Citrus Sinensis ID: 032288

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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---
Protein Sequence
MADEDYNDLDMGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHcccccEEEEEEcccccEEEEEccEEEEccHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHHccccEEEEEEccccccccccccEEEEccccHHccccc
Coil and Loop (DISEMBL)
madedyndldmgyedeppepeieegaeedaeninnddingepietEEKEEQEQKEAARKTSKYMTKYERARILGTRAlqismnapvmvelegetdPLEIAMKELRErkipftirrylpdgsyedwgvdelivedswkrqvggd
Flexible Loop (DISEMBL)
madedyndldmgyedeppePEIEegaeedaeninnDDINGEPIETEEKEEQEQKeaarktskymtkYERARILGTRALQISMNAPVMVELEGETDPLEIAMKElrerkipftirrylpdgsyedwgvdelivedswkrqvggd
Low Complexity Region (SEG)
MADEDYNDLDMGYedeppepeieegaeedaeninnddingepieteekeeqeqkeAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD
Disordered region (IsUnstruct)
*****************************************************************KYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSW*******
Disordered Region (DISOPRED)
*ADEDYNDLDMGYEDEPPEPE*****************************************YMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQ****
Disordered Region (DISEMBL)
********LDMGYE**************DAENINNDDINGEPIE*****************KYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD
Disordered Region (DISPRO)
********************************************************ARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWK******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MADEDYNDLDMGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWKRQVGGD
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	143	2.2.26 [Sep-21-2011]
Q32PE0	127	DNA-directed RNA polymera	yes	no	0.713	0.803	0.657	6e-33
O88828	127	DNA-directed RNA polymera	yes	no	0.657	0.740	0.723	1e-32
P61219	127	DNA-directed RNA polymera	yes	no	0.657	0.740	0.723	1e-32
Q5R592	127	DNA-directed RNA polymera	yes	no	0.657	0.740	0.723	1e-32
P61218	127	DNA-directed RNA polymera	yes	no	0.657	0.740	0.723	1e-32
P61217	127	DNA-directed RNA polymera	yes	no	0.657	0.740	0.723	1e-32
P20435	155	DNA-directed RNA polymera	yes	no	0.867	0.8	0.532	2e-31
Q24320	131	DNA-directed RNA polymera	yes	no	0.713	0.778	0.605	5e-31
P36595	142	DNA-directed RNA polymera	yes	no	0.643	0.647	0.666	6e-31
Q54FA8	133	DNA-directed RNA polymera	yes	no	0.524	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 (350), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 73/111 (65%), Positives = 85/111 (76%), Gaps = 9/111 (8%)

Query: 24  EGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMN 83
           E AEE+ +      +N E + + E+ +  QK   R T+ YMTKYERAR+LGTRALQI+M 
Sbjct: 26  ENAEEEGQ------VNVEILPSGERPQANQK---RITTPYMTKYERARVLGTRALQIAMC 76

Query: 84  APVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 134
           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 =  138 bits (348), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 68/94 (72%), Positives = 75/94 (79%)

Query: 41  EPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIA 100
           E +E     E+ Q    R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IA
Sbjct: 34  ENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIA 93

Query: 101 MKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 134
           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 =  138 bits (348), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 68/94 (72%), Positives = 75/94 (79%)

Query: 41  EPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIA 100
           E +E     E+ Q    R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IA
Sbjct: 34  ENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIA 93

Query: 101 MKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 134
           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 (347), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 68/94 (72%), Positives = 75/94 (79%)

Query: 41  EPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIA 100
           E +E     E+ Q    R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IA
Sbjct: 34  ENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIA 93

Query: 101 MKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 134
           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 (347), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 68/94 (72%), Positives = 75/94 (79%)

Query: 41  EPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIA 100
           E +E     E+ Q    R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IA
Sbjct: 34  ENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIA 93

Query: 101 MKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 134
           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 (347), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 68/94 (72%), Positives = 75/94 (79%)

Query: 41  EPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIA 100
           E +E     E+ Q    R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IA
Sbjct: 34  ENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIA 93

Query: 101 MKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 134
           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 (337), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 81/152 (53%), Positives = 100/152 (65%), Gaps = 28/152 (18%)

Query: 2   ADEDYNDLDM-GYEDEPP---EPEIEEGAEEDAENINNDDINGEPIET-----EEKEEQE 52
            +E++ D D+  + DE     +P+ ++G   DA        NG+ I T     E+ ++ E
Sbjct: 11  GNENFEDFDVEHFSDEETYEEKPQFKDGETTDA--------NGKTIVTGGNGPEDFQQHE 62

Query: 53  Q------KEAA-----RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAM 101
           Q      KE A     R T+ YMTKYERARILGTRALQISMNAPV V+LEGETDPL IAM
Sbjct: 63  QIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAM 122

Query: 102 KELRERKIPFTIRRYLPDGSYEDWGVDELIVE 133
           KEL E+KIP  IRRYLPDGS+EDW V+ELIV+
Sbjct: 123 KELAEKKIPLVIRRYLPDGSFEDWSVEELIVD 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 =  132 bits (333), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 66/109 (60%), Positives = 82/109 (75%), Gaps = 7/109 (6%)

Query: 27  EEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPV 86
           EE+A+NI       E I           ++ R T+KYMTKYERAR+LGTRALQI+M AP+
Sbjct: 30  EEEADNI-------EIIAPGGAGGGGVPKSKRITTKYMTKYERARVLGTRALQIAMCAPI 82

Query: 87  MVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDS 135
           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 =  132 bits (332), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 68/102 (66%), Positives = 75/102 (73%), Gaps = 10/102 (9%)

Query: 40  GEPIET-------EEKEEQEQKEAA---RKTSKYMTKYERARILGTRALQISMNAPVMVE 89
           GEP  T         K  Q  K  A   R T+ YMTKYERARILGTRALQISMNAPV+V+
Sbjct: 41  GEPSTTVITEDVASSKTAQSGKAVAKEDRTTTPYMTKYERARILGTRALQISMNAPVLVD 100

Query: 90  LEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELI 131
           LEGETDPL+IAMKEL ++KIP  +RRYLPDGSYEDW V ELI
Sbjct: 101 LEGETDPLQIAMKELAQKKIPLLVRRYLPDGSYEDWSVAELI 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: 58  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 117
           RKT++YMTKYERAR+LG+RALQISMNAP+MVELEGETDPL+IA KELR +KIP  IRR+L
Sbjct: 59  RKTTRYMTKYERARLLGSRALQISMNAPIMVELEGETDPLQIAWKELRAKKIPLIIRRFL 118

