Query gi|254780785|ref|YP_003065198.1| 30S ribosomal protein S15 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 89
No_of_seqs 106 out of 1519
Neff 5.0
Searched_HMMs 39220
Date Sun May 29 20:53:45 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780785.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00952 S15_bact ribosomal p 100.0 2.5E-43 0 260.4 10.7 86 4-89 1-86 (86)
2 PRK05626 rpsO 30S ribosomal pr 100.0 1.2E-38 3.1E-43 234.4 12.1 89 1-89 1-89 (89)
3 pfam00312 Ribosomal_S15 Riboso 100.0 4.8E-34 1.2E-38 209.0 11.1 82 7-88 2-83 (83)
4 CHL00027 rps15 ribosomal prote 100.0 6.5E-33 1.7E-37 202.8 10.0 79 11-89 8-86 (90)
5 COG0184 RpsO Ribosomal protein 100.0 1.5E-32 3.8E-37 200.8 10.5 89 1-89 1-89 (89)
6 cd00353 Ribosomal_S15p_S13e Ri 100.0 2.8E-32 7E-37 199.3 10.3 80 7-86 1-80 (80)
7 PTZ00119 40S ribosomal protein 99.9 3.6E-22 9.3E-27 143.4 8.4 85 4-88 106-190 (302)
8 KOG2815 consensus 99.7 8.2E-18 2.1E-22 119.4 4.2 74 15-88 176-249 (256)
9 cd00677 S15_NS1_EPRS_RNA-bind 99.4 2.1E-13 5.3E-18 95.0 4.9 46 26-71 1-46 (46)
10 PTZ00072 40S ribosomal protein 97.9 4.9E-05 1.2E-09 48.8 7.5 68 3-74 63-130 (148)
11 PRK08561 rps15p 30S ribosomal 97.9 4.2E-05 1.1E-09 49.1 7.1 66 5-74 68-133 (151)
12 KOG2815 consensus 97.6 6.3E-05 1.6E-09 48.2 3.2 81 7-87 90-170 (256)
13 KOG0400 consensus 90.7 0.4 1E-05 27.2 4.1 67 4-74 67-133 (151)
14 pfam10078 DUF2316 Uncharacteri 69.7 2.4 6.2E-05 22.8 1.5 46 1-46 1-47 (89)
15 pfam04778 LMP LMP repeated reg 38.4 37 0.00094 16.3 5.7 75 10-86 26-102 (157)
16 TIGR01240 mevDPdecarb diphosph 34.8 42 0.0011 16.0 4.3 44 43-86 196-254 (325)
17 COG4191 Signal transduction hi 30.4 48 0.0012 15.7 2.7 39 23-61 422-463 (603)
18 COG4259 Uncharacterized protei 29.3 50 0.0013 15.6 2.6 37 23-59 47-83 (121)
19 COG4367 Uncharacterized protei 22.9 70 0.0018 14.8 2.7 42 1-42 1-49 (97)
20 COG3799 Mal Methylaspartate am 20.3 79 0.002 14.5 2.8 24 17-40 270-293 (410)
No 1
>TIGR00952 S15_bact ribosomal protein S15; InterPro: IPR005290 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 of 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 , . This family includes specifically bacterial, chloroplast, and mitochondrial ribosomal protein S15. The homologous proteins of Archaea and Eukarya are designated S13. Escherichia coli ribosomal protein S15 has been shown to regulate the expression of its own mRNA by a feedback mechanism at the translational level. The translational operator overlaps the ribosome binding site and folds into two mutually exclusive structures, one consisting of two stem-loops (I and II) and the other one forming a pseudoknot. The two structures, which seem to be energetically equivalent are in dynamic equilibrium, and the pseudoknot is stabilized by binding of S15. However, binding of S15 does not prevent 30 S subunit binding but traps the subunit into an incompetent translation initiation complex. Repression can be alleviated by 16 S rRNA, which is able to displace the bound S15, thus allowing translation to proceed .; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome.
Probab=100.00 E-value=2.5e-43 Score=260.36 Aligned_cols=86 Identities=57% Similarity=0.862 Sum_probs=84.7
Q ss_pred CHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf 88999999999545888788899999997799999999999778413527789999997899999998409999999999
Q gi|254780785|r 4 TLERKRELMKEYAVSPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLERKDVERYKRLVQ 83 (89)
Q Consensus 4 ~~~~k~~~i~~f~~~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~~d~~~Y~~~i~ 83 (89)
+++.|++||++||.||+||||||||||+||+||++|||||+.||||++|+|||+.||++||+||+||+++|.++|..+|+
T Consensus 1 ~~e~K~~ii~~f~~hE~DTGS~~VQiAlLT~rI~~LteHLk~nkKDh~SRRGLL~lVg~RRrLL~Yl~~~d~e~Y~~LI~ 80 (86)
T TIGR00952 1 TKERKQEIIKEFQLHEKDTGSPEVQIALLTERINQLTEHLKANKKDHHSRRGLLKLVGRRRRLLKYLKRTDVERYRSLIK 80 (86)
T ss_pred CHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
T ss_conf 91248999998545899855889999999999988878875178983302799999997788999971016799999998
Q ss_pred HHCCCC
Q ss_conf 836899
Q gi|254780785|r 84 SLKLRR 89 (89)
Q Consensus 84 ~LglRk 89 (89)
.||||+
T Consensus 81 ~LGLR~ 86 (86)
T TIGR00952 81 KLGLRR 86 (86)
T ss_pred HCCCCC
T ss_conf 447999
No 2
>PRK05626 rpsO 30S ribosomal protein S15; Reviewed
Probab=100.00 E-value=1.2e-38 Score=234.43 Aligned_cols=89 Identities=56% Similarity=0.859 Sum_probs=88.5
Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf 98888999999999545888788899999997799999999999778413527789999997899999998409999999
Q gi|254780785|r 1 MSITLERKRELMKEYAVSPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLERKDVERYKR 80 (89)
Q Consensus 1 m~~~~~~k~~~i~~f~~~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~~d~~~Y~~ 80 (89)
|++++++|+++|++|++||+||||||||||+||+||.+|++||+.||||++|+|||.++|++|++||+||+++|+++|.+
T Consensus 1 M~~~k~~k~~li~kf~~~~~DTGS~eVQiA~LT~rI~~Lt~Hl~~n~KD~~s~RgL~~lv~kRkrlL~YL~~~d~~~Y~~ 80 (89)
T PRK05626 1 MSLTKEKKAEIIKEFGRHEGDTGSPEVQVALLTERINHLTEHLKEHKKDHHSRRGLLKMVGQRRKLLDYLKKKDVERYRA 80 (89)
T ss_pred CCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH
T ss_conf 99888999999999769999878789999999999999999998876625789999999999999999998668999999
Q ss_pred HHHHHCCCC
Q ss_conf 999836899
Q gi|254780785|r 81 LVQSLKLRR 89 (89)
Q Consensus 81 ~i~~LglRk 89 (89)
+|++|||||
T Consensus 81 ~i~~LgLRk 89 (89)
T PRK05626 81 LIEKLGLRR 89 (89)
T ss_pred HHHHHCCCC
T ss_conf 999958999
No 3
>pfam00312 Ribosomal_S15 Ribosomal protein S15.
Probab=100.00 E-value=4.8e-34 Score=209.04 Aligned_cols=82 Identities=45% Similarity=0.653 Sum_probs=80.3
Q ss_pred HHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHC
Q ss_conf 99999999545888788899999997799999999999778413527789999997899999998409999999999836
Q gi|254780785|r 7 RKRELMKEYAVSPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLERKDVERYKRLVQSLK 86 (89)
Q Consensus 7 ~k~~~i~~f~~~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~~d~~~Y~~~i~~Lg 86 (89)
.|+.+|++|+++|+||||||||||+||+||.+|++||+.||||++|+|||..+|++|++||+||+++|+++|.++|++||
T Consensus 2 ~k~~~I~~f~~~~~DTGS~evQiA~lT~rI~~Lt~Hl~~~~KD~~srRgL~~lv~kRrrlL~YL~~~d~~~Y~~~i~~Lg 81 (83)
T pfam00312 2 AKGLKISEFLKAEKDTGSVEVQLALLTERIVRLRKHLEEHKKDYSSKRGLIKLVSKRRRLLRYLKKKNTVRYENLIEQLG 81 (83)
T ss_pred CHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHC
T ss_conf 47689999769999868899999999999999999998578863269999999999999999998579999999999838
Q ss_pred CC
Q ss_conf 89
Q gi|254780785|r 87 LR 88 (89)
Q Consensus 87 lR 88 (89)
||
T Consensus 82 lR 83 (83)
T pfam00312 82 LR 83 (83)
T ss_pred CC
T ss_conf 89
No 4
>CHL00027 rps15 ribosomal protein S15
Probab=100.00 E-value=6.5e-33 Score=202.76 Aligned_cols=79 Identities=35% Similarity=0.514 Sum_probs=76.0
Q ss_pred HHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCC
Q ss_conf 9999545888788899999997799999999999778413527789999997899999998409999999999836899
Q gi|254780785|r 11 LMKEYAVSPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLERKDVERYKRLVQSLKLRR 89 (89)
Q Consensus 11 ~i~~f~~~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~~d~~~Y~~~i~~LglRk 89 (89)
.+..++.+++||||||||||+||+||.+|++||+.|+||+||+|||++||++|++||+||+++|+++|..+|++||||+
T Consensus 8 ~~~s~~~~e~DTGS~eVQIAlLT~rI~~Lt~Hlk~~kKD~~srRgL~~lV~kRrrLL~YL~~kd~~~Y~~li~~LgiRk 86 (90)
T CHL00027 8 SVISQEEKEENRGSVEFQVFSFTNKIRRLTSHLELHKKDYSSQRGLRKILGKRQRLLAYLSKKNRVRYKELISQLGIRE 86 (90)
T ss_pred HHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCC
T ss_conf 8888872368878954657768989999999998779830029999999999999999998569999999999919987
No 5
>COG0184 RpsO Ribosomal protein S15P/S13E [Translation, ribosomal structure and biogenesis]
Probab=99.98 E-value=1.5e-32 Score=200.80 Aligned_cols=89 Identities=58% Similarity=0.770 Sum_probs=88.1
Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf 98888999999999545888788899999997799999999999778413527789999997899999998409999999
Q gi|254780785|r 1 MSITLERKRELMKEYAVSPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLERKDVERYKR 80 (89)
Q Consensus 1 m~~~~~~k~~~i~~f~~~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~~d~~~Y~~ 80 (89)
|+++.+.+++++++|+.++.||||+|||||+||+||++|++||+.||||+||+|||+.||++|++||+||+++|.++|.|
T Consensus 1 m~~~~~~k~~l~~eyg~~~~dtgs~evq~a~Lt~ri~~L~~Hlk~hkKD~~srRGL~~~vskrrrLl~Ylk~~~~~~y~~ 80 (89)
T COG0184 1 MSLTSEIKQELRDEYGIPEVDTGSGEVQLALLTERINNLTEHLKEHKKDHHSRRGLLLLVSKRRRLLKYLKRKDVLRYRW 80 (89)
T ss_pred CCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 98608999999999388988899849999999999999999999777605679879999999999999987558531899
Q ss_pred HHHHHCCCC
Q ss_conf 999836899
Q gi|254780785|r 81 LVQSLKLRR 89 (89)
Q Consensus 81 ~i~~LglRk 89 (89)
+++.||||+
T Consensus 81 li~~lglr~ 89 (89)
T COG0184 81 LIKKLGLRR 89 (89)
T ss_pred HHHHHHCCC
T ss_conf 887762459
No 6
>cd00353 Ribosomal_S15p_S13e Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome. S15 also plays an important autoregulatory role by binding and preventing its own mRNA from being translated. S15 has a predominantly alpha-helical fold that is highly structured except for the N-terminal alpha helix.
Probab=99.98 E-value=2.8e-32 Score=199.31 Aligned_cols=80 Identities=56% Similarity=0.827 Sum_probs=78.5
Q ss_pred HHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHC
Q ss_conf 99999999545888788899999997799999999999778413527789999997899999998409999999999836
Q gi|254780785|r 7 RKRELMKEYAVSPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLERKDVERYKRLVQSLK 86 (89)
Q Consensus 7 ~k~~~i~~f~~~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~~d~~~Y~~~i~~Lg 86 (89)
+++++|++|+.+|+||||+|||||+||+||.+|++||+.||||++|+|||+.+|++|++||+||+++|+++|.+++++||
T Consensus 1 ~k~~ii~~~~~~~~DtGS~evQia~LT~rI~~L~~Hl~~~kkD~~skrgL~~lv~kRrrLL~YLkr~d~~~y~~~i~~Lg 80 (80)
T cd00353 1 KKQEILKEFGLAEGDTGSPEVQLALLTERIVNLTEHLEKNKKDKHSKRGLLLLVSKRRRLLKYLKRKDRLRYEWLIEKLG 80 (80)
T ss_pred CHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCC
T ss_conf 97899998779999878799999999999999999998877621789999999999999999998668999999999829
No 7
>PTZ00119 40S ribosomal protein S15; Provisional
Probab=99.87 E-value=3.6e-22 Score=143.39 Aligned_cols=85 Identities=35% Similarity=0.443 Sum_probs=81.0
Q ss_pred CHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf 88999999999545888788899999997799999999999778413527789999997899999998409999999999
Q gi|254780785|r 4 TLERKRELMKEYAVSPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLERKDVERYKRLVQ 83 (89)
Q Consensus 4 ~~~~k~~~i~~f~~~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~~d~~~Y~~~i~ 83 (89)
...++-.+.+..|+.|.||||++||||.||++|.++.+|+..|++|...+|.+.+++++|.++|+||.++|||.|.++|.
T Consensus 106 h~~rkl~l~r~LQR~PfDTgS~pVqiacLTeKIlNlRaHli~~~rD~~~Kr~m~i~L~RR~klMK~Ly~~dfelykhvc~ 185 (302)
T PTZ00119 106 HKYKKLIIRRHLQRRPFDTGSAPVQIGCLTEKILNLRAHLIRRCKDHCKKRTMSILLARRQKLMKYLYKTDFELYKHTCQ 185 (302)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCCEEHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999604887679955311788999988999986443103778999999998999999998600699999999
Q ss_pred HHCCC
Q ss_conf 83689
Q gi|254780785|r 84 SLKLR 88 (89)
Q Consensus 84 ~LglR 88 (89)
.|+|+
T Consensus 186 ~L~ik 190 (302)
T PTZ00119 186 LLKIK 190 (302)
T ss_pred HHCCE
T ss_conf 75533
No 8
>KOG2815 consensus
Probab=99.70 E-value=8.2e-18 Score=119.35 Aligned_cols=74 Identities=41% Similarity=0.513 Sum_probs=73.1
Q ss_pred HCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCC
Q ss_conf 54588878889999999779999999999977841352778999999789999999840999999999983689
Q gi|254780785|r 15 YAVSPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLERKDVERYKRLVQSLKLR 88 (89)
Q Consensus 15 f~~~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~~d~~~Y~~~i~~LglR 88 (89)
|++++.||||++||+|.+|.+|.+++.|++.|+||.++.+||..+|.+|+++|+||++.|+++|..++++||+|
T Consensus 176 ~~~~e~dtgs~~vQ~~~~t~~i~~~~r~~~~Hkkd~~~~~~l~~~~qkR~r~Lkyl~~~~~~~y~~~~~kl~~r 249 (256)
T KOG2815 176 FQRFESDTGSAEVQAAFPTVEIRKLSRHEELHKKDQASVRGLRQEVQKRQRALKYLARANRQRYVRTIKKLALR 249 (256)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCC
T ss_conf 52011224466576776889999998899998889888889999999999999999986785414532220225
No 9
>cd00677 S15_NS1_EPRS_RNA-bind S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism.
Probab=99.41 E-value=2.1e-13 Score=95.01 Aligned_cols=46 Identities=59% Similarity=0.757 Sum_probs=44.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999997799999999999778413527789999997899999998
Q gi|254780785|r 26 EVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLE 71 (89)
Q Consensus 26 evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk 71 (89)
|||||++|++|++|++|++.||||+++++||..+|++|++|++||+
T Consensus 1 ~vqia~lt~rI~~L~~h~~~~~kD~~~kr~L~~~v~kr~~Ll~ylk 46 (46)
T cd00677 1 EVQIALLTERIRNLKEHLAKNKKDKHSKRGLDLLVSKRLRLLKYLK 46 (46)
T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf 9103579999999999998779963018779999999999987719
No 10
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=97.94 E-value=4.9e-05 Score=48.79 Aligned_cols=68 Identities=22% Similarity=0.319 Sum_probs=53.4
Q ss_pred CCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 888999999999545888788899999997799999999999778413527789999997899999998409
Q gi|254780785|r 3 ITLERKRELMKEYAVSPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLERKD 74 (89)
Q Consensus 3 ~~~~~k~~~i~~f~~~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~~d 74 (89)
++..+..++.++-+..|. -||--..++ .+-.++..||+.|+||.+++|+|...-++-+||-+|.+++.
T Consensus 63 vtG~ki~~ILk~~gl~p~---iPEDL~~Li-kKAv~irkHLe~n~KD~~~kr~L~LiESkI~RL~rYYk~~~ 130 (148)
T PTZ00072 63 VTGRKILRILKHRGLAPE---IPEDLYFLI-KKAVQMRKHLERNRKDKDSKFRLILVESRIHRLARYYKRVK 130 (148)
T ss_pred CCCCHHHHHHHHCCCCCC---CCHHHHHHH-HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 135639999998799899---958999999-99999999998765532457899999999999999986067
No 11
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=97.93 E-value=4.2e-05 Score=49.12 Aligned_cols=66 Identities=27% Similarity=0.446 Sum_probs=50.2
Q ss_pred HHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 8999999999545888788899999997799999999999778413527789999997899999998409
Q gi|254780785|r 5 LERKRELMKEYAVSPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLERKD 74 (89)
Q Consensus 5 ~~~k~~~i~~f~~~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~~d 74 (89)
..+..++.++-+..|. -||--..+ -.+-.++..|++.|+||.+++|+|...-++-+||-+|.+++.
T Consensus 68 Gkki~~iLk~~gl~p~---iPEDL~~L-ikkAv~lrkHLe~n~kD~~~Kr~L~LiESkI~RL~rYYk~~~ 133 (151)
T PRK08561 68 GKKITEILEENGLAPE---IPEDLMNL-IKKAVNLRKHLEENPKDLHNKRGLQLIESKIRRLVKYYKRTG 133 (151)
T ss_pred CCCHHHHHHHCCCCCC---CCHHHHHH-HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 7839999997699888---96799999-999999999998756426668999999999999999987148
No 12
>KOG2815 consensus
Probab=97.55 E-value=6.3e-05 Score=48.15 Aligned_cols=81 Identities=28% Similarity=0.347 Sum_probs=76.7
Q ss_pred HHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHC
Q ss_conf 99999999545888788899999997799999999999778413527789999997899999998409999999999836
Q gi|254780785|r 7 RKRELMKEYAVSPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLERKDVERYKRLVQSLK 86 (89)
Q Consensus 7 ~k~~~i~~f~~~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~~d~~~Y~~~i~~Lg 86 (89)
..++++++.+.|+.|.+|.|.++|-+|+-|..-+.|+.....+.+....+..+..+|.+.++||+..|..++.++...|.
T Consensus 90 ~~~el~ke~~~~~~~~~~~e~k~~k~t~a~~~d~~~~~~~~~e~~~~~r~~l~~~kr~~~lril~~~n~ss~e~~k~~lk 169 (256)
T KOG2815 90 EKAELSKEVKNHKQDNNSLEEKFAKKTAAIRRDTFELEAIIIELSGKIRIKLLIDKREKILRILRRRNLSSFEKIKIKLK 169 (256)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCHHHHHCHHHHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 99999999998788877889999998886101088772300555130247534537889999862311114999999998
Q ss_pred C
Q ss_conf 8
Q gi|254780785|r 87 L 87 (89)
Q Consensus 87 l 87 (89)
+
T Consensus 170 ~ 170 (256)
T KOG2815 170 L 170 (256)
T ss_pred H
T ss_conf 7
No 13
>KOG0400 consensus
Probab=90.71 E-value=0.4 Score=27.18 Aligned_cols=67 Identities=21% Similarity=0.301 Sum_probs=50.0
Q ss_pred CHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 88999999999545888788899999997799999999999778413527789999997899999998409
Q gi|254780785|r 4 TLERKRELMKEYAVSPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLERKD 74 (89)
Q Consensus 4 ~~~~k~~~i~~f~~~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~~d 74 (89)
+.++.-.+.+.-|.-|. -|| -...|-.+-..+..||+.|+||..++-.|+..-++--|+-.|.+++-
T Consensus 67 ~G~kI~Rilk~~Gl~Pe---iPe-DLy~likkAv~iRkHLer~RKD~d~K~RLILveSRihRlARYYk~~~ 133 (151)
T KOG0400 67 TGNKILRILKSNGLAPE---IPE-DLYHLIKKAVAIRKHLERNRKDKDAKFRLILVESRIHRLARYYKTKM 133 (151)
T ss_pred HHHHHHHHHHHCCCCCC---CCH-HHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEHHHHHHHHHHHHHCC
T ss_conf 00699999997699889---938-89999999999999998741266642578863678999999997414
No 14
>pfam10078 DUF2316 Uncharacterized protein conserved in bacteria (DUF2316). Members of this family of hypothetical bacterial proteins have no known function.
Probab=69.73 E-value=2.4 Score=22.82 Aligned_cols=46 Identities=20% Similarity=0.138 Sum_probs=34.6
Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCCHHHHHHH-HHHHHHHHHHHHHHC
Q ss_conf 9888899999999954588878889999999-779999999999977
Q gi|254780785|r 1 MSITLERKRELMKEYAVSPGDTGSPEVQVAV-CTERIANLTEHFKSA 46 (89)
Q Consensus 1 m~~~~~~k~~~i~~f~~~~~DtGS~evQIA~-lT~rI~~L~~Hl~~~ 46 (89)
||+++++++...+++|.|-.-+|-+..|||- |..-+..+..-|..+
T Consensus 1 MSLn~~Q~~~T~~ELqeNf~~~~ls~~~iA~dL~~s~~~ve~vL~m~ 47 (89)
T pfam10078 1 MSLNIEEMQATRKELQANFELSGLTIEQVAKDLNTTPEKVEALLQLK 47 (89)
T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC
T ss_conf 99889999999999999998838989999989499999999999734
No 15
>pfam04778 LMP LMP repeated region. This family consists of a repeated sequence element found in the LMP group of surface-located membrane proteins of Mycoplasma hominis. The the number of repeats in the protein affects the tendency of cells to spontaneously aggregate. Agglutination may be an important factor in colonisation. Non-agglutinating microorganisms might easily be distributed whereas aggregation might provide a better chance to avoid an antibody response since some of the epitopes may be buried.
Probab=38.41 E-value=37 Score=16.31 Aligned_cols=75 Identities=20% Similarity=0.363 Sum_probs=59.0
Q ss_pred HHHHHHCC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHH-CCHHHHHHHHHHHC
Q ss_conf 99999545-8887888999999977999999999997784135277899999978999999984-09999999999836
Q gi|254780785|r 10 ELMKEYAV-SPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLER-KDVERYKRLVQSLK 86 (89)
Q Consensus 10 ~~i~~f~~-~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~-~d~~~Y~~~i~~Lg 86 (89)
++.+.-|. ..+||.|.+.-=..|+.+|...+.-|..+.+|+..+ +-.+-.-|+..=.++.. ++..-|..+|.+|.
T Consensus 26 EI~kAnq~v~sNnt~smqsak~SLd~KvtEi~~kL~~Fn~dKeak--F~eLeqtRk~IdeFi~~~knnpnYs~Lv~~L~ 102 (157)
T pfam04778 26 EIQKANQAVASNNTASMQSAKSSLDAKVTEITKKLETFNKDKDAK--FKELEQTRKDIDEFINTNKNNPNYSTLVKDLT 102 (157)
T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf 999999999807889998788889999999999999971008888--89999999989998712457930999999999
No 16
>TIGR01240 mevDPdecarb diphosphomevalonate decarboxylase; InterPro: IPR005935 Synonyms: mevalonate diphosphate decarboxylase; pyrophosphomevalonate decarboxylase. This group of enzymes belongs to the GHMP kinase domain superfamily. GHMP kinases are a unique class of ATP-dependent enzymes (the abbreviation of which refers to the original members: galactokinase, homoserine kinase, mevalonate kinase, and phosphomevalonate kinase) . Enzymes belonging to this superfamily contain three well-conserved motifs, the second of which has the typical sequence Pro-X-X-X-Gly-Leu-X-Ser-Ser-Ala and is involved in ATP binding . The phosphate binding loop in GHMP kinases is distinct from the classical P-loops found in many ATP/GTP binding proteins. The bound ADP molecule adopts a rare syn conformation and is in the opposite orientation from those bound to the P-loop-containing proteins . GHMP kinases display a distinctly bilobal appearance with their N-terminal subdomains dominated by a mixed beta-sheet flanked on one side by alpha-helices and their C-terminal subdomains containing a four stranded anti-parallel beta-sheet , , , . Diphosphomevalonate decarboxylase (mevalonate pyrophosphate decarboxylase, (4.1.1.33 from EC) catalyzes the decarboxylation of mevalonate pyrophosphate to isopentyl pyrophosphate (IPP) , the last step in the synthesis of IPP in the mevalonate pathway. Mevalonate is a key intermediate in the biosynthesis of sterols and non-sterol isoprenes in the mevalonate pathway. In mammals, the majority of mevalonate is converted into cholesterol. ATP + (R)-5-diphosphomevalonate = ADP + phosphate + isopentenyl diphosphate + CO2 ; GO: 0004163 diphosphomevalonate decarboxylase activity, 0008299 isoprenoid biosynthetic process.
Probab=34.81 E-value=42 Score=15.98 Aligned_cols=44 Identities=23% Similarity=0.279 Sum_probs=34.6
Q ss_pred HHHCCCCCCHHHHHHHHH--------------H-HHHHHHHHHHHCCHHHHHHHHHHHC
Q ss_conf 997784135277899999--------------9-7899999998409999999999836
Q gi|254780785|r 43 FKSAKKDVNSKIGLGRLI--------------S-LRSSLLKYLERKDVERYKRLVQSLK 86 (89)
Q Consensus 43 l~~~kKD~~s~rgL~~lv--------------~-kRkklL~YLk~~d~~~Y~~~i~~Lg 86 (89)
+..-|||.+|+.|+..-| . |=..|++|++.+||+...+..+.=+
T Consensus 196 ~nd~KK~vSSr~GM~ltv~TS~~f~ew~e~v~~dr~~~m~~aik~kdF~~~g~~t~~n~ 254 (325)
T TIGR01240 196 VNDIKKDVSSREGMKLTVETSELFKEWVESVVIDRFEVMKKAIKTKDFEKLGKETEANS 254 (325)
T ss_pred EECCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 31368874530356888987776422343100058999999973212899999998745
No 17
>COG4191 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]
Probab=30.43 E-value=48 Score=15.67 Aligned_cols=39 Identities=28% Similarity=0.396 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCC---CCCHHHHHHHHHH
Q ss_conf 88999999977999999999997784---1352778999999
Q gi|254780785|r 23 GSPEVQVAVCTERIANLTEHFKSAKK---DVNSKIGLGRLIS 61 (89)
Q Consensus 23 GS~evQIA~lT~rI~~L~~Hl~~~kK---D~~s~rgL~~lv~ 61 (89)
+--.-.|+-||+|+-.+++|++.+-. +....-.+..+|.
T Consensus 422 ~~Nl~~I~~LteRma~It~~Lk~FArk~~~a~~~v~l~~ai~ 463 (603)
T COG4191 422 RENLERISALTERMAAITAHLKSFARKSRDAAGPVSLREAIE 463 (603)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHH
T ss_conf 767999999999998899999998336766667765799999
No 18
>COG4259 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.32 E-value=50 Score=15.55 Aligned_cols=37 Identities=16% Similarity=0.148 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHH
Q ss_conf 8899999997799999999999778413527789999
Q gi|254780785|r 23 GSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRL 59 (89)
Q Consensus 23 GS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~l 59 (89)
-|+|.|+|-|-+-|.....---.-|--+|+.-||+.-
T Consensus 47 es~e~Q~~~le~~~ek~~ak~~~vpPG~HAhLGlLys 83 (121)
T COG4259 47 ESKEAQTAALEKYLEKIGAKNGAVPPGYHAHLGLLYS 83 (121)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH
T ss_conf 8788999999999999751489999727888777886
No 19
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.89 E-value=70 Score=14.78 Aligned_cols=42 Identities=21% Similarity=0.241 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCCHHHHHHH-H------HHHHHHHHHH
Q ss_conf 9888899999999954588878889999999-7------7999999999
Q gi|254780785|r 1 MSITLERKRELMKEYAVSPGDTGSPEVQVAV-C------TERIANLTEH 42 (89)
Q Consensus 1 m~~~~~~k~~~i~~f~~~~~DtGS~evQIA~-l------T~rI~~L~~H 42 (89)
||+++++++..-++||.|-.-+--+---||- | -++|.+++.|
T Consensus 1 MSLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr 49 (97)
T COG4367 1 MSLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQR 49 (97)
T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHC
T ss_conf 9889899998899999754406452999999958879999999988506
No 20
>COG3799 Mal Methylaspartate ammonia-lyase [Amino acid transport and metabolism]
Probab=20.34 E-value=79 Score=14.48 Aligned_cols=24 Identities=29% Similarity=0.362 Sum_probs=18.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 588878889999999779999999
Q gi|254780785|r 17 VSPGDTGSPEVQVAVCTERIANLT 40 (89)
Q Consensus 17 ~~~~DtGS~evQIA~lT~rI~~L~ 40 (89)
-.|-|.||.+.||-.+++=..-|+
T Consensus 270 EgP~DaGs~~aQI~~~a~i~~~L~ 293 (410)
T COG3799 270 EGPVDAGSKPAQIRLLAAITKELT 293 (410)
T ss_pred ECCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 266567888899999999999986
Done!