Psyllid ID: psy12830

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90----
Protein Sequence
MPYANQPSVHITDLTDENVKFQVEDTELSKRTNGNWKENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQTGFRKTFCSPNQSPENPGNLI
Secondary Structure (PSIPRED)
cccccccEEEEEEcccccEEEEEEEccEEEEEccccccccccccccEEEEEccccHHHHHHHHHHcccEEcccccccEEccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccEEEEEEcccccEEEEEEccccccccccccHHHHHHHcHHHHHHHcccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccc
Coil and Loop (DISEMBL)
mpyanqpsvhitdltdenvkfqvedtelskrtngnwkenMEWKGLSAQLLLCSRPSFLFAFLCIYENRLAlsqtgfrktfcspnqspenpgnli
Flexible Loop (DISEMBL)
mpyanqpsvhitdltdenvkfqvedtelskrtngnwkenMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQTGFrktfcspnqspenpgnli
Low Complexity Region (SEG)
MPYANQPSVHITDLTDENVKFQVEDTELSKRTNGNWKENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQTGFRKTFCSPNQSPENPGNLI
Disordered region (IsUnstruct)
*********************************GNWKENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQTGFRKTFC*************
Disordered Region (DISOPRED)
******PSVHITDLTDENVKFQVEDTELSKRTNGNWKENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQTGFRKTF**************
Disordered Region (DISEMBL)
MPYANQPSVHITDLTDENVKFQVEDTELSKRTNGNWKENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQTGFRKTFC*************
Disordered Region (DISPRO)
*PYANQPSVHITDLTDENVKFQVEDTELSKRTNGNWKENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQTGFRKTFCSPNQ*********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MPYANQPSVHITDLTDENVKFQVEDTELSKRTNGNWKENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQTGFRKTFCSPNQSPENPGNLI
Positional Conservation
no confident homologs detected

---

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	94	2.2.26 [Sep-21-2011]
P19387	275	DNA-directed RNA polymera	yes	N/A	0.308	0.105	0.724	9e-06
Q3T0Q3	275	DNA-directed RNA polymera	yes	N/A	0.308	0.105	0.724	1e-05
P97760	275	DNA-directed RNA polymera	yes	N/A	0.308	0.105	0.689	3e-05

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

 Score = 48.9 bits (115), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 21/29 (72%), Positives = 27/29 (93%)

Query: 1  MPYANQPSVHITDLTDENVKFQVEDTELS 29
          MPYANQP+V IT+LTDENVKF +E+T+L+
Sbjct: 1  MPYANQPTVRITELTDENVKFIIENTDLA 29

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)

>sp|Q3T0Q3|RPB3_BOVIN DNA-directed RNA polymerase II subunit RPB3 OS=Bos taurus GN=POLR2C PE=2 SV=1

 Score = 48.9 bits (115), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/29 (72%), Positives = 27/29 (93%)

Query: 1  MPYANQPSVHITDLTDENVKFQVEDTELS 29
          MPYANQP+V IT+LTDENVKF +E+T+L+
Sbjct: 1  MPYANQPTVRITELTDENVKFIIENTDLA 29

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.

Bos taurus (taxid: 9913)

>sp|P97760|RPB3_MOUSE DNA-directed RNA polymerase II subunit RPB3 OS=Mus musculus GN=Polr2c PE=2 SV=1

 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/29 (68%), Positives = 27/29 (93%)

Query: 1  MPYANQPSVHITDLTDENVKFQVEDTELS 29
          MPYANQP+V IT+LT+ENVKF +E+T+L+
Sbjct: 1  MPYANQPTVRITELTEENVKFIIENTDLA 29


  Database: swissprot
    Posted date:  Mar 23, 2013  2:32 AM
  Number of letters in database: 191,569,459
  Number of sequences in database:  539,616
  
Lambda     K      H
   0.317    0.132    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 35,341,573
Number of Sequences: 539616
Number of extensions: 1141694
Number of successful extensions: 2312
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 2309
Number of HSP's gapped (non-prelim): 3
length of query: 94
length of database: 191,569,459
effective HSP length: 64
effective length of query: 30
effective length of database: 157,034,035
effective search space: 4711021050
effective search space used: 4711021050
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)

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.

Mus musculus (taxid: 10090)

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	94
242011218	275	DNA-directed RNA polymerase II 33 kDa po	0.308	0.105	0.965	3e-08
332017912	256	DNA-directed RNA polymerase II subunit R	0.308	0.113	0.931	1e-07
322793846	325	hypothetical protein SINV_07940 [Solenop	0.308	0.089	0.931	2e-07
66517558	276	PREDICTED: DNA-directed RNA polymerase I	0.308	0.105	0.931	2e-07
350400985	276	PREDICTED: DNA-directed RNA polymerase I	0.308	0.105	0.931	2e-07
383848177	276	PREDICTED: DNA-directed RNA polymerase I	0.308	0.105	0.931	2e-07
307175611	276	DNA-directed RNA polymerase II subunit R	0.308	0.105	0.931	2e-07
332376707	275	unknown [Dendroctonus ponderosae]	0.308	0.105	0.931	3e-07
91094813	274	PREDICTED: similar to DNA-directed RNA p	0.308	0.105	0.862	9e-07
114051193	275	DNA-directed RNA polymerase II polypepti	0.308	0.105	0.896	1e-06

>gi|242011218|ref|XP_002426352.1| DNA-directed RNA polymerase II 33 kDa polypeptide, putative [Pediculus humanus corporis] gi|212510429|gb|EEB13614.1| DNA-directed RNA polymerase II 33 kDa polypeptide, putative [Pediculus humanus corporis]

 Score = 62.4 bits (150), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 28/29 (96%), Positives = 29/29 (100%)

Query: 1  MPYANQPSVHITDLTDENVKFQVEDTELS 29
          MPYANQPSVHITDLTDENVKFQ+EDTELS
Sbjct: 1  MPYANQPSVHITDLTDENVKFQIEDTELS 29

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332017912|gb|EGI58566.1| DNA-directed RNA polymerase II subunit RPB3 [Acromyrmex echinatior]

 Score = 60.5 bits (145), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/29 (93%), Positives = 29/29 (100%)

Query: 1  MPYANQPSVHITDLTDENVKFQVEDTELS 29
          MPYANQPSVHI+DLT+ENVKFQVEDTELS
Sbjct: 1  MPYANQPSVHISDLTEENVKFQVEDTELS 29

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322793846|gb|EFZ17186.1| hypothetical protein SINV_07940 [Solenopsis invicta]

 Score = 60.1 bits (144), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/29 (93%), Positives = 29/29 (100%)

Query: 1  MPYANQPSVHITDLTDENVKFQVEDTELS 29
          MPYANQPSVHI+DLT+ENVKFQVEDTELS
Sbjct: 1  MPYANQPSVHISDLTEENVKFQVEDTELS 29

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66517558|ref|XP_624836.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Apis mellifera] gi|380029804|ref|XP_003698555.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Apis florea]

