Psyllid ID: psy8360

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150--
Protein Sequence
MVSQCSNTDLCCTYGSWLGWAFTLLLDENAPTPSKANKWMGDLNLILGIKGERALVLILNHYMKVKSKNQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKIIDR
Secondary Structure (PSIPRED)
cccccccccEEEEccccccHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHcccccEEEEEEcccccEEEEEccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccHHHHHHHHHHHHccccccccccccHcccccHHccccccccccEEEcccccccccccccccccccccHHcHHHHHHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHHccccEEEEEEccccccccccccEEEEEcc
Coil and Loop (DISEMBL)
mvsqcsntdlcctygswLGWAFTLLldenaptpskankwMGDLNLILGIKGERALVLILNHYMKVksknqiknnnklNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIrrylpdnsyedwgidelkiidr
Flexible Loop (DISEMBL)
MVSQCSNTDLCCTYGSWLGWAFTLLLDENAPTPSKANKWMGDLNLILGIKGERALVLILNHYMKvksknqiknnnklnikQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKElkarkipiiirrylpdnsyedwgidelkiidr
Low Complexity Region (SEG)
MVSQCSNTDLCCTYGSWLGWAFTLLLDENAPTPSKANKWMGDLNLILGIKGERALVLILNHYMKVksknqiknnnklnikqiRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKIIDR
Disordered region (IsUnstruct)
******NTDLCCTYGSWLGWAFTLLLDENAPTPSKANKWMGDLNLILGIKGERALVLILNHYMKVKSKNQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKII**
Disordered Region (DISOPRED)
*****SN*DLCCTYGSWLGWAFTLLLDE****************************************************QIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKIID*
Disordered Region (DISEMBL)
********DLCCTYGSWLGWAFTLLLDENAPTPSKANKWMGDLNLILGIKGERALVLILNHYMKVKSKNQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKIIDR
Disordered Region (DISPRO)
****CSNTDLCCTYGSWLGWAFTLLLDENA************************LV****************NNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKIIDR
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVSQCSNTDLCCTYGSWLGWAFTLLLDENAPTPSKANKWMGDLNLILGIKGERALVLILNHYMKVKSKNQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKIIDR
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	152	2.2.26 [Sep-21-2011]
Q32PE0	127	DNA-directed RNA polymera	yes	N/A	0.453	0.543	0.913	2e-30
Q5R592	127	DNA-directed RNA polymera	yes	N/A	0.453	0.543	0.913	2e-30
P61218	127	DNA-directed RNA polymera	yes	N/A	0.453	0.543	0.913	2e-30
P61217	127	DNA-directed RNA polymera	yes	N/A	0.453	0.543	0.913	2e-30
O88828	127	DNA-directed RNA polymera	yes	N/A	0.453	0.543	0.913	3e-30
P61219	127	DNA-directed RNA polymera	yes	N/A	0.453	0.543	0.913	3e-30
Q24320	131	DNA-directed RNA polymera	yes	N/A	0.453	0.526	0.855	1e-29
Q17684	137	Probable DNA-directed RNA	yes	N/A	0.453	0.503	0.797	1e-26
A8WSV7	138	Probable DNA-directed RNA	N/A	N/A	0.453	0.5	0.782	3e-26
P36595	142	DNA-directed RNA polymera	yes	N/A	0.638	0.683	0.544	6e-25

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

 Score =  131 bits (329), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 63/69 (91%), Positives = 65/69 (94%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct: 59  KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 118

Query: 143 GIDELKIID 151
           G+DEL I D
Sbjct: 119 GVDELIITD 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|Q5R592|RPAB2_PONAB DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Pongo abelii GN=POLR2F PE=2 SV=1

 Score =  131 bits (329), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 63/69 (91%), Positives = 65/69 (94%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct: 59  KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 118

Query: 143 GIDELKIID 151
           G+DEL I D
Sbjct: 119 GVDELIITD 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 =  131 bits (329), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 63/69 (91%), Positives = 65/69 (94%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct: 59  KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 118

Query: 143 GIDELKIID 151
           G+DEL I D
Sbjct: 119 GVDELIITD 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 =  131 bits (329), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 63/69 (91%), Positives = 65/69 (94%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct: 59  KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 118

Query: 143 GIDELKIID 151
           G+DEL I D
Sbjct: 119 GVDELIITD 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|O88828|RPAB2_RAT DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Rattus norvegicus GN=Polr2f PE=1 SV=1

 Score =  130 bits (328), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 63/69 (91%), Positives = 65/69 (94%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct: 59  KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 118

Query: 143 GIDELKIID 151
           G+DEL I D
Sbjct: 119 GVDELIISD 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 =  130 bits (328), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 63/69 (91%), Positives = 65/69 (94%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct: 59  KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 118

Query: 143 GIDELKIID 151
           G+DEL I D
Sbjct: 119 GVDELIISD 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 =  128 bits (322), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 59/69 (85%), Positives = 66/69 (95%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERARVLGTRALQIAMCAP+MVEL+GETDPLQIAMKELK +KIPIIIRRYLPD+SYEDW
Sbjct: 62  KYERARVLGTRALQIAMCAPIMVELDGETDPLQIAMKELKQKKIPIIIRRYLPDHSYEDW 121

Query: 143 GIDELKIID 151
            IDEL ++D
Sbjct: 122 SIDELIMVD 130

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 =  118 bits (295), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 55/69 (79%), Positives = 62/69 (89%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERARVLGTRALQIAM APVMVELEGETDPL+IA KELK R+IPII+RRYLPD SYEDW
Sbjct: 68  KYERARVLGTRALQIAMGAPVMVELEGETDPLEIARKELKQRRIPIIVRRYLPDGSYEDW 127

Query: 143 GIDELKIID 151
             D+L++ D
Sbjct: 128 PTDQLQLAD 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 =  117 bits (292), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 54/69 (78%), Positives = 62/69 (89%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERARVLGTRALQIAM APVMVELEGETDPL+IA KELK R++PIIIRRYLPD SYEDW
Sbjct: 69  KYERARVLGTRALQIAMGAPVMVELEGETDPLEIARKELKQRRVPIIIRRYLPDGSYEDW 128

Query: 143 GIDELKIID 151
             ++L++ D
Sbjct: 129 PTEQLQLAD 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 (281), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 55/101 (54%), Positives = 69/101 (68%), Gaps = 4/101 (3%)

Query: 51  GERALVLILNHYMKVKS----KNQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVE 106
           GE +  +I       K+    K   K +        +YERAR+LGTRALQI+M APV+V+
Sbjct: 41  GEPSTTVITEDVASSKTAQSGKAVAKEDRTTTPYMTKYERARILGTRALQISMNAPVLVD 100

