Query 027713
Match_columns 220
No_of_seqs 143 out of 1237
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 14:04:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027713.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027713hhsearch_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 6.1E-45 1.3E-49 300.6 20.3 170 43-215 1-171 (172)
2 cd05797 Ribosomal_L10 Ribosoma 100.0 5.6E-41 1.2E-45 272.9 17.7 155 44-201 1-156 (157)
3 COG0244 RplJ Ribosomal protein 100.0 1.1E-38 2.3E-43 264.4 17.8 172 41-215 1-174 (175)
4 cd00379 Ribosomal_L10_P0 Ribos 100.0 7.3E-34 1.6E-38 229.5 17.1 153 46-201 1-154 (155)
5 PF00466 Ribosomal_L10: Riboso 99.9 4.9E-24 1.1E-28 160.8 7.9 98 43-141 1-100 (100)
6 KOG4241 Mitochondrial ribosoma 99.8 1.1E-20 2.4E-25 157.9 11.0 160 50-214 77-237 (245)
7 cd05795 Ribosomal_P0_L10e Ribo 99.8 1.4E-20 3.1E-25 156.0 10.0 94 46-140 1-99 (175)
8 cd05796 Ribosomal_P0_like Ribo 99.8 3.2E-20 6.8E-25 152.3 9.9 93 46-140 1-100 (163)
9 PRK04019 rplP0 acidic ribosoma 99.8 9.3E-20 2E-24 164.7 10.4 96 43-139 3-101 (330)
10 PTZ00135 60S acidic ribosomal 99.8 3.1E-19 6.6E-24 159.9 10.2 98 44-142 6-108 (310)
11 PTZ00240 60S ribosomal protein 99.6 1.1E-15 2.3E-20 137.4 11.1 96 43-139 3-112 (323)
12 KOG0815 60S acidic ribosomal p 99.1 3.7E-10 8.1E-15 95.7 9.2 96 42-138 4-104 (245)
13 KOG0816 Protein involved in mR 99.1 1.1E-09 2.5E-14 91.7 10.0 116 42-159 17-146 (223)
14 PRK10343 RNA-binding protein Y 73.5 14 0.00029 27.9 6.0 72 52-125 8-87 (97)
15 PF11909 NdhN: NADH-quinone ox 68.6 2.6 5.7E-05 34.1 1.2 26 150-175 106-131 (154)
16 COG1534 Predicted RNA-binding 66.6 32 0.0007 26.0 6.6 70 53-124 8-85 (97)
17 TIGR00253 RNA_bind_YhbY putati 64.3 33 0.00071 25.7 6.3 72 52-125 6-85 (95)
18 cd05797 Ribosomal_L10 Ribosoma 60.3 7.4 0.00016 31.2 2.4 28 185-212 129-156 (157)
19 PRK00099 rplJ 50S ribosomal pr 43.8 26 0.00056 28.5 3.1 26 176-201 143-168 (172)
20 PF14226 DIOX_N: non-haem diox 39.2 79 0.0017 23.2 5.0 42 44-86 9-50 (116)
21 PF01740 STAS: STAS domain; I 37.0 89 0.0019 22.9 5.0 63 50-112 26-105 (117)
22 PF00619 CARD: Caspase recruit 35.3 1.5E+02 0.0033 20.5 6.3 60 149-208 20-83 (85)
23 COG2429 Archaeal GTP cyclohydr 32.5 89 0.0019 27.4 4.7 47 108-157 173-219 (250)
24 KOG0951 RNA helicase BRR2, DEA 32.5 77 0.0017 34.5 5.1 61 21-84 499-569 (1674)
25 PF08496 Peptidase_S49_N: Pept 28.4 1.2E+02 0.0026 24.7 4.6 26 61-86 96-122 (155)
26 PF08800 VirE_N: VirE N-termin 26.5 71 0.0015 25.1 3.0 32 57-88 25-56 (136)
27 PF13758 Prefoldin_3: Prefoldi 26.4 1.2E+02 0.0025 23.1 3.9 23 151-173 38-60 (99)
28 COG5178 PRP8 U5 snRNP spliceos 25.4 57 0.0012 35.2 2.7 55 18-74 11-65 (2365)
29 PF02700 PurS: Phosphoribosylf 25.2 1.3E+02 0.0029 21.6 3.9 45 98-142 20-64 (80)
30 TIGR00377 ant_ant_sig anti-ant 23.0 2.9E+02 0.0062 19.7 6.4 62 53-114 32-102 (108)
31 PLN02276 gibberellin 20-oxidas 22.1 2E+02 0.0044 26.3 5.5 71 15-86 14-94 (361)
32 PF09949 DUF2183: Uncharacteri 21.1 3.6E+02 0.0078 20.1 6.3 51 46-96 49-99 (100)
No 1
>PRK00099 rplJ 50S ribosomal protein L10; Reviewed
Probab=100.00 E-value=6.1e-45 Score=300.61 Aligned_cols=170 Identities=39% Similarity=0.578 Sum_probs=163.8
Q ss_pred cChhHHHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHhcCCC-CEEEEEchHHHHHHHhcCCcccccccccCceEE
Q 027713 43 ISRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN-TKLIVAKNTLVYKAIEGTQWEALKPCMSGMNAW 121 (220)
Q Consensus 43 ~~r~~K~~~v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr~~-~~l~VvKNtL~k~Al~~t~~~~L~~~l~G~tal 121 (220)
|+|++|.++|+++++.|++|++++++||+|++++++++||++||++ ++++|+|||||++|+++++++++.++|+|++|+
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 6789999999999999999999999999999999999999999985 899999999999999999999999999999999
Q ss_pred EEeecCChhHHhHHHHHHHhhcCcCCcceeeeeeCCeecCHhhHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHhhchHH
Q 027713 122 LFVHTEEIPAAIKPYRNFQKEKKLEENDFAGAVFEGKFYAPGDFKALESMPTRAEIYAKLLGALQGSAIGLVGTLQAPAR 201 (220)
Q Consensus 122 vfs~~~~~~~~aK~l~~f~K~~~~~~l~l~gg~veg~~l~~~~v~~lakLPs~e~l~aqlv~~L~~p~~~l~~~L~~~~~ 201 (220)
+|++ +||.+++|++.+|.|+++ ++.++||++||+++|.+++++||+|||+|+++++|+|+|++|+++++++|+++++
T Consensus 81 ~fs~-~d~~~~~k~l~~f~K~~~--~~~l~gg~~eg~~l~~~~i~~la~LPs~~el~a~l~~~l~~p~~~l~~~L~~~~~ 157 (172)
T PRK00099 81 AFSY-EDPVAAAKVLKDFAKDNK--KLEIKGGAIEGKVLDAEEVKALAKLPSREELLAKLLGVLQAPATKLAGVLNAPPS 157 (172)
T ss_pred EEeC-CChHHHHHHHHHHHhhCc--CceEEEEEECCEEcCHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Confidence 9997 577789999999999985 5899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhh
Q 027713 202 DLLMVLKAYAKKLE 215 (220)
Q Consensus 202 ~L~~~L~~~~~k~e 215 (220)
