Query psy35
Match_columns 69
No_of_seqs 20 out of 22
Neff 1.8
Searched_HMMs 46136
Date Fri Aug 16 18:16:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy35.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/35hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PHA00028 rep RNA replicase, be 55.8 6.6 0.00014 33.2 1.4 28 34-61 247-275 (561)
2 PF03431 RNA_replicase_B: RNA 39.5 11 0.00023 31.9 0.2 21 41-61 247-267 (542)
3 COG0415 PhrB Deoxyribodipyrimi 23.7 23 0.0005 28.7 -0.3 36 4-40 348-387 (461)
4 COG5528 Predicted integral mem 18.1 65 0.0014 23.5 1.1 14 53-66 66-79 (155)
5 TIGR03768 RPA4764 metallophosp 17.5 1.4E+02 0.003 24.9 2.9 19 27-45 127-145 (492)
6 KOG4245|consensus 16.8 62 0.0013 25.5 0.7 15 53-67 143-157 (297)
7 PF10429 Mtr2: Nuclear pore RN 14.8 80 0.0017 23.0 0.8 12 2-13 130-141 (166)
8 TIGR03767 P_acnes_RR metalloph 14.3 1.8E+02 0.0038 24.2 2.7 18 27-44 123-140 (496)
9 PF09572 RE_XamI: XamI restric 14.2 83 0.0018 24.2 0.8 13 1-13 171-183 (251)
10 PF14979 TMEM52: Transmembrane 13.9 92 0.002 22.6 0.9 12 49-60 14-25 (154)
No 1
>PHA00028 rep RNA replicase, beta subunit
Probab=55.80 E-value=6.6 Score=33.18 Aligned_cols=28 Identities=32% Similarity=0.376 Sum_probs=22.5
Q ss_pred CCCC-CCCCCCCccCCchhHHHHHHHHhc
Q psy35 34 SASH-DGASTPDVGCLPVHLSLWLVWLMG 61 (69)
Q Consensus 34 stsH-DgasTPDv~~~~~~ls~~~~~~~~ 61 (69)
.+|- +.-.|=|..+.|.|+|+||||+.-
T Consensus 247 ~gS~d~sLATIDLSsASDSISl~LV~lll 275 (561)
T PHA00028 247 LGSVDGSLATIDLSSASDSISLKLVWLLL 275 (561)
T ss_pred hccccCceeeEeccccccHHHHHHHHHHc
Confidence 3455 345789999999999999999874
No 2
>PF03431 RNA_replicase_B: RNA replicase, beta-chain ; InterPro: IPR005093 RNA-directed RNA polymerase (RdRp) (2.7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This is a family of Leviviridae RNA replicases.; GO: 0003968 RNA-directed RNA polymerase activity, 0019079 viral genome replication; PDB: 3MMP_G 3AVU_A 3AVW_A 3AGQ_A 3AGP_A 3AVT_A 3AVY_A 3AVX_A 3AVV_A.
Probab=39.53 E-value=11 Score=31.89 Aligned_cols=21 Identities=38% Similarity=0.522 Sum_probs=17.3
Q ss_pred CCCCccCCchhHHHHHHHHhc
Q psy35 41 STPDVGCLPVHLSLWLVWLMG 61 (69)
Q Consensus 41 sTPDv~~~~~~ls~~~~~~~~ 61 (69)
-|=|..+.|.++|+||||+.-
T Consensus 247 aTIDLSsASDsis~~Lv~~ll 267 (542)
T PF03431_consen 247 ATIDLSSASDSISLWLVELLL 267 (542)
T ss_dssp EEEEBTTCCCT-BHHHHHHHS
T ss_pred eeEeccccccHhHHHHHHHhC
Confidence 577889999999999999864
No 3
>COG0415 PhrB Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]
Probab=23.66 E-value=23 Score=28.67 Aligned_cols=36 Identities=39% Similarity=0.524 Sum_probs=25.4
Q ss_pred ceeeecCCCCC----CCCCCCCCcCCCCCCCCCCCCCCCCC
Q psy35 4 DLVIDERDSTK----PLPELGGTTNGNDGRSNADSASHDGA 40 (69)
Q Consensus 4 DLVIDERd~~k----p~pelg~~~Ngn~~rsnadstsHDga 40 (69)
||-||.|.|.+ -+=+ |+.+|||+|=+=+.|+++|.+
T Consensus 348 ~L~IdWR~GE~~F~~~LiD-~D~asN~ggWQW~AstG~Da~ 387 (461)
T COG0415 348 DLLIDWREGEKYFMRQLID-GDPASNNGGWQWAASTGTDAA 387 (461)
T ss_pred hcCCCHHHHHHHHHHhccC-CCcccCCCCeeEEeccCCCCC
Confidence 78899999876 2222 666777777666777777764
No 4
>COG5528 Predicted integral membrane protein [Function unknown]
Probab=18.14 E-value=65 Score=23.48 Aligned_cols=14 Identities=36% Similarity=0.477 Sum_probs=12.0
Q ss_pred HHHHHHHhcccchh
Q psy35 53 SLWLVWLMGFPLIT 66 (69)
Q Consensus 53 s~~~~~~~~~~~~~ 66 (69)
..||+|+.|+||-+
T Consensus 66 G~aLa~~aG~pL~~ 79 (155)
T COG5528 66 GWALAHLAGWPLGQ 79 (155)
T ss_pred HHHHHHHcCCCccc
Confidence 57999999999854
No 5
>TIGR03768 RPA4764 metallophosphoesterase, RPA4764 family. This model describes a small collection of probable metallophosphoresterases, related to pfam00149. Members of this protein family usually have a Sec-independent TAT (twin-arginine translocation) signal sequence, N-terminal to the region modeled by this alignment. This model and TIGR03767 divide a narrow clade of pfam00149-related enzymes.
