Citrus Sinensis ID: 045556

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90------
Protein Sequence
MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLRHFDERYKQKGSRKLVLSKLYKACKQTANPCKTLDGQMGNPFKEHVL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccEEEccccccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHcccccccEEEEccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHEccHHHHHHHcccccccccccEEEEEccccccccccHHHHEHEEcccccHHccHHHHHHHHHHHHHHHHccccccEEEEEcccccccccccc
Coil and Loop (DISEMBL)
mlleiahfedvellwpffthhrfsnidiifnplevpprmnighifecsLRHFDERYKQKGSRKLVLSKLYKAckqtanpcktldgqmgnpfkehvl
Flexible Loop (DISEMBL)
MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLRHFDERYKQKGSRKLVLSKLYKACkqtanpcktldgqmgnpfkehvl
Low Complexity Region (SEG)
MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLRHFDERYKQKGSRKLVLSKLYKACKQTANPCKTLDGQMGNPFKEHVL
Disordered region (IsUnstruct)
**LEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLRHFDERYKQKGSRKLVLSKLYKACKQTA*******************
Disordered Region (DISOPRED)
***EIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLRHFDERYKQKGSRKLVLSKLYKACKQTANPCKTLDGQMGNPFKEHVL
Disordered Region (DISEMBL)
MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLRHFDERYKQKGSRKLVLSKLYKACKQTANPCKTLDGQMGNPFKEHVL
Disordered Region (DISPRO)
MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLRHFDERYKQKGSRKLVLSKLYKACKQTANPCKTLDGQMGNPF*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLRHFDERYKQKGSRKLVLSKLYKACKQTANPCKTLDGQMGNPFKEHVL
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	96	2.2.26 [Sep-21-2011]
Q09G54	1070	DNA-directed RNA polymera	N/A	no	0.739	0.066	0.521	1e-19
A0A327	1066	DNA-directed RNA polymera	N/A	no	0.739	0.066	0.510	2e-19
Q68S14	1071	DNA-directed RNA polymera	N/A	no	0.739	0.066	0.5	2e-19
Q33C46	1070	DNA-directed RNA polymera	N/A	no	0.822	0.073	0.471	2e-19
P06271	1070	DNA-directed RNA polymera	N/A	no	0.822	0.073	0.471	2e-19
Q3C1G7	1070	DNA-directed RNA polymera	N/A	no	0.822	0.073	0.471	2e-19
Q8S8X9	1070	DNA-directed RNA polymera	N/A	no	0.822	0.073	0.471	2e-19
Q2MIJ5	1070	DNA-directed RNA polymera	N/A	no	0.822	0.073	0.471	3e-19
Q2VEI4	1070	DNA-directed RNA polymera	N/A	no	0.822	0.073	0.471	3e-19
Q2MIA8	1070	DNA-directed RNA polymera	N/A	no	0.822	0.073	0.471	3e-19

>sp|Q09G54|RPOB_PLAOC DNA-directed RNA polymerase subunit beta OS=Platanus occidentalis GN=rpoB PE=3 SV=1

 Score = 94.7 bits (234), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 49/94 (52%), Positives = 60/94 (63%), Gaps = 23/94 (24%)

Query: 26  IDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSRKLVLSKLYKA 72
           ID++FNPL VP RMN+G IFECSL        RH     FDERY+Q+ SRKLV S+LYKA
Sbjct: 848 IDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYKA 907

Query: 73  CKQTANP----------CKTLDGQMGNPFKEHVL 96
            KQTANP           +  DG+ G+PF++ VL
Sbjct: 908 SKQTANPWVFEPEYPGKSRIFDGRTGDPFEQPVL 941

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
Platanus occidentalis (taxid: 4403)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6

>sp|A0A327|RPOB_COFAR DNA-directed RNA polymerase subunit beta OS=Coffea arabica GN=rpoB PE=3 SV=1

 Score = 94.4 bits (233), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/94 (51%), Positives = 60/94 (63%), Gaps = 23/94 (24%)

Query: 26  IDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSRKLVLSKLYKA 72
           +D++FNPL VP RMN+G IFECSL        RH     FDERY+Q+ SRKLV S+LY+A
Sbjct: 844 VDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYQA 903

Query: 73  CKQTANP----------CKTLDGQMGNPFKEHVL 96
            KQTANP           +  DG+ GNPF++ VL
Sbjct: 904 SKQTANPWVFEAEYPGKSRIFDGRTGNPFEQPVL 937

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Coffea arabica (taxid: 13443)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|Q68S14|RPOB_PANGI DNA-directed RNA polymerase subunit beta OS=Panax ginseng GN=rpoB PE=3 SV=1

 Score = 94.0 bits (232), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 47/94 (50%), Positives = 61/94 (64%), Gaps = 23/94 (24%)

Query: 26  IDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSRKLVLSKLYKA 72
           +D++FNPL VPPRMN+G IFECSL        RH     FDERY+Q+ SRKLV S+LY+A
Sbjct: 849 VDMVFNPLGVPPRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEA 908

Query: 73  CKQTANP----------CKTLDGQMGNPFKEHVL 96
            KQTANP           +  DG+ G+PF++ V+
Sbjct: 909 GKQTANPWVFEPEYPGKSRIFDGRTGDPFEQPVI 942

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Panax ginseng (taxid: 4054)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|Q33C46|RPOB_NICTO DNA-directed RNA polymerase subunit beta OS=Nicotiana tomentosiformis GN=rpoB PE=3 SV=1

 Score = 94.0 bits (232), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 49/104 (47%), Positives = 64/104 (61%), Gaps = 25/104 (24%)

Query: 16  PFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSR 62
           P+    R  ++D++FNPL VP RMN+G IFECSL        RH     FDERY+Q+ SR
Sbjct: 840 PYLQDGR--SVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASR 897

Query: 63  KLVLSKLYKACKQTANP----------CKTLDGQMGNPFKEHVL 96
           KLV S+LY+A KQTANP           +  DG+ GNPF++ V+
Sbjct: 898 KLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGNPFEQPVI 941

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Nicotiana tomentosiformis (taxid: 4098)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|P06271|RPOB_TOBAC DNA-directed RNA polymerase subunit beta OS=Nicotiana tabacum GN=rpoB PE=3 SV=1

 Score = 94.0 bits (232), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 49/104 (47%), Positives = 64/104 (61%), Gaps = 25/104 (24%)

Query: 16  PFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSR 62
           P+    R  ++D++FNPL VP RMN+G IFECSL        RH     FDERY+Q+ SR
Sbjct: 840 PYLQDGR--SVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASR 897

Query: 63  KLVLSKLYKACKQTANP----------CKTLDGQMGNPFKEHVL 96
           KLV S+LY+A KQTANP           +  DG+ GNPF++ V+
Sbjct: 898 KLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGNPFEQPVI 941

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Nicotiana tabacum (taxid: 4097)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|Q3C1G7|RPOB_NICSY DNA-directed RNA polymerase subunit beta OS=Nicotiana sylvestris GN=rpoB PE=3 SV=1

 Score = 94.0 bits (232), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 49/104 (47%), Positives = 64/104 (61%), Gaps = 25/104 (24%)

Query: 16  PFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSR 62
           P+    R  ++D++FNPL VP RMN+G IFECSL        RH     FDERY+Q+ SR
Sbjct: 840 PYLQDGR--SVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASR 897

Query: 63  KLVLSKLYKACKQTANP----------CKTLDGQMGNPFKEHVL 96
           KLV S+LY+A KQTANP           +  DG+ GNPF++ V+
Sbjct: 898 KLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGNPFEQPVI 941

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Nicotiana sylvestris (taxid: 4096)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|Q8S8X9|RPOB_ATRBE DNA-directed RNA polymerase subunit beta OS=Atropa belladonna GN=rpoB PE=3 SV=1

 Score = 94.0 bits (232), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 49/104 (47%), Positives = 64/104 (61%), Gaps = 25/104 (24%)

Query: 16  PFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSR 62
           P+    R  ++D++FNPL VP RMN+G IFECSL        RH     FDERY+Q+ SR
Sbjct: 840 PYLQDGR--SVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASR 897

Query: 63  KLVLSKLYKACKQTANP----------CKTLDGQMGNPFKEHVL 96
           KLV S+LY+A KQTANP           +  DG+ GNPF++ V+
Sbjct: 898 KLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGNPFEQPVI 941

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Atropa belladonna (taxid: 33113)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|Q2MIJ5|RPOB_SOLBU DNA-directed RNA polymerase subunit beta OS=Solanum bulbocastanum GN=rpoB PE=3 SV=1

 Score = 93.6 bits (231), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 49/104 (47%), Positives = 64/104 (61%), Gaps = 25/104 (24%)

Query: 16  PFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSR 62
           P+    R  ++D++FNPL VP RMN+G IFECSL        RH     FDERY+Q+ SR
Sbjct: 840 PYLQDGR--SVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASR 897

Query: 63  KLVLSKLYKACKQTANP----------CKTLDGQMGNPFKEHVL 96
           KLV S+LY+A KQTANP           +  DG+ GNPF++ V+
Sbjct: 898 KLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGNPFEQPVI 941

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Solanum bulbocastanum (taxid: 147425)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|Q2VEI4|RPOB_SOLTU DNA-directed RNA polymerase subunit beta OS=Solanum tuberosum GN=rpoB PE=3 SV=1

 Score = 93.6 bits (231), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 49/104 (47%), Positives = 64/104 (61%), Gaps = 25/104 (24%)

Query: 16  PFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSR 62
           P+    R  ++D++FNPL VP RMN+G IFECSL        RH     FDERY+Q+ SR
Sbjct: 840 PYLQDGR--SVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASR 897

Query: 63  KLVLSKLYKACKQTANP----------CKTLDGQMGNPFKEHVL 96
           KLV S+LY+A KQTANP           +  DG+ GNPF++ V+
Sbjct: 898 KLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGNPFEQPVI 941

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Solanum tuberosum (taxid: 4113)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|Q2MIA8|RPOB_SOLLC DNA-directed RNA polymerase subunit beta OS=Solanum lycopersicum GN=rpoB PE=3 SV=1

