Citrus Sinensis ID: 027312

---

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-------210-------220-----
Protein Sequence
MEKGGGGKGGGVGGGGKTSLKSIPASLGGKDDNSAKSKRGRKVQFNTEGLSEGKFTFSSKSDGKFETTYGKGGLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKST
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHccccHHHHHHHHccccccHHHHHHHcccccccccccHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccHHHcccccccccccHHHHcccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccHccHHHcccccHccccHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccHHHHHHHHccccccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
mekggggkgggvggggktslksipaslggkddnsakskrgrkvqfnteglsegkftfssksdgkfettygkggltkggkgdkvangakVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMAllsadptikipvsfdkgllyakthshftnpqAVKGLFQSLsehgvtdgeicVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKST
Flexible Loop (DISEMBL)
mekggggkgggvggggktslksipaslggkddnsakskrgrkvqfnteglsegkftfssksdgkfettygkggltkggkgdkvangAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKST
Low Complexity Region (SEG)
MEkggggkgggvggggkTSLKSIPASLGGKDDNSAKSKRGRKVQFNTEGLSEGKFTFSSKSDGKFEttygkggltkggkgDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKST
Disordered region (IsUnstruct)
**************************************************************************************AKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLA*****
Disordered Region (DISOPRED)
******************************************************************************************************EQELPKNAKCLMDCEAAHILE*******************SFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKF***
Disordered Region (DISEMBL)
***************GKTSLKSIPAS***************KVQFNTEGLSEGKFTFSSKSDGKFETTYGKGGLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKST
Disordered Region (DISPRO)
************************************************************************************************PLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAK****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MEKGGGGKGGGVGGGGKTSLKSIPASLGGKDDNSAKSKRGRKVQFNTEGLSEGKFTFSSKSDGKFETTYGKGGLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKST
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	225	2.2.26 [Sep-21-2011]
Q54S04	155	DNA-directed RNA polymera	yes	no	0.502	0.729	0.310	6e-08
Q9D7M8	142	DNA-directed RNA polymera	yes	no	0.422	0.669	0.298	1e-05
O15514	142	DNA-directed RNA polymera	yes	no	0.422	0.669	0.298	1e-05

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

 Score = 57.8 bits (138), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 40/129 (31%), Positives = 68/129 (52%), Gaps = 16/129 (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 SHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKE 214
           S + N  ++K +  +LS+  + + EI  +AN+CPE  +EA +++PSLK      +D L+ 
Sbjct: 87  SRYKNKTSIKQVRTALSKQNLEEFEIASLANLCPEISDEAKSLIPSLKKME---DDELQA 143

Query: 215 VLIQLAKFK 223
           +L +L+  +
Sbjct: 144 ILDELSNLR 152

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 = 50.1 bits (118), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 29/97 (29%), Positives = 52/97 (53%), Gaps = 2/97 (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 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAK 204
             L +  +   E+  +AN+CPET EE+ A++PSL+ +
Sbjct: 85  SLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR 121

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 = 50.1 bits (118), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 29/97 (29%), Positives = 52/97 (53%), Gaps = 2/97 (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 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAK 204
             L +  +   E+  +AN+CPET EE+ A++PSL+ +
Sbjct: 85  SLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR 121

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	225
225468957	239	PREDICTED: uncharacterized protein LOC10	0.977	0.920	0.594	1e-65
255568114	203	conserved hypothetical protein [Ricinus	0.88	0.975	0.564	2e-63
449491225	220	PREDICTED: DNA-directed RNA polymerase I	0.888	0.909	0.548	2e-55
449434414	242	PREDICTED: uncharacterized protein LOC10	0.888	0.826	0.548	4e-55
224124738	197	predicted protein [Populus trichocarpa]	0.728	0.832	0.545	8e-51
356532865	211	PREDICTED: DNA-directed RNA polymerase I	0.915	0.976	0.475	7e-50
388515433	201	unknown [Medicago truncatula]	0.853	0.955	0.490	2e-45
357448135	223	DNA-directed RNA polymerase II subunit r	0.782	0.789	0.507	2e-43
297804626	210	At4g15950 [Arabidopsis lyrata subsp. lyr	0.897	0.961	0.437	3e-39
334186572	205	RNA polymerase II, Rpb4, core protein [A	0.88	0.965	0.415	5e-36

>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 =  255 bits (651), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 132/222 (59%), Positives = 168/222 (75%), Gaps = 2/222 (0%)

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 ANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKST 225
           AN CPET++E +A+VPSLK K S L + LK+VL  LA+ K +
Sbjct: 185 ANTCPETIDEVFALVPSLKPKWSTLREPLKDVLRGLAELKHS 226

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 =  247 bits (631), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 127/225 (56%), Positives = 166/225 (73%), Gaps = 27/225 (12%)

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 EICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFK 223
           EIC IAN+CP+ V+E +A+VPSLK+K++ L + LK++L QL++ K
Sbjct: 156 EICTIANVCPDGVDEVFALVPSLKSKKNVLREPLKDILGQLSELK 200

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 =  221 bits (564), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 118/215 (54%), Positives = 154/215 (71%), Gaps = 15/215 (6%)

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 VEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKST 225
            +E +A++PSLK KRS+L++ +  VL +LAK KS+
Sbjct: 186 TDEVFALLPSLKRKRSKLSEPINNVLSELAKVKSS 220

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 =  219 bits (559), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 118/215 (54%), Positives = 153/215 (71%), Gaps = 15/215 (6%)

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 VEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKST 225
            +E +A++PSLK KRS+L++ +  VL +LAK KS 
Sbjct: 186 TDEVFALLPSLKRKRSKLSEPINNVLSELAKVKSC 220

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  206 bits (523), Expect = 8e-51,   Method: Compositional matrix adjust.
 Identities = 102/187 (54%), Positives = 133/187 (71%), Gaps = 23/187 (12%)

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 FTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVL 216
           +TNPQ+V+ + ++L ++GV+DGEI +IAN+ PET +EA+A+VPSLK+K S L + LK++L
Sbjct: 128 YTNPQSVRRVLEALRKYGVSDGEISLIANVFPETADEAFALVPSLKSKASTLREPLKDIL 187

Query: 217 IQLAKFK 223
            +LAKFK
Sbjct: 188 GELAKFK 194

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  202 bits (515), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 109/229 (47%), Positives = 151/229 (65%), Gaps = 23/229 (10%)

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 DGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKST 225
           D EICVI N+CPET++E +A++PSLK +R+  + +LK+ L +LAKF+ T
Sbjct: 162 DSEICVIGNVCPETIDEVFALLPSLKDRRNIDSQVLKDSLSELAKFRQT 210

