Query 044692
Match_columns 61
No_of_seqs 103 out of 218
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 05:50:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044692.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044692hhsearch_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 2.5E-34 5.4E-39 190.3 5.7 57 1-61 32-120 (120)
2 KOG0887 60S ribosomal protein 100.0 2.2E-32 4.8E-37 179.3 5.6 57 1-61 23-111 (111)
3 PF01247 Ribosomal_L35Ae: Ribo 99.9 9.8E-29 2.1E-33 157.8 4.1 51 1-55 13-95 (95)
4 PRK04337 50S ribosomal protein 99.9 6.4E-28 1.4E-32 152.6 4.2 51 1-55 13-87 (87)
5 COG2451 Ribosomal protein L35A 99.9 1.1E-27 2.4E-32 154.9 5.2 57 1-61 19-100 (100)
6 PF09853 DUF2080: Putative tra 87.7 0.34 7.5E-06 28.4 1.4 36 14-57 14-49 (53)
7 PF01782 RimM: RimM N-terminal 73.4 1.1 2.3E-05 26.2 -0.1 18 6-23 53-70 (84)
8 TIGR02273 16S_RimM 16S rRNA pr 71.6 1.6 3.4E-05 28.8 0.5 18 6-23 55-72 (165)
9 PRK13829 rimM 16S rRNA-process 64.7 2.7 5.8E-05 28.0 0.5 19 5-23 48-66 (162)
10 PRK14592 rimM 16S rRNA-process 63.9 3.2 6.9E-05 27.6 0.7 19 5-23 51-69 (165)
11 PRK14591 rimM 16S rRNA-process 61.0 3.4 7.3E-05 27.7 0.4 19 5-23 59-77 (169)
12 PRK13828 rimM 16S rRNA-process 59.8 3.8 8.1E-05 27.2 0.5 19 5-23 39-57 (161)
13 PRK00122 rimM 16S rRNA-process 54.7 5.1 0.00011 26.6 0.5 18 6-23 60-77 (172)
14 PRK14594 rimM 16S rRNA-process 54.1 5.1 0.00011 26.8 0.4 18 6-23 57-74 (166)
15 PRK14590 rimM 16S rRNA-process 47.9 7.5 0.00016 26.2 0.5 18 6-23 56-73 (171)
16 COG3466 ISA1214 Putative trans 36.1 21 0.00046 21.0 1.1 24 23-56 26-49 (52)
17 PF12150 MFP2b: Cytosolic moti 31.4 45 0.00097 26.1 2.4 28 27-58 50-81 (362)
18 PRK00893 aspartate carbamoyltr 30.3 72 0.0016 22.0 3.1 35 9-43 55-102 (152)
19 PF13509 S1_2: S1 domain; PDB: 30.0 50 0.0011 18.5 2.0 30 26-59 22-51 (61)
20 PF01713 Smr: Smr domain; Int 30.0 41 0.00088 19.3 1.6 13 24-36 71-83 (83)
21 TIGR00240 ATCase_reg aspartate 29.3 68 0.0015 22.1 2.8 36 8-43 52-100 (150)
22 COG0806 RimM RimM protein, req 28.7 26 0.00057 24.2 0.7 19 5-23 60-78 (174)
23 PF14047 DCR: Dppa2/4 conserve 20.5 1.9E+02 0.0042 17.6 3.4 32 27-61 14-46 (66)
24 PF09499 RE_ApaLI: ApaLI-like 20.5 55 0.0012 23.6 1.1 11 50-60 144-155 (191)
25 COG4919 Ribosomal protein S30 20.3 46 0.001 19.6 0.5 20 24-43 3-32 (54)
No 1
>PTZ00041 60S ribosomal protein L35a; Provisional
Probab=100.00 E-value=2.5e-34 Score=190.26 Aligned_cols=57 Identities=68% Similarity=1.168 Sum_probs=56.0
Q ss_pred CCccccCCeeEEEecCcCCCCCC--------------------------------CCCCCcEEEEEecCCCCCCccccCC
Q 044692 1 SKSNQYPNTSLIHIEGVNTKEEV--------------------------------PHGNSGVVRAKFKSNLPPSPWYLNH 48 (61)
