Psyllid ID: psy11162

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-
Protein Sequence
MIRKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEERF
Secondary Structure (PSIPRED)
ccEEEEEEcccccccEEEEEEEcccccHHHHHHHHHHccccEEEEcEEccccccccEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccEEEEEEccccccEEEEEEEccccHHHHHHHHHHHccccEEEEEEEcccccccEEEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
MIRKIIKELdtkvpnaaiftvnkedhtlgnmirnqllkdphvlfagykqphplehKFILRIQttaestphdALMNAITDLLAELSLFEERF
Flexible Loop (DISEMBL)
mirkiikeldtkvpnaaiftvnkedhtlGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEERF
Low Complexity Region (SEG)
MIRKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEERF
Disordered region (IsUnstruct)
*****IKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSL*****
Disordered Region (DISOPRED)
**RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEERF
Disordered Region (DISEMBL)
MIRKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEERF
Disordered Region (DISPRO)
MIRKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEERF
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MIRKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEERF
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	91	2.2.26 [Sep-21-2011]
Q7PVQ9	117	DNA-directed RNA polymera	yes	N/A	0.978	0.760	0.876	7e-41
Q9VJE4	117	DNA-directed RNA polymera	yes	N/A	0.978	0.760	0.853	1e-39
Q60SM4	122	Probable DNA-directed RNA	N/A	N/A	0.978	0.729	0.730	4e-32
P52435	117	DNA-directed RNA polymera	yes	N/A	0.978	0.760	0.696	5e-32
Q32P79	117	DNA-directed RNA polymera	yes	N/A	0.978	0.760	0.696	5e-32
O08740	117	DNA-directed RNA polymera	yes	N/A	0.978	0.760	0.696	5e-32
Q9GZM3	115	DNA-directed RNA polymera	yes	N/A	0.967	0.765	0.704	1e-31
Q9H1A7	115	DNA-directed RNA polymera	yes	N/A	0.967	0.765	0.704	2e-31
Q9XVH6	122	Probable DNA-directed RNA	yes	N/A	0.967	0.721	0.727	1e-30
P87123	123	DNA-directed RNA polymera	yes	N/A	0.890	0.658	0.555	4e-21

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

 Score =  165 bits (418), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 78/89 (87%), Positives = 85/89 (95%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
           +KIIKELD KVPNAAIFTVNKEDHTLGNMIRNQLLKDP+VLFAGYK PHPLEHKF+LRIQ
Sbjct: 17  KKIIKELDMKVPNAAIFTVNKEDHTLGNMIRNQLLKDPNVLFAGYKLPHPLEHKFVLRIQ 76

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           TT+E +PH+A MNAITDLL+ELSLFEERF
Sbjct: 77  TTSEYSPHEAFMNAITDLLSELSLFEERF 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|Q9VJE4|RPB11_DROME DNA-directed RNA polymerase II subunit RPB11 OS=Drosophila melanogaster GN=Rpb11 PE=3 SV=1

 Score =  161 bits (407), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 76/89 (85%), Positives = 84/89 (94%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
           +KIIKELDTKV NAAIFT+NKEDHTLGNMIRNQLLKDP+VLFAGYK PHPLEHKF++RIQ
Sbjct: 17  KKIIKELDTKVTNAAIFTINKEDHTLGNMIRNQLLKDPNVLFAGYKVPHPLEHKFVIRIQ 76

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           TTA+ +P +A MNAITDLLAELSLFEERF
Sbjct: 77  TTADYSPQEAFMNAITDLLAELSLFEERF 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.

Drosophila melanogaster (taxid: 7227)

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

 Score =  136 bits (342), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 65/89 (73%), Positives = 73/89 (82%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
           +KI  E DTKVPNAAIFT+NKEDHTLGNM++ QLLKDP VLFAGYK PHPLEHK +LR+Q
Sbjct: 16  KKIYIEKDTKVPNAAIFTINKEDHTLGNMLKIQLLKDPEVLFAGYKNPHPLEHKILLRVQ 75

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           TT  +TP DAL  AITDL+ ELSL E R 
Sbjct: 76  TTNATTPADALTTAITDLVGELSLLEHRI 104

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB11 is part of the core element with the central large cleft.

Caenorhabditis briggsae (taxid: 6238)

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

 Score =  136 bits (342), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 62/89 (69%), Positives = 75/89 (84%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
           +KI    DTKVPNA +FT+NKEDHTLGN+I++QLLKDP VLFAGYK PHPLEHK I+R+Q
Sbjct: 17  KKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQ 76

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           TT + +P +A  NAITDL++ELSL EERF
Sbjct: 77  TTPDYSPQEAFTNAITDLISELSLLEERF 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 =  136 bits (342), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 62/89 (69%), Positives = 75/89 (84%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
           +KI    DTKVPNA +FT+NKEDHTLGN+I++QLLKDP VLFAGYK PHPLEHK I+R+Q
Sbjct: 17  KKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQ 76

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           TT + +P +A  NAITDL++ELSL EERF
Sbjct: 77  TTPDYSPQEAFTNAITDLISELSLLEERF 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 =  136 bits (342), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 62/89 (69%), Positives = 75/89 (84%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
           +KI    DTKVPNA +FT+NKEDHTLGN+I++QLLKDP VLFAGYK PHPLEHK I+R+Q
Sbjct: 17  KKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQ 76

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           TT + +P +A  NAITDL++ELSL EERF
Sbjct: 77  TTPDYSPQEAFTNAITDLISELSLLEERF 105

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB11 is part of the core element with the central large cleft.

Mus musculus (taxid: 10090)

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

 Score =  135 bits (339), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 62/88 (70%), Positives = 74/88 (84%)

Query: 4   KIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQT 63
           KI    DTKVPNA +FT+NKEDHTLGN+I++QLLKDP VLFAGYK PHPLEHK I+R+QT
Sbjct: 17  KITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQT 76

Query: 64  TAESTPHDALMNAITDLLAELSLFEERF 91
           T + +P +A  NAITDL++ELSL EERF
Sbjct: 77  TPDYSPQEAFTNAITDLISELSLLEERF 104

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB11 is part of the core element with the central large cleft.

Homo sapiens (taxid: 9606)

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

 Score =  134 bits (337), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 62/88 (70%), Positives = 74/88 (84%)

Query: 4   KIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQT 63
           KI    DTKVPNA +FT+NKEDHTLGN+I++QLLKDP VLFAGYK PHPLEHK I+R+QT
Sbjct: 17  KITINKDTKVPNACLFTMNKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQT 76

Query: 64  TAESTPHDALMNAITDLLAELSLFEERF 91
           T + +P +A  NAITDL++ELSL EERF
Sbjct: 77  TPDYSPQEAFTNAITDLISELSLLEERF 104

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB11 is part of the core element with the central large cleft.

Homo sapiens (taxid: 9606)

>sp|Q9XVH6|RPB11_CAEEL Probable DNA-directed RNA polymerase II subunit RPB11 OS=Caenorhabditis elegans GN=rpb-11 PE=3 SV=1

 Score =  131 bits (329), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 64/88 (72%), Positives = 71/88 (80%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
           +K   E DTKVPNAAIFT+ KEDHTLGNM++ QLLKDP VLFAGYK PHPLEHK +LRIQ
Sbjct: 16  KKFYIEKDTKVPNAAIFTIMKEDHTLGNMLKIQLLKDPEVLFAGYKNPHPLEHKILLRIQ 75

Query: 63  TTAESTPHDALMNAITDLLAELSLFEER 90
           TT  +TP DAL  AITDL+ ELSL E R
Sbjct: 76  TTNNTTPADALTTAITDLVGELSLLEHR 103

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 elegans (taxid: 6239)

>sp|P87123|RPB11_SCHPO DNA-directed RNA polymerase II subunit RPB11 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb11 PE=1 SV=1

 Score =  100 bits (248), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 45/81 (55%), Positives = 57/81 (70%)

Query: 4  KIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQT 63
          K+  ELD+K PNAA+ T+ KEDHTL NM+ NQLL D  VLFAGYK PHPL H FILR+QT
Sbjct: 17 KVTYELDSKSPNAAVVTLEKEDHTLANMLANQLLSDERVLFAGYKVPHPLNHNFILRVQT 76

Query: 64 TAESTPHDALMNAITDLLAEL 84
            + +P   +++A   L+  L
Sbjct: 77 VEDCSPKQVIVDAAKSLITHL 97

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.

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

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	91
58393315	117	AGAP009209-PA [Anopheles gambiae str. PE	0.978	0.760	0.876	3e-39
340711267	117	PREDICTED: DNA-directed RNA polymerase I	0.978	0.760	0.865	1e-38
242003519	117	DNA-directed RNA polymerase II subunit J	0.978	0.760	0.853	1e-38
125985605	117	GA19897 [Drosophila pseudoobscura pseudo	0.978	0.760	0.865	2e-38
170037676	117	DNA-directed RNA polymerase II subunit J	0.978	0.760	0.853	2e-38
157136940	117	DNA-directed RNA polymerase II 13.3 kDa	0.978	0.760	0.853	2e-38
156542813	117	PREDICTED: DNA-directed RNA polymerase I	0.978	0.760	0.842	2e-38
66530114	117	PREDICTED: DNA-directed RNA polymerase I	0.978	0.760	0.853	3e-38
332030496	137	DNA-directed RNA polymerase II subunit R	0.978	0.649	0.842	3e-38
242247465	117	DNA-directed RNA polymerase II subunit R	0.978	0.760	0.865	4e-38

>gi|58393315|ref|XP_319985.2| AGAP009209-PA [Anopheles gambiae str. PEST] gi|74839219|sp|Q7PVQ9.2|RPB11_ANOGA RecName: Full=DNA-directed RNA polymerase II subunit RPB11; Short=RNA polymerase II subunit B11; AltName: Full=DNA-directed RNA polymerase II subunit J gi|55235548|gb|EAA14713.2| AGAP009209-PA [Anopheles gambiae str. PEST]

 Score =  165 bits (418), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 78/89 (87%), Positives = 85/89 (95%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
           +KIIKELD KVPNAAIFTVNKEDHTLGNMIRNQLLKDP+VLFAGYK PHPLEHKF+LRIQ
Sbjct: 17  KKIIKELDMKVPNAAIFTVNKEDHTLGNMIRNQLLKDPNVLFAGYKLPHPLEHKFVLRIQ 76

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           TT+E +PH+A MNAITDLL+ELSLFEERF
Sbjct: 77  TTSEYSPHEAFMNAITDLLSELSLFEERF 105

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340711267|ref|XP_003394200.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB11-like [Bombus terrestris] gi|350411736|ref|XP_003489439.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB11-like [Bombus impatiens]

 Score =  163 bits (413), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 77/89 (86%), Positives = 84/89 (94%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
           +KIIKE DTKVPNAAIFTVNKEDHTLGNMIRNQLLKDP VLFAGYK PHPLEHKF++RIQ
Sbjct: 17  KKIIKEQDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPQVLFAGYKVPHPLEHKFVIRIQ 76

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           TT++ TPHDA M+AITDL+AELSLFEERF
Sbjct: 77  TTSDYTPHDAFMHAITDLIAELSLFEERF 105

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242003519|ref|XP_002422761.1| DNA-directed RNA polymerase II subunit J, putative [Pediculus humanus corporis] gi|212505604|gb|EEB10023.1| DNA-directed RNA polymerase II subunit J, putative [Pediculus humanus corporis]

 Score =  163 bits (412), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 76/89 (85%), Positives = 85/89 (95%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
           +KI+KELD KVPNAAIFT+NKEDHTLGNMIR+QLLKDP+VLFAGYK PHPLEHKF+LRIQ
Sbjct: 17  KKIVKELDQKVPNAAIFTINKEDHTLGNMIRDQLLKDPNVLFAGYKVPHPLEHKFVLRIQ 76

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           TT++ TP DALMNAITDLL+ELSLFEERF
Sbjct: 77  TTSDYTPQDALMNAITDLLSELSLFEERF 105

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|125985605|ref|XP_001356566.1| GA19897 [Drosophila pseudoobscura pseudoobscura] gi|195147658|ref|XP_002014796.1| GL18757 [Drosophila persimilis] gi|54644890|gb|EAL33630.1| GA19897 [Drosophila pseudoobscura pseudoobscura] gi|194106749|gb|EDW28792.1| GL18757 [Drosophila persimilis]

 Score =  162 bits (411), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 77/89 (86%), Positives = 84/89 (94%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
           +KIIKELDTKV NAAIFT+NKEDHTLGNMIRNQLLKDP+VLFAGYK PHPLEHKF++RIQ
Sbjct: 17  KKIIKELDTKVTNAAIFTINKEDHTLGNMIRNQLLKDPNVLFAGYKVPHPLEHKFVIRIQ 76