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  187 bits (476), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 108/220 (49%), Positives = 143/220 (65%), Gaps = 28/220 (12%)

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 ANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFK 223
           AN+CPET +E +A++PSLK+KR   +  ++E L +LAKFK
Sbjct: 159 ANVCPETADEVFALLPSLKSKRGINSQPVEEALSELAKFK 198

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 =  181 bits (460), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 99/195 (50%), Positives = 133/195 (68%), Gaps = 19/195 (9%)

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 LYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRL 208
             + + S ++NP++V+   + L  H +T+ EICVIAN+CPET +E +A++PSLK+KR   
Sbjct: 146 AKSSSSSKYSNPESVRHTLEPLMNHDLTESEICVIANVCPETADEVFALLPSLKSKRGIN 205

Query: 209 NDLLKEVLIQLAKFK 223
           +  ++E L +LAKFK
Sbjct: 206 SQPVEEALSELAKFK 220

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 =  167 bits (423), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 94/215 (43%), Positives = 135/215 (62%), Gaps = 13/215 (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 VEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKST 225
           V+E  A +PSLKAK+  +N  L++ L++LAK K +
Sbjct: 175 VDEVLAFIPSLKAKKEVINQPLQDALVELAKLKKS 209

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 =  156 bits (395), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 89/214 (41%), Positives = 133/214 (62%), Gaps = 16/214 (7%)

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 EEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKST 225
           +E  A +PSLK K+  +N  L++ L +L+K K +
Sbjct: 171 DEVLAFIPSLKTKKEVINQPLQDALEELSKLKKS 204

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	225
TAIR|locus:2178158	138	NRPB4 [Arabidopsis thaliana (t	0.551	0.898	0.444	1.6e-22
DICTYBASE|DDB_G0282739	155	rpb4 "DNA-directed RNA polymer	0.591	0.858	0.326	1.8e-09
WB|WBGene00018391	144	rpb-4 [Caenorhabditis elegans	0.448	0.701	0.342	5.9e-09
ZFIN|ZDB-GENE-040714-2	145	polr2d "polymerase (RNA) II (D	0.568	0.882	0.283	5.3e-08
UNIPROTKB|F1P2S1	147	POLR2D "Uncharacterized protei	0.471	0.721	0.290	1.1e-07
UNIPROTKB|Q1JQ91	142	POLR2D "Polymerase (RNA) II (D	0.471	0.746	0.281	2.5e-07
UNIPROTKB|E2RPH1	142	POLR2D "Uncharacterized protei	0.471	0.746	0.281	2.5e-07
UNIPROTKB|O15514	142	POLR2D "DNA-directed RNA polym	0.471	0.746	0.281	2.5e-07
MGI|MGI:1916491	142	Polr2d "polymerase (RNA) II (D	0.471	0.746	0.281	2.5e-07
RGD|1308565	142	Polr2d "polymerase (RNA) II (D	0.471	0.746	0.281	2.5e-07

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

 Score = 261 (96.9 bits), Expect = 1.6e-22, P = 1.6e-22
 Identities = 56/126 (44%), Positives = 83/126 (65%)

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 NPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAK-RSRLNDLLKEVLI 217
             NP AV+ + + LS H +T+ E+CV+ N+CPETVEEA A+VPSLK K R+  ++ ++++L 
Sbjct:    70 NPDAVRQVREILSRHQLTEFELCVLGNLCPETVEEAVAMVPSLKTKGRAHDDEAIEKMLN 129

Query:   218 QLAKFK 223
              L+  K
Sbjct:   130 DLSLVK 135

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 = 138 (53.6 bits), Expect = 1.8e-09, P = 1.8e-09
 Identities = 49/150 (32%), Positives = 77/150 (51%)

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 AYAIVPSLKAKRS-RLNDLLKEVLIQLAKF 222
             A +++PSLK      L  +L E L  L KF
Sbjct:   126 AKSLIPSLKKMEDDELQAILDE-LSNLRKF 154

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

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

 Score = 133 (51.9 bits), Expect = 5.9e-09, P = 5.9e-09
 Identities = 36/105 (34%), Positives = 56/105 (53%)

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

Query:   173 HGVTDGEICVIANICPETVEEAYAIVPSL--KAKRSRLNDLLKEV 215
               +   E+  IAN+CPE  EEA A+VPSL  K + S L ++LK++
Sbjct:    93 KHLHKFEVAQIANLCPENAEEAKALVPSLENKIEESELEEVLKDL 137

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

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

 Score = 124 (48.7 bits), Expect = 5.3e-08, P = 5.3e-08
 Identities = 38/134 (28%), Positives = 67/134 (50%)

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 FDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKA 203
             F K L Y    S F N + +  +   L +  +   E+  +AN+CPE  EEA A++PSL+ 
Sbjct:    64 FMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELASLANLCPEAAEEAKALIPSLEG 123

Query:   204 K--RSRLNDLLKEV 215
             +     L  +L ++
Sbjct:   124 RFEDEELQQILDDI 137

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 = 121 (47.7 bits), Expect = 1.1e-07, P = 1.1e-07
 Identities = 32/110 (29%), Positives = 57/110 (51%)

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

Query:   168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAK--RSRLNDLLKEV 215
               L +  +   E+  +AN+CPET EEA A++PSL+ +     L  +L ++
Sbjct:    90 SLLLQKKLHKFELACLANLCPETAEEAKALIPSLEGRFEDEELQQILDDI 139

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

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

 Score = 118 (46.6 bits), Expect = 2.5e-07, P = 2.5e-07
 Identities = 31/110 (28%), Positives = 57/110 (51%)

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

Query:   168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAK--RSRLNDLLKEV 215
               L +  +   E+  +AN+CPET EE+ A++PSL+ +     L  +L ++
Sbjct:    85 SLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDI 134

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 = 118 (46.6 bits), Expect = 2.5e-07, P = 2.5e-07
 Identities = 31/110 (28%), Positives = 57/110 (51%)

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

Query:   168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAK--RSRLNDLLKEV 215
               L +  +   E+  +AN+CPET EE+ A++PSL+ +     L  +L ++
Sbjct:    85 SLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDI 134

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 = 118 (46.6 bits), Expect = 2.5e-07, P = 2.5e-07
 Identities = 31/110 (28%), Positives = 57/110 (51%)

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

Query:   168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAK--RSRLNDLLKEV 215
               L +  +   E+  +AN+CPET EE+ A++PSL+ +     L  +L ++
Sbjct:    85 SLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDI 134

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 = 118 (46.6 bits), Expect = 2.5e-07, P = 2.5e-07
 Identities = 31/110 (28%), Positives = 57/110 (51%)

