Query 029973
Match_columns 184
No_of_seqs 157 out of 397
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 06:32:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029973.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029973hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01159 Ribosomal_L6e: Riboso 99.9 1.3E-24 2.8E-29 168.3 -1.9 57 126-182 1-58 (108)
2 KOG1694 60s ribosomal protein 99.9 2.6E-22 5.6E-27 163.4 4.9 90 61-182 12-102 (152)
3 COG2163 RPL14A Ribosomal prote 99.7 3.1E-17 6.8E-22 130.1 6.7 81 85-165 1-82 (125)
4 PF03868 Ribosomal_L6e_N: Ribo 99.6 3.1E-17 6.6E-22 115.3 -1.6 40 1-40 1-40 (59)
5 PTZ00471 60S ribosomal protein 99.5 4.4E-14 9.5E-19 113.4 6.7 62 88-149 4-90 (134)
6 PRK04333 50S ribosomal protein 99.2 7.3E-11 1.6E-15 87.9 6.6 70 88-162 3-72 (84)
7 KOG3418 60S ribosomal protein 98.7 3E-08 6.6E-13 80.0 5.1 64 86-152 2-93 (136)
8 PTZ00065 60S ribosomal protein 98.2 4.4E-06 9.5E-11 67.2 6.4 61 88-149 7-67 (130)
9 CHL00141 rpl24 ribosomal prote 95.3 0.022 4.8E-07 42.4 3.7 65 86-153 6-76 (83)
10 PRK12281 rplX 50S ribosomal pr 95.2 0.027 5.9E-07 41.3 3.8 63 88-153 6-74 (76)
11 PRK01191 rpl24p 50S ribosomal 95.0 0.043 9.4E-07 43.8 4.7 63 88-159 45-110 (120)
12 TIGR01080 rplX_A_E ribosomal p 94.5 0.065 1.4E-06 42.3 4.5 63 88-159 41-106 (114)
13 PTZ00194 60S ribosomal protein 94.3 0.1 2.3E-06 42.8 5.5 63 88-159 46-111 (143)
14 KOG3421 60S ribosomal protein 93.9 0.073 1.6E-06 43.4 3.7 61 86-148 4-64 (136)
15 KOG1694 60s ribosomal protein 93.7 0.0077 1.7E-07 49.7 -2.2 122 8-138 1-152 (152)
16 PRK00004 rplX 50S ribosomal pr 93.2 0.11 2.5E-06 39.9 3.6 63 88-153 4-72 (105)
17 TIGR01079 rplX_bact ribosomal 92.6 0.18 3.9E-06 39.0 3.9 63 88-153 3-72 (104)
18 COG0198 RplX Ribosomal protein 92.2 0.27 5.7E-06 38.4 4.5 60 89-155 5-72 (104)
19 smart00739 KOW KOW (Kyprides, 87.6 0.86 1.9E-05 25.8 3.1 24 89-112 2-25 (28)
20 PF00467 KOW: KOW motif; Inte 80.6 2.7 5.9E-05 25.5 3.2 26 91-116 1-26 (32)
21 PF10543 ORF6N: ORF6N domain; 43.7 2.9 6.2E-05 30.8 -2.3 28 101-138 6-33 (88)
22 COG2350 Uncharacterized protei 35.0 12 0.00026 28.4 -0.2 18 108-125 26-44 (92)
23 KOG0116 RasGAP SH3 binding pro 31.0 38 0.00082 32.2 2.4 49 112-161 87-137 (419)
24 KOG1999 RNA polymerase II tran 28.5 79 0.0017 33.4 4.3 43 81-123 452-494 (1024)
25 PF08134 cIII: cIII protein fa 26.0 22 0.00047 23.9 -0.1 10 60-69 11-20 (44)
26 TIGR00922 nusG transcription t 25.2 1.4E+02 0.003 23.7 4.4 35 87-121 118-153 (172)
27 PF06080 DUF938: Protein of un 23.7 32 0.00069 29.6 0.5 17 114-130 133-149 (204)
28 PRK08666 5'-methylthioadenosin 22.8 62 0.0014 27.9 2.1 50 91-144 30-84 (261)
29 PRK05609 nusG transcription an 22.6 1.5E+02 0.0032 23.6 4.2 34 87-120 125-159 (181)
30 KOG1999 RNA polymerase II tran 20.6 2.2E+02 0.0048 30.3 5.8 57 87-143 406-492 (1024)
31 PF00122 E1-E2_ATPase: E1-E2 A 20.2 2.2E+02 0.0048 22.9 4.8 54 85-148 48-114 (230)
32 COG2805 PilT Tfp pilus assembl 20.1 57 0.0012 30.6 1.4 10 115-124 125-134 (353)
33 TIGR01955 RfaH transcriptional 20.0 2E+02 0.0044 22.4 4.3 34 87-120 107-140 (159)
No 1
>PF01159 Ribosomal_L6e: Ribosomal protein L6e ; InterPro: IPR000915 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 [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes mammalian ribosomal protein L6 (L6 was previously known as TAX-responsive enhancer element binding protein 107); Caenorhabditis elegans ribosomal protein L6 (R151.3); Saccharomyces cerevisiae (Baker's yeast) ribosomal protein YL16A/YL16B; and Mesembryanthemum crystallinum (Common ice plant) ribosomal protein YL16-like. These proteins have 175 (yeast) to 287 (mammalian) amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A18_E 4A1D_E 4A19_E 4A1B_E 3IZR_G 3O58_F 3O5H_F 3IZS_G.