Query: 118 PDGSYEDWGVDELIV 132
           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	143
224136924	143	predicted protein [Populus trichocarpa]	1.0	1.0	0.888	7e-65
297792515	144	hypothetical protein ARALYDRAFT_495261 [	1.0	0.993	0.840	1e-55
15242235	144	RNA polymerase Rpb6 [Arabidopsis thalian	1.0	0.993	0.840	1e-55
297835766	144	hypothetical protein ARALYDRAFT_899271 [	1.0	0.993	0.833	5e-55
356535896	142	PREDICTED: DNA-directed RNA polymerases	0.993	1.0	0.881	4e-54
351724737	142	uncharacterized protein LOC100305739 [Gl	0.993	1.0	0.881	8e-54
224120092	143	predicted protein [Populus trichocarpa]	1.0	1.0	0.909	4e-53
15224039	144	RNA polymerase Rpb6 [Arabidopsis thalian	1.0	0.993	0.812	6e-53
326495054	142	predicted protein [Hordeum vulgare subsp	0.979	0.985	0.790	1e-52
449437154	142	PREDICTED: DNA-directed RNA polymerases	0.986	0.992	0.866	1e-52

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

 Score =  251 bits (641), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 127/143 (88%), Positives = 134/143 (93%)

Query: 1   MADEDYNDLDMGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKT 60
           MAD++YND+DMGYEDEP EPEIEEGA+EDAEN NN+D  GEPIETE+KEEQ   E  RKT
Sbjct: 1   MADDEYNDVDMGYEDEPAEPEIEEGADEDAENNNNEDDTGEPIETEDKEEQAPVERPRKT 60

Query: 61  SKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG 120
           SK+MTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG
Sbjct: 61  SKFMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG 120

Query: 121 SYEDWGVDELIVEDSWKRQVGGD 143
           SYEDWGVDELIVEDSWKRQVGGD
Sbjct: 121 SYEDWGVDELIVEDSWKRQVGGD 143

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  220 bits (561), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 121/144 (84%), Positives = 132/144 (91%), Gaps = 1/144 (0%)

Query: 1   MADEDYNDLD-MGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARK 59
           MADEDYN++D +GYEDEP EPEIEEG EEDAE   NDD+NGEP+ETE+K E E  +  RK
Sbjct: 1   MADEDYNEVDDLGYEDEPVEPEIEEGVEEDAEMKENDDVNGEPLETEDKVETEPVQRPRK 60

Query: 60  TSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPD 119
           TSK+MTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELR+RKIPFTIRRYLPD
Sbjct: 61  TSKFMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRQRKIPFTIRRYLPD 120

Query: 120 GSYEDWGVDELIVEDSWKRQVGGD 143
           GS+E+WGVDELIVEDSWKRQVGGD
Sbjct: 121 GSFEEWGVDELIVEDSWKRQVGGD 144

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  220 bits (560), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 121/144 (84%), Positives = 130/144 (90%), Gaps = 1/144 (0%)

Query: 1   MADEDYNDLD-MGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARK 59
           MADEDYND+D +GYEDEP EPEIEEG EED E   NDD+NGEPIE E+K E E  +  RK
Sbjct: 1   MADEDYNDVDDLGYEDEPAEPEIEEGVEEDVEMKENDDVNGEPIEAEDKVETEPVQRPRK 60

Query: 60  TSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPD 119
           TSK+MTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELR+RKIPFTIRRYLPD
Sbjct: 61  TSKFMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRQRKIPFTIRRYLPD 120

Query: 120 GSYEDWGVDELIVEDSWKRQVGGD 143
           GS+E+WGVDELIVEDSWKRQVGGD
Sbjct: 121 GSFEEWGVDELIVEDSWKRQVGGD 144

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

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 =  218 bits (556), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 120/144 (83%), Positives = 132/144 (91%), Gaps = 1/144 (0%)

Query: 1   MADEDYNDLD-MGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARK 59
           MADEDYN++D +GYEDEP EPEIEEG EEDA+   NDD+NGEP+ETE+K E E  +  RK
Sbjct: 1   MADEDYNEVDDLGYEDEPVEPEIEEGVEEDADIKENDDVNGEPMETEDKVETEPVQRPRK 60

Query: 60  TSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPD 119
           TSK+MTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELR+RKIPFTIRRYLPD
Sbjct: 61  TSKFMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRQRKIPFTIRRYLPD 120

Query: 120 GSYEDWGVDELIVEDSWKRQVGGD 143
           GS+E+WGVDELIVEDSWKRQVGGD
Sbjct: 121 GSFEEWGVDELIVEDSWKRQVGGD 144

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  215 bits (548), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 126/143 (88%), Positives = 134/143 (93%), Gaps = 1/143 (0%)

Query: 1   MADEDYNDLDMGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKT 60
           MAD+DY D+DMGYEDEPPEPEIEEGAEED EN  ND++ GEPI+TE+KEE++  E  RKT
Sbjct: 1   MADDDYEDIDMGYEDEPPEPEIEEGAEEDLEN-KNDELTGEPIDTEDKEEEQPVERPRKT 59

Query: 61  SKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG 120
           SKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG
Sbjct: 60  SKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG 119

Query: 121 SYEDWGVDELIVEDSWKRQVGGD 143
           SYEDWGVDELIVEDSWKRQVGGD
Sbjct: 120 SYEDWGVDELIVEDSWKRQVGGD 142

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  214 bits (546), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 126/143 (88%), Positives = 133/143 (93%), Gaps = 1/143 (0%)

Query: 1   MADEDYNDLDMGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKT 60
           MADEDY D+DMGYEDEPPEPEIEEGAEED EN  ND+I GE I+TE+KEE++  +  RKT
Sbjct: 1   MADEDYEDIDMGYEDEPPEPEIEEGAEEDVEN-KNDEITGESIDTEDKEEEQPVKRPRKT 59

Query: 61  SKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG 120
           SKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG
Sbjct: 60  SKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG 119

Query: 121 SYEDWGVDELIVEDSWKRQVGGD 143
           SYEDWGVDELIVEDSWKRQVGGD
Sbjct: 120 SYEDWGVDELIVEDSWKRQVGGD 142

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  212 bits (539), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 130/143 (90%), Positives = 135/143 (94%)

Query: 1   MADEDYNDLDMGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKT 60
           MADEDYND+DMGYEDEPPEPEIEEG EEDA+N NN+D  GEPIETE+KEEQE  E  RKT
Sbjct: 1   MADEDYNDVDMGYEDEPPEPEIEEGVEEDADNDNNEDDKGEPIETEDKEEQEPVERPRKT 60

Query: 61  SKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG 120
           SK+MTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG
Sbjct: 61  SKFMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG 120

Query: 121 SYEDWGVDELIVEDSWKRQVGGD 143
           SYEDWGVDELIVEDSWKRQVGGD
Sbjct: 121 SYEDWGVDELIVEDSWKRQVGGD 143

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15224039|ref|NP_178540.1| RNA polymerase Rpb6 [Arabidopsis thaliana] gi|4544434|gb|AAD22343.1| putative DNA-directed RNA polymerase II subunit [Arabidopsis thaliana] gi|33589774|gb|AAQ22653.1| At2g04630 [Arabidopsis thaliana] gi|110738832|dbj|BAF01339.1| putative DNA-directed RNA polymerase II subunit [Arabidopsis thaliana] gi|330250757|gb|AEC05851.1| RNA polymerase Rpb6 [Arabidopsis thaliana]

