Query 028968
Match_columns 201
No_of_seqs 139 out of 900
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 05:22:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028968.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028968hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0335 RplS Ribosomal protein 100.0 1.3E-28 2.8E-33 195.1 8.4 70 132-201 7-77 (115)
2 CHL00084 rpl19 ribosomal prote 100.0 2.8E-28 6E-33 193.5 9.9 75 125-201 4-79 (117)
3 PRK05338 rplS 50S ribosomal pr 99.9 6.3E-28 1.4E-32 191.1 8.9 70 132-201 5-75 (116)
4 TIGR01024 rplS_bact ribosomal 99.9 8.2E-28 1.8E-32 189.7 9.0 70 132-201 5-75 (113)
5 PF01245 Ribosomal_L19: Riboso 99.9 5.4E-27 1.2E-31 184.4 11.2 74 126-201 1-75 (113)
6 KOG1698 Mitochondrial/chloropl 99.9 2.1E-23 4.5E-28 178.2 10.3 144 42-201 6-152 (201)
7 PF05641 Agenet: Agenet domain 85.2 2.8 6E-05 29.7 5.2 38 146-188 1-38 (68)
8 smart00743 Agenet Tudor-like d 81.5 9 0.0002 25.9 6.4 49 144-200 1-49 (61)
9 PF02211 NHase_beta: Nitrile h 62.5 7.6 0.00016 34.2 3.0 36 142-177 131-170 (222)
10 PF12969 DUF3857: Domain of Un 61.9 15 0.00033 28.6 4.3 21 141-161 85-105 (177)
11 TIGR03170 flgA_cterm flagella 60.3 33 0.00072 26.0 5.8 47 142-193 62-108 (122)
12 PF02765 POT1: Telomeric singl 58.9 8.9 0.00019 30.6 2.6 39 142-187 69-109 (146)
13 cd00493 FabA_FabZ FabA/Z, beta 58.1 18 0.0004 26.6 4.0 30 145-174 88-117 (131)
14 TIGR01750 fabZ beta-hydroxyacy 52.1 25 0.00054 27.0 4.0 28 145-172 97-124 (140)
15 cd01288 FabZ FabZ is a 17kD be 52.1 49 0.0011 24.4 5.5 28 145-172 87-114 (131)
16 PF13144 SAF_2: SAF-like 49.3 61 0.0013 26.5 6.1 47 141-192 135-181 (196)
17 smart00739 KOW KOW (Kyprides, 46.1 40 0.00086 19.0 3.3 27 145-177 1-27 (28)
18 PF02752 Arrestin_C: Arrestin 46.1 35 0.00076 24.9 3.9 31 145-175 15-46 (136)
19 cd04497 hPOT1_OB1_like hPOT1_O 46.1 35 0.00075 27.1 4.1 41 141-188 64-104 (138)
20 PRK00006 fabZ (3R)-hydroxymyri 44.4 34 0.00074 26.5 3.7 28 146-173 102-129 (147)
21 PF07977 FabA: FabA-like domai 42.5 27 0.00059 26.9 2.9 30 144-173 95-128 (138)
22 COG1566 EmrA Multidrug resista 42.4 74 0.0016 29.9 6.2 63 134-199 247-318 (352)
23 TIGR02266 gmx_TIGR02266 Myxoco 42.1 97 0.0021 22.0 5.6 35 144-179 35-69 (96)
24 cd03451 FkbR2 FkbR2 is a Strep 41.4 43 0.00094 25.5 3.8 16 145-160 91-106 (146)
25 cd04455 S1_NusA S1_NusA: N-uti 41.4 39 0.00085 23.3 3.3 22 145-166 40-62 (67)
26 cd05690 S1_RPS1_repeat_ec5 S1_ 41.3 29 0.00063 23.2 2.6 22 145-166 45-67 (69)
27 PRK07018 flgA flagellar basal 40.3 87 0.0019 27.1 5.9 47 142-193 173-219 (235)
28 cd00164 S1_like S1_like: Ribos 40.1 35 0.00075 21.5 2.7 16 145-160 41-56 (65)
29 cd04471 S1_RNase_R S1_RNase_R: 40.1 29 0.00063 23.9 2.5 23 144-166 56-79 (83)
30 PF00238 Ribosomal_L14: Riboso 39.9 59 0.0013 26.0 4.5 36 142-177 29-67 (122)
31 COG2030 MaoC Acyl dehydratase 39.7 41 0.00089 27.2 3.6 17 144-160 105-121 (159)
32 cd05708 S1_Rrp5_repeat_sc12 S1 39.0 36 0.00078 23.0 2.8 21 145-165 47-68 (77)
33 cd05703 S1_Rrp5_repeat_hs12_sc 38.0 40 0.00087 23.8 3.0 23 145-167 46-69 (73)
34 cd03450 NodN NodN (nodulation 37.2 75 0.0016 25.6 4.8 33 146-178 98-134 (149)
35 cd04452 S1_IF2_alpha S1_IF2_al 36.5 42 0.00092 22.8 2.8 15 146-160 50-64 (76)
36 PF07238 PilZ: PilZ domain; I 36.1 1.1E+02 0.0024 20.8 5.0 32 145-178 44-75 (102)
37 COG2139 RPL21A Ribosomal prote 35.9 40 0.00086 26.9 2.9 40 141-180 28-71 (98)
38 cd05706 S1_Rrp5_repeat_sc10 S1 35.9 46 0.001 22.7 2.9 15 146-160 48-62 (73)
39 cd04491 SoSSB_OBF SoSSB_OBF: A 35.8 49 0.0011 23.4 3.1 26 143-168 46-72 (82)
40 cd05688 S1_RPS1_repeat_ec3 S1_ 35.5 41 0.0009 22.0 2.6 15 146-160 45-59 (68)
41 cd08544 Reeler Reeler, the N-t 35.5 86 0.0019 24.2 4.7 31 145-179 29-59 (135)
42 cd05705 S1_Rrp5_repeat_hs14 S1 35.0 44 0.00095 23.8 2.8 22 145-166 50-72 (74)
43 PF08207 EFP_N: Elongation fac 35.0 1.4E+02 0.003 20.6 5.2 49 145-200 4-53 (58)
44 PF09926 DUF2158: Uncharacteri 34.6 26 0.00056 24.6 1.5 10 146-155 1-10 (53)
45 PRK06005 flgA flagellar basal 34.4 1.1E+02 0.0024 25.3 5.5 48 142-194 97-144 (160)
46 PRK04424 fatty acid biosynthes 34.4 64 0.0014 26.9 4.1 30 144-173 137-166 (185)
47 PRK05483 rplN 50S ribosomal pr 34.4 70 0.0015 25.9 4.1 34 144-177 31-67 (122)
48 cd06462 Peptidase_S24_S26 The 34.2 84 0.0018 21.2 4.0 43 143-193 11-53 (84)
49 TIGR00405 L26e_arch ribosomal 34.1 1.7E+02 0.0037 23.0 6.3 43 144-194 85-127 (145)
50 PRK08571 rpl14p 50S ribosomal 34.0 1.5E+02 0.0032 24.5 6.0 36 142-177 43-78 (132)
51 cd03441 R_hydratase_like (R)-h 34.0 1.2E+02 0.0027 21.8 5.1 17 144-160 79-95 (127)
52 cd05685 S1_Tex S1_Tex: The C-t 33.2 53 0.0012 21.3 2.8 20 146-165 45-65 (68)
53 cd05686 S1_pNO40 S1_pNO40: pNO 32.1 55 0.0012 22.8 2.8 21 146-166 49-69 (73)
54 TIGR00008 infA translation ini 31.5 34 0.00074 25.2 1.8 26 140-165 39-65 (68)
55 cd05697 S1_Rrp5_repeat_hs5 S1_ 30.7 63 0.0014 21.9 2.9 22 145-166 44-66 (69)
56 PRK15136 multidrug efflux syst 30.7 91 0.002 28.7 4.8 33 141-176 261-293 (390)
57 PRK02268 hypothetical protein; 30.6 64 0.0014 26.8 3.4 36 141-176 31-68 (141)
58 PRK03999 translation initiatio 30.4 1.2E+02 0.0026 24.4 4.8 54 142-200 7-60 (129)
59 PRK06461 single-stranded DNA-b 30.2 55 0.0012 25.9 2.9 28 143-170 62-90 (129)
60 TIGR01067 rplN_bact ribosomal 30.2 97 0.0021 25.0 4.3 34 144-177 31-67 (122)
61 PF00717 Peptidase_S24: Peptid 30.0 42 0.00091 22.4 1.9 40 143-190 8-47 (70)
62 cd05698 S1_Rrp5_repeat_hs6_sc5 29.9 67 0.0015 21.6 2.9 15 146-160 45-59 (70)
63 PRK08559 nusG transcription an 29.8 2.3E+02 0.005 23.0 6.5 41 144-192 93-133 (153)
64 cd05689 S1_RPS1_repeat_ec4 S1_ 29.3 60 0.0013 22.0 2.6 21 145-165 48-69 (72)
65 PF13437 HlyD_3: HlyD family s 29.1 1.7E+02 0.0037 21.0 5.2 44 140-187 44-90 (105)
66 cd05704 S1_Rrp5_repeat_hs13 S1 29.0 67 0.0014 22.5 2.9 22 144-166 47-68 (72)
67 PF10447 EXOSC1: Exosome compo 28.7 40 0.00087 25.4 1.8 14 143-156 66-79 (82)
68 cd05707 S1_Rrp5_repeat_sc11 S1 28.6 69 0.0015 21.6 2.8 21 145-165 44-65 (68)
69 PTZ00054 60S ribosomal protein 28.5 1.2E+02 0.0026 25.3 4.7 35 142-176 50-84 (139)
70 TIGR03673 rpl14p_arch 50S ribo 28.4 2E+02 0.0044 23.7 5.9 36 142-177 42-77 (131)
71 PF04319 NifZ: NifZ domain; I 28.4 69 0.0015 24.2 3.0 34 144-177 3-36 (75)
72 smart00316 S1 Ribosomal protei 28.3 72 0.0016 20.3 2.8 16 145-160 46-61 (72)
73 TIGR01956 NusG_myco NusG famil 28.1 1E+02 0.0022 28.1 4.5 30 142-177 202-231 (258)
74 PF02014 Reeler: Reeler domain 28.0 61 0.0013 25.1 2.8 33 144-180 28-60 (132)
75 PF11302 DUF3104: Protein of u 27.3 2.1E+02 0.0046 21.7 5.4 51 143-193 3-58 (75)
76 PF00575 S1: S1 RNA binding do 27.2 69 0.0015 21.7 2.6 25 142-166 45-70 (74)
77 PF03061 4HBT: Thioesterase su 27.2 1E+02 0.0022 20.3 3.4 28 145-172 43-70 (79)
78 cd03452 MaoC_C MaoC_C The C-t 27.1 93 0.002 24.3 3.7 15 146-160 89-103 (142)
79 PF11717 Tudor-knot: RNA bindi 27.1 2E+02 0.0044 19.4 5.0 36 146-187 1-36 (55)
80 cd03440 hot_dog The hotdog fol 26.8 1.6E+02 0.0034 17.9 4.3 21 144-164 56-76 (100)
81 PRK12617 flgA flagellar basal 26.7 1.9E+02 0.0042 25.2 5.9 47 144-195 154-200 (214)
82 PRK08515 flgA flagellar basal 26.6 1.8E+02 0.0039 25.2 5.6 47 141-193 161-207 (222)
83 PRK12618 flgA flagellar basal 26.4 1.8E+02 0.0038 23.7 5.2 47 143-194 79-125 (141)
84 cd01289 FabA_like Domain of un 26.2 91 0.002 24.5 3.5 30 144-173 91-121 (138)
85 cd03447 FAS_MaoC FAS_MaoC, the 26.2 1.2E+02 0.0026 23.5 4.1 16 145-160 80-95 (126)
86 TIGR02754 sod_Ni_protease nick 26.0 1.6E+02 0.0035 21.0 4.5 13 143-155 9-21 (90)
87 cd04461 S1_Rrp5_repeat_hs8_sc7 26.0 84 0.0018 22.2 3.0 21 145-165 58-79 (83)
88 TIGR01000 bacteriocin_acc bact 25.9 1.3E+02 0.0029 28.1 5.0 46 140-187 366-415 (457)
89 cd05691 S1_RPS1_repeat_ec6 S1_ 25.9 86 0.0019 20.9 2.9 16 145-160 44-59 (73)
90 cd03449 R_hydratase (R)-hydrat 25.9 1.6E+02 0.0035 21.4 4.6 16 145-160 82-97 (128)
91 PRK13692 (3R)-hydroxyacyl-ACP 25.8 1.3E+02 0.0029 24.4 4.5 16 145-160 96-111 (159)
92 TIGR00074 hypC_hupF hydrogenas 25.7 51 0.0011 24.6 1.9 15 143-157 33-47 (76)
93 PF01575 MaoC_dehydratas: MaoC 25.6 75 0.0016 23.9 2.8 28 144-171 87-114 (122)
94 KOG0494 Transcription factor C 25.3 14 0.0003 34.5 -1.5 68 99-168 120-188 (332)
95 PRK09014 rfaH transcriptional 25.2 83 0.0018 25.2 3.1 27 145-177 109-135 (162)
96 PF08605 Rad9_Rad53_bind: Fung 24.8 38 0.00083 27.7 1.1 14 143-156 57-70 (131)
97 PF12148 DUF3590: Protein of u 24.5 44 0.00096 25.8 1.3 22 143-164 63-84 (85)
98 TIGR01955 RfaH transcriptional 24.2 1.1E+02 0.0024 24.1 3.6 29 144-178 107-135 (159)
99 COG1499 NMD3 NMD protein affec 24.0 46 0.00099 31.4 1.6 15 142-156 243-257 (355)
100 PF11325 DUF3127: Domain of un 23.9 73 0.0016 24.4 2.4 18 143-160 50-67 (84)
101 COG0361 InfA Translation initi 23.8 58 0.0013 24.6 1.8 27 139-165 40-67 (75)
102 cd04486 YhcR_OBF_like YhcR_OBF 23.7 95 0.0021 22.7 2.9 24 143-166 42-65 (78)
103 cd05696 S1_Rrp5_repeat_hs4 S1_ 23.5 99 0.0021 21.5 2.9 21 145-165 46-67 (71)
104 PF14326 DUF4384: Domain of un 23.3 78 0.0017 22.9 2.4 17 144-160 1-17 (83)
105 cd05687 S1_RPS1_repeat_ec1_hs1 23.3 1.1E+02 0.0023 20.7 2.9 15 146-160 45-59 (70)
106 smart00276 GLECT Galectin. Gal 23.0 1.1E+02 0.0024 23.6 3.3 50 141-190 3-57 (128)
107 PRK12442 translation initiatio 23.0 60 0.0013 25.3 1.8 24 139-162 40-64 (87)
108 PF04225 OapA: Opacity-associa 22.5 1.1E+02 0.0023 22.9 3.0 19 139-157 36-54 (85)
109 KOG3416 Predicted nucleic acid 22.3 1E+02 0.0022 25.8 3.1 29 145-179 61-89 (134)
110 cd00070 GLECT Galectin/galacto 22.2 1.2E+02 0.0025 23.3 3.3 25 141-165 4-29 (127)
111 PF01052 SpoA: Surface present 21.9 66 0.0014 22.6 1.8 35 143-177 26-64 (77)
112 PRK10800 acyl-CoA thioesterase 21.9 1.6E+02 0.0035 22.0 4.0 27 144-170 65-92 (130)
113 cd05692 S1_RPS1_repeat_hs4 S1_ 21.6 1.3E+02 0.0028 19.4 3.1 13 145-157 44-56 (69)
114 PRK06804 flgA flagellar basal 21.3 2.2E+02 0.0047 25.7 5.3 47 143-194 200-246 (261)
115 cd03446 MaoC_like MoaC_like 21.3 1.5E+02 0.0034 22.2 3.8 16 145-160 90-105 (140)
116 TIGR02799 thio_ybgC tol-pal sy 21.2 1.7E+02 0.0038 21.3 4.0 28 145-172 65-93 (126)
117 cd05693 S1_Rrp5_repeat_hs1_sc1 20.7 1.1E+02 0.0023 23.3 2.8 16 145-160 66-81 (100)
118 PRK13691 (3R)-hydroxyacyl-ACP 20.6 1.3E+02 0.0028 24.8 3.4 16 145-160 96-111 (166)
119 cd03455 SAV4209 SAV4209 is a S 20.6 1.9E+02 0.004 21.7 4.1 16 145-160 79-94 (123)
120 CHL00057 rpl14 ribosomal prote 20.6 1.9E+02 0.0041 23.4 4.3 34 144-177 31-67 (122)
121 PRK11281 hypothetical protein; 20.5 2.1E+02 0.0045 31.1 5.7 36 145-180 938-979 (1113)
122 PF01455 HupF_HypC: HupF/HypC 20.5 77 0.0017 23.0 1.9 14 143-156 35-48 (68)
123 TIGR00922 nusG transcription t 20.4 4.5E+02 0.0098 21.0 7.4 28 144-177 118-145 (172)
124 COG5496 Predicted thioesterase 20.4 2.5E+02 0.0054 23.4 5.0 47 143-190 68-114 (130)
125 PF01281 Ribosomal_L9_N: Ribos 20.3 76 0.0017 21.8 1.7 17 139-155 5-22 (48)
126 PRK12786 flgA flagellar basal 20.3 2.6E+02 0.0056 26.0 5.7 47 143-194 256-302 (338)