+|+++|+++.++++
T Consensus 158 ~l~~~L~~~~~~~~ 171 (172)
T PRK00099 158 KLARVLKALAEKKE 171 (172)
T ss_pred HHHHHHHHHHHhhc
Confidence 99999999999874
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=100.00 E-value=5.6e-41 Score=272.88 Aligned_cols=155 Identities=42% Similarity=0.616 Sum_probs=148.3
Q ss_pred ChhHHHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHhcCCC-CEEEEEchHHHHHHHhcCCcccccccccCceEEE
Q 027713 44 SRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN-TKLIVAKNTLVYKAIEGTQWEALKPCMSGMNAWL 122 (220)
Q Consensus 44 ~r~~K~~~v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr~~-~~l~VvKNtL~k~Al~~t~~~~L~~~l~G~talv 122 (220)
.|++|.+++++++++|+++++++++||+|++++++++||++||+. ++++|+||||+++|+++++++++.++|+|++|++
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 378999999999999999999999999999999999999999976 8999999999999999999999999999999999
Q ss_pred EeecCChhHHhHHHHHHHhhcCcCCcceeeeeeCCeecCHhhHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHhhchHH
Q 027713 123 FVHTEEIPAAIKPYRNFQKEKKLEENDFAGAVFEGKFYAPGDFKALESMPTRAEIYAKLLGALQGSAIGLVGTLQAPAR 201 (220)
Q Consensus 123 fs~~~~~~~~aK~l~~f~K~~~~~~l~l~gg~veg~~l~~~~v~~lakLPs~e~l~aqlv~~L~~p~~~l~~~L~~~~~ 201 (220)
|++ +||.+++|++.+|.|+++ ++.++||++||+++|.+++++||+|||+|++++||+|+|++|+++++++|+++++
T Consensus 81 f~~-~d~~~~~k~l~~f~k~~~--~~~~~gg~~eg~~l~~~~v~~la~LPs~e~l~a~l~~~l~~p~~~l~~~L~~~~~ 156 (157)
T cd05797 81 FSE-EDPVAAAKVLKDFAKENK--KLEIKGGVVEGKVLDAEEVKALAKLPSREELLAQLLGLLQAPATKLVRVLNAPAS 156 (157)
T ss_pred EeC-CChHHHHHHHHHHHHhCC--CcEEEEEEECCEecCHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 997 578789999999999985 6899999999999999999999999999999999999999999999999998865
No 3
>COG0244 RplJ Ribosomal protein L10 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-38 Score=264.45 Aligned_cols=172 Identities=33% Similarity=0.456 Sum_probs=164.3
Q ss_pred hccChhHHHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHhcCCC-CEEEEEchHHHHHHHhcCCcccccccccCce
Q 027713 41 AAISRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN-TKLIVAKNTLVYKAIEGTQWEALKPCMSGMN 119 (220)
Q Consensus 41 ~a~~r~~K~~~v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr~~-~~l~VvKNtL~k~Al~~t~~~~L~~~l~G~t 119 (220)
|++.+++|.++|+++++.|++|++++|+||+|+++.++++||++||+. ++++|+||||+++|+++++++.+.++|+||+
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 678889999999999999999999999999999999999999999975 9999999999999999999999999999999
Q ss_pred EEEEeecCChhHHhHHHHHHHhhc-CcCCcceeeeeeCCeecCHhhHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHhhc
Q 027713 120 AWLFVHTEEIPAAIKPYRNFQKEK-KLEENDFAGAVFEGKFYAPGDFKALESMPTRAEIYAKLLGALQGSAIGLVGTLQA 198 (220)
Q Consensus 120 alvfs~~~~~~~~aK~l~~f~K~~-~~~~l~l~gg~veg~~l~~~~v~~lakLPs~e~l~aqlv~~L~~p~~~l~~~L~~ 198 (220)
|++|++ +||.+++|++.+|+|.+ . .+.++||++||..++..+++++++||++++++++++|.+++|.+++++.|++
T Consensus 81 ai~fs~-~dp~~~~K~~~~f~k~~~~--~~~~~~~~~eg~~l~~~~v~~~aklp~~~el~~~l~g~~~ap~~~~~~~L~a 157 (175)
T COG0244 81 AIAFSN-EDPVAAAKLLKDFAKEAGD--KAPIKGGVPEGKVLGAAEVIALAKLPSKEELVVMLLGVLQAPATKLLRALKA 157 (175)
T ss_pred EEEEec-CCHHHHHHHHHHHhhhhcc--cceEEEEEecCcccCHHHHHHHhcCCcHHHHHHHHHHhhHhhHHHHHHHHhc
Confidence 999997 47889999999999995 4 6899999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHhhh
Q 027713 199 PARDLLMVLKAYAKKLE 215 (220)
Q Consensus 199 ~~~~L~~~L~~~~~k~e 215 (220)
.+..+.+.+.++.+++.
T Consensus 158 ~~~~~~~~~~a~~~~g~ 174 (175)
T COG0244 158 VPDKVGLKLLAAYEKGV 174 (175)
T ss_pred cHHHHhhHHHHhhccCC
Confidence 99999999999887653
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=100.00 E-value=7.3e-34 Score=229.50 Aligned_cols=153 Identities=37% Similarity=0.558 Sum_probs=145.1
Q ss_pred hHHHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHhcCCC-CEEEEEchHHHHHHHhcCCcccccccccCceEEEEe
Q 027713 46 TKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN-TKLIVAKNTLVYKAIEGTQWEALKPCMSGMNAWLFV 124 (220)
Q Consensus 46 ~~K~~~v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr~~-~~l~VvKNtL~k~Al~~t~~~~L~~~l~G~talvfs 124 (220)
++|.+++++++++|++|+.++++||+|+++++++++|++|++. ++++|+|||||++|+++++++.+.++|+|+++++|+
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 4799999999999999999999999999999999999999977 999999999999999999999999999999999999
Q ss_pred ecCChhHHhHHHHHHHhhcCcCCcceeeeeeCCeecCHhhHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHhhchHH
Q 027713 125 HTEEIPAAIKPYRNFQKEKKLEENDFAGAVFEGKFYAPGDFKALESMPTRAEIYAKLLGALQGSAIGLVGTLQAPAR 201 (220)
Q Consensus 125 ~~~~~~~~aK~l~~f~K~~~~~~l~l~gg~veg~~l~~~~v~~lakLPs~e~l~aqlv~~L~~p~~~l~~~L~~~~~ 201 (220)
+ +|+.+++|++.+|.+.++ ++.++||++||++++++++..++++|+++++++++++++++|+.++++.|+++..
