Query 040909
Match_columns 98
No_of_seqs 102 out of 237
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 13:00:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040909.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040909hhsearch_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 2E-53 4.4E-58 302.4 11.1 96 3-98 11-120 (120)
2 KOG0887 60S ribosomal protein 100.0 1.3E-49 2.9E-54 278.7 10.6 96 3-98 2-111 (111)
3 PF01247 Ribosomal_L35Ae: Ribo 100.0 4.7E-46 1E-50 255.7 9.7 81 12-92 1-95 (95)
4 COG2451 Ribosomal protein L35A 100.0 1.6E-42 3.5E-47 239.3 11.1 93 6-98 1-100 (100)
5 PRK04337 50S ribosomal protein 100.0 1E-41 2.2E-46 231.3 9.0 79 14-92 3-87 (87)
6 PF09853 DUF2080: Putative tra 95.9 0.016 3.6E-07 36.4 4.1 34 57-95 17-50 (53)
7 PF01782 RimM: RimM N-terminal 89.6 0.45 9.8E-06 30.3 3.1 28 59-86 2-29 (84)
8 PRK00122 rimM 16S rRNA-process 89.0 0.48 1E-05 34.5 3.2 30 56-85 7-36 (172)
9 PRK14594 rimM 16S rRNA-process 88.7 0.44 9.6E-06 34.8 2.8 27 57-83 2-28 (166)
10 PF01782 RimM: RimM N-terminal 87.7 1.7 3.7E-05 27.6 4.8 31 16-51 45-75 (84)
11 TIGR02273 16S_RimM 16S rRNA pr 86.9 1.1 2.4E-05 32.3 3.9 30 57-86 2-31 (165)
12 PRK14593 rimM 16S rRNA-process 83.8 1.1 2.4E-05 33.1 2.8 29 57-85 5-33 (184)
13 PRK14592 rimM 16S rRNA-process 83.8 1.3 2.9E-05 32.1 3.2 29 57-85 3-31 (165)
14 PRK14591 rimM 16S rRNA-process 81.9 1.9 4.2E-05 31.5 3.4 29 56-84 5-33 (169)
15 TIGR02273 16S_RimM 16S rRNA pr 81.2 1.3 2.8E-05 32.0 2.2 20 29-48 55-74 (165)
16 PF04950 DUF663: Protein of un 79.8 3.6 7.9E-05 33.0 4.6 59 29-94 231-294 (297)
17 PRK14590 rimM 16S rRNA-process 78.7 1.9 4.2E-05 31.7 2.5 27 58-84 2-28 (171)
18 PRK14592 rimM 16S rRNA-process 74.4 3.3 7E-05 30.1 2.7 21 28-48 51-71 (165)
19 PRK13829 rimM 16S rRNA-process 73.8 2.8 6E-05 30.5 2.2 22 28-49 48-69 (162)
20 PRK13829 rimM 16S rRNA-process 73.3 6 0.00013 28.7 3.9 24 56-82 3-26 (162)
21 PRK14591 rimM 16S rRNA-process 71.9 3 6.5E-05 30.5 2.0 21 28-48 59-79 (169)
22 PRK13828 rimM 16S rRNA-process 70.7 3.7 8E-05 29.8 2.2 21 28-48 39-59 (161)
23 PRK14594 rimM 16S rRNA-process 67.3 4.3 9.4E-05 29.6 2.0 20 29-48 57-76 (166)
24 PRK00122 rimM 16S rRNA-process 66.1 4.8 0.00011 29.2 2.1 20 29-48 60-79 (172)
25 COG3466 ISA1214 Putative trans 63.5 18 0.00038 22.8 3.9 32 56-93 18-49 (52)
26 PF14444 S1-like: S1-like 61.1 29 0.00063 22.1 4.7 36 56-93 2-44 (58)
27 PRK14590 rimM 16S rRNA-process 60.1 7.3 0.00016 28.6 2.1 22 28-49 55-76 (171)
28 PRK14593 rimM 16S rRNA-process 55.8 17 0.00037 26.8 3.4 15 34-48 66-80 (184)
29 COG0806 RimM RimM protein, req 50.3 30 0.00066 25.9 4.1 40 55-94 6-45 (174)
30 cd04479 RPA3 RPA3: A subfamily 49.5 76 0.0016 21.2 5.6 39 52-92 15-61 (101)
31 KOG0189 Phosphoadenosine phosp 45.5 22 0.00048 28.6 2.8 32 11-42 147-178 (261)
32 COG0806 RimM RimM protein, req 42.2 27 0.00059 26.2 2.7 24 25-48 57-80 (174)
33 PF12150 MFP2b: Cytosolic moti 32.1 61 0.0013 27.4 3.5 38 55-95 40-81 (362)
34 PF06312 Neurexophilin: Neurex 30.8 91 0.002 24.4 4.1 34 58-96 85-118 (219)
35 COG5192 BMS1 GTP-binding prote 30.3 20 0.00044 33.0 0.5 22 58-79 889-910 (1077)
36 KOG0461 Selenocysteine-specifi 28.5 79 0.0017 27.6 3.6 34 60-93 470-505 (522)
37 PRK00893 aspartate carbamoyltr 25.7 2.1E+02 0.0046 21.3 5.1 48 30-86 53-104 (152)
38 PF08661 Rep_fac-A_3: Replicat 23.0 2.4E+02 0.0052 18.8 4.9 38 52-91 18-65 (109)
39 KOG0148 Apoptosis-promoting RN 22.7 74 0.0016 26.4 2.4 30 31-63 201-238 (321)
40 PF01713 Smr: Smr domain; Int 21.2 56 0.0012 20.4 1.2 15 63-77 69-83 (83)
41 TIGR00240 ATCase_reg aspartate 20.1 2.8E+02 0.006 20.7 4.8 47 31-86 52-102 (150)
No 1
>PTZ00041 60S ribosomal protein L35a; Provisional
Probab=100.00 E-value=2e-53 Score=302.35 Aligned_cols=96 Identities=59% Similarity=1.118 Sum_probs=89.3
Q ss_pred CCCCCceeceEEEEEEEeeecccCCCCCCeeEEEecCccchHHhh--------------hcCCCceeeEEEeEEEeecCC
Q 040909 3 KGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAK--------------TKKNGTHYRCIWGKVARSHSN 68 (98)
Q Consensus 3 ~~~~~~~~Rly~kg~~lgykRg~~~Q~~~~aLlKieGV~~k~~Ak--------------~~~~~~k~RviwGKV~r~HGn 68 (98)
+++..++.|||+||+|+|||||++||+|||||||||||+++|||. +.++++++|+|||||+|+|||
