Citrus Sinensis ID: 030872

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170
Protein Sequence
MEKGGGGKGGGVGGGGKTSLKSIPASLGGKDDNSAKSKRGRKVQFNTEGLSEGKFTFSSKSDGKFETTYGKGGLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQYP
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHccccccHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccHHccccccccEcccccccccccccccccccccccccccccccccccccccccccccccccccccHEcccccccHccHHHHcHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHccccccHHHHHHHHccc
Coil and Loop (DISEMBL)
mekggggkgggvggggktslksipaslggkddnsakskrgrkvqfnteglsegkftfssksdgkfettygkggltkggkgdkvangakVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMAllsadptikipvsfdkgllyakthshftnpqavkglfqyp
Flexible Loop (DISEMBL)
mekggggkgggvggggktslksipaslggkddnsakskrgrkvqfnteglsegkftfssksdgkfettygkggltkggkgdkvangAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHshftnpqavkglfqyp
Low Complexity Region (SEG)
MEkggggkgggvggggkTSLKSIPASLGGKDDNSAKSKRGRKVQFNTEGLSEGKFTFSSKSDGKFEttygkggltkggkgDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQYP
Disordered region (IsUnstruct)
**************************************************************************************AKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAV*******
Disordered Region (DISOPRED)
*******************************************************************************************************QELPKNAKCLMDCEAAHILEGIQEQ**********KIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ**
Disordered Region (DISEMBL)
***************GKTSLKSIPAS***************KVQFNTEGLSEGKFTFSSKSDGKFETTYGKGGLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQYP
Disordered Region (DISPRO)
************************************************************************************************PLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQYP
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MEKGGGGKGGGVGGGGKTSLKSIPASLGGKDDNSAKSKRGRKVQFNTEGLSEGKFTFSSKSDGKFETTYGKGGLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQYP
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

No hits with e-value below 0.001 by BLAST

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	170
225468957	239	PREDICTED: uncharacterized protein LOC10	0.958	0.682	0.593	5e-45
255568114	203	conserved hypothetical protein [Ricinus	0.841	0.704	0.576	4e-44
449491225	220	PREDICTED: DNA-directed RNA polymerase I	0.841	0.65	0.544	3e-34
449434414	242	PREDICTED: uncharacterized protein LOC10	0.841	0.590	0.544	3e-34
224124738	197	predicted protein [Populus trichocarpa]	0.641	0.553	0.530	4e-31
356532865	211	PREDICTED: DNA-directed RNA polymerase I	0.870	0.701	0.461	4e-30
388515433	201	unknown [Medicago truncatula]	0.805	0.681	0.478	1e-26
357448135	223	DNA-directed RNA polymerase II subunit r	0.711	0.542	0.5	5e-25
51970310	158	unnamed protein product [Arabidopsis tha	0.835	0.898	0.412	8e-22
51971721	155	unnamed protein product [Arabidopsis tha	0.835	0.916	0.412	8e-22

>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 =  185 bits (470), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 98/165 (59%), Positives = 123/165 (74%), Gaps = 2/165 (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 GIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ 168
           GIQEQM +LS DPTIKIP+SF+KGL YA++ + + +PQ+V+ + +
Sbjct: 125 GIQEQMVVLSEDPTIKIPLSFNKGLQYAQSSNCYASPQSVRLVLE 169

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 =  182 bits (462), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 98/170 (57%), Positives = 121/170 (71%), Gaps = 27/170 (15%)

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 AHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ 168
           A +L+GIQEQM LLS DPTIK+PVSFD+ L +A+T + FTNPQ+V+ + +
Sbjct: 96  AQVLQGIQEQMVLLSRDPTIKLPVSFDRALQHARTGARFTNPQSVRRILE 145

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 =  150 bits (378), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 86/158 (54%), Positives = 107/158 (67%), Gaps = 15/158 (9%)

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 LLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ 168
            LSADPTIKIP SFD+GL YAK  +H+ N ++V+ + +
Sbjct: 126 FLSADPTIKIPTSFDRGLQYAKRANHYVNAESVRPVLE 163

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 =  149 bits (377), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 86/158 (54%), Positives = 107/158 (67%), Gaps = 15/158 (9%)

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 LLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ 168
            LSADPTIKIP SFD+GL YAK  +H+ N ++V+ + +
Sbjct: 126 FLSADPTIKIPTSFDRGLQYAKRANHYVNAESVRPVLE 163

