Query 033505
Match_columns 118
No_of_seqs 129 out of 904
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 03:03:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033505.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033505hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00096 40S ribosomal protein 100.0 1.7E-55 3.7E-60 328.1 8.4 116 1-116 28-143 (143)
2 TIGR01025 rpsS_arch ribosomal 100.0 7.4E-55 1.6E-59 322.2 8.5 118 1-118 18-135 (135)
3 PRK04038 rps19p 30S ribosomal 100.0 1.4E-53 3.1E-58 315.1 9.9 115 1-118 20-134 (134)
4 KOG0898 40S ribosomal protein 100.0 1.6E-52 3.5E-57 311.3 5.2 118 1-118 35-152 (152)
5 COG0185 RpsS Ribosomal protein 100.0 2.3E-42 5E-47 241.6 6.3 90 18-111 1-93 (93)
6 CHL00050 rps19 ribosomal prote 100.0 5.2E-37 1.1E-41 214.6 7.7 81 18-102 1-84 (92)
7 TIGR01050 rpsS_bact ribosomal 100.0 2.7E-36 5.9E-41 211.0 7.1 83 18-104 1-86 (92)
8 PF00203 Ribosomal_S19: Riboso 100.0 2.3E-36 5.1E-41 206.6 6.0 81 20-101 1-81 (81)
9 PRK00357 rpsS 30S ribosomal pr 100.0 4.3E-36 9.2E-41 210.1 7.0 82 18-103 1-85 (92)
10 PLN03147 ribosomal protein S19 100.0 3.1E-34 6.8E-39 200.6 7.1 79 20-104 1-81 (92)
11 KOG0899 Mitochondrial/chloropl 100.0 2.8E-34 6E-39 198.8 4.9 84 17-104 9-92 (93)
12 PRK01110 rpmF 50S ribosomal pr 53.0 8.7 0.00019 24.8 1.3 48 12-78 9-56 (60)
13 PF01783 Ribosomal_L32p: Ribos 45.1 9.2 0.0002 24.0 0.5 48 12-77 8-55 (56)
14 TIGR01031 rpmF_bact ribosomal 26.8 39 0.00084 21.3 1.2 20 57-76 35-54 (55)
15 KOG3265 Histone chaperone invo 23.7 65 0.0014 26.5 2.2 20 59-78 86-109 (250)
16 PF02229 PC4: Transcriptional 22.3 1.3E+02 0.0028 18.7 3.0 30 65-97 11-40 (56)
17 PRK12286 rpmF 50S ribosomal pr 20.7 58 0.0013 20.7 1.2 47 12-76 9-55 (57)
No 1
>PTZ00096 40S ribosomal protein S15; Provisional
Probab=100.00 E-value=1.7e-55 Score=328.07 Aligned_cols=116 Identities=72% Similarity=1.237 Sum_probs=113.7
Q ss_pred CChHHHHHHhhHHHHhhhhcCCCCChhhHHHHHHHHhhhCCCCCCCCceEeccCCccccccccceEEEEecCceeeeeee
Q 033505 1 MSTDELAKLFSARARRRFQRGLKRKPMALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEI 80 (118)
Q Consensus 1 m~~~e~~~l~~ar~RR~m~Rs~~k~~~~ll~~~rk~k~~~~~~~k~~~ikt~~R~s~IlP~~vg~~~~VyNGk~f~~v~I 80 (118)
||+|||++|+||||||++.||+...+..|+++++++++.+++++|+++|+||+|+|+|+|+|||++|+|||||+|++|+|
T Consensus 28 m~~~e~~~L~~aR~RR~~~RGl~~~~~~LlkKirk~~~~~~~~~k~~~ikT~~R~~~IlP~mVG~ti~VyNGK~fv~V~I 107 (143)
T PTZ00096 28 LPEEELVELFRARQRRRINRGIKRKHPTLLKKLRKAKKATKPGEKPKAVKTHLRDMIIVPEMVGSVVGVYNGKQFNNVEI 107 (143)
T ss_pred CCHHHHHHHcCcccccccccCCCHHHHHHHHHHHHHhhhcccccCCcceeEecccCeeCccccCcEEEEEcCCeeEeeEe
Confidence 89999999999999999999999999999999999998888888889999999999999999999999999999999999
Q ss_pred cCCcceeeeeeeeeeeecccCCCCCCCCCCCcCcee
Q 033505 81 KPEMIGHYLAEFSISYKPVKHGRPGIGATHSSRFIP 116 (118)
Q Consensus 81 ~~eMIGhklGEF~~Trk~~~h~~~g~gat~ss~fvp 116 (118)
+||||||||||||+||+++.||+||+|||+||+|||
T Consensus 108 ~~eMIGhkLGEFa~Trk~~~Hg~pGigATrSS~fvp 143 (143)
T PTZ00096 108 KPEMIGHYLGEFSITYKPVRHGKPGVGATHSSRFIP 143 (143)
T ss_pred ccCeeceeeccccCCcccccCCCCCcCcccccccCC
Confidence 999999999999999999999999999999999998
No 2
>TIGR01025 rpsS_arch ribosomal protein S19(archaeal)/S15(eukaryotic). This model represents eukaryotic ribosomal protein S15 and its archaeal equivalent. It excludes bacterial and organellar ribosomal protein S19. The nomenclature for the archaeal members is unresolved and given variously as S19 (after the more distant bacterial homologs) or S15.
