Query 031097
Match_columns 166
No_of_seqs 112 out of 762
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 09:10:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031097.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031097hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0093 RplN Ribosomal protein 100.0 5.5E-53 1.2E-57 324.0 12.4 120 47-166 1-122 (122)
2 CHL00057 rpl14 ribosomal prote 100.0 1.1E-51 2.5E-56 318.5 13.2 120 47-166 1-122 (122)
3 PRK05483 rplN 50S ribosomal pr 100.0 2.1E-51 4.6E-56 317.0 13.1 120 47-166 1-122 (122)
4 TIGR01067 rplN_bact ribosomal 100.0 3.3E-51 7.1E-56 315.8 13.1 120 47-166 1-122 (122)
5 PF00238 Ribosomal_L14: Riboso 100.0 1.1E-49 2.4E-54 306.7 10.2 120 47-166 1-122 (122)
6 TIGR03673 rpl14p_arch 50S ribo 100.0 3.7E-49 8.1E-54 307.9 12.5 116 47-166 10-131 (131)
7 PTZ00054 60S ribosomal protein 100.0 3.9E-49 8.4E-54 310.3 12.4 116 47-166 18-139 (139)
8 PRK08571 rpl14p 50S ribosomal 100.0 7.8E-49 1.7E-53 306.4 12.7 116 47-166 11-132 (132)
9 PTZ00320 ribosomal protein L14 100.0 1.1E-47 2.4E-52 312.5 12.8 117 50-166 62-188 (188)
10 KOG0901 60S ribosomal protein 100.0 4.4E-35 9.6E-40 231.6 11.0 125 41-166 12-145 (145)
11 KOG3441 Mitochondrial ribosoma 99.9 3.1E-23 6.7E-28 161.8 7.8 106 48-166 32-149 (149)
12 cd03696 selB_II selB_II: this 50.8 34 0.00074 23.6 4.2 54 48-102 27-81 (83)
13 cd03695 CysN_NodQ_II CysN_NodQ 49.2 60 0.0013 22.6 5.3 61 35-102 18-79 (81)
14 cd03693 EF1_alpha_II EF1_alpha 40.1 56 0.0012 23.1 4.0 54 48-102 31-85 (91)
15 cd03698 eRF3_II_like eRF3_II_l 40.1 62 0.0013 22.4 4.2 54 48-102 27-81 (83)
16 PF08447 PAS_3: PAS fold; Int 38.3 47 0.001 21.9 3.3 32 108-139 55-86 (91)
17 cd04089 eRF3_II eRF3_II: domai 35.3 77 0.0017 21.9 4.1 54 48-102 26-80 (82)
18 PF10382 DUF2439: Protein of u 32.2 57 0.0012 23.3 3.0 28 116-144 20-49 (83)
19 cd03694 GTPBP_II Domain II of 30.5 1E+02 0.0023 21.6 4.1 61 36-101 19-84 (87)
20 PF01245 Ribosomal_L19: Riboso 29.8 1.4E+02 0.003 22.8 5.0 35 76-112 18-52 (113)
21 PF14578 GTP_EFTU_D4: Elongati 29.7 1.2E+02 0.0027 22.0 4.4 59 34-103 20-80 (81)
22 TIGR01024 rplS_bact ribosomal 29.0 1.1E+02 0.0024 23.6 4.3 34 76-111 18-51 (113)
23 PF00575 S1: S1 RNA binding do 28.5 1.3E+02 0.0028 19.7 4.1 31 96-131 2-32 (74)
24 CHL00084 rpl19 ribosomal prote 26.1 1.4E+02 0.003 23.2 4.4 34 76-111 22-55 (117)
25 smart00047 LYZ2 Lysozyme subfa 25.9 35 0.00076 26.8 1.1 23 3-28 37-59 (147)
26 COG1705 FlgJ Muramidase (flage 24.7 33 0.00071 29.1 0.8 24 3-29 72-95 (201)
27 PRK05338 rplS 50S ribosomal pr 24.3 1.5E+02 0.0033 22.9 4.3 34 76-111 18-51 (116)
28 COG0231 Efp Translation elonga 22.2 3.8E+02 0.0082 20.8 8.8 49 80-134 36-88 (131)
29 cd04497 hPOT1_OB1_like hPOT1_O 22.1 1.6E+02 0.0034 22.6 4.0 34 51-85 38-77 (138)
30 PF01272 GreA_GreB: Transcript 21.4 24 0.00053 24.4 -0.5 14 6-19 40-53 (77)
31 PF12508 DUF3714: Protein of u 20.6 89 0.0019 26.2 2.6 46 99-148 52-97 (200)
No 1
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.5e-53 Score=323.96 Aligned_cols=120 Identities=56% Similarity=0.863 Sum_probs=117.2
Q ss_pred hhhcCceEEEeeCcCcceEEEEEeeCC--ccccccCcEEEEEEeeecCCCccccceEEEEEEEeeeeeccCCCCeeEeec
Q 031097 47 FIQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSEVRFD 124 (166)
Q Consensus 47 MIq~~T~L~VaDNSGak~v~cI~vl~~--~k~a~vGD~I~vsVKk~~~~~kvKKg~V~kAvIVRtKk~~~R~dG~~ikFd 124 (166)
|||.+|+|+|||||||+.++||+++++ +++|.+||+|++|||++.|...+||||+++|||||||++++|+||++++||
T Consensus 1 miq~~t~l~vADNSGAk~v~~I~V~gg~~r~~A~vGD~ivvsVKka~P~~~vKkg~V~~AViVRtkk~~rR~DGs~i~Fd 80 (122)
T COG0093 1 MIQVQTRLNVADNSGAKEVMCIKVLGGSRRRYAGVGDIIVVSVKKAIPRGMVKKGDVVKAVVVRTKKEVRRPDGSYIKFD 80 (122)
T ss_pred CcccccEEEEccCCCCcEEEEEEEeccccccccCCCCEEEEEEeeccCCcceeccceEEEEEEEeCCceEcCCCCEEEeC
Confidence 899999999999999999999999976 569999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEcCCCCccceEEeccchhhhhcCCCchheccccccC
Q 031097 125 DNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 166 (166)
Q Consensus 125 dNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~ii 166 (166)
||||||+|++++|+||||||||++|||+++|+||+|||++++
T Consensus 81 dNA~Viin~~g~P~GtrI~GPVaRElr~~~~~kI~SlA~eVv 122 (122)
T COG0093 81 DNAAVIINPDGEPRGTRIFGPVARELRERGFMKIASLAPEVV 122 (122)
T ss_pred CceEEEECCCCCcccceEecchhHHHHhcCCceeeecceecC
Confidence 999999999999999999999999999999999999999975
No 2
>CHL00057 rpl14 ribosomal protein L14
Probab=100.00 E-value=1.1e-51 Score=318.54 Aligned_cols=120 Identities=48% Similarity=0.787 Sum_probs=116.9
Q ss_pred hhhcCceEEEeeCcCcceEEEEEeeCC--ccccccCcEEEEEEeeecCCCccccceEEEEEEEeeeeeccCCCCeeEeec
Q 031097 47 FIQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSEVRFD 124 (166)