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

Query:   168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAK--RSRLNDLLKEV 215
               L +  +   E+  +AN+CPET EE+ A++PSL+ +     L  +L ++
Sbjct:    85 SLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDI 134

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 = 118 (46.6 bits), Expect = 2.5e-07, P = 2.5e-07
 Identities = 31/110 (28%), Positives = 57/110 (51%)

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

Query:   168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAK--RSRLNDLLKEV 215
               L +  +   E+  +AN+CPET EE+ A++PSL+ +     L  +L ++
Sbjct:    85 SLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDI 134

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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	225
pfam03874	110	pfam03874, RNA_pol_Rpb4, RNA polymerase Rpb4	2e-22
smart00657	118	smart00657, RPOL4c, DNA-directed RNA-polymerase II	9e-13
COG5250	138	COG5250, RPB4, RNA polymerase II, fourth largest s	4e-06

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

 Score = 87.2 bits (217), Expect = 2e-22
 Identities = 30/106 (28%), Positives = 49/106 (46%), Gaps = 2/106 (1%)

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

Query: 172 EHGVTDGEICVIANICPETVEEAYAIVPSLKAKRS--RLNDLLKEV 215
           E  +T  E   I N+ PET +E  AI+ SL+++ S  +L ++L  +
Sbjct: 61  EFELTKFEALQIVNLLPETADELRAIIESLESRFSEEQLEEILDIL 106

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 = 9e-13
 Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 4/111 (3%)

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

Query: 168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRS--RLNDLLKEVL 216
             L    +   EI  + N+ PET EEA  ++PSL+ +     L +LL ++ 
Sbjct: 62  TLLKSKKLHKFEIAQLGNLRPETAEEAQLLIPSLEERIDEEELEELLDDLS 112

Length = 118

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

 Score = 44.6 bits (105), Expect = 4e-06
 Identities = 31/132 (23%), Positives = 60/132 (45%), Gaps = 5/132 (3%)

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

Query: 149 LYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRL 208
            Y      F + +  + L  +LS  G  + EI  + ++  ++ EEA  ++PSL  K    
Sbjct: 63  GYLDDFCRFKDKEVAEALRTTLSGLGFHEFEIAQLGSLFCQSAEEAKTLIPSLGNKID-- 120

Query: 209 NDLLKEVLIQLA 220
           + +L+ +L +L+
Sbjct: 121 DAILQAILKELS 132

Length = 138

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	225
KOG2351	134	consensus RNA polymerase II, fourth largest subuni	100.0
COG5250	138	RPB4 RNA polymerase II, fourth largest subunit [Tr	99.97
smart00657	118	RPOL4c DNA-directed RNA-polymerase II subunit.	99.97
PRK14981	112	DNA-directed RNA polymerase subunit F; Provisional	99.94
PF03874	117	RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR00	99.94
COG1460	114	Uncharacterized protein conserved in archaea [Func	99.57
KOG4168	149	consensus Predicted RNA polymerase III subunit C17	98.64
PF06569	71	DUF1128: Protein of unknown function (DUF1128); In	87.47

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

Probab=100.00  E-value=1.2e-41  Score=275.44  Aligned_cols=130  Identities=35%  Similarity=0.460  Sum_probs=123.8

Q ss_pred             cccccCccccccCcccccccccccHHHHHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHh
Q 027312           91 VVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSL  170 (225)
Q Consensus        91 ~~~eE~aaeLkLG~eF~~nakcLsnsEV~~ILe~~~e~~~~~s~d~~~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL  170 (225)
                      ...|||||+|+||+||. ++.|||+|||++||+++.++.+ .+.|+..++++||.||+.|+++||||+|++++.+||++|
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 9999999999999999998864 367888999999999999999999999999999999999


Q ss_pred             hhCCCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhc
Q 027312          171 SEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS  224 (225)
Q Consensus       171 ~~~~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~  224 (225)
                      ...+||+||+|||+||||+|+|||++|||||+.|  ++|+.|++||++|+.+|.
T Consensus        81 s~~~lhkFE~A~lgnLcpetaEEAkaLvPSL~nk--idD~~le~iL~dls~lr~  132 (134)
T KOG2351|consen   81 SGKGLHKFEVAQLGNLCPETAEEAKALVPSLENK--IDDDELEQILKDLSTLRT  132 (134)
T ss_pred             hhCCcchhhHHHHhccCcccHHHHHHhccccccc--cCHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999998  999999999999999885

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

Probab=99.97  E-value=2.8e-32  Score=219.80  Aligned_cols=131  Identities=24%  Similarity=0.330  Sum_probs=117.2

Q ss_pred             cccccCccccccCcccccccccccHHHHHHHHHHHHHHhhhhcCCCCCCchH--HHHHHHHHHHhcCCCCCHHHHHHHHH
Q 027312           91 VVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPV--SFDKGLLYAKTHSHFTNPQAVKGLFQ  168 (225)
Q Consensus        91 ~~~eE~aaeLkLG~eF~~nakcLsnsEV~~ILe~~~e~~~~~s~d~~~~~s~--Vf~KTleYl~rFSk~k~~esv~~Vre  168 (225)
                      +..|||||+|+|||||+ |...||++||+++|+....+++.+-.......++  +|++|+.|++.||+|++.+.+.+++.
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            45799999999999998 9999999999999999887764221112333444  49999999999999999999999999


Q ss_pred             HhhhCCCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhc
Q 027312          169 SLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS  224 (225)
Q Consensus       169 lL~~~~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~  224 (225)
                      +|...|+|+||+||+++|||+++||||+|||||..|  ++|..+|.||++++.+|+
T Consensus        83 ~L~~~gfh~fEiAqlGsL~c~saeEAktLiPSL~nk--idD~~lq~ilkels~l~~  136 (138)
T COG5250          83 TLSGLGFHEFEIAQLGSLFCQSAEEAKTLIPSLGNK--IDDAILQAILKELSLLRK  136 (138)
T ss_pred             HHccCCcchhhHHHhhccccccHHHHHhhccccccc--ccHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999999999999998  999999999999999986

>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit

Probab=99.97  E-value=2.5e-31  Score=211.96  Aligned_cols=116  Identities=28%  Similarity=0.393  Sum_probs=105.3

Q ss_pred             cccccccccccHHHHHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhCCCCchhhhhh
Q 027312          104 QELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVI  183 (225)
Q Consensus       104 ~eF~~nakcLsnsEV~~ILe~~~e~~~~~s~d~~~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL~~~~L~kfEiAqL  183 (225)
                      ++|. |++|||||||++||+.++...  .+.++..+++.|+++|++|+++|+++++++++.++++.|..++||+||+|||
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 999999999999999654322  2344556788999999999999999999999999999999999999999999


