Query 026573
Match_columns 236
No_of_seqs 149 out of 982
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 09:46:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026573.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026573hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00084 rpl19 ribosomal prote 100.0 9E-42 2E-46 276.0 12.6 103 132-234 9-112 (117)
2 PRK05338 rplS 50S ribosomal pr 100.0 9.7E-42 2.1E-46 275.4 11.6 103 132-234 5-108 (116)
3 TIGR01024 rplS_bact ribosomal 100.0 1.3E-41 2.8E-46 273.7 11.8 103 132-234 5-108 (113)
4 PF01245 Ribosomal_L19: Riboso 100.0 4.8E-41 1E-45 269.5 13.5 105 126-232 1-106 (113)
5 COG0335 RplS Ribosomal protein 100.0 1.1E-40 2.4E-45 269.1 11.2 100 132-231 7-107 (115)
6 KOG1698 Mitochondrial/chloropl 100.0 2.7E-40 5.8E-45 287.2 11.1 179 42-236 6-187 (201)
7 PF05641 Agenet: Agenet domain 78.3 7 0.00015 28.3 5.3 38 146-188 1-38 (68)
8 PRK01191 rpl24p 50S ribosomal 78.0 4.8 0.0001 33.5 4.9 81 133-222 34-116 (120)
9 smart00743 Agenet Tudor-like d 75.3 17 0.00036 25.2 6.4 49 144-200 1-49 (61)
10 TIGR01080 rplX_A_E ribosomal p 68.8 9.6 0.00021 31.3 4.5 73 140-221 37-111 (114)
11 PF14153 Spore_coat_CotO: Spor 58.6 28 0.00061 30.7 5.8 69 113-197 104-172 (185)
12 PF12969 DUF3857: Domain of Un 57.6 20 0.00043 28.7 4.4 20 141-160 85-104 (177)
13 TIGR03170 flgA_cterm flagella 49.0 56 0.0012 25.5 5.6 46 142-192 62-107 (122)
14 PF02765 POT1: Telomeric singl 48.4 23 0.00049 29.0 3.4 47 142-196 69-117 (146)
15 COG2139 RPL21A Ribosomal prote 47.9 20 0.00043 29.2 2.9 45 141-185 28-76 (98)
16 smart00739 KOW KOW (Kyprides, 45.0 49 0.0011 19.1 3.7 27 145-177 1-27 (28)
17 PRK04183 glutamyl-tRNA(Gln) am 44.1 45 0.00096 32.7 5.2 56 145-215 2-57 (419)
18 PTZ00194 60S ribosomal protein 43.8 40 0.00086 29.0 4.3 71 132-211 34-106 (143)
19 cd04497 hPOT1_OB1_like hPOT1_O 41.9 43 0.00094 27.2 4.1 41 141-188 64-104 (138)
20 COG1566 EmrA Multidrug resista 40.2 54 0.0012 31.5 5.0 64 134-200 247-319 (352)
21 PF03888 MucB_RseB: MucB/RseB 39.8 1.1E+02 0.0023 28.1 6.8 49 164-215 9-57 (285)
22 cd08544 Reeler Reeler, the N-t 39.0 68 0.0015 25.5 4.7 31 145-179 29-59 (135)
23 PF02211 NHase_beta: Nitrile h 38.8 32 0.00069 31.1 3.1 36 142-177 131-170 (222)
24 PF13144 SAF_2: SAF-like 37.9 1.1E+02 0.0023 25.8 6.0 47 141-192 135-181 (196)
25 cd00493 FabA_FabZ FabA/Z, beta 35.9 59 0.0013 24.5 3.8 29 145-173 88-116 (131)
26 cd01737 LSm16_N LSm16 belongs 33.1 83 0.0018 23.8 4.0 46 148-200 5-54 (62)
27 cd01288 FabZ FabZ is a 17kD be 33.1 66 0.0014 24.4 3.7 28 145-172 87-114 (131)
28 cd06462 Peptidase_S24_S26 The 33.0 1.6E+02 0.0036 20.3 5.5 43 143-193 11-53 (84)
29 PF12148 DUF3590: Protein of u 32.9 27 0.00058 27.6 1.5 23 142-164 62-84 (85)
30 TIGR01750 fabZ beta-hydroxyacy 32.7 70 0.0015 25.1 3.9 28 145-172 97-124 (140)
31 PRK03999 translation initiatio 31.8 1E+02 0.0023 25.4 4.9 56 142-202 7-62 (129)
32 TIGR00405 L26e_arch ribosomal 31.4 2.4E+02 0.0053 22.8 6.9 43 144-194 85-127 (145)
33 PF08207 EFP_N: Elongation fac 28.9 2E+02 0.0043 20.4 5.3 19 182-200 35-53 (58)
34 PRK07018 flgA flagellar basal 28.8 1.4E+02 0.0029 26.6 5.4 47 142-193 173-219 (235)
35 TIGR00922 nusG transcription t 28.2 3.4E+02 0.0073 22.3 7.8 28 144-177 118-145 (172)
36 PRK08571 rpl14p 50S ribosomal 28.0 1.3E+02 0.0029 25.4 4.9 36 142-177 43-78 (132)
37 COG0250 NusG Transcription ant 27.7 2.6E+02 0.0055 24.4 6.8 33 140-178 118-150 (178)
38 PF08572 PRP3: pre-mRNA proces 27.4 39 0.00085 30.5 1.8 22 113-134 170-191 (223)
39 PRK00006 fabZ (3R)-hydroxymyri 27.1 90 0.002 24.8 3.7 27 146-172 102-128 (147)
40 PF02014 Reeler: Reeler domain 26.9 63 0.0014 25.7 2.7 32 144-179 28-59 (132)
41 PRK09455 rseB anti-sigma E fac 26.9 2.3E+02 0.005 26.7 6.8 49 163-215 39-88 (319)
42 PF09926 DUF2158: Uncharacteri 25.6 46 0.00099 23.9 1.5 11 146-156 1-11 (53)
43 PF07977 FabA: FabA-like domai 25.5 74 0.0016 25.1 2.9 29 144-172 95-127 (138)
44 PRK05609 nusG transcription an 25.5 3.9E+02 0.0084 22.1 7.9 46 143-196 124-169 (181)
45 TIGR01955 RfaH transcriptional 25.4 1.5E+02 0.0032 24.0 4.7 29 144-178 107-135 (159)
46 PF00717 Peptidase_S24: Peptid 25.2 90 0.002 21.4 3.0 43 143-194 8-51 (70)
47 TIGR00008 infA translation ini 24.8 54 0.0012 24.8 1.9 23 142-164 41-64 (68)
48 PF02752 Arrestin_C: Arrestin 24.6 1.1E+02 0.0024 22.8 3.6 30 145-174 15-45 (136)
49 PF00238 Ribosomal_L14: Riboso 24.6 1.4E+02 0.003 24.5 4.3 36 142-177 29-67 (122)
50 TIGR03673 rpl14p_arch 50S ribo 24.3 1.6E+02 0.0035 24.8 4.8 35 143-177 43-77 (131)
51 PTZ00054 60S ribosomal protein 23.9 1.6E+02 0.0035 25.1 4.8 35 143-177 51-85 (139)
52 TIGR02266 gmx_TIGR02266 Myxoco 23.7 2.9E+02 0.0063 20.0 5.9 45 144-196 35-79 (96)
53 PRK06005 flgA flagellar basal 23.3 2.3E+02 0.0049 24.1 5.5 49 142-195 97-145 (160)
54 PF07238 PilZ: PilZ domain; I 23.0 2.7E+02 0.0059 19.4 5.3 32 145-178 44-75 (102)
55 COG0361 InfA Translation initi 22.8 63 0.0014 25.0 1.9 23 142-164 43-66 (75)
56 PRK15136 multidrug efflux syst 22.2 1.7E+02 0.0036 27.7 5.0 32 142-176 262-293 (390)
57 PF01458 UPF0051: Uncharacteri 22.1 4.4E+02 0.0096 22.8 7.3 61 164-228 145-214 (229)
58 PRK04306 50S ribosomal protein 22.0 1.1E+02 0.0024 24.7 3.2 44 143-186 32-79 (98)
59 PRK05483 rplN 50S ribosomal pr 21.8 1.7E+02 0.0038 24.2 4.4 34 144-177 31-67 (122)
60 PF10447 EXOSC1: Exosome compo 21.3 66 0.0014 24.9 1.8 13 144-156 67-79 (82)
61 cd00164 S1_like S1_like: Ribos 21.3 1.1E+02 0.0023 19.7 2.6 15 145-159 41-55 (65)
62 PRK08559 nusG transcription an 21.2 2.8E+02 0.006 23.1 5.6 29 144-178 93-121 (153)
63 PF12945 YcgR_2: Flagellar pro 21.1 2.8E+02 0.006 19.7 5.0 33 144-179 46-78 (87)
64 cd05708 S1_Rrp5_repeat_sc12 S1 20.5 1.1E+02 0.0023 21.2 2.6 16 145-160 47-62 (77)
65 PF03946 Ribosomal_L11_N: Ribo 20.4 3.1E+02 0.0068 19.9 5.1 43 112-162 13-58 (60)
66 cd05690 S1_RPS1_repeat_ec5 S1_ 20.3 1E+02 0.0022 21.0 2.4 21 145-165 45-66 (69)
No 1
>CHL00084 rpl19 ribosomal protein L19
Probab=100.00 E-value=9e-42 Score=276.05 Aligned_cols=103 Identities=40% Similarity=0.785 Sum_probs=98.4
Q ss_pred HHHHhhhcCCCCCCCCCCCEEEEEEEeec-CccccceEEEEEEEEecCCccceEEEEeeeCCeeEEEEeeccCCccceEE
Q 026573 132 RAVEASESERPIPDIRTGDVVEIKLEVPE-NRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVEIVFPLYSPNIKEIK 210 (236)
Q Consensus 132 ~~ie~~~~kk~iP~f~~GDiV~V~~~i~E-~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~GvGVEr~FpLySP~I~~Ie 210 (236)
+.+++.+.+.++|+|++||||+|++.+.| +|+|+|.|+|+||+++|+|+++||||||+++|+|||++||||||.|++|+
T Consensus 9 ~~~~~~~~~~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvRki~~gvGVEr~fpl~SP~I~~Ie 88 (117)
T CHL00084 9 KEIESEFLKKNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVRKVFQGIGVERVFLLHSPKLASIE 88 (117)
T ss_pred HHHHHHHhhcCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEEEeccCccEEEEEecCCCccceEE
Confidence 57888888899999999999999999999 89999999999999999999999999999999999999999999999999
Q ss_pred EeeecccCCcceeeeccCCCCCCC
Q 026573 211 VVSHRKVRRARLYYLRDKLPRLST 234 (236)
Q Consensus 211 Vlrr~KVRRAKLYYLRdk~~r~ST 234 (236)
|++++|||||||||||++.++-..
