Psyllid ID: psy548

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80----
Protein Sequence
MVFSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKIIDR
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHHHHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHcccccEEEEEEcccccEEEEEccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccHHHHHHHHHHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHHccccEEEEEEccccccccccccEEEEEcc
Coil and Loop (DISEMBL)
MVFSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIrrylpdnsyedwgidelkiidr
Flexible Loop (DISEMBL)
MVFSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKElkarkipiiirrylpdnsyedwgidelkiidr
Low Complexity Region (SEG)
MVFSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKIIDR
Disordered region (IsUnstruct)
****PSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKII**
Disordered Region (DISOPRED)
******F***IVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKIID*
Disordered Region (DISEMBL)
MVFSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKIIDR
Disordered Region (DISPRO)
*****SFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKIIDR
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MVFSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKIIDR
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	84	2.2.26 [Sep-21-2011]
Q5R592	127	DNA-directed RNA polymera	yes	N/A	0.904	0.598	0.855	7e-31
P61218	127	DNA-directed RNA polymera	yes	N/A	0.904	0.598	0.855	7e-31
P61217	127	DNA-directed RNA polymera	yes	N/A	0.904	0.598	0.855	7e-31
Q32PE0	127	DNA-directed RNA polymera	yes	N/A	0.904	0.598	0.855	8e-31
O88828	127	DNA-directed RNA polymera	yes	N/A	0.904	0.598	0.855	1e-30
P61219	127	DNA-directed RNA polymera	yes	N/A	0.904	0.598	0.855	1e-30
Q24320	131	DNA-directed RNA polymera	yes	N/A	0.916	0.587	0.792	5e-30
Q17684	137	Probable DNA-directed RNA	yes	N/A	0.976	0.598	0.695	5e-27
A8WSV7	138	Probable DNA-directed RNA	N/A	N/A	0.976	0.594	0.682	1e-26
P36595	142	DNA-directed RNA polymera	yes	N/A	0.857	0.507	0.694	6e-25

>sp|Q5R592|RPAB2_PONAB DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Pongo abelii GN=POLR2F PE=2 SV=1

 Score =  132 bits (331), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 65/76 (85%), Positives = 68/76 (89%)

Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
           I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLP
Sbjct: 52  ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLP 111

Query: 68  DNSYEDWGIDELKIID 83
           D SYEDWG+DEL I D
Sbjct: 112 DGSYEDWGVDELIITD 127

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, POLR2F/RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds.
Pongo abelii (taxid: 9601)

>sp|P61218|RPAB2_HUMAN DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Homo sapiens GN=POLR2F PE=1 SV=1

 Score =  132 bits (331), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 65/76 (85%), Positives = 68/76 (89%)

Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
           I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLP
Sbjct: 52  ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLP 111

Query: 68  DNSYEDWGIDELKIID 83
           D SYEDWG+DEL I D
Sbjct: 112 DGSYEDWGVDELIITD 127

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II, and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, POLR2F/RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds.

Homo sapiens (taxid: 9606)

>sp|P61217|RPAB2_CRIGR DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Cricetulus griseus GN=POLR2F PE=2 SV=1

 Score =  132 bits (331), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 65/76 (85%), Positives = 68/76 (89%)

Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
           I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLP
Sbjct: 52  ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLP 111

Query: 68  DNSYEDWGIDELKIID 83
           D SYEDWG+DEL I D
Sbjct: 112 DGSYEDWGVDELIITD 127

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II, and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, POLR2F/RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds.

Cricetulus griseus (taxid: 10029)

>sp|Q32PE0|RPAB2_BOVIN DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Bos taurus GN=POLR2F PE=2 SV=1

 Score =  132 bits (331), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 65/76 (85%), Positives = 68/76 (89%)

Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
           I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLP
Sbjct: 52  ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLP 111

Query: 68  DNSYEDWGIDELKIID 83
           D SYEDWG+DEL I D
Sbjct: 112 DGSYEDWGVDELIITD 127

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II, and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, POLR2F/RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds.

Bos taurus (taxid: 9913)

>sp|O88828|RPAB2_RAT DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Rattus norvegicus GN=Polr2f PE=1 SV=1

 Score =  131 bits (330), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 65/76 (85%), Positives = 68/76 (89%)

Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
           I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLP
Sbjct: 52  ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLP 111

Query: 68  DNSYEDWGIDELKIID 83
           D SYEDWG+DEL I D
Sbjct: 112 DGSYEDWGVDELIISD 127

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, POLR2F/RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds.

Rattus norvegicus (taxid: 10116)

>sp|P61219|RPAB2_MOUSE DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Mus musculus GN=Polr2f PE=2 SV=1

 Score =  131 bits (330), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 65/76 (85%), Positives = 68/76 (89%)

Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
           I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLP
Sbjct: 52  ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLP 111

Query: 68  DNSYEDWGIDELKIID 83
           D SYEDWG+DEL I D
Sbjct: 112 DGSYEDWGVDELIISD 127

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, POLR2F/RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds.

Mus musculus (taxid: 10090)

>sp|Q24320|RPAB2_DROME DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Drosophila melanogaster GN=RpII18 PE=2 SV=1

 Score =  129 bits (324), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 61/77 (79%), Positives = 69/77 (89%)

Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
           I T  + +YERARVLGTRALQIAMCAP+MVEL+GETDPLQIAMKELK +KIPIIIRRYLP
Sbjct: 55  ITTKYMTKYERARVLGTRALQIAMCAPIMVELDGETDPLQIAMKELKQKKIPIIIRRYLP 114

Query: 68  DNSYEDWGIDELKIIDR 84
           D+SYEDW IDEL ++D 
Sbjct: 115 DHSYEDWSIDELIMVDN 131

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds.

Drosophila melanogaster (taxid: 7227)

>sp|Q17684|RPAB2_CAEEL Probable DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Caenorhabditis elegans GN=rpb-6 PE=3 SV=1

 Score =  119 bits (298), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 57/82 (69%), Positives = 67/82 (81%)

Query: 2   VFSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPII 61
           V +   + T  + +YERARVLGTRALQIAM APVMVELEGETDPL+IA KELK R+IPII
Sbjct: 55  VPTSEHVTTPFMTKYERARVLGTRALQIAMGAPVMVELEGETDPLEIARKELKQRRIPII 114

Query: 62  IRRYLPDNSYEDWGIDELKIID 83
           +RRYLPD SYEDW  D+L++ D
Sbjct: 115 VRRYLPDGSYEDWPTDQLQLAD 136

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds.

Caenorhabditis elegans (taxid: 6239)

>sp|A8WSV7|RPAB2_CAEBR Probable DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Caenorhabditis briggsae GN=rpb-6 PE=3 SV=1

 Score =  118 bits (296), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 56/82 (68%), Positives = 67/82 (81%)

Query: 2   VFSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPII 61
           V +   + T  + +YERARVLGTRALQIAM APVMVELEGETDPL+IA KELK R++PII
Sbjct: 56  VPTSEHVTTPFMTKYERARVLGTRALQIAMGAPVMVELEGETDPLEIARKELKQRRVPII 115

Query: 62  IRRYLPDNSYEDWGIDELKIID 83
           IRRYLPD SYEDW  ++L++ D
Sbjct: 116 IRRYLPDGSYEDWPTEQLQLAD 137

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds.

Caenorhabditis briggsae (taxid: 6238)

>sp|P36595|RPAB2_SCHPO DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb6 PE=1 SV=1

 Score =  112 bits (280), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 50/72 (69%), Positives = 61/72 (84%)

Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
             T  + +YERAR+LGTRALQI+M APV+V+LEGETDPLQIAMKEL  +KIP+++RRYLP
Sbjct: 70  TTTPYMTKYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRYLP 129

Query: 68  DNSYEDWGIDEL 79
           D SYEDW + EL
Sbjct: 130 DGSYEDWSVAEL 141

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds.

