Citrus Sinensis ID: 033968

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------
Protein Sequence
MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEKVQAMKIDSKE
Secondary Structure (PSIPRED)
ccccccccccEEEEEEccccccHHHHHHHHHHcccccEEEEccccccccccEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccEEEEEEcccccHHHHHHHHHHccccEEEEEEEccccccccEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccc
Coil and Loop (DISEMBL)
mehgafgdqsnatfslteedHTLANAVRFTlnqdprvtfcgysiphpsdarvnirvqttgdparEVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEKVQAMKIDSKE
Flexible Loop (DISEMBL)
mehgafgdqsnatfSLTEEDHTLANAVRFTLNQDPRVTFCGYsiphpsdarvNIRVQTTGDPAREVLKDSCQELMLMCRHVRSTFAkavddfrtsekvqamkidske
Low Complexity Region (SEG)
MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEKVQAMKIDSKE
Disordered region (IsUnstruct)
********************HTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDPAREVLKDSCQELMLMCRHVRSTFAKAVDD****************
Disordered Region (DISOPRED)
*********SNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDPAREVLKDSCQELMLMCRHVRSTFAK********************
Disordered Region (DISEMBL)
*********SNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEKVQAMKIDSKE
Disordered Region (DISPRO)
********QSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTS************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEKVQAMKIDSKE
Positional Conservation
no confident homologs detected

---

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	107	2.2.26 [Sep-21-2011]
Q5XK67	114	DNA-directed RNA polymera	N/A	no	0.803	0.754	0.436	7e-18
Q9Y2S0	133	DNA-directed RNA polymera	yes	no	0.869	0.699	0.414	1e-17
P97304	133	DNA-directed RNA polymera	yes	no	0.869	0.699	0.404	2e-17
P28000	142	DNA-directed RNA polymera	yes	no	0.766	0.577	0.457	3e-17
Q6DRI4	112	DNA-directed RNA polymera	yes	no	0.841	0.803	0.428	6e-17
Q1RMG8	133	DNA-directed RNA polymera	yes	no	0.869	0.699	0.393	2e-16
Q54ES6	116	DNA-directed RNA polymera	yes	no	0.738	0.681	0.475	2e-15
Q09177	125	DNA-directed RNA polymera	yes	no	0.785	0.672	0.411	7e-15
Q9VIZ0	105	Probable DNA-directed RNA	yes	no	0.869	0.885	0.368	1e-14
Q61IX2	145	Probable DNA-directed RNA	N/A	no	0.775	0.572	0.380	2e-10

>sp|Q5XK67|RPAC2_XENLA DNA-directed RNA polymerases I and III subunit RPAC2 OS=Xenopus laevis GN=polr1d PE=3 SV=1

 Score = 89.4 bits (220), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 38/87 (43%), Positives = 60/87 (68%), Gaps = 1/87 (1%)

Query: 8   DQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQT-TGDPAREV 66
           ++S  TF L EEDHTL N++R+ + ++P V FCGYSI HPS+ ++N R+QT  G PA E 
Sbjct: 20  EESCVTFVLHEEDHTLGNSLRYMVMKNPEVEFCGYSITHPSETKINFRIQTRNGIPAVEP 79

Query: 67  LKDSCQELMLMCRHVRSTFAKAVDDFR 93
            +    EL+ +C+HV +TF  ++ +++
Sbjct: 80  FRRGLNELVDVCQHVLNTFETSIKEYK 106

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common core component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively.
Xenopus laevis (taxid: 8355)

>sp|Q9Y2S0|RPAC2_HUMAN DNA-directed RNA polymerases I and III subunit RPAC2 OS=Homo sapiens GN=POLR1D PE=1 SV=1

 Score = 88.2 bits (217), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 39/94 (41%), Positives = 60/94 (63%), Gaps = 1/94 (1%)

Query: 1   MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
           M   A  D+   TF L EEDHTL N++R+ + ++P V FCGY+  HPS++++N+R+QT G
Sbjct: 29  MVQAAGTDRHCVTFVLHEEDHTLGNSLRYMIMKNPEVEFCGYTTTHPSESKINLRIQTRG 88

Query: 61  D-PAREVLKDSCQELMLMCRHVRSTFAKAVDDFR 93
             PA E  +    ELM +C+HV   F  ++ D++
Sbjct: 89  TLPAVEPFQRGLNELMNVCQHVLDKFEASIKDYK 122

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common core component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively.

Homo sapiens (taxid: 9606)

>sp|P97304|RPAC2_MOUSE DNA-directed RNA polymerases I and III subunit RPAC2 OS=Mus musculus GN=Polr1d PE=2 SV=1

 Score = 87.4 bits (215), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 38/94 (40%), Positives = 59/94 (62%), Gaps = 1/94 (1%)

Query: 1   MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
           M   A  D+   TF L EEDHTL N +R+ + ++P V FCGY+  HPS++++N+R+QT G
Sbjct: 29  MVQAAGTDRQCVTFVLHEEDHTLGNCLRYIIMKNPEVEFCGYTTTHPSESKINLRIQTRG 88

Query: 61  D-PAREVLKDSCQELMLMCRHVRSTFAKAVDDFR 93
             PA E  +    EL+ +C+HV   F  ++ D++
Sbjct: 89  ALPAVEPFQKGLNELLNVCQHVLVKFEASIKDYK 122

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common core component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively.

Mus musculus (taxid: 10090)

>sp|P28000|RPAC2_YEAST DNA-directed RNA polymerases I and III subunit RPAC2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPC19 PE=1 SV=1

 Score = 87.0 bits (214), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 38/83 (45%), Positives = 58/83 (69%), Gaps = 1/83 (1%)

Query: 8   DQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREV 66
           D ++A+F + EEDHTL NA+R+ + ++P V FCGYSIPHPS+  +NIR+QT G+  A + 
Sbjct: 57  DGTSASFQIVEEDHTLGNALRYVIMKNPDVEFCGYSIPHPSENLLNIRIQTYGETTAVDA 116

Query: 67  LKDSCQELMLMCRHVRSTFAKAV 89
           L+   ++LM +C  V S F + +
Sbjct: 117 LQKGLKDLMDLCDVVESKFTEKI 139

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common core component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively.

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

>sp|Q6DRI4|RPAC2_DANRE DNA-directed RNA polymerases I and III subunit RPAC2 OS=Danio rerio GN=polr1d PE=3 SV=1

 Score = 85.9 bits (211), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 39/91 (42%), Positives = 58/91 (63%), Gaps = 1/91 (1%)

Query: 8   DQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTT-GDPAREV 66
           D+   TF L EEDHTL N++R+ + +   V FCGYSI HPS++++N R+QT  G PA E 
Sbjct: 19  DEGCVTFVLNEEDHTLGNSLRYMIMKSQDVEFCGYSITHPSESKINFRIQTRDGVPASEP 78

Query: 67  LKDSCQELMLMCRHVRSTFAKAVDDFRTSEK 97
           L++    L  +C+HV  TF   + +F+  E+
Sbjct: 79  LRNGLNNLTDVCKHVLQTFEARMKEFKEQEE 109

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common core component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively.

Danio rerio (taxid: 7955)

>sp|Q1RMG8|RPAC2_BOVIN DNA-directed RNA polymerases I and III subunit RPAC2 OS=Bos taurus GN=POLR1D PE=2 SV=1

 Score = 84.3 bits (207), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 60/94 (63%), Gaps = 1/94 (1%)

Query: 1   MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
           M   A  D+   TF L EEDHTL N++R+ + ++P V FCGY+  HPS++++N+R+QT G
Sbjct: 29  MVQAAGTDRHCVTFVLHEEDHTLGNSLRYMIMKNPEVEFCGYTTTHPSESKINLRIQTRG 88

Query: 61  D-PAREVLKDSCQELMLMCRHVRSTFAKAVDDFR 93
             PA E  +    +LM +C+HV   F  ++ +++
Sbjct: 89  ALPAVEPFQRGLTDLMNVCQHVLDKFEASIKEYK 122

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common core component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively.

Bos taurus (taxid: 9913)

>sp|Q54ES6|RPC19_DICDI DNA-directed RNA polymerases I and III subunit rpc19 OS=Dictyostelium discoideum GN=rpc19 PE=3 SV=1

 Score = 81.3 bits (199), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/80 (47%), Positives = 54/80 (67%), Gaps = 1/80 (1%)

Query: 12  ATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDS 70
           ATF  T+EDHTL NA+ + L ++P+V F GYSIPHPSD R+N+R+QT  +  A+E L   
Sbjct: 36  ATFIFTDEDHTLGNALHYVLMKNPKVDFSGYSIPHPSDNRMNLRIQTKSNITAQESLLQG 95

Query: 71  CQELMLMCRHVRSTFAKAVD 90
             ++  + RH+  TF  A+D
Sbjct: 96  LTDIKDISRHIFETFNNALD 115

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common core component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively.

Dictyostelium discoideum (taxid: 44689)

>sp|Q09177|RPAC2_SCHPO DNA-directed RNA polymerases I and III subunit RPAC2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpc19 PE=2 SV=1

 Score = 79.3 bits (194), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 35/85 (41%), Positives = 55/85 (64%), Gaps = 1/85 (1%)

Query: 4   GAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTT-GDP 62
           G   D ++ TF + +EDHTL N++R+ + ++P V FCGYSIPHPS+A++N R+QT     
Sbjct: 27  GHSADLTSVTFQIQKEDHTLGNSLRYVIMKNPEVEFCGYSIPHPSEAKMNFRIQTAPSTT 86

Query: 63  AREVLKDSCQELMLMCRHVRSTFAK 87
           A +VL+    +L+ +C  V   F +
Sbjct: 87  AVDVLRKGLDDLIDLCDAVTEKFTE 111

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common core component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively.

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

>sp|Q9VIZ0|RPAC2_DROME Probable DNA-directed RNA polymerases I and III subunit RPAC2 OS=Drosophila melanogaster GN=l(2)37Cg PE=3 SV=1

 Score = 78.2 bits (191), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 38/103 (36%), Positives = 61/103 (59%), Gaps = 10/103 (9%)

Query: 7   GDQSNA----TFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDP 62
           GD+ N     TF  T E HTL NA++  + + P V FCGY+IPHP++ +++ R+Q+  D 
Sbjct: 9   GDEKNGEGSRTFVFTNEGHTLGNALKTIIARYPEVDFCGYTIPHPTEQKLHFRIQSRRDR 68

Query: 63  AREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEKVQAMKIDS 105
           A ++LK   ++L  +C H   TF K + +F       AMK+++
Sbjct: 69  AIDILKRGLEDLEGLCDHTIVTFEKEMAEF------NAMKVEN 105

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common core component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively.

Drosophila melanogaster (taxid: 7227)

>sp|Q61IX2|RPAC2_CAEBR Probable DNA-directed RNA polymerases I and III subunit RPAC2 OS=Caenorhabditis briggsae GN=CBG10036 PE=3 SV=1

 Score = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/84 (38%), Positives = 49/84 (58%), Gaps = 1/84 (1%)

Query: 8   DQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTT-GDPAREV 66
           D SN T  L EEDHT+ N+++  L++   V FCGY++PHP + ++  RVQT  G  A EV
Sbjct: 58  DPSNLTLILYEEDHTIGNSIKHILSRMDEVEFCGYNVPHPLEDKILFRVQTKDGINALEV 117

Query: 67  LKDSCQELMLMCRHVRSTFAKAVD 90
           L  + + +  +   +R  F  A +
Sbjct: 118 LVKAFESVEQVFSTIRGKFEAAYE 141

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common core component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively.

