Query 018444
Match_columns 356
No_of_seqs 227 out of 644
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 09:04:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018444.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018444hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 7.9E-24 1.7E-28 170.0 8.2 84 112-195 1-84 (84)
2 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 3.3E-23 7.1E-28 166.4 8.1 76 2-77 9-84 (84)
3 TIGR00253 RNA_bind_YhbY putati 99.9 3.8E-22 8.1E-27 165.0 10.3 77 4-80 11-87 (95)
4 TIGR00253 RNA_bind_YhbY putati 99.9 4.3E-22 9.3E-27 164.7 10.5 86 112-197 1-86 (95)
5 PRK10343 RNA-binding protein Y 99.9 6.7E-22 1.5E-26 164.2 10.5 86 112-197 3-88 (97)
6 PRK10343 RNA-binding protein Y 99.9 8.6E-22 1.9E-26 163.6 10.6 77 4-80 13-89 (97)
7 COG1534 Predicted RNA-binding 99.8 8.3E-21 1.8E-25 157.8 9.4 79 2-80 10-88 (97)
8 COG1534 Predicted RNA-binding 99.8 4.2E-20 9.1E-25 153.6 10.7 84 112-195 2-85 (97)
9 KOG1990 Poly(A)-specific exori 99.8 4E-20 8.7E-25 191.7 7.7 192 16-208 34-273 (564)
10 KOG1990 Poly(A)-specific exori 99.3 1.7E-12 3.6E-17 135.3 4.1 209 3-211 184-487 (564)
11 PF04472 DUF552: Protein of un 53.7 95 0.0021 24.2 7.6 56 25-81 12-70 (73)
12 PRK06934 flavodoxin; Provision 49.0 12 0.00026 35.7 2.2 93 44-153 67-187 (221)
13 PF11830 DUF3350: Domain of un 39.5 38 0.00082 26.4 3.2 23 233-255 22-44 (56)
14 PF01918 Alba: Alba; InterPro 33.7 85 0.0018 23.8 4.4 58 130-187 2-64 (70)
15 COG1799 Uncharacterized protei 31.8 87 0.0019 29.2 4.8 58 25-83 87-147 (167)
16 cd05797 Ribosomal_L10 Ribosoma 31.4 53 0.0011 28.8 3.3 31 110-140 28-58 (157)
17 PF11623 DUF3252: Protein of u 30.2 40 0.00087 26.0 2.0 18 65-82 23-42 (53)
18 cd08619 PI-PLCXDc_plant Cataly 28.4 1.3E+02 0.0028 30.2 5.7 65 21-85 93-173 (285)
19 cd01461 vWA_interalpha_trypsin 27.5 1.5E+02 0.0032 25.0 5.3 52 135-188 110-161 (171)
20 PF04530 Viral_Beta_CD: Viral 26.6 61 0.0013 28.8 2.8 21 13-34 93-113 (122)
21 cd08619 PI-PLCXDc_plant Cataly 26.3 2.2E+02 0.0049 28.5 7.0 73 138-210 92-180 (285)
22 PF11609 DUF3248: Protein of u 24.5 44 0.00095 26.6 1.3 13 59-71 2-14 (63)
23 COG2511 GatE Archaeal Glu-tRNA 23.2 3E+02 0.0065 30.4 7.6 118 15-137 351-481 (631)
24 PF10369 ALS_ss_C: Small subun 22.9 2.1E+02 0.0045 22.6 4.9 39 35-75 2-40 (75)
25 KOG1257 NADP+-dependent malic 21.9 98 0.0021 33.8 3.7 73 6-81 385-463 (582)
26 COG1514 LigT 2'-5' RNA ligase 21.7 83 0.0018 28.9 2.8 101 38-152 40-146 (180)
27 TIGR01056 topB DNA topoisomera 21.7 4.4E+02 0.0096 29.0 8.7 83 64-151 36-121 (660)
28 COG1098 VacB Predicted RNA bin 20.8 82 0.0018 28.3 2.5 27 20-46 38-64 (129)
29 cd05796 Ribosomal_P0_like Ribo 20.3 96 0.0021 27.8 2.9 29 110-140 26-54 (163)
No 1
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=99.90 E-value=7.9e-24 Score=169.95 Aligned_cols=84 Identities=27% Similarity=0.439 Sum_probs=75.7
Q ss_pred CCHHHHHHHHHccCCCcceeecccccccHHHHHHHHHHhhcCceEEEEeeCCCCCcHHHHHHHHHhhcCcEEEEEeCCEE
Q 018444 112 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQI 191 (356)
Q Consensus 112 LT~kErtyLRrla~~l~Pif~LGKngv~~gLv~aI~ea~Ek~ELVKI~vkg~~~~D~keiA~eLk~lTg~vLVs~~g~~I 191 (356)
||++|+.+||++|+.++|+++|||+|++++++.+|+.+|++||||||.|+++|..+.+++|++|++.|||++|+++|+++
T Consensus 1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG~~~ 80 (84)
T PF01985_consen 1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIGRTI 80 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEETTEE
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEECCEE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEe
Q 018444 192 LMWR 195 (356)
Q Consensus 192 VLYR 195 (356)
||||
T Consensus 81 vlyR 84 (84)
T PF01985_consen 81 VLYR 84 (84)
T ss_dssp EEEE
T ss_pred EEEC
Confidence 9998
No 2
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=99.89 E-value=3.3e-23 Score=166.38 Aligned_cols=76 Identities=28% Similarity=0.476 Sum_probs=68.2
Q ss_pred cccCcccCCCeeeeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEEEEEe
Q 018444 2 LVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFR 77 (356)
Q Consensus 2 l~K~~lkmkpvV~IGK~GVTd~VVeeIh~awk~rELVKVK~l~~~~~dmk~iae~Le~kTGg~VVqrIG~~iVLYR 77 (356)
|-+.|++++|+|+|||+|||++|+++|+++|++||||||||.+++..+++++++.|+++|||++||++|+++||||
T Consensus 9 Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG~~~vlyR 84 (84)
T PF01985_consen 9 LRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIGRTIVLYR 84 (84)
T ss_dssp HHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEETTEEEEEE
T ss_pred HHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEECCEEEEEC
Confidence 4578999999999999999999999999999999999999999999999999999999999999999999999998
No 3
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=99.87 E-value=3.8e-22 Score=165.03 Aligned_cols=77 Identities=22% Similarity=0.315 Sum_probs=74.9
Q ss_pred cCcccCCCeeeeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEEEEEeccC
Q 018444 4 KPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRN 80 (356)
Q Consensus 4 K~~lkmkpvV~IGK~GVTd~VVeeIh~awk~rELVKVK~l~~~~~dmk~iae~Le~kTGg~VVqrIG~~iVLYRg~n 80 (356)
..|++++|+|+|||+|||++|+++|+++|++|||||||+++++..+.+++++.|+++|||++||.||+++||||++.
