Query psy3777
Match_columns 99
No_of_seqs 112 out of 1009
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 17:02:03 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3777.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3777hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0335 RplS Ribosomal protein 100.0 2.4E-44 5.1E-49 249.0 12.8 95 1-98 1-98 (115)
2 PRK05338 rplS 50S ribosomal pr 100.0 1.1E-43 2.4E-48 246.8 12.2 95 1-98 1-96 (116)
3 TIGR01024 rplS_bact ribosomal 100.0 1.2E-43 2.6E-48 245.7 12.2 95 1-98 1-96 (113)
4 CHL00084 rpl19 ribosomal prote 100.0 2.7E-43 5.8E-48 245.1 12.0 94 2-98 6-100 (117)
5 PF01245 Ribosomal_L19: Riboso 100.0 5E-43 1.1E-47 242.4 12.0 95 1-98 1-96 (113)
6 KOG1698|consensus 100.0 6.2E-29 1.3E-33 185.5 9.2 95 3-98 76-173 (201)
7 PF05641 Agenet: Agenet domain 89.2 1.5 3.3E-05 27.0 5.2 38 22-65 1-38 (68)
8 smart00743 Agenet Tudor-like d 87.7 4.1 8.8E-05 24.1 6.4 50 20-78 1-50 (61)
9 cd04497 hPOT1_OB1_like hPOT1_O 76.6 6.2 0.00013 27.4 4.5 41 17-65 64-104 (138)
10 PF02765 POT1: Telomeric singl 72.4 4.4 9.6E-05 28.3 2.9 49 17-73 68-117 (146)
11 PRK01191 rpl24p 50S ribosomal 71.1 8.8 0.00019 27.0 4.1 60 20-88 44-105 (120)
12 TIGR03170 flgA_cterm flagella 70.6 16 0.00035 24.3 5.3 47 18-70 62-108 (122)
13 PF12969 DUF3857: Domain of Un 68.9 5.1 0.00011 27.6 2.6 20 17-36 85-104 (177)
14 PF03888 MucB_RseB: MucB/RseB 67.4 23 0.0005 27.6 6.2 51 40-93 8-58 (285)
15 PRK03999 translation initiatio 66.5 16 0.00035 25.5 4.7 57 17-79 6-62 (129)
16 PF02752 Arrestin_C: Arrestin 66.5 13 0.00029 23.9 4.1 32 21-52 15-46 (136)
17 PF11302 DUF3104: Protein of u 59.6 41 0.00089 21.9 5.3 52 19-70 3-58 (75)
18 cd08544 Reeler Reeler, the N-t 59.4 26 0.00057 23.7 4.7 31 21-56 29-59 (135)
19 COG2139 RPL21A Ribosomal prote 57.5 13 0.00027 25.5 2.7 41 17-57 28-71 (98)
20 PF02211 NHase_beta: Nitrile h 57.4 9.3 0.0002 29.2 2.4 36 18-54 131-170 (222)
21 PF10447 EXOSC1: Exosome compo 55.7 9.1 0.0002 25.0 1.8 14 19-32 66-79 (82)
22 TIGR00008 infA translation ini 54.9 11 0.00023 24.0 1.9 26 16-41 39-64 (68)
23 cd05688 S1_RPS1_repeat_ec3 S1_ 54.5 19 0.00042 20.6 3.0 17 21-37 44-60 (68)
24 TIGR01080 rplX_A_E ribosomal p 53.6 36 0.00079 23.6 4.6 61 19-88 39-101 (114)
25 PF09926 DUF2158: Uncharacteri 53.3 9.7 0.00021 23.0 1.5 11 22-32 1-11 (53)
26 PF13144 SAF_2: SAF-like 53.0 61 0.0013 23.2 6.0 46 18-69 136-181 (196)
27 cd00164 S1_like S1_like: Ribos 52.2 23 0.0005 19.6 3.0 15 21-35 41-55 (65)
28 cd05708 S1_Rrp5_repeat_sc12 S1 52.0 22 0.00048 21.0 3.0 16 21-36 47-62 (77)
29 cd05690 S1_RPS1_repeat_ec5 S1_ 51.8 22 0.00047 20.8 2.9 22 21-42 45-66 (69)
30 smart00739 KOW KOW (Kyprides, 51.7 29 0.00062 16.9 3.6 27 21-54 1-27 (28)
31 cd06462 Peptidase_S24_S26 The 50.9 45 0.00098 19.7 4.3 43 19-70 11-53 (84)
32 PF11717 Tudor-knot: RNA bindi 50.1 51 0.0011 19.3 4.6 35 22-63 1-35 (55)
33 TIGR00038 efp translation elon 49.1 86 0.0019 23.0 6.3 49 20-80 4-57 (184)
34 PRK07018 flgA flagellar basal 49.1 50 0.0011 24.9 5.2 48 17-70 172-219 (235)
35 cd05705 S1_Rrp5_repeat_hs14 S1 49.0 27 0.00058 21.6 3.1 22 21-42 50-71 (74)
36 cd05685 S1_Tex S1_Tex: The C-t 48.8 29 0.00063 19.7 3.1 16 22-37 45-60 (68)
37 cd04452 S1_IF2_alpha S1_IF2_al 48.7 26 0.00057 20.8 3.0 15 22-36 50-64 (76)
