Psyllid ID: psy1865

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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--
Protein Sequence
MDKNLRLKYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIEKKPNAGVVA
Secondary Structure (PSIPRED)
cccccccccccccccEEEEEEEEEEcccccccccccccccccccEEEEcccEEEEccccccccccccccccccccEEEEcccccEEEEEEEEEEccccccccccccEEEEEEEEEEEEEcccccHHHHHHHHHHcccccEEEEcccccEEEc
Secondary Structure Prediction (SSPRO)
cccccccccccccccEEEEEEEEEEccccccccccccHHHcccccEEcccEEEEEcccHHHHccccccccccccEEEEEEccccEEEEEEEEEccccccccccccHHHHHHEcccEEEEEccccHHHHHHHHHHccccEEEEEcccccEEEc
Coil and Loop (DISEMBL)
mdknlrlkyepceqdTLQFQLKikctksasfshsshaddmyEKHKVftkdiqwvpigsqgdmykssdvgpihddiliaklrpgheidvTMFAVKSigrdhakfspVATAFYRLLPKITLTQEIEGEMAQRLQTmfspgvisiekkpnagvva
Flexible Loop (DISEMBL)
mdknlrlkyepceqDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMfspgvisiekkpnagvva
Low Complexity Region (SEG)
MDKNLRLKYEPCEQDTLQFQLKIKCTKsasfshsshaddMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIEKKPNAGVVA
Disordered region (IsUnstruct)
**************DTLQFQLKIKCTK************MYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMF*****************
Disordered Region (DISOPRED)
******L*YEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVP**************PIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIEKKP******
Disordered Region (DISEMBL)
MDKNLRLKYEPCEQDTLQFQLKIKCT***********DDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIEKKPNAGVVA
Disordered Region (DISPRO)
*****RLKYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIEKKPNAGVVA
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDKNLRLKYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIEKKPNAGVVA
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	152	2.2.26 [Sep-21-2011]
P52432	346	DNA-directed RNA polymera	yes	N/A	0.888	0.390	0.544	2e-40
O15160	346	DNA-directed RNA polymera	yes	N/A	0.888	0.390	0.529	1e-39
Q32L22	346	DNA-directed RNA polymera	yes	N/A	0.868	0.381	0.533	3e-39
P07703	335	DNA-directed RNA polymera	yes	N/A	0.993	0.450	0.394	4e-26
O94616	348	DNA-directed RNA polymera	yes	N/A	0.855	0.373	0.417	2e-24
Q54SN4	345	DNA-directed RNA polymera	yes	N/A	0.809	0.356	0.401	3e-18
Q54DH7	302	DNA-directed RNA polymera	no	N/A	0.631	0.317	0.3	1e-07
Q39212	319	DNA-directed RNA polymera	no	N/A	0.684	0.326	0.333	1e-07
Q39211	319	DNA-directed RNA polymera	no	N/A	0.671	0.319	0.312	4e-07
P19387	275	DNA-directed RNA polymera	no	N/A	0.690	0.381	0.271	8e-06

>sp|P52432|RPAC1_MOUSE DNA-directed RNA polymerases I and III subunit RPAC1 OS=Mus musculus GN=Polr1c PE=1 SV=3

 Score =  164 bits (415), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 74/136 (54%), Positives = 102/136 (75%), Gaps = 1/136 (0%)

Query: 10  EPCEQDTLQFQLKIKCTKSASFSH-SSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDV 68
           E  E DTLQF+L+++CT++ + +  SS  +++Y  HKV+T+ + WVP+G+Q D++    +
Sbjct: 131 EGTEIDTLQFRLQVRCTRNPNAAKDSSDPNELYVNHKVYTRHMTWVPLGNQADVFPEGTI 190

Query: 69  GPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMA 128
            P+HDDILIA+LRPG EID+ M  VK IG+DHAKFSPVATA YRLLP ITL + +EGE A
Sbjct: 191 RPVHDDILIAQLRPGQEIDLMMHCVKGIGKDHAKFSPVATASYRLLPAITLLEPVEGEAA 250

Query: 129 QRLQTMFSPGVISIEK 144
           + L   FSPGVI +E+
Sbjct: 251 EELSQCFSPGVIEVEE 266

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. RPAC1 is part of the Pol core element with the central large cleft and probably a clamp element that moves to open and close the cleft.
Mus musculus (taxid: 10090)

>sp|O15160|RPAC1_HUMAN DNA-directed RNA polymerases I and III subunit RPAC1 OS=Homo sapiens GN=POLR1C PE=1 SV=1

 Score =  161 bits (408), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 72/136 (52%), Positives = 101/136 (74%), Gaps = 1/136 (0%)

Query: 10  EPCEQDTLQFQLKIKCTKSA-SFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDV 68
           E  E DTLQF+L+++CT++  +   SS  +++Y  HKV+T+ + W+P+G+Q D++    +
Sbjct: 131 EGTEIDTLQFRLQVRCTRNPHAAKDSSDPNELYVNHKVYTRHMTWIPLGNQADLFPEGTI 190

Query: 69  GPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMA 128
            P+HDDILIA+LRPG EID+ M  VK IG+DHAKFSPVATA YRLLP ITL + +EGE A
Sbjct: 191 RPVHDDILIAQLRPGQEIDLLMHCVKGIGKDHAKFSPVATASYRLLPDITLLEPVEGEAA 250

Query: 129 QRLQTMFSPGVISIEK 144
           + L   FSPGVI +++
Sbjct: 251 EELSRCFSPGVIEVQE 266

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. RPAC1 is part of the Pol core element with the central large cleft and probably a clamp element that moves to open and close the cleft.

Homo sapiens (taxid: 9606)

>sp|Q32L22|RPAC1_BOVIN DNA-directed RNA polymerases I and III subunit RPAC1 OS=Bos taurus GN=POLR1C PE=2 SV=1

 Score =  160 bits (405), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 71/133 (53%), Positives = 100/133 (75%), Gaps = 1/133 (0%)

Query: 13  EQDTLQFQLKIKCTKSA-SFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPI 71
           E DTLQF+L+++CT++  +   SS  +++Y  H+V+T+ + WVP+G+Q D++    + P+
Sbjct: 134 EIDTLQFRLQVRCTRNPHAAKDSSDPNELYVNHRVYTRHMTWVPLGNQADLFPEGAIRPV 193

Query: 72  HDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRL 131
           HDDILIA+LRPG EID+ M  VK IG+DHAKFSPVATA YRLLP ITL + +EGE A+ L
Sbjct: 194 HDDILIAQLRPGQEIDLLMHCVKGIGKDHAKFSPVATASYRLLPDITLLEPVEGEAAEEL 253

Query: 132 QTMFSPGVISIEK 144
              FSPGVI +++
Sbjct: 254 SRCFSPGVIEVQE 266

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. RPAC1 is part of the Pol core element with the central large cleft and probably a clamp element that moves to open and close the cleft.

Bos taurus (taxid: 9913)

>sp|P07703|RPAC1_YEAST DNA-directed RNA polymerases I and III subunit RPAC1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPC40 PE=1 SV=1

 Score =  117 bits (292), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 60/152 (39%), Positives = 89/152 (58%), Gaps = 1/152 (0%)

Query: 1   MDKNLRLKYEPCEQDTLQFQLKIKCTKSASFSH-SSHADDMYEKHKVFTKDIQWVPIGSQ 59
           +D NL    +  +++T+   L +KCT++      S+   ++Y    V+ +D+++ P G Q
Sbjct: 116 VDSNLPDDEKFTDENTIVLSLNVKCTRNPDAPKGSTDPKELYNNAHVYARDLKFEPQGRQ 175

Query: 60  GDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITL 119
              +    V P   DIL+AKLRPG EI +    +  IG DHAKFSPV+TA YRLLP+I +
Sbjct: 176 STTFADCPVVPADPDILLAKLRPGQEISLKAHCILGIGGDHAKFSPVSTASYRLLPQINI 235

Query: 120 TQEIEGEMAQRLQTMFSPGVISIEKKPNAGVV 151
            Q I+GE A+R Q  F PGVI I++  +   V
Sbjct: 236 LQPIKGESARRFQKCFPPGVIGIDEGSDEAYV 267

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. RPAC1 is part of the Pol core element with the central large cleft and probably a clamp element that moves to open and close the cleft.

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

>sp|O94616|RPAC1_SCHPO DNA-directed RNA polymerases I and III subunit RPAC1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpc40 PE=3 SV=1

 Score =  110 bits (276), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 58/139 (41%), Positives = 84/139 (60%), Gaps = 9/139 (6%)

Query: 15  DTLQFQLKIKCTKSASFSHSSHADD-----MYEKHKVFTKDIQWVPIGSQGDMYKSSDVG 69
           DT+ F L  KC     F+ ++  D+     +Y   +V++ D+ W P G Q + +  + + 
Sbjct: 137 DTVVFSLNKKC----EFNKNAATDEKDPKRLYVNSEVYSGDLIWKPQGRQEERFADNPIR 192

Query: 70  PIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQ 129
            ++ DI++AKLRPG EID+   A+  IG+DHAKFSPVATA YRLLP I +   IEGE A 
Sbjct: 193 VVNPDIVVAKLRPGQEIDLEAHAILGIGQDHAKFSPVATASYRLLPTIHILSPIEGEDAV 252

Query: 130 RLQTMFSPGVISIEKKPNA 148
           + Q  F  GVI +E+ P+ 
Sbjct: 253 KFQKCFPKGVIELEEGPDG 271

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. RPAC1 is part of the Pol core element with the central large cleft and probably a clamp element that moves to open and close the cleft.

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

>sp|Q54SN4|RPAC1_DICDI DNA-directed RNA polymerases I and III subunit rpac1 OS=Dictyostelium discoideum GN=polr1c PE=3 SV=1

 Score = 90.5 bits (223), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 53/132 (40%), Positives = 74/132 (56%), Gaps = 9/132 (6%)

Query: 14  QDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSD--VGPI 71
           +DTL FQLK+KC K  S +     +    KH +      WVP   Q +M+ + +    P+
Sbjct: 144 EDTLIFQLKVKCEKD-SVTGKIINETALSKHLI------WVPTQDQEEMFPNEEDRPRPM 196

Query: 72  HDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRL 131
            DDI I KLRPG  ID+  +  K+IGR+H K+SPV TA YRL P I++ + I+G+ A +L
Sbjct: 197 EDDIPIMKLRPGQVIDIQCYCEKNIGREHIKWSPVCTASYRLQPVISVDKSIKGDKANQL 256

Query: 132 QTMFSPGVISIE 143
                  V  IE
Sbjct: 257 LEKCPKKVFDIE 268

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. RPAC1 is part of the Pol core element with the central large cleft and probably a clamp element that moves to open and close the cleft.

Dictyostelium discoideum (taxid: 44689)

>sp|Q54DH7|RPB3_DICDI DNA-directed RNA polymerase II subunit rpb3 OS=Dictyostelium discoideum GN=polr2c PE=3 SV=1

 Score = 55.8 bits (133), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 33/110 (30%), Positives = 55/110 (50%), Gaps = 14/110 (12%)

Query: 12  CEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPI 71
           C+Q +++ +L +KCT++     +S          + +++   +P+ SQ     S      
Sbjct: 98  CDQCSVELRLNVKCTENRPRDVTSS--------DLLSQNSAVIPVSSQVTSSNS------ 143

Query: 72  HDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQ 121
             +I I KLR G EI +   A K +G++HAK+SP   A Y+  P I L Q
Sbjct: 144 EQEIPIVKLRRGQEIKLRAIAKKGVGKEHAKWSPSCVATYQFQPIIVLNQ 193

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. 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. Rpb3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft.

Dictyostelium discoideum (taxid: 44689)

>sp|Q39212|RPB3B_ARATH DNA-directed RNA polymerase II subunit RPB3-B OS=Arabidopsis thaliana GN=RPB36B PE=1 SV=2

 Score = 55.5 bits (132), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 38/114 (33%), Positives = 55/114 (48%), Gaps = 10/114 (8%)

Query: 10  EPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVG 69
           E CE  +++F L  KC    +   +S   D+Y      + D    P+    +   S    
Sbjct: 97  EHCEFCSVEFPLSAKCVTDQTLDVTSR--DLY------SADPTVTPVDFTSNSSTSDSSE 148

Query: 70  PIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEI 123
             H  I+IAKLR G E+ +   A K IG+DHAK+SP AT  Y   P I + +E+
Sbjct: 149 --HKGIIIAKLRRGQELKLKALARKGIGKDHAKWSPAATVTYMYEPDIIINEEM 200

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. 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. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft.

Arabidopsis thaliana (taxid: 3702)

>sp|Q39211|RPB3A_ARATH DNA-directed RNA polymerase II subunit RPB3-A OS=Arabidopsis thaliana GN=RPB36A PE=2 SV=1

 Score = 53.9 bits (128), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 35/112 (31%), Positives = 54/112 (48%), Gaps = 10/112 (8%)

Query: 12  CEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPI 71
           CE  +++F+L  KC    +   +S   D+Y      T     V       +  SS+    
Sbjct: 99  CEFCSVEFRLSSKCVTDQTLDVTSR--DLYSADPTVTP----VDFTIDSSVSDSSE---- 148

Query: 72  HDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEI 123
           H  I+I KLR G E+ +   A K IG+DHAK+SP AT  +   P I + +++
Sbjct: 149 HKGIIIVKLRRGQELKLRAIARKGIGKDHAKWSPAATVTFMYEPDIIINEDM 200

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. 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. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft.