127 PRK08572 rps17p 30S ribosomal 20.0 1.2E+02 0.0025 24.4 3.0 22 164-188 28-49 (108)
128 PF01336 tRNA_anti-codon: OB-f 20.0 1.3E+02 0.0028 19.9 2.8 19 145-163 44-62 (75)
No 1
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=1.3e-28 Score=195.13 Aligned_cols=70 Identities=36% Similarity=0.763 Sum_probs=67.2
Q ss_pred HHHHhhhcCCCCCCCCCCCEEEEEEEeec-CCcccceEEEEEEEeecCCccceEEEEeeeCCeeeEEEeeC
Q 028968 132 RAVEASESERPIPDIRTGDVVEIKLEVPE-NRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVEIVFPL 201 (201)
Q Consensus 132 e~IE~~q~kkdiPeFr~GDtVrV~v~I~E-nKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~GVGVER~FPL 201 (201)
+++++.|+++++|+|+|||||+|+++|.| +|+|+|.|+|+||+++|+|+++||||||+++|+||||+||+
T Consensus 7 ~~le~~q~~~~iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~~~tftvRkis~G~GVEr~Fp~ 77 (115)
T COG0335 7 QQLEQEQIKKDIPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGISETFTVRKISYGVGVERVFPL 77 (115)
T ss_pred HHHHHHHHHhhCCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCCCccceEEEEEeecCceEEEEeec
Confidence 56788888889999999999999999999 99999999999999999999999999999999999999996
No 2
>CHL00084 rpl19 ribosomal protein L19
Probab=99.95 E-value=2.8e-28 Score=193.45 Aligned_cols=75 Identities=36% Similarity=0.753 Sum_probs=69.9
Q ss_pred HHHHHHHHHHHhhhcCCCCCCCCCCCEEEEEEEeec-CCcccceEEEEEEEeecCCccceEEEEeeeCCeeeEEEeeC
Q 028968 125 IMGILNKRAVEASESERPIPDIRTGDVVEIKLEVPE-NRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVEIVFPL 201 (201)
Q Consensus 125 lM~iLnke~IE~~q~kkdiPeFr~GDtVrV~v~I~E-nKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~GVGVER~FPL 201 (201)
+++++ +++++.++++++|+|++||||+|+++|.| +|+|+|.|+|+||+++|+|+++||||||+++|+||||+|||
T Consensus 4 ~~~~i--~~~~~~~~~~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvRki~~gvGVEr~fpl 79 (117)
T CHL00084 4 LQQLV--KEIESEFLKKNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVRKVFQGIGVERVFLL 79 (117)
T ss_pred HHHHH--HHHHHHHhhcCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEEEeccCccEEEEEec
Confidence 34455 56888888999999999999999999999 99999999999999999999999999999999999999996
No 3
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=99.95 E-value=6.3e-28 Score=191.07 Aligned_cols=70 Identities=37% Similarity=0.798 Sum_probs=66.4
Q ss_pred HHHHhhhcCCCCCCCCCCCEEEEEEEeec-CCcccceEEEEEEEeecCCccceEEEEeeeCCeeeEEEeeC
Q 028968 132 RAVEASESERPIPDIRTGDVVEIKLEVPE-NRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVEIVFPL 201 (201)
Q Consensus 132 e~IE~~q~kkdiPeFr~GDtVrV~v~I~E-nKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~GVGVER~FPL 201 (201)
+.+|+.++++++|+|++||||+|+++|.| +|+|+|.|+|+||+++|+|+++||||||+++|+||||+|||
T Consensus 5 ~~~~~~~~~~~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki~~gvGVEr~fpl 75 (116)
T PRK05338 5 KEIEAEQLRKDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKISYGVGVERTFPL 75 (116)
T ss_pred HHHHHHHhhcCCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEcccCccEEEEecC
Confidence 45677777889999999999999999999 89999999999999999999999999999999999999997
No 4
>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=99.95 E-value=8.2e-28 Score=189.70 Aligned_cols=70 Identities=34% Similarity=0.808 Sum_probs=66.6
Q ss_pred HHHHhhhcCCCCCCCCCCCEEEEEEEeec-CCcccceEEEEEEEeecCCccceEEEEeeeCCeeeEEEeeC
Q 028968 132 RAVEASESERPIPDIRTGDVVEIKLEVPE-NRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVEIVFPL 201 (201)
Q Consensus 132 e~IE~~q~kkdiPeFr~GDtVrV~v~I~E-nKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~GVGVER~FPL 201 (201)
+.+|+.++++++|+|++||||+|+++|.| +|+|+|.|+|+||+++|+|+++||||||+++|+||||+|||
T Consensus 5 ~~~e~~~~~~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i~~gvGVEr~fpl 75 (113)
T TIGR01024 5 KQIEQEQLKKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKISYGVGVERIFPL 75 (113)
T ss_pred HHHHHHHhhcCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEeccCccEEEEEEc
Confidence 45677778899999999999999999999 99999999999999999999999999999999999999997
No 5
>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=99.94 E-value=5.4e-27 Score=184.38 Aligned_cols=74 Identities=35% Similarity=0.814 Sum_probs=70.1
Q ss_pred HHHHHHHHHHhhhcCCCCCCCCCCCEEEEEEEeec-CCcccceEEEEEEEeecCCccceEEEEeeeCCeeeEEEeeC
Q 028968 126 MGILNKRAVEASESERPIPDIRTGDVVEIKLEVPE-NRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVEIVFPL 201 (201)
Q Consensus 126 M~iLnke~IE~~q~kkdiPeFr~GDtVrV~v~I~E-nKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~GVGVER~FPL 201 (201)
|++| +++|+.++++++|+|++||+|+|++++.| +|+|+|.|+|+||+++|+|+++||||||+++|+||||+|||
T Consensus 1 ~~~i--~~~e~~~~~~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~~~~g~gVE~~f~l 75 (113)
T PF01245_consen 1 MNLI--EEVEREQIKKDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRNISQGVGVERVFPL 75 (113)
T ss_dssp -HHH--HHHHHTTCSSSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEEEETTEEEEEEEET
T ss_pred ChHH--HHHHHHHhhcCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEEEecCccEEEEEEc
Confidence 6666 67889989999999999999999999999 99999999999999999999999999999999999999997
No 6
>KOG1698 consensus Mitochondrial/chloroplast ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=2.1e-23 Score=178.20 Aligned_cols=144 Identities=31% Similarity=0.450 Sum_probs=112.7
Q ss_pred eeeeec---CCCccccceeeccccceeEEeeccchhhhcchhhHHHhHHHHhhccceeeeecccccccchhhhccCCCCC
Q 028968 42 VSVSAK---PIGWNLGFFVNAQVKDSFVVRAEANEEAEANESIEEEQNEAVQAQGDVVVAVEAESEDKVEEEEVKAPRKP 118 (201)
Q Consensus 42 ~~~~~~---~~~~~~~~~~~~~~~~~~v~~a~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~e~~~~~~~e~~~~~p~r~~ 118 (201)
+++++. +..|++.+.+.....++|+..+|.-..+.....+ ..++.-+...-.....+..+.
T Consensus 6 ~~~~r~~~~~~a~~~~v~l~~~~~~~~~~~~e~~~~a~~~~~~----------------~~~~~~~~~~~~~~~~~f~~~ 69 (201)
T KOG1698|consen 6 LGFDRFPMFRAASYRNVSLKGKWFSSFIAISEERCFAPTKRPS----------------VNEPSPESPCVVEQYPEFLPL 69 (201)
T ss_pred eeeecccccchhhhheeecccceeeeeccccccccccCCCCcc----------------cccCCCCCccccccCcccccc
Confidence 444444 3566777777778888999888764333322220 123322222222344556667
Q ss_pred CCchhHHHHHHHHHHHHhhhcCCCCCCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEeeeCCeeeEEE
Q 028968 119 RVKLGDIMGILNKRAVEASESERPIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVEIV 198 (201)
Q Consensus 119 ~~klg~lM~iLnke~IE~~q~kkdiPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~GVGVER~ 198 (201)
++..+++|++|++++++...+.+++|+|++||+|+|++..+++|.++..|.||||+|+|.|+++||+|||++.|+|||.+
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 77789999999999999998889999999999999999999999999999999999999999999999999999999999
Q ss_pred eeC
Q 028968 199 FPL 201 (201)
Q Consensus 199 FPL 201 (201)
|||
T Consensus 150 ~pL 152 (201)
T KOG1698|consen 150 FPL 152 (201)
T ss_pred Eec
Confidence 997
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=85.18 E-value=2.8 Score=29.69 Aligned_cols=38 Identities=18% Similarity=0.318 Sum_probs=26.0
Q ss_pred CCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEe
Q 028968 146 IRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRR 188 (201)
Q Consensus 146 Fr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRK 188 (201)
|++||.|+|... |+.-|-.=|.|+|++..+.+ +|.|+-
T Consensus 1 F~~G~~VEV~s~--e~g~~gaWf~a~V~~~~~~~---~~~V~Y 38 (68)
T PF05641_consen 1 FKKGDEVEVSSD--EDGFRGAWFPATVLKENGDD---KYLVEY 38 (68)
T ss_dssp --TT-EEEEEE---SBTT--EEEEEEEEEEETT----EEEEEE
T ss_pred CCCCCEEEEEEc--CCCCCcEEEEEEEEEeCCCc---EEEEEE
Confidence 789999999753 34459999999999999876 788875
No 8
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=81.46 E-value=9 Score=25.88 Aligned_cols=49 Identities=16% Similarity=0.193 Sum_probs=35.7
Q ss_pred CCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEeeeCCeeeEEEee
Q 028968 144 PDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVEIVFP 200 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~GVGVER~FP 200 (201)
..|++||.|.+.... .-.=|.|+|++..+ +..|.|+=...+.|-+-+|+
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 368999999998752 56789999999887 45688887654466554443
No 9
>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=62.47 E-value=7.6 Score=34.18 Aligned_cols=36 Identities=25% Similarity=0.424 Sum_probs=20.6
Q ss_pred CCCCCCCCCEEEEEEEeecCCcccceE----EEEEEEeec
Q 028968 142 PIPDIRTGDVVEIKLEVPENRRRLSIY----KGIVMSRQN 177 (201)
Q Consensus 142 diPeFr~GDtVrV~v~I~EnKeRiQ~F----eGIVIarrn 177 (201)
.-|.|++||.|+|.-.-+..-.|+..| .|+|.+.+|
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 468999999999997766678888887 788887665
No 10
>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=61.90 E-value=15 Score=28.64 Aligned_cols=21 Identities=29% Similarity=0.668 Sum_probs=13.5
Q ss_pred CCCCCCCCCCEEEEEEEeecC
Q 028968 141 RPIPDIRTGDVVEIKLEVPEN 161 (201)
Q Consensus 141 kdiPeFr~GDtVrV~v~I~En 161 (201)
-.+|++++||+|...+.+...
T Consensus 85 ~~~p~v~~GdiIe~~y~~~~~ 105 (177)
T PF12969_consen 85 FAFPDVRVGDIIEYSYTIKSK 105 (177)
T ss_dssp EE--S--TT-EEEEEEEEEE-
T ss_pred EEcCCCCCCcEEEEEEEEEec
Confidence 479999999999999999763
No 11
>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=60.30 E-value=33 Score=26.04 Aligned_cols=47 Identities=21% Similarity=0.259 Sum_probs=34.5
Q ss_pred CCCCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEeeeCCe
Q 028968 142 PIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGI 193 (201)
Q Consensus 142 diPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~GV 193 (201)
..|-++-||+|.|.+...- ++ .+-...|..+++++.++.|||...|-
T Consensus 62 ~~~~V~~G~~V~i~~~~~~----~~-i~~~g~Al~~g~~G~~I~V~N~~s~k 108 (122)
T TIGR03170 62 PPWLVKRGDTVTVIARGGG----LS-VTTEGKALEDGAVGDQIRVRNLSSGK 108 (122)
T ss_pred CccEEcCCCEEEEEEecCC----EE-EEEEEEEccccCCCCEEEEEECCCCC
Confidence 4578999999999886431 11 22345788899999999999976653
No 12
>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=58.89 E-value=8.9 Score=30.60 Aligned_cols=39 Identities=15% Similarity=0.508 Sum_probs=26.6
Q ss_pred CCCCCCC-CCEEEEE-EEeecCCcccceEEEEEEEeecCCccceEEEE
Q 028968 142 PIPDIRT-GDVVEIK-LEVPENRRRLSIYKGIVMSRQNAGIHTTIRIR 187 (201)
Q Consensus 142 diPeFr~-GDtVrV~-v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVR 187 (201)
.+|.+.. ||+|.++ ++ +|.|.|-..+..+.+-+++|-|=
T Consensus 69 ~LP~v~~~GDii~l~r~k-------v~~~~~~~~~~~~~~~~ss~~vf 109 (146)
T PF02765_consen 69 SLPNVKSVGDIIRLRRVK-------VQSYNGKPQGLSNSTSNSSWAVF 109 (146)
T ss_dssp HSCTTCSTTHEEEEEEEE-------EEEETTEEEEEEECECTEEEEEE
T ss_pred HCCCCCCCCCEEEEEEEE-------EEEECCEEEEEecCCCcEEEEEE
Confidence 5799998 9999998 55 45555555555555555666665
No 13
>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=58.14 E-value=18 Score=26.58 Aligned_cols=30 Identities=23% Similarity=0.452 Sum_probs=24.0
Q ss_pred CCCCCCEEEEEEEeecCCcccceEEEEEEE
Q 028968 145 DIRTGDVVEIKLEVPENRRRLSIYKGIVMS 174 (201)
Q Consensus 145 eFr~GDtVrV~v~I~EnKeRiQ~FeGIVIa 174 (201)
..+|||++.+.+++.+.+.++-.|.+.+..
