Citrus Sinensis ID: 032987

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------13
MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRLL
cEEEEEEEEEEEEccccccccHHHHHHHHHHHHHHcEEEccEEEEEEEEEccEEccEEEEcccccEEEEEEEEEEEEEEccccEEEEEEEEEcccEEEEEEccccEEEEcccccccccccccccccccc
cEEEEEEEEEEEccHHHccccHHHHHHHHHHHHHHcccHHccEEEEEEEEEEEccccEEEcccccEEEEEEEEEEEEEccccEEEEEEEEEcccccEEEEEcccccEEEcHHHcccccccccccccccc
mfylskiehtlrlpphllrlplNEAIKLELENVFLDKVIANLGLCIsiydikeieggfvypgegasthtVKFRLVVFRPFVGEIIAAKLKesdanglrlslgffediyvpshllpspsrsepdpygrll
mfylskiehtlrlpphllRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPshllpspsrsepdpygrll
MFYLSKIEHTlrlpphllrlplNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRLL
**YLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSH*****************
MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRLL
MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLP**************
MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDP*****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRLL
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 ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query129 2.2.26 [Sep-21-2011]
Q9Y535204 DNA-directed RNA polymera yes no 0.922 0.583 0.428 5e-24
Q9D2C6204 DNA-directed RNA polymera yes no 0.922 0.583 0.428 8e-24
Q2T9X1204 DNA-directed RNA polymera yes no 0.922 0.583 0.428 1e-23
P35718212 DNA-directed RNA polymera yes no 0.883 0.537 0.443 8e-23
O94285203 DNA-directed RNA polymera yes no 0.953 0.605 0.373 9e-21
Q557J3 252 DNA-directed RNA polymera yes no 0.914 0.468 0.369 2e-17
P39466183 DNA-directed RNA polymera yes no 0.782 0.551 0.310 9e-10
Q7ZW41172 DNA-directed RNA polymera no no 0.945 0.709 0.284 7e-09
P62489172 DNA-directed RNA polymera no no 0.945 0.709 0.284 8e-09
P62488172 DNA-directed RNA polymera no no 0.945 0.709 0.284 8e-09
>sp|Q9Y535|RPC8_HUMAN DNA-directed RNA polymerase III subunit RPC8 OS=Homo sapiens GN=POLR3H PE=1 SV=1 Back     alignment and function desciption
 Score =  109 bits (272), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 51/119 (42%), Positives = 76/119 (63%)

Query: 1   MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVY 60
           MF L ++  T+R+PP      LN++I  EL     +KV+ N+GLCI ++DI ++E  +V+
Sbjct: 1   MFVLVEMVDTVRIPPWQFERKLNDSIAEELNKKLANKVVYNVGLCICLFDITKLEDAYVF 60

Query: 61  PGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSR 119
           PG+GAS   V FR VVF PF+ EI+  K+K     G+ +SLGFF+DI +P   L  P++
Sbjct: 61  PGDGASHTKVHFRCVVFHPFLDEILIGKIKGCSPEGVHVSLGFFDDILIPPESLQQPAK 119
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts, such as Epstein-Barr virus-encoded RNAs (EBERs) induce type I interferon and NF- Kappa-B through the RIG-I pathway.
Homo sapiens (taxid: 9606)
>sp|Q9D2C6|RPC8_MOUSE DNA-directed RNA polymerase III subunit RPC8 OS=Mus musculus GN=Polr3h PE=2 SV=2 Back     alignment and function description
>sp|Q2T9X1|RPC8_BOVIN DNA-directed RNA polymerase III subunit RPC8 OS=Bos taurus GN=POLR3H PE=2 SV=1 Back     alignment and function description
>sp|P35718|RPC8_YEAST DNA-directed RNA polymerase III subunit RPC8 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPC25 PE=1 SV=1 Back     alignment and function description
>sp|O94285|RPC8_SCHPO DNA-directed RNA polymerase III subunit rpc8 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpc25 PE=1 SV=1 Back     alignment and function description
>sp|Q557J3|RPC8_DICDI DNA-directed RNA polymerase III subunit rpc8 OS=Dictyostelium discoideum GN=polr3h-1 PE=2 SV=1 Back     alignment and function description
>sp|P39466|RPOE_SULAC DNA-directed RNA polymerase subunit E OS=Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) GN=rpoE PE=1 SV=2 Back     alignment and function description
>sp|Q7ZW41|RPB7_DANRE DNA-directed RNA polymerase II subunit RPB7 OS=Danio rerio GN=polr2g PE=2 SV=1 Back     alignment and function description
>sp|P62489|RPB7_RAT DNA-directed RNA polymerase II subunit RPB7 OS=Rattus norvegicus GN=Polr2g PE=2 SV=1 Back     alignment and function description
>sp|P62488|RPB7_MOUSE DNA-directed RNA polymerase II subunit RPB7 OS=Mus musculus GN=Polr2g PE=2 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query129
297843474204 predicted protein [Arabidopsis lyrata su 0.984 0.622 0.732 1e-50
15222202204 RNA polymerase Rpb7 N-terminal domain-co 0.984 0.622 0.732 2e-50
42571371189 RNA polymerase Rpb7 N-terminal domain-co 0.984 0.671 0.732 2e-50
225437229192 PREDICTED: DNA-directed RNA polymerase I 0.961 0.645 0.806 1e-44
359479790192 PREDICTED: DNA-directed RNA polymerase I 0.984 0.661 0.771 3e-44
255559937194 DNA-directed RNA polymerase III 25 kD po 0.984 0.654 0.740 1e-42
449436395226 PREDICTED: DNA-directed RNA polymerase I 0.953 0.544 0.650 5e-42
224062241186 predicted protein [Populus trichocarpa] 0.984 0.682 0.700 2e-39
363807592214 uncharacterized protein LOC100800770 [Gl 0.914 0.551 0.652 2e-39
356572779212 PREDICTED: DNA-directed RNA polymerase I 0.914 0.556 0.652 3e-39
>gi|297843474|ref|XP_002889618.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297335460|gb|EFH65877.1| predicted protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
 Score =  204 bits (518), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 93/127 (73%), Positives = 114/127 (89%)