Q Consensus 1 ~~~nQ~~~taLlkiegV~~k~~a--------------------------------~HGnsGvvrAkFk~nLPp~a~~~~~ 48 (61)
|++||+|||||||||||++++|| +|||||+|||+|++||||+| |
T Consensus 32 g~~nQ~~~~aLlKieGV~~~~~a~fYlGKrvayvyka~~~~~~~k~RviwGKVtR~HGnsGvVrAkF~~nLPp~A----~ 107 (120)
T PTZ00041 32 SKVNQYPNVALLKIEGVNTREDARFYLGKRVAYVYKAKKLKNGTKFRAIWGKITRPHGNSGVVRARFNKNLPPKA----I 107 (120)
T ss_pred ccccCCCceEEEEecCcCChhhhHhhccceEEEEEcCccccCCcceeEEEEEEEcccCCCcEEEEEeCCCCChHH----c
Confidence 68999999999999999999999 99999999999999999999 9
Q ss_pred CCeEEEEEeecCC
Q 044692 49 GDRVRVVMYPGNI 61 (61)
Q Consensus 49 g~~VrV~lYPs~i 61 (61)
|++||||||||+|
T Consensus 108 G~~VrVmlyPs~i 120 (120)
T PTZ00041 108 GSRVRVFLYPSNI 120 (120)
T ss_pred CCeEEEEEccCCC
Confidence 9999999999997
No 2
>KOG0887 consensus 60S ribosomal protein L35A/L37 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=2.2e-32 Score=179.34 Aligned_cols=57 Identities=72% Similarity=1.121 Sum_probs=55.9
Q ss_pred CCccccCCeeEEEecCcCCCCCC--------------------------------CCCCCcEEEEEecCCCCCCccccCC
Q 044692 1 SKSNQYPNTSLIHIEGVNTKEEV--------------------------------PHGNSGVVRAKFKSNLPPSPWYLNH 48 (61)
Q Consensus 1 ~~~nQ~~~taLlkiegV~~k~~a--------------------------------~HGnsGvvrAkFk~nLPp~a~~~~~ 48 (61)
|+++|+|+|+|||||||+++||| +|||||+|||||.+||||++ |
T Consensus 23 ~~r~~~~~t~llkIEGv~skeEa~fYlGkR~~yvYKa~~~~~~~k~RvIWGkVTr~HGNsG~VrAkF~~Nlp~Ka----~ 98 (111)
T KOG0887|consen 23 GKRNQHPNTSLLKIEGVYSKEEASFYLGKRCVYVYKAKPEVRGSKTRVIWGKVTRPHGNSGVVRAKFTSNLPPKA----M 98 (111)
T ss_pred cccccCCCcEEEEEecccchhhhheeecCcEEEEEecCCCCCCceEEEEEEEEecccCCcceEEEEeccCCChhH----c
Confidence 68999999999999999999999 99999999999999999999 9
Q ss_pred CCeEEEEEeecCC
Q 044692 49 GDRVRVVMYPGNI 61 (61)
Q Consensus 49 g~~VrV~lYPs~i 61 (61)
|++||||||||+|
T Consensus 99 G~rvrVmLYps~i 111 (111)
T KOG0887|consen 99 GHRVRVMLYPSNI 111 (111)
T ss_pred CcEEEEEEecccC
Confidence 9999999999998
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=99.95 E-value=9.8e-29 Score=157.77 Aligned_cols=51 Identities=73% Similarity=1.110 Sum_probs=47.0
Q ss_pred CCccccCCeeEEEecCcCCCCCC--------------------------------CCCCCcEEEEEecCCCCCCccccCC
Q 044692 1 SKSNQYPNTSLIHIEGVNTKEEV--------------------------------PHGNSGVVRAKFKSNLPPSPWYLNH 48 (61)
Q Consensus 1 ~~~nQ~~~taLlkiegV~~k~~a--------------------------------~HGnsGvvrAkFk~nLPp~a~~~~~ 48 (61)
|++||+|||||||||||++++|| +|||||+|||||++||||+| |
T Consensus 13 g~~~Q~~~~aLlKiegV~~~~~a~fylGKrv~yvyk~~~~~~~~k~r~iwGkV~r~HGnsGvVrAkF~~nLP~~a----~ 88 (95)