Query: 107 LEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDEL 147
           LEGETDPLQIAMKEL  +KIP+++RRYLPD SYEDW + EL
Sbjct: 101 LEGETDPLQIAMKELAQKKIPLLVRRYLPDGSYEDWSVAEL 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	152
350536293	132	uncharacterized protein LOC100165288 [Ac	0.572	0.659	0.761	1e-31
307168238	129	DNA-directed RNA polymerases I, II, and	0.460	0.542	0.942	1e-30
66524012	130	PREDICTED: DNA-directed RNA polymerases	0.460	0.538	0.942	1e-30
332027163	130	DNA-directed RNA polymerases I, II, and	0.460	0.538	0.942	1e-30
307201767	130	DNA-directed RNA polymerases I, II, and	0.460	0.538	0.928	2e-30
322784320	149	hypothetical protein SINV_10192 [Solenop	0.467	0.476	0.943	2e-30
383854730	130	PREDICTED: DNA-directed RNA polymerases	0.460	0.538	0.928	2e-30
307197591	109	DNA-directed RNA polymerases I, II, and	0.453	0.633	0.942	2e-30
241558215	129	RNA polymerase subunit K, putative [Ixod	0.559	0.658	0.793	3e-30
242007913	132	DNA-directed RNA polymerases I, II, and	0.592	0.681	0.725	3e-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 =  141 bits (355), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 67/88 (76%), Positives = 80/88 (90%), Gaps = 1/88 (1%)

Query: 66  KSKNQIKNNNKLNIKQI-RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKAR 124
           ++++Q++ + ++  K + +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK R
Sbjct: 45  EAQSQVQKSKRITTKYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKKR 104

Query: 125 KIPIIIRRYLPDNSYEDWGIDELKIIDR 152
           KIPIIIRRYLPDNSYEDWGIDEL I+D+
Sbjct: 105 KIPIIIRRYLPDNSYEDWGIDELIIVDQ 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 =  137 bits (346), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 66/70 (94%), Positives = 67/70 (95%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK RKIPIIIRRYLPDNSYEDW
Sbjct: 60  KYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKQRKIPIIIRRYLPDNSYEDW 119

Query: 143 GIDELKIIDR 152
           GIDEL IID 
Sbjct: 120 GIDELIIIDH 129

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

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 =  137 bits (345), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 66/70 (94%), Positives = 67/70 (95%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK RKIPIIIRRYLPDNSYEDW
Sbjct: 61  KYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKQRKIPIIIRRYLPDNSYEDW 120

Query: 143 GIDELKIIDR 152
           GIDEL IID 
Sbjct: 121 GIDELIIIDH 130

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

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 =  137 bits (345), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 66/70 (94%), Positives = 67/70 (95%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK RKIPIIIRRYLPDNSYEDW
Sbjct: 61  KYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKQRKIPIIIRRYLPDNSYEDW 120

Query: 143 GIDELKIIDR 152
           GIDEL IID 
Sbjct: 121 GIDELIIIDH 130

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

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 (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 65/70 (92%), Positives = 67/70 (95%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK RKIPI+IRRYLPDNSYEDW
Sbjct: 61  KYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKQRKIPIVIRRYLPDNSYEDW 120

Query: 143 GIDELKIIDR 152
           GIDEL IID 
Sbjct: 121 GIDELIIIDH 130

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 =  137 bits (344), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 67/71 (94%), Positives = 67/71 (94%)

Query: 82  IRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYED 141
           I YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK RKIPIIIRRYLPDNSYED
Sbjct: 79  ILYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKQRKIPIIIRRYLPDNSYED 138

Query: 142 WGIDELKIIDR 152
           WGIDEL IID 
Sbjct: 139 WGIDELIIIDH 149

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

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 (344), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 65/70 (92%), Positives = 67/70 (95%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK RKIPI+IRRYLPDNSYEDW
Sbjct: 61  KYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKQRKIPIVIRRYLPDNSYEDW 120

Query: 143 GIDELKIIDR 152
           GIDEL IID 
Sbjct: 121 GIDELIIIDH 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 =  136 bits (343), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 65/69 (94%), Positives = 67/69 (97%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK RKIPI+IRRYLPDNSYEDW
Sbjct: 40  KYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKQRKIPIVIRRYLPDNSYEDW 99

Query: 143 GIDELKIID 151
           GIDEL IID
Sbjct: 100 GIDELIIID 108

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 =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 69/87 (79%), Positives = 72/87 (82%), Gaps = 2/87 (2%)

Query: 67  SKNQIKNNNK--LNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKAR 124
           S  Q + N K    +   +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKAR
Sbjct: 43  SDGQPQQNQKRITTMYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKAR 102

Query: 125 KIPIIIRRYLPDNSYEDWGIDELKIID 151
           KIPIIIRRYLPD SYEDWGIDEL I D
Sbjct: 103 KIPIIIRRYLPDGSYEDWGIDELIITD 129

Source: Ixodes scapularis

Species: Ixodes scapularis

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242007913|ref|XP_002424760.1| DNA-directed RNA polymerases I, II, and III 14.4 kDa polypeptide, putative [Pediculus humanus corporis] gi|212508274|gb|EEB12022.1| DNA-directed RNA polymerases I, II, and III 14.4 kDa polypeptide, putative [Pediculus humanus corporis]

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 66/91 (72%), Positives = 77/91 (84%), Gaps = 1/91 (1%)

Query: 63  MKVKSKNQIKNNNKLNIKQI-RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKEL 121
           + +++K  +  + ++  K + +YERARVLGTRALQIAM APVMVELEGETDPLQIAMKEL
Sbjct: 42  ISIEAKGSVAKSKRITTKYMTKYERARVLGTRALQIAMGAPVMVELEGETDPLQIAMKEL 101

Query: 122 KARKIPIIIRRYLPDNSYEDWGIDELKIIDR 152
           K RKIPIIIRRYLPD+SYEDWGIDEL IID 
Sbjct: 102 KQRKIPIIIRRYLPDHSYEDWGIDELIIIDH 132