Q ss_pred             hccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhc
Q 027312          184 ANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS  224 (225)
Q Consensus       184 aNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~  224 (225)
                      +||||+|++||++|||||++|  |+|++|++||++|+++|.
T Consensus        78 ~Nl~P~s~~E~~~lI~sl~~r--~~ee~l~~iL~~i~~~~~  116 (118)
T smart00657       78 GNLRPETAEEAQLLIPSLEER--IDEEELEELLDDLSSLLP  116 (118)
T ss_pred             hCCCCCCHHHHHHHhhhhhcc--CCHHHHHHHHHHHHHhcC
Confidence            999999999999999999987  999999999999999985

>PRK14981 DNA-directed RNA polymerase subunit F; Provisional

Probab=99.94  E-value=1.2e-26  Score=184.50  Aligned_cols=105  Identities=23%  Similarity=0.277  Sum_probs=92.6

Q ss_pred             ccccccHHHHHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhCCCCchhhhhhhccCC
Q 027312          109 NAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICP  188 (225)
Q Consensus       109 nakcLsnsEV~~ILe~~~e~~~~~s~d~~~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL~~~~L~kfEiAqLaNL~P  188 (225)
                      ..+|||++||+.||+++.+..         ++++++++|++|+++|++++..++.+.+++++...+|++|++|+|+||||
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            567999999999999876531         67899999999999999997666777666777777799999999999999


Q ss_pred             CCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhc
Q 027312          189 ETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS  224 (225)
Q Consensus       189 eT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~  224 (225)
                      +|+||||+|||++..  ++++++|++|||+|.+||.
T Consensus        79 ~~~dElrai~~~~~~--~~~~e~l~~ILd~l~k~~~  112 (112)
T PRK14981         79 ETRDELRAIFAKERY--TLSPEELDEILDIVKKYRE  112 (112)
T ss_pred             CCHHHHHHHHHHhcc--CCCHHHHHHHHHHHHHhhC
Confidence            999999999999844  5999999999999999973

>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=99.94  E-value=1.6e-26  Score=181.37  Aligned_cols=110  Identities=32%  Similarity=0.416  Sum_probs=93.9

Q ss_pred             cccHHHHHHHHHHHHHHhhhh-------cCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhCCCCchhhhhhh
Q 027312          112 CLMDCEAAHILEGIQEQMALL-------SADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIA  184 (225)
Q Consensus       112 cLsnsEV~~ILe~~~e~~~~~-------s~d~~~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL~~~~L~kfEiAqLa  184 (225)
                      ||||+||+.||+++.+.....       ...+..+++.++++|++|+++|+++++++++..+++.|..++|+++|++||+
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            799999999999655433211       1245678889999999999999999999999999999999999999999999


Q ss_pred             ccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhh
Q 027312          185 NICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFK  223 (225)
Q Consensus       185 NL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r  223 (225)
                      ||||+|++|+++|||+++.|  |+|++|++||++|++||
T Consensus        81 Nl~P~~~~El~~ii~~~~~r--~~ee~l~~iL~~v~~~~  117 (117)
T PF03874_consen   81 NLRPTTAVELRAIIESLESR--FSEEDLEEILDLVSKYR  117 (117)
T ss_dssp             HH--SSHHHHHHHSTTGTTT--STHHHHHHHHHHHHHHT
T ss_pred             cCCCCCHHHHHHHHHHhccC--CCHHHHHHHHHHHHHhC
Confidence            99999999999999999986  99999999999999987

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=99.57  E-value=2e-14  Score=115.32  Aligned_cols=105  Identities=20%  Similarity=0.316  Sum_probs=85.8

Q ss_pred             ccccccHHHHHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhh-CCCCchhhhhhhccC
Q 027312          109 NAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSE-HGVTDGEICVIANIC  187 (225)
Q Consensus       109 nakcLsnsEV~~ILe~~~e~~~~~s~d~~~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL~~-~~L~kfEiAqLaNL~  187 (225)
                      +-+.+|++||+.||..+         ....++++.++.||+|+++|+++. |+.++++.+-|.. .++.+.-++-|+.||
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            44689999999999977         233567899999999999999997 7777777766654 445444355599999


Q ss_pred             CCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhcC
Q 027312          188 PETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKST  225 (225)
Q Consensus       188 PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~~  225 (225)
                      |+|.+|+|+|+.+  ++..+++|+|++|||.+.+||.+
T Consensus        79 P~t~~ElRsIla~--e~~~~s~E~l~~Ildiv~Ky~~~  114 (114)
T COG1460          79 PRTPDELRSILAK--ERVMLSDEELDKILDIVDKYREE  114 (114)
T ss_pred             CCCHHHHHHHHHH--ccCCCCHHHHHHHHHHHHHHhcC
Confidence            9999999999995  44578999999999999999863

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

Probab=98.64  E-value=6.7e-08  Score=80.73  Aligned_cols=113  Identities=18%  Similarity=0.224  Sum_probs=91.3

Q ss_pred             cccccccHHHHHHHHHHHHHHhhh--h-c-CCCC-----CCchHHHHHHHHHHHhc--CCCCCHHHHHHHHHHhhhCCCC
Q 027312          108 KNAKCLMDCEAAHILEGIQEQMAL--L-S-ADPT-----IKIPVSFDKGLLYAKTH--SHFTNPQAVKGLFQSLSEHGVT  176 (225)
Q Consensus       108 ~nakcLsnsEV~~ILe~~~e~~~~--~-s-~d~~-----~~~s~Vf~KTleYl~rF--Sk~k~~esv~~VrelL~~~~L~  176 (225)
                      .+.-.|+|.||...|.....+...  + + +...     .+++.+.+.|+.|+..=  +.-.++|.+.++..-+..++|+
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            355689999999999887632110  0 0 1111     34788999999999983  5666788888888888999999


Q ss_pred             chhhhhhhccCCCCHHHHHHhhccccccCCC-CHHHHHHHHHHHHhh
Q 027312          177 DGEICVIANICPETVEEAYAIVPSLKAKRSR-LNDLLKEVLIQLAKF  222 (225)
Q Consensus       177 kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~-~de~Lq~ILd~Lsk~  222 (225)
                      +.|+.||.|+.|-++-|...+|.-+++|  | ++++|.++|..+..+
T Consensus        86 KAE~LqiiN~rPss~vel~~~iE~~eeR--f~~ee~i~elv~~i~~~  130 (149)
T KOG4168|consen   86 KAEILQIINLRPSSSVELYLIIEEVEER--FQDEEDIEELVETISKT  130 (149)
T ss_pred             HHHHHHHhccCcchHHHHHHHHHHHHHh--ccchhcHHHHHHhcccc
Confidence            9999999999999999999999999987  7 999999999888653