Q Consensus 47 MIq~~T~L~VaDNSGak~v~cI~vl~~--~k~a~vGD~I~vsVKk~~~~~kvKKg~V~kAvIVRtKk~~~R~dG~~ikFd 124 (166)
|||.+|+|+|+|||||+.++||++|++ +++|++||+|+||||+++|+++++|||+++|||||||++++|+||++++||
T Consensus 1 MIq~~t~l~v~DNSGak~v~cI~v~~~~~~~~a~vGD~IvvsVk~~~~~~k~kkg~v~kAvIVrtk~~~~r~dG~~i~F~ 80 (122)
T CHL00057 1 MIQPQTYLNVADNSGARKLMCIRVLGASNRKYAHIGDVIIAVVKEAVPNMPLKRSEVVRAVIVRTCKELKRDNGMIIRFD 80 (122)
T ss_pred CCCcCCEEEEeECCCCcEEEEEEEeCCCCCccccCCCEEEEEEEeccCCCceecCCEEEEEEEEeccccCcCCCcEEEcC
Confidence 999999999999999999999999974 578999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEcCCCCccceEEeccchhhhhcCCCchheccccccC
Q 031097 125 DNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 166 (166)
Q Consensus 125 dNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~ii 166 (166)
|||+||+|++++|+||||+||||+|||+++|+||+|||++++
T Consensus 81 ~Na~VLin~~~~p~GTrI~Gpv~~elr~k~~~Ki~sla~~vi 122 (122)
T CHL00057 81 DNAAVVIDQEGNPKGTRVFGPIARELREKNFTKIVSLAPEVL 122 (122)
T ss_pred CceEEEECCCCCEeEeEEEccchHHHhhcCCeEEEecccccC
Confidence 999999999999999999999999999999999999999885
No 3
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=100.00 E-value=2.1e-51 Score=316.97 Aligned_cols=120 Identities=61% Similarity=0.897 Sum_probs=116.7
Q ss_pred hhhcCceEEEeeCcCcceEEEEEeeCC--ccccccCcEEEEEEeeecCCCccccceEEEEEEEeeeeeccCCCCeeEeec
Q 031097 47 FIQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSEVRFD 124 (166)
Q Consensus 47 MIq~~T~L~VaDNSGak~v~cI~vl~~--~k~a~vGD~I~vsVKk~~~~~kvKKg~V~kAvIVRtKk~~~R~dG~~ikFd 124 (166)
|||.+|+|+|+|||||+.++||+++++ +++|++||+|+||||+..|+++++||++++|||||||++++|+||++++||
T Consensus 1 MIq~~t~l~v~DNSGak~v~cI~v~g~~~~~~a~iGD~I~vsVkk~~~~~~~kkg~v~~AvIVrtkk~~~r~dG~~i~F~ 80 (122)
T PRK05483 1 MIQQETRLNVADNSGAKEVMCIKVLGGSKRRYASIGDVIVVSVKEAIPRGKVKKGDVVKAVVVRTKKGVRRPDGSYIRFD 80 (122)
T ss_pred CCCCCCEEEEeECCCCCEEEEEEEeCCCCCCccccCCEEEEEEEEcCCCCcccCCCEeeEEEEEeccceecCCCCEEEcC
Confidence 999999999999999999999999975 568999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEcCCCCccceEEeccchhhhhcCCCchheccccccC
Q 031097 125 DNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 166 (166)
Q Consensus 125 dNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~ii 166 (166)
|||+||+|++++|+||||+||||+|||+++|+||+|||++++
T Consensus 81 dNavVLin~~~~p~GTrI~Gpv~~elr~~~~~Ki~sla~~v~ 122 (122)
T PRK05483 81 DNAAVLLNNDGEPRGTRIFGPVARELRDKKFMKIVSLAPEVL 122 (122)
T ss_pred CCEEEEECCCCCEeEeEEeccchHHHhhcCCcEEEecccccC
Confidence 999999999999999999999999999999999999999875
No 4
>TIGR01067 rplN_bact ribosomal protein L14, bacterial/organelle. This model distinguishes bacterial and most organellar examples of ribosomal protein L14 from all archaeal and eukaryotic forms.
Probab=100.00 E-value=3.3e-51 Score=315.83 Aligned_cols=120 Identities=56% Similarity=0.849 Sum_probs=116.8
Q ss_pred hhhcCceEEEeeCcCcceEEEEEeeCC--ccccccCcEEEEEEeeecCCCccccceEEEEEEEeeeeeccCCCCeeEeec
Q 031097 47 FIQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSEVRFD 124 (166)
Q Consensus 47 MIq~~T~L~VaDNSGak~v~cI~vl~~--~k~a~vGD~I~vsVKk~~~~~kvKKg~V~kAvIVRtKk~~~R~dG~~ikFd 124 (166)
|||.+|+|+|+|||||+.++||++|++ +++|++||+|+||||+++|+++++|||+++|||||||++++|+||++++||
T Consensus 1 MIq~~t~l~v~DNSGak~v~cI~v~~~~~~~~a~iGD~I~vsVk~~~~~~~~kkg~v~~AvIVrtkk~~~r~dG~~i~F~ 80 (122)
T TIGR01067 1 MIQQQSRLNVADNSGAKKVQCIKVLGGSRRRYATVGDVIVVVVKDAIPNGKVKKGDVVKAVIVRTKKGVRRKDGSYIRFD 80 (122)
T ss_pred CCCcCCEEEEeECCCCcEEEEEEEeCCCCCCccccCCEEEEEEEEcCCCCccccccEEEEEEEEeecceEeCCCCEEECC
Confidence 999999999999999999999999975 468999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEcCCCCccceEEeccchhhhhcCCCchheccccccC
Q 031097 125 DNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 166 (166)
Q Consensus 125 dNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~ii 166 (166)
|||+||+|++++|+||||+||||+|||+++|+||+|||++++
T Consensus 81 ~Na~VLin~~~~p~GTrI~Gpv~~elr~~~~~Ki~sla~~i~ 122 (122)
T TIGR01067 81 DNACVLINKNKEPRGTRIFGPVARELRDKGFMKIVSLAPEVI 122 (122)
T ss_pred CceEEEECCCCCEeeeEEEccchHHHhhcCCceeeeccchhC
Confidence 999999999999999999999999999999999999999885
No 5
>PF00238 Ribosomal_L14: Ribosomal protein L14p/L23e; InterPro: IPR000218 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 L14 is one of the proteins from the large ribosomal subunit. In eubacteria, L14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities []. Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins []. L14 is a protein of 119 to 137 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_M 4A1C_J 4A1E_J 4A1A_J 4A17_J 1VSP_I 3D5D_O 1VSA_I 3MRZ_K 3F1F_O ....
