Citrus Sinensis ID: 028639

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200------
Protein Sequence
MEKGGGGKGGGVGGGGKTSLKSIPASLGGKDDNSAKSKRGRKVQFNTEGLSEGKFTFSSKSDGKFETTYGKGGLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKVWLV
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccHHHHHcccEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHccccccHHHHHHHHHHHHHccccHHHHHHHHHcccccHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccHHHHcccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccHccHHHcccccHccccHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccHHHHHHHHccccccHHHHHHHcccHEEEEc
Coil and Loop (DISEMBL)
mekggggkgggvggggktslksipaslggkddnsakskrgrkvqfnteglsegkftfssksdgkfettygkggltkggkgdkvangakVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMAllsadptikipvsfdkgllyakthshftnpqAVKGLFQSLsehgvtdgeicVIANICPETVEEAYAIVPSLKVWLV
Flexible Loop (DISEMBL)
mekggggkgggvggggktslksipaslggkddnsakskrgrkvqfnteglsegkftfssksdgkfettygkggltkggkgdkvangAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKVWLV
Low Complexity Region (SEG)
MEkggggkgggvggggkTSLKSIPASLGGKDDNSAKSKRGRKVQFNTEGLSEGKFTFSSKSDGKFEttygkggltkggkgDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKVWLV
Disordered region (IsUnstruct)
**************************************************************************************AKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKVWL*
Disordered Region (DISOPRED)
******************************************************************************************************EQELPKNAKCLMDCEAAHILE*******************SFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKVWLV
Disordered Region (DISEMBL)
***************GKTSLKSIPAS***************KVQFNTEGLSEGKFTFSSKSDGKFETTYGKGGLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKVWLV
Disordered Region (DISPRO)
***********************************************************************************************LPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKVWLV
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEKGGGGKGGGVGGGGKTSLKSIPASLGGKDDNSAKSKRGRKVQFNTEGLSEGKFTFSSKSDGKFETTYGKGGLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKVWLV
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	206	2.2.26 [Sep-21-2011]
Q54S04	155	DNA-directed RNA polymera	yes	no	0.461	0.612	0.333	9e-08
Q9D7M8	142	DNA-directed RNA polymera	yes	no	0.451	0.654	0.305	9e-06
O15514	142	DNA-directed RNA polymera	yes	no	0.451	0.654	0.305	9e-06

>sp|Q54S04|RPB4_DICDI DNA-directed RNA polymerase II subunit rpb4 OS=Dictyostelium discoideum GN=polr2d PE=3 SV=1

 Score = 57.0 bits (136), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 36/108 (33%), Positives = 58/108 (53%), Gaps = 13/108 (12%)

Query: 108 KNAKCLMDCEAAHILE---GIQEQ----------MALLSADPTIKIPVSFDKGLLYAKTH 154
           K+AK L++ E A +LE   GI E           +  L  +    I  +F K L YA+  
Sbjct: 27  KDAKFLLNSEVAILLEHRKGISESEGTEFPQNTLLIHLYYNSINDIIRTFHKTLAYAEKF 86

Query: 155 SHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLK 202
           S + N  ++K +  +LS+  + + EI  +AN+CPE  +EA +++PSLK
Sbjct: 87  SRYKNKTSIKQVRTALSKQNLEEFEIASLANLCPEISDEAKSLIPSLK 134

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. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA.
Dictyostelium discoideum (taxid: 44689)

>sp|Q9D7M8|RPB4_MOUSE DNA-directed RNA polymerase II subunit RPB4 OS=Mus musculus GN=Polr2d PE=2 SV=2

 Score = 50.4 bits (119), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 29/95 (30%), Positives = 51/95 (53%), Gaps = 2/95 (2%)

Query: 108 KNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF 167
           + A+ L++ E   +LE  ++Q    SA+   ++   F K L Y    S F N + +  + 
Sbjct: 27  ETAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNYTARFSRFKNRETIASVR 84

Query: 168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLK 202
             L +  +   E+  +AN+CPET EE+ A++PSL+
Sbjct: 85  SLLLQKKLHKFELACLANLCPETAEESKALIPSLE 119

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. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA.

Mus musculus (taxid: 10090)

>sp|O15514|RPB4_HUMAN DNA-directed RNA polymerase II subunit RPB4 OS=Homo sapiens GN=POLR2D PE=1 SV=1

 Score = 50.4 bits (119), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 29/95 (30%), Positives = 51/95 (53%), Gaps = 2/95 (2%)

Query: 108 KNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF 167
           + A+ L++ E   +LE  ++Q    SA+   ++   F K L Y    S F N + +  + 
Sbjct: 27  ETAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNYTARFSRFKNRETIASVR 84

Query: 168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLK 202
             L +  +   E+  +AN+CPET EE+ A++PSL+
Sbjct: 85  SLLLQKKLHKFELACLANLCPETAEESKALIPSLE 119

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. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	206
225468957	239	PREDICTED: uncharacterized protein LOC10	0.956	0.824	0.613	2e-61
255568114	203	conserved hypothetical protein [Ricinus	0.859	0.871	0.583	3e-59
449491225	220	PREDICTED: DNA-directed RNA polymerase I	0.859	0.804	0.557	4e-50
449434414	242	PREDICTED: uncharacterized protein LOC10	0.859	0.731	0.557	1e-49
356532865	211	PREDICTED: DNA-directed RNA polymerase I	0.888	0.867	0.485	3e-45
224124738	197	predicted protein [Populus trichocarpa]	0.694	0.725	0.548	3e-45
388515433	201	unknown [Medicago truncatula]	0.830	0.850	0.497	3e-41
357448135	223	DNA-directed RNA polymerase II subunit r	0.752	0.695	0.517	1e-39
297804626	210	At4g15950 [Arabidopsis lyrata subsp. lyr	0.868	0.852	0.442	8e-34
334186572	205	RNA polymerase II, Rpb4, core protein [A	0.854	0.858	0.427	3e-32

>gi|225468957|ref|XP_002274855.1| PREDICTED: uncharacterized protein LOC100246461 isoform 1 [Vitis vinifera] gi|359495604|ref|XP_003635035.1| PREDICTED: uncharacterized protein LOC100246461 isoform 2 [Vitis vinifera] gi|297736694|emb|CBI25730.3| unnamed protein product [Vitis vinifera]

 Score =  240 bits (613), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 122/199 (61%), Positives = 154/199 (77%), Gaps = 2/199 (1%)

Query: 6   GGKGGGVGGG-GKTSLKS-IPASLGGKDDNSAKSKRGRKVQFNTEGLSEGKFTFSSKSDG 63
           GGKG  +    GK+S KS + ASL GKDD++AKSKRGRKVQFN  GL E + T S  S G
Sbjct: 5   GGKGFSLNSNLGKSSTKSPLEASLTGKDDSAAKSKRGRKVQFNNGGLPEARLTSSLMSGG 64

Query: 64  KFETTYGKGGLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILE 123
           K +    KG L+KGGKG +V NG K +V K   PLELR+EQELPKNAKC+MDCEAA IL+
Sbjct: 65  KTDIPIAKGDLSKGGKGGRVLNGEKSAVPKPPAPLELRIEQELPKNAKCMMDCEAALILK 124

Query: 124 GIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVI 183
           GIQEQM +LS DPTIKIP+SF+KGL YA++ + + +PQ+V+ + + LS++GV+DGEICVI
Sbjct: 125 GIQEQMVVLSEDPTIKIPLSFNKGLQYAQSSNCYASPQSVRLVLEPLSKYGVSDGEICVI 184

Query: 184 ANICPETVEEAYAIVPSLK 202
           AN CPET++E +A+VPSLK
Sbjct: 185 ANTCPETIDEVFALVPSLK 203

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255568114|ref|XP_002525033.1| conserved hypothetical protein [Ricinus communis] gi|223535695|gb|EEF37360.1| conserved hypothetical protein [Ricinus communis]

 Score =  233 bits (594), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 119/204 (58%), Positives = 150/204 (73%), Gaps = 27/204 (13%)

Query: 1   MEKGGGGKGGGVGGGG-KTSLKSI-PASLGGKDDNSAKSKRGRKVQFNTEGLSEGKFTFS 58
           MEKGG  KG  + G G K+SLKSI PAS  GKDD SAKSKRG+KVQFN++G         
Sbjct: 1   MEKGG--KGFSLPGKGLKSSLKSITPASTKGKDDTSAKSKRGKKVQFNSQG--------- 49

Query: 59  SKSDGKFETTYGKGGLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEA 118
                          ++KGGKGDKV+NG K+S  KE  PLEL++EQ+LPKNAKCLMDCEA
Sbjct: 50  --------------NMSKGGKGDKVSNGVKISSTKEPQPLELKIEQDLPKNAKCLMDCEA 95

Query: 119 AHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDG 178
           A +L+GIQEQM LLS DPTIK+PVSFD+ L +A+T + FTNPQ+V+ + + L +HGV++G
Sbjct: 96  AQVLQGIQEQMVLLSRDPTIKLPVSFDRALQHARTGARFTNPQSVRRILEGLKKHGVSEG 155

Query: 179 EICVIANICPETVEEAYAIVPSLK 202
           EIC IAN+CP+ V+E +A+VPSLK
Sbjct: 156 EICTIANVCPDGVDEVFALVPSLK 179

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449491225|ref|XP_004158834.1| PREDICTED: DNA-directed RNA polymerase II subunit rpb4-like [Cucumis sativus]

 Score =  203 bits (516), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 107/192 (55%), Positives = 137/192 (71%), Gaps = 15/192 (7%)

Query: 16  GKTSLKSIP---ASLGGKDDNSAKSKRGRKVQFNTEGLSEGKFTFSSKSDGKFETTYGKG 72
            K+SLKS     ASL GKDD+ +K K+GRKVQF+ +G  +   TFS K  GK       G
Sbjct: 16  AKSSLKSSALKDASLKGKDDSLSKLKKGRKVQFDAQGSVDATNTFSMKYSGK------NG 69

Query: 73  GLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKC--LMDCEAAHILEGIQEQMA 130
            L KGGKG   AN  K S+ KE   LEL++EQELPKN KC  LMDCEAA +L+GIQ+QM 
Sbjct: 70  DLGKGGKG---AN-TKASIAKEPQALELKIEQELPKNVKCQCLMDCEAAQLLQGIQDQMV 125

Query: 131 LLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPET 190
            LSADPTIKIP SFD+GL YAK  +H+ N ++V+ + ++L ++GVTD EICVIAN+CP+T
Sbjct: 126 FLSADPTIKIPTSFDRGLQYAKRANHYVNAESVRPVLETLKKYGVTDSEICVIANVCPDT 185