T Consensus 81 ~-~~~~~~~k~~~~~~k~~~--~~~~k~g~~~~~v~~~~~~~~l~~lp~~~~~~~~~v~~l~~~~~~l~~~L~~~~~ 154 (155)
T cd00379 81 N-EDPVEVAKVLKDFAKENK--KLFAKGGVVAGKVLDPAGVTALAKLPSREELLAMLIGLLKAPIAKLARLLNALGI 154 (155)
T ss_pred C-CChHHHHHHHHHHHHhCC--CceEEEEEEcCEecCHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 7 577789999999999875 5899999999999999999999999999999999999999999999998887653
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=99.90 E-value=4.9e-24 Score=160.75 Aligned_cols=98 Identities=35% Similarity=0.576 Sum_probs=92.9
Q ss_pred cChhHHHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHhcCCC-CEEEEEchHHHHHHHhcCCcc-cccccccCceE
Q 027713 43 ISRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN-TKLIVAKNTLVYKAIEGTQWE-ALKPCMSGMNA 120 (220)
Q Consensus 43 ~~r~~K~~~v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr~~-~~l~VvKNtL~k~Al~~t~~~-~L~~~l~G~ta 120 (220)
|+|++|.++++++.+.|++++.+++++|+|++++++++||++|+++ ++++|+||+|+++|+++++++ .+.++|.|++|
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 6889999999999999999999999999999999999999999987 999999999999999999998 89999999999
Q ss_pred EEEeecCChhHHhHHHHHHHh
Q 027713 121 WLFVHTEEIPAAIKPYRNFQK 141 (220)
Q Consensus 121 lvfs~~~~~~~~aK~l~~f~K 141 (220)
++|++ +|+.+++|++.+|+|
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 99995 678889999999875
No 6
>KOG4241 consensus Mitochondrial ribosomal protein L10 [Translation, ribosomal structure and biogenesis]
Probab=99.84 E-value=1.1e-20 Score=157.90 Aligned_cols=160 Identities=16% Similarity=0.201 Sum_probs=143.3
Q ss_pred HHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHhcCCC-CEEEEEchHHHHHHHhcCCcccccccccCceEEEEeecCC
Q 027713 50 ETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN-TKLIVAKNTLVYKAIEGTQWEALKPCMSGMNAWLFVHTEE 128 (220)
Q Consensus 50 ~~v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr~~-~~l~VvKNtL~k~Al~~t~~~~L~~~l~G~talvfs~~~~ 128 (220)
-+..|+..+++++.+++++++..+++.++.-.|.+||++ +.|+.+.|.+++.++++|.|+.|.++|.|+.+++|++ |
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 456678889999999999999999999999999999876 9999999999999999999999999999999999986 3
Q ss_pred hhHHhHHHHHHHhhcCcCCcceeeeeeCCeecCHhhHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHhhchHHHHHHHHH
Q 027713 129 IPAAIKPYRNFQKEKKLEENDFAGAVFEGKFYAPGDFKALESMPTRAEIYAKLLGALQGSAIGLVGTLQAPARDLLMVLK 208 (220)
Q Consensus 129 ~~~~aK~l~~f~K~~~~~~l~l~gg~veg~~l~~~~v~~lakLPs~e~l~aqlv~~L~~p~~~l~~~L~~~~~~L~~~L~ 208 (220)
++.+ |.+....++- +.+.+.||+++..+++..++.+||+|||++.++|+++.++....+++...++..++++..+|+
T Consensus 155 ~~ki-k~~lri~r~v--P~~~llgG~I~dtvlsRnqlv~yaklpsL~~vqa~lvQ~l~qq~~~l~~ql~~~qr~~~svld 231 (245)
T KOG4241|consen 155 ISKI-KSILRITRKV--PLVMLLGGRIVDTVLSRNQLVEYAKLPSLEDVQAHLVQLLGQQVAQLTIQLDTVQRHLPSVLD 231 (245)
T ss_pred hHHH-HHHHHHHhhc--chheecccchHHHHHHHHHHHHHhhCCChHHHHHHHHHHhhhhHHHHHHHHHHHHhccchHhh
Confidence 4333 4444443443 468999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhh
Q 027713 209 AYAKKL 214 (220)
Q Consensus 209 ~~~~k~ 214 (220)
++.+-.
T Consensus 232 ~h~k~~ 237 (245)
T KOG4241|consen 232 SHIKTN 237 (245)
T ss_pred ccCCCC
Confidence 998754
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=99.83 E-value=1.4e-20 Score=155.97 Aligned_cols=94 Identities=23% Similarity=0.342 Sum_probs=88.3
Q ss_pred hHHHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHhcCCCCEEEEEchHHHHHHHhcCC-----cccccccccCceE
Q 027713 46 TKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGTQ-----WEALKPCMSGMNA 120 (220)
Q Consensus 46 ~~K~~~v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr~~~~l~VvKNtL~k~Al~~t~-----~~~L~~~l~G~ta 120 (220)
+||.++|+++++.+++|+.+++++|+|++++++++||++||+.++++|+|||||++|+++++ ++.|.++|+|++|
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 58999999999999999999999999999999999999999889999999999999999986 6788999999999
Q ss_pred EEEeecCChhHHhHHHHHHH
Q 027713 121 WLFVHTEEIPAAIKPYRNFQ 140 (220)
Q Consensus 121 lvfs~~~~~~~~aK~l~~f~ 140 (220)
++|++ +|+.+++|++.+|.
T Consensus 81 liFt~-~dp~~v~k~l~~~~ 99 (175)
T cd05795 81 FIFTN-GDPFEIRKILEENK 99 (175)
T ss_pred EEEEC-CCHHHHHHHHHHcC
Confidence 99997 67888999999873
No 8
>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=99.83 E-value=3.2e-20 Score=152.33 Aligned_cols=93 Identities=16% Similarity=0.347 Sum_probs=87.3
Q ss_pred hHHHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHhcCCCCEEEEEchHHHHHHHhcCC-------cccccccccCc
Q 027713 46 TKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGTQ-------WEALKPCMSGM 118 (220)
Q Consensus 46 ~~K~~~v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr~~~~l~VvKNtL~k~Al~~t~-------~~~L~~~l~G~ 118 (220)
+||.++++++++.|++|+.+++++|+|++++++++||++||+. +++|+|||||++|+++++ ++.|.++|+|+
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 5899999999999999999999999999999999999999988 999999999999999875 67899999999
Q ss_pred eEEEEeecCChhHHhHHHHHHH
Q 027713 119 NAWLFVHTEEIPAAIKPYRNFQ 140 (220)
Q Consensus 119 talvfs~~~~~~~~aK~l~~f~ 140 (220)
+|++|++ +|+.+++|++.+|.
