Psyllid ID: psy11392

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-------130-------140-------150-------160-------17
MLYDITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVKDILKYFAEKDKPDPVRDFLMGAIAPALRSLPRHLFLKAKKEIFEAVHKYEMIAEEQSGDQYEYTLGA
ccEEEEEEEEEEEEccccccccccccccEEEEEEEEEEEEcccEEEccccccEEEEEEEEEEEEEccccEEEEEEEEEEcccEEEEcccccccccccccccccEEEEEcccccccccccEEEccccccEEcccccEEEEEHHHHHHHHHHHHHHHHHHHcccEEEEccc
ccHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEEEEEccccEEEcccccEEEEEEEEEEEEEccccEEEEEEEEEcccccEEEEEcccccccccccccccccEEEEcccccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEccc
mlyditkiedsviipgdgashtkvfpnvgLCMMLYDitkiedsviipgdgashtkvEFRYVVFRPFVSEIIIGKirscskegvhdsqssnqpeqpisdsTVKDILKYFaekdkpdpvrDFLMGAIAPALRSLPRHLFLKAKKEIFEAVHKYEMIAeeqsgdqyeytlga
MLYDITKIedsviipgdgashtKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVhdsqssnqpeqpisdsTVKDILKYFaekdkpdpvRDFLMGAIAPALRSLPRHLFLKAKKEIFEAVHKYEMiaeeqsgdqyeytlga
MLYDITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVKDILKYFAEKDKPDPVRDFLMGAIAPALRSLPRHLFLKAKKEIFEAVHKYEMIAEEQSGDQYEYTLGA
**YDITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSC************************DILKYFAEK***DPVRDFLMGAIAPALRSLPRHLFLKAKKEIFEAVHKYEMIA**************
MLYDITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVKDILKYFAEKDKPDPVRDFLMGAIAPALRSLPRHLFLKAKKEIFEAVH**************EYTLG*
MLYDITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRS*******************SDSTVKDILKYFAEKDKPDPVRDFLMGAIAPALRSLPRHLFLKAKKEIFEAVHKYEMIAEEQSGDQYEYTLGA
MLYDITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVKDILKYFAEKDKPDPVRDFLMGAIAPALRSLPRHLFLKAKKEIFEAVHKYEMIAEEQSGDQYEYTLGA
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MLYDITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVKDILKYFAEKDKPDPVRDFLMGAIAPALRSLPRHLFLKAKKEIFEAVHKYEMIAEEQSGDQYEYTLGA
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 ?
Query169 2.2.26 [Sep-21-2011]
Q9D2C6204 DNA-directed RNA polymera yes N/A 0.473 0.392 0.6 2e-21
Q2T9X1204 DNA-directed RNA polymera yes N/A 0.473 0.392 0.6 3e-21
Q9Y535204 DNA-directed RNA polymera yes N/A 0.473 0.392 0.587 2e-20
P35718212 DNA-directed RNA polymera yes N/A 0.502 0.400 0.39 2e-14
O94285203 DNA-directed RNA polymera yes N/A 0.372 0.310 0.476 2e-12
Q557J3252 DNA-directed RNA polymera yes N/A 0.372 0.25 0.428 1e-08
P34087171 DNA-directed RNA polymera no N/A 0.313 0.309 0.415 3e-06
>sp|Q9D2C6|RPC8_MOUSE DNA-directed RNA polymerase III subunit RPC8 OS=Mus musculus GN=Polr3h PE=2 SV=2 Back     alignment and function desciption
 Score =  101 bits (252), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 48/80 (60%), Positives = 59/80 (73%)

Query: 7   KIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPF 66
           K+ DS+    +     KV  NVGLC+ L+DITK+ED+ + PGDGASHTKV FRYVVF PF
Sbjct: 21  KLNDSIAEELNKKLANKVVYNVGLCICLFDITKLEDAYVFPGDGASHTKVHFRYVVFHPF 80