 Score = 60.1 bits (144), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/29 (93%), Positives = 29/29 (100%)

Query: 1  MPYANQPSVHITDLTDENVKFQVEDTELS 29
          MPYANQPSVHI+DLT+ENVKFQVEDTELS
Sbjct: 1  MPYANQPSVHISDLTEENVKFQVEDTELS 29

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350400985|ref|XP_003486021.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Bombus impatiens]

 Score = 60.1 bits (144), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/29 (93%), Positives = 29/29 (100%)

Query: 1  MPYANQPSVHITDLTDENVKFQVEDTELS 29
          MPYANQPSVHI+DLT+ENVKFQVEDTELS
Sbjct: 1  MPYANQPSVHISDLTEENVKFQVEDTELS 29

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383848177|ref|XP_003699728.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Megachile rotundata]

 Score = 60.1 bits (144), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/29 (93%), Positives = 29/29 (100%)

Query: 1  MPYANQPSVHITDLTDENVKFQVEDTELS 29
          MPYANQPSVHI+DLT+ENVKFQVEDTELS
Sbjct: 1  MPYANQPSVHISDLTEENVKFQVEDTELS 29

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307175611|gb|EFN65520.1| DNA-directed RNA polymerase II subunit RPB3 [Camponotus floridanus]

 Score = 60.1 bits (144), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/29 (93%), Positives = 29/29 (100%)

Query: 1  MPYANQPSVHITDLTDENVKFQVEDTELS 29
          MPYANQPSVHI+DLT+ENVKFQVEDTELS
Sbjct: 1  MPYANQPSVHISDLTEENVKFQVEDTELS 29

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332376707|gb|AEE63493.1| unknown [Dendroctonus ponderosae]

 Score = 59.3 bits (142), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 27/29 (93%), Positives = 28/29 (96%)

Query: 1  MPYANQPSVHITDLTDENVKFQVEDTELS 29
          MPYANQPSVHITDLTDENVKF VEDT+LS
Sbjct: 1  MPYANQPSVHITDLTDENVKFYVEDTDLS 29

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91094813|ref|XP_970635.1| PREDICTED: similar to DNA-directed RNA polymerase II subunit [Tribolium castaneum] gi|270006567|gb|EFA03015.1| hypothetical protein TcasGA2_TC010438 [Tribolium castaneum]

 Score = 57.4 bits (137), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 25/29 (86%), Positives = 28/29 (96%)

Query: 1  MPYANQPSVHITDLTDENVKFQVEDTELS 29
          MPYANQPSVHITDLTD+NVKF +EDT+LS
Sbjct: 1  MPYANQPSVHITDLTDDNVKFYIEDTDLS 29

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|114051193|ref|NP_001040388.1| DNA-directed RNA polymerase II polypeptide [Bombyx mori] gi|95102714|gb|ABF51298.1| DNA-directed RNA polymerase II polypeptide [Bombyx mori]

 Score = 57.4 bits (137), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/29 (89%), Positives = 28/29 (96%)

Query: 1  MPYANQPSVHITDLTDENVKFQVEDTELS 29
          MPYANQPSVHIT+L+DENVKF VEDTELS
Sbjct: 1  MPYANQPSVHITELSDENVKFVVEDTELS 29

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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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	94
FB|FBgn0026373	275	RpII33 "RNA polymerase II 33kD	0.308	0.105	0.827	1e-07
UNIPROTKB|D4A8A8	330	Polr2c "Protein Polr2c" [Rattu	0.308	0.087	0.689	2.4e-07
UNIPROTKB|H3BRR2	46	POLR2C "DNA-directed RNA polym	0.308	0.630	0.724	3.8e-07
UNIPROTKB|E1BV97	275	POLR2C "Uncharacterized protei	0.308	0.105	0.724	1.3e-06
UNIPROTKB|Q3T0Q3	275	POLR2C "DNA-directed RNA polym	0.308	0.105	0.724	1.3e-06
UNIPROTKB|E2RQ42	275	POLR2C "Uncharacterized protei	0.308	0.105	0.724	1.3e-06
UNIPROTKB|P19387	275	POLR2C "DNA-directed RNA polym	0.308	0.105	0.724	1.3e-06
UNIPROTKB|I3LCH3	275	POLR2C "Uncharacterized protei	0.308	0.105	0.724	1.3e-06
MGI|MGI:109299	275	Polr2c "polymerase (RNA) II (D	0.308	0.105	0.689	3.7e-06
RGD|1306935	275	Polr2c "polymerase (RNA) II (D	0.308	0.105	0.689	3.7e-06

FB|FBgn0026373 RpII33 "RNA polymerase II 33kD subunit" [Drosophila melanogaster (taxid:7227)]

 Score = 126 (49.4 bits), Expect = 1.0e-07, P = 1.0e-07
 Identities = 24/29 (82%), Positives = 27/29 (93%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELS 29
             MPYANQPSV IT+LTD+NVKF +EDTELS
Sbjct:     1 MPYANQPSVQITELTDDNVKFVLEDTELS 29

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

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

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

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0034605 "cellular response to heat" evidence=IEP

GO:0005634 "nucleus" evidence=IDA

GO:0005703 "polytene chromosome puff" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005875 "microtubule associated complex" evidence=IDA

GO:0003677 "DNA binding" evidence=IDA

UNIPROTKB|D4A8A8 Polr2c "Protein Polr2c" [Rattus norvegicus (taxid:10116)]

 Score = 112 (44.5 bits), Expect = 2.4e-07, Sum P(2) = 2.4e-07
 Identities = 20/29 (68%), Positives = 27/29 (93%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELS 29
             MPYANQP+V IT+LT+ENVKF +E+T+L+
Sbjct:     1 MPYANQPTVRITELTEENVKFIIENTDLA 29

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|H3BRR2 POLR2C "DNA-directed RNA polymerase II subunit RPB3" [Homo sapiens (taxid:9606)]

 Score = 116 (45.9 bits), Expect = 3.8e-07, P = 3.8e-07
 Identities = 21/29 (72%), Positives = 27/29 (93%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELS 29
             MPYANQP+V IT+LTDENVKF +E+T+L+
Sbjct:     1 MPYANQPTVRITELTDENVKFIIENTDLA 29

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|E1BV97 POLR2C "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 116 (45.9 bits), Expect = 1.3e-06, P = 1.3e-06
 Identities = 21/29 (72%), Positives = 27/29 (93%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELS 29
             MPYANQP+V IT+LTDENVKF +E+T+L+
Sbjct:     1 MPYANQPTVRITELTDENVKFIIENTDLA 29

GO:0003677 "DNA binding" evidence=IEA

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

GO:0046983 "protein dimerization activity" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0015630 "microtubule cytoskeleton" evidence=IEA

UNIPROTKB|Q3T0Q3 POLR2C "DNA-directed RNA polymerase II subunit RPB3" [Bos taurus (taxid:9913)]