Probab=100.00 E-value=7.4e-55 Score=322.22 Aligned_cols=118 Identities=74% Similarity=1.154 Sum_probs=112.8
Q ss_pred CChHHHHHHhhHHHHhhhhcCCCCChhhHHHHHHHHhhhCCCCCCCCceEeccCCccccccccceEEEEecCceeeeeee
Q 033505 1 MSTDELAKLFSARARRRFQRGLKRKPMALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEI 80 (118)
Q Consensus 1 m~~~e~~~l~~ar~RR~m~Rs~~k~~~~ll~~~rk~k~~~~~~~k~~~ikt~~R~s~IlP~~vg~~~~VyNGk~f~~v~I 80 (118)
|+++||++|+||||||++.|++...+..|+++++++++....++++++|+||+|+|+|+|+|||++|+||||++|++|+|
T Consensus 18 m~~~e~~~l~~ar~RRs~~RG~~~~~~~Llkki~k~~~~~~~g~k~~~IKT~sR~s~IlP~~VG~ti~VyNGk~fv~v~I 97 (135)
T TIGR01025 18 MSLEELAKLLPARQRRRLKRGLTPKQKKLLKKLRKAKKEAPKGEKPEVIRTHCRDMIILPEMVGSTVGVYNGKEFVQVEI 97 (135)
T ss_pred CCHHHHHHHcCcccCcccccCCchhhHHHHHHHHHHHhccccccCCcceEEeccCCeeChhhcCcEEEEEcCCeeEEEEe
Confidence 89999999999999999999999999999999998876555567789999999999999999999999999999999999
Q ss_pred cCCcceeeeeeeeeeeecccCCCCCCCCCCCcCceecC
Q 033505 81 KPEMIGHYLAEFSISYKPVKHGRPGIGATHSSRFIPLK 118 (118)
Q Consensus 81 ~~eMIGhklGEF~~Trk~~~h~~~g~gat~ss~fvplk 118 (118)
+||||||||||||+||+++.|++||+|||+||+|||||
T Consensus 98 ~~eMVGhklGEFa~Trk~~~Hg~pGigAt~ss~fvplK 135 (135)
T TIGR01025 98 KPEMIGHYLGEFSITRKPVKHGRPGIGATRSSMFVPLK 135 (135)
T ss_pred cCCeeceeecccccCcccCcCCCCCcCccccccceeCc
Confidence 99999999999999999999999999999999999997
No 3
>PRK04038 rps19p 30S ribosomal protein S19P; Provisional
Probab=100.00 E-value=1.4e-53 Score=315.07 Aligned_cols=115 Identities=58% Similarity=0.982 Sum_probs=108.2
Q ss_pred CChHHHHHHhhHHHHhhhhcCCCCChhhHHHHHHHHhhhCCCCCCCCceEeccCCccccccccceEEEEecCceeeeeee
Q 033505 1 MSTDELAKLFSARARRRFQRGLKRKPMALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEI 80 (118)
Q Consensus 1 m~~~e~~~l~~ar~RR~m~Rs~~k~~~~ll~~~rk~k~~~~~~~k~~~ikt~~R~s~IlP~~vg~~~~VyNGk~f~~v~I 80 (118)
||+|||++|+||||||++.|+....+..|+++++++++. ++++++|+||+|+|+|+|+|||++|+|||||+|++|+|
T Consensus 20 m~~~~~~~l~~ar~RRsl~KGp~~~~~~LlkKi~k~~~~---~~k~~~ikT~sR~s~IlP~~VG~ti~VyNGk~fv~v~I 96 (134)
T PRK04038 20 MSLEEFAELLPARQRRSLKRGLTPEQRKLLEKIRKARRE---KKKGRVIRTHVRDMIILPEMVGLTIAVYNGKEFVEVEI 96 (134)
T ss_pred CCHHHHHHHcchhhhhhhccCCCcchHHHHHHHHHHHhc---ccCCcceeEeccCCeeChhhcCeEEEEecCceeEeEEe
