Query 027812
Match_columns 218
No_of_seqs 129 out of 1036
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 15:33:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027812.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027812hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00160 rpl9 ribosomal protei 100.0 2.9E-47 6.4E-52 313.0 16.2 148 40-217 4-152 (153)
2 TIGR00158 L9 ribosomal protein 100.0 7.3E-47 1.6E-51 309.2 16.2 146 42-217 1-147 (148)
3 PRK00137 rplI 50S ribosomal pr 100.0 3.3E-46 7.2E-51 305.0 16.6 146 42-217 1-146 (147)
4 COG0359 RplI Ribosomal protein 100.0 1.1E-44 2.4E-49 295.3 15.1 146 42-217 1-146 (148)
5 PRK14538 putative bifunctional 100.0 1.5E-37 3.2E-42 310.0 13.1 146 41-216 688-833 (838)
6 KOG4607 Mitochondrial ribosoma 99.9 3.5E-24 7.6E-29 182.6 8.2 156 29-215 36-192 (222)
7 PF01281 Ribosomal_L9_N: Ribos 99.9 2.3E-24 5E-29 145.3 3.0 47 42-88 1-47 (48)
8 PF03948 Ribosomal_L9_C: Ribos 99.9 1.5E-22 3.3E-27 152.1 10.4 85 115-217 2-86 (87)
9 PF10045 DUF2280: Uncharacteri 62.8 3 6.4E-05 32.6 0.5 32 157-188 21-52 (104)
10 PF08766 DEK_C: DEK C terminal 46.9 9.6 0.00021 25.7 0.9 23 154-176 19-41 (54)
11 PF00571 CBS: CBS domain CBS d 38.8 28 0.00061 22.3 2.2 17 150-166 40-56 (57)
12 PF07523 Big_3: Bacterial Ig-l 30.5 74 0.0016 21.8 3.3 25 183-215 43-67 (67)
13 PF13592 HTH_33: Winged helix- 25.0 39 0.00085 23.0 1.1 26 154-179 3-28 (60)
14 PRK09184 acyl carrier protein; 21.7 48 0.001 24.7 1.1 24 155-178 44-67 (89)
15 PF06560 GPI: Glucose-6-phosph 21.2 66 0.0014 27.4 1.9 26 43-68 94-128 (182)
No 1
>CHL00160 rpl9 ribosomal protein L9; Provisional
Probab=100.00 E-value=2.9e-47 Score=312.97 Aligned_cols=148 Identities=22% Similarity=0.420 Sum_probs=132.0
Q ss_pred cceEEEEeccccccCCCCceEEeCCCcccccccccCccccchHHHHHHHHHHHHhcCCchHHHHHHHhhhhhhhHHHHHH
Q 027812 40 RRLEVILTTKVDKLGKAGETVKVAPGYFRNHLMPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEK 119 (218)
Q Consensus 40 kkmkVILlkdV~~LGk~GdiV~Vk~GYARNfLiP~glAv~at~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~a~~ 119 (218)
++|+|||++||++||++||+|+|+||||||||||+|+|++||+.|++.++..++..+ +++++..++|++
T Consensus 4 kkmkVIL~~dV~~LGk~Gdiv~Vk~GYaRNyLiP~glA~~AT~~n~~~~e~~~~~~~-----------~~~~~~~~~a~~ 72 (153)
T CHL00160 4 KKIQVILKENIQKLGKSGTVIKVKSGYARNYLIPNKMAKVATQGSLKQQKMYQKILD-----------LKLKEAKEKCLK 72 (153)
T ss_pred ceEEEEEcccccccCCCCCEEEEcCchHhhhhcccCchhhCCHHHHHHHHHHHHHHH-----------HHHHHHHHHHHH
Confidence 569999999999999999999999999999999999999999999998887776421 233456778899
Q ss_pred HHHHHhcC-ceEEEEeccccccccccCCCCCceeeeccCHHHHHHHHHhhcCCcccCCcccCCCCCccceeEEEEEEcCC
Q 027812 120 AARRLENA-RLVLRRFPNIEKLRSRESKDVPIELRSPVTKEELVAEVSRQLSISIEPENLHLPSPLSAFGEYEVPMRLPK 198 (218)
Q Consensus 120 ~~~kL~~~-~l~~~~~~~~~~~~~k~g~~~~~klfGSVT~~dI~~~L~~q~gi~Idk~~I~l~~pIk~~G~y~V~I~L~~ 198 (218)
++++|++. .++|.++++++ |+||||||+.||+++|.+++|++||+++|.||+ |+++|+|.|+|+||+
T Consensus 73 la~~l~~~~~~~i~~k~ge~-----------gklfGSVt~~dIa~~l~~~~g~~idk~~I~l~~-Ik~~G~~~v~v~L~~ 140 (153)
T CHL00160 73 VKQLLEEIQKFSVKKKVGEN-----------NQIFGSVTEKEISQIIKNKTNIDLEKQNIELPE-IKTIGIYNIEIKLTS 140 (153)
T ss_pred HHHHhhCCceEEEEEEeCCC-----------CeEEcccCHHHHHHHHHHhhCCccccceeehhh-ccccEeEEEEEEecC
Confidence 99999998 58888777443 399999999999999988889999999999998 999999999999999
Q ss_pred CCCCCCceEEEEEEEEEEe
Q 027812 199 AIPLPEGKVQWTLNVKVRG 217 (218)
Q Consensus 199 ~v~~p~~~~~~~l~V~V~~ 217 (218)
+| +++++|+|..