Query: 67  VSEIIIGKIRSCSKEGVHDS 86
           + EI+IGKI+ CS EGVH S
Sbjct: 81  LDEILIGKIKGCSPEGVHVS 100
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 tRNA. 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 induce type I interferon and NF- Kappa-B through the RIG-I pathway.
Mus musculus (taxid: 10090)
>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|Q9Y535|RPC8_HUMAN DNA-directed RNA polymerase III subunit RPC8 OS=Homo sapiens GN=POLR3H PE=1 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|P34087|RPB7_YEAST DNA-directed RNA polymerase II subunit RPB7 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPB7 PE=1 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 ?
Query169
260824541203 hypothetical protein BRAFLDRAFT_104488 [ 0.473 0.394 0.637 8e-22
91092914199 PREDICTED: similar to DNA-directed RNA p 0.461 0.391 0.589 7e-21
291243945204 PREDICTED: hypothetical protein isoform 0.473 0.392 0.612 1e-20
118404162207 polymerase (RNA) III (DNA directed) poly 0.473 0.386 0.612 1e-20
224095057206 PREDICTED: DNA-directed RNA polymerase I 0.384 0.315 0.723 2e-20
48096324203 PREDICTED: DNA-directed RNA polymerase I 0.461 0.384 0.628 2e-20
47206295251 unnamed protein product [Tetraodon nigro 0.372 0.250 0.746 2e-20
380018290203 PREDICTED: DNA-directed RNA polymerase I 0.461 0.384 0.628 2e-20
344296182204 PREDICTED: DNA-directed RNA polymerase I 0.473 0.392 0.6 2e-20
383853110204 PREDICTED: DNA-directed RNA polymerase I 0.461 0.382 0.628 2e-20
>gi|260824541|ref|XP_002607226.1| hypothetical protein BRAFLDRAFT_104488 [Branchiostoma floridae] gi|229292572|gb|EEN63236.1| hypothetical protein BRAFLDRAFT_104488 [Branchiostoma floridae] Back     alignment and taxonomy information
 Score =  108 bits (270), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 51/80 (63%), Positives = 62/80 (77%)

Query: 7   KIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPF 66
           K+ D+VI   +     KV  NVGLC+ L+DITK+EDS I PGDGASHT+V FRYVVFRPF
Sbjct: 21  KLNDAVIEELNNKFANKVVYNVGLCIALFDITKLEDSFIFPGDGASHTRVHFRYVVFRPF 80

Query: 67  VSEIIIGKIRSCSKEGVHDS 86
           + EI+ G+IRSCS+EGVH S
Sbjct: 81  MDEILQGRIRSCSREGVHVS 100

Source: Branchiostoma floridae

Species: Branchiostoma floridae

Genus: Branchiostoma

Family: Branchiostomidae

Order:

Class:

Phylum: Chordata

Superkingdom: Eukaryota
>gi|91092914|ref|XP_971430.1| PREDICTED: similar to DNA-directed RNA polymerase III 25 kDa polypeptide [Tribolium castaneum] gi|270003098|gb|EEZ99545.1| hypothetical protein TcasGA2_TC000127 [Tribolium castaneum] Back     alignment and taxonomy information
>gi|291243945|ref|XP_002741858.1| PREDICTED: hypothetical protein isoform 1 [Saccoglossus kowalevskii] Back     alignment and taxonomy information
>gi|118404162|ref|NP_001072397.1| polymerase (RNA) III (DNA directed) polypeptide H (22.9kD) [Xenopus (Silurana) tropicalis] gi|111306182|gb|AAI21598.1| hypothetical protein MGC147203 [Xenopus (Silurana) tropicalis] Back     alignment and taxonomy information
>gi|224095057|ref|XP_002197392.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC8 isoform 1 [Taeniopygia guttata] Back     alignment and taxonomy information
>gi|48096324|ref|XP_394665.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC8-like isoform 1 [Apis mellifera] Back     alignment and taxonomy information
>gi|47206295|emb|CAF93183.1| unnamed protein product [Tetraodon nigroviridis] Back     alignment and taxonomy information
>gi|380018290|ref|XP_003693065.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC8-like isoform 1 [Apis florea] Back     alignment and taxonomy information
>gi|344296182|ref|XP_003419788.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC8-like isoform 1 [Loxodonta africana] Back     alignment and taxonomy information
>gi|383853110|ref|XP_003702067.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC8-like isoform 1 [Megachile rotundata] 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 ?
Query169
UNIPROTKB|E1BV29209 POLR3H "Uncharacterized protei 0.473 0.382 0.6 1.1e-21
ZFIN|ZDB-GENE-040718-179214 polr3h "polymerase (RNA) III ( 0.378 0.299 0.734 1.5e-21
UNIPROTKB|F1ML03204 POLR3H "DNA-directed RNA polym 0.473 0.392 0.6 1.9e-21
UNIPROTKB|F1SRD6204 POLR3H "Uncharacterized protei 0.473 0.392 0.6 1.9e-21
MGI|MGI:1926179204 Polr3h "polymerase (RNA) III ( 0.473 0.392 0.6 1.9e-21
RGD|1305889204 Polr3h "polymerase (RNA) III ( 0.473 0.392 0.6 1.9e-21
UNIPROTKB|Q2T9X1204 POLR3H "DNA-directed RNA polym 0.473 0.392 0.6 2.4e-21
UNIPROTKB|F8WDV1123 POLR3H "DNA-directed RNA polym 0.520 0.715 0.522 1.7e-20
UNIPROTKB|Q9Y535204 POLR3H "DNA-directed RNA polym 0.473 0.392 0.587 1.7e-20
UNIPROTKB|E2RRG9204 POLR3H "Uncharacterized protei 0.473 0.392 0.562 2.7e-20
UNIPROTKB|E1BV29 POLR3H "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
 Score = 253 (94.1 bits), Expect = 1.1e-21, P = 1.1e-21
 Identities = 48/80 (60%), Positives = 61/80 (76%)