Probab=17.51 E-value=1.4e+02 Score=24.94 Aligned_cols=19 Identities=32% Similarity=0.354 Sum_probs=14.5
Q ss_pred CCCCCCCCCCCCCCCCCCc
Q psy35 27 DGRSNADSASHDGASTPDV 45 (69)
Q Consensus 27 ~~rsnadstsHDgasTPDv 45 (69)
+++-.++|+.|+|+..-|-
T Consensus 127 G~~I~p~SG~~~~~e~v~~ 145 (492)
T TIGR03768 127 GKPITPSSGAHAGADTIDY 145 (492)
T ss_pred CCeeccCCCCCCCccCCCC
Confidence 3577889999988777654
No 6
>KOG4245|consensus
Probab=16.77 E-value=62 Score=25.50 Aligned_cols=15 Identities=53% Similarity=1.179 Sum_probs=12.7
Q ss_pred HHHHHHHhcccchhc
Q psy35 53 SLWLVWLMGFPLITA 67 (69)
Q Consensus 53 s~~~~~~~~~~~~~~ 67 (69)
-.|+-||.|.|--||
T Consensus 143 kywlpwlvgmpaeta 157 (297)
T KOG4245|consen 143 KYWLPWLVGMPAETA 157 (297)
T ss_pred hhhhHHHhCCchHHH
Confidence 479999999997665
No 7
>PF10429 Mtr2: Nuclear pore RNA shuttling protein Mtr2; InterPro: IPR019488 Mtr2 is a monomeric, dual-action, RNA-shuttle protein found in yeasts. Transport across the nuclear-cytoplasmic membrane is via the macro-molecular membrane-spanning nuclear pore complex, NPC. The pore is lined by a subset of NPC members called nucleoporins that present FG (Phe-Gly) receptors, characteristically GLFG and FXFG motifs, for shuttling RNAs and proteins. RNA cargo is bound to soluble transport proteins (nuclear export factors) such as Mex67 in yeasts, and TAP in metazoa, which pass along the pore by binding to successive FG receptors. Mtr2 when bound to Mex67 maximises this FG-binding. Mtr2 also acts independently of Mex67 in transporting the large ribosomal RNA subunit through the pore []. ; PDB: 1Q40_A 1Q42_A 1OF5_B.
Probab=14.81 E-value=80 Score=22.96 Aligned_cols=12 Identities=42% Similarity=0.578 Sum_probs=9.2
Q ss_pred CcceeeecCCCC
Q psy35 2 PIDLVIDERDST 13 (69)
Q Consensus 2 PIDLVIDERd~~ 13 (69)
.+-||||||--.
T Consensus 130 sl~lvvDe~i~~ 141 (166)
T PF10429_consen 130 SLQLVVDERIFR 141 (166)
T ss_dssp EEEEEEECGCCC
T ss_pred eEEEEEechhhc
Confidence 356999999755
No 8
>TIGR03767 P_acnes_RR metallophosphoesterase, PPA1498 family. This model describes a small collection of probable metallophosphoresterases, related to pfam00149 but with long inserts separating some of the shared motifs such that the homology is apparent only through multiple sequence alignment. Members of this protein family, in general, have a Sec-independent TAT (twin-arginine translocation) signal sequence, N-terminal to the region modeled by this alignment. Members include YP_056203.1 from Propionibacterium acnes KPA171202.
Probab=14.32 E-value=1.8e+02 Score=24.25 Aligned_cols=18 Identities=17% Similarity=0.176 Sum_probs=13.3
Q ss_pred CCCCCCCCCCCCCCCCCC
Q psy35 27 DGRSNADSASHDGASTPD 44 (69)
Q Consensus 27 ~~rsnadstsHDgasTPD 44 (69)
++.-.++|+.||++...|
T Consensus 123 G~~i~p~sG~~~~~e~v~ 140 (496)
T TIGR03767 123 GGTIVPNSGDPDRYESVQ 140 (496)
T ss_pred CCeeccCCCCCCCccccc
Confidence 357778999998766555
No 9
>PF09572 RE_XamI: XamI restriction endonuclease; InterPro: IPR019072 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the XamI restriction endonuclease which recognises GTCGAC but cleavage site unknown. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=14.25 E-value=83 Score=24.25 Aligned_cols=13 Identities=38% Similarity=0.815 Sum_probs=10.4
Q ss_pred CCcceeeecCCCC
Q psy35 1 MPIDLVIDERDST 13 (69)
Q Consensus 1 MPIDLVIDERd~~ 13 (69)
||+|+||=--+++
T Consensus 171 ~pvD~vI~p~~~~ 183 (251)
T PF09572_consen 171 IPVDVVIRPHDGR 183 (251)
T ss_pred CcccEEEecCCCC
Confidence 7999999766655
No 10
>PF14979 TMEM52: Transmembrane 52
Probab=13.92 E-value=92 Score=22.64 Aligned_cols=12 Identities=42% Similarity=1.093 Sum_probs=9.3
Q ss_pred chhHHHHHHHHh
Q psy35 49 PVHLSLWLVWLM 60 (69)
Q Consensus 49 ~~~ls~~~~~~~ 60 (69)
....+||-|||.
T Consensus 14 ~~W~~LWyIwLi 25 (154)
T PF14979_consen 14 TRWSSLWYIWLI 25 (154)
T ss_pred cceehhhHHHHH
Confidence 456788999986
Done!