Query 030853
Match_columns 170
No_of_seqs 121 out of 1053
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 05:34:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030853.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030853hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00099 rplJ 50S ribosomal pr 100.0 7.2E-31 1.6E-35 208.0 13.1 120 43-165 1-121 (172)
2 cd05797 Ribosomal_L10 Ribosoma 100.0 2.8E-30 6E-35 201.5 13.2 119 44-165 1-120 (157)
3 COG0244 RplJ Ribosomal protein 100.0 2E-29 4.4E-34 201.1 12.1 123 41-166 1-125 (175)
4 cd00379 Ribosomal_L10_P0 Ribos 99.9 6.5E-27 1.4E-31 180.9 12.4 118 46-166 1-119 (155)
5 PF00466 Ribosomal_L10: Riboso 99.9 3.7E-26 8E-31 165.6 7.8 98 43-141 1-100 (100)
6 cd05796 Ribosomal_P0_like Ribo 99.9 5.6E-24 1.2E-28 167.7 10.0 123 46-170 1-137 (163)
7 cd05795 Ribosomal_P0_L10e Ribo 99.9 6E-24 1.3E-28 169.3 9.6 123 46-170 1-135 (175)
8 PRK04019 rplP0 acidic ribosoma 99.9 7.6E-23 1.6E-27 177.2 10.3 126 44-170 4-139 (330)
9 PTZ00135 60S acidic ribosomal 99.9 6.3E-22 1.4E-26 170.3 10.3 98 44-142 6-108 (310)
10 PTZ00240 60S ribosomal protein 99.8 3.7E-18 8E-23 147.5 11.6 110 44-154 4-134 (323)
11 KOG0816 Protein involved in mR 99.6 1.8E-15 4E-20 122.3 10.2 130 39-170 14-157 (223)
12 KOG0815 60S acidic ribosomal p 99.4 1.7E-12 3.7E-17 106.4 9.4 98 42-140 4-106 (245)
13 KOG4241 Mitochondrial ribosoma 99.2 3.2E-11 6.9E-16 98.4 4.6 112 50-166 77-189 (245)
14 TIGR00253 RNA_bind_YhbY putati 73.9 16 0.00036 26.4 6.3 72 52-125 6-85 (95)
15 COG1534 Predicted RNA-binding 72.7 22 0.00048 26.0 6.7 70 53-124 8-85 (97)
16 PRK10343 RNA-binding protein Y 71.0 19 0.0004 26.2 6.0 72 52-125 8-87 (97)
17 PF14226 DIOX_N: non-haem diox 46.4 63 0.0014 22.8 5.2 41 44-85 9-49 (116)
18 PF08800 VirE_N: VirE N-termin 44.7 27 0.00058 26.5 3.1 32 57-88 25-56 (136)
19 COG2429 Archaeal GTP cyclohydr 41.7 60 0.0013 27.5 4.9 54 96-155 164-217 (250)
20 CHL00197 carA carbamoyl-phosph 36.7 76 0.0016 28.5 5.2 81 63-161 193-277 (382)
21 COG4825 Uncharacterized membra 34.4 62 0.0013 28.6 4.1 43 103-145 166-208 (395)
22 PF08496 Peptidase_S49_N: Pept 33.9 97 0.0021 24.3 4.8 26 61-86 96-122 (155)
23 PF02700 PurS: Phosphoribosylf 33.3 78 0.0017 22.0 3.8 45 99-143 21-65 (80)
24 PF01591 6PF2K: 6-phosphofruct 32.5 73 0.0016 26.3 4.1 40 49-88 81-121 (222)
25 PF10678 DUF2492: Protein of u 30.4 1.1E+02 0.0023 21.5 4.0 37 45-81 19-55 (78)
26 TIGR03853 matur_matur probable 30.3 1.1E+02 0.0024 21.4 4.1 36 47-82 19-54 (77)
27 PF01740 STAS: STAS domain; I 29.0 1.1E+02 0.0023 21.5 4.1 64 49-112 25-105 (117)
28 PF01985 CRS1_YhbY: CRS1 / Yhb 26.8 55 0.0012 22.7 2.1 47 52-98 6-54 (84)
29 PF01583 APS_kinase: Adenylyls 26.0 2.2E+02 0.0048 22.2 5.6 50 45-94 56-107 (156)
30 PRK05783 hypothetical protein; 25.9 1.7E+02 0.0037 20.6 4.5 45 99-143 23-67 (84)
31 PF05165 GGDN: GGDN family; I 25.6 1.3E+02 0.0029 25.5 4.5 54 95-154 159-212 (246)
32 PF03993 DUF349: Domain of Unk 24.1 39 0.00085 22.3 0.9 40 43-89 31-70 (77)
33 PRK03511 minC septum formation 23.7 1.8E+02 0.004 24.0 5.0 59 51-109 28-96 (228)
34 PF01692 Paramyxo_C: Paramyxov 22.3 1.3E+02 0.0027 24.5 3.6 55 3-57 28-84 (204)
35 PRK00513 minC septum formation 21.5 3E+02 0.0065 22.4 5.9 45 49-93 29-81 (214)
36 PF09949 DUF2183: Uncharacteri 20.6 3.3E+02 0.0073 19.6 6.4 50 46-95 49-98 (100)
37 PF13716 CRAL_TRIO_2: Divergen 20.6 3.2E+02 0.0069 20.0 5.4 59 48-106 30-104 (149)
38 PF08140 Cuticle_1: Crustacean 20.6 49 0.0011 20.3 0.7 16 114-129 23-38 (40)
39 PF03802 CitX: Apo-citrate lya 20.5 2.7E+02 0.0058 21.9 5.2 56 100-162 59-118 (170)
No 1
>PRK00099 rplJ 50S ribosomal protein L10; Reviewed
Probab=99.97 E-value=7.2e-31 Score=207.96 Aligned_cols=120 Identities=32% Similarity=0.456 Sum_probs=115.1
Q ss_pred cChHHHHHHHHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCC-cEEEEEchHHHHHHHhCCCcccccccCcCcEEE
Q 030853 43 ISRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN-TKLIVAKNTLVYKAIEGTQWEALKPCMSGMNAW 121 (170)
Q Consensus 43 ~~r~~K~~~v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~-~~i~VvKNtL~r~AL~~t~~e~L~~~l~G~~al 121 (170)
|+|++|.+++++|++.|++|+.++++||+|++++++++||++|++. ++++|+|||||++||+++++++|.++|+|++++
T Consensus 1 m~r~~K~~~v~~l~~~l~~~~~v~v~~~~gl~~~~~~~lR~~lr~~~~~~~V~KNtL~~~Al~~~~~~~l~~~l~G~~al 80 (172)
T PRK00099 1 MNREEKKEIVAELAEKLKKAQSAVVADYRGLTVAQMTELRKKLREAGVEYKVVKNTLARRALEGTGFEGLDDLLKGPTAI 80 (172)
T ss_pred CCHHHHHHHHHHHHHHHHhCCEEEEEecCCCcHHHHHHHHHHHHHcCCEEEEehhHHHHHHHhcCCchhhhhhCcCCeEE
Confidence 5789999999999999999999999999999999999999999986 899999999999999999999999999999999
Q ss_pred EEeeCCChHHHHHHHHHHhhhcCCCcceeeEEEEcCeeeccccc
Q 030853 122 LFVHTEEIPAAIKPYRNFQKEKKLEENDFAGAVFEGVGYWIGGD 165 (170)
Q Consensus 122 vFs~~d~~~~~~K~i~~f~K~~~~~~l~ikgG~~dg~~ls~~~~ 165 (170)
+|++ +||.+++|++.+|+|+++ ++.++||++||++++.+++
T Consensus 81 ~fs~-~d~~~~~k~l~~f~K~~~--~~~l~gg~~eg~~l~~~~i 121 (172)
T PRK00099 81 AFSY-EDPVAAAKVLKDFAKDNK--KLEIKGGAIEGKVLDAEEV 121 (172)
T ss_pred EEeC-CChHHHHHHHHHHHhhCc--CceEEEEEECCEEcCHHHH
Confidence 9998 678899999999999987 7999999999999999865
No 2
>cd05797 Ribosomal_L10 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein and forms the base of the L7/L12 stalk, while the extended C-terminal helix binds to two or three dimers of the NTD of L7/L12 (L7 and L12 are identical except for an acetylated N-terminus). The L7/L12 stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-in
Probab=99.97 E-value=2.8e-30 Score=201.45 Aligned_cols=119 Identities=38% Similarity=0.516 Sum_probs=114.0