Query:     7 KIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPF 66
             K+ +S+    +     KV  NVGLC+ LYDITK+EDS I PGDGASHTKV FRYVVF PF
Sbjct:    21 KLNESIAEELNKKLANKVVYNVGLCICLYDITKLEDSYIFPGDGASHTKVHFRYVVFHPF 80

Query:    67 VSEIIIGKIRSCSKEGVHDS 86
             + EI++G+I+SCS++GVH S
Sbjct:    81 LDEILVGEIKSCSQDGVHVS 100
GO:0003677 "DNA binding" evidence=IEA
GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA
GO:0005666 "DNA-directed RNA polymerase III complex" evidence=IEA
GO:0005813 "centrosome" evidence=IEA
GO:0006383 "transcription from RNA polymerase III promoter" evidence=IEA
ZFIN|ZDB-GENE-040718-179 polr3h "polymerase (RNA) III (DNA directed) polypeptide H" [Danio rerio (taxid:7955)] 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|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
UNIPROTKB|F8WDV1 POLR3H "DNA-directed RNA polymerase III subunit RPC8" [Homo sapiens (taxid:9606)] 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|E2RRG9 POLR3H "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] 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

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q9Y535RPC8_HUMANNo assigned EC number0.58750.47330.3921yesN/A
Q2T9X1RPC8_BOVINNo assigned EC number0.60.47330.3921yesN/A
Q9D2C6RPC8_MOUSENo assigned EC number0.60.47330.3921yesN/A

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query169
cd0433080 cd04330, RNAP_III_Rpc25_N, RNAP_III_Rpc25_N: Rpc25 7e-21
COG1095183 COG1095, RPB7, DNA-directed RNA polymerase, subuni 4e-15
TIGR00448179 TIGR00448, rpoE, DNA-directed RNA polymerase (rpoE 3e-13
pfam0387670 pfam03876, SHS2_Rpb7-N, SHS2 domain found in N ter 5e-11
cd0065580 cd00655, RNAP_Rpb7_N_like, RNAP_Rpb7_N_like: This 1e-08
PRK08563187 PRK08563, PRK08563, DNA-directed RNA polymerase su 2e-07
cd0433180 cd04331, RNAP_E_N, RNAP_E_N: RpoE, N-terminal ribo 2e-05
pfam08292121 pfam08292, RNA_pol_Rbc25, RNA polymerase III subun 7e-05
pfam0294437 pfam02944, BESS, BESS motif 0.004
>gnl|CDD|239822 cd04330, RNAP_III_Rpc25_N, RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain Back     alignment and domain information 
 Score = 81.1 bits (201), Expect = 7e-21
 Identities = 32/45 (71%), Positives = 36/45 (80%)

