Query 033755
Match_columns 112
No_of_seqs 103 out of 224
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 05:56:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033755.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033755hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00041 60S ribosomal protein 100.0 9.2E-64 2E-68 363.9 12.3 110 3-112 11-120 (120)
2 KOG0887 60S ribosomal protein 100.0 6.4E-60 1.4E-64 338.7 12.4 110 3-112 2-111 (111)
3 PF01247 Ribosomal_L35Ae: Ribo 100.0 1.2E-56 2.6E-61 315.6 10.7 95 12-106 1-95 (95)
4 PRK04337 50S ribosomal protein 100.0 1E-50 2.3E-55 281.9 9.4 85 14-106 3-87 (87)
5 COG2451 Ribosomal protein L35A 100.0 1.3E-48 2.9E-53 275.9 11.7 100 6-112 1-100 (100)
6 PF09853 DUF2080: Putative tra 95.6 0.023 5E-07 36.6 4.0 34 71-109 17-50 (53)
7 PF01782 RimM: RimM N-terminal 93.7 0.14 3E-06 33.6 4.2 36 16-56 45-80 (84)
8 TIGR02273 16S_RimM 16S rRNA pr 90.9 0.17 3.7E-06 37.5 2.1 28 29-56 55-82 (165)
9 PRK14591 rimM 16S rRNA-process 90.4 0.27 5.8E-06 36.9 2.8 29 28-56 59-87 (169)
10 PRK14592 rimM 16S rRNA-process 89.6 0.28 6E-06 36.6 2.3 32 28-60 51-82 (165)
11 PRK13829 rimM 16S rRNA-process 89.5 0.26 5.6E-06 36.8 2.1 32 28-60 48-79 (162)
12 PRK13828 rimM 16S rRNA-process 88.4 0.35 7.5E-06 36.0 2.1 32 28-60 39-70 (161)
13 PF01782 RimM: RimM N-terminal 87.9 0.66 1.4E-05 30.3 3.0 28 73-100 2-29 (84)
14 PRK14594 rimM 16S rRNA-process 87.2 0.38 8.2E-06 36.1 1.7 32 28-60 56-87 (166)
15 PRK00122 rimM 16S rRNA-process 87.2 0.43 9.3E-06 35.6 2.0 29 28-56 59-87 (172)
16 PRK00122 rimM 16S rRNA-process 87.1 0.74 1.6E-05 34.4 3.2 30 70-99 7-36 (172)
17 PRK14590 rimM 16S rRNA-process 87.0 0.45 9.7E-06 35.9 2.0 32 28-60 55-86 (171)
18 PRK14594 rimM 16S rRNA-process 87.0 0.67 1.4E-05 34.7 2.9 28 71-98 2-29 (166)
19 TIGR02273 16S_RimM 16S rRNA pr 84.1 1.7 3.6E-05 32.2 3.9 29 71-99 2-30 (165)
20 PRK14593 rimM 16S rRNA-process 81.2 1.7 3.7E-05 33.0 3.0 29 71-99 5-33 (184)
21 PRK14592 rimM 16S rRNA-process 80.5 2.1 4.5E-05 31.9 3.2 29 71-99 3-31 (165)
22 PRK14591 rimM 16S rRNA-process 79.0 2.7 5.9E-05 31.5 3.4 29 70-98 5-33 (169)
23 PRK14593 rimM 16S rRNA-process 77.2 4.2 9.1E-05 30.8 4.1 26 34-60 66-91 (184)
24 PRK14590 rimM 16S rRNA-process 75.2 3 6.4E-05 31.5 2.7 27 72-98 2-28 (171)
25 PF04950 DUF663: Protein of un 72.2 3.3 7.1E-05 34.1 2.5 63 30-108 232-294 (297)
26 PRK13829 rimM 16S rRNA-process 69.1 8.9 0.00019 28.6 4.1 24 70-96 3-26 (162)
27 COG0806 RimM RimM protein, req 59.3 8.5 0.00018 29.6 2.4 31 25-55 57-87 (174)
28 cd04479 RPA3 RPA3: A subfamily 54.7 56 0.0012 22.5 5.7 34 72-106 20-61 (101)
29 PF12150 MFP2b: Cytosolic moti 51.5 41 0.00089 29.1 5.5 37 70-109 41-81 (362)
30 PF14444 S1-like: S1-like 49.7 55 0.0012 21.4 4.7 36 70-107 2-44 (58)
31 KOG0189 Phosphoadenosine phosp 45.1 22 0.00048 29.3 2.8 32 11-42 147-178 (261)
32 KOG0461 Selenocysteine-specifi 44.5 42 0.00091 29.9 4.6 43 47-101 455-497 (522)
33 COG3466 ISA1214 Putative trans 42.4 93 0.002 20.1 5.2 27 75-107 23-49 (52)
34 COG0806 RimM RimM protein, req 41.5 45 0.00097 25.7 3.9 40 69-108 6-45 (174)
35 TIGR01129 secD protein-export 33.3 19 0.00041 30.6 0.8 33 28-60 62-94 (397)
36 PRK05812 secD preprotein trans 27.5 28 0.0006 30.8 0.8 33 28-60 148-180 (498)
37 PF01123 Stap_Strp_toxin: Stap 26.3 19 0.00042 24.7 -0.3 46 30-77 35-85 (87)
38 PRK14726 bifunctional preprote 24.4 33 0.00072 32.4 0.8 34 27-60 186-219 (855)
39 COG5192 BMS1 GTP-binding prote 24.4 30 0.00066 32.7 0.5 23 72-94 889-911 (1077)
40 PF05798 Phage_FRD3: Bacteriop 23.5 21 0.00046 24.4 -0.5 10 42-51 62-71 (75)
41 cd09232 Snurportin-1_C C-termi 22.6 1.5E+02 0.0033 22.8 4.0 35 50-98 30-64 (186)
42 PRK13023 bifunctional preprote 22.4 44 0.00095 31.3 1.1 33 28-60 93-125 (758)
43 cd04713 BAH_plant_3 BAH, or Br 22.1 3.2E+02 0.0069 19.9 6.6 32 80-111 77-108 (146)
44 PRK12933 secD preprotein trans 21.9 46 0.001 30.5 1.2 29 28-56 256-284 (604)
45 COG4680 Uncharacterized protei 20.3 1.1E+02 0.0023 22.1 2.5 24 44-73 47-70 (98)
No 1
>PTZ00041 60S ribosomal protein L35a; Provisional
Probab=100.00 E-value=9.2e-64 Score=363.91 Aligned_cols=110 Identities=66% Similarity=1.193 Sum_probs=106.3
Q ss_pred CCCCCceeeeEEEEEEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEEEEecccccCCceeEEEEEEEEceeCC
Q 033755 3 KGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGN 82 (112)
Q Consensus 3 ~~~~~~~~RLy~kgv~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~k~~~~g~k~rviwGKV~r~HGn 82 (112)
+++..++.|||+||+|+|||||++||+|||||||||||+++|||+|||||||||||+++++++|+++|+|||||+|+|||
T Consensus 11 ~~~~~~~~Rly~kgv~lgYkRg~~nQ~~~~aLlKieGV~~~~~a~fYlGKrvayvyka~~~~~~~k~RviwGKVtR~HGn 90 (120)
T PTZ00041 11 TNRKKKPVRLYVKAVFLGYKRSKVNQYPNVALLKIEGVNTREDARFYLGKRVAYVYKAKKLKNGTKFRAIWGKITRPHGN 90 (120)