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

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	84
350536293	132	uncharacterized protein LOC100165288 [Ac	0.916	0.583	0.870	3e-31
307168238	129	DNA-directed RNA polymerases I, II, and	0.916	0.596	0.883	4e-31
332027163	130	DNA-directed RNA polymerases I, II, and	0.916	0.592	0.883	4e-31
346470037	129	hypothetical protein [Amblyomma maculatu	0.904	0.589	0.881	5e-31
66524012	130	PREDICTED: DNA-directed RNA polymerases	0.916	0.592	0.883	6e-31
307201767	130	DNA-directed RNA polymerases I, II, and	0.916	0.592	0.870	6e-31
241558215	129	RNA polymerase subunit K, putative [Ixod	0.904	0.589	0.881	6e-31
383854730	130	PREDICTED: DNA-directed RNA polymerases	0.916	0.592	0.870	7e-31
307197591	109	DNA-directed RNA polymerases I, II, and	0.916	0.706	0.870	8e-31
322784320	149	hypothetical protein SINV_10192 [Solenop	0.821	0.463	0.956	2e-30

>gi|350536293|ref|NP_001233048.1| uncharacterized protein LOC100165288 [Acyrthosiphon pisum] gi|239788305|dbj|BAH70841.1| ACYPI005782 [Acyrthosiphon pisum] gi|239790530|dbj|BAH71820.1| ACYPI006245 [Acyrthosiphon pisum]

 Score =  139 bits (349), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 67/77 (87%), Positives = 71/77 (92%)

Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
           I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK RKIPIIIRRYLP
Sbjct: 56  ITTKYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKKRKIPIIIRRYLP 115

Query: 68  DNSYEDWGIDELKIIDR 84
           DNSYEDWGIDEL I+D+
Sbjct: 116 DNSYEDWGIDELIIVDQ 132

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307168238|gb|EFN61464.1| DNA-directed RNA polymerases I, II, and III subunit RPABC2 [Camponotus floridanus]

 Score =  138 bits (348), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 68/77 (88%), Positives = 70/77 (90%)

Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
           I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK RKIPIIIRRYLP
Sbjct: 53  ITTRYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKQRKIPIIIRRYLP 112

Query: 68  DNSYEDWGIDELKIIDR 84
           DNSYEDWGIDEL IID 
Sbjct: 113 DNSYEDWGIDELIIIDH 129

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332027163|gb|EGI67256.1| DNA-directed RNA polymerases I, II, and III subunit RPABC2 [Acromyrmex echinatior]

 Score =  138 bits (347), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 68/77 (88%), Positives = 70/77 (90%)

Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
           I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK RKIPIIIRRYLP
Sbjct: 54  ITTRYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKQRKIPIIIRRYLP 113

Query: 68  DNSYEDWGIDELKIIDR 84
           DNSYEDWGIDEL IID 
Sbjct: 114 DNSYEDWGIDELIIIDH 130

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|346470037|gb|AEO34863.1| hypothetical protein [Amblyomma maculatum]

 Score =  138 bits (347), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 67/76 (88%), Positives = 70/76 (92%)

Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
           I T+ + +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP
Sbjct: 54  ITTMYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 113

Query: 68  DNSYEDWGIDELKIID 83
           D SYEDWGIDEL I D
Sbjct: 114 DGSYEDWGIDELLITD 129

Source: Amblyomma maculatum

Species: Amblyomma maculatum

Genus: Amblyomma

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66524012|ref|XP_393973.2| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC2-like [Apis mellifera] gi|340724588|ref|XP_003400663.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC2-like [Bombus terrestris] gi|350397886|ref|XP_003485021.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC2-like [Bombus impatiens] gi|380021021|ref|XP_003694373.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC2-like [Apis florea]

 Score =  138 bits (347), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 68/77 (88%), Positives = 70/77 (90%)

Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
           I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK RKIPIIIRRYLP
Sbjct: 54  ITTRYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKQRKIPIIIRRYLP 113

Query: 68  DNSYEDWGIDELKIIDR 84
           DNSYEDWGIDEL IID 
Sbjct: 114 DNSYEDWGIDELIIIDH 130

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307201767|gb|EFN81440.1| DNA-directed RNA polymerases I, II, and III subunit RPABC2 [Harpegnathos saltator] gi|307202651|gb|EFN81971.1| DNA-directed RNA polymerases I, II, and III subunit RPABC2 [Harpegnathos saltator]

 Score =  137 bits (346), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 67/77 (87%), Positives = 70/77 (90%)

Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
           I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK RKIPI+IRRYLP
Sbjct: 54  ITTRYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKQRKIPIVIRRYLP 113

Query: 68  DNSYEDWGIDELKIIDR 84
           DNSYEDWGIDEL IID 
Sbjct: 114 DNSYEDWGIDELIIIDH 130

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|241558215|ref|XP_002400181.1| RNA polymerase subunit K, putative [Ixodes scapularis] gi|215499742|gb|EEC09236.1| RNA polymerase subunit K, putative [Ixodes scapularis] gi|442752305|gb|JAA68312.1| Putative rna polymerase subunit k [Ixodes ricinus]

 Score =  137 bits (346), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 67/76 (88%), Positives = 70/76 (92%)

Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
           I T+ + +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP
Sbjct: 54  ITTMYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 113

Query: 68  DNSYEDWGIDELKIID 83
           D SYEDWGIDEL I D
Sbjct: 114 DGSYEDWGIDELIITD 129

Source: Ixodes scapularis

Species: Ixodes scapularis

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383854730|ref|XP_003702873.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC2-like [Megachile rotundata]

 Score =  137 bits (346), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 67/77 (87%), Positives = 70/77 (90%)

Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
           I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK RKIPI+IRRYLP
Sbjct: 54  ITTRYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKQRKIPIVIRRYLP 113

Query: 68  DNSYEDWGIDELKIIDR 84
           DNSYEDWGIDEL IID 
Sbjct: 114 DNSYEDWGIDELIIIDH 130

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307197591|gb|EFN78795.1| DNA-directed RNA polymerases I, II, and III subunit RPABC2 [Harpegnathos saltator]

 Score =  137 bits (345), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 67/77 (87%), Positives = 70/77 (90%)

Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
           I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK RKIPI+IRRYLP
Sbjct: 33  ITTRYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKQRKIPIVIRRYLP 92

Query: 68  DNSYEDWGIDELKIIDR 84
           DNSYEDWGIDEL IID 
Sbjct: 93  DNSYEDWGIDELIIIDH 109

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322784320|gb|EFZ11308.1| hypothetical protein SINV_10192 [Solenopsis invicta]

 Score =  135 bits (341), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 66/69 (95%), Positives = 66/69 (95%)

Query: 16  YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWG 75
           YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK RKIPIIIRRYLPDNSYEDWG
Sbjct: 81  YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKQRKIPIIIRRYLPDNSYEDWG 140

Query: 76  IDELKIIDR 84
           IDEL IID 
Sbjct: 141 IDELIIIDH 149

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	84
UNIPROTKB|F1ND65	135	POLR2F "Uncharacterized protei	0.904	0.562	0.855	2.1e-29
UNIPROTKB|Q9PT88	127	RPB6 "RNA polymerase common su	0.904	0.598	0.855	2.1e-29
UNIPROTKB|F2Z4C9	127	POLR2F "DNA-directed RNA polym	0.904	0.598	0.855	2.1e-29
UNIPROTKB|Q32PE0	127	POLR2F "DNA-directed RNA polym	0.904	0.598	0.855	2.1e-29
UNIPROTKB|E2RPD9	127	POLR2F "Uncharacterized protei	0.904	0.598	0.855	2.1e-29
UNIPROTKB|P61218	127	POLR2F "DNA-directed RNA polym	0.904	0.598	0.855	2.1e-29
UNIPROTKB|P61217	127	POLR2F "DNA-directed RNA polym	0.904	0.598	0.855	2.1e-29
UNIPROTKB|Q5R592	127	POLR2F "DNA-directed RNA polym	0.904	0.598	0.855	2.1e-29
ZFIN|ZDB-GENE-040718-279	127	polr2f "polymerase (RNA) II (D	0.904	0.598	0.855	2.1e-29
MGI|MGI:1349393	127	Polr2f "polymerase (RNA) II (D	0.904	0.598	0.855	2.7e-29

UNIPROTKB|F1ND65 POLR2F "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 65/76 (85%), Positives = 68/76 (89%)

Query:     8 IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
             I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLP
Sbjct:    60 ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLP 119

Query:    68 DNSYEDWGIDELKIID 83
             D SYEDWG+DEL I D
Sbjct:   120 DGSYEDWGVDELIITD 135

GO:0003677 "DNA binding" evidence=IEA

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

GO:0004672 "protein kinase activity" evidence=IEA

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

GO:0005730 "nucleolus" evidence=IEA

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

UNIPROTKB|Q9PT88 RPB6 "RNA polymerase common subunit RPB6" [Gallus gallus (taxid:9031)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 65/76 (85%), Positives = 68/76 (89%)