Query: 191 VEEAYAIVPSLK 202
            +E +A++PSLK
Sbjct: 186 TDEVFALLPSLK 197

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434414|ref|XP_004134991.1| PREDICTED: uncharacterized protein LOC101213971 [Cucumis sativus]

 Score =  201 bits (512), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 107/192 (55%), Positives = 137/192 (71%), Gaps = 15/192 (7%)

Query: 16  GKTSLKSIP---ASLGGKDDNSAKSKRGRKVQFNTEGLSEGKFTFSSKSDGKFETTYGKG 72
            K+SLKS     ASL GKDD+ +K K+GRKVQF+ +G  +   TFS K  GK       G
Sbjct: 16  AKSSLKSSALKDASLKGKDDSLSKLKKGRKVQFDAQGSVDATNTFSMKYSGK------NG 69

Query: 73  GLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKC--LMDCEAAHILEGIQEQMA 130
            L KGGKG   AN  K S+ KE   LEL++EQELPKN KC  LMDCEAA +L+GIQ+QM 
Sbjct: 70  DLGKGGKG---AN-TKASIAKEPQALELKIEQELPKNVKCQCLMDCEAAQLLQGIQDQMV 125

Query: 131 LLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPET 190
            LSADPTIKIP SFD+GL YAK  +H+ N ++V+ + ++L ++GVTD EICVIAN+CP+T
Sbjct: 126 FLSADPTIKIPTSFDRGLQYAKRANHYVNAESVRPVLETLKKYGVTDSEICVIANVCPDT 185

Query: 191 VEEAYAIVPSLK 202
            +E +A++PSLK
Sbjct: 186 TDEVFALLPSLK 197

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356532865|ref|XP_003534990.1| PREDICTED: DNA-directed RNA polymerase II subunit rpb4-like [Glycine max]

 Score =  187 bits (474), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 100/206 (48%), Positives = 135/206 (65%), Gaps = 23/206 (11%)

Query: 1   MEKGGGGKG----GGVGGGGKTSLKSIPASLGGKDDNSAKSKRGRKVQFNTEGLSEGKFT 56
           MEKGG G      GG+G            SL GKDD + KS +GR+VQF+T+G       
Sbjct: 1   MEKGGKGASLFSKGGLG------------SLKGKDDIATKSAKGRRVQFSTDGP-----L 43

Query: 57  FSSKSDGKFETTYGKGGLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDC 116
           F S       T+   GG  KGG GD VA G K S  K++ P + RV+Q+LP+N KCLMDC
Sbjct: 44  FESGVSSNSATSLKSGG--KGGMGDNVAKGGKNSQSKDSHPSDYRVDQKLPENIKCLMDC 101

Query: 117 EAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVT 176
           EA  IL+GIQE+M +LS D T+K+P+SFDKGL YAK++S + + Q+++ +   L++ GVT
Sbjct: 102 EAVDILQGIQERMVMLSRDSTVKMPISFDKGLQYAKSNSKYLDLQSIRHILDRLAKCGVT 161

Query: 177 DGEICVIANICPETVEEAYAIVPSLK 202
           D EICVI N+CPET++E +A++PSLK
Sbjct: 162 DSEICVIGNVCPETIDEVFALLPSLK 187

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224124738|ref|XP_002329936.1| predicted protein [Populus trichocarpa] gi|222871958|gb|EEF09089.1| predicted protein [Populus trichocarpa]

 Score =  187 bits (474), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 91/166 (54%), Positives = 117/166 (70%), Gaps = 23/166 (13%)

Query: 37  SKRGRKVQFNTEGLSEGKFTFSSKSDGKFETTYGKGGLTKGGKGDKVANGAKVSVVKEAL 96
           S  GRK+ F +EG                        L+KGGKG K+ANG K  + KE  
Sbjct: 31  SNNGRKIHFESEG-----------------------NLSKGGKGGKIANGGKSPMTKEPP 67

Query: 97  PLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSH 156
           PLEL++E ELP+NAK LMDCEAA IL+GIQ+QM LLS DPTIK+PVSFDKGL YAK  +H
Sbjct: 68  PLELKIESELPQNAKPLMDCEAAQILQGIQDQMVLLSQDPTIKLPVSFDKGLQYAKNGAH 127

Query: 157 FTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLK 202
           +TNPQ+V+ + ++L ++GV+DGEI +IAN+ PET +EA+A+VPSLK
Sbjct: 128 YTNPQSVRRVLEALRKYGVSDGEISLIANVFPETADEAFALVPSLK 173

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388515433|gb|AFK45778.1| unknown [Medicago truncatula]

 Score =  174 bits (440), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 99/199 (49%), Positives = 129/199 (64%), Gaps = 28/199 (14%)

Query: 6   GGKGGGVGGGGKTSLKSIPASLGGKDDNSAKSKRGRKVQFNTEGLSEGKFTFSSKSDGKF 65
           GGKGG +   G          L GKDD++ KS + RKVQF +EGL      F S+S+G  
Sbjct: 5   GGKGGSLLSKG---------GLKGKDDSATKSAKARKVQF-SEGL------FESRSNGP- 47

Query: 66  ETTYGKGGLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGI 125
                    T GGKGDKVANG K S  K+    E RV+QELP+N KCLMDCEAA +L+GI
Sbjct: 48  ---------TSGGKGDKVANGGKSSAAKDPHQFEHRVDQELPENFKCLMDCEAAVMLQGI 98

Query: 126 QEQMALLSADPTIKIPVSFDKGL--LYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVI 183
           Q+QM  LS DP+IK+P SFDKGL    + + S ++NP++V+   + L  H +T+ EICVI
Sbjct: 99  QDQMVALSRDPSIKMPASFDKGLYYAKSSSSSKYSNPESVRHTLEPLMNHDLTESEICVI 158

Query: 184 ANICPETVEEAYAIVPSLK 202
           AN+CPET +E +A++PSLK
Sbjct: 159 ANVCPETADEVFALLPSLK 177

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357448135|ref|XP_003594343.1| DNA-directed RNA polymerase II subunit rpb4 [Medicago truncatula] gi|124360902|gb|ABN08874.1| RNA polymerase Rpb4 [Medicago truncatula] gi|355483391|gb|AES64594.1| DNA-directed RNA polymerase II subunit rpb4 [Medicago truncatula]

 Score =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 90/174 (51%), Positives = 119/174 (68%), Gaps = 19/174 (10%)

Query: 31  DDNSAKSKRGRKVQFNTEGLSEGKFTFSSKSDGKFETTYGKGGLTKGGKGDKVANGAKVS 90
           DD++ KS + RKVQF +EGL      F S+S+G           T GGKGDKVANG K S
Sbjct: 43  DDSATKSAKARKVQF-SEGL------FESRSNGP----------TSGGKGDKVANGGKSS 85

Query: 91  VVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGL-- 148
             K+    E RV+QELP+N KCLMDCEAA +L+GIQ+QM  LS DP+IK+P SFDKGL  
Sbjct: 86  AAKDPHQFEHRVDQELPENFKCLMDCEAAVMLQGIQDQMVALSRDPSIKMPASFDKGLYY 145

Query: 149 LYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLK 202
             + + S ++NP++V+   + L  H +T+ EICVIAN+CPET +E +A++PSLK
Sbjct: 146 AKSSSSSKYSNPESVRHTLEPLMNHDLTESEICVIANVCPETADEVFALLPSLK 199

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297804626|ref|XP_002870197.1| At4g15950 [Arabidopsis lyrata subsp. lyrata] gi|297316033|gb|EFH46456.1| At4g15950 [Arabidopsis lyrata subsp. lyrata]

 Score =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 85/192 (44%), Positives = 119/192 (61%), Gaps = 13/192 (6%)

Query: 13  GGGGKTSLKSIPASL--GGKDDNSAKSKRGRKVQFNTEGLSEGKFTFSSKSDGKFETTYG 70
           G G K+SLKS    L  GGKD NS K K+GRK+ F+ +G     +      +G  +    
Sbjct: 6   GKGLKSSLKSKDGFLVAGGKDGNSTKLKKGRKIHFD-QGTPPPNYKIL---NGSSDPLPF 61

Query: 71  KGGLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMA 130
           +    K GKGDK    +K S+       EL+   +LP+NA+C+MDCEA  IL+GI+  + 
Sbjct: 62  QSSAAKVGKGDKPTKSSKNSLQS----FELK---DLPENAECMMDCEAFQILDGIKGHLV 114

Query: 131 LLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPET 190
            LS DP+IKIPVS+D+ L Y  +  H++NPQ+V+ + + L  HGV+DGE+CVIAN  P+T
Sbjct: 115 GLSEDPSIKIPVSYDRALAYVDSCVHYSNPQSVRKVLEPLKTHGVSDGEMCVIANASPDT 174

Query: 191 VEEAYAIVPSLK 202
           V+E  A +PSLK
Sbjct: 175 VDEVLAFIPSLK 186

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334186572|ref|NP_193330.2| RNA polymerase II, Rpb4, core protein [Arabidopsis thaliana] gi|332658269|gb|AEE83669.1| RNA polymerase II, Rpb4, core protein [Arabidopsis thaliana]

 Score =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 82/192 (42%), Positives = 119/192 (61%), Gaps = 16/192 (8%)

Query: 13  GGGGKTSLKSIPASLGGKDDNSAKSKRGRKVQFNTEGLSEGKFTFSSKSDGK-FETTYGK 71
           G G K+SLKS     GGKD +S K K+GRK+ F+           +  SD + F+++  K
Sbjct: 6   GKGLKSSLKS---KDGGKDGSSTKLKKGRKIHFDQRTPPANYKILNVSSDQQPFQSSAAK 62

Query: 72  GGLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMAL 131
            G     K DK    +K S+       EL+   +LP+NA+C+MDCEA  IL+GI+ Q+  
Sbjct: 63  CG-----KSDKPTKSSKNSLHS----FELK---DLPENAECMMDCEAFQILDGIKGQLVG 110

Query: 132 LSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETV 191
           LS DP+IKIPVS+D+ L Y ++  H+TNPQ+V+ + + L  +G++DGE+CVIAN   E+V
Sbjct: 111 LSEDPSIKIPVSYDRALAYVESCVHYTNPQSVRKVLEPLKTYGISDGEMCVIANASSESV 170