T ss_pred ccCCcCCcceEEEEEEEEeccccccCCCceEEEEecCcCChhhhHhhccceEEEEEcCccccCCcceeEEEEEEEcccCC
Confidence 44556689999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEecCCCCccCCCCeEEEEEeecCC
Q 033755 83 SGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112 (112)
Q Consensus 83 sGvVrAkF~~nLPp~aiG~~vrVmLyps~i 112 (112)
||+|||+|++||||||||++||||||||+|
T Consensus 91 sGvVrAkF~~nLPp~A~G~~VrVmlyPs~i 120 (120)
T PTZ00041 91 SGVVRARFNKNLPPKAIGSRVRVFLYPSNI 120 (120)
T ss_pred CcEEEEEeCCCCChHHcCCeEEEEEccCCC
Confidence 999999999999999999999999999997
No 2
>KOG0887 consensus 60S ribosomal protein L35A/L37 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.4e-60 Score=338.71 Aligned_cols=110 Identities=71% Similarity=1.153 Sum_probs=107.2
Q ss_pred CCCCCceeeeEEEEEEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEEEEecccccCCceeEEEEEEEEceeCC
Q 033755 3 KGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGN 82 (112)
Q Consensus 3 ~~~~~~~~RLy~kgv~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~k~~~~g~k~rviwGKV~r~HGn 82 (112)
+..|.+.+|||+||+|+||+||+++|+|||+|||||||+++|||+||+||||+||||+++..+++++|+|||||||+|||
T Consensus 2 k~~~~e~~rl~vk~~~~~~kr~~r~~~~~t~llkIEGv~skeEa~fYlGkR~~yvYKa~~~~~~~k~RvIWGkVTr~HGN 81 (111)
T KOG0887|consen 2 KGMMGERGRLYVKGTFLGYKRGKRNQHPNTSLLKIEGVYSKEEASFYLGKRCVYVYKAKPEVRGSKTRVIWGKVTRPHGN 81 (111)
T ss_pred CCcccccceeEeeeEEeeeeecccccCCCcEEEEEecccchhhhheeecCcEEEEEecCCCCCCceEEEEEEEEecccCC
Confidence 45678889999999999999999999999999999999999999999999999999999988999999999999999999
Q ss_pred CceEEEEecCCCCccCCCCeEEEEEeecCC
Q 033755 83 SGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112 (112)
Q Consensus 83 sGvVrAkF~~nLPp~aiG~~vrVmLyps~i 112 (112)
||+|||+|.+||||+|||++||||||||+|
T Consensus 82 sG~VrAkF~~Nlp~Ka~G~rvrVmLYps~i 111 (111)
T KOG0887|consen 82 SGVVRAKFTSNLPPKAMGHRVRVMLYPSNI 111 (111)
T ss_pred cceEEEEeccCCChhHcCcEEEEEEecccC
Confidence 999999999999999999999999999998
No 3
>PF01247 Ribosomal_L35Ae: Ribosomal protein L35Ae; InterPro: IPR001780 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 ribosomal L35A eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of: Vertebrate L35A. Caenorhabditis elegans L35A (F10E7.7). Saccharomyces cerevisiae L37A/L37B (Rp47). Plant L35A. Pyrococcus woesei L35A homologue []. These proteins have 87 to 110 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_j 2LP6_A 1SQR_A 4A18_H 4A1D_H 4A19_H 4A1B_H 3IZS_j.
Probab=100.00 E-value=1.2e-56 Score=315.59 Aligned_cols=95 Identities=73% Similarity=1.200 Sum_probs=88.5
Q ss_pred eEEEEEEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEEEEecccccCCceeEEEEEEEEceeCCCceEEEEec
Q 033755 12 LYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFK 91 (112)
Q Consensus 12 Ly~kgv~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~k~~~~g~k~rviwGKV~r~HGnsGvVrAkF~ 91 (112)
||+||+|+|||||++||+|||||||||||+|+|||+|||||||+|||++++++++++.|+|||||+|+|||||+|||+|+
T Consensus 1 ly~kgv~~gykRg~~~Q~~~~aLlKiegV~~~~~a~fylGKrv~yvyk~~~~~~~~k~r~iwGkV~r~HGnsGvVrAkF~ 80 (95)
T PF01247_consen 1 LYVKGVFLGYKRGKRNQHPNTALLKIEGVNTKEDAQFYLGKRVAYVYKAKNKKNGSKGRVIWGKVTRPHGNSGVVRAKFK 80 (95)
T ss_dssp -EEEEEEEEEEEETSTTCEEEEEEEESS-STCHHHHTTTT-EEEEEECE-SSSTTECSEEEEEEEEEESTTTTEEEEEES
T ss_pred CeeeEEEEeecccccccCCCeeEEeecCccCHHHHHhhcCcEEEEEEecccccCCCcEeEEEEEEEeEEcCCCEEEEEeC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccCCCCeEEEE
Q 033755 92 SNLPPKSMGDRVRVF 106 (112)
Q Consensus 92 ~nLPp~aiG~~vrVm 106 (112)
+||||||||++||||
T Consensus 81 ~nLP~~a~G~~VrVm 95 (95)
T PF01247_consen 81 KNLPPQAIGSRVRVM 95 (95)
T ss_dssp S--STTGCSSEEEEE
T ss_pred CCCChHHcCCEEEeC
Confidence 999999999999998
No 4
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=100.00 E-value=1e-50 Score=281.88 Aligned_cols=85 Identities=36% Similarity=0.689 Sum_probs=82.2
Q ss_pred EEEEEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEEEEecccccCCceeEEEEEEEEceeCCCceEEEEecCC
Q 033755 14 VRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSN 93 (112)
Q Consensus 14 ~kgv~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~k~~~~g~k~rviwGKV~r~HGnsGvVrAkF~~n 93 (112)
+||+|+|||||++||+|||||||||||+++|||+|||||||+|||++ | |+|||||+|+|||||+|||+|++|
T Consensus 3 ~kgv~~gykRg~~nQ~~~~aLlkiegv~~~~~a~fylGKrv~yvyk~-----g---rviwGKItR~HGnsGvVrAkF~~n 74 (87)
T PRK04337 3 MKGVILSYRRGKNTQYNRQVIIKPLGVDDREEAAKLIGRKVIWKDPT-----G---NKYVGKIVRVHGNRGEVRARFKPG 74 (87)
T ss_pred ceEEEEEeccccCccCCceEEEEEcCcCCHHHHHhhcCceEEEEeCC-----C---CEEEEEEEeeeCCCceEEEEECCC
Confidence 69999999999999999999999999999999999999999999986 3 799999999999999999999999
Q ss_pred CCccCCCCeEEEE
Q 033755 94 LPPKSMGDRVRVF 106 (112)
Q Consensus 94 LPp~aiG~~vrVm 106 (112)
|||||||++|||.