T Consensus 141 ~V-------~a~i~v~V~~ 152 (153)
T CHL00160 141 DV-------KANINLQILP 152 (153)
T ss_pred Cc-------EEEEEEEEEE
Confidence 98 7999999974
No 2
>TIGR00158 L9 ribosomal protein L9. Ribosomal protein L9 appears to be universal in, but restricted to, eubacteria and chloroplast.
Probab=100.00 E-value=7.3e-47 Score=309.20 Aligned_cols=146 Identities=27% Similarity=0.398 Sum_probs=130.4
Q ss_pred eEEEEeccccccCCCCceEEeCCCcccccccccCccccchHHHHHHHHHHHHhcCCchHHHHHHHhhhhhhhHHHHHHHH
Q 027812 42 LEVILTTKVDKLGKAGETVKVAPGYFRNHLMPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAA 121 (218)
Q Consensus 42 mkVILlkdV~~LGk~GdiV~Vk~GYARNfLiP~glAv~at~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~a~~~~ 121 (218)
|+|||++||+|||++||+|+|+||||||||||+|+|++||++|++.++.+++..+ +..++...+|++++
T Consensus 1 MkVIL~~dV~~lGk~GdiV~Vk~GYaRNyLiP~g~A~~aT~~nl~~~e~~~~~~~-----------~~~~~~~~~a~~l~ 69 (148)
T TIGR00158 1 MKVILLEDVANLGKRGDVVEVKDGYARNFLIPKGLAVPATKKNIEFFEARRKKLE-----------EKLAANKAAAARLK 69 (148)
T ss_pred CeEEEcccccccCCCCCEEEEcccchhhhhcccCchhhCCHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHH
Confidence 8999999999999999999999999999999999999999999998888776422 23345577888999
Q ss_pred HHHhcCceEEEEeccccccccccCCCCCceeeeccCHHHHHHHHHhhcCCcccCCcccCCCC-CccceeEEEEEEcCCCC
Q 027812 122 RRLENARLVLRRFPNIEKLRSRESKDVPIELRSPVTKEELVAEVSRQLSISIEPENLHLPSP-LSAFGEYEVPMRLPKAI 200 (218)
Q Consensus 122 ~kL~~~~l~~~~~~~~~~~~~k~g~~~~~klfGSVT~~dI~~~L~~q~gi~Idk~~I~l~~p-Ik~~G~y~V~I~L~~~v 200 (218)
++|++..++|.++++++ |+||||||++||+++|.++ |++||+++|.||+| |+++|+|+|+|+||++|
T Consensus 70 ~~l~~~~~~i~~k~ge~-----------gklfGSVt~~~I~~~l~~~-g~~idk~~I~l~~~~Ik~~G~y~v~i~L~~~V 137 (148)
T TIGR00158 70 EVLELGTLTISKKVGDE-----------GKLFGSITTKQIADALKAA-GLDLDKKKIELPDGVIRTTGEHEVTIKLHEEV 137 (148)
T ss_pred HHhcCcEEEEEEEeCCC-----------CeEEEeECHHHHHHHHHHc-CCcccHhhEECCCCceeceEEEEEEEEEcCCc
Confidence 99999888888777443 3999999999999999865 99999999999986 99999999999999998
Q ss_pred CCCCceEEEEEEEEEEe
Q 027812 201 PLPEGKVQWTLNVKVRG 217 (218)
Q Consensus 201 ~~p~~~~~~~l~V~V~~ 217 (218)
+++++|+|..