Query: 23 KVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFV 67
          KV  NVGLC+ LYDI ++ED  I+PGDGASH KV FR VVFRPFV
Sbjct: 36 KVIQNVGLCICLYDILEVEDGYILPGDGASHYKVTFRMVVFRPFV 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|202794 pfam03876, SHS2_Rpb7-N, SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 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|236289 PRK08563, PRK08563, DNA-directed RNA polymerase subunit E'; Provisional 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|202479 pfam02944, BESS, BESS motif Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 169
COG1095183 RPB7 DNA-directed RNA polymerase, subunit E' [Tran 99.97
PTZ00162176 DNA-directed RNA polymerase II subunit 7; Provisio 99.96
TIGR00448179 rpoE DNA-directed RNA polymerase (rpoE), archaeal 99.96
PRK08563187 DNA-directed RNA polymerase subunit E'; Provisiona 99.95
KOG3297|consensus202 99.92
KOG3298|consensus170 99.89
cd0433080 RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-termin 99.81
cd0065580 RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved 99.79
cd0432980 RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ri 99.79
cd0433180 RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprot 99.76
PF0387670 SHS2_Rpb7-N: SHS2 domain found in N terminus of Rp 99.47
COG0539 541 RpsA Ribosomal protein S1 [Translation, ribosomal 99.32
cd0432889 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal r 99.0
PRK07899 486 rpsA 30S ribosomal protein S1; Reviewed 98.75
PRK07400318 30S ribosomal protein S1; Reviewed 98.68
cd0568673 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom 98.62
cd0446288 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly 98.61
PRK06299 565 rpsA 30S ribosomal protein S1; Reviewed 98.6
PF0057574 S1: S1 RNA binding domain; InterPro: IPR003029 Rib 98.59
PRK13806 491 rpsA 30S ribosomal protein S1; Provisional 98.47
PRK12269 863 bifunctional cytidylate kinase/ribosomal protein S 98.44
cd0445276 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr 98.4
PF08292122 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I 98.39
TIGR00717 516 rpsA ribosomal protein S1. This model provides tru 98.39
COG0539 541 RpsA Ribosomal protein S1 [Translation, ribosomal 98.39
PRK12269 863 bifunctional cytidylate kinase/ribosomal protein S 98.38
cd0570574 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a 98.38
PRK06676390 rpsA 30S ribosomal protein S1; Reviewed 98.37
cd0569474 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp 98.32
PTZ00248 319 eukaryotic translation initiation factor 2 subunit 98.29
cd0445388 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik 98.26
cd0570673 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a 98.25
cd0446183 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp 98.23
cd0569069 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p 98.21
cd0570877 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a 98.21
cd0569269 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p 98.2
cd0570768 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a 98.2
cd0568479 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal 98.19
cd0568868 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p 98.18
PRK13806491 rpsA 30S ribosomal protein S1; Provisional 98.15
cd0447183 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai 98.14
PRK08582139 hypothetical protein; Provisional 98.14
cd0570472 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a 98.13
cd0569870 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp 98.11
cd0569769 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t 98.1
PRK07899486 rpsA 30S ribosomal protein S1; Reviewed 98.09
PRK07252120 hypothetical protein; Provisional 98.08
cd0569671 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t 98.08
cd0568972 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p 98.07
PRK00087647 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 98.07
cd0578986 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. 98.06
COG1098129 VacB Predicted RNA binding protein (contains ribos 98.02
PRK07400318 30S ribosomal protein S1; Reviewed 98.02
PRK05807136 hypothetical protein; Provisional 98.0
cd0570373 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R 97.96
TIGR03591684 polynuc_phos polyribonucleotide nucleotidyltransfe 97.95
cd0569173 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p 97.95
cd0447268 S1_PNPase S1_PNPase: Polynucleotide phosphorylase 97.9
cd0568770 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib 97.89
TIGR02696719 pppGpp_PNP guanosine pentaphosphate synthetase I/p 97.89
cd0446567 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib 97.84
cd0568568 S1_Tex S1_Tex: The C-terminal S1 domain of a trans 97.79
PRK03987 262 translation initiation factor IF-2 subunit alpha; 97.75
smart0031672 S1 Ribosomal protein S1-like RNA-binding domain. 97.75
PLN00207891 polyribonucleotide nucleotidyltransferase; Provisi 97.68
PRK04163235 exosome complex RNA-binding protein Rrp4; Provisio 97.68
cd0446099 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. 97.67
cd0445567 S1_NusA S1_NusA: N-utilizing substance A protein ( 97.62
PRK06676390 rpsA 30S ribosomal protein S1; Reviewed 97.6
TIGR00717516 rpsA ribosomal protein S1. This model provides tru 97.6
PRK08059123 general stress protein 13; Validated 97.59
cd0570270 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R 97.59
PRK09521189 exosome complex RNA-binding protein Csl4; Provisio 97.58
cd0569566 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t 97.51
PRK11824693 polynucleotide phosphorylase/polyadenylase; Provis 97.5
cd0447377 S1_RecJ_like S1_RecJ_like: The S1 domain of the ar 97.45
PRK06299565 rpsA 30S ribosomal protein S1; Reviewed 97.44
cd0445482 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA- 97.41
cd05693100 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp 97.37
COG1093 269 SUI2 Translation initiation factor 2, alpha subuni 97.37
PHA0294588 interferon resistance protein; Provisional 97.37
PRK00087647 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 97.15
cd0016465 S1_like S1_like: Ribosomal protein S1-like RNA-bin 97.09
KOG4134|consensus253 97.0
TIGR02063709 RNase_R ribonuclease R. This family consists of an 96.86
PRK11642813 exoribonuclease R; Provisional 96.7
TIGR00358654 3_prime_RNase VacB and RNase II family 3'-5' exori 96.54
COG1185692 Pnp Polyribonucleotide nucleotidyltransferase (pol 96.28
COG2183780 Tex Transcriptional accessory protein [Transcripti 96.28
PRK09202 470 nusA transcription elongation factor NusA; Validat 96.19
PRK12327 362 nusA transcription elongation factor NusA; Provisi 95.75
TIGR01953 341 NusA transcription termination factor NusA. This m 95.19
cd0579192 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. 94.71
TIGR00757 414 RNaseEG ribonuclease, Rne/Rng family. The C-termin 94.0
PRK05054644 exoribonuclease II; Provisional 92.18
cd0579086 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai 91.2
PRK12328 374 nusA transcription elongation factor NusA; Provisi 89.46
PF1350961 S1_2: S1 domain; PDB: 3GO5_A. 88.6
COG0557706 VacB Exoribonuclease R [Transcription] 87.89
COG1097239 RRP4 RNA-binding protein Rrp4 and related proteins 86.23
PHA0285886 EIF2a-like PKR inhibitor; Provisional 84.22
KOG2916|consensus 304 83.49
TIGR02062639 RNase_B exoribonuclease II. This family consists o 80.75
KOG1067|consensus760 80.37
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription] Back     alignment and domain information 
Probab=99.97  E-value=1.6e-30  Score=213.30  Aligned_cols=102  Identities=25%  Similarity=0.459  Sum_probs=97.4