>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function

Probab=87.47  E-value=1.2  Score=33.60  Aligned_cols=40  Identities=15%  Similarity=0.195  Sum_probs=33.8

Q ss_pred             ccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhc
Q 027312          185 NICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS  224 (225)
Q Consensus       185 NL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~  224 (225)
                      ++-....|+.+-|+.....|.+|+..+++.|.++|.++|+
T Consensus        32 ~f~~~~yedl~diy~~V~~K~~fS~sEm~aI~~ELG~LRK   71 (71)
T PF06569_consen   32 DFSEEKYEDLKDIYEMVMSKDSFSPSEMQAIAEELGQLRK   71 (71)
T ss_pred             hCChhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHhhcC
Confidence            4455668888888887777778999999999999999996

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	225
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 = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/97 (29%), Positives = 52/97 (53%), Gaps = 2/97 (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 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAK 204
             L +  +   E+  +AN+CPET EE+ A++PSL+ +
Sbjct: 95  SLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR 131

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	225
2c35_A	152	Human RPB4, DNA-directed RNA polymerase II 16 kDa	1e-30
3h0g_D	135	DNA-directed RNA polymerase II subunit RPB4; trans	3e-28
3hou_D	221	DNA-directed RNA polymerase II subunit RPB4; RNA p	7e-25
1y14_A	187	B32, RPB4, DNA-directed RNA polymerase II 32 kDa p	6e-16
3ayh_A	136	DNA-directed RNA polymerase III subunit RPC9; tran	2e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
4ayb_F	113	DNA-directed RNA polymerase; transferase, multi-su	3e-05

>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 =  109 bits (274), Expect = 1e-30
 Identities = 40/156 (25%), Positives = 75/156 (48%), Gaps = 11/156 (7%)

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 ETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS 224
           ET EE+ A++PSL+ +    ++ L+++L  +   +S
Sbjct: 116 ETAEESKALIPSLEGRFE--DEELQQILDDIQTKRS 149

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

 Score =  102 bits (256), Expect = 3e-28
 Identities = 27/126 (21%), Positives = 52/126 (41%), Gaps = 5/126 (3%)

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

Query: 159 NPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQ 218
             +A     + +  +     E   +  +C E  EEA  ++PSL  K    +  L+ +L +
Sbjct: 70  TAEATYAC-ERILGNRFHKFERAQLGTLCCEDAEEARTLIPSLANKID--DQNLQGILDE 126

Query: 219 LAKFKS 224
           L+  + 
Sbjct: 127 LSTLRK 132

>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 = 96.6 bits (239), Expect = 7e-25
 Identities = 29/154 (18%), Positives = 61/154 (39%), Gaps = 7/154 (4%)

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 VEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS 224
            +EA  ++PSL  K S  +D L+ +L +L+  ++
Sbjct: 188 ADEAKTLIPSLNNKIS--DDELERILKELSNLET 219

>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 = 72.3 bits (176), Expect = 6e-16
 Identities = 25/113 (22%), Positives = 48/113 (42%), Gaps = 2/113 (1%)

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

Query: 172 EHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS 224
             G+   E+  + ++  +T +EA  ++PSL  K S  +D L+ +L +L+  ++
Sbjct: 135 STGLHPFEVAQLGSLACDTADEAKTLIPSLNNKIS--DDELERILKELSNLET 185

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

 Score = 42.0 bits (98), Expect = 2e-05
 Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 3/71 (4%)

Query: 149 LYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRL 208
           L ++ +      +         +E  +T  EI VI N  P +V E YA +  ++    R 
Sbjct: 63  LSSQGNCEGLTKERFLDCIAIFNEFELTKAEILVILNNKPSSVPELYACIEGIE---ERF 119

Query: 209 NDLLKEVLIQL 219
            +     L++ 
Sbjct: 120 KEEDIFKLVEK 130

>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 = 44.1 bits (103), Expect = 2e-05
 Identities = 35/236 (14%), Positives = 74/236 (31%), Gaps = 55/236 (23%)

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--------SLKAKRSRLNDLLKEVLIQLAKFKST 225
           + +   +  P+ +  E     P        S++   +  ++      +   K  + 
Sbjct: 306 LLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKH---VNCDKLTTI 358

>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 = 41.5 bits (97), Expect = 3e-05
 Identities = 13/76 (17%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 150 YAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLN 209
           Y  +     + ++ + + + LS     +    V+A+ICP T +E  +I+  + + R+  +
Sbjct: 40  YLNSVEK-CDAESAQKVVEELSSIISREDVRAVLASICPITPDEVRSIL-IMDSNRTYTS 97

Query: 210 DLLKEVLIQLAKFKST 225
           + +++++  + K+  +
Sbjct: 98  EDIQKIIDIIRKYIKS 113

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	225
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	99.98
1y14_A	187	B32, RPB4, DNA-directed RNA polymerase II 32 kDa p	99.95
1go3_F	107	DNA-directed RNA polymerase subunit F; transferase	99.95
4ayb_F	113	DNA-directed RNA polymerase; transferase, multi-su	99.91
3ayh_A	136	DNA-directed RNA polymerase III subunit RPC9; tran	99.82
2ckz_A	161	DNA-directed RNA polymerase III 18 KD polypeptide;	99.75

>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=8.2e-42  Score=278.28  Aligned_cols=129  Identities=22%  Similarity=0.297  Sum_probs=118.6

Q ss_pred             cccccCccccccCcccccccccccHHHHHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHh
Q 027312           91 VVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSL  170 (225)
Q Consensus        91 ~~~eE~aaeLkLG~eF~~nakcLsnsEV~~ILe~~~e~~~~~s~d~~~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL  170 (225)
                      +++||||++|+||+||+ |++|||||||++||+.++++++. ...+..+++.||+||++|+++|++|++++++.+||++|
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             hhCCCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhc
Q 027312          171 SEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS  224 (225)
Q Consensus       171 ~~~~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~  224 (225)
                      .. +||+||+|||+||||+|+||||+|||||++|  ++|++|++||++|++||.
T Consensus        82 ~~-~L~~fEia~L~NL~P~t~dEak~LIpsL~~r--~~de~L~~IL~~l~~~r~  132 (135)
T 3h0g_D           82 GN-RFHKFERAQLGTLCCEDAEEARTLIPSLANK--IDDQNLQGILDELSTLRK  132 (135)
T ss_dssp             CC-CSCHHHHHHHHHHCCCCHHHHHHHCGGGTTT--SCSHHHHHHHHHHHHHTT
T ss_pred             Hh-cCCHHHHHHHccCCCCCHHHHHHHHHHhccc--CCHHHHHHHHHHHHHHhc
Confidence            99 9999999999999999999999999999987  899999999999999985