Caenorhabditis briggsae (taxid: 6238)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	107
225434732	105	PREDICTED: DNA-directed RNA polymerases	0.971	0.990	0.759	2e-42
388495242	115	unknown [Medicago truncatula]	0.934	0.869	0.76	1e-41
351725297	107	uncharacterized protein LOC100500695 [Gl	0.897	0.897	0.802	1e-41
388497488	104	unknown [Lotus japonicus]	0.971	1.0	0.740	2e-41
158828223	109	RNApol24 [Cleome spinosa]	0.962	0.944	0.766	3e-41
357461253	218	DNA-directed RNA polymerases I and III s	0.934	0.458	0.75	3e-41
357502661	115	DNA-directed RNA polymerases I and III s	0.934	0.869	0.75	4e-41
356573936	106	PREDICTED: DNA-directed RNA polymerases	0.990	1.0	0.716	4e-40
224059388	102	predicted protein [Populus trichocarpa]	0.887	0.931	0.768	8e-39
449459084	104	PREDICTED: DNA-directed RNA polymerases	0.962	0.990	0.699	1e-38

>gi|225434732|ref|XP_002281351.1| PREDICTED: DNA-directed RNA polymerases I and III subunit RPAC2 isoform 1 [Vitis vinifera] gi|297745971|emb|CBI16027.3| unnamed protein product [Vitis vinifera]

 Score =  176 bits (446), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 79/104 (75%), Positives = 93/104 (89%)

Query: 1   MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
           MEHG+F D S +TFSL++EDHTLAN++RFTLNQDPRV FCGYSIPHPSDARVNIRVQTTG
Sbjct: 1   MEHGSFSDHSKSTFSLSDEDHTLANSIRFTLNQDPRVAFCGYSIPHPSDARVNIRVQTTG 60

Query: 61  DPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEKVQAMKID 104
           D AREVLKD+CQ+LMLMC+HVRSTF KAV D++ S+ V+ M I+
Sbjct: 61  DSAREVLKDACQDLMLMCQHVRSTFDKAVVDYKMSKPVKDMSIE 104

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388495242|gb|AFK35687.1| unknown [Medicago truncatula]

 Score =  173 bits (439), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 76/100 (76%), Positives = 90/100 (90%)

Query: 1   MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
           MEHG++ D S +TFSL +EDHT AN+VRFTLNQDPRVTFCGYSIPHPS+ RVN+RVQTTG
Sbjct: 1   MEHGSYSDLSKSTFSLVDEDHTFANSVRFTLNQDPRVTFCGYSIPHPSENRVNVRVQTTG 60

Query: 61  DPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEKVQA 100
           DPA EVLKD CQ+LMLMC+HVRSTF KAV+DF+TS+ V++
Sbjct: 61  DPASEVLKDGCQDLMLMCQHVRSTFGKAVNDFKTSKSVRS 100

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351725297|ref|NP_001238111.1| uncharacterized protein LOC100500695 [Glycine max] gi|255630968|gb|ACU15848.1| unknown [Glycine max]

 Score =  173 bits (438), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 77/96 (80%), Positives = 88/96 (91%)

Query: 1  MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
          MEHG++ DQS +TFSL +EDHT ANAVRFTLNQDPRV+FCGYSIPHPSD RVNIRVQTTG
Sbjct: 1  MEHGSYTDQSKSTFSLVDEDHTFANAVRFTLNQDPRVSFCGYSIPHPSDNRVNIRVQTTG 60

Query: 61 DPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSE 96
          DP+REVLKD+CQ+LMLMC+HVRSTF KAV DF+ S+
Sbjct: 61 DPSREVLKDACQDLMLMCQHVRSTFDKAVSDFKISK 96

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388497488|gb|AFK36810.1| unknown [Lotus japonicus]

 Score =  172 bits (436), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 77/104 (74%), Positives = 91/104 (87%)

Query: 1   MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
           MEHG+  D+S +TFSLT+EDHT ANA+R+TLNQDPRVTFCGYSIPHPSD RVNIRVQTTG
Sbjct: 1   MEHGSHSDESRSTFSLTDEDHTFANAIRYTLNQDPRVTFCGYSIPHPSDNRVNIRVQTTG 60

Query: 61  DPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEKVQAMKID 104
           +PAREVLKDSCQ +MLMC+HVR TF KAV+DF++ +  + M ID
Sbjct: 61  EPAREVLKDSCQHMMLMCQHVRGTFDKAVNDFKSKKGGKDMDID 104

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|158828223|gb|ABW81101.1| RNApol24 [Cleome spinosa]

 Score =  172 bits (435), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 79/103 (76%), Positives = 88/103 (85%)

Query: 1   MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
           MEHG+F D S+ATFSLTEEDHTLANAVRF LNQDPRVTFCGYSIPHPS ARVNIRVQTTG
Sbjct: 1   MEHGSFTDHSHATFSLTEEDHTLANAVRFVLNQDPRVTFCGYSIPHPSHARVNIRVQTTG 60

Query: 61  DPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEKVQAMKI 103
           DPAREVLKD+CQ+LMLM RHVR  F  AV DF+   + ++M +
Sbjct: 61  DPAREVLKDACQDLMLMNRHVRGVFDNAVADFKKGNQTESMDV 103

Source: Cleome spinosa

Species: Cleome spinosa

Genus: Cleome

Family: Cleomaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357461253|ref|XP_003600908.1| DNA-directed RNA polymerases I and III subunit RPAC2 [Medicago truncatula] gi|355489956|gb|AES71159.1| DNA-directed RNA polymerases I and III subunit RPAC2 [Medicago truncatula]

 Score =  172 bits (435), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 75/100 (75%), Positives = 88/100 (88%)

Query: 1   MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
           MEHG + D S +TFSL  EDHT +N+VRFTLNQDPRVTFCGYSIPHPS+ RVN+RVQTTG
Sbjct: 104 MEHGLYSDLSKSTFSLVNEDHTFSNSVRFTLNQDPRVTFCGYSIPHPSENRVNVRVQTTG 163

Query: 61  DPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEKVQA 100
           DPA EVLKD CQ+LMLMC+HVRSTF KAV+DF+TS+ V++
Sbjct: 164 DPASEVLKDGCQDLMLMCQHVRSTFGKAVNDFKTSKSVRS 203

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357502661|ref|XP_003621619.1| DNA-directed RNA polymerases I and III subunit RPAC2 [Medicago truncatula] gi|355496634|gb|AES77837.1| DNA-directed RNA polymerases I and III subunit RPAC2 [Medicago truncatula]

 Score =  171 bits (434), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 75/100 (75%), Positives = 89/100 (89%)

Query: 1   MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
           MEHG++ D S +TFSL +EDHT AN+VRF LNQDPRVTFCGYSIPHPS+ RVN+RVQTTG
Sbjct: 1   MEHGSYSDLSKSTFSLVDEDHTFANSVRFILNQDPRVTFCGYSIPHPSENRVNVRVQTTG 60

Query: 61  DPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEKVQA 100
           DPA EVLKD CQ+LMLMC+HVRSTF KAV+DF+TS+ V++
Sbjct: 61  DPASEVLKDGCQDLMLMCQHVRSTFGKAVNDFKTSKSVRS 100

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356573936|ref|XP_003555110.1| PREDICTED: DNA-directed RNA polymerases I and III subunit RPAC2-like [Glycine max]

 Score =  168 bits (426), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 76/106 (71%), Positives = 90/106 (84%)

Query: 1   MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
           ME G++ DQS +TFSL +EDHT AN+VRFTLNQDPRVTFCGYSIPHPSD RVNIRVQTTG
Sbjct: 1   MELGSYSDQSKSTFSLVDEDHTFANSVRFTLNQDPRVTFCGYSIPHPSDNRVNIRVQTTG 60

Query: 61  DPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEKVQAMKIDSK 106
           DPAREVLKD CQ+LMLMC+HVRSTF  A+ DF+ ++     ++D+K
Sbjct: 61  DPAREVLKDGCQDLMLMCQHVRSTFDNAMTDFKRTQTNTEQEMDTK 106

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224059388|ref|XP_002299838.1| predicted protein [Populus trichocarpa] gi|222847096|gb|EEE84643.1| predicted protein [Populus trichocarpa]

 Score =  164 bits (414), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 73/95 (76%), Positives = 85/95 (89%)

Query: 1  MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
          MEHG+  D S+ATF   +EDHTLAN+VRF LNQDPRV+FCGYSIPHPSDA+VNIRVQTTG
Sbjct: 1  MEHGSVRDPSSATFCFVDEDHTLANSVRFALNQDPRVSFCGYSIPHPSDAKVNIRVQTTG 60

Query: 61 DPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTS 95
          DPAREVLKD+CQ LM+MC+HVRST  KAVDD+R++
Sbjct: 61 DPAREVLKDACQNLMVMCQHVRSTLDKAVDDYRSN 95

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449459084|ref|XP_004147276.1| PREDICTED: DNA-directed RNA polymerases I and III subunit RPAC2-like [Cucumis sativus]

 Score =  163 bits (412), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 72/103 (69%), Positives = 89/103 (86%)

Query: 1   MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
           MEHG+F D++ +TFS+ +EDHTLAN +R+TLNQDPRVTFCGYSIPHPSD RVNIRVQTTG
Sbjct: 1   MEHGSFTDETKSTFSMADEDHTLANTLRYTLNQDPRVTFCGYSIPHPSDNRVNIRVQTTG 60

Query: 61  DPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEKVQAMKI 103
           DPAREVLKD+CQ LM++C+HVR+TF KAV D + +  V+ + I
Sbjct: 61  DPAREVLKDACQNLMVVCQHVRNTFDKAVLDVKLTNPVRDINI 103

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	107
TAIR|locus:2043092	139	RPC14 "RNApolymerase 14 kDa su	0.588	0.453	0.682	1.7e-18
UNIPROTKB|Q9Y2S0	133	POLR1D "DNA-directed RNA polym	0.869	0.699	0.414	5.3e-17
ZFIN|ZDB-GENE-040930-4	112	polr1d "polymerase (RNA) I pol	0.841	0.803	0.428	5.3e-17
MGI|MGI:108403	133	Polr1d "polymerase (RNA) I pol	0.897	0.721	0.391	1.4e-16
UNIPROTKB|E2RI73	133	POLR1D "Uncharacterized protei	0.869	0.699	0.404	1.8e-16
SGD|S000005057	142	RPC19 "RNA polymerase subunit	0.766	0.577	0.457	2.9e-16
UNIPROTKB|G3MYF3	133	G3MYF3 "Uncharacterized protei	0.869	0.699	0.393	4.7e-16
UNIPROTKB|Q1RMG8	133	POLR1D "DNA-directed RNA polym	0.869	0.699	0.393	4.7e-16
UNIPROTKB|F1RSW6	130	POLR1D "Uncharacterized protei	0.906	0.746	0.415	4.7e-16
UNIPROTKB|I3LRD0	139	POLR1D "Uncharacterized protei	0.906	0.697	0.415	4.7e-16

TAIR|locus:2043092 RPC14 "RNApolymerase 14 kDa subunit" [Arabidopsis thaliana (taxid:3702)]

 Score = 223 (83.6 bits), Expect = 1.7e-18, P = 1.7e-18
 Identities = 43/63 (68%), Positives = 50/63 (79%)

Query:    35 PRVTFCGYSIPHPSDARVNIRVQTTGDPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRT 94
             PRVT   Y+IPHPS  +VNIRVQTTGDPAREV KD+CQELM M RHVRS F KAV +++ 
Sbjct:    52 PRVTVAAYTIPHPSLEQVNIRVQTTGDPAREVFKDACQELMQMNRHVRSVFDKAVAEYKD 111

Query:    95 SEK 97
              +K
Sbjct:   112 EQK 114

GO:0003677 "DNA binding" evidence=IEA;ISS

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0009304 "tRNA transcription" evidence=TAS

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005666 "DNA-directed RNA polymerase III complex" evidence=ISS;IDA

UNIPROTKB|Q9Y2S0 POLR1D "DNA-directed RNA polymerases I and III subunit RPAC2" [Homo sapiens (taxid:9606)]

 Score = 209 (78.6 bits), Expect = 5.3e-17, P = 5.3e-17
 Identities = 39/94 (41%), Positives = 60/94 (63%)

Query:     1 MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
             M   A  D+   TF L EEDHTL N++R+ + ++P V FCGY+  HPS++++N+R+QT G
Sbjct:    29 MVQAAGTDRHCVTFVLHEEDHTLGNSLRYMIMKNPEVEFCGYTTTHPSESKINLRIQTRG 88

Query:    61 D-PAREVLKDSCQELMLMCRHVRSTFAKAVDDFR 93
               PA E  +    ELM +C+HV   F  ++ D++
Sbjct:    89 TLPAVEPFQRGLNELMNVCQHVLDKFEASIKDYK 122

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005736 "DNA-directed RNA polymerase I complex" evidence=IEA

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006360 "transcription from RNA polymerase I promoter" evidence=TAS

GO:0006361 "transcription initiation from RNA polymerase I promoter" evidence=TAS

GO:0006362 "transcription elongation from RNA polymerase I promoter" evidence=TAS

GO:0006363 "termination of RNA polymerase I transcription" evidence=TAS

GO:0006383 "transcription from RNA polymerase III promoter" evidence=TAS

GO:0006385 "transcription elongation from RNA polymerase III promoter" evidence=TAS

GO:0006386 "termination of RNA polymerase III transcription" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

ZFIN|ZDB-GENE-040930-4 polr1d "polymerase (RNA) I polypeptide D" [Danio rerio (taxid:7955)]

 Score = 209 (78.6 bits), Expect = 5.3e-17, P = 5.3e-17
 Identities = 39/91 (42%), Positives = 58/91 (63%)

Query:     8 DQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTT-GDPAREV 66
             D+   TF L EEDHTL N++R+ + +   V FCGYSI HPS++++N R+QT  G PA E 
Sbjct:    19 DEGCVTFVLNEEDHTLGNSLRYMIMKSQDVEFCGYSITHPSESKINFRIQTRDGVPASEP 78

Query:    67 LKDSCQELMLMCRHVRSTFAKAVDDFRTSEK 97
             L++    L  +C+HV  TF   + +F+  E+
Sbjct:    79 LRNGLNNLTDVCKHVLQTFEARMKEFKEQEE 109