T Consensus 138 -------~a~i~v~V~~ 147 (148)
T TIGR00158 138 -------FAVLKVIVVP 147 (148)
T ss_pred -------EEEEEEEEEE
Confidence 7999999975
No 3
>PRK00137 rplI 50S ribosomal protein L9; Reviewed
Probab=100.00 E-value=3.3e-46 Score=304.96 Aligned_cols=146 Identities=29% Similarity=0.473 Sum_probs=131.8
Q ss_pred eEEEEeccccccCCCCceEEeCCCcccccccccCccccchHHHHHHHHHHHHhcCCchHHHHHHHhhhhhhhHHHHHHHH
Q 027812 42 LEVILTTKVDKLGKAGETVKVAPGYFRNHLMPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAA 121 (218)
Q Consensus 42 mkVILlkdV~~LGk~GdiV~Vk~GYARNfLiP~glAv~at~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~a~~~~ 121 (218)
|+|||++||+|||++||+|+|+||||||||||+|+|+|||+++++.++.+++.. ++++++.+.+|++++
T Consensus 1 mkVIL~~dv~~lGk~Gdiv~Vk~GYaRNyLiP~~lA~~aT~~~~~~~~~~~~~~-----------~~~~~~~~~~a~~l~ 69 (147)
T PRK00137 1 MKVILLEDVKNLGKKGDVVEVKDGYARNFLIPQGKAVRATKGNLKQLEARRAEL-----------EAKAAEELAEAEALA 69 (147)
T ss_pred CeEEEcccccccCCCCCEEEEcCcchhhhhccCCceeeCCHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHH
Confidence 899999999999999999999999999999999999999999999888777542 223456688899999
Q ss_pred HHHhcCceEEEEeccccccccccCCCCCceeeeccCHHHHHHHHHhhcCCcccCCcccCCCCCccceeEEEEEEcCCCCC
Q 027812 122 RRLENARLVLRRFPNIEKLRSRESKDVPIELRSPVTKEELVAEVSRQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIP 201 (218)
Q Consensus 122 ~kL~~~~l~~~~~~~~~~~~~k~g~~~~~klfGSVT~~dI~~~L~~q~gi~Idk~~I~l~~pIk~~G~y~V~I~L~~~v~ 201 (218)
+.|++..++|.++++++ |+||||||++||+++|.++ |++||+++|.||+||+++|+|.|+|+||++|
T Consensus 70 ~~l~~~~l~i~~k~g~~-----------gklfGsVt~~~I~~~l~~~-g~~idk~~I~l~~~Ik~~G~y~v~i~L~~~v- 136 (147)
T PRK00137 70 EKLEGLTVTIKAKAGED-----------GKLFGSVTTKDIAEALKKQ-GIEIDKRKIELPGPIKTLGEYEVPVKLHPEV- 136 (147)
T ss_pred HHhhCCEEEEEEEcCCC-----------CeEEeeeCHHHHHHHHHHc-CCccCHHHeECCCcccccEEEEEEEEECCCc-
Confidence 99999889888877433 3999999999999999877 9999999999999999999999999999998
Q ss_pred CCCceEEEEEEEEEEe
Q 027812 202 LPEGKVQWTLNVKVRG 217 (218)
Q Consensus 202 ~p~~~~~~~l~V~V~~ 217 (218)
+++|+|+|..
