Query psy12975
Match_columns 205
No_of_seqs 12 out of 14
Neff 1.9
Searched_HMMs 46136
Date Fri Aug 16 15:56:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12975.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12975hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1031 Uncharacterized Fe-S o 53.3 6.5 0.00014 38.8 1.1 51 150-201 174-236 (560)
2 PHA02681 ORF089 virion membran 44.9 15 0.00032 29.1 1.7 27 165-191 25-60 (92)
3 PF06568 DUF1127: Domain of un 30.0 22 0.00048 22.9 0.5 17 182-198 22-38 (40)
4 TIGR01021 rpsE_bact ribosomal 19.3 98 0.0021 25.5 2.5 46 149-194 67-112 (154)
5 PRK15124 2'-5' RNA ligase; Pro 17.1 77 0.0017 25.0 1.3 17 186-202 108-124 (176)
6 PLN00010 cyclin-dependent kina 15.4 86 0.0019 24.5 1.2 41 145-195 8-48 (86)
7 PRK00550 rpsE 30S ribosomal pr 13.3 1.5E+02 0.0033 24.7 2.2 44 151-194 80-123 (168)
8 PF03719 Ribosomal_S5_C: Ribos 12.9 94 0.002 22.5 0.7 36 159-194 2-37 (74)
9 CHL00138 rps5 ribosomal protei 12.6 1.4E+02 0.0031 24.4 1.8 44 151-194 92-135 (143)
10 COG1996 RPC10 DNA-directed RNA 12.5 1E+02 0.0023 21.6 0.8 29 154-191 21-49 (49)
No 1
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=53.34 E-value=6.5 Score=38.81 Aligned_cols=51 Identities=37% Similarity=0.656 Sum_probs=38.2
Q ss_pred CCCccee-ee-----eecccccee------eecCCCCCCCCCCCCCchhhhhhhccCccccccC
Q psy12975 150 GQHDTYR-HV-----TFEPCARKV------CVTPRPRRSGTASPPLVPKQIKAIGLDRDERHFR 201 (205)
Q Consensus 150 ~~~~~~~-~~-----~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 (205)
-||-.|- || |++-|+|.| |..|...+.-.-.+--|-+.|||+ .+-.-||||
T Consensus 174 ~qHP~yp~~vi~EiETyRGC~r~~~ggCSFCtEp~~g~~~~R~~e~Vv~EVkaL-Y~~GvrhFR 236 (560)
T COG1031 174 KQHPNYPEYVICEIETYRGCPRRVSGGCSFCTEPVRGRPEFRPPEDVVEEVKAL-YRAGVRHFR 236 (560)
T ss_pred HhCCCCcceEEEEEeeccCCcccccCCCccccCcCcCCcccCCHHHHHHHHHHH-HHhccceee
Confidence 4888887 76 566899986 777776666677777788888886 344568887
No 2
>PHA02681 ORF089 virion membrane protein; Provisional
Probab=44.89 E-value=15 Score=29.08 Aligned_cols=27 Identities=30% Similarity=0.615 Sum_probs=19.4
Q ss_pred ceeeec-CCCCCCCCCCC--------CCchhhhhhh
Q psy12975 165 RKVCVT-PRPRRSGTASP--------PLVPKQIKAI 191 (205)
Q Consensus 165 ~~~~~~-~~~~~~~~~~~--------~~~~~~~~~~ 191 (205)
|+-|++ |+++|-+..-. -|-|.||||+
T Consensus 25 RR~~i~~p~~~r~~D~L~~~ds~F~D~lTpDQVrAl 60 (92)
T PHA02681 25 RRSCVSAPAVPRNKDLLPPGASSFEDKMTDDQVRAF 60 (92)
T ss_pred HhccCCCCCCCcccccCCCCCchhhccCCHHHHHHH
Confidence 566887 88776655444 3678999996
No 3
>PF06568 DUF1127: Domain of unknown function (DUF1127); InterPro: IPR009506 This family is found in several hypothetical bacterial proteins. In some cases it represents it represents the C-terminal region whereas in others it represents the whole sequence.