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 345566899999999999999999999999999999999999954 345688999999999999999
Q ss_pred CceEEEEeCCCCCccCCCCeEEEEEeecCC
Q 040909 69 SGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98 (98)
Q Consensus 69 sGvVrAkF~~nLPp~AiG~~VrVmLyps~i 98 (98)
||+|||+|++||||||||++||||||||+|
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=1.3e-49 Score=278.71 Aligned_cols=96 Identities=66% Similarity=1.061 Sum_probs=90.3
Q ss_pred CCCCCceeceEEEEEEEeeecccCCCCCCeeEEEecCccchHHhh--------------hcCCCceeeEEEeEEEeecCC
Q 040909 3 KGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAK--------------TKKNGTHYRCIWGKVARSHSN 68 (98)
Q Consensus 3 ~~~~~~~~Rly~kg~~lgykRg~~~Q~~~~aLlKieGV~~k~~Ak--------------~~~~~~k~RviwGKV~r~HGn 68 (98)
+..|.+.+|||+||+|+||+||+++|+|||+|||||||+++|||. ...+++++|+|||||||+|||
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 566788899999999999999999999999999999999999954 334679999999999999999
Q ss_pred CceEEEEeCCCCCccCCCCeEEEEEeecCC
Q 040909 69 SGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98 (98)
Q Consensus 69 sGvVrAkF~~nLPp~AiG~~VrVmLyps~i 98 (98)
||+|||+|.+||||+|||++||||||||+|
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=4.7e-46 Score=255.70 Aligned_cols=81 Identities=67% Similarity=1.117 Sum_probs=73.5
Q ss_pred eEEEEEEEeeecccCCCCCCeeEEEecCccchHHhh--------------hcCCCceeeEEEeEEEeecCCCceEEEEeC
Q 040909 12 LYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAK--------------TKKNGTHYRCIWGKVARSHSNSGVVRAKFK 77 (98)
Q Consensus 12 ly~kg~~lgykRg~~~Q~~~~aLlKieGV~~k~~Ak--------------~~~~~~k~RviwGKV~r~HGnsGvVrAkF~ 77 (98)
||+||+|+|||||++||+|||||||||||+++|||. +.++++++|+|||||+|+|||||+|||+|+
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 899999999999999999999999999999999964 345688999999999999999999999999
Q ss_pred CCCCccCCCCeEEEE
Q 040909 78 SNLPPKSVGDRVRVF 92 (98)
Q Consensus 78 ~nLPp~AiG~~VrVm 92 (98)
+||||||||++||||
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
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-42 Score=239.26 Aligned_cols=93 Identities=47% Similarity=0.738 Sum_probs=85.7
Q ss_pred CCceeceEEEEEEEeeecccCCCCCCeeEEEecCccchHHhhhcCC-------CceeeEEEeEEEeecCCCceEEEEeCC
Q 040909 6 QGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKKN-------GTHYRCIWGKVARSHSNSGVVRAKFKS 78 (98)
Q Consensus 6 ~~~~~Rly~kg~~lgykRg~~~Q~~~~aLlKieGV~~k~~Ak~~~~-------~~k~RviwGKV~r~HGnsGvVrAkF~~ 78 (98)
|.+..|+++||+|+|||||+++|||+++|||||||+|+|||..... .+..|||||+|+|+|||||+|||+|.+
T Consensus 1 ~~~~~r~~ikgv~lsyrR~k~~q~P~~~liKi~gv~s~~eA~~y~gk~v~yk~~~~G~Vi~G~V~R~HGnsGaVrarF~~ 80 (100)
T COG2451 1 MAEGHRLRIKGVVLSYRRSKRTQHPNVSLIKIEGVDSPEEAQFYLGKRVCYKYRSSGRVIKGKVVRTHGNSGAVRARFER 80 (100)
T ss_pred CCccceEEEeeEEEEEEecccccCCceEEEEEecCCCHHHHHhhhccEEEEEeCCCCcEEEEEEEEecCCcceEEEEecC
Confidence 3456899999999999999999999999999999999999986532 344699999999999999999999999
Q ss_pred CCCccCCCCeEEEEEeecCC
Q 040909 79 NLPPKSVGDRVRVFMYPNNI 98 (98)
Q Consensus 79 nLPp~AiG~~VrVmLyps~i 98 (98)
||||||+|+.|+||||||+|
T Consensus 81 ~LP~qa~G~~v~v~ly~~~~ 100 (100)
T COG2451 81 NLPGQALGTSVEVKLYPSNI 100 (100)
T ss_pred CCCchhcCcEEEEEEccCCC
Confidence 99999999999999999986
No 5
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=100.00 E-value=1e-41 Score=231.28 Aligned_cols=79 Identities=38% Similarity=0.612 Sum_probs=71.9
Q ss_pred EEEEEEeeecccCCCCCCeeEEEecCccchHHhhhcCCC------ceeeEEEeEEEeecCCCceEEEEeCCCCCccCCCC
Q 040909 14 VRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKKNG------THYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGD 87 (98)
Q Consensus 14 ~kg~~lgykRg~~~Q~~~~aLlKieGV~~k~~Ak~~~~~------~k~RviwGKV~r~HGnsGvVrAkF~~nLPp~AiG~ 87 (98)
+||+|+|||||++||+|||||||||||+++|||+..... ...|+|||||||+|||||+|||+|++||||||||+
T Consensus 3 ~kgv~~gykRg~~nQ~~~~aLlkiegv~~~~~a~fylGKrv~yvyk~grviwGKItR~HGnsGvVrAkF~~nLP~~a~G~ 82 (87)
T PRK04337 3 MKGVILSYRRGKNTQYNRQVIIKPLGVDDREEAAKLIGRKVIWKDPTGNKYVGKIVRVHGNRGEVRARFKPGLPGQALGD 82 (87)
T ss_pred ceEEEEEeccccCccCCceEEEEEcCcCCHHHHHhhcCceEEEEeCCCCEEEEEEEeeeCCCceEEEEECCCCChHHcCC
Confidence 699999999999999999999999999999998865321 12489999999999999999999999999999999
Q ss_pred eEEEE
Q 040909 88 RVRVF 92 (98)
Q Consensus 88 ~VrVm 92 (98)
+|||.
