Psyllid ID: psy6025

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--------9
MIINMFHENPLVKRVQEEELSSTDSSIEFLLCPSHVGIAGNEEAKQATNDDVTHQELFFDEIKINIEKKYLEEWNIQNGPILLVQTKTN
cEEEcccccHHHHHHHHHHHccccccEEEEEccccccccccHHHHHHccccccHHHEEHHHHHHHHHHHHHHHHHcccccEEEEEEEcc
cEEEccccccHHHHHHHHHcccccccHEEEcccccccEcccHHHHHHccccccHHHHHHHHHEEHHHHHHHHHHHcccccEEEEEEccc
miinmfhenplvkrvqeeelsstdssiefllcpshvgiagneeakqatnddvthqelFFDEIKINIEKKYLEewniqngpiLLVQTKTN
miinmfhenplvkrvqeEELSSTDSSIEFLLCPSHVGIAGNEEAKQATNDDVTHQELFFDEIKINIEKKYLeewniqngpillvqtktn
MIINMFHENPLVKRVQEEELSSTDSSIEFLLCPSHVGIAGNEEAKQATNDDVTHQELFFDEIKINIEKKYLEEWNIQNGPILLVQTKTN
**************************IEFLLCPSHVGIAG*********DDVTHQELFFDEIKINIEKKYLEEWNIQNGPILLV*****
MIINMF*ENPLV*************SIEFLLCPSHVGI*************VTHQELFFDEIKINIEKKYLEEWNIQNGPILLVQT***
MIINMFHENPLVKRVQ********SSIEFLLCPSHVGIAGNEEAKQATNDDVTHQELFFDEIKINIEKKYLEEWNIQNGPILLVQTKTN
MIINMFHENPLVKRVQEEELSSTDSSIEFLLCPSHVGIAGNEEAKQATNDDVTHQELFFDEIKINIEKKYLEEWNIQNGPILLVQTK**
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MIINMFHENPLVKRVQEEELSSTDSSIEFLLCPSHVGIAGNEEAKQATNDDVTHQELFFDEIKINIEKKYLEEWNIQNGPILLVQTKTN
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

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

Original result of BLAST against Nonredundant Database

No hits with e-value below 0.001 by BLAST

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

No hits with e-value below 0.001 by BLAST

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 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 ?
Query89
cd09276128 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom 5e-05
>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse transcriptases Back     alignment and domain information 
 Score = 38.8 bits (91), Expect = 5e-05
 Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 6/55 (10%)

Query: 1   MIINMFHENPLVKRVQE--EELSSTDSSIEFLLCPSHVGIAGNEE----AKQATN 49
            + +    +PLV R+++   EL++    +     P H GI GNE     AK+A  
Sbjct: 74  ALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADRLAKEAAK 128

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 128

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 89
PF00075132 RNase_H: RNase H; InterPro: IPR002156 The RNase H 99.14
PRK08719147 ribonuclease H; Reviewed 99.09
PRK00203150 rnhA ribonuclease H; Reviewed 99.08
PRK06548161 ribonuclease H; Provisional 98.87
COG0328154 RnhA Ribonuclease HI [DNA replication, recombinati 98.73
cd06222130 RnaseH RNase H (RNase HI) is an endonuclease that 98.68
KOG3752|consensus371 98.18
PRK13907128 rnhA ribonuclease H; Provisional 96.41
PF1345687 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH 95.26
PRK07708219 hypothetical protein; Validated 94.64
PRK07238 372 bifunctional RNase H/acid phosphatase; Provisional 94.22
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site Back     alignment and domain information 
Probab=99.14  E-value=2.1e-11  Score=79.73  Aligned_cols=41  Identities=29%  Similarity=0.546  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHhhcCCCceEEEEecCccCC-CccHHHHHhhhhhh
Q psy6025          10 PLVKRVQEEELSSTDSSIEFLLCPSHVGI-AGNEEAKQATNDDV   52 (89)
Q Consensus        10 ~i~~~Iq~~el~~~~~~i~~~WvP~H~GI-~GNE~AD~~Ak~a~   52 (89)
                      ++...|.+ .+ ..+..|.|.|||||+|+ .|||+||+||++|+
T Consensus        90 ~i~~~i~~-~~-~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   90 PIKNEIWE-LL-SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             BHTHHHHH-HH-HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             cchhheee-cc-ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence            57777773 44 44788999999999999 69999999999885