38 PF12961 DUF3850: Domain of Un 48.4 26 0.00057 22.6 3.0 31 16-53 23-53 (72)
39 cd05703 S1_Rrp5_repeat_hs12_sc 47.9 28 0.00062 21.3 3.1 23 21-43 46-68 (73)
40 COG1499 NMD3 NMD protein affec 47.6 12 0.00026 30.6 1.6 15 18-32 243-257 (355)
41 PF08207 EFP_N: Elongation fac 47.3 61 0.0013 19.3 5.3 49 21-77 4-53 (58)
42 cd04471 S1_RNase_R S1_RNase_R: 47.1 24 0.00052 21.3 2.7 17 20-36 56-72 (83)
43 PF00924 MS_channel: Mechanose 47.0 26 0.00055 24.9 3.1 21 21-53 60-80 (206)
44 PRK15136 multidrug efflux syst 46.6 50 0.0011 26.5 5.1 33 17-53 261-293 (390)
45 PRK09455 rseB anti-sigma E fac 46.3 1.3E+02 0.0028 24.0 7.3 52 38-93 37-89 (319)
46 cd05706 S1_Rrp5_repeat_sc10 S1 45.9 32 0.0007 20.4 3.1 16 21-36 47-62 (73)
47 COG1566 EmrA Multidrug resista 45.5 44 0.00096 27.2 4.6 57 16-76 253-318 (352)
48 PF00238 Ribosomal_L14: Riboso 44.4 40 0.00087 23.3 3.7 37 18-54 29-67 (122)
49 PF11325 DUF3127: Domain of un 44.3 26 0.00055 23.1 2.6 17 19-35 50-66 (84)
50 cd04455 S1_NusA S1_NusA: N-uti 44.1 37 0.00081 20.3 3.2 16 21-36 40-55 (67)
51 smart00333 TUDOR Tudor domain. 43.8 60 0.0013 18.3 6.3 46 20-77 1-46 (57)
52 cd05698 S1_Rrp5_repeat_hs6_sc5 43.5 38 0.00083 19.9 3.1 16 22-37 45-60 (70)
53 COG0361 InfA Translation initi 42.9 21 0.00045 23.2 1.9 20 16-35 41-60 (75)
54 cd05686 S1_pNO40 S1_pNO40: pNO 42.7 33 0.00071 20.8 2.8 16 22-37 49-64 (73)
55 cd05702 S1_Rrp5_repeat_hs11_sc 42.6 34 0.00074 20.4 2.8 16 21-36 46-61 (70)
56 cd05689 S1_RPS1_repeat_ec4 S1_ 42.5 37 0.00081 20.1 3.0 21 21-41 48-68 (72)
57 cd05707 S1_Rrp5_repeat_sc11 S1 42.4 41 0.0009 19.8 3.1 16 21-36 44-59 (68)
58 PTZ00194 60S ribosomal protein 41.9 98 0.0021 22.4 5.5 56 21-85 46-103 (143)
59 PF07076 DUF1344: Protein of u 41.8 31 0.00068 21.6 2.5 22 16-37 32-53 (61)
60 cd00493 FabA_FabZ FabA/Z, beta 41.5 60 0.0013 20.9 4.1 29 21-50 88-116 (131)
61 cd01737 LSm16_N LSm16 belongs 41.4 56 0.0012 20.6 3.6 34 24-65 5-38 (62)
62 PRK00276 infA translation init 41.3 34 0.00073 21.3 2.7 25 22-53 47-71 (72)
63 PF01835 A2M_N: MG2 domain; I 41.0 91 0.002 19.6 6.2 21 17-37 6-26 (99)
64 PRK12442 translation initiatio 40.9 18 0.0004 24.1 1.5 32 16-54 41-72 (87)
65 PRK04183 glutamyl-tRNA(Gln) am 40.4 1E+02 0.0022 25.6 6.1 55 21-93 2-58 (419)
66 PF02014 Reeler: Reeler domain 40.1 22 0.00049 24.0 1.9 33 20-57 28-60 (132)
67 PF11604 CusF_Ec: Copper bindi 40.0 50 0.0011 20.4 3.3 21 17-37 38-58 (70)
68 TIGR01955 RfaH transcriptional 39.8 57 0.0012 22.5 3.9 28 20-54 107-134 (159)
69 smart00316 S1 Ribosomal protei 39.8 46 0.00099 18.6 3.0 16 21-36 46-61 (72)
70 cd01288 FabZ FabZ is a 17kD be 39.7 60 0.0013 21.0 3.9 28 21-49 87-114 (131)
71 TIGR01956 NusG_myco NusG famil 39.6 1.5E+02 0.0031 23.5 6.5 30 18-54 202-231 (258)
72 cd05697 S1_Rrp5_repeat_hs5 S1_ 39.2 48 0.001 19.5 3.1 21 21-41 44-64 (69)
73 COG5636 Uncharacterized conser 38.6 21 0.00046 28.1 1.7 16 18-33 259-274 (284)
74 cd05691 S1_RPS1_repeat_ec6 S1_ 38.5 49 0.0011 19.3 3.0 15 21-35 44-58 (73)
75 TIGR01750 fabZ beta-hydroxyacy 38.4 66 0.0014 21.5 4.0 28 21-49 97-124 (140)
76 PF12148 DUF3590: Protein of u 38.3 15 0.00032 24.4 0.7 23 18-41 62-84 (85)
77 COG2030 MaoC Acyl dehydratase 37.6 69 0.0015 22.5 4.1 17 20-36 105-121 (159)