 Score = 116 (45.9 bits), Expect = 1.3e-06, P = 1.3e-06
 Identities = 21/29 (72%), Positives = 27/29 (93%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELS 29
             MPYANQP+V IT+LTDENVKF +E+T+L+
Sbjct:     1 MPYANQPTVRITELTDENVKFIIENTDLA 29

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

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

GO:0015630 "microtubule cytoskeleton" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2RQ42 POLR2C "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 116 (45.9 bits), Expect = 1.3e-06, P = 1.3e-06
 Identities = 21/29 (72%), Positives = 27/29 (93%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELS 29
             MPYANQP+V IT+LTDENVKF +E+T+L+
Sbjct:     1 MPYANQPTVRITELTDENVKFIIENTDLA 29

GO:0015630 "microtubule cytoskeleton" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0046983 "protein dimerization activity" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|P19387 POLR2C "DNA-directed RNA polymerase II subunit RPB3" [Homo sapiens (taxid:9606)]

 Score = 116 (45.9 bits), Expect = 1.3e-06, P = 1.3e-06
 Identities = 21/29 (72%), Positives = 27/29 (93%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELS 29
             MPYANQP+V IT+LTDENVKF +E+T+L+
Sbjct:     1 MPYANQPTVRITELTDENVKFIIENTDLA 29

GO:0003677 "DNA binding" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IDA

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

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

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

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

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

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

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

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

GO:0005730 "nucleolus" evidence=IDA

GO:0015630 "microtubule cytoskeleton" evidence=IDA

UNIPROTKB|I3LCH3 POLR2C "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 116 (45.9 bits), Expect = 1.3e-06, P = 1.3e-06
 Identities = 21/29 (72%), Positives = 27/29 (93%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELS 29
             MPYANQP+V IT+LTDENVKF +E+T+L+
Sbjct:     1 MPYANQPTVRITELTDENVKFIIENTDLA 29

GO:0015630 "microtubule cytoskeleton" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0046983 "protein dimerization activity" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

MGI|MGI:109299 Polr2c "polymerase (RNA) II (DNA directed) polypeptide C" [Mus musculus (taxid:10090)]

 Score = 112 (44.5 bits), Expect = 3.7e-06, P = 3.7e-06
 Identities = 20/29 (68%), Positives = 27/29 (93%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELS 29
             MPYANQP+V IT+LT+ENVKF +E+T+L+
Sbjct:     1 MPYANQPTVRITELTEENVKFIIENTDLA 29

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;IDA

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

GO:0005737 "cytoplasm" evidence=IDA

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

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

GO:0046983 "protein dimerization activity" evidence=IEA

RGD|1306935 Polr2c "polymerase (RNA) II (DNA directed) polypeptide C" [Rattus norvegicus (taxid:10116)]

 Score = 112 (44.5 bits), Expect = 3.7e-06, P = 3.7e-06
 Identities = 20/29 (68%), Positives = 27/29 (93%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELS 29
             MPYANQP+V IT+LT+ENVKF +E+T+L+
Sbjct:     1 MPYANQPTVRITELTEENVKFIIENTDLA 29

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISO

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

GO:0005737 "cytoplasm" evidence=IEA;ISO

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

GO:0015630 "microtubule cytoskeleton" evidence=IEA;ISO

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by 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	94
cd07031	265	cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic	3e-04

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

 Score = 37.2 bits (87), Expect = 3e-04
 Identities = 14/23 (60%), Positives = 19/23 (82%)

Query: 7  PSVHITDLTDENVKFQVEDTELS 29
          P V IT+LTD+ VKF +E+T+LS
Sbjct: 1  PRVEITELTDDKVKFILENTDLS 23

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	94
KOG1522|consensus	285		99.94
cd07032	291	RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA poly	99.83
cd07031	265	RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polyme	99.79
cd07028	212	RNAP_RPB3_like RPB3 subunit of RNA polymerase. The	99.75
PRK00783	263	DNA-directed RNA polymerase subunit D; Provisional	99.69
cd07030	259	RNAP_D D subunit of Archaeal RNA polymerase. The D	99.69
PRK14979	195	DNA-directed RNA polymerase subunit D; Provisional	99.53
KOG1521|consensus	338		99.51
smart00662	224	RPOLD RNA polymerases D. DNA-directed RNA polymera	99.13
COG0202	317	RpoA DNA-directed RNA polymerase, alpha subunit/40	99.04
cd06928	215	RNAP_alpha_NTD N-terminal domain of the Alpha subu	98.09
PRK05182	310	DNA-directed RNA polymerase subunit alpha; Provisi	98.05
PF01193	66	RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation	97.2
cd00460	86	RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA pol	96.2
PF01000	112	RNA_pol_A_bac: RNA polymerase Rpb3/RpoA insert dom	96.16
CHL00013	327	rpoA RNA polymerase alpha subunit	94.99
PRK01146	85	DNA-directed RNA polymerase subunit L; Provisional	93.8
TIGR02027	297	rpoA DNA-directed RNA polymerase, alpha subunit, b	88.53
cd06927	83	RNAP_L L subunit of Archaeal RNA polymerase. The a	84.47
cd07027	83	RNAP_RPB11_like RPB11 subunit of RNA polymerase. T	83.18

>KOG1522|consensus

Probab=99.94  E-value=1.4e-27  Score=188.79  Aligned_cols=72  Identities=28%  Similarity=0.401  Sum_probs=69.9

Q ss_pred             CCCCCCeEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceecccc
Q psy12830          2 PYANQPSVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQT   74 (94)
Q Consensus         2 py~~qP~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~t   74 (94)
                      ||++||.|+|+||++++|||+|+|||+|+||||||+       +|||||+|+.|||||+|     ||++||+|+|||.|.
T Consensus         1 ~y~~~p~v~I~Elt~d~vkF~L~nTdlsvANsLRRV~iaEvPTiAID~VeIe~NssVL~D-----EFiAHRLGLIPl~S~   75 (285)
T KOG1522|consen    1 PYANQPTVKIRELTDDNVKFVLSNTDLSVANSLRRVMIAEVPTIAIDLVEIEVNSSVLPD-----EFIAHRLGLIPLISD   75 (285)
T ss_pred             CCCCCCceEEEecCCCceEEEEecChHHHHHHHHHHHHhcCceeEEEEEEEecccccccH-----HHHHhhhcceeccch
Confidence            799999999999999999999999999999999999       99999999999999999     999999999999998


Q ss_pred             ccee
Q psy12830         75 GFRK   78 (94)
Q Consensus        75 ~~~~   78 (94)
                      .+-+
T Consensus        76 ~~~~   79 (285)
T KOG1522|consen   76 RIVE   79 (285)
T ss_pred             hhhh
Confidence            8755

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

Probab=99.83  E-value=1.9e-21  Score=153.68  Aligned_cols=62  Identities=13%  Similarity=0.109  Sum_probs=57.6