Query: 1   MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVY 60
           MFYLS++EH+LR+PPHLL LPL +AIK  L+NVFLDKV+A+LGLC+S+YDIK IEGGFV 
Sbjct: 1   MFYLSELEHSLRVPPHLLNLPLEDAIKSVLQNVFLDKVLADLGLCVSVYDIKSIEGGFVL 60

Query: 61  PGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRS 120
           PG+GA+T+ V FR+VVFRPFVGE+IAAK KESD+NGLRL+LGFF+DIYVP+ L+P P+R 
Sbjct: 61  PGDGAATYKVGFRIVVFRPFVGEVIAAKFKESDSNGLRLTLGFFDDIYVPAPLMPKPNRC 120

Query: 121 EPDPYGR 127
           EPDPY R
Sbjct: 121 EPDPYNR 127

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|15222202|ref|NP_172164.1| RNA polymerase Rpb7 N-terminal domain-containing protein [Arabidopsis thaliana] gi|7523702|gb|AAF63141.1|AC011001_11 hypothetical protein [Arabidopsis thaliana] gi|17529108|gb|AAL38764.1| putative RNA polymerase [Arabidopsis thaliana] gi|23296904|gb|AAN13199.1| putative RNA polymerase [Arabidopsis thaliana] gi|332189917|gb|AEE28038.1| RNA polymerase Rpb7 N-terminal domain-containing protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|42571371|ref|NP_973776.1| RNA polymerase Rpb7 N-terminal domain-containing protein [Arabidopsis thaliana] gi|332189916|gb|AEE28037.1| RNA polymerase Rpb7 N-terminal domain-containing protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|225437229|ref|XP_002281971.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC8 [Vitis vinifera] gi|297735498|emb|CBI17938.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|359479790|ref|XP_002271507.2| PREDICTED: DNA-directed RNA polymerase III subunit RPC8-like [Vitis vinifera] gi|296086693|emb|CBI32328.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|255559937|ref|XP_002520987.1| DNA-directed RNA polymerase III 25 kD polypeptide, putative [Ricinus communis] gi|223539824|gb|EEF41404.1| DNA-directed RNA polymerase III 25 kD polypeptide, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|449436395|ref|XP_004135978.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC8-like [Cucumis sativus] gi|449523449|ref|XP_004168736.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC8-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|224062241|ref|XP_002300802.1| predicted protein [Populus trichocarpa] gi|222842528|gb|EEE80075.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|363807592|ref|NP_001241897.1| uncharacterized protein LOC100800770 [Glycine max] gi|255644932|gb|ACU22966.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|356572779|ref|XP_003554543.1| PREDICTED: DNA-directed RNA polymerase III subunit rpc8-like [Glycine max] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query129
TAIR|locus:2033077204 AT1G06790 [Arabidopsis thalian 0.984 0.622 0.653 8.4e-42
ZFIN|ZDB-GENE-040718-179214 polr3h "polymerase (RNA) III ( 0.922 0.556 0.411 3e-21
WB|WBGene00014111 239 rpc-25 [Caenorhabditis elegans 0.906 0.489 0.444 3.9e-21
UNIPROTKB|E1BV29209 POLR3H "Uncharacterized protei 0.914 0.564 0.389 5.7e-20
UNIPROTKB|F1ML03204 POLR3H "DNA-directed RNA polym 0.922 0.583 0.394 1.2e-19
UNIPROTKB|Q9Y535204 POLR3H "DNA-directed RNA polym 0.922 0.583 0.394 1.2e-19
UNIPROTKB|F1SRD6204 POLR3H "Uncharacterized protei 0.922 0.583 0.394 1.2e-19
MGI|MGI:1926179204 Polr3h "polymerase (RNA) III ( 0.922 0.583 0.394 1.2e-19
RGD|1305889204 Polr3h "polymerase (RNA) III ( 0.922 0.583 0.394 1.2e-19
UNIPROTKB|Q2T9X1204 POLR3H "DNA-directed RNA polym 0.922 0.583 0.394 1.9e-19
TAIR|locus:2033077 AT1G06790 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 443 (161.0 bits), Expect = 8.4e-42, P = 8.4e-42
 Identities = 83/127 (65%), Positives = 102/127 (80%)

Query:     1 MFYLSKIEHTXXXXXXXXXXXXNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVY 60
             MFYLS++EH+             +AIK  L+NVFLDKV+A+LGLC+SIYDIK +EGGFV 
Sbjct:     1 MFYLSELEHSLRVPPHLLNLPLEDAIKSVLQNVFLDKVLADLGLCVSIYDIKSVEGGFVL 60

Query:    61 PGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRS 120
             PG+GA+T+ V  R+VVFRPFVGE+IAAK KESDANGLRL+LGFF+DIYVP+ L+P P+R 
Sbjct:    61 PGDGAATYKVGLRIVVFRPFVGEVIAAKFKESDANGLRLTLGFFDDIYVPAPLMPKPNRC 120