Confidence 899999999999999999999988788899999987653 33457899999999999999999999999999999999
Q ss_pred cCCcceeeeeeeeeeeecccCCCCCCCCCCCcCceecC
Q 033505 81 KPEMIGHYLAEFSISYKPVKHGRPGIGATHSSRFIPLK 118 (118)
Q Consensus 81 ~~eMIGhklGEF~~Trk~~~h~~~g~gat~ss~fvplk 118 (118)
+||||||||||||+||+++.|++||+|||+||+|||||
T Consensus 97 ~~eMVGhklGEFa~Trk~~~Hg~pGigAT~sS~fvplK 134 (134)
T PRK04038 97 VPEMIGHYLGEFALTRKRVQHGSPGIGATRSSKFVPLK 134 (134)
T ss_pred ccCccceeeccccCCcccCcCCCCCcCccccccceeCc
Confidence 99999999999999999999999999999999999997
No 4
>KOG0898 consensus 40S ribosomal protein S15 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-52 Score=311.28 Aligned_cols=118 Identities=84% Similarity=1.321 Sum_probs=116.6
Q ss_pred CChHHHHHHhhHHHHhhhhcCCCCChhhHHHHHHHHhhhCCCCCCCCceEeccCCccccccccceEEEEecCceeeeeee
Q 033505 1 MSTDELAKLFSARARRRFQRGLKRKPMALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEI 80 (118)
Q Consensus 1 m~~~e~~~l~~ar~RR~m~Rs~~k~~~~ll~~~rk~k~~~~~~~k~~~ikt~~R~s~IlP~~vg~~~~VyNGk~f~~v~I 80 (118)
||.+|+++|+|||+||+++||+|++|..|+++||++++++++.+||++|+||.|||+|+|+|||..|+|||||.|.+|+|
T Consensus 35 ms~~~~~~l~~ar~rrR~~RGL~~k~~~liKklrkAkk~A~~~ekpe~VkTHlR~mII~PEMvGs~VGVyNGK~FnqvEi 114 (152)
T KOG0898|consen 35 MSTEQLVKLFPARQRRRLNRGLTRKPHSLIKKLRKAKKEAPPMEKPEVVKTHLRNMIIVPEMVGSMVGVYNGKTFNQVEI 114 (152)
T ss_pred CCHHHHHHHHHHHHHHHHHcccccchHHHHHHHHHHHhhcCcccCcHHHHHHhhcceeeHhhhcceEEEecCcccceeec
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCcceeeeeeeeeeeecccCCCCCCCCCCCcCceecC
Q 033505 81 KPEMIGHYLAEFSISYKPVKHGRPGIGATHSSRFIPLK 118 (118)
Q Consensus 81 ~~eMIGhklGEF~~Trk~~~h~~~g~gat~ss~fvplk 118 (118)
+|||||||||||++|+||++|++||+|||+||.|+|||
T Consensus 115 KPEMIGhYL~eFsiTykpvkHgrpgigat~SsrfipLk 152 (152)
T KOG0898|consen 115 KPEMIGHYLGEFSITYKPVKHGRPGIGATHSSRFIPLK 152 (152)
T ss_pred cHHHHhhhhhhccccccccccCCCCCCcccccccccCC
Confidence 99999999999999999999999999999999999997
No 5
>COG0185 RpsS Ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-42 Score=241.58 Aligned_cols=90 Identities=49% Similarity=0.754 Sum_probs=81.9
Q ss_pred hhcCCCCChh---hHHHHHHHHhhhCCCCCCCCceEeccCCccccccccceEEEEecCceeeeeeecCCcceeeeeeeee
