Psyllid ID: psy7584

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60-------
Protein Sequence
MHLEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT
Secondary Structure (PSIPRED)
cccccccccEEEcEEcEEcccccccEEEEEEEEEcccccEEEEEEEccccccccccHHHcccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccEEEEEEEEcccccEEEEEEEEEEEcccccccHccccccccc
Coil and Loop (DISEMBL)
mhlegttkrfskrdgstflrnsetgivDQVMLTLnvdgykfckirvrsvripqigdkfasrhgqkgt
Flexible Loop (DISEMBL)
mhlegttkrfskrdgstflrnsetgivdqvMLTLNVDGYKFCKIrvrsvripqigdkfasrhgqkgt
Low Complexity Region (SEG)
MHLEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT
Disordered region (IsUnstruct)
*********************SETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIG************
Disordered Region (DISOPRED)
****************TFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQK**
Disordered Region (DISEMBL)
************RDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDK**********
Disordered Region (DISPRO)
***********************TGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGD***********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MHLEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT
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	67	2.2.26 [Sep-21-2011]
P08266	1176	DNA-directed RNA polymera	yes	N/A	0.970	0.055	0.907	3e-29
Q8CFI7	1174	DNA-directed RNA polymera	yes	N/A	0.970	0.055	0.846	4e-27
P30876	1174	DNA-directed RNA polymera	yes	N/A	0.970	0.055	0.846	4e-27
Q10578	1193	DNA-directed RNA polymera	yes	N/A	0.970	0.054	0.769	1e-23
Q54J75	1170	DNA-directed RNA polymera	yes	N/A	0.910	0.052	0.737	8e-21
Q42877	1191	DNA-directed RNA polymera	N/A	N/A	0.955	0.053	0.687	2e-20
P38420	1188	DNA-directed RNA polymera	yes	N/A	0.955	0.053	0.687	3e-20
P08518	1224	DNA-directed RNA polymera	yes	N/A	0.910	0.049	0.704	1e-18
Q6FLD5	1223	DNA-directed RNA polymera	yes	N/A	0.910	0.049	0.688	1e-18
Q02061	1210	DNA-directed RNA polymera	yes	N/A	0.910	0.050	0.704	3e-18

>sp|P08266|RPB2_DROME DNA-directed RNA polymerase II subunit RPB2 OS=Drosophila melanogaster GN=RpII140 PE=2 SV=2

 Score =  126 bits (317), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 59/65 (90%), Positives = 61/65 (93%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           L+  TKRFSKRD STFLRNSETGIVDQVMLTLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct: 882 LDSNTKRFSKRDASTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRH 941

Query: 63  GQKGT 67
           GQKGT
Sbjct: 942 GQKGT 946

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB2 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template.
Drosophila melanogaster (taxid: 7227)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6

>sp|Q8CFI7|RPB2_MOUSE DNA-directed RNA polymerase II subunit RPB2 OS=Mus musculus GN=Polr2b PE=2 SV=2

 Score =  119 bits (299), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 55/65 (84%), Positives = 60/65 (92%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           LE T +R++KRD STFLR SETGIVDQVM+TLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct: 880 LESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRH 939

Query: 63  GQKGT 67
           GQKGT
Sbjct: 940 GQKGT 944

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB2 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template.

Mus musculus (taxid: 10090)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|P30876|RPB2_HUMAN DNA-directed RNA polymerase II subunit RPB2 OS=Homo sapiens GN=POLR2B PE=1 SV=1

 Score =  119 bits (299), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 55/65 (84%), Positives = 60/65 (92%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           LE T +R++KRD STFLR SETGIVDQVM+TLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct: 880 LESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRH 939

Query: 63  GQKGT 67
           GQKGT
Sbjct: 940 GQKGT 944

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB2 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template.

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|Q10578|RPB2_CAEEL DNA-directed RNA polymerase II subunit RPB2 OS=Caenorhabditis elegans GN=rpb-2 PE=2 SV=2

 Score =  108 bits (270), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 50/65 (76%), Positives = 58/65 (89%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           L+ + K++ KRD STFLR+SETGIVDQVML+LN DG KF KIR+RSVR+PQIGDKFASRH
Sbjct: 886 LDASGKKYPKRDASTFLRSSETGIVDQVMLSLNSDGNKFVKIRMRSVRLPQIGDKFASRH 945

Query: 63  GQKGT 67
           GQKGT
Sbjct: 946 GQKGT 950

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB2 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template.

Caenorhabditis elegans (taxid: 6239)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|Q54J75|RPB2_DICDI DNA-directed RNA polymerase II subunit rpb2 OS=Dictyostelium discoideum GN=polr2b PE=3 SV=1

 Score = 99.0 bits (245), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 45/61 (73%), Positives = 56/61 (91%)

Query: 7   TKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKG 66
           T+R +KRD ST LR+SETGIVDQV+LT + +G+KFCK+RVRS+R+PQIGDKF+SRHGQKG
Sbjct: 880 TRRHTKRDSSTALRSSETGIVDQVILTTSGEGFKFCKVRVRSMRVPQIGDKFSSRHGQKG 939

Query: 67  T 67
           T
Sbjct: 940 T 940

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. rpb2 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template.

Dictyostelium discoideum (taxid: 44689)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|Q42877|RPB2_SOLLC DNA-directed RNA polymerase II subunit RPB2 OS=Solanum lycopersicum GN=RPB2 PE=2 SV=1

 Score = 97.4 bits (241), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 44/64 (68%), Positives = 55/64 (85%)

Query: 4   EGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHG 63
           +G   R++++D ST LR+SETG+VDQV+LT N DG +F K+RVRSVRIPQIGDKF+SRHG
Sbjct: 886 QGQASRYTRKDHSTSLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHG 945

Query: 64  QKGT 67
           QKGT
Sbjct: 946 QKGT 949

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB2 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template.

Solanum lycopersicum (taxid: 4081)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|P38420|RPB2_ARATH DNA-directed RNA polymerase II subunit RPB2 OS=Arabidopsis thaliana GN=RPB135 PE=2 SV=2

 Score = 97.1 bits (240), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 44/64 (68%), Positives = 55/64 (85%)

Query: 4   EGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHG 63
           +G + R+++RD S  LR+SETG+VDQV+LT N DG +F K+RVRSVRIPQIGDKF+SRHG
Sbjct: 887 QGQSSRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHG 946

Query: 64  QKGT 67
           QKGT
Sbjct: 947 QKGT 950

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB2 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template.

Arabidopsis thaliana (taxid: 3702)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|P08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPB2 PE=1 SV=2

 Score = 91.7 bits (226), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 43/61 (70%), Positives = 50/61 (81%)

Query: 7   TKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKG 66
           T   SKRD ST LR++E GIVDQV++T N DG KF K+RVR+ +IPQIGDKFASRHGQKG
Sbjct: 929 TAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKG 988

Query: 67  T 67
           T
Sbjct: 989 T 989

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerases II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw. The jaws are thought to grab the incoming DNA template. The fork loop 1 (RPB2) interacts with the RNA-DNA hybrid, possibly stabilizing it.

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

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|Q6FLD5|RPB2_CANGA DNA-directed RNA polymerase II subunit RPB2 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=RPB2 PE=3 SV=1

 Score = 91.7 bits (226), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 42/61 (68%), Positives = 50/61 (81%)

Query: 7   TKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKG 66
           T   SKRD ST LR++E GIVDQV++T N DG KF K+RVR+ ++PQIGDKFASRHGQKG
Sbjct: 928 TAYHSKRDASTPLRSTENGIVDQVLITTNQDGLKFVKVRVRTTKVPQIGDKFASRHGQKG 987

Query: 67  T 67
           T
Sbjct: 988 T 988

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB2 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template.

Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (taxid: 284593)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|Q02061|RPB2_SCHPO DNA-directed RNA polymerase II subunit RPB2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb2 PE=1 SV=2

 Score = 90.5 bits (223), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 43/61 (70%), Positives = 52/61 (85%)

Query: 7   TKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKG 66
           T+  +KRD ST LR++E+GIVDQVM+T N +G KF K+R+RS RIPQIGDKFASRHGQKG
Sbjct: 918 TQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTRIPQIGDKFASRHGQKG 977

Query: 67  T 67
           T
Sbjct: 978 T 978

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB2 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template.

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

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	67
312381454	1954	hypothetical protein AND_06234 [Anophele	0.970	0.033	0.938	2e-29
170042980	1176	DNA-directed RNA polymerase II 140 kDa p	0.970	0.055	0.938	4e-29
324120616	1150	RNA polymerase II second largest subunit	0.970	0.056	0.938	5e-29
324120626	1175	RNA polymerase II second largest subunit	0.970	0.055	0.938	5e-29
324120640	1175	RNA polymerase II second largest subunit	0.970	0.055	0.938	5e-29
357621065	1176	hypothetical protein KGM_12615 [Danaus p	0.970	0.055	0.938	5e-29
324120622	1176	RNA polymerase II second largest subunit	0.970	0.055	0.938	5e-29
324120638	1175	RNA polymerase II second largest subunit	0.970	0.055	0.938	6e-29
324120652	1176	RNA polymerase II second largest subunit	0.970	0.055	0.938	7e-29
324120636	1173	RNA polymerase II second largest subunit	0.970	0.055	0.938	7e-29

>gi|312381454|gb|EFR27200.1| hypothetical protein AND_06234 [Anopheles darlingi]

 Score =  132 bits (333), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 61/65 (93%), Positives = 64/65 (98%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           L+GTTKRF+KRDGSTFLRNSETGIVDQVMLTLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct: 881 LDGTTKRFTKRDGSTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRH 940

Query: 63  GQKGT 67
           GQKGT
Sbjct: 941 GQKGT 945

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170042980|ref|XP_001849183.1| DNA-directed RNA polymerase II 140 kDa polypeptide [Culex quinquefasciatus] gi|167866385|gb|EDS29768.1| DNA-directed RNA polymerase II 140 kDa polypeptide [Culex quinquefasciatus]

 Score =  131 bits (330), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 61/65 (93%), Positives = 64/65 (98%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           L+GTTKR+SKRDGSTFLRNSETGIVDQVMLTLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct: 882 LDGTTKRYSKRDGSTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRH 941

Query: 63  GQKGT 67
           GQKGT
Sbjct: 942 GQKGT 946

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|324120616|dbj|BAJ78699.1| RNA polymerase II second largest subunit [Phraortes illepidus]

 Score =  131 bits (330), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 61/65 (93%), Positives = 63/65 (96%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           LEGTTKRF+KRD STFLRNSETGIVDQVMLTLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct: 856 LEGTTKRFTKRDASTFLRNSETGIVDQVMLTLNAEGYKFCKIRVRSVRIPQIGDKFASRH 915

Query: 63  GQKGT 67
           GQKGT
Sbjct: 916 GQKGT 920

Source: Phraortes illepidus

Species: Phraortes illepidus

Genus: Phraortes

Family: Phasmatidae

Order: Phasmatodea

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|324120626|dbj|BAJ78704.1| RNA polymerase II second largest subunit [Euconocephalus varius]

 Score =  131 bits (330), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 61/65 (93%), Positives = 63/65 (96%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           LEGTTKRF+KRD STFLRNSETGIVDQVMLTLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct: 881 LEGTTKRFTKRDASTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRH 940

Query: 63  GQKGT 67
           GQKGT
Sbjct: 941 GQKGT 945

Source: Euconocephalus varius

Species: Euconocephalus varius

Genus: Euconocephalus

Family: Tettigoniidae

Order: Orthoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|324120640|dbj|BAJ78711.1| RNA polymerase II second largest subunit [Blattella nipponica]

 Score =  131 bits (329), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 61/65 (93%), Positives = 63/65 (96%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           LEGTTKRF+KRD STFLRNSETGIVDQVMLTLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct: 881 LEGTTKRFTKRDASTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRH 940

Query: 63  GQKGT 67
           GQKGT
Sbjct: 941 GQKGT 945

Source: Blattella nipponica

Species: Blattella nipponica

Genus: Blattella

Family: Ectobiidae

Order: Blattodea

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357621065|gb|EHJ73034.1| hypothetical protein KGM_12615 [Danaus plexippus]

 Score =  131 bits (329), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 61/65 (93%), Positives = 63/65 (96%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           LEGTTKRF+KRD STFLRNSETGIVDQVMLTLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct: 881 LEGTTKRFTKRDASTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRH 940

Query: 63  GQKGT 67
           GQKGT
Sbjct: 941 GQKGT 945

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|324120622|dbj|BAJ78702.1| RNA polymerase II second largest subunit [Karoophasma biedouwense]

 Score =  131 bits (329), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 61/65 (93%), Positives = 63/65 (96%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           LEGTTKRF+KRD STFLRNSETGIVDQVMLTLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct: 881 LEGTTKRFTKRDASTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRH 940

Query: 63  GQKGT 67
           GQKGT
Sbjct: 941 GQKGT 945

Source: Karoophasma biedouwense

Species: Karoophasma biedouwense

Genus: Karoophasma

Family: Austrophasmatidae

Order: Mantophasmatodea

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|324120638|dbj|BAJ78710.1| RNA polymerase II second largest subunit [Tenodera aridifolia]

 Score =  131 bits (329), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 61/65 (93%), Positives = 63/65 (96%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           LEGTTKRF+KRD STFLRNSETGIVDQVMLTLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct: 881 LEGTTKRFTKRDASTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRH 940

Query: 63  GQKGT 67
           GQKGT
Sbjct: 941 GQKGT 945

Source: Tenodera aridifolia

Species: Tenodera aridifolia

Genus: Tenodera

Family: Mantidae

Order: Mantodea

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|324120652|dbj|BAJ78717.1| RNA polymerase II second largest subunit [Bemisia tabaci]

 Score =  130 bits (328), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 61/65 (93%), Positives = 63/65 (96%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           LEGTTKR+SKRD STFLRNSETGIVDQVMLTLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct: 881 LEGTTKRYSKRDASTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRH 940

Query: 63  GQKGT 67
           GQKGT
Sbjct: 941 GQKGT 945

Source: Bemisia tabaci

Species: Bemisia tabaci

Genus: Bemisia

Family: Aleyrodidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|324120636|dbj|BAJ78709.1| RNA polymerase II second largest subunit [Zorotypus sp. 154-1]

 Score =  130 bits (328), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 61/65 (93%), Positives = 63/65 (96%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           LEGTTKRF+KRD STFLRNSETGIVDQVMLTLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct: 879 LEGTTKRFTKRDASTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRH 938