Query:     8 IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
             I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLP
Sbjct:    52 ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLP 111

Query:    68 DNSYEDWGIDELKIID 83
             D SYEDWG+DEL I D
Sbjct:   112 DGSYEDWGVDELIITD 127

GO:0003677 "DNA binding" evidence=IEA

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

GO:0004672 "protein kinase activity" evidence=IEA

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

GO:0005730 "nucleolus" evidence=IEA

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

UNIPROTKB|F2Z4C9 POLR2F "DNA-directed RNA polymerases I, II, and III subunit RPABC2" [Bos taurus (taxid:9913)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 65/76 (85%), Positives = 68/76 (89%)

Query:     8 IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
             I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLP
Sbjct:    52 ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLP 111

Query:    68 DNSYEDWGIDELKIID 83
             D SYEDWG+DEL I D
Sbjct:   112 DGSYEDWGVDELIITD 127

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

GO:0005730 "nucleolus" evidence=IEA

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

GO:0004672 "protein kinase activity" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q32PE0 POLR2F "DNA-directed RNA polymerases I, II, and III subunit RPABC2" [Bos taurus (taxid:9913)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 65/76 (85%), Positives = 68/76 (89%)

Query:     8 IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
             I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLP
Sbjct:    52 ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLP 111

Query:    68 DNSYEDWGIDELKIID 83
             D SYEDWG+DEL I D
Sbjct:   112 DGSYEDWGVDELIITD 127

GO:0006468 "protein phosphorylation" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISS

GO:0004672 "protein kinase activity" evidence=ISS

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

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2RPD9 POLR2F "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 65/76 (85%), Positives = 68/76 (89%)

Query:     8 IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
             I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLP
Sbjct:    52 ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLP 111

Query:    68 DNSYEDWGIDELKIID 83
             D SYEDWG+DEL I D
Sbjct:   112 DGSYEDWGVDELIITD 127

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

GO:0005730 "nucleolus" evidence=IEA

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

GO:0004672 "protein kinase activity" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|P61218 POLR2F "DNA-directed RNA polymerases I, II, and III subunit RPABC2" [Homo sapiens (taxid:9606)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 65/76 (85%), Positives = 68/76 (89%)

Query:     8 IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
             I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLP
Sbjct:    52 ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLP 111

Query:    68 DNSYEDWGIDELKIID 83
             D SYEDWG+DEL I D
Sbjct:   112 DGSYEDWGVDELIITD 127

GO:0003677 "DNA binding" evidence=IEA

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

GO:0004672 "protein kinase activity" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

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

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

GO:0000398 "mRNA splicing, via spliceosome" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=TAS

GO:0006289 "nucleotide-excision repair" evidence=TAS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=TAS

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=TAS

GO:0006370 "7-methylguanosine mRNA capping" evidence=TAS

GO: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:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0050434 "positive regulation of viral transcription" evidence=TAS

GO:0006468 "protein phosphorylation" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|P61217 POLR2F "DNA-directed RNA polymerases I, II, and III subunit RPABC2" [Cricetulus griseus (taxid:10029)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 65/76 (85%), Positives = 68/76 (89%)

Query:     8 IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
             I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLP
Sbjct:    52 ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLP 111

Query:    68 DNSYEDWGIDELKIID 83
             D SYEDWG+DEL I D
Sbjct:   112 DGSYEDWGVDELIITD 127

GO:0005634 "nucleus" evidence=ISS

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

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

GO:0006468 "protein phosphorylation" evidence=ISS

GO:0004672 "protein kinase activity" evidence=ISS

UNIPROTKB|Q5R592 POLR2F "DNA-directed RNA polymerases I, II, and III subunit RPABC2" [Pongo abelii (taxid:9601)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 65/76 (85%), Positives = 68/76 (89%)

Query:     8 IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
             I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLP
Sbjct:    52 ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLP 111

Query:    68 DNSYEDWGIDELKIID 83
             D SYEDWG+DEL I D
Sbjct:   112 DGSYEDWGVDELIITD 127

GO:0005634 "nucleus" evidence=ISS

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

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

GO:0004672 "protein kinase activity" evidence=ISS

ZFIN|ZDB-GENE-040718-279 polr2f "polymerase (RNA) II (DNA directed) polypeptide F" [Danio rerio (taxid:7955)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 65/76 (85%), Positives = 68/76 (89%)

Query:     8 IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
             I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK+RKIPIIIRRYLP
Sbjct:    52 ITTQYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKSRKIPIIIRRYLP 111

Query:    68 DNSYEDWGIDELKIID 83
             D SYEDWG DEL I D
Sbjct:   112 DGSYEDWGCDELIITD 127

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0030880 "RNA polymerase complex" evidence=IEA

MGI|MGI:1349393 Polr2f "polymerase (RNA) II (DNA directed) polypeptide F" [Mus musculus (taxid:10090)]

 Score = 325 (119.5 bits), Expect = 2.7e-29, P = 2.7e-29
 Identities = 65/76 (85%), Positives = 68/76 (89%)

Query:     8 IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
             I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLP
Sbjct:    52 ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLP 111

Query:    68 DNSYEDWGIDELKIID 83
             D SYEDWG+DEL I D
Sbjct:   112 DGSYEDWGVDELIISD 127

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISO

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

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

GO:0030880 "RNA polymerase complex" evidence=IEA

GO:0032774 "RNA biosynthetic process" evidence=IDA

---

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)
Q8TT40	RPOK_METAC	2, ., 7, ., 7, ., 6	0.6	0.5952	0.8333	yes	N/A
P61217	RPAB2_CRIGR	No assigned EC number	0.8552	0.9047	0.5984	yes	N/A
O26148	RPOK_METTH	2, ., 7, ., 7, ., 6	0.4807	0.6190	0.8524	yes	N/A
Q9YDJ9	RPOK_AERPE	2, ., 7, ., 7, ., 6	0.3768	0.7976	0.7528	yes	N/A
Q8PW42	RPOK_METMA	2, ., 7, ., 7, ., 6	0.62	0.5952	0.6024	yes	N/A
O29134	RPOK_ARCFU	2, ., 7, ., 7, ., 6	0.54	0.5833	0.6533	yes	N/A
P61219	RPAB2_MOUSE	No assigned EC number	0.8552	0.9047	0.5984	yes	N/A
O88828	RPAB2_RAT	No assigned EC number	0.8552	0.9047	0.5984	yes	N/A
A1RWX0	RPOK_THEPD	2, ., 7, ., 7, ., 6	0.4285	0.8214	0.8518	yes	N/A
Q9HQJ0	RPOK_HALSA	2, ., 7, ., 7, ., 6	0.4615	0.6071	0.85	yes	N/A
Q32PE0	RPAB2_BOVIN	No assigned EC number	0.8552	0.9047	0.5984	yes	N/A
P61218	RPAB2_HUMAN	No assigned EC number	0.8552	0.9047	0.5984	yes	N/A
A2SSV2	RPOK_METLZ	2, ., 7, ., 7, ., 6	0.5	0.6547	0.8870	yes	N/A
Q8ZTF9	RPOK_PYRAE	2, ., 7, ., 7, ., 6	0.3918	0.8571	0.6792	yes	N/A
Q5R592	RPAB2_PONAB	No assigned EC number	0.8552	0.9047	0.5984	yes	N/A
P36595	RPAB2_SCHPO	No assigned EC number	0.6944	0.8571	0.5070	yes	N/A
P20435	RPAB2_YEAST	No assigned EC number	0.68	0.8809	0.4774	yes	N/A
Q24320	RPAB2_DROME	No assigned EC number	0.7922	0.9166	0.5877	yes	N/A
Q54FA8	RPAB2_DICDI	No assigned EC number	0.7083	0.8571	0.5413	yes	N/A
B0R4Y7	RPOK_HALS3	2, ., 7, ., 7, ., 6	0.4615	0.6071	0.85	yes	N/A
Q17684	RPAB2_CAEEL	No assigned EC number	0.6951	0.9761	0.5985	yes	N/A

EC Number Prediction by EFICAz Software

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	84
PLN00152	130	PLN00152, PLN00152, DNA-directed RNA polymerase; P	6e-39
PRK01099	62	PRK01099, rpoK, DNA-directed RNA polymerase subuni	1e-19
pfam01192	57	pfam01192, RNA_pol_Rpb6, RNA polymerase Rpb6	3e-12
COG1758	74	COG1758, RpoZ, DNA-directed RNA polymerase, subuni	7e-11