Q 033505 18 FQRGLKRKPM---ALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSI 94 (118)
Q Consensus 18 m~Rs~~k~~~---~ll~~~rk~k~~~~~~~k~~~ikt~~R~s~IlP~~vg~~~~VyNGk~f~~v~I~~eMIGhklGEF~~ 94 (118)
|+||+||+|+ .|++++++++.. +. +++|+||||+|+|||+|||++|+||||++|+||+|+||||||||||||+
T Consensus 1 ~~RSlkkGp~~~~~Ll~Kv~~~~~~---~~-k~~IkT~sR~stIlPemVG~ti~VhNGk~~vpV~I~~eMVGHkLGEFap 76 (93)
T COG0185 1 MRRSLKKGPFVDKHLLKKVRKAKES---GK-KKPIKTWSRRSTILPEMVGLTIAVHNGKKFVPVEITEEMVGHKLGEFAP 76 (93)
T ss_pred CCcccccCccccHHHHHHHHHHHhc---cC-CCcceeeecccEechhhcCcEEEEEcCceEEEEEechhhcceecccccc
Confidence 5788999988 678888877652 32 3899999999999999999999999999999999999999999999999
Q ss_pred eeecccCCCCCCCCCCC
Q 033505 95 SYKPVKHGRPGIGATHS 111 (118)
Q Consensus 95 Trk~~~h~~~g~gat~s 111 (118)
||++++|+.+|++||+|
T Consensus 77 TR~~~~H~~~~~~atr~ 93 (93)
T COG0185 77 TRTFVGHGADGIKATRS 93 (93)
T ss_pred eecccccCCCCcCcccC
Confidence 99999999999999986
No 6
>CHL00050 rps19 ribosomal protein S19
Probab=100.00 E-value=5.2e-37 Score=214.62 Aligned_cols=81 Identities=37% Similarity=0.555 Sum_probs=71.5
Q ss_pred hhcCCCCChhh---HHHHHHHHhhhCCCCCCCCceEeccCCccccccccceEEEEecCceeeeeeecCCcceeeeeeeee
Q 033505 18 FQRGLKRKPMA---LIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSI 94 (118)
Q Consensus 18 m~Rs~~k~~~~---ll~~~rk~k~~~~~~~k~~~ikt~~R~s~IlP~~vg~~~~VyNGk~f~~v~I~~eMIGhklGEF~~ 94 (118)
|+||+||+||. |+++++++.. ..++++|+||+|+|+|+|+|||++|+||||++|++|+|+||||||||||||+
T Consensus 1 M~RS~wKgpfv~~~Ll~ki~~~~~----~~~~~~ikT~sR~s~IlP~~vg~t~~VyNGk~fv~v~I~~eMVGhklGEFa~ 76 (92)
T CHL00050 1 MTRSLKKNPFVANHLLKKIEKLNT----KEEKEIIVTWSRASTIIPTMIGHTIAVHNGKEHIPIYITDQMVGHKLGEFAP 76 (92)
T ss_pred CCCccccCcccCHHHHHHHHHhhh----ccCCccceEEccccEeChhhcCcEEEEEcCceEEEEEEccccccceeeeEee
Confidence 78999999994 5555555432 2235789999999999999999999999999999999999999999999999
Q ss_pred eeecccCC
Q 033505 95 SYKPVKHG 102 (118)
Q Consensus 95 Trk~~~h~ 102 (118)
||++++|+
T Consensus 77 TRk~~~h~ 84 (92)
T CHL00050 77 TRNFRGHA 84 (92)
T ss_pred eecccccc
Confidence 99999995
No 7
>TIGR01050 rpsS_bact ribosomal protein S19, bacterial/organelle. the Archaea may be designated S15 or S19.