Q ss_pred ChHHHHHHHHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCC-cEEEEEchHHHHHHHhCCCcccccccCcCcEEEE
Q 030853 44 SRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN-TKLIVAKNTLVYKAIEGTQWEALKPCMSGMNAWL 122 (170)
Q Consensus 44 ~r~~K~~~v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~-~~i~VvKNtL~r~AL~~t~~e~L~~~l~G~~alv 122 (170)
.|++|.+++++|++.|++|+.++++||+|++++++++||++||+. ++++|+|||||++|+++++++++.++|+|+++++
T Consensus 1 ~~~~K~~~v~~l~~~l~~~~~v~v~~~~gl~~~~~~~lR~~lr~~~~~~~V~KNtL~~~Al~~t~~~~l~~~l~G~~al~ 80 (157)
T cd05797 1 NREKKEEIVAELKEKLKEAKSVVVADYRGLTVAQLTELRKELREAGVKLKVVKNTLAKRALEGTGFEDLDDLLKGPTAIA 80 (157)
T ss_pred ChHHHHHHHHHHHHHHHhCCEEEEEecCCCcHHHHHHHHHHHHHcCCEEEEehhHHHHHHHhcCCchhhHhhCcCCEEEE
Confidence 478999999999999999999999999999999999999999987 8999999999999999999999999999999999
Q ss_pred EeeCCChHHHHHHHHHHhhhcCCCcceeeEEEEcCeeeccccc
Q 030853 123 FVHTEEIPAAIKPYRNFQKEKKLEENDFAGAVFEGVGYWIGGD 165 (170)
Q Consensus 123 Fs~~d~~~~~~K~i~~f~K~~~~~~l~ikgG~~dg~~ls~~~~ 165 (170)
|++ +||.+++|++.+|.|+++ ++.++||++||++++.+++
T Consensus 81 f~~-~d~~~~~k~l~~f~k~~~--~~~~~gg~~eg~~l~~~~v 120 (157)
T cd05797 81 FSE-EDPVAAAKVLKDFAKENK--KLEIKGGVVEGKVLDAEEV 120 (157)
T ss_pred EeC-CChHHHHHHHHHHHHhCC--CcEEEEEEECCEecCHHHH
Confidence 998 579899999999999987 7999999999999999865
No 3
>COG0244 RplJ Ribosomal protein L10 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=2e-29 Score=201.07 Aligned_cols=123 Identities=33% Similarity=0.438 Sum_probs=116.1
Q ss_pred hccChHHHHHHHHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCC-cEEEEEchHHHHHHHhCCCcccccccCcCcE
Q 030853 41 AAISRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN-TKLIVAKNTLVYKAIEGTQWEALKPCMSGMN 119 (170)
Q Consensus 41 ~~~~r~~K~~~v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~-~~i~VvKNtL~r~AL~~t~~e~L~~~l~G~~ 119 (170)
|.+.+++|.++|++|++.|++|++++++||+|+++.|+++||++||+. ++++|+||||+++||++++++.|.++++||+
T Consensus 1 ~~~~~e~K~~~v~el~e~~~~s~~~~i~dy~Gl~~~ql~~lR~~lr~~g~~lkV~KNtL~~rAl~~~~~e~l~~~l~Gp~ 80 (175)
T COG0244 1 MALAREWKKELVAELKELIKESPSVVIVDYRGLTVAQLTELRKKLREAGAKLKVVKNTLLRRALEEAGLEGLDDLLKGPT 80 (175)
T ss_pred CCccHHHHHHHHHHHHHHHhhCCEEEEEEeCCCcHHHHHHHHHHHHhCCcEEEEEhhHHHHHHHHhcchhhHHHhccCCe
Confidence 457789999999999999999999999999999999999999999986 9999999999999999999999999999999
Q ss_pred EEEEeeCCChHHHHHHHHHHhhhc-CCCcceeeEEEEcCeeecccccc
Q 030853 120 AWLFVHTEEIPAAIKPYRNFQKEK-KLEENDFAGAVFEGVGYWIGGDF 166 (170)
Q Consensus 120 alvFs~~d~~~~~~K~i~~f~K~~-~~~~l~ikgG~~dg~~ls~~~~~ 166 (170)
+++|++ +||.+++|.+.+|+|.+ + ++.++||++||..++.+++-
T Consensus 81 ai~fs~-~dp~~~~K~~~~f~k~~~~--~~~~~~~~~eg~~l~~~~v~ 125 (175)
T COG0244 81 AIAFSN-EDPVAAAKLLKDFAKEAGD--KAPIKGGVPEGKVLGAAEVI 125 (175)
T ss_pred EEEEec-CCHHHHHHHHHHHhhhhcc--cceEEEEEecCcccCHHHHH
Confidence 999998 57999999999999995 6 79999999999999887653
No 4
>cd00379 Ribosomal_L10_P0 Ribosomal protein L10 family; composed of the large subunit ribosomal protein called L10 in bacteria, P0 in eukaryotes, and L10e in archaea, as well as uncharacterized P0-like eukaryotic proteins. In all three kingdoms, L10 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein and forms the base of the L7/L12 stalk, while the extended C-terminal helix binds to two or three dimers of the NTD of L7/L12 (L7 and L12 are identical except for an acetylated N-terminus). The L7/L12 stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been sho
Probab=99.94 E-value=6.5e-27 Score=180.92 Aligned_cols=118 Identities=36% Similarity=0.517 Sum_probs=111.8
Q ss_pred HHHHHHHHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCC-cEEEEEchHHHHHHHhCCCcccccccCcCcEEEEEe
Q 030853 46 TKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN-TKLIVAKNTLVYKAIEGTQWEALKPCMSGMNAWLFV 124 (170)
Q Consensus 46 ~~K~~~v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~-~~i~VvKNtL~r~AL~~t~~e~L~~~l~G~~alvFs 124 (170)
++|.+++++++++|++|+.++++||++++++++++||++|++. ++++|+|||||++||++++++++.++|+|+++++|+
T Consensus 1 ~~K~~~v~~l~~~l~~~~~v~v~~~~~l~~~~~~~lR~~l~~~~~~~~v~KNtl~~~Al~~t~~~~~~~~l~G~~~~~f~ 80 (155)
T cd00379 1 EKKEELVEELKELLKKYKSVVVVDYRGLTVAQLTELRKELRESGAKLKVGKNTLMRRALKGTGFEELKPLLKGPTALAFT 80 (155)
T ss_pred CchHHHHHHHHHHHHhCCEEEEEecCCCcHHHHHHHHHHHHHcCCEEEEEehHHHHHHHcCCCccchhhhCcCCEEEEEe
Confidence 4699999999999999999999999999999999999999988 999999999999999999999999999999999999
Q ss_pred eCCChHHHHHHHHHHhhhcCCCcceeeEEEEcCeeecccccc
Q 030853 125 HTEEIPAAIKPYRNFQKEKKLEENDFAGAVFEGVGYWIGGDF 166 (170)
Q Consensus 125 ~~d~~~~~~K~i~~f~K~~~~~~l~ikgG~~dg~~ls~~~~~ 166 (170)
+ +||.+++|++.+|.+.++ ++.++||++||++++++++.
T Consensus 81 ~-~~~~~~~k~~~~~~k~~~--~~~~k~g~~~~~v~~~~~~~ 119 (155)
T cd00379 81 N-EDPVEVAKVLKDFAKENK--KLFAKGGVVAGKVLDPAGVT 119 (155)
T ss_pred C-CChHHHHHHHHHHHHhCC--CceEEEEEEcCEecCHHHHH
Confidence 7 578899999999999887 68999999999999988653
No 5
>PF00466 Ribosomal_L10: Ribosomal protein L10; InterPro: IPR001790 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 [, ]. On the basis of sequence similarities the following prokaryotic and eukaryotic ribosomal proteins can be grouped: Bacterial 50S ribosomal protein L10; Archaebacterial acidic ribosomal protein P0 homologue (L10E); Eukaryotic 60S ribosomal protein P0 (L10E). This entry represents the ribosomal protein L10P family, with includes the above mentioned ribosomal proteins.; GO: 0042254 ribosome biogenesis, 0005622 intracellular; PDB: 3A1Y_G 3D5D_J 3PYT_I 3PYV_I 3D5B_J 3PYO_I 3PYR_I 3MS1_I 3MRZ_I 1VQ9_G ....