Query: 192 EEAYAIVPSLKV 203
           +E  A +PSLK 
Sbjct: 171 DEVLAFIPSLKT 182

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	206
TAIR|locus:2178158	138	NRPB4 [Arabidopsis thaliana (t	0.5	0.746	0.490	3.9e-21
DICTYBASE|DDB_G0282739	155	rpb4 "DNA-directed RNA polymer	0.553	0.735	0.325	1.2e-08
ZFIN|ZDB-GENE-040714-2	145	polr2d "polymerase (RNA) II (D	0.558	0.793	0.302	1.1e-07
UNIPROTKB|F1P2S1	147	POLR2D "Uncharacterized protei	0.451	0.632	0.315	2.3e-07
WB|WBGene00018391	144	rpb-4 [Caenorhabditis elegans	0.427	0.611	0.344	2.9e-07
UNIPROTKB|Q1JQ91	142	POLR2D "Polymerase (RNA) II (D	0.451	0.654	0.305	4.8e-07
UNIPROTKB|E2RPH1	142	POLR2D "Uncharacterized protei	0.451	0.654	0.305	4.8e-07
UNIPROTKB|O15514	142	POLR2D "DNA-directed RNA polym	0.451	0.654	0.305	4.8e-07
MGI|MGI:1916491	142	Polr2d "polymerase (RNA) II (D	0.451	0.654	0.305	4.8e-07
RGD|1308565	142	Polr2d "polymerase (RNA) II (D	0.451	0.654	0.305	4.8e-07

TAIR|locus:2178158 NRPB4 [Arabidopsis thaliana (taxid:3702)]

 Score = 248 (92.4 bits), Expect = 3.9e-21, P = 3.9e-21
 Identities = 51/104 (49%), Positives = 70/104 (67%)

Query:    99 ELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFT 158
             EL++  E  K AKCLM+CE + ILE   EQ+  +S DP  ++   F+K L Y K  S + 
Sbjct:    11 ELKIGDEFLK-AKCLMNCEVSLILEHKFEQLQQISEDPMNQVSQVFEKSLQYVKRFSRYK 69

Query:   159 NPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLK 202
             NP AV+ + + LS H +T+ E+CV+ N+CPETVEEA A+VPSLK
Sbjct:    70 NPDAVRQVREILSRHQLTEFELCVLGNLCPETVEEAVAMVPSLK 113

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM

GO:0008152 "metabolic process" evidence=IEA

GO:0032774 "RNA biosynthetic process" evidence=IEA

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

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

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

DICTYBASE|DDB_G0282739 rpb4 "DNA-directed RNA polymerase II subunit 4" [Dictyostelium discoideum (taxid:44689)]

 Score = 130 (50.8 bits), Expect = 1.2e-08, P = 1.2e-08
 Identities = 42/129 (32%), Positives = 69/129 (53%)

Query:    88 KVSVVKEALPLE-LRVEQELPKNAKCLMDCEAAHILE---GIQEQMALLSADPTIKIPV- 142
             K S ++E   L  L+  ++L K+AK L++ E A +LE   GI E         T+ I + 
Sbjct:     7 KRSGIQEEEDLTTLKFPRDL-KDAKFLLNSEVAILLEHRKGISESEGTEFPQNTLLIHLY 65

Query:   143 ---------SFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEE 193
                      +F K L YA+  S + N  ++K +  +LS+  + + EI  +AN+CPE  +E
Sbjct:    66 YNSINDIIRTFHKTLAYAEKFSRYKNKTSIKQVRTALSKQNLEEFEIASLANLCPEISDE 125

Query:   194 AYAIVPSLK 202
             A +++PSLK
Sbjct:   126 AKSLIPSLK 134

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

GO:0005737 "cytoplasm" evidence=IDA

GO:0005634 "nucleus" evidence=IEA;IDA

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

GO:0044237 "cellular metabolic process" evidence=IEA

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

GO:0003824 "catalytic activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0044351 "macropinocytosis" evidence=RCA

ZFIN|ZDB-GENE-040714-2 polr2d "polymerase (RNA) II (DNA directed) polypeptide D" [Danio rerio (taxid:7955)]

 Score = 121 (47.7 bits), Expect = 1.1e-07, P = 1.1e-07
 Identities = 36/119 (30%), Positives = 61/119 (51%)

Query:    84 ANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVS 143
             A   +V  V+E    +L   +E  +NA+ L++ E   +LE  ++Q    SA+   ++   
Sbjct:     8 AGATQVGDVEEDAS-QLMFPKEF-ENAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEV 63

Query:   144 FDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLK 202
             F K L Y    S F N + +  +   L +  +   E+  +AN+CPE  EEA A++PSL+
Sbjct:    64 FMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELASLANLCPEAAEEAKALIPSLE 122

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0044237 "cellular metabolic process" evidence=IEA

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

GO:0003824 "catalytic activity" evidence=IEA

UNIPROTKB|F1P2S1 POLR2D "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 118 (46.6 bits), Expect = 2.3e-07, P = 2.3e-07
 Identities = 30/95 (31%), Positives = 51/95 (53%)

Query:   108 KNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF 167
             + A+ L++ E   +LE  ++Q    SA+   ++   F K L Y    S F N + +  + 
Sbjct:    32 ETAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNYTARFSRFKNRETIASVR 89

Query:   168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLK 202
               L +  +   E+  +AN+CPET EEA A++PSL+
Sbjct:    90 SLLLQKKLHKFELACLANLCPETAEEAKALIPSLE 124

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" 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

WB|WBGene00018391 rpb-4 [Caenorhabditis elegans (taxid:6239)]

 Score = 117 (46.2 bits), Expect = 2.9e-07, P = 2.9e-07
 Identities = 31/90 (34%), Positives = 47/90 (52%)

Query:   113 LMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSE 172
             L+  E   +LE    + +  S D   ++   F K L YA+  S F N + ++ +    SE
Sbjct:    35 LLTAEVYLLLE--HRRQSSESKDEIEEMSEVFIKTLNYARRMSRFKNRETIRAVRAIFSE 92

Query:   173 HGVTDGEICVIANICPETVEEAYAIVPSLK 202
               +   E+  IAN+CPE  EEA A+VPSL+
Sbjct:    93 KHLHKFEVAQIANLCPENAEEAKALVPSLE 122

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

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

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

UNIPROTKB|Q1JQ91 POLR2D "Polymerase (RNA) II (DNA directed) polypeptide D" [Bos taurus (taxid:9913)]

 Score = 115 (45.5 bits), Expect = 4.8e-07, P = 4.8e-07
 Identities = 29/95 (30%), Positives = 51/95 (53%)

Query:   108 KNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF 167
             + A+ L++ E   +LE  ++Q    SA+   ++   F K L Y    S F N + +  + 
Sbjct:    27 ETAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNYTARFSRFKNRETIASVR 84

Query:   168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLK 202
               L +  +   E+  +AN+CPET EE+ A++PSL+
Sbjct:    85 SLLLQKKLHKFELACLANLCPETAEESKALIPSLE 119

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

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

GO:0004672 "protein kinase activity" evidence=IEA

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

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2RPH1 POLR2D "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 115 (45.5 bits), Expect = 4.8e-07, P = 4.8e-07
 Identities = 29/95 (30%), Positives = 51/95 (53%)

Query:   108 KNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF 167
             + A+ L++ E   +LE  ++Q    SA+   ++   F K L Y    S F N + +  + 
Sbjct:    27 ETAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNYTARFSRFKNRETIASVR 84

Query:   168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLK 202
               L +  +   E+  +AN+CPET EE+ A++PSL+
Sbjct:    85 SLLLQKKLHKFELACLANLCPETAEESKALIPSLE 119

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

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

GO:0004672 "protein kinase activity" evidence=IEA

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

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|O15514 POLR2D "DNA-directed RNA polymerase II subunit RPB4" [Homo sapiens (taxid:9606)]

 Score = 115 (45.5 bits), Expect = 4.8e-07, P = 4.8e-07
 Identities = 29/95 (30%), Positives = 51/95 (53%)

Query:   108 KNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF 167
             + A+ L++ E   +LE  ++Q    SA+   ++   F K L Y    S F N + +  + 
Sbjct:    27 ETAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNYTARFSRFKNRETIASVR 84

Query:   168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLK 202
               L +  +   E+  +AN+CPET EE+ A++PSL+
Sbjct:    85 SLLLQKKLHKFELACLANLCPETAEESKALIPSLE 119

GO:0000166 "nucleotide binding" evidence=IEA

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

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

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

GO:0004672 "protein kinase activity" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

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

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

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

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

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

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

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

GO:0006468 "protein phosphorylation" evidence=IDA

MGI|MGI:1916491 Polr2d "polymerase (RNA) II (DNA directed) polypeptide D" [Mus musculus (taxid:10090)]

 Score = 115 (45.5 bits), Expect = 4.8e-07, P = 4.8e-07
 Identities = 29/95 (30%), Positives = 51/95 (53%)

Query:   108 KNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF 167
             + A+ L++ E   +LE  ++Q    SA+   ++   F K L Y    S F N + +  + 
Sbjct:    27 ETAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNYTARFSRFKNRETIASVR 84

Query:   168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLK 202
               L +  +   E+  +AN+CPET EE+ A++PSL+
Sbjct:    85 SLLLQKKLHKFELACLANLCPETAEESKALIPSLE 119

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

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

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:0044237 "cellular metabolic process" evidence=IEA

RGD|1308565 Polr2d "polymerase (RNA) II (DNA directed) polypeptide D" [Rattus norvegicus (taxid:10116)]

 Score = 115 (45.5 bits), Expect = 4.8e-07, P = 4.8e-07
 Identities = 29/95 (30%), Positives = 51/95 (53%)

Query:   108 KNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF 167
             + A+ L++ E   +LE  ++Q    SA+   ++   F K L Y    S F N + +  + 
Sbjct:    27 ETAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNYTARFSRFKNRETIASVR 84

Query:   168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLK 202
               L +  +   E+  +AN+CPET EE+ A++PSL+
Sbjct:    85 SLLLQKKLHKFELACLANLCPETAEESKALIPSLE 119

GO:0000166 "nucleotide binding" evidence=IEA

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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: GSVIVG00013100001 SubName- Full=Chromosome undetermined scaffold_435, whole genome shotgun sequence; (244 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	206
pfam03874	110	pfam03874, RNA_pol_Rpb4, RNA polymerase Rpb4	1e-21
smart00657	118	smart00657, RPOL4c, DNA-directed RNA-polymerase II	7e-13
COG5250	138	COG5250, RPB4, RNA polymerase II, fourth largest s	2e-06

>gnl|CDD|217775 pfam03874, RNA_pol_Rpb4, RNA polymerase Rpb4

 Score = 84.9 bits (211), Expect = 1e-21
 Identities = 27/91 (29%), Positives = 40/91 (43%)

Query: 112 CLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLS 171
            L + E   IL+   E+    S      +     K L Y    S   NP++ + L + L 
Sbjct: 1   YLTNSEVLEILKKELEERRRESRYVEENLNTILRKTLEYLNKFSRLKNPESARELVEELK 60