Query:   121 EPDPYGR 127
             EPDPY R
Sbjct:   121 EPDPYNR 127
GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM
GO:0006351 "transcription, DNA-dependent" evidence=IEA;ISS
GO:0009507 "chloroplast" evidence=ISM
GO:0009062 "fatty acid catabolic process" evidence=RCA
ZFIN|ZDB-GENE-040718-179 polr3h "polymerase (RNA) III (DNA directed) polypeptide H" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
WB|WBGene00014111 rpc-25 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
UNIPROTKB|E1BV29 POLR3H "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|F1ML03 POLR3H "DNA-directed RNA polymerase III subunit RPC8" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|Q9Y535 POLR3H "DNA-directed RNA polymerase III subunit RPC8" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1SRD6 POLR3H "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
MGI|MGI:1926179 Polr3h "polymerase (RNA) III (DNA directed) polypeptide H" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1305889 Polr3h "polymerase (RNA) III (DNA directed) polypeptide H" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|Q2T9X1 POLR3H "DNA-directed RNA polymerase III subunit RPC8" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
Al_scaffold_0001_618
annotation not avaliable (204 aa)
(Arabidopsis lyrata)
Predicted Functional Partners:
fgenesh2_kg.8__1958__AT5G60040.1
annotation not avaliable (1376 aa)
  • ••• 0.844
fgenesh2_kg.7__493__AT4G35800.1
annotation not avaliable (1839 aa)
  • ••• 0.744
scaffold_800415.1
annotation not avaliable (1165 aa)
  • ••• 0.719
Al_scaffold_0007_3549
annotation not avaliable (52 aa)
   • •• 0.711
fgenesh2_kg.8__1077__AT5G51940.1
annotation not avaliable (144 aa)
   •••• 0.705
scaffold_303241.1
annotation not avaliable (144 aa)
   •••• 0.703
fgenesh1_pm.C_scaffold_7002163
annotation not avaliable (187 aa)
   •    0.702
Al_scaffold_0004_1372
annotation not avaliable (122 aa)
   •••• 0.702
scaffold_502273.1
annotation not avaliable (116 aa)
   •••• 0.699
fgenesh2_kg.7__2974__AT4G13720.1
annotation not avaliable (224 aa)
•  • •  0.678

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query129
cd0433080 cd04330, RNAP_III_Rpc25_N, RNAP_III_Rpc25_N: Rpc25 3e-36
COG1095183 COG1095, RPB7, DNA-directed RNA polymerase, subuni 8e-32
TIGR00448179 TIGR00448, rpoE, DNA-directed RNA polymerase (rpoE 2e-28
PRK08563187 PRK08563, PRK08563, DNA-directed RNA polymerase su 7e-22
pfam0387670 pfam03876, SHS2_Rpb7-N, SHS2 domain found in N ter 1e-21
cd0433180 cd04331, RNAP_E_N, RNAP_E_N: RpoE, N-terminal ribo 3e-18
pfam08292121 pfam08292, RNA_pol_Rbc25, RNA polymerase III subun 2e-16
cd0065580 cd00655, RNAP_Rpb7_N_like, RNAP_Rpb7_N_like: This 5e-14
cd0432980 cd04329, RNAP_II_Rpb7_N, RNAP_II_Rpb7_N: Rpb7, N-t 4e-10
PTZ00162176 PTZ00162, PTZ00162, DNA-directed RNA polymerase II 1e-06
>gnl|CDD|239822 cd04330, RNAP_III_Rpc25_N, RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain Back     alignment and domain information 
 Score =  118 bits (298), Expect = 3e-36
 Identities = 45/80 (56%), Positives = 60/80 (75%)

Query: 2  FYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYP 61
          F LS+IE T+R+PP     PLN+AI+ EL   + +KVI N+GLCI +YDI E+E G++ P
Sbjct: 1  FILSEIEDTVRIPPSQFSRPLNDAIEDELNKKYANKVIQNVGLCICLYDILEVEDGYILP 60

