Query 038179
Match_columns 221
No_of_seqs 125 out of 1035
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 08:22:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038179.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038179hhsearch_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 1.2E-46 2.6E-51 311.4 16.3 148 40-220 4-152 (153)
2 TIGR00158 L9 ribosomal protein 100.0 3.6E-46 7.8E-51 307.0 16.0 146 42-220 1-147 (148)
3 PRK00137 rplI 50S ribosomal pr 100.0 1.4E-45 3.1E-50 303.0 16.2 146 42-220 1-146 (147)
4 COG0359 RplI Ribosomal protein 100.0 2.9E-44 6.3E-49 295.2 14.8 146 42-220 1-146 (148)
5 PRK14538 putative bifunctional 100.0 4.6E-37 1E-41 308.0 13.0 146 41-219 688-833 (838)
6 KOG4607 Mitochondrial ribosoma 99.9 4.2E-23 9.1E-28 177.6 7.6 157 29-218 36-192 (222)
7 PF03948 Ribosomal_L9_C: Ribos 99.9 2.2E-22 4.7E-27 152.3 10.2 85 118-220 2-86 (87)
8 PF01281 Ribosomal_L9_N: Ribos 99.9 1.6E-23 3.4E-28 142.7 2.9 48 42-92 1-48 (48)
9 PF10045 DUF2280: Uncharacteri 51.7 6.3 0.00014 31.1 0.6 32 160-191 21-52 (104)
10 PF08766 DEK_C: DEK C terminal 41.0 14 0.00031 25.0 1.0 24 157-180 19-42 (54)
11 PF07523 Big_3: Bacterial Ig-l 38.1 46 0.001 23.1 3.3 24 187-218 44-67 (67)
12 cd05887 Ig1_Nectin-3_like Firs 28.7 1.1E+02 0.0023 23.2 4.2 27 187-218 69-95 (96)
13 PF13592 HTH_33: Winged helix- 22.9 48 0.001 22.7 1.2 25 157-181 3-27 (60)
14 cd05718 Ig1_PVR_like First imm 22.7 1.7E+02 0.0037 20.8 4.2 27 187-218 71-97 (98)
15 PF00571 CBS: CBS domain CBS d 21.4 76 0.0016 20.3 1.9 16 154-169 41-56 (57)
16 TIGR00074 hypC_hupF hydrogenas 20.9 1.1E+02 0.0023 22.7 2.8 29 38-73 24-52 (76)
No 1
>CHL00160 rpl9 ribosomal protein L9; Provisional
Probab=100.00 E-value=1.2e-46 Score=311.41 Aligned_cols=148 Identities=22% Similarity=0.410 Sum_probs=133.5
Q ss_pred eeeEEEEccCCccccCCCCCCceEEeCCceeeccccccCccccchHHHHHHHHHHHHhcCchhHHHHHHhhhhhhhhHHH
Q 038179 40 RRWNLDLLTNQPKVDKLGKAGETVKVAPGYFRNHLMPKLLAVPNIEKFAHLIRKQRRICQPVEEEKVKVIRKSEDNMSRE 119 (221)
Q Consensus 40 kkmkVILled~~~V~~LGk~GdvV~Vk~GYARNfLiP~glAv~at~~~~~~~~~~~~~~~~~e~e~~~~~~~~~~~~~~e 119 (221)
++|+|||++| |++||++||+|+|+||||||||||+|+|++||++|++.++..++.. ++++++.+++
T Consensus 4 kkmkVIL~~d---V~~LGk~Gdiv~Vk~GYaRNyLiP~glA~~AT~~n~~~~e~~~~~~-----------~~~~~~~~~~ 69 (153)
T CHL00160 4 KKIQVILKEN---IQKLGKSGTVIKVKSGYARNYLIPNKMAKVATQGSLKQQKMYQKIL-----------DLKLKEAKEK 69 (153)
T ss_pred ceEEEEEccc---ccccCCCCCEEEEcCchHhhhhcccCchhhCCHHHHHHHHHHHHHH-----------HHHHHHHHHH
Confidence 6799999999 9999999999999999999999999999999999999988877642 2234466778
Q ss_pred HHHHHHHhhcC-cEEEEEeecccccccccCCCCCceeeeccCHHHHHHHHHhhcCCcccCCcccCCCCCccceeEEEEEE
Q 038179 120 FEKAARRLENA-RLVLRRFSNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMR 198 (221)
Q Consensus 120 a~~~~~kL~~~-~l~~~~~~~~~~i~~~~g~~g~~klfGsVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~~G~y~V~I~ 198 (221)
|++++++|++. .++|.+++ |++| +||||||+.||+++|.+++|++||+++|.||+ |+++|+|+|+|+
T Consensus 70 a~~la~~l~~~~~~~i~~k~---------ge~g--klfGSVt~~dIa~~l~~~~g~~idk~~I~l~~-Ik~~G~~~v~v~ 137 (153)
T CHL00160 70 CLKVKQLLEEIQKFSVKKKV---------GENN--QIFGSVTEKEISQIIKNKTNIDLEKQNIELPE-IKTIGIYNIEIK 137 (153)
T ss_pred HHHHHHHhhCCceEEEEEEe---------CCCC--eEEcccCHHHHHHHHHHhhCCccccceeehhh-ccccEeEEEEEE
Confidence 99999999998 58888776 4555 99999999999999998899999999999997 999999999999
Q ss_pred cCCCCCCCCceEEEEEEEEEEe
Q 038179 199 LPKAIPLPEGKVQWTLNVKVRG 220 (221)
Q Consensus 199 L~~~V~~p~~~v~~~l~V~V~~ 220 (221)
||++| +++++|.|+.
