Citrus Sinensis ID: 034762

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80----
Protein Sequence
MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSRVY
Secondary Structure (PSIPRED)
cccccccccEEcccccEEEEEEcccccccEEEEEEcccccHHHHHHHHHHHccccEEEEEcccccccccEEEEEEEEccccccc
Secondary Structure Prediction (SSPRO)
cccccccEEEEEccccEEEEEEEcccccccEEEEEEccccHHHHHHHHHHHccccEEEEEEEcccccccEEEEEEEEccccccc
Coil and Loop (DISEMBL)
mnapdryerfvvpegtkkvsyERDTKIINAASFTIEREEHTIGNILRMQLhrdenvlfagyklphplqYKIIVRAELAKHSRVY
Flexible Loop (DISEMBL)
mnapdryerfvvpegtkkvsyerdtkiinaasftiereeHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSRVY
Low Complexity Region (SEG)
MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSRVY
Disordered region (IsUnstruct)
*********FVV****KKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAEL*******
Disordered Region (DISOPRED)
**APDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELA******
Disordered Region (DISEMBL)
MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSRVY
Disordered Region (DISPRO)
****DRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHS***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSRVY
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	84	2.2.26 [Sep-21-2011]
Q38859	116	DNA-directed RNA polymera	yes	no	0.964	0.698	0.839	6e-36
Q86JJ5	120	DNA-directed RNA polymera	yes	no	0.964	0.675	0.543	3e-23
P52435	117	DNA-directed RNA polymera	yes	no	0.904	0.649	0.552	6e-21
Q32P79	117	DNA-directed RNA polymera	yes	no	0.904	0.649	0.552	6e-21
O08740	117	DNA-directed RNA polymera	yes	no	0.904	0.649	0.552	7e-21
Q9VJE4	117	DNA-directed RNA polymera	yes	no	0.880	0.632	0.581	8e-21
Q7PVQ9	117	DNA-directed RNA polymera	yes	no	0.880	0.632	0.567	7e-20
Q9GZM3	115	DNA-directed RNA polymera	yes	no	0.892	0.652	0.539	2e-19
Q9H1A7	115	DNA-directed RNA polymera	yes	no	0.892	0.652	0.526	5e-19
Q60SM4	122	Probable DNA-directed RNA	N/A	no	0.892	0.614	0.539	2e-18

>sp|Q38859|RPB11_ARATH DNA-directed RNA polymerase II subunit RPB11 OS=Arabidopsis thaliana GN=RPB13.6 PE=2 SV=1

 Score =  149 bits (375), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 68/81 (83%), Positives = 75/81 (92%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAP+RYERFVVPEGTKKVSY+RDTKIINAASFT+ERE+HTIGNI+RMQLHRDENVLFAG
Sbjct: 1  MNAPERYERFVVPEGTKKVSYDRDTKIINAASFTVEREDHTIGNIVRMQLHRDENVLFAG 60

Query: 61 YKLPHPLQYKIIVRAELAKHS 81
          Y+LPHPL+YKIIVR      S
Sbjct: 61 YQLPHPLKYKIIVRIHTTSQS 81

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. RPB11 is part of the core element with the central large cleft.
Arabidopsis thaliana (taxid: 3702)

>sp|Q86JJ5|RPB11_DICDI DNA-directed RNA polymerase II subunit rpb11 OS=Dictyostelium discoideum GN=polr2j PE=3 SV=1

 Score =  107 bits (266), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 44/81 (54%), Positives = 66/81 (81%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAPDR+E FV+P+G KKV+  RDTKI NA+ FTI +E+HTIGN++RMQL  D++++FAG
Sbjct: 1  MNAPDRFELFVLPDGAKKVTMVRDTKIPNASMFTILKEDHTIGNLIRMQLIADQDIIFAG 60

Query: 61 YKLPHPLQYKIIVRAELAKHS 81
          Y++PHPL++ + +R +   ++
Sbjct: 61 YRMPHPLEHNVNIRIQTNNNT 81

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. RPB11 is part of the core element with the central large cleft.

Dictyostelium discoideum (taxid: 44689)

>sp|P52435|RPB11_HUMAN DNA-directed RNA polymerase II subunit RPB11-a OS=Homo sapiens GN=POLR2J PE=1 SV=1

 Score = 99.4 bits (246), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 42/76 (55%), Positives = 60/76 (78%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct: 1  MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 60

Query: 61 YKLPHPLQYKIIVRAE 76
          YK+PHPL++KII+R +
Sbjct: 61 YKVPHPLEHKIIIRVQ 76

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. RPB11 is part of the core element with the central large cleft.

Homo sapiens (taxid: 9606)

>sp|Q32P79|RPB11_BOVIN DNA-directed RNA polymerase II subunit RPB11 OS=Bos taurus GN=POLR2J PE=3 SV=1

 Score = 99.4 bits (246), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 42/76 (55%), Positives = 60/76 (78%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct: 1  MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 60

Query: 61 YKLPHPLQYKIIVRAE 76
          YK+PHPL++KII+R +
Sbjct: 61 YKVPHPLEHKIIIRVQ 76

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. RPB11 is part of the core element with the central large cleft.

Bos taurus (taxid: 9913)

>sp|O08740|RPB11_MOUSE DNA-directed RNA polymerase II subunit RPB11 OS=Mus musculus GN=Polr2j PE=2 SV=1

 Score = 99.0 bits (245), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 42/76 (55%), Positives = 60/76 (78%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct: 1  MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 60

Query: 61 YKLPHPLQYKIIVRAE 76
          YK+PHPL++KII+R +
Sbjct: 61 YKVPHPLEHKIIIRVQ 76

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. RPB11 is part of the core element with the central large cleft.

Mus musculus (taxid: 10090)

>sp|Q9VJE4|RPB11_DROME DNA-directed RNA polymerase II subunit RPB11 OS=Drosophila melanogaster GN=Rpb11 PE=3 SV=1

 Score = 99.0 bits (245), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 43/74 (58%), Positives = 59/74 (79%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAP  +E F++ EG KK+  E DTK+ NAA FTI +E+HT+GN++R QL +D NVLFAG
Sbjct: 1  MNAPPTFESFLLYEGEKKIIKELDTKVTNAAIFTINKEDHTLGNMIRNQLLKDPNVLFAG 60

Query: 61 YKLPHPLQYKIIVR 74
          YK+PHPL++K ++R
Sbjct: 61 YKVPHPLEHKFVIR 74

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. RPB11 is part of the core element with the central large cleft.

Drosophila melanogaster (taxid: 7227)

>sp|Q7PVQ9|RPB11_ANOGA DNA-directed RNA polymerase II subunit RPB11 OS=Anopheles gambiae GN=Rpb11 PE=2 SV=2

 Score = 95.9 bits (237), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 42/74 (56%), Positives = 58/74 (78%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAP  +E F++ EG KK+  E D K+ NAA FT+ +E+HT+GN++R QL +D NVLFAG
Sbjct: 1  MNAPPTFESFLLYEGEKKIIKELDMKVPNAAIFTVNKEDHTLGNMIRNQLLKDPNVLFAG 60

Query: 61 YKLPHPLQYKIIVR 74
          YKLPHPL++K ++R
Sbjct: 61 YKLPHPLEHKFVLR 74

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. RPB11 is part of the core element with the central large cleft.

Anopheles gambiae (taxid: 7165)

>sp|Q9GZM3|RPB1B_HUMAN DNA-directed RNA polymerase II subunit RPB11-b1 OS=Homo sapiens GN=POLR2J2 PE=1 SV=1

 Score = 94.0 bits (232), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 41/76 (53%), Positives = 60/76 (78%), Gaps = 1/76 (1%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAP  +E F++ EG +K++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct: 1  MNAPPAFESFLLFEG-EKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 59

Query: 61 YKLPHPLQYKIIVRAE 76
          YK+PHPL++KII+R +
Sbjct: 60 YKVPHPLEHKIIIRVQ 75

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. RPB11 is part of the core element with the central large cleft.

Homo sapiens (taxid: 9606)

>sp|Q9H1A7|RPB1C_HUMAN DNA-directed RNA polymerase II subunit RPB11-b2 OS=Homo sapiens GN=POLR2J3 PE=2 SV=1

 Score = 93.2 bits (230), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 40/76 (52%), Positives = 60/76 (78%), Gaps = 1/76 (1%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAP  +E F++ EG +K++  +DTK+ NA  FT+ +E+HT+GNI++ QL +D  VLFAG
Sbjct: 1  MNAPPAFESFLLFEG-EKITINKDTKVPNACLFTMNKEDHTLGNIIKSQLLKDPQVLFAG 59

Query: 61 YKLPHPLQYKIIVRAE 76
          YK+PHPL++KII+R +
Sbjct: 60 YKVPHPLEHKIIIRVQ 75

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. RPB11 is part of the core element with the central large cleft.

Homo sapiens (taxid: 9606)

>sp|Q60SM4|RPB11_CAEBR Probable DNA-directed RNA polymerase II subunit RPB11 OS=Caenorhabditis briggsae GN=rpb-11 PE=3 SV=1

 Score = 91.3 bits (225), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 41/76 (53%), Positives = 60/76 (78%), Gaps = 1/76 (1%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAP  +E F++ +  KK+  E+DTK+ NAA FTI +E+HT+GN+L++QL +D  VLFAG
Sbjct: 1  MNAPAAFESFLLLDD-KKIYIEKDTKVPNAAIFTINKEDHTLGNMLKIQLLKDPEVLFAG 59

Query: 61 YKLPHPLQYKIIVRAE 76
          YK PHPL++KI++R +
Sbjct: 60 YKNPHPLEHKILLRVQ 75

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. RPB11 is part of the core element with the central large cleft.

