Citrus Sinensis ID: 033231

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120----
Protein Sequence
MAGQEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD
Secondary Structure (PSIPRED)
cccccccHHHHHccccccccccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHcccccEEEEEEcccccEEEEEccEEEEEcHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccHHcHHHHHHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHHccccEEEEEEccccccccccccEEEEccccHHccccc
Coil and Loop (DISEMBL)
magqegaeedaeninnddingepietEEKEEQEQKEAARKTSKYMTKYERARILGTRAlqismnapvmvelegetdPLEIAMKELRErkipftirrylpdgsyedwgvdelivedswkrqvggd
Flexible Loop (DISEMBL)
magqegaeedaeninnddingepieteekeeqeqkeaarktskymtkYERARILGTRALQISMNAPVMVELEGETDPLEIAMKElrerkipftirrylpdgsyedwgvdelivedswkrqvggd
Low Complexity Region (SEG)
MAGQegaeedaeninnddingePIeteekeeqeqkeAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD
Disordered region (IsUnstruct)
**********************************************KYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSW*******
Disordered Region (DISOPRED)
*******************************************YMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQ****
Disordered Region (DISEMBL)
***********ENINNDDINGEPIE*****************KYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD
Disordered Region (DISPRO)
*************************************ARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSW*******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAGQEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD
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	124	2.2.26 [Sep-21-2011]
Q32PE0	127	DNA-directed RNA polymera	yes	no	0.822	0.803	0.657	4e-33
O88828	127	DNA-directed RNA polymera	yes	no	0.758	0.740	0.723	6e-33
P61219	127	DNA-directed RNA polymera	yes	no	0.758	0.740	0.723	6e-33
Q5R592	127	DNA-directed RNA polymera	yes	no	0.758	0.740	0.723	8e-33
P61218	127	DNA-directed RNA polymera	yes	no	0.758	0.740	0.723	8e-33
P61217	127	DNA-directed RNA polymera	yes	no	0.758	0.740	0.723	8e-33
P20435	155	DNA-directed RNA polymera	yes	no	0.612	0.490	0.815	2e-31
Q24320	131	DNA-directed RNA polymera	yes	no	0.822	0.778	0.605	3e-31
P36595	142	DNA-directed RNA polymera	yes	no	0.596	0.521	0.810	4e-31
Q54FA8	133	DNA-directed RNA polymera	yes	no	0.604	0.563	0.773	1e-29

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

 Score =  139 bits (351), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 73/111 (65%), Positives = 85/111 (76%), Gaps = 9/111 (8%)

Query: 5   EGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMN 64
           E AEE+ +      +N E + + E+ +  QK   R T+ YMTKYERAR+LGTRALQI+M 
Sbjct: 26  ENAEEEGQ------VNVEILPSGERPQANQK---RITTPYMTKYERARVLGTRALQIAMC 76

Query: 65  APVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 115
           APVMVELEGETDPL IAMKEL+ RKIP  IRRYLPDGSYEDWGVDELI+ D
Sbjct: 77  APVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITD 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 =  139 bits (349), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 68/94 (72%), Positives = 75/94 (79%)

Query: 22  EPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIA 81
           E +E     E+ Q    R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IA
Sbjct: 34  ENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIA 93

Query: 82  MKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 115
           MKEL+ RKIP  IRRYLPDGSYEDWGVDELI+ D
Sbjct: 94  MKELKARKIPIIIRRYLPDGSYEDWGVDELIISD 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 =  139 bits (349), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 68/94 (72%), Positives = 75/94 (79%)

Query: 22  EPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIA 81
           E +E     E+ Q    R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IA
Sbjct: 34  ENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIA 93

Query: 82  MKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 115
           MKEL+ RKIP  IRRYLPDGSYEDWGVDELI+ D
Sbjct: 94  MKELKARKIPIIIRRYLPDGSYEDWGVDELIISD 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|Q5R592|RPAB2_PONAB DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Pongo abelii GN=POLR2F PE=2 SV=1

 Score =  138 bits (348), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 68/94 (72%), Positives = 75/94 (79%)

Query: 22  EPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIA 81
           E +E     E+ Q    R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IA
Sbjct: 34  ENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIA 93

Query: 82  MKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 115
           MKEL+ RKIP  IRRYLPDGSYEDWGVDELI+ D
Sbjct: 94  MKELKARKIPIIIRRYLPDGSYEDWGVDELIITD 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 =  138 bits (348), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 68/94 (72%), Positives = 75/94 (79%)

Query: 22  EPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIA 81
           E +E     E+ Q    R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IA
Sbjct: 34  ENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIA 93

Query: 82  MKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 115
           MKEL+ RKIP  IRRYLPDGSYEDWGVDELI+ D
Sbjct: 94  MKELKARKIPIIIRRYLPDGSYEDWGVDELIITD 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 =  138 bits (348), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 68/94 (72%), Positives = 75/94 (79%)

Query: 22  EPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIA 81
           E +E     E+ Q    R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IA
Sbjct: 34  ENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIA 93

Query: 82  MKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 115
           MKEL+ RKIP  IRRYLPDGSYEDWGVDELI+ D
Sbjct: 94  MKELKARKIPIIIRRYLPDGSYEDWGVDELIITD 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|P20435|RPAB2_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPO26 PE=1 SV=1

 Score =  134 bits (336), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 62/76 (81%), Positives = 68/76 (89%)

Query: 39  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
           R T+ YMTKYERARILGTRALQISMNAPV V+LEGETDPL IAMKEL E+KIP  IRRYL
Sbjct: 79  RATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYL 138

Query: 99  PDGSYEDWGVDELIVE 114
           PDGS+EDW V+ELIV+
Sbjct: 139 PDGSFEDWSVEELIVD 154

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.

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

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

 Score =  133 bits (335), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 66/109 (60%), Positives = 82/109 (75%), Gaps = 7/109 (6%)

Query: 8   EEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPV 67
           EE+A+NI       E I           ++ R T+KYMTKYERAR+LGTRALQI+M AP+
Sbjct: 30  EEEADNI-------EIIAPGGAGGGGVPKSKRITTKYMTKYERARVLGTRALQIAMCAPI 82

Query: 68  MVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDS 116
           MVEL+GETDPL+IAMKEL+++KIP  IRRYLPD SYEDW +DELI+ D+
Sbjct: 83  MVELDGETDPLQIAMKELKQKKIPIIIRRYLPDHSYEDWSIDELIMVDN 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|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 =  133 bits (334), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 60/74 (81%), Positives = 67/74 (90%)

Query: 39  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
           R T+ YMTKYERARILGTRALQISMNAPV+V+LEGETDPL+IAMKEL ++KIP  +RRYL
Sbjct: 69  RTTTPYMTKYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRYL 128

Query: 99  PDGSYEDWGVDELI 112
           PDGSYEDW V ELI
Sbjct: 129 PDGSYEDWSVAELI 142

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)

>sp|Q54FA8|RPAB2_DICDI DNA-directed RNA polymerases I, II, and III subunit rpabc2 OS=Dictyostelium discoideum GN=polr2f PE=3 SV=1

 Score =  128 bits (321), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 58/75 (77%), Positives = 68/75 (90%)

Query: 39  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
           RKT++YMTKYERAR+LG+RALQISMNAP+MVELEGETDPL+IA KELR +KIP  IRR+L
Sbjct: 59  RKTTRYMTKYERARLLGSRALQISMNAPIMVELEGETDPLQIAWKELRAKKIPLIIRRFL 118

Query: 99  PDGSYEDWGVDELIV 113
           P+G YEDW VDEL +
Sbjct: 119 PNGMYEDWSVDELSI 133

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.