Probab=99.88 E-value=1.3e-24 Score=168.26 Aligned_cols=57 Identities=68% Similarity=1.083 Sum_probs=50.0
Q ss_pred ecCcceeeeecceEEeeeeEEecCCcccC-ccChHhhhhhhhhhhccccccccccccc
Q 029973 126 INGVPLRRVNQSYVIGTSTKVDISGVNVD-KFDDKYFAKEVERKKKKGENEFFESEKE 182 (184)
Q Consensus 126 lN~vPlrRv~q~~VIaTstkidis~vki~-~l~D~YFkk~k~~k~~~~e~eiF~~~ke 182 (184)
|||||||||||+|||||||+||||+|+|| +|||+||++.+.++++++|++||++++|
T Consensus 1 iNGVPLRRVnQ~yVIATSTkvDis~v~ip~~~~D~YF~~~~~~k~k~~e~~~f~~~~~ 58 (108)
T PF01159_consen 1 INGVPLRRVNQAYVIATSTKVDISGVKIPEKIDDAYFKRKKKKKKKKGEGDFFAEKKE 58 (108)
T ss_dssp SSS--SEEESSCCCEECSCESCHCCHHH-CCTTGSSSCHCCCCHHHHHHCHCCHHHHH
T ss_pred CCCCcceecccceEEEEeeEEeccccchhhccchHHHHhhhhccccccHHHHHhcccc
Confidence 79999999999999999999999999995 6999999998877889999999997653
No 2
>KOG1694 consensus 60s ribosomal protein L6 [Translation, ribosomal structure and biogenesis]
Probab=99.86 E-value=2.6e-22 Score=163.42 Aligned_cols=90 Identities=56% Similarity=0.841 Sum_probs=80.9
Q ss_pred CCCCCCCCCCCCccCCCCCCCCcccccccCCCcEEEEeeceecCceEEEeeecCCceEEEeccceecCcceeeeecceEE
Q 029973 61 PPKFYPADDVKKPLVNKRKPKPTKLRASITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSYVI 140 (184)
Q Consensus 61 ~p~yYptedv~~~~~~~~~~~~~klR~sitpGtvlIiL~Gr~~GKRvVfLKqL~sglllVtGP~~lN~vPlrRv~q~~VI 140 (184)
+|.|||+ ...+.+.++++||+||+||||||||+ .+||+|++|++|+|+|
T Consensus 12 ~~~~yp~------~k~~~~~~~~k~r~~l~~gtvliil~-------------------------~~ng~~~~~v~~~~~~ 60 (152)
T KOG1694|consen 12 PPADYPR------KKARYSAKPSKLRASLTPGTVLIILA-------------------------PINGVPLKRVNERYVA 60 (152)
T ss_pred Chhhccc------hhccccccchhhhhccCCCeeEEEec-------------------------ccCCcCcccccceEEe
Confidence 8889988 22334577899999999999999999 6999999999999999
Q ss_pred eeeeEEecCCcccC-ccChHhhhhhhhhhhccccccccccccc
Q 029973 141 GTSTKVDISGVNVD-KFDDKYFAKEVERKKKKGENEFFESEKE 182 (184)
Q Consensus 141 aTstkidis~vki~-~l~D~YFkk~k~~k~~~~e~eiF~~~ke 182 (184)
+||+ ||++||+++ ++||+||.+.+.++++++|+|||++++|
T Consensus 61 ~ts~-i~~~~vk~~e~~td~yf~K~k~~~~k~~e~~i~~~eke 102 (152)
T KOG1694|consen 61 TTSK-IDPSNVKIPEHLTDAYFKKKKLKKKKTQEGEIFAEEKE 102 (152)
T ss_pred eeee-eccccccccccccHHHHhhhhccccccccchhhccccc
Confidence 9988 999999996 5999999999888999999999999875
No 3
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=99.69 E-value=3.1e-17 Score=130.06 Aligned_cols=81 Identities=36% Similarity=0.589 Sum_probs=72.5
Q ss_pred cccccCCCcEEEEeeceecCceEEEeeecCCceEEEeccceecCcceeeeecceEEeeeeEEecCCccc-CccChHhhhh
Q 029973 85 LRASITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVDISGVNV-DKFDDKYFAK 163 (184)
Q Consensus 85 lR~sitpGtvlIiL~Gr~~GKRvVfLKqL~sglllVtGP~~lN~vPlrRv~q~~VIaTstkidis~vki-~~l~D~YFkk 163 (184)
++++|.||+|+++++||++|++||+|+++|.+.++++||..+||+|++|+|-+|+++|++.+|+..... +.+.-+|+..
T Consensus 1 ~~~~l~~GrVvvv~~GR~aGkk~VIv~~iDd~~v~i~gp~~v~gv~r~r~n~~~l~~t~~~~~~~rg~~~~~v~~~~~a~ 80 (125)
T COG2163 1 MRASLEVGRVVVVTAGRFAGKKVVIVKIIDDNFVLITGPKKVKGVPRRRINIKHLEPTDKVIDLVRGASDEKVKKANEAA 80 (125)
T ss_pred CCccccCCeEEEEecceeCCceEEEEEEccCCEEEEeCCccccCCccccccceeeeccceeeeecccccHHHHHHHHHhh
Confidence 478899999999999999999999999999999999999999999999999999999999999866544 4567677765
Q ss_pred hh
Q 029973 164 EV 165 (184)
Q Consensus 164 ~k 165 (184)
..
T Consensus 81 ~~ 82 (125)
T COG2163 81 GV 82 (125)
T ss_pred hh
Confidence 53
No 4
>PF03868 Ribosomal_L6e_N: Ribosomal protein L6, N-terminal domain; InterPro: IPR005568 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 [, ]. L6 is a protein from the large (50S) subunit. In Escherichia coli, it is located in the aminoacyl-tRNA binding site of the peptidyltransferase centre, and is known to bind directly to 23S rRNA. It belongs to a family of ribosomal proteins, including L6 from bacteria, cyanelles (structures that perform similar functions to chloroplasts, but have structural and biochemical characteristics of Cyanobacteria) and mitochondria; and L9 from mammals, Drosophila, plants and yeast. L6 contains two domains with almost identical folds, suggesting that is was derived by the duplication of an ancient RNA-binding protein gene. Analysis reveals several sites on the protein surface where interactions with other ribosome components may occur, the N terminus being involved in protein-protein interactions and the C terminus containing possible RNA-binding sites [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_G.
