Query psy3772
Match_columns 119
No_of_seqs 139 out of 1052
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 16:54:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3772.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3772hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05338 rplS 50S ribosomal pr 100.0 8.7E-55 1.9E-59 314.9 13.8 115 1-118 1-115 (116)
2 COG0335 RplS Ribosomal protein 100.0 1.4E-54 3E-59 312.4 13.5 112 1-115 1-114 (115)
3 TIGR01024 rplS_bact ribosomal 100.0 2.4E-54 5.1E-59 311.4 13.6 112 1-115 1-112 (113)
4 CHL00084 rpl19 ribosomal prote 100.0 4.1E-54 8.9E-59 311.7 13.2 112 2-116 6-117 (117)
5 PF01245 Ribosomal_L19: Riboso 100.0 1.6E-53 3.5E-58 306.7 10.6 113 1-116 1-113 (113)
6 KOG1698|consensus 100.0 6.5E-34 1.4E-38 221.1 9.3 107 3-110 76-184 (201)
7 smart00743 Agenet Tudor-like d 87.2 4.9 0.00011 24.7 6.6 50 20-78 1-50 (61)
8 PF05641 Agenet: Agenet domain 85.7 2.9 6.4E-05 26.8 5.1 38 22-65 1-38 (68)
9 PRK01191 rpl24p 50S ribosomal 73.2 9.2 0.0002 28.1 4.8 68 21-97 45-114 (120)
10 TIGR03170 flgA_cterm flagella 69.6 17 0.00038 25.1 5.5 47 18-70 62-108 (122)
11 PF02765 POT1: Telomeric singl 65.7 5.8 0.00013 28.8 2.5 48 17-73 68-117 (146)
12 TIGR01080 rplX_A_E ribosomal p 65.6 18 0.0004 26.1 5.0 62 19-89 39-102 (114)
13 PRK03999 translation initiatio 65.2 13 0.00028 27.1 4.2 57 17-79 6-62 (129)
14 PF02752 Arrestin_C: Arrestin 65.1 13 0.00028 25.0 4.0 33 21-53 15-47 (136)
15 COG2139 RPL21A Ribosomal prote 63.2 9 0.0002 27.3 2.9 42 17-58 28-72 (98)
16 cd04497 hPOT1_OB1_like hPOT1_O 63.0 15 0.00033 26.5 4.2 41 17-65 64-104 (138)
17 PF11302 DUF3104: Protein of u 61.9 39 0.00084 23.0 5.7 52 19-70 3-58 (75)
18 PF03888 MucB_RseB: MucB/RseB 61.5 39 0.00086 27.4 6.8 51 40-93 8-58 (285)
19 PF12969 DUF3857: Domain of Un 60.7 8.5 0.00019 27.6 2.5 20 17-36 85-104 (177)
20 cd01737 LSm16_N LSm16 belongs 58.6 20 0.00043 23.6 3.7 34 24-65 5-38 (62)
21 PF13144 SAF_2: SAF-like 57.6 45 0.00098 24.9 6.1 47 17-69 135-181 (196)
22 PF08207 EFP_N: Elongation fac 54.5 41 0.00089 21.0 4.6 49 21-77 4-53 (58)
23 cd08544 Reeler Reeler, the N-t 53.6 34 0.00073 24.1 4.6 31 21-56 29-59 (135)
24 PF02211 NHase_beta: Nitrile h 50.6 15 0.00031 29.4 2.5 36 18-54 131-170 (222)
25 smart00739 KOW KOW (Kyprides, 48.3 37 0.00081 17.2 3.6 27 21-54 1-27 (28)
26 PRK07018 flgA flagellar basal 48.2 57 0.0012 25.6 5.6 48 17-70 172-219 (235)
27 PF11717 Tudor-knot: RNA bindi 47.7 64 0.0014 19.7 4.8 35 22-63 1-35 (55)
28 PF10447 EXOSC1: Exosome compo 47.1 14 0.00031 25.1 1.7 13 20-32 67-79 (82)
29 cd06462 Peptidase_S24_S26 The 45.8 71 0.0015 19.7 5.4 43 19-70 11-53 (84)
30 PF09926 DUF2158: Uncharacteri 45.3 15 0.00033 23.1 1.5 11 22-32 1-11 (53)
31 TIGR00405 L26e_arch ribosomal 45.2 1.1E+02 0.0024 21.8 6.4 43 20-71 85-127 (145)
32 COG1499 NMD3 NMD protein affec 45.2 13 0.00029 31.7 1.6 16 17-32 242-257 (355)
33 PRK15136 multidrug efflux syst 45.2 52 0.0011 27.6 5.2 32 18-53 262-293 (390)
34 PTZ00194 60S ribosomal protein 44.9 86 0.0019 23.7 5.8 61 17-87 43-105 (143)
35 TIGR00922 nusG transcription t 44.8 1.1E+02 0.0023 22.4 6.3 29 20-55 118-146 (172)
36 TIGR01956 NusG_myco NusG famil 44.2 1E+02 0.0023 25.3 6.6 38 19-63 203-240 (258)
37 COG1566 EmrA Multidrug resista 44.1 92 0.002 26.5 6.5 56 17-76 254-318 (352)
38 PRK09455 rseB anti-sigma E fac 44.1 1.1E+02 0.0025 25.4 7.0 52 38-93 37-89 (319)
39 COG0250 NusG Transcription ant 42.5 1E+02 0.0022 23.6 6.1 32 17-55 119-150 (178)
40 PF12961 DUF3850: Domain of Un 42.0 36 0.00077 22.9 3.0 31 16-53 23-53 (72)
41 PF00238 Ribosomal_L14: Riboso 42.0 66 0.0014 23.2 4.7 37 18-54 29-67 (122)
42 cd05688 S1_RPS1_repeat_ec3 S1_ 41.9 34 0.00075 20.4 2.8 15 22-36 45-59 (68)
43 TIGR02754 sod_Ni_protease nick 40.8 71 0.0015 20.7 4.4 45 19-67 9-53 (90)
44 cd00164 S1_like S1_like: Ribos 40.7 39 0.00084 19.4 2.8 15 21-35 41-55 (65)
45 TIGR01955 RfaH transcriptional 40.4 53 0.0011 23.6 4.0 29 20-55 107-135 (159)
46 PRK09014 rfaH transcriptional 40.3 50 0.0011 24.1 3.9 27 21-54 109-135 (162)
47 PF00717 Peptidase_S24: Peptid 40.2 22 0.00049 21.7 1.8 44 19-71 8-51 (70)
48 KOG3409|consensus 40.1 59 0.0013 25.7 4.4 16 18-33 119-134 (193)
49 PRK06005 flgA flagellar basal 39.5 1.1E+02 0.0024 22.9 5.7 49 18-72 97-145 (160)
50 cd05708 S1_Rrp5_repeat_sc12 S1 38.4 42 0.00091 20.6 2.8 15 22-36 48-62 (77)
51 PRK00529 elongation factor P; 38.3 98 0.0021 23.7 5.4 51 19-81 4-59 (186)
52 PF02014 Reeler: Reeler domain 38.1 33 0.00072 24.2 2.6 32 20-56 28-59 (132)
53 smart00333 TUDOR Tudor domain. 37.6 87 0.0019 18.4 6.3 35 20-64 1-35 (57)
54 cd00493 FabA_FabZ FabA/Z, beta 37.3 75 0.0016 21.3 4.2 29 21-50 88-116 (131)
55 PRK05483 rplN 50S ribosomal pr 37.0 73 0.0016 23.2 4.2 35 20-54 31-67 (122)
56 cd05690 S1_RPS1_repeat_ec5 S1_ 36.9 45 0.00097 20.2 2.8 20 22-41 46-65 (69)
57 PF01835 A2M_N: MG2 domain; I 36.9 1.2E+02 0.0026 19.8 6.3 20 17-36 6-25 (99)
58 TIGR00192 urease_beta urease, 36.8 33 0.00071 24.6 2.3 33 16-49 60-97 (101)
59 TIGR00008 infA translation ini 36.5 28 0.00061 23.0 1.8 18 18-35 41-58 (68)
60 cd05705 S1_Rrp5_repeat_hs14 S1 36.3 49 0.0011 21.3 3.0 22 21-42 50-71 (74)
61 TIGR00038 efp translation elon 35.9 1.3E+02 0.0027 23.1 5.6 49 20-80 4-57 (184)
62 cd05685 S1_Tex S1_Tex: The C-t 35.5 56 0.0012 19.3 3.0 15 22-36 45-59 (68)
63 cd04452 S1_IF2_alpha S1_IF2_al 35.4 50 0.0011 20.4 2.9 15 22-36 50-64 (76)
64 PF14085 DUF4265: Domain of un 35.3 1.3E+02 0.0028 21.2 5.3 33 21-63 25-57 (117)
65 TIGR01750 fabZ beta-hydroxyacy 35.1 78 0.0017 22.0 4.1 27 22-49 98-124 (140)
66 PF06507 Auxin_resp: Auxin res 34.7 89 0.0019 21.3 4.2 32 20-54 37-68 (83)
67 PF00386 C1q: C1q domain; Int 34.5 76 0.0016 21.8 3.9 30 21-50 94-127 (127)
68 PRK13203 ureB urease subunit b 34.2 38 0.00083 24.3 2.3 33 16-49 60-97 (102)
69 PF14438 SM-ATX: Ataxin 2 SM d 34.1 1.2E+02 0.0027 19.4 4.7 36 23-65 10-45 (77)
70 cd05703 S1_Rrp5_repeat_hs12_sc 34.1 56 0.0012 20.8 3.0 21 22-42 47-67 (73)
71 PF12701 LSM14: Scd6-like Sm d 33.9 1.6E+02 0.0036 20.5 6.2 60 23-93 6-81 (96)
72 cd01288 FabZ FabZ is a 17kD be 33.8 81 0.0018 21.2 3.9 27 22-49 88-114 (131)
73 cd04455 S1_NusA S1_NusA: N-uti 33.7 79 0.0017 19.6 3.6 17 21-37 40-56 (67)
74 PRK08559 nusG transcription an 33.5 1.2E+02 0.0025 22.4 4.9 28 21-55 94-121 (153)
75 cd05706 S1_Rrp5_repeat_sc10 S1 33.2 60 0.0013 20.0 2.9 14 22-35 48-61 (73)
76 COG0361 InfA Translation initi 33.1 34 0.00075 23.2 1.9 17 18-34 43-59 (75)
77 cd01735 LSm12_N LSm12 belongs 33.0 98 0.0021 20.0 3.9 28 21-55 2-29 (61)
78 cd04471 S1_RNase_R S1_RNase_R: 32.9 47 0.001 20.8 2.4 16 21-36 57-72 (83)
79 TIGR01067 rplN_bact ribosomal 32.6 99 0.0022 22.5 4.4 35 20-54 31-67 (122)
80 PF07076 DUF1344: Protein of u 32.5 49 0.0011 21.7 2.5 21 17-37 33-53 (61)
81 cd05698 S1_Rrp5_repeat_hs6_sc5 32.4 62 0.0013 19.7 2.9 16 22-37 45-60 (70)
82 PF01281 Ribosomal_L9_N: Ribos 30.9 32 0.0007 21.2 1.3 16 16-31 6-22 (48)
83 PF11325 DUF3127: Domain of un 30.9 52 0.0011 22.6 2.5 17 19-35 50-66 (84)
84 cd05702 S1_Rrp5_repeat_hs11_sc 30.9 68 0.0015 19.9 2.9 16 21-36 46-61 (70)
85 cd00407 Urease_beta Urease bet 30.8 47 0.001 23.8 2.3 33 16-49 60-97 (101)
86 PF11132 SplA: Transcriptional 30.5 53 0.0012 22.4 2.4 17 18-34 2-18 (75)
87 smart00110 C1Q Complement comp 30.3 91 0.002 22.5 3.9 31 21-51 99-133 (135)
88 COG5636 Uncharacterized conser 30.3 35 0.00075 28.1 1.8 17 17-33 258-274 (284)
89 PRK04183 glutamyl-tRNA(Gln) am 30.3 1.9E+02 0.0041 25.2 6.3 55 21-93 2-58 (419)
90 PRK05609 nusG transcription an 30.2 2.2E+02 0.0048 20.8 6.2 44 20-72 125-168 (181)
91 PF01472 PUA: PUA domain; Int 30.1 36 0.00078 21.9 1.6 14 19-32 28-41 (74)
92 cd05686 S1_pNO40 S1_pNO40: pNO 30.0 66 0.0014 20.2 2.8 16 22-37 49-64 (73)
93 cd05707 S1_Rrp5_repeat_sc11 S1 29.9 76 0.0016 19.4 3.0 15 22-36 45-59 (68)
94 TIGR02266 gmx_TIGR02266 Myxoco 29.6 1.6E+02 0.0034 18.9 5.8 45 20-73 35-79 (96)
95 PRK13201 ureB urease subunit b 29.5 46 0.00099 25.1 2.2 35 16-51 60-99 (136)
96 PRK13202 ureB urease subunit b 29.4 49 0.0011 23.9 2.2 33 16-49 61-98 (104)
97 PF11604 CusF_Ec: Copper bindi 29.4 68 0.0015 20.7 2.8 21 17-37 38-58 (70)
98 PRK02268 hypothetical protein; 29.4 83 0.0018 23.6 3.6 35 18-52 32-67 (141)
99 PRK00276 infA translation init 29.2 51 0.0011 21.4 2.1 25 22-53 47-71 (72)
100 PRK00006 fabZ (3R)-hydroxymyri 29.1 1E+02 0.0022 21.7 3.9 27 22-49 102-128 (147)
101 smart00316 S1 Ribosomal protei 29.0 76 0.0017 18.4 2.8 14 22-35 47-60 (72)
102 PF12945 YcgR_2: Flagellar pro 29.0 1.5E+02 0.0033 18.6 5.0 31 21-55 47-77 (87)
103 PF10610 Tafi-CsgC: Thin aggre 29.0 63 0.0014 23.4 2.7 20 22-41 75-94 (106)
104 PRK13198 ureB urease subunit b 28.9 51 0.0011 25.4 2.4 36 16-52 88-128 (158)
105 KOG3416|consensus 28.9 34 0.00073 25.7 1.4 23 21-51 61-83 (134)
106 PRK08571 rpl14p 50S ribosomal 28.6 1.5E+02 0.0033 21.9 4.8 35 19-54 44-78 (132)
107 TIGR00074 hypC_hupF hydrogenas 28.1 48 0.001 22.3 1.9 14 19-32 33-46 (76)
108 TIGR01000 bacteriocin_acc bact 27.8 1.6E+02 0.0034 25.1 5.5 80 17-103 367-450 (457)
109 PTZ00054 60S ribosomal protein 27.5 1.6E+02 0.0035 22.1 4.8 35 19-54 51-85 (139)
110 PF09671 Spore_GerQ: Spore coa 27.3 76 0.0016 21.9 2.8 42 7-52 5-46 (81)
111 cd05697 S1_Rrp5_repeat_hs5 S1_ 27.2 88 0.0019 19.1 3.0 16 21-36 44-59 (69)
112 PF07238 PilZ: PilZ domain; I 27.2 1.6E+02 0.0035 18.3 5.0 32 21-55 44-75 (102)
113 TIGR03673 rpl14p_arch 50S ribo 27.2 1.7E+02 0.0038 21.6 4.9 35 19-54 43-77 (131)
114 PRK13204 ureB urease subunit b 27.1 56 0.0012 25.2 2.3 37 16-53 83-124 (159)
115 PF01455 HupF_HypC: HupF/HypC 26.8 53 0.0011 21.4 1.9 15 18-32 34-48 (68)
116 cd05689 S1_RPS1_repeat_ec4 S1_ 26.7 84 0.0018 19.3 2.8 20 21-40 48-67 (72)
117 PRK08515 flgA flagellar basal 26.7 2E+02 0.0044 22.5 5.5 47 17-70 161-207 (222)
118 PF07977 FabA: FabA-like domai 26.6 85 0.0018 22.0 3.1 29 21-49 96-127 (138)
119 PRK14578 elongation factor P; 26.5 1.3E+02 0.0029 23.3 4.4 63 20-91 5-70 (187)
120 TIGR02728 spore_gerQ spore coa 26.3 52 0.0011 22.8 1.8 41 7-51 3-43 (82)
121 cd05691 S1_RPS1_repeat_ec6 S1_ 26.3 92 0.002 18.9 2.9 14 22-35 45-58 (73)
122 cd05687 S1_RPS1_repeat_ec1_hs1 26.3 97 0.0021 18.9 3.0 14 22-35 45-58 (70)
123 PRK12786 flgA flagellar basal 26.1 1.8E+02 0.0038 24.5 5.4 48 19-72 256-303 (338)
124 cd03692 mtIF2_IVc mtIF2_IVc: t 26.1 41 0.00089 22.1 1.3 13 17-29 71-83 (84)
125 PRK04306 50S ribosomal protein 25.8 1E+02 0.0022 21.8 3.3 43 19-61 32-77 (98)
126 TIGR01451 B_ant_repeat conserv 25.7 1.6E+02 0.0035 17.8 4.9 31 18-51 4-34 (53)
127 COG1945 Pyruvoyl-dependent arg 25.4 1.3E+02 0.0029 23.2 4.1 37 18-54 58-96 (163)
128 PRK13205 ureB urease subunit b 24.8 67 0.0014 24.8 2.4 34 16-50 60-98 (162)
129 CHL00057 rpl14 ribosomal prote 24.8 1.8E+02 0.0039 21.2 4.5 35 20-54 31-67 (122)
130 PF02563 Poly_export: Polysacc 24.7 54 0.0012 21.4 1.7 13 21-33 12-24 (82)
131 cd05791 S1_CSL4 S1_CSL4: CSL4, 24.7 61 0.0013 21.9 2.0 14 21-34 60-73 (92)
132 PF00963 Cohesin: Cohesin doma 24.7 1.3E+02 0.0028 21.1 3.8 32 18-53 6-37 (141)
133 cd03451 FkbR2 FkbR2 is a Strep 24.6 79 0.0017 21.9 2.6 15 22-36 92-106 (146)
134 cd05692 S1_RPS1_repeat_hs4 S1_ 24.5 1.1E+02 0.0024 17.9 3.0 14 22-35 45-58 (69)
135 PF14326 DUF4384: Domain of un 24.5 77 0.0017 20.7 2.4 16 20-35 1-16 (83)
136 PF04319 NifZ: NifZ domain; I 24.4 90 0.0019 21.1 2.7 18 19-36 2-19 (75)
137 PF01345 DUF11: Domain of unkn 24.4 1.9E+02 0.0041 18.1 4.9 32 17-51 32-63 (76)
138 PRK12442 translation initiatio 24.3 60 0.0013 22.6 1.9 31 17-54 42-72 (87)
139 PF12148 DUF3590: Protein of u 24.1 43 0.00092 23.2 1.1 23 18-41 62-84 (85)
140 PF12700 HlyD_2: HlyD family s 24.1 1.1E+02 0.0025 23.7 3.7 43 17-64 205-247 (328)
141 PF08605 Rad9_Rad53_bind: Fung 23.8 43 0.00093 24.7 1.2 14 19-32 57-70 (131)
142 cd05704 S1_Rrp5_repeat_hs13 S1 23.8 98 0.0021 19.5 2.7 15 21-35 48-62 (72)
143 COG5235 RFA2 Single-stranded D 23.6 1.7E+02 0.0037 24.0 4.6 31 44-77 70-101 (258)
144 COG2030 MaoC Acyl dehydratase 23.5 1.3E+02 0.0028 22.0 3.7 16 21-36 106-121 (159)
145 PF13358 DDE_3: DDE superfamil 23.5 37 0.0008 22.7 0.7 43 47-89 81-126 (146)
146 PRK12618 flgA flagellar basal 23.4 2.7E+02 0.006 20.4 5.4 48 19-72 79-126 (141)
147 cd06530 S26_SPase_I The S26 Ty 23.3 2E+02 0.0044 18.1 4.7 46 19-68 11-56 (85)
148 PF04970 LRAT: Lecithin retino 23.3 54 0.0012 22.8 1.5 15 18-32 3-17 (125)
149 PF09931 DUF2163: Uncharacteri 23.1 2.6E+02 0.0056 20.4 5.3 46 23-68 92-137 (163)
150 PF08206 OB_RNB: Ribonuclease 23.0 1.6E+02 0.0035 18.1 3.5 27 21-51 31-57 (58)
151 PF04225 OapA: Opacity-associa 22.5 64 0.0014 21.7 1.7 17 17-33 38-54 (85)
152 TIGR00998 8a0101 efflux pump m 22.4 1.2E+02 0.0027 24.0 3.6 36 17-56 250-285 (334)
153 PRK12617 flgA flagellar basal 22.1 3.2E+02 0.0069 21.5 5.8 47 21-73 155-201 (214)
154 PF13437 HlyD_3: HlyD family s 22.1 2.4E+02 0.0051 18.4 5.3 33 17-54 45-78 (105)
155 PF07154 DUF1392: Protein of u 22.0 1.7E+02 0.0036 22.4 4.0 33 16-51 82-114 (150)
156 COG2100 Predicted Fe-S oxidore 21.9 1.5E+02 0.0033 25.9 4.2 31 17-54 346-377 (414)
157 cd05693 S1_Rrp5_repeat_hs1_sc1 21.6 1.1E+02 0.0023 21.0 2.7 16 21-36 66-81 (100)
158 PRK13986 urease subunit alpha; 21.4 71 0.0015 25.9 2.0 34 16-50 165-203 (225)
159 cd02853 MTHase_N_term Maltooli 21.4 92 0.002 20.1 2.3 16 75-90 11-26 (85)
160 PF00575 S1: S1 RNA binding do 21.2 1.1E+02 0.0025 18.7 2.6 21 20-40 47-67 (74)
161 cd04461 S1_Rrp5_repeat_hs8_sc7 21.2 1.3E+02 0.0028 19.2 3.0 13 22-34 59-71 (83)
162 PRK04163 exosome complex RNA-b 21.1 2E+02 0.0044 22.6 4.6 17 19-35 109-125 (235)
163 cd03450 NodN NodN (nodulation 21.1 2.7E+02 0.0059 20.2 5.0 15 22-36 98-112 (149)
164 cd01289 FabA_like Domain of un 21.0 1.6E+02 0.0035 20.9 3.7 30 20-50 91-121 (138)
165 PF01828 Peptidase_A4: Peptida 20.9 2.7E+02 0.0059 21.7 5.2 15 21-35 90-104 (208)
166 PRK13188 bifunctional UDP-3-O- 20.8 1.5E+02 0.0032 26.3 4.0 29 22-50 416-444 (464)
167 PF06819 Arc_PepC: Archaeal Pe 20.8 1.2E+02 0.0027 21.9 3.0 34 3-37 16-49 (110)
168 PRK04424 fatty acid biosynthes 20.4 2E+02 0.0042 21.8 4.2 27 21-48 138-164 (185)
169 COG0231 Efp Translation elonga 20.4 2E+02 0.0043 21.0 4.1 51 20-78 7-58 (131)
170 cd04491 SoSSB_OBF SoSSB_OBF: A 20.1 1.5E+02 0.0032 18.9 3.0 18 19-36 46-64 (82)
171 PRK10413 hydrogenase 2 accesso 20.0 80 0.0017 21.5 1.8 13 20-32 41-53 (82)
172 TIGR00376 DNA helicase, putati 20.0 1.6E+02 0.0034 26.8 4.1 30 21-55 57-86 (637)
173 COG3097 Uncharacterized protei 20.0 68 0.0015 23.1 1.5 13 21-33 32-44 (106)
No 1
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=100.00 E-value=8.7e-55 Score=314.87 Aligned_cols=115 Identities=61% Similarity=0.976 Sum_probs=112.6
Q ss_pred CchHHHHHHHHHHHhcCCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCeeEEEEEeecC
Q psy3772 1 MNLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQLYS 80 (119)
Q Consensus 1 m~li~~~e~~~~~~~~~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gvGVEr~f~l~S 80 (119)
|++|+.+|++|+ +.++|+|+|||||+|+++|.||+|+|+|.|+|+||+++++|+++||||||+++|+|||++||+||
T Consensus 1 ~~~i~~~~~~~~---~~~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki~~gvGVEr~fpl~S 77 (116)
T PRK05338 1 MNLIKEIEAEQL---RKDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKISYGVGVERTFPLHS 77 (116)
T ss_pred CcHHHHHHHHHh---hcCCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEcccCccEEEEecCCC
Confidence 899999999999 78999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccceEEEEEeccccccceeeecCCCCcceeeeeeccc
Q psy3772 81 PIISSIIVKRRGDVRRAKLYYLRKCSGKSARIKEKLLK 118 (119)
Q Consensus 81 P~I~~IeVl~~~kvrRakLyYLR~~~gK~arike~~~~ 118 (119)
|.|++|+|+++|++|||||||||++.||+|||||+...
