Query psy14541
Match_columns 103
No_of_seqs 134 out of 1080
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 22:33:08 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14541.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14541hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3419|consensus 100.0 5E-31 1.1E-35 186.0 6.2 82 1-83 27-108 (112)
2 TIGR00002 S16 ribosomal protei 99.9 2.6E-25 5.6E-30 148.8 5.9 54 1-58 25-78 (78)
3 PRK14525 rpsP 30S ribosomal pr 99.9 4E-25 8.7E-30 151.0 6.0 58 1-62 27-84 (88)
4 CHL00005 rps16 ribosomal prote 99.9 3.6E-25 7.7E-30 149.5 5.4 55 1-61 26-80 (82)
5 PRK14524 rpsP 30S ribosomal pr 99.9 5.1E-25 1.1E-29 152.0 6.1 59 1-63 26-84 (94)
6 PRK14521 rpsP 30S ribosomal pr 99.9 1.9E-24 4.1E-29 164.1 7.3 58 1-62 27-84 (186)
7 PRK14523 rpsP 30S ribosomal pr 99.9 5.8E-24 1.2E-28 155.1 7.0 69 1-71 26-94 (137)
8 PRK14522 rpsP 30S ribosomal pr 99.9 2.1E-23 4.5E-28 148.7 9.1 60 1-65 27-88 (116)
9 COG0228 RpsP Ribosomal protein 99.9 6.4E-24 1.4E-28 144.9 5.3 53 1-56 26-78 (87)
10 PRK14520 rpsP 30S ribosomal pr 99.9 1.1E-23 2.3E-28 156.3 6.0 56 1-60 27-82 (155)
11 PRK00040 rpsP 30S ribosomal pr 99.9 9.7E-24 2.1E-28 140.3 4.7 50 1-52 26-75 (75)
12 PF00886 Ribosomal_S16: Riboso 99.8 1.2E-20 2.5E-25 121.2 3.6 44 1-45 19-62 (62)
13 PF11875 DUF3395: Domain of un 66.3 4 8.7E-05 29.8 1.7 21 7-27 108-128 (151)
14 PF03484 B5: tRNA synthetase B 54.5 25 0.00054 22.1 3.6 36 24-61 2-37 (70)
15 COG0669 CoaD Phosphopantethein 41.9 9.2 0.0002 28.9 0.2 10 12-21 9-18 (159)
16 smart00874 B5 tRNA synthetase 36.5 74 0.0016 19.4 3.7 34 24-59 2-35 (71)
17 KOG0363|consensus 33.7 21 0.00047 31.1 1.1 63 9-78 67-134 (527)
18 PF09330 Lact-deh-memb: D-lact 30.9 22 0.00048 29.3 0.8 58 7-71 51-109 (291)
19 KOG0135|consensus 29.5 38 0.00083 30.7 2.0 35 4-40 170-204 (661)
20 PF03649 UPF0014: Uncharacteri 28.9 50 0.0011 26.1 2.4 35 25-60 151-188 (250)
21 PF13592 HTH_33: Winged helix- 28.7 75 0.0016 19.2 2.7 38 27-65 4-44 (60)
22 KOG0718|consensus 26.2 42 0.0009 29.8 1.7 17 10-28 499-515 (546)
23 TIGR00245 conserved hypothetic 25.4 62 0.0013 25.6 2.4 35 25-60 145-182 (248)
24 KOG1476|consensus 25.3 38 0.00082 28.4 1.2 48 35-82 119-174 (330)
25 cd00218 GlcAT-I Beta1,3-glucur 24.4 42 0.0009 26.5 1.2 48 35-82 33-90 (223)
26 PF07022 Phage_CI_repr: Bacter 22.8 81 0.0018 19.4 2.1 33 25-58 21-54 (66)
27 PF09494 Slx4: Slx4 endonuclea 22.4 1.3E+02 0.0027 18.7 2.9 40 7-58 15-60 (64)
28 TIGR00125 cyt_tran_rel cytidyl 21.7 37 0.00081 20.0 0.4 11 11-21 5-15 (66)
29 TIGR03830 CxxCG_CxxCG_HTH puta 21.1 77 0.0017 21.1 1.9 35 25-60 87-121 (127)
30 smart00708 PhBP Insect pheromo 20.6 1.1E+02 0.0024 19.0 2.5 39 7-54 39-77 (103)
No 1
>KOG3419|consensus
Probab=99.97 E-value=5e-31 Score=185.95 Aligned_cols=82 Identities=52% Similarity=0.888 Sum_probs=77.3
Q ss_pred CCCCCccccccceecCCCCCCCcceeeeeHHHHHHHHhCCCcccCHHHHHHHHHcCCCCcchhhhhHHhhchhHHHHHHH
Q psy14541 1 MRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHITSPVRELFGLAGLFPIYHRTYMNAWRNRNKAEAEIE 80 (103)
Q Consensus 1 ~~RdGk~IE~LG~YdP~~~~~~ek~v~ln~eRi~yWL~~G~AqPS~tV~~LL~~ag~lp~~p~~~~~~~~~~~k~~~~~~ 80 (103)
++|||++||+||+|||+++..+++.|.||++||+|||++| ||||++|.+||+++|++|.||++++.+|++|+..+++.+
T Consensus 27 ~~rdgk~iE~lG~ydPlp~~~~~~~v~Ln~dRikyWl~~G-AqpS~tv~~Ll~~aGl~p~~p~~~~~a~~~rr~~a~~~~ 105 (112)
T KOG3419|consen 27 KRRDGKPIEQLGTYDPLPNQDNEKLVALNFDRIKYWLGVG-AQPSDTVEELLGKAGLFPIHPMTFMNAKRNRRLTAEQVL 105 (112)
T ss_pred ccccCCchhheecccCCCCCCCCcceeecHHHHHHHHhcC-CccChHHHHHHHhcCCCCCchhhhhccccchhhhhhhcc
Confidence 4799999999999999999999999999999999999999 999999999999999999999999999999999877765
Q ss_pred HHH
Q psy14541 81 KQK 83 (103)
Q Consensus 81 ~~~ 83 (103)
...
T Consensus 106 ~~~ 108 (112)
T KOG3419|consen 106 PVE 108 (112)
T ss_pred chh
Confidence 544
No 2
>TIGR00002 S16 ribosomal protein S16. This model describes ribosomal S16 of bacteria and organelles.
Probab=99.92 E-value=2.6e-25 Score=148.84 Aligned_cols=54 Identities=46% Similarity=0.830 Sum_probs=50.8
Q ss_pred CCCCCccccccceecCCCCCCCcceeeeeHHHHHHHHhCCCcccCHHHHHHHHHcCCC
Q psy14541 1 MRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHITSPVRELFGLAGLF 58 (103)
Q Consensus 1 ~~RdGk~IE~LG~YdP~~~~~~ek~v~ln~eRi~yWL~~G~AqPS~tV~~LL~~ag~l 58 (103)
++|||+|||+||+|||++++ +.|.||++|++|||++| ||||++|.+||+++|++
T Consensus 25 ~~RdGk~iE~lG~YnP~~~~---~~i~l~~~ri~~Wl~~G-Aqps~tV~~Ll~~~g~~ 78 (78)
T TIGR00002 25 SRRDGRYIEELGFYNPLTKE---SRVKLNVERIKYWLSKG-AQPTDTVRNLLKKAGVF 78 (78)
T ss_pred CCCCCCceeEeeeccCCCCC---cEEEEcHHHHHHHHHCC-CccCHHHHHHHHHccCC
Confidence 57999999999999999864 68999999999999999 99999999999999975
No 3
>PRK14525 rpsP 30S ribosomal protein S16; Provisional
Probab=99.91 E-value=4e-25 Score=150.98 Aligned_cols=58 Identities=22% Similarity=0.387 Sum_probs=53.1
Q ss_pred CCCCCccccccceecCCCCCCCcceeeeeHHHHHHHHhCCCcccCHHHHHHHHHcCCCCcch
Q psy14541 1 MRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHITSPVRELFGLAGLFPIYH 62 (103)
Q Consensus 1 ~~RdGk~IE~LG~YdP~~~~~~ek~v~ln~eRi~yWL~~G~AqPS~tV~~LL~~ag~lp~~p 62 (103)
++|||+|||+||||||+.++ +.|.||++||+|||++| ||||+||++||+++|+...+|
T Consensus 27 ~~RdGk~IE~lG~YnP~~~~---~~i~ln~eri~~WL~~G-AqpT~tV~~Ll~~~g~~~~~~ 84 (88)
T PRK14525 27 NARDGKYLEDVGIYDPTKRP---ERIELKVERIEHWLKAG-AKPSQTVAMILKRAAKAAAPA 84 (88)
T ss_pred CCCCCCceeEEecccCCCCC---ceEEEcHHHHHHHHHCC-CccCHHHHHHHHHcCccCCCC
Confidence 57999999999999999753 58999999999999999 999999999999999996543
No 4
>CHL00005 rps16 ribosomal protein S16
Probab=99.91 E-value=3.6e-25 Score=149.53 Aligned_cols=55 Identities=29% Similarity=0.510 Sum_probs=50.9
Q ss_pred CCCCCccccccceecCCCCCCCcceeeeeHHHHHHHHhCCCcccCHHHHHHHHHcCCCCcc
Q psy14541 1 MRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHITSPVRELFGLAGLFPIY 61 (103)
Q Consensus 1 ~~RdGk~IE~LG~YdP~~~~~~ek~v~ln~eRi~yWL~~G~AqPS~tV~~LL~~ag~lp~~ 61 (103)
++|||+|||+||+|||+.+ .+.||++|++|||++| ||||++|++||+++|+++.+
T Consensus 26 ~~RdGk~iE~lG~YnP~~~-----~~~ln~eri~~Wl~~G-Aqpt~tV~~Ll~~~g~~~~~ 80 (82)
T CHL00005 26 SRREGRDLEKVGFYDPIKN-----QTYLNVPAILYFLEKG-AQPTETVYDILKKAEVFKEL 80 (82)
T ss_pred CCCCCcceeEeeeccCCCc-----ccEEeHHHHHHHHHCc-CccCHHHHHHHHHcCchhhh
Confidence 5899999999999999965 4699999999999999 99999999999999998754
No 5
>PRK14524 rpsP 30S ribosomal protein S16; Provisional
Probab=99.91 E-value=5.1e-25 Score=151.95 Aligned_cols=59 Identities=25% Similarity=0.488 Sum_probs=53.9
Q ss_pred CCCCCccccccceecCCCCCCCcceeeeeHHHHHHHHhCCCcccCHHHHHHHHHcCCCCcchh
Q psy14541 1 MRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHITSPVRELFGLAGLFPIYHR 63 (103)
Q Consensus 1 ~~RdGk~IE~LG~YdP~~~~~~ek~v~ln~eRi~yWL~~G~AqPS~tV~~LL~~ag~lp~~p~ 63 (103)
++|||+|||+||||||++++ ..|.||++|++|||++| ||||+||.+||+++|++++...
T Consensus 26 ~~RdGk~iE~lG~YnP~~~~---~~i~l~~eri~~Wl~~G-AqpT~tV~~Llkk~g~~~~~~~ 84 (94)
T PRK14524 26 KRRDGAYIESLGYYNPLKEP---YEIKVDVERAVEWILKG-AQPSDTVRDILRKFGVMKKVHE 84 (94)
T ss_pred CCCCCCceeEeeecCCCCCC---ceEEEcHHHHHHHHHcC-CccCHHHHHHHHHccchhhhHH
Confidence 58999999999999999764 58999999999999999 9999999999999999876443
No 6
>PRK14521 rpsP 30S ribosomal protein S16; Provisional
Probab=99.91 E-value=1.9e-24 Score=164.14 Aligned_cols=58 Identities=31% Similarity=0.576 Sum_probs=54.2
Q ss_pred CCCCCccccccceecCCCCCCCcceeeeeHHHHHHHHhCCCcccCHHHHHHHHHcCCCCcch
Q psy14541 1 MRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHITSPVRELFGLAGLFPIYH 62 (103)
Q Consensus 1 ~~RdGk~IE~LG~YdP~~~~~~ek~v~ln~eRi~yWL~~G~AqPS~tV~~LL~~ag~lp~~p 62 (103)
++|||+|||+||||||+.++ ..|.||++||+|||++| ||||+||++||++.|+|++++
T Consensus 27 ~~RDGk~IE~lG~YnP~~~~---~~i~Ln~eRi~~WL~~G-AqPTdtV~~lL~~~g~~~k~~ 84 (186)
T PRK14521 27 APRDGKFIEKIGTYNPNTNP---ATVDLNFDRAVYWLMNG-AQPTDTARNILSYEGVLLKKH 84 (186)
T ss_pred CCCCCCceeeeeecCCCCCC---ceEEEcHHHHHHHHHCC-CcCCHHHHHHHHHcccchhhh
Confidence 58999999999999999764 68999999999999999 999999999999999998765
No 7
>PRK14523 rpsP 30S ribosomal protein S16; Provisional
Probab=99.90 E-value=5.8e-24 Score=155.05 Aligned_cols=69 Identities=20% Similarity=0.266 Sum_probs=59.2
Q ss_pred CCCCCccccccceecCCCCCCCcceeeeeHHHHHHHHhCCCcccCHHHHHHHHHcCCCCcchhhhhHHhhc
Q psy14541 1 MRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHITSPVRELFGLAGLFPIYHRTYMNAWRN 71 (103)
Q Consensus 1 ~~RdGk~IE~LG~YdP~~~~~~ek~v~ln~eRi~yWL~~G~AqPS~tV~~LL~~ag~lp~~p~~~~~~~~~ 71 (103)
++|||+|||.||||||+++.. ++.|.||++||+|||++| ||||++|.+||+++|++|.++..-.....+
T Consensus 26 s~RDGK~IE~LG~YdP~~~~~-~~~i~Ln~eRi~yWL~~G-AQPS~tV~~LLkkag~~~~~~~~~g~~~~~ 94 (137)
T PRK14523 26 KPRDGRFIERVGYYNPMARGQ-DIRLQLEKERISHWLNQG-AQTSLRVKHLIKKLEKSPEEAQKGGMRKGE 94 (137)
T ss_pred CCCCCCceeeeeecCCCCCCC-CceEEECHHHHHHHHHCC-CccCHHHHHHHHHcccchHHHHhcccccCC
Confidence 579999999999999998764 358999999999999999 999999999999999999876543333333
No 8
>PRK14522 rpsP 30S ribosomal protein S16; Provisional
Probab=99.90 E-value=2.1e-23 Score=148.66 Aligned_cols=60 Identities=28% Similarity=0.457 Sum_probs=54.8
Q ss_pred CCCCCccccccceecCCCCCCCcceeeeeHHHHHHHHhCCCcccCHHHHHHHHH--cCCCCcchhhh
Q psy14541 1 MRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHITSPVRELFGL--AGLFPIYHRTY 65 (103)
Q Consensus 1 ~~RdGk~IE~LG~YdP~~~~~~ek~v~ln~eRi~yWL~~G~AqPS~tV~~LL~~--ag~lp~~p~~~ 65 (103)
++|||+|||+||||||+.+ +.|.||++||.|||++| ||||++|..||++ .|++++.....