Probab=99.61 E-value=3.1e-17 Score=115.27 Aligned_cols=40 Identities=65% Similarity=1.074 Sum_probs=24.4
Q ss_pred CCCCCCCCCCCCCcccccCccccchhhhhhccccceeeec
Q 029973 1 MAPKQGKPRVSRNPELIRGIGKFSRSKMYHKRGLWAIKAK 40 (184)
Q Consensus 1 ma~kkg~p~~~rn~~l~~Gi~r~Srs~~y~rk~~~k~k~k 40 (184)
||+++++|||+|||+|++||+|||||+||+|+|||+.|.+
T Consensus 1 m~~kK~k~~~~RN~~L~~GI~RySrS~my~kralyk~K~k 40 (59)
T PF03868_consen 1 MAPKKKKPHCSRNPVLVRGIGRYSRSAMYHKRALYKRKKK 40 (59)
T ss_dssp ------------HHHHHTTTSHHHHHHHHHHHHH-S-THH
T ss_pred CccccccccccCChhhhCccccccHHHHHHHHHHHHHhcc
Confidence 8999999999999999999999999999999999986643
No 5
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=99.49 E-value=4.4e-14 Score=113.39 Aligned_cols=62 Identities=37% Similarity=0.675 Sum_probs=58.0
Q ss_pred ccCCCcEEEEeeceecCceEEEeeecCC-------ceEEEec----ccee--------------cCcceeeeecceEEee
Q 029973 88 SITPGTVLIILAGRFKGKRVVFLKQLPS-------GLLLVSG----PFKI--------------NGVPLRRVNQSYVIGT 142 (184)
Q Consensus 88 sitpGtvlIiL~Gr~~GKRvVfLKqL~s-------glllVtG----P~~l--------------N~vPlrRv~q~~VIaT 142 (184)
-+.||.|+|+|+|||+|+++|+||++|+ |.+||+| |.++ ....+..+|.+|+++|
T Consensus 4 ~~kpgkVVivL~GR~AGkKaVivk~~ddgt~drpy~halVaGIdryP~kVtk~M~kkki~KRskiK~FvK~vNynHlmPT 83 (134)
T PTZ00471 4 FLKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYPKKVVRGMSKRTIARRSQVGVFLRVVNHKHFLPT 83 (134)
T ss_pred cccCCEEEEEEccccCCcEEEEEeecCCCCccCcCceEEEEeecccchhhhhhccHHHHHHHhccccceEEEeeceeccc
Confidence 4689999999999999999999999998 5999999 8888 7778889999999999
Q ss_pred eeEEecC
Q 029973 143 STKVDIS 149 (184)
Q Consensus 143 stkidis 149 (184)
++.+||+
T Consensus 84 RY~vdi~ 90 (134)
T PTZ00471 84 RYNMDMS 90 (134)
T ss_pred ceeeecc
Confidence 9999998
No 6
>PRK04333 50S ribosomal protein L14e; Validated
Probab=99.17 E-value=7.3e-11 Score=87.94 Aligned_cols=70 Identities=33% Similarity=0.448 Sum_probs=62.3
Q ss_pred ccCCCcEEEEeeceecCceEEEeeecCCceEEEeccceecCcceeeeecceEEeeeeEEecCCcccCccChHhhh
Q 029973 88 SITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVDISGVNVDKFDDKYFA 162 (184)
Q Consensus 88 sitpGtvlIiL~Gr~~GKRvVfLKqL~sglllVtGP~~lN~vPlrRv~q~~VIaTstkidis~vki~~l~D~YFk 162 (184)
.+.+|.++++++|+++|+.+|+++.++++.+||.||+. +++|.++.|.+|+..|+++++++. ..+|+..+
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d~~~vlVdg~~~-~~~~rk~kn~khl~lt~~ki~~~~----~~~~~~vr 72 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIIDKNFVLVTGPSL-TGVKRRRCNIKHLEPTDKKVDIEK----GASDEEVK 72 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEecCCEEEEECCCc-CCCCCeeechHHEEEeeEEEECCC----CCCCHHHH
Confidence 57899999999999999999999999999999999987 999999999999999999998643 24555544
No 7
>KOG3418 consensus 60S ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=98.67 E-value=3e-08 Score=79.97 Aligned_cols=64 Identities=30% Similarity=0.615 Sum_probs=57.4
Q ss_pred ccccCCCcEEEEeeceecCceEEEeeecCCc-------eEEEeccceecCccee---------------------eeecc
Q 029973 86 RASITPGTVLIILAGRFKGKRVVFLKQLPSG-------LLLVSGPFKINGVPLR---------------------RVNQS 137 (184)
Q Consensus 86 R~sitpGtvlIiL~Gr~~GKRvVfLKqL~sg-------lllVtGP~~lN~vPlr---------------------Rv~q~ 137 (184)
.+-+.||.||++++|+++|+++|++||.++| .+||.| |.+.|+. -+|-.
T Consensus 2 ~kflkPgkvv~v~sG~yAg~KaVivk~~Ddg~~d~p~~h~LvAg---i~ryP~kvt~~~gkkk~~krsk~k~flKv~ny~ 78 (136)
T KOG3418|consen 2 AKFLKPGKVVLVLSGRYAGKKAVIVKNIDDGTEDKPYGHALVAG---VDRYPRKVTKSMGKKKLAKRSKVKPFLKVINYN 78 (136)
T ss_pred cccccCCcEEEeecccccCccEEEEeecccCCccCCCceeeeee---hhhccccccccccchhhhhcccceeEEEEeecc
Confidence 3567899999999999999999999999987 999999 8888886 58999
Q ss_pred eEEeeeeEEecCCcc
Q 029973 138 YVIGTSTKVDISGVN 152 (184)
Q Consensus 138 ~VIaTstkidis~vk 152 (184)
++++|...+|+...+
T Consensus 79 hlMptRy~vdv~~~k 93 (136)
T KOG3418|consen 79 HLMPTRYTVDVLALK 93 (136)
T ss_pred cccCcceEEeehhhh
Confidence 999999999997543
No 8
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=98.18 E-value=4.4e-06 Score=67.19 Aligned_cols=61 Identities=25% Similarity=0.337 Sum_probs=57.6
Q ss_pred ccCCCcEEEEeeceecCceEEEeeecCCceEEEeccceecCcceeeeecceEEeeeeEEecC
Q 029973 88 SITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVDIS 149 (184)
Q Consensus 88 sitpGtvlIiL~Gr~~GKRvVfLKqL~sglllVtGP~~lN~vPlrRv~q~~VIaTstkidis 149 (184)
-+.+|.|+.|..|.+.||-||++..++.+-+||.|| ...|||.+.+|-+++..|..+|+|+
T Consensus 7 fVEiGRVvli~~Gp~~GKL~vIVDIID~nRvLVDGP-~~tgV~Rq~i~~k~l~LT~~~v~i~ 67 (130)
T PTZ00065 7 FVEPGRLCLIQYGPDAGKLCFIVDIVTPTRVLVDGA-FITGVKRQSIPLKRLKLTDEKIKIN 67 (130)