 Score = 93.6 bits (231), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 49/104 (47%), Positives = 64/104 (61%), Gaps = 25/104 (24%)

Query: 16  PFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSR 62
           P+    R  ++D++FNPL VP RMN+G IFECSL        RH     FDERY+Q+ SR
Sbjct: 840 PYLQDGR--SVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASR 897

Query: 63  KLVLSKLYKACKQTANP----------CKTLDGQMGNPFKEHVL 96
           KLV S+LY+A KQTANP           +  DG+ GNPF++ V+
Sbjct: 898 KLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGNPFEQPVI 941

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Solanum lycopersicum (taxid: 4081)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

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	96
114329738	1070	RNA polymerase beta subunit [Platanus oc	0.739	0.066	0.521	6e-18
290489620	1070	RNA polymerase beta subunit protein [Ner	0.739	0.066	0.510	7e-18
116617100	1066	RNA polymerase beta subunit [Coffea arab	0.739	0.066	0.510	9e-18
313183985	1073	RNA polymerase beta subunit [Castanea mo	0.822	0.073	0.480	9e-18
52220802	1071	RNA polymerase beta subunit [Panax ginse	0.739	0.066	0.5	9e-18
225282	1000	RNA polymerase beta	0.822	0.079	0.471	1e-17
290489608	1072	RNA polymerase beta subunit protein [Dil	0.822	0.073	0.480	1e-17
81301554	1070	RNA polymerase beta subunit [Nicotiana t	0.822	0.073	0.471	1e-17
350996418	1070	RNA polymerase beta subunit (chloroplast	0.822	0.073	0.471	1e-17
394831094	1070	RNA polymerase beta subunit (chloroplast	0.822	0.073	0.471	1e-17

>gi|114329738|ref|YP_740557.1| RNA polymerase beta subunit [Platanus occidentalis] gi|122166043|sp|Q09G54.1|RPOB_PLAOC RecName: Full=DNA-directed RNA polymerase subunit beta; AltName: Full=PEP; AltName: Full=Plastid-encoded RNA polymerase subunit beta; Short=RNA polymerase subunit beta gi|114054376|gb|ABI49770.1| RNA polymerase beta subunit [Platanus occidentalis]

 Score = 94.7 bits (234), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 49/94 (52%), Positives = 60/94 (63%), Gaps = 23/94 (24%)

Query: 26  IDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSRKLVLSKLYKA 72
           ID++FNPL VP RMN+G IFECSL        RH     FDERY+Q+ SRKLV S+LYKA
Sbjct: 848 IDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYKA 907

Query: 73  CKQTANP----------CKTLDGQMGNPFKEHVL 96
            KQTANP           +  DG+ G+PF++ VL
Sbjct: 908 SKQTANPWVFEPEYPGKSRIFDGRTGDPFEQPVL 941

Source: Platanus occidentalis

Species: Platanus occidentalis

Genus: Platanus

Family: Platanaceae

Order: Proteales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|290489620|gb|ADD31194.1| RNA polymerase beta subunit protein [Nerium oleander]

 Score = 94.7 bits (234), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 48/94 (51%), Positives = 60/94 (63%), Gaps = 23/94 (24%)

Query: 26  IDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSRKLVLSKLYKA 72
           +D++FNPL VP RMN+G IFECSL        RH     FDERY+Q+ SRKLV S+LY+A
Sbjct: 848 VDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYQA 907

Query: 73  CKQTANP----------CKTLDGQMGNPFKEHVL 96
            KQTANP           +  DG+ GNPF++ VL
Sbjct: 908 SKQTANPWVFEPEYPGKSRIFDGRTGNPFEQPVL 941

Source: Nerium oleander

Species: Nerium oleander

Genus: Nerium

Family: Apocynaceae

Order: Gentianales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116617100|ref|YP_817474.1| RNA polymerase beta subunit [Coffea arabica] gi|122153613|sp|A0A327.1|RPOB_COFAR RecName: Full=DNA-directed RNA polymerase subunit beta; AltName: Full=PEP; AltName: Full=Plastid-encoded RNA polymerase subunit beta; Short=RNA polymerase subunit beta gi|116242156|gb|ABJ89671.1| RNA polymerase beta subunit [Coffea arabica]

 Score = 94.4 bits (233), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 48/94 (51%), Positives = 60/94 (63%), Gaps = 23/94 (24%)

Query: 26  IDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSRKLVLSKLYKA 72
           +D++FNPL VP RMN+G IFECSL        RH     FDERY+Q+ SRKLV S+LY+A
Sbjct: 844 VDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYQA 903

Query: 73  CKQTANP----------CKTLDGQMGNPFKEHVL 96
            KQTANP           +  DG+ GNPF++ VL
Sbjct: 904 SKQTANPWVFEAEYPGKSRIFDGRTGNPFEQPVL 937

Source: Coffea arabica

Species: Coffea arabica

Genus: Coffea

Family: Rubiaceae

Order: Gentianales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|313183985|ref|YP_004021142.1| RNA polymerase beta subunit [Castanea mollissima] gi|309321512|gb|ADO65052.1| RNA polymerase beta subunit [Castanea mollissima]

 Score = 94.4 bits (233), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 50/104 (48%), Positives = 65/104 (62%), Gaps = 25/104 (24%)

Query: 16  PFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSR 62
           P+    R  ++D++FNPL VP RMN+G IFECSL        RH     FDERY+Q+ SR
Sbjct: 843 PYLQDGR--SVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLGRHYRIAPFDERYEQEASR 900

Query: 63  KLVLSKLYKACKQTANP----------CKTLDGQMGNPFKEHVL 96
           KLV S+LY+A KQTANP           + LDG+ G+PF++ VL
Sbjct: 901 KLVFSELYEASKQTANPWVFDPEYPGKSRILDGRTGDPFEQPVL 944

Source: Castanea mollissima

Species: Castanea mollissima

Genus: Castanea

Family: Fagaceae

Order: Fagales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|52220802|ref|YP_086958.1| RNA polymerase beta subunit [Panax ginseng] gi|68053101|sp|Q68S14.1|RPOB_PANGI RecName: Full=DNA-directed RNA polymerase subunit beta; AltName: Full=PEP; AltName: Full=Plastid-encoded RNA polymerase subunit beta; Short=RNA polymerase subunit beta gi|51235305|gb|AAT98501.1| RNA polymerase beta subunit [Panax ginseng]

 Score = 94.0 bits (232), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 47/94 (50%), Positives = 61/94 (64%), Gaps = 23/94 (24%)

Query: 26  IDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSRKLVLSKLYKA 72
           +D++FNPL VPPRMN+G IFECSL        RH     FDERY+Q+ SRKLV S+LY+A
Sbjct: 849 VDMVFNPLGVPPRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEA 908

Query: 73  CKQTANP----------CKTLDGQMGNPFKEHVL 96
            KQTANP           +  DG+ G+PF++ V+
Sbjct: 909 GKQTANPWVFEPEYPGKSRIFDGRTGDPFEQPVI 942

Source: Panax ginseng

Species: Panax ginseng

Genus: Panax

Family: Araliaceae

Order: Apiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225282|prf||1211235T RNA polymerase beta

 Score = 94.0 bits (232), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 49/104 (47%), Positives = 64/104 (61%), Gaps = 25/104 (24%)

Query: 16  PFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSR 62
           P+    R  ++D++FNPL VP RMN+G IFECSL        RH     FDERY+Q+ SR
Sbjct: 840 PYLQDGR--SVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASR 897

Query: 63  KLVLSKLYKACKQTANP----------CKTLDGQMGNPFKEHVL 96
           KLV S+LY+A KQTANP           +  DG+ GNPF++ V+
Sbjct: 898 KLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGNPFEQPVI 941

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|290489608|gb|ADD31188.1| RNA polymerase beta subunit protein [Dillenia indica]

 Score = 94.0 bits (232), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 50/104 (48%), Positives = 64/104 (61%), Gaps = 25/104 (24%)

Query: 16  PFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSR 62
           P+F     S +D++FNPL VP RMN+G IFECSL        RH     FDERY+Q+ SR
Sbjct: 842 PYFQDG--SPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLNRHYRILPFDERYEQEASR 899

Query: 63  KLVLSKLYKACKQTANP----------CKTLDGQMGNPFKEHVL 96
           KLV S+LYKA KQTANP           +  DG+ G+PF++ V+
Sbjct: 900 KLVFSELYKASKQTANPWIFEPEYPGKSRIFDGRTGDPFEQPVI 943

Source: Dillenia indica

Species: Dillenia indica

Genus: Dillenia

Family: Dilleniaceae

Order: Dilleniales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|81301554|ref|YP_398851.1| RNA polymerase beta subunit [Nicotiana tomentosiformis] gi|88909146|sp|Q33C46.1|RPOB_NICTO RecName: Full=DNA-directed RNA polymerase subunit beta; AltName: Full=PEP; AltName: Full=Plastid-encoded RNA polymerase subunit beta; Short=RNA polymerase subunit beta gi|80750913|dbj|BAE47989.1| RNA polymerase beta subunit [Nicotiana tomentosiformis]

 Score = 94.0 bits (232), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 49/104 (47%), Positives = 64/104 (61%), Gaps = 25/104 (24%)

Query: 16  PFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSR 62
           P+    R  ++D++FNPL VP RMN+G IFECSL        RH     FDERY+Q+ SR
Sbjct: 840 PYLQDGR--SVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASR 897

Query: 63  KLVLSKLYKACKQTANP----------CKTLDGQMGNPFKEHVL 96
           KLV S+LY+A KQTANP           +  DG+ GNPF++ V+
Sbjct: 898 KLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGNPFEQPVI 941

Source: Nicotiana tomentosiformis

Species: Nicotiana tomentosiformis

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|350996418|gb|AEQ36930.1| RNA polymerase beta subunit (chloroplast) [Datura stramonium]

 Score = 94.0 bits (232), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 49/104 (47%), Positives = 64/104 (61%), Gaps = 25/104 (24%)