Arabidopsis thaliana (taxid: 3702)

>sp|P19387|RPB3_HUMAN DNA-directed RNA polymerase II subunit RPB3 OS=Homo sapiens GN=POLR2C PE=1 SV=2

 Score = 49.3 bits (116), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 31/114 (27%), Positives = 55/114 (48%), Gaps = 9/114 (7%)

Query: 10  EPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVG 69
           E C + +++F L ++C +  +  H +  D +    +V       +P+ S+      +D  
Sbjct: 92  EFCPECSVEFTLDVRCNEDQT-RHVTSRDLISNSPRV-------IPVTSRNRDNDPNDYV 143

Query: 70  PIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEI 123
              DDILI KLR G E+ +  +A K  G++HAK++P A   +   P   L   +
Sbjct: 144 E-QDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVAFEYDPDNALRHTV 196

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. 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. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft.

Homo sapiens (taxid: 9606)

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	152
189239160	338	PREDICTED: similar to CG3756 CG3756-PA [	0.927	0.417	0.636	5e-44
270010836	335	hypothetical protein TcasGA2_TC014519 [T	0.927	0.420	0.636	8e-44
195035209	333	GH11517 [Drosophila grimshawi] gi|193905	0.907	0.414	0.575	3e-41
242021511	347	DNA-directed RNA polymerase I 40 kDa pol	0.875	0.383	0.559	2e-40
225707230	351	DNA-directed RNA polymerase I 40 kDa pol	0.901	0.390	0.568	2e-40
195386486	333	GJ24400 [Drosophila virilis] gi|19414839	0.907	0.414	0.553	4e-40
195114368	333	GI17014 [Drosophila mojavensis] gi|19391	0.907	0.414	0.561	6e-40
449283222	323	DNA-directed RNA polymerases I and III s	0.888	0.417	0.602	9e-40
195437356	332	GK24584 [Drosophila willistoni] gi|19416	0.907	0.415	0.561	9e-40
170033286	335	DNA-directed RNA polymerase I 40 kDa pol	0.901	0.408	0.550	1e-39

>gi|189239160|ref|XP_971966.2| PREDICTED: similar to CG3756 CG3756-PA [Tribolium castaneum]

 Score =  182 bits (461), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 93/146 (63%), Positives = 110/146 (75%), Gaps = 5/146 (3%)

Query: 10  EPCEQDTLQFQLKIKCTKSASFSHSS-HADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDV 68
           E  EQDTL+F LKIKCT +   S  S  A+DMY+ + V++K I+WVPIG Q + +  SDV
Sbjct: 128 EGTEQDTLEFALKIKCTNNKDSSKDSLRAEDMYKNNNVYSKHIKWVPIGKQKERF--SDV 185

Query: 69  GPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMA 128
           GPIH DILIAK+RPGHE+D+ + AVKS GRDHAKFSPVATAFYRLLP I L +E+EGE A
Sbjct: 186 GPIHPDILIAKMRPGHELDLKLLAVKSNGRDHAKFSPVATAFYRLLPDIKLLREVEGEAA 245

Query: 129 QRLQTMFSPGVISI--EKKPNAGVVA 152
           +RLQ  FSPGVISI  EK     VVA
Sbjct: 246 ERLQKCFSPGVISIRHEKGRKYAVVA 271

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270010836|gb|EFA07284.1| hypothetical protein TcasGA2_TC014519 [Tribolium castaneum]

 Score =  181 bits (459), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 93/146 (63%), Positives = 110/146 (75%), Gaps = 5/146 (3%)

Query: 10  EPCEQDTLQFQLKIKCTKSASFSHSS-HADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDV 68
           E  EQDTL+F LKIKCT +   S  S  A+DMY+ + V++K I+WVPIG Q + +  SDV
Sbjct: 125 EGTEQDTLEFALKIKCTNNKDSSKDSLRAEDMYKNNNVYSKHIKWVPIGKQKERF--SDV 182

Query: 69  GPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMA 128
           GPIH DILIAK+RPGHE+D+ + AVKS GRDHAKFSPVATAFYRLLP I L +E+EGE A
Sbjct: 183 GPIHPDILIAKMRPGHELDLKLLAVKSNGRDHAKFSPVATAFYRLLPDIKLLREVEGEAA 242

Query: 129 QRLQTMFSPGVISI--EKKPNAGVVA 152
           +RLQ  FSPGVISI  EK     VVA
Sbjct: 243 ERLQKCFSPGVISIRHEKGRKYAVVA 268

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195035209|ref|XP_001989070.1| GH11517 [Drosophila grimshawi] gi|193905070|gb|EDW03937.1| GH11517 [Drosophila grimshawi]

 Score =  172 bits (437), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 80/139 (57%), Positives = 106/139 (76%), Gaps = 1/139 (0%)

Query: 13  EQDTLQFQLKIKCTKSASFS-HSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPI 71
           EQDTL+++LK+KCT+    +   S+ DD+Y+ HKV++  ++W+P G QG +Y  S V  I
Sbjct: 127 EQDTLEYELKVKCTRRKDATKEQSNFDDIYKNHKVYSGHLKWLPKGKQGQIYSESSVNCI 186

Query: 72  HDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRL 131
           HDDILIA+LRPGHE+D+ + AVK IG+DHAKFSPVATAFYRLLP+ITLT+E+ G+ A  L
Sbjct: 187 HDDILIAQLRPGHELDLRLIAVKGIGKDHAKFSPVATAFYRLLPQITLTREVSGKDAYLL 246

Query: 132 QTMFSPGVISIEKKPNAGV 150
           Q  FSPGVI I++   A V
Sbjct: 247 QNCFSPGVIGIDENECAYV 265

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242021511|ref|XP_002431188.1| DNA-directed RNA polymerase I 40 kDa polypeptide, putative [Pediculus humanus corporis] gi|212516437|gb|EEB18450.1| DNA-directed RNA polymerase I 40 kDa polypeptide, putative [Pediculus humanus corporis]

 Score =  170 bits (430), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 75/134 (55%), Positives = 100/134 (74%), Gaps = 1/134 (0%)

Query: 10  EPCEQDTLQFQLKIKCT-KSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDV 68
           EP EQDTL+F+LKIKC+       +S   DD+Y  H V++K ++WVPIGSQG  Y   ++
Sbjct: 125 EPNEQDTLEFELKIKCSVNKEGHKNSYQIDDLYINHSVYSKHLKWVPIGSQGTTYDEKNI 184

Query: 69  GPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMA 128
           GP+  DIL+ KLRPG E+D+ + AVK +G+DH KFSPVATAFYR+LP+IT+ +++ GE A
Sbjct: 185 GPVLPDILLNKLRPGQELDLKLHAVKGLGKDHTKFSPVATAFYRMLPEITMVKKVTGEAA 244

Query: 129 QRLQTMFSPGVISI 142
           +RLQ  FSPGVI I
Sbjct: 245 ERLQNCFSPGVIEI 258

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|225707230|gb|ACO09461.1| DNA-directed RNA polymerase I 40 kDa polypeptide [Osmerus mordax]

 Score =  169 bits (429), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 79/139 (56%), Positives = 107/139 (76%), Gaps = 2/139 (1%)

Query: 15  DTLQFQLKIKCTKSA-SFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHD 73
           DT+Q QLKIKCT++  +   SS   ++Y  H V++KD++WVPIG+Q D++  +++GP+H 
Sbjct: 141 DTIQLQLKIKCTRNPRAPKDSSDPRELYLNHMVYSKDMKWVPIGNQADVFADANIGPVHG 200

Query: 74  DILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQT 133
           DILIA+LRPG E+DV M  VK IG+DHAKFSPVATA YRLLP+ITL + +EGE A+RL++
Sbjct: 201 DILIAQLRPGQELDVVMSCVKGIGKDHAKFSPVATASYRLLPEITLMETVEGEKAERLKS 260

Query: 134 MFSPGVISIEKKPNAGVVA 152
            FSPGVI +E   N  V+A
Sbjct: 261 CFSPGVIELE-NCNGKVIA 278

Source: Osmerus mordax

Species: Osmerus mordax

Genus: Osmerus

Family: Osmeridae

Order: Osmeriformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|195386486|ref|XP_002051935.1| GJ24400 [Drosophila virilis] gi|194148392|gb|EDW64090.1| GJ24400 [Drosophila virilis]

 Score =  169 bits (427), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 77/139 (55%), Positives = 107/139 (76%), Gaps = 1/139 (0%)

Query: 13  EQDTLQFQLKIKCTKSASFSH-SSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPI 71
           EQDTL+++LK+KCT+    S   S+ DD+Y+ HKV++  ++W+P G QG +Y  + VG I
Sbjct: 127 EQDTLEYELKVKCTRRKDASKDQSNFDDIYKNHKVYSGHLKWLPKGKQGQIYTENSVGCI 186

Query: 72  HDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRL 131
           H+DILIA+LRPGHE+D+ + AVK +G+DHAKFSPVATA+YRLLP+I LT+E+ G+ A  L
Sbjct: 187 HEDILIAQLRPGHELDLRLIAVKGLGKDHAKFSPVATAYYRLLPQINLTREVTGKDAYLL 246

Query: 132 QTMFSPGVISIEKKPNAGV 150
           Q+ FSPGVI I++   A V
Sbjct: 247 QSCFSPGVIGIDENECAYV 265

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195114368|ref|XP_002001739.1| GI17014 [Drosophila mojavensis] gi|193912314|gb|EDW11181.1| GI17014 [Drosophila mojavensis]

 Score =  168 bits (426), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 78/139 (56%), Positives = 105/139 (75%), Gaps = 1/139 (0%)

Query: 13  EQDTLQFQLKIKCTKSASFSH-SSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPI 71
           EQDTL+++LK+KCT+    S   S+ DD+Y  HKV++  ++W+P G Q  +Y  S VG I
Sbjct: 127 EQDTLEYELKVKCTRRKDASKDQSNFDDIYRNHKVYSGHLKWLPKGKQAQIYSESSVGCI 186

Query: 72  HDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRL 131
           H+DILIA+LRPGHE+D+ + AVK IG+DHAKFSPVATA+YRLLP+I LT+E+ G+ A  L
Sbjct: 187 HEDILIAQLRPGHELDLRLIAVKGIGKDHAKFSPVATAYYRLLPQINLTREVRGKDAYLL 246

Query: 132 QTMFSPGVISIEKKPNAGV 150
           Q+ FSPGVI I++   A V
Sbjct: 247 QSCFSPGVIGIDENECAYV 265

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|449283222|gb|EMC89903.1| DNA-directed RNA polymerases I and III subunit RPAC1, partial [Columba livia]

 Score =  168 bits (425), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 82/136 (60%), Positives = 101/136 (74%), Gaps = 1/136 (0%)

Query: 10  EPCEQDTLQFQLKIKCTKSASFS-HSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDV 68
           E  E DTLQFQLKIKC+++   +  SS  +++Y  HKV++K + WVP+G+Q D++  +D 
Sbjct: 108 EGTEIDTLQFQLKIKCSRNPQAAKESSDPNELYFNHKVYSKHMTWVPLGNQTDLFPDADF 167

Query: 69  GPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMA 128
            P+HDDILIA LRPG EIDV M  VK IG+DHAKFSPVATA YRLLP ITL Q IE E A
Sbjct: 168 RPVHDDILIALLRPGQEIDVLMHCVKGIGKDHAKFSPVATASYRLLPDITLLQPIEDEAA 227

Query: 129 QRLQTMFSPGVISIEK 144
           + LQ  FSPGVI I+K
Sbjct: 228 ETLQKCFSPGVIEIQK 243

Source: Columba livia

Species: Columba livia

Genus: Columba

Family: Columbidae

Order: Columbiformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|195437356|ref|XP_002066606.1| GK24584 [Drosophila willistoni] gi|194162691|gb|EDW77592.1| GK24584 [Drosophila willistoni]

 Score =  167 bits (424), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 78/139 (56%), Positives = 105/139 (75%), Gaps = 1/139 (0%)

Query: 13  EQDTLQFQLKIKCTKSASFSH-SSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPI 71
           EQDTL+++LK+KCT+    S   S  D++Y+ HKVF+  ++W+P G QG +Y  S VG I
Sbjct: 126 EQDTLEYELKVKCTRRKDASKDQSTFDEIYKNHKVFSGHLKWLPKGKQGQIYTESSVGCI 185

Query: 72  HDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRL 131
           H+DILIA+LRPGHE+D+ + AVK +G+DHAKFSPVATA+YRLLP I L +E+ G+ A  L
Sbjct: 186 HEDILIAQLRPGHEMDLRLIAVKGLGKDHAKFSPVATAYYRLLPLIKLNREVSGKDAYLL 245