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

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	152
UNIPROTKB|F1ND65	135	POLR2F "Uncharacterized protei	0.453	0.511	0.913	5.6e-29
UNIPROTKB|Q9PT88	127	RPB6 "RNA polymerase common su	0.453	0.543	0.913	5.6e-29
UNIPROTKB|F2Z4C9	127	POLR2F "DNA-directed RNA polym	0.453	0.543	0.913	5.6e-29
UNIPROTKB|Q32PE0	127	POLR2F "DNA-directed RNA polym	0.453	0.543	0.913	5.6e-29
UNIPROTKB|E2RPD9	127	POLR2F "Uncharacterized protei	0.453	0.543	0.913	5.6e-29
UNIPROTKB|P61218	127	POLR2F "DNA-directed RNA polym	0.453	0.543	0.913	5.6e-29
UNIPROTKB|P61217	127	POLR2F "DNA-directed RNA polym	0.453	0.543	0.913	5.6e-29
UNIPROTKB|Q5R592	127	POLR2F "DNA-directed RNA polym	0.453	0.543	0.913	5.6e-29
ZFIN|ZDB-GENE-040718-279	127	polr2f "polymerase (RNA) II (D	0.453	0.543	0.913	5.6e-29
MGI|MGI:1349393	127	Polr2f "polymerase (RNA) II (D	0.453	0.543	0.913	7.1e-29

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

 Score = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 63/69 (91%), Positives = 65/69 (94%)

Query:    83 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
             +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct:    67 KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 126

Query:   143 GIDELKIID 151
             G+DEL I D
Sbjct:   127 GVDELIITD 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 = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 63/69 (91%), Positives = 65/69 (94%)

Query:    83 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
             +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct:    59 KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 118

Query:   143 GIDELKIID 151
             G+DEL I D
Sbjct:   119 GVDELIITD 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 = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 63/69 (91%), Positives = 65/69 (94%)

Query:    83 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
             +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct:    59 KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 118

Query:   143 GIDELKIID 151
             G+DEL I D
Sbjct:   119 GVDELIITD 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 = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 63/69 (91%), Positives = 65/69 (94%)

Query:    83 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
             +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct:    59 KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 118

Query:   143 GIDELKIID 151
             G+DEL I D
Sbjct:   119 GVDELIITD 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 = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 63/69 (91%), Positives = 65/69 (94%)

Query:    83 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
             +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct:    59 KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 118

Query:   143 GIDELKIID 151
             G+DEL I D
Sbjct:   119 GVDELIITD 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 = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 63/69 (91%), Positives = 65/69 (94%)

Query:    83 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
             +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct:    59 KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 118

Query:   143 GIDELKIID 151
             G+DEL I D
Sbjct:   119 GVDELIITD 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 = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 63/69 (91%), Positives = 65/69 (94%)

Query:    83 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
             +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct:    59 KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 118

Query:   143 GIDELKIID 151
             G+DEL I D
Sbjct:   119 GVDELIITD 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 = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 63/69 (91%), Positives = 65/69 (94%)

Query:    83 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
             +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct:    59 KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 118

Query:   143 GIDELKIID 151
             G+DEL I D
Sbjct:   119 GVDELIITD 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 = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 63/69 (91%), Positives = 65/69 (94%)

Query:    83 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
             +YERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK+RKIPIIIRRYLPD SYEDW
Sbjct:    59 KYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKSRKIPIIIRRYLPDGSYEDW 118

Query:   143 GIDELKIID 151
             G DEL I D
Sbjct:   119 GCDELIITD 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 = 321 (118.1 bits), Expect = 7.1e-29, P = 7.1e-29
 Identities = 63/69 (91%), Positives = 65/69 (94%)

Query:    83 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
             +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct:    59 KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 118

Query:   143 GIDELKIID 151
             G+DEL I D
Sbjct:   119 GVDELIISD 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	0.5849	0.3486	0.8833	yes	N/A
P61217	RPAB2_CRIGR	No assigned EC number	0.9130	0.4539	0.5433	yes	N/A
Q8PW42	RPOK_METMA	2, ., 7, ., 7, ., 6	0.62	0.3289	0.6024	yes	N/A
P61219	RPAB2_MOUSE	No assigned EC number	0.9130	0.4539	0.5433	yes	N/A
O88828	RPAB2_RAT	No assigned EC number	0.9130	0.4539	0.5433	yes	N/A
Q32PE0	RPAB2_BOVIN	No assigned EC number	0.9130	0.4539	0.5433	yes	N/A
P61218	RPAB2_HUMAN	No assigned EC number	0.9130	0.4539	0.5433	yes	N/A
A2SSV2	RPOK_METLZ	2, ., 7, ., 7, ., 6	0.54	0.3223	0.7903	yes	N/A
Q5R592	RPAB2_PONAB	No assigned EC number	0.9130	0.4539	0.5433	yes	N/A
P36595	RPAB2_SCHPO	No assigned EC number	0.5445	0.6381	0.6830	yes	N/A
P20435	RPAB2_YEAST	No assigned EC number	0.7246	0.4473	0.4387	yes	N/A
Q24320	RPAB2_DROME	No assigned EC number	0.8550	0.4539	0.5267	yes	N/A
Q54FA8	RPAB2_DICDI	No assigned EC number	0.7462	0.4407	0.5037	yes	N/A
Q17684	RPAB2_CAEEL	No assigned EC number	0.7971	0.4539	0.5036	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

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	152
PLN00152	130	PLN00152, PLN00152, DNA-directed RNA polymerase; P	2e-41
PRK01099	62	PRK01099, rpoK, DNA-directed RNA polymerase subuni	9e-23
pfam01192	57	pfam01192, RNA_pol_Rpb6, RNA polymerase Rpb6	2e-13
COG1758	74	COG1758, RpoZ, DNA-directed RNA polymerase, subuni	6e-13

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

 Score =  134 bits (338), Expect = 2e-41
 Identities = 55/69 (79%), Positives = 62/69 (89%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERAR+LGTRALQI+M APVMVELEGETDPL+IAMKEL+ RKIP  IRRYLPD SYEDW
Sbjct: 62  KYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDW 121

Query: 143 GIDELKIID 151
           G+DEL + D
Sbjct: 122 GVDELIVED 130

Length = 130

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

 Score = 84.6 bits (210), Expect = 9e-23
 Identities = 28/54 (51%), Positives = 41/54 (75%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPD 136
           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 = 60.7 bits (148), Expect = 2e-13
 Identities = 21/48 (43%), Positives = 31/48 (64%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIII 130
           RYE AR++  RA Q++  AP +V+ E E  P+ IA++E+   KIP  I
Sbjct: 10  RYELARIIAKRAKQLSYGAPPLVDEESEIKPVVIALEEIADGKIPPEI 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 = 60.0 bits (146), Expect = 6e-13
 Identities = 24/59 (40%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELEGE-TDPLQIAMKELKARKIPIIIRRYLPDNSYE 140
           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	152
KOG3405|consensus	136		100.0
PLN00152	130	DNA-directed RNA polymerase; Provisional	100.0
PRK01099	62	rpoK DNA-directed RNA polymerase subunit K; Provis	99.92
COG1758	74	RpoZ DNA-directed RNA polymerase, subunit K/omega	99.72
PF01192	57	RNA_pol_Rpb6: RNA polymerase Rpb6 ; InterPro: IPR0	99.62
PRK00392	69	rpoZ DNA-directed RNA polymerase subunit omega; Re	99.26
TIGR00690	59	rpoZ DNA-directed RNA polymerase, omega subunit. T	99.19
PF05320	167	Pox_RNA_Pol_19: Poxvirus DNA-directed RNA polymera	82.78