T Consensus 137 ------~a~l~v~V~~ 146 (147)
T PRK00137 137 ------TATIKVNVVA 146 (147)
T ss_pred ------EEEEEEEEEE
Confidence 7999999975
No 4
>COG0359 RplI Ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-44 Score=295.34 Aligned_cols=146 Identities=28% Similarity=0.425 Sum_probs=131.4
Q ss_pred eEEEEeccccccCCCCceEEeCCCcccccccccCccccchHHHHHHHHHHHHhcCCchHHHHHHHhhhhhhhHHHHHHHH
Q 027812 42 LEVILTTKVDKLGKAGETVKVAPGYFRNHLMPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAA 121 (218)
Q Consensus 42 mkVILlkdV~~LGk~GdiV~Vk~GYARNfLiP~glAv~at~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~a~~~~ 121 (218)
|+|||++||++||+.||+|+|++|||||||||+|+|++||+.|++.++.+++.. ++..++.+.+++.++
T Consensus 1 MkVILl~dV~~lGk~Gdiv~VkdGYarNfLiPkglAv~At~~n~~~~e~~r~~~-----------e~~~~~~~~~a~~lk 69 (148)
T COG0359 1 MKVILLEDVKGLGKKGDIVEVKDGYARNFLIPKGLAVPATKGNLKLLEARRAKL-----------EKKAAEELAEAEALK 69 (148)
T ss_pred CeEEEecchhhcCCCCCEEEecchhhhhhhccccchhhCCHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999888866542 223455678899999
Q ss_pred HHHhcCceEEEEeccccccccccCCCCCceeeeccCHHHHHHHHHhhcCCcccCCcccCCCCCccceeEEEEEEcCCCCC
Q 027812 122 RRLENARLVLRRFPNIEKLRSRESKDVPIELRSPVTKEELVAEVSRQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIP 201 (218)
Q Consensus 122 ~kL~~~~l~~~~~~~~~~~~~k~g~~~~~klfGSVT~~dI~~~L~~q~gi~Idk~~I~l~~pIk~~G~y~V~I~L~~~v~ 201 (218)
++|+...++|.++++++ |+||||||++||++++.++ |++||++.|.+|++|+++|+|+|+|+||++|
T Consensus 70 ~~Le~~~~~i~~kag~~-----------GklfGSVt~~dIa~~l~~~-g~~idk~~i~l~~~ik~~G~~~V~vkLh~eV- 136 (148)
T COG0359 70 EKLEGKTVEIAVKAGED-----------GKLFGSVTSKDIAEALKAA-GFKLDKRKIRLPNGIKTLGEHEVEVKLHEEV- 136 (148)
T ss_pred HHhhCceEEEEEEcCCC-----------CceeccccHHHHHHHHHHc-CCCcchheeEcCchhhhcceeEEEEEecCce-
Confidence 99999778888877543 3999999999999999987 9999999999999999999999999999998
Q ss_pred CCCceEEEEEEEEEEe
Q 027812 202 LPEGKVQWTLNVKVRG 217 (218)
Q Consensus 202 ~p~~~~~~~l~V~V~~ 217 (218)
+++++|.|..
T Consensus 137 ------~a~v~v~V~~ 146 (148)
T COG0359 137 ------TATVKVNVVA 146 (148)
T ss_pred ------EEEEEEEEEe
Confidence 7999999975
No 5
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=100.00 E-value=1.5e-37 Score=309.96 Aligned_cols=146 Identities=22% Similarity=0.308 Sum_probs=131.4
Q ss_pred ceEEEEeccccccCCCCceEEeCCCcccccccccCccccchHHHHHHHHHHHHhcCCchHHHHHHHhhhhhhhHHHHHHH
Q 027812 41 RLEVILTTKVDKLGKAGETVKVAPGYFRNHLMPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKA 120 (218)
Q Consensus 41 kmkVILlkdV~~LGk~GdiV~Vk~GYARNfLiP~glAv~at~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~a~~~ 120 (218)
.|||||++||+|||++||+|+|+|||| |||||+|+|++||++|++.++.+++.. ++++++..++|+++
T Consensus 688 ~MkVIL~~dv~~lGk~Gdvv~Vk~GYa-NfLiP~~~A~~aT~~nlk~~e~~~~~~-----------~~~~~~~~~~a~~l 755 (838)
T PRK14538 688 NMEIILLTDIKNKGKKHEIIKVNNGYG-NFLIQNKKALLADKENLAKIKKKKILE-----------QEKKRNHELLMKKL 755 (838)