Probab=100.00 E-value=1.1e-49 Score=306.68 Aligned_cols=120 Identities=60% Similarity=0.879 Sum_probs=114.1
Q ss_pred hhhcCceEEEeeCcCcceEEEEEeeCC--ccccccCcEEEEEEeeecCCCccccceEEEEEEEeeeeeccCCCCeeEeec
Q 031097 47 FIQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSEVRFD 124 (166)
Q Consensus 47 MIq~~T~L~VaDNSGak~v~cI~vl~~--~k~a~vGD~I~vsVKk~~~~~kvKKg~V~kAvIVRtKk~~~R~dG~~ikFd 124 (166)
|||.+|+|+|+|||||++++||+++++ +++|++||+|++|||+.+|+.++|||++++|+|||||++++|.||++++||
T Consensus 1 MIq~~t~L~v~DNSGak~v~cI~v~~~~~~~~a~vGD~I~vsVkk~~~~~~vkkg~v~~avIVrtk~~~~r~dg~~i~F~ 80 (122)
T PF00238_consen 1 MIQKGTILKVADNSGAKKVKCIKVLGGKRRKYASVGDIIVVSVKKGRPKSKVKKGQVYKAVIVRTKKPIRRKDGSFIKFD 80 (122)
T ss_dssp -BETTEEEEESBSSSEEEEEEEEETSSTTTSEE-TTSEEEEEEEEE-SSSSSTTTEEEEEEEEECSSEEETTTSEEEEES
T ss_pred CCCCCCEEEEeeCCCCcEEEEEEEeCCcCccccccceEEEEEEeecccCccccccceEEEEEEEEeEEEEEeCCcEEEeC
Confidence 999999999999999999999999975 678999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEcCCCCccceEEeccchhhhhcCCCchheccccccC
Q 031097 125 DNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 166 (166)
Q Consensus 125 dNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~ii 166 (166)
|||+||+|++++|+||||+||||+|||+++|+||+|||++||
T Consensus 81 ~Na~VLln~~~~p~GtrI~Gpv~~elr~~~~~ki~sla~~iv 122 (122)
T PF00238_consen 81 DNAVVLLNKKGNPLGTRIFGPVPRELRKKKFPKILSLASRIV 122 (122)
T ss_dssp SEEEEEEETTSSBSSSSBCSEEEHHHHHTTSHHHHHHSSCEE
T ss_pred CccEEEEcCCCCEeeeEEEeeehHHhhHcCCchHHhhccccC
Confidence 999999999999999999999999999999999999999885
No 6
>TIGR03673 rpl14p_arch 50S ribosomal protein L14P. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in 2 intersubunit bridges.
Probab=100.00 E-value=3.7e-49 Score=307.86 Aligned_cols=116 Identities=40% Similarity=0.574 Sum_probs=109.9
Q ss_pred hhhcCceEEEeeCcCcceEEEEEeeC---C--c-cccccCcEEEEEEeeecCCCccccceEEEEEEEeeeeeccCCCCee
Q 031097 47 FIQMRTVLKVVDNSGAKTVMCIQPLK---G--R-KVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSE 120 (166)
Q Consensus 47 MIq~~T~L~VaDNSGak~v~cI~vl~---~--~-k~a~vGD~I~vsVKk~~~~~kvKKg~V~kAvIVRtKk~~~R~dG~~ 120 (166)
|||.+|+|+|+|||||++++||++++ + + ++|.+||+|+||||++.| ++|||+++|||||||++++|+||++
T Consensus 10 mIq~~t~L~VaDNSGak~v~cI~vl~~~g~~~r~~~a~iGD~IvvsVK~~~p---~~kg~v~kAVIVRtkk~~~R~dGs~ 86 (131)
T TIGR03673 10 ALPVGSLLVCADNTGAKEVEVISVKGYKGVKRRLPCAGVGDMVVVSVKKGTP---EMRKQVFKAVVVRQRKEYRRPDGTR 86 (131)
T ss_pred eeccCCEEEEeeCCCCceEEEEEEeeeCCCcccCCccccCCEEEEEEEECCc---cccCCEeEEEEEEeCcceecCCCcE
Confidence 99999999999999999999999983 2 3 569999999999999999 5789999999999999999999999
Q ss_pred EeecCceEEEEcCCCCccceEEeccchhhhhcCCCchheccccccC
Q 031097 121 VRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 166 (166)
Q Consensus 121 ikFddNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~ii 166 (166)
++|||||+||+|++++|+|||||||||+|| +++|+||+|||++++
T Consensus 87 i~FddNa~VLin~~~~P~GTRI~GpV~rEl-~~~~~Ki~SlA~~vi 131 (131)
T TIGR03673 87 VKFEDNAVVIVTPDGEPKGTEIKGPVAREA-AERWPKIASIASIIV 131 (131)
T ss_pred EEeCCcEEEEECCCCCEeeeEEEccchHHH-HhCccHheeccchhC
Confidence 999999999999999999999999999999 567999999999885
No 7
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=100.00 E-value=3.9e-49 Score=310.35 Aligned_cols=116 Identities=34% Similarity=0.475 Sum_probs=110.4
Q ss_pred hhhcCceEEEeeCcCcceEEEEEeeC---C--c-cccccCcEEEEEEeeecCCCccccceEEEEEEEeeeeeccCCCCee
Q 031097 47 FIQMRTVLKVVDNSGAKTVMCIQPLK---G--R-KVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSE 120 (166)
Q Consensus 47 MIq~~T~L~VaDNSGak~v~cI~vl~---~--~-k~a~vGD~I~vsVKk~~~~~kvKKg~V~kAvIVRtKk~~~R~dG~~ 120 (166)
|||.+|+|+|+|||||++++||++++ + + ++|.+||+|+||||++.| ++|||+++|||||||++++|+||++
T Consensus 18 mIq~~t~L~vaDNSGAk~v~cI~vlg~~g~~~r~~~a~iGD~IvvsVKk~~p---~~kg~V~kAVIVRtKk~~rR~dGs~ 94 (139)
T PTZ00054 18 GLPVGAVVNCADNSGAKNLYIIAVKGIHGRLNRLPSASLGDMVLATVKKGKP---ELRKKVLNAVIIRQRKAWRRKDGVF 94 (139)
T ss_pred eecCCCEEEEeeCCCccEEEEEEEeccCcCCccCcccccCCEEEEEEEECCC---cccCCEeeEEEEEECcceEcCCCcE