T Consensus 138 L~~~V-------~a~i~v~V~~ 152 (153)
T CHL00160 138 LTSDV-------KANINLQILP 152 (153)
T ss_pred ecCCc-------EEEEEEEEEE
Confidence 99998 9999999974
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=3.6e-46 Score=307.00 Aligned_cols=146 Identities=25% Similarity=0.398 Sum_probs=131.7
Q ss_pred eEEEEccCCccccCCCCCCceEEeCCceeeccccccCccccchHHHHHHHHHHHHhcCchhHHHHHHhhhhhhhhHHHHH
Q 038179 42 WNLDLLTNQPKVDKLGKAGETVKVAPGYFRNHLMPKLLAVPNIEKFAHLIRKQRRICQPVEEEKVKVIRKSEDNMSREFE 121 (221)
Q Consensus 42 mkVILled~~~V~~LGk~GdvV~Vk~GYARNfLiP~glAv~at~~~~~~~~~~~~~~~~~e~e~~~~~~~~~~~~~~ea~ 121 (221)
|+|||++| |++||++||+|+|+||||||||||+|+|++||++|++.++.+++.. ++++++.+++|+
T Consensus 1 MkVIL~~d---V~~lGk~GdiV~Vk~GYaRNyLiP~g~A~~aT~~nl~~~e~~~~~~-----------~~~~~~~~~~a~ 66 (148)
T TIGR00158 1 MKVILLED---VANLGKRGDVVEVKDGYARNFLIPKGLAVPATKKNIEFFEARRKKL-----------EEKLAANKAAAA 66 (148)
T ss_pred CeEEEccc---ccccCCCCCEEEEcccchhhhhcccCchhhCCHHHHHHHHHHHHHH-----------HHHHHHHHHHHH
Confidence 89999999 9999999999999999999999999999999999999988877642 223445678889
Q ss_pred HHHHHhhcCcEEEEEeecccccccccCCCCCceeeeccCHHHHHHHHHhhcCCcccCCcccCCCC-CccceeEEEEEEcC
Q 038179 122 KAARRLENARLVLRRFSNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSP-LSAFGEYEVPMRLP 200 (221)
Q Consensus 122 ~~~~kL~~~~l~~~~~~~~~~i~~~~g~~g~~klfGsVT~~dI~~~l~~q~gi~Idk~~I~l~~p-Ik~~G~y~V~I~L~ 200 (221)
+++++|++..++|.+++ |++| +||||||++||+++|.++ |++||+++|.||+| |+++|+|+|+|+||
T Consensus 67 ~l~~~l~~~~~~i~~k~---------ge~g--klfGSVt~~~I~~~l~~~-g~~idk~~I~l~~~~Ik~~G~y~v~i~L~ 134 (148)
T TIGR00158 67 RLKEVLELGTLTISKKV---------GDEG--KLFGSITTKQIADALKAA-GLDLDKKKIELPDGVIRTTGEHEVTIKLH 134 (148)
T ss_pred HHHHHhcCcEEEEEEEe---------CCCC--eEEEeECHHHHHHHHHHc-CCcccHhhEECCCCceeceEEEEEEEEEc
Confidence 99999999999888776 4555 999999999999999876 99999999999986 99999999999999
Q ss_pred CCCCCCCceEEEEEEEEEEe
Q 038179 201 KAIPLPEGKVQWTLNVKVRG 220 (221)
Q Consensus 201 ~~V~~p~~~v~~~l~V~V~~ 220 (221)
++| +++++|+|..