Query: 132 QTMFSPGVISIEKKPNAGV 150
           Q+ FSPGVI I++  NA V
Sbjct: 246 QSCFSPGVIGIDENENAYV 264

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170033286|ref|XP_001844509.1| DNA-directed RNA polymerase I 40 kDa polypeptide [Culex quinquefasciatus] gi|167873916|gb|EDS37299.1| DNA-directed RNA polymerase I 40 kDa polypeptide [Culex quinquefasciatus]

 Score =  167 bits (424), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 76/138 (55%), Positives = 103/138 (74%), Gaps = 1/138 (0%)

Query: 14  QDTLQFQLKIKCTK-SASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIH 72
           QDTL+F+LK+KCTK +   +  ++ D MY+ H +++  I+WVP+G+Q  +YK +DVGPI 
Sbjct: 130 QDTLEFELKVKCTKKNKDSTEVTNNDSMYKNHSIYSGQIKWVPVGNQASIYKEADVGPID 189

Query: 73  DDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQ 132
           DDILI+++RPGHE D+ +FAVK +G+DHAKFSPVATA YRLLP+I L + + G  A  LQ
Sbjct: 190 DDILISRMRPGHEFDIKLFAVKGVGKDHAKFSPVATASYRLLPEIHLKRPVVGNQALLLQ 249

Query: 133 TMFSPGVISIEKKPNAGV 150
             FSPGVI I+K   A V
Sbjct: 250 KCFSPGVIEIDKDDQAYV 267

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	152
ZFIN|ZDB-GENE-040426-1495	362	polr1c "polymerase (RNA) I pol	0.881	0.370	0.533	1.7e-38
MGI|MGI:103288	346	Polr1c "polymerase (RNA) I pol	0.888	0.390	0.529	1.7e-38
UNIPROTKB|Q5RJK9	346	Polr1c "Protein Polr1c" [Rattu	0.888	0.390	0.529	9.3e-38
UNIPROTKB|E1C548	346	POLR1C "Uncharacterized protei	0.881	0.387	0.577	2.1e-36
UNIPROTKB|F1LXY3	260	Polr1c "Protein Polr1c" [Rattu	0.888	0.519	0.529	9.2e-36
UNIPROTKB|O15160	346	POLR1C "DNA-directed RNA polym	0.888	0.390	0.514	1.9e-35
UNIPROTKB|F1RRJ4	351	POLR1C "Uncharacterized protei	0.888	0.384	0.514	4e-35
UNIPROTKB|Q32L22	346	POLR1C "DNA-directed RNA polym	0.868	0.381	0.518	6.5e-35
UNIPROTKB|E2RH57	346	POLR1C "Uncharacterized protei	0.888	0.390	0.507	8.3e-35
FB|FBgn0031657	333	CG3756 [Drosophila melanogaste	0.907	0.414	0.525	1.3e-34

ZFIN|ZDB-GENE-040426-1495 polr1c "polymerase (RNA) I polypeptide C" [Danio rerio (taxid:7955)]

 Score = 391 (142.7 bits), Expect = 1.7e-38, Sum P(2) = 1.7e-38
 Identities = 72/135 (53%), Positives = 97/135 (71%)

Query:    10 EPCEQDTLQFQLKIKCTKXXXXXXXXXX-XXMYEKHKVFTKDIQWVPIGSQGDMYKSSDV 68
             E  E DT+Q QLK+KCT+             +Y  H +++ DI+W+PIG+Q D++  + +
Sbjct:   147 EGTEIDTIQLQLKVKCTRNPRAPKDSSDPKELYLNHMIYSGDIKWLPIGNQADVFADAKI 206

Query:    69 GPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMA 128
             GP+H DIL+A++RPG E+D+ M  VK IG+DHAKFSPVATA YRLLP+ITL Q IEGE A
Sbjct:   207 GPVHGDILLAQVRPGQELDIVMHCVKGIGKDHAKFSPVATASYRLLPEITLLQTIEGEQA 266

Query:   129 QRLQTMFSPGVISIE 143
             +RL+  FSPGVI +E
Sbjct:   267 ERLKRCFSPGVIELE 281

GO:0046983 "protein dimerization activity" evidence=IEA

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

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

GO:0003677 "DNA binding" evidence=IEA

MGI|MGI:103288 Polr1c "polymerase (RNA) I polypeptide C" [Mus musculus (taxid:10090)]

 Score = 386 (140.9 bits), Expect = 1.7e-38, Sum P(2) = 1.7e-38
 Identities = 72/136 (52%), Positives = 95/136 (69%)

Query:    10 EPCEQDTLQFQLKIKCTKXXXXXXXXXX-XXMYEKHKVFTKDIQWVPIGSQGDMYKSSDV 68
             E  E DTLQF+L+++CT+             +Y  HKV+T+ + WVP+G+Q D++    +
Sbjct:   131 EGTEIDTLQFRLQVRCTRNPNAAKDSSDPNELYVNHKVYTRHMTWVPLGNQADVFPEGTI 190

Query:    69 GPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMA 128
              P+HDDILIA+LRPG EID+ M  VK IG+DHAKFSPVATA YRLLP ITL + +EGE A
Sbjct:   191 RPVHDDILIAQLRPGQEIDLMMHCVKGIGKDHAKFSPVATASYRLLPAITLLEPVEGEAA 250

Query:   129 QRLQTMFSPGVISIEK 144
             + L   FSPGVI +E+
Sbjct:   251 EELSQCFSPGVIEVEE 266

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|Q5RJK9 Polr1c "Protein Polr1c" [Rattus norvegicus (taxid:10116)]

 Score = 386 (140.9 bits), Expect = 9.3e-38, Sum P(2) = 9.3e-38
 Identities = 72/136 (52%), Positives = 96/136 (70%)

Query:    10 EPCEQDTLQFQLKIKCTKXXXXXXXXXX-XXMYEKHKVFTKDIQWVPIGSQGDMYKSSDV 68
             E  E DTLQF+L+++CT+             +Y  HKV+T+ + WVP+G+Q D++    V
Sbjct:   131 EGTEIDTLQFRLQVRCTRNPSAAKDSSDPNELYVNHKVYTRHMTWVPLGNQADVFPEGTV 190

Query:    69 GPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMA 128
              P+HDDILIA+LRPG EID+ M  VK IG+DHAKFSPVATA YRLLP ITL + +EGE A
Sbjct:   191 RPVHDDILIAQLRPGQEIDLMMHCVKGIGKDHAKFSPVATASYRLLPDITLLEPVEGEAA 250

Query:   129 QRLQTMFSPGVISIEK 144
             + L   FSPGVI++++
Sbjct:   251 EELSQCFSPGVIAVQE 266

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|E1C548 POLR1C "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 392 (143.0 bits), Expect = 2.1e-36, P = 2.1e-36
 Identities = 78/135 (57%), Positives = 94/135 (69%)

Query:    10 EPCEQDTLQFQLKIKCTKXXXXXXXXXX-XXMYEKHKVFTKDIQWVPIGSQGDMYKSSDV 68
             E  E DTLQFQLKIKC++             +Y  HKV++K + WVP+G+Q D++  +D 
Sbjct:   131 EGTEIDTLQFQLKIKCSRNPQAAKESSDPNELYFNHKVYSKHMTWVPLGNQTDLFPDADF 190

Query:    69 GPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMA 128
              P+HDDILIA LRPG EIDV M  VK IG+DHAKFSPVATA YRLLP ITL Q +E E A
Sbjct:   191 RPVHDDILIALLRPGQEIDVLMHCVKGIGKDHAKFSPVATASYRLLPDITLLQPVEDEAA 250

Query:   129 QRLQTMFSPGVISIE 143
             + LQ  FSPGVI I+
Sbjct:   251 ETLQKCFSPGVIEIQ 265

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|F1LXY3 Polr1c "Protein Polr1c" [Rattus norvegicus (taxid:10116)]

 Score = 386 (140.9 bits), Expect = 9.2e-36, P = 9.2e-36
 Identities = 72/136 (52%), Positives = 96/136 (70%)

Query:    10 EPCEQDTLQFQLKIKCTKXXXXXXXXXX-XXMYEKHKVFTKDIQWVPIGSQGDMYKSSDV 68
             E  E DTLQF+L+++CT+             +Y  HKV+T+ + WVP+G+Q D++    V
Sbjct:    45 EGTEIDTLQFRLQVRCTRNPSAAKDSSDPNELYVNHKVYTRHMTWVPLGNQADVFPEGTV 104

Query:    69 GPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMA 128
              P+HDDILIA+LRPG EID+ M  VK IG+DHAKFSPVATA YRLLP ITL + +EGE A
Sbjct:   105 RPVHDDILIAQLRPGQEIDLMMHCVKGIGKDHAKFSPVATASYRLLPDITLLEPVEGEAA 164

Query:   129 QRLQTMFSPGVISIEK 144
             + L   FSPGVI++++
Sbjct:   165 EELSQCFSPGVIAVQE 180

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|O15160 POLR1C "DNA-directed RNA polymerases I and III subunit RPAC1" [Homo sapiens (taxid:9606)]

 Score = 383 (139.9 bits), Expect = 1.9e-35, P = 1.9e-35
 Identities = 70/136 (51%), Positives = 95/136 (69%)

Query:    10 EPCEQDTLQFQLKIKCTKXXXXXXXXXX-XXMYEKHKVFTKDIQWVPIGSQGDMYKSSDV 68
             E  E DTLQF+L+++CT+             +Y  HKV+T+ + W+P+G+Q D++    +
Sbjct:   131 EGTEIDTLQFRLQVRCTRNPHAAKDSSDPNELYVNHKVYTRHMTWIPLGNQADLFPEGTI 190

Query:    69 GPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMA 128
              P+HDDILIA+LRPG EID+ M  VK IG+DHAKFSPVATA YRLLP ITL + +EGE A
Sbjct:   191 RPVHDDILIAQLRPGQEIDLLMHCVKGIGKDHAKFSPVATASYRLLPDITLLEPVEGEAA 250

Query:   129 QRLQTMFSPGVISIEK 144
             + L   FSPGVI +++
Sbjct:   251 EELSRCFSPGVIEVQE 266

GO:0003677 "DNA binding" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

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

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

GO:0005654 "nucleoplasm" evidence=TAS

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

GO:0006361 "transcription initiation from RNA polymerase I promoter" evidence=TAS

GO:0006362 "transcription elongation from RNA polymerase I promoter" evidence=TAS

GO:0006363 "termination of RNA polymerase I transcription" evidence=TAS

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

GO:0006385 "transcription elongation from RNA polymerase III promoter" evidence=TAS

GO:0006386 "termination of RNA polymerase III transcription" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

UNIPROTKB|F1RRJ4 POLR1C "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 380 (138.8 bits), Expect = 4.0e-35, P = 4.0e-35
 Identities = 70/136 (51%), Positives = 95/136 (69%)

Query:    10 EPCEQDTLQFQLKIKCTKXXXXXXXXXX-XXMYEKHKVFTKDIQWVPIGSQGDMYKSSDV 68
             E  E DTLQF+L+++CT+             +Y  HKV+T+ + WVP+G+Q D++    +
Sbjct:   136 EGTEIDTLQFRLQVRCTRNPSAAKDSSDPNELYVNHKVYTRHMTWVPLGNQADLFPEGTI 195

Query:    69 GPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMA 128
              P+HDDILIA+LRPG EID+ M  VK IG+DHAKFSPVATA YRLLP ITL + +EG+ A
Sbjct:   196 RPVHDDILIAQLRPGQEIDLLMQCVKGIGKDHAKFSPVATASYRLLPDITLLEPVEGDAA 255

Query:   129 QRLQTMFSPGVISIEK 144
             + L   FSPGVI +++
Sbjct:   256 EELSRCFSPGVIEVQE 271

GO:0046983 "protein dimerization activity" evidence=IEA

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

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q32L22 POLR1C "DNA-directed RNA polymerases I and III subunit RPAC1" [Bos taurus (taxid:9913)]

 Score = 378 (138.1 bits), Expect = 6.5e-35, P = 6.5e-35
 Identities = 69/133 (51%), Positives = 94/133 (70%)

Query:    13 EQDTLQFQLKIKCTKXXXXXXXXXX-XXMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPI 71
             E DTLQF+L+++CT+             +Y  H+V+T+ + WVP+G+Q D++    + P+
Sbjct:   134 EIDTLQFRLQVRCTRNPHAAKDSSDPNELYVNHRVYTRHMTWVPLGNQADLFPEGAIRPV 193

Query:    72 HDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRL 131
             HDDILIA+LRPG EID+ M  VK IG+DHAKFSPVATA YRLLP ITL + +EGE A+ L
Sbjct:   194 HDDILIAQLRPGQEIDLLMHCVKGIGKDHAKFSPVATASYRLLPDITLLEPVEGEAAEEL 253

Query:   132 QTMFSPGVISIEK 144
                FSPGVI +++
Sbjct:   254 SRCFSPGVIEVQE 266

GO:0005634 "nucleus" evidence=IEA

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

GO:0046983 "protein dimerization activity" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2RH57 POLR1C "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 377 (137.8 bits), Expect = 8.3e-35, P = 8.3e-35
 Identities = 69/136 (50%), Positives = 95/136 (69%)