 Score =  211 bits (538), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 117/144 (81%), Positives = 130/144 (90%), Gaps = 1/144 (0%)

Query: 1   MADEDYNDLD-MGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARK 59
           MAD+DYN++D +GYEDEP EPEIEEG EEDA+   NDD+N +P+ETE+K E E  +  RK
Sbjct: 1   MADDDYNEVDDLGYEDEPAEPEIEEGVEEDADIKENDDVNVDPLETEDKVETEPVQRPRK 60

Query: 60  TSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPD 119
           TSK+MTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELR+RKIPFTIRRYLPD
Sbjct: 61  TSKFMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRQRKIPFTIRRYLPD 120

Query: 120 GSYEDWGVDELIVEDSWKRQVGGD 143
            SYE+WGVDELIVEDSWKRQVGGD
Sbjct: 121 MSYEEWGVDELIVEDSWKRQVGGD 144

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326495054|dbj|BAJ85623.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  211 bits (536), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 113/143 (79%), Positives = 126/143 (88%), Gaps = 3/143 (2%)

Query: 1   MADEDYNDLDMGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEA-ARK 59
           MAD+DYN++DMGYEDEPPE +IEEG EED EN  N+D   + +  E +E++++K A  R 
Sbjct: 1   MADDDYNEVDMGYEDEPPEADIEEGVEEDPEN--NEDAPDDVVGGEGEEKEQEKTARPRN 58

Query: 60  TSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPD 119
           T+KYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELR RKIPFTIRRYLPD
Sbjct: 59  TTKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRARKIPFTIRRYLPD 118

Query: 120 GSYEDWGVDELIVEDSWKRQVGG 142
           GSYEDWGVDELIVEDSWKRQVGG
Sbjct: 119 GSYEDWGVDELIVEDSWKRQVGG 141

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449437154|ref|XP_004136357.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC2-like [Cucumis sativus]

 Score =  211 bits (536), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 123/142 (86%), Positives = 131/142 (92%), Gaps = 1/142 (0%)

Query: 1   MADEDYNDLDMGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKT 60
           MAD+DYNDLDMGYEDEPPEPEIEEGAEE+ +  N DD+ GEP+E E KE++E  E  RKT
Sbjct: 1   MADDDYNDLDMGYEDEPPEPEIEEGAEEELDT-NTDDVPGEPVEAEGKEDEEPVERVRKT 59

Query: 61  SKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG 120
           SK+MTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG
Sbjct: 60  SKFMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG 119

Query: 121 SYEDWGVDELIVEDSWKRQVGG 142
           SYEDWGVDELIVEDSWKRQVGG
Sbjct: 120 SYEDWGVDELIVEDSWKRQVGG 141

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	143
TAIR|locus:2173058	144	NRPB6A [Arabidopsis thaliana (	0.601	0.597	0.953	6.7e-45
TAIR|locus:2049213	144	NRPB6B [Arabidopsis thaliana (	0.601	0.597	0.953	1.2e-43
FB|FBgn0003275	131	RpII18 "RNA polymerase II 18kD	0.545	0.595	0.756	2.6e-30
CGD|CAL0003456	157	RPO26 [Candida albicans (taxid	0.531	0.484	0.815	6.2e-30
UNIPROTKB|Q59QT0	157	RPO26 "Potential subunit commo	0.531	0.484	0.815	6.2e-30
ZFIN|ZDB-GENE-040718-279	127	polr2f "polymerase (RNA) II (D	0.538	0.606	0.818	6.2e-30
MGI|MGI:1349393	127	Polr2f "polymerase (RNA) II (D	0.538	0.606	0.831	1e-29
RGD|708567	127	Polr2f "polymerase (RNA) II (D	0.538	0.606	0.831	1e-29
UNIPROTKB|F1ND65	135	POLR2F "Uncharacterized protei	0.538	0.570	0.831	1.3e-29
UNIPROTKB|Q9PT88	127	RPB6 "RNA polymerase common su	0.538	0.606	0.831	1.3e-29

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

 Score = 431 (156.8 bits), Expect = 6.7e-45, Sum P(2) = 6.7e-45
 Identities = 82/86 (95%), Positives = 86/86 (100%)

Query:    58 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 117
             RKTSK+MTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELR+RKIPFTIRRYL
Sbjct:    59 RKTSKFMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRQRKIPFTIRRYL 118

Query:   118 PDGSYEDWGVDELIVEDSWKRQVGGD 143
             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 = 1.2e-43, Sum P(2) = 1.2e-43
 Identities = 82/86 (95%), Positives = 85/86 (98%)

Query:    58 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 117
             RKTSK+MTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELR+RKIPFTIRRYL
Sbjct:    59 RKTSKFMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRQRKIPFTIRRYL 118

Query:   118 PDGSYEDWGVDELIVEDSWKRQVGGD 143
             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

FB|FBgn0003275 RpII18 "RNA polymerase II 18kD subunit" [Drosophila melanogaster (taxid:7227)]

 Score = 318 (117.0 bits), Expect = 2.6e-30, Sum P(2) = 2.6e-30
 Identities = 59/78 (75%), Positives = 71/78 (91%)

Query:    58 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 117
             R T+KYMTKYERAR+LGTRALQI+M AP+MVEL+GETDPL+IAMKEL+++KIP  IRRYL
Sbjct:    54 RITTKYMTKYERARVLGTRALQIAMCAPIMVELDGETDPLQIAMKELKQKKIPIIIRRYL 113

Query:   118 PDGSYEDWGVDELIVEDS 135
             PD SYEDW +DELI+ D+
Sbjct:   114 PDHSYEDWSIDELIMVDN 131

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

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0007095 "mitotic G2 DNA damage checkpoint" evidence=IGI

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:    58 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 117
             R T+ YMTKYERARILGTRALQIS+NAPV+V++EGETDPL+IAMKEL +RKIP  IRRYL
Sbjct:    81 RTTTPYMTKYERARILGTRALQISLNAPVLVDIEGETDPLQIAMKELAQRKIPLVIRRYL 140

Query:   118 PDGSYEDWGVDELIVE 133
             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:    58 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 117
             R T+ YMTKYERARILGTRALQIS+NAPV+V++EGETDPL+IAMKEL +RKIP  IRRYL
Sbjct:    81 RTTTPYMTKYERARILGTRALQISLNAPVLVDIEGETDPLQIAMKELAQRKIPLVIRRYL 140

Query:   118 PDGSYEDWGVDELIVE 133
             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:    58 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 117
             R T++YMTKYERAR+LGTRALQI+M APVMVELEGETDPL+IAMKEL+ RKIP  IRRYL
Sbjct:    51 RITTQYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKSRKIPIIIRRYL 110

Query:   118 PDGSYEDWGVDELIVED 134
             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:    58 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 117
             R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IAMKEL+ RKIP  IRRYL
Sbjct:    51 RITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYL 110

Query:   118 PDGSYEDWGVDELIVED 134
             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:    58 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 117
             R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IAMKEL+ RKIP  IRRYL
Sbjct:    51 RITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYL 110