Q ss_pred             ccchHHHHHHHhhhhcCceeeCCeeEEEEEeeeeeeccceEeeCCCceeEEEEEEEEEEecCCCcEEEEEEEEEecceeE
Q psy11392          5 ITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVH   84 (169)
Q Consensus         5 ~t~l~~~I~~eL~ekyegKVi~~vGLiV~V~dI~~I~eG~I~pgDG~~~~~V~FraIvFrPf~GEVVeG~V~~vt~~GiF   84 (169)
                      +.++++++.+.|+++|+||+++++|+||+|+++.++++|+|.||||++|++|+|+|++|+|+.||||+|+|++++++|+|
T Consensus        19 g~~~~~~v~~~L~~k~eG~~~~~~G~~v~V~~v~~igeG~I~~GDG~~y~~V~f~al~fkP~~gEVV~GeVv~~~~~G~f   98 (183)
T COG1095          19 GEDLEEAVKEELKEKYEGKLDGDVGLVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALVFKPFRGEVVEGEVVEVVEFGAF   98 (183)
T ss_pred             CccHHHHHHHHHHHHhcceEccccCEEEEEEEeeEeeccEEecCCCcEEEEEEEEEEEEEeccccEEEEEEEEEeecceE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCCCccCCccccccccce
Q psy11392         85 DSQSSNQPEQPISDSTVKDILKY  107 (169)
Q Consensus        85 V~lGp~dGlIhISd~s~~e~i~~  107 (169)
                      |++||+||++|+| +-+|+|+.+
T Consensus        99 V~igp~dglvh~s-qi~dd~~~~  120 (183)
T COG1095          99 VRIGPLDGLVHVS-QIMDDYIDY  120 (183)
T ss_pred             EEeccccccccHh-hccCccccc
Confidence            9999999999999 666666655

>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional Back     alignment and domain information
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form Back     alignment and domain information
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional Back     alignment and domain information
>KOG3297|consensus Back     alignment and domain information
>KOG3298|consensus 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
>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
>cd04329 RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain 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
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] 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
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK07400 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain 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
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed 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
>PRK13806 rpsA 30S ribosomal protein S1; Provisional Back     alignment and domain information
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional 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
>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
>TIGR00717 rpsA ribosomal protein S1 Back     alignment and domain information
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional 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
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed 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
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional 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
>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
>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
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain 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
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain 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
>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
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>PRK13806 rpsA 30S ribosomal protein S1; Provisional Back     alignment and domain information
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain Back     alignment and domain information
>PRK08582 hypothetical protein; Provisional 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
>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
>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
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK07252 hypothetical protein; Provisional 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
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) 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
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain 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
>PRK07400 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK05807 hypothetical protein; Provisional 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
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase Back     alignment and domain information
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: 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
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase 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
>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
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated Back     alignment and domain information
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional Back     alignment and domain information
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional Back     alignment and domain information
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain 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
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>TIGR00717 rpsA ribosomal protein S1 Back     alignment and domain information
>PRK08059 general stress protein 13; Validated 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
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional 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
>PRK11824 polynucleotide phosphorylase/polyadenylase; 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
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain 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
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PHA02945 interferon resistance protein; Provisional 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
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>KOG4134|consensus Back     alignment and domain information
>TIGR02063 RNase_R ribonuclease R Back     alignment and domain information
>PRK11642 exoribonuclease R; Provisional Back     alignment and domain information
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases Back     alignment and domain information
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG2183 Tex Transcriptional accessory protein [Transcription] Back     alignment and domain information
>PRK09202 nusA transcription elongation factor NusA; Validated Back     alignment and domain information
>PRK12327 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>TIGR01953 NusA transcription termination factor NusA Back     alignment and domain information
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain Back     alignment and domain information
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family Back     alignment and domain information
>PRK05054 exoribonuclease II; Provisional Back     alignment and domain information
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain Back     alignment and domain information
>PRK12328 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>PF13509 S1_2: S1 domain; PDB: 3GO5_A Back     alignment and domain information
>COG0557 VacB Exoribonuclease R [Transcription] Back     alignment and domain information
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PHA02858 EIF2a-like PKR inhibitor; Provisional Back     alignment and domain information
>KOG2916|consensus Back     alignment and domain information
>TIGR02062 RNase_B exoribonuclease II Back     alignment and domain information
>KOG1067|consensus 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 ?
Query169
2ckz_B218 X-Ray Structure Of Rna Polymerase Iii Subcomplex C1 2e-15
3ayh_B203 Crystal Structure Of The C1725 SUBCOMPLEX FROM S. P 2e-13
2b8k_G215 12-Subunit Rna Polymerase Ii Length = 215 2e-07
1nt9_G171 Complete 12-Subunit Rna Polymerase Ii Length = 171 2e-07
>pdb|2CKZ|B Chain B, X-Ray Structure Of Rna Polymerase Iii Subcomplex C17-C25. Length = 218 Back     alignment and structure 
Iteration: 1