>gnl|CDD|177755 PLN00152, PLN00152, DNA-directed RNA polymerase; Provisional

 Score =  125 bits (315), Expect = 6e-39
 Identities = 55/71 (77%), Positives = 63/71 (88%)

Query: 13  IKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYE 72
           + +YERAR+LGTRALQI+M APVMVELEGETDPL+IAMKEL+ RKIP  IRRYLPD SYE
Sbjct: 60  MTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYE 119

Query: 73  DWGIDELKIID 83
           DWG+DEL + D
Sbjct: 120 DWGVDELIVED 130

Length = 130

>gnl|CDD|179220 PRK01099, rpoK, DNA-directed RNA polymerase subunit K; Provisional

 Score = 74.2 bits (183), Expect = 1e-19
 Identities = 28/54 (51%), Positives = 41/54 (75%)

Query: 15 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPD 68
          R+ERAR++G RALQI+M APV++++   TDPL IA +E K   +PI ++R LP+
Sbjct: 9  RFERARIIGARALQISMGAPVLIDIPESTDPLDIAEEEFKRGVLPITVKRPLPN 62

Length = 62

>gnl|CDD|201652 pfam01192, RNA_pol_Rpb6, RNA polymerase Rpb6

 Score = 55.4 bits (134), Expect = 3e-12
 Identities = 21/55 (38%), Positives = 34/55 (61%)

Query: 8  IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIII 62
          + +  + RYE AR++  RA Q++  AP +V+ E E  P+ IA++E+   KIP  I
Sbjct: 3  LTSKYLNRYELARIIAKRAKQLSYGAPPLVDEESEIKPVVIALEEIADGKIPPEI 57

Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and III. This family also contains the bacterial equivalent to Rpb6, the omega subunit. Rpb6 and omega are structurally conserved and both function in polymerase assembly. Length = 57

>gnl|CDD|224672 COG1758, RpoZ, DNA-directed RNA polymerase, subunit K/omega [Transcription]

 Score = 52.3 bits (126), Expect = 7e-11
 Identities = 24/59 (40%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 15 RYERARVLGTRALQIAMCAPVMVELEGE-TDPLQIAMKELKARKIPIIIRRYLPDNSYE 72
          RYE   V   RA Q+A  AP +V+ E     P+ IA++E+   KIPI I R L  +S +
Sbjct: 16 RYELVVVAAKRARQLAAGAPPLVDDEENKDKPVVIALREIAEGKIPIEILRELLIHSLQ 74

Length = 74

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	84
KOG3405|consensus	136		100.0
PLN00152	130	DNA-directed RNA polymerase; Provisional	100.0
PRK01099	62	rpoK DNA-directed RNA polymerase subunit K; Provis	99.95
COG1758	74	RpoZ DNA-directed RNA polymerase, subunit K/omega	99.83
PF01192	57	RNA_pol_Rpb6: RNA polymerase Rpb6 ; InterPro: IPR0	99.78
PRK00392	69	rpoZ DNA-directed RNA polymerase subunit omega; Re	99.55
TIGR00690	59	rpoZ DNA-directed RNA polymerase, omega subunit. T	99.55
PF05320	167	Pox_RNA_Pol_19: Poxvirus DNA-directed RNA polymera	83.77

>KOG3405|consensus

Probab=100.00  E-value=6e-38  Score=218.34  Aligned_cols=82  Identities=71%  Similarity=1.051  Sum_probs=80.3

Q ss_pred             CCCCCcccCCCccHHHHHHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCCCeEEEEecCCCcEEEeeccccce
Q psy548            2 VFSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKI   81 (84)
Q Consensus         2 ~~~~~r~t~~~ltrYelari~g~RArQL~~GA~plV~~~~~~kp~~IAl~Ei~~gkI~~~i~R~~p~~~~e~~~l~el~~   81 (84)
                      ||.++|+|.|||||||+||++|.||+|||||||+||+.++.++|+.||.+||+++||||+|||+||||+||||+++||++
T Consensus        55 v~~s~R~TtpyMTKYErArvLGtRAlQIsm~APvmVeLegETdPL~IAmkEL~qkKIP~iIRRyLPDgSyEDW~vdELiv  134 (136)
T KOG3405|consen   55 VPKSERKTTPYMTKYERARVLGTRALQISMNAPVMVELEGETDPLEIAMKELKQKKIPFIIRRYLPDGSYEDWSVDELIV  134 (136)
T ss_pred             ccccccccCcchhHHHHHHhhhHHHHHHhcCCCeEEecCCCCCHHHHHHHHHhhccCceEEeeeCCCCCccccccceeec
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ec
Q psy548           82 ID   83 (84)
Q Consensus        82 ~~   83 (84)
                      .|
T Consensus       135 ~d  136 (136)
T KOG3405|consen  135 ED  136 (136)
T ss_pred             cC
Confidence            65

>PLN00152 DNA-directed RNA polymerase; Provisional

Probab=100.00  E-value=2.2e-36  Score=210.20  Aligned_cols=82  Identities=68%  Similarity=1.054  Sum_probs=78.6

Q ss_pred             CCCCCcccCCCccHHHHHHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCCCeEEEEecCCCcEEEeeccccce
Q psy548            2 VFSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKI   81 (84)
Q Consensus         2 ~~~~~r~t~~~ltrYelari~g~RArQL~~GA~plV~~~~~~kp~~IAl~Ei~~gkI~~~i~R~~p~~~~e~~~l~el~~   81 (84)
                      ++.++|+|++||||||+||++|.||+|||+|||+||+.++.++|+.||.+|+.+|+|||+|+|++|||+||+|+++||.+
T Consensus        49 ~~~~~R~T~p~lTkyErARIiG~RALQIsmgApvlV~~~g~tdPl~IA~~El~~~~iP~iVrR~lPdG~yEd~~v~EL~~  128 (130)
T PLN00152         49 PVQRPRKTTPYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIV  128 (130)
T ss_pred             ccccccccccchhHHHHHhhHhHHHHHHhcCCceEEccCCCcCHHHHHHHHHHcCCCCeEEEEECCCCCEEeeEeeeEee
Confidence            35678999999999999999999999999999999999878899999999999999999999999999999999999998


Q ss_pred             ec
Q psy548           82 ID   83 (84)
Q Consensus        82 ~~   83 (84)
                      .|
T Consensus       129 ~~  130 (130)
T PLN00152        129 ED  130 (130)
T ss_pred             cC
Confidence            76

>PRK01099 rpoK DNA-directed RNA polymerase subunit K; Provisional

Probab=99.95  E-value=4.1e-28  Score=150.52  Aligned_cols=61  Identities=46%  Similarity=0.824  Sum_probs=58.3

Q ss_pred             ccCCCccHHHHHHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCCCeEEEEecCC
Q psy548            8 IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPD   68 (84)
Q Consensus         8 ~t~~~ltrYelari~g~RArQL~~GA~plV~~~~~~kp~~IAl~Ei~~gkI~~~i~R~~p~   68 (84)
                      .++++|||||+|+++|+||+||++||+|+|+.++++||++||++||++|+|+++|+|++||
T Consensus         2 ~~~~~ltrfe~a~i~akRArQl~~Ga~~lv~~~~~~kPv~iAl~Ei~~gkI~~~v~r~~p~   62 (62)
T PRK01099          2 MGPMKLTRFERARIIGARALQISMGAPVLIDIPESTDPLDIAEEEFKRGVLPITVKRPLPN   62 (62)
T ss_pred             CCCcccCHHHHHHHHHHHHHHHHcCCCceecCCCCCCHHHHHHHHHHcCCCCeEeecCCCC
Confidence            5789999999999999999999999999999855799999999999999999999999997

>COG1758 RpoZ DNA-directed RNA polymerase, subunit K/omega [Transcription]

Probab=99.83  E-value=6.2e-21  Score=120.81  Aligned_cols=70  Identities=36%  Similarity=0.401  Sum_probs=62.7