Query:   118 PDGSYEDWGVDELIVED 134
             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:    58 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 117
             R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IAMKEL+ RKIP  IRRYL
Sbjct:    59 RITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYL 118

Query:   118 PDGSYEDWGVDELIVED 134
             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:    58 RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 117
             R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IAMKEL+ RKIP  IRRYL
Sbjct:    51 RITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYL 110

Query:   118 PDGSYEDWGVDELIVED 134
             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

---

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	0.6573	0.7401	yes	no
P61219	RPAB2_MOUSE	No assigned EC number	0.7234	0.6573	0.7401	yes	no
O88828	RPAB2_RAT	No assigned EC number	0.7234	0.6573	0.7401	yes	no
Q32PE0	RPAB2_BOVIN	No assigned EC number	0.6576	0.7132	0.8031	yes	no
P61218	RPAB2_HUMAN	No assigned EC number	0.7234	0.6573	0.7401	yes	no
Q5R592	RPAB2_PONAB	No assigned EC number	0.7234	0.6573	0.7401	yes	no
P36595	RPAB2_SCHPO	No assigned EC number	0.6666	0.6433	0.6478	yes	no
P20435	RPAB2_YEAST	No assigned EC number	0.5328	0.8671	0.8	yes	no
Q24320	RPAB2_DROME	No assigned EC number	0.6055	0.7132	0.7786	yes	no
Q54FA8	RPAB2_DICDI	No assigned EC number	0.7733	0.5244	0.5639	yes	no
Q17684	RPAB2_CAEEL	No assigned EC number	0.7466	0.5244	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	0.691

---

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

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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	143
PLN00152	130	PLN00152, PLN00152, DNA-directed RNA polymerase; P	2e-60
PRK01099	62	PRK01099, rpoK, DNA-directed RNA polymerase subuni	1e-23
pfam01192	57	pfam01192, RNA_pol_Rpb6, RNA polymerase Rpb6	6e-17
COG1758	74	COG1758, RpoZ, DNA-directed RNA polymerase, subuni	1e-13

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

 Score =  182 bits (463), Expect = 2e-60
 Identities = 110/130 (84%), Positives = 118/130 (90%)

Query: 5   DYNDLDMGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYM 64
           DYND+DMGYEDEP EPEIEEGAEED+E+ NND++ G   E E+KEEQE  +  RKT+ YM
Sbjct: 1   DYNDMDMGYEDEPSEPEIEEGAEEDSESNNNDEVKGSIGENEDKEEQEPVQRPRKTTPYM 60

Query: 65  TKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYED 124
           TKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYED
Sbjct: 61  TKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYED 120

Query: 125 WGVDELIVED 134
           WGVDELIVED
Sbjct: 121 WGVDELIVED 130

Length = 130

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

 Score = 86.5 bits (215), Expect = 1e-23
 Identities = 29/59 (49%), Positives = 44/59 (74%)

Query: 61  SKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPD 119
              +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 = 69.6 bits (171), Expect = 6e-17
 Identities = 27/56 (48%), Positives = 38/56 (67%)

Query: 58  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTI 113
           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 = 61.6 bits (150), Expect = 1e-13
 Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 60  TSKYMTKYERARILGTRALQISMNAPVMVELEGE-TDPLEIAMKELRERKIPFTIRRYLP 118
             K   +YE   +   RA Q++  AP +V+ E     P+ IA++E+ E KIP  I R L 
Sbjct: 10  LDKVGNRYELVVVAAKRARQLAAGAPPLVDDEENKDKPVVIALREIAEGKIPIEILRELL 69

Query: 119 DGSYE 123
             S +
Sbjct: 70  IHSLQ 74

Length = 74

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	143
KOG3405	136	consensus RNA polymerase subunit K [Transcription]	100.0
PLN00152	130	DNA-directed RNA polymerase; Provisional	100.0
PRK01099	62	rpoK DNA-directed RNA polymerase subunit K; Provis	99.93
COG1758	74	RpoZ DNA-directed RNA polymerase, subunit K/omega	99.77
PF01192	57	RNA_pol_Rpb6: RNA polymerase Rpb6 ; InterPro: IPR0	99.69
PRK00392	69	rpoZ DNA-directed RNA polymerase subunit omega; Re	99.31
TIGR00690	59	rpoZ DNA-directed RNA polymerase, omega subunit. T	99.25
PF05320	167	Pox_RNA_Pol_19: Poxvirus DNA-directed RNA polymera	96.0

>KOG3405 consensus RNA polymerase subunit K [Transcription]

Probab=100.00  E-value=1.6e-44  Score=277.98  Aligned_cols=130  Identities=68%  Similarity=1.075  Sum_probs=98.2

Q ss_pred             ccccCCC-CCCCCCCCCccccccchhhh---cccCCCCCC-CCCccchhhhHhhhhhhhhcCCccccHHHHHHHHHHHHH
Q 032288            4 EDYNDLD-MGYEDEPPEPEIEEGAEEDA---ENINNDDIN-GEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRAL   78 (143)
Q Consensus         4 ~~~~~~~-~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~-~~~~~~~~~~~~~~~~~~r~t~~~lTKYElARIiG~RAl   78 (143)
                      .||++++ .|++++..++..++..+++.   .|...++++ .+.+...+.. ...+.++|+|+|||||||+|||+|+||+
T Consensus         2 ~dy~n~~~~g~~~~~~~~~~~~~veed~~~~~ne~~~~e~~e~~~e~~~~g-~~v~~s~R~TtpyMTKYErArvLGtRAl   80 (136)
T KOG3405|consen    2 SDYENDDFLGDDDEPEEPSIEEDVEEDPQDKDNEDEDEEPNEDVVEIEDAG-KAVPKSERKTTPYMTKYERARVLGTRAL   80 (136)
T ss_pred             ccccccccCCCccccccccccccccccccccccccccCcchhhhhcccccc-ccccccccccCcchhHHHHHHhhhHHHH
Confidence            3565443 44444444444444444433   222222222 2333333332 4457899999999999999999999999


Q ss_pred             HHhhcCCceecCCCCCChHHHHHHHHHcCCCCeEEEeecCCCcEEEeecceeeecc
Q 032288           79 QISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED  134 (143)
Q Consensus        79 QLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lPdg~yEdw~l~eL~~~~  134 (143)
                      |||||||+||++++.|+|+.||++||+++||||+|||||||||||+|+++||++.+
T Consensus        81 QIsm~APvmVeLegETdPL~IAmkEL~qkKIP~iIRRyLPDgSyEDW~vdELiv~d  136 (136)
T KOG3405|consen   81 QISMNAPVMVELEGETDPLEIAMKELKQKKIPFIIRRYLPDGSYEDWSVDELIVED  136 (136)
T ss_pred             HHhcCCCeEEecCCCCCHHHHHHHHHhhccCceEEeeeCCCCCccccccceeeccC
Confidence            99999999999999999999999999999999999999999999999999999864