T Consensus 80 ~~lift~-~dp~~v~k~l~~~~ 100 (163)
T cd05796 80 VGLLFTN-EPPEEVIEYFDSYS 100 (163)
T ss_pred EEEEEEC-CCHHHHHHHHHHcC
Confidence 9999997 67888999999883
No 9
>PRK04019 rplP0 acidic ribosomal protein P0; Validated
Probab=99.81 E-value=9.3e-20 Score=164.66 Aligned_cols=96 Identities=25% Similarity=0.369 Sum_probs=91.4
Q ss_pred cChhHHHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHhcCCCCEEEEEchHHHHHHHhcCC---cccccccccCce
Q 027713 43 ISRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGTQ---WEALKPCMSGMN 119 (220)
Q Consensus 43 ~~r~~K~~~v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr~~~~l~VvKNtL~k~Al~~t~---~~~L~~~l~G~t 119 (220)
..++||.++|++++++|++|+.++|+||+|++++++++||++||+.++++|+|||||++||++++ ++.|.++|+|++
T Consensus 3 ~~~e~K~~~v~el~~~l~~~~~v~iv~~~gl~~~ql~~lR~~lr~~~~~~v~KNtL~~~Al~~~~~~~~~~L~~~l~G~~ 82 (330)
T PRK04019 3 HVPEWKKEEVEELKELIKSYPVVGIVDLEGIPARQLQEIRRKLRGKAELKVSKNTLIKRALEEAGEEDLEKLEDYLEGQV 82 (330)
T ss_pred chHHHHHHHHHHHHHHHHhCCEEEEEEcCCCCHHHHHHHHHHHHcCCEEEEEehHHHHHHHHhcCcccHHHHHhhccCCE
Confidence 45799999999999999999999999999999999999999999889999999999999999998 899999999999
Q ss_pred EEEEeecCChhHHhHHHHHH
Q 027713 120 AWLFVHTEEIPAAIKPYRNF 139 (220)
Q Consensus 120 alvfs~~~~~~~~aK~l~~f 139 (220)
+++|++ +||..++|++.+|
T Consensus 83 alift~-~dp~~v~k~l~~~ 101 (330)
T PRK04019 83 ALIFTN-MNPFKLYKLLEKS 101 (330)
T ss_pred EEEEEC-CCHHHHHHHHHHc
Confidence 999997 6788899999987
No 10
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=99.79 E-value=3.1e-19 Score=159.90 Aligned_cols=98 Identities=26% Similarity=0.373 Sum_probs=91.0
Q ss_pred ChhHHHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHhcCCCCEEEEEchHHHHHHHhcC-----CcccccccccCc
Q 027713 44 SRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGT-----QWEALKPCMSGM 118 (220)
Q Consensus 44 ~r~~K~~~v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr~~~~l~VvKNtL~k~Al~~t-----~~~~L~~~l~G~ 118 (220)
.|++|.+++++|++.|++|+.++|++|+|++++|+++||++||+++.++|+|||||++||+++ +++.|.++|+|+
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 368999999999999999999999999999999999999999988899999999999999987 478899999999
Q ss_pred eEEEEeecCChhHHhHHHHHHHhh
Q 027713 119 NAWLFVHTEEIPAAIKPYRNFQKE 142 (220)
Q Consensus 119 talvfs~~~~~~~~aK~l~~f~K~ 142 (220)
++++||+ +|+.+++|++.+|.+.
T Consensus 86 ~gliFTn-~dp~ev~k~l~~~k~~ 108 (310)
T PTZ00135 86 VGFVFTK-DDLFEVKPVILENKVP 108 (310)
T ss_pred EEEEEEC-CCHHHHHHHHHHcCCc
Confidence 9999997 5687899999998553
No 11
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=99.64 E-value=1.1e-15 Score=137.43 Aligned_cols=96 Identities=21% Similarity=0.284 Sum_probs=86.5
Q ss_pred cChhHHHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHhcCCCCEEEEEchHHHHHHHhcCC-------cccc----
Q 027713 43 ISRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGTQ-------WEAL---- 111 (220)
Q Consensus 43 ~~r~~K~~~v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr~~~~l~VvKNtL~k~Al~~t~-------~~~L---- 111 (220)
..++||.+++++|++++++|+.++||+++|++++|++++|+.||+.+++.|+|||||++||++++ ++.+
T Consensus 3 ~~~~~K~~~v~~l~~~l~~y~~v~Iv~~~nv~s~qlq~IR~~lrg~a~~~~GKNtlm~~AL~~~~~~~~~~~~~~ll~~~ 82 (323)
T PTZ00240 3 SITTAKREYEERLVDCLTKYSCVLFVGMDNVRSQQVHDVRRALRGKAEFVMGKKTLQAKIVEKRAQAKKASAEAKLFNDQ 82 (323)
T ss_pred chhHHHHHHHHHHHHHHHhCCEEEEEEecCCCcHHHHHHHHHhhCCcEEEEecHHHHHHHHhhccccccchhHHHHhhhh
Confidence 34688999999999999999999999999999999999999999989999999999999999864 3455
Q ss_pred ---cccccCceEEEEeecCChhHHhHHHHHH
Q 027713 112 ---KPCMSGMNAWLFVHTEEIPAAIKPYRNF 139 (220)
Q Consensus 112 ---~~~l~G~talvfs~~~~~~~~aK~l~~f 139 (220)
.++++|+++++||+ +++..+.++|.++
T Consensus 83 ~~~~~~l~GnvgliFTn-~~p~ev~~~l~~~ 112 (323)
T PTZ00240 83 CEEKNLLSGNTGLIFTN-NEVQEITSVLDSH 112 (323)
T ss_pred ccccccccCCEEEEEeC-CCHHHHHHHHHHc
Confidence 48999999999998 6787888888766
No 12
>KOG0815 consensus 60S acidic ribosomal protein P0 [Translation, ribosomal structure and biogenesis]
Probab=99.11 E-value=3.7e-10 Score=95.69 Aligned_cols=96 Identities=21% Similarity=0.309 Sum_probs=84.2
Q ss_pred ccChhHHHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHhcCCCCEEEEEchHHHHHHHhcCC-----ccccccccc
Q 027713 42 AISRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGTQ-----WEALKPCMS 116 (220)
Q Consensus 42 a~~r~~K~~~v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr~~~~l~VvKNtL~k~Al~~t~-----~~~L~~~l~ 116 (220)
+...++|..+..++.++|+++..++++.-+++...|++++|+.||..+.+.+.|||++|+|+++.+ ++.+.+++.