Query: 16  PFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSR 62
           P+    R  ++D++FNPL VP RMN+G IFECSL        RH     FDERY+Q+ SR
Sbjct: 840 PYLQDGR--SVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASR 897

Query: 63  KLVLSKLYKACKQTANP----------CKTLDGQMGNPFKEHVL 96
           KLV S+LY+A KQTANP           +  DG+ GNPF++ V+
Sbjct: 898 KLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGNPFEQPVI 941

Source: Datura stramonium

Species: Datura stramonium

Genus: Datura

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|394831094|ref|YP_006503783.1| RNA polymerase beta subunit (chloroplast) [Datura stramonium] gi|350996505|gb|AEQ37016.1| RNA polymerase beta subunit [Datura stramonium]

 Score = 94.0 bits (232), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 49/104 (47%), Positives = 64/104 (61%), Gaps = 25/104 (24%)

Query: 16  PFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSR 62
           P+    R  ++D++FNPL VP RMN+G IFECSL        RH     FDERY+Q+ SR
Sbjct: 840 PYLQDGR--SVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASR 897

Query: 63  KLVLSKLYKACKQTANP----------CKTLDGQMGNPFKEHVL 96
           KLV S+LY+A KQTANP           +  DG+ GNPF++ V+
Sbjct: 898 KLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGNPFEQPVI 941

Source: Datura stramonium

Species: Datura stramonium

Genus: Datura

Family: Solanaceae

Order: Solanales

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	96
UNIPROTKB|P0C501	1075	rpoB "DNA-directed RNA polymer	0.739	0.066	0.468	1.5e-12
UNIPROTKB|P0C502	1075	rpoB "DNA-directed RNA polymer	0.739	0.066	0.468	1.5e-12
UNIPROTKB|P0C503	1075	rpoB "DNA-directed RNA polymer	0.739	0.066	0.468	1.5e-12
UNIPROTKB|Q6ENI4	1075	rpoB "DNA-directed RNA polymer	0.739	0.066	0.468	1.5e-12

UNIPROTKB|P0C501 rpoB "DNA-directed RNA polymerase subunit beta" [Oryza sativa (taxid:4530)]

 Score = 180 (68.4 bits), Expect = 1.5e-12, P = 1.5e-12
 Identities = 44/94 (46%), Positives = 58/94 (61%)

Query:    26 IDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSRKLVLSKLYKA 72
             +D++FNPL VP RMN+G IFE SL        +H     FDERY+Q+ SRKLV S+LY+A
Sbjct:   853 VDMVFNPLGVPSRMNVGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEA 912

Query:    73 CKQTANP----------CKTLDGQMGNPFKEHVL 96
              KQT NP           +  DG+ G+PF++ VL
Sbjct:   913 SKQTKNPWVFEPEYPGKSRIFDGRTGDPFEQPVL 946

GO:0009536 "plastid" evidence=IC

UNIPROTKB|P0C502 rpoB "DNA-directed RNA polymerase subunit beta" [Oryza sativa Indica Group (taxid:39946)]

 Score = 180 (68.4 bits), Expect = 1.5e-12, P = 1.5e-12
 Identities = 44/94 (46%), Positives = 58/94 (61%)

Query:    26 IDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSRKLVLSKLYKA 72
             +D++FNPL VP RMN+G IFE SL        +H     FDERY+Q+ SRKLV S+LY+A
Sbjct:   853 VDMVFNPLGVPSRMNVGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEA 912

Query:    73 CKQTANP----------CKTLDGQMGNPFKEHVL 96
              KQT NP           +  DG+ G+PF++ VL
Sbjct:   913 SKQTKNPWVFEPEYPGKSRIFDGRTGDPFEQPVL 946

GO:0009536 "plastid" evidence=IC

UNIPROTKB|P0C503 rpoB "DNA-directed RNA polymerase subunit beta" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 180 (68.4 bits), Expect = 1.5e-12, P = 1.5e-12
 Identities = 44/94 (46%), Positives = 58/94 (61%)

Query:    26 IDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSRKLVLSKLYKA 72
             +D++FNPL VP RMN+G IFE SL        +H     FDERY+Q+ SRKLV S+LY+A
Sbjct:   853 VDMVFNPLGVPSRMNVGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEA 912

Query:    73 CKQTANP----------CKTLDGQMGNPFKEHVL 96
              KQT NP           +  DG+ G+PF++ VL
Sbjct:   913 SKQTKNPWVFEPEYPGKSRIFDGRTGDPFEQPVL 946

GO:0009536 "plastid" evidence=IC

UNIPROTKB|Q6ENI4 rpoB "DNA-directed RNA polymerase subunit beta" [Oryza nivara (taxid:4536)]

 Score = 180 (68.4 bits), Expect = 1.5e-12, P = 1.5e-12
 Identities = 44/94 (46%), Positives = 58/94 (61%)

Query:    26 IDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSRKLVLSKLYKA 72
             +D++FNPL VP RMN+G IFE SL        +H     FDERY+Q+ SRKLV S+LY+A
Sbjct:   853 VDMVFNPLGVPSRMNVGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEA 912

Query:    73 CKQTANP----------CKTLDGQMGNPFKEHVL 96
              KQT NP           +  DG+ G+PF++ VL
Sbjct:   913 SKQTKNPWVFEPEYPGKSRIFDGRTGDPFEQPVL 946


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.327   0.142   0.457    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0       96        96   0.00091  102 3  11 22  0.46    29
                                                     29  0.43    31


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  4
  No. of states in DFA:  577 (61 KB)
  Total size of DFA:  127 KB (2080 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  10.99u 0.12s 11.11t   Elapsed:  00:00:00
  Total cpu time:  10.99u 0.12s 11.11t   Elapsed:  00:00:00
  Start:  Thu May  9 18:06:45 2013   End:  Thu May  9 18:06:45 2013

GO:0009536 "plastid" evidence=IC

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	RPOB	unknown protein; Chloroplast DNA-dependent RNA polymerase B subunit. The transcription of this gene is regulated by a nuclear encoded RNA polymerase. This gene has been transferred to mitochondrial genome during crucifer evolution. ; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity) (1072 aa)
		(Arabidopsis thaliana)
Predicted Functional Partners:
	RPOC1	unknown protein; RNA polymerase beta' subunit-1 ; DNA-dependent RNA polymerase catalyzes the tr [...] (680 aa)	•	•	•	•	•		•		0.999
	RPOA	unknown protein; RNA polymerase alpha subunit ; DNA-dependent RNA polymerase catalyzes the tran [...] (329 aa)	•		•	•	•		•		0.999
	ATCG00790.1-P	unknown protein; chloroplast gene encoding a ribosomal protein L16, which is a constituent of 5 [...] (135 aa)	•			•			•		0.995
	RPOC2	unknown protein; RNA polymerase beta' subunit-2 ; DNA-dependent RNA polymerase catalyzes the tr [...] (1376 aa)	•	•	•		•		•		0.991
	ATCG00800.1-P	unknown protein; encodes a chloroplast ribosomal protein S3, a constituent of the small subunit [...] (218 aa)	•			•	•		•		0.991
	RPL2.2	unknown protein; encodes a chloroplast ribosomal protein L2, a constituent of the large subunit [...] (274 aa)	•			•			•		0.988
	RPL2.1	unknown protein; encodes a chloroplast ribosomal protein L2, a constituent of the large subunit [...] (274 aa)	•			•			•		0.988
	TUFA	elongation factor Tu, putative / EF-Tu, putative; elongation factor Tu, putative / EF-Tu, putat [...] (454 aa)	•			•	•		•		0.985
	ATRABE1B	ATRABE1B (ARABIDOPSIS RAB GTPASE HOMOLOG E1B); GTP binding / GTPase/ translation elongation fac [...] (476 aa)	•			•	•		•		0.984
	AT3G13120	30S ribosomal protein S10, chloroplast, putative; 30S ribosomal protein S10, chloroplast, putat [...] (191 aa)	•			•	•		•		0.983

---

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	96
CHL00001	1070	CHL00001, rpoB, RNA polymerase beta subunit	2e-26
pfam00562	373	pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, do	2e-09
cd00653	866	cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun	1e-08
CHL00207	1077	CHL00207, rpoB, RNA polymerase beta subunit; Provi	2e-08
PRK00405	1112	PRK00405, rpoB, DNA-directed RNA polymerase subuni	5e-08
COG0085	1060	COG0085, RpoB, DNA-directed RNA polymerase, beta s	2e-07
TIGR02013	1065	TIGR02013, rpoB, DNA-directed RNA polymerase, beta	3e-07
PRK09603	2890	PRK09603, PRK09603, bifunctional DNA-directed RNA	8e-05
PRK14844	2836	PRK14844, PRK14844, bifunctional DNA-directed RNA	4e-04
TIGR03670	599	TIGR03670, rpoB_arch, DNA-directed RNA polymerase	0.001
PRK07225	605	PRK07225, PRK07225, DNA-directed RNA polymerase su	0.003

>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit

 Score =  101 bits (253), Expect = 2e-26
 Identities = 44/94 (46%), Positives = 57/94 (60%), Gaps = 23/94 (24%)

Query: 26  IDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSRKLVLSKLYKA 72
           +D++ NPL VP RMN+G IFEC L        RH     FDERY+Q+ SRKLV S+LY+A
Sbjct: 848 VDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEASRKLVFSELYEA 907

Query: 73  CKQTANP----------CKTLDGQMGNPFKEHVL 96
            KQTANP           +  DG+ G+PF++ V 
Sbjct: 908 SKQTANPWVFEPEYPGKSRLFDGRTGDPFEQPVT 941

Length = 1070

>gnl|CDD|215994 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, domain 6

 Score = 52.2 bits (126), Expect = 2e-09
 Identities = 24/85 (28%), Positives = 32/85 (37%), Gaps = 20/85 (23%)

Query: 26  IDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSRKLVLSKLYKA 72
            DII NP  VP RM IG + E  L        +      FD         + +   L +A
Sbjct: 255 PDIILNPHGVPSRMTIGQLLESLLGKAAALLGKFIDATPFDGA---SEDVEDIGELLKEA 311