Confidence 99999999999999999999999996 3 2 479999999999999999 6789999999999999999999999
Q ss_pred EeecCceEEEEcCCCCccceEEeccchhhhhcCCCchheccccccC
Q 031097 121 VRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 166 (166)
Q Consensus 121 ikFddNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~ii 166 (166)
++|||||+||+|++++|+|||||||||+|| +++|+||+|||++++
T Consensus 95 i~F~dNA~VLin~~~~p~GTRI~GpV~rEl-~~~~~KI~SLA~~vi 139 (139)
T PTZ00054 95 IYFEDNAGVIVNPKGEMKGSAITGPVAKEC-ADLWPKISSAAPAIV 139 (139)
T ss_pred EEeCCcEEEEECCCCCEeeeEEeCchhHHH-HhCccHhhccccccC
Confidence 999999999999999999999999999999 567999999999986
No 8
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=100.00 E-value=7.8e-49 Score=306.39 Aligned_cols=116 Identities=38% Similarity=0.530 Sum_probs=109.8
Q ss_pred hhhcCceEEEeeCcCcceEEEEEeeC---C-c--cccccCcEEEEEEeeecCCCccccceEEEEEEEeeeeeccCCCCee
Q 031097 47 FIQMRTVLKVVDNSGAKTVMCIQPLK---G-R--KVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSE 120 (166)
Q Consensus 47 MIq~~T~L~VaDNSGak~v~cI~vl~---~-~--k~a~vGD~I~vsVKk~~~~~kvKKg~V~kAvIVRtKk~~~R~dG~~ 120 (166)
|||.+|+|+|+|||||+.++||++++ + + ++|.+||+|+||||++.| ++|||+++|||||||++++|+||++
T Consensus 11 mIq~~T~L~VaDNSGAk~v~cI~vlg~~g~~~r~~~a~iGD~IvvsVK~~~p---~~kg~v~kAVIVRtkk~~~R~dGs~ 87 (132)
T PRK08571 11 GLPVGARLVCADNTGAKEVEIISVKGYKGVKRRLPKAGVGDMVVVSVKKGTP---EMRKQVLRAVVVRQRKEYRRPDGTR 87 (132)
T ss_pred eecCCCEEEEeeCCCCCeEEEEEEeccCCCCccCCccccCCEEEEEEEECCC---cccCCEeEEEEEEeccceEcCCCcE
Confidence 99999999999999999999999985 2 2 469999999999999999 5789999999999999999999999
Q ss_pred EeecCceEEEEcCCCCccceEEeccchhhhhcCCCchheccccccC
Q 031097 121 VRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 166 (166)
Q Consensus 121 ikFddNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~ii 166 (166)
++|||||+||+|++++|+||||+||||+|| +++|+||+|||++++
T Consensus 88 i~F~dNa~VLin~~~~p~GTRI~GpV~~El-~~~~~Ki~sLA~~vi 132 (132)
T PRK08571 88 VKFEDNAAVIVTPEGTPKGTEIKGPVAREA-AERWPKIASIASIIV 132 (132)
T ss_pred EEeCCcEEEEECCCCCEeeeEEeccchHHH-hhCCchheeccchhC
Confidence 999999999999999999999999999999 567999999999885
No 9
>PTZ00320 ribosomal protein L14; Provisional
Probab=100.00 E-value=1.1e-47 Score=312.53 Aligned_cols=117 Identities=25% Similarity=0.332 Sum_probs=113.6
Q ss_pred cCceEEEeeCcCcceEEEEEeeCCccccccCcE----EEEEEeeecC------CCccccceEEEEEEEeeeeeccCCCCe
Q 031097 50 MRTVLKVVDNSGAKTVMCIQPLKGRKVARLGDT----IVASVKEAMP------TGKVKKGQVVHAVVVRAAMQHGRFDGS 119 (166)
Q Consensus 50 ~~T~L~VaDNSGak~v~cI~vl~~~k~a~vGD~----I~vsVKk~~~------~~kvKKg~V~kAvIVRtKk~~~R~dG~ 119 (166)
-+|+|+|+||||||+++||+++.++++|++||+ |+||||++.| ++++|||||++|||||||++++|+||+
T Consensus 62 ~qT~L~VaDNSGAK~V~CIkVl~~rr~A~IGDi~~~~IvVsVKka~P~~~~~~~~kVKKG~V~kAVIVRTKK~irR~DGs 141 (188)
T PTZ00320 62 DQVKLHCVDNTNCKHVRLISKATAERFAHCRVFPAVAHRVSVQRFKSGRGEVSRHRVKPGNIYWVCLLSRRQTNTRMSGL 141 (188)
T ss_pred CCcEEEEEeCCCCcEEEEEEEecCCCceeeccccCceEEEEEeecccCccccccCceecCCEEEEEEEEECcccCCCCCC
Confidence 379999999999999999999977899999999 9999999999 789999999999999999999999999
Q ss_pred eEeecCceEEEEcCCCCccceEEeccchhhhhcCCCchheccccccC
Q 031097 120 EVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 166 (166)
Q Consensus 120 ~ikFddNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~ii 166 (166)
+++||||||||+|++++|+||||||||++|||+++|+||+|||+.|+
T Consensus 142 ~IrFDdNAaVLIN~qgePlGTRIfGPVaRELR~k~f~KIvSLAp~~~ 188 (188)
T PTZ00320 142 QTNFDRNTCILMNDQRVPLGTRVMYCAGRHVNHKYHLKAVVLANFFV 188 (188)
T ss_pred EEEeCCcEEEEECCCCCEeeeEEecchhHHHhhcCCceeeecccccC
Confidence 99999999999999999999999999999999999999999999875
No 10
>KOG0901 consensus 60S ribosomal protein L14/L17/L23 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.4e-35 Score=231.59 Aligned_cols=125 Identities=39% Similarity=0.546 Sum_probs=116.5
Q ss_pred chhhhh-hhhcCceEEEeeCcCcceEEEEEeeC--C----ccccccCcEEEEEEee--ecCCCccccceEEEEEEEeeee
Q 031097 41 SQQQRT-FIQMRTVLKVVDNSGAKTVMCIQPLK--G----RKVARLGDTIVASVKE--AMPTGKVKKGQVVHAVVVRAAM 111 (166)