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           TTAE +P +A MNAITDLLAELSLFEERF
Sbjct: 77  TTAEYSPQEAFMNAITDLLAELSLFEERF 105

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170037676|ref|XP_001846682.1| DNA-directed RNA polymerase II subunit J [Culex quinquefasciatus] gi|167880966|gb|EDS44349.1| DNA-directed RNA polymerase II subunit J [Culex quinquefasciatus]

 Score =  162 bits (411), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 76/89 (85%), Positives = 85/89 (95%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
           +KIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDP+VLFAGYK PHPLEHKF++RIQ
Sbjct: 17  KKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPNVLFAGYKLPHPLEHKFVIRIQ 76

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           TT++ +P +A MNAITDLL+ELSLFEERF
Sbjct: 77  TTSDYSPQEAFMNAITDLLSELSLFEERF 105

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157136940|ref|XP_001663871.1| DNA-directed RNA polymerase II 13.3 kDa polypeptide [Aedes aegypti] gi|108869812|gb|EAT34037.1| AAEL013700-PA [Aedes aegypti]

 Score =  162 bits (411), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 76/89 (85%), Positives = 85/89 (95%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
           +KIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDP+VLFAGYK PHPLEHKF++RIQ
Sbjct: 17  KKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPNVLFAGYKLPHPLEHKFVIRIQ 76

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           TT++ +P +A MNAITDLL+ELSLFEERF
Sbjct: 77  TTSDYSPQEAFMNAITDLLSELSLFEERF 105

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156542813|ref|XP_001607873.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB11-like [Nasonia vitripennis]

 Score =  162 bits (410), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 75/89 (84%), Positives = 84/89 (94%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
           +KIIKE DTKVPNAAIFT+NKEDHTLGNMIRNQLLKDP VLFAGYK PHPLEHKF++RIQ
Sbjct: 17  KKIIKEQDTKVPNAAIFTINKEDHTLGNMIRNQLLKDPQVLFAGYKLPHPLEHKFVIRIQ 76

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           TT++ TPH+A MNA+TDL+AELSLFEERF
Sbjct: 77  TTSDHTPHEAFMNAVTDLIAELSLFEERF 105

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66530114|ref|XP_624001.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB11 [Apis mellifera] gi|380030239|ref|XP_003698760.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB11-like [Apis florea] gi|383860640|ref|XP_003705797.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB11-like [Megachile rotundata] gi|307206928|gb|EFN84774.1| DNA-directed RNA polymerase II subunit RPB11 [Harpegnathos saltator]

 Score =  162 bits (409), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 76/89 (85%), Positives = 84/89 (94%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
           +KIIKE DTKVPNAAIFTVNKEDHTLGNMIRNQLLKDP VLFAGYK PHPLEHKF++RIQ
Sbjct: 17  KKIIKEQDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPQVLFAGYKVPHPLEHKFVIRIQ 76

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           TT++ TPH+A M+AITDL+AELSLFEERF
Sbjct: 77  TTSDYTPHEAFMHAITDLIAELSLFEERF 105

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332030496|gb|EGI70184.1| DNA-directed RNA polymerase II subunit RPB11 [Acromyrmex echinatior]

 Score =  162 bits (409), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 75/89 (84%), Positives = 84/89 (94%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
           +KIIKE DTKVPNAAIFT+NKEDHTLGNMIRNQLLKDP VLFAGYK PHPLEHKF++RIQ
Sbjct: 17  KKIIKEQDTKVPNAAIFTINKEDHTLGNMIRNQLLKDPQVLFAGYKVPHPLEHKFVIRIQ 76

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           TT++ TPH+A M+AITDL+AELSLFEERF
Sbjct: 77  TTSDYTPHEAFMHAITDLIAELSLFEERF 105

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242247465|ref|NP_001156261.1| DNA-directed RNA polymerase II subunit RPB11-a [Acyrthosiphon pisum] gi|239799164|dbj|BAH70515.1| ACYPI008208 [Acyrthosiphon pisum]

 Score =  161 bits (408), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 77/89 (86%), Positives = 84/89 (94%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
           +KI+KE+DTKV NAAIFTVNKEDHTLGNMIRNQLLKDP+VLFAGYKQPHPLEHKF LRIQ
Sbjct: 17  KKIVKEVDTKVTNAAIFTVNKEDHTLGNMIRNQLLKDPNVLFAGYKQPHPLEHKFELRIQ 76

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           TT++ TP DAL N+ITDLLAELSLFEERF
Sbjct: 77  TTSDYTPQDALTNSITDLLAELSLFEERF 105

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

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	91
FB|FBgn0032634	117	Rpb11 "Rpb11" [Drosophila mela	0.978	0.760	0.853	3e-37
UNIPROTKB|Q32P79	117	POLR2J "DNA-directed RNA polym	0.978	0.760	0.696	1.4e-30
UNIPROTKB|E2RD80	117	LOC100686835 "Uncharacterized	0.978	0.760	0.696	1.4e-30
UNIPROTKB|F1PXE5	130	LOC100686835 "Uncharacterized	0.978	0.684	0.696	1.4e-30
UNIPROTKB|P52435	117	POLR2J "DNA-directed RNA polym	0.978	0.760	0.696	1.4e-30
UNIPROTKB|Q9H1A6	127	POLR2J1 "DNA-directed RNA poly	0.978	0.700	0.696	1.4e-30
MGI|MGI:109582	117	Polr2j "polymerase (RNA) II (D	0.978	0.760	0.696	1.4e-30
RGD|1310198	117	Polr2j "polymerase (RNA) II (D	0.978	0.760	0.696	1.4e-30
UNIPROTKB|E2QRJ6	158	POLR2J3 "DNA-directed RNA poly	0.967	0.556	0.704	2.3e-30
UNIPROTKB|Q9GZM3	115	POLR2J2 "DNA-directed RNA poly	0.967	0.765	0.704	2.3e-30

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

 Score = 400 (145.9 bits), Expect = 3.0e-37, P = 3.0e-37
 Identities = 76/89 (85%), Positives = 84/89 (94%)

Query:     3 RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
             +KIIKELDTKV NAAIFT+NKEDHTLGNMIRNQLLKDP+VLFAGYK PHPLEHKF++RIQ
Sbjct:    17 KKIIKELDTKVTNAAIFTINKEDHTLGNMIRNQLLKDPNVLFAGYKVPHPLEHKFVIRIQ 76

Query:    63 TTAESTPHDALMNAITDLLAELSLFEERF 91
             TTA+ +P +A MNAITDLLAELSLFEERF
Sbjct:    77 TTADYSPQEAFMNAITDLLAELSLFEERF 105

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

 Score = 337 (123.7 bits), Expect = 1.4e-30, P = 1.4e-30
 Identities = 62/89 (69%), Positives = 75/89 (84%)

Query:     3 RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
             +KI    DTKVPNA +FT+NKEDHTLGN+I++QLLKDP VLFAGYK PHPLEHK I+R+Q
Sbjct:    17 KKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQ 76

Query:    63 TTAESTPHDALMNAITDLLAELSLFEERF 91
             TT + +P +A  NAITDL++ELSL EERF
Sbjct:    77 TTPDYSPQEAFTNAITDLISELSLLEERF 105

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 = 337 (123.7 bits), Expect = 1.4e-30, P = 1.4e-30
 Identities = 62/89 (69%), Positives = 75/89 (84%)

Query:     3 RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
             +KI    DTKVPNA +FT+NKEDHTLGN+I++QLLKDP VLFAGYK PHPLEHK I+R+Q
Sbjct:    17 KKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQ 76

Query:    63 TTAESTPHDALMNAITDLLAELSLFEERF 91
             TT + +P +A  NAITDL++ELSL EERF
Sbjct:    77 TTPDYSPQEAFTNAITDLISELSLLEERF 105

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

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

GO:0003677 "DNA binding" evidence=IEA

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

 Score = 337 (123.7 bits), Expect = 1.4e-30, P = 1.4e-30
 Identities = 62/89 (69%), Positives = 75/89 (84%)

Query:     3 RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
             +KI    DTKVPNA +FT+NKEDHTLGN+I++QLLKDP VLFAGYK PHPLEHK I+R+Q
Sbjct:    38 KKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQ 97

Query:    63 TTAESTPHDALMNAITDLLAELSLFEERF 91
             TT + +P +A  NAITDL++ELSL EERF
Sbjct:    98 TTPDYSPQEAFTNAITDLISELSLLEERF 126

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 = 337 (123.7 bits), Expect = 1.4e-30, P = 1.4e-30
 Identities = 62/89 (69%), Positives = 75/89 (84%)

Query:     3 RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
             +KI    DTKVPNA +FT+NKEDHTLGN+I++QLLKDP VLFAGYK PHPLEHK I+R+Q
Sbjct:    17 KKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQ 76

Query:    63 TTAESTPHDALMNAITDLLAELSLFEERF 91
             TT + +P +A  NAITDL++ELSL EERF
Sbjct:    77 TTPDYSPQEAFTNAITDLISELSLLEERF 105

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

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

 Score = 337 (123.7 bits), Expect = 1.4e-30, P = 1.4e-30
 Identities = 62/89 (69%), Positives = 75/89 (84%)

Query:     3 RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
             +KI    DTKVPNA +FT+NKEDHTLGN+I++QLLKDP VLFAGYK PHPLEHK I+R+Q
Sbjct:    17 KKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQ 76

Query:    63 TTAESTPHDALMNAITDLLAELSLFEERF 91
             TT + +P +A  NAITDL++ELSL EERF
Sbjct:    77 TTPDYSPQEAFTNAITDLISELSLLEERF 105

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

GO:0003677 "DNA binding" evidence=IEA

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

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

 Score = 337 (123.7 bits), Expect = 1.4e-30, P = 1.4e-30
 Identities = 62/89 (69%), Positives = 75/89 (84%)

Query:     3 RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
             +KI    DTKVPNA +FT+NKEDHTLGN+I++QLLKDP VLFAGYK PHPLEHK I+R+Q
Sbjct:    17 KKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQ 76

Query:    63 TTAESTPHDALMNAITDLLAELSLFEERF 91
             TT + +P +A  NAITDL++ELSL EERF
Sbjct:    77 TTPDYSPQEAFTNAITDLISELSLLEERF 105

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;IDA

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

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

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

GO:0030275 "LRR domain binding" evidence=ISO

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

 Score = 337 (123.7 bits), Expect = 1.4e-30, P = 1.4e-30
 Identities = 62/89 (69%), Positives = 75/89 (84%)

Query:     3 RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
             +KI    DTKVPNA +FT+NKEDHTLGN+I++QLLKDP VLFAGYK PHPLEHK I+R+Q
Sbjct:    17 KKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQ 76

Query:    63 TTAESTPHDALMNAITDLLAELSLFEERF 91
             TT + +P +A  NAITDL++ELSL EERF
Sbjct:    77 TTPDYSPQEAFTNAITDLISELSLLEERF 105

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

UNIPROTKB|E2QRJ6 POLR2J3 "DNA-directed RNA polymerase II subunit RPB11-b2" [Homo sapiens (taxid:9606)]

 Score = 335 (123.0 bits), Expect = 2.3e-30, P = 2.3e-30
 Identities = 62/88 (70%), Positives = 74/88 (84%)

Query:     4 KIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQT 63
             KI    DTKVPNA +FT+NKEDHTLGN+I++QLLKDP VLFAGYK PHPLEHK I+R+QT
Sbjct:    17 KITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQT 76

Query:    64 TAESTPHDALMNAITDLLAELSLFEERF 91
             T + +P +A  NAITDL++ELSL EERF
Sbjct:    77 TPDYSPQEAFTNAITDLISELSLLEERF 104

GO:0003677 "DNA binding" evidence=IEA

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

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

UNIPROTKB|Q9GZM3 POLR2J2 "DNA-directed RNA polymerase II subunit RPB11-b1" [Homo sapiens (taxid:9606)]

 Score = 335 (123.0 bits), Expect = 2.3e-30, P = 2.3e-30
 Identities = 62/88 (70%), Positives = 74/88 (84%)

Query:     4 KIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQT 63
             KI    DTKVPNA +FT+NKEDHTLGN+I++QLLKDP VLFAGYK PHPLEHK I+R+QT
Sbjct:    17 KITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQT 76

Query:    64 TAESTPHDALMNAITDLLAELSLFEERF 91
             T + +P +A  NAITDL++ELSL EERF
Sbjct:    77 TPDYSPQEAFTNAITDLISELSLLEERF 104