Query: 62 GEGASTHTVKFRLVVFRPFV 81
          G+GAS + V FR+VVFRPFV
Sbjct: 61 GDGASHYKVTFRMVVFRPFV 80

Rpc25 is a subunit of eukaryotic RNA polymerase (RNAP) III and is homologous to Rpa43 of eukaryotic RNAP I, Rpb7 of eukaryotic RNAP II, and RpoE of archaeal RNAP. Rpc25 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which are thought to bind single-stranded RNA. Rpc25 heterodimerizes with Rpc17 and plays an important role in transcription initiation. RNAP III transcribes diverse structural and catalytic RNAs including 5S ribosomal RNAs, tRNAs, and a small number of snRNAs involved in RNA and protein synthesis. Length = 80
>gnl|CDD|224020 COG1095, RPB7, DNA-directed RNA polymerase, subunit E' [Transcription] Back     alignment and domain information
>gnl|CDD|129540 TIGR00448, rpoE, DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form Back     alignment and domain information
>gnl|CDD|236289 PRK08563, PRK08563, DNA-directed RNA polymerase subunit E'; Provisional Back     alignment and domain information
>gnl|CDD|202794 pfam03876, SHS2_Rpb7-N, SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 Back     alignment and domain information
>gnl|CDD|239823 cd04331, RNAP_E_N, RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain Back     alignment and domain information
>gnl|CDD|219782 pfam08292, RNA_pol_Rbc25, RNA polymerase III subunit Rpc25 Back     alignment and domain information
>gnl|CDD|238354 cd00655, RNAP_Rpb7_N_like, RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP Back     alignment and domain information
>gnl|CDD|239821 cd04329, RNAP_II_Rpb7_N, RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain Back     alignment and domain information
>gnl|CDD|240298 PTZ00162, PTZ00162, DNA-directed RNA polymerase II subunit 7; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 129
PTZ00162176 DNA-directed RNA polymerase II subunit 7; Provisio 100.0
KOG3297202 consensus DNA-directed RNA polymerase subunit E' [ 100.0
TIGR00448179 rpoE DNA-directed RNA polymerase (rpoE), archaeal 100.0
COG1095183 RPB7 DNA-directed RNA polymerase, subunit E' [Tran 100.0
PRK08563187 DNA-directed RNA polymerase subunit E'; Provisiona 100.0
KOG3298170 consensus DNA-directed RNA polymerase subunit E' [ 100.0
cd0433080 RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-termin 99.97
cd0432980 RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ri 99.97
cd0065580 RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved 99.97
cd0433180 RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprot 99.97
PF0387670 SHS2_Rpb7-N: SHS2 domain found in N terminus of Rp 99.88
cd0432889 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal r 99.79
PF08292122 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I 99.6
cd0446288 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly 98.99
KOG4134253 consensus DNA-dependent RNA polymerase I [Transcri 98.83
PF0057574 S1: S1 RNA binding domain; InterPro: IPR003029 Rib 97.69
cd0447183 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai 96.91
cd0569870 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp 96.55
cd0568673 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom 96.47
cd0569769 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t 96.46
cd0570574 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a 96.24
cd0446567 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib 96.23
smart0031672 S1 Ribosomal protein S1-like RNA-binding domain. 96.17
cd0446183 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp 96.16
cd0445567 S1_NusA S1_NusA: N-utilizing substance A protein ( 96.1
cd0569269 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p 96.08
cd0446099 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. 96.06
cd0578986 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. 96.02
cd0568568 S1_Tex S1_Tex: The C-terminal S1 domain of a trans 96.01
cd0570768 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a 96.0
cd0570673 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a 95.86
cd0569474 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp 95.77
cd0445482 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA- 95.73
cd0568972 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p 95.48
cd0569566 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t 95.43
cd0569069 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p 95.41
cd0447268 S1_PNPase S1_PNPase: Polynucleotide phosphorylase 95.4
cd0445276 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr 95.33
cd0569671 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t 95.29
PRK08582139 hypothetical protein; Provisional 95.27
cd0570877 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a 95.22
cd0568770 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib 95.2
cd0568868 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p 95.12
cd0569173 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p 95.08
cd0445388 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik 94.88
cd0570373 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R 94.77
COG0539 541 RpsA Ribosomal protein S1 [Translation, ribosomal 94.74
cd0568479 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal 94.54
PF1350961 S1_2: S1 domain; PDB: 3GO5_A. 94.48
TIGR03591684 polynuc_phos polyribonucleotide nucleotidyltransfe 94.4
PRK07252120 hypothetical protein; Provisional 94.36
TIGR02063709 RNase_R ribonuclease R. This family consists of an 93.92
PTZ00248 319 eukaryotic translation initiation factor 2 subunit 93.57
cd0447377 S1_RecJ_like S1_RecJ_like: The S1 domain of the ar 93.46
PRK11642 813 exoribonuclease R; Provisional 93.21
PRK05807136 hypothetical protein; Provisional 93.12
PHA0294588 interferon resistance protein; Provisional 93.09
cd0570270 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R 92.53
PRK08059123 general stress protein 13; Validated 92.45
TIGR02696719 pppGpp_PNP guanosine pentaphosphate synthetase I/p 92.42
cd0570472 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a 92.26
PRK04163 235 exosome complex RNA-binding protein Rrp4; Provisio 91.71
COG1098129 VacB Predicted RNA binding protein (contains ribos 91.39
TIGR00358654 3_prime_RNase VacB and RNase II family 3'-5' exori 91.36
cd0016465 S1_like S1_like: Ribosomal protein S1-like RNA-bin 91.24
PF03293160 Pox_RNA_pol: Poxvirus DNA-directed RNA polymerase, 90.72
PRK07899 486 rpsA 30S ribosomal protein S1; Reviewed 90.49
PRK07400318 30S ribosomal protein S1; Reviewed 89.78
PRK07400 318 30S ribosomal protein S1; Reviewed 89.73
PRK03987 262 translation initiation factor IF-2 subunit alpha; 89.72
PRK09202 470 nusA transcription elongation factor NusA; Validat 89.51
PRK09521189 exosome complex RNA-binding protein Csl4; Provisio 89.51
PRK06676 390 rpsA 30S ribosomal protein S1; Reviewed 89.47
PRK11824693 polynucleotide phosphorylase/polyadenylase; Provis 88.68
COG1093 269 SUI2 Translation initiation factor 2, alpha subuni 88.43
PRK12327 362 nusA transcription elongation factor NusA; Provisi 88.09
PRK13806 491 rpsA 30S ribosomal protein S1; Provisional 87.55
PRK13806 491 rpsA 30S ribosomal protein S1; Provisional 87.47
cd05693100 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp 87.3
PRK06676 390 rpsA 30S ribosomal protein S1; Reviewed 87.06
PRK07899 486 rpsA 30S ribosomal protein S1; Reviewed 86.76
TIGR01953 341 NusA transcription termination factor NusA. This m 85.88
TIGR00717 516 rpsA ribosomal protein S1. This model provides tru 85.48
PLN00207891 polyribonucleotide nucleotidyltransferase; Provisi 84.52
cd0579086 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai 83.97
TIGR00717 516 rpsA ribosomal protein S1. This model provides tru 83.38
cd0579192 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. 81.84
PRK00087 647 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 81.33
PRK06299 565 rpsA 30S ribosomal protein S1; Reviewed 81.33
PRK06299 565 rpsA 30S ribosomal protein S1; Reviewed 80.98
PRK12269 863 bifunctional cytidylate kinase/ribosomal protein S 80.62
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional Back     alignment and domain information 
Probab=100.00  E-value=2.2e-46  Score=280.70  Aligned_cols=124  Identities=23%  Similarity=0.361  Sum_probs=121.0