Dictyostelium discoideum (taxid: 44689)

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	124
224136924	143	predicted protein [Populus trichocarpa]	0.975	0.846	0.892	2e-54
147794797	140	hypothetical protein VITISV_000776 [Viti	0.951	0.842	0.883	2e-50
255539539	124	DNA-directed RNA polymerase subunit rpb6	1.0	1.0	0.895	3e-50
356535896	142	PREDICTED: DNA-directed RNA polymerases	0.919	0.802	0.878	3e-50
297792515	144	hypothetical protein ARALYDRAFT_495261 [	0.927	0.798	0.852	8e-50
297835766	144	hypothetical protein ARALYDRAFT_899271 [	0.927	0.798	0.843	3e-49
351724737	142	uncharacterized protein LOC100305739 [Gl	0.919	0.802	0.869	3e-49
357509805	145	DNA-directed RNA polymerases I, II, and	0.927	0.793	0.870	3e-49
15242235	144	RNA polymerase Rpb6 [Arabidopsis thalian	0.927	0.798	0.843	4e-49
224120092	143	predicted protein [Populus trichocarpa]	0.846	0.734	0.933	5e-49

>gi|224136924|ref|XP_002322450.1| predicted protein [Populus trichocarpa] gi|222869446|gb|EEF06577.1| predicted protein [Populus trichocarpa]

 Score =  215 bits (548), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 108/121 (89%), Positives = 113/121 (93%)

Query: 4   QEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISM 63
           +EGA+EDAEN NN+D  GEPIETE+KEEQ   E  RKTSK+MTKYERARILGTRALQISM
Sbjct: 23  EEGADEDAENNNNEDDTGEPIETEDKEEQAPVERPRKTSKFMTKYERARILGTRALQISM 82

Query: 64  NAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGG 123
           NAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGG
Sbjct: 83  NAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGG 142

Query: 124 D 124
           D
Sbjct: 143 D 143

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147794797|emb|CAN62586.1| hypothetical protein VITISV_000776 [Vitis vinifera]

 Score =  202 bits (515), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 106/120 (88%), Positives = 110/120 (91%), Gaps = 2/120 (1%)

Query: 5   EGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMN 64
           EGAEEDA+N NN+DI  + IET EKE Q   E +RKTSKYMTKYERARILGTRALQISMN
Sbjct: 23  EGAEEDADNNNNEDI-PDAIETAEKE-QVPVERSRKTSKYMTKYERARILGTRALQISMN 80

Query: 65  APVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD 124
           APVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD
Sbjct: 81  APVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD 140

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255539539|ref|XP_002510834.1| DNA-directed RNA polymerase subunit rpb6, putative [Ricinus communis] gi|223549949|gb|EEF51436.1| DNA-directed RNA polymerase subunit rpb6, putative [Ricinus communis]

 Score =  201 bits (512), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 111/124 (89%), Positives = 115/124 (92%)

Query: 1   MAGQEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQ 60
           M  QEGAEED EN NN+D+ G+PIETE+KEEQE  E  RKTSKYMTKYERARILGTRALQ
Sbjct: 1   MIWQEGAEEDVENNNNEDVPGDPIETEDKEEQEAAERPRKTSKYMTKYERARILGTRALQ 60

Query: 61  ISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQ 120
           ISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQ
Sbjct: 61  ISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQ 120

Query: 121 VGGD 124
           VGGD
Sbjct: 121 VGGD 124

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356535896|ref|XP_003536478.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC2-like [Glycine max]

 Score =  201 bits (512), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 101/115 (87%), Positives = 107/115 (93%), Gaps = 1/115 (0%)

Query: 10  DAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMV 69
           D EN  ND++ GEPI+TE+KEE++  E  RKTSKYMTKYERARILGTRALQISMNAPVMV
Sbjct: 29  DLEN-KNDELTGEPIDTEDKEEEQPVERPRKTSKYMTKYERARILGTRALQISMNAPVMV 87

Query: 70  ELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD 124
           ELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD
Sbjct: 88  ELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD 142

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297792515|ref|XP_002864142.1| hypothetical protein ARALYDRAFT_495261 [Arabidopsis lyrata subsp. lyrata] gi|297309977|gb|EFH40401.1| hypothetical protein ARALYDRAFT_495261 [Arabidopsis lyrata subsp. lyrata]

 Score =  200 bits (509), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 98/115 (85%), Positives = 106/115 (92%)

Query: 10  DAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMV 69
           DAE   NDD+NGEP+ETE+K E E  +  RKTSK+MTKYERARILGTRALQISMNAPVMV
Sbjct: 30  DAEMKENDDVNGEPLETEDKVETEPVQRPRKTSKFMTKYERARILGTRALQISMNAPVMV 89

Query: 70  ELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD 124
           ELEGETDPLEIAMKELR+RKIPFTIRRYLPDGS+E+WGVDELIVEDSWKRQVGGD
Sbjct: 90  ELEGETDPLEIAMKELRQRKIPFTIRRYLPDGSFEEWGVDELIVEDSWKRQVGGD 144

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297835766|ref|XP_002885765.1| hypothetical protein ARALYDRAFT_899271 [Arabidopsis lyrata subsp. lyrata] gi|297331605|gb|EFH62024.1| hypothetical protein ARALYDRAFT_899271 [Arabidopsis lyrata subsp. lyrata]

 Score =  198 bits (504), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 97/115 (84%), Positives = 106/115 (92%)

Query: 10  DAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMV 69
           DA+   NDD+NGEP+ETE+K E E  +  RKTSK+MTKYERARILGTRALQISMNAPVMV
Sbjct: 30  DADIKENDDVNGEPMETEDKVETEPVQRPRKTSKFMTKYERARILGTRALQISMNAPVMV 89

Query: 70  ELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD 124
           ELEGETDPLEIAMKELR+RKIPFTIRRYLPDGS+E+WGVDELIVEDSWKRQVGGD
Sbjct: 90  ELEGETDPLEIAMKELRQRKIPFTIRRYLPDGSFEEWGVDELIVEDSWKRQVGGD 144

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351724737|ref|NP_001236044.1| uncharacterized protein LOC100305739 [Glycine max] gi|255626491|gb|ACU13590.1| unknown [Glycine max]

 Score =  198 bits (504), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 100/115 (86%), Positives = 106/115 (92%), Gaps = 1/115 (0%)

Query: 10  DAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMV 69
           D EN  ND+I GE I+TE+KEE++  +  RKTSKYMTKYERARILGTRALQISMNAPVMV
Sbjct: 29  DVEN-KNDEITGESIDTEDKEEEQPVKRPRKTSKYMTKYERARILGTRALQISMNAPVMV 87

Query: 70  ELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD 124
           ELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD
Sbjct: 88  ELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD 142

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357509805|ref|XP_003625191.1| DNA-directed RNA polymerases I, II, and III subunit RPABC2 [Medicago truncatula] gi|124360124|gb|ABN08140.1| DNA-directed RNA polymerase, 14 to 18 kDa subunit [Medicago truncatula] gi|355500206|gb|AES81409.1| DNA-directed RNA polymerases I, II, and III subunit RPABC2 [Medicago truncatula] gi|388508874|gb|AFK42503.1| unknown [Medicago truncatula] gi|388517849|gb|AFK46986.1| unknown [Medicago truncatula]

 Score =  198 bits (504), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 101/116 (87%), Positives = 105/116 (90%), Gaps = 1/116 (0%)