Probab=99.93 E-value=3.7e-26 Score=165.59 Aligned_cols=98 Identities=35% Similarity=0.576 Sum_probs=93.8
Q ss_pred cChHHHHHHHHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCC-cEEEEEchHHHHHHHhCCCcc-cccccCcCcEE
Q 030853 43 ISRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN-TKLIVAKNTLVYKAIEGTQWE-ALKPCMSGMNA 120 (170)
Q Consensus 43 ~~r~~K~~~v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~-~~i~VvKNtL~r~AL~~t~~e-~L~~~l~G~~a 120 (170)
|+|++|.+++++++++|++|+.+++++|+|++++++++||++|+++ ++++|+||+||++||++++++ +|.++|+|+++
T Consensus 1 m~~~~K~~~v~~~~~~l~~~~~v~v~~~~~l~~~~~~~lR~~l~~~~~~~~v~KN~l~~~Al~~~~~~~~l~~~l~G~~~ 80 (100)
T PF00466_consen 1 MTKEKKEEIVEELKELLKKSKYVIVVDYNGLSANQLQELRKELRKKGGKFKVVKNTLMKKALKNTGFEEALSPLLKGPTA 80 (100)
T ss_dssp -SCHHHHHHHHHHHHHHHCSSEEEEEECTTSCHHHHHHHHHHHHHHTEEEEECSHHHHHHHHHHHHTSSSSSCCTSSSEE
T ss_pred CcHHHHHHHHHHHHHHHHhCCEEEEEEeCCCCHHHHHHHHHHHHhcCcEEEEecHHHHHHHHhcCccccCccccccCCEE
Confidence 6799999999999999999999999999999999999999999988 999999999999999999998 89999999999
Q ss_pred EEEeeCCChHHHHHHHHHHhh
Q 030853 121 WLFVHTEEIPAAIKPYRNFQK 141 (170)
Q Consensus 121 lvFs~~d~~~~~~K~i~~f~K 141 (170)
++|++ +||.+++|++.+|+|
T Consensus 81 ~if~~-~d~~~~~k~l~~~~K 100 (100)
T PF00466_consen 81 LIFSN-EDPFEIAKILKKFAK 100 (100)
T ss_dssp EEEES-SSHHHHHHHHHHSTT
T ss_pred EEEEC-CCHHHHHHHHHHhcC
Confidence 99996 679999999999986
No 6
>cd05796 Ribosomal_P0_like Ribosomal protein L10 family, P0-like protein subfamily; composed of uncharacterized eukaryotic proteins with similarity to the 60S ribosomal protein P0, including the Saccharomyces cerevisiae protein called mRNA turnover protein 4 (MRT4). MRT4 may be involved in mRNA decay. P0 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. It occupies the L7/L12 stalk of the ribosome. The stalk is known to contain the binding site for elongation factors EF-G and EF-Tu; however, there is disagreement as to whether or not P0 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, P0 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WAS
Probab=99.90 E-value=5.6e-24 Score=167.75 Aligned_cols=123 Identities=15% Similarity=0.276 Sum_probs=103.1
Q ss_pred HHHHHHHHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCCcEEEEEchHHHHHHHhCCC-------cccccccCcCc
Q 030853 46 TKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGTQ-------WEALKPCMSGM 118 (170)
Q Consensus 46 ~~K~~~v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~~~i~VvKNtL~r~AL~~t~-------~e~L~~~l~G~ 118 (170)
++|.+++++|++.|++|+.+++++|+|++++|+++||+.||+. +++|+|||||++||++++ ++.|.++|+|+
T Consensus 1 e~K~~~v~~l~e~l~~y~~v~iv~~~gl~~~ql~~iR~~lr~~-~~~v~KNtl~~~Al~~~~~~~~~~~~~~L~~~l~G~ 79 (163)
T cd05796 1 ELKQKLVENIREAVDKYKYIYVFSVDNMRNNKLKDIRQEWKDS-RFFFGKNKVMQVALGRTPEDEYKPNLHKLSKYLKGQ 79 (163)
T ss_pred ChHHHHHHHHHHHHHhCCEEEEEEecCCCHHHHHHHHHHhcCC-EEEEEchHHHHHHHhhCccccccccHHHHHHHhCCC
Confidence 4699999999999999999999999999999999999999987 999999999999999874 78899999999
Q ss_pred EEEEEeeCCChHHHHHHHHHH-----hhhcC--CCcceeeEEEEcCeeeccccccccCC
Q 030853 119 NAWLFVHTEEIPAAIKPYRNF-----QKEKK--LEENDFAGAVFEGVGYWIGGDFAGSG 170 (170)
Q Consensus 119 ~alvFs~~d~~~~~~K~i~~f-----~K~~~--~~~l~ikgG~~dg~~ls~~~~~~~~~ 170 (170)
++++||+ +||.+++|++.+| +|.+. +..+.|..|-.+.-.-+....|+++|
T Consensus 80 ~~lift~-~dp~~v~k~l~~~~~~~~ar~G~iA~~dvvi~~G~~~~~p~~~~~~~~~lg 137 (163)
T cd05796 80 VGLLFTN-EPPEEVIEYFDSYSEPDFARAGSIATETVTLPEGPLEQFPHSMEPQLRKLG 137 (163)
T ss_pred EEEEEEC-CCHHHHHHHHHHcCCcccccCCCCCCceEEEeCCCCCCCCCCcchHHHHcC
Confidence 9999998 6799999999984 44442 33477777755443333344566554
No 7
>cd05795 Ribosomal_P0_L10e Ribosomal protein L10 family, P0 and L10e subfamily; composed of eukaryotic 60S ribosomal protein P0 and the archaeal P0 homolog, L10e. P0 or L10e forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). These eukaryotic and archaeal P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2.
Probab=99.90 E-value=6e-24 Score=169.31 Aligned_cols=123 Identities=20% Similarity=0.220 Sum_probs=104.1
Q ss_pred HHHHHHHHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCCcEEEEEchHHHHHHHhCCC-----cccccccCcCcEE
Q 030853 46 TKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGTQ-----WEALKPCMSGMNA 120 (170)
Q Consensus 46 ~~K~~~v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~~~i~VvKNtL~r~AL~~t~-----~e~L~~~l~G~~a 120 (170)
++|.+++++|++.+++|+.+++++|+|++++++++||+.||+.++++|+|||||++||++++ ++.|.++|+|+++
T Consensus 1 ~~K~~~v~el~e~l~~~~~v~v~~~~gl~~~ql~~lR~~lr~~~~~~v~KNtL~~~Al~~~~~~~~~~~~L~~~l~G~~~ 80 (175)
T cd05795 1 EWKKEYVEKLTELLKSYPKVLIVDADNVGSKQLQKIRRSLRGKAEILMGKNTLIRRALRNLGDENPELEKLLPYLKGNVG 80 (175)
T ss_pred ChHHHHHHHHHHHHHhCCEEEEEEecCCChHHHHHHHHHhhCCCEEEEechHHHHHHHHhcccccccHHHHHHHhcCCEE
Confidence 46999999999999999999999999999999999999999889999999999999999985 7889999999999
Q ss_pred EEEeeCCChHHHHHHHHH-----HhhhcC--CCcceeeEEEEcCeeeccccccccCC
Q 030853 121 WLFVHTEEIPAAIKPYRN-----FQKEKK--LEENDFAGAVFEGVGYWIGGDFAGSG 170 (170)
Q Consensus 121 lvFs~~d~~~~~~K~i~~-----f~K~~~--~~~l~ikgG~~dg~~ls~~~~~~~~~ 170 (170)
++||+ +||.+++|++.+ |+|.+. +..+.|..|..+ -.-++...|+++|
T Consensus 81 liFt~-~dp~~v~k~l~~~~~~~~ar~G~iA~~dvvi~~G~t~-~~p~~~~~~~~lg 135 (175)
T cd05795 81 FIFTN-GDPFEIRKILEENKVPAPAKPGAIAPCDVVVPAGPTG-MPPGPTSFFQALG 135 (175)
T ss_pred EEEEC-CCHHHHHHHHHHcCCcccccCCCccCceEEEcCCCcC-CCCCchHHHHHcC
Confidence 99998 679999999997 455542 345788888664 2223334666655
No 8
>PRK04019 rplP0 acidic ribosomal protein P0; Validated
Probab=99.88 E-value=7.6e-23 Score=177.20 Aligned_cols=126 Identities=22% Similarity=0.258 Sum_probs=107.9
Q ss_pred ChHHHHHHHHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCCcEEEEEchHHHHHHHhCCC---cccccccCcCcEE
Q 030853 44 SRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGTQ---WEALKPCMSGMNA 120 (170)
Q Consensus 44 ~r~~K~~~v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~~~i~VvKNtL~r~AL~~t~---~e~L~~~l~G~~a 120 (170)
-+++|.++|++|++.|++|++++|+||+|++++|+++||+.||+.++++|+|||||++||++++ ++.|.++|+|+++
T Consensus 4 ~~e~K~~~v~el~~~l~~~~~v~iv~~~gl~~~ql~~lR~~lr~~~~~~v~KNtL~~~Al~~~~~~~~~~L~~~l~G~~a 83 (330)
T PRK04019 4 VPEWKKEEVEELKELIKSYPVVGIVDLEGIPARQLQEIRRKLRGKAELKVSKNTLIKRALEEAGEEDLEKLEDYLEGQVA 83 (330)
T ss_pred hHHHHHHHHHHHHHHHHhCCEEEEEEcCCCCHHHHHHHHHHHHcCCEEEEEehHHHHHHHHhcCcccHHHHHhhccCCEE
Confidence 4788999999999999999999999999999999999999999889999999999999999998 9999999999999
Q ss_pred EEEeeCCChHHHHHHHHHHh-----hhcC--CCcceeeEEEEcCeeeccccccccCC
Q 030853 121 WLFVHTEEIPAAIKPYRNFQ-----KEKK--LEENDFAGAVFEGVGYWIGGDFAGSG 170 (170)
Q Consensus 121 lvFs~~d~~~~~~K~i~~f~-----K~~~--~~~l~ikgG~~dg~~ls~~~~~~~~~ 170 (170)
++||+ +||++++|++.+|. |.+. +..+.|..|..+.........|.++|
T Consensus 84 lift~-~dp~~v~k~l~~~~~~~~ak~G~iA~~divip~G~t~~~P~~~~~~l~~lg 139 (330)
T PRK04019 84 LIFTN-MNPFKLYKLLEKSKTPAPAKPGDIAPEDIVVPAGPTGFPPGPILSELQKLG 139 (330)
T ss_pred EEEEC-CCHHHHHHHHHHcCCcccCCCCCCCCCeEEEcCCCCCCCCcccHHHHHHcC
Confidence 99998 67999999999854 4432 23477777766655544445555554
No 9
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=99.87 E-value=6.3e-22 Score=170.30 Aligned_cols=98 Identities=26% Similarity=0.373 Sum_probs=92.4
Q ss_pred ChHHHHHHHHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCCcEEEEEchHHHHHHHhCC-----CcccccccCcCc
Q 030853 44 SRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGT-----QWEALKPCMSGM 118 (170)
Q Consensus 44 ~r~~K~~~v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~~~i~VvKNtL~r~AL~~t-----~~e~L~~~l~G~ 118 (170)
+|++|.+++++|++.|++|+.++|++|+|++++|+++||+.||++++++|+|||||++||+++ +++.|.++|+|+
T Consensus 6 ~re~K~~~v~~l~e~l~~y~~v~vv~~~nv~s~ql~~iR~~LR~~a~~~vgKNTL~r~AL~~~~~~~~~l~~L~~~LkG~ 85 (310)
T PTZ00135 6 KKAKKKAYFEKLYELLEKYKKILIVSVDNVGSKQMQDIRRSLRGKAELLMGKNTLIRKALKQRLEELPELEKLLPHVKGN 85 (310)
T ss_pred hHHHHHHHHHHHHHHHHhCCEEEEEEcCCCCHHHHHHHHHHHhcCCEEEEEehHHHHHHHhhCcccccChHHHHhhccCC
Confidence 588899999999999999999999999999999999999999988999999999999999986 588999999999
Q ss_pred EEEEEeeCCChHHHHHHHHHHhhh
Q 030853 119 NAWLFVHTEEIPAAIKPYRNFQKE 142 (170)
Q Consensus 119 ~alvFs~~d~~~~~~K~i~~f~K~ 142 (170)
++++||+ +|+.+++|++.+|.+.