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 =  139 bits (350), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 70/132 (53%), Positives = 87/132 (65%), Gaps = 23/132 (17%)

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 FTNPQAVKGLFQ 168
           +TNPQ+V+ + +
Sbjct: 128 YTNPQSVRRVLE 139

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 =  135 bits (341), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 79/171 (46%), Positives = 106/171 (61%), Gaps = 23/171 (13%)

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 EAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF 167
           EA  IL+GIQE+M +LS D T+K+P+SFDKGL YAK++S + + Q+++ + 
Sbjct: 102 EAVDILQGIQERMVMLSRDSTVKMPISFDKGLQYAKSNSKYLDLQSIRHIL 152

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 =  124 bits (312), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 79/165 (47%), Positives = 102/165 (61%), Gaps = 28/165 (16%)

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--LYAKTHSHFTNPQAVKGLFQ 168
           Q+QM  LS DP+IK+P SFDKGL    + + S ++NP++V+   +
Sbjct: 99  QDQMVALSRDPSIKMPASFDKGLYYAKSSSSSKYSNPESVRHTLE 143

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 =  119 bits (297), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 70/140 (50%), Positives = 92/140 (65%), Gaps = 19/140 (13%)

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 LYAKTHSHFTNPQAVKGLFQ 168
             + + S ++NP++V+   +
Sbjct: 146 AKSSSSSKYSNPESVRHTLE 165

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|51970310|dbj|BAD43847.1| unnamed protein product [Arabidopsis thaliana]

 Score =  108 bits (270), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 66/160 (41%), Positives = 98/160 (61%), Gaps = 18/160 (11%)

Query: 13  GGGGKTSLKSIPASLGGKDDNSAKSKRGRKVQFNTEGLSEGKFTFSSKSDGK--FETTYG 70
           G G K+SLKS     GGKD +S K K+GRK+ F+ +G     +   + S  +  F+++  
Sbjct: 6   GKGLKSSLKS---KDGGKDGSSTKLKKGRKIHFD-QGTPPANYKILNVSSDQQPFQSS-- 59

Query: 71  KGGLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMA 130
                K GK DK    +K S+       EL+   +LP+NA+C+MDCEA  IL+GI+ Q+ 
Sbjct: 60  ---AAKCGKSDKPTKSSKNSLHS----FELK---DLPENAECMMDCEAFQILDGIKGQLV 109

Query: 131 LLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQYP 170
            LS DP+IKIPVS+D+ L Y ++  H+TNPQ+V+ + +YP
Sbjct: 110 GLSEDPSIKIPVSYDRALAYVESCVHYTNPQSVRKVLEYP 149

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|51971721|dbj|BAD44525.1| unnamed protein product [Arabidopsis thaliana]

 Score =  108 bits (270), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 66/160 (41%), Positives = 98/160 (61%), Gaps = 18/160 (11%)

Query: 13  GGGGKTSLKSIPASLGGKDDNSAKSKRGRKVQFNTEGLSEGKFTFSSKSDGK--FETTYG 70
           G G K+SLKS     GGKD +S K K+GRK+ F+ +G     +   + S  +  F+++  
Sbjct: 3   GKGLKSSLKS---KDGGKDGSSTKLKKGRKIHFD-QGTPPANYKILNVSSDQQPFQSS-- 56

Query: 71  KGGLTKGGKGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMA 130
                K GK DK    +K S+       EL+   +LP+NA+C+MDCEA  IL+GI+ Q+ 
Sbjct: 57  ---AAKCGKSDKPTKSSKNSLHS----FELK---DLPENAECMMDCEAFQILDGIKGQLV 106

Query: 131 LLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQYP 170
            LS DP+IKIPVS+D+ L Y ++  H+TNPQ+V+ + +YP
Sbjct: 107 GLSEDPSIKIPVSYDRALAYVESCVHYTNPQSVRKVLEYP 146

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	170
TAIR|locus:2178158	138	NRPB4 [Arabidopsis thaliana (t	0.382	0.471	0.439	9.7e-09

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

 Score = 131 (51.2 bits), Expect = 9.7e-09, P = 9.7e-09
 Identities = 29/66 (43%), Positives = 40/66 (60%)

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 NPQAVK 164
             NP AV+
Sbjct:    70 NPDAVR 75