T ss_pred ceeeceEEEEecCCCCCCEEEEEEEEcCCeEEEeCC-CcCCcceeEEeccceEEccEEEecC
Confidence 467999999999999999999999999999999999 5779999999999999999999985
No 9
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=95.35 E-value=0.022 Score=42.36 Aligned_cols=65 Identities=23% Similarity=0.236 Sum_probs=48.7
Q ss_pred ccccCCCcEEEEeeceecCceEEEeeec-CCceEEEeccceecCcce-----eeeecceEEeeeeEEecCCccc
Q 029973 86 RASITPGTVLIILAGRFKGKRVVFLKQL-PSGLLLVSGPFKINGVPL-----RRVNQSYVIGTSTKVDISGVNV 153 (184)
Q Consensus 86 R~sitpGtvlIiL~Gr~~GKRvVfLKqL-~sglllVtGP~~lN~vPl-----rRv~q~~VIaTstkidis~vki 153 (184)
.-.|.+|+.+++++|+++||.-.+++-+ +++.++|.| +|-+-- ..-.+.-++.-..-|++|||.+
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg---vn~~~k~~k~~~~~~~g~i~~~e~pI~~SnV~l 76 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKG---INIKFKHIKPNKENEVGEIKQFEAPIHSSNVML 76 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcC---cEEEEEEcCCccCCCCCCEEEEECCCCHHHEEE
Confidence 3478899999999999999999999985 478899999 553221 1123345666666788888876
No 10
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=95.21 E-value=0.027 Score=41.30 Aligned_cols=63 Identities=22% Similarity=0.304 Sum_probs=46.0
Q ss_pred ccCCCcEEEEeeceecCceEEEeeec-CCceEEEeccceecCcce-----eeeecceEEeeeeEEecCCccc
Q 029973 88 SITPGTVLIILAGRFKGKRVVFLKQL-PSGLLLVSGPFKINGVPL-----RRVNQSYVIGTSTKVDISGVNV 153 (184)
Q Consensus 88 sitpGtvlIiL~Gr~~GKRvVfLKqL-~sglllVtGP~~lN~vPl-----rRv~q~~VIaTstkidis~vki 153 (184)
.|..|+-+++++|.++||.-.+++-+ .++-++|.| +|-+-- ..-.+--++....-|++|||.+
T Consensus 6 ~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg---vn~~kkh~kp~~~~~~G~i~~~e~pI~~SnV~l 74 (76)
T PRK12281 6 KVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEG---VKIAKKAIKPSQKNPNGGFIEKEMPIHISNVKK 74 (76)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcC---cEEEEEEcCCCccCCCCCEEEEEcCcCHHHcee
Confidence 58899999999999999999999985 578899999 665421 1111234555555677777743
No 11
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=95.01 E-value=0.043 Score=43.77 Aligned_cols=63 Identities=17% Similarity=0.330 Sum_probs=48.2
Q ss_pred ccCCCcEEEEeeceecCceEEEeeec-CCceEEEeccceecCcceeeeecceEEeeeeEEecCCcccC--ccChH
Q 029973 88 SITPGTVLIILAGRFKGKRVVFLKQL-PSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVDISGVNVD--KFDDK 159 (184)
Q Consensus 88 sitpGtvlIiL~Gr~~GKRvVfLKqL-~sglllVtGP~~lN~vPlrRv~q~~VIaTstkidis~vki~--~l~D~ 159 (184)
.|..|+.|+|++|.++|+..-+++-+ ..+-++|.| +|-+- .+- +....-|++|||.+- .++|.
T Consensus 45 ~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeG---vn~~k----~~G--~~~e~pIh~SNV~l~~l~l~~~ 110 (120)
T PRK01191 45 PVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEG---VTVKK----ADG--TEVPRPIHPSNVMITKLDLSDE 110 (120)
T ss_pred eEeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeC---cEEEC----CCC--eEEEcccchhHeEEEeCccCCH
Confidence 47799999999999999999999986 478899999 55322 122 445567899999883 36554
No 12
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=94.48 E-value=0.065 Score=42.25 Aligned_cols=63 Identities=24% Similarity=0.325 Sum_probs=48.4
Q ss_pred ccCCCcEEEEeeceecCceEEEeeec-CCceEEEeccceecCcceeeeecceEEeeeeEEecCCcccC--ccChH
Q 029973 88 SITPGTVLIILAGRFKGKRVVFLKQL-PSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVDISGVNVD--KFDDK 159 (184)
Q Consensus 88 sitpGtvlIiL~Gr~~GKRvVfLKqL-~sglllVtGP~~lN~vPlrRv~q~~VIaTstkidis~vki~--~l~D~ 159 (184)
.|.-|+.|+|++|.|+|+.-.+++-+ ..+.++|.| ||-+- -+ - +....-|++|||.+- .|+|+
T Consensus 41 ~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Veg---vn~~k---~~-G--~~~e~pIh~SnV~l~~l~l~~~ 106 (114)
T TIGR01080 41 PVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEG---VTKEK---VN-G--TEVPVPIHPSNVMITKLNLDDE 106 (114)
T ss_pred eeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcC---eEEEC---CC-C--eEEEeeechHHeEEEeccCChH
Confidence 47789999999999999999999986 467799999 55322 12 2 456667999999883 46665
No 13
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=94.35 E-value=0.1 Score=42.76 Aligned_cols=63 Identities=13% Similarity=0.199 Sum_probs=49.8
Q ss_pred ccCCCcEEEEeeceecCceEEEeeec-CCceEEEeccceecCcceeeeecceEEeeeeEEecCCccc--CccChH
Q 029973 88 SITPGTVLIILAGRFKGKRVVFLKQL-PSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVDISGVNV--DKFDDK 159 (184)
Q Consensus 88 sitpGtvlIiL~Gr~~GKRvVfLKqL-~sglllVtGP~~lN~vPlrRv~q~~VIaTstkidis~vki--~~l~D~ 159 (184)
.|.-|+.|+|++|.|+|++--+++-+ .++-++|.| || +..-|.+- ...-|++|||-| +.++|.