>PLN00152 DNA-directed RNA polymerase; Provisional

Probab=100.00  E-value=3e-43  Score=270.26  Aligned_cols=130  Identities=85%  Similarity=1.275  Sum_probs=112.8

Q ss_pred             cccCCCCCCCCCCCCccccccchhhhcccCCCCCCCCCccchhhhHhhhhhhhhcCCccccHHHHHHHHHHHHHHHhhcC
Q 032288            5 DYNDLDMGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNA   84 (143)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~t~~~lTKYElARIiG~RAlQLs~GA   84 (143)
                      ||++++.++.+++.+.+++++.+++.+++++.+.+..+.....+...+....+|+|++||||||+|||+|+||+||||||
T Consensus         1 ~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~T~p~lTkyErARIiG~RALQIsmgA   80 (130)
T PLN00152          1 DYNDMDMGYEDEPSEPEIEEGAEEDSESNNNDEVKGSIGENEDKEEQEPVQRPRKTTPYMTKYERARILGTRALQISMNA   80 (130)
T ss_pred             CCcccccccccCCCCccccccccccccccCcccccccccchhccccccccccccccccchhHHHHHhhHhHHHHHHhcCC
Confidence            68888888989999999999888877776666544333334344445556888999999999999999999999999999


Q ss_pred             CceecCCCCCChHHHHHHHHHcCCCCeEEEeecCCCcEEEeecceeeecc
Q 032288           85 PVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED  134 (143)
Q Consensus        85 pplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lPdg~yEdw~l~eL~~~~  134 (143)
                      |+||++++.++|+.||++||.+|+|||+|||+||||+||+|+|+||++.+
T Consensus        81 pvlV~~~g~tdPl~IA~~El~~~~iP~iVrR~lPdG~yEd~~v~EL~~~~  130 (130)
T PLN00152         81 PVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED  130 (130)
T ss_pred             ceEEccCCCcCHHHHHHHHHHcCCCCeEEEEECCCCCEEeeEeeeEeecC
Confidence            99999988899999999999999999999999999999999999999864

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

Probab=99.93  E-value=2.3e-26  Score=157.04  Aligned_cols=61  Identities=48%  Similarity=0.838  Sum_probs=58.4

Q ss_pred             cCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCCCeEEEeecCC
Q 032288           59 KTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPD  119 (143)
Q Consensus        59 ~t~~~lTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lPd  119 (143)
                      .++++|||||+||++|+||+||++||||+|+...+.||+.||++||++|+||++|+|++||
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            5789999999999999999999999999999855899999999999999999999999997

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

Probab=99.77  E-value=4.3e-19  Score=123.46  Aligned_cols=69  Identities=32%  Similarity=0.406  Sum_probs=62.0

Q ss_pred             hhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCC-CChHHHHHHHHHcCCCCeEEEeecCCCcEE
Q 032288           55 EAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGE-TDPLEIAMKELRERKIPFTIRRYLPDGSYE  123 (143)
Q Consensus        55 ~~~r~t~~~lTKYElARIiG~RAlQLs~GApplVd~~~~-~dPv~IA~~EL~eGkIpi~IrR~lPdg~yE  123 (143)
                      ..+....++.|||++|+++|+||+||++||+++++.... .||+.||++||.+|+||+.|.|.+++++.+
T Consensus         5 ~~~~l~~~~~~ryelv~~aa~RA~Ql~~ga~~~~~~~~~~~kpv~iAl~Ei~~g~i~~~i~~~~~~~~~~   74 (74)
T COG1758           5 TIEDLLDKVGNRYELVVVAAKRARQLAAGAPPLVDDEENKDKPVVIALREIAEGKIPIEILRELLIHSLQ   74 (74)
T ss_pred             CHHHHHhhccCHHHHHHHHHHHHHHHHcCCCCccccccccCChHHHHHHHHHcCCCCcccchhhhccccC
Confidence            345667789999999999999999999999999987654 899999999999999999999999998753

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

Probab=99.69  E-value=2.7e-17  Score=108.46  Aligned_cols=55  Identities=36%  Similarity=0.491  Sum_probs=50.6

Q ss_pred             cCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCCCeEE
Q 032288           59 KTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTI  113 (143)
Q Consensus        59 ~t~~~lTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~I  113 (143)
                      ...++.|||++++++|+||+||++||+|+++.....+|+.||++||.+|+|+|.|
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            4567899999999999999999999999998765669999999999999999987

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=99.31  E-value=4.3e-12  Score=86.00  Aligned_cols=51  Identities=27%  Similarity=0.405  Sum_probs=46.0

Q ss_pred             cccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCCCeEEE
Q 032288           63 YMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIR  114 (143)
Q Consensus        63 ~lTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~Ir  114 (143)
                      +-+||.++.++++||+||+.|++++++.. ..+|+.||++||.+|+|.|..-
T Consensus        13 v~~ry~Lv~~aakRArql~~~~~~~~~~~-~~K~~~~Al~EI~~gki~~~~~   63 (69)
T PRK00392         13 VDNRYELVLLAAKRARQLRAGAKPPVDKS-SDKPVVIALREIAEGKVTYEIL   63 (69)
T ss_pred             cCCHHHHHHHHHHHHHHHHcCCCCCCCCc-CCChHHHHHHHHHcCCCceecc
Confidence            44999999999999999999999987654 6899999999999999998763

>TIGR00690 rpoZ DNA-directed RNA polymerase, omega subunit

Probab=99.25  E-value=1.2e-11  Score=83.17  Aligned_cols=48  Identities=23%  Similarity=0.376  Sum_probs=41.0

Q ss_pred             ccccHHHHHHHHHHHHHHHhhcC-CceecCCCCCChHHHHHHHHHcCCCC
Q 032288           62 KYMTKYERARILGTRALQISMNA-PVMVELEGETDPLEIAMKELRERKIP  110 (143)
Q Consensus        62 ~~lTKYElARIiG~RAlQLs~GA-pplVd~~~~~dPv~IA~~EL~eGkIp  110 (143)
                      .+.+||.++.++++||+||+.|+ |++++.. +.+|+.||++||.+|+|.
T Consensus        11 ~v~srY~Lv~~aakRArqL~~~~~~~~~~~~-~~Kp~~iAl~EIa~gkvs   59 (59)
T TIGR00690        11 KIGSRYDLVLVAARRARQLQLKGTDPIVPEE-NDKPTVIALREIAAGLVS   59 (59)
T ss_pred             hcCCHhHHHHHHHHHHHHHHhCCCCCccCcc-cCchHHHHHHHHHcCCCC
Confidence            45699999999999999999876 5555553 789999999999999983

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=96.00  E-value=0.024  Score=45.99  Aligned_cols=64  Identities=16%  Similarity=0.290  Sum_probs=53.2