T Consensus 89 V~r~gkvRRAKLyYLR~~~gKaar 112 (117)
T CHL00084 89 VLRRSKVRRAKLYYLRNRVGKAAR 112 (117)
T ss_pred EEEeCccchheeEEeccCcChhhe
Confidence 999999999999999999887543
No 2
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=100.00 E-value=9.7e-42 Score=275.43 Aligned_cols=103 Identities=41% Similarity=0.778 Sum_probs=97.3
Q ss_pred HHHHhhhcCCCCCCCCCCCEEEEEEEeec-CccccceEEEEEEEEecCCccceEEEEeeeCCeeEEEEeeccCCccceEE
Q 026573 132 RAVEASESERPIPDIRTGDVVEIKLEVPE-NRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVEIVFPLYSPNIKEIK 210 (236)
Q Consensus 132 ~~ie~~~~kk~iP~f~~GDiV~V~~~i~E-~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~GvGVEr~FpLySP~I~~Ie 210 (236)
+.+|+.++++++|+|++||||+|+++|.| +|+|+|.|+|+||+++|+|+++||||||+++|+|||++||||||.|++|+
T Consensus 5 ~~~~~~~~~~~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki~~gvGVEr~fpl~SP~I~~Ie 84 (116)
T PRK05338 5 KEIEAEQLRKDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKISYGVGVERTFPLHSPRIDSIE 84 (116)
T ss_pred HHHHHHHhhcCCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEcccCccEEEEecCCCCcccEEE
Confidence 45777777899999999999999999999 89999999999999999999999999999999999999999999999999
Q ss_pred EeeecccCCcceeeeccCCCCCCC
Q 026573 211 VVSHRKVRRARLYYLRDKLPRLST 234 (236)
Q Consensus 211 Vlrr~KVRRAKLYYLRdk~~r~ST 234 (236)
|++++|+|||||||||++.++-..
T Consensus 85 V~r~gkvRRAKLyYLR~~~gK~ar 108 (116)
T PRK05338 85 VVRRGKVRRAKLYYLRELRGKAAR 108 (116)
T ss_pred EEEecccchhheeeeccCcchhhe
Confidence 999999999999999999876543
No 3
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=100.00 E-value=1.3e-41 Score=273.69 Aligned_cols=103 Identities=40% Similarity=0.811 Sum_probs=97.7
Q ss_pred HHHHhhhcCCCCCCCCCCCEEEEEEEeec-CccccceEEEEEEEEecCCccceEEEEeeeCCeeEEEEeeccCCccceEE
Q 026573 132 RAVEASESERPIPDIRTGDVVEIKLEVPE-NRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVEIVFPLYSPNIKEIK 210 (236)
Q Consensus 132 ~~ie~~~~kk~iP~f~~GDiV~V~~~i~E-~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~GvGVEr~FpLySP~I~~Ie 210 (236)
+.+|+.+.++++|+|++||+|+|++.+.| +|+|+|.|+|+||+++|+|+++||||||+++|+|||++||||||.|++|+
T Consensus 5 ~~~e~~~~~~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i~~gvGVEr~fpl~SP~I~~Ie 84 (113)
T TIGR01024 5 KQIEQEQLKKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKISYGVGVERIFPLHSPNIDSIE 84 (113)
T ss_pred HHHHHHHhhcCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEeccCccEEEEEEcCCCccceEE
Confidence 45677777899999999999999999999 89999999999999999999999999999999999999999999999999
Q ss_pred EeeecccCCcceeeeccCCCCCCC
Q 026573 211 VVSHRKVRRARLYYLRDKLPRLST 234 (236)
Q Consensus 211 Vlrr~KVRRAKLYYLRdk~~r~ST 234 (236)
|++++|+|||||||||++.++-+.
T Consensus 85 Vl~~~kvrRaKLyYLR~~~gK~ar 108 (113)
T TIGR01024 85 VVRRGKVRRAKLYYLRERRGKAAR 108 (113)
T ss_pred EEEeCccchhheeeeccCcchhhe
Confidence 999999999999999999887544
No 4
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 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 [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=100.00 E-value=4.8e-41 Score=269.53 Aligned_cols=105 Identities=42% Similarity=0.848 Sum_probs=99.2
Q ss_pred HHHHHHHHHHhhhcCCCCCCCCCCCEEEEEEEeec-CccccceEEEEEEEEecCCccceEEEEeeeCCeeEEEEeeccCC
Q 026573 126 MGILNKRAVEASESERPIPDIRTGDVVEIKLEVPE-NRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVEIVFPLYSP 204 (236)
Q Consensus 126 M~iLe~~~ie~~~~kk~iP~f~~GDiV~V~~~i~E-~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~GvGVEr~FpLySP 204 (236)
|++| +++|+.+.+.++|+|++||+|+|++.+.| +|+|+|.|+|+||+++|+|+++||||||+++|+|||++||||||
T Consensus 1 ~~~i--~~~e~~~~~~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~~~~g~gVE~~f~l~SP 78 (113)
T PF01245_consen 1 MNLI--EEVEREQIKKDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRNISQGVGVERVFPLYSP 78 (113)
T ss_dssp -HHH--HHHHHTTCSSSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEEEETTEEEEEEEETTST
T ss_pred ChHH--HHHHHHHhhcCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEEEecCccEEEEEEcCCC
Confidence 5666 68888888999999999999999999998 89999999999999999999999999999999999999999999
Q ss_pred ccceEEEeeecccCCcceeeeccCCCCC
Q 026573 205 NIKEIKVVSHRKVRRARLYYLRDKLPRL 232 (236)
Q Consensus 205 ~I~~IeVlrr~KVRRAKLYYLRdk~~r~ 232 (236)
.|++|+|++++|+|||||||||++.++.
T Consensus 79 ~I~~IeV~~~~kvrRaKLyYLR~~~gK~ 106 (113)
T PF01245_consen 79 LIKSIEVLRRGKVRRAKLYYLRDRKGKA 106 (113)
T ss_dssp TEEEEEEEEEBECSSSSTGGGGCTTSHH
T ss_pred CeEEEEEEEecccchhhhhhhhcCccch
Confidence 9999999999999999999999988753
No 5
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-40 Score=269.06 Aligned_cols=100 Identities=41% Similarity=0.785 Sum_probs=95.7
Q ss_pred HHHHhhhcCCCCCCCCCCCEEEEEEEeec-CccccceEEEEEEEEecCCccceEEEEeeeCCeeEEEEeeccCCccceEE
Q 026573 132 RAVEASESERPIPDIRTGDVVEIKLEVPE-NRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVEIVFPLYSPNIKEIK 210 (236)
Q Consensus 132 ~~ie~~~~kk~iP~f~~GDiV~V~~~i~E-~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~GvGVEr~FpLySP~I~~Ie 210 (236)
+.+++.|.++++|+|+|||||+|++++.| +|+|+|.|+|+||+++|+|+++|||||++++|+|||++||+|||.|++|+
T Consensus 7 ~~le~~q~~~~iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~~~tftvRkis~G~GVEr~Fp~~SP~Ie~Ie 86 (115)
T COG0335 7 QQLEQEQIKKDIPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGISETFTVRKISYGVGVERVFPLHSPLIESIE 86 (115)
T ss_pred HHHHHHHHHhhCCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCCCccceEEEEEeecCceEEEEeecCCCceeEEE
Confidence 56777777888999999999999999999 89999999999999999999999999999999999999999999999999
Q ss_pred EeeecccCCcceeeeccCCCC
Q 026573 211 VVSHRKVRRARLYYLRDKLPR 231 (236)
Q Consensus 211 Vlrr~KVRRAKLYYLRdk~~r 231 (236)
|+++|+||||||||||++..+
T Consensus 87 V~rrGkVRRAKLYYLR~~~GK 107 (115)
T COG0335 87 VVRRGKVRRAKLYYLRERRGK 107 (115)
T ss_pred EEecCceeeeeeEeeeccccc
Confidence 999999999999999998765
No 6
>KOG1698 consensus Mitochondrial/chloroplast ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.7e-40 Score=287.22 Aligned_cols=179 Identities=40% Similarity=0.578 Sum_probs=149.9
Q ss_pred eeeeec---ccccccccceecccccceEEeecchhhhhcchhHHHHHHHhhhhcCCeeeeeeccccchhhhhhcCCCCCC
Q 026573 42 VSVSAK---PIGWNLGFFVNAQVKDSFVVRAEANEEAEANESIEEEQNEAVQAQGDVVVAVEAESEDKVEEEEVKAPRKP 118 (236)
Q Consensus 42 ~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pp~k~ 118 (236)
+.++|+ +..|++.+.+.....++|+..++.-..+ +-++. .+.+...++..-.+..++.+.-
T Consensus 6 ~~~~r~~~~~~a~~~~v~l~~~~~~~~~~~~e~~~~a---------------~~~~~-~~~~~~~~~~~~~~~~~~f~~~ 69 (201)
T KOG1698|consen 6 LGFDRFPMFRAASYRNVSLKGKWFSSFIAISEERCFA---------------PTKRP-SVNEPSPESPCVVEQYPEFLPL 69 (201)
T ss_pred eeeecccccchhhhheeecccceeeeecccccccccc---------------CCCCc-ccccCCCCCccccccCcccccc
Confidence 455555 3566666666666777888766652222 22222 1234444444455566777777
Q ss_pred ccchhhHHHHHHHHHHHhhhcCCCCCCCCCCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEeeeCCeeEEEE
Q 026573 119 RVKLGDIMGILNKRAVEASESERPIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVEIV 198 (236)
Q Consensus 119 r~KL~dlM~iLe~~~ie~~~~kk~iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~GvGVEr~ 198 (236)
+...+++|++|++++++...+.+++|+|++||+|+|++.+++++.++..|.||||.++|+|+++||+|||+++|+|||..
