Query 031865
Match_columns 151
No_of_seqs 163 out of 944
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 06:26:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031865.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031865hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00103 rpl35 ribosomal prote 99.9 5.8E-27 1.2E-31 162.9 5.4 65 80-144 1-65 (65)
2 PRK00172 rpmI 50S ribosomal pr 99.9 2.3E-26 5.1E-31 159.2 5.5 65 80-144 1-65 (65)
3 TIGR00001 rpmI_bact ribosomal 99.9 2.4E-26 5.2E-31 158.5 5.3 63 81-143 1-63 (63)
4 COG0291 RpmI Ribosomal protein 99.9 5.7E-26 1.2E-30 158.6 4.6 65 80-144 1-65 (65)
5 PF01632 Ribosomal_L35p: Ribos 99.9 7.2E-24 1.6E-28 144.6 2.3 61 81-141 1-61 (61)
6 KOG4316 Uncharacterized conser 95.7 0.002 4.3E-08 52.4 -0.7 74 70-143 67-141 (172)
7 PF10571 UPF0547: Uncharacteri 43.3 12 0.00026 21.8 0.7 17 3-19 8-24 (26)
8 PF08772 NOB1_Zn_bind: Nin one 29.6 22 0.00048 25.4 0.5 20 7-26 22-41 (73)
9 PF04423 Rad50_zn_hook: Rad50 29.3 18 0.00039 23.4 -0.0 10 11-20 22-31 (54)
10 PF03811 Zn_Tnp_IS1: InsA N-te 26.5 43 0.00094 20.8 1.3 15 4-19 1-15 (36)
11 PRK00432 30S ribosomal protein 26.4 35 0.00076 22.4 1.0 11 7-17 18-28 (50)
12 PF14169 YdjO: Cold-inducible 26.0 30 0.00065 24.0 0.6 8 11-18 41-48 (59)
13 PF14803 Nudix_N_2: Nudix N-te 24.6 30 0.00065 21.3 0.4 17 10-26 1-17 (34)
No 1
>CHL00103 rpl35 ribosomal protein L35
Probab=99.93 E-value=5.8e-27 Score=162.88 Aligned_cols=65 Identities=51% Similarity=0.673 Sum_probs=63.6
Q ss_pred ccCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhCCCc
Q 031865 80 GYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYL 144 (151)
Q Consensus 80 ~~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlLPY~ 144 (151)
++|||||+||+|||++||+|||+|.+||++|++++|+++++|+|+++.+|+++|.++|++||||+
T Consensus 1 MpKmKT~k~a~KRFKvT~sGKvkr~~a~k~H~l~kKs~krkR~L~~~~~v~~~d~~~ik~~lp~~ 65 (65)
T CHL00103 1 MPKLKTRKAAAKRYKKTGNGKFLRRKAFKSHLLQKKSSKQKRKLSQTVCVSKGDSKSIKLMLPYL 65 (65)
T ss_pred CCccccchhhhheeEecCCCCEEeccCCccccccCCCHHHHHhcCCCeeECHHHHHHHHHhcCCC
Confidence 58999999999999999999999999999999999999999999999999999999999999995
No 2
>PRK00172 rpmI 50S ribosomal protein L35; Reviewed
Probab=99.93 E-value=2.3e-26 Score=159.21 Aligned_cols=65 Identities=51% Similarity=0.707 Sum_probs=63.6
Q ss_pred ccCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhCCCc
Q 031865 80 GYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYL 144 (151)
Q Consensus 80 ~~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlLPY~ 144 (151)
|+|||||+||+|||++||+|||+|++||++|++++|+.+++|+|+++.+|+++|.++|++||||+
T Consensus 1 MpKmKT~k~akKRFk~T~~GKi~r~~a~k~H~~~~Ks~k~kR~lr~~~~v~~~~~k~ik~~lpy~ 65 (65)
T PRK00172 1 MPKMKTKSGAAKRFKVTGSGKVKRKHAGKRHILTKKSTKRKRQLRGTTVVSKADAKRVKRMLPYA 65 (65)
T ss_pred CCCcccchhhhheeEEcCCCCEEeccCCCccccccCCHHHHHhcCCCeeECHHHHHHHHHhcCCC
Confidence 57999999999999999999999999999999999999999999999999999999999999995
No 3
>TIGR00001 rpmI_bact ribosomal protein L35. This ribosomal protein is found in bacteria and organelles only. It is not closely related to any eukaryotic or archaeal ribosomal protein.
