Citrus Sinensis ID: 045123

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------22
Protein Sequence
MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER
Secondary Structure (PSIPRED)
ccccccccccccccccEEEEEcccHHHHHHccEEEEEccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccHHHHHHHHHHHHcccccccccccccHHHHHHHHHccHHHHHHHHHHHccccccccccccccHHcccccccccccccccccccccccEEEEEEEEEEEEEccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccEEEEEEEEcccHHHHHHccEEEEEcccHccccccccccccccccccEcccccccccccccccccccccHHHHcccHHHHHHHHHHHHHHHHHHHHcccEEcccccHHHHHHHHcccHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccEEEcccEEEEEEcccccccccccccccccccEEEccccc
Coil and Loop (DISEMBL)
mencftfspfkvAKVRMVQFSILSPDEIRKMSVTeidhgkttergmpmagglsdlrlgtidkrfkcetcssnmgecpghfghlelakpmfhIGFMKTLLTIMRCVCfncskiladeeDDKFKLALKIRHPKSRLEQILCACKtknkceggdeiDVLSllghdgeeplrkrksgcgalqptltidGMNMIAEYKAQrkknddqgqlpepverkqtltaer
Flexible Loop (DISEMBL)
mencftfspfkvakvrMVQFSilspdeirkMSVTEidhgkttergmpmagglSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALkirhpksrlEQILCACktknkceggDEIDVLSLLGHDgeeplrkrksgcgalqptltidGMNMIAEYKAQrkknddqgqlpepverkqtltaer
Low Complexity Region (SEG)
MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER
Disordered region (IsUnstruct)
***CFTFSPFKVAKVRMVQFSILSPDEI**********************GLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGH**************ALQPTLTIDGMNMI******************************
Disordered Region (DISOPRED)
***********VAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPKSRLEQILCACKTKNKC*************************GCGALQPTLTIDGMNMIAEY********************QTL****
Disordered Region (DISEMBL)
MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTIDGMNMIAEYKA***********PEPVER********
Disordered Region (DISPRO)
****FTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPKSRLEQILCACKTKNKC************************SGCGALQPTLTIDGMNMIAEYKAQ************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER
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	219	2.2.26 [Sep-21-2011]
P18616	1839	DNA-directed RNA polymera	yes	no	0.990	0.117	0.675	2e-87
P35084	1727	DNA-directed RNA polymera	yes	no	0.958	0.121	0.468	1e-49
P08775	1970	DNA-directed RNA polymera	yes	no	0.885	0.098	0.457	1e-45
P24928	1970	DNA-directed RNA polymera	yes	no	0.885	0.098	0.457	1e-45
A5DCV3	1579	DNA-directed RNA polymera	N/A	no	0.913	0.126	0.430	4e-45
P04052	1887	DNA-directed RNA polymera	yes	no	0.917	0.106	0.443	4e-45
P36594	1752	DNA-directed RNA polymera	yes	no	0.867	0.108	0.438	3e-43
P35074	1853	DNA-directed RNA polymera	N/A	no	0.876	0.103	0.444	1e-41
P16356	1856	DNA-directed RNA polymera	yes	no	0.904	0.106	0.420	3e-39
Q75A34	1745	DNA-directed RNA polymera	yes	no	0.913	0.114	0.365	5e-38

>sp|P18616|RPB1_ARATH DNA-directed RNA polymerase II subunit RPB1 OS=Arabidopsis thaliana GN=RPB205 PE=1 SV=3

 Score =  321 bits (823), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 148/219 (67%), Positives = 182/219 (83%), Gaps = 2/219 (0%)

Query: 1   MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTI 60
           M+  F FSP +V+KVR+VQF ILSPDEIR+MSV  ++H +TTE+G P  GGLSD RLGTI
Sbjct: 1   MDTRFPFSPAEVSKVRVVQFGILSPDEIRQMSVIHVEHSETTEKGKPKVGGLSDTRLGTI 60

Query: 61  DKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDK 120
           D++ KCETC +NM ECPGHFG+LELAKPM+H+GFMKT+L+IMRCVCFNCSKILADEE+ K
Sbjct: 61  DRKVKCETCMANMAECPGHFGYLELAKPMYHVGFMKTVLSIMRCVCFNCSKILADEEEHK 120

Query: 121 FKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPT 180
           FK A+KI++PK+RL++IL ACK K KC+GGD+ID   +  H  +EP++K + GCGA QP 
Sbjct: 121 FKQAMKIKNPKNRLKKILDACKNKTKCDGGDDID--DVQSHSTDEPVKKSRGGCGAQQPK 178

Query: 181 LTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219
           LTI+GM MIAEYK QRKKND+  QLPEP ERKQTL A+R
Sbjct: 179 LTIEGMKMIAEYKIQRKKNDEPDQLPEPAERKQTLGADR 217

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second 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. RPB1 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. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.
Arabidopsis thaliana (taxid: 3702)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6

>sp|P35084|RPB1_DICDI DNA-directed RNA polymerase II subunit rpb1 OS=Dictyostelium discoideum GN=polr2a PE=2 SV=2

 Score =  196 bits (498), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 103/220 (46%), Positives = 137/220 (62%), Gaps = 10/220 (4%)

Query: 1   MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTI 60
           M   F  S  ++ KV+ VQF ILSPDEIR MSV  ++H +T E G P AGGL D  +GTI
Sbjct: 1   MAAFFPPSSAELRKVKRVQFGILSPDEIRNMSVARVEHPETYENGKPKAGGLLDPAMGTI 60

Query: 61  DKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDK 120
           DK  +C+TCS  M ECPGHFGH+ELAKP+FHIGF+ T+L I+RCVC++CSK+L D  +  
Sbjct: 61  DKTQRCQTCSGTMAECPGHFGHIELAKPVFHIGFIDTVLKILRCVCYHCSKLLTDTNEHS 120

Query: 121 FKLALKIRHPKSRLEQILCACKTKNKCE-GGDEIDVLSLLGHDGEEPLRKRKSGCGALQP 179
           F+ ALKIR+ K RL  ++  CK K  C  GG+E +   L   D E     +  GCG + P
Sbjct: 121 FRQALKIRNQKHRLNAVVDCCKNKKVCAIGGEEEEEHDLSKTDEELDKPVKHGGCGNVLP 180

Query: 180 TLTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219
            +T + + +I E+K             E +E+K  L+AER
Sbjct: 181 KITKEDLKIIVEFKDVTD---------ESIEKKSVLSAER 211

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second 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. RPB1 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. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.

Dictyostelium discoideum (taxid: 44689)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|P08775|RPB1_MOUSE DNA-directed RNA polymerase II subunit RPB1 OS=Mus musculus GN=Polr2a PE=1 SV=3

 Score =  182 bits (463), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 92/201 (45%), Positives = 128/201 (63%), Gaps = 7/201 (3%)

Query: 15  VRMVQFSILSPDEIRKMSVTE--IDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSN 72
           ++ VQF +LSPDE+++MSVTE  I + +TTE G P  GGL D R G I++  +C+TC+ N
Sbjct: 18  IKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGN 77

Query: 73  MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFK--LALKIRHP 130
           M ECPGHFGH+ELAKP+FH+GF+   + ++RCVCF CSK+L D  + K K  LA     P
Sbjct: 78  MTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQP 137

Query: 131 KSRLEQILCACKTKNKCEGGDEID-VLSLLGHDGEEPLRKRK--SGCGALQPTLTIDGMN 187
           K RL  +   CK KN CEGG+E+D    +   +G+E L K K   GCG  QP +   G+ 
Sbjct: 138 KKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLE 197

Query: 188 MIAEYKAQRKKNDDQGQLPEP 208
           + AE+K   + + ++  L  P
Sbjct: 198 LYAEWKHVNEDSQEKKILLSP 218

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second 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. RPB1 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. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.

Mus musculus (taxid: 10090)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|P24928|RPB1_HUMAN DNA-directed RNA polymerase II subunit RPB1 OS=Homo sapiens GN=POLR2A PE=1 SV=2

 Score =  182 bits (463), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 92/201 (45%), Positives = 128/201 (63%), Gaps = 7/201 (3%)

Query: 15  VRMVQFSILSPDEIRKMSVTE--IDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSN 72
           ++ VQF +LSPDE+++MSVTE  I + +TTE G P  GGL D R G I++  +C+TC+ N
Sbjct: 18  IKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGN 77

Query: 73  MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFK--LALKIRHP 130
           M ECPGHFGH+ELAKP+FH+GF+   + ++RCVCF CSK+L D  + K K  LA     P
Sbjct: 78  MTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQP 137

Query: 131 KSRLEQILCACKTKNKCEGGDEID-VLSLLGHDGEEPLRKRK--SGCGALQPTLTIDGMN 187
           K RL  +   CK KN CEGG+E+D    +   +G+E L K K   GCG  QP +   G+ 
Sbjct: 138 KKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLE 197

Query: 188 MIAEYKAQRKKNDDQGQLPEP 208
           + AE+K   + + ++  L  P
Sbjct: 198 LYAEWKHVNEDSQEKKILLSP 218

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second 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. RPB1 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. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing. Acts as a RNA-dependent RNA polymerase when associated with small delta antigen of Hepatitis delta virus, acting both as a replicate and transcriptase for the viral RNA circular genome.

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 4

EC: 8

>sp|A5DCV3|RPB1_PICGU DNA-directed RNA polymerase II subunit RPB1 (Fragments) OS=Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) GN=RPB1 PE=3 SV=2

 Score =  181 bits (458), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 90/209 (43%), Positives = 127/209 (60%), Gaps = 9/209 (4%)

Query: 1   MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGM--PMAGGLSDLRLG 58
           M   F  S   +  V+ VQF +LSP+E+R +SV +I++ +T ++    P  GGL+D RLG
Sbjct: 1   MSRQFPHSSAPLRSVKEVQFGLLSPEEVRAISVAKIEYPETMDQATKRPREGGLNDPRLG 60

Query: 59  TIDKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEED 118
           +ID+ FKC+TC  +M ECPGHFGH+ELAKP+FHIGF+  +  +  CVC +C K+L DE +
Sbjct: 61  SIDRNFKCQTCGEDMAECPGHFGHIELAKPVFHIGFIAKIKKVCECVCMHCGKLLLDESN 120

Query: 119 DKFKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQ 178
                A++IR PK R   +   CK K  CE     DVL   G +G EP R  + GCG  Q
Sbjct: 121 PAMAQAIRIRDPKKRFNAVWNLCKGKMICEA----DVLQDDG-EGNEPKRTSRGGCGHTQ 175

Query: 179 PTLTIDGMNMIAEYKAQRKKNDDQGQLPE 207
           P +  DG+ +   +K  + KN D+ + PE
Sbjct: 176 PVVRKDGLKLWGTWK--QNKNYDETEQPE 202

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second 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. RPB1 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. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.

Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) (taxid: 294746)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|P04052|RPB1_DROME DNA-directed RNA polymerase II subunit RPB1 OS=Drosophila melanogaster GN=RpII215 PE=3 SV=4

 Score =  181 bits (458), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 98/221 (44%), Positives = 137/221 (61%), Gaps = 20/221 (9%)

Query: 6   TFSPFKVAKVRMVQFSILSPDEIRKMSVTE--IDHGKTTERGMPMAGGLSDLRLGTIDKR 63
           T S   + +V+ VQF ILSPDEIR+MSVTE  +   +T E G P  GGL D R G ID+ 
Sbjct: 5   TDSKAPLRQVKRVQFGILSPDEIRRMSVTEGGVQFAETMEGGRPKLGGLMDPRQGVIDRT 64

Query: 64  FKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFK- 122
            +C+TC+ NM ECPGHFGH++LAKP+FHIGF+   + I+RCVCF CSK+L    + K K 
Sbjct: 65  SRCQTCAGNMTECPGHFGHIDLAKPVFHIGFITKTIKILRCVCFYCSKMLVSPHNPKIKE 124

Query: 123 LALKIR-HPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRK---SGCGALQ 178
           + +K R  P+ RL  +   CK K  CEGG+++D    L  + ++P   +K    GCG  Q
Sbjct: 125 IVMKSRGQPRKRLAYVYDLCKGKTICEGGEDMD----LTKENQQPDPNKKPGHGGCGHYQ 180

Query: 179 PTLTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219
           P++   G+++ AE+K Q +  D Q       E+K  ++AER
Sbjct: 181 PSIRRTGLDLTAEWKHQNE--DSQ-------EKKIVVSAER 212

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second 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. RPB1 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. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.

Drosophila melanogaster (taxid: 7227)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|P36594|RPB1_SCHPO DNA-directed RNA polymerase II subunit rpb1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb1 PE=1 SV=1

 Score =  174 bits (442), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 92/210 (43%), Positives = 123/210 (58%), Gaps = 20/210 (9%)

Query: 7   FSPFKVA--KVRMVQFSILSPDEIRKMSVTEIDHGKTTERG--MPMAGGLSDLRLGTIDK 62
           FSP  V   +V  VQF ILSP+EIR MSV +I+  +T +     P  GGL D RLGTID+
Sbjct: 6   FSPSSVPLRRVEEVQFGILSPEEIRSMSVAKIEFPETMDESGQRPRVGGLLDPRLGTIDR 65

Query: 63  RFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFK 122
           +FKC+TC   M +CPGHFGH+ELAKP+FHIGF+  +  I+ CVC+NC K+  D  + KF 
Sbjct: 66  QFKCQTCGETMADCPGHFGHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPKFN 125

Query: 123 LALKIRHPKSRLEQILCACKTKNKCE-----GGDEIDVLSLLGHDGEEPLRKRKSGCGAL 177
              + R PK+RL  +   CKTK  C+     G D  D+ +   + G         GCGA 
Sbjct: 126 DTQRYRDPKNRLNAVWNVCKTKMVCDTGLSAGSDNFDLSNPSANMGH-------GGCGAA 178

Query: 178 QPTLTIDGMNMIAEYKAQRKKNDDQGQLPE 207
           QPT+  DG+ +   +    K+  D+  LPE
Sbjct: 179 QPTIRKDGLRLWGSW----KRGKDESDLPE 204

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second 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. RPB1 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. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.

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

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|P35074|RPB1_CAEBR DNA-directed RNA polymerase II subunit RPB1 OS=Caenorhabditis briggsae GN=rpb-1 PE=3 SV=2

 Score =  169 bits (428), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 92/207 (44%), Positives = 127/207 (61%), Gaps = 15/207 (7%)

Query: 18  VQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSNMGECP 77
           VQF IL P+EI++MSV  ++  +  E G P  GGL D R G ID+R +C TC+ N+ +CP
Sbjct: 18  VQFGILGPEEIKRMSVAHVEFPEVYENGKPKMGGLMDPRQGVIDRRGRCMTCAGNLTDCP 77

Query: 78  GHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIR--HPKSRLE 135
           GHFGHLELAKP+FHIGF+   L I+RCVCF C ++L D+ + +    LK    +PK RL 
Sbjct: 78  GHFGHLELAKPVFHIGFLTKSLKILRCVCFYCGRLLIDKTNPRVMDILKKTSGNPKKRLA 137

Query: 136 QILCACKTKNKCEGGDEIDVLSLLGHDGEEPL---RKRKSGCGALQPTLTIDGMNMIAEY 192
            I   CK+K+ CEG  E +    L  D ++P+   +K  +GCG  QP+    G+++ AE+
Sbjct: 138 LIYDLCKSKSVCEGAAEKE--DGLPDDMDDPMNEGKKVPAGCGRYQPSYRRVGIDINAEW 195

Query: 193 KAQRKKNDDQGQLPEPVERKQTLTAER 219
           K  +  N+D        ERK  LTAER
Sbjct: 196 K--KNVNEDTQ------ERKIMLTAER 214

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second 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. RPB1 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. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.

Caenorhabditis briggsae (taxid: 6238)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|P16356|RPB1_CAEEL DNA-directed RNA polymerase II subunit RPB1 OS=Caenorhabditis elegans GN=ama-1 PE=1 SV=3

 Score =  161 bits (408), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 92/219 (42%), Positives = 125/219 (57%), Gaps = 21/219 (9%)

Query: 8   SPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTIDKRFKCE 67
           +P ++  V  VQF IL P+EI++MSV  ++  +  E G P  GGL D R G ID+R +C 
Sbjct: 10  APLRI--VSRVQFGILGPEEIKRMSVAHVEFPEVYENGKPKLGGLMDPRQGVIDRRGRCM 67

Query: 68  TCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKI 127
           TC+ N+ +CPGHFGHLELAKP+FHIGF+   L I+RCVCF C ++L D+   +    LK 
Sbjct: 68  TCAGNLTDCPGHFGHLELAKPVFHIGFLTKTLKILRCVCFYCGRLLIDKSAPRVLEILKK 127

Query: 128 --RHPKSRLEQILCACKTKNKCEGGDEID-----VLSLLGHDGEEPLRKRKSGCGALQPT 180
              + K RL  I   CK K+ CEG  E +           +DG    +K   GCG  QP+
Sbjct: 128 TGTNSKKRLTMIYDLCKAKSVCEGAAEKEEGMPDDPDDPMNDG----KKVAGGCGRYQPS 183

Query: 181 LTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219
               G+++ AE+K  +  N+D        ERK  LTAER
Sbjct: 184 YRRVGIDINAEWK--KNVNEDTQ------ERKIMLTAER 214

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second 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. RPB1 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. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.

Caenorhabditis elegans (taxid: 6239)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|Q75A34|RPB1_ASHGO DNA-directed RNA polymerase II subunit RPB1 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=RPB1 PE=3 SV=2

 Score =  157 bits (397), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 79/216 (36%), Positives = 127/216 (58%), Gaps = 16/216 (7%)

Query: 5   FTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMA--GGLSDLRLGTIDK 62
           F +S   +  ++ VQF + SP+E+R +SV +I+  +T +     A  GGL+D RLG+ID+
Sbjct: 4   FPYSSAPLRTIKEVQFGLFSPEEVRAISVAKIEFPETMDETQMRAKVGGLNDPRLGSIDR 63

Query: 63  RFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFK 122
            FKC+TC   M +CPGHFGH+ELAKP+FHIGF+  +  +  CVC +C K+L DE ++  +
Sbjct: 64  NFKCQTCGEGMNDCPGHFGHIELAKPVFHIGFISKIKKVCECVCMHCGKLLLDEYNELMR 123

Query: 123 LALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLT 182
            A+KI+ PK R   +   CK K  C+        + +  + +      + GCG  QP++ 
Sbjct: 124 QAIKIKDPKRRFNAVWSLCKAKMVCD--------TEVPSEDDPSKYISRGGCGNAQPSIR 175

Query: 183 IDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAE 218
            DG++++  +K  + KN +    PE    K+ ++AE
Sbjct: 176 KDGLSLVGTWK--KDKNAEDADQPE----KRIISAE 205

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second 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. RPB1 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. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.

Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (taxid: 284811)

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	219
356538329	1827	PREDICTED: DNA-directed RNA polymerase I	0.986	0.118	0.739	6e-93
255579596	1855	DNA-directed RNA polymerase II largest s	0.986	0.116	0.744	1e-92
356496595	1827	PREDICTED: DNA-directed RNA polymerase I	0.986	0.118	0.739	3e-92
449524332	1853	PREDICTED: DNA-directed RNA polymerase I	0.986	0.116	0.726	9e-91
449456849	1832	PREDICTED: LOW QUALITY PROTEIN: DNA-dire	0.986	0.117	0.726	1e-90
225459758	1848	PREDICTED: DNA-directed RNA polymerase I	0.986	0.116	0.730	2e-90
302141712	1565	unnamed protein product [Vitis vinifera]	0.986	0.138	0.642	9e-86
334187204	1839	DNA-directed RNA polymerase II subunit R	0.990	0.117	0.675	1e-85
357483939	1864	DNA-directed RNA polymerase [Medicago tr	0.986	0.115	0.666	2e-85
242078217	1857	hypothetical protein SORBIDRAFT_07g00368	0.981	0.115	0.671	5e-83

>gi|356538329|ref|XP_003537656.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB1-like [Glycine max]

 Score =  345 bits (886), Expect = 6e-93,   Method: Compositional matrix adjust.
 Identities = 162/219 (73%), Positives = 190/219 (86%), Gaps = 3/219 (1%)

Query: 1   MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTI 60
           M+  F FSP +VAKVRMVQF ILSPDEIR+MSV +I+HG+TTERG P  GGLSD RLGTI
Sbjct: 1   MDIRFPFSPAEVAKVRMVQFGILSPDEIRQMSVVQIEHGETTERGKPKVGGLSDPRLGTI 60

Query: 61  DKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDK 120
           D++ KCETC+++M ECPGHFGHLELAKPMFHIGF+KT+LTIMRCVCFNCSKILADE D K
Sbjct: 61  DRKLKCETCTASMAECPGHFGHLELAKPMFHIGFLKTVLTIMRCVCFNCSKILADENDHK 120

Query: 121 FKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPT 180
           FK AL+IR+PK+RL++IL ACK K+KCEGGDEID+    G D +EP++K + GCGA QP 
Sbjct: 121 FKQALRIRNPKNRLKKILDACKNKSKCEGGDEIDI---PGQDTDEPVKKSRGGCGAQQPK 177

Query: 181 LTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219
           +TI+GM MIAEYKAQRKK+DDQ QLPEPVERKQTL+AER
Sbjct: 178 ITIEGMKMIAEYKAQRKKSDDQEQLPEPVERKQTLSAER 216

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255579596|ref|XP_002530639.1| DNA-directed RNA polymerase II largest subunit, putative [Ricinus communis] gi|223529812|gb|EEF31747.1| DNA-directed RNA polymerase II largest subunit, putative [Ricinus communis]

 Score =  344 bits (883), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 163/219 (74%), Positives = 189/219 (86%), Gaps = 3/219 (1%)

Query: 1   MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTI 60
           M+  F +SP +VAKVRMVQF ILSPDEIR+MSV +I+  +TTERG P  GGLSDLRLGTI
Sbjct: 1   MDMRFPYSPAEVAKVRMVQFGILSPDEIRQMSVVQIEFSETTERGKPKPGGLSDLRLGTI 60

Query: 61  DKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDK 120
           D++ KCETC++NM ECPGHFGHLELAKPMFHIGF+KT+L+IMRCVCFNCSKILADEED K
Sbjct: 61  DRKMKCETCTANMAECPGHFGHLELAKPMFHIGFLKTVLSIMRCVCFNCSKILADEEDHK 120

Query: 121 FKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPT 180
           FK ALKI++PK+RL++IL ACK K KCEGGD+IDV S    D +EP++K + GCGA QP 
Sbjct: 121 FKQALKIKNPKNRLKKILDACKNKTKCEGGDDIDVHS---QDTDEPVKKSRGGCGAQQPR 177

Query: 181 LTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219
           +TI+GM MIAEYKAQRKKNDDQ QLPEPVERKQTLTAER
Sbjct: 178 MTIEGMKMIAEYKAQRKKNDDQEQLPEPVERKQTLTAER 216

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496595|ref|XP_003517152.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB1-like [Glycine max]

 Score =  343 bits (880), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 162/219 (73%), Positives = 189/219 (86%), Gaps = 3/219 (1%)

Query: 1   MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTI 60
           M+  F FSP +VAKVRMVQF ILSPDEIR+MSV +I+HG+TTERG P  GGLSD RLGTI
Sbjct: 1   MDIRFPFSPAEVAKVRMVQFGILSPDEIRQMSVVQIEHGETTERGKPKVGGLSDPRLGTI 60

Query: 61  DKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDK 120
           D++ KCETC+++M ECPGHFGHLELAKPMFHIGF+KT+LTIMRCVCFNCSKILADE D K
Sbjct: 61  DRKLKCETCTASMAECPGHFGHLELAKPMFHIGFLKTVLTIMRCVCFNCSKILADENDHK 120

Query: 121 FKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPT 180
           FK AL+IR+PK+RL++IL ACK K+KCEGGDEID+    G D EE ++K + GCGA QP 
Sbjct: 121 FKQALRIRNPKNRLKKILDACKNKSKCEGGDEIDI---PGQDTEESVKKSRGGCGAQQPK 177

Query: 181 LTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219
           +TI+GM MIAEYKAQRKK+DDQ QLPEPVERKQTL+AER
Sbjct: 178 ITIEGMKMIAEYKAQRKKSDDQEQLPEPVERKQTLSAER 216

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449524332|ref|XP_004169177.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB1-like [Cucumis sativus]

 Score =  338 bits (867), Expect = 9e-91,   Method: Compositional matrix adjust.
 Identities = 159/219 (72%), Positives = 184/219 (84%), Gaps = 3/219 (1%)

Query: 1   MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTI 60
           M+  F +SP +VAKVRMVQF ILSPDEIR+MSV +I+HG+TTERG P   GLSD RLGTI
Sbjct: 1   MDLRFPYSPAEVAKVRMVQFGILSPDEIRQMSVVQIEHGETTERGKPKVAGLSDPRLGTI 60

Query: 61  DKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDK 120
           D++ KCETC++NM ECPGHFGHLELAKPMFHIGFMKT+LTIMR VCFNCSKIL DEED K
Sbjct: 61  DRKMKCETCTANMAECPGHFGHLELAKPMFHIGFMKTVLTIMRSVCFNCSKILVDEEDPK 120

Query: 121 FKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPT 180
           FK AL+I++PK+RL +IL ACK K KCEGGDEIDV    G D ++P++K + GCGA QP 
Sbjct: 121 FKQALRIKNPKNRLRKILDACKNKTKCEGGDEIDV---QGQDSDQPVKKSRGGCGAQQPK 177

Query: 181 LTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219
           ++I+GM M AEYKAQRKKNDD  QLPEPVERKQTLTAER
Sbjct: 178 ISIEGMKMTAEYKAQRKKNDDPEQLPEPVERKQTLTAER 216

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449456849|ref|XP_004146161.1| PREDICTED: LOW QUALITY PROTEIN: DNA-directed RNA polymerase II subunit RPB1-like [Cucumis sativus]

 Score =  338 bits (867), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 159/219 (72%), Positives = 184/219 (84%), Gaps = 3/219 (1%)

Query: 1   MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTI 60
           M+  F +SP +VAKVRMVQF ILSPDEIR+MSV +I+HG+TTERG P   GLSD RLGTI
Sbjct: 1   MDLRFPYSPAEVAKVRMVQFGILSPDEIRQMSVVQIEHGETTERGKPKVAGLSDPRLGTI 60

Query: 61  DKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDK 120
           D++ KCETC++NM ECPGHFGHLELAKPMFHIGFMKT+LTIMR VCFNCSKIL DEED K
Sbjct: 61  DRKMKCETCTANMAECPGHFGHLELAKPMFHIGFMKTVLTIMRSVCFNCSKILVDEEDPK 120

Query: 121 FKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPT 180
           FK AL+I++PK+RL +IL ACK K KCEGGDEIDV    G D ++P++K + GCGA QP 
Sbjct: 121 FKQALRIKNPKNRLRKILDACKNKTKCEGGDEIDV---QGQDSDQPVKKSRGGCGAQQPK 177

Query: 181 LTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219
           ++I+GM M AEYKAQRKKNDD  QLPEPVERKQTLTAER
Sbjct: 178 ISIEGMKMTAEYKAQRKKNDDPEQLPEPVERKQTLTAER 216

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225459758|ref|XP_002285900.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB1-like [Vitis vinifera]

 Score =  337 bits (865), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 160/219 (73%), Positives = 186/219 (84%), Gaps = 3/219 (1%)

Query: 1   MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTI 60
           M+  F +SP +VAKVRMVQF ILSPDEIR+MSV +I+H +TTERG P  GGLSD RLGTI
Sbjct: 1   MDMRFPYSPAEVAKVRMVQFGILSPDEIRQMSVVQIEHSETTERGKPKPGGLSDPRLGTI 60

Query: 61  DKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDK 120
           D++ KCETC++NM ECPGHFGHLELAKPMFHIGFMKT+L+IMRCVCFNCSKILADEED K
Sbjct: 61  DRKMKCETCTANMAECPGHFGHLELAKPMFHIGFMKTVLSIMRCVCFNCSKILADEEDHK 120

Query: 121 FKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPT 180
           FK A KIR+PK+RL++IL ACK K+KCEGGDEI+  +L   D +EP++K + GCGA QP 
Sbjct: 121 FKQAQKIRNPKNRLKKILDACKNKSKCEGGDEIETQAL---DSDEPVKKSRGGCGAQQPK 177

Query: 181 LTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219
           LTI+GM MIAEYK QRKKNDD  QLPEPVERKQ L+AER
Sbjct: 178 LTIEGMKMIAEYKIQRKKNDDPEQLPEPVERKQQLSAER 216

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302141712|emb|CBI18915.3| unnamed protein product [Vitis vinifera]

 Score =  322 bits (824), Expect = 9e-86,   Method: Compositional matrix adjust.
 Identities = 160/249 (64%), Positives = 186/249 (74%), Gaps = 33/249 (13%)

Query: 1   MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTI 60
           M+  F +SP +VAKVRMVQF ILSPDEIR+MSV +I+H +TTERG P  GGLSD RLGTI
Sbjct: 1   MDMRFPYSPAEVAKVRMVQFGILSPDEIRQMSVVQIEHSETTERGKPKPGGLSDPRLGTI 60

Query: 61  DKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADE---- 116
           D++ KCETC++NM ECPGHFGHLELAKPMFHIGFMKT+L+IMRCVCFNCSKILADE    
Sbjct: 61  DRKMKCETCTANMAECPGHFGHLELAKPMFHIGFMKTVLSIMRCVCFNCSKILADELTEN 120

Query: 117 --------------------------EDDKFKLALKIRHPKSRLEQILCACKTKNKCEGG 150
                                     ED KFK A KIR+PK+RL++IL ACK K+KCEGG
Sbjct: 121 VKWISKSKFANMKSLKLGHSLLHCKSEDHKFKQAQKIRNPKNRLKKILDACKNKSKCEGG 180

Query: 151 DEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTIDGMNMIAEYKAQRKKNDDQGQLPEPVE 210
           DEI+  +L   D +EP++K + GCGA QP LTI+GM MIAEYK QRKKNDD  QLPEPVE
Sbjct: 181 DEIETQAL---DSDEPVKKSRGGCGAQQPKLTIEGMKMIAEYKIQRKKNDDPEQLPEPVE 237

Query: 211 RKQTLTAER 219
           RKQ L+AER
Sbjct: 238 RKQQLSAER 246

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334187204|ref|NP_195305.2| DNA-directed RNA polymerase II subunit RPB1 [Arabidopsis thaliana] gi|322510106|sp|P18616.3|RPB1_ARATH RecName: Full=DNA-directed RNA polymerase II subunit RPB1; Short=RNA polymerase II subunit B1; AltName: Full=DNA-directed RNA polymerase III largest subunit gi|332661173|gb|AEE86573.1| DNA-directed RNA polymerase II subunit RPB1 [Arabidopsis thaliana]

 Score =  321 bits (823), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 148/219 (67%), Positives = 182/219 (83%), Gaps = 2/219 (0%)

Query: 1   MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTI 60
           M+  F FSP +V+KVR+VQF ILSPDEIR+MSV  ++H +TTE+G P  GGLSD RLGTI
Sbjct: 1   MDTRFPFSPAEVSKVRVVQFGILSPDEIRQMSVIHVEHSETTEKGKPKVGGLSDTRLGTI 60

Query: 61  DKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDK 120
           D++ KCETC +NM ECPGHFG+LELAKPM+H+GFMKT+L+IMRCVCFNCSKILADEE+ K
Sbjct: 61  DRKVKCETCMANMAECPGHFGYLELAKPMYHVGFMKTVLSIMRCVCFNCSKILADEEEHK 120

Query: 121 FKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPT 180
           FK A+KI++PK+RL++IL ACK K KC+GGD+ID   +  H  +EP++K + GCGA QP 
Sbjct: 121 FKQAMKIKNPKNRLKKILDACKNKTKCDGGDDID--DVQSHSTDEPVKKSRGGCGAQQPK 178

Query: 181 LTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219
           LTI+GM MIAEYK QRKKND+  QLPEP ERKQTL A+R
Sbjct: 179 LTIEGMKMIAEYKIQRKKNDEPDQLPEPAERKQTLGADR 217

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357483939|ref|XP_003612256.1| DNA-directed RNA polymerase [Medicago truncatula] gi|355513591|gb|AES95214.1| DNA-directed RNA polymerase [Medicago truncatula]

 Score =  320 bits (820), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 158/237 (66%), Positives = 187/237 (78%), Gaps = 21/237 (8%)

Query: 1   MENCFTFSPFKVAKVRMVQFSILSPDEI------RKMSVTEIDHGKTTERGMPMAGGLSD 54
           M+  F FSP +VAKVRMVQF ILSPDEI      R+M+V +I+HG+TTERG P  GGLSD
Sbjct: 1   MDIRFPFSPAEVAKVRMVQFGILSPDEIVIFSILRQMAVVQIEHGETTERGKPKIGGLSD 60

Query: 55  LRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILA 114
            RLGTID++ KCETC+++M ECPGHFG+LELAKPMFHIGF+KT+L+IMRCVCFNCSKILA
Sbjct: 61  PRLGTIDRKMKCETCTASMAECPGHFGYLELAKPMFHIGFLKTVLSIMRCVCFNCSKILA 120

Query: 115 DE------------EDDKFKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHD 162
           DE             D KFK A++I++PK RL +IL ACK K KCEGGD+ID   L  HD
Sbjct: 121 DEVLSRPFKPVLLINDHKFKQAMRIKNPKHRLRKILDACKNKTKCEGGDDID---LPEHD 177

Query: 163 GEEPLRKRKSGCGALQPTLTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219
            +EPL+K + GCGA QP +TI+GM MIAEYKAQRKK+DDQ QLPEPVERKQTL+AER
Sbjct: 178 TKEPLKKSRGGCGAQQPKITIEGMKMIAEYKAQRKKSDDQEQLPEPVERKQTLSAER 234

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242078217|ref|XP_002443877.1| hypothetical protein SORBIDRAFT_07g003680 [Sorghum bicolor] gi|241940227|gb|EES13372.1| hypothetical protein SORBIDRAFT_07g003680 [Sorghum bicolor]

 Score =  312 bits (800), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 147/219 (67%), Positives = 180/219 (82%), Gaps = 4/219 (1%)

Query: 1   MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTI 60
           M+  F +SP +VAKV +VQF ILSPDEIR+MSV +I+H +T ERG P  GGLSD RLGTI
Sbjct: 1   MDARFPYSPAEVAKVELVQFGILSPDEIRQMSVVQIEHAETMERGKPKPGGLSDPRLGTI 60

Query: 61  DKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDK 120
           D++ KCETC + M ECPGHFGHLELAKPMFHIGF+KT+L+IMRCVCFNCSKILADE++ K
Sbjct: 61  DRKIKCETCMAGMAECPGHFGHLELAKPMFHIGFIKTVLSIMRCVCFNCSKILADEDETK 120

Query: 121 FKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPT 180
           FK ALKIR+PK+RL++I  ACK+K  C GGD++DV      D +EP++KR  GCGA QP 
Sbjct: 121 FKQALKIRNPKNRLKRIYDACKSKKVCAGGDDLDVQE---QDTDEPVKKR-GGCGAQQPN 176

Query: 181 LTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219
           +T+DGM M+AE+KA +KK+DDQ QLPEPVERKQ L+AER
Sbjct: 177 ITVDGMKMVAEFKAPKKKSDDQDQLPEPVERKQILSAER 215

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

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	219
DICTYBASE|DDB_G0279193	1727	rpb1 "RNA polymerase II core s	0.940	0.119	0.476	5.5e-47
UNIPROTKB|Q6NX41	566	POLR2A "DNA-directed RNA polym	0.894	0.346	0.460	9.1e-45
UNIPROTKB|I3LJR4	1010	POLR2A "DNA-directed RNA polym	0.894	0.194	0.460	1e-43
UNIPROTKB|J9NW09	1789	POLR2A "DNA-directed RNA polym	0.894	0.109	0.460	3.1e-43
UNIPROTKB|F1PGS0	1969	POLR2A "DNA-directed RNA polym	0.894	0.099	0.460	3.6e-43
UNIPROTKB|G3MZY8	1970	POLR2A "DNA-directed RNA polym	0.894	0.099	0.460	3.6e-43
UNIPROTKB|P24928	1970	POLR2A "DNA-directed RNA polym	0.894	0.099	0.460	3.6e-43
MGI|MGI:98086	1970	Polr2a "polymerase (RNA) II (D	0.894	0.099	0.460	3.6e-43
RGD|1587326	1970	Polr2a "polymerase (RNA) II (D	0.894	0.099	0.460	3.6e-43
ZFIN|ZDB-GENE-041008-78	1965	polr2a "polymerase (RNA) II (D	0.894	0.099	0.443	1.1e-41

DICTYBASE|DDB_G0279193 rpb1 "RNA polymerase II core subunit" [Dictyostelium discoideum (taxid:44689)]