T Consensus 70 ~~~~~~~~e~Ldr~a~~~rr~~r~iPe~~~G~Iv~V~s~~p~~k~k~s~f~Gi~I~R~~~Gl~atf~LRnvIagvGVEi~ 149 (201)
T KOG1698|consen 70 RKVAKRIMEILDRQAVLERRKVRDIPEFKVGSIVRVTSEDPENKRKVSRFKGICIRRRNAGLNATFLLRNVIAGVGVEIV 149 (201)
T ss_pred hhHHHHHHHhhCHHHHHHHHhcccCCccccccEEEEEecCCccCCceeEEEEEEEEecccCCcceEEeeehhhCceeEEE
Confidence 88899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeccCCccceEEEeeecccCCcceeeeccCCCCCCCCC
Q 026573 199 FPLYSPNIKEIKVVSHRKVRRARLYYLRDKLPRLSTFK 236 (236)
Q Consensus 199 FpLySP~I~~IeVlrr~KVRRAKLYYLRdk~~r~STf~ 236 (236)
||||||+|++|+|+++.|+|||+||||||.+++|||||
T Consensus 150 ~pLYsP~IkeI~Vlk~~k~rra~LyYLRd~lp~lstfd 187 (201)
T KOG1698|consen 150 FPLYSPNIKEIKVLKLEKRRRAKLYYLRDALPELSTFD 187 (201)
T ss_pred EeccCCCeeEEEEechhhcccchhhhhhccccccCchh
Confidence 99999999999999999999999999999999999996
No 7
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=78.31 E-value=7 Score=28.34 Aligned_cols=38 Identities=16% Similarity=0.270 Sum_probs=25.0
Q ss_pred CCCCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEe
Q 026573 146 IRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRR 188 (236)
Q Consensus 146 f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRn 188 (236)
|++||.|+|.... +.-|-.=|.|.|+...+.+ +++|+-
T Consensus 1 F~~G~~VEV~s~e--~g~~gaWf~a~V~~~~~~~---~~~V~Y 38 (68)
T PF05641_consen 1 FKKGDEVEVSSDE--DGFRGAWFPATVLKENGDD---KYLVEY 38 (68)
T ss_dssp --TT-EEEEEE-S--BTT--EEEEEEEEEEETT----EEEEEE
T ss_pred CCCCCEEEEEEcC--CCCCcEEEEEEEEEeCCCc---EEEEEE
Confidence 7899999998644 3447789999999999876 677764
No 8
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=78.02 E-value=4.8 Score=33.51 Aligned_cols=81 Identities=19% Similarity=0.196 Sum_probs=47.1
Q ss_pred HHHhhhcCCCCCCCCCCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEe--eeCCeeEEEEeeccCCccceEE
Q 026573 133 AVEASESERPIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRR--IIAGIGVEIVFPLYSPNIKEIK 210 (236)
Q Consensus 133 ~ie~~~~kk~iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRn--ii~GvGVEr~FpLySP~I~~Ie 210 (236)
++.+....+.+ .++.||.|.|.-=- .|. =+|.|+.+-...- .++|-. +....|+|+-+|||.-+|.=++
T Consensus 34 eLr~~y~ir~~-~IkkGD~V~VisG~--~KG----k~GkV~~V~~~~~--~V~VeGvn~~k~~G~~~e~pIh~SNV~l~~ 104 (120)
T PRK01191 34 ELREKYGIRSL-PVRKGDTVKVMRGD--FKG----EEGKVVEVDLKRG--RIYVEGVTVKKADGTEVPRPIHPSNVMITK 104 (120)
T ss_pred HHHHHhCCccc-eEeCCCEEEEeecC--CCC----ceEEEEEEEcCCC--EEEEeCcEEECCCCeEEEcccchhHeEEEe
Confidence 44444444555 59999999996421 122 2488888854321 233322 2234568999999988876555
Q ss_pred EeeecccCCcce
Q 026573 211 VVSHRKVRRARL 222 (236)
Q Consensus 211 Vlrr~KVRRAKL 222 (236)
..--.+.|.++|
T Consensus 105 l~l~~~~R~~~l 116 (120)
T PRK01191 105 LDLSDERREKIL 116 (120)
T ss_pred CccCCHHHHHHh
Confidence 543344444443
No 9
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=75.29 E-value=17 Score=25.19 Aligned_cols=49 Identities=16% Similarity=0.193 Sum_probs=34.6
Q ss_pred CCCCCCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEeeeCCeeEEEEee
Q 026573 144 PDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVEIVFP 200 (236)
Q Consensus 144 P~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~GvGVEr~Fp 200 (236)
+.|++||.|.+.+.. .-.=|.|+|++..+ +..+.|+=.-.+.|-+..|+
T Consensus 1 ~~~~~G~~Ve~~~~~-----~~~W~~a~V~~~~~---~~~~~V~~~~~~~~~~e~v~ 49 (61)
T smart00743 1 SDFKKGDRVEVFSKE-----EDSWWEAVVTKVLG---DGKYLVRYLTESEPLKETVD 49 (61)
T ss_pred CCcCCCCEEEEEECC-----CCEEEEEEEEEECC---CCEEEEEECCCCcccEEEEe
Confidence 368999999999853 23579999999877 34577765433366666655
No 10
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=68.76 E-value=9.6 Score=31.33 Aligned_cols=73 Identities=21% Similarity=0.221 Sum_probs=42.6
Q ss_pred CCCCCCCCCCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEee--eCCeeEEEEeeccCCccceEEEeeeccc
Q 026573 140 ERPIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRI--IAGIGVEIVFPLYSPNIKEIKVVSHRKV 217 (236)
Q Consensus 140 kk~iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRni--i~GvGVEr~FpLySP~I~~IeVlrr~KV 217 (236)
.+.+ .++-||.|.|.- ++. .-.+|.|+.+.++.. .+.|-.+ ....|++.-.|+|--+|.=+...--...
T Consensus 37 ~r~~-~IkkGD~V~Vi~----Gk~--KGk~GkV~~V~~~~~--~V~Vegvn~~k~~G~~~e~pIh~SnV~l~~l~l~~~~ 107 (114)
T TIGR01080 37 KRAL-PVRKGDKVRIMR----GDF--KGHEGKVSKVDLKRY--RIYVEGVTKEKVNGTEVPVPIHPSNVMITKLNLDDEK 107 (114)
T ss_pred cccc-eeecCCEEEEec----CCC--CCCEEEEEEEEcCCC--EEEEcCeEEECCCCeEEEeeechHHeEEEeccCChHH
Confidence 3444 699999999964 221 125699998875432 2222221 1123578888898877766655333333
Q ss_pred CCcc
Q 026573 218 RRAR 221 (236)
Q Consensus 218 RRAK 221 (236)
|+.+
T Consensus 108 R~~~ 111 (114)
T TIGR01080 108 RKKI 111 (114)
T ss_pred HHHH
Confidence 4443
No 11
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=58.57 E-value=28 Score=30.73 Aligned_cols=69 Identities=25% Similarity=0.295 Sum_probs=37.0
Q ss_pred CCCCCCccchhhHHHHHHHHHHHhhhcCCCCCCCCCCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEeeeCC
Q 026573 113 KAPRKPRVKLGDIMGILNKRAVEASESERPIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAG 192 (236)
Q Consensus 113 ~pp~k~r~KL~dlM~iLe~~~ie~~~~kk~iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~G 192 (236)
..+.+++.|-..-|++.+ .|+=.. ++|..-|-=.+.|... -..|.|+|+..++ ..+.|+-.-.|
T Consensus 104 ~~~~~~~~K~Fk~M~~~E--KI~fL~---~~P~~lp~i~C~i~t~-------~~~Y~G~I~~~~~----~~v~i~~~~~~ 167 (185)
T PF14153_consen 104 QVPTFPRKKSFKEMNIEE--KIDFLI---NLPHHLPPIKCEIETK-------DKSYRGIILSYDE----GEVSIMPFNQG 167 (185)
T ss_pred ccccccccCChhhccHHH--HHHHHH---hCcccCCCCceEEEeC-------CceEEEEEEeccC----CEEEEeccCCC
Confidence 345555666666787764 332222 2333222222344332 2479999999887 36777665455
Q ss_pred eeEEE
Q 026573 193 IGVEI 197 (236)
Q Consensus 193 vGVEr 197 (236)
.-++.
T Consensus 168 ~~~~i 172 (185)
T PF14153_consen 168 EEIEI 172 (185)
T ss_pred cceEe
Confidence 44443
No 12
>PF12969 DUF3857: Domain of Unknown Function with PDB structure (DUF3857); InterPro: IPR024618 This domain is based on the first domain of the PDB structure 3KD4 (residues 1-228). It is structurally similar to domains in other hydrolases, eg. M1 family aminopeptidase, despite lack of any significant sequence similarity. The domain is N-terminal to a transglutaminase domain, which is found in many proteins known to have transglutaminase activity. The function of this domain is unknown. ; PDB: 3KD4_A.
Probab=57.59 E-value=20 Score=28.71 Aligned_cols=20 Identities=30% Similarity=0.688 Sum_probs=13.1
Q ss_pred CCCCCCCCCCEEEEEEEeec
Q 026573 141 RPIPDIRTGDVVEIKLEVPE 160 (236)
Q Consensus 141 k~iP~f~~GDiV~V~~~i~E 160 (236)
-.+|++++||+|...|.+..
T Consensus 85 ~~~p~v~~GdiIe~~y~~~~ 104 (177)
T PF12969_consen 85 FAFPDVRVGDIIEYSYTIKS 104 (177)
T ss_dssp EE--S--TT-EEEEEEEEEE
T ss_pred EEcCCCCCCcEEEEEEEEEe
Confidence 46999999999999999865
No 13
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=48.97 E-value=56 Score=25.45 Aligned_cols=46 Identities=20% Similarity=0.251 Sum_probs=33.7
Q ss_pred CCCCCCCCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEeeeCC
Q 026573 142 PIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAG 192 (236)
Q Consensus 142 ~iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~G 192 (236)
.-|-++-||.|.|.+.... + ...-...|..+.+++.+++|||...|
T Consensus 62 ~~~~V~~G~~V~i~~~~~~----~-~i~~~g~Al~~g~~G~~I~V~N~~s~ 107 (122)
T TIGR03170 62 PPWLVKRGDTVTVIARGGG----L-SVTTEGKALEDGAVGDQIRVRNLSSG 107 (122)
T ss_pred CccEEcCCCEEEEEEecCC----E-EEEEEEEEccccCCCCEEEEEECCCC
Confidence 4577999999999986532 1 12334457778899999999996544
No 14
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold []. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....
Probab=48.38 E-value=23 Score=29.00 Aligned_cols=47 Identities=19% Similarity=0.489 Sum_probs=31.5
Q ss_pred CCCCCCC-CCEEEEE-EEeecCccccceEEEEEEEEecCCccceEEEEeeeCCeeEE
Q 026573 142 PIPDIRT-GDVVEIK-LEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVE 196 (236)
Q Consensus 142 ~iP~f~~-GDiV~V~-~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~GvGVE 196 (236)
.+|.+.. ||+|.++ +++ |.|.|-..+..+.+-++++.|= .-++.|..
T Consensus 69 ~LP~v~~~GDii~l~r~kv-------~~~~~~~~~~~~~~~~ss~~vf-~~~~~~~~ 117 (146)
T PF02765_consen 69 SLPNVKSVGDIIRLRRVKV-------QSYNGKPQGLSNSTSNSSWAVF-SSGGSGAP 117 (146)
T ss_dssp HSCTTCSTTHEEEEEEEEE-------EEETTEEEEEEECECTEEEEEE-CTSSTTTC
T ss_pred HCCCCCCCCCEEEEEEEEE-------EEECCEEEEEecCCCcEEEEEE-ecCCCCCC
Confidence 4799888 9999998 554 5677766676666656777664 23444433
No 15
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=47.93 E-value=20 Score=29.22 Aligned_cols=45 Identities=18% Similarity=0.324 Sum_probs=33.4
Q ss_pred CCCCCCCCCCEEEEEEEee--c--CccccceEEEEEEEEecCCccceEE
Q 026573 141 RPIPDIRTGDVVEIKLEVP--E--NRRRLSIYKGIVMSRQNAGIHTTIR 185 (236)
Q Consensus 141 k~iP~f~~GDiV~V~~~i~--E--~K~RiQ~F~GVVIa~r~~Gl~sTFt 185 (236)
+-+-+|.+||.|-|.+.=. . .-.|.|=..|+|+.++++...-.+.
