Query psy4327
Match_columns 187
No_of_seqs 110 out of 225
Neff 3.0
Searched_HMMs 46136
Date Fri Aug 16 22:47:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4327.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4327hhsearch_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 1E-59 2.2E-64 370.6 12.6 112 70-187 9-120 (120)
2 KOG0887|consensus 100.0 2E-55 4.3E-60 342.0 11.6 105 77-187 7-111 (111)
3 PF01247 Ribosomal_L35Ae: Ribo 100.0 1E-52 2.2E-57 319.3 10.9 95 81-181 1-95 (95)
4 PRK04337 50S ribosomal protein 100.0 1.6E-47 3.4E-52 287.7 10.2 85 83-181 3-87 (87)
5 COG2451 Ribosomal protein L35A 100.0 1E-44 2.2E-49 277.9 11.9 97 78-187 4-100 (100)
6 PF09853 DUF2080: Putative tra 94.8 0.051 1.1E-06 38.3 4.1 34 146-184 17-50 (53)
7 PF01782 RimM: RimM N-terminal 91.1 0.66 1.4E-05 32.8 5.2 40 81-125 41-80 (84)
8 PRK14591 rimM 16S rRNA-process 87.6 0.84 1.8E-05 37.1 4.0 31 97-128 59-89 (169)
9 TIGR02273 16S_RimM 16S rRNA pr 85.9 0.78 1.7E-05 36.7 3.0 28 98-125 55-82 (165)
10 PRK14592 rimM 16S rRNA-process 85.2 1.5 3.3E-05 35.4 4.4 29 97-125 51-79 (165)
11 PRK13829 rimM 16S rRNA-process 83.7 1.1 2.4E-05 36.2 3.0 31 97-128 48-78 (162)
12 PF01782 RimM: RimM N-terminal 82.8 1.3 2.8E-05 31.3 2.7 28 148-175 2-29 (84)
13 PRK13828 rimM 16S rRNA-process 81.7 1.4 3E-05 35.5 2.9 29 97-125 39-67 (161)
14 PRK00122 rimM 16S rRNA-process 80.2 1.7 3.6E-05 35.1 2.8 28 98-125 60-87 (172)
15 PRK14590 rimM 16S rRNA-process 79.9 1.7 3.8E-05 35.6 2.8 31 97-128 55-85 (171)
16 PRK14594 rimM 16S rRNA-process 79.5 1.6 3.5E-05 35.4 2.5 31 98-129 57-87 (166)
17 PRK14593 rimM 16S rRNA-process 65.7 13 0.00029 30.6 4.8 26 103-129 66-91 (184)
18 PF04950 DUF663: Protein of un 64.3 14 0.00031 33.0 5.1 64 98-183 231-294 (297)
19 cd04479 RPA3 RPA3: A subfamily 56.5 48 0.001 24.8 6.0 34 147-181 20-61 (101)
20 COG3466 ISA1214 Putative trans 48.3 33 0.00071 24.4 3.7 31 146-182 19-49 (52)
21 PF14444 S1-like: S1-like 46.6 46 0.00099 24.0 4.3 35 145-181 2-43 (58)
22 COG0806 RimM RimM protein, req 44.9 25 0.00055 29.5 3.2 31 94-124 57-87 (174)
23 PF01123 Stap_Strp_toxin: Stap 43.1 52 0.0011 24.7 4.4 48 99-152 35-85 (87)
24 KOG0189|consensus 38.6 27 0.0006 31.5 2.6 44 67-110 134-177 (261)
25 PF12150 MFP2b: Cytosolic moti 37.0 70 0.0015 30.3 5.1 37 145-184 41-81 (362)
26 cd09232 Snurportin-1_C C-termi 20.7 1.4E+02 0.0031 25.0 3.8 21 153-173 44-64 (186)
No 1
>PTZ00041 60S ribosomal protein L35a; Provisional