 Score = 506 (183.2 bits), Expect = 5.5e-47, P = 5.5e-47
 Identities = 103/216 (47%), Positives = 137/216 (63%)

Query:     5 FTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTIDKRF 64
             F  S  ++ KV+ VQF ILSPDEIR MSV  ++H +T E G P AGGL D  +GTIDK  
Sbjct:     5 FPPSSAELRKVKRVQFGILSPDEIRNMSVARVEHPETYENGKPKAGGLLDPAMGTIDKTQ 64

Query:    65 KCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLA 124
             +C+TCS  M ECPGHFGH+ELAKP+FHIGF+ T+L I+RCVC++CSK+L D  +  F+ A
Sbjct:    65 RCQTCSGTMAECPGHFGHIELAKPVFHIGFIDTVLKILRCVCYHCSKLLTDTNEHSFRQA 124

Query:   125 LKIRHPKSRLEQILCACKTKNKCE-GGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTI 183
             LKIR+ K RL  ++  CK K  C  GG+E +   L   D E     +  GCG + P +T 
Sbjct:   125 LKIRNQKHRLNAVVDCCKNKKVCAIGGEEEEEHDLSKTDEELDKPVKHGGCGNVLPKITK 184

Query:   184 DGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219
             + + +I E+K      D      E +E+K  L+AER
Sbjct:   185 EDLKIIVEFK---DVTD------ESIEKKSVLSAER 211

GO:0005634 "nucleus" evidence=IEA;IDA

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

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

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0046872 "metal ion binding" evidence=IEA

GO:0016779 "nucleotidyltransferase activity" evidence=IEA

GO:0016740 "transferase activity" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

UNIPROTKB|Q6NX41 POLR2A "DNA-directed RNA polymerase" [Homo sapiens (taxid:9606)]

 Score = 471 (170.9 bits), Expect = 9.1e-45, P = 9.1e-45
 Identities = 94/204 (46%), Positives = 130/204 (63%)

Query:    15 VRMVQFSILSPDEIRKMSVTE--IDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSN 72
             ++ VQF +LSPDE+++MSVTE  I + +TTE G P  GGL D R G I++  +C+TC+ N
Sbjct:    18 IKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGN 77

Query:    73 MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFK--LALKIRHP 130
             M ECPGHFGH+ELAKP+FH+GF+   + ++RCVCF CSK+L D  + K K  LA     P
Sbjct:    78 MTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQP 137

Query:   131 KSRLEQILCACKTKNKCEGGDEID-VLSLLGHDGEEPLRKRKS--GCGALQPTLTIDGMN 187
             K RL  +   CK KN CEGG+E+D    +   +G+E L K K   GCG  QP +   G+ 
Sbjct:   138 KKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLE 197

Query:   188 MIAEYKAQRKKNDDQGQLPEPVER 211
             + AE+K   + + ++  L  P ER
Sbjct:   198 LYAEWKHVNEDSQEKKILLSP-ER 220

GO:0003677 "DNA binding" evidence=IEA

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

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

UNIPROTKB|I3LJR4 POLR2A "DNA-directed RNA polymerase" [Sus scrofa (taxid:9823)]

 Score = 471 (170.9 bits), Expect = 1.0e-43, P = 1.0e-43
 Identities = 94/204 (46%), Positives = 130/204 (63%)

Query:    15 VRMVQFSILSPDEIRKMSVTE--IDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSN 72
             ++ VQF +LSPDE+++MSVTE  I + +TTE G P  GGL D R G I++  +C+TC+ N
Sbjct:    18 IKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGN 77

Query:    73 MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFK--LALKIRHP 130
             M ECPGHFGH+ELAKP+FH+GF+   + ++RCVCF CSK+L D  + K K  LA     P
Sbjct:    78 MTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQP 137

Query:   131 KSRLEQILCACKTKNKCEGGDEID-VLSLLGHDGEEPLRKRKS--GCGALQPTLTIDGMN 187
             K RL  +   CK KN CEGG+E+D    +   +G+E L K K   GCG  QP +   G+ 
Sbjct:   138 KKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLE 197

Query:   188 MIAEYKAQRKKNDDQGQLPEPVER 211
             + AE+K   + + ++  L  P ER
Sbjct:   198 LYAEWKHVNEDSQEKKILLSP-ER 220

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

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|J9NW09 POLR2A "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)]

 Score = 471 (170.9 bits), Expect = 3.1e-43, P = 3.1e-43
 Identities = 94/204 (46%), Positives = 130/204 (63%)

Query:    15 VRMVQFSILSPDEIRKMSVTE--IDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSN 72
             ++ VQF +LSPDE+++MSVTE  I + +TTE G P  GGL D R G I++  +C+TC+ N
Sbjct:    18 IKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGN 77

Query:    73 MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFK--LALKIRHP 130
             M ECPGHFGH+ELAKP+FH+GF+   + ++RCVCF CSK+L D  + K K  LA     P
Sbjct:    78 MTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQP 137

Query:   131 KSRLEQILCACKTKNKCEGGDEID-VLSLLGHDGEEPLRKRKS--GCGALQPTLTIDGMN 187
             K RL  +   CK KN CEGG+E+D    +   +G+E L K K   GCG  QP +   G+ 
Sbjct:   138 KKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLE 197

Query:   188 MIAEYKAQRKKNDDQGQLPEPVER 211
             + AE+K   + + ++  L  P ER
Sbjct:   198 LYAEWKHVNEDSQEKKILLSP-ER 220

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

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

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1PGS0 POLR2A "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)]

 Score = 471 (170.9 bits), Expect = 3.6e-43, P = 3.6e-43
 Identities = 94/204 (46%), Positives = 130/204 (63%)

Query:    15 VRMVQFSILSPDEIRKMSVTE--IDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSN 72
             ++ VQF +LSPDE+++MSVTE  I + +TTE G P  GGL D R G I++  +C+TC+ N
Sbjct:    18 IKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGN 77

Query:    73 MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFK--LALKIRHP 130
             M ECPGHFGH+ELAKP+FH+GF+   + ++RCVCF CSK+L D  + K K  LA     P
Sbjct:    78 MTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQP 137

Query:   131 KSRLEQILCACKTKNKCEGGDEID-VLSLLGHDGEEPLRKRKS--GCGALQPTLTIDGMN 187
             K RL  +   CK KN CEGG+E+D    +   +G+E L K K   GCG  QP +   G+ 
Sbjct:   138 KKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLE 197

Query:   188 MIAEYKAQRKKNDDQGQLPEPVER 211
             + AE+K   + + ++  L  P ER
Sbjct:   198 LYAEWKHVNEDSQEKKILLSP-ER 220

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

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

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|G3MZY8 POLR2A "DNA-directed RNA polymerase" [Bos taurus (taxid:9913)]

 Score = 471 (170.9 bits), Expect = 3.6e-43, P = 3.6e-43
 Identities = 94/204 (46%), Positives = 130/204 (63%)

Query:    15 VRMVQFSILSPDEIRKMSVTE--IDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSN 72
             ++ VQF +LSPDE+++MSVTE  I + +TTE G P  GGL D R G I++  +C+TC+ N
Sbjct:    18 IKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGN 77

Query:    73 MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFK--LALKIRHP 130
             M ECPGHFGH+ELAKP+FH+GF+   + ++RCVCF CSK+L D  + K K  LA     P
Sbjct:    78 MTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQP 137

Query:   131 KSRLEQILCACKTKNKCEGGDEID-VLSLLGHDGEEPLRKRKS--GCGALQPTLTIDGMN 187
             K RL  +   CK KN CEGG+E+D    +   +G+E L K K   GCG  QP +   G+ 
Sbjct:   138 KKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLE 197

Query:   188 MIAEYKAQRKKNDDQGQLPEPVER 211
             + AE+K   + + ++  L  P ER
Sbjct:   198 LYAEWKHVNEDSQEKKILLSP-ER 220

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

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

GO:0004672 "protein kinase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

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

UNIPROTKB|P24928 POLR2A "DNA-directed RNA polymerase II subunit RPB1" [Homo sapiens (taxid:9606)]

 Score = 471 (170.9 bits), Expect = 3.6e-43, P = 3.6e-43
 Identities = 94/204 (46%), Positives = 130/204 (63%)

Query:    15 VRMVQFSILSPDEIRKMSVTE--IDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSN 72
             ++ VQF +LSPDE+++MSVTE  I + +TTE G P  GGL D R G I++  +C+TC+ N
Sbjct:    18 IKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGN 77

Query:    73 MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFK--LALKIRHP 130
             M ECPGHFGH+ELAKP+FH+GF+   + ++RCVCF CSK+L D  + K K  LA     P
Sbjct:    78 MTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQP 137

Query:   131 KSRLEQILCACKTKNKCEGGDEID-VLSLLGHDGEEPLRKRKS--GCGALQPTLTIDGMN 187
             K RL  +   CK KN CEGG+E+D    +   +G+E L K K   GCG  QP +   G+ 
Sbjct:   138 KKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLE 197

Query:   188 MIAEYKAQRKKNDDQGQLPEPVER 211
             + AE+K   + + ++  L  P ER
Sbjct:   198 LYAEWKHVNEDSQEKKILLSP-ER 220

GO:0046872 "metal ion binding" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0003677 "DNA binding" evidence=NAS

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

GO:0006355 "regulation of transcription, DNA-dependent" evidence=NAS

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

GO:0005634 "nucleus" evidence=IDA;NAS

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

GO:0004672 "protein kinase activity" evidence=IDA

GO:0005730 "nucleolus" 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:0031625 "ubiquitin protein ligase binding" evidence=IPI

GO:0006468 "protein phosphorylation" evidence=IDA

MGI|MGI:98086 Polr2a "polymerase (RNA) II (DNA directed) polypeptide A" [Mus musculus (taxid:10090)]

 Score = 471 (170.9 bits), Expect = 3.6e-43, P = 3.6e-43
 Identities = 94/204 (46%), Positives = 130/204 (63%)

Query:    15 VRMVQFSILSPDEIRKMSVTE--IDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSN 72
             ++ VQF +LSPDE+++MSVTE  I + +TTE G P  GGL D R G I++  +C+TC+ N
Sbjct:    18 IKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGN 77

Query:    73 MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFK--LALKIRHP 130
             M ECPGHFGH+ELAKP+FH+GF+   + ++RCVCF CSK+L D  + K K  LA     P
Sbjct:    78 MTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQP 137

Query:   131 KSRLEQILCACKTKNKCEGGDEID-VLSLLGHDGEEPLRKRKS--GCGALQPTLTIDGMN 187
             K RL  +   CK KN CEGG+E+D    +   +G+E L K K   GCG  QP +   G+ 
Sbjct:   138 KKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLE 197

Query:   188 MIAEYKAQRKKNDDQGQLPEPVER 211
             + AE+K   + + ++  L  P ER
Sbjct:   198 LYAEWKHVNEDSQEKKILLSP-ER 220

GO:0003677 "DNA binding" evidence=IDA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO

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

GO:0005730 "nucleolus" 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:0031625 "ubiquitin protein ligase binding" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

RGD|1587326 Polr2a "polymerase (RNA) II (DNA directed) polypeptide A" [Rattus norvegicus (taxid:10116)]

 Score = 471 (170.9 bits), Expect = 3.6e-43, P = 3.6e-43
 Identities = 94/204 (46%), Positives = 130/204 (63%)

Query:    15 VRMVQFSILSPDEIRKMSVTE--IDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSN 72
             ++ VQF +LSPDE+++MSVTE  I + +TTE G P  GGL D R G I++  +C+TC+ N
Sbjct:    18 IKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGN 77

Query:    73 MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFK--LALKIRHP 130
             M ECPGHFGH+ELAKP+FH+GF+   + ++RCVCF CSK+L D  + K K  LA     P
Sbjct:    78 MTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQP 137

Query:   131 KSRLEQILCACKTKNKCEGGDEID-VLSLLGHDGEEPLRKRKS--GCGALQPTLTIDGMN 187
             K RL  +   CK KN CEGG+E+D    +   +G+E L K K   GCG  QP +   G+ 
Sbjct:   138 KKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLE 197

Query:   188 MIAEYKAQRKKNDDQGQLPEPVER 211
             + AE+K   + + ++  L  P ER
Sbjct:   198 LYAEWKHVNEDSQEKKILLSP-ER 220

GO:0003674 "molecular_function" evidence=ND

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

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

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

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=ISO

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

GO:0008150 "biological_process" evidence=ND

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

ZFIN|ZDB-GENE-041008-78 polr2a "polymerase (RNA) II (DNA directed) polypeptide A" [Danio rerio (taxid:7955)]

 Score = 457 (165.9 bits), Expect = 1.1e-41, P = 1.1e-41
 Identities = 90/203 (44%), Positives = 129/203 (63%)

Query:    15 VRMVQFSILSPDEIRKMSVTE--IDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSN 72
             ++ VQF +LSPDE+++MSVTE  I + +TTE G P  GGL D R G I++  +C+TC+ N
Sbjct:    16 IKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERSGRCQTCAGN 75

Query:    73 MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFK-LALKIR-HP 130
             M ECPGHFGH+ELAKP+FH+GF+  ++ ++RCVCF CSK+L D  + K K +  K +  P
Sbjct:    76 MTECPGHFGHIELAKPVFHVGFITKIMKVLRCVCFFCSKLLVDANNPKIKDILTKSKGQP 135

Query:   131 KSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKS--GCGALQPTLTIDGMNM 188
             + RL  +   CK KN CEGG+E+D    +     E + K K   GCG  QP +   G+ +
Sbjct:   136 RKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPESEDITKEKGHGGCGRYQPRIRRSGLEL 195

Query:   189 IAEYKAQRKKNDDQGQLPEPVER 211
              AE+K   + + ++  L  P ER
Sbjct:   196 YAEWKHVNEDSQEKKILLSP-ER 217

GO:0003677 "DNA binding" evidence=IEA

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

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

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

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

GO:0016740 "transferase activity" evidence=IEA

GO:0016779 "nucleotidyltransferase activity" 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

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

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.7	LOW CONFIDENCE prediction!
4th Layer	2.7.7.6	0.737

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	219
pfam04997	330	pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, do	3e-52
PRK08566	882	PRK08566, PRK08566, DNA-directed RNA polymerase su	9e-38
COG0086	808	COG0086, RpoC, DNA-directed RNA polymerase, beta'	3e-34
TIGR02390	867	TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer	7e-34
PRK14977	1321	PRK14977, PRK14977, bifunctional DNA-directed RNA	2e-28

>gnl|CDD|218370 pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, domain 1

 Score =  170 bits (434), Expect = 3e-52
 Identities = 77/178 (43%), Positives = 101/178 (56%), Gaps = 17/178 (9%)

Query: 14  KVRMVQFSILSPDEIRKMSVTEIDHGKTTERGM--PMAGGLSDLRLGTIDKRFKCETCSS 71
           K++ +QF I SP+EIRK SV E+   +T   G   P  GGL D R+GTI K+  CETC  
Sbjct: 3   KIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEPGGLLDERMGTIKKKSICETCGV 62

Query: 72  NMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEED----DKFKLALKI 127
            + ECPGHFGH+ELAKP+FHIGF K +L+I+RCVC  CS +L +E       K  +  K 
Sbjct: 63  EVTECPGHFGHIELAKPVFHIGFFKKILSILRCVCKLCSSLLLNESVKYFFLKVVIDPKG 122

Query: 128 RHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTIDG 185
           ++ K RL++I   CK K+ C    E                K   GCG  QP ++ DG
Sbjct: 123 KNSKKRLKKINNLCKKKSICSKCGED-----------NGGLKAFEGCGKYQPKISKDG 169

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, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand. Length = 330

>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated

 Score =  138 bits (351), Expect = 9e-38
 Identities = 53/141 (37%), Positives = 81/141 (57%), Gaps = 7/141 (4%)

Query: 14  KVRMVQFSILSPDEIRKMSVTEIDHGKT-TERGMPMAGGLSDLRLGTIDKRFKCETCSSN 72
           ++  ++F +LSP+EIRKMSVT+I    T  + G P+ GGL D RLG ID   +C+TC   
Sbjct: 8   RIGSIKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGR 67

Query: 73  MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEED-----DKFKLALKI 127
            GECPGHFGH+ELA+P+ H+GF K +  ++R  C  C ++   EE+     +K +   + 
Sbjct: 68  AGECPGHFGHIELARPVIHVGFAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLERLKEW 127

Query: 128 RHPKSRL-EQILCACKTKNKC 147
                 L +++      +  C
Sbjct: 128 GSLADDLIKEVKKEAAKRMVC 148

Length = 882

>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]

 Score =  128 bits (324), Expect = 3e-34
 Identities = 37/97 (38%), Positives = 56/97 (57%), Gaps = 3/97 (3%)

Query: 18  VQFSILSPDEIRKMSVTEIDHGKT-TERGMPMAGGLSDLRLGTIDKRFKCETCSSNMGEC 76
           ++F + SP+EIR     E+   +T   R  P  GGL D R+   DK ++C TC      C
Sbjct: 7   IKFGLASPEEIRS-WSGEVKKPETINYRTKPERGGLFDERIFGPDKDYEC-TCGKYKRIC 64

Query: 77  PGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKIL 113
           PG FGH+ELA P+ HI F K++ +++   C +C ++L
Sbjct: 65  PGGFGHIELAAPVAHIWFFKSIPSLLDMTCRDCERVL 101

Length = 808

>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'

 Score =  127 bits (321), Expect = 7e-34
 Identities = 51/106 (48%), Positives = 71/106 (66%), Gaps = 1/106 (0%)

Query: 14  KVRMVQFSILSPDEIRKMSVTEIDHGKTTER-GMPMAGGLSDLRLGTIDKRFKCETCSSN 72
           K+  ++F +LSP+EIRKMSV E+    T +  G P+ GGL D RLG I+   +C+TC   
Sbjct: 3   KIGSIKFGLLSPEEIRKMSVVEVVTADTYDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGK 62

Query: 73  MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEED 118
           +GECPGHFGH+ELA+P+ H+GF K +  I+R  C  C +I   EE+
Sbjct: 63  VGECPGHFGHIELARPVVHVGFAKEIYKILRATCRKCGRITLTEEE 108

This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. Length = 867

>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional

 Score =  111 bits (279), Expect = 2e-28
 Identities = 44/117 (37%), Positives = 67/117 (57%), Gaps = 1/117 (0%)

Query: 18  VQFSILSPDEIRKMSVTEIDHGKT-TERGMPMAGGLSDLRLGTIDKRFKCETCSSNMGEC 76
           + F ++SP + RK+   EI   +   E G+P+ GGL D RLGTI+   KC TC +    C
Sbjct: 12  IIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANC 71

