Query 034541
Match_columns 92
No_of_seqs 116 out of 765
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 03:55:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034541.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034541hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01025 rpsS_arch ribosomal 100.0 5.6E-46 1.2E-50 264.5 7.6 91 2-92 45-135 (135)
2 PTZ00096 40S ribosomal protein 100.0 1.2E-45 2.6E-50 264.8 7.4 89 2-90 55-143 (143)
3 PRK04038 rps19p 30S ribosomal 100.0 2.8E-45 6.1E-50 260.6 7.4 88 2-92 47-134 (134)
4 KOG0898 40S ribosomal protein 100.0 3.8E-42 8.2E-47 247.0 2.2 92 1-92 61-152 (152)
5 COG0185 RpsS Ribosomal protein 100.0 8.9E-41 1.9E-45 225.4 6.5 80 2-85 14-93 (93)
6 CHL00050 rps19 ribosomal prote 100.0 9.5E-34 2.1E-38 190.7 6.9 71 2-76 14-84 (92)
7 TIGR01050 rpsS_bact ribosomal 100.0 1.7E-33 3.7E-38 189.5 6.7 73 2-78 14-86 (92)
8 PRK00357 rpsS 30S ribosomal pr 100.0 2.5E-33 5.3E-38 188.8 6.1 72 2-77 14-85 (92)
9 PF00203 Ribosomal_S19: Riboso 100.0 1.4E-32 3E-37 180.7 4.4 56 20-75 26-81 (81)
10 PLN03147 ribosomal protein S19 100.0 9.1E-32 2E-36 181.4 6.1 69 5-79 14-82 (92)
11 KOG0899 Mitochondrial/chloropl 100.0 2.5E-30 5.4E-35 173.3 3.0 58 21-78 35-92 (93)
12 KOG3265 Histone chaperone invo 22.0 65 0.0014 25.5 1.9 20 33-52 86-109 (250)
13 PF02229 PC4: Transcriptional 21.1 87 0.0019 18.7 1.9 30 39-71 11-40 (56)
14 PF07833 Cu_amine_oxidN1: Copp 20.8 15 0.00033 22.4 -1.5 21 44-64 1-21 (93)
No 1
>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=5.6e-46 Score=264.53 Aligned_cols=91 Identities=78% Similarity=1.247 Sum_probs=86.5
Q ss_pred hHHHHHHHHhhhCCCCCCCCceEeeccCceecccccccEEEEecCcceeeeccCCCcceeeeeEEeeeEecccCCCCCCC
Q 034541 2 ALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRPGIG 81 (92)
Q Consensus 2 ~ll~k~~k~~~~~~~~~k~~~ikt~sR~s~IlP~~vg~~~~VyNGk~f~~v~I~~eMIG~klGEFa~Trk~~~h~k~G~g 81 (92)
+||++++++++....++++++|+||+|+|+|+|+|||++|.||||++|++|+|+||||||||||||+||+++.|++||+|
T Consensus 45 ~Llkki~k~~~~~~~g~k~~~IKT~sR~s~IlP~~VG~ti~VyNGk~fv~v~I~~eMVGhklGEFa~Trk~~~Hg~pGig 124 (135)
T TIGR01025 45 KLLKKLRKAKKEAPKGEKPEVIRTHCRDMIILPEMVGSTVGVYNGKEFVQVEIKPEMIGHYLGEFSITRKPVKHGRPGIG 124 (135)
T ss_pred HHHHHHHHHHhccccccCCcceEEeccCCeeChhhcCcEEEEEcCCeeEEEEecCCeeceeecccccCcccCcCCCCCcC
Confidence 58999999887655567789999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccccceecC
Q 034541 82 ATHSSRFIPLK 92 (92)
Q Consensus 82 at~ss~f~plk 92 (92)
||+||+|||||
T Consensus 125 At~ss~fvplK 135 (135)
T TIGR01025 125 ATRSSMFVPLK 135 (135)
T ss_pred ccccccceeCc
Confidence 99999999997
No 2
>PTZ00096 40S ribosomal protein S15; Provisional
