Citrus Sinensis ID: 035172

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70-
Protein Sequence
MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNTLDKSDTS
Secondary Structure (PSIPRED)
cccccccccccccHHcHHHHHHHHHHccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEccccHHHHHHHHHHHHHHccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHccccccccccc
Coil and Loop (DISEMBL)
miipvrcftcgkvignkWDTYLDLLQadypegdaldALGLVRYCCRRMLMTHVDLIEKLLnyntldksdts
Flexible Loop (DISEMBL)
MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEkllnyntldksdts
Low Complexity Region (SEG)
MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNTLDKSDTS
Disordered region (IsUnstruct)
*IIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNT*******
Disordered Region (DISOPRED)
MIIPVRCFTCGKVIGNKWDTYLDLLQA*****DALDALGLVRYCCRRMLMTHVDLIEKLL***********
Disordered Region (DISEMBL)
MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNTLDKSDTS
Disordered Region (DISPRO)
MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNTL******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNTLDKSDTS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	71	2.2.26 [Sep-21-2011]
Q9SYA6	71	DNA-directed RNA polymera	yes	no	1.0	1.0	0.901	1e-32
Q39290	71	DNA-directed RNA polymera	N/A	no	1.0	1.0	0.915	5e-32
Q9VC49	67	DNA-directed RNA polymera	yes	no	0.943	1.0	0.820	4e-27
P62876	67	DNA-directed RNA polymera	yes	no	0.943	1.0	0.805	5e-27
P62875	67	DNA-directed RNA polymera	yes	no	0.943	1.0	0.805	5e-27
Q6QN04	67	DNA-directed RNA polymera	N/A	no	0.943	1.0	0.805	5e-27
Q32P78	67	DNA-directed RNA polymera	yes	no	0.943	1.0	0.805	5e-27
Q9GR61	67	DNA-directed RNA polymera	yes	no	0.943	1.0	0.791	1e-26
A8Y1E9	67	DNA-directed RNA polymera	N/A	no	0.943	1.0	0.791	1e-26
Q55AB6	70	DNA-directed RNA polymera	yes	no	0.915	0.928	0.861	2e-26

>sp|Q9SYA6|RPAB5_ARATH DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Arabidopsis thaliana GN=At1g61700 PE=3 SV=1

 Score =  138 bits (347), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 64/71 (90%), Positives = 69/71 (97%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MI+PVRCFTCGKVIGNKWDTYL+LLQADY EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIVPVRCFTCGKVIGNKWDTYLELLQADYAEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 61 NYNTLDKSDTS 71
          NYNT++KSD +
Sbjct: 61 NYNTMEKSDPN 71

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft.
Arabidopsis thaliana (taxid: 3702)

>sp|Q39290|RPAB5_BRANA DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Brassica napus PE=3 SV=1

 Score =  135 bits (341), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 65/71 (91%), Positives = 66/71 (92%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCFTCGKVIGNKWD YLDLLQ DY EGDALDAL LVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDAYLDLLQLDYTEGDALDALNLVRYCCRRMLMTHVDLIEKLL 60

Query: 61 NYNTLDKSDTS 71
          NYNTL+KSD S
Sbjct: 61 NYNTLEKSDNS 71

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft.

Brassica napus (taxid: 3708)

>sp|Q9VC49|RPAB5_DROME DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Drosophila melanogaster GN=Rpb10 PE=1 SV=1

 Score =  119 bits (299), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 55/67 (82%), Positives = 61/67 (91%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIP+RCFTCGKVIGNKW++YL LLQA+Y EGDALDALGL RYCCRRML+ HVDLIEKLL
Sbjct: 1  MIIPIRCFTCGKVIGNKWESYLGLLQAEYTEGDALDALGLKRYCCRRMLLGHVDLIEKLL 60

Query: 61 NYNTLDK 67
          NY  L+K
Sbjct: 61 NYAPLEK 67

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft.

Drosophila melanogaster (taxid: 7227)

>sp|P62876|RPAB5_MOUSE DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Mus musculus GN=Polr2l PE=2 SV=1

 Score =  119 bits (299), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 54/67 (80%), Positives = 60/67 (89%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCFTCGK++GNKW+ YL LLQA+Y EGDALDALGL RYCCRRML+ HVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL 60

Query: 61 NYNTLDK 67
          NY  L+K
Sbjct: 61 NYAPLEK 67

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, POLR2L/RBP10 is part of the core element with the central large cleft.

Mus musculus (taxid: 10090)

>sp|P62875|RPAB5_HUMAN DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Homo sapiens GN=POLR2L PE=1 SV=1

 Score =  119 bits (299), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 54/67 (80%), Positives = 60/67 (89%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCFTCGK++GNKW+ YL LLQA+Y EGDALDALGL RYCCRRML+ HVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL 60

Query: 61 NYNTLDK 67
          NY  L+K
Sbjct: 61 NYAPLEK 67

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, POLR2L/RBP10 is part of the core element with the central large cleft.

Homo sapiens (taxid: 9606)

>sp|Q6QN04|RPAB5_CHILA DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Chinchilla lanigera GN=POLR2L PE=3 SV=1

 Score =  119 bits (299), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 54/67 (80%), Positives = 60/67 (89%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCFTCGK++GNKW+ YL LLQA+Y EGDALDALGL RYCCRRML+ HVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL 60

Query: 61 NYNTLDK 67
          NY  L+K
Sbjct: 61 NYAPLEK 67

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, POLR2L/RBP10 is part of the core element with the central large cleft.

Chinchilla lanigera (taxid: 34839)

>sp|Q32P78|RPAB5_BOVIN DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Bos taurus GN=POLR2L PE=3 SV=1

 Score =  119 bits (299), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 54/67 (80%), Positives = 60/67 (89%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCFTCGK++GNKW+ YL LLQA+Y EGDALDALGL RYCCRRML+ HVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL 60

Query: 61 NYNTLDK 67
          NY  L+K
Sbjct: 61 NYAPLEK 67

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, POLR2L/RBP10 is part of the core element with the central large cleft.

Bos taurus (taxid: 9913)

>sp|Q9GR61|RPAB5_CAEEL DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Caenorhabditis elegans GN=rpb-10 PE=3 SV=1

 Score =  117 bits (294), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 53/67 (79%), Positives = 61/67 (91%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIP+RCFTCGKVIG+KW+TYL  LQ++Y EGDALDALGL RYCCRRML+ HVDLIEKLL
Sbjct: 1  MIIPIRCFTCGKVIGDKWETYLGFLQSEYSEGDALDALGLRRYCCRRMLLAHVDLIEKLL 60

Query: 61 NYNTLDK 67
          NY+ L+K
Sbjct: 61 NYHPLEK 67

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft.

Caenorhabditis elegans (taxid: 6239)

>sp|A8Y1E9|RPAB5_CAEBR DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Caenorhabditis briggsae GN=rpb-10 PE=3 SV=1

 Score =  117 bits (294), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 53/67 (79%), Positives = 61/67 (91%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIP+RCFTCGKVIG+KW+TYL  LQ++Y EGDALDALGL RYCCRRML+ HVDLIEKLL
Sbjct: 1  MIIPIRCFTCGKVIGDKWETYLGFLQSEYSEGDALDALGLRRYCCRRMLLAHVDLIEKLL 60

Query: 61 NYNTLDK 67
          NY+ L+K
Sbjct: 61 NYHPLEK 67

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft.