Q ss_pred             CeEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeec
Q 032987            1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF   80 (129)
Q Consensus         1 MF~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~   80 (129)
                      ||++++++|+|+|||++|+++++++++++|+++|+||+.+++|+||||+||.++++|+|.||||+++|+|+|||+|||||
T Consensus         1 MF~~~~l~d~v~i~P~~f~~~~~~~i~~~L~~~~egkv~~~~GliV~v~di~~i~~G~I~~gdG~~~~~V~FraivFrPf   80 (176)
T PTZ00162          1 MFFVVELWKNVSLKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPF   80 (176)
T ss_pred             CcEEEEEEEEEEECHHHcCccHHHHHHHHHHHHHCCCCcCcccEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEEecC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCCcCCCCCCC
Q 032987           81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGR  127 (129)
Q Consensus        81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~f~~d~~~~  127 (129)
                      +|||++|+|++++++|+|+++||+| +|||+++||+++.|  |++++
T Consensus        81 ~gEVv~g~V~~v~~~G~~v~~Gp~~-ifI~~~~l~~~~~f--d~~~~  124 (176)
T PTZ00162         81 KDEVLDAIVTDVNKLGFFAQAGPLK-AFVSRSAIPPDFVY--DSDSA  124 (176)
T ss_pred             CCCEEEEEEEEEecceEEEEeeCeE-EEEcHHHCCCccEE--CCCCC
Confidence            9999999999999999999999998 99999999999999  65544

>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription] Back     alignment and domain information
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form Back     alignment and domain information
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription] Back     alignment and domain information
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional Back     alignment and domain information
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription] Back     alignment and domain information
>cd04330 RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain Back     alignment and domain information
>cd04329 RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain Back     alignment and domain information
>cd00655 RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP Back     alignment and domain information
>cd04331 RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain Back     alignment and domain information
>PF03876 SHS2_Rpb7-N: SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; InterPro: IPR005576 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core Back     alignment and domain information
>cd04328 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain Back     alignment and domain information
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit Back     alignment and domain information
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain Back     alignment and domain information
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription] Back     alignment and domain information
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain Back     alignment and domain information
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain Back     alignment and domain information
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains Back     alignment and domain information
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain Back     alignment and domain information
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain Back     alignment and domain information
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain Back     alignment and domain information
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa Back     alignment and domain information
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain Back     alignment and domain information
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain Back     alignment and domain information
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain Back     alignment and domain information
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>PRK08582 hypothetical protein; Provisional Back     alignment and domain information
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain Back     alignment and domain information
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide Back     alignment and domain information
>PF13509 S1_2: S1 domain; PDB: 3GO5_A Back     alignment and domain information
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase Back     alignment and domain information
>PRK07252 hypothetical protein; Provisional Back     alignment and domain information
>TIGR02063 RNase_R ribonuclease R Back     alignment and domain information
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional Back     alignment and domain information
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease Back     alignment and domain information
>PRK11642 exoribonuclease R; Provisional Back     alignment and domain information
>PRK05807 hypothetical protein; Provisional Back     alignment and domain information
>PHA02945 interferon resistance protein; Provisional Back     alignment and domain information
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>PRK08059 general stress protein 13; Validated Back     alignment and domain information
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase Back     alignment and domain information
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional Back     alignment and domain information
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases Back     alignment and domain information
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>PF03293 Pox_RNA_pol: Poxvirus DNA-directed RNA polymerase, 18 kD subunit; InterPro: IPR004973 DNA-directed RNA polymerases 2 Back     alignment and domain information
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK07400 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK07400 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated Back     alignment and domain information
>PRK09202 nusA transcription elongation factor NusA; Validated Back     alignment and domain information
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional Back     alignment and domain information
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional Back     alignment and domain information
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK12327 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>PRK13806 rpsA 30S ribosomal protein S1; Provisional Back     alignment and domain information
>PRK13806 rpsA 30S ribosomal protein S1; Provisional Back     alignment and domain information
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>TIGR01953 NusA transcription termination factor NusA Back     alignment and domain information
>TIGR00717 rpsA ribosomal protein S1 Back     alignment and domain information
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional Back     alignment and domain information
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain Back     alignment and domain information
>TIGR00717 rpsA ribosomal protein S1 Back     alignment and domain information
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain Back     alignment and domain information
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed Back     alignment and domain information
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query129
2ckz_B218 X-Ray Structure Of Rna Polymerase Iii Subcomplex C1 3e-20
3ayh_B203 Crystal Structure Of The C1725 SUBCOMPLEX FROM S. P 3e-19
2b8k_G215 12-Subunit Rna Polymerase Ii Length = 215 3e-08
1nt9_G171 Complete 12-Subunit Rna Polymerase Ii Length = 171 3e-08
2c35_B172 Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii L 1e-07
3h0g_G172 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 3e-07
2pmz_E180 Archaeal Rna Polymerase From Sulfolobus Solfataricu 2e-04
2waq_E180 The Complete Structure Of The Archaeal 13-Subunit D 2e-04
2y0s_E180 Crystal Structure Of Sulfolobus Shibatae Rna Polyme 2e-04
>pdb|2CKZ|B Chain B, X-Ray Structure Of Rna Polymerase Iii Subcomplex C17-C25. Length = 218 Back     alignment and structure 
Iteration: 1