Probab=100.00 E-value=1.2e-45 Score=264.81 Aligned_cols=89 Identities=78% Similarity=1.351 Sum_probs=87.0
Q ss_pred hHHHHHHHHhhhCCCCCCCCceEeeccCceecccccccEEEEecCcceeeeccCCCcceeeeeEEeeeEecccCCCCCCC
Q 034541 2 ALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRPGIG 81 (92)
Q Consensus 2 ~ll~k~~k~~~~~~~~~k~~~ikt~sR~s~IlP~~vg~~~~VyNGk~f~~v~I~~eMIG~klGEFa~Trk~~~h~k~G~g 81 (92)
.||+||+++++.+++++++++|+||+|+|+|+|+|||++|+|||||+|++|+|+||||||||||||+||+++.||+||+|
T Consensus 55 ~LlkKirk~~~~~~~~~k~~~ikT~~R~~~IlP~mVG~ti~VyNGK~fv~V~I~~eMIGhkLGEFa~Trk~~~Hg~pGig 134 (143)
T PTZ00096 55 TLLKKLRKAKKATKPGEKPKAVKTHLRDMIIVPEMVGSVVGVYNGKQFNNVEIKPEMIGHYLGEFSITYKPVRHGKPGVG 134 (143)
T ss_pred HHHHHHHHHhhhcccccCCcceeEecccCeeCccccCcEEEEEcCCeeEeeEeccCeeceeeccccCCcccccCCCCCcC
Confidence 69999999998888888999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccccee
Q 034541 82 ATHSSRFIP 90 (92)
Q Consensus 82 at~ss~f~p 90 (92)
||+||+|||
T Consensus 135 ATrSS~fvp 143 (143)
T PTZ00096 135 ATHSSRFIP 143 (143)
T ss_pred cccccccCC
Confidence 999999998
No 3
>PRK04038 rps19p 30S ribosomal protein S19P; Provisional
Probab=100.00 E-value=2.8e-45 Score=260.65 Aligned_cols=88 Identities=63% Similarity=1.068 Sum_probs=82.9
Q ss_pred hHHHHHHHHhhhCCCCCCCCceEeeccCceecccccccEEEEecCcceeeeccCCCcceeeeeEEeeeEecccCCCCCCC
Q 034541 2 ALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRPGIG 81 (92)
Q Consensus 2 ~ll~k~~k~~~~~~~~~k~~~ikt~sR~s~IlP~~vg~~~~VyNGk~f~~v~I~~eMIG~klGEFa~Trk~~~h~k~G~g 81 (92)
.||++++++++. .+++++|+||||+|+|+|+|||++|.|||||+|++|+|+||||||||||||+||+++.|++||+|
T Consensus 47 ~LlkKi~k~~~~---~~k~~~ikT~sR~s~IlP~~VG~ti~VyNGk~fv~v~I~~eMVGhklGEFa~Trk~~~Hg~pGig 123 (134)
T PRK04038 47 KLLEKIRKARRE---KKKGRVIRTHVRDMIILPEMVGLTIAVYNGKEFVEVEIVPEMIGHYLGEFALTRKRVQHGSPGIG 123 (134)
T ss_pred HHHHHHHHHHhc---ccCCcceeEeccCCeeChhhcCeEEEEecCceeEeEEeccCccceeeccccCCcccCcCCCCCcC
Confidence 589999998754 34557899999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccccceecC
Q 034541 82 ATHSSRFIPLK 92 (92)
Q Consensus 82 at~ss~f~plk 92 (92)
||+||+|||||
T Consensus 124 AT~sS~fvplK 134 (134)
T PRK04038 124 ATRSSKFVPLK 134 (134)
T ss_pred ccccccceeCc
Confidence 99999999997
No 4
>KOG0898 consensus 40S ribosomal protein S15 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.8e-42 Score=246.96 Aligned_cols=92 Identities=88% Similarity=1.380 Sum_probs=90.2
Q ss_pred ChHHHHHHHHhhhCCCCCCCCceEeeccCceecccccccEEEEecCcceeeeccCCCcceeeeeEEeeeEecccCCCCCC
Q 034541 1 MALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRPGI 80 (92)
Q Consensus 1 ~~ll~k~~k~~~~~~~~~k~~~ikt~sR~s~IlP~~vg~~~~VyNGk~f~~v~I~~eMIG~klGEFa~Trk~~~h~k~G~ 80 (92)
+.|+++||+|++.+++.++|++++||.||++|+|+|||..|+|||||.|.+|+|+||||||+||||++|+||++|++||+