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0005634 "nucleus" 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	0.4494	0.9780	0.7416	yes	N/A
Q9GZM3	RPB1B_HUMAN	No assigned EC number	0.7045	0.9670	0.7652	yes	N/A
Q8U4N1	RPOL_PYRFU	2, ., 7, ., 7, ., 6	0.3661	0.7582	0.7263	yes	N/A
Q96YA7	RPOL_SULTO	2, ., 7, ., 7, ., 6	0.4406	0.6483	0.6344	yes	N/A
P52435	RPB11_HUMAN	No assigned EC number	0.6966	0.9780	0.7606	yes	N/A
Q8IER7	RPB11_PLAF7	No assigned EC number	0.3636	0.8351	0.6031	yes	N/A
P87123	RPB11_SCHPO	No assigned EC number	0.5555	0.8901	0.6585	yes	N/A
Q9VJE4	RPB11_DROME	No assigned EC number	0.8539	0.9780	0.7606	yes	N/A
P57671	RPOL_PYRHO	2, ., 7, ., 7, ., 6	0.3833	0.6373	0.6105	yes	N/A
P38902	RPB11_YEAST	No assigned EC number	0.5243	0.9010	0.6833	yes	N/A
O08740	RPB11_MOUSE	No assigned EC number	0.6966	0.9780	0.7606	yes	N/A
Q7PVQ9	RPB11_ANOGA	No assigned EC number	0.8764	0.9780	0.7606	yes	N/A
C3NFY8	RPOL_SULIN	2, ., 7, ., 7, ., 6	0.5087	0.6263	0.6195	yes	N/A
C4KIP6	RPOL_SULIK	2, ., 7, ., 7, ., 6	0.5087	0.6263	0.6195	yes	N/A
P46217	RPOL_SULAC	2, ., 7, ., 7, ., 6	0.4035	0.6263	0.6333	yes	N/A
Q32P79	RPB11_BOVIN	No assigned EC number	0.6966	0.9780	0.7606	yes	N/A
Q980K0	RPOL_SULSO	2, ., 7, ., 7, ., 6	0.4833	0.6593	0.6521	yes	N/A
C3N7I8	RPOL_SULIY	2, ., 7, ., 7, ., 6	0.5087	0.6263	0.6195	yes	N/A
A4YHV0	RPOL_METS5	2, ., 7, ., 7, ., 6	0.4	0.6593	0.6666	yes	N/A
Q60SM4	RPB11_CAEBR	No assigned EC number	0.7303	0.9780	0.7295	N/A	N/A
C3MRD1	RPOL_SULIL	2, ., 7, ., 7, ., 6	0.5087	0.6263	0.6195	yes	N/A
Q9XVH6	RPB11_CAEEL	No assigned EC number	0.7272	0.9670	0.7213	yes	N/A
C3MZG6	RPOL_SULIA	2, ., 7, ., 7, ., 6	0.5087	0.6263	0.6195	yes	N/A
C3MXM0	RPOL_SULIM	2, ., 7, ., 7, ., 6	0.5087	0.6263	0.6195	yes	N/A
Q38859	RPB11_ARATH	No assigned EC number	0.5168	0.9780	0.7672	yes	N/A
Q9H1A7	RPB1C_HUMAN	No assigned EC number	0.7045	0.9670	0.7652	yes	N/A

EC Number Prediction by EFICAz Software

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	91
cd06926	93	cd06926, RNAP_II_RPB11, RPB11 subunit of Eukaryoti	2e-49
pfam13656	77	pfam13656, RNA_pol_L_2, RNA polymerase Rpb3/Rpb11	2e-26
COG1761	99	COG1761, RPB11, DNA-directed RNA polymerase, subun	2e-24
cd07027	83	cd07027, RNAP_RPB11_like, RPB11 subunit of RNA pol	1e-21
cd07029	85	cd07029, RNAP_I_III_AC19, AC19 subunit of Eukaryot	5e-19
PRK01146	85	PRK01146, PRK01146, DNA-directed RNA polymerase su	6e-15
cd06927	83	cd06927, RNAP_L, L subunit of Archaeal RNA polymer	3e-14
pfam01193	88	pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 di	2e-13
cd00460	86	cd00460, RNAP_RPB11_RPB3, RPB11 and RPB3 subunits	2e-13

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

 Score =  150 bits (382), Expect = 2e-49
 Identities = 63/89 (70%), Positives = 74/89 (83%)

Query: 3  RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
          +KI ++ DTKVPNAA FT+NKEDHTLGN++R QLLKDP+VLFAGYK PHPLEHK  LRIQ
Sbjct: 5  KKITEKKDTKVPNAATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIELRIQ 64

Query: 63 TTAESTPHDALMNAITDLLAELSLFEERF 91
          T    TP +AL NAITDL++ELSL +E F
Sbjct: 65 TDGSITPKEALKNAITDLISELSLLKEEF 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 = 92.2 bits (230), Expect = 2e-26
 Identities = 40/77 (51%), Positives = 49/77 (63%)

Query: 15 NAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALM 74
          N A F +  EDHTLGN++R +LLKDP V FAGY  PHPLE K  LRIQT +   P D L 
Sbjct: 1  NEATFEIEGEDHTLGNLLREELLKDPDVEFAGYSVPHPLEDKINLRIQTKSGKDPLDVLK 60

Query: 75 NAITDLLAELSLFEERF 91
           A+ DL++     E+ 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 = 87.8 bits (218), Expect = 2e-24
 Identities = 32/84 (38%), Positives = 45/84 (53%)

Query: 8  ELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAES 67
           +  K  N+    +  EDHTLGN++R +LLKD  V FA Y  PHPL     +RI+T    
Sbjct: 8  RIIKKDDNSLELEIEGEDHTLGNLLREELLKDEDVEFAAYSIPHPLIDNPKIRIKTKGGV 67

Query: 68 TPHDALMNAITDLLAELSLFEERF 91
           P +AL  A   +L +L    ++F
Sbjct: 68 DPKEALKRAARKILKDLEELLDQF 91

Length = 99

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

 Score = 80.2 bits (198), Expect = 1e-21
 Identities = 30/66 (45%), Positives = 39/66 (59%)

Query: 15 NAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALM 74
          N+    +  EDHTLGN++R +LLKD  V FA Y   HP+  K  +RIQT +   P DAL 
Sbjct: 9  NSVTVEMENEDHTLGNLLREELLKDDQVDFARYYIKHPVIDKIQIRIQTKSGIKPKDALK 68

Query: 75 NAITDL 80
           A+  L
Sbjct: 69 RAVNKL 74

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

 Score = 73.4 bits (181), Expect = 5e-19
 Identities = 31/74 (41%), Positives = 39/74 (52%)

Query: 7  KELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAE 66
           E +    + A F    EDHTLGN +R  ++K+P V F GY  PHP E+K  LRIQT   
Sbjct: 1  VEGEGTDESCATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSIPHPSENKINLRIQTKGG 60

Query: 67 STPHDALMNAITDL 80
              D L   + DL
Sbjct: 61 EPAVDVLKKGLEDL 74

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

 Score = 63.3 bits (155), Expect = 6e-15
 Identities = 27/89 (30%), Positives = 46/89 (51%), Gaps = 4/89 (4%)

Query: 1  MIRKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILR 60
          M  K++++ D ++       +  EDHTL N+++ +LL+DP V  A Y   HPL    +L+
Sbjct: 1  MEIKVLEKEDNEL----ELEIEGEDHTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLK 56

Query: 61 IQTTAESTPHDALMNAITDLLAELSLFEE 89
          I+T     P +AL  A   ++     F +
Sbjct: 57 IKTDGGIDPLEALKEAAKRIIDLCDEFLD 85

Length = 85

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

 Score = 61.4 bits (150), Expect = 3e-14
 Identities = 28/86 (32%), Positives = 45/86 (52%), Gaps = 4/86 (4%)

Query: 4  KIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQT 63
          K+I++ D ++       +  EDHTL N+++ +LL+DP V  A Y   HPL    +L+I+T
Sbjct: 2  KVIEKEDNEL----ELEIEGEDHTLLNLLKEELLRDPGVKVASYDIEHPLLSNPVLKIKT 57

Query: 64 TAESTPHDALMNAITDLLAELSLFEE 89
               P +AL  A   L+     F +
Sbjct: 58 DGGVDPLEALKEAAKRLIDLCEEFLD 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|216354 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimerisation domain

 Score = 59.6 bits (145), Expect = 2e-13
 Identities = 33/88 (37%), Positives = 41/88 (46%), Gaps = 19/88 (21%)

Query: 17 AIFTVNKEDHTLGNMIRNQLLKD-PHVLFAGYKQPHPLEH------------------KF 57
            F +  EDHTLGN +R  LL D P V  AG K PHP +                   K 
Sbjct: 1  IEFLLEGEDHTLGNALRRVLLSDVPGVAIAGVKIPHPAKFSPVKKVNYRVVGVGTDYDKL 60

Query: 58 ILRIQTTAESTPHDALMNAITDLLAELS 85
          ILRI+T    TP +AL  A+  L+ +L 
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|132901 cd00460, RNAP_RPB11_RPB3, RPB11 and RPB3 subunits of RNA polymerase

 Score = 59.4 bits (144), Expect = 2e-13
 Identities = 33/75 (44%), Positives = 40/75 (53%), Gaps = 7/75 (9%)

Query: 12 KVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEH------KFILRIQTTA 65
          K  N   F +  EDHTLGN +R  LLK P V FA Y   HP++       KFILRI+T  
Sbjct: 6  KEKNYVDFVLENEDHTLGNSLRRILLKSP-VEFAAYYVEHPVKLQRTDEDKFILRIETVG 64

Query: 66 ESTPHDALMNAITDL 80
             P +AL  A+  L
Sbjct: 65 SIPPEEALRRAVEIL 79

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	91
cd06926	93	RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA poly	100.0
cd07029	85	RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA pol	100.0
PF13656	77	RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisatio	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
KOG4392|consensus	117		100.0
KOG3438|consensus	105		99.97
cd00460	86	RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA pol	99.95
PF01193	66	RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation	99.74
cd07028	212	RNAP_RPB3_like RPB3 subunit of RNA polymerase. The	96.32
PRK14979	195	DNA-directed RNA polymerase subunit D; Provisional	96.09
cd06928	215	RNAP_alpha_NTD N-terminal domain of the Alpha subu	95.93
smart00662	224	RPOLD RNA polymerases D. DNA-directed RNA polymera	95.76
TIGR02027	297	rpoA DNA-directed RNA polymerase, alpha subunit, b	95.67
PRK00783	263	DNA-directed RNA polymerase subunit D; Provisional	95.38
PRK05182	310	DNA-directed RNA polymerase subunit alpha; Provisi	95.17
CHL00013	327	rpoA RNA polymerase alpha subunit	95.01
cd07030	259	RNAP_D D subunit of Archaeal RNA polymerase. The D	94.78
cd06928	215	RNAP_alpha_NTD N-terminal domain of the Alpha subu	94.55
PRK05182	310	DNA-directed RNA polymerase subunit alpha; Provisi	94.39
cd07028	212	RNAP_RPB3_like RPB3 subunit of RNA polymerase. The	94.38
CHL00013	327	rpoA RNA polymerase alpha subunit	92.75
cd07031	265	RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polyme	92.51
PRK14979	195	DNA-directed RNA polymerase subunit D; Provisional	92.39
smart00662	224	RPOLD RNA polymerases D. DNA-directed RNA polymera	92.05
cd07031	265	RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polyme	92.04
COG0202	317	RpoA DNA-directed RNA polymerase, alpha subunit/40	91.58
cd07030	259	RNAP_D D subunit of Archaeal RNA polymerase. The D	89.5
PRK00783	263	DNA-directed RNA polymerase subunit D; Provisional	88.73
cd07032	291	RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA poly	88.62
TIGR02027	297	rpoA DNA-directed RNA polymerase, alpha subunit, b	83.73

>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II

Probab=100.00  E-value=4.9e-39  Score=210.68  Aligned_cols=90  Identities=70%  Similarity=1.037  Sum_probs=88.1

Q ss_pred             ceeeeeecCCCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHH
Q psy11162          2 IRKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLL   81 (91)
Q Consensus         2 ~~kv~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~   81 (91)
                      .+||+++.|++.+|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++.+|.+||++|+++|.
T Consensus         4 ~~kv~~~~d~k~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~fagY~vpHPl~~~~~l~i~t~~~~~p~~al~~a~~~l~   83 (93)
T cd06926           4 EKKITEKKDTKVPNAATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIELRIQTDGSITPKEALKNAITDLI   83 (93)
T ss_pred             ccceEEeecCCCCcEEEEEEeCCCchHHHHHHHHHhcCCCeeEEeeccCCCCCCceEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            37999999999999999999999999999999999999999999999999999999999999998999999999999999


Q ss_pred             HHHHHHHhhC
Q psy11162         82 AELSLFEERF   91 (91)
Q Consensus        82 ~~~~~l~~~f   91 (91)
                      +.|+.++++|
T Consensus        84 ~~~~~~~~~f   93 (93)
T cd06926          84 SELSLLKEEF   93 (93)
T ss_pred             HHHHHHHhhC
Confidence            9999999987

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.