Query: 77  PGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPKSR 133
           PGHFGH+ELA+P+ HI F+  +  ++   C  C+K+   +ED      ++  H  +R
Sbjct: 72  PGHFGHIELAEPVIHIAFIDNIKDLLNSTCHKCAKLKLPQEDLNVFKLIEEAHAAAR 128

Length = 1321

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	219
KOG0260	1605	consensus RNA polymerase II, large subunit [Transc	100.0
PRK08566	882	DNA-directed RNA polymerase subunit A'; Validated	100.0
TIGR02390	868	RNA_pol_rpoA1 DNA-directed RNA polymerase subunit	100.0
PRK14977	1321	bifunctional DNA-directed RNA polymerase A'/A'' su	100.0
PF04997	337	RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; Int	100.0
KOG0261	1386	consensus RNA polymerase III, large subunit [Trans	100.0
KOG0262	1640	consensus RNA polymerase I, large subunit [Transcr	99.97
COG0086	808	RpoC DNA-directed RNA polymerase, beta' subunit/16	99.94
TIGR02386	1140	rpoC_TIGR DNA-directed RNA polymerase, beta' subun	99.77
PRK00566	1156	DNA-directed RNA polymerase subunit beta'; Provisi	99.58
PRK02625	627	rpoC1 DNA-directed RNA polymerase subunit gamma; P	99.1
PRK14906	1460	DNA-directed RNA polymerase subunit beta'/alpha do	99.09
TIGR02387	619	rpoC1_cyan DNA-directed RNA polymerase, gamma subu	99.09
PRK14844	2836	bifunctional DNA-directed RNA polymerase subunit b	99.08
CHL00018	663	rpoC1 RNA polymerase beta' subunit	98.99
PRK09603	2890	bifunctional DNA-directed RNA polymerase subunit b	98.96

>KOG0260 consensus RNA polymerase II, large subunit [Transcription]

Probab=100.00  E-value=6e-50  Score=393.86  Aligned_cols=197  Identities=50%  Similarity=0.828  Sum_probs=178.2

Q ss_pred             CCCCCCCCccccceeeeEEEEeCCHHHHhcCcccEEecCccccCCCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcc
Q 045123            1 MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHF   80 (219)
Q Consensus         1 ~~~~~~~~~~~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHf   80 (219)
                      |+..+..+++++++|++||||++||+||++|||.+|..|++++.++|..|||.|||||++|+...|+||+.++.+|||||
T Consensus         1 m~~~~~~~~~pl~~v~~vqFgi~spdeir~mSV~~i~~~e~~e~~~pk~ggl~D~RlG~idr~~~CqTC~g~~~~CpGHF   80 (1605)
T KOG0260|consen    1 MGDDCEFSQAPLRTVKSVQFGILSPDEIRRMSVAEIEFPETMEGGRPKLGGLMDPRLGTIDRDSLCQTCGGNMFECPGHF   80 (1605)
T ss_pred             CCCCcccccCcceeeeEEEeeccChhhhhcceeEEeecccccccCCCCcCCccccccCCCCccchhhhhccccccCCccc
Confidence            78899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeecccceeeeeehhhhhhhhhhhcccccccccCccCHHHHHHHHhcC-chhHHHHHHHHhccccccCCCCcccccccC
Q 045123           81 GHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRH-PKSRLEQILCACKTKNKCEGGDEIDVLSLL  159 (219)
Q Consensus        81 GhIeL~~Pv~h~~f~~~i~~iL~~vC~~C~rll~~~~~~~~~~~~~~~~-~k~r~~~i~~~ck~~~~Ce~~~~~d~~~~~  159 (219)
                      |||+||+|||||+|+++|.+||+|||++|+++++++..+++.++++.+. ++.|+..||.+||++.+|+.+.+.+.+   
T Consensus        81 GhieLAkPvfH~gFl~kv~kiL~cVC~~C~ki~~~~~~~~~~~~~~~~~~~k~rl~~v~~vck~k~~ce~g~~~e~~---  157 (1605)
T KOG0260|consen   81 GHIELAKPVFHPGFLKKVKKILRCVCFYCSKILKDKFNPKEDQILRKRYCSKGRLLMVLDVCKGKVVCEGGIDVESD---  157 (1605)
T ss_pred             ceeeeccccccHHHHHHHHHHHHHhhhcchheeecccCcchhhhhhhhcCCcchHHHHHHhhccceeeecccccccc---
Confidence            9999999999999999999999999999999999998888878877666 999999999999999999875443322   


Q ss_pred             CCCCCCCCccCCCCCCCCCCeEEEeceEEEEEEccccccCCCCCCCCCCCCcccccCCCC
Q 045123          160 GHDGEEPLRKRKSGCGALQPTLTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER  219 (219)
Q Consensus       160 ~~~~~~~~~~~~~gCG~~qP~irk~glkl~~~~k~~~~~~~~~~~~~~~~~~k~~ltae~  219 (219)
                                .|+|||+.||.||+.|+++|++||.+.    ++.     +|+|+.|+|++
T Consensus       158 ----------g~sgcg~kqP~i~r~gl~l~a~~k~~~----e~~-----~e~k~~ls~e~  198 (1605)
T KOG0260|consen  158 ----------GRSGCGLKQPSIRRLGLDLWAFWKQGD----EDS-----QESKRKLSAER  198 (1605)
T ss_pred             ----------ccccccccCCceeccCchhhhhhhccC----ccC-----CcccccCcHHH
Confidence                      358999999999999999999998521    111     23588898864

>PRK08566 DNA-directed RNA polymerase subunit A'; Validated

Probab=100.00  E-value=1.5e-43  Score=353.60  Aligned_cols=154  Identities=36%  Similarity=0.735  Sum_probs=137.0

Q ss_pred             ccceeeeEEEEeCCHHHHhcCcccEEecCccccC-CCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcceeeecccce
Q 045123           11 KVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTER-GMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPM   89 (219)
Q Consensus        11 ~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~-~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~Pv   89 (219)
                      ..++|++|+|++||++||+++||++|+++++||. ++|++|||+|||||++++...|+|||++..+||||||||+|++||
T Consensus         5 ~~~~I~~I~F~~~S~eEI~klSv~~It~~~~~d~~g~P~~gGL~D~RLG~~~~~~~C~TCg~~~~~CPGHFGhIeL~~PV   84 (882)
T PRK08566          5 IPKRIGSIKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPV   84 (882)
T ss_pred             CceeeeeEEEecCCHHHHHHhCeEEEecccccCCCCCcCCCCCCCcccCCCCCCCCCCCCCCCCCcCCCcceEEeccccc
Confidence            3478999999999999999999999999999984 899999999999999999999999999999999999999999999


Q ss_pred             eeeeehhhhhhhhhhhcccccccccCccCHH-HHHHHHhcC-----chhHHHHHHHHhccccccCCCCcccccccCCCCC
Q 045123           90 FHIGFMKTLLTIMRCVCFNCSKILADEEDDK-FKLALKIRH-----PKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDG  163 (219)
Q Consensus        90 ~h~~f~~~i~~iL~~vC~~C~rll~~~~~~~-~~~~~~~~~-----~k~r~~~i~~~ck~~~~Ce~~~~~d~~~~~~~~~  163 (219)
                      |||+||+.|++||+|+|++|+||++++++.+ |...++..+     .+.+++++++.|+++.+|                
T Consensus        85 fhpgf~~~v~~iL~~iC~~C~rll~~~~~~~~~~~~l~~~~~~~~~~~~l~k~i~k~~k~~~~C----------------  148 (882)
T PRK08566         85 IHVGFAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLERLKEWGSLADDLIKEVKKEAAKRMVC----------------  148 (882)
T ss_pred             cchhHHHHHHHHHHHhhhhhCceeccccchHHHHHHHhchhhhhhhHHHHHHHHHHHhcCCCCC----------------
Confidence            9999999999999999999999999876543 433333211     235789999999999999                


Q ss_pred             CCCCccCCCCCCCCCCeEEEeceEE
Q 045123          164 EEPLRKRKSGCGALQPTLTIDGMNM  188 (219)
Q Consensus       164 ~~~~~~~~~gCG~~qP~irk~glkl  188 (219)
                              ++||+.||+|+++++..
T Consensus       149 --------~~Cg~~~~ki~~~~~~~  165 (882)
T PRK08566        149 --------PHCGEKQYKIKFEKPTT  165 (882)
T ss_pred             --------CCcCCCCceEEEeccee
Confidence                    68999999999997643

>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'

Probab=100.00  E-value=1.7e-42  Score=345.31  Aligned_cols=151  Identities=38%  Similarity=0.829  Sum_probs=134.6

Q ss_pred             ceeeeEEEEeCCHHHHhcCcccEEecCcccc-CCCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcceeeecccceee
Q 045123           13 AKVRMVQFSILSPDEIRKMSVTEIDHGKTTE-RGMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPMFH   91 (219)
Q Consensus        13 ~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~-~~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~Pv~h   91 (219)
                      ++|++|+|++||++||+++||++|+++++|| .|+|++|||||||||++++...|+|||++..+||||||||+|++||||
T Consensus         2 ~~I~~I~F~~~S~eEI~k~Sv~~It~~~~~d~~g~P~~gGL~D~RLG~~~~~~~C~TCg~~~~~CpGHFGhIeL~~PVfh   81 (868)
T TIGR02390         2 KKIGSIKFGLLSPEEIRKMSVVEVVTADTYDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVH   81 (868)
T ss_pred             ceeeEEEEeCCCHHHHHHhCeeEEecccccCCCCCcCCCCccCcccCCCCCCCCCCCCCCCCCcCCCcceEEeccccccc
Confidence            5799999999999999999999999999998 489999999999999999999999999999999999999999999999


Q ss_pred             eeehhhhhhhhhhhcccccccccCccC-HHHHHHHH-hcC----c-hhHHHHHHHHhccccccCCCCcccccccCCCCCC
Q 045123           92 IGFMKTLLTIMRCVCFNCSKILADEED-DKFKLALK-IRH----P-KSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGE  164 (219)
Q Consensus        92 ~~f~~~i~~iL~~vC~~C~rll~~~~~-~~~~~~~~-~~~----~-k~r~~~i~~~ck~~~~Ce~~~~~d~~~~~~~~~~  164 (219)
                      |+|++.|++||+|+|++|+||++++++ +.+...++ .++    + +.+++++++.|+++++|                 
T Consensus        82 pgf~~~i~kiL~~vC~~C~rll~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~i~~~~~~~~~C-----------------  144 (868)
T TIGR02390        82 VGFAKEIYKILRATCRKCGRITLTEEEIEQYLEKINKLKEEGGDLASTLIEKIVKEAAKRMKC-----------------  144 (868)
T ss_pred             hhHHHHHHHHHHHHhhhcCceeeCccccHHHHHHHHhcccchhhhHHHHHHHHHHHhhcCCCC-----------------
Confidence            999999999999999999999998754 33544433 222    1 45678899999988899                 


Q ss_pred             CCCccCCCCCCCCCCeEEEeceE
Q 045123          165 EPLRKRKSGCGALQPTLTIDGMN  187 (219)
Q Consensus       165 ~~~~~~~~gCG~~qP~irk~glk  187 (219)
                             ++||+.||+||++++.
T Consensus       145 -------~~Cg~~~p~ir~~~~~  160 (868)
T TIGR02390       145 -------PHCGEEQKKIKFEKPT  160 (868)
T ss_pred             -------CCCCCcCceEEEeeee
Confidence                   6899999999998743

This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.

>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional

Probab=100.00  E-value=4.1e-42  Score=351.90  Aligned_cols=156  Identities=33%  Similarity=0.691  Sum_probs=134.8

Q ss_pred             cccceeeeEEEEeCCHHHHhcCcccEEecCccccC-CCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcceeeecccc
Q 045123           10 FKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTER-GMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKP   88 (219)
Q Consensus        10 ~~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~-~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~P   88 (219)
                      .++++|++|+|++||+|||+++||++|+++++||. ++|++|||||||||++++...|.||++++.+||||||||+|++|
T Consensus         4 ~~~~~I~~I~Fg~~S~eeIrk~Sv~~It~~~~~d~~g~P~~gGl~DprlG~~d~~~~C~TCg~~~~~CpGHFGHIELa~P   83 (1321)
T PRK14977          4 LAVKAIDGIIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAEP   83 (1321)
T ss_pred             CccceeceEEEecCCHHHHHHhCeEEEecccccCCCCCcCCCCCCccccCCCCCCCCCCCCCCCCCcCCCeeEEEEccCC
Confidence            56789999999999999999999999999999985 79999999999999999999999999999999999999999999


Q ss_pred             eeeeeehhhhhhhhhhhcccccccccCccCHHHHHHHH-hc-----CchhHHH-----H----HHHHhccccccCCCCcc
Q 045123           89 MFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALK-IR-----HPKSRLE-----Q----ILCACKTKNKCEGGDEI  153 (219)
Q Consensus        89 v~h~~f~~~i~~iL~~vC~~C~rll~~~~~~~~~~~~~-~~-----~~k~r~~-----~----i~~~ck~~~~Ce~~~~~  153 (219)
                      ||||+||+.|++||+|+|++|+||++++++.++..+++ .+     ++++|+.     +    ++.+|++.++|      
T Consensus        84 VfHpgf~k~i~~iLr~iC~~C~rlll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~C------  157 (1321)
T PRK14977         84 VIHIAFIDNIKDLLNSTCHKCAKLKLPQEDLNVFKLIEEAHAAARDIPEKRIDDEIIEEVRDQVKVYAKKAKEC------  157 (1321)
T ss_pred             ceecccHHHHHHHHHHHHHHhchhhcCcccHHHHHHHHHHhhhcccchhhhhhHHHHHHHHhhhhhhhccCCcC------
Confidence            99999999999999999999999999987766433322 11     2334432     2    23458888899      


Q ss_pred             cccccCCCCCCCCCccCCCCCCCCCCeEEEeceEEE
Q 045123          154 DVLSLLGHDGEEPLRKRKSGCGALQPTLTIDGMNMI  189 (219)
Q Consensus       154 d~~~~~~~~~~~~~~~~~~gCG~~qP~irk~glkl~  189 (219)
                                        ++||+.||+|++++...+
T Consensus       158 ------------------~~C~~~~~~i~~~~~~~~  175 (1321)
T PRK14977        158 ------------------PHCGAPQHELEFEEPTIF  175 (1321)
T ss_pred             ------------------CCCCCCCCeEEEeeceee
Confidence                              689999999999875543

>PF04997 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; InterPro: IPR007080 RNA polymerases catalyse the DNA-dependent polymerisation of RNA

Probab=100.00  E-value=3.2e-42  Score=303.02  Aligned_cols=176  Identities=43%  Similarity=0.782  Sum_probs=138.1

Q ss_pred             ceeeeEEEEeCCHHHHhcCcccEEecCccccC--CCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcceeeeccccee
Q 045123           13 AKVRMVQFSILSPDEIRKMSVTEIDHGKTTER--GMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPMF   90 (219)
Q Consensus        13 ~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~Pv~   90 (219)
                      ++|++|+|++||++||++|||++|+++.+|+.  ++|+.|||||||||+.++...|+|||+++.+||||||||+|+.|||
T Consensus         2 ~~i~~i~f~~~s~~eI~~~Sv~~i~~~~~~~~~~~~p~~~Gl~d~rlG~~~~~~~C~tC~~~~~~CpGHfGhI~L~~PV~   81 (337)
T PF04997_consen    2 KKIKSIQFGIYSPEEIRKLSVKEITNPETFDNLTGKPIKGGLYDPRLGPIDKKQICSTCGLNYTECPGHFGHIELALPVY   81 (337)
T ss_dssp             EEEEEEEEEE--HHHHHHHEEEB--SSTSBCTSSSSCBSSSSSSSSSS-SSSSSTSSSSSSSSSSCCCSEEEEEEEEEEE
T ss_pred             CeeeEEEEEeCCHHHHHHhCcEEEechhhccCCCCCCccccccChhhcCCCcccccccccccccccCCceeEEEeCHHHH
Confidence            68999999999999999999999999999995  5999999999999999999999999999999999999999999999


Q ss_pred             eeeehhhhhhhhhhhcccccccccCccCHHHHH-HHH---hcCchhHHHHHHHHhccccccCCCCcccccccCCCCCCCC
Q 045123           91 HIGFMKTLLTIMRCVCFNCSKILADEEDDKFKL-ALK---IRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEP  166 (219)
Q Consensus        91 h~~f~~~i~~iL~~vC~~C~rll~~~~~~~~~~-~~~---~~~~k~r~~~i~~~ck~~~~Ce~~~~~d~~~~~~~~~~~~  166 (219)
                      ||+|++.+++||+++|++|+++++++.+..+.. .+.   ......+++.|++.|++...|......+...     ....
T Consensus        82 h~~f~~~i~~iL~~~C~~C~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~-----~~~~  156 (337)
T PF04997_consen   82 HPGFFKEIPKILRCICKKCSRLLLSEKEKYFYLKILLKLKKKKKKERLKIISKECKKKSICSHCKAINGKI-----KKVE  156 (337)
T ss_dssp             TCCCHHHHHHHHTTSCTTTSCTSTCCCCHTSCHHHCHCSHSSSHHHHHHHHHHHHHHTCSSTSTCC-SSS--------SS
T ss_pred             hhcccccceeeecccccccccccccccccccccccccccccccchhHHHHHHHhhhhhhhhcccccccccc-----cccc
Confidence            999999999999999999999999987653211 111   2345678999999999999996432211100     0000


Q ss_pred             CccCCCCCCCCCCeEEEec-eEEEEEEc
Q 045123          167 LRKRKSGCGALQPTLTIDG-MNMIAEYK  193 (219)
Q Consensus       167 ~~~~~~gCG~~qP~irk~g-lkl~~~~k  193 (219)
                      ......+|+..++.++++| ..+...|+
T Consensus       157 ~~~~~~~~~~~~~~~~~~~~~~i~~~i~  184 (337)
T PF04997_consen  157 KSKKCEGCGKKNPKIRKEGAEKIQEEIK  184 (337)
T ss_dssp             SEETSSSSSSBSCEEEEESHCCCCCHHH
T ss_pred             cchhcccccccCcccccchhhhcccccc
Confidence            0012368999999999998 55555554

Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which is a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_W 3QQC_A 1YNJ_D 1HQM_D 1YNN_D 1I6V_D 2GHO_D 2AUJ_D 1ZYR_D 1SMY_D ....