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

MGI|MGI:108403 Polr1d "polymerase (RNA) I polypeptide D" [Mus musculus (taxid:10090)]

 Score = 205 (77.2 bits), Expect = 1.4e-16, P = 1.4e-16
 Identities = 38/97 (39%), Positives = 60/97 (61%)

Query:     1 MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
             M   A  D+   TF L EEDHTL N +R+ + ++P V FCGY+  HPS++++N+R+QT G
Sbjct:    29 MVQAAGTDRQCVTFVLHEEDHTLGNCLRYIIMKNPEVEFCGYTTTHPSESKINLRIQTRG 88

Query:    61 D-PAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSE 96
               PA E  +    EL+ +C+HV   F  ++ D++  +
Sbjct:    89 ALPAVEPFQKGLNELLNVCQHVLVKFEASIKDYKAKK 125

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=IEA

GO:0005736 "DNA-directed RNA polymerase I complex" evidence=IDA

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

UNIPROTKB|E2RI73 POLR1D "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 204 (76.9 bits), Expect = 1.8e-16, P = 1.8e-16
 Identities = 38/94 (40%), Positives = 60/94 (63%)

Query:     1 MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
             M   A  D+   TF L EEDHTL N++R+ + ++P V FCGY+  HPS++++N+R+QT G
Sbjct:    29 MVQAAGTDRHCVTFVLHEEDHTLGNSLRYMIMKNPEVEFCGYTTTHPSESKINLRIQTRG 88

Query:    61 D-PAREVLKDSCQELMLMCRHVRSTFAKAVDDFR 93
               PA E  +    ELM +C+HV   F  ++ +++
Sbjct:    89 ALPAVEPFQRGLNELMNVCQHVLDKFEASIKEYK 122

GO:0005736 "DNA-directed RNA polymerase I complex" evidence=IEA

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

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

GO:0003677 "DNA binding" evidence=IEA

SGD|S000005057 RPC19 "RNA polymerase subunit AC19" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 202 (76.2 bits), Expect = 2.9e-16, P = 2.9e-16
 Identities = 38/83 (45%), Positives = 58/83 (69%)

Query:     8 DQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDP-AREV 66
             D ++A+F + EEDHTL NA+R+ + ++P V FCGYSIPHPS+  +NIR+QT G+  A + 
Sbjct:    57 DGTSASFQIVEEDHTLGNALRYVIMKNPDVEFCGYSIPHPSENLLNIRIQTYGETTAVDA 116

Query:    67 LKDSCQELMLMCRHVRSTFAKAV 89
             L+   ++LM +C  V S F + +
Sbjct:   117 LQKGLKDLMDLCDVVESKFTEKI 139

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

GO:0042797 "tRNA transcription from RNA polymerase III promoter" evidence=IDA

GO:0006360 "transcription from RNA polymerase I promoter" evidence=IC

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005736 "DNA-directed RNA polymerase I complex" evidence=IDA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|G3MYF3 G3MYF3 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 200 (75.5 bits), Expect = 4.7e-16, P = 4.7e-16
 Identities = 37/94 (39%), Positives = 60/94 (63%)

Query:     1 MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
             M   A  D+   TF L EEDHTL N++R+ + ++P V FCGY+  HPS++++N+R+QT G
Sbjct:    29 MVQAAGTDRHCVTFVLHEEDHTLGNSLRYMIMKNPEVEFCGYTTTHPSESKINLRIQTRG 88

Query:    61 D-PAREVLKDSCQELMLMCRHVRSTFAKAVDDFR 93
               PA E  +    +LM +C+HV   F  ++ +++
Sbjct:    89 ALPAVEPFQRGVTDLMNVCQHVLDKFEASIKEYK 122

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

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q1RMG8 POLR1D "DNA-directed RNA polymerases I and III subunit RPAC2" [Bos taurus (taxid:9913)]

 Score = 200 (75.5 bits), Expect = 4.7e-16, P = 4.7e-16
 Identities = 37/94 (39%), Positives = 60/94 (63%)

Query:     1 MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
             M   A  D+   TF L EEDHTL N++R+ + ++P V FCGY+  HPS++++N+R+QT G
Sbjct:    29 MVQAAGTDRHCVTFVLHEEDHTLGNSLRYMIMKNPEVEFCGYTTTHPSESKINLRIQTRG 88

Query:    61 D-PAREVLKDSCQELMLMCRHVRSTFAKAVDDFR 93
               PA E  +    +LM +C+HV   F  ++ +++
Sbjct:    89 ALPAVEPFQRGLTDLMNVCQHVLDKFEASIKEYK 122

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1RSW6 POLR1D "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 200 (75.5 bits), Expect = 4.7e-16, P = 4.7e-16
 Identities = 42/101 (41%), Positives = 60/101 (59%)

Query:     1 MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
             M   A  D+   TF L EEDHTL N++R+ + ++P V FCGY+  HPS++++N+R+QT G
Sbjct:    26 MVQAAGTDRHCVTFVLHEEDHTLGNSLRYMIMKNPEVEFCGYTTTHPSESKINLRIQTRG 85

Query:    61 D-PAREVLKDSCQELMLMCRHVRSTFA---KAVDDFRTSEK 97
               PA E  +    ELM +C+HV   F    KA  D +   K
Sbjct:    86 ALPAVEPFQRGLTELMNVCQHVLDKFEASIKAYKDHKAGRK 126

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

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|I3LRD0 POLR1D "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 200 (75.5 bits), Expect = 4.7e-16, P = 4.7e-16
 Identities = 42/101 (41%), Positives = 60/101 (59%)

Query:     1 MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60
             M   A  D+   TF L EEDHTL N++R+ + ++P V FCGY+  HPS++++N+R+QT G
Sbjct:    35 MVQAAGTDRHCVTFVLHEEDHTLGNSLRYMIMKNPEVEFCGYTTTHPSESKINLRIQTRG 94

Query:    61 D-PAREVLKDSCQELMLMCRHVRSTFA---KAVDDFRTSEK 97
               PA E  +    ELM +C+HV   F    KA  D +   K
Sbjct:    95 ALPAVEPFQRGLTELMNVCQHVLDKFEASIKAYKDHKAGRK 135

GO:0005736 "DNA-directed RNA polymerase I complex" evidence=IEA

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

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

GO:0003677 "DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q6DRI4	RPAC2_DANRE	No assigned EC number	0.4285	0.8411	0.8035	yes	no
Q9VIZ0	RPAC2_DROME	No assigned EC number	0.3689	0.8691	0.8857	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.7	LOW CONFIDENCE prediction!
4th Layer	2.7.7.6	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00024190001	SubName- Full=Chromosome chr6 scaffold_3, whole genome shotgun sequence; (105 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00020457001	SubName- Full=Chromosome chr5 scaffold_2, whole genome shotgun sequence; (208 aa)				•		•			0.925
	GSVIVG00028076001	SubName- Full=Chromosome chr7 scaffold_42, whole genome shotgun sequence; (533 aa)				•		•			0.911
	GSVIVG00002744001	SubName- Full=Chromosome chr1 scaffold_135, whole genome shotgun sequence; (78 aa)				•	•	•	•		0.910
	GSVIVG00002140001	SubName- Full=Chromosome chr19 scaffold_126, whole genome shotgun sequence; (528 aa)				•		•			0.907
	GSVIVG00038611001	RecName- Full=Pyruvate kinase; EC=2.7.1.40; (573 aa)						•			0.899
	GSVIVG00036953001	SubName- Full=Chromosome chr1 scaffold_84, whole genome shotgun sequence; (417 aa)						•			0.899
	GSVIVG00034786001	SubName- Full=Chromosome chr5 scaffold_72, whole genome shotgun sequence; (471 aa)						•			0.899
	GSVIVG00034055001	RecName- Full=Nucleoside diphosphate kinase; EC=2.7.4.6; (159 aa)						•			0.899
	26N20_30	RecName- Full=Pyruvate kinase; EC=2.7.1.40; (493 aa)						•			0.899
	GSVIVG00025495001	RecName- Full=Pyruvate kinase; EC=2.7.1.40; (475 aa)						•			0.899

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	107
cd07029	85	cd07029, RNAP_I_III_AC19, AC19 subunit of Eukaryot	3e-41
pfam13656	77	pfam13656, RNA_pol_L_2, RNA polymerase Rpb3/Rpb11	7e-30
cd07027	83	cd07027, RNAP_RPB11_like, RPB11 subunit of RNA pol	2e-21
COG1761	99	COG1761, RPB11, DNA-directed RNA polymerase, subun	5e-20
cd06926	93	cd06926, RNAP_II_RPB11, RPB11 subunit of Eukaryoti	2e-19
pfam01193	88	pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 di	1e-14
PRK01146	85	PRK01146, PRK01146, DNA-directed RNA polymerase su	6e-14
cd06927	83	cd06927, RNAP_L, L subunit of Archaeal RNA polymer	9e-14
cd00460	86	cd00460, RNAP_RPB11_RPB3, RPB11 and RPB3 subunits	2e-12

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

 Score =  130 bits (329), Expect = 3e-41
 Identities = 40/79 (50%), Positives = 57/79 (72%), Gaps = 1/79 (1%)

Query: 8  DQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREV 66
          D+S ATF    EDHTL N++R+ + ++P V FCGYSIPHPS+ ++N+R+QT G  PA +V
Sbjct: 7  DESCATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSIPHPSENKINLRIQTKGGEPAVDV 66

Query: 67 LKDSCQELMLMCRHVRSTF 85
          LK   ++L  +C H+ STF
Sbjct: 67 LKKGLEDLEQICDHILSTF 85

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

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

 Score =  101 bits (254), Expect = 7e-30
 Identities = 31/77 (40%), Positives = 49/77 (63%), Gaps = 1/77 (1%)

Query: 10 SNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLK 68
          + ATF +  EDHTL N +R  L +DP V F GYS+PHP + ++N+R+QT       +VLK
Sbjct: 1  NEATFEIEGEDHTLGNLLREELLKDPDVEFAGYSVPHPLEDKINLRIQTKSGKDPLDVLK 60

Query: 69 DSCQELMLMCRHVRSTF 85
          ++ ++L+ +C  +   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|132905 cd07027, RNAP_RPB11_like, RPB11 subunit of RNA polymerase

 Score = 80.2 bits (198), Expect = 2e-21
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 7  GDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PARE 65
           ++++ T  +  EDHTL N +R  L +D +V F  Y I HP   ++ IR+QT      ++
Sbjct: 6  KEKNSVTVEMENEDHTLGNLLREELLKDDQVDFARYYIKHPVIDKIQIRIQTKSGIKPKD 65

Query: 66 VLKDSCQELMLMCRHV 81
           LK +  +L  +  H+
Sbjct: 66 ALKRAVNKLSKLYEHL 81

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

 Score = 77.4 bits (191), Expect = 5e-20
 Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 1/81 (1%)

Query: 8  DQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDP-AREV 66
          D ++    +  EDHTL N +R  L +D  V F  YSIPHP      IR++T G    +E 
Sbjct: 13 DDNSLELEIEGEDHTLGNLLREELLKDEDVEFAAYSIPHPLIDNPKIRIKTKGGVDPKEA 72

Query: 67 LKDSCQELMLMCRHVRSTFAK 87
          LK + ++++     +   F +
Sbjct: 73 LKRAARKILKDLEELLDQFEE 93

Length = 99

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

 Score = 75.3 bits (186), Expect = 2e-19
 Identities = 29/75 (38%), Positives = 47/75 (62%), Gaps = 1/75 (1%)

Query: 12 ATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDPA-REVLKDS 70
          ATF++ +EDHTL N +R  L +DP V F GY +PHP + ++ +R+QT G    +E LK++
Sbjct: 19 ATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIELRIQTDGSITPKEALKNA 78

Query: 71 CQELMLMCRHVRSTF 85
            +L+     ++  F
Sbjct: 79 ITDLISELSLLKEEF 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|216354 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimerisation domain

 Score = 63.0 bits (154), Expect = 1e-14
 Identities = 26/88 (29%), Positives = 37/88 (42%), Gaps = 20/88 (22%)

Query: 12 ATFSLTEEDHTLANAVRFTLNQD-PRVTFCGYSIPHPS------------------DARV 52
            F L  EDHTL NA+R  L  D P V   G  IPHP+                    ++
Sbjct: 1  IEFLLEGEDHTLGNALRRVLLSDVPGVAIAGVKIPHPAKFSPVKKVNYRVVGVGTDYDKL 60

Query: 53 NIRVQTTGD-PAREVLKDSCQELMLMCR 79
           +R++T G     E LK++ + 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|234909 PRK01146, PRK01146, DNA-directed RNA polymerase subunit L; Provisional

 Score = 61.4 bits (150), Expect = 6e-14
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 14 FSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHP--SDARVNIRVQTTGDPAREVLKDSC 71
            +  EDHTL N ++  L +DP V    Y I HP  S+  + I+     DP  E LK++ 
Sbjct: 15 LEIEGEDHTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLKIKTDGGIDP-LEALKEAA 73