Q ss_pred             hhhhhhcCCccccHHHHHHHHHHHHHHHhhcCCceec-CCC---CCChHHHHHHHHHcCCCCeEEEee
Q 032288           53 QKEAARKTSKYMTKYERARILGTRALQISMNAPVMVE-LEG---ETDPLEIAMKELRERKIPFTIRRY  116 (143)
Q Consensus        53 ~~~~~r~t~~~lTKYElARIiG~RAlQLs~GApplVd-~~~---~~dPv~IA~~EL~eGkIpi~IrR~  116 (143)
                      +..-+|+-++.++=||+.=|+|.--.-|..|--|||. +..   ..+-+.|.++||.+|.-|++|...
T Consensus        69 I~~iK~RYTRRiSLfEiTGIiaESyNLLqRGRlPLv~dlsdeT~k~n~L~vvi~EIeEg~CPIVIeKN  136 (167)
T PF05320_consen   69 ISAIKKRYTRRISLFEITGIIAESYNLLQRGRLPLVSDLSDETLKDNILHVVIKEIEEGTCPIVIEKN  136 (167)
T ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHHHHHccccccccccchHHHHHhHHHHHHHHHhcCCCcEEEeeC
Confidence            3455677778899999999999999999999999995 322   246789999999999999999763

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

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	143
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 =  134 bits (336), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 64/77 (83%), Positives = 69/77 (89%)
Query: 58  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 117
           R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IAMKEL+ RKIP  IRRYL
Sbjct: 51  RITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYL 110
Query: 118 PDGSYEDWGVDELIVED 134
           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 (330), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 62/76 (81%), Positives = 68/76 (89%)
Query: 58  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 117
           R T+ YMTKYERARILGTRALQISMNAPV V+LEGETDPL IAMKEL E+KIP  IRRYL
Sbjct: 79  RATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYL 138
Query: 118 PDGSYEDWGVDELIVE 133
           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 (327), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 62/76 (81%), Positives = 68/76 (89%)
Query: 58  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 117
           R T+ YMTKYERARILGTRALQISMNAPV V+LEGETDPL IAMKEL E+KIP  IRRYL
Sbjct: 8   RATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYL 67
Query: 118 PDGSYEDWGVDELIVE 133
           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 (327), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 60/74 (81%), Positives = 67/74 (90%)
Query: 58  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 117
           R T+ YMTKYERARILGTRALQISMNAPV+V+LEGETDPL+IAMKEL ++KIP  +RRYL
Sbjct: 69  RTTTPYMTKYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRYL 128
Query: 118 PDGSYEDWGVDELI 131
           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 = 56.6 bits (135), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 40/59 (67%), Gaps = 2/59 (3%)
Query: 64  MTKYERARILGTRALQISMNAPVMVELE--GETDPLEIAMKELRERKIPFTIRRYLPDG 120
           +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 = 56.6 bits (135), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 40/59 (67%), Gaps = 2/59 (3%)
Query: 64  MTKYERARILGTRALQISMNAPVMVELE--GETDPLEIAMKELRERKIPFTIRRYLPDG 120
           +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 = 55.5 bits (132), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/59 (42%), Positives = 40/59 (67%), Gaps = 2/59 (3%)
Query: 64  MTKYERARILGTRALQISMNAPVMVELE--GETDPLEIAMKELRERKIPFTIRRYLPDG 120
           +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	143
4ayb_K	95	DNA-directed RNA polymerase; transferase, multi-su	1e-31
1qkl_A	127	RPB6, DNA-directed RNA polymerase II 14.4 KD polyp	8e-31
3h0g_F	142	DNA-directed RNA polymerases I, II, and III subuni	9e-30
1twf_F	155	ABC23, DNA-directed RNA polymerases I, II, and III	1e-27

>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 =  107 bits (269), Expect = 1e-31
 Identities = 28/100 (28%), Positives = 48/100 (48%), Gaps = 9/100 (9%)

Query: 32  NINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELE 91
            +  D I  + +   E                +T+YE AR++  RALQ++M AP ++++ 
Sbjct: 2   GLERDGILSQDLHFNEVFV-------SLWQNKLTRYEIARVISARALQLAMGAPALIDIN 54

Query: 92  --GETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDE 129
               TD + IA +E +   +P TIRR LP+G      + +
Sbjct: 55  NISSTDVISIAEEEFKRGVLPITIRRRLPNGKIILLSLRK 94

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

 Score =  106 bits (266), Expect = 8e-31
 Identities = 75/134 (55%), Positives = 92/134 (68%), Gaps = 7/134 (5%)

Query: 1   MADEDYNDLDMGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKT 60
           M+D + N     ++ +  +   E+   +D EN   ++   E +E     E+ Q    R T
Sbjct: 1   MSDNEDN-----FDGDDFDDVEEDEGLDDLEN--AEEEGQENVEILPSGERPQANQKRIT 53

Query: 61  SKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG 120
           + YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IAMKEL+ RKIP  IRRYLPDG
Sbjct: 54  TPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDG 113

Query: 121 SYEDWGVDELIVED 134
           SYEDWGVDELI+ D
Sbjct: 114 SYEDWGVDELIITD 127

>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 =  104 bits (260), Expect = 9e-30
 Identities = 63/130 (48%), Positives = 82/130 (63%), Gaps = 2/130 (1%)

Query: 2   ADEDYNDLDMGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTS 61
           A  +    ++   DE  + +       +       +        +  +   +++  R T+
Sbjct: 15  AVMEEEVDELEMIDENGQSQQGVSHPGEPSTTVITEDVASSKTAQSGKAVAKED--RTTT 72

Query: 62  KYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGS 121
            YMTKYERARILGTRALQISMNAPV+V+LEGETDPL+IAMKEL ++KIP  +RRYLPDGS
Sbjct: 73  PYMTKYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRYLPDGS 132

Query: 122 YEDWGVDELI 131
           YEDW V ELI
Sbjct: 133 YEDWSVAELI 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 = 99.4 bits (247), Expect = 1e-27
 Identities = 70/137 (51%), Positives = 89/137 (64%), Gaps = 6/137 (4%)

Query: 3   DEDYNDLDMGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEK------EEQEQKEA 56
            +  +  D    +E P+ +  E  + + + I       E  +  E+      +E+   + 
Sbjct: 18  FDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKD 77

Query: 57  ARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRY 116
            R T+ YMTKYERARILGTRALQISMNAPV V+LEGETDPL IAMKEL E+KIP  IRRY
Sbjct: 78  QRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRY 137

Query: 117 LPDGSYEDWGVDELIVE 133
           LPDGS+EDW V+ELIV+
Sbjct: 138 LPDGSFEDWSVEELIVD 154

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	143
1qkl_A	127	RPB6, DNA-directed RNA polymerase II 14.4 KD polyp	100.0
1twf_F	155	ABC23, DNA-directed RNA polymerases I, II, and III	100.0
3h0g_F	142	DNA-directed RNA polymerases I, II, and III subuni	100.0
4ayb_K	95	DNA-directed RNA polymerase; transferase, multi-su	99.97
3lu0_E	91	DNA-directed RNA polymerase subunit omega; E. coli	99.29
2a6h_E	99	RNA polymerase omega chain; RNA polymerase holoenz	99.19

>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=1.5e-41  Score=259.15  Aligned_cols=127  Identities=57%  Similarity=0.837  Sum_probs=99.0