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

Probab=100.00  E-value=9.2e-38  Score=201.87  Aligned_cols=83  Identities=37%  Similarity=0.539  Sum_probs=80.8

Q ss_pred             cCCCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy11162          9 LDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFE   88 (91)
Q Consensus         9 ~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~   88 (91)
                      ..++.+|+++|+|.||||||||+||++|+++|+|.||||+||||+++++.|||||+++.+|.+||++|+++|.+.|+++.
T Consensus         3 ~~~~~~n~~~~~i~~EdHTLgNlLr~~L~~~p~V~fagY~vpHPl~~~~~lriqT~~~~~p~~al~~a~~~l~~~~~~~~   82 (85)
T cd07029           3 GEGTDESCATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSIPHPSENKINLRIQTKGGEPAVDVLKKGLEDLEQICDHIL   82 (85)
T ss_pred             cccCCCCeEEEEEeCCCcchHHHHHHHHhhCCCceEEeecccCCCCCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            56789999999999999999999999999999999999999999999999999999989999999999999999999999


Q ss_pred             hhC
Q psy11162         89 ERF   91 (91)
Q Consensus        89 ~~f   91 (91)
                      ++|
T Consensus        83 ~~f   85 (85)
T cd07029          83 STF   85 (85)
T ss_pred             hcC
Confidence            987

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

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

Probab=100.00  E-value=1.2e-37  Score=197.86  Aligned_cols=77  Identities=52%  Similarity=0.817  Sum_probs=72.6

Q ss_pred             ceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhhC
Q psy11162         15 NAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEERF   91 (91)
Q Consensus        15 n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~f   91 (91)
                      |+++|+|.+|||||||+||++|+++|+|.||||++||||++++.|||||+++.+|.+||++|+++|.++|+.|+++|
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            78999999999999999999999999999999999999999999999999998999999999999999999999987

...

>PRK01146 DNA-directed RNA polymerase subunit L; Provisional

Probab=100.00  E-value=6.3e-37  Score=197.95  Aligned_cols=83  Identities=31%  Similarity=0.442  Sum_probs=78.7

Q ss_pred             eecCCCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Q psy11162          7 KELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSL   86 (91)
Q Consensus         7 ~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~   86 (91)
                      ++..++.+|+++|+|.||||||||+||++|+++|+|.||||++||||+++++|||||+++.+|.+||++|+++|++.|++
T Consensus         3 ikvi~~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqt~~~~~p~~al~~a~~~L~~~~~~   82 (85)
T PRK01146          3 IKVLEKEDNELELEIEGEDHTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLKIKTDGGIDPLEALKEAAKRIIDLCDE   82 (85)
T ss_pred             EEEEecCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEeecCCCCCCccEEEEEECCCCCHHHHHHHHHHHHHHHHHH
Confidence            44557888999999999999999999999999999999999999999999999999998899999999999999999999


Q ss_pred             HHh
Q psy11162         87 FEE   89 (91)
Q Consensus        87 l~~   89 (91)
                      |++
T Consensus        83 ~~~   85 (85)
T PRK01146         83 FLD   85 (85)
T ss_pred             HhC
Confidence            864

>cd06927 RNAP_L L subunit of Archaeal RNA polymerase

Probab=100.00  E-value=2.3e-36  Score=194.55  Aligned_cols=79  Identities=34%  Similarity=0.500  Sum_probs=75.9

Q ss_pred             CCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHh
Q psy11162         11 TKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEE   89 (91)
Q Consensus        11 ~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~   89 (91)
                      ++.+|+++|+|.||||||||+||++|+++|+|.||||++||||+++++|||||+++.+|.+||++|+++|++.|+.|.+
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            5667999999999999999999999999999999999999999999999999999889999999999999999999864

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=4.3e-36  Score=193.33  Aligned_cols=78  Identities=40%  Similarity=0.578  Sum_probs=75.0

Q ss_pred             CCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy11162         11 TKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFE   88 (91)
Q Consensus        11 ~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~   88 (91)
                      ++.+|+++|+|.||||||||+||++|+++|+|.||||++|||++++++|||||+++.+|.+||++|+++|.+.|+.|.
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            456699999999999999999999999999999999999999999999999999988999999999999999999986

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=3.2e-34  Score=190.25  Aligned_cols=91  Identities=36%  Similarity=0.565  Sum_probs=87.3

Q ss_pred             CceeeeeecCCCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHH
Q psy11162          1 MIRKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDL   80 (91)
Q Consensus         1 ~~~kv~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l   80 (91)
                      |-+++.+...++.+|+++|++.||||||||+|+++|+++|+|.||||+||||+.+++.+||||+++++|.+||++|++.+
T Consensus         1 ~~~~~~l~ii~~~~n~~~i~i~gEdHTL~NlL~~~L~~d~~V~~a~Y~i~HP~~~~~~i~Ikt~~~~dp~~aL~~A~~~i   80 (99)
T COG1761           1 MTPEMELRIIKKDDNSLELEIEGEDHTLGNLLREELLKDEDVEFAAYSIPHPLIDNPKIRIKTKGGVDPKEALKRAARKI   80 (99)
T ss_pred             CCCceEEEEeccCCCEEEEEEecCCchHHHHHHHHHhCCCCeeEEEEeCCCCCCCCceEEEEECCCCCHHHHHHHHHHHH
Confidence            55788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhC
Q psy11162         81 LAELSLFEERF   91 (91)
Q Consensus        81 ~~~~~~l~~~f   91 (91)
                      ++.|++|.++|
T Consensus        81 ~~~~~~l~~~~   91 (99)
T COG1761          81 LKDLEELLDQF   91 (99)
T ss_pred             HHHHHHHHHHH
Confidence            99999999843

>KOG4392|consensus

Probab=100.00  E-value=1.4e-33  Score=190.40  Aligned_cols=89  Identities=72%  Similarity=1.110  Sum_probs=86.8

Q ss_pred             eeeeeecCCCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHH
Q psy11162          3 RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLA   82 (91)
Q Consensus         3 ~kv~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~   82 (91)
                      +||++..|+|++|++.|+|++|||||||+||.+|++||+|.||||++|||+..++.|||||..+++|.+|+..|+.++..
T Consensus        17 kKvtin~DtKvpNA~~fTiekEDHTLGNii~~qLl~D~~vLFagYkvpHPl~~~~~LRiqtt~d~~p~~al~~a~~~l~~   96 (117)
T KOG4392|consen   17 KKITINKDTKVPNAALFTIEKEDHTLGNIIKSQLLKDPRVLFAGYKVPHPLEHKIILRVQTTEDCSPADALTNAITDLIE   96 (117)
T ss_pred             ceeEEecCCCCCceEEEEEecccchHHHHHHHHHccCccceEeeecCCCcccccEEEEEecCCCCCHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhC
Q psy11162         83 ELSLFEERF   91 (91)
Q Consensus        83 ~~~~l~~~f   91 (91)
                      ..+.++..|
T Consensus        97 el~~l~~~f  105 (117)
T KOG4392|consen   97 ELSLLENRF  105 (117)
T ss_pred             HHHHHHHHH
Confidence            999998765

>KOG3438|consensus

Probab=99.97  E-value=6.1e-31  Score=174.91  Aligned_cols=79  Identities=35%  Similarity=0.616  Sum_probs=76.4

Q ss_pred             CCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhhC
Q psy11162         13 VPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEERF   91 (91)
Q Consensus        13 ~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~f   91 (91)
                      ..++.+|++..|||||||+||+.|+++|.|+||||.||||+++++.|||||.++..+.++|++|+++|.+.|+.+.++|
T Consensus        14 d~~~~Tf~~~eEDHTlgNalR~vI~k~peVefcGYtIPHPse~k~niRIQt~~~~~A~evl~kgl~el~~~c~~v~~kF   92 (105)
T KOG3438|consen   14 DLSSATFQLREEDHTLGNALRYVIMKNPEVEFCGYTIPHPSEDKINIRIQTRDGDPAVEVLKKGLEELMQLCDHVRSKF   92 (105)
T ss_pred             CCCceEEEEEecCcchhHHHHHHHhcCCceEEEeccCCCCchhhheEEEEecCCCcchHHHHHHHHHHHHHHHHHHHHH
Confidence            6789999999999999999999999999999999999999999999999999888999999999999999999999876

>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase

Probab=99.95  E-value=2e-27  Score=152.95  Aligned_cols=76  Identities=45%  Similarity=0.628  Sum_probs=72.4

Q ss_pred             CCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCC------CCeeEEEEEeCCCCCHHHHHHHHHHHHHHHH
Q psy11162         11 TKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPL------EHKFILRIQTTAESTPHDALMNAITDLLAEL   84 (91)
Q Consensus        11 ~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl------~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~   84 (91)
                      ++.+|+++|+|.||||||||+||++|++ +.|.||||+||||+      .+++.|+|+|+|+.+|.+||++|++.|.+.|
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            4566999999999999999999999999 99999999999999      9999999999999999999999999999998


Q ss_pred             HHH
Q psy11162         85 SLF   87 (91)
Q Consensus        85 ~~l   87 (91)
                      +.|
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=99.74  E-value=3.2e-18  Score=104.91  Aligned_cols=65  Identities=46%  Similarity=0.729  Sum_probs=61.4

Q ss_pred             EEEEEecCCcchHHHHHHHHhcC-CCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q psy11162         17 AIFTVNKEDHTLGNMIRNQLLKD-PHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELS   85 (91)
Q Consensus        17 ~~~~i~~EdHTlgNlLr~~L~~~-~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~   85 (91)
                      ++|.+.|+|||+||+||..|+++ |.|.+++    ||..+++.++|+|+|+.+|.++|.+|++.|.+.|+
T Consensus         1 i~~~~~g~~~tl~N~LRr~ll~~vp~~ai~~----~~~~~~~~~~IeT~g~~~p~~~l~~A~~~l~~~~~   66 (66)
T PF01193_consen    1 IEFLLKGEDHTLGNALRRILLSEVPGVAIDG----HPNEDKFVFRIETDGSLTPKEALLKAIKILKEKLN   66 (66)
T ss_dssp             EEEEEESHHHHHHHHHHHHHHSSSEEEEEEE----SSEEEEEEEEEEEBSSS-HHHHHHHHHHHHHHHHC
T ss_pred             CEeEEcCCchHHHHHHHHHHHhcCCCceEEe----cCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHhcC
Confidence            57999999999999999999999 9999999    99999999999999999999999999999998874

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 ....