T ss_pred hhhHHHHHHHHhcCCCCCEEEECCCch-hhhccCCchhhcCHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHH
Confidence 599999999999999999999999999 999999999999999999888877642 22345567788999
Q ss_pred HHHHhcCceEEEEeccccccccccCCCCCceeeeccCHHHHHHHHHhhcCCcccCCcccCCCCCccceeEEEEEEcCCCC
Q 027812 121 ARRLENARLVLRRFPNIEKLRSRESKDVPIELRSPVTKEELVAEVSRQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAI 200 (218)
Q Consensus 121 ~~kL~~~~l~~~~~~~~~~~~~k~g~~~~~klfGSVT~~dI~~~L~~q~gi~Idk~~I~l~~pIk~~G~y~V~I~L~~~v 200 (218)
+++|++..+++.++++++ |+||||||++||+++|++++|++||++.|.||+|||++|+|.|+|+||++|
T Consensus 756 ~~~l~~~~~~i~~k~ge~-----------gklfGSVt~~~I~~~l~~~~g~~idk~~I~l~~~Ik~~G~~~v~i~L~~~V 824 (838)
T PRK14538 756 KSEIDNKKITLDIQLGPK-----------GKIYGKITLKQIVEEFHKIHNITIDRKKISLENEIISVGIYPVDVFLTDQI 824 (838)
T ss_pred HHHhhCcEEEEEEEeCCC-----------CeeeeccCHHHHHHHHHHhhCCccccceeeCCCcccccEEEEEEEEEcCCe
Confidence 999999888888877544 399999999999999998899999999999999999999999999999998
Q ss_pred CCCCceEEEEEEEEEE
Q 027812 201 PLPEGKVQWTLNVKVR 216 (218)
Q Consensus 201 ~~p~~~~~~~l~V~V~ 216 (218)
+++++|+|.
T Consensus 825 -------~a~i~v~V~ 833 (838)
T PRK14538 825 -------KATFFLNVI 833 (838)
T ss_pred -------EEEEEEEEE
Confidence 799999886
No 6
>KOG4607 consensus Mitochondrial ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=99.90 E-value=3.5e-24 Score=182.63 Aligned_cols=156 Identities=28% Similarity=0.317 Sum_probs=116.7
Q ss_pred ceeEeeccccccceEEEEeccccccCCCCceEEeCCCcccccccccCccccchHHHHHHHHHHHHhcCCchHHHHHHHhh
Q 027812 29 PLLYSCQGVRYRRLEVILTTKVDKLGKAGETVKVAPGYFRNHLMPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRK 108 (218)
Q Consensus 29 ~l~~~~~~~~~kkmkVILlkdV~~LGk~GdiV~Vk~GYARNfLiP~glAv~at~~~~~~~~~~~~~~~~~~~e~~~~~~~ 108 (218)
+|+..+++++++.++|||++||+|||++||+|+|++||+||+|+|+|+|+|+||.+...+...+.. . .
T Consensus 36 ~lv~~~~~k~k~~levIL~~~Ve~lG~qGdvVsVk~g~~RN~Llp~glAvy~tp~~~~~~k~~~~e-------~----~- 103 (222)
T KOG4607|consen 36 ELVEFTQKKPKPNLEVILKTDVEKLGKQGDVVSVKRGYFRNFLLPKGLAVYNTPLNLKKYKLREQE-------E----E- 103 (222)
T ss_pred hHhHhhhccCCcceeeeeehhhhhhcccCcEEEeecchhhhhcccccccccCChhhHHHHHHHHHH-------H----H-
Confidence 899999999999999999999999999999999999999999999999999999986543333221 0 0
Q ss_pred hhhhhHHHHHHHHHHHhcCceEEEEeccccccccccCCCCCcee-eeccCHHHHHHHHHhhcCCcccCCcccCCCCCccc
Q 027812 109 SEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRESKDVPIEL-RSPVTKEELVAEVSRQLSISIEPENLHLPSPLSAF 187 (218)
Q Consensus 109 ~~~~~~~~a~~~~~kL~~~~l~~~~~~~~~~~~~k~g~~~~~kl-fGSVT~~dI~~~L~~q~gi~Idk~~I~l~~pIk~~ 187 (218)
.+..+.++..+....|+...+.+.++.+.. ..| +|+|+++.....+.++.-+++|++.|..|. ++.-
T Consensus 104 ~~k~~vk~e~k~V~~lqt~v~~~~~~k~~k-----------w~l~~~~V~~~l~~gv~~~~~t~~l~k~~vs~P~-~k~e 171 (222)