T Consensus 78 P~I~~IeV~r~gkvRRAKLyYLR~~~gK~arike~~~~ 115 (116)
T PRK05338 78 PRIDSIEVVRRGKVRRAKLYYLRELRGKAARIKERRDA 115 (116)
T ss_pred CcccEEEEEEecccchhheeeeccCcchhheeeeeccC
Confidence 99999999999999999999999999999999998764
No 2
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-54 Score=312.40 Aligned_cols=112 Identities=61% Similarity=1.020 Sum_probs=109.7
Q ss_pred Cc--hHHHHHHHHHHHhcCCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCeeEEEEEee
Q psy3772 1 MN--LIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQL 78 (119)
Q Consensus 1 m~--li~~~e~~~~~~~~~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gvGVEr~f~l 78 (119)
|+ +|+.+|++|+ +.++|+|+|||||+|++++.||+|+|+|.|+|+||+++|+|+++|||||++++|+|||++||+
T Consensus 1 m~~~~i~~le~~q~---~~~iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~~~tftvRkis~G~GVEr~Fp~ 77 (115)
T COG0335 1 MNIPIIQQLEQEQI---KKDIPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGISETFTVRKISYGVGVERVFPL 77 (115)
T ss_pred CCcHHHHHHHHHHH---HhhCCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCCCccceEEEEEeecCceEEEEeec
Confidence 66 8999999999 778999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCccceEEEEEeccccccceeeecCCCCcceeeeee
Q psy3772 79 YSPIISSIIVKRRGDVRRAKLYYLRKCSGKSARIKEK 115 (119)
Q Consensus 79 ~SP~I~~IeVl~~~kvrRakLyYLR~~~gK~arike~ 115 (119)
|||.|++|||+++|+||||||||||++.||+|||||+
T Consensus 78 ~SP~Ie~IeV~rrGkVRRAKLYYLR~~~GKaArIke~ 114 (115)
T COG0335 78 HSPLIESIEVVRRGKVRRAKLYYLRERRGKAARIKEK 114 (115)
T ss_pred CCCceeEEEEEecCceeeeeeEeeecccccceeeeec
Confidence 9999999999999999999999999999999999996
No 3
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=100.00 E-value=2.4e-54 Score=311.39 Aligned_cols=112 Identities=59% Similarity=0.972 Sum_probs=110.5
Q ss_pred CchHHHHHHHHHHHhcCCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCeeEEEEEeecC
Q psy3772 1 MNLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQLYS 80 (119)
Q Consensus 1 m~li~~~e~~~~~~~~~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gvGVEr~f~l~S 80 (119)
|++|+.+|++|+ +.++|+|+|||+|+|++++.||+|+|+|.|+|+||+++|+|+++||||||+++|+|||++||+||
T Consensus 1 m~~i~~~e~~~~---~~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i~~gvGVEr~fpl~S 77 (113)
T TIGR01024 1 QNLIKQIEQEQL---KKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKISYGVGVERIFPLHS 77 (113)
T ss_pred CcHHHHHHHHHh---hcCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEeccCccEEEEEEcCC
Confidence 899999999999 88999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccceEEEEEeccccccceeeecCCCCcceeeeee
Q psy3772 81 PIISSIIVKRRGDVRRAKLYYLRKCSGKSARIKEK 115 (119)
Q Consensus 81 P~I~~IeVl~~~kvrRakLyYLR~~~gK~arike~ 115 (119)
|.|++|+|+++|++|||||||||++.||+|||||+
T Consensus 78 P~I~~IeVl~~~kvrRaKLyYLR~~~gK~arike~ 112 (113)
T TIGR01024 78 PNIDSIEVVRRGKVRRAKLYYLRERRGKAARIKER 112 (113)
T ss_pred CccceEEEEEeCccchhheeeeccCcchhheeeec
Confidence 99999999999999999999999999999999996
No 4
>CHL00084 rpl19 ribosomal protein L19
Probab=100.00 E-value=4.1e-54 Score=311.74 Aligned_cols=112 Identities=50% Similarity=0.800 Sum_probs=109.2
Q ss_pred chHHHHHHHHHHHhcCCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCeeEEEEEeecCC
Q psy3772 2 NLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQLYSP 81 (119)
Q Consensus 2 ~li~~~e~~~~~~~~~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gvGVEr~f~l~SP 81 (119)
++|+.+|++|+ +.++|+|+|||||+|++++.||+|+|+|.|+|+||+++|+|+++||||||+++|+|||++||+|||
T Consensus 6 ~~i~~~~~~~~---~~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvRki~~gvGVEr~fpl~SP 82 (117)
T CHL00084 6 QLVKEIESEFL---KKNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVRKVFQGIGVERVFLLHSP 82 (117)
T ss_pred HHHHHHHHHHh---hcCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEEEeccCccEEEEEecCCC
Confidence 57899999999 889999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccceEEEEEeccccccceeeecCCCCcceeeeeec
Q psy3772 82 IISSIIVKRRGDVRRAKLYYLRKCSGKSARIKEKL 116 (119)
Q Consensus 82 ~I~~IeVl~~~kvrRakLyYLR~~~gK~arike~~ 116 (119)
.|++|||+++|++|||||||||++.||+|||||++
T Consensus 83 ~I~~IeV~r~gkvRRAKLyYLR~~~gKaarike~~ 117 (117)
T CHL00084 83 KLASIEVLRRSKVRRAKLYYLRNRVGKAARLKQKF 117 (117)
T ss_pred ccceEEEEEeCccchheeEEeccCcChhheeeccC
Confidence 99999999999999999999999999999999964
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=100.00 E-value=1.6e-53 Score=306.70 Aligned_cols=113 Identities=60% Similarity=0.984 Sum_probs=109.7
Q ss_pred CchHHHHHHHHHHHhcCCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCeeEEEEEeecC
Q psy3772 1 MNLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQLYS 80 (119)
Q Consensus 1 m~li~~~e~~~~~~~~~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gvGVEr~f~l~S 80 (119)
||||+.+|++|+ +.++|+|+|||+|+|++.+.||+++|+|.|+|+||+++++|+++||||||+++|+|||++|||||
T Consensus 1 ~~~i~~~e~~~~---~~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~~~~g~gVE~~f~l~S 77 (113)
T PF01245_consen 1 MNLIEEVEREQI---KKDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRNISQGVGVERVFPLYS 77 (113)
T ss_dssp -HHHHHHHHTTC---SSSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEEEETTEEEEEEEETTS
T ss_pred ChHHHHHHHHHh---hcCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEEEecCccEEEEEEcCC
Confidence 899999999998 89999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccceEEEEEeccccccceeeecCCCCcceeeeeec
Q psy3772 81 PIISSIIVKRRGDVRRAKLYYLRKCSGKSARIKEKL 116 (119)
Q Consensus 81 P~I~~IeVl~~~kvrRakLyYLR~~~gK~arike~~ 116 (119)
|.|++|+|++++++||||||||||++||+|||||+.
T Consensus 78 P~I~~IeV~~~~kvrRaKLyYLR~~~gK~arike~~ 113 (113)
T PF01245_consen 78 PLIKSIEVLRRGKVRRAKLYYLRDRKGKAARIKEKR 113 (113)
T ss_dssp TTEEEEEEEEEBECSSSSTGGGGCTTSHHHHHHBT-
T ss_pred CCeEEEEEEEecccchhhhhhhhcCccchhhhcccC
Confidence 999999999999999999999999999999999963
No 6
>KOG1698|consensus
Probab=100.00 E-value=6.5e-34 Score=221.14 Aligned_cols=107 Identities=34% Similarity=0.659 Sum_probs=99.5
Q ss_pred hHHHHHHHHHHHhc--CCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCeeEEEEEeecC
Q psy3772 3 LIQKIEQEEIIRLK--KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQLYS 80 (119)
Q Consensus 3 li~~~e~~~~~~~~--~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gvGVEr~f~l~S 80 (119)
+++.||.+++...+ .++|+|+|||+|+|++.+++ ++.++..|.|+||.+++.|+++||+|||+++|+|||..|||||
T Consensus 76 ~~e~Ldr~a~~~rr~~r~iPe~~~G~Iv~V~s~~p~-~k~k~s~f~Gi~I~R~~~Gl~atf~LRnvIagvGVEi~~pLYs 154 (201)
T KOG1698|consen 76 IMEILDRQAVLERRKVRDIPEFKVGSIVRVTSEDPE-NKRKVSRFKGICIRRRNAGLNATFLLRNVIAGVGVEIVFPLYS 154 (201)
T ss_pred HHHhhCHHHHHHHHhcccCCccccccEEEEEecCCc-cCCceeEEEEEEEEecccCCcceEEeeehhhCceeEEEEeccC
Confidence 67888888886643 89999999999999999996 6999999999999999999999999999999999999999999
Q ss_pred CccceEEEEEeccccccceeeecCCCCcce
Q psy3772 81 PIISSIIVKRRGDVRRAKLYYLRKCSGKSA 110 (119)
Q Consensus 81 P~I~~IeVl~~~kvrRakLyYLR~~~gK~a 110 (119)
|+|++|+|++..|++||+||||||......
T Consensus 155 P~IkeI~Vlk~~k~rra~LyYLRd~lp~ls 184 (201)
T KOG1698|consen 155 PNIKEIKVLKLEKRRRAKLYYLRDALPELS 184 (201)
T ss_pred CCeeEEEEechhhcccchhhhhhccccccC
Confidence 999999999999999999999999877544
No 7
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=87.20 E-value=4.9 Score=24.71 Aligned_cols=50 Identities=24% Similarity=0.393 Sum_probs=36.0
Q ss_pred CCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCeeEEEEEee
Q psy3772 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQL 78 (119)
Q Consensus 20 P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gvGVEr~f~l 78 (119)
+.|.+||.|.+.... ++ .=|.|+|++..+ +..+.|+=...+.|-+-.|+.
T Consensus 1 ~~~~~G~~Ve~~~~~-~~-----~W~~a~V~~~~~---~~~~~V~~~~~~~~~~e~v~~ 50 (61)
T smart00743 1 SDFKKGDRVEVFSKE-ED-----SWWEAVVTKVLG---DGKYLVRYLTESEPLKETVDW 50 (61)
T ss_pred CCcCCCCEEEEEECC-CC-----EEEEEEEEEECC---CCEEEEEECCCCcccEEEEeH
Confidence 468999999999853 23 589999999887 345777654444666666653
No 8
>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=85.70 E-value=2.9 Score=26.82 Aligned_cols=38 Identities=21% Similarity=0.404 Sum_probs=25.3
Q ss_pred CCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEE
Q psy3772 22 FVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRK 65 (119)
Q Consensus 22 f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~ 65 (119)
|++||.|.|.... +|. +-.=|.|.|+...+.+ ++.|+-
T Consensus 1 F~~G~~VEV~s~e-~g~--~gaWf~a~V~~~~~~~---~~~V~Y 38 (68)
T PF05641_consen 1 FKKGDEVEVSSDE-DGF--RGAWFPATVLKENGDD---KYLVEY 38 (68)
T ss_dssp --TT-EEEEEE-S-BTT----EEEEEEEEEEETT----EEEEEE
T ss_pred CCCCCEEEEEEcC-CCC--CcEEEEEEEEEeCCCc---EEEEEE
Confidence 7899999998753 343 6689999999999876 777765
No 9
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=73.20 E-value=9.2 Score=28.08 Aligned_cols=68 Identities=21% Similarity=0.175 Sum_probs=40.7
Q ss_pred CCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEE--eecCeeEEEEEeecCCccceEEEEEecccccc
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRK--ISYNEGIERTFQLYSPIISSIIVKRRGDVRRA 97 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~--i~~gvGVEr~f~l~SP~I~~IeVl~~~kvrRa 97 (119)
.++.||.|.|.. |.-. -=+|.|+.+-...- .++|-. +....|+|.-+|+|..+|.=+...-.-+.|.+
T Consensus 45 ~IkkGD~V~Vis----G~~K---Gk~GkV~~V~~~~~--~V~VeGvn~~k~~G~~~e~pIh~SNV~l~~l~l~~~~R~~ 114 (120)
T PRK01191 45 PVRKGDTVKVMR----GDFK---GEEGKVVEVDLKRG--RIYVEGVTVKKADGTEVPRPIHPSNVMITKLDLSDERREK 114 (120)
T ss_pred eEeCCCEEEEee----cCCC---CceEEEEEEEcCCC--EEEEeCcEEECCCCeEEEcccchhHeEEEeCccCCHHHHH
Confidence 599999999965 4211 12499999864321 233322 22345689999999888765544332333333
No 10
>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=69.58 E-value=17 Score=25.13 Aligned_cols=47 Identities=17% Similarity=0.070 Sum_probs=34.7
Q ss_pred CCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCe
Q psy3772 18 NIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNE 70 (119)
Q Consensus 18 ~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gv 70 (119)
.-|-++-||.|.+.+.. |+ =..+-...|..+..++.++.|||...|-
T Consensus 62 ~~~~V~~G~~V~i~~~~--~~----~~i~~~g~Al~~g~~G~~I~V~N~~s~k 108 (122)
T TIGR03170 62 PPWLVKRGDTVTVIARG--GG----LSVTTEGKALEDGAVGDQIRVRNLSSGK 108 (122)
T ss_pred CccEEcCCCEEEEEEec--CC----EEEEEEEEEccccCCCCEEEEEECCCCC
Confidence 45679999999999863 32 1344455777788999999999976553
No 11
>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=65.65 E-value=5.8 Score=28.84 Aligned_cols=48 Identities=27% Similarity=0.410 Sum_probs=32.5
Q ss_pred CCCCCCCC-CCEEEEE-EEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCeeEE
Q psy3772 17 KNIPDFVT-GDTIIVN-LNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIE 73 (119)
Q Consensus 17 ~~~P~f~~-GD~v~V~-~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gvGVE 73 (119)
..+|.+.. ||+|.++ ++ +|.|.|-..+..+.+-+++|.|= ..++.|..
T Consensus 68 ~~LP~v~~~GDii~l~r~k--------v~~~~~~~~~~~~~~~~ss~~vf-~~~~~~~~ 117 (146)
T PF02765_consen 68 ESLPNVKSVGDIIRLRRVK--------VQSYNGKPQGLSNSTSNSSWAVF-SSGGSGAP 117 (146)
T ss_dssp HHSCTTCSTTHEEEEEEEE--------EEEETTEEEEEEECECTEEEEEE-CTSSTTTC
T ss_pred HHCCCCCCCCCEEEEEEEE--------EEEECCEEEEEecCCCcEEEEEE-ecCCCCCC
Confidence 46899888 9999988 44 45677776676666656777764 23444543
No 12
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=65.58 E-value=18 Score=26.14 Aligned_cols=62 Identities=16% Similarity=0.133 Sum_probs=38.2
Q ss_pred CCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEe--ecCeeEEEEEeecCCccceEEEE
Q psy3772 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKI--SYNEGIERTFQLYSPIISSIIVK 89 (119)
Q Consensus 19 ~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i--~~gvGVEr~f~l~SP~I~~IeVl 89 (119)
-..++.||.|.|.- |.- .--+|.|+.+..... .+.|-.+ ....|+|.-.|+|.-+|+=+..-
T Consensus 39 ~~~IkkGD~V~Vi~----Gk~---KGk~GkV~~V~~~~~--~V~Vegvn~~k~~G~~~e~pIh~SnV~l~~l~ 102 (114)
T TIGR01080 39 ALPVRKGDKVRIMR----GDF---KGHEGKVSKVDLKRY--RIYVEGVTKEKVNGTEVPVPIHPSNVMITKLN 102 (114)
T ss_pred cceeecCCEEEEec----CCC---CCCEEEEEEEEcCCC--EEEEcCeEEECCCCeEEEeeechHHeEEEecc
Confidence 33699999999964 432 135699999875432 2222221 11235788889987777655443
No 13
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=65.24 E-value=13 Score=27.12 Aligned_cols=57 Identities=7% Similarity=0.102 Sum_probs=35.5
Q ss_pred CCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCeeEEEEEeec
Q psy3772 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQLY 79 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gvGVEr~f~l~ 79 (119)
...|+|++|++|.. +|..-.+..++-.--+++ ++....+.+||+..|.=+|.+|+-.
T Consensus 6 ~~~~~lrkG~~i~~-----~g~p~~V~~~~~~kpGkh-g~a~vr~k~knL~tG~~~e~~~~s~ 62 (129)
T PRK03999 6 VEVGELKEGSYVVI-----DGEPCKIVEISKSKPGKH-GSAKARIVAIGIFDGQKRSLVQPVD 62 (129)
T ss_pred ccHHHccCCCEEEE-----CCEEEEEEEEEeecCCCC-CcEEEEEEEEECCCCCEEEEEecCC
Confidence 35688999999954 343222223322222221 1235678899999999999999743
No 14
>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=65.14 E-value=13 Score=24.97 Aligned_cols=33 Identities=27% Similarity=0.492 Sum_probs=21.9
Q ss_pred CCCCCCEEEEEEEEecCCccccceEEEEEEEEe
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRR 53 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r 53 (119)
.|.|||++.|++.+.+.++..++...--++..-
T Consensus 15 ~~~~Ge~i~v~v~i~n~s~~~i~~I~v~L~~~~ 47 (136)
T PF02752_consen 15 AYVPGETIPVNVEIDNQSKKKIKKIKVSLVERI 47 (136)
T ss_dssp EEETT--EEEEEEEEE-SSSEEEEEEEEEEEEE
T ss_pred EECCCCEEEEEEEEEECCCCEEEEEEEEEEEEE
Confidence 489999999999998777766666555555433
No 15
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=63.20 E-value=9 Score=27.35 Aligned_cols=42 Identities=19% Similarity=0.503 Sum_probs=30.8
Q ss_pred CCCCCCCCCCEEEEEEEE--ecC-CccccceEEEEEEEEecCCCc
Q psy3772 17 KNIPDFVTGDTIIVNLNV--IEG-TRKRIQAYEGIVISRRNKGLN 58 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~i--~eg-~k~r~q~f~GvvI~~r~~g~~ 58 (119)
+-+-+|.+||.|-+.+.= ..| .-.|.|-..|+|+..+++...
T Consensus 28 r~l~ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~ 72 (98)
T COG2139 28 RYLQEYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYK 72 (98)
T ss_pred hHHhhccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEE
Confidence 456689999999887631 112 357889999999999987543
No 16
>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=62.97 E-value=15 Score=26.48 Aligned_cols=41 Identities=27% Similarity=0.419 Sum_probs=31.0
Q ss_pred CCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEE
Q psy3772 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRK 65 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~ 65 (119)
.++|.+.+||+|.++=. ++|.|.|-..+..+. -.+++-|=+
T Consensus 64 ~~LP~v~~GDVIll~~~-------kv~~~~g~~~~~~~~-~~ss~avf~ 104 (138)
T cd04497 64 ESLPIVKVGDIILLRRV-------KIQSYNGKPQGISND-RGSSWAVFR 104 (138)
T ss_pred hhCCCCCCCCEEEEEEE-------EEEEECCceEEEECC-CceeEEEEc
Confidence 56898899999999742 367888988888776 456676633
No 17
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=61.90 E-value=39 Score=22.99 Aligned_cols=52 Identities=21% Similarity=0.253 Sum_probs=36.2
Q ss_pred CCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCC----CceeEEEEEeecCe
Q psy3772 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKG----LNSNFIVRKISYNE 70 (119)
Q Consensus 19 ~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g----~~~tftlR~i~~gv 70 (119)
+..++|||+|-|.-.-..++...-.-..|-||...+.. ..|=|.+=++-.|+
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 56789999999976543334445567899999987642 35558887765553
No 18
>PF03888 MucB_RseB: MucB/RseB family; InterPro: IPR005588 The members of this family are regulators of the anti-sigma E protein RseD.; PDB: 2P4B_B 2V42_B 2V43_A 3M4W_A.
Probab=61.45 E-value=39 Score=27.40 Aligned_cols=51 Identities=31% Similarity=0.342 Sum_probs=36.8
Q ss_pred cccceEEEEEEEEecCCCceeEEEEEeecCeeEEEEEeecCCccceEEEEEecc
Q psy3772 40 KRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQLYSPIISSIIVKRRGD 93 (119)
Q Consensus 40 ~r~q~f~GvvI~~r~~g~~~tftlR~i~~gvGVEr~f~l~SP~I~~IeVl~~~k 93 (119)
-+.+.|+|+.+-.++..+.+.=.+....+|.-.|+.-.|..|.. ||+|++.