T Consensus 27 ~~RDGk~IE~lG~YdP~~~----~~v~Ln~eRi~yWL~~G-AqPS~tV~~LLkk~~~Gi~~~~~~~k 88 (116)
T PRK14522 27 SPRDGKYIELLGWYDPHSE----QNYQLKSERIFYWLNQG-AELTEKAGALVKQGAPGVYSELMAKK 88 (116)
T ss_pred CCCCCCcceeeeccCCCCC----CceEECHHHHHHHHHCC-CccCHHHHHHHHhhhcccchhHHHHH
Confidence 5899999999999999875 36999999999999999 9999999999999 69999976644
No 9
>COG0228 RpsP Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=6.4e-24 Score=144.93 Aligned_cols=53 Identities=42% Similarity=0.663 Sum_probs=49.3
Q ss_pred CCCCCccccccceecCCCCCCCcceeeeeHHHHHHHHhCCCcccCHHHHHHHHHcC
Q psy14541 1 MRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHITSPVRELFGLAG 56 (103)
Q Consensus 1 ~~RdGk~IE~LG~YdP~~~~~~ek~v~ln~eRi~yWL~~G~AqPS~tV~~LL~~ag 56 (103)
+||||+|||.||+|||+. ..+..|.||.||+.|||++| |||||||++||+++|
T Consensus 26 s~RDGr~IE~lG~ynP~~--~~~~~v~l~~eri~~Wl~~G-AqpSdtV~~ll~~~g 78 (87)
T COG0228 26 SPRDGRFIERLGTYNPLL--GKEERVKLDEERILYWLSQG-AQPSDTVRRLLKKAG 78 (87)
T ss_pred CCCCCcchhhhcccCCCC--CccceEEEcHHHHHHHHHcC-CcccHHHHHHHHHhh
Confidence 589999999999999977 23468999999999999999 999999999999998
No 10
>PRK14520 rpsP 30S ribosomal protein S16; Provisional
Probab=99.89 E-value=1.1e-23 Score=156.29 Aligned_cols=56 Identities=29% Similarity=0.644 Sum_probs=51.9
Q ss_pred CCCCCccccccceecCCCCCCCcceeeeeHHHHHHHHhCCCcccCHHHHHHHHHcCCCCc
Q psy14541 1 MRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHITSPVRELFGLAGLFPI 60 (103)
Q Consensus 1 ~~RdGk~IE~LG~YdP~~~~~~ek~v~ln~eRi~yWL~~G~AqPS~tV~~LL~~ag~lp~ 60 (103)
++|||+|||+||||||+.++ ..|.||++||+|||++| ||||++|.+||++.|++.+
T Consensus 27 ~~RDGk~IE~lG~YnP~~~~---~~i~ln~eRi~yWL~~G-AQPT~~V~~LLk~~g~~~~ 82 (155)
T PRK14520 27 TKRDGRAIEEIGRYHPKEEP---SLIEIDSERAQYWLSVG-AQPTEPVLALLKITGDWQK 82 (155)
T ss_pred CCCCCCceeeeeccCCCCCC---ceEEEcHHHHHHHHHCC-CccCHHHHHHHHHcchhhh
Confidence 57999999999999998764 68999999999999999 9999999999999998754
No 11
>PRK00040 rpsP 30S ribosomal protein S16; Reviewed
Probab=99.89 E-value=9.7e-24 Score=140.34 Aligned_cols=50 Identities=38% Similarity=0.678 Sum_probs=46.1
Q ss_pred CCCCCccccccceecCCCCCCCcceeeeeHHHHHHHHhCCCcccCHHHHHHH
Q psy14541 1 MRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHITSPVRELF 52 (103)
Q Consensus 1 ~~RdGk~IE~LG~YdP~~~~~~ek~v~ln~eRi~yWL~~G~AqPS~tV~~LL 52 (103)
++|||+|||+||+|||+++.. ++.|.||++||+|||++| ||||++|++||
T Consensus 26 ~~RdGk~iE~lG~ydP~~~~~-~~~i~ln~eri~~Wl~~G-Aqpt~~V~~Ll 75 (75)
T PRK00040 26 SPRDGRFIERVGFYNPLAKPA-EEEVKLDEERVLYWLGQG-AQPTDTVRRLL 75 (75)
T ss_pred CCCCCCceeEEeecCCCCCCC-cceEEEcHHHHHHHHHCC-CccCHHHHHhC
Confidence 579999999999999998653 579999999999999999 99999999986
No 12
>PF00886 Ribosomal_S16: Ribosomal protein S16; InterPro: IPR000307 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 S16 is one of the proteins from the small ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [], groups: Eubacterial S16. Algal and plant chloroplast S16. Cyanelle S16. Neurospora crassa mitochondrial S24 (cyt-21). S16 proteins have about 100 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2Y14_P 3UZ6_S 2J02_P 1HNZ_P 3V26_P 3KNL_P 1N34_P 2J00_P 1HNW_P 3OHC_P ....
Probab=99.81 E-value=1.2e-20 Score=121.17 Aligned_cols=44 Identities=45% Similarity=0.829 Sum_probs=41.4
Q ss_pred CCCCCccccccceecCCCCCCCcceeeeeHHHHHHHHhCCCcccC
Q psy14541 1 MRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHIT 45 (103)
Q Consensus 1 ~~RdGk~IE~LG~YdP~~~~~~ek~v~ln~eRi~yWL~~G~AqPS 45 (103)
++|||++||+||+|||++++.+++.+.||++||+|||++| ||||
T Consensus 19 ~~RdGk~iE~lG~YdP~~~~~~~~~~~l~~eri~~Wl~~G-AqpT 62 (62)
T PF00886_consen 19 SPRDGKFIEELGFYDPIPNPDEEKQIKLNFERIKYWLSKG-AQPT 62 (62)
T ss_dssp SSTTSSESEEEEEEETTSSSSSSTSEEETHHHHHHHHHTT-EEEE
T ss_pred cccccchhhccceEcCCCCCCCceeEEeCHHHHHHHHHcC-cCCC
Confidence 5799999999999999999766789999999999999999 9998
No 13
>PF11875 DUF3395: Domain of unknown function (DUF3395); InterPro: IPR024586 Chaperone DnaJ was originally characterised from Escherichia coli as a 41 kDa heat shock protein. DnaJ has a modular structure consisting of a J-domain, a proximal G/F-domain, and a distal zinc finger domain, followed by less conserved C-terminal sequences. Since then, a large number of DnaJ-related proteins containing a J-domain have been characterised from a variety of different organisms. In the genome of Arabidopsis thaliana a total of 89 J-domain proteins have been identified []. This entry represents a C-terminal domain found in some eukaryotic DnaJ-like proteins, including member 11 from the subfamily C1 and protein DnaJ 13 from Arabidopsis. This domain is typically between 147 to 176 amino acids in length.