T KOG4607|consen 104 AEKIRVKEEAKVVAVLQTVVLFKVMNKGGK-----------WKLNPNLVKASLRKGVIVAELTIKLDKELVSGPI-TKEE 171 (222)
T ss_pred hhhhccHHHHHHHHHHHhhhhhheeccCCc-----------eeecHHHHHHHHhcceEeccccccCcccccCCCc-cccc
Confidence 012223333333346776666555554322 244 778888777777777777888999888885 7888
Q ss_pred eeEEEEEEcCCCCCCCCceEEEEEEEEE
Q 027812 188 GEYEVPMRLPKAIPLPEGKVQWTLNVKV 215 (218)
Q Consensus 188 G~y~V~I~L~~~v~~p~~~~~~~l~V~V 215 (218)
|+|.+.|+++++. ++-+...|
T Consensus 172 ~~~~~~V~in~~~-------~vr~~~~v 192 (222)
T KOG4607|consen 172 GEYICEVKINPDV-------TVRVKIRV 192 (222)
T ss_pred ceEEEEEEECCcc-------eEEeeeee
Confidence 8999999999887 45555544
No 7
>PF01281 Ribosomal_L9_N: Ribosomal protein L9, N-terminal domain; InterPro: IPR020070 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 L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....
Probab=99.89 E-value=2.3e-24 Score=145.35 Aligned_cols=47 Identities=43% Similarity=0.634 Sum_probs=43.4
Q ss_pred eEEEEeccccccCCCCceEEeCCCcccccccccCccccchHHHHHHH
Q 027812 42 LEVILTTKVDKLGKAGETVKVAPGYFRNHLMPKLLAVPNIEKFAHLI 88 (218)
Q Consensus 42 mkVILlkdV~~LGk~GdiV~Vk~GYARNfLiP~glAv~at~~~~~~~ 88 (218)
|+|||++||+|||++||+|+|++|||||||+|+|+|+|||+++++.+
T Consensus 1 m~ViL~~dv~~lG~~Gdiv~V~~Gy~RN~L~p~~~A~~at~~~~~~~ 47 (48)
T PF01281_consen 1 MKVILLKDVPGLGKKGDIVEVKPGYARNFLIPQGLAVYATPENLKQL 47 (48)
T ss_dssp -EEEESSCCTTSBSTTEEEE-SHHHHHHTTTTTTSEEECSHHHHHHH
T ss_pred CEEEEcccccccCCCCCEEEEccceeeehccCCCceeeCCHHHHHhc
Confidence 89999999999999999999999999999999999999999998765
No 8
>PF03948 Ribosomal_L9_C: Ribosomal protein L9, C-terminal domain; InterPro: IPR020069 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 L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....
Probab=99.88 E-value=1.5e-22 Score=152.11 Aligned_cols=85 Identities=27% Similarity=0.469 Sum_probs=78.3
Q ss_pred HHHHHHHHHHhcCceEEEEeccccccccccCCCCCceeeeccCHHHHHHHHHhhcCCcccCCcccCCCCCccceeEEEEE
Q 027812 115 REFEKAARRLENARLVLRRFPNIEKLRSRESKDVPIELRSPVTKEELVAEVSRQLSISIEPENLHLPSPLSAFGEYEVPM 194 (218)
Q Consensus 115 ~~a~~~~~kL~~~~l~~~~~~~~~~~~~k~g~~~~~klfGSVT~~dI~~~L~~q~gi~Idk~~I~l~~pIk~~G~y~V~I 194 (218)
++|++++++|++..++|.++++++ |+||||||++||+++|.+++|++||+++|.||+|||++|+|.|+|
T Consensus 2 ~~A~~l~~~l~~~~l~i~~k~g~~-----------gklfGSVt~~dIa~~l~~~~g~~Idk~~I~l~~~IK~~G~~~v~v 70 (87)
T PF03948_consen 2 AEAQALAEKLEGITLTIKRKAGEN-----------GKLFGSVTSKDIAKALKEQTGIEIDKKKIELPEPIKSLGEYEVKV 70 (87)
T ss_dssp HHHHHHHHHHCSSEEEEEECBSSC-----------SSBSSEBSHHHHHHHHHHCCSSSSSSSSBCSSSTBESSEEEEEEE
T ss_pred HHHHHHHHHhcCCEEEEEEEecCC-----------cceecCcCHHHHHHHHHHhhCCeEeccEEECCCchhccEEEEEEE
Confidence 467789999999999999888544 399999999999999999999999999999999999999999999
Q ss_pred EcCCCCCCCCceEEEEEEEEEEe
Q 027812 195 RLPKAIPLPEGKVQWTLNVKVRG 217 (218)
Q Consensus 195 ~L~~~v~~p~~~~~~~l~V~V~~ 217 (218)
+||++| .++++|.|..