T PF01247_consen 13 GKRNQHPNTALLKIEGVNTKEDAQFYLGKRVAYVYKAKNKKNGSKGRVIWGKVTRPHGNSGVVRAKFKKNLPPQA----I 88 (95)
T ss_dssp ETSTTCEEEEEEEESS-STCHHHHTTTT-EEEEEECE-SSSTTECSEEEEEEEEEESTTTTEEEEEESS--STTG----C
T ss_pred cccccCCCeeEEeecCccCHHHHHhhcCcEEEEEEecccccCCCcEeEEEEEEEeEEcCCCEEEEEeCCCCChHH----c
Confidence 68999999999999999999999 99999999999999999999 9
Q ss_pred CCeEEEE
Q 044692 49 GDRVRVV 55 (61)
Q Consensus 49 g~~VrV~ 55 (61)
|++||||
T Consensus 89 G~~VrVm 95 (95)
T PF01247_consen 89 GSRVRVM 95 (95)
T ss_dssp SSEEEEE
T ss_pred CCEEEeC
Confidence 9999998
No 4
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=99.94 E-value=6.4e-28 Score=152.57 Aligned_cols=51 Identities=43% Similarity=0.716 Sum_probs=49.5
Q ss_pred CCccccCCeeEEEecCcCCCCCC------------------------CCCCCcEEEEEecCCCCCCccccCCCCeEEEE
Q 044692 1 SKSNQYPNTSLIHIEGVNTKEEV------------------------PHGNSGVVRAKFKSNLPPSPWYLNHGDRVRVV 55 (61)
Q Consensus 1 ~~~nQ~~~taLlkiegV~~k~~a------------------------~HGnsGvvrAkFk~nLPp~a~~~~~g~~VrV~ 55 (61)
|++||+|||||||||||++++|| +|||||+|||+|++||||+| ||++|||.
T Consensus 13 g~~nQ~~~~aLlkiegv~~~~~a~fylGKrv~yvyk~grviwGKItR~HGnsGvVrAkF~~nLP~~a----~G~~vrv~ 87 (87)
T PRK04337 13 GKNTQYNRQVIIKPLGVDDREEAAKLIGRKVIWKDPTGNKYVGKIVRVHGNRGEVRARFKPGLPGQA----LGDYVEII 87 (87)
T ss_pred ccCccCCceEEEEEcCcCCHHHHHhhcCceEEEEeCCCCEEEEEEEeeeCCCceEEEEECCCCChHH----cCCEEEeC
Confidence 68999999999999999999999 99999999999999999999 99999983
No 5
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=1.1e-27 Score=154.90 Aligned_cols=57 Identities=58% Similarity=0.898 Sum_probs=55.7
Q ss_pred CCccccCCeeEEEecCcCCCCCC-------------------------CCCCCcEEEEEecCCCCCCccccCCCCeEEEE
Q 044692 1 SKSNQYPNTSLIHIEGVNTKEEV-------------------------PHGNSGVVRAKFKSNLPPSPWYLNHGDRVRVV 55 (61)
Q Consensus 1 ~~~nQ~~~taLlkiegV~~k~~a-------------------------~HGnsGvvrAkFk~nLPp~a~~~~~g~~VrV~ 55 (61)
|+++|||+++|||||||++++|| +|||||+|||+|.+|||||| +|+.|+||
T Consensus 19 ~k~~q~P~~~liKi~gv~s~~eA~~y~gk~v~yk~~~~G~Vi~G~V~R~HGnsGaVrarF~~~LP~qa----~G~~v~v~ 94 (100)
T COG2451 19 SKRTQHPNVSLIKIEGVDSPEEAQFYLGKRVCYKYRSSGRVIKGKVVRTHGNSGAVRARFERNLPGQA----LGTSVEVK 94 (100)
T ss_pred cccccCCceEEEEEecCCCHHHHHhhhccEEEEEeCCCCcEEEEEEEEecCCcceEEEEecCCCCchh----cCcEEEEE
Confidence 68999999999999999999999 99999999999999999999 99999999
Q ss_pred EeecCC
Q 044692 56 MYPGNI 61 (61)
Q Consensus 56 lYPs~i 61 (61)
||||+|
T Consensus 95 ly~~~~ 100 (100)
T COG2451 95 LYPSNI 100 (100)
T ss_pred EccCCC
Confidence 999986
No 6
>PF09853 DUF2080: Putative transposon-encoded protein (DUF2080); InterPro: IPR019205 This entry, found in various hypothetical archaeal proteins, has no known function.