>KOG0261 consensus RNA polymerase III, large subunit [Transcription]

Probab=100.00  E-value=8.4e-36  Score=290.00  Aligned_cols=157  Identities=41%  Similarity=0.802  Sum_probs=141.7

Q ss_pred             ceeeeEEEEeCCHHHHhcCcccEEecCccccC--C-CCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcceeeecccce
Q 045123           13 AKVRMVQFSILSPDEIRKMSVTEIDHGKTTER--G-MPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPM   89 (219)
Q Consensus        13 ~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~-~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~Pv   89 (219)
                      .+|++|+|+++|++||++.|+++|.+..+|+.  + .|+++|++|||||++++...|.|||+++.+|+|||||+.|++||
T Consensus        11 kki~~i~F~~~s~~ei~~~a~v~v~~~~LY~~~~~~~P~~~G~LD~rMGvs~K~~~C~TCg~~la~C~GHfGy~~L~LPV   90 (1386)
T KOG0261|consen   11 KKIKHIQFSILSPEEIRQQAEVEVSSKDLYDISTQRAPLPNGPLDPRMGVSNKKDKCATCGEGLADCIGHFGYLKLALPV   90 (1386)
T ss_pred             ceeeeEeeccCCHHHHHhcceEEeeccchhhhhcccCCCcCCCcCcccCCCCCCCccchhccchhhcccccceEeeccee
Confidence            69999999999999999999999999999984  2 49999999999999999999999999999999999999999999


Q ss_pred             eeeeehhhhhhhhhhhcccccccccCccCHHHHHHHHhcCch-------hHHHHHHHHhccccccCCCCcccccccCCCC
Q 045123           90 FHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPK-------SRLEQILCACKTKNKCEGGDEIDVLSLLGHD  162 (219)
Q Consensus        90 ~h~~f~~~i~~iL~~vC~~C~rll~~~~~~~~~~~~~~~~~k-------~r~~~i~~~ck~~~~Ce~~~~~d~~~~~~~~  162 (219)
                      ||+|||+.+++||+|+|++|+.+|+++++.+. ...++++|.       ..+++|++.||+..+|               
T Consensus        91 FhiGyfk~ti~iLq~ICK~Cs~ilL~~~~k~~-fl~~lr~p~~~~l~k~~l~kri~~~CkK~~~C---------------  154 (1386)
T KOG0261|consen   91 FHIGYFKATIQILQCICKNCSSILLSEEDKRQ-FLKKLRNPGLDNLRKKALLKRIVAKCKKVNTC---------------  154 (1386)
T ss_pred             eeehhHHHHHHHHHHHHHhhhhhhcCHHHHHH-HHHHhhCCCCChHHHHHHHHHHHHHhhccccc---------------
Confidence            99999999999999999999999999765443 344677763       3479999999999999               


Q ss_pred             CCCCCccCCCCCCCCCCeEEEe--ceEEEEE-Ecc
Q 045123          163 GEEPLRKRKSGCGALQPTLTID--GMNMIAE-YKA  194 (219)
Q Consensus       163 ~~~~~~~~~~gCG~~qP~irk~--glkl~~~-~k~  194 (219)
                               .+||..|+.++|.  +|+|+++ |+-
T Consensus       155 ---------~hCg~~NG~VKK~~~~lkIiHd~~~~  180 (1386)
T KOG0261|consen  155 ---------SHCGALNGTVKKAAALLKIIHDRFKL  180 (1386)
T ss_pred             ---------cccCCcCceeeccccceeEeeehhhc
Confidence                     5799999999994  4899988 653

>KOG0262 consensus RNA polymerase I, large subunit [Transcription]

Probab=99.97  E-value=3.6e-31  Score=262.68  Aligned_cols=109  Identities=36%  Similarity=0.667  Sum_probs=101.6

Q ss_pred             cc-ceeeeEEEEeCCHHHHhcCcccEEecCccccC-CCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcceeeecccc
Q 045123           11 KV-AKVRMVQFSILSPDEIRKMSVTEIDHGKTTER-GMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKP   88 (219)
Q Consensus        11 ~~-~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~-~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~P   88 (219)
                      ++ +.+..|+|++|+++||+++||++|++|.++|+ |+|++|||||++||+.+....|.||++...+||||||||+|+.|
T Consensus         8 pv~~~~~~v~Fg~yt~~ei~klSv~kIt~p~~~D~lGhPi~GGLYDl~LGp~~~~~~C~TC~~~~~~CPGH~GHIeL~~p   87 (1640)
T KOG0262|consen    8 PVMSFQPSVSFGSYTDQEIRKLSVKKITNPITFDNLGHPIPGGLYDLALGPLDNSDVCSTCNQDELNCPGHMGHIELPVP   87 (1640)
T ss_pred             cccccccceeeeccCHHHHhhcceeEecCceeecccCCCCCCcccccccCCccchhhhhhhcchhhcCCCccCeeeeccc
Confidence            44 34555999999999999999999999999998 99999999999999888888999999999999999999999999


Q ss_pred             eeeeeehhhhhhhhhhhcccccccccCccCH
Q 045123           89 MFHIGFMKTLLTIMRCVCFNCSKILADEEDD  119 (219)
Q Consensus        89 v~h~~f~~~i~~iL~~vC~~C~rll~~~~~~  119 (219)
                      ||||+||+.++.+|++.|++|++|.+...+-
T Consensus        88 vynPlfF~~ly~lLr~sCl~Chhf~~k~~~v  118 (1640)
T KOG0262|consen   88 VYNPLFFDFLYNLLRGSCLFCHHFRCKNVDV  118 (1640)
T ss_pred             ccCHHHHHHHHHHHHHHHHhhhhcccCcHHH
Confidence            9999999999999999999999999987543

>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]

Probab=99.94  E-value=1.8e-28  Score=242.77  Aligned_cols=147  Identities=31%  Similarity=0.550  Sum_probs=119.3

Q ss_pred             eeeeEEEEeCCHHHHhcCcccEEecCccccC-CCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcceeeecccceeee
Q 045123           14 KVRMVQFSILSPDEIRKMSVTEIDHGKTTER-GMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPMFHI   92 (219)
Q Consensus        14 ~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~-~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~Pv~h~   92 (219)
                      .++ |+|+++||++|++ |+.||+.|++||. ++|..+||+|+|||..+++..| |||+....||||||||||+.||+|+
T Consensus         4 ~~~-i~~gl~sp~~ir~-~s~ev~~pet~~~~~~P~~~Gl~d~ri~~~~~~~~C-~Cg~~~~~~~~~~GhIeLa~Pv~hi   80 (808)
T COG0086           4 IFD-IKFGLASPEEIRS-WSGEVKKPETINYRTKPERGGLFDERIFGPDKDYEC-TCGKYKRICPGGFGHIELAAPVAHI   80 (808)
T ss_pred             cce-eEEecCCHHHHHh-cceEEcCccccCCCCcccCCCccchhhcCCCCCcee-cCCCCcCcCCCCceeEEeecceEEe
Confidence            344 9999999999999 5599999999996 5999999999999999999999 9999999999999999999999999


Q ss_pred             eehhhhhhhhhhhcccccccccCccCHHHHHHHHhcCchhHHHHHHHHhccccccCCCCcccccccCCCCCCCCCccCCC
Q 045123           93 GFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKS  172 (219)
Q Consensus        93 ~f~~~i~~iL~~vC~~C~rll~~~~~~~~~~~~~~~~~k~r~~~i~~~ck~~~~Ce~~~~~d~~~~~~~~~~~~~~~~~~  172 (219)
                      +|++.+.++|++.|..|+++++..   .+  .+. .   ..+.+.+-+.+....      .|              ...+
T Consensus        81 ~f~k~~~~~L~~~~~~~~~v~~~~---~~--~~~-~---~~l~~~~~~~~~~~~------~~--------------~~~~  131 (808)
T COG0086          81 WFFKSIPSLLDMTCRDCERVLYFE---AY--VVL-G---TDLEKIQLLNETEYV------YD--------------SFCA  131 (808)
T ss_pred             chhhccHHHHhhhHHhhhhhhhHh---HH--HHh-c---cchhhhcccchheee------cc--------------ccCC
Confidence            999999999999999999998882   12  111 1   233333333332220      00              1126


Q ss_pred             CCCCCCCeEEEeceEEEEEE
Q 045123          173 GCGALQPTLTIDGMNMIAEY  192 (219)
Q Consensus       173 gCG~~qP~irk~glkl~~~~  192 (219)
                      +||+.|++++++++.+..+.
T Consensus       132 ~~Ga~~~~~~~~~~~~~~~~  151 (808)
T COG0086         132 HCGAEAIKILLEKPDLETER  151 (808)
T ss_pred             CCCchhHHHHHhCcchhhhh
Confidence            89999999999998776655

>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form

Probab=99.77  E-value=3.4e-19  Score=180.61  Aligned_cols=105  Identities=30%  Similarity=0.473  Sum_probs=95.5

Q ss_pred             eEEEEeCCHHHHhcCcccEEecCccccCC--CCCCCCCccCCC-CCC--------------CCCcccCCCCCCCCccC--
Q 045123           17 MVQFSILSPDEIRKMSVTEIDHGKTTERG--MPMAGGLSDLRL-GTI--------------DKRFKCETCSSNMGECP--   77 (219)
Q Consensus        17 ~i~F~~~s~eeI~~~Sv~ei~~~~~~~~~--~p~~~Gl~D~rl-G~~--------------~~~~~C~TC~~~~~~Cp--   77 (219)
                      +|+++++|||+|++||+.||++|++++.+  +|..+||+|+|+ |+.              .+...|.+||..+..|+  
T Consensus         1 ~i~i~laSPe~I~~ws~geV~~petiny~t~kPe~~GLfcerIFGp~k~~ec~Cgkyk~~~~~~~~C~~Cgve~t~~~vr   80 (1140)
T TIGR02386         1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR   80 (1140)
T ss_pred             CeEEEecCHHHHHhhhceEEeccceecCCCCccCCCCcccchhcCCccCceeccccccccCcCCcCCCCCCCCcccchhh
Confidence            48999999999999999999999999964  999999999999 987              45678999999999998  


Q ss_pred             -Ccceeeecccceeeeeehhh-----------hhhhhhhhcccccccccCccCHHH
Q 045123           78 -GHFGHLELAKPMFHIGFMKT-----------LLTIMRCVCFNCSKILADEEDDKF  121 (219)
Q Consensus        78 -GHfGhIeL~~Pv~h~~f~~~-----------i~~iL~~vC~~C~rll~~~~~~~~  121 (219)
                       +|||||+|+.||+|++|++.           ..+.|+++|++|+.+.+++.++.+
T Consensus        81 r~rmGhI~La~Pv~Hiwy~k~~ps~~~~ll~~~~k~le~v~y~~~~~v~~~~~~~~  136 (1140)
T TIGR02386        81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKL  136 (1140)
T ss_pred             hhcccceeecCCceeehhcCCCchHHHHHhCCCHHHhhheeeccceEEeCCCCCch
Confidence             99999999999999999998           589999999999999888754433

Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain.

>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional

Probab=99.58  E-value=1.6e-15  Score=154.30  Aligned_cols=101  Identities=30%  Similarity=0.473  Sum_probs=88.2

Q ss_pred             eeeeEEEEeCCHHHHhcCcccEEecCccccC--CCCCCCCCccCCC-CCCCCCcccCCCCCCC------CccC-------
Q 045123           14 KVRMVQFSILSPDEIRKMSVTEIDHGKTTER--GMPMAGGLSDLRL-GTIDKRFKCETCSSNM------GECP-------   77 (219)
Q Consensus        14 ~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~~~~~C~TC~~~~------~~Cp-------   77 (219)
                      ++..|++++.|||+|++||+.||++|++.+.  .+|..+||+|.|+ |+. ++..| .||.-.      ..|+       
T Consensus         6 ~~~~i~i~laspe~I~~ws~GeV~~petinyrt~kPe~~GLfcerIFgp~-kd~eC-~Cgkyk~~~~~~~~C~~cgve~~   83 (1156)
T PRK00566          6 DFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPT-KDYEC-LCGKYKRVRYKGIICERCGVEVT   83 (1156)
T ss_pred             CcceEEEEccCHHHHHHhhcceEccccccccCCCccCCCCcccchhcCcc-cCcEE-eCccccccCcCCcCCCCCCceee
Confidence            6889999999999999999999999999884  5999999999999 654 46677 777422      3677       


Q ss_pred             ------Ccceeeecccceeeeeehh-----------hhhhhhhhhcccccccccCc
Q 045123           78 ------GHFGHLELAKPMFHIGFMK-----------TLLTIMRCVCFNCSKILADE  116 (219)
Q Consensus        78 ------GHfGhIeL~~Pv~h~~f~~-----------~i~~iL~~vC~~C~rll~~~  116 (219)
                            +|||||+|+.||.|++|++           ...+.|+++|++|+.+++++
T Consensus        84 ~~~vrr~rmGhI~La~Pv~Hiwy~k~~ps~i~~ll~~~~k~le~v~y~~~~~v~~~  139 (1156)
T PRK00566         84 RSKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDP  139 (1156)
T ss_pred             echhhhhhcceeeecCceeeeeecCCCchHHHHHhCCCHHHhhheeecceEEEeCC
Confidence                  9999999999999999999           44899999999999987765

>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional

Probab=99.10  E-value=7.8e-11  Score=113.76  Aligned_cols=86  Identities=26%  Similarity=0.496  Sum_probs=72.0

Q ss_pred             ceeeeEEEEeCCHHHHhcCc---------ccEEecCccccC--CCCCCCCCccCCC-CCCC--------------CCccc
Q 045123           13 AKVRMVQFSILSPDEIRKMS---------VTEIDHGKTTER--GMPMAGGLSDLRL-GTID--------------KRFKC   66 (219)
Q Consensus        13 ~~i~~i~F~~~s~eeI~~~S---------v~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~--------------~~~~C   66 (219)
                      .++..|+.++.|||+|++||         +.||++|++++.  .+|..+||++.|. |+..              +...|
T Consensus         7 ~~~~~i~I~laSPe~I~~Ws~r~lpng~i~GeV~kpeTinyrT~KPE~dGLFCerIFGP~k~~eC~CGkyk~~~~~~~~C   86 (627)
T PRK02625          7 NRFDYVKIGLASPERIRQWGQRTLPNGQVVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVC   86 (627)
T ss_pred             cccceEEEEecCHHHHHHHHHhhcCCCceeeEECCCcccccCCCCCCCCCEeechhcCCccCcEEeCCCccccCcCCcCC
Confidence            46788999999999999999         999999999884  6999999999997 8763              22357


Q ss_pred             CCCCCCCCcc---CCcceeeecccceeeeeehhhh
Q 045123           67 ETCSSNMGEC---PGHFGHLELAKPMFHIGFMKTL   98 (219)
Q Consensus        67 ~TC~~~~~~C---pGHfGhIeL~~Pv~h~~f~~~i   98 (219)
                      ..||....+-   .=.+|||+|+.||-|++|++.+
T Consensus        87 ~~CgvE~t~s~vRR~RMG~I~La~PV~HiWylk~~  121 (627)
T PRK02625         87 ERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGI  121 (627)
T ss_pred             CCCCcEecchhhhHhhcCceeecCCceEeeccCCC
Confidence            7887665433   4569999999999999999854

>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional

Probab=99.09  E-value=5.9e-11  Score=122.44  Aligned_cols=104  Identities=27%  Similarity=0.417  Sum_probs=80.6

Q ss_pred             cceeeeEEEEeCCHHHHhcCcccEEecCccccC--CCCCCCCCccCCC-CCCC--------------CCcccCCCCCCCC
Q 045123           12 VAKVRMVQFSILSPDEIRKMSVTEIDHGKTTER--GMPMAGGLSDLRL-GTID--------------KRFKCETCSSNMG   74 (219)
Q Consensus        12 ~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~--------------~~~~C~TC~~~~~   74 (219)
                      ...+..|+.++.||++|++||+.||++|++.+.  .+|..+||++.|. |+..              ++..|..||..+.
T Consensus         6 ~~~f~~i~I~lASPe~Ir~WS~GEV~kpeTINyrT~KPE~dGLFCerIFGP~kd~eC~CGKyk~~~~~g~~C~~CGVEvt   85 (1460)
T PRK14906          6 VTNFDALRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEVT   85 (1460)
T ss_pred             ccccceEEEEecCHHHHHhhhceeEcCccccccccCCCCCCCeeeceeccCccCcEEeCccccccCcCCeEcCCCCcEec
Confidence            347889999999999999999999999999885  5999999999998 8763              2335777776543


Q ss_pred             cc---CCcceeeecccceeeeeehhhhh-----------hhhhhhcccccccccC
Q 045123           75 EC---PGHFGHLELAKPMFHIGFMKTLL-----------TIMRCVCFNCSKILAD  115 (219)
Q Consensus        75 ~C---pGHfGhIeL~~Pv~h~~f~~~i~-----------~iL~~vC~~C~rll~~  115 (219)
                      .-   .=.||||+|+.||-|++|++.+.           +-|+.+.++=+.+.++
T Consensus        86 ~s~vRR~RMGhI~La~PV~HiWylk~~ps~i~~lL~~~~k~le~viYf~~~iv~~  140 (1460)
T PRK14906         86 RAKVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIITS  140 (1460)
T ss_pred             chHHHHHhcCcccccCcchhhhhccCCcHHHHHHhCCCHHHhhhhhccceeEEec
Confidence            22   45799999999999999998653           4445555544444443

>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit

Probab=99.09  E-value=8.7e-11  Score=113.30  Aligned_cols=84  Identities=25%  Similarity=0.469  Sum_probs=69.1

Q ss_pred             eeeEEEEeCCHHHHhcCc---------ccEEecCccccC--CCCCCCCCccCCC-CCCC--------------CCcccCC
Q 045123           15 VRMVQFSILSPDEIRKMS---------VTEIDHGKTTER--GMPMAGGLSDLRL-GTID--------------KRFKCET   68 (219)
Q Consensus        15 i~~i~F~~~s~eeI~~~S---------v~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~--------------~~~~C~T   68 (219)
                      +..|+.++.|||+|++||         +.||++|++++.  .+|..+||++.|. |+..              +...|..
T Consensus         2 ~~~i~I~laSPe~I~~Ws~r~lpng~i~GeV~kp~TinyrT~KPE~dGLFCerIFGP~k~~eC~CGkyk~~~~~~~~C~~   81 (619)
T TIGR02387         2 FDYVKITIASPERVMEWGQRTLPNGQVVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCER   81 (619)
T ss_pred             CceEEEEecCHHHHHHHHHhhCCCCceeeEECCCcccccCCCCCCCCCEeechhcCCCcCcEEeCCCccccCcCCcCCCC
Confidence            467999999999999999         999999999884  6999999999998 8764              2235667


Q ss_pred             CCCCCCcc---CCcceeeecccceeeeeehhhh
Q 045123           69 CSSNMGEC---PGHFGHLELAKPMFHIGFMKTL   98 (219)
Q Consensus        69 C~~~~~~C---pGHfGhIeL~~Pv~h~~f~~~i   98 (219)
                      ||....+-   .=.+|||+|+.||-|++|++.+
T Consensus        82 CgvE~t~s~vRR~RMG~I~La~PV~HiWylk~~  114 (619)
T TIGR02387        82 CGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGI  114 (619)
T ss_pred             CCCEEchhhhHHHhcCceeccCcceeeeecCCC
Confidence            76554332   4469999999999999999854

The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.