Q ss_pred             eEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceecccc
Q psy12830          8 SVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQT   74 (94)
Q Consensus         8 ~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~t   74 (94)
                      +|+|.+++++.++|.|+|+|+||||||||+       ||||.|.|++|||||+|     |||+||+|+|||.+.
T Consensus         2 ~i~i~~~~~~~~~f~l~~~d~s~ANAlRRimiaEVPt~AId~V~i~~NTSvl~D-----E~lAHRLGLIPL~~d   70 (291)
T cd07032           2 KIEIISLSDEELEFDLIGVDASIANAFRRILLAEVPTMAIEKVYIYNNTSVIQD-----EVLAHRLGLIPIKAD   70 (291)
T ss_pred             eEEEEECCCCEEEEEEecCCHHHHHHHHHHHHhcCcceeEEEEEEEECCccchh-----HHHHHhhcCceeecC
Confidence            689999999999999999999999999999       99999999999999999     778888888887764

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

>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II

Probab=99.79  E-value=9.3e-20  Score=141.03  Aligned_cols=65  Identities=25%  Similarity=0.346  Sum_probs=60.5

Q ss_pred             CeEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceecccccc
Q psy12830          7 PSVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQTGF   76 (94)
Q Consensus         7 P~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~t~~   76 (94)
                      |+|+|.++++++++|+|+|+|.++||||||+       +|||.|.|++|||||+|     |||+||+++||+-+..+
T Consensus         1 p~i~i~~~~~~~~~F~l~~~~~s~aNALRRillsevPt~AI~~V~I~~NtSvl~D-----E~iaHRlglIPl~~e~~   72 (265)
T cd07031           1 PRVEITELTDDKVKFILENTDLSVANSLRRVMIAEVPTLAIDLVEIEENTSVLHD-----EFIAHRLGLIPLTSDDV   72 (265)
T ss_pred             CcEEEEEcCCCEEEEEEEcCcHHHHHHHHHHHHHcCccceEEEEEEecCCccccc-----ceeeeecccCCCccCcH
Confidence            6899999999999999999999999999999       99999999999999999     88888888888877654

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.

>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase

Probab=99.75  E-value=8.9e-19  Score=132.50  Aligned_cols=63  Identities=14%  Similarity=0.186  Sum_probs=57.3

Q ss_pred             CeEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceecccc
Q psy12830          7 PSVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQT   74 (94)
Q Consensus         7 P~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~t   74 (94)
                      |+|+|.++++++++|.|+|+++++||||||+       +|||.|.|++|||+++|     |+++||.+.||+-+.
T Consensus         1 ~~i~i~~~~~~~~~f~l~g~~~t~aNaLRRiLLsevP~~AI~~V~I~~NtS~~~D-----E~iaHrlglIP~~~e   70 (212)
T cd07028           1 PQVKIREADKDNVDFILSGVDLAMANALRRVMIAEVPTMAVDSVEVETNTSVLAD-----EILAHRLGLIPLQSM   70 (212)
T ss_pred             CcEEEEEcCCCEEEEEEEccChhHHHHHHHHHHHcCcceEEEEEEEEcCCCcccc-----eeeeeeeeecccccC
Confidence            6899999999999999999999999999999       99999999999999999     666666667776654

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

>PRK00783 DNA-directed RNA polymerase subunit D; Provisional

Probab=99.69  E-value=1.2e-17  Score=126.94  Aligned_cols=62  Identities=13%  Similarity=0.086  Sum_probs=54.3

Q ss_pred             CeEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceeccc
Q psy12830          7 PSVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQ   73 (94)
Q Consensus         7 P~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~   73 (94)
                      |+|+|.+.+++.++|.++|.+.++||||||+       +|||.|.|++|||+++||     |++||+++||+-+
T Consensus         1 ~~~~~~~~~~~~~~f~~~g~~~t~~NalRRvlls~vp~~Ai~~v~i~~n~s~~~de-----~i~hrl~lip~~~   69 (263)
T PRK00783          1 MEIEILELDDRSARFVVEGVTPAFANAIRRAMIADVPTMAIDDVRFYENTSVLFDE-----ILAHRLGLIPLTT   69 (263)
T ss_pred             CceEEEEcCCcEEEEEEeCCCHHHHHHHHHHHHHcCCeeeEEEEEEEECCcchhHH-----HHHHhhcCccccc
Confidence            6799999999999999999999999999999       999999999999999995     4555555555544

>cd07030 RNAP_D D subunit of Archaeal RNA polymerase

Probab=99.69  E-value=1.2e-17  Score=126.62  Aligned_cols=64  Identities=9%  Similarity=0.058  Sum_probs=55.9

Q ss_pred             CeEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceeccccc
Q psy12830          7 PSVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQTG   75 (94)
Q Consensus         7 P~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~t~   75 (94)
                      |+|+|.+++++.++|+++|.+.++||||||+       +|||.|.|++|||+++|     ||++||.+.||+-+..
T Consensus         1 ~~~~~~~~~~~~~~f~~~g~~~s~~NalRRills~vp~~Ai~~V~i~~n~s~~~d-----e~i~hrl~~ip~~~e~   71 (259)
T cd07030           1 MEIEVLELDDDRARFVLEGVPPAFANAIRRAIISEVPTLAIDDVNIYENTSVLFD-----EMLAHRLGLIPLRTDL   71 (259)
T ss_pred             CceEEEecCCCEEEEEEeCCCHHHHHHHHHHHHhcCCeeeEEEEEEEeCCchhhH-----HHHHHhhcCcccccCH
Confidence            6899999999999999999999999999999       99999999999999999     5555555555554443

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

>PRK14979 DNA-directed RNA polymerase subunit D; Provisional

Probab=99.53  E-value=7.2e-15  Score=111.02  Aligned_cols=62  Identities=10%  Similarity=-0.046  Sum_probs=53.3

Q ss_pred             CCeEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceeccc
Q psy12830          6 QPSVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQ   73 (94)
Q Consensus         6 qP~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~   73 (94)
                      .+++++..-++++++|.|+ ++++++|||||+       +||+.|.|+.|||+++|     |+++|+.+.|||-+
T Consensus         3 ~~~~~~~~~~~~~~~f~l~-~~~tlgNaLRRvLLssipg~AI~~V~I~~Nts~~~D-----EivaHe~~lIpLK~   71 (195)
T PRK14979          3 TIKEKEKTRIGEEFKFSLK-APISFSSALRRIMISEVPTYAIENVYFYENSSSMYD-----EILAHRLGLIPIKG   71 (195)
T ss_pred             ccceeeeccCCcEEEEEEE-cCccHHHHHHHHHHhcCcceeEEEEEEecCcccccc-----hheeeeeeeeeeee
Confidence            3678999999999999999 999999999999       99999999999999999     55555555555444

>KOG1521|consensus

Probab=99.51  E-value=3.5e-15  Score=120.90  Aligned_cols=65  Identities=14%  Similarity=0.078  Sum_probs=59.6