T Consensus 135 ~~V-------~a~i~v~V~~ 147 (148)
T TIGR00158 135 EEV-------FAVLKVIVVP 147 (148)
T ss_pred CCc-------EEEEEEEEEE
Confidence 998 9999999975
No 3
>PRK00137 rplI 50S ribosomal protein L9; Reviewed
Probab=100.00 E-value=1.4e-45 Score=303.01 Aligned_cols=146 Identities=29% Similarity=0.482 Sum_probs=132.8
Q ss_pred eEEEEccCCccccCCCCCCceEEeCCceeeccccccCccccchHHHHHHHHHHHHhcCchhHHHHHHhhhhhhhhHHHHH
Q 038179 42 WNLDLLTNQPKVDKLGKAGETVKVAPGYFRNHLMPKLLAVPNIEKFAHLIRKQRRICQPVEEEKVKVIRKSEDNMSREFE 121 (221)
Q Consensus 42 mkVILled~~~V~~LGk~GdvV~Vk~GYARNfLiP~glAv~at~~~~~~~~~~~~~~~~~e~e~~~~~~~~~~~~~~ea~ 121 (221)
|+|||++| |++||++||+|+|+||||||||||+|+|+|||++|++.++..++.. ++++++.+++|+
T Consensus 1 mkVIL~~d---v~~lGk~Gdiv~Vk~GYaRNyLiP~~lA~~aT~~~~~~~~~~~~~~-----------~~~~~~~~~~a~ 66 (147)
T PRK00137 1 MKVILLED---VKNLGKKGDVVEVKDGYARNFLIPQGKAVRATKGNLKQLEARRAEL-----------EAKAAEELAEAE 66 (147)
T ss_pred CeEEEccc---ccccCCCCCEEEEcCcchhhhhccCCceeeCCHHHHHHHHHHHHHH-----------HHHHHHHHHHHH
Confidence 89999999 9999999999999999999999999999999999999988877542 223456788899
Q ss_pred HHHHHhhcCcEEEEEeecccccccccCCCCCceeeeccCHHHHHHHHHhhcCCcccCCcccCCCCCccceeEEEEEEcCC
Q 038179 122 KAARRLENARLVLRRFSNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPK 201 (221)
Q Consensus 122 ~~~~kL~~~~l~~~~~~~~~~i~~~~g~~g~~klfGsVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~~G~y~V~I~L~~ 201 (221)
++++.|++..++|.+++ |++| +||||||++||+++|.++ |++||+++|.||+||+++|+|+|+|+||+
T Consensus 67 ~l~~~l~~~~l~i~~k~---------g~~g--klfGsVt~~~I~~~l~~~-g~~idk~~I~l~~~Ik~~G~y~v~i~L~~ 134 (147)
T PRK00137 67 ALAEKLEGLTVTIKAKA---------GEDG--KLFGSVTTKDIAEALKKQ-GIEIDKRKIELPGPIKTLGEYEVPVKLHP 134 (147)
T ss_pred HHHHHhhCCEEEEEEEc---------CCCC--eEEeeeCHHHHHHHHHHc-CCccCHHHeECCCcccccEEEEEEEEECC
Confidence 99999999999998876 4455 999999999999999877 99999999999999999999999999999
Q ss_pred CCCCCCceEEEEEEEEEEe
Q 038179 202 AIPLPEGKVQWTLNVKVRG 220 (221)
Q Consensus 202 ~V~~p~~~v~~~l~V~V~~ 220 (221)
+| +++|+|+|..