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

Probab=99.08  E-value=9.6e-11  Score=125.89  Aligned_cols=103  Identities=31%  Similarity=0.503  Sum_probs=83.0

Q ss_pred             ceeeeEEEEeCCHHHHhcCcccEEecCccccC--CCCCCCCCccCCC-CCCC--------------CCcccCCCCCCCCc
Q 045123           13 AKVRMVQFSILSPDEIRKMSVTEIDHGKTTER--GMPMAGGLSDLRL-GTID--------------KRFKCETCSSNMGE   75 (219)
Q Consensus        13 ~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~--------------~~~~C~TC~~~~~~   75 (219)
                      ..+..|+.++.||++|++||+.||++|++.+.  .+|..+||++.|. |+..              +...|..||..+..
T Consensus      1446 ~~~~~i~i~laSPe~I~~Ws~GeV~kpeTinyrt~kPE~dGLFcerIFGp~kd~eC~Cgkyk~~~~~g~~C~~Cgvevt~ 1525 (2836)
T PRK14844       1446 QSFNEVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVTS 1525 (2836)
T ss_pred             cccceEEEEecCHHHHHhhhceeECCcccccccCCCCCCCCeehhhhcCCCcCcEEecccccccccCCcCcCCCCcEeee
Confidence            57889999999999999999999999999985  5999999999995 9864              33578889877654


Q ss_pred             c---CCcceeeecccceeeeeehhhh-----------hhhhhhhcccccccccC
Q 045123           76 C---PGHFGHLELAKPMFHIGFMKTL-----------LTIMRCVCFNCSKILAD  115 (219)
Q Consensus        76 C---pGHfGhIeL~~Pv~h~~f~~~i-----------~~iL~~vC~~C~rll~~  115 (219)
                      .   .-.+|||+|+.||.|++|++.+           .+-|+.+.++=+.+.++
T Consensus      1526 s~vRR~RmGhI~La~PV~HiWy~k~~ps~i~~lL~~~~k~le~v~y~~~~~v~~ 1579 (2836)
T PRK14844       1526 SKVRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVID 1579 (2836)
T ss_pred             chhhHhhcCceeecCcceeeecccCCcHHHHHHhCCCHHHhhheeeeeeEEEec
Confidence            4   4789999999999999999855           34455555554444443

>CHL00018 rpoC1 RNA polymerase beta' subunit

Probab=98.99  E-value=3.6e-10  Score=109.98  Aligned_cols=87  Identities=26%  Similarity=0.420  Sum_probs=70.2

Q ss_pred             ceeeeEEEEeCCHHHHhcCcc---------cEEecCccccC--CCCCCCCCccCCC-CCCCC-----------------C
Q 045123           13 AKVRMVQFSILSPDEIRKMSV---------TEIDHGKTTER--GMPMAGGLSDLRL-GTIDK-----------------R   63 (219)
Q Consensus        13 ~~i~~i~F~~~s~eeI~~~Sv---------~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~~-----------------~   63 (219)
                      ..+..|+.++.||++|++||.         .||++|++++.  .+|..+||++.|. |+...                 .
T Consensus         5 ~~~~~i~I~laSPe~I~~Ws~r~lpng~ivGeV~kp~TinyrT~KPE~dGLFCErIFGP~k~~~C~CGkyk~~~~~~~~~   84 (663)
T CHL00018          5 YKHQQLRIGLASPQQIRAWAERILPNGEIVGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDEKEDP   84 (663)
T ss_pred             cCcCeEEEEecCHHHHHHHHHhhCCCCceeeEECCCccccccCCCCCCCCEeechhcCCCcCCEEeCCCccccCccccCC
Confidence            467889999999999999995         89999999884  6999999999998 88741                 1


Q ss_pred             cccCCCCCCCCcc---CCcceeeecccceeeeeehhhhh
Q 045123           64 FKCETCSSNMGEC---PGHFGHLELAKPMFHIGFMKTLL   99 (219)
Q Consensus        64 ~~C~TC~~~~~~C---pGHfGhIeL~~Pv~h~~f~~~i~   99 (219)
                      ..|..||....+-   .=.+|||+|+.||-|++|++.+.
T Consensus        85 ~~C~~CgVE~t~s~vRR~RMG~I~La~PV~HiWylk~~p  123 (663)
T CHL00018         85 KFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLP  123 (663)
T ss_pred             CccCCcCCEechhhhhHhhcCceeecCcceeehhhcCCc
Confidence            2566666544322   34689999999999999998553

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

Probab=98.96  E-value=4.6e-10  Score=121.14  Aligned_cols=88  Identities=27%  Similarity=0.498  Sum_probs=72.7

Q ss_pred             ccceeeeEEEEeCCHHHHhcCcccEEecCccccC--CCCCCCCCccCCC-CCCC--------------CCc-ccCCCCCC
Q 045123           11 KVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTER--GMPMAGGLSDLRL-GTID--------------KRF-KCETCSSN   72 (219)
Q Consensus        11 ~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~--------------~~~-~C~TC~~~   72 (219)
                      ....+..|+.++.||++|++||+.||++|++.+.  .+|..+||++.|. |+..              ++. .|..||..
T Consensus      1392 ~~~~~~~i~i~lASpe~I~~ws~GeV~kpeTinyrt~kPe~dGLFcerIFGp~kd~eC~Cgkyk~~~~~g~~~C~~Cgve 1471 (2890)
T PRK09603       1392 RPKDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIGTCEKCGVA 1471 (2890)
T ss_pred             cccCcceEEEEecCHHHHHHhhceeEccccccccccCccCCCCEeeceeccCccCcEEeCCCcccccCCCCEEcCCCCcE
Confidence            4467889999999999999999999999999885  5999999999997 8753              112 47777765


Q ss_pred             CCcc---CCcceeeecccceeeeeehhhh
Q 045123           73 MGEC---PGHFGHLELAKPMFHIGFMKTL   98 (219)
Q Consensus        73 ~~~C---pGHfGhIeL~~Pv~h~~f~~~i   98 (219)
                      ...-   .-.+|||+|+.||.|++|++.+
T Consensus      1472 vt~s~vRR~RmGhI~La~Pv~HiWy~k~~ 1500 (2890)
T PRK09603       1472 ITHSKVRRFRMGHIELATPVAHIWYVNSL 1500 (2890)
T ss_pred             echhHhHHHhcCceeecCcceeeeccCCC
Confidence            4322   4579999999999999999855

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	219
3h0g_A	1752	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		2e-44
1i3q_A	1733	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		3e-38
4a3c_A	1732	Rna Polymerase Ii Initial Transcribing Complex With		3e-38
3j0k_A	1455	Orientation Of Rna Polymerase Ii Within The Human V		3e-38
3qqc_A	436	Crystal Structure Of Archaeal Spt45 BOUND TO THE RN		1e-26
2waq_A	880	The Complete Structure Of The Archaeal 13-Subunit D		4e-24
2pmz_A	880	Archaeal Rna Polymerase From Sulfolobus Solfataricu		1e-23

>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1752

Iteration: 1
 Score =  174 bits (442), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 92/210 (43%), Positives = 123/210 (58%), Gaps = 20/210 (9%)
Query: 7   FSPFKVA--KVRMVQFSILSPDEIRKMSVTEIDHGKTTERG--MPMAGGLSDLRLGTIDK 62
           FSP  V   +V  VQF ILSP+EIR MSV +I+  +T +     P  GGL D RLGTID+
Sbjct: 6   FSPSSVPLRRVEEVQFGILSPEEIRSMSVAKIEFPETMDESGQRPRVGGLLDPRLGTIDR 65
Query: 63  RFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFK 122
           +FKC+TC   M +CPGHFGH+ELAKP+FHIGF+  +  I+ CVC+NC K+  D  + KF 
Sbjct: 66  QFKCQTCGETMADCPGHFGHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPKFN 125
Query: 123 LALKIRHPKSRLEQILCACKTKNKCE-----GGDEIDVLSLLGHDGEEPLRKRKSGCGAL 177
              + R PK+RL  +   CKTK  C+     G D  D+ +   + G         GCGA 
Sbjct: 126 DTQRYRDPKNRLNAVWNVCKTKMVCDTGLSAGSDNFDLSNPSANMGH-------GGCGAA 178
Query: 178 QPTLTIDGMNMIAEYKAQRKKNDDQGQLPE 207
           QPT+  DG+ +   +    K+  D+  LPE
Sbjct: 179 QPTIRKDGLRLWGSW----KRGKDESDLPE 204

>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1733

Iteration: 1
 Score =  154 bits (390), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 81/196 (41%), Positives = 113/196 (57%), Gaps = 10/196 (5%)
Query: 7   FSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMA--GGLSDLRLGTIDKRF 64
           +S   +  V+ VQF + SP+E+R +SV +I   +T +     A  GGL+D RLG+ID+  
Sbjct: 6   YSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNL 65
Query: 65  KCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLA 124
           KC+TC   M ECPGHFGH++LAKP+FH+GF+  +  +  CVC +C K+L DE ++  + A
Sbjct: 66  KCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQA 125
Query: 125 LKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTID 184
           L I+  K R   I   CKTK  C    E DV S    D    L  R  GCG  QPT+  D
Sbjct: 126 LAIKDSKKRFAAIWTLCKTKMVC----ETDVPS---EDDPTQLVSR-GGCGNTQPTIRKD 177
Query: 185 GMNMIAEYKAQRKKND 200
           G+ ++  +K  R   D
Sbjct: 178 GLKLVGSWKKDRATGD 193

>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt Dna-Rna Hybrid Length = 1732

Iteration: 1
 Score =  154 bits (390), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 81/196 (41%), Positives = 113/196 (57%), Gaps = 10/196 (5%)
Query: 7   FSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMA--GGLSDLRLGTIDKRF 64
           +S   +  V+ VQF + SP+E+R +SV +I   +T +     A  GGL+D RLG+ID+  
Sbjct: 6   YSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNL 65
Query: 65  KCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLA 124
           KC+TC   M ECPGHFGH++LAKP+FH+GF+  +  +  CVC +C K+L DE ++  + A
Sbjct: 66  KCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQA 125
Query: 125 LKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTID 184
           L I+  K R   I   CKTK  C    E DV S    D    L  R  GCG  QPT+  D
Sbjct: 126 LAIKDSKKRFAAIWTLCKTKMVC----ETDVPS---EDDPTQLVSR-GGCGNTQPTIRKD 177
Query: 185 GMNMIAEYKAQRKKND 200
           G+ ++  +K  R   D
Sbjct: 178 GLKLVGSWKKDRATGD 193

>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human Vp16-Mediator-Pol Ii-Tfiif Assembly Length = 1455

Iteration: 1
 Score =  154 bits (390), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 81/196 (41%), Positives = 113/196 (57%), Gaps = 10/196 (5%)
Query: 7   FSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMA--GGLSDLRLGTIDKRF 64
           +S   +  V+ VQF + SP+E+R +SV +I   +T +     A  GGL+D RLG+ID+  
Sbjct: 6   YSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNL 65
Query: 65  KCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLA 124
           KC+TC   M ECPGHFGH++LAKP+FH+GF+  +  +  CVC +C K+L DE ++  + A
Sbjct: 66  KCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQA 125
Query: 125 LKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTID 184
           L I+  K R   I   CKTK  C    E DV S    D    L  R  GCG  QPT+  D
Sbjct: 126 LAIKDSKKRFAAIWTLCKTKMVC----ETDVPS---EDDPTQLVSR-GGCGNTQPTIRKD 177
Query: 185 GMNMIAEYKAQRKKND 200
           G+ ++  +K  R   D
Sbjct: 178 GLKLVGSWKKDRATGD 193

>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP CLAMP DOMAIN Length = 436

Iteration: 1
 Score =  115 bits (289), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 57/132 (43%), Positives = 82/132 (62%), Gaps = 3/132 (2%)
Query: 18  VQFSILSPDEIRKMSVTEIDHGKTTER-GMPMAGGLSDLRLGTIDKRFKCETCSSNMGEC 76
           ++F ILSP EIRKMS  E+    T +  G P+ GG+ D R+G ID   +CETC    GEC
Sbjct: 72  IEFGILSPQEIRKMSAVEVTVPDTYDDDGYPIEGGVMDKRMGVIDPGLRCETCGGRAGEC 131
Query: 77  PGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKI-LADEEDDKFKLALKI-RHPKSRL 134
           PGHFGH+ELA+P+ H+GF KT+  I+   C  C +I L DEE +++   +++ R+ +S  
Sbjct: 132 PGHFGHIELARPVIHVGFAKTIYRILESTCRECGRIKLTDEEIEEYMKKIELARNRRSEF 191
Query: 135 EQILCACKTKNK 146
            +I+     K K
Sbjct: 192 NEIIKEIHKKAK 203

>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 880

Iteration: 1
 Score =  107 bits (268), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 66/209 (31%), Positives = 103/209 (49%), Gaps = 25/209 (11%)
Query: 15  VRMVQFSILSPDEIRKMSVTEIDHGKT-TERGMPMAGGLSDLRLGTIDKRFKCETCSSNM 73
           ++ ++F ILSPDEIRKMSVT I       E G P+ G + D RLG I+   KC TC + +
Sbjct: 6   IKGIKFGILSPDEIRKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCGNTL 65
Query: 74  GECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKI-LADEEDDKFKL---ALKIRH 129
           G CPGHFGH+EL +P+ H+GF+K +   ++  C  C ++ ++++E +K+     A+K R 
Sbjct: 66  GNCPGHFGHIELVRPVIHVGFVKHVYEFLKATCRRCGRVKISEDEIEKYSRIYNAIKKRW 125
Query: 130 PKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLR-----------KRKSGCGALQ 178
           P +         KT  K +         +  H GE+  +           +RK G   L 
Sbjct: 126 PSAARRLTEYVKKTAMKAQ---------VCPHCGEKQFKIKLEKPYNFYEERKEGVAKLT 176
Query: 179 PTLTIDGMNMIAEYKAQRKKNDDQGQLPE 207
           P+   + +  + E   +    D     PE
Sbjct: 177 PSDIRERLEKVPESDVEILGYDPTTSRPE 205

>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 880

Iteration: 1
 Score =  105 bits (263), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 50/123 (40%), Positives = 77/123 (62%), Gaps = 5/123 (4%)
Query: 15  VRMVQFSILSPDEIRKMSVTEIDHGKT-TERGMPMAGGLSDLRLGTIDKRFKCETCSSNM 73
           ++ ++F ILSPDEIRKMSVT I       E G P+ G + D RLG I+   KC TC + +
Sbjct: 6   IKGIKFGILSPDEIRKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCGNTL 65
Query: 74  GECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKI-LADEEDDKFKL---ALKIRH 129
           G CPGHFGH+EL +P+ H+G +K +   ++  C  C ++ ++++E +K+     A+K R 
Sbjct: 66  GNCPGHFGHIELVRPVIHVGLVKHIYEFLKATCRRCGRVKISEDEIEKYSRIYNAIKKRW 125
Query: 130 PKS 132
           P +
Sbjct: 126 PSA 128

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	219
3qqc_A	436	DNA-directed RNA polymerase subunit B, DNA-direct	2e-66
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	5e-66
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	1e-63
4ayb_A	880	DNA-directed RNA polymerase; transferase, multi-su	1e-48
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-04

>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase subunit A', DNA-directed...; transcription, fusion protein, chimera protein, multiprotein; 3.30A {Pyrococcus furiosus} Length = 436

 Score =  209 bits (535), Expect = 2e-66
 Identities = 65/203 (32%), Positives = 96/203 (47%), Gaps = 24/203 (11%)

Query: 14  KVRMVQFSILSPDEIRKMSVTEIDHGKT-TERGMPMAGGLSDLRLGTIDKRFKCETCSSN 72
            +  ++F ILSP EIRKMS  E+    T  + G P+ GG+ D R+G ID   +CETC   
Sbjct: 68  VIGSIEFGILSPQEIRKMSAVEVTVPDTYDDDGYPIEGGVMDKRMGVIDPGLRCETCGGR 127

Query: 73  MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKF--KLALKIRHP 130
            GECPGHFGH+ELA+P+ H+GF KT+  I+   C  C +I   +E+ +   K     R+ 
Sbjct: 128 AGECPGHFGHIELARPVIHVGFAKTIYRILESTCRECGRIKLTDEEIEEYMKKIELARNR 187

Query: 131 KSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTIDGMNMIA 190
           +S   +I+     K K                     R     CGA Q  +  +   +  
Sbjct: 188 RSEFNEIIKEIHKKAKE--------------------RMVCPHCGAPQYPIKFEKPTIYW 227

Query: 191 EYKAQRKKNDDQGQL-PEPVERK 212
           E +   + N+ + +L P  V   
Sbjct: 228 EIRKDEQGNEYRHRLMPTEVRDW 250

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score =  219 bits (558), Expect = 5e-66
 Identities = 84/202 (41%), Positives = 117/202 (57%), Gaps = 4/202 (1%)

Query: 5   FTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTE--RGMPMAGGLSDLRLGTIDK 62
           F+ S   + +V  VQF ILSP+EIR MSV +I+  +T +     P  GGL D RLGTID+
Sbjct: 6   FSPSSVPLRRVEEVQFGILSPEEIRSMSVAKIEFPETMDESGQRPRVGGLLDPRLGTIDR 65

Query: 63  RFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFK 122
           +FKC+TC   M +CPGHFGH+ELAKP+FHIGF+  +  I+ CVC+NC K+  D  + KF 
Sbjct: 66  QFKCQTCGETMADCPGHFGHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPKFN 125

Query: 123 LALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLT 182
              + R PK+RL  +   CKTK  C+ G      +               GCGA QPT+ 
Sbjct: 126 DTQRYRDPKNRLNAVWNVCKTKMVCDTGLSAGSDN--FDLSNPSANMGHGGCGAAQPTIR 183