T Consensus 83 ~vrv~ 87 (87)
T PRK04337 83 YVEII 87 (87)
T ss_pred EEEeC
Confidence 99983
No 6
>PF09853 DUF2080: Putative transposon-encoded protein (DUF2080); InterPro: IPR019205 This entry, found in various hypothetical archaeal proteins, has no known function.
Probab=95.93 E-value=0.016 Score=36.41 Aligned_cols=34 Identities=26% Similarity=0.471 Sum_probs=27.9
Q ss_pred EEEeEEEeecCCCceEEEEeCCCCCccCCCCeEEEEEee
Q 040909 57 CIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYP 95 (98)
Q Consensus 57 viwGKV~r~HGnsGvVrAkF~~nLPp~AiG~~VrVmLyp 95 (98)
+++++|+ +|||| |++..+||+.-+|.++.|.+..
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 5667766 99999 5677999999999999887643
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=89.61 E-value=0.45 Score=30.32 Aligned_cols=28 Identities=18% Similarity=0.445 Sum_probs=22.8
Q ss_pred EeEEEeecCCCceEEEEeCCCCCccCCC
Q 040909 59 WGKVARSHSNSGVVRAKFKSNLPPKSVG 86 (98)
Q Consensus 59 wGKV~r~HGnsGvVrAkF~~nLPp~AiG 86 (98)
-|+|.+|||-.|-|++..-.+.|.....
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 3999999999999999999887765443
No 8
>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional
Probab=89.02 E-value=0.48 Score=34.46 Aligned_cols=30 Identities=23% Similarity=0.403 Sum_probs=26.2
Q ss_pred eEEEeEEEeecCCCceEEEEeCCCCCccCC
Q 040909 56 RCIWGKVARSHSNSGVVRAKFKSNLPPKSV 85 (98)
Q Consensus 56 RviwGKV~r~HGnsGvVrAkF~~nLPp~Ai 85 (98)
.+..|+|++|||-.|-|+++.-...|...+
T Consensus 7 ~v~iG~i~~~hGlkGevkv~~~td~p~~~~ 36 (172)
T PRK00122 7 LLVVGKIVSAHGIKGEVKVKSFTDFPERIF 36 (172)
T ss_pred eEEEEEEECCCcccEEEEEEEecCCHHHHc
Confidence 477899999999999999999988886544
No 9
>PRK14594 rimM 16S rRNA-processing protein RimM; Provisional
Probab=88.66 E-value=0.44 Score=34.80 Aligned_cols=27 Identities=22% Similarity=0.086 Sum_probs=23.6
Q ss_pred EEEeEEEeecCCCceEEEEeCCCCCcc
Q 040909 57 CIWGKVARSHSNSGVVRAKFKSNLPPK 83 (98)
Q Consensus 57 viwGKV~r~HGnsGvVrAkF~~nLPp~ 83 (98)
++.|+|++|||=.|-|+++.-..-|+.
T Consensus 2 ~~iG~I~~~hGlkGevkV~~~td~~~~ 28 (166)
T PRK14594 2 FVKGIILSSYGINGYAKVKSISNNFCD 28 (166)
T ss_pred EEEEEEECceeeeEEEEEEEccCCHHH
Confidence 578999999999999999988776655
No 10
>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=87.74 E-value=1.7 Score=27.65 Aligned_cols=31 Identities=10% Similarity=0.253 Sum_probs=22.1
Q ss_pred EEEEeeecccCCCCCCeeEEEecCccchHHhhhcCC
Q 040909 16 GTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKKN 51 (98)
Q Consensus 16 g~~lgykRg~~~Q~~~~aLlKieGV~~k~~Ak~~~~ 51 (98)
-.+.+++ .+.+..|++++||+|+++|...++
T Consensus 45 ~~v~~~~-----~~~~~~i~~~~gi~~r~~Ae~l~g 75 (84)
T PF01782_consen 45 LKVESVR-----PHGKSLIVKFEGIDDREAAEALRG 75 (84)
T ss_dssp EEEEEEE-----EETTEEEEEETT--SHHHHHTTTT
T ss_pred EEEEEEE-----EeCCEEEEEEcCCCCHHHHHhhCC
Confidence 4555555 337899999999999999987654
No 11
>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=86.85 E-value=1.1 Score=32.30 Aligned_cols=30 Identities=23% Similarity=0.385 Sum_probs=25.5
Q ss_pred EEEeEEEeecCCCceEEEEeCCCCCccCCC
Q 040909 57 CIWGKVARSHSNSGVVRAKFKSNLPPKSVG 86 (98)
Q Consensus 57 viwGKV~r~HGnsGvVrAkF~~nLPp~AiG 86 (98)
+..|+|++|||=.|-|+++.-...|...+.