Caenorhabditis briggsae (taxid: 6238)

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	84
449464004	116	PREDICTED: DNA-directed RNA polymerase I	0.964	0.698	0.925	7e-37
255553542	156	DNA-directed RNA polymerase II 13.6 kD p	0.964	0.519	0.888	3e-36
388516987	116	unknown [Lotus japonicus]	0.964	0.698	0.913	3e-36
225430537	116	PREDICTED: DNA-directed RNA polymerase I	0.964	0.698	0.888	3e-36
358248360	116	uncharacterized protein LOC100784219 [Gl	0.964	0.698	0.913	4e-36
356531671	116	PREDICTED: DNA-directed RNA polymerase I	0.964	0.698	0.913	4e-36
115470799	120	Os07g0172500 [Oryza sativa Japonica Grou	0.964	0.675	0.876	2e-35
224103945	116	predicted protein [Populus trichocarpa]	0.964	0.698	0.876	2e-35
413937790	112	hypothetical protein ZEAMMB73_270623 [Ze	0.964	0.723	0.864	3e-35
226504996	120	uncharacterized protein LOC100274213 [Ze	0.964	0.675	0.864	3e-35

>gi|449464004|ref|XP_004149719.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB11-like [Cucumis sativus] gi|449516703|ref|XP_004165386.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB11-like [Cucumis sativus]

 Score =  157 bits (397), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 75/81 (92%), Positives = 75/81 (92%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG
Sbjct: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60

Query: 61 YKLPHPLQYKIIVRAELAKHS 81
          YKLPHPLQYKIIVR      S
Sbjct: 61 YKLPHPLQYKIIVRIHTTSQS 81

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255553542|ref|XP_002517812.1| DNA-directed RNA polymerase II 13.6 kD polypeptide, putative [Ricinus communis] gi|223543084|gb|EEF44619.1| DNA-directed RNA polymerase II 13.6 kD polypeptide, putative [Ricinus communis]

 Score =  155 bits (392), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 72/81 (88%), Positives = 75/81 (92%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAPDRYERFVVPEGTKKVSYERDTKIINAASFT+ERE+HTIGNILRMQLHRDENVLFAG
Sbjct: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTVEREDHTIGNILRMQLHRDENVLFAG 60

Query: 61 YKLPHPLQYKIIVRAELAKHS 81
          Y+LPHPLQYKIIVR      S
Sbjct: 61 YRLPHPLQYKIIVRIHTTSQS 81

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388516987|gb|AFK46555.1| unknown [Lotus japonicus]

 Score =  155 bits (392), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 74/81 (91%), Positives = 75/81 (92%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIERE+HTIGNILRMQLHRD NVLFAG
Sbjct: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREDHTIGNILRMQLHRDPNVLFAG 60

Query: 61 YKLPHPLQYKIIVRAELAKHS 81
          YKLPHPLQYKIIVR   A  S
Sbjct: 61 YKLPHPLQYKIIVRIHTASQS 81

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225430537|ref|XP_002285578.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB11 [Vitis vinifera] gi|296082163|emb|CBI21168.3| unnamed protein product [Vitis vinifera]

 Score =  155 bits (391), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 72/81 (88%), Positives = 75/81 (92%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAPDRYERFVVPEGTKKVSYERDTKIINAASFT+ERE+HTIGNILRMQLHRDENVLFAG
Sbjct: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTVEREDHTIGNILRMQLHRDENVLFAG 60

Query: 61 YKLPHPLQYKIIVRAELAKHS 81
          YKLPHPLQYKII+R      S
Sbjct: 61 YKLPHPLQYKIIIRIHTTSQS 81

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358248360|ref|NP_001240124.1| uncharacterized protein LOC100784219 [Glycine max] gi|255626235|gb|ACU13462.1| unknown [Glycine max]

 Score =  155 bits (391), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 74/81 (91%), Positives = 74/81 (91%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD NVLFAG
Sbjct: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDPNVLFAG 60

Query: 61 YKLPHPLQYKIIVRAELAKHS 81
          YKLPHPLQYKIIVR      S
Sbjct: 61 YKLPHPLQYKIIVRIHTTSQS 81

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356531671|ref|XP_003534400.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB11 [Glycine max]

 Score =  155 bits (391), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 74/81 (91%), Positives = 74/81 (91%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD NVLFAG
Sbjct: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDPNVLFAG 60

Query: 61 YKLPHPLQYKIIVRAELAKHS 81
          YKLPHPLQYKIIVR      S
Sbjct: 61 YKLPHPLQYKIIVRIHTTSQS 81

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115470799|ref|NP_001058998.1| Os07g0172500 [Oryza sativa Japonica Group] gi|34394446|dbj|BAC83620.1| putative DNA-directed RNA polymerase II 13.6K chain [Oryza sativa Japonica Group] gi|113610534|dbj|BAF20912.1| Os07g0172500 [Oryza sativa Japonica Group] gi|215704597|dbj|BAG94225.1| unnamed protein product [Oryza sativa Japonica Group]

 Score =  152 bits (385), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 71/81 (87%), Positives = 74/81 (91%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAPDRYERFVVPEGTKKVSYERDTKI+NA SFTIERE+HTIGNILRMQLHRD NVLFAG
Sbjct: 1  MNAPDRYERFVVPEGTKKVSYERDTKIVNAGSFTIEREDHTIGNILRMQLHRDPNVLFAG 60

Query: 61 YKLPHPLQYKIIVRAELAKHS 81
          YKLPHPLQYKI+VR   A  S
Sbjct: 61 YKLPHPLQYKILVRVHTANQS 81

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224103945|ref|XP_002313254.1| predicted protein [Populus trichocarpa] gi|118484276|gb|ABK94017.1| unknown [Populus trichocarpa] gi|222849662|gb|EEE87209.1| predicted protein [Populus trichocarpa]

 Score =  152 bits (384), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 71/81 (87%), Positives = 75/81 (92%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAPDRYERFVVPEGTKKVSYERDTKIINAASFT+ERE+HTIGNILRMQLHRD+NVLFAG
Sbjct: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTVEREDHTIGNILRMQLHRDDNVLFAG 60

Query: 61 YKLPHPLQYKIIVRAELAKHS 81
          YKLPHPL+YKIIVR      S
Sbjct: 61 YKLPHPLKYKIIVRIHTTSQS 81

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413937790|gb|AFW72341.1| hypothetical protein ZEAMMB73_270623 [Zea mays]

 Score =  152 bits (384), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 70/81 (86%), Positives = 74/81 (91%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAPDRYERFVVPEGTKKVSYERDTKI+NAASFT+ERE+HT+GNILRMQLHRD NVLFAG
Sbjct: 1  MNAPDRYERFVVPEGTKKVSYERDTKIVNAASFTVEREDHTVGNILRMQLHRDPNVLFAG 60

Query: 61 YKLPHPLQYKIIVRAELAKHS 81
          YKLPHPLQYKIIVR      S
Sbjct: 61 YKLPHPLQYKIIVRIHTTSQS 81

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226504996|ref|NP_001142057.1| uncharacterized protein LOC100274213 [Zea mays] gi|194696560|gb|ACF82364.1| unknown [Zea mays] gi|194699868|gb|ACF84018.1| unknown [Zea mays] gi|194706942|gb|ACF87555.1| unknown [Zea mays] gi|195615212|gb|ACG29436.1| DNA-directed RNA polymerase II subunit J [Zea mays] gi|195628620|gb|ACG36140.1| DNA-directed RNA polymerase II subunit J [Zea mays] gi|195656859|gb|ACG47897.1| DNA-directed RNA polymerase II subunit J [Zea mays] gi|413937791|gb|AFW72342.1| DNA-directed RNA polymerase II subunit J isoform 1 [Zea mays] gi|413937792|gb|AFW72343.1| DNA-directed RNA polymerase II subunit J isoform 2 [Zea mays] gi|413937793|gb|AFW72344.1| DNA-directed RNA polymerase II subunit J isoform 3 [Zea mays] gi|413937794|gb|AFW72345.1| DNA-directed RNA polymerase II subunit J isoform 4 [Zea mays] gi|413937795|gb|AFW72346.1| DNA-directed RNA polymerase II subunit J isoform 5 [Zea mays]

 Score =  152 bits (384), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 70/81 (86%), Positives = 74/81 (91%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAPDRYERFVVPEGTKKVSYERDTKI+NAASFT+ERE+HT+GNILRMQLHRD NVLFAG
Sbjct: 1  MNAPDRYERFVVPEGTKKVSYERDTKIVNAASFTVEREDHTVGNILRMQLHRDPNVLFAG 60

Query: 61 YKLPHPLQYKIIVRAELAKHS 81
          YKLPHPLQYKIIVR      S
Sbjct: 61 YKLPHPLQYKIIVRIHTTSQS 81

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	84
DICTYBASE|DDB_G0277677	120	rpb11 "RNA polymerase II core	0.904	0.633	0.578	3.4e-22
FB|FBgn0032634	117	Rpb11 "Rpb11" [Drosophila mela	0.904	0.649	0.565	1e-20
UNIPROTKB|Q32P79	117	POLR2J "DNA-directed RNA polym	0.904	0.649	0.552	2.1e-20
UNIPROTKB|E2RD80	117	LOC100686835 "Uncharacterized	0.904	0.649	0.552	2.1e-20
UNIPROTKB|F1PXE5	130	LOC100686835 "Uncharacterized	0.904	0.584	0.552	2.1e-20
UNIPROTKB|P52435	117	POLR2J "DNA-directed RNA polym	0.904	0.649	0.552	2.1e-20
UNIPROTKB|Q9H1A6	127	POLR2J1 "DNA-directed RNA poly	0.904	0.598	0.552	2.1e-20
MGI|MGI:109582	117	Polr2j "polymerase (RNA) II (D	0.904	0.649	0.552	2.1e-20
RGD|1310198	117	Polr2j "polymerase (RNA) II (D	0.904	0.649	0.552	2.1e-20
ZFIN|ZDB-GENE-050522-120	117	polr2j "polymerase (RNA) II (D	0.904	0.649	0.526	3.5e-20

DICTYBASE|DDB_G0277677 rpb11 "RNA polymerase II core subunit" [Dictyostelium discoideum (taxid:44689)]

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 44/76 (57%), Positives = 64/76 (84%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAPDR+E FV+P+G KKV+  RDTKI NA+ FTI +E+HTIGN++RMQL  D++++FAG
Sbjct:     1 MNAPDRFELFVLPDGAKKVTMVRDTKIPNASMFTILKEDHTIGNLIRMQLIADQDIIFAG 60

Query:    61 YKLPHPLQYKIIVRAE 76
             Y++PHPL++ + +R +
Sbjct:    61 YRMPHPLEHNVNIRIQ 76

GO:0046983 "protein dimerization activity" evidence=IEA

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

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

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

FB|FBgn0032634 Rpb11 "Rpb11" [Drosophila melanogaster (taxid:7227)]