Query: 10  DAENINND-DINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVM 68
           D +N N+D D  GEPIETEEKE+    E  R+TSKYMTKYERARILGTRALQISMNAPVM
Sbjct: 30  DPDNKNDDLDAEGEPIETEEKEDAAPVERPRRTSKYMTKYERARILGTRALQISMNAPVM 89

Query: 69  VELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD 124
           VELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD
Sbjct: 90  VELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD 145

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15242235|ref|NP_200007.1| RNA polymerase Rpb6 [Arabidopsis thaliana] gi|13878077|gb|AAK44116.1|AF370301_1 putative DNA-directed RNA polymerase II subunit [Arabidopsis thaliana] gi|10177729|dbj|BAB11042.1| DNA-directed RNA polymerase II subunit-like protein [Arabidopsis thaliana] gi|17104747|gb|AAL34262.1| putative DNA-directed RNA polymerase II subunit [Arabidopsis thaliana] gi|21595784|gb|AAM66131.1| DNA-directed RNA polymerase II subunit-like protein [Arabidopsis thaliana] gi|332008765|gb|AED96148.1| RNA polymerase Rpb6 [Arabidopsis thaliana]

 Score =  198 bits (503), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 97/115 (84%), Positives = 104/115 (90%)

Query: 10  DAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMV 69
           D E   NDD+NGEPIE E+K E E  +  RKTSK+MTKYERARILGTRALQISMNAPVMV
Sbjct: 30  DVEMKENDDVNGEPIEAEDKVETEPVQRPRKTSKFMTKYERARILGTRALQISMNAPVMV 89

Query: 70  ELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD 124
           ELEGETDPLEIAMKELR+RKIPFTIRRYLPDGS+E+WGVDELIVEDSWKRQVGGD
Sbjct: 90  ELEGETDPLEIAMKELRQRKIPFTIRRYLPDGSFEEWGVDELIVEDSWKRQVGGD 144

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224120092|ref|XP_002318240.1| predicted protein [Populus trichocarpa] gi|222858913|gb|EEE96460.1| predicted protein [Populus trichocarpa]

 Score =  197 bits (502), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 98/105 (93%), Positives = 100/105 (95%)

Query: 20  NGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLE 79
            GEPIETE+KEEQE  E  RKTSK+MTKYERARILGTRALQISMNAPVMVELEGETDPLE
Sbjct: 39  KGEPIETEDKEEQEPVERPRKTSKFMTKYERARILGTRALQISMNAPVMVELEGETDPLE 98

Query: 80  IAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD 124
           IAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD
Sbjct: 99  IAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD 143

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	124
TAIR|locus:2173058	144	NRPB6A [Arabidopsis thaliana (	0.693	0.597	0.953	1.6e-40
TAIR|locus:2049213	144	NRPB6B [Arabidopsis thaliana (	0.693	0.597	0.953	5.3e-40
CGD|CAL0003456	157	RPO26 [Candida albicans (taxid	0.612	0.484	0.815	6.2e-30
UNIPROTKB|Q59QT0	157	RPO26 "Potential subunit commo	0.612	0.484	0.815	6.2e-30
ZFIN|ZDB-GENE-040718-279	127	polr2f "polymerase (RNA) II (D	0.620	0.606	0.818	6.2e-30
MGI|MGI:1349393	127	Polr2f "polymerase (RNA) II (D	0.620	0.606	0.831	1e-29
RGD|708567	127	Polr2f "polymerase (RNA) II (D	0.620	0.606	0.831	1e-29
UNIPROTKB|F1ND65	135	POLR2F "Uncharacterized protei	0.620	0.570	0.831	1.3e-29
UNIPROTKB|Q9PT88	127	RPB6 "RNA polymerase common su	0.620	0.606	0.831	1.3e-29
UNIPROTKB|F2Z4C9	127	POLR2F "DNA-directed RNA polym	0.620	0.606	0.831	1.3e-29

TAIR|locus:2173058 NRPB6A [Arabidopsis thaliana (taxid:3702)]

 Score = 431 (156.8 bits), Expect = 1.6e-40, P = 1.6e-40
 Identities = 82/86 (95%), Positives = 86/86 (100%)

Query:    39 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
             RKTSK+MTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELR+RKIPFTIRRYL
Sbjct:    59 RKTSKFMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRQRKIPFTIRRYL 118

Query:    99 PDGSYEDWGVDELIVEDSWKRQVGGD 124
             PDGS+E+WGVDELIVEDSWKRQVGGD
Sbjct:   119 PDGSFEEWGVDELIVEDSWKRQVGGD 144

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

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0030880 "RNA polymerase complex" evidence=IEA

GO:0000418 "DNA-directed RNA polymerase IV complex" evidence=IPI

GO:0000419 "DNA-directed RNA polymerase V complex" evidence=IPI

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

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

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

TAIR|locus:2049213 NRPB6B [Arabidopsis thaliana (taxid:3702)]

 Score = 426 (155.0 bits), Expect = 5.3e-40, P = 5.3e-40
 Identities = 82/86 (95%), Positives = 85/86 (98%)

Query:    39 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
             RKTSK+MTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELR+RKIPFTIRRYL
Sbjct:    59 RKTSKFMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRQRKIPFTIRRYL 118

Query:    99 PDGSYEDWGVDELIVEDSWKRQVGGD 124
             PD SYE+WGVDELIVEDSWKRQVGGD
Sbjct:   119 PDMSYEEWGVDELIVEDSWKRQVGGD 144

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

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0030880 "RNA polymerase complex" evidence=IEA

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

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

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

CGD|CAL0003456 RPO26 [Candida albicans (taxid:5476)]

 Score = 331 (121.6 bits), Expect = 6.2e-30, P = 6.2e-30
 Identities = 62/76 (81%), Positives = 70/76 (92%)

Query:    39 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
             R T+ YMTKYERARILGTRALQIS+NAPV+V++EGETDPL+IAMKEL +RKIP  IRRYL
Sbjct:    81 RTTTPYMTKYERARILGTRALQISLNAPVLVDIEGETDPLQIAMKELAQRKIPLVIRRYL 140

Query:    99 PDGSYEDWGVDELIVE 114
             PDGSYEDWG DELIV+
Sbjct:   141 PDGSYEDWGCDELIVD 156

GO:0042493 "response to drug" evidence=IMP

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

GO:0005829 "cytosol" evidence=IEA

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

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

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

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

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

GO:0003968 "RNA-directed RNA polymerase activity" evidence=IEA

UNIPROTKB|Q59QT0 RPO26 "Potential subunit common to RNA polymerase I, II and III" [Candida albicans SC5314 (taxid:237561)]

 Score = 331 (121.6 bits), Expect = 6.2e-30, P = 6.2e-30
 Identities = 62/76 (81%), Positives = 70/76 (92%)

Query:    39 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
             R T+ YMTKYERARILGTRALQIS+NAPV+V++EGETDPL+IAMKEL +RKIP  IRRYL
Sbjct:    81 RTTTPYMTKYERARILGTRALQISLNAPVLVDIEGETDPLQIAMKELAQRKIPLVIRRYL 140

Query:    99 PDGSYEDWGVDELIVE 114
             PDGSYEDWG DELIV+
Sbjct:   141 PDGSYEDWGCDELIVD 156

GO:0042493 "response to drug" evidence=IMP

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

 Score = 331 (121.6 bits), Expect = 6.2e-30, P = 6.2e-30
 Identities = 63/77 (81%), Positives = 70/77 (90%)

Query:    39 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
             R T++YMTKYERAR+LGTRALQI+M APVMVELEGETDPL+IAMKEL+ RKIP  IRRYL
Sbjct:    51 RITTQYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKSRKIPIIIRRYL 110

Query:    99 PDGSYEDWGVDELIVED 115
             PDGSYEDWG DELI+ D
Sbjct:   111 PDGSYEDWGCDELIITD 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 = 329 (120.9 bits), Expect = 1.0e-29, P = 1.0e-29
 Identities = 64/77 (83%), Positives = 69/77 (89%)

Query:    39 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
             R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IAMKEL+ RKIP  IRRYL
Sbjct:    51 RITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYL 110

Query:    99 PDGSYEDWGVDELIVED 115
             PDGSYEDWGVDELI+ D
Sbjct:   111 PDGSYEDWGVDELIISD 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

RGD|708567 Polr2f "polymerase (RNA) II (DNA directed) polypeptide F" [Rattus norvegicus (taxid:10116)]

 Score = 329 (120.9 bits), Expect = 1.0e-29, P = 1.0e-29
 Identities = 64/77 (83%), Positives = 69/77 (89%)

Query:    39 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
             R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IAMKEL+ RKIP  IRRYL
Sbjct:    51 RITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYL 110

Query:    99 PDGSYEDWGVDELIVED 115
             PDGSYEDWGVDELI+ D
Sbjct:   111 PDGSYEDWGVDELIISD 127

GO:0003677 "DNA binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISO;TAS

GO:0004672 "protein kinase activity" evidence=ISO;ISS

GO:0005634 "nucleus" evidence=ISO;ISS

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

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

GO:0005730 "nucleolus" evidence=ISO

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

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

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

GO:0032774 "RNA biosynthetic process" evidence=ISO

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

 Score = 328 (120.5 bits), Expect = 1.3e-29, P = 1.3e-29
 Identities = 64/77 (83%), Positives = 69/77 (89%)

Query:    39 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
             R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IAMKEL+ RKIP  IRRYL
Sbjct:    59 RITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYL 118

Query:    99 PDGSYEDWGVDELIVED 115
             PDGSYEDWGVDELI+ D
Sbjct:   119 PDGSYEDWGVDELIITD 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 = 328 (120.5 bits), Expect = 1.3e-29, P = 1.3e-29
 Identities = 64/77 (83%), Positives = 69/77 (89%)

Query:    39 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
             R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IAMKEL+ RKIP  IRRYL
Sbjct:    51 RITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYL 110

Query:    99 PDGSYEDWGVDELIVED 115
             PDGSYEDWGVDELI+ D
Sbjct:   111 PDGSYEDWGVDELIITD 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 = 328 (120.5 bits), Expect = 1.3e-29, P = 1.3e-29
 Identities = 64/77 (83%), Positives = 69/77 (89%)

Query:    39 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
             R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IAMKEL+ RKIP  IRRYL
Sbjct:    51 RITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYL 110

Query:    99 PDGSYEDWGVDELIVED 115
             PDGSYEDWGVDELI+ D
Sbjct:   111 PDGSYEDWGVDELIITD 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

---

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)
P61217	RPAB2_CRIGR	No assigned EC number	0.7234	0.7580	0.7401	yes	no
P61219	RPAB2_MOUSE	No assigned EC number	0.7234	0.7580	0.7401	yes	no
O88828	RPAB2_RAT	No assigned EC number	0.7234	0.7580	0.7401	yes	no
Q32PE0	RPAB2_BOVIN	No assigned EC number	0.6576	0.8225	0.8031	yes	no
P61218	RPAB2_HUMAN	No assigned EC number	0.7234	0.7580	0.7401	yes	no
Q5R592	RPAB2_PONAB	No assigned EC number	0.7234	0.7580	0.7401	yes	no
P36595	RPAB2_SCHPO	No assigned EC number	0.8108	0.5967	0.5211	yes	no
P20435	RPAB2_YEAST	No assigned EC number	0.8157	0.6129	0.4903	yes	no
Q24320	RPAB2_DROME	No assigned EC number	0.6055	0.8225	0.7786	yes	no
Q54FA8	RPAB2_DICDI	No assigned EC number	0.7733	0.6048	0.5639	yes	no
Q17684	RPAB2_CAEEL	No assigned EC number	0.7466	0.6048	0.5474	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_fgenesh4_pg.C_LG_XV1089	DNA-directed RNA polymerase (143 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	fgenesh4_pg.C_LG_XII000913	hypothetical protein (152 aa)						•	•		0.908
	eugene3.00400106	RecName- Full=Nucleoside diphosphate kinase; EC=2.7.4.6; (149 aa)						•	•		0.908
	grail3.0014029901	hypothetical protein (52 aa)				•	•	•	•		0.907
	gw1.II.1445.1	SubName- Full=Putative uncharacterized protein; (164 aa)						•	•		0.907
	estExt_Genewise1_v1.C_LG_XIV2383	CTP synthase (EC-6.3.4.2) (562 aa)				•		•	•		0.904
	gw1.X.1387.1	CTP synthase (EC-6.3.4.2) (589 aa)				•		•	•		0.903
	estExt_Genewise1_v1.C_LG_III0729	CTP synthase (EC-6.3.4.2) (596 aa)				•		•	•		0.902
	gw1.I.8101.1	CTP synthase (EC-6.3.4.2) (591 aa)				•		•	•		0.902
	estExt_fgenesh4_pg.C_LG_I0458	hypothetical protein (204 aa)				•		•			0.902
	fgenesh4_pm.C_LG_VIII000317	CTP synthase (EC-6.3.4.2) (605 aa)				•		•	•		0.902

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	124
PLN00152	130	PLN00152, PLN00152, DNA-directed RNA polymerase; P	3e-54
PRK01099	62	PRK01099, rpoK, DNA-directed RNA polymerase subuni	6e-24
pfam01192	57	pfam01192, RNA_pol_Rpb6, RNA polymerase Rpb6	2e-17
COG1758	74	COG1758, RpoZ, DNA-directed RNA polymerase, subuni	3e-14

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

 Score =  165 bits (419), Expect = 3e-54
 Identities = 93/112 (83%), Positives = 101/112 (90%)

Query: 4   QEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISM 63
           +EGAEED+E+ NND++ G   E E+KEEQE  +  RKT+ YMTKYERARILGTRALQISM
Sbjct: 19  EEGAEEDSESNNNDEVKGSIGENEDKEEQEPVQRPRKTTPYMTKYERARILGTRALQISM 78

Query: 64  NAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 115
           NAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED
Sbjct: 79  NAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 130

Length = 130

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

 Score = 86.9 bits (216), Expect = 6e-24
 Identities = 29/59 (49%), Positives = 44/59 (74%)

Query: 42  SKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPD 100
              +T++ERARI+G RALQISM APV++++   TDPL+IA +E +   +P T++R LP+
Sbjct: 4   PMKLTRFERARIIGARALQISMGAPVLIDIPESTDPLDIAEEEFKRGVLPITVKRPLPN 62

Length = 62

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

 Score = 70.0 bits (172), Expect = 2e-17
 Identities = 27/56 (48%), Positives = 38/56 (67%)

Query: 39 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTI 94
          R TSKY+ +YE ARI+  RA Q+S  AP +V+ E E  P+ IA++E+ + KIP  I
Sbjct: 2  RLTSKYLNRYELARIIAKRAKQLSYGAPPLVDEESEIKPVVIALEEIADGKIPPEI 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 = 62.3 bits (152), Expect = 3e-14
 Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 41  TSKYMTKYERARILGTRALQISMNAPVMVELEGE-TDPLEIAMKELRERKIPFTIRRYLP 99
             K   +YE   +   RA Q++  AP +V+ E     P+ IA++E+ E KIP  I R L 
Sbjct: 10  LDKVGNRYELVVVAAKRARQLAAGAPPLVDDEENKDKPVVIALREIAEGKIPIEILRELL 69