Probab=66.30 E-value=4 Score=29.84 Aligned_cols=21 Identities=24% Similarity=0.245 Sum_probs=12.7
Q ss_pred cccccceecCCCCCCCcceee
Q psy14541 7 PIEQLGTFDPLPNEYQEKLVS 27 (103)
Q Consensus 7 ~IE~LG~YdP~~~~~~ek~v~ 27 (103)
.=..+|||||.+....+|.+.
T Consensus 108 Ks~L~GF~DP~p~~ge~K~L~ 128 (151)
T PF11875_consen 108 KSGLPGFYDPCPFLGEPKQLR 128 (151)
T ss_pred hhhCCCCCCCccccCCccEEE
Confidence 335689999987222235444
No 14
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=54.49 E-value=25 Score=22.05 Aligned_cols=36 Identities=17% Similarity=0.256 Sum_probs=27.3
Q ss_pred ceeeeeHHHHHHHHhCCCcccCHHHHHHHHHcCCCCcc
Q psy14541 24 KLVSLNIERIRYWLGTSDIHITSPVRELFGLAGLFPIY 61 (103)
Q Consensus 24 k~v~ln~eRi~yWL~~G~AqPS~tV~~LL~~ag~lp~~ 61 (103)
+.+.++.+++...|+.- -..+.+.++|++.|+--..
T Consensus 2 ~~i~~~~~~i~~~lG~~--i~~~~i~~~L~~lg~~~~~ 37 (70)
T PF03484_consen 2 KKITLSLDKINKLLGID--ISPEEIIKILKRLGFKVEK 37 (70)
T ss_dssp EEEEEEHHHHHHHHTS-----HHHHHHHHHHTT-EEEE
T ss_pred eEEEecHHHHHHHhCCC--CCHHHHHHHHHHCCCEEEE
Confidence 57899999999999874 4557889999999876553
No 15
>COG0669 CoaD Phosphopantetheine adenylyltransferase [Coenzyme metabolism]
Probab=41.89 E-value=9.2 Score=28.95 Aligned_cols=10 Identities=50% Similarity=1.036 Sum_probs=8.9
Q ss_pred ceecCCCCCC
Q psy14541 12 GTFDPLPNEY 21 (103)
Q Consensus 12 G~YdP~~~~~ 21 (103)
|+|||+++.+
T Consensus 9 GSFDPiTnGH 18 (159)
T COG0669 9 GSFDPITNGH 18 (159)
T ss_pred CCCCCCccch
Confidence 8999999975
No 16
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=36.54 E-value=74 Score=19.35 Aligned_cols=34 Identities=24% Similarity=0.403 Sum_probs=27.4
Q ss_pred ceeeeeHHHHHHHHhCCCcccCHHHHHHHHHcCCCC
Q psy14541 24 KLVSLNIERIRYWLGTSDIHITSPVRELFGLAGLFP 59 (103)
Q Consensus 24 k~v~ln~eRi~yWL~~G~AqPS~tV~~LL~~ag~lp 59 (103)
..|.++.+++...|+.- -. .+.+.++|.+.|+--
T Consensus 2 ~~i~~~~~~i~~llG~~-i~-~~ei~~~L~~lg~~~ 35 (71)
T smart00874 2 RTITLRRERINRLLGLD-LS-AEEIEEILKRLGFEV 35 (71)
T ss_pred cEEEecHHHHHHHHCCC-CC-HHHHHHHHHHCCCeE
Confidence 35899999999999976 44 466899999999643
No 17
>KOG0363|consensus
Probab=33.72 E-value=21 Score=31.06 Aligned_cols=63 Identities=21% Similarity=0.222 Sum_probs=45.9
Q ss_pred cccceecCCCCCCCcceeeeeHHHHHHHHhCCCcccCHHH--HHHHHHcCCCCc---chhhhhHHhhchhHHHHH
Q psy14541 9 EQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHITSPV--RELFGLAGLFPI---YHRTYMNAWRNRNKAEAE 78 (103)
Q Consensus 9 E~LG~YdP~~~~~~ek~v~ln~eRi~yWL~~G~AqPS~tV--~~LL~~ag~lp~---~p~~~~~~~~~~~k~~~~ 78 (103)
-.||.=||-. .|-+|+.+++.| .+||-.-|=+| ..||+.++.|-. ||.+++..||--.+.+..