 Score = 93.6 bits (231), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 48/115 (41%), Positives = 71/115 (61%), Gaps = 1/115 (0%)
Query: 1   MFYLSKIEHTXXXXXXXXXXXXNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVY 60
           MF LSKI                 AI  +L N F +K+I N+GLCI+IYD+  +E G + 
Sbjct: 1   MFILSKIADLVRIPPDQFHRDTISAITHQLNNKFANKIIPNVGLCITIYDLLTVEEGQLK 60
Query: 61  PGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLS-LGFFEDIYVPSHLL 114
           PG+G+S   V FR VVF+PF+GEI+   + +  A G+++S LG F+DI++P ++L
Sbjct: 61  PGDGSSYINVTFRAVVFKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNML 115
>pdb|3AYH|B Chain B, Crystal Structure Of The C1725 SUBCOMPLEX FROM S. POMBE RNA Polymerase Iii Length = 203 Back     alignment and structure
>pdb|2B8K|G Chain G, 12-Subunit Rna Polymerase Ii Length = 215 Back     alignment and structure
>pdb|1NT9|G Chain G, Complete 12-Subunit Rna Polymerase Ii Length = 171 Back     alignment and structure
>pdb|2C35|B Chain B, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii Length = 172 Back     alignment and structure
>pdb|3H0G|G Chain G, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 172 Back     alignment and structure
>pdb|2PMZ|E Chain E, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 180 Back     alignment and structure
>pdb|2WAQ|E Chain E, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 180 Back     alignment and structure
>pdb|2Y0S|E Chain E, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In P21 Space Group Length = 180 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query129
2ckz_B218 C25, DNA-directed RNA polymerase III 25 KD polypep 1e-40
3ayh_B203 DNA-directed RNA polymerase III subunit RPC8; tran 2e-40
4ayb_E180 DNA-directed RNA polymerase; transferase, multi-su 2e-37
1go3_E187 DNA-directed RNA polymerase subunit E; transferase 1e-36
2c35_B172 Human RPB7, DNA-directed RNA polymerase II 19 kDa 1e-35
2b8k_G215 B16, DNA-directed RNA polymerase II 19 kDa polypep 5e-34
1y14_B171 B16, RPB7, DNA-directed RNA polymerase II 19 kDa p 4e-33
3h0g_G172 DNA-directed RNA polymerase II subunit RPB7; trans 1e-28
2rf4_A214 DNA-directed RNA polymerase I subunit RPA4; transf 8e-05
>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae} Length = 218 Back     alignment and structure
 Score =  134 bits (337), Expect = 1e-40
 Identities = 52/124 (41%), Positives = 78/124 (62%), Gaps = 1/124 (0%)

Query: 1   MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVY 60
           MF LSKI   +R+PP         AI  +L N F +K+I N+GLCI+IYD+  +E G + 
Sbjct: 1   MFILSKIADLVRIPPDQFHRDTISAITHQLNNKFANKIIPNVGLCITIYDLLTVEEGQLK 60

Query: 61  PGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLS-LGFFEDIYVPSHLLPSPSR 119
           PG+G+S   V FR VVF+PF+GEI+   + +  A G+++S LG F+DI++P ++L     
Sbjct: 61  PGDGSSYINVTFRAVVFKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCY 120