Query: 63  GQKGT 67
           GQKGT
Sbjct: 939 GQKGT 943

Source: Zorotypus sp. 154-1

Species: Zorotypus sp. 154-1

Genus: Zorotypus

Family: Zorotypidae

Order: Zoraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	67
FB|FBgn0262955	1176	RpII140 "RNA polymerase II 140	0.970	0.055	0.907	1e-25
UNIPROTKB|I3LGP4	1167	POLR2B "DNA-directed RNA polym	0.970	0.055	0.861	1.9e-24
UNIPROTKB|A5PJW8	1174	POLR2B "DNA-directed RNA polym	0.970	0.055	0.861	2e-24
UNIPROTKB|E2RNN5	1174	POLR2B "DNA-directed RNA polym	0.970	0.055	0.861	2e-24
UNIPROTKB|F1NCB0	1174	POLR2B "DNA-directed RNA polym	0.970	0.055	0.861	4.1e-24
UNIPROTKB|F1P4F2	1176	POLR2B "DNA-directed RNA polym	0.970	0.055	0.861	4.1e-24
UNIPROTKB|C9J4M6	1099	POLR2B "DNA-directed RNA polym	0.970	0.059	0.846	7.8e-24
UNIPROTKB|C9J2Y9	1167	POLR2B "DNA-directed RNA polym	0.970	0.055	0.846	8.5e-24
UNIPROTKB|P30876	1174	POLR2B "DNA-directed RNA polym	0.970	0.055	0.846	8.6e-24
MGI|MGI:2388280	1174	Polr2b "polymerase (RNA) II (D	0.970	0.055	0.846	8.6e-24

FB|FBgn0262955 RpII140 "RNA polymerase II 140kD subunit" [Drosophila melanogaster (taxid:7227)]

 Score = 304 (112.1 bits), Expect = 1.0e-25, P = 1.0e-25
 Identities = 59/65 (90%), Positives = 61/65 (93%)

Query:     3 LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
             L+  TKRFSKRD STFLRNSETGIVDQVMLTLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct:   882 LDSNTKRFSKRDASTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRH 941

Query:    63 GQKGT 67
             GQKGT
Sbjct:   942 GQKGT 946

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

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0032549 "ribonucleoside binding" evidence=IEA

UNIPROTKB|I3LGP4 POLR2B "DNA-directed RNA polymerase" [Sus scrofa (taxid:9823)]

 Score = 292 (107.8 bits), Expect = 1.9e-24, P = 1.9e-24
 Identities = 56/65 (86%), Positives = 61/65 (93%)

Query:     3 LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
             LEGT +R++KRD STFLR SETGIVDQVM+TLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct:   873 LEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRH 932

Query:    63 GQKGT 67
             GQKGT
Sbjct:   933 GQKGT 937

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

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

GO:0004672 "protein kinase activity" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

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

GO:0032549 "ribonucleoside binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|A5PJW8 POLR2B "DNA-directed RNA polymerase" [Bos taurus (taxid:9913)]

 Score = 292 (107.8 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 56/65 (86%), Positives = 61/65 (93%)

Query:     3 LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
             LEGT +R++KRD STFLR SETGIVDQVM+TLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct:   880 LEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRH 939

Query:    63 GQKGT 67
             GQKGT
Sbjct:   940 GQKGT 944

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

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

GO:0004672 "protein kinase activity" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

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

GO:0032549 "ribonucleoside binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2RNN5 POLR2B "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)]

 Score = 292 (107.8 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 56/65 (86%), Positives = 61/65 (93%)

Query:     3 LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
             LEGT +R++KRD STFLR SETGIVDQVM+TLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct:   880 LEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRH 939

Query:    63 GQKGT 67
             GQKGT
Sbjct:   940 GQKGT 944

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

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

GO:0004672 "protein kinase activity" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

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

GO:0032549 "ribonucleoside binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1NCB0 POLR2B "DNA-directed RNA polymerase" [Gallus gallus (taxid:9031)]

 Score = 289 (106.8 bits), Expect = 4.1e-24, P = 4.1e-24
 Identities = 56/65 (86%), Positives = 60/65 (92%)

Query:     3 LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
             LE T +RF+KRD STFLR SETGIVDQVM+TLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct:   880 LESTNRRFTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRH 939

Query:    63 GQKGT 67
             GQKGT
Sbjct:   940 GQKGT 944

GO:0003677 "DNA binding" evidence=IEA

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

GO:0032549 "ribonucleoside binding" evidence=IEA

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

UNIPROTKB|F1P4F2 POLR2B "DNA-directed RNA polymerase" [Gallus gallus (taxid:9031)]

 Score = 289 (106.8 bits), Expect = 4.1e-24, P = 4.1e-24
 Identities = 56/65 (86%), Positives = 60/65 (92%)

Query:     3 LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
             LE T +RF+KRD STFLR SETGIVDQVM+TLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct:   882 LESTNRRFTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRH 941

Query:    63 GQKGT 67
             GQKGT
Sbjct:   942 GQKGT 946

GO:0003677 "DNA binding" evidence=IEA

GO:0032549 "ribonucleoside binding" evidence=IEA

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

GO:0003682 "chromatin binding" evidence=IEA

GO:0004672 "protein kinase activity" evidence=IEA

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

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

UNIPROTKB|C9J4M6 POLR2B "DNA-directed RNA polymerase" [Homo sapiens (taxid:9606)]

 Score = 286 (105.7 bits), Expect = 7.8e-24, P = 7.8e-24
 Identities = 55/65 (84%), Positives = 60/65 (92%)

Query:     3 LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
             LE T +R++KRD STFLR SETGIVDQVM+TLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct:   805 LESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRH 864

Query:    63 GQKGT 67
             GQKGT
Sbjct:   865 GQKGT 869

GO:0003677 "DNA binding" evidence=IEA

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

GO:0032549 "ribonucleoside binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|C9J2Y9 POLR2B "DNA-directed RNA polymerase" [Homo sapiens (taxid:9606)]

 Score = 286 (105.7 bits), Expect = 8.5e-24, P = 8.5e-24
 Identities = 55/65 (84%), Positives = 60/65 (92%)

Query:     3 LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
             LE T +R++KRD STFLR SETGIVDQVM+TLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct:   873 LESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRH 932

Query:    63 GQKGT 67
             GQKGT
Sbjct:   933 GQKGT 937

GO:0003677 "DNA binding" evidence=IEA

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

GO:0032549 "ribonucleoside binding" evidence=IEA

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

GO:0003682 "chromatin binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|P30876 POLR2B "DNA-directed RNA polymerase II subunit RPB2" [Homo sapiens (taxid:9606)]

 Score = 286 (105.7 bits), Expect = 8.6e-24, P = 8.6e-24
 Identities = 55/65 (84%), Positives = 60/65 (92%)

Query:     3 LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
             LE T +R++KRD STFLR SETGIVDQVM+TLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct:   880 LESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRH 939

Query:    63 GQKGT 67
             GQKGT
Sbjct:   940 GQKGT 944

GO:0003677 "DNA binding" evidence=IEA

GO:0032549 "ribonucleoside binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

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

GO:0003682 "chromatin binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0004672 "protein kinase activity" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

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

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

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

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

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

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

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

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

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

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

GO:0006468 "protein phosphorylation" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

MGI|MGI:2388280 Polr2b "polymerase (RNA) II (DNA directed) polypeptide B" [Mus musculus (taxid:10090)]

 Score = 286 (105.7 bits), Expect = 8.6e-24, P = 8.6e-24
 Identities = 55/65 (84%), Positives = 60/65 (92%)

Query:     3 LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
             LE T +R++KRD STFLR SETGIVDQVM+TLN +GYKFCKIRVRSVRIPQIGDKFASRH
Sbjct:   880 LESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRH 939

Query:    63 GQKGT 67
             GQKGT
Sbjct:   940 GQKGT 944

GO:0003677 "DNA binding" evidence=IEA

GO:0003682 "chromatin binding" evidence=IDA

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

GO:0005634 "nucleus" evidence=IC;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:0016740 "transferase activity" evidence=IEA

