Query psy1444
Match_columns 71
No_of_seqs 7 out of 9
Neff 2.5
Searched_HMMs 46136
Date Fri Aug 16 19:54:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1444.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1444hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0151 PurD Phosphoribosylami 8.4 2E+02 0.0043 23.9 1.2 10 31-40 219-228 (428)
2 PF01830 Peptidase_C7: Peptida 5.4 3E+02 0.0066 21.4 0.8 17 1-17 1-17 (243)
3 PF12546 Cryptochrome_C: Blue/ 4.8 3E+02 0.0065 19.0 0.4 11 2-12 25-35 (121)
4 PF06390 NESP55: Neuroendocrin 4.7 9.5E+02 0.021 18.9 3.1 30 8-37 223-252 (257)
5 PF01071 GARS_A: Phosphoribosy 4.6 1.3E+02 0.0028 21.8 -1.6 8 32-39 120-127 (194)
6 COG2350 Uncharacterized protei 4.2 5.1E+02 0.011 16.7 1.2 7 11-17 41-47 (92)
7 KOG4536|consensus 3.8 3.9E+02 0.0085 21.8 0.4 9 1-9 213-221 (347)
8 KOG0237|consensus 3.4 6.1E+02 0.013 22.9 1.2 10 31-40 225-234 (788)
9 PF01200 Ribosomal_S28e: Ribos 2.3 9.5E+02 0.021 15.2 0.8 8 26-33 47-54 (69)
10 PF11291 DUF3091: Protein of u 2.2 6.8E+02 0.015 16.7 0.1 5 1-5 44-48 (100)
No 1
>COG0151 PurD Phosphoribosylamine-glycine ligase [Nucleotide transport and metabolism]
Probab=8.39 E-value=2e+02 Score=23.87 Aligned_cols=10 Identities=30% Similarity=0.674 Sum_probs=5.6
Q ss_pred CCCCCCCCCC
Q psy1444 31 NRDKGPRADR 40 (71)
Q Consensus 31 ~~d~GP~~d~ 40 (71)
+.|+||||.+
T Consensus 219 dgD~GPNTGG 228 (428)
T COG0151 219 DGDTGPNTGG 228 (428)
T ss_pred CCCCCCCCCC
Confidence 4556666654
No 2
>PF01830 Peptidase_C7: Peptidase C7 family; InterPro: IPR002704 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C7 (clan CA). These are found in fungi and viruses (Hypoviridae). They are involved in transmissible hypovirulence and may indicate the possible origins of hypovirulence-associated dsRNAs [].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis
Probab=5.40 E-value=3e+02 Score=21.40 Aligned_cols=17 Identities=29% Similarity=0.458 Sum_probs=13.9
Q ss_pred CcchhhhhccCCCCCCC
Q psy1444 1 MTCSRKREKSMPGADRN 17 (71)
Q Consensus 1 ~~~~~~~~~~gP~~d~d 17 (71)
|+|+||-..++...++-
T Consensus 1 ms~lr~psq~lvl~~S~ 17 (243)
T PF01830_consen 1 MSCLRKPSQSLVLPESV 17 (243)
T ss_pred CCcccCCcccccccCCC
Confidence 89999998888777654
No 3
>PF12546 Cryptochrome_C: Blue/Ultraviolet sensing protein C terminal; InterPro: IPR020978 Cryptochromes are blue/ultraviolet-A light sensing photoreceptors involved in regulating various growth and developmental responses in plants []. This signature is found in eukaryotic proteins at the C-terminal end and are typically between 113 and 125 amino acids in length. The family is found in association with PF03441 from PFAM and PF00875 from PFAM.
Probab=4.79 E-value=3e+02 Score=19.00 Aligned_cols=11 Identities=36% Similarity=0.465 Sum_probs=6.8
Q ss_pred cchhhhhccCC
Q psy1444 2 TCSRKREKSMP 12 (71)
Q Consensus 2 ~~~~~~~~~gP 12 (71)
+|.|.|+||+.
T Consensus 25 ~~~Rr~~DQMV 35 (121)
T PF12546_consen 25 TITRRYEDQMV 35 (121)
T ss_pred ccccccccccc
Confidence 45666666664
No 4
>PF06390 NESP55: Neuroendocrine-specific golgi protein P55 (NESP55); InterPro: IPR009434 This family consists of several mammalian neuroendocrine-specific golgi protein P55 (NESP55) sequences. NESP55 is a novel member of the chromogranin family and is a soluble, acidic, heat-stable secretory protein that is expressed exclusively in endocrine and nervous tissues, although less widely than chromogranins [].
Probab=4.73 E-value=9.5e+02 Score=18.91 Aligned_cols=30 Identities=33% Similarity=0.478 Sum_probs=13.4
Q ss_pred hccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy1444 8 EKSMPGADRNKGPRADRDKGPGANRDKGPR 37 (71)
Q Consensus 8 ~~~gP~~d~d~GP~~d~d~GP~~~~d~GP~ 37 (71)
||+-+-.=+-+-|-.-+|+-|-+-+-+||.
T Consensus 223 EK~q~rrckp~k~~~rrd~spesp~~~gpi 252 (257)
T PF06390_consen 223 EKQQQRRCKPKKPTRRRDPSPESPSKKGPI 252 (257)
T ss_pred HhhccccCCCCCCccccCCCCCCcccCCCC
Confidence 344444444444444444444444444443
No 5
>PF01071 GARS_A: Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; InterPro: IPR020561 Phosphoribosylglycinamide synthetase (6.3.4.13 from EC) (GARS) (phosphoribosylamine glycine ligase) [] catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by phosphoribosylglycinamide synthetase is the ATP-dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide: ATP + 5-phosphoribosylamine + glycine = ADP + Pi + 5'-phosphoribosylglycinamide In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS) (IPR000728 from INTERPRO). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS (IPR000728 from INTERPRO) and with phosphoribosylglycinamide formyltransferase (GART) (), forming GARS-AIRS-GART. This entry represents the A-domain of the enzyme, and is related to the ATP-grasp domain of biotin carboxylase/carbamoyl phosphate synthetase.; PDB: 1GSO_A 3LP8_A 2IP4_A 1VKZ_A 2QK4_A 2XD4_A 2XCL_A 3MJF_A 2YRW_A 2YS6_A ....
Probab=4.62 E-value=1.3e+02 Score=21.82 Aligned_cols=8 Identities=38% Similarity=0.792 Sum_probs=3.5
Q ss_pred CCCCCCCC
Q psy1444 32 RDKGPRAD 39 (71)
Q Consensus 32 ~d~GP~~d 39 (71)
.|+||||.
T Consensus 120 gd~GpnTG 127 (194)
T PF01071_consen 120 GDTGPNTG 127 (194)
T ss_dssp TTEEEEES
T ss_pred CCCCCCCC
Confidence 34444443
No 6
>COG2350 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=4.25 E-value=5.1e+02 Score=16.73 Aligned_cols=7 Identities=43% Similarity=0.515 Sum_probs=2.6
Q ss_pred CCCCCCC
Q psy1444 11 MPGADRN 17 (71)
Q Consensus 11 gP~~d~d 17 (71)
||..+++
T Consensus 41 GP~~~~d 47 (92)
T COG2350 41 GPFPDRD 47 (92)
T ss_pred CCCCCCC
Confidence 3333333
No 7
>KOG4536|consensus
Probab=3.75 E-value=3.9e+02 Score=21.81 Aligned_cols=9 Identities=56% Similarity=0.501 Sum_probs=6.3
Q ss_pred Ccchhhhhc
Q psy1444 1 MTCSRKREK 9 (71)
Q Consensus 1 ~~~~~~~~~ 9 (71)
|+|+++||+
T Consensus 213 ~~~~k~r~k 221 (347)
T KOG4536|consen 213 MYNSKWREK 221 (347)
T ss_pred ccchhhhhc
Confidence 677777765
No 8
>KOG0237|consensus
Probab=3.39 E-value=6.1e+02 Score=22.90 Aligned_cols=10 Identities=30% Similarity=0.674 Sum_probs=5.1
Q ss_pred CCCCCCCCCC
Q psy1444 31 NRDKGPRADR 40 (71)
Q Consensus 31 ~~d~GP~~d~ 40 (71)
++|+||||.+
T Consensus 225 dgD~GpNTGg 234 (788)
T KOG0237|consen 225 DGDTGPNTGG 234 (788)
T ss_pred CCCCCCCCCC
Confidence 4455555543
No 9
>PF01200 Ribosomal_S28e: Ribosomal protein S28e; InterPro: IPR000289 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 [, ]. A number of eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. Examples are: Mammalian S28 [] Plant S28 [] Fungi S33 [] Archaebacterial S28e. These proteins have from 64 to 78 amino acids and a highly conserved C-terminal region.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_Y 2XZN_1 2XZM_1 1NY4_A 1NE3_A 3U5C_c 3U5G_c 3O30_R 3O2Z_R 3IZB_Y.
Probab=2.26 E-value=9.5e+02 Score=15.24 Aligned_cols=8 Identities=50% Similarity=0.754 Sum_probs=0.0
Q ss_pred CCCCCCCC
Q psy1444 26 KGPGANRD 33 (71)
Q Consensus 26 ~GP~~~~d 33 (71)
|||++..|
T Consensus 47 kGPVr~GD 54 (69)
T PF01200_consen 47 KGPVREGD 54 (69)
T ss_dssp CSTTSTT-
T ss_pred cCCcccCc
No 10
>PF11291 DUF3091: Protein of unknown function (DUF3091); InterPro: IPR021442 This eukaryotic family of proteins has no known function.
Probab=2.21 E-value=6.8e+02 Score=16.72 Aligned_cols=5 Identities=80% Similarity=1.590 Sum_probs=0.0
Q ss_pred Ccchh
Q psy1444 1 MTCSR 5 (71)
Q Consensus 1 ~~~~~ 5 (71)
|||.+
T Consensus 44 mTC~~ 48 (100)
T PF11291_consen 44 MTCNR 48 (100)
T ss_pred cccCC
Done!