Q Consensus 41 ~~~~~~-MIq~~T~L~VaDNSGak~v~cI~vl~--~----~k~a~vGD~I~vsVKk--~~~~~kvKKg~V~kAvIVRtKk 111 (166)
.++|.. |||.+|.++|+||||||.++||++.+ + .+.|.+||+++++||+ ..|+.++|.|+++.|+|||+++
T Consensus 12 ~k~r~s~~~~~g~~incaDNSgAknL~~isv~g~~Grlnrl~~A~~GD~vva~vKka~~~Pe~r~k~g~~~~avvVr~~k 91 (145)
T KOG0901|consen 12 VKFRISLGLPVGAVINCADNSGAKNLYCISVKGIKGRLNRLPAAGVGDMVVATVKKAHGKPELRKKVGEVLPAVVVRQKK 91 (145)
T ss_pred hhhhhhhccccceEEEecCCCCcceEEEEEEeccccccccccCCCcCCEEEEEEecccCCCccCcEecccceeeEEeecc
Confidence 334443 99999999999999999999999987 4 3589999999999999 7999999999999999999999
Q ss_pred eccCCCCeeEeecCceEEEEcCCCCccceEEeccchhhhhcCCCchheccccccC
Q 031097 112 QHGRFDGSEVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 166 (166)
Q Consensus 112 ~~~R~dG~~ikFddNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~ii 166 (166)
+..|.||++++|+|||+|++|++++|.||+|+|||++|++. .|++|+|+|+.++
T Consensus 92 ~~~r~dgs~~~f~dnA~v~~~~~~e~~gs~i~G~v~~e~~~-~~~kias~A~~i~ 145 (145)
T KOG0901|consen 92 SKRRKDGSIAYFEDNAGVIVNNKGEPKGSAITGPVGKELAD-LWPKIASLAGLVV 145 (145)
T ss_pred ccccCCCcEEEEcCceEEEEcccCccccceeccccChhHhh-hhHHHHhhccccC
Confidence 99999999999999999999999999999999999999999 7999999998764
No 11
>KOG3441 consensus Mitochondrial ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=3.1e-23 Score=161.85 Aligned_cols=106 Identities=39% Similarity=0.628 Sum_probs=94.5
Q ss_pred hhcCceEEEeeCcCc--------ceEEEEEeeCCccccccCcEEEEEEeeecCCCccccceEEEEEEEeeeeeccCCCCe
Q 031097 48 IQMRTVLKVVDNSGA--------KTVMCIQPLKGRKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGS 119 (166)
Q Consensus 48 Iq~~T~L~VaDNSGa--------k~v~cI~vl~~~k~a~vGD~I~vsVKk~~~~~kvKKg~V~kAvIVRtKk~~~R~dG~ 119 (166)
|++.|+|+|+|||.. +..+||++|+++..+.+||.|+|+|| ||..+|+||....+. +.|
T Consensus 32 I~k~tRlrVVDNSaLGk~a~~~gr~PrCIHVYkkrgvg~~GDkiLvAIk----------GQmkKa~vVGh~~~~--k~~- 98 (149)
T KOG3441|consen 32 IHKRTRLRVVDNSALGKEADTTGRLPRCIHVYKKRGVGELGDKILVAIK----------GQMKKAYVVGHVHYR--KHG- 98 (149)
T ss_pred hhhhheEEEecchhhcccccccCCCCceEEEEecccccccccEEEEEEe----------cceeeeEEEEeeccC--CCC-
Confidence 788999999999954 67899999998889999999999997 899999999966543 334
Q ss_pred eEeecCceEEEEcCCCCccceEEeccchhhhhcC----CCchheccccccC
Q 031097 120 EVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRK----KHVSILTLAEHLA 166 (166)
Q Consensus 120 ~ikFddNavVLln~k~~plGTRI~GpV~~Elr~k----k~~KI~SLA~~ii 166 (166)
.++||.|.+||+|++|+|+||||.-|||..||.. .|+|++++|++||
T Consensus 99 ~P~fDsNniVLiddnGnPlGtRI~~PIPT~Lr~~~~~~~ysKVLAiA~~fv 149 (149)
T KOG3441|consen 99 VPVFDSNNIVLIDDNGNPLGTRITAPIPTKLRANRGNVQYSKVLAIANKFV 149 (149)
T ss_pred CcccCCCcEEEECCCCCcccceEeccCcHHHHhccCCcchhhHHHHHhhcC
Confidence 4799999999999999999999999999999832 5999999999886
No 12
>cd03696 selB_II selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.
Probab=50.84 E-value=34 Score=23.57 Aligned_cols=54 Identities=15% Similarity=0.257 Sum_probs=34.0
Q ss_pred hhcCceEEEeeCcCcceEEEEEeeCC-ccccccCcEEEEEEeeecCCCccccceEE
Q 031097 48 IQMRTVLKVVDNSGAKTVMCIQPLKG-RKVARLGDTIVASVKEAMPTGKVKKGQVV 102 (166)
Q Consensus 48 Iq~~T~L~VaDNSGak~v~cI~vl~~-~k~a~vGD~I~vsVKk~~~~~kvKKg~V~ 102 (166)
|+.+..+.+.++--.-.++=|+.... ...|..||.|-+.++...+ ..+++|++.
T Consensus 27 i~~g~~v~~~p~~~~~~V~sI~~~~~~~~~a~aGd~v~i~l~~~~~-~~i~~G~vl 81 (83)
T cd03696 27 VKVGDKVEILPLGEETRVRSIQVHGKDVEEAKAGDRVALNLTGVDA-KDLERGDVL 81 (83)
T ss_pred EeCCCEEEECCCCceEEEEEEEECCcCcCEEcCCCEEEEEEcCCCH-HHcCCccEE
Confidence 67788888887432333444443222 3578899999999976544 346666653
No 13
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=49.22 E-value=60 Score=22.58 Aligned_cols=61 Identities=20% Similarity=0.364 Sum_probs=39.8
Q ss_pred ccccccchhhhhhhhcCceEEEeeCcCcceEEEEEeeCC-ccccccCcEEEEEEeeecCCCccccceEE
Q 031097 35 ASGNFLSQQQRTFIQMRTVLKVVDNSGAKTVMCIQPLKG-RKVARLGDTIVASVKEAMPTGKVKKGQVV 102 (166)
Q Consensus 35 ~c~~~~~~~~~~MIq~~T~L~VaDNSGak~v~cI~vl~~-~k~a~vGD~I~vsVKk~~~~~kvKKg~V~ 102 (166)
.++...++. ++.+..+.+.+.-=.-.++-|+.... -..|..||.|-+.++. ...+++|++.