This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
>PRK08719 ribonuclease H; Reviewed Back     alignment and domain information
>PRK00203 rnhA ribonuclease H; Reviewed Back     alignment and domain information
>PRK06548 ribonuclease H; Provisional Back     alignment and domain information
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair] Back     alignment and domain information
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner Back     alignment and domain information
>KOG3752|consensus Back     alignment and domain information
>PRK13907 rnhA ribonuclease H; Provisional Back     alignment and domain information
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B Back     alignment and domain information
>PRK07708 hypothetical protein; Validated Back     alignment and domain information
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query89
3qio_A150 GAG-POL polyprotein; RNAse H, inhibitor, nuclease, 99.2
3h08_A146 RNH (ribonuclease H); RNAse H, 3D-structure, endon 99.19
1jl1_A155 Ribonuclease HI; RNAse HI, protein stability, ther 99.15
2qkb_A154 Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy 99.15
2kq2_A147 Ribonuclease H-related protein; PSI, NESG, protein 99.14
2e4l_A158 Ribonuclease HI, RNAse HI; hydrolase, endoribonucl 99.11
3p1g_A165 Xenotropic murine leukemia virus-related virus (X 99.03
1ril_A166 Ribonuclease H; hydrolase(endoribonuclease); 2.80A 98.99
2lsn_A165 Reverse transcriptase; RNAse H, viral protein; NMR 98.83
1mu2_A555 HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym 98.81
2zd1_A557 Reverse transcriptase/ribonuclease H; P51/P66, het 98.71
3hst_B141 Protein RV2228C/MT2287; ribonuclease H1, RV2228C N 98.08
3u3g_D140 Ribonuclease H, RNAse H1; hydrolase, cleave the RN 98.04
2ehg_A149 Ribonuclease HI; RNAse HI, hyperthermophilic archa 97.9
>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase, hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} SCOP: c.55.3.1 PDB: 3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A Back     alignment and structure
Probab=99.20  E-value=9.8e-12  Score=86.03  Aligned_cols=45  Identities=24%  Similarity=0.465  Sum_probs=36.0

Q ss_pred             CcHHHHHHHHHHhhcCCCceEEEEecCccCCCccHHHHHhhhhhhhc
Q psy6025           8 ENPLVKRVQEEELSSTDSSIEFLLCPSHVGIAGNEEAKQATNDDVTH   54 (89)
Q Consensus         8 ~n~i~~~Iq~~el~~~~~~i~~~WvP~H~GI~GNE~AD~~Ak~a~~~   54 (89)
                      ..++.+.+.+ ++ .....|.|.|||||+|++|||+||+||++|+..
T Consensus       103 n~~l~~~l~~-~l-~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A          103 NVDLVNQIIE-QL-IKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             CHHHHHHHHH-HH-TTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             cHHHHHHHHH-HH-hhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            3456666652 23 456789999999999999999999999999864
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease, hydrolase, magnesium, metal-binding; 1.60A {Chlorobaculum tepidum} Back     alignment and structure
>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability, hydrogen exchange, cooperativity, hydrolase; 1.30A {Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A 1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A 1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A 3aa5_X 1rbv_A ... Back     alignment and structure
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A* Back     alignment and structure
>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A Back     alignment and structure
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A {Shewanella oneidensis} PDB: 2zqb_A Back     alignment and structure
>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A 4e89_A Back     alignment and structure
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A Back     alignment and structure
>2lsn_A Reverse transcriptase; RNAse H, viral protein; NMR {Simian foamy virus} Back     alignment and structure
>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B Back     alignment and structure
>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ... Back     alignment and structure
>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal domain, fusion protein, maltose binding protein, HYDR; HET: MLR TAR; 2.25A {Mycobacterium tuberculosis} Back     alignment and structure
>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of RNA/DNA hybrid; 1.40A {Uncultured organism} Back     alignment and structure
>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus tokodaii} PDB: 3aly_A Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query89
d1jl1a_152 RNase H (RNase HI) {Escherichia coli [TaxId: 562]} 99.45
d1rila_147 RNase H (RNase HI) {Thermus thermophilus [TaxId: 2 99.34
d1mu2a1126 HIV RNase H (Domain of reverse transcriptase) {Hum 99.33
d1s1ta1110 HIV RNase H (Domain of reverse transcriptase) {Hum 94.74
>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Escherichia coli [TaxId: 562]

Probab=99.45  E-value=2.5e-14  Score=93.55  Aligned_cols=45  Identities=20%  Similarity=0.277  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHhhcCCCceEEEEecCccCCCccHHHHHhhhhhhhcccc
Q psy6025          10 PLVKRVQEEELSSTDSSIEFLLCPSHVGIAGNEEAKQATNDDVTHQEL   57 (89)
Q Consensus        10 ~i~~~Iq~~el~~~~~~i~~~WvP~H~GI~GNE~AD~~Ak~a~~~~~~   57 (89)
                      ++.+.+.+  + .....|.|.|||||+|++|||+||+||++|+.++.+
T Consensus       100 ~~~~~i~~--~-~~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~  144 (152)
T d1jl1a_         100 DLWQRLDA--A-LGQHQIKWEWVKGHAGHPENERADELARAAAMNPTL  144 (152)
T ss_dssp             HHHHHHHH--H-TTTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCB
T ss_pred             HHHHHHHH--H-hhcceeEEEEecccCCCccHHHHHHHHHHHHhCCCC
Confidence            44555542  2 334689999999999999999999999999987643
>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]} Back     information, alignment and structure
>d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 1 [TaxId: 11676]} Back     information, alignment and structure