>KOG3405|consensus

Probab=100.00  E-value=1.6e-36  Score=235.94  Aligned_cols=84  Identities=70%  Similarity=1.043  Sum_probs=81.9

Q ss_pred             ccccccccccCCCCcchhhhHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCccEEEEEEcCCCcEEEEecccc
Q psy8360          68 KNQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDEL  147 (152)
Q Consensus        68 k~i~d~~~~t~~~lTKYElARIIG~RAlQLs~GAppLVd~~~~~dPv~IAl~EL~eGkIpiiIrR~lP~g~yEdw~l~eL  147 (152)
                      |.|++.+|+|.|++||||+|||+|+||+|||||||+||++++.+||+.||++||+|+||||+||||||||+||||+++||
T Consensus        53 ~~v~~s~R~TtpyMTKYErArvLGtRAlQIsm~APvmVeLegETdPL~IAmkEL~qkKIP~iIRRyLPDgSyEDW~vdEL  132 (136)
T KOG3405|consen   53 KAVPKSERKTTPYMTKYERARVLGTRALQISMNAPVMVELEGETDPLEIAMKELKQKKIPFIIRRYLPDGSYEDWSVDEL  132 (136)
T ss_pred             ccccccccccCcchhHHHHHHhhhHHHHHHhcCCCeEEecCCCCCHHHHHHHHHhhccCceEEeeeCCCCCcccccccee
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceec
Q psy8360         148 KIID  151 (152)
Q Consensus       148 ~i~~  151 (152)
                      ++.|
T Consensus       133 iv~d  136 (136)
T KOG3405|consen  133 IVED  136 (136)
T ss_pred             eccC
Confidence            9864

>PLN00152 DNA-directed RNA polymerase; Provisional

Probab=100.00  E-value=1.5e-34  Score=224.39  Aligned_cols=83  Identities=67%  Similarity=1.072  Sum_probs=79.2

Q ss_pred             cccccccccCCCCcchhhhHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCccEEEEEEcCCCcEEEEeccccc
Q psy8360          69 NQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELK  148 (152)
Q Consensus        69 ~i~d~~~~t~~~lTKYElARIIG~RAlQLs~GAppLVd~~~~~dPv~IAl~EL~eGkIpiiIrR~lP~g~yEdw~l~eL~  148 (152)
                      ......|+|+|+|||||+|||+|+||+|||||||++|++++.+||+.||++||.+|+|||+|||++|||+||+|+++||+
T Consensus        48 ~~~~~~R~T~p~lTkyErARIiG~RALQIsmgApvlV~~~g~tdPl~IA~~El~~~~iP~iVrR~lPdG~yEd~~v~EL~  127 (130)
T PLN00152         48 EPVQRPRKTTPYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELI  127 (130)
T ss_pred             cccccccccccchhHHHHHhhHhHHHHHHhcCCceEEccCCCcCHHHHHHHHHHcCCCCeEEEEECCCCCEEeeEeeeEe
Confidence            55677799999999999999999999999999999999987899999999999999999999999999999999999999


Q ss_pred             eec
Q psy8360         149 IID  151 (152)
Q Consensus       149 i~~  151 (152)
                      +.|
T Consensus       128 ~~~  130 (130)
T PLN00152        128 VED  130 (130)
T ss_pred             ecC
Confidence            875

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

Probab=99.92  E-value=2.6e-25  Score=153.16  Aligned_cols=61  Identities=48%  Similarity=0.797  Sum_probs=58.1

Q ss_pred             ccCCCCcchhhhHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCccEEEEEEcCC
Q psy8360          76 KLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPD  136 (152)
Q Consensus        76 ~t~~~lTKYElARIIG~RAlQLs~GAppLVd~~~~~dPv~IAl~EL~eGkIpiiIrR~lP~  136 (152)
                      .++++|||||+||++|+||+||++||||+|+.+++.||++||++||++|+||++|+|++||
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            3689999999999999999999999999999855899999999999999999999999997

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

Probab=99.72  E-value=4.5e-18  Score=119.29  Aligned_cols=65  Identities=38%  Similarity=0.444  Sum_probs=59.0

Q ss_pred             ccCCCCcchhhhHHHHHHHHHHhcCCCceeeCCCC-CChHHHHHHHHHcCCccEEEEEEcCCCcEE
Q psy8360          76 KLNIKQIRYERARVLGTRALQIAMCAPVMVELEGE-TDPLQIAMKELKARKIPIIIRRYLPDNSYE  140 (152)
Q Consensus        76 ~t~~~lTKYElARIIG~RAlQLs~GAppLVd~~~~-~dPv~IAl~EL~eGkIpiiIrR~lP~g~yE  140 (152)
                      -+....||||+|+++|+||+||++||+++++.+.. .||+.||++|+++|+||+.+.|..++++.+
T Consensus         9 l~~~~~~ryelv~~aa~RA~Ql~~ga~~~~~~~~~~~kpv~iAl~Ei~~g~i~~~i~~~~~~~~~~   74 (74)
T COG1758           9 LLDKVGNRYELVVVAAKRARQLAAGAPPLVDDEENKDKPVVIALREIAEGKIPIEILRELLIHSLQ   74 (74)
T ss_pred             HHhhccCHHHHHHHHHHHHHHHHcCCCCccccccccCChHHHHHHHHHcCCCCcccchhhhccccC
Confidence            45678899999999999999999999999987643 899999999999999999999999998753

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

Probab=99.62  E-value=5.2e-16  Score=103.16  Aligned_cols=53  Identities=36%  Similarity=0.468  Sum_probs=49.1

Q ss_pred             CCCCcchhhhHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCccEEE
Q psy8360          78 NIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIII  130 (152)
Q Consensus        78 ~~~lTKYElARIIG~RAlQLs~GAppLVd~~~~~dPv~IAl~EL~eGkIpiiI  130 (152)
                      ....+||++++++|+||+||++||+|+++.+...+|+++|++||.+|+++|.|
T Consensus         5 ~~~~~rY~Lv~~~akRArql~~g~~~~~~~~~~~k~v~iAl~EI~~gki~~~i   57 (57)
T PF01192_consen    5 EKVDNRYELVILAAKRARQLSEGAPPLVEEDNEMKPVSIALEEIAEGKIKIEI   57 (57)
T ss_dssp             HSSSSHHHHHHHHHHHHHHHHTTSTTSSSSSSSSSSSHHHHHHHHTTSSCEEE
T ss_pred             hccCCHhHHHHHHHHHHHHHHcCcccccccccCCCcHHHHHHHHHcCCCCCcC
Confidence            45679999999999999999999999998775669999999999999999986