T Consensus 75 LP~~a~G~~vrv~ 87 (87)
T PRK04337 75 LPGQALGDYVEII 87 (87)
T ss_pred CChHHcCCEEEeC
Confidence 9999999999983
No 5
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-48 Score=275.94 Aligned_cols=100 Identities=53% Similarity=0.922 Sum_probs=94.9
Q ss_pred CCceeeeEEEEEEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEEEEecccccCCceeEEEEEEEEceeCCCce
Q 033755 6 QGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGV 85 (112)
Q Consensus 6 ~~~~~RLy~kgv~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~k~~~~g~k~rviwGKV~r~HGnsGv 85 (112)
|.+..|+++||+++|||||+++|||+++|||||||+|+|||+|||||+|+|+|+.. | |+|||+|+|+|||||+
T Consensus 1 ~~~~~r~~ikgv~lsyrR~k~~q~P~~~liKi~gv~s~~eA~~y~gk~v~yk~~~~----G---~Vi~G~V~R~HGnsGa 73 (100)
T COG2451 1 MAEGHRLRIKGVVLSYRRSKRTQHPNVSLIKIEGVDSPEEAQFYLGKRVCYKYRSS----G---RVIKGKVVRTHGNSGA 73 (100)
T ss_pred CCccceEEEeeEEEEEEecccccCCceEEEEEecCCCHHHHHhhhccEEEEEeCCC----C---cEEEEEEEEecCCcce
Confidence 34558999999999999999999999999999999999999999999999988762 5 8999999999999999
Q ss_pred EEEEecCCCCccCCCCeEEEEEeecCC
Q 033755 86 VRAKFKSNLPPKSMGDRVRVFMYPSNI 112 (112)
Q Consensus 86 VrAkF~~nLPp~aiG~~vrVmLyps~i 112 (112)
|||+|.+||||||+|+.|+||||||+|
T Consensus 74 VrarF~~~LP~qa~G~~v~v~ly~~~~ 100 (100)
T COG2451 74 VRARFERNLPGQALGTSVEVKLYPSNI 100 (100)
T ss_pred EEEEecCCCCchhcCcEEEEEEccCCC
Confidence 999999999999999999999999986
No 6
>PF09853 DUF2080: Putative transposon-encoded protein (DUF2080); InterPro: IPR019205 This entry, found in various hypothetical archaeal proteins, has no known function.
Probab=95.61 E-value=0.023 Score=36.64 Aligned_cols=34 Identities=32% Similarity=0.597 Sum_probs=27.4
Q ss_pred EEEEEEEceeCCCceEEEEecCCCCccCCCCeEEEEEee
Q 033755 71 CIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYP 109 (112)
Q Consensus 71 viwGKV~r~HGnsGvVrAkF~~nLPp~aiG~~vrVmLyp 109 (112)
+++++|+ +|||| |++..+||+.-+|.++.|.+..
T Consensus 17 ~~~~~vk-~~Gns----a~v~p~lPkeyiGK~v~iiil~ 50 (53)
T PF09853_consen 17 TFIGVVK-PFGNS----ARVYPSLPKEYIGKKVIIIILE 50 (53)
T ss_pred EEEEEEE-ecCcc----eeEcCCCChHHcCcEEEEEEeC
Confidence 4566665 99999 5678999999999999887643
No 7
>PF01782 RimM: RimM N-terminal domain; InterPro: IPR002676 The RimM protein is essential for efficient processing of 16S rRNA []. The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes [].; GO: 0006364 rRNA processing; PDB: 2QGG_A 3A1P_C 2DOG_A 2DYI_A 3H9N_A 2F1L_A.
Probab=93.68 E-value=0.14 Score=33.56 Aligned_cols=36 Identities=11% Similarity=0.208 Sum_probs=26.2
Q ss_pred EEEEeeecccCCCCCCeeEEEecCcCCcchhceeecceEEE
Q 033755 16 GTILGYKRSKSNQYPNTSLIQIEGVNTKEDVSWYCGKRMAY 56 (112)
Q Consensus 16 gv~~gykRg~~~Q~~~~aLlKIegV~~~~~a~fylGKrvay 56 (112)
-.+.+++ .+.+..|++++|++|+++|+.+.|..+..
T Consensus 45 ~~v~~~~-----~~~~~~i~~~~gi~~r~~Ae~l~g~~l~v 80 (84)
T PF01782_consen 45 LKVESVR-----PHGKSLIVKFEGIDDREAAEALRGCELYV 80 (84)
T ss_dssp EEEEEEE-----EETTEEEEEETT--SHHHHHTTTT-EEEE
T ss_pred EEEEEEE-----EeCCEEEEEEcCCCCHHHHHhhCCCEEEE
Confidence 4555555 33789999999999999999999987753
No 8
>TIGR02273 16S_RimM 16S rRNA processing protein RimM. This family consists of the bacterial protein RimM (YfjA, 21K), a 30S ribosomal subunit-binding protein implicated in 16S ribsomal RNA processing. It has been partially characterized in Escherichia coli, is found with other translation-associated genes such as trmD. It is broadly distributed among bacteria, including some minimal genomes such the aphid endosymbiont Buchnera aphidicola. The protein contains a PRC-barrel domain that it shares with other protein families (pfam05239) and a unique domain (pfam01782). This model describes the full-length protein. A member from Arabidopsis (plant) has additional N-terminal sequence likely to represent a chloroplast transit peptide.
Probab=90.86 E-value=0.17 Score=37.49 Aligned_cols=28 Identities=18% Similarity=0.326 Sum_probs=24.7
Q ss_pred CCCeeEEEecCcCCcchhceeecceEEE
Q 033755 29 YPNTSLIQIEGVNTKEDVSWYCGKRMAY 56 (112)
Q Consensus 29 ~~~~aLlKIegV~~~~~a~fylGKrvay 56 (112)
+.+..||+++|++|+++|+.+.|..+..
T Consensus 55 ~~~~~lv~f~gi~~~~~Ae~L~g~~l~i 82 (165)
T TIGR02273 55 QNNKLIVKFEGIDDREAAEALKGLELFV 82 (165)
T ss_pred ECCEEEEEECCCCCHHHHHHhcCCEEEE
Confidence 4567899999999999999999998764
No 9
>PRK14591 rimM 16S rRNA-processing protein RimM; Provisional
Probab=90.40 E-value=0.27 Score=36.89 Aligned_cols=29 Identities=10% Similarity=0.276 Sum_probs=25.4
Q ss_pred CCCCeeEEEecCcCCcchhceeecceEEE
Q 033755 28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAY 56 (112)
Q Consensus 28 Q~~~~aLlKIegV~~~~~a~fylGKrvay 56 (112)
++.+..|++++|++|+++|+.+.|..+..
T Consensus 59 ~~~~~~lv~f~gi~dr~~Ae~l~g~~l~v 87 (169)
T PRK14591 59 KRADKVYIKLANINNADTAKKYVNALIGV 87 (169)
T ss_pred EECCEEEEEEcCCCCHHHHHHhcCCEEEE
Confidence 45677899999999999999999998753
No 10
>PRK14592 rimM 16S rRNA-processing protein RimM; Provisional
Probab=89.59 E-value=0.28 Score=36.63 Aligned_cols=32 Identities=16% Similarity=0.295 Sum_probs=26.4
Q ss_pred CCCCeeEEEecCcCCcchhceeecceEEEEEec
Q 033755 28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60 (112)
Q Consensus 28 Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~ 60 (112)
++.+..|++++|++|+++|+.+.|..+.. .++
T Consensus 51 ~~~~~~lv~f~gi~~~~~Ae~l~g~~l~v-~~~ 82 (165)
T PRK14592 51 IGANLVIAKISGINSRTEAELLRNKKLYV-ERS 82 (165)
T ss_pred ecCCEEEEEEcCCCCHHHHHHhcCCEEEE-EHH
Confidence 44567899999999999999999998764 443
No 11
>PRK13829 rimM 16S rRNA-processing protein RimM; Provisional
Probab=89.47 E-value=0.26 Score=36.84 Aligned_cols=32 Identities=19% Similarity=0.286 Sum_probs=26.5
Q ss_pred CCCCeeEEEecCcCCcchhceeecceEEEEEec
Q 033755 28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60 (112)
Q Consensus 28 Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~ 60 (112)
++.+..|++++|++|+++|+.+.|..+. |.++
T Consensus 48 ~~~~~~l~~f~gi~~r~~Ae~l~g~~l~-v~~~ 79 (162)
T PRK13829 48 RVGPELVLHLAGVTSREGAEALVGLRVY-ADDA 79 (162)
T ss_pred EECCEEEEEECCCCCHHHHHHhcCCEEE-EEHH
Confidence 4466789999999999999999999876 3443
No 12
>PRK13828 rimM 16S rRNA-processing protein RimM; Provisional
Probab=88.40 E-value=0.35 Score=36.05 Aligned_cols=32 Identities=16% Similarity=0.199 Sum_probs=26.5
Q ss_pred CCCCeeEEEecCcCCcchhceeecceEEEEEec
Q 033755 28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60 (112)
Q Consensus 28 Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~ 60 (112)
++.+..|++++|++|+++|+.+.|..+.. .+.
