Query psy13912
Match_columns 76
No_of_seqs 112 out of 148
Neff 2.6
Searched_HMMs 46136
Date Fri Aug 16 23:39:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13912.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13912hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4655|consensus 99.9 7.4E-29 1.6E-33 181.7 1.6 58 2-59 1-58 (181)
2 TIGR01018 rpsD_arch ribosomal 98.5 2.2E-08 4.8E-13 71.8 0.7 44 17-60 14-57 (162)
3 PRK04051 rps4p 30S ribosomal p 98.4 6E-08 1.3E-12 70.2 0.6 42 19-60 16-57 (177)
4 PTZ00155 40S ribosomal protein 97.9 2.1E-06 4.6E-11 62.5 0.0 43 20-62 18-60 (181)
5 PLN00189 40S ribosomal protein 97.8 3.8E-06 8.2E-11 62.1 0.2 43 19-61 19-61 (194)
6 PF00163 Ribosomal_S4: Ribosom 93.9 0.0032 6.8E-08 39.8 -3.3 42 5-52 3-44 (94)
7 COG0522 RpsD Ribosomal protein 78.6 0.51 1.1E-05 35.0 -0.6 36 1-37 1-36 (205)
8 PF07014 Hs1pro-1_C: Hs1pro-1 40.0 12 0.00025 29.6 0.5 12 65-76 87-98 (261)
9 KOG0722|consensus 35.2 23 0.00051 28.7 1.5 46 8-55 279-324 (329)
10 PF09185 DUF1948: Domain of un 29.5 33 0.00071 24.8 1.3 23 42-64 74-96 (140)
11 PRK14750 kdpF potassium-transp 28.7 70 0.0015 17.9 2.3 15 56-70 9-23 (29)
12 PF06400 Alpha-2-MRAP_N: Alpha 28.1 46 0.001 23.6 1.9 41 4-45 68-117 (120)
13 PF06459 RR_TM4-6: Ryanodine R 25.8 52 0.0011 25.4 1.9 11 63-73 177-187 (274)
14 KOG4779|consensus 22.4 34 0.00074 22.9 0.3 51 8-73 23-73 (82)
No 1
>KOG4655|consensus
Probab=99.95 E-value=7.4e-29 Score=181.68 Aligned_cols=58 Identities=45% Similarity=0.758 Sum_probs=55.6
Q ss_pred cccchhHHhhhhhhcccceecccCchhHHHHHHhhcCCCChhhHHhhcCCCCCchHHH
Q psy13912 2 VRKLKYHEQKLLKKVDFISWEADNNLHEVKIMRRFGIQKRQDYTTAGFKPNPVPPELT 59 (76)
Q Consensus 2 mRkLK~HEqKLLKKVdFl~WK~d~n~RE~~vmrRY~iq~ReDY~kYNkl~~~~~~~~t 59 (76)
|||||||||||||||||++||.|+++||..|++||||++||||++||++||.+|.+--
T Consensus 1 vRKLK~HEQKLLKkVdFLnWkv~d~~re~~v~rrY~l~~REdY~kyn~l~~~~r~la~ 58 (181)
T KOG4655|consen 1 VRKLKFHEQKLLKKVDFLNWKVTDHHRELCVLRRYHLKKREDYTKYNRLAGKVRKLAN 58 (181)
T ss_pred CchhhHHHHHHHHhcccceeeecCchhhHHHHHHHhcccHHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999999999999999999999999999999999999999887644
No 2
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=98.53 E-value=2.2e-08 Score=71.78 Aligned_cols=44 Identities=11% Similarity=0.203 Sum_probs=38.8
Q ss_pred ccceecccCchhHHHHHHhhcCCCChhhHHhhcCCCCCchHHHH
Q psy13912 17 DFISWEADNNLHEVKIMRRFGIQKRQDYTTAGFKPNPVPPELTV 60 (76)
Q Consensus 17 dFl~WK~d~n~RE~~vmrRY~iq~ReDY~kYNkl~~~~~~~~t~ 60 (76)
---.|+.|++.+|.++|++|+|++++||.+||+++|.+|.+---
T Consensus 14 P~~pw~ker~~~E~~l~~kYgLknk~E~wk~~~~~~kiR~~Ar~ 57 (162)
T TIGR01018 14 PRHPWIKERLDRELKLVGKYGLRNKKEVWKAETTLRKYRRAARE 57 (162)
T ss_pred CCCChhhhhCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 34589999999999999999999999999999999988765433