Caenorhabditis briggsae (taxid: 6238)

>sp|Q55AB6|RPAB5_DICDI DNA-directed RNA polymerases I, II, and III subunit rpabc5 OS=Dictyostelium discoideum GN=polr2l PE=3 SV=1

 Score =  117 bits (293), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 56/65 (86%), Positives = 57/65 (87%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCFTCGKVIGNKWD YL LLQ DY EGDALDAL L RYCCRRML+THVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDAYLSLLQIDYTEGDALDALCLKRYCCRRMLLTHVDLIEKLL 60

Query: 61 NYNTL 65
          NY  L
Sbjct: 61 NYTPL 65

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft.

Dictyostelium discoideum (taxid: 44689)

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	71
449441830	71	PREDICTED: DNA-directed RNA polymerases	1.0	1.0	0.971	2e-32
225425585	71	PREDICTED: DNA-directed RNA polymerases	1.0	1.0	0.957	2e-32
388499416	71	unknown [Lotus japonicus] gi|388514409|g	1.0	1.0	0.957	4e-32
356497696	71	PREDICTED: DNA-directed RNA polymerases	1.0	1.0	0.957	4e-32
356515720	71	PREDICTED: DNA-directed RNA polymerases	0.971	0.971	0.985	4e-32
356508029	71	PREDICTED: DNA-directed RNA polymerases	1.0	1.0	0.957	6e-32
224069248	71	predicted protein [Populus trichocarpa]	1.0	1.0	0.943	9e-32
116778557	71	unknown [Picea sitchensis] gi|116781551|	1.0	1.0	0.929	9e-32
326497947	71	predicted protein [Hordeum vulgare subsp	1.0	1.0	0.929	2e-31
449435392	71	PREDICTED: DNA-directed RNA polymerases	0.971	0.971	0.942	2e-31

>gi|449441830|ref|XP_004138685.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC5-like [Cucumis sativus] gi|449522728|ref|XP_004168378.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC5-like [Cucumis sativus]

 Score =  143 bits (360), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 69/71 (97%), Positives = 69/71 (97%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCFTCGKVIGNKWD YLDLLQADY EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 61 NYNTLDKSDTS 71
          NYNTLDKSDTS
Sbjct: 61 NYNTLDKSDTS 71

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225425585|ref|XP_002263065.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC5 [Vitis vinifera] gi|297739069|emb|CBI28558.3| unnamed protein product [Vitis vinifera]

 Score =  143 bits (360), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 68/71 (95%), Positives = 70/71 (98%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCFTCGKVIGNKWDTYLDLLQADY EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYTEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 61 NYNTLDKSDTS 71
          NYNTL+KS+TS
Sbjct: 61 NYNTLEKSETS 71

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388499416|gb|AFK37774.1| unknown [Lotus japonicus] gi|388514409|gb|AFK45266.1| unknown [Lotus japonicus]

 Score =  141 bits (356), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 68/71 (95%), Positives = 69/71 (97%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCFTCGKVIGNKWD YLDLLQ+DY EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDPYLDLLQSDYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 61 NYNTLDKSDTS 71
          NYNTLDKSDTS
Sbjct: 61 NYNTLDKSDTS 71

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356497696|ref|XP_003517695.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC5 [Glycine max] gi|356502404|ref|XP_003520009.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC5-like [Glycine max] gi|255631340|gb|ACU16037.1| unknown [Glycine max]

 Score =  141 bits (356), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 68/71 (95%), Positives = 69/71 (97%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCFTCGKVIGNKWDTYLDLLQ+DY EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQSDYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 61 NYNTLDKSDTS 71
          NYNTLDKSD S
Sbjct: 61 NYNTLDKSDPS 71

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356515720|ref|XP_003526546.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC5-like [Glycine max]

 Score =  141 bits (356), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 68/69 (98%), Positives = 68/69 (98%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCFTCGKVIGNKWDTYLDLLQADY EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 61 NYNTLDKSD 69
          NYNTLDKSD
Sbjct: 61 NYNTLDKSD 69

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356508029|ref|XP_003522765.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC5-like [Glycine max]

 Score =  141 bits (355), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 68/71 (95%), Positives = 69/71 (97%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCFTCGKVIGNKWDTYLDLLQADY EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 61 NYNTLDKSDTS 71
          NYNTLDKSD +
Sbjct: 61 NYNTLDKSDPN 71

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224069248|ref|XP_002326311.1| predicted protein [Populus trichocarpa] gi|224071453|ref|XP_002303467.1| predicted protein [Populus trichocarpa] gi|118486243|gb|ABK94963.1| unknown [Populus trichocarpa] gi|222833504|gb|EEE71981.1| predicted protein [Populus trichocarpa] gi|222840899|gb|EEE78446.1| predicted protein [Populus trichocarpa]

 Score =  140 bits (353), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 67/71 (94%), Positives = 69/71 (97%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCFTCGKVIGNKWDTYLDLLQADY EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYTEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 61 NYNTLDKSDTS 71
          NYNTL+KS+ S
Sbjct: 61 NYNTLEKSEGS 71

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116778557|gb|ABK20909.1| unknown [Picea sitchensis] gi|116781551|gb|ABK22149.1| unknown [Picea sitchensis] gi|116789545|gb|ABK25286.1| unknown [Picea sitchensis]

 Score =  140 bits (353), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 66/71 (92%), Positives = 70/71 (98%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCFTCGKVIGNKWDTYLDLLQADY EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYTEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 61 NYNTLDKSDTS 71
          NYNTL++S+T+
Sbjct: 61 NYNTLERSETN 71

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326497947|dbj|BAJ94836.1| predicted protein [Hordeum vulgare subsp. vulgare] gi|326520229|dbj|BAK04039.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  139 bits (351), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 66/71 (92%), Positives = 69/71 (97%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCFTCGKVIGNKWD YLDLLQADY EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDHYLDLLQADYTEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 61 NYNTLDKSDTS 71
          NYNTL+K++TS
Sbjct: 61 NYNTLEKTETS 71

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449435392|ref|XP_004135479.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC5-like [Cucumis sativus] gi|449478734|ref|XP_004155405.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC5-like [Cucumis sativus]

 Score =  139 bits (350), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 65/69 (94%), Positives = 68/69 (98%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEG+ALD LGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGEALDMLGLVRYCCRRMLMTHVDLIEKLL 60

Query: 61 NYNTLDKSD 69
          NYNT+DKS+
Sbjct: 61 NYNTMDKSE 69

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	71
TAIR|locus:2195718	71	AT1G61700 [Arabidopsis thalian	0.971	0.971	0.927	1.4e-32
TAIR|locus:2823924	71	NRPB10 [Arabidopsis thaliana (	1.0	1.0	0.915	9.8e-32
FB|FBgn0039218	67	Rpb10 "Rpb10" [Drosophila mela	0.943	1.0	0.820	5.7e-27
UNIPROTKB|E1BSY6	67	POLR2L "Uncharacterized protei	0.943	1.0	0.805	5.7e-27
UNIPROTKB|Q32P78	67	POLR2L "DNA-directed RNA polym	0.943	1.0	0.805	5.7e-27
UNIPROTKB|P62875	67	POLR2L "DNA-directed RNA polym	0.943	1.0	0.805	5.7e-27
UNIPROTKB|F2Z551	67	LOC100511241 "Uncharacterized	0.943	1.0	0.805	5.7e-27
UNIPROTKB|Q6QN04	67	POLR2L "DNA-directed RNA polym	0.943	1.0	0.805	5.7e-27
MGI|MGI:1913741	67	Polr2l "polymerase (RNA) II (D	0.943	1.0	0.805	5.7e-27
RGD|1566209	323	Polr2l "polymerase (RNA) II (D	0.943	0.207	0.805	5.7e-27

TAIR|locus:2195718 AT1G61700 [Arabidopsis thaliana (taxid:3702)]

