Query psy8882
Match_columns 204
No_of_seqs 72 out of 74
Neff 3.5
Searched_HMMs 46136
Date Fri Aug 16 21:47:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8882.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8882hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14324 PINIT: PINIT domain; 99.9 1.3E-28 2.9E-33 197.6 5.2 110 65-204 1-113 (144)
2 KOG2169|consensus 99.9 6.7E-22 1.4E-26 190.4 8.3 119 65-204 107-226 (636)
3 PF01479 S4: S4 domain; Inter 32.6 38 0.00082 21.7 2.0 16 170-185 27-42 (48)
4 PRK10856 cytoskeletal protein 22.2 82 0.0018 29.1 2.9 25 163-187 297-321 (331)
5 PF13464 DUF4115: Domain of un 20.2 92 0.002 22.2 2.2 19 165-183 46-64 (77)
6 PRK06944 sulfur carrier protei 12.8 1.6E+02 0.0036 19.8 1.9 14 169-182 1-14 (65)
7 PRK05659 sulfur carrier protei 11.9 1.8E+02 0.0039 19.8 1.9 13 170-182 2-14 (66)
8 TIGR02988 YaaA_near_RecF S4 do 11.4 1.8E+02 0.004 19.6 1.8 14 170-183 35-48 (59)
9 COG0522 RpsD Ribosomal protein 10.9 1.5E+02 0.0031 26.1 1.4 26 161-186 111-136 (205)
10 KOG2305|consensus 10.5 89 0.0019 29.2 -0.0 20 77-96 102-121 (313)
No 1
>PF14324 PINIT: PINIT domain; PDB: 3I2D_A.
Probab=99.95 E-value=1.3e-28 Score=197.56 Aligned_cols=110 Identities=32% Similarity=0.451 Sum_probs=74.5
Q ss_pred CCCCCceeeecCCccccccccccceeccCCCCCCcceeeeEEEeCHHHHHHHhhcCccCCCccccceeeccccceecccc
Q psy8882 65 DRHPAVKFKVLPFFDMKHELIPISSLQPTNTSSRNQEVSFQFKLTNQQAAELGENREIIPGVRNDWHYQRTHCAIFSLIL 144 (204)
Q Consensus 65 ~~~P~VrfK~LPFYdvldeLLkPT~L~~s~~~~r~qe~~f~F~LTpqQv~~I~~srd~~pg~k~e~~v~rt~~~~~~~~~ 144 (204)
|+||+++||++||||++ ++|.++.+.+.. .+..++..|.|.||++|+++|+++ ++.+
T Consensus 1 ~~~~~~~Fk~sPFY~~~-~~i~~~~~~~~~-~~~r~~~~~~F~L~~~~~~~l~~~---------~~~~------------ 57 (144)
T PF14324_consen 1 PVHPDLRFKPSPFYKVL-RLIHPTPLLPAS-SSGRQTCSFSFKLSPDQVELLKSS---------NPSY------------ 57 (144)
T ss_dssp -------B--BTTEEEE-EEEEEEEEEE---EEEEEEEEEEE---HHHHHHHHST---------T--E------------
T ss_pred CCCCccEeccCCCccee-EEcCCccccccc-cCCCCeEEEEEEECHHHHHHHhcC---------CCCe------------
Confidence 57999999999999999 889999999988 678889999999999999999996 3456
Q ss_pred CCeEEEE---eeecCCCCCCccCCCCccEEEECCeeecCCCCCCCCCCCCCCCCCCCCccCCC
Q psy8882 145 YPQVQLR---IASLNTTTEQDDHYPPNLAIKVNQRAVQLPNPIPSRVQNKEPIRPSRLIEETN 204 (204)
Q Consensus 145 ~~QVQLR---fc~~etsceQ~D~fPpnl~VKVN~k~c~LP~~iP~~k~g~EpkRP~RPINIT~ 204 (204)
||+|| ||.++++|+|+|+||++|+|||||+.|.+|+..+.||+|. .||||||+
T Consensus 58 --~v~L~c~~~~~~~~~~~q~i~FP~~~evkvN~~~v~~~~~glknKpGt-----~rPvdIT~ 113 (144)
T PF14324_consen 58 --QVYLFCGKFCLSESSGNQPIEFPPPCEVKVNGKQVKLNNRGLKNKPGT-----ARPVDITP 113 (144)
T ss_dssp --EEEEEEEESS-SS-GGGB-----SSEEEEETTEE--S--SS-TTS-GG-----GS-EE-GG
T ss_pred --EEEEEEeccccCCCCCccccccCCCeEEEEeCEEcccCccCCCCCCCC-----CCCcccch
Confidence 99999 8999999999999999999999999999999999999999 89999995
No 2
>KOG2169|consensus
Probab=99.86 E-value=6.7e-22 Score=190.45 Aligned_cols=119 Identities=38% Similarity=0.632 Sum_probs=113.7
Q ss_pred CCCCCceeeecCCccccccccccceeccCCCCCCcceeeeEEEeCHHHHHHHhhcCccCCCccccceeeccccceecccc
Q psy8882 65 DRHPAVKFKVLPFFDMKHELIPISSLQPTNTSSRNQEVSFQFKLTNQQAAELGENREIIPGVRNDWHYQRTHCAIFSLIL 144 (204)
Q Consensus 65 ~~~P~VrfK~LPFYdvldeLLkPT~L~~s~~~~r~qe~~f~F~LTpqQv~~I~~srd~~pg~k~e~~v~rt~~~~~~~~~ 144 (204)
+.|++|+|++++|||++.++++|+.+..++ +.+++|+.|.|+||++++..|..++|+.+|.|.++.
