Citrus Sinensis ID: 033562

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110------
Protein Sequence
MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKHSRVY
Secondary Structure (PSIPRED)
ccccccccccccccccEEEEEEcccccccEEEEEEEcccccHHHHHHHHHHcccccEEEEEccccccccEEEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccEEEEcccccEEEEEEEccccccEEEEEEEccccHHHHHHHHHHHccccEEEEEEEcccccccEEEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
mnapdryerfvvpegtkkvsyERDTKIINAASFTIEREEHTIGNILRMQLhrdenvlfagyklphplqYKIIVRIhttsqsspmqAYNQAINDLDKELDTLKSAFEAELAKHSRVY
Flexible Loop (DISEMBL)
mnapdryerfvvpegtkkvsyerdtkiinaasftiereeHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEaelakhsrvy
Low Complexity Region (SEG)
MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKHSRVY
Disordered region (IsUnstruct)
*********FVV****KKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHT***************************************
Disordered Region (DISOPRED)
**APDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKHS***
Disordered Region (DISEMBL)
MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKHSRVY
Disordered Region (DISPRO)
****DRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKHSRVY
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPxxxxxxxxxxxxxxxxxxxxxxxxxxxxHSRVY
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	116	2.2.26 [Sep-21-2011]
Q38859	116	DNA-directed RNA polymera	yes	no	0.974	0.974	0.893	4e-56
Q86JJ5	120	DNA-directed RNA polymera	yes	no	0.991	0.958	0.460	2e-29
P52435	117	DNA-directed RNA polymera	yes	no	0.905	0.897	0.523	5e-28
Q32P79	117	DNA-directed RNA polymera	yes	no	0.905	0.897	0.523	5e-28
O08740	117	DNA-directed RNA polymera	yes	no	0.939	0.931	0.504	5e-28
Q9VJE4	117	DNA-directed RNA polymera	yes	no	0.913	0.905	0.528	9e-28
Q7PVQ9	117	DNA-directed RNA polymera	yes	no	0.905	0.897	0.533	2e-27
Q9GZM3	115	DNA-directed RNA polymera	yes	no	0.931	0.939	0.504	1e-26
Q9H1A7	115	DNA-directed RNA polymera	yes	no	0.931	0.939	0.495	3e-26
Q60SM4	122	Probable DNA-directed RNA	N/A	no	0.974	0.926	0.464	1e-24

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

 Score =  216 bits (550), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 101/113 (89%), Positives = 110/113 (97%)

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

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKHS 113
           Y+LPHPL+YKIIVRIHTTSQSSPMQAYNQAINDLDKELD LK+ FEAE+AK S
Sbjct: 61  YQLPHPLKYKIIVRIHTTSQSSPMQAYNQAINDLDKELDYLKNQFEAEVAKFS 113

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 =  127 bits (319), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 53/115 (46%), Positives = 87/115 (75%)

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

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKHSRV 115
           Y++PHPL++ + +RI T + ++P++   +++  L +E  +L+++F  ++ K   V
Sbjct: 61  YRMPHPLEHNVNIRIQTNNNTNPLECVQKSMECLSREFTSLENSFIEQVQKKRNV 115

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 =  122 bits (307), Expect = 5e-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.

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 =  122 bits (307), Expect = 5e-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.

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 (307), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 55/109 (50%), Positives = 77/109 (70%)

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

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAEL 109
           YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F   +
Sbjct: 61  YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRGAI 109

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 =  122 bits (305), Expect = 9e-28,   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 (302), Expect = 2e-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 (294), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 55/109 (50%), Positives = 77/109 (70%), Gaps = 1/109 (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  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAEL 109
           YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F   L
Sbjct: 60  YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRTCL 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.

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 =  116 bits (291), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 54/109 (49%), Positives = 77/109 (70%), Gaps = 1/109 (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  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAEL 109
           YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F   L
Sbjct: 60  YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRTCL 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.

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 =  111 bits (278), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 53/114 (46%), Positives = 81/114 (71%), Gaps = 1/114 (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  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKHSR 114
           YK PHPL++KI++R+ TT+ ++P  A   AI DL  EL  L+   ++ + K ++
Sbjct: 60  YKNPHPLEHKILLRVQTTNATTPADALTTAITDLVGELSLLEHRIDSAIKKCTQ 113

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	116
225430537	116	PREDICTED: DNA-directed RNA polymerase I	1.0	1.0	0.939	6e-59
449464004	116	PREDICTED: DNA-directed RNA polymerase I	1.0	1.0	0.956	1e-58
356531671	116	PREDICTED: DNA-directed RNA polymerase I	1.0	1.0	0.931	4e-57
358248360	116	uncharacterized protein LOC100784219 [Gl	1.0	1.0	0.922	6e-57
217070988	116	unknown [Medicago truncatula] gi|3885194	1.0	1.0	0.905	1e-56
147832705	129	hypothetical protein VITISV_015574 [Viti	1.0	0.899	0.844	2e-56
224103945	116	predicted protein [Populus trichocarpa]	1.0	1.0	0.905	1e-55
388516987	116	unknown [Lotus japonicus]	1.0	1.0	0.896	2e-55
255553542	156	DNA-directed RNA polymerase II 13.6 kD p	0.939	0.698	0.944	3e-55
297819918	116	ATRPB13.6 [Arabidopsis lyrata subsp. lyr	0.974	0.974	0.911	3e-55

>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 =  231 bits (588), Expect = 6e-59,   Method: Compositional matrix adjust.
 Identities = 109/116 (93%), Positives = 113/116 (97%)

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

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKHSRVY 116
           YKLPHPLQYKII+RIHTTSQSSPMQAYNQAINDLDKELD LK+AFE ELAKHSR Y
Sbjct: 61  YKLPHPLQYKIIIRIHTTSQSSPMQAYNQAINDLDKELDYLKNAFEVELAKHSREY 116

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>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 =  229 bits (585), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 111/116 (95%), Positives = 112/116 (96%)

Query: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
           MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG
Sbjct: 1   MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKHSRVY 116
           YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELD LK+AFEAE AK SR Y
Sbjct: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDHLKNAFEAEFAKFSRDY 116

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  224 bits (572), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 108/116 (93%), Positives = 111/116 (95%)

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

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKHSRVY 116
           YKLPHPLQYKIIVRIHTTSQSSPMQAYNQ+INDLD+ELD LKSAFEAE+ K SR Y
Sbjct: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQSINDLDRELDHLKSAFEAEMLKFSRDY 116

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 =  224 bits (571), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 107/116 (92%), Positives = 111/116 (95%)

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

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKHSRVY 116
           YKLPHPLQYKIIVRIHTTSQSSPMQAYNQ++NDLD+ELD LKSAFEAE+ K SR Y
Sbjct: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQSVNDLDRELDHLKSAFEAEMLKFSRDY 116

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 =  223 bits (567), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 105/116 (90%), Positives = 111/116 (95%)

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

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKHSRVY 116
           YKLPHPLQYKII+RIHTTSQSSPMQAYNQ+INDLDKELDTLKS FEAEL K S+ Y
Sbjct: 61  YKLPHPLQYKIIIRIHTTSQSSPMQAYNQSINDLDKELDTLKSGFEAELLKFSKDY 116

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  222 bits (566), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 109/129 (84%), Positives = 113/129 (87%), Gaps = 13/129 (10%)

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

Query: 48  MQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEA 107
           MQLHRDENVLFAGYKLPHPLQYKII+RIHTTSQSSPMQAYNQAINDLDKELD LK+AFE 
Sbjct: 61  MQLHRDENVLFAGYKLPHPLQYKIIIRIHTTSQSSPMQAYNQAINDLDKELDYLKNAFEV 120

Query: 108 ELAKHSRVY 116
           ELAKHSR Y
Sbjct: 121 ELAKHSREY 129

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  220 bits (560), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 105/116 (90%), Positives = 110/116 (94%)

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

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKHSRVY 116
           YKLPHPL+YKIIVRIHTTSQSSPMQAYNQAINDLDKELD LK+AFEAELA     Y
Sbjct: 61  YKLPHPLKYKIIVRIHTTSQSSPMQAYNQAINDLDKELDHLKNAFEAELANRPGQY 116

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 =  218 bits (556), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 104/116 (89%), Positives = 110/116 (94%)

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

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKHSRVY 116
           YKLPHPLQYKIIVRIHT SQSSPMQAYNQ+INDLDKELD LK+AFEA++ + SR Y
Sbjct: 61  YKLPHPLQYKIIVRIHTASQSSPMQAYNQSINDLDKELDHLKNAFEADMLRFSRDY 116

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

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 (556), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 103/109 (94%), Positives = 106/109 (97%)

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

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAEL 109
           Y+LPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELD LKSAFE  L
Sbjct: 61  YRLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDHLKSAFEECL 109

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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 =  218 bits (556), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 103/113 (91%), Positives = 110/113 (97%)