Query: 183 IDGMNMIAEYKAQRKKNDDQGQ 204
            DG+ +   +K  + ++D   +
Sbjct: 184 KDGLRLWGSWKRGKDESDLPEK 205

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score =  212 bits (541), Expect = 1e-63
 Identities = 76/216 (35%), Positives = 113/216 (52%), Gaps = 16/216 (7%)

Query: 6   TFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKT--TERGMPMAGGLSDLRLGTIDKR 63
            +S   +  V+ VQF + SP+E+R +SV +I   +T    +     GGL+D RLG+ID+ 
Sbjct: 5   QYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRN 64

Query: 64  FKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKL 123
            KC+TC   M ECPGHFGH++LAKP+FH+GF+  +  +  CVC +C K+L DE ++  + 
Sbjct: 65  LKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQ 124

Query: 124 ALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTI 183
           AL I+  K R   I   CKTK  CE             + +      + GCG  QPT+  
Sbjct: 125 ALAIKDSKKRFAAIWTLCKTKMVCETDVP--------SEDDPTQLVSRGGCGNTQPTIRK 176

Query: 184 DGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219
           DG+ ++  +K  R   D            + L+ E 
Sbjct: 177 DGLKLVGSWKKDRATGDADE------PELRVLSTEE 206

>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Length = 880

 Score =  169 bits (429), Expect = 1e-48
 Identities = 52/186 (27%), Positives = 82/186 (44%), Gaps = 18/186 (9%)

Query: 14  KVRMVQFSILSPDEIRKMSVTEIDHGKT-TERGMPMAGGLSDLRLGTIDKRFKCETCSSN 72
            ++ ++F ILSPDEIRKMSVT I       E G P+ G + D RLG I+   KC TC + 
Sbjct: 5   NIKGIKFGILSPDEIRKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCGNT 64

Query: 73  MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPKS 132
           +G CPGHFGH+EL +P+ H+GF+K +   ++  C  C ++   E++ +    +     K 
Sbjct: 65  LGNCPGHFGHIELVRPVIHVGFVKHVYEFLKATCRRCGRVKISEDEIEKYSRIYNAIKKR 124

Query: 133 RLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTIDGMNMIAEY 192
                    +   K                      +    CG  Q  + ++      E 
Sbjct: 125 WPSAARRLTEYVKKTAMK-----------------AQVCPHCGEKQFKIKLEKPYNFYEE 167

Query: 193 KAQRKK 198
           + +   
Sbjct: 168 RKEGVA 173

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 40.6 bits (94), Expect = 3e-04
 Identities = 25/115 (21%), Positives = 39/115 (33%), Gaps = 18/115 (15%)

Query: 82  HLELAKPMFHI------GFMKTLLTIMRCVCFNCSKILADEEDDKFKLAL-KIRHPKSRL 134
            L   +P  ++      G  KT + +   VC +  K+    +   F L L     P++ L
Sbjct: 143 ALLELRPAKNVLIDGVLGSGKTWVALD--VCLS-YKVQCKMDFKIFWLNLKNCNSPETVL 199

Query: 135 EQI--LCACKTKNKCEGGDEIDVLSLLGHDGEEPLR---KRKSGCGALQPTLTID 184
           E +  L      N     D    + L  H  +  LR   K K     L   L + 
Sbjct: 200 EMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL---LVLL 251

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 40.2 bits (93), Expect = 4e-04
 Identities = 33/219 (15%), Positives = 64/219 (29%), Gaps = 59/219 (26%)

Query: 11  KVAKVRMVQFSILSPDEIRKM----SVTEID------------HGKTTERGMPMAGGLSD 54
           K+  +     ++L P E RKM    SV                        M +   L  
Sbjct: 354 KLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHK 413

Query: 55  LRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFM-KTLLT---IMRCVCFNCS 110
             L  ++K+ K  T S           +LEL   + +   + ++++    I +    +  
Sbjct: 414 YSL--VEKQPKESTISI-------PSIYLELKVKLENEYALHRSIVDHYNIPKTFDSD-- 462

Query: 111 KILADEEDDKF--KLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLR 168
            ++    D  F   +     H K                E  + + +  ++  D     R
Sbjct: 463 DLIPPYLDQYFYSHIG---HHLK--------------NIEHPERMTLFRMVFLD----FR 501

Query: 169 ----K-RKSGCGALQPTLTIDGMNMIAEYKAQRKKNDDQ 202
               K R            ++ +  +  YK     ND +
Sbjct: 502 FLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPK 540

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 39.5 bits (91), Expect = 7e-04
 Identities = 28/158 (17%), Positives = 47/158 (29%), Gaps = 36/158 (22%)

Query: 79  HFGHLELAKPMFHIGFMKTLLTIMRCVC--FNCS-------KILADEEDDKFKLALKIRH 129
           H  H++         +   L          F+C         IL+ EE D     +  + 
Sbjct: 3   HHHHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHI---IMSKD 59

Query: 130 PKSRLEQILCACKTKNK------CEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTI 183
             S   ++     +K +       E    I+   L+      P++         QP++  
Sbjct: 60  AVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLM-----SPIKTE-----QRQPSMMT 109

Query: 184 DGMNMIAEYKAQRKK--NDDQGQLPEPVERKQTLTAER 219
                   Y  QR +  ND+Q      V R Q     R
Sbjct: 110 R------MYIEQRDRLYNDNQVFAKYNVSRLQPYLKLR 141

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	219
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	100.0
3qqc_A	436	DNA-directed RNA polymerase subunit B, DNA-direct	100.0
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	100.0
4ayb_A	880	DNA-directed RNA polymerase; transferase, multi-su	100.0
1hqm_D	1265	DNA-directed RNA polymerase; transferase, transcri	99.91
3lu0_D	1407	DNA-directed RNA polymerase subunit beta'; E. coli	99.58
2a6h_D	1524	DNA-directed RNA polymerase beta' chain; RNA polym	99.45

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=100.00  E-value=2.7e-53  Score=441.83  Aligned_cols=207  Identities=42%  Similarity=0.780  Sum_probs=178.1

Q ss_pred             CCCCCCccccceeeeEEEEeCCHHHHhcCcccEEecCccccC--CCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcc
Q 045123            3 NCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTER--GMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHF   80 (219)
Q Consensus         3 ~~~~~~~~~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHf   80 (219)
                      ..|++|+++.++|++|+|++||+|||+++||++|+++++||.  ++|+.|||+|||||++++...|.|||+++.+|||||
T Consensus         4 ~~~~~s~~~~~~i~~i~Fg~~S~eeI~~~Sv~~I~~~~~~d~~~~~P~~~Gl~D~rlG~~~~~~~C~TCg~~~~~CpGHF   83 (1752)
T 3h0g_A            4 IQFSPSSVPLRRVEEVQFGILSPEEIRSMSVAKIEFPETMDESGQRPRVGGLLDPRLGTIDRQFKCQTCGETMADCPGHF   83 (1752)
T ss_dssp             CSSCCCSSCCCCCCCBEECCCCHHHHHHHCCCCCCCTTCTTCSSSSSCCSSSSSSSCCCSSSSCCCTTSCCSSSSCCCCC
T ss_pred             ccCCCCcCcceeeeeEEEecCCHHHHHHhCeeEEecccccccccCCCCCCCCcCccccCCCCCCCCCCCCCCCCcCCCcc
Confidence            478999999999999999999999999999999999999996  499999999999999999999999999999999999


Q ss_pred             eeeecccceeeeeehhhhhhhhhhhcccccccccCccCHHHHHHHHhcCchhHHHHHHHHhccccccCCCCcccccccCC
Q 045123           81 GHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLG  160 (219)
Q Consensus        81 GhIeL~~Pv~h~~f~~~i~~iL~~vC~~C~rll~~~~~~~~~~~~~~~~~k~r~~~i~~~ck~~~~Ce~~~~~d~~~~~~  160 (219)
                      |||||++||||||||+.|++||+|+|++|+||++++++++|+.+++++++++||++||++||++++|+.+...++++ +.
T Consensus        84 GHIELa~PVfHpgF~~~I~kILr~vC~~C~klll~~~~~~f~~~lrlrd~k~r~~~V~~~ck~k~~Ce~~~~~~~~~-~~  162 (1752)
T 3h0g_A           84 GHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPKFNDTQRYRDPKNRLNAVWNVCKTKMVCDTGLSAGSDN-FD  162 (1752)
T ss_dssp             EECCCCSCBCCHHHHHHHHHHSSSSCTTTCCCSCCSCSHHHHHHHHSSCTTTTHHHHHHHHHHCCCCCSSTTCCSSC-CC
T ss_pred             eeeecccceEeehhhHHHHHHHHHHHHHhcccccccccHHHHHHHHccCHHHHHHHHHHHhccccccCCCCcccccc-hh
Confidence            99999999999999999999999999999999999988999999999999999999999999999998643322111 00


Q ss_pred             CCCCCCCccCCCCCCCCCCeEEEeceEEEEEEccccccCCCCCCCCCCCCcccccCCCC
Q 045123          161 HDGEEPLRKRKSGCGALQPTLTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER  219 (219)
Q Consensus       161 ~~~~~~~~~~~~gCG~~qP~irk~glkl~~~~k~~~~~~~~~~~~~~~~~~k~~ltae~  219 (219)
                       .........|+|||+.||+|||+|++|+++|+..+++  +++  +    +++.|||++
T Consensus       163 -~~~~~~~~~~~gCG~~qP~IRKeglkl~~~~k~~k~~--~~~--~----~k~~LtP~e  212 (1752)
T 3h0g_A          163 -LSNPSANMGHGGCGAAQPTIRKDGLRLWGSWKRGKDE--SDL--P----EKRLLSPLE  212 (1752)
T ss_dssp             -SSCCCCCCSSCSSCCCCCCCEEETTEEECCBCCSSSS--CBC--S----SCCCCCHHH
T ss_pred             -cccccccccCCCcCCcCCcEEeeccEEEEEEcccccc--ccc--c----cceecCHHH
Confidence             1111123457999999999999999999999853321  111  1    378888863

>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase subunit A', DNA-directed...; transcription, fusion protein, chimera protein, multiprotein; 3.30A {Pyrococcus furiosus}

Probab=100.00  E-value=5.9e-50  Score=371.98  Aligned_cols=175  Identities=34%  Similarity=0.705  Sum_probs=141.9

Q ss_pred             ccceeeeEEEEeCCHHHHhcCcccEEecCccccC-CCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcceeeecccce
Q 045123           11 KVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTER-GMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPM   89 (219)
Q Consensus        11 ~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~-~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~Pv   89 (219)
                      ..++|++|+||+||++||+++||++|+++++||. ++|++|||+|||||++++...|+|||+++.+||||||||+|+.||
T Consensus        65 ~~~~i~~i~F~~~s~eeI~~~Sv~~I~~~~~~d~~~~P~~gGl~D~rlG~~~~~~~C~TCg~~~~~CpGHfGhIeL~~PV  144 (436)
T 3qqc_A           65 GGKVIGSIEFGILSPQEIRKMSAVEVTVPDTYDDDGYPIEGGVMDKRMGVIDPGLRCETCGGRAGECPGHFGHIELARPV  144 (436)
T ss_dssp             --CEEEEEECCBCCHHHHHHTEEEECCBCCCCC----CCCSBSSCSSSCCCSSCCCCSSSCCCSSSCCCCEEEEEEEEEE
T ss_pred             ccceeeeeeeccCCHHHHHHhCCeEEecccccCCCCCccCCCccCccccCCCCCCCCCCCCCCCCcCCCCceeEeechHH
Confidence            4479999999999999999999999999999985 799999999999999999999999999999999999999999999


Q ss_pred             eeeeehhhhhhhhhhhcccccccccCccC-HHHHHHHHhc-----CchhHHHHHHHHhccccccCCCCcccccccCCCCC
Q 045123           90 FHIGFMKTLLTIMRCVCFNCSKILADEED-DKFKLALKIR-----HPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDG  163 (219)
Q Consensus        90 ~h~~f~~~i~~iL~~vC~~C~rll~~~~~-~~~~~~~~~~-----~~k~r~~~i~~~ck~~~~Ce~~~~~d~~~~~~~~~  163 (219)
                      |||+|++.|++||+|+|++|+|+++++++ ++|..+++..     +++.|+++||+.|+++++|                
T Consensus       145 fh~gF~~~I~kILr~vC~~C~klll~~~~~~~f~~~lr~~~~~~~~~k~~~~~i~~~~k~~~~C----------------  208 (436)
T 3qqc_A          145 IHVGFAKTIYRILESTCRECGRIKLTDEEIEEYMKKIELARNRRSEFNEIIKEIHKKAKERMVC----------------  208 (436)
T ss_dssp             ECGGGHHHHHHHHHHSCSTTCCCSSCHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHHHHTCCSC----------------
T ss_pred             HHHHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHhhhhccccHHHHHHHHHHHcccCCcC----------------
Confidence            99999999999999999999999999765 4677666632     4788999999999999999                


Q ss_pred             CCCCccCCCCCCCCCCeEEEeceEEEEEEccccccCCCCCCCCCCCCcccccCCCC
Q 045123          164 EEPLRKRKSGCGALQPTLTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER  219 (219)
Q Consensus       164 ~~~~~~~~~gCG~~qP~irk~glkl~~~~k~~~~~~~~~~~~~~~~~~k~~ltae~  219 (219)
                              +|||+.||+||++|++++.+..  +.   ++++ ++    ++.|||++
T Consensus       209 --------~gCG~~qp~Ir~e~~~~~~~~~--~~---~~~~-~~----k~~LtP~~  246 (436)
T 3qqc_A          209 --------PHCGAPQYPIKFEKPTIYWEIR--KD---EQGN-EY----RHRLMPTE  246 (436)
T ss_dssp             --------C-------CCCBCSSSCEEEEC--CC------C-CC----EEEECHHH
T ss_pred             --------cccCCcCceEEEecceeeeecc--cc---cccc-cc----ccccCHHH
Confidence                    6999999999999987654332  11   1111 22    78888863

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...

Probab=100.00  E-value=8.9e-47  Score=393.16  Aligned_cols=185  Identities=39%  Similarity=0.785  Sum_probs=166.4

Q ss_pred             CCCCCCCCccccceeeeEEEEeCCHHHHhcCcccEEecCccccCC--CCCCCCCccCCCCCCCCCcccCCCCCCCCccCC
Q 045123            1 MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERG--MPMAGGLSDLRLGTIDKRFKCETCSSNMGECPG   78 (219)
Q Consensus         1 ~~~~~~~~~~~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~~--~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpG   78 (219)
                      |. .|++|+++.++|++|+|+++|+|||++||++||+++++||.+  +|..|||+|||||++++...|.|||.+..+|||
T Consensus         1 ~~-~~~~~~~~~~~i~~I~f~l~SpeeIr~~Sv~eI~~pet~~~~~~~P~~~GL~d~rlG~~~~~~~C~tCg~~~~~C~G   79 (1733)
T 1twf_A            1 MV-GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPG   79 (1733)
T ss_dssp             -C-CCSCCCSCBCCCCEEECCBCCHHHHHHTCCCCCCCSCCSCTTSCCSCCSSSSCSSSCCCTTCCCSSSCCCCTTSCCC
T ss_pred             CC-CCCCCcCCccccceEEEEeCCHHHHHHhCeeEEecccccccccCCCCcCCCcCcccCcccCCCEeCCCCCCCCcCCC
Confidence            56 899999999999999999999999999999999999999976  999999999999999999999999999999999


Q ss_pred             cceeeecccceeeeeehhhhhhhhhhhcccccccccCccCHHHHHHHHhcCchhHHHHHHHHhccccccCCCCccccccc
Q 045123           79 HFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSL  158 (219)
Q Consensus        79 HfGhIeL~~Pv~h~~f~~~i~~iL~~vC~~C~rll~~~~~~~~~~~~~~~~~k~r~~~i~~~ck~~~~Ce~~~~~d~~~~  158 (219)
                      |||||||++|||||+||+.++++|+++|++|+++++++.+++|.+++++++|++|+++||++|+++++|+.+...+.+  
T Consensus        80 HfGHIELa~PV~HigF~k~i~kiLe~VC~~Cskllld~~~~~~~~~L~~~~pk~r~~~v~e~ck~k~~Ce~~~~~~~e--  157 (1733)
T 1twf_A           80 HFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDD--  157 (1733)
T ss_dssp             CCCCEEEEEEEECGGGHHHHHHHHHHBCTTTCCBSCCTTSHHHHHHHTCCSHHHHHHHHHHHHTTCCBCCSEECCSSC--
T ss_pred             ccceeecccccccHHHHhhHHHHHHHHhHhcceeeeccchHHHHHHHHhcCHHHHHHHHHHHhcccccccccccchhc--
Confidence            999999999999999999999999999999999999988888888888889999999999999999999642111110  


Q ss_pred             CCCCCCCCCccCCCCCCCCCCeEEEeceEEEEEEcc
Q 045123          159 LGHDGEEPLRKRKSGCGALQPTLTIDGMNMIAEYKA  194 (219)
Q Consensus       159 ~~~~~~~~~~~~~~gCG~~qP~irk~glkl~~~~k~  194 (219)
                          .  .....|+|||+.||.||++||+++++|+.
T Consensus       158 ----~--~~~~~~~gCGa~qp~irk~gl~l~~e~k~  187 (1733)
T 1twf_A          158 ----P--TQLVSRGGCGNTQPTIRKDGLKLVGSWKK  187 (1733)
T ss_dssp             ----T--TSCEECCSCCCBCCCCEECSSCEEEEECS
T ss_pred             ----c--ccccccCCCCCccHHHHhcCCceEEeecc
Confidence                0  11223689999999999999999999974

>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A

Probab=100.00  E-value=1.9e-36  Score=301.58  Aligned_cols=156  Identities=35%  Similarity=0.736  Sum_probs=130.1