T Consensus 88 ~v~pgd~l~i~~~i~~~~~~~~~~~~~~~~ 117 (131)
T cd00493 88 PVLPGDTLTLEVELLKVRRGLGKFDGRAYV 117 (131)
T ss_pred CcCCCCEEEEEEEEEEeeCCEEEEEEEEEE
Confidence 467999999999999865677777777654
No 14
>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=52.08 E-value=25 Score=26.98 Aligned_cols=28 Identities=25% Similarity=0.483 Sum_probs=21.8
Q ss_pred CCCCCCEEEEEEEeecCCcccceEEEEE
Q 028968 145 DIRTGDVVEIKLEVPENRRRLSIYKGIV 172 (201)
Q Consensus 145 eFr~GDtVrV~v~I~EnKeRiQ~FeGIV 172 (201)
..+|||++.+++++.+...+.-.|.|.+
T Consensus 97 ~v~pGd~l~i~~~i~~~~~~~~~~~~~~ 124 (140)
T TIGR01750 97 PVVPGDQLILHAEFLKKRRKIGKFKGEA 124 (140)
T ss_pred ccCCCCEEEEEEEEEEccCCEEEEEEEE
Confidence 3678999999999988556666777765
No 15
>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=52.07 E-value=49 Score=24.42 Aligned_cols=28 Identities=25% Similarity=0.464 Sum_probs=22.6
Q ss_pred CCCCCCEEEEEEEeecCCcccceEEEEE
Q 028968 145 DIRTGDVVEIKLEVPENRRRLSIYKGIV 172 (201)
Q Consensus 145 eFr~GDtVrV~v~I~EnKeRiQ~FeGIV 172 (201)
...|||++++.+++.+.+.+.-.|++.+
T Consensus 87 pv~pgd~l~i~~~v~~~~~~~~~~~~~~ 114 (131)
T cd01288 87 PVVPGDQLILEVELLKLRRGIGKFKGKA 114 (131)
T ss_pred ccCCCCEEEEEEEEEEeeCCEEEEEEEE
Confidence 3568999999999998666777777776
No 16
>PF13144 SAF_2: SAF-like
Probab=49.25 E-value=61 Score=26.55 Aligned_cols=47 Identities=21% Similarity=0.400 Sum_probs=34.9
Q ss_pred CCCCCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEeeeCC
Q 028968 141 RPIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAG 192 (201)
Q Consensus 141 kdiPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~G 192 (201)
+..|-++-||.|.|.+...- ++ .+-..+|..++.++.+++|||...|
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----IS-ISTEGKALEDGALGDTIRVKNLSSG 181 (196)
T ss_pred ccceecCCCCEEEEEEEeCC----EE-EEEEEEEccCCCCCCEEEEEECCCC
Confidence 34588999999999876431 22 2234578889999999999997655
No 17
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=46.13 E-value=40 Score=19.04 Aligned_cols=27 Identities=19% Similarity=0.235 Sum_probs=18.0
Q ss_pred CCCCCCEEEEEEEeecCCcccceEEEEEEEeec
Q 028968 145 DIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQN 177 (201)
Q Consensus 145 eFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn 177 (201)
.|.+||.|+|.- -...-+.|+++...+
T Consensus 1 ~~~~G~~V~I~~------G~~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIA------GPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeE------CCCCCcEEEEEEEcC
Confidence 378999999863 334445777776643
No 18
>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=46.11 E-value=35 Score=24.87 Aligned_cols=31 Identities=13% Similarity=0.400 Sum_probs=21.5
Q ss_pred CCCCCCEEEEEEEeec-CCcccceEEEEEEEe
Q 028968 145 DIRTGDVVEIKLEVPE-NRRRLSIYKGIVMSR 175 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E-nKeRiQ~FeGIVIar 175 (201)
.|.+||+|.|++.|.. .+.+++..+--++.+
T Consensus 15 ~~~~Ge~i~v~v~i~n~s~~~i~~I~v~L~~~ 46 (136)
T PF02752_consen 15 AYVPGETIPVNVEIDNQSKKKIKKIKVSLVER 46 (136)
T ss_dssp EEETT--EEEEEEEEE-SSSEEEEEEEEEEEE
T ss_pred EECCCCEEEEEEEEEECCCCEEEEEEEEEEEE
Confidence 3889999999999997 566666666555544
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=46.05 E-value=35 Score=27.09 Aligned_cols=41 Identities=17% Similarity=0.379 Sum_probs=31.1
Q ss_pred CCCCCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEe
Q 028968 141 RPIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRR 188 (201)
Q Consensus 141 kdiPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRK 188 (201)
..+|.+.+||+|.++= =++|.|.|-..+..+. -.++|-|=+
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 4689899999999973 4788888888888776 346665544
No 20
>PRK00006 fabZ (3R)-hydroxymyristoyl-ACP dehydratase; Reviewed
Probab=44.41 E-value=34 Score=26.50 Aligned_cols=28 Identities=25% Similarity=0.527 Sum_probs=21.8
Q ss_pred CCCCCEEEEEEEeecCCcccceEEEEEE
Q 028968 146 IRTGDVVEIKLEVPENRRRLSIYKGIVM 173 (201)
Q Consensus 146 Fr~GDtVrV~v~I~EnKeRiQ~FeGIVI 173 (201)
.++||+|.+.+++.+.++++=.|.+.+.
T Consensus 102 v~pGd~l~i~~~i~~~~~~~v~~~~~~~ 129 (147)
T PRK00006 102 VVPGDQLILEVELLKQRRGIWKFKGVAT 129 (147)
T ss_pred cCCCCEEEEEEEEEEeeCCEEEEEEEEE
Confidence 3589999999999886566667777663
No 21
>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=42.50 E-value=27 Score=26.91 Aligned_cols=30 Identities=20% Similarity=0.501 Sum_probs=22.8
Q ss_pred CCCCCCC-EEEEEEEeec---CCcccceEEEEEE
Q 028968 144 PDIRTGD-VVEIKLEVPE---NRRRLSIYKGIVM 173 (201)
Q Consensus 144 PeFr~GD-tVrV~v~I~E---nKeRiQ~FeGIVI 173 (201)
=.+.||| ++++.+.+.+ ....+-.|+|.+.
T Consensus 95 ~~v~Pg~~~l~~~v~i~~~~~~~~~~~~~~~~~~ 128 (138)
T PF07977_consen 95 GPVYPGDKTLRIEVEIKKIRRREGGMAIFDGTAY 128 (138)
T ss_dssp S-B-TTE-EEEEEEEEEEEEEEETTEEEEEEEEE
T ss_pred ccEeCCCcEEEEEEEEEEeecccCCEEEEEEEEE
Confidence 3578999 9999999988 6777777887664
No 22
>COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms]
Probab=42.39 E-value=74 Score=29.86 Aligned_cols=63 Identities=24% Similarity=0.316 Sum_probs=45.7
Q ss_pred HHhhhcCCCCCCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCC---------ccceEEEEeeeCCeeeEEEe
Q 028968 134 VEASESERPIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAG---------IHTTIRIRRIIAGIGVEIVF 199 (201)
Q Consensus 134 IE~~q~kkdiPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~G---------i~sTFTVRKIs~GVGVER~F 199 (201)
|...+.+.+|..+++|+-++|++-.-... ..|+|+|-++...- .+.|+..-|+.+.+.|...|
T Consensus 247 V~AnFkETqL~~~r~Gq~a~I~~da~~~~---~~~~G~v~~i~~~tg~~fsllp~~natgN~tkvvQRvPVrI~l 318 (352)
T COG1566 247 VVANFKETQLARVRPGQPAEITLDAYPGN---GVVEGIVEGIAPATGSAFSLLPAQNATGNWTKVVQRVPVRIEL 318 (352)
T ss_pred EEeeeeeeecCcccCCCeEEEEEEcCCCc---eEEEEEEEEecCCcccccccCCCccCCCCEEEEEEeeeEEEEe
Confidence 33445667899999999999998766532 89999999986431 24455556777877776655
No 23
>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=42.12 E-value=97 Score=21.97 Aligned_cols=35 Identities=31% Similarity=0.490 Sum_probs=25.7
Q ss_pred CCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCC
Q 028968 144 PDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAG 179 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~G 179 (201)
..+.+||.|.|.+.++.+...+. ..|.|+..+..+
T Consensus 35 ~~~~~g~~v~l~l~l~~~~~~i~-~~g~Vv~~~~~~ 69 (96)
T TIGR02266 35 KPLAVGTRVELKLTLPGGERPVE-LKGVVAWVRPAA 69 (96)
T ss_pred CCcCCCCEEEEEEEcCCCCeEEE-EEEEEEEeCCCC
Confidence 35789999999999987533333 579998877544
No 24
>cd03451 FkbR2 FkbR2 is a Streptomyces hygroscopicus protein with a hot dog fold that belongs to a conserved family of proteins found in prokaryotes and archaea but not in eukaryotes. FkbR2 has sequence similarity to (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. The function of FkbR2 is unknown.
Probab=41.40 E-value=43 Score=25.45 Aligned_cols=16 Identities=25% Similarity=0.262 Sum_probs=14.2
Q ss_pred CCCCCCEEEEEEEeec
Q 028968 145 DIRTGDVVEIKLEVPE 160 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E 160 (201)
.+++||+|.+..+|.+
T Consensus 91 pv~~GDtl~~~~~v~~ 106 (146)
T cd03451 91 PVFHGDTLYAESEVLS 106 (146)
T ss_pred CCCCCCEEEEEEEEEE
Confidence 4689999999999987
No 25
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=41.39 E-value=39 Score=23.26 Aligned_cols=22 Identities=14% Similarity=0.167 Sum_probs=16.1
Q ss_pred CCCCCCEEEEEEEeec-CCcccc
Q 028968 145 DIRTGDVVEIKLEVPE-NRRRLS 166 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E-nKeRiQ 166 (201)
.|++||.|+|.+.-.+ ++++.|
T Consensus 40 ~~~~Gd~v~v~v~~v~~~~~~~~ 62 (67)
T cd04455 40 SYRPGDRIKAYVLEVRKTSKGPQ 62 (67)
T ss_pred cCCCCCEEEEEEEEEecCCCCCE
Confidence 5899999999987666 344433
No 26
>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=41.26 E-value=29 Score=23.20 Aligned_cols=22 Identities=27% Similarity=0.320 Sum_probs=16.0
Q ss_pred CCCCCCEEEEEEEeec-CCcccc
Q 028968 145 DIRTGDVVEIKLEVPE-NRRRLS 166 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E-nKeRiQ 166 (201)
.|++||.|+|.+.-.. .+.|+.
T Consensus 45 ~~~~G~~v~v~v~~id~~~~~i~ 67 (69)
T cd05690 45 IYKKGQEVEAVVLNIDVERERIS 67 (69)
T ss_pred EECCCCEEEEEEEEEECCcCEEe
Confidence 3899999999975554 555553
No 27
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=40.26 E-value=87 Score=27.07 Aligned_cols=47 Identities=19% Similarity=0.181 Sum_probs=33.8
Q ss_pred CCCCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEeeeCCe
Q 028968 142 PIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGI 193 (201)
Q Consensus 142 diPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~GV 193 (201)
.-|-++-||+|.|.+.-. -++ ..-...|..+++++.+++|||...|-
T Consensus 173 ~~~~V~~G~~V~i~~~~g----~~~-i~~~G~Al~~G~~Gd~IrVrN~~Sgk 219 (235)
T PRK07018 173 QAWVVCKGQTVSIIARGD----GFS-VKTEGEALNDGAVGQQIRVRNMASGQ 219 (235)
T ss_pred CccEeCCCCEEEEEEecC----CEE-EEEEEEEcCCCCCCCeEEEEECCCCC
Confidence 467799999999987632 111 12334778889999999999876653
No 28
>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=40.11 E-value=35 Score=21.48 Aligned_cols=16 Identities=31% Similarity=0.449 Sum_probs=13.0
Q ss_pred CCCCCCEEEEEEEeec
Q 028968 145 DIRTGDVVEIKLEVPE 160 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E 160 (201)
.|++||+|++.+.-..
T Consensus 41 ~~~~G~~v~~~v~~~d 56 (65)
T cd00164 41 VFKVGDEVEVKVLEVD 56 (65)
T ss_pred EeCCCCEEEEEEEEEc
Confidence 4999999999886544
No 29
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=40.07 E-value=29 Score=23.87 Aligned_cols=23 Identities=26% Similarity=0.541 Sum_probs=16.1
Q ss_pred CCCCCCCEEEEEEEeec-CCcccc
Q 028968 144 PDIRTGDVVEIKLEVPE-NRRRLS 166 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~E-nKeRiQ 166 (201)
-.|++||+|+|.+.-.. .+.+++
T Consensus 56 ~~~~~gd~v~v~v~~vd~~~~~i~ 79 (83)
T cd04471 56 KVFRLGDKVKVRVVRVDLDRRKID 79 (83)
T ss_pred CEEcCCCEEEEEEEEeccccCEEE
Confidence 45899999999876654 344443
No 30
>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=39.89 E-value=59 Score=26.00 Aligned_cols=36 Identities=11% Similarity=0.337 Sum_probs=27.5
Q ss_pred CCCCCCCCCEEEEEEEee--c-CCcccceEEEEEEEeec
Q 028968 142 PIPDIRTGDVVEIKLEVP--E-NRRRLSIYKGIVMSRQN 177 (201)
Q Consensus 142 diPeFr~GDtVrV~v~I~--E-nKeRiQ~FeGIVIarrn 177 (201)
..+.-..||+|.|.++-. . .-++=|+|.|+|+..+.
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 456678999999999877 3 33555999999998765
No 31
>COG2030 MaoC Acyl dehydratase [Lipid metabolism]
Probab=39.68 E-value=41 Score=27.18 Aligned_cols=17 Identities=24% Similarity=0.458 Sum_probs=15.1
Q ss_pred CCCCCCCEEEEEEEeec
Q 028968 144 PDIRTGDVVEIKLEVPE 160 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~E 160 (201)
-.+++||||++.+.+.+
T Consensus 105 ~PV~~Gdtl~~~~~v~~ 121 (159)
T COG2030 105 KPVFPGDTLRARVEVLD 121 (159)
T ss_pred CCCCCCCEEEEEEEEEE
Confidence 45899999999999987
No 32
>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=39.00 E-value=36 Score=23.00 Aligned_cols=21 Identities=29% Similarity=0.457 Sum_probs=15.2
Q ss_pred CCCCCCEEEEEEEeec-CCccc
Q 028968 145 DIRTGDVVEIKLEVPE-NRRRL 165 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E-nKeRi 165 (201)
.|++||.|+|.+.=.. ++.|+
T Consensus 47 ~~~~Gd~v~v~i~~vd~~~~~i 68 (77)
T cd05708 47 LFRVGDKVRAKVLKIDAEKKRI 68 (77)
T ss_pred eecCCCEEEEEEEEEeCCCCEE
Confidence 4899999999875544 45554
No 33
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: 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 H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=38.00 E-value=40 Score=23.81 Aligned_cols=23 Identities=13% Similarity=0.278 Sum_probs=17.0
Q ss_pred CCCCCCEEEEEEEeec-CCcccce
Q 028968 145 DIRTGDVVEIKLEVPE-NRRRLSI 167 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E-nKeRiQ~ 167 (201)
.|++||.|++.+.-.. +++|+.+
T Consensus 46 ~~~vG~~v~~kV~~id~~~~~i~L 69 (73)
T cd05703 46 KFPIGQALKAKVVGVDKEHKLLRL 69 (73)
T ss_pred hCCCCCEEEEEEEEEeCCCCEEEE
Confidence 4999999999976554 5666553
No 34
>cd03450 NodN NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their legume hosts, a symbiotic process that requires production of Nod factors, which are signal molecules involved in root hair deformation and meristematic cell division. The nodulation gene products, including NodN, are involved in producing the Nod factors, however the role played by NodN is unclear.
Probab=37.20 E-value=75 Score=25.63 Aligned_cols=33 Identities=6% Similarity=0.166 Sum_probs=23.2
Q ss_pred CCCCCEEEEEEEeec--CCc--ccceEEEEEEEeecC
Q 028968 146 IRTGDVVEIKLEVPE--NRR--RLSIYKGIVMSRQNA 178 (201)
Q Consensus 146 Fr~GDtVrV~v~I~E--nKe--RiQ~FeGIVIarrn~ 178 (201)
+++||+|.+..+|.+ .++ |.++..=..|.++|.