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

Query: 61  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKHS 113
           Y+LPHPL+YKIIVRIHTTSQSSPMQAYNQAINDLDKELD LK+ FEAE+AK S
Sbjct: 61  YQLPHPLKYKIIVRIHTTSQSSPMQAYNQAINDLDKELDYLKNQFEAEVAKFS 113

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	116
DICTYBASE|DDB_G0277677	120	rpb11 "RNA polymerase II core	0.991	0.958	0.460	1.7e-27
UNIPROTKB|Q32P79	117	POLR2J "DNA-directed RNA polym	0.939	0.931	0.504	5.7e-27
UNIPROTKB|E2RD80	117	LOC100686835 "Uncharacterized	0.939	0.931	0.504	5.7e-27
UNIPROTKB|P52435	117	POLR2J "DNA-directed RNA polym	0.939	0.931	0.504	5.7e-27
MGI|MGI:109582	117	Polr2j "polymerase (RNA) II (D	0.939	0.931	0.504	5.7e-27
RGD|1310198	117	Polr2j "polymerase (RNA) II (D	0.939	0.931	0.504	5.7e-27
FB|FBgn0032634	117	Rpb11 "Rpb11" [Drosophila mela	0.913	0.905	0.528	7.3e-27
UNIPROTKB|F1PXE5	130	LOC100686835 "Uncharacterized	0.905	0.807	0.523	7.3e-27
UNIPROTKB|Q9H1A6	127	POLR2J1 "DNA-directed RNA poly	0.905	0.826	0.523	7.3e-27
ZFIN|ZDB-GENE-050522-120	117	polr2j "polymerase (RNA) II (D	0.939	0.931	0.486	9.4e-27

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

 Score = 308 (113.5 bits), Expect = 1.7e-27, P = 1.7e-27
 Identities = 53/115 (46%), Positives = 87/115 (75%)

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

Query:    61 YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKHSRV 115
             Y++PHPL++ + +RI T + ++P++   +++  L +E  +L+++F  ++ K   V
Sbjct:    61 YRMPHPLEHNVNIRIQTNNNTNPLECVQKSMECLSREFTSLENSFIEQVQKKRNV 115

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

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

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 55/109 (50%), Positives = 77/109 (70%)

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

Query:    61 YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAEL 109
             YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F   +
Sbjct:    61 YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAI 109

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 = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 55/109 (50%), Positives = 77/109 (70%)

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

Query:    61 YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAEL 109
             YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F   +
Sbjct:    61 YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAI 109

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 = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 55/109 (50%), Positives = 77/109 (70%)

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

Query:    61 YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAEL 109
             YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F   +
Sbjct:    61 YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAI 109

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

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

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 55/109 (50%), Positives = 77/109 (70%)

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

Query:    61 YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAEL 109
             YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F   +
Sbjct:    61 YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRGAI 109

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

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

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 55/109 (50%), Positives = 77/109 (70%)

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

Query:    61 YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAEL 109
             YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F   +
Sbjct:    61 YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAI 109

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

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

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

 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:    22 MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 81

Query:    61 YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105
             YK+PHPL++KII+R+ TT   SP +A+  AI DL  EL  L+  F
Sbjct:    82 YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERF 126

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

GO:0003677 "DNA binding" evidence=IEA

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

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

 Score = 301 (111.0 bits), Expect = 9.4e-27, P = 9.4e-27
 Identities = 53/109 (48%), Positives = 77/109 (70%)

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 YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAEL 109
             YK+PHPL++K+++R+ TT   SP +A+  AI DL  EL  L+  F   +
Sbjct:    61 YKVPHPLEHKVVIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAI 109

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

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

GO:0003677 "DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q86JJ5	RPB11_DICDI	No assigned EC number	0.4608	0.9913	0.9583	yes	no
Q9GZM3	RPB1B_HUMAN	No assigned EC number	0.5045	0.9310	0.9391	yes	no
P52435	RPB11_HUMAN	No assigned EC number	0.5238	0.9051	0.8974	yes	no
Q8IER7	RPB11_PLAF7	No assigned EC number	0.3333	0.9396	0.8650	yes	no
P87123	RPB11_SCHPO	No assigned EC number	0.4666	0.8965	0.8455	yes	no
Q9VJE4	RPB11_DROME	No assigned EC number	0.5283	0.9137	0.9059	yes	no
P38902	RPB11_YEAST	No assigned EC number	0.4444	0.9310	0.9	yes	no
O08740	RPB11_MOUSE	No assigned EC number	0.5045	0.9396	0.9316	yes	no
Q7PVQ9	RPB11_ANOGA	No assigned EC number	0.5333	0.9051	0.8974	yes	no
Q32P79	RPB11_BOVIN	No assigned EC number	0.5238	0.9051	0.8974	yes	no
Q9XVH6	RPB11_CAEEL	No assigned EC number	0.4824	0.9741	0.9262	yes	no
Q38859	RPB11_ARATH	No assigned EC number	0.8938	0.9741	0.9741	yes	no
Q9H1A7	RPB1C_HUMAN	No assigned EC number	0.4954	0.9310	0.9391	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	LOW CONFIDENCE prediction!
4th Layer	2.7.7.6	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00032808001	SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (116 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00033123001	SubName- Full=Putative uncharacterized protein (Chromosome chr5 scaffold_64, whole genome shotg [...] (114 aa)	•			•	•	•	•		0.979
	GSVIVG00002744001	SubName- Full=Chromosome chr1 scaffold_135, whole genome shotgun sequence; (78 aa)				•	•	•	•		0.975
	GSVIVG00036639001	SubName- Full=Chromosome chr3 scaffold_8, whole genome shotgun sequence; (318 aa)				•	•	•	•		0.945
	GSVIVG00024229001	SubName- Full=Putative uncharacterized protein (Chromosome chr6 scaffold_3, whole genome shotgu [...] (176 aa)				•	•	•	•		0.936
	GSVIVG00020457001	SubName- Full=Chromosome chr5 scaffold_2, whole genome shotgun sequence; (208 aa)				•		•			0.922
	GSVIVG00016705001	SubName- Full=Chromosome chr11 scaffold_13, whole genome shotgun sequence; (206 aa)				•	•	•	•		0.921
	GSVIVG00028076001	SubName- Full=Chromosome chr7 scaffold_42, whole genome shotgun sequence; (533 aa)				•		•			0.902
	Ndpk	RecName- Full=Nucleoside diphosphate kinase; EC=2.7.4.6; (148 aa)				•		•			0.900
	GSVIVG00038611001	RecName- Full=Pyruvate kinase; EC=2.7.1.40; (573 aa)						•			0.899
	GSVIVG00036953001	SubName- Full=Chromosome chr1 scaffold_84, whole genome shotgun sequence; (417 aa)						•			0.899

---

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	116
cd06926	93	cd06926, RNAP_II_RPB11, RPB11 subunit of Eukaryoti	6e-48
pfam13656	77	pfam13656, RNA_pol_L_2, RNA polymerase Rpb3/Rpb11	5e-24
COG1761	99	COG1761, RPB11, DNA-directed RNA polymerase, subun	3e-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 =  148 bits (375), Expect = 6e-48
 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 = 86.9 bits (216), Expect = 5e-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 = 75.5 bits (186), Expect = 3e-19
 Identities = 34/93 (36%), Positives = 50/93 (53%)

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  IHTTSQSSPMQAYNQAINDLDKELDTLKSAFEA 107
           I T     P +A  +A   + K+L+ L   FE 
Sbjct: 61  IKTKGGVDPKEALKRAARKILKDLEELLDQFEE 93

Length = 99

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

 Score = 68.8 bits (169), 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 = 67.5 bits (165), 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 = 57.6 bits (140), 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 = 55.3 bits (134), 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 = 54.9 bits (133), 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	116
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 [	100.0
cd00460	86	RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA pol	99.93
PF01193	66	RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation	99.7
PRK14979	195	DNA-directed RNA polymerase subunit D; Provisional	95.61
cd06928	215	RNAP_alpha_NTD N-terminal domain of the Alpha subu	95.44
cd07028	212	RNAP_RPB3_like RPB3 subunit of RNA polymerase. The	95.26
TIGR02027	297	rpoA DNA-directed RNA polymerase, alpha subunit, b	95.07
smart00662	224	RPOLD RNA polymerases D. DNA-directed RNA polymera	94.93
PRK05182	310	DNA-directed RNA polymerase subunit alpha; Provisi	94.3
PRK00783	263	DNA-directed RNA polymerase subunit D; Provisional	94.11
CHL00013	327	rpoA RNA polymerase alpha subunit	94.1
cd07030	259	RNAP_D D subunit of Archaeal RNA polymerase. The D	93.03
cd07031	265	RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polyme	93.02
CHL00013	327	rpoA RNA polymerase alpha subunit	91.93
PRK05182	310	DNA-directed RNA polymerase subunit alpha; Provisi	91.79
cd06928	215	RNAP_alpha_NTD N-terminal domain of the Alpha subu	91.14
cd07028	212	RNAP_RPB3_like RPB3 subunit of RNA polymerase. The	91.04
cd07031	265	RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polyme	90.2
PRK14979	195	DNA-directed RNA polymerase subunit D; Provisional	89.86
smart00662	224	RPOLD RNA polymerases D. DNA-directed RNA polymera	89.81
COG0202	317	RpoA DNA-directed RNA polymerase, alpha subunit/40	89.24
PRK00783	263	DNA-directed RNA polymerase subunit D; Provisional	89.07
cd07030	259	RNAP_D D subunit of Archaeal RNA polymerase. The D	86.59
cd07032	291	RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA poly	83.91
TIGR02027	297	rpoA DNA-directed RNA polymerase, alpha subunit, b	81.82
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	80.34