T Consensus 28 r~l~ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~ 76 (98)
T COG2139 28 RYLQEYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVY 76 (98)
T ss_pred hHHhhccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEe
Confidence 3467899999998886432 1 3678999999999999976544443
No 16
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=44.96 E-value=49 Score=19.14 Aligned_cols=27 Identities=19% Similarity=0.238 Sum_probs=18.6
Q ss_pred CCCCCCEEEEEEEeecCccccceEEEEEEEEec
Q 026573 145 DIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQN 177 (236)
Q Consensus 145 ~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~ 177 (236)
.|.+||.|.|.-= ...-+.|+++.+.+
T Consensus 1 ~~~~G~~V~I~~G------~~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIAG------PFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeEC------CCCCcEEEEEEEcC
Confidence 3789999999742 23346788887654
No 17
>PRK04183 glutamyl-tRNA(Gln) amidotransferase subunit D; Validated
Probab=44.08 E-value=45 Score=32.69 Aligned_cols=56 Identities=27% Similarity=0.525 Sum_probs=35.2
Q ss_pred CCCCCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEeeeCCeeEEEEeeccCCccceEEEeeec
Q 026573 145 DIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVEIVFPLYSPNIKEIKVVSHR 215 (236)
Q Consensus 145 ~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~GvGVEr~FpLySP~I~~IeVlrr~ 215 (236)
.+.+||.|+|.... ..|+|++|-... +-.-.+.|.|=+ ++|+.+ -.|.+|+++.++
T Consensus 2 ~~~~gd~v~~~~~~-------~~~~g~~~p~~~-~~~~~~kl~~gy-n~g~~~------~~~~~~~~~~~~ 57 (419)
T PRK04183 2 GMEVGDRVRVEKDD-------VVYEGILMPSYE-DDHIVIKLDNGY-NIGIDI------DKIAEIELLEKG 57 (419)
T ss_pred CCCCCCEEEEEECC-------eEEEEEEecCCC-CCEEEEEcCCCc-eeeecc------ccccceEEcccc
Confidence 37789999997532 689999997665 222334444433 366643 246667777654
No 18
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=43.79 E-value=40 Score=28.97 Aligned_cols=71 Identities=18% Similarity=0.221 Sum_probs=40.4
Q ss_pred HHHHhhhcCCCCCCCCCCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEee--eCCeeEEEEeeccCCccceE
Q 026573 132 RAVEASESERPIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRI--IAGIGVEIVFPLYSPNIKEI 209 (236)
Q Consensus 132 ~~ie~~~~kk~iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRni--i~GvGVEr~FpLySP~I~~I 209 (236)
+++.+....+.+ .++.||+|.|.-=- .|. -+|.|+.+-...- .+.|-.+ ....|-..-+|+|..+|.=+
T Consensus 34 keLr~k~~~Rs~-~IkkGD~V~Vi~Gk--~KG----k~GkV~~V~~k~~--~ViVEgvn~~Kk~gk~~e~PIh~SNV~iv 104 (143)
T PTZ00194 34 KELRAKYNVRSM-PVRKDDEVMVVRGH--HKG----REGKVTAVYRKKW--VIHIEKITREKANGEPVQIGIHPSNVIIT 104 (143)
T ss_pred HHHHHHhCCccc-eeecCCEEEEecCC--CCC----CceEEEEEEcCCC--EEEEeCeEEEecCCCEeecCcCchheEEE
Confidence 344444555666 59999999986421 122 2399998865332 3333222 22233445678888877644
Q ss_pred EE
Q 026573 210 KV 211 (236)
Q Consensus 210 eV 211 (236)
+.
T Consensus 105 ~l 106 (143)
T PTZ00194 105 KL 106 (143)
T ss_pred cc
Confidence 43
No 19
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=41.86 E-value=43 Score=27.22 Aligned_cols=41 Identities=17% Similarity=0.379 Sum_probs=30.0
Q ss_pred CCCCCCCCCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEe
Q 026573 141 RPIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRR 188 (236)
Q Consensus 141 k~iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRn 188 (236)
..+|.+.+||+|.++= =++|.|.|-..+..+. -.+++-|=+
T Consensus 64 ~~LP~v~~GDVIll~~------~kv~~~~g~~~~~~~~-~~ss~avf~ 104 (138)
T cd04497 64 ESLPIVKVGDIILLRR------VKIQSYNGKPQGISND-RGSSWAVFR 104 (138)
T ss_pred hhCCCCCCCCEEEEEE------EEEEEECCceEEEECC-CceeEEEEc
Confidence 3589899999999983 2357788888888776 346666633
No 20
>COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms]
Probab=40.16 E-value=54 Score=31.52 Aligned_cols=64 Identities=25% Similarity=0.347 Sum_probs=46.9
Q ss_pred HHhhhcCCCCCCCCCCCEEEEEEEeecCccccceEEEEEEEEecC-C--------ccceEEEEeeeCCeeEEEEee
Q 026573 134 VEASESERPIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNA-G--------IHTTIRIRRIIAGIGVEIVFP 200 (236)
Q Consensus 134 ie~~~~kk~iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~-G--------l~sTFtLRnii~GvGVEr~Fp 200 (236)
|....++..+..+++|+-++|++...... ..|+|+|-++-.. | .+.|...=++.+++.|...|.
T Consensus 247 V~AnFkETqL~~~r~Gq~a~I~~da~~~~---~~~~G~v~~i~~~tg~~fsllp~~natgN~tkvvQRvPVrI~ld 319 (352)
T COG1566 247 VVANFKETQLARVRPGQPAEITLDAYPGN---GVVEGIVEGIAPATGSAFSLLPAQNATGNWTKVVQRVPVRIELD 319 (352)
T ss_pred EEeeeeeeecCcccCCCeEEEEEEcCCCc---eEEEEEEEEecCCcccccccCCCccCCCCEEEEEEeeeEEEEec
Confidence 34445667899999999999999776532 6799999999753 2 245555567788888876664
No 21
>PF03888 MucB_RseB: MucB/RseB family; InterPro: IPR005588 The members of this family are regulators of the anti-sigma E protein RseD.; PDB: 2P4B_B 2V42_B 2V43_A 3M4W_A.
Probab=39.82 E-value=1.1e+02 Score=28.07 Aligned_cols=49 Identities=16% Similarity=0.167 Sum_probs=36.6
Q ss_pred ccceEEEEEEEEecCCccceEEEEeeeCCeeEEEEeeccCCccceEEEeeec
Q 026573 164 RLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVEIVFPLYSPNIKEIKVVSHR 215 (236)
Q Consensus 164 RiQ~F~GVVIa~r~~Gl~sTFtLRnii~GvGVEr~FpLySP~I~~IeVlrr~ 215 (236)
|.+.|+|+.+-.++..+.+.=.+..+.+|.-.|+...|..|.. ||+|++
T Consensus 9 ~~lnY~g~fv~~~~~~~~s~ri~H~~~~~~e~ErL~~LdG~~r---eviR~~ 57 (285)
T PF03888_consen 9 RQLNYEGTFVYQRGGQMESMRIRHAVDDGGEYERLESLDGPPR---EVIRRG 57 (285)
T ss_dssp HHSEEEEEEEEEETTEEEEEEEEEEEETTEEEEEEEE-SSS-----EEEEET
T ss_pred HhCCeEEEEEEEeCCeEEEEEEEEEeeCCEEEEEEEecCCCcE---EEEEEC
Confidence 5578999999999887655444555578888999999999875 788776
No 22
>cd08544 Reeler Reeler, the N-terminal domain of reelin, F-spondin, and a variety of other proteins. This domain is found at the N-terminus of F-spondin, a protein attached to the extracellular matrix, which plays roles in neuronal development and vascular remodelling. The F-spondin reeler domain has been reported to bind heparin. The reeler domain is also found at the N-terminus of reelin, an extracellular glycoprotein involved in the development of the brain cortex, and in a variety of other eukaryotic proteins with different domain architectures, including the animal ferric-chelate reductase 1 or stromal cell-derived receptor 2, a member of the cytochrome B561 family, which reduces ferric iron before its transport from the endosome to the cytoplasm. Also included is the insect putative defense protein 1, which is expressed upon bacterial infection and appears to contain a single reeler domain.
Probab=38.98 E-value=68 Score=25.49 Aligned_cols=31 Identities=16% Similarity=0.383 Sum_probs=26.3
Q ss_pred CCCCCCEEEEEEEeecCccccceEEEEEEEEecCC
Q 026573 145 DIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAG 179 (236)
Q Consensus 145 ~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~G 179 (236)
.+.||+.+.|++..... ..|.|..|.-|+.+
T Consensus 29 ~y~pG~~~~Vtl~~~~~----~~F~GF~lqAr~~~ 59 (135)
T cd08544 29 SYVPGETYTVTLSGSSP----SPFRGFLLQARDAS 59 (135)
T ss_pred EECCCCEEEEEEECCCC----CceeEEEEEEEcCC
Confidence 68999999999987543 68999999999865
No 23
>PF02211 NHase_beta: Nitrile hydratase beta subunit; InterPro: IPR024690 Nitrile hydratases (EC:4.2.1.84) are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit []. This entry represents the structural domain of nitrile hydratase beta subunit which contains irregular array of helices in the N-terminal extension.; GO: 0018822 nitrile hydratase activity; PDB: 2DXB_H 2DD5_K 2DD4_H 2ZZD_B 2DXC_H 1AHJ_F 2ZPE_B 2ZCF_B 2D0Q_B 2CZ7_B ....
Probab=38.80 E-value=32 Score=31.06 Aligned_cols=36 Identities=25% Similarity=0.424 Sum_probs=19.7
Q ss_pred CCCCCCCCCEEEEEEEeecCccccceE----EEEEEEEec
Q 026573 142 PIPDIRTGDVVEIKLEVPENRRRLSIY----KGIVMSRQN 177 (236)
Q Consensus 142 ~iP~f~~GDiV~V~~~i~E~K~RiQ~F----~GVVIa~r~ 177 (236)
.-|.|.+||.|+|.-..+..-.|+..| .|+|....+
T Consensus 131 ~~~~F~vGd~Vrv~~~~~~~HtR~P~Y~rg~~G~I~~~~g 170 (222)
T PF02211_consen 131 APPRFAVGDRVRVRNLPPPGHTRLPRYVRGKTGTIERVHG 170 (222)
T ss_dssp SS-SS-TT-EEEE-----SS--SS-GGGTT-EEEEEEEEE
T ss_pred CCCCCCCCCEEEECCCCCCCcccccHhhCCCeeEEEEEec
Confidence 468999999999997666666676665 688887766
No 24
>PF13144 SAF_2: SAF-like
Probab=37.91 E-value=1.1e+02 Score=25.76 Aligned_cols=47 Identities=19% Similarity=0.372 Sum_probs=34.5
Q ss_pred CCCCCCCCCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEeeeCC
Q 026573 141 RPIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAG 192 (236)
Q Consensus 141 k~iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~G 192 (236)
...|-++-||.|.|.+.... + ...--.+|..+..++.+++|||.-.|
T Consensus 135 ~~~~~V~~G~~V~v~~~~g~----i-~i~~~g~Al~~G~~G~~I~V~N~~S~ 181 (196)
T PF13144_consen 135 EPPPLVKRGDIVTVIARSGG----I-SISTEGKALEDGALGDTIRVKNLSSG 181 (196)
T ss_pred ccceecCCCCEEEEEEEeCC----E-EEEEEEEEccCCCCCCEEEEEECCCC
Confidence 34588999999999986532 1 12334467788899999999997544
No 25
>cd00493 FabA_FabZ FabA/Z, beta-hydroxyacyl-acyl carrier protein (ACP)-dehydratases: One of several distinct enzyme types of the dissociative, type II, fatty acid synthase system (found in bacteria and plants) required to complete successive cycles of fatty acid elongation. The third step of the elongation cycle, the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, is catalyzed by FabA or FabZ. FabA is bifunctional and catalyzes an additional isomerization reaction of trans-2-acyl-ACP to cis-3-acyl-ACP, an essential reaction to unsaturated fatty acid synthesis. FabZ is the primary dehydratase that participates in the elongation cycles of saturated as well as unsaturated fatty acid biosynthesis, whereas FabA is more active in the dehydration of beta-hydroxydecanoyl-ACP. The FabA structure is homodimeric with two independent active sites located at the dimer interface.