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.312   0.130   0.359    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      170       141   0.00091  102 3  11 23  0.37    32
                                                     30  0.47    33


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  545 (58 KB)
  Total size of DFA:  116 KB (2077 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  12.10u 0.10s 12.20t   Elapsed:  00:00:01
  Total cpu time:  12.10u 0.10s 12.20t   Elapsed:  00:00:01
  Start:  Fri May 10 01:30:56 2013   End:  Fri May 10 01:30:57 2013

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

---

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	170
pfam03874	110	pfam03874, RNA_pol_Rpb4, RNA polymerase Rpb4	6e-04

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

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 13/57 (22%), Positives = 21/57 (36%)

Query: 112 CLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ 168
            L + E   IL+   E+    S      +     K L Y    S   NP++ + L +
Sbjct: 1   YLTNSEVLEILKKELEERRRESRYVEENLNTILRKTLEYLNKFSRLKNPESARELVE 57

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	170
KOG2351	134	consensus RNA polymerase II, fourth largest subuni	99.93
smart00657	118	RPOL4c DNA-directed RNA-polymerase II subunit.	99.54
COG5250	138	RPB4 RNA polymerase II, fourth largest subunit [Tr	99.06
PF03874	117	RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR00	98.77
PRK14981	112	DNA-directed RNA polymerase subunit F; Provisional	98.71
COG1460	114	Uncharacterized protein conserved in archaea [Func	94.26

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

Probab=99.93  E-value=1.2e-26  Score=183.54  Aligned_cols=77  Identities=30%  Similarity=0.324  Sum_probs=73.3

Q ss_pred             cccccCCccccccCcccccchhhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872           90 SVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ  168 (170)
Q Consensus        90 sa~~eEdAaELkf~~EF~~NAkcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~  168 (170)
                      .+..||||++|+||+||+ +++|||+|||.+||||+.+|.++ |+|+.+++++||.|||+|+.|||||||+++|++||.
T Consensus         2 ~g~~EEdAa~lk~g~EFe-~~~~L~~sEa~lllE~~~~q~~r-s~d~~~~~s~Vf~kTl~Y~~~FsRfKn~etv~avr~   78 (134)
T KOG2351|consen    2 RGEEEEDAAELKLGKEFE-TADALMLSEARLLLEHRLEQRRR-SEDDESEMSDVFKKTLQYLDRFSRFKNRETVRAVRT   78 (134)
T ss_pred             cchhhccHHhccccHHHH-HHHHHHHHHHHHHHHHHHHHHhh-cccccchHHHHHHHHHHHHHHHHHhcCHHHHHHHHH
Confidence            467899999999999998 69999999999999999999874 999999999999999999999999999999999995

>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit

Probab=99.54  E-value=9.3e-15  Score=110.71  Aligned_cols=62  Identities=24%  Similarity=0.380  Sum_probs=55.0

Q ss_pred             cccccchhhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872          104 QELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ  168 (170)
Q Consensus       104 ~EF~~NAkcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~  168 (170)
                      ++|. ||+||+||||++||+++++.-.  +.++...++.||.|||+|+++|++|+|+++|+++|+
T Consensus         1 ~~f~-~a~~L~n~Ev~~ll~~k~~~~~--~~~~~~~l~~v~~~tl~Yl~~~~~~~~~e~i~~~~~   62 (118)
T smart00657        1 PEFK-NATCLTNSEVQLLLELKRQSKE--SEEEQQPLSTVMKKTLKYLSKFARFKNREIVRAVRT   62 (118)
T ss_pred             CCcc-chhHhHHHHHHHHHHHHHHhhc--cccccchHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            4787 8999999999999998765332  777788899999999999999999999999999985

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

Probab=99.06  E-value=1.5e-10  Score=92.23  Aligned_cols=75  Identities=21%  Similarity=0.282  Sum_probs=63.3