T Consensus 8 ~~~lnY~g~fv~~~~~~~~s~ri~H~~~~~~e~ErL~~LdG~~r---eviR~~d 58 (285)
T PF03888_consen 8 ARQLNYEGTFVYQRGGQMESMRIRHAVDDGGEYERLESLDGPPR---EVIRRGD 58 (285)
T ss_dssp HHHSEEEEEEEEEETTEEEEEEEEEEEETTEEEEEEEE-SSS-----EEEEETT
T ss_pred HHhCCeEEEEEEEeCCeEEEEEEEEEeeCCEEEEEEEecCCCcE---EEEEECC
Confidence 35689999999998876554434444567778999999999875 8888864
No 19
>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=60.65 E-value=8.5 Score=27.57 Aligned_cols=20 Identities=25% Similarity=0.356 Sum_probs=13.0
Q ss_pred CCCCCCCCCCEEEEEEEEec
Q psy3772 17 KNIPDFVTGDTIIVNLNVIE 36 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~i~e 36 (119)
-.+|++++||+|...+.+..
T Consensus 85 ~~~p~v~~GdiIe~~y~~~~ 104 (177)
T PF12969_consen 85 FAFPDVRVGDIIEYSYTIKS 104 (177)
T ss_dssp EE--S--TT-EEEEEEEEEE
T ss_pred EEcCCCCCCcEEEEEEEEEe
Confidence 57999999999999999864
No 20
>cd01737 LSm16_N LSm16 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function.
Probab=58.56 E-value=20 Score=23.64 Aligned_cols=34 Identities=15% Similarity=0.341 Sum_probs=22.4
Q ss_pred CCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEE
Q psy3772 24 TGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRK 65 (119)
Q Consensus 24 ~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~ 65 (119)
.|+.|.++-- +-+-.|+|.|.++.-.- -|+.+++
T Consensus 5 iGs~VSI~C~------~~lGVyQG~i~~V~~~~--qTI~l~~ 38 (62)
T cd01737 5 LGSIVSINCG------ETLGVYQGLVSAVDQES--QTISLAF 38 (62)
T ss_pred cceEEEEecC------CceEEEEEEEEEeCccc--eEEEEee
Confidence 5777777653 23559999999987643 3454444
No 21
>PF13144 SAF_2: SAF-like
Probab=57.63 E-value=45 Score=24.90 Aligned_cols=47 Identities=17% Similarity=0.156 Sum_probs=35.3
Q ss_pred CCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecC
Q psy3772 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYN 69 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~g 69 (119)
...|.++.||.|.|.+.. |. =..+--.+|..+..++.++.|+|...|
T Consensus 135 ~~~~~V~~G~~V~v~~~~--g~----i~i~~~g~Al~~G~~G~~I~V~N~~S~ 181 (196)
T PF13144_consen 135 EPPPLVKRGDIVTVIARS--GG----ISISTEGKALEDGALGDTIRVKNLSSG 181 (196)
T ss_pred ccceecCCCCEEEEEEEe--CC----EEEEEEEEEccCCCCCCEEEEEECCCC
Confidence 345789999999998864 32 234445578888899999999997654
No 22
>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=54.46 E-value=41 Score=20.99 Aligned_cols=49 Identities=18% Similarity=0.393 Sum_probs=28.7
Q ss_pred CCCCCCEEEEEEEEecCCccccceEEEEEEEEecCC-CceeEEEEEeecCeeEEEEEe
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKG-LNSNFIVRKISYNEGIERTFQ 77 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g-~~~tftlR~i~~gvGVEr~f~ 77 (119)
++++|.+|.+ +|+--.+..++-+ .-++| .--.+.+||+..|.-+|.+|.
T Consensus 4 dlr~G~~i~~-----~g~~~~V~~~~~~---k~gkg~a~v~~klknl~tG~~~e~tf~ 53 (58)
T PF08207_consen 4 DLRKGMVIEI-----DGEPYVVLDFQHV---KPGKGGAFVRVKLKNLRTGSKVEKTFR 53 (58)
T ss_dssp G--TTSEEEE-----TTEEEEEEEEEEE---CCTTSSSEEEEEEEETTTTEEEEEEEE
T ss_pred HccCCCEEEE-----CCEEEEEEEEEEE---CCCCCCeEEEEEEEECCCCCEEEEEEC
Confidence 5788988865 4533333333211 12333 233566999999999999995
No 23
>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=53.60 E-value=34 Score=24.14 Aligned_cols=31 Identities=23% Similarity=0.502 Sum_probs=25.4
Q ss_pred CCCCCCEEEEEEEEecCCccccceEEEEEEEEecCC
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKG 56 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g 56 (119)
.+.||+.+.|++.-.++ ..|.|..|.-+..+
T Consensus 29 ~y~pG~~~~Vtl~~~~~-----~~F~GF~lqAr~~~ 59 (135)
T cd08544 29 SYVPGETYTVTLSGSSP-----SPFRGFLLQARDAS 59 (135)
T ss_pred EECCCCEEEEEEECCCC-----CceeEEEEEEEcCC
Confidence 68999999999974322 69999999988865
No 24
>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=50.65 E-value=15 Score=29.40 Aligned_cols=36 Identities=25% Similarity=0.399 Sum_probs=18.9
Q ss_pred CCCCCCCCCEEEEEEEEecCCccccceE----EEEEEEEec
Q psy3772 18 NIPDFVTGDTIIVNLNVIEGTRKRIQAY----EGIVISRRN 54 (119)
Q Consensus 18 ~~P~f~~GD~v~V~~~i~eg~k~r~q~f----~GvvI~~r~ 54 (119)
.-|.|.+||.|+|.-.-+.+ -+|+..| .|+|....+
T Consensus 131 ~~~~F~vGd~Vrv~~~~~~~-HtR~P~Y~rg~~G~I~~~~g 170 (222)
T PF02211_consen 131 APPRFAVGDRVRVRNLPPPG-HTRLPRYVRGKTGTIERVHG 170 (222)
T ss_dssp SS-SS-TT-EEEE-----SS---SS-GGGTT-EEEEEEEEE
T ss_pred CCCCCCCCCEEEECCCCCCC-cccccHhhCCCeeEEEEEec
Confidence 46789999999998766653 6777665 688887665
No 25
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=48.28 E-value=37 Score=17.20 Aligned_cols=27 Identities=30% Similarity=0.423 Sum_probs=18.3
Q ss_pred CCCCCCEEEEEEEEecCCccccceEEEEEEEEec
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~ 54 (119)
.|.+||.|.|.- |. ..-+.|.++.+.+
T Consensus 1 ~~~~G~~V~I~~----G~---~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIA----GP---FKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeE----CC---CCCcEEEEEEEcC
Confidence 378999999874 42 2345788777654
No 26
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=48.21 E-value=57 Score=25.61 Aligned_cols=48 Identities=8% Similarity=0.039 Sum_probs=34.4
Q ss_pred CCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCe
Q psy3772 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNE 70 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gv 70 (119)
..-|-++.||.|.|.+.. |. =...--..|..+.+++.++.|||...|-
T Consensus 172 ~~~~~V~~G~~V~i~~~~--g~----~~i~~~G~Al~~G~~Gd~IrVrN~~Sgk 219 (235)
T PRK07018 172 RQAWVVCKGQTVSIIARG--DG----FSVKTEGEALNDGAVGQQIRVRNMASGQ 219 (235)
T ss_pred cCccEeCCCCEEEEEEec--CC----EEEEEEEEEcCCCCCCCeEEEEECCCCC
Confidence 345679999999999863 21 1233444677788999999999976653
No 27
>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=47.73 E-value=64 Score=19.73 Aligned_cols=35 Identities=26% Similarity=0.535 Sum_probs=24.2
Q ss_pred CCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEE
Q psy3772 22 FVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIV 63 (119)
Q Consensus 22 f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftl 63 (119)
|.+|+.|.+.. .+| +.+++-|+.++..+-...|.|
T Consensus 1 ~~vG~~v~~~~--~~~-----~~y~A~I~~~r~~~~~~~YyV 35 (55)
T PF11717_consen 1 FEVGEKVLCKY--KDG-----QWYEAKILDIREKNGEPEYYV 35 (55)
T ss_dssp --TTEEEEEEE--TTT-----EEEEEEEEEEEECTTCEEEEE
T ss_pred CCcCCEEEEEE--CCC-----cEEEEEEEEEEecCCCEEEEE
Confidence 67899998887 233 699999999997654444444
No 28
>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=47.10 E-value=14 Score=25.12 Aligned_cols=13 Identities=23% Similarity=0.381 Sum_probs=8.4
Q ss_pred CCCCCCCEEEEEE
Q psy3772 20 PDFVTGDTIIVNL 32 (119)
Q Consensus 20 P~f~~GD~v~V~~ 32 (119)
-.|+|||+|+=.+
T Consensus 67 ~~FrpGDIVrA~V 79 (82)
T PF10447_consen 67 DCFRPGDIVRARV 79 (82)
T ss_dssp GT--SSSEEEEEE
T ss_pred hccCCCCEEEEEE
Confidence 3599999998654
No 29
>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=45.76 E-value=71 Score=19.66 Aligned_cols=43 Identities=19% Similarity=0.318 Sum_probs=28.6
Q ss_pred CCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCe
Q psy3772 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNE 70 (119)
Q Consensus 19 ~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gv 70 (119)
.|.|.+||+|-|.-... ..-.|-+++.+..| ..+++|++....
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 58899999998875321 23445555555444 568888887765
No 30
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=45.25 E-value=15 Score=23.14 Aligned_cols=11 Identities=27% Similarity=0.537 Sum_probs=9.2
Q ss_pred CCCCCEEEEEE
Q psy3772 22 FVTGDTIIVNL 32 (119)
Q Consensus 22 f~~GD~v~V~~ 32 (119)
|.+||+|+...
T Consensus 1 f~~GDvV~LKS 11 (53)
T PF09926_consen 1 FKIGDVVQLKS 11 (53)
T ss_pred CCCCCEEEEcc
Confidence 78999998864
No 31
>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=45.23 E-value=1.1e+02 Score=21.84 Aligned_cols=43 Identities=14% Similarity=0.138 Sum_probs=28.2
Q ss_pred CCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCee
Q psy3772 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEG 71 (119)
Q Consensus 20 P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gvG 71 (119)
+.|.+||.|+|. +|. .+-|+|.++...+... -.+|.=...+.-
T Consensus 85 ~~~~~Gd~V~I~----~GP---f~G~~g~v~~~d~~k~--~v~v~l~~~~~~ 127 (145)
T TIGR00405 85 ESIKKGDIVEII----SGP---FKGERAKVIRVDESKE--EVTLELIEAAVP 127 (145)
T ss_pred cccCCCCEEEEe----ecC---CCCCeEEEEEEcCCCC--EEEEEEEEcCcc
Confidence 469999999986 364 4678899999876443 344433334443
No 32
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=45.22 E-value=13 Score=31.66 Aligned_cols=16 Identities=38% Similarity=0.611 Sum_probs=13.6
Q ss_pred CCCCCCCCCCEEEEEE
Q psy3772 17 KNIPDFVTGDTIIVNL 32 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~ 32 (119)
--+|+|+|||+|.+.-
T Consensus 242 vrip~~~~gDiV~~~~ 257 (355)
T COG1499 242 VRIPEFRPGDIVSVRG 257 (355)
T ss_pred EECCCCCCCCEEEECC
Confidence 3589999999999864
No 33
>PRK15136 multidrug efflux system protein EmrA; Provisional
Probab=45.22 E-value=52 Score=27.62 Aligned_cols=32 Identities=13% Similarity=0.333 Sum_probs=24.0
Q ss_pred CCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEe
Q psy3772 18 NIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRR 53 (119)
Q Consensus 18 ~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r 53 (119)
++..+++|+.|.|.+-.-.+. ..|.|.|..+.
T Consensus 262 ~l~~v~~Gq~V~I~~da~p~~----~~~~G~V~~I~ 293 (390)
T PRK15136 262 QLANMRIGQPATITSDIYGDD----VVYTGKVVGLD 293 (390)
T ss_pred HHhcCCCCCEEEEEEecCCCC----ceEEEEEEEEC
Confidence 566799999999987532221 37999999984
No 34
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=44.91 E-value=86 Score=23.68 Aligned_cols=61 Identities=18% Similarity=0.190 Sum_probs=35.7
Q ss_pred CCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEe--ecCeeEEEEEeecCCccceEE
Q psy3772 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKI--SYNEGIERTFQLYSPIISSII 87 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i--~~gvGVEr~f~l~SP~I~~Ie 87 (119)
+.+ .++.||+|.|.. |.-. -=+|.|+++-...- .+.|-.+ ....|-..-+|+|..+|.=+.
T Consensus 43 Rs~-~IkkGD~V~Vi~----Gk~K---Gk~GkV~~V~~k~~--~ViVEgvn~~Kk~gk~~e~PIh~SNV~iv~ 105 (143)
T PTZ00194 43 RSM-PVRKDDEVMVVR----GHHK---GREGKVTAVYRKKW--VIHIEKITREKANGEPVQIGIHPSNVIITK 105 (143)
T ss_pred ccc-eeecCCEEEEec----CCCC---CCceEEEEEEcCCC--EEEEeCeEEEecCCCEeecCcCchheEEEc
Confidence 444 599999999964 4322 12399999865432 3333222 223344456788888775443
No 35
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=44.79 E-value=1.1e+02 Score=22.40 Aligned_cols=29 Identities=28% Similarity=0.503 Sum_probs=22.3
Q ss_pred CCCCCCCEEEEEEEEecCCccccceEEEEEEEEecC
Q psy3772 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNK 55 (119)
Q Consensus 20 P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~ 55 (119)
+.|.+||.|+|. +|. .+-|+|+++...+.
T Consensus 118 ~~~~~G~~V~I~----~Gp---f~G~~g~v~~~~~~ 146 (172)
T TIGR00922 118 IDFEVGEQVRVN----DGP---FANFTGTVEEVDYE 146 (172)
T ss_pred cCCCCCCEEEEe----ecC---CCCcEEEEEEEcCC
Confidence 348999999986 464 46789999998743
No 36
>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=44.15 E-value=1e+02 Score=25.34 Aligned_cols=38 Identities=13% Similarity=0.193 Sum_probs=26.6
Q ss_pred CCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEE
Q psy3772 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIV 63 (119)
Q Consensus 19 ~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftl 63 (119)
.++|.+||.|+|.- |. .+-|+|.++......-...+.|
T Consensus 203 ~~~f~vGd~VrI~d----GP---F~GfeG~I~eid~~k~Rv~VlV 240 (258)
T TIGR01956 203 LSKFRVGNFVKIVD----GP---FKGIVGKIKKIDQEKKKAIVEV 240 (258)
T ss_pred ccCCCCCCEEEEEe----cC---CCCcEEEEEEEeCCCCEEEEEE
Confidence 46699999999863 54 5689999999975332333333
No 37
>COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms]
Probab=44.11 E-value=92 Score=26.52 Aligned_cols=56 Identities=18% Similarity=0.202 Sum_probs=41.4
Q ss_pred CCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecC-C--------CceeEEEEEeecCeeEEEEE
Q psy3772 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNK-G--------LNSNFIVRKISYNEGIERTF 76 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~-g--------~~~tftlR~i~~gvGVEr~f 76 (119)
.+++.++||+-++|++..-.++ ..|+|+|-++... | .+.|+..=++.+.+.|...|
T Consensus 254 TqL~~~r~Gq~a~I~~da~~~~----~~~~G~v~~i~~~tg~~fsllp~~natgN~tkvvQRvPVrI~l 318 (352)
T COG1566 254 TQLARVRPGQPAEITLDAYPGN----GVVEGIVEGIAPATGSAFSLLPAQNATGNWTKVVQRVPVRIEL 318 (352)
T ss_pred eecCcccCCCeEEEEEEcCCCc----eEEEEEEEEecCCcccccccCCCccCCCCEEEEEEeeeEEEEe
Confidence 5789999999999999754332 6899999999843 2 13455555678888877666
No 38
>PRK09455 rseB anti-sigma E factor; Provisional
Probab=44.09 E-value=1.1e+02 Score=25.37 Aligned_cols=52 Identities=19% Similarity=0.291 Sum_probs=39.2
Q ss_pred CccccceEEEEEEEEecCCCceeEEEEEee-cCeeEEEEEeecCCccceEEEEEecc
Q psy3772 38 TRKRIQAYEGIVISRRNKGLNSNFIVRKIS-YNEGIERTFQLYSPIISSIIVKRRGD 93 (119)
Q Consensus 38 ~k~r~q~f~GvvI~~r~~g~~~tftlR~i~-~gvGVEr~f~l~SP~I~~IeVl~~~k 93 (119)
+..+.+.|+|+.+-.++..+ +|+.++-.. +|.=.|+.-.|..|.- ||+|++.
T Consensus 37 ~A~~~lnY~g~fV~~~~~~i-~s~ri~H~~~~~~e~erL~~LdG~~r---EviR~~d 89 (319)
T PRK09455 37 EASQSLNYELSFINITKQGI-ESLRYRHARLDNKPLAQLLQMDGPRR---EIIQRGN 89 (319)
T ss_pred HHHHhCCeEEEEEEEeCCeE-EEEEEEEEEeCCEEEEEEEecCCCce---EEEEECC
Confidence 45677999999999997655 456666554 4566999999988874 8888763
No 39
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=42.55 E-value=1e+02 Score=23.62 Aligned_cols=32 Identities=22% Similarity=0.314 Sum_probs=23.8
Q ss_pred CCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecC
Q psy3772 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNK 55 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~ 55 (119)
....+|.+||.|+|.- |. .-.|.|.|+.....
T Consensus 119 ~~~~~~e~Gd~VrI~~----Gp---Fa~f~g~V~evd~e 150 (178)
T COG0250 119 KPKVDFEPGDVVRIID----GP---FAGFKAKVEEVDEE 150 (178)
T ss_pred cccccCCCCCEEEEec----cC---CCCccEEEEEEcCc
Confidence 4456799999999853 53 23688899998865
No 40
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=41.96 E-value=36 Score=22.91 Aligned_cols=31 Identities=32% Similarity=0.457 Sum_probs=22.2
Q ss_pred cCCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEe
Q psy3772 16 KKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRR 53 (119)
Q Consensus 16 ~~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r 53 (119)
+++=-+|++||++...-+.. | .|.|-.+..+
T Consensus 23 RkNDRdf~VGD~L~L~E~~~-~------~YTGr~~~~~ 53 (72)
T PF12961_consen 23 RKNDRDFQVGDILVLREWDN-G------EYTGREIEAE 53 (72)
T ss_pred EecCCCCCCCCEEEEEEecC-C------CccccEEEEE
Confidence 35555899999999987643 3 6777776544
No 41
>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=41.95 E-value=66 Score=23.22 Aligned_cols=37 Identities=19% Similarity=0.321 Sum_probs=27.7
Q ss_pred CCCCCCCCCEEEEEEEEe--cCCccccceEEEEEEEEec
Q psy3772 18 NIPDFVTGDTIIVNLNVI--EGTRKRIQAYEGIVISRRN 54 (119)
Q Consensus 18 ~~P~f~~GD~v~V~~~i~--eg~k~r~q~f~GvvI~~r~ 54 (119)
..+.-..||+|.|.++-. .+.-++-|.+.|+|+..+.
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 456678999999999764 4444555899999999775
No 42
>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=41.88 E-value=34 Score=20.36 Aligned_cols=15 Identities=27% Similarity=0.390 Sum_probs=12.5
Q ss_pred CCCCCEEEEEEEEec
Q psy3772 22 FVTGDTIIVNLNVIE 36 (119)
Q Consensus 22 f~~GD~v~V~~~i~e 36 (119)
|++||.|.|.+.-.+
T Consensus 45 ~~~Gd~v~v~i~~vd 59 (68)
T cd05688 45 VNVGDEVEVKVLKID 59 (68)
T ss_pred ECCCCEEEEEEEEEE
Confidence 899999999876544
No 43
>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=40.84 E-value=71 Score=20.73 Aligned_cols=45 Identities=24% Similarity=0.257 Sum_probs=25.0
Q ss_pred CCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEee
Q psy3772 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKIS 67 (119)
Q Consensus 19 ~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~ 67 (119)
.|.|.+||+|-|.-.... .. ..-.|-++..+..+-...+.++++.
T Consensus 9 ~P~l~~GD~vlv~~~~~~---~~-~~~~Gdivv~~~~~~~~~~~vkRv~ 53 (90)
T TIGR02754 9 SPTLPPGDRIIVVPWLKI---FR-VPPIGNVVVVRHPLQPYGLIIKRLA 53 (90)
T ss_pred cCccCCCCEEEEEEcccc---CC-CCCCCeEEEEecCCCCcceEEEEee
Confidence 589999999988742110 11 1112655554443333457777764
No 44
>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=40.73 E-value=39 Score=19.37 Aligned_cols=15 Identities=27% Similarity=0.406 Sum_probs=12.5
Q ss_pred CCCCCCEEEEEEEEe
Q psy3772 21 DFVTGDTIIVNLNVI 35 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~ 35 (119)
.|++||+|.+.+.-.
T Consensus 41 ~~~~G~~v~~~v~~~ 55 (65)
T cd00164 41 VFKVGDEVEVKVLEV 55 (65)
T ss_pred EeCCCCEEEEEEEEE
Confidence 499999999998643
No 45
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=40.40 E-value=53 Score=23.63 Aligned_cols=29 Identities=17% Similarity=0.402 Sum_probs=22.3
Q ss_pred CCCCCCCEEEEEEEEecCCccccceEEEEEEEEecC
Q psy3772 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNK 55 (119)
Q Consensus 20 P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~ 55 (119)
+.|.+||.|+|. +|. .+-|+|++....+.