Probab=100.00 E-value=1e-59 Score=370.58 Aligned_cols=112 Identities=55% Similarity=0.985 Sum_probs=106.2
Q ss_pred hccccccCCCceEEEEEEEeeecccCCCCCCeeEEeecCCCChhhhhhhccceEEEEEeccccccCCCCCCCCceeeEEe
Q psy4327 70 KHKRLRLRHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWG 149 (187)
Q Consensus 70 k~~~~~~~~~RLyvKgvflGYKRG~rnQ~pntALLKIEGV~tkedA~FYlGKRVaYVYKaK~~~~~pg~~k~sk~RvIWG 149 (187)
+..+....++|||++|+|+|||||++||+|||||||||||++++||+|||||||||||++++. .+++++|+|||
T Consensus 9 ~~~~~~~~~~Rly~kgv~lgYkRg~~nQ~~~~aLlKieGV~~~~~a~fYlGKrvayvyka~~~------~~~~k~RviwG 82 (120)
T PTZ00041 9 KKTNRKKKPVRLYVKAVFLGYKRSKVNQYPNVALLKIEGVNTREDARFYLGKRVAYVYKAKKL------KNGTKFRAIWG 82 (120)
T ss_pred ecccCCcCCcceEEEEEEEEeccccccCCCceEEEEecCcCChhhhHhhccceEEEEEcCccc------cCCcceeEEEE
Confidence 344566788899999999999999999999999999999999999999999999999999876 47899999999
Q ss_pred EEEcccCCCceEEEEeCCCCCccCCCCeEEEEEeecCC
Q psy4327 150 KVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187 (187)
Q Consensus 150 KVtR~HGNSGvVRAKFk~NLPpqAiG~rVRVmLYPS~I 187 (187)
||+|+|||||+|||+|++||||||||++||||||||+|
T Consensus 83 KVtR~HGnsGvVrAkF~~nLPp~A~G~~VrVmlyPs~i 120 (120)
T PTZ00041 83 KITRPHGNSGVVRARFNKNLPPKAIGSRVRVFLYPSNI 120 (120)
T ss_pred EEEcccCCCcEEEEEeCCCCChHHcCCeEEEEEccCCC
Confidence 99999999999999999999999999999999999998
No 2
>KOG0887|consensus
Probab=100.00 E-value=2e-55 Score=342.03 Aligned_cols=105 Identities=66% Similarity=1.137 Sum_probs=101.1
Q ss_pred CCCceEEEEEEEeeecccCCCCCCeeEEeecCCCChhhhhhhccceEEEEEeccccccCCCCCCCCceeeEEeEEEcccC
Q psy4327 77 RHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHG 156 (187)
Q Consensus 77 ~~~RLyvKgvflGYKRG~rnQ~pntALLKIEGV~tkedA~FYlGKRVaYVYKaK~~~~~pg~~k~sk~RvIWGKVtR~HG 156 (187)
..+|||++|+|+||+||+++|+||++|||||||+++|||+|||||||+||||++.. .+++++|+|||||||+||
T Consensus 7 e~~rl~vk~~~~~~kr~~r~~~~~t~llkIEGv~skeEa~fYlGkR~~yvYKa~~~------~~~~k~RvIWGkVTr~HG 80 (111)
T KOG0887|consen 7 ERGRLYVKGTFLGYKRGKRNQHPNTSLLKIEGVYSKEEASFYLGKRCVYVYKAKPE------VRGSKTRVIWGKVTRPHG 80 (111)
T ss_pred ccceeEeeeEEeeeeecccccCCCcEEEEEecccchhhhheeecCcEEEEEecCCC------CCCceEEEEEEEEecccC
Confidence 34899999999999999999999999999999999999999999999999999743 478999999999999999
Q ss_pred CCceEEEEeCCCCCccCCCCeEEEEEeecCC
Q psy4327 157 SSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187 (187)
Q Consensus 157 NSGvVRAKFk~NLPpqAiG~rVRVmLYPS~I 187 (187)
|||+|||+|.+||||+|||++||||||||+|
T Consensus 81 NsG~VrAkF~~Nlp~Ka~G~rvrVmLYps~i 111 (111)
T KOG0887|consen 81 NSGVVRAKFTSNLPPKAMGHRVRVMLYPSNI 111 (111)