Probab=35.91 E-value=59 Score=24.48 Aligned_cols=29 Identities=24% Similarity=0.479 Sum_probs=21.8
Q ss_pred CCCCCCEEEEEEEeecCccccceEEEEEE
Q 026573 145 DIRTGDVVEIKLEVPENRRRLSIYKGIVM 173 (236)
Q Consensus 145 ~f~~GDiV~V~~~i~E~K~RiQ~F~GVVI 173 (236)
...+||+|.+.+++.+.+.+.-.|.+.+.
T Consensus 88 ~v~pgd~l~i~~~i~~~~~~~~~~~~~~~ 116 (131)
T cd00493 88 PVLPGDTLTLEVELLKVRRGLGKFDGRAY 116 (131)
T ss_pred CcCCCCEEEEEEEEEEeeCCEEEEEEEEE
Confidence 46799999999999875556666766654
No 26
>cd01737 LSm16_N LSm16 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function.
Probab=33.13 E-value=83 Score=23.81 Aligned_cols=46 Identities=24% Similarity=0.409 Sum_probs=27.4
Q ss_pred CCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEe----eeCCeeEEEEee
Q 026573 148 TGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRR----IIAGIGVEIVFP 200 (236)
Q Consensus 148 ~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRn----ii~GvGVEr~Fp 200 (236)
.|..|.|+- .+-+-.|+|+|.++...- -||.+|+ =+...-+|.+|.
T Consensus 5 iGs~VSI~C-----~~~lGVyQG~i~~V~~~~--qTI~l~~~~~ngik~~~~EVt~~ 54 (62)
T cd01737 5 LGSIVSINC-----GETLGVYQGLVSAVDQES--QTISLAFPFHNGVKCLVPEVTFR 54 (62)
T ss_pred cceEEEEec-----CCceEEEEEEEEEeCccc--eEEEEeecccCCccccCceEEEE
Confidence 477777764 345678999999887643 2344443 333334555553
No 27
>cd01288 FabZ FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid biosynthesis pathway.
Probab=33.08 E-value=66 Score=24.39 Aligned_cols=28 Identities=25% Similarity=0.464 Sum_probs=20.9
Q ss_pred CCCCCCEEEEEEEeecCccccceEEEEE
Q 026573 145 DIRTGDVVEIKLEVPENRRRLSIYKGIV 172 (236)
Q Consensus 145 ~f~~GDiV~V~~~i~E~K~RiQ~F~GVV 172 (236)
...|||+|++..++.+...+.-.|.+.+
T Consensus 87 pv~pgd~l~i~~~v~~~~~~~~~~~~~~ 114 (131)
T cd01288 87 PVVPGDQLILEVELLKLRRGIGKFKGKA 114 (131)
T ss_pred ccCCCCEEEEEEEEEEeeCCEEEEEEEE
Confidence 3668999999999887555566666665
No 28
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=32.97 E-value=1.6e+02 Score=20.29 Aligned_cols=43 Identities=21% Similarity=0.302 Sum_probs=28.7
Q ss_pred CCCCCCCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEeeeCCe
Q 026573 143 IPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGI 193 (236)
Q Consensus 143 iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~Gv 193 (236)
.|.|..||+|-|.-... ..-.|=++..+..| ..+++|++....
T Consensus 11 ~P~i~~gd~v~i~~~~~------~~~~G~iv~~~~~~--~~~~ikrl~~~~ 53 (84)
T cd06462 11 EPTIPDGDLVLVDKSSY------EPKRGDIVVFRLPG--GELTVKRVIGLP 53 (84)
T ss_pred cCcccCCCEEEEEecCC------CCcCCEEEEEEcCC--CcEEEEEEEEEC
Confidence 47899999998875322 23445555555544 568888887665
No 29
>PF12148 DUF3590: Protein of unknown function (DUF3590); InterPro: IPR021991 This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with PF00097 from PFAM, PF02182 from PFAM, PF00628 from PFAM, PF00240 from PFAM. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed. ; PDB: 3DB4_A 3ASK_A 3DB3_A 2L3R_A.
Probab=32.93 E-value=27 Score=27.63 Aligned_cols=23 Identities=26% Similarity=0.514 Sum_probs=14.6
Q ss_pred CCCCCCCCCEEEEEEEeecCccc
Q 026573 142 PIPDIRTGDVVEIKLEVPENRRR 164 (236)
Q Consensus 142 ~iP~f~~GDiV~V~~~i~E~K~R 164 (236)
+.-++.+|++|.|.|.+.+.|+|
T Consensus 62 ~w~~L~VG~~VMvNYN~d~P~er 84 (85)
T PF12148_consen 62 KWDELKVGQVVMVNYNVDEPKER 84 (85)
T ss_dssp -GGG--TT-EEEEEE-TTSTTS-
T ss_pred cHHhCCcccEEEEecCCCCcccC
Confidence 35578999999999999887776
No 30
>TIGR01750 fabZ beta-hydroxyacyl-[acyl carrier protein] dehydratase FabZ. This enzyme, FabZ, shows overlapping substrate specificity with FabA with regard to chain length in fatty acid biosynthesis. FabZ works preferentially on shorter chains and is often designated (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase, although its actual specificity is broader. Unlike FabA, FabZ does not function as an isomerase and cannot initiate unsaturated fatty acid biosynthesis. However, only FabZ can act during the elongation of unsaturated fatty acid chains.
Probab=32.74 E-value=70 Score=25.13 Aligned_cols=28 Identities=25% Similarity=0.483 Sum_probs=20.1
Q ss_pred CCCCCCEEEEEEEeecCccccceEEEEE
Q 026573 145 DIRTGDVVEIKLEVPENRRRLSIYKGIV 172 (236)
Q Consensus 145 ~f~~GDiV~V~~~i~E~K~RiQ~F~GVV 172 (236)
.++|||+|.+++++.....+.-.|.|.+
T Consensus 97 ~v~pGd~l~i~~~i~~~~~~~~~~~~~~ 124 (140)
T TIGR01750 97 PVVPGDQLILHAEFLKKRRKIGKFKGEA 124 (140)
T ss_pred ccCCCCEEEEEEEEEEccCCEEEEEEEE
Confidence 3678999999999876444555566654
No 31
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=31.81 E-value=1e+02 Score=25.36 Aligned_cols=56 Identities=16% Similarity=0.188 Sum_probs=33.2
Q ss_pred CCCCCCCCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEeeeCCeeEEEEeecc
Q 026573 142 PIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVEIVFPLY 202 (236)
Q Consensus 142 ~iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~GvGVEr~FpLy 202 (236)
..++|+.|++|.+.=. --.+..++-.--+++| +---.+.+||+..|.=+|.+|+-.
T Consensus 7 ~~~~lrkG~~i~~~g~----p~~V~~~~~~kpGkhg-~a~vr~k~knL~tG~~~e~~~~s~ 62 (129)
T PRK03999 7 EVGELKEGSYVVIDGE----PCKIVEISKSKPGKHG-SAKARIVAIGIFDGQKRSLVQPVD 62 (129)
T ss_pred cHHHccCCCEEEECCE----EEEEEEEEeecCCCCC-cEEEEEEEEECCCCCEEEEEecCC
Confidence 4678999999965310 1111112211111111 224668899999999999999854
No 32
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=31.35 E-value=2.4e+02 Score=22.76 Aligned_cols=43 Identities=21% Similarity=0.268 Sum_probs=27.5
Q ss_pred CCCCCCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEeeeCCee
Q 026573 144 PDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIG 194 (236)
Q Consensus 144 P~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~GvG 194 (236)
..|.+||.|+|.= .=.+-|+|.|+...+... -.+|.=...+.-
T Consensus 85 ~~~~~Gd~V~I~~------GPf~G~~g~v~~~d~~k~--~v~v~l~~~~~~ 127 (145)
T TIGR00405 85 ESIKKGDIVEIIS------GPFKGERAKVIRVDESKE--EVTLELIEAAVP 127 (145)
T ss_pred cccCCCCEEEEee------cCCCCCeEEEEEEcCCCC--EEEEEEEEcCcc
Confidence 4599999999963 224568999999876443 344433333333
No 33
>PF08207 EFP_N: Elongation factor P (EF-P) KOW-like domain; InterPro: IPR013185 This entry represents the N-terminal domain of homologues of elongation factor P, which probably are translation initiation factors. ; PDB: 3TRE_A 1YBY_A 1IZ6_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H 3OYY_B.
Probab=28.94 E-value=2e+02 Score=20.39 Aligned_cols=19 Identities=21% Similarity=0.476 Sum_probs=16.5
Q ss_pred ceEEEEeeeCCeeEEEEee
Q 026573 182 TTIRIRRIIAGIGVEIVFP 200 (236)
Q Consensus 182 sTFtLRnii~GvGVEr~Fp 200 (236)
-.+.+||+..|.-+|.+|.
T Consensus 35 v~~klknl~tG~~~e~tf~ 53 (58)
T PF08207_consen 35 VRVKLKNLRTGSKVEKTFR 53 (58)
T ss_dssp EEEEEEETTTTEEEEEEEE
T ss_pred EEEEEEECCCCCEEEEEEC
Confidence 4456999999999999996
No 34
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=28.77 E-value=1.4e+02 Score=26.56 Aligned_cols=47 Identities=17% Similarity=0.155 Sum_probs=33.3
Q ss_pred CCCCCCCCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEeeeCCe
Q 026573 142 PIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGI 193 (236)
Q Consensus 142 ~iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~Gv 193 (236)
.-+-++-||.|.|.+.... + ...--..|..+.+++-.++|||...|-
T Consensus 173 ~~~~V~~G~~V~i~~~~g~----~-~i~~~G~Al~~G~~Gd~IrVrN~~Sgk 219 (235)
T PRK07018 173 QAWVVCKGQTVSIIARGDG----F-SVKTEGEALNDGAVGQQIRVRNMASGQ 219 (235)
T ss_pred CccEeCCCCEEEEEEecCC----E-EEEEEEEEcCCCCCCCeEEEEECCCCC
Confidence 4567999999999986532 1 122333577788999999999875543
No 35
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=28.25 E-value=3.4e+02 Score=22.33 Aligned_cols=28 Identities=18% Similarity=0.284 Sum_probs=21.5
Q ss_pred CCCCCCCEEEEEEEeecCccccceEEEEEEEEec
Q 026573 144 PDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQN 177 (236)
Q Consensus 144 P~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~ 177 (236)
..|.+||.|+|.= .=.+-|+|+|+.+.+
T Consensus 118 ~~~~~G~~V~I~~------Gpf~G~~g~v~~~~~ 145 (172)
T TIGR00922 118 IDFEVGEQVRVND------GPFANFTGTVEEVDY 145 (172)
T ss_pred cCCCCCCEEEEee------cCCCCcEEEEEEEcC
Confidence 5589999999962 225668999999864
No 36
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=28.04 E-value=1.3e+02 Score=25.39 Aligned_cols=36 Identities=17% Similarity=0.409 Sum_probs=28.1
Q ss_pred CCCCCCCCCEEEEEEEeecCccccceEEEEEEEEec
Q 026573 142 PIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQN 177 (236)
Q Consensus 142 ~iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~ 177 (236)
.+|.-.+||+|.|.++--..-.|-|.+.|||+..+.