T Consensus 107 ~~~~~G~~V~V~----~GP---f~g~~g~v~~~~~~ 135 (159)
T TIGR01955 107 TLPYKGDKVRIT----DGA---FAGFEAIFLEPDGE 135 (159)
T ss_pred cCCCCCCEEEEe----ccC---CCCcEEEEEEECCC
Confidence 348999999875 464 46799999998743
No 46
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=40.27 E-value=50 Score=24.05 Aligned_cols=27 Identities=22% Similarity=0.428 Sum_probs=21.8
Q ss_pred CCCCCCEEEEEEEEecCCccccceEEEEEEEEec
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~ 54 (119)
.|.+||.|+|. +|. .+-|+|++....+
T Consensus 109 ~~~~G~~V~I~----~Gp---~~g~eg~v~~~~~ 135 (162)
T PRK09014 109 TPKPGDKVIIT----EGA---FEGLQAIYTEPDG 135 (162)
T ss_pred CCCCCCEEEEe----cCC---CCCcEEEEEEeCC
Confidence 48899999885 464 5789999998874
No 47
>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=40.19 E-value=22 Score=21.67 Aligned_cols=44 Identities=16% Similarity=0.397 Sum_probs=24.5
Q ss_pred CCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCee
Q psy3772 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEG 71 (119)
Q Consensus 19 ~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gvG 71 (119)
.|.|.+||+|-|.-.. ....|=++.....|-. ..+++++....|
T Consensus 8 ~P~i~~Gd~v~v~~~~--------~~~~gdivv~~~~~~~-~~~iKrv~~~~~ 51 (70)
T PF00717_consen 8 EPTIKDGDIVLVDPSS--------EPKDGDIVVVKIDGDE-ELYIKRVVGEPG 51 (70)
T ss_dssp GGTSSTTEEEEEEETS-----------TTSEEEEEETTEE-SEEEEEEEEETT
T ss_pred ccCeeCCCEEEEEEcC--------CCccCeEEEEEECCce-eeEEEEEEEeCC
Confidence 4889999999887422 2333333333333211 588888775443
No 48
>KOG3409|consensus
Probab=40.09 E-value=59 Score=25.75 Aligned_cols=16 Identities=19% Similarity=0.389 Sum_probs=12.4
Q ss_pred CCCCCCCCCEEEEEEE
Q psy3772 18 NIPDFVTGDTIIVNLN 33 (119)
Q Consensus 18 ~~P~f~~GD~v~V~~~ 33 (119)
-+-.|+|||+|.-.+-
T Consensus 119 v~ksFrPgDiVlAkVi 134 (193)
T KOG3409|consen 119 VYKSFRPGDIVLAKVI 134 (193)
T ss_pred hhhccCCCcEEEEEEe
Confidence 4556999999987663
No 49
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=39.50 E-value=1.1e+02 Score=22.95 Aligned_cols=49 Identities=8% Similarity=0.033 Sum_probs=33.8
Q ss_pred CCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCeeE
Q psy3772 18 NIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGI 72 (119)
Q Consensus 18 ~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gvGV 72 (119)
+-|-++-||.|.+.+... | =...-.-+|..+.+.+.++.|||...|-=|
T Consensus 97 ~p~~V~rG~~V~i~~~~~-g-----~~i~~~G~Al~~G~~Gd~IrVrN~~Sgkiv 145 (160)
T PRK06005 97 EPSLVTRGSPVKLVFSAG-G-----LTITAAGTPLQSGAAGDLIRVRNVDSGVIV 145 (160)
T ss_pred CCcEEeCCCEEEEEEecC-C-----EEEEEEEEEcccCCCCCEEEEEECCCCCEE
Confidence 445699999999998632 2 122233366678889999999998666444
No 50
>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=38.41 E-value=42 Score=20.63 Aligned_cols=15 Identities=27% Similarity=0.485 Sum_probs=12.2
Q ss_pred CCCCCEEEEEEEEec
Q psy3772 22 FVTGDTIIVNLNVIE 36 (119)
Q Consensus 22 f~~GD~v~V~~~i~e 36 (119)
|++||.|+|.+.-.+
T Consensus 48 ~~~Gd~v~v~i~~vd 62 (77)
T cd05708 48 FRVGDKVRAKVLKID 62 (77)
T ss_pred ecCCCEEEEEEEEEe
Confidence 899999999876543
No 51
>PRK00529 elongation factor P; Validated
Probab=38.30 E-value=98 Score=23.66 Aligned_cols=51 Identities=22% Similarity=0.338 Sum_probs=33.2
Q ss_pred CCCCCCCCEEEEEEEEecCCccccceEEEEEEEEe----cCC-CceeEEEEEeecCeeEEEEEeecCC
Q psy3772 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRR----NKG-LNSNFIVRKISYNEGIERTFQLYSP 81 (119)
Q Consensus 19 ~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r----~~g-~~~tftlR~i~~gvGVEr~f~l~SP 81 (119)
.-+|++||+|.+ +|. .| .|+... |+| .--.+.+|++..|.-.|.+|+-...
T Consensus 4 a~~ik~G~~I~~-----~g~-----~~--~V~~~~~~kpGkg~A~vrvk~knL~tG~~~e~~f~~~e~ 59 (186)
T PRK00529 4 ANDLRKGLVIEI-----DGE-----PY--VVLEFEHVKPGKGQAFVRTKLKNLLTGSVVEKTFKAGDK 59 (186)
T ss_pred hhhcCCCCEEEE-----CCE-----EE--EEEEEEEeeCCCCceEEEEEEEECCCCCeEEEEeCCCCE
Confidence 346899999965 342 33 233322 332 2346779999999999999987543
No 52
>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=38.08 E-value=33 Score=24.19 Aligned_cols=32 Identities=19% Similarity=0.454 Sum_probs=23.5
Q ss_pred CCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCC
Q psy3772 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKG 56 (119)
Q Consensus 20 P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g 56 (119)
..+.||+.+.|++.. ...+.|.|..|.-+...
T Consensus 28 ~~y~pg~~~~Vtl~~-----~~~~~F~GFllqAr~~~ 59 (132)
T PF02014_consen 28 SSYEPGQTYTVTLSS-----SGSSSFRGFLLQARDAN 59 (132)
T ss_dssp SSB-TTBEEEEEEEE-----TTTEEBSEEEEEEEETT
T ss_pred CeEcCCCEEEEEEEC-----CCCCceeEEEEEEEeCC
Confidence 358999999999932 22479999999888543
No 53
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=37.61 E-value=87 Score=18.39 Aligned_cols=35 Identities=23% Similarity=0.416 Sum_probs=27.7
Q ss_pred CCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEE
Q psy3772 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVR 64 (119)
Q Consensus 20 P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR 64 (119)
+.+.+|+.+.+.+ .+| +-|.|.|+...+. .++.|.
T Consensus 1 ~~~~~G~~~~a~~--~d~-----~wyra~I~~~~~~---~~~~V~ 35 (57)
T smart00333 1 PTFKVGDKVAARW--EDG-----EWYRARIIKVDGE---QLYEVF 35 (57)
T ss_pred CCCCCCCEEEEEe--CCC-----CEEEEEEEEECCC---CEEEEE
Confidence 3689999999998 345 5999999999875 456665
No 54
>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=37.26 E-value=75 Score=21.27 Aligned_cols=29 Identities=17% Similarity=0.549 Sum_probs=20.2
Q ss_pred CCCCCCEEEEEEEEecCCccccceEEEEEE
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVI 50 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI 50 (119)
...|||++.+.+.+.+ .....-.|.+.+.
T Consensus 88 ~v~pgd~l~i~~~i~~-~~~~~~~~~~~~~ 116 (131)
T cd00493 88 PVLPGDTLTLEVELLK-VRRGLGKFDGRAY 116 (131)
T ss_pred CcCCCCEEEEEEEEEE-eeCCEEEEEEEEE
Confidence 3679999999999875 2345566666554
No 55
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=36.97 E-value=73 Score=23.21 Aligned_cols=35 Identities=20% Similarity=0.325 Sum_probs=25.8
Q ss_pred CCCCCCCEEEEEEEE--ecCCccccceEEEEEEEEec
Q psy3772 20 PDFVTGDTIIVNLNV--IEGTRKRIQAYEGIVISRRN 54 (119)
Q Consensus 20 P~f~~GD~v~V~~~i--~eg~k~r~q~f~GvvI~~r~ 54 (119)
+.-..||+|.|.++- +++.-.+-|.+.|+|+..+.
T Consensus 31 ~~a~iGD~I~vsVkk~~~~~~~kkg~v~~AvIVrtkk 67 (122)
T PRK05483 31 RYASIGDVIVVSVKEAIPRGKVKKGDVVKAVVVRTKK 67 (122)
T ss_pred CccccCCEEEEEEEEcCCCCcccCCCEeeEEEEEecc
Confidence 567899999999873 22223455899999998774
No 56
>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=36.95 E-value=45 Score=20.22 Aligned_cols=20 Identities=20% Similarity=0.330 Sum_probs=14.4
Q ss_pred CCCCCEEEEEEEEecCCccc
Q psy3772 22 FVTGDTIIVNLNVIEGTRKR 41 (119)
Q Consensus 22 f~~GD~v~V~~~i~eg~k~r 41 (119)
|++||.|.|.+.-.+-++.|
T Consensus 46 ~~~G~~v~v~v~~id~~~~~ 65 (69)
T cd05690 46 YKKGQEVEAVVLNIDVERER 65 (69)
T ss_pred ECCCCEEEEEEEEEECCcCE
Confidence 89999999997654434443
No 57
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=36.85 E-value=1.2e+02 Score=19.79 Aligned_cols=20 Identities=20% Similarity=0.330 Sum_probs=15.6
Q ss_pred CCCCCCCCCCEEEEEEEEec
Q psy3772 17 KNIPDFVTGDTIIVNLNVIE 36 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~i~e 36 (119)
.|-|-.+|||+|.+...+..
T Consensus 6 TDr~iYrPGetV~~~~~~~~ 25 (99)
T PF01835_consen 6 TDRPIYRPGETVHFRAIVRD 25 (99)
T ss_dssp ESSSEE-TTSEEEEEEEEEE
T ss_pred CCccCcCCCCEEEEEEEEec
Confidence 46788999999999998643
No 58
>TIGR00192 urease_beta urease, beta subunit. In a number of species, including B.subtilis, Synechocystis, and Haemophilus influenzae, urease subunits beta and gamma are encoded as separate polypeptides. In Helicobacter pylori UreA and in the fission yeast Schizosaccharomyces pombe, beta subunit-like sequence follows gamma subunit-like sequence in a single chain; the fission yeast protein contains additional C-terminal regions.
Probab=36.82 E-value=33 Score=24.60 Aligned_cols=33 Identities=36% Similarity=0.711 Sum_probs=24.2
Q ss_pred cCCCCC-----CCCCCEEEEEEEEecCCccccceEEEEE
Q psy3772 16 KKNIPD-----FVTGDTIIVNLNVIEGTRKRIQAYEGIV 49 (119)
Q Consensus 16 ~~~~P~-----f~~GD~v~V~~~i~eg~k~r~q~f~Gvv 49 (119)
+-|+|. |.|||+-.|++--- |-+.++.=|.|.|
T Consensus 60 RLdIpaGTavRFEPG~~k~V~LV~~-gG~r~v~G~~gl~ 97 (101)
T TIGR00192 60 RLDIPSGTAVRFEPGEEKSVELVAI-GGNRRIYGFNGLV 97 (101)
T ss_pred ccccCCCCeEeECCCCeEEEEEEEc-cCceEEEccCccc
Confidence 468886 99999999998654 4455566666654
No 59
>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=36.45 E-value=28 Score=23.05 Aligned_cols=18 Identities=22% Similarity=0.364 Sum_probs=13.9
Q ss_pred CCCCCCCCCEEEEEEEEe
Q psy3772 18 NIPDFVTGDTIIVNLNVI 35 (119)
Q Consensus 18 ~~P~f~~GD~v~V~~~i~ 35 (119)
..--+.+||.|.|...--
T Consensus 41 ~rI~I~~GD~V~Ve~spy 58 (68)
T TIGR00008 41 HYIRILPGDKVKVELSPY 58 (68)
T ss_pred ccEEECCCCEEEEEECcc
Confidence 444588999999998753
No 60
>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=36.28 E-value=49 Score=21.26 Aligned_cols=22 Identities=5% Similarity=0.194 Sum_probs=16.1
Q ss_pred CCCCCCEEEEEEEEecCCcccc
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRI 42 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~ 42 (119)
.|.+||.|.+.+.-.+.++.|+
T Consensus 50 ~~~~G~~v~~kVl~id~~~~~i 71 (74)
T cd05705 50 YLPEGKLLTAKVLSVNSEKNLV 71 (74)
T ss_pred ccCCCCEEEEEEEEEECCCCEE
Confidence 4899999999987655444443
No 61
>TIGR00038 efp translation elongation factor P. function: involved in peptide bond synthesis. stimulate efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (by similarity). The trusted cutoff of this model is set high enough to exclude members of TIGR02178, an EFP-like protein of certain Gammaproteobacteria.
Probab=35.92 E-value=1.3e+02 Score=23.08 Aligned_cols=49 Identities=20% Similarity=0.279 Sum_probs=32.5
Q ss_pred CCCCCCCEEEEEEEEecCCccccceEEEEEEEEe----cC-CCceeEEEEEeecCeeEEEEEeecC
Q psy3772 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRR----NK-GLNSNFIVRKISYNEGIERTFQLYS 80 (119)
Q Consensus 20 P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r----~~-g~~~tftlR~i~~gvGVEr~f~l~S 80 (119)
-+|++||+|.. +|. .|. |+... |+ +.--.+.+|++..|.-+|++|+-..
T Consensus 4 ~~ik~G~~I~~-----~g~-----~~~--V~~~~~~kpGkg~A~~rvk~knL~tG~~~e~~f~~~~ 57 (184)
T TIGR00038 4 NDLRKGLVIEL-----DGE-----PYV--VLEFEHVKPGKGQAFVRVKLKNLLTGKVLEKTFRSGE 57 (184)
T ss_pred hhccCCCEEEE-----CCE-----EEE--EEEEEEeeCCCCceEEEEEEEECCCCCEEEEEeCCCC
Confidence 46899999955 242 333 33322 23 2234678999999999999998654
No 62
>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=35.53 E-value=56 Score=19.27 Aligned_cols=15 Identities=27% Similarity=0.426 Sum_probs=12.3
Q ss_pred CCCCCEEEEEEEEec
Q psy3772 22 FVTGDTIIVNLNVIE 36 (119)
Q Consensus 22 f~~GD~v~V~~~i~e 36 (119)
|++||.|.|.+.-.+
T Consensus 45 ~~~Gd~v~v~i~~vd 59 (68)
T cd05685 45 VSVGDIVEVKVISID 59 (68)
T ss_pred cCCCCEEEEEEEEEE
Confidence 799999999876544
No 63
>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=35.41 E-value=50 Score=20.39 Aligned_cols=15 Identities=13% Similarity=0.273 Sum_probs=12.2
Q ss_pred CCCCCEEEEEEEEec
Q psy3772 22 FVTGDTIIVNLNVIE 36 (119)
Q Consensus 22 f~~GD~v~V~~~i~e 36 (119)
|++||+|+|.+.-.+
T Consensus 50 ~~~Gd~v~vkv~~~d 64 (76)
T cd04452 50 VKVGRKEVVKVIRVD 64 (76)
T ss_pred eCCCCEEEEEEEEEE
Confidence 899999999876443
No 64
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=35.28 E-value=1.3e+02 Score=21.20 Aligned_cols=33 Identities=27% Similarity=0.426 Sum_probs=20.4
Q ss_pred CCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEE
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIV 63 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftl 63 (119)
.+..||+|.+... +| .-.|.++|.+ +| |+|+.|
T Consensus 25 glA~gDvV~~~~~--~g----~~~~~~~v~~---sG-nsTiRv 57 (117)
T PF14085_consen 25 GLALGDVVRAEPD--DG----ELWFQKVVES---SG-NSTIRV 57 (117)
T ss_pred CCCCCCEEEEEeC--CC----eEEEEEEEec---CC-CEEEEE
Confidence 5788999999863 22 3466666543 33 555554
No 65
>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=35.08 E-value=78 Score=22.04 Aligned_cols=27 Identities=26% Similarity=0.637 Sum_probs=18.6
Q ss_pred CCCCCEEEEEEEEecCCccccceEEEEE
Q psy3772 22 FVTGDTIIVNLNVIEGTRKRIQAYEGIV 49 (119)
Q Consensus 22 f~~GD~v~V~~~i~eg~k~r~q~f~Gvv 49 (119)
..|||++.++..+.. .....-.|.|.+
T Consensus 98 v~pGd~l~i~~~i~~-~~~~~~~~~~~~ 124 (140)
T TIGR01750 98 VVPGDQLILHAEFLK-KRRKIGKFKGEA 124 (140)
T ss_pred cCCCCEEEEEEEEEE-ccCCEEEEEEEE
Confidence 678999999998874 234445555554
No 66
>PF06507 Auxin_resp: Auxin response factor; InterPro: IPR010525 This pattern represents a conserved region of auxin-responsive transcription factors. The plant hormone auxin (indole-3-acetic acid) can regulate the gene expression of several families, including Aux/IAA, GH3 and SAUR families. Two related families of proteins, Aux/IAA proteins (IPR003311 from INTERPRO) and the auxin response factors (ARF), are key regulators of auxin-modulated gene expression []. There are multiple ARF proteins, some of which activate, while others repress transcription. ARF proteins bind to auxin-responsive cis-acting promoter elements (AuxREs) using an N-terminal DNA-binding domain. It is thought that Aux/IAA proteins activate transcription by modifying ARF activity through the C-terminal protein-protein interaction domains (IPR011525 from INTERPRO) found in both Aux/IAA and ARF proteins. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0009725 response to hormone stimulus, 0005634 nucleus
Probab=34.71 E-value=89 Score=21.29 Aligned_cols=32 Identities=6% Similarity=0.240 Sum_probs=24.3
Q ss_pred CCCCCCCEEEEEEEEecCCccccceEEEEEEEEec
Q psy3772 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (119)
Q Consensus 20 P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~ 54 (119)
-.|.+|--++..+. ++......|.|+|+++..
T Consensus 37 ~~~~~GmRfkM~fE---~eds~~~~~~GtI~~v~~ 68 (83)
T PF06507_consen 37 HPWSVGMRFKMRFE---TEDSSERRWQGTIVGVSD 68 (83)
T ss_pred CCCCCCcEEEEEec---cCCCccceeeeEEeEeec
Confidence 46899999988874 444444678999999876
No 67
>PF00386 C1q: C1q domain; InterPro: IPR001073 This entry represents the C-terminal domain of C1q. C1q is a subunit of the C1 enzyme complex that activates the serum complement system. C1q comprises 6 A, 6 B and 6 C chains. These share the same topology, each possessing a small, globular N-terminal domain, a collagen-like Gly/Pro-rich central region, and a conserved C-terminal region, the C1q domain []. The C1q protein is produced in collagen-producing cells and shows sequence and structural similarity to collagens VIII and X [, ]. This domain is also found in multimerin and EMILIN proteins.; PDB: 1O91_C 2JG8_D 2JG9_A 2WNV_A 2WNU_A 1PK6_A 4DOU_A 1C3H_C 1C28_C 2OII_A ....
Probab=34.46 E-value=76 Score=21.85 Aligned_cols=30 Identities=20% Similarity=0.413 Sum_probs=17.5
Q ss_pred CCCCCCEEEEEEEEe----cCCccccceEEEEEE
Q psy3772 21 DFVTGDTIIVNLNVI----EGTRKRIQAYEGIVI 50 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~----eg~k~r~q~f~GvvI 50 (119)
++.+||.|.|..... ...-..-..|.|..|
T Consensus 94 ~L~~GD~V~v~~~~~~~~~~~~~~~~stFsGfLl 127 (127)
T PF00386_consen 94 QLNKGDTVWVRLDSGNGIYSSGSNPYSTFSGFLL 127 (127)
T ss_dssp EE-TT-EEEEEEEEEEEEEBBTTSBTEEEEEEEE
T ss_pred EeCCCCEEEEEEecCceEEeCCCCCCEEEEEEEC
Confidence 478999999988742 112224567777654
No 68
>PRK13203 ureB urease subunit beta; Reviewed
Probab=34.15 E-value=38 Score=24.32 Aligned_cols=33 Identities=33% Similarity=0.550 Sum_probs=23.8
Q ss_pred cCCCCC-----CCCCCEEEEEEEEecCCccccceEEEEE
Q psy3772 16 KKNIPD-----FVTGDTIIVNLNVIEGTRKRIQAYEGIV 49 (119)
Q Consensus 16 ~~~~P~-----f~~GD~v~V~~~i~eg~k~r~q~f~Gvv 49 (119)
+-|+|. |.|||+-+|.+--- |-..++.=|.|.+
T Consensus 60 RLdIpaGTavRFEPG~~k~V~LV~~-gG~r~v~G~ngl~ 97 (102)
T PRK13203 60 RLNIPAGTAVRFEPGQTREVELVPL-AGARRVYGFRGKV 97 (102)
T ss_pred ccccCCCCeEeECCCCeEEEEEEEc-cCceEEEccCccc
Confidence 478996 99999999998654 4455565565544
No 69
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=34.13 E-value=1.2e+02 Score=19.38 Aligned_cols=36 Identities=25% Similarity=0.455 Sum_probs=22.1
Q ss_pred CCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEE
Q psy3772 23 VTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRK 65 (119)
Q Consensus 23 ~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~ 65 (119)
-.|-.|.|+++ +| ..|+|+.-+..-.+-+..+.|..
T Consensus 10 lvG~~V~V~~~--~G-----~~yeGif~s~s~~~~~~~vvLk~ 45 (77)
T PF14438_consen 10 LVGQTVEVTTK--NG-----SVYEGIFHSASPESNEFDVVLKM 45 (77)
T ss_dssp TTTSEEEEEET--TS------EEEEEEEEE-T---T--EEEEE
T ss_pred CcCCEEEEEEC--CC-----CEEEEEEEeCCCcccceeEEEEe
Confidence 47888999874 67 48999999887654455666543
No 70
>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=34.10 E-value=56 Score=20.83 Aligned_cols=21 Identities=14% Similarity=0.313 Sum_probs=15.2
Q ss_pred CCCCCEEEEEEEEecCCcccc
Q psy3772 22 FVTGDTIIVNLNVIEGTRKRI 42 (119)
Q Consensus 22 f~~GD~v~V~~~i~eg~k~r~ 42 (119)
|.+||.|.+.+.-.+.++.|+
T Consensus 47 ~~vG~~v~~kV~~id~~~~~i 67 (73)
T cd05703 47 FPIGQALKAKVVGVDKEHKLL 67 (73)
T ss_pred CCCCCEEEEEEEEEeCCCCEE
Confidence 999999999976544444443
No 71
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=33.94 E-value=1.6e+02 Score=20.47 Aligned_cols=60 Identities=20% Similarity=0.212 Sum_probs=39.6
Q ss_pred CCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEe-ecCe---------------eEEEEEeecCCccceE
Q psy3772 23 VTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKI-SYNE---------------GIERTFQLYSPIISSI 86 (119)
Q Consensus 23 ~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i-~~gv---------------GVEr~f~l~SP~I~~I 86 (119)
..|..|.+..+ .+ -.|+|++..+.. -++|++|.|+ .+|. --+.+| ..--|+++
T Consensus 6 ~IGs~ISlisk--~~-----iRYeG~L~~Id~--~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~F--r~sDIkdL 74 (96)
T PF12701_consen 6 YIGSKISLISK--SD-----IRYEGILYSIDT--EDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVF--RGSDIKDL 74 (96)
T ss_dssp CTTCEEEEEET--TT-----EEEEEEEEEEET--TTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEE--ETTTEEEE
T ss_pred ccCCEEEEEEC--CC-----cEEEEEEEEEcC--CCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEE--EccccceE
Confidence 35888887653 11 489999999985 3689999997 4565 122233 55678888
Q ss_pred EEEEecc
Q psy3772 87 IVKRRGD 93 (119)
Q Consensus 87 eVl~~~k 93 (119)
+|+.-..