78 KOG3409|consensus 37.6 73 0.0016 24.2 4.4 18 17-34 118-135 (193)
79 cd05687 S1_RPS1_repeat_ec1_hs1 36.4 58 0.0013 19.1 3.1 15 21-35 44-58 (70)
80 PRK00529 elongation factor P; 36.1 1.7E+02 0.0037 21.4 6.5 55 19-81 4-59 (186)
81 COG0250 NusG Transcription ant 36.0 1.3E+02 0.0028 22.1 5.5 32 17-55 119-150 (178)
82 PF11132 SplA: Transcriptional 35.9 40 0.00086 22.0 2.4 17 18-34 2-18 (75)
83 PRK05483 rplN 50S ribosomal pr 35.7 78 0.0017 22.1 4.1 35 20-54 31-67 (122)
84 KOG4020|consensus 35.3 25 0.00054 27.7 1.6 15 18-32 237-251 (257)
85 PF10610 Tafi-CsgC: Thin aggre 35.1 51 0.0011 22.8 3.0 21 21-41 74-94 (106)
86 PRK08515 flgA flagellar basal 35.1 1.3E+02 0.0028 22.6 5.5 47 17-70 161-207 (222)
87 PRK06005 flgA flagellar basal 35.1 1.2E+02 0.0026 21.8 5.1 50 18-73 97-146 (160)
88 cd05704 S1_Rrp5_repeat_hs13 S1 34.8 55 0.0012 19.8 2.9 16 20-35 47-62 (72)
89 PF07154 DUF1392: Protein of u 34.8 67 0.0015 23.5 3.7 33 16-51 82-114 (150)
90 PRK00006 fabZ (3R)-hydroxymyri 34.7 76 0.0016 21.4 3.9 27 22-49 102-128 (147)
91 KOG3416|consensus 34.7 24 0.00052 25.3 1.4 20 21-47 61-80 (134)
92 PRK09014 rfaH transcriptional 34.2 64 0.0014 22.5 3.5 27 21-54 109-135 (162)
93 PRK02268 hypothetical protein; 33.9 69 0.0015 23.0 3.6 34 17-50 31-65 (141)
94 COG3269 Predicted RNA-binding 33.8 1.3E+02 0.0029 19.4 6.3 47 17-63 8-54 (73)
95 PRK08571 rpl14p 50S ribosomal 33.8 1.2E+02 0.0026 21.6 4.8 35 19-54 44-78 (132)
96 TIGR00074 hypC_hupF hydrogenas 33.7 34 0.00074 22.0 1.9 14 19-32 33-46 (76)
97 PF04225 OapA: Opacity-associa 33.6 33 0.00072 22.1 1.8 18 16-33 37-54 (85)
98 cd05696 S1_Rrp5_repeat_hs4 S1_ 33.4 64 0.0014 19.5 3.0 16 21-36 46-61 (71)
99 cd05791 S1_CSL4 S1_CSL4: CSL4, 33.1 37 0.00079 22.0 2.0 15 21-35 60-74 (92)
100 cd05693 S1_Rrp5_repeat_hs1_sc1 33.0 57 0.0012 21.5 2.9 16 21-36 66-81 (100)
101 PF12945 YcgR_2: Flagellar pro 32.5 1.2E+02 0.0025 18.4 5.0 32 20-55 46-77 (87)
102 cd04461 S1_Rrp5_repeat_hs8_sc7 32.3 69 0.0015 19.6 3.1 15 21-35 58-72 (83)
103 TIGR02754 sod_Ni_protease nick 32.2 1.1E+02 0.0025 18.9 4.1 45 19-67 9-53 (90)
104 cd03692 mtIF2_IVc mtIF2_IVc: t 32.1 28 0.00061 22.0 1.3 13 17-29 71-83 (84)
105 cd05692 S1_RPS1_repeat_hs4 S1_ 32.0 68 0.0015 18.1 2.9 15 21-35 44-58 (69)
106 PF08605 Rad9_Rad53_bind: Fung 31.6 26 0.00057 24.7 1.2 14 19-32 57-70 (131)
107 PF01472 PUA: PUA domain; Int 31.5 34 0.00073 21.1 1.5 13 20-32 29-41 (74)
108 TIGR03673 rpl14p_arch 50S ribo 31.2 1.3E+02 0.0029 21.3 4.7 35 19-54 43-77 (131)
109 cd05793 S1_IF1A S1_IF1A: Trans 31.2 50 0.0011 21.1 2.3 15 20-34 37-51 (77)
110 PF01455 HupF_HypC: HupF/HypC 31.0 43 0.00093 20.9 1.9 15 18-32 34-48 (68)
111 PF14326 DUF4384: Domain of un 31.0 52 0.0011 20.6 2.4 38 20-65 1-38 (83)
112 PTZ00054 60S ribosomal protein 30.9 1.3E+02 0.0029 21.5 4.7 35 19-54 51-85 (139)
113 CHL00010 infA translation init 30.3 59 0.0013 20.6 2.5 26 22-54 47-72 (78)
114 PF02563 Poly_export: Polysacc 30.0 39 0.00085 21.1 1.7 14 21-34 12-25 (82)
115 PF00386 C1q: C1q domain; Int 30.0 88 0.0019 20.6 3.5 30 21-50 94-127 (127)
116 PF06507 Auxin_resp: Auxin res 29.9 1.1E+02 0.0023 20.0 3.7 32 20-54 37-68 (83)
117 PF07977 FabA: FabA-like domai 29.8 61 0.0013 21.8 2.7 30 20-49 95-127 (138)
118 PF00575 S1: S1 RNA binding do 29.6 66 0.0014 19.0 2.6 22 20-41 47-68 (74)