 Score = 356 (130.4 bits), Expect = 1.4e-32, P = 1.4e-32
 Identities = 64/69 (92%), Positives = 68/69 (98%)

Query:     1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
             MI+PVRCFTCGKVIGNKWDTYL+LLQADY EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct:     1 MIVPVRCFTCGKVIGNKWDTYLELLQADYAEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query:    61 NYNTLDKSD 69
             NYNT++KSD
Sbjct:    61 NYNTMEKSD 69

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2823924 NRPB10 [Arabidopsis thaliana (taxid:3702)]

 Score = 348 (127.6 bits), Expect = 9.8e-32, P = 9.8e-32
 Identities = 65/71 (91%), Positives = 66/71 (92%)

Query:     1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
             MIIPVRCFTCGKVIGNKWD YLDLLQ DY EGDALDAL LVRYCCRRMLMTHVDLIEKLL
Sbjct:     1 MIIPVRCFTCGKVIGNKWDQYLDLLQLDYTEGDALDALQLVRYCCRRMLMTHVDLIEKLL 60

Query:    61 NYNTLDKSDTS 71
             NYNTL+KSD S
Sbjct:    61 NYNTLEKSDNS 71

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000418 "DNA-directed RNA polymerase IV complex" evidence=IPI

GO:0000419 "DNA-directed RNA polymerase V complex" evidence=IPI

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

FB|FBgn0039218 Rpb10 "Rpb10" [Drosophila melanogaster (taxid:7227)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 55/67 (82%), Positives = 61/67 (91%)

Query:     1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
             MIIP+RCFTCGKVIGNKW++YL LLQA+Y EGDALDALGL RYCCRRML+ HVDLIEKLL
Sbjct:     1 MIIPIRCFTCGKVIGNKWESYLGLLQAEYTEGDALDALGLKRYCCRRMLLGHVDLIEKLL 60

Query:    61 NYNTLDK 67
             NY  L+K
Sbjct:    61 NYAPLEK 67

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

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

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

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

GO:0005634 "nucleus" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E1BSY6 POLR2L "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 54/67 (80%), Positives = 60/67 (89%)

Query:     1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
             MIIPVRCFTCGK++GNKW+ YL LLQA+Y EGDALDALGL RYCCRRML+ HVDLIEKLL
Sbjct:     1 MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL 60

Query:    61 NYNTLDK 67
             NY  L+K
Sbjct:    61 NYAPLEK 67

GO:0003677 "DNA binding" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0004672 "protein kinase activity" evidence=IEA

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

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

UNIPROTKB|Q32P78 POLR2L "DNA-directed RNA polymerases I, II, and III subunit RPABC5" [Bos taurus (taxid:9913)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 54/67 (80%), Positives = 60/67 (89%)

Query:     1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
             MIIPVRCFTCGK++GNKW+ YL LLQA+Y EGDALDALGL RYCCRRML+ HVDLIEKLL
Sbjct:     1 MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL 60

Query:    61 NYNTLDK 67
             NY  L+K
Sbjct:    61 NYAPLEK 67

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=ISS

GO:0004672 "protein kinase activity" evidence=ISS

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|P62875 POLR2L "DNA-directed RNA polymerases I, II, and III subunit RPABC5" [Homo sapiens (taxid:9606)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 54/67 (80%), Positives = 60/67 (89%)

Query:     1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
             MIIPVRCFTCGK++GNKW+ YL LLQA+Y EGDALDALGL RYCCRRML+ HVDLIEKLL
Sbjct:     1 MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL 60

Query:    61 NYNTLDK 67
             NY  L+K
Sbjct:    61 NYAPLEK 67

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0004672 "protein kinase activity" evidence=IDA

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

GO:0005634 "nucleus" evidence=IDA

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

GO:0006356 "regulation of transcription from RNA polymerase I promoter" evidence=TAS

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

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

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

GO: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|F2Z551 LOC100511241 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 54/67 (80%), Positives = 60/67 (89%)

Query:     1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
             MIIPVRCFTCGK++GNKW+ YL LLQA+Y EGDALDALGL RYCCRRML+ HVDLIEKLL
Sbjct:     1 MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL 60

Query:    61 NYNTLDK 67
             NY  L+K
Sbjct:    61 NYAPLEK 67

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q6QN04 POLR2L "DNA-directed RNA polymerases I, II, and III subunit RPABC5" [Chinchilla lanigera (taxid:34839)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 54/67 (80%), Positives = 60/67 (89%)

Query:     1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
             MIIPVRCFTCGK++GNKW+ YL LLQA+Y EGDALDALGL RYCCRRML+ HVDLIEKLL
Sbjct:     1 MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL 60

Query:    61 NYNTLDK 67
             NY  L+K
Sbjct:    61 NYAPLEK 67

GO:0005634 "nucleus" evidence=ISS

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

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

GO:0006468 "protein phosphorylation" evidence=ISS

GO:0004672 "protein kinase activity" evidence=ISS

MGI|MGI:1913741 Polr2l "polymerase (RNA) II (DNA directed) polypeptide L" [Mus musculus (taxid:10090)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 54/67 (80%), Positives = 60/67 (89%)

Query:     1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
             MIIPVRCFTCGK++GNKW+ YL LLQA+Y EGDALDALGL RYCCRRML+ HVDLIEKLL
Sbjct:     1 MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL 60

Query:    61 NYNTLDK 67
             NY  L+K
Sbjct:    61 NYAPLEK 67

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISO

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

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

RGD|1566209 Polr2l "polymerase (RNA) II (DNA directed) polypeptide L" [Rattus norvegicus (taxid:10116)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 54/67 (80%), Positives = 60/67 (89%)

Query:     1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
             MIIPVRCFTCGK++GNKW+ YL LLQA+Y EGDALDALGL RYCCRRML+ HVDLIEKLL
Sbjct:   257 MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL 316