T Consensus 18 v~Gkv~~G~----v~~Gd~v~~~P~~~~~~V~si~~~~~~~~~a~aGd~v~l~l~~---~~~i~~G~vl 79 (81)
T cd03695 18 YAGTIASGS----IRVGDEVVVLPSGKTSRVKSIETFDGELDEAGAGESVTLTLED---EIDVSRGDVI 79 (81)
T ss_pred EEEEEccce----EECCCEEEEcCCCCeEEEEEEEECCcEeCEEcCCCEEEEEECC---ccccCCCCEE
Confidence 455555554 56777888877532335667765544 4578999999999973 3446777764
No 14
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=40.13 E-value=56 Score=23.11 Aligned_cols=54 Identities=19% Similarity=0.211 Sum_probs=34.7
Q ss_pred hhcCceEEEeeCcCcceEEEEEeeCC-ccccccCcEEEEEEeeecCCCccccceEE
Q 031097 48 IQMRTVLKVVDNSGAKTVMCIQPLKG-RKVARLGDTIVASVKEAMPTGKVKKGQVV 102 (166)
Q Consensus 48 Iq~~T~L~VaDNSGak~v~cI~vl~~-~k~a~vGD~I~vsVKk~~~~~kvKKg~V~ 102 (166)
|+.+..+.+.-+-=.-.++-|+..+. ...|..||.+-+.++...+ ..+++|++.
T Consensus 31 i~~gd~v~i~P~~~~~~V~sI~~~~~~~~~a~aG~~v~i~l~~i~~-~~v~~G~vl 85 (91)
T cd03693 31 LKPGMVVTFAPAGVTGEVKSVEMHHEPLEEALPGDNVGFNVKNVSK-KDIKRGDVA 85 (91)
T ss_pred eecCCEEEECCCCcEEEEEEEEECCcCcCEECCCCEEEEEECCCCH-HHcCCcCEE
Confidence 66777777776422234566655443 4678899999999975432 456677764
No 15
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=40.12 E-value=62 Score=22.36 Aligned_cols=54 Identities=20% Similarity=0.185 Sum_probs=33.7
Q ss_pred hhcCceEEEeeCcCcceEEEEEeeCC-ccccccCcEEEEEEeeecCCCccccceEE
Q 031097 48 IQMRTVLKVVDNSGAKTVMCIQPLKG-RKVARLGDTIVASVKEAMPTGKVKKGQVV 102 (166)
Q Consensus 48 Iq~~T~L~VaDNSGak~v~cI~vl~~-~k~a~vGD~I~vsVKk~~~~~kvKKg~V~ 102 (166)
|+.+..+.+.-.--.-.++-|+.... ...|..||.+-+.++...+ ..+++|++.
T Consensus 27 i~~Gd~v~i~P~~~~~~V~si~~~~~~~~~a~aGd~v~~~l~~~~~-~~v~~G~vl 81 (83)
T cd03698 27 IQKGDTLLVMPSKESVEVKSIYVDDEEVDYAVAGENVRLKLKGIDE-EDISPGDVL 81 (83)
T ss_pred EeCCCEEEEeCCCcEEEEEEEEECCeECCEECCCCEEEEEECCCCH-HHCCCCCEE
Confidence 55677777766432234566655443 4578999999999975433 245667654
No 16
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=38.27 E-value=47 Score=21.85 Aligned_cols=32 Identities=16% Similarity=0.230 Sum_probs=25.7
Q ss_pred eeeeeccCCCCeeEeecCceEEEEcCCCCccc
Q 031097 108 RAAMQHGRFDGSEVRFDDNAVVLVNKAGEPTG 139 (166)
Q Consensus 108 RtKk~~~R~dG~~ikFddNavVLln~k~~plG 139 (166)
.....++++||.+.-+...+.++-|++|+|..
T Consensus 55 ~~e~R~~~~~G~~~wi~~~~~~~~d~~g~~~~ 86 (91)
T PF08447_consen 55 EIEYRIRRKDGEYRWIEVRGRPIFDENGKPIR 86 (91)
T ss_dssp EEEEEEEGTTSTEEEEEEEEEEEETTTS-EEE
T ss_pred EEEEEEECCCCCEEEEEEEEEEEECCCCCEEE
Confidence 34455678999999999999999999998853
No 17
>cd04089 eRF3_II eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-li
Probab=35.29 E-value=77 Score=21.87 Aligned_cols=54 Identities=22% Similarity=0.229 Sum_probs=33.1
Q ss_pred hhcCceEEEeeCcCcceEEEEEeeCC-ccccccCcEEEEEEeeecCCCccccceEE
Q 031097 48 IQMRTVLKVVDNSGAKTVMCIQPLKG-RKVARLGDTIVASVKEAMPTGKVKKGQVV 102 (166)
Q Consensus 48 Iq~~T~L~VaDNSGak~v~cI~vl~~-~k~a~vGD~I~vsVKk~~~~~kvKKg~V~ 102 (166)
++.+-.+.+...--.-.++-|+..+. ...|..||.+-+.++...+ ..+++|++.
T Consensus 26 i~~G~~v~i~P~~~~~~V~si~~~~~~~~~a~aGd~v~l~l~~i~~-~~v~~G~vl 80 (82)
T cd04089 26 IKKGDKLLVMPNKTQVEVLSIYNEDVEVRYARPGENVRLRLKGIEE-EDISPGFVL 80 (82)
T ss_pred EecCCEEEEeCCCcEEEEEEEEECCEECCEECCCCEEEEEecCCCH-HHCCCCCEE
Confidence 55566666665422234555654433 3568899999999975443 346667664
No 18
>PF10382 DUF2439: Protein of unknown function (DUF2439); InterPro: IPR018838 This domain is found at the N-terminal of proteins implicated in telomere maintenance in Saccharomyces cerevisiae (Baker's yeast) [] and in meiotic chromosome segregation in Schizosaccharomyces pombe (Fission yeast) [].