Q ss_pred             ccccCCccccccCcccccchhhhhhHHHHHHHHHHHHHHHhhhcC--CCCcchHH--HHHHHHHHHhcCCCCCHHHHHhh
Q 030872           91 VVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSAD--PTIKIPVS--FDKGLLYAKTHSHFTNPQAVKGL  166 (170)
Q Consensus        91 a~~eEdAaELkf~~EF~~NAkcLmnsEVa~ILE~rkeq~~~lSeD--p~~eiseV--F~KTL~YakrFSrfkN~eSVr~V  166 (170)
                      +.-||||+.|++++||+ |.+.||.||+..|+|...++-.  .+.  -+..+.+|  |.+|++|-..|+||++.+++..+
T Consensus         4 ~~~ee~aa~lklg~efe-~ed~l~lsEAr~lie~~l~~rr--retn~~e~~s~dvk~~k~T~~Yl~~F~Rfkd~e~~~a~   80 (138)
T COG5250           4 AIFEEDAAQLKLGPEFE-NEDMLMLSEARYLIEGQLERRR--RETNGAEFRSNDVKVFKSTLGYLDDFCRFKDKEVAEAL   80 (138)
T ss_pred             hHhhhhHHHhhcCcccc-chHHHHHHHHHHHHHHHHHHHH--HhcccccccchhHHHHHHHHHHHHHHHHhhhHHHHHHH
Confidence            56789999999999998 8999999999999998877543  222  24556666  99999999999999999999888


Q ss_pred             hc
Q 030872          167 FQ  168 (170)
Q Consensus       167 R~  168 (170)
                      |.
T Consensus        81 ~~   82 (138)
T COG5250          81 RT   82 (138)
T ss_pred             HH
Confidence            74

>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=98.77  E-value=8.5e-09  Score=76.19  Aligned_cols=57  Identities=32%  Similarity=0.376  Sum_probs=46.6

Q ss_pred             hhhhHHHHHHHHHHH-HHHHh------hhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872          112 CLMDCEAAHILEGIQ-EQMAL------LSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ  168 (170)
Q Consensus       112 cLmnsEVa~ILE~rk-eq~~~------lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~  168 (170)
                      ||.|+||..||+++. ++...      ..+++...++.++.+|++|+++|++++|+++++++++
T Consensus         1 ~Lsn~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Yl~~~~~~~~~e~~~~l~~   64 (117)
T PF03874_consen    1 LLSNYEVLQILEKRREEQKNKSKKKQKNKEDPPENLNTIQYKTLEYLEKFSKFQNPESIKELRE   64 (117)
T ss_dssp             EE-HHHHHHHHHHHHHHHHCHCHHHHHHHHHCSSCHCHHHHHHHHHHHHH-SSSSHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHHHHhhhccccccccccccchHHHHHHHHHHHHccccCCCHHHHHHHHH
Confidence            799999999999554 44332      2467889999999999999999999999999999885

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 ....

>PRK14981 DNA-directed RNA polymerase subunit F; Provisional

Probab=98.71  E-value=1.4e-08  Score=77.34  Aligned_cols=48  Identities=21%  Similarity=0.272  Sum_probs=40.0

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhh
Q 030872          110 AKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGL  166 (170)
Q Consensus       110 AkcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~V  166 (170)
                      .+||.++||+.||+++.+.         .+++.+|.|||+|+++|++|++.++...|
T Consensus         9 e~~lt~sEa~~iL~~~~~~---------~els~~~~ktl~y~~kFsk~~~e~a~elv   56 (112)
T PRK14981          9 EEYITIAEAKEILSEIEEE---------RELSYELRRTLDYLNRFSKLDPEDAEELV   56 (112)
T ss_pred             cccccHHHHHHHHHHHHhc---------cchhHHHHHHHHHHHHHhCCCHHHHHHHH
Confidence            6899999999999998763         18999999999999999999644444443

>COG1460 Uncharacterized protein conserved in archaea [Function unknown]

Probab=94.26  E-value=0.09  Score=41.48  Aligned_cols=48  Identities=21%  Similarity=0.360  Sum_probs=40.1

Q ss_pred             hhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872          111 KCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ  168 (170)
Q Consensus       111 kcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~  168 (170)
                      +-+-.+||+.||..+         +.+.+++-.+..||.|+++|++.- |+.++++.+
T Consensus        11 ~yiti~Eak~il~~~---------~~~~eL~y~~~~al~y~~kFakld-pe~a~e~ve   58 (114)
T COG1460          11 KYITISEAKKILSKV---------EREEELTYEQREALEYAEKFAKLD-PEKARELVE   58 (114)
T ss_pred             cCccHHHHHHHHHHh---------cccccchHHHHHHHHHHHHHhcCC-HHHHHHHHH
Confidence            456689999999998         224789999999999999999987 998887753