T Consensus 135 ~v-------~a~l~v~V~~ 146 (147)
T PRK00137 135 EV-------TATIKVNVVA 146 (147)
T ss_pred Cc-------EEEEEEEEEE
Confidence 98 9999999975
No 4
>COG0359 RplI Ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.9e-44 Score=295.17 Aligned_cols=146 Identities=28% Similarity=0.433 Sum_probs=132.8
Q ss_pred eEEEEccCCccccCCCCCCceEEeCCceeeccccccCccccchHHHHHHHHHHHHhcCchhHHHHHHhhhhhhhhHHHHH
Q 038179 42 WNLDLLTNQPKVDKLGKAGETVKVAPGYFRNHLMPKLLAVPNIEKFAHLIRKQRRICQPVEEEKVKVIRKSEDNMSREFE 121 (221)
Q Consensus 42 mkVILled~~~V~~LGk~GdvV~Vk~GYARNfLiP~glAv~at~~~~~~~~~~~~~~~~~e~e~~~~~~~~~~~~~~ea~ 121 (221)
|+|||++| |++||+.||+|+|++|||||||||+|+|++||+.|++.++.++... +++..+++++|+
T Consensus 1 MkVILl~d---V~~lGk~Gdiv~VkdGYarNfLiPkglAv~At~~n~~~~e~~r~~~-----------e~~~~~~~~~a~ 66 (148)
T COG0359 1 MKVILLED---VKGLGKKGDIVEVKDGYARNFLIPKGLAVPATKGNLKLLEARRAKL-----------EKKAAEELAEAE 66 (148)
T ss_pred CeEEEecc---hhhcCCCCCEEEecchhhhhhhccccchhhCCHHHHHHHHHHHHHH-----------HHHHHHHHHHHH
Confidence 89999999 9999999999999999999999999999999999999999866531 233456678999
Q ss_pred HHHHHhhcCcEEEEEeecccccccccCCCCCceeeeccCHHHHHHHHHhhcCCcccCCcccCCCCCccceeEEEEEEcCC
Q 038179 122 KAARRLENARLVLRRFSNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPK 201 (221)
Q Consensus 122 ~~~~kL~~~~l~~~~~~~~~~i~~~~g~~g~~klfGsVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~~G~y~V~I~L~~ 201 (221)
+++++|++..++|.+++ |++| +||||||++||++++.++ |++||+++|.+|++|+++|+|+|+|+||+
T Consensus 67 ~lk~~Le~~~~~i~~ka---------g~~G--klfGSVt~~dIa~~l~~~-g~~idk~~i~l~~~ik~~G~~~V~vkLh~ 134 (148)
T COG0359 67 ALKEKLEGKTVEIAVKA---------GEDG--KLFGSVTSKDIAEALKAA-GFKLDKRKIRLPNGIKTLGEHEVEVKLHE 134 (148)
T ss_pred HHHHHhhCceEEEEEEc---------CCCC--ceeccccHHHHHHHHHHc-CCCcchheeEcCchhhhcceeEEEEEecC
Confidence 99999999778888776 4555 999999999999999988 99999999999999999999999999999
Q ss_pred CCCCCCceEEEEEEEEEEe
Q 038179 202 AIPLPEGKVQWTLNVKVRG 220 (221)
Q Consensus 202 ~V~~p~~~v~~~l~V~V~~ 220 (221)
+| +++++|.|.+
T Consensus 135 eV-------~a~v~v~V~~ 146 (148)
T COG0359 135 EV-------TATVKVNVVA 146 (148)
T ss_pred ce-------EEEEEEEEEe
Confidence 98 9999999975
No 5
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=100.00 E-value=4.6e-37 Score=307.98 Aligned_cols=146 Identities=22% Similarity=0.308 Sum_probs=132.5
Q ss_pred eeEEEEccCCccccCCCCCCceEEeCCceeeccccccCccccchHHHHHHHHHHHHhcCchhHHHHHHhhhhhhhhHHHH
Q 038179 41 RWNLDLLTNQPKVDKLGKAGETVKVAPGYFRNHLMPKLLAVPNIEKFAHLIRKQRRICQPVEEEKVKVIRKSEDNMSREF 120 (221)
Q Consensus 41 kmkVILled~~~V~~LGk~GdvV~Vk~GYARNfLiP~glAv~at~~~~~~~~~~~~~~~~~e~e~~~~~~~~~~~~~~ea 120 (221)
.|||||++| |++||++||+|+|+|||| |||||+|+|++||++|++.++.+++.. ++++++.+++|
T Consensus 688 ~MkVIL~~d---v~~lGk~Gdvv~Vk~GYa-NfLiP~~~A~~aT~~nlk~~e~~~~~~-----------~~~~~~~~~~a 752 (838)
T PRK14538 688 NMEIILLTD---IKNKGKKHEIIKVNNGYG-NFLIQNKKALLADKENLAKIKKKKILE-----------QEKKRNHELLM 752 (838)