Query: 172 EHGVTDGEICVIANICPETVEEAYAIVPSLK 202
           E  +T  E   I N+ PET +E  AI+ SL+
Sbjct: 61  EFELTKFEALQIVNLLPETADELRAIIESLE 91

This family includes the Rpb4 protein. This family also includes C17 (aka CGRP-RCP) is an essential subunit of RNA polymerase III. C17 forms a subcomplex with C25 which is likely to be the counterpart of subcomplex Rpb4/7 in Pol II. Length = 110

>gnl|CDD|128904 smart00657, RPOL4c, DNA-directed RNA-polymerase II subunit

 Score = 62.4 bits (152), Expect = 7e-13
 Identities = 28/95 (29%), Positives = 44/95 (46%), Gaps = 2/95 (2%)

Query: 108 KNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF 167
           KNA CL + E   +LE  ++     S +    +     K L Y    + F N + V+ + 
Sbjct: 4   KNATCLTNSEVQLLLELKRQSKE--SEEEQQPLSTVMKKTLKYLSKFARFKNREIVRAVR 61

Query: 168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLK 202
             L    +   EI  + N+ PET EEA  ++PSL+
Sbjct: 62  TLLKSKKLHKFEIAQLGNLRPETAEEAQLLIPSLE 96

Length = 118

>gnl|CDD|227575 COG5250, RPB4, RNA polymerase II, fourth largest subunit [Transcription]

 Score = 45.0 bits (106), Expect = 2e-06
 Identities = 27/113 (23%), Positives = 50/113 (44%), Gaps = 3/113 (2%)

Query: 91  VVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVS--FDKGL 148
            + E    +L++  E  +N   LM  EA +++EG  E+    +     +      F   L
Sbjct: 4   AIFEEDAAQLKLGPEF-ENEDMLMLSEARYLIEGQLERRRRETNGAEFRSNDVKVFKSTL 62

Query: 149 LYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSL 201
            Y      F + +  + L  +LS  G  + EI  + ++  ++ EEA  ++PSL
Sbjct: 63  GYLDDFCRFKDKEVAEALRTTLSGLGFHEFEIAQLGSLFCQSAEEAKTLIPSL 115

Length = 138

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	206
KOG2351	134	consensus RNA polymerase II, fourth largest subuni	100.0
COG5250	138	RPB4 RNA polymerase II, fourth largest subunit [Tr	99.96
smart00657	118	RPOL4c DNA-directed RNA-polymerase II subunit.	99.93
PRK14981	112	DNA-directed RNA polymerase subunit F; Provisional	99.88
PF03874	117	RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR00	99.84
COG1460	114	Uncharacterized protein conserved in archaea [Func	99.03
KOG4168	149	consensus Predicted RNA polymerase III subunit C17	95.0

>KOG2351 consensus RNA polymerase II, fourth largest subunit [Transcription]

Probab=100.00  E-value=2.3e-39  Score=259.83  Aligned_cols=112  Identities=36%  Similarity=0.444  Sum_probs=106.3

Q ss_pred             cccccCccccccCcccccccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 028639           91 VVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSL  170 (206)
Q Consensus        91 ~~~eEdaaeLkLG~eF~ena~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL  170 (206)
                      ..+||||++|+||+||. +++|||+|||++||+++.++++ .++|+..++++||+||++|+++||||+|+++|.+||.+|
T Consensus         3 g~~EEdAa~lk~g~EFe-~~~~L~~sEa~lllE~~~~q~~-rs~d~~~~~s~Vf~kTl~Y~~~FsRfKn~etv~avr~iL   80 (134)
T KOG2351|consen    3 GEEEEDAAELKLGKEFE-TADALMLSEARLLLEHRLEQRR-RSEDDESEMSDVFKKTLQYLDRFSRFKNRETVRAVRTIL   80 (134)
T ss_pred             chhhccHHhccccHHHH-HHHHHHHHHHHHHHHHHHHHHh-hcccccchHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            46899999999999998 9999999999999999998874 367888999999999999999999999999999999999


Q ss_pred             HhCCCCcchhhhhhccCCCCHHHHHHhhcccccc
Q 028639          171 SEHGVTDGEICVIANICPETVEEAYAIVPSLKVW  204 (206)
Q Consensus       171 ~~~gL~kFEIAqLaNLcPeTaEEAKALIPSL~~~  204 (206)
                      ...+||+||+|||+||||+|+||||+|||||+.-
T Consensus        81 s~~~lhkFE~A~lgnLcpetaEEAkaLvPSL~nk  114 (134)
T KOG2351|consen   81 SGKGLHKFEVAQLGNLCPETAEEAKALVPSLENK  114 (134)
T ss_pred             hhCCcchhhHHHHhccCcccHHHHHHhccccccc
Confidence            9999999999999999999999999999999864

>COG5250 RPB4 RNA polymerase II, fourth largest subunit [Transcription]

Probab=99.96  E-value=3.1e-30  Score=206.43  Aligned_cols=113  Identities=24%  Similarity=0.304  Sum_probs=99.6

Q ss_pred             cccccCccccccCcccccccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHH--HHHHHHHHHhcCCCCCHHHHHHHHH
Q 028639           91 VVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVS--FDKGLLYAKTHSHFTNPQAVKGLFQ  168 (206)
Q Consensus        91 ~~~eEdaaeLkLG~eF~ena~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~v--f~KTleYv~rFSkfkn~Esv~aVRe  168 (206)
                      +..||||++|+|||||+ |.+.||++||+++|+....+++..-...+...++|  |++|+.|++.|+||++.+.+.++|.
T Consensus         4 ~~~ee~aa~lklg~efe-~ed~l~lsEAr~lie~~l~~rrretn~~e~~s~dvk~~k~T~~Yl~~F~Rfkd~e~~~a~~~   82 (138)
T COG5250           4 AIFEEDAAQLKLGPEFE-NEDMLMLSEARYLIEGQLERRRRETNGAEFRSNDVKVFKSTLGYLDDFCRFKDKEVAEALRT   82 (138)
T ss_pred             hHhhhhHHHhhcCcccc-chHHHHHHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence            46899999999999998 99999999999999998877642211223344454  9999999999999999999999999


Q ss_pred             HHHhCCCCcchhhhhhccCCCCHHHHHHhhcccccc
Q 028639          169 SLSEHGVTDGEICVIANICPETVEEAYAIVPSLKVW  204 (206)
Q Consensus       169 lL~~~gL~kFEIAqLaNLcPeTaEEAKALIPSL~~~  204 (206)
                      +|...|+|+|||||+++|||+++||||+|||||..-
T Consensus        83 ~L~~~gfh~fEiAqlGsL~c~saeEAktLiPSL~nk  118 (138)
T COG5250          83 TLSGLGFHEFEIAQLGSLFCQSAEEAKTLIPSLGNK  118 (138)
T ss_pred             HHccCCcchhhHHHhhccccccHHHHHhhccccccc
Confidence            999999999999999999999999999999999763

>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit

Probab=99.93  E-value=1.9e-26  Score=181.38  Aligned_cols=98  Identities=29%  Similarity=0.404  Sum_probs=87.2

Q ss_pred             cccccccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcchhhhh
Q 028639          104 QELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVI  183 (206)
Q Consensus       104 ~eF~ena~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kFEIAqL  183 (206)
                      ++|. |++|||||||++||+.+++..  .+.++..+++.++++|++|+++|+++++++++.+++++|..++||+||+|||
T Consensus         1 ~~f~-~a~~L~n~Ev~~ll~~k~~~~--~~~~~~~~l~~v~~~tl~Yl~~~~~~~~~e~i~~~~~~L~~~~L~k~E~~~i   77 (118)
T smart00657        1 PEFK-NATCLTNSEVQLLLELKRQSK--ESEEEQQPLSTVMKKTLKYLSKFARFKNREIVRAVRTLLKSKKLHKFEIAQL   77 (118)
T ss_pred             CCcc-chhHhHHHHHHHHHHHHHHhh--ccccccchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCCHHHHHHH
Confidence            4787 999999999999999654432  2344556678999999999999999999999999999999999999999999


Q ss_pred             hccCCCCHHHHHHhhcccccc
Q 028639          184 ANICPETVEEAYAIVPSLKVW  204 (206)
Q Consensus       184 aNLcPeTaEEAKALIPSL~~~  204 (206)
                      +||||.|++||++|||||++.
T Consensus        78 ~Nl~P~s~~E~~~lI~sl~~r   98 (118)
T smart00657       78 GNLRPETAEEAQLLIPSLEER   98 (118)
T ss_pred             hCCCCCCHHHHHHHhhhhhcc
Confidence            999999999999999999843

>PRK14981 DNA-directed RNA polymerase subunit F; Provisional

Probab=99.88  E-value=7.2e-23  Score=160.73  Aligned_cols=85  Identities=24%  Similarity=0.278  Sum_probs=76.2

Q ss_pred             ccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcchhhhhhccCC
Q 028639          109 NAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICP  188 (206)
Q Consensus       109 na~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kFEIAqLaNLcP  188 (206)
                      +.+|||++||+.||+++.+.+         ++++++++|++|+++|++++..++.+.+++++...+||+|++|+|+||||
T Consensus         8 ~e~~lt~sEa~~iL~~~~~~~---------els~~~~ktl~y~~kFsk~~~e~a~elve~L~~~~~l~e~~a~~I~nL~P   78 (112)
T PRK14981          8 EEEYITIAEAKEILSEIEEER---------ELSYELRRTLDYLNRFSKLDPEDAEELVEELLELEKMKEKTAVKIADILP   78 (112)
T ss_pred             hcccccHHHHHHHHHHHHhcc---------chhHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHccCCCHHHHHHHHhcCC
Confidence            567999999999999876541         67899999999999999998777777788888887899999999999999


Q ss_pred             CCHHHHHHhhcccc
Q 028639          189 ETVEEAYAIVPSLK  202 (206)
Q Consensus       189 eTaEEAKALIPSL~  202 (206)
                      +|+||||+||||+.
T Consensus        79 ~~~dElrai~~~~~   92 (112)
T PRK14981         79 ETRDELRAIFAKER   92 (112)
T ss_pred             CCHHHHHHHHHHhc
Confidence            99999999999994

>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core

Probab=99.84  E-value=2.8e-21  Score=149.39  Aligned_cols=93  Identities=33%  Similarity=0.402  Sum_probs=77.0

Q ss_pred             cccHHHHHHHHHHHHHHHhhh-------cCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcchhhhhh
Q 028639          112 CLMDCEAAHILEGIQEQMALL-------SADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIA  184 (206)
Q Consensus       112 cLslsEV~lILe~~~e~~~~~-------s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kFEIAqLa  184 (206)
                      ||||+||..||+++.+..+..       ...+..+++.++.+|++|+++|+++.+++++..+++.|..++|++||++||+
T Consensus         1 ~Lsn~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Yl~~~~~~~~~e~~~~l~~~L~~~~L~~~E~~qi~   80 (117)
T PF03874_consen    1 LLSNYEVLQILEKRREEQKNKSKKKQKNKEDPPENLNTIQYKTLEYLEKFSKFQNPESIKELREELKKFGLTEFEILQII   80 (117)
T ss_dssp             EE-HHHHHHHHHHHHHHHHCHCHHHHHHHHHCSSCHCHHHHHHHHHHHHH-SSSSHHHHHHHHHHHTTSTS-HHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHHHHhhhccccccccccccchHHHHHHHHHHHHccccCCCHHHHHHHHHHHhcccCCHHHHHHHh
Confidence            799999999999665543211       1345667889999999999999999999999999999999999999999999


Q ss_pred             ccCCCCHHHHHHhhcccccc
Q 028639          185 NICPETVEEAYAIVPSLKVW  204 (206)
Q Consensus       185 NLcPeTaEEAKALIPSL~~~  204 (206)
                      ||||.|++|+++|||+++..
T Consensus        81 Nl~P~~~~El~~ii~~~~~r  100 (117)
T PF03874_consen   81 NLRPTTAVELRAIIESLESR  100 (117)
T ss_dssp             HH--SSHHHHHHHSTTGTTT
T ss_pred             cCCCCCHHHHHHHHHHhccC
Confidence            99999999999999999853

Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....