Query: 73  CKQTANPCKTL--DGQMGNPFKEHV 95
                   K +  DG+ G PFK  +
Sbjct: 312 GYN--AYGKEVLYDGRTGEPFKAPI 334

RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII). Length = 373

>gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit

 Score = 50.3 bits (121), Expect = 1e-08
 Identities = 22/85 (25%), Positives = 30/85 (35%), Gaps = 22/85 (25%)

Query: 26  IDIIFNPLEVPPRMNIGHIFECSL---------RH----FDERYKQKGSRKLVLSKLYKA 72
            DII NP   P RM IG + E  L               FD   ++  S  L  + L   
Sbjct: 664 PDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLN-- 721

Query: 73  CKQTANPCKTL--DGQMGNPFKEHV 95
                   K +  DG+ G P +  +
Sbjct: 722 -----YYGKEVLYDGRTGEPLEAPI 741

RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation. Length = 866

>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional

 Score = 49.3 bits (118), Expect = 2e-08
 Identities = 34/94 (36%), Positives = 43/94 (45%), Gaps = 23/94 (24%)

Query: 26  IDIIFNPLEVPPRMNIGHIFECSL-------------RHFDERYKQKGSRKLVLSKLYKA 72
            DII NPL VP RMN+G +FEC L               FDE Y  + SR L+ +KL +A
Sbjct: 844 PDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMYGSEYSRILINNKLNQA 903

Query: 73  CKQTAN--------PCKTL--DGQMGNPFKEHVL 96
             +           P K +  DG+ G  FK  V 
Sbjct: 904 SIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVT 937

Length = 1077

>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed

 Score = 48.2 bits (116), Expect = 5e-08
 Identities = 15/24 (62%), Positives = 17/24 (70%)

Query: 26  IDIIFNPLEVPPRMNIGHIFECSL 49
           +DI+ NPL VP RMNIG I E  L
Sbjct: 914 VDIVLNPLGVPSRMNIGQILETHL 937

Length = 1112

>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]

 Score = 46.8 bits (112), Expect = 2e-07
 Identities = 16/24 (66%), Positives = 16/24 (66%)

Query: 26  IDIIFNPLEVPPRMNIGHIFECSL 49
            DII NPL VP RMNIG I E  L
Sbjct: 863 PDIILNPLGVPSRMNIGQILETHL 886

Length = 1060

>gnl|CDD|233685 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit

 Score = 46.2 bits (110), Expect = 3e-07
 Identities = 26/81 (32%), Positives = 35/81 (43%), Gaps = 11/81 (13%)

Query: 26  IDIIFNPLEVPPRMNIGHIFECSLRHFDERYKQKG-----------SRKLVLSKLYKACK 74
           +DI+ NPL VP RMNIG I E  L    ++  +KG           S + +   L KA  
Sbjct: 871 VDIVLNPLGVPSRMNIGQILETHLGWAGKKLGRKGVPIATPVFDGASEEEIKEYLEKAGL 930

Query: 75  QTANPCKTLDGQMGNPFKEHV 95
                 +  DG+ G  F   V
Sbjct: 931 PRDGKVRLYDGRTGEQFDNPV 951

This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit [Transcription, DNA-dependent RNA polymerase]. Length = 1065

>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed

 Score = 39.5 bits (92), Expect = 8e-05
 Identities = 16/39 (41%), Positives = 23/39 (58%)

Query: 26   IDIIFNPLEVPPRMNIGHIFECSLRHFDERYKQKGSRKL 64
            +DI+ NPL VP RMNIG I E  L    + + ++ +  L
Sbjct: 1122 VDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASML 1160

Length = 2890

>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional

 Score = 37.7 bits (87), Expect = 4e-04
 Identities = 14/21 (66%), Positives = 16/21 (76%)

Query: 26   IDIIFNPLEVPPRMNIGHIFE 46
            +DII NPL VP RMN+G I E
Sbjct: 1115 VDIILNPLGVPSRMNVGQILE 1135

Length = 2836

>gnl|CDD|132709 TIGR03670, rpoB_arch, DNA-directed RNA polymerase subunit B

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 9/20 (45%), Positives = 13/20 (65%)

Query: 27  DIIFNPLEVPPRMNIGHIFE 46
           D+I NP  +P RM +G + E
Sbjct: 387 DLIINPHAIPSRMTVGQLLE 406

This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes. Length = 599

>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B'; Validated

 Score = 34.9 bits (81), Expect = 0.003
 Identities = 10/20 (50%), Positives = 14/20 (70%)

Query: 27  DIIFNPLEVPPRMNIGHIFE 46
           D+I NP  +P RM +GH+ E
Sbjct: 393 DLIINPHAIPSRMTVGHVLE 412

Length = 605

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	96
COG0085	1060	RpoB DNA-directed RNA polymerase, beta subunit/140	100.0
TIGR03670	599	rpoB_arch DNA-directed RNA polymerase subunit B. T	100.0
PRK07225	605	DNA-directed RNA polymerase subunit B'; Validated	100.0
PF00562	386	RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; Int	100.0
PRK08565	1103	DNA-directed RNA polymerase subunit B; Provisional	99.97
PRK00405	1112	rpoB DNA-directed RNA polymerase subunit beta; Rev	99.97
TIGR02013	1065	rpoB DNA-directed RNA polymerase, beta subunit. Th	99.97
cd00653	866	RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA po	99.97
CHL00207	1077	rpoB RNA polymerase beta subunit; Provisional	99.97
CHL00001	1070	rpoB RNA polymerase beta subunit	99.96
PRK09603	2890	bifunctional DNA-directed RNA polymerase subunit b	99.96
KOG0215	1153	consensus RNA polymerase III, second largest subun	99.94
PRK14844	2836	bifunctional DNA-directed RNA polymerase subunit b	99.94
KOG0216	1111	consensus RNA polymerase I, second largest subunit	99.94
KOG0214	1141	consensus RNA polymerase II, second largest subuni	99.93

>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]

Probab=100.00  E-value=6.7e-36  Score=261.14  Aligned_cols=90  Identities=32%  Similarity=0.470  Sum_probs=86.7

Q ss_pred             CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc--------cccccccCCCcHHHHHHHHHHh
Q 045556            1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR--------HFDERYKQKGSRKLVLSKLYKA   72 (96)
Q Consensus         1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG--------~~dg~~~~~~~~~~i~~~L~~~   72 (96)
                      .||+|||+||    |||++||+  +||||||||||||||||||++|+|+|        .++++.|++.+.+++++.|+++
T Consensus       844 Vis~i~p~eD----MPf~~~G~--~~DiilNP~gvPSRM~iGqilE~~lG~a~~~~G~~~~~~~F~g~~~~~~~~~l~~~  917 (1060)
T COG0085         844 VVSKIVPQED----MPFLEDGT--PPDIILNPLGVPSRMNIGQILETHLGKAAALLGIPVDTPVFDGAPEEDIRELLKEA  917 (1060)
T ss_pred             eeeeecCccc----CCcCCCCC--cccEEECCCCCCccccHHHHHHHHHHHHHHhcCceeccCCcCCCCHHHHHHHHHHc
Confidence            4899999999    99999999  99999999999999999999999999        6788889999999999999999


Q ss_pred             ccCCCCCceeecCCCCccCCCCCC
Q 045556           73 CKQTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        73 g~~~~g~e~lydG~TGe~~~~~I~   96 (96)
                      ||+++|+++||||+|||+|+++|+
T Consensus       918 g~~~~Gk~~lydG~TGe~~~~~i~  941 (1060)
T COG0085         918 GFPYSGKEVLYDGRTGEPFDAPIF  941 (1060)
T ss_pred             CCCCCCCEEeecCCCCCcccccEE
Confidence            999999999999999999999985

>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B

Probab=100.00  E-value=1.2e-34  Score=242.89  Aligned_cols=90  Identities=22%  Similarity=0.318  Sum_probs=85.7

Q ss_pred             CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc--------cccccccCCCcHHHHHHHHHHh
Q 045556            1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR--------HFDERYKQKGSRKLVLSKLYKA   72 (96)
Q Consensus         1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG--------~~dg~~~~~~~~~~i~~~L~~~   72 (96)
                      .||.|+|+||    |||++||+  +|||||||||||||||||||+|+++|        .+|+++|.+.+.+++.+.|+++
T Consensus       367 vvs~i~~~eD----MPft~~G~--~pDiIiNPhg~PSRMTiGqllE~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~L~~~  440 (599)
T TIGR03670       367 VIGMIVPQED----MPFTEDGI--VPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKL  440 (599)
T ss_pred             eEEeEeccCC----CCcCCCCC--CCCEEECcccccccccHHHHHHHHHHHHHHhcCCEEEeCCCCCccHHHHHHHHHHc
Confidence            3789999999    99999999  99999999999999999999999999        6688889888899999999999


Q ss_pred             ccCCCCCceeecCCCCccCCCCCC
Q 045556           73 CKQTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        73 g~~~~g~e~lydG~TGe~~~~~I~   96 (96)
                      ||+++|+|+||||+||++|+++|+
T Consensus       441 g~~~~G~e~ly~G~TG~~~~~~if  464 (599)
T TIGR03670       441 GFKPDGKEVMYDGITGEKLEAEIF  464 (599)
T ss_pred             CCCCCCCEEEEcCCCCCCccccEE
Confidence            999999999999999999999885

This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.