T Consensus 75 ~v~e~~~ 81 (96)
T PF12701_consen 75 KVIEPPP 81 (96)
T ss_dssp EECE-S-
T ss_pred EEEcCCC
Confidence 8876543
No 72
>cd01288 FabZ FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid biosynthesis pathway.
Probab=33.77 E-value=81 Score=21.22 Aligned_cols=27 Identities=26% Similarity=0.636 Sum_probs=18.8
Q ss_pred CCCCCEEEEEEEEecCCccccceEEEEE
Q psy3772 22 FVTGDTIIVNLNVIEGTRKRIQAYEGIV 49 (119)
Q Consensus 22 f~~GD~v~V~~~i~eg~k~r~q~f~Gvv 49 (119)
..|||++.+...+.+ .....-.|++.+
T Consensus 88 v~pgd~l~i~~~v~~-~~~~~~~~~~~~ 114 (131)
T cd01288 88 VVPGDQLILEVELLK-LRRGIGKFKGKA 114 (131)
T ss_pred cCCCCEEEEEEEEEE-eeCCEEEEEEEE
Confidence 568999999999875 334455556554
No 73
>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=33.66 E-value=79 Score=19.63 Aligned_cols=17 Identities=18% Similarity=0.290 Sum_probs=13.4
Q ss_pred CCCCCCEEEEEEEEecC
Q psy3772 21 DFVTGDTIIVNLNVIEG 37 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg 37 (119)
.|++||.|.|.+.-.+.
T Consensus 40 ~~~~Gd~v~v~v~~v~~ 56 (67)
T cd04455 40 SYRPGDRIKAYVLEVRK 56 (67)
T ss_pred cCCCCCEEEEEEEEEec
Confidence 58999999998875443
No 74
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=33.48 E-value=1.2e+02 Score=22.36 Aligned_cols=28 Identities=14% Similarity=0.234 Sum_probs=22.4
Q ss_pred CCCCCCEEEEEEEEecCCccccceEEEEEEEEecC
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNK 55 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~ 55 (119)
.|.+||.|+|.- |. .+-|+|.|+...+.
T Consensus 94 ~~~~G~~V~I~~----Gp---f~g~~g~V~~vd~~ 121 (153)
T PRK08559 94 GIKEGDIVELIA----GP---FKGEKARVVRVDES 121 (153)
T ss_pred CCCCCCEEEEec----cC---CCCceEEEEEEcCC
Confidence 599999999863 53 46789999999764
No 75
>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=33.17 E-value=60 Score=20.03 Aligned_cols=14 Identities=14% Similarity=0.235 Sum_probs=11.9
Q ss_pred CCCCCEEEEEEEEe
Q psy3772 22 FVTGDTIIVNLNVI 35 (119)
Q Consensus 22 f~~GD~v~V~~~i~ 35 (119)
|++||+|++.+.-.
T Consensus 48 ~~~Gd~v~~~V~~~ 61 (73)
T cd05706 48 FKKNDIVRACVLSV 61 (73)
T ss_pred cCCCCEEEEEEEEE
Confidence 99999999987644
No 76
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=33.11 E-value=34 Score=23.15 Aligned_cols=17 Identities=29% Similarity=0.511 Sum_probs=13.5
Q ss_pred CCCCCCCCCEEEEEEEE
Q psy3772 18 NIPDFVTGDTIIVNLNV 34 (119)
Q Consensus 18 ~~P~f~~GD~v~V~~~i 34 (119)
..--+.|||.|.|...-
T Consensus 43 ~~i~I~~GD~V~Ve~~~ 59 (75)
T COG0361 43 NRIRILPGDVVLVELSP 59 (75)
T ss_pred eeEEeCCCCEEEEEecc
Confidence 34558999999999864
No 77
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=33.04 E-value=98 Score=20.04 Aligned_cols=28 Identities=18% Similarity=0.163 Sum_probs=22.4
Q ss_pred CCCCCCEEEEEEEEecCCccccceEEEEEEEEecC
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNK 55 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~ 55 (119)
-|.+|++|.+.+- .| +.|+|=|.+-...
T Consensus 2 ~f~iGs~V~~kTc--~g-----~~ieGEV~afD~~ 29 (61)
T cd01735 2 CFSVGSQVSCRTC--FE-----QRLQGEVVAFDYP 29 (61)
T ss_pred ccccccEEEEEec--CC-----ceEEEEEEEecCC
Confidence 4889999999886 35 5899999987653
No 78
>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=32.90 E-value=47 Score=20.78 Aligned_cols=16 Identities=25% Similarity=0.424 Sum_probs=12.9
Q ss_pred CCCCCCEEEEEEEEec
Q psy3772 21 DFVTGDTIIVNLNVIE 36 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (119)
.|++||.|+|.+.-.+
T Consensus 57 ~~~~gd~v~v~v~~vd 72 (83)
T cd04471 57 VFRLGDKVKVRVVRVD 72 (83)
T ss_pred EEcCCCEEEEEEEEec
Confidence 4899999999886543
No 79
>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=32.58 E-value=99 Score=22.47 Aligned_cols=35 Identities=17% Similarity=0.303 Sum_probs=25.7
Q ss_pred CCCCCCCEEEEEEEE--ecCCccccceEEEEEEEEec
Q psy3772 20 PDFVTGDTIIVNLNV--IEGTRKRIQAYEGIVISRRN 54 (119)
Q Consensus 20 P~f~~GD~v~V~~~i--~eg~k~r~q~f~GvvI~~r~ 54 (119)
+.-..||++.|.++- +++.-.+-|.+.++|+..+.
T Consensus 31 ~~a~iGD~I~vsVk~~~~~~~~kkg~v~~AvIVrtkk 67 (122)
T TIGR01067 31 RYATVGDVIVVVVKDAIPNGKVKKGDVVKAVIVRTKK 67 (122)
T ss_pred CccccCCEEEEEEEEcCCCCccccccEEEEEEEEeec
Confidence 567899999999873 22223446899999998774
No 80
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=32.53 E-value=49 Score=21.65 Aligned_cols=21 Identities=14% Similarity=0.360 Sum_probs=17.6
Q ss_pred CCCCCCCCCCEEEEEEEEecC
Q psy3772 17 KNIPDFVTGDTIIVNLNVIEG 37 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~i~eg 37 (119)
.+++.+.||..|.|.|....|
T Consensus 33 f~~~~L~~G~kV~V~yd~~~g 53 (61)
T PF07076_consen 33 FDFDGLKPGMKVVVFYDEVDG 53 (61)
T ss_pred ccccccCCCCEEEEEEEccCC
Confidence 467889999999999987654
No 81
>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=32.43 E-value=62 Score=19.73 Aligned_cols=16 Identities=19% Similarity=0.324 Sum_probs=13.1
Q ss_pred CCCCCEEEEEEEEecC
Q psy3772 22 FVTGDTIIVNLNVIEG 37 (119)
Q Consensus 22 f~~GD~v~V~~~i~eg 37 (119)
|++||.+.|.+.-.+.
T Consensus 45 ~~~G~~i~v~v~~~d~ 60 (70)
T cd05698 45 FRVGQVVKVKVLSCDP 60 (70)
T ss_pred ccCCCEEEEEEEEEcC
Confidence 9999999999865543
No 82
>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=30.93 E-value=32 Score=21.18 Aligned_cols=16 Identities=31% Similarity=0.621 Sum_probs=12.5
Q ss_pred cCCCCCC-CCCCEEEEE
Q psy3772 16 KKNIPDF-VTGDTIIVN 31 (119)
Q Consensus 16 ~~~~P~f-~~GD~v~V~ 31 (119)
.+|+|.+ +.||+|.|.
T Consensus 6 ~~dv~~lG~~Gdiv~V~ 22 (48)
T PF01281_consen 6 LKDVPGLGKKGDIVEVK 22 (48)
T ss_dssp SSCCTTSBSTTEEEE-S
T ss_pred cccccccCCCCCEEEEc
Confidence 5789985 899999984
No 83
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=30.86 E-value=52 Score=22.62 Aligned_cols=17 Identities=29% Similarity=0.638 Sum_probs=14.7
Q ss_pred CCCCCCCCEEEEEEEEe
Q psy3772 19 IPDFVTGDTIIVNLNVI 35 (119)
Q Consensus 19 ~P~f~~GD~v~V~~~i~ 35 (119)
+-.|.+||.|+|.+.+.
T Consensus 50 l~~~~~Gd~V~Vsf~i~ 66 (84)
T PF11325_consen 50 LDNFQVGDEVKVSFNIE 66 (84)
T ss_pred hccCCCCCEEEEEEEee
Confidence 36799999999999874
No 84
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: 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 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=30.85 E-value=68 Score=19.90 Aligned_cols=16 Identities=19% Similarity=0.142 Sum_probs=12.8
Q ss_pred CCCCCCEEEEEEEEec
Q psy3772 21 DFVTGDTIIVNLNVIE 36 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (119)
.|++||+|.+.+.-..
T Consensus 46 ~~~~Gd~i~~kVl~~d 61 (70)
T cd05702 46 KFKIGQKIKARVIGGH 61 (70)
T ss_pred hCCCCCEEEEEEEEEe
Confidence 3999999999986443
No 85
>cd00407 Urease_beta Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of external and internally-generated urea as a nitrogen source. The enzyme consists of three subunits, alpha, beta and gamma, which can exist as separate proteins or can be fused on a single protein chain. The alpha-beta-gamma heterotrimer forms multimers, mainly trimers. The large alpha subunit is the catalytic domain containing an active site with a bi-nickel center complexed by a carbamylated lysine. The beta and gamma subunits play a role in subunit association to form the higher order trimers.
Probab=30.78 E-value=47 Score=23.79 Aligned_cols=33 Identities=33% Similarity=0.690 Sum_probs=23.6
Q ss_pred cCCCCC-----CCCCCEEEEEEEEecCCccccceEEEEE
Q psy3772 16 KKNIPD-----FVTGDTIIVNLNVIEGTRKRIQAYEGIV 49 (119)
Q Consensus 16 ~~~~P~-----f~~GD~v~V~~~i~eg~k~r~q~f~Gvv 49 (119)
+-|+|. |.|||+-+|++--- |-+..+.=|.|.+
T Consensus 60 RLdIpaGTavRFEPG~~k~V~LV~~-~G~r~v~G~~~l~ 97 (101)
T cd00407 60 RLDIPAGTAVRFEPGEEKEVELVPI-GGKRRVYGFNGLV 97 (101)
T ss_pred eecccCCCeEEECCCCeEEEEEEEc-cCceEEEccCccc
Confidence 468886 99999999998544 4455555555544
No 86
>PF11132 SplA: Transcriptional regulator protein (SplA); InterPro: IPR022608 The SplA protein functions in trans as a negative regulator of the level of splB-lacZ expression in the developing forespore [].
Probab=30.51 E-value=53 Score=22.39 Aligned_cols=17 Identities=18% Similarity=0.372 Sum_probs=14.2
Q ss_pred CCCCCCCCCEEEEEEEE
Q psy3772 18 NIPDFVTGDTIIVNLNV 34 (119)
Q Consensus 18 ~~P~f~~GD~v~V~~~i 34 (119)
++..+++||+|-|-+.-
T Consensus 2 ~~~~~~~GD~VyViYrN 18 (75)
T PF11132_consen 2 DMKPYHAGDIVYVIYRN 18 (75)
T ss_pred CccccCCCCEEEEEEcC
Confidence 46789999999998863
No 87
>smart00110 C1Q Complement component C1q domain. Globular domain found in many collagens and eponymously in complement C1q. When part of full length proteins these domains form a 'bouquet' due to the multimerization of heterotrimers. The C1q fold is similar to that of tumour necrosis factor.
Probab=30.33 E-value=91 Score=22.53 Aligned_cols=31 Identities=13% Similarity=0.200 Sum_probs=21.8
Q ss_pred CCCCCCEEEEEEEEe----cCCccccceEEEEEEE
Q psy3772 21 DFVTGDTIIVNLNVI----EGTRKRIQAYEGIVIS 51 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~----eg~k~r~q~f~GvvI~ 51 (119)
.+.+||.|-|..... .++.++..+|.|..|-
T Consensus 99 ~L~~GD~Vwl~l~~~~~~i~~~~~~~stFSGfLl~ 133 (135)
T smart00110 99 QLRQGDQVWLELPDEKNGLYAGEYVDSTFSGFLLF 133 (135)
T ss_pred EECCCCEEEEEEeCCCCceecCCCCcEEEEEEEEe
Confidence 478999999887531 1334677889988763
No 88
>COG5636 Uncharacterized conserved protein, contains Zn-ribbon-like motif [Function unknown]
Probab=30.28 E-value=35 Score=28.11 Aligned_cols=17 Identities=29% Similarity=0.663 Sum_probs=14.0
Q ss_pred CCCCCCCCCCEEEEEEE
Q psy3772 17 KNIPDFVTGDTIIVNLN 33 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~ 33 (119)
--+|.|.|||+|.....
T Consensus 258 lGlPaf~PGd~v~~~~n 274 (284)
T COG5636 258 LGLPAFEPGDVVSFSMN 274 (284)
T ss_pred cCCCCCCCCceeeeecc
Confidence 35899999999987664
No 89
>PRK04183 glutamyl-tRNA(Gln) amidotransferase subunit D; Validated
Probab=30.27 E-value=1.9e+02 Score=25.17 Aligned_cols=55 Identities=24% Similarity=0.492 Sum_probs=34.9
Q ss_pred CCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecC--eeEEEEEeecCCccceEEEEEecc
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYN--EGIERTFQLYSPIISSIIVKRRGD 93 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~g--vGVEr~f~l~SP~I~~IeVl~~~k 93 (119)
.+.+||.|+|... + ..|+|++|-... +-.++| |+.+| +|+.. -.|.+||++.++.
T Consensus 2 ~~~~gd~v~~~~~---~-----~~~~g~~~p~~~---~~~~~~-kl~~gyn~g~~~------~~~~~~~~~~~~~ 58 (419)
T PRK04183 2 GMEVGDRVRVEKD---D-----VVYEGILMPSYE---DDHIVI-KLDNGYNIGIDI------DKIAEIELLEKGE 58 (419)
T ss_pred CCCCCCEEEEEEC---C-----eEEEEEEecCCC---CCEEEE-EcCCCceeeecc------ccccceEEccccc
Confidence 3678999999652 2 699999996655 223333 44443 66542 2456777776653
No 90
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=30.15 E-value=2.2e+02 Score=20.79 Aligned_cols=44 Identities=18% Similarity=0.276 Sum_probs=27.9
Q ss_pred CCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCeeE
Q psy3772 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGI 72 (119)
Q Consensus 20 P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gvGV 72 (119)
..|.+||.|+|. +|. .+-|+|.|.......- ..+|.=-+.|-.+
T Consensus 125 ~~~~~Gd~VrI~----~GP---f~G~~g~v~~i~~~~~--r~~v~l~~~G~~~ 168 (181)
T PRK05609 125 VDFEVGEMVRVI----DGP---FADFNGTVEEVDYEKS--KLKVLVSIFGRET 168 (181)
T ss_pred cCCCCCCEEEEe----ccC---CCCCEEEEEEEeCCCC--EEEEEEEECCCce
Confidence 458999999986 354 4678999999864332 3344333444433
No 91
>PF01472 PUA: PUA domain; InterPro: IPR002478 The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was named after the proteins in which it was first found []. PUA is a highly conserved RNA-binding motif found in a wide range of archaeal, bacterial and eukaryotic proteins, including enzymes that catalyse tRNA and rRNA post-transcriptional modifications, proteins involved in ribosome biogenesis and translation, as well as in enzymes involved in proline biosynthesis [, ]. The structures of several PUA-RNA complexes reveal a common RNA recognition surface, but also some versatility in the way in which the motif binds to RNA []. PUA motifs are involved in dyskeratosis congenita and cancer, pointing to links between RNA metabolism and human diseases [].; GO: 0003723 RNA binding; PDB: 1ZE2_A 1ZE1_A 1R3E_A 2AB4_A 3R90_D 2J5T_A 2J5V_B 1Q7H_A 2APO_A 2RFK_A ....
Probab=30.11 E-value=36 Score=21.86 Aligned_cols=14 Identities=29% Similarity=0.354 Sum_probs=9.6
Q ss_pred CCCCCCCCEEEEEE
Q psy3772 19 IPDFVTGDTIIVNL 32 (119)
Q Consensus 19 ~P~f~~GD~v~V~~ 32 (119)
-++|++||.|.|..
T Consensus 28 ~~~f~~gd~V~i~~ 41 (74)
T PF01472_consen 28 DGDFRKGDEVAIVD 41 (74)
T ss_dssp ETT--TTSEEEEEE
T ss_pred CCCcCCCCEEEEEc
Confidence 35699999999875
No 92
>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=29.99 E-value=66 Score=20.23 Aligned_cols=16 Identities=19% Similarity=0.117 Sum_probs=12.7
Q ss_pred CCCCCEEEEEEEEecC
Q psy3772 22 FVTGDTIIVNLNVIEG 37 (119)
Q Consensus 22 f~~GD~v~V~~~i~eg 37 (119)
|++||.|.|.+.-.+.
T Consensus 49 ~~~Gd~v~vkv~~vd~ 64 (73)
T cd05686 49 VDVGEKVWVKVIGREM 64 (73)
T ss_pred ECCCCEEEEEEEEECC
Confidence 7999999999865443
No 93
>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=29.94 E-value=76 Score=19.38 Aligned_cols=15 Identities=20% Similarity=0.364 Sum_probs=12.4
Q ss_pred CCCCCEEEEEEEEec
Q psy3772 22 FVTGDTIIVNLNVIE 36 (119)
Q Consensus 22 f~~GD~v~V~~~i~e 36 (119)
|++||.|++.+.-..
T Consensus 45 ~~~Gd~v~~~v~~~d 59 (68)
T cd05707 45 FKVGQLVKGKIVSID 59 (68)
T ss_pred cCCCCEEEEEEEEEe
Confidence 999999999876443
No 94
>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=29.61 E-value=1.6e+02 Score=18.93 Aligned_cols=45 Identities=16% Similarity=0.245 Sum_probs=30.2
Q ss_pred CCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCeeEE
Q psy3772 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIE 73 (119)
Q Consensus 20 P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gvGVE 73 (119)
..+.+||.|.|.+..+.+. . .-...|.|......+-+. ..+.||+
T Consensus 35 ~~~~~g~~v~l~l~l~~~~-~-~i~~~g~Vv~~~~~~~~~-------~~~~Gv~ 79 (96)
T TIGR02266 35 KPLAVGTRVELKLTLPGGE-R-PVELKGVVAWVRPAADGG-------PPGMGVR 79 (96)
T ss_pred CCcCCCCEEEEEEEcCCCC-e-EEEEEEEEEEeCCCCCCC-------CCeeEEE
Confidence 4579999999999987532 1 234679988887544322 2466776
No 95
>PRK13201 ureB urease subunit beta; Reviewed
Probab=29.52 E-value=46 Score=25.07 Aligned_cols=35 Identities=29% Similarity=0.497 Sum_probs=26.3
Q ss_pred cCCCCC-----CCCCCEEEEEEEEecCCccccceEEEEEEE
Q psy3772 16 KKNIPD-----FVTGDTIIVNLNVIEGTRKRIQAYEGIVIS 51 (119)
Q Consensus 16 ~~~~P~-----f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~ 51 (119)
+-|+|. |.|||+-.|.+--- |-..++.=|.|.|-+
T Consensus 60 RLdIPAGTAVRFEPG~~k~V~LV~i-gG~r~V~Gfnglv~G 99 (136)
T PRK13201 60 HLDIPAGAAVRFEPGDKKEVQLVEY-AGKRKIFGFRGMVNG 99 (136)
T ss_pred ccccCCCCeEeECCCCeEEEEEEEc-cCceEEEccCccccC
Confidence 578996 99999999998544 446667777776643
No 96
>PRK13202 ureB urease subunit beta; Reviewed
Probab=29.40 E-value=49 Score=23.86 Aligned_cols=33 Identities=27% Similarity=0.390 Sum_probs=23.6
Q ss_pred cCCCCC-----CCCCCEEEEEEEEecCCccccceEEEEE
Q psy3772 16 KKNIPD-----FVTGDTIIVNLNVIEGTRKRIQAYEGIV 49 (119)
Q Consensus 16 ~~~~P~-----f~~GD~v~V~~~i~eg~k~r~q~f~Gvv 49 (119)
+-|+|. |.|||+-.|++--- |-+.++.=|.|.+
T Consensus 61 RLdIpaGTavRFEPG~~k~V~LV~~-gG~r~v~G~~~~~ 98 (104)
T PRK13202 61 RLDIPAATAVRFEPGIPQIVGLVPL-GGRREVPGLTLNP 98 (104)
T ss_pred ccccCCCCeEEECCCCeEEEEEEEc-cCCeEEEcCCccc
Confidence 468886 99999999998654 4455555555544
No 97
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=29.37 E-value=68 Score=20.70 Aligned_cols=21 Identities=10% Similarity=0.317 Sum_probs=14.9
Q ss_pred CCCCCCCCCCEEEEEEEEecC
Q psy3772 17 KNIPDFVTGDTIIVNLNVIEG 37 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~i~eg 37 (119)
.++..|++||.|.+.+...++
T Consensus 38 ~~l~~l~~Gd~V~F~~~~~~~ 58 (70)
T PF11604_consen 38 VDLAGLKPGDKVRFTFERTDD 58 (70)
T ss_dssp SEESS-STT-EEEEEEEEETT
T ss_pred hhhhcCCCCCEEEEEEEECCC
Confidence 356679999999999987654
No 98
>PRK02268 hypothetical protein; Provisional
Probab=29.36 E-value=83 Score=23.55 Aligned_cols=35 Identities=23% Similarity=0.319 Sum_probs=24.8
Q ss_pred CCCCCCCCCEEEEEE-EEecCCccccceEEEEEEEE
Q psy3772 18 NIPDFVTGDTIIVNL-NVIEGTRKRIQAYEGIVISR 52 (119)
Q Consensus 18 ~~P~f~~GD~v~V~~-~i~eg~k~r~q~f~GvvI~~ 52 (119)
.+-.++|||.|-.-. +..-|.++..|.|.|+=.-.