Query:    10 EPCEQDTLQFQLKIKCTKXXXXXXXXXX-XXMYEKHKVFTKDIQWVPIGSQGDMYKSSDV 68
             E  E DTLQF+L+++CT+             +Y  HKV+++ + WVP+G+Q D++    +
Sbjct:   131 EGTEIDTLQFRLQVRCTRNPHAAKDSSDPNELYVNHKVYSRHMTWVPLGNQADLFPEGTI 190

Query:    69 GPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMA 128
              P+HDDILIA+LRPG EID+ M  VK IG+DHAKFSPVATA YRLLP ITL + +EG+ A
Sbjct:   191 RPVHDDILIAQLRPGQEIDLLMHCVKGIGKDHAKFSPVATASYRLLPDITLLEPVEGDAA 250

Query:   129 QRLQTMFSPGVISIEK 144
             + L   FSPGVI +++
Sbjct:   251 EELSRCFSPGVIEVQE 266

GO:0046983 "protein dimerization activity" evidence=IEA

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

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

GO:0003677 "DNA binding" evidence=IEA

FB|FBgn0031657 CG3756 [Drosophila melanogaster (taxid:7227)]

 Score = 375 (137.1 bits), Expect = 1.3e-34, P = 1.3e-34
 Identities = 73/139 (52%), Positives = 96/139 (69%)

Query:    13 EQDTLQFQLKIKCTKXXXXXXXXXXXX-MYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPI 71
             EQDTL+F+LK+KC++             +Y+ HKV++  ++W+P G Q  +Y  S V  I
Sbjct:   127 EQDTLEFELKVKCSRRRDAGKDQSNFDDIYKNHKVYSGHLKWLPKGKQAQIYSESAVNCI 186

Query:    72 HDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRL 131
             HDDILIA+LRPGHE+D+ + AVK +GRDHAKFSPVATA YRLLP I L +E+ G+ A  L
Sbjct:   187 HDDILIAQLRPGHELDLRLVAVKGLGRDHAKFSPVATATYRLLPMIKLNREVTGKDAYLL 246

Query:   132 QTMFSPGVISIEKKPNAGV 150
             Q  FSPGVI I++   A V
Sbjct:   247 QNCFSPGVIGIDENETAYV 265

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

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

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

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

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

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

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005875 "microtubule associated complex" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q32L22	RPAC1_BOVIN	No assigned EC number	0.5338	0.8684	0.3815	yes	N/A
O15160	RPAC1_HUMAN	No assigned EC number	0.5294	0.8881	0.3901	yes	N/A
P52432	RPAC1_MOUSE	No assigned EC number	0.5441	0.8881	0.3901	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	152
cd07032	291	cd07032, RNAP_I_II_AC40, AC40 subunit of Eukaryoti	1e-65
smart00662	224	smart00662, RPOLD, RNA polymerases D	6e-27
cd07028	212	cd07028, RNAP_RPB3_like, RPB3 subunit of RNA polym	7e-26
cd07031	265	cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic	4e-15
pfam01000	117	pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA	7e-15
COG0202	317	COG0202, RpoA, DNA-directed RNA polymerase, alpha	4e-14
PRK00783	263	PRK00783, PRK00783, DNA-directed RNA polymerase su	3e-13
cd07030	259	cd07030, RNAP_D, D subunit of Archaeal RNA polymer	3e-12

>gnl|CDD|132910 cd07032, RNAP_I_II_AC40, AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

 Score =  201 bits (513), Expect = 1e-65
 Identities = 76/136 (55%), Positives = 101/136 (74%), Gaps = 1/136 (0%)

Query: 10  EPCEQDTLQFQLKIKCTKSASFSHSSH-ADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDV 68
           EP E++TL F+LK+KCT++ +    S   D++Y  HKV++ D++WVPIGSQ   +  + +
Sbjct: 83  EPTEENTLVFELKVKCTRNPNAPKDSTDPDELYINHKVYSGDLKWVPIGSQEKRFADNPI 142

Query: 69  GPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMA 128
            P+H DILIAKLRPG EID+ +  VK IG+DHAKFSPVATA YRLLP+ITL + I GE A
Sbjct: 143 RPVHPDILIAKLRPGQEIDLELHCVKGIGKDHAKFSPVATASYRLLPEITLLKPITGEDA 202

Query: 129 QRLQTMFSPGVISIEK 144
           ++LQ  F PGVI IE+
Sbjct: 203 EKLQKCFPPGVIDIEE 218

The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC40 to RPB3 suggests a similar function. The AC40 subunit is likely to associate with the RPB11 counterpart, AC19, to form a heterodimer, which stabilizes the association of the two largest subunits of RNAP I and RNAP III. Length = 291

>gnl|CDD|214766 smart00662, RPOLD, RNA polymerases D

 Score =   99 bits (250), Expect = 6e-27
 Identities = 34/134 (25%), Positives = 51/134 (38%), Gaps = 26/134 (19%)

Query: 10  EPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVG 69
           E CE+ ++   L +K                     V   D++              DV 
Sbjct: 72  EGCEKCSVTLTLDVKGPGE-----------------VTAGDLKSDS---------DPDVE 105

Query: 70  PIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQ 129
            ++ DI IAKLR G E+++   A K  G  HAK+SPV+T  YR +P+I +          
Sbjct: 106 IVNPDIPIAKLREGQELELEARAEKGRGYVHAKWSPVSTVEYRYIPRIPVDASFSPVDRV 165

Query: 130 RLQTMFSPGVISIE 143
             Q      V   +
Sbjct: 166 AYQVECPRVVQRTD 179

DNA-directed RNA polymerase subunit D and bacterial alpha chain. Length = 224

>gnl|CDD|132906 cd07028, RNAP_RPB3_like, RPB3 subunit of RNA polymerase

 Score = 96.9 bits (241), Expect = 7e-26
 Identities = 36/110 (32%), Positives = 48/110 (43%), Gaps = 12/110 (10%)

Query: 6   RLKYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKS 65
           R   E CE +    +  +  T  A                V++KD+  V      ++   
Sbjct: 77  RSPEEDCECEDHCDKCSVVLTLQAFAESE-------STTNVYSKDLVIVSNLMGRNI--- 126

Query: 66  SDVGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLP 115
               PI  DILI KLR G EI +T  A K IG++HAKF PVA   +R  P
Sbjct: 127 --GHPIIQDILICKLRKGQEIKLTCVAKKGIGKEHAKFGPVAAIEFRYDP 174

The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts. Length = 212

>gnl|CDD|132909 cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic RNA polymerase II

 Score = 69.9 bits (172), Expect = 4e-15
 Identities = 32/111 (28%), Positives = 50/111 (45%), Gaps = 9/111 (8%)

Query: 12  CEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPI 71
           C++ +++  L +KCT   +      + D+        K    VP+  + D    S+    
Sbjct: 88  CDKCSVELTLDVKCTGDQTRE--VTSRDLV---SSGPKVNDVVPVPIRND----SEDNGE 138

Query: 72  HDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQE 122
            D ILI KLR G E+ +   A K IG++HAK+SP A   +   P   L   
Sbjct: 139 EDGILIVKLRKGQELKLRCIAKKGIGKEHAKWSPTAAVTFEYDPDNALRHT 189

The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. Length = 265

>gnl|CDD|110031 pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA insert domain

 Score = 66.1 bits (162), Expect = 7e-15
 Identities = 27/100 (27%), Positives = 40/100 (40%), Gaps = 28/100 (28%)

Query: 3   KNLRLKYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDM 62
           K L  K E CE+ ++   L +K                    +V   D++          
Sbjct: 28  KELVCKIEGCEECSVTLTLDVKGPG-----------------EVTAGDLES--------- 61

Query: 63  YKSSDVGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAK 102
               DV  ++ DILIA LR G E+++  +A K  G  HAK
Sbjct: 62  --DPDVEIVNPDILIATLRKGQELELEAYAKKGRGYVHAK 99

Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal. Length = 117

>gnl|CDD|223280 COG0202, RpoA, DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]

 Score = 67.4 bits (165), Expect = 4e-14
 Identities = 31/161 (19%), Positives = 54/161 (33%), Gaps = 19/161 (11%)

Query: 3   KNLRLKYEPCEQDTLQFQLKIKCTKSAS-FSHSS----HADDMYEKH-----------KV 46
           K L +K +  E+ TL+   +     +AS  +          D                +V
Sbjct: 79  KPLAVKLDGDEEVTLELDKEGPGEVTASDITVPLDLEVVNPDHVIATLTEDAKLEMELRV 138

Query: 47  FTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPV 106
           ++ D      G++ D      VGPI  D   + +R    I       +   +DH K+ P 
Sbjct: 139 YSGDGYVPAEGNREDD---PPVGPIAVDAPFSPVRKVQYIVEEARVGQGTDKDHLKWEPE 195

Query: 107 ATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIEKKPN 147
                R    + +  +I  E  +    +    V   E+KP 
Sbjct: 196 TNGSIRPEEALAIAAKILIEHLEVFVELCPKAVEIEEEKPE 236

Length = 317

>gnl|CDD|234837 PRK00783, PRK00783, DNA-directed RNA polymerase subunit D; Provisional

 Score = 64.5 bits (158), Expect = 3e-13
 Identities = 22/68 (32%), Positives = 41/68 (60%), Gaps = 3/68 (4%)

Query: 60  GDMYKSSD--VGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKI 117
           GD+ KSSD  V P+  +I I KL+ G ++ +  +A    G++HAK+ P +   Y+  P+I
Sbjct: 107 GDL-KSSDPDVKPVDPNIPIVKLKEGQKLVLEAYARLGRGKEHAKWQPGSACGYKYYPRI 165

Query: 118 TLTQEIEG 125
            ++++ + 
Sbjct: 166 EVSEDCDE 173

Length = 263

>gnl|CDD|132908 cd07030, RNAP_D, D subunit of Archaeal RNA polymerase

 Score = 61.9 bits (151), Expect = 3e-12
 Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 3/61 (4%)

Query: 60  GDMYKSSD--VGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKI 117
           GD+ KSSD  V P++D+I I KL  G ++ +  +A    G++HAK+ P     Y+  P I
Sbjct: 107 GDL-KSSDPDVKPVYDNIPIVKLGKGQKLVLEAYARLGRGKEHAKWQPTTACGYKYYPVI 165

Query: 118 T 118
            
Sbjct: 166 E 166

The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer. Length = 259

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	152
KOG1521|consensus	338		100.0
cd07032	291	RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA poly	100.0
KOG1522|consensus	285		100.0
cd07031	265	RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polyme	99.97
PRK00783	263	DNA-directed RNA polymerase subunit D; Provisional	99.95
cd07030	259	RNAP_D D subunit of Archaeal RNA polymerase. The D	99.95
smart00662	224	RPOLD RNA polymerases D. DNA-directed RNA polymera	99.92
cd07028	212	RNAP_RPB3_like RPB3 subunit of RNA polymerase. The	99.92
PF01000	112	RNA_pol_A_bac: RNA polymerase Rpb3/RpoA insert dom	99.75
COG0202	317	RpoA DNA-directed RNA polymerase, alpha subunit/40	99.67
PRK14979	195	DNA-directed RNA polymerase subunit D; Provisional	99.64
cd06928	215	RNAP_alpha_NTD N-terminal domain of the Alpha subu	99.09
PRK05182	310	DNA-directed RNA polymerase subunit alpha; Provisi	99.01
TIGR02027	297	rpoA DNA-directed RNA polymerase, alpha subunit, b	98.66
CHL00013	327	rpoA RNA polymerase alpha subunit	96.48
PRK15449	95	ferredoxin-like protein FixX; Provisional	81.32

>KOG1521|consensus

Probab=100.00  E-value=1.2e-50  Score=339.13  Aligned_cols=137  Identities=54%  Similarity=0.910  Sum_probs=133.7

Q ss_pred             CeEEEEEEEEecCCCCC-ccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEEEEEEEe
Q psy1865          15 DTLQFQLKIKCTKSASF-SHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAV   93 (152)
Q Consensus        15 csV~f~L~V~c~~~~~~-~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~l~~~A~   93 (152)
                      +|++|+|+|+|++++.+ ++++||..||.|+.|||+|++|.|+|.|.+.|.+..++|+++||+|+||||||+|+|+|||+
T Consensus       133 ntlvF~L~VkC~~n~~a~~~~sdpk~Ly~ns~vyS~~~~w~P~g~Q~~~f~e~~i~~~~~DILiAkLrPGQEI~le~hav  212 (338)
T KOG1521|consen  133 NTLVFKLNVKCTKNPNAKKDSSDPKELYNNSEVYSRDLTWKPKGYQAEIFAENPIRPVHDDILIAKLRPGQEIELEAHAV  212 (338)
T ss_pred             ceEEEEEEeeccCCCCcccCCCChhHhccCcEEecCcceeccccchhhhcccCCccccCcceEEEecCCCCEeeeeeeee
Confidence            99999999999999999 99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCcceeeeccceeEEeEeeeeeEEccccChHHHHHHHhhCCCccEEeccCCC---ceee
Q psy1865          94 KSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIEKKPN---AGVV  151 (152)
Q Consensus        94 kGiGk~HAKwsPv~~~~yr~~P~i~i~~~~~~~~~~~~~~~cp~~Vf~i~~~~~---a~v~  151 (152)
                      |||||+||||||||||+||++|.|.|+.++.||+|++|++|||+|||+|+++++   |+|+
T Consensus       213 kGIGkdHAKfSPVaTAsYRLlP~I~l~~ei~ge~A~~lqkcfs~gVi~iee~~~kk~A~Va  273 (338)
T KOG1521|consen  213 KGIGKDHAKFSPVATASYRLLPTIVLLAEIEGEDAERLQKCFSPGVIDIEEMGGKKRAYVA  273 (338)
T ss_pred             cccCcccccccCcccceeeccceeEecCcccchhHHHHHhhCCCCeEeeecCCCceEEEec
Confidence            999999999999999999999999999999999999999999999999999876   7664