Q ss_pred             CCCCcccCCCccHHHHHHHHHHHHHHHhcCCCceeeCCCC-CChHHHHHHHHHcCCCCeEEEEecCCCcEE
Q psy548            3 FSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGE-TDPLQIAMKELKARKIPIIIRRYLPDNSYE   72 (84)
Q Consensus         3 ~~~~r~t~~~ltrYelari~g~RArQL~~GA~plV~~~~~-~kp~~IAl~Ei~~gkI~~~i~R~~p~~~~e   72 (84)
                      |..+.......|||++|+++|+||+||++|++++++.+.. +||+.+|++||++|++++.+.+..++++.+
T Consensus         4 ~~~~~l~~~~~~ryelv~~aa~RA~Ql~~ga~~~~~~~~~~~kpv~iAl~Ei~~g~i~~~i~~~~~~~~~~   74 (74)
T COG1758           4 PTIEDLLDKVGNRYELVVVAAKRARQLAAGAPPLVDDEENKDKPVVIALREIAEGKIPIEILRELLIHSLQ   74 (74)
T ss_pred             cCHHHHHhhccCHHHHHHHHHHHHHHHHcCCCCccccccccCChHHHHHHHHHcCCCCcccchhhhccccC
Confidence            4455667788999999999999999999999999988754 899999999999999999999999998753

>PF01192 RNA_pol_Rpb6: RNA polymerase Rpb6 ; InterPro: IPR006110 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2

Probab=99.78  E-value=2.2e-19  Score=108.04  Aligned_cols=56  Identities=36%  Similarity=0.467  Sum_probs=51.0

Q ss_pred             cccCCCccHHHHHHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCCCeEE
Q psy548            7 FIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIII   62 (84)
Q Consensus         7 r~t~~~ltrYelari~g~RArQL~~GA~plV~~~~~~kp~~IAl~Ei~~gkI~~~i   62 (84)
                      +......|||++++++|+||+||++|++|+++.++..||+++|++||++|+++|+|
T Consensus         2 ~l~~~~~~rY~Lv~~~akRArql~~g~~~~~~~~~~~k~v~iAl~EI~~gki~~~i   57 (57)
T PF01192_consen    2 DLLEKVDNRYELVILAAKRARQLSEGAPPLVEEDNEMKPVSIALEEIAEGKIKIEI   57 (57)
T ss_dssp             HHHHSSSSHHHHHHHHHHHHHHHHTTSTTSSSSSSSSSSSHHHHHHHHTTSSCEEE
T ss_pred             hhhhccCCHhHHHHHHHHHHHHHHcCcccccccccCCCcHHHHHHHHHcCCCCCcC
Confidence            34567789999999999999999999999998876669999999999999999986

7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. A component of 14 to 18 kDa shared by all three forms of eukaryotic RNA polymerases and which has been sequenced in budding yeast (gene RPB6 or RPO26), in Schizosaccharomyces pombe (Fission yeast) (gene rpb6 or rpo15), in human and in African swine fever virus (ASFV) is evolutionary related to the archaebacterial subunit K (gene rpoK). The archaebacterial protein is colinear with the C-terminal part of the eukaryotic subunit. The structures of the omega subunit and RBP6, and the structures of the omega/beta' and RPB6/RPB1 interfaces, suggest a molecular mechanism for the function of omega and RPB6 in promoting RNAP assembly and/or stability. The conserved regions of omega and RPB6 form a compact structural domain that interacts simultaneously with conserved regions of the largest RNAP subunit and with the C-terminal tail following a conserved region of the largest RNAP subunit. The second half of the conserved region of omega and RPB6 forms an arc that projects away from the remainder of the structural domain and wraps over and around the C-terminal tail of the largest RNAP subunit, clamping it in a crevice, and threading the C-terminal tail of the largest RNAP subunit through the narrow gap between omega and RPB6 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_R 2Y0S_I 3HKZ_U 2PMZ_K 3M3Y_F 3HOX_F 3GTJ_F 4A3K_F 2VUM_F 3S14_F ....

>PRK00392 rpoZ DNA-directed RNA polymerase subunit omega; Reviewed

Probab=99.55  E-value=1e-14  Score=90.21  Aligned_cols=49  Identities=29%  Similarity=0.362  Sum_probs=45.6

Q ss_pred             cHHHHHHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCCCeEEE
Q psy548           14 KRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIR   63 (84)
Q Consensus        14 trYelari~g~RArQL~~GA~plV~~~~~~kp~~IAl~Ei~~gkI~~~i~   63 (84)
                      |||.|+.++|+||+||+.|+++.++.. +.||+++|++||++|+|.+...
T Consensus        15 ~ry~Lv~~aakRArql~~~~~~~~~~~-~~K~~~~Al~EI~~gki~~~~~   63 (69)
T PRK00392         15 NRYELVLLAAKRARQLRAGAKPPVDKS-SDKPVVIALREIAEGKVTYEIL   63 (69)
T ss_pred             CHHHHHHHHHHHHHHHHcCCCCCCCCc-CCChHHHHHHHHHcCCCceecc
Confidence            899999999999999999999997765 6899999999999999999864

>TIGR00690 rpoZ DNA-directed RNA polymerase, omega subunit

Probab=99.55  E-value=1e-14  Score=89.13  Aligned_cols=46  Identities=28%  Similarity=0.366  Sum_probs=39.7

Q ss_pred             ccHHHHHHHHHHHHHHHhcCC-CceeeCCCCCChHHHHHHHHHcCCCC
Q psy548           13 IKRYERARVLGTRALQIAMCA-PVMVELEGETDPLQIAMKELKARKIP   59 (84)
Q Consensus        13 ltrYelari~g~RArQL~~GA-~plV~~~~~~kp~~IAl~Ei~~gkI~   59 (84)
                      =|||.||.++++|||||+.|+ +++++.. ++||+++|++||++|+|.
T Consensus        13 ~srY~Lv~~aakRArqL~~~~~~~~~~~~-~~Kp~~iAl~EIa~gkvs   59 (59)
T TIGR00690        13 GSRYDLVLVAARRARQLQLKGTDPIVPEE-NDKPTVIALREIAAGLVS   59 (59)
T ss_pred             CCHhHHHHHHHHHHHHHHhCCCCCccCcc-cCchHHHHHHHHHcCCCC
Confidence            389999999999999999766 5555554 699999999999999974

The trusted cutoff excludes archaeal homologs but captures some organellar sequences.

>PF05320 Pox_RNA_Pol_19: Poxvirus DNA-directed RNA polymerase 19 kDa subunit; InterPro: IPR007984 DNA-directed RNA polymerases 2

Probab=83.77  E-value=2.5  Score=30.98  Aligned_cols=56  Identities=18%  Similarity=0.239  Sum_probs=46.4

Q ss_pred             cCCCccHHHHHHHHHHHHHHHhcCCCceeeCC--C--CCChHHHHHHHHHcCCCCeEEEE
Q psy548            9 ITIVIKRYERARVLGTRALQIAMCAPVMVELE--G--ETDPLQIAMKELKARKIPIIIRR   64 (84)
Q Consensus         9 t~~~ltrYelari~g~RArQL~~GA~plV~~~--~--~~kp~~IAl~Ei~~gkI~~~i~R   64 (84)
                      -..+++=||+.=++|.==.-|+-|--|||.--  .  ..+-+.+-++||.+|.-|++|-+
T Consensus        76 YTRRiSLfEiTGIiaESyNLLqRGRlPLv~dlsdeT~k~n~L~vvi~EIeEg~CPIVIeK  135 (167)
T PF05320_consen   76 YTRRISLFEITGIIAESYNLLQRGRLPLVSDLSDETLKDNILHVVIKEIEEGTCPIVIEK  135 (167)
T ss_pred             HHhhhhHHHHHHHHHHHHHHHHccccccccccchHHHHHhHHHHHHHHHhcCCCcEEEee
Confidence            34567889999999999999999999999632  1  24567899999999999999986

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. The poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses the transcription of DNA into RNA. It consists of at least eight subunits, this is the 19 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	84
1qkl_A	127	Hrpabc14.4, Essential Subunit Of Human Rna Polymera		6e-32
3h0g_F	142	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		5e-26
1i3q_F	155	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		2e-25
3j0k_F	84	Orientation Of Rna Polymerase Ii Within The Human V		7e-25
2y0s_I	95	Crystal Structure Of Sulfolobus Shibatae Rna Polyme		6e-08
2waq_K	95	The Complete Structure Of The Archaeal 13-Subunit D		2e-07
2pmz_K	95	Archaeal Rna Polymerase From Sulfolobus Solfataricu		2e-07

>pdb|1QKL|A Chain A, Hrpabc14.4, Essential Subunit Of Human Rna Polymerases I, Ii And Iii Length = 127