119 cd03451 FkbR2 FkbR2 is a Strep 29.6 62 0.0013 21.5 2.7 16 21-36 91-106 (146)
120 TIGR02728 spore_gerQ spore coa 29.3 33 0.00071 22.7 1.2 41 7-51 3-43 (82)
121 PF01828 Peptidase_A4: Peptida 29.2 1.6E+02 0.0036 22.0 5.2 15 21-35 90-104 (208)
122 TIGR01000 bacteriocin_acc bact 29.0 1.3E+02 0.0028 24.6 4.9 70 17-90 367-440 (457)
123 PF04319 NifZ: NifZ domain; I 29.0 69 0.0015 20.7 2.7 17 19-35 2-18 (75)
124 PF04970 LRAT: Lecithin retino 28.5 40 0.00086 22.5 1.6 15 18-32 3-17 (125)
125 PF13358 DDE_3: DDE superfamil 28.3 26 0.00056 22.5 0.6 41 47-87 81-124 (146)
126 PF09671 Spore_GerQ: Spore coa 27.9 57 0.0012 21.6 2.2 41 7-51 5-45 (81)
127 PRK04163 exosome complex RNA-b 27.7 1.3E+02 0.0028 22.8 4.4 17 19-35 109-125 (235)
128 cd04472 S1_PNPase S1_PNPase: P 27.4 87 0.0019 17.8 2.8 15 21-35 44-58 (68)
129 PRK08059 general stress protei 27.3 84 0.0018 21.2 3.1 15 21-35 51-65 (123)
130 TIGR02266 gmx_TIGR02266 Myxoco 27.2 1.6E+02 0.0034 18.1 5.9 45 20-73 35-79 (96)
131 PF00963 Cohesin: Cohesin doma 27.2 1.1E+02 0.0025 20.5 3.7 31 19-53 7-37 (141)
132 PRK04424 fatty acid biosynthes 27.2 1.2E+02 0.0026 22.0 4.0 17 20-36 137-153 (185)
133 COG3097 Uncharacterized protei 27.1 46 0.001 22.9 1.7 14 20-33 31-44 (106)
134 PRK07252 hypothetical protein; 26.9 83 0.0018 21.5 3.0 16 21-36 47-62 (120)
135 TIGR01067 rplN_bact ribosomal 26.5 1.7E+02 0.0037 20.3 4.5 35 20-54 31-67 (122)
136 PRK13188 bifunctional UDP-3-O- 26.5 98 0.0021 26.2 3.9 30 21-50 415-444 (464)
137 PF07238 PilZ: PilZ domain; I 26.4 1.5E+02 0.0033 17.6 5.2 32 21-55 44-75 (102)
138 PF03069 FmdA_AmdA: Acetamidas 26.3 92 0.002 25.5 3.6 34 22-57 79-113 (369)
139 PF12700 HlyD_2: HlyD family s 25.8 1.2E+02 0.0026 22.6 4.0 43 17-64 205-247 (328)
140 cd03452 MaoC_C MaoC_C The C-t 25.8 1.1E+02 0.0024 20.8 3.4 16 21-36 88-103 (142)
141 TIGR03027 pepcterm_export puta 25.6 54 0.0012 23.1 1.9 13 22-34 3-15 (165)
142 PF11213 DUF3006: Protein of u 25.6 86 0.0019 19.4 2.6 19 17-35 28-51 (71)
143 PRK08572 rps17p 30S ribosomal 25.0 1E+02 0.0022 21.3 3.1 19 43-64 30-48 (108)
144 cd04486 YhcR_OBF_like YhcR_OBF 25.0 96 0.0021 19.5 2.8 18 19-36 42-59 (78)
145 TIGR00405 L26e_arch ribosomal 25.0 2.3E+02 0.005 19.3 6.0 43 20-71 85-127 (145)
146 cd01735 LSm12_N LSm12 belongs 24.9 1.4E+02 0.0031 18.4 3.5 28 21-55 2-29 (61)
147 PF13437 HlyD_3: HlyD family s 24.9 1.8E+02 0.004 18.1 5.2 33 17-54 45-78 (105)
148 PF06819 Arc_PepC: Archaeal Pe 24.9 96 0.0021 21.5 3.0 34 3-37 16-49 (110)
149 TIGR01451 B_ant_repeat conserv 24.8 1.1E+02 0.0024 17.8 2.9 31 18-51 4-34 (53)
150 PF08206 OB_RNB: Ribonuclease 24.7 1.3E+02 0.0029 17.7 3.3 27 21-51 31-57 (58)
151 cd04328 RNAP_I_Rpa43_N RNAP_I_ 24.4 1.1E+02 0.0024 19.5 3.0 41 43-83 45-89 (89)
152 cd03454 YdeM YdeM is a Bacillu 24.2 89 0.0019 20.8 2.7 16 21-36 88-103 (140)
153 PF13550 Phage-tail_3: Putativ 24.1 61 0.0013 21.8 1.9 16 18-33 136-151 (164)
154 PRK04012 translation initiatio 24.0 79 0.0017 21.3 2.4 16 20-35 58-73 (100)
155 PF02107 FlgH: Flagellar L-rin 24.0 76 0.0016 23.2 2.5 18 17-34 20-37 (179)
156 cd03446 MaoC_like MoaC_like 23.9 91 0.002 20.5 2.7 16 21-36 90-105 (140)
157 PRK06461 single-stranded DNA-b 23.9 1E+02 0.0023 21.1 3.0 14 18-31 61-74 (129)