T Consensus 67 ksi~vDnpaA------kvLv~~S~vQD~-EvGDGTTSV~vlaaeLlreAeklv~~kiHPq~Ii~GyR~A~~~a~e 134 (527)
T KOG0363|consen 67 KSIGVDNPAA------KVLVDISKVQDD-EVGDGTTSVTVLAAELLREAEKLVNQKIHPQTIISGYRMATAAALE 134 (527)
T ss_pred HhcCCCCchh------hheecccccccc-ccCCCceehHHHHHHHHHHHHHHHhcccCcHHHHHHHHHHHHHHHH
Confidence 4567777754 478999999999 34444555555 578999887766 999999999975554444
No 18
>PF09330 Lact-deh-memb: D-lactate dehydrogenase, membrane binding; InterPro: IPR015409 Members of this entry are predominantly found in prokaryotic D-lactate dehydrogenase, forming the cap-membrane-binding domain, which consists of a large seven-stranded antiparallel beta-sheet flanked on both sides by alpha-helices. They allow for membrane association []. ; GO: 0050660 flavin adenine dinucleotide binding, 0055085 transmembrane transport; PDB: 1F0X_A.
Probab=30.92 E-value=22 Score=29.29 Aligned_cols=58 Identities=24% Similarity=0.362 Sum_probs=5.0
Q ss_pred cccccceecCCCCCCCcceeeeeHHHHHHHHhC-CCcccCHHHHHHHHHcCCCCcchhhhhHHhhc
Q psy14541 7 PIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGT-SDIHITSPVRELFGLAGLFPIYHRTYMNAWRN 71 (103)
Q Consensus 7 ~IE~LG~YdP~~~~~~ek~v~ln~eRi~yWL~~-G~AqPS~tV~~LL~~ag~lp~~p~~~~~~~~~ 71 (103)
.|+.+|+ |-+|.-. .++-.+|++..+|.- + ..+||+|...++ .++|.|-+.-|..+|.
T Consensus 51 ~I~~lGt-~~lP~lF---a~K~~~D~~~~k~~~lp-~~lsDr~lQ~~s--~l~P~hLP~Rm~~yr~ 109 (291)
T PF09330_consen 51 MIKKLGT-DRLPRLF---ALKARIDALLEKLPFLP-PNLSDRVLQALS--NLLPNHLPKRMRDYRD 109 (291)
T ss_dssp ----------------------------------------------------------HHHHHHHH
T ss_pred HHHHhCc-hhHHHHH---HHHHHHHHHHHhcCCCC-CCccHHHHHHHH--hhChhhcCHHHHHHHH
Confidence 6899999 7777764 467788898888887 5 789999887764 6899987766666664
No 19
>KOG0135|consensus
Probab=29.54 E-value=38 Score=30.70 Aligned_cols=35 Identities=26% Similarity=0.659 Sum_probs=25.5
Q ss_pred CCccccccceecCCCCCCCcceeeeeHHHHHHHHhCC
Q psy14541 4 NDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTS 40 (103)
Q Consensus 4 dGk~IE~LG~YdP~~~~~~ek~v~ln~eRi~yWL~~G 40 (103)
+-+-|+..-+|||..... -.=.=|++.++||+++=
T Consensus 170 Nt~~I~TtatyDP~t~Ef--VinTP~~~A~K~WiGn~ 204 (661)
T KOG0135|consen 170 NTKGIQTTATYDPTTEEF--VINTPDFSAIKCWIGNA 204 (661)
T ss_pred cccceeeeeeecCCCCee--EecCCcHHHHHHHhccc
Confidence 346688899999987642 01145789999999875
No 20
>PF03649 UPF0014: Uncharacterised protein family (UPF0014); InterPro: IPR005226 This family has no known function. It includes potential membrane proteins.
Probab=28.93 E-value=50 Score=26.10 Aligned_cols=35 Identities=20% Similarity=0.202 Sum_probs=28.6
Q ss_pred eeeeeHHHHHHHHhCCCcccCHHHHHHHHHc---CCCCc
Q psy14541 25 LVSLNIERIRYWLGTSDIHITSPVRELFGLA---GLFPI 60 (103)
Q Consensus 25 ~v~ln~eRi~yWL~~G~AqPS~tV~~LL~~a---g~lp~ 60 (103)
.++-+.+++.++|+.| |.|.+.++.+++++ +++|.
T Consensus 151 ~l~~~~~~ie~~LalG-at~~eA~~~~~r~ai~~al~P~ 188 (250)
T PF03649_consen 151 ELRERRDEIEALLALG-ATPREAVRPFIRRAIRAALIPT 188 (250)
T ss_pred HHHHhHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHhHhH
Confidence 3456788999999999 99999999988854 66665
No 21
>PF13592 HTH_33: Winged helix-turn helix
Probab=28.71 E-value=75 Score=19.25 Aligned_cols=38 Identities=16% Similarity=0.184 Sum_probs=27.9
Q ss_pred eeeHHHHHHHHhC--CCcccC-HHHHHHHHHcCCCCcchhhh
Q psy14541 27 SLNIERIRYWLGT--SDIHIT-SPVRELFGLAGLFPIYHRTY 65 (103)
Q Consensus 27 ~ln~eRi~yWL~~--G~AqPS-~tV~~LL~~ag~lp~~p~~~ 65 (103)
.+....|..||.. | ...| .+|.+||++.|+-.+-|...