>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

Probab=100.00  E-value=1.7e-45  Score=310.13  Aligned_cols=137  Identities=55%  Similarity=0.964  Sum_probs=131.4

Q ss_pred             CCCCCCCCeEEEEEEEEecCCCCC-ccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEE
Q psy1865           8 KYEPCEQDTLQFQLKIKCTKSASF-SHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEI   86 (152)
Q Consensus         8 ~~~~c~~csV~f~L~V~c~~~~~~-~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I   86 (152)
                      ++++|++|||+|+|+|+|++++.. +++++|.++|.+..|||+||+|.|.|.|...+.++++.|++++|+|+||++||+|
T Consensus        81 ~~~~~~~~~v~f~L~v~c~~~~~~~~~~~~~~~~~~~~~VyS~dl~~~p~g~q~~~~~~~~v~~v~~dI~I~kL~~gQ~l  160 (291)
T cd07032          81 DDEPTEENTLVFELKVKCTRNPNAPKDSTDPDELYINHKVYSGDLKWVPIGSQEKRFADNPIRPVHPDILIAKLRPGQEI  160 (291)
T ss_pred             ccCCCCCcEEEEEEEEEccCCcccccccccccccccccEEECCCCEecCCCccccccCCCCcEEeCCCcEEEEECCCCEE
Confidence            578999999999999999988777 8888999999999999999999999999888889999999999999999999999


Q ss_pred             EEEEEEeecCCcceeeeccceeEEeEeeeeeEEccccChHHHHHHHhhCCCccEEecc
Q psy1865          87 DVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIEK  144 (152)
Q Consensus        87 ~l~~~A~kGiGk~HAKwsPv~~~~yr~~P~i~i~~~~~~~~~~~~~~~cp~~Vf~i~~  144 (152)
                      +|+|+|+||+||+||||||||+|+|||+|+|+|++++.++++++|+++||+|||++++
T Consensus       161 ~le~~a~kG~Gk~HAKwsPv~ta~yr~~P~I~i~~~~~~~~~~~~~~~cP~~Vf~i~~  218 (291)
T cd07032         161 DLELHCVKGIGKDHAKFSPVATASYRLLPEITLLKPITGEDAEKLQKCFPPGVIDIEE  218 (291)
T ss_pred             EEEEEEEcCcccccceecCceeEEEEecceEEEcCcCCHHHHHHHHhhCCCccEEecc
Confidence            9999999999999999999999999999999999999999999999999999999975

The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun

>KOG1522|consensus

Probab=100.00  E-value=2.5e-34  Score=235.92  Aligned_cols=124  Identities=27%  Similarity=0.407  Sum_probs=96.5

Q ss_pred             cCCCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeE-----EeecCCCCCCCCCCCCcccCCCceEEEcC
Q psy1865           7 LKYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQ-----WVPIGSQGDMYKSSDVGPIHDDILIAKLR   81 (152)
Q Consensus         7 ~~~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~-----~~p~~~q~~~~~~~~~~p~~~~I~I~KL~   81 (152)
                      +|+++|++|||.|+|+++|+.+++             .+|||+||.     ..|+.+...  ......+-+++|+|+|||
T Consensus        87 ~C~~~C~eCSVef~L~~kc~~d~T-------------~~VtsrDL~s~~~~v~pv~~~~~--~~~~~~~e~~gilI~KLR  151 (285)
T KOG1522|consen   87 ECDEFCPECSVEFTLDVKCTDDQT-------------RDVTSRDLVSLDPTVTPVDSNRG--SEIDDDSESKGILIVKLR  151 (285)
T ss_pred             chhccCCcceEEEEEeeeecccce-------------eeeehHhhhccCCcccccccCCC--CccccccccCCcEEEEee
Confidence            489999999999999999998865             466666666     345543211  111123447899999999


Q ss_pred             CCCEEEEEEEEeecCCcceeeeccceeEEeEeeeeeEEccccChHHHHHHHhhCCCccEEeccC
Q psy1865          82 PGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIEKK  145 (152)
Q Consensus        82 ~GQ~I~l~~~A~kGiGk~HAKwsPv~~~~yr~~P~i~i~~~~~~~~~~~~~~~cp~~Vf~i~~~  145 (152)
                      +||+|+|+|+|+|||||+||||||+|++.|+|+|.+.+++.+..++...+.+--+...+++++.
T Consensus       152 kgQELkLra~akKGigKeHAKWsPta~V~FeYDPdn~lrhT~y~~e~~~~~Ewp~sk~~e~~~~  215 (285)
T KOG1522|consen  152 KGQELKLRAIAKKGIGKEHAKWSPTAAVAFEYDPDNKLRHTLYWFEEDDLIEWPKSKNSELEED  215 (285)
T ss_pred             cCCceeeeeeecccccccccccCCcceEEEEECccHhhhccCCCccccchhhCCcccccCCCCC
Confidence            9999999999999999999999999999999999999998877655544444445566777665

>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II

Probab=99.97  E-value=7.4e-31  Score=218.58  Aligned_cols=103  Identities=28%  Similarity=0.420  Sum_probs=85.9

Q ss_pred             CCCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCc------ccCCCceEEEcC
Q psy1865           8 KYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVG------PIHDDILIAKLR   81 (152)
Q Consensus         8 ~~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~------p~~~~I~I~KL~   81 (152)
                      +++.|+.|++.|+|+|+|+++.             ...|||+||+|.|.+.|...  ...+.      +++++|+|+||+
T Consensus        84 ~~~~~~~~~v~~~L~v~~~~~~-------------~~~V~s~Dl~~~~~~~~~~~--~~pi~~~~~~~~~~~~i~I~kL~  148 (265)
T cd07031          84 CDEFCDKCSVELTLDVKCTGDQ-------------TREVTSRDLVSSGPKVNDVV--PVPIRNDSEDNGEEDGILIVKLR  148 (265)
T ss_pred             ccCCCCCCeEEEEEEEEeccCC-------------CceEEHHHcccccccccccC--CcccccccccccCCCCeEEEEEC
Confidence            4567999999999999998753             26899999999876554421  11111      346899999999


Q ss_pred             CCCEEEEEEEEeecCCcceeeeccceeEEeEeeeeeEEccccCh
Q psy1865          82 PGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEG  125 (152)
Q Consensus        82 ~GQ~I~l~~~A~kGiGk~HAKwsPv~~~~yr~~P~i~i~~~~~~  125 (152)
                      |||+|+|+|+|+||+||+||||||||+|+|||+|+|+|+++..+
T Consensus       149 ~gq~i~le~~a~kG~Gk~HAKwsPv~~~~y~~~p~i~i~~~~~~  192 (265)
T cd07031         149 KGQELKLRCIAKKGIGKEHAKWSPTAAVTFEYDPDNALRHTDYW  192 (265)
T ss_pred             CCCEEEEEEEEECCEeccCCEeccceEEEEEEccceEEcccccc
Confidence            99999999999999999999999999999999999999976544

The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.

>PRK00783 DNA-directed RNA polymerase subunit D; Provisional

Probab=99.95  E-value=1.5e-27  Score=197.21  Aligned_cols=108  Identities=23%  Similarity=0.501  Sum_probs=95.2

Q ss_pred             CCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEEE
Q psy1865           9 YEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDV   88 (152)
Q Consensus         9 ~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~l   88 (152)
                      +++|++|++.|+|+++.+                 ..|||+||++          .++.+.|++++|+|++|++||+|+|
T Consensus        84 ~~~~~~~~~~~~l~~~~~-----------------~~V~a~dl~~----------~~~~v~~v~~~~~I~~L~~~~~l~~  136 (263)
T PRK00783         84 GEGCPDCTVTLSLEVEGP-----------------KTVYSGDLKS----------SDPDVKPVDPNIPIVKLKEGQKLVL  136 (263)
T ss_pred             CCCCCCcEEEEEEEecCC-----------------CcEEcccccc----------CCCCceecCCCcEEEEeCCCCEEEE
Confidence            468999999999999832                 4699999985          2456789999999999999999999


Q ss_pred             EEEEeecCCcceeeeccceeEEeEeeeeeEEccccChHHHHHHHhhCCCccEEeccC
Q psy1865          89 TMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIEKK  145 (152)
Q Consensus        89 ~~~A~kGiGk~HAKwsPv~~~~yr~~P~i~i~~~~~~~~~~~~~~~cp~~Vf~i~~~  145 (152)
                      +|+|+||+|++||||||+++++||+.|.|.+.+.+.+  +..+++.||.++|.++++
T Consensus       137 e~~~~~G~G~~HAKw~p~~~~~yr~~p~I~i~~~C~~--C~~C~~~CP~~vi~~~~~  191 (263)
T PRK00783        137 EAYARLGRGKEHAKWQPGSACGYKYYPRIEVSEDCDE--CEKCVEACPRGVLELKEG  191 (263)
T ss_pred             EEEEEcCcccccCccCcceEeeecccccccccccCCc--hHHHHHhCCccccEecCC
Confidence            9999999999999999999999999999999555543  778999999999999764

>cd07030 RNAP_D D subunit of Archaeal RNA polymerase

Probab=99.95  E-value=2.8e-27  Score=195.26  Aligned_cols=108  Identities=25%  Similarity=0.480  Sum_probs=97.4

Q ss_pred             CCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEEE
Q psy1865           9 YEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDV   88 (152)
Q Consensus         9 ~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~l   88 (152)
                      ...|+.|++.|+|+++++                 ..|||+||+|          .+..+.|++++|+|+||++||+|+|
T Consensus        84 ~~~~~~~~~~~~l~~~~~-----------------~~v~s~dl~~----------~~~~v~~~~~~~~I~~l~~~~~l~~  136 (259)
T cd07030          84 GAGCPLCTVTLTLSVEGP-----------------GTVYSGDLKS----------SDPDVKPVYDNIPIVKLGKGQKLVL  136 (259)
T ss_pred             CCCCCCcEEEEEEEccCC-----------------ceEEcccccc----------CCCCccccCCCcEEEEeCCCCEEEE
Confidence            467889999999999854                 4699999987          3456789999999999999999999


Q ss_pred             EEEEeecCCcceeeeccceeEEeEeeeeeEEccccChHHHHHHHhhCCCccEEeccC
Q psy1865          89 TMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIEKK  145 (152)
Q Consensus        89 ~~~A~kGiGk~HAKwsPv~~~~yr~~P~i~i~~~~~~~~~~~~~~~cp~~Vf~i~~~  145 (152)
                      +++|+||+||+||||+|+++++||++|.|.+++.+.+  +..+++.||.++|.++++
T Consensus       137 ~~~~~kg~g~~hakw~p~~~~~yr~~P~i~i~~~C~~--C~~C~~~CP~~vi~~d~~  191 (259)
T cd07030         137 EAYARLGRGKEHAKWQPTTACGYKYYPVIEIDEDCDG--CGKCVEECPRGVLELEEG  191 (259)
T ss_pred             EEEEecCccCCCCCCCCccEEEEEeecceechhhCCC--hHHHHHhCCccceEccCC
Confidence            9999999999999999999999999999999987765  778999999999998764

The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w

>smart00662 RPOLD RNA polymerases D

Probab=99.92  E-value=8.6e-26  Score=183.79  Aligned_cols=111  Identities=31%  Similarity=0.384  Sum_probs=100.3

Q ss_pred             cCCCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEE
Q psy1865           7 LKYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEI   86 (152)
Q Consensus         7 ~~~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I   86 (152)
                      +|+.+|+.|++.|+|+++|+                 ..|||+||+|.         .|+.+.|++++|+|++|++||+|
T Consensus        70 ~~~~~~~~~~~~~~L~~~gp-----------------~~V~a~Dl~~~---------~~~~v~~vnp~~~I~~L~~gq~l  123 (224)
T smart00662       70 ECEEGCEKCSVTLTLDVKGP-----------------GEVTAGDLKSD---------SDPDVEIVNPDIPIAKLREGQEL  123 (224)
T ss_pred             cccccCCCceEEEEEEEEcC-----------------CcEEHHHcccC---------CCCCcEEeCCCcEEEEECCCCEE
Confidence            46789999999999999965                 35999999972         15578899999999999999999