T Consensus 61 ~~liKklrkAkk~A~~~ekpe~VkTHlR~mII~PEMvGs~VGVyNGK~FnqvEiKPEMIGhYL~eFsiTykpvkHgrpgi 140 (152)
T KOG0898|consen 61 HSLIKKLRKAKKEAPPMEKPEVVKTHLRNMIIVPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFSITYKPVKHGRPGI 140 (152)
T ss_pred HHHHHHHHHHHhhcCcccCcHHHHHHhhcceeeHhhhcceEEEecCcccceeeccHHHHhhhhhhccccccccccCCCCC
Confidence 46999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCccccceecC
Q 034541 81 GATHSSRFIPLK 92 (92)
Q Consensus 81 gat~ss~f~plk 92 (92)
|||+||+|+|||
T Consensus 141 gat~SsrfipLk 152 (152)
T KOG0898|consen 141 GATHSSRFIPLK 152 (152)
T ss_pred CcccccccccCC
Confidence 999999999997
No 5
>COG0185 RpsS Ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.9e-41 Score=225.36 Aligned_cols=80 Identities=51% Similarity=0.755 Sum_probs=75.1
Q ss_pred hHHHHHHHHhhhCCCCCCCCceEeeccCceecccccccEEEEecCcceeeeccCCCcceeeeeEEeeeEecccCCCCCCC
Q 034541 2 ALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRPGIG 81 (92)
Q Consensus 2 ~ll~k~~k~~~~~~~~~k~~~ikt~sR~s~IlP~~vg~~~~VyNGk~f~~v~I~~eMIG~klGEFa~Trk~~~h~k~G~g 81 (92)
.||+|++++++. +++ ++|+||||+|+|||+|||++|+||||++|+||+|+||||||||||||+||+++.|+.+|++
T Consensus 14 ~Ll~Kv~~~~~~---~~k-~~IkT~sR~stIlPemVG~ti~VhNGk~~vpV~I~~eMVGHkLGEFapTR~~~~H~~~~~~ 89 (93)
T COG0185 14 HLLKKVRKAKES---GKK-KPIKTWSRRSTILPEMVGLTIAVHNGKKFVPVEITEEMVGHKLGEFAPTRTFVGHGADGIK 89 (93)
T ss_pred HHHHHHHHHHhc---cCC-CcceeeecccEechhhcCcEEEEEcCceEEEEEechhhcceecccccceecccccCCCCcC
Confidence 589999999863 334 8999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcc
Q 034541 82 ATHS 85 (92)
Q Consensus 82 at~s 85 (92)
||+|
T Consensus 90 atr~ 93 (93)
T COG0185 90 ATRS 93 (93)
T ss_pred cccC
Confidence 9986
No 6
>CHL00050 rps19 ribosomal protein S19
Probab=100.00 E-value=9.5e-34 Score=190.66 Aligned_cols=71 Identities=37% Similarity=0.505 Sum_probs=64.7
Q ss_pred hHHHHHHHHhhhCCCCCCCCceEeeccCceecccccccEEEEecCcceeeeccCCCcceeeeeEEeeeEecccCC
Q 034541 2 ALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHG 76 (92)
Q Consensus 2 ~ll~k~~k~~~~~~~~~k~~~ikt~sR~s~IlP~~vg~~~~VyNGk~f~~v~I~~eMIG~klGEFa~Trk~~~h~ 76 (92)
.||+++++++. ..++++|+||||+|+|||+|||++|+||||++|++|+|+||||||||||||+||+++.|+
T Consensus 14 ~Ll~ki~~~~~----~~~~~~ikT~sR~s~IlP~~vg~t~~VyNGk~fv~v~I~~eMVGhklGEFa~TRk~~~h~ 84 (92)
T CHL00050 14 HLLKKIEKLNT----KEEKEIIVTWSRASTIIPTMIGHTIAVHNGKEHIPIYITDQMVGHKLGEFAPTRNFRGHA 84 (92)
T ss_pred HHHHHHHHhhh----ccCCccceEEccccEeChhhcCcEEEEEcCceEEEEEEccccccceeeeEeeeecccccc
Confidence 57888887753 234578999999999999999999999999999999999999999999999999999995
No 7
>TIGR01050 rpsS_bact ribosomal protein S19, bacterial/organelle. the Archaea may be designated S15 or S19.