Iteration: 1
 Score =  132 bits (331), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 65/76 (85%), Positives = 68/76 (89%)
Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
           I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLP
Sbjct: 52  ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLP 111
Query: 68  DNSYEDWGIDELKIID 83
           D SYEDWG+DEL I D
Sbjct: 112 DGSYEDWGVDELIITD 127

>pdb|3H0G|F Chain F, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 142

Iteration: 1
 Score =  112 bits (280), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 50/72 (69%), Positives = 61/72 (84%)
Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
             T  + +YERAR+LGTRALQI+M APV+V+LEGETDPLQIAMKEL  +KIP+++RRYLP
Sbjct: 70  TTTPYMTKYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRYLP 129
Query: 68  DNSYEDWGIDEL 79
           D SYEDW + EL
Sbjct: 130 DGSYEDWSVAEL 141

>pdb|1I3Q|F Chain F, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 155

Iteration: 1
 Score =  110 bits (275), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 51/75 (68%), Positives = 64/75 (85%), Gaps = 1/75 (1%)
Query: 9   ITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPD 68
            T  + +YERAR+LGTRALQI+M APV V+LEGETDPL+IAMKEL  +KIP++IRRYLPD
Sbjct: 81  TTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPD 140
Query: 69  NSYEDWGIDELKIID 83
            S+EDW ++EL I+D
Sbjct: 141 GSFEDWSVEEL-IVD 154

>pdb|3J0K|F Chain F, Orientation Of Rna Polymerase Ii Within The Human Vp16-Mediator-Pol Ii-Tfiif Assembly Length = 84

Iteration: 1
 Score =  108 bits (270), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 51/74 (68%), Positives = 64/74 (86%), Gaps = 1/74 (1%)
Query: 10 TIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDN 69
          T  + +YERAR+LGTRALQI+M APV V+LEGETDPL+IAMKEL  +KIP++IRRYLPD 
Sbjct: 11 TPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDG 70
Query: 70 SYEDWGIDELKIID 83
          S+EDW ++EL I+D
Sbjct: 71 SFEDWSVEEL-IVD 83

>pdb|2Y0S|I Chain I, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In P21 Space Group Length = 95

Iteration: 1
 Score = 52.4 bits (124), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 27/58 (46%), Positives = 38/58 (65%), Gaps = 2/58 (3%)
Query: 13 IKRYERARVLGTRALQIAMCAPVMVELEG--ETDPLQIAMKELKARKIPIIIRRYLPD 68
          + RYE ARV+  RALQ+AM AP ++++     TD + IA +E K   +PI IRR LP+
Sbjct: 27 LTRYEIARVISARALQLAMGAPALIDINNISSTDVISIAEEEFKRGVLPITIRRRLPN 84

>pdb|2WAQ|K Chain K, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 95

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/58 (44%), Positives = 38/58 (65%), Gaps = 2/58 (3%)
Query: 13 IKRYERARVLGTRALQIAMCAPVMVELEG--ETDPLQIAMKELKARKIPIIIRRYLPD 68
          + RYE ARV+  RALQ+AM AP ++++     TD + IA +E +   +PI IRR LP+
Sbjct: 27 LTRYEIARVISARALQLAMGAPALIDINNLSSTDVISIAEEEFRRGVLPITIRRRLPN 84

>pdb|2PMZ|K Chain K, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 95

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/58 (44%), Positives = 38/58 (65%), Gaps = 2/58 (3%)
Query: 13 IKRYERARVLGTRALQIAMCAPVMVELEG--ETDPLQIAMKELKARKIPIIIRRYLPD 68
          + RYE ARV+  RALQ+AM AP ++++     TD + IA +E +   +PI IRR LP+
Sbjct: 27 LTRYEIARVISARALQLAMGAPALIDINNLSSTDVISIAEEEFRRGVLPITIRRRLPN 84
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	84
1qkl_A	127	RPB6, DNA-directed RNA polymerase II 14.4 KD polyp	4e-30
1twf_F	155	ABC23, DNA-directed RNA polymerases I, II, and III	9e-30
3h0g_F	142	DNA-directed RNA polymerases I, II, and III subuni	7e-29
4ayb_K	95	DNA-directed RNA polymerase; transferase, multi-su	3e-27

>1qkl_A RPB6, DNA-directed RNA polymerase II 14.4 KD polypeptide; transcription; NMR {Homo sapiens} SCOP: a.143.1.2 Length = 127

 Score =  102 bits (255), Expect = 4e-30
 Identities = 63/69 (91%), Positives = 65/69 (94%)

Query: 15  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 74
           +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct: 59  KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 118

Query: 75  GIDELKIID 83
           G+DEL I D
Sbjct: 119 GVDELIITD 127

>1twf_F ABC23, DNA-directed RNA polymerases I, II, and III 23 KD polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: a.143.1.2 PDB: 1i3q_F 1i6h_F 1k83_F* 1nik_F 1nt9_F 1pqv_F 1r5u_F 1r9s_F* 1r9t_F* 1sfo_F* 1twa_F* 1twc_F* 1i50_F* 1twg_F* 1twh_F* 1wcm_F 1y1v_F 1y1w_F 1y1y_F 1y77_F* ... Length = 155

 Score =  102 bits (254), Expect = 9e-30
 Identities = 48/67 (71%), Positives = 60/67 (89%)

Query: 15  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 74
           +YERAR+LGTRALQI+M APV V+LEGETDPL+IAMKEL  +KIP++IRRYLPD S+EDW
Sbjct: 87  KYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDW 146

Query: 75  GIDELKI 81
            ++EL +
Sbjct: 147 SVEELIV 153

>3h0g_F DNA-directed RNA polymerases I, II, and III subunit rpabc2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 142

 Score = 99.4 bits (247), Expect = 7e-29
 Identities = 49/65 (75%), Positives = 59/65 (90%)

Query: 15  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 74
           +YERAR+LGTRALQI+M APV+V+LEGETDPLQIAMKEL  +KIP+++RRYLPD SYEDW
Sbjct: 77  KYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRYLPDGSYEDW 136

Query: 75  GIDEL 79
            + EL
Sbjct: 137 SVAEL 141

>4ayb_K DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_I 4b1o_K 4b1p_I 2waq_K 2wb1_I 2pmz_K 3hkz_K Length = 95

 Score = 94.1 bits (234), Expect = 3e-27
 Identities = 27/66 (40%), Positives = 39/66 (59%), Gaps = 2/66 (3%)

Query: 15 RYERARVLGTRALQIAMCAPVMVELE--GETDPLQIAMKELKARKIPIIIRRYLPDNSYE 72
          RYE ARV+  RALQ+AM AP ++++     TD + IA +E K   +PI IRR LP+    
Sbjct: 29 RYEIARVISARALQLAMGAPALIDINNISSTDVISIAEEEFKRGVLPITIRRRLPNGKII 88

Query: 73 DWGIDE 78
             + +
Sbjct: 89 LLSLRK 94

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	84
1qkl_A	127	RPB6, DNA-directed RNA polymerase II 14.4 KD polyp	100.0
1twf_F	155	ABC23, DNA-directed RNA polymerases I, II, and III	100.0
3h0g_F	142	DNA-directed RNA polymerases I, II, and III subuni	100.0
4ayb_K	95	DNA-directed RNA polymerase; transferase, multi-su	99.97
3lu0_E	91	DNA-directed RNA polymerase subunit omega; E. coli	99.56
2a6h_E	99	RNA polymerase omega chain; RNA polymerase holoenz	99.49

>1qkl_A RPB6, DNA-directed RNA polymerase II 14.4 KD polypeptide; transcription; NMR {Homo sapiens} SCOP: a.143.1.2

Probab=100.00  E-value=1.9e-37  Score=214.23  Aligned_cols=82  Identities=79%  Similarity=1.176  Sum_probs=79.1