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 445789999999999999999999999999999999999999999999999999999999999863 578999999
Q ss_pred CceEEEEeecCChhHHhHHHHH
Q 027713 117 GMNAWLFVHTEEIPAAIKPYRN 138 (220)
Q Consensus 117 G~talvfs~~~~~~~~aK~l~~ 138 (220)
|+++++|++++ ..++-+.+.+
T Consensus 84 g~vgfvftk~~-L~ei~~~i~~ 104 (245)
T KOG0815|consen 84 GNVGFVFTKGD-LKEIRKEIIE 104 (245)
T ss_pred eceeEEEEecc-HHHHHHHHHh
Confidence 99999999844 4444444433
No 13
>KOG0816 consensus Protein involved in mRNA turnover [RNA processing and modification]
Probab=99.06 E-value=1.1e-09 Score=91.66 Aligned_cols=116 Identities=15% Similarity=0.271 Sum_probs=93.6
Q ss_pred ccChhHHHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHhcCCCCEEEEEchHHHHHHHhcCC-------ccccccc
Q 027713 42 AISRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGTQ-------WEALKPC 114 (220)
Q Consensus 42 a~~r~~K~~~v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr~~~~l~VvKNtL~k~Al~~t~-------~~~L~~~ 114 (220)
...+++|..+++++++.+++|++++|++..||...-+.++|.+|+ +..+.++||++|..|+..+. +..+..+
T Consensus 17 KKg~e~K~~i~~~ir~~vd~Y~~v~Vf~~~nMRn~~lk~iR~~~k-~sr~f~GknKVm~vaLG~~~~dE~~~~l~klskl 95 (223)
T KOG0816|consen 17 KKGKEKKEAIVEEIREAVDKYPYVFVFEVPNMRNTTLKEIRQDFK-NSRFFFGKNKVMQVALGRSREDEYKENLYKLSKL 95 (223)
T ss_pred hhhHHHHHHHHHHHHHHHhhCCeEEEEEcCCcchHHHHHHHHHhh-ccceecchhhHHHHHhcCCchhhHHHHHHHhhhh
Confidence 345789999999999999999999999999999999999999999 78999999999999999874 4567889
Q ss_pred ccCceEEEEeecCChhHHhHHHHH-----HHhhcC--cCCcceeeeeeCCee
Q 027713 115 MSGMNAWLFVHTEEIPAAIKPYRN-----FQKEKK--LEENDFAGAVFEGKF 159 (220)
Q Consensus 115 l~G~talvfs~~~~~~~~aK~l~~-----f~K~~~--~~~l~l~gg~veg~~ 159 (220)
++|.++++|++ .+..++.-.+.. |++.+. ...+.|-.|.++..-
T Consensus 96 l~G~~GLlFTd-~~keeV~e~f~sy~~~DyaR~g~vA~~Tv~ip~Gpl~~f~ 146 (223)
T KOG0816|consen 96 LKGSVGLLFTD-MSKEEVIEWFRSYVEEDYARAGDVAPETVTIPEGPLEQFA 146 (223)
T ss_pred ccCceEEEecC-CCHHHHHHHHHHHHHHhhhccCCcCcceEeecCcchhhcc
Confidence 99999999996 445555555543 444441 234556666666544
No 14
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=73.53 E-value=14 Score=27.92 Aligned_cols=72 Identities=14% Similarity=0.130 Sum_probs=53.3
Q ss_pred HHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHhcCCC--CEEEEEchHHHH-HHH-----hcCCcccccccccCceEEEE
Q 027713 52 VDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN--TKLIVAKNTLVY-KAI-----EGTQWEALKPCMSGMNAWLF 123 (220)
Q Consensus 52 v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr~~--~~l~VvKNtL~k-~Al-----~~t~~~~L~~~l~G~talvf 123 (220)
.+.|+..-.+-+-++.+--+|+|.+-+.+++..|..+ ++++|.+|.--. +.+ +.++-+-+ ...|.++++|
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 4567777788888999999999999999999999665 899998886432 122 12333322 3679999999
Q ss_pred ee
Q 027713 124 VH 125 (220)
Q Consensus 124 s~ 125 (220)
=.
T Consensus 86 R~ 87 (97)
T PRK10343 86 RP 87 (97)
T ss_pred ec
Confidence 65
No 15
>PF11909 NdhN: NADH-quinone oxidoreductase cyanobacterial subunit N; InterPro: IPR020874 NAD(P)H-quinone oxidoreductase (NDH-1) shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. It couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. NDH-1 can be composed of about 15 different subunits, although different subcomplexes with different compositions have been identified which probably have different functions. This entry represents subunit N. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process, 0016020 membrane
Probab=68.56 E-value=2.6 Score=34.12 Aligned_cols=26 Identities=19% Similarity=0.385 Sum_probs=23.0
Q ss_pred eeeeeeCCeecCHhhHHHhhcCCCHH
Q 027713 150 FAGAVFEGKFYAPGDFKALESMPTRA 175 (220)
Q Consensus 150 l~gg~veg~~l~~~~v~~lakLPs~e 175 (220)
+.-=.+||+++|.+|++.|++||.+|
T Consensus 106 lvLWiiEG~vLS~~El~~L~~Lp~~e 131 (154)
T PF11909_consen 106 LVLWIIEGQVLSRQELEYLCNLPQRE 131 (154)
T ss_pred EEEEEEeccccCHHHHHHHHhccccC
Confidence 55568999999999999999999875
No 16
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=66.64 E-value=32 Score=25.98 Aligned_cols=70 Identities=21% Similarity=0.224 Sum_probs=51.9
Q ss_pred HHHHHHHhcCCeEEEEEeCCCChhhHHHHHHhcCCC--CEEEEEchHHHHH------HHhcCCcccccccccCceEEEEe
Q 027713 53 DTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN--TKLIVAKNTLVYK------AIEGTQWEALKPCMSGMNAWLFV 124 (220)
Q Consensus 53 ~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr~~--~~l~VvKNtL~k~------Al~~t~~~~L~~~l~G~talvfs 124 (220)
+.++..-.+-..++.+.-+|+|..-+.++++.|..+ ++++|.+|..-.+ -.+.++.+-+ ...|.++++|=
T Consensus 8 ~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lV--qviG~~~vlyr 85 (97)
T COG1534 8 RFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELV--QVIGKTLVLYR 85 (97)
T ss_pred HHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEe--eeeeeEEEEEe
Confidence 455666667788999999999999999999999654 8999999865422 2222444433 27799999985
No 17
>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=64.26 E-value=33 Score=25.71 Aligned_cols=72 Identities=15% Similarity=0.136 Sum_probs=53.0
Q ss_pred HHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHhcCCC--CEEEEEchHHHHH-HHh-----cCCcccccccccCceEEEE
Q 027713 52 VDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPEN--TKLIVAKNTLVYK-AIE-----GTQWEALKPCMSGMNAWLF 123 (220)
Q Consensus 52 v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr~~--~~l~VvKNtL~k~-Al~-----~t~~~~L~~~l~G~talvf 123 (220)
-+.|+....+-+.++.+--+|+|.+-+.++...|..+ ++++|.+|.--.+ .+. .++-+ +.. ..|.++++|
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 KRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGAC-NVQ-VIGKTIVLY 83 (95)
T ss_pred HHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCE-EEE-EEccEEEEE
Confidence 4567777777788999999999999999999999765 8999999854322 122 23333 222 459999999
Q ss_pred ee
Q 027713 124 VH 125 (220)
Q Consensus 124 s~ 125 (220)
=.