T Consensus 32 pl~RmkpGD~ivyYsp~~~~~~~~~~qaftAig~V~ 67 (141)
T PRK02268 32 PLRRMKPGDWIIYYSPKTTFGGKDKLQAFTAIGKVK 67 (141)
T ss_pred hhhcCCCCCEEEEEeceEecCCCcccceEEEEEEEc
Confidence 455689999998633 23346788899999976533
No 99
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=29.23 E-value=51 Score=21.38 Aligned_cols=25 Identities=24% Similarity=0.417 Sum_probs=17.2
Q ss_pred CCCCCEEEEEEEEecCCccccceEEEEEEEEe
Q psy3772 22 FVTGDTIIVNLNVIEGTRKRIQAYEGIVISRR 53 (119)
Q Consensus 22 f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r 53 (119)
..+||.|.|.....+. -+|.+|-+.
T Consensus 47 i~vGD~V~ve~~~~~~-------~~g~Iv~r~ 71 (72)
T PRK00276 47 ILPGDKVTVELSPYDL-------TKGRITYRH 71 (72)
T ss_pred cCCCCEEEEEEcccCC-------CeEEEEEEe
Confidence 6889999999764332 247777653
No 100
>PRK00006 fabZ (3R)-hydroxymyristoyl-ACP dehydratase; Reviewed
Probab=29.11 E-value=1e+02 Score=21.71 Aligned_cols=27 Identities=26% Similarity=0.683 Sum_probs=18.1
Q ss_pred CCCCCEEEEEEEEecCCccccceEEEEE
Q psy3772 22 FVTGDTIIVNLNVIEGTRKRIQAYEGIV 49 (119)
Q Consensus 22 f~~GD~v~V~~~i~eg~k~r~q~f~Gvv 49 (119)
..|||+|.+...+.+- +...-.|.+-+
T Consensus 102 v~pGd~l~i~~~i~~~-~~~~v~~~~~~ 128 (147)
T PRK00006 102 VVPGDQLILEVELLKQ-RRGIWKFKGVA 128 (147)
T ss_pred cCCCCEEEEEEEEEEe-eCCEEEEEEEE
Confidence 4699999999988642 33444455554
No 101
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=29.00 E-value=76 Score=18.40 Aligned_cols=14 Identities=21% Similarity=0.420 Sum_probs=12.1
Q ss_pred CCCCCEEEEEEEEe
Q psy3772 22 FVTGDTIIVNLNVI 35 (119)
Q Consensus 22 f~~GD~v~V~~~i~ 35 (119)
|++||.|.+.+.-.
T Consensus 47 ~~~G~~v~~~V~~~ 60 (72)
T smart00316 47 LKVGDEVKVKVLSV 60 (72)
T ss_pred ecCCCEEEEEEEEE
Confidence 99999999988654
No 102
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=28.99 E-value=1.5e+02 Score=18.61 Aligned_cols=31 Identities=26% Similarity=0.480 Sum_probs=22.3
Q ss_pred CCCCCCEEEEEEEEecCCccccceEEEEEEEEecC
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNK 55 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~ 55 (119)
.|..|+.|.|.+...++ +=.|+..|+++...
T Consensus 47 ~l~~g~~v~v~~~~~~~----~y~F~s~V~~~~~~ 77 (87)
T PF12945_consen 47 PLREGEEVIVRFISEDG----VYAFKSKVIGRISE 77 (87)
T ss_dssp CS-TT-EEEEEEEE-SC----EEEEEEEEEEEE-S
T ss_pred eecCCCEEEEEEEECCe----EEEEEEEEEEEEcC
Confidence 58899999999975433 78999999998744
No 103
>PF10610 Tafi-CsgC: Thin aggregative fimbriae synthesis protein; InterPro: IPR014491 Thin aggressive fibres known as curli fibres or fimbriae (curli; Tafi) are cell-surface protein polymers found in Salmonella typhimurium and Escherichia coli that mediate interactions important for host and environmental persistence, development of biofilms, motility, colonisation and invasion of cells, and conjugation []. Four general assembly pathways for different fimbriae have been proposed, one of which is extracellular nucleation-precipitation (ENP), which differs from the others in that fibre-growth occurs extracellularly. Thin aggregative fimbriae are the only fimbriae dependent on the ENP pathway. Tafi were first identified in Salmonella spp and the controlling operon termed agf; however subsequent isolation of the homologous operon in E coli led to its being called csg. Tafi are known as curli because, in the absence of extracellular polysaccharides, their morphology appears curled; however, when expressed with such polysaccharides their morphology appears as a tangled amorphous matrix. The gene agfC is found to be transcribed at low levels, localised to the periplasm in a mature form, and in combination with AgfE is important for AgfA extracellular assembly, which facilitates the synthesis of Tafi. The genes involved in Tafi production are organised into two adjacent divergently transcribed operons, agfBAC and agfDEFG, both of which are required for biosynthesis and assembly [].; PDB: 2XSK_A 2Y2T_A 2Y2Y_A.
Probab=28.99 E-value=63 Score=23.40 Aligned_cols=20 Identities=20% Similarity=0.408 Sum_probs=13.2
Q ss_pred CCCCCEEEEEEEEecCCccc
Q psy3772 22 FVTGDTIIVNLNVIEGTRKR 41 (119)
Q Consensus 22 f~~GD~v~V~~~i~eg~k~r 41 (119)
+.|||.|.+.+.+.+|.+-+
T Consensus 75 i~p~D~v~I~VtvSDG~sl~ 94 (106)
T PF10610_consen 75 ISPGDKVKIIVTVSDGKSLH 94 (106)
T ss_dssp --TT-EEEEEEEEE-SSS-E
T ss_pred eCCCCeEEEEEEEcCCCeEE
Confidence 78999999999999986543
No 104
>PRK13198 ureB urease subunit beta; Reviewed
Probab=28.88 E-value=51 Score=25.41 Aligned_cols=36 Identities=25% Similarity=0.409 Sum_probs=26.9
Q ss_pred cCCCCC-----CCCCCEEEEEEEEecCCccccceEEEEEEEE
Q psy3772 16 KKNIPD-----FVTGDTIIVNLNVIEGTRKRIQAYEGIVISR 52 (119)
Q Consensus 16 ~~~~P~-----f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~ 52 (119)
+-|+|. |.|||+-.|.+--- |...++.=|.|.|-+.
T Consensus 88 RLdIPAGTAVRFEPG~~k~V~LV~~-gG~r~V~Gfnglv~G~ 128 (158)
T PRK13198 88 RLNISSTTAIRFEPGDETEVPLIPF-GGKQTLYGFNNLVDGW 128 (158)
T ss_pred ccccCCCCeEeeCCCCeeEEEEEEc-cCceEEEccCccccCc
Confidence 578886 99999999998544 4466677777766543
No 105
>KOG3416|consensus
Probab=28.87 E-value=34 Score=25.70 Aligned_cols=23 Identities=17% Similarity=0.312 Sum_probs=15.8
Q ss_pred CCCCCCEEEEEEEEecCCccccceEEEEEEE
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVIS 51 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~ 51 (119)
.|.|||+|+.+=-. .+.|+| |..
T Consensus 61 ~~~PGDIirLt~Gy-------~Si~qg-~Lt 83 (134)
T KOG3416|consen 61 LIQPGDIIRLTGGY-------ASIFQG-CLT 83 (134)
T ss_pred ccCCccEEEecccc-------hhhhcC-ceE
Confidence 49999999986322 257777 443
No 106
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=28.59 E-value=1.5e+02 Score=21.93 Aligned_cols=35 Identities=23% Similarity=0.410 Sum_probs=26.8
Q ss_pred CCCCCCCCEEEEEEEEecCCccccceEEEEEEEEec
Q psy3772 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (119)
Q Consensus 19 ~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~ 54 (119)
+|.-.+||+|.|.++-... -.+-|.+.++|+..+.
T Consensus 44 ~~~a~iGD~IvvsVK~~~p-~~kg~v~kAVIVRtkk 78 (132)
T PRK08571 44 LPKAGVGDMVVVSVKKGTP-EMRKQVLRAVVVRQRK 78 (132)
T ss_pred CCccccCCEEEEEEEECCC-cccCCEeEEEEEEecc
Confidence 4678899999999985433 3345899999998774
No 107
>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=28.07 E-value=48 Score=22.27 Aligned_cols=14 Identities=21% Similarity=0.579 Sum_probs=12.6
Q ss_pred CCCCCCCCEEEEEE
Q psy3772 19 IPDFVTGDTIIVNL 32 (119)
Q Consensus 19 ~P~f~~GD~v~V~~ 32 (119)
+|+..|||.|-||.
T Consensus 33 v~~~~vGD~VLVH~ 46 (76)
T TIGR00074 33 VGEVKVGDYVLVHV 46 (76)
T ss_pred eCCCCCCCEEEEec
Confidence 58899999999986
No 108
>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=27.83 E-value=1.6e+02 Score=25.12 Aligned_cols=80 Identities=10% Similarity=0.108 Sum_probs=45.7
Q ss_pred CCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCC----ceeEEEEEeecCeeEEEEEeecCCccceEEEEEec
Q psy3772 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGL----NSNFIVRKISYNEGIERTFQLYSPIISSIIVKRRG 92 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~----~~tftlR~i~~gvGVEr~f~l~SP~I~~IeVl~~~ 92 (119)
.+++.+++|+.|.|++.- ...+...|.|.|..+..... +.+|+++=-+.-.. .-.++|..-+-.++.+.-
T Consensus 367 ~di~~v~~Gq~V~v~~~a---~~~~~~~~~G~V~~Is~~~~~~~~~~~y~v~v~l~~~~-~~~~~L~pGM~a~v~I~~-- 440 (457)
T TIGR01000 367 NDISGIKVGQKVRFKLTQ---NVPKPIILDGTITSISSAPTATKKGNFYKVIATIKITK-NQAELIRYGLTGKISTIT-- 440 (457)
T ss_pred HHHhhcCCCCeEEEEEec---CCCCceEEEEEEEEEcCCCccCCCCCEEEEEEEecCCc-ccccccCCCCEEEEEEEE--
Confidence 467789999998888753 22222479999999875432 24666653331000 012356666666666653
Q ss_pred cccccceeeec
Q psy3772 93 DVRRAKLYYLR 103 (119)
Q Consensus 93 kvrRakLyYLR 103 (119)
-.|.-|.||=
T Consensus 441 -~~rt~l~yll 450 (457)
T TIGR01000 441 -GKKTYFNYYK 450 (457)
T ss_pred -cceeHHHHHH
Confidence 2344455543
No 109
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=27.49 E-value=1.6e+02 Score=22.05 Aligned_cols=35 Identities=17% Similarity=0.386 Sum_probs=27.0
Q ss_pred CCCCCCCCEEEEEEEEecCCccccceEEEEEEEEec
Q psy3772 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (119)
Q Consensus 19 ~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~ 54 (119)
+|.-.+||+|.|.++-... -.+-|.+.++|+..+.
T Consensus 51 ~~~a~iGD~IvvsVKk~~p-~~kg~V~kAVIVRtKk 85 (139)
T PTZ00054 51 LPSASLGDMVLATVKKGKP-ELRKKVLNAVIIRQRK 85 (139)
T ss_pred CcccccCCEEEEEEEECCC-cccCCEeeEEEEEECc
Confidence 4678899999999986433 3455999999998773
No 110
>PF09671 Spore_GerQ: Spore coat protein (Spore_GerQ); InterPro: IPR014099 Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria). This protein is cross-linked by a spore coat-associated transglutaminase.
Probab=27.32 E-value=76 Score=21.94 Aligned_cols=42 Identities=17% Similarity=0.257 Sum_probs=31.5
Q ss_pred HHHHHHHHhcCCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEE
Q psy3772 7 IEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISR 52 (119)
Q Consensus 7 ~e~~~~~~~~~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~ 52 (119)
+|+..++ ++-.+..|-..++.+.-.+++.-+...|.|++-+-
T Consensus 5 ~eqsYiE----NILRlN~GK~~T~Y~Tyenn~ewnakvf~GviE~a 46 (81)
T PF09671_consen 5 LEQSYIE----NILRLNRGKLATFYMTYENNSEWNAKVFRGVIEAA 46 (81)
T ss_pred chHHHHH----HHHHhcCCceEEEEEEecCchhhhheeeEEEehhc
Confidence 4555653 66678889999998887666666788999998653
No 111
>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=27.22 E-value=88 Score=19.13 Aligned_cols=16 Identities=19% Similarity=0.301 Sum_probs=13.0
Q ss_pred CCCCCCEEEEEEEEec
Q psy3772 21 DFVTGDTIIVNLNVIE 36 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (119)
.|.+||.+.+.+.-.+
T Consensus 44 ~~~~Gd~i~~~V~~id 59 (69)
T cd05697 44 KFKPGLKVKCRVLSVE 59 (69)
T ss_pred cCCCCCEEEEEEEEEE
Confidence 3999999999886544
No 112
>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=27.17 E-value=1.6e+02 Score=18.25 Aligned_cols=32 Identities=16% Similarity=0.276 Sum_probs=22.8
Q ss_pred CCCCCCEEEEEEEEecCCccccceEEEEEEEEecC
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNK 55 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~ 55 (119)
.+.+||.|.+.+.+..+.. ..+.|.|+...+.
T Consensus 44 ~~~~~~~v~l~~~~~~~~~---~~~~~~V~~~~~~ 75 (102)
T PF07238_consen 44 PLEPGDRVRLSFSLPGGGF---PIVTGRVVRIQKD 75 (102)
T ss_dssp G--TTSEEEEEEECTTTSC---EEEEEEEEEEEEE
T ss_pred CCCCCCEEEEEEEeCCCCe---eEEEEEEEEEECC
Confidence 6899999999998765432 1299999988876
No 113
>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=27.16 E-value=1.7e+02 Score=21.63 Aligned_cols=35 Identities=23% Similarity=0.431 Sum_probs=26.4
Q ss_pred CCCCCCCCEEEEEEEEecCCccccceEEEEEEEEec
Q psy3772 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (119)
Q Consensus 19 ~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~ 54 (119)
.|.-.+||+|.|.++-... ..+-|.+.++++..+.
T Consensus 43 ~~~a~iGD~IvvsVK~~~p-~~kg~v~kAVIVRtkk 77 (131)
T TIGR03673 43 LPCAGVGDMVVVSVKKGTP-EMRKQVFKAVVVRQRK 77 (131)
T ss_pred CCccccCCEEEEEEEECCc-cccCCEeEEEEEEeCc
Confidence 3667899999999985333 2345899999998774
No 114
>PRK13204 ureB urease subunit beta; Reviewed
Probab=27.09 E-value=56 Score=25.18 Aligned_cols=37 Identities=24% Similarity=0.375 Sum_probs=27.1
Q ss_pred cCCCCC-----CCCCCEEEEEEEEecCCccccceEEEEEEEEe
Q psy3772 16 KKNIPD-----FVTGDTIIVNLNVIEGTRKRIQAYEGIVISRR 53 (119)
Q Consensus 16 ~~~~P~-----f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r 53 (119)
+-|+|. |.|||+-.|.+--- |-..++.=|.|.|-+.-
T Consensus 83 RLdIPAGTAVRFEPG~~k~V~LV~~-gG~r~V~Gfnglv~G~l 124 (159)
T PRK13204 83 RLDIPANTAVRFEPGDEKEVTLVPF-AGKRFIFGFNNLVDGWS 124 (159)
T ss_pred ccccCCCCeEeECCCCeeEEEEEEc-cCceEEEccCccccccc
Confidence 578886 99999999998544 44666777777665433
No 115
>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=26.79 E-value=53 Score=21.43 Aligned_cols=15 Identities=33% Similarity=0.656 Sum_probs=10.8
Q ss_pred CCCCCCCCCEEEEEE
Q psy3772 18 NIPDFVTGDTIIVNL 32 (119)
Q Consensus 18 ~~P~f~~GD~v~V~~ 32 (119)
=+|+..|||.|-||.
T Consensus 34 lv~~v~~Gd~VLVHa 48 (68)
T PF01455_consen 34 LVPDVKVGDYVLVHA 48 (68)
T ss_dssp TCTSB-TT-EEEEET
T ss_pred EeCCCCCCCEEEEec
Confidence 467899999999984
No 116
>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=26.68 E-value=84 Score=19.28 Aligned_cols=20 Identities=25% Similarity=0.282 Sum_probs=14.1
Q ss_pred CCCCCCEEEEEEEEecCCcc
Q psy3772 21 DFVTGDTIIVNLNVIEGTRK 40 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~ 40 (119)
.|+.||.|.|.+.-.+.++.
T Consensus 48 ~~~~Gd~v~v~v~~id~~~~ 67 (72)
T cd05689 48 VVSLGDEVEVMVLDIDEERR 67 (72)
T ss_pred EeCCCCEEEEEEEEeeCCcC
Confidence 38999999998765443333
No 117
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=26.66 E-value=2e+02 Score=22.48 Aligned_cols=47 Identities=15% Similarity=0.038 Sum_probs=32.1
Q ss_pred CCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCe
Q psy3772 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNE 70 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gv 70 (119)
...|-++-||.|.|.+.- |. =+ =..+| .|..+..++.++.||| ..|-
T Consensus 161 ~~~~lV~rGd~V~i~~~~--gg-~~-I~~~G--~Al~~G~~Gd~IrVrN-~Sgk 207 (222)
T PRK08515 161 KALILVRKNDIINGVLKE--GG-VS-IEISL--KALQDGNLGDIIQAKN-KSNK 207 (222)
T ss_pred CCcceEecCCEEEEEEEC--CC-EE-EEEEE--EEcccCCCCCEEEEEe-CCCC
Confidence 345679999999998852 21 11 12334 5666788999999999 5553
No 118
>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=26.57 E-value=85 Score=21.98 Aligned_cols=29 Identities=14% Similarity=0.352 Sum_probs=17.7
Q ss_pred CCCCCC-EEEEEEEEecC--CccccceEEEEE
Q psy3772 21 DFVTGD-TIIVNLNVIEG--TRKRIQAYEGIV 49 (119)
Q Consensus 21 ~f~~GD-~v~V~~~i~eg--~k~r~q~f~Gvv 49 (119)
.+.||| ++++++.+.+. .....-.|+|.+
T Consensus 96 ~v~Pg~~~l~~~v~i~~~~~~~~~~~~~~~~~ 127 (138)
T PF07977_consen 96 PVYPGDKTLRIEVEIKKIRRREGGMAIFDGTA 127 (138)
T ss_dssp -B-TTE-EEEEEEEEEEEEEEETTEEEEEEEE
T ss_pred cEeCCCcEEEEEEEEEEeecccCCEEEEEEEE
Confidence 478999 99998888651 233445555544
No 119
>PRK14578 elongation factor P; Provisional
Probab=26.55 E-value=1.3e+02 Score=23.33 Aligned_cols=63 Identities=16% Similarity=0.165 Sum_probs=35.8
Q ss_pred CCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCcee---EEEEEeecCeeEEEEEeecCCccceEEEEEe
Q psy3772 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSN---FIVRKISYNEGIERTFQLYSPIISSIIVKRR 91 (119)
Q Consensus 20 P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~t---ftlR~i~~gvGVEr~f~l~SP~I~~IeVl~~ 91 (119)
-+|++|.++... |.--++..|+ -.+-++|-+.+ ..+||+..|.-+|.+|.-- -.++...|.++
T Consensus 5 ~dik~G~~i~~d-----g~~~~V~~~~---~~kpg~~g~~a~vr~klknl~tG~~~e~tf~s~-d~ve~a~ve~~ 70 (187)
T PRK14578 5 SDFKKGLVIQLD-----GAPCLLLDVT---FQSPSARGANTMVKTKYRNLLTGQVLEKTFRSG-DKVEEADFERH 70 (187)
T ss_pred hhcCCCCEEEEC-----CEEEEEEEEE---EEcCCCCCCceEEEEEEEECCCCCEEEEEECCC-CEEEEeEEEEe
Confidence 468888887762 4222222221 11122332333 4799999999999999643 34555555543
No 120
>TIGR02728 spore_gerQ spore coat protein GerQ. Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria). This protein is cross-linked by a spore coat-associated transglutaminase.
Probab=26.32 E-value=52 Score=22.77 Aligned_cols=41 Identities=22% Similarity=0.274 Sum_probs=31.2
Q ss_pred HHHHHHHHhcCCCCCCCCCCEEEEEEEEecCCccccceEEEEEEE
Q psy3772 7 IEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVIS 51 (119)
Q Consensus 7 ~e~~~~~~~~~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~ 51 (119)
+|+..++ ++-.+..|-+.++.+.-.++++-+-..|.|++-+
T Consensus 3 ~eqSyie----NILRlN~GK~~T~y~Tfenn~ew~akvf~G~iE~ 43 (82)
T TIGR02728 3 VEQSYIE----NILRMNRGKTATVYMTFENSPEWAARVFRGQIEN 43 (82)
T ss_pred chHHHHH----HHHHhcCCceEEEEEEEcCChHhhhhheeeehhh
Confidence 4566653 5667888999999888766667777899998754
No 121
>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=26.31 E-value=92 Score=18.86 Aligned_cols=14 Identities=21% Similarity=0.525 Sum_probs=11.8
Q ss_pred CCCCCEEEEEEEEe
Q psy3772 22 FVTGDTIIVNLNVI 35 (119)
Q Consensus 22 f~~GD~v~V~~~i~ 35 (119)
|++||++++.+.-.
T Consensus 45 ~~~Gd~v~~~v~~~ 58 (73)
T cd05691 45 FKVGDEVEAKITNV 58 (73)
T ss_pred cCCCCEEEEEEEEE
Confidence 89999999987644
No 122
>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=26.30 E-value=97 Score=18.88 Aligned_cols=14 Identities=21% Similarity=0.285 Sum_probs=11.9
Q ss_pred CCCCCEEEEEEEEe
Q psy3772 22 FVTGDTIIVNLNVI 35 (119)
Q Consensus 22 f~~GD~v~V~~~i~ 35 (119)
|++||++.+.+.-.
T Consensus 45 ~~~Gd~i~~~i~~~ 58 (70)
T cd05687 45 VKVGDEVEVYVLRV 58 (70)
T ss_pred CCCCCEEEEEEEEE
Confidence 99999999987643
No 123
>PRK12786 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=26.15 E-value=1.8e+02 Score=24.51 Aligned_cols=48 Identities=6% Similarity=-0.047 Sum_probs=33.6
Q ss_pred CCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCeeE
Q psy3772 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGI 72 (119)
Q Consensus 19 ~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gvGV 72 (119)
-+-++-||.|.|.+... | =....-..+..+.+.+.++.|||...|-=|
T Consensus 256 p~lV~rGd~V~i~~~~g-g-----l~v~~~G~ALe~G~~Gd~IrV~N~~S~kiv 303 (338)
T PRK12786 256 PDLVQRGQLVTLIYQTP-G-----IYLTARGKALEDGAEGDVVRVLNLQSKRTV 303 (338)
T ss_pred ccEEcCCCEEEEEEEcC-C-----EEEEEEEEEccccCCCCEEEEEECCCCCEE
Confidence 34589999999998632 2 133444566777888999999998655433
No 124
>cd03692 mtIF2_IVc mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor EF-Tu. The C-terminal part of mtIF2 contains the entire fMet-tRNAfmet binding site of IF-2 and is resistant to proteolysis. This C-terminal portion consists of two domains, IF2 C1 and IF2 C2. IF2 C2 been shown to contain all molecular determinants necessary and sufficient for the recognition and binding of fMet-tRNAfMet. Like IF2 from certain prokaryotes such as Thermus thermophilus, mtIF2lacks domain II which is thought to be involved in binding of E.coli IF-2 to 30S subunits.