Query:    61 NYNTLDK 67
             NY  L+K
Sbjct:   317 NYAPLEK 323

GO:0005634 "nucleus" evidence=ISO

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

GO:0004672 "protein kinase activity" evidence=ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O13877	RPAB5_SCHPO	No assigned EC number	0.7647	0.9577	0.9577	yes	no
B8GEG1	RPON_METPE	2, ., 7, ., 7, ., 6	0.5161	0.8732	1.0	yes	no
Q8TT41	RPON_METAC	2, ., 7, ., 7, ., 6	0.5	0.8732	1.0	yes	no
C3N8S2	RPON_SULIY	2, ., 7, ., 7, ., 6	0.4761	0.8873	0.9545	yes	no
P62876	RPAB5_MOUSE	No assigned EC number	0.8059	0.9436	1.0	yes	no
P62875	RPAB5_HUMAN	No assigned EC number	0.8059	0.9436	1.0	yes	no
Q9VC49	RPAB5_DROME	No assigned EC number	0.8208	0.9436	1.0	yes	no
A4WNA8	RPON_PYRAR	2, ., 7, ., 7, ., 6	0.5396	0.8873	0.9692	yes	no
Q6QN04	RPAB5_CHILA	No assigned EC number	0.8059	0.9436	1.0	N/A	no
Q8PW43	RPON_METMA	2, ., 7, ., 7, ., 6	0.5161	0.8732	1.0	yes	no
O29135	RPON_ARCFU	2, ., 7, ., 7, ., 6	0.4590	0.8591	0.8026	yes	no
Q5JJC9	RPON_PYRKO	2, ., 7, ., 7, ., 6	0.4843	0.9014	0.9846	yes	no
Q9YB47	RPON_AERPE	2, ., 7, ., 7, ., 6	0.4761	0.8873	0.8181	yes	no
P22139	RPAB5_YEAST	No assigned EC number	0.6857	0.9718	0.9857	yes	no
A8Y1E9	RPAB5_CAEBR	No assigned EC number	0.7910	0.9436	1.0	N/A	no
B9LPW4	RPON_HALLT	2, ., 7, ., 7, ., 6	0.4531	0.8873	0.9843	yes	no
B6YSQ7	RPON_THEON	2, ., 7, ., 7, ., 6	0.4843	0.9014	0.9846	yes	no
Q8SRS6	RPAB5_ENCCU	No assigned EC number	0.5384	0.9154	0.9027	yes	no
A8M9S4	RPON_CALMQ	2, ., 7, ., 7, ., 6	0.4328	0.9436	1.0	yes	no
B1YC34	RPON_PYRNV	2, ., 7, ., 7, ., 6	0.4761	0.8873	0.9545	yes	no
P29199	RPON_HALMA	2, ., 7, ., 7, ., 6	0.4545	0.8873	0.9545	yes	no
C4KJ97	RPON_SULIK	2, ., 7, ., 7, ., 6	0.4761	0.8873	0.9545	yes	no
Q8TVB4	RPON_METKA	2, ., 7, ., 7, ., 6	0.5384	0.9014	0.8888	yes	no
A2SSV3	RPON_METLZ	2, ., 7, ., 7, ., 6	0.5	0.8732	1.0	yes	no
A3DMR0	RPON_STAMF	2, ., 7, ., 7, ., 6	0.4242	0.9295	1.0	yes	no
Q9GR61	RPAB5_CAEEL	No assigned EC number	0.7910	0.9436	1.0	yes	no
Q9SYA6	RPAB5_ARATH	No assigned EC number	0.9014	1.0	1.0	yes	no
C3MZ09	RPON_SULIM	2, ., 7, ., 7, ., 6	0.4761	0.8873	0.9545	yes	no
Q46CK8	RPON_METBF	2, ., 7, ., 7, ., 6	0.5161	0.8732	1.0	yes	no
A4YIM8	RPON_METS5	2, ., 7, ., 7, ., 6	0.5238	0.8873	0.9545	yes	no
Q32P78	RPAB5_BOVIN	No assigned EC number	0.8059	0.9436	1.0	yes	no
Q18G60	RPON_HALWD	2, ., 7, ., 7, ., 6	0.4687	0.8873	0.9843	yes	no
Q75BV8	RPAB5_ASHGO	No assigned EC number	0.6571	0.9718	0.9857	yes	no
A3MXZ9	RPON_PYRCJ	2, ., 7, ., 7, ., 6	0.5396	0.8873	0.9545	yes	no
A7IAH1	RPON_METB6	2, ., 7, ., 7, ., 6	0.5	0.8732	1.0	yes	no
Q0W8C7	RPON_UNCMA	2, ., 7, ., 7, ., 6	0.4788	0.8732	0.8732	yes	no
C3MJQ1	RPON_SULIL	2, ., 7, ., 7, ., 6	0.4761	0.8873	0.9545	yes	no
Q39290	RPAB5_BRANA	No assigned EC number	0.9154	1.0	1.0	N/A	no
A0B6E7	RPON_METTP	2, ., 7, ., 7, ., 6	0.5	0.8591	1.0	yes	no
P39472	RPON_SULAC	2, ., 7, ., 7, ., 6	0.4516	0.8732	0.9393	yes	no
Q55AB6	RPAB5_DICDI	No assigned EC number	0.8615	0.9154	0.9285	yes	no
Q96YW4	RPON_SULTO	2, ., 7, ., 7, ., 6	0.5079	0.8873	0.9545	yes	no
O59298	RPON_PYRHO	2, ., 7, ., 7, ., 6	0.5468	0.9014	0.9846	yes	no
C3N058	RPON_SULIA	2, ., 7, ., 7, ., 6	0.4761	0.8873	0.9545	yes	no
A1RSD9	RPON_PYRIL	2, ., 7, ., 7, ., 6	0.4920	0.8873	0.9545	yes	no
C3NMP6	RPON_SULIN	2, ., 7, ., 7, ., 6	0.4761	0.8873	0.9545	yes	no
P60291	RPON_PYRAB	2, ., 7, ., 7, ., 6	0.5312	0.9014	0.9846	yes	no
P60292	RPON_PYRFU	2, ., 7, ., 7, ., 6	0.5312	0.9014	0.9846	yes	no
A3CWI3	RPON_METMJ	2, ., 7, ., 7, ., 6	0.5	0.8732	1.0	yes	no
Q980Z8	RPON_SULSO	2, ., 7, ., 7, ., 6	0.5	0.8732	0.9393	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

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_Genewise1_v1.C_LG_III2262	SubName- Full=Putative uncharacterized protein; (71 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.IX.2304.1	hypothetical protein (321 aa)	•			•	•	•	•		0.930
	grail3.0014029901	hypothetical protein (52 aa)				•	•	•	•		0.895
	estExt_fgenesh4_pg.C_1570036	hypothetical protein (206 aa)				•	•	•	•		0.880
	estExt_Genewise1_v1.C_LG_IX3069	SubName- Full=Putative uncharacterized protein; (117 aa)				•	•	•	•		0.857
	estExt_fgenesh4_pg.C_LG_XV1089	DNA-directed RNA polymerase (143 aa)	•			•	•	•	•		0.840
	estExt_Genewise1_v1.C_LG_I4990	hypothetical protein (176 aa)					•	•	•		0.835
	estExt_fgenesh4_kg.C_LG_XII0035	DNA-directed RNA polymerase (143 aa)	•			•	•	•	•		0.831
	gw1.I.2689.1	hypothetical protein (1334 aa)	•				•	•	•		0.744
	eugene3.00012667	hypothetical protein (390 aa)	•			•	•	•	•		0.734
	estExt_fgenesh4_pg.C_LG_X0832	SubName- Full=Putative uncharacterized protein; (145 aa)	•			•					0.615

---

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	71
PLN00032	71	PLN00032, PLN00032, DNA-directed RNA polymerase; P	8e-49
pfam01194	60	pfam01194, RNA_pol_N, RNA polymerases N / 8 kDa su	4e-36
COG1644	63	COG1644, RPB10, DNA-directed RNA polymerase, subun	4e-32
PRK04016	62	PRK04016, PRK04016, DNA-directed RNA polymerase su	1e-28

>gnl|CDD|215034 PLN00032, PLN00032, DNA-directed RNA polymerase; Provisional

 Score =  147 bits (373), Expect = 8e-49
 Identities = 67/71 (94%), Positives = 69/71 (97%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCFTCGKVIGNKWDTYLDLLQADY EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 61 NYNTLDKSDTS 71
          NYNTL+KS+ S
Sbjct: 61 NYNTLEKSENS 71

Length = 71

>gnl|CDD|189881 pfam01194, RNA_pol_N, RNA polymerases N / 8 kDa subunit

 Score =  115 bits (290), Expect = 4e-36
 Identities = 45/60 (75%), Positives = 51/60 (85%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCFTCGKVIG+KW+ YL+ L+     GDALD LGL RYCCRRML+THVDLI+KLL
Sbjct: 1  MIIPVRCFTCGKVIGDKWEEYLERLEEGEDPGDALDDLGLKRYCCRRMLLTHVDLIDKLL 60

Length = 60

>gnl|CDD|224558 COG1644, RPB10, DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]

 Score =  105 bits (263), Expect = 4e-32
 Identities = 38/63 (60%), Positives = 50/63 (79%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIPVRCF+CGKVIG+KW+ Y   ++     G+ LD LG+ RYCCRRML++HVDLI++LL
Sbjct: 1  MIIPVRCFSCGKVIGHKWEEYKRRVEEGEDPGEVLDDLGVKRYCCRRMLLSHVDLIDELL 60