>KOG4392 consensus RNA polymerase, subunit L [Transcription]

Probab=100.00  E-value=8.8e-44  Score=249.92  Aligned_cols=111  Identities=54%  Similarity=0.849  Sum_probs=110.0

Q ss_pred             CCCCccccceeeCCCCeeeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCC
Q 033562            1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQ   80 (116)
Q Consensus         1 ~n~p~~~~~~~l~~~~~Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~   80 (116)
                      ||||+|||+|+|.+|++||++..|+|++|++.|+|.+|||||||+|+.+|+++|+|.||||++|||++.++.+||||..+
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             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033562           81 SSPMQAYNQAINDLDKELDTLKSAFEAELAK  111 (116)
Q Consensus        81 ~~p~e~l~~a~~~l~~~~~~l~~~f~~a~~~  111 (116)
                      ++|.++|.+|+.++...++.++..|..+++.
T Consensus        81 ~~p~~al~~a~~~l~~el~~l~~~f~~~~~~  111 (117)
T KOG4392|consen   81 CSPADALTNAITDLIEELSLLENRFKAEAAL  111 (117)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999999999999986

>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II

Probab=100.00  E-value=5.1e-39  Score=220.15  Aligned_cols=93  Identities=57%  Similarity=0.903  Sum_probs=91.2

Q ss_pred             CCCCeeeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHH
Q 033562           13 PEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAIN   92 (116)
Q Consensus        13 ~~~~~Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~   92 (116)
                      |+|++||++..|++++|+++|+|.||||||||+||+.|+++|+|.||||+||||++++++|||||+++.+|.+||++|++
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 033562           93 DLDKELDTLKSAF  105 (116)
Q Consensus        93 ~l~~~~~~l~~~f  105 (116)
                      +|.+.|++++++|
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=2e-36  Score=200.87  Aligned_cols=77  Identities=47%  Similarity=0.788  Sum_probs=72.7

Q ss_pred             ceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 033562           29 NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF  105 (116)
Q Consensus        29 n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f  105 (116)
                      |+++|+|.+|||||||+||++|+++|+|.||||+|||||+++++|||||+++++|.+||++|+++|.++|++++++|
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=6.9e-36  Score=201.78  Aligned_cols=82  Identities=32%  Similarity=0.575  Sum_probs=79.4

Q ss_pred             cCCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033562           24 DTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS  103 (116)
Q Consensus        24 ~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~  103 (116)
                      ..+.+|+++|+|.||||||||+||+.|+++|+|.||||+||||++++++|||||+++.+|.+||++|+++|.+.|+++++
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            46889999999999999999999999999999999999999999999999999999899999999999999999999998


Q ss_pred             HH
Q 033562          104 AF  105 (116)
Q Consensus       104 ~f  105 (116)
                      +|
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=8.9e-35  Score=196.36  Aligned_cols=79  Identities=29%  Similarity=0.413  Sum_probs=76.3

Q ss_pred             CCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033562           25 TKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS  103 (116)
Q Consensus        25 ~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~  103 (116)
                      .+.+|+++|+|.||||||||+||+.|+++|+|.||||+|||||+++++|||||+++.+|.+||++|+++|.+.|++|++
T Consensus         7 ~~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqt~~~~~p~~al~~a~~~L~~~~~~~~~   85 (85)
T PRK01146          7 EKEDNELELEIEGEDHTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLKIKTDGGIDPLEALKEAAKRIIDLCDEFLD   85 (85)
T ss_pred             ecCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEeecCCCCCCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence            5788999999999999999999999999999999999999999999999999999999999999999999999999863

>cd06927 RNAP_L L subunit of Archaeal RNA polymerase

Probab=100.00  E-value=1.8e-34  Score=194.13  Aligned_cols=79  Identities=30%  Similarity=0.443  Sum_probs=75.7

Q ss_pred             CCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033562           25 TKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS  103 (116)
Q Consensus        25 ~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~  103 (116)
                      .+..|+++|+|.||||||||+||++|+++|+|.||||++||||+++++|||||+++.+|.+||++|+++|++.|++|++
T Consensus         5 ~~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~p~~al~~a~~~l~~~~~~~~~   83 (83)
T cd06927           5 EKEDNELELEIEGEDHTLLNLLKEELLRDPGVKVASYDIEHPLLSNPVLKIKTDGGVDPLEALKEAAKRLIDLCEEFLD   83 (83)
T ss_pred             EcCCCEEEEEEeCCCchHHHHHHHHHhcCCCeEEEEeecCCCCCCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence            3578999999999999999999999999999999999999999999999999999899999999999999999999863

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=2.8e-34  Score=193.14  Aligned_cols=78  Identities=40%  Similarity=0.614  Sum_probs=74.9

Q ss_pred             CCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q 033562           25 TKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLK  102 (116)
Q Consensus        25 ~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~  102 (116)
                      ++..|+++|+|.||||||||+||++|+++|+|.||||+|||||+++++|||||+++.+|.+||++|+++|.+.|++++
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            356799999999999999999999999999999999999999999999999999989999999999999999999985

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=1.2e-33  Score=195.80  Aligned_cols=97  Identities=36%  Similarity=0.545  Sum_probs=91.1

Q ss_pred             CeeeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHH
Q 033562           16 TKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLD   95 (116)
Q Consensus        16 ~~Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~   95 (116)
                      .++.++....+..|+++|++.||||||||+|++.|+++++|+||||+||||+.+++++||||+++++|.+||++|++.++
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            45667777778999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhh
Q 033562           96 KELDTLKSAFEAELAKHS  113 (116)
Q Consensus        96 ~~~~~l~~~f~~a~~~~~  113 (116)
                      +.|++|.++| ++++++.
T Consensus        82 ~~~~~l~~~~-~~~e~~~   98 (99)
T COG1761          82 KDLEELLDQF-EEFEKKE   98 (99)
T ss_pred             HHHHHHHHHH-HHHHhhc
Confidence            9999999999 8887764

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

Probab=100.00  E-value=4.1e-34  Score=198.00  Aligned_cols=89  Identities=30%  Similarity=0.585  Sum_probs=86.0

Q ss_pred             CcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 033562           27 IINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE  106 (116)
Q Consensus        27 ~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f~  106 (116)
                      ..++++|++.+|||||||.||++|+++|.|+||||+||||++++++|||||.++..++++|++|+++|.++|++++.+|+
T Consensus        14 d~~~~Tf~~~eEDHTlgNalR~vI~k~peVefcGYtIPHPse~k~niRIQt~~~~~A~evl~kgl~el~~~c~~v~~kF~   93 (105)
T KOG3438|consen   14 DLSSATFQLREEDHTLGNALRYVIMKNPEVEFCGYTIPHPSEDKINIRIQTRDGDPAVEVLKKGLEELMQLCDHVRSKFE   93 (105)
T ss_pred             CCCceEEEEEecCcchhHHHHHHHhcCCceEEEeccCCCCchhhheEEEEecCCCcchHHHHHHHHHHHHHHHHHHHHHH
Confidence            67899999999999999999999999999999999999999999999999998889999999999999999999999999


Q ss_pred             HHHHhhhcc
Q 033562          107 AELAKHSRV  115 (116)
Q Consensus       107 ~a~~~~~~~  115 (116)
                      +++++|+.+
T Consensus        94 ~~i~~~k~~  102 (105)
T KOG3438|consen   94 EEIEEYKDQ  102 (105)
T ss_pred             HHHHHhhhh
Confidence            999999754

>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase

Probab=99.93  E-value=5.9e-26  Score=152.82  Aligned_cols=76  Identities=39%  Similarity=0.592  Sum_probs=72.0

Q ss_pred             CCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCC------CceeEEEEEeCCCCCHHHHHHHHHHHHHHHH
Q 033562           25 TKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPL------QYKIIVRIHTTSQSSPMQAYNQAINDLDKEL   98 (116)
Q Consensus        25 ~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl------~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~   98 (116)
                      .+..|+++|+|.||||||||+||+.|++ +.|.||||+||||+      .+++.|+|+|+|+.+|.+||++|++.|.+.|
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            3567999999999999999999999999 99999999999999      9999999999999999999999999999988


Q ss_pred             HHH
Q 033562           99 DTL  101 (116)
Q Consensus        99 ~~l  101 (116)
                      +.|
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=2.1e-17  Score=105.89  Aligned_cols=65  Identities=35%  Similarity=0.556  Sum_probs=61.0