Query: 100 DGSYE 104
             S +
Sbjct: 70  IHSLQ 74

Length = 74

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	124
PLN00152	130	DNA-directed RNA polymerase; Provisional	100.0
KOG3405	136	consensus RNA polymerase subunit K [Transcription]	100.0
PRK01099	62	rpoK DNA-directed RNA polymerase subunit K; Provis	99.93
COG1758	74	RpoZ DNA-directed RNA polymerase, subunit K/omega	99.74
PF01192	57	RNA_pol_Rpb6: RNA polymerase Rpb6 ; InterPro: IPR0	99.67
PRK00392	69	rpoZ DNA-directed RNA polymerase subunit omega; Re	99.3
TIGR00690	59	rpoZ DNA-directed RNA polymerase, omega subunit. T	99.22
PF05320	167	Pox_RNA_Pol_19: Poxvirus DNA-directed RNA polymera	88.45

>PLN00152 DNA-directed RNA polymerase; Provisional

Probab=100.00  E-value=3.1e-40  Score=248.45  Aligned_cols=112  Identities=83%  Similarity=1.219  Sum_probs=101.1

Q ss_pred             cCccchhhhccCCCCCCCCCCcchhHHHHHhHHhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHH
Q 033231            4 QEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMK   83 (124)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~T~~~LTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~   83 (124)
                      +++++++.+++|+++.++......++..++....+|+|++||||||+|||+|+||+|||||||+||++++.++|+.||++
T Consensus        19 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~T~p~lTkyErARIiG~RALQIsmgApvlV~~~g~tdPl~IA~~   98 (130)
T PLN00152         19 EEGAEEDSESNNNDEVKGSIGENEDKEEQEPVQRPRKTTPYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMK   98 (130)
T ss_pred             cccccccccccCcccccccccchhccccccccccccccccchhHHHHHhhHhHHHHHHhcCCceEEccCCCcCHHHHHHH
Confidence            35666666777777767777777777777778889999999999999999999999999999999999878999999999


Q ss_pred             HHHcCCccEEEEEecCCCcEEEeecceeeecc
Q 033231           84 ELRERKIPFTIRRYLPDGSYEDWGVDELIVED  115 (124)
Q Consensus        84 EL~eGkIpi~IrR~lpdg~yE~~~l~eL~i~~  115 (124)
                      ||.+|+|||+|||+||||+||+|+|+||++++
T Consensus        99 El~~~~iP~iVrR~lPdG~yEd~~v~EL~~~~  130 (130)
T PLN00152         99 ELRERKIPFTIRRYLPDGSYEDWGVDELIVED  130 (130)
T ss_pred             HHHcCCCCeEEEEECCCCCEEeeEeeeEeecC
Confidence            99999999999999999999999999999875

>KOG3405 consensus RNA polymerase subunit K [Transcription]

Probab=100.00  E-value=8.9e-40  Score=246.66  Aligned_cols=94  Identities=76%  Similarity=1.178  Sum_probs=86.7

Q ss_pred             CCCCcchhHHHHHhHHhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCccEEEEEecCC
Q 033231           21 GEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPD  100 (124)
Q Consensus        21 ~~~~~~~~~~~~~~~~~~r~T~~~LTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lpd  100 (124)
                      .+.+++.+-. +.++.++|+|.|||||||+|||+|+||+|||||||+||++++.+||+.||++||+++||||+|||||||
T Consensus        43 e~~~e~~~~g-~~v~~s~R~TtpyMTKYErArvLGtRAlQIsm~APvmVeLegETdPL~IAmkEL~qkKIP~iIRRyLPD  121 (136)
T KOG3405|consen   43 EDVVEIEDAG-KAVPKSERKTTPYMTKYERARVLGTRALQISMNAPVMVELEGETDPLEIAMKELKQKKIPFIIRRYLPD  121 (136)
T ss_pred             hhhhcccccc-ccccccccccCcchhHHHHHHhhhHHHHHHhcCCCeEEecCCCCCHHHHHHHHHhhccCceEEeeeCCC
Confidence            4555555554 566788999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcEEEeecceeeecc
Q 033231          101 GSYEDWGVDELIVED  115 (124)
Q Consensus       101 g~yE~~~l~eL~i~~  115 (124)
                      |+||+|+++||+|++
T Consensus       122 gSyEDW~vdELiv~d  136 (136)
T KOG3405|consen  122 GSYEDWSVDELIVED  136 (136)
T ss_pred             CCccccccceeeccC
Confidence            999999999999875

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

Probab=99.93  E-value=2.6e-26  Score=153.53  Aligned_cols=61  Identities=48%  Similarity=0.838  Sum_probs=58.3

Q ss_pred             cCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCccEEEEEecCC
Q 033231           40 KTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPD  100 (124)
Q Consensus        40 ~T~~~LTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lpd  100 (124)
                      .+++||||||+||++|+||+||++||+|+|+.+.++||+.||++||++|+||++|+|++||
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            4789999999999999999999999999999855899999999999999999999999997

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

Probab=99.74  E-value=2e-18  Score=117.58  Aligned_cols=67  Identities=33%  Similarity=0.422  Sum_probs=60.3

Q ss_pred             hhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCC-CChHHHHHHHHHcCCccEEEEEecCCCcEE
Q 033231           38 ARKTSKYMTKYERARILGTRALQISMNAPVMVELEGE-TDPLEIAMKELRERKIPFTIRRYLPDGSYE  104 (124)
Q Consensus        38 ~r~T~~~LTKYElARIiG~RAlQLs~GApplVd~~~~-~dPv~IA~~EL~eGkIpi~IrR~lpdg~yE  104 (124)
                      +.......|||++|+++|+||+||++||+++++.... .+|+.||++||.+|+||+.+.|..++++.+
T Consensus         7 ~~l~~~~~~ryelv~~aa~RA~Ql~~ga~~~~~~~~~~~kpv~iAl~Ei~~g~i~~~i~~~~~~~~~~   74 (74)
T COG1758           7 EDLLDKVGNRYELVVVAAKRARQLAAGAPPLVDDEENKDKPVVIALREIAEGKIPIEILRELLIHSLQ   74 (74)
T ss_pred             HHHHhhccCHHHHHHHHHHHHHHHHcCCCCccccccccCChHHHHHHHHHcCCCCcccchhhhccccC
Confidence            4456788899999999999999999999999988753 899999999999999999999999988753

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

Probab=99.67  E-value=7.6e-17  Score=104.07  Aligned_cols=55  Identities=36%  Similarity=0.491  Sum_probs=50.3

Q ss_pred             cCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCccEEE
Q 033231           40 KTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTI   94 (124)
Q Consensus        40 ~T~~~LTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~I   94 (124)
                      ......|||++++++|+||+||++||+|+++.+...+|+.||++||.+|+|+|.|
T Consensus         3 l~~~~~~rY~Lv~~~akRArql~~g~~~~~~~~~~~k~v~iAl~EI~~gki~~~i   57 (57)
T PF01192_consen    3 LLEKVDNRYELVILAAKRARQLSEGAPPLVEEDNEMKPVSIALEEIAEGKIKIEI   57 (57)
T ss_dssp             HHHSSSSHHHHHHHHHHHHHHHHTTSTTSSSSSSSSSSSHHHHHHHHTTSSCEEE
T ss_pred             hhhccCCHhHHHHHHHHHHHHHHcCcccccccccCCCcHHHHHHHHHcCCCCCcC
Confidence            3457789999999999999999999999998875669999999999999999986