T Consensus 98 V~~GDtl~~~~~V~~~~~~~~~~~~~~~~~~~~~~~~ 134 (149)
T cd03450 98 VPVGSRVRGRFTLLSVEELKGGGVQVTLEVTVEIEGE 134 (149)
T ss_pred eeCCcEEEEEEEEEEEEEcCCCeEEEEEEEEEEEeCC
Confidence 689999999999987 222 245666566666654
No 35
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=36.46 E-value=42 Score=22.80 Aligned_cols=15 Identities=13% Similarity=0.244 Sum_probs=12.2
Q ss_pred CCCCCEEEEEEEeec
Q 028968 146 IRTGDVVEIKLEVPE 160 (201)
Q Consensus 146 Fr~GDtVrV~v~I~E 160 (201)
|+.||+|+|.+.-.+
T Consensus 50 ~~~Gd~v~vkv~~~d 64 (76)
T cd04452 50 VKVGRKEVVKVIRVD 64 (76)
T ss_pred eCCCCEEEEEEEEEE
Confidence 899999999866444
No 36
>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=36.15 E-value=1.1e+02 Score=20.83 Aligned_cols=32 Identities=22% Similarity=0.379 Sum_probs=23.5
Q ss_pred CCCCCCEEEEEEEeecCCcccceEEEEEEEeecC
Q 028968 145 DIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNA 178 (201)
Q Consensus 145 eFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~ 178 (201)
.+.+||.|.|.+.+.....-. +.|.|+..++.
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 789999999988777633322 99999998877
No 37
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=35.93 E-value=40 Score=26.88 Aligned_cols=40 Identities=20% Similarity=0.324 Sum_probs=30.2
Q ss_pred CCCCCCCCCCEEEEEEEeec----CCcccceEEEEEEEeecCCc
Q 028968 141 RPIPDIRTGDVVEIKLEVPE----NRRRLSIYKGIVMSRQNAGI 180 (201)
Q Consensus 141 kdiPeFr~GDtVrV~v~I~E----nKeRiQ~FeGIVIarrn~Gi 180 (201)
+-|-+|++||.|-+.+.=.= --.|.|=..|+|+..+|+..
T Consensus 28 r~l~ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay 71 (98)
T COG2139 28 RYLQEYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAY 71 (98)
T ss_pred hHHhhccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEE
Confidence 44668999999877654322 25799999999999998653
No 38
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: 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 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=35.86 E-value=46 Score=22.66 Aligned_cols=15 Identities=13% Similarity=0.248 Sum_probs=12.5
Q ss_pred CCCCCEEEEEEEeec
Q 028968 146 IRTGDVVEIKLEVPE 160 (201)
Q Consensus 146 Fr~GDtVrV~v~I~E 160 (201)
|++||+|++.+.-..
T Consensus 48 ~~~Gd~v~~~V~~~d 62 (73)
T cd05706 48 FKKNDIVRACVLSVD 62 (73)
T ss_pred cCCCCEEEEEEEEEe
Confidence 999999999876554
No 39
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=35.75 E-value=49 Score=23.41 Aligned_cols=26 Identities=38% Similarity=0.493 Sum_probs=20.4
Q ss_pred CCCCCCCCEEEEE-EEeecCCcccceE
Q 028968 143 IPDIRTGDVVEIK-LEVPENRRRLSIY 168 (201)
Q Consensus 143 iPeFr~GDtVrV~-v~I~EnKeRiQ~F 168 (201)
.+.+.+||+|++. .++.+-+.+.|+.
T Consensus 46 ~~~~~~G~vv~i~~~~v~~~~g~~ql~ 72 (82)
T cd04491 46 ADDLEPGDVVRIENAYVREFNGRLELS 72 (82)
T ss_pred cccCCCCCEEEEEeEEEEecCCcEEEE
Confidence 6779999999999 8888755556654
No 40
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: 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 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=35.54 E-value=41 Score=21.97 Aligned_cols=15 Identities=33% Similarity=0.523 Sum_probs=12.4
Q ss_pred CCCCCEEEEEEEeec
Q 028968 146 IRTGDVVEIKLEVPE 160 (201)
Q Consensus 146 Fr~GDtVrV~v~I~E 160 (201)
|++||.|+|.+.-..
T Consensus 45 ~~~Gd~v~v~i~~vd 59 (68)
T cd05688 45 VNVGDEVEVKVLKID 59 (68)
T ss_pred ECCCCEEEEEEEEEE
Confidence 899999999876554
No 41
>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=35.48 E-value=86 Score=24.24 Aligned_cols=31 Identities=16% Similarity=0.383 Sum_probs=26.3
Q ss_pred CCCCCCEEEEEEEeecCCcccceEEEEEEEeecCC
Q 028968 145 DIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAG 179 (201)
Q Consensus 145 eFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~G 179 (201)
.+.||+.+.|++.-... ..|+|..|.-|+.+
T Consensus 29 ~y~pG~~~~Vtl~~~~~----~~F~GF~lqAr~~~ 59 (135)
T cd08544 29 SYVPGETYTVTLSGSSP----SPFRGFLLQARDAS 59 (135)
T ss_pred EECCCCEEEEEEECCCC----CceeEEEEEEEcCC
Confidence 68999999999986543 89999999988865
No 42
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: 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 H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=35.03 E-value=44 Score=23.79 Aligned_cols=22 Identities=9% Similarity=0.196 Sum_probs=17.0
Q ss_pred CCCCCCEEEEEEEeec-CCcccc
Q 028968 145 DIRTGDVVEIKLEVPE-NRRRLS 166 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E-nKeRiQ 166 (201)
.|++||.|++.+.-.+ ++.|+.
T Consensus 50 ~~~~G~~v~~kVl~id~~~~~i~ 72 (74)
T cd05705 50 YLPEGKLLTAKVLSVNSEKNLVE 72 (74)
T ss_pred ccCCCCEEEEEEEEEECCCCEEe
Confidence 4899999999987665 566654
No 43
>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=34.96 E-value=1.4e+02 Score=20.63 Aligned_cols=49 Identities=22% Similarity=0.374 Sum_probs=26.6
Q ss_pred CCCCCCEEEEEEEeecCCcccceEEEEEEEeecCC-ccceEEEEeeeCCeeeEEEee
Q 028968 145 DIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAG-IHTTIRIRRIIAGIGVEIVFP 200 (201)
Q Consensus 145 eFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~G-i~sTFTVRKIs~GVGVER~FP 200 (201)
+|+.|.+|.+.= .--++.-| .-.+.|+| .--...+|++..|.-+|++|.
T Consensus 4 dlr~G~~i~~~g----~~~~V~~~---~~~k~gkg~a~v~~klknl~tG~~~e~tf~ 53 (58)
T PF08207_consen 4 DLRKGMVIEIDG----EPYVVLDF---QHVKPGKGGAFVRVKLKNLRTGSKVEKTFR 53 (58)
T ss_dssp G--TTSEEEETT----EEEEEEEE---EEECCTTSSSEEEEEEEETTTTEEEEEEEE
T ss_pred HccCCCEEEECC----EEEEEEEE---EEECCCCCCeEEEEEEEECCCCCEEEEEEC
Confidence 578888876620 00112222 22233444 123345999999999999995
No 44
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=34.59 E-value=26 Score=24.60 Aligned_cols=10 Identities=50% Similarity=0.963 Sum_probs=8.6
Q ss_pred CCCCCEEEEE
Q 028968 146 IRTGDVVEIK 155 (201)
Q Consensus 146 Fr~GDtVrV~ 155 (201)
|++||+|+++
T Consensus 1 f~~GDvV~LK 10 (53)
T PF09926_consen 1 FKIGDVVQLK 10 (53)
T ss_pred CCCCCEEEEc
Confidence 7899999876
No 45
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=34.43 E-value=1.1e+02 Score=25.32 Aligned_cols=48 Identities=17% Similarity=0.223 Sum_probs=33.9
Q ss_pred CCCCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEeeeCCee
Q 028968 142 PIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIG 194 (201)
Q Consensus 142 diPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~GVG 194 (201)
.-+-++-||.|.+.+.-.- =++ ...| +|..+.+.+.++.|||...|-=
T Consensus 97 ~p~~V~rG~~V~i~~~~~g--~~i-~~~G--~Al~~G~~Gd~IrVrN~~Sgki 144 (160)
T PRK06005 97 EPSLVTRGSPVKLVFSAGG--LTI-TAAG--TPLQSGAAGDLIRVRNVDSGVI 144 (160)
T ss_pred CCcEEeCCCEEEEEEecCC--EEE-EEEE--EEcccCCCCCEEEEEECCCCCE
Confidence 4567999999999886432 111 1223 6777889999999999876643
No 46
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=34.43 E-value=64 Score=26.93 Aligned_cols=30 Identities=20% Similarity=0.166 Sum_probs=21.7
Q ss_pred CCCCCCCEEEEEEEeecCCcccceEEEEEE
Q 028968 144 PDIRTGDVVEIKLEVPENRRRLSIYKGIVM 173 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~EnKeRiQ~FeGIVI 173 (201)
-..+|||++.++.++.+.+.++-.+++.+-
T Consensus 137 kPV~pGD~L~~ea~v~~~~~~~~~v~~~~~ 166 (185)
T PRK04424 137 RPVKLGERVVAKAEVVRKKGNKYIVEVKSY 166 (185)
T ss_pred cCCCCCCEEEEEEEEEEccCCEEEEEEEEE
Confidence 357899999999999985555445555444
No 47
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=34.36 E-value=70 Score=25.87 Aligned_cols=34 Identities=15% Similarity=0.277 Sum_probs=26.2
Q ss_pred CCCCCCCEEEEEEEeec--C-CcccceEEEEEEEeec
Q 028968 144 PDIRTGDVVEIKLEVPE--N-RRRLSIYKGIVMSRQN 177 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~E--n-KeRiQ~FeGIVIarrn 177 (201)
+.-.+||+|.|.++-.. . -.|=|++.|+|+..+.
T Consensus 31 ~~a~iGD~I~vsVkk~~~~~~~kkg~v~~AvIVrtkk 67 (122)
T PRK05483 31 RYASIGDVIVVSVKEAIPRGKVKKGDVVKAVVVRTKK 67 (122)
T ss_pred CccccCCEEEEEEEEcCCCCcccCCCEeeEEEEEecc
Confidence 56789999999987433 2 3567999999998763
No 48
>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=34.19 E-value=84 Score=21.21 Aligned_cols=43 Identities=21% Similarity=0.302 Sum_probs=26.4
Q ss_pred CCCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEeeeCCe
Q 028968 143 IPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGI 193 (201)
Q Consensus 143 iPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~GV 193 (201)
.|.|..||+|-|.-.-. ..-.|-+++.+..| ..+++|++...-
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 47899999998873211 33445444444444 568888876543
No 49
>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=34.07 E-value=1.7e+02 Score=23.02 Aligned_cols=43 Identities=21% Similarity=0.283 Sum_probs=28.6
Q ss_pred CCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEeeeCCee
Q 028968 144 PDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIG 194 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~GVG 194 (201)
..|.+||.|+|. ..=++=|+|+|+...+... -.+|.=+..|.-
T Consensus 85 ~~~~~Gd~V~I~------~GPf~G~~g~v~~~d~~k~--~v~v~l~~~~~~ 127 (145)
T TIGR00405 85 ESIKKGDIVEII------SGPFKGERAKVIRVDESKE--EVTLELIEAAVP 127 (145)
T ss_pred cccCCCCEEEEe------ecCCCCCeEEEEEEcCCCC--EEEEEEEEcCcc
Confidence 459999999985 2557778899988865433 344444444444
No 50
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=34.03 E-value=1.5e+02 Score=24.53 Aligned_cols=36 Identities=17% Similarity=0.409 Sum_probs=28.1
Q ss_pred CCCCCCCCCEEEEEEEeecCCcccceEEEEEEEeec
Q 028968 142 PIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQN 177 (201)
Q Consensus 142 diPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn 177 (201)
.+|.-.+||+|.|.++-.....|=|++.++|+..+.
T Consensus 43 r~~~a~iGD~IvvsVK~~~p~~kg~v~kAVIVRtkk 78 (132)
T PRK08571 43 RLPKAGVGDMVVVSVKKGTPEMRKQVLRAVVVRQRK 78 (132)
T ss_pred cCCccccCCEEEEEEEECCCcccCCEeEEEEEEecc
Confidence 357789999999998765533456999999998663
No 51
>cd03441 R_hydratase_like (R)-hydratase [(R)-specific enoyl-CoA hydratase]. Catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. The structure of the monomer includes a five-strand antiparallel beta-sheet wrapped around a central alpha helix, referred to as a hot dog fold. The active site lies within a substrate-binding tunnel formed by the homodimer. Other enzymes with this fold include MaoC dehydratase, Hydratase-Dehydrogenase-Epimerase protein (HDE), and the fatty acid synthase beta subunit.
Probab=33.97 E-value=1.2e+02 Score=21.83 Aligned_cols=17 Identities=24% Similarity=0.454 Sum_probs=14.9
Q ss_pred CCCCCCCEEEEEEEeec
Q 028968 144 PDIRTGDVVEIKLEVPE 160 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~E 160 (201)
=.+++||+|.+..+|.+
T Consensus 79 ~Pv~~Gd~l~~~~~v~~ 95 (127)
T cd03441 79 APVFPGDTLRVEVEVLG 95 (127)
T ss_pred CCcCCCCEEEEEEEEEE
Confidence 35799999999999987
No 52
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=33.22 E-value=53 Score=21.28 Aligned_cols=20 Identities=35% Similarity=0.682 Sum_probs=14.6
Q ss_pred CCCCCEEEEEEEeec-CCccc
Q 028968 146 IRTGDVVEIKLEVPE-NRRRL 165 (201)
Q Consensus 146 Fr~GDtVrV~v~I~E-nKeRi 165 (201)
|++||.|+|.+.=.. .+.++
T Consensus 45 ~~~Gd~v~v~i~~vd~~~~~i 65 (68)
T cd05685 45 VSVGDIVEVKVISIDEERGRI 65 (68)
T ss_pred cCCCCEEEEEEEEEECCCCEE
Confidence 899999999876554 34444
No 53
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=32.10 E-value=55 Score=22.79 Aligned_cols=21 Identities=19% Similarity=0.321 Sum_probs=14.5
Q ss_pred CCCCCEEEEEEEeecCCcccc
Q 028968 146 IRTGDVVEIKLEVPENRRRLS 166 (201)
Q Consensus 146 Fr~GDtVrV~v~I~EnKeRiQ 166 (201)
|+.||+|+|.+.=.+...|++
T Consensus 49 ~~~Gd~v~vkv~~vd~~~ki~ 69 (73)
T cd05686 49 VDVGEKVWVKVIGREMKDKMK 69 (73)
T ss_pred ECCCCEEEEEEEEECCCCcEE
Confidence 799999999876554222544
No 54
>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=31.48 E-value=34 Score=25.24 Aligned_cols=26 Identities=27% Similarity=0.362 Sum_probs=18.5
Q ss_pred CCCCCCCCCCCEEEEEEEeec-CCccc
Q 028968 140 ERPIPDIRTGDVVEIKLEVPE-NRRRL 165 (201)
Q Consensus 140 kkdiPeFr~GDtVrV~v~I~E-nKeRi 165 (201)
++.---+.+||.|.|.+.--+ +|-||
T Consensus 39 r~~rI~I~~GD~V~Ve~spyd~tkgrI 65 (68)
T TIGR00008 39 RMHYIRILPGDKVKVELSPYDLTRGRI 65 (68)
T ss_pred hhccEEECCCCEEEEEECcccCCcEeE
Confidence 334455899999999987665 55554
No 55
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: 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 H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=30.74 E-value=63 Score=21.89 Aligned_cols=22 Identities=27% Similarity=0.413 Sum_probs=15.9
Q ss_pred CCCCCCEEEEEEEeec-CCcccc
Q 028968 145 DIRTGDVVEIKLEVPE-NRRRLS 166 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E-nKeRiQ 166 (201)
.|+.||+|++.+.-.. .+.|+.
T Consensus 44 ~~~~Gd~i~~~V~~id~~~~~i~ 66 (69)
T cd05697 44 KFKPGLKVKCRVLSVEPERKRLV 66 (69)
T ss_pred cCCCCCEEEEEEEEEECCCCEEE
Confidence 4999999999876555 444543
No 56
>PRK15136 multidrug efflux system protein EmrA; Provisional
Probab=30.69 E-value=91 Score=28.70 Aligned_cols=33 Identities=18% Similarity=0.384 Sum_probs=23.4
Q ss_pred CCCCCCCCCCEEEEEEEeecCCcccceEEEEEEEee
Q 028968 141 RPIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQ 176 (201)
Q Consensus 141 kdiPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarr 176 (201)
.++..+++|+.|.|.+-.-.+ -+.|.|.|..+.