T Consensus 84 R~ 85 (95)
T TIGR00253 84 RP 85 (95)
T ss_pred ec
Confidence 54
No 18
>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=60.33 E-value=7.4 Score=31.17 Aligned_cols=28 Identities=43% Similarity=0.456 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHhhchHHHHHHHHHHHHH
Q 027713 185 LQGSAIGLVGTLQAPARDLLMVLKAYAK 212 (220)
Q Consensus 185 L~~p~~~l~~~L~~~~~~L~~~L~~~~~ 212 (220)
...-.++++++|++|+++|+++|+++.+
T Consensus 129 ~e~l~a~l~~~l~~p~~~l~~~L~~~~~ 156 (157)
T cd05797 129 REELLAQLLGLLQAPATKLVRVLNAPAS 156 (157)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 3455689999999999999999999764
No 19
>PRK00099 rplJ 50S ribosomal protein L10; Reviewed
Probab=43.84 E-value=26 Score=28.55 Aligned_cols=26 Identities=31% Similarity=0.296 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhchHH
Q 027713 176 EIYAKLLGALQGSAIGLVGTLQAPAR 201 (220)
Q Consensus 176 ~l~aqlv~~L~~p~~~l~~~L~~~~~ 201 (220)
.-..+++++|++|..+++++|++...
T Consensus 143 ~p~~~l~~~L~~~~~~l~~~L~~~~~ 168 (172)
T PRK00099 143 APATKLAGVLNAPPSKLARVLKALAE 168 (172)
T ss_pred HHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence 33457777777777777777776554
No 20
>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=39.24 E-value=79 Score=23.23 Aligned_cols=42 Identities=10% Similarity=0.188 Sum_probs=34.3
Q ss_pred ChhHHHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHhcC
Q 027713 44 SRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLP 86 (220)
Q Consensus 44 ~r~~K~~~v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr 86 (220)
..+.+..++++|.+.+.+..++.|+++ |++.+.+.++....+
T Consensus 9 ~~~~~~~~~~~l~~A~~~~GFf~l~nh-Gi~~~l~~~~~~~~~ 50 (116)
T PF14226_consen 9 DPADREEVAEQLRDACEEWGFFYLVNH-GIPQELIDRVFAAAR 50 (116)
T ss_dssp CHHHHHHHHHHHHHHHHHTSEEEEESS-SSSHHHHHHHHHHHH
T ss_pred CCccHHHHHHHHHHHHHhCCEEEEecc-cccchhhHHHHHHHH
Confidence 357788999999999999998877776 999988877765543
No 21
>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=37.01 E-value=89 Score=22.92 Aligned_cols=63 Identities=14% Similarity=0.224 Sum_probs=44.9
Q ss_pred HHHHHHHHHHhcCC---------eEEEEEeCCCChhh------HHHHHHhcCC-CCEEEEEc-hHHHHHHHhcCCccccc
Q 027713 50 ETVDTVKTHLENCH---------LIAAIKYKGFTVKQ------FQDLRRSLPE-NTKLIVAK-NTLVYKAIEGTQWEALK 112 (220)
Q Consensus 50 ~~v~~l~e~l~~s~---------~v~vv~y~gl~~~~------~~~LR~~Lr~-~~~l~VvK-NtL~k~Al~~t~~~~L~ 112 (220)
.+.+.+.+.+.... ..+|+|+++++.-+ +.+++++++. ++.+.++. +.-++..++.+|+....
T Consensus 26 ~~~~~i~~~~~~~~~~~~~~~~~~~vIlD~s~v~~iDssgi~~L~~~~~~~~~~g~~~~l~~~~~~v~~~l~~~~~~~~~ 105 (117)
T PF01740_consen 26 EFRDRIRKLIDEDPERIKKRQTIKNVILDMSGVSFIDSSGIQALVDIIKELRRRGVQLVLVGLNPDVRRILERSGLIDFI 105 (117)
T ss_dssp HHHHHHHHHHCCSSS--HTSSSSSEEEEEETTESEESHHHHHHHHHHHHHHHHTTCEEEEESHHHHHHHHHHHTTGHHHS
T ss_pred HHHHHHHHhhhcccccccccccceEEEEEEEeCCcCCHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHcCCChhc
Confidence 45666777777764 89999999987644 4566777863 46666544 77777889999886543
No 22
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=35.26 E-value=1.5e+02 Score=20.48 Aligned_cols=60 Identities=20% Similarity=0.241 Sum_probs=45.8
Q ss_pred ceeeeeeCCeecCHhhHHHhhcCCCHHHHHHHHHHHHHH----HHHHHHHHhhchHHHHHHHHH
Q 027713 149 DFAGAVFEGKFYAPGDFKALESMPTRAEIYAKLLGALQG----SAIGLVGTLQAPARDLLMVLK 208 (220)
Q Consensus 149 ~l~gg~veg~~l~~~~v~~lakLPs~e~l~aqlv~~L~~----p~~~l~~~L~~~~~~L~~~L~ 208 (220)
.+....++..+++.++.+.+...|+..+=..+|+-+|.. ....|..+|......|+..|.