T ss_pred hhhHHHHHH---HHhcCCCCCEEEECCCch-hhhccCCchhhcCHHHHHHHHHHHHHH-----------HHHHHHHHHHH
Confidence 499999999 999999999999999999 999999999999999999988877642 23345667889
Q ss_pred HHHHHHhhcCcEEEEEeecccccccccCCCCCceeeeccCHHHHHHHHHhhcCCcccCCcccCCCCCccceeEEEEEEcC
Q 038179 121 EKAARRLENARLVLRRFSNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLP 200 (221)
Q Consensus 121 ~~~~~kL~~~~l~~~~~~~~~~i~~~~g~~g~~klfGsVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~~G~y~V~I~L~ 200 (221)
++++++|++..++|.+++ |++| +||||||++||+++|++++|++||++.|.||+|||++|+|.|+|+||
T Consensus 753 ~~l~~~l~~~~~~i~~k~---------ge~g--klfGSVt~~~I~~~l~~~~g~~idk~~I~l~~~Ik~~G~~~v~i~L~ 821 (838)
T PRK14538 753 KKLKSEIDNKKITLDIQL---------GPKG--KIYGKITLKQIVEEFHKIHNITIDRKKISLENEIISVGIYPVDVFLT 821 (838)
T ss_pred HHHHHHhhCcEEEEEEEe---------CCCC--eeeeccCHHHHHHHHHHhhCCccccceeeCCCcccccEEEEEEEEEc
Confidence 999999999988888776 4556 99999999999999998899999999999999999999999999999
Q ss_pred CCCCCCCceEEEEEEEEEE
Q 038179 201 KAIPLPEGKVQWTLNVKVR 219 (221)
Q Consensus 201 ~~V~~p~~~v~~~l~V~V~ 219 (221)
++| +++++|.|+
T Consensus 822 ~~V-------~a~i~v~V~ 833 (838)
T PRK14538 822 DQI-------KATFFLNVI 833 (838)
T ss_pred CCe-------EEEEEEEEE
Confidence 998 999999986
No 6
>KOG4607 consensus Mitochondrial ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=4.2e-23 Score=177.58 Aligned_cols=157 Identities=24% Similarity=0.245 Sum_probs=116.7
Q ss_pred ceeeeecceeeeeeEEEEccCCccccCCCCCCceEEeCCceeeccccccCccccchHHHHHHHHHHHHhcCchhHHHHHH
Q 038179 29 PLLFSCQGVRYRRWNLDLLTNQPKVDKLGKAGETVKVAPGYFRNHLMPKLLAVPNIEKFAHLIRKQRRICQPVEEEKVKV 108 (221)
Q Consensus 29 ~~~~~~~~~r~kkmkVILled~~~V~~LGk~GdvV~Vk~GYARNfLiP~glAv~at~~~~~~~~~~~~~~~~~e~e~~~~ 108 (221)
+|+.-++++++..++|||++| |++||++||+|+|++||+||+|+|+|+|+|+||.+.+.+...+.. +.
T Consensus 36 ~lv~~~~~k~k~~levIL~~~---Ve~lG~qGdvVsVk~g~~RN~Llp~glAvy~tp~~~~~~k~~~~e-------~~-- 103 (222)
T KOG4607|consen 36 ELVEFTQKKPKPNLEVILKTD---VEKLGKQGDVVSVKRGYFRNFLLPKGLAVYNTPLNLKKYKLREQE-------EE-- 103 (222)
T ss_pred hHhHhhhccCCcceeeeeehh---hhhhcccCcEEEeecchhhhhcccccccccCChhhHHHHHHHHHH-------HH--
Confidence 889999999999999999999 999999999999999999999999999999999996654433321 10
Q ss_pred hhhhhhhhHHHHHHHHHHhhcCcEEEEEeecccccccccCCCCCceeeeccCHHHHHHHHHhhcCCcccCCcccCCCCCc
Q 038179 109 IRKSEDNMSREFEKAARRLENARLVLRRFSNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLS 188 (221)
Q Consensus 109 ~~~~~~~~~~ea~~~~~kL~~~~l~~~~~~~~~~i~~~~g~~g~~klfGsVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk 188 (221)
.+..+..+..+....|....+.+.++.+... - -.+|+|+++.....+..++.+++|++.|+.|. ++
T Consensus 104 ---~~k~~vk~e~k~V~~lqt~v~~~~~~k~~kw--------~--l~~~~V~~~l~~gv~~~~~t~~l~k~~vs~P~-~k 169 (222)
T KOG4607|consen 104 ---AEKIRVKEEAKVVAVLQTVVLFKVMNKGGKW--------K--LNPNLVKASLRKGVIVAELTIKLDKELVSGPI-TK 169 (222)
T ss_pred ---hhhhccHHHHHHHHHHHhhhhhheeccCCce--------e--ecHHHHHHHHhcceEeccccccCcccccCCCc-cc