Q ss_pred             EEEEEEeecCCcceeeeccceeEEeEeeeeeEEccccChHHHHHHHhhCCCccEEec
Q psy1865          87 DVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIE  143 (152)
Q Consensus        87 ~l~~~A~kGiGk~HAKwsPv~~~~yr~~P~i~i~~~~~~~~~~~~~~~cp~~Vf~i~  143 (152)
                      +++++|+||+|++||||+|+++++|++.|.|.++..+++.++..+...||++++..+
T Consensus       124 ~~e~~~~~G~G~~hak~~p~~~~~~~~~~~i~id~~~~pv~~v~~~~~~~~~~~~~~  180 (224)
T smart00662      124 ELEARAEKGRGYVHAKWSPVSTVEYRYIPRIPVDASFSPVDRVAYQVECPRVVQRTD  180 (224)
T ss_pred             EEEEEEECCcccccCccccccCCCcCcCCEEEECCCCChhhheeeeccCCccceecc
Confidence            999999999999999999999999999999999998888888889999999888765

DNA-directed RNA polymerase subunit D and bacterial alpha chain

>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase

Probab=99.92  E-value=2.3e-25  Score=180.64  Aligned_cols=91  Identities=35%  Similarity=0.500  Sum_probs=79.5

Q ss_pred             cCCCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEE
Q psy1865           7 LKYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEI   86 (152)
Q Consensus         7 ~~~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I   86 (152)
                      ++...|+.|++.|+|+++++.+             .+..|||+||+|.+.+.     +++.+.|++++|+|+||++||+|
T Consensus        84 ~~~~~~~~~~v~~~l~~~g~~~-------------~~~~V~s~DL~~~~~~~-----~~~~v~pv~~di~I~kL~~gq~i  145 (212)
T cd07028          84 ECEDHCDKCSVVLTLQAFAESE-------------STTNVYSKDLVIVSNLM-----GRNIGHPIIQDILICKLRKGQEI  145 (212)
T ss_pred             cccccccceeEEEEEEccCCCC-------------CcceEEHHHcccCCccc-----cCCCeEEeCCCcEEEEECCCCEE
Confidence            3567788899999999997653             12579999999965443     34678899999999999999999


Q ss_pred             EEEEEEeecCCcceeeeccceeEEeEeee
Q psy1865          87 DVTMFAVKSIGRDHAKFSPVATAFYRLLP  115 (152)
Q Consensus        87 ~l~~~A~kGiGk~HAKwsPv~~~~yr~~P  115 (152)
                      +|+|+|+||+|++|||||||++++|+++|
T Consensus       146 ~le~~~~~G~G~~hAk~sPV~~v~y~~~~  174 (212)
T cd07028         146 KLTCVAKKGIGKEHAKFGPVAAIEFRYDP  174 (212)
T ss_pred             EEEEEEECCCcCCCCEeCCceEEEEEEEc
Confidence            99999999999999999999999999999

The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and

>PF01000 RNA_pol_A_bac: RNA polymerase Rpb3/RpoA insert domain; InterPro: IPR011262 DNA-directed RNA polymerases 2

Probab=99.75  E-value=3.2e-18  Score=125.21  Aligned_cols=70  Identities=31%  Similarity=0.516  Sum_probs=63.4

Q ss_pred             CCCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEE
Q psy1865           8 KYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEID   87 (152)
Q Consensus         8 ~~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~   87 (152)
                      ++.+|+.|++.|.|+++|+.                 .|||+||++          .+..+++++++++|++|++||+|+
T Consensus        43 ~~~~~~~~~~~~~L~~~g~~-----------------~V~a~di~~----------~~~~i~ivn~d~~I~tl~~~~~l~   95 (112)
T PF01000_consen   43 CEEGCDDCSVTFSLKVKGPG-----------------EVTAGDIKL----------EPSGIEIVNPDIYIATLSEGQKLE   95 (112)
T ss_dssp             SSSSTTTSEEEEEEEEESSS-----------------CEEGGGSEE----------SBTTEEESSTTSEEEEEESSTEEE
T ss_pred             cccCCCCceEEEEEEecCCC-----------------ccccceeEe----------cCCceEEecCCeEEEEECCCCEEE
Confidence            56899999999999999763                 499999998          356678999999999999999999


Q ss_pred             EEEEEeecCCcceeeec
Q psy1865          88 VTMFAVKSIGRDHAKFS  104 (152)
Q Consensus        88 l~~~A~kGiGk~HAKws  104 (152)
                      |+|+|++|+|+.|||||
T Consensus        96 ~e~~i~~G~Gy~~ak~~  112 (112)
T PF01000_consen   96 MELYIEKGRGYVHAKWS  112 (112)
T ss_dssp             EEEEEEEEESEECCTS-
T ss_pred             EEEEEECCCcccccccC
Confidence            99999999999999997

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha (RpoA) subunit homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. The dimerisation domains differ between the different subunit families. In eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain is comprised of a central insert domain, which interrupts an Rpb11-like domain (IPR009025 from INTERPRO), dividing it into two halves []. In eukaryotic Rpb11 and archaeal L subunits, the insert domain is lacking, leaving the Rpb11-like domain intact and contiguous.; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_O 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3GTK_C 1TWH_C 3HOV_C 3S17_C ....

>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]

Probab=99.67  E-value=5.5e-17  Score=138.57  Aligned_cols=127  Identities=15%  Similarity=0.140  Sum_probs=110.5

Q ss_pred             CCCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEE
Q psy1865           8 KYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEID   87 (152)
Q Consensus         8 ~~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~   87 (152)
                      |+.+|..|++.++|+|.|+...-+ +-+++.+++....||++++.|-+.+.+   ..++++.|+..|+++++|+++|.+.
T Consensus       101 g~v~a~d~~~~~~lEv~np~~~ia-~~~~~~~l~~~~~V~~G~gyv~~~~~~---~~~~~v~~i~~D~~~spv~kvqy~v  176 (317)
T COG0202         101 GEVTASDITVPLDLEVVNPDHVIA-TLTEDAKLEMELRVYSGDGYVPAEGNR---EDDPPVGPIAVDAPFSPVRKVQYIV  176 (317)
T ss_pred             ccccHhhcccceeEEEECCCceee-eccCCcceEEEEEEEcCccEecccccc---ccCCCceeeeCCCceeeeeeceEEE
Confidence            566899999999999999866443 223367778889999999999665555   3667889999999999999999999


Q ss_pred             EEEEEeecCCcceeeeccceeEEeEeeeeeEEccccChHHHHHHHhhCCCc
Q psy1865          88 VTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPG  138 (152)
Q Consensus        88 l~~~A~kGiGk~HAKwsPv~~~~yr~~P~i~i~~~~~~~~~~~~~~~cp~~  138 (152)
                      ++|+|.+|+|++||||+|++..+|+++|.+.+-..+..++...++++||..
T Consensus       177 e~~r~~~~~~~Dhl~~~~~T~gsi~~~~a~~~aa~il~e~~~~~~~~~~~~  227 (317)
T COG0202         177 EEARVGQGTDKDHLKWEPETNGSIRPEEALAIAAKILIEHLEVFVELCPKA  227 (317)
T ss_pred             EeEEEeccCCceeEEEEEeeccEeehHHHHHHHHHHHHHHHHHHHhhcccc
Confidence            999999999999999999999999999988887778788999999999976

>PRK14979 DNA-directed RNA polymerase subunit D; Provisional

Probab=99.64  E-value=5e-16  Score=124.86  Aligned_cols=76  Identities=22%  Similarity=0.440  Sum_probs=62.6

Q ss_pred             CCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEEEEEEEe
Q psy1865          14 QDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAV   93 (152)
Q Consensus        14 ~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~l~~~A~   93 (152)
                      .+++.|+|+++.+                 ..|||+||++          .+.  .|++++++|++|++||+|+|+|+|+
T Consensus        77 ~~~~~l~L~~~gp-----------------~~Vta~Di~~----------~~~--~ivnpdi~I~tL~~g~~l~~e~~~~  127 (195)
T PRK14979         77 DEVITFTLSKEGP-----------------CTVYSSDLKS----------ENG--EVAFKNIPIVKLAEGQKLEIECEAL  127 (195)
T ss_pred             CCcEEEEEEEeCC-----------------ceEEHHHcCC----------CCC--cccCCCcEEEEECCCCEEEEEEEEE
Confidence            4688999988621                 4699999986          222  4789999999999999999999999


Q ss_pred             ecCCcceeeeccceeEEeEeeeeeEE
Q psy1865          94 KSIGRDHAKFSPVATAFYRLLPKITL  119 (152)
Q Consensus        94 kGiGk~HAKwsPv~~~~yr~~P~i~i  119 (152)
                      +|+|++||||+|+ .+.|++.+.=++
T Consensus       128 ~G~Gy~hAk~~pv-da~y~~~~~dkl  152 (195)
T PRK14979        128 VGTGKIHAKWQPC-NAVYKQISNDEV  152 (195)
T ss_pred             CCCccccccccce-eeEEecCCCcEE
Confidence            9999999999995 567877765444

>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase

Probab=99.09  E-value=4.5e-10  Score=91.27  Aligned_cols=76  Identities=26%  Similarity=0.300  Sum_probs=65.7

Q ss_pred             CCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEEEEEE
Q psy1865          12 CEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMF   91 (152)
Q Consensus        12 c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~l~~~   91 (152)
                      |.+|++.++|+++++                 ..|||+||.+           +..+.+++++++|++|.+||+|+++|+
T Consensus        81 ~~~~~~~~~l~~~gp-----------------~~V~a~Di~~-----------~~~i~ivnp~~~IatL~~~~~l~ie~~  132 (215)
T cd06928          81 SEDEPQVLRLKVKGP-----------------GVVTAADIEL-----------PSGVEIVNPDQYIATLTEDASLEMELR  132 (215)
T ss_pred             CCCceEEEEEEEecC-----------------eEEEhHhcCc-----------CCCcEEeCCCcEEEEECCCCEEEEEEE
Confidence            447899999999843                 4699999986           224789999999999999999999999


Q ss_pred             EeecCCcceeee-----------------ccceeEEeEeee
Q psy1865          92 AVKSIGRDHAKF-----------------SPVATAFYRLLP  115 (152)
Q Consensus        92 A~kGiGk~HAKw-----------------sPv~~~~yr~~P  115 (152)
                      |++|+|+.+|+|                 |||--+.|....
T Consensus       133 i~~G~Gy~~~~~~~~~~~~~~~~~iDa~f~PV~~vny~v~~  173 (215)
T cd06928         133 IEKGRGYVPAEENKSEEKPIGFIPIDAIFSPVRKVNYSVES  173 (215)
T ss_pred             EECcCcceeccccccccCCCceEEeCCCcCCeEEEEEEEEE
Confidence            999999999988                 899989897554

The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac

>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional

Probab=99.01  E-value=8.1e-10  Score=94.30  Aligned_cols=73  Identities=26%  Similarity=0.397  Sum_probs=62.5

Q ss_pred             CeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEEEEEEEee
Q psy1865          15 DTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAVK   94 (152)
Q Consensus        15 csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~l~~~A~k   94 (152)
                      |++.++|+++++                 ..|||+||.+           ++.+.|++++++|++|++||+|+++++|++
T Consensus        93 ~~~~~~l~~~gp-----------------~~VtA~Di~~-----------~~~v~ivn~d~~IatL~~~~~l~ie~~~~k  144 (310)
T PRK05182         93 EPVTLTLSKKGP-----------------GEVTAGDIET-----------DGDVEIVNPDLVIATLNEGAKLEMELTVER  144 (310)
T ss_pred             ceEEEEEEecCC-----------------eEEEHHHcCC-----------CCCcEEeCCCeEEEEECCCCEEEEEEEEEC
Confidence            899999999732                 4799999985           234789999999999999999999999999


Q ss_pred             cCCcceee----------------eccceeEEeEeee
Q psy1865          95 SIGRDHAK----------------FSPVATAFYRLLP  115 (152)
Q Consensus        95 GiGk~HAK----------------wsPv~~~~yr~~P  115 (152)
                      |+|..+|+                |+||.-+.|...+
T Consensus       145 G~Gy~~~~~~~~~~~~g~i~iDa~f~PV~~vny~ve~  181 (310)
T PRK05182        145 GRGYVPAEENKEDAPIGRIPVDAIFSPVKKVNYTVEN  181 (310)
T ss_pred             cCCCcccccccccCCcccEEecCCcCCccceEEEecc
Confidence            99987665                9999989996444

>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type

Probab=98.66  E-value=9.8e-08  Score=81.10  Aligned_cols=62  Identities=26%  Similarity=0.332  Sum_probs=53.1

Q ss_pred             ceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEEEEEEEeecCCccee-----------------eeccc
Q psy1865          44 HKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHA-----------------KFSPV  106 (152)
Q Consensus        44 ~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~l~~~A~kGiGk~HA-----------------KwsPv  106 (152)
                      ..|+++||+|.          ++.+.++.++++|++|.+||+|++++++.+|+|..+|                 -||||
T Consensus        86 ~~VtA~Di~~~----------p~~ieivnpd~~IatL~~~~~L~iel~i~~G~Gy~~~~~~~~~~~~~~~i~iDa~FsPV  155 (297)
T TIGR02027        86 GVVTAGDIKAP----------PGDVEIVNPDLVIATLTEPADLEIELRVERGRGYVPAEENREEDRPVGVIAVDAIFSPV  155 (297)
T ss_pred             EEEEhhhcccC----------CCCcEEeCCCeEEEEECCCCEEEEEEEEEcccccCcccccccccCccccccccccccCe
Confidence            57999999973          3457889999999999999999999999999997544                 49999


Q ss_pred             eeEEeEeee
Q psy1865         107 ATAFYRLLP  115 (152)
Q Consensus       107 ~~~~yr~~P  115 (152)
                      --+.|....
T Consensus       156 ~~Vny~ve~  164 (297)
T TIGR02027       156 LKVNYEVEN  164 (297)
T ss_pred             EEEEEEEee
Confidence            989997654

This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.