Probab=32.24 E-value=57 Score=23.33 Aligned_cols=28 Identities=21% Similarity=0.541 Sum_probs=22.2
Q ss_pred CCCeeEeec--CceEEEEcCCCCccceEEec
Q 031097 116 FDGSEVRFD--DNAVVLVNKAGEPTGTRVFG 144 (166)
Q Consensus 116 ~dG~~ikFd--dNavVLln~k~~plGTRI~G 144 (166)
.||. ++|. .|-+.|.|+++..+|+.+.-
T Consensus 20 ~DG~-l~~~~~~~kv~Lyde~~~~i~~~~~~ 49 (83)
T PF10382_consen 20 HDGF-LKYHSFNKKVMLYDEDGNLIGSDFLK 49 (83)
T ss_pred ECCE-EEEEeCCCEEEEEcCCCCEEeEEEEe
Confidence 4887 4555 77799999999999998764
No 19
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=30.45 E-value=1e+02 Score=21.56 Aligned_cols=61 Identities=23% Similarity=0.318 Sum_probs=37.9
Q ss_pred cccccchhhhhhhhcCceEEEeeCc-C---cceEEEEEeeCC-ccccccCcEEEEEEeeecCCCccccceE
Q 031097 36 SGNFLSQQQRTFIQMRTVLKVVDNS-G---AKTVMCIQPLKG-RKVARLGDTIVASVKEAMPTGKVKKGQV 101 (166)
Q Consensus 36 c~~~~~~~~~~MIq~~T~L~VaDNS-G---ak~v~cI~vl~~-~k~a~vGD~I~vsVKk~~~~~kvKKg~V 101 (166)
++...++. ++++..+.+...- | .-.++-|+..+. -..|..||.+-+.++...+ ..+++|.+
T Consensus 19 ~G~v~~G~----v~~g~~v~~~P~~~g~~~~~~V~sI~~~~~~~~~a~aGd~v~l~l~~i~~-~~i~~G~v 84 (87)
T cd03694 19 GGTVSKGV----IRLGDTLLLGPDQDGSFRPVTVKSIHRNRSPVRVVRAGQSASLALKKIDR-SLLRKGMV 84 (87)
T ss_pred EEEEecCE----EeCCCEEEECCCCCCCEeEEEEEEEEECCeECCEECCCCEEEEEEcCCCH-HHcCCccE
Confidence 44444444 5567777777642 3 235666665443 3578999999999976544 34555654
No 20
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 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 L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=29.77 E-value=1.4e+02 Score=22.84 Aligned_cols=35 Identities=26% Similarity=0.283 Sum_probs=25.8
Q ss_pred ccccCcEEEEEEeeecCCCccccceEEEEEEEeeeee
Q 031097 76 VARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQ 112 (166)
Q Consensus 76 ~a~vGD~I~vsVKk~~~~~kvKKg~V~kAvIVRtKk~ 112 (166)
.-.+||+|.|.++...... .+-|.+.|+++.-+..
T Consensus 18 ~f~~GD~v~V~~~i~e~~k--~r~q~f~GvvIa~~~~ 52 (113)
T PF01245_consen 18 EFRVGDTVRVTYKISEGNK--ERIQVFEGVVIARRRR 52 (113)
T ss_dssp SSSSSSEEEEEEEEESSSS--EEEEEEEEEEEEEEBS
T ss_pred CcCCCCEEEEEEEEecCCC--ceeEEEEEEEEEEECC
Confidence 4579999999998653321 2468999999987763
No 21
>PF14578 GTP_EFTU_D4: Elongation factor Tu domain 4; PDB: 1G7R_A 1G7S_A 1G7T_A 1XE1_A.
Probab=29.73 E-value=1.2e+02 Score=21.98 Aligned_cols=59 Identities=22% Similarity=0.381 Sum_probs=36.1
Q ss_pred cccccccchhhhhhhhcCceEEEeeCcCcceEEEEEeeCCc--cccccCcEEEEEEeeecCCCccccceEEE
Q 031097 34 MASGNFLSQQQRTFIQMRTVLKVVDNSGAKTVMCIQPLKGR--KVARLGDTIVASVKEAMPTGKVKKGQVVH 103 (166)
Q Consensus 34 ~~c~~~~~~~~~~MIq~~T~L~VaDNSGak~v~cI~vl~~~--k~a~vGD~I~vsVKk~~~~~kvKKg~V~k 103 (166)
..|++.+.+. |..++.| |..-+-.++=|+. +++ ..|..||.|=+++.... .++.||+.+
T Consensus 20 ~IvG~V~~G~----ik~G~~l---~G~~iG~I~sIe~-~~k~v~~A~~G~eVai~Ieg~~---~i~eGDiLy 80 (81)
T PF14578_consen 20 AIVGEVLEGI----IKPGYPL---DGRKIGRIKSIED-NGKNVDEAKKGDEVAISIEGPT---QIKEGDILY 80 (81)
T ss_dssp EEEEEEEEEE----EETT-EE---CSSCEEEEEEEEE-TTEEESEEETT-EEEEEEET-----TB-TT-EEE
T ss_pred eEEEEEeeeE----EeCCCcc---CCEEEEEEEEeEE-CCcCccccCCCCEEEEEEeCCc---cCCCCCEEe
Confidence 4555665555 6778888 6655555666653 332 57999999999998644 788888875
No 22
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=28.98 E-value=1.1e+02 Score=23.58 Aligned_cols=34 Identities=32% Similarity=0.287 Sum_probs=24.2
Q ss_pred ccccCcEEEEEEeeecCCCccccceEEEEEEEeeee
Q 031097 76 VARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAM 111 (166)
Q Consensus 76 ~a~vGD~I~vsVKk~~~~~kvKKg~V~kAvIVRtKk 111 (166)
.-.+||+|.|.++-... .-++-|.+.++++..+.
T Consensus 18 ~f~~GD~v~V~~~i~eg--~k~R~q~f~GvvI~~~~ 51 (113)
T TIGR01024 18 DFRVGDTVRVHVKIVEG--KKERIQVFEGVVIARRG 51 (113)
T ss_pred ccCCCCEEEEEEEEccC--CceEcccEEEEEEEEeC
Confidence 45799999998874332 22346889999998774
No 23
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 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 S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=28.48 E-value=1.3e+02 Score=19.65 Aligned_cols=31 Identities=19% Similarity=0.241 Sum_probs=21.9
Q ss_pred cccceEEEEEEEeeeeeccCCCCeeEeecCceEEEE
Q 031097 96 VKKGQVVHAVVVRAAMQHGRFDGSEVRFDDNAVVLV 131 (166)
Q Consensus 96 vKKg~V~kAvIVRtKk~~~R~dG~~ikFddNavVLl 131 (166)
.+.|+++.|.|.+-. ++|.++.++++.-.++
T Consensus 2 ~~~G~iv~g~V~~v~-----~~g~~V~l~~~~~g~i 32 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVE-----DFGVFVDLGNGIEGFI 32 (74)
T ss_dssp SSTTSEEEEEEEEEE-----TTEEEEEESTSSEEEE
T ss_pred CCCCCEEEEEEEEEE-----CCEEEEEECCcEEEEE
Confidence 457888888888654 3688888885555544
No 24
>CHL00084 rpl19 ribosomal protein L19
Probab=26.10 E-value=1.4e+02 Score=23.19 Aligned_cols=34 Identities=21% Similarity=0.198 Sum_probs=23.3
Q ss_pred ccccCcEEEEEEeeecCCCccccceEEEEEEEeeee
Q 031097 76 VARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAM 111 (166)
Q Consensus 76 ~a~vGD~I~vsVKk~~~~~kvKKg~V~kAvIVRtKk 111 (166)
.-.+||+|.|.++-...+. .+-|.+.++|+..+.
T Consensus 22 ~f~~GDtV~V~~~i~eg~k--~R~q~F~GvvI~~r~ 55 (117)
T CHL00084 22 KIRVGDTVKVGVLIQEGNK--ERVQFYEGTVIAKKN 55 (117)
T ss_pred ccCCCCEEEEEEEEecCCe--eEeceEEEEEEEEeC
Confidence 4579999999986433211 235789999998653
No 25
>smart00047 LYZ2 Lysozyme subfamily 2. Eubacterial enzymes distantly related to eukaryotic lysozymes.
Probab=25.86 E-value=35 Score=26.79 Aligned_cols=23 Identities=48% Similarity=0.651 Sum_probs=18.3
Q ss_pred hhhhhcccccccccccCccccccccc
Q 031097 3 ASLASKWSRVGRSLLGGLGNNLSGLS 28 (166)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 28 (166)
|-|.|-| |+|.+..=.|||||.-
T Consensus 37 AiLESgw---G~S~La~~~nNlFGIK 59 (147)
T smart00047 37 AALESGW---GTSKLAKKYNNLFGIK 59 (147)
T ss_pred HHHHcCC---CCCCccCCCCCeeccc
Confidence 3455555 8999999999999994
No 26
>COG1705 FlgJ Muramidase (flagellum-specific) [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=24.73 E-value=33 Score=29.08 Aligned_cols=24 Identities=50% Similarity=0.787 Sum_probs=19.1
Q ss_pred hhhhhcccccccccccCcccccccccc
Q 031097 3 ASLASKWSRVGRSLLGGLGNNLSGLSS 29 (166)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 29 (166)
|-|.|-| |++.|..-+|||||.-.
T Consensus 72 AiLESgw---Gks~l~~~~~NLFGIK~ 95 (201)
T COG1705 72 AILESGW---GKSELASKGNNLFGIKG 95 (201)
T ss_pred HHHHcCC---cchhhccCCCCeeeeee
Confidence 3455555 99999999999999765
No 27
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=24.31 E-value=1.5e+02 Score=22.93 Aligned_cols=34 Identities=26% Similarity=0.206 Sum_probs=23.2
Q ss_pred ccccCcEEEEEEeeecCCCccccceEEEEEEEeeee
Q 031097 76 VARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAM 111 (166)
Q Consensus 76 ~a~vGD~I~vsVKk~~~~~kvKKg~V~kAvIVRtKk 111 (166)
.-.+||+|.|.++-.... -++-|.+.++++..+.
T Consensus 18 ~f~~GD~V~V~~~i~eg~--k~R~q~f~GvvI~~~~ 51 (116)
T PRK05338 18 EFRPGDTVRVHVKVVEGN--KERIQAFEGVVIARRG 51 (116)
T ss_pred CcCCCCEEEEEEEEccCC--ceEeccEEEEEEEEeC
Confidence 346999999988632221 1235789999998774
No 28
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=22.16 E-value=3.8e+02 Score=20.80 Aligned_cols=49 Identities=16% Similarity=0.233 Sum_probs=33.6
Q ss_pred CcEEEEEEeeecCCCc----cccceEEEEEEEeeeeeccCCCCeeEeecCceEEEEcCC
Q 031097 80 GDTIVASVKEAMPTGK----VKKGQVVHAVVVRAAMQHGRFDGSEVRFDDNAVVLVNKA 134 (166)
Q Consensus 80 GD~I~vsVKk~~~~~k----vKKg~V~kAvIVRtKk~~~R~dG~~ikFddNavVLln~k 134 (166)
|-++.+..|.+....+ .+-++.+...+|..+. .+++++|++..+++|.+
T Consensus 36 ~a~vrvk~k~l~tG~~~e~~f~~~~kve~a~ie~~~------~q~lY~dg~~~~FMD~e 88 (131)
T COG0231 36 GAFVRVKLKNLFTGKKVEKTFKADDKVEVAIVERKT------AQYLYIDGDFYVFMDLE 88 (131)
T ss_pred CcEEEEEEEEccCCCEEEEEEcCCCEEEEeEEeeee------EEEEEcCCCeEEEccCC
Confidence 3478888887666432 3445666666666443 57899999999999854
No 29
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=22.13 E-value=1.6e+02 Score=22.58 Aligned_cols=34 Identities=21% Similarity=0.367 Sum_probs=22.7
Q ss_pred CceEEEeeCcCc--ceEEEEEeeCCc----cccccCcEEEE
Q 031097 51 RTVLKVVDNSGA--KTVMCIQPLKGR----KVARLGDTIVA 85 (166)
Q Consensus 51 ~T~L~VaDNSGa--k~v~cI~vl~~~----k~a~vGD~I~v 85 (166)
...|+++|-|++ ..+ .++++... ....+||+|.+
T Consensus 38 ~~tl~i~D~S~~~~~~l-~v~~F~~~~~~LP~v~~GDVIll 77 (138)
T cd04497 38 CCTLTITDPSLANSDGL-TVKLFRPNEESLPIVKVGDIILL 77 (138)
T ss_pred EEEEEEECCCCCCCCcE-EEEEECCChhhCCCCCCCCEEEE
Confidence 456999999997 444 44456542 23489997754
No 30
>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.
Probab=21.44 E-value=24 Score=24.37 Aligned_cols=14 Identities=43% Similarity=0.503 Sum_probs=10.0
Q ss_pred hhcccccccccccC
Q 031097 6 ASKWSRVGRSLLGG 19 (166)
Q Consensus 6 ~~~~~~~~~~~~~~ 19 (166)
-|-.||+|+.|||-
T Consensus 40 IS~~SPLG~ALlG~ 53 (77)
T PF01272_consen 40 ISIDSPLGKALLGK 53 (77)
T ss_dssp EETTSHHHHHHTT-
T ss_pred EEecCHHHHHhcCC
Confidence 35578888888873
No 31
>PF12508 DUF3714: Protein of unknown function (DUF3714) ; InterPro: IPR022187 Proteins in this entry are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage.
Probab=20.63 E-value=89 Score=26.22 Aligned_cols=46 Identities=28% Similarity=0.351 Sum_probs=35.5
Q ss_pred ceEEEEEEEeeeeeccCCCCeeEeecCceEEEEcCCCCccceEEeccchh
Q 031097 99 GQVVHAVVVRAAMQHGRFDGSEVRFDDNAVVLVNKAGEPTGTRVFGPVPH 148 (166)
Q Consensus 99 g~V~kAvIVRtKk~~~R~dG~~ikFddNavVLln~k~~plGTRI~GpV~~ 148 (166)
..-.+|+|-.+.+ -.+|++++|.=---+.++...-|.||.++| +++
T Consensus 52 ~n~I~A~V~~~qt---v~~Gs~vrlRLle~i~i~g~~IPkgt~l~G-~~~ 97 (200)
T PF12508_consen 52 KNTIRAVVDGTQT---VVDGSRVRLRLLEDIQIGGILIPKGTYLYG-VAS 97 (200)
T ss_pred CCeEEEEEecceE---EeCCCEEEEEEcCceEECCEEeCCCCEEEE-EEe
Confidence 4677899988854 367888887766666778888999999999 443
Done!