Query: 72 QELMLMCRHVRS 83
          + ++ +C     
Sbjct: 74 KRIIDLCDEFLD 85

Length = 85

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

 Score = 60.7 bits (148), Expect = 9e-14
 Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 19 EDHTLANAVRFTLNQDPRVTFCGYSIPHP--SDARVNIRVQTTGDPAREVLKDSCQELML 76
          EDHTL N ++  L +DP V    Y I HP  S+  + I+     DP  E LK++ + L+ 
Sbjct: 18 EDHTLLNLLKEELLRDPGVKVASYDIEHPLLSNPVLKIKTDGGVDP-LEALKEAAKRLID 76

Query: 77 MCRHVRS 83
          +C     
Sbjct: 77 LCEEFLD 83

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

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

 Score = 57.8 bits (140), Expect = 2e-12
 Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 8/82 (9%)

Query: 7  GDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSD------ARVNIRVQTTG 60
           +++   F L  EDHTL N++R  L + P V F  Y + HP         +  +R++T G
Sbjct: 6  KEKNYVDFVLENEDHTLGNSLRRILLKSP-VEFAAYYVEHPVKLQRTDEDKFILRIETVG 64

Query: 61 D-PAREVLKDSCQELMLMCRHV 81
            P  E L+ + + L     H+
Sbjct: 65 SIPPEEALRRAVEILRKKLEHL 86

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	107
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
KOG3438	105	consensus DNA-directed RNA polymerase, subunit L [	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
cd06926	93	RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA poly	100.0
COG1761	99	RPB11 DNA-directed RNA polymerase, subunit L [Tran	99.98
KOG4392	117	consensus RNA polymerase, subunit L [Transcription	99.97
cd00460	86	RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA pol	99.94
PF01193	66	RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation	99.69
PRK14979	195	DNA-directed RNA polymerase subunit D; Provisional	95.13
cd07028	212	RNAP_RPB3_like RPB3 subunit of RNA polymerase. The	95.02
smart00662	224	RPOLD RNA polymerases D. DNA-directed RNA polymera	94.39
cd06928	215	RNAP_alpha_NTD N-terminal domain of the Alpha subu	94.17
TIGR02027	297	rpoA DNA-directed RNA polymerase, alpha subunit, b	93.93
cd07031	265	RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polyme	93.53
PRK00783	263	DNA-directed RNA polymerase subunit D; Provisional	93.24
PRK05182	310	DNA-directed RNA polymerase subunit alpha; Provisi	92.7
cd07028	212	RNAP_RPB3_like RPB3 subunit of RNA polymerase. The	92.61
cd06928	215	RNAP_alpha_NTD N-terminal domain of the Alpha subu	92.31
CHL00013	327	rpoA RNA polymerase alpha subunit	92.22
cd07030	259	RNAP_D D subunit of Archaeal RNA polymerase. The D	91.87
PRK14979	195	DNA-directed RNA polymerase subunit D; Provisional	90.56
smart00662	224	RPOLD RNA polymerases D. DNA-directed RNA polymera	89.78
PRK05182	310	DNA-directed RNA polymerase subunit alpha; Provisi	89.18
PRK00783	263	DNA-directed RNA polymerase subunit D; Provisional	88.89
cd07031	265	RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polyme	85.51
cd07030	259	RNAP_D D subunit of Archaeal RNA polymerase. The D	84.75
COG0202	317	RpoA DNA-directed RNA polymerase, alpha subunit/40	84.18
cd07032	291	RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA poly	83.53
CHL00013	327	rpoA RNA polymerase alpha subunit	83.12

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

Probab=100.00  E-value=1.4e-36  Score=203.39  Aligned_cols=83  Identities=49%  Similarity=0.907  Sum_probs=80.3

Q ss_pred             CCCCCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHH
Q 033968            3 HGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHV   81 (107)
Q Consensus         3 ~~~~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l   81 (107)
                      .+.++++|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++ +|.+||++|+++|.+.|+++
T Consensus         2 ~~~~~~~n~~~~~i~~EdHTLgNlLr~~L~~~p~V~fagY~vpHPl~~~~~lriqT~~~~~p~~al~~a~~~l~~~~~~~   81 (85)
T cd07029           2 EGEGTDESCATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSIPHPSENKINLRIQTKGGEPAVDVLKKGLEDLEQICDHI   81 (85)
T ss_pred             CcccCCCCeEEEEEeCCCcchHHHHHHHHhhCCCceEEeecccCCCCCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999999999999999999999999999997 99999999999999999999


Q ss_pred             HHHH
Q 033968           82 RSTF   85 (107)
Q Consensus        82 ~~~f   85 (107)
                      ++.|
T Consensus        82 ~~~f   85 (85)
T cd07029          82 LSTF   85 (85)
T ss_pred             HhcC
Confidence            9876

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=1.8e-36  Score=199.29  Aligned_cols=76  Identities=39%  Similarity=0.824  Sum_probs=71.9

Q ss_pred             CeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHHH
Q 033968           10 SNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRSTF   85 (107)
Q Consensus        10 n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~f   85 (107)
                      |+++|+|.+|||||||+||++|+++|+|.||||+|||||+++++|||||+++ +|.+||++|+++|.++|++++++|
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            7899999999999999999999999999999999999999999999999999 999999999999999999999988

...

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

Probab=100.00  E-value=1.8e-35  Score=203.68  Aligned_cols=96  Identities=50%  Similarity=0.952  Sum_probs=91.8

Q ss_pred             CCCCCCCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHH
Q 033968            1 MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCR   79 (107)
Q Consensus         1 ~~~~~~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~   79 (107)
                      |.+++..+.++.+|++..|||||||+||++|+++|.|+||||.||||++++++|||||.++ +++++|++||++|.+.|+
T Consensus         7 m~~~~~~d~~~~Tf~~~eEDHTlgNalR~vI~k~peVefcGYtIPHPse~k~niRIQt~~~~~A~evl~kgl~el~~~c~   86 (105)
T KOG3438|consen    7 MSQASFTDLSSATFQLREEDHTLGNALRYVIMKNPEVEFCGYTIPHPSEDKINIRIQTRDGDPAVEVLKKGLEELMQLCD   86 (105)
T ss_pred             hccCcccCCCceEEEEEecCcchhHHHHHHHhcCCceEEEeccCCCCchhhheEEEEecCCCcchHHHHHHHHHHHHHHH
Confidence            5678888999999999999999999999999999999999999999999999999999977 999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhh
Q 033968           80 HVRSTFAKAVDDFRTSE   96 (107)
Q Consensus        80 ~l~~~f~~a~~~~~~~~   96 (107)
                      +++..|.+++++|+...
T Consensus        87 ~v~~kF~~~i~~~k~~~  103 (105)
T KOG3438|consen   87 HVRSKFEEEIEEYKDQK  103 (105)
T ss_pred             HHHHHHHHHHHHhhhhc
Confidence            99999999999998654

>PRK01146 DNA-directed RNA polymerase subunit L; Provisional

Probab=100.00  E-value=6e-35  Score=195.51  Aligned_cols=78  Identities=26%  Similarity=0.458  Sum_probs=74.9

Q ss_pred             CCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHH
Q 033968            6 FGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRS   83 (107)
Q Consensus         6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~   83 (107)
                      .+++|+++|+|.||||||||+||++|+++|+|.||||+|||||+++++|||||+++ +|.+||++|+++|.+.|++|++
T Consensus         7 ~~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqt~~~~~p~~al~~a~~~L~~~~~~~~~   85 (85)
T PRK01146          7 EKEDNELELEIEGEDHTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLKIKTDGGIDPLEALKEAAKRIIDLCDEFLD   85 (85)
T ss_pred             ecCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEeecCCCCCCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence            46789999999999999999999999999999999999999999999999999977 9999999999999999999863

>cd06927 RNAP_L L subunit of Archaeal RNA polymerase

Probab=100.00  E-value=6.4e-35  Score=194.63  Aligned_cols=78  Identities=27%  Similarity=0.474  Sum_probs=74.9

Q ss_pred             CCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHH
Q 033968            6 FGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRS   83 (107)
Q Consensus         6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~   83 (107)
                      .+++|+++|+|.||||||||+||++|+++|+|.||||+|||||+++++|||||+++ +|.+||++|+++|++.|+++++
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            46789999999999999999999999999999999999999999999999999997 9999999999999999999863

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

>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase

Probab=100.00  E-value=9.7e-35  Score=193.76  Aligned_cols=77  Identities=31%  Similarity=0.520  Sum_probs=74.4

Q ss_pred             CCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHH
Q 033968            6 FGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVR   82 (107)
Q Consensus         6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~   82 (107)
                      +.++|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++ +|.+||++|+++|.+.|++++
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            46789999999999999999999999999999999999999999999999999997 999999999999999999985

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/

>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II

Probab=100.00  E-value=1.5e-34  Score=196.26  Aligned_cols=81  Identities=36%  Similarity=0.683  Sum_probs=78.4

Q ss_pred             CCCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHH
Q 033968            5 AFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRS   83 (107)
Q Consensus         5 ~~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~   83 (107)
                      -++.+|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++ +|.+||++|+++|.+.|+++++
T Consensus        12 d~k~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~fagY~vpHPl~~~~~l~i~t~~~~~p~~al~~a~~~l~~~~~~~~~   91 (93)
T cd06926          12 DTKVPNAATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIELRIQTDGSITPKEALKNAITDLISELSLLKE   91 (93)
T ss_pred             cCCCCcEEEEEEeCCCchHHHHHHHHHhcCCCeeEEeeccCCCCCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            368899999999999999999999999999999999999999999999999999997 9999999999999999999998


Q ss_pred             HH
Q 033968           84 TF   85 (107)
Q Consensus        84 ~f   85 (107)
                      .|
T Consensus        92 ~f   93 (93)
T cd06926          92 EF   93 (93)
T ss_pred             hC
Confidence            76

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.

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

Probab=99.98  E-value=7.1e-32  Score=185.53  Aligned_cols=86  Identities=30%  Similarity=0.490  Sum_probs=82.6

Q ss_pred             CCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHH
Q 033968            6 FGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRST   84 (107)
Q Consensus         6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~   84 (107)
                      .+++|+++|+|.||||||||+||++|++||+|.||||+||||+.++++|||||+++ +|.+||++|++.+.+.|++|.++
T Consensus        11 ~~~~n~~~i~i~gEdHTL~NlL~~~L~~d~~V~~a~Y~i~HP~~~~~~i~Ikt~~~~dp~~aL~~A~~~i~~~~~~l~~~   90 (99)
T COG1761          11 KKDDNSLELEIEGEDHTLGNLLREELLKDEDVEFAAYSIPHPLIDNPKIRIKTKGGVDPKEALKRAARKILKDLEELLDQ   90 (99)
T ss_pred             ccCCCEEEEEEecCCchHHHHHHHHHhCCCCeeEEEEeCCCCCCCCceEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            36799999999999999999999999999999999999999999999999999999 99999999999999999999999


Q ss_pred             HHHHHHHH
Q 033968           85 FAKAVDDF   92 (107)
Q Consensus        85 f~~a~~~~   92 (107)
                      | ++++++
T Consensus        91 ~-~~~e~~   97 (99)
T COG1761          91 F-EEFEKK   97 (99)
T ss_pred             H-HHHHhh
Confidence            9 887765

>KOG4392 consensus RNA polymerase, subunit L [Transcription]

Probab=99.97  E-value=3.5e-30  Score=180.17  Aligned_cols=86  Identities=33%  Similarity=0.555  Sum_probs=84.1

Q ss_pred             CCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHH
Q 033968            6 FGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRST   84 (107)
Q Consensus         6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~   84 (107)
                      ++.+|++.|+|++|||||||+||.+|++||+|.||||++|||++.++.|||||..+ +|.++|.+|+.+|...++.++.+
T Consensus        25 tKvpNA~~fTiekEDHTLGNii~~qLl~D~~vLFagYkvpHPl~~~~~LRiqtt~d~~p~~al~~a~~~l~~el~~l~~~  104 (117)
T KOG4392|consen   25 TKVPNAALFTIEKEDHTLGNIIKSQLLKDPRVLFAGYKVPHPLEHKIILRVQTTEDCSPADALTNAITDLIEELSLLENR  104 (117)
T ss_pred             CCCCceEEEEEecccchHHHHHHHHHccCccceEeeecCCCcccccEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999999999999999999999999999999988 99999999999999999999999


Q ss_pred             HHHHHHH
Q 033968           85 FAKAVDD   91 (107)
Q Consensus        85 f~~a~~~   91 (107)
                      |..+++.
T Consensus       105 f~~~~~~  111 (117)
T KOG4392|consen  105 FKAEAAL  111 (117)
T ss_pred             HHHHHhc
Confidence            9999987

>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase

Probab=99.94  E-value=3.7e-26  Score=152.33  Aligned_cols=75  Identities=31%  Similarity=0.539  Sum_probs=71.6