T Consensus 39 ~~~~~~lv~f~gi~dr~~Ae~L~g~~l~i-~~~ 70 (161)
T PRK13828 39 PAKDGLVARLKGVATREAAEALRGLELYV-PRD 70 (161)
T ss_pred EECCEEEEEECCCCCHHHHHHhcCCEEEE-EHH
Confidence 44566899999999999999999998764 443
No 13
>PF01782 RimM: RimM N-terminal domain; InterPro: IPR002676 The RimM protein is essential for efficient processing of 16S rRNA []. The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes [].; GO: 0006364 rRNA processing; PDB: 2QGG_A 3A1P_C 2DOG_A 2DYI_A 3H9N_A 2F1L_A.
Probab=87.93 E-value=0.66 Score=30.30 Aligned_cols=28 Identities=25% Similarity=0.622 Sum_probs=22.8
Q ss_pred EEEEEceeCCCceEEEEecCCCCccCCC
Q 033755 73 WGKVARPHGNSGVVRAKFKSNLPPKSMG 100 (112)
Q Consensus 73 wGKV~r~HGnsGvVrAkF~~nLPp~aiG 100 (112)
-|+|.+|||-.|-|++..-.+.|.....
T Consensus 2 vG~I~~~hGlkG~vkv~~~td~~~~~~~ 29 (84)
T PF01782_consen 2 VGRIGKPHGLKGEVKVRPFTDFPERLFN 29 (84)
T ss_dssp EEEEEEEETTTTEEEEEE-SSSGGGGGG
T ss_pred EEEECCCEecCEEEEEEEecCCHHHHcC
Confidence 4999999999999999998887765443
No 14
>PRK14594 rimM 16S rRNA-processing protein RimM; Provisional
Probab=87.17 E-value=0.38 Score=36.06 Aligned_cols=32 Identities=19% Similarity=0.193 Sum_probs=26.2
Q ss_pred CCCCeeEEEecCcCCcchhceeecceEEEEEec
Q 033755 28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60 (112)
Q Consensus 28 Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~ 60 (112)
.+.+..|++++|++|+++|+.+.|..+. |.++
T Consensus 56 ~~~~~~lvkf~gi~dr~~Ae~L~g~~l~-v~~~ 87 (166)
T PRK14594 56 LKNNSLLLKFEEFNAPEPIKPLIGFELW-VDDE 87 (166)
T ss_pred EECCEEEEEEcCCCCHHHHHHhcCCEEE-EEHH
Confidence 3456689999999999999999998775 4554
No 15
>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional
Probab=87.16 E-value=0.43 Score=35.63 Aligned_cols=29 Identities=14% Similarity=0.182 Sum_probs=24.9
Q ss_pred CCCCeeEEEecCcCCcchhceeecceEEE
Q 033755 28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAY 56 (112)
Q Consensus 28 Q~~~~aLlKIegV~~~~~a~fylGKrvay 56 (112)
.+.+..|+|++|++|+++|+.|.|..+..
T Consensus 59 ~~~~~~lvkf~gi~~~~~Ae~l~g~~l~i 87 (172)
T PRK00122 59 FHKGFLIVKFEGVDDRNAAEALKGCELFV 87 (172)
T ss_pred EECCEEEEEECCCCCHHHHHHhCCCEEEE
Confidence 34566899999999999999999998764
No 16
>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional
Probab=87.13 E-value=0.74 Score=34.36 Aligned_cols=30 Identities=27% Similarity=0.480 Sum_probs=26.3
Q ss_pred EEEEEEEEceeCCCceEEEEecCCCCccCC
Q 033755 70 RCIWGKVARPHGNSGVVRAKFKSNLPPKSM 99 (112)
Q Consensus 70 rviwGKV~r~HGnsGvVrAkF~~nLPp~ai 99 (112)
.+..|+|++|||-.|-|+++.-.+.|...+
T Consensus 7 ~v~iG~i~~~hGlkGevkv~~~td~p~~~~ 36 (172)
T PRK00122 7 LLVVGKIVSAHGIKGEVKVKSFTDFPERIF 36 (172)
T ss_pred eEEEEEEECCCcccEEEEEEEecCCHHHHc
Confidence 478999999999999999999988886544
No 17
>PRK14590 rimM 16S rRNA-processing protein RimM; Provisional
Probab=87.01 E-value=0.45 Score=35.95 Aligned_cols=32 Identities=19% Similarity=0.257 Sum_probs=26.7
Q ss_pred CCCCeeEEEecCcCCcchhceeecceEEEEEec
Q 033755 28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60 (112)
Q Consensus 28 Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~ 60 (112)
++.+..|++++|++|+++|+.+.|..+.. .++
T Consensus 55 ~~~~~~lv~f~gi~~~e~Ae~L~g~~l~i-~~~ 86 (171)
T PRK14590 55 PHGGKFLVRFEGYDTPEEAVKWRGGSLFL-PQE 86 (171)
T ss_pred EECCEEEEEECCCCCHHHHHHhcCCEEEE-EHH
Confidence 44566899999999999999999998864 453
No 18
>PRK14594 rimM 16S rRNA-processing protein RimM; Provisional
Probab=86.96 E-value=0.67 Score=34.74 Aligned_cols=28 Identities=21% Similarity=0.102 Sum_probs=24.0
Q ss_pred EEEEEEEceeCCCceEEEEecCCCCccC
Q 033755 71 CIWGKVARPHGNSGVVRAKFKSNLPPKS 98 (112)
Q Consensus 71 viwGKV~r~HGnsGvVrAkF~~nLPp~a 98 (112)
+++|+|++|||=.|-|+++.-..-|+..
T Consensus 2 ~~iG~I~~~hGlkGevkV~~~td~~~~~ 29 (166)
T PRK14594 2 FVKGIILSSYGINGYAKVKSISNNFCDF 29 (166)
T ss_pred EEEEEEECceeeeEEEEEEEccCCHHHh
Confidence 5789999999999999999887766553
No 19
>TIGR02273 16S_RimM 16S rRNA processing protein RimM. This family consists of the bacterial protein RimM (YfjA, 21K), a 30S ribosomal subunit-binding protein implicated in 16S ribsomal RNA processing. It has been partially characterized in Escherichia coli, is found with other translation-associated genes such as trmD. It is broadly distributed among bacteria, including some minimal genomes such the aphid endosymbiont Buchnera aphidicola. The protein contains a PRC-barrel domain that it shares with other protein families (pfam05239) and a unique domain (pfam01782). This model describes the full-length protein. A member from Arabidopsis (plant) has additional N-terminal sequence likely to represent a chloroplast transit peptide.