 Score = 244 (91.0 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 43/76 (56%), Positives = 60/76 (78%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAP  +E F++ EG KK+  E DTK+ NAA FTI +E+HT+GN++R QL +D NVLFAG
Sbjct:     1 MNAPPTFESFLLYEGEKKIIKELDTKVTNAAIFTINKEDHTLGNMIRNQLLKDPNVLFAG 60

Query:    61 YKLPHPLQYKIIVRAE 76
             YK+PHPL++K ++R +
Sbjct:    61 YKVPHPLEHKFVIRIQ 76

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

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

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

GO:0005634 "nucleus" evidence=NAS

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q32P79 POLR2J "DNA-directed RNA polymerase II subunit RPB11" [Bos taurus (taxid:9913)]

 Score = 241 (89.9 bits), Expect = 2.1e-20, P = 2.1e-20
 Identities = 42/76 (55%), Positives = 60/76 (78%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct:     1 MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 60

Query:    61 YKLPHPLQYKIIVRAE 76
             YK+PHPL++KII+R +
Sbjct:    61 YKVPHPLEHKIIIRVQ 76

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

GO:0004672 "protein kinase activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

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

GO:0030275 "LRR domain binding" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2RD80 LOC100686835 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 241 (89.9 bits), Expect = 2.1e-20, P = 2.1e-20
 Identities = 42/76 (55%), Positives = 60/76 (78%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct:     1 MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 60

Query:    61 YKLPHPLQYKIIVRAE 76
             YK+PHPL++KII+R +
Sbjct:    61 YKVPHPLEHKIIIRVQ 76

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

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1PXE5 LOC100686835 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 241 (89.9 bits), Expect = 2.1e-20, P = 2.1e-20
 Identities = 42/76 (55%), Positives = 60/76 (78%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct:    22 MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 81

Query:    61 YKLPHPLQYKIIVRAE 76
             YK+PHPL++KII+R +
Sbjct:    82 YKVPHPLEHKIIIRVQ 97

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

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|P52435 POLR2J "DNA-directed RNA polymerase II subunit RPB11-a" [Homo sapiens (taxid:9606)]

 Score = 241 (89.9 bits), Expect = 2.1e-20, P = 2.1e-20
 Identities = 42/76 (55%), Positives = 60/76 (78%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct:     1 MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 60

Query:    61 YKLPHPLQYKIIVRAE 76
             YK+PHPL++KII+R +
Sbjct:    61 YKVPHPLEHKIIIRVQ 76

GO:0003677 "DNA binding" evidence=IEA

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

GO:0004672 "protein kinase activity" evidence=IDA

GO:0030275 "LRR domain binding" evidence=IPI

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

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

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

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

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

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

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

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

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

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

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

GO:0006468 "protein phosphorylation" evidence=IDA

UNIPROTKB|Q9H1A6 POLR2J1 "DNA-directed RNA polymerase II subunit RPB11-a" [Homo sapiens (taxid:9606)]

 Score = 241 (89.9 bits), Expect = 2.1e-20, P = 2.1e-20
 Identities = 42/76 (55%), Positives = 60/76 (78%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct:     1 MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 60

Query:    61 YKLPHPLQYKIIVRAE 76
             YK+PHPL++KII+R +
Sbjct:    61 YKVPHPLEHKIIIRVQ 76

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

GO:0003677 "DNA binding" evidence=IEA

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

MGI|MGI:109582 Polr2j "polymerase (RNA) II (DNA directed) polypeptide J" [Mus musculus (taxid:10090)]

 Score = 241 (89.9 bits), Expect = 2.1e-20, P = 2.1e-20
 Identities = 42/76 (55%), Positives = 60/76 (78%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct:     1 MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 60

Query:    61 YKLPHPLQYKIIVRAE 76
             YK+PHPL++KII+R +
Sbjct:    61 YKVPHPLEHKIIIRVQ 76

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

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

GO:0030275 "LRR domain binding" evidence=ISO

RGD|1310198 Polr2j "polymerase (RNA) II (DNA directed) polypeptide J" [Rattus norvegicus (taxid:10116)]

 Score = 241 (89.9 bits), Expect = 2.1e-20, P = 2.1e-20
 Identities = 42/76 (55%), Positives = 60/76 (78%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAP  +E F++ EG KK++  +DTK+ NA  FTI +E+HT+GNI++ QL +D  VLFAG
Sbjct:     1 MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG 60

Query:    61 YKLPHPLQYKIIVRAE 76
             YK+PHPL++KII+R +
Sbjct:    61 YKVPHPLEHKIIIRVQ 76

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=ISO

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

GO:0030275 "LRR domain binding" evidence=IEA;ISO

ZFIN|ZDB-GENE-050522-120 polr2j "polymerase (RNA) II (DNA directed) polypeptide J" [Danio rerio (taxid:7955)]

 Score = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 40/76 (52%), Positives = 60/76 (78%)

Query:     1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
             MNAP  +E F++ EG KK++  +DTK+ NA  FT+ +E+HT+GNI+R QL +D  VLFAG
Sbjct:     1 MNAPPAFESFLLFEGEKKITITKDTKVPNACLFTLNKEDHTLGNIIRSQLLKDPQVLFAG 60

Query:    61 YKLPHPLQYKIIVRAE 76
             YK+PHPL++K+++R +
Sbjct:    61 YKVPHPLEHKVVIRVQ 76

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

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

GO:0003677 "DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q86JJ5	RPB11_DICDI	No assigned EC number	0.5432	0.9642	0.675	yes	no
Q9GZM3	RPB1B_HUMAN	No assigned EC number	0.5394	0.8928	0.6521	yes	no
P52435	RPB11_HUMAN	No assigned EC number	0.5526	0.9047	0.6495	yes	no
P87123	RPB11_SCHPO	No assigned EC number	0.5263	0.8928	0.6097	yes	no
Q9VJE4	RPB11_DROME	No assigned EC number	0.5810	0.8809	0.6324	yes	no
O08740	RPB11_MOUSE	No assigned EC number	0.5526	0.9047	0.6495	yes	no
Q7PVQ9	RPB11_ANOGA	No assigned EC number	0.5675	0.8809	0.6324	yes	no
Q32P79	RPB11_BOVIN	No assigned EC number	0.5526	0.9047	0.6495	yes	no
Q9XVH6	RPB11_CAEEL	No assigned EC number	0.5061	0.9523	0.6557	yes	no
Q38859	RPB11_ARATH	No assigned EC number	0.8395	0.9642	0.6982	yes	no
Q9H1A7	RPB1C_HUMAN	No assigned EC number	0.5263	0.8928	0.6521	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	84
cd06926	93	cd06926, RNAP_II_RPB11, RPB11 subunit of Eukaryoti	2e-34
pfam13656	77	pfam13656, RNA_pol_L_2, RNA polymerase Rpb3/Rpb11	1e-15
COG1761	99	COG1761, RPB11, DNA-directed RNA polymerase, subun	2e-13
cd07029	85	cd07029, RNAP_I_III_AC19, AC19 subunit of Eukaryot	6e-12
cd07027	83	cd07027, RNAP_RPB11_like, RPB11 subunit of RNA pol	5e-11
PRK01146	85	PRK01146, PRK01146, DNA-directed RNA polymerase su	2e-07
pfam01193	88	pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 di	2e-07
cd06927	83	cd06927, RNAP_L, L subunit of Archaeal RNA polymer	2e-06
cd00460	86	cd00460, RNAP_RPB11_RPB3, RPB11 and RPB3 subunits	0.001

>gnl|CDD|132902 cd06926, RNAP_II_RPB11, RPB11 subunit of Eukaryotic RNA polymerase II

 Score =  112 bits (283), Expect = 2e-34
 Identities = 40/62 (64%), Positives = 55/62 (88%)

Query: 13 PEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKII 72
          PEG KK++ ++DTK+ NAA+FTI +E+HT+GN+LRMQL +D NVLFAGYK+PHPL++KI 
Sbjct: 1  PEGEKKITEKKDTKVPNAATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIE 60

Query: 73 VR 74
          +R
Sbjct: 61 LR 62

The eukaryotic RPB11 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 RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. Length = 93

>gnl|CDD|222292 pfam13656, RNA_pol_L_2, RNA polymerase Rpb3/Rpb11 dimerisation domain

 Score = 64.5 bits (158), Expect = 1e-15
 Identities = 26/46 (56%), Positives = 36/46 (78%)

Query: 29 NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVR 74
          N A+F IE E+HT+GN+LR +L +D +V FAGY +PHPL+ KI +R
Sbjct: 1  NEATFEIEGEDHTLGNLLREELLKDPDVEFAGYSVPHPLEDKINLR 46

The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Many of the members of this family carry only the N-terminal region of Rpb11. Length = 77

>gnl|CDD|224675 COG1761, RPB11, DNA-directed RNA polymerase, subunit L [Transcription]

 Score = 59.7 bits (145), Expect = 2e-13
 Identities = 24/60 (40%), Positives = 35/60 (58%)

Query: 15 GTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVR 74
           T ++      K  N+    IE E+HT+GN+LR +L +DE+V FA Y +PHPL     +R
Sbjct: 1  MTPEMELRIIKKDDNSLELEIEGEDHTLGNLLREELLKDEDVEFAAYSIPHPLIDNPKIR 60

Length = 99

>gnl|CDD|132907 cd07029, RNAP_I_III_AC19, AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

 Score = 55.3 bits (134), Expect = 6e-12
 Identities = 19/46 (41%), Positives = 29/46 (63%)

Query: 29 NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVR 74
          + A+F    E+HT+GN LR  + ++  V F GY +PHP + KI +R
Sbjct: 9  SCATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSIPHPSENKINLR 54

The eukaryotic AC19 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 AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to associate with the RPB3 counterpart, AC40, to form a heterodimer, which stabilizes the association of the two largest subunits of RNAP I and RNAP III. Length = 85

>gnl|CDD|132905 cd07027, RNAP_RPB11_like, RPB11 subunit of RNA polymerase

 Score = 52.9 bits (127), Expect = 5e-11
 Identities = 20/46 (43%), Positives = 32/46 (69%)

Query: 29 NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVR 74
          N+ +  +E E+HT+GN+LR +L +D+ V FA Y + HP+  KI +R
Sbjct: 9  NSVTVEMENEDHTLGNLLREELLKDDQVDFARYYIKHPVIDKIQIR 54

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/L subunits) and bacterial (alpha subunit) counterparts. Length = 83

>gnl|CDD|234909 PRK01146, PRK01146, DNA-directed RNA polymerase subunit L; Provisional