Probab=100.00 E-value=1.7e-33 Score=189.47 Aligned_cols=73 Identities=38% Similarity=0.571 Sum_probs=66.1
Q ss_pred hHHHHHHHHhhhCCCCCCCCceEeeccCceecccccccEEEEecCcceeeeccCCCcceeeeeEEeeeEecccCCCC
Q 034541 2 ALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRP 78 (92)
Q Consensus 2 ~ll~k~~k~~~~~~~~~k~~~ikt~sR~s~IlP~~vg~~~~VyNGk~f~~v~I~~eMIG~klGEFa~Trk~~~h~k~ 78 (92)
+|++++++++. ..++++|+||||+|+|+|+|||++|+||||++|++|+|++|||||||||||+||++..|++.
T Consensus 14 ~Ll~ki~k~~~----~~~~~~ikT~sR~s~IlP~~vg~~i~VynGk~fv~v~I~~~MvGhklGEFa~TRk~~~h~~~ 86 (92)
T TIGR01050 14 HLLKKVEKLNE----SGKKKVIKTWSRRSTIIPEMIGHTIAVHNGKKFIPVYITEDMVGHKLGEFAPTRTFKGHAKS 86 (92)
T ss_pred HHHHHHHHhhc----ccCCCceEEEecccEEChHHCCcEEEEEcCceEEEEEeCcCeecceeeeeeceeeccccccC
Confidence 57888888762 23467899999999999999999999999999999999999999999999999999999753
No 8
>PRK00357 rpsS 30S ribosomal protein S19; Reviewed
Probab=100.00 E-value=2.5e-33 Score=188.79 Aligned_cols=72 Identities=33% Similarity=0.522 Sum_probs=65.6
Q ss_pred hHHHHHHHHhhhCCCCCCCCceEeeccCceecccccccEEEEecCcceeeeccCCCcceeeeeEEeeeEecccCCC
Q 034541 2 ALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGR 77 (92)
Q Consensus 2 ~ll~k~~k~~~~~~~~~k~~~ikt~sR~s~IlP~~vg~~~~VyNGk~f~~v~I~~eMIG~klGEFa~Trk~~~h~k 77 (92)
+||+++++++.. + ++++|+||||+|+|+|+|||++|.||||++|++|+|+||||||||||||+||+++.|+.