Probab=87.70 E-value=0.34 Score=28.40 Aligned_cols=36 Identities=28% Similarity=0.406 Sum_probs=27.0
Q ss_pred ecCcCCCCCCCCCCCcEEEEEecCCCCCCccccCCCCeEEEEEe
Q 044692 14 IEGVNTKEEVPHGNSGVVRAKFKSNLPPSPWYLNHGDRVRVVMY 57 (61)
Q Consensus 14 iegV~~k~~a~HGnsGvvrAkFk~nLPp~a~~~~~g~~VrV~lY 57 (61)
|+++..+.-.+||||| ++..+||+.- +|.++.|.+-
T Consensus 14 i~~~~~~~vk~~Gnsa----~v~p~lPkey----iGK~v~iiil 49 (53)
T PF09853_consen 14 IEPTFIGVVKPFGNSA----RVYPSLPKEY----IGKKVIIIIL 49 (53)
T ss_pred EEEEEEEEEEecCcce----eEcCCCChHH----cCcEEEEEEe
Confidence 3444444445999996 5678999999 9999988754
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=73.43 E-value=1.1 Score=26.20 Aligned_cols=18 Identities=17% Similarity=0.479 Sum_probs=13.9
Q ss_pred cCCeeEEEecCcCCCCCC
Q 044692 6 YPNTSLIHIEGVNTKEEV 23 (61)
Q Consensus 6 ~~~taLlkiegV~~k~~a 23 (61)
+.+..|+|++||+|+++|
T Consensus 53 ~~~~~i~~~~gi~~r~~A 70 (84)
T PF01782_consen 53 HGKSLIVKFEGIDDREAA 70 (84)
T ss_dssp ETTEEEEEETT--SHHHH
T ss_pred eCCEEEEEEcCCCCHHHH
Confidence 467889999999999887
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=71.59 E-value=1.6 Score=28.79 Aligned_cols=18 Identities=22% Similarity=0.530 Sum_probs=15.9
Q ss_pred cCCeeEEEecCcCCCCCC
Q 044692 6 YPNTSLIHIEGVNTKEEV 23 (61)
Q Consensus 6 ~~~taLlkiegV~~k~~a 23 (61)
+.+..|||++|++|+++|
T Consensus 55 ~~~~~lv~f~gi~~~~~A 72 (165)
T TIGR02273 55 QNNKLIVKFEGIDDREAA 72 (165)
T ss_pred ECCEEEEEECCCCCHHHH
Confidence 455789999999999999
No 9
>PRK13829 rimM 16S rRNA-processing protein RimM; Provisional
Probab=64.70 E-value=2.7 Score=28.03 Aligned_cols=19 Identities=21% Similarity=0.469 Sum_probs=16.5
Q ss_pred ccCCeeEEEecCcCCCCCC
Q 044692 5 QYPNTSLIHIEGVNTKEEV 23 (61)
Q Consensus 5 Q~~~taLlkiegV~~k~~a 23 (61)
.+.+..|+|++||+|+++|
T Consensus 48 ~~~~~~l~~f~gi~~r~~A 66 (162)
T PRK13829 48 RVGPELVLHLAGVTSREGA 66 (162)
T ss_pred EECCEEEEEECCCCCHHHH
Confidence 4466789999999999999
No 10
>PRK14592 rimM 16S rRNA-processing protein RimM; Provisional
Probab=63.90 E-value=3.2 Score=27.62 Aligned_cols=19 Identities=26% Similarity=0.422 Sum_probs=16.2
Q ss_pred ccCCeeEEEecCcCCCCCC
Q 044692 5 QYPNTSLIHIEGVNTKEEV 23 (61)
Q Consensus 5 Q~~~taLlkiegV~~k~~a 23 (61)
+..+..|+|++||+|+++|
T Consensus 51 ~~~~~~lv~f~gi~~~~~A 69 (165)
T PRK14592 51 IGANLVIAKISGINSRTEA 69 (165)
T ss_pred ecCCEEEEEEcCCCCHHHH
Confidence 3456679999999999999
No 11
>PRK14591 rimM 16S rRNA-processing protein RimM; Provisional