Q ss_pred             CCCCeEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceeccc
Q psy12830          4 ANQPSVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQ   73 (94)
Q Consensus         4 ~~qP~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~   73 (94)
                      ..+-+|.|.+++++.+.|.+.|+|.|+|||+||+       ||||.|.|..||||..|     |+||||+|+|||.-
T Consensus        43 ~~~~~V~iv~~~~~~leFDligIda~IANAfRRILiaEVPtmAiEkVyi~nNTSViqD-----EvLaHRlGLvPl~a  114 (338)
T KOG1521|consen   43 KDNFKVDIVSLDEETLEFDLIGIDASIANAFRRILIAEVPTMAIEKVYIYNNTSVIQD-----EVLAHRLGLVPLRA  114 (338)
T ss_pred             hhceEEEEEeccCcceeEEEeeccHHHHHHHHHHHHhhcchhheeeeEEecCccccHH-----HHHHHhhcCccccc
Confidence            3457899999999999999999999999999999       99999999999999999     78888888888753

>smart00662 RPOLD RNA polymerases D

Probab=99.13  E-value=1.4e-11  Score=92.92  Aligned_cols=50  Identities=8%  Similarity=-0.038  Sum_probs=42.8

Q ss_pred             eEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcc--cceeeeeeecc
Q psy12830         18 NVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPS--FLFAFLCIYEN   67 (94)
Q Consensus        18 ~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~--~~~~fl~~~~~   67 (94)
                      +++|+|++.++++||||||+       +|||.|.|+.|+|.+.|++  |||++.+++.+
T Consensus         1 ~~~f~l~~~~~t~~NaLRRilLs~vp~~aI~~V~I~~n~~~v~eev~~~rLnL~pl~~~   59 (224)
T smart00662        1 RAKFVLEPYGLTLANALRRVLLSSVPGMAVTEVEIEGNTSGVQDEVLAHRLGLKPLASD   59 (224)
T ss_pred             CeEEEEEcCCchHHHHHHHHHHHcCccceEEEEEEecCCcchhHHHHHHHhCCeeEEEe
Confidence            37999999999999999999       9999999999999999955  55555555543

DNA-directed RNA polymerase subunit D and bacterial alpha chain

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

Probab=99.04  E-value=1.5e-10  Score=92.52  Aligned_cols=79  Identities=9%  Similarity=-0.024  Sum_probs=63.7

Q ss_pred             EEEeecC----CceEEEEEccCCchhhhcceee-------EEeeeEEEee------cccccCCcc--cceeeeeeeccce
Q psy12830          9 VHITDLT----DENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSA------QLLLCSRPS--FLFAFLCIYENRL   69 (94)
Q Consensus         9 V~I~eLt----d~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~------NTSVL~d~~--~~~~fl~~~~~~~   69 (94)
                      |+|.+++    +..+.|.++|.+.++||||||+       +||+.|+|..      +.+.+.|++  |||++.++..+.-
T Consensus         7 i~i~~~~~~~~~~~ieplerG~g~tlgNALRRvLLSsiPg~Av~~V~I~~v~hef~s~~gv~Edvl~~~LnLk~L~~~~~   86 (317)
T COG0202           7 VKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEIDGVLHEFDSIEGVQEDVLAHRLNLKPLAVKLD   86 (317)
T ss_pred             eEEEEcccccccEEEEEeeeCCcchhHHHHHHHHHHcCccceEEEEEEeccccccccCcCcHHHHHHHHhcCceeeeecc
Confidence            9999999    8899999999999999999999       9999999999      334999988  8888888777655


Q ss_pred             -------ecccccceeeecCCCCCC
Q psy12830         70 -------ALSQTGFRKTFCSPNQSP   87 (94)
Q Consensus        70 -------~l~~t~~~~~~~~~~~~~   87 (94)
                             -++..|--..+|+-.+.+
T Consensus        87 ~~~~~~~~~~~~g~g~v~a~d~~~~  111 (317)
T COG0202          87 GDEEVTLELDKEGPGEVTASDITVP  111 (317)
T ss_pred             cccceEEEEeccCCccccHhhcccc
Confidence                   344445455556555555

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

Probab=98.09  E-value=2.4e-06  Score=64.57  Aligned_cols=48  Identities=4%  Similarity=-0.017  Sum_probs=40.9

Q ss_pred             EEeecCCceEEEEE----ccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeee
Q psy12830         10 HITDLTDENVKFQV----EDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCI   64 (94)
Q Consensus        10 ~I~eLtd~~vkFiL----~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~   64 (94)
                      ++.+.++.+.+|.+    .|..+++||||||+       +||+.|+|+.|       .|+|+.+|.
T Consensus         2 ~~~~~~~~~~~F~i~pl~~g~~~tlgNaLRRvLLs~ipg~aI~~v~I~~~-------~He~~~Ipg   60 (215)
T cd06928           2 KVENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEGV-------LHEFSTIPG   60 (215)
T ss_pred             eeccCCCcEEEEEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEEEEEccc-------ccccccCCC
Confidence            35567889999999    67999999999999       99999999988       467777664

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=98.05  E-value=5.7e-06  Score=65.91  Aligned_cols=52  Identities=10%  Similarity=0.054  Sum_probs=42.4

Q ss_pred             CCCeEEEeecC--CceEEEEEc----cCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeee
Q psy12830          5 NQPSVHITDLT--DENVKFQVE----DTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLC   63 (94)
Q Consensus         5 ~qP~V~I~eLt--d~~vkFiL~----ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~   63 (94)
                      +-..+++.+.+  +.+.+|+++    |...++||||||+       +||+.|.|+.       ..|+|+.+|
T Consensus         5 ~~~~i~~~e~~~~~~~~~F~i~Ple~G~g~tlgNaLRRvLLs~ipg~aI~~VkI~g-------v~hEf~~Ip   69 (310)
T PRK05182          5 KPQKIEVEEESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKIDG-------VLHEFSTIP   69 (310)
T ss_pred             cCcEEEEEeccCCCcEEEEEEeccCCCchhHHHHHHHHHHHhcCCeeEEEEEEEcc-------eeeeccccC
Confidence            33468899986  899999997    9999999999999       9999999931       226666655

>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2

Probab=97.20  E-value=9.5e-05  Score=46.24  Aligned_cols=24  Identities=4%  Similarity=0.048  Sum_probs=22.4

Q ss_pred             EEEEEccCCchhhhcceee-------EEeee
Q psy12830         19 VKFQVEDTELSKRTNGNWK-------ENMEW   42 (94)
Q Consensus        19 vkFiL~ntDlS~ANaLRRi-------lAID~   42 (94)
                      ++|.++|.|.+++|+|||+       +||+.
T Consensus         1 i~~~~~g~~~tl~N~LRr~ll~~vp~~ai~~   31 (66)
T PF01193_consen    1 IEFLLKGEDHTLGNALRRILLSEVPGVAIDG   31 (66)
T ss_dssp             EEEEEESHHHHHHHHHHHHHHSSSEEEEEEE
T ss_pred             CEeEEcCCchHHHHHHHHHHHhcCCCceEEe
Confidence            5899999999999999999       88887

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 subunit (RpoA) 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 []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....