T ss_pred CcceEEEEeccCCChhHcCcEEEEEEecccC
Confidence 9999999999999999999999999999998
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=1e-52 Score=319.32 Aligned_cols=95 Identities=64% Similarity=1.107 Sum_probs=86.9
Q ss_pred eEEEEEEEeeecccCCCCCCeeEEeecCCCChhhhhhhccceEEEEEeccccccCCCCCCCCceeeEEeEEEcccCCCce
Q psy4327 81 LYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHGSSGS 160 (187)
Q Consensus 81 LyvKgvflGYKRG~rnQ~pntALLKIEGV~tkedA~FYlGKRVaYVYKaK~~~~~pg~~k~sk~RvIWGKVtR~HGNSGv 160 (187)
||+||+|+|||||++||||||||||||||++++||+|||||||+|||++++. .++++.|+|||||+|+|||||+
T Consensus 1 ly~kgv~~gykRg~~~Q~~~~aLlKiegV~~~~~a~fylGKrv~yvyk~~~~------~~~~k~r~iwGkV~r~HGnsGv 74 (95)
T PF01247_consen 1 LYVKGVFLGYKRGKRNQHPNTALLKIEGVNTKEDAQFYLGKRVAYVYKAKNK------KNGSKGRVIWGKVTRPHGNSGV 74 (95)
T ss_dssp -EEEEEEEEEEEETSTTCEEEEEEEESS-STCHHHHTTTT-EEEEEECE-SS------STTECSEEEEEEEEEESTTTTE
T ss_pred CeeeEEEEeecccccccCCCeeEEeecCccCHHHHHhhcCcEEEEEEecccc------cCCCcEeEEEEEEEeEEcCCCE
Confidence 8999999999999999999999999999999999999999999999999887 3689999999999999999999
Q ss_pred EEEEeCCCCCccCCCCeEEEE
Q psy4327 161 VRAKFHRNLPAIYMGRKVRIM 181 (187)
Q Consensus 161 VRAKFk~NLPpqAiG~rVRVm 181 (187)
|||+|++||||||||++||||
T Consensus 75 VrAkF~~nLP~~a~G~~VrVm 95 (95)
T PF01247_consen 75 VRAKFKKNLPPQAIGSRVRVM 95 (95)
T ss_dssp EEEEESS--STTGCSSEEEEE
T ss_pred EEEEeCCCCChHHcCCEEEeC
Confidence 999999999999999999999
No 4
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=100.00 E-value=1.6e-47 Score=287.70 Aligned_cols=85 Identities=25% Similarity=0.503 Sum_probs=81.9
Q ss_pred EEEEEEeeecccCCCCCCeeEEeecCCCChhhhhhhccceEEEEEeccccccCCCCCCCCceeeEEeEEEcccCCCceEE
Q psy4327 83 ARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHGSSGSVR 162 (187)
Q Consensus 83 vKgvflGYKRG~rnQ~pntALLKIEGV~tkedA~FYlGKRVaYVYKaK~~~~~pg~~k~sk~RvIWGKVtR~HGNSGvVR 162 (187)
+||+|+|||||++||+|||||||||||++++||+|||||||+|||++ | |+|||||||+|||||+||
T Consensus 3 ~kgv~~gykRg~~nQ~~~~aLlkiegv~~~~~a~fylGKrv~yvyk~-------g-------rviwGKItR~HGnsGvVr 68 (87)
T PRK04337 3 MKGVILSYRRGKNTQYNRQVIIKPLGVDDREEAAKLIGRKVIWKDPT-------G-------NKYVGKIVRVHGNRGEVR 68 (87)
T ss_pred ceEEEEEeccccCccCCceEEEEEcCcCCHHHHHhhcCceEEEEeCC-------C-------CEEEEEEEeeeCCCceEE
Confidence 69999999999999999999999999999999999999999999975 1 799999999999999999
Q ss_pred EEeCCCCCccCCCCeEEEE
Q psy4327 163 AKFHRNLPAIYMGRKVRIM 181 (187)
Q Consensus 163 AKFk~NLPpqAiG~rVRVm 181 (187)
|+|++||||||||++|||.