 Score = 78.2 bits (191), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 39/100 (39%), Positives = 58/100 (58%), Gaps = 15/100 (15%)
Query: 2   LYDITKIEDSVIIPGD--------GASH-------TKVFPNVGLCMMLYDITKIEDSVII 46
           ++ ++KI D V IP D          +H        K+ PNVGLC+ +YD+  +E+  + 
Sbjct: 1   MFILSKIADLVRIPPDQFHRDTISAITHQLNNKFANKIIPNVGLCITIYDLLTVEEGQLK 60
Query: 47  PGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVHDS 86
           PGDG+S+  V FR VVF+PF+ EI+ G I  C+ EG+  S
Sbjct: 61  PGDGSSYINVTFRAVVFKPFLGEIVTGWISKCTAEGIKVS 100
>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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query169
2ckz_B218 C25, DNA-directed RNA polymerase III 25 KD polypep 1e-17
3ayh_B203 DNA-directed RNA polymerase III subunit RPC8; tran 2e-15
1go3_E187 DNA-directed RNA polymerase subunit E; transferase 4e-12
2c35_B172 Human RPB7, DNA-directed RNA polymerase II 19 kDa 5e-12
4ayb_E180 DNA-directed RNA polymerase; transferase, multi-su 1e-11
2b8k_G215 B16, DNA-directed RNA polymerase II 19 kDa polypep 4e-10
1y14_B171 B16, RPB7, DNA-directed RNA polymerase II 19 kDa p 7e-10
3h0g_G172 DNA-directed RNA polymerase II subunit RPB7; trans 5e-09
2rf4_A214 DNA-directed RNA polymerase I subunit RPA4; transf 3e-04
>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 = 75.5 bits (185), Expect = 1e-17
 Identities = 34/92 (36%), Positives = 53/92 (57%)

Query: 23  KVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEG 82
           K+ PNVGLC+ +YD+  +E+  + PGDG+S+  V FR VVF+PF+ EI+ G I  C+ EG
Sbjct: 37  KIIPNVGLCITIYDLLTVEEGQLKPGDGSSYINVTFRAVVFKPFLGEIVTGWISKCTAEG 96