T Consensus 261 ~~l~~v~~Gq~V~I~~da~p~---~~~~~G~V~~I~ 293 (390)
T PRK15136 261 TQLANMRIGQPATITSDIYGD---DVVYTGKVVGLD 293 (390)
T ss_pred HHHhcCCCCCEEEEEEecCCC---CceEEEEEEEEC
Confidence 356788899988887654322 136999999883
No 57
>PRK02268 hypothetical protein; Provisional
Probab=30.60 E-value=64 Score=26.81 Aligned_cols=36 Identities=14% Similarity=0.301 Sum_probs=26.3
Q ss_pred CCCCCCCCCCEEEEEEEeec--CCcccceEEEEEEEee
Q 028968 141 RPIPDIRTGDVVEIKLEVPE--NRRRLSIYKGIVMSRQ 176 (201)
Q Consensus 141 kdiPeFr~GDtVrV~v~I~E--nKeRiQ~FeGIVIarr 176 (201)
..|-.+++||.|-....-.. ++...|.|.||=.-..
T Consensus 31 apl~RmkpGD~ivyYsp~~~~~~~~~~qaftAig~V~~ 68 (141)
T PRK02268 31 APLRRMKPGDWIIYYSPKTTFGGKDKLQAFTAIGKVKD 68 (141)
T ss_pred chhhcCCCCCEEEEEeceEecCCCcccceEEEEEEEcC
Confidence 45778999999987653322 7889999999765433
No 58
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=30.35 E-value=1.2e+02 Score=24.43 Aligned_cols=54 Identities=17% Similarity=0.195 Sum_probs=30.6
Q ss_pred CCCCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEeeeCCeeeEEEee
Q 028968 142 PIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGVEIVFP 200 (201)
Q Consensus 142 diPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~GVGVER~FP 200 (201)
..++|+.|++|.+.=.. -++--++-.--.++| +.--.+.+|++..|-=+|++|+
T Consensus 7 ~~~~lrkG~~i~~~g~p----~~V~~~~~~kpGkhg-~a~vr~k~knL~tG~~~e~~~~ 60 (129)
T PRK03999 7 EVGELKEGSYVVIDGEP----CKIVEISKSKPGKHG-SAKARIVAIGIFDGQKRSLVQP 60 (129)
T ss_pred cHHHccCCCEEEECCEE----EEEEEEEeecCCCCC-cEEEEEEEEECCCCCEEEEEec
Confidence 56899999999754100 011111111111111 2245677899999988888886
No 59
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=30.22 E-value=55 Score=25.88 Aligned_cols=28 Identities=25% Similarity=0.400 Sum_probs=21.1
Q ss_pred CCCCCCCCEEEEE-EEeecCCcccceEEE
Q 028968 143 IPDIRTGDVVEIK-LEVPENRRRLSIYKG 170 (201)
Q Consensus 143 iPeFr~GDtVrV~-v~I~EnKeRiQ~FeG 170 (201)
.+.|++||+|+|. -++.+-+.++|+--|
T Consensus 62 a~~l~~GdvV~I~na~v~~f~G~lqL~i~ 90 (129)
T PRK06461 62 AGSLKEGEVVEIENAWTTLYRGKVQLNVG 90 (129)
T ss_pred cccCCCCCEEEEECcEEeeeCCEEEEEEC
Confidence 4568999999999 777775566776655
No 60
>TIGR01067 rplN_bact ribosomal protein L14, bacterial/organelle. This model distinguishes bacterial and most organellar examples of ribosomal protein L14 from all archaeal and eukaryotic forms.
Probab=30.17 E-value=97 Score=25.01 Aligned_cols=34 Identities=12% Similarity=0.253 Sum_probs=26.3
Q ss_pred CCCCCCCEEEEEEEeec--C-CcccceEEEEEEEeec
Q 028968 144 PDIRTGDVVEIKLEVPE--N-RRRLSIYKGIVMSRQN 177 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~E--n-KeRiQ~FeGIVIarrn 177 (201)
+.-.+||+|.|.++-.. . -.|=|++.|+|+..+.
T Consensus 31 ~~a~iGD~I~vsVk~~~~~~~~kkg~v~~AvIVrtkk 67 (122)
T TIGR01067 31 RYATVGDVIVVVVKDAIPNGKVKKGDVVKAVIVRTKK 67 (122)
T ss_pred CccccCCEEEEEEEEcCCCCccccccEEEEEEEEeec
Confidence 55889999999987433 2 3567999999998763
No 61
>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=30.03 E-value=42 Score=22.45 Aligned_cols=40 Identities=23% Similarity=0.405 Sum_probs=21.7
Q ss_pred CCCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEeee
Q 028968 143 IPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRII 190 (201)
Q Consensus 143 iPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs 190 (201)
.|.|+.||+|-|.-.. .++.-. +|+.+.+.+ . ..+++++.
T Consensus 8 ~P~i~~Gd~v~v~~~~-----~~~~gd-ivv~~~~~~-~-~~~iKrv~ 47 (70)
T PF00717_consen 8 EPTIKDGDIVLVDPSS-----EPKDGD-IVVVKIDGD-E-ELYIKRVV 47 (70)
T ss_dssp GGTSSTTEEEEEEETS--------TTS-EEEEEETTE-E-SEEEEEEE
T ss_pred ccCeeCCCEEEEEEcC-----CCccCe-EEEEEECCc-e-eeEEEEEE
Confidence 4889999999887322 222222 333333222 1 57788875
No 62
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: 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 H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=29.88 E-value=67 Score=21.59 Aligned_cols=15 Identities=33% Similarity=0.558 Sum_probs=12.5
Q ss_pred CCCCCEEEEEEEeec
Q 028968 146 IRTGDVVEIKLEVPE 160 (201)
Q Consensus 146 Fr~GDtVrV~v~I~E 160 (201)
|++||+|+|.+.-..
T Consensus 45 ~~~G~~i~v~v~~~d 59 (70)
T cd05698 45 FRVGQVVKVKVLSCD 59 (70)
T ss_pred ccCCCEEEEEEEEEc
Confidence 999999999876554
No 63
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=29.76 E-value=2.3e+02 Score=22.97 Aligned_cols=41 Identities=20% Similarity=0.275 Sum_probs=28.4
Q ss_pred CCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEeeeCC
Q 028968 144 PDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAG 192 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~G 192 (201)
-.|++||.|+|. ..=.+-|+|.|+...+.. ...+|.=+-+.
T Consensus 93 ~~~~~G~~V~I~------~Gpf~g~~g~V~~vd~~k--~~v~v~ll~~~ 133 (153)
T PRK08559 93 EGIKEGDIVELI------AGPFKGEKARVVRVDESK--EEVTVELLEAA 133 (153)
T ss_pred cCCCCCCEEEEe------ccCCCCceEEEEEEcCCC--CEEEEEEECCc
Confidence 359999999996 356777899999987542 22555544444
No 64
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: 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 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=29.35 E-value=60 Score=22.03 Aligned_cols=21 Identities=33% Similarity=0.490 Sum_probs=15.2
Q ss_pred CCCCCCEEEEEEEeec-CCccc
Q 028968 145 DIRTGDVVEIKLEVPE-NRRRL 165 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E-nKeRi 165 (201)
.|+.||.|+|.+.=.+ .+.|+
T Consensus 48 ~~~~Gd~v~v~v~~id~~~~~i 69 (72)
T cd05689 48 VVSLGDEVEVMVLDIDEERRRI 69 (72)
T ss_pred EeCCCCEEEEEEEEeeCCcCEE
Confidence 4899999999875544 44554
No 65
>PF13437 HlyD_3: HlyD family secretion protein
Probab=29.10 E-value=1.7e+02 Score=21.02 Aligned_cols=44 Identities=25% Similarity=0.351 Sum_probs=30.2
Q ss_pred CCCCCCCC-CCCEEEEEEEeecCCcccceEEEEEEEeecCCc--cceEEEE
Q 028968 140 ERPIPDIR-TGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGI--HTTIRIR 187 (201)
Q Consensus 140 kkdiPeFr-~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi--~sTFTVR 187 (201)
.+++..++ +||.|++++. ...+ +.|.|.|..+....- +.+|.++
T Consensus 44 ~~~~~~i~~~g~~v~v~~~--~~~~--~~~~g~V~~I~~~~~~~~~~~~v~ 90 (105)
T PF13437_consen 44 EKDIARIKDPGQKVTVRLD--PGPE--KTIEGKVSSISPSPDPQGGTYRVE 90 (105)
T ss_pred hHhhcceEeCCCEEEEEEC--CCCC--cEEEEEEEEEeCcccCCCcEEEEE
Confidence 35677887 9999999987 2222 299999999877322 2356554
No 66
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: 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 H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=28.98 E-value=67 Score=22.48 Aligned_cols=22 Identities=9% Similarity=0.218 Sum_probs=15.4
Q ss_pred CCCCCCCEEEEEEEeecCCcccc
Q 028968 144 PDIRTGDVVEIKLEVPENRRRLS 166 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~EnKeRiQ 166 (201)
..|++||.|++.+.-. ++.|++
T Consensus 47 ~~~~~Gd~v~~kV~~~-~~~~i~ 68 (72)
T cd05704 47 EGFKPGKIVRCCILSK-KDGKYQ 68 (72)
T ss_pred HhCCCCCEEEEEEEEe-cCCEEE
Confidence 4599999999987544 335554
No 67
>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=28.68 E-value=40 Score=25.44 Aligned_cols=14 Identities=29% Similarity=0.551 Sum_probs=8.9
Q ss_pred CCCCCCCCEEEEEE
Q 028968 143 IPDIRTGDVVEIKL 156 (201)
Q Consensus 143 iPeFr~GDtVrV~v 156 (201)
.-.|+|||+|+=.+
T Consensus 66 ~~~FrpGDIVrA~V 79 (82)
T PF10447_consen 66 YDCFRPGDIVRARV 79 (82)
T ss_dssp GGT--SSSEEEEEE
T ss_pred HhccCCCCEEEEEE
Confidence 34699999998654
No 68
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: 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 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=28.56 E-value=69 Score=21.60 Aligned_cols=21 Identities=19% Similarity=0.398 Sum_probs=14.8
Q ss_pred CCCCCCEEEEEEEeec-CCccc
Q 028968 145 DIRTGDVVEIKLEVPE-NRRRL 165 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E-nKeRi 165 (201)
.|++||.|++.+.-.. .+.|+
T Consensus 44 ~~~~Gd~v~~~v~~~d~~~~~i 65 (68)
T cd05707 44 RFKVGQLVKGKIVSIDPDNGRI 65 (68)
T ss_pred ccCCCCEEEEEEEEEeCCCCEE
Confidence 3999999999876544 34444
No 69
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=28.53 E-value=1.2e+02 Score=25.28 Aligned_cols=35 Identities=14% Similarity=0.357 Sum_probs=27.8
Q ss_pred CCCCCCCCCEEEEEEEeecCCcccceEEEEEEEee
Q 028968 142 PIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQ 176 (201)
Q Consensus 142 diPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarr 176 (201)
.+|.-.+||+|.|.++-...-.|=|++.++|+..+
T Consensus 50 r~~~a~iGD~IvvsVKk~~p~~kg~V~kAVIVRtK 84 (139)
T PTZ00054 50 RLPSASLGDMVLATVKKGKPELRKKVLNAVIIRQR 84 (139)
T ss_pred cCcccccCCEEEEEEEECCCcccCCEeeEEEEEEC
Confidence 35778899999999876553446699999999865
No 70
>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=28.42 E-value=2e+02 Score=23.67 Aligned_cols=36 Identities=19% Similarity=0.426 Sum_probs=27.6
Q ss_pred CCCCCCCCCEEEEEEEeecCCcccceEEEEEEEeec
Q 028968 142 PIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQN 177 (201)
Q Consensus 142 diPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn 177 (201)
.+|.-.+||+|.|.++-.....|=|++.|+|+..+.
T Consensus 42 r~~~a~iGD~IvvsVK~~~p~~kg~v~kAVIVRtkk 77 (131)
T TIGR03673 42 RLPCAGVGDMVVVSVKKGTPEMRKQVFKAVVVRQRK 77 (131)
T ss_pred cCCccccCCEEEEEEEECCccccCCEeEEEEEEeCc
Confidence 346778999999998864433455999999998764
No 71
>PF04319 NifZ: NifZ domain; InterPro: IPR007415 NifZ is a short protein is found in the nif (nitrogen fixation) operon. It is required for the maturation of the nitrogenase MoFe protein. In the absence of NifZ, only one of the two P-clusters of the MoFe protein is matured to the ultimate [8Fe-7S] structure. The other P-cluster site in the protein contains a [4Fe-4S] cluster pair, suggesting that NifZ is specifically required for the formation of the second P-cluster [, , ].; GO: 0009399 nitrogen fixation
Probab=28.38 E-value=69 Score=24.18 Aligned_cols=34 Identities=18% Similarity=0.269 Sum_probs=24.4
Q ss_pred CCCCCCCEEEEEEEeecCCcccceEEEEEEEeec
Q 028968 144 PDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQN 177 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn 177 (201)
|.|..||.|++.-.|..+-+=.-.=.|-+++++|
T Consensus 3 p~f~~G~~V~a~~~irNDGt~Pg~~~g~lLv~~G 36 (75)
T PF04319_consen 3 PRFEWGDKVRARKDIRNDGTFPGKEIGELLVRKG 36 (75)
T ss_pred CccCCCCEEEEEEEeEcCCCCCCCCCCCEEEcCC
Confidence 8899999999999998743333333466666665
No 72
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=28.32 E-value=72 Score=20.33 Aligned_cols=16 Identities=25% Similarity=0.455 Sum_probs=13.0
Q ss_pred CCCCCCEEEEEEEeec
Q 028968 145 DIRTGDVVEIKLEVPE 160 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E 160 (201)
.|++||+|++.+.-..
T Consensus 46 ~~~~G~~v~~~V~~~~ 61 (72)
T smart00316 46 VLKVGDEVKVKVLSVD 61 (72)
T ss_pred eecCCCEEEEEEEEEe
Confidence 4999999999876554
No 73
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=28.06 E-value=1e+02 Score=28.11 Aligned_cols=30 Identities=17% Similarity=0.214 Sum_probs=24.2
Q ss_pred CCCCCCCCCEEEEEEEeecCCcccceEEEEEEEeec
Q 028968 142 PIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQN 177 (201)
Q Consensus 142 diPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn 177 (201)
..++|.+||.|+|.- .=++-|+|+|+...+
T Consensus 202 ~~~~f~vGd~VrI~d------GPF~GfeG~I~eid~ 231 (258)
T TIGR01956 202 NLSKFRVGNFVKIVD------GPFKGIVGKIKKIDQ 231 (258)
T ss_pred cccCCCCCCEEEEEe------cCCCCcEEEEEEEeC
Confidence 356799999999963 567889999999875
No 74
>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=27.98 E-value=61 Score=25.11 Aligned_cols=33 Identities=15% Similarity=0.358 Sum_probs=25.2
Q ss_pred CCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCc
Q 028968 144 PDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGI 180 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi 180 (201)
..+.+|++++|++ +...-+.|+|..|.-+...-
T Consensus 28 ~~y~pg~~~~Vtl----~~~~~~~F~GFllqAr~~~~ 60 (132)
T PF02014_consen 28 SSYEPGQTYTVTL----SSSGSSSFRGFLLQARDANN 60 (132)
T ss_dssp SSB-TTBEEEEEE----EETTTEEBSEEEEEEEETT-
T ss_pred CeEcCCCEEEEEE----ECCCCCceeEEEEEEEeCCC
Confidence 3589999999999 55677889999998776543
No 75
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=27.30 E-value=2.1e+02 Score=21.75 Aligned_cols=51 Identities=16% Similarity=0.329 Sum_probs=34.7
Q ss_pred CCCCCCCCEEEEEEEeec-CCcccceEEEEEEEeecCC----ccceEEEEeeeCCe
Q 028968 143 IPDIRTGDVVEIKLEVPE-NRRRLSIYKGIVMSRQNAG----IHTTIRIRRIIAGI 193 (201)
Q Consensus 143 iPeFr~GDtVrV~v~I~E-nKeRiQ~FeGIVIarrn~G----i~sTFTVRKIs~GV 193 (201)
+..+++||+|-|.-.-.- .+..-.=..|-||...|.. ..+-|-|-.+-.|+
T Consensus 3 FL~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggaR~P~~~tlFQVadVDtG~ 58 (75)
T PF11302_consen 3 FLSVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGARDPKVPTLFQVADVDTGV 58 (75)
T ss_pred ccccCCCCEEEEecCccccccCCCCcEEEEEEEEeccccCCCCCceEEEEEccCCe
Confidence 567899999998744311 2334466789999987654 34558887776664
No 76
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=27.17 E-value=69 Score=21.71 Aligned_cols=25 Identities=20% Similarity=0.396 Sum_probs=18.2
Q ss_pred CCCCCCCCCEEEEEEEeec-CCcccc
Q 028968 142 PIPDIRTGDVVEIKLEVPE-NRRRLS 166 (201)
Q Consensus 142 diPeFr~GDtVrV~v~I~E-nKeRiQ 166 (201)
.-..|++||+|+|.+.-.+ ++.|+.