Q ss_pred             CCCCCcccCCCccHHHHHHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCCCeEEEEecCCCcEEEeeccccce
Q psy548            2 VFSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKI   81 (84)
Q Consensus         2 ~~~~~r~t~~~ltrYelari~g~RArQL~~GA~plV~~~~~~kp~~IAl~Ei~~gkI~~~i~R~~p~~~~e~~~l~el~~   81 (84)
                      +|.++|+|+|||||||+||++|+||+||++||+|||+.++.+||++||++||++|+||++|+|++|||+||+|+++||.+
T Consensus        46 ~~~~~r~t~p~lTRYElARIiG~RAlQLs~GAppLVd~e~~~dPl~IAl~ElaeGkIpi~VrR~lPdg~yEd~~~~eL~i  125 (127)
T 1qkl_A           46 QANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELII  125 (127)
T ss_dssp             TTCCCSSCCSSCCHHHHHHHHHHHHHHHHHSCCSSSCSSSSCSSSHHHHHHHHHTCCCEEEEEEETTTEEEEESSSSSCS
T ss_pred             CCccccccCCCcCHHHHHHHHHHHHHHHhcCCcceEcCCCCCCHHHHHHHHHHcCCCCeEEEEECCCCCEEEeehhheec
Confidence            68899999999999999999999999999999999999877899999999999999999999999999999999999998


Q ss_pred             ec
Q psy548           82 ID   83 (84)
Q Consensus        82 ~~   83 (84)
                      .|
T Consensus       126 ~~  127 (127)
T 1qkl_A          126 TD  127 (127)
T ss_dssp             CC
T ss_pred             cC
Confidence            65

>1twf_F ABC23, DNA-directed RNA polymerases I, II, and III 23 KD polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: a.143.1.2 PDB: 1i3q_F 1i6h_F 1k83_F* 1nik_F 1nt9_F 1pqv_F 1r5u_F 1r9s_F* 1r9t_F* 1sfo_F* 1twa_F* 1twc_F* 1i50_F* 1twg_F* 1twh_F* 1wcm_F 1y1v_F 1y1w_F 1y1y_F 1y77_F* ...

Probab=100.00  E-value=2.2e-36  Score=214.46  Aligned_cols=82  Identities=60%  Similarity=0.965  Sum_probs=79.1

Q ss_pred             CCCCCcccCCCccHHHHHHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCCCeEEEEecCCCcEEEeeccccce
Q psy548            2 VFSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKI   81 (84)
Q Consensus         2 ~~~~~r~t~~~ltrYelari~g~RArQL~~GA~plV~~~~~~kp~~IAl~Ei~~gkI~~~i~R~~p~~~~e~~~l~el~~   81 (84)
                      +|..+|+|++||||||+||++|+||+||++||+|||+.++.+||++||++||++|+||++|+|++|||+||+|+++||++
T Consensus        74 ~~~~~r~t~p~lTRYElARIiG~RAlQLsmGAppLVd~e~~~dPl~IAl~ElaeGkIPl~IrR~lPdG~yEd~~v~eL~~  153 (155)
T 1twf_F           74 IPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIV  153 (155)
T ss_dssp             CCSSSCCSCSBCCHHHHHHHHHHHHHHHHTTCCCSSCCSSCCSHHHHHHHHHHTTCCCEEEEEECTTSCEEEEETTTSBC
T ss_pred             CCcccccCCCCcCHHHHHHHHHHHHHHHhcCCCcEEecCCCCCHHHHHHHHHHcCCCCeEEEEECCCCCEEEeeHHHhcc
Confidence            68899999999999999999999999999999999999877899999999999999999999999999999999999998


Q ss_pred             ec
Q psy548           82 ID   83 (84)
Q Consensus        82 ~~   83 (84)
                      .|
T Consensus       154 ~~  155 (155)
T 1twf_F          154 DL  155 (155)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>3h0g_F DNA-directed RNA polymerases I, II, and III subunit rpabc2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=100.00  E-value=1.1e-36  Score=213.48  Aligned_cols=79  Identities=65%  Similarity=1.035  Sum_probs=76.8

Q ss_pred             CCCCCcccCCCccHHHHHHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCCCeEEEEecCCCcEEEeeccccc
Q psy548            2 VFSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELK   80 (84)
Q Consensus         2 ~~~~~r~t~~~ltrYelari~g~RArQL~~GA~plV~~~~~~kp~~IAl~Ei~~gkI~~~i~R~~p~~~~e~~~l~el~   80 (84)
                      +|.++|+|+|||||||+||++|+||+||++||||||+.++++||++||++||++|+|||+|+|++|||+||+|+++||.
T Consensus        64 ~~~~~R~T~pylTRYElARIiG~RAlQIsmGAp~LVd~~~~tdPl~IA~~EL~egkIPiiVrR~lPdgkyEdw~l~EL~  142 (142)
T 3h0g_F           64 VAKEDRTTTPYMTKYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRYLPDGSYEDWSVAELI  142 (142)
T ss_dssp             CCTTSCCSCSSCCHHHHHHHHHHHHHHHHTCCCCCSCCCSCCCTTHHHHHHHHTTCCCCEEECCCSSSCCCEEETTTCC
T ss_pred             CCcccccCCCccCHHHHHHHHHHHHHHHHCCCCceEcCCCCCCHHHHHHHHHHcCCCceEEEEECCCCCEEEeEHHHcC
Confidence            6899999999999999999999999999999999999987899999999999999999999999999999999999984

>4ayb_K DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_I 4b1o_K 4b1p_I 2waq_K 2wb1_I 2pmz_K 3hkz_K

Probab=99.97  E-value=1.2e-30  Score=172.84  Aligned_cols=68  Identities=40%  Similarity=0.618  Sum_probs=64.4

Q ss_pred             CCccHHHHHHHHHHHHHHHhcCCCceeeCC--CCCChHHHHHHHHHcCCCCeEEEEecCCCcEEEeeccc
Q psy548           11 IVIKRYERARVLGTRALQIAMCAPVMVELE--GETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDE   78 (84)
Q Consensus        11 ~~ltrYelari~g~RArQL~~GA~plV~~~--~~~kp~~IAl~Ei~~gkI~~~i~R~~p~~~~e~~~l~e   78 (84)
                      +.|||||+||++|.||+||++||+|+|+++  +..||+.||.+|+.+|+|||+|+|++|||+||+|+|+|
T Consensus        25 ~kLTKYEkaRIiG~RA~Qis~GA~~~I~~~~~~~~Dp~~IA~~EL~~~kiP~iIrR~lPnG~~E~~~l~e   94 (95)
T 4ayb_K           25 NKLTRYEIARVISARALQLAMGAPALIDINNISSTDVISIAEEEFKRGVLPITIRRRLPNGKIILLSLRK   94 (95)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHTCCCCSSCTTTSCSSCTHHHHHHHHHTTCCCEEEEEECTTSCEEEECCCC
T ss_pred             ccccHHHHHHHHHHHHHHHHCCCCceEeCCCCCCCCHHHHHHHHHHcCCCCEEEEEeCCCCCEEEEEecc
Confidence            449999999999999999999999999986  36899999999999999999999999999999999987

>3lu0_E DNA-directed RNA polymerase subunit omega; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_E*

Probab=99.56  E-value=1.1e-15  Score=99.96  Aligned_cols=53  Identities=23%  Similarity=0.227  Sum_probs=48.4

Q ss_pred             cHHHHHHHHHHHHHHHhc-CCCceeeCCCCCChHHHHHHHHHcCCCCeEEEEecC
Q psy548           14 KRYERARVLGTRALQIAM-CAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP   67 (84)
Q Consensus        14 trYelari~g~RArQL~~-GA~plV~~~~~~kp~~IAl~Ei~~gkI~~~i~R~~p   67 (84)
                      |||+|+.++++|||||+. |++|+|+.+ ++||++||++||++|+|.+.+....+
T Consensus        15 nRY~LV~~AAKRARQL~~~G~~plv~~~-~~Kpv~iALrEIa~GkV~~~~l~~~~   68 (91)
T 3lu0_E           15 NRFDLVLVAARRARQMQVGGKDPLVPEE-NDKTTVIALREIEEGLINNQILDVRE   68 (91)
T ss_dssp             SHHHHHHHHHHHHHHHHHTCCCSCCSSS-CCCSSCCSHHHHHSSSCEEESSSSCC
T ss_pred             CHhHHHHHHHHHHHHHHhcCCCCccCCC-CCChHHHHHHHHHcCCCceeeCChhh
Confidence            899999999999999998 999999987 79999999999999999998765443

>2a6h_E RNA polymerase omega chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.143.1.1 PDB: 1smy_E* 1zyr_E* 1iw7_E* 2a69_E* 2a6e_E 2a68_E* 2be5_E* 2cw0_E 3dxj_E* 2o5i_E 2o5j_E* 2ppb_E* 3aoh_E* 3aoi_E* 3eql_E* 1ynj_K* 1i6v_E* 1l9u_E 1l9z_E 1hqm_E* ...