T Consensus 43 r~~~a~iGD~IvvsVK~~~p~~kg~v~kAVIVRtkk 78 (132)
T PRK08571 43 RLPKAGVGDMVVVSVKKGTPEMRKQVLRAVVVRQRK 78 (132)
T ss_pred cCCccccCCEEEEEEEECCCcccCCEeEEEEEEecc
Confidence 347789999999998765434456999999998774
No 37
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=27.70 E-value=2.6e+02 Score=24.36 Aligned_cols=33 Identities=27% Similarity=0.355 Sum_probs=24.3
Q ss_pred CCCCCCCCCCCEEEEEEEeecCccccceEEEEEEEEecC
Q 026573 140 ERPIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNA 178 (236)
Q Consensus 140 kk~iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~ 178 (236)
.+...+|.+||.|+|.- .=+..|.|.|+.+...
T Consensus 118 ~~~~~~~e~Gd~VrI~~------GpFa~f~g~V~evd~e 150 (178)
T COG0250 118 KKPKVDFEPGDVVRIID------GPFAGFKAKVEEVDEE 150 (178)
T ss_pred CcccccCCCCCEEEEec------cCCCCccEEEEEEcCc
Confidence 34567899999999863 1234588899988764
No 38
>PF08572 PRP3: pre-mRNA processing factor 3 (PRP3); InterPro: IPR013881 Pre-mRNA processing factor 3 (PRP3) is a U4/U6-associated splicing factor. The human PRP3 has been implicated in autosomal retinitis pigmentosa [].
Probab=27.37 E-value=39 Score=30.48 Aligned_cols=22 Identities=41% Similarity=0.783 Sum_probs=18.4
Q ss_pred CCCCCCccchhhHHHHHHHHHH
Q 026573 113 KAPRKPRVKLGDIMGILNKRAV 134 (236)
Q Consensus 113 ~pp~k~r~KL~dlM~iLe~~~i 134 (236)
.||..|+.||.++|..|..++|
T Consensus 170 ~ppP~PKVKlSNLMrVL~~eAV 191 (223)
T PF08572_consen 170 EPPPPPKVKLSNLMRVLGNEAV 191 (223)
T ss_pred CCCCCCcccHHHHHHHhhcchh
Confidence 6888999999999998876544
No 39
>PRK00006 fabZ (3R)-hydroxymyristoyl-ACP dehydratase; Reviewed
Probab=27.08 E-value=90 Score=24.79 Aligned_cols=27 Identities=26% Similarity=0.554 Sum_probs=19.2
Q ss_pred CCCCCEEEEEEEeecCccccceEEEEE
Q 026573 146 IRTGDVVEIKLEVPENRRRLSIYKGIV 172 (236)
Q Consensus 146 f~~GDiV~V~~~i~E~K~RiQ~F~GVV 172 (236)
.++||+|.+..++.+.+.++-.|.+-+
T Consensus 102 v~pGd~l~i~~~i~~~~~~~v~~~~~~ 128 (147)
T PRK00006 102 VVPGDQLILEVELLKQRRGIWKFKGVA 128 (147)
T ss_pred cCCCCEEEEEEEEEEeeCCEEEEEEEE
Confidence 468999999999876444455555554
No 40
>PF02014 Reeler: Reeler domain Schematic picture including Reeler domain; InterPro: IPR002861 Extracellular matrix (ECM) proteins play an important role in early cortical development, specifically in the formation of neural connections and in controlling the cyto-architecture of the central nervous system. The product of the reeler gene in mouse is reelin,a large extracellular protein secreted by pioneer neurons that coordinates cell positioning during neurodevelopment []. F-spondin and mindin are a family of matrix-attached adhesion molecules that share structural similarities and overlapping domains of expression. Both F-spondin and mindin promote adhesion and outgrowth of hippocampal embryonic neurons and bind to a putative receptor(s) expressed on both hippocampal and sensory neurons []. This domain of unknown function is found at the N terminus of reelin and F-spondin.; PDB: 2ZOT_B 2ZOU_B 3COO_A.
Probab=26.92 E-value=63 Score=25.69 Aligned_cols=32 Identities=16% Similarity=0.398 Sum_probs=24.0
Q ss_pred CCCCCCCEEEEEEEeecCccccceEEEEEEEEecCC
Q 026573 144 PDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAG 179 (236)
Q Consensus 144 P~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~G 179 (236)
..+.+|+.++|++ +......|+|..|.-+..+
T Consensus 28 ~~y~pg~~~~Vtl----~~~~~~~F~GFllqAr~~~ 59 (132)
T PF02014_consen 28 SSYEPGQTYTVTL----SSSGSSSFRGFLLQARDAN 59 (132)
T ss_dssp SSB-TTBEEEEEE----EETTTEEBSEEEEEEEETT
T ss_pred CeEcCCCEEEEEE----ECCCCCceeEEEEEEEeCC
Confidence 4589999999999 2334567999999888643
No 41
>PRK09455 rseB anti-sigma E factor; Provisional
Probab=26.87 E-value=2.3e+02 Score=26.65 Aligned_cols=49 Identities=12% Similarity=0.263 Sum_probs=36.8
Q ss_pred cccceEEEEEEEEecCCccceEEEEee-eCCeeEEEEeeccCCccceEEEeeec
Q 026573 163 RRLSIYKGIVMSRQNAGIHTTIRIRRI-IAGIGVEIVFPLYSPNIKEIKVVSHR 215 (236)
Q Consensus 163 ~RiQ~F~GVVIa~r~~Gl~sTFtLRni-i~GvGVEr~FpLySP~I~~IeVlrr~ 215 (236)
.|-+.|+|+.+-.++..+. ++.++.. .+|.=.|+.-.|.-|.- ||+|++
T Consensus 39 ~~~lnY~g~fV~~~~~~i~-s~ri~H~~~~~~e~erL~~LdG~~r---EviR~~ 88 (319)
T PRK09455 39 SQSLNYELSFINITKQGIE-SLRYRHARLDNKPLAQLLQMDGPRR---EIIQRG 88 (319)
T ss_pred HHhCCeEEEEEEEeCCeEE-EEEEEEEEeCCEEEEEEEecCCCce---EEEEEC
Confidence 3457899999999987664 4565554 56666999999998864 788775
No 42
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=25.63 E-value=46 Score=23.93 Aligned_cols=11 Identities=45% Similarity=0.812 Sum_probs=9.0
Q ss_pred CCCCCEEEEEE
Q 026573 146 IRTGDVVEIKL 156 (236)
Q Consensus 146 f~~GDiV~V~~ 156 (236)
|++||+|+.+-
T Consensus 1 f~~GDvV~LKS 11 (53)
T PF09926_consen 1 FKIGDVVQLKS 11 (53)
T ss_pred CCCCCEEEEcc
Confidence 78999998763
No 43
>PF07977 FabA: FabA-like domain; InterPro: IPR013114 Fatty acids biosynthesis occurs by two distinct pathways: in fungi, mammals and mycobacteria, type I or associative fatty-acid biosynthesis (type I FAS) is accomplished by multifunctional proteins in which distinct domains catalyse specific reactions; in plants and most bacteria, type II or dissociative fatty-acid biosynthesis (type II FAS) is accomplished by distinct enzymes []. Both FabZ and FabA catalyse the dehydration of beta-hydroxyacyl acyl carrier protein (ACP) to trans 2-enoyl ACP. However, FabZ and FabA display subtle differences in substrate specificities, whereby FabA is most effective on acyl ACPs of 9-11 carbon atoms in length, while FabZ is less specific. Unlike FabA, FabZ does not function as an isomerase and cannot initiate unsaturated fatty acid biosynthesis. However, only FabZ can act during the elongation of unsaturated fatty acid chains. This enzyme domain has a HotDog fold.; PDB: 3D6X_F 2GLV_J 2GLM_E 2GLP_E 2GLL_C 1U1Z_F 3ESI_A 3AZB_T 3AZA_M 3AZ9_U ....
Probab=25.48 E-value=74 Score=25.14 Aligned_cols=29 Identities=21% Similarity=0.520 Sum_probs=20.2
Q ss_pred CCCCCCC-EEEEEEEeec---CccccceEEEEE
Q 026573 144 PDIRTGD-VVEIKLEVPE---NRRRLSIYKGIV 172 (236)
Q Consensus 144 P~f~~GD-iV~V~~~i~E---~K~RiQ~F~GVV 172 (236)
-.+.||| ++++++.+.+ .......|+|.+
T Consensus 95 ~~v~Pg~~~l~~~v~i~~~~~~~~~~~~~~~~~ 127 (138)
T PF07977_consen 95 GPVYPGDKTLRIEVEIKKIRRREGGMAIFDGTA 127 (138)
T ss_dssp S-B-TTE-EEEEEEEEEEEEEEETTEEEEEEEE
T ss_pred ccEeCCCcEEEEEEEEEEeecccCCEEEEEEEE
Confidence 3578999 9999998877 556666666654
No 44
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=25.47 E-value=3.9e+02 Score=22.06 Aligned_cols=46 Identities=15% Similarity=0.195 Sum_probs=28.4
Q ss_pred CCCCCCCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEeeeCCeeEE
Q 026573 143 IPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVE 196 (236)
Q Consensus 143 iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~GvGVE 196 (236)
...|.+||.|+|.- .=.+-|+|+|..+.+..- .++|.=-+.|-.+.
T Consensus 124 ~~~~~~Gd~VrI~~------GPf~G~~g~v~~i~~~~~--r~~v~l~~~G~~~~ 169 (181)
T PRK05609 124 KVDFEVGEMVRVID------GPFADFNGTVEEVDYEKS--KLKVLVSIFGRETP 169 (181)
T ss_pred ccCCCCCCEEEEec------cCCCCCEEEEEEEeCCCC--EEEEEEEECCCceE
Confidence 35699999999972 225668999999864332 33443334444433
No 45
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=25.40 E-value=1.5e+02 Score=24.03 Aligned_cols=29 Identities=17% Similarity=0.209 Sum_probs=21.9
Q ss_pred CCCCCCCEEEEEEEeecCccccceEEEEEEEEecC
Q 026573 144 PDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNA 178 (236)
Q Consensus 144 P~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~ 178 (236)
..|.+||.|+|.- + =.+-|+|+|....+.