Probab=30.04 E-value=22 Score=22.86 Aligned_cols=17 Identities=35% Similarity=0.577 Sum_probs=14.1
Q ss_pred CCchhhhhhhccCcccc
Q psy12975 182 PLVPKQIKAIGLDRDER 198 (205)
Q Consensus 182 ~~~~~~~~~~~~~~~~~ 198 (205)
-|-..|++.|||.|++.
T Consensus 22 ~Lsd~~L~DIGl~R~di 38 (40)
T PF06568_consen 22 ELSDRQLADIGLTRSDI 38 (40)
T ss_pred cCCHHHHHHcCCCHHHh
Confidence 46678999999999875
No 4
>TIGR01021 rpsE_bact ribosomal protein S5, bacterial/organelle type. This model finds chloroplast ribosomal protein S5 as well as bacterial ribosomal protein S5. A candidate mitochondrial form (Saccharomyces cerevisiae YBR251W and its homolog) differs substantially and is not included in this model.
Probab=19.32 E-value=98 Score=25.46 Aligned_cols=46 Identities=17% Similarity=0.129 Sum_probs=37.2
Q ss_pred CCCCcceeeeeeccccceeeecCCCCCCCCCCCCCchhhhhhhccC
Q psy12975 149 PGQHDTYRHVTFEPCARKVCVTPRPRRSGTASPPLVPKQIKAIGLD 194 (205)
Q Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 (205)
-++|-.|.-|...-|+-+|.+.|+|+-.|-...+.+-+-+..+||.
T Consensus 67 ~~~~Ti~~~v~gk~gs~~V~l~Pap~G~Gi~a~~~~~~il~laGI~ 112 (154)
T TIGR01021 67 LTKGTIPHEVIGVSGAAKVLLKPASPGTGVIAGGAVRAILELAGVK 112 (154)
T ss_pred cCCCccceEEEEEECcEEEEEEECCCCCceEeCcHHHHHHHHcCcc
Confidence 3455445556777789999999999999998888888888888985
No 5
>PRK15124 2'-5' RNA ligase; Provisional
Probab=17.06 E-value=77 Score=25.03 Aligned_cols=17 Identities=24% Similarity=0.366 Sum_probs=14.1
Q ss_pred hhhhhhccCccccccCC
Q psy12975 186 KQIKAIGLDRDERHFRP 202 (205)
Q Consensus 186 ~~~~~~~~~~~~~~~~~ 202 (205)
+.++++|+..|+|.|+|
T Consensus 108 ~~l~~~G~~~e~r~f~P 124 (176)
T PRK15124 108 SQAARSGCYQSPQPFHP 124 (176)
T ss_pred HHHHHcCCCCCCCCCCC
Confidence 34567899999999998
No 6
>PLN00010 cyclin-dependent kinases regulatory subunit; Provisional
Probab=15.44 E-value=86 Score=24.54 Aligned_cols=41 Identities=34% Similarity=0.579 Sum_probs=24.1
Q ss_pred cccCCCCCcceeeeeeccccceeeecCCCCCCCCCCCCCchhhhhhhccCc
Q psy12975 145 EKYSPGQHDTYRHVTFEPCARKVCVTPRPRRSGTASPPLVPKQIKAIGLDR 195 (205)
Q Consensus 145 ~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 195 (205)
.+|.|..+ .||||.+-.=..|. -|. .--|--.+.+.||+..
T Consensus 8 ~kY~Dd~y-eYRhViLPk~~~k~--ipk-------~~LL~E~EWR~LGIqq 48 (86)
T PLN00010 8 EKYFDDTY-EYRHVVLPPEVAKL--LPK-------NRLLSENEWRAIGVQQ 48 (86)
T ss_pred CceeCCCc-EEEEEEeCHHHHHh--CCc-------CcccCHHHHHHhcccc
Confidence 46777764 69999985433331 111 1235556777788764
No 7
>PRK00550 rpsE 30S ribosomal protein S5; Validated
Probab=13.31 E-value=1.5e+02 Score=24.72 Aligned_cols=44 Identities=18% Similarity=0.146 Sum_probs=37.5
Q ss_pred CCcceeeeeeccccceeeecCCCCCCCCCCCCCchhhhhhhccC
Q psy12975 151 QHDTYRHVTFEPCARKVCVTPRPRRSGTASPPLVPKQIKAIGLD 194 (205)
Q Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 (205)
.|-.|.-|...-++-+|.+-|+|+-.|-...+.+-+-+..+||.