T Consensus 46 ~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEg---vn---~~Kk~gk~---~e~PIh~SNV~iv~l~l~~~ 111 (143)
T PTZ00194 46 PVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEK---IT---REKANGEP---VQIGIHPSNVIITKLKLNKD 111 (143)
T ss_pred eeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeC---eE---EEecCCCE---eecCcCchheEEEccccCch
Confidence 47889999999999999999999986 467899888 44 34444443 355799999998 468887
No 14
>KOG3421 consensus 60S ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=93.87 E-value=0.073 Score=43.42 Aligned_cols=61 Identities=25% Similarity=0.344 Sum_probs=52.8
Q ss_pred ccccCCCcEEEEeeceecCceEEEeeecCCceEEEeccceecCcceeeeecceEEeeeeEEec
Q 029973 86 RASITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVDI 148 (184)
Q Consensus 86 R~sitpGtvlIiL~Gr~~GKRvVfLKqL~sglllVtGP~~lN~vPlrRv~q~~VIaTstkidi 148 (184)
..+...|.|.++..|.+.||-|+++-+.++..+|+-|| ..+||..-+|-+-+.-|-..+|+
T Consensus 4 ~r~veVGrva~v~~G~~~GkL~AIVdviDqnr~lvDGp--~t~v~rq~~~~~~~~LT~~~~kf 64 (136)
T KOG3421|consen 4 KRFVEVGRVALVSFGPDAGKLVAIVDVIDQNRALVDGP--CTGVPRQAMNLKCLQLTDFVLKF 64 (136)
T ss_pred hhhhhcceEEEEEecCCCceEEEEEEeecchhhhccCc--ccccchhhcchhheeeeeeeEec
Confidence 45678899999999999999999999999999999999 56888887777777777766665
No 15
>KOG1694 consensus 60s ribosomal protein L6 [Translation, ribosomal structure and biogenesis]
Probab=93.73 E-value=0.0077 Score=49.65 Aligned_cols=122 Identities=16% Similarity=0.098 Sum_probs=83.9
Q ss_pred CCCCCCcccccCccccchhhhhhccccceee-----ec-----CCCcC-----CCCCCC----Cc--ceeecCCCCC---
Q 029973 8 PRVSRNPELIRGIGKFSRSKMYHKRGLWAIK-----AK-----NGGVF-----PRHDPK----PK--AAAPAEKPPK--- 63 (184)
Q Consensus 8 p~~~rn~~l~~Gi~r~Srs~~y~rk~~~k~k-----~k-----~gg~~-----pkng~k----g~--r~v~l~k~p~--- 63 (184)
+||++|+ |++| .++||.+ +++. ++ .-|.+ +.||.. ++ .+.....++.
T Consensus 1 ~~~~~~~----~~~~--~~~~yp~---~k~~~~~~~~k~r~~l~~gtvliil~~~ng~~~~~v~~~~~~~ts~i~~~~vk 71 (152)
T KOG1694|consen 1 PHCSKNP----GIGR--PPADYPR---KKARYSAKPSKLRASLTPGTVLIILAPINGVPLKRVNERYVATTSKIDPSNVK 71 (152)
T ss_pred CCcccCC----CCCC--Chhhccc---hhccccccchhhhhccCCCeeEEEecccCCcCcccccceEEeeeeeecccccc
Confidence 6899998 8888 8888887 3211 11 01110 233321 22 2233444554
Q ss_pred --CCCCCCCCCccCCCC----CCCCcccccccCCCcEEEEeeceecCceEEEeeecCCceEEEeccceecCcceeeeecc
Q 029973 64 --FYPADDVKKPLVNKR----KPKPTKLRASITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQS 137 (184)
Q Consensus 64 --yYptedv~~~~~~~~----~~~~~klR~sitpGtvlIiL~Gr~~GKRvVfLKqL~sglllVtGP~~lN~vPlrRv~q~ 137 (184)
+|.+++........+ .++....+++..+.|......+.+.+.++++..++-.++..+.|+...+..++...++.
T Consensus 72 ~~e~~td~yf~K~k~~~~k~~e~~i~~~ekekyeIteq~kiDqKaVDs~il~~iK~ip~lk~yl~~~f~l~~g~~Ph~l~ 151 (152)
T KOG1694|consen 72 IPEHLTDAYFKKKKLKKKKTQEGEIFAEEKEKYEITEQRKIDQKAVDSQILPKIKAIPQLKKYLGSVFALTNGIYPHKLK 151 (152)
T ss_pred ccccccHHHHhhhhccccccccchhhcccccccccchhhhhhHHHHHHHHHHHHhhchHhhhccchhhhccCCCCccccc
Confidence 557777655432222 35678889999999999999999999999999988888889999998888888887776
Q ss_pred e
Q 029973 138 Y 138 (184)
Q Consensus 138 ~ 138 (184)
|
T Consensus 152 f 152 (152)
T KOG1694|consen 152 F 152 (152)
T ss_pred C
Confidence 5
No 16
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=93.20 E-value=0.11 Score=39.94 Aligned_cols=63 Identities=33% Similarity=0.455 Sum_probs=48.4
Q ss_pred ccCCCcEEEEeeceecCceEEEeeec-CCceEEEeccceecCccee-----eeecceEEeeeeEEecCCccc
Q 029973 88 SITPGTVLIILAGRFKGKRVVFLKQL-PSGLLLVSGPFKINGVPLR-----RVNQSYVIGTSTKVDISGVNV 153 (184)
Q Consensus 88 sitpGtvlIiL~Gr~~GKRvVfLKqL-~sglllVtGP~~lN~vPlr-----Rv~q~~VIaTstkidis~vki 153 (184)
.|.+|+.|.+++|.++|+.-.+++-+ .++-++|.| +|-+... .-++-=++....-|++|||.+
T Consensus 4 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Veg---vn~~k~h~k~~~~~~~G~i~~~e~pI~~SnV~l 72 (105)
T PRK00004 4 KIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEG---VNIVKKHQKPNQENPQGGIIEKEAPIHISNVAL 72 (105)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcC---cEEEEEecCCCCCCCCCceEEEECCcCHHHEEE
Confidence 57899999999999999999999986 478899999 6643221 112345567777899999977
No 17
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=92.58 E-value=0.18 Score=38.95 Aligned_cols=63 Identities=32% Similarity=0.476 Sum_probs=49.2
Q ss_pred ccCCCcEEEEeeceecCceEEEeeecC-CceEEEeccceecCccee----eee--cceEEeeeeEEecCCccc
Q 029973 88 SITPGTVLIILAGRFKGKRVVFLKQLP-SGLLLVSGPFKINGVPLR----RVN--QSYVIGTSTKVDISGVNV 153 (184)
Q Consensus 88 sitpGtvlIiL~Gr~~GKRvVfLKqL~-sglllVtGP~~lN~vPlr----Rv~--q~~VIaTstkidis~vki 153 (184)
.|..|+-+.+++|.++||.-.+++-+. .+.++|.| +|-+.-+ ..+ +--++....-|++|||.+
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg---vN~~kkh~k~~~~~~~~g~i~~~e~pI~~SnV~l 72 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEG---VNMVKKHVKPKPTQRSQGGIIEKEAPIHISNVML 72 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECC---cEEEEEecCcccCCCCCCceEEEEccCCHHHeEE
Confidence 478999999999999999999999864 78899999 6643222 112 456677777899999976
No 18
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=92.23 E-value=0.27 Score=38.44 Aligned_cols=60 Identities=28% Similarity=0.446 Sum_probs=47.3
Q ss_pred cCCCcEEEEeeceecCceEEEeeecCCceEEEeccceecCcceeeeecc--------eEEeeeeEEecCCcccCc
Q 029973 89 ITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQS--------YVIGTSTKVDISGVNVDK 155 (184)
Q Consensus 89 itpGtvlIiL~Gr~~GKRvVfLKqL~sglllVtGP~~lN~vPlrRv~q~--------~VIaTstkidis~vki~~ 155 (184)
|.-|+.+++++|.++|+.-..|+-+... ++|.| |-+...|++ =+|-.-.-|++|||.|-.