T Consensus 69 AkF~~nLP~~a~G~~vrv~ 87 (87)
T PRK04337 69 ARFKPGLPGQALGDYVEII 87 (87)
T ss_pred EEECCCCChHHcCCEEEeC
Confidence 9999999999999999983
No 5
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1e-44 Score=277.91 Aligned_cols=97 Identities=47% Similarity=0.846 Sum_probs=92.7
Q ss_pred CCceEEEEEEEeeecccCCCCCCeeEEeecCCCChhhhhhhccceEEEEEeccccccCCCCCCCCceeeEEeEEEcccCC
Q psy4327 78 HGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHGS 157 (187)
Q Consensus 78 ~~RLyvKgvflGYKRG~rnQ~pntALLKIEGV~tkedA~FYlGKRVaYVYKaK~~~~~pg~~k~sk~RvIWGKVtR~HGN 157 (187)
..|++++|+|+|||||+++|||+++|||||||+|++||+|||||+|+|+|+.. .|||||+|+|+|||
T Consensus 4 ~~r~~ikgv~lsyrR~k~~q~P~~~liKi~gv~s~~eA~~y~gk~v~yk~~~~-------------G~Vi~G~V~R~HGn 70 (100)
T COG2451 4 GHRLRIKGVVLSYRRSKRTQHPNVSLIKIEGVDSPEEAQFYLGKRVCYKYRSS-------------GRVIKGKVVRTHGN 70 (100)
T ss_pred cceEEEeeEEEEEEecccccCCceEEEEEecCCCHHHHHhhhccEEEEEeCCC-------------CcEEEEEEEEecCC
Confidence 36999999999999999999999999999999999999999999999998641 28999999999999
Q ss_pred CceEEEEeCCCCCccCCCCeEEEEEeecCC
Q psy4327 158 SGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187 (187)
Q Consensus 158 SGvVRAKFk~NLPpqAiG~rVRVmLYPS~I 187 (187)
||+|||+|.+||||||+|..|+||||||+|
T Consensus 71 sGaVrarF~~~LP~qa~G~~v~v~ly~~~~ 100 (100)
T COG2451 71 SGAVRARFERNLPGQALGTSVEVKLYPSNI 100 (100)
T ss_pred cceEEEEecCCCCchhcCcEEEEEEccCCC
Confidence 999999999999999999999999999986
No 6
>PF09853 DUF2080: Putative transposon-encoded protein (DUF2080); InterPro: IPR019205 This entry, found in various hypothetical archaeal proteins, has no known function.
Probab=94.79 E-value=0.051 Score=38.34 Aligned_cols=34 Identities=38% Similarity=0.681 Sum_probs=27.2
Q ss_pred eEEeEEEcccCCCceEEEEeCCCCCccCCCCeEEEEEee
Q psy4327 146 AIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYP 184 (187)
Q Consensus 146 vIWGKVtR~HGNSGvVRAKFk~NLPpqAiG~rVRVmLYP 184 (187)
+++|+|+ +|||| |++..+||+.-+|.++.|.+..
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 4555555 99999 4677999999999999987643
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=91.05 E-value=0.66 Score=32.80 Aligned_cols=40 Identities=13% Similarity=0.161 Sum_probs=28.3
Q ss_pred eEEEEEEEeeecccCCCCCCeeEEeecCCCChhhhhhhccceEEE
Q psy4327 81 LYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVF 125 (187)
Q Consensus 81 LyvKgvflGYKRG~rnQ~pntALLKIEGV~tkedA~FYlGKRVaY 125 (187)
.|..-.+.+++ .+.+..|++++||+|+++|+.|.|..+..
T Consensus 41 ~~~~~~v~~~~-----~~~~~~i~~~~gi~~r~~Ae~l~g~~l~v 80 (84)
T PF01782_consen 41 EWRPLKVESVR-----PHGKSLIVKFEGIDDREAAEALRGCELYV 80 (84)
T ss_dssp EEEEEEEEEEE-----EETTEEEEEETT--SHHHHHTTTT-EEEE
T ss_pred ceEEEEEEEEE-----EeCCEEEEEEcCCCCHHHHHhhCCCEEEE
Confidence 34445566665 33789999999999999999999987643
No 8
>PRK14591 rimM 16S rRNA-processing protein RimM; Provisional
Probab=87.55 E-value=0.84 Score=37.08 Aligned_cols=31 Identities=16% Similarity=0.254 Sum_probs=25.8
Q ss_pred CCCCeeEEeecCCCChhhhhhhccceEEEEEe
Q psy4327 97 QHPNTSLLAIEKCNTKEDARFYVGKRCVFLYK 128 (187)
Q Consensus 97 Q~pntALLKIEGV~tkedA~FYlGKRVaYVYK 128 (187)
++.+..|++++||+++++|+.|.|..+. +.+
T Consensus 59 ~~~~~~lv~f~gi~dr~~Ae~l~g~~l~-v~~ 89 (169)
T PRK14591 59 KRADKVYIKLANINNADTAKKYVNALIG-VPK 89 (169)
T ss_pred EECCEEEEEEcCCCCHHHHHHhcCCEEE-EEH
Confidence 3457789999999999999999998774 444
No 9
>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=85.89 E-value=0.78 Score=36.74 Aligned_cols=28 Identities=18% Similarity=0.232 Sum_probs=24.2
Q ss_pred CCCeeEEeecCCCChhhhhhhccceEEE
Q psy4327 98 HPNTSLLAIEKCNTKEDARFYVGKRCVF 125 (187)
Q Consensus 98 ~pntALLKIEGV~tkedA~FYlGKRVaY 125 (187)
+.+..||+++|++|+++|+.+.|..+..