158 cd05695 S1_Rrp5_repeat_hs3 S1_ 23.9 1.3E+02 0.0029 17.8 3.2 16 21-36 42-57 (66)
159 TIGR00922 nusG transcription t 23.8 2.6E+02 0.0056 19.5 6.3 28 20-54 118-145 (172)
160 cd04454 S1_Rrp4_like S1_Rrp4_l 23.8 77 0.0017 19.4 2.2 17 19-35 48-64 (82)
161 PF12701 LSM14: Scd6-like Sm d 23.7 1.8E+02 0.0038 19.4 4.0 59 24-92 7-80 (96)
162 PF00717 Peptidase_S24: Peptid 23.4 52 0.0011 19.2 1.3 44 19-71 8-51 (70)
163 smart00110 C1Q Complement comp 23.4 1.4E+02 0.0029 20.7 3.6 32 20-51 98-133 (135)
164 PF01575 MaoC_dehydratas: MaoC 23.3 1.2E+02 0.0025 19.9 3.1 17 20-36 87-103 (122)
165 cd01289 FabA_like Domain of un 23.3 1.4E+02 0.0029 20.4 3.5 30 20-49 91-120 (138)
166 PRK10413 hydrogenase 2 accesso 23.1 65 0.0014 21.0 1.8 13 20-32 41-53 (82)
167 cd04491 SoSSB_OBF SoSSB_OBF: A 23.1 1.2E+02 0.0026 18.5 3.0 18 19-36 46-64 (82)
168 cd03453 SAV4209_like SAV4209_l 23.0 96 0.0021 20.4 2.7 16 21-36 80-95 (127)
169 COG0668 MscS Small-conductance 22.9 1.7E+02 0.0038 21.7 4.3 38 20-57 146-189 (316)
170 PRK11507 ribosome-associated p 22.8 62 0.0014 20.7 1.6 12 20-31 51-62 (70)
171 cd05684 S1_DHX8_helicase S1_DH 22.6 1.1E+02 0.0024 18.4 2.8 13 22-34 49-61 (79)
172 PRK12786 flgA flagellar basal 22.5 2.6E+02 0.0056 22.6 5.4 47 20-72 257-303 (338)
173 cd05694 S1_Rrp5_repeat_hs2_sc2 22.4 1.3E+02 0.0029 18.5 3.1 16 20-35 42-57 (74)
174 cd03441 R_hydratase_like (R)-h 22.4 1E+02 0.0022 19.5 2.7 17 20-36 79-95 (127)
175 cd08548 Type_I_cohesin_like Ty 22.4 1.3E+02 0.0028 20.7 3.3 47 22-74 10-57 (135)
176 smart00326 SH3 Src homology 3 22.2 79 0.0017 16.9 1.8 13 21-33 20-32 (58)
177 cd05794 S1_EF-P_repeat_2 S1_EF 22.2 78 0.0017 19.3 1.9 16 18-33 33-49 (56)
178 PRK12618 flgA flagellar basal 22.1 2.9E+02 0.0063 19.4 5.1 48 19-72 79-126 (141)
179 PRK14578 elongation factor P; 22.1 3.4E+02 0.0073 20.2 6.2 63 19-90 4-69 (187)
180 PF01281 Ribosomal_L9_N: Ribos 22.0 67 0.0014 18.9 1.5 16 16-31 6-22 (48)
181 PF01176 eIF-1a: Translation i 22.0 49 0.0011 20.1 1.0 16 19-34 39-54 (65)
182 TIGR00998 8a0101 efflux pump m 21.9 1.4E+02 0.003 22.7 3.7 36 17-56 250-285 (334)
183 PRK09838 periplasmic copper-bi 21.6 97 0.0021 21.3 2.5 19 18-36 85-103 (115)
184 PRK13692 (3R)-hydroxyacyl-ACP 21.6 1E+02 0.0022 21.8 2.7 16 21-36 96-111 (159)
185 PRK12269 bifunctional cytidyla 21.6 2.2E+02 0.0047 26.1 5.2 37 21-57 710-768 (863)
186 TIGR00192 urease_beta urease, 21.6 93 0.002 21.3 2.3 33 16-49 60-97 (101)
187 COG2100 Predicted Fe-S oxidore 21.5 2.6E+02 0.0056 23.5 5.3 32 16-54 345-377 (414)
188 PF04246 RseC_MucC: Positive r 21.5 96 0.0021 21.1 2.5 17 17-33 47-63 (135)
189 PRK04306 50S ribosomal protein 21.5 1.3E+02 0.0027 20.5 3.0 44 18-61 31-77 (98)
190 TIGR03635 S17_bact 30S ribosom 21.5 1.2E+02 0.0027 19.1 2.8 19 43-64 2-20 (71)
191 cd02853 MTHase_N_term Maltooli 21.5 96 0.0021 19.2 2.3 16 75-90 11-26 (85)
192 PF01191 RNA_pol_Rpb5_C: RNA p 21.4 71 0.0015 20.5 1.7 14 21-34 48-61 (74)
193 PRK13691 (3R)-hydroxyacyl-ACP 21.3 1E+02 0.0022 22.0 2.7 16 21-36 96-111 (166)
194 TIGR01843 type_I_hlyD type I s 21.2 1.1E+02 0.0023 23.9 2.9 38 16-55 318-355 (423)
195 PF13509 S1_2: S1 domain; PDB: 21.2 1.2E+02 0.0025 18.1 2.5 20 17-36 32-52 (61)
196 TIGR00849 gutA PTS system, glu 21.0 82 0.0018 21.9 2.1 15 17-31 105-119 (121)