T Consensus 11 ~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~iG~~~vlYR~~~ 87 (95)
T TIGR00253 11 GKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGKTIVLYRPTK 87 (95)
T ss_pred HHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEccEEEEEecCC
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999974
No 4
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=99.87 E-value=4.3e-22 Score=164.70 Aligned_cols=86 Identities=22% Similarity=0.348 Sum_probs=85.0
Q ss_pred CCHHHHHHHHHccCCCcceeecccccccHHHHHHHHHHhhcCceEEEEeeCCCCCcHHHHHHHHHhhcCcEEEEEeCCEE
Q 018444 112 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQI 191 (356)
Q Consensus 112 LT~kErtyLRrla~~l~Pif~LGKngv~~gLv~aI~ea~Ek~ELVKI~vkg~~~~D~keiA~eLk~lTg~vLVs~~g~~I 191 (356)
||++|+.+||++|+.+.|+++|||+|++++++..|.++|++||||||.++++|..|.+++|++|++.|||++||++|+.+
T Consensus 1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~iG~~~ 80 (95)
T TIGR00253 1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGKTI 80 (95)
T ss_pred CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEccEE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecC
Q 018444 192 LMWRGK 197 (356)
Q Consensus 192 VLYRGk 197 (356)
||||+.
T Consensus 81 vlYR~~ 86 (95)
T TIGR00253 81 VLYRPT 86 (95)
T ss_pred EEEecC
Confidence 999986
No 5
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.87 E-value=6.7e-22 Score=164.23 Aligned_cols=86 Identities=15% Similarity=0.256 Sum_probs=85.2
Q ss_pred CCHHHHHHHHHccCCCcceeecccccccHHHHHHHHHHhhcCceEEEEeeCCCCCcHHHHHHHHHhhcCcEEEEEeCCEE
Q 018444 112 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQI 191 (356)
Q Consensus 112 LT~kErtyLRrla~~l~Pif~LGKngv~~gLv~aI~ea~Ek~ELVKI~vkg~~~~D~keiA~eLk~lTg~vLVs~~g~~I 191 (356)
||++|+.|||++|+++.|+++|||+|++++++..|.+++++||||||.++++|..+.+++|++|++.|||++||++|+++
T Consensus 3 Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~IG~~~ 82 (97)
T PRK10343 3 LSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTL 82 (97)
T ss_pred CCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeeeCcEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecC
Q 018444 192 LMWRGK 197 (356)
Q Consensus 192 VLYRGk 197 (356)
||||..
T Consensus 83 vlYR~~ 88 (97)
T PRK10343 83 VLYRPT 88 (97)
T ss_pred EEEecC
Confidence 999986
No 6
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.87 E-value=8.6e-22 Score=163.59 Aligned_cols=77 Identities=21% Similarity=0.241 Sum_probs=75.0
Q ss_pred cCcccCCCeeeeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEEEEEeccC
Q 018444 4 KPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRN 80 (356)
Q Consensus 4 K~~lkmkpvV~IGK~GVTd~VVeeIh~awk~rELVKVK~l~~~~~dmk~iae~Le~kTGg~VVqrIG~~iVLYRg~n 80 (356)
..|++++|+|+|||+|||++|+++|.++|++|||||||+++++.++.++++++|+++||+++||+||+++||||++.
T Consensus 13 ~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~IG~~~vlYR~~~ 89 (97)
T PRK10343 13 GLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTLVLYRPTK 89 (97)
T ss_pred HhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeeeCcEEEEEecCC
Confidence 56899999999999999999999999999999999999999999999999999999999999999999999999985
No 7
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.84 E-value=8.3e-21 Score=157.77 Aligned_cols=79 Identities=24% Similarity=0.403 Sum_probs=75.7
Q ss_pred cccCcccCCCeeeeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEEEEEeccC
Q 018444 2 LVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRN 80 (356)
Q Consensus 2 l~K~~lkmkpvV~IGK~GVTd~VVeeIh~awk~rELVKVK~l~~~~~dmk~iae~Le~kTGg~VVqrIG~~iVLYRg~n 80 (356)
|.+.|++++|+|+|||+|||++|+++|.++|++||||||++.+++.++.+++|+.|++++|+.+||+||+++||||.+.
T Consensus 10 Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqviG~~~vlyr~~~ 88 (97)
T COG1534 10 LRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIGKTLVLYRESK 88 (97)
T ss_pred HHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeeeeEEEEEecCc
Confidence 5678999999999999999999999999999999999999999999999999999999999999999999999999443
No 8
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.82 E-value=4.2e-20 Score=153.58 Aligned_cols=84 Identities=26% Similarity=0.416 Sum_probs=83.6
Q ss_pred CCHHHHHHHHHccCCCcceeecccccccHHHHHHHHHHhhcCceEEEEeeCCCCCcHHHHHHHHHhhcCcEEEEEeCCEE
Q 018444 112 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQI 191 (356)
Q Consensus 112 LT~kErtyLRrla~~l~Pif~LGKngv~~gLv~aI~ea~Ek~ELVKI~vkg~~~~D~keiA~eLk~lTg~vLVs~~g~~I 191 (356)
||.+|+.+||++|+++.|+|++||||++.++++.|..+++.+|||||.+++++..|-+++|++|++.|||.+||++|+.+
T Consensus 2 Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqviG~~~ 81 (97)
T COG1534 2 LTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIGKTL 81 (97)
T ss_pred CcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeeeeEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEe
Q 018444 192 LMWR 195 (356)
Q Consensus 192 VLYR 195 (356)
||||
T Consensus 82 vlyr 85 (97)
T COG1534 82 VLYR 85 (97)
T ss_pred EEEe
Confidence 9999
No 9
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.80 E-value=4e-20 Score=191.67 Aligned_cols=192 Identities=21% Similarity=0.182 Sum_probs=172.3
Q ss_pred CCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCC-eEEEEECcEEEEEeccCCCCCC---------
Q 018444 16 GRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGG-KIIFRVGGLVYLFRGRNYNYRT--------- 85 (356)
Q Consensus 16 GK~GVTd~VVeeIh~awk~rELVKVK~l~~~~~dmk~iae~Le~kTGg-~VVqrIG~~iVLYRg~nY~~~~--------- 85 (356)
+++|+|+++++.|++.|+.+|+++++|....+.+|.+.++.++..||| .+||+.|-+...|++..|..+.