Q ss_pred             eEEEEecCCcchHHHHHHHhhcC-CCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 033562           31 ASFTIEREEHTIGNILRMQLHRD-ENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELD   99 (116)
Q Consensus        31 ~~~~i~~EDHTLgNlLr~~L~~~-~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~   99 (116)
                      ++|.+.|+|||+||+||..|+++ |+|.+++    ||..+++.++|+|+|+.+|.++|.+|++.|.+.|+
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            47999999999999999999999 9999999    99999999999999999999999999999998763

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=95.61  E-value=0.06  Score=41.43  Aligned_cols=51  Identities=14%  Similarity=0.171  Sum_probs=41.1

Q ss_pred             CCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033562           53 DENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEA  107 (116)
Q Consensus        53 ~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f~~  107 (116)
                      .| |. |.|+..-  .++..+.|.|+|+++|.+||..|++-|.+.++.|.+.+..
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 5554322  4999999999999999999999999999999998777643

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

Probab=95.44  E-value=0.03  Score=43.21  Aligned_cols=45  Identities=27%  Similarity=0.240  Sum_probs=37.3

Q ss_pred             CeeeeeecCCC------CCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 033562           55 NVLFAGYKLPH------PLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELD   99 (116)
Q Consensus        55 ~V~fAgY~ipH------Pl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~   99 (116)
                      =|.-+.|.|.-      .-.+++.|-|.|+|.++|.+||..|++.|.+.+.
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            36677787643      3457899999999999999999999999988775

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=95.26  E-value=0.057  Score=41.81  Aligned_cols=52  Identities=17%  Similarity=0.262  Sum_probs=43.8

Q ss_pred             hcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033562           51 HRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS  103 (116)
Q Consensus        51 ~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~  103 (116)
                      .+-.=|.-|+|++. |-.++..|.|-|+|..+|.+|+.+|++-|++.++.|.+
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            34445677888864 36799999999999999999999999999999998875

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

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

Probab=95.07  E-value=0.072  Score=43.13  Aligned_cols=49  Identities=24%  Similarity=0.310  Sum_probs=40.8

Q ss_pred             CeeeeeecCCC------CCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033562           55 NVLFAGYKLPH------PLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS  103 (116)
Q Consensus        55 ~V~fAgY~ipH------Pl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~  103 (116)
                      -|.-+.|.|..      ...+++.+.|.|+|.++|.+||.+|++-|.+.+..|.+
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      23478999999999999999999999999999988865

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.

>smart00662 RPOLD RNA polymerases D

Probab=94.93  E-value=0.059  Score=41.72  Aligned_cols=45  Identities=24%  Similarity=0.313  Sum_probs=37.4

Q ss_pred             eeeeeecCCCCC----------------CceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Q 033562           56 VLFAGYKLPHPL----------------QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDT  100 (116)
Q Consensus        56 V~fAgY~ipHPl----------------~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~  100 (116)
                      |..+.|.+.-|.                .+++.|.|.|+|..+|.+||.+|++-|...++.
T Consensus       163 v~~v~~~~~~~~~~~~~~~~~~c~~~~~~d~l~f~IeT~G~i~p~~al~~A~~iL~~k~~~  223 (224)
T smart00662      163 VDRVAYQVECPRVVQRTDCCRECDEGEEYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEA  223 (224)
T ss_pred             hhheeeeccCCccceecccchhhhccCCCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHhh
Confidence            555667766664                588999999999999999999999999887764

DNA-directed RNA polymerase subunit D and bacterial alpha chain

>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional

Probab=94.30  E-value=0.13  Score=41.93  Aligned_cols=49  Identities=20%  Similarity=0.232  Sum_probs=40.7

Q ss_pred             CeeeeeecCCCC------CCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033562           55 NVLFAGYKLPHP------LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS  103 (116)
Q Consensus        55 ~V~fAgY~ipHP------l~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~  103 (116)
                      -|.-+.|.+.-.      -.+++.+.|.|+|.++|.+||.+|++-|.+.+..|.+
T Consensus       171 PV~~vny~ve~~~~~~~~~~e~L~leI~TnGsi~P~eAl~~A~~iL~~~l~~f~~  225 (310)
T PRK05182        171 PVKKVNYTVENTRVGQRTDYDKLILEVETDGSITPEEALALAAKILVEQLSVFVD  225 (310)
T ss_pred             CccceEEEecccccCCCCcceEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence            366677876542      1468999999999999999999999999999988765

>PRK00783 DNA-directed RNA polymerase subunit D; Provisional

Probab=94.11  E-value=0.064  Score=42.14  Aligned_cols=36  Identities=17%  Similarity=0.172  Sum_probs=28.6

Q ss_pred             eeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcC-CC
Q 033562           18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-EN   55 (116)
Q Consensus        18 Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~   55 (116)
                      ++++.+.  ..+.++|.+.|-|+||||.||-.|+.. |+
T Consensus         2 ~~~~~~~--~~~~~~f~~~g~~~t~~NalRRvlls~vp~   38 (263)
T PRK00783          2 EIEILEL--DDRSARFVVEGVTPAFANAIRRAMIADVPT   38 (263)
T ss_pred             ceEEEEc--CCcEEEEEEeCCCHHHHHHHHHHHHHcCCe
Confidence            3555543  347899999999999999999999985 54

>CHL00013 rpoA RNA polymerase alpha subunit

Probab=94.10  E-value=0.13  Score=42.39  Aligned_cols=49  Identities=18%  Similarity=0.169  Sum_probs=41.2

Q ss_pred             CeeeeeecCCCC-----CCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033562           55 NVLFAGYKLPHP-----LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS  103 (116)
Q Consensus        55 ~V~fAgY~ipHP-----l~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~  103 (116)
                      =|.-+.|.|..-     ..+++.+-|.|+|.++|.+||..|++-|.+.+.-+.+
T Consensus       170 PV~kVny~Ve~~~~~~~~~e~L~lEI~TnGsi~P~~Al~~Aa~il~~~~~~~~~  223 (327)
T CHL00013        170 PVRNVNYSIHSYGNGNEKQEILFLEIWTNGSITPKEALHEASRNLIDLFIPFLH  223 (327)
T ss_pred             CeeEEEEEEEEcccCCcccceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            366777887651     2578999999999999999999999999999887764

>cd07030 RNAP_D D subunit of Archaeal RNA polymerase

Probab=93.03  E-value=0.13  Score=40.33  Aligned_cols=36  Identities=14%  Similarity=0.149  Sum_probs=28.9

Q ss_pred             eeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcC-CC
Q 033562           18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-EN   55 (116)
Q Consensus        18 Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~   55 (116)
                      ++++.+.  .++.+.|.+.|-|+|+||.||-.|+.. |+
T Consensus         2 ~~~~~~~--~~~~~~f~~~g~~~s~~NalRRills~vp~   38 (259)
T cd07030           2 EIEVLEL--DDDRARFVLEGVPPAFANAIRRAIISEVPT   38 (259)
T ss_pred             ceEEEec--CCCEEEEEEeCCCHHHHHHHHHHHHhcCCe
Confidence            4555543  358899999999999999999999884 54

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

>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II

Probab=93.02  E-value=0.21  Score=39.85  Aligned_cols=53  Identities=17%  Similarity=0.140  Sum_probs=43.8

Q ss_pred             CeeeeeecCCCCC-----------CceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033562           55 NVLFAGYKLPHPL-----------QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEA  107 (116)
Q Consensus        55 ~V~fAgY~ipHPl-----------~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f~~  107 (116)
                      ...||-..+.||-           .+.+.+.|-|.|..+|.++|.+|++-|.+.++.|.+.+..
T Consensus       201 ~c~~c~~c~~~~~~~~~~v~i~~~~~~fiF~VES~Gsl~p~~Iv~~Al~iL~~K~~~l~~~l~~  264 (265)
T cd07031         201 WPKSENACIEEPPEKDALFDIDAKPDKFYFNVESTGALPPEQIVLSGLEILKKKLADLQLQLSE  264 (265)
T ss_pred             cCchhHHHhhcccccCCceEEEeeCCEEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3455555566653           5789999999999999999999999999999999988653

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.