No 3
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=98.42 E-value=6e-08 Score=70.15 Aligned_cols=42 Identities=10% Similarity=0.270 Sum_probs=37.6
Q ss_pred ceecccCchhHHHHHHhhcCCCChhhHHhhcCCCCCchHHHH
Q psy13912 19 ISWEADNNLHEVKIMRRFGIQKRQDYTTAGFKPNPVPPELTV 60 (76)
Q Consensus 19 l~WK~d~n~RE~~vmrRY~iq~ReDY~kYNkl~~~~~~~~t~ 60 (76)
--|+.|++.+|.++|++|+|++++||.+||+++|.+|.+---
T Consensus 16 ~pw~~~r~~~E~~l~~~YgLknk~E~wk~~~~~~~iR~~Ar~ 57 (177)
T PRK04051 16 HPWQKERIAEERELLGKYGLRNKRELWKAQSILRKYRRQARS 57 (177)
T ss_pred CchhhhhcHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 359999999999999999999999999999999988765433
No 4
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=97.92 E-value=2.1e-06 Score=62.51 Aligned_cols=43 Identities=14% Similarity=0.304 Sum_probs=37.8
Q ss_pred eecccCchhHHHHHHhhcCCCChhhHHhhcCCCCCchHHHHHH
Q psy13912 20 SWEADNNLHEVKIMRRFGIQKRQDYTTAGFKPNPVPPELTVLL 62 (76)
Q Consensus 20 ~WK~d~n~RE~~vmrRY~iq~ReDY~kYNkl~~~~~~~~t~~~ 62 (76)
-|+.+.=.+|.++|++|+|++++||.+||+++|.++.+-.-++
T Consensus 18 P~~k~rl~~E~~li~kYgLknk~E~wk~~~~~~kiR~~Ar~L~ 60 (181)
T PTZ00155 18 PFEKERLDAELKLCGEYGLKNKREIWRVQYTLAKIRKAARELL 60 (181)
T ss_pred chhHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4888888999999999999999999999999999887655443
No 5
>PLN00189 40S ribosomal protein S9; Provisional
Probab=97.84 E-value=3.8e-06 Score=62.08 Aligned_cols=43 Identities=12% Similarity=0.311 Sum_probs=37.4
Q ss_pred ceecccCchhHHHHHHhhcCCCChhhHHhhcCCCCCchHHHHH
Q psy13912 19 ISWEADNNLHEVKIMRRFGIQKRQDYTTAGFKPNPVPPELTVL 61 (76)
Q Consensus 19 l~WK~d~n~RE~~vmrRY~iq~ReDY~kYNkl~~~~~~~~t~~ 61 (76)
--|+.+.=.+|.++|++|+|++++||.+||+++|.+|.+..-+
T Consensus 19 ~P~ek~Rl~~E~kli~kYgLknK~E~wky~~ll~kiRk~Ar~L 61 (194)
T PLN00189 19 RPYEKERLDAELKLVGEYGLRNKRELWRVQYALSRIRNAARML 61 (194)
T ss_pred CchhhHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHH
Confidence 3588888889999999999999999999999999998864433
No 6
>PF00163 Ribosomal_S4: Ribosomal protein S4/S9 N-terminal domain; InterPro: IPR001912 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 [, ]. Ribosomal protein S4 is one of the proteins from the small ribosomal subunit. S4 is known to bind directly to 16S ribosomal RNA. The crystal structure of a bacterial S4 protein revealed a two domain molecule. The first domain is composed of four helices in the known structure. The second domain is an insertion within domain 1 and displays some structural homology with the ETS DNA binding domain []. This entry represents the domain found at the N terminus of small ribosomal subunits S4 and S9. ; GO: 0019843 rRNA binding, 0005622 intracellular; PDB: 3BBN_D 2WWL_D 3OR9_D 3OFA_D 2QBB_D 3OFP_D 4A2I_D 2QB9_D 3OFO_D 2QBF_D ....