Probab=100.00 E-value=2.7e-36 Score=211.02 Aligned_cols=83 Identities=39% Similarity=0.606 Sum_probs=72.7
Q ss_pred hhcCCCCChhh---HHHHHHHHhhhCCCCCCCCceEeccCCccccccccceEEEEecCceeeeeeecCCcceeeeeeeee
Q 033505 18 FQRGLKRKPMA---LIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSI 94 (118)
Q Consensus 18 m~Rs~~k~~~~---ll~~~rk~k~~~~~~~k~~~ikt~~R~s~IlP~~vg~~~~VyNGk~f~~v~I~~eMIGhklGEF~~ 94 (118)
|+||+||+||. |+++++++.. ..++++|+||||+|+|+|+|||++|+||||++|++|+|++|||||||||||+
T Consensus 1 MsRS~wKgpfv~~~Ll~ki~k~~~----~~~~~~ikT~sR~s~IlP~~vg~~i~VynGk~fv~v~I~~~MvGhklGEFa~ 76 (92)
T TIGR01050 1 MSRSLKKGPFVDHHLLKKVEKLNE----SGKKKVIKTWSRRSTIIPEMIGHTIAVHNGKKFIPVYITEDMVGHKLGEFAP 76 (92)
T ss_pred CCcccccCccccHHHHHHHHHhhc----ccCCCceEEEecccEEChHHCCcEEEEEcCceEEEEEeCcCeecceeeeeec
Confidence 78999999994 5565555431 2346789999999999999999999999999999999999999999999999
Q ss_pred eeecccCCCC
Q 033505 95 SYKPVKHGRP 104 (118)
Q Consensus 95 Trk~~~h~~~ 104 (118)
||+++.|++.
T Consensus 77 TRk~~~h~~~ 86 (92)
T TIGR01050 77 TRTFKGHAKS 86 (92)
T ss_pred eeeccccccC
Confidence 9999999753
No 8
>PF00203 Ribosomal_S19: Ribosomal protein S19; InterPro: IPR002222 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 [, ]. The small subunit ribosomal proteins can be categorised as: primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S19 contains 88-144 amino acid residues. In Escherichia coli, S19 is known to form a complex with S13 that binds strongly to 16S ribosomal RNA. Experimental evidence [] has revealed that S19 is moderately exposed on the ribosomal surface, and is designated a secondary rRNA binding protein. S19 belongs to a family of ribosomal proteins [, ] that includes: eubacterial S19; algal and plant chloroplast S19; cyanelle S19; archaebacterial S19; plant mitochondrial S19; and eukaryotic S15 ('rig' protein).; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 2XZM_S 2XZN_S 2ZKQ_s 3U5C_P 3O30_I 3U5G_P 3O2Z_I 3IZB_R 1S1H_S 1XMO_S ....
Probab=100.00 E-value=2.3e-36 Score=206.56 Aligned_cols=81 Identities=51% Similarity=0.838 Sum_probs=75.5
Q ss_pred cCCCCChhhHHHHHHHHhhhCCCCCCCCceEeccCCccccccccceEEEEecCceeeeeeecCCcceeeeeeeeeeeecc
Q 033505 20 RGLKRKPMALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPV 99 (118)
Q Consensus 20 Rs~~k~~~~ll~~~rk~k~~~~~~~k~~~ikt~~R~s~IlP~~vg~~~~VyNGk~f~~v~I~~eMIGhklGEF~~Trk~~ 99 (118)
||+||+|+.+...++++++.+..+++ ++++||+|+|+|+|+|||++|+||||++|++|+|++|||||||||||+||+++
T Consensus 1 Rs~~K~~~~~~~~l~k~~~~~~~~~k-~~ikt~~R~s~IlP~~vg~~i~VyNGk~f~~i~I~~~miG~klGEF~~Trk~~ 79 (81)
T PF00203_consen 1 RSLWKGPFVLKKLLKKIKKLNPSKKK-KVIKTHSRSSTILPEMVGKTIGVYNGKKFVPIKITPEMIGHKLGEFAPTRKPV 79 (81)