GO:0016779 "nucleotidyltransferase activity" evidence=IEA

GO:0032549 "ribonucleoside binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8SR75	RPB2_ENCCU	2, ., 7, ., 7, ., 6	0.6551	0.8507	0.0499	yes	N/A
B0R8D5	RPOB1_HALS3	2, ., 7, ., 7, ., 6	0.5454	0.8208	0.0904	yes	N/A
Q8CFI7	RPB2_MOUSE	2, ., 7, ., 7, ., 6	0.8461	0.9701	0.0553	yes	N/A
P08518	RPB2_YEAST	2, ., 7, ., 7, ., 6	0.7049	0.9104	0.0498	yes	N/A
P08266	RPB2_DROME	2, ., 7, ., 7, ., 6	0.9076	0.9701	0.0552	yes	N/A
P30876	RPB2_HUMAN	2, ., 7, ., 7, ., 6	0.8461	0.9701	0.0553	yes	N/A
P38420	RPB2_ARATH	2, ., 7, ., 7, ., 6	0.6875	0.9552	0.0538	yes	N/A
Q02061	RPB2_SCHPO	2, ., 7, ., 7, ., 6	0.7049	0.9104	0.0504	yes	N/A
Q10578	RPB2_CAEEL	2, ., 7, ., 7, ., 6	0.7692	0.9701	0.0544	yes	N/A
Q54J75	RPB2_DICDI	2, ., 7, ., 7, ., 6	0.7377	0.9104	0.0521	yes	N/A
O27124	RPOB1_METTH	2, ., 7, ., 7, ., 6	0.5818	0.8208	0.0912	yes	N/A
Q6FLD5	RPB2_CANGA	2, ., 7, ., 7, ., 6	0.6885	0.9104	0.0498	yes	N/A
O28392	RPOB1_ARCFU	2, ., 7, ., 7, ., 6	0.5454	0.8208	0.0910	yes	N/A
P0CX03	RPOB1_HALSA	2, ., 7, ., 7, ., 6	0.5454	0.8208	0.0904	yes	N/A
Q03587	RPOB_THEAC	2, ., 7, ., 7, ., 6	0.5357	0.8358	0.0468	yes	N/A
Q60181	RPOB1_METJA	2, ., 7, ., 7, ., 6	0.5272	0.8208	0.0864	yes	N/A
P41557	RPOB1_METVS	2, ., 7, ., 7, ., 6	0.5272	0.8208	0.0900	yes	N/A
Q753Q4	RPB2_ASHGO	2, ., 7, ., 7, ., 6	0.7017	0.8507	0.0466	yes	N/A
P11513	RPOB_SULAC	2, ., 7, ., 7, ., 6	0.5892	0.8358	0.0497	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.7	0.691

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	67
PRK08565	1103	PRK08565, PRK08565, DNA-directed RNA polymerase su	7e-24
cd00653	866	cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun	9e-24
TIGR03670	599	TIGR03670, rpoB_arch, DNA-directed RNA polymerase	4e-23
pfam00562	373	pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, do	4e-22
PRK07225	605	PRK07225, PRK07225, DNA-directed RNA polymerase su	8e-22
COG0085	1060	COG0085, RpoB, DNA-directed RNA polymerase, beta s	2e-19
CHL00207	1077	CHL00207, rpoB, RNA polymerase beta subunit; Provi	0.001

>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B; Provisional

 Score = 91.9 bits (229), Expect = 7e-24
 Identities = 32/57 (56%), Positives = 43/57 (75%)

Query: 10  FSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKG 66
             +RD S  +R+ E GIVD V++T + +G K  K+RVR +RIP++GDKFASRHGQKG
Sbjct: 814 QERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKG 870

Length = 1103

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

 Score = 91.5 bits (228), Expect = 9e-24
 Identities = 32/64 (50%), Positives = 35/64 (54%), Gaps = 3/64 (4%)

Query: 7   TKRFSKRDGSTFLRNSETGIVDQVMLT---LNVDGYKFCKIRVRSVRIPQIGDKFASRHG 63
            K    RD S      E GIVD V +    LN  G K  K+ +R  R PQIGDKFASRHG
Sbjct: 582 EKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHG 641

Query: 64  QKGT 67
           QKG 
Sbjct: 642 QKGV 645

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

 Score = 89.7 bits (223), Expect = 4e-23
 Identities = 32/55 (58%), Positives = 43/55 (78%)

Query: 12  KRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKG 66
           +RD S  +R+ E GIVD+V++T   +G K  K+RVR +RIP++GDKFASRHGQKG
Sbjct: 312 RRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKG 366

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|215994 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, domain 6

 Score = 86.4 bits (215), Expect = 4e-22
 Identities = 29/61 (47%), Positives = 37/61 (60%)

Query: 7   TKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKG 66
            K    +D S  +++ E G VD V + LN  G K  K+ +R  R PQ+GDKFASRHGQKG
Sbjct: 176 EKARDVKDTSLKVKHGEEGRVDDVKIDLNPGGIKKVKVYIRQKRKPQVGDKFASRHGQKG 235

Query: 67  T 67
            
Sbjct: 236 V 236

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

 Score = 86.2 bits (214), Expect = 8e-22
 Identities = 31/55 (56%), Positives = 42/55 (76%)

Query: 12  KRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKG 66
           +R+ S  +R+ E GIVD V+LT   +G +  K+RVR +RIP++GDKFASRHGQKG
Sbjct: 318 RRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKG 372

Length = 605

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

 Score = 79.5 bits (197), Expect = 2e-19
 Identities = 27/61 (44%), Positives = 31/61 (50%), Gaps = 4/61 (6%)

Query: 11  SKRDGSTFLRNSETGIVDQVMLTLNVDG----YKFCKIRVRSVRIPQIGDKFASRHGQKG 66
             RD S  + + E GIVD V +    DG     K  K+ V   R PQIGDK A RHG KG
Sbjct: 784 KVRDTSLRVPHGEEGIVDDVQVFTREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHGNKG 843

Query: 67  T 67
            
Sbjct: 844 V 844

Length = 1060

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

 Score = 34.7 bits (80), Expect = 0.001
 Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 7/62 (11%)

Query: 13  RDGSTFLRNSETG-IVDQVMLTLNV-DGYKF-----CKIRVRSVRIPQIGDKFASRHGQK 65
           +D S  + N   G ++   + + +  D  KF      ++ +  +R  Q+GDK A RHG K
Sbjct: 764 KDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNK 823

Query: 66  GT 67
           G 
Sbjct: 824 GI 825

Length = 1077

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	67
PRK07225	605	DNA-directed RNA polymerase subunit B'; Validated	99.85
TIGR03670	599	rpoB_arch DNA-directed RNA polymerase subunit B. T	99.85
COG0085	1060	RpoB DNA-directed RNA polymerase, beta subunit/140	99.83
PRK08565	1103	DNA-directed RNA polymerase subunit B; Provisional	99.81
PF00562	386	RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; Int	99.81
KOG0214|consensus	1141		99.79
TIGR02013	1065	rpoB DNA-directed RNA polymerase, beta subunit. Th	99.78
PRK00405	1112	rpoB DNA-directed RNA polymerase subunit beta; Rev	99.77
CHL00001	1070	rpoB RNA polymerase beta subunit	99.76
cd00653	866	RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA po	99.76
KOG0215|consensus	1153		99.76
CHL00207	1077	rpoB RNA polymerase beta subunit; Provisional	99.75
KOG0216|consensus	1111		99.65
PRK09603	2890	bifunctional DNA-directed RNA polymerase subunit b	99.49
PRK14844	2836	bifunctional DNA-directed RNA polymerase subunit b	99.21
PF04941	748	LEF-8: Late expression factor 8 (LEF-8); InterPro:	94.04
PHA03394	865	lef-8 DNA-directed RNA polymerase subunit beta-lik	93.8