>CHL00013 rpoA RNA polymerase alpha subunit

Probab=91.93  E-value=0.31  Score=40.20  Aligned_cols=47  Identities=26%  Similarity=0.262  Sum_probs=36.8

Q ss_pred             eEeeccCCCcceeEEEE----ecCCcchHHHHHHHhhc-CCCeeeeeecCCC
Q 033562           19 VSYERDTKIINAASFTI----EREEHTIGNILRMQLHR-DENVLFAGYKLPH   65 (116)
Q Consensus        19 v~~~~~~k~~n~~~~~i----~~EDHTLgNlLr~~L~~-~~~V~fAgY~ipH   65 (116)
                      +....+....+.+.|.|    .|..|||||+||-.|+. .|+.-+.+-+|.+
T Consensus        10 ie~~~~~~~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~g   61 (327)
T CHL00013         10 VESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEG   61 (327)
T ss_pred             eeEEEecCCCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECC
Confidence            44455556678899999    67889999999999998 4887777777654

>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional

Probab=91.79  E-value=0.38  Score=39.20  Aligned_cols=47  Identities=26%  Similarity=0.311  Sum_probs=34.8

Q ss_pred             eeEeeccCCCcceeEEEEe----cCCcchHHHHHHHhhcC-CCeeeeeecCC
Q 033562           18 KVSYERDTKIINAASFTIE----REEHTIGNILRMQLHRD-ENVLFAGYKLP   64 (116)
Q Consensus        18 Kv~~~~~~k~~n~~~~~i~----~EDHTLgNlLr~~L~~~-~~V~fAgY~ip   64 (116)
                      ++++...+...+.+.|.+.    |.++|+||+||-.|+.. |+.-..+-+|.
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            3444433334689999996    99999999999999984 77666666654

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

Probab=91.14  E-value=0.32  Score=37.53  Aligned_cols=39  Identities=28%  Similarity=0.336  Sum_probs=30.7

Q ss_pred             CCcceeEEEE----ecCCcchHHHHHHHhhcC-CCeeeeeecCC
Q 033562           26 KIINAASFTI----EREEHTIGNILRMQLHRD-ENVLFAGYKLP   64 (116)
Q Consensus        26 k~~n~~~~~i----~~EDHTLgNlLr~~L~~~-~~V~fAgY~ip   64 (116)
                      ...+.+.|.|    .|.++|+||.||-.|+.. |+.-.-+-+|.
T Consensus         6 ~~~~~~~F~i~pl~~g~~~tlgNaLRRvLLs~ipg~aI~~v~I~   49 (215)
T cd06928           6 KRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIE   49 (215)
T ss_pred             CCCcEEEEEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEEEEEc
Confidence            3468899999    779999999999999884 77665555553

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=91.04  E-value=0.26  Score=38.19  Aligned_cols=31  Identities=13%  Similarity=0.216  Sum_probs=27.0

Q ss_pred             CCcceeEEEEecCCcchHHHHHHHhhcC-CCe
Q 033562           26 KIINAASFTIEREEHTIGNILRMQLHRD-ENV   56 (116)
Q Consensus        26 k~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~V   56 (116)
                      +.++.+.|.+.|-|+|+||+||-.|+.. |+.
T Consensus         8 ~~~~~~~f~l~g~~~t~aNaLRRiLLsevP~~   39 (212)
T cd07028           8 ADKDNVDFILSGVDLAMANALRRVMIAEVPTM   39 (212)
T ss_pred             cCCCEEEEEEEccChhHHHHHHHHHHHcCcce
Confidence            5678899999999999999999999985 553

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=90.20  E-value=0.63  Score=37.09  Aligned_cols=39  Identities=15%  Similarity=0.260  Sum_probs=30.0

Q ss_pred             eeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcC-CCeee
Q 033562           18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-ENVLF   58 (116)
Q Consensus        18 Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~V~f   58 (116)
                      +|++.+.  .++.++|.+.+=|+|+||+||-.|+.. |..-.
T Consensus         2 ~i~i~~~--~~~~~~F~l~~~~~s~aNALRRillsevPt~AI   41 (265)
T cd07031           2 RVEITEL--TDDKVKFILENTDLSVANSLRRVMIAEVPTLAI   41 (265)
T ss_pred             cEEEEEc--CCCEEEEEEEcCcHHHHHHHHHHHHHcCccceE
Confidence            3555543  458899999999999999999999884 65433

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=89.86  E-value=0.6  Score=35.93  Aligned_cols=37  Identities=14%  Similarity=0.222  Sum_probs=29.8

Q ss_pred             ccCCCcceeEEEEecCCcchHHHHHHHhhcC-CCeeeee
Q 033562           23 RDTKIINAASFTIEREEHTIGNILRMQLHRD-ENVLFAG   60 (116)
Q Consensus        23 ~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~V~fAg   60 (116)
                      .-++..+.++|.+. -|.|+||.||-.|+.. |+.-.-+
T Consensus         8 ~~~~~~~~~~f~l~-~~~tlgNaLRRvLLssipg~AI~~   45 (195)
T PRK14979          8 EKTRIGEEFKFSLK-APISFSSALRRIMISEVPTYAIEN   45 (195)
T ss_pred             eeccCCcEEEEEEE-cCccHHHHHHHHHHhcCcceeEEE
Confidence            33678889999999 9999999999999884 6644444

>smart00662 RPOLD RNA polymerases D

Probab=89.81  E-value=0.44  Score=36.84  Aligned_cols=33  Identities=24%  Similarity=0.299  Sum_probs=26.4

Q ss_pred             eEEEEecCCcchHHHHHHHhhcC-CCeeeeeecC
Q 033562           31 ASFTIEREEHTIGNILRMQLHRD-ENVLFAGYKL   63 (116)
Q Consensus        31 ~~~~i~~EDHTLgNlLr~~L~~~-~~V~fAgY~i   63 (116)
                      +.|++.+-++|+||+||-.|+.. |+.-.-+.+|
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 6655554444

DNA-directed RNA polymerase subunit D and bacterial alpha chain

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

Probab=89.24  E-value=0.8  Score=37.58  Aligned_cols=45  Identities=18%  Similarity=0.017  Sum_probs=31.8

Q ss_pred             eEeeccC--CCcceeEEEEecCCcchHHHHHHHhhc-CCCeeeeeecC
Q 033562           19 VSYERDT--KIINAASFTIEREEHTIGNILRMQLHR-DENVLFAGYKL   63 (116)
Q Consensus        19 v~~~~~~--k~~n~~~~~i~~EDHTLgNlLr~~L~~-~~~V~fAgY~i   63 (116)
                      |++...+  ...-.++|...|-+|||||+||-.|+. .|+.-.-+-+|
T Consensus         7 i~i~~~~~~~~~~~ieplerG~g~tlgNALRRvLLSsiPg~Av~~V~I   54 (317)
T COG0202           7 VKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEI   54 (317)
T ss_pred             eEEEEcccccccEEEEEeeeCCcchhHHHHHHHHHHcCccceEEEEEE
Confidence            4444333  336688999999999999999999988 47644433333

>PRK00783 DNA-directed RNA polymerase subunit D; Provisional

Probab=89.07  E-value=1.2  Score=34.98  Aligned_cols=41  Identities=20%  Similarity=0.231  Sum_probs=37.0

Q ss_pred             CCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033562           67 LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEA  107 (116)
Q Consensus        67 l~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f~~  107 (116)
                      ..++..+.+.|.|..+|.+++..|++-|...++.|.++++.
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            36778899999999999999999999999999999988764

>cd07030 RNAP_D D subunit of Archaeal RNA polymerase

Probab=86.59  E-value=1.8  Score=33.87  Aligned_cols=37  Identities=19%  Similarity=0.302  Sum_probs=33.2

Q ss_pred             CceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 033562           68 QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSA  104 (116)
Q Consensus        68 ~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~  104 (116)
                      .+...+.|.|.|..+|.++|+.|++-|.+.++.|.++
T Consensus       222 ~~~~if~vEs~Gsl~p~~il~~A~~~l~~k~~~~~~~  258 (259)
T cd07030         222 EDRFIFEVESDGSLPPKEILLEALRILKEKADELIEA  258 (259)
T ss_pred             CCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            4567888999999999999999999999999998765

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=83.91  E-value=3  Score=33.93  Aligned_cols=37  Identities=22%  Similarity=0.266  Sum_probs=33.8

Q ss_pred             CCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033562           67 LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS  103 (116)
Q Consensus        67 l~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~  103 (116)
                      -.+.+.+.|-|.|...|.+.+.+|++-|.+.|+.+++
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            4677999999999999999999999999999998875

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=81.82  E-value=1.7  Score=35.22  Aligned_cols=29  Identities=24%  Similarity=0.236  Sum_probs=23.6

Q ss_pred             ecCCcchHHHHHHHhhcC-CCeeeeeecCC
Q 033562           36 EREEHTIGNILRMQLHRD-ENVLFAGYKLP   64 (116)
Q Consensus        36 ~~EDHTLgNlLr~~L~~~-~~V~fAgY~ip   64 (116)
                      .|..|||||+||-.|+.. |++-..+-+|.
T Consensus        11 ~g~g~TlGNaLRRvLLs~i~g~aI~~vkI~   40 (297)
T TIGR02027        11 RGFGITLGNALRRVLLSSIPGAAITAVKID   40 (297)
T ss_pred             CCchhHHHHHHHHHHHhcCCceEEEEEEEc
Confidence            688999999999999984 87776666654

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.