>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=7e-38  Score=259.15  Aligned_cols=132  Identities=27%  Similarity=0.372  Sum_probs=118.7

Q ss_pred             CcccccccCccccccCcccccccccccHHHHHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHH
Q 027312           88 KVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF  167 (225)
Q Consensus        88 k~~~~~eE~aaeLkLG~eF~~nakcLsnsEV~~ILe~~~e~~~~~s~d~~~~~s~Vf~KTleYl~rFSk~k~~esv~~Vr  167 (225)
                      +..+.+||||++|+||++|. |++|||||||+.||++++.+..  +.++..++++++++|++||++|++|++++++++|+
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  34556788999999999999999999999999999


Q ss_pred             HHhhhCCCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhc
Q 027312          168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS  224 (225)
Q Consensus       168 elL~~~~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~  224 (225)
                      ++|..++||+||+|+|+||||+|+||||+|||||+.|  ++|++|++||++|++||.
T Consensus        95 e~L~~~~L~~~E~a~L~NL~P~t~dEar~lipsl~~r--~sdEeLe~ILd~l~k~r~  149 (152)
T 2c35_A           95 SLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR--FEDEELQQILDDIQTKRS  149 (152)
T ss_dssp             HHHHTSSCCHHHHHHHHHHCCSSHHHHHHHCGGGTTT--SCHHHHHHHHHHHHHHCC
T ss_pred             HHHHhcCCCHHHHHHhccCCCCCHHHHHHHHHhhccC--CCHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999876  999999999999999986

>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=99.98  E-value=1.5e-32  Score=238.38  Aligned_cols=132  Identities=23%  Similarity=0.315  Sum_probs=113.3

Q ss_pred             cccccCccccccCcccc----------cccccccHHHHHHHHHHHH-HHhhh--hc------------------------
Q 027312           91 VVKEALPLELRVEQELP----------KNAKCLMDCEAAHILEGIQ-EQMAL--LS------------------------  133 (225)
Q Consensus        91 ~~~eE~aaeLkLG~eF~----------~nakcLsnsEV~~ILe~~~-e~~~~--~s------------------------  133 (225)
                      .++||+||.|+|||||+          +...+|+++|+++|+.... ++++.  .+                        
T Consensus        18 ~~~eenaa~l~lg~efql~q~~~~g~~~~lialnlsearl~i~~al~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (221)
T 3hou_D           18 VEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKHKKKHLKHENANDETTAVEDE   97 (221)
T ss_dssp             CCCCCCCSSSCCCGGGCSEEECTTSCEEECCBCCTTHHHHHHHHHHHHHHHHHHHTTCC---------------------
T ss_pred             ccchhhhHHhhcCcccceeecccCCchhHhHhhhhHHHHHHHHHHHHHHHHHhhcccccccccccccccccccccccccc
Confidence            57999999999999998          4667999999999996532 21110  00                        


Q ss_pred             -----------CCC----------------------CCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhCCCCchhh
Q 027312          134 -----------ADP----------------------TIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEI  180 (225)
Q Consensus       134 -----------~d~----------------------~~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL~~~~L~kfEi  180 (225)
                                 .+.                      ....+.||+|||+||++|++|++++++..||++|..++||+||+
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~e~e~~~~~~~~~~~~g~~seVf~KTLdYl~rFSKfkn~EAv~aVrELL~~~gLheFEi  177 (221)
T 3hou_D           98 DDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEV  177 (221)
T ss_dssp             --------------------CTHHHHHHHHHHHHHHSCSCCHHHHHHHHHHHHSCSCCCHHHHHHHHHHHTTSCCCHHHH
T ss_pred             cccccccccccccchhhhccchHHHHHHHHHHHhhcCCCccHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHhcCCChHHh
Confidence                       000                      11457899999999999999999999999999999999999999


Q ss_pred             hhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhc
Q 027312          181 CVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS  224 (225)
Q Consensus       181 AqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~  224 (225)
                      |+||||||+|+||||+|||||+.+  +++++|++||++|++||.
T Consensus       178 AqLANLcPeTaDEARALIPSL~~k--~sDEeLqeILdeLskyR~  219 (221)
T 3hou_D          178 AQLGSLACDTADEAKTLIPSLNNK--ISDDELERILKELSNLET  219 (221)
T ss_dssp             HHHHHSCCCSHHHHHHHCTTCTTS--SCHHHHHHHHHHHHHHSC
T ss_pred             heecccCCCCHHHHHHHHHhhccc--CCHHHHHHHHHHHHHhhc
Confidence            999999999999999999999986  899999999999999984

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

Probab=99.95  E-value=1.1e-28  Score=210.74  Aligned_cols=85  Identities=22%  Similarity=0.373  Sum_probs=81.9

Q ss_pred             CCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhCCCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHH
Q 027312          138 IKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLI  217 (225)
Q Consensus       138 ~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL~~~~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd  217 (225)
                      .+++++|++||+||++|++|++++++++|+++|..++||+||+|+|+||||+|++|||+|||||+.+  +++++|++||+
T Consensus       101 ~~ls~v~~KTLeYl~rFsk~kn~Esa~elre~L~~~kL~efE~aqLaNL~PeTadEaraLIpSle~r--lsdEeLeeILd  178 (187)
T 1y14_A          101 GGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNK--ISDDELERILK  178 (187)
T ss_dssp             CSCCHHHHHHHHHHHHHCSCCSHHHHHHHHHHHHTTTCCHHHHHHHHHSCCSSHHHHHHHSGGGTTT--SCHHHHHHHHH
T ss_pred             ccccHHHHHHHHHHHHccCCCCHHHHHHHHHHHHhcCCCHHHHHHcCcCCCCCHHHHHHHHHhhccC--CCHHHHHHHHH
Confidence            4788999999999999999999999999999999999999999999999999999999999999876  99999999999


Q ss_pred             HHHhhhc
Q 027312          218 QLAKFKS  224 (225)
Q Consensus       218 ~Lsk~r~  224 (225)
                      +|++||.
T Consensus       179 ~L~k~r~  185 (187)
T 1y14_A          179 ELSNLET  185 (187)
T ss_dssp             HHHHHCC
T ss_pred             HHHHhhc
Confidence            9999985

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

Probab=99.95  E-value=4.2e-28  Score=190.44  Aligned_cols=106  Identities=19%  Similarity=0.258  Sum_probs=95.3

Q ss_pred             cCcccccccccccHHHHHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhCCCCchhhh
Q 027312          102 VEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEIC  181 (225)
Q Consensus       102 LG~eF~~nakcLsnsEV~~ILe~~~e~~~~~s~d~~~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL~~~~L~kfEiA  181 (225)
                      +|.+|. +.+|||+|||+.||+++.+.         .++++++++|++|+++|++| +++.+.++++.|.+.+||+|++|
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            466887 99999999999999988653         35779999999999999999 68888888888878899999999