>CHL00013 rpoA RNA polymerase alpha subunit

Probab=96.48  E-value=0.016  Score=50.20  Aligned_cols=61  Identities=21%  Similarity=0.276  Sum_probs=53.2

Q ss_pred             ceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEEEEEEEeecCCcc--------------eeeeccceeE
Q psy1865          44 HKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAVKSIGRD--------------HAKFSPVATA  109 (152)
Q Consensus        44 ~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~l~~~A~kGiGk~--------------HAKwsPv~~~  109 (152)
                      ..|+++|+.+           ++.+..+.++..|+.|..|+.|++++...+|.|-.              -|-||||--+
T Consensus       106 ~~vtA~Di~~-----------p~~ieivnpd~~Iatl~~~~~l~~el~ie~G~GY~~~~~~~~~~g~i~iDa~FsPV~kV  174 (327)
T CHL00013        106 KYVTAQDIIL-----------PPSVEIVDPTQHIATITEPIDLEIELKIEKGRGYRLKTPKNFQDGSFPIDAVFMPVRNV  174 (327)
T ss_pred             eEEEeeeecc-----------CCCeEEeCCCeEEEEeCCCCEEEEEEEEECccCceeccccccCCCcEEeCCCCCCeeEE
Confidence            5799999975           34578899999999999999999999999999984              3479999999


Q ss_pred             EeEeee
Q psy1865         110 FYRLLP  115 (152)
Q Consensus       110 ~yr~~P  115 (152)
                      .|...+
T Consensus       175 ny~Ve~  180 (327)
T CHL00013        175 NYSIHS  180 (327)
T ss_pred             EEEEEE
Confidence            997776

>PRK15449 ferredoxin-like protein FixX; Provisional

Probab=81.32  E-value=1.7  Score=31.41  Aligned_cols=39  Identities=10%  Similarity=0.240  Sum_probs=27.9

Q ss_pred             EEeEe---eeeeEEccccChHHHHHHHhhCCCccEEeccCCC
Q psy1865         109 AFYRL---LPKITLTQEIEGEMAQRLQTMFSPGVISIEKKPN  147 (152)
Q Consensus       109 ~~yr~---~P~i~i~~~~~~~~~~~~~~~cp~~Vf~i~~~~~  147 (152)
                      ..|..   .|+|.++.+......+.+++.||.|+|..++.+.
T Consensus        14 ~~y~vd~~~~HI~i~~~~~~~~~k~C~~aCPagA~~~~e~G~   55 (95)
T PRK15449         14 NKFNVDEEHPHIVVKADADKQALELLVKACPAGLYKKQDDGS   55 (95)
T ss_pred             ceeECCCCCCcEEEcCCCCchhhhHHHHHCCHhhcEeCCCCC
Confidence            45653   4899998665445566789999999998765443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	152
3how_C	347	Complete Rna Polymerase Ii Elongation Complex Iii W		9e-04

>pdb|3HOW|C Chain C, Complete Rna Polymerase Ii Elongation Complex Iii With A T-U Mismatch And A Frayed Rna 3'-Uridine Length = 347

Iteration: 1
 Score = 39.3 bits (90), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 17/41 (41%), Positives = 24/41 (58%)
Query: 75  ILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLP 115
           +LI KLR G E+ +T  A K I ++HAK+ P A   +   P
Sbjct: 171 VLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDP 211

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	152
1twf_C	318	B44.5, DNA-directed RNA polymerase II 45 kDa polyp	3e-19
2pa8_D	265	DNA-directed RNA polymerase subunit D; ferredoxin-	5e-15
3h0g_C	297	DNA-directed RNA polymerase II subunit RPB3; trans	7e-15

>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1 d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C 1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C* 1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C 1y77_C* ... Length = 318

 Score = 81.2 bits (199), Expect = 3e-19
 Identities = 27/141 (19%), Positives = 47/141 (33%), Gaps = 13/141 (9%)

Query: 7   LKYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSS 66
              + C++ ++   L+                       V++KD+  V      ++    
Sbjct: 87  FCEDHCDKCSVVLTLQAFGES-------------ESTTNVYSKDLVIVSNLMGRNIGHPI 133

Query: 67  DVGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGE 126
                 + +LI KLR G E+ +T  A K I ++HAK+ P A   +   P   L       
Sbjct: 134 IQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWY 193

Query: 127 MAQRLQTMFSPGVISIEKKPN 147
                +          E  PN
Sbjct: 194 EQDSAKEWPQSKNCEYEDPPN 214

>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D 2y0s_D Length = 265

 Score = 69.2 bits (168), Expect = 5e-15
 Identities = 27/138 (19%), Positives = 50/138 (36%), Gaps = 29/138 (21%)

Query: 8   KYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSD 67
             E CE+   +  ++ +                 E   +++KDI+           +   
Sbjct: 85  CTENCEKCYTKIYIEAEAPN--------------EPRMIYSKDIKS----------EDPS 120

Query: 68  VGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEM 127
           V PI  DI I  L    +I +        G++HAKF PV+ +  R  PK+ +        
Sbjct: 121 VVPISGDIPIVLLGTNQKISLEARLRLGYGKEHAKFIPVSLSVVRYYPKVEILAN----- 175

Query: 128 AQRLQTMFSPGVISIEKK 145
            ++   +   GV  ++  
Sbjct: 176 CEKAVNVCPEGVFELKDG 193

>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 297

 Score = 68.8 bits (167), Expect = 7e-15
 Identities = 26/119 (21%), Positives = 42/119 (35%), Gaps = 16/119 (13%)

Query: 8   KYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSD 67
             + C + +++  L  KCT                  +++ +D+      S G       
Sbjct: 92  CDQYCPKCSVELFLNAKCTGE-------------GTMEIYARDLVVSSNSSLGHPIL--- 135

Query: 68  VGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGE 126
             P     LI KLR   EI +   A K I ++HAK+SP +   +   P   L       
Sbjct: 136 ADPKSRGPLICKLRKEQEISLRCIAKKGIAKEHAKWSPTSAVAFEYDPWNKLQHTDYWF 194

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	152
2pa8_D	265	DNA-directed RNA polymerase subunit D; ferredoxin-	99.96
3h0g_C	297	DNA-directed RNA polymerase II subunit RPB3; trans	99.96
1twf_C	318	B44.5, DNA-directed RNA polymerase II 45 kDa polyp	99.95
2a6h_A	315	DNA-directed RNA polymerase alpha chain; RNA polym	99.61
1bdf_A	235	RNA polymerase alpha subunit; nucleotidyltransfera	99.52
3lu0_A	329	DNA-directed RNA polymerase subunit alpha; E. coli	98.89

>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D 2y0s_D

Probab=99.96  E-value=7.7e-30  Score=210.12  Aligned_cols=110  Identities=24%  Similarity=0.402  Sum_probs=98.6

Q ss_pred             cCCCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEE
Q psy1865           7 LKYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEI   86 (152)
Q Consensus         7 ~~~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I   86 (152)
                      +|+++|+.|+++|+|+|+|++++              ..|||+||++          .++.++|++++|+|+||++||+|
T Consensus        84 ~~~~~~~~~~~~~~l~~~~~~g~--------------~~V~a~Di~~----------~~~~v~~~~~~i~I~~L~~g~~l  139 (265)
T 2pa8_D           84 ECTENCEKCYTKIYIEAEAPNEP--------------RMIYSKDIKS----------EDPSVVPISGDIPIVLLGTNQKI  139 (265)
T ss_dssp             TCCSSCTTTEEEEEEEEECCSSC--------------EEEEGGGCEE----------SSTTCCBSCSCCEEEEECTTCEE
T ss_pred             ccccCCCCcEEEEEEEEEecCCC--------------cEEEhhhccc----------CCCCceecCCCcEEEEeCCCCEE
Confidence            46789999999999999996542              6899999986          46778999999999999999999


Q ss_pred             EEEEEEeecCCcceeeeccceeEEeEeeeeeEEccccChHHHHHHHhhCCCccEEeccC
Q psy1865          87 DVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIEKK  145 (152)
Q Consensus        87 ~l~~~A~kGiGk~HAKwsPv~~~~yr~~P~i~i~~~~~~~~~~~~~~~cp~~Vf~i~~~  145 (152)
                      +|+|+|+||+|++||||+|+++++||++|.|.++     ..+.++++.||.|+|.++++
T Consensus       140 ~~e~~~~~G~G~~~ak~~pv~t~~yr~~p~I~i~-----~~C~~C~~~CP~g~I~id~~  193 (265)
T 2pa8_D          140 SLEARLRLGYGKEHAKFIPVSLSVVRYYPKVEIL-----ANCEKAVNVCPEGVFELKDG  193 (265)
T ss_dssp             EEEEEEEEECTTTCGGGCCEEEEEEEEEEEEEEC-----SCCTTHHHHCTTCCEEEETT
T ss_pred             EEEEEEecCccccccCcccceeeeeccccchhhh-----hhHHHHHHhCcccCeEecCC
Confidence            9999999999999999999999999999999998     22556888999999998763

>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=99.96  E-value=1.3e-30  Score=219.20  Aligned_cols=116  Identities=22%  Similarity=0.293  Sum_probs=90.9

Q ss_pred             CCCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCC-cccCCCceEEEcCCCCEE
Q psy1865           8 KYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDV-GPIHDDILIAKLRPGHEI   86 (152)
Q Consensus         8 ~~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~-~p~~~~I~I~KL~~GQ~I   86 (152)
                      |+++|+.|+++|+|+|+|+++.             +..|||+||+|.|.  +  .|..+.. .|++++|+|+||++||+|
T Consensus        92 ~~~~~~~~~v~l~L~v~g~~~~-------------~~~Vta~Dl~~~~~--~--~~~~pv~~~~~n~di~IakL~~gq~l  154 (297)
T 3h0g_C           92 CDQYCPKCSVELFLNAKCTGEG-------------TMEIYARDLVVSSN--S--SLGHPILADPKSRGPLICKLRKEQEI  154 (297)
T ss_dssp             SSSSCGGGSCEEEEEECCCCSS-------------CEEEEGGGCBCCSC--C--SSCCBCCCSTTSCCSEEEEECSSCCE
T ss_pred             cccCCCCceEEEEEEEEeccCC-------------CceEEcccccccCc--c--cccccccccCCCCCeEEEEECCCCEE
Confidence            5678999999999999998652             36899999998541  1  1111111 256899999999999999


Q ss_pred             EEEEEEeecCCcceeeeccceeEEeEeeeeeEEccccC-hHHHHHHHhhCCCccEEe
Q psy1865          87 DVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIE-GEMAQRLQTMFSPGVISI  142 (152)
Q Consensus        87 ~l~~~A~kGiGk~HAKwsPv~~~~yr~~P~i~i~~~~~-~~~~~~~~~~cp~~Vf~i  142 (152)
                      +|+|+|+||+|++||||||||+|+|||+|+|+|++... .+  +..++.||.++|..
T Consensus       155 ~le~~a~kG~G~~HAKwsPv~~~~y~~~P~i~l~~~~~~~e--~~~~~~~P~~~~~~  209 (297)
T 3h0g_C          155 SLRCIAKKGIAKEHAKWSPTSAVAFEYDPWNKLQHTDYWFE--NDADAEWPKSKNAD  209 (297)
T ss_dssp             EEEEEEEEECGGGCTTSCCBCCCCCCSSSSCSSCCSCCCCS--SCSTTTSCCCGGGT
T ss_pred             EEEEEEECCEeccccccCcceEEEEEeccceEEcccccccc--chhHhhCCccccce
Confidence            99999999999999999999999999999999997421 10  13556788887643

>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1 d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C 1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C* 1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C 1y77_C* ...