Probab=61.01 E-value=3.4 Score=27.66 Aligned_cols=19 Identities=11% Similarity=0.331 Sum_probs=16.2
Q ss_pred ccCCeeEEEecCcCCCCCC
Q 044692 5 QYPNTSLIHIEGVNTKEEV 23 (61)
Q Consensus 5 Q~~~taLlkiegV~~k~~a 23 (61)
++.+..|+|++||+++++|
T Consensus 59 ~~~~~~lv~f~gi~dr~~A 77 (169)
T PRK14591 59 KRADKVYIKLANINNADTA 77 (169)
T ss_pred EECCEEEEEEcCCCCHHHH
Confidence 3456789999999999999
No 12
>PRK13828 rimM 16S rRNA-processing protein RimM; Provisional
Probab=59.76 E-value=3.8 Score=27.23 Aligned_cols=19 Identities=21% Similarity=0.356 Sum_probs=16.3
Q ss_pred ccCCeeEEEecCcCCCCCC
Q 044692 5 QYPNTSLIHIEGVNTKEEV 23 (61)
Q Consensus 5 Q~~~taLlkiegV~~k~~a 23 (61)
++.+..|+|++||+|+++|
T Consensus 39 ~~~~~~lv~f~gi~dr~~A 57 (161)
T PRK13828 39 PAKDGLVARLKGVATREAA 57 (161)
T ss_pred EECCEEEEEECCCCCHHHH
Confidence 3456689999999999999
No 13
>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional
Probab=54.67 E-value=5.1 Score=26.62 Aligned_cols=18 Identities=17% Similarity=0.377 Sum_probs=15.6
Q ss_pred cCCeeEEEecCcCCCCCC
Q 044692 6 YPNTSLIHIEGVNTKEEV 23 (61)
Q Consensus 6 ~~~taLlkiegV~~k~~a 23 (61)
+.+..|+|++|++++++|
T Consensus 60 ~~~~~lvkf~gi~~~~~A 77 (172)
T PRK00122 60 HKGFLIVKFEGVDDRNAA 77 (172)
T ss_pred ECCEEEEEECCCCCHHHH
Confidence 345679999999999999
No 14
>PRK14594 rimM 16S rRNA-processing protein RimM; Provisional
Probab=54.13 E-value=5.1 Score=26.77 Aligned_cols=18 Identities=28% Similarity=0.399 Sum_probs=15.5
Q ss_pred cCCeeEEEecCcCCCCCC
Q 044692 6 YPNTSLIHIEGVNTKEEV 23 (61)
Q Consensus 6 ~~~taLlkiegV~~k~~a 23 (61)
+.+..|+|++|++++++|
T Consensus 57 ~~~~~lvkf~gi~dr~~A 74 (166)
T PRK14594 57 KNNSLLLKFEEFNAPEPI 74 (166)
T ss_pred ECCEEEEEEcCCCCHHHH
Confidence 345679999999999999
No 15
>PRK14590 rimM 16S rRNA-processing protein RimM; Provisional
Probab=47.92 E-value=7.5 Score=26.19 Aligned_cols=18 Identities=33% Similarity=0.429 Sum_probs=15.5
Q ss_pred cCCeeEEEecCcCCCCCC
Q 044692 6 YPNTSLIHIEGVNTKEEV 23 (61)
Q Consensus 6 ~~~taLlkiegV~~k~~a 23 (61)
+.+..|+|++||+++++|
T Consensus 56 ~~~~~lv~f~gi~~~e~A 73 (171)
T PRK14590 56 HGGKFLVRFEGYDTPEEA 73 (171)
T ss_pred ECCEEEEEECCCCCHHHH
Confidence 345679999999999999
No 16
>COG3466 ISA1214 Putative transposon-encoded protein [Function unknown]
Probab=36.12 E-value=21 Score=20.96 Aligned_cols=24 Identities=42% Similarity=0.697 Sum_probs=19.3
Q ss_pred CCCCCCcEEEEEecCCCCCCccccCCCCeEEEEE
Q 044692 23 VPHGNSGVVRAKFKSNLPPSPWYLNHGDRVRVVM 56 (61)
Q Consensus 23 a~HGnsGvvrAkFk~nLPp~a~~~~~g~~VrV~l 56 (61)
+|-||||.| ..|-.- +|.+|-|..