T Consensus 107 ~~~~~G~~V~V~~----G--Pf~g~~g~v~~~~~~ 135 (159)
T TIGR01955 107 TLPYKGDKVRITD----G--AFAGFEAIFLEPDGE 135 (159)
T ss_pred cCCCCCCEEEEec----c--CCCCcEEEEEEECCC
Confidence 4599999998863 2 256799999998743
No 46
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 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) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=25.22 E-value=90 Score=21.36 Aligned_cols=43 Identities=28% Similarity=0.513 Sum_probs=23.9
Q ss_pred CCCCCCCCEEEEEEEeecCccccceEEE-EEEEEecCCccceEEEEeeeCCee
Q 026573 143 IPDIRTGDVVEIKLEVPENRRRLSIYKG-IVMSRQNAGIHTTIRIRRIIAGIG 194 (236)
Q Consensus 143 iP~f~~GDiV~V~~~i~E~K~RiQ~F~G-VVIa~r~~Gl~sTFtLRnii~GvG 194 (236)
.|.|+.||+|-|.-.. ....| +|+.... |-. ..+++++...-|
T Consensus 8 ~P~i~~Gd~v~v~~~~-------~~~~gdivv~~~~-~~~-~~~iKrv~~~~~ 51 (70)
T PF00717_consen 8 EPTIKDGDIVLVDPSS-------EPKDGDIVVVKID-GDE-ELYIKRVVGEPG 51 (70)
T ss_dssp GGTSSTTEEEEEEETS----------TTSEEEEEET-TEE-SEEEEEEEEETT
T ss_pred ccCeeCCCEEEEEEcC-------CCccCeEEEEEEC-Cce-eeEEEEEEEeCC
Confidence 4889999999887433 12222 3333332 211 578888864443
No 47
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=24.76 E-value=54 Score=24.78 Aligned_cols=23 Identities=30% Similarity=0.387 Sum_probs=16.6
Q ss_pred CCCCCCCCCEEEEEEEeec-Cccc
Q 026573 142 PIPDIRTGDVVEIKLEVPE-NRRR 164 (236)
Q Consensus 142 ~iP~f~~GDiV~V~~~i~E-~K~R 164 (236)
..-.+.+||.|.|.+.-.. +|.|
T Consensus 41 ~rI~I~~GD~V~Ve~spyd~tkgr 64 (68)
T TIGR00008 41 HYIRILPGDKVKVELSPYDLTRGR 64 (68)
T ss_pred ccEEECCCCEEEEEECcccCCcEe
Confidence 3456899999999987654 4444
No 48
>PF02752 Arrestin_C: Arrestin (or S-antigen), C-terminal domain; InterPro: IPR011022 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The C-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=24.64 E-value=1.1e+02 Score=22.82 Aligned_cols=30 Identities=10% Similarity=0.361 Sum_probs=18.7
Q ss_pred CCCCCCEEEEEEEeec-CccccceEEEEEEE
Q 026573 145 DIRTGDVVEIKLEVPE-NRRRLSIYKGIVMS 174 (236)
Q Consensus 145 ~f~~GDiV~V~~~i~E-~K~RiQ~F~GVVIa 174 (236)
.|.+||.|.|++.+.. .+.+++...--++.
T Consensus 15 ~~~~Ge~i~v~v~i~n~s~~~i~~I~v~L~~ 45 (136)
T PF02752_consen 15 AYVPGETIPVNVEIDNQSKKKIKKIKVSLVE 45 (136)
T ss_dssp EEETT--EEEEEEEEE-SSSEEEEEEEEEEE
T ss_pred EECCCCEEEEEEEEEECCCCEEEEEEEEEEE
Confidence 4889999999999986 45454444444433
No 49
>PF00238 Ribosomal_L14: Ribosomal protein L14p/L23e; InterPro: IPR000218 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 [, ]. Ribosomal protein L14 is one of the proteins from the large ribosomal subunit. In eubacteria, L14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities []. Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins []. L14 is a protein of 119 to 137 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_M 4A1C_J 4A1E_J 4A1A_J 4A17_J 1VSP_I 3D5D_O 1VSA_I 3MRZ_K 3F1F_O ....
Probab=24.62 E-value=1.4e+02 Score=24.54 Aligned_cols=36 Identities=11% Similarity=0.337 Sum_probs=26.9
Q ss_pred CCCCCCCCCEEEEEEEee--c-CccccceEEEEEEEEec
Q 026573 142 PIPDIRTGDVVEIKLEVP--E-NRRRLSIYKGIVMSRQN 177 (236)
Q Consensus 142 ~iP~f~~GDiV~V~~~i~--E-~K~RiQ~F~GVVIa~r~ 177 (236)
..+.-..||+|.|.++-. . .-++-+.+.|+|+..+.
T Consensus 29 ~~~~a~vGD~I~vsVkk~~~~~~vkkg~v~~avIVrtk~ 67 (122)
T PF00238_consen 29 RRKYASVGDIIVVSVKKGRPKSKVKKGQVYKAVIVRTKK 67 (122)
T ss_dssp TTSEE-TTSEEEEEEEEE-SSSSSTTTEEEEEEEEECSS
T ss_pred CccccccceEEEEEEeecccCccccccceEEEEEEEEeE
Confidence 456678999999998765 3 34455899999998876
No 50
>TIGR03673 rpl14p_arch 50S ribosomal protein L14P. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in 2 intersubunit bridges.
Probab=24.34 E-value=1.6e+02 Score=24.82 Aligned_cols=35 Identities=20% Similarity=0.447 Sum_probs=27.3
Q ss_pred CCCCCCCCEEEEEEEeecCccccceEEEEEEEEec
Q 026573 143 IPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQN 177 (236)
Q Consensus 143 iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~ 177 (236)
+|.-.+||+|.|.++--....+-+.+.|||+..+.
T Consensus 43 ~~~a~iGD~IvvsVK~~~p~~kg~v~kAVIVRtkk 77 (131)
T TIGR03673 43 LPCAGVGDMVVVSVKKGTPEMRKQVFKAVVVRQRK 77 (131)
T ss_pred CCccccCCEEEEEEEECCccccCCEeEEEEEEeCc
Confidence 46678999999998764434456999999998774
No 51
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=23.93 E-value=1.6e+02 Score=25.11 Aligned_cols=35 Identities=14% Similarity=0.373 Sum_probs=28.0
Q ss_pred CCCCCCCCEEEEEEEeecCccccceEEEEEEEEec
Q 026573 143 IPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQN 177 (236)
Q Consensus 143 iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~ 177 (236)
+|.-.+||+|.|.++--..-.|-+.+.+||+..+.
T Consensus 51 ~~~a~iGD~IvvsVKk~~p~~kg~V~kAVIVRtKk 85 (139)
T PTZ00054 51 LPSASLGDMVLATVKKGKPELRKKVLNAVIIRQRK 85 (139)
T ss_pred CcccccCCEEEEEEEECCCcccCCEeeEEEEEECc
Confidence 47788999999998765544566999999998774
No 52
>TIGR02266 gmx_TIGR02266 Myxococcus xanthus paralogous domain TIGR02266. This domain is related to Type IV pilus assembly protein PilZ (Pfam model pfam07238). It is found in at least 12 copies in Myxococcus xanthus DK 1622.
Probab=23.71 E-value=2.9e+02 Score=20.01 Aligned_cols=45 Identities=31% Similarity=0.420 Sum_probs=30.5
Q ss_pred CCCCCCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEeeeCCeeEE
Q 026573 144 PDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVE 196 (236)
Q Consensus 144 P~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~GvGVE 196 (236)
..+.+|+.|.|.+..+.+... -...|.|+..+..+-+. ..|+||+
T Consensus 35 ~~~~~g~~v~l~l~l~~~~~~-i~~~g~Vv~~~~~~~~~-------~~~~Gv~ 79 (96)
T TIGR02266 35 KPLAVGTRVELKLTLPGGERP-VELKGVVAWVRPAADGG-------PPGMGVR 79 (96)
T ss_pred CCcCCCCEEEEEEEcCCCCeE-EEEEEEEEEeCCCCCCC-------CCeeEEE
Confidence 357899999999999764322 34679888877544322 2566776
No 53
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=23.30 E-value=2.3e+02 Score=24.14 Aligned_cols=49 Identities=18% Similarity=0.210 Sum_probs=33.8
Q ss_pred CCCCCCCCCEEEEEEEeecCccccceEEEEEEEEecCCccceEEEEeeeCCeeE
Q 026573 142 PIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGV 195 (236)
Q Consensus 142 ~iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~Gl~sTFtLRnii~GvGV 195 (236)
.-+-++-||.|.|.+.... + ...-.-++..+.+.+..+.|||...|-=|
T Consensus 97 ~p~~V~rG~~V~i~~~~~g----~-~i~~~G~Al~~G~~Gd~IrVrN~~Sgkiv 145 (160)
T PRK06005 97 EPSLVTRGSPVKLVFSAGG----L-TITAAGTPLQSGAAGDLIRVRNVDSGVIV 145 (160)
T ss_pred CCcEEeCCCEEEEEEecCC----E-EEEEEEEEcccCCCCCEEEEEECCCCCEE
Confidence 4457999999999987542 1 11222346678889999999997655433
No 54
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=23.03 E-value=2.7e+02 Score=19.42 Aligned_cols=32 Identities=22% Similarity=0.379 Sum_probs=23.2
Q ss_pred CCCCCCEEEEEEEeecCccccceEEEEEEEEecC
Q 026573 145 DIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNA 178 (236)
Q Consensus 145 ~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~ 178 (236)
.+.+||.|.|.+.+.....-. +.|.|+..++.
T Consensus 44 ~~~~~~~v~l~~~~~~~~~~~--~~~~V~~~~~~ 75 (102)
T PF07238_consen 44 PLEPGDRVRLSFSLPGGGFPI--VTGRVVRIQKD 75 (102)
T ss_dssp G--TTSEEEEEEECTTTSCEE--EEEEEEEEEEE
T ss_pred CCCCCCEEEEEEEeCCCCeeE--EEEEEEEEECC
Confidence 689999999999876533322 99999998876
No 55
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=22.80 E-value=63 Score=25.00 Aligned_cols=23 Identities=30% Similarity=0.352 Sum_probs=16.6
Q ss_pred CCCCCCCCCEEEEEEEeec-Cccc
Q 026573 142 PIPDIRTGDVVEIKLEVPE-NRRR 164 (236)
Q Consensus 142 ~iP~f~~GDiV~V~~~i~E-~K~R 164 (236)
..-.+.+||+|.|..+... +|.|
T Consensus 43 ~~i~I~~GD~V~Ve~~~~d~~kg~ 66 (75)
T COG0361 43 NRIRILPGDVVLVELSPYDLTKGR 66 (75)
T ss_pred eeEEeCCCCEEEEEeccccccccc
Confidence 3556899999999987654 4433
No 56
>PRK15136 multidrug efflux system protein EmrA; Provisional
Probab=22.15 E-value=1.7e+02 Score=27.69 Aligned_cols=32 Identities=19% Similarity=0.437 Sum_probs=23.7
Q ss_pred CCCCCCCCCEEEEEEEeecCccccceEEEEEEEEe
Q 026573 142 PIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQ 176 (236)
Q Consensus 142 ~iP~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r 176 (236)
++..+++|+.|.|++....+. ..|.|.|..+-
T Consensus 262 ~l~~v~~Gq~V~I~~da~p~~---~~~~G~V~~I~ 293 (390)
T PRK15136 262 QLANMRIGQPATITSDIYGDD---VVYTGKVVGLD 293 (390)
T ss_pred HHhcCCCCCEEEEEEecCCCC---ceEEEEEEEEC
Confidence 467899999999987543221 26999999984
No 57
>PF01458 UPF0051: Uncharacterized protein family (UPF0051); InterPro: IPR000825 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents SufB and SufD proteins that form part of the SufBCD complex in the SUF system. No specific functions have been assigned to these proteins.; GO: 0016226 iron-sulfur cluster assembly; PDB: 1VH4_B 2ZU0_A 4DN7_A.