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=99.26  E-value=7.7e-12  Score=85.41  Aligned_cols=49  Identities=29%  Similarity=0.337  Sum_probs=45.1

Q ss_pred             cchhhhHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCccEEEE
Q psy8360          82 IRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIR  131 (152)
Q Consensus        82 TKYElARIIG~RAlQLs~GAppLVd~~~~~dPv~IAl~EL~eGkIpiiIr  131 (152)
                      +||+++.++++||+||+.|+++.++.. ..+|+.||++||.+|+|.+..-
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            899999999999999999999997764 7799999999999999998764

>TIGR00690 rpoZ DNA-directed RNA polymerase, omega subunit

Probab=99.19  E-value=2.7e-11  Score=82.24  Aligned_cols=45  Identities=29%  Similarity=0.393  Sum_probs=39.0

Q ss_pred             cchhhhHHHHHHHHHHhcCC-CceeeCCCCCChHHHHHHHHHcCCcc
Q psy8360          82 IRYERARVLGTRALQIAMCA-PVMVELEGETDPLQIAMKELKARKIP  127 (152)
Q Consensus        82 TKYElARIIG~RAlQLs~GA-ppLVd~~~~~dPv~IAl~EL~eGkIp  127 (152)
                      +||+++.++++||+||+.|+ +++++.. +.+|+.||++||++|+|.
T Consensus        14 srY~Lv~~aakRArqL~~~~~~~~~~~~-~~Kp~~iAl~EIa~gkvs   59 (59)
T TIGR00690        14 SRYDLVLVAARRARQLQLKGTDPIVPEE-NDKPTVIALREIAAGLVS   59 (59)
T ss_pred             CHhHHHHHHHHHHHHHHhCCCCCccCcc-cCchHHHHHHHHHcCCCC
Confidence            89999999999999999776 5555543 789999999999999973

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=82.78  E-value=1.2  Score=36.63  Aligned_cols=64  Identities=13%  Similarity=0.197  Sum_probs=52.2

Q ss_pred             cccccccccCCCCcchhhhHHHHHHHHHHhcCCCceeeC-CC---CCChHHHHHHHHHcCCccEEEEE
Q psy8360          69 NQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVEL-EG---ETDPLQIAMKELKARKIPIIIRR  132 (152)
Q Consensus        69 ~i~d~~~~t~~~lTKYElARIIG~RAlQLs~GAppLVd~-~~---~~dPv~IAl~EL~eGkIpiiIrR  132 (152)
                      +|..-++.+.-+++=||..=|+|.--.-|..|--|||.- ..   ..+-+.|-++||.+|.-|++|..
T Consensus        68 kI~~iK~RYTRRiSLfEiTGIiaESyNLLqRGRlPLv~dlsdeT~k~n~L~vvi~EIeEg~CPIVIeK  135 (167)
T PF05320_consen   68 KISAIKKRYTRRISLFEITGIIAESYNLLQRGRLPLVSDLSDETLKDNILHVVIKEIEEGTCPIVIEK  135 (167)
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHccccccccccchHHHHHhHHHHHHHHHhcCCCcEEEee
Confidence            344555667778899999999999989999999999952 11   34568899999999999999986

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	152
1qkl_A	127	Hrpabc14.4, Essential Subunit Of Human Rna Polymera		4e-31
3h0g_F	142	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		1e-25
1i3q_F	155	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		3e-25
3j0k_F	84	Orientation Of Rna Polymerase Ii Within The Human V		1e-24
2y0s_I	95	Crystal Structure Of Sulfolobus Shibatae Rna Polyme		7e-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 =  130 bits (326), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 63/69 (91%), Positives = 65/69 (94%)
Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct: 59  KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 118
Query: 143 GIDELKIID 151
           G+DEL I D
Sbjct: 119 GVDELIITD 127

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

Iteration: 1
 Score =  112 bits (279), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 49/65 (75%), Positives = 59/65 (90%)
Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERAR+LGTRALQI+M APV+V+LEGETDPLQIAMKEL  +KIP+++RRYLPD SYEDW
Sbjct: 77  KYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRYLPDGSYEDW 136
Query: 143 GIDEL 147
            + EL
Sbjct: 137 SVAEL 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 = 3e-25,   Method: Compositional matrix adjust.
 Identities = 50/69 (72%), Positives = 62/69 (89%), Gaps = 1/69 (1%)
Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERAR+LGTRALQI+M APV V+LEGETDPL+IAMKEL  +KIP++IRRYLPD S+EDW
Sbjct: 87  KYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDW 146
Query: 143 GIDELKIID 151
            ++EL I+D
Sbjct: 147 SVEEL-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 (271), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 50/69 (72%), Positives = 62/69 (89%), Gaps = 1/69 (1%)
Query: 83  RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
           +YERAR+LGTRALQI+M APV V+LEGETDPL+IAMKEL  +KIP++IRRYLPD S+EDW
Sbjct: 16  KYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDW 75
Query: 143 GIDELKIID 151
            ++EL I+D
Sbjct: 76  SVEEL-IVD 83

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 27/56 (48%), Positives = 37/56 (66%), Gaps = 2/56 (3%)
Query: 83  RYERARVLGTRALQIAMCAPVMVELE--GETDPLQIAMKELKARKIPIIIRRYLPD 136
           RYE ARV+  RALQ+AM AP ++++     TD + IA +E K   +PI IRR LP+
Sbjct: 29  RYEIARVISARALQLAMGAPALIDINNISSTDVISIAEEEFKRGVLPITIRRRLPN 84

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/56 (46%), Positives = 37/56 (66%), Gaps = 2/56 (3%)
Query: 83  RYERARVLGTRALQIAMCAPVMVELE--GETDPLQIAMKELKARKIPIIIRRYLPD 136
           RYE ARV+  RALQ+AM AP ++++     TD + IA +E +   +PI IRR LP+
Sbjct: 29  RYEIARVISARALQLAMGAPALIDINNLSSTDVISIAEEEFRRGVLPITIRRRLPN 84