 Score = 43.7 bits (104), Expect = 2e-07
 Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 4/53 (7%)

Query: 26 KII----NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVR 74
          K++    N     IE E+HT+ N+L+ +L  D  V  A Y + HPL    +++
Sbjct: 4  KVLEKEDNELELEIEGEDHTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLK 56

Length = 85

>gnl|CDD|216354 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimerisation domain

 Score = 43.8 bits (104), Expect = 2e-07
 Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 31 ASFTIEREEHTIGNILRMQLHRD-ENVLFAGYKLPHPLQYKIIVRA 75
            F +E E+HT+GN LR  L  D   V  AG K+PHP ++  + + 
Sbjct: 1  IEFLLEGEDHTLGNALRRVLLSDVPGVAIAGVKIPHPAKFSPVKKV 46

The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Length = 88

>gnl|CDD|132903 cd06927, RNAP_L, L subunit of Archaeal RNA polymerase

 Score = 41.4 bits (98), Expect = 2e-06
 Identities = 16/42 (38%), Positives = 25/42 (59%)

Query: 33 FTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVR 74
            IE E+HT+ N+L+ +L RD  V  A Y + HPL    +++
Sbjct: 13 LEIEGEDHTLLNLLKEELLRDPGVKVASYDIEHPLLSNPVLK 54

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. Length = 83

>gnl|CDD|132901 cd00460, RNAP_RPB11_RPB3, RPB11 and RPB3 subunits of RNA polymerase

 Score = 33.9 bits (78), Expect = 0.001
 Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 1/42 (2%)

Query: 29 NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYK 70
          N   F +E E+HT+GN LR  L +   V FA Y + HP++ +
Sbjct: 9  NYVDFVLENEDHTLGNSLRRILLKSP-VEFAAYYVEHPVKLQ 49

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 archaeal (D/L subunits) and bacterial (alpha subunit) counterparts. Length = 86

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	84
KOG4392	117	consensus RNA polymerase, subunit L [Transcription	100.0
cd06926	93	RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA poly	99.97
PRK01146	85	DNA-directed RNA polymerase subunit L; Provisional	99.96
cd07029	85	RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA pol	99.95
cd06927	83	RNAP_L L subunit of Archaeal RNA polymerase. The a	99.95
cd07027	83	RNAP_RPB11_like RPB11 subunit of RNA polymerase. T	99.95
PF13656	77	RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisatio	99.95
COG1761	99	RPB11 DNA-directed RNA polymerase, subunit L [Tran	99.93
KOG3438	105	consensus DNA-directed RNA polymerase, subunit L [	99.92
cd00460	86	RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA pol	99.85
PF01193	66	RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation	99.32
PRK00783	263	DNA-directed RNA polymerase subunit D; Provisional	96.32
cd07030	259	RNAP_D D subunit of Archaeal RNA polymerase. The D	95.98
cd07028	212	RNAP_RPB3_like RPB3 subunit of RNA polymerase. The	95.49
PRK05182	310	DNA-directed RNA polymerase subunit alpha; Provisi	94.68
PRK14979	195	DNA-directed RNA polymerase subunit D; Provisional	94.61
cd07031	265	RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polyme	94.44
cd06928	215	RNAP_alpha_NTD N-terminal domain of the Alpha subu	93.86
COG0202	317	RpoA DNA-directed RNA polymerase, alpha subunit/40	92.67
smart00662	224	RPOLD RNA polymerases D. DNA-directed RNA polymera	92.04
CHL00013	327	rpoA RNA polymerase alpha subunit	89.4
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	82.31
TIGR02027	297	rpoA DNA-directed RNA polymerase, alpha subunit, b	82.04

>KOG4392 consensus RNA polymerase, subunit L [Transcription]

Probab=100.00  E-value=2.6e-38  Score=214.66  Aligned_cols=82  Identities=54%  Similarity=0.904  Sum_probs=80.3

Q ss_pred             CCCCcccceeeeCCCceeeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccC
Q 034762            1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKH   80 (84)
Q Consensus         1 mn~p~~~~~~~l~~ge~Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~   80 (84)
                      ||||+|||+|+|++|++||++..++|.+|++.|+|.+|||||||+|+.+|++||+|.||||++|||+.+++.|||||+.+
T Consensus         1 MNaP~~fE~fll~eg~kKvtin~DtKvpNA~~fTiekEDHTLGNii~~qLl~D~~vLFagYkvpHPl~~~~~LRiqtt~d   80 (117)
T KOG4392|consen    1 MNAPPAFESFLLFEGEKKITINKDTKVPNAALFTIEKEDHTLGNIIKSQLLKDPRVLFAGYKVPHPLEHKIILRVQTTED   80 (117)
T ss_pred             CCCchhhhhheeccCCceeEEecCCCCCceEEEEEecccchHHHHHHHHHccCccceEeeecCCCcccccEEEEEecCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cc
Q 034762           81 SR   82 (84)
Q Consensus        81 ~~   82 (84)
                      .+
T Consensus        81 ~~   82 (117)
T KOG4392|consen   81 CS   82 (117)
T ss_pred             CC
Confidence            54

>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II

Probab=99.97  E-value=4.1e-32  Score=177.70  Aligned_cols=70  Identities=57%  Similarity=0.929  Sum_probs=67.8

Q ss_pred             CCCceeeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccCcc
Q 034762           13 PEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSR   82 (84)
Q Consensus        13 ~~ge~Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~~~   82 (84)
                      |+|++||++..+++++|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++.+
T Consensus         1 ~~~~~kv~~~~d~k~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~fagY~vpHPl~~~~~l~i~t~~~~~   70 (93)
T cd06926           1 PEGEKKITEKKDTKVPNAATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIELRIQTDGSIT   70 (93)
T ss_pred             CCCccceEEeecCCCCcEEEEEEeCCCchHHHHHHHHHhcCCCeeEEeeccCCCCCCceEEEEEeCCCCC
Confidence            6899999999999999999999999999999999999999999999999999999999999999998654

The eukaryotic RPB11 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 RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.

>PRK01146 DNA-directed RNA polymerase subunit L; Provisional

Probab=99.96  E-value=6.2e-29  Score=160.55  Aligned_cols=63  Identities=27%  Similarity=0.363  Sum_probs=57.7

Q ss_pred             eeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccCcc
Q 034762           18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSR   82 (84)
Q Consensus        18 Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~~~   82 (84)
                      ++++..  +.+|+++|+|.||||||||+||++|+++|+|.||||+|||||+++++|||||+++.+
T Consensus         2 ~ikvi~--~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqt~~~~~   64 (85)
T PRK01146          2 EIKVLE--KEDNELELEIEGEDHTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLKIKTDGGID   64 (85)
T ss_pred             eEEEEe--cCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEeecCCCCCCccEEEEEECCCCC
Confidence            345554  679999999999999999999999999999999999999999999999999997754

>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

Probab=99.95  E-value=8.6e-29  Score=159.89  Aligned_cols=59  Identities=32%  Similarity=0.546  Sum_probs=56.0

Q ss_pred             cCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccCcc
Q 034762           24 DTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSR   82 (84)
Q Consensus        24 ~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~~~   82 (84)
                      ..+.+|+++|+|.||||||||+||++|+++|+|+||||+||||+++++.|||||+++.+
T Consensus         4 ~~~~~n~~~~~i~~EdHTLgNlLr~~L~~~p~V~fagY~vpHPl~~~~~lriqT~~~~~   62 (85)
T cd07029           4 EGTDESCATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSIPHPSENKINLRIQTKGGEP   62 (85)
T ss_pred             ccCCCCeEEEEEeCCCcchHHHHHHHHhhCCCceEEeecccCCCCCccEEEEEeCCCCC
Confidence            45789999999999999999999999999999999999999999999999999998654

The eukaryotic AC19 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 AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass

>cd06927 RNAP_L L subunit of Archaeal RNA polymerase

Probab=99.95  E-value=1.5e-28  Score=158.22  Aligned_cols=61  Identities=30%  Similarity=0.395  Sum_probs=56.3

Q ss_pred             EEeecCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccCcc
Q 034762           20 SYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSR   82 (84)
Q Consensus        20 ~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~~~   82 (84)
                      ++.+  +.+|+++|+|.||||||||+||++|+++|+|.||||+|||||+++++|||||+++.+
T Consensus         2 kvi~--~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~   62 (83)
T cd06927           2 KVIE--KEDNELELEIEGEDHTLLNLLKEELLRDPGVKVASYDIEHPLLSNPVLKIKTDGGVD   62 (83)
T ss_pred             eEEE--cCCCEEEEEEeCCCchHHHHHHHHHhcCCCeEEEEeecCCCCCCccEEEEEeCCCCC
Confidence            3444  569999999999999999999999999999999999999999999999999999654

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=99.95  E-value=2.3e-28  Score=157.31  Aligned_cols=57  Identities=37%  Similarity=0.595  Sum_probs=54.2

Q ss_pred             CCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccCcc
Q 034762           26 KIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSR   82 (84)
Q Consensus        26 ~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~~~   82 (84)
                      +.+|+++|+|.||||||||+||++|+++|+|+||||+||||++++++|||||+++.+
T Consensus         6 ~~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrI~T~~~~~   62 (83)
T cd07027           6 KEKNSVTVEMENEDHTLGNLLREELLKDDQVDFARYYIKHPVIDKIQIRIQTKSGIK   62 (83)
T ss_pred             cCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEEecCCCCCCccEEEEEECCCCC
Confidence            558999999999999999999999999999999999999999999999999998653

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/

>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K

Probab=99.95  E-value=1.1e-28  Score=156.56  Aligned_cols=54  Identities=46%  Similarity=0.781  Sum_probs=49.5

Q ss_pred             ceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccCcc
Q 034762           29 NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSR   82 (84)
Q Consensus        29 n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~~~   82 (84)
                      |+++|+|.+|||||||+||++|+++|+|+||||+|||||+++++|||||+++.+
T Consensus         1 n~~~f~i~~EDHTlgNlLr~~L~~~p~V~fagY~vpHPl~~~i~l~Iqt~~~~~   54 (77)
T PF13656_consen    1 NEITFTIYGEDHTLGNLLRYELLKDPDVEFAGYRVPHPLENKINLRIQTKGGIT   54 (77)
T ss_dssp             TEEEEEEES--HHHHHHHHHCCTTSTTEEEEEEEESETTSSEEEEEEEESTTS-
T ss_pred             CeEEEEEeCCCccHHHHHHHHHhhCCCeEEEEeccCCCCCCceEEEEEECCCCC
Confidence            689999999999999999999999999999999999999999999999998843

...