>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase

Probab=96.20  E-value=0.0024  Score=42.05  Aligned_cols=29  Identities=17%  Similarity=0.196  Sum_probs=27.8

Q ss_pred             EEEeecCCceEEEEEccCCchhhhcceee
Q psy12830          9 VHITDLTDENVKFQVEDTELSKRTNGNWK   37 (94)
Q Consensus         9 V~I~eLtd~~vkFiL~ntDlS~ANaLRRi   37 (94)
                      |+|.+.+++.++|+++|-|-.++|+||+.
T Consensus         1 ~ki~~~~~~~~~~~~~~edhTl~n~L~~~   29 (86)
T cd00460           1 VKILEKEKNYVDFVLENEDHTLGNSLRRI   29 (86)
T ss_pred             CceecCCCCEEEEEEeCCCchHHHHHHHH
Confidence            57889999999999999999999999999

The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, 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 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

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

Probab=96.16  E-value=0.0011  Score=44.71  Aligned_cols=23  Identities=4%  Similarity=-0.092  Sum_probs=16.7

Q ss_pred             EEEeecccccCCcc--cceeeeeee
Q psy12830         43 KGLSAQLLLCSRPS--FLFAFLCIY   65 (94)
Q Consensus        43 V~I~~NTSVL~d~~--~~~~fl~~~   65 (94)
                      |.|.+||||++||+  |||+.+|..
T Consensus         1 v~i~~n~s~~~dE~v~He~~~Ipgv   25 (112)
T PF01000_consen    1 VYIYENTSVLPDEGVAHEFGLIPGV   25 (112)
T ss_dssp             EEEEEETSSS-HHHHHCHHHBSTCB
T ss_pred             CEEEECCCeeccceeEeccccCCcc
Confidence            78999999999965  555555554

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 ....

>CHL00013 rpoA RNA polymerase alpha subunit

Probab=94.99  E-value=0.027  Score=45.69  Aligned_cols=41  Identities=2%  Similarity=-0.128  Sum_probs=37.5

Q ss_pred             CeEEEeecCCceEEEEEccCCc----hhhhcceee-------EEeeeEEEee
Q psy12830          7 PSVHITDLTDENVKFQVEDTEL----SKRTNGNWK-------ENMEWKGLSA   47 (94)
Q Consensus         7 P~V~I~eLtd~~vkFiL~ntDl----S~ANaLRRi-------lAID~V~I~~   47 (94)
                      .+.++.+.++.+.+|.++....    .++|||||+       .||..|.|+.
T Consensus        10 ie~~~~~~~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~g   61 (327)
T CHL00013         10 VESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEG   61 (327)
T ss_pred             eeEEEecCCCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECC
Confidence            5678889999999999999998    999999999       9999999965

>PRK01146 DNA-directed RNA polymerase subunit L; Provisional

Probab=93.80  E-value=0.062  Score=35.91  Aligned_cols=39  Identities=5%  Similarity=0.002  Sum_probs=34.3

Q ss_pred             CeEEEeecCCceEEEEEccCCchhhhcceee-EEeeeEEE
Q psy12830          7 PSVHITDLTDENVKFQVEDTELSKRTNGNWK-ENMEWKGL   45 (94)
Q Consensus         7 P~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-lAID~V~I   45 (94)
                      |+|+|.+.+++.+.|.+.|=|=.+.|+||-. +.-+.|.+
T Consensus         1 m~ikvi~~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~f   40 (85)
T PRK01146          1 MEIKVLEKEDNELELEIEGEDHTLMNLLKEELLEDPGVEA   40 (85)
T ss_pred             CeEEEEecCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeE
Confidence            6899999999999999999999999999988 55555544

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

Probab=88.53  E-value=0.2  Score=39.82  Aligned_cols=28  Identities=11%  Similarity=0.058  Sum_probs=23.1

Q ss_pred             EEEEc----cCCchhhhcceee-------EEeeeEEEee
Q psy12830         20 KFQVE----DTELSKRTNGNWK-------ENMEWKGLSA   47 (94)
Q Consensus        20 kFiL~----ntDlS~ANaLRRi-------lAID~V~I~~   47 (94)
                      +|+++    |...+++|||||+       .||..|.|+.
T Consensus         3 ~f~i~Ple~g~g~TlGNaLRRvLLs~i~g~aI~~vkI~g   41 (297)
T TIGR02027         3 KFVLEPLERGFGITLGNALRRVLLSSIPGAAITAVKIDG   41 (297)
T ss_pred             EEEEecCCCCchhHHHHHHHHHHHhcCCceEEEEEEEcc
Confidence            45553    6678999999999       9999999974

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.

>cd06927 RNAP_L L subunit of Archaeal RNA polymerase

Probab=84.47  E-value=0.78  Score=30.48  Aligned_cols=37  Identities=5%  Similarity=0.030  Sum_probs=31.0

Q ss_pred             EEEeecCCceEEEEEccCCchhhhcceee-EEeeeEEE
Q psy12830          9 VHITDLTDENVKFQVEDTELSKRTNGNWK-ENMEWKGL   45 (94)
Q Consensus         9 V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-lAID~V~I   45 (94)
                      |+|.+.+++.++|++.|=|=.+.|+||-. +.-+.|.+
T Consensus         1 ikvi~~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~f   38 (83)
T cd06927           1 LKVIEKEDNELELEIEGEDHTLLNLLKEELLRDPGVKV   38 (83)
T ss_pred             CeEEEcCCCEEEEEEeCCCchHHHHHHHHHhcCCCeEE
Confidence            57899999999999999999999999987 44444443

The archaeal L subunit of 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 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.

>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase

Probab=83.18  E-value=0.9  Score=30.17  Aligned_cols=37  Identities=8%  Similarity=0.038  Sum_probs=31.1

Q ss_pred             EEEeecCCceEEEEEccCCchhhhcceee-EEeeeEEE
Q psy12830          9 VHITDLTDENVKFQVEDTELSKRTNGNWK-ENMEWKGL   45 (94)
Q Consensus         9 V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-lAID~V~I   45 (94)
                      |+|.+.+++.++|+++|=|=.+.|+||-. +.-+.|.+
T Consensus         1 ~kii~~~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~f   38 (83)
T cd07027           1 LRIISKEKNSVTVEMENEDHTLGNLLREELLKDDQVDF   38 (83)
T ss_pred             CeeEecCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeE
Confidence            57889999999999999999999999987 44444443

The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L 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 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/