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

Probab=99.85  E-value=9.4e-22  Score=153.08  Aligned_cols=58  Identities=53%  Similarity=0.888  Sum_probs=55.5

Q ss_pred             cceeeeeEEcCCCCCeEEEEEEEEeccCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584          10 FSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus        10 ~~~rd~S~~~k~~e~g~Vd~V~~~~~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      ...+|+|++++++|+|+||+|.++.+.+|.+.|+|++|+.|+|+||||||||||||||
T Consensus       316 ~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~ir~~R~p~iGDKfssRHGQKGv  373 (605)
T PRK07225        316 EKRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGV  373 (605)
T ss_pred             cCcceeeEEecCCCcEEEEEEEEEecCCCCEEEEEEEEEEEeccccchhhhcccCcee
Confidence            3479999999999999999999999999999999999999999999999999999997

>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B

Probab=99.85  E-value=1.7e-21  Score=151.52  Aligned_cols=58  Identities=55%  Similarity=0.902  Sum_probs=55.4

Q ss_pred             cceeeeeEEcCCCCCeEEEEEEEEeccCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584          10 FSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus        10 ~~~rd~S~~~k~~e~g~Vd~V~~~~~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      ...+|+|++++++|+|+||+|.++.++++.+.|+|++|+.|+|+||||||||||||||
T Consensus       310 ~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~~r~~R~p~iGDKfssRHGQKGv  367 (599)
T TIGR03670       310 ERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGV  367 (599)
T ss_pred             ccCceEEEEecCCCcEEEEEEEEEecCCCcEEEEEEEeeeecCcchhhhhhhccCcce
Confidence            3479999999999999999999999999999999999999999999999999999997

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

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

Probab=99.83  E-value=5.9e-21  Score=155.40  Aligned_cols=56  Identities=46%  Similarity=0.617  Sum_probs=54.4

Q ss_pred             eeeeeEEcCCCCCeEEEEEEEEeccC----CcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584          12 KRDGSTFLRNSETGIVDQVMLTLNVD----GYKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus        12 ~rd~S~~~k~~e~g~Vd~V~~~~~~~----g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      +||+|++++++|+|+||+|.++++++    +++.|||++|+.|+|++|||||||||||||
T Consensus       785 ~rdtsl~~~~g~~G~V~~V~~~~~~~~~~g~~~~vkV~v~~~R~~~~GDK~a~RHG~KGV  844 (1060)
T COG0085         785 VRDTSLRVPHGEEGIVDDVQVFTREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHGNKGV  844 (1060)
T ss_pred             eeccceeecCCCCeEEEEEEEEeccCCCcCceEEEEEEEEEeccCCccccccccCCCCce
Confidence            89999999999999999999999987    789999999999999999999999999997

>PRK08565 DNA-directed RNA polymerase subunit B; Provisional

Probab=99.81  E-value=2e-20  Score=152.31  Aligned_cols=58  Identities=55%  Similarity=0.908  Sum_probs=55.5

Q ss_pred             cceeeeeEEcCCCCCeEEEEEEEEeccCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584          10 FSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus        10 ~~~rd~S~~~k~~e~g~Vd~V~~~~~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      ...+|+|++++.+|+|+||+|.++.+.++.+.|+|++|+.|+|+||||||||||||||
T Consensus       814 ~~~~~~s~~~~~~e~g~V~~V~~~~~~~~~~~vkv~ir~~R~p~iGDKfssRhGqKGv  871 (1103)
T PRK08565        814 QERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGV  871 (1103)
T ss_pred             CccccceEEecCCCceEEEEEEEEecCCCcEEEEEEEEEEecCchhhhhhhhccCcce
Confidence            3479999999999999999999999999999999999999999999999999999997

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

Probab=99.81  E-value=3.8e-20  Score=137.04  Aligned_cols=57  Identities=58%  Similarity=0.865  Sum_probs=50.0

Q ss_pred             ceeeeeEEcCCCCCeEEEEEEE-------EeccCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584          11 SKRDGSTFLRNSETGIVDQVML-------TLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus        11 ~~rd~S~~~k~~e~g~Vd~V~~-------~~~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      ..+|+|++++.+|.|+||+|.+       ..+.++...|+|++|+.|+|++|||||||||||||
T Consensus       188 ~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~~~~~~~~iki~ir~~R~p~iGDKfssRHGqKGV  251 (386)
T PF00562_consen  188 NYRDTSIKYKSGESGRVDKVIIFSNEKKDTSNNEGYKKIKIRIRSTRRPQIGDKFSSRHGQKGV  251 (386)
T ss_dssp             SEEEEEEES-TT-EEEEEEEEEECCCSSBEEETTCEEEEEEEEEEEEE--TTEEEEETTSEEEE
T ss_pred             cccceeecccccEEeEeccccccccccccccccCcceEEEEEecccccchhHHHHhhhhcCceE
Confidence            3799999999999999999999       66788899999999999999999999999999997

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 ....

>KOG0214|consensus

Probab=99.79  E-value=1e-19  Score=147.04  Aligned_cols=64  Identities=66%  Similarity=0.944  Sum_probs=60.3

Q ss_pred             CCCCCccceeeeeEEcCCCCCeEEEEEEEEeccCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584           4 EGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus         4 ~~~~~~~~~rd~S~~~k~~e~g~Vd~V~~~~~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      +..++.+.++|+|+.++++|.|+||+|.++.|.+|.+|++|++|+.|.|++|||||||||||||
T Consensus       848 ~~~~~~~t~~d~s~~Lr~~e~Givd~V~vt~n~~G~kF~kv~vr~~ripqiGDKfasrHgqKG~  911 (1141)
T KOG0214|consen  848 GPEDRLYTKRDHSTKLRHTERGIVDQVWVTKNSEGPKFVKVRVRQVRIPQIGDKFASRHGQKGT  911 (1141)
T ss_pred             cccccccccccceeecccCCcceEEEEEEecCCCCCceeEEEEeecccccccchhccccccCcc
Confidence            3455678899999999999999999999999999999999999999999999999999999997

>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit

Probab=99.78  E-value=2.3e-19  Score=146.22  Aligned_cols=57  Identities=35%  Similarity=0.452  Sum_probs=53.4

Q ss_pred             ceeeeeEEcCCCCCeEEEEEEEEeccCC-------cEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584          11 SKRDGSTFLRNSETGIVDQVMLTLNVDG-------YKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus        11 ~~rd~S~~~k~~e~g~Vd~V~~~~~~~g-------~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      .++|+|++++++|+|+||+|.++.++++       ...|+|++|+.|+|+||||||||||||||
T Consensus       789 ~~~d~s~~~~~~~~g~V~~V~~~~~~~~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGv  852 (1065)
T TIGR02013       789 DVRDTSLRVPPGVEGTVIDVKVFSRKQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGV  852 (1065)
T ss_pred             cccccceEccCCCCEEEEEEEEEeccCCCccCcCccEEEEEEEeecccccccchhhhcccCcee
Confidence            4789999999999999999999988776       57899999999999999999999999997

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.

