Query psy9580
Match_columns 71
No_of_seqs 115 out of 953
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 23:18:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9580.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9580hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00103 rpl35 ribosomal prote 100.0 4.6E-32 9.9E-37 162.5 5.1 65 7-71 1-65 (65)
2 PRK00172 rpmI 50S ribosomal pr 100.0 1.7E-31 3.6E-36 159.7 5.2 65 7-71 1-65 (65)
3 COG0291 RpmI Ribosomal protein 100.0 5.5E-31 1.2E-35 158.0 4.5 65 7-71 1-65 (65)
4 TIGR00001 rpmI_bact ribosomal 100.0 2.4E-30 5.3E-35 154.0 5.0 63 8-70 1-63 (63)
5 PF01632 Ribosomal_L35p: Ribos 99.9 2.9E-27 6.3E-32 139.6 2.1 61 8-68 1-61 (61)
6 KOG4316|consensus 93.6 0.024 5.1E-07 39.4 0.4 61 8-68 78-138 (172)
7 PF06463 Mob_synth_C: Molybden 32.3 29 0.00063 22.4 1.3 12 18-29 76-87 (128)
8 PF09585 Lin0512_fam: Conserve 16.1 98 0.0021 20.3 1.4 14 58-71 62-75 (113)
9 PF10636 hemP: Hemin uptake pr 15.9 95 0.0021 16.6 1.1 17 13-29 19-35 (38)
10 PF15249 GLTSCR1: Glioma tumor 15.2 80 0.0017 19.8 0.8 10 61-70 25-34 (109)
No 1
>CHL00103 rpl35 ribosomal protein L35
Probab=99.97 E-value=4.6e-32 Score=162.52 Aligned_cols=65 Identities=40% Similarity=0.543 Sum_probs=64.3
Q ss_pred CcCcccCcccccceeecCCccEEeeccCcccccCCCChHHHHhhcCCeeeccCcHHHHHhhCCCC
Q psy9580 7 VFKIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLRGLASVHKSNIASVRAMMPNS 71 (71)
Q Consensus 7 mpKmKT~k~aaKRFk~T~sGk~kr~~ag~~H~~~~Ks~krkR~Lrk~~~v~~~~~k~ik~llpy~ 71 (71)
|||||||+||+|||++||||+|+|.+||++|++++||++++|+|++..+|+++|+++|++||||+
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 89999999999999999999999999999999999999999999999999999999999999996
No 2
>PRK00172 rpmI 50S ribosomal protein L35; Reviewed
Probab=99.97 E-value=1.7e-31 Score=159.73 Aligned_cols=65 Identities=52% Similarity=0.677 Sum_probs=64.3
Q ss_pred CcCcccCcccccceeecCCccEEeeccCcccccCCCChHHHHhhcCCeeeccCcHHHHHhhCCCC
Q psy9580 7 VFKIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLRGLASVHKSNIASVRAMMPNS 71 (71)
Q Consensus 7 mpKmKT~k~aaKRFk~T~sGk~kr~~ag~~H~~~~Ks~krkR~Lrk~~~v~~~~~k~ik~llpy~ 71 (71)
|||||||+||+|||++||||+|+|++||++|++++||++++|+|+++.+|+++|++.|+.||||+
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 89999999999999999999999999999999999999999999999999999999999999996
No 3
>COG0291 RpmI Ribosomal protein L35 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=5.5e-31 Score=158.04 Aligned_cols=65 Identities=51% Similarity=0.593 Sum_probs=64.0
Q ss_pred CcCcccCcccccceeecCCccEEeeccCcccccCCCChHHHHhhcCCeeeccCcHHHHHhhCCCC
Q psy9580 7 VFKIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLRGLASVHKSNIASVRAMMPNS 71 (71)
Q Consensus 7 mpKmKT~k~aaKRFk~T~sGk~kr~~ag~~H~~~~Ks~krkR~Lrk~~~v~~~~~k~ik~llpy~ 71 (71)
|||||||+||+|||++||||+|+|++||++|++++||++++|+||+..+|+++|.++|.+||||.
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 89999999999999999999999999999999999999999999999999999999999999984
No 4
>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=99.96 E-value=2.4e-30 Score=153.99 Aligned_cols=63 Identities=48% Similarity=0.604 Sum_probs=62.6
Q ss_pred cCcccCcccccceeecCCccEEeeccCcccccCCCChHHHHhhcCCeeeccCcHHHHHhhCCC
Q psy9580 8 FKIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLRGLASVHKSNIASVRAMMPN 70 (71)
Q Consensus 8 pKmKT~k~aaKRFk~T~sGk~kr~~ag~~H~~~~Ks~krkR~Lrk~~~v~~~~~k~ik~llpy 70 (71)
||||||+||+|||++||||+|++++||++|++++||++++|+|+++++|+++|++.|++||||
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 899999999999999999999999999999999999999999999999999999999999998
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=99.93 E-value=2.9e-27 Score=139.57 Aligned_cols=61 Identities=48% Similarity=0.656 Sum_probs=55.4
Q ss_pred cCcccCcccccceeecCCccEEeeccCcccccCCCChHHHHhhcCCeeeccCcHHHHHhhC
Q psy9580 8 FKIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLRGLASVHKSNIASVRAMM 68 (71)
Q Consensus 8 pKmKT~k~aaKRFk~T~sGk~kr~~ag~~H~~~~Ks~krkR~Lrk~~~v~~~~~k~ik~ll 68 (71)
||||||+||+|||++||||+|+|++||++|+++++|++++|+|++..+|+++|++.|++||
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 8999999999999999999999999999999999999999999999999999999999987
No 6
>KOG4316|consensus
Probab=93.60 E-value=0.024 Score=39.39 Aligned_cols=61 Identities=23% Similarity=0.160 Sum_probs=56.5
Q ss_pred cCcccCcccccceeecCCccEEeeccCcccccCCCChHHHHhhcCCeeeccCcHHHHHhhC
Q psy9580 8 FKIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLRGLASVHKSNIASVRAMM 68 (71)
Q Consensus 8 pKmKT~k~aaKRFk~T~sGk~kr~~ag~~H~~~~Ks~krkR~Lrk~~~v~~~~~k~ik~ll 68 (71)
-|-||-+++-+||+.-..|-..|.|+|+.-.+.+|+.-.+++|.--..-+++|-..+-+|+
T Consensus 78 GkrktvkaVldRFkRL~~G~WIr~h~Gr~Kkl~kK~~a~~krl~~~vfcnktQs~lLDKm~ 138 (172)
T KOG4316|consen 78 GKRKTVKAVLDRFKRLHCGLWIRAHPGRHKKLYKKDEAWQKRLLYYVFCNKTQSELLDKMM 138 (172)
T ss_pred cccccHHHHHHHHHhcccCeeeeecCchhhhhhhcCHHHHHHHHHhheechHHHHHHHHHh
Confidence 3678999999999999999999999999999999999999999999999999988887775
No 7
>PF06463 Mob_synth_C: Molybdenum Cofactor Synthesis C; InterPro: IPR010505 The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cis-dithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism [, ]. In Escherichia coli, biosynthesis of MoCF is a three stage process. It begins with the MoaA and MoaC conversion of GTP to the meta-stable pterin intermediate precursor Z. The second stage involves MPT synthase (MoaD and MoaE), which converts precursor Z to MPT; MoeB is involved in the recycling of MPT synthase. The final step in MoCF synthesis is the attachment of mononuclear Mo to MPT, a process that requires MoeA and which is enhanced by MogA in an Mg2 ATP-dependent manner []. MoCF is the active co-factor in eukaryotic and some prokaryotic molybdo-enzymes, but the majority of bacterial enzymes requiring MoCF, need a modification of MTP for it to be active; MobA is involved in the attachment of a nucleotide monophosphate to MPT resulting in the MGD co-factor, the active co-factor for most prokaryotic molybdo-enzymes. Bacterial two-hybrid studies have revealed the close interactions between MoeA, MogA, and MobA in the synthesis of MoCF []. Moreover the close functional association of MoeA and MogA in the synthesis of MoCF is supported by fact that the known eukaryotic homologues to MoeA and MogA exist as fusion proteins: CNX1 (Q39054 from SWISSPROT) of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. Q9NQX3 from SWISSPROT) and Drosophila melanogaster (Fruit fly) Cinnamon (P39205 from SWISSPROT) []. This entry represents MoaA, which belongs to a family of enzymes involved in the synthesis of metallo-cofactors (IPR000385 from INTERPRO). Each subunit of the MoaA dimer is comprised of an N-terminal SAM domain (IPR007197 from INTERPRO) that contains the [4Fe-4S] cluster typical for this family of enzymes, as well as an additional [4Fe-4S] cluster in the C-terminal domain that is unique to MoaA proteins []. The unique Fe site of the C-terminal [4Fe-4S] cluster is thought to be involved in the binding and activation of 5'-GTP. Mutations in the human MoCF biosynthesis proteins MOCS1, MOCS2 or GEPH cause MoCF Deficiency type A (MOCOD), causing the loss of activity of MoCF-containing enzymes, resulting in neurological abnormalities and death [].; GO: 0051539 4 iron, 4 sulfur cluster binding, 0006777 Mo-molybdopterin cofactor biosynthetic process, 0019008 molybdopterin synthase complex; PDB: 2FB2_A 2FB3_A 1TV8_B 1TV7_A.
Probab=32.25 E-value=29 Score=22.39 Aligned_cols=12 Identities=25% Similarity=0.512 Sum_probs=8.5
Q ss_pred cceeecCCccEE
Q psy9580 18 KRFFIRTGGVIK 29 (71)
Q Consensus 18 KRFk~T~sGk~k 29 (71)
.|.+||++|+++
T Consensus 76 NRiRlTsdG~l~ 87 (128)
T PF06463_consen 76 NRIRLTSDGKLK 87 (128)
T ss_dssp -EEEE-TTSEEE
T ss_pred CEEEEccCccEE
Confidence 588999999875
No 8
>PF09585 Lin0512_fam: Conserved hypothetical protein (Lin0512_fam); InterPro: IPR011719 This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N terminus.
Probab=16.11 E-value=98 Score=20.26 Aligned_cols=14 Identities=36% Similarity=0.662 Sum_probs=11.5
Q ss_pred cCcHHHHHhhCCCC
Q psy9580 58 KSNIASVRAMMPNS 71 (71)
Q Consensus 58 ~~~~k~ik~llpy~ 71 (71)
.-|...|+..|||+
T Consensus 62 ~vD~e~v~~~~PyG 75 (113)
T PF09585_consen 62 KVDIEAVKAVFPYG 75 (113)
T ss_pred ccCHHHHHHhCCCC
Confidence 34788999999996
No 9
>PF10636 hemP: Hemin uptake protein hemP; InterPro: IPR019600 This entry represents bacterial proteins that are involved in the uptake of the iron source hemin []. ; PDB: 2JRA_B 2LOJ_A.
Probab=15.88 E-value=95 Score=16.63 Aligned_cols=17 Identities=18% Similarity=0.173 Sum_probs=12.3
Q ss_pred CcccccceeecCCccEE
Q psy9580 13 KSSAKKRFFIRTGGVIK 29 (71)
Q Consensus 13 ~k~aaKRFk~T~sGk~k 29 (71)
|-+.-=|.++|.+||+-
T Consensus 19 H~g~~Y~LR~Tr~gKLI 35 (38)
T PF10636_consen 19 HGGQIYRLRITRQGKLI 35 (38)
T ss_dssp ETTEEEEEEEETTTEEE
T ss_pred eCCeEEEeeEccCCcEE
Confidence 44555688999999863
No 10
>PF15249 GLTSCR1: Glioma tumor suppressor candidate region
Probab=15.22 E-value=80 Score=19.82 Aligned_cols=10 Identities=20% Similarity=0.438 Sum_probs=8.4
Q ss_pred HHHHHhhCCC
Q psy9580 61 IASVRAMMPN 70 (71)
Q Consensus 61 ~k~ik~llpy 70 (71)
...+.+||||
T Consensus 25 ~DA~~RLLPY 34 (109)
T PF15249_consen 25 EDAVERLLPY 34 (109)
T ss_pred HHHHHHhcch
Confidence 3679999999
Done!