Query: 83  VHDSQSSNQPEQPISDSTVKDILKYFAEKDKP 114
           +  S      +  I  + + +   Y  E+   
Sbjct: 97  IKVSLLGIFDDIFIPQNMLFEGCYYTPEESAW 128
>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe} Length = 203 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
>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
>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 ?
Query169
3ayh_B203 DNA-directed RNA polymerase III subunit RPC8; tran 99.95
4ayb_E180 DNA-directed RNA polymerase; transferase, multi-su 99.95
2ckz_B218 C25, DNA-directed RNA polymerase III 25 KD polypep 99.94
3h0g_G172 DNA-directed RNA polymerase II subunit RPB7; trans 99.94
1go3_E187 DNA-directed RNA polymerase subunit E; transferase 99.91
2c35_B172 Human RPB7, DNA-directed RNA polymerase II 19 kDa 99.89
1y14_B171 B16, RPB7, DNA-directed RNA polymerase II 19 kDa p 99.88
2b8k_G215 B16, DNA-directed RNA polymerase II 19 kDa polypep 99.87
2rf4_A214 DNA-directed RNA polymerase I subunit RPA4; transf 99.67
2bh8_A101 1B11; transcription, molecular evolution, unique a 98.8
1kl9_A182 Eukaryotic translation initiation factor 2 subuni; 98.71
1luz_A88 Protein K3, protein K2; stranded anti-parallel bet 98.65
2a19_A175 EIF-2- alpha, eukaryotic translation initiation fa 98.64
2cqo_A119 Nucleolar protein of 40 kDa; S1 domain, OB-fold, s 98.63
2k52_A80 Uncharacterized protein MJ1198; metal-binding, zin 98.62
2eqs_A103 ATP-dependent RNA helicase DHX8; S1 domain, OB-fol 98.56
2khi_A115 30S ribosomal protein S1; acetylation, phosphoprot 98.45
2khj_A109 30S ribosomal protein S1; OB fold, acetylation, ph 98.45
2k4k_A130 GSP13, general stress protein 13; cytoplasm, stres 98.44
1q8k_A 308 Eukaryotic translation initiation factor 2 subunit 98.35
3aev_A 275 Translation initiation factor 2 subunit alpha; pro 98.3
3cw2_C 266 Translation initiation factor 2 subunit alpha; AIF 98.23
3cdi_A723 Polynucleotide phosphorylase; mRNA turnover, RNAse 98.16
4aid_A726 Polyribonucleotide nucleotidyltransferase; transfe 98.1
1e3p_A757 Guanosine pentaphosphate synthetase; polyribonucle 98.04
2nn6_I209 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, 98.02
3m7n_A179 Putative uncharacterized protein AF_0206; exosome, 97.93
3go5_A 285 Multidomain protein with S1 RNA-binding domains; s 97.9
2ba0_A229 Archeal exosome RNA binding protein RRP4; RNAse PH 97.85
2je6_I251 RRP4, exosome complex RNA-binding protein 1; nucle 97.74
2z0s_A235 Probable exosome complex RNA-binding protein 1; al 97.67
3bzc_A785 TEX; helix-turn-helix, helix-hairpin-helix, S1 dom 97.66
3psi_A 1219 Transcription elongation factor SPT6; nucleus; 3.3 97.57
1wi5_A119 RRP5 protein homolog; S1 domain, OB-fold, structur 97.49
3psf_A1030 Transcription elongation factor SPT6; nucleus; 2.5 97.34
3go5_A 285 Multidomain protein with S1 RNA-binding domains; s 97.33
2ja9_A175 Exosome complex exonuclease RRP40; RNA-binding pro 97.14
2nn6_H 308 Exosome complex exonuclease RRP4; RNA, exosome, PM 97.13
2id0_A644 Exoribonuclease 2; RNAse, exonuclease, hydrolyase, 96.63
2bx2_L 517 Ribonuclease E, RNAse E; RNA-binding, RNA turnover 96.62
1hh2_P 344 NUSA, N utilization substance protein A; transcrip 96.61
2wp8_J977 Exosome complex exonuclease DIS3; nucleus, hydrola 95.36
1k0r_A 366 NUSA; two component arrangement, S1 domain, two K- 95.06
2vnu_D760 Exosome complex exonuclease RRP44; hydrolase-RNA c 93.22
2asb_A 251 Transcription elongation protein NUSA; protein-RNA 93.07
2bh8_A101 1B11; transcription, molecular evolution, unique a 89.33
1kl9_A182 Eukaryotic translation initiation factor 2 subuni; 87.57
2nn6_G289 Exosome complex exonuclease RRP40; RNA, exosome, P 83.37
>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe} Back     alignment and structure
Probab=99.95  E-value=1e-27  Score=195.67  Aligned_cols=98  Identities=33%  Similarity=0.520  Sum_probs=94.1

Q ss_pred             ccchHHHHHHHhhhhcCceeeCCeeEEEEEeeeeeeccceEeeCCCceeEEEEEEEEEEecCCCcEEEEEEEEEecceeE
Q psy11392          5 ITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVH   84 (169)
Q Consensus         5 ~t~l~~~I~~eL~ekyegKVi~~vGLiV~V~dI~~I~eG~I~pgDG~~~~~V~FraIvFrPf~GEVVeG~V~~vt~~GiF   84 (169)
                      +.++.+++.++|+++|+||+++++|+||||+|+.++++|+|.||||+++++|+|++++|+|++||+++|+|+++|++|+|
T Consensus        19 ~~~~~~~i~~~L~~~~egkv~~~~Gl~I~v~di~~i~~g~I~~GdG~~~~~V~fk~~~f~p~~GEv~~G~Vs~vt~~Gif   98 (203)
T 3ayh_B           19 WKPTKEALAEEIHKKYANKVIQNIGLAICVYDFLKIGEGIIKYGDGSSYMNVVFRLIIFRPFRGEVMLGKIKSCSEEGIR   98 (203)
T ss_dssp             TSCHHHHHHHHHHHHHTTEEETTTEEEEEEEEEEEECCCEECTTTCCEEEEEEEEEEEECCCTTCEEEEEEEEEETTEEE
T ss_pred             CChHHHHHHHHhhhhhCCEEeCCccEEEEEEEeeEecccEEeCCCCCEEEEEEEEEEEEccCCCCEEEEEEEEEeccEEE
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCCCccCCccccc
Q psy11392         85 DSQSSNQPEQPISDSTVK  102 (169)
Q Consensus        85 V~lGp~dGlIhISd~s~~  102 (169)
                      |++||++|++|+|++..+
T Consensus        99 V~lg~~eglv~~~~l~~d  116 (203)
T 3ayh_B           99 VTISFFDDIFIPKDMLFD  116 (203)
T ss_dssp             EECSSCCCEEEEGGGBCT
T ss_pred             EEEeCceEEEEcHHhCCC
Confidence            999999999999977654
>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
>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
>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
>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
>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
>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
>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
>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} 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
>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Back     alignment and structure
>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Back     alignment and structure
>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} 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
>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
>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
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Back     alignment and structure
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A 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
>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
>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
>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
>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
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} 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
>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} 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
>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_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
>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
>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonu nuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A 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
>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {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
>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 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
>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli} 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
>2nn6_G Exosome complex exonuclease RRP40; 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