T Consensus 26 tpfGnsakV------dvPK~y----iG~rv~viI 49 (52)
T COG3466 26 TPFGNSAKV------DVPKRY----IGKRVYVII 49 (52)
T ss_pred EecCCccee------eCchHH----cCcEEEEEE
Confidence 389999988 467777 999988764
No 17
>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=31.42 E-value=45 Score=26.13 Aligned_cols=28 Identities=32% Similarity=0.632 Sum_probs=21.1
Q ss_pred CCcEEEEEec---CCCCC-CccccCCCCeEEEEEee
Q 044692 27 NSGVVRAKFK---SNLPP-SPWYLNHGDRVRVVMYP 58 (61)
Q Consensus 27 nsGvvrAkFk---~nLPp-~a~~~~~g~~VrV~lYP 58 (61)
|+|||-+-|- .+|-+ +. +|+.|+|..|-
T Consensus 50 n~GvveCSF~~~~~elt~~~d----lgg~IQiLqy~ 81 (362)
T PF12150_consen 50 NSGVVECSFPYDKAELTGKDD----LGGQIQILQYK 81 (362)
T ss_dssp ETTEEEEEEEETTEEE-SCCC----CTSEEEEEE-S
T ss_pred CCceEEEEEEcccceeccccc----cCCEEEEEEEc
Confidence 6999999993 34655 66 99999999884
No 18
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=30.33 E-value=72 Score=21.97 Aligned_cols=35 Identities=34% Similarity=0.397 Sum_probs=26.6
Q ss_pred eeEEEecCcC-CCCCC-------CCC-----CCcEEEEEecCCCCCCc
Q 044692 9 TSLIHIEGVN-TKEEV-------PHG-----NSGVVRAKFKSNLPPSP 43 (61)
Q Consensus 9 taLlkiegV~-~k~~a-------~HG-----nsGvvrAkFk~nLPp~a 43 (61)
--+|||||.. +.+|+ |+- ..|.|.-||+-.||..-
T Consensus 55 KDIIKIE~~~l~~~e~~~laliaP~aTiNiI~d~~VveK~~v~lP~~i 102 (152)
T PRK00893 55 KDIIKIENRFLSEEEVDQLALIAPNATINIIRDYEVVEKRKVELPEEI 102 (152)
T ss_pred CCEEEECCcccCHhHhhheEEECCCCEEEEEeCCEEEEeccCCCCccc
Confidence 3489999986 34555 443 38999999999999875
No 19
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=30.02 E-value=50 Score=18.49 Aligned_cols=30 Identities=30% Similarity=0.449 Sum_probs=15.8
Q ss_pred CCCcEEEEEecCCCCCCccccCCCCeEEEEEeec
Q 044692 26 GNSGVVRAKFKSNLPPSPWYLNHGDRVRVVMYPG 59 (61)
Q Consensus 26 GnsGvvrAkFk~nLPp~a~~~~~g~~VrV~lYPs 59 (61)
|.++-+.--++ .+|.. ..+|..|.||+|-.
T Consensus 22 ~~~~~vlLp~~-e~~~~---~~~Gd~v~VFvY~D 51 (61)
T PF13509_consen 22 GEGKEVLLPKS-EVPEP---LKVGDEVEVFVYLD 51 (61)
T ss_dssp TT-EEEEEEGG-G---------TTSEEEEEEEE-
T ss_pred CCCCEEEechH-HcCCC---CCCCCEEEEEEEEC
Confidence 44455555544 33422 23899999999964
No 20
>PF01713 Smr: Smr domain; InterPro: IPR002625 This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 (P23909 from SWISSPROT) protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2, P94545 from SWISSPROT [].; PDB: 3QD7_X 2D9I_A 3FAU_A 2VKC_A 2ZQE_A.
Probab=30.00 E-value=41 Score=19.31 Aligned_cols=13 Identities=38% Similarity=0.514 Sum_probs=10.6
Q ss_pred CCCCCcEEEEEec
Q 044692 24 PHGNSGVVRAKFK 36 (61)
Q Consensus 24 ~HGnsGvvrAkFk 36 (61)
.+||+|++...+|
T Consensus 71 ~~g~~G~~~V~lk 83 (83)
T PF01713_consen 71 EDGNSGATIVYLK 83 (83)
T ss_dssp CCTGGGEEEEEE-
T ss_pred CCCCCeEEEEEeC
Confidence 6799999998875
No 21
>TIGR00240 ATCase_reg aspartate carbamoyltransferase, regulatory subunit. The presence of this regulatory subunit allows feedback inhibition by CTP on aspartate carbamoyltransferase, the first step in the synthesis of CTP from aspartate. In many species, this regulatory subunit is not present. In Thermotoga maritima, the catalytic and regulatory subunits are encoded by a fused gene and the regulatory region has enough sequence differences to score below the trusted cutoff.