>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase

Probab=96.32  E-value=0.017  Score=42.71  Aligned_cols=50  Identities=14%  Similarity=0.313  Sum_probs=42.3

Q ss_pred             CCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162         40 PHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEER   90 (91)
Q Consensus        40 ~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~   90 (91)
                      .=|.-|.|++. |-.+...|.|.|+|..+|.+|+.+|++-|.+.+++|.++
T Consensus       163 sPV~~v~y~~~-~~~d~li~~VeT~Gsi~p~~~l~~A~~iL~~~~~~~~~~  212 (212)
T cd07028         163 GPVAAIEFRYD-PVADTYIMNVESVGSLPPDQVVVEAIKTLQKKVASILLA  212 (212)
T ss_pred             CCceEEEEEEE-ccCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHhhC
Confidence            33566778854 356889999999999999999999999999999998763

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

>PRK14979 DNA-directed RNA polymerase subunit D; Provisional

Probab=96.09  E-value=0.03  Score=41.13  Aligned_cols=48  Identities=21%  Similarity=0.280  Sum_probs=39.6

Q ss_pred             CCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162         39 DPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEER   90 (91)
Q Consensus        39 ~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~   90 (91)
                      .| |. |.|+..-  .++..|.|.|+|+.+|.+|+..|++-|.+.++.|.+.
T Consensus       138 ~p-vd-a~y~~~~--~dkl~leIeTdGsi~P~~al~~Aa~iL~~~l~~~~~~  185 (195)
T PRK14979        138 QP-CN-AVYKQIS--NDEVEFKVESFGQMDAEDILRSALEILKNKAEKFLQE  185 (195)
T ss_pred             cc-ee-eEEecCC--CcEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            45 44 5565332  4899999999999999999999999999999998764

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

Probab=95.93  E-value=0.019  Score=42.24  Aligned_cols=45  Identities=29%  Similarity=0.298  Sum_probs=36.9

Q ss_pred             eeeeeeeCCC------CCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Q psy11162         42 VLFAGYKQPH------PLEHKFILRIQTTAESTPHDALMNAITDLLAELSL   86 (91)
Q Consensus        42 V~fAgY~vpH------Pl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~   86 (91)
                      |.-+.|.|.-      .-.+...|.|.|+|+.+|.+||..|++.|.+.+..
T Consensus       164 V~~vny~v~~~~~~~~~~~e~L~leI~TnGsi~P~~Al~~A~~il~~~~~~  214 (215)
T cd06928         164 VRKVNYSVESTRVGQRTDYEKLILEIWTNGSISPEEALAQAAKILINHFSP  214 (215)
T ss_pred             eEEEEEEEEEeecCCCCCceeEEEEEEECCCCCHHHHHHHHHHHHHHHhhc
Confidence            6666777543      23567899999999999999999999999988753

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

>smart00662 RPOLD RNA polymerases D

Probab=95.76  E-value=0.026  Score=41.64  Aligned_cols=34  Identities=26%  Similarity=0.439  Sum_probs=30.9

Q ss_pred             CCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Q psy11162         54 EHKFILRIQTTAESTPHDALMNAITDLLAELSLF   87 (91)
Q Consensus        54 ~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l   87 (91)
                      .++..|.|.|+|..+|.+||.+|++-|.+.++.|
T Consensus       191 ~d~l~f~IeT~G~i~p~~al~~A~~iL~~k~~~~  224 (224)
T smart00662      191 YDKLIFDVETNGSLKPEEAVLEAAKILKEKLEAF  224 (224)
T ss_pred             CCEEEEEEEecCCcCHHHHHHHHHHHHHHHHhhC
Confidence            5789999999999999999999999999988753

DNA-directed RNA polymerase subunit D and bacterial alpha chain

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

Probab=95.67  E-value=0.047  Score=42.10  Aligned_cols=48  Identities=33%  Similarity=0.429  Sum_probs=39.1

Q ss_pred             eeeeeeeCCC------CCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHh
Q psy11162         42 VLFAGYKQPH------PLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEE   89 (91)
Q Consensus        42 V~fAgY~vpH------Pl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~   89 (91)
                      |.-+.|.+..      ...+...|.|.|+|..+|.+|+.+|++-|.+.|..|.+
T Consensus       155 V~~Vny~ve~~rv~~~~~~d~li~eIeT~Gsi~P~~al~~A~~iL~~~~~~~~~  208 (297)
T TIGR02027       155 VLKVNYEVENTRVGQRTDYDKLILEIETNGSITPKDAIAEAAKILIEHLEPFVN  208 (297)
T ss_pred             eEEEEEEEeeeeccCCccccEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            4556677653      23467999999999999999999999999999987753

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

>PRK00783 DNA-directed RNA polymerase subunit D; Provisional

Probab=95.38  E-value=0.015  Score=43.56  Aligned_cols=34  Identities=24%  Similarity=0.233  Sum_probs=28.0

Q ss_pred             eeeeecCCCCCceEEEEEecCCcchHHHHHHHHhcC
Q psy11162          4 KIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKD   39 (91)
Q Consensus         4 kv~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~   39 (91)
                      ++.+...+  ++.++|.+.|-|+|+||+||-.|+.+
T Consensus         2 ~~~~~~~~--~~~~~f~~~g~~~t~~NalRRvlls~   35 (263)
T PRK00783          2 EIEILELD--DRSARFVVEGVTPAFANAIRRAMIAD   35 (263)
T ss_pred             ceEEEEcC--CcEEEEEEeCCCHHHHHHHHHHHHHc
Confidence            34454444  48899999999999999999999986

>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional

Probab=95.17  E-value=0.078  Score=41.18  Aligned_cols=48  Identities=31%  Similarity=0.392  Sum_probs=39.4

Q ss_pred             eeeeeeeCCCC------CCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHh
Q psy11162         42 VLFAGYKQPHP------LEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEE   89 (91)
Q Consensus        42 V~fAgY~vpHP------l~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~   89 (91)
                      |.-+.|.+.-.      -.+...|.|.|+|+.+|.+||.+|++-|.+.+..|.+
T Consensus       172 V~~vny~ve~~~~~~~~~~e~L~leI~TnGsi~P~eAl~~A~~iL~~~l~~f~~  225 (310)
T PRK05182        172 VKKVNYTVENTRVGQRTDYDKLILEVETDGSITPEEALALAAKILVEQLSVFVD  225 (310)
T ss_pred             ccceEEEecccccCCCCcceEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence            56677776542      1467999999999999999999999999999987754

>CHL00013 rpoA RNA polymerase alpha subunit

Probab=95.01  E-value=0.079  Score=41.59  Aligned_cols=47  Identities=26%  Similarity=0.260  Sum_probs=39.3

Q ss_pred             eeeeeeeCCCC-----CCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy11162         42 VLFAGYKQPHP-----LEHKFILRIQTTAESTPHDALMNAITDLLAELSLFE   88 (91)
Q Consensus        42 V~fAgY~vpHP-----l~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~   88 (91)
                      |.-+.|.|..-     -.+...|-|.|+|+++|.+||..|++-|.+.+.-|.
T Consensus       171 V~kVny~Ve~~~~~~~~~e~L~lEI~TnGsi~P~~Al~~Aa~il~~~~~~~~  222 (327)
T CHL00013        171 VRNVNYSIHSYGNGNEKQEILFLEIWTNGSITPKEALHEASRNLIDLFIPFL  222 (327)
T ss_pred             eeEEEEEEEEcccCCcccceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            66677777651     257899999999999999999999999999987764

>cd07030 RNAP_D D subunit of Archaeal RNA polymerase

Probab=94.78  E-value=0.042  Score=41.01  Aligned_cols=36  Identities=19%  Similarity=0.258  Sum_probs=28.8

Q ss_pred             eeeeecCCCCCceEEEEEecCCcchHHHHHHHHhcC-CC
Q psy11162          4 KIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKD-PH   41 (91)
Q Consensus         4 kv~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~-~~   41 (91)
                      +|++...+  ++.+.|.+.|-|+|+||+||-.|+.. |.
T Consensus         2 ~~~~~~~~--~~~~~f~~~g~~~s~~NalRRills~vp~   38 (259)
T cd07030           2 EIEVLELD--DDRARFVLEGVPPAFANAIRRAIISEVPT   38 (259)
T ss_pred             ceEEEecC--CCEEEEEEeCCCHHHHHHHHHHHHhcCCe
Confidence            34554444  48999999999999999999999986 44

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

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

Probab=94.55  E-value=0.065  Score=39.45  Aligned_cols=41  Identities=29%  Similarity=0.427  Sum_probs=32.2

Q ss_pred             CCCCCceEEEEE----ecCCcchHHHHHHHHhcC-CCeeeeeeeCC
Q psy11162         10 DTKVPNAAIFTV----NKEDHTLGNMIRNQLLKD-PHVLFAGYKQP   50 (91)
Q Consensus        10 ~~k~~n~~~~~i----~~EdHTlgNlLr~~L~~~-~~V~fAgY~vp   50 (91)
                      ++..++.+.|.+    .|.++|+||+||..|+.+ |+...-+-++.
T Consensus         4 ~~~~~~~~~F~i~pl~~g~~~tlgNaLRRvLLs~ipg~aI~~v~I~   49 (215)
T cd06928           4 ENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIE   49 (215)
T ss_pred             ccCCCcEEEEEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEEEEEc
Confidence            445579999999    789999999999999885 66655555544

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

>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional

Probab=94.39  E-value=0.12  Score=40.16  Aligned_cols=47  Identities=30%  Similarity=0.333  Sum_probs=35.6

Q ss_pred             eeeeecCCCCCceEEEEEe----cCCcchHHHHHHHHhcC-CCeeeeeeeCC
Q psy11162          4 KIIKELDTKVPNAAIFTVN----KEDHTLGNMIRNQLLKD-PHVLFAGYKQP   50 (91)
Q Consensus         4 kv~~~~~~k~~n~~~~~i~----~EdHTlgNlLr~~L~~~-~~V~fAgY~vp   50 (91)
                      ++.+...+..++.+.|.+.    |.++|+||+||-.|+.+ |+...-+-++.
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            4555543334799999997    99999999999999885 76666666654

>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase

Probab=94.38  E-value=0.045  Score=40.41  Aligned_cols=33  Identities=15%  Similarity=0.346  Sum_probs=28.1

Q ss_pred             cCCCCCceEEEEEecCCcchHHHHHHHHhcC-CC
Q psy11162          9 LDTKVPNAAIFTVNKEDHTLGNMIRNQLLKD-PH   41 (91)
Q Consensus         9 ~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~-~~   41 (91)
                      .-++.++.+.|.+.|-|+|+||+||-.|+.. |.
T Consensus         5 i~~~~~~~~~f~l~g~~~t~aNaLRRiLLsevP~   38 (212)
T cd07028           5 IREADKDNVDFILSGVDLAMANALRRVMIAEVPT   38 (212)
T ss_pred             EEEcCCCEEEEEEEccChhHHHHHHHHHHHcCcc
Confidence            3456668999999999999999999999986 44

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

>CHL00013 rpoA RNA polymerase alpha subunit

Probab=92.75  E-value=0.32  Score=38.18  Aligned_cols=50  Identities=18%  Similarity=0.203  Sum_probs=40.8

Q ss_pred             ceeeeeecCCCCCceEEEEEe----cCCcchHHHHHHHHhcC-CCeeeeeeeCCC
Q psy11162          2 IRKIIKELDTKVPNAAIFTVN----KEDHTLGNMIRNQLLKD-PHVLFAGYKQPH   51 (91)
Q Consensus         2 ~~kv~~~~~~k~~n~~~~~i~----~EdHTlgNlLr~~L~~~-~~V~fAgY~vpH   51 (91)
                      ++-+....++...+++.|.|.    |..|||||+||..|+.+ |+..+.+-++.+
T Consensus         7 ~~~ie~~~~~~~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~g   61 (327)
T CHL00013          7 WKCVESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEG   61 (327)
T ss_pred             ccceeEEEecCCCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECC
Confidence            455777788888999999996    57779999999999985 887777777654

>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II

Probab=92.51  E-value=0.38  Score=36.54  Aligned_cols=37  Identities=16%  Similarity=0.345  Sum_probs=34.0

Q ss_pred             CCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162         54 EHKFILRIQTTAESTPHDALMNAITDLLAELSLFEER   90 (91)
Q Consensus        54 ~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~   90 (91)
                      .+.+.|.|.|.|..+|.++|.+|++-|.+.++.|.+.
T Consensus       225 ~~~fiF~VES~Gsl~p~~Iv~~Al~iL~~K~~~l~~~  261 (265)
T cd07031         225 PDKFYFNVESTGALPPEQIVLSGLEILKKKLADLQLQ  261 (265)
T ss_pred             CCEEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            4678999999999999999999999999999998764

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

>PRK14979 DNA-directed RNA polymerase subunit D; Provisional

Probab=92.39  E-value=0.19  Score=36.92  Aligned_cols=43  Identities=12%  Similarity=0.273  Sum_probs=33.3

Q ss_pred             eeeecCCCCCceEEEEEecCCcchHHHHHHHHhcC-CCeeeeeee
Q psy11162          5 IIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKD-PHVLFAGYK   48 (91)
Q Consensus         5 v~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~-~~V~fAgY~   48 (91)
                      +.++.-++..+.+.|.+. -|.|+||+||-.|+.. |+...-+-+
T Consensus         4 ~~~~~~~~~~~~~~f~l~-~~~tlgNaLRRvLLssipg~AI~~V~   47 (195)
T PRK14979          4 IKEKEKTRIGEEFKFSLK-APISFSSALRRIMISEVPTYAIENVY   47 (195)
T ss_pred             cceeeeccCCcEEEEEEE-cCccHHHHHHHHHHhcCcceeEEEEE
Confidence            345556778899999999 9999999999999985 654444433

>smart00662 RPOLD RNA polymerases D

Probab=92.05  E-value=0.25  Score=36.43  Aligned_cols=33  Identities=27%  Similarity=0.351  Sum_probs=26.2