T Consensus 86 ~gliFTn-~dp~ev~k~l~~~k~~ 108 (310)
T PTZ00135 86 VGFVFTK-DDLFEVKPVILENKVP 108 (310)
T ss_pred EEEEEEC-CCHHHHHHHHHHcCCc
Confidence 9999998 6799999999998764
No 10
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=99.76 E-value=3.7e-18 Score=147.53 Aligned_cols=110 Identities=18% Similarity=0.215 Sum_probs=93.9
Q ss_pred ChHHHHHHHHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCCcEEEEEchHHHHHHHhCCC-------cccc-----
Q 030853 44 SRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGTQ-------WEAL----- 111 (170)
Q Consensus 44 ~r~~K~~~v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~~~i~VvKNtL~r~AL~~t~-------~e~L----- 111 (170)
.+++|.+++++|++++++|+.++||++.|++++|++++|+.||+.++++|+|||||++||++++ +++|
T Consensus 4 ~~~~K~~~v~~l~~~l~~y~~v~Iv~~~nv~s~qlq~IR~~lrg~a~~~~GKNtlm~~AL~~~~~~~~~~~~~~ll~~~~ 83 (323)
T PTZ00240 4 ITTAKREYEERLVDCLTKYSCVLFVGMDNVRSQQVHDVRRALRGKAEFVMGKKTLQAKIVEKRAQAKKASAEAKLFNDQC 83 (323)
T ss_pred hhHHHHHHHHHHHHHHHhCCEEEEEEecCCCcHHHHHHHHHhhCCcEEEEecHHHHHHHHhhccccccchhHHHHhhhhc
Confidence 3456999999999999999999999999999999999999999889999999999999999763 4566
Q ss_pred --cccCcCcEEEEEeeCCChHHHHHHHHH-----HhhhcC--CCcceeeEEE
Q 030853 112 --KPCMSGMNAWLFVHTEEIPAAIKPYRN-----FQKEKK--LEENDFAGAV 154 (170)
Q Consensus 112 --~~~l~G~~alvFs~~d~~~~~~K~i~~-----f~K~~~--~~~l~ikgG~ 154 (170)
.++++|+++++||+ +||.++.++|.+ ++|.+. +..+.|..|-
T Consensus 84 ~~~~~l~GnvgliFTn-~~p~ev~~~l~~~k~~a~AraG~IAp~dVvvpaG~ 134 (323)
T PTZ00240 84 EEKNLLSGNTGLIFTN-NEVQEITSVLDSHRVKAPARVGAIAPCDVIVPAGS 134 (323)
T ss_pred cccccccCCEEEEEeC-CCHHHHHHHHHHcCCcccccCCCCCCceEEECCCC
Confidence 48999999999998 679999999987 445442 2346666663
No 11
>KOG0816 consensus Protein involved in mRNA turnover [RNA processing and modification]
Probab=99.63 E-value=1.8e-15 Score=122.26 Aligned_cols=130 Identities=15% Similarity=0.261 Sum_probs=112.3
Q ss_pred hhhccChHHHHHHHHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCCcEEEEEchHHHHHHHhCC-------Ccccc
Q 030853 39 IRAAISRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGT-------QWEAL 111 (170)
Q Consensus 39 ~~~~~~r~~K~~~v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~~~i~VvKNtL~r~AL~~t-------~~e~L 111 (170)
.+-...++.|+.++++|++.+++|+.++|++..||+..-+.+||.+|+ +++++++||++|.+||+.+ ++..+
T Consensus 14 kt~KKg~e~K~~i~~~ir~~vd~Y~~v~Vf~~~nMRn~~lk~iR~~~k-~sr~f~GknKVm~vaLG~~~~dE~~~~l~kl 92 (223)
T KOG0816|consen 14 KTAKKGKEKKEAIVEEIREAVDKYPYVFVFEVPNMRNTTLKEIRQDFK-NSRFFFGKNKVMQVALGRSREDEYKENLYKL 92 (223)
T ss_pred HhhhhhHHHHHHHHHHHHHHHhhCCeEEEEEcCCcchHHHHHHHHHhh-ccceecchhhHHHHHhcCCchhhHHHHHHHh
Confidence 444567999999999999999999999999999999999999999999 8999999999999999987 47788
Q ss_pred cccCcCcEEEEEeeCCChHHHHHHHH-----HHhhhcC--CCcceeeEEEEcCeeeccccccccCC
Q 030853 112 KPCMSGMNAWLFVHTEEIPAAIKPYR-----NFQKEKK--LEENDFAGAVFEGVGYWIGGDFAGSG 170 (170)
Q Consensus 112 ~~~l~G~~alvFs~~d~~~~~~K~i~-----~f~K~~~--~~~l~ikgG~~dg~~ls~~~~~~~~~ 170 (170)
..+++|.++++||+ .+..++..++. +|++.+. ++.+.|..|.++...-+-+-+++++|
T Consensus 93 skll~G~~GLlFTd-~~keeV~e~f~sy~~~DyaR~g~vA~~Tv~ip~Gpl~~f~hsmEP~lRklg 157 (223)
T KOG0816|consen 93 SKLLKGSVGLLFTD-MSKEEVIEWFRSYVEEDYARAGDVAPETVTIPEGPLEQFAHSMEPQLRKLG 157 (223)
T ss_pred hhhccCceEEEecC-CCHHHHHHHHHHHHHHhhhccCCcCcceEeecCcchhhcccccchhhHhhc
Confidence 99999999999997 55767777766 4677664 45688899999988887777777665
No 12
>KOG0815 consensus 60S acidic ribosomal protein P0 [Translation, ribosomal structure and biogenesis]
Probab=99.39 E-value=1.7e-12 Score=106.37 Aligned_cols=98 Identities=20% Similarity=0.303 Sum_probs=88.8
Q ss_pred ccChHHHHHHHHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCCcEEEEEchHHHHHHHhCC-----CcccccccCc
Q 030853 42 AISRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGT-----QWEALKPCMS 116 (170)
Q Consensus 42 ~~~r~~K~~~v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~~~i~VvKNtL~r~AL~~t-----~~e~L~~~l~ 116 (170)
.-.+++|.....++.++|++|+.++++..+++.+.|++++|+.||+.+++.|+|||+||+|+.+. .++.+.++++
T Consensus 4 ~~~~e~k~~y~~K~~~L~~~y~~~~~v~~dnv~s~ql~~ir~~lrg~a~vlmgkntm~rrair~~~~~~~~~~~llp~~~ 83 (245)
T KOG0815|consen 4 ADKAEKKAVYFTKLRQLFEEYPKCFVVGADNVGSTQLQNIRKQLRGDAVVLMGKNTMMRRAIRGHLENNPALEKLLPVVK 83 (245)
T ss_pred hhhhHHHHHHHHHHHHHHHhcCceEEEeecchhhHHHHHHHHHhcCceeeeechhHHHHHHHHhccCCcHHHHhhcccee
Confidence 34578899999999999999999999999999999999999999999999999999999999986 3688999999
Q ss_pred CcEEEEEeeCCChHHHHHHHHHHh
Q 030853 117 GMNAWLFVHTEEIPAAIKPYRNFQ 140 (170)
Q Consensus 117 G~~alvFs~~d~~~~~~K~i~~f~ 140 (170)
|+++++|++ .|..++-+.+.+..
T Consensus 84 g~vgfvftk-~~L~ei~~~i~~n~ 106 (245)
T KOG0815|consen 84 GNVGFVFTK-GDLKEIRKEIIENK 106 (245)
T ss_pred eceeEEEEe-ccHHHHHHHHHhcc
Confidence 999999999 45777777777663
No 13
>KOG4241 consensus Mitochondrial ribosomal protein L10 [Translation, ribosomal structure and biogenesis]
Probab=99.16 E-value=3.2e-11 Score=98.35 Aligned_cols=112 Identities=14% Similarity=0.148 Sum_probs=98.2
Q ss_pred HHHHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCC-cEEEEEchHHHHHHHhCCCcccccccCcCcEEEEEeeCCC
Q 030853 50 ETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN-TKLIVAKNTLVYKAIEGTQWEALKPCMSGMNAWLFVHTEE 128 (170)
Q Consensus 50 ~~v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~-~~i~VvKNtL~r~AL~~t~~e~L~~~l~G~~alvFs~~d~ 128 (170)
-+..|+..+++++.++++|++..+++.++--.|.+|+++ ++++.+-|.+++.+++++.|+.|.++|.|+.+++|+. |
T Consensus 77 ~~~re~~~v~~~~R~~Avcq~~~v~a~d~~~~r~QLrk~ni~~ksygnkIlk~~~~~t~y~~l~plfvgnh~ill~~-d- 154 (245)
T KOG4241|consen 77 SNLREDWMVREEFRVMAVCQFLPVPARDLWFARNQLRKKNIEFKSYGNKILKKIFDKTPYSSLNPLFVGNHAILLAK-D- 154 (245)
T ss_pred HHHHHHHHHHhhhhheeeeecccCcHHHHHHHHHHHHhccchhhhchHHHHHHHHhcCchhhhhhheeccceEEEcC-C-
Confidence 356778889999999999999999999999999999987 9999999999999999999999999999999999997 4
Q ss_pred hHHHHHHHHHHhhhcCCCcceeeEEEEcCeeecccccc
Q 030853 129 IPAAIKPYRNFQKEKKLEENDFAGAVFEGVGYWIGGDF 166 (170)
Q Consensus 129 ~~~~~K~i~~f~K~~~~~~l~ikgG~~dg~~ls~~~~~ 166 (170)
+. ..|.+....++-+ .+.+.||+++..+++..+..