T Consensus 107 ~~~~~~~~~~~~~y~~l~~~~~p~~~~~~~-~~~~~~~~~~f~lt~~~~~~i~~~~~~~~~~k~~~~------------- 172 (636)
T KOG2169|consen 107 PFHPDVKLKKLPFYDVLSELIKPHVLHSSN-SPSLSESPFLFALTPEQVSGISSRPDVLPGSKSEGS------------- 172 (636)
T ss_pred cCCCcccccCCchheecccccCceeecCcC-CCCcccccchhhcchhhhhhcccccccccccccccc-------------
Confidence 699999999999999999999999999998 689999999999999999999999999999886644
Q ss_pred CCeEEEEeeecCCCCCCccCCCCccEEEECCeeecCC-CCCCCCCCCCCCCCCCCCccCCC
Q psy8882 145 YPQVQLRIASLNTTTEQDDHYPPNLAIKVNQRAVQLP-NPIPSRVQNKEPIRPSRLIEETN 204 (204)
Q Consensus 145 ~~QVQLRfc~~etsceQ~D~fPpnl~VKVN~k~c~LP-~~iP~~k~g~EpkRP~RPINIT~ 204 (204)
+ |+.+++|+++|+||.++.|+||++.|+|| |++|+++.++|+||++||+|||.
T Consensus 173 ---~----~~~~~s~p~e~~~p~~~~~~vn~~~~~l~~~~~~~n~~~~~~~~~~~P~n~t~ 226 (636)
T KOG2169|consen 173 ---V----CLMETSCPQEDHFPPNVQVKVNNSPCQLPFGYMPNNKHGLEPKRPSRPGNITS 226 (636)
T ss_pred ---e----eeccccCccccccCceeEEEecCCcceeeccccCCCCcccccCCCCCCCcCcc
Confidence 3 99999999999999999999999999999 99999999999999999999995
No 3
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=32.58 E-value=38 Score=21.73 Aligned_cols=16 Identities=38% Similarity=0.484 Sum_probs=13.3
Q ss_pred EEEECCeeecCCCCCC
Q psy8882 170 AIKVNQRAVQLPNPIP 185 (204)
Q Consensus 170 ~VKVN~k~c~LP~~iP 185 (204)
.|+|||+.|.-|++.-
T Consensus 27 ~V~VNg~~v~~~~~~v 42 (48)
T PF01479_consen 27 RVKVNGKVVKDPSYIV 42 (48)
T ss_dssp TEEETTEEESSTTSBE
T ss_pred EEEECCEEEcCCCCCC
Confidence 4899999999888743
No 4
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=22.20 E-value=82 Score=29.11 Aligned_cols=25 Identities=20% Similarity=0.255 Sum_probs=21.3
Q ss_pred cCCCCccEEEECCeeecCCCCCCCC
Q psy8882 163 DHYPPNLAIKVNQRAVQLPNPIPSR 187 (204)
Q Consensus 163 D~fPpnl~VKVN~k~c~LP~~iP~~ 187 (204)
-.+|.+..|++||+.+.|.+++..+
T Consensus 297 iG~~~~v~i~~nG~~vdl~~~~~~g 321 (331)
T PRK10856 297 IGAPAAVQIQYQGKPVDLSRFIRTN 321 (331)
T ss_pred EcCCCceEEEECCEEccCCccCcCC
Confidence 4579999999999999999996544
No 5
>PF13464 DUF4115: Domain of unknown function (DUF4115)
Probab=20.19 E-value=92 Score=22.15 Aligned_cols=19 Identities=26% Similarity=0.443 Sum_probs=16.5
Q ss_pred CCCccEEEECCeeecCCCC
Q psy8882 165 YPPNLAIKVNQRAVQLPNP 183 (204)
Q Consensus 165 fPpnl~VKVN~k~c~LP~~ 183 (204)
.+.++.|++||+.+.+++.