Probab=84.10 E-value=1.7 Score=32.17 Aligned_cols=29 Identities=31% Similarity=0.567 Sum_probs=25.0
Q ss_pred EEEEEEEceeCCCceEEEEecCCCCccCC
Q 033755 71 CIWGKVARPHGNSGVVRAKFKSNLPPKSM 99 (112)
Q Consensus 71 viwGKV~r~HGnsGvVrAkF~~nLPp~ai 99 (112)
+..|+|.+|||=.|-|+++.-...|...+
T Consensus 2 v~iG~I~~~hGlkGevkv~~~td~p~~~~ 30 (165)
T TIGR02273 2 LVVGKIGGPHGIKGEVKVKSFTDFPESLF 30 (165)
T ss_pred EEEEEEECCcccCEEEEEEEcCCCHHHHc
Confidence 46799999999999999999888886554
No 20
>PRK14593 rimM 16S rRNA-processing protein RimM; Provisional
Probab=81.20 E-value=1.7 Score=32.98 Aligned_cols=29 Identities=17% Similarity=0.401 Sum_probs=25.2
Q ss_pred EEEEEEEceeCCCceEEEEecCCCCccCC
Q 033755 71 CIWGKVARPHGNSGVVRAKFKSNLPPKSM 99 (112)
Q Consensus 71 viwGKV~r~HGnsGvVrAkF~~nLPp~ai 99 (112)
+..|+|.++||-.|-|++..-..-|....
T Consensus 5 i~iG~I~~~hGikGevkv~~~td~pe~~~ 33 (184)
T PRK14593 5 LLVGRIGKSVGLNGGLKLHLESDFPECLK 33 (184)
T ss_pred EEEEEEECCEeeeEEEEEEECCCCHHHhc
Confidence 57899999999999999999988777543
No 21
>PRK14592 rimM 16S rRNA-processing protein RimM; Provisional
Probab=80.45 E-value=2.1 Score=31.94 Aligned_cols=29 Identities=28% Similarity=0.389 Sum_probs=25.2
Q ss_pred EEEEEEEceeCCCceEEEEecCCCCccCC
Q 033755 71 CIWGKVARPHGNSGVVRAKFKSNLPPKSM 99 (112)
Q Consensus 71 viwGKV~r~HGnsGvVrAkF~~nLPp~ai 99 (112)
+..|+|++|||=.|-|+++.-.+-|....
T Consensus 3 v~iG~I~~~hGlkGevkv~~~td~p~~~~ 31 (165)
T PRK14592 3 ICLGVITSPHGIKGHVKIKTFTEDPENIS 31 (165)
T ss_pred EEEEEEECCCccCEEEEEEECCCCHHHhc
Confidence 56899999999999999999988777543
No 22
>PRK14591 rimM 16S rRNA-processing protein RimM; Provisional
Probab=78.97 E-value=2.7 Score=31.49 Aligned_cols=29 Identities=10% Similarity=-0.123 Sum_probs=25.4
Q ss_pred EEEEEEEEceeCCCceEEEEecCCCCccC
Q 033755 70 RCIWGKVARPHGNSGVVRAKFKSNLPPKS 98 (112)
Q Consensus 70 rviwGKV~r~HGnsGvVrAkF~~nLPp~a 98 (112)
-+..|+|.+|||=.|-|+++.-...|...
T Consensus 5 ~v~vG~I~~~hGlkGevkv~~~td~p~~~ 33 (169)
T PRK14591 5 FVEIAKIGATYKLNGELNLYPLANSIETL 33 (169)
T ss_pred EEEEEEEeCCccccEEEEEEECCCCHHHh
Confidence 47789999999999999999988877744
No 23
>PRK14593 rimM 16S rRNA-processing protein RimM; Provisional
Probab=77.24 E-value=4.2 Score=30.84 Aligned_cols=26 Identities=19% Similarity=0.222 Sum_probs=22.5
Q ss_pred EEEecCcCCcchhceeecceEEEEEec
Q 033755 34 LIQIEGVNTKEDVSWYCGKRMAYIYKA 60 (112)
Q Consensus 34 LlKIegV~~~~~a~fylGKrvayvyk~ 60 (112)
+++++|++|+++|+.+.|..+. |.++
T Consensus 66 ~v~f~gi~dr~~Ae~l~g~~l~-i~~~ 91 (184)
T PRK14593 66 LLFLETIHTPEKAKELTNLGLF-MSEA 91 (184)
T ss_pred EEEEcCCCCHHHHHHhcCCEEE-EEHH
Confidence 6899999999999999999876 4554
No 24
>PRK14590 rimM 16S rRNA-processing protein RimM; Provisional
Probab=75.21 E-value=3 Score=31.51 Aligned_cols=27 Identities=19% Similarity=0.382 Sum_probs=23.5
Q ss_pred EEEEEEceeCCCceEEEEecCCCCccC
Q 033755 72 IWGKVARPHGNSGVVRAKFKSNLPPKS 98 (112)
Q Consensus 72 iwGKV~r~HGnsGvVrAkF~~nLPp~a 98 (112)
..|+|.+|||-.|-|++..-..-|...
T Consensus 2 ~vG~I~~~hGlkGevkv~~~td~pe~~ 28 (171)
T PRK14590 2 SLGQLGKPFGIKGWLRVNVRGETLHTL 28 (171)
T ss_pred eEEEEeCCEeeCeEEEEEEccCCHHHh
Confidence 479999999999999999888877653
No 25
>PF04950 DUF663: Protein of unknown function (DUF663); InterPro: IPR007034 This domain is found at the C terminus of the ribosome biogenesis protein BMS1 and TSR1 families, which may act as a molecular switch during maturation of the 40S ribosomal subunit in the nucleolus.; PDB: 1WB1_D 1WB3_B 1WB2_A.
Probab=72.18 E-value=3.3 Score=34.11 Aligned_cols=63 Identities=27% Similarity=0.535 Sum_probs=37.1
Q ss_pred CCeeEEEecCcCCcchhceeecceEEEEEecccccCCceeEEEEEEEEceeCCCceEEEEecCCCCccCCCCeEEEEEe
Q 033755 30 PNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMY 108 (112)
Q Consensus 30 ~~~aLlKIegV~~~~~a~fylGKrvayvyk~k~~~~g~k~rviwGKV~r~HGnsGvVrAkF~~nLPp~aiG~~vrVmLy 108 (112)
-++|.|+-= -++.+|..++.|-.+-= +.| .| |.|..+-|..|.++|-|...|=. .+.|..-||
T Consensus 232 k~~a~vr~M-F~~~~dv~~F~~~~l~T-------~~G--~r---G~Ik~~lgt~G~fka~F~~~i~~---~D~V~~~ly 294 (297)
T PF04950_consen 232 KRTAVVRGM-FFNPEDVAWFKGAELRT-------KSG--IR---GHIKESLGTHGYFKATFEDKIKQ---SDIVFMRLY 294 (297)
T ss_dssp SSSCEECSS-SSTCCHHHHS-S--BEE-------TTS---B---EEEEE-BTTTTBBEEEESS---S---S-EEEEE--
T ss_pred CceEEhhhh-cCCHHHHHhhcCCEEEe-------ecc--CC---CEECeeECCCCcEEEEECCcCCC---CCEEEEecC
Confidence 356666644 56777888887765531 123 34 99999999999999999988854 355655555
No 26
>PRK13829 rimM 16S rRNA-processing protein RimM; Provisional
Probab=69.10 E-value=8.9 Score=28.57 Aligned_cols=24 Identities=25% Similarity=0.421 Sum_probs=20.3
Q ss_pred EEEEEEEEceeCCCceEEEEecCCCCc
Q 033755 70 RCIWGKVARPHGNSGVVRAKFKSNLPP 96 (112)
Q Consensus 70 rviwGKV~r~HGnsGvVrAkF~~nLPp 96 (112)
.+..|+|++|||=.|-|+++ .-|.