T Consensus 155 ~~-kik~~lri~r~vP--~~~llgG~I~dtvlsRnqlv 189 (245)
T KOG4241|consen 155 IS-KIKSILRITRKVP--LVMLLGGRIVDTVLSRNQLV 189 (245)
T ss_pred hH-HHHHHHHHHhhcc--hheecccchHHHHHHHHHHH
Confidence 43 4466666666656 68999999999999886543
No 14
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=73.91 E-value=16 Score=26.37 Aligned_cols=72 Identities=15% Similarity=0.178 Sum_probs=52.4
Q ss_pred HHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCC--cEEEEEchHHHHH-HH-----hCCCcccccccCcCcEEEEE
Q 030853 52 VDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN--TKLIVAKNTLVYK-AI-----EGTQWEALKPCMSGMNAWLF 123 (170)
Q Consensus 52 v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~--~~i~VvKNtL~r~-AL-----~~t~~e~L~~~l~G~~alvF 123 (170)
.+.|+...-.-+-++.+.-+|+|.+-+.++...|..+ ++++|.+|.--.+ .+ +.++-+-+. .-|.++++|
T Consensus 6 r~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq--~iG~~~vlY 83 (95)
T TIGR00253 6 KRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQ--VIGKTIVLY 83 (95)
T ss_pred HHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEE--EEccEEEEE
Confidence 3457777777788999999999999999999999876 9999999853222 11 223433222 448999988
Q ss_pred ee
Q 030853 124 VH 125 (170)
Q Consensus 124 s~ 125 (170)
=.
T Consensus 84 R~ 85 (95)
T TIGR00253 84 RP 85 (95)
T ss_pred ec
Confidence 64
No 15
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=72.68 E-value=22 Score=25.98 Aligned_cols=70 Identities=21% Similarity=0.243 Sum_probs=51.5
Q ss_pred HHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCC--cEEEEEchHHHHH------HHhCCCcccccccCcCcEEEEEe
Q 030853 53 DTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN--TKLIVAKNTLVYK------AIEGTQWEALKPCMSGMNAWLFV 124 (170)
Q Consensus 53 ~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~--~~i~VvKNtL~r~------AL~~t~~e~L~~~l~G~~alvFs 124 (170)
..|+..--.-+-++.+.-+|+|.+-+.++.+.|..+ ++++|.+|...-+ -.+.++.+.+. .-|.++++|=
T Consensus 8 ~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVq--viG~~~vlyr 85 (97)
T COG1534 8 RFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQ--VIGKTLVLYR 85 (97)
T ss_pred HHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEee--eeeeEEEEEe
Confidence 345555666778999999999999999999999766 8999999875422 22224444333 6688888885
No 16
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=71.02 E-value=19 Score=26.23 Aligned_cols=72 Identities=14% Similarity=0.130 Sum_probs=52.3
Q ss_pred HHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCC--cEEEEEchHHHH-HHH-----hCCCcccccccCcCcEEEEE
Q 030853 52 VDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN--TKLIVAKNTLVY-KAI-----EGTQWEALKPCMSGMNAWLF 123 (170)
Q Consensus 52 v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~--~~i~VvKNtL~r-~AL-----~~t~~e~L~~~l~G~~alvF 123 (170)
.+.|+..-..-+-++.+.-+|+|.+-+.++...|..+ ++++|.+|.-.. +.+ +.++-+.. ..-|.++++|
T Consensus 8 r~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~V--q~IG~~~vlY 85 (97)
T PRK10343 8 KQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNV--QVIGKTLVLY 85 (97)
T ss_pred HHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEE--eeeCcEEEEE
Confidence 3457777777788999999999999999999999876 999999886332 111 12333322 2568899988
Q ss_pred ee
Q 030853 124 VH 125 (170)
Q Consensus 124 s~ 125 (170)
=.
T Consensus 86 R~ 87 (97)
T PRK10343 86 RP 87 (97)
T ss_pred ec
Confidence 64
No 17
>PF14226 DIOX_N: non-haem dioxygenase in morphine synthesis N-terminal; PDB: 3OOX_A 1BK0_A 1IPS_B 1QIQ_A 1OC1_A 2Y86_A 2Y60_A 1W03_A 2VE1_A 1QJF_A ....
Probab=46.44 E-value=63 Score=22.77 Aligned_cols=41 Identities=10% Similarity=0.199 Sum_probs=34.0
Q ss_pred ChHHHHHHHHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhc
Q 030853 44 SRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSL 85 (170)
Q Consensus 44 ~r~~K~~~v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~L 85 (170)
..+.+.+++++|.+.+.+...++|++. |++...++++.+..
T Consensus 9 ~~~~~~~~~~~l~~A~~~~GFf~l~nh-Gi~~~l~~~~~~~~ 49 (116)
T PF14226_consen 9 DPADREEVAEQLRDACEEWGFFYLVNH-GIPQELIDRVFAAA 49 (116)
T ss_dssp CHHHHHHHHHHHHHHHHHTSEEEEESS-SSSHHHHHHHHHHH
T ss_pred CCccHHHHHHHHHHHHHhCCEEEEecc-cccchhhHHHHHHH
Confidence 457788899999999999998887776 99998888877554
No 18
>PF08800 VirE_N: VirE N-terminal domain; InterPro: IPR014907 This domain is associated with the N terminus of Virulence E proteins. The function of the domain is unknown.
Probab=44.70 E-value=27 Score=26.48 Aligned_cols=32 Identities=16% Similarity=0.262 Sum_probs=28.1
Q ss_pred HHHhhCCeEEEEEeCCCChhHHHHHHHhcCCC
Q 030853 57 THLENCHLIAAIKYKGFTVKQFQDLRRSLPEN 88 (170)
Q Consensus 57 e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~ 88 (170)
..+..++.++++|+.++...++.++|+.+...
T Consensus 25 ~~l~~~sglv~lDiD~l~~ee~~~~r~~l~~~ 56 (136)
T PF08800_consen 25 DNLKAYSGLVVLDIDHLDPEEAEELRQLLFED 56 (136)
T ss_pred hhhhhCCCcEEEEeCCCCHHHHHHHHHHHhcC
Confidence 45677999999999999999999999998765
No 19
>COG2429 Archaeal GTP cyclohydrolase III [Nucleotide transport and metabolism]
Probab=41.71 E-value=60 Score=27.48 Aligned_cols=54 Identities=13% Similarity=0.017 Sum_probs=41.6
Q ss_pred hHHHHHHHhCCCcccccccCcCcEEEEEeeCCChHHHHHHHHHHhhhcCCCcceeeEEEE
Q 030853 96 NTLVYKAIEGTQWEALKPCMSGMNAWLFVHTEEIPAAIKPYRNFQKEKKLEENDFAGAVF 155 (170)
Q Consensus 96 NtL~r~AL~~t~~e~L~~~l~G~~alvFs~~d~~~~~~K~i~~f~K~~~~~~l~ikgG~~ 155 (170)
-+||+...+ +..|.-++-|-|.+.++++.++..+.+.+..+.++.+ +.++.|+=
T Consensus 164 ~~L~~~l~k---~gal~fflGGDN~ma~~p~~s~g~v~d~i~~v~~~~~---v~lkvGIG 217 (250)
T COG2429 164 ATLMRFLEK---IGALLFFLGGDNIMAVCPGLSAGDVLDAIAEVLDDAE---VDLKVGIG 217 (250)
T ss_pred HHHHHHHHh---cCcEEEEecCcceEEECCCCCchhHHHHHHHHHHhhc---cceEeeec
Confidence 345555544 6678889999999999988777778889988888764 67888863
No 20
>CHL00197 carA carbamoyl-phosphate synthase arginine-specific small subunit; Provisional
Probab=36.71 E-value=76 Score=28.49 Aligned_cols=81 Identities=12% Similarity=0.111 Sum_probs=47.2
Q ss_pred CeEEEEEeCCCChhHHHHHHHhcCCCcEEEEEchHHHHHHHhCCCcccccccCcCcEEEEEeeC-CChHHHHH---HHHH
Q 030853 63 HLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGTQWEALKPCMSGMNAWLFVHT-EEIPAAIK---PYRN 138 (170)
Q Consensus 63 ~~v~v~~~~~lta~q~~~LRk~Lr~~~~i~VvKNtL~r~AL~~t~~e~L~~~l~G~~alvFs~~-d~~~~~~K---~i~~ 138 (170)
..|+++|+ |++.+-+..|++. ...+.|++|.. ..+.+... .+.+++++++ .+|..... .+.+
T Consensus 193 ~~I~viD~-g~k~ni~~~L~~~---G~~v~vvp~~~--------~~~~i~~~--~~dgIilSgGPg~p~~~~~~i~~i~~ 258 (382)
T CHL00197 193 LKIIVIDF-GVKYNILRRLKSF---GCSITVVPATS--------PYQDILSY--QPDGILLSNGPGDPSAIHYGIKTVKK 258 (382)
T ss_pred CEEEEEEC-CcHHHHHHHHHHC---CCeEEEEcCCC--------CHHHHhcc--CCCEEEEcCCCCChhHHHHHHHHHHH
Confidence 47999999 7777755555532 47888998752 23333221 4678999865 34433322 3333
Q ss_pred HhhhcCCCcceeeEEEEcCeeec
Q 030853 139 FQKEKKLEENDFAGAVFEGVGYW 161 (170)
Q Consensus 139 f~K~~~~~~l~ikgG~~dg~~ls 161 (170)
+.+. .+.+.|=|+.-|+|.