T Consensus 55 ~~~~~lv~f~gi~~~~~Ae~L~g~~l~i 82 (165)
T TIGR02273 55 QNNKLIVKFEGIDDREAAEALKGLELFV 82 (165)
T ss_pred ECCEEEEEECCCCCHHHHHHhcCCEEEE
Confidence 3457899999999999999999987644
No 10
>PRK14592 rimM 16S rRNA-processing protein RimM; Provisional
Probab=85.21 E-value=1.5 Score=35.39 Aligned_cols=29 Identities=17% Similarity=0.219 Sum_probs=24.9
Q ss_pred CCCCeeEEeecCCCChhhhhhhccceEEE
Q psy4327 97 QHPNTSLLAIEKCNTKEDARFYVGKRCVF 125 (187)
Q Consensus 97 Q~pntALLKIEGV~tkedA~FYlGKRVaY 125 (187)
++.+..|++++||+|+++|+.|.|..+..
T Consensus 51 ~~~~~~lv~f~gi~~~~~Ae~l~g~~l~v 79 (165)
T PRK14592 51 IGANLVIAKISGINSRTEAELLRNKKLYV 79 (165)
T ss_pred ecCCEEEEEEcCCCCHHHHHHhcCCEEEE
Confidence 44567899999999999999999998754
No 11
>PRK13829 rimM 16S rRNA-processing protein RimM; Provisional
Probab=83.68 E-value=1.1 Score=36.24 Aligned_cols=31 Identities=19% Similarity=0.200 Sum_probs=25.9
Q ss_pred CCCCeeEEeecCCCChhhhhhhccceEEEEEe
Q psy4327 97 QHPNTSLLAIEKCNTKEDARFYVGKRCVFLYK 128 (187)
Q Consensus 97 Q~pntALLKIEGV~tkedA~FYlGKRVaYVYK 128 (187)
.+.+..|++++||+|+++|+.|.|..+. +.+
T Consensus 48 ~~~~~~l~~f~gi~~r~~Ae~l~g~~l~-v~~ 78 (162)
T PRK13829 48 RVGPELVLHLAGVTSREGAEALVGLRVY-ADD 78 (162)
T ss_pred EECCEEEEEECCCCCHHHHHHhcCCEEE-EEH
Confidence 4456689999999999999999998764 444
No 12
>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=82.77 E-value=1.3 Score=31.30 Aligned_cols=28 Identities=25% Similarity=0.627 Sum_probs=23.0
Q ss_pred EeEEEcccCCCceEEEEeCCCCCccCCC
Q psy4327 148 WGKVTRPHGSSGSVRAKFHRNLPAIYMG 175 (187)
Q Consensus 148 WGKVtR~HGNSGvVRAKFk~NLPpqAiG 175 (187)
.|+|.++||-.|-|++..-.+.|.....
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 4999999999999999999887765443
No 13
>PRK13828 rimM 16S rRNA-processing protein RimM; Provisional
Probab=81.72 E-value=1.4 Score=35.53 Aligned_cols=29 Identities=14% Similarity=0.110 Sum_probs=24.8
Q ss_pred CCCCeeEEeecCCCChhhhhhhccceEEE
Q psy4327 97 QHPNTSLLAIEKCNTKEDARFYVGKRCVF 125 (187)
Q Consensus 97 Q~pntALLKIEGV~tkedA~FYlGKRVaY 125 (187)
++.+..|++++||+|+++|+.|.|..+..