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	94
3h0g_C	297	DNA-directed RNA polymerase II subunit RPB3; trans	99.73
2pa8_D	265	DNA-directed RNA polymerase subunit D; ferredoxin-	99.72
1twf_C	318	B44.5, DNA-directed RNA polymerase II 45 kDa polyp	99.71
1bdf_A	235	RNA polymerase alpha subunit; nucleotidyltransfera	98.87
2a6h_A	315	DNA-directed RNA polymerase alpha chain; RNA polym	98.79
3lu0_A	329	DNA-directed RNA polymerase subunit alpha; E. coli	98.25
2pa8_L	92	DNA-directed RNA polymerase subunit L; ferredoxin-	90.64
1xpp_A	115	TA1416, DNA-directed RNA polymerase subunit L; str	87.72

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

Probab=99.73  E-value=3.2e-19  Score=140.12  Aligned_cols=67  Identities=12%  Similarity=0.228  Sum_probs=59.7

Q ss_pred             CCCCeEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceeccccc
Q psy12830          4 ANQPSVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQTG   75 (94)
Q Consensus         4 ~~qP~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~t~   75 (94)
                      .++|+|+|.++++++++|+|+|+|+++||||||+       +|||.|.|+.|||||+|     |||+||++.||+-+..
T Consensus         2 ~~~p~I~i~~~~~~~~~F~l~g~~~tiaNALRRiLLSeVPt~AI~~V~I~~NtSvl~D-----E~laHrlglIP~v~ed   75 (297)
T 3h0g_C            2 DSETHITIRNISKNSVDFVLTNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPD-----EFLAHRLGMIPLDSSN   75 (297)
T ss_dssp             --CCSBCCCCBCSSEEEEEECSCCHHHHHHHHHHHHSSCCEEEEEEEEEEEECSSSCH-----HHHHHHHHHSCBCCTT
T ss_pred             CCCCeEEEEEccCCEEEEEEECCChhHHHHHHHHHHHcCccceEEEEEEEeCCccccc-----cceeeeeccCCccccc
Confidence            4689999999999999999999999999999999       99999999999999999     7777777777776543

>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=99.72  E-value=7.7e-19  Score=132.70  Aligned_cols=64  Identities=8%  Similarity=-0.063  Sum_probs=57.9

Q ss_pred             CeEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceeccccc
Q psy12830          7 PSVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQTG   75 (94)
Q Consensus         7 P~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~t~   75 (94)
                      |+|+|.++++++++|+|+|.+.++||||||+       +|||.|+|+.|||||+|     |||+||.+.||+-+..
T Consensus         1 ~~i~i~~~~~~~~~f~l~g~~~t~~NalRRills~vp~~AI~~V~i~~Ntsvl~D-----E~v~Hr~~~Ip~~~ed   71 (265)
T 2pa8_D            1 MSINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYD-----EILAHRLALIPFMSEE   71 (265)
T ss_dssp             -CEEEEEECSSEEEEEEESSCHHHHHHHHHHHHHSCCEEEEEEEEEEEECSSSCH-----HHHHHHHTTSCBCCTT
T ss_pred             CeEEEEEcCCCEEEEEEeCCCHHHHHHHHHHHHHcCccceEEEEEEEeCCCcccc-----HHHHHhhcCCcCcccC
Confidence            6799999999999999999999999999999       99999999999999999     7777777777776654

>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=99.71  E-value=7.4e-19  Score=138.52  Aligned_cols=68  Identities=13%  Similarity=0.229  Sum_probs=60.9

Q ss_pred             CCCCeEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceecccccc
Q psy12830          4 ANQPSVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQTGF   76 (94)
Q Consensus         4 ~~qP~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~t~~   76 (94)
                      .++|+|+|.++++++++|+|+|.++++||||||+       +|||.|+|+.|||||+|     |||+||++.||+-+..+
T Consensus         3 ~~~p~I~i~~~~~~~~kF~leG~~~tlaNALRRiLLSevPg~AI~~V~I~~NTSvl~D-----E~vaHrlglIP~v~eDv   77 (318)
T 1twf_C            3 EEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLAD-----EFIAHRLGLIPLQSMDI   77 (318)
T ss_dssp             CCSSBCCCSCCCSSEECCEEBSSCHHHHHHHHHHHHHCCCEEEEEEEEEEEECSSSCH-----HHHHHHHHTSCEEETTG
T ss_pred             ccCCeEEEEEecCCEEEEEEEccChhHHHHHHHHHHHcCccceEEEEEEEeCCccccc-----ceeEeecccCCCcccCh
Confidence            4789999999999999999999999999999999       99999999999999999     77777777777765443

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

Probab=98.87  E-value=7.2e-10  Score=83.76  Aligned_cols=54  Identities=11%  Similarity=-0.044  Sum_probs=45.1

Q ss_pred             CCe-EEEeecCCceEEEEEc----cCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceeccc
Q psy12830          6 QPS-VHITDLTDENVKFQVE----DTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQ   73 (94)
Q Consensus         6 qP~-V~I~eLtd~~vkFiL~----ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~   73 (94)
                      .|. |+|.+.++.+++|+++    |.+.++||||||+       +||+.|.|              ++++|+.+.||+-+
T Consensus        10 ~p~~i~i~~~~~~~~~F~l~Ple~G~~~tlgNaLRRiLLsevpg~AI~~V~I--------------e~v~He~~~Ipgv~   75 (235)
T 1bdf_A           10 KPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVTEVEI--------------DGVLHEYSTKEGVQ   75 (235)
T ss_dssp             CCCEEEEEESSSSEEEEEEEEEETTHHHHHHHHHHHHHTTSCCCEEEEEEEE--------------TTCCSTTCCCTTBS
T ss_pred             CCceEEEEEccCCEEEEEEEecCCCCchHHHHHHHHHHHhcCCceEEEEEEE--------------cceeeccccCCCcc
Confidence            344 9999999999999996    9999999999999       99999999              24555555555554

>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=98.79  E-value=2.4e-09  Score=84.27  Aligned_cols=42  Identities=10%  Similarity=0.010  Sum_probs=39.8

Q ss_pred             CCeEEEeecCCceEEEEEc----cCCchhhhcceee-------EEeeeEEEee
Q psy12830          6 QPSVHITDLTDENVKFQVE----DTELSKRTNGNWK-------ENMEWKGLSA   47 (94)
Q Consensus         6 qP~V~I~eLtd~~vkFiL~----ntDlS~ANaLRRi-------lAID~V~I~~   47 (94)
                      .|+|+|.+.++.+++|+++    |.+.++||||||+       +||+.|.|+.
T Consensus         8 ~p~i~i~~~~~~~~~F~l~Ple~G~~~TlgNaLRRiLLsevpg~AI~~V~I~~   60 (315)
T 2a6h_A            8 APVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIED   60 (315)
T ss_dssp             CCEEEEEEETTTEEEEEEEEECTTCHHHHHHHHHHHHHHTCEEEEEEEEEESS
T ss_pred             CCeEEEEEccCCEEEEEEEccCCCchhHHHHHHHHHHHhcCCceEEEEEEEec
Confidence            5899999999999999995    9999999999999       9999999975