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

Probab=99.77  E-value=3.8e-19  Score=145.34  Aligned_cols=57  Identities=35%  Similarity=0.488  Sum_probs=53.0

Q ss_pred             ceeeeeEEcCCCCCeEEEEEEEEec-cCC-------cEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584          11 SKRDGSTFLRNSETGIVDQVMLTLN-VDG-------YKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus        11 ~~rd~S~~~k~~e~g~Vd~V~~~~~-~~g-------~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      .++|+|++++++|+|+||+|.++.+ .+|       ...|+|++|+.|+|+||||||||||||||
T Consensus       831 ~~~d~s~~~~~~~~g~V~~v~~~~~~~~~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGv  895 (1112)
T PRK00405        831 DVKDTSLRVPHGEEGTVIDVKVFTRIEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGV  895 (1112)
T ss_pred             ccccceEEcCCCCCEEEEEEEEeeccccCCccCcCcceEEEEEEeeecccCcccchhhccCCcee
Confidence            4799999999999999999999987 665       47899999999999999999999999997

>CHL00001 rpoB RNA polymerase beta subunit

Probab=99.76  E-value=8.7e-19  Score=143.01  Aligned_cols=58  Identities=26%  Similarity=0.261  Sum_probs=53.4

Q ss_pred             cceeeeeEEcCCCCCeEEEEEEEEec----cCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584          10 FSKRDGSTFLRNSETGIVDQVMLTLN----VDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus        10 ~~~rd~S~~~k~~e~g~Vd~V~~~~~----~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      ..++|+|+++++++.|+|++|.++.+    .++...|+|++|+.|+|++|||||||||||||
T Consensus       768 ~~~~d~sl~~~~~~~g~V~~v~~~~~~~~~~~~~~~vkv~i~~~R~~~vGDK~asRHGqKGv  829 (1070)
T CHL00001        768 STSKETCLKLPIGGRGRVIDVRWIQKKGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGI  829 (1070)
T ss_pred             CcceeCeEECCCCCceEEEEEEEEecccCCCCCcEEEEEEEEEEecCCCCcccccccCCcce
Confidence            45899999999999999999999874    45678999999999999999999999999997

>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit

Probab=99.76  E-value=9.5e-19  Score=139.79  Aligned_cols=57  Identities=53%  Similarity=0.722  Sum_probs=53.9

Q ss_pred             ceeeeeEEcCCCCCeEEEEEEEEe---ccCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584          11 SKRDGSTFLRNSETGIVDQVMLTL---NVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus        11 ~~rd~S~~~k~~e~g~Vd~V~~~~---~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      ..+|+|++++.+|+|+||+|.++.   +.++...|+|++|+.|+|+||||||||||||||
T Consensus       586 ~~~~~~~~~~~~~~g~v~~v~~~~~~~~~~~~~~v~v~~r~~R~p~iGDKfssRhGqKGv  645 (866)
T cd00653         586 DVRDTSLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGV  645 (866)
T ss_pred             cceEEEEEecCCCceEEEEEEEeccccCCCCcEEEEEEEeEEecCCcccccccccCCCcE
Confidence            479999999999999999999988   567789999999999999999999999999997

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.

>KOG0215|consensus

Probab=99.76  E-value=4.7e-20  Score=148.36  Aligned_cols=58  Identities=38%  Similarity=0.590  Sum_probs=55.9

Q ss_pred             cceeeeeEEcCCCCCeEEEEEEEEeccCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584          10 FSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus        10 ~~~rd~S~~~k~~e~g~Vd~V~~~~~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      ..|+|.++.|+..|+++||+|++++|+++...||+.+||+|.|++|||||||||||||
T Consensus       869 ~~Yk~~pitykgpepsyidkVmls~n~~dq~LIK~llRQTRrPElGDKFSSRHGQKGV  926 (1153)
T KOG0215|consen  869 VQYKAVPITYKGPEPSYIDRVMLTSNDEDQFLIKVLLRQTRRPELGDKFSSRHGQKGV  926 (1153)
T ss_pred             cccccccceecCCCcchhheeEeecCccccHHHHHHHhhccCcccccccccccCCCce
Confidence            3599999999999999999999999999999999999999999999999999999997

>CHL00207 rpoB RNA polymerase beta subunit; Provisional

Probab=99.75  E-value=1.9e-18  Score=141.11  Aligned_cols=58  Identities=31%  Similarity=0.396  Sum_probs=51.5

Q ss_pred             cceeeeeEEcCCCCCeEEEEEEEEeccCC--c-----EEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584          10 FSKRDGSTFLRNSETGIVDQVMLTLNVDG--Y-----KFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus        10 ~~~rd~S~~~k~~e~g~Vd~V~~~~~~~g--~-----~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      ...+|+|++++++++|+|++|.++.++++  .     ..|+|++|+.|+|++|||||||||||||
T Consensus       761 ~~~kd~sl~~~~~~~g~V~~V~~~~~~~~~~~~~~~~~~vkv~i~~~R~p~vGDKfasRHGqKGV  825 (1077)
T CHL00207        761 KDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGI  825 (1077)
T ss_pred             CcceEeEEEcCCCCcEEEEEEEEEecCCCCcccccccEEEEEEEEEEecCCcccccccccCCcee
Confidence            35799999999999999999999986433  2     3589999999999999999999999997

>KOG0216|consensus

Probab=99.65  E-value=1e-16  Score=129.45  Aligned_cols=53  Identities=47%  Similarity=0.601  Sum_probs=49.1

Q ss_pred             eeEEcCCCCCeEEEEEEEEeccCCc--EEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584          15 GSTFLRNSETGIVDQVMLTLNVDGY--KFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus        15 ~S~~~k~~e~g~Vd~V~~~~~~~g~--~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      .-.+|+..|+|+||.|.++.++.|.  +.+.|++|.+|+|.||||||||||||||
T Consensus       817 ~~~~~~~~ep~~vd~vr~~~~~~~~~~k~~~i~~Ri~R~p~IGDKFsSRhGQKGi  871 (1111)
T KOG0216|consen  817 RIKKYHGTEPGIVDEVRVLGNDMGDQEKCATITLRIPRNPIIGDKFSSRHGQKGI  871 (1111)
T ss_pred             EEEEecCCCCeeeEEEEEccccCCCccceEEEEEEecCCCcccchhhhhcccccc
Confidence            3468999999999999999998876  7899999999999999999999999997

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

Probab=99.49  E-value=3.2e-14  Score=123.49  Aligned_cols=29  Identities=41%  Similarity=0.652  Sum_probs=27.3

Q ss_pred             cEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584          39 YKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus        39 ~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      .+.|+|+||+.|+|++|||||||||||||
T Consensus      1075 ~~~VkV~ia~kR~~qvGDK~AgRHGnKGV 1103 (2890)
T PRK09603       1075 IKKVKLYIATKRKLKVGDKMAGRHGNKGI 1103 (2890)
T ss_pred             ceEEEEEEEEeecccccchhhhccCCCee
Confidence            35799999999999999999999999997

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

Probab=99.21  E-value=2.3e-11  Score=106.13  Aligned_cols=28  Identities=39%  Similarity=0.501  Sum_probs=26.9

Q ss_pred             EEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584          40 KFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus        40 ~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      +.|+|+|.+.|++++|||+|+|||||||
T Consensus      1069 ~~VkVyia~KRkiqvGDKmAGRHGNKGV 1096 (2836)
T PRK14844       1069 MSVKVFIAVKHSLQPGDKMAGRHGNKGV 1096 (2836)
T ss_pred             eEEEEEEEEeecCCccccccccCCCCce
Confidence            5799999999999999999999999997

>PF04941 LEF-8: Late expression factor 8 (LEF-8); InterPro: IPR007025 Late expression factor 8 (LEF-8) is one of the primary components of RNA polymerase produced by polyhedrosis viruses

Probab=94.04  E-value=0.19  Score=41.30  Aligned_cols=30  Identities=27%  Similarity=0.347  Sum_probs=22.5