T Consensus 4 ~wt~~~i~~~I~~~fg-v~ys~~~v~~lL~r~G~s~~kp~~~ 44 (60)
T PF13592_consen 4 RWTLKEIAAYIEEEFG-VKYSPSGVYRLLKRLGFSYQKPRPR 44 (60)
T ss_pred cccHHHHHHHHHHHHC-CEEcHHHHHHHHHHcCCccccCCCC
Confidence 3566777777753 6 5555 46899999999998876643
No 22
>KOG0718|consensus
Probab=26.18 E-value=42 Score=29.84 Aligned_cols=17 Identities=35% Similarity=0.641 Sum_probs=12.4
Q ss_pred ccceecCCCCCCCcceeee
Q psy14541 10 QLGTFDPLPNEYQEKLVSL 28 (103)
Q Consensus 10 ~LG~YdP~~~~~~ek~v~l 28 (103)
..|||||++.. +|.+.|
T Consensus 499 lpGFydpc~ge--~K~L~I 515 (546)
T KOG0718|consen 499 LPGFYDPCPGE--PKELEI 515 (546)
T ss_pred CCcccCCCCCC--ccEEEE
Confidence 46999999875 465554
No 23
>TIGR00245 conserved hypothetical protein TIGR00245.
Probab=25.37 E-value=62 Score=25.57 Aligned_cols=35 Identities=17% Similarity=0.264 Sum_probs=29.8
Q ss_pred eeeeeHHHHHHHHhCCCcccCHHHHHHHHH---cCCCCc
Q psy14541 25 LVSLNIERIRYWLGTSDIHITSPVRELFGL---AGLFPI 60 (103)
Q Consensus 25 ~v~ln~eRi~yWL~~G~AqPS~tV~~LL~~---ag~lp~ 60 (103)
.++-+.+.+.++|+.| |.|-+.++.+++. ++++|.
T Consensus 145 ~l~~~~~~ie~~LaLG-at~~~A~~~~~r~Ai~aaliP~ 182 (248)
T TIGR00245 145 MVKSERDEIQGYLSLG-ATPKQAIAPFIRNAIKASLIPT 182 (248)
T ss_pred HHHHhhHHHHHHHHCC-CCHHHHHHHHHHHHHHHHhhch
Confidence 3566789999999999 9999999999984 477776
No 24
>KOG1476|consensus
Probab=25.35 E-value=38 Score=28.41 Aligned_cols=48 Identities=25% Similarity=0.321 Sum_probs=36.4
Q ss_pred HHHhCCC-cccCHHHHHHHHHcCCCCcc-----hhhhh--HHhhchhHHHHHHHHH
Q psy14541 35 YWLGTSD-IHITSPVRELFGLAGLFPIY-----HRTYM--NAWRNRNKAEAEIEKQ 82 (103)
Q Consensus 35 yWL~~G~-AqPS~tV~~LL~~ag~lp~~-----p~~~~--~~~~~~~k~~~~~~~~ 82 (103)
+||=+-| ...|+.|..+|.+.|+.-.| |+.|. ++|.+|.++.+.++.+
T Consensus 119 hWIVVEd~~~~~p~v~~~L~rtgl~ythl~~~t~~~~~~~rg~~qRn~aL~~ir~~ 174 (330)
T KOG1476|consen 119 HWIVVEDGEGTTPEVSGILRRTGLPYTHLVHKTPMGYKARRGWEQRNMALRWIRSR 174 (330)
T ss_pred eEEEEecCCCCCHHHHHHHHHcCCceEEEeccCCCCCccccchhHHHHHHHHHHHh
Confidence 4654433 48999999999999999876 44444 4599999999988843
No 25
>cd00218 GlcAT-I Beta1,3-glucuronyltransferase I (GlcAT-I) is involved in the initial steps of proteoglycan synthesis. Beta1,3-glucuronyltransferase I (GlcAT-I) domain; GlcAT-I is a Key enzyme involved in the initial steps of proteoglycan synthesis. GlcAT-I catalyzes the transfer of a glucuronic acid moiety from the uridine diphosphate-glucuronic acid (UDP-GlcUA) to the common linkage region of trisaccharide Gal-beta-(1-3)-Gal-beta-(1-4)-Xyl of proteoglycans. The enzyme has two subdomains that bind the donor and acceptor substrate separately. The active site is located at the cleft between both subdomains in which the trisaccharide molecule is oriented perpendicular to the UDP. This family has been classified as Glycosyltransferase family 43 (GT-43).
Probab=24.41 E-value=42 Score=26.51 Aligned_cols=48 Identities=25% Similarity=0.210 Sum_probs=34.2
Q ss_pred HHHhCCCcc-cCHHHHHHHHHcCCCCcchh---------hhhHHhhchhHHHHHHHHH
Q psy14541 35 YWLGTSDIH-ITSPVRELFGLAGLFPIYHR---------TYMNAWRNRNKAEAEIEKQ 82 (103)
Q Consensus 35 yWL~~G~Aq-PS~tV~~LL~~ag~lp~~p~---------~~~~~~~~~~k~~~~~~~~ 82 (103)
+||=+.++. .|+.|++||.+.|++-.|-. ...+.|.+|...-++++..