Probab=99.49  E-value=3.3e-14  Score=93.90  Aligned_cols=48  Identities=23%  Similarity=0.237  Sum_probs=42.2

Q ss_pred             cHHHHHHHHHHHHHHHhcCC--CceeeC---CCCC---------ChHHHHHHHHHcCCCCeE
Q psy548           14 KRYERARVLGTRALQIAMCA--PVMVEL---EGET---------DPLQIAMKELKARKIPII   61 (84)
Q Consensus        14 trYelari~g~RArQL~~GA--~plV~~---~~~~---------kp~~IAl~Ei~~gkI~~~   61 (84)
                      |||+||.++|+||+||+.|+  .|+++.   ..+.         ||++||++||++|+|.+.
T Consensus        15 nrY~LV~~aAKRARQI~~g~~k~~lv~~l~~~~~~~l~e~~~~~Kpv~iAL~EI~~Gki~~~   76 (99)
T 2a6h_E           15 SKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAETWAMKELLTGRLVFG   76 (99)
T ss_dssp             SHHHHHHHHHHHHHHHHHTCTTCCSCCSSSCCCCSSSSGGGTSSCSHHHHHHHHTTTCCEEE
T ss_pred             CHhHHHHHHHHHHHHHHcCCccccchhhhhhcccccccccccCCCHHHHHHHHHHcCCeeec
Confidence            89999999999999999999  999872   1133         999999999999999864

---

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	84
d1qkla_	127	a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId:	4e-34
d1twff_	84	a.143.1.2 (F:) RPB6 {Baker's yeast (Saccharomyces	2e-32

>d1qkla_ a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId: 9606]} Length = 127

class: All alpha proteins
fold: RPB6/omega subunit-like
superfamily: RPB6/omega subunit-like
family: RPB6
domain: RPB6
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  111 bits (279), Expect = 4e-34
 Identities = 65/76 (85%), Positives = 68/76 (89%)

Query: 8   IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
           I T  + +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLP
Sbjct: 52  ITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLP 111

Query: 68  DNSYEDWGIDELKIID 83
           D SYEDWG+DEL I D
Sbjct: 112 DGSYEDWGVDELIITD 127

>d1twff_ a.143.1.2 (F:) RPB6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 84

class: All alpha proteins
fold: RPB6/omega subunit-like
superfamily: RPB6/omega subunit-like
family: RPB6
domain: RPB6
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  105 bits (264), Expect = 2e-32
 Identities = 49/74 (66%), Positives = 62/74 (83%)

Query: 8  IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67
            T  + +YERAR+LGTRALQI+M APV V+LEGETDPL+IAMKEL  +KIP++IRRYLP
Sbjct: 9  ATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLP 68

Query: 68 DNSYEDWGIDELKI 81
          D S+EDW ++EL +
Sbjct: 69 DGSFEDWSVEELIV 82

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	84
d1twff_	84	RPB6 {Baker's yeast (Saccharomyces cerevisiae) [Ta	100.0
d1qkla_	127	RPB6 {Human (Homo sapiens) [TaxId: 9606]}	100.0
d1smye_	95	RNA polymerase omega subunit {Thermus thermophilus	97.9

>d1twff_ a.143.1.2 (F:) RPB6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: RPB6/omega subunit-like
superfamily: RPB6/omega subunit-like
family: RPB6
domain: RPB6
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=8.2e-36  Score=192.28  Aligned_cols=80  Identities=61%  Similarity=1.022  Sum_probs=77.7

Q ss_pred             CCCCCcccCCCccHHHHHHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCCCeEEEEecCCCcEEEeeccccce
Q psy548            2 VFSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKI   81 (84)
Q Consensus         2 ~~~~~r~t~~~ltrYelari~g~RArQL~~GA~plV~~~~~~kp~~IAl~Ei~~gkI~~~i~R~~p~~~~e~~~l~el~~   81 (84)
                      +|+++|+|+|+|||||.+|++|.||+||++||+|+|+.++.++|++||.+|+.+|++||+|+|++|||+||+|+++||.|
T Consensus         3 i~~~~~~T~p~LTkYE~ariiG~Ra~Ql~~Ga~p~I~~~~~~d~~~IA~~El~~~kiP~iIrR~lP~g~~E~w~l~dL~i   82 (84)
T d1twff_           3 IPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIV   82 (84)
T ss_dssp             CCSSSCCSCSBCCHHHHHHHHHHHHHHHHTTCCCSSCCSSCCSHHHHHHHHHHTTCCCEEEEEECTTSCEEEEETTTSBC
T ss_pred             cCCcCcccCccccHHHHHHHHHHHHHHHHcCCCceecCCCCCCHHHHHHHHHHcCCCCEEEEEECCCCCEEEEEHHHeee
Confidence            68999999999999999999999999999999999999878999999999999999999999999999999999999965

>d1qkla_ a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RPB6/omega subunit-like
superfamily: RPB6/omega subunit-like
family: RPB6
domain: RPB6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3.6e-35  Score=201.03  Aligned_cols=82  Identities=79%  Similarity=1.176  Sum_probs=79.4

Q ss_pred             CCCCCcccCCCccHHHHHHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCCCeEEEEecCCCcEEEeeccccce
Q psy548            2 VFSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKI   81 (84)
Q Consensus         2 ~~~~~r~t~~~ltrYelari~g~RArQL~~GA~plV~~~~~~kp~~IAl~Ei~~gkI~~~i~R~~p~~~~e~~~l~el~~   81 (84)
                      ++..+|+|+|+|||||++|++|.||+||++||+|+|+.++.++|+.||.+||.+|+|||+|+|++|||+||+|+|++|.|
T Consensus        46 ~~~~~~~T~p~lTkYE~arilG~Ra~Qi~~ga~~~i~~~~~~d~~~IA~~EL~~kkiPfiIrR~lp~g~~E~w~l~dL~i  125 (127)
T d1qkla_          46 QANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELII  125 (127)
T ss_dssp             TTCCCSSCCSSCCHHHHHHHHHHHHHHHHHSCCSSSCSSSSCSSSHHHHHHHHHTCCCEEEEEEETTTEEEEESSSSSCS
T ss_pred             ccCcccccCCcccHHHHHHHHHHHHHHHhcCCCceecCCCCCCHHHHHHHHHHcCCCCEEEEEECCCCCEEEEEhHheEe
Confidence            57789999999999999999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             ec
Q psy548           82 ID   83 (84)
Q Consensus        82 ~~   83 (84)
                      +|
T Consensus       126 ~~  127 (127)
T d1qkla_         126 TD  127 (127)
T ss_dssp             CC
T ss_pred             cC
Confidence            86

>d1smye_ a.143.1.1 (E:) RNA polymerase omega subunit {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: RPB6/omega subunit-like
superfamily: RPB6/omega subunit-like
family: RNA polymerase omega subunit
domain: RNA polymerase omega subunit
species: Thermus thermophilus [TaxId: 274]

Probab=97.90  E-value=8.6e-06  Score=51.71  Aligned_cols=51  Identities=25%  Similarity=0.336  Sum_probs=39.4

Q ss_pred             cHHHHHHHHHHHHHH-HhcCCC-ceeeCCC----C--------CChHHHHHHHHHcCCCCeEEEEec
Q psy548           14 KRYERARVLGTRALQ-IAMCAP-VMVELEG----E--------TDPLQIAMKELKARKIPIIIRRYL   66 (84)
Q Consensus        14 trYelari~g~RArQ-L~~GA~-plV~~~~----~--------~kp~~IAl~Ei~~gkI~~~i~R~~   66 (84)
                      |||-|..++|+||.| |-.|.+ .+++.+.    .        -+++..|++|+.-|+  +.+---+
T Consensus        14 SkYRLsvVvakRA~QlLr~g~~ntvL~pde~p~~~tleg~~~dpN~vt~AMkEL~tGr--l~~GenL   78 (95)
T d1smye_          14 SKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAETWAMKELLTGR--LVFGENL   78 (95)
T ss_dssp             SHHHHHHHHHHHHHHHHHTCTTCCSCCSSSCCCCSSSSGGGTSSCSHHHHHHHHTTTC--EEEESSS
T ss_pred             cceeeehhhHHHHHHHHHcCCCccccChhhhhhhhcccccCCCCcHHHHHHHHHHhCc--eeecCCC
Confidence            799999999999999 788998 5555431    1        268999999999999  4443333