T Consensus 71 ~L~~~V-------~a~i~v~V~~ 86 (87)
T PF03948_consen 71 KLHPEV-------SAKIKVNVVA 86 (87)
T ss_dssp EEETTE-------EEEEEEEEEE
T ss_pred EeCCCe-------EEEEEEEEEe
Confidence 999998 7999999975
No 9
>PF10045 DUF2280: Uncharacterized conserved protein (DUF2280); InterPro: IPR018738 This entry is represented by Burkholderia phage Bups phi1, Orf2.36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=62.84 E-value=3 Score=32.57 Aligned_cols=32 Identities=19% Similarity=0.340 Sum_probs=27.5
Q ss_pred CHHHHHHHHHhhcCCcccCCcccCCCCCccce
Q 027812 157 TKEELVAEVSRQLSISIEPENLHLPSPLSAFG 188 (218)
Q Consensus 157 T~~dI~~~L~~q~gi~Idk~~I~l~~pIk~~G 188 (218)
||.++++++++.+|++|++.+++.-+|=|.-|
T Consensus 21 TPs~v~~aVk~eFgi~vsrQqve~yDPTK~aG 52 (104)
T PF10045_consen 21 TPSEVAEAVKEEFGIDVSRQQVESYDPTKRAG 52 (104)
T ss_pred CHHHHHHHHHHHhCCccCHHHHHHcCchHHHH
Confidence 89999999999999999999988766665544
No 10
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=46.89 E-value=9.6 Score=25.65 Aligned_cols=23 Identities=13% Similarity=0.404 Sum_probs=15.8
Q ss_pred eccCHHHHHHHHHhhcCCcccCC
Q 027812 154 SPVTKEELVAEVSRQLSISIEPE 176 (218)
Q Consensus 154 GSVT~~dI~~~L~~q~gi~Idk~ 176 (218)
.+||.++|..+|.+.+|+++..+
T Consensus 19 ~~vT~k~vr~~Le~~~~~dL~~~ 41 (54)
T PF08766_consen 19 DTVTKKQVREQLEERFGVDLSSR 41 (54)
T ss_dssp GG--HHHHHHHHHHH-SS--SHH
T ss_pred hHhhHHHHHHHHHHHHCCCcHHH
Confidence 57999999999999999988754
No 11
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=38.82 E-value=28 Score=22.28 Aligned_cols=17 Identities=12% Similarity=0.233 Sum_probs=15.3
Q ss_pred ceeeeccCHHHHHHHHH
Q 027812 150 IELRSPVTKEELVAEVS 166 (218)
Q Consensus 150 ~klfGSVT~~dI~~~L~ 166 (218)
+++-|.||..||...+.
T Consensus 40 ~~~~G~is~~dl~~~l~ 56 (57)
T PF00571_consen 40 GKLVGIISRSDLLKALL 56 (57)
T ss_dssp SBEEEEEEHHHHHHHHH
T ss_pred CEEEEEEEHHHHHhhhh
Confidence 49999999999999885
No 12
>PF07523 Big_3: Bacterial Ig-like domain (group 3); InterPro: IPR011080 This entry represents bacterial domains with an Ig-like fold. These domains are found in a variety of bacterial surface proteins.; PDB: 2L7Y_A 2KPN_A.