T Consensus 5 IrkGD~V~Vi~GkdKGk~GkVl~v~~k~-V~VEG------vnv~kkh~k~~~~~~~ggii~~EapIh~SnV~i~~ 72 (104)
T COG0198 5 VKKGDTVKVIAGKDKGKEGKVLKVLPKK-VVVEG------VNVVKKHIKPSQENPEGGIINKEAPIHISNVAIID 72 (104)
T ss_pred eecCCEEEEEecCCCCcceEEEEEecCe-EEEEC------cEEEEecCCCCCcCCCCceeeeeecccHHHeEEec
Confidence 5679999999999999999999999877 88877 445666666 245555678999997743
No 19
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=87.62 E-value=0.86 Score=25.83 Aligned_cols=24 Identities=33% Similarity=0.499 Sum_probs=21.7
Q ss_pred cCCCcEEEEeeceecCceEEEeee
Q 029973 89 ITPGTVLIILAGRFKGKRVVFLKQ 112 (184)
Q Consensus 89 itpGtvlIiL~Gr~~GKRvVfLKq 112 (184)
+.+|+.+.|+.|.|+|.-.++++.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i 25 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEV 25 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEE
Confidence 579999999999999999988875
No 20
>PF00467 KOW: KOW motif; InterPro: IPR005824 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 KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=80.62 E-value=2.7 Score=25.50 Aligned_cols=26 Identities=27% Similarity=0.362 Sum_probs=23.0
Q ss_pred CCcEEEEeeceecCceEEEeeecCCc
Q 029973 91 PGTVLIILAGRFKGKRVVFLKQLPSG 116 (184)
Q Consensus 91 pGtvlIiL~Gr~~GKRvVfLKqL~sg 116 (184)
+|+.+.|+.|+|+|.-..+++-..+.
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~ 26 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSK 26 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTT
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCC
Confidence 68999999999999999999887654
No 21
>PF10543 ORF6N: ORF6N domain; InterPro: IPR018873 This entry represents an N-terminal DNA-binding domain found in a wide range of proteins from bacterial and eukaryotic DNA viruses and there bacterial homologues, they include the poxvirus D6R/N1R and baculoviral Bro protein families. The KilA-N domain is considered to be homologous to the fungal DNA-binding APSES domain. Both the KilA-N and APSES domains share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease []. This entry represents the amino-terminal domain of the Enterobacteria phage P22 antirepressor ((P03037 from SWISSPROT) []. It is found associated with IPR018876 from INTERPRO.
Probab=43.71 E-value=2.9 Score=30.82 Aligned_cols=28 Identities=25% Similarity=0.630 Sum_probs=23.2
Q ss_pred eecCceEEEeeecCCceEEEeccceecCcceeeeecce
Q 029973 101 RFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSY 138 (184)
Q Consensus 101 r~~GKRvVfLKqL~sglllVtGP~~lN~vPlrRv~q~~ 138 (184)
.|+|+|||-.++|+. +.|+|-.++++.|
T Consensus 6 e~rg~rV~t~~~lA~----------~yg~~~~~i~~~~ 33 (88)
T PF10543_consen 6 EYRGQRVMTDEDLAE----------LYGVETKTINRNF 33 (88)
T ss_pred EEcCEEEEEHHHHHH----------HhCcCHHHHHHHH
Confidence 589999999999985 7788888777754
No 22
>COG2350 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.98 E-value=12 Score=28.43 Aligned_cols=18 Identities=61% Similarity=0.798 Sum_probs=14.7
Q ss_pred EEeeecC-CceEEEeccce
Q 029973 108 VFLKQLP-SGLLLVSGPFK 125 (184)
Q Consensus 108 VfLKqL~-sglllVtGP~~ 125 (184)
=+|+|+. +|.|+++|||.