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 169
d1go3e278 d.230.1.1 (E:1-78) N-terminal, heterodimerisation 3e-12
d1go3e278 d.230.1.1 (E:1-78) N-terminal, heterodimerisation 0.002
d1y14b280 d.230.1.1 (B:1-80) N-terminal, heterodimerisation 2e-10
d2c35b277 d.230.1.1 (B:1-77) N-terminal, heterodimerisation 5e-10
>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 = 57.0 bits (138), Expect = 3e-12
 Identities = 10/41 (24%), Positives = 24/41 (58%)

Query: 23 KVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVF 63
          ++  +VG  + + D+  I +  ++ GDG+++  V F  +V+
Sbjct: 37 RLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVY 77
>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
>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
>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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query169
d1go3e278 N-terminal, heterodimerisation domain of RBP7 (Rpo 99.68
d2c35b277 N-terminal, heterodimerisation domain of RBP7 (Rpo 99.63
d1y14b280 N-terminal, heterodimerisation domain of RBP7 (Rpo 99.6
d2c35b194 C-terminal domain of RNA polymerase II subunit RBP 99.22
d1y14b191 C-terminal domain of RNA polymerase II subunit RBP 99.17
d1go3e1106 C-terminal domain of RNA polymerase II subunit RBP 98.99
d1sroa_76 S1 RNA-binding domain of polyribonucleotide phosph 98.78
d2je6i187 S1-domain of exosome complex RNA-binding protein 1 98.72
d2ba0a183 S1-domain of exosome complex RNA-binding protein 1 98.72
d1kl9a286 Eukaryotic initiation factor 2alpha, eIF2alpha, N- 98.7
d2ahob284 Eukaryotic initiation factor 2alpha, eIF2alpha, N- 98.7
d2z0sa188 S1-domain of exosome complex RNA-binding protein 1 98.57
d2nn6h195 S1-domain of Ribosomal RNA-processing protein 4, R 98.54
d1e3pa262 S1 RNA-binding domain of polyribonucleotide phosph 98.39
d3bzka494 Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287] 98.22
d2ix0a387 Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5 97.87
d1wi5a_119 S1-domain of RRP5 protein homolog (PDCD11, KIAA018 97.73
d2nn6g188 S1-domain of exosome component 3 (RRP40) {Human (H 97.43
d1hh2p172 S1 domain of NusA {Thermotoga maritima [TaxId: 233 96.9
d2ja9a190 S1-domain of exosome component 3 (RRP40) {Saccharo 96.85
d2nn6i1125 Exosome component 1, EXOSC1 {Human (Homo sapiens) 95.21
d2asba176 S1 domain of NusA {Mycobacterium tuberculosis [Tax 90.11
d1smxa_87 S1-domain of Ribonuclease E {Escherichia coli [Tax 89.95
d1k3ra171 Hypothetical protein MTH1 (MT0001), insert domain 82.78
>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=99.68  E-value=3.1e-17  Score=114.79  Aligned_cols=59  Identities=19%  Similarity=0.334  Sum_probs=57.7

Q ss_pred             ccchHHHHHHHhhhhcCceeeCCeeEEEEEeeeeeeccceEeeCCCceeEEEEEEEEEE
Q psy11392          5 ITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVF   63 (169)
Q Consensus         5 ~t~l~~~I~~eL~ekyegKVi~~vGLiV~V~dI~~I~eG~I~pgDG~~~~~V~FraIvF   63 (169)
                      +.++++++.++|+++|+||+.+++|+||+|+|+.++++|+|.||||+++++|+||+++|
T Consensus        19 g~~~~~~i~~~L~~~~egkv~~~~G~ii~v~di~~i~eG~I~~gdG~~~~~V~F~~lvF   77 (78)
T d1go3e2          19 GKDLKETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVY   77 (78)
T ss_dssp             TSCHHHHHHHHHHHHHTTCEETTTEEEEEEEEEEEECCCBCCTTCCSEEEEEEEEEEEE
T ss_pred             CcCHHHHHHHHHHHHhCCcCcCCcCEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEE
Confidence            57899999999999999999999999999999999999999999999999999999998
>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
>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} 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
>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
>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
>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
>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
>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
>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
>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} 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
>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]} 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
>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]} 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
>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2asba1 b.40.4.5 (A:108-183) S1 domain of NusA {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1k3ra1 b.40.4.10 (A:93-163) Hypothetical protein MTH1 (MT0001), insert domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure