Query psy2852
Match_columns 488
No_of_seqs 3 out of 5
Neff 1.3
Searched_HMMs 46136
Date Fri Aug 16 18:31:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2852.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2852hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00199 WAP whey acidic protei 1.9 2.3E+03 0.05 16.3 2.6 9 159-167 16-24 (60)
2 KOG1141|consensus 1.0 2.2E+03 0.047 25.6 1.0 20 145-164 936-955 (1262)
3 KOG1141|consensus 1.0 2.2E+03 0.048 25.5 1.0 21 404-424 935-955 (1262)
4 PF04565 RNA_pol_Rpb2_3: RNA p 0.9 2.7E+03 0.059 16.1 1.1 7 163-169 45-51 (68)
5 COG5661 Predicted secreted Zn- 0.9 2.3E+03 0.05 21.1 0.5 10 15-24 81-90 (210)
6 COG0853 PanD Aspartate 1-decar 0.8 1.8E+03 0.039 20.3 -0.4 24 100-123 14-37 (126)
7 PF04758 Ribosomal_S30: Riboso 0.7 2.7E+03 0.058 17.0 0.4 7 390-396 5-11 (59)
8 PF12225 MTHFR_C: Methylene-te 0.7 4.1E+03 0.089 16.8 1.6 27 446-477 35-62 (97)
9 PF01589 Alpha_E1_glycop: Alph 0.7 2.6E+03 0.056 23.0 0.2 12 197-208 387-398 (502)
10 PF00095 WAP: WAP-type (Whey A 0.7 4.4E+03 0.096 13.1 1.3 29 159-193 1-29 (43)
No 1
>cd00199 WAP whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease.
Probab=1.87 E-value=2.3e+03 Score=16.29 Aligned_cols=9 Identities=22% Similarity=0.999 Sum_probs=3.8
Q ss_pred ccccccccc
Q psy2852 159 RAGKCQITS 167 (488)
Q Consensus 159 ~AG~C~I~~ 167 (488)
.+|.||...
T Consensus 16 k~G~CP~~~ 24 (60)
T cd00199 16 KPGRCPMVN 24 (60)
T ss_pred ccCcCcCCC
Confidence 344444433
No 2
>KOG1141|consensus
Probab=1.01 E-value=2.2e+03 Score=25.62 Aligned_cols=20 Identities=30% Similarity=0.579 Sum_probs=8.5
Q ss_pred cccccccccccccccccccc
Q psy2852 145 SRAGKCQITSPSLSRAGKCQ 164 (488)
Q Consensus 145 S~AG~C~I~~~~~S~AG~C~ 164 (488)
+.+|+|-|+++.--+-+.||
T Consensus 936 ~d~~~~~~~~~~~~~~~~cp 955 (1262)
T KOG1141|consen 936 SDASKCECQQLSIEAMKRCP 955 (1262)
T ss_pred cccCcccCCCCChhhhcCCC
Confidence 33444444444444444443
No 3
>KOG1141|consensus
Probab=0.98 E-value=2.2e+03 Score=25.52 Aligned_cols=21 Identities=29% Similarity=0.515 Sum_probs=9.8
Q ss_pred cccccceeccccccccccccc
Q psy2852 404 LSRAGKCQITSPSLSRAGKCQ 424 (488)
Q Consensus 404 ~S~AG~C~I~~~~~S~AG~C~ 424 (488)
++.+|+|.|+++.--+.+.||
T Consensus 935 p~d~~~~~~~~~~~~~~~~cp 955 (1262)
T KOG1141|consen 935 PSDASKCECQQLSIEAMKRCP 955 (1262)
T ss_pred CcccCcccCCCCChhhhcCCC
Confidence 344444444444444444444
No 4
>PF04565 RNA_pol_Rpb2_3: RNA polymerase Rpb2, domain 3; InterPro: IPR007645 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 3, is also known as the fork domain and is proximal to catalytic site [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_B 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C 3AOH_H 1IW7_M 2O5J_C 2CW0_M ....