T Consensus 33 ~WIVVEd~~~~t~~va~lL~~sgl~y~HL~~~~~~~~~~~~~rg~~qRn~AL~~ir~~ 90 (223)
T cd00218 33 HWIVVEDSEEKTPLVAELLRRSGLMYTHLNAKTPSDPTWLKPRGVEQRNLALRWIREH 90 (223)
T ss_pred EEEEEeCCCCCCHHHHHHHHHcCCceEEeccCCCCCcccCCcccHHHHHHHHHHHHhc
Confidence 576555455 99999999999999766521 2345677777777777665
No 26
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=22.79 E-value=81 Score=19.42 Aligned_cols=33 Identities=6% Similarity=0.036 Sum_probs=22.3
Q ss_pred eeeeeHHHHH-HHHhCCCcccCHHHHHHHHHcCCC
Q psy14541 25 LVSLNIERIR-YWLGTSDIHITSPVRELFGLAGLF 58 (103)
Q Consensus 25 ~v~ln~eRi~-yWL~~G~AqPS~tV~~LL~~ag~l 58 (103)
.+.|...-+. .|...| .-|.+-+.+|-...|+=
T Consensus 21 ~lgis~st~s~~~~~r~-~~P~~~l~~ia~~~gvs 54 (66)
T PF07022_consen 21 RLGISKSTLSNNWKKRG-SIPAEWLIKIALETGVS 54 (66)
T ss_dssp CTT--HHHHH-HHHHSS-S--HHHHHHHHHHH---
T ss_pred HhCcCHHHhhHHHHhCC-CCCHHHHHHHHHHHCcC
Confidence 4678888999 999999 99988888887777753
No 27
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=22.35 E-value=1.3e+02 Score=18.70 Aligned_cols=40 Identities=25% Similarity=0.549 Sum_probs=27.3
Q ss_pred cccccceecCCCCCCCcceeeeeHHHHHHHHh-CCCc----c-cCHHHHHHHHHcCCC
Q psy14541 7 PIEQLGTFDPLPNEYQEKLVSLNIERIRYWLG-TSDI----H-ITSPVRELFGLAGLF 58 (103)
Q Consensus 7 ~IE~LG~YdP~~~~~~ek~v~ln~eRi~yWL~-~G~A----q-PS~tV~~LL~~ag~l 58 (103)
.-|+|=.|+| |+++.+..||. .| . + ....+++.|...||.
T Consensus 15 l~ekIL~YeP-----------I~L~el~~~L~~~g-~~~~~~~~~~~l~~~lD~~gIt 60 (64)
T PF09494_consen 15 LYEKILMYEP-----------INLEELHAWLKASG-IGFDRKVDPSKLKEWLDSQGIT 60 (64)
T ss_pred HHHHHHcCCC-----------ccHHHHHHHHHHcC-CCccceeCHHHHHHHHHHCCce
Confidence 3466777888 67888999998 77 4 3 334566666666653
No 28
>TIGR00125 cyt_tran_rel cytidyltransferase-related domain. Protein families that contain at least one copy of this domain include citrate lyase ligase, pantoate-beta-alanine ligase, glycerol-3-phosphate cytidyltransferase, ADP-heptose synthase, phosphocholine cytidylyltransferase, lipopolysaccharide core biosynthesis protein KdtB, the bifunctional protein NadR, and a number whose function is unknown. Many of these proteins are known to use CTP or ATP and release pyrophosphate.
Probab=21.69 E-value=37 Score=19.99 Aligned_cols=11 Identities=45% Similarity=0.760 Sum_probs=8.5
Q ss_pred cceecCCCCCC
Q psy14541 11 LGTFDPLPNEY 21 (103)
Q Consensus 11 LG~YdP~~~~~ 21 (103)
.|+|||+...+
T Consensus 5 ~G~Fdp~H~GH 15 (66)
T TIGR00125 5 VGTFDPFHLGH 15 (66)
T ss_pred cCccCCCCHHH
Confidence 69999987653
No 29
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=21.15 E-value=77 Score=21.12 Aligned_cols=35 Identities=11% Similarity=0.195 Sum_probs=27.0
Q ss_pred eeeeeHHHHHHHHhCCCcccCHHHHHHHHHcCCCCc
Q psy14541 25 LVSLNIERIRYWLGTSDIHITSPVRELFGLAGLFPI 60 (103)
Q Consensus 25 ~v~ln~eRi~yWL~~G~AqPS~tV~~LL~~ag~lp~ 60 (103)
.+.+....|..|..-. ..|+..+..||+..++-|.
T Consensus 87 ~lg~~~~tis~~e~g~-~~p~~~~~~l~~~l~~~p~ 121 (127)
T TIGR03830 87 LLGGGVNAFSRYERGE-VRPSKALDKLLRLLDKHPE 121 (127)
T ss_pred HhCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHHChH
Confidence 4567778888897666 7799888888888776664
No 30
>smart00708 PhBP Insect pheromone/odorant binding protein domains.
Probab=20.61 E-value=1.1e+02 Score=18.95 Aligned_cols=39 Identities=13% Similarity=0.228 Sum_probs=26.6
Q ss_pred cccccceecCCCCCCCcceeeeeHHHHHHHHhCCCcccCHHHHHHHHH
Q psy14541 7 PIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHITSPVRELFGL 54 (103)
Q Consensus 7 ~IE~LG~YdP~~~~~~ek~v~ln~eRi~yWL~~G~AqPS~tV~~LL~~ 54 (103)
+++.+|++|+- . .|+.+++..-+..+ ....+.|..++..
T Consensus 39 ~~~~~g~~~~~--g------~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 77 (103)
T smart00708 39 VLKKLGLVDDD--G------KFDAEKLLEQLKAD-DEMAEELEDIIEK 77 (103)
T ss_pred HHHHcCCcCCC--C------CcCHHHHHHHHHcC-hhHHHHHHHHHHH
Confidence 56788988872 1 37888887777654 5566666666654
Done!