K+  + DTK  NA   T E+E+HT+GN++R +L  D  VLFA 
Sbjct: 1   MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAA 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE 106
           YK+ HP   +  +RI TT    P  A   A N +  +L  LK+ FE
Sbjct: 61  YKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFE 106

>d1xppa_ d.74.3.2 (A:) DNA-directed RNA polymerase subunit L, RpoL {Thermoplasma acidophilum [TaxId: 2303]} Length = 99

class: Alpha and beta proteins (a+b)
fold: DCoH-like
superfamily: RBP11-like subunits of RNA polymerase
family: RBP11/RpoL
domain: DNA-directed RNA polymerase subunit L, RpoL
species: Thermoplasma acidophilum [TaxId: 2303]

 Score = 82.9 bits (205), Expect = 7e-23
 Identities = 19/89 (21%), Positives = 40/89 (44%), Gaps = 1/89 (1%)

Query: 18  KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHT 77
           + S    +K  N+ +  +   ++T+   L  ++ +D+ V  A Y + HP+     + +  
Sbjct: 2   ESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRV 61

Query: 78  TSQSSPMQAYNQAINDLDKELDTLKSAFE 106
            S   P  A  +A+  L K  + L + F+
Sbjct: 62  KS-GKPQSAIKRAVRKLSKLYEDLGTQFQ 89

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	110
d1twfk_	114	RPB11 {Baker's yeast (Saccharomyces cerevisiae) [T	100.0
d1xppa_	99	DNA-directed RNA polymerase subunit L, RpoL {Therm	100.0
d1bdfa1	105	RNA polymerase alpha {Escherichia coli [TaxId: 562	98.37
d1smya1	106	RNA polymerase alpha {Thermus thermophilus [TaxId:	98.17
d1twfc1	135	RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta	97.26

>d1twfk_ d.74.3.2 (K:) RPB11 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: DCoH-like
superfamily: RBP11-like subunits of RNA polymerase
family: RBP11/RpoL
domain: RPB11
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.5e-45  Score=253.33  Aligned_cols=110  Identities=43%  Similarity=0.683  Sum_probs=108.6

Q ss_pred             CCCCccccceecCCCceeeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCC
Q 033845            1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQ   80 (110)
Q Consensus         1 mn~p~~~~~~~l~~~~~Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~   80 (110)
                      ||||||+|+|+|++|++||++..+++.+|+++|+|.+|||||||+|++.|+++|+|.||||++|||+++++.|||||+++
T Consensus         1 mn~p~~~~~~~l~~~e~ki~i~~~~~~~n~~~~~i~~EdhTlGnlL~~~L~~~~~V~fagY~~pHPl~~~i~irI~t~~~   80 (114)
T d1twfk_           1 MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG   80 (114)
T ss_dssp             CCSCCSGGGTSCCTTCCSCCEEECSSSTTEEEEEEESCCHHHHHHHHHHHTTCTTEEEEEEECSCTTSCEEEEEEEECTT
T ss_pred             CCCcchhhhcccCCCCceEEEEecCCCCceEEEEEeCCCchHHHHHHHHHhcCCCceEEEeecCCCCCCeeEEEEEeCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHhhhC
Q 033845           81 SSPMQAYNQAINDLDKELDTLKSAFEVKHL  110 (110)
Q Consensus        81 ~~P~~al~~a~~~l~~~~~~l~~~f~~~~~  110 (110)
                      .+|.++|++|+++|++.|+.+++.|+++|.
T Consensus        81 ~~p~~~l~~a~~~l~~~~~~l~~~f~~e~~  110 (114)
T d1twfk_          81 YDPKDALKNACNSIINKLGALKTNFETEWN  110 (114)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            999999999999999999999999999993

>d1xppa_ d.74.3.2 (A:) DNA-directed RNA polymerase subunit L, RpoL {Thermoplasma acidophilum [TaxId: 2303]}

class: Alpha and beta proteins (a+b)
fold: DCoH-like
superfamily: RBP11-like subunits of RNA polymerase
family: RBP11/RpoL
domain: DNA-directed RNA polymerase subunit L, RpoL
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=100.00  E-value=5.5e-35  Score=196.69  Aligned_cols=91  Identities=20%  Similarity=0.272  Sum_probs=85.5