>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]

Probab=99.93  E-value=1.1e-25  Score=149.78  Aligned_cols=65  Identities=37%  Similarity=0.532  Sum_probs=60.7

Q ss_pred             ceeeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccC
Q 034762           16 TKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKH   80 (84)
Q Consensus        16 e~Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~   80 (84)
                      .+++++...++.+|+++|++.||||||||+|+++|+++++|+||+|+||||+.+++.+||||+++
T Consensus         2 ~~~~~l~ii~~~~n~~~i~i~gEdHTL~NlL~~~L~~d~~V~~a~Y~i~HP~~~~~~i~Ikt~~~   66 (99)
T COG1761           2 TPEMELRIIKKDDNSLELEIEGEDHTLGNLLREELLKDEDVEFAAYSIPHPLIDNPKIRIKTKGG   66 (99)
T ss_pred             CCceEEEEeccCCCEEEEEEecCCchHHHHHHHHHhCCCCeeEEEEeCCCCCCCCceEEEEECCC
Confidence            45666666668899999999999999999999999999999999999999999999999999998

>KOG3438 consensus DNA-directed RNA polymerase, subunit L [Transcription]

Probab=99.92  E-value=2.1e-25  Score=149.36  Aligned_cols=56  Identities=34%  Similarity=0.654  Sum_probs=53.2

Q ss_pred             CcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccCcc
Q 034762           27 IINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSR   82 (84)
Q Consensus        27 ~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~~~   82 (84)
                      ..++.+|++..|||||||+||++|+++|+|+||||.||||+++++.|||||.++..
T Consensus        14 d~~~~Tf~~~eEDHTlgNalR~vI~k~peVefcGYtIPHPse~k~niRIQt~~~~~   69 (105)
T KOG3438|consen   14 DLSSATFQLREEDHTLGNALRYVIMKNPEVEFCGYTIPHPSEDKINIRIQTRDGDP   69 (105)
T ss_pred             CCCceEEEEEecCcchhHHHHHHHhcCCceEEEeccCCCCchhhheEEEEecCCCc
Confidence            67899999999999999999999999999999999999999999999999997653

>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase

Probab=99.85  E-value=1.9e-21  Score=124.78  Aligned_cols=56  Identities=39%  Similarity=0.559  Sum_probs=53.3

Q ss_pred             CCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCC------CcceEEEEEeccCcc
Q 034762           26 KIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPL------QYKIIVRAELAKHSR   82 (84)
Q Consensus        26 ~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl------~~~i~l~Iqt~~~~~   82 (84)
                      +.+|+++|+|.||||||||+||++|++ +.|.||||+|+||+      .++++|+|+|+|+.+
T Consensus         6 ~~~~~~~~~~~~edhTl~n~L~~~l~~-~pV~~a~Y~v~hp~~~~~~~~d~~~~~VeT~Gs~~   67 (86)
T cd00460           6 KEKNYVDFVLENEDHTLGNSLRRILLK-SPVEFAAYYVEHPVKLQRTDEDKFILRIETVGSIP   67 (86)
T ss_pred             CCCCEEEEEEeCCCchHHHHHHHHHhC-CCceEEEEEeCCCccCCCCCCCeEEEEEEECCCCC
Confidence            568999999999999999999999999 99999999999999      999999999999754

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

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

Probab=99.32  E-value=1.5e-12  Score=79.41  Aligned_cols=48  Identities=33%  Similarity=0.512  Sum_probs=45.0

Q ss_pred             eEEEEecCCcchHHHHHHHHhcC-CceeEEeeeCCCCCCcceEEEEEeccCcc
Q 034762           31 ASFTIEREEHTIGNILRMQLHRD-ENVLFAGYKLPHPLQYKIIVRAELAKHSR   82 (84)
Q Consensus        31 ~~~~i~~EdHTLgNlLr~~Ll~~-~~V~fAgY~vpHPl~~~i~l~Iqt~~~~~   82 (84)
                      ++|.+.|+|||+||+||..|+++ |.|.+++    ||..++++|+|+|+|+.+
T Consensus         1 i~~~~~g~~~tl~N~LRr~ll~~vp~~ai~~----~~~~~~~~~~IeT~g~~~   49 (66)
T PF01193_consen    1 IEFLLKGEDHTLGNALRRILLSEVPGVAIDG----HPNEDKFVFRIETDGSLT   49 (66)
T ss_dssp             EEEEEESHHHHHHHHHHHHHHSSSEEEEEEE----SSEEEEEEEEEEEBSSS-
T ss_pred             CEeEEcCCchHHHHHHHHHHHhcCCCceEEe----cCCCCEEEEEEEECCCCC
Confidence            57999999999999999999999 9999999    999999999999999854

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 ....

>PRK00783 DNA-directed RNA polymerase subunit D; Provisional

Probab=96.32  E-value=0.0054  Score=45.60  Aligned_cols=34  Identities=18%  Similarity=0.220  Sum_probs=29.4

Q ss_pred             eeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcC
Q 034762           18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD   53 (84)
Q Consensus        18 Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~   53 (84)
                      ||++.+.+  ++.++|.+.|-++||||+||..|+..
T Consensus         2 ~~~~~~~~--~~~~~f~~~g~~~t~~NalRRvlls~   35 (263)
T PRK00783          2 EIEILELD--DRSARFVVEGVTPAFANAIRRAMIAD   35 (263)
T ss_pred             ceEEEEcC--CcEEEEEEeCCCHHHHHHHHHHHHHc
Confidence            56776654  68899999999999999999999975

>cd07030 RNAP_D D subunit of Archaeal RNA polymerase

Probab=95.98  E-value=0.01  Score=44.04  Aligned_cols=34  Identities=15%  Similarity=0.195  Sum_probs=29.4

Q ss_pred             eeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcC
Q 034762           18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD   53 (84)
Q Consensus        18 Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~   53 (84)
                      +|++.+.+  ++.++|.+.|-|+|+||+||..|+..
T Consensus         2 ~~~~~~~~--~~~~~f~~~g~~~s~~NalRRills~   35 (259)
T cd07030           2 EIEVLELD--DDRARFVLEGVPPAFANAIRRAIISE   35 (259)
T ss_pred             ceEEEecC--CCEEEEEEeCCCHHHHHHHHHHHHhc
Confidence            56776644  68999999999999999999999875

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

>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase

Probab=95.49  E-value=0.024  Score=41.81  Aligned_cols=40  Identities=15%  Similarity=0.184  Sum_probs=32.0

Q ss_pred             eEEeecCCCcceeEEEEecCCcchHHHHHHHHhcC-C-----ceeEEe
Q 034762           19 VSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-E-----NVLFAG   60 (84)
Q Consensus        19 i~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~-~-----~V~fAg   60 (84)
                      |++.+  +.++.++|.+.|-|+|+||+||..|+.. |     .|.+.+
T Consensus         3 i~i~~--~~~~~~~f~l~g~~~t~aNaLRRiLLsevP~~AI~~V~I~~   48 (212)
T cd07028           3 VKIRE--ADKDNVDFILSGVDLAMANALRRVMIAEVPTMAVDSVEVET   48 (212)
T ss_pred             EEEEE--cCCCEEEEEEEccChhHHHHHHHHHHHcCcceEEEEEEEEc
Confidence            45555  5589999999999999999999999985 3     555555

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

>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional

Probab=94.68  E-value=0.054  Score=41.93  Aligned_cols=46  Identities=26%  Similarity=0.323  Sum_probs=33.3

Q ss_pred             eeEEeecCCCcceeEEEEe----cCCcchHHHHHHHHhcC-CceeEEeeeC
Q 034762           18 KVSYERDTKIINAASFTIE----REEHTIGNILRMQLHRD-ENVLFAGYKL   63 (84)
Q Consensus        18 Ki~~~~~~~~~n~~~~~i~----~EdHTLgNlLr~~Ll~~-~~V~fAgY~v   63 (84)
                      ++++...+..++.++|.+.    |.++|+||+||..|+.. |+.-.-+-+|
T Consensus         8 ~i~~~e~~~~~~~~~F~i~Ple~G~g~tlgNaLRRvLLs~ipg~aI~~VkI   58 (310)
T PRK05182          8 KIEVEEESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKI   58 (310)
T ss_pred             EEEEEeccCCCcEEEEEEeccCCCchhHHHHHHHHHHHhcCCeeEEEEEEE
Confidence            4555543335789999997    99999999999999884 5544444433

>PRK14979 DNA-directed RNA polymerase subunit D; Provisional

Probab=94.61  E-value=0.048  Score=40.01  Aligned_cols=37  Identities=14%  Similarity=0.197  Sum_probs=29.9

Q ss_pred             EEeecCCCcceeEEEEecCCcchHHHHHHHHhcC-Ccee
Q 034762           20 SYERDTKIINAASFTIEREEHTIGNILRMQLHRD-ENVL   57 (84)
Q Consensus        20 ~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~-~~V~   57 (84)
                      ++...++..+.++|.+. -+.|+||+||..|+.. |..-
T Consensus         5 ~~~~~~~~~~~~~f~l~-~~~tlgNaLRRvLLssipg~A   42 (195)
T PRK14979          5 KEKEKTRIGEEFKFSLK-APISFSSALRRIMISEVPTYA   42 (195)
T ss_pred             ceeeeccCCcEEEEEEE-cCccHHHHHHHHHHhcCccee
Confidence            34445578999999999 9999999999999874 5433

>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II

Probab=94.44  E-value=0.059  Score=40.75  Aligned_cols=34  Identities=21%  Similarity=0.312  Sum_probs=28.9

Q ss_pred             eeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcC
Q 034762           18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD   53 (84)
Q Consensus        18 Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~   53 (84)
                      +|++.+.+  ++.++|.+.+=|+|+||+||..|+..
T Consensus         2 ~i~i~~~~--~~~~~F~l~~~~~s~aNALRRillse   35 (265)
T cd07031           2 RVEITELT--DDKVKFILENTDLSVANSLRRVMIAE   35 (265)
T ss_pred             cEEEEEcC--CCEEEEEEEcCcHHHHHHHHHHHHHc
Confidence            46666644  78999999999999999999999874

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.