T Consensus 45 ~~~~~~~G~~v~v~v~~vd~~~~~i~ 70 (74)
T PF00575_consen 45 PSEVYKIGQTVRVKVIKVDKEKGRIR 70 (74)
T ss_dssp SHGTCETTCEEEEEEEEEETTTTEEE
T ss_pred cccccCCCCEEEEEEEEEECCCCeEE
Confidence 4457999999999887666 555543
No 77
>PF03061 4HBT: Thioesterase superfamily; InterPro: IPR006683 This family contains a wide variety of enzymes, principally thioesterases. This family includes 4HBT (3.1.2.23 from EC) which catalyses the final step in the biosynthesis of 4-hydroxybenzoate from 4-chlorobenzoate in the soil dwelling microbe Pseudomonas CBS-3. This family includes various cytosolic long-chain acyl-CoA thioester hydrolases. Long-chain acyl-CoA hydrolases hydrolyse palmitoyl-CoA to CoA and palmitate, they also catalyse the hydrolysis of other long chain fatty acyl-CoA thioesters. ; PDB: 3F5O_F 2F0X_D 2H4U_C 2PRX_A 2OV9_D 1YLI_B 3BJK_F 1IXL_A 3DKZ_B 2EIS_B ....
Probab=27.17 E-value=1e+02 Score=20.28 Aligned_cols=28 Identities=21% Similarity=0.268 Sum_probs=19.1
Q ss_pred CCCCCCEEEEEEEeecCCcccceEEEEE
Q 028968 145 DIRTGDVVEIKLEVPENRRRLSIYKGIV 172 (201)
Q Consensus 145 eFr~GDtVrV~v~I~EnKeRiQ~FeGIV 172 (201)
..++||+|+++.++..-.++.-.++..+
T Consensus 43 p~~~gd~l~~~~~v~~~g~~~~~~~~~v 70 (79)
T PF03061_consen 43 PVRPGDTLRVEARVVRVGRKSFTVEVEV 70 (79)
T ss_dssp -BBTTSEEEEEEEEEEEESSEEEEEEEE
T ss_pred ccCCCeEEEEEEEEEEECCEEEEEEEEE
Confidence 4789999999999988444444444444
No 78
>cd03452 MaoC_C MaoC_C The C-terminal hot dog fold of the MaoC (monoamine oxidase C) dehydratase regulatory protein. Orthologs of MaoC include PaaZ [Escherichia coli] and PaaN [Pseudomonas putida], which are putative ring-opening enzymes involved in phenylacetic acid degradation. The C-terminal domain of MaoC has sequence similarity to (R)-specific enoyl-CoA hydratase,Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. MaoC also has an N-terminal PutA domain like that found in the E. coli PutA proline dehydrogenase and other members of the aldehyde dehydrogenase family.
Probab=27.12 E-value=93 Score=24.27 Aligned_cols=15 Identities=20% Similarity=0.600 Sum_probs=13.8
Q ss_pred CCCCCEEEEEEEeec
Q 028968 146 IRTGDVVEIKLEVPE 160 (201)
Q Consensus 146 Fr~GDtVrV~v~I~E 160 (201)
.++||+|.+..+|.+
T Consensus 89 V~~GDtl~~~~~V~~ 103 (142)
T cd03452 89 VYPGDTIQVRLTCKR 103 (142)
T ss_pred CCCCCEEEEEEEEEE
Confidence 689999999999987
No 79
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=27.06 E-value=2e+02 Score=19.42 Aligned_cols=36 Identities=11% Similarity=0.178 Sum_probs=25.9
Q ss_pred CCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEE
Q 028968 146 IRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIR 187 (201)
Q Consensus 146 Fr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVR 187 (201)
|.+|+.|-+.. ..-+.|++.|+.++..+-..-|-|.
T Consensus 1 ~~vG~~v~~~~------~~~~~y~A~I~~~r~~~~~~~YyVH 36 (55)
T PF11717_consen 1 FEVGEKVLCKY------KDGQWYEAKILDIREKNGEPEYYVH 36 (55)
T ss_dssp --TTEEEEEEE------TTTEEEEEEEEEEEECTTCEEEEEE
T ss_pred CCcCCEEEEEE------CCCcEEEEEEEEEEecCCCEEEEEE
Confidence 67899888875 4568899999999987655555553
No 80
>cd03440 hot_dog The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold. These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate. This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis.
Probab=26.80 E-value=1.6e+02 Score=17.94 Aligned_cols=21 Identities=29% Similarity=0.466 Sum_probs=15.7
Q ss_pred CCCCCCCEEEEEEEeecCCcc
Q 028968 144 PDIRTGDVVEIKLEVPENRRR 164 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~EnKeR 164 (201)
-...+||.|.+..++.....+
T Consensus 56 ~~~~~g~~v~~~~~~~~~~~~ 76 (100)
T cd03440 56 RPVRPGDTLTVEAEVVRVGRS 76 (100)
T ss_pred cCCCCCCEEEEEEEEEecccc
Confidence 346679999999999883333
No 81
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=26.70 E-value=1.9e+02 Score=25.16 Aligned_cols=47 Identities=17% Similarity=0.169 Sum_probs=32.4
Q ss_pred CCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEeeeCCeee
Q 028968 144 PDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIGV 195 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~GVGV 195 (201)
+-++-||+|.|.+.-.- =++ ..+| .|..+++.+..+.|||...|-=|
T Consensus 154 ~lV~rG~~V~I~a~~~g--~~V-s~~G--~AL~~G~~Ge~IrVrN~~SgrvV 200 (214)
T PRK12617 154 RLVRRGDTVPLVSRNGG--LEV-RMSG--RALSDAGENERVSVENSSSRRVV 200 (214)
T ss_pred ceEcCCCEEEEEEecCC--EEE-EEEE--EEccCCCCCCEEEEEECCCCCEE
Confidence 45899999999875321 111 1235 56778899999999997666433
No 82
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=26.59 E-value=1.8e+02 Score=25.21 Aligned_cols=47 Identities=11% Similarity=0.116 Sum_probs=33.0
Q ss_pred CCCCCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEeeeCCe
Q 028968 141 RPIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGI 193 (201)
Q Consensus 141 kdiPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~GV 193 (201)
+..|-++-||.|.|.+.-.- =++ .++| .|..++.++.+++||+ ..|-
T Consensus 161 ~~~~lV~rGd~V~i~~~~gg--~~I-~~~G--~Al~~G~~Gd~IrVrN-~Sgk 207 (222)
T PRK08515 161 KALILVRKNDIINGVLKEGG--VSI-EISL--KALQDGNLGDIIQAKN-KSNK 207 (222)
T ss_pred CCcceEecCCEEEEEEECCC--EEE-EEEE--EEcccCCCCCEEEEEe-CCCC
Confidence 34677999999999875321 111 2344 6778889999999998 6553
No 83
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=26.40 E-value=1.8e+02 Score=23.74 Aligned_cols=47 Identities=11% Similarity=0.198 Sum_probs=32.4
Q ss_pred CCCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEeeeCCee
Q 028968 143 IPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIG 194 (201)
Q Consensus 143 iPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~GVG 194 (201)
-+-++-||.|.|.+...- =++. -+| .|..+++++.++.|||...|-=
T Consensus 79 p~lV~rG~~V~i~~~~gg--l~i~-~~G--~AL~~G~~Gd~IrV~N~~S~ri 125 (141)
T PRK12618 79 PAIVDRNQLVPLAYRLGG--LEIR-TEG--RALSRGGVGDEIRVMNLSSRTT 125 (141)
T ss_pred ccEEeCCCEEEEEEecCC--EEEE-EEE--EEcccCCCCCEEEEEECCCCCE
Confidence 456899999999876431 1111 234 5667888999999999876643
No 84
>cd01289 FabA_like Domain of unknown function, appears to be related to a diverse group of beta-hydroxydecanoyl ACP dehydratases (FabA) and beta-hydroxyacyl ACP dehydratases (FabZ). This group appears to lack the conserved active site histidine of FabA and FabZ.
Probab=26.25 E-value=91 Score=24.51 Aligned_cols=30 Identities=10% Similarity=0.140 Sum_probs=22.7
Q ss_pred CCCCCCCEEEEEEEeecCC-cccceEEEEEE
Q 028968 144 PDIRTGDVVEIKLEVPENR-RRLSIYKGIVM 173 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~EnK-eRiQ~FeGIVI 173 (201)
|-+.+||++.++++....+ +.+-.|+|.+.
T Consensus 91 ~v~p~Gd~l~i~~~~~~~~~~~~~~~~~~~~ 121 (138)
T cd01289 91 DRFDLGSTLLIVVAELLQGDSGLGVFECTIE 121 (138)
T ss_pred ceeCCCCeeEEEeeeeeeCCCcEEEEEEEEE
Confidence 4455699999999987755 47888887754
No 85
>cd03447 FAS_MaoC FAS_MaoC, the MaoC-like hot dog fold of the fatty acid synthase, beta subunit. Other enzymes with this fold include MaoC dehydratase, Hydratase-Dehydrogenase-Epimerase protein (HDE), and 17-beta-hydroxysteriod dehydrogenase (HSD).
Probab=26.17 E-value=1.2e+02 Score=23.49 Aligned_cols=16 Identities=25% Similarity=0.322 Sum_probs=14.1
Q ss_pred CCCCCCEEEEEEEeec
Q 028968 145 DIRTGDVVEIKLEVPE 160 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E 160 (201)
...+||+|++.+++.+
T Consensus 80 PV~~gdtl~~~~~v~~ 95 (126)
T cd03447 80 MVLPNDELEVRLEHVG 95 (126)
T ss_pred cCcCCCEEEEEEEEEE
Confidence 4679999999999987
No 86
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.
Probab=26.02 E-value=1.6e+02 Score=20.99 Aligned_cols=13 Identities=23% Similarity=0.486 Sum_probs=11.1
Q ss_pred CCCCCCCCEEEEE
Q 028968 143 IPDIRTGDVVEIK 155 (201)
Q Consensus 143 iPeFr~GDtVrV~ 155 (201)
.|.|+.||.|-|.
T Consensus 9 ~P~l~~GD~vlv~ 21 (90)
T TIGR02754 9 SPTLPPGDRIIVV 21 (90)
T ss_pred cCccCCCCEEEEE
Confidence 4889999999776
No 87
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. 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 S. cerevisiae Rrp5 and 14 S1 repeats in H. 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 H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=25.95 E-value=84 Score=22.17 Aligned_cols=21 Identities=19% Similarity=0.469 Sum_probs=14.4
Q ss_pred CCCCCCEEEEEEEeec-CCccc
Q 028968 145 DIRTGDVVEIKLEVPE-NRRRL 165 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E-nKeRi 165 (201)
.|+.||+|+|.+.=.. .+.|+
T Consensus 58 ~~~~Gd~v~vkV~~id~~~~~i 79 (83)
T cd04461 58 GFKKGQSVTAKVTSVDEEKQRF 79 (83)
T ss_pred hcCCCCEEEEEEEEEcCCCCEE
Confidence 3999999999875433 34444
No 88
>TIGR01000 bacteriocin_acc bacteriocin secretion accessory protein. This family represents an accessory protein that works with the bacteriocin maturation and ABC transport secretion protein described by TIGR01193.
Probab=25.94 E-value=1.3e+02 Score=28.09 Aligned_cols=46 Identities=24% Similarity=0.294 Sum_probs=30.4
Q ss_pred CCCCCCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCc----cceEEEE
Q 028968 140 ERPIPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGI----HTTIRIR 187 (201)
Q Consensus 140 kkdiPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi----~sTFTVR 187 (201)
..++..+++|+.|.|++.- ...+-..|.|.|..+..... +.+|+|+
T Consensus 366 e~di~~v~~Gq~V~v~~~a--~~~~~~~~~G~V~~Is~~~~~~~~~~~y~v~ 415 (457)
T TIGR01000 366 SNDISGIKVGQKVRFKLTQ--NVPKPIILDGTITSISSAPTATKKGNFYKVI 415 (457)
T ss_pred HHHHhhcCCCCeEEEEEec--CCCCceEEEEEEEEEcCCCccCCCCCEEEEE
Confidence 3567888899988777653 22233479999998875432 2467664
No 89
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: 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 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=25.92 E-value=86 Score=20.93 Aligned_cols=16 Identities=31% Similarity=0.493 Sum_probs=12.4
Q ss_pred CCCCCCEEEEEEEeec
Q 028968 145 DIRTGDVVEIKLEVPE 160 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E 160 (201)
.|++||+|++.+.=..
T Consensus 44 ~~~~Gd~v~~~v~~~d 59 (73)
T cd05691 44 RFKVGDEVEAKITNVD 59 (73)
T ss_pred ccCCCCEEEEEEEEEe
Confidence 3899999999865443
No 90
>cd03449 R_hydratase (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase II, and beta-hydroxydecanoyl-ACP dehydratase, MaoC dehydratase, Hydratase-Dehydrogenase-Epimerase protein (HDE), and the fatty acid synthase beta subunit. The active site lies within a substrate-binding tunnel formed by the (R)-hydratase homodimer. A subset of the bacterial (R)-hydratases contain a C-terminal phosphotransacetylase (PTA) domain.
Probab=25.92 E-value=1.6e+02 Score=21.41 Aligned_cols=16 Identities=31% Similarity=0.445 Sum_probs=13.8
Q ss_pred CCCCCCEEEEEEEeec
Q 028968 145 DIRTGDVVEIKLEVPE 160 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E 160 (201)
.+.+||++.+..++.+
T Consensus 82 Pv~~gd~l~~~~~v~~ 97 (128)
T cd03449 82 PVFIGDTVTATVTVTE 97 (128)
T ss_pred CccCCCEEEEEEEEEE
Confidence 4688999999999887
No 91
>PRK13692 (3R)-hydroxyacyl-ACP dehydratase subunit HadA; Provisional
Probab=25.80 E-value=1.3e+02 Score=24.42 Aligned_cols=16 Identities=25% Similarity=0.252 Sum_probs=14.2
Q ss_pred CCCCCCEEEEEEEeec
Q 028968 145 DIRTGDVVEIKLEVPE 160 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E 160 (201)
.+++||+|.+.++|.+
T Consensus 96 PV~~GDtL~~~~eV~~ 111 (159)
T PRK13692 96 PIVAGDKLYCDVYVDS 111 (159)
T ss_pred CccCCCEEEEEEEEEE
Confidence 4899999999999976
No 92
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=25.71 E-value=51 Score=24.61 Aligned_cols=15 Identities=20% Similarity=0.567 Sum_probs=13.0
Q ss_pred CCCCCCCCEEEEEEE
Q 028968 143 IPDIRTGDVVEIKLE 157 (201)
Q Consensus 143 iPeFr~GDtVrV~v~ 157 (201)
+|+.++||.|-||.=
T Consensus 33 v~~~~vGD~VLVH~G 47 (76)
T TIGR00074 33 VGEVKVGDYVLVHVG 47 (76)
T ss_pred eCCCCCCCEEEEecC
Confidence 478999999999973
No 93
>PF01575 MaoC_dehydratas: MaoC like domain; InterPro: IPR002539 The C terminus of the MaoC protein is found to share similarity with a wide variety of enzymes. All these enzymes contain multiple domains. This domain is found in parts of two enzymes that have been assigned dehydratase activities. A deletion mutant of the C-terminal 271 amino acids in Q02207 from SWISSPROT abolished its 2-enoyl-CoA hydratase activity, suggesting that this region may be a hydratase enzyme []. The maoC gene is part of a operon with maoA which is involved in the synthesis of monoamine oxidase [].; GO: 0016491 oxidoreductase activity, 0008152 metabolic process; PDB: 3HMJ_H 2UV8_I 2VKZ_G 1PN4_C 1PN2_B 1S9C_K 3OML_A 1Q6W_B 2B3M_A 3K67_B ....