>COG1460 Uncharacterized protein conserved in archaea [Function unknown]

Probab=99.03  E-value=8.7e-10  Score=87.87  Aligned_cols=82  Identities=22%  Similarity=0.307  Sum_probs=63.3

Q ss_pred             ccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHH-HHHHHHhCCCCcchhhhhhccC
Q 028639          109 NAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKG-LFQSLSEHGVTDGEICVIANIC  187 (206)
Q Consensus       109 na~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~a-VRelL~~~gL~kFEIAqLaNLc  187 (206)
                      +-+.+|++||+.||..+         ....++++.++.||+|+++|+++. |+.++. |.+++.-.++.+-=++-|++||
T Consensus         9 e~~yiti~Eak~il~~~---------~~~~eL~y~~~~al~y~~kFakld-pe~a~e~veEL~~i~~~~e~~avkIadI~   78 (114)
T COG1460           9 EEKYITISEAKKILSKV---------EREEELTYEQREALEYAEKFAKLD-PEKARELVEELLSIVKMSEKIAVKIADIM   78 (114)
T ss_pred             hccCccHHHHHHHHHHh---------cccccchHHHHHHHHHHHHHhcCC-HHHHHHHHHHHHhhccccHHHHHHHHHhC
Confidence            44689999999999877         234467899999999999999998 666655 5555555555333344499999


Q ss_pred             CCCHHHHHHhhcc
Q 028639          188 PETVEEAYAIVPS  200 (206)
Q Consensus       188 PeTaEEAKALIPS  200 (206)
                      |+|.+|.|+++-.
T Consensus        79 P~t~~ElRsIla~   91 (114)
T COG1460          79 PRTPDELRSILAK   91 (114)
T ss_pred             CCCHHHHHHHHHH
Confidence            9999999998743

>KOG4168 consensus Predicted RNA polymerase III subunit C17 [Transcription]

Probab=95.00  E-value=0.087  Score=44.10  Aligned_cols=97  Identities=18%  Similarity=0.204  Sum_probs=69.0

Q ss_pred             cccccccHHHHHHHHHHHHHHHhh----hcCC-----CCCCchHHHHHHHHHHHhcC--CCCCHHHHHHHHHHHHhCCCC
Q 028639          108 KNAKCLMDCEAAHILEGIQEQMAL----LSAD-----PTIKIPVSFDKGLLYAKTHS--HFTNPQAVKGLFQSLSEHGVT  176 (206)
Q Consensus       108 ena~cLslsEV~lILe~~~e~~~~----~s~d-----~~~~~s~vf~KTleYv~rFS--kfkn~Esv~aVRelL~~~gL~  176 (206)
                      .+.-.|++-||...|+....+...    ..+.     .-.+++-+...|+.|+..-.  .-.+.|.+.++-.-|..++|+
T Consensus         6 ar~a~LtnyEVl~fL~el~~~n~~~~k~s~r~~~Q~~~~~~l~ti~~et~kYls~~~n~~~qt~E~i~el~~k~~~fkLt   85 (149)
T KOG4168|consen    6 ARNAALTNYEVLQFLNELECMNEEADKSSHRLGAQNILQNDLPTITYETLKYLSDNKNASTQTNESIIELITKLKSFKLT   85 (149)
T ss_pred             hhHHHhhhHHHHHHHHHhhhhhhhhhhhhhhhhcccccccccchhHHHHHHHHhcCcccccccHHHHHHHHHHhccccch
Confidence            455689999999999876521110    0011     11236678889999998755  333466777777777788999


Q ss_pred             cchhhhhhccCCCCHHHHHHhhcccccc
Q 028639          177 DGEICVIANICPETVEEAYAIVPSLKVW  204 (206)
Q Consensus       177 kFEIAqLaNLcPeTaEEAKALIPSL~~~  204 (206)
                      +-|+-||.|+.|-++=|...+|--+++.
T Consensus        86 KAE~LqiiN~rPss~vel~~~iE~~eeR  113 (149)
T KOG4168|consen   86 KAEILQIINLRPSSSVELYLIIEEVEER  113 (149)
T ss_pred             HHHHHHHhccCcchHHHHHHHHHHHHHh
Confidence            9999999999999998888887655443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	206
2c35_A	152	Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii L		1e-06

>pdb|2C35|A Chain A, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii Length = 152

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/95 (30%), Positives = 51/95 (53%), Gaps = 2/95 (2%)
Query: 108 KNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF 167
           + A+ L++ E   +LE  ++Q    SA+   ++   F K L Y    S F N + +  + 
Sbjct: 37  ETAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNYTARFSRFKNRETIASVR 94
Query: 168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLK 202
             L +  +   E+  +AN+CPET EE+ A++PSL+
Sbjct: 95  SLLLQKKLHKFELACLANLCPETAEESKALIPSLE 129

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	206
2c35_A	152	Human RPB4, DNA-directed RNA polymerase II 16 kDa	7e-29
3h0g_D	135	DNA-directed RNA polymerase II subunit RPB4; trans	5e-26
3hou_D	221	DNA-directed RNA polymerase II subunit RPB4; RNA p	7e-23
1y14_A	187	B32, RPB4, DNA-directed RNA polymerase II 32 kDa p	1e-13
3ayh_A	136	DNA-directed RNA polymerase III subunit RPC9; tran	5e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
4ayb_F	113	DNA-directed RNA polymerase; transferase, multi-su	8e-04

>2c35_A Human RPB4, DNA-directed RNA polymerase II 16 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: a.60.8.2 Length = 152

 Score =  104 bits (261), Expect = 7e-29
 Identities = 37/134 (27%), Positives = 64/134 (47%), Gaps = 9/134 (6%)

Query: 73  GLTKGGKGDKVANGAK----VSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQ 128
           G  +   G ++A G        V ++A  L    E    + A+ L++ E   +LE  ++Q
Sbjct: 1   GSRRASVGSQMAAGGSDPRAGDVEEDASQLIFPKE---FETAETLLNSEVHMLLEHRKQQ 57

Query: 129 MALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICP 188
               SA+   ++   F K L Y    S F N + +  +   L +  +   E+  +AN+CP
Sbjct: 58  --NESAEDEQELSEVFMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCP 115

Query: 189 ETVEEAYAIVPSLK 202
           ET EE+ A++PSL+
Sbjct: 116 ETAEESKALIPSLE 129

>3h0g_D DNA-directed RNA polymerase II subunit RPB4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 135

 Score = 96.6 bits (240), Expect = 5e-26
 Identities = 23/104 (22%), Positives = 42/104 (40%), Gaps = 3/104 (2%)

Query: 99  ELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFT 158
           +L++  E  +N   L   EA  ++E +  Q A    +  I +     K + Y    + F 
Sbjct: 12  QLKLGPEF-ENEDMLTVSEAKILIETVLAQRAR-ETNGEIPMTDVMKKTVAYFNVFARFK 69

Query: 159 NPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLK 202
             +A     + +  +     E   +  +C E  EEA  ++PSL 
Sbjct: 70  TAEATYAC-ERILGNRFHKFERAQLGTLCCEDAEEARTLIPSLA 112

>3hou_D DNA-directed RNA polymerase II subunit RPB4; RNA polymerase II, metal-binding, transcription bubble; HET: BRU; 3.20A {Saccharomyces cerevisiae} PDB: 1nt9_D 1y1w_D 1y1y_D 1y77_D* 2b63_D* 2b8k_D 2ja5_D* 2ja6_D* 2ja7_D* 2ja8_D* 2r7z_D 2r92_D 2r93_D 1y1v_D* 3fki_D 3h3v_E 2vum_D* 3hov_D* 3how_D* 3hox_D* ... Length = 221

 Score = 90.8 bits (224), Expect = 7e-23
 Identities = 23/132 (17%), Positives = 48/132 (36%), Gaps = 5/132 (3%)

Query: 76  KGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSAD 135
           +  K  +  +  K    + A      VE E     +  ++ +    +     +  L S D
Sbjct: 68  RAFKRSQKKHKKKHLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETREKELESID 127

Query: 136 PTIKIPVS-----FDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPET 190
             ++             + Y    S F + + V  + Q L   G+   E+  + ++  +T
Sbjct: 128 VLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDT 187

Query: 191 VEEAYAIVPSLK 202
            +EA  ++PSL 
Sbjct: 188 ADEAKTLIPSLN 199

>1y14_A B32, RPB4, DNA-directed RNA polymerase II 32 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: a.60.8.2 Length = 187

 Score = 65.3 bits (158), Expect = 1e-13
 Identities = 19/91 (20%), Positives = 35/91 (38%)

Query: 112 CLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLS 171
              D   +   E   E + +L    T          + Y    S F + + V  + Q L 
Sbjct: 75  DDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLK 134

Query: 172 EHGVTDGEICVIANICPETVEEAYAIVPSLK 202
             G+   E+  + ++  +T +EA  ++PSL 
Sbjct: 135 STGLHPFEVAQLGSLACDTADEAKTLIPSLN 165

>3ayh_A DNA-directed RNA polymerase III subunit RPC9; transcription; 2.19A {Schizosaccharomyces pombe} Length = 136

 Score = 40.8 bits (95), Expect = 5e-05
 Identities = 13/57 (22%), Positives = 23/57 (40%)