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

Probab=93.86  E-value=0.065  Score=39.29  Aligned_cols=38  Identities=29%  Similarity=0.329  Sum_probs=29.1

Q ss_pred             CCCcceeEEEE----ecCCcchHHHHHHHHhcC-CceeEEeee
Q 034762           25 TKIINAASFTI----EREEHTIGNILRMQLHRD-ENVLFAGYK   62 (84)
Q Consensus        25 ~~~~n~~~~~i----~~EdHTLgNlLr~~Ll~~-~~V~fAgY~   62 (84)
                      +...++++|.|    .|.++|+||+||..|+.. |+.-+-+-+
T Consensus         5 ~~~~~~~~F~i~pl~~g~~~tlgNaLRRvLLs~ipg~aI~~v~   47 (215)
T cd06928           5 NKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVK   47 (215)
T ss_pred             cCCCcEEEEEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEEEE
Confidence            34478899999    779999999999999885 554444433

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

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

Probab=92.67  E-value=0.19  Score=39.16  Aligned_cols=42  Identities=19%  Similarity=-0.005  Sum_probs=31.2

Q ss_pred             eEEeecC--CCcceeEEEEecCCcchHHHHHHHHhc-CCceeEEe
Q 034762           19 VSYERDT--KIINAASFTIEREEHTIGNILRMQLHR-DENVLFAG   60 (84)
Q Consensus        19 i~~~~~~--~~~n~~~~~i~~EdHTLgNlLr~~Ll~-~~~V~fAg   60 (84)
                      |++...+  ..+-.+++.+.|-+|||||+||..|+. .|..-.-+
T Consensus         7 i~i~~~~~~~~~~~ieplerG~g~tlgNALRRvLLSsiPg~Av~~   51 (317)
T COG0202           7 VKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTA   51 (317)
T ss_pred             eEEEEcccccccEEEEEeeeCCcchhHHHHHHHHHHcCccceEEE
Confidence            5555443  347789999999999999999999987 46544333

>smart00662 RPOLD RNA polymerases D

Probab=92.04  E-value=0.15  Score=37.40  Aligned_cols=32  Identities=25%  Similarity=0.279  Sum_probs=25.2

Q ss_pred             eEEEEecCCcchHHHHHHHHhcC-CceeEEeee
Q 034762           31 ASFTIEREEHTIGNILRMQLHRD-ENVLFAGYK   62 (84)
Q Consensus        31 ~~~~i~~EdHTLgNlLr~~Ll~~-~~V~fAgY~   62 (84)
                      ++|.+.+-++|+||+||..|+.. |..-.-+.+
T Consensus         2 ~~f~l~~~~~t~~NaLRRilLs~vp~~aI~~V~   34 (224)
T smart00662        2 AKFVLEPYGLTLANALRRVLLSSVPGMAVTEVE   34 (224)
T ss_pred             eEEEEEcCCchHHHHHHHHHHHcCccceEEEEE
Confidence            67999999999999999999884 554444433

DNA-directed RNA polymerase subunit D and bacterial alpha chain

>CHL00013 rpoA RNA polymerase alpha subunit

Probab=89.40  E-value=1.2  Score=34.95  Aligned_cols=47  Identities=26%  Similarity=0.301  Sum_probs=34.6

Q ss_pred             eEEeecCCCcceeEEEEe----cCCcchHHHHHHHHhcC-CceeEEeeeCCC
Q 034762           19 VSYERDTKIINAASFTIE----REEHTIGNILRMQLHRD-ENVLFAGYKLPH   65 (84)
Q Consensus        19 i~~~~~~~~~n~~~~~i~----~EdHTLgNlLr~~Ll~~-~~V~fAgY~vpH   65 (84)
                      ++........++.+|.|.    |..|||||+||..|+.. |+.-+.+-++.+
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            455555667888999986    56679999999999984 666666655533

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=82.31  E-value=1.2  Score=35.66  Aligned_cols=23  Identities=30%  Similarity=0.592  Sum_probs=21.3

Q ss_pred             CCcchHHHHHHHHhcCCceeEEe
Q 034762           38 EEHTIGNILRMQLHRDENVLFAG   60 (84)
Q Consensus        38 EdHTLgNlLr~~Ll~~~~V~fAg   60 (84)
                      -+|++.|.||..|.+||+|.+.|
T Consensus       183 dT~sF~~aLraALReDPDVIlvG  205 (353)
T COG2805         183 DTLSFANALRAALREDPDVILVG  205 (353)
T ss_pred             cHHHHHHHHHHHhhcCCCEEEEe
Confidence            45999999999999999999988

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

Probab=82.04  E-value=1.3  Score=33.99  Aligned_cols=28  Identities=25%  Similarity=0.253  Sum_probs=21.1

Q ss_pred             ecCCcchHHHHHHHHhcC-CceeEEeeeC
Q 034762           36 EREEHTIGNILRMQLHRD-ENVLFAGYKL   63 (84)
Q Consensus        36 ~~EdHTLgNlLr~~Ll~~-~~V~fAgY~v   63 (84)
                      .|-++||||+||..|+.. |++-..+-+|
T Consensus        11 ~g~g~TlGNaLRRvLLs~i~g~aI~~vkI   39 (297)
T TIGR02027        11 RGFGITLGNALRRVLLSSIPGAAITAVKI   39 (297)
T ss_pred             CCchhHHHHHHHHHHHhcCCceEEEEEEE
Confidence            477899999999999985 6655555443

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	84
3h0g_K	123	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		5e-17
1i3q_K	120	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		2e-15
2pa8_L	92	X-Ray Crystal Structure Of The DL SUBCOMPLEX OF THE		1e-05
2waq_L	92	The Complete Structure Of The Archaeal 13-Subunit D		3e-05

>pdb|3H0G|K Chain K, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 123

Iteration: 1
 Score = 82.8 bits (203), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 40/76 (52%), Positives = 53/76 (69%), Gaps = 1/76 (1%)
Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MN P+RYE  +   G  KV+YE D+K  NAA  T+E+E+HT+ N+L  QL  DE VLFAG
Sbjct: 1  MNQPERYE-LIELMGLPKVTYELDSKSPNAAVVTLEKEDHTLANMLANQLLSDERVLFAG 59
Query: 61 YKLPHPLQYKIIVRAE 76
          YK+PHPL +  I+R +
Sbjct: 60 YKVPHPLNHNFILRVQ 75

>pdb|1I3Q|K Chain K, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 120

Iteration: 1
 Score = 77.8 bits (190), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 35/74 (47%), Positives = 49/74 (66%)
Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAPDR+E F++ EG  K+  + DTK  NA   T E+E+HT+GN++R +L  D  VLFA 
Sbjct: 1  MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAA 60
Query: 61 YKLPHPLQYKIIVR 74
          YK+ HP   +  +R
Sbjct: 61 YKVEHPFFARFKLR 74

>pdb|2PA8|L Chain L, X-Ray Crystal Structure Of The DL SUBCOMPLEX OF THE SULFOLOBUS Solfataricus Rna Polymerase Length = 92

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/46 (47%), Positives = 27/46 (58%)
Query: 29 NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVR 74
          N     IE E+HT+GN++   L R   V FA Y  PHPL  KIIV+
Sbjct: 11 NYLELEIEGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVK 56

>pdb|2WAQ|L Chain L, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 92

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 27/46 (58%)
Query: 29 NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVR 74
          N     IE E+HT+GN++   L +   V FA Y  PHPL  KIIV+
Sbjct: 11 NYLELEIEGEDHTLGNLIAGTLRKISGVSFASYYQPHPLTDKIIVK 56

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	84
1twf_K	120	B13.6, DNA-directed RNA polymerase II 13.6 kDa pol	7e-32
3h0g_K	123	DNA-directed RNA polymerase II subunit RPB11; tran	7e-30
2pa8_L	92	DNA-directed RNA polymerase subunit L; ferredoxin-	4e-17
1xpp_A	115	TA1416, DNA-directed RNA polymerase subunit L; str	4e-16

>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB: 1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K 1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K* 1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ... Length = 120

 Score =  106 bits (266), Expect = 7e-32
 Identities = 35/74 (47%), Positives = 49/74 (66%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAPDR+E F++ EG  K+  + DTK  NA   T E+E+HT+GN++R +L  D  VLFA 
Sbjct: 1  MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAA 60

Query: 61 YKLPHPLQYKIIVR 74
          YK+ HP   +  +R
Sbjct: 61 YKVEHPFFARFKLR 74

>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 123

 Score =  101 bits (253), Expect = 7e-30
 Identities = 40/74 (54%), Positives = 51/74 (68%), Gaps = 1/74 (1%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MN P+RYE      G  KV+YE D+K  NAA  T+E+E+HT+ N+L  QL  DE VLFAG
Sbjct: 1  MNQPERYELIE-LMGLPKVTYELDSKSPNAAVVTLEKEDHTLANMLANQLLSDERVLFAG 59

Query: 61 YKLPHPLQYKIIVR 74
          YK+PHPL +  I+R
Sbjct: 60 YKVPHPLNHNFILR 73

>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 Length = 92

 Score = 68.0 bits (166), Expect = 4e-17
 Identities = 22/51 (43%), Positives = 27/51 (52%)

Query: 24 DTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVR 74
               N     IE E+HT+GN++   L R   V FA Y  PHPL  KIIV+
Sbjct: 6  LKSESNYLELEIEGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVK 56

>1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural genomics, protein structure initiative, MCSG; 1.60A {Thermoplasma acidophilum} SCOP: d.74.3.2 Length = 115

 Score = 66.1 bits (161), Expect = 4e-16
 Identities = 13/61 (21%), Positives = 28/61 (45%)

Query: 14 EGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIV 73
          E T + S    +K  N+ +  +   ++T+   L  ++ +D+ V  A Y + HP+     +
Sbjct: 6  ERTAESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQI 65

Query: 74 R 74
           
Sbjct: 66 Y 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	84
1twf_K	120	B13.6, DNA-directed RNA polymerase II 13.6 kDa pol	100.0
3h0g_K	123	DNA-directed RNA polymerase II subunit RPB11; tran	100.0
1xpp_A	115	TA1416, DNA-directed RNA polymerase subunit L; str	99.97
2pa8_L	92	DNA-directed RNA polymerase subunit L; ferredoxin-	99.96
2pa8_D	265	DNA-directed RNA polymerase subunit D; ferredoxin-	96.41
1bdf_A	235	RNA polymerase alpha subunit; nucleotidyltransfera	95.36
1twf_C	318	B44.5, DNA-directed RNA polymerase II 45 kDa polyp	95.34
3h0g_C	297	DNA-directed RNA polymerase II subunit RPB3; trans	94.95
2a6h_A	315	DNA-directed RNA polymerase alpha chain; RNA polym	94.02
3lu0_A	329	DNA-directed RNA polymerase subunit alpha; E. coli	93.68

>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB: 1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K 1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K* 1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ...