Query: 61 NYN 63
           Y+
Sbjct: 61 PYD 63

Length = 63

>gnl|CDD|235200 PRK04016, PRK04016, DNA-directed RNA polymerase subunit N; Provisional

 Score = 96.5 bits (241), Expect = 1e-28
 Identities = 34/62 (54%), Positives = 48/62 (77%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          M+IPVRCFTCGKVI  KW+ + + ++A    G  LD LG+ RYCCRRML++HV+LI++++
Sbjct: 1  MMIPVRCFTCGKVIAEKWEEFKERVEAGEDPGKVLDDLGVKRYCCRRMLLSHVELIDEVI 60

Query: 61 NY 62
           Y
Sbjct: 61 PY 62

Length = 62

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	71
PLN00032	71	DNA-directed RNA polymerase; Provisional	100.0
PRK04016	62	DNA-directed RNA polymerase subunit N; Provisional	100.0
COG1644	63	RPB10 DNA-directed RNA polymerase, subunit N (RpoN	100.0
KOG3497	69	consensus DNA-directed RNA polymerase, subunit RPB	100.0
PF01194	60	RNA_pol_N: RNA polymerases N / 8 kDa subunit; Inte	100.0
PHA03082	63	DNA-dependent RNA polymerase subunit; Provisional	99.33
PF05864	63	Chordopox_RPO7: Chordopoxvirus DNA-directed RNA po	99.32
PRK00418	62	DNA gyrase inhibitor; Reviewed	87.17
COG3024	65	Uncharacterized protein conserved in bacteria [Fun	80.36

>PLN00032 DNA-directed RNA polymerase; Provisional

Probab=100.00  E-value=3e-48  Score=243.21  Aligned_cols=70  Identities=94%  Similarity=1.577  Sum_probs=67.6

Q ss_pred             CcccccccCCCccccchHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhHHHHHHHhccCcccccCC
Q 035172            1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNTLDKSDT   70 (71)
Q Consensus         1 MiiPvRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthvdlid~ll~y~~~~~~~~   70 (71)
                      |||||||||||||||++||+|++++++|++|++|||+||++|||||||||||||+||+|++|++.++...
T Consensus         1 MiiPVRCFTCGkvig~~we~y~~~~~~g~~~~~~LD~LG~~RYCCRRMllsHvdlid~ll~y~~~~~~~~   70 (71)
T PLN00032          1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNTLEKSEN   70 (71)
T ss_pred             CCCceeecCCCCCcHHHHHHHHHHHhcCCCHHHHHHHhCchhhhhhhHHHHHHHHHHHHHccCchhhhcc
Confidence            9999999999999999999999999999999999999999999999999999999999999998877654

>PRK04016 DNA-directed RNA polymerase subunit N; Provisional

Probab=100.00  E-value=4.8e-46  Score=228.20  Aligned_cols=62  Identities=55%  Similarity=1.195  Sum_probs=61.5

Q ss_pred             CcccccccCCCccccchHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhHHHHHHHhcc
Q 035172            1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLLNY   62 (71)
Q Consensus         1 MiiPvRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthvdlid~ll~y   62 (71)
                      ||||||||||||+||++||+|++++++|++|++|||+||++|||||||||||||+||+|++|
T Consensus         1 MiiPvRCFTCGkvi~~~we~y~~~~~~g~~~~~vLd~Lg~~RyCCRRMllthvdlid~l~~y   62 (62)
T PRK04016          1 MMIPVRCFTCGKVIAEKWEEFKERVEAGEDPGKVLDDLGVKRYCCRRMLLSHVELIDEVIPY   62 (62)
T ss_pred             CCCCeEecCCCCChHHHHHHHHHHHHcCCCHHHHHHHcCCcchhhhhHHHHHHHHHHHHHcC
Confidence            99999999999999999999999999999999999999999999999999999999999998

>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]

Probab=100.00  E-value=6.1e-46  Score=228.43  Aligned_cols=63  Identities=60%  Similarity=1.250  Sum_probs=62.2

Q ss_pred             CcccccccCCCccccchHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhHHHHHHHhccC
Q 035172            1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYN   63 (71)
Q Consensus         1 MiiPvRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthvdlid~ll~y~   63 (71)
                      ||||||||||||+||++|++|++++++|++|++|||+||++||||||||+||||+||++++|+
T Consensus         1 MiiPiRCFsCGkvi~~~w~~y~~rv~~ge~p~~vLDdLGv~RYCCRRM~lsHvd~id~~~~y~   63 (63)
T COG1644           1 MIIPVRCFSCGKVIGHKWEEYKRRVEEGEDPGEVLDDLGVKRYCCRRMLLSHVDLIDELLPYD   63 (63)
T ss_pred             CCCceEeecCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCcHHHHHHHHHHHHHHHHHhhccCC
Confidence            999999999999999999999999999999999999999999999999999999999999985

>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]

Probab=100.00  E-value=3.9e-45  Score=227.03  Aligned_cols=68  Identities=85%  Similarity=1.509  Sum_probs=66.8

Q ss_pred             CcccccccCCCccccchHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhHHHHHHHhccCccccc
Q 035172            1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNTLDKS   68 (71)
Q Consensus         1 MiiPvRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthvdlid~ll~y~~~~~~   68 (71)
                      ||||||||||||+||+|||.|++++|+.+++++|||+||++|||||||+|||||+||+||+|++.+++
T Consensus         1 MIiPiRCFtCGKvig~KWe~Yl~lLq~d~~eg~ALd~LGl~RyCCRRM~l~HVDlieKlL~y~~lek~   68 (69)
T KOG3497|consen    1 MIIPIRCFTCGKVIGDKWETYLELLQADYTEGDALDALGLKRYCCRRMLLTHVDLIEKLLNYNPLEKF   68 (69)
T ss_pred             CeeeeEeeeccccccccHHHHHHHHHHhhccchHHHHhhhHHHHHHHHHHHHHHHHHHHHccCccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999998875

>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2

Probab=100.00  E-value=4.4e-45  Score=222.64  Aligned_cols=60  Identities=75%  Similarity=1.389  Sum_probs=51.4

Q ss_pred             CcccccccCCCccccchHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhHHHHHHHh
Q 035172            1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL   60 (71)
Q Consensus         1 MiiPvRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthvdlid~ll   60 (71)
                      ||||||||||||+|||+||+|++++++|++|++|||+||++|||||||||||||+||+|+
T Consensus         1 MiiPVRCFTCGkvi~~~~e~y~~~~~~~~~~~~~Ld~LG~~ryCCRrmlLshvdli~~ll   60 (60)
T PF01194_consen    1 MIIPVRCFTCGKVIGNKWEEYLERLENGEDPGDALDDLGLKRYCCRRMLLSHVDLIDKLL   60 (60)
T ss_dssp             ---SSS-STTTSBTCGHHHHHHHHHHTTS-HHHHHHHTT-SSHHHHHHHHTB--THHHHH
T ss_pred             CCCceecCCCCCChhHhHHHHHHHHHcCCCHHHHHHHhCCceeehhhHHHHHHHHHHHhC
Confidence            999999999999999999999999999999999999999999999999999999999986

7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....