Q ss_pred             CcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584          38 GYKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus        38 g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      +.-++|+.+--.=.--.|=|.||-||||||
T Consensus       704 d~v~vKl~~V~st~dLeGlKICgIHGQKGV  733 (748)
T PF04941_consen  704 DTVYVKLTLVTSTSDLEGLKICGIHGQKGV  733 (748)
T ss_pred             CEEEEEEEEEEEecCccceEEeeeeccccc
Confidence            345566665555556679999999999997

LEF-8 shows homology to the second largest subunit of prokaryotic DNA-directed RNA polymerase[].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent

>PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional

Probab=93.80  E-value=0.21  Score=41.57  Aligned_cols=29  Identities=34%  Similarity=0.410  Sum_probs=20.9

Q ss_pred             cEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584          39 YKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus        39 ~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      .-++|+++--.=.--.|=|.||-||||||
T Consensus       695 ~v~lKl~~Vtst~dLeGlKICgIHGQKGV  723 (865)
T PHA03394        695 TVYLKIRLVTSTSDLEGLKICGIHGQKGV  723 (865)
T ss_pred             EEEEEEEEEEEecCcceeEEeeecccccc
Confidence            33455555444455679999999999997

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	67
1i3q_B	1224	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		8e-20
3h0g_B	1210	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		2e-19
2pmz_B	1124	Archaeal Rna Polymerase From Sulfolobus Solfataricu		3e-14
2waq_B	1131	The Complete Structure Of The Archaeal 13-Subunit D		3e-14

>pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1224

Iteration: 1
 Score = 91.7 bits (226), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 43/61 (70%), Positives = 50/61 (81%)
Query: 7   TKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKG 66
           T   SKRD ST LR++E GIVDQV++T N DG KF K+RVR+ +IPQIGDKFASRHGQKG
Sbjct: 929 TAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKG 988
Query: 67  T 67
           T
Sbjct: 989 T 989

>pdb|3H0G|B Chain B, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1210

Iteration: 1
 Score = 90.5 bits (223), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 43/61 (70%), Positives = 52/61 (85%)
Query: 7   TKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKG 66
           T+  +KRD ST LR++E+GIVDQVM+T N +G KF K+R+RS RIPQIGDKFASRHGQKG
Sbjct: 918 TQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTRIPQIGDKFASRHGQKG 977
Query: 67  T 67
           T
Sbjct: 978 T 978

>pdb|2PMZ|B Chain B, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 1124

Iteration: 1
 Score = 73.2 bits (178), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 34/56 (60%), Positives = 41/56 (73%)
Query: 11  SKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKG 66
           +KRD S   R+ E GIVD V++T   +G K  K+RVR +RIP IGDKFASRHGQKG
Sbjct: 831 AKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRDLRIPTIGDKFASRHGQKG 886

>pdb|2WAQ|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 1131

Iteration: 1
 Score = 73.2 bits (178), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 34/56 (60%), Positives = 41/56 (73%)
Query: 11  SKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKG 66
           +KRD S   R+ E GIVD V++T   +G K  K+RVR +RIP IGDKFASRHGQKG
Sbjct: 834 AKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRDLRIPSIGDKFASRHGQKG 889

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	67
1twf_B	1224	DNA-directed RNA polymerase II 140 kDa polypeptid;	1e-29
3h0g_B	1210	DNA-directed RNA polymerase II subunit RPB2; trans	2e-29
4ayb_B	1131	DNA-directed RNA polymerase; transferase, multi-su	8e-29

>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* ... Length = 1224

 Score =  107 bits (269), Expect = 1e-29
 Identities = 44/65 (67%), Positives = 51/65 (78%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           L   T   SKRD ST LR++E GIVDQV++T N DG KF K+RVR+ +IPQIGDKFASRH
Sbjct: 925 LGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRH 984

Query: 63  GQKGT 67
           GQKGT
Sbjct: 985 GQKGT 989

>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1210

 Score =  107 bits (269), Expect = 2e-29
 Identities = 44/65 (67%), Positives = 53/65 (81%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           L   T+  +KRD ST LR++E+GIVDQVM+T N +G KF K+R+RS RIPQIGDKFASRH
Sbjct: 914 LGQRTQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTRIPQIGDKFASRH 973

Query: 63  GQKGT 67
           GQKGT
Sbjct: 974 GQKGT 978

>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 Length = 1131

 Score =  105 bits (263), Expect = 8e-29
 Identities = 34/67 (50%), Positives = 43/67 (64%)

Query: 1   MHLEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFAS 60
              +  +   +KRD S   R+ E GIVD V++T   +G K  K+RVR +RIP IGDKFAS
Sbjct: 824 QEFKELSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRDLRIPSIGDKFAS 883

Query: 61  RHGQKGT 67
           RHGQKG 
Sbjct: 884 RHGQKGV 890

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	67
1twf_B	1224	DNA-directed RNA polymerase II 140 kDa polypeptid;	99.87
4ayb_B	1131	DNA-directed RNA polymerase; transferase, multi-su	99.82
3h0g_B	1210	DNA-directed RNA polymerase II subunit RPB2; trans	99.82
2a6h_C	1119	DNA-directed RNA polymerase beta chain; RNA polyme	99.82
3lu0_C	1342	DNA-directed RNA polymerase subunit beta; E. coli	99.66
3tbi_B	228	DNA-directed RNA polymerase subunit beta; transcri	95.32

>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=99.87  E-value=1.2e-22  Score=165.35  Aligned_cols=60  Identities=70%  Similarity=1.019  Sum_probs=56.0

Q ss_pred             CccceeeeeEEcCCCCCeEEEEEEEEeccCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584           8 KRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus         8 ~~~~~rd~S~~~k~~e~g~Vd~V~~~~~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      +...++|+|++++++|.|+||+|+++.+++|.++|||++|++|+|+||||||||||||||
T Consensus       930 ~~~~~rd~s~~~~~~e~g~Vd~V~~~~~~~g~~~vkV~ir~~R~p~iGDKfasRHGqKGv  989 (1224)
T 1twf_B          930 AYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGT  989 (1224)
T ss_dssp             ---CCBBCCEECCTTCCEEEEEEEEEECSSSCEEEEEEEEEEECCCTTCEEECTTSCEEE
T ss_pred             ccCccceeEEEeeCCCCeEEEEEEEEecCCCCEEEEEEEEecCCCCchhhhhhhccCcce
Confidence            446789999999999999999999999999999999999999999999999999999997

>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=99.82  E-value=7.4e-21  Score=153.13  Aligned_cols=57  Identities=60%  Similarity=0.933  Sum_probs=55.3

Q ss_pred             ceeeeeEEcCCCCCeEEEEEEEEeccCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584          11 SKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus        11 ~~rd~S~~~k~~e~g~Vd~V~~~~~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      .++|+|++++++|.|+||.|.++.+++|++.|+|+||+.|+|++|||||||||||||
T Consensus       834 ~~~d~sl~~~~g~~g~Vd~v~~~~~~~~~~~vkV~i~~~R~~~vGDK~agRHGnKGv  890 (1131)
T 4ayb_B          834 AKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRDLRIPSIGDKFASRHGQKGV  890 (1131)
T ss_dssp             CCCCCCEECCTTCCEEEEEEEEEECSSSCEEEEEEEEEEECCCTTCEEEETTSCEEE
T ss_pred             eeeeeeEEccCCCceEEEEEEEeeccCCceEEEEEEeccccCcccccccccccccce
Confidence            468999999999999999999999999999999999999999999999999999997

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

Probab=99.82  E-value=2.7e-21  Score=157.72  Aligned_cols=60  Identities=70%  Similarity=1.007  Sum_probs=57.5