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=99.30  E-value=5.2e-12  Score=83.73  Aligned_cols=49  Identities=29%  Similarity=0.449  Sum_probs=45.2

Q ss_pred             cHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCccEEEE
Q 033231           46 TKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIR   95 (124)
Q Consensus        46 TKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~Ir   95 (124)
                      +||.++.++++||+||+.|++++++.. ..+|+.||++||.+|+|.|..-
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            899999999999999999999987765 6899999999999999998764

>TIGR00690 rpoZ DNA-directed RNA polymerase, omega subunit

Probab=99.22  E-value=2.4e-11  Score=80.04  Aligned_cols=45  Identities=22%  Similarity=0.408  Sum_probs=39.5

Q ss_pred             cHHHHHHHHHHHHHHHhhcC-CceecCCCCCChHHHHHHHHHcCCcc
Q 033231           46 TKYERARILGTRALQISMNA-PVMVELEGETDPLEIAMKELRERKIP   91 (124)
Q Consensus        46 TKYElARIiG~RAlQLs~GA-pplVd~~~~~dPv~IA~~EL~eGkIp   91 (124)
                      +||.++.++++||+||+.|+ +++++.. +.+|+.||++||.+|+|.
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            89999999999999999876 5555554 799999999999999974

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=88.45  E-value=1.2  Score=35.61  Aligned_cols=61  Identities=16%  Similarity=0.322  Sum_probs=49.9

Q ss_pred             HhhhcCCccccHHHHHHHHHHHHHHHhhcCCceec-CCC---CCChHHHHHHHHHcCCccEEEEE
Q 033231           36 EAARKTSKYMTKYERARILGTRALQISMNAPVMVE-LEG---ETDPLEIAMKELRERKIPFTIRR   96 (124)
Q Consensus        36 ~~~r~T~~~LTKYElARIiG~RAlQLs~GApplVd-~~~---~~dPv~IA~~EL~eGkIpi~IrR   96 (124)
                      +-.|+-...++=||+.=|+|.--.-|..|-.|||. ...   ..+-+.|-++||.+|.-|++|..
T Consensus        71 ~iK~RYTRRiSLfEiTGIiaESyNLLqRGRlPLv~dlsdeT~k~n~L~vvi~EIeEg~CPIVIeK  135 (167)
T PF05320_consen   71 AIKKRYTRRISLFEITGIIAESYNLLQRGRLPLVSDLSDETLKDNILHVVIKEIEEGTCPIVIEK  135 (167)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHHHHccccccccccchHHHHHhHHHHHHHHHhcCCCcEEEee
Confidence            33455557789999999999999999999999995 221   24568899999999999999986

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	124
1qkl_A	127	Hrpabc14.4, Essential Subunit Of Human Rna Polymera		3e-32
1i3q_F	155	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		1e-31
3j0k_F	84	Orientation Of Rna Polymerase Ii Within The Human V		2e-31
3h0g_F	142	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		3e-31
2waq_K	95	The Complete Structure Of The Archaeal 13-Subunit D		5e-09
2pmz_K	95	Archaeal Rna Polymerase From Sulfolobus Solfataricu		5e-09
2y0s_I	95	Crystal Structure Of Sulfolobus Shibatae Rna Polyme		1e-08

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

Iteration: 1
 Score =  133 bits (334), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 64/77 (83%), Positives = 69/77 (89%)
Query: 39  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
           R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IAMKEL+ RKIP  IRRYL
Sbjct: 51  RITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYL 110
Query: 99  PDGSYEDWGVDELIVED 115
           PDGSYEDWGVDELI+ D
Sbjct: 111 PDGSYEDWGVDELIITD 127

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

Iteration: 1
 Score =  131 bits (329), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 62/76 (81%), Positives = 68/76 (89%)
Query: 39  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
           R T+ YMTKYERARILGTRALQISMNAPV V+LEGETDPL IAMKEL E+KIP  IRRYL
Sbjct: 79  RATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYL 138
Query: 99  PDGSYEDWGVDELIVE 114
           PDGS+EDW V+ELIV+
Sbjct: 139 PDGSFEDWSVEELIVD 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 =  130 bits (328), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 62/76 (81%), Positives = 68/76 (89%)
Query: 39  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
           R T+ YMTKYERARILGTRALQISMNAPV V+LEGETDPL IAMKEL E+KIP  IRRYL
Sbjct: 8   RATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYL 67
Query: 99  PDGSYEDWGVDELIVE 114
           PDGS+EDW V+ELIV+
Sbjct: 68  PDGSFEDWSVEELIVD 83

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

Iteration: 1
 Score =  130 bits (326), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 60/74 (81%), Positives = 67/74 (90%)
Query: 39  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
           R T+ YMTKYERARILGTRALQISMNAPV+V+LEGETDPL+IAMKEL ++KIP  +RRYL
Sbjct: 69  RTTTPYMTKYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRYL 128
Query: 99  PDGSYEDWGVDELI 112
           PDGSYEDW V ELI
Sbjct: 129 PDGSYEDWSVAELI 142

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 40/59 (67%), Gaps = 2/59 (3%)
Query: 45  MTKYERARILGTRALQISMNAPVMVELEG--ETDPLEIAMKELRERKIPFTIRRYLPDG 101
           +T+YE AR++  RALQ++M AP ++++     TD + IA +E R   +P TIRR LP+G
Sbjct: 27  LTRYEIARVISARALQLAMGAPALIDINNLSSTDVISIAEEEFRRGVLPITIRRRLPNG 85

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 40/59 (67%), Gaps = 2/59 (3%)
Query: 45  MTKYERARILGTRALQISMNAPVMVELEG--ETDPLEIAMKELRERKIPFTIRRYLPDG 101
           +T+YE AR++  RALQ++M AP ++++     TD + IA +E R   +P TIRR LP+G
Sbjct: 27  LTRYEIARVISARALQLAMGAPALIDINNLSSTDVISIAEEEFRRGVLPITIRRRLPNG 85

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/59 (42%), Positives = 40/59 (67%), Gaps = 2/59 (3%)
Query: 45  MTKYERARILGTRALQISMNAPVMVELEG--ETDPLEIAMKELRERKIPFTIRRYLPDG 101
           +T+YE AR++  RALQ++M AP ++++     TD + IA +E +   +P TIRR LP+G
Sbjct: 27  LTRYEIARVISARALQLAMGAPALIDINNISSTDVISIAEEEFKRGVLPITIRRRLPNG 85

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	124
1qkl_A	127	RPB6, DNA-directed RNA polymerase II 14.4 KD polyp	1e-33
4ayb_K	95	DNA-directed RNA polymerase; transferase, multi-su	1e-32
3h0g_F	142	DNA-directed RNA polymerases I, II, and III subuni	6e-31
1twf_F	155	ABC23, DNA-directed RNA polymerases I, II, and III	5e-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 (283), Expect = 1e-33
 Identities = 71/111 (63%), Positives = 81/111 (72%)

Query: 5   EGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMN 64
           E  E   +  N ++   E +E     E+ Q    R T+ YMTKYERAR+LGTRALQI+M 
Sbjct: 17  EEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMC 76

Query: 65  APVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 115
           APVMVELEGETDPL IAMKEL+ RKIP  IRRYLPDGSYEDWGVDELI+ D
Sbjct: 77  APVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITD 127

>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 =  109 bits (274), Expect = 1e-32
 Identities = 28/100 (28%), Positives = 48/100 (48%), Gaps = 9/100 (9%)