T Consensus 34 ~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~n~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~~ 113 (564)
T KOG1990|consen 34 WKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMSTGGNFVVWSRGDSISSPEFLCQRSPVDFVARQQEN 113 (564)
T ss_pred cccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccCCCceeeeecCccccCCccceeecchhhhhhhchh
Confidence 999999999999999999999999999999999999999999999999 9999999999999777776541
Q ss_pred --------------------CCCCCccccCCCCCCCc-----------cccccCCC----CCCHHHHHHHHHccCCCcce
Q 018444 86 --------------------RPQYPLMLWKPAAPVYP-----------KLIQEAPE----GLTKHEADELRRKGKSLLPI 130 (356)
Q Consensus 86 --------------------rPr~~~m~w~p~~Pv~p-----------~l~~~~Pe----~LT~kErtyLRrla~~l~Pi 130 (356)
.|++-+|+..++.|++. .+++.+|. .||..+.+++|++|...+||
T Consensus 114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~ 193 (564)
T KOG1990|consen 114 QAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPH 193 (564)
T ss_pred hhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhccccccc
Confidence 15555666566666544 44555554 49999999999999999999
Q ss_pred eecccccccHHHHHHHHHHhhcCceEEEEee-CCCCCcHHHHHHHH--HhhcCcEEEEEeCCEEEEEecCCCCCCCCCCC
Q 018444 131 CKLAKNGVYLTLVRDVRNAFEGSSLVKVNCK-GMHASDYKKLGAKL--KELVPCVLLSFDDEQILMWRGKDWKSMYPEPP 207 (356)
Q Consensus 131 f~LGKngv~~gLv~aI~ea~Ek~ELVKI~vk-g~~~~D~keiA~eL--k~lTg~vLVs~~g~~IVLYRGkd~~~~~v~~~ 207 (356)
|.+|+++..++++.+++.+|++++.+|+.|+ |.+.+..+.+|.++ ..+||++||.+|+..+|+|||++|++ .++.+
T Consensus 194 ~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~hN~~~dv~y~~~~Fl~-~lp~~ 272 (564)
T KOG1990|consen 194 FALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVLHNKLLDVMYRYKNFLS-PLPST 272 (564)
T ss_pred ceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEeeccceeeeeehhhccc-ccchh
Confidence 9999999999999999999999999999999 99999999999999 99999999999999999999999999 66555
Q ss_pred C
Q 018444 208 S 208 (356)
Q Consensus 208 ~ 208 (356)
.
T Consensus 273 l 273 (564)
T KOG1990|consen 273 L 273 (564)
T ss_pred H
Confidence 3
No 10
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.28 E-value=1.7e-12 Score=135.35 Aligned_cols=209 Identities=21% Similarity=0.271 Sum_probs=168.7
Q ss_pred ccCcccCCCeeeeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCC-hhhHHHHHHHH--HHHhCCeEEEEECcEEEEEecc
Q 018444 3 VKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVP-TVDMDNVCRRL--EEKTGGKIIFRVGGLVYLFRGR 79 (356)
Q Consensus 3 ~K~~lkmkpvV~IGK~GVTd~VVeeIh~awk~rELVKVK~l~~~-~~dmk~iae~L--e~kTGg~VVqrIG~~iVLYRg~ 79 (356)
-+++-+..+.+.+|..+.-+++.-.+...|..|+..|+.+...- ......++..+ -..||+.+|-+-|-..+.||++
T Consensus 184 r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~hN~~~dv~y~~~ 263 (564)
T KOG1990|consen 184 RRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVLHNKLLDVMYRYK 263 (564)
T ss_pred HHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEeeccceeeeeehh
Confidence 35677788999999999999999999999999999998887653 44556778888 8899999999999999999998
Q ss_pred CCCCCC-------CC---CCCcc-----------------------------ccC-CCCC--------------------
Q 018444 80 NYNYRT-------RP---QYPLM-----------------------------LWK-PAAP-------------------- 99 (356)
Q Consensus 80 nY~~~~-------rP---r~~~m-----------------------------~w~-p~~P-------------------- 99 (356)
+|-.+- +. .||.+ .|- |+.+
T Consensus 264 ~Fl~~lp~~l~~f~~~~~~fp~~~~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~ 343 (564)
T KOG1990|consen 264 NFLSPLPSTLEEFTDSSSMFPNIEDTKRLAKLSEYQKLNLKATLLELARAKAKKEKEIERRSISSRLKLEFEKASSEKLT 343 (564)
T ss_pred hcccccchhHHHhhhhhhhhhhhHHHHHhhccccccchhhhhhHHHHHHHhcccccCcccccccchhhhhhhccchhhHH
Confidence 887631 11 12211 011 1111
Q ss_pred ---------------------------CCccccccCCCCCCHHHHHHHHHccCCCcceeecccccccHHHHHHHHHHhhc
Q 018444 100 ---------------------------VYPKLIQEAPEGLTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEG 152 (356)
Q Consensus 100 ---------------------------v~p~l~~~~Pe~LT~kErtyLRrla~~l~Pif~LGKngv~~gLv~aI~ea~Ek 152 (356)
-.|..-+..|+..|.+++.++++.|..+....-+|+.|+++|++.+++.+|..