Q ss_pred             ceeeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHH
Q 033845           16 TKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLD   95 (110)
Q Consensus        16 ~~Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l~   95 (110)
                      +.++++.  ++++|+++|+|.||||||||+||++|+++|+|.||||++|||+++++.|+|||+++ +|.++|++|+++++
T Consensus         2 ~~~ikvi--~~~~n~~~~~i~~EdHTlgn~L~~~L~~~~~V~fagY~ipHPl~~~~~l~I~t~~~-~p~~~l~~a~~~li   78 (99)
T d1xppa_           2 ESSLRVI--SKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSG-KPQSAIKRAVRKLS   78 (99)
T ss_dssp             CCEEEEE--EECSSEEEEEEESCCHHHHHHHHHHHTTCTTEEEEEEECSSTTTSCCEEEEEESSS-CHHHHHHHHHHHHH
T ss_pred             CceEEEE--ecCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEEecCCcccCCeEEEEEeCCC-CHHHHHHHHHHHHH
Confidence            4455555  57899999999999999999999999999999999999999999999999999977 89999999999999


Q ss_pred             HHHHHHHHHHHhhh
Q 033845           96 KELDTLKSAFEVKH  109 (110)
Q Consensus        96 ~~~~~l~~~f~~~~  109 (110)
                      +.|+.|+++|+++|
T Consensus        79 ~~~~~l~~~~~~~~   92 (99)
T d1xppa_          79 KLYEDLGTQFQKEF   92 (99)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999999998

>d1bdfa1 d.74.3.1 (A:2-52,A:179-232) RNA polymerase alpha {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: DCoH-like
superfamily: RBP11-like subunits of RNA polymerase
family: RNA polymerase alpha subunit dimerisation domain
domain: RNA polymerase alpha
species: Escherichia coli [TaxId: 562]

Probab=98.37  E-value=8.7e-07  Score=58.59  Aligned_cols=73  Identities=25%  Similarity=0.294  Sum_probs=59.6

Q ss_pred             cceeEEEE----ccCCcchHHHHHHHHhc-CCCeeeeeeeCC---CCC---CcceEEEEEeCCCCCHHHHHHHHHHHHHH
Q 033845           28 INAASFTI----EREEHTIGNILRMQLHR-DENVLFAGYKLP---HPL---QYKIIVRIHTTSQSSPMQAYNQAINDLDK   96 (110)
Q Consensus        28 ~n~~~~~i----~~EDHTlgNlLr~~L~~-~~~V~fAgY~vp---HPl---~~~~~lrIqT~~~~~P~~al~~a~~~l~~   96 (110)
                      ++.+.|++    .|-.||+||.+|..|+. .+.|.-++|+|.   |=.   .+++.|.|.|+|.++|.+|+..|++-|.+
T Consensus        20 ~~~~k~~~eplErG~Gyt~gn~lr~~llSs~sPV~~V~y~Ve~~~~e~~td~d~L~lei~TnGsi~p~eA~~~Aa~il~~   99 (105)
T d1bdfa1          20 STHAKVTLEPLERGFGHTLGNALRAILLSSMPPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAE   99 (105)
T ss_dssp             SSEEEEEEEEEETTHHHHHHHHHHHHHTTSCCSEEEEEEECCBCCCSSCSSEEEEEEEEEECSSSCHHHHHHHHHHHHHH
T ss_pred             CceEEEEEEEccCCcccccccccchhhhhcccceeEEEEeeeeeecCCCCcceEEEEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            34455554    57789999999999887 599999999985   321   36899999999999999999999998887


Q ss_pred             HHHH
Q 033845           97 ELDT  100 (110)
Q Consensus        97 ~~~~  100 (110)
                      .+.-
T Consensus       100 ~~~~  103 (105)
T d1bdfa1         100 QLEA  103 (105)
T ss_dssp             HGGG
T ss_pred             HHHh
Confidence            6643

>d1smya1 d.74.3.1 (A:1-49,A:173-229) RNA polymerase alpha {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: DCoH-like
superfamily: RBP11-like subunits of RNA polymerase
family: RNA polymerase alpha subunit dimerisation domain
domain: RNA polymerase alpha
species: Thermus thermophilus [TaxId: 274]

Probab=98.17  E-value=1.8e-06  Score=57.25  Aligned_cols=76  Identities=25%  Similarity=0.272  Sum_probs=61.6

Q ss_pred             CCcceeEEEE----ccCCcchHHHHHHHHhc-CCCeeeeeeeCCC------CCCcceEEEEEeCCCCCHHHHHHHHHHHH
Q 033845           26 KIINAASFTI----EREEHTIGNILRMQLHR-DENVLFAGYKLPH------PLQYKIIVRIHTTSQSSPMQAYNQAINDL   94 (110)
Q Consensus        26 k~~n~~~~~i----~~EDHTlgNlLr~~L~~-~~~V~fAgY~vpH------Pl~~~~~lrIqT~~~~~P~~al~~a~~~l   94 (110)
                      ...+.+.|.+    .|..+|+||.+|..|.. .|-|.-+.|.|..      .-.+++.|-|.|+|+++|.+||..|++-|
T Consensus        16 ~~~~y~~~v~~p~erG~g~~~gn~l~~il~ss~~PV~kV~y~Ve~~rvg~~~d~dkL~LeI~TnGsi~P~eAl~~Aa~il   95 (106)
T d1smya1          16 QGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEIL   95 (106)
T ss_dssp             CSSSCEEEEEEEECTTHHHHHHHHHHHHHHHTCECEEEEEEEEEECCCSSCSCCEEEEEEEEECSSSCHHHHHHHHHHHH
T ss_pred             cCCceeEEEeeccCCCcccccccccceeehhcCChhhEEEEEecccccCcccceeEEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            4555666665    37789999999997776 6999999999863      12468999999999999999999999988


Q ss_pred             HHHHHHH
Q 033845           95 DKELDTL  101 (110)
Q Consensus        95 ~~~~~~l  101 (110)
                      .+-+..|
T Consensus        96 ~~h~~~f  102 (106)
T d1smya1          96 REHLTYF  102 (106)
T ss_dssp             HHHHHTS
T ss_pred             HHHHHhh
Confidence            8776543

>d1twfc1 d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: DCoH-like
superfamily: RBP11-like subunits of RNA polymerase
family: RNA polymerase alpha subunit dimerisation domain
domain: RPB3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.26  E-value=0.0023  Score=43.48  Aligned_cols=89  Identities=13%  Similarity=0.238  Sum_probs=70.0

Q ss_pred             ceeeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcC-CCeeeeeeeC-------------------------------
Q 033845           16 TKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-ENVLFAGYKL-------------------------------   63 (110)
Q Consensus        16 ~~Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~-~~V~fAgY~v-------------------------------   63 (110)
                      .++|++..  ..++.+.|.+.|-|-+++|+||-.++.. |-  ++++.+                               
T Consensus         3 ~P~i~i~~--~~~~~~~F~l~~~d~s~ANalRRi~iaeV~t--~v~feyDp~N~lrHtdyw~e~~~~~ewP~s~~~~~e~   78 (135)
T d1twfc1           3 GPQVKIRE--ASKDNVDFILSNVDLAMANSLRRVMIAEIAA--AIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYED   78 (135)
T ss_dssp             SSBCCCSC--CCSSEECCEEBSSCHHHHHHHHHHHHHCCEE--EEEEEECSSTTSCCSCCCCSSCHHHHSCCCGGGTTSC
T ss_pred             CCEEEEEE--cCCCEEEEEEeCCCHHHHHHHHHHHHHhhhh--heeeeecccccccceeecccCCccccCCcccCCCCCC
Confidence            35566654  5778899999999999999999999875 32  232111                               


Q ss_pred             -CC---CC-----CcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033845           64 -PH---PL-----QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVK  108 (110)
Q Consensus        64 -pH---Pl-----~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~~f~~~  108 (110)
                       +.   |+     .+.+.+.|-|.|...|.+.+.+|++-|+..|..|...+...
T Consensus        79 ~~~e~e~fd~~akpd~F~f~VEs~G~l~p~~Iv~~ai~iL~~Kl~~l~~~L~~~  132 (135)
T d1twfc1          79 PPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQM  132 (135)
T ss_dssp             CCCSSSCCCTTCCCCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcccccCCCCCCCCCEEEEEEEeccCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             11   23     25688999999999999999999999999999999988653