T Consensus 2 v~iG~I~~~hGlkGevkv~~~td~p~~~~~ 31 (165)
T TIGR02273 2 LVVGKIGGPHGIKGEVKVKSFTDFPESLFD 31 (165)
T ss_pred EEEEEEECCcccCEEEEEEEcCCCHHHHcC
Confidence 467999999999999999998888875543
No 12
>PRK14593 rimM 16S rRNA-processing protein RimM; Provisional
Probab=83.83 E-value=1.1 Score=33.11 Aligned_cols=29 Identities=17% Similarity=0.347 Sum_probs=25.0
Q ss_pred EEEeEEEeecCCCceEEEEeCCCCCccCC
Q 040909 57 CIWGKVARSHSNSGVVRAKFKSNLPPKSV 85 (98)
Q Consensus 57 viwGKV~r~HGnsGvVrAkF~~nLPp~Ai 85 (98)
+..|+|+++||-.|-|++..-..-|....
T Consensus 5 i~iG~I~~~hGikGevkv~~~td~pe~~~ 33 (184)
T PRK14593 5 LLVGRIGKSVGLNGGLKLHLESDFPECLK 33 (184)
T ss_pred EEEEEEECCEeeeEEEEEEECCCCHHHhc
Confidence 56799999999999999999988777543
No 13
>PRK14592 rimM 16S rRNA-processing protein RimM; Provisional
Probab=83.81 E-value=1.3 Score=32.12 Aligned_cols=29 Identities=21% Similarity=0.240 Sum_probs=25.1
Q ss_pred EEEeEEEeecCCCceEEEEeCCCCCccCC
Q 040909 57 CIWGKVARSHSNSGVVRAKFKSNLPPKSV 85 (98)
Q Consensus 57 viwGKV~r~HGnsGvVrAkF~~nLPp~Ai 85 (98)
+..|+|++|||=.|-|+++.-+.-|....
T Consensus 3 v~iG~I~~~hGlkGevkv~~~td~p~~~~ 31 (165)
T PRK14592 3 ICLGVITSPHGIKGHVKIKTFTEDPENIS 31 (165)
T ss_pred EEEEEEECCCccCEEEEEEECCCCHHHhc
Confidence 56799999999999999999988777543
No 14
>PRK14591 rimM 16S rRNA-processing protein RimM; Provisional
Probab=81.88 E-value=1.9 Score=31.45 Aligned_cols=29 Identities=10% Similarity=-0.094 Sum_probs=25.3
Q ss_pred eEEEeEEEeecCCCceEEEEeCCCCCccC
Q 040909 56 RCIWGKVARSHSNSGVVRAKFKSNLPPKS 84 (98)
Q Consensus 56 RviwGKV~r~HGnsGvVrAkF~~nLPp~A 84 (98)
-+..|+|.+|||=.|-|+++.-...|...
T Consensus 5 ~v~vG~I~~~hGlkGevkv~~~td~p~~~ 33 (169)
T PRK14591 5 FVEIAKIGATYKLNGELNLYPLANSIETL 33 (169)
T ss_pred EEEEEEEeCCccccEEEEEEECCCCHHHh
Confidence 46789999999999999999988877744
No 15
>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=81.18 E-value=1.3 Score=31.98 Aligned_cols=20 Identities=20% Similarity=0.458 Sum_probs=17.1
Q ss_pred CCCeeEEEecCccchHHhhh
Q 040909 29 YPNTSLIQIKGVNIKEEAKT 48 (98)
Q Consensus 29 ~~~~aLlKieGV~~k~~Ak~ 48 (98)
+.+..||+++|++|+++|..
T Consensus 55 ~~~~~lv~f~gi~~~~~Ae~ 74 (165)
T TIGR02273 55 QNNKLIVKFEGIDDREAAEA 74 (165)
T ss_pred ECCEEEEEECCCCCHHHHHH
Confidence 35578999999999999875
No 16
>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=79.77 E-value=3.6 Score=32.98 Aligned_cols=59 Identities=20% Similarity=0.264 Sum_probs=35.2
Q ss_pred CCCeeEEEecCccchHHhhhcCC-----CceeeEEEeEEEeecCCCceEEEEeCCCCCccCCCCeEEEEEe
Q 040909 29 YPNTSLIQIKGVNIKEEAKTKKN-----GTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMY 94 (98)
Q Consensus 29 ~~~~aLlKieGV~~k~~Ak~~~~-----~~k~RviwGKV~r~HGnsGvVrAkF~~nLPp~AiG~~VrVmLy 94 (98)
+-++|.||-= -++.+|..+.++ .+..| |.|..+-|..|.++|-|...|=. .+.|..-||
T Consensus 231 ~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 231 HKRTAVVRGM-FFNPEDVAWFKGAELRTKSGIR---GHIKESLGTHGYFKATFEDKIKQ---SDIVFMRLY 294 (297)
T ss_dssp ESSSCEECSS-SSTCCHHHHS-S--BEETTS-B---EEEEE-BTTTTBBEEEESS---S---S-EEEEE--
T ss_pred ECceEEhhhh-cCCHHHHHhhcCCEEEeeccCC---CEECeeECCCCcEEEEECCcCCC---CCEEEEecC
Confidence 3456766644 455666655433 24445 99999999999999999988754 466766666
No 17
>PRK14590 rimM 16S rRNA-processing protein RimM; Provisional
Probab=78.70 E-value=1.9 Score=31.68 Aligned_cols=27 Identities=11% Similarity=0.217 Sum_probs=23.5
Q ss_pred EEeEEEeecCCCceEEEEeCCCCCccC
Q 040909 58 IWGKVARSHSNSGVVRAKFKSNLPPKS 84 (98)
Q Consensus 58 iwGKV~r~HGnsGvVrAkF~~nLPp~A 84 (98)
..|+|++|||-.|-|++..-..-|...