Q ss_pred             CCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCC------CCceeEEEEeCCC-CHHHHHHHHHHHHHHHH
Q 033968            6 FGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPS------DARVNIRVQTTGD-PAREVLKDSCQELMLMC   78 (107)
Q Consensus         6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPl------e~~i~lrIqT~~~-~p~eal~~Al~~L~~~~   78 (107)
                      .+++|+++|+|.||||||||+||++|++ |.|.||||+||||+      .+++.|+|+|+|+ +|.+||++|++.|.+.|
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            4678999999999999999999999999 99999999999999      9999999999998 99999999999999998


Q ss_pred             HHH
Q 033968           79 RHV   81 (107)
Q Consensus        79 ~~l   81 (107)
                      +.|
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=99.69  E-value=3.3e-17  Score=103.96  Aligned_cols=64  Identities=34%  Similarity=0.517  Sum_probs=60.2

Q ss_pred             eEEEEecCCcchHHHHHHHHhcC-CCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHH
Q 033968           12 ATFSLTEEDHTLANAVRFTLNQD-PRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCR   79 (107)
Q Consensus        12 ~~~~i~~EDHTLgNlLr~~L~~~-~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~   79 (107)
                      ++|.+.|+|||+||+||..|+++ |.|.+++    ||..+++.|+|+|+|+ +|.++|.+|++.|.+.|+
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    9999999999999999 999999999999998773

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

>PRK14979 DNA-directed RNA polymerase subunit D; Provisional

Probab=95.13  E-value=0.097  Score=39.89  Aligned_cols=39  Identities=15%  Similarity=0.296  Sum_probs=35.1

Q ss_pred             CCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968           49 DARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRSTFAK   87 (107)
Q Consensus        49 e~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~f~~   87 (107)
                      .++..|.|.|+|. +|.+||..|++-|.+.++.|.+.++.
T Consensus       149 ~dkl~leIeTdGsi~P~~al~~Aa~iL~~~l~~~~~~l~~  188 (195)
T PRK14979        149 NDEVEFKVESFGQMDAEDILRSALEILKNKAEKFLQELEG  188 (195)
T ss_pred             CcEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4899999999999 99999999999999999998776653

>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase

Probab=95.02  E-value=0.066  Score=41.05  Aligned_cols=47  Identities=15%  Similarity=0.251  Sum_probs=40.3

Q ss_pred             CeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHH
Q 033968           36 RVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRS   83 (107)
Q Consensus        36 ~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~   83 (107)
                      =|.-|.|++. |-.++..|.|.|+|. +|.+||.+|++-|++.++.|.+
T Consensus       164 PV~~v~y~~~-~~~d~li~~VeT~Gsi~p~~~l~~A~~iL~~~~~~~~~  211 (212)
T cd07028         164 PVAAIEFRYD-PVADTYIMNVESVGSLPPDQVVVEAIKTLQKKVASILL  211 (212)
T ss_pred             CceEEEEEEE-ccCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHhh
Confidence            3566778854 466899999999999 9999999999999999998875

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

>smart00662 RPOLD RNA polymerases D

Probab=94.39  E-value=0.089  Score=40.28  Aligned_cols=32  Identities=16%  Similarity=0.185  Sum_probs=29.1

Q ss_pred             CCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHH
Q 033968           49 DARVNIRVQTTGD-PAREVLKDSCQELMLMCRH   80 (107)
Q Consensus        49 e~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~   80 (107)
                      .+++.|.|.|+|. +|.+||.+|++-|.+.++.
T Consensus       191 ~d~l~f~IeT~G~i~p~~al~~A~~iL~~k~~~  223 (224)
T smart00662      191 YDKLIFDVETNGSLKPEEAVLEAAKILKEKLEA  223 (224)
T ss_pred             CCEEEEEEEecCCcCHHHHHHHHHHHHHHHHhh
Confidence            5789999999999 9999999999999987764

DNA-directed RNA polymerase subunit D and bacterial alpha chain

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

Probab=94.17  E-value=0.094  Score=40.06  Aligned_cols=43  Identities=19%  Similarity=0.287  Sum_probs=35.0

Q ss_pred             eeeeeecCCC------CCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHH
Q 033968           37 VTFCGYSIPH------PSDARVNIRVQTTGD-PAREVLKDSCQELMLMCR   79 (107)
Q Consensus        37 V~fAgY~vpH------Ple~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~   79 (107)
                      |.-+.|.|.-      .-..++.|.|.|+|. +|.+||..|++.|.+.+.
T Consensus       164 V~~vny~v~~~~~~~~~~~e~L~leI~TnGsi~P~~Al~~A~~il~~~~~  213 (215)
T cd06928         164 VRKVNYSVESTRVGQRTDYEKLILEIWTNGSISPEEALAQAAKILINHFS  213 (215)
T ss_pred             eEEEEEEEEEeecCCCCCceeEEEEEEECCCCCHHHHHHHHHHHHHHHhh
Confidence            5666777543      234678999999999 999999999999988775

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

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

Probab=93.93  E-value=0.17  Score=40.50  Aligned_cols=47  Identities=11%  Similarity=0.277  Sum_probs=38.4

Q ss_pred             eeeeeecCCC------CCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHH
Q 033968           37 VTFCGYSIPH------PSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRS   83 (107)
Q Consensus        37 V~fAgY~vpH------Ple~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~   83 (107)
                      |.-+.|.|..      ...+++.|.|.|+|. +|.+||.+|++-|.+.+..|.+
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            5556676653      234689999999999 9999999999999999998865

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.

>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II

Probab=93.53  E-value=0.14  Score=40.40  Aligned_cols=52  Identities=13%  Similarity=0.209  Sum_probs=42.9

Q ss_pred             CeeeeeecCCCCC-----------CCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968           36 RVTFCGYSIPHPS-----------DARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRSTFAK   87 (107)
Q Consensus        36 ~V~fAgY~vpHPl-----------e~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~f~~   87 (107)
                      ...||...+.||-           .+++.|.|.|.|. +|.++|.+|++-|.+.++.|.+.++.
T Consensus       201 ~c~~c~~c~~~~~~~~~~v~i~~~~~~fiF~VES~Gsl~p~~Iv~~Al~iL~~K~~~l~~~l~~  264 (265)
T cd07031         201 WPKSENACIEEPPEKDALFDIDAKPDKFYFNVESTGALPPEQIVLSGLEILKKKLADLQLQLSE  264 (265)
T ss_pred             cCchhHHHhhcccccCCceEEEeeCCEEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4556666666652           5778999999999 99999999999999999999988754

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.

>PRK00783 DNA-directed RNA polymerase subunit D; Provisional

Probab=93.24  E-value=0.087  Score=40.91  Aligned_cols=28  Identities=29%  Similarity=0.345  Sum_probs=23.8

Q ss_pred             CCCCeeEEEEecCCcchHHHHHHHHhcC
Q 033968            7 GDQSNATFSLTEEDHTLANAVRFTLNQD   34 (107)
Q Consensus         7 ~~~n~~~~~i~~EDHTLgNlLr~~L~~~   34 (107)
                      .+++.++|.+.|-++||||+||-.|+..
T Consensus         8 ~~~~~~~f~~~g~~~t~~NalRRvlls~   35 (263)
T PRK00783          8 LDDRSARFVVEGVTPAFANAIRRAMIAD   35 (263)
T ss_pred             cCCcEEEEEEeCCCHHHHHHHHHHHHHc
Confidence            3567889999999999999999888875

>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional

Probab=92.70  E-value=0.32  Score=39.25  Aligned_cols=47  Identities=17%  Similarity=0.229  Sum_probs=38.5

Q ss_pred             eeeeeecCCCC------CCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHH
Q 033968           37 VTFCGYSIPHP------SDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRS   83 (107)
Q Consensus        37 V~fAgY~vpHP------le~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~   83 (107)
                      |.-+.|.|.-.      -..++.|.|.|+|. +|.+||.+|+..|...+..|.+
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            55667766542      13579999999999 9999999999999999988765

>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase

Probab=92.61  E-value=0.14  Score=39.31  Aligned_cols=31  Identities=32%  Similarity=0.465  Sum_probs=26.9

Q ss_pred             CCCCCeeEEEEecCCcchHHHHHHHHhcC-CC
Q 033968            6 FGDQSNATFSLTEEDHTLANAVRFTLNQD-PR   36 (107)
Q Consensus         6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~   36 (107)
                      ..+++.+.|.+.|-|+|+||+||-.|+.. |.
T Consensus         7 ~~~~~~~~f~l~g~~~t~aNaLRRiLLsevP~   38 (212)
T cd07028           7 EADKDNVDFILSGVDLAMANALRRVMIAEVPT   38 (212)
T ss_pred             EcCCCEEEEEEEccChhHHHHHHHHHHHcCcc
Confidence            35788999999999999999999888875 54

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

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

Probab=92.31  E-value=0.21  Score=38.16  Aligned_cols=39  Identities=23%  Similarity=0.330  Sum_probs=30.3

Q ss_pred             CCCCeeEEEE----ecCCcchHHHHHHHHhcC-CCeeeeeecCC
Q 033968            7 GDQSNATFSL----TEEDHTLANAVRFTLNQD-PRVTFCGYSIP   45 (107)
Q Consensus         7 ~~~n~~~~~i----~~EDHTLgNlLr~~L~~~-~~V~fAgY~vp   45 (107)
                      .+++.+.|.|    .|.++|+||+||-.|+.. |+.-+-+-+|.
T Consensus         6 ~~~~~~~F~i~pl~~g~~~tlgNaLRRvLLs~ipg~aI~~v~I~   49 (215)
T cd06928           6 KRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIE   49 (215)
T ss_pred             CCCcEEEEEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEEEEEc
Confidence            4568899999    779999999999888875 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

>CHL00013 rpoA RNA polymerase alpha subunit

Probab=92.22  E-value=0.35  Score=39.46  Aligned_cols=47  Identities=19%  Similarity=0.268  Sum_probs=39.0

Q ss_pred             eeeeeecCCCC-----CCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHH
Q 033968           37 VTFCGYSIPHP-----SDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRS   83 (107)
Q Consensus        37 V~fAgY~vpHP-----le~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~   83 (107)
                      |.-+.|.|..-     ...++.|-|.|+|. +|.+||..|++.|...+..+.+
T Consensus       171 V~kVny~Ve~~~~~~~~~e~L~lEI~TnGsi~P~~Al~~Aa~il~~~~~~~~~  223 (327)
T CHL00013        171 VRNVNYSIHSYGNGNEKQEILFLEIWTNGSITPKEALHEASRNLIDLFIPFLH  223 (327)
T ss_pred             eeEEEEEEEEcccCCcccceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            66677777641     25689999999999 9999999999999999988754

>cd07030 RNAP_D D subunit of Archaeal RNA polymerase

Probab=91.87  E-value=0.17  Score=39.15  Aligned_cols=28  Identities=29%  Similarity=0.345  Sum_probs=24.7

Q ss_pred             CCCCeeEEEEecCCcchHHHHHHHHhcC
Q 033968            7 GDQSNATFSLTEEDHTLANAVRFTLNQD   34 (107)
Q Consensus         7 ~~~n~~~~~i~~EDHTLgNlLr~~L~~~   34 (107)
                      .+++.+.|.+.|-++|+||+||-.|+..
T Consensus         8 ~~~~~~~f~~~g~~~s~~NalRRills~   35 (259)
T cd07030           8 LDDDRARFVLEGVPPAFANAIRRAIISE   35 (259)
T ss_pred             cCCCEEEEEEeCCCHHHHHHHHHHHHhc
Confidence            4568899999999999999999888875

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

>PRK14979 DNA-directed RNA polymerase subunit D; Provisional

Probab=90.56  E-value=0.32  Score=37.11  Aligned_cols=36  Identities=17%  Similarity=0.184  Sum_probs=29.5

Q ss_pred             CCCCCCeeEEEEecCCcchHHHHHHHHhcC-CCeeeee
Q 033968            5 AFGDQSNATFSLTEEDHTLANAVRFTLNQD-PRVTFCG   41 (107)
Q Consensus         5 ~~~~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~V~fAg   41 (107)
                      ++++++.++|.+. -+.|+||+||-.|+.. |+.-.-+
T Consensus         9 ~~~~~~~~~f~l~-~~~tlgNaLRRvLLssipg~AI~~   45 (195)
T PRK14979          9 KTRIGEEFKFSLK-APISFSSALRRIMISEVPTYAIEN   45 (195)
T ss_pred             eccCCcEEEEEEE-cCccHHHHHHHHHHhcCcceeEEE
Confidence            5788999999999 9999999999888875 6544433

>smart00662 RPOLD RNA polymerases D

Probab=89.78  E-value=0.45  Score=36.42  Aligned_cols=33  Identities=36%  Similarity=0.387  Sum_probs=25.9