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	170
2c35_A	152	Human RPB4, DNA-directed RNA polymerase II 16 kDa	2e-11
3h0g_D	135	DNA-directed RNA polymerase II subunit RPB4; trans	9e-11
3hou_D	221	DNA-directed RNA polymerase II subunit RPB4; RNA p	3e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-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 = 58.2 bits (140), Expect = 2e-11
 Identities = 23/100 (23%), Positives = 41/100 (41%), Gaps = 9/100 (9%)

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 MALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ 168
               SA+   ++   F K L Y    S F N + +  +  
Sbjct: 58  --NESAEDEQELSEVFMKTLNYTARFSRFKNRETIASVRS 95

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

 Score = 55.8 bits (134), Expect = 9e-11
 Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 2/66 (3%)

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

Query: 159 NPQAVK 164
             +A  
Sbjct: 70  TAEATY 75

>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 = 47.3 bits (111), Expect = 3e-07
 Identities = 13/94 (13%), Positives = 28/94 (29%), Gaps = 5/94 (5%)

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

Query: 136 PTIKIPVS-----FDKGLLYAKTHSHFTNPQAVK 164
             ++             + Y    S F + + V 
Sbjct: 128 VLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVG 161

>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 = 39.1 bits (90), Expect = 4e-04
 Identities = 32/177 (18%), Positives = 58/177 (32%), Gaps = 46/177 (25%)

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---LYAKTHSH---------FTNPQAVKGLF 167
            +Q   A  + + + KI + +  K +   L A T +H          T  +  K L 
Sbjct: 252 NVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV-KSLL 307

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	170
3h0g_D	135	DNA-directed RNA polymerase II subunit RPB4; trans	99.86
2c35_A	152	Human RPB4, DNA-directed RNA polymerase II 16 kDa	99.82
1go3_F	107	DNA-directed RNA polymerase subunit F; transferase	99.16
3hou_D	221	DNA-directed RNA polymerase II subunit RPB4; RNA p	98.71
1y14_A	187	B32, RPB4, DNA-directed RNA polymerase II 32 kDa p	98.44
4ayb_F	113	DNA-directed RNA polymerase; transferase, multi-su	97.78
3ayh_A	136	DNA-directed RNA polymerase III subunit RPC9; tran	97.52
2ckz_A	161	DNA-directed RNA polymerase III 18 KD polypeptide;	96.01

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

Probab=99.86  E-value=2.7e-22  Score=155.68  Aligned_cols=76  Identities=20%  Similarity=0.237  Sum_probs=67.2

Q ss_pred             ccccCCccccccCcccccchhhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872           91 VVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ  168 (170)
Q Consensus        91 a~~eEdAaELkf~~EF~~NAkcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~  168 (170)
                      +..||||++|+||+||+ ||+||+||||++||+.+++|... .....++++.||.|||+|+++|+||+|+++|++||+
T Consensus         4 ~~~ee~a~~L~lg~eF~-~a~~Ls~sEv~~lL~~~~~~r~~-~~~~~~~~~~v~~kTl~Yl~~Fsk~~~~e~~~~v~~   79 (135)
T 3h0g_D            4 AIFEEDAAQLKLGPEFE-NEDMLTVSEAKILIETVLAQRAR-ETNGEIPMTDVMKKTVAYFNVFARFKTAEATYACER   79 (135)
T ss_dssp             --CCCCCTTTCSCHHHH-HSCBCCHHHHHHHHHHHHHHHHT-TCCSCCCCTTHHHHHHHHHHTTCTTCSHHHHHHHHH
T ss_pred             hHHHHhHHhhCCCHhhc-CcccccHHHHHHHHHHHHHHHHh-cccCCcchhHHHHHHHHHHHHccCCCCHHHHHHHHH
Confidence            67899999999999998 89999999999999999877652 234568899999999999999999999999999986

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

Probab=99.82  E-value=1e-20  Score=148.72  Aligned_cols=78  Identities=23%  Similarity=0.260  Sum_probs=68.1

Q ss_pred             CccccccCCccccccCcccccchhhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhh
Q 030872           88 KVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF  167 (170)
Q Consensus        88 kssa~~eEdAaELkf~~EF~~NAkcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR  167 (170)
                      ......||||++|+|++||. |++||+||||+.||++|+++..  +.|+..+++.+|.|||+|+++|++|+|+++|++||
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            55667899999999999997 7999999999999999999875  57788999999999999999999999999999998