T Consensus 14 ~Ll~ki~k~~~~---~-~~~~ikT~sR~s~IlP~~vg~~i~VyNGk~fv~v~I~~emiGhklGEFa~Tr~~~~H~~ 85 (92)
T PRK00357 14 HLLKKVEKANES---G-DKKVIKTWSRRSTILPEFVGLTIAVHNGRKHVPVYVTENMVGHKLGEFAPTRTFRGHAA 85 (92)
T ss_pred HHHHHHHHHhhc---c-CCCceEEeeccCCcCHHHCCceEEEEcCCeeEeEEeccCccceeeeeecceeccccccc
Confidence 588999988632 2 45789999999999999999999999999999999999999999999999999999974
No 9
>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=99.97 E-value=1.4e-32 Score=180.69 Aligned_cols=56 Identities=55% Similarity=0.953 Sum_probs=54.7
Q ss_pred CCceEeeccCceecccccccEEEEecCcceeeeccCCCcceeeeeEEeeeEecccC
Q 034541 20 PEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKH 75 (92)
Q Consensus 20 ~~~ikt~sR~s~IlP~~vg~~~~VyNGk~f~~v~I~~eMIG~klGEFa~Trk~~~h 75 (92)
+++++||+|+|+|+|+|||++|+||||++|++|+|++||||||||||++||+++.|
T Consensus 26 k~~ikt~~R~s~IlP~~vg~~i~VyNGk~f~~i~I~~~miG~klGEF~~Trk~~~H 81 (81)
T PF00203_consen 26 KKVIKTHSRSSTILPEMVGKTIGVYNGKKFVPIKITPEMIGHKLGEFAPTRKPVKH 81 (81)
T ss_dssp TSEEEESSTTSBBSGTGTTSEEEEESSSSEEEEECSSTGTSSBCGCGSSSSSTSCT
T ss_pred CcceEEEeCCCCcccceeceEEEEecCceEEEEEecccccceEeeceeeecccCCC
Confidence 38999999999999999999999999999999999999999999999999999988
No 10
>PLN03147 ribosomal protein S19; Provisional
Probab=99.97 E-value=9.1e-32 Score=181.38 Aligned_cols=69 Identities=22% Similarity=0.341 Sum_probs=61.3
Q ss_pred HHHHHHhhhCCCCCCCCceEeeccCceecccccccEEEEecCcceeeeccCCCcceeeeeEEeeeEecccCCCCC
Q 034541 5 KKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRPG 79 (92)
Q Consensus 5 ~k~~k~~~~~~~~~k~~~ikt~sR~s~IlP~~vg~~~~VyNGk~f~~v~I~~eMIG~klGEFa~Trk~~~h~k~G 79 (92)
.+++++++. .++|+||||+|+|+|+|||++|+||||++|++|+|+||||||||||||+||+++.|..+.
T Consensus 14 ~k~~~~~~~------~~~iktwSR~S~IlP~~vg~ti~VyNGk~fv~v~It~~MVGhKlGEFa~Trk~~~hk~~~ 82 (92)
T PLN03147 14 ARIKKKRDL------LLGKKIWSHRSSILPDFVDCSVLIYNGKTHIRCKITEGKVGHKFGEFAFTRKRRPHRAII 82 (92)
T ss_pred HHHHHHHhc------CCceeEEcccceECHHHcCCEEEEeCCCceEEEEecCCccceeeeccccEecccCCCCcc
Confidence 356655532 158999999999999999999999999999999999999999999999999999998773
No 11
>KOG0899 consensus Mitochondrial/chloroplast ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=2.5e-30 Score=173.26 Aligned_cols=58 Identities=34% Similarity=0.605 Sum_probs=55.7
Q ss_pred CceEeeccCceecccccccEEEEecCcceeeeccCCCcceeeeeEEeeeEecccCCCC
Q 034541 21 EPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRP 78 (92)
Q Consensus 21 ~~ikt~sR~s~IlP~~vg~~~~VyNGk~f~~v~I~~eMIG~klGEFa~Trk~~~h~k~ 78 (92)
-+|+||||+|||||+|||.+|.|||||+|++|+|+|+|||||||||++|||.+.|.+.