Probab=93.86 E-value=0.0032 Score=39.84 Aligned_cols=42 Identities=21% Similarity=0.328 Sum_probs=37.1
Q ss_pred chhHHhhhhhhcccceecccCchhHHHHHHhhcCCCChhhHHhhcCCC
Q psy13912 5 LKYHEQKLLKKVDFISWEADNNLHEVKIMRRFGIQKRQDYTTAGFKPN 52 (76)
Q Consensus 5 LK~HEqKLLKKVdFl~WK~d~n~RE~~vmrRY~iq~ReDY~kYNkl~~ 52 (76)
+.+|+.|+.+++++..|..+. ..++++|+ .+.+++.|+..++
T Consensus 3 ~~~~~~k~~Rr~g~~~~~~~~----~~~~~~~~--~~~~~~~~~~~~~ 44 (94)
T PF00163_consen 3 YRGPKCKLPRRLGEKLWLTEK----AKLIRRYG--LRPGQHGWRRKSR 44 (94)
T ss_dssp SHSCCCHHHHHCTSHCTCSCC----CSHCCSSS--SSSSSSTTSHHHH
T ss_pred cCCCccccCCCCCCCccCCCc----cccccccc--ccccccccccccc
Confidence 788999999999999998774 88899999 8888898888765
No 7
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=78.60 E-value=0.51 Score=34.97 Aligned_cols=36 Identities=25% Similarity=0.383 Sum_probs=27.7
Q ss_pred CcccchhHHhhhhhhcccceecccCchhHHHHHHhhc
Q psy13912 1 MVRKLKYHEQKLLKKVDFISWEADNNLHEVKIMRRFG 37 (76)
Q Consensus 1 MmRkLK~HEqKLLKKVdFl~WK~d~n~RE~~vmrRY~ 37 (76)
|+|..+ |.+|++++++|.-|..+.--.|.+-+.+|.
T Consensus 1 M~r~~~-~~~K~~rr~g~~~~~~~~~~~~~~~~~~pG 36 (205)
T COG0522 1 MARYPG-PKKKLSRRLGFNPWLKERLCKERKLPYKPG 36 (205)
T ss_pred CCCCcC-cccceeeecCCChHHHHHHHHHhhcCCCcc
Confidence 899999 999999999999999854444444444444
No 8
>PF07014 Hs1pro-1_C: Hs1pro-1 protein C-terminus; InterPro: IPR009743 This entry represents the C terminus (approximately 270 residues) of a number of plant Hs1pro-1 proteins, which are believed to confer nematode resistance [].