Query: 120 SEPD 123
             P+
Sbjct: 121 YTPE 124
>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe} Length = 203 Back     alignment and structure
>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E Length = 180 Back     alignment and structure
>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1 Length = 187 Back     alignment and structure
>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1 Length = 172 Back     alignment and structure
>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 Length = 215 Back     alignment and structure
>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ... Length = 171 Back     alignment and structure
>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 172 Back     alignment and structure
>2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA, DNA-binding, phosphorylation, POL I, POLI, rpoli, nuclear protein; 3.10A {Saccharomyces cerevisiae} Length = 214 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query129
2ckz_B218 C25, DNA-directed RNA polymerase III 25 KD polypep 100.0
3ayh_B203 DNA-directed RNA polymerase III subunit RPC8; tran 100.0
4ayb_E180 DNA-directed RNA polymerase; transferase, multi-su 100.0
3h0g_G172 DNA-directed RNA polymerase II subunit RPB7; trans 100.0
1go3_E187 DNA-directed RNA polymerase subunit E; transferase 100.0
2c35_B172 Human RPB7, DNA-directed RNA polymerase II 19 kDa 99.97
1y14_B171 B16, RPB7, DNA-directed RNA polymerase II 19 kDa p 99.97
2b8k_G215 B16, DNA-directed RNA polymerase II 19 kDa polypep 99.97
2rf4_A214 DNA-directed RNA polymerase I subunit RPA4; transf 99.97
2bh8_A101 1B11; transcription, molecular evolution, unique a 97.57
2cqo_A119 Nucleolar protein of 40 kDa; S1 domain, OB-fold, s 96.87
2khi_A115 30S ribosomal protein S1; acetylation, phosphoprot 96.86
2eqs_A103 ATP-dependent RNA helicase DHX8; S1 domain, OB-fol 96.85
2k52_A80 Uncharacterized protein MJ1198; metal-binding, zin 96.72
1wi5_A119 RRP5 protein homolog; S1 domain, OB-fold, structur 96.7
1luz_A88 Protein K3, protein K2; stranded anti-parallel bet 96.61
1kl9_A 182 Eukaryotic translation initiation factor 2 subuni; 96.46
3cdi_A723 Polynucleotide phosphorylase; mRNA turnover, RNAse 96.38
2khj_A109 30S ribosomal protein S1; OB fold, acetylation, ph 96.33
2a19_A 175 EIF-2- alpha, eukaryotic translation initiation fa 96.2
2k4k_A130 GSP13, general stress protein 13; cytoplasm, stres 95.96
1e3p_A757 Guanosine pentaphosphate synthetase; polyribonucle 95.87
2ba0_A 229 Archeal exosome RNA binding protein RRP4; RNAse PH 95.43
2je6_I 251 RRP4, exosome complex RNA-binding protein 1; nucle 95.08
2z0s_A 235 Probable exosome complex RNA-binding protein 1; al 94.9
4aid_A726 Polyribonucleotide nucleotidyltransferase; transfe 94.85
3aev_A 275 Translation initiation factor 2 subunit alpha; pro 94.84
2ja9_A 175 Exosome complex exonuclease RRP40; RNA-binding pro 94.74
2nn6_I209 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, 94.65
1q8k_A 308 Eukaryotic translation initiation factor 2 subunit 94.4
3cw2_C 266 Translation initiation factor 2 subunit alpha; AIF 94.17
3m7n_A179 Putative uncharacterized protein AF_0206; exosome, 93.88
3go5_A 285 Multidomain protein with S1 RNA-binding domains; s 93.49
3go5_A 285 Multidomain protein with S1 RNA-binding domains; s 92.85
1hh2_P 344 NUSA, N utilization substance protein A; transcrip 92.76
3bzc_A785 TEX; helix-turn-helix, helix-hairpin-helix, S1 dom 92.69
2nn6_H 308 Exosome complex exonuclease RRP4; RNA, exosome, PM 91.73
3psi_A 1219 Transcription elongation factor SPT6; nucleus; 3.3 90.04
1k0r_A 366 NUSA; two component arrangement, S1 domain, two K- 89.79
2id0_A644 Exoribonuclease 2; RNAse, exonuclease, hydrolyase, 89.65
2asb_A 251 Transcription elongation protein NUSA; protein-RNA 86.95
2wp8_J977 Exosome complex exonuclease DIS3; nucleus, hydrola 85.82
>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae} Back     alignment and structure
Probab=100.00  E-value=4.4e-41  Score=258.21  Aligned_cols=126  Identities=41%  Similarity=0.768  Sum_probs=122.8

Q ss_pred             CeEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeec
Q 032987            1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF   80 (129)
Q Consensus         1 MF~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~   80 (129)
                      ||++++++|+|+|||++|+++++++|+++|+++|+||+++++|+|||++||.++++|+|.||||+++|+|+|+|++|||+
T Consensus         1 MF~l~~l~d~V~I~P~~f~~~l~~~i~~~L~~kyegkv~~~~Gl~I~v~di~~i~eG~I~~GdG~~~~~V~fk~~~f~p~   80 (218)
T 2ckz_B            1 MFILSKIADLVRIPPDQFHRDTISAITHQLNNKFANKIIPNVGLCITIYDLLTVEEGQLKPGDGSSYINVTFRAVVFKPF   80 (218)
T ss_dssp             CEEEEEEEEEEEECGGGTTSCHHHHHHHHHHHHHTTEEETTTEEEEEEEEEEEECCCEECSSSSCEEEEEEEEEEEECCC
T ss_pred             CeEEEEEEEEEEECHHHcCchHHHHHHHHHHHHhcCcCcCCccEEEEEEEeeeccCcEEeCCCCCEEEEEEEEEEEecCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCEEEEEEEEEccCceEEEe-CccceEEecCCCCCCCCCcCCCCCCCC
Q 032987           81 VGEIIAAKLKESDANGLRLSL-GFFEDIYVPSHLLPSPSRSEPDPYGRL  128 (129)
Q Consensus        81 ~~EVl~g~V~~v~~~Gi~v~~-G~~~~i~i~~~~lp~~~~f~~d~~~~~  128 (129)
                      +||+++|+|++++++|+|+++ ||+++++||++.+|+++.|  |++++.
T Consensus        81 vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~s~l~~d~~~f--d~~~~~  127 (218)
T 2ckz_B           81 LGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYY--TPEESA  127 (218)
T ss_dssp             TTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTSCTTCEE--ETTTTE
T ss_pred             CCCEEEEEEEEEccCcEEEEccCccceEEEcHHHCCCCcEE--cCcCce
Confidence            999999999999999999999 9999999999999999999  766653
>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe} Back     alignment and structure
>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E Back     alignment and structure
>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1 Back     alignment and structure
>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1 Back     alignment and structure
>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ... Back     alignment and structure
>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 Back     alignment and structure
>2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA, DNA-binding, phosphorylation, POL I, POLI, rpoli, nuclear protein; 3.10A {Saccharomyces cerevisiae} Back     alignment and structure
>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli} Back     alignment and structure
>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Back     alignment and structure
>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Back     alignment and structure
>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5 Back     alignment and structure
>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5 Back     alignment and structure
>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 Back     alignment and structure
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Back     alignment and structure
>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Back     alignment and structure
>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A Back     alignment and structure
>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} Back     alignment and structure
>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A Back     alignment and structure
>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 Back     alignment and structure
>2je6_I RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 PDB: 2jea_I* 2jeb_I* 3l7z_C Back     alignment and structure
>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} SCOP: b.40.4.5 d.51.1.1 Back     alignment and structure
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Back     alignment and structure
>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A Back     alignment and structure
>2ja9_A Exosome complex exonuclease RRP40; RNA-binding protein, RNA, S1 domain, KH domain, hydrolase, RNA-binding, nuclear protein; 2.20A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.51.1.1 Back     alignment and structure
>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 Back     alignment and structure
>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1 Back     alignment and structure
>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B* Back     alignment and structure
>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A Back     alignment and structure
>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae} Back     alignment and structure
>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae} Back     alignment and structure
>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A Back     alignment and structure
>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A Back     alignment and structure
>2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 Back     alignment and structure
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} Back     alignment and structure
>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 Back     alignment and structure
>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A Back     alignment and structure
>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A Back     alignment and structure
>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 129
d1go3e278 d.230.1.1 (E:1-78) N-terminal, heterodimerisation 5e-29
d2c35b277 d.230.1.1 (B:1-77) N-terminal, heterodimerisation 3e-26
d1y14b280 d.230.1.1 (B:1-80) N-terminal, heterodimerisation 3e-26
d2c35b194 b.40.4.5 (B:78-171) C-terminal domain of RNA polym 9e-05
>d1go3e2 d.230.1.1 (E:1-78) N-terminal, heterodimerisation domain of RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 78 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Dodecin subunit-like
superfamily: N-terminal, heterodimerisation domain of RBP7 (RpoE)
family: N-terminal, heterodimerisation domain of RBP7 (RpoE)
domain: N-terminal, heterodimerisation domain of RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 98.6 bits (246), Expect = 5e-29
 Identities = 22/77 (28%), Positives = 42/77 (54%)