T Consensus 26 ~~L~~~~a~G~ll~sGP~~ 44 (92)
T COG2350 26 ARLKQLYAEGRLLTSGPFP 44 (92)
T ss_pred HHHHHhhhcCeEEEeCCCC
Confidence 3688874 79999999985
No 23
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=31.04 E-value=38 Score=32.18 Aligned_cols=49 Identities=20% Similarity=0.389 Sum_probs=34.4
Q ss_pred ecC-CceEEEeccceecCcceeeeecceEEeeeeE-EecCCcccCccChHhh
Q 029973 112 QLP-SGLLLVSGPFKINGVPLRRVNQSYVIGTSTK-VDISGVNVDKFDDKYF 161 (184)
Q Consensus 112 qL~-sglllVtGP~~lN~vPlrRv~q~~VIaTstk-idis~vki~~l~D~YF 161 (184)
.|. .-+++|||=|..|+-|+||..|.|++|-.-+ ..|-| ||=.+-|++|
T Consensus 87 S~~~GvvI~VtG~lt~~~~~rRkF~QtFfLapq~~~yfVlN-DiFRfvde~~ 137 (419)
T KOG0116|consen 87 SLEKGVVIMVTGYLTNKDGPRRKFSQTFFLAPQEKGYFVLN-DIFRFVDEEF 137 (419)
T ss_pred hccCCeEEEEEEEEEeCCCcceEEEEEEEEeecCCceEEEe-chhhhccccc
Confidence 344 3567899999999999999999999997665 44433 3323444455
No 24
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=28.49 E-value=79 Score=33.44 Aligned_cols=43 Identities=23% Similarity=0.496 Sum_probs=34.9
Q ss_pred CCcccccccCCCcEEEEeeceecCceEEEeeecCCceEEEecc
Q 029973 81 KPTKLRASITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGP 123 (184)
Q Consensus 81 ~~~klR~sitpGtvlIiL~Gr~~GKRvVfLKqL~sglllVtGP 123 (184)
..+.||+-+.||+.+=+++|+|.|..-++++--.+-++|.+--
T Consensus 452 ~~~eLrKyF~~GDhVKVi~G~~eG~tGlVvrVe~~~vi~~Sd~ 494 (1024)
T KOG1999|consen 452 PASELRKYFEPGDHVKVIAGRYEGDTGLVVRVEQGDVILLSDL 494 (1024)
T ss_pred chHhhhhhccCCCeEEEEeccccCCcceEEEEeCCeEEEEecC
Confidence 3678999999999999999999999988887765555555443
No 25
>PF08134 cIII: cIII protein family; InterPro: IPR012995 This family consists of the CIII family of regulatory proteins. The lambda CIII protein has 54 amino acids and it forms an amphipathic helix within its amino acid sequence. Lambda CIII stabilises the lambda CII protein and the host sigma factor 32, responsible for transcribing genes of the heat shock regulon [].
Probab=25.95 E-value=22 Score=23.95 Aligned_cols=10 Identities=20% Similarity=0.673 Sum_probs=8.2
Q ss_pred CCCCCCCCCC
Q 029973 60 KPPKFYPADD 69 (184)
Q Consensus 60 k~p~yYpted 69 (184)
-|..|||+|.
T Consensus 11 vmSAyYP~ES 20 (44)
T PF08134_consen 11 VMSAYYPTES 20 (44)
T ss_pred eeeeecCcHH
Confidence 4788999995
No 26
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=25.23 E-value=1.4e+02 Score=23.72 Aligned_cols=35 Identities=17% Similarity=0.072 Sum_probs=27.8
Q ss_pred cccCCCcEEEEeeceecCceEEEeeec-CCceEEEe
Q 029973 87 ASITPGTVLIILAGRFKGKRVVFLKQL-PSGLLLVS 121 (184)
Q Consensus 87 ~sitpGtvlIiL~Gr~~GKRvVfLKqL-~sglllVt 121 (184)
..+.+|+.+.|..|.++|-..++.+.- ..+-+.|.
T Consensus 118 ~~~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~ 153 (172)
T TIGR00922 118 IDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVS 153 (172)
T ss_pred cCCCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEE
Confidence 447899999999999999999999875 34455543
No 27
>PF06080 DUF938: Protein of unknown function (DUF938); InterPro: IPR010342 This family consists of several hypothetical proteins from both prokaryotes and eukaryotes. The function of this family is unknown.
Probab=23.71 E-value=32 Score=29.65 Aligned_cols=17 Identities=47% Similarity=0.929 Sum_probs=14.7
Q ss_pred CCceEEEeccceecCcc
Q 029973 114 PSGLLLVSGPFKINGVP 130 (184)
Q Consensus 114 ~sglllVtGP~~lN~vP 130 (184)
++|+|++=|||..||..
T Consensus 133 ~gG~L~~YGPF~~~G~~ 149 (204)
T PF06080_consen 133 PGGLLFLYGPFNRDGKF 149 (204)
T ss_pred CCCEEEEeCCcccCCEe
Confidence 37999999999999943
No 28
>PRK08666 5'-methylthioadenosine phosphorylase; Validated
Probab=22.80 E-value=62 Score=27.89 Aligned_cols=50 Identities=30% Similarity=0.480 Sum_probs=33.0
Q ss_pred CCcEEEEeeceecCceEEEeeecCCceEEEeccceec-----CcceeeeecceEEeeee
Q 029973 91 PGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKIN-----GVPLRRVNQSYVIGTST 144 (184)
Q Consensus 91 pGtvlIiL~Gr~~GKRvVfLKqL~sglllVtGP~~lN-----~vPlrRv~q~~VIaTst 144 (184)
-|.+ =+..|.+.|+.||||-+-.-|..+ -|.++| .+ +....-+.+|.|.+
T Consensus 30 ~g~~-~~~~G~~~g~~Vv~l~~~G~gh~~--~~~kVn~~a~~~~-l~~~Gv~~II~tgs 84 (261)
T PRK08666 30 YGEV-KVKIGTYAGEEVAFLARHGEGHSV--PPHKINYRANIWA-LKELGVERILATSA 84 (261)
T ss_pred CCCC-EEEEEEECCEEEEEEeCCCCCCcc--ChhhcchHHHHHH-HHHCCCCEEEEecc
Confidence 3443 366789999999998865444332 466776 22 55667777887775
No 29
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=22.64 E-value=1.5e+02 Score=23.61 Aligned_cols=34 Identities=15% Similarity=0.150 Sum_probs=26.9
Q ss_pred cccCCCcEEEEeeceecCceEEEeeec-CCceEEE
Q 029973 87 ASITPGTVLIILAGRFKGKRVVFLKQL-PSGLLLV 120 (184)
Q Consensus 87 ~sitpGtvlIiL~Gr~~GKRvVfLKqL-~sglllV 120 (184)
..+.+|+.+-|..|.++|-..++++.- +.+-+.|
T Consensus 125 ~~~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v 159 (181)
T PRK05609 125 VDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKV 159 (181)
T ss_pred cCCCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEE
Confidence 447899999999999999999999975 3434433
No 30
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=20.60 E-value=2.2e+02 Score=30.28 Aligned_cols=57 Identities=26% Similarity=0.388 Sum_probs=43.1
Q ss_pred cccCCCcEEEEeeceecCceEEEeeecCCceEEE------eccceecCccee------------------------eeec
Q 029973 87 ASITPGTVLIILAGRFKGKRVVFLKQLPSGLLLV------SGPFKINGVPLR------------------------RVNQ 136 (184)
Q Consensus 87 ~sitpGtvlIiL~Gr~~GKRvVfLKqL~sglllV------tGP~~lN~vPlr------------------------Rv~q 136 (184)
..+.||+.++++.|...|-+.++.+.=..-.+++ .+||.+|.--|| ||.|
T Consensus 406 ~~F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~~e~l~~pl~~~~~eLrKyF~~GDhVKVi~G~~eG~tGlVvrVe~ 485 (1024)
T KOG1999|consen 406 HLFSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSKHEDLKGPLEVPASELRKYFEPGDHVKVIAGRYEGDTGLVVRVEQ 485 (1024)
T ss_pred cccCCCCeEEEeeeeeccceeEEEeccCceEEEeeccccCCCccccchHhhhhhccCCCeEEEEeccccCCcceEEEEeC
Confidence 3489999999999999999998887754444443 467777766565 8888
Q ss_pred ceEEeee
Q 029973 137 SYVIGTS 143 (184)
Q Consensus 137 ~~VIaTs 143 (184)
..||--|
T Consensus 486 ~~vi~~S 492 (1024)
T KOG1999|consen 486 GDVILLS 492 (1024)
T ss_pred CeEEEEe
Confidence 8877655
No 31
>PF00122 E1-E2_ATPase: E1-E2 ATPase p-type cation-transporting ATPase superfamily signature H+-transporting ATPase (proton pump) signature sodium/potassium-transporting ATPase signature; InterPro: IPR008250 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the actuator (A) domain, and some transmembrane helices found in P-type ATPases []. It contains the TGES-loop which is essential for the metal ion binding which results in tight association between the A and P (phosphorylation) domains []. It does not contain the phosphorylation site. It is thought that the large movement of the actuator domain, which is transmitted to the transmembrane helices, is essential to the long distance coupling between formation/decomposition of the acyl phosphate in the cytoplasmic P-domain and the changes in the ion-binding sites buried deep in the membranous region []. This domain has a modulatory effect on the phosphoenzyme processing steps through its nucleotide binding [],[]. P-type (or E1-E2-type) ATPases that form an aspartyl phosphate intermediate in the course of ATP hydrolysis, can be divided into 4 major groups []: (1) Ca2+-transporting ATPases; (2) Na+/K+- and gastric H+/K+-transporting ATPases; (3) plasma membrane H+-transporting ATPases (proton pumps) of plants, fungi and lower eukaryotes; and (4) all bacterial P-type ATPases, except the g2+-ATPase of Salmonella typhimurium, which is more similar to the eukaryotic sequences. However, great variety of sequence analysis methods results in diversity of classification. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0000166 nucleotide binding, 0046872 metal ion binding; PDB: 2XZB_A 1MHS_B 3TLM_A 3A3Y_A 2ZXE_A 3NAL_A 3NAM_A 3NAN_A 2YJ6_B 2IYE_A ....
Probab=20.21 E-value=2.2e+02 Score=22.95 Aligned_cols=54 Identities=20% Similarity=0.433 Sum_probs=33.6
Q ss_pred cccccCCCcEEEEeeceecCceEEEeeecCCceEEEe-ccceec-------Ccceeee-----ecceEEeeeeEEec
Q 029973 85 LRASITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVS-GPFKIN-------GVPLRRV-----NQSYVIGTSTKVDI 148 (184)
Q Consensus 85 lR~sitpGtvlIiL~Gr~~GKRvVfLKqL~sglllVt-GP~~lN-------~vPlrRv-----~q~~VIaTstkidi 148 (184)
.-++|.||+++++-.|..= +...+++. |...+| ..|..+. ...++.+-|.-++-
T Consensus 48 ~~~~L~~GDiI~l~~g~~v----------PaD~~ll~~g~~~vd~s~ltGes~pv~k~~~~~~~~~~i~~Gs~v~~g 114 (230)
T PF00122_consen 48 PSSELVPGDIIILKAGDIV----------PADGILLESGSAYVDESALTGESEPVKKTPLPLNPGNIIFAGSIVVSG 114 (230)
T ss_dssp EGGGT-TTSEEEEETTEBE----------SSEEEEEESSEEEEECHHHHSBSSEEEESSSCCCTTTEE-TTEEEEEE
T ss_pred hHhhccceeeeeccccccc----------ccCccceeccccccccccccccccccccccccccccchhhcccccccc
Confidence 3567899999999887632 43223333 555555 3788888 77777776665543
No 32
>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=20.10 E-value=57 Score=30.56 Aligned_cols=10 Identities=60% Similarity=1.135 Sum_probs=8.8
Q ss_pred CceEEEeccc
Q 029973 115 SGLLLVSGPF 124 (184)
Q Consensus 115 sglllVtGP~ 124 (184)
.||+|||||=
T Consensus 125 ~GLILVTGpT 134 (353)
T COG2805 125 RGLILVTGPT 134 (353)
T ss_pred CceEEEeCCC
Confidence 4999999994
No 33
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=20.01 E-value=2e+02 Score=22.36 Aligned_cols=34 Identities=21% Similarity=0.251 Sum_probs=26.8
Q ss_pred cccCCCcEEEEeeceecCceEEEeeecCCceEEE
Q 029973 87 ASITPGTVLIILAGRFKGKRVVFLKQLPSGLLLV 120 (184)
Q Consensus 87 ~sitpGtvlIiL~Gr~~GKRvVfLKqL~sglllV 120 (184)
..+.+|+.+.|..|.++|--.++++.-+.+-+.|
T Consensus 107 ~~~~~G~~V~V~~GPf~g~~g~v~~~~~~~r~~v 140 (159)
T TIGR01955 107 TLPYKGDKVRITDGAFAGFEAIFLEPDGEKRSML 140 (159)
T ss_pred cCCCCCCEEEEeccCCCCcEEEEEEECCCceEEE
Confidence 3478999999999999999999998744443333
Done!