Probab=39.96 E-value=12 Score=29.63 Aligned_cols=12 Identities=50% Similarity=1.179 Sum_probs=10.4
Q ss_pred HHHHHHhhhhcC
Q psy13912 65 YLCFAINRIWKL 76 (76)
Q Consensus 65 ~~~~~~~~~~~~ 76 (76)
--|+++.|||||
T Consensus 87 ~dc~~vERiWKL 98 (261)
T PF07014_consen 87 SDCWIVERIWKL 98 (261)
T ss_pred hHHHHHHHHHHH
Confidence 359999999996
No 9
>KOG0722|consensus
Probab=35.22 E-value=23 Score=28.73 Aligned_cols=46 Identities=15% Similarity=0.268 Sum_probs=34.2
Q ss_pred HHhhhhhhcccceecccCchhHHHHHHhhcCCCChhhHHhhcCCCCCc
Q psy13912 8 HEQKLLKKVDFISWEADNNLHEVKIMRRFGIQKRQDYTTAGFKPNPVP 55 (76)
Q Consensus 8 HEqKLLKKVdFl~WK~d~n~RE~~vmrRY~iq~ReDY~kYNkl~~~~~ 55 (76)
-|.++-+|.||..||.+...-|.+-|.--. .-.-|..|-+-.|+++
T Consensus 279 ~~~~~W~~~n~~~wkaeq~e~~~~k~a~~p--rYk~y~rymkn~g~~~ 324 (329)
T KOG0722|consen 279 FERECWLKLNCATWKAEQDEAEQEKMAQSP--RYKRYKRYMKNAGTIS 324 (329)
T ss_pred HHHHHHHhcCchhhhccCcHHHHHhhhcCc--cHHHHHHHHhcCCCee
Confidence 467888999999999998888877764211 1146888888888765
No 10
>PF09185 DUF1948: Domain of unknown function (DUF1948); InterPro: IPR015268 Members of this family of Mycoplasma hypothetical proteins adopt a helical structure, with one central alpha-helix surrounded by five others, in a NusB-like fold. Their function has not, as yet, been determined []. ; PDB: 1Q8C_A.
Probab=29.55 E-value=33 Score=24.77 Aligned_cols=23 Identities=9% Similarity=-0.168 Sum_probs=6.2
Q ss_pred hhhHHhhcCCCCCchHHHHHHHH
Q psy13912 42 QDYTTAGFKPNPVPPELTVLLHF 64 (76)
Q Consensus 42 eDY~kYNkl~~~~~~~~t~~~~~ 64 (76)
|--++||++||.--.++|-+.+.
T Consensus 74 eiq~kynkisgkkidllt~avil 96 (140)
T PF09185_consen 74 EIQSKYNKISGKKIDLLTKAVIL 96 (140)
T ss_dssp S--------------HHHHHHHH
T ss_pred HHHHHhcccccchhhHHHHHHHH
Confidence 44589999999999999987653
No 11
>PRK14750 kdpF potassium-transporting ATPase subunit F; Provisional
Probab=28.66 E-value=70 Score=17.86 Aligned_cols=15 Identities=40% Similarity=0.585 Sum_probs=12.0
Q ss_pred hHHHHHHHHHHHHHH
Q psy13912 56 PELTVLLHFYLCFAI 70 (76)
Q Consensus 56 ~~~t~~~~~~~~~~~ 70 (76)
.++-+++..|+|||.
T Consensus 9 ~llv~lLl~YLvYAL 23 (29)
T PRK14750 9 ALLVLLLLGYLVYAL 23 (29)
T ss_pred HHHHHHHHHHHHHHH
Confidence 456788899999985
No 12
>PF06400 Alpha-2-MRAP_N: Alpha-2-macroglobulin RAP, N-terminal domain; InterPro: IPR009066 The alpha-2-macroglobulin receptor-associated protein (RAP) is a glycoprotein that binds to the alpha-2-macroglobulin receptor, as well as to other members of the low density lipoprotein receptor family (IPR002172 from INTERPRO). RAP acts to inhibit the binding of all know ligands for these receptors, and may prevent receptor aggregation and degradation in the endoplasmic reticulum, thereby acting as a molecular chaperone []. RAP may be under the regulatory control of calmodulin, since it is able to bind calmodulin and be phosphorylated by calmodulin-dependent kinase II (IPR002048 from INTERPRO). RAP is comprised of three domains. Both domains 1 and 3 are involved in binding to the alpha-2-macroglobulin receptor, while domain 1 is also involved in inhibiting the binding of activated alpha-2-macroglobulin (IPR001599 from INTERPRO). Structural studies have revealed the RAP domain 1 to be comprised of a partly opened bundle of three helices, the first one being shorter than the other two.; PDB: 1NRE_A 2P03_A 1OV2_A 1LRE_A 2FYL_A 1OP1_A 2P01_A.