T Consensus 344 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~ 423 (564)
T KOG1990|consen 344 EAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKS 423 (564)
T ss_pred HHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhh
Confidence 01111124567899999999999999999999999999999999999999999
Q ss_pred CceEEEEee-CCCCCcHHHHHHHHHhhcCcEEEEEeCC-E---EEEEecCCCCCCCCCCCCCCC
Q 018444 153 SSLVKVNCK-GMHASDYKKLGAKLKELVPCVLLSFDDE-Q---ILMWRGKDWKSMYPEPPSFSN 211 (356)
Q Consensus 153 ~ELVKI~vk-g~~~~D~keiA~eLk~lTg~vLVs~~g~-~---IVLYRGkd~~~~~v~~~~~~~ 211 (356)
+|++|+.|+ .+.+...+..|..+...+|+++|+++.. . |+.|||++|..+....|....
T Consensus 424 ~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~P~~~l 487 (564)
T KOG1990|consen 424 RELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLRPRNLL 487 (564)
T ss_pred cccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcccCchhhh
Confidence 999999999 6666999999999999999999998543 2 899999999997776665533
No 11
>PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A.
Probab=53.67 E-value=95 Score=24.17 Aligned_cols=56 Identities=11% Similarity=0.170 Sum_probs=38.7
Q ss_pred HHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHH---HhCCeEEEEECcEEEEEeccCC
Q 018444 25 LELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEE---KTGGKIIFRVGGLVYLFRGRNY 81 (356)
Q Consensus 25 VeeIh~awk~rELVKVK~l~~~~~dmk~iae~Le~---kTGg~VVqrIG~~iVLYRg~nY 81 (356)
+.+|-++++....|-+.+..-.....+++.+.|.. ..+|.+.+. |..++|+=+++.
T Consensus 12 ~~~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~G~~~al~G~i~~i-~~~~~l~~P~~V 70 (73)
T PF04472_consen 12 AREIVDALREGKIVIVNLENLDDEEAQRILDFLSGAVYALDGDIQKI-SEKVFLLTPKGV 70 (73)
T ss_dssp HHHHHHHHHTT--EEEE-TTS-HHHHHHHHHHHHHHHHHTT-EEEEE-ETTEEEEE----
T ss_pred HHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHhchheeeCCEEEEE-cCCEEEEECCCc
Confidence 45688999999999999999888899999999875 778887665 666777766554
No 12
>PRK06934 flavodoxin; Provisional
Probab=49.04 E-value=12 Score=35.71 Aligned_cols=93 Identities=19% Similarity=0.346 Sum_probs=58.0
Q ss_pred CCChhhHHHHHHHHHHHhCCeEEEEECcEEEEEeccCCCCC-----------CCC-----------------CCCccccC
Q 018444 44 GVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRNYNYR-----------TRP-----------------QYPLMLWK 95 (356)
Q Consensus 44 ~~~~~dmk~iae~Le~kTGg~VVqrIG~~iVLYRg~nY~~~-----------~rP-----------------r~~~m~w~ 95 (356)
+...-+.+.+|+.|++++||.+.... ..-.|-. +|+.. .|| -||.|||.
T Consensus 67 ~~~~GnTk~vAe~Ia~~~gaDl~eI~--~~~~Y~~-~yd~~~~~a~~E~~~~~~P~L~~~~~dl~~YD~I~IG~PIWwg~ 143 (221)
T PRK06934 67 GEVLGSTQYVAQIIQEETGGDLFRIE--TVKPYPR-QHDPLLKYAEQEVKEGGRPEMREKIQNLADYDQIFIGYPIWWYK 143 (221)
T ss_pred CCCCCHHHHHHHHHHHHHCCCEEEEE--EccccCC-CCchhhhHHHHhhhcCCCHHHHHHHHhHHhCCEEEEEcchhhcc
Confidence 33446889999999999999888764 2233433 33321 134 35778888
Q ss_pred CCCCCCccccccCCCCCCHHHHHHHHHccCCCcceeecccccccHHHHHHHHHHhhcC
Q 018444 96 PAAPVYPKLIQEAPEGLTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGS 153 (356)
Q Consensus 96 p~~Pv~p~l~~~~Pe~LT~kErtyLRrla~~l~Pif~LGKngv~~gLv~aI~ea~Ek~ 153 (356)
++.||.-=|= +..+ .++++-|+|.-|-+| ..+-++.|+++..+.
T Consensus 144 ~P~~V~tFLe-----------~~d~--~GK~I~pF~T~ggsg-~g~s~~~i~~l~~~a 187 (221)
T PRK06934 144 MPMVMYSFFE-----------QHDF--SGKTLIPFTTHGGSR-FSDSLREIKRLQPNA 187 (221)
T ss_pred ccHHHHHHHH-----------hcCC--CCCEEEEEEecCCCC-ccchHHHHHHHcCCc
Confidence 7555543221 1111 267888999887665 344677787777666
No 13
>PF11830 DUF3350: Domain of unknown function (DUF3350); InterPro: IPR021785 This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 50 to 64 amino acids in length.
Probab=39.53 E-value=38 Score=26.42 Aligned_cols=23 Identities=22% Similarity=0.482 Sum_probs=17.6
Q ss_pred ccccccchhHHHHHHHHhhhccc
Q 018444 233 QGTIRSSPKMISLWKRAIESTKA 255 (356)
Q Consensus 233 ~~~~~~~~~~~~lw~~ai~~~~a 255 (356)
...-+++...-.||+.||..-..
T Consensus 22 ~~~krt~eelR~LWrkAI~QqIl 44 (56)
T PF11830_consen 22 EKKKRTREELRELWRKAIHQQIL 44 (56)
T ss_pred cccccCHHHHHHHHHHHHHHHHH
Confidence 45567778899999999966543
No 14
>PF01918 Alba: Alba; InterPro: IPR002775 Members of this family include the archaeal protein Alba and a number of eukaryotic proteins with no known function. The DNA/RNA-binding protein Alba binds double-stranded DNA tightly but without sequence specificity. It binds rRNA and mRNA in vivo, and may play a role in maintaining the structural and functional stability of RNA, and, perhaps, ribosomes. It is distributed uniformly and abundantly on the chromosome. Alba has been shown to bind DNA and affect DNA supercoiling in a temperature dependent manner []. It is regulated by acetylation (alba = acetylation lowers binding affinity) by the Sir2 protein. Alba is proposed to play a role in establishment or maintenance of chromatin architecture and thereby in transcription repression. For further information see [].; GO: 0003676 nucleic acid binding; PDB: 3TOE_B 3IAB_A 1NFJ_A 1NFH_B 2Q3V_B 1VM0_B 1NH9_A 1Y9X_A 3U6Y_C 2H9U_A ....