T Consensus 2 ~vG~I~~~hGlkGevkv~~~td~pe~~ 28 (171)
T PRK14590 2 SLGQLGKPFGIKGWLRVNVRGETLHTL 28 (171)
T ss_pred eEEEEeCCEeeCeEEEEEEccCCHHHh
Confidence 469999999999999999888877743
No 18
>PRK14592 rimM 16S rRNA-processing protein RimM; Provisional
Probab=74.40 E-value=3.3 Score=30.09 Aligned_cols=21 Identities=29% Similarity=0.378 Sum_probs=17.4
Q ss_pred CCCCeeEEEecCccchHHhhh
Q 040909 28 QYPNTSLIQIKGVNIKEEAKT 48 (98)
Q Consensus 28 Q~~~~aLlKieGV~~k~~Ak~ 48 (98)
+..+..|++++||+|+++|..
T Consensus 51 ~~~~~~lv~f~gi~~~~~Ae~ 71 (165)
T PRK14592 51 IGANLVIAKISGINSRTEAEL 71 (165)
T ss_pred ecCCEEEEEEcCCCCHHHHHH
Confidence 345678999999999999874
No 19
>PRK13829 rimM 16S rRNA-processing protein RimM; Provisional
Probab=73.79 E-value=2.8 Score=30.50 Aligned_cols=22 Identities=18% Similarity=0.308 Sum_probs=18.0
Q ss_pred CCCCeeEEEecCccchHHhhhc
Q 040909 28 QYPNTSLIQIKGVNIKEEAKTK 49 (98)
Q Consensus 28 Q~~~~aLlKieGV~~k~~Ak~~ 49 (98)
.+.+..|++++||+|+++|...
T Consensus 48 ~~~~~~l~~f~gi~~r~~Ae~l 69 (162)
T PRK13829 48 RVGPELVLHLAGVTSREGAEAL 69 (162)
T ss_pred EECCEEEEEECCCCCHHHHHHh
Confidence 4456689999999999998753
No 20
>PRK13829 rimM 16S rRNA-processing protein RimM; Provisional
Probab=73.27 E-value=6 Score=28.71 Aligned_cols=24 Identities=17% Similarity=0.235 Sum_probs=20.1
Q ss_pred eEEEeEEEeecCCCceEEEEeCCCCCc
Q 040909 56 RCIWGKVARSHSNSGVVRAKFKSNLPP 82 (98)
Q Consensus 56 RviwGKV~r~HGnsGvVrAkF~~nLPp 82 (98)
.+..|+|++|||=.|-|+++ .-|.
T Consensus 3 ~i~iG~I~~~hGikGevkv~---d~p~ 26 (162)
T PRK13829 3 RTEIGRFGGPYGVQGGLKFR---GEPV 26 (162)
T ss_pred EEEEEEEeCCeeecEEEEEe---cchH
Confidence 35679999999999999998 4454
No 21
>PRK14591 rimM 16S rRNA-processing protein RimM; Provisional
Probab=71.92 E-value=3 Score=30.46 Aligned_cols=21 Identities=19% Similarity=0.344 Sum_probs=17.7
Q ss_pred CCCCeeEEEecCccchHHhhh
Q 040909 28 QYPNTSLIQIKGVNIKEEAKT 48 (98)
Q Consensus 28 Q~~~~aLlKieGV~~k~~Ak~ 48 (98)
++.+..|++++||+++++|..
T Consensus 59 ~~~~~~lv~f~gi~dr~~Ae~ 79 (169)
T PRK14591 59 KRADKVYIKLANINNADTAKK 79 (169)
T ss_pred EECCEEEEEEcCCCCHHHHHH
Confidence 445778999999999999875
No 22
>PRK13828 rimM 16S rRNA-processing protein RimM; Provisional
Probab=70.66 E-value=3.7 Score=29.75 Aligned_cols=21 Identities=24% Similarity=0.384 Sum_probs=17.4
Q ss_pred CCCCeeEEEecCccchHHhhh
Q 040909 28 QYPNTSLIQIKGVNIKEEAKT 48 (98)
Q Consensus 28 Q~~~~aLlKieGV~~k~~Ak~ 48 (98)
++.+..|++++||+|+++|+.
T Consensus 39 ~~~~~~lv~f~gi~dr~~Ae~ 59 (161)
T PRK13828 39 PAKDGLVARLKGVATREAAEA 59 (161)
T ss_pred EECCEEEEEECCCCCHHHHHH
Confidence 345668999999999999874
No 23
>PRK14594 rimM 16S rRNA-processing protein RimM; Provisional
Probab=67.31 E-value=4.3 Score=29.58 Aligned_cols=20 Identities=25% Similarity=0.301 Sum_probs=16.8
Q ss_pred CCCeeEEEecCccchHHhhh
Q 040909 29 YPNTSLIQIKGVNIKEEAKT 48 (98)
Q Consensus 29 ~~~~aLlKieGV~~k~~Ak~ 48 (98)
+.+..|++++|++|+++|..
T Consensus 57 ~~~~~lvkf~gi~dr~~Ae~ 76 (166)
T PRK14594 57 KNNSLLLKFEEFNAPEPIKP 76 (166)
T ss_pred ECCEEEEEEcCCCCHHHHHH
Confidence 35568999999999999874
No 24
>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional
Probab=66.08 E-value=4.8 Score=29.19 Aligned_cols=20 Identities=15% Similarity=0.320 Sum_probs=16.8
Q ss_pred CCCeeEEEecCccchHHhhh
Q 040909 29 YPNTSLIQIKGVNIKEEAKT 48 (98)
Q Consensus 29 ~~~~aLlKieGV~~k~~Ak~ 48 (98)
+.+..|+|++|++|+++|..