>PRK07225 DNA-directed RNA polymerase subunit B'; Validated

Probab=100.00  E-value=1.2e-34  Score=243.04  Aligned_cols=90  Identities=23%  Similarity=0.299  Sum_probs=85.8

Q ss_pred             CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc--------cccccccCCCcHHHHHHHHHHh
Q 045556            1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR--------HFDERYKQKGSRKLVLSKLYKA   72 (96)
Q Consensus         1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG--------~~dg~~~~~~~~~~i~~~L~~~   72 (96)
                      .||.|+|+||    |||++||+  +|||||||||||||||||||+|+++|        .+|+++|.+.+.+++.+.|+++
T Consensus       373 vvs~i~~~eD----MPft~~G~--~PDiIiNPhg~PSRMTiGql~E~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~L~~~  446 (605)
T PRK07225        373 VIGLIVPQED----MPFTESGV--VPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKL  446 (605)
T ss_pred             eEEeEecccc----CCcCCCCC--cccEEECcccccccCcHHHHHHHHHHHHHHhcCceEeecCCCCchHHHHHHHHHHh
Confidence            3789999999    99999999  99999999999999999999999999        6688889988899999999999


Q ss_pred             ccCCCCCceeecCCCCccCCCCCC
Q 045556           73 CKQTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        73 g~~~~g~e~lydG~TGe~~~~~I~   96 (96)
                      ||+++|+|+||||+||++|+++|+
T Consensus       447 g~~~~G~e~my~G~TG~~~~~~if  470 (605)
T PRK07225        447 GFEHTGKEVMYDGITGEKIEAEIF  470 (605)
T ss_pred             CcCCCCeEEEEcCCCCCEecccEE
Confidence            999999999999999999999885

>PF00562 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; InterPro: IPR007120 DNA-directed RNA polymerases 2

Probab=100.00  E-value=2.1e-34  Score=230.03  Aligned_cols=89  Identities=29%  Similarity=0.386  Sum_probs=80.7

Q ss_pred             cceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc--------cccccccCCCcHHHHHHHHHHhc
Q 045556            2 LLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR--------HFDERYKQKGSRKLVLSKLYKAC   73 (96)
Q Consensus         2 ~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG--------~~dg~~~~~~~~~~i~~~L~~~g   73 (96)
                      ||.|+|+||    ||||+||+  +|||||||||||||||||||+|+++|        .+|.++|.+.+.+++.+.|.++|
T Consensus       252 vs~i~~~eD----MPft~~G~--~pDiIiNPhgiPSRMtiGqllE~~~g~~~~~~g~~~~~t~F~~~~~~~i~~~l~~~g  325 (386)
T PF00562_consen  252 VSKILPQED----MPFTEDGI--VPDIIINPHGIPSRMTIGQLLESLLGKAGALNGRFVDATPFDESSEEDISELLKKAG  325 (386)
T ss_dssp             EEEEE-TTT----SEEETTSE--B-SEEE-GGGSTTTTBTHHHHHHHHHHHHHHSTCEEB-TTTSSS-HHHHHHHHHHTT
T ss_pred             Eeeeecccc----CccccCCC--cceeeecccccccccchHHHHhhhhhhhhhccccceecCCCCCcchhhhHhhhhccc
Confidence            799999999    99999999  99999999999999999999999999        66888899999999999999999


Q ss_pred             cCCCCCceeecCCCCccCCCCCC
Q 045556           74 KQTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        74 ~~~~g~e~lydG~TGe~~~~~I~   96 (96)
                      |+++|+++||||+||++|+++|+
T Consensus       326 ~~~~g~~~l~~g~tG~~~~~~i~  348 (386)
T PF00562_consen  326 YNYPGKEVLYDGRTGEKFEAPIF  348 (386)
T ss_dssp             SHTTSEEEEBESSSSSBESSEEE
T ss_pred             ccccceEEEEcCccCceEEeEEE
Confidence            99999999999999999999875

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerases (2.7.7.6 from EC) catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain represents the hybrid-binding domain and the wall domain []. The hybrid-binding domain binds the nascent RNA strand/template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion []. This domain is also involved in binding to Rpb1 and Rpb3 []. Many of the bacterial members contain large insertions within this domain, which are known as dispensable region 2 (DRII).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_R 3HKZ_B 2PMZ_R 3H0G_B 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B ....

>PRK08565 DNA-directed RNA polymerase subunit B; Provisional

Probab=99.97  E-value=4.1e-33  Score=244.98  Aligned_cols=90  Identities=22%  Similarity=0.323  Sum_probs=85.4

Q ss_pred             CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc--------cccccccCCCcHHHHHHHHHHh
Q 045556            1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR--------HFDERYKQKGSRKLVLSKLYKA   72 (96)
Q Consensus         1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG--------~~dg~~~~~~~~~~i~~~L~~~   72 (96)
                      .||.|+|+||    |||++||+  +|||||||||||||||||||+|+++|        .+|+++|.+.+.+++.+.|+++
T Consensus       871 v~s~i~~~ed----mPf~~~G~--~pDiI~NPh~~PSRMtiG~l~E~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~L~~~  944 (1103)
T PRK08565        871 VIGMLVPQED----MPFTEDGI--VPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKL  944 (1103)
T ss_pred             eeeeeccccc----CCcCCCCC--CccEEECCCCCcccccHHHHHHHHHHHHHHhcCceeeecCcCCchHHHHHHHHHHc
Confidence            3789999999    99999999  99999999999999999999999999        5678888888899999999999


Q ss_pred             ccCCCCCceeecCCCCccCCCCCC
Q 045556           73 CKQTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        73 g~~~~g~e~lydG~TGe~~~~~I~   96 (96)
                      ||+++|+|+||||+||++|+++|+
T Consensus       945 g~~~~G~e~l~~G~tG~~~~~~if  968 (1103)
T PRK08565        945 GYKPDGTEVMYDGRTGEKIKAPIF  968 (1103)
T ss_pred             CCCCCCcEEEEcCCCCCCcccceE
Confidence            999999999999999999999985

>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed

Probab=99.97  E-value=3.4e-32  Score=239.63  Aligned_cols=90  Identities=30%  Similarity=0.441  Sum_probs=84.1

Q ss_pred             CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc-------cccccc-cCCCcHHHHHHHHHHh
Q 045556            1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR-------HFDERY-KQKGSRKLVLSKLYKA   72 (96)
Q Consensus         1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG-------~~dg~~-~~~~~~~~i~~~L~~~   72 (96)
                      .||.|+|+||    |||++||+  +|||||||||||||||||||+||++|       .+++++ |.+.+.+++.+.|+++
T Consensus       895 vis~i~~~eD----MPf~~~G~--~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~~g~~~~tp~f~~~~~~~~~~~l~~~  968 (1112)
T PRK00405        895 VVSRILPVED----MPYLEDGT--PVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPVFDGAKEEEIKELLEEA  968 (1112)
T ss_pred             eEEeEeccCC----CCcCCCCC--CCcEEECCCCCcccccHHHHHHHHhhHHHHhcCCeEecCccCCccHHHHHHHHHHc
Confidence            3799999999    99999999  99999999999999999999999999       445666 7778899999999999


Q ss_pred             ccCCCCCceeecCCCCccCCCCCC
Q 045556           73 CKQTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        73 g~~~~g~e~lydG~TGe~~~~~I~   96 (96)
                      ||+++|+++||||+||++|+++|+
T Consensus       969 g~~~~G~e~l~~G~tG~~~~~~if  992 (1112)
T PRK00405        969 GLPEDGKTTLYDGRTGEPFDRPVT  992 (1112)
T ss_pred             CcCCCCCEEEECCCCCCCCcccEE
Confidence            999999999999999999999985

>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit

Probab=99.97  E-value=6e-32  Score=237.33  Aligned_cols=90  Identities=32%  Similarity=0.463  Sum_probs=82.5

Q ss_pred             CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc---c-------ccccc-cCCCcHHHHHHHH
Q 045556            1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR---H-------FDERY-KQKGSRKLVLSKL   69 (96)
Q Consensus         1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG---~-------~dg~~-~~~~~~~~i~~~L   69 (96)
                      .||.|+|+||    |||++||+  +|||||||||||||||||||+||++|   .       +++++ |.+.+.+++.+.|
T Consensus       852 vis~i~~~eD----MPf~~~G~--~pDiIiNPhg~PSRMtiGqllE~~~gka~~~~~~~~~~~~tp~f~~~~~~~~~~~l  925 (1065)
T TIGR02013       852 VVSKILPIED----MPFLEDGT--PVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVPIATPVFDGASEEEIKEYL  925 (1065)
T ss_pred             eEEeEecCCC----CCccCCCC--CccEEECCCCCcccccHHHHHHHHHHHHHHhccCCCeEEeccCcCCccHHHHHHHH
Confidence            3799999999    99999999  99999999999999999999999988   1       23444 6777899999999


Q ss_pred             HHhccCCCCCceeecCCCCccCCCCCC
Q 045556           70 YKACKQTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        70 ~~~g~~~~g~e~lydG~TGe~~~~~I~   96 (96)
                      +++||+++|+++||||+||++|+++|+
T Consensus       926 ~~~g~~~~G~e~l~~G~TG~~~~~~if  952 (1065)
T TIGR02013       926 EKAGLPRDGKVRLYDGRTGEQFDRPVT  952 (1065)
T ss_pred             HHcCCCCCCCEEEEcCCCCCCccccEE
Confidence            999999999999999999999999985

This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.

>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit

Probab=99.97  E-value=8.3e-32  Score=232.19  Aligned_cols=90  Identities=27%  Similarity=0.342  Sum_probs=85.7

Q ss_pred             CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc--------cccccccCCCcHHHHHHHHHHh
Q 045556            1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR--------HFDERYKQKGSRKLVLSKLYKA   72 (96)
Q Consensus         1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG--------~~dg~~~~~~~~~~i~~~L~~~   72 (96)
                      .||.|+|+||    |||++||+  +||||||||||||||||||++|+++|        ..|+++|.+...+++.+.|.++
T Consensus       645 v~s~i~~~~d----mPf~~~G~--~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~t~f~~~~~~~~~~~l~~~  718 (866)
T cd00653         645 VISKILPQED----MPFTEDGI--PPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEA  718 (866)
T ss_pred             EEEEEecccc----CCcccCCC--CCcEEecCCcCcccccHHHHHHHHHHHHHHhcCCcccccccCcchHHHHHHHHHHc
Confidence            3789999999    99999999  99999999999999999999999999        6688899888899999999999


Q ss_pred             ccCCCCCceeecCCCCccCCCCCC
Q 045556           73 CKQTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        73 g~~~~g~e~lydG~TGe~~~~~I~   96 (96)
                      ||+++|+|+||||+||++|+++|+
T Consensus       719 g~~~~G~e~~y~g~tG~~~~~~if  742 (866)
T cd00653         719 GLNYYGKEVLYDGRTGEPLEAPIF  742 (866)
T ss_pred             CCCCCCcEEEEcCCCCCCcccceE
Confidence            999999999999999999999985

RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.