T ss_dssp CCSSSSTHHHHHHHHHHHHHHCTTST-SEEEESSTTSBBSGTGTTSEEEEESSSSEEEEECSSTGTSSBCGCGSSSSSTS
T ss_pred CCCCcccchhHHHHHHHHHHhhcCCC-cceEEEeCCCCcccceeceEEEEecCceEEEEEecccccceEeeceeeecccC
Confidence 89999999999999888766555554 89999999999999999999999999999999999999999999999999999
Q ss_pred cC
Q 033505 100 KH 101 (118)
Q Consensus 100 ~h 101 (118)
+|
T Consensus 80 ~H 81 (81)
T PF00203_consen 80 KH 81 (81)
T ss_dssp CT
T ss_pred CC
Confidence 88
No 9
>PRK00357 rpsS 30S ribosomal protein S19; Reviewed
Probab=100.00 E-value=4.3e-36 Score=210.07 Aligned_cols=82 Identities=34% Similarity=0.558 Sum_probs=72.3
Q ss_pred hhcCCCCChh---hHHHHHHHHhhhCCCCCCCCceEeccCCccccccccceEEEEecCceeeeeeecCCcceeeeeeeee
Q 033505 18 FQRGLKRKPM---ALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSI 94 (118)
Q Consensus 18 m~Rs~~k~~~---~ll~~~rk~k~~~~~~~k~~~ikt~~R~s~IlP~~vg~~~~VyNGk~f~~v~I~~eMIGhklGEF~~ 94 (118)
|+||+||+|+ .|+++++++.. .+ ++++|+||+|+|+|+|+|||++|+||||++|++|+|+||||||||||||+
T Consensus 1 M~RS~~Kgp~v~~~Ll~ki~k~~~---~~-~~~~ikT~sR~s~IlP~~vg~~i~VyNGk~fv~v~I~~emiGhklGEFa~ 76 (92)
T PRK00357 1 MARSLKKGPFVDGHLLKKVEKANE---SG-DKKVIKTWSRRSTILPEFVGLTIAVHNGRKHVPVYVTENMVGHKLGEFAP 76 (92)
T ss_pred CCcccccCccccHHHHHHHHHHhh---cc-CCCceEEeeccCCcCHHHCCceEEEEcCCeeEeEEeccCccceeeeeecc
Confidence 7899999999 46666665542 22 35789999999999999999999999999999999999999999999999
Q ss_pred eeecccCCC
Q 033505 95 SYKPVKHGR 103 (118)
Q Consensus 95 Trk~~~h~~ 103 (118)
||++++|+.
T Consensus 77 Tr~~~~H~~ 85 (92)
T PRK00357 77 TRTFRGHAA 85 (92)
T ss_pred eeccccccc
Confidence 999999974
No 10
>PLN03147 ribosomal protein S19; Provisional
Probab=100.00 E-value=3.1e-34 Score=200.62 Aligned_cols=79 Identities=19% Similarity=0.308 Sum_probs=68.3
Q ss_pred cCCCCChhhHHH--HHHHHhhhCCCCCCCCceEeccCCccccccccceEEEEecCceeeeeeecCCcceeeeeeeeeeee
Q 033505 20 RGLKRKPMALIK--KLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYK 97 (118)
Q Consensus 20 Rs~~k~~~~ll~--~~rk~k~~~~~~~k~~~ikt~~R~s~IlP~~vg~~~~VyNGk~f~~v~I~~eMIGhklGEF~~Trk 97 (118)
||+||+||.... ++.++.+ ...+|+||||+|+|+|+|||++|+||||++|++|+|+||||||||||||+||+
T Consensus 1 RS~wKGPfv~~~L~k~~~~~~------~~~~iktwSR~S~IlP~~vg~ti~VyNGk~fv~v~It~~MVGhKlGEFa~Trk 74 (92)
T PLN03147 1 QAIWKGAFVDAFLARIKKKRD------LLLGKKIWSHRSSILPDFVDCSVLIYNGKTHIRCKITEGKVGHKFGEFAFTRK 74 (92)
T ss_pred CCCccCccccHHHHHHHHHHh------cCCceeEEcccceECHHHcCCEEEEeCCCceEEEEecCCccceeeeccccEec
Confidence 899999995332 3433322 12589999999999999999999999999999999999999999999999999
Q ss_pred cccCCCC
Q 033505 98 PVKHGRP 104 (118)
Q Consensus 98 ~~~h~~~ 104 (118)
++.|...