Probab=33.66 E-value=85 Score=23.84 Aligned_cols=58 Identities=14% Similarity=0.069 Sum_probs=48.0
Q ss_pred eeecccccccHHHHHHHHHHh-----hcCceEEEEeeCCCCCcHHHHHHHHHhhcCcEEEEEe
Q 018444 130 ICKLAKNGVYLTLVRDVRNAF-----EGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFD 187 (356)
Q Consensus 130 if~LGKngv~~gLv~aI~ea~-----Ek~ELVKI~vkg~~~~D~keiA~eLk~lTg~vLVs~~ 187 (356)
.+.++++.-....+..+..+| .+..-|.|.-.|..-...=.+|+.++++.+..++|++
T Consensus 2 ~I~V~~~~~~~~~v~~~~~~L~~~~~~~~~~V~l~g~G~aI~kaI~vaei~K~~~~~~~~qv~ 64 (70)
T PF01918_consen 2 EIYVSSNSPIKSYVKRALKLLEGRENGKNDEVVLKGRGKAISKAISVAEILKRRFGEGLYQVN 64 (70)
T ss_dssp EEEE-STS-HHHHHHHHHHHHT-TTHTTCSEEEEEEECCHHHHHHHHHHHHHHHTSTTTEEEE
T ss_pred EEEECCCCCHHHHHHHHHHHHhhhhcCCCCEEEEEEEcHHHHHHHHHHHHHHHhhcCCCEEEE
Confidence 467889999999999999999 8888899999999989999999999999865555543
No 15
>COG1799 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.80 E-value=87 Score=29.16 Aligned_cols=58 Identities=19% Similarity=0.296 Sum_probs=48.0
Q ss_pred HHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHH---HhCCeEEEEECcEEEEEeccCCCC
Q 018444 25 LELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEE---KTGGKIIFRVGGLVYLFRGRNYNY 83 (356)
Q Consensus 25 VeeIh~awk~rELVKVK~l~~~~~dmk~iae~Le~---kTGg~VVqrIG~~iVLYRg~nY~~ 83 (356)
..+|-++++.++-|-|.+..-...+.+++.+.|+- .++|. +|+||..++|.=+.|-+.
T Consensus 87 a~~ia~~lk~~k~Vvinl~~m~~~qArRivDFlaG~~~al~G~-~qkVg~~ifL~tP~nv~V 147 (167)
T COG1799 87 AQEIADYLKNRKAVVINLQRMDPAQARRIVDFLAGAVFALRGS-IQKVGSKIFLLTPSNVDV 147 (167)
T ss_pred HHHHHHHHhcCceEEEEeeeCCHHHHHHHHHHhcchhhhhccc-HHhhcceeEEecccceee
Confidence 46788899999999999999888999999999874 34444 378999999998888763
No 16
>cd05797 Ribosomal_L10 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein and forms the base of the L7/L12 stalk, while the extended C-terminal helix binds to two or three dimers of the NTD of L7/L12 (L7 and L12 are identical except for an acetylated N-terminus). The L7/L12 stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-in
Probab=31.41 E-value=53 Score=28.79 Aligned_cols=31 Identities=29% Similarity=0.257 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHHHccCCCcceeecccccccH
Q 018444 110 EGLTKHEADELRRKGKSLLPICKLAKNGVYL 140 (356)
Q Consensus 110 e~LT~kErtyLRrla~~l~Pif~LGKngv~~ 140 (356)
.+||..|.+.||+.-+.....|.++||.+..
T Consensus 28 ~gl~~~~~~~lR~~lr~~~~~~~V~KNtL~~ 58 (157)
T cd05797 28 RGLTVAQLTELRKELREAGVKLKVVKNTLAK 58 (157)
T ss_pred CCCcHHHHHHHHHHHHHcCCEEEEehhHHHH
Confidence 4799999999999988877899999998743
No 17
>PF11623 DUF3252: Protein of unknown function (DUF3252); InterPro: IPR021659 This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function. ; PDB: 3C4S_B 2JZ2_A.
Probab=30.16 E-value=40 Score=25.99 Aligned_cols=18 Identities=39% Similarity=0.741 Sum_probs=16.2
Q ss_pred EEEEE--CcEEEEEeccCCC
Q 018444 65 IIFRV--GGLVYLFRGRNYN 82 (356)
Q Consensus 65 VVqrI--G~~iVLYRg~nY~ 82 (356)
+|||+ |++.|||-|.|++
T Consensus 23 ~VQRvsdgkaaVLFEGGnWd 42 (53)
T PF11623_consen 23 FVQRVSDGKAAVLFEGGNWD 42 (53)
T ss_dssp EEEEEETTEEEEEEEETTEE
T ss_pred EEEEeeCCeEEEEecCCCce
Confidence 68988 9999999999986
No 18
>cd08619 PI-PLCXDc_plant Catalytic domain of phosphatidylinositol-specific phospholipase C, X domain containing proteins found in plants. The CD corresponds to the catalytic domain present in uncharacterized plant phosphatidylinositol-specific phospholipase C, X domain containing proteins (PI-PLCXD). The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) has a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, plant PI-PLCXDs contain a single TIM-barrel type catalytic domain, X domain, and are more closely related to bacterial PI-PLCs, which participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although the biological function of plant PI-PLCXDs still remains u
Probab=28.41 E-value=1.3e+02 Score=30.19 Aligned_cols=65 Identities=12% Similarity=0.137 Sum_probs=48.6
Q ss_pred CHHHHHHHHHHHHhC--CeEEEEecCCChh-hHHHHHHHHHHHhCCeEEEEE-------------CcEEEEEeccCCCCC
Q 018444 21 THNMLELIHSHWKRR--RVIKIKCKGVPTV-DMDNVCRRLEEKTGGKIIFRV-------------GGLVYLFRGRNYNYR 84 (356)
Q Consensus 21 Td~VVeeIh~awk~r--ELVKVK~l~~~~~-dmk~iae~Le~kTGg~VVqrI-------------G~~iVLYRg~nY~~~ 84 (356)
.++++++|.+-+..| |+|-+.+...... +..+....|.++.|..++.+. .+++++|+...|.-+
T Consensus 93 ~~dvL~~i~~FL~~hp~EvVIL~~k~ey~~~~~~~~~~~li~~lGd~l~~~~~~~~~~TL~eL~~krVIviy~~~~~~~~ 172 (285)
T cd08619 93 VDVVLNDIKRFLSETKSEFVILEIRTEYGHEDPPQFDLWLVEQLGDHLIHQDDSVFSKTLAELLPKRVICIWKPRKSPAP 172 (285)
T ss_pred HHHHHHHHHHHHHHCCCeEEEEEEeecccCCCchHHHHHHHHHhcchhccCCCccccccHHHHhCCcEEEEEcCCCCCcc
Confidence 478999999999776 9999999765322 223566778888899888652 356888999988744
Q ss_pred C
Q 018444 85 T 85 (356)
Q Consensus 85 ~ 85 (356)
+
T Consensus 173 ~ 173 (285)
T cd08619 173 A 173 (285)
T ss_pred C
Confidence 3
No 19
>cd01461 vWA_interalpha_trypsin_inhibitor vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin). Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to the extracellular matrix by binding to hyaluronic acid. The heavy chains carry the VWA domain with a conserved MIDAS motif. Although the exact role of the VWA domains remains unknown, it has been speculated to be involved in mediating protein-protein interactions with the components of the extracellular matrix.