>CHL00207 rpoB RNA polymerase beta subunit; Provisional

Probab=99.97  E-value=3.8e-31  Score=232.40  Aligned_cols=90  Identities=30%  Similarity=0.427  Sum_probs=78.2

Q ss_pred             CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc--------cccccccCCCcHHHHHHHHHHh
Q 045556            1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR--------HFDERYKQKGSRKLVLSKLYKA   72 (96)
Q Consensus         1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG--------~~dg~~~~~~~~~~i~~~L~~~   72 (96)
                      .||+|+|+||    |||++||+  +|||||||||||||||||||+||++|        .++.++|.+...+++.+.|.+.
T Consensus       825 Vvs~i~p~eD----MPf~~dG~--~pDiIlNPhg~PSRMtiGqllE~~lGka~~~l~~~~~~tpF~~~~~~~~~~~l~~~  898 (1077)
T CHL00207        825 IISRILPRQD----MPYLPDGT--PPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMYGSEYSRILINN  898 (1077)
T ss_pred             eEEeeeccCC----CCccCCCC--CccEEECCccccccccHHHHHHHHHHHHHHhcCCcEeeccCCCCcHHHHHHHHHhh
Confidence            3799999999    99999999  99999999999999999999999999        3455677777666666666554


Q ss_pred             ---------------ccCCCCCceeecCCCCccCCCCCC
Q 045556           73 ---------------CKQTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        73 ---------------g~~~~g~e~lydG~TGe~~~~~I~   96 (96)
                                     +|+++|+++||||+||++|+++|+
T Consensus       899 ~l~~~~~~~~~~~~~~~~~~Gk~~lydG~TGe~~~~~i~  937 (1077)
T CHL00207        899 KLNQASIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVT  937 (1077)
T ss_pred             hhhhccchhccccccCCCCCCCEEEECCCCCCCccCceE
Confidence                           377789999999999999999985

>CHL00001 rpoB RNA polymerase beta subunit

Probab=99.96  E-value=3.4e-31  Score=232.65  Aligned_cols=90  Identities=33%  Similarity=0.661  Sum_probs=77.4

Q ss_pred             CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc--------cccccccCCCcHHHH-----HH
Q 045556            1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR--------HFDERYKQKGSRKLV-----LS   67 (96)
Q Consensus         1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG--------~~dg~~~~~~~~~~i-----~~   67 (96)
                      .||.|+|+||    |||++||+  +|||||||||||||||||||+||++|        .+++++|.+...+++     .+
T Consensus       829 vvs~i~~~eD----MPf~~dG~--~pDiIlNP~gvPSRMtiGqllE~~~G~a~~~~g~~~~~~pf~~~~~~~~~~~~~~~  902 (1070)
T CHL00001        829 IISKILPRQD----MPYLQDGT--PVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEASRKLVFS  902 (1070)
T ss_pred             eEeeeecccC----CCcccCCC--CCceeeccccccccccHHHHHHHHhHHHHhhcCceeeeccCCCcchhhhhhhhhhH
Confidence            3799999999    99999999  99999999999999999999999999        456666765544444     37


Q ss_pred             HHHHhcc---C-------CCCCceeecCCCCccCCCCCC
Q 045556           68 KLYKACK---Q-------TANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        68 ~L~~~g~---~-------~~g~e~lydG~TGe~~~~~I~   96 (96)
                      .|.++|+   +       ..|+++||||+||++|+++|+
T Consensus       903 ~l~~~~~~~~~~~~~~~~~~Gk~~l~dG~TG~~~~~~i~  941 (1070)
T CHL00001        903 ELYEASKQTANPWVFEPEYPGKSRLFDGRTGDPFEQPVT  941 (1070)
T ss_pred             HHHHHHHhcCCceeccCCCCCeEEEEcCCCCCCccceEE
Confidence            7888887   3       349999999999999999985

>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed

Probab=99.96  E-value=6.4e-30  Score=236.27  Aligned_cols=90  Identities=29%  Similarity=0.396  Sum_probs=80.8

Q ss_pred             CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCccccccccccccc-------c------c--------------
Q 045556            1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLRH-------F------D--------------   53 (96)
Q Consensus         1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG~-------~------d--------------   53 (96)
                      .||+|+|+||    |||++||+  +|||||||||||||||||||+|+|+|.       +      +              
T Consensus      1103 ViS~I~p~ED----MPfl~dG~--~pDIIlNPlGvPSRMnIGQilE~~LG~aa~~lg~~i~~~~~~~~~~~~~~~~~~~~ 1176 (2890)
T PRK09603       1103 IVSNIVPVAD----MPYTADGE--PVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLEDKTKDFAKELRAKML 1176 (2890)
T ss_pred             eEEEEEchhc----CCCCCCCC--CCcEEECCCCCCccccHHHHHHHHHHHHHHhcCcChhhhhhhcchhhhHHHHHHHH
Confidence            3799999999    99999999  999999999999999999999999991       0      0              


Q ss_pred             --------------------------------------ccc-cCCCcHHHHHHHHHHhccCCCCCceeecCCCCccCCCC
Q 045556           54 --------------------------------------ERY-KQKGSRKLVLSKLYKACKQTANPCKTLDGQMGNPFKEH   94 (96)
Q Consensus        54 --------------------------------------g~~-~~~~~~~~i~~~L~~~g~~~~g~e~lydG~TGe~~~~~   94 (96)
                                                            +++ |++.+.+++.+.|+++||+++|++.||||+|||+|+++
T Consensus      1177 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~tpvF~g~~~~~i~~~l~~aG~~~~Gk~~LyDGrTGe~f~~~ 1256 (2890)
T PRK09603       1177 EIANAINEKDPLTIHALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRER 1256 (2890)
T ss_pred             hhhcccccccccccccccccchHHHHhhhhhhccCCcccCCCCCCCCHHHHHHHHHHcCCCCCCCEEEEcCCCCCCccce
Confidence                                                  112 56677899999999999999999999999999999999


Q ss_pred             CC
Q 045556           95 VL   96 (96)
Q Consensus        95 I~   96 (96)
                      |+
T Consensus      1257 V~ 1258 (2890)
T PRK09603       1257 VN 1258 (2890)
T ss_pred             EE
Confidence            85

>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]

Probab=99.94  E-value=2.2e-28  Score=210.36  Aligned_cols=90  Identities=21%  Similarity=0.251  Sum_probs=83.1

Q ss_pred             CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc---ccc-----ccccCCCcHHHHHHHHHHh
Q 045556            1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR---HFD-----ERYKQKGSRKLVLSKLYKA   72 (96)
Q Consensus         1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG---~~d-----g~~~~~~~~~~i~~~L~~~   72 (96)
                      .|+.||+|||    |||...|+  +|||||||||||||||+|+++|.+.|   +.+     |+.|.+.+++++++.|.++
T Consensus       926 VcGlIv~QED----MPFnD~GI--cPDiIMNPHGFPSRMTVGK~iELlsGKAGVl~G~~hYGTaFGgskVed~~~~Lv~h  999 (1153)
T KOG0215|consen  926 VCGLIVQQED----MPFNDQGI--CPDIIMNPHGFPSRMTVGKMIELLSGKAGVLEGTFHYGTAFGGSKVEDISEELVEH  999 (1153)
T ss_pred             eeeEEeeccC----CCCcccCC--CcccccCCCCCcccchHHHHHHHhccccceeeeeEeeccccCCchHHHHHHHHHHh
Confidence            3688999999    99999999  99999999999999999999999988   444     5568889999999999999


Q ss_pred             ccCCCCCceeecCCCCccCCCCCC
Q 045556           73 CKQTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        73 g~~~~g~e~lydG~TGe~~~~~I~   96 (96)
                      ||++.||..+|+|.|||++++-|+
T Consensus      1000 GfnY~GKD~ltSGITGepLeAYIf 1023 (1153)
T KOG0215|consen 1000 GFNYSGKDMLTSGITGEPLEAYIF 1023 (1153)
T ss_pred             ccCccCccccccCCCCCcceeeEE
Confidence            999999999999999999998764

>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional

Probab=99.94  E-value=3.1e-28  Score=224.86  Aligned_cols=44  Identities=39%  Similarity=0.772  Sum_probs=43.0

Q ss_pred             CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc
Q 045556            1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR   50 (96)
Q Consensus         1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG   50 (96)
                      .||+|+|.||    |||++|||  |+|||+||+|||||||||||+|||||
T Consensus      1096 VIS~IlP~eD----MPyL~DGt--pvDIvLNPLGVPSRMNvGQilE~hLG 1139 (2836)
T PRK14844       1096 VISRVVPVED----MPYLEDGT--PVDIILNPLGVPSRMNVGQILETHVG 1139 (2836)
T ss_pred             eEeEEcccCC----CCcCCCCC--CceEEeCCCCCCccccHHHHHHHHHH
Confidence            4899999999    99999999  99999999999999999999999999

>KOG0216 consensus RNA polymerase I, second largest subunit [Transcription]

Probab=99.94  E-value=2.2e-28  Score=210.59  Aligned_cols=90  Identities=22%  Similarity=0.191  Sum_probs=81.6

Q ss_pred             CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc--------cccccccC----CCcHHHHHHH
Q 045556            1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR--------HFDERYKQ----KGSRKLVLSK   68 (96)
Q Consensus         1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG--------~~dg~~~~----~~~~~~i~~~   68 (96)
                      .+|..||.+|    |||++.|.  .|||||||||||||||||+++|+++|        ..|+++|.    ....+.+.+.
T Consensus       871 icS~~wP~~d----mPFtesGm--~PDii~NPH~FPSRMTIgM~iEs~AgK~~alhG~~~Datpf~~~E~~t~~dyfg~~  944 (1111)
T KOG0216|consen  871 ICSQKWPTID----MPFTESGM--VPDIIINPHAFPSRMTIGMLIESMAGKAGALHGNAQDATPFIFSEENTAIDYFGEM  944 (1111)
T ss_pred             cccccCCCCC----CCccccCc--CcceeeCCCCCcccccHHHHHHHHhchhhccccccccCCceeecCcccHHHHHHHH
Confidence            4789999999    99999999  99999999999999999999999999        56777753    2336889999