T Consensus 259 ~~~~----~~PilGIClGhQlLa 277 (382)
T CHL00197 259 LLKY----NIPIFGICMGHQILS 277 (382)
T ss_pred HHhC----CCCEEEEcHHHHHHH
Confidence 3321 355677666655543
No 21
>COG4825 Uncharacterized membrane-anchored protein conserved in bacteria [Function unknown]
Probab=34.38 E-value=62 Score=28.64 Aligned_cols=43 Identities=19% Similarity=0.294 Sum_probs=36.3
Q ss_pred HhCCCcccccccCcCcEEEEEeeCCChHHHHHHHHHHhhhcCC
Q 030853 103 IEGTQWEALKPCMSGMNAWLFVHTEEIPAAIKPYRNFQKEKKL 145 (170)
Q Consensus 103 L~~t~~e~L~~~l~G~~alvFs~~d~~~~~~K~i~~f~K~~~~ 145 (170)
+++.+++++...++|...++.+.+++...-.|.++.|.|++.+
T Consensus 166 idg~gIPD~~n~~~gR~VlIva~~~~~~~dLk~lk~fi~ey~p 208 (395)
T COG4825 166 IDGIGIPDLDNDLRGRHVLIVADEPSFEDDLKSLKPFIKEYQP 208 (395)
T ss_pred hcCCCCCcccchhcccEEEEEeCCCChHhHHHHHHHHHHhhCC
Confidence 4556899999999999999999877666678999999999874
No 22
>PF08496 Peptidase_S49_N: Peptidase family S49 N-terminal; InterPro: IPR013703 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found to the N terminus of bacterial signal peptidases that belong to the MEROPS peptidase family S49 (protease IV family, clan SK) (see also IPR002142 from INTERPRO) [, ]. ; GO: 0004252 serine-type endopeptidase activity, 0005886 plasma membrane
Probab=33.95 E-value=97 Score=24.30 Aligned_cols=26 Identities=15% Similarity=0.381 Sum_probs=23.2
Q ss_pred hCCeEEEEEeCC-CChhHHHHHHHhcC
Q 030853 61 NCHLIAAIKYKG-FTVKQFQDLRRSLP 86 (170)
Q Consensus 61 ~s~~v~v~~~~~-lta~q~~~LRk~Lr 86 (170)
..+.+||+||+| +.+.+...||.++-
T Consensus 96 ~~~r~~VldF~Gdi~A~~v~~LReeis 122 (155)
T PF08496_consen 96 PKPRLFVLDFKGDIKASEVESLREEIS 122 (155)
T ss_pred CCCeEEEEecCCCccHHHHHHHHHHHH
Confidence 368999999998 99999999998874
No 23
>PF02700 PurS: Phosphoribosylformylglycinamidine (FGAM) synthase; InterPro: IPR003850 Phosphoribosylformylglycinamidine(FGAM) synthetase, 6.3.5.3 from EC, catalyses the fourth step in the de novo purine biosynthetic pathway []. 5-phosphoribosylformylglycinamide (FGAR) + glutamine + ATP = FGAM + glutamate + ADP + Pi In eukaryotes and many bacterial systems (including Escherichia coli and Salmonella typhimurium), the FGAM synthetase is encoded by the large form of PurL (lgPurL), which contains an N-terminal ATPase domain and a C-terminal glutamine-binding domain. In archaeal and other bacterial systems, however, FGAM synthetase is encoded by separate genes, making it a multisubunit (rather than multidomain) enzyme. The protein is composed of the small form of PurL (smPurL), which is homologus to the ATPase domain of lgPurL, PurQ which is homologous to the glutamine-binding domain of of lgPurL, and PurS, whose function is not known. This entry represents the PurS subunit of the multisubunit FGAM synthetase. Recent studies showed that disruption of the purS gene in Bacillus subtilis resulted in a purine auxotrophic phenotype, due to defective FGAM synthetase activity. Therefore, the PurS protein appears to be required for the function of the PurL and PurQ subunits of the FGAM synthetase, but the molecular mechanism for the functional role of PurS is currently not known. For additional information please see [, ].; GO: 0016879 ligase activity, forming carbon-nitrogen bonds; PDB: 2ZW2_B 3D54_B 1VQ3_B 1GTD_A 2YX5_A 2CUW_A 1TWJ_B 1T4A_B 2DGB_B.
Probab=33.30 E-value=78 Score=21.97 Aligned_cols=45 Identities=11% Similarity=0.139 Sum_probs=35.8
Q ss_pred HHHHHhCCCcccccccCcCcEEEEEeeCCChHHHHHHHHHHhhhc
Q 030853 99 VYKAIEGTQWEALKPCMSGMNAWLFVHTEEIPAAIKPYRNFQKEK 143 (170)
Q Consensus 99 ~r~AL~~t~~e~L~~~l~G~~alvFs~~d~~~~~~K~i~~f~K~~ 143 (170)
+++||...|+..+.+.=.|...-+....+|..++.+.+.+++++.
T Consensus 21 i~~al~~lG~~~v~~Vr~GK~~~l~~~~~~~e~a~~~v~~i~~~L 65 (80)
T PF02700_consen 21 IKRALHRLGYDGVKDVRVGKYIELELEADDEEEAEEQVEEICEKL 65 (80)
T ss_dssp HHHHHHHTT-TTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHT
T ss_pred HHHHHHHcCCcccCcEEEEEEEEEEEeCCCHHHHHHHHHHHHHHh
Confidence 577888889999999889999988888777777788888888764
No 24
>PF01591 6PF2K: 6-phosphofructo-2-kinase; InterPro: IPR013079 6-Phosphofructo-2-kinase (2.7.1.105 from EC, 3.1.3.46 from EC) is a bifunctional enzyme that catalyses both the synthesis and the degradation of fructose-2, 6-bisphosphate. The fructose-2,6-bisphosphatase reaction involves a phosphohistidine intermediate. The catalytic pathway is: ATP + D-fructose 6-phosphate = ADP + D-fructose 2,6-bisphosphate D-fructose 2,6-bisphosphate + H2O = 6-fructose 6-phosphate + Pi The enzyme is important in the regulation of hepatic carbohydrate metabolism and is found in greatest quantities in the liver, kidney and heart. In mammals, several genes often encode different isoforms, each of which differs in its tissue distribution and enzymatic activity []. The family described here bears a resemblance to the ATP-driven phospho-fructokinases, however, they share little sequence similarity, although a few residues seem key to their interaction with fructose 6-phosphate []. This domain forms the N-terminal region of this enzyme, while IPR013078 from INTERPRO forms the C-terminal domain.; GO: 0003873 6-phosphofructo-2-kinase activity, 0005524 ATP binding, 0006000 fructose metabolic process; PDB: 2DWO_A 3QPW_A 3QPV_A 3QPU_A 2I1V_B 2DWP_A 2AXN_A 1K6M_B 3BIF_A 2BIF_A ....
Probab=32.52 E-value=73 Score=26.34 Aligned_cols=40 Identities=15% Similarity=0.160 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHh-hCCeEEEEEeCCCChhHHHHHHHhcCCC
Q 030853 49 EETVDTVKTHLE-NCHLIAAIKYKGFTVKQFQDLRRSLPEN 88 (170)
Q Consensus 49 ~~~v~el~e~~~-~s~~v~v~~~~~lta~q~~~LRk~Lr~~ 88 (170)
...++++.++|. +...|+|+|-.+.|.+..+.|...+++.
T Consensus 81 ~~~l~dl~~~l~~~~G~VAI~DATN~T~~RR~~l~~~~~~~ 121 (222)
T PF01591_consen 81 KEALEDLIEWLQEEGGQVAIFDATNSTRERRKMLVERFKEH 121 (222)
T ss_dssp HHHHHHHHHHHHTS--SEEEEES---SHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHhcCCCeEEEEeCCCCCHHHHHHHHHHHHHc
Confidence 457888899998 6668999999999999999999888765
No 25
>PF10678 DUF2492: Protein of unknown function (DUF2492); InterPro: IPR019620 This entry describes a family of small cytosolic proteins, about 80 amino acids in length, in which the eight invariant residues include three His residues and two Cys residues. Two pairs of these invariant residues occur in motifs HxH (where x is A or G) and CxH, both of which suggest metal-binding activity. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulphatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulphur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulphatase/maturase systems.
Probab=30.40 E-value=1.1e+02 Score=21.51 Aligned_cols=37 Identities=16% Similarity=0.195 Sum_probs=33.2
Q ss_pred hHHHHHHHHHHHHHHhhCCeEEEEEeCCCChhHHHHH
Q 030853 45 RTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDL 81 (170)
Q Consensus 45 r~~K~~~v~el~e~~~~s~~v~v~~~~~lta~q~~~L 81 (170)
...|.++++.|.+.|.....+.-|.-.++++.++-++
T Consensus 19 ~~t~~~L~~ai~~~FG~~arFhTCSae~m~a~eLv~F 55 (78)
T PF10678_consen 19 PYTKEELKAAIIEKFGEDARFHTCSAEGMTADELVDF 55 (78)
T ss_pred CcCHHHHHHHHHHHhCCCceEEecCCCCCCHHHHHHH
Confidence 3457889999999999999999999999999999876
No 26
>TIGR03853 matur_matur probable metal-binding protein. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulfatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulfur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulfatase/maturase systems.
Probab=30.27 E-value=1.1e+02 Score=21.39 Aligned_cols=36 Identities=8% Similarity=0.165 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHhhCCeEEEEEeCCCChhHHHHHH
Q 030853 47 KKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLR 82 (170)
Q Consensus 47 ~K~~~v~el~e~~~~s~~v~v~~~~~lta~q~~~LR 82 (170)
-|.++++.|.+.|.+...+.-|..++|++.++-++=
T Consensus 19 t~~~L~~~i~~~FG~~arFhTCSa~~m~a~~Li~FL 54 (77)
T TIGR03853 19 TRESLKAAIEQKFGEDARFHTCSAEGMTADELLQFL 54 (77)
T ss_pred CHHHHHHHHHHHhCCCceEeecccccCCHHHHHHHH
Confidence 477899999999999999999999999999988773
No 27
>PF01740 STAS: STAS domain; InterPro: IPR002645 The STAS (Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function. The establishment of differential gene expression in sporulating Bacillus subtilis involves four protein components one of which is SpoIIAA (P10727 from SWISSPROT). The four components regulate the sporulation sigma factor F. Early in sporulation, SpoIIAA is in the phosphorylated state (SpoIIAA-P), as a result of the activity of the ATP-dependent protein kinase SpoIIAB (P10728 from SWISSPROT). The site at which this protein is a conserved serine. SpoIIAB is an anti-sigma factor that in its free form inhibits F by binding to it. Competition by SpoIIAA (the anti-anti-sigma factor) for binding to SpoIIAB releases Sigma F activity []. The STAS domain is found in the anti-sigma factor antagonist SpoIIAA.; PDB: 3T6O_B 3LKL_B 1H4Z_A 1H4Y_B 1H4X_B 3NY7_A 3OIZ_A 1T6R_A 1VC1_B 1SBO_A ....