197 PRK05609 nusG transcription an 20.9 3E+02 0.0066 19.2 6.1 47 20-75 125-171 (181)
198 COG2012 RPB5 DNA-directed RNA 20.9 56 0.0012 21.6 1.1 14 17-30 38-51 (80)
199 COG5235 RFA2 Single-stranded D 20.9 2E+02 0.0044 22.6 4.3 31 44-77 70-101 (258)
200 PRK06299 rpsA 30S ribosomal pr 20.8 2.5E+02 0.0055 23.5 5.3 37 21-57 331-389 (565)
201 COG1945 Pyruvoyl-dependent arg 20.8 2E+02 0.0043 21.3 4.1 38 17-54 57-96 (163)
202 COG0231 Efp Translation elonga 20.6 2.2E+02 0.0048 19.8 4.2 52 19-78 6-58 (131)
203 TIGR00717 rpsA ribosomal prote 20.5 2.6E+02 0.0056 23.0 5.2 35 22-56 318-374 (516)
204 PRK10334 mechanosensitive chan 20.5 1.5E+02 0.0033 23.1 3.7 12 20-31 128-139 (286)
205 PF13538 UvrD_C_2: UvrD-like h 20.4 60 0.0013 20.2 1.2 11 22-32 1-11 (104)
206 COG0425 SirA Predicted redox p 20.4 56 0.0012 20.8 1.0 49 16-65 23-76 (78)
207 cd05829 Sortase_E Sortase E (S 20.3 82 0.0018 21.9 1.9 16 17-32 68-83 (144)
208 PF08755 YccV-like: Hemimethyl 20.3 96 0.0021 20.4 2.2 25 20-54 2-26 (100)
209 PF01345 DUF11: Domain of unkn 20.1 1.5E+02 0.0032 17.8 2.9 31 18-51 33-63 (76)
210 cd06529 S24_LexA-like Peptidas 20.1 1.6E+02 0.0035 17.3 3.1 40 19-70 11-51 (81)
No 1
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.4e-44 Score=248.96 Aligned_cols=95 Identities=55% Similarity=0.959 Sum_probs=92.9
Q ss_pred Cc--hHHHHHHHHHHhhcCCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCeeEEEEEee
Q psy3777 1 MN--LIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQL 78 (99)
Q Consensus 1 m~--li~~~e~~~~~~~~~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gvGVEr~fpl 78 (99)
|+ +++.+|++|+ ++++|+|+|||||+|++++.||+|+|+|.|+|+|||++|+|+++|||||++++|+|||++||+
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 55 8999999999 788999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCccceEEEEEeee-eeeee
Q psy3777 79 YSPIISSIIVKRRGD-RNAYI 98 (99)
Q Consensus 79 ~SP~I~~I~V~~~~k-rra~l 98 (99)
|||.|++|+|+++|| |||||
T Consensus 78 ~SP~Ie~IeV~rrGkVRRAKL 98 (115)
T COG0335 78 HSPLIESIEVVRRGKVRRAKL 98 (115)
T ss_pred CCCceeEEEEEecCceeeeee
Confidence 999999999999999 99998
No 2
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=100.00 E-value=1.1e-43 Score=246.78 Aligned_cols=95 Identities=58% Similarity=0.960 Sum_probs=93.5
Q ss_pred CchHHHHHHHHHHhhcCCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCeeEEEEEeecC
Q psy3777 1 MNLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQLYS 80 (99)
Q Consensus 1 m~li~~~e~~~~~~~~~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gvGVEr~fpl~S 80 (99)
|++++.+|++|+ ++++|+|+|||+|+|++++.||+|+|+|.|+|+||+++++|+++||||||+++|+|||++||+||
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 CccceEEEEEeee-eeeee
Q psy3777 81 PIISSIIVKRRGD-RNAYI 98 (99)
Q Consensus 81 P~I~~I~V~~~~k-rra~l 98 (99)
|.|++|+|+++|| |||+|
T Consensus 78 P~I~~IeV~r~gkvRRAKL 96 (116)
T PRK05338 78 PRIDSIEVVRRGKVRRAKL 96 (116)
T ss_pred CcccEEEEEEecccchhhe
Confidence 9999999999999 99998
No 3
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=100.00 E-value=1.2e-43 Score=245.65 Aligned_cols=95 Identities=54% Similarity=0.905 Sum_probs=93.6
Q ss_pred CchHHHHHHHHHHhhcCCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCeeEEEEEeecC
Q psy3777 1 MNLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQLYS 80 (99)
Q Consensus 1 m~li~~~e~~~~~~~~~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gvGVEr~fpl~S 80 (99)
|++++.+|++|+ +.++|+|+|||+|+|++.+.||+|+|+|.|+|+||+++++|+++||||||+++|+|||++||+||
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 78999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccceEEEEEeee-eeeee
Q psy3777 81 PIISSIIVKRRGD-RNAYI 98 (99)
Q Consensus 81 P~I~~I~V~~~~k-rra~l 98 (99)
|.|++|+|+++|| |||+|
T Consensus 78 P~I~~IeVl~~~kvrRaKL 96 (113)
T TIGR01024 78 PNIDSIEVVRRGKVRRAKL 96 (113)
T ss_pred CccceEEEEEeCccchhhe
Confidence 9999999999999 99998
No 4
>CHL00084 rpl19 ribosomal protein L19
Probab=100.00 E-value=2.7e-43 Score=245.15 Aligned_cols=94 Identities=45% Similarity=0.716 Sum_probs=91.7
Q ss_pred chHHHHHHHHHHhhcCCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCeeEEEEEeecCC
Q psy3777 2 NLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQLYSP 81 (99)
Q Consensus 2 ~li~~~e~~~~~~~~~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gvGVEr~fpl~SP 81 (99)
++++.+|++|+ ++++|+|+|||+|+|++.+.||+|+|+|.|+|+||+++++|+++||||||+++|+|||++||+|||
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 47899999999 789999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccceEEEEEeee-eeeee
Q psy3777 82 IISSIIVKRRGD-RNAYI 98 (99)
Q Consensus 82 ~I~~I~V~~~~k-rra~l 98 (99)
.|++|+|+++|| |||+|
T Consensus 83 ~I~~IeV~r~gkvRRAKL 100 (117)
T CHL00084 83 KLASIEVLRRSKVRRAKL 100 (117)
T ss_pred ccceEEEEEeCccchhee
Confidence 999999999999 99998
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=5e-43 Score=242.36 Aligned_cols=95 Identities=55% Similarity=0.937 Sum_probs=92.8
Q ss_pred CchHHHHHHHHHHhhcCCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCeeEEEEEeecC
Q psy3777 1 MNLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQLYS 80 (99)
Q Consensus 1 m~li~~~e~~~~~~~~~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gvGVEr~fpl~S 80 (99)
|||++.+|++|+ +.++|+|+|||+|+|++.+.||+|+|+|.|+|+|||++++|+++||||||+++|+|||++||+||
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 899999999999 89999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccceEEEEEeee-eeeee
Q psy3777 81 PIISSIIVKRRGD-RNAYI 98 (99)
Q Consensus 81 P~I~~I~V~~~~k-rra~l 98 (99)
|.|++|+|+++|+ |||+|
T Consensus 78 P~I~~IeV~~~~kvrRaKL 96 (113)
T PF01245_consen 78 PLIKSIEVLRRGKVRRAKL 96 (113)
T ss_dssp TTEEEEEEEEEBECSSSST
T ss_pred CCeEEEEEEEecccchhhh
Confidence 9999999999999 99998
No 6
>KOG1698|consensus
Probab=99.96 E-value=6.2e-29 Score=185.50 Aligned_cols=95 Identities=31% Similarity=0.619 Sum_probs=88.8
Q ss_pred hHHHHHHHHHHhh--cCCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCeeEEEEEeecC
Q psy3777 3 LIQKIEQEEIIRL--KKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQLYS 80 (99)
Q Consensus 3 li~~~e~~~~~~~--~~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gvGVEr~fpl~S 80 (99)
+++.||.++|... ..++|+|+|||+|+|++.+++ ++.++..|.|+||+++++|+++||+|||++.|+|||-.|||||
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 6788888887744 579999999999999999996 6999999999999999999999999999999999999999999
Q ss_pred CccceEEEEEeee-eeeee
Q psy3777 81 PIISSIIVKRRGD-RNAYI 98 (99)
Q Consensus 81 P~I~~I~V~~~~k-rra~l 98 (99)