T Consensus 60 ~~~~~lvkf~gi~~~~~Ae~ 79 (172)
T PRK00122 60 HKGFLIVKFEGVDDRNAAEA 79 (172)
T ss_pred ECCEEEEEECCCCCHHHHHH
Confidence 34568999999999999774
No 25
>COG3466 ISA1214 Putative transposon-encoded protein [Function unknown]
Probab=63.49 E-value=18 Score=22.77 Aligned_cols=32 Identities=28% Similarity=0.511 Sum_probs=24.7
Q ss_pred eEEEeEEEeecCCCceEEEEeCCCCCccCCCCeEEEEE
Q 040909 56 RCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFM 93 (98)
Q Consensus 56 RviwGKV~r~HGnsGvVrAkF~~nLPp~AiG~~VrVmL 93 (98)
.+..=+...|-||||.|- .|-.-+|.+|.|..
T Consensus 18 e~~~ek~VtpfGnsakVd------vPK~yiG~rv~viI 49 (52)
T COG3466 18 EVVFEKRVTPFGNSAKVD------VPKRYIGKRVYVII 49 (52)
T ss_pred EEEEEEEEEecCCcceee------CchHHcCcEEEEEE
Confidence 344445555999999985 68999999998865
No 26
>PF14444 S1-like: S1-like
Probab=61.12 E-value=29 Score=22.12 Aligned_cols=36 Identities=36% Similarity=0.548 Sum_probs=28.1
Q ss_pred eEEEeEEEeecCCCceE--EEEeC-----CCCCccCCCCeEEEEE
Q 040909 56 RCIWGKVARSHSNSGVV--RAKFK-----SNLPPKSVGDRVRVFM 93 (98)
Q Consensus 56 RviwGKV~r~HGnsGvV--rAkF~-----~nLPp~AiG~~VrVmL 93 (98)
|+.-|-||..|++-|.+ -.-|. -++| ..|++|.+--
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 68899999999999998 44454 3566 5999998753
No 27
>PRK14590 rimM 16S rRNA-processing protein RimM; Provisional
Probab=60.08 E-value=7.3 Score=28.63 Aligned_cols=22 Identities=23% Similarity=0.237 Sum_probs=17.8
Q ss_pred CCCCeeEEEecCccchHHhhhc
Q 040909 28 QYPNTSLIQIKGVNIKEEAKTK 49 (98)
Q Consensus 28 Q~~~~aLlKieGV~~k~~Ak~~ 49 (98)
++.+..|++++||+|+++|+..
T Consensus 55 ~~~~~~lv~f~gi~~~e~Ae~L 76 (171)
T PRK14590 55 PHGGKFLVRFEGYDTPEEAVKW 76 (171)
T ss_pred EECCEEEEEECCCCCHHHHHHh
Confidence 4456689999999999998753
No 28
>PRK14593 rimM 16S rRNA-processing protein RimM; Provisional
Probab=55.80 E-value=17 Score=26.84 Aligned_cols=15 Identities=27% Similarity=0.457 Sum_probs=13.3
Q ss_pred EEEecCccchHHhhh
Q 040909 34 LIQIKGVNIKEEAKT 48 (98)
Q Consensus 34 LlKieGV~~k~~Ak~ 48 (98)
+++++||+|+++|..
T Consensus 66 ~v~f~gi~dr~~Ae~ 80 (184)
T PRK14593 66 LLFLETIHTPEKAKE 80 (184)
T ss_pred EEEEcCCCCHHHHHH
Confidence 689999999999764
No 29
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=50.28 E-value=30 Score=25.90 Aligned_cols=40 Identities=20% Similarity=0.261 Sum_probs=31.7
Q ss_pred eeEEEeEEEeecCCCceEEEEeCCCCCccCCCCeEEEEEe
Q 040909 55 YRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMY 94 (98)
Q Consensus 55 ~RviwGKV~r~HGnsGvVrAkF~~nLPp~AiG~~VrVmLy 94 (98)
-.+.-|||..+||=.|-||.+=.+.-|...+.-...+.+-
T Consensus 6 ~~~~vGkI~~t~Gi~GevrV~s~Td~~~~~~~~~~~~~~~ 45 (174)
T COG0806 6 NLLLVGKIVSTHGIRGEVRVKSFTDFPESLFDYGPWLLLK 45 (174)
T ss_pred ceEEEEEEEecccccEEEEEEECCCCHHHhcCcCcEEEec
Confidence 4578899999999999999998888887766655544443
No 30
>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=49.51 E-value=76 Score=21.21 Aligned_cols=39 Identities=28% Similarity=0.445 Sum_probs=26.1
Q ss_pred CceeeEEEeEEEeecCC-------Cc-eEEEEeCCCCCccCCCCeEEEE
Q 040909 52 GTHYRCIWGKVARSHSN-------SG-VVRAKFKSNLPPKSVGDRVRVF 92 (98)
Q Consensus 52 ~~k~RviwGKV~r~HGn-------sG-vVrAkF~~nLPp~AiG~~VrVm 92 (98)
+...| ++|||++.||+ .| .|.+.....+ ...+++-|.|.