Confidence 1122233334444478777776666543111 1 34577777777666666777888888888874 77
Q ss_pred cceeEEEEEEcCCCCCCCCceEEEEEEEEE
Q 038179 189 AFGEYEVPMRLPKAIPLPEGKVQWTLNVKV 218 (221)
Q Consensus 189 ~~G~y~V~I~L~~~V~~p~~~v~~~l~V~V 218 (221)
.-|+|.+.|+++++. ++-+...|
T Consensus 170 ~e~~~~~~V~in~~~-------~vr~~~~v 192 (222)
T KOG4607|consen 170 EEGEYICEVKINPDV-------TVRVKIRV 192 (222)
T ss_pred ccceEEEEEEECCcc-------eEEeeeee
Confidence 777999999999876 55555544
No 7
>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=2.2e-22 Score=152.28 Aligned_cols=85 Identities=27% Similarity=0.508 Sum_probs=78.8
Q ss_pred HHHHHHHHHhhcCcEEEEEeecccccccccCCCCCceeeeccCHHHHHHHHHhhcCCcccCCcccCCCCCccceeEEEEE
Q 038179 118 REFEKAARRLENARLVLRRFSNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPM 197 (221)
Q Consensus 118 ~ea~~~~~kL~~~~l~~~~~~~~~~i~~~~g~~g~~klfGsVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~~G~y~V~I 197 (221)
++|++++++|++..++|.++++ ++| +||||||++||+++|.+++|++||+++|.||+|||++|+|.|+|
T Consensus 2 ~~A~~l~~~l~~~~l~i~~k~g---------~~g--klfGSVt~~dIa~~l~~~~g~~Idk~~I~l~~~IK~~G~~~v~v 70 (87)
T PF03948_consen 2 AEAQALAEKLEGITLTIKRKAG---------ENG--KLFGSVTSKDIAKALKEQTGIEIDKKKIELPEPIKSLGEYEVKV 70 (87)
T ss_dssp HHHHHHHHHHCSSEEEEEECBS---------SCS--SBSSEBSHHHHHHHHHHCCSSSSSSSSBCSSSTBESSEEEEEEE
T ss_pred HHHHHHHHHhcCCEEEEEEEec---------CCc--ceecCcCHHHHHHHHHHhhCCeEeccEEECCCchhccEEEEEEE
Confidence 4688999999999999998764 455 99999999999999999999999999999999999999999999
Q ss_pred EcCCCCCCCCceEEEEEEEEEEe
Q 038179 198 RLPKAIPLPEGKVQWTLNVKVRG 220 (221)
Q Consensus 198 ~L~~~V~~p~~~v~~~l~V~V~~ 220 (221)
+||++| .++++|.|.+
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 9999999975
No 8
>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=99.88 E-value=1.6e-23 Score=142.67 Aligned_cols=48 Identities=40% Similarity=0.578 Sum_probs=44.2
Q ss_pred eEEEEccCCccccCCCCCCceEEeCCceeeccccccCccccchHHHHHHHH
Q 038179 42 WNLDLLTNQPKVDKLGKAGETVKVAPGYFRNHLMPKLLAVPNIEKFAHLIR 92 (221)
Q Consensus 42 mkVILled~~~V~~LGk~GdvV~Vk~GYARNfLiP~glAv~at~~~~~~~~ 92 (221)
|+|||++| |++||++||+|+|++|||||||+|+|+|+|||+++++.++
T Consensus 1 m~ViL~~d---v~~lG~~Gdiv~V~~Gy~RN~L~p~~~A~~at~~~~~~~e 48 (48)
T PF01281_consen 1 MKVILLKD---VPGLGKKGDIVEVKPGYARNFLIPQGLAVYATPENLKQLE 48 (48)
T ss_dssp -EEEESSC---CTTSBSTTEEEE-SHHHHHHTTTTTTSEEECSHHHHHHHH
T ss_pred CEEEEccc---ccccCCCCCEEEEccceeeehccCCCceeeCCHHHHHhcC
Confidence 89999999 9999999999999999999999999999999999998764
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=51.73 E-value=6.3 Score=31.11 Aligned_cols=32 Identities=19% Similarity=0.335 Sum_probs=26.5
Q ss_pred CHHHHHHHHHhhcCCcccCCcccCCCCCccce
Q 038179 160 TKEELVAEVARQLSISIEPENLHLPSPLSAFG 191 (221)
Q Consensus 160 T~~dI~~~l~~q~gi~Idk~~I~l~~pIk~~G 191 (221)
||.+++++++++||++|++..++-=+|=|.-|
T Consensus 21 TPs~v~~aVk~eFgi~vsrQqve~yDPTK~aG 52 (104)
T PF10045_consen 21 TPSEVAEAVKEEFGIDVSRQQVESYDPTKRAG 52 (104)