Q ss_pred             c
Q 030872          168 Q  168 (170)
Q Consensus       168 ~  168 (170)
                      +
T Consensus        95 e   95 (152)
T 2c35_A           95 S   95 (152)
T ss_dssp             H
T ss_pred             H
Confidence            5

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

Probab=99.16  E-value=2.6e-11  Score=90.57  Aligned_cols=56  Identities=14%  Similarity=0.206  Sum_probs=49.7

Q ss_pred             cCcccccchhhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872          102 VEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ  168 (170)
Q Consensus       102 f~~EF~~NAkcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~  168 (170)
                      ++++|. +++||++|||+.||++|.+.         .+++.+|.|||+|+++|++| +++.++++++
T Consensus         2 i~kei~-~~~~lt~sEa~~iL~~~~~~---------~e~s~~~~ktl~y~~kFsk~-~~e~a~~l~e   57 (107)
T 1go3_F            2 IGKKIL-GERYVTVSEAAEIMYNRAQI---------GELSYEQGCALDYLQKFAKL-DKEEAKKLVE   57 (107)
T ss_dssp             CSSEEE-EEEEECHHHHHHHHHHHHHH---------SCCCHHHHHHHHHHHHHCCS-CHHHHHHHHH
T ss_pred             chHHHh-cccccCHHHHHHHHHHHHhc---------ccccHHHHHHHHHHHHHhCC-CHHHHHHHHH
Confidence            567887 69999999999999999772         68999999999999999999 7888887764

>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=98.71  E-value=2.1e-08  Score=84.39  Aligned_cols=30  Identities=17%  Similarity=0.298  Sum_probs=28.2

Q ss_pred             cchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872          139 KIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ  168 (170)
Q Consensus       139 eiseVF~KTL~YakrFSrfkN~eSVr~VR~  168 (170)
                      ..++||+|||+|+++|+||+|+++|+.||+
T Consensus       136 ~~seVf~KTLdYl~rFSKfkn~EAv~aVrE  165 (221)
T 3hou_D          136 GNNKDLKNTMQYLTNFSRFRDQETVGAVIQ  165 (221)
T ss_dssp             SCCHHHHHHHHHHHHSCSCCCHHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHhcCCCcHHHHHHHHH
Confidence            368999999999999999999999999996

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

Probab=98.44  E-value=1.8e-07  Score=76.81  Aligned_cols=49  Identities=16%  Similarity=0.143  Sum_probs=41.9

Q ss_pred             chhhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872          109 NAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ  168 (170)
Q Consensus       109 NAkcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~  168 (170)
                      |.+-.-++||+.||+.+           ..+++.+|.|||+|+.+|++|+||++|++||+
T Consensus        83 ~~~~~~i~~v~~lle~~-----------~~~ls~v~~KTLeYl~rFsk~kn~Esa~elre  131 (187)
T 1y14_A           83 ETREKELESIDVLLEQT-----------TGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQ  131 (187)
T ss_dssp             -CHHHHHHHHHHHHHHH-----------SCSCCHHHHHHHHHHHHHCSCCSHHHHHHHHH
T ss_pred             chhhhhHHHHHHHHhhc-----------cccccHHHHHHHHHHHHccCCCCHHHHHHHHH
Confidence            34455679999999954           35899999999999999999999999999985

>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=97.78  E-value=1.7e-06  Score=64.92  Aligned_cols=48  Identities=6%  Similarity=0.089  Sum_probs=38.3

Q ss_pred             hhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872          111 KCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ  168 (170)
Q Consensus       111 kcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~  168 (170)
                      +-+.++||..||+.+         .++.+++++|.|||+|+++|++| +++.++++|+
T Consensus        10 ~~it~~eakeiL~~~---------~~~~~~s~~~~ktl~y~~~Fsk~-~~e~a~~l~e   57 (113)
T 4ayb_F           10 HYIPYSVAKKLLSDV---------IKSGSSSNLLQRTYDYLNSVEKC-DAESAQKVVE   57 (113)
T ss_dssp             EEECTTGGGGTTTTT---------SSSSCCCTTHHHHHHHTTTTCSS-CHHHHHHHHH
T ss_pred             cccCHHHHHHHHHHH---------HhcccccHHHHHHHHHHHHHcCC-CHHHHHHHHH
Confidence            456688888888654         23468899999999999999999 7777777764