Q ss_pred             hhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhh
Q 027312          182 VIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFK  223 (225)
Q Consensus       182 qLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r  223 (225)
                      +|+||||+|+||||+||||+.    + +++|++||++|++||
T Consensus        71 ~I~nl~P~t~dElraii~~~~----~-~eel~~ILd~l~k~~  107 (107)
T 1go3_F           71 KIADILPEDLDDLRAIYYKRE----L-PENAEEILEIVRKYI  107 (107)
T ss_dssp             HHHHHCCCSHHHHHHHSTTSC----C-CTTHHHHHHHHTTCC
T ss_pred             HHHHhCCCCHHHHHHHHhccc----C-cHHHHHHHHHHHHcC
Confidence            999999999999999999974    4 999999999999986

>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=99.91  E-value=7.6e-27  Score=184.70  Aligned_cols=106  Identities=13%  Similarity=0.195  Sum_probs=88.4

Q ss_pred             ccccccHHHHHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhCCCCchhhhhhhccCC
Q 027312          109 NAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICP  188 (225)
Q Consensus       109 nakcLsnsEV~~ILe~~~e~~~~~s~d~~~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL~~~~L~kfEiAqLaNL~P  188 (225)
                      +.+.++++||+.||..+         .+..++++++++||+|+++|++| +++.+.++++.|...++++||+|+|+||||
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            45689999999999743         23345678999999999999999 677888888888888999999999999999


Q ss_pred             CCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhcC
Q 027312          189 ETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKST  225 (225)
Q Consensus       189 eT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~~  225 (225)
                      +|+||||+||||++++ .+++++|++||++|++|.++
T Consensus        78 ~~~dElrali~s~e~~-~~~deeL~~IL~~l~ky~~s  113 (113)
T 4ayb_F           78 ITPDEVRSILIMDSNR-TYTSEDIQKIIDIIRKYIKS  113 (113)
T ss_dssp             CSSCCCCTTTTTTCCC-CCCCTHHHHHHHHC------
T ss_pred             CCHHHHHHHHHhhccC-CCCHHHHHHHHHHHHHHhcC
Confidence            9999999999998765 78999999999999999875

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

Probab=99.82  E-value=6e-21  Score=154.84  Aligned_cols=113  Identities=15%  Similarity=0.150  Sum_probs=97.2

Q ss_pred             cccccccHHHHHHHHHHHHHHhhhh--cCC-----CCCCchHHHHHHHHHHHhc--CCCCCHHHHHHHHHHhhhCCCCch
Q 027312          108 KNAKCLMDCEAAHILEGIQEQMALL--SAD-----PTIKIPVSFDKGLLYAKTH--SHFTNPQAVKGLFQSLSEHGVTDG  178 (225)
Q Consensus       108 ~nakcLsnsEV~~ILe~~~e~~~~~--s~d-----~~~~~s~Vf~KTleYl~rF--Sk~k~~esv~~VrelL~~~~L~kf  178 (225)
                      .++.+|||+||..+|++++.+....  ...     ...+++.|+++|++|+++|  +.+++++++.++++.|..++|+++
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            3678999999999999987643210  011     1256889999999999998  445789999999999999999999


Q ss_pred             hhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhh
Q 027312          179 EICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKF  222 (225)
Q Consensus       179 EiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~  222 (225)
                      |++||+||||.|+.|+++||+.+++|  |+||++++||++|+.+
T Consensus        93 E~LqivNl~P~t~vel~~iIEe~e~R--fsee~ie~IL~~i~~~  134 (136)
T 3ayh_A           93 EILVILNNKPSSVPELYACIEGIEER--FKEEDIFKLVEKINTT  134 (136)
T ss_dssp             HHHHHHHHCCCSHHHHHHHSTTHHHH--HTTTTHHHHHHHHHHH
T ss_pred             HHHHHhccCCCCHHHHHHHHHhcccC--CCHHHHHHHHHHHHHh
Confidence            99999999999999999999999987  9999999999999875

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

Probab=99.75  E-value=3.1e-19  Score=149.06  Aligned_cols=113  Identities=15%  Similarity=0.180  Sum_probs=33.1

Q ss_pred             ccccccHHHHHHHHHHHHHHhhh---------------hcCC--CCCCchHHHHHHHHHHHhcCC---------------
Q 027312          109 NAKCLMDCEAAHILEGIQEQMAL---------------LSAD--PTIKIPVSFDKGLLYAKTHSH---------------  156 (225)
Q Consensus       109 nakcLsnsEV~~ILe~~~e~~~~---------------~s~d--~~~~~s~Vf~KTleYl~rFSk---------------  156 (225)
                      +..+|||.||..+|+.+..+..-               ....  +..+++.|++.|++||.++.+               
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            56799999999999998765310               0011  224578899999999999987               


Q ss_pred             ----------CCCHHHHHHHHHHhhhCCCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhh
Q 027312          157 ----------FTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFK  223 (225)
Q Consensus       157 ----------~k~~esv~~VrelL~~~~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r  223 (225)
                                ..+++++..+++.|..++|+++|++||+||||.+++|+++||+.+++|  |+|+++++||++|+.++
T Consensus        87 ~~~~~~~~~~~~~~e~i~~l~~~L~~~~Ltk~E~lqivNl~P~s~vel~~iIEe~e~R--fsee~ie~IL~ii~~~~  161 (161)
T 2ckz_A           87 AKDAEKSGISKMSDESFAELMTKLNSFKLFKAEKLQIVNQLPANMVHLYSIVEECDAR--FDEKTIEEMLEIISAYA  161 (161)
T ss_dssp             -----------------------------------------------------------------------------
T ss_pred             ccccccccccccCHHHHHHHHHHHHhcCCCHHHHHHHhccCCCCHHHHHHHHHhcccC--CCHHHHHHHHHHHHHhC
Confidence                      356889999999999999999999999999999999999999999886  99999999999998764

---

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	225
d1y14a_	176	a.60.8.2 (A:) RNA polymerase II subunit RBP4 (RpoF	7e-34
d2c35a1	129	a.60.8.2 (A:14-142) RNA polymerase II subunit RBP4	5e-27
d1go3f_	107	a.60.8.2 (F:) RNA polymerase II subunit RBP4 (RpoF	1e-11

>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 =  117 bits (295), Expect = 7e-34
 Identities = 29/154 (18%), Positives = 61/154 (39%), Gaps = 7/154 (4%)