T Consensus 35 ~pikt~sRasTIlP~~Vg~~~~IhNGk~~v~vkIte~mVGHKlGEFapTrk~~~~akt 92 (93)
T KOG0899|consen 35 APIKTWSRASTILPTMVGHTFAIHNGKEHVPVKITEDMVGHKLGEFAPTRKFFGHAKT 92 (93)
T ss_pred CceeehhhhcchhhhhhCceEEEecCcceeeEEeecchhccccccccchhhhhccccC
Confidence 4799999999999999999999999999999999999999999999999999999763
No 12
>KOG3265 consensus Histone chaperone involved in gene silencing [Transcription; Chromatin structure and dynamics]
Probab=22.05 E-value=65 Score=25.51 Aligned_cols=20 Identities=25% Similarity=0.559 Sum_probs=16.3
Q ss_pred cccccccEEE----EecCcceeee
Q 034541 33 VPEMIGSIIG----VYNGKTFNQV 52 (92)
Q Consensus 33 lP~~vg~~~~----VyNGk~f~~v 52 (92)
+.++||.|+- =|+|++|++|
T Consensus 86 ~~d~vGVTviLltC~Y~gQEFIRv 109 (250)
T KOG3265|consen 86 EDDIVGVTVILLTCSYRGQEFIRV 109 (250)
T ss_pred ccceeeeEEEEEEEEEcCceeEEE
Confidence 5688998765 3999999986
No 13
>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=21.06 E-value=87 Score=18.68 Aligned_cols=30 Identities=17% Similarity=0.189 Sum_probs=19.6
Q ss_pred cEEEEecCcceeeeccCCCcceeeeeEEeeeEe
Q 034541 39 SIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYK 71 (92)
Q Consensus 39 ~~~~VyNGk~f~~v~I~~eMIG~klGEFa~Trk 71 (92)
.++.-|+|+.++.|..=-+ . .-||..||+|
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 4677899998877743333 2 2488888775
No 14
>PF07833 Cu_amine_oxidN1: Copper amine oxidase N-terminal domain; InterPro: IPR012854 Amine oxidases (AO) are enzymes that catalyse the oxidation of a wide range of biogenic amines including many neurotransmitters, histamine and xenobiotic amines. There are two classes of amine oxidases: flavin-containing (1.4.3.4 from EC) and copper-containing (1.4.3.6 from EC). Copper-containing AO act as a disulphide-linked homodimer. They catalyse the oxidation of primary amines to aldehydes, with the subsequent release of ammonia and hydrogen peroxide, which requires one copper ion per subunit and topaquinone as cofactor []: RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2 Copper-containing amine oxidases are found in bacteria, fungi, plants and animals. In prokaryotes, the enzyme enables various amine substrates to be used as sources of carbon and nitrogen [, ]. In eukaryotes they have a broader range of functions, including cell differentiation and growth, wound healing, detoxification and cell signalling []. The copper amine oxidases occur as mushroom-shaped homodimers of 70-95 kDa, each monomer containing a copper ion and a covalently bound redox cofactor, topaquinone (TPQ). TPQ is formed by post-translational modification of a conserved tyrosine residue. The copper ion is coordinated with three histidine residues and two water molecules in a distorted square pyramidal geometry, and has a dual function in catalysis and TPQ biogenesis. The catalytic domain is the largest of the 3-4 domains found in copper amine oxidases, and consists of a beta sandwich of 18 strands in two sheets. The active site is buried and requires a conformational change to allow the substrate access. The two N-terminal domains share a common structural fold, its core consisting of a five-stranded antiparallel beta sheet twisted around an alpha helix. The D1 domains from the two subunits comprise the stalk, of the mushroom-shaped dimer, and interact with each other but do not pack tightly against each other [, ]. This entry represents a domain found at the N-terminal of certain copper amine oxidases, as well as in related proteins such as cell wall hydrolase and N-acetylmuramoyl-L-alanine amidase. This domain consists of a five-stranded antiparallel beta-sheet twisted around an alpha helix [, ]. ; PDB: 1SPU_A 2WGQ_A 2WO0_A 1JRQ_A 1QAF_B 1D6U_B 1QAL_A 2WOF_A 1OAC_B 1QAK_A ....
Probab=20.77 E-value=15 Score=22.40 Aligned_cols=21 Identities=24% Similarity=0.458 Sum_probs=12.0
Q ss_pred ecCcceeeeccCCCcceeeee
Q 034541 44 YNGKTFNQVEIKPEMIGHYLA 64 (92)
Q Consensus 44 yNGk~f~~v~I~~eMIG~klG 64 (92)
+||+.|+|+..-.+.+|..+-
T Consensus 1 ~~g~~~vPl~~i~~~lg~~v~ 21 (93)
T PF07833_consen 1 KDGKTYVPLRFIAEALGAKVS 21 (93)
T ss_dssp -----EEEHHHHHHHHT-EEE
T ss_pred CCcEEEEEHHHHHHHcCCEEE
Confidence 588889998888888887654
Done!