T Consensus 20 ~ild~L~~~~vlt~~e~e~I~~~~t~~~k~~~LLd~l~~kg~~a~~~F~~~L~~~~~~La~~L~ 83 (85)
T PF00619_consen 20 DILDHLLSRGVLTEEEYEEIRSEPTRQDKARKLLDILKRKGPEAFDIFCQALRENQPHLADDLE 83 (85)
T ss_dssp HHHHHHHHTTSSSHHHHHHHHTSSSHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHCCCCCHHHHHHHHccCChHHHHHHHHHHHHHHCHHHHHHHHHHHHhhCHHHHHHHc
Confidence 355667788899999999999999999999999999973 334566666666666665543
No 23
>COG2429 Archaeal GTP cyclohydrolase III [Nucleotide transport and metabolism]
Probab=32.54 E-value=89 Score=27.37 Aligned_cols=47 Identities=13% Similarity=0.046 Sum_probs=37.3
Q ss_pred cccccccccCceEEEEeecCChhHHhHHHHHHHhhcCcCCcceeeeeeCC
Q 027713 108 WEALKPCMSGMNAWLFVHTEEIPAAIKPYRNFQKEKKLEENDFAGAVFEG 157 (220)
Q Consensus 108 ~~~L~~~l~G~talvfs~~~~~~~~aK~l~~f~K~~~~~~l~l~gg~veg 157 (220)
+..|.-++-|-+.+.++++.+...+.+++..+.++++ +.++.|+=-|
T Consensus 173 ~gal~fflGGDN~ma~~p~~s~g~v~d~i~~v~~~~~---v~lkvGIGig 219 (250)
T COG2429 173 IGALLFFLGGDNIMAVCPGLSAGDVLDAIAEVLDDAE---VDLKVGIGIG 219 (250)
T ss_pred cCcEEEEecCcceEEECCCCCchhHHHHHHHHHHhhc---cceEeeeccC
Confidence 5678889999999999997766667788888888873 5788887444
No 24
>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]
Probab=32.51 E-value=77 Score=34.48 Aligned_cols=61 Identities=21% Similarity=0.265 Sum_probs=46.8
Q ss_pred CCCCCCCCCCCCCC----------CCchhhhccChhHHHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHh
Q 027713 21 NPLFHFHPSKRSKP----------PPTHIRAAISRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRS 84 (220)
Q Consensus 21 ~~~~~~~~~~~~~~----------~~~~~~~a~~r~~K~~~v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~ 84 (220)
.-+|||-|+=+|.| |-+.+++- .-....++++-+...+++.+++||++.=|++--..+|..
T Consensus 499 ~glf~fd~syRpvPL~qq~Igi~ek~~~~~~q---amNe~~yeKVm~~agk~qVLVFVHsRkET~ktA~aIRd~ 569 (1674)
T KOG0951|consen 499 EGLFYFDSSYRPVPLKQQYIGITEKKPLKRFQ---AMNEACYEKVLEHAGKNQVLVFVHSRKETAKTARAIRDK 569 (1674)
T ss_pred ccccccCcccCcCCccceEeccccCCchHHHH---HHHHHHHHHHHHhCCCCcEEEEEEechHHHHHHHHHHHH
Confidence 45799999999988 22232211 113367888899999999999999999999999999944
No 25
>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=28.40 E-value=1.2e+02 Score=24.71 Aligned_cols=26 Identities=15% Similarity=0.381 Sum_probs=23.2
Q ss_pred cCCeEEEEEeCC-CChhhHHHHHHhcC
Q 027713 61 NCHLIAAIKYKG-FTVKQFQDLRRSLP 86 (220)
Q Consensus 61 ~s~~v~vv~y~g-l~~~~~~~LR~~Lr 86 (220)
..+.++|+||+| +.+.+...||.++.
T Consensus 96 ~~~r~~VldF~Gdi~A~~v~~LReeis 122 (155)
T PF08496_consen 96 PKPRLFVLDFKGDIKASEVESLREEIS 122 (155)
T ss_pred CCCeEEEEecCCCccHHHHHHHHHHHH
Confidence 468899999998 99999999999864
No 26
>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=26.47 E-value=71 Score=25.10 Aligned_cols=32 Identities=16% Similarity=0.262 Sum_probs=27.7
Q ss_pred HHHhcCCeEEEEEeCCCChhhHHHHHHhcCCC
Q 027713 57 THLENCHLIAAIKYKGFTVKQFQDLRRSLPEN 88 (220)
Q Consensus 57 e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr~~ 88 (220)
..+..+..++++|+.++..+++.++|+.+...
T Consensus 25 ~~l~~~sglv~lDiD~l~~ee~~~~r~~l~~~ 56 (136)
T PF08800_consen 25 DNLKAYSGLVVLDIDHLDPEEAEELRQLLFED 56 (136)
T ss_pred hhhhhCCCcEEEEeCCCCHHHHHHHHHHHhcC
Confidence 45667888999999999999999999998765
No 27
>PF13758 Prefoldin_3: Prefoldin subunit
Probab=26.35 E-value=1.2e+02 Score=23.07 Aligned_cols=23 Identities=13% Similarity=0.164 Sum_probs=17.7
Q ss_pred eeeeeCCeecCHhhHHHhhcCCC
Q 027713 151 AGAVFEGKFYAPGDFKALESMPT 173 (220)
Q Consensus 151 ~gg~veg~~l~~~~v~~lakLPs 173 (220)
.|--++|.+++..+|+.+-.-++
T Consensus 38 i~r~f~g~lv~~kEi~~ilG~~~ 60 (99)
T PF13758_consen 38 IRRDFGGSLVTEKEIKEILGEGQ 60 (99)
T ss_pred HHHhcCcccccHHHHHHHhCCCC
Confidence 34456799999999998877654
No 28
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=25.39 E-value=57 Score=35.18 Aligned_cols=55 Identities=22% Similarity=0.293 Sum_probs=32.4
Q ss_pred CCCCCCCCCCCCCCCCCCCchhhhccChhHHHHHHHHHHHHHhcCCeEEEEEeCCCC
Q 027713 18 PSTNPLFHFHPSKRSKPPPTHIRAAISRTKKEETVDTVKTHLENCHLIAAIKYKGFT 74 (220)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~a~~r~~K~~~v~~l~e~l~~s~~v~vv~y~gl~ 74 (220)
|..-|+-+=||+|||.|+|+..--.....++..++..+...+.+ -++..+.+...