T Consensus 39 ~~~~~~lv~f~gi~dr~~Ae~L~g~~l~i 67 (161)
T PRK13828 39 PAKDGLVARLKGVATREAAEALRGLELYV 67 (161)
T ss_pred EECCEEEEEECCCCCHHHHHHhcCCEEEE
Confidence 34566899999999999999999987754
No 14
>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional
Probab=80.19 E-value=1.7 Score=35.14 Aligned_cols=28 Identities=14% Similarity=0.197 Sum_probs=24.0
Q ss_pred CCCeeEEeecCCCChhhhhhhccceEEE
Q psy4327 98 HPNTSLLAIEKCNTKEDARFYVGKRCVF 125 (187)
Q Consensus 98 ~pntALLKIEGV~tkedA~FYlGKRVaY 125 (187)
+.+..||+++|++++++|+.|.|..+..
T Consensus 60 ~~~~~lvkf~gi~~~~~Ae~l~g~~l~i 87 (172)
T PRK00122 60 HKGFLIVKFEGVDDRNAAEALKGCELFV 87 (172)
T ss_pred ECCEEEEEECCCCCHHHHHHhCCCEEEE
Confidence 3456899999999999999999987644
No 15
>PRK14590 rimM 16S rRNA-processing protein RimM; Provisional
Probab=79.86 E-value=1.7 Score=35.56 Aligned_cols=31 Identities=26% Similarity=0.281 Sum_probs=25.7
Q ss_pred CCCCeeEEeecCCCChhhhhhhccceEEEEEe
Q psy4327 97 QHPNTSLLAIEKCNTKEDARFYVGKRCVFLYK 128 (187)
Q Consensus 97 Q~pntALLKIEGV~tkedA~FYlGKRVaYVYK 128 (187)
++.+..|++++||+++++|+.+.|..+. +.+
T Consensus 55 ~~~~~~lv~f~gi~~~e~Ae~L~g~~l~-i~~ 85 (171)
T PRK14590 55 PHGGKFLVRFEGYDTPEEAVKWRGGSLF-LPQ 85 (171)
T ss_pred EECCEEEEEECCCCCHHHHHHhcCCEEE-EEH
Confidence 3455689999999999999999999875 444
No 16
>PRK14594 rimM 16S rRNA-processing protein RimM; Provisional
Probab=79.50 E-value=1.6 Score=35.44 Aligned_cols=31 Identities=23% Similarity=0.310 Sum_probs=25.4
Q ss_pred CCCeeEEeecCCCChhhhhhhccceEEEEEec
Q psy4327 98 HPNTSLLAIEKCNTKEDARFYVGKRCVFLYKA 129 (187)
Q Consensus 98 ~pntALLKIEGV~tkedA~FYlGKRVaYVYKa 129 (187)
+.+..||+++|++++++|+.|.|..+ |+.+.
T Consensus 57 ~~~~~lvkf~gi~dr~~Ae~L~g~~l-~v~~~ 87 (166)
T PRK14594 57 KNNSLLLKFEEFNAPEPIKPLIGFEL-WVDDE 87 (166)
T ss_pred ECCEEEEEEcCCCCHHHHHHhcCCEE-EEEHH
Confidence 34568999999999999999999875 55554
No 17
>PRK14593 rimM 16S rRNA-processing protein RimM; Provisional
Probab=65.66 E-value=13 Score=30.55 Aligned_cols=26 Identities=27% Similarity=0.257 Sum_probs=22.0
Q ss_pred EEeecCCCChhhhhhhccceEEEEEec
Q psy4327 103 LLAIEKCNTKEDARFYVGKRCVFLYKA 129 (187)
Q Consensus 103 LLKIEGV~tkedA~FYlGKRVaYVYKa 129 (187)
+|+++||+++++|+.|.|..+. +.+.
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 6899999999999999998764 4443
No 18
>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=64.27 E-value=14 Score=33.02 Aligned_cols=64 Identities=25% Similarity=0.400 Sum_probs=37.9
Q ss_pred CCCeeEEeecCCCChhhhhhhccceEEEEEeccccccCCCCCCCCceeeEEeEEEcccCCCceEEEEeCCCCCccCCCCe
Q psy4327 98 HPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRK 177 (187)
Q Consensus 98 ~pntALLKIEGV~tkedA~FYlGKRVaYVYKaK~~~~~pg~~k~sk~RvIWGKVtR~HGNSGvVRAKFk~NLPpqAiG~r 177 (187)
+-++|.|+-= -++.+|..++.|-.+-= + +..| |.|..+.|.+|.+||-|...|= +.+.