Probab=0.93 E-value=2.7e+03 Score=16.07 Aligned_cols=7 Identities=29% Similarity=1.123 Sum_probs=2.4
Q ss_pred ccccccc
Q psy2852 163 CQITSPS 169 (488)
Q Consensus 163 C~I~~~~ 169 (488)
||+..||
T Consensus 45 CPveTPE 51 (68)
T PF04565_consen 45 CPVETPE 51 (68)
T ss_dssp SSSSS-S
T ss_pred eecccCC
Confidence 3443333
No 5
>COG5661 Predicted secreted Zn-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=0.87 E-value=2.3e+03 Score=21.05 Aligned_cols=10 Identities=50% Similarity=0.973 Sum_probs=4.9
Q ss_pred ccCcceeecc
Q psy2852 15 SRAGKCQITS 24 (488)
Q Consensus 15 sragkcqits 24 (488)
+++|+|+|+.
T Consensus 81 ~~~g~C~v~~ 90 (210)
T COG5661 81 STAGQCQVGD 90 (210)
T ss_pred ecCCceeeee
Confidence 4455555544
No 6
>COG0853 PanD Aspartate 1-decarboxylase [Coenzyme metabolism]
Probab=0.80 E-value=1.8e+03 Score=20.26 Aligned_cols=24 Identities=29% Similarity=0.385 Sum_probs=0.0
Q ss_pred ccccccCcccceeccccccccccc
Q psy2852 100 ITSPSLSRAGKCQITSPSLSRAGK 123 (488)
Q Consensus 100 I~~~~~~~AG~C~I~~~~~S~AG~ 123 (488)
+|++++|--|-+.|.+--+.+||.
T Consensus 14 VT~A~L~Y~GSitID~dlldaagi 37 (126)
T COG0853 14 VTEADLNYVGSITIDEDLLDAAGI 37 (126)
T ss_pred EeecccceEEeEEECHHHHhhcCC
No 7
>PF04758 Ribosomal_S30: Ribosomal protein S30; InterPro: IPR006846 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 entry is for the ribosomal protein S30.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_X 2XZM_X 3IZB_Z 3U5G_e 3U5C_e 3J16_E 3IZ6_Z.
Probab=0.75 E-value=2.7e+03 Score=16.97 Aligned_cols=7 Identities=86% Similarity=1.151 Sum_probs=0.0
Q ss_pred ccccccc
Q psy2852 390 SLSRAGK 396 (488)
Q Consensus 390 slsrAG~ 396 (488)
||.|||+
T Consensus 5 SLarAGK 11 (59)
T PF04758_consen 5 SLARAGK 11 (59)
T ss_dssp CCTTTTH
T ss_pred chhhccc
No 8
>PF12225 MTHFR_C: Methylene-tetrahydrofolate reductase C terminal; InterPro: IPR022026 This family is found in bacteria and archaea, and is approximately 100 amino acids in length. There is a conserved NGPCGG sequence motif. This family is the C-terminal of methylene-tetrahydrofolate reductase. This protein reduces FAD using the reducing equivalents from reduced FAD, subsequently reduces tetrahydrofolate. The C-terminal of MTHFR contains the FAD binding site and is the catalytic portion of the enzyme.