T Consensus 11 ppppppg~epps~pppPppPg~~~~~r~~k~~~~~g~~~~~~g~--~~~~~r~S~k~ 65 (2365)
T COG5178 11 PPPPPPGFEPPSQPPPPPPPGVNVKKRSRKQLSIVGDILGHSGN--PIYSLRVSDKP 65 (2365)
T ss_pred ccccCCCCCCCCCCCCccCCCcchhhhccccHHHhhhhhhhcCC--cceeeecccch
Confidence 44556777899999888887755333334455566666554443 34444444443
No 29
>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=25.20 E-value=1.3e+02 Score=21.58 Aligned_cols=45 Identities=11% Similarity=0.146 Sum_probs=33.8
Q ss_pred HHHHHHhcCCcccccccccCceEEEEeecCChhHHhHHHHHHHhh
Q 027713 98 LVYKAIEGTQWEALKPCMSGMNAWLFVHTEEIPAAIKPYRNFQKE 142 (220)
Q Consensus 98 L~k~Al~~t~~~~L~~~l~G~talvfs~~~~~~~~aK~l~~f~K~ 142 (220)
-+++||...||..+.+.=.|...-+....++...+.+.+.+.+++
T Consensus 20 ai~~al~~lG~~~v~~Vr~GK~~~l~~~~~~~e~a~~~v~~i~~~ 64 (80)
T PF02700_consen 20 AIKRALHRLGYDGVKDVRVGKYIELELEADDEEEAEEQVEEICEK 64 (80)
T ss_dssp HHHHHHHHTT-TTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCcccCcEEEEEEEEEEEeCCCHHHHHHHHHHHHHH
Confidence 356788899999999999999999988877776666666666654
No 30
>TIGR00377 ant_ant_sig anti-anti-sigma factor. This superfamily includes small (105-125 residue) proteins related to SpoIIAA of Bacillus subtilis, an anti-anti-sigma factor. SpoIIAA can bind to and inhibit the anti-sigma F factor SpoIIAB. Also, it can be phosphorylated by SpoIIAB on a Ser residue at position 59 of the seed alignment. A similar arrangement is inferred for RsbV, an anti-anti-sigma factor for sigma B. This Ser is fairly well conserved within a motif resembling MXS[STA]G[VIL]X[VIL][VILF] among homologous known or predicted anti-anti-sigma factors. Regions similar to SpoIIAA and apparently homologous, but differing considerably near the phosphorlated Ser of SpoIIAA, appear in a single copy in several longer proteins.
Probab=23.04 E-value=2.9e+02 Score=19.68 Aligned_cols=62 Identities=10% Similarity=0.104 Sum_probs=41.3
Q ss_pred HHHHHHHh-cCCeEEEEEeCCCCh------hhHHHHHHhcCCC-CEEEEEc-hHHHHHHHhcCCccccccc
Q 027713 53 DTVKTHLE-NCHLIAAIKYKGFTV------KQFQDLRRSLPEN-TKLIVAK-NTLVYKAIEGTQWEALKPC 114 (220)
Q Consensus 53 ~~l~e~l~-~s~~v~vv~y~gl~~------~~~~~LR~~Lr~~-~~l~VvK-NtL~k~Al~~t~~~~L~~~ 114 (220)
+.+.+.+. .....+++|+++++- .-+..+++++++. +.+.++. |.=+++.++.+++..+.++
T Consensus 32 ~~l~~~~~~~~~~~vvidls~v~~iDssgl~~L~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~l~~~~~i 102 (108)
T TIGR00377 32 EKVTPAAERTGPRPIVLDLEDLEFMDSSGLGVLLGRYKQVRRVGGQLVLVSVSPRVARLLDITGLLRIIPI 102 (108)
T ss_pred HHHHHHHHhcCCCeEEEECCCCeEEccccHHHHHHHHHHHHhcCCEEEEEeCCHHHHHHHHHhChhheecc
Confidence 44556665 356678888888665 3445666777654 6766654 8888889988887765543
No 31
>PLN02276 gibberellin 20-oxidase
Probab=22.08 E-value=2e+02 Score=26.31 Aligned_cols=71 Identities=11% Similarity=0.128 Sum_probs=46.3
Q ss_pred CCCCCCCCCCCCCCCCC-CCCCCc-----hhhhcc----ChhHHHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHh
Q 027713 15 TLKPSTNPLFHFHPSKR-SKPPPT-----HIRAAI----SRTKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRS 84 (220)
Q Consensus 15 ~~~~~~~~~~~~~~~~~-~~~~~~-----~~~~a~----~r~~K~~~v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~ 84 (220)
+.+.++.|..|+.|... |+..+. .+-.+. ..+.+..++++|.+..++..++.|++ +|++.+.+.+++..
T Consensus 14 ~~~~~~vp~~~~~~~~~~p~~~~~~~~iPvIDls~~~~~~~~~~~~~~~~l~~Ac~~~GFF~l~n-HGI~~~l~~~~~~~ 92 (361)
T PLN02276 14 LQKQSNIPAQFIWPDEEKPSAAVPELAVPLIDLGGFLSGDEAATAEAARLVREACLKHGFFQVVN-HGVDAALIRAAHEY 92 (361)
T ss_pred hcCCCCCCHHhcCCccccCCCCCcCCCCCeEEChhhcCCChHHHHHHHHHHHHHHHHCcEEEEEc-CCCCHHHHHHHHHH
Confidence 33556788888877633 321111 111211 23456779999999999999888887 68999888888765
Q ss_pred cC
Q 027713 85 LP 86 (220)
Q Consensus 85 Lr 86 (220)
.+
T Consensus 93 ~~ 94 (361)
T PLN02276 93 MD 94 (361)
T ss_pred HH
Confidence 44
No 32
>PF09949 DUF2183: Uncharacterized conserved protein (DUF2183); InterPro: IPR019236 This domain, found in various bacterial and fungal proteins, has no known function.
Probab=21.15 E-value=3.6e+02 Score=20.13 Aligned_cols=51 Identities=10% Similarity=0.229 Sum_probs=43.7
Q ss_pred hHHHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHHhcCCCCEEEEEch
Q 027713 46 TKKEETVDTVKTHLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKN 96 (220)
Q Consensus 46 ~~K~~~v~~l~e~l~~s~~v~vv~y~gl~~~~~~~LR~~Lr~~~~l~VvKN 96 (220)
+.|...++++-+.+-+.+.|+|-|-..-+.+--.++.++..+.+.-..+|+
T Consensus 49 ~~K~~~i~~i~~~fP~~kfiLIGDsgq~DpeiY~~ia~~~P~~i~ai~IR~ 99 (100)
T PF09949_consen 49 EHKRDNIERILRDFPERKFILIGDSGQHDPEIYAEIARRFPGRILAIYIRD 99 (100)
T ss_pred hHHHHHHHHHHHHCCCCcEEEEeeCCCcCHHHHHHHHHHCCCCEEEEEEEe
Confidence 589999999999999999999999999999988999999887755444443
Done!