Probab=99.95  E-value=2.8e-28  Score=206.56  Aligned_cols=101  Identities=25%  Similarity=0.393  Sum_probs=87.5

Q ss_pred             cCCCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCC-cccCCCceEEEcCCCCE
Q psy1865           7 LKYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDV-GPIHDDILIAKLRPGHE   85 (152)
Q Consensus         7 ~~~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~-~p~~~~I~I~KL~~GQ~   85 (152)
                      +|+++|+.|+++|+|+|+|+++.             ...|||+||+|.| +.+...+.++.+ .+++++|+|+||++||+
T Consensus        87 ~~~~~c~~~~v~l~L~v~c~~~g-------------~~~Vta~Di~~~~-~~~~~~~~~p~v~ei~npdi~IakL~~gq~  152 (318)
T 1twf_C           87 FCEDHCDKCSVVLTLQAFGESES-------------TTNVYSKDLVIVS-NLMGRNIGHPIIQDKEGNGVLICKLRKGQE  152 (318)
T ss_dssp             SSSSCCTTTEEEEEEEEECCSSS-------------CEEEEGGGEEECS-CCTTCSEEEECCCSTTSCCSEEEEECTTCE
T ss_pred             ccccCCCCceEEEEEEEEecCCC-------------CeeEEhHhccccC-ccccccccCCCccccCCCCeEEEEECCCCE
Confidence            46789999999999999998763             2689999999965 223334556666 47899999999999999


Q ss_pred             EEEEEEEeecCCcceeeeccceeEEeEeeeeeEEcc
Q psy1865          86 IDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQ  121 (152)
Q Consensus        86 I~l~~~A~kGiGk~HAKwsPv~~~~yr~~P~i~i~~  121 (152)
                      |+|+|+|+||+|++|||||||++++|||+|++++.+
T Consensus       153 L~me~~a~kG~G~~hAk~sPva~~~y~~~P~~~~~~  188 (318)
T 1twf_C          153 LKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKH  188 (318)
T ss_dssp             EEEEEEEEEECTTTCGGGCCEEEEEEEECSSTTSCC
T ss_pred             EEEEEEEEcCcccccccccccccceecccccccccc
Confidence            999999999999999999999999999999998875

>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3aoh_A* 3aoi_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* ...

Probab=99.61  E-value=3.3e-16  Score=132.49  Aligned_cols=66  Identities=21%  Similarity=0.245  Sum_probs=59.7

Q ss_pred             CCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEEEEEE
Q psy1865          12 CEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMF   91 (152)
Q Consensus        12 c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~l~~~   91 (152)
                      |+.|++.|+|+|+++                 ..|||+||+|           ++.+.|++++++|++|++||+|+|+|+
T Consensus        92 ~~~~~~~~~L~v~gp-----------------~~VtA~Di~~-----------~~~v~ivnpd~~IatL~~g~~l~me~~  143 (315)
T 2a6h_A           92 PSLQTVTLLLKAEGP-----------------KEVKARDFLP-----------VADVEIMNPDLHIATLEEGGRLNMEVR  143 (315)
T ss_dssp             TTCSBCCEEEEEESS-----------------CEEEGGGSCC-----------CTTEEESCTTCEEEEBCSSCEEEEEEE
T ss_pred             CCCCeEEEEEEEecC-----------------eeEEhhhCCc-----------CCCcEEcCCCeEEEEECCCCEEEEEEE
Confidence            578999999999943                 5799999985           456789999999999999999999999


Q ss_pred             EeecCCcceeeecc
Q psy1865          92 AVKSIGRDHAKFSP  105 (152)
Q Consensus        92 A~kGiGk~HAKwsP  105 (152)
                      |.||+|++||||++
T Consensus       144 ~~kG~Gy~~ak~~~  157 (315)
T 2a6h_A          144 VDRGVGYVPAEKHG  157 (315)
T ss_dssp             EEEEESEECHHHHC
T ss_pred             EEecCCccccccCc
Confidence            99999999999985

>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1

Probab=99.52  E-value=2.4e-14  Score=116.58  Aligned_cols=63  Identities=19%  Similarity=0.202  Sum_probs=57.0

Q ss_pred             CCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCC-CCEEEEEEEE
Q psy1865          14 QDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRP-GHEIDVTMFA   92 (152)
Q Consensus        14 ~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~-GQ~I~l~~~A   92 (152)
                      .|++.|+|+++++                 ..|||+||+.           ++.+.|++++++|++|++ ||+|+|+|+|
T Consensus        95 ~~~~~~~L~v~gp-----------------~~VtA~Di~~-----------~~~v~ivnpd~~IatL~~~g~~l~~e~~~  146 (235)
T 1bdf_A           95 KDEVILTLNKSGI-----------------GPVTAADITH-----------DGDVEIVKPQHVICHLTDENASISMRIKV  146 (235)
T ss_dssp             CSEEEEEEEEESS-----------------EEEEGGGBCC-----------CSSCEESCTTCEEEEECSTTCEEEEEEEE
T ss_pred             CceEEEEEEEecC-----------------eEEEhHhCCC-----------CCCCEEcCCCeEEEEECCCCCEEEEEEEE
Confidence            6999999999843                 5799999973           456889999999999999 9999999999


Q ss_pred             eecCCcceeeec
Q psy1865          93 VKSIGRDHAKFS  104 (152)
Q Consensus        93 ~kGiGk~HAKws  104 (152)
                      .||+|++|||||
T Consensus       147 ~kG~Gy~~ak~s  158 (235)
T 1bdf_A          147 QRGRGYVPASTR  158 (235)
T ss_dssp             EECCSEECGGGT
T ss_pred             Eecccceecccc
Confidence            999999999993

>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A

Probab=98.89  E-value=1.2e-09  Score=92.91  Aligned_cols=76  Identities=21%  Similarity=0.264  Sum_probs=63.9

Q ss_pred             CCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcC-CCCEEEEEE
Q psy1865          12 CEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLR-PGHEIDVTM   90 (152)
Q Consensus        12 c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~-~GQ~I~l~~   90 (152)
                      |..|++.++|+++.+                 ..|||+||++           ++.+.+++++++|++|+ +||+|+|++
T Consensus        93 ~~~~~~~~~L~~~Gp-----------------~~VtA~DI~~-----------~~~veivnpd~~IatL~~~~~~L~me~  144 (329)
T 3lu0_A           93 QGKDEVILTLNKSGI-----------------GPVTAADITH-----------DGDVEIVKPQHVICHLTDENASISMRI  144 (329)
T ss_dssp             SSCSCEEEEECCCSS-----------------SCEETTSSCC-----------CSSEECSCTTCEEECBCSSCCCCCEEE
T ss_pred             CCCceEEEEEEEeCC-----------------eEEEeeeecc-----------CCCCEEeCCCcEEEEEccCCcEEEEEE
Confidence            467899999998632                 5799999975           34578899999999999 999999999


Q ss_pred             EEeecCCcceee--------------------eccceeEEeEeee
Q psy1865          91 FAVKSIGRDHAK--------------------FSPVATAFYRLLP  115 (152)
Q Consensus        91 ~A~kGiGk~HAK--------------------wsPv~~~~yr~~P  115 (152)
                      +|.+|+|..+|.                    |+||--+.|.-.+
T Consensus       145 ~i~~G~GY~~a~~~~~~~~~~~~ig~i~iDa~fsPV~~Vny~Ve~  189 (329)
T 3lu0_A          145 KVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEA  189 (329)
T ss_dssp             EEEEESSEECTTTSCCCSTTSSSCCCEECCEECCCEEEEEEEEEE
T ss_pred             EEECcccceechhccccccccCcCceEeeCCCCCceeeEEEEEec
Confidence            999999987653                    8999999996554

---

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	152
d1twfc2	131	d.181.1.1 (C:42-172) RPB3 {Baker's yeast (Saccharo	3e-20

>d1twfc2 d.181.1.1 (C:42-172) RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 131

class: Alpha and beta proteins (a+b)
fold: Insert subdomain of RNA polymerase alpha subunit
superfamily: Insert subdomain of RNA polymerase alpha subunit
family: Insert subdomain of RNA polymerase alpha subunit
domain: RPB3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 78.9 bits (194), Expect = 3e-20
 Identities = 21/97 (21%), Positives = 39/97 (40%), Gaps = 13/97 (13%)

Query: 9   YEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDV 68
            + C++ ++   L+                       V++KD+  V      ++      
Sbjct: 48  EDHCDKCSVVLTLQAFGESE-------------STTNVYSKDLVIVSNLMGRNIGHPIIQ 94

Query: 69  GPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHAKFSP 105
               + +LI KLR G E+ +T  A K I ++HAK+ P
Sbjct: 95  DKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGP 131

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	152
d1twfc2	131	RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.94
d1bdfa2	126	RNA polymerase alpha subunit {Escherichia coli [Ta	94.4
d1smya2	123	RNA polymerase alpha subunit {Thermus thermophilus	92.21

>d1twfc2 d.181.1.1 (C:42-172) RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Insert subdomain of RNA polymerase alpha subunit
superfamily: Insert subdomain of RNA polymerase alpha subunit
family: Insert subdomain of RNA polymerase alpha subunit
domain: RPB3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.94  E-value=9.7e-28  Score=177.60  Aligned_cols=87  Identities=24%  Similarity=0.365  Sum_probs=70.9

Q ss_pred             ccCCCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCE
Q psy1865           6 RLKYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHE   85 (152)
Q Consensus         6 ~~~~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~   85 (152)
                      ..|+++|+.|+|.|+|+|+|+++.             ...|||+||+|.+...+...+......+..++|+|+||+|||+
T Consensus        45 ~~~~~~~~~~~v~~~L~v~~~~~~-------------~~~V~s~Dl~~~~~~~~~~~~~~~~~~~~~~~IlI~kL~pGQ~  111 (131)
T d1twfc2          45 CFCEDHCDKCSVVLTLQAFGESES-------------TTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQE  111 (131)
T ss_dssp             SSSSSCCTTTEEEEEEEEECCSSS-------------CEEEEGGGEEECSCCTTCSEEEECCCSTTSCCSEEEEECTTCE
T ss_pred             ccccCCCCCceEEEEeEcccCCCC-------------CceEEhhheEEcCCccccccCCccccCCcCCCCEEEEeCCCCE
Confidence            346789999999999999998652             3689999999976544433222223345678999999999999


Q ss_pred             EEEEEEEeecCCcceeeecc
Q psy1865          86 IDVTMFAVKSIGRDHAKFSP  105 (152)
Q Consensus        86 I~l~~~A~kGiGk~HAKwsP  105 (152)
                      |+|+|+|+||+||+||||||
T Consensus       112 i~l~a~a~kG~Gk~HAK~sP  131 (131)
T d1twfc2         112 LKLTCVAKKGIAKEHAKWGP  131 (131)
T ss_dssp             EEEEEEEEEECTTTCGGGCC
T ss_pred             EEEEEEEEecccccCcEeCc
Confidence            99999999999999999999

>d1bdfa2 d.181.1.1 (A:53-178) RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Insert subdomain of RNA polymerase alpha subunit
superfamily: Insert subdomain of RNA polymerase alpha subunit
family: Insert subdomain of RNA polymerase alpha subunit
domain: RNA polymerase alpha subunit
species: Escherichia coli [TaxId: 562]

Probab=94.40  E-value=0.069  Score=37.41  Aligned_cols=61  Identities=20%  Similarity=0.223  Sum_probs=46.7

Q ss_pred             CCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcC-CCCEEEEEEEE
Q psy1865          14 QDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLR-PGHEIDVTMFA   92 (152)
Q Consensus        14 ~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~-~GQ~I~l~~~A   92 (152)
                      ......+|+++.+                 ..|+++|+..           +..+.-+.++-.|+.|. +|-+|+|+++.
T Consensus        43 ~~~~~~~l~~~gp-----------------~~VtA~di~~-----------~~~veIvNpd~~Iatlt~~~~~l~mel~v   94 (126)
T d1bdfa2          43 KDEVILTLNKSGI-----------------GPVTAADITH-----------DGDVEIVKPQHVICHLTDENASISMRIKV   94 (126)
T ss_dssp             CSEEEEEEEEESS-----------------EEEEGGGBCC-----------CSSCEESCTTCEEEEECSTTCEEEEEEEE
T ss_pred             CCceEEEEEecCc-----------------ccEEEecccC-----------CCCEEEeCCceEEEEEecCCceEEEEEEE
Confidence            3456677777632                 5789999874           23456678899999995 89999999999


Q ss_pred             eecCCcceee
Q psy1865          93 VKSIGRDHAK  102 (152)
Q Consensus        93 ~kGiGk~HAK  102 (152)
                      .+|+|-..|-
T Consensus        95 ~~GrGYv~ae  104 (126)
T d1bdfa2          95 QRGRGYVPAS  104 (126)
T ss_dssp             EECCSEECGG
T ss_pred             eCCCCeeccc
Confidence            9999975543

>d1smya2 d.181.1.1 (A:50-172) RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Insert subdomain of RNA polymerase alpha subunit
superfamily: Insert subdomain of RNA polymerase alpha subunit
family: Insert subdomain of RNA polymerase alpha subunit
domain: RNA polymerase alpha subunit
species: Thermus thermophilus [TaxId: 274]

Probab=92.21  E-value=0.05  Score=37.95  Aligned_cols=47  Identities=23%  Similarity=0.322  Sum_probs=38.1

Q ss_pred             ceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEEEEEEEeecCCccee
Q psy1865          44 HKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHA  101 (152)
Q Consensus        44 ~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~l~~~A~kGiGk~HA  101 (152)
                      ..|+++|+.+           +..+.-++++-.|+.|..+-+|+|+++..+|+|-..|
T Consensus        58 ~~VtA~Di~~-----------~~~veIvNpd~~IaTl~~~~~l~mel~v~~GrGYv~a  104 (123)
T d1smya2          58 KEVKARDFLP-----------VADVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPA  104 (123)
T ss_dssp             BCCBGGGSCC-----------CTTEEESCTTCBCCCBCTTCCEEEEEEEEEEESEECH
T ss_pred             CeEEeeeecC-----------CCcEEEECCcEEEEEEcCCcEEEEEEEEcccccceEc
Confidence            4578888864           2345667889999999999999999999999996443