Q ss_pred             HHHhccCCCCCceeecCCCCccCCCCCC
Q 045556           69 LYKACKQTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        69 L~~~g~~~~g~e~lydG~TGe~~~~~I~   96 (96)
                      |+++||+++|+|.||+|.+|+.|++.|+
T Consensus       945 L~~~GyNyyGnE~~YSGv~G~e~~adIf  972 (1111)
T KOG0216|consen  945 LKKAGYNYYGNEPMYSGVDGREMRADIF  972 (1111)
T ss_pred             HHHcCcCccCCcccccccccceeeeeEE
Confidence            9999999999999999999999999874

>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]

Probab=99.93  E-value=5.8e-27  Score=202.80  Aligned_cols=89  Identities=25%  Similarity=0.331  Sum_probs=82.4

Q ss_pred             cceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc--------cccccccCCCcHHHHHHHHHHhc
Q 045556            2 LLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR--------HFDERYKQKGSRKLVLSKLYKAC   73 (96)
Q Consensus         2 ~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG--------~~dg~~~~~~~~~~i~~~L~~~g   73 (96)
                      ++.+.++||    ||||.+|+  +||||+|||||||||||||++||++|        ..|+++|.+..+..+.+.|+++|
T Consensus       912 ig~~~~qed----mpft~eGi--~pDiiiNPhaiPSRmtig~liEc~lgk~~a~~~e~~~atpFs~v~v~~is~~l~~~g  985 (1141)
T KOG0214|consen  912 IGITYRQED----MPFTIEGI--VPDIIINPHAIPSRMTIGQLIECLLGKVAAYEGEEGDATPFSDVTVSKISANLHVYG  985 (1141)
T ss_pred             ccceeecCC----CCccccCC--CcceEECcccCccccchhhhHHHhhhhhhhcccccccCCCCCccchhcccchHHHhc
Confidence            566777777    99999999  99999999999999999999999999        44677888899999999999999


Q ss_pred             cCCCCCceeecCCCCccCCCCCC
Q 045556           74 KQTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        74 ~~~~g~e~lydG~TGe~~~~~I~   96 (96)
                      |+..|+|+||||+||++|.++|+
T Consensus       986 ~~~~G~e~~ynGrtG~~~~~~if 1008 (1141)
T KOG0214|consen  986 YQYRGNERMYNGRTGRKLRAQIF 1008 (1141)
T ss_pred             cccCCCEEEecCCCCceeeeeee
Confidence            99999999999999999999875

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	96
2a6h_C	1119	DNA-directed RNA polymerase beta chain; RNA polyme	8e-12

>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ... Length = 1119

 Score = 58.5 bits (142), Expect = 8e-12
 Identities = 18/67 (26%), Positives = 26/67 (38%), Gaps = 13/67 (19%)

Query: 26  IDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSRKLVLSKLYKA 72
           +D+I NPL VP RMN+G I E  L        +      FD   + +    L  +     
Sbjct: 867 VDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYF 926

Query: 73  CKQTANP 79
            K+    
Sbjct: 927 GKRKGEG 933

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	96
4ayb_B	1131	DNA-directed RNA polymerase; transferase, multi-su	100.0
1twf_B	1224	DNA-directed RNA polymerase II 140 kDa polypeptid;	100.0
2a6h_C	1119	DNA-directed RNA polymerase beta chain; RNA polyme	99.97
3h0g_B	1210	DNA-directed RNA polymerase II subunit RPB2; trans	99.97
3lu0_C	1342	DNA-directed RNA polymerase subunit beta; E. coli	99.97

>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B 2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B

Probab=100.00  E-value=2.1e-35  Score=257.72  Aligned_cols=90  Identities=22%  Similarity=0.284  Sum_probs=85.5

Q ss_pred             CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc--------cccccccCCCcHHHHHHHHHHh
Q 045556            1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR--------HFDERYKQKGSRKLVLSKLYKA   72 (96)
Q Consensus         1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG--------~~dg~~~~~~~~~~i~~~L~~~   72 (96)
                      .||+|+|+||    |||++||+  +|||||||||||||||||||+|+++|        ..|+++|.+...+++.+.|.++
T Consensus       890 vvs~i~p~eD----MPf~~dG~--~~DiilNP~gvPSRMniGqilE~~~gk~~~~~g~~~~atpf~~~~~e~~~~~l~~~  963 (1131)
T 4ayb_B          890 VIGMLIPQVD----MPYTVKGV--VPDVILNPHALPSRMTLGQIMEGIAGKYAALSGNIVDATPFYKTPIEQLQNEILKY  963 (1131)
T ss_dssp             EEEEEECTTT----SEEETTSC--CCSEECCTTSSTTTTCHHHHHHHHHHHHHHHHCCCCBCCTTSSCCTHHHHHHHHHT
T ss_pred             eeeeeccccc----CCcCCCCC--CccEEECCCCCcccCcHHHHHHHHHHHHHHhCCCceecCccCCCcHHHHHHHHHHc
Confidence            3799999999    99999999  99999999999999999999999999        5678888888889999999999


Q ss_pred             ccCCCCCceeecCCCCccCCCCCC
Q 045556           73 CKQTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        73 g~~~~g~e~lydG~TGe~~~~~I~   96 (96)
                      ||+++|+++||||+|||+|+++|+
T Consensus       964 g~~~~g~~~lydG~TGe~~~~~i~  987 (1131)
T 4ayb_B          964 GYLPDATEVTYDGRTGQKIKSRIY  987 (1131)
T ss_dssp             TSCTTSEECEEETTTCCBCSSCEE
T ss_pred             CCCCCCCEEEeCCCCCCEecCcEE
Confidence            999999999999999999999985

>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B 1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B* 1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B* 1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ...

Probab=100.00  E-value=2.1e-35  Score=260.21  Aligned_cols=89  Identities=22%  Similarity=0.287  Sum_probs=86.0

Q ss_pred             cceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc--------cccccccCCCcHHHHHHHHHHhc
Q 045556            2 LLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR--------HFDERYKQKGSRKLVLSKLYKAC   73 (96)
Q Consensus         2 ~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG--------~~dg~~~~~~~~~~i~~~L~~~g   73 (96)
                      ||.|+|+||    |||++||+  +|||||||||||||||||||+||++|        ..|+++|.+.+++++.+.|+++|
T Consensus       990 is~i~p~eD----MPf~~dG~--~pDiIiNPhg~PSRMtiGqllE~~lgka~~~~G~~~datpF~~~~~~~i~~~L~~~g 1063 (1224)
T 1twf_B          990 IGITYRRED----MPFTAEGI--VPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHG 1063 (1224)
T ss_dssp             EEEEECTTT----SCEETTSC--CCSEEECGGGSTTTTCHHHHHHHHHHHHHHHHCSCEECCSSSSCCHHHHHHHHHTTT
T ss_pred             eeeeccccc----CCcCCCCC--CccEEeCCCcCccccccchhHHHHhhHHHHhcCceeecCCCCCccHHHHHHHHHHcC
Confidence            799999999    99999999  99999999999999999999999999        56888999999999999999999


Q ss_pred             cCCCCCceeecCCCCccCCCCCC
Q 045556           74 KQTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        74 ~~~~g~e~lydG~TGe~~~~~I~   96 (96)
                      |+++|+++||||+||++|+++|+
T Consensus      1064 ~~~~G~e~ly~G~TG~~~~~~i~ 1086 (1224)
T 1twf_B         1064 YQSRGFEVMYNGHTGKKLMAQIF 1086 (1224)
T ss_dssp             SCTTSEECEECTTTCCBCSSCEE
T ss_pred             CCCCCCEEeecCCCCCCccceEE
Confidence            99999999999999999999985

>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ...

Probab=99.97  E-value=3.1e-33  Score=245.06  Aligned_cols=90  Identities=27%  Similarity=0.399  Sum_probs=83.2

Q ss_pred             CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc-------cccccc-cCCCcHHHHHHHHHHh
Q 045556            1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR-------HFDERY-KQKGSRKLVLSKLYKA   72 (96)
Q Consensus         1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG-------~~dg~~-~~~~~~~~i~~~L~~~   72 (96)
                      .||+|+|+||    |||++||+  +|||||||||||||||||||+||++|       ...+++ |++.+.+++.+.|+++
T Consensus       848 Vis~i~p~eD----MPf~~dG~--~pDiIlNPhgvPSRMtiGqllE~~lG~a~~~~g~~~atp~F~~~~~~~i~~~L~~~  921 (1119)
T 2a6h_C          848 VVAKILPVED----MPHLPDGT--PVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQA  921 (1119)
T ss_dssp             EEEEEECTTT----SCBCSSSC--BCSEECCSTTTTTTTBTHHHHHHHHHHHHHHTTEEEECCTTTSCCHHHHHHHHHHH
T ss_pred             eEEeeeccCC----CccccCCC--CccEEeCCCcCccccchhhhhHHHhhhHHhhcCCceEecccCCCCHHHHHHHHHHh
Confidence            3799999999    99999999  99999999999999999999999999       223566 7778999999999999


Q ss_pred             -----------------------------cc--------------CCCCCceeecCCCCccCCCCCC
Q 045556           73 -----------------------------CK--------------QTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        73 -----------------------------g~--------------~~~g~e~lydG~TGe~~~~~I~   96 (96)
                                                   ||              +++|+++||||+|||+|+++|+
T Consensus       922 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~Gk~~lydG~TGe~~~~~I~  988 (1119)
T 2a6h_C          922 FEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPEEQLKELFLQGKVVLYDGRTGEPIEGPIV  988 (1119)
T ss_dssp             HHHHHHHHHHHTCCCBHHHHHHHHHHHTTTSSCTTSCHHHHHHHHHHTTEECCBCSSSCCBCSSCEE
T ss_pred             hhhccccccccccccchhhhhhhhhhhcCCcccccccchhhhcccCCCCceEeecCCCCCCccceEE
Confidence                                         99              9999999999999999999985