Query: 149 LYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKVWL 205
           L ++ +      +         +E  +T  EI VI N  P +V E YA +  ++   
Sbjct: 63  LSSQGNCEGLTKERFLDCIAIFNEFELTKAEILVILNNKPSSVPELYACIEGIEERF 119

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

 Score = 41.4 bits (96), Expect = 1e-04
 Identities = 33/202 (16%), Positives = 65/202 (32%), Gaps = 44/202 (21%)

Query: 11  GVGGGGKTSLKSIPASLGGKDDNSAKSKRGRKV-------QFNTEGLSEGKFTFSSKSDG 63
           GV G GKT +    A          + K   K+         + E + E       + D 
Sbjct: 157 GVLGSGKTWV----ALDVCLSY-KVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDP 211

Query: 64  KFETTYGKGGLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILE 123
            + +           + D  +N   + +   ++  ELR   +      CL+      +L 
Sbjct: 212 NWTS-----------RSDHSSN---IKLRIHSIQAELRRLLKSKPYENCLL------VLL 251

Query: 124 GIQEQMALLSADPTIKIPV-SFDKGL---LYAKTHSHFTNPQAVKGLFQSLSEHGVTDGE 179
            +Q   A  + + + KI + +  K +   L A T +H +       L     +       
Sbjct: 252 NVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVK------S 305

Query: 180 ICV-IANICPETV-EEAYAIVP 199
           + +   +  P+ +  E     P
Sbjct: 306 LLLKYLDCRPQDLPREVLTTNP 327

>4ayb_F DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_F 2y0s_F 2waq_F 4b1o_F 4b1p_U 2pmz_F 3hkz_F Length = 113

 Score = 36.8 bits (85), Expect = 8e-04
 Identities = 13/81 (16%), Positives = 31/81 (38%), Gaps = 10/81 (12%)

Query: 117 EAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVT 176
            A  +L  + +  +  +            +   Y  +     + ++ + + + LS     
Sbjct: 16  VAKKLLSDVIKSGSSSNL---------LQRTYDYLNSVEK-CDAESAQKVVEELSSIISR 65

Query: 177 DGEICVIANICPETVEEAYAI 197
           +    V+A+ICP T +E  +I
Sbjct: 66  EDVRAVLASICPITPDEVRSI 86

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	206
3h0g_D	135	DNA-directed RNA polymerase II subunit RPB4; trans	100.0
2c35_A	152	Human RPB4, DNA-directed RNA polymerase II 16 kDa	100.0
3hou_D	221	DNA-directed RNA polymerase II subunit RPB4; RNA p	99.96
1go3_F	107	DNA-directed RNA polymerase subunit F; transferase	99.91
1y14_A	187	B32, RPB4, DNA-directed RNA polymerase II 32 kDa p	99.91
4ayb_F	113	DNA-directed RNA polymerase; transferase, multi-su	99.82
3ayh_A	136	DNA-directed RNA polymerase III subunit RPC9; tran	99.51
2ckz_A	161	DNA-directed RNA polymerase III 18 KD polypeptide;	99.31

>3h0g_D DNA-directed RNA polymerase II subunit RPB4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=100.00  E-value=1.8e-37  Score=249.47  Aligned_cols=110  Identities=23%  Similarity=0.292  Sum_probs=100.2

Q ss_pred             cccccCccccccCcccccccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 028639           91 VVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSL  170 (206)
Q Consensus        91 ~~~eEdaaeLkLG~eF~ena~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL  170 (206)
                      +++||||++|+||+||+ |++|||||||++||+.++++++. ...+..+++.+|+||++|+++|+||++++++.+||++|
T Consensus         4 ~~~ee~a~~L~lg~eF~-~a~~Ls~sEv~~lL~~~~~~r~~-~~~~~~~~~~v~~kTl~Yl~~Fsk~~~~e~~~~v~~lL   81 (135)
T 3h0g_D            4 AIFEEDAAQLKLGPEFE-NEDMLTVSEAKILIETVLAQRAR-ETNGEIPMTDVMKKTVAYFNVFARFKTAEATYACERIL   81 (135)
T ss_dssp             --CCCCCTTTCSCHHHH-HSCBCCHHHHHHHHHHHHHHHHT-TCCSCCCCTTHHHHHHHHHHTTCTTCSHHHHHHHHHHC
T ss_pred             hHHHHhHHhhCCCHhhc-CcccccHHHHHHHHHHHHHHHHh-cccCCcchhHHHHHHHHHHHHccCCCCHHHHHHHHHHH
Confidence            67999999999999998 99999999999999999887642 12345678899999999999999999999999999999


Q ss_pred             HhCCCCcchhhhhhccCCCCHHHHHHhhccccc
Q 028639          171 SEHGVTDGEICVIANICPETVEEAYAIVPSLKV  203 (206)
Q Consensus       171 ~~~gL~kFEIAqLaNLcPeTaEEAKALIPSL~~  203 (206)
                      .. +||+||+|||+||||+|+||||+|||||++
T Consensus        82 ~~-~L~~fEia~L~NL~P~t~dEak~LIpsL~~  113 (135)
T 3h0g_D           82 GN-RFHKFERAQLGTLCCEDAEEARTLIPSLAN  113 (135)
T ss_dssp             CC-CSCHHHHHHHHHHCCCCHHHHHHHCGGGTT
T ss_pred             Hh-cCCHHHHHHHccCCCCCHHHHHHHHHHhcc
Confidence            99 999999999999999999999999999985

>2c35_A Human RPB4, DNA-directed RNA polymerase II 16 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: a.60.8.2

Probab=100.00  E-value=4.2e-33  Score=227.51  Aligned_cols=113  Identities=28%  Similarity=0.380  Sum_probs=100.5

Q ss_pred             CcccccccCccccccCcccccccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHH
Q 028639           88 KVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF  167 (206)
Q Consensus        88 k~~~~~eEdaaeLkLG~eF~ena~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVR  167 (206)
                      +..+.+||||++|+||++|. |++|||||||++||+++++++.  ..++..+++++|++||+|+++|++|++++++++|+
T Consensus        18 ~~~~~~ee~a~~l~~gkef~-~~~~Lt~sEV~~lL~~~~~~~~--~~~~~~els~v~~kTl~Yl~~F~k~k~~e~~~~l~   94 (152)
T 2c35_A           18 PRAGDVEEDASQLIFPKEFE-TAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNYTARFSRFKNRETIASVR   94 (152)
T ss_dssp             ------CCBGGGTBCCSSSS-SCEECCHHHHHHHHHHHHHHHH--SSCSSCCCCHHHHHHHHHHHHTCSCCSHHHHHHHH
T ss_pred             CCCCCccccHHHHhcchhhc-ccccccHHHHHHHHHHHHHhhc--ccccccchHHHHHHHHHHHHHccCCCCHHHHHHHH
Confidence            55677999999999999998 9999999999999999987653  34566788999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhhhhccCCCCHHHHHHhhccccc
Q 028639          168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKV  203 (206)
Q Consensus       168 elL~~~gL~kFEIAqLaNLcPeTaEEAKALIPSL~~  203 (206)
                      ++|..++||+||+|+|+||||+|+||||+|||||+.
T Consensus        95 e~L~~~~L~~~E~a~L~NL~P~t~dEar~lipsl~~  130 (152)
T 2c35_A           95 SLLLQKKLHKFELACLANLCPETAEESKALIPSLEG  130 (152)
T ss_dssp             HHHHTSSCCHHHHHHHHHHCCSSHHHHHHHCGGGTT
T ss_pred             HHHHhcCCCHHHHHHhccCCCCCHHHHHHHHHhhcc
Confidence            999999999999999999999999999999999974

>3hou_D DNA-directed RNA polymerase II subunit RPB4; RNA polymerase II, metal-binding, transcription bubble; HET: BRU; 3.20A {Saccharomyces cerevisiae} PDB: 1nt9_D 1y1w_D 1y1y_D 1y77_D* 2b63_D* 2b8k_D 2ja5_D* 2ja6_D* 2ja7_D* 2ja8_D* 2r7z_D 2r92_D 2r93_D 1y1v_D* 3fki_D 3h3v_E 2vum_D* 3hov_D* 3how_D* 3hox_D* ...

Probab=99.96  E-value=4.3e-29  Score=214.52  Aligned_cols=114  Identities=22%  Similarity=0.268  Sum_probs=95.9

Q ss_pred             ccccccCccccccCcccc----------cccccccHHHHHHHHHHHHH-HHhh--hc-----------------------
Q 028639           90 SVVKEALPLELRVEQELP----------KNAKCLMDCEAAHILEGIQE-QMAL--LS-----------------------  133 (206)
Q Consensus        90 ~~~~eEdaaeLkLG~eF~----------ena~cLslsEV~lILe~~~e-~~~~--~s-----------------------  133 (206)
                      -.++||+|+.|+||+||+          +...+|++||+++|+..... +++.  .+                       
T Consensus        17 ~~~~eenaa~l~lg~efql~q~~~~g~~~~lialnlsearl~i~~al~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (221)
T 3hou_D           17 KVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKHKKKHLKHENANDETTAVED   96 (221)
T ss_dssp             CCCCCCCCSSSCCCGGGCSEEECTTSCEEECCBCCTTHHHHHHHHHHHHHHHHHHHTTCC--------------------
T ss_pred             cccchhhhHHhhcCcccceeecccCCchhHhHhhhhHHHHHHHHHHHHHHHHHhhccccccccccccccccccccccccc
Confidence            357999999999999999          56779999999999965422 2110  00                       


Q ss_pred             ------------CCC----------------------CCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcch
Q 028639          134 ------------ADP----------------------TIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGE  179 (206)
Q Consensus       134 ------------~d~----------------------~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kFE  179 (206)
                                  .+.                      ....+.||+|||+||++|+||++++++.+||++|..++||+||
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~e~e~~~~~~~~~~~~g~~seVf~KTLdYl~rFSKfkn~EAv~aVrELL~~~gLheFE  176 (221)
T 3hou_D           97 EDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFE  176 (221)
T ss_dssp             ---------------------CTHHHHHHHHHHHHHHSCSCCHHHHHHHHHHHHSCSCCCHHHHHHHHHHHTTSCCCHHH
T ss_pred             ccccccccccccccchhhhccchHHHHHHHHHHHhhcCCCccHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHhcCCChHH
Confidence                        000                      1145789999999999999999999999999999999999999