Q ss_pred             EEEEEecCCcchHHHHHHHHhcC-CCeeeeeeeC
Q psy11162         17 AIFTVNKEDHTLGNMIRNQLLKD-PHVLFAGYKQ   49 (91)
Q Consensus        17 ~~~~i~~EdHTlgNlLr~~L~~~-~~V~fAgY~v   49 (91)
                      +.|.+.+-++|+||+||-.|+.. |....-+.++
T Consensus         2 ~~f~l~~~~~t~~NaLRRilLs~vp~~aI~~V~I   35 (224)
T smart00662        2 AKFVLEPYGLTLANALRRVLLSSVPGMAVTEVEI   35 (224)
T ss_pred             eEEEEEcCCchHHHHHHHHHHHcCccceEEEEEE
Confidence            67999999999999999999985 6555444443

DNA-directed RNA polymerase subunit D and bacterial alpha chain

>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II

Probab=92.04  E-value=0.32  Score=36.96  Aligned_cols=35  Identities=14%  Similarity=0.327  Sum_probs=28.1

Q ss_pred             CCCceEEEEEecCCcchHHHHHHHHhcC-CCeeeee
Q psy11162         12 KVPNAAIFTVNKEDHTLGNMIRNQLLKD-PHVLFAG   46 (91)
Q Consensus        12 k~~n~~~~~i~~EdHTlgNlLr~~L~~~-~~V~fAg   46 (91)
                      ..++.++|.+.+=|+|+||+||-.|+.. |....-.
T Consensus         8 ~~~~~~~F~l~~~~~s~aNALRRillsevPt~AI~~   43 (265)
T cd07031           8 LTDDKVKFILENTDLSVANSLRRVMIAEVPTLAIDL   43 (265)
T ss_pred             cCCCEEEEEEEcCcHHHHHHHHHHHHHcCccceEEE
Confidence            4458999999999999999999999885 5543333

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

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

Probab=91.58  E-value=0.28  Score=38.32  Aligned_cols=46  Identities=20%  Similarity=0.089  Sum_probs=33.3

Q ss_pred             eeeecCCC--CCceEEEEEecCCcchHHHHHHHHhcC-CCeeeeeeeCC
Q psy11162          5 IIKELDTK--VPNAAIFTVNKEDHTLGNMIRNQLLKD-PHVLFAGYKQP   50 (91)
Q Consensus         5 v~~~~~~k--~~n~~~~~i~~EdHTlgNlLr~~L~~~-~~V~fAgY~vp   50 (91)
                      |++...++  .+-.+++...|-+|||||+||-.|+.. |....-+-++.
T Consensus         7 i~i~~~~~~~~~~~ieplerG~g~tlgNALRRvLLSsiPg~Av~~V~I~   55 (317)
T COG0202           7 VKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEID   55 (317)
T ss_pred             eEEEEcccccccEEEEEeeeCCcchhHHHHHHHHHHcCccceEEEEEEe
Confidence            44444443  478899999999999999999999885 66544443333

>cd07030 RNAP_D D subunit of Archaeal RNA polymerase

Probab=89.50  E-value=1.3  Score=33.09  Aligned_cols=37  Identities=22%  Similarity=0.416  Sum_probs=33.3

Q ss_pred             CCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162         54 EHKFILRIQTTAESTPHDALMNAITDLLAELSLFEER   90 (91)
Q Consensus        54 ~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~   90 (91)
                      .+...+.|.|.|..+|.+++++|++-|.+.++.|.++
T Consensus       222 ~~~~if~vEs~Gsl~p~~il~~A~~~l~~k~~~~~~~  258 (259)
T cd07030         222 EDRFIFEVESDGSLPPKEILLEALRILKEKADELIEA  258 (259)
T ss_pred             CCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            4557789999999999999999999999999999765

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

>PRK00783 DNA-directed RNA polymerase subunit D; Provisional

Probab=88.73  E-value=1.3  Score=33.16  Aligned_cols=38  Identities=21%  Similarity=0.289  Sum_probs=34.2

Q ss_pred             CCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162         53 LEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEER   90 (91)
Q Consensus        53 l~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~   90 (91)
                      ..+...+.+.|.|..+|.++++.|++-|.+.+++|.+.
T Consensus       221 ~~~~~if~vEs~G~l~p~~iv~~A~~~l~~k~~~~~~~  258 (263)
T PRK00783        221 DENKFIFTVESDGSLPVEEILLEALKILKRKADELIEA  258 (263)
T ss_pred             cCCeEEEEeccCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            35678899999999999999999999999999998764

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

Probab=88.62  E-value=1.3  Score=34.28  Aligned_cols=37  Identities=24%  Similarity=0.349  Sum_probs=33.8

Q ss_pred             CCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHh
Q psy11162         53 LEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEE   89 (91)
Q Consensus        53 l~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~   89 (91)
                      -.+.+.+.|.+.|..+|.+.+.+|++-|.+.|+.|.+
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            3566999999999999999999999999999999876

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=83.73  E-value=1.1  Score=34.68  Aligned_cols=29  Identities=31%  Similarity=0.358  Sum_probs=23.1

Q ss_pred             ecCCcchHHHHHHHHhcC-CCeeeeeeeCC
Q psy11162         22 NKEDHTLGNMIRNQLLKD-PHVLFAGYKQP   50 (91)
Q Consensus        22 ~~EdHTlgNlLr~~L~~~-~~V~fAgY~vp   50 (91)
                      .|.+||+||+||-.|+.+ |++...+-++.
T Consensus        11 ~g~g~TlGNaLRRvLLs~i~g~aI~~vkI~   40 (297)
T TIGR02027        11 RGFGITLGNALRRVLLSSIPGAAITAVKID   40 (297)
T ss_pred             CCchhHHHHHHHHHHHhcCCceEEEEEEEc
Confidence            478999999999999985 77766665554

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	91
3h0g_K	123	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		3e-22
1i3q_K	120	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		3e-18
2pa8_L	92	X-Ray Crystal Structure Of The DL SUBCOMPLEX OF THE		9e-11
2waq_L	92	The Complete Structure Of The Archaeal 13-Subunit D		3e-10

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

Iteration: 1
 Score =  100 bits (248), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 45/81 (55%), Positives = 57/81 (70%)
Query: 4  KIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQT 63
          K+  ELD+K PNAA+ T+ KEDHTL NM+ NQLL D  VLFAGYK PHPL H FILR+QT
Sbjct: 17 KVTYELDSKSPNAAVVTLEKEDHTLANMLANQLLSDERVLFAGYKVPHPLNHNFILRVQT 76
Query: 64 TAESTPHDALMNAITDLLAEL 84
            + +P   +++A   L+  L
Sbjct: 77 VEDCSPKQVIVDAAKSLITHL 97

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

Iteration: 1
 Score = 87.0 bits (214), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 43/82 (52%), Positives = 51/82 (62%)
Query: 10  DTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTP 69
           DTK PNA + T  KEDHTLGN+IR +LL D  VLFA YK  HP   +F LRIQTT    P
Sbjct: 24  DTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDP 83
Query: 70  HDALMNAITDLLAELSLFEERF 91
            DAL NA   ++ +L   +  F
Sbjct: 84  KDALKNACNSIINKLGALKTNF 105

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

Iteration: 1
 Score = 61.6 bits (148), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 29/60 (48%), Positives = 37/60 (61%)
Query: 21 VNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDL 80
          +  EDHTLGN+I   L +   V FA Y QPHPL  K I++I T    TP DAL+ AI ++
Sbjct: 17 IEGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVKILTDGSITPKDALLKAIENI 76

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

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 34/57 (59%)
Query: 21 VNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAI 77
          +  EDHTLGN+I   L K   V FA Y QPHPL  K I++I T     P DAL+ AI
Sbjct: 17 IEGEDHTLGNLIAGTLRKISGVSFASYYQPHPLTDKIIVKILTDGSIAPKDALLKAI 73

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	91
3h0g_K	123	DNA-directed RNA polymerase II subunit RPB11; tran	2e-33
1twf_K	120	B13.6, DNA-directed RNA polymerase II 13.6 kDa pol	3e-32
2pa8_L	92	DNA-directed RNA polymerase subunit L; ferredoxin-	2e-30
1xpp_A	115	TA1416, DNA-directed RNA polymerase subunit L; str	5e-28

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

 Score =  110 bits (277), Expect = 2e-33
 Identities = 46/89 (51%), Positives = 59/89 (66%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
            K+  ELD+K PNAA+ T+ KEDHTL NM+ NQLL D  VLFAGYK PHPL H FILR+Q
Sbjct: 16  PKVTYELDSKSPNAAVVTLEKEDHTLANMLANQLLSDERVLFAGYKVPHPLNHNFILRVQ 75

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           T  + +P   +++A   L+  L   +  F
Sbjct: 76  TVEDCSPKQVIVDAAKSLITHLEEIKVNF 104

>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 =  107 bits (269), Expect = 3e-32
 Identities = 44/89 (49%), Positives = 54/89 (60%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
            K+  + DTK PNA + T  KEDHTLGN+IR +LL D  VLFA YK  HP   +F LRIQ
Sbjct: 17  SKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQ 76

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           TT    P DAL NA   ++ +L   +  F
Sbjct: 77  TTEGYDPKDALKNACNSIINKLGALKTNF 105

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

 Score =  101 bits (254), Expect = 2e-30
 Identities = 31/84 (36%), Positives = 42/84 (50%)

Query: 8  ELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAES 67
           +     N     +  EDHTLGN+I   L +   V FA Y QPHPL  K I++I T    
Sbjct: 4  RILKSESNYLELEIEGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVKILTDGSI 63

Query: 68 TPHDALMNAITDLLAELSLFEERF 91
          TP DAL+ AI ++    S + +  
Sbjct: 64 TPKDALLKAIENIRGMTSHYIDEI 87

>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 = 96.9 bits (241), Expect = 5e-28
 Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 1/84 (1%)

Query: 8  ELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAES 67
           + +K  N+    +   D+TL   +  ++LKD  V  A Y   HP+     + ++     
Sbjct: 14 RVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVK-SG 72

Query: 68 TPHDALMNAITDLLAELSLFEERF 91
           P  A+  A+  L         +F
Sbjct: 73 KPQSAIKRAVRKLSKLYEDLGTQF 96

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	91
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
2pa8_L	92	DNA-directed RNA polymerase subunit L; ferredoxin-	100.0
1xpp_A	115	TA1416, DNA-directed RNA polymerase subunit L; str	100.0
2pa8_D	265	DNA-directed RNA polymerase subunit D; ferredoxin-	95.62
3h0g_C	297	DNA-directed RNA polymerase II subunit RPB3; trans	95.54
1twf_C	318	B44.5, DNA-directed RNA polymerase II 45 kDa polyp	95.22
1bdf_A	235	RNA polymerase alpha subunit; nucleotidyltransfera	94.05
1twf_C	318	B44.5, DNA-directed RNA polymerase II 45 kDa polyp	93.94
1bdf_A	235	RNA polymerase alpha subunit; nucleotidyltransfera	93.91
3lu0_A	329	DNA-directed RNA polymerase subunit alpha; E. coli	93.71
2a6h_A	315	DNA-directed RNA polymerase alpha chain; RNA polym	93.67
3lu0_A	329	DNA-directed RNA polymerase subunit alpha; E. coli	91.77
2a6h_A	315	DNA-directed RNA polymerase alpha chain; RNA polym	91.74
3h0g_C	297	DNA-directed RNA polymerase II subunit RPB3; trans	90.33
2pa8_D	265	DNA-directed RNA polymerase subunit D; ferredoxin-	90.25

>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=6.4e-40  Score=223.48  Aligned_cols=89  Identities=52%  Similarity=0.863  Sum_probs=87.5

Q ss_pred             eeeeeecCCCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHH
Q psy11162          3 RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLA   82 (91)
Q Consensus         3 ~kv~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~   82 (91)
                      +||++..|+|++|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++.+|.+||++|+++|++
T Consensus        16 ~Kv~~~~dtk~~n~~~f~i~~EDHTLgNlLr~~Llk~p~V~fAgY~vpHPle~~~~lrIqT~~~~~p~eaL~~al~~L~~   95 (123)
T 3h0g_K           16 PKVTYELDSKSPNAAVVTLEKEDHTLANMLANQLLSDERVLFAGYKVPHPLNHNFILRVQTVEDCSPKQVIVDAAKSLIT   95 (123)
T ss_dssp             CSCCEEECSSSTTEEEEEEESCCSSHHHHHHHTGGGSTTCSCBCCBCSCTTSCEEEEEEECCSSSCSHHHHHHHHHHHHH
T ss_pred             cceEEecCCCCCceEEEEEeCCCcchHHHHHHHHhcCCCeeEeeecCCCCCCCceEEEEEECCCCCHHHHHHHHHHHHHH
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhC
Q psy11162         83 ELSLFEERF   91 (91)
Q Consensus        83 ~~~~l~~~f   91 (91)
                      .|+.|++.|
T Consensus        96 ~~~~l~~~F  104 (123)
T 3h0g_K           96 HLEEIKVNF  104 (123)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999999876