T Consensus 75 ~~~hk~~ 81 (92)
T PLN03147 75 RRPHRAI 81 (92)
T ss_pred ccCCCCc
Confidence 9999776
No 11
>KOG0899 consensus Mitochondrial/chloroplast ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.8e-34 Score=198.80 Aligned_cols=84 Identities=30% Similarity=0.498 Sum_probs=73.8
Q ss_pred hhhcCCCCChhhHHHHHHHHhhhCCCCCCCCceEeccCCccccccccceEEEEecCceeeeeeecCCcceeeeeeeeeee
Q 033505 17 RFQRGLKRKPMALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISY 96 (118)
Q Consensus 17 ~m~Rs~~k~~~~ll~~~rk~k~~~~~~~k~~~ikt~~R~s~IlP~~vg~~~~VyNGk~f~~v~I~~eMIGhklGEF~~Tr 96 (118)
+|+||+||+||+.-..+++..... .+-+|+||+|+++|||+|||.+|.|||||+|++|+|+|+|||||||||++||
T Consensus 9 Sm~RSvwK~P~V~~~~~rk~~~~~----~~~pikt~sRasTIlP~~Vg~~~~IhNGk~~v~vkIte~mVGHKlGEFapTr 84 (93)
T KOG0899|consen 9 SMTRSVWKGPFVVKFLLRKIEKLK----GKAPIKTWSRASTILPTMVGHTFAIHNGKEHVPVKITEDMVGHKLGEFAPTR 84 (93)
T ss_pred HHHHHhhcCcchhHHHHHHHHHhc----CCCceeehhhhcchhhhhhCceEEEecCcceeeEEeecchhccccccccchh
Confidence 399999999997666666554321 1358999999999999999999999999999999999999999999999999
Q ss_pred ecccCCCC
Q 033505 97 KPVKHGRP 104 (118)
Q Consensus 97 k~~~h~~~ 104 (118)
|...|.+.
T Consensus 85 k~~~~akt 92 (93)
T KOG0899|consen 85 KFFGHAKT 92 (93)
T ss_pred hhhccccC
Confidence 99999763
No 12
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=53.02 E-value=8.7 Score=24.77 Aligned_cols=48 Identities=17% Similarity=0.348 Sum_probs=29.6
Q ss_pred HHHHhhhhcCCCCChhhHHHHHHHHhhhCCCCCCCCceEeccCCccccccccceEEEEecCceeeee
Q 033505 12 ARARRRFQRGLKRKPMALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQV 78 (118)
Q Consensus 12 ar~RR~m~Rs~~k~~~~ll~~~rk~k~~~~~~~k~~~ikt~~R~s~IlP~~vg~~~~VyNGk~f~~v 78 (118)
|++|+.+.|+-|+-....+ .+.. .=...++|--|-. -+.|+|++.+.+
T Consensus 9 Sksr~~~RRa~~~~~~~~~-----------------~~c~-~cg~~~~pH~vc~-cG~Y~gr~v~~~ 56 (60)
T PRK01110 9 SKSKRRMRRSHWKLTAPTL-----------------SVDK-TTGEYHLPHHVSP-KGYYKGRKVLKK 56 (60)
T ss_pred chhhchhhhhhhhccCCce-----------------eEcC-CCCceeccceecC-CcccCCeEeecc
Confidence 6788999998884322111 1111 1123467777766 789999988764
No 13
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=45.09 E-value=9.2 Score=24.03 Aligned_cols=48 Identities=19% Similarity=0.331 Sum_probs=27.2
Q ss_pred HHHHhhhhcCCCCChhhHHHHHHHHhhhCCCCCCCCceEeccCCccccccccceEEEEecCceeee
Q 033505 12 ARARRRFQRGLKRKPMALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQ 77 (118)
Q Consensus 12 ar~RR~m~Rs~~k~~~~ll~~~rk~k~~~~~~~k~~~ikt~~R~s~IlP~~vg~~~~VyNGk~f~~ 77 (118)
|++|+++.|+.|+-.. +..+.--.=....+|-.|-..-+.|+|++.+.