>PHA03082 DNA-dependent RNA polymerase subunit; Provisional

Probab=99.33  E-value=1.8e-13  Score=84.22  Aligned_cols=49  Identities=27%  Similarity=0.575  Sum_probs=46.4

Q ss_pred             CcccccccCCCccccchHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhHH
Q 035172            1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVD   54 (71)
Q Consensus         1 MiiPvRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthvd   54 (71)
                      |+||+.|.|||+.+|+  |+|..++ ...+.++||.  ++++.|||-.|.||+|
T Consensus         1 MVf~lVCsTCGrDlSe--eRy~Lli-~~~~L~~Vl~--~v~~~CCRlKLsTQIE   49 (63)
T PHA03082          1 MVFQLVCSTCGRDLSE--ERYRLLI-KKKSLKKVLR--TVKNSCCRLKLSTQIE   49 (63)
T ss_pred             CeeeeeecccCcchhH--HHHHHHH-HHhhHHHHHH--Hhhccceeeeeecccc
Confidence            8999999999999999  9999999 5589999999  9999999999999987

>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 DNA-directed RNA polymerases 2

Probab=99.32  E-value=2.2e-13  Score=83.87  Aligned_cols=49  Identities=27%  Similarity=0.603  Sum_probs=46.3

Q ss_pred             CcccccccCCCccccchHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhHH
Q 035172            1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVD   54 (71)
Q Consensus         1 MiiPvRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthvd   54 (71)
                      |+||+.|.|||+.||+  |+|..++ +..+.++||.  ++++.|||-.|.||+|
T Consensus         1 MVf~lvCSTCGrDlSe--eRy~Lli-~~~~Lk~Vl~--~v~n~CCRlKLsTQIE   49 (63)
T PF05864_consen    1 MVFQLVCSTCGRDLSE--ERYRLLI-KEMSLKKVLR--TVKNSCCRLKLSTQIE   49 (63)
T ss_pred             CeeeeeecccCCcchH--HHHHHHH-HHhhHHHHHH--Hhhccceeeeeccccc
Confidence            8999999999999999  9999999 5589999999  9999999999999987

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. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent

>PRK00418 DNA gyrase inhibitor; Reviewed

Probab=87.17  E-value=0.18  Score=31.01  Aligned_cols=14  Identities=50%  Similarity=0.904  Sum_probs=11.5

Q ss_pred             CcccccccCCCccc
Q 035172            1 MIIPVRCFTCGKVI   14 (71)
Q Consensus         1 MiiPvRCfTCGkvi   14 (71)
                      |...|+|++|||.+
T Consensus         3 ~~~~v~CP~C~k~~   16 (62)
T PRK00418          3 ETITVNCPTCGKPV   16 (62)
T ss_pred             CCccccCCCCCCcc
Confidence            34568999999997

>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=80.36  E-value=0.78  Score=28.60  Aligned_cols=13  Identities=54%  Similarity=0.948  Sum_probs=10.8

Q ss_pred             cccccccCCCccc
Q 035172            2 IIPVRCFTCGKVI   14 (71)
Q Consensus         2 iiPvRCfTCGkvi   14 (71)
                      ++-|-|+||||++
T Consensus         5 ~~~v~CP~Cgkpv   17 (65)
T COG3024           5 RITVPCPTCGKPV   17 (65)
T ss_pred             cccccCCCCCCcc
Confidence            3557799999998

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	71
3h0g_J	71	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		7e-26
1i3q_J	70	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		1e-23
2pmz_N	66	Archaeal Rna Polymerase From Sulfolobus Solfataricu		8e-16
2waq_N	66	The Complete Structure Of The Archaeal 13-Subunit D		2e-15
1ef4_A	55	Solution Structure Of The Essential Rna Polymerase		1e-08

>pdb|3H0G|J Chain J, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 71

Iteration: 1
 Score =  112 bits (279), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 52/68 (76%), Positives = 58/68 (85%)
Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIP+RCF+CGKVIG+KWDTYL LLQ D  EG+ALD LGL RYCCRRM++THVDLIEKLL
Sbjct: 1  MIIPIRCFSCGKVIGDKWDTYLTLLQEDNTEGEALDKLGLQRYCCRRMILTHVDLIEKLL 60
Query: 61 NYNTLDKS 68
           YN L K 
Sbjct: 61 CYNPLSKQ 68

>pdb|1I3Q|J Chain J, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 70

Iteration: 1
 Score =  104 bits (260), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 48/70 (68%), Positives = 58/70 (82%), Gaps = 1/70 (1%)
Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQAD-YPEGDALDALGLVRYCCRRMLMTHVDLIEKL 59
          MI+PVRCF+CGKV+G+KW++YL+LLQ D   EG AL  LGL RYCCRRM++THVDLIEK 
Sbjct: 1  MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF 60
Query: 60 LNYNTLDKSD 69
          L YN L+K D
Sbjct: 61 LRYNPLEKRD 70

>pdb|2PMZ|N Chain N, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 66

Iteration: 1
 Score = 78.6 bits (192), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 31/62 (50%), Positives = 47/62 (75%)
Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          M+IP+RCFTCG +I +KW +++  + A    G  LD LG+ RYCCRRML++HVD+I +++
Sbjct: 1  MLIPIRCFTCGSLIADKWQSFITRVNAGENPGKVLDDLGVKRYCCRRMLLSHVDIINEVI 60
Query: 61 NY 62
          +Y
Sbjct: 61 HY 62

>pdb|2WAQ|N Chain N, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 66

Iteration: 1
 Score = 77.4 bits (189), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 30/63 (47%), Positives = 46/63 (73%)
Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          M+IP+RCFTCG +I +KW  ++  + A    G  LD LG+ RYCCRRML++H+D+I +++
Sbjct: 1  MMIPIRCFTCGSLIADKWQPFITRVNAGENPGKVLDDLGVKRYCCRRMLLSHIDIISEVI 60
Query: 61 NYN 63
          +Y 
Sbjct: 61 HYT 63

>pdb|1EF4|A Chain A, Solution Structure Of The Essential Rna Polymerase Subunit Rpb10 From Methanobacterium Thermoautotrophicum Length = 55

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/52 (48%), Positives = 33/52 (63%)
Query: 3  IPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVD 54
          IPVRC +CGK +   ++ Y   +       D LD LGL RYCCRRML++HV+
Sbjct: 2  IPVRCLSCGKPVSAYFNEYQRRVADGEDPKDVLDDLGLKRYCCRRMLISHVE 53
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	71
1twf_J	70	DNA-directed RNA polymerases I, II, and III 8.3 K	3e-37
4ayb_N	66	DNA-directed RNA polymerase; transferase, multi-su	5e-36
1ef4_A	55	Subunit N, DNA-directed RNA polymerase; three heli	3e-30

>1twf_J DNA-directed RNA polymerases I, II, and III 8.3 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.11.1 PDB: 1i3q_J 1i6h_J 1k83_J* 1nik_J 1nt9_J 1pqv_J 1r5u_J 1r9s_J* 1r9t_J* 1sfo_J* 1twa_J* 1twc_J* 1i50_J* 1twg_J* 1twh_J* 1wcm_J 1y1v_J 1y1w_J 1y1y_J 1y77_J* ... Length = 70

 Score =  117 bits (295), Expect = 3e-37
 Identities = 48/70 (68%), Positives = 58/70 (82%), Gaps = 1/70 (1%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQAD-YPEGDALDALGLVRYCCRRMLMTHVDLIEKL 59
          MI+PVRCF+CGKV+G+KW++YL+LLQ D   EG AL  LGL RYCCRRM++THVDLIEK 
Sbjct: 1  MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF 60

Query: 60 LNYNTLDKSD 69
          L YN L+K D
Sbjct: 61 LRYNPLEKRD 70

>4ayb_N DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_N 2y0s_N 2waq_N 4b1o_N 4b1p_O 2pmz_N 3hkz_N Length = 66