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

Probab=97.52  E-value=6.2e-05  Score=57.69  Aligned_cols=61  Identities=8%  Similarity=-0.024  Sum_probs=47.9

Q ss_pred             cchhhhhhHHHHHHHHHHHHHHHhh--hc-----CCCCcchHHHHHHHHHHHhc--CCCCCHHHHHhhhc
Q 030872          108 KNAKCLMDCEAAHILEGIQEQMALL--SA-----DPTIKIPVSFDKGLLYAKTH--SHFTNPQAVKGLFQ  168 (170)
Q Consensus       108 ~NAkcLmnsEVa~ILE~rkeq~~~l--Se-----Dp~~eiseVF~KTL~YakrF--SrfkN~eSVr~VR~  168 (170)
                      .|+.+|.|.||..+|++++.+...-  .+     .....+..|+.+|++|..++  ..+.|+++|+++++
T Consensus        13 ~~~a~LsN~EVl~~L~~~~~~~~~~~~~~~~~~~~~~~~l~ti~~e~l~YL~~~p~~~~q~~e~i~~l~~   82 (136)
T 3ayh_A           13 ARDAYLTNAEVFFHLKEMENEQNARTQERGAAQALVCENLRTIQFEILKYLSSQGNCEGLTKERFLDCIA   82 (136)
T ss_dssp             EEEEEECHHHHHHHHHHHHHHHHHHHHHHGGGGCCCCHHHHHHHHHHHHHHHTTTCCTTCCHHHHHHHHH
T ss_pred             cccccccHHHHHHHHHHHHhhhcccccccCCccccccchHHHHHHHHHHHHHhCCCccccCHHHHHHHHH
Confidence            4688999999999999998654311  11     12366899999999999999  56689999999874

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

Probab=96.01  E-value=0.0028  Score=50.29  Aligned_cols=50  Identities=12%  Similarity=0.140  Sum_probs=34.0

Q ss_pred             cchhhhhhHHHHHHHHHHHHHHHh---------------hhcC--CCCcchHHHHHHHHHHHhcCCC
Q 030872          108 KNAKCLMDCEAAHILEGIQEQMAL---------------LSAD--PTIKIPVSFDKGLLYAKTHSHF  157 (170)
Q Consensus       108 ~NAkcLmnsEVa~ILE~rkeq~~~---------------lSeD--p~~eiseVF~KTL~YakrFSrf  157 (170)
                      .++.+|.|.||..+|++++.+...               -.+.  +...+..|+.++++|..++++|
T Consensus         6 ~~~a~LSN~EVl~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ti~~e~~~YL~~~p~~   72 (161)
T 2ckz_A            6 ERNAFLSDYEVLKFLTDLEKKHLWDQKSLAALKKSRSKGKQNRPYNHPELQGITRNVVNYLSINKNF   72 (161)
T ss_dssp             EEEEEECHHHHHHHHHHHHHHTTCSHHHHHCC----------CCCCCHHHHHHHHHHHHHHTC----
T ss_pred             hhhhhhhHHHHHHHHHHhhhhccccccchhhhhcccccccccCCCCCccHHHHHHHHHHHHHhCCcc
Confidence            357899999999999999875320               0011  1245788999999999999984

---

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	170
d1y14a_	176	a.60.8.2 (A:) RNA polymerase II subunit RBP4 (RpoF	6e-15
d2c35a1	129	a.60.8.2 (A:14-142) RNA polymerase II subunit RBP4	3e-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 = 66.5 bits (162), Expect = 6e-15
 Identities = 13/94 (13%), Positives = 28/94 (29%), Gaps = 5/94 (5%)

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

Query: 136 PTIKIPVS-----FDKGLLYAKTHSHFTNPQAVK 164
             ++             + Y    S F + + V 
Sbjct: 83  VLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVG 116

>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 = 55.5 bits (134), Expect = 3e-11
 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 3/66 (4%)

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 NPQAVK 164
           N + + 
Sbjct: 63  NRETIA 68

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	170
d2c35a1	129	RNA polymerase II subunit RBP4 (RpoF) {Human (Homo	99.82
d1y14a_	176	RNA polymerase II subunit RBP4 (RpoF) {Baker's yea	99.43
d1go3f_	107	RNA polymerase II subunit RBP4 (RpoF) {Archaeon Me	98.49

>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=99.82  E-value=4.5e-21  Score=144.34  Aligned_cols=72  Identities=25%  Similarity=0.325  Sum_probs=68.4

Q ss_pred             cCCccccccCcccccchhhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872           94 EALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ  168 (170)
Q Consensus        94 eEdAaELkf~~EF~~NAkcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~  168 (170)
                      ||||++|+|++||. |++||+||||+.||++|+++..  +.++..+++.||.|||+|+.+|++|+|+++|+.||+
T Consensus         1 ee~a~~l~~~~ef~-~~~~Lt~~Ev~~iL~~~~~~~~--~~~~~~~l~~~~~ktl~Yl~~fak~~~~es~~~~~~   72 (129)
T d2c35a1           1 EEDASQLIFPKEFE-TAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNYTARFSRFKNRETIASVRS   72 (129)
T ss_dssp             CCBGGGTBCCSSSS-SCEECCHHHHHHHHHHHHHHHH--SSCSSCCCCHHHHHHHHHHHHTCSCCSHHHHHHHHH
T ss_pred             CcchhhhcccHhhc-chhhhhHHHHHHHHHHHHHHHh--cccccccHHHHHHHHHHHHHHhccCCCHHHHHHHHH
Confidence            69999999999998 8999999999999999998764  888999999999999999999999999999999985

>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=99.43  E-value=4.3e-15  Score=118.93  Aligned_cols=90  Identities=16%  Similarity=0.133  Sum_probs=40.1

Q ss_pred             CCCcccCCCCccccccCCccccccCcccccchhhhhhHHHHHHHHHHH-----HHHHhhhcCCCCcchHHHHHHHHHHHh
Q 030872           79 KGDKVANGAKVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQ-----EQMALLSADPTIKIPVSFDKGLLYAKT  153 (170)
Q Consensus        79 k~~k~a~g~kssa~~eEdAaELkf~~EF~~NAkcLmnsEVa~ILE~rk-----eq~~~lSeDp~~eiseVF~KTL~Yakr  153 (170)
                      +..+..++.+..........++.++.+.++|+.++|+||.+.+++...     +++..+++++....++||+|||+|+++
T Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~l~~~~~~~e~~sg~~~~v~~kTldYl~~  105 (176)
T d1y14a_          26 KRSQKKHKKKHLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTN  105 (176)
T ss_dssp             HSCC-------------------------------------------CHHHHHHHHHHHHHHHSCSCCHHHHHHHHHHHH
T ss_pred             cccccccccccccccCCchhhhcccccCchhhhhhccchhhhhhhhhhhHHHHHhhhhhcccCCCCchHHHHHHHHHHHH
Confidence            333333444444445556778889999999999999998777766554     445557888999999999999999999


Q ss_pred             cCCCCCHHHHHhhhc
Q 030872          154 HSHFTNPQAVKGLFQ  168 (170)
Q Consensus       154 FSrfkN~eSVr~VR~  168 (170)
                      |+||+|+++|++||+
T Consensus       106 Fsk~k~~es~~~vre  120 (176)
T d1y14a_         106 FSRFRDQETVGAVIQ  120 (176)
T ss_dssp             HCSCCSHHHHHHHHH
T ss_pred             hccCCCHHHHHHHHH
Confidence            999999999999996

>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=98.49  E-value=6.3e-08  Score=70.76  Aligned_cols=55  Identities=15%  Similarity=0.190  Sum_probs=46.3

Q ss_pred             CcccccchhhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872          103 EQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ  168 (170)
Q Consensus       103 ~~EF~~NAkcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~  168 (170)
                      ++++-+ -+.|.++||..||+.|.+         +.+|+.+|.|||+|+++|++| ||++++++++
T Consensus         3 ~keii~-e~~lt~ae~keiL~~~~~---------~~elsye~~~tL~y~~~fak~-~~e~~~~l~~   57 (107)
T d1go3f_           3 GKKILG-ERYVTVSEAAEIMYNRAQ---------IGELSYEQGCALDYLQKFAKL-DKEEAKKLVE   57 (107)
T ss_dssp             SSEEEE-EEEECHHHHHHHHHHHHH---------HSCCCHHHHHHHHHHHHHCCS-CHHHHHHHHH
T ss_pred             chhhhh-ccccCHHHHHHHHHHhhc---------cccccHHHHHHHHHHHHHHcC-CHHHHHHHHH
Confidence            445553 688999999999998754         157999999999999999999 8999998874