T Consensus 15 gk~V~-ivGkV~~~~~~~~~~~~~Dg~~v~v~l~~~~-~~~~~~~vEVi 61 (101)
T cd04479 15 GKTVR-IVGKVEKVDGDSLTLISSDGVNVTVELNRPL-DLPISGYVEVI 61 (101)
T ss_pred CCEEE-EEEEEEEecCCeEEEEcCCCCEEEEEeCCCC-CcccCCEEEEE
Confidence 34566 66999999998 44 7777777654 34555556553
No 31
>KOG0189 consensus Phosphoadenosine phosphosulfate reductase [Amino acid transport and metabolism]
Probab=45.54 E-value=22 Score=28.57 Aligned_cols=32 Identities=19% Similarity=0.307 Sum_probs=27.8
Q ss_pred ceEEEEEEEeeecccCCCCCCeeEEEecCccc
Q 040909 11 KLYVRGTILGYKRSKSNQYPNTSLIQIKGVNI 42 (98)
Q Consensus 11 Rly~kg~~lgykRg~~~Q~~~~aLlKieGV~~ 42 (98)
-|-++|+|.|=|+++--.+..-.+|+|++|..
T Consensus 147 ~L~v~A~~TGrRksQ~gtRselpiVqvD~~fe 178 (261)
T KOG0189|consen 147 GLNVKAVFTGRRKSQGGTRSELPIVQVDPVFE 178 (261)
T ss_pred ccceeeEEecccccCCCcccccceEEecCccc
Confidence 36689999999999999999999999998843
No 32
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=42.17 E-value=27 Score=26.15 Aligned_cols=24 Identities=17% Similarity=0.358 Sum_probs=19.9
Q ss_pred cCCCCCCeeEEEecCccchHHhhh
Q 040909 25 KSNQYPNTSLIQIKGVNIKEEAKT 48 (98)
Q Consensus 25 ~~~Q~~~~aLlKieGV~~k~~Ak~ 48 (98)
....+.|-.+++++|++++++|..
T Consensus 57 ~~r~~~~~~i~kf~gi~dr~~ae~ 80 (174)
T COG0806 57 SVRKHKNLLILKFKGIDDRNAAEA 80 (174)
T ss_pred EeeecCCEEEEEeCCCCCHHHHHH
Confidence 344578899999999999999764
No 33
>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=32.12 E-value=61 Score=27.42 Aligned_cols=38 Identities=29% Similarity=0.584 Sum_probs=28.5
Q ss_pred eeEEEeEEEeecCCCceEEEEeC---CCCCc-cCCCCeEEEEEee
Q 040909 55 YRCIWGKVARSHSNSGVVRAKFK---SNLPP-KSVGDRVRVFMYP 95 (98)
Q Consensus 55 ~RviwGKV~r~HGnsGvVrAkF~---~nLPp-~AiG~~VrVmLyp 95 (98)
.+.|+|+- .-|+|+|-+-|- .+|-+ +.+|..|+|..|-
T Consensus 40 GkPihGrA---WNn~GvveCSF~~~~~elt~~~dlgg~IQiLqy~ 81 (362)
T PF12150_consen 40 GKPIHGRA---WNNSGVVECSFPYDKAELTGKDDLGGQIQILQYK 81 (362)
T ss_dssp TEEEEEEE---EEETTEEEEEEEETTEEE-SCCCCTSEEEEEE-S
T ss_pred CCCcccce---ecCCceEEEEEEcccceeccccccCCEEEEEEEc
Confidence 34777765 578999999994 45766 8899999999883
No 34
>PF06312 Neurexophilin: Neurexophilin
Probab=30.78 E-value=91 Score=24.38 Aligned_cols=34 Identities=29% Similarity=0.354 Sum_probs=27.7
Q ss_pred EEeEEEeecCCCceEEEEeCCCCCccCCCCeEEEEEeec
Q 040909 58 IWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPN 96 (98)
Q Consensus 58 iwGKV~r~HGnsGvVrAkF~~nLPp~AiG~~VrVmLyps 96 (98)
+-|+|+ =||| |..-|.|.-+-|+++ .|.|.|-++
T Consensus 85 ~~G~V~-Dh~N-GTYtv~F~L~W~G~v---~vsV~LVHP 118 (219)
T PF06312_consen 85 AAGKVT-DHGN-GTYTVSFPLLWPGQV---SVSVSLVHP 118 (219)
T ss_pred ceEEEE-ECCC-CeEEEEEEeecCceE---EEEEEEEcc
Confidence 459999 7887 999999999999986 677777543
No 35
>COG5192 BMS1 GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=30.31 E-value=20 Score=33.01 Aligned_cols=22 Identities=32% Similarity=0.579 Sum_probs=19.5
Q ss_pred EEeEEEeecCCCceEEEEeCCC
Q 040909 58 IWGKVARSHSNSGVVRAKFKSN 79 (98)
Q Consensus 58 iwGKV~r~HGnsGvVrAkF~~n 79 (98)
|.|.|.+|||..|..||-|.--
T Consensus 889 lrgqvk~~~~k~g~yra~fe~k 910 (1077)
T COG5192 889 LRGQVKGPHGKNGEYRAVFEGK 910 (1077)
T ss_pred ccccccCccCCCccchheeccc
Confidence 4499999999999999999854
No 36
>KOG0461 consensus Selenocysteine-specific elongation factor [Translation, ribosomal structure and biogenesis]
Probab=28.48 E-value=79 Score=27.57 Aligned_cols=34 Identities=26% Similarity=0.581 Sum_probs=28.3
Q ss_pred eEEEeecCCCceEEEEeCCCCCccCCCC--eEEEEE
Q 040909 60 GKVARSHSNSGVVRAKFKSNLPPKSVGD--RVRVFM 93 (98)
Q Consensus 60 GKV~r~HGnsGvVrAkF~~nLPp~AiG~--~VrVmL 93 (98)
|+|-++-|.||.++.-|.-.|.|..+.. .|.|.|