 Score =  114 bits (288), Expect = 5e-36
 Identities = 30/63 (47%), Positives = 46/63 (73%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          M+IP+RCFTCG +I +KW  ++  + A    G  LD LG+ RYCCRRML++H+D+I +++
Sbjct: 1  MMIPIRCFTCGSLIADKWQPFITRVNAGENPGKVLDDLGVKRYCCRRMLLSHIDIISEVI 60

Query: 61 NYN 63
          +Y 
Sbjct: 61 HYT 63

>1ef4_A Subunit N, DNA-directed RNA polymerase; three helix bundle, zinc binding, structural genomics, PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: a.4.11.1 Length = 55

 Score = 99.7 bits (249), Expect = 3e-30
 Identities = 25/53 (47%), Positives = 34/53 (64%)

Query: 2  IIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVD 54
          +IPVRC +CGK +   ++ Y   +       D LD LGL RYCCRRML++HV+
Sbjct: 1  MIPVRCLSCGKPVSAYFNEYQRRVADGEDPKDVLDDLGLKRYCCRRMLISHVE 53

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	71
1twf_J	70	DNA-directed RNA polymerases I, II, and III 8.3 K	100.0
4ayb_N	66	DNA-directed RNA polymerase; transferase, multi-su	100.0
1ef4_A	55	Subunit N, DNA-directed RNA polymerase; three heli	100.0
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	85.83
2fk4_A	75	Protein E6; zinc binding domain, oncoprotein, meta	83.88
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	82.59

>1twf_J DNA-directed RNA polymerases I, II, and III 8.3 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.11.1 PDB: 1i3q_J 1i6h_J 1k83_J* 1nik_J 1nt9_J 1pqv_J 1r5u_J 1r9s_J* 1r9t_J* 1sfo_J* 1twa_J* 1twc_J* 1i50_J* 1twg_J* 1twh_J* 1wcm_J 1y1v_J 1y1w_J 1y1y_J 1y77_J* ...

Probab=100.00  E-value=2.8e-47  Score=237.22  Aligned_cols=68  Identities=69%  Similarity=1.344  Sum_probs=63.6

Q ss_pred             CcccccccCCCccccchHHHHHHHHHccC-ChhhHHHhcCCcchhhhhHHHHhHHHHHHHhccCccccc
Q 035172            1 MIIPVRCFTCGKVIGNKWDTYLDLLQADY-PEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNTLDKS   68 (71)
Q Consensus         1 MiiPvRCfTCGkvi~~~~e~y~~~v~~~~-~~~~vLd~Lg~~ryCCRrmllthvdlid~ll~y~~~~~~   68 (71)
                      ||||||||||||+|||+||+|++++++|+ +|++|||+||++|||||||||||||+||+|++|++.+++
T Consensus         1 MiiPVRCFTCGkvi~~~we~y~~~~~~g~l~~~~~LD~Lg~~RyCCRrMllthvdlie~ll~y~~~~~~   69 (70)
T 1twf_J            1 MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNPLEKR   69 (70)
T ss_dssp             CCCCSBCTTTCCBCTTCHHHHHHHHHTSCCCHHHHHHHTTCCSHHHHHHHHTBCCTHHHHHTCCC----
T ss_pred             CCCCeecCCCCCChHHHHHHHHHHHHcCCCCHHHHHHHcCCcccchhhHHHHHHHHHHHHhcCCccccC
Confidence            99999999999999999999999999999 999999999999999999999999999999999987764

>4ayb_N DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_N 2y0s_N 2waq_N 4b1o_N 4b1p_O 2pmz_N 3hkz_N

Probab=100.00  E-value=2.2e-46  Score=231.16  Aligned_cols=64  Identities=47%  Similarity=1.137  Sum_probs=63.1

Q ss_pred             CcccccccCCCccccchHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhHHHHHHHhccCc
Q 035172            1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNT   64 (71)
Q Consensus         1 MiiPvRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthvdlid~ll~y~~   64 (71)
                      ||||||||||||+|||+|++|++++++|+++++|||+||++|||||||||||||+||+|++|+.
T Consensus         1 MiIPVRCFTCGkvi~~k~~~y~~~~~~~~~~g~~LD~Lgl~ryCCRRm~LtHVdlid~ll~y~~   64 (66)
T 4ayb_N            1 MMIPIRCFTCGSLIADKWQPFITRVNAGENPGKVLDDLGVKRYCCRRMLLSHIDIISEVIHYTR   64 (66)
T ss_dssp             CCCCSBCTTTCCBCHHHHHHHHHHHHTTCCHHHHHHHSSCCSSHHHHHHHTCCCCTTTTSTTCC
T ss_pred             CCCCcccCCCcHhHHHHHHHHHHHHhcCCCHHHHHHHhCCceechhhhHHHHHHHHHHHHccCC
Confidence            9999999999999999999999999999999999999999999999999999999999999984

>1ef4_A Subunit N, DNA-directed RNA polymerase; three helix bundle, zinc binding, structural genomics, PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: a.4.11.1

Probab=100.00  E-value=1e-42  Score=208.51  Aligned_cols=55  Identities=45%  Similarity=0.944  Sum_probs=53.8

Q ss_pred             cccccccCCCccccchHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhHHHH
Q 035172            2 IIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLI   56 (71)
Q Consensus         2 iiPvRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthvdli   56 (71)
                      |||||||||||+|||+||+|++++++|++|+||||+||++|||||||||||||+|
T Consensus         1 iiPVRCFTCGkvi~~~we~y~~~~~~~~~~~~~LD~Lg~~RyCCRRMlLthvdli   55 (55)
T 1ef4_A            1 MIPVRCLSCGKPVSAYFNEYQRRVADGEDPKDVLDDLGLKRYCCRRMLISHVETW   55 (55)
T ss_dssp             CCSSSCSCTTSCCHHHHHHHHHHHHHTCCHHHHHHHHTCSSHHHHHHHTTTCCCC
T ss_pred             CCCeecCCCCCChhHHHHHHHHHHHcCCCHHHHHHHcCCceEeccccceeheecC
Confidence            7999999999999999999999999999999999999999999999999999975

>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A

Probab=85.83  E-value=0.25  Score=24.50  Aligned_cols=10  Identities=50%  Similarity=1.364  Sum_probs=8.4

Q ss_pred             cccccCCCcc
Q 035172            4 PVRCFTCGKV   13 (71)
Q Consensus         4 PvRCfTCGkv   13 (71)
                      ++.||.||+.
T Consensus         6 ~~~C~nCgk~   15 (29)
T 1nc8_A            6 VIRCWNCGKE   15 (29)
T ss_dssp             CCBCTTTSCB
T ss_pred             CCEEEECCcc
Confidence            4679999986

>2fk4_A Protein E6; zinc binding domain, oncoprotein, metal binding protein; NMR {Human papillomavirus type 16} SCOP: g.90.1.1 PDB: 2ljz_A

Probab=83.88  E-value=0.7  Score=27.84  Aligned_cols=25  Identities=20%  Similarity=0.474  Sum_probs=17.4

Q ss_pred             ccccccCCCccccchHHHHHHHHHccC
Q 035172            3 IPVRCFTCGKVIGNKWDTYLDLLQADY   29 (71)
Q Consensus         3 iPvRCfTCGkvi~~~~e~y~~~v~~~~   29 (71)
                      |+|||..|+|+++.  .|=+..+..++
T Consensus        23 i~IRC~~C~k~L~~--~EK~~~~~~~~   47 (75)
T 2fk4_A           23 LLIRCINCQKPLSP--EEKQRHLDKKQ   47 (75)
T ss_dssp             SCCCCSSSCCCCCH--HHHHHHHHHCS
T ss_pred             EEEEhHHcCCcCCH--HHHHHHHHCCC
Confidence            78999999999976  44344343443