>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=99.97  E-value=7.6e-33  Score=243.92  Aligned_cols=89  Identities=26%  Similarity=0.312  Sum_probs=85.4

Q ss_pred             cceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc--------cccccccCCCcHHHHHHHHHHhc
Q 045556            2 LLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR--------HFDERYKQKGSRKLVLSKLYKAC   73 (96)
Q Consensus         2 ~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG--------~~dg~~~~~~~~~~i~~~L~~~g   73 (96)
                      ||+|+|+||    |||++||+  +||||||||||||||||||++|+++|        ..|+++|.+.+.+++.+.|+++|
T Consensus       979 i~~i~~~ed----mPf~~~G~--~pDii~NP~~~PSRMtigq~~E~~~g~~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g 1052 (1210)
T 3h0g_B          979 IGMTYRHED----MPFSAQGI--VPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVTVEAVSKLLRSHG 1052 (1210)
T ss_dssp             EEEEECTTT----SCCBTTTB--CCSEECCGGGSTTSCCHHHHHHHHHHHHSSSSCCCCBCCSSCSCCHHHHHHHHHTTT
T ss_pred             eeEEecccc----CCcCCCCC--CCeEEECCCcCCCCccchhhhHhHHHHHHHhcCCceeeccCCCCcHHHHHHHHHHcC
Confidence            789999999    99999999  99999999999999999999999999        35788899999999999999999


Q ss_pred             cCCCCCceeecCCCCccCCCCCC
Q 045556           74 KQTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        74 ~~~~g~e~lydG~TGe~~~~~I~   96 (96)
                      |+++|+++||||+||++|+++|+
T Consensus      1053 ~~~~G~~~l~~g~tg~~~~~~i~ 1075 (1210)
T 3h0g_B         1053 FQSRGFEVMYHGHTGRKLVAQVF 1075 (1210)
T ss_dssp             SCTTSCBCCBCSSSCCBCSSCBE
T ss_pred             cCCCCCEEEEcCCCCCCccccEE
Confidence            99999999999999999999985

>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C*

Probab=99.97  E-value=1.3e-32  Score=243.30  Aligned_cols=90  Identities=29%  Similarity=0.413  Sum_probs=82.0

Q ss_pred             CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccccc---c------------------------
Q 045556            1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLRHF---D------------------------   53 (96)
Q Consensus         1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG~~---d------------------------   53 (96)
                      .||+|+|+||    |||++||+  +|||||||||||||||||||+|||+|..   -                        
T Consensus      1075 Vis~I~p~ED----MPf~~dG~--~pDIIlNP~gvPSRMnIGqilE~~lG~aa~~~G~~i~~~~~~~~~~~~~r~~~~~~ 1148 (1342)
T 3lu0_C         1075 VISKINPIED----MPYDENGT--PVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRA 1148 (1342)
T ss_dssp             EECCCCCTTT----SCEETTEE--ECSEECCGGGTTSSCBTHHHHHHHHHHGGGTSSTHHHHTTTHHHHCTTTHHHHHHH
T ss_pred             eEEEEecccC----CCCCCCCC--CCcEEeCCCCCCCccchhhhhHHhhhHHHHhcCchHHHHHHhhhhhHHHHHHHHHH
Confidence            3799999999    99999999  9999999999999999999999999910   0                        


Q ss_pred             ----------------------------------ccc-cCCCcHHHHHHHHHHhccCCCCCceeecCCCCccCCCCCC
Q 045556           54 ----------------------------------ERY-KQKGSRKLVLSKLYKACKQTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        54 ----------------------------------g~~-~~~~~~~~i~~~L~~~g~~~~g~e~lydG~TGe~~~~~I~   96 (96)
                                                        +++ |.+++.+++.+.|.++||+++|+++||||+|||+|+++|+
T Consensus      1149 y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~aTPvFdga~~~~i~~~L~~aG~~~~Gk~~LydGrTGe~f~~~V~ 1226 (1342)
T 3lu0_C         1149 YDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVT 1226 (1342)
T ss_dssp             TTTTCCCSSSCCTTTSCHHHHHHTTTTTSSCTTCBCCSSSSCCHHHHHHHTSSSSSCSSSCBCCBCSSSCSBCSSCBC
T ss_pred             hhcccccchhhhhcccchHHHHHHhhhhccCCcccCCCCCCCCHHHHHHHHHHcCCCCCCCEEEEcCCCCCCccccee
Confidence                                              222 6778899999999999999999999999999999999996

---

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	96
d1twfb_	1207	e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces c	8e-07
d1smyc_	1119	e.29.1.1 (C:) RNA-polymerase beta {Thermus thermop	4e-04

>d1twfb_ e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1207

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta
domain: RBP2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 43.4 bits (101), Expect = 8e-07
 Identities = 11/24 (45%), Positives = 15/24 (62%)

Query: 26   IDIIFNPLEVPPRMNIGHIFECSL 49
             D+I NP  +P RM + H+ EC L
Sbjct: 991  PDLIINPHAIPSRMTVAHLIECLL 1014

>d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} Length = 1119

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta
domain: RNA-polymerase beta
species: Thermus thermophilus [TaxId: 274]

 Score = 35.5 bits (81), Expect = 4e-04
 Identities = 14/24 (58%), Positives = 17/24 (70%)

Query: 26  IDIIFNPLEVPPRMNIGHIFECSL 49
           +D+I NPL VP RMN+G I E  L
Sbjct: 867 VDVILNPLGVPSRMNLGQILETHL 890

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	96
d1twfb_	1207	RBP2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	100.0
d1smyc_	1119	RNA-polymerase beta {Thermus thermophilus [TaxId:	99.97

>d1twfb_ e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta
domain: RBP2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.2e-35  Score=255.44  Aligned_cols=89  Identities=22%  Similarity=0.287  Sum_probs=86.2

Q ss_pred             cceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc--------cccccccCCCcHHHHHHHHHHhc
Q 045556            2 LLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR--------HFDERYKQKGSRKLVLSKLYKAC   73 (96)
Q Consensus         2 ~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG--------~~dg~~~~~~~~~~i~~~L~~~g   73 (96)
                      ||.|+|+||    |||++||+  +|||||||||||||||||||+|+++|        .+|+++|++.+.+++.+.|.++|
T Consensus       973 ~s~i~p~eD----MPf~~dG~--~pDiI~NP~g~PSRMtiGql~E~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~L~~~g 1046 (1207)
T d1twfb_         973 IGITYRRED----MPFTAEGI--VPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHG 1046 (1207)
T ss_dssp             EEEEECTTT----SCEETTSC--CCSEEECGGGSTTTTCHHHHHHHHHHHHHHHHCSCEECCSSSSCCHHHHHHHHHTTT
T ss_pred             eeeeechhh----CCcCCCCC--CccEEECCCcCcccCcHHHHHHHHHHHHHHhcCCccccCCCCCccHHHHHHHHHHcC
Confidence            799999999    99999999  99999999999999999999999999        67889999999999999999999


Q ss_pred             cCCCCCceeecCCCCccCCCCCC
Q 045556           74 KQTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        74 ~~~~g~e~lydG~TGe~~~~~I~   96 (96)
                      |+++|+|.||||+|||+|+++|+
T Consensus      1047 ~~~~G~e~ly~G~tG~~~~~~i~ 1069 (1207)
T d1twfb_        1047 YQSRGFEVMYNGHTGKKLMAQIF 1069 (1207)
T ss_dssp             SCTTSEECEECTTTCCBCSSCEE
T ss_pred             CCCCCCEEEECCCCCCCccceEE
Confidence            99999999999999999999985

>d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]}

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta
domain: RNA-polymerase beta
species: Thermus thermophilus [TaxId: 274]

Probab=99.97  E-value=9.7e-34  Score=242.62  Aligned_cols=89  Identities=27%  Similarity=0.436  Sum_probs=81.5

Q ss_pred             cceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc--------cccccccCCCcHHHHHHHHHHh-
Q 045556            2 LLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR--------HFDERYKQKGSRKLVLSKLYKA-   72 (96)
Q Consensus         2 ~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG--------~~dg~~~~~~~~~~i~~~L~~~-   72 (96)
                      ||.|+|+||    ||||++|+  +|||||||||||||||||||+||++|        ..|+++|.+.+.+++.+.|.++ 
T Consensus       849 ~g~i~~~eD----MPft~~Gi--~PDiIiNPhg~PSRMTiG~liE~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~l~~~~  922 (1119)
T d1smyc_         849 VAKILPVED----MPHLPDGT--PVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAF  922 (1119)
T ss_dssp             EEEEECTTT----SCBCSSSC--BCSEEECSTTTTTTTBTHHHHHHHHHHHHHHTTCEEECCSSSSCCHHHHHHHHHHHH
T ss_pred             ceeeechhh----CccccCCc--ceeEEeccccccccccHHHHHHHHHHHHHhhcCceeeccCCCCCcHHHHHHHHHHHH
Confidence            789999999    99999999  99999999999999999999999999        6788999988888888877664 


Q ss_pred             ------------------------------------------ccCCCCCceeecCCCCccCCCCCC
Q 045556           73 ------------------------------------------CKQTANPCKTLDGQMGNPFKEHVL   96 (96)
Q Consensus        73 ------------------------------------------g~~~~g~e~lydG~TGe~~~~~I~   96 (96)
                                                                ||+++|+|+||||+||++|+++|+
T Consensus       923 ~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~G~e~my~G~TG~~~~~~If  988 (1119)
T d1smyc_         923 EVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPEEQLKELFLQGKVVLYDGRTGEPIEGPIV  988 (1119)
T ss_dssp             HHHHHHHHHTTCCCBHHHHHHHHHHHTTTSSCTTSCHHHHHHHHHHTTEECCBCTTTSCBCSSCEE
T ss_pred             HhhccccccccccccchhHHHHHHHhhcccCCCCCChHHHHhhccCCCCEEEECCCCCCEeCCeEE
Confidence                                                      455679999999999999999985