T Consensus 231 ~k~~a~vr~M-F~~~~dv~~F~~~~l~T----~-----------~G~r---G~Ik~~lgt~G~fka~F~~~i~---~~D~ 288 (297)
T PF04950_consen 231 HKRTAVVRGM-FFNPEDVAWFKGAELRT----K-----------SGIR---GHIKESLGTHGYFKATFEDKIK---QSDI 288 (297)
T ss_dssp ESSSCEECSS-SSTCCHHHHS-S--BEE----T-----------TS-B---EEEEE-BTTTTBBEEEESS------SS-E
T ss_pred ECceEEhhhh-cCCHHHHHhhcCCEEEe----e-----------ccCC---CEECeeECCCCcEEEEECCcCC---CCCE
Confidence 3456666644 56778888888765432 1 2244 9999999999999999998875 4456
Q ss_pred EEEEEe
Q psy4327 178 VRIMLY 183 (187)
Q Consensus 178 VRVmLY 183 (187)
|..-||
T Consensus 289 V~~~ly 294 (297)
T PF04950_consen 289 VFMRLY 294 (297)
T ss_dssp EEEE--
T ss_pred EEEecC
Confidence 666665
No 19
>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=56.47 E-value=48 Score=24.84 Aligned_cols=34 Identities=29% Similarity=0.540 Sum_probs=22.7
Q ss_pred EEeEEEcccCC-------Cc-eEEEEeCCCCCccCCCCeEEEE
Q psy4327 147 IWGKVTRPHGS-------SG-SVRAKFHRNLPAIYMGRKVRIM 181 (187)
Q Consensus 147 IWGKVtR~HGN-------SG-vVRAKFk~NLPpqAiG~rVRVm 181 (187)
|+|+|++.||+ .| .|.+.....+ ...+|+-|.|.
T Consensus 20 ivGkV~~~~~~~~~~~~~Dg~~v~v~l~~~~-~~~~~~~vEVi 61 (101)
T cd04479 20 IVGKVEKVDGDSLTLISSDGVNVTVELNRPL-DLPISGYVEVI 61 (101)
T ss_pred EEEEEEEecCCeEEEEcCCCCEEEEEeCCCC-CcccCCEEEEE
Confidence 45899999988 44 7777777654 34555555553
No 20
>COG3466 ISA1214 Putative transposon-encoded protein [Function unknown]
Probab=48.28 E-value=33 Score=24.45 Aligned_cols=31 Identities=29% Similarity=0.718 Sum_probs=24.5
Q ss_pred eEEeEEEcccCCCceEEEEeCCCCCccCCCCeEEEEE
Q psy4327 146 AIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIML 182 (187)
Q Consensus 146 vIWGKVtR~HGNSGvVRAKFk~NLPpqAiG~rVRVmL 182 (187)
+.+-+...|-||||.|- .|-.-+|.+|.|..
T Consensus 19 ~~~ek~VtpfGnsakVd------vPK~yiG~rv~viI 49 (52)
T COG3466 19 VVFEKRVTPFGNSAKVD------VPKRYIGKRVYVII 49 (52)
T ss_pred EEEEEEEEecCCcceee------CchHHcCcEEEEEE
Confidence 44445556999999984 69999999999875
No 21
>PF14444 S1-like: S1-like
Probab=46.57 E-value=46 Score=24.02 Aligned_cols=35 Identities=29% Similarity=0.434 Sum_probs=27.6
Q ss_pred eeEEeEEEcccCCCceE--EEEeC-----CCCCccCCCCeEEEE
Q psy4327 145 RAIWGKVTRPHGSSGSV--RAKFH-----RNLPAIYMGRKVRIM 181 (187)
Q Consensus 145 RvIWGKVtR~HGNSGvV--RAKFk-----~NLPpqAiG~rVRVm 181 (187)
|++-|-||..|++-|.| -.-|. -++| ..|++|.|-
T Consensus 2 r~~~GvVTkl~~~yG~IDe~vFF~~~vv~G~~P--~vGdrV~v~ 43 (58)
T PF14444_consen 2 RVFTGVVTKLCDDYGFIDEDVFFQTDVVKGNVP--KVGDRVLVE 43 (58)
T ss_pred ceEEEEEEEEeCCcceEcccEEEEcccEecCCC--ccCCEEEEE
Confidence 68889999999999988 33443 4567 599999875
No 22
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=44.91 E-value=25 Score=29.47 Aligned_cols=31 Identities=16% Similarity=0.221 Sum_probs=27.0
Q ss_pred cCCCCCCeeEEeecCCCChhhhhhhccceEE
Q psy4327 94 QRNQHPNTSLLAIEKCNTKEDARFYVGKRCV 124 (187)
Q Consensus 94 ~rnQ~pntALLKIEGV~tkedA~FYlGKRVa 124 (187)
....+.|-.+|+++|++++++|+-+.|-.+.