>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} SCOP: g.40.1.1

Probab=82.59  E-value=0.44  Score=23.12  Aligned_cols=10  Identities=50%  Similarity=1.195  Sum_probs=8.2

Q ss_pred             cccccCCCcc
Q 035172            4 PVRCFTCGKV   13 (71)
Q Consensus         4 PvRCfTCGkv   13 (71)
                      ++.||.||+.
T Consensus         2 ~~~Cf~CG~~   11 (26)
T 1dsq_A            2 GPVCFSCGKT   11 (26)
T ss_dssp             CCBCTTTCCB
T ss_pred             CCeeEeCCCC
Confidence            4689999985

---

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	71
d1twfj_	65	a.4.11.1 (J:) RNA polymerase subunit RPB10 {Baker'	8e-36
d1ef4a_	55	a.4.11.1 (A:) RNA polymerase subunit RPB10 {Archae	7e-32

>d1twfj_ a.4.11.1 (J:) RNA polymerase subunit RPB10 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 65

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: RNA polymerase subunit RPB10
family: RNA polymerase subunit RPB10
domain: RNA polymerase subunit RPB10
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  112 bits (283), Expect = 8e-36
 Identities = 45/64 (70%), Positives = 54/64 (84%), Gaps = 1/64 (1%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQAD-YPEGDALDALGLVRYCCRRMLMTHVDLIEKL 59
          MI+PVRCF+CGKV+G+KW++YL+LLQ D   EG AL  LGL RYCCRRM++THVDLIEK 
Sbjct: 1  MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF 60

Query: 60 LNYN 63
          L YN
Sbjct: 61 LRYN 64

>d1ef4a_ a.4.11.1 (A:) RNA polymerase subunit RPB10 {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 55

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: RNA polymerase subunit RPB10
family: RNA polymerase subunit RPB10
domain: RNA polymerase subunit RPB10
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

 Score =  102 bits (257), Expect = 7e-32
 Identities = 25/53 (47%), Positives = 34/53 (64%)

Query: 2  IIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVD 54
          +IPVRC +CGK +   ++ Y   +       D LD LGL RYCCRRML++HV+
Sbjct: 1  MIPVRCLSCGKPVSAYFNEYQRRVADGEDPKDVLDDLGLKRYCCRRMLISHVE 53

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	71
d1twfj_	65	RNA polymerase subunit RPB10 {Baker's yeast (Sacch	100.0
d1ef4a_	55	RNA polymerase subunit RPB10 {Archaeon Methanobact	100.0
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	91.15
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	90.75
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	84.0

>d1twfj_ a.4.11.1 (J:) RNA polymerase subunit RPB10 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: RNA polymerase subunit RPB10
family: RNA polymerase subunit RPB10
domain: RNA polymerase subunit RPB10
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.7e-45  Score=225.04  Aligned_cols=64  Identities=70%  Similarity=1.377  Sum_probs=62.5

Q ss_pred             CcccccccCCCccccchHHHHHHHHHccC-ChhhHHHhcCCcchhhhhHHHHhHHHHHHHhccCc
Q 035172            1 MIIPVRCFTCGKVIGNKWDTYLDLLQADY-PEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNT   64 (71)
Q Consensus         1 MiiPvRCfTCGkvi~~~~e~y~~~v~~~~-~~~~vLd~Lg~~ryCCRrmllthvdlid~ll~y~~   64 (71)
                      ||||||||||||+|||+|++|++++++|+ ++++|||+||++|||||||||||||+||++++|+|
T Consensus         1 MiIPVRCFTCgkvi~~k~~~y~~~~~~~~~~~~~~Ld~Lgl~RyCCRrm~Lshvdlid~l~~y~p   65 (65)
T d1twfj_           1 MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNP   65 (65)
T ss_dssp             CCCCSBCTTTCCBCTTCHHHHHHHHHTSCCCHHHHHHHTTCCSHHHHHHHHTBCCTHHHHHTCCC
T ss_pred             CCCCcccCCCCcChHHHHHHHHHHHHcCCCCHHHHHHHcCCceeehhhHHHHHHHHHHHhhcCCC
Confidence            99999999999999999999999999997 88999999999999999999999999999999986

>d1ef4a_ a.4.11.1 (A:) RNA polymerase subunit RPB10 {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: RNA polymerase subunit RPB10
family: RNA polymerase subunit RPB10
domain: RNA polymerase subunit RPB10
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=100.00  E-value=3e-40  Score=196.36  Aligned_cols=54  Identities=46%  Similarity=0.973  Sum_probs=52.9

Q ss_pred             cccccccCCCccccchHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhHHH
Q 035172            2 IIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDL   55 (71)
Q Consensus         2 iiPvRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthvdl   55 (71)
                      |||||||||||+||++|++|++++++|+++++|||+||++|||||||||||||.
T Consensus         1 iIPVRCFTCGkvia~k~~~y~~~~~~~~~~~~~LD~Lgl~RyCCRRm~LshVD~   54 (55)
T d1ef4a_           1 MIPVRCLSCGKPVSAYFNEYQRRVADGEDPKDVLDDLGLKRYCCRRMLISHVET   54 (55)
T ss_dssp             CCSSSCSCTTSCCHHHHHHHHHHHHHTCCHHHHHHHHTCSSHHHHHHHTTTCCC
T ss_pred             CCCcCcCCCchhHHHHHHHHHHHHHcCCCHHHHHHHcCCeeeccchhHHhcccc
Confidence            799999999999999999999999999999999999999999999999999984

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=91.15  E-value=0.031  Score=28.00  Aligned_cols=10  Identities=50%  Similarity=1.364  Sum_probs=8.7

Q ss_pred             cccccCCCcc
Q 035172            4 PVRCFTCGKV   13 (71)
Q Consensus         4 PvRCfTCGkv   13 (71)
                      +|.||.|||.
T Consensus         6 ~ikCfNCGke   15 (29)
T d1nc8a_           6 VIRCWNCGKE   15 (29)
T ss_dssp             CCBCTTTSCB
T ss_pred             eeEeecCCcc
Confidence            5889999985

>d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=90.75  E-value=0.033  Score=27.11  Aligned_cols=8  Identities=63%  Similarity=1.634  Sum_probs=6.9

Q ss_pred             cccCCCcc
Q 035172            6 RCFTCGKV   13 (71)
Q Consensus         6 RCfTCGkv   13 (71)
                      .||||||-
T Consensus         4 vcfscgkt   11 (26)
T d1dsqa_           4 VCFSCGKT   11 (26)
T ss_dssp             BCTTTCCB
T ss_pred             EEEecCCc
Confidence            59999984

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=84.00  E-value=0.41  Score=25.24  Aligned_cols=30  Identities=13%  Similarity=0.088  Sum_probs=26.6

Q ss_pred             ccchHHHHHHHHHccCChhhHHHhcCCcch
Q 035172           14 IGNKWDTYLDLLQADYPEGDALDALGLVRY   43 (71)
Q Consensus        14 i~~~~e~y~~~v~~~~~~~~vLd~Lg~~ry   43 (71)
                      -.+.|++-+.++++|++..++-..+|+.|-
T Consensus         7 t~~q~~~a~~l~~~G~s~~~iA~~~gVSr~   36 (47)
T d1ijwc_           7 NKHEQEQISRLLEKGHPRQQLAIIFGIGVS   36 (47)
T ss_dssp             CHHHHHHHHHHHHTTCCHHHHHHHHTCCHH
T ss_pred             CHHHHHHHHHHHHCCCCHHHHHHHHCcCHH
Confidence            356899999999999999999999999863