Q ss_pred             eEEEEecCCcchHHHHHHHHhcC-CCeeeeeecC
Q 033968           12 ATFSLTEEDHTLANAVRFTLNQD-PRVTFCGYSI   44 (107)
Q Consensus        12 ~~~~i~~EDHTLgNlLr~~L~~~-~~V~fAgY~v   44 (107)
                      +.|.+.+-++|+||+||-.|+.. |..-.-+.+|
T Consensus         2 ~~f~l~~~~~t~~NaLRRilLs~vp~~aI~~V~I   35 (224)
T smart00662        2 AKFVLEPYGLTLANALRRVLLSSVPGMAVTEVEI   35 (224)
T ss_pred             eEEEEEcCCchHHHHHHHHHHHcCccceEEEEEE
Confidence            67999999999999999888874 6655544443

DNA-directed RNA polymerase subunit D and bacterial alpha chain

>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional

Probab=89.18  E-value=0.59  Score=37.71  Aligned_cols=38  Identities=29%  Similarity=0.339  Sum_probs=30.7

Q ss_pred             CCCeeEEEEe----cCCcchHHHHHHHHhcC-CCeeeeeecCC
Q 033968            8 DQSNATFSLT----EEDHTLANAVRFTLNQD-PRVTFCGYSIP   45 (107)
Q Consensus         8 ~~n~~~~~i~----~EDHTLgNlLr~~L~~~-~~V~fAgY~vp   45 (107)
                      +++.+.|.|.    |.++|+||+||-.|+.. |+.-.-+-+|.
T Consensus        17 ~~~~~~F~i~Ple~G~g~tlgNaLRRvLLs~ipg~aI~~VkI~   59 (310)
T PRK05182         17 DDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKID   59 (310)
T ss_pred             CCcEEEEEEeccCCCchhHHHHHHHHHHHhcCCeeEEEEEEEc
Confidence            4688999996    99999999999888874 76666666653

>PRK00783 DNA-directed RNA polymerase subunit D; Provisional

Probab=88.89  E-value=1.2  Score=34.62  Aligned_cols=40  Identities=15%  Similarity=0.320  Sum_probs=36.0

Q ss_pred             CCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968           48 SDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRSTFAK   87 (107)
Q Consensus        48 le~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~f~~   87 (107)
                      ..++..+.|.|.|. +|.++++.|++-|++.++.|.+..+.
T Consensus       221 ~~~~~if~vEs~G~l~p~~iv~~A~~~l~~k~~~~~~~~~~  261 (263)
T PRK00783        221 DENKFIFTVESDGSLPVEEILLEALKILKRKADELIEALEE  261 (263)
T ss_pred             cCCeEEEEeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            46678889999999 99999999999999999999988765

>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II

Probab=85.51  E-value=0.9  Score=35.81  Aligned_cols=32  Identities=22%  Similarity=0.386  Sum_probs=26.5

Q ss_pred             CCCCeeEEEEecCCcchHHHHHHHHhcC-CCee
Q 033968            7 GDQSNATFSLTEEDHTLANAVRFTLNQD-PRVT   38 (107)
Q Consensus         7 ~~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~V~   38 (107)
                      .+++.++|.+.+=|+|+||+||-.|+.. |..-
T Consensus         8 ~~~~~~~F~l~~~~~s~aNALRRillsevPt~A   40 (265)
T cd07031           8 LTDDKVKFILENTDLSVANSLRRVMIAEVPTLA   40 (265)
T ss_pred             cCCCEEEEEEEcCcHHHHHHHHHHHHHcCccce
Confidence            4568899999999999999999888774 5433

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

>cd07030 RNAP_D D subunit of Archaeal RNA polymerase

Probab=84.75  E-value=2.3  Score=32.86  Aligned_cols=36  Identities=19%  Similarity=0.362  Sum_probs=31.9

Q ss_pred             CCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHH
Q 033968           49 DARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRST   84 (107)
Q Consensus        49 e~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~   84 (107)
                      .+...+.|.|.|. +|.++|++|+.-|.+.++.|.++
T Consensus       222 ~~~~if~vEs~Gsl~p~~il~~A~~~l~~k~~~~~~~  258 (259)
T cd07030         222 EDRFIFEVESDGSLPPKEILLEALRILKEKADELIEA  258 (259)
T ss_pred             CCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            4567788999999 99999999999999999998765

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

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

Probab=84.18  E-value=0.96  Score=36.74  Aligned_cols=29  Identities=24%  Similarity=0.055  Sum_probs=24.6

Q ss_pred             CCCeeEEEEecCCcchHHHHHHHHhcC-CC
Q 033968            8 DQSNATFSLTEEDHTLANAVRFTLNQD-PR   36 (107)
Q Consensus         8 ~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~   36 (107)
                      ..-.++|.+.|-+|||||+||-.|+.. |+
T Consensus        17 ~~~~ieplerG~g~tlgNALRRvLLSsiPg   46 (317)
T COG0202          17 AKFVIEPLERGFGVTLGNALRRVLLSSIPG   46 (317)
T ss_pred             ccEEEEEeeeCCcchhHHHHHHHHHHcCcc
Confidence            466789999999999999999888874 54

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

Probab=83.53  E-value=2.9  Score=33.65  Aligned_cols=37  Identities=16%  Similarity=0.319  Sum_probs=33.1

Q ss_pred             CCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHH
Q 033968           47 PSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRS   83 (107)
Q Consensus        47 Ple~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~   83 (107)
                      +-.+.+.+.|.+.|. +|.+.+.+|++-|.+.|+.+.+
T Consensus       253 ~~~d~fiF~VES~G~l~p~~i~~~Ai~iL~~K~~~l~~  290 (291)
T cd07032         253 RVRDHFIFSIESTGALPPDVLFLEAIKILKEKCRKLLE  290 (291)
T ss_pred             EeCCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHhh
Confidence            346678999999999 9999999999999999998875

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

>CHL00013 rpoA RNA polymerase alpha subunit

Probab=83.12  E-value=1  Score=36.80  Aligned_cols=40  Identities=18%  Similarity=0.129  Sum_probs=30.3

Q ss_pred             CCCCeeEEEEe----cCCcchHHHHHHHHhcC-CCeeeeeecCCC
Q 033968            7 GDQSNATFSLT----EEDHTLANAVRFTLNQD-PRVTFCGYSIPH   46 (107)
Q Consensus         7 ~~~n~~~~~i~----~EDHTLgNlLr~~L~~~-~~V~fAgY~vpH   46 (107)
                      ..++.+.|.|.    |..|||||+||-.|+.. |+.-+.+-+|.+
T Consensus        17 ~~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~g   61 (327)
T CHL00013         17 KRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEG   61 (327)
T ss_pred             CCCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECC
Confidence            34566777775    57789999999888875 877777776654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	107
3h0g_K	123	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		2e-09
1i3q_K	120	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		2e-08
2waq_L	92	The Complete Structure Of The Archaeal 13-Subunit D		5e-05
2pa8_L	92	X-Ray Crystal Structure Of The DL SUBCOMPLEX OF THE		6e-04

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 12  ATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDS 70
           A  +L +EDHTLAN +   L  D RV F GY +PHP +    +RVQT  D   ++V+ D+
Sbjct: 30  AVVTLEKEDHTLANMLANQLLSDERVLFAGYKVPHPLNHNFILRVQTVEDCSPKQVIVDA 89
Query: 71  CQELMLMCRHVRSTFAK 87
            + L+     ++  F +
Sbjct: 90  AKSLITHLEEIKVNFMR 106

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 15  SLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTT-GDPAREVLKDSCQE 73
           +  +EDHTL N +R  L  D +V F  Y + HP  AR  +R+QTT G   ++ LK++C  
Sbjct: 34  TFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDPKDALKNACNS 93
Query: 74  LMLMCRHVRSTF 85
           ++     +++ F
Sbjct: 94  IINKLGALKTNF 105

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 2/82 (2%)
Query: 1  MEHGAFGDQSNAT-FSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTT 59
          ME      +SN     +  EDHTL N +  TL +   V+F  Y  PHP   ++ +++ T 
Sbjct: 1  MEIKILKSESNYLELEIEGEDHTLGNLIAGTLRKISGVSFASYYQPHPLTDKIIVKILTD 60
Query: 60 GDPA-REVLKDSCQELMLMCRH 80
          G  A ++ L  + + + +M  H
Sbjct: 61 GSIAPKDALLKAIETVRVMASH 82

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

Iteration: 1
 Score = 38.9 bits (89), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 19 EDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD--PAREVLK 68
          EDHTL N +  TL +   V+F  Y  PHP   ++ +++ T G   P   +LK
Sbjct: 20 EDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVKILTDGSITPKDALLK 71

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	107
1xpp_A	115	TA1416, DNA-directed RNA polymerase subunit L; str	9e-32
3h0g_K	123	DNA-directed RNA polymerase II subunit RPB11; tran	3e-29
2pa8_L	92	DNA-directed RNA polymerase subunit L; ferredoxin-	2e-27
1twf_K	120	B13.6, DNA-directed RNA polymerase II 13.6 kDa pol	3e-27

>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 =  106 bits (267), Expect = 9e-32
 Identities = 17/95 (17%), Positives = 42/95 (44%)

Query: 8   DQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDPAREVL 67
           ++++ T  +   D+TL   +   + +D +V    Y I HP      I V+      +  +
Sbjct: 19  EKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSGKPQSAI 78

Query: 68  KDSCQELMLMCRHVRSTFAKAVDDFRTSEKVQAMK 102
           K + ++L  +   + + F K    + +   ++A++
Sbjct: 79  KRAVRKLSKLYEDLGTQFQKEFQRYESDHMIKAVE 113

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

 Score =  100 bits (251), Expect = 3e-29
 Identities = 30/97 (30%), Positives = 49/97 (50%), Gaps = 1/97 (1%)

Query: 8   DQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREV 66
             + A  +L +EDHTLAN +   L  D RV F GY +PHP +    +RVQT  D   ++V
Sbjct: 26  SPNAAVVTLEKEDHTLANMLANQLLSDERVLFAGYKVPHPLNHNFILRVQTVEDCSPKQV 85

Query: 67  LKDSCQELMLMCRHVRSTFAKAVDDFRTSEKVQAMKI 103
           + D+ + L+     ++  F +  +    S +   M+ 
Sbjct: 86  IVDAAKSLITHLEEIKVNFMREWELKMISVEGVEMEF 122

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

 Score = 95.3 bits (237), Expect = 2e-27
 Identities = 19/84 (22%), Positives = 35/84 (41%), Gaps = 1/84 (1%)

Query: 7  GDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PARE 65
           + +     +  EDHTL N +  TL +   V+F  Y  PHP   ++ +++ T G    ++
Sbjct: 8  SESNYLELEIEGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVKILTDGSITPKD 67

Query: 66 VLKDSCQELMLMCRHVRSTFAKAV 89
           L  + + +  M  H         
Sbjct: 68 ALLKAIENIRGMTSHYIDEIKGLT 91

>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 = 95.4 bits (237), Expect = 3e-27
 Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 1/89 (1%)

Query: 8   DQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREV 66
             +    +  +EDHTL N +R  L  D +V F  Y + HP  AR  +R+QTT     ++ 
Sbjct: 27  APNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDPKDA 86

Query: 67  LKDSCQELMLMCRHVRSTFAKAVDDFRTS 95
           LK++C  ++     +++ F    +    +
Sbjct: 87  LKNACNSIINKLGALKTNFETEWNLQTLA 115

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	107
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
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_D	265	DNA-directed RNA polymerase subunit D; ferredoxin-	93.83
1twf_C	318	B44.5, DNA-directed RNA polymerase II 45 kDa polyp	93.57
2pa8_D	265	DNA-directed RNA polymerase subunit D; ferredoxin-	90.81
1twf_C	318	B44.5, DNA-directed RNA polymerase II 45 kDa polyp	90.57
1bdf_A	235	RNA polymerase alpha subunit; nucleotidyltransfera	90.52
2a6h_A	315	DNA-directed RNA polymerase alpha chain; RNA polym	90.2
2a6h_A	315	DNA-directed RNA polymerase alpha chain; RNA polym	90.04
1bdf_A	235	RNA polymerase alpha subunit; nucleotidyltransfera	90.02
3h0g_C	297	DNA-directed RNA polymerase II subunit RPB3; trans	89.29
3lu0_A	329	DNA-directed RNA polymerase subunit alpha; E. coli	89.08
3h0g_C	297	DNA-directed RNA polymerase II subunit RPB3; trans	88.53
3lu0_A	329	DNA-directed RNA polymerase subunit alpha; E. coli	87.69

>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=2.2e-38  Score=213.63  Aligned_cols=84  Identities=23%  Similarity=0.396  Sum_probs=81.3