Q ss_pred             CCcccccCCCCCCCCCCCCccccccchhhhcccCCCCCCCCCccchhhhHhhhhhhhhcCCccccHHHHHHHHHHHHHHH
Q 032288            1 MADEDYNDLDMGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQI   80 (143)
Q Consensus         1 m~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~t~~~lTKYElARIiG~RAlQL   80 (143)
                      |+|++|+.+++  +|++.+++.  +.++-++..++.+.|++++...   ...++..+|+|+||||||++|||+|+||+||
T Consensus         1 m~d~~~~~~~~--~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~r~t~p~lTRYElARIiG~RAlQL   73 (127)
T 1qkl_A            1 MSDNEDNFDGD--DFDDVEEDE--GLDDLENAEEEGQENVEILPSG---ERPQANQKRITTPYMTKYERARVLGTRALQI   73 (127)
T ss_dssp             CCCCCCCSCCC--SSSSSCCCC--TTTTCCCSCCCCSCEEEEEESC---CCTTTCCCSSCCSSCCHHHHHHHHHHHHHHH
T ss_pred             CCcccccCCCc--ccccccccc--CccccccccccCcccceecccc---CcCCCccccccCCCcCHHHHHHHHHHHHHHH
Confidence            88988833333  344332222  1111011123334678888642   3345789999999999999999999999999


Q ss_pred             hhcCCceecCCCCCChHHHHHHHHHcCCCCeEEEeecCCCcEEEeecceeeecc
Q 032288           81 SMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED  134 (143)
Q Consensus        81 s~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lPdg~yEdw~l~eL~~~~  134 (143)
                      ||||||||++++.+||+.||++||++|||||+|||+||||+||+|+|++|++++
T Consensus        74 s~GAppLVd~e~~~dPl~IAl~ElaeGkIpi~VrR~lPdg~yEd~~~~eL~i~~  127 (127)
T 1qkl_A           74 AMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITD  127 (127)
T ss_dssp             HHSCCSSSCSSSSCSSSHHHHHHHHHTCCCEEEEEEETTTEEEEESSSSSCSCC
T ss_pred             hcCCcceEcCCCCCCHHHHHHHHHHcCCCCeEEEEECCCCCEEEeehhheeccC
Confidence            999999999987789999999999999999999999999999999999999864

>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=1.9e-37  Score=242.92  Aligned_cols=85  Identities=74%  Similarity=1.149  Sum_probs=80.1

Q ss_pred             HhhhhhhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCCCeEEEeecCCCcEEEeecce
Q 032288           50 EQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDE  129 (143)
Q Consensus        50 ~~~~~~~~r~t~~~lTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lPdg~yEdw~l~e  129 (143)
                      .++++..+|+|++||||||+|||+|+||+||||||||||++++.+||+.||++||++|||||+|||+||||+||+|+|+|
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            45567889999999999999999999999999999999999877899999999999999999999999999999999999


Q ss_pred             eeecc
Q 032288          130 LIVED  134 (143)
Q Consensus       130 L~~~~  134 (143)
                      |++++
T Consensus       151 L~~~~  155 (155)
T 1twf_F          151 LIVDL  155 (155)
T ss_dssp             SBCCC
T ss_pred             hccCC
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=1.8e-37  Score=240.21  Aligned_cols=82  Identities=73%  Similarity=1.162  Sum_probs=78.4

Q ss_pred             HhhhhhhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCCCeEEEeecCCCcEEEeecce
Q 032288           50 EQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDE  129 (143)
Q Consensus        50 ~~~~~~~~r~t~~~lTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lPdg~yEdw~l~e  129 (143)
                      ..+.+..+|+|+|||||||+|||+|+||+||||||||||+++++++|+.||++||++|||||+|||++|||+||+|+|+|
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            34567999999999999999999999999999999999999878999999999999999999999999999999999999


Q ss_pred             ee
Q 032288          130 LI  131 (143)
Q Consensus       130 L~  131 (143)
                      |+
T Consensus       141 L~  142 (142)
T 3h0g_F          141 LI  142 (142)
T ss_dssp             CC
T ss_pred             cC
Confidence            96

>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=2.9e-31  Score=193.95  Aligned_cols=69  Identities=36%  Similarity=0.659  Sum_probs=65.2

Q ss_pred             CccccHHHHHHHHHHHHHHHhhcCCceecCC--CCCChHHHHHHHHHcCCCCeEEEeecCCCcEEEeecce
Q 032288           61 SKYMTKYERARILGTRALQISMNAPVMVELE--GETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDE  129 (143)
Q Consensus        61 ~~~lTKYElARIiG~RAlQLs~GApplVd~~--~~~dPv~IA~~EL~eGkIpi~IrR~lPdg~yEdw~l~e  129 (143)
                      .+.|||||+|||+|+||+||||||||||+++  +.+||+.||++||.+|+|||+|||+||||+||+|+|+|
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            3569999999999999999999999999986  36899999999999999999999999999999999986

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

Probab=99.29  E-value=8.5e-13  Score=95.16  Aligned_cols=53  Identities=23%  Similarity=0.271  Sum_probs=47.8

Q ss_pred             ccccHHHHHHHHHHHHHHHhh-cCCceecCCCCCChHHHHHHHHHcCCCCeEEEe
Q 032288           62 KYMTKYERARILGTRALQISM-NAPVMVELEGETDPLEIAMKELRERKIPFTIRR  115 (143)
Q Consensus        62 ~~lTKYElARIiG~RAlQLs~-GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR  115 (143)
                      .+.+||+|+.++++||+||+. |++|+|+.. +.||+.||++||.+|+|.+.+-.
T Consensus        12 kV~nRY~LV~~AAKRARQL~~~G~~plv~~~-~~Kpv~iALrEIa~GkV~~~~l~   65 (91)
T 3lu0_E           12 KIGNRFDLVLVAARRARQMQVGGKDPLVPEE-NDKTTVIALREIEEGLINNQILD   65 (91)
T ss_dssp             HSSSHHHHHHHHHHHHHHHHHTCCCSCCSSS-CCCSSCCSHHHHHSSSCEEESSS
T ss_pred             HcCCHhHHHHHHHHHHHHHHhcCCCCccCCC-CCChHHHHHHHHHcCCCceeeCC
Confidence            355999999999999999998 999999976 78999999999999999987533

>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=99.19  E-value=1.8e-11  Score=88.99  Aligned_cols=50  Identities=24%  Similarity=0.278  Sum_probs=43.0