Probab=22.13 E-value=4.4e+02 Score=22.79 Aligned_cols=61 Identities=16% Similarity=0.399 Sum_probs=38.5
Q ss_pred ccceEEEEEEEEec-CCccceEEEEeeeC-CeeEEEEee---ccCCccceEEEeee----cccCCcceeeeccC
Q 026573 164 RLSIYKGIVMSRQN-AGIHTTIRIRRIIA-GIGVEIVFP---LYSPNIKEIKVVSH----RKVRRARLYYLRDK 228 (236)
Q Consensus 164 RiQ~F~GVVIa~r~-~Gl~sTFtLRnii~-GvGVEr~Fp---LySP~I~~IeVlrr----~KVRRAKLYYLRdk 228 (236)
-...|.|.++-.++ .|.+....-|.++- +.+.=...| ++...| +. .| |+....+||||+.|
T Consensus 145 s~~vf~G~i~i~~~a~~s~~~q~~~~llls~~A~~~s~P~LeI~~~dV---~a-~H~AtvG~idee~LFYL~SR 214 (229)
T PF01458_consen 145 SKVVFRGRIKIEKGAQGSDAHQECRNLLLSDEARAYSIPELEIDEDDV---KA-SHGATVGQIDEEQLFYLMSR 214 (229)
T ss_dssp SEEEEEEEEEEECTSTTEEEEEEEEEEE-STT-EEEEEEEEEE-SSSE---EE-EEEEEEEES-HHHHHHHHCT
T ss_pred ceEEEEeEEEEhhhhhCChheeeEeeEEccCCeEEEEEEhHhcccCCc---EE-EEeeEeecCCHHHHHHHHHc
Confidence 34589998776665 57777778888865 334433444 444444 22 33 69999999999976
No 58
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=22.04 E-value=1.1e+02 Score=24.71 Aligned_cols=44 Identities=16% Similarity=0.291 Sum_probs=31.2
Q ss_pred CCCCCCCCEEEEEEEeec----CccccceEEEEEEEEecCCccceEEE
Q 026573 143 IPDIRTGDVVEIKLEVPE----NRRRLSIYKGIVMSRQNAGIHTTIRI 186 (236)
Q Consensus 143 iP~f~~GDiV~V~~~i~E----~K~RiQ~F~GVVIa~r~~Gl~sTFtL 186 (236)
+-.|+.||+|.|...-.- .-.|.+=-.|.|+.++++.+.--+.+
T Consensus 32 l~~y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A~~V~v~v 79 (98)
T PRK04306 32 LQEFEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRAYIVEVKD 79 (98)
T ss_pred HHhccCCCEEEEEecCceecCCccccccCCCEEEEeecCeEEEEEEEE
Confidence 446999999999874321 35667777899999988765554433
No 59
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=21.78 E-value=1.7e+02 Score=24.18 Aligned_cols=34 Identities=15% Similarity=0.281 Sum_probs=26.1
Q ss_pred CCCCCCCEEEEEEEeec---CccccceEEEEEEEEec
Q 026573 144 PDIRTGDVVEIKLEVPE---NRRRLSIYKGIVMSRQN 177 (236)
Q Consensus 144 P~f~~GDiV~V~~~i~E---~K~RiQ~F~GVVIa~r~ 177 (236)
+.-..||+|.|.++-.. .-.|-+.+.|+|+..+.
T Consensus 31 ~~a~iGD~I~vsVkk~~~~~~~kkg~v~~AvIVrtkk 67 (122)
T PRK05483 31 RYASIGDVIVVSVKEAIPRGKVKKGDVVKAVVVRTKK 67 (122)
T ss_pred CccccCCEEEEEEEEcCCCCcccCCCEeeEEEEEecc
Confidence 56889999999986433 13456899999998874
No 60
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=21.31 E-value=66 Score=24.87 Aligned_cols=13 Identities=31% Similarity=0.611 Sum_probs=8.6
Q ss_pred CCCCCCCEEEEEE
Q 026573 144 PDIRTGDVVEIKL 156 (236)
Q Consensus 144 P~f~~GDiV~V~~ 156 (236)
-.|+|||+|+=++
T Consensus 67 ~~FrpGDIVrA~V 79 (82)
T PF10447_consen 67 DCFRPGDIVRARV 79 (82)
T ss_dssp GT--SSSEEEEEE
T ss_pred hccCCCCEEEEEE
Confidence 4599999998664
No 61
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=21.29 E-value=1.1e+02 Score=19.66 Aligned_cols=15 Identities=33% Similarity=0.419 Sum_probs=12.5
Q ss_pred CCCCCCEEEEEEEee
Q 026573 145 DIRTGDVVEIKLEVP 159 (236)
Q Consensus 145 ~f~~GDiV~V~~~i~ 159 (236)
.|++||+|++.+.-.
T Consensus 41 ~~~~G~~v~~~v~~~ 55 (65)
T cd00164 41 VFKVGDEVEVKVLEV 55 (65)
T ss_pred EeCCCCEEEEEEEEE
Confidence 499999999997654
No 62
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=21.17 E-value=2.8e+02 Score=23.10 Aligned_cols=29 Identities=24% Similarity=0.313 Sum_probs=22.6
Q ss_pred CCCCCCCEEEEEEEeecCccccceEEEEEEEEecC
Q 026573 144 PDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNA 178 (236)
Q Consensus 144 P~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~ 178 (236)
-.|.+||.|+|.- .=.+-|.|.|+...+.
T Consensus 93 ~~~~~G~~V~I~~------Gpf~g~~g~V~~vd~~ 121 (153)
T PRK08559 93 EGIKEGDIVELIA------GPFKGEKARVVRVDES 121 (153)
T ss_pred cCCCCCCEEEEec------cCCCCceEEEEEEcCC
Confidence 3599999999973 2356689999999764
No 63
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=21.10 E-value=2.8e+02 Score=19.73 Aligned_cols=33 Identities=18% Similarity=0.335 Sum_probs=23.5
Q ss_pred CCCCCCCEEEEEEEeecCccccceEEEEEEEEecCC
Q 026573 144 PDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAG 179 (236)
Q Consensus 144 P~f~~GDiV~V~~~i~E~K~RiQ~F~GVVIa~r~~G 179 (236)
..|+.|+.|.|.+....+ +-.|+..|+++....
T Consensus 46 ~~l~~g~~v~v~~~~~~~---~y~F~s~V~~~~~~p 78 (87)
T PF12945_consen 46 IPLREGEEVIVRFISEDG---VYAFKSKVIGRISEP 78 (87)
T ss_dssp CCS-TT-EEEEEEEE-SC---EEEEEEEEEEEE-SS
T ss_pred EeecCCCEEEEEEEECCe---EEEEEEEEEEEEcCC
Confidence 358899999999977544 778999999988544
No 64
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.49 E-value=1.1e+02 Score=21.21 Aligned_cols=16 Identities=31% Similarity=0.312 Sum_probs=12.5
Q ss_pred CCCCCCEEEEEEEeec
Q 026573 145 DIRTGDVVEIKLEVPE 160 (236)
Q Consensus 145 ~f~~GDiV~V~~~i~E 160 (236)
.|++||.|+|.+.-..
T Consensus 47 ~~~~Gd~v~v~i~~vd 62 (77)
T cd05708 47 LFRVGDKVRAKVLKID 62 (77)
T ss_pred eecCCCEEEEEEEEEe
Confidence 4899999999975443
No 65
>PF03946 Ribosomal_L11_N: Ribosomal protein L11, N-terminal domain; InterPro: IPR020784 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 [, ]. Ribosomal protein L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacteria, plant chloroplast, red algal chloroplast, cyanelle and archaeabacterial L11; and mammalian, plant and yeast L12 (YL15). L11 is a protein of 140 to 165 amino-acid residues. In E. coli, the C-terminal half of L11 has been shown [] to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure.; PDB: 2ZJQ_F 2ZJP_F 3CF5_F 2WRJ_K 2WH4_K 2WRL_K 3FIN_L 2X9U_K 3I8I_L 2XUX_K ....
Probab=20.35 E-value=3.1e+02 Score=19.95 Aligned_cols=43 Identities=16% Similarity=0.342 Sum_probs=27.3
Q ss_pred cCCCCCCcc---chhhHHHHHHHHHHHhhhcCCCCCCCCCCCEEEEEEEeecCc
Q 026573 112 VKAPRKPRV---KLGDIMGILNKRAVEASESERPIPDIRTGDVVEIKLEVPENR 162 (236)
Q Consensus 112 ~~pp~k~r~---KL~dlM~iLe~~~ie~~~~kk~iP~f~~GDiV~V~~~i~E~K 162 (236)
|.||..|.. -+ ++|++- +++++.... ++.|..|.|.+.+.+++
T Consensus 13 p~pplgp~LG~~Gi-n~~~f~--k~fN~~T~~-----~k~G~~v~V~i~v~~d~ 58 (60)
T PF03946_consen 13 PAPPLGPALGPLGI-NIKKFC--KDFNKATKD-----YKPGIPVPVKITVYNDK 58 (60)
T ss_dssp STTTSTHHHHTTTS--HHHHH--HHHHHHTTT-----CTTSSEEEEEEEEETTS
T ss_pred CCCCcCcccccCCC-CHHHHH--HHHHHHHhc-----ccCCCEEEEEEEEeCCC
Confidence 456666632 23 555554 466655433 88899999999987644
No 66
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=20.33 E-value=1e+02 Score=21.02 Aligned_cols=21 Identities=24% Similarity=0.300 Sum_probs=14.8
Q ss_pred CCCCCCEEEEEEEeec-Ccccc
Q 026573 145 DIRTGDVVEIKLEVPE-NRRRL 165 (236)
Q Consensus 145 ~f~~GDiV~V~~~i~E-~K~Ri 165 (236)
.|++||.|+|.+.-.. .+.|+
T Consensus 45 ~~~~G~~v~v~v~~id~~~~~i 66 (69)
T cd05690 45 IYKKGQEVEAVVLNIDVERERI 66 (69)
T ss_pred EECCCCEEEEEEEEEECCcCEE
Confidence 3899999999965443 44443
Done!