T Consensus 3 ~i~iG~I~~~hGikGevkv~---d~p~ 26 (162)
T PRK13829 3 RTEIGRFGGPYGVQGGLKFR---GEPV 26 (162)
T ss_pred EEEEEEEeCCeeecEEEEEe---cchH
Confidence 36789999999999999998 4454
No 27
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=59.30 E-value=8.5 Score=29.64 Aligned_cols=31 Identities=10% Similarity=0.238 Sum_probs=27.1
Q ss_pred cCCCCCCeeEEEecCcCCcchhceeecceEE
Q 033755 25 KSNQYPNTSLIQIEGVNTKEDVSWYCGKRMA 55 (112)
Q Consensus 25 ~~~Q~~~~aLlKIegV~~~~~a~fylGKrva 55 (112)
....+.|-.+++++|++++++|+-+.|-.+.
T Consensus 57 ~~r~~~~~~i~kf~gi~dr~~ae~l~G~~i~ 87 (174)
T COG0806 57 SVRKHKNLLILKFKGIDDRNAAEALKGYEIF 87 (174)
T ss_pred EeeecCCEEEEEeCCCCCHHHHHHhcCcEEE
Confidence 3456889999999999999999999998765
No 28
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=54.68 E-value=56 Score=22.45 Aligned_cols=34 Identities=29% Similarity=0.460 Sum_probs=22.4
Q ss_pred EEEEEEceeCC-------Cc-eEEEEecCCCCccCCCCeEEEE
Q 033755 72 IWGKVARPHGN-------SG-VVRAKFKSNLPPKSMGDRVRVF 106 (112)
Q Consensus 72 iwGKV~r~HGn-------sG-vVrAkF~~nLPp~aiG~~vrVm 106 (112)
++|||++.||+ .| .|.+.....+ ...+++-|.|.
T Consensus 20 ivGkV~~~~~~~~~~~~~Dg~~v~v~l~~~~-~~~~~~~vEVi 61 (101)
T cd04479 20 IVGKVEKVDGDSLTLISSDGVNVTVELNRPL-DLPISGYVEVI 61 (101)
T ss_pred EEEEEEEecCCeEEEEcCCCCEEEEEeCCCC-CcccCCEEEEE
Confidence 46899999988 34 7777777654 34455555543
No 29
>PF12150 MFP2b: Cytosolic motility protein; InterPro: IPR021010 This entry represents proteins found in nematodes. They complex with MSP (major sperm protein) to allow motility []. Their action is quite similar to the action of bacterial actin molecules.; PDB: 2BJQ_A 2BJR_A.
Probab=51.53 E-value=41 Score=29.13 Aligned_cols=37 Identities=30% Similarity=0.640 Sum_probs=29.1
Q ss_pred EEEEEEEEceeCCCceEEEEec---CCCCc-cCCCCeEEEEEee
Q 033755 70 RCIWGKVARPHGNSGVVRAKFK---SNLPP-KSMGDRVRVFMYP 109 (112)
Q Consensus 70 rviwGKV~r~HGnsGvVrAkF~---~nLPp-~aiG~~vrVmLyp 109 (112)
+.|+|+- .-|+|+|-+-|- .+|-+ +.+|..|+|..|-
T Consensus 41 kPihGrA---WNn~GvveCSF~~~~~elt~~~dlgg~IQiLqy~ 81 (362)
T PF12150_consen 41 KPIHGRA---WNNSGVVECSFPYDKAELTGKDDLGGQIQILQYK 81 (362)
T ss_dssp EEEEEEE---EEETTEEEEEEEETTEEE-SCCCCTSEEEEEE-S
T ss_pred CCcccce---ecCCceEEEEEEcccceeccccccCCEEEEEEEc
Confidence 5889976 589999999994 45766 8899999999873
No 30
>PF14444 S1-like: S1-like
Probab=49.72 E-value=55 Score=21.43 Aligned_cols=36 Identities=33% Similarity=0.526 Sum_probs=27.9
Q ss_pred EEEEEEEEceeCCCceE--EEEec-----CCCCccCCCCeEEEEE
Q 033755 70 RCIWGKVARPHGNSGVV--RAKFK-----SNLPPKSMGDRVRVFM 107 (112)
Q Consensus 70 rviwGKV~r~HGnsGvV--rAkF~-----~nLPp~aiG~~vrVmL 107 (112)
|+.-|-||..|++-|.+ -.-|. -++| ..|++|.+--
T Consensus 2 r~~~GvVTkl~~~yG~IDe~vFF~~~vv~G~~P--~vGdrV~v~A 44 (58)
T PF14444_consen 2 RVFTGVVTKLCDDYGFIDEDVFFQTDVVKGNVP--KVGDRVLVEA 44 (58)
T ss_pred ceEEEEEEEEeCCcceEcccEEEEcccEecCCC--ccCCEEEEEE
Confidence 68899999999999988 34444 4566 5999998753
No 31
>KOG0189 consensus Phosphoadenosine phosphosulfate reductase [Amino acid transport and metabolism]
Probab=45.15 E-value=22 Score=29.29 Aligned_cols=32 Identities=19% Similarity=0.358 Sum_probs=28.0
Q ss_pred eeEEEEEEEeeecccCCCCCCeeEEEecCcCC
Q 033755 11 RLYVRGTILGYKRSKSNQYPNTSLIQIEGVNT 42 (112)
Q Consensus 11 RLy~kgv~~gykRg~~~Q~~~~aLlKIegV~~ 42 (112)
-|-++|+|+|=|+++--.+..-.+++|++|..
T Consensus 147 ~L~v~A~~TGrRksQ~gtRselpiVqvD~~fe 178 (261)
T KOG0189|consen 147 GLNVKAVFTGRRKSQGGTRSELPIVQVDPVFE 178 (261)
T ss_pred ccceeeEEecccccCCCcccccceEEecCccc
Confidence 36689999999999999999999999998854
No 32
>KOG0461 consensus Selenocysteine-specific elongation factor [Translation, ribosomal structure and biogenesis]
Probab=44.54 E-value=42 Score=29.91 Aligned_cols=43 Identities=28% Similarity=0.585 Sum_probs=35.0
Q ss_pred ceeecceEEEEEecccccCCceeEEEEEEEEceeCCCceEEEEecCCCCccCCCC
Q 033755 47 SWYCGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGD 101 (112)
Q Consensus 47 ~fylGKrvayvyk~k~~~~g~k~rviwGKV~r~HGnsGvVrAkF~~nLPp~aiG~ 101 (112)
+-|+|+.|+- . .| -| |+|-++-|.||.++.-|.-.|.|..+..