Probab=28.13 E-value=46 Score=23.60 Aligned_cols=41 Identities=24% Similarity=0.417 Sum_probs=24.0
Q ss_pred cchhHHhhhhh--hcccceecccCchhHH-------HHHHhhcCCCChhhH
Q psy13912 4 KLKYHEQKLLK--KVDFISWEADNNLHEV-------KIMRRFGIQKRQDYT 45 (76)
Q Consensus 4 kLK~HEqKLLK--KVdFl~WK~d~n~RE~-------~vmrRY~iq~ReDY~ 45 (76)
-||.||+.-|. |+.--.= .+++..|+ .||.+|++.+..|=.
T Consensus 68 dLKi~dkeEl~wKklk~~g~-D~dG~kEa~Lrrkl~~Im~kYgL~g~~D~~ 117 (120)
T PF06400_consen 68 DLKIHDKEELAWKKLKAEGK-DKDGEKEAELRRKLNVIMSKYGLDGKKDTE 117 (120)
T ss_dssp HHHHHHHHHHHHHHHHHHTS--SSSHHHHHHHHHHHHHHHHHTSSSSSSS-
T ss_pred HHHHhHHHHHHHHHHhhhCC-CccccHHHHHHHHHHHHHHHhCCCCCcccc
Confidence 37888887542 2211111 23466774 588999998887743
No 13
>PF06459 RR_TM4-6: Ryanodine Receptor TM 4-6; InterPro: IPR009460 The release of Ca2+ ions from intracellular stores is a key step in a wide variety of cellular functions. In striated muscle, the release of Ca2+ from the sarcoplasmic reticulum (SR) leads to muscle contraction. Ca2+ release occurs through large, high-conductance Ca2+ release channels, also known as ryanodine receptors (RyRs) because they bind the plant alkaloid ryanodine with high affinity and specificity []. This region covers TM regions 4-6 of the ryanodine receptor 1 family.; GO: 0005219 ryanodine-sensitive calcium-release channel activity, 0006874 cellular calcium ion homeostasis, 0016021 integral to membrane
Probab=25.81 E-value=52 Score=25.44 Aligned_cols=11 Identities=55% Similarity=0.872 Sum_probs=8.9
Q ss_pred HHHHHHHHhhh
Q psy13912 63 HFYLCFAINRI 73 (76)
Q Consensus 63 ~~~~~~~~~~~ 73 (76)
..|++||||=|
T Consensus 177 ALflAFaINFI 187 (274)
T PF06459_consen 177 ALFLAFAINFI 187 (274)
T ss_pred HHHHHHHHHHH
Confidence 45789999976
No 14
>KOG4779|consensus
Probab=22.37 E-value=34 Score=22.95 Aligned_cols=51 Identities=29% Similarity=0.428 Sum_probs=34.0
Q ss_pred HHhhhhhhcccceecccCchhHHHHHHhhcCCCChhhHHhhcCCCCCchHHHHHHHHHHHHHHhhh
Q psy13912 8 HEQKLLKKVDFISWEADNNLHEVKIMRRFGIQKRQDYTTAGFKPNPVPPELTVLLHFYLCFAINRI 73 (76)
Q Consensus 8 HEqKLLKKVdFl~WK~d~n~RE~~vmrRY~iq~ReDY~kYNkl~~~~~~~~t~~~~~~~~~~~~~~ 73 (76)
||.+-||. +-|..|.+. ...++++ +.=+++..++|+.+|+.- +--.+||-|
T Consensus 23 sEeRFL~r---iGws~d~~~---------gFG~~q~-tiKS~~~~LIravrTvmr--vPLI~iN~i 73 (82)
T KOG4779|consen 23 SEERFLKR---IGWSTDQGI---------GFGEDQP-TIKSQLMNLIRAVRTVMR--VPLIIINSI 73 (82)
T ss_pred hHHHHHHH---hCcCcccCc---------ccCCCCc-cHHHHHHHHHHHHHHHHh--cchhhhhHH
Confidence 78888888 678877543 2345555 445788889999999875 333455543
Done!