Probab=26.10 E-value=41 Score=22.12 Aligned_cols=13 Identities=38% Similarity=0.542 Sum_probs=8.8
Q ss_pred CCCCCCCCCCEEE
Q psy3772 17 KNIPDFVTGDTII 29 (119)
Q Consensus 17 ~~~P~f~~GD~v~ 29 (119)
.++.+|++||++.
T Consensus 71 ~~~~d~~~Gdvi~ 83 (84)
T cd03692 71 ENFNDIKVGDIIE 83 (84)
T ss_pred eCcccCCCCCEEE
Confidence 4555777788775
No 125
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=25.77 E-value=1e+02 Score=21.85 Aligned_cols=43 Identities=19% Similarity=0.456 Sum_probs=27.7
Q ss_pred CCCCCCCCEEEEEEEE--ecC-CccccceEEEEEEEEecCCCceeE
Q psy3772 19 IPDFVTGDTIIVNLNV--IEG-TRKRIQAYEGIVISRRNKGLNSNF 61 (119)
Q Consensus 19 ~P~f~~GD~v~V~~~i--~eg-~k~r~q~f~GvvI~~r~~g~~~tf 61 (119)
+-+|++||.|.+...= ..| .-.+.+--.|.|...+++.+.-.+
T Consensus 32 l~~y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A~~V~v 77 (98)
T PRK04306 32 LQEFEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRAYIVEV 77 (98)
T ss_pred HHhccCCCEEEEEecCceecCCccccccCCCEEEEeecCeEEEEEE
Confidence 4469999999987631 111 134555668899988877544444
No 126
>TIGR01451 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.
Probab=25.70 E-value=1.6e+02 Score=17.81 Aligned_cols=31 Identities=19% Similarity=0.277 Sum_probs=21.1
Q ss_pred CCCCCCCCCEEEEEEEEecCCccccceEEEEEEE
Q psy3772 18 NIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVIS 51 (119)
Q Consensus 18 ~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~ 51 (119)
+-....|||+|..++.+.+... ..-.+++|.
T Consensus 4 d~~~~~~Gd~v~Yti~v~N~g~---~~a~~v~v~ 34 (53)
T TIGR01451 4 DKTVATIGDTITYTITVTNNGN---VPATNVVVT 34 (53)
T ss_pred CccccCCCCEEEEEEEEEECCC---CceEeEEEE
Confidence 4566899999999998864322 244565554
No 127
>COG1945 Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) [Amino acid transport and metabolism]
Probab=25.44 E-value=1.3e+02 Score=23.25 Aligned_cols=37 Identities=19% Similarity=0.383 Sum_probs=23.6
Q ss_pred CCCCCCCCCEEEEEEE--EecCCccccceEEEEEEEEec
Q psy3772 18 NIPDFVTGDTIIVNLN--VIEGTRKRIQAYEGIVISRRN 54 (119)
Q Consensus 18 ~~P~f~~GD~v~V~~~--i~eg~k~r~q~f~GvvI~~r~ 54 (119)
.+|+|.||.+|-+-+. ..++.-+.+..=-|++|.+.+
T Consensus 58 gl~kl~pG~iv~~V~Ar~~S~~~G~~isaaig~a~p~D~ 96 (163)
T COG1945 58 GLPKLPPGAILFCVMARGTSNEPGRTISAAIGVAIPRDK 96 (163)
T ss_pred cCCcCCCCcEEeEEEeecccCCCCceeeeeeeEEecCCC
Confidence 5899999999998776 233323344455555555553
No 128
>PRK13205 ureB urease subunit beta; Reviewed
Probab=24.81 E-value=67 Score=24.83 Aligned_cols=34 Identities=29% Similarity=0.530 Sum_probs=25.5
Q ss_pred cCCCCC-----CCCCCEEEEEEEEecCCccccceEEEEEE
Q psy3772 16 KKNIPD-----FVTGDTIIVNLNVIEGTRKRIQAYEGIVI 50 (119)
Q Consensus 16 ~~~~P~-----f~~GD~v~V~~~i~eg~k~r~q~f~GvvI 50 (119)
+-|+|. |.|||+-.|.+--- |-..++.=|.|.|-
T Consensus 60 RLdIPAGTAVRFEPGe~ktV~LV~i-gG~R~V~Gfnglv~ 98 (162)
T PRK13205 60 RLDIPSGTAVRLEPGDARTVNLVAI-GGDRIVAGFRDLVD 98 (162)
T ss_pred ccccCCCCeEeECCCCeEEEEEEEc-cCceEEEccCcccc
Confidence 478996 99999999998654 44666777777653
No 129
>CHL00057 rpl14 ribosomal protein L14
Probab=24.79 E-value=1.8e+02 Score=21.19 Aligned_cols=35 Identities=17% Similarity=0.169 Sum_probs=25.6
Q ss_pred CCCCCCCEEEEEEEE--ecCCccccceEEEEEEEEec
Q psy3772 20 PDFVTGDTIIVNLNV--IEGTRKRIQAYEGIVISRRN 54 (119)
Q Consensus 20 P~f~~GD~v~V~~~i--~eg~k~r~q~f~GvvI~~r~ 54 (119)
+.-.+||++.|.++- +++.-.+-|.+.++|+..+.
T Consensus 31 ~~a~vGD~IvvsVk~~~~~~k~kkg~v~kAvIVrtk~ 67 (122)
T CHL00057 31 KYAHIGDVIIAVVKEAVPNMPLKRSEVVRAVIVRTCK 67 (122)
T ss_pred ccccCCCEEEEEEEeccCCCceecCCEEEEEEEEecc
Confidence 667899999998873 22223355899999998774
No 130
>PF02563 Poly_export: Polysaccharide biosynthesis/export protein; InterPro: IPR003715 The extracellular polysaccharide colanic acid (CA) is produced by species of the family Enterobacteriaceae. In Escherichia coli (strain K12) the CA cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The CA gene clusters may be involved in the export of polysaccharide from the cell [].; GO: 0015159 polysaccharide transmembrane transporter activity, 0015774 polysaccharide transport, 0016020 membrane; PDB: 2W8I_E 2W8H_E 2J58_D.
Probab=24.75 E-value=54 Score=21.39 Aligned_cols=13 Identities=15% Similarity=0.332 Sum_probs=8.4
Q ss_pred CCCCCCEEEEEEE
Q psy3772 21 DFVTGDTIIVNLN 33 (119)
Q Consensus 21 ~f~~GD~v~V~~~ 33 (119)
.+.|||.|.|.++
T Consensus 12 ~l~pGD~l~i~v~ 24 (82)
T PF02563_consen 12 RLGPGDVLRISVF 24 (82)
T ss_dssp ---TT-EEEEEET
T ss_pred EECCCCEEEEEEe
Confidence 4899999999986
No 131
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=24.74 E-value=61 Score=21.89 Aligned_cols=14 Identities=21% Similarity=0.292 Sum_probs=11.8
Q ss_pred CCCCCCEEEEEEEE
Q psy3772 21 DFVTGDTIIVNLNV 34 (119)
Q Consensus 21 ~f~~GD~v~V~~~i 34 (119)
.|+|||+|+-.+.-
T Consensus 60 ~f~~GDiV~AkVis 73 (92)
T cd05791 60 CFRPGDIVRAKVIS 73 (92)
T ss_pred hcCCCCEEEEEEEE
Confidence 49999999988853
No 132
>PF00963 Cohesin: Cohesin domain; InterPro: IPR002102 Cohesin domains interact with a complementary domain, termed the dockerin domain (see IPR002105 from INTERPRO). The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome []. The scaffoldin component of the cellulolytic bacterium Clostridium thermocellum is a non-hydrolytic protein which organises the hydrolytic enzymes in a large complex, called the cellulosome. Scaffoldin comprises a series of functional domains, amongst which is a single cellulose-binding domain and nine cohesin domains which are responsible for integrating the individual enzymatic subunits into the complex.; GO: 0030246 carbohydrate binding, 0000272 polysaccharide catabolic process; PDB: 2BM3_A 3P0D_I 3KCP_A 2B59_A 3L8Q_B 3FNK_C 3GHP_B 2CCL_A 1ANU_A 1OHZ_A ....
Probab=24.71 E-value=1.3e+02 Score=21.09 Aligned_cols=32 Identities=19% Similarity=0.269 Sum_probs=20.7
Q ss_pred CCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEe
Q psy3772 18 NIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRR 53 (119)
Q Consensus 18 ~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r 53 (119)
+-++..|||+|.|.+.+...... +.|+-+...
T Consensus 6 ~~~~a~~G~tv~V~V~v~~~~~~----i~~~~~~l~ 37 (141)
T PF00963_consen 6 DSVSAKPGETVTVPVNVSNVSNS----IAGMQFTLS 37 (141)
T ss_dssp SECEE-TTSEEEEEEEEESCTTT----EEEEEEEEE
T ss_pred CCceECCCCEEEEEEEEEcCCCc----EEEEEEEEE
Confidence 34567899999999999764322 555555444
No 133
>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=24.55 E-value=79 Score=21.88 Aligned_cols=15 Identities=27% Similarity=0.490 Sum_probs=13.0
Q ss_pred CCCCCEEEEEEEEec
Q psy3772 22 FVTGDTIIVNLNVIE 36 (119)
Q Consensus 22 f~~GD~v~V~~~i~e 36 (119)
+.|||+|.++..+.+
T Consensus 92 v~~GDtl~~~~~v~~ 106 (146)
T cd03451 92 VFHGDTLYAESEVLS 106 (146)
T ss_pred CCCCCEEEEEEEEEE
Confidence 789999999998864
No 134
>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=24.52 E-value=1.1e+02 Score=17.91 Aligned_cols=14 Identities=29% Similarity=0.444 Sum_probs=11.5
Q ss_pred CCCCCEEEEEEEEe
Q psy3772 22 FVTGDTIIVNLNVI 35 (119)
Q Consensus 22 f~~GD~v~V~~~i~ 35 (119)
|++||.|.|.+.-.
T Consensus 45 ~~~Gd~v~v~v~~~ 58 (69)
T cd05692 45 LKEGDKVKVKVLSI 58 (69)
T ss_pred cCCCCEEEEEEEEE
Confidence 89999999987433
No 135
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=24.48 E-value=77 Score=20.69 Aligned_cols=16 Identities=6% Similarity=0.189 Sum_probs=13.5
Q ss_pred CCCCCCCEEEEEEEEe
Q psy3772 20 PDFVTGDTIIVNLNVI 35 (119)
Q Consensus 20 P~f~~GD~v~V~~~i~ 35 (119)
|.|+.||.|++.+...
T Consensus 1 ~~~~~Ge~v~~~~~~~ 16 (83)
T PF14326_consen 1 TVYRVGERVRFRVTSN 16 (83)
T ss_pred CcccCCCEEEEEEEeC
Confidence 5689999999999763
No 136
>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=24.45 E-value=90 Score=21.10 Aligned_cols=18 Identities=22% Similarity=0.381 Sum_probs=15.3
Q ss_pred CCCCCCCCEEEEEEEEec
Q psy3772 19 IPDFVTGDTIIVNLNVIE 36 (119)
Q Consensus 19 ~P~f~~GD~v~V~~~i~e 36 (119)
-|.|.+||.|++.-.+.+
T Consensus 2 ~p~f~~G~~V~a~~~irN 19 (75)
T PF04319_consen 2 PPRFEWGDKVRARKDIRN 19 (75)
T ss_pred CCccCCCCEEEEEEEeEc
Confidence 388999999999988853
No 137
>PF01345 DUF11: Domain of unknown function DUF11; InterPro: IPR001434 This group of sequences is represented by a conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis (Streptococcus faecalis), and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydia trachomatis outer membrane proteins. In C. trachomatis, three cysteine-rich proteins (also believed to be lipoproteins), MOMP, OMP6 and OMP3, make up the extracellular matrix of the outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. They are thought to be involved in porin formation and, as these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism.; GO: 0005727 extrachromosomal circular DNA
Probab=24.43 E-value=1.9e+02 Score=18.11 Aligned_cols=32 Identities=19% Similarity=0.256 Sum_probs=21.4
Q ss_pred CCCCCCCCCCEEEEEEEEecCCccccceEEEEEEE
Q psy3772 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVIS 51 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~ 51 (119)
-+.+...+||+|..++.+.+... ....+++|.
T Consensus 32 ~~~~~~~~Gd~v~ytitvtN~G~---~~a~nv~v~ 63 (76)
T PF01345_consen 32 VNPSTANPGDTVTYTITVTNTGP---APATNVVVT 63 (76)
T ss_pred cCCCcccCCCEEEEEEEEEECCC---CeeEeEEEE
Confidence 35567999999999998864322 245555554
No 138
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=24.27 E-value=60 Score=22.64 Aligned_cols=31 Identities=19% Similarity=0.322 Sum_probs=20.9
Q ss_pred CCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEec
Q psy3772 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~ 54 (119)
+..-.+.+||.|.|.+.--. .-.|-+|-+..
T Consensus 42 ~~rIrIl~GD~V~VE~spYD-------ltkGRIiyR~~ 72 (87)
T PRK12442 42 KHRIRILAGDRVTLELSPYD-------LTKGRINFRHK 72 (87)
T ss_pred eeeEEecCCCEEEEEECccc-------CCceeEEEEec
Confidence 44456889999999987422 22477777664
No 139
>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=24.13 E-value=43 Score=23.24 Aligned_cols=23 Identities=30% Similarity=0.541 Sum_probs=13.0
Q ss_pred CCCCCCCCCEEEEEEEEecCCccc
Q psy3772 18 NIPDFVTGDTIIVNLNVIEGTRKR 41 (119)
Q Consensus 18 ~~P~f~~GD~v~V~~~i~eg~k~r 41 (119)
+.-++.+|++|.|.|.+.+ .++|
T Consensus 62 ~w~~L~VG~~VMvNYN~d~-P~er 84 (85)
T PF12148_consen 62 KWDELKVGQVVMVNYNVDE-PKER 84 (85)
T ss_dssp -GGG--TT-EEEEEE-TTS-TTS-
T ss_pred cHHhCCcccEEEEecCCCC-cccC
Confidence 4457999999999998755 3554
No 140
>PF12700 HlyD_2: HlyD family secretion protein; PDB: 3LNN_B 4DK0_A 4DK1_C 3FPP_B 2K32_A 2K33_A 3OW7_B 3OOC_A 3T53_B 4DNT_C ....
Probab=24.06 E-value=1.1e+02 Score=23.70 Aligned_cols=43 Identities=19% Similarity=0.326 Sum_probs=29.4
Q ss_pred CCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEE
Q psy3772 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVR 64 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR 64 (119)
.+++.+.+|+.+.|++....+ -+.|.|.|..+.... +.+|+++
T Consensus 205 ~~~~~i~~g~~~~v~~~~~~~----~~~~~g~v~~i~~~~-~~~~~v~ 247 (328)
T PF12700_consen 205 SDASKIKVGQKVEVTIDAPDN----GKSFTGKVSSISPSA-SRTFKVR 247 (328)
T ss_dssp CGTTTHTTTGEEEEEETTSS-----SSEEEEEEEEEESSE-TTEEEEE
T ss_pred HHHHhccCCcEEEEEEEeecC----CCceeeEEeecCCcc-ceeeEEE
Confidence 467789999998887754331 258999998887664 3344443
No 141
>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=23.84 E-value=43 Score=24.70 Aligned_cols=14 Identities=36% Similarity=0.408 Sum_probs=11.5
Q ss_pred CCCCCCCCEEEEEE
Q psy3772 19 IPDFVTGDTIIVNL 32 (119)
Q Consensus 19 ~P~f~~GD~v~V~~ 32 (119)
.-++++||+|.|..
T Consensus 57 ~LDlRIGD~Vkv~~ 70 (131)
T PF08605_consen 57 YLDLRIGDTVKVDG 70 (131)
T ss_pred eeeeecCCEEEECC
Confidence 45799999999954
No 142
>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=23.84 E-value=98 Score=19.52 Aligned_cols=15 Identities=13% Similarity=0.171 Sum_probs=12.5
Q ss_pred CCCCCCEEEEEEEEe
Q psy3772 21 DFVTGDTIIVNLNVI 35 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~ 35 (119)
.|++||.|++.+.-.
T Consensus 48 ~~~~Gd~v~~kV~~~ 62 (72)
T cd05704 48 GFKPGKIVRCCILSK 62 (72)
T ss_pred hCCCCCEEEEEEEEe
Confidence 499999999998644
No 143
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=23.64 E-value=1.7e+02 Score=24.02 Aligned_cols=31 Identities=29% Similarity=0.475 Sum_probs=26.4
Q ss_pred eEEEEEEEEecCCCceeEEEEEeecCee-EEEEEe
Q psy3772 44 AYEGIVISRRNKGLNSNFIVRKISYNEG-IERTFQ 77 (119)
Q Consensus 44 ~f~GvvI~~r~~g~~~tftlR~i~~gvG-VEr~f~ 77 (119)
.|.|+|-.++-.-.+++|++ -.|.| ||-+|-
T Consensus 70 ~fVGvvrni~~~ttn~~~~i---EDGTG~Ievr~W 101 (258)
T COG5235 70 QFVGVVRNIKTSTTNSMFVI---EDGTGSIEVRFW 101 (258)
T ss_pred EEEEEEEeeeecccceEEEE---ecCCceEEEEec
Confidence 79999999998888998886 67998 887773
No 144
>COG2030 MaoC Acyl dehydratase [Lipid metabolism]
Probab=23.54 E-value=1.3e+02 Score=22.02 Aligned_cols=16 Identities=25% Similarity=0.538 Sum_probs=13.9
Q ss_pred CCCCCCEEEEEEEEec
Q psy3772 21 DFVTGDTIIVNLNVIE 36 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (119)
.+.+||+|++...+.+
T Consensus 106 PV~~Gdtl~~~~~v~~ 121 (159)
T COG2030 106 PVFPGDTLRARVEVLD 121 (159)
T ss_pred CCCCCCEEEEEEEEEE
Confidence 4889999999999875
No 145
>PF13358 DDE_3: DDE superfamily endonuclease
Probab=23.51 E-value=37 Score=22.71 Aligned_cols=43 Identities=28% Similarity=0.312 Sum_probs=34.1
Q ss_pred EEEEEEecCCCceeEEEEEeecC--eeEEEEE-eecCCccceEEEE
Q psy3772 47 GIVISRRNKGLNSNFIVRKISYN--EGIERTF-QLYSPIISSIIVK 89 (119)
Q Consensus 47 GvvI~~r~~g~~~tftlR~i~~g--vGVEr~f-~l~SP~I~~IeVl 89 (119)
++++-..|.....+=.++..+.. .|++..| |-|||.+.=||-+
T Consensus 81 ~~~li~DNa~~H~~~~~~~~l~~~~~~~~~~~~P~~sPdLNpiE~~ 126 (146)
T PF13358_consen 81 RIVLIMDNASIHKSKKVQEWLEEHERGIELLFLPPYSPDLNPIENV 126 (146)
T ss_pred EEEEecccccccccccccceeeccccccccccccCcCCccCHHHHH
Confidence 77787888888777778888776 8888777 8899998877744
No 146
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=23.45 E-value=2.7e+02 Score=20.37 Aligned_cols=48 Identities=13% Similarity=0.118 Sum_probs=31.6
Q ss_pred CCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCeeE
Q psy3772 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGI 72 (119)
Q Consensus 19 ~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gvGV 72 (119)
-+-++-||.|.+.+.. |. =+ =.-+| .|..+.+.+.++.|||...|-=|
T Consensus 79 p~lV~rG~~V~i~~~~--gg-l~-i~~~G--~AL~~G~~Gd~IrV~N~~S~riV 126 (141)
T PRK12618 79 PAIVDRNQLVPLAYRL--GG-LE-IRTEG--RALSRGGVGDEIRVMNLSSRTTV 126 (141)
T ss_pred ccEEeCCCEEEEEEec--CC-EE-EEEEE--EEcccCCCCCEEEEEECCCCCEE
Confidence 3458999999998863 21 11 11223 45557788999999997665433
No 147
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=23.32 E-value=2e+02 Score=18.10 Aligned_cols=46 Identities=20% Similarity=0.224 Sum_probs=27.5
Q ss_pred CCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeec
Q psy3772 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISY 68 (119)
Q Consensus 19 ~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~ 68 (119)
.|.|.+||.|-|.-..... ...-.|=++..+..+......++++..
T Consensus 11 ~P~i~~gd~v~v~~~~~~~----~~~~~GDiv~~~~~~~~~~~~vkRv~~ 56 (85)
T cd06530 11 EPTLQPGDLVLVNKLSYGF----REPKRGDVVVFKSPGDPGKPIIKRVIG 56 (85)
T ss_pred cCcccCCCEEEEEEeeccc----CCCCCCCEEEEeCCCCCCCEEEEEEEE
Confidence 5789999999886432211 023346555555554344567777765
No 148
>PF04970 LRAT: Lecithin retinol acyltransferase; InterPro: IPR007053 This entry represents a conserved sequence region found in proteins from viruses, bacteria and eukaryotes. It contains a well-conserved NCEHF motif, though its function in these proteins is unknown.; PDB: 2KYT_A 4DOT_A 4FA0_A.
Probab=23.30 E-value=54 Score=22.82 Aligned_cols=15 Identities=27% Similarity=0.273 Sum_probs=7.8
Q ss_pred CCCCCCCCCEEEEEE
Q psy3772 18 NIPDFVTGDTIIVNL 32 (119)
Q Consensus 18 ~~P~f~~GD~v~V~~ 32 (119)
+.+.++|||.|.+.-
T Consensus 3 ~~~~~~~GD~I~~~r 17 (125)
T PF04970_consen 3 DKKRLKPGDHIEVPR 17 (125)
T ss_dssp ---S--TT-EEEEEE
T ss_pred cccCCCCCCEEEEec
Confidence 467899999999865
No 149
>PF09931 DUF2163: Uncharacterized conserved protein (DUF2163); InterPro: IPR019228 This entry describes the N-terminal region of a family of proteins found almost exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus (Rhodopseudomonas capsulata) gene transfer agent, which packages DNA. An apparent exception is Wolbachia pipientis wMel, a bacterial endosymbiont of the fruit fly, which has several candidate phage-related genes physically separate from obvious prophage regions.