Probab=25.64 E-value=75 Score=23.93 Aligned_cols=28 Identities=21% Similarity=0.285 Sum_probs=17.8
Q ss_pred CCCCCCCEEEEEEEeecCCcccceEEEE
Q 028968 144 PDIRTGDVVEIKLEVPENRRRLSIYKGI 171 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~EnKeRiQ~FeGI 171 (201)
-...+||+|.+.+++.+.+..-+...+.
T Consensus 87 ~PV~~gdtl~~~~~v~~~~~~~~~~~v~ 114 (122)
T PF01575_consen 87 APVFPGDTLTAEVEVTEKREGKERVRVT 114 (122)
T ss_dssp S--BTTEEEEEEEEEEEEEEEEEEEEEE
T ss_pred ccccCCCEEEEEEEEEEEEEcCceEEEE
Confidence 4588999999999998833333444333
No 94
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=25.33 E-value=14 Score=34.49 Aligned_cols=68 Identities=24% Similarity=0.332 Sum_probs=46.1
Q ss_pred ecccccccchhhhccC-CCCCCCchhHHHHHHHHHHHHhhhcCCCCCCCCCCCEEEEEEEeecCCcccceE
Q 028968 99 VEAESEDKVEEEEVKA-PRKPRVKLGDIMGILNKRAVEASESERPIPDIRTGDVVEIKLEVPENRRRLSIY 168 (201)
Q Consensus 99 ~e~~~~~~~e~~~~~p-~r~~~~klg~lM~iLnke~IE~~q~kkdiPeFr~GDtVrV~v~I~EnKeRiQ~F 168 (201)
+-++.++-.-.-.... .+++|.....+...+..+++|+.++..-+||++.-..+.+..+++| .|||++
T Consensus 120 ~g~~~ln~~~~s~~~~kkk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpE--DRIqVW 188 (332)
T KOG0494|consen 120 VGGESLNGSGGSPDNAKKKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPE--DRIQVW 188 (332)
T ss_pred cCCccccCCCCCCcccccccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCch--hhhhHH
Confidence 3445555433322222 2234444566776666689999988889999999999999999988 577764
No 95
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=25.23 E-value=83 Score=25.15 Aligned_cols=27 Identities=19% Similarity=0.199 Sum_probs=22.4
Q ss_pred CCCCCCEEEEEEEeecCCcccceEEEEEEEeec
Q 028968 145 DIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQN 177 (201)
Q Consensus 145 eFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn 177 (201)
.|.+||.|+|. ..-++-|+|+|....+
T Consensus 109 ~~~~G~~V~I~------~Gp~~g~eg~v~~~~~ 135 (162)
T PRK09014 109 TPKPGDKVIIT------EGAFEGLQAIYTEPDG 135 (162)
T ss_pred CCCCCCEEEEe------cCCCCCcEEEEEEeCC
Confidence 58999999995 3568899999988764
No 96
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=24.85 E-value=38 Score=27.68 Aligned_cols=14 Identities=36% Similarity=0.565 Sum_probs=11.7
Q ss_pred CCCCCCCCEEEEEE
Q 028968 143 IPDIRTGDVVEIKL 156 (201)
Q Consensus 143 iPeFr~GDtVrV~v 156 (201)
.-++|+||+|+|..
T Consensus 57 ~LDlRIGD~Vkv~~ 70 (131)
T PF08605_consen 57 YLDLRIGDTVKVDG 70 (131)
T ss_pred eeeeecCCEEEECC
Confidence 35799999999975
No 97
>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=24.47 E-value=44 Score=25.82 Aligned_cols=22 Identities=27% Similarity=0.546 Sum_probs=14.3
Q ss_pred CCCCCCCCEEEEEEEeecCCcc
Q 028968 143 IPDIRTGDVVEIKLEVPENRRR 164 (201)
Q Consensus 143 iPeFr~GDtVrV~v~I~EnKeR 164 (201)
.-++.+|+.|-|++.+.+.|+|
T Consensus 63 w~~L~VG~~VMvNYN~d~P~er 84 (85)
T PF12148_consen 63 WDELKVGQVVMVNYNVDEPKER 84 (85)
T ss_dssp GGG--TT-EEEEEE-TTSTTS-
T ss_pred HHhCCcccEEEEecCCCCcccC
Confidence 4468899999999999887776
No 98
>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=24.18 E-value=1.1e+02 Score=24.12 Aligned_cols=29 Identities=17% Similarity=0.235 Sum_probs=22.7
Q ss_pred CCCCCCCEEEEEEEeecCCcccceEEEEEEEeecC
Q 028968 144 PDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNA 178 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~ 178 (201)
..|.+||.|+|. ..=++-|+|+|....++
T Consensus 107 ~~~~~G~~V~V~------~GPf~g~~g~v~~~~~~ 135 (159)
T TIGR01955 107 TLPYKGDKVRIT------DGAFAGFEAIFLEPDGE 135 (159)
T ss_pred cCCCCCCEEEEe------ccCCCCcEEEEEEECCC
Confidence 459999999885 24478899999998743
No 99
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=24.03 E-value=46 Score=31.38 Aligned_cols=15 Identities=40% Similarity=0.857 Sum_probs=13.0
Q ss_pred CCCCCCCCCEEEEEE
Q 028968 142 PIPDIRTGDVVEIKL 156 (201)
Q Consensus 142 diPeFr~GDtVrV~v 156 (201)
-||+|++||+|.+.-
T Consensus 243 rip~~~~gDiV~~~~ 257 (355)
T COG1499 243 RIPEFRPGDIVSVRG 257 (355)
T ss_pred ECCCCCCCCEEEECC
Confidence 389999999999863
No 100
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=23.93 E-value=73 Score=24.37 Aligned_cols=18 Identities=17% Similarity=0.532 Sum_probs=15.0
Q ss_pred CCCCCCCCEEEEEEEeec
Q 028968 143 IPDIRTGDVVEIKLEVPE 160 (201)
Q Consensus 143 iPeFr~GDtVrV~v~I~E 160 (201)
+-.|++||.|+|.+.|.-
T Consensus 50 l~~~~~Gd~V~Vsf~i~~ 67 (84)
T PF11325_consen 50 LDNFQVGDEVKVSFNIEG 67 (84)
T ss_pred hccCCCCCEEEEEEEeec
Confidence 367999999999998853
No 101
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=23.79 E-value=58 Score=24.61 Aligned_cols=27 Identities=26% Similarity=0.356 Sum_probs=18.6
Q ss_pred cCCCCCCCCCCCEEEEEEEeec-CCccc
Q 028968 139 SERPIPDIRTGDVVEIKLEVPE-NRRRL 165 (201)
Q Consensus 139 ~kkdiPeFr~GDtVrV~v~I~E-nKeRi 165 (201)
+++.---+.+||.|.|.+.--. +|-|+
T Consensus 40 mr~~~i~I~~GD~V~Ve~~~~d~~kg~I 67 (75)
T COG0361 40 MRKNRIRILPGDVVLVELSPYDLTKGRI 67 (75)
T ss_pred chheeEEeCCCCEEEEEecccccccccE
Confidence 3444456899999999987655 55443
No 102
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=23.66 E-value=95 Score=22.66 Aligned_cols=24 Identities=25% Similarity=0.254 Sum_probs=18.6
Q ss_pred CCCCCCCCEEEEEEEeecCCcccc
Q 028968 143 IPDIRTGDVVEIKLEVPENRRRLS 166 (201)
Q Consensus 143 iPeFr~GDtVrV~v~I~EnKeRiQ 166 (201)
.+.+.+||.|+|.=++.|-...+|
T Consensus 42 ~~~~~~Gd~V~vtG~v~ey~g~tq 65 (78)
T cd04486 42 GADVAVGDLVRVTGTVTEYYGLTQ 65 (78)
T ss_pred CCCCCCCCEEEEEEEEEeeCCeEE
Confidence 678999999999988888333444
No 103
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: 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 H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=23.49 E-value=99 Score=21.54 Aligned_cols=21 Identities=10% Similarity=0.058 Sum_probs=15.0
Q ss_pred CCCCCCEEEEEEEeec-CCccc
Q 028968 145 DIRTGDVVEIKLEVPE-NRRRL 165 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E-nKeRi 165 (201)
.|++||.|++.+.-.. .+.|+
T Consensus 46 ~~~vG~~v~~kV~~id~~~~~i 67 (71)
T cd05696 46 PFKAGTTHKARIIGYSPMDGLL 67 (71)
T ss_pred ccCCCCEEEEEEEEEeCCCCEE
Confidence 3999999999976544 33344
No 104
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=23.28 E-value=78 Score=22.87 Aligned_cols=17 Identities=18% Similarity=0.319 Sum_probs=14.0
Q ss_pred CCCCCCCEEEEEEEeec
Q 028968 144 PDIRTGDVVEIKLEVPE 160 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~E 160 (201)
|.|+.||.|++.++..+
T Consensus 1 ~~~~~Ge~v~~~~~~~~ 17 (83)
T PF14326_consen 1 TVYRVGERVRFRVTSNR 17 (83)
T ss_pred CcccCCCEEEEEEEeCC
Confidence 56899999999988743
No 105
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: 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 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=23.27 E-value=1.1e+02 Score=20.68 Aligned_cols=15 Identities=33% Similarity=0.490 Sum_probs=12.3
Q ss_pred CCCCCEEEEEEEeec
Q 028968 146 IRTGDVVEIKLEVPE 160 (201)
Q Consensus 146 Fr~GDtVrV~v~I~E 160 (201)
|++||.|++.+.-..
T Consensus 45 ~~~Gd~i~~~i~~~~ 59 (70)
T cd05687 45 VKVGDEVEVYVLRVE 59 (70)
T ss_pred CCCCCEEEEEEEEEE
Confidence 999999999876543
No 106
>smart00276 GLECT Galectin. Galectin - galactose-binding lectin
Probab=23.04 E-value=1.1e+02 Score=23.64 Aligned_cols=50 Identities=18% Similarity=0.294 Sum_probs=29.3
Q ss_pred CCCC-CCCCCCEEEEEEEeecCCcccc--eEEEE-EEEe-ecCCccceEEEEeee
Q 028968 141 RPIP-DIRTGDVVEIKLEVPENRRRLS--IYKGI-VMSR-QNAGIHTTIRIRRII 190 (201)
Q Consensus 141 kdiP-eFr~GDtVrV~v~I~EnKeRiQ--~FeGI-VIar-rn~Gi~sTFTVRKIs 190 (201)
..|| .|++|++|.|+=++..+.+|.+ ...|- -|+- =|--.+....|||-.
T Consensus 3 ~~lp~~l~~G~~i~i~G~~~~~~~~F~inl~~~~~di~lH~n~rf~~~~iV~Ns~ 57 (128)
T smart00276 3 LPIPGGLKPGQTLTVRGIVLPDAKRFSINLLTGGDDIALHFNPRFNENKIVCNSK 57 (128)
T ss_pred ccCCCCCCCCCEEEEEEEECCCCCEEEEEeecCCCCEEEEEeccCCCCEEEEeCc
Confidence 3577 7999999999999987544443 33331 1111 112233456677754
No 107
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=23.01 E-value=60 Score=25.28 Aligned_cols=24 Identities=21% Similarity=0.273 Sum_probs=17.4
Q ss_pred cCCCCCCCCCCCEEEEEEEeec-CC
Q 028968 139 SERPIPDIRTGDVVEIKLEVPE-NR 162 (201)
Q Consensus 139 ~kkdiPeFr~GDtVrV~v~I~E-nK 162 (201)
+++..-.+.+||.|.|.+.--. +|
T Consensus 40 mR~~rIrIl~GD~V~VE~spYDltk 64 (87)
T PRK12442 40 MRKHRIRILAGDRVTLELSPYDLTK 64 (87)
T ss_pred eeeeeEEecCCCEEEEEECcccCCc
Confidence 4455566899999999987544 44
No 108
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=22.46 E-value=1.1e+02 Score=22.89 Aligned_cols=19 Identities=21% Similarity=0.716 Sum_probs=10.7
Q ss_pred cCCCCCCCCCCCEEEEEEE
Q 028968 139 SERPIPDIRTGDVVEIKLE 157 (201)
Q Consensus 139 ~kkdiPeFr~GDtVrV~v~ 157 (201)
..+.+-.++|||+|.+.+.
T Consensus 36 ~~k~L~~L~pGq~l~f~~d 54 (85)
T PF04225_consen 36 EAKPLTRLKPGQTLEFQLD 54 (85)
T ss_dssp GT--GGG--TT-EEEEEE-
T ss_pred ccchHhhCCCCCEEEEEEC
Confidence 3467888999999998864
No 109
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=22.30 E-value=1e+02 Score=25.84 Aligned_cols=29 Identities=24% Similarity=0.439 Sum_probs=20.0
Q ss_pred CCCCCCEEEEEEEeecCCcccceEEEEEEEeecCC
Q 028968 145 DIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAG 179 (201)
Q Consensus 145 eFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~G 179 (201)
-|+|||+|+++ +.=..+|+|-.+-.-|+|
T Consensus 61 ~~~PGDIirLt------~Gy~Si~qg~LtL~~GK~ 89 (134)
T KOG3416|consen 61 LIQPGDIIRLT------GGYASIFQGCLTLYVGKG 89 (134)
T ss_pred ccCCccEEEec------ccchhhhcCceEEEecCC
Confidence 38999999984 556778888444444544
No 110
>cd00070 GLECT Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation.
Probab=22.24 E-value=1.2e+02 Score=23.32 Aligned_cols=25 Identities=28% Similarity=0.611 Sum_probs=19.7
Q ss_pred CCCC-CCCCCCEEEEEEEeecCCccc
Q 028968 141 RPIP-DIRTGDVVEIKLEVPENRRRL 165 (201)
Q Consensus 141 kdiP-eFr~GDtVrV~v~I~EnKeRi 165 (201)
..+| .|++|+.|.|+-.+..+.+|.
T Consensus 4 ~~l~~~l~~G~~i~i~G~~~~~~~~f 29 (127)
T cd00070 4 LPLPGGLKPGSTLTVKGRVLPNAKRF 29 (127)
T ss_pred cccCCCCcCCCEEEEEEEECCCCCEE
Confidence 3566 799999999999998854443
No 111
>PF01052 SpoA: Surface presentation of antigens (SPOA); InterPro: IPR001543 Proteins in this group are involved in a secretory pathway responsible for the surface presentation of invasion plasmid antigen needed for the entry of Salmonella and other species into mammalian cells [, ].They could play a role in preserving the translocation competence of the IPA antigens and are required for secretion of the three IPA proteins []. The C-terminal region of flagellar motor switch proteins FliN and FliM is also included in this entry. ; PDB: 3UEP_A 1O9Y_B 1YAB_A.