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=80.34  E-value=1.4  Score=36.83  Aligned_cols=24  Identities=29%  Similarity=0.530  Sum_probs=21.8

Q ss_pred             CCcchHHHHHHHhhcCCCeeeeee
Q 033562           38 EEHTIGNILRMQLHRDENVLFAGY   61 (116)
Q Consensus        38 EDHTLgNlLr~~L~~~~~V~fAgY   61 (116)
                      ..|++.|.||..|.+||+|.+.|=
T Consensus       183 dT~sF~~aLraALReDPDVIlvGE  206 (353)
T COG2805         183 DTLSFANALRAALREDPDVILVGE  206 (353)
T ss_pred             cHHHHHHHHHHHhhcCCCEEEEec
Confidence            349999999999999999999993

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	116
1i3q_K	120	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		4e-22
3h0g_K	123	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		7e-21
2pa8_L	92	X-Ray Crystal Structure Of The DL SUBCOMPLEX OF THE		2e-08
2waq_L	92	The Complete Structure Of The Archaeal 13-Subunit D		9e-08

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

Iteration: 1
 Score = 99.4 bits (246), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 48/108 (44%), 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  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAE 108
           YK+ HP   +  +RI TT    P  A   A N +  +L  LK+ FE E
Sbjct: 61  YKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETE 108

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

Iteration: 1
 Score = 95.5 bits (236), Expect = 7e-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 = 2e-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 = 52.0 bits (123), Expect = 9e-08,   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	116
1twf_K	120	B13.6, DNA-directed RNA polymerase II 13.6 kDa pol	8e-44
3h0g_K	123	DNA-directed RNA polymerase II subunit RPB11; tran	7e-42
2pa8_L	92	DNA-directed RNA polymerase subunit L; ferredoxin-	6e-28
1xpp_A	115	TA1416, DNA-directed RNA polymerase subunit L; str	4e-26

>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 =  138 bits (348), Expect = 8e-44
 Identities = 48/112 (42%), Positives = 65/112 (58%)

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  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKH 112
           YK+ HP   +  +RI TT    P  A   A N +  +L  LK+ FE E    
Sbjct: 61  YKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQ 112

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

 Score =  133 bits (335), Expect = 7e-42
 Identities = 50/112 (44%), Positives = 64/112 (57%), Gaps = 1/112 (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  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKH 112
           YK+PHPL +  I+R+ T    SP Q    A   L   L+ +K  F  E    
Sbjct: 60  YKVPHPLNHNFILRVQTVEDCSPKQVIVDAAKSLITHLEEIKVNFMREWELK 111

>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 = 96.8 bits (241), Expect = 6e-28
 Identities = 28/86 (32%), Positives = 38/86 (44%)

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  MQAYNQAINDLDKELDTLKSAFEAEL 109
             A  +AI ++           +   
Sbjct: 66  KDALLKAIENIRGMTSHYIDEIKGLT 91

>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 = 93.1 bits (231), Expect = 4e-26
 Identities = 22/99 (22%), Positives = 45/99 (45%), Gaps = 1/99 (1%)

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

Query: 74  RIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKH 112
            +   S   P  A  +A+  L K  + L + F+ E  ++
Sbjct: 66  YVRVKS-GKPQSAIKRAVRKLSKLYEDLGTQFQKEFQRY 103

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	116
3h0g_K	123	DNA-directed RNA polymerase II subunit RPB11; tran	100.0
1twf_K	120	B13.6, DNA-directed RNA polymerase II 13.6 kDa pol	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-	94.58
1twf_C	318	B44.5, DNA-directed RNA polymerase II 45 kDa polyp	94.24
1bdf_A	235	RNA polymerase alpha subunit; nucleotidyltransfera	92.83
3lu0_A	329	DNA-directed RNA polymerase subunit alpha; E. coli	92.62
2pa8_D	265	DNA-directed RNA polymerase subunit D; ferredoxin-	92.54
2a6h_A	315	DNA-directed RNA polymerase alpha chain; RNA polym	92.26
1bdf_A	235	RNA polymerase alpha subunit; nucleotidyltransfera	92.22
2a6h_A	315	DNA-directed RNA polymerase alpha chain; RNA polym	91.62
1twf_C	318	B44.5, DNA-directed RNA polymerase II 45 kDa polyp	91.03
3h0g_C	297	DNA-directed RNA polymerase II subunit RPB3; trans	90.81
3h0g_C	297	DNA-directed RNA polymerase II subunit RPB3; trans	89.99
3lu0_A	329	DNA-directed RNA polymerase subunit alpha; E. coli	88.51

>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=2.8e-51  Score=292.38  Aligned_cols=113  Identities=44%  Similarity=0.656  Sum_probs=111.1

Q ss_pred             CCCCccccceeeCCCCeeeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCC
Q 033562            1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQ   80 (116)
Q Consensus         1 ~n~p~~~~~~~l~~~~~Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~   80 (116)
                      ||||||||+|+| +|++||++.+|+|++|+++|+|.+|||||||+||++|+++|+|.||||+|||||+++++|||||+++
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             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 033562           81 SSPMQAYNQAINDLDKELDTLKSAFEAELAKHSR  114 (116)
Q Consensus        81 ~~p~e~l~~a~~~l~~~~~~l~~~f~~a~~~~~~  114 (116)
                      ++|.+||++|+++|++.|++++++|.++++.++.
T Consensus        80 ~~p~eaL~~al~~L~~~~~~l~~~F~~~~~~~~~  113 (123)
T 3h0g_K           80 CSPKQVIVDAAKSLITHLEEIKVNFMREWELKMI  113 (123)
T ss_dssp             SCSHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTS
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            9999999999999999999999999999998764

>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=1e-50  Score=288.28  Aligned_cols=114  Identities=42%  Similarity=0.678  Sum_probs=110.1

Q ss_pred             CCCCccccceeeCCCCeeeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCC
Q 033562            1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQ   80 (116)
Q Consensus         1 ~n~p~~~~~~~l~~~~~Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~   80 (116)
                      ||||||||+|+||+|++|+++..+++.+|+++|+|.||||||||+||++|+++|+|.||||+|||||+++++|||||+|+
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             CCHHHHHHHHHHHHHHHHHHHHHHHHH--HHHhhhc
Q 033562           81 SSPMQAYNQAINDLDKELDTLKSAFEA--ELAKHSR  114 (116)
Q Consensus        81 ~~p~e~l~~a~~~l~~~~~~l~~~f~~--a~~~~~~  114 (116)
                      .+|.+||++|+++|++.|++++++|++  ++++|..
T Consensus        81 ~~p~eaL~~a~~~L~~~~~~l~~~f~~e~~~~~~~~  116 (120)
T 1twf_K           81 YDPKDALKNACNSIINKLGALKTNFETEWNLQTLAA  116 (120)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCC--
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            999999999999999999999999999  7777654

>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=3.4e-40  Score=232.75  Aligned_cols=102  Identities=22%  Similarity=0.268  Sum_probs=94.9

Q ss_pred             eCCCCeeeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHH
Q 033562           12 VPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAI   91 (116)
Q Consensus        12 l~~~~~Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~   91 (116)
                      -|+|++|+++..+++.+|+++|+|.+|||||||+||+.|+++|+|.||||+|||||+++++|||||+|+. |.+||++|+
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            3789999999999999999999999999999999999999999999999999999999999999999987 999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhc
Q 033562           92 NDLDKELDTLKSAFEAELAKHSR  114 (116)
Q Consensus        92 ~~l~~~~~~l~~~f~~a~~~~~~  114 (116)
                      ++|.+.|++|+++|++++++|+.
T Consensus        83 ~~L~~~~~~l~~~f~~a~~~~~~  105 (115)
T 1xpp_A           83 RKLSKLYEDLGTQFQKEFQRYES  105 (115)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhch
Confidence            99999999999999999998853

>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=1.6e-38  Score=216.27  Aligned_cols=89  Identities=31%  Similarity=0.401  Sum_probs=84.9

Q ss_pred             eccCCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Q 033562           22 ERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTL  101 (116)
Q Consensus        22 ~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l  101 (116)
                      ...++.+|+++|+|.||||||||+||+.|+++|+|.||||+|||||+++++|||||+++.+|.+||++|+++|.+.|+++
T Consensus         4 kvi~k~~n~~~f~i~~EDHTLgN~Lr~~L~~~p~V~fagY~vpHPl~~~~~lrIqT~~~~~p~~al~~a~~~l~~~~~~~   83 (92)
T 2pa8_L            4 RILKSESNYLELEIEGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVKILTDGSITPKDALLKAIENIRGMTSHY   83 (92)
T ss_dssp             EEEEEETTEEEEEEETCCHHHHHHHHHHHHTSTTEEEEEEECSSTTSCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEecCCCeEEEEEecCchhHHHHHHHHHhcCCCeeEEEeecCCCCCCceEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Confidence            34457899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHH
Q 033562          102 KSAFEAELA  110 (116)
Q Consensus       102 ~~~f~~a~~  110 (116)
                      +++|+++++
T Consensus        84 ~~~f~~~~k   92 (92)
T 2pa8_L           84 IDEIKGLTK   92 (92)
T ss_dssp             HHHHHHHHC
T ss_pred             HHHHHHHhC
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=94.58  E-value=0.027  Score=43.28  Aligned_cols=29  Identities=10%  Similarity=-0.146  Sum_probs=22.5