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/56 (46%), Positives = 37/56 (66%), Gaps = 2/56 (3%)
Query: 83  RYERARVLGTRALQIAMCAPVMVELE--GETDPLQIAMKELKARKIPIIIRRYLPD 136
           RYE ARV+  RALQ+AM AP ++++     TD + IA +E +   +PI IRR LP+
Sbjct: 29  RYEIARVISARALQLAMGAPALIDINNLSSTDVISIAEEEFRRGVLPITIRRRLPN 84
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	152
1qkl_A	127	RPB6, DNA-directed RNA polymerase II 14.4 KD polyp	2e-33
1twf_F	155	ABC23, DNA-directed RNA polymerases I, II, and III	2e-32
3h0g_F	142	DNA-directed RNA polymerases I, II, and III subuni	9e-32
4ayb_K	95	DNA-directed RNA polymerase; transferase, multi-su	8e-30

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

 Score =  113 bits (284), Expect = 2e-33
 Identities = 65/94 (69%), Positives = 72/94 (76%), Gaps = 4/94 (4%)

Query: 58  ILNHYMKVKSKNQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIA 117
           IL    + ++  +      +     +YERARVLGTRALQIAMCAPVMVELEGETDPL IA
Sbjct: 38  ILPSGERPQANQKRITTPYMT----KYERARVLGTRALQIAMCAPVMVELEGETDPLLIA 93

Query: 118 MKELKARKIPIIIRRYLPDNSYEDWGIDELKIID 151
           MKELKARKIPIIIRRYLPD SYEDWG+DEL I D
Sbjct: 94  MKELKARKIPIIIRRYLPDGSYEDWGVDELIITD 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 =  112 bits (280), Expect = 2e-32
 Identities = 54/109 (49%), Positives = 69/109 (63%)

Query: 41  GDLNLILGIKGERALVLILNHYMKVKSKNQIKNNNKLNIKQIRYERARVLGTRALQIAMC 100
           G   +  G   E            +K K   K+         +YERAR+LGTRALQI+M 
Sbjct: 45  GKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMN 104

Query: 101 APVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKI 149
           APV V+LEGETDPL+IAMKEL  +KIP++IRRYLPD S+EDW ++EL +
Sbjct: 105 APVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIV 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 =  109 bits (274), Expect = 9e-32
 Identities = 51/82 (62%), Positives = 62/82 (75%)

Query: 66  KSKNQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARK 125
             K   K +        +YERAR+LGTRALQI+M APV+V+LEGETDPLQIAMKEL  +K
Sbjct: 60  SGKAVAKEDRTTTPYMTKYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKK 119

Query: 126 IPIIIRRYLPDNSYEDWGIDEL 147
           IP+++RRYLPD SYEDW + EL
Sbjct: 120 IPLLVRRYLPDGSYEDWSVAEL 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 =  102 bits (257), Expect = 8e-30
 Identities = 27/66 (40%), Positives = 39/66 (59%), Gaps = 2/66 (3%)

Query: 83  RYERARVLGTRALQIAMCAPVMVELE--GETDPLQIAMKELKARKIPIIIRRYLPDNSYE 140
           RYE ARV+  RALQ+AM AP ++++     TD + IA +E K   +PI IRR LP+    
Sbjct: 29  RYEIARVISARALQLAMGAPALIDINNISSTDVISIAEEEFKRGVLPITIRRRLPNGKII 88

Query: 141 DWGIDE 146
              + +
Sbjct: 89  LLSLRK 94

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	152
1qkl_A	127	RPB6, DNA-directed RNA polymerase II 14.4 KD polyp	100.0
3h0g_F	142	DNA-directed RNA polymerases I, II, and III subuni	100.0
1twf_F	155	ABC23, DNA-directed RNA polymerases I, II, and III	100.0
4ayb_K	95	DNA-directed RNA polymerase; transferase, multi-su	99.96
3lu0_E	91	DNA-directed RNA polymerase subunit omega; E. coli	99.21
2a6h_E	99	RNA polymerase omega chain; RNA polymerase holoenz	99.1

>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=1.3e-34  Score=222.85  Aligned_cols=85  Identities=75%  Similarity=1.130  Sum_probs=81.6

Q ss_pred             cccccccccccCCCCcchhhhHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCccEEEEEEcCCCcEEEEeccc
Q psy8360          67 SKNQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDE  146 (152)
Q Consensus        67 ~k~i~d~~~~t~~~lTKYElARIIG~RAlQLs~GAppLVd~~~~~dPv~IAl~EL~eGkIpiiIrR~lP~g~yEdw~l~e  146 (152)
                      .+.+++.+|+|+|++||||+||++|+||+||||||||||+.++.+||+.||++||++|+||++|||++|||+||+|+++|
T Consensus        43 ~~~~~~~~r~t~p~lTRYElARIiG~RAlQLs~GAppLVd~e~~~dPl~IAl~ElaeGkIpi~VrR~lPdg~yEd~~~~e  122 (127)
T 1qkl_A           43 ERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDE  122 (127)
T ss_dssp             CCTTTCCCSSCCSSCCHHHHHHHHHHHHHHHHHSCCSSSCSSSSCSSSHHHHHHHHHTCCCEEEEEEETTTEEEEESSSS
T ss_pred             CcCCCccccccCCCcCHHHHHHHHHHHHHHHhcCCcceEcCCCCCCHHHHHHHHHHcCCCCeEEEEECCCCCEEEeehhh
Confidence            56789999999999999999999999999999999999999877899999999999999999999999999999999999


Q ss_pred             cceec
Q psy8360         147 LKIID  151 (152)
Q Consensus       147 L~i~~  151 (152)
                      |+|.|
T Consensus       123 L~i~~  127 (127)
T 1qkl_A          123 LIITD  127 (127)
T ss_dssp             SCSCC
T ss_pred             eeccC
Confidence            99864

>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=1.9e-34  Score=225.40  Aligned_cols=82  Identities=62%  Similarity=1.007  Sum_probs=79.7

Q ss_pred             cccccccccccCCCCcchhhhHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCccEEEEEEcCCCcEEEEeccc
Q psy8360          67 SKNQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDE  146 (152)
Q Consensus        67 ~k~i~d~~~~t~~~lTKYElARIIG~RAlQLs~GAppLVd~~~~~dPv~IAl~EL~eGkIpiiIrR~lP~g~yEdw~l~e  146 (152)
                      .+++++++|+|+|+|||||+|||+|+||+||+|||||||+.++++||++||++||++|+|||+|||++|||+||+|+++|
T Consensus        61 ~~~~~~~~R~T~pylTRYElARIiG~RAlQIsmGAp~LVd~~~~tdPl~IA~~EL~egkIPiiVrR~lPdgkyEdw~l~E  140 (142)
T 3h0g_F           61 GKAVAKEDRTTTPYMTKYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRYLPDGSYEDWSVAE  140 (142)
T ss_dssp             CCCCCTTSCCSCSSCCHHHHHHHHHHHHHHHHTCCCCCSCCCSCCCTTHHHHHHHHTTCCCCEEECCCSSSCCCEEETTT
T ss_pred             cccCCcccccCCCccCHHHHHHHHHHHHHHHHCCCCceEcCCCCCCHHHHHHHHHHcCCCceEEEEECCCCCEEEeEHHH
Confidence            67899999999999999999999999999999999999999878999999999999999999999999999999999999


Q ss_pred             cc
Q psy8360         147 LK  148 (152)
Q Consensus       147 L~  148 (152)
                      |+
T Consensus       141 L~  142 (142)
T 3h0g_F          141 LI  142 (142)
T ss_dssp             CC
T ss_pred             cC
Confidence            95

>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=5.3e-34  Score=225.45  Aligned_cols=91  Identities=56%  Similarity=0.886  Sum_probs=81.5

Q ss_pred             hhhhcccccccccccccCCCCcchhhhHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCccEEEEEEcCCCcEE
Q psy8360          61 HYMKVKSKNQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYE  140 (152)
Q Consensus        61 ~~~~~~~k~i~d~~~~t~~~lTKYElARIIG~RAlQLs~GAppLVd~~~~~dPv~IAl~EL~eGkIpiiIrR~lP~g~yE  140 (152)
                      ...+.+.++|++.+|+|+|+|||||+|||+|+||+||+|||||||++++.+||+.||++||++|+||++|||++|||+||
T Consensus        65 ~~~~~~~~~~~~~~r~t~p~lTRYElARIiG~RAlQLsmGAppLVd~e~~~dPl~IAl~ElaeGkIPl~IrR~lPdG~yE  144 (155)
T 1twf_F           65 RRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFE  144 (155)
T ss_dssp             -------CCCCSSSCCSCSBCCHHHHHHHHHHHHHHHHTTCCCSSCCSSCCSHHHHHHHHHHTTCCCEEEEEECTTSCEE
T ss_pred             cccccccccCCcccccCCCCcCHHHHHHHHHHHHHHHhcCCCcEEecCCCCCHHHHHHHHHHcCCCCeEEEEECCCCCEE
Confidence            44567778999999999999999999999999999999999999999877899999999999999999999999999999


Q ss_pred             EEeccccceec
Q psy8360         141 DWGIDELKIID  151 (152)
Q Consensus       141 dw~l~eL~i~~  151 (152)
                      +|+++||++.+
T Consensus       145 d~~v~eL~~~~  155 (155)
T 1twf_F          145 DWSVEELIVDL  155 (155)
T ss_dssp             EEETTTSBCCC
T ss_pred             EeeHHHhccCC
Confidence            99999999864

>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=99.96  E-value=6.4e-31  Score=193.83  Aligned_cols=69  Identities=41%  Similarity=0.611  Sum_probs=65.0

Q ss_pred             CCCCcchhhhHHHHHHHHHHhcCCCceeeCC--CCCChHHHHHHHHHcCCccEEEEEEcCCCcEEEEeccc
Q psy8360          78 NIKQIRYERARVLGTRALQIAMCAPVMVELE--GETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDE  146 (152)
Q Consensus        78 ~~~lTKYElARIIG~RAlQLs~GAppLVd~~--~~~dPv~IAl~EL~eGkIpiiIrR~lP~g~yEdw~l~e  146 (152)
                      .+.|||||+|||+|+||+||++||||+|+++  ..+||++||.+||.+|+|||+|||++|||+||+|+|+|
T Consensus        24 ~~kLTKYEkaRIiG~RA~Qis~GA~~~I~~~~~~~~Dp~~IA~~EL~~~kiP~iIrR~lPnG~~E~~~l~e   94 (95)
T 4ayb_K           24 QNKLTRYEIARVISARALQLAMGAPALIDINNISSTDVISIAEEEFKRGVLPITIRRRLPNGKIILLSLRK   94 (95)
T ss_dssp             TSSCCHHHHHHHHHHHHHHHHTCCCCSSCTTTSCSSCTHHHHHHHHHTTCCCEEEEEECTTSCEEEECCCC
T ss_pred             cccccHHHHHHHHHHHHHHHHCCCCceEeCCCCCCCCHHHHHHHHHHcCCCCEEEEEeCCCCCEEEEEecc
Confidence            3459999999999999999999999999986  36899999999999999999999999999999999987

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

Probab=99.21  E-value=3.5e-12  Score=92.77  Aligned_cols=50  Identities=24%  Similarity=0.242  Sum_probs=46.2

Q ss_pred             cchhhhHHHHHHHHHHhc-CCCceeeCCCCCChHHHHHHHHHcCCccEEEEE
Q psy8360          82 IRYERARVLGTRALQIAM-CAPVMVELEGETDPLQIAMKELKARKIPIIIRR  132 (152)
Q Consensus        82 TKYElARIIG~RAlQLs~-GAppLVd~~~~~dPv~IAl~EL~eGkIpiiIrR  132 (152)
                      +||+++.++++||+||+. |++|+|+.+ +.||+.||++||++|+|.+.+-.
T Consensus        15 nRY~LV~~AAKRARQL~~~G~~plv~~~-~~Kpv~iALrEIa~GkV~~~~l~   65 (91)
T 3lu0_E           15 NRFDLVLVAARRARQMQVGGKDPLVPEE-NDKTTVIALREIEEGLINNQILD   65 (91)
T ss_dssp             SHHHHHHHHHHHHHHHHHTCCCSCCSSS-CCCSSCCSHHHHHSSSCEEESSS
T ss_pred             CHhHHHHHHHHHHHHHHhcCCCCccCCC-CCChHHHHHHHHHcCCCceeeCC
Confidence            799999999999999998 999999976 88999999999999999987543

>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=99.10  E-value=6.7e-11  Score=86.76  Aligned_cols=48  Identities=23%  Similarity=0.223  Sum_probs=41.8

Q ss_pred             cchhhhHHHHHHHHHHhcCC--CceeeC---CCCC---------ChHHHHHHHHHcCCccEE
Q psy8360          82 IRYERARVLGTRALQIAMCA--PVMVEL---EGET---------DPLQIAMKELKARKIPII  129 (152)
Q Consensus        82 TKYElARIIG~RAlQLs~GA--ppLVd~---~~~~---------dPv~IAl~EL~eGkIpii  129 (152)
                      +||+++.++++||+||+.|+  .|+++.   ..+.         +|+.||++||++|+|.+.
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            79999999999999999999  999873   1133         999999999999998763