T Consensus 455 dlfvG~~v~l--S-----tG--e~---G~Ie~aFGqsgKf~itf~~~lspe~~~~ 497 (522)
T KOG0461|consen 455 DLFVGFQVCL--S-----TG--ER---GKIEGAFGQSGKFRITFAEKLSPELISN 497 (522)
T ss_pred ceeeeeEEEe--c-----cC--Cc---cceeccccCcceEEEEecccCChhhhcc
Confidence 4588998886 2 23 23 8999999999999999999999988653
No 33
>COG3466 ISA1214 Putative transposon-encoded protein [Function unknown]
Probab=42.42 E-value=93 Score=20.07 Aligned_cols=27 Identities=41% Similarity=0.685 Sum_probs=22.0
Q ss_pred EEEceeCCCceEEEEecCCCCccCCCCeEEEEE
Q 033755 75 KVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFM 107 (112)
Q Consensus 75 KV~r~HGnsGvVrAkF~~nLPp~aiG~~vrVmL 107 (112)
+...|-||||.|- .|-.-+|.+|.|..
T Consensus 23 k~VtpfGnsakVd------vPK~yiG~rv~viI 49 (52)
T COG3466 23 KRVTPFGNSAKVD------VPKRYIGKRVYVII 49 (52)
T ss_pred EEEEecCCcceee------CchHHcCcEEEEEE
Confidence 4455999999984 69999999998764
No 34
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=41.47 E-value=45 Score=25.67 Aligned_cols=40 Identities=23% Similarity=0.313 Sum_probs=31.5
Q ss_pred eEEEEEEEEceeCCCceEEEEecCCCCccCCCCeEEEEEe
Q 033755 69 YRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGDRVRVFMY 108 (112)
Q Consensus 69 ~rviwGKV~r~HGnsGvVrAkF~~nLPp~aiG~~vrVmLy 108 (112)
-.+..|||..+||=.|-||.+=.+.-|...+.....+.+-
T Consensus 6 ~~~~vGkI~~t~Gi~GevrV~s~Td~~~~~~~~~~~~~~~ 45 (174)
T COG0806 6 NLLLVGKIVSTHGIRGEVRVKSFTDFPESLFDYGPWLLLK 45 (174)
T ss_pred ceEEEEEEEecccccEEEEEEECCCCHHHhcCcCcEEEec
Confidence 3688999999999999999998888777666655544443
No 35
>TIGR01129 secD protein-export membrane protein SecD. SecD from Mycobacterium tuberculosis has a long Pro-rich insert.
Probab=33.27 E-value=19 Score=30.65 Aligned_cols=33 Identities=12% Similarity=0.200 Sum_probs=28.0
Q ss_pred CCCCeeEEEecCcCCcchhceeecceEEEEEec
Q 033755 28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60 (112)
Q Consensus 28 Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~ 60 (112)
|-++.-+|+++|+.+.++|...||+.----++.
T Consensus 62 ~G~~~I~V~lPg~~d~~~~~~~lg~~a~l~f~~ 94 (397)
T TIGR01129 62 QGKDRIVVELPGVTDTSRAKDILGGTATLEFRL 94 (397)
T ss_pred eCCceEEEECCCCCCHHHHHHHhCCceEEEEEE
Confidence 457889999999999999999999987765543
No 36
>PRK05812 secD preprotein translocase subunit SecD; Reviewed
Probab=27.51 E-value=28 Score=30.77 Aligned_cols=33 Identities=15% Similarity=0.261 Sum_probs=27.7
Q ss_pred CCCCeeEEEecCcCCcchhceeecceEEEEEec
Q 033755 28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60 (112)
Q Consensus 28 Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~ 60 (112)
|-++.-+|+++|+.+.+++...||+.----++.
T Consensus 148 ~G~~rI~V~lPG~~d~~~~~~~ig~ta~L~f~~ 180 (498)
T PRK05812 148 QGADRIVVELPGVQDTARAKEILGKTATLEFRL 180 (498)
T ss_pred eCCCeEEEECCCCCCHHHHHHHhcCceEEEEEE
Confidence 457889999999999999999999987654543
No 37
>PF01123 Stap_Strp_toxin: Staphylococcal/Streptococcal toxin, OB-fold domain; InterPro: IPR006173 Staphylococcus aureus is a Gram-positive coccus that grows in clusters or pairs, and is the major cause of nosocomial infections due to its multiple antibiotic resistant nature []. Patients who are immunocompromised (e.g., those suffering from third degree burns or chronic illness) are at risk from deep staphylococcal infections, such as osteomyelitis and pneumonia. Most skin infections are also caused by this bacterium. Many virulence mechanisms are employed by Staphylococci to induce pathogenesis: these can include polysaccharide capsules and exotoxins []. One of the major virulence exotoxins is toxic shock syndrome toxin (TSST), which is secreted by the organism upon successful invasion. It causes a major inflammatory response in the host via superantigenic properties, and is the causative agent of toxic shock syndrome. The structure of the TSST protein was originally determined to 2.5A by means of X-ray crystallography []. The N- and C-terminal domains both contain regions involved in MHC class II association; the C-terminal domain is also implicated in binding the T-cell receptor. Overall, the structure resembles that of Staphylococcal enterotoxin B (SEB), but differs in its N terminus and in the degree to which a long central helix is covered by surface loops []. The region around the carboxyl end of this helix is proposed to govern the superantigenic properties of TSST. An adjacent region along this helix is thought to be critical in the ability of TSST to induce toxic shock syndrome. Most recently, the structures of five mutants of TSST have been determined to 1.95A []. The mutations are in the central alpha-helix, and allow mapping of portions of TSST involved in superantigenicity and lethality.; GO: 0009405 pathogenesis; PDB: 1XXG_A 1KTK_D 1HQR_D 2NTS_A 1FNW_E 1FNU_C 1L0X_B 1FNV_D 1UUP_B 1HA5_C ....
Probab=26.31 E-value=19 Score=24.70 Aligned_cols=46 Identities=17% Similarity=0.433 Sum_probs=31.4
Q ss_pred CCeeEEEecCcCCcchhceeecceEEEEEecc-----cccCCceeEEEEEEEE
Q 033755 30 PNTSLIQIEGVNTKEDVSWYCGKRMAYIYKAK-----VKKNGSHYRCIWGKVA 77 (112)
Q Consensus 30 ~~~aLlKIegV~~~~~a~fylGKrvayvyk~k-----~~~~g~k~rviwGKV~ 77 (112)
.+.--|++| .++.+.|++|-||+|-- |=.. ....+.+..++.|=||
T Consensus 35 ~~~~~l~~e-f~~~~~a~~fKgKkVDI-fG~~Y~~~C~~~~~~~~~c~YGGVT 85 (87)
T PF01123_consen 35 SSYNDLKVE-FNSEDLAKKFKGKKVDI-FGLSYYYNCYGSEGNKTACMYGGVT 85 (87)
T ss_dssp TTESEEEEE--SSHHHHHHHTTSEEEE-EEEEBETTSSSSSSSEEEEEESEEE
T ss_pred CcceeEEEE-eCCHHHHHhhcCCEEEE-EecccccccccCCCCceEEEecCEe
Confidence 555667777 89999999999999972 2111 1012456788888887
No 38
>PRK14726 bifunctional preprotein translocase subunit SecD/SecF; Provisional
Probab=24.43 E-value=33 Score=32.45 Aligned_cols=34 Identities=9% Similarity=0.171 Sum_probs=28.6
Q ss_pred CCCCCeeEEEecCcCCcchhceeecceEEEEEec
Q 033755 27 NQYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60 (112)
Q Consensus 27 ~Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~ 60 (112)
.|-++.-+++++|+.|.++|...||+.----++.