Probab=99.93 E-value=2.4e-26 Score=158.48 Aligned_cols=63 Identities=59% Similarity=0.799 Sum_probs=62.3
Q ss_pred cCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhCCC
Q 031865 81 YKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPY 143 (151)
Q Consensus 81 ~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlLPY 143 (151)
+|||||+||+|||++||+|||+|++||++|++++|+.+++|+|+++.+|+++|+++|++||||
T Consensus 1 pKmKT~~~akKRFK~T~tGKvkr~~a~k~H~l~~Ks~k~kR~L~~~~~v~~~~~~~ik~~lpy 63 (63)
T TIGR00001 1 PKMKTHKAAAKRFKITGSGKIKRKKAGKRHLLTKKSSKRKRNLRKKAIVSAGDLKRVKLLLPY 63 (63)
T ss_pred CCcccchhhhhheEEcCCCCEEecccCcccccccCCHHHHHhcCCCeeECHHHHHHHHHhcCC
Confidence 599999999999999999999999999999999999999999999999999999999999998
No 4
>COG0291 RpmI Ribosomal protein L35 [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=5.7e-26 Score=158.60 Aligned_cols=65 Identities=52% Similarity=0.698 Sum_probs=63.5
Q ss_pred ccCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhCCCc
Q 031865 80 GYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCLPYL 144 (151)
Q Consensus 80 ~~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlLPY~ 144 (151)
++|||||+||+|||++||+|+|+|++||++|++++|+.+++|+||+..+|+++|.++|++||||.
T Consensus 1 MPKmKT~k~aaKRFK~T~~Gkikr~~A~k~H~l~kKs~k~kR~Lr~~~~v~~~d~k~v~~~l~~~ 65 (65)
T COG0291 1 MPKMKTKKGAAKRFKITGTGKIKRKHAGKRHILTKKSTKRKRHLRKTAVVSKADLKRVKRLLLYA 65 (65)
T ss_pred CCccchhhhhHhheeecCCCcEEecccccccccccCCHHHHHhccCCceeCHHHHHHHHHhccCC
Confidence 57999999999999999999999999999999999999999999999999999999999999984
No 5
>PF01632 Ribosomal_L35p: Ribosomal protein L35; InterPro: IPR021137 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 [, ]. L35 is a basic protein of 60 to 70 amino-acid residues from the large subunit []. Like many basic polypeptides, L35 completely inhibits ornithine decarboxylase when present unbound in the cell, but the inhibitory function is abolished upon its incorporation into ribosomes []. It belongs to a family of ribosomal proteins, including L35 from bacteria, plant chloroplast, red algae chloroplasts and cyanelles. In plants it is a nuclear encoded gene product, which suggests a chloroplast-to-nucleus relocation during the evolution of higher plants [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2QBE_3 2QBG_3 3SGF_7 2QOV_3 3J0Y_6 3I22_3 3E1D_W 1VS6_3 2VHN_3 1VS8_3 ....
Probab=99.88 E-value=7.2e-24 Score=144.64 Aligned_cols=61 Identities=57% Similarity=0.796 Sum_probs=55.4
Q ss_pred cCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhC
Q 031865 81 YKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL 141 (151)
Q Consensus 81 ~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlL 141 (151)
+|||||+|++|||++||+|+|+|++||++|++++||.+++|+|+++.+|+++|.++|++||
T Consensus 1 pKmKT~k~a~KRFk~t~sGkikr~~agk~H~~~~Ks~krkr~Lr~~~~v~~~~~k~ikklL 61 (61)
T PF01632_consen 1 PKMKTHKSAAKRFKVTGSGKIKRKRAGKRHLLTKKSSKRKRRLRKTTLVHKADVKRIKKLL 61 (61)
T ss_dssp ---S-HHHHHTTEEEESSSEEEEE-SSSSSSSSSSSCHCTTTTSCEEESSSHHHHHHTTTT
T ss_pred CCccchhhhHhheeEcCCCeEEeccCCcccccccCCHHHHHHcCCCEEECHHHHHHHHHhC
Confidence 6999999999999999999999999999999999999999999999999999999999987
No 6
>KOG4316 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.75 E-value=0.002 Score=52.45 Aligned_cols=74 Identities=26% Similarity=0.294 Sum_probs=68.8
Q ss_pred CceEEEeeccccCcccCcccccceEEccCcceEeeccCcccccCCCChHHHhhcCCCeeeccccHHHHHHhC-CC
Q 031865 70 PQTVTVFAAKGYKMKTHKASAKRFRVTGKGKILRRRAGKQHLLAKKNTKRKLRLSKMHEVSRSDYDNVIGCL-PY 143 (151)