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

Probab=98.25  E-value=2.8e-07  Score=73.27  Aligned_cols=49  Identities=8%  Similarity=-0.027  Sum_probs=41.7

Q ss_pred             eEEEeecCCceEEEEEc----cCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeee
Q psy12830          8 SVHITDLTDENVKFQVE----DTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLC   63 (94)
Q Consensus         8 ~V~I~eLtd~~vkFiL~----ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~   63 (94)
                      .++|.+.++.+.+|+++    |.+.++||||||+       +||+.|+|+ |  |    .|+|+.+|
T Consensus        13 ~~~v~~~~~~~~kF~l~PlerG~g~TlgNaLRRvLLssvpg~AIt~V~I~-g--v----~Hefs~Ip   72 (329)
T 3lu0_A           13 LVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEID-G--V----LHEYSTKE   72 (329)
T ss_dssp             CCCEEECTTSEEEEEECCCCTTCHHHHHHHHHHHTTTSSCEEEEEEEEES-S--C----SSTTCCCT
T ss_pred             eEEEEEcCCCEEEEEEEecCCCChhHHHHHHHHHHHhcCCceEEEEEEEe-C--c----cccccccc
Confidence            57889999999999999    9999999999999       999999994 3  1    25566555

>2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L 2y0s_L

Probab=90.64  E-value=0.16  Score=33.21  Aligned_cols=31  Identities=6%  Similarity=0.044  Sum_probs=29.8

Q ss_pred             CeEEEeecCCceEEEEEccCCchhhhcceee
Q psy12830          7 PSVHITDLTDENVKFQVEDTELSKRTNGNWK   37 (94)
Q Consensus         7 P~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi   37 (94)
                      |+|+|.+.+++.+.|++.|=|=.+.|+||-.
T Consensus         1 Meikvi~k~~n~~~f~i~~EDHTLgN~Lr~~   31 (92)
T 2pa8_L            1 MEIRILKSESNYLELEIEGEDHTLGNLIAGT   31 (92)
T ss_dssp             CEEEEEEEETTEEEEEEETCCHHHHHHHHHH
T ss_pred             CceEEEecCCCeEEEEEecCchhHHHHHHHH
Confidence            6899999999999999999999999999988

>1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural genomics, protein structure initiative, MCSG; 1.60A {Thermoplasma acidophilum} SCOP: d.74.3.2

Probab=87.72  E-value=0.47  Score=32.56  Aligned_cols=42  Identities=2%  Similarity=-0.057  Sum_probs=34.7

Q ss_pred             CCCCeEEEeecCCceEEEEEccCCchhhhcceee-EEeeeEEE
Q psy12830          4 ANQPSVHITDLTDENVKFQVEDTELSKRTNGNWK-ENMEWKGL   45 (94)
Q Consensus         4 ~~qP~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-lAID~V~I   45 (94)
                      .+.|+++|.+.+++.+.|++.+=|=.+.|+||-. +.-+.|.+
T Consensus         8 ~~kmeiki~~k~~n~~~f~i~~EDHTLgNlLr~~Llkdp~V~f   50 (115)
T 1xpp_A            8 TAESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDE   50 (115)
T ss_dssp             -CCCEEEEEEECSSEEEEEEESCCHHHHHHHHHHHTTCTTEEE
T ss_pred             ccceEEEEEcCCCCEEEEEEeCCCchhHHHHHHHHhcCCCeEE
Confidence            3569999999999999999999999999999988 44344433

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	94
d1twfc1	135	RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.13
d1twfc2	131	RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta	98.8
d1xppa_	99	DNA-directed RNA polymerase subunit L, RpoL {Therm	85.38

>d1twfc1 d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: DCoH-like
superfamily: RBP11-like subunits of RNA polymerase
family: RNA polymerase alpha subunit dimerisation domain
domain: RPB3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.13  E-value=2.9e-12  Score=90.26  Aligned_cols=46  Identities=17%  Similarity=0.154  Sum_probs=43.2

Q ss_pred             CCCeEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeeccc
Q psy12830          5 NQPSVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLL   50 (94)
Q Consensus         5 ~qP~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTS   50 (94)
                      .+|+|+|+++++++++|+|+|+|+|+||||||+       ++++.|....|++
T Consensus         2 ~~P~i~i~~~~~~~~~F~l~~~d~s~ANalRRi~iaeV~t~v~feyDp~N~lr   54 (135)
T d1twfc1           2 EGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIAAAIEFEYDPWNKLK   54 (135)
T ss_dssp             CSSBCCCSCCCSSEECCEEBSSCHHHHHHHHHHHHHCCEEEEEEEECSSTTSC
T ss_pred             CCCEEEEEEcCCCEEEEEEeCCCHHHHHHHHHHHHHhhhhheeeeeccccccc
Confidence            689999999999999999999999999999999       8999998888865

>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=98.80  E-value=3e-10  Score=76.43  Aligned_cols=32  Identities=6%  Similarity=0.072  Sum_probs=27.4

Q ss_pred             EEeeeEEEeecccccCCcccceeeeeeeccceecccc
Q psy12830         38 ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQT   74 (94)
Q Consensus        38 lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~t   74 (94)
                      ||||.|.|++|||+|+|     |||+||+++|||-+.
T Consensus         3 lAid~V~I~~NTS~l~D-----E~iaHRLglIPi~~~   34 (131)
T d1twfc2           3 LAIDSVEVETNTTVLAD-----EFIAHRLGLIPLQSM   34 (131)
T ss_dssp             EEEEEEEEEEECSSSCH-----HHHHHHHHTSCEEET
T ss_pred             EEEEEEEEEECCcccch-----HHHHHhhcCceeecc
Confidence            89999999999999999     777777777777543

>d1xppa_ d.74.3.2 (A:) DNA-directed RNA polymerase subunit L, RpoL {Thermoplasma acidophilum [TaxId: 2303]}

class: Alpha and beta proteins (a+b)
fold: DCoH-like
superfamily: RBP11-like subunits of RNA polymerase
family: RBP11/RpoL
domain: DNA-directed RNA polymerase subunit L, RpoL
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=85.38  E-value=0.2  Score=31.30  Aligned_cols=32  Identities=3%  Similarity=0.018  Sum_probs=30.3

Q ss_pred             CCeEEEeecCCceEEEEEccCCchhhhcceee
Q psy12830          6 QPSVHITDLTDENVKFQVEDTELSKRTNGNWK   37 (94)
Q Consensus         6 qP~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi   37 (94)
                      +-+|+|.+.+++.++|.|.|=|=.+.|+||..
T Consensus         2 ~~~ikvi~~~~n~~~~~i~~EdHTlgn~L~~~   33 (99)
T d1xppa_           2 ESSLRVISKEKNSITVEMINYDNTLLRTLVEE   33 (99)
T ss_dssp             CCEEEEEEECSSEEEEEEESCCHHHHHHHHHH
T ss_pred             CceEEEEecCCCEEEEEEeCCCchHHHHHHHH
Confidence            45799999999999999999999999999998