T Consensus 186 ~~G~~rI~VelPG~~D~~~a~~~ig~ta~L~f~~ 219 (855)
T PRK14726 186 RQGDDRIVVQVPGLVDPQRLKNLLNQPAKLSFRL 219 (855)
T ss_pred EeCCceEEEECCCCCCHHHHHHHhCCceEEEEEE
Confidence 3567889999999999999999999987655544
No 39
>COG5192 BMS1 GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=24.39 E-value=30 Score=32.75 Aligned_cols=23 Identities=39% Similarity=0.788 Sum_probs=19.9
Q ss_pred EEEEEEceeCCCceEEEEecCCC
Q 033755 72 IWGKVARPHGNSGVVRAKFKSNL 94 (112)
Q Consensus 72 iwGKV~r~HGnsGvVrAkF~~nL 94 (112)
+.|.|.+|||..|..||-|.--+
T Consensus 889 lrgqvk~~~~k~g~yra~fe~km 911 (1077)
T COG5192 889 LRGQVKGPHGKNGEYRAVFEGKM 911 (1077)
T ss_pred ccccccCccCCCccchheeccch
Confidence 45999999999999999998543
No 40
>PF05798 Phage_FRD3: Bacteriophage FRD3 protein; InterPro: IPR008765 This is a group of proteins of unknown function from bacteriophage T2 and related phage.
Probab=23.54 E-value=21 Score=24.43 Aligned_cols=10 Identities=40% Similarity=0.833 Sum_probs=7.8
Q ss_pred Ccchhceeec
Q 033755 42 TKEDVSWYCG 51 (112)
Q Consensus 42 ~~~~a~fylG 51 (112)
+.|||+||.|
T Consensus 62 ~~EDa~FY~g 71 (75)
T PF05798_consen 62 DPEDAKFYMG 71 (75)
T ss_pred CHHHHHHHHH
Confidence 3488999987
No 41
>cd09232 Snurportin-1_C C-terminal m3G cap-binding domain of nuclear import adaptor snurportin-1. Snurportin-1 (SPN1 or SNUPN) is a nuclear import adaptor for m3G-capped spliceosomal U small nucleoproteins (snRNPs), which are assembled in the cytoplasm. After capping and assembly, the U snRNPs are transported into the nucleus by SPN1 and importin beta; SPN1 is then returned to the cytoplasm by exportin 1 (CRM1), which also transports the non-capped U snRNPs. The U snRNPs are essential elements of the spliceosome, which catalyzes the excision of introns and the ligation of exons to form a mature mRNA. SPN1 contains two domains, an N-terminal importin beta-binding (IBB) domain and a C-terminal m3G cap-binding domain.
Probab=22.64 E-value=1.5e+02 Score=22.75 Aligned_cols=35 Identities=31% Similarity=0.437 Sum_probs=26.1
Q ss_pred ecceEEEEEecccccCCceeEEEEEEEEceeCCCceEEEEecCCCCccC
Q 033755 50 CGKRMAYIYKAKVKKNGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKS 98 (112)
Q Consensus 50 lGKrvayvyk~k~~~~g~k~rviwGKV~r~HGnsGvVrAkF~~nLPp~a 98 (112)
.||||.-|-. + |++ .+...+|-+...|.+.||+-.
T Consensus 30 ~G~R~lvv~~--~-----------g~t-~~~~r~g~~~~~f~s~lP~g~ 64 (186)
T cd09232 30 VGKRCLVVAS--K-----------GKT-VARSKNGRTLHRFSSALPGGS 64 (186)
T ss_pred CceEEEEEEe--C-----------CEE-EEEeCCCCEEEecccCCCCCC
Confidence 4888886542 1 333 377889999999999999954
No 42
>PRK13023 bifunctional preprotein translocase subunit SecD/SecF; Reviewed
Probab=22.36 E-value=44 Score=31.27 Aligned_cols=33 Identities=12% Similarity=0.092 Sum_probs=28.0
Q ss_pred CCCCeeEEEecCcCCcchhceeecceEEEEEec
Q 033755 28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAYIYKA 60 (112)
Q Consensus 28 Q~~~~aLlKIegV~~~~~a~fylGKrvayvyk~ 60 (112)
|-++.-++++||+.|.|+|...||+.----++.
T Consensus 93 ~G~~rI~VelPG~~d~~~a~~~ig~ta~L~F~~ 125 (758)
T PRK13023 93 EGRNQIRVEVPGLYDAQLLKDILTIRGNLSFRA 125 (758)
T ss_pred ECCceEEEECCCCCCHHHHHHHhCCceEEEEEE
Confidence 557789999999999999999999987665554
No 43
>cd04713 BAH_plant_3 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=22.11 E-value=3.2e+02 Score=19.92 Aligned_cols=32 Identities=13% Similarity=0.238 Sum_probs=24.5
Q ss_pred eCCCceEEEEecCCCCccCCCCeEEEEEeecC
Q 033755 80 HGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSN 111 (112)
Q Consensus 80 HGnsGvVrAkF~~nLPp~aiG~~vrVmLyps~ 111 (112)
|..+=++..-....+|..+|-+.+.|+.+|..
T Consensus 77 ~~~~ElF~S~~~d~~~~~~I~gkc~V~~~~~~ 108 (146)
T cd04713 77 EDPRELFYSFHRDEVPAESVLHPCKVAFVPKG 108 (146)
T ss_pred CCCCeEEEeCCCCcCCHHHCcceeEEEECCcc
Confidence 34455666666677899999999999988754
No 44
>PRK12933 secD preprotein translocase subunit SecD; Reviewed
Probab=21.92 E-value=46 Score=30.46 Aligned_cols=29 Identities=17% Similarity=0.161 Sum_probs=25.0
Q ss_pred CCCCeeEEEecCcCCcchhceeecceEEE
Q 033755 28 QYPNTSLIQIEGVNTKEDVSWYCGKRMAY 56 (112)
Q Consensus 28 Q~~~~aLlKIegV~~~~~a~fylGKrvay 56 (112)
|-.+.-+++++|+.|.++|...||+.---
T Consensus 256 qG~~rI~VelPGv~D~~~ak~iig~tA~L 284 (604)
T PRK12933 256 QGEHRIRIELPGVQDPAAAKNVIGATASL 284 (604)
T ss_pred ecCceEEEECCCCCCHHHHHHHhCCceEE
Confidence 56788999999999999999999976543
No 45
>COG4680 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.35 E-value=1.1e+02 Score=22.13 Aligned_cols=24 Identities=29% Similarity=0.437 Sum_probs=17.5
Q ss_pred chhceeecceEEEEEecccccCCceeEEEE
Q 033755 44 EDVSWYCGKRMAYIYKAKVKKNGSHYRCIW 73 (112)
Q Consensus 44 ~~a~fylGKrvayvyk~k~~~~g~k~rviw 73 (112)
-|+.||..+++++ ...|+++|.|.
T Consensus 47 ~d~~~~~Dnr~Vf------di~GN~yRLIv 70 (98)
T COG4680 47 LDNFKYLDNRVVF------DIGGNKYRLIV 70 (98)
T ss_pred cccceeccceEEE------EcCCCEEEEEE
Confidence 3567788888887 24689999774
Done!