T Consensus 80 ~~Ti~~~v~gk~gs~kV~l~Pap~G~Gl~a~~~i~~il~laGI~ 123 (168)
T PRK00550 80 GGTIPHEVIGKFGAAKVLLKPASEGTGVIAGGAVRAVLELAGVK 123 (168)
T ss_pred CCccceeEEEEEceEEEEEEeCCCCCceEeChHHHHHHHHcCcc
Confidence 66677778888899999999999999988888887888888885
No 8
>PF03719 Ribosomal_S5_C: Ribosomal protein S5, C-terminal domain; InterPro: IPR005324 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 [, ]. This is a family of proteins related to the 30S ribosomal protein S5P from Sulfolobus acidocaldarius (O05641 from SWISSPROT). Ribosomal protein S5 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S5 is known to be important in the assembly and function of the 30S ribosomal subunit. Mutations in S5 have been shown to increase translational error frequencies.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_E 2XZM_E 2WDK_E 3KNJ_E 3HUY_E 2B9M_E 2Y18_E 1XMQ_E 1IBM_E 3TVF_H ....
Probab=12.92 E-value=94 Score=22.53 Aligned_cols=36 Identities=25% Similarity=0.289 Sum_probs=29.8
Q ss_pred eeccccceeeecCCCCCCCCCCCCCchhhhhhhccC
Q psy12975 159 TFEPCARKVCVTPRPRRSGTASPPLVPKQIKAIGLD 194 (205)
Q Consensus 159 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 (205)
.-.-++-+|.+-|+|+-.|-...+.+-+-++.+|+.
T Consensus 2 ~gk~g~~~V~l~Pap~G~Gl~a~~~vr~il~laGI~ 37 (74)
T PF03719_consen 2 TGKFGATKVFLKPAPPGTGLVAGGAVRAILELAGIK 37 (74)
T ss_dssp EEEETTEEEEEEESCTTSCEESSHHHHHHHHHTTES
T ss_pred EEEEeeEEEEEEeCCCCcceeechhHHHHHHhcccc
Confidence 334578899999999999998888888888888875
No 9
>CHL00138 rps5 ribosomal protein S5; Validated
Probab=12.64 E-value=1.4e+02 Score=24.44 Aligned_cols=44 Identities=20% Similarity=0.163 Sum_probs=37.1
Q ss_pred CCcceeeeeeccccceeeecCCCCCCCCCCCCCchhhhhhhccC
Q psy12975 151 QHDTYRHVTFEPCARKVCVTPRPRRSGTASPPLVPKQIKAIGLD 194 (205)
Q Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 (205)
.|-.|.-|.-.-++-+|.+-|+|+-.|-..-+.+-+-+.++|+.
T Consensus 92 ~~TI~~~v~gk~gs~~V~l~Pap~G~Gi~a~~~i~~vlelaGI~ 135 (143)
T CHL00138 92 SNSIPHNITGIFGAAKVILRPSAPGSGVIAGGSVRIVLELAGIK 135 (143)
T ss_pred CCeEeeEEEEEEeeEEEEEEECCCCCcEEECcHHHHHHHHcCcc
Confidence 35566667778889999999999999998888888888888885
No 10
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=12.49 E-value=1e+02 Score=21.65 Aligned_cols=29 Identities=31% Similarity=0.581 Sum_probs=22.8
Q ss_pred ceeeeeeccccceeeecCCCCCCCCCCCCCchhhhhhh
Q psy12975 154 TYRHVTFEPCARKVCVTPRPRRSGTASPPLVPKQIKAI 191 (205)
Q Consensus 154 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 191 (205)
.|+-|.-.-|.-++-|-+|+.+ +|++||+
T Consensus 21 ~~~~irCp~Cg~rIl~K~R~~~---------~krvkA~ 49 (49)
T COG1996 21 ETRGIRCPYCGSRILVKERPKV---------PKRVKAR 49 (49)
T ss_pred ccCceeCCCCCcEEEEeccCCc---------cEEEecC
Confidence 4556666779999999999765 8888885
Done!