Probab=29.31 E-value=68 Score=22.12 Aligned_cols=36 Identities=31% Similarity=0.411 Sum_probs=26.3
Q ss_pred CeeEEEecCcC-CCCCC-------CCC-----CCcEEEEEecCCCCCCc
Q 044692 8 NTSLIHIEGVN-TKEEV-------PHG-----NSGVVRAKFKSNLPPSP 43 (61)
Q Consensus 8 ~taLlkiegV~-~k~~a-------~HG-----nsGvvrAkFk~nLPp~a 43 (61)
.--+|||||.. +.+|+ |.- ..|.|.-||+-.||..-
T Consensus 52 kKDIIKIE~~~l~~~e~~~laliaP~aTiNiI~d~~Vv~K~~v~lP~~i 100 (150)
T TIGR00240 52 KKDIVKIENTFLKEEEVDQIALIAPQATINIIRNYEVVEKSKPSLPEEI 100 (150)
T ss_pred cCCEEEECCcccCHhHhhheEEECCCCEEEEEeCCEEEEeccCCCChhe
Confidence 34589999998 23555 332 38999999999999765
No 22
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=28.74 E-value=26 Score=24.17 Aligned_cols=19 Identities=11% Similarity=0.406 Sum_probs=16.9
Q ss_pred ccCCeeEEEecCcCCCCCC
Q 044692 5 QYPNTSLIHIEGVNTKEEV 23 (61)
Q Consensus 5 Q~~~taLlkiegV~~k~~a 23 (61)
.+.|-.++|++||+++++|
T Consensus 60 ~~~~~~i~kf~gi~dr~~a 78 (174)
T COG0806 60 KHKNLLILKFKGIDDRNAA 78 (174)
T ss_pred ecCCEEEEEeCCCCCHHHH
Confidence 4678889999999999988
No 23
>PF14047 DCR: Dppa2/4 conserved region
Probab=20.52 E-value=1.9e+02 Score=17.58 Aligned_cols=32 Identities=25% Similarity=0.590 Sum_probs=23.6
Q ss_pred CCcEEEEEecCCCCCCccccCC-CCeEEEEEeecCC
Q 044692 27 NSGVVRAKFKSNLPPSPWYLNH-GDRVRVVMYPGNI 61 (61)
Q Consensus 27 nsGvvrAkFk~nLPp~a~~~~~-g~~VrV~lYPs~i 61 (61)
..|-|+-.|... |+|--.. |..|-.+|.|+.|
T Consensus 14 ~~gwv~LqfhaG---qawVp~~~~r~i~LfLlPac~ 46 (66)
T PF14047_consen 14 TEGWVRLQFHAG---QAWVPETPGRMISLFLLPACI 46 (66)
T ss_pred cccceeeeeecC---ceeccCCCCcEeeeeeccccc
Confidence 378889999765 7754433 8888899988754
No 24
>PF09499 RE_ApaLI: ApaLI-like restriction endonuclease; InterPro: IPR019036 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes R.ApaLI and R.XbaI restriction endonucleases. ApaLI recognises and cleaves the sequence GTGCAC.
Probab=20.48 E-value=55 Score=23.61 Aligned_cols=11 Identities=27% Similarity=0.902 Sum_probs=7.6
Q ss_pred CeEEEEE-eecC
Q 044692 50 DRVRVVM-YPGN 60 (61)
Q Consensus 50 ~~VrV~l-YPs~ 60 (61)
..||||+ ||.+
T Consensus 144 ~PIrimf~~P~r 155 (191)
T PF09499_consen 144 KPIRIMFYYPNR 155 (191)
T ss_pred cceEEEEeCCCH
Confidence 3688888 7753
No 25
>COG4919 Ribosomal protein S30 [Translation, ribosomal structure and biogenesis]
Probab=20.27 E-value=46 Score=19.63 Aligned_cols=20 Identities=55% Similarity=0.846 Sum_probs=13.2
Q ss_pred CCCC---CcEEE-------EEecCCCCCCc
Q 044692 24 PHGN---SGVVR-------AKFKSNLPPSP 43 (61)
Q Consensus 24 ~HGn---sGvvr-------AkFk~nLPp~a 43 (61)
.||. .|.|| ||=++|+||.-
T Consensus 3 sHGSLTKAGKVR~QTPkipaK~kkn~~PR~ 32 (54)
T COG4919 3 SHGSLTKAGKVRKQTPKIPAKQKKNYPPRL 32 (54)
T ss_pred CccccccccchhccCCCCCccccccCChhH
Confidence 4664 67666 66777887754
Done!