T Consensus 470 G~Ie~aFGqsgKf~itf~~~lspe~~~~~~~v~~sL 505 (522)
T KOG0461|consen 470 GKIEGAFGQSGKFRITFAEKLSPELISNTEKVEISL 505 (522)
T ss_pred cceeccccCcceEEEEecccCChhhhccccceEEEE
Confidence 8999999999999999999999988643 344444
No 37
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=25.75 E-value=2.1e+02 Score=21.25 Aligned_cols=48 Identities=23% Similarity=0.208 Sum_probs=31.4
Q ss_pred CCeeEEEecCcc-chHHhhhc---CCCceeeEEEeEEEeecCCCceEEEEeCCCCCccCCC
Q 040909 30 PNTSLIQIKGVN-IKEEAKTK---KNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVG 86 (98)
Q Consensus 30 ~~~aLlKieGV~-~k~~Ak~~---~~~~k~RviwGKV~r~HGnsGvVrAkF~~nLPp~AiG 86 (98)
-..-+|||||.. +.+|+... ...-.+.+| ..+.|.-||+-.||.+..|
T Consensus 53 GkKDIIKIE~~~l~~~e~~~laliaP~aTiNiI---------~d~~VveK~~v~lP~~i~g 104 (152)
T PRK00893 53 GRKDIIKIENRFLSEEEVDQLALIAPNATINII---------RDYEVVEKRKVELPEEIEG 104 (152)
T ss_pred CcCCEEEECCcccCHhHhhheEEECCCCEEEEE---------eCCEEEEeccCCCCccccc
Confidence 345689999986 33555442 122344444 3688888999999987766
No 38
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=23.05 E-value=2.4e+02 Score=18.78 Aligned_cols=38 Identities=26% Similarity=0.368 Sum_probs=21.9
Q ss_pred CceeeEEEeEEEeec--CC--------CceEEEEeCCCCCccCCCCeEEE
Q 040909 52 GTHYRCIWGKVARSH--SN--------SGVVRAKFKSNLPPKSVGDRVRV 91 (98)
Q Consensus 52 ~~k~RviwGKV~r~H--Gn--------sGvVrAkF~~nLPp~AiG~~VrV 91 (98)
+...| |+|||.+.+ |. .|.|.+.+...++.+ .+.-|.|
T Consensus 18 gk~Vr-ivGkv~~~~~~g~~~~l~~~d~~~V~v~l~~~~~~~-~~~~vEv 65 (109)
T PF08661_consen 18 GKTVR-IVGKVESVDPDGGSATLSTSDGGQVTVSLNPPSDEE-LSKYVEV 65 (109)
T ss_dssp TSEEE-EEEEEEEE-TTSSEEEEE-TTS-EEEEEESS--SS----SEEEE
T ss_pred CCeEE-EEEEEeeEcCCCCEEEEEcCCCCEEEEEeCCCCCCC-CCCEEEE
Confidence 45566 669999999 65 477788888777653 3455544
No 39
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=22.66 E-value=74 Score=26.43 Aligned_cols=30 Identities=30% Similarity=0.627 Sum_probs=20.4
Q ss_pred CeeEEEecCccchHHhhh--------cCCCceeeEEEeEEE
Q 040909 31 NTSLIQIKGVNIKEEAKT--------KKNGTHYRCIWGKVA 63 (98)
Q Consensus 31 ~~aLlKieGV~~k~~Ak~--------~~~~~k~RviwGKV~ 63 (98)
-.|.||.| ++|.|.. ++.+.-.||.|||=.
T Consensus 201 GYaFVrF~---tkEaAahAIv~mNntei~G~~VkCsWGKe~ 238 (321)
T KOG0148|consen 201 GYAFVRFE---TKEAAAHAIVQMNNTEIGGQLVRCSWGKEG 238 (321)
T ss_pred ceEEEEec---chhhHHHHHHHhcCceeCceEEEEeccccC
Confidence 45778854 6665442 345788999999953
No 40
>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=21.18 E-value=56 Score=20.44 Aligned_cols=15 Identities=27% Similarity=0.304 Sum_probs=10.2
Q ss_pred EeecCCCceEEEEeC
Q 040909 63 ARSHSNSGVVRAKFK 77 (98)
Q Consensus 63 ~r~HGnsGvVrAkF~ 77 (98)
...+||+|++.+.|+
T Consensus 69 ~~~~g~~G~~~V~lk 83 (83)
T PF01713_consen 69 EPEDGNSGATIVYLK 83 (83)
T ss_dssp -CCCTGGGEEEEEE-
T ss_pred CCCCCCCeEEEEEeC
Confidence 346788888888775
No 41
>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=20.14 E-value=2.8e+02 Score=20.65 Aligned_cols=47 Identities=23% Similarity=0.287 Sum_probs=29.6
Q ss_pred CeeEEEecCccch-HHhhhc---CCCceeeEEEeEEEeecCCCceEEEEeCCCCCccCCC
Q 040909 31 NTSLIQIKGVNIK-EEAKTK---KNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVG 86 (98)
Q Consensus 31 ~~aLlKieGV~~k-~~Ak~~---~~~~k~RviwGKV~r~HGnsGvVrAkF~~nLPp~AiG 86 (98)
..-+|||||..-. +|+... ...-.+.+| ..+.|.-||+-.||...-|
T Consensus 52 kKDIIKIE~~~l~~~e~~~laliaP~aTiNiI---------~d~~Vv~K~~v~lP~~i~g 102 (150)
T TIGR00240 52 KKDIVKIENTFLKEEEVDQIALIAPQATINII---------RNYEVVEKSKPSLPEEIEG 102 (150)
T ss_pred cCCEEEECCcccCHhHhhheEEECCCCEEEEE---------eCCEEEEeccCCCChheee
Confidence 4568999999833 444432 122234444 2577888888888877654
Done!