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 VEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS 224
            +EA  ++PSL  K S  +D L+ +L +L+  ++
Sbjct: 143 ADEAKTLIPSLNNKIS--DDELERILKELSNLET 174

>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 = 98.3 bits (245), Expect = 5e-27
 Identities = 34/126 (26%), Positives = 66/126 (52%), Gaps = 5/126 (3%)

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 NPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQ 218
           N + +  +   L +  +   E+  +AN+CPET EE+ A++PSL+ +    ++ L+++L  
Sbjct: 63  NRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFE--DEELQQILDD 120

Query: 219 LAKFKS 224
           +   +S
Sbjct: 121 IQTKRS 126

>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 = 57.1 bits (138), Expect = 1e-11
 Identities = 17/106 (16%), Positives = 42/106 (39%), Gaps = 12/106 (11%)

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

Query: 171 SEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRS--RLNDLLKE 214
              G+ +     IA+I PE +++  AI    +   +   + +++++
Sbjct: 60  ISLGIDEKTAVKIADILPEDLDDLRAIYYKRELPENAEEILEIVRK 105

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	225
d2c35a1	129	RNA polymerase II subunit RBP4 (RpoF) {Human (Homo	100.0
d1y14a_	176	RNA polymerase II subunit RBP4 (RpoF) {Baker's yea	99.97
d1go3f_	107	RNA polymerase II subunit RBP4 (RpoF) {Archaeon Me	99.88

>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=100.00  E-value=7.4e-38  Score=250.04  Aligned_cols=126  Identities=28%  Similarity=0.407  Sum_probs=119.2

Q ss_pred             ccCccccccCcccccccccccHHHHHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhC
Q 027312           94 EALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEH  173 (225)
Q Consensus        94 eE~aaeLkLG~eF~~nakcLsnsEV~~ILe~~~e~~~~~s~d~~~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL~~~  173 (225)
                      ||||++|+||+||. |++|||||||+.||+.++++.  .+.++..++++++++|++|+++||++++++++..|+++|..+
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  345667788999999999999999999999999999999999


Q ss_pred             CCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhc
Q 027312          174 GVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS  224 (225)
Q Consensus       174 ~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~  224 (225)
                      +|+++|+|||+||||+|++||++|||+++.|  |++++|++||+.|++||+
T Consensus        78 ~L~~~E~~~i~Nl~P~~~~El~~li~~l~~r--~see~l~~iLd~l~~~r~  126 (129)
T d2c35a1          78 KLHKFELACLANLCPETAEESKALIPSLEGR--FEDEELQQILDDIQTKRS  126 (129)
T ss_dssp             SCCHHHHHHHHHHCCSSHHHHHHHCGGGTTT--SCHHHHHHHHHHHHHHCC
T ss_pred             CCCHHHHHHHhCCCCCCHHHHHHHHHHhccC--CCHHHHHHHHHHHHHHhc
Confidence            9999999999999999999999999999876  999999999999999986

>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=99.97  E-value=1.2e-32  Score=231.28  Aligned_cols=139  Identities=19%  Similarity=0.247  Sum_probs=87.8

Q ss_pred             CCCCCcccccccCccccccCcccccccccccHHHHHHHHHHHHHHhhh-----hcCCCCCCchHHHHHHHHHHHhcCCCC
Q 027312           84 ANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMAL-----LSADPTIKIPVSFDKGLLYAKTHSHFT  158 (225)
Q Consensus        84 ~~~~k~~~~~eE~aaeLkLG~eF~~nakcLsnsEV~~ILe~~~e~~~~-----~s~d~~~~~s~Vf~KTleYl~rFSk~k  158 (225)
                      .+|.+.......+..++.+..+-+++..+++.||...+++...++++.     ..+++....+.||+||++||++|++|+
T Consensus        31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~l~~~~~~~e~~sg~~~~v~~kTldYl~~Fsk~k  110 (176)
T d1y14a_          31 KHKKKHLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFR  110 (176)
T ss_dssp             ------------------------------------------CHHHHHHHHHHHHHHHSCSCCHHHHHHHHHHHHHCSCC
T ss_pred             ccccccccccCCchhhhcccccCchhhhhhccchhhhhhhhhhhHHHHHhhhhhcccCCCCchHHHHHHHHHHHHhccCC
Confidence            344444444444455555555555677888888888777655443332     334566778899999999999999999


Q ss_pred             CHHHHHHHHHHhhhCCCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhc
Q 027312          159 NPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS  224 (225)
Q Consensus       159 ~~esv~~VrelL~~~~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~  224 (225)
                      +++++++||++|.+++||+||+|+|+||||+|+||||+|||||+.+  ++|++|++||++|++||.
T Consensus       111 ~~es~~~vrelL~~~~L~~fE~a~L~NLcPet~eEAkaLiPSL~~k--~~de~Lq~IL~~L~~~r~  174 (176)
T d1y14a_         111 DQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNK--ISDDELERILKELSNLET  174 (176)
T ss_dssp             SHHHHHHHHHHHHTTTCCHHHHHHHHHSCCSSHHHHHHHSGGGTTT--SCHHHHHHHHHHHHHHCC
T ss_pred             CHHHHHHHHHHHHhcCCCHHHHHHhhccCCCCHHHHHHHhhhhccc--CCHHHHHHHHHHHHHhhc
Confidence            9999999999999999999999999999999999999999999976  899999999999999985

>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=99.88  E-value=8.2e-23  Score=158.74  Aligned_cols=104  Identities=18%  Similarity=0.247  Sum_probs=87.2

Q ss_pred             CcccccccccccHHHHHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhCCCCchhhhh
Q 027312          103 EQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICV  182 (225)
Q Consensus       103 G~eF~~nakcLsnsEV~~ILe~~~e~~~~~s~d~~~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL~~~~L~kfEiAq  182 (225)
                      |.++- +.++||++||+.||..+.+.         .++++++++|++|+++|++| +++.+.++++.|...++|+|++|+
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            55665 77899999999999876432         25789999999999999999 799999999999889999999999


Q ss_pred             hhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhh
Q 027312          183 IANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKF  222 (225)
Q Consensus       183 LaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~  222 (225)
                      ||||||+|+||+|+|+|++..  .+++++   ||++|.+|
T Consensus        72 IanL~P~~~dElrai~~~~~~--~~~~ee---Il~il~~y  106 (107)
T d1go3f_          72 IADILPEDLDDLRAIYYKREL--PENAEE---ILEIVRKY  106 (107)
T ss_dssp             HHHHCCCSHHHHHHHSTTSCC--CTTHHH---HHHHHTTC
T ss_pred             HHHhCCCCHHHHHHHHHHhcc--CCCHHH---HHHHHHHh
Confidence            999999999999999998543  355554   55555543