>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=3.3e-39  Score=219.01  Aligned_cols=89  Identities=49%  Similarity=0.753  Sum_probs=87.3

Q ss_pred             eeeeeecCCCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHH
Q psy11162          3 RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLA   82 (91)
Q Consensus         3 ~kv~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~   82 (91)
                      +||+++.++|.+|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+|+.+|.+||++|+++|++
T Consensus        17 ~K~~~~~~~k~~n~~~f~i~~EDHTLgNlLr~~Llk~p~V~fAgY~vpHPl~~~~~lrIqT~~~~~p~eaL~~a~~~L~~   96 (120)
T 1twf_K           17 SKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIIN   96 (120)
T ss_dssp             CSCCEEECSSSTTEEEEEEESCCHHHHHHHHHHHTTCTTEEEEEEECSCTTSCEEEEEEEECTTCCHHHHHHHHHHHHHH
T ss_pred             ceEEEEeccCCCCeEEEEEeCCCchHHHHHHHHHhhCCCeeEEeeecCCCCCCccEEEEEECCCCCHHHHHHHHHHHHHH
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhC
Q psy11162         83 ELSLFEERF   91 (91)
Q Consensus        83 ~~~~l~~~f   91 (91)
                      .|+.++++|
T Consensus        97 ~~~~l~~~f  105 (120)
T 1twf_K           97 KLGALKTNF  105 (120)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999999876

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

Probab=100.00  E-value=2.8e-39  Score=210.39  Aligned_cols=86  Identities=36%  Similarity=0.518  Sum_probs=82.4

Q ss_pred             eeecCCCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q psy11162          6 IKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELS   85 (91)
Q Consensus         6 ~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~   85 (91)
                      .+...++.+|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++.+|.+||++|+++|.+.|+
T Consensus         2 eikvi~k~~n~~~f~i~~EDHTLgN~Lr~~L~~~p~V~fagY~vpHPl~~~~~lrIqT~~~~~p~~al~~a~~~l~~~~~   81 (92)
T 2pa8_L            2 EIRILKSESNYLELEIEGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVKILTDGSITPKDALLKAIENIRGMTS   81 (92)
T ss_dssp             EEEEEEEETTEEEEEEETCCHHHHHHHHHHHHTSTTEEEEEEECSSTTSCCEEEEEEECSSSCHHHHHHHHHHHHHHHHH
T ss_pred             ceEEEecCCCeEEEEEecCchhHHHHHHHHHhcCCCeeEEEeecCCCCCCceEEEEEECCCCCHHHHHHHHHHHHHHHHH
Confidence            45667789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhC
Q psy11162         86 LFEERF   91 (91)
Q Consensus        86 ~l~~~f   91 (91)
                      .++++|
T Consensus        82 ~~~~~f   87 (92)
T 2pa8_L           82 HYIDEI   87 (92)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            999876

>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=1.6e-38  Score=214.45  Aligned_cols=88  Identities=20%  Similarity=0.230  Sum_probs=85.9

Q ss_pred             eeeeeecCCCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHH
Q psy11162          3 RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLA   82 (91)
Q Consensus         3 ~kv~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~   82 (91)
                      +|+.++.+++.+|+++|+|.+|||||||+||++|+++|+|.||||+|||||+++++|||||+|+. |.+||++|+++|.+
T Consensus         9 ~kmeiki~~k~~n~~~f~i~~EDHTLgNlLr~~Llkdp~V~fAgY~vpHPle~~~~lrIqT~~~~-p~eaL~~al~~L~~   87 (115)
T 1xpp_A            9 AESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSGK-PQSAIKRAVRKLSK   87 (115)
T ss_dssp             CCCEEEEEEECSSEEEEEEESCCHHHHHHHHHHHTTCTTEEEEEEECSSTTTSCCEEEEEESSSC-HHHHHHHHHHHHHH
T ss_pred             cceEEEEEcCCCCEEEEEEeCCCchhHHHHHHHHhcCCCeEEEEeecCCCCCCccEEEEEeCCCC-hHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999987 99999999999999


Q ss_pred             HHHHHHhhC
Q psy11162         83 ELSLFEERF   91 (91)
Q Consensus        83 ~~~~l~~~f   91 (91)
                      .|+.|++.|
T Consensus        88 ~~~~l~~~f   96 (115)
T 1xpp_A           88 LYEDLGTQF   96 (115)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999999876

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

Probab=95.62  E-value=0.0086  Score=43.84  Aligned_cols=27  Identities=11%  Similarity=-0.064  Sum_probs=24.3

Q ss_pred             CCceEEEEEecCCcchHHHHHHHHhcC
Q psy11162         13 VPNAAIFTVNKEDHTLGNMIRNQLLKD   39 (91)
Q Consensus        13 ~~n~~~~~i~~EdHTlgNlLr~~L~~~   39 (91)
                      .++.+.|.+.|-|+||||+||-.|+..
T Consensus         9 ~~~~~~f~l~g~~~t~~NalRRills~   35 (265)
T 2pa8_D            9 DDTRIDLVFEGYPLEFVNAIRRASMLY   35 (265)
T ss_dssp             CSSEEEEEEESSCHHHHHHHHHHHHHS
T ss_pred             CCCEEEEEEeCCCHHHHHHHHHHHHHc
Confidence            468999999999999999999998875

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

Probab=95.54  E-value=0.0089  Score=45.23  Aligned_cols=42  Identities=19%  Similarity=0.287  Sum_probs=33.1

Q ss_pred             CceeeeeecCCCCCceEEEEEecCCcchHHHHHHHHhcC-CCe
Q psy11162          1 MIRKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKD-PHV   42 (91)
Q Consensus         1 ~~~kv~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~-~~V   42 (91)
                      |..|-++......++.+.|.+.|-|.||||+||-.|+.. |..
T Consensus         1 m~~~p~I~i~~~~~~~~~F~l~g~~~tiaNALRRiLLSeVPt~   43 (297)
T 3h0g_C            1 MDSETHITIRNISKNSVDFVLTNTSLAVANSLRRVVLAEIPTV   43 (297)
T ss_dssp             ---CCSBCCCCBCSSEEEEEECSCCHHHHHHHHHHHHSSCCEE
T ss_pred             CCCCCeEEEEEccCCEEEEEEECCChhHHHHHHHHHHHcCccc
Confidence            566666777777889999999999999999999999885 543

>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=95.22  E-value=0.0086  Score=45.59  Aligned_cols=29  Identities=14%  Similarity=0.282  Sum_probs=18.5

Q ss_pred             CCCCCceEEEEEecCCcchHHHHHHHHhc
Q psy11162         10 DTKVPNAAIFTVNKEDHTLGNMIRNQLLK   38 (91)
Q Consensus        10 ~~k~~n~~~~~i~~EdHTlgNlLr~~L~~   38 (91)
                      ....++.+.|.+.|-|+||||+||-.|+.
T Consensus        11 ~~~~~~~~kF~leG~~~tlaNALRRiLLS   39 (318)
T 1twf_C           11 REASKDNVDFILSNVDLAMANSLRRVMIA   39 (318)
T ss_dssp             SCCCSSEECCEEBSSCHHHHHHHHHHHHH
T ss_pred             EEecCCEEEEEEEccChhHHHHHHHHHHH
Confidence            33445666777777777777776666554

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

Probab=94.05  E-value=0.022  Score=41.44  Aligned_cols=34  Identities=32%  Similarity=0.401  Sum_probs=23.2

Q ss_pred             CCceEEEEEe----cCCcchHHHHHHHHhcC-CCeeeee
Q psy11162         13 VPNAAIFTVN----KEDHTLGNMIRNQLLKD-PHVLFAG   46 (91)
Q Consensus        13 ~~n~~~~~i~----~EdHTlgNlLr~~L~~~-~~V~fAg   46 (91)
                      .++.+.|.+.    |-++|+||+||-.|+.. |+...-+
T Consensus        20 ~~~~~~F~l~Ple~G~~~tlgNaLRRiLLsevpg~AI~~   58 (235)
T 1bdf_A           20 SSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVTE   58 (235)
T ss_dssp             SSSEEEEEEEEEETTHHHHHHHHHHHHHTTSCCCEEEEE
T ss_pred             cCCEEEEEEEecCCCCchHHHHHHHHHHHhcCCceEEEE
Confidence            3577788885    88888888888777764 5544333

>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=93.94  E-value=0.11  Score=39.43  Aligned_cols=37  Identities=8%  Similarity=0.198  Sum_probs=33.8

Q ss_pred             CCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162         54 EHKFILRIQTTAESTPHDALMNAITDLLAELSLFEER   90 (91)
Q Consensus        54 ~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~   90 (91)
                      .++..|.|.|+|..+|.+||.+|++-|.+.|+.|.+.
T Consensus       225 ~dkfif~VET~Gsi~Peeav~~A~kIL~~kl~~f~~~  261 (318)
T 1twf_C          225 ADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLA  261 (318)
T ss_dssp             CCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999999999988653

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

Probab=93.91  E-value=0.047  Score=39.71  Aligned_cols=47  Identities=23%  Similarity=0.296  Sum_probs=38.2

Q ss_pred             eeeeeeeCCCC------CCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy11162         42 VLFAGYKQPHP------LEHKFILRIQTTAESTPHDALMNAITDLLAELSLFE   88 (91)
Q Consensus        42 V~fAgY~vpHP------l~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~   88 (91)
                      |.-+.|++.-.      -.++..|.|.|+|+.+|.+|+.+|++-|.+.|+.|.
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            44567776422      236799999999999999999999999999988764

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

Probab=93.71  E-value=0.062  Score=41.14  Aligned_cols=48  Identities=23%  Similarity=0.322  Sum_probs=38.0

Q ss_pred             CCeeeeeeeCC-----CCC-CCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Q psy11162         40 PHVLFAGYKQP-----HPL-EHKFILRIQTTAESTPHDALMNAITDLLAELSLF   87 (91)
Q Consensus        40 ~~V~fAgY~vp-----HPl-~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l   87 (91)
                      .=|.-+.|.|.     ... .++..|.|.|+|+.+|.+|+..|++-|++.+..|
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            33556777654     333 4789999999999999999999999999877654

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

Probab=93.67  E-value=0.09  Score=39.89  Aligned_cols=46  Identities=30%  Similarity=0.338  Sum_probs=37.3

Q ss_pred             eeeeeeeCC------CCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Q psy11162         42 VLFAGYKQP------HPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLF   87 (91)
Q Consensus        42 V~fAgY~vp------HPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l   87 (91)
                      |.-+.|.+.      -.-.+...|.|.|+|+.+|.+|+.+|++-|.+.|..|
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            445666553      1234789999999999999999999999999998876

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

Probab=91.77  E-value=0.063  Score=41.11  Aligned_cols=41  Identities=29%  Similarity=0.353  Sum_probs=31.7

Q ss_pred             CCceEEEEEe----cCCcchHHHHHHHHhcC-CCeeeeeee---CCCCC
Q psy11162         13 VPNAAIFTVN----KEDHTLGNMIRNQLLKD-PHVLFAGYK---QPHPL   53 (91)
Q Consensus        13 ~~n~~~~~i~----~EdHTlgNlLr~~L~~~-~~V~fAgY~---vpHPl   53 (91)
                      .++.+.|.+.    |-++|+||+||-.|+.. |+...-+-+   +.|-+
T Consensus        20 ~~~~~kF~l~PlerG~g~TlgNaLRRvLLssvpg~AIt~V~I~gv~Hef   68 (329)
T 3lu0_A           20 SSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEY   68 (329)
T ss_dssp             TTSEEEEEECCCCTTCHHHHHHHHHHHTTTSSCEEEEEEEEESSCSSTT
T ss_pred             CCCEEEEEEEecCCCChhHHHHHHHHHHHhcCCceEEEEEEEeCccccc
Confidence            5799999999    99999999999999985 654444433   44543

>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=91.74  E-value=0.069  Score=40.54  Aligned_cols=42  Identities=24%  Similarity=0.278  Sum_probs=30.9

Q ss_pred             CCCceEEEEEe----cCCcchHHHHHHHHhcC-CCeeeeee---eCCCCC
Q psy11162         12 KVPNAAIFTVN----KEDHTLGNMIRNQLLKD-PHVLFAGY---KQPHPL   53 (91)
Q Consensus        12 k~~n~~~~~i~----~EdHTlgNlLr~~L~~~-~~V~fAgY---~vpHPl   53 (91)
                      ..++.+.|.+.    |-++|+||+||-.|+.. |+...-+-   .+.|-+
T Consensus        16 ~~~~~~~F~l~Ple~G~~~TlgNaLRRiLLsevpg~AI~~V~I~~v~He~   65 (315)
T 2a6h_A           16 QGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEF   65 (315)
T ss_dssp             ETTTEEEEEEEEECTTCHHHHHHHHHHHHHHTCEEEEEEEEEESSCCSTT
T ss_pred             ccCCEEEEEEEccCCCchhHHHHHHHHHHHhcCCceEEEEEEEecchhcc
Confidence            34789999995    99999999999999885 54433332   255654