Probab=29.00 E-value=1.1e+02 Score=21.51 Aligned_cols=64 Identities=16% Similarity=0.223 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHhhCC---------eEEEEEeCCCChhHHH------HHHHhcCCC-cEEEEEc-hHHHHHHHhCCCcccc
Q 030853 49 EETVDTVKTHLENCH---------LIAAIKYKGFTVKQFQ------DLRRSLPEN-TKLIVAK-NTLVYKAIEGTQWEAL 111 (170)
Q Consensus 49 ~~~v~el~e~~~~s~---------~v~v~~~~~lta~q~~------~LRk~Lr~~-~~i~VvK-NtL~r~AL~~t~~e~L 111 (170)
..+.+.+.+.+.... ..+|+|+++++.-+.. ++++.++.. +.+.++- +.-++..|+.+++...
T Consensus 25 ~~~~~~i~~~~~~~~~~~~~~~~~~~vIlD~s~v~~iDssgi~~L~~~~~~~~~~g~~~~l~~~~~~v~~~l~~~~~~~~ 104 (117)
T PF01740_consen 25 EEFRDRIRKLIDEDPERIKKRQTIKNVILDMSGVSFIDSSGIQALVDIIKELRRRGVQLVLVGLNPDVRRILERSGLIDF 104 (117)
T ss_dssp HHHHHHHHHHHCCSSS--HTSSSSSEEEEEETTESEESHHHHHHHHHHHHHHHHTTCEEEEESHHHHHHHHHHHTTGHHH
T ss_pred HHHHHHHHHhhhcccccccccccceEEEEEEEeCCcCCHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHcCCChh
Confidence 346667777777764 7899999998765544 455777644 6555444 7778888998887654
Q ss_pred c
Q 030853 112 K 112 (170)
Q Consensus 112 ~ 112 (170)
.
T Consensus 105 ~ 105 (117)
T PF01740_consen 105 I 105 (117)
T ss_dssp S
T ss_pred c
Confidence 4
No 28
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=26.84 E-value=55 Score=22.68 Aligned_cols=47 Identities=15% Similarity=0.187 Sum_probs=31.7
Q ss_pred HHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCC--cEEEEEchHH
Q 030853 52 VDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN--TKLIVAKNTL 98 (170)
Q Consensus 52 v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~--~~i~VvKNtL 98 (170)
.+.|+..-..-+-++.+.-+|+|.+-+.+++..|..+ +++++-+|.-
T Consensus 6 ~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~ 54 (84)
T PF01985_consen 6 RKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCR 54 (84)
T ss_dssp HHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--H
T ss_pred HHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCH
Confidence 3456666666677788888999999999999998765 8888888643
No 29
>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....
Probab=26.01 E-value=2.2e+02 Score=22.18 Aligned_cols=50 Identities=14% Similarity=0.196 Sum_probs=35.3
Q ss_pred hHHHHHHHHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCC--cEEEEE
Q 030853 45 RTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN--TKLIVA 94 (170)
Q Consensus 45 r~~K~~~v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~--~~i~Vv 94 (170)
|++...-+.++..+|.++..++|+..-..........|+.+... .++.|-
T Consensus 56 R~e~~rr~~~~A~ll~~~G~ivIva~isp~~~~R~~~R~~~~~~~f~eVyv~ 107 (156)
T PF01583_consen 56 REENIRRIAEVAKLLADQGIIVIVAFISPYREDREWARELIPNERFIEVYVD 107 (156)
T ss_dssp HHHHHHHHHHHHHHHHHTTSEEEEE----SHHHHHHHHHHHHTTEEEEEEEE
T ss_pred HHHHHHHHHHHHHHHHhCCCeEEEeeccCchHHHHHHHHhCCcCceEEEEeC
Confidence 44455556667778899999999999999999999999999863 555543
No 30
>PRK05783 hypothetical protein; Provisional
Probab=25.86 E-value=1.7e+02 Score=20.64 Aligned_cols=45 Identities=7% Similarity=-0.020 Sum_probs=35.9
Q ss_pred HHHHHhCCCcccccccCcCcEEEEEeeCCChHHHHHHHHHHhhhc
Q 030853 99 VYKAIEGTQWEALKPCMSGMNAWLFVHTEEIPAAIKPYRNFQKEK 143 (170)
Q Consensus 99 ~r~AL~~t~~e~L~~~l~G~~alvFs~~d~~~~~~K~i~~f~K~~ 143 (170)
++.||...|+..+.+.=.|...-+...+++..++.+.+.+++++.
T Consensus 23 I~~aL~~lg~~~V~~VRvGK~iel~l~~~~~e~a~~~v~~mc~~L 67 (84)
T PRK05783 23 IQRYVIERYTGNIIEVRAGKYLVFKIEANSPEEAKELALKIAREG 67 (84)
T ss_pred HHHHHHHcCCCCcceEEeeEEEEEEEcCCCHHHHHHHHHHHHHhc
Confidence 577888888988888889999888777666766778888887764
No 31
>PF05165 GGDN: GGDN family; InterPro: IPR007839 GTP cyclohydrolase III catalyses the formation of 2-amino-5-formylamino-6- ribofuranosylamino-4(3H)-pyrimidinone ribonucleotide monophosphate and inorganic phosphate from GTP. The enzyme also has an independent pyrophosphate phosphohydrolase activity. The proteins are 200-270 amino acids in length.; GO: 0003933 GTP cyclohydrolase activity, 0009058 biosynthetic process; PDB: 2QV6_B.
Probab=25.59 E-value=1.3e+02 Score=25.49 Aligned_cols=54 Identities=13% Similarity=0.128 Sum_probs=32.7
Q ss_pred chHHHHHHHhCCCcccccccCcCcEEEEEeeCCChHHHHHHHHHHhhhcCCCcceeeEEE
Q 030853 95 KNTLVYKAIEGTQWEALKPCMSGMNAWLFVHTEEIPAAIKPYRNFQKEKKLEENDFAGAV 154 (170)
Q Consensus 95 KNtL~r~AL~~t~~e~L~~~l~G~~alvFs~~d~~~~~~K~i~~f~K~~~~~~l~ikgG~ 154 (170)
.+.||+.. . ++..|.-++-|-|.++++++.+..++.+.+.....+.+ +.++.|+
T Consensus 159 ~~~l~~~~-~--~~G~L~fylGGDNi~~v~p~~~~~~~~~~i~~V~~~~~---i~lkvGI 212 (246)
T PF05165_consen 159 YAKLMKYL-E--KYGSLAFYLGGDNIMAVCPDLDEDDLLDAIEHVEEEVG---IDLKVGI 212 (246)
T ss_dssp HHHHHHHH-H--TTT---EEEETTEEEEE-TT--HHHHHHHHHHHHHHHS-----EEEEE
T ss_pred HHHHHHHH-H--hcCCEEEEecCceEEEECCCCCHHHHHHHHHHHHhhcC---ceEEEee
Confidence 35666666 3 35667889999999999987666666677766655543 5788886
No 32
>PF03993 DUF349: Domain of Unknown Function (DUF349); InterPro: IPR007139 This motif is found singly or as up to five tandem repeats in a small set of bacterial proteins. There are two or three alpha-helices, and possibly a beta-strand.
Probab=24.14 E-value=39 Score=22.28 Aligned_cols=40 Identities=15% Similarity=0.143 Sum_probs=29.3
Q ss_pred cChHHHHHHHHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCCc
Q 030853 43 ISRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPENT 89 (170)
Q Consensus 43 ~~r~~K~~~v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~~ 89 (170)
...+.|..+|+++..+..... -.-..+.+.+|+.+|+..+
T Consensus 31 ~n~~~K~~Li~~~~~l~~~~d-------~~~~~~~~k~l~~~Wk~iG 70 (77)
T PF03993_consen 31 ENLEKKEALIEEAEALAESED-------WKEAAEEIKELQQEWKEIG 70 (77)
T ss_pred HHHHHHHHHHHHHHHhccccc-------HHHHHHHHHHHHHHHHHcC
Confidence 356779999999988777654 3455677888888887543
No 33
>PRK03511 minC septum formation inhibitor; Reviewed
Probab=23.67 E-value=1.8e+02 Score=24.01 Aligned_cols=59 Identities=7% Similarity=0.161 Sum_probs=35.5
Q ss_pred HHHHHHHHHhhCC-----eEEEEEeCCCC-hhHHHHHHHhcCCC-cEEEEE---chHHHHHHHhCCCcc
Q 030853 51 TVDTVKTHLENCH-----LIAAIKYKGFT-VKQFQDLRRSLPEN-TKLIVA---KNTLVYKAIEGTQWE 109 (170)
Q Consensus 51 ~v~el~e~~~~s~-----~v~v~~~~~lt-a~q~~~LRk~Lr~~-~~i~Vv---KNtL~r~AL~~t~~e 109 (170)
+.++|.+.+++++ .-+++|+.+++ ..++..|..-++.. ....-+ .+...+.++...++.