T Consensus 46 na~~v~v~~nG~~~~~~~~ 64 (77)
T PF13464_consen 46 NAGAVEVTVNGKPVDLLGP 64 (77)
T ss_pred CCCcEEEEECCEECCCCCC
Confidence 5788999999999999754
No 6
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=12.80 E-value=1.6e+02 Score=19.85 Aligned_cols=14 Identities=36% Similarity=0.814 Sum_probs=11.6
Q ss_pred cEEEECCeeecCCC
Q psy8882 169 LAIKVNQRAVQLPN 182 (204)
Q Consensus 169 l~VKVN~k~c~LP~ 182 (204)
+.|+|||+.+.+|.
T Consensus 1 m~i~vNg~~~~~~~ 14 (65)
T PRK06944 1 MDIQLNQQTLSLPD 14 (65)
T ss_pred CEEEECCEEEECCC
Confidence 36899999999874
No 7
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=11.89 E-value=1.8e+02 Score=19.78 Aligned_cols=13 Identities=31% Similarity=0.616 Sum_probs=11.2
Q ss_pred EEEECCeeecCCC
Q psy8882 170 AIKVNQRAVQLPN 182 (204)
Q Consensus 170 ~VKVN~k~c~LP~ 182 (204)
.|+|||+.+.++.
T Consensus 2 ~i~vNG~~~~~~~ 14 (66)
T PRK05659 2 NIQLNGEPRELPD 14 (66)
T ss_pred EEEECCeEEEcCC
Confidence 6899999998874
No 8
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=11.36 E-value=1.8e+02 Score=19.58 Aligned_cols=14 Identities=14% Similarity=0.048 Sum_probs=10.5
Q ss_pred EEEECCeeecCCCC
Q psy8882 170 AIKVNQRAVQLPNP 183 (204)
Q Consensus 170 ~VKVN~k~c~LP~~ 183 (204)
.|+|||+.|.-|++
T Consensus 35 ~V~VNg~~~~~~~~ 48 (59)
T TIGR02988 35 EVLVNGELENRRGK 48 (59)
T ss_pred CEEECCEEccCCCC
Confidence 48899998876554
No 9
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=10.93 E-value=1.5e+02 Score=26.05 Aligned_cols=26 Identities=27% Similarity=0.304 Sum_probs=19.1
Q ss_pred CccCCCCccEEEECCeeecCCCCCCC
Q psy8882 161 QDDHYPPNLAIKVNQRAVQLPNPIPS 186 (204)
Q Consensus 161 Q~D~fPpnl~VKVN~k~c~LP~~iP~ 186 (204)
|.-.|=.+=+|.|||+.+..|+|+=+
T Consensus 111 qARQlV~HGHI~VnGk~V~iPSy~V~ 136 (205)
T COG0522 111 QARQLVSHGHILVNGKRVNIPSYLVS 136 (205)
T ss_pred HHHHHhhcceEEECCEEeccCcEEec
Confidence 33444455579999999999998644
No 10
>KOG2305|consensus
Probab=10.54 E-value=89 Score=29.19 Aligned_cols=20 Identities=15% Similarity=0.315 Sum_probs=0.0
Q ss_pred CccccccccccceeccCCCC
Q psy8882 77 FFDMKHELIPISSLQPTNTS 96 (204)
Q Consensus 77 FYdvldeLLkPT~L~~s~~~ 96 (204)
||++||+++.|+.+.+++|+
T Consensus 102 ly~qlD~i~d~~tIlaSSTS 121 (313)
T KOG2305|consen 102 LYKQLDEIADPTTILASSTS 121 (313)
T ss_pred HHHHHHHhcCCceEEecccc
Done!