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

Probab=90.33  E-value=0.2  Score=37.75  Aligned_cols=37  Identities=11%  Similarity=0.386  Sum_probs=34.0

Q ss_pred             CCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162         54 EHKFILRIQTTAESTPHDALMNAITDLLAELSLFEER   90 (91)
Q Consensus        54 ~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~   90 (91)
                      .++..|.|.|+|..+|.+++.+|++-|.+.++.|.+.
T Consensus       226 ~dkfif~VET~Gsl~p~eiv~~A~~iL~~kl~~f~~~  262 (297)
T 3h0g_C          226 PRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLVRD  262 (297)
T ss_dssp             CCCEEEEEEBCSSSCTTTTTHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999999999988753

>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=90.25  E-value=0.59  Score=33.97  Aligned_cols=37  Identities=24%  Similarity=0.502  Sum_probs=32.9

Q ss_pred             CCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162         54 EHKFILRIQTTAESTPHDALMNAITDLLAELSLFEER   90 (91)
Q Consensus        54 ~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~   90 (91)
                      .+...+.|.|+|..+|.+++.+|++-|.+.++.|.+.
T Consensus       223 ~d~~i~~VEt~Gsl~Pee~v~~A~~iL~~~~~~~~~~  259 (265)
T 2pa8_D          223 EDKYILEIESVGSLKPERILLEAGKSIIRKIEELEKK  259 (265)
T ss_dssp             EEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEeccCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            3567899999999999999999999999999988764

---

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	91
d1twfk_	114	d.74.3.2 (K:) RPB11 {Baker's yeast (Saccharomyces	1e-32
d1xppa_	99	d.74.3.2 (A:) DNA-directed RNA polymerase subunit	6e-25

>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 =  107 bits (269), Expect = 1e-32
 Identities = 44/89 (49%), Positives = 54/89 (60%)

Query: 3   RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
            K+  + DTK PNA + T  KEDHTLGN+IR +LL D  VLFA YK  HP   +F LRIQ
Sbjct: 17  SKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQ 76

Query: 63  TTAESTPHDALMNAITDLLAELSLFEERF 91
           TT    P DAL NA   ++ +L   +  F
Sbjct: 77  TTEGYDPKDALKNACNSIINKLGALKTNF 105

>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 = 87.6 bits (217), Expect = 6e-25
 Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 1/84 (1%)

Query: 8  ELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAES 67
           + +K  N+    +   D+TL   +  ++LKD  V  A Y   HP+     + ++     
Sbjct: 6  RVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVK-SG 64

Query: 68 TPHDALMNAITDLLAELSLFEERF 91
           P  A+  A+  L         +F
Sbjct: 65 KPQSAIKRAVRKLSKLYEDLGTQF 88

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	91
d1xppa_	99	DNA-directed RNA polymerase subunit L, RpoL {Therm	100.0
d1twfk_	114	RPB11 {Baker's yeast (Saccharomyces cerevisiae) [T	100.0
d1bdfa1	105	RNA polymerase alpha {Escherichia coli [TaxId: 562	98.28
d1smya1	106	RNA polymerase alpha {Thermus thermophilus [TaxId:	98.19
d1twfc1	135	RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta	96.65

>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=1e-34  Score=188.90  Aligned_cols=86  Identities=21%  Similarity=0.233  Sum_probs=80.4

Q ss_pred             eeeecCCCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHH
Q psy11162          5 IIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAEL   84 (91)
Q Consensus         5 v~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~   84 (91)
                      +.++.-++.+|+++|+|.||||||||+||++|+++|+|.||||++||||+++|.|+|||+++ +|.+||++|++++++.|
T Consensus         3 ~~ikvi~~~~n~~~~~i~~EdHTlgn~L~~~L~~~~~V~fagY~ipHPl~~~~~l~I~t~~~-~p~~~l~~a~~~li~~~   81 (99)
T d1xppa_           3 SSLRVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSG-KPQSAIKRAVRKLSKLY   81 (99)
T ss_dssp             CEEEEEEECSSEEEEEEESCCHHHHHHHHHHHTTCTTEEEEEEECSSTTTSCCEEEEEESSS-CHHHHHHHHHHHHHHHH
T ss_pred             ceEEEEecCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEEecCCcccCCeEEEEEeCCC-CHHHHHHHHHHHHHHHH
Confidence            34555677789999999999999999999999999999999999999999999999999987 89999999999999999


Q ss_pred             HHHHhhC
Q psy11162         85 SLFEERF   91 (91)
Q Consensus        85 ~~l~~~f   91 (91)
                      +.|.+.|
T Consensus        82 ~~l~~~~   88 (99)
T d1xppa_          82 EDLGTQF   88 (99)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9998875

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

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

Probab=100.00  E-value=2.2e-34  Score=191.51  Aligned_cols=89  Identities=49%  Similarity=0.753  Sum_probs=86.5

Q ss_pred             eeeeeecCCCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHH
Q psy11162          3 RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLA   82 (91)
Q Consensus         3 ~kv~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~   82 (91)
                      +||.+..+++.+|+++|+|.+|||||||+|++.|+++|+|.||||++|||+++++.|||||+++.+|.++|++|+++|++
T Consensus        17 ~ki~i~~~~~~~n~~~~~i~~EdhTlGnlL~~~L~~~~~V~fagY~~pHPl~~~i~irI~t~~~~~p~~~l~~a~~~l~~   96 (114)
T d1twfk_          17 SKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIIN   96 (114)
T ss_dssp             CSCCEEECSSSTTEEEEEEESCCHHHHHHHHHHHTTCTTEEEEEEECSCTTSCEEEEEEEECTTCCHHHHHHHHHHHHHH
T ss_pred             ceEEEEecCCCCceEEEEEeCCCchHHHHHHHHHhcCCCceEEEeecCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999998999999999999999


Q ss_pred             HHHHHHhhC
Q psy11162         83 ELSLFEERF   91 (91)
Q Consensus        83 ~~~~l~~~f   91 (91)
                      .|+.|++.|
T Consensus        97 ~~~~l~~~f  105 (114)
T d1twfk_          97 KLGALKTNF  105 (114)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999998875

>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=98.28  E-value=2.9e-06  Score=54.16  Aligned_cols=73  Identities=29%  Similarity=0.338  Sum_probs=60.2

Q ss_pred             CceEEEEE----ecCCcchHHHHHHHHhc-CCCeeeeeeeCC---CC---CCCeeEEEEEeCCCCCHHHHHHHHHHHHHH
Q psy11162         14 PNAAIFTV----NKEDHTLGNMIRNQLLK-DPHVLFAGYKQP---HP---LEHKFILRIQTTAESTPHDALMNAITDLLA   82 (91)
Q Consensus        14 ~n~~~~~i----~~EdHTlgNlLr~~L~~-~~~V~fAgY~vp---HP---l~~~~~l~Iqt~~~~~p~~al~~a~~~l~~   82 (91)
                      ++.+.|++    .|-++|+||.+|..|+. .+.|.-++|+|.   |=   -.++..|.|.|+|.++|.+|+..|++-|.+
T Consensus        20 ~~~~k~~~eplErG~Gyt~gn~lr~~llSs~sPV~~V~y~Ve~~~~e~~td~d~L~lei~TnGsi~p~eA~~~Aa~il~~   99 (105)
T d1bdfa1          20 STHAKVTLEPLERGFGHTLGNALRAILLSSMPPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAE   99 (105)
T ss_dssp             SSEEEEEEEEEETTHHHHHHHHHHHHHTTSCCSEEEEEEECCBCCCSSCSSEEEEEEEEEECSSSCHHHHHHHHHHHHHH
T ss_pred             CceEEEEEEEccCCcccccccccchhhhhcccceeEEEEeeeeeecCCCCcceEEEEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            34455554    57889999999999777 589999999987   43   245899999999999999999999999988


Q ss_pred             HHHH
Q psy11162         83 ELSL   86 (91)
Q Consensus        83 ~~~~   86 (91)
                      .+.-
T Consensus       100 ~~~~  103 (105)
T d1bdfa1         100 QLEA  103 (105)
T ss_dssp             HGGG
T ss_pred             HHHh
Confidence            7654

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

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

Probab=98.19  E-value=2.1e-06  Score=55.07  Aligned_cols=76  Identities=30%  Similarity=0.326  Sum_probs=62.0

Q ss_pred             CCCceEEEEEe----cCCcchHHHHHHHHhc-CCCeeeeeeeCCC------CCCCeeEEEEEeCCCCCHHHHHHHHHHHH
Q psy11162         12 KVPNAAIFTVN----KEDHTLGNMIRNQLLK-DPHVLFAGYKQPH------PLEHKFILRIQTTAESTPHDALMNAITDL   80 (91)
Q Consensus        12 k~~n~~~~~i~----~EdHTlgNlLr~~L~~-~~~V~fAgY~vpH------Pl~~~~~l~Iqt~~~~~p~~al~~a~~~l   80 (91)
                      +..+...|.+.    |..+|+||.||..|.. .|-|.-+.|+|..      .-.++..|-|.|+|.++|.+|+..|++-|
T Consensus        16 ~~~~y~~~v~~p~erG~g~~~gn~l~~il~ss~~PV~kV~y~Ve~~rvg~~~d~dkL~LeI~TnGsi~P~eAl~~Aa~il   95 (106)
T d1smya1          16 QGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEIL   95 (106)
T ss_dssp             CSSSCEEEEEEEECTTHHHHHHHHHHHHHHHTCECEEEEEEEEEECCCSSCSCCEEEEEEEEECSSSCHHHHHHHHHHHH
T ss_pred             cCCceeEEEeeccCCCcccccccccceeehhcCChhhEEEEEecccccCcccceeEEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            44456666654    7789999999997766 5899999999873      22467999999999999999999999999


Q ss_pred             HHHHHHH
Q psy11162         81 LAELSLF   87 (91)
Q Consensus        81 ~~~~~~l   87 (91)
                      .+.+..|
T Consensus        96 ~~h~~~f  102 (106)
T d1smya1          96 REHLTYF  102 (106)
T ss_dssp             HHHHHTS
T ss_pred             HHHHHhh
Confidence            9887654

>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=96.65  E-value=0.011  Score=38.76  Aligned_cols=80  Identities=11%  Similarity=0.291  Sum_probs=62.4

Q ss_pred             cCCCCCceEEEEEecCCcchHHHHHHHHhcC-CCeeeeeeeC--------------------------------C---CC
Q psy11162          9 LDTKVPNAAIFTVNKEDHTLGNMIRNQLLKD-PHVLFAGYKQ--------------------------------P---HP   52 (91)
Q Consensus         9 ~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~-~~V~fAgY~v--------------------------------p---HP   52 (91)
                      .-+..++.+.|.+.|-|-++.|+||-.++.+ |-  ++++.+                                +   .|
T Consensus         8 i~~~~~~~~~F~l~~~d~s~ANalRRi~iaeV~t--~v~feyDp~N~lrHtdyw~e~~~~~ewP~s~~~~~e~~~~e~e~   85 (135)
T d1twfc1           8 IREASKDNVDFILSNVDLAMANSLRRVMIAEIAA--AIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDP   85 (135)
T ss_dssp             CSCCCSSEECCEEBSSCHHHHHHHHHHHHHCCEE--EEEEEECSSTTSCCSCCCCSSCHHHHSCCCGGGTTSCCCCSSSC
T ss_pred             EEEcCCCEEEEEEeCCCHHHHHHHHHHHHHhhhh--heeeeecccccccceeecccCCccccCCcccCCCCCCCcccccC
Confidence            3445568999999999999999999999876 42  222111                                1   12


Q ss_pred             C-----CCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162         53 L-----EHKFILRIQTTAESTPHDALMNAITDLLAELSLFEER   90 (91)
Q Consensus        53 l-----~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~   90 (91)
                      +     -+.+.+.|.|.|...|.+++.+|++-|...|..|...
T Consensus        86 fd~~akpd~F~f~VEs~G~l~p~~Iv~~ai~iL~~Kl~~l~~~  128 (135)
T d1twfc1          86 FDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLA  128 (135)
T ss_dssp             CCTTCCCCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCEEEEEEEeccCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            3     2568899999999999999999999999999988754