Query: 13  NINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELE 72
            +  D I  + +   E                +T+YE AR++  RALQ++M AP ++++ 
Sbjct: 2   GLERDGILSQDLHFNEVFV-------SLWQNKLTRYEIARVISARALQLAMGAPALIDIN 54

Query: 73  --GETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDE 110
               TD + IA +E +   +P TIRR LP+G      + +
Sbjct: 55  NISSTDVISIAEEEFKRGVLPITIRRRLPNGKIILLSLRK 94

>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 =  106 bits (265), Expect = 6e-31
 Identities = 62/108 (57%), Positives = 73/108 (67%)

Query: 5   EGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMN 64
           +G     E                +  +   +  R T+ YMTKYERARILGTRALQISMN
Sbjct: 35  QGVSHPGEPSTTVITEDVASSKTAQSGKAVAKEDRTTTPYMTKYERARILGTRALQISMN 94

Query: 65  APVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELI 112
           APV+V+LEGETDPL+IAMKEL ++KIP  +RRYLPDGSYEDW V ELI
Sbjct: 95  APVLVDLEGETDPLQIAMKELAQKKIPLLVRRYLPDGSYEDWSVAELI 142

>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 =  104 bits (260), Expect = 5e-30
 Identities = 67/117 (57%), Positives = 81/117 (69%), Gaps = 6/117 (5%)

Query: 4   QEGAEEDAENINNDDINGEPIETEEK------EEQEQKEAARKTSKYMTKYERARILGTR 57
            E  + + + I       E  +  E+      +E+   +  R T+ YMTKYERARILGTR
Sbjct: 38  GETTDANGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTR 97

Query: 58  ALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVE 114
           ALQISMNAPV V+LEGETDPL IAMKEL E+KIP  IRRYLPDGS+EDW V+ELIV+
Sbjct: 98  ALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVD 154

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	124
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	99.97
3lu0_E	91	DNA-directed RNA polymerase subunit omega; E. coli	99.26
2a6h_E	99	RNA polymerase omega chain; RNA polymerase holoenz	99.15

>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=3.8e-37  Score=230.01  Aligned_cols=94  Identities=72%  Similarity=1.097  Sum_probs=85.4

Q ss_pred             CCCcchhHHHHHhHHhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCccEEEEEecCCC
Q 033231           22 EPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG  101 (124)
Q Consensus        22 ~~~~~~~~~~~~~~~~~r~T~~~LTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lpdg  101 (124)
                      +.+++.......+....|+|+|||||||+|||+|+||+||||||||||++++.+||+.||++||++|+|||+|||+||||
T Consensus        34 ~~~~~~~~~~~~~~~~~r~t~p~lTRYElARIiG~RAlQLs~GAppLVd~e~~~dPl~IAl~ElaeGkIpi~VrR~lPdg  113 (127)
T 1qkl_A           34 ENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDG  113 (127)
T ss_dssp             CEEEEEESCCCTTTCCCSSCCSSCCHHHHHHHHHHHHHHHHHSCCSSSCSSSSCSSSHHHHHHHHHTCCCEEEEEEETTT
T ss_pred             ccceeccccCcCCCccccccCCCcCHHHHHHHHHHHHHHHhcCCcceEcCCCCCCHHHHHHHHHHcCCCCeEEEEECCCC
Confidence            44455545556677889999999999999999999999999999999999877899999999999999999999999999


Q ss_pred             cEEEeecceeeecc
Q 033231          102 SYEDWGVDELIVED  115 (124)
Q Consensus       102 ~yE~~~l~eL~i~~  115 (124)
                      +||+|++++|+|++
T Consensus       114 ~yEd~~~~eL~i~~  127 (127)
T 1qkl_A          114 SYEDWGVDELIITD  127 (127)
T ss_dssp             EEEEESSSSSCSCC
T ss_pred             CEEEeehhheeccC
Confidence            99999999999874

>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=6.2e-36  Score=226.86  Aligned_cols=81  Identities=74%  Similarity=1.180  Sum_probs=77.0

Q ss_pred             HHhHHhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCccEEEEEecCCCcEEEeeccee
Q 033231           32 QEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDEL  111 (124)
Q Consensus        32 ~~~~~~~r~T~~~LTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lpdg~yE~~~l~eL  111 (124)
                      ++.+..+|+|+|||||||+|||+|+||+||||||||||+++++++|++||++||++|+|||+|||++|||+||+|+|+||
T Consensus        62 ~~~~~~~R~T~pylTRYElARIiG~RAlQIsmGAp~LVd~~~~tdPl~IA~~EL~egkIPiiVrR~lPdgkyEdw~l~EL  141 (142)
T 3h0g_F           62 KAVAKEDRTTTPYMTKYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRYLPDGSYEDWSVAEL  141 (142)
T ss_dssp             CCCCTTSCCSCSSCCHHHHHHHHHHHHHHHHTCCCCCSCCCSCCCTTHHHHHHHHTTCCCCEEECCCSSSCCCEEETTTC
T ss_pred             ccCCcccccCCCccCHHHHHHHHHHHHHHHHCCCCceEcCCCCCCHHHHHHHHHHcCCCceEEEEECCCCCEEEeEHHHc
Confidence            34557889999999999999999999999999999999998789999999999999999999999999999999999999


Q ss_pred             e
Q 033231          112 I  112 (124)
Q Consensus       112 ~  112 (124)
                      +
T Consensus       142 ~  142 (142)
T 3h0g_F          142 I  142 (142)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=3.5e-35  Score=225.30  Aligned_cols=85  Identities=74%  Similarity=1.149  Sum_probs=79.4

Q ss_pred             HHHhHHhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCccEEEEEecCCCcEEEeecce
Q 033231           31 EQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDE  110 (124)
Q Consensus        31 ~~~~~~~~r~T~~~LTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lpdg~yE~~~l~e  110 (124)
                      .++++...|+|++||||||+|||+|+||+||||||||||++++.+||+.||++||++|+|||+|||+||||+||+|+|+|
T Consensus        71 ~~~~~~~~r~t~p~lTRYElARIiG~RAlQLsmGAppLVd~e~~~dPl~IAl~ElaeGkIPl~IrR~lPdG~yEd~~v~e  150 (155)
T 1twf_F           71 EKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEE  150 (155)
T ss_dssp             -CCCCSSSCCSCSBCCHHHHHHHHHHHHHHHHTTCCCSSCCSSCCSHHHHHHHHHHTTCCCEEEEEECTTSCEEEEETTT
T ss_pred             cccCCcccccCCCCcCHHHHHHHHHHHHHHHhcCCCcEEecCCCCCHHHHHHHHHHcCCCCeEEEEECCCCCEEEeeHHH
Confidence            34455678999999999999999999999999999999999877899999999999999999999999999999999999


Q ss_pred             eeecc
Q 033231          111 LIVED  115 (124)
Q Consensus       111 L~i~~  115 (124)
                      |+|++
T Consensus       151 L~~~~  155 (155)
T 1twf_F          151 LIVDL  155 (155)
T ss_dssp             SBCCC
T ss_pred             hccCC
Confidence            99974

>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=4.3e-31  Score=189.02  Aligned_cols=69  Identities=36%  Similarity=0.659  Sum_probs=65.2