Probab=21.94 E-value=66 Score=22.59 Aligned_cols=35 Identities=17% Similarity=0.368 Sum_probs=21.5
Q ss_pred CCCCCCCCEEEEEEEeec----CCcccceEEEEEEEeec
Q 028968 143 IPDIRTGDVVEIKLEVPE----NRRRLSIYKGIVMSRQN 177 (201)
Q Consensus 143 iPeFr~GDtVrV~v~I~E----nKeRiQ~FeGIVIarrn 177 (201)
+=.+++||++.+.....+ .-.-...|.|......+
T Consensus 26 l~~L~~Gdvi~l~~~~~~~v~l~v~g~~~~~g~lg~~~~ 64 (77)
T PF01052_consen 26 LLNLKVGDVIPLDKPADEPVELRVNGQPIFRGELGRVNG 64 (77)
T ss_dssp HHC--TT-EEEECCESSTEEEEEETTEEEEEEEEEEETT
T ss_pred HhcCCCCCEEEeCCCCCCCEEEEECCEEEEEEEEEEECC
Confidence 446889999988777433 23556788888876554
No 112
>PRK10800 acyl-CoA thioesterase YbgC; Provisional
Probab=21.94 E-value=1.6e+02 Score=22.01 Aligned_cols=27 Identities=19% Similarity=0.341 Sum_probs=20.3
Q ss_pred CCCCCCCEEEEEEEeec-CCcccceEEE
Q 028968 144 PDIRTGDVVEIKLEVPE-NRRRLSIYKG 170 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~E-nKeRiQ~FeG 170 (201)
-..+.||+|.|+..+.+ ++.++....-
T Consensus 65 ~~~~~~d~i~v~t~v~~~~~~s~~~~~~ 92 (130)
T PRK10800 65 APARLDDMLEVQSEITSMRGTSLTFTQR 92 (130)
T ss_pred CcccCCCEEEEEEEEEeeCcEEEEEEEE
Confidence 35678999999999999 7666554433
No 113
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: 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 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=21.60 E-value=1.3e+02 Score=19.35 Aligned_cols=13 Identities=31% Similarity=0.565 Sum_probs=10.9
Q ss_pred CCCCCCEEEEEEE
Q 028968 145 DIRTGDVVEIKLE 157 (201)
Q Consensus 145 eFr~GDtVrV~v~ 157 (201)
.|++||.|+|.+.
T Consensus 44 ~~~~Gd~v~v~v~ 56 (69)
T cd05692 44 VLKEGDKVKVKVL 56 (69)
T ss_pred ccCCCCEEEEEEE
Confidence 4899999999864
No 114
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=21.34 E-value=2.2e+02 Score=25.68 Aligned_cols=47 Identities=13% Similarity=0.112 Sum_probs=32.5
Q ss_pred CCCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEeeeCCee
Q 028968 143 IPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIG 194 (201)
Q Consensus 143 iPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~GVG 194 (201)
-+-++-||.|.|.+.-.- =++ ..+| +|..+++.+.++.|||...|-=
T Consensus 200 p~lV~rG~~V~Iva~~gg--~~i-~~~G--~AL~~G~~Gd~IrVrN~~Sgkv 246 (261)
T PRK06804 200 PVLVERGQHVLMIAAQDG--IEA-QTLG--IAQKNGRKGELIKVKNLSSGRV 246 (261)
T ss_pred CcEEecCCEEEEEEecCC--EEE-EEEE--EEccCCCCCCEEEEEECCCCCE
Confidence 456899999999875321 111 1234 6777889999999999776643
No 115
>cd03446 MaoC_like MoaC_like Similar to the MaoC (monoamine oxidase C) dehydratase regulatory protein but without the N-terminal PutA domain. This protein family has a hot-dog fold similar to that of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
Probab=21.25 E-value=1.5e+02 Score=22.22 Aligned_cols=16 Identities=31% Similarity=0.447 Sum_probs=14.2
Q ss_pred CCCCCCEEEEEEEeec
Q 028968 145 DIRTGDVVEIKLEVPE 160 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E 160 (201)
.+++||+|.+..+|.+
T Consensus 90 pv~~GD~l~~~~~v~~ 105 (140)
T cd03446 90 PVFIGDTIRAEAEVVE 105 (140)
T ss_pred CCCCCCEEEEEEEEEE
Confidence 3789999999999986
No 116
>TIGR02799 thio_ybgC tol-pal system-associated acyl-CoA thioesterase. The tol-pal system consists of five critical genes. Inner membrane proteins TolQ and TolR convert protomotive force to energy that is transduced through TolA to an outer membrane complex of TolB and Pal. The system is known to be required to maintain outer membrane integrity. In a system with several homologous parts, ExbB and ExbD transduces energy through TonB to a variety of outer membrane proteins, many of which are siderophore receptors. The tol-pal system therefore may also be involved in transport. This family consists of a protein nearly always found in operons with the genes of the tol-pal system. The significance of this thioesterase to the tol-pal system is unclear, but either of two observations may be relevant. First, Pal, or peptidoglycan-associated lipoprotein, has a conserved N-terminal cleavage and acylation that makes it a lipoprotein. Second, the tol-pal system is implicated not only in the import o
Probab=21.23 E-value=1.7e+02 Score=21.30 Aligned_cols=28 Identities=18% Similarity=0.243 Sum_probs=21.9
Q ss_pred CCCCCCEEEEEEEeec-CCcccceEEEEE
Q 028968 145 DIRTGDVVEIKLEVPE-NRRRLSIYKGIV 172 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E-nKeRiQ~FeGIV 172 (201)
..+.||+|.|+..+.+ ++.+......+.
T Consensus 65 ~~~~gd~v~v~~~v~~~~~~~~~~~~~i~ 93 (126)
T TIGR02799 65 PARLDDLLTVTTRVVELKGASLVFAQEVR 93 (126)
T ss_pred cccCCCEEEEEEEEEecCceEEEEEEEEE
Confidence 5678999999999999 777777654444
No 117
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: 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 H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.67 E-value=1.1e+02 Score=23.26 Aligned_cols=16 Identities=19% Similarity=0.237 Sum_probs=13.1
Q ss_pred CCCCCCEEEEEEEeec
Q 028968 145 DIRTGDVVEIKLEVPE 160 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E 160 (201)
.|++||+|++.+.-..
T Consensus 66 ~f~vGd~V~~kVi~~d 81 (100)
T cd05693 66 LFSVGQLVRCKVVSLD 81 (100)
T ss_pred hccCCCEEEEEEEEcc
Confidence 4999999999876554
No 118
>PRK13691 (3R)-hydroxyacyl-ACP dehydratase subunit HadC; Provisional
Probab=20.64 E-value=1.3e+02 Score=24.83 Aligned_cols=16 Identities=13% Similarity=0.366 Sum_probs=14.3
Q ss_pred CCCCCCEEEEEEEeec
Q 028968 145 DIRTGDVVEIKLEVPE 160 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E 160 (201)
.+++||+|.+.++|.+
T Consensus 96 PV~~GDtL~~~~~V~~ 111 (166)
T PRK13691 96 PVLAGDKLWARMDIHS 111 (166)
T ss_pred CcCCCCEEEEEEEEEE
Confidence 3799999999999976
No 119
>cd03455 SAV4209 SAV4209 is a Streptomyces avermitilis protein with a hot dog fold that is similar to those of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. The alpha- and gamma-proteobacterial members of this CD have, in addition to a hot dog fold, an N-terminal extension.
Probab=20.62 E-value=1.9e+02 Score=21.68 Aligned_cols=16 Identities=19% Similarity=0.289 Sum_probs=14.2
Q ss_pred CCCCCCEEEEEEEeec
Q 028968 145 DIRTGDVVEIKLEVPE 160 (201)
Q Consensus 145 eFr~GDtVrV~v~I~E 160 (201)
...+||+|.+..+|.+
T Consensus 79 pv~~Gdtl~~~~~v~~ 94 (123)
T cd03455 79 PLYAGDTLRFGGRVTA 94 (123)
T ss_pred cccCCCEEEEEEEEEe
Confidence 4689999999999987
No 120
>CHL00057 rpl14 ribosomal protein L14
Probab=20.56 E-value=1.9e+02 Score=23.40 Aligned_cols=34 Identities=12% Similarity=0.198 Sum_probs=26.0
Q ss_pred CCCCCCCEEEEEEEeec--C-CcccceEEEEEEEeec
Q 028968 144 PDIRTGDVVEIKLEVPE--N-RRRLSIYKGIVMSRQN 177 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~E--n-KeRiQ~FeGIVIarrn 177 (201)
+.-.+||+|.|.++-.. . -.|=|++.++|+..+.
T Consensus 31 ~~a~vGD~IvvsVk~~~~~~k~kkg~v~kAvIVrtk~ 67 (122)
T CHL00057 31 KYAHIGDVIIAVVKEAVPNMPLKRSEVVRAVIVRTCK 67 (122)
T ss_pred ccccCCCEEEEEEEeccCCCceecCCEEEEEEEEecc
Confidence 56789999999887533 2 3467999999998764
No 121
>PRK11281 hypothetical protein; Provisional
Probab=20.52 E-value=2.1e+02 Score=31.06 Aligned_cols=36 Identities=19% Similarity=0.249 Sum_probs=23.7
Q ss_pred CCCCCCEEEEEEE---eec---CCcccceEEEEEEEeecCCc
Q 028968 145 DIRTGDVVEIKLE---VPE---NRRRLSIYKGIVMSRQNAGI 180 (201)
Q Consensus 145 eFr~GDtVrV~v~---I~E---nKeRiQ~FeGIVIarrn~Gi 180 (201)
.|++||+|+|.=. |.+ --+|+..+.|..|-+-|+-+
T Consensus 938 PfrIGD~I~I~~~~G~V~~I~lRsT~Irt~D~~~ViIPNs~~ 979 (1113)
T PRK11281 938 PVRIGDTVTIGTFSGTVSKIRIRATTITDFDRKEVIVPNKAF 979 (1113)
T ss_pred CcCCCCEEEECCEEEEEEEEEeEEEEEEcCCCCEEEEechhh
Confidence 4999999998521 222 24667777777777766654
No 122
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=20.47 E-value=77 Score=22.98 Aligned_cols=14 Identities=36% Similarity=0.821 Sum_probs=10.5
Q ss_pred CCCCCCCCEEEEEE
Q 028968 143 IPDIRTGDVVEIKL 156 (201)
Q Consensus 143 iPeFr~GDtVrV~v 156 (201)
+|+..+||.|-||.
T Consensus 35 v~~v~~Gd~VLVHa 48 (68)
T PF01455_consen 35 VPDVKVGDYVLVHA 48 (68)
T ss_dssp CTSB-TT-EEEEET
T ss_pred eCCCCCCCEEEEec
Confidence 68899999999984
No 123
>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=20.37 E-value=4.5e+02 Score=21.00 Aligned_cols=28 Identities=18% Similarity=0.328 Sum_probs=22.5
Q ss_pred CCCCCCCEEEEEEEeecCCcccceEEEEEEEeec
Q 028968 144 PDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQN 177 (201)
Q Consensus 144 PeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn 177 (201)
..|++||.|+|. ..=++-|+|+|+...+
T Consensus 118 ~~~~~G~~V~I~------~Gpf~G~~g~v~~~~~ 145 (172)
T TIGR00922 118 IDFEVGEQVRVN------DGPFANFTGTVEEVDY 145 (172)
T ss_pred cCCCCCCEEEEe------ecCCCCcEEEEEEEcC
Confidence 559999999995 3567788999998764
No 124
>COG5496 Predicted thioesterase [General function prediction only]
Probab=20.36 E-value=2.5e+02 Score=23.42 Aligned_cols=47 Identities=19% Similarity=0.210 Sum_probs=27.5
Q ss_pred CCCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEeee
Q 028968 143 IPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRII 190 (201)
Q Consensus 143 iPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs 190 (201)
+-..-+|++|+|..++.+-..|--.|.+++. --+.-|++--+.|.|.
T Consensus 68 la~~~~G~~V~i~~~l~~v~Gr~v~f~i~a~-~~~~~Ig~g~h~R~iv 114 (130)
T COG5496 68 LAATPPGLTVTIGARLEKVEGRKVKFRIIAM-EGGDKIGEGTHTRVIV 114 (130)
T ss_pred ccCCCCCCeEEEEEEEEEEeccEEEEEEEEe-eCCcEEeeeEEEEEEe
Confidence 3456799999999999883333345666554 1122234444445443
No 125
>PF01281 Ribosomal_L9_N: Ribosomal protein L9, N-terminal domain; InterPro: IPR020070 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 L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....
Probab=20.31 E-value=76 Score=21.81 Aligned_cols=17 Identities=35% Similarity=0.808 Sum_probs=13.5
Q ss_pred cCCCCCCC-CCCCEEEEE
Q 028968 139 SERPIPDI-RTGDVVEIK 155 (201)
Q Consensus 139 ~kkdiPeF-r~GDtVrV~ 155 (201)
+.+|+|.+ +.||+|.|.
T Consensus 5 L~~dv~~lG~~Gdiv~V~ 22 (48)
T PF01281_consen 5 LLKDVPGLGKKGDIVEVK 22 (48)
T ss_dssp ESSCCTTSBSTTEEEE-S
T ss_pred EcccccccCCCCCEEEEc
Confidence 56899986 999999984
No 126
>PRK12786 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=20.26 E-value=2.6e+02 Score=25.97 Aligned_cols=47 Identities=9% Similarity=0.140 Sum_probs=33.4
Q ss_pred CCCCCCCCEEEEEEEeecCCcccceEEEEEEEeecCCccceEEEEeeeCCee
Q 028968 143 IPDIRTGDVVEIKLEVPENRRRLSIYKGIVMSRQNAGIHTTIRIRRIIAGIG 194 (201)
Q Consensus 143 iPeFr~GDtVrV~v~I~EnKeRiQ~FeGIVIarrn~Gi~sTFTVRKIs~GVG 194 (201)
-+-++-||.|.|.+...- ++ ...-..|..+.+++.+++|||...|-=
T Consensus 256 p~lV~rGd~V~i~~~~gg----l~-v~~~G~ALe~G~~Gd~IrV~N~~S~ki 302 (338)
T PRK12786 256 PDLVQRGQLVTLIYQTPG----IY-LTARGKALEDGAEGDVVRVLNLQSKRT 302 (338)
T ss_pred ccEEcCCCEEEEEEEcCC----EE-EEEEEEEccccCCCCEEEEEECCCCCE
Confidence 456899999999886432 21 123446777888999999999866643
No 127
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=20.05 E-value=1.2e+02 Score=24.40 Aligned_cols=22 Identities=32% Similarity=0.600 Sum_probs=17.0
Q ss_pred ccceEEEEEEEeecCCccceEEEEe
Q 028968 164 RLSIYKGIVMSRQNAGIHTTIRIRR 188 (201)
Q Consensus 164 RiQ~FeGIVIarrn~Gi~sTFTVRK 188 (201)
|-|.|+|+|++.+ ++.|.+|+-
T Consensus 28 rgk~l~G~VvS~K---m~KTvvV~v 49 (108)
T PRK08572 28 RGQVLEGTVVSDK---MHKTVVVER 49 (108)
T ss_pred eeEEEEEEEEecC---CCceEEEEE
Confidence 4578999999975 678888753
No 128
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=20.01 E-value=1.3e+02 Score=19.91 Aligned_cols=19 Identities=21% Similarity=0.489 Sum_probs=13.9
Q ss_pred CCCCCCEEEEEEEeecCCc
Q 028968 145 DIRTGDVVEIKLEVPENRR 163 (201)
Q Consensus 145 eFr~GDtVrV~v~I~EnKe 163 (201)
.+++||.|.|.=++...+.
T Consensus 44 ~l~~g~~v~v~G~v~~~~~ 62 (75)
T PF01336_consen 44 KLKEGDIVRVRGKVKRYNG 62 (75)
T ss_dssp TS-TTSEEEEEEEEEEETT
T ss_pred cCCCCeEEEEEEEEEEECC
Confidence 3779999999977777433
Done!