Query: 1  MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVY 60
          M+ + +I   +++PP      L E +K  L   +  ++  ++G  +SI D+K+I  G V 
Sbjct: 1  MYKILEIADVVKVPPEEFGKDLKETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVV 60

Query: 61 PGEGASTHTVKFRLVVF 77
           G+G++ H V F  +V+
Sbjct: 61 HGDGSAYHPVVFETLVY 77
>d2c35b2 d.230.1.1 (B:1-77) N-terminal, heterodimerisation domain of RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]} Length = 77 Back     information, alignment and structure
>d1y14b2 d.230.1.1 (B:1-80) N-terminal, heterodimerisation domain of RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 80 Back     information, alignment and structure
>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]} Length = 94 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query129
d1go3e278 N-terminal, heterodimerisation domain of RBP7 (Rpo 99.97
d2c35b277 N-terminal, heterodimerisation domain of RBP7 (Rpo 99.96
d1y14b280 N-terminal, heterodimerisation domain of RBP7 (Rpo 99.96
d2c35b194 C-terminal domain of RNA polymerase II subunit RBP 99.38
d1y14b191 C-terminal domain of RNA polymerase II subunit RBP 99.31
d1go3e1106 C-terminal domain of RNA polymerase II subunit RBP 98.33
d2ba0a183 S1-domain of exosome complex RNA-binding protein 1 97.43
d2je6i187 S1-domain of exosome complex RNA-binding protein 1 97.23
d2z0sa188 S1-domain of exosome complex RNA-binding protein 1 97.21
d2ahob284 Eukaryotic initiation factor 2alpha, eIF2alpha, N- 96.95
d1kl9a286 Eukaryotic initiation factor 2alpha, eIF2alpha, N- 96.8
d1sroa_76 S1 RNA-binding domain of polyribonucleotide phosph 96.76
d2nn6h195 S1-domain of Ribosomal RNA-processing protein 4, R 96.63
d2ix0a387 Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5 96.47
d2ja9a190 S1-domain of exosome component 3 (RRP40) {Saccharo 95.79
d3bzka494 Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287] 95.71
d1hh2p172 S1 domain of NusA {Thermotoga maritima [TaxId: 233 95.48
d2nn6g188 S1-domain of exosome component 3 (RRP40) {Human (H 94.97
d1wi5a_119 S1-domain of RRP5 protein homolog (PDCD11, KIAA018 93.65
d1e3pa262 S1 RNA-binding domain of polyribonucleotide phosph 91.41
>d1go3e2 d.230.1.1 (E:1-78) N-terminal, heterodimerisation domain of RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Dodecin subunit-like
superfamily: N-terminal, heterodimerisation domain of RBP7 (RpoE)
family: N-terminal, heterodimerisation domain of RBP7 (RpoE)
domain: N-terminal, heterodimerisation domain of RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.97  E-value=9.4e-31  Score=170.37  Aligned_cols=77  Identities=29%  Similarity=0.550  Sum_probs=76.6

Q ss_pred             CeEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEe
Q 032987            1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVF   77 (129)
Q Consensus         1 MF~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvf   77 (129)
                      ||++++++|+|+|||++||++++++++++|+++|+||+.+++|+||+|+|+.++++|+|.||||+++|+|+|||+||
T Consensus         1 MF~~~~l~d~v~i~P~~~g~~~~~~i~~~L~~~~egkv~~~~G~ii~v~di~~i~eG~I~~gdG~~~~~V~F~~lvF   77 (78)
T d1go3e2           1 MYKILEIADVVKVPPEEFGKDLKETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVY   77 (78)
T ss_dssp             CEEEEEEEEEEEECGGGTTSCHHHHHHHHHHHHHTTCEETTTEEEEEEEEEEEECCCBCCTTCCSEEEEEEEEEEEE
T ss_pred             CcEEEEEEEEEEECHHHhCcCHHHHHHHHHHHHhCCcCcCCcCEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999
>d2c35b2 d.230.1.1 (B:1-77) N-terminal, heterodimerisation domain of RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1y14b2 d.230.1.1 (B:1-80) N-terminal, heterodimerisation domain of RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]} Back     information, alignment and structure
>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]} Back     information, alignment and structure