Q ss_pred             cccHHHHHHHHHHHHHHHhhcC--CceecC---CCCC---------ChHHHHHHHHHcCCCCeE
Q 032288           63 YMTKYERARILGTRALQISMNA--PVMVEL---EGET---------DPLEIAMKELRERKIPFT  112 (143)
Q Consensus        63 ~lTKYElARIiG~RAlQLs~GA--pplVd~---~~~~---------dPv~IA~~EL~eGkIpi~  112 (143)
                      +.+||+++.++++||+||+.|+  .|+++.   ..+.         ||+.||++||.+|+|.|.
T Consensus        13 v~nrY~LV~~aAKRARQI~~g~~k~~lv~~l~~~~~~~l~e~~~~~Kpv~iAL~EI~~Gki~~~   76 (99)
T 2a6h_E           13 VDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAETWAMKELLTGRLVFG   76 (99)
T ss_dssp             SSSHHHHHHHHHHHHHHHHHTCTTCCSCCSSSCCCCSSSSGGGTSSCSHHHHHHHHTTTCCEEE
T ss_pred             cCCHhHHHHHHHHHHHHHHcCCccccchhhhhhcccccccccccCCCHHHHHHHHHHcCCeeec
Confidence            5689999999999999999999  999872   1123         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	143
d1twff_	84	a.143.1.2 (F:) RPB6 {Baker's yeast (Saccharomyces	4e-40
d1qkla_	127	a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId:	4e-37

>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 =  127 bits (321), Expect = 4e-40
 Identities = 62/76 (81%), Positives = 68/76 (89%)

Query: 58  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 117
           R T+ YMTKYERARILGTRALQISMNAPV V+LEGETDPL IAMKEL E+KIP  IRRYL
Sbjct: 8   RATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYL 67

Query: 118 PDGSYEDWGVDELIVE 133
           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 =  121 bits (305), Expect = 4e-37
 Identities = 76/134 (56%), Positives = 92/134 (68%), Gaps = 7/134 (5%)

Query: 1   MADEDYNDLDMGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKT 60
           M+D + N     ++D     E +EG ++          N E + + E+ +  QK   R T
Sbjct: 1   MSDNEDNFDGDDFDDV----EEDEGLDDLENAEEEGQENVEILPSGERPQANQK---RIT 53

Query: 61  SKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG 120
           + YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IAMKEL+ RKIP  IRRYLPDG
Sbjct: 54  TPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDG 113

Query: 121 SYEDWGVDELIVED 134
           SYEDWGVDELI+ D
Sbjct: 114 SYEDWGVDELIITD 127

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	143
d1qkla_	127	RPB6 {Human (Homo sapiens) [TaxId: 9606]}	100.0
d1twff_	84	RPB6 {Baker's yeast (Saccharomyces cerevisiae) [Ta	100.0
d1smye_	95	RNA polymerase omega subunit {Thermus thermophilus	97.94

>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=9.7e-38  Score=235.70  Aligned_cols=82  Identities=79%  Similarity=1.220  Sum_probs=78.7

Q ss_pred             hhhhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCCCeEEEeecCCCcEEEeecceeee
Q 032288           53 QKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIV  132 (143)
Q Consensus        53 ~~~~~r~t~~~lTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lPdg~yEdw~l~eL~~  132 (143)
                      ..+.+|+|+|+|||||+|||+|.||+|||+||||||++.+.++|+.||++||.+|||||+|||+||||+||+|+|++|++
T Consensus        46 ~~~~~~~T~p~lTkYE~arilG~Ra~Qi~~ga~~~i~~~~~~d~~~IA~~EL~~kkiPfiIrR~lp~g~~E~w~l~dL~i  125 (127)
T d1qkla_          46 QANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELII  125 (127)
T ss_dssp             TTCCCSSCCSSCCHHHHHHHHHHHHHHHHHSCCSSSCSSSSCSSSHHHHHHHHHTCCCEEEEEEETTTEEEEESSSSSCS
T ss_pred             ccCcccccCCcccHHHHHHHHHHHHHHHhcCCCceecCCCCCCHHHHHHHHHHcCCCCEEEEEECCCCCEEEEEhHheEe
Confidence            46889999999999999999999999999999999999888999999999999999999999999999999999999998


Q ss_pred             cc
Q 032288          133 ED  134 (143)
Q Consensus       133 ~~  134 (143)
                      .+
T Consensus       126 ~~  127 (127)
T d1qkla_         126 TD  127 (127)
T ss_dssp             CC
T ss_pred             cC
Confidence            64

>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=4.1e-35  Score=208.33  Aligned_cols=81  Identities=77%  Similarity=1.201  Sum_probs=77.9

Q ss_pred             hhhhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCCCeEEEeecCCCcEEEeecceeee
Q 032288           53 QKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIV  132 (143)
Q Consensus        53 ~~~~~r~t~~~lTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lPdg~yEdw~l~eL~~  132 (143)
                      +++++|+|+|+|||||+|||+|.||+|||+||||+|++++.++|+.||.+||.+|+|||+|||++|||+||+|+|++|+|
T Consensus         3 i~~~~~~T~p~LTkYE~ariiG~Ra~Ql~~Ga~p~I~~~~~~d~~~IA~~El~~~kiP~iIrR~lP~g~~E~w~l~dL~i   82 (84)
T d1twff_           3 IPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIV   82 (84)
T ss_dssp             CCSSSCCSCSBCCHHHHHHHHHHHHHHHHTTCCCSSCCSSCCSHHHHHHHHHHTTCCCEEEEEECTTSCEEEEETTTSBC
T ss_pred             cCCcCcccCccccHHHHHHHHHHHHHHHHcCCCceecCCCCCCHHHHHHHHHHcCCCCEEEEEECCCCCEEEEEHHHeee
Confidence            35789999999999999999999999999999999999878999999999999999999999999999999999999998


Q ss_pred             c
Q 032288          133 E  133 (143)
Q Consensus       133 ~  133 (143)
                      +
T Consensus        83 d   83 (84)
T d1twff_          83 D   83 (84)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=97.94  E-value=8.3e-06  Score=57.58  Aligned_cols=55  Identities=25%  Similarity=0.280  Sum_probs=42.9

Q ss_pred             ccccHHHHHHHHHHHHHH-HhhcCC-ceecCCC----CC--------ChHHHHHHHHHcCCCCeEEEeecC
Q 032288           62 KYMTKYERARILGTRALQ-ISMNAP-VMVELEG----ET--------DPLEIAMKELRERKIPFTIRRYLP  118 (143)
Q Consensus        62 ~~lTKYElARIiG~RAlQ-Ls~GAp-plVd~~~----~~--------dPv~IA~~EL~eGkIpi~IrR~lP  118 (143)
                      -.++||-+..++|+||.| |-.|.| .+++.+.    .+        ++++.|++||.-|+  +.+--.||
T Consensus        11 ltDSkYRLsvVvakRA~QlLr~g~~ntvL~pde~p~~~tleg~~~dpN~vt~AMkEL~tGr--l~~GenL~   79 (95)
T d1smye_          11 MVDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAETWAMKELLTGR--LVFGENLV   79 (95)
T ss_dssp             TSSSHHHHHHHHHHHHHHHHHTCTTCCSCCSSSCCCCSSSSGGGTSSCSHHHHHHHHTTTC--EEEESSSS
T ss_pred             ccccceeeehhhHHHHHHHHHcCCCccccChhhhhhhhcccccCCCCcHHHHHHHHHHhCc--eeecCCCC
Confidence            357999999999999999 888999 5555432    22        78999999999999  55554444