Q ss_pred             ccceeeeEEEEeCCHHHHhcCcccEEecCccccC-CCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcceeeecccce
Q 045123           11 KVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTER-GMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPM   89 (219)
Q Consensus        11 ~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~-~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~Pv   89 (219)
                      ..++|++|+||++|||||++||++||++|++||. |.|+.|||+|||||+.++...|+|||.++.+||||||||+|+.||
T Consensus         2 ~~k~i~~I~f~l~SpeeIr~~S~~eV~~p~t~n~~g~p~~ggl~D~~lG~~~~~~~C~tCg~~~~~c~ghfGhIeLa~PV   81 (880)
T 4ayb_A            2 SEKNIKGIKFGILSPDEIRKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCGNTLGNCPGHFGHIELVRPV   81 (880)
T ss_dssp             -CEEEEEEEEECCCHHHHHHHTCSCBCCSCCCBSSSSSBCSSSSCGGGCCCSSSCCCTTTCCCGGGCCCCCEEEEEEEEE
T ss_pred             CCceeceEEEEeCCHHHHHHhcceEEeCcceECCCCCccCCCCCChhhCCCCCCCCCCCCCCCCCCCCCCCeeecccccc
Confidence            3578999999999999999999999999999985 899999999999999999999999999999999999999999999


Q ss_pred             eeeeehhhhhhhhhhhcccccccccCccCHH-HHHHHH---hcCc--hhHH-HHHHHHhccccccCCCCcccccccCCCC
Q 045123           90 FHIGFMKTLLTIMRCVCFNCSKILADEEDDK-FKLALK---IRHP--KSRL-EQILCACKTKNKCEGGDEIDVLSLLGHD  162 (219)
Q Consensus        90 ~h~~f~~~i~~iL~~vC~~C~rll~~~~~~~-~~~~~~---~~~~--k~r~-~~i~~~ck~~~~Ce~~~~~d~~~~~~~~  162 (219)
                      |||+|++.|.++|+++|++|+|+++++++.+ +.....   .+.+  .+++ +.+.+.+.+...|               
T Consensus        82 ~h~~f~~~i~~lL~~~c~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c---------------  146 (880)
T 4ayb_A           82 IHVGFVKHVYEFLKATCRRCGRVKISEDEIEKYSRIYNAIKKRWPSAARRLTEYVKKTAMKAQVC---------------  146 (880)
T ss_dssp             ECGGGTTHHHHHHHTSCTTSSCCCSSCCHHHHHHHHHHHHGGGCHHHHHHHHHHHHHHHTTCSSC---------------
T ss_pred             cchhHHHHHHHHHhCccccccCCcCCHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHhcccccc---------------
Confidence            9999999999999999999999999865432 222222   1222  1223 4455666777777               


Q ss_pred             CCCCCccCCCCCCCCCCeEEEec-eEEEE
Q 045123          163 GEEPLRKRKSGCGALQPTLTIDG-MNMIA  190 (219)
Q Consensus       163 ~~~~~~~~~~gCG~~qP~irk~g-lkl~~  190 (219)
                               ++||+.||+|++++ +++..
T Consensus       147 ---------~~cg~~~~~i~~~~~~~~~~  166 (880)
T 4ayb_A          147 ---------PHCGEKQFKIKLEKPYNFYE  166 (880)
T ss_dssp             ---------TTTTCCCCCCEEEETTEEEE
T ss_pred             ---------hhccchhhhhhhcCcCCHHH
Confidence                     58999999999886 34433

>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D

Probab=99.91  E-value=3.9e-26  Score=232.55  Aligned_cols=104  Identities=33%  Similarity=0.501  Sum_probs=77.7

Q ss_pred             ceeeeEEEEeCCHHHHhcCcccEEecCcccc--CCCCCCCCCccCCC-CCCC--------------CCcccCCCCCCCCc
Q 045123           13 AKVRMVQFSILSPDEIRKMSVTEIDHGKTTE--RGMPMAGGLSDLRL-GTID--------------KRFKCETCSSNMGE   75 (219)
Q Consensus        13 ~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~--~~~p~~~Gl~D~rl-G~~~--------------~~~~C~TC~~~~~~   75 (219)
                      ++|++|+|+++|||+|++||+.||++|++|+  +++|..+||+|+|| |+..              +...|.|||..+.+
T Consensus         3 ~~~~~i~~gl~Spe~Ir~~S~geV~~pet~ny~t~kP~~~GLfd~rifGp~k~~~C~Cgkyk~~~~~~~~C~~Cg~~~~~   82 (1265)
T 1hqm_D            3 KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTR   82 (1265)
T ss_dssp             CCBCCCCCCCCCTTTHHHHTTTCCCCCCC-------------------------------------CCSCSSSSSSSSCC
T ss_pred             cccceEEEecCCHHHHHHhhEEEEcchhheecCCCcccCCCCcCccccCCCccceecCCCccccCCCCCCCCCCCCcccc
Confidence            4689999999999999999999999999998  37999999999999 7653              67899999999999


Q ss_pred             c---CCcceeeecccceeeeeehhh-----------hhhhhhhhcccccccccCc
Q 045123           76 C---PGHFGHLELAKPMFHIGFMKT-----------LLTIMRCVCFNCSKILADE  116 (219)
Q Consensus        76 C---pGHfGhIeL~~Pv~h~~f~~~-----------i~~iL~~vC~~C~rll~~~  116 (219)
                      |   |||||||+|+.||||+||++.           +.+.|+++|++|+++++++
T Consensus        83 ~~vrrg~~GhIeLa~PV~Hi~y~k~~~s~l~~lL~~~~k~le~v~y~~s~v~~~~  137 (1265)
T 1hqm_D           83 SIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLFATELEQVLYFNKYIVLDP  137 (1265)
T ss_dssp             SSSCCCSCCCCCCCSCCCSTTSTTHHHHTTTCTTTHHHHTTSSSCCCCSCCCCSS
T ss_pred             cccccCccceEEecCceeeeeecccchHHHHHHhcCCHHhhccEeeecceEeecC
Confidence            9   899999999999999999996           4577889999999988764

>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D*

Probab=99.58  E-value=5.3e-16  Score=157.82  Aligned_cols=104  Identities=28%  Similarity=0.470  Sum_probs=91.8

Q ss_pred             cccceeeeEEEEeCCHHHHhcCcccEEecCccccC--CCCCCCCCccCCC-CCCC--------------CCcccCCCCCC
Q 045123           10 FKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTER--GMPMAGGLSDLRL-GTID--------------KRFKCETCSSN   72 (219)
Q Consensus        10 ~~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~--------------~~~~C~TC~~~   72 (219)
                      .+...+++|++++.||++|++||..||++|++++.  .+|..+||+++|+ |+..              +...|.+||..
T Consensus        12 ~~~~~~~~i~i~laSpe~I~~ws~GEV~kpetinyrt~kPe~dGLFcerIFGp~kd~eC~Cgkyk~~~~~g~~C~~Cgve   91 (1407)
T 3lu0_D           12 TKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVE   91 (1407)
T ss_dssp             --CCCCCCEEECCCCHHHHHHHBCSCCCSCCCCCSSCCSCCSSSSSCTTTTCCSSSSCCSSCSCCSTTCSSSCCSSSCCC
T ss_pred             cccCccceEEEEeCCHHHHHhhcCeEECCccccccCCCCCCCCCccchhhcCCCcCcEEeCccccccccCCCCCCCCCCc
Confidence            45678999999999999999999999999999985  6999999999999 9873              45789999999


Q ss_pred             CCccC---Ccceeeecccceeeeeehhhh----hhhhhhhcccccccc
Q 045123           73 MGECP---GHFGHLELAKPMFHIGFMKTL----LTIMRCVCFNCSKIL  113 (219)
Q Consensus        73 ~~~Cp---GHfGhIeL~~Pv~h~~f~~~i----~~iL~~vC~~C~rll  113 (219)
                      ...|.   .|||||+|+.||.|++||+.+    -.+|...+..+.+++
T Consensus        92 vt~~~vRr~rmGhI~La~PV~Hiwy~k~~ps~i~~lL~~~~k~le~vi  139 (1407)
T 3lu0_D           92 VTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVL  139 (1407)
T ss_dssp             CCCTTHHHHCBCEEEEEEEECCTHHHHSSSCTTTTTTTSCSSTTHHHH
T ss_pred             cccCcchhhhcceeeecCceeEeeeccCCchHHHHHhCCCHHHhhhhe
Confidence            99997   999999999999999999987    567777877776654

>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D

Probab=99.45  E-value=3.4e-14  Score=146.14  Aligned_cols=102  Identities=33%  Similarity=0.511  Sum_probs=87.7

Q ss_pred             eeeeEEEEeCCHHHHhcCcccEEecCccccC--CCCCCCCCccCCC-CCCC--------------CCcccCCCCCCCCcc
Q 045123           14 KVRMVQFSILSPDEIRKMSVTEIDHGKTTER--GMPMAGGLSDLRL-GTID--------------KRFKCETCSSNMGEC   76 (219)
Q Consensus        14 ~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~--------------~~~~C~TC~~~~~~C   76 (219)
                      .+..|++++.||++|++||+.||++|++.+.  .+|..+||++.|. |+..              ....|..||..+.++
T Consensus         4 ~~~~i~i~laSP~~I~~ws~GeV~~peTiny~t~kPe~~GLFcerIFGp~~~~~C~Cgkyk~~~~~~~~C~~Cgve~t~s   83 (1524)
T 2a6h_D            4 EVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTKS   83 (1524)
T ss_dssp             CCCEEEEECCCHHHHHHHEEEECCSCCCBCTTSCSBCSSSTTCTTTTCCSSSSCCSSCSSCSSTTTTCCCSSSCCCCSST
T ss_pred             ccceEEEEecCHHHHHHhhcceecCcccccccCCCCCCCCcccchhcCccccceEcCccccccCcCCCCCCCCCCccccc
Confidence            5678999999999999999999999999884  6999999999999 9875              223466677666666


Q ss_pred             C---Ccceeeecccceeeeeehhhh-----------hhhhhhhcccccccccC
Q 045123           77 P---GHFGHLELAKPMFHIGFMKTL-----------LTIMRCVCFNCSKILAD  115 (219)
Q Consensus        77 p---GHfGhIeL~~Pv~h~~f~~~i-----------~~iL~~vC~~C~rll~~  115 (219)
                      .   .+||||+|+.||.|++|++.+           .+.|+.++++++.+.+.
T Consensus        84 ~VRR~rmG~I~La~PV~HiWylk~~PS~l~~LLd~s~k~le~i~yf~~y~v~~  136 (1524)
T 2a6h_D           84 IVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLD  136 (1524)
T ss_dssp             HHHHHCEEEEEEEEEEECHHHHSSSSCHHHHHTTSCTTHHHHHHHHSCCEEEC
T ss_pred             hHHhhhcCeeeecCceeehhhhcCCchHHHHHhcCCHHHHhHhhcceeeEeec
Confidence            4   999999999999999999988           78899999998776554

---

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	219
d1twfa_	1449	e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c	1e-56

>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449

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-prime
domain: RBP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  191 bits (486), Expect = 1e-56
 Identities = 79/216 (36%), Positives = 115/216 (53%), Gaps = 16/216 (7%)

Query: 6   TFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTE--RGMPMAGGLSDLRLGTIDKR 63
            +S   +  V+ VQF + SP+E+R +SV +I   +T +  +     GGL+D RLG+ID+ 
Sbjct: 4   QYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRN 63

Query: 64  FKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKL 123
            KC+TC   M ECPGHFGH++LAKP+FH+GF+  +  +  CVC +C K+L DE ++  + 
Sbjct: 64  LKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQ 123

Query: 124 ALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTI 183
           AL I+  K R   I   CKTK  CE         +   D    L  R  GCG  QPT+  
Sbjct: 124 ALAIKDSKKRFAAIWTLCKTKMVCET-------DVPSEDDPTQLVSRG-GCGNTQPTIRK 175

Query: 184 DGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219
           DG+ ++  +K  R   D            + L+ E 
Sbjct: 176 DGLKLVGSWKKDRATGDADE------PELRVLSTEE 205

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	219
d1twfa_	1449	RBP1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	100.0
d1smyd_	1504	RNA-polymerase beta-prime {Thermus thermophilus [T	99.22
d1jmab2	46	Cellular receptor HveA {Human (Homo sapiens) [TaxI	84.3

>d1twfa_ e.29.1.2 (A:) RBP1 {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-prime
domain: RBP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=5.4e-41  Score=345.73  Aligned_cols=184  Identities=39%  Similarity=0.806  Sum_probs=163.2

Q ss_pred             CCCCCccccceeeeEEEEeCCHHHHhcCcccEEecCccccC--CCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcce
Q 045123            4 CFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTER--GMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFG   81 (219)
Q Consensus         4 ~~~~~~~~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfG   81 (219)
                      ...||.+++++|++|+|+++||+||++||++||++|++||.  +.|..|||||||||+.++...|.||+++..+||||||
T Consensus         2 ~~~~~~~p~~~i~~i~f~~~s~eeIr~~S~~ei~~~~~~~~~~~~p~~~Gl~d~rlG~~~~~~~C~tC~~~~~~CpGHfG   81 (1449)
T d1twfa_           2 GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFG   81 (1449)
T ss_dssp             CCSCCCSCBCCCCEEECCBCCHHHHHHTCCCCCCCSCCSCTTSCCSCCSSSSCSSSCCCTTCCCSSSCCCCTTSCCCCCC
T ss_pred             CCCCCcCccceeceEEEEecCHHHHHHhcceEEcCCCcccCCCCCCCCCCCcchhhCCCCCcCCCCCCCCCCcCCCCCCE
Confidence            46899999999999999999999999999999999999985  5799999999999999999999999999999999999


Q ss_pred             eeecccceeeeeehhhhhhhhhhhcccccccccCccCHHHHHHHHhcCchhHHHHHHHHhccccccCCCCcccccccCCC
Q 045123           82 HLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGH  161 (219)
Q Consensus        82 hIeL~~Pv~h~~f~~~i~~iL~~vC~~C~rll~~~~~~~~~~~~~~~~~k~r~~~i~~~ck~~~~Ce~~~~~d~~~~~~~  161 (219)
                      ||+|+.|||||+|++.++++|+++|++|++++++.....++.++...+++.++..++++++.+..|+.....+       
T Consensus        82 hIeL~~PV~h~~f~~~~~~~L~~~C~~C~~l~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------  154 (1449)
T d1twfa_          82 HIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSE-------  154 (1449)
T ss_dssp             CEEEEEEEECGGGHHHHHHHHHHBCTTTCCBSCCTTSHHHHHHHTCCSHHHHHHHHHHHHTTCCBCCSEECCS-------
T ss_pred             eeEecccchhHHHHHHHHHHHHHhhhccCCEeecccHHHHHHHHhhcchhhhhHHHHHHhhhheeccccccch-------
Confidence            9999999999999999999999999999999999888888888888899999999999999999996421111       


Q ss_pred             CCCCCCccCCCCCCCCCCeEEEeceEEEEEEccc
Q 045123          162 DGEEPLRKRKSGCGALQPTLTIDGMNMIAEYKAQ  195 (219)
Q Consensus       162 ~~~~~~~~~~~gCG~~qP~irk~glkl~~~~k~~  195 (219)
                       .........+||++.||.|+++++++..+|+..
T Consensus       155 -~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~  187 (1449)
T d1twfa_         155 -DDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKD  187 (1449)
T ss_dssp             -SCTTSCEECCSCCCBCCCCEECSSCEEEEECSS
T ss_pred             -hhhhhhhhcCCCCcCChhhhhhhHHHHHHHHHh
Confidence             001111124799999999999999999998754

>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {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-prime
domain: RNA-polymerase beta-prime
species: Thermus thermophilus [TaxId: 274]

Probab=99.22  E-value=1.7e-12  Score=132.69  Aligned_cols=88  Identities=34%  Similarity=0.544  Sum_probs=73.2

Q ss_pred             ceeeeEEEEeCCHHHHhcCcccEEecCccccC--CCCCCCCCccCCC-CCCC--------------CCcccCCCCCCCCc
Q 045123           13 AKVRMVQFSILSPDEIRKMSVTEIDHGKTTER--GMPMAGGLSDLRL-GTID--------------KRFKCETCSSNMGE   75 (219)
Q Consensus        13 ~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~--------------~~~~C~TC~~~~~~   75 (219)
                      ++|++|+.++.|||+|+.||+.||+.|+|.+.  .+|-.+||+|.|. ||..              ++..|.-||-.+..
T Consensus         2 ~~~~~i~i~lASpe~Ir~Ws~GeV~kpeTinYrT~KPE~dGLFcerIFGP~kd~eC~CGKyk~~~~~g~vC~~CgVevt~   81 (1504)
T d1smyd_           2 KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTK   81 (1504)
T ss_dssp             CCCCEEEEECCCHHHHHHHEEEECCSCCCBCTTSSSBCSSSSSCHHHHCCSSSSSCSSCSCCSSSSSSCCCSSSCCCCSS
T ss_pred             CccceEEEEecCHHHHHHhcCcccCCCCccccCCCCCCCCCeeeccccCCCcCceEeCCCccccccCCEECCCCCcEECc
Confidence            46889999999999999999999999999986  4999999999998 9875              23466666654432


Q ss_pred             ---cCCcceeeecccceeeeeehhhhhh
Q 045123           76 ---CPGHFGHLELAKPMFHIGFMKTLLT  100 (219)
Q Consensus        76 ---CpGHfGhIeL~~Pv~h~~f~~~i~~  100 (219)
                         -.=.+|||+|+.||-|++|++.+.+
T Consensus        82 s~vRR~RmGhIeLa~PV~HiWy~k~~PS  109 (1504)
T d1smyd_          82 SIVRRYRMGHIELATPAAHIWFVKDVPS  109 (1504)
T ss_dssp             THHHHHCEEEEEEEEEEECGGGTSSSSC
T ss_pred             cchHhhccCCccccCCceeeCccCCcch
Confidence               2457999999999999999996543

>d1jmab2 g.24.1.1 (B:60-105) Cellular receptor HveA {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: TNF receptor-like
superfamily: TNF receptor-like
family: TNF receptor-like
domain: Cellular receptor HveA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.30  E-value=0.099  Score=31.55  Aligned_cols=31  Identities=26%  Similarity=0.586  Sum_probs=20.9

Q ss_pred             CccCCCCCCCCCcccCCCCCCCCcc-CCcceee
Q 045123           52 LSDLRLGTIDKRFKCETCSSNMGEC-PGHFGHL   83 (219)
Q Consensus        52 l~D~rlG~~~~~~~C~TC~~~~~~C-pGHfGhI   83 (219)
                      +-||.||... ...|++=....-.| ||||=-+
T Consensus         1 mCDPaMgL~t-~~~CS~t~ntvC~C~~GhFC~~   32 (46)
T d1jmab2           1 MCDPAMGLRA-SRNCSRTENAVCGCSPGHFCIV   32 (46)
T ss_dssp             CCCTTTTEEE-EECCCSSSCCEEEECTTEEEEE
T ss_pred             CCCcchhhhh-hhhcccccCceecccCcceEEe
Confidence            3599999765 45677755544455 9999644