Q ss_pred             CCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHHH
Q 033968            7 GDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRSTF   85 (107)
Q Consensus         7 ~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~f   85 (107)
                      +++|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++ +|.+||++|+++|.+.|++++++|
T Consensus         8 k~~n~~~f~i~~EDHTLgN~Lr~~L~~~p~V~fagY~vpHPl~~~~~lrIqT~~~~~p~~al~~a~~~l~~~~~~~~~~f   87 (92)
T 2pa8_L            8 SESNYLELEIEGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVKILTDGSITPKDALLKAIENIRGMTSHYIDEI   87 (92)
T ss_dssp             EETTEEEEEEETCCHHHHHHHHHHHHTSTTEEEEEEECSSTTSCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCeEEEEEecCchhHHHHHHHHHhcCCCeeEEEeecCCCCCCceEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999999988 999999999999999999999999


Q ss_pred             HHHHH
Q 033968           86 AKAVD   90 (107)
Q Consensus        86 ~~a~~   90 (107)
                      ++|++
T Consensus        88 ~~~~k   92 (92)
T 2pa8_L           88 KGLTK   92 (92)
T ss_dssp             HHHHC
T ss_pred             HHHhC
Confidence            99863

>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=8.1e-38  Score=218.76  Aligned_cols=90  Identities=18%  Similarity=0.302  Sum_probs=86.7

Q ss_pred             CCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968            7 GDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDPAREVLKDSCQELMLMCRHVRSTFA   86 (107)
Q Consensus         7 ~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~~p~eal~~Al~~L~~~~~~l~~~f~   86 (107)
                      +++|+++|+|.+|||||||+||++|++||+|.||||+|||||+++++|||||+|+.|.+||++|+++|.+.|++|++.|+
T Consensus        18 k~~n~~~f~i~~EDHTLgNlLr~~Llkdp~V~fAgY~vpHPle~~~~lrIqT~~~~p~eaL~~al~~L~~~~~~l~~~f~   97 (115)
T 1xpp_A           18 KEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSGKPQSAIKRAVRKLSKLYEDLGTQFQ   97 (115)
T ss_dssp             ECSSEEEEEEESCCHHHHHHHHHHHTTCTTEEEEEEECSSTTTSCCEEEEEESSSCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEeCCCchhHHHHHHHHhcCCCeEEEEeecCCCCCCccEEEEEeCCCChHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57999999999999999999999999999999999999999999999999999888999999999999999999999999


Q ss_pred             HHHHHHHhhh
Q 033968           87 KAVDDFRTSE   96 (107)
Q Consensus        87 ~a~~~~~~~~   96 (107)
                      +|+++|+.++
T Consensus        98 ~a~~~~~~~~  107 (115)
T 1xpp_A           98 KEFQRYESDH  107 (115)
T ss_dssp             HHHHHHHHHC
T ss_pred             HHHHHhchhh
Confidence            9999997653

>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=6.5e-38  Score=221.40  Aligned_cols=97  Identities=31%  Similarity=0.460  Sum_probs=90.6

Q ss_pred             CCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHH
Q 033968            6 FGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRST   84 (107)
Q Consensus         6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~   84 (107)
                      ++.+|+++|+|.+|||||||+||++|+++|+|.||||+||||++++++|||||+|+ +|.+||++||++|++.|++|++.
T Consensus        24 tk~~n~~~f~i~~EDHTLgNlLr~~Llk~p~V~fAgY~vpHPle~~~~lrIqT~~~~~p~eaL~~al~~L~~~~~~l~~~  103 (123)
T 3h0g_K           24 SKSPNAAVVTLEKEDHTLANMLANQLLSDERVLFAGYKVPHPLNHNFILRVQTVEDCSPKQVIVDAAKSLITHLEEIKVN  103 (123)
T ss_dssp             SSSTTEEEEEEESCCSSHHHHHHHTGGGSTTCSCBCCBCSCTTSCEEEEEEECCSSSCSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCceEEEEEeCCCcchHHHHHHHHhcCCCeeEeeecCCCCCCCceEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            67899999999999999999999999999999999999999999999999999988 99999999999999999999999


Q ss_pred             HHHHHHHHHhhhhhhhcc
Q 033968           85 FAKAVDDFRTSEKVQAMK  102 (107)
Q Consensus        85 f~~a~~~~~~~~~~~~~~  102 (107)
                      |.++++.++...+...|+
T Consensus       104 F~~~~~~~~~~~~~~~~~  121 (123)
T 3h0g_K          104 FMREWELKMISVEGVEME  121 (123)
T ss_dssp             HHHHTTTTTSSSCCCC--
T ss_pred             HHHHHHhccccccceeec
Confidence            999999988776654554

>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=3.4e-37  Score=216.77  Aligned_cols=89  Identities=27%  Similarity=0.511  Sum_probs=83.6

Q ss_pred             CCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHH
Q 033968            6 FGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRST   84 (107)
Q Consensus         6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~   84 (107)
                      ++++|+++|+|.||||||||+||++|+++|+|.||||+|||||+++++|||||+|+ +|.+||++||++|++.|++++++
T Consensus        25 ~k~~n~~~f~i~~EDHTLgNlLr~~Llk~p~V~fAgY~vpHPl~~~~~lrIqT~~~~~p~eaL~~a~~~L~~~~~~l~~~  104 (120)
T 1twf_K           25 TKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTN  104 (120)
T ss_dssp             SSSTTEEEEEEESCCHHHHHHHHHHHTTCTTEEEEEEECSCTTSCEEEEEEEECTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCeEEEEEeCCCchHHHHHHHHHhhCCCeeEEeeecCCCCCCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999999999999999999999999998 99999999999999999999999


Q ss_pred             HHH--HHHHHHh
Q 033968           85 FAK--AVDDFRT   94 (107)
Q Consensus        85 f~~--a~~~~~~   94 (107)
                      |.+  ++++|..
T Consensus       105 f~~e~~~~~~~~  116 (120)
T 1twf_K          105 FETEWNLQTLAA  116 (120)
T ss_dssp             HHHHTTTCCC--
T ss_pred             HHHHHHHHhhhc
Confidence            999  7666554

>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=93.83  E-value=0.038  Score=41.89  Aligned_cols=26  Identities=15%  Similarity=0.142  Sum_probs=16.0

Q ss_pred             CCCeeEEEEecCCcchHHHHHHHHhc
Q 033968            8 DQSNATFSLTEEDHTLANAVRFTLNQ   33 (107)
Q Consensus         8 ~~n~~~~~i~~EDHTLgNlLr~~L~~   33 (107)
                      +++.+.|.+.|-|+||||+||-.|+.
T Consensus         9 ~~~~~~f~l~g~~~t~~NalRRills   34 (265)
T 2pa8_D            9 DDTRIDLVFEGYPLEFVNAIRRASML   34 (265)
T ss_dssp             CSSEEEEEEESSCHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEeCCCHHHHHHHHHHHHH
Confidence            35556666666666666666655554

>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=93.57  E-value=0.16  Score=40.02  Aligned_cols=41  Identities=12%  Similarity=0.208  Sum_probs=36.7

Q ss_pred             CCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968           49 DARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRSTFAKAV   89 (107)
Q Consensus        49 e~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~f~~a~   89 (107)
                      .+++.|.|.|+|. +|.+||.+|++-|++.|..|.+.+....
T Consensus       225 ~dkfif~VET~Gsi~Peeav~~A~kIL~~kl~~f~~~l~~~~  266 (318)
T 1twf_C          225 ADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMD  266 (318)
T ss_dssp             CCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            4589999999999 9999999999999999999988876643

>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=90.81  E-value=0.35  Score=36.53  Aligned_cols=40  Identities=5%  Similarity=0.285  Sum_probs=35.2

Q ss_pred             CCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968           49 DARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRSTFAKA   88 (107)
Q Consensus        49 e~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~f~~a   88 (107)
                      .++..+.|.|+|. +|.+++..|++-|++.++.|.+.+...
T Consensus       223 ~d~~i~~VEt~Gsl~Pee~v~~A~~iL~~~~~~~~~~l~~~  263 (265)
T 2pa8_D          223 EDKYILEIESVGSLKPERILLEAGKSIIRKIEELEKKLVEV  263 (265)
T ss_dssp             EEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3567888999999 999999999999999999999887654

>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=90.57  E-value=0.13  Score=40.64  Aligned_cols=28  Identities=25%  Similarity=0.428  Sum_probs=24.6

Q ss_pred             CCCCeeEEEEecCCcchHHHHHHHHhcC
Q 033968            7 GDQSNATFSLTEEDHTLANAVRFTLNQD   34 (107)
Q Consensus         7 ~~~n~~~~~i~~EDHTLgNlLr~~L~~~   34 (107)
                      .+++.+.|.+.|-|+||||+||-.|+..
T Consensus        13 ~~~~~~kF~leG~~~tlaNALRRiLLSe   40 (318)
T 1twf_C           13 ASKDNVDFILSNVDLAMANSLRRVMIAE   40 (318)
T ss_dssp             CCSSEECCEEBSSCHHHHHHHHHHHHHC
T ss_pred             ecCCEEEEEEEccChhHHHHHHHHHHHc
Confidence            4678899999999999999999888764

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

Probab=90.52  E-value=0.11  Score=39.14  Aligned_cols=25  Identities=36%  Similarity=0.405  Sum_probs=12.7

Q ss_pred             CCeeEEEEe----cCCcchHHHHHHHHhc
Q 033968            9 QSNATFSLT----EEDHTLANAVRFTLNQ   33 (107)
Q Consensus         9 ~n~~~~~i~----~EDHTLgNlLr~~L~~   33 (107)
                      ++.+.|.+.    |-++||||+||-.|+.
T Consensus        21 ~~~~~F~l~Ple~G~~~tlgNaLRRiLLs   49 (235)
T 1bdf_A           21 STHAKVTLEPLERGFGHTLGNALRAILLS   49 (235)
T ss_dssp             SSEEEEEEEEEETTHHHHHHHHHHHHHTT
T ss_pred             CCEEEEEEEecCCCCchHHHHHHHHHHHh
Confidence            344555553    5555555555544444

>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=90.20  E-value=0.36  Score=37.95  Aligned_cols=46  Identities=15%  Similarity=0.217  Sum_probs=36.9

Q ss_pred             eeeeeecCC------CCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHH
Q 033968           37 VTFCGYSIP------HPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVR   82 (107)
Q Consensus        37 V~fAgY~vp------HPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~   82 (107)
                      |.-|.|.+.      -.-.+++.|.|.|+|. +|.+||.+|++-|.+.|..|.
T Consensus       174 v~~v~y~ve~~rv~~~~~~dkli~eIeT~Gsi~P~eal~~A~~iL~~~l~~f~  226 (315)
T 2a6h_A          174 VRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFS  226 (315)
T ss_dssp             EEEEEEEEEECCBTTBCCCEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHTTC
T ss_pred             ceeEEEEeeeeeecccccccEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            445566543      1234689999999999 999999999999999999884

>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=90.04  E-value=0.13  Score=40.54  Aligned_cols=30  Identities=27%  Similarity=0.292  Sum_probs=25.0

Q ss_pred             CCCeeEEEE----ecCCcchHHHHHHHHhcC-CCe
Q 033968            8 DQSNATFSL----TEEDHTLANAVRFTLNQD-PRV   37 (107)
Q Consensus         8 ~~n~~~~~i----~~EDHTLgNlLr~~L~~~-~~V   37 (107)
                      +++.+.|.+    .|-++||||+||-.|+.. |+.
T Consensus        17 ~~~~~~F~l~Ple~G~~~TlgNaLRRiLLsevpg~   51 (315)
T 2a6h_A           17 GREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGT   51 (315)
T ss_dssp             TTTEEEEEEEEECTTCHHHHHHHHHHHHHHTCEEE
T ss_pred             cCCEEEEEEEccCCCchhHHHHHHHHHHHhcCCce
Confidence            477899999    499999999999888875 543

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

Probab=90.02  E-value=0.18  Score=38.03  Aligned_cols=46  Identities=15%  Similarity=0.216  Sum_probs=36.4

Q ss_pred             eeeeeecCCCC------CCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHH
Q 033968           37 VTFCGYSIPHP------SDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVR   82 (107)
Q Consensus        37 V~fAgY~vpHP------le~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~   82 (107)
                      |.-+.|.++-.      -.+++.|.|.|+|. +|.+||.+|++-|.+.|..|.
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            44466776422      23579999999999 999999999999999887664

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

Probab=89.29  E-value=0.33  Score=37.98  Aligned_cols=40  Identities=15%  Similarity=0.252  Sum_probs=36.2

Q ss_pred             CCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968           48 SDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRSTFAK   87 (107)
Q Consensus        48 le~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~f~~   87 (107)
                      -.+++.|.|.|+|. +|.+++.+|++-|+..++.|.+.+++
T Consensus       225 ~~dkfif~VET~Gsl~p~eiv~~A~~iL~~kl~~f~~~L~~  265 (297)
T 3h0g_C          225 EPRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLVRDLDE  265 (297)
T ss_dssp             CCCCEEEEEEBCSSSCTTTTTHHHHHHHHHHHHHHHHHHHC
T ss_pred             cCCEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            35789999999999 99999999999999999999888764