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 3456889999999999999999999998764
No 23
>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=43.13 E-value=52 Score=24.71 Aligned_cols=48 Identities=21% Similarity=0.262 Sum_probs=33.5
Q ss_pred CCeeEEeecCCCChhhhhhhccceEEE---EEeccccccCCCCCCCCceeeEEeEEE
Q psy4327 99 PNTSLLAIEKCNTKEDARFYVGKRCVF---LYKAKTKELKPHSKRKSRLRAIWGKVT 152 (187)
Q Consensus 99 pntALLKIEGV~tkedA~FYlGKRVaY---VYKaK~~~~~pg~~k~sk~RvIWGKVt 152 (187)
.+.--|++| .++.+.|++|-||+|-- -|.. .+.+ ..+.+..+|.|=||
T Consensus 35 ~~~~~l~~e-f~~~~~a~~fKgKkVDIfG~~Y~~----~C~~-~~~~~~~c~YGGVT 85 (87)
T PF01123_consen 35 SSYNDLKVE-FNSEDLAKKFKGKKVDIFGLSYYY----NCYG-SEGNKTACMYGGVT 85 (87)
T ss_dssp TTESEEEEE--SSHHHHHHHTTSEEEEEEEEBET----TSSS-SSSSEEEEEESEEE
T ss_pred CcceeEEEE-eCCHHHHHhhcCCEEEEEeccccc----cccc-CCCCceEEEecCEe
Confidence 555667777 89999999999999962 1211 1223 34567899999888
No 24
>KOG0189|consensus
Probab=38.55 E-value=27 Score=31.48 Aligned_cols=44 Identities=18% Similarity=0.314 Sum_probs=33.7
Q ss_pred hhhhccccccCCCceEEEEEEEeeecccCCCCCCeeEEeecCCC
Q psy4327 67 KTKKHKRLRLRHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCN 110 (187)
Q Consensus 67 ~~~k~~~~~~~~~RLyvKgvflGYKRG~rnQ~pntALLKIEGV~ 110 (187)
.+.|-.-.++...-|-++|+|+|-|+++.-.+..-.+|+|++|.
T Consensus 134 ~l~KV~P~~RA~k~L~v~A~~TGrRksQ~gtRselpiVqvD~~f 177 (261)
T KOG0189|consen 134 RLRKVEPARRAYKGLNVKAVFTGRRKSQGGTRSELPIVQVDPVF 177 (261)
T ss_pred hhhhccHHHHHhhccceeeEEecccccCCCcccccceEEecCcc
Confidence 34443333444556889999999999999999999999999884
No 25
>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=37.03 E-value=70 Score=30.31 Aligned_cols=37 Identities=27% Similarity=0.536 Sum_probs=28.8
Q ss_pred eeEEeEEEcccCCCceEEEEeC---CCCCc-cCCCCeEEEEEee
Q psy4327 145 RAIWGKVTRPHGSSGSVRAKFH---RNLPA-IYMGRKVRIMLYP 184 (187)
Q Consensus 145 RvIWGKVtR~HGNSGvVRAKFk---~NLPp-qAiG~rVRVmLYP 184 (187)
+.|+|+. .-|+|+|-+-|- .+|-+ ..+|..|+|..|-
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 5788876 488999999993 46776 8899999999883
No 26
>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=20.68 E-value=1.4e+02 Score=25.01 Aligned_cols=21 Identities=19% Similarity=0.294 Sum_probs=18.1
Q ss_pred cccCCCceEEEEeCCCCCccC
Q psy4327 153 RPHGSSGSVRAKFHRNLPAIY 173 (187)
Q Consensus 153 R~HGNSGvVRAKFk~NLPpqA 173 (187)
.....+|-+...|...||+-.
T Consensus 44 ~~~~r~g~~~~~f~s~lP~g~ 64 (186)
T cd09232 44 VARSKNGRTLHRFSSALPGGS 64 (186)
T ss_pred EEEeCCCCEEEecccCCCCCC
Confidence 367889999999999999954
Done!