|+|++|+|++..| |||+|
T Consensus 155 P~IkeI~Vlk~~k~rra~L 173 (201)
T KOG1698|consen 155 PNIKEIKVLKLEKRRRAKL 173 (201)
T ss_pred CCeeEEEEechhhcccchh
Confidence 9999999999988 99987
No 7
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=89.23 E-value=1.5 Score=27.02 Aligned_cols=38 Identities=21% Similarity=0.394 Sum_probs=25.0
Q ss_pred cCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEE
Q psy3777 22 FVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRK 65 (99)
Q Consensus 22 f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~ 65 (99)
|++||.|+|.... +| -+-.=|.|.|++..+.+ ++.|+-
T Consensus 1 F~~G~~VEV~s~e-~g--~~gaWf~a~V~~~~~~~---~~~V~Y 38 (68)
T PF05641_consen 1 FKKGDEVEVSSDE-DG--FRGAWFPATVLKENGDD---KYLVEY 38 (68)
T ss_dssp --TT-EEEEEE-S-BT--T--EEEEEEEEEEETT----EEEEEE
T ss_pred CCCCCEEEEEEcC-CC--CCcEEEEEEEEEeCCCc---EEEEEE
Confidence 7899999998754 34 37789999999998765 777764
No 8
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=87.71 E-value=4.1 Score=24.07 Aligned_cols=50 Identities=24% Similarity=0.367 Sum_probs=35.5
Q ss_pred CCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCeeEEEEEee
Q psy3777 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQL 78 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gvGVEr~fpl 78 (99)
+.|++||.|.+.+.. + -.=|.|+|++..+ +..+.|+=...+.|-+-.|+.
T Consensus 1 ~~~~~G~~Ve~~~~~-~-----~~W~~a~V~~~~~---~~~~~V~~~~~~~~~~e~v~~ 50 (61)
T smart00743 1 SDFKKGDRVEVFSKE-E-----DSWWEAVVTKVLG---DGKYLVRYLTESEPLKETVDW 50 (61)
T ss_pred CCcCCCCEEEEEECC-C-----CEEEEEEEEEECC---CCEEEEEECCCCcccEEEEeH
Confidence 468999999998853 2 2589999999886 445777544433776666653
No 9
>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=76.64 E-value=6.2 Score=27.38 Aligned_cols=41 Identities=27% Similarity=0.423 Sum_probs=32.0
Q ss_pred CCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEE
Q psy3777 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRK 65 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~ 65 (99)
..+|.+.+||+|.++= =++|.|.|-..+..+. -.+++-|=+
T Consensus 64 ~~LP~v~~GDVIll~~-------~kv~~~~g~~~~~~~~-~~ss~avf~ 104 (138)
T cd04497 64 ESLPIVKVGDIILLRR-------VKIQSYNGKPQGISND-RGSSWAVFR 104 (138)
T ss_pred hhCCCCCCCCEEEEEE-------EEEEEECCceEEEECC-CceeEEEEc
Confidence 5789899999999873 4578999998888776 456777633
No 10
>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=72.36 E-value=4.4 Score=28.27 Aligned_cols=49 Identities=29% Similarity=0.423 Sum_probs=32.2
Q ss_pred CCCCCcCC-CCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCeeEE
Q psy3777 17 KNIPDFVT-GDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIE 73 (99)
Q Consensus 17 ~~~p~f~~-GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gvGVE 73 (99)
..+|.+.. ||+|.++ .-++|.|.|-..+..+.+-++++-|= ..++.|..
T Consensus 68 ~~LP~v~~~GDii~l~-------r~kv~~~~~~~~~~~~~~~~ss~~vf-~~~~~~~~ 117 (146)
T PF02765_consen 68 ESLPNVKSVGDIIRLR-------RVKVQSYNGKPQGLSNSTSNSSWAVF-SSGGSGAP 117 (146)
T ss_dssp HHSCTTCSTTHEEEEE-------EEEEEEETTEEEEEEECECTEEEEEE-CTSSTTTC
T ss_pred HHCCCCCCCCCEEEEE-------EEEEEEECCEEEEEecCCCcEEEEEE-ecCCCCCC
Confidence 46899888 9999987 12356777776666666656777763 23444443
No 11
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