Probab=0.74 E-value=4.1e+03 Score=16.78 Aligned_cols=27 Identities=30% Similarity=0.768 Sum_probs=0.0
Q ss_pred ccccccc-ccccccccceeecCcccccCcceee
Q psy2852 446 AGKCQIT-SPSLSRAGKCQITSPSLSRAGKCQI 477 (488)
Q Consensus 446 AG~C~I~-~~~~S~AG~Cqitspslsragkcqi 477 (488)
+|.|||+ =|-=-+.|-|--+ +.|+|.|
T Consensus 35 ggiCP~~~CpK~l~NGPCGG~-----~~G~CEV 62 (97)
T PF12225_consen 35 GGICPMSRCPKSLLNGPCGGS-----QDGKCEV 62 (97)
T ss_pred cccCccccCcCccccCCCCCC-----CCCceec
No 9
>PF01589 Alpha_E1_glycop: Alphavirus E1 glycoprotein; InterPro: IPR002548 Alphaviruses are enveloped RNA viruses that use arthropods such as mosquitoes for transmission to their vertebrate hosts, and include Semliki Forest and Sindbis viruses []. Alphaviruses consist of three structural proteins: the core nucleocapsid protein C, and the envelope proteins P62 and E1 that associate as a heterodimer. The viral membrane-anchored surface glycoproteins are responsible for receptor recognition and entry into target cells through membrane fusion. The proteolytic maturation of P62 into E2 (IPR000936 from INTERPRO) and E3 (IPR002533 from INTERPRO) causes a change in the viral surface. Together the E1, E2, and sometimes E3, glycoprotein "spikes" form an E1/E2 dimer or an E1/E2/E3 trimer, where E2 extends from the centre to the vertices, E1 fills the space between the vertices, and E3, if present, is at the distal end of the spike []. Upon exposure of the virus to the acidity of the endosome, E1 dissociates from E2 to form an E1 homotrimer, which is necessary for the fusion step to drive the cellular and viral membranes together. The alphaviral glycoprotein E1 is a class II viral fusion protein, which is structurally different from the class I fusion proteins found in influenza virus and HIV. The structure of the Semliki Forest virus revealed a structure that is similar to that of flaviviral glycoprotein E, with three structural domains in the same primary sequence arrangement []. This entry represents all three domains of the alphaviral E1 glycoprotein.; GO: 0004252 serine-type endopeptidase activity, 0019028 viral capsid, 0055036 virion membrane; PDB: 2YEW_L 1LD4_P 1Z8Y_K 3MUU_B 3N44_F 2XFB_F 3N42_F 2XFC_H 3N40_F 3N41_F ....
Probab=0.70 E-value=2.6e+03 Score=22.98 Aligned_cols=12 Identities=50% Similarity=0.911 Sum_probs=0.0
Q ss_pred cccccceecCcc
Q psy2852 197 SRAGKCQITSPS 208 (488)
Q Consensus 197 S~AGK~~itsps 208 (488)
+++|||+|-|+|
T Consensus 387 ~k~GkCaVHs~S 398 (502)
T PF01589_consen 387 DKAGKCAVHSHS 398 (502)
T ss_dssp SS-EEEEEEESS
T ss_pred CCCccCceeccC
No 10
>PF00095 WAP: WAP-type (Whey Acidic Protein) 'four-disulfide core'; InterPro: IPR008197 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. Whey acidic protein (WAP) is a major component of the whey fraction of milk, which contains a significant number of different proteins. WAP proteins share limited sequence identity, except for their conserved cysteine-rich regions, known as 4-disulphide core (4-DSC) domains, and the positional conservation of specific residues []. Several non-milk proteins also contain 4-DSC patterns, such as certain serine protease inhibitors. WAP itself appears to have a protease-inhibitor function, as seen with its inhibitory effect on the progression of cancer cells [].; GO: 0030414 peptidase inhibitor activity, 0005576 extracellular region; PDB: 1FLE_I 2REL_A 2Z7F_I 3NGG_B.
Probab=0.69 E-value=4.4e+03 Score=13.06 Aligned_cols=29 Identities=24% Similarity=0.629 Sum_probs=0.0
Q ss_pred ccccccccccccccccccccccccccccCcccccc
Q psy2852 159 RAGKCQITSPSLSRAGKCQITSPSLSRAGKCQITS 193 (488)
Q Consensus 159 ~AG~C~I~~~~~S~AG~C~I~~~~~S~AG~C~~~~ 193 (488)
+.|.|| ......+.|. ..|..-..|+..+
T Consensus 1 K~G~CP---~~~~~~~~c~---~~C~~D~dC~~~~ 29 (43)
T PF00095_consen 1 KPGSCP---PPSPDSGDCR---DECSSDSDCPGGQ 29 (43)
T ss_dssp SSSB----------SCEES---BS-SSGGGSSTT-
T ss_pred CCCcCc---CCCCccCccc---ccCcCccccCCcC
Done!