T ss_pred CHHHHHHHHHHHhCCccCHHHHHHcCchHHHH
Confidence 89999999999999999999887655555444
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=41.00 E-value=14 Score=24.99 Aligned_cols=24 Identities=13% Similarity=0.396 Sum_probs=16.2
Q ss_pred eccCHHHHHHHHHhhcCCcccCCc
Q 038179 157 SPVTKEELVAEVARQLSISIEPEN 180 (221)
Q Consensus 157 GsVT~~dI~~~l~~q~gi~Idk~~ 180 (221)
..||.++|...|.+.+|+++..++
T Consensus 19 ~~vT~k~vr~~Le~~~~~dL~~~K 42 (54)
T PF08766_consen 19 DTVTKKQVREQLEERFGVDLSSRK 42 (54)
T ss_dssp GG--HHHHHHHHHHH-SS--SHHH
T ss_pred hHhhHHHHHHHHHHHHCCCcHHHH
Confidence 579999999999999999987543
No 11
>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=38.10 E-value=46 Score=23.07 Aligned_cols=24 Identities=29% Similarity=0.351 Sum_probs=19.2
Q ss_pred CccceeEEEEEEcCCCCCCCCceEEEEEEEEE
Q 038179 187 LSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKV 218 (221)
Q Consensus 187 Ik~~G~y~V~I~L~~~V~~p~~~v~~~l~V~V 218 (221)
-...|.|.|++.... . +++++|.|
T Consensus 44 ~~~~G~y~Vt~~y~~-~-------t~t~~VtV 67 (67)
T PF07523_consen 44 TSKAGTYTVTYTYKG-V-------TATFTVTV 67 (67)
T ss_dssp TTS-CCEEEEEEECT-E-------EEEEEEEE
T ss_pred cCCCceEEEEEEECC-E-------EEEEEEEC
Confidence 567899999999996 3 88888876
No 12
>cd05887 Ig1_Nectin-3_like First immunoglobulin (Ig) domain of nectin-3 (also known as poliovirus receptor related protein 3) and similar proteins. Ig1_Nectin-3_like: domain similar to the first immunoglobulin (Ig) domain of nectin-3 (also known as poliovirus receptor related protein 3). Nectin-3 belongs to the nectin family comprised of four transmembrane glycoproteins (nectins-1 through -4). Nectins are synaptic cell adhesion molecules (CAMs) which participate in adhesion and signaling at various intracellular junctions. Nectins form homophilic cis-dimers, followed by homophilic and heterophilic trans-dimers involved in cell-cell adhesion. For example, during spermatid development, the nectin-3,-2 trans-interaction is required for the formation of Sertoli cell-spermatid junctions in testis, and during morphogenesis of the ciliary body, the nectin-3,-1 trans-interaction is important for apex-apex adhesion between the pigment and non-pigment layers of the ciliary epithelia. Nectins also
Probab=28.73 E-value=1.1e+02 Score=23.25 Aligned_cols=27 Identities=30% Similarity=0.316 Sum_probs=23.0
Q ss_pred CccceeEEEEEEcCCCCCCCCceEEEEEEEEE
Q 038179 187 LSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKV 218 (221)
Q Consensus 187 Ik~~G~y~V~I~L~~~V~~p~~~v~~~l~V~V 218 (221)
...-|.|.+.+.-+ |.|..++++.+.|
T Consensus 69 ~~D~G~Y~C~v~tf-----P~G~~~~~~~l~~ 95 (96)
T cd05887 69 FSDIGVYICKAVTF-----PLGNTQSSTTVTV 95 (96)
T ss_pred ccccEEEEEEEEeC-----CCCCeeEEEEEEE
Confidence 35679999999998 7788899998887
No 13
>PF13592 HTH_33: Winged helix-turn helix
Probab=22.87 E-value=48 Score=22.73 Aligned_cols=25 Identities=16% Similarity=0.335 Sum_probs=21.0