T Consensus 8 Sksr~~~Rrs~~~l~~------------------~~l~~c~~cg~~~~~H~vc~~cG~y~~r~v~~ 55 (56)
T PF01783_consen 8 SKSRKRMRRSHWKLKA------------------PNLVKCPNCGEPKLPHRVCPSCGYYKGRQVIE 55 (56)
T ss_dssp CHHHHHHHTTTTS--T------------------TSEEESSSSSSEESTTSBCTTTBBSSSSSSST
T ss_pred ChhHccchhccccccc------------------cceeeeccCCCEecccEeeCCCCeECCEEEee
Confidence 6789999999884311 11111111223456666654446899988764
No 14
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=26.79 E-value=39 Score=21.30 Aligned_cols=20 Identities=20% Similarity=0.436 Sum_probs=15.8
Q ss_pred cccccccceEEEEecCceee
Q 033505 57 IIVPEMIGSIIGVYNGKTFN 76 (118)
Q Consensus 57 ~IlP~~vg~~~~VyNGk~f~ 76 (118)
..+|-.|-..-+.|+|++.+
T Consensus 35 ~~~~H~vc~~cG~Y~gr~v~ 54 (55)
T TIGR01031 35 FKLPHRVCPSCGYYKGRQVL 54 (55)
T ss_pred cccCeeECCccCeECCEEcc
Confidence 57788888788899998764
No 15
>KOG3265 consensus Histone chaperone involved in gene silencing [Transcription; Chromatin structure and dynamics]
Probab=23.72 E-value=65 Score=26.51 Aligned_cols=20 Identities=25% Similarity=0.559 Sum_probs=16.6
Q ss_pred cccccceEEE----EecCceeeee
Q 033505 59 VPEMIGSIIG----VYNGKTFNQV 78 (118)
Q Consensus 59 lP~~vg~~~~----VyNGk~f~~v 78 (118)
+.++||.|+- =|+|.+|++|
T Consensus 86 ~~d~vGVTviLltC~Y~gQEFIRv 109 (250)
T KOG3265|consen 86 EDDIVGVTVILLTCSYRGQEFIRV 109 (250)
T ss_pred ccceeeeEEEEEEEEEcCceeEEE
Confidence 6789998765 4999999986
No 16
>PF02229 PC4: Transcriptional Coactivator p15 (PC4); InterPro: IPR003173 p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain []. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.; GO: 0003677 DNA binding, 0003713 transcription coactivator activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3PM7_B 2LTD_A 2LTT_B 3OBH_B 2L3A_B 2PHE_B 1PCF_B 2C62_B.
Probab=22.25 E-value=1.3e+02 Score=18.68 Aligned_cols=30 Identities=17% Similarity=0.189 Sum_probs=20.6
Q ss_pred eEEEEecCceeeeeeecCCcceeeeeeeeeeee
Q 033505 65 SIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYK 97 (118)
Q Consensus 65 ~~~~VyNGk~f~~v~I~~eMIGhklGEF~~Trk 97 (118)
.++.-|+|+.++.|..--+ + .-||..||+|
T Consensus 11 v~v~~fkG~~~vdIRe~y~--~-~~g~~~P~kK 40 (56)
T PF02229_consen 11 VSVSEFKGKPYVDIREWYE--K-KDGEWKPTKK 40 (56)
T ss_dssp EEEEEETTSEEEEEEEEET--T-SSS-EEEEEE
T ss_pred EEEEEeCCeEEEEEEeeEE--c-CCCcCcCcCC
Confidence 5678899998887754434 3 2488888876
No 17
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=20.73 E-value=58 Score=20.70 Aligned_cols=47 Identities=19% Similarity=0.268 Sum_probs=27.3
Q ss_pred HHHHhhhhcCCCCChhhHHHHHHHHhhhCCCCCCCCceEeccCCccccccccceEEEEecCceee
Q 033505 12 ARARRRFQRGLKRKPMALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFN 76 (118)
Q Consensus 12 ar~RR~m~Rs~~k~~~~ll~~~rk~k~~~~~~~k~~~ikt~~R~s~IlP~~vg~~~~VyNGk~f~ 76 (118)
|+.||.+.|+-|+-.. +..+.=-.=...++|--|-..-+.|+|+.-+
T Consensus 9 S~srr~~RRsh~~l~~------------------~~l~~C~~CG~~~~~H~vC~~CG~Y~gr~v~ 55 (57)
T PRK12286 9 SKSRKRKRRAHFKLKA------------------PGLVECPNCGEPKLPHRVCPSCGYYKGREVV 55 (57)
T ss_pred ChhhcchhcccccccC------------------CcceECCCCCCccCCeEECCCCCcCCCEEee
Confidence 6788888888775311 1111111113346677777677889998744
Done!