Q ss_pred             hhhhhccCCCCHHHHHHhhccccc
Q 028639          180 ICVIANICPETVEEAYAIVPSLKV  203 (206)
Q Consensus       180 IAqLaNLcPeTaEEAKALIPSL~~  203 (206)
                      +|+||||||+|+||||+|||||..
T Consensus       177 iAqLANLcPeTaDEARALIPSL~~  200 (221)
T 3hou_D          177 VAQLGSLACDTADEAKTLIPSLNN  200 (221)
T ss_dssp             HHHHHHSCCCSHHHHHHHCTTCTT
T ss_pred             hheecccCCCCHHHHHHHHHhhcc
Confidence            999999999999999999999984

>1go3_F DNA-directed RNA polymerase subunit F; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: a.60.8.2

Probab=99.91  E-value=5.7e-25  Score=170.46  Aligned_cols=90  Identities=19%  Similarity=0.266  Sum_probs=79.9

Q ss_pred             cCcccccccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcchhh
Q 028639          102 VEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEIC  181 (206)
Q Consensus       102 LG~eF~ena~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kFEIA  181 (206)
                      +|.+|. +.+|||+|||+.||+++.+.         .++++++++|++|+++|+|| +++.+.++++.|.+.+||+||+|
T Consensus         2 i~kei~-~~~~lt~sEa~~iL~~~~~~---------~e~s~~~~ktl~y~~kFsk~-~~e~a~~l~e~L~~~~l~e~~a~   70 (107)
T 1go3_F            2 IGKKIL-GERYVTVSEAAEIMYNRAQI---------GELSYEQGCALDYLQKFAKL-DKEEAKKLVEELISLGIDEKTAV   70 (107)
T ss_dssp             CSSEEE-EEEEECHHHHHHHHHHHHHH---------SCCCHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHTTCCHHHHH
T ss_pred             chHHHh-cccccCHHHHHHHHHHHHhc---------ccccHHHHHHHHHHHHHhCC-CHHHHHHHHHHHHhCCCCHHHHH
Confidence            456787 99999999999999987653         35779999999999999999 57777777777778889999999


Q ss_pred             hhhccCCCCHHHHHHhhcccc
Q 028639          182 VIANICPETVEEAYAIVPSLK  202 (206)
Q Consensus       182 qLaNLcPeTaEEAKALIPSL~  202 (206)
                      +|+||||+|+||||+||||+.
T Consensus        71 ~I~nl~P~t~dElraii~~~~   91 (107)
T 1go3_F           71 KIADILPEDLDDLRAIYYKRE   91 (107)
T ss_dssp             HHHHHCCCSHHHHHHHSTTSC
T ss_pred             HHHHhCCCCHHHHHHHHhccc
Confidence            999999999999999999985

>1y14_A B32, RPB4, DNA-directed RNA polymerase II 32 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: a.60.8.2

Probab=99.91  E-value=1.4e-24  Score=183.21  Aligned_cols=66  Identities=21%  Similarity=0.341  Sum_probs=63.7

Q ss_pred             CCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcchhhhhhccCCCCHHHHHHhhccccc
Q 028639          138 IKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKV  203 (206)
Q Consensus       138 ~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kFEIAqLaNLcPeTaEEAKALIPSL~~  203 (206)
                      .+++++|.+||+|+++|++|++++++++||++|..++||+||+|+|+||||+|+||||+|||||..
T Consensus       101 ~~ls~v~~KTLeYl~rFsk~kn~Esa~elre~L~~~kL~efE~aqLaNL~PeTadEaraLIpSle~  166 (187)
T 1y14_A          101 GGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN  166 (187)
T ss_dssp             CSCCHHHHHHHHHHHHHCSCCSHHHHHHHHHHHHTTTCCHHHHHHHHHSCCSSHHHHHHHSGGGTT
T ss_pred             ccccHHHHHHHHHHHHccCCCCHHHHHHHHHHHHhcCCCHHHHHHcCcCCCCCHHHHHHHHHhhcc
Confidence            478899999999999999999999999999999999999999999999999999999999999984

>4ayb_F DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_F 2y0s_F 2waq_F 4b1o_F 4b1p_U 2pmz_F 3hkz_F

Probab=99.82  E-value=1.8e-22  Score=157.60  Aligned_cols=86  Identities=15%  Similarity=0.163  Sum_probs=74.2

Q ss_pred             ccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcchhhhhhccCC
Q 028639          109 NAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICP  188 (206)
Q Consensus       109 na~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kFEIAqLaNLcP  188 (206)
                      +.+.++++||+.||..+         .+..+.++++++||+|+++|+|| +++.+.++++.|...++|+||+|+|+||||
T Consensus         8 ~e~~it~~eakeiL~~~---------~~~~~~s~~~~ktl~y~~~Fsk~-~~e~a~~l~e~L~~~~l~~~~~a~IanL~P   77 (113)
T 4ayb_F            8 EEHYIPYSVAKKLLSDV---------IKSGSSSNLLQRTYDYLNSVEKC-DAESAQKVVEELSSIISREDVRAVLASICP   77 (113)
T ss_dssp             EEEEECTTGGGGTTTTT---------SSSSCCCTTHHHHHHHTTTTCSS-CHHHHHHHHHHHHTTCCCHHHHHHHHHHCC
T ss_pred             cccccCHHHHHHHHHHH---------HhcccccHHHHHHHHHHHHHcCC-CHHHHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence            44679999999999643         23345678999999999999999 567777788888888999999999999999


Q ss_pred             CCHHHHHHhhcccccc
Q 028639          189 ETVEEAYAIVPSLKVW  204 (206)
Q Consensus       189 eTaEEAKALIPSL~~~  204 (206)
                      +|+||||+||||+.++
T Consensus        78 ~~~dElrali~s~e~~   93 (113)
T 4ayb_F           78 ITPDEVRSILIMDSNR   93 (113)
T ss_dssp             CSSCCCCTTTTTTCCC
T ss_pred             CCHHHHHHHHHhhccC
Confidence            9999999999999875

>3ayh_A DNA-directed RNA polymerase III subunit RPC9; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=99.51  E-value=7.6e-15  Score=117.37  Aligned_cols=97  Identities=18%  Similarity=0.160  Sum_probs=80.4

Q ss_pred             cccccccHHHHHHHHHHHHHHHhhh--cCC-----CCCCchHHHHHHHHHHHhc--CCCCCHHHHHHHHHHHHhCCCCcc
Q 028639          108 KNAKCLMDCEAAHILEGIQEQMALL--SAD-----PTIKIPVSFDKGLLYAKTH--SHFTNPQAVKGLFQSLSEHGVTDG  178 (206)
Q Consensus       108 ena~cLslsEV~lILe~~~e~~~~~--s~d-----~~~~~s~vf~KTleYv~rF--Skfkn~Esv~aVRelL~~~gL~kF  178 (206)
                      .++.+|||.||..+|+++..+....  ...     ...+.+.++.+|++|+++|  +.+.+++++.++++.|..++|+++
T Consensus        13 ~~~a~LsN~EVl~~L~~~~~~~~~~~~~~~~~~~~~~~~l~ti~~e~l~YL~~~p~~~~q~~e~i~~l~~~L~~~~Ltk~   92 (136)
T 3ayh_A           13 ARDAYLTNAEVFFHLKEMENEQNARTQERGAAQALVCENLRTIQFEILKYLSSQGNCEGLTKERFLDCIAIFNEFELTKA   92 (136)
T ss_dssp             EEEEEECHHHHHHHHHHHHHHHHHHHHHHGGGGCCCCHHHHHHHHHHHHHHHTTTCCTTCCHHHHHHHHHTTTTTCCCHH
T ss_pred             cccccccHHHHHHHHHHHHhhhcccccccCCccccccchHHHHHHHHHHHHHhCCCccccCHHHHHHHHHHHHhcCCCHH
Confidence            4678999999999999887643210  111     1245778999999999999  445689999999999999999999


Q ss_pred             hhhhhhccCCCCHHHHHHhhcccccc
Q 028639          179 EICVIANICPETVEEAYAIVPSLKVW  204 (206)
Q Consensus       179 EIAqLaNLcPeTaEEAKALIPSL~~~  204 (206)
                      |+.||+||||.|+.|+++||+..+..
T Consensus        93 E~LqivNl~P~t~vel~~iIEe~e~R  118 (136)
T 3ayh_A           93 EILVILNNKPSSVPELYACIEGIEER  118 (136)
T ss_dssp             HHHHHHHHCCCSHHHHHHHSTTHHHH
T ss_pred             HHHHHhccCCCCHHHHHHHHHhcccC
Confidence            99999999999999999999998744

>2ckz_A DNA-directed RNA polymerase III 18 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=99.31  E-value=5.7e-13  Score=109.77  Aligned_cols=96  Identities=15%  Similarity=0.155  Sum_probs=32.1

Q ss_pred             ccccccHHHHHHHHHHHHHHHhh---------------hcCC--CCCCchHHHHHHHHHHHhcCC---------------
Q 028639          109 NAKCLMDCEAAHILEGIQEQMAL---------------LSAD--PTIKIPVSFDKGLLYAKTHSH---------------  156 (206)
Q Consensus       109 na~cLslsEV~lILe~~~e~~~~---------------~s~d--~~~~~s~vf~KTleYv~rFSk---------------  156 (206)
                      +..+|||.||..+|..+..+...               ....  +..+++.|+..|++|+.++++               
T Consensus         7 ~~a~LSN~EVl~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ti~~e~~~YL~~~p~~~~~~~~~~~~~~~~   86 (161)
T 2ckz_A            7 RNAFLSDYEVLKFLTDLEKKHLWDQKSLAALKKSRSKGKQNRPYNHPELQGITRNVVNYLSINKNFINQEDEGEERESSG   86 (161)
T ss_dssp             EEEEECHHHHHHHHHHHHHHTTCSHHHHHCC----------CCCCCHHHHHHHHHHHHHHTC------------------
T ss_pred             hhhhhhHHHHHHHHHHhhhhccccccchhhhhcccccccccCCCCCccHHHHHHHHHHHHHhCCcccccccccccccccc
Confidence            56799999999999988765310               0011  113466799999999999998               


Q ss_pred             ----------CCCHHHHHHHHHHHHhCCCCcchhhhhhccCCCCHHHHHHhhcccccc
Q 028639          157 ----------FTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKVW  204 (206)
Q Consensus       157 ----------fkn~Esv~aVRelL~~~gL~kFEIAqLaNLcPeTaEEAKALIPSL~~~  204 (206)
                                +.+++++..+.+.|..++|+++|+.||+||||.++.|+++||+.++..
T Consensus        87 ~~~~~~~~~~~~~~e~i~~l~~~L~~~~Ltk~E~lqivNl~P~s~vel~~iIEe~e~R  144 (161)
T 2ckz_A           87 AKDAEKSGISKMSDESFAELMTKLNSFKLFKAEKLQIVNQLPANMVHLYSIVEECDAR  144 (161)
T ss_dssp             ----------------------------------------------------------
T ss_pred             ccccccccccccCHHHHHHHHHHHHhcCCCHHHHHHHhccCCCCHHHHHHHHHhcccC
Confidence                      355788888888888999999999999999999999999999988754