Probab=100.00  E-value=9e-43  Score=236.30  Aligned_cols=82  Identities=43%  Similarity=0.717  Sum_probs=80.4

Q ss_pred             CCCCcccceeeeCCCceeeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccC
Q 034762            1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKH   80 (84)
Q Consensus         1 mn~p~~~~~~~l~~ge~Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~   80 (84)
                      ||||||||+|+|+||++||++..+++.+|+++|+|.||||||||+||++|+++|+|+||||+|||||+++++|||||+|+
T Consensus         1 mnap~~~e~f~l~~ge~K~~~~~~~k~~n~~~f~i~~EDHTLgNlLr~~Llk~p~V~fAgY~vpHPl~~~~~lrIqT~~~   80 (120)
T 1twf_K            1 MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG   80 (120)
T ss_dssp             CCSCCSGGGTSCCTTCCSCCEEECSSSTTEEEEEEESCCHHHHHHHHHHHTTCTTEEEEEEECSCTTSCEEEEEEEECTT
T ss_pred             CCCCCccceeecCCCCceEEEEeccCCCCeEEEEEeCCCchHHHHHHHHHhhCCCeeEEeeecCCCCCCccEEEEEECCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cc
Q 034762           81 SR   82 (84)
Q Consensus        81 ~~   82 (84)
                      .+
T Consensus        81 ~~   82 (120)
T 1twf_K           81 YD   82 (120)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=100.00  E-value=8.4e-43  Score=237.66  Aligned_cols=81  Identities=49%  Similarity=0.783  Sum_probs=79.4

Q ss_pred             CCCCcccceeeeCCCceeeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccC
Q 034762            1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKH   80 (84)
Q Consensus         1 mn~p~~~~~~~l~~ge~Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~   80 (84)
                      ||||||||+|+| +|++||++..+++.+|+++|+|.||||||||+||++|+++|+|+||||+||||++++++|||||+|+
T Consensus         1 mnap~~~e~f~l-~ge~Kv~~~~dtk~~n~~~f~i~~EDHTLgNlLr~~Llk~p~V~fAgY~vpHPle~~~~lrIqT~~~   79 (123)
T 3h0g_K            1 MNQPERYELIEL-MGLPKVTYELDSKSPNAAVVTLEKEDHTLANMLANQLLSDERVLFAGYKVPHPLNHNFILRVQTVED   79 (123)
T ss_dssp             CCCCCGGGTSSC-SSCCSCCEEECSSSTTEEEEEEESCCSSHHHHHHHTGGGSTTCSCBCCBCSCTTSCEEEEEEECCSS
T ss_pred             CCCCCccceeEe-CCCcceEEecCCCCCceEEEEEeCCCcchHHHHHHHHhcCCCeeEeeecCCCCCCCceEEEEEECCC
Confidence            999999999999 9999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cc
Q 034762           81 SR   82 (84)
Q Consensus        81 ~~   82 (84)
                      .+
T Consensus        80 ~~   81 (123)
T 3h0g_K           80 CS   81 (123)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>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=99.97  E-value=6e-32  Score=182.31  Aligned_cols=70  Identities=19%  Similarity=0.163  Sum_probs=63.8

Q ss_pred             eCCCceeeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccCc
Q 034762           12 VPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHS   81 (84)
Q Consensus        12 l~~ge~Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~~   81 (84)
                      -+||++|+++..+++.+|+++|+|.+|||||||+||++|+++|+|+||||+|||||+++++|||||+|+.
T Consensus         4 ~~~~~~kmeiki~~k~~n~~~f~i~~EDHTLgNlLr~~Llkdp~V~fAgY~vpHPle~~~~lrIqT~~~~   73 (115)
T 1xpp_A            4 QRERTAESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSGK   73 (115)
T ss_dssp             -----CCCEEEEEEECSSEEEEEEESCCHHHHHHHHHHHTTCTTEEEEEEECSSTTTSCCEEEEEESSSC
T ss_pred             ccccccceEEEEEcCCCCEEEEEEeCCCchhHHHHHHHHhcCCCeEEEEeecCCCCCCccEEEEEeCCCC
Confidence            4789999999999999999999999999999999999999999999999999999999999999999875

>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=99.96  E-value=3.2e-30  Score=167.43  Aligned_cols=61  Identities=36%  Similarity=0.444  Sum_probs=56.6

Q ss_pred             eecCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccCcc
Q 034762           22 ERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSR   82 (84)
Q Consensus        22 ~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~~~   82 (84)
                      ...++.+|+++|+|.||||||||+||++|+++|+|+||||+||||++++++|||||+++.+
T Consensus         4 kvi~k~~n~~~f~i~~EDHTLgN~Lr~~L~~~p~V~fagY~vpHPl~~~~~lrIqT~~~~~   64 (92)
T 2pa8_L            4 RILKSESNYLELEIEGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVKILTDGSIT   64 (92)
T ss_dssp             EEEEEETTEEEEEEETCCHHHHHHHHHHHHTSTTEEEEEEECSSTTSCCEEEEEEECSSSC
T ss_pred             EEEecCCCeEEEEEecCchhHHHHHHHHHhcCCCeeEEEeecCCCCCCceEEEEEECCCCC
Confidence            3344779999999999999999999999999999999999999999999999999998754

>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=96.41  E-value=0.0028  Score=46.19  Aligned_cols=41  Identities=12%  Similarity=0.028  Sum_probs=32.6

Q ss_pred             eeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcC-C-----ceeEEe
Q 034762           18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-E-----NVLFAG   60 (84)
Q Consensus        18 Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~-~-----~V~fAg   60 (84)
                      +|++...  .++.++|.+.|-|+||||+||..|+.. |     .|.+.|
T Consensus         2 ~i~i~~~--~~~~~~f~l~g~~~t~~NalRRills~vp~~AI~~V~i~~   48 (265)
T 2pa8_D            2 SINLLHK--DDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIE   48 (265)
T ss_dssp             CEEEEEE--CSSEEEEEEESSCHHHHHHHHHHHHHSCCEEEEEEEEEEE
T ss_pred             eEEEEEc--CCCEEEEEEeCCCHHHHHHHHHHHHHcCccceEEEEEEEe
Confidence            4566554  388999999999999999999999874 4     556666

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

Probab=95.36  E-value=0.012  Score=42.77  Aligned_cols=42  Identities=29%  Similarity=0.287  Sum_probs=32.3

Q ss_pred             eeeEEeecCCCcceeEEEEe----cCCcchHHHHHHHHhcC-CceeEEe
Q 034762           17 KKVSYERDTKIINAASFTIE----REEHTIGNILRMQLHRD-ENVLFAG   60 (84)
Q Consensus        17 ~Ki~~~~~~~~~n~~~~~i~----~EdHTLgNlLr~~Ll~~-~~V~fAg   60 (84)
                      .+|++...  .++.++|.+.    |-++||||+||..|+.. |+.-.-+
T Consensus        12 ~~i~i~~~--~~~~~~F~l~Ple~G~~~tlgNaLRRiLLsevpg~AI~~   58 (235)
T 1bdf_A           12 RLVDIEQV--SSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVTE   58 (235)
T ss_dssp             CEEEEEES--SSSEEEEEEEEEETTHHHHHHHHHHHHHTTSCCCEEEEE
T ss_pred             ceEEEEEc--cCCEEEEEEEecCCCCchHHHHHHHHHHHhcCCceEEEE
Confidence            44677664  4889999996    99999999999999974 6544433

>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=95.34  E-value=0.0066  Score=46.09  Aligned_cols=35  Identities=14%  Similarity=0.241  Sum_probs=28.8

Q ss_pred             eeeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcC
Q 034762           17 KKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD   53 (84)
Q Consensus        17 ~Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~   53 (84)
                      .+|++..  ..++.++|.+.|-|+||||.||..|+..
T Consensus         6 p~I~i~~--~~~~~~kF~leG~~~tlaNALRRiLLSe   40 (318)
T 1twf_C            6 PQVKIRE--ASKDNVDFILSNVDLAMANSLRRVMIAE   40 (318)
T ss_dssp             SBCCCSC--CCSSEECCEEBSSCHHHHHHHHHHHHHC
T ss_pred             CeEEEEE--ecCCEEEEEEEccChhHHHHHHHHHHHc
Confidence            3455555  3488999999999999999999999874

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

Probab=94.95  E-value=0.015  Score=43.97  Aligned_cols=36  Identities=14%  Similarity=0.232  Sum_probs=30.3

Q ss_pred             ceeeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcC
Q 034762           16 TKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD   53 (84)
Q Consensus        16 e~Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~   53 (84)
                      ..+|++...  .++.++|.+.|-|.||||.||..|+..
T Consensus         4 ~p~I~i~~~--~~~~~~F~l~g~~~tiaNALRRiLLSe   39 (297)
T 3h0g_C            4 ETHITIRNI--SKNSVDFVLTNTSLAVANSLRRVVLAE   39 (297)
T ss_dssp             CCSBCCCCB--CSSEEEEEECSCCHHHHHHHHHHHHSS
T ss_pred             CCeEEEEEc--cCCEEEEEEECCChhHHHHHHHHHHHc
Confidence            456666664  479999999999999999999999984

>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=94.02  E-value=0.038  Score=41.84  Aligned_cols=37  Identities=22%  Similarity=0.170  Sum_probs=29.3

Q ss_pred             eeEEeecCCCcceeEEEEe----cCCcchHHHHHHHHhcC-Cce
Q 034762           18 KVSYERDTKIINAASFTIE----REEHTIGNILRMQLHRD-ENV   56 (84)
Q Consensus        18 Ki~~~~~~~~~n~~~~~i~----~EdHTLgNlLr~~Ll~~-~~V   56 (84)
                      +|++...  .++.++|.+.    |-++||||+||..|+.. |+.
T Consensus        10 ~i~i~~~--~~~~~~F~l~Ple~G~~~TlgNaLRRiLLsevpg~   51 (315)
T 2a6h_A           10 VFTVRTQ--GREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGT   51 (315)
T ss_dssp             EEEEEEE--TTTEEEEEEEEECTTCHHHHHHHHHHHHHHTCEEE
T ss_pred             eEEEEEc--cCCEEEEEEEccCCCchhHHHHHHHHHHHhcCCce
Confidence            3666553  3889999995    99999999999999874 543