Probab=23.05 E-value=2.6e+02 Score=20.42 Aligned_cols=46 Identities=9% Similarity=0.061 Sum_probs=30.6
Q ss_pred CCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeec
Q psy3772 23 VTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISY 68 (119)
Q Consensus 23 ~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~ 68 (119)
..|-.|++...--....+.+-.|.|.|..++..|..-+++++-...
T Consensus 92 ~d~a~v~i~~~~~~d~~~~~~l~~G~i~ev~~~~~~~~~~~~~~~~ 137 (163)
T PF09931_consen 92 FDGARVEIFRVNWSDPEGAVLLFSGRIGEVTRGGSAFTAELRSLAA 137 (163)
T ss_pred CCCcEEEEEEEecCCCcceEEEEEEEEEEEEecCCEEEEEEecchH
Confidence 3455666554332223567779999999999988666666766544
No 150
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=23.00 E-value=1.6e+02 Score=18.05 Aligned_cols=27 Identities=26% Similarity=0.412 Sum_probs=17.1
Q ss_pred CCCCCCEEEEEEEEecCCccccceEEEEEEE
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVIS 51 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~ 51 (119)
..-.||.|.|.+.- ..+-..-+|-|+.
T Consensus 31 ~A~~gD~V~v~i~~----~~~~~~~eg~vv~ 57 (58)
T PF08206_consen 31 GAMDGDKVLVRITP----PSRGKRPEGEVVE 57 (58)
T ss_dssp TS-TT-EEEEEEEE----SSSEEEEEEEEEE
T ss_pred CCCCCCEEEEEEec----CCCCCCCCEEEEe
Confidence 45679999999864 2233567787775
No 151
>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=22.47 E-value=64 Score=21.69 Aligned_cols=17 Identities=24% Similarity=0.440 Sum_probs=9.9
Q ss_pred CCCCCCCCCCEEEEEEE
Q psy3772 17 KNIPDFVTGDTIIVNLN 33 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~ 33 (119)
+.+-.++|||+|.+.+-
T Consensus 38 k~L~~L~pGq~l~f~~d 54 (85)
T PF04225_consen 38 KPLTRLKPGQTLEFQLD 54 (85)
T ss_dssp --GGG--TT-EEEEEE-
T ss_pred chHhhCCCCCEEEEEEC
Confidence 57778999999999874
No 152
>TIGR00998 8a0101 efflux pump membrane protein (multidrug resistance protein A).
Probab=22.38 E-value=1.2e+02 Score=23.98 Aligned_cols=36 Identities=14% Similarity=0.309 Sum_probs=26.4
Q ss_pred CCCCCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCC
Q psy3772 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKG 56 (119)
Q Consensus 17 ~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g 56 (119)
.+++.+++|+.|.|++... +.. +.|.|.|..+....
T Consensus 250 ~~~~~i~~G~~v~v~~~~~-~~~---~~~~G~V~~Is~~~ 285 (334)
T TIGR00998 250 TQLKNVRIGQPVTIRSDLY-GSD---VVFEGKVTGISMGT 285 (334)
T ss_pred HHHhhCCCCCEEEEEEecC-CCC---CEEEEEEEEECCCc
Confidence 4567799999999997432 211 37999999998653
No 153
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=22.15 E-value=3.2e+02 Score=21.52 Aligned_cols=47 Identities=19% Similarity=0.133 Sum_probs=31.4
Q ss_pred CCCCCCEEEEEEEEecCCccccceEEEEEEEEecCCCceeEEEEEeecCeeEE
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIE 73 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g~~~tftlR~i~~gvGVE 73 (119)
-++-||+|.|.+.-. | =+ =.-+| .|..+.+.+..+.|||...|-=|+
T Consensus 155 lV~rG~~V~I~a~~~-g--~~-Vs~~G--~AL~~G~~Ge~IrVrN~~SgrvV~ 201 (214)
T PRK12617 155 LVRRGDTVPLVSRNG-G--LE-VRMSG--RALSDAGENERVSVENSSSRRVVQ 201 (214)
T ss_pred eEcCCCEEEEEEecC-C--EE-EEEEE--EEccCCCCCCEEEEEECCCCCEEE
Confidence 589999999988521 1 11 12234 455678889999999976664443
No 154
>PF13437 HlyD_3: HlyD family secretion protein
Probab=22.13 E-value=2.4e+02 Score=18.40 Aligned_cols=33 Identities=30% Similarity=0.466 Sum_probs=25.3
Q ss_pred CCCCCCC-CCCEEEEEEEEecCCccccceEEEEEEEEec
Q psy3772 17 KNIPDFV-TGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (119)
Q Consensus 17 ~~~P~f~-~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~ 54 (119)
.++..++ +||-+++++. .+. + +.|.|.|..+..
T Consensus 45 ~~~~~i~~~g~~v~v~~~--~~~-~--~~~~g~V~~I~~ 78 (105)
T PF13437_consen 45 KDIARIKDPGQKVTVRLD--PGP-E--KTIEGKVSSISP 78 (105)
T ss_pred HhhcceEeCCCEEEEEEC--CCC-C--cEEEEEEEEEeC
Confidence 4677787 9999999986 232 2 399999999887
No 155
>PF07154 DUF1392: Protein of unknown function (DUF1392); InterPro: IPR009824 This family consists of several hypothetical cyanobacterial proteins of around 150 residues in length, which seem to be specific to Anabaena species. The function of this family is unknown.
Probab=22.04 E-value=1.7e+02 Score=22.43 Aligned_cols=33 Identities=21% Similarity=0.444 Sum_probs=23.9
Q ss_pred cCCCCCCCCCCEEEEEEEEecCCccccceEEEEEEE
Q psy3772 16 KKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVIS 51 (119)
Q Consensus 16 ~~~~P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~ 51 (119)
..+-|.|.-||.|.+.+. .+|.|.| ...|+..-
T Consensus 82 tv~kp~F~LGd~V~~~f~-~~~pkqR--lIlGv~lv 114 (150)
T PF07154_consen 82 TVQKPAFRLGDRVEFRFY-SDGPKQR--LILGVFLV 114 (150)
T ss_pred eccCCceecCCEEEEEec-CCCCceE--EEEEEEEe
Confidence 357899999999999985 2455555 56776543
No 156
>COG2100 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=21.86 E-value=1.5e+02 Score=25.89 Aligned_cols=31 Identities=16% Similarity=0.455 Sum_probs=23.4
Q ss_pred CCCCC-CCCCCEEEEEEEEecCCccccceEEEEEEEEec
Q psy3772 17 KNIPD-FVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (119)
Q Consensus 17 ~~~P~-f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~ 54 (119)
..+|. |+.||+|++.+-. +| .++|=.+++-.
T Consensus 346 p~lp~PF~rGevv~aevV~-~G------r~kGEmlavAr 377 (414)
T COG2100 346 PRLPKPFKRGEVVKAEVVL-PG------RLKGEMLAVAR 377 (414)
T ss_pred CCCCCccccCcEEEEEEEe-cc------eecceEEEEec
Confidence 56774 9999999999865 45 67777776654
No 157
>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=21.61 E-value=1.1e+02 Score=21.02 Aligned_cols=16 Identities=13% Similarity=0.289 Sum_probs=12.9
Q ss_pred CCCCCCEEEEEEEEec
Q psy3772 21 DFVTGDTIIVNLNVIE 36 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (119)
.|++||+|++.+.-..
T Consensus 66 ~f~vGd~V~~kVi~~d 81 (100)
T cd05693 66 LFSVGQLVRCKVVSLD 81 (100)
T ss_pred hccCCCEEEEEEEEcc
Confidence 3999999999886543
No 158
>PRK13986 urease subunit alpha; Provisional
Probab=21.45 E-value=71 Score=25.92 Aligned_cols=34 Identities=29% Similarity=0.488 Sum_probs=25.0
Q ss_pred cCCCCC-----CCCCCEEEEEEEEecCCccccceEEEEEE
Q psy3772 16 KKNIPD-----FVTGDTIIVNLNVIEGTRKRIQAYEGIVI 50 (119)
Q Consensus 16 ~~~~P~-----f~~GD~v~V~~~i~eg~k~r~q~f~GvvI 50 (119)
+-|+|. |.|||+-.|++--- |.+.++.=|.|.+-
T Consensus 165 RLdIpAGTavRFEPG~~k~V~LV~~-gG~r~v~G~ngl~~ 203 (225)
T PRK13986 165 RLDIASGTAVRFEPGEEKSVELIDI-GGNRRIFGFNALVN 203 (225)
T ss_pred ccccCCCCeEeECCCCeeEEEEEEc-cCceEEecCCcccC
Confidence 468896 99999999998544 44666666666553
No 159
>cd02853 MTHase_N_term Maltooligosyl trehalose synthase (MTSase) N-terminus domain. MTSase and maltooligosyl trehalose trehalohydrolase (MTHase) work together to produce trehalose. MTSase is responsible for converting the alpha-1,4-glucosidic linkage to an alpha,alpha-1,1-glucosidic linkage at the reducing end of the maltooligosaccharide through an intramolecular transglucosylation reaction, while MTHase hydrolyzes the penultimate alpha-1,4 linkage of the reducing end, resulting in the release of trehalose. The N-terminus of MTSase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase.
Probab=21.40 E-value=92 Score=20.15 Aligned_cols=16 Identities=19% Similarity=0.526 Sum_probs=14.4
Q ss_pred EEeecCCccceEEEEE
Q psy3772 75 TFQLYSPIISSIIVKR 90 (119)
Q Consensus 75 ~f~l~SP~I~~IeVl~ 90 (119)
+|.|+||.-++++|+-
T Consensus 11 ~F~vwAP~A~~V~l~l 26 (85)
T cd02853 11 RFRLWAPDAKRVTLRL 26 (85)
T ss_pred EEEEeCCCCCEEEEEe
Confidence 6999999999999984
No 160
>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=21.18 E-value=1.1e+02 Score=18.66 Aligned_cols=21 Identities=14% Similarity=0.284 Sum_probs=15.3
Q ss_pred CCCCCCCEEEEEEEEecCCcc
Q psy3772 20 PDFVTGDTIIVNLNVIEGTRK 40 (119)
Q Consensus 20 P~f~~GD~v~V~~~i~eg~k~ 40 (119)
+.|.+||+|.|.+.-.+-++.
T Consensus 47 ~~~~~G~~v~v~v~~vd~~~~ 67 (74)
T PF00575_consen 47 EVYKIGQTVRVKVIKVDKEKG 67 (74)
T ss_dssp GTCETTCEEEEEEEEEETTTT
T ss_pred cccCCCCEEEEEEEEEECCCC
Confidence 459999999998875544333
No 161
>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=21.17 E-value=1.3e+02 Score=19.17 Aligned_cols=13 Identities=15% Similarity=0.491 Sum_probs=11.4
Q ss_pred CCCCCEEEEEEEE
Q psy3772 22 FVTGDTIIVNLNV 34 (119)
Q Consensus 22 f~~GD~v~V~~~i 34 (119)
|++||.|.|.+.-
T Consensus 59 ~~~Gd~v~vkV~~ 71 (83)
T cd04461 59 FKKGQSVTAKVTS 71 (83)
T ss_pred cCCCCEEEEEEEE
Confidence 9999999998754
No 162
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=21.10 E-value=2e+02 Score=22.61 Aligned_cols=17 Identities=24% Similarity=0.272 Sum_probs=13.7
Q ss_pred CCCCCCCCEEEEEEEEe
Q psy3772 19 IPDFVTGDTIIVNLNVI 35 (119)
Q Consensus 19 ~P~f~~GD~v~V~~~i~ 35 (119)
-|.|++||.|...+.-.
T Consensus 109 ~~~~~~GDlV~akV~~i 125 (235)
T PRK04163 109 RKYLDIGDYIIAKVKDV 125 (235)
T ss_pred HhhCCCCCEEEEEEEEE
Confidence 45699999999998644
No 163
>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=21.06 E-value=2.7e+02 Score=20.21 Aligned_cols=15 Identities=7% Similarity=0.228 Sum_probs=12.8
Q ss_pred CCCCCEEEEEEEEec
Q psy3772 22 FVTGDTIIVNLNVIE 36 (119)
Q Consensus 22 f~~GD~v~V~~~i~e 36 (119)
..+||+|.+...|.+
T Consensus 98 V~~GDtl~~~~~V~~ 112 (149)
T cd03450 98 VPVGSRVRGRFTLLS 112 (149)
T ss_pred eeCCcEEEEEEEEEE
Confidence 679999999998864
No 164
>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=21.01 E-value=1.6e+02 Score=20.95 Aligned_cols=30 Identities=13% Similarity=0.268 Sum_probs=19.0
Q ss_pred CCCCCCCEEEEEEEEecCCc-cccceEEEEEE
Q psy3772 20 PDFVTGDTIIVNLNVIEGTR-KRIQAYEGIVI 50 (119)
Q Consensus 20 P~f~~GD~v~V~~~i~eg~k-~r~q~f~GvvI 50 (119)
|-+.+||++.++..... .. ...-.|.|.+.
T Consensus 91 ~v~p~Gd~l~i~~~~~~-~~~~~~~~~~~~~~ 121 (138)
T cd01289 91 DRFDLGSTLLIVVAELL-QGDSGLGVFECTIE 121 (138)
T ss_pred ceeCCCCeeEEEeeeee-eCCCcEEEEEEEEE
Confidence 44555999999887653 23 25666666643
No 165
>PF01828 Peptidase_A4: Peptidase A4 family; InterPro: IPR000250 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. The peptidases in family G1 form a subset of what were formerly termed 'pepstatin-insensitive carboxyl proteinases'. After its discovery in about 1970, the pentapeptide pepstatin soon came to be thought of as a very general inhibitor of the endopeptidases that are active at acidic pH. But more recently several acid-acting endopeptidases from bacteria and fungi had been found to be resistant to pepstatin. The unusual active sites of the 'pepstatin-insensitive carboxyl peptidases' proved difficult to characterise, but it has now been established that the enzymes from bacteria are acid-acting serine peptidases in family S53 (clan SB), IPR000209 from INTERPRO, whereas the fungal enzymes are in family G1 (formerly A4). The importance of glutamate ('E') and glutamine ('Q') residues in the active sites of the family G1 enzymes led to the family name, Eqolisin []. This group of glutamate/glutamine peptidases belong to MEROPS peptidase family G1 (eqolisin family, clan GA). An example of this group is scytalidoglutamic peptidase. The proteins are thermostable, pepstatin insensitive and are active at low pH ranges []. The enzyme has a unique heterodimeric structure, with a 39-residue light chain and a 173-residue heavy chain bound to each other non-covalently []. The tertiary structure of the active site of scytalidoglutamic peptidase (MEROPS G01.001) with a bound tripeptide product has been interpreted as showing that Glu136 is the primary catalytic residue. The most likely mechanism is suggested to be nucleophilic attack by a water molecule activated by the Glu136 side chain on the si-face of the scissile peptide bond carbon atom to form the tetrahedral intermediate. Electrophilic assistance, and oxyanion stabilisation, are provided by the side-chain amide of Gln53. Both scytalidoglutamic peptidase (MEROPS G01.001) and aspergilloglutamic peptidase (MEROPS G01.002) cleave the Tyr26 Thr27 bond in the B chain of oxidized insulin; a bond not cleaved by other acid-acting endopeptidases. Scytalidoglutamic peptidase is most active on casein at pH 2 and is inhibited by 1,2-epoxy-3-(p-nitrophenoxy)propane (EPNP), a compound that also inhibits pepsin. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis; PDB: 1Y43_B 1S2B_A 2IFR_A 1S2K_A 2IFW_A.
Probab=20.88 E-value=2.7e+02 Score=21.74 Aligned_cols=15 Identities=33% Similarity=0.437 Sum_probs=9.4
Q ss_pred CCCCCCEEEEEEEEe
Q psy3772 21 DFVTGDTIIVNLNVI 35 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~ 35 (119)
.+.|||.|.|++.-.
T Consensus 90 ~v~~GD~i~~~V~a~ 104 (208)
T PF01828_consen 90 PVSPGDTIRVTVTAT 104 (208)
T ss_dssp ---TT-EEEEEEEEE
T ss_pred eECCCCEEEEEEEec
Confidence 489999999999753
No 166
>PRK13188 bifunctional UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase/(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase; Reviewed
Probab=20.80 E-value=1.5e+02 Score=26.29 Aligned_cols=29 Identities=28% Similarity=0.502 Sum_probs=20.5
Q ss_pred CCCCCEEEEEEEEecCCccccceEEEEEE
Q psy3772 22 FVTGDTIIVNLNVIEGTRKRIQAYEGIVI 50 (119)
Q Consensus 22 f~~GD~v~V~~~i~eg~k~r~q~f~GvvI 50 (119)
..|||++.+++.+.+-....+-.|+|.+.
T Consensus 416 V~PGDtL~I~veI~~~~~~giv~f~g~~~ 444 (464)
T PRK13188 416 VVPGDTLIFKVELLSPIRRGICQMQGKAY 444 (464)
T ss_pred CCCCCEEEEEEEEEEEecCCEEEEEEEEE
Confidence 57899999999876522344556777664
No 167
>PF06819 Arc_PepC: Archaeal Peptidase A24 C-terminal Domain; InterPro: IPR009639 This region is of unknown function found at the C terminus of some archael proteins that have multiple transmembrane domains and are predicted to be aspartic peptidases belonging to the MEROPS peptidase subfamily A24A (type 4 prepilin peptidase 1.
Probab=20.79 E-value=1.2e+02 Score=21.92 Aligned_cols=34 Identities=18% Similarity=0.280 Sum_probs=25.6
Q ss_pred hHHHHHHHHHHHhcCCCCCCCCCCEEEEEEEEecC
Q psy3772 3 LIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEG 37 (119)
Q Consensus 3 li~~~e~~~~~~~~~~~P~f~~GD~v~V~~~i~eg 37 (119)
++..+..+.+.. ++.+.+++.||++.=.++..++
T Consensus 16 ~v~al~~e~l~~-~~~VeELkEgdIL~e~I~~k~~ 49 (110)
T PF06819_consen 16 VVYALRGEELSD-KKPVEELKEGDILGEIIYEKDD 49 (110)
T ss_pred HHHHHHHHHHhh-cccHhhcCccceehheEEEeCC
Confidence 455666666643 5788899999999988887655
No 168
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=20.42 E-value=2e+02 Score=21.77 Aligned_cols=27 Identities=11% Similarity=0.156 Sum_probs=17.8
Q ss_pred CCCCCCEEEEEEEEecCCccccceEEEE
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGI 48 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~Gv 48 (119)
...|||++.++..+.+. +.+.-.+.+.
T Consensus 138 PV~pGD~L~~ea~v~~~-~~~~~~v~~~ 164 (185)
T PRK04424 138 PVKLGERVVAKAEVVRK-KGNKYIVEVK 164 (185)
T ss_pred CCCCCCEEEEEEEEEEc-cCCEEEEEEE
Confidence 47899999999998742 3333344443
No 169
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=20.36 E-value=2e+02 Score=20.99 Aligned_cols=51 Identities=16% Similarity=0.291 Sum_probs=30.6
Q ss_pred CCCCCCCEEEEEEEEecCCccccceEEEEEEEEecCC-CceeEEEEEeecCeeEEEEEee
Q psy3772 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKG-LNSNFIVRKISYNEGIERTFQL 78 (119)
Q Consensus 20 P~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~g-~~~tftlR~i~~gvGVEr~f~l 78 (119)
-+|++|-+|.+ +|..-++..++ -.+-|+| --..+.++++..|.-+|.+|+-
T Consensus 7 ~~lr~G~~i~~-----dg~~~~V~~~~---~~KpGKg~a~vrvk~k~l~tG~~~e~~f~~ 58 (131)
T COG0231 7 SELRKGLYIVI-----DGEPYVVVEIS---HVKPGKGGAFVRVKLKNLFTGKKVEKTFKA 58 (131)
T ss_pred HHccCCCEEEE-----CCeEEEEEEEE---EccCCCCCcEEEEEEEEccCCCEEEEEEcC
Confidence 36889988774 23222222221 1122333 2445669999999999999975
No 170
>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=20.08 E-value=1.5e+02 Score=18.94 Aligned_cols=18 Identities=28% Similarity=0.397 Sum_probs=14.3
Q ss_pred CCCCCCCCEEEEE-EEEec
Q psy3772 19 IPDFVTGDTIIVN-LNVIE 36 (119)
Q Consensus 19 ~P~f~~GD~v~V~-~~i~e 36 (119)
.+.+.+||++.+. -++.+
T Consensus 46 ~~~~~~G~vv~i~~~~v~~ 64 (82)
T cd04491 46 ADDLEPGDVVRIENAYVRE 64 (82)
T ss_pred cccCCCCCEEEEEeEEEEe
Confidence 6779999999988 66654
No 171
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=20.04 E-value=80 Score=21.51 Aligned_cols=13 Identities=23% Similarity=0.503 Sum_probs=11.7
Q ss_pred CCCCCCCEEEEEE
Q psy3772 20 PDFVTGDTIIVNL 32 (119)
Q Consensus 20 P~f~~GD~v~V~~ 32 (119)
|+..+||-|-||.
T Consensus 41 ~~~~vGDyVLVHa 53 (82)
T PRK10413 41 PADLLGQWVLVHV 53 (82)
T ss_pred cccccCCEEEEec
Confidence 6789999999986
No 172
>TIGR00376 DNA helicase, putative. The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.
Probab=20.03 E-value=1.6e+02 Score=26.79 Aligned_cols=30 Identities=20% Similarity=0.406 Sum_probs=22.0
Q ss_pred CCCCCCEEEEEEEEecCCccccceEEEEEEEEecC
Q psy3772 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNK 55 (119)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI~~r~~ 55 (119)
.|.+||.|.|.. ++ .....+.|+|..+...
T Consensus 57 ~~~~GD~v~i~~----~~-~~~~~~~g~V~~v~~~ 86 (637)
T TIGR00376 57 EISVGDIVLVSR----GN-PLQSDLTGVVTRVGKR 86 (637)
T ss_pred cCCCCCEEEEec----CC-CCCCCcEEEEEEEcCc
Confidence 699999999873 22 2235689999998764
No 173
>COG3097 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.02 E-value=68 Score=23.06 Aligned_cols=13 Identities=31% Similarity=0.411 Sum_probs=11.4
Q ss_pred CCCCCCEEEEEEE
Q psy3772 21 DFVTGDTIIVNLN 33 (119)
Q Consensus 21 ~f~~GD~v~V~~~ 33 (119)
.|+|||+++|...
T Consensus 32 hf~~g~vlrV~r~ 44 (106)
T COG3097 32 HFKPGDVLRVGRF 44 (106)
T ss_pred cCCCCCEEEEEEe
Confidence 4999999999875
Done!