---

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	152
d1qkla_	127	a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId:	8e-38
d1twff_	84	a.143.1.2 (F:) RPB6 {Baker's yeast (Saccharomyces	4e-35

>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 =  123 bits (310), Expect = 8e-38
 Identities = 65/94 (69%), Positives = 72/94 (76%), Gaps = 4/94 (4%)

Query: 58  ILNHYMKVKSKNQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIA 117
           IL    + ++  +      +     +YERARVLGTRALQIAMCAPVMVELEGETDPL IA
Sbjct: 38  ILPSGERPQANQKRITTPYMT----KYERARVLGTRALQIAMCAPVMVELEGETDPLLIA 93

Query: 118 MKELKARKIPIIIRRYLPDNSYEDWGIDELKIID 151
           MKELKARKIPIIIRRYLPD SYEDWG+DEL I D
Sbjct: 94  MKELKARKIPIIIRRYLPDGSYEDWGVDELIITD 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 =  115 bits (289), Expect = 4e-35
 Identities = 49/79 (62%), Positives = 62/79 (78%)

Query: 71  IKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIII 130
            K+         +YERAR+LGTRALQI+M APV V+LEGETDPL+IAMKEL  +KIP++I
Sbjct: 4   PKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVI 63

Query: 131 RRYLPDNSYEDWGIDELKI 149
           RRYLPD S+EDW ++EL +
Sbjct: 64  RRYLPDGSFEDWSVEELIV 82

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	152
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	97.51

>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=1.4e-34  Score=207.33  Aligned_cols=82  Identities=61%  Similarity=1.003  Sum_probs=79.2

Q ss_pred             ccccccccccCCCCcchhhhHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCccEEEEEEcCCCcEEEEecccc
Q psy8360          68 KNQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDEL  147 (152)
Q Consensus        68 k~i~d~~~~t~~~lTKYElARIIG~RAlQLs~GAppLVd~~~~~dPv~IAl~EL~eGkIpiiIrR~lP~g~yEdw~l~eL  147 (152)
                      |.|+|++|+|+|+|||||+||++|.||+||++||+|+|+.++.+||++||.+||.+|+|||+|||++|||+||+|+++||
T Consensus         1 k~i~~~~~~T~p~LTkYE~ariiG~Ra~Ql~~Ga~p~I~~~~~~d~~~IA~~El~~~kiP~iIrR~lP~g~~E~w~l~dL   80 (84)
T d1twff_           1 KAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEEL   80 (84)
T ss_dssp             CCCCSSSCCSCSBCCHHHHHHHHHHHHHHHHTTCCCSSCCSSCCSHHHHHHHHHHTTCCCEEEEEECTTSCEEEEETTTS
T ss_pred             CCcCCcCcccCccccHHHHHHHHHHHHHHHHcCCCceecCCCCCCHHHHHHHHHHcCCCCEEEEEECCCCCEEEEEHHHe
Confidence            46899999999999999999999999999999999999998789999999999999999999999999999999999999


Q ss_pred             ce
Q psy8360         148 KI  149 (152)
Q Consensus       148 ~i  149 (152)
                      +|
T Consensus        81 ~i   82 (84)
T d1twff_          81 IV   82 (84)
T ss_dssp             BC
T ss_pred             ee
Confidence            75

>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=5.5e-34  Score=216.88  Aligned_cols=86  Identities=74%  Similarity=1.112  Sum_probs=82.4

Q ss_pred             ccccccccccccCCCCcchhhhHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCccEEEEEEcCCCcEEEEecc
Q psy8360          66 KSKNQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGID  145 (152)
Q Consensus        66 ~~k~i~d~~~~t~~~lTKYElARIIG~RAlQLs~GAppLVd~~~~~dPv~IAl~EL~eGkIpiiIrR~lP~g~yEdw~l~  145 (152)
                      +.+.+.+.+|+|+|+|||||+|||+|.||+||++||||+|++++.++|++||.+||.+|||||+|||++|||+||+|+++
T Consensus        42 ~~~~~~~~~~~T~p~lTkYE~arilG~Ra~Qi~~ga~~~i~~~~~~d~~~IA~~EL~~kkiPfiIrR~lp~g~~E~w~l~  121 (127)
T d1qkla_          42 GERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVD  121 (127)
T ss_dssp             CCCTTTCCCSSCCSSCCHHHHHHHHHHHHHHHHHSCCSSSCSSSSCSSSHHHHHHHHHTCCCEEEEEEETTTEEEEESSS
T ss_pred             ccccccCcccccCCcccHHHHHHHHHHHHHHHhcCCCceecCCCCCCHHHHHHHHHHcCCCCEEEEEECCCCCEEEEEhH
Confidence            34678999999999999999999999999999999999999988899999999999999999999999999999999999


Q ss_pred             ccceec
Q psy8360         146 ELKIID  151 (152)
Q Consensus       146 eL~i~~  151 (152)
                      +|.|+|
T Consensus       122 dL~i~~  127 (127)
T d1qkla_         122 ELIITD  127 (127)
T ss_dssp             SSCSCC
T ss_pred             heEecC
Confidence            999986

>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=97.51  E-value=4.6e-05  Score=54.27  Aligned_cols=54  Identities=24%  Similarity=0.290  Sum_probs=41.7

Q ss_pred             CCcchhhhHHHHHHHHH-HhcCCC-ceeeCCC----C--------CChHHHHHHHHHcCCccEEEEEEcC
Q psy8360          80 KQIRYERARVLGTRALQ-IAMCAP-VMVELEG----E--------TDPLQIAMKELKARKIPIIIRRYLP  135 (152)
Q Consensus        80 ~lTKYElARIIG~RAlQ-Ls~GAp-pLVd~~~----~--------~dPv~IAl~EL~eGkIpiiIrR~lP  135 (152)
                      .-+||-+..++|+||.| |-.|.| .+++.+.    .        -++++.|++||.-|+  +.+--.+|
T Consensus        12 tDSkYRLsvVvakRA~QlLr~g~~ntvL~pde~p~~~tleg~~~dpN~vt~AMkEL~tGr--l~~GenL~   79 (95)
T d1smye_          12 VDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAETWAMKELLTGR--LVFGENLV   79 (95)
T ss_dssp             SSSHHHHHHHHHHHHHHHHHTCTTCCSCCSSSCCCCSSSSGGGTSSCSHHHHHHHHTTTC--EEEESSSS
T ss_pred             cccceeeehhhHHHHHHHHHcCCCccccChhhhhhhhcccccCCCCcHHHHHHHHHHhCc--eeecCCCC
Confidence            34799999999999999 889999 5555442    1        278999999999999  44443333