Q Consensus 70 ~~s~~~~~~~~~KmKThKgAaKRFKvTgSGKIkR~rAgkrHlltkKS~KrKRrLrk~~~V~~~d~k~IKrlL-PY 143 (151)
..+++-|+.++.|-||-+++-+||+.-..|-..|.++|+.-.+-+|+.-.+++|..-..-+++|-+.+-+|+ ||
T Consensus 67 ~r~~t~Fs~~kGkrktvkaVldRFkRL~~G~WIr~h~Gr~Kkl~kK~~a~~krl~~~vfcnktQs~lLDKm~Tsy 141 (172)
T KOG4316|consen 67 VRSLTYFSARKGKRKTVKAVLDRFKRLHCGLWIRAHPGRHKKLYKKDEAWQKRLLYYVFCNKTQSELLDKMMTSY 141 (172)
T ss_pred hhhhhhhhhhhcccccHHHHHHHHHhcccCeeeeecCchhhhhhhcCHHHHHHHHHhheechHHHHHHHHHhhHH
Confidence 348889999999999999999999999999999999999999999999999999999999999999998877 44
No 7
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=43.34 E-value=12 Score=21.80 Aligned_cols=17 Identities=29% Similarity=0.618 Sum_probs=12.7
Q ss_pred cceeeeeeeccCCCCCC
Q 031865 3 SMISFNLKFCPLCPSSS 19 (151)
Q Consensus 3 ~~~~~~~~~~~~~~~~~ 19 (151)
..++.+..+||+|+..+
T Consensus 8 ~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 8 AEVPESAKFCPHCGYDF 24 (26)
T ss_pred CCchhhcCcCCCCCCCC
Confidence 34667788899998765
No 8
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=29.61 E-value=22 Score=25.37 Aligned_cols=20 Identities=30% Similarity=0.675 Sum_probs=9.8
Q ss_pred eeeeeccCCCCCCccccccc
Q 031865 7 FNLKFCPLCPSSSSVRASRG 26 (151)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~ 26 (151)
.+-.|||-|+..+-.||+..
T Consensus 22 ~~k~FCp~CGn~TL~rvsvs 41 (73)
T PF08772_consen 22 MTKQFCPKCGNATLKRVSVS 41 (73)
T ss_dssp SS--S-SSS--S--EEEE-B
T ss_pred CCceeCcccCCCcceEEEEE
Confidence 35578999999999999875
No 9
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=29.30 E-value=18 Score=23.39 Aligned_cols=10 Identities=40% Similarity=1.026 Sum_probs=4.8
Q ss_pred eccCCCCCCc
Q 031865 11 FCPLCPSSSS 20 (151)
Q Consensus 11 ~~~~~~~~~~ 20 (151)
.||+|.++..
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp E-TTT--EE-
T ss_pred cCCCCCCCCC
Confidence 7999988654
No 10
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=26.53 E-value=43 Score=20.79 Aligned_cols=15 Identities=33% Similarity=0.902 Sum_probs=10.5
Q ss_pred ceeeeeeeccCCCCCC
Q 031865 4 MISFNLKFCPLCPSSS 19 (151)
Q Consensus 4 ~~~~~~~~~~~~~~~~ 19 (151)
|+.+++ .||.|.+..
T Consensus 1 Ma~i~v-~CP~C~s~~ 15 (36)
T PF03811_consen 1 MAKIDV-HCPRCQSTE 15 (36)
T ss_pred CCcEee-eCCCCCCCC
Confidence 566665 499998766
No 11
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=26.37 E-value=35 Score=22.43 Aligned_cols=11 Identities=55% Similarity=1.023 Sum_probs=8.7
Q ss_pred eeeeeccCCCC
Q 031865 7 FNLKFCPLCPS 17 (151)
Q Consensus 7 ~~~~~~~~~~~ 17 (151)
.+..|||.|++
T Consensus 18 ~~~~fCP~Cg~ 28 (50)
T PRK00432 18 RKNKFCPRCGS 28 (50)
T ss_pred EccCcCcCCCc
Confidence 46778999986
No 12
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=26.00 E-value=30 Score=24.02 Aligned_cols=8 Identities=63% Similarity=1.526 Sum_probs=6.2
Q ss_pred eccCCCCC
Q 031865 11 FCPLCPSS 18 (151)
Q Consensus 11 ~~~~~~~~ 18 (151)
.||||.++
T Consensus 41 ~CPlC~s~ 48 (59)
T PF14169_consen 41 VCPLCKSP 48 (59)
T ss_pred cCCCcCCc
Confidence 49999765
No 13
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=24.58 E-value=30 Score=21.29 Aligned_cols=17 Identities=41% Similarity=0.898 Sum_probs=7.5
Q ss_pred eeccCCCCCCccccccc
Q 031865 10 KFCPLCPSSSSVRASRG 26 (151)
Q Consensus 10 ~~~~~~~~~~~~~~~~~ 26 (151)
+|||-|+.+-..+++.|
T Consensus 1 kfC~~CG~~l~~~ip~g 17 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEG 17 (34)
T ss_dssp -B-TTT--B-EEE--TT
T ss_pred CccccccChhhhhcCCC
Confidence 58999998876676654
Done!