Probab=27.51 E-value=1.5e+02 Score=24.95 Aligned_cols=52 Identities=13% Similarity=0.129 Sum_probs=36.3
Q ss_pred cccccHHHHHHHHHHhhcCceEEEEeeCCCCCcHHHHHHHHHhhcCcEEEEEeC
Q 018444 135 KNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDD 188 (356)
Q Consensus 135 Kngv~~gLv~aI~ea~Ek~ELVKI~vkg~~~~D~keiA~eLk~lTg~vLVs~~g 188 (356)
...-.++++.++..++.. =++|.+-++...-..++...|++.|||..+.+.+
T Consensus 110 ~~~~~~~~~~~~~~~~~~--~i~i~~i~~g~~~~~~~l~~ia~~~gG~~~~~~~ 161 (171)
T cd01461 110 EVTNESQILKNVREALSG--RIRLFTFGIGSDVNTYLLERLAREGRGIARRIYE 161 (171)
T ss_pred CCCCHHHHHHHHHHhcCC--CceEEEEEeCCccCHHHHHHHHHcCCCeEEEecC
Confidence 333345566777666543 3677777776655568899999999999988754
No 20
>PF04530 Viral_Beta_CD: Viral Beta C/D like family; InterPro: IPR007617 This is a family of ssRNA positive-strand viral proteins. Conserved region is found in the Beta C and Beta D transcripts.
Probab=26.61 E-value=61 Score=28.84 Aligned_cols=21 Identities=24% Similarity=0.686 Sum_probs=18.8
Q ss_pred eeeCCCCCCHHHHHHHHHHHHh
Q 018444 13 VNLGRDGLTHNMLELIHSHWKR 34 (356)
Q Consensus 13 V~IGK~GVTd~VVeeIh~awk~ 34 (356)
+++|+.-|.++||+.|| ||.+
T Consensus 93 ik~~~~PIDP~VIaAIH-HwQk 113 (122)
T PF04530_consen 93 IKLAPVPIDPEVIAAIH-HWQK 113 (122)
T ss_pred EecCCCCCCHHHHHHHH-HHHh
Confidence 56899999999999999 8865
No 21
>cd08619 PI-PLCXDc_plant Catalytic domain of phosphatidylinositol-specific phospholipase C, X domain containing proteins found in plants. The CD corresponds to the catalytic domain present in uncharacterized plant phosphatidylinositol-specific phospholipase C, X domain containing proteins (PI-PLCXD). The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) has a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, plant PI-PLCXDs contain a single TIM-barrel type catalytic domain, X domain, and are more closely related to bacterial PI-PLCs, which participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although the biological function of plant PI-PLCXDs still remains u
Probab=26.32 E-value=2.2e+02 Score=28.49 Aligned_cols=73 Identities=16% Similarity=0.220 Sum_probs=51.4
Q ss_pred ccHHHHHHHHHHhhcC--ceEEEEeeCC-CCCcHHHHHHHHHhhcCcEEEEEeC-------------CEEEEEecCCCCC
Q 018444 138 VYLTLVRDVRNAFEGS--SLVKVNCKGM-HASDYKKLGAKLKELVPCVLLSFDD-------------EQILMWRGKDWKS 201 (356)
Q Consensus 138 v~~gLv~aI~ea~Ek~--ELVKI~vkg~-~~~D~keiA~eLk~lTg~vLVs~~g-------------~~IVLYRGkd~~~ 201 (356)
....++..|+..+..+ |+|-+.++.. ...+..+....|.+..|..++.... .-||+|+...|..
T Consensus 92 ~~~dvL~~i~~FL~~hp~EvVIL~~k~ey~~~~~~~~~~~li~~lGd~l~~~~~~~~~~TL~eL~~krVIviy~~~~~~~ 171 (285)
T cd08619 92 PVDVVLNDIKRFLSETKSEFVILEIRTEYGHEDPPQFDLWLVEQLGDHLIHQDDSVFSKTLAELLPKRVICIWKPRKSPA 171 (285)
T ss_pred cHHHHHHHHHHHHHHCCCeEEEEEEeecccCCCchHHHHHHHHHhcchhccCCCccccccHHHHhCCcEEEEEcCCCCCc
Confidence 4577888888888554 9999999833 3444445667777777888876533 3389999888877
Q ss_pred CCCCCCCCC
Q 018444 202 MYPEPPSFS 210 (356)
Q Consensus 202 ~~v~~~~~~ 210 (356)
+.+..+...
T Consensus 172 ~~~~~~~~~ 180 (285)
T cd08619 172 PAVGSPLWS 180 (285)
T ss_pred cCCCCCccC
Confidence 766655544
No 22
>PF11609 DUF3248: Protein of unknown function (DUF3248); InterPro: IPR021650 This family of proteins is thought to be the product of the gene TT1592 from Thermus thermophilus however this cannot be confirmed. Currently there is no known function. ; PDB: 2E6X_A.