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

Probab=89.08  E-value=0.27  Score=39.05  Aligned_cols=47  Identities=15%  Similarity=0.218  Sum_probs=37.4

Q ss_pred             CeeeeeecCC-----CCC-CCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHH
Q 033968           36 RVTFCGYSIP-----HPS-DARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVR   82 (107)
Q Consensus        36 ~V~fAgY~vp-----HPl-e~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~   82 (107)
                      =|.-+.|.|.     -.. ..+..|.|.|+|. +|.+||..|++-|++.+.-|.
T Consensus       179 PV~~Vny~Ve~~rvgq~td~dkL~leI~TdGsi~P~eAl~~Aa~iL~~~l~~f~  232 (329)
T 3lu0_A          179 PVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFV  232 (329)
T ss_dssp             CEEEEEEEEEEECCSSCSCEEEEEEEEEECSSSCHHHHHHHHHHHHHHHTTTSS
T ss_pred             ceeeEEEEEeccccCCCcccceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            3556777654     333 4689999999999 999999999999999877654

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

Probab=88.53  E-value=0.3  Score=38.21  Aligned_cols=30  Identities=23%  Similarity=0.368  Sum_probs=26.0

Q ss_pred             CCCCeeEEEEecCCcchHHHHHHHHhcC-CC
Q 033968            7 GDQSNATFSLTEEDHTLANAVRFTLNQD-PR   36 (107)
Q Consensus         7 ~~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~   36 (107)
                      .+++.+.|.+.|-|.||||+||-.|+.. |.
T Consensus        12 ~~~~~~~F~l~g~~~tiaNALRRiLLSeVPt   42 (297)
T 3h0g_C           12 ISKNSVDFVLTNTSLAVANSLRRVVLAEIPT   42 (297)
T ss_dssp             BCSSEEEEEECSCCHHHHHHHHHHHHSSCCE
T ss_pred             ccCCEEEEEEECCChhHHHHHHHHHHHcCcc
Confidence            4678999999999999999999888874 53

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

Probab=87.69  E-value=0.25  Score=39.21  Aligned_cols=34  Identities=29%  Similarity=0.358  Sum_probs=27.6

Q ss_pred             CCCeeEEEEe----cCCcchHHHHHHHHhcC-CCeeeee
Q 033968            8 DQSNATFSLT----EEDHTLANAVRFTLNQD-PRVTFCG   41 (107)
Q Consensus         8 ~~n~~~~~i~----~EDHTLgNlLr~~L~~~-~~V~fAg   41 (107)
                      +++.+.|.+.    |-++||||+||-.|+.. |+.-.-+
T Consensus        20 ~~~~~kF~l~PlerG~g~TlgNaLRRvLLssvpg~AIt~   58 (329)
T 3lu0_A           20 SSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTE   58 (329)
T ss_dssp             TTSEEEEEECCCCTTCHHHHHHHHHHHTTTSSCEEEEEE
T ss_pred             CCCEEEEEEEecCCCChhHHHHHHHHHHHhcCCceEEEE
Confidence            5788999998    99999999999988884 6543333

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	107
d1xppa_	99	d.74.3.2 (A:) DNA-directed RNA polymerase subunit	6e-27
d1twfk_	114	d.74.3.2 (K:) RPB11 {Baker's yeast (Saccharomyces	1e-26

>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 = 93.3 bits (232), Expect = 6e-27
 Identities = 16/88 (18%), Positives = 37/88 (42%)

Query: 8  DQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDPAREVL 67
          ++++ T  +   D+TL   +   + +D +V    Y I HP      I V+      +  +
Sbjct: 11 EKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSGKPQSAI 70

Query: 68 KDSCQELMLMCRHVRSTFAKAVDDFRTS 95
          K + ++L  +   + + F K    + + 
Sbjct: 71 KRAVRKLSKLYEDLGTQFQKEFQRYESD 98

>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 = 92.5 bits (230), Expect = 1e-26
 Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 12  ATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDS 70
              +  +EDHTL N +R  L  D +V F  Y + HP  AR  +R+QTT     ++ LK++
Sbjct: 31  VVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDPKDALKNA 90

Query: 71  CQELMLMCRHVRSTFAK 87
           C  ++     +++ F  
Sbjct: 91  CNSIINKLGALKTNFET 107

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	107
d1xppa_	99	DNA-directed RNA polymerase subunit L, RpoL {Therm	100.0
d1twfk_	114	RPB11 {Baker's yeast (Saccharomyces cerevisiae) [T	99.97
d1bdfa1	105	RNA polymerase alpha {Escherichia coli [TaxId: 562	97.98
d1smya1	106	RNA polymerase alpha {Thermus thermophilus [TaxId:	97.81
d1twfc1	135	RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta	97.09

>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=2.7e-36  Score=203.50  Aligned_cols=91  Identities=18%  Similarity=0.289  Sum_probs=87.7

Q ss_pred             CCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 033968            6 FGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDPAREVLKDSCQELMLMCRHVRSTF   85 (107)
Q Consensus         6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~~p~eal~~Al~~L~~~~~~l~~~f   85 (107)
                      ++++|+++|+|.||||||||+||+.|+++|+|.||||++||||+++|.|||||++++|.++|++|+++|++.|+.|.++|
T Consensus         9 ~~~~n~~~~~i~~EdHTlgn~L~~~L~~~~~V~fagY~ipHPl~~~~~l~I~t~~~~p~~~l~~a~~~li~~~~~l~~~~   88 (99)
T d1xppa_           9 SKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSGKPQSAIKRAVRKLSKLYEDLGTQF   88 (99)
T ss_dssp             EECSSEEEEEEESCCHHHHHHHHHHHTTCTTEEEEEEECSSTTTSCCEEEEEESSSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ecCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEEecCCcccCCeEEEEEeCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35789999999999999999999999999999999999999999999999999988999999999999999999999999


Q ss_pred             HHHHHHHHhhh
Q 033968           86 AKAVDDFRTSE   96 (107)
Q Consensus        86 ~~a~~~~~~~~   96 (107)
                      .+++++|++.+
T Consensus        89 ~~~~~~~~~~~   99 (99)
T d1xppa_          89 QKEFQRYESDH   99 (99)
T ss_dssp             HHHHHHHHHHC
T ss_pred             HHHHHHHhhcC
Confidence            99999999763

>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=99.97  E-value=4.3e-32  Score=186.96  Aligned_cols=86  Identities=28%  Similarity=0.494  Sum_probs=82.3

Q ss_pred             CCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHH
Q 033968            6 FGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRST   84 (107)
Q Consensus         6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~   84 (107)
                      ++.+|+++|+|.+|||||||+|++.|+++|+|.||||++||||++++.|||||+++ +|.++|++|+++|++.|+.|++.
T Consensus        25 ~~~~n~~~~~i~~EdhTlGnlL~~~L~~~~~V~fagY~~pHPl~~~i~irI~t~~~~~p~~~l~~a~~~l~~~~~~l~~~  104 (114)
T d1twfk_          25 TKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTN  104 (114)
T ss_dssp             SSSTTEEEEEEESCCHHHHHHHHHHHTTCTTEEEEEEECSCTTSCEEEEEEEECTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCceEEEEEeCCCchHHHHHHHHHhcCCCceEEEeecCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            45689999999999999999999999999999999999999999999999999988 99999999999999999999999


Q ss_pred             HHHHHHH
Q 033968           85 FAKAVDD   91 (107)
Q Consensus        85 f~~a~~~   91 (107)
                      |+++++.
T Consensus       105 f~~e~~~  111 (114)
T d1twfk_         105 FETEWNL  111 (114)
T ss_dssp             HHHHTTT
T ss_pred             HHHHhhh
Confidence            9998754

>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=97.98  E-value=1.1e-05  Score=53.16  Aligned_cols=72  Identities=24%  Similarity=0.295  Sum_probs=57.6

Q ss_pred             CCeeEEEE----ecCCcchHHHHHHHHhc-CCCeeeeeecCC---CC---CCCceeEEEEeCCC-CHHHHHHHHHHHHHH
Q 033968            9 QSNATFSL----TEEDHTLANAVRFTLNQ-DPRVTFCGYSIP---HP---SDARVNIRVQTTGD-PAREVLKDSCQELML   76 (107)
Q Consensus         9 ~n~~~~~i----~~EDHTLgNlLr~~L~~-~~~V~fAgY~vp---HP---le~~i~lrIqT~~~-~p~eal~~Al~~L~~   76 (107)
                      +....|++    +|-.+|+||.+|..|+. .+.|.-++|+|.   |=   -..++.|.|.|+|. +|.+||..|++-|.+
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    56679999999988766 589999999987   32   23489999999999 999999999998887


Q ss_pred             HHHH
Q 033968           77 MCRH   80 (107)
Q Consensus        77 ~~~~   80 (107)
                      .+..
T Consensus       100 ~~~~  103 (105)
T d1bdfa1         100 QLEA  103 (105)
T ss_dssp             HGGG
T ss_pred             HHHh
Confidence            6643

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

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

Probab=97.81  E-value=1.6e-05  Score=52.68  Aligned_cols=74  Identities=20%  Similarity=0.235  Sum_probs=58.4

Q ss_pred             CCCeeEEEEe----cCCcchHHHHHHHHhc-CCCeeeeeecCCC------CCCCceeEEEEeCCC-CHHHHHHHHHHHHH
Q 033968            8 DQSNATFSLT----EEDHTLANAVRFTLNQ-DPRVTFCGYSIPH------PSDARVNIRVQTTGD-PAREVLKDSCQELM   75 (107)
Q Consensus         8 ~~n~~~~~i~----~EDHTLgNlLr~~L~~-~~~V~fAgY~vpH------Ple~~i~lrIqT~~~-~p~eal~~Al~~L~   75 (107)
                      ..+...|.+.    |..+|+||.||..|.. .|-|.-+.|.|.-      .-..++.|-|.|+|. +|.+||..|++-|.
T Consensus        17 ~~~y~~~v~~p~erG~g~~~gn~l~~il~ss~~PV~kV~y~Ve~~rvg~~~d~dkL~LeI~TnGsi~P~eAl~~Aa~il~   96 (106)
T d1smya1          17 GREYGEFVLEPLERGFGVTLGNPLRRILLSSIPPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILR   96 (106)
T ss_dssp             SSSCEEEEEEEECTTHHHHHHHHHHHHHHHTCECEEEEEEEEEECCCSSCSCCEEEEEEEEECSSSCHHHHHHHHHHHHH
T ss_pred             CCceeEEEeeccCCCcccccccccceeehhcCChhhEEEEEecccccCcccceeEEEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            3444556654    6779999999986655 6999999999873      124579999999999 99999999999888


Q ss_pred             HHHHHH
Q 033968           76 LMCRHV   81 (107)
Q Consensus        76 ~~~~~l   81 (107)
                      +.+..|
T Consensus        97 ~h~~~f  102 (106)
T d1smya1          97 EHLTYF  102 (106)
T ss_dssp             HHHHTS
T ss_pred             HHHHhh
Confidence            776543

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

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

Probab=97.09  E-value=0.0023  Score=43.70  Aligned_cols=83  Identities=19%  Similarity=0.332  Sum_probs=64.3

Q ss_pred             CCCCCeeEEEEecCCcchHHHHHHHHhcC-CC-eeeee----------e-------------------cCCC---CC---
Q 033968            6 FGDQSNATFSLTEEDHTLANAVRFTLNQD-PR-VTFCG----------Y-------------------SIPH---PS---   48 (107)
Q Consensus         6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~-V~fAg----------Y-------------------~vpH---Pl---   48 (107)
                      ..+++.+.|.+.|-|-++.|+||-.++.+ |- |.|-.          |                   ..|.   |+   
T Consensus        10 ~~~~~~~~F~l~~~d~s~ANalRRi~iaeV~t~v~feyDp~N~lrHtdyw~e~~~~~ewP~s~~~~~e~~~~e~e~fd~~   89 (135)
T d1twfc1          10 EASKDNVDFILSNVDLAMANSLRRVMIAEIAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYK   89 (135)
T ss_dssp             CCCSSEECCEEBSSCHHHHHHHHHHHHHCCEEEEEEEECSSTTSCCSCCCCSSCHHHHSCCCGGGTTSCCCCSSSCCCTT
T ss_pred             EcCCCEEEEEEeCCCHHHHHHHHHHHHHhhhhheeeeecccccccceeecccCCccccCCcccCCCCCCCcccccCCCCC
Confidence            45778899999999999999999888775 42 22211          1                   1111   22   


Q ss_pred             --CCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968           49 --DARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRSTFAKA   88 (107)
Q Consensus        49 --e~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~f~~a   88 (107)
                        .+++.+.|.+.|. .|.+++.+|++-|+..|..|...+...
T Consensus        90 akpd~F~f~VEs~G~l~p~~Iv~~ai~iL~~Kl~~l~~~L~~~  132 (135)
T d1twfc1          90 AQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQM  132 (135)
T ss_dssp             CCCCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEEeccCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence              2468899999999 999999999999999999999888653