Q ss_pred eccCHHHHHHHHHhhcCCcccCCcc
Q 038179 157 SPVTKEELVAEVARQLSISIEPENL 181 (221)
Q Consensus 157 GsVT~~dI~~~l~~q~gi~Idk~~I 181 (221)
+--|..+|++.|.+++|+.+.+..|
T Consensus 3 ~~wt~~~i~~~I~~~fgv~ys~~~v 27 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKYSPSGV 27 (60)
T ss_pred CcccHHHHHHHHHHHHCCEEcHHHH
Confidence 4678999999999999998877655
No 14
>cd05718 Ig1_PVR_like First immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155) and similar proteins. Ig1_PVR_like: domain similar to the first immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155). Poliovirus (PV) binds to its cellular receptor (PVR/CD155) to initiate infection. CD155 is a membrane-anchored, single-span glycoprotein; its extracellular region has three Ig-like domains. There are four different isotypes of CD155 (referred to as alpha, beta, gamma, and delta), that result from alternate splicing of the CD155 mRNA, and have identical extracellular domains. CD155-beta and - gamma, are secreted, CD155-alpha and delta are membrane-bound and function as PV receptors. The virus recognition site is contained in the amino-terminal domain, D1. Having the virus attachment site on the receptor distal from the plasma membrane, may be important for successful initiation of infection of cells by the virus. CD155 binds in the poliovirus "c
Probab=22.72 E-value=1.7e+02 Score=20.80 Aligned_cols=27 Identities=26% Similarity=0.327 Sum_probs=21.1
Q ss_pred CccceeEEEEEEcCCCCCCCCceEEEEEEEEE
Q 038179 187 LSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKV 218 (221)
Q Consensus 187 Ik~~G~y~V~I~L~~~V~~p~~~v~~~l~V~V 218 (221)
...-|.|.+.+..+ |.+..++++++.|
T Consensus 71 ~~D~G~Y~C~v~~~-----~~g~~~~~~~l~V 97 (98)
T cd05718 71 LEDEGNYICEFATF-----PQGNRQKVTTLTV 97 (98)
T ss_pred cccCEEEEEEEEeC-----CCCcEEEEEEEEe
Confidence 45679999999865 5566788888876
No 15
>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=21.39 E-value=76 Score=20.30 Aligned_cols=16 Identities=13% Similarity=0.360 Sum_probs=14.6
Q ss_pred eeeeccCHHHHHHHHH
Q 038179 154 ELRSPVTKEELVAEVA 169 (221)
Q Consensus 154 klfGsVT~~dI~~~l~ 169 (221)
++.|.||..||...+.
T Consensus 41 ~~~G~is~~dl~~~l~ 56 (57)
T PF00571_consen 41 KLVGIISRSDLLKALL 56 (57)
T ss_dssp BEEEEEEHHHHHHHHH
T ss_pred EEEEEEEHHHHHhhhh
Confidence 8999999999998875
No 16
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=20.95 E-value=1.1e+02 Score=22.68 Aligned_cols=29 Identities=31% Similarity=0.368 Sum_probs=22.9
Q ss_pred eeeeeEEEEccCCccccCCCCCCceEEeCCceeecc
Q 038179 38 RYRRWNLDLLTNQPKVDKLGKAGETVKVAPGYFRNH 73 (221)
Q Consensus 38 r~kkmkVILled~~~V~~LGk~GdvV~Vk~GYARNf 73 (221)
.++.+.+.|+.+ ++ .||.|-|-.|||+.-
T Consensus 24 ~~~~v~l~lv~~---~~----vGD~VLVH~G~Ai~~ 52 (76)
T TIGR00074 24 IKRDVSLDLVGE---VK----VGDYVLVHVGFAISV 52 (76)
T ss_pred eEEEEEEEeeCC---CC----CCCEEEEecChhhhh
Confidence 335588888877 53 899999999999853
Done!