Q ss_pred             CccceeeeeEEcCCCCCeEEEEEEEEeccCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584           8 KRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus         8 ~~~~~rd~S~~~k~~e~g~Vd~V~~~~~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      +.+.++|+|++++++|.|+||+|+++.+++|.++|+|++|++|+|++|||||||||||||
T Consensus       919 ~~~~~rd~s~~~~~~e~g~Vd~V~~~~~~~g~~~vkv~~~~~R~~~~GDK~a~RhGqKGv  978 (1210)
T 3h0g_B          919 QLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTRIPQIGDKFASRHGQKGT  978 (1210)
T ss_dssp             CCCCCCCCCCCCCTTCCCCCCEEEEEECSSSSEEEEEEECCCBCCCTTCEEECTTCCCEE
T ss_pred             cccccceeeEEecCCCCeEEEEEEEEEecCCCeEEEEEEEEecCCCchhhhhcccCCCce
Confidence            456789999999999999999999999999999999999999999999999999999997

>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=99.82  E-value=1.1e-20  Score=153.39  Aligned_cols=60  Identities=35%  Similarity=0.452  Sum_probs=55.6

Q ss_pred             CccceeeeeEEcCCCCCeEEEEEEEEeccC-Cc-------EEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584           8 KRFSKRDGSTFLRNSETGIVDQVMLTLNVD-GY-------KFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus         8 ~~~~~rd~S~~~k~~e~g~Vd~V~~~~~~~-g~-------~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      +...++|+|++++++|.|+|++|.++.+++ |.       +.|+|++|++|+|++|||||||||||||
T Consensus       781 k~~~~rd~Sl~~~~~e~G~V~~V~~~~~~~~g~~l~~~~~~~vkV~i~~~R~~~vGDKfasRHGqKGV  848 (1119)
T 2a6h_C          781 KARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGV  848 (1119)
T ss_dssp             CCCCEEECCEECCSSCCCEEEEEEEECSSCSSCCCCTTEEEEEEEEEEEEEECCTTCEEECTTSCEEE
T ss_pred             cccccceeeEEccCCccEEEEEEEEEccCCCCcccCCCcceEEEEEEcccCCcccCchhhhccCCCce
Confidence            345789999999999999999999998887 64       8999999999999999999999999997

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

Probab=99.66  E-value=3.9e-17  Score=134.31  Aligned_cols=30  Identities=43%  Similarity=0.561  Sum_probs=28.4

Q ss_pred             CcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584          38 GYKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus        38 g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      ..++|||++|++|+|++|||||||||||||
T Consensus      1046 v~k~VkV~ia~kRk~qvGDK~AgRHGnKGV 1075 (1342)
T 3lu0_C         1046 VLKIVKVYLAVKRRIQPGDKMAGRHGNKGV 1075 (1342)
T ss_dssp             SSCEEEEEEEEEECCCTTCEEECSSSCCEE
T ss_pred             CceEEEEEEEEeccCCCCCCcccccCCCce
Confidence            468999999999999999999999999997

>3tbi_B DNA-directed RNA polymerase subunit beta; transcription accessory protein, transcription; 3.00A {Escherichia coli}

Probab=95.32  E-value=0.021  Score=39.96  Aligned_cols=29  Identities=24%  Similarity=0.156  Sum_probs=25.7

Q ss_pred             CccceeeeeEEcCCCCCeEEEEEEEEecc
Q psy7584           8 KRFSKRDGSTFLRNSETGIVDQVMLTLNV   36 (67)
Q Consensus         8 ~~~~~rd~S~~~k~~e~g~Vd~V~~~~~~   36 (67)
                      +....+|+|+++++++.|+|+.|.+++..
T Consensus        80 k~~~vkDtSL~vp~G~~G~VidV~if~r~  108 (228)
T 3tbi_B           80 KASDVKDSSLRVPNGVSGTVIDVQVFTRD  108 (228)
T ss_dssp             TSSCEEECCEECCSSCBEEEEEEEEEEBT
T ss_pred             ccccceeCcEecCCCCcEEEEEEEEEecC
Confidence            45678999999999999999999998754

---

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	67
d1twfb_	1207	e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces c	7e-16
d1smyc_	1119	e.29.1.1 (C:) RNA-polymerase beta {Thermus thermop	8e-11

>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 = 67.6 bits (164), Expect = 7e-16
 Identities = 44/65 (67%), Positives = 51/65 (78%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           L   T   SKRD ST LR++E GIVDQV++T N DG KF K+RVR+ +IPQIGDKFASRH
Sbjct: 908 LGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRH 967

Query: 63  GQKGT 67
           GQKGT
Sbjct: 968 GQKGT 972

>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 = 53.2 bits (127), Expect = 8e-11
 Identities = 20/69 (28%), Positives = 29/69 (42%), Gaps = 8/69 (11%)

Query: 7   TKRFSKRDGSTFLRNSETGIVDQV--------MLTLNVDGYKFCKIRVRSVRIPQIGDKF 58
            K    +D S  +   E GIV +          + L     +  ++ V   R  Q+GDK 
Sbjct: 780 EKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKL 839

Query: 59  ASRHGQKGT 67
           A+RHG KG 
Sbjct: 840 ANRHGNKGV 848

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	67
d1twfb_	1207	RBP2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.81
d1smyc_	1119	RNA-polymerase beta {Thermus thermophilus [TaxId:	99.8

>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=99.81  E-value=1.1e-20  Score=149.94  Aligned_cols=59  Identities=71%  Similarity=1.038  Sum_probs=55.4

Q ss_pred             ccceeeeeEEcCCCCCeEEEEEEEEeccCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584           9 RFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus         9 ~~~~rd~S~~~k~~e~g~Vd~V~~~~~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      ...++|+|+.++.+|.|+||+|..+.+.++.+.++|+||+.|+|+||||||||||||||
T Consensus       914 ~~~~~~~s~~~~~~~~g~V~~v~~~~~~~~~~~~kv~i~~~R~p~iGDKfasRhGqKGv  972 (1207)
T d1twfb_         914 YHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGT  972 (1207)
T ss_dssp             --CCBBCCEECCTTCCEEEEEEEEEECSSSCEEEEEEEEEEECCCTTCEEECTTSCEEE
T ss_pred             cccccceeEEccCCCCeEEEEEEEeecccccceeeEEEEEEeccchhhhhhhccCCcce
Confidence            34578999999999999999999999999999999999999999999999999999997

>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=99.80  E-value=2.2e-20  Score=146.71  Aligned_cols=59  Identities=32%  Similarity=0.391  Sum_probs=52.8

Q ss_pred             ccceeeeeEEcCCCCCeEEEEEEEEeccCC--------cEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584           9 RFSKRDGSTFLRNSETGIVDQVMLTLNVDG--------YKFCKIRVRSVRIPQIGDKFASRHGQKGT   67 (67)
Q Consensus         9 ~~~~rd~S~~~k~~e~g~Vd~V~~~~~~~g--------~~~vkV~vR~~R~P~iGDKFsSRHGQKGv   67 (67)
                      ...++|+|+.++.++.|+||+|.++.+.++        ...|+|++|++|+|+||||||||||||||
T Consensus       782 ~~~~k~~s~~~~~~~~g~v~~v~~~~~~~~~~~~~~~~~~~vkv~~r~~R~p~iGDKfssRHGQKGv  848 (1119)
T d1smyc_         782 ARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGV  848 (1119)
T ss_dssp             SCCCEECCEECCSSCCCEEEEEEEECSSCSSCCCCTTEEEEEEEEEEEEECCCTTCEEECTTSCEEE
T ss_pred             cceeeeeeeccCCCCCCEEEEEEEEeccccccccCCCcceEEEEEEeeeeeccccchhhhhccCCcc
Confidence            345799999999999999999998866443        47899999999999999999999999997