Q ss_pred             CcceeEEEEecCCcchHHHHHHHhhcC-CC
Q 033562           27 IINAASFTIEREEHTIGNILRMQLHRD-EN   55 (116)
Q Consensus        27 ~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~   55 (116)
                      .++.+.|.+.|-|+||||.||-.|+.. |+
T Consensus         9 ~~~~~~f~l~g~~~t~~NalRRills~vp~   38 (265)
T 2pa8_D            9 DDTRIDLVFEGYPLEFVNAIRRASMLYVPI   38 (265)
T ss_dssp             CSSEEEEEEESSCHHHHHHHHHHHHHSCCE
T ss_pred             CCCEEEEEEeCCCHHHHHHHHHHHHHcCcc
Confidence            366788888888888888888877763 44

>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=94.24  E-value=0.12  Score=41.29  Aligned_cols=41  Identities=12%  Similarity=0.160  Sum_probs=37.7

Q ss_pred             CceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033562           68 QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAE  108 (116)
Q Consensus        68 ~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f~~a  108 (116)
                      .++..|.|-|+|.++|.+||.+|++-|.+.|+.|.+.+...
T Consensus       225 ~dkfif~VET~Gsi~Peeav~~A~kIL~~kl~~f~~~l~~~  265 (318)
T 1twf_C          225 ADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQM  265 (318)
T ss_dssp             CCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            47899999999999999999999999999999999887654

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

Probab=92.83  E-value=0.12  Score=39.36  Aligned_cols=47  Identities=19%  Similarity=0.278  Sum_probs=38.2

Q ss_pred             eeeeeecCCCC------CCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q 033562           56 VLFAGYKLPHP------LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLK  102 (116)
Q Consensus        56 V~fAgY~ipHP------l~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~  102 (116)
                      |.-+.|+++-.      -.++..+.|-|+|+.+|.+||.+|++-|.+.|+.|.
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      247899999999999999999999999998887664

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

Probab=92.62  E-value=0.091  Score=42.18  Aligned_cols=48  Identities=19%  Similarity=0.304  Sum_probs=38.6

Q ss_pred             CCeeeeeecCC-----CCC-CceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Q 033562           54 ENVLFAGYKLP-----HPL-QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTL  101 (116)
Q Consensus        54 ~~V~fAgY~ip-----HPl-~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l  101 (116)
                      .=|.-+.|.|.     ... .++..+-|.|+|+++|.+||..|++-|.+.+.-|
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            34666777654     333 5899999999999999999999999999877654

>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=92.54  E-value=0.22  Score=38.10  Aligned_cols=41  Identities=15%  Similarity=0.227  Sum_probs=36.9

Q ss_pred             CceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033562           68 QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAE  108 (116)
Q Consensus        68 ~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f~~a  108 (116)
                      .++..+.|.|+|..+|.+++..|++-|.+.++.|.+.+...
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            46778999999999999999999999999999999888664

>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=92.26  E-value=0.19  Score=40.02  Aligned_cols=46  Identities=26%  Similarity=0.367  Sum_probs=38.1

Q ss_pred             eeeeeecCC------CCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Q 033562           56 VLFAGYKLP------HPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTL  101 (116)
Q Consensus        56 V~fAgY~ip------HPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l  101 (116)
                      |.-+.|.+.      -.-.++..+.|-|+|+.+|.+||.+|++-|.+.|+.|
T Consensus       174 v~~v~y~ve~~rv~~~~~~dkli~eIeT~Gsi~P~eal~~A~~iL~~~l~~f  225 (315)
T 2a6h_A          174 VRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYF  225 (315)
T ss_dssp             EEEEEEEEEECCBTTBCCCEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHTT
T ss_pred             ceeEEEEeeeeeecccccccEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHH
Confidence            455667653      1235889999999999999999999999999999877

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

Probab=92.22  E-value=0.14  Score=39.04  Aligned_cols=43  Identities=28%  Similarity=0.233  Sum_probs=32.0

Q ss_pred             eeEeeccCCCcceeEEEEe----cCCcchHHHHHHHhhc-CCCeeeeeec
Q 033562           18 KVSYERDTKIINAASFTIE----REEHTIGNILRMQLHR-DENVLFAGYK   62 (116)
Q Consensus        18 Kv~~~~~~k~~n~~~~~i~----~EDHTLgNlLr~~L~~-~~~V~fAgY~   62 (116)
                      +|++...  .++.+.|.+.    |.++||||.||-.|+. .|+.-.-+-+
T Consensus        13 ~i~i~~~--~~~~~~F~l~Ple~G~~~tlgNaLRRiLLsevpg~AI~~V~   60 (235)
T 1bdf_A           13 LVDIEQV--SSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVTEVE   60 (235)
T ss_dssp             EEEEEES--SSSEEEEEEEEEETTHHHHHHHHHHHHHTTSCCCEEEEEEE
T ss_pred             eEEEEEc--cCCEEEEEEEecCCCCchHHHHHHHHHHHhcCCceEEEEEE
Confidence            3555543  4678999996    9999999999999988 4765444433

>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=91.62  E-value=0.11  Score=41.25  Aligned_cols=36  Identities=19%  Similarity=0.160  Sum_probs=28.3

Q ss_pred             eEeeccCCCcceeEEEE----ecCCcchHHHHHHHhhcC-CCe
Q 033562           19 VSYERDTKIINAASFTI----EREEHTIGNILRMQLHRD-ENV   56 (116)
Q Consensus        19 v~~~~~~k~~n~~~~~i----~~EDHTLgNlLr~~L~~~-~~V   56 (116)
                      |++...  ..+.+.|.+    .|.++||||+||-.|+.. |+.
T Consensus        11 i~i~~~--~~~~~~F~l~Ple~G~~~TlgNaLRRiLLsevpg~   51 (315)
T 2a6h_A           11 FTVRTQ--GREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGT   51 (315)
T ss_dssp             EEEEEE--TTTEEEEEEEEECTTCHHHHHHHHHHHHHHTCEEE
T ss_pred             EEEEEc--cCCEEEEEEEccCCCchhHHHHHHHHHHHhcCCce
Confidence            555433  367899999    599999999999999884 553

>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=91.03  E-value=0.095  Score=41.77  Aligned_cols=36  Identities=14%  Similarity=0.240  Sum_probs=28.2

Q ss_pred             eeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcC-CC
Q 033562           18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-EN   55 (116)
Q Consensus        18 Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~   55 (116)
                      +|++..  ..++.+.|.+.|-|+||||.||-.|+.. |+
T Consensus         7 ~I~i~~--~~~~~~kF~leG~~~tlaNALRRiLLSevPg   43 (318)
T 1twf_C            7 QVKIRE--ASKDNVDFILSNVDLAMANSLRRVMIAEIPT   43 (318)
T ss_dssp             BCCCSC--CCSSEECCEEBSSCHHHHHHHHHHHHHCCCE
T ss_pred             eEEEEE--ecCCEEEEEEEccChhHHHHHHHHHHHcCcc
Confidence            444443  3477899999999999999999988874 54

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

Probab=90.81  E-value=0.22  Score=39.42  Aligned_cols=40  Identities=13%  Similarity=0.255  Sum_probs=36.8

Q ss_pred             CceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033562           68 QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEA  107 (116)
Q Consensus        68 ~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f~~  107 (116)
                      .++..+.|.|+|..+|.+++.+|++-|.+.++.|.+.+++
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            5789999999999999999999999999999999887753

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

Probab=89.99  E-value=0.27  Score=38.92  Aligned_cols=37  Identities=14%  Similarity=0.242  Sum_probs=29.7

Q ss_pred             eeeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcC-CC
Q 033562           17 KKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-EN   55 (116)
Q Consensus        17 ~Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~   55 (116)
                      .+|++..  ..++.+.|.+.|-|.||||.||-.|+.. |.
T Consensus         5 p~I~i~~--~~~~~~~F~l~g~~~tiaNALRRiLLSeVPt   42 (297)
T 3h0g_C            5 THITIRN--ISKNSVDFVLTNTSLAVANSLRRVVLAEIPT   42 (297)
T ss_dssp             CSBCCCC--BCSSEEEEEECSCCHHHHHHHHHHHHSSCCE
T ss_pred             CeEEEEE--ccCCEEEEEEECCChhHHHHHHHHHHHcCcc
Confidence            4555554  3458999999999999999999999884 55

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

Probab=88.51  E-value=0.3  Score=39.18  Aligned_cols=34  Identities=29%  Similarity=0.285  Sum_probs=27.9

Q ss_pred             CcceeEEEEe----cCCcchHHHHHHHhhcC-CCeeeee
Q 033562           27 IINAASFTIE----REEHTIGNILRMQLHRD-ENVLFAG   60 (116)
Q Consensus        27 ~~n~~~~~i~----~EDHTLgNlLr~~L~~~-~~V~fAg   60 (116)
                      ..+.+.|.+.    |.++||||.||-.|+.. |+.-.-+
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            4689999998    99999999999999984 6644333