Probab=24.53 E-value=44 Score=26.55 Aligned_cols=13 Identities=31% Similarity=0.792 Sum_probs=9.4
Q ss_pred HHhCCeEEEEECc
Q 018444 59 EKTGGKIIFRVGG 71 (356)
Q Consensus 59 ~kTGg~VVqrIG~ 71 (356)
+++|+.+|||||+
T Consensus 2 ~~Lg~~LvWRiGk 14 (63)
T PF11609_consen 2 EALGQHLVWRIGK 14 (63)
T ss_dssp HHTT--EEEEEEE
T ss_pred hhhcceeEEEecc
Confidence 4689999999987
No 23
>COG2511 GatE Archaeal Glu-tRNAGln amidotransferase subunit E (contains GAD domain) [Translation, ribosomal structure and biogenesis]
Probab=23.18 E-value=3e+02 Score=30.41 Aligned_cols=118 Identities=19% Similarity=0.136 Sum_probs=67.5
Q ss_pred eCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHh----CCeEEEEE-----CcEEEEEeccCCCCCC
Q 018444 15 LGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKT----GGKIIFRV-----GGLVYLFRGRNYNYRT 85 (356)
Q Consensus 15 IGK~GVTd~VVeeIh~awk~rELVKVK~l~~~~~dmk~iae~Le~kT----Gg~VVqrI-----G~~iVLYRg~nY~~~~ 85 (356)
+.+-|||+.=|+.+.+++-+.+.--+.+........+.+.+.+.++. .|..=-+. |.|.+| |+..=. -
T Consensus 351 LP~YGIteeEV~~v~d~lga~~~Davvlva~~~~~~~~a~~~V~~Ra~~ai~gvpeETR~a~~DGtT~yL-RPlPGa--a 427 (631)
T COG2511 351 LPGYGITEEEVEAVRDALGAGEEDAVVLVAGEEERAKRALEAVIERAKEAIEGVPEETRGALPDGTTVYL-RPLPGA--A 427 (631)
T ss_pred CccCCCCHHHHHHHHHHhCCCCCceEEEEeCCHHHHHHHHHHHHHHHHHHHcCCCHhhccCCCCCCceee-cCCCCc--c
Confidence 34679999999999999999887777776666666666666655433 22222211 333332 111000 0
Q ss_pred CCCCCccccCCCCCCCccccc----cCCCCCCHHHHHHHHHccCCCcceeeccccc
Q 018444 86 RPQYPLMLWKPAAPVYPKLIQ----EAPEGLTKHEADELRRKGKSLLPICKLAKNG 137 (356)
Q Consensus 86 rPr~~~m~w~p~~Pv~p~l~~----~~Pe~LT~kErtyLRrla~~l~Pif~LGKng 137 (356)
| -||...- |+.-+...+++ .+|++++.+-..|.+..+....---++-+..
T Consensus 428 R-MYPETDI-Ppi~i~~~~l~~~~~~~Pe~~~ek~~r~~~eygLs~~LA~~~~~~~ 481 (631)
T COG2511 428 R-MYPETDI-PPIRIDEELLEKIKENLPELPEEKVERYVKEYGLSKELAEQLASDP 481 (631)
T ss_pred c-cCCcCCC-CCcccCHHHHHHHhhhCCCCHHHHHHHHHHHhCCCHHHHHHHHhhh
Confidence 0 2333332 22334555553 5788888888888887766544333444333
No 24
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=22.93 E-value=2.1e+02 Score=22.65 Aligned_cols=39 Identities=18% Similarity=0.166 Sum_probs=24.5
Q ss_pred CCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEEEE
Q 018444 35 RRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYL 75 (356)
Q Consensus 35 rELVKVK~l~~~~~dmk~iae~Le~kTGg~VVqrIG~~iVL 75 (356)
|||+=||+.. .. +.+.-...|++..+|.+|.....++++
T Consensus 2 rEl~LiKV~~-~~-~~r~ei~~l~~~f~a~ivd~~~~~~ii 40 (75)
T PF10369_consen 2 RELALIKVKA-TP-ENRSEILQLAEIFRARIVDVSPDSIII 40 (75)
T ss_dssp EEEEEEEEE--SC-HHHHHHHHHHHHTT-EEEEEETTEEEE
T ss_pred eEEEEEEEEC-Cc-cCHHHHHHHHHHhCCEEEEECCCEEEE
Confidence 5666555555 23 334445667778999999988776665
No 25
>KOG1257 consensus NADP+-dependent malic enzyme [Energy production and conversion]
Probab=21.89 E-value=98 Score=33.80 Aligned_cols=73 Identities=21% Similarity=0.294 Sum_probs=57.5
Q ss_pred cccCCCeeeeCCCCC----CHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEE--EEEecc
Q 018444 6 LLKDNRQVNLGRDGL----THNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLV--YLFRGR 79 (356)
Q Consensus 6 ~lkmkpvV~IGK~GV----Td~VVeeIh~awk~rELVKVK~l~~~~~dmk~iae~Le~kTGg~VVqrIG~~i--VLYRg~ 79 (356)
....||-+.||-.|+ |+.|++.++.+ +|==-|--+.|++..+.-+|+..=.-|+|.+|-..|+-+ |-|-|+
T Consensus 385 V~~vKPtvLiG~S~~~g~Fteevl~~Ma~~---~erPiIFalSNPT~~aECtae~ay~~t~Gr~ifaSGSPF~pV~~~gK 461 (582)
T KOG1257|consen 385 VKEVKPTVLIGASGVGGAFTEEVLRAMAKS---NERPIIFALSNPTSKAECTAEQAYKWTKGRAIFASGSPFPPVEYNGK 461 (582)
T ss_pred HHhcCCcEEEecccCCccCCHHHHHHHHhc---CCCceEEecCCCccccccCHHHHhhhcCCcEEEecCCCCCCceeCCc
Confidence 346899999999986 78888888765 555556677889999999999999999999999998843 444444
Q ss_pred CC
Q 018444 80 NY 81 (356)
Q Consensus 80 nY 81 (356)
.|
T Consensus 462 ~~ 463 (582)
T KOG1257|consen 462 VY 463 (582)
T ss_pred Ee
Confidence 44
No 26
>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]
Probab=21.74 E-value=83 Score=28.93 Aligned_cols=101 Identities=18% Similarity=0.190 Sum_probs=50.7
Q ss_pred EEEEecCCCh-hhHHHHHHHHHHHhCCeEEEEECcEEEEEeccCCCCCCCCCCCccccCCCCCCCccccccCCCCCCHHH
Q 018444 38 IKIKCKGVPT-VDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHE 116 (356)
Q Consensus 38 VKVK~l~~~~-~dmk~iae~Le~kTGg~VVqrIG~~iVLYRg~nY~~~~rPr~~~m~w~p~~Pv~p~l~~~~Pe~LT~kE 116 (356)
|-++|++... ...+++++.|.+-..+ +.-.+-|..=..+. +|.++..+|-++.. ...|.+ |-..=
T Consensus 40 iTL~flGev~e~~~~~l~~~l~~i~~~-----~~f~i~l~g~g~F~---~~~~~rvi~~~v~~-~~~L~~-----L~~~l 105 (180)
T COG1514 40 ITLKFLGEVDEDKADELIEALARIAAP-----EPFPITLDGAGSFP---NPRRPRVIWVGVEE-TEELRA-----LAEEL 105 (180)
T ss_pred EEEEccCCcCchHHHHHHHHHHHhhcC-----CceEEEEeeEcccC---CCCCCcEEEEcCCC-cHHHHH-----HHHHH
Confidence 4577788644 4566666666664443 01122222222222 13344456766333 222221 11111
Q ss_pred HHHHHHc-----cCCCcceeecccccccHHHHHHHHHHhhc
Q 018444 117 ADELRRK-----GKSLLPICKLAKNGVYLTLVRDVRNAFEG 152 (356)
Q Consensus 117 rtyLRrl-----a~~l~Pif~LGKngv~~gLv~aI~ea~Ek 152 (356)
...+.++ .+.--||+.|||....++++....+....