Probab=30.48 E-value=74 Score=21.83 Aligned_cols=25 Identities=28% Similarity=0.328 Sum_probs=18.7
Q ss_pred CCccceeEEEEEEcCCCCCCCCceEEEEEEEEE
Q 027812 183 PLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKV 215 (218)
Q Consensus 183 pIk~~G~y~V~I~L~~~v~~p~~~~~~~l~V~V 215 (218)
.-...|.|.|++.... . +++++|.|
T Consensus 43 d~~~~G~y~Vt~~y~~-~-------t~t~~VtV 67 (67)
T PF07523_consen 43 DTSKAGTYTVTYTYKG-V-------TATFTVTV 67 (67)
T ss_dssp -TTS-CCEEEEEEECT-E-------EEEEEEEE
T ss_pred ecCCCceEEEEEEECC-E-------EEEEEEEC
Confidence 3568899999999996 2 67777776
No 13
>PF13592 HTH_33: Winged helix-turn helix
Probab=25.01 E-value=39 Score=22.98 Aligned_cols=26 Identities=15% Similarity=0.296 Sum_probs=21.1
Q ss_pred eccCHHHHHHHHHhhcCCcccCCccc
Q 027812 154 SPVTKEELVAEVSRQLSISIEPENLH 179 (218)
Q Consensus 154 GSVT~~dI~~~L~~q~gi~Idk~~I~ 179 (218)
+--|..+|++.|.+++|+.+.+..|.
T Consensus 3 ~~wt~~~i~~~I~~~fgv~ys~~~v~ 28 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKYSPSGVY 28 (60)
T ss_pred CcccHHHHHHHHHHHHCCEEcHHHHH
Confidence 45788999999999999988776553
No 14
>PRK09184 acyl carrier protein; Provisional
Probab=21.72 E-value=48 Score=24.71 Aligned_cols=24 Identities=13% Similarity=0.292 Sum_probs=20.6
Q ss_pred ccCHHHHHHHHHhhcCCcccCCcc
Q 027812 155 PVTKEELVAEVSRQLSISIEPENL 178 (218)
Q Consensus 155 SVT~~dI~~~L~~q~gi~Idk~~I 178 (218)
|+..-+|+-++.+.||+.|+....
T Consensus 44 Sld~velv~~lE~~fgi~i~~~~~ 67 (89)
T PRK09184 44 SIDILEIALVISKRYGFQLRSDNP 67 (89)
T ss_pred HHHHHHHHHHHHHHHCCcCCCcch
Confidence 788999999999999999975543
No 15
>PF06560 GPI: Glucose-6-phosphate isomerase (GPI); InterPro: IPR010551 This entry consists of several bacterial and archaeal glucose-6-phosphate isomerase (GPI) proteins (5.3.1.9 from EC), which are involved in glycolysis and in gluconeogenesis and catalyse the conversion of D-glucose 6-phosphate to D-fructose 6-phosphate. The deduced amino acid sequence of the first archaeal PGI isolated from Pyrococcus furiosus revealed that it is not related to its eukaryotic and many of its bacterial counterparts. In contrast, this archaeal PGI shares similarity with the cupin superfamily that consists of a variety of proteins that are generally involved in sugar metabolism in both prokaryotes and eukaryotes [].; GO: 0004347 glucose-6-phosphate isomerase activity, 0006094 gluconeogenesis, 0006096 glycolysis, 0005737 cytoplasm; PDB: 1J3Q_B 1J3R_B 1J3P_A 2GC0_A 1X8E_A 1X82_A 1QY4_B 2GC2_B 1QXJ_A 1QXR_B ....
Probab=21.19 E-value=66 Score=27.38 Aligned_cols=26 Identities=35% Similarity=0.592 Sum_probs=15.9
Q ss_pred EEEEeccccc---------cCCCCceEEeCCCccc
Q 027812 43 EVILTTKVDK---------LGKAGETVKVAPGYFR 68 (218)
Q Consensus 43 kVILlkdV~~---------LGk~GdiV~Vk~GYAR 68 (218)
=++|+++..+ -..+||+|-|.||||-
T Consensus 94 g~~lLq~~~~~~~~~~~~v~~~~G~~v~IPp~yaH 128 (182)
T PF06560_consen 94 GLILLQKEEGDDVGDVIAVEAKPGDVVYIPPGYAH 128 (182)
T ss_dssp EEEEEE-TTS-----EEEEEE-TTEEEEE-TT-EE
T ss_pred EEEEEEecCCCcceeEEEEEeCCCCEEEECCCceE
Confidence 3678888776 1467888888888884
Done!