---

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	206
d1y14a_	176	a.60.8.2 (A:) RNA polymerase II subunit RBP4 (RpoF	1e-32
d2c35a1	129	a.60.8.2 (A:14-142) RNA polymerase II subunit RBP4	2e-26
d1go3f_	107	a.60.8.2 (F:) RNA polymerase II subunit RBP4 (RpoF	2e-12

>d1y14a_ a.60.8.2 (A:) RNA polymerase II subunit RBP4 (RpoF) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 176

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: RNA polymerase II subunit RBP4 (RpoF)
domain: RNA polymerase II subunit RBP4 (RpoF)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  113 bits (285), Expect = 1e-32
 Identities = 23/132 (17%), Positives = 48/132 (36%), Gaps = 5/132 (3%)

Query: 76  KGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSAD 135
           +  K  +  +  K    + A      VE E     +  ++ +    +     +  L S D
Sbjct: 23  RAFKRSQKKHKKKHLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETREKELESID 82

Query: 136 PTIKIPVS-----FDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPET 190
             ++             + Y    S F + + V  + Q L   G+   E+  + ++  +T
Sbjct: 83  VLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDT 142

Query: 191 VEEAYAIVPSLK 202
            +EA  ++PSL 
Sbjct: 143 ADEAKTLIPSLN 154

>d2c35a1 a.60.8.2 (A:14-142) RNA polymerase II subunit RBP4 (RpoF) {Human (Homo sapiens) [TaxId: 9606]} Length = 129

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: RNA polymerase II subunit RBP4 (RpoF)
domain: RNA polymerase II subunit RBP4 (RpoF)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 96.4 bits (240), Expect = 2e-26
 Identities = 31/104 (29%), Positives = 55/104 (52%), Gaps = 3/104 (2%)

Query: 99  ELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFT 158
           +L   +E  + A+ L++ E   +LE  ++Q    SA+   ++   F K L Y    S F 
Sbjct: 6   QLIFPKEF-ETAETLLNSEVHMLLEHRKQQN--ESAEDEQELSEVFMKTLNYTARFSRFK 62

Query: 159 NPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLK 202
           N + +  +   L +  +   E+  +AN+CPET EE+ A++PSL+
Sbjct: 63  NRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLE 106

>d1go3f_ a.60.8.2 (F:) RNA polymerase II subunit RBP4 (RpoF) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 107

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: RNA polymerase II subunit RBP4 (RpoF)
domain: RNA polymerase II subunit RBP4 (RpoF)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 59.0 bits (143), Expect = 2e-12
 Identities = 17/93 (18%), Positives = 36/93 (38%), Gaps = 10/93 (10%)

Query: 111 KCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSL 170
           + +   EAA I+    +           ++       L Y +  +   + +  K L + L
Sbjct: 10  RYVTVSEAAEIMYNRAQ---------IGELSYEQGCALDYLQKFAKL-DKEEAKKLVEEL 59

Query: 171 SEHGVTDGEICVIANICPETVEEAYAIVPSLKV 203
              G+ +     IA+I PE +++  AI    ++
Sbjct: 60  ISLGIDEKTAVKIADILPEDLDDLRAIYYKREL 92

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	206
d2c35a1	129	RNA polymerase II subunit RBP4 (RpoF) {Human (Homo	99.98
d1y14a_	176	RNA polymerase II subunit RBP4 (RpoF) {Baker's yea	99.94
d1go3f_	107	RNA polymerase II subunit RBP4 (RpoF) {Archaeon Me	99.85

>d2c35a1 a.60.8.2 (A:14-142) RNA polymerase II subunit RBP4 (RpoF) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: RNA polymerase II subunit RBP4 (RpoF)
domain: RNA polymerase II subunit RBP4 (RpoF)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.98  E-value=9.1e-33  Score=217.38  Aligned_cols=108  Identities=30%  Similarity=0.413  Sum_probs=101.2

Q ss_pred             ccCccccccCcccccccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhC
Q 028639           94 EALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEH  173 (206)
Q Consensus        94 eEdaaeLkLG~eF~ena~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~  173 (206)
                      ||||++|+||+||. |++|||||||++||+++++++  ...++..+++.++.+|++|+++|++|++++++.+|+++|..+
T Consensus         1 ee~a~~l~~~~ef~-~~~~Lt~~Ev~~iL~~~~~~~--~~~~~~~~l~~~~~ktl~Yl~~fak~~~~es~~~~~~ll~~~   77 (129)
T d2c35a1           1 EEDASQLIFPKEFE-TAETLLNSEVHMLLEHRKQQN--ESAEDEQELSEVFMKTLNYTARFSRFKNRETIASVRSLLLQK   77 (129)
T ss_dssp             CCBGGGTBCCSSSS-SCEECCHHHHHHHHHHHHHHH--HSSCSSCCCCHHHHHHHHHHHHTCSCCSHHHHHHHHHHHHTS
T ss_pred             CcchhhhcccHhhc-chhhhhHHHHHHHHHHHHHHH--hcccccccHHHHHHHHHHHHHHhccCCCHHHHHHHHHHhccc
Confidence            79999999999998 999999999999999988765  355677788999999999999999999999999999999999


Q ss_pred             CCCcchhhhhhccCCCCHHHHHHhhcccccc
Q 028639          174 GVTDGEICVIANICPETVEEAYAIVPSLKVW  204 (206)
Q Consensus       174 gL~kFEIAqLaNLcPeTaEEAKALIPSL~~~  204 (206)
                      +|++||+|||+||||.|++||++||||++..
T Consensus        78 ~L~~~E~~~i~Nl~P~~~~El~~li~~l~~r  108 (129)
T d2c35a1          78 KLHKFELACLANLCPETAEESKALIPSLEGR  108 (129)
T ss_dssp             SCCHHHHHHHHHHCCSSHHHHHHHCGGGTTT
T ss_pred             CCCHHHHHHHhCCCCCCHHHHHHHHHHhccC
Confidence            9999999999999999999999999999743

>d1y14a_ a.60.8.2 (A:) RNA polymerase II subunit RBP4 (RpoF) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: RNA polymerase II subunit RBP4 (RpoF)
domain: RNA polymerase II subunit RBP4 (RpoF)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.94  E-value=6.8e-29  Score=205.87  Aligned_cols=122  Identities=17%  Similarity=0.199  Sum_probs=69.8

Q ss_pred             ccCCCCCcccccccCccccccCcccccccccccHHHHHHHHHHHHHHHh-----hhcCCCCCCchHHHHHHHHHHHhcCC
Q 028639           82 KVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMA-----LLSADPTIKIPVSFDKGLLYAKTHSH  156 (206)
Q Consensus        82 ~~~~~~k~~~~~eEdaaeLkLG~eF~ena~cLslsEV~lILe~~~e~~~-----~~s~d~~~~~s~vf~KTleYv~rFSk  156 (206)
                      +..++.++......+..++.+..+-+++..+++.+|...++....++++     ...+++....++||+|||+|+++|+|
T Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~l~~~~~~~e~~sg~~~~v~~kTldYl~~Fsk  108 (176)
T d1y14a_          29 QKKHKKKHLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSR  108 (176)
T ss_dssp             C-------------------------------------------CHHHHHHHHHHHHHHHSCSCCHHHHHHHHHHHHHCS
T ss_pred             ccccccccccccCCchhhhcccccCchhhhhhccchhhhhhhhhhhHHHHHhhhhhcccCCCCchHHHHHHHHHHHHhcc
Confidence            3344444444444455555555555567778888877777755433332     23456677788999999999999999


Q ss_pred             CCCHHHHHHHHHHHHhCCCCcchhhhhhccCCCCHHHHHHhhccccc
Q 028639          157 FTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKV  203 (206)
Q Consensus       157 fkn~Esv~aVRelL~~~gL~kFEIAqLaNLcPeTaEEAKALIPSL~~  203 (206)
                      |++++++++||++|.+++||+||+|+|+||||+|+||||+|||||+.
T Consensus       109 ~k~~es~~~vrelL~~~~L~~fE~a~L~NLcPet~eEAkaLiPSL~~  155 (176)
T d1y14a_         109 FRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN  155 (176)
T ss_dssp             CCSHHHHHHHHHHHHTTTCCHHHHHHHHHSCCSSHHHHHHHSGGGTT
T ss_pred             CCCHHHHHHHHHHHHhcCCCHHHHHHhhccCCCCHHHHHHHhhhhcc
Confidence            99999999999999999999999999999999999999999999973

>d1go3f_ a.60.8.2 (F:) RNA polymerase II subunit RBP4 (RpoF) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: RNA polymerase II subunit RBP4 (RpoF)
domain: RNA polymerase II subunit RBP4 (RpoF)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.85  E-value=8.6e-22  Score=151.07  Aligned_cols=89  Identities=19%  Similarity=0.258  Sum_probs=78.8

Q ss_pred             CcccccccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcchhhh
Q 028639          103 EQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICV  182 (206)
Q Consensus       103 G~eF~ena~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kFEIAq  182 (206)
                      |.++- +.++||++||+.||..+.+.         .++++++++||+|+++|++| +++.+.++++.|...++|+|++|+
T Consensus         3 ~keii-~e~~lt~ae~keiL~~~~~~---------~elsye~~~tL~y~~~fak~-~~e~~~~l~~~L~~~~~~~~~aak   71 (107)
T d1go3f_           3 GKKIL-GERYVTVSEAAEIMYNRAQI---------GELSYEQGCALDYLQKFAKL-DKEEAKKLVEELISLGIDEKTAVK   71 (107)
T ss_dssp             SSEEE-EEEEECHHHHHHHHHHHHHH---------SCCCHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHTTCCHHHHHH
T ss_pred             chhhh-hccccCHHHHHHHHHHhhcc---------ccccHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHhcCCCHHHHHH
Confidence            44555 67899999999999876432         25789999999999999999 789999988888889999999999


Q ss_pred             hhccCCCCHHHHHHhhcccc
Q 028639          183 IANICPETVEEAYAIVPSLK  202 (206)
Q Consensus       183 LaNLcPeTaEEAKALIPSL~  202 (206)
                      ||||||+|+||+|+||||+.
T Consensus        72 IanL~P~~~dElrai~~~~~   91 (107)
T d1go3f_          72 IADILPEDLDDLRAIYYKRE   91 (107)
T ss_dssp             HHHHCCCSHHHHHHHSTTSC
T ss_pred             HHHhCCCCHHHHHHHHHHhc
Confidence            99999999999999999975