Q ss_pred             CccccHHHHHHHHHHHHHHHhhcCCceecCCC--CCChHHHHHHHHHcCCccEEEEEecCCCcEEEeecce
Q 033231           42 SKYMTKYERARILGTRALQISMNAPVMVELEG--ETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDE  110 (124)
Q Consensus        42 ~~~LTKYElARIiG~RAlQLs~GApplVd~~~--~~dPv~IA~~EL~eGkIpi~IrR~lpdg~yE~~~l~e  110 (124)
                      .+.|||||+|||+|+||+||||||||||+++.  .+||+.||++||.+|+|||+|||++|||+||+|+|+|
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            35699999999999999999999999999863  6899999999999999999999999999999999986

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

Probab=99.26  E-value=2.1e-12  Score=91.09  Aligned_cols=50  Identities=22%  Similarity=0.294  Sum_probs=46.4

Q ss_pred             cHHHHHHHHHHHHHHHhh-cCCceecCCCCCChHHHHHHHHHcCCccEEEEE
Q 033231           46 TKYERARILGTRALQISM-NAPVMVELEGETDPLEIAMKELRERKIPFTIRR   96 (124)
Q Consensus        46 TKYElARIiG~RAlQLs~-GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR   96 (124)
                      +||+++.++++||+||+. |++|+|+.+ +.+|+.||++||.+|+|.+.+..
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            899999999999999998 999999976 79999999999999999987543

>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=99.15  E-value=4.1e-11  Score=85.26  Aligned_cols=48  Identities=25%  Similarity=0.317  Sum_probs=41.8

Q ss_pred             cHHHHHHHHHHHHHHHhhcC--CceecC---CCCC---------ChHHHHHHHHHcCCccEE
Q 033231           46 TKYERARILGTRALQISMNA--PVMVEL---EGET---------DPLEIAMKELRERKIPFT   93 (124)
Q Consensus        46 TKYElARIiG~RAlQLs~GA--pplVd~---~~~~---------dPv~IA~~EL~eGkIpi~   93 (124)
                      +||+++.++++||+||+.|+  .++++.   ..+.         +|+.||++||.+|+|.|.
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  999872   1123         999999999999999763

---

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	124
d1twff_	84	a.143.1.2 (F:) RPB6 {Baker's yeast (Saccharomyces	4e-41
d1qkla_	127	a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId:	1e-38

>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 =  129 bits (326), Expect = 4e-41
 Identities = 62/76 (81%), Positives = 68/76 (89%)

Query: 39  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
           R T+ YMTKYERARILGTRALQISMNAPV V+LEGETDPL IAMKEL E+KIP  IRRYL
Sbjct: 8   RATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYL 67

Query: 99  PDGSYEDWGVDELIVE 114
           PDGS+EDW V+ELIV+
Sbjct: 68  PDGSFEDWSVEELIVD 83

>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 =  124 bits (313), Expect = 1e-38
 Identities = 71/112 (63%), Positives = 82/112 (73%), Gaps = 3/112 (2%)

Query: 4   QEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISM 63
            EG ++          N E + + E+ +  QK   R T+ YMTKYERAR+LGTRALQI+M
Sbjct: 19  DEGLDDLENAEEEGQENVEILPSGERPQANQK---RITTPYMTKYERARVLGTRALQIAM 75

Query: 64  NAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 115
            APVMVELEGETDPL IAMKEL+ RKIP  IRRYLPDGSYEDWGVDELI+ D
Sbjct: 76  CAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITD 127

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	124
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	97.66

>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=1.5e-35  Score=206.21  Aligned_cols=80  Identities=78%  Similarity=1.224  Sum_probs=77.3

Q ss_pred             HHhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCccEEEEEecCCCcEEEeecceeeec
Q 033231           35 KEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVE  114 (124)
Q Consensus        35 ~~~~r~T~~~LTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lpdg~yE~~~l~eL~i~  114 (124)
                      ....|+|+|+|||||+|||+|.||+|||+||+|+|++++.++|+.||.+||.+|+|||+|+|++|||+||+|+|++|+||
T Consensus         4 ~~~~~~T~p~LTkYE~ariiG~Ra~Ql~~Ga~p~I~~~~~~d~~~IA~~El~~~kiP~iIrR~lP~g~~E~w~l~dL~id   83 (84)
T d1twff_           4 PKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVD   83 (84)
T ss_dssp             CSSSCCSCSBCCHHHHHHHHHHHHHHHHTTCCCSSCCSSCCSHHHHHHHHHHTTCCCEEEEEECTTSCEEEEETTTSBCC
T ss_pred             CCcCcccCccccHHHHHHHHHHHHHHHHcCCCceecCCCCCCHHHHHHHHHHcCCCCEEEEEECCCCCEEEEEHHHeeec
Confidence            45789999999999999999999999999999999998789999999999999999999999999999999999999987

>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=6.8e-36  Score=220.81  Aligned_cols=91  Identities=74%  Similarity=1.112  Sum_probs=83.3

Q ss_pred             cchhHHHHHhHHhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCccEEEEEecCCCcEE
Q 033231           25 ETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYE  104 (124)
Q Consensus        25 ~~~~~~~~~~~~~~r~T~~~LTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lpdg~yE  104 (124)
                      .+....+..+.+..|+|+|||||||+|||+|.||+|||+||||||++++.++|+.||++||.+|+|||+|||++|||+||
T Consensus        37 ~i~~~~~~~~~~~~~~T~p~lTkYE~arilG~Ra~Qi~~ga~~~i~~~~~~d~~~IA~~EL~~kkiPfiIrR~lp~g~~E  116 (127)
T d1qkla_          37 EILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYE  116 (127)
T ss_dssp             EEEESCCCTTTCCCSSCCSSCCHHHHHHHHHHHHHHHHHSCCSSSCSSSSCSSSHHHHHHHHHTCCCEEEEEEETTTEEE
T ss_pred             hhhhcccccccCcccccCCcccHHHHHHHHHHHHHHHhcCCCceecCCCCCCHHHHHHHHHHcCCCCEEEEEECCCCCEE
Confidence            34344445567889999999999999999999999999999999999888999999999999999999999999999999


Q ss_pred             Eeecceeeecc
Q 033231          105 DWGVDELIVED  115 (124)
Q Consensus       105 ~~~l~eL~i~~  115 (124)
                      +|+|++|+|++
T Consensus       117 ~w~l~dL~i~~  127 (127)
T d1qkla_         117 DWGVDELIITD  127 (127)
T ss_dssp             EESSSSSCSCC
T ss_pred             EEEhHheEecC
Confidence            99999999874

>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=97.66  E-value=3e-05  Score=53.54  Aligned_cols=45  Identities=27%  Similarity=0.361  Sum_probs=37.4

Q ss_pred             cHHHHHHHHHHHHHH-HhhcCC-ceecCCC----C--------CChHHHHHHHHHcCCc
Q 033231           46 TKYERARILGTRALQ-ISMNAP-VMVELEG----E--------TDPLEIAMKELRERKI   90 (124)
Q Consensus        46 TKYElARIiG~RAlQ-Ls~GAp-plVd~~~----~--------~dPv~IA~~EL~eGkI   90 (124)
                      |||-+..++|+||.| |-.|.| .+++.+.    .        -++++.|++||.-|++
T Consensus        14 SkYRLsvVvakRA~QlLr~g~~ntvL~pde~p~~~tleg~~~dpN~vt~AMkEL~tGrl   72 (95)
T d1smye_          14 SKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAETWAMKELLTGRL   72 (95)
T ss_dssp             SHHHHHHHHHHHHHHHHHTCTTCCSCCSSSCCCCSSSSGGGTSSCSHHHHHHHHTTTCE
T ss_pred             cceeeehhhHHHHHHHHHcCCCccccChhhhhhhhcccccCCCCcHHHHHHHHHHhCce
Confidence            799999999999999 888998 5555432    1        2789999999999993