T Consensus 106 ~~~~~~~g~~~~~r~F~PHvTl~r~k~~~~~~~~~~~~~~~ 146 (180)
T COG1514 106 ERALARLGLRPEERPFVPHVTLARVKSKDKLVEALGEFKNV 146 (180)
T ss_pred HHHHHhcCCCCCCCCcCCCEEEEeecccchhhhhhhhhccc
Confidence 1133333 46778999999998777777776655443
No 27
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=21.66 E-value=4.4e+02 Score=29.02 Aligned_cols=83 Identities=18% Similarity=0.150 Sum_probs=49.4
Q ss_pred eEEEEECcEEEEEeccCCCCCCCCCCCccccCCCCCCCccccccCCCCCCHHHHHHHHHccC--CCcceeecccccccHH
Q 018444 64 KIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELRRKGK--SLLPICKLAKNGVYLT 141 (356)
Q Consensus 64 ~VVqrIG~~iVLYRg~nY~~~~rPr~~~m~w~p~~Pv~p~l~~~~Pe~LT~kErtyLRrla~--~l~Pif~LGKngv~~g 141 (356)
.|.|..||.+-|.-+..| .|.|..|-|.+ .|+.|..|+-.+..=+.++...||++++ ...-++.=+=..-=.+
T Consensus 36 ~V~~~~GHl~~L~~p~~~----~~~~~~W~~~~-lp~~p~~f~~~~~~~~~~~~~~ik~l~k~~~ad~Ii~AtDpDREGE 110 (660)
T TIGR01056 36 FVTWAVGHLVELAEPEEY----DEKYKNWRTYD-LPLEPEDWQLVVSDKTKKQFNVIKRILKENKVDEVVIATDPDREGE 110 (660)
T ss_pred EEEeCchhhhcCCChhhc----ccccCccccCC-CCcccccceeeeccchHHHHHHHHHHhhhcCCCEEEECCCCCcchH
Confidence 578899999888766555 35666665543 6777765543333335677889999988 6555554433333333
Q ss_pred HHHH-HHHHhh
Q 018444 142 LVRD-VRNAFE 151 (356)
Q Consensus 142 Lv~a-I~ea~E 151 (356)
++.. |.+++.
T Consensus 111 ~I~~~i~~~l~ 121 (660)
T TIGR01056 111 LIAREILDYLK 121 (660)
T ss_pred HHHHHHHHHhC
Confidence 3332 444443
No 28
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=20.80 E-value=82 Score=28.30 Aligned_cols=27 Identities=22% Similarity=0.414 Sum_probs=24.7
Q ss_pred CCHHHHHHHHHHHHhCCeEEEEecCCC
Q 018444 20 LTHNMLELIHSHWKRRRVIKIKCKGVP 46 (356)
Q Consensus 20 VTd~VVeeIh~awk~rELVKVK~l~~~ 46 (356)
|+++.|..||++|+--+=|+||++...
T Consensus 38 Ia~~fVkdI~d~L~vG~eV~vKVl~id 64 (129)
T COG1098 38 IADGFVKDIHDHLKVGQEVKVKVLDID 64 (129)
T ss_pred hhhhhHHhHHHHhcCCCEEEEEEEeec
Confidence 689999999999999999999998754
No 29
>cd05796 Ribosomal_P0_like Ribosomal protein L10 family, P0-like protein subfamily; composed of uncharacterized eukaryotic proteins with similarity to the 60S ribosomal protein P0, including the Saccharomyces cerevisiae protein called mRNA turnover protein 4 (MRT4). MRT4 may be involved in mRNA decay. P0 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. It occupies the L7/L12 stalk of the ribosome. The stalk is known to contain the binding site for elongation factors EF-G and EF-Tu; however, there is disagreement as to whether or not P0 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, P0 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WAS
Probab=20.34 E-value=96 Score=27.83 Aligned_cols=29 Identities=17% Similarity=0.257 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHHHccCCCcceeecccccccH
Q 018444 110 EGLTKHEADELRRKGKSLLPICKLAKNGVYL 140 (356)
Q Consensus 110 e~LT~kErtyLRrla~~l~Pif~LGKngv~~ 140 (356)
.+|+..|...||+.-+.. .|.+|||.+..
T Consensus 26 ~gl~~~ql~~iR~~lr~~--~~~v~KNtl~~ 54 (163)
T cd05796 26 DNMRNNKLKDIRQEWKDS--RFFFGKNKVMQ 54 (163)
T ss_pred cCCCHHHHHHHHHHhcCC--EEEEEchHHHH
Confidence 479999999999998875 78899998754
Done!