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

Probab=93.68  E-value=0.032  Score=42.66  Aligned_cols=39  Identities=31%  Similarity=0.279  Sum_probs=30.3

Q ss_pred             eeEEeecCCCcceeEEEEe----cCCcchHHHHHHHHhcC-CceeE
Q 034762           18 KVSYERDTKIINAASFTIE----REEHTIGNILRMQLHRD-ENVLF   58 (84)
Q Consensus        18 Ki~~~~~~~~~n~~~~~i~----~EdHTLgNlLr~~Ll~~-~~V~f   58 (84)
                      ++.+...  .++.++|.+.    |-++||||+||..|+.. |+.-.
T Consensus        13 ~~~v~~~--~~~~~kF~l~PlerG~g~TlgNaLRRvLLssvpg~AI   56 (329)
T 3lu0_A           13 LVDIEQV--SSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAV   56 (329)
T ss_dssp             CCCEEEC--TTSEEEEEECCCCTTCHHHHHHHHHHHTTTSSCEEEE
T ss_pred             eEEEEEc--CCCEEEEEEEecCCCChhHHHHHHHHHHHhcCCceEE
Confidence            4444443  4889999999    99999999999999984 54433

---

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	84
d1twfk_	114	d.74.3.2 (K:) RPB11 {Baker's yeast (Saccharomyces	1e-32
d1xppa_	99	d.74.3.2 (A:) DNA-directed RNA polymerase subunit	3e-15

>d1twfk_ d.74.3.2 (K:) RPB11 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 114

class: Alpha and beta proteins (a+b)
fold: DCoH-like
superfamily: RBP11-like subunits of RNA polymerase
family: RBP11/RpoL
domain: RPB11
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  107 bits (268), Expect = 1e-32
 Identities = 35/74 (47%), Positives = 49/74 (66%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAPDR+E F++ EG  K+  + DTK  NA   T E+E+HT+GN++R +L  D  VLFA 
Sbjct: 1  MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAA 60

Query: 61 YKLPHPLQYKIIVR 74
          YK+ HP   +  +R
Sbjct: 61 YKVEHPFFARFKLR 74

>d1xppa_ d.74.3.2 (A:) DNA-directed RNA polymerase subunit L, RpoL {Thermoplasma acidophilum [TaxId: 2303]} Length = 99

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]

 Score = 62.5 bits (152), Expect = 3e-15
 Identities = 11/57 (19%), Positives = 26/57 (45%), Gaps = 4/57 (7%)

Query: 22 ERDTKII----NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVR 74
          E   ++I    N+ +  +   ++T+   L  ++ +D+ V  A Y + HP+     + 
Sbjct: 2  ESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIY 58

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	84
d1twfk_	114	RPB11 {Baker's yeast (Saccharomyces cerevisiae) [T	100.0
d1xppa_	99	DNA-directed RNA polymerase subunit L, RpoL {Therm	99.94
d1bdfa1	105	RNA polymerase alpha {Escherichia coli [TaxId: 562	95.96
d1smya1	106	RNA polymerase alpha {Thermus thermophilus [TaxId:	94.15
d1twfc1	135	RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta	88.94

>d1twfk_ d.74.3.2 (K:) RPB11 {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: RBP11/RpoL
domain: RPB11
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=8.9e-38  Score=207.51  Aligned_cols=82  Identities=43%  Similarity=0.717  Sum_probs=80.1

Q ss_pred             CCCCcccceeeeCCCceeeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccC
Q 034762            1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKH   80 (84)
Q Consensus         1 mn~p~~~~~~~l~~ge~Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~   80 (84)
                      ||||||||+|+|++|++||++..+++.+|+++|+|.+|||||||+|++.|+++|+|.||||++|||+++++.|||||+++
T Consensus         1 mn~p~~~~~~~l~~~e~ki~i~~~~~~~n~~~~~i~~EdhTlGnlL~~~L~~~~~V~fagY~~pHPl~~~i~irI~t~~~   80 (114)
T d1twfk_           1 MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG   80 (114)
T ss_dssp             CCSCCSGGGTSCCTTCCSCCEEECSSSTTEEEEEEESCCHHHHHHHHHHHTTCTTEEEEEEECSCTTSCEEEEEEEECTT
T ss_pred             CCCcchhhhcccCCCCceEEEEecCCCCceEEEEEeCCCchHHHHHHHHHhcCCCceEEEeecCCCCCCeeEEEEEeCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cc
Q 034762           81 SR   82 (84)
Q Consensus        81 ~~   82 (84)
                      .+
T Consensus        81 ~~   82 (114)
T d1twfk_          81 YD   82 (114)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.94  E-value=8.8e-28  Score=155.35  Aligned_cols=65  Identities=15%  Similarity=0.163  Sum_probs=60.0

Q ss_pred             CceeeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccCc
Q 034762           15 GTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHS   81 (84)
Q Consensus        15 ge~Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~~   81 (84)
                      |+.+|++..  +.+|+++|+|.||||||||+||+.|+++|+|.||||++||||+++|.|+|||+++.
T Consensus         1 ~~~~ikvi~--~~~n~~~~~i~~EdHTlgn~L~~~L~~~~~V~fagY~ipHPl~~~~~l~I~t~~~~   65 (99)
T d1xppa_           1 AESSLRVIS--KEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSGK   65 (99)
T ss_dssp             CCCEEEEEE--ECSSEEEEEEESCCHHHHHHHHHHHTTCTTEEEEEEECSSTTTSCCEEEEEESSSC
T ss_pred             CCceEEEEe--cCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEEecCCcccCCeEEEEEeCCCC
Confidence            466777776  56999999999999999999999999999999999999999999999999998764

>d1bdfa1 d.74.3.1 (A:2-52,A:179-232) RNA polymerase alpha {Escherichia coli [TaxId: 562]}

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: RNA polymerase alpha
species: Escherichia coli [TaxId: 562]

Probab=95.96  E-value=0.017  Score=35.98  Aligned_cols=55  Identities=24%  Similarity=0.193  Sum_probs=42.5

Q ss_pred             cceeEEEE----ecCCcchHHHHHHHHhc-CCceeEEeeeCC---CC---CCcceEEEEEeccCcc
Q 034762           28 INAASFTI----EREEHTIGNILRMQLHR-DENVLFAGYKLP---HP---LQYKIIVRAELAKHSR   82 (84)
Q Consensus        28 ~n~~~~~i----~~EdHTLgNlLr~~Ll~-~~~V~fAgY~vp---HP---l~~~i~l~Iqt~~~~~   82 (84)
                      +...+|++    .|-.+|+||.+|..|+. .+.|.-++|+|.   |=   -.+++.|.|.|+|..+
T Consensus        20 ~~~~k~~~eplErG~Gyt~gn~lr~~llSs~sPV~~V~y~Ve~~~~e~~td~d~L~lei~TnGsi~   85 (105)
T d1bdfa1          20 STHAKVTLEPLERGFGHTLGNALRAILLSSMPPVERIAYNVEAARVEQRTDLDKLVIEMETNGTID   85 (105)
T ss_dssp             SSEEEEEEEEEETTHHHHHHHHHHHHHTTSCCSEEEEEEECCBCCCSSCSSEEEEEEEEEECSSSC
T ss_pred             CceEEEEEEEccCCcccccccccchhhhhcccceeEEEEeeeeeecCCCCcceEEEEEEEeCCCCC
Confidence            44455554    56679999999999776 699999999986   32   2358999999999864

>d1smya1 d.74.3.1 (A:1-49,A:173-229) RNA polymerase alpha {Thermus thermophilus [TaxId: 274]}

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: RNA polymerase alpha
species: Thermus thermophilus [TaxId: 274]

Probab=94.15  E-value=0.05  Score=33.97  Aligned_cols=56  Identities=20%  Similarity=0.088  Sum_probs=43.2

Q ss_pred             CcceeEEEEe----cCCcchHHHHHHHHhc-CCceeEEeeeCCC------CCCcceEEEEEeccCcc
Q 034762           27 IINAASFTIE----REEHTIGNILRMQLHR-DENVLFAGYKLPH------PLQYKIIVRAELAKHSR   82 (84)
Q Consensus        27 ~~n~~~~~i~----~EdHTLgNlLr~~Ll~-~~~V~fAgY~vpH------Pl~~~i~l~Iqt~~~~~   82 (84)
                      ......|.+.    |..+|+||.||..|.. .+-|.-+.|.|..      .-..++.|-|.|+|..+
T Consensus        17 ~~~y~~~v~~p~erG~g~~~gn~l~~il~ss~~PV~kV~y~Ve~~rvg~~~d~dkL~LeI~TnGsi~   83 (106)
T d1smya1          17 GREYGEFVLEPLERGFGVTLGNPLRRILLSSIPPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVT   83 (106)
T ss_dssp             SSSCEEEEEEEECTTHHHHHHHHHHHHHHHTCECEEEEEEEEEECCCSSCSCCEEEEEEEEECSSSC
T ss_pred             CCceeEEEeeccCCCcccccccccceeehhcCChhhEEEEEecccccCcccceeEEEEEEEeCCCCC
Confidence            3555666654    7789999999997665 7999999999863      12368999999999864

>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=88.94  E-value=0.093  Score=34.13  Aligned_cols=36  Identities=14%  Similarity=0.224  Sum_probs=30.1

Q ss_pred             ceeeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcC
Q 034762           16 TKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD   53 (84)
Q Consensus        16 e~Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~   53 (84)
                      ..+|++..  ..++.++|.+.|-|-++.|.||..|+.+
T Consensus         3 ~P~i~i~~--~~~~~~~F~l~~~d~s~ANalRRi~iae   38 (135)
T d1twfc1           3 GPQVKIRE--ASKDNVDFILSNVDLAMANSLRRVMIAE   38 (135)
T ss_dssp             SSBCCCSC--CCSSEECCEEBSSCHHHHHHHHHHHHHC
T ss_pred             CCEEEEEE--cCCCEEEEEEeCCCHHHHHHHHHHHHHh
Confidence            35666666  4478899999999999999999999875