---

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	116
d1twfk_	114	d.74.3.2 (K:) RPB11 {Baker's yeast (Saccharomyces	5e-44
d1xppa_	99	d.74.3.2 (A:) DNA-directed RNA polymerase subunit	5e-24

>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 =  137 bits (346), Expect = 5e-44
 Identities = 48/108 (44%), 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  YKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAE 108
           YK+ HP   +  +RI TT    P  A   A N +  +L  LK+ FE E
Sbjct: 61  YKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETE 108

>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 = 86.0 bits (213), Expect = 5e-24
 Identities = 20/94 (21%), Positives = 42/94 (44%), Gaps = 1/94 (1%)

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

Query: 78  TSQSSPMQAYNQAINDLDKELDTLKSAFEAELAK 111
            S   P  A  +A+  L K  + L + F+ E  +
Sbjct: 62  KS-GKPQSAIKRAVRKLSKLYEDLGTQFQKEFQR 94

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	116
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	98.22
d1smya1	106	RNA polymerase alpha {Thermus thermophilus [TaxId:	97.96
d1twfc1	135	RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta	96.91

>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=1.9e-44  Score=251.82  Aligned_cols=111  Identities=43%  Similarity=0.688  Sum_probs=108.8

Q ss_pred             CCCCccccceeeCCCCeeeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCC
Q 033562            1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQ   80 (116)
Q Consensus         1 ~n~p~~~~~~~l~~~~~Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~   80 (116)
                      ||||||+|+|+||+|++||++..+++.+|+.+|+|.+|||||||+|++.|+++|+|.||||++||||++++.|||||+++
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             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033562           81 SSPMQAYNQAINDLDKELDTLKSAFEAELAK  111 (116)
Q Consensus        81 ~~p~e~l~~a~~~l~~~~~~l~~~f~~a~~~  111 (116)
                      .+|.++|++|+++|++.|+.+++.|+++++-
T Consensus        81 ~~p~~~l~~a~~~l~~~~~~l~~~f~~e~~~  111 (114)
T d1twfk_          81 YDPKDALKNACNSIINKLGALKTNFETEWNL  111 (114)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            9999999999999999999999999998764

>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=1.6e-35  Score=201.59  Aligned_cols=96  Identities=20%  Similarity=0.279  Sum_probs=89.9

Q ss_pred             CeeeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHH
Q 033562           16 TKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLD   95 (116)
Q Consensus        16 ~~Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~   95 (116)
                      +.++++.  ++.+|+++|+|.||||||||+||+.|+++|+|.||||++||||++++.|+|+|+++ +|.++|++|+++++
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  46889999999999999999999999999999999999999999999999999977 89999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhhc
Q 033562           96 KELDTLKSAFEAELAKHSR  114 (116)
Q Consensus        96 ~~~~~l~~~f~~a~~~~~~  114 (116)
                      +.|+.|+++|++++++|++
T Consensus        79 ~~~~~l~~~~~~~~~~~~~   97 (99)
T d1xppa_          79 KLYEDLGTQFQKEFQRYES   97 (99)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhh
Confidence            9999999999999999986

>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=98.22  E-value=2.6e-06  Score=56.88  Aligned_cols=72  Identities=25%  Similarity=0.296  Sum_probs=58.9

Q ss_pred             ceeEEEE----ecCCcchHHHHHHHhhc-CCCeeeeeecCC---CC---CCceeEEEEEeCCCCCHHHHHHHHHHHHHHH
Q 033562           29 NAASFTI----EREEHTIGNILRMQLHR-DENVLFAGYKLP---HP---LQYKIIVRIHTTSQSSPMQAYNQAINDLDKE   97 (116)
Q Consensus        29 n~~~~~i----~~EDHTLgNlLr~~L~~-~~~V~fAgY~ip---HP---l~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~   97 (116)
                      +.+.|++    .|-.||+||.+|..|.. .+.|.-++|+|.   |=   -.+++.|.|.|+|.++|.+|+..|++-|.+.
T Consensus        21 ~~~k~~~eplErG~Gyt~gn~lr~~llSs~sPV~~V~y~Ve~~~~e~~td~d~L~lei~TnGsi~p~eA~~~Aa~il~~~  100 (105)
T d1bdfa1          21 THAKVTLEPLERGFGHTLGNALRAILLSSMPPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQ  100 (105)
T ss_dssp             SEEEEEEEEEETTHHHHHHHHHHHHHTTSCCSEEEEEEECCBCCCSSCSSEEEEEEEEEECSSSCHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEEccCCcccccccccchhhhhcccceeEEEEeeeeeecCCCCcceEEEEEEEeCCCCCHHHHHHHHHHHHHHH
Confidence            3444544    67789999999999777 699999999985   32   2469999999999999999999999888876


Q ss_pred             HHH
Q 033562           98 LDT  100 (116)
Q Consensus        98 ~~~  100 (116)
                      +..
T Consensus       101 ~~~  103 (105)
T d1bdfa1         101 LEA  103 (105)
T ss_dssp             GGG
T ss_pred             HHh
Confidence            643

>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=97.96  E-value=3.4e-06  Score=56.57  Aligned_cols=73  Identities=26%  Similarity=0.288  Sum_probs=59.3

Q ss_pred             cceeEEEE----ecCCcchHHHHHHHhhc-CCCeeeeeecCCC------CCCceeEEEEEeCCCCCHHHHHHHHHHHHHH
Q 033562           28 INAASFTI----EREEHTIGNILRMQLHR-DENVLFAGYKLPH------PLQYKIIVRIHTTSQSSPMQAYNQAINDLDK   96 (116)
Q Consensus        28 ~n~~~~~i----~~EDHTLgNlLr~~L~~-~~~V~fAgY~ipH------Pl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~   96 (116)
                      .+...|.+    .|..+|+||.||..|.. .|-|.-+.|.|..      .-.+++.|-|.|+|.++|.+||..|++-|.+
T Consensus        18 ~~y~~~v~~p~erG~g~~~gn~l~~il~ss~~PV~kV~y~Ve~~rvg~~~d~dkL~LeI~TnGsi~P~eAl~~Aa~il~~   97 (106)
T d1smya1          18 REYGEFVLEPLERGFGVTLGNPLRRILLSSIPPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILRE   97 (106)
T ss_dssp             SSCEEEEEEEECTTHHHHHHHHHHHHHHHTCECEEEEEEEEEECCCSSCSCCEEEEEEEEECSSSCHHHHHHHHHHHHHH
T ss_pred             CceeEEEeeccCCCcccccccccceeehhcCChhhEEEEEecccccCcccceeEEEEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            34455555    47789999999997766 6999999999863      1257899999999999999999999988887


Q ss_pred             HHHH
Q 033562           97 ELDT  100 (116)
Q Consensus        97 ~~~~  100 (116)
                      .+..
T Consensus        98 h~~~  101 (106)
T d1smya1          98 HLTY  101 (106)
T ss_dssp             HHHT
T ss_pred             HHHh
Confidence            6654

>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=96.91  E-value=0.0077  Score=41.28  Aligned_cols=90  Identities=16%  Similarity=0.268  Sum_probs=68.9

Q ss_pred             eeeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcC-CC-eeeee----------e-------------------cCCC
Q 033562           17 KKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-EN-VLFAG----------Y-------------------KLPH   65 (116)
Q Consensus        17 ~Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~-V~fAg----------Y-------------------~ipH   65 (116)
                      .+|++..  ...+.+.|++.|-|-++.|.||-.++.. |- |.|-.          |                   ..+.
T Consensus         4 P~i~i~~--~~~~~~~F~l~~~d~s~ANalRRi~iaeV~t~v~feyDp~N~lrHtdyw~e~~~~~ewP~s~~~~~e~~~~   81 (135)
T d1twfc1           4 PQVKIRE--ASKDNVDFILSNVDLAMANSLRRVMIAEIAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPN   81 (135)
T ss_dssp             SBCCCSC--CCSSEECCEEBSSCHHHHHHHHHHHHHCCEEEEEEEECSSTTSCCSCCCCSSCHHHHSCCCGGGTTSCCCC
T ss_pred             CEEEEEE--cCCCEEEEEEeCCCHHHHHHHHHHHHHhhhhheeeeecccccccceeecccCCccccCCcccCCCCCCCcc
Confidence            4555554  4567899999999999999999998875 42 22211          1                   0111


Q ss_pred             ---CC-----CceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033562           66 ---PL-----QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAE  108 (116)
Q Consensus        66 ---Pl-----~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f~~a  108 (116)
                         |+     .+...+.|-|.|...|.+.+.+|++-|+..|..|...+...
T Consensus        82 e~e~fd~~akpd~F~f~VEs~G~l~p~~Iv~~ai~iL~~Kl~~l~~~L~~~  132 (135)
T d1twfc1          82 EGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQM  132 (135)
T ss_dssp             SSSCCCTTCCCCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCCCCCCCCEEEEEEEeccCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence               22     27788999999999999999999999999999999888764