T Consensus 28 l~~~L~~ki~~a~~FF~~apvvld~~~l~~~~~~~~L~~~l~~~gl~~vgv~~~~~~~~~~~~~~~gl~ 96 (228)
T PRK03511 28 IRQALEDKIAQAPAFLKNAPVVINVSALEDPVNWSALHKAVSSTGLRVVGVSGCKDAQLKAEIARAGLP 96 (228)
T ss_pred HHHHHHHHHHhChHHhCCCeEEEEeccCCChHHHHHHHHHHHHCCCEEEEEEcCChHHHHHHHHhcCCc
Confidence 4444444444332 23689999998 67899999999876 322222 344455555555553
No 34
>PF01692 Paramyxo_C: Paramyxovirus non-structural protein c; InterPro: IPR002608 This family consist of the C proteins (C', C, Y1, Y2) found in the Paramyxovirinae, e.g. Human parainfluenza virus 3, and Sendai virus. The C proteins effect viral RNA synthesis having both a positive and negative effect during the course of infection []. The paramyxovirinae have a negative-strand ssRNA genome of 15.3 kb from which six mRNAs are transcribed, five of these are monocistronic. The P/C mRNA is polycistronic and has two overlapping open reading frames P and C, C encodes the nested C proteins C', C, Y1 and Y2 [].; GO: 0030683 evasion by virus of host immune response
Probab=22.26 E-value=1.3e+02 Score=24.51 Aligned_cols=55 Identities=16% Similarity=0.131 Sum_probs=27.1
Q ss_pred cccccccccccccCCccCCCCCCCCCCCCCCCCCchhhhccChHH--HHHHHHHHHH
Q 030853 3 VSLLSLSSSQNLTLKPSTNPLFHFHPSKRSKPPPTHIRAAISRTK--KEETVDTVKT 57 (170)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~--K~~~v~el~e 57 (170)
-|+.|-+++||.+-.+-....-++++.+-..-+.....+..+++. --.+|+++..
T Consensus 28 ssl~Sy~~s~~~~~kt~~~st~ss~~~k~~a~~~~~sv~~~~kq~~~~~KIiDQv~r 84 (204)
T PF01692_consen 28 SSLNSYPVSAPTPEKTEAGSTTSSTEPKNQALPAEPSVNQKPKQQKRRPKIIDQVRR 84 (204)
T ss_pred hhhhccccCCCCccccccccccccCCcccccccCCcccccCccchhhcchHHHHHHh
Confidence 356777888888766544433345554433322222223332222 2336666654
No 35
>PRK00513 minC septum formation inhibitor; Reviewed
Probab=21.54 E-value=3e+02 Score=22.36 Aligned_cols=45 Identities=20% Similarity=0.334 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHhhC------CeEEEEEeCC--CChhHHHHHHHhcCCCcEEEE
Q 030853 49 EETVDTVKTHLENC------HLIAAIKYKG--FTVKQFQDLRRSLPENTKLIV 93 (170)
Q Consensus 49 ~~~v~el~e~~~~s------~~v~v~~~~~--lta~q~~~LRk~Lr~~~~i~V 93 (170)
.++.++|.+.|+++ +.-+++++.+ ++..++++|..-++....+.+
T Consensus 29 ~~l~~~L~~kl~~~~~ff~~~~~v~l~~~~r~l~~~~~~~l~~~l~~~~~~~v 81 (214)
T PRK00513 29 DELLQELKEKLSKGKYFWKGKATVHVKVGNRLLDEEQLQELKDVITERRQTAV 81 (214)
T ss_pred HHHHHHHHHHHHhCchhcCCCeEEEEEECCCCCCHHHHHHHHHHHHhCCCeEE
Confidence 34555555555443 2455666655 888999999999876643333
No 36
>PF09949 DUF2183: Uncharacterized conserved protein (DUF2183); InterPro: IPR019236 This domain, found in various bacterial and fungal proteins, has no known function.
Probab=20.57 E-value=3.3e+02 Score=19.55 Aligned_cols=50 Identities=10% Similarity=0.219 Sum_probs=43.0
Q ss_pred HHHHHHHHHHHHHHhhCCeEEEEEeCCCChhHHHHHHHhcCCCcEEEEEc
Q 030853 46 TKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAK 95 (170)
Q Consensus 46 ~~K~~~v~el~e~~~~s~~v~v~~~~~lta~q~~~LRk~Lr~~~~i~VvK 95 (170)
+.|...+++|-+.+-+.+.|+|-|-..-+.+--.++.++..+.+.-..++
T Consensus 49 ~~K~~~i~~i~~~fP~~kfiLIGDsgq~DpeiY~~ia~~~P~~i~ai~IR 98 (100)
T PF09949_consen 49 EHKRDNIERILRDFPERKFILIGDSGQHDPEIYAEIARRFPGRILAIYIR 98 (100)
T ss_pred hHHHHHHHHHHHHCCCCcEEEEeeCCCcCHHHHHHHHHHCCCCEEEEEEE
Confidence 58999999999999999999999999999998899999988775444444
No 37
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=20.57 E-value=3.2e+02 Score=19.97 Aligned_cols=59 Identities=17% Similarity=0.197 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHH----hhCCeEEEEEeCCCChh---HHHHHHHhc-------CCC-cEEEEEc-hHHHHHHHhCC
Q 030853 48 KEETVDTVKTHL----ENCHLIAAIKYKGFTVK---QFQDLRRSL-------PEN-TKLIVAK-NTLVYKAIEGT 106 (170)
Q Consensus 48 K~~~v~el~e~~----~~s~~v~v~~~~~lta~---q~~~LRk~L-------r~~-~~i~VvK-NtL~r~AL~~t 106 (170)
=+.++.-+-..+ .+.+.++|+|.++.+.. .+..+++-+ +++ ..+.+++ |..+|.++...
T Consensus 30 ~~~ll~yl~~~l~~~~~~~~f~vVid~~~~~~~~~~~~~~l~~~~~~l~~~~~~nl~~vyiv~p~~~~k~~~~~~ 104 (149)
T PF13716_consen 30 LERLLLYLLSTLSEEVVDKPFSVVIDHTGFSRSSEPSLSWLKQLYKLLPRKYKKNLKKVYIVHPNWFLKKILATL 104 (149)
T ss_dssp HHHHHHHHHHHH-TTTTTS-EEEEEE-TT--GGG---HHHHHHTTTSS-HHHHHTEEEEEEES--HHHHHHHHHT
T ss_pred HHHHHHHHHHhhhHHhcCCCEEEEEEcCCCccccCCchHHHHHHHHHHHHHHhhceEEEEEECCCHHHHHHHHHH
Confidence 334455555555 34579999999998543 467776543 335 5666666 88888888544
No 38
>PF08140 Cuticle_1: Crustacean cuticle protein repeat; InterPro: IPR012539 This family consists of the cuticle proteins from the Cancer pagurus (Rock crab) and the Homarus americanus (American lobster). These proteins are isolated from the calcified regions of the crustacean and they contain two copies of an 18 residue sequence motif, which thus far has been found only in crustacean calcified exoskeletons [].; GO: 0042302 structural constituent of cuticle
Probab=20.55 E-value=49 Score=20.34 Aligned_cols=16 Identities=6% Similarity=0.216 Sum_probs=13.3
Q ss_pred cCcCcEEEEEeeCCCh
Q 030853 114 CMSGMNAWLFVHTEEI 129 (170)
Q Consensus 114 ~l~G~~alvFs~~d~~ 129 (170)
.+.|+.++|+++++++
T Consensus 23 vl~GpSG~v~sdG~nv 38 (40)
T PF08140_consen 23 VLIGPSGAVLSDGKNV 38 (40)
T ss_pred EEECCceEEeeCCcEe
Confidence 5789999999987754
No 39
>PF03802 CitX: Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase; InterPro: IPR005551 Members of this protein family are annotated as CitX, containing the CitX domain, the domain is also found in the CitXG bifunctional protein, of the citrate lyase system. CitX transfers the prosthetic group 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA to the citrate lyase gamma chain, an acyl carrier protein. This enzyme may be designated holo-ACP synthase, holo-citrate lyase synthase, or apo-citrate lyase phosphoribosyl-dephospho-CoA transferase. In a few genera, including Haemophilus, this protein occurs as a fusion protein with CitG (2.7.8.25 from EC), an enzyme involved in prosthetic group biosynthesis. This CitX family is easily separated from the holo-ACP synthases of other enzyme systems.; GO: 0051191 prosthetic group biosynthetic process
Probab=20.49 E-value=2.7e+02 Score=21.94 Aligned_cols=56 Identities=13% Similarity=0.083 Sum_probs=36.2
Q ss_pred HHHHhCCCccccc----ccCcCcEEEEEeeCCChHHHHHHHHHHhhhcCCCcceeeEEEEcCeeecc
Q 030853 100 YKAIEGTQWEALK----PCMSGMNAWLFVHTEEIPAAIKPYRNFQKEKKLEENDFAGAVFEGVGYWI 162 (170)
Q Consensus 100 r~AL~~t~~e~L~----~~l~G~~alvFs~~d~~~~~~K~i~~f~K~~~~~~l~ikgG~~dg~~ls~ 162 (170)
...+...++..+. ..-.|+.+++..+ .++..+.+...++...++ .|-.+|=.+++.
T Consensus 59 ~~~l~~~~~~~~~~~~~~~~tGpe~~~~v~-~~a~~vK~~~i~iEe~hp------lGRL~DiDV~~~ 118 (170)
T PF03802_consen 59 EQQLSANGIFKLEQEILNDPTGPEAFLVVD-GDAEEVKRIMIEIEESHP------LGRLFDIDVLDP 118 (170)
T ss_pred HHHHHHcCCeEeeeeeeecCCcceeeEEeC-CCHHHHHHHHHHHHccCc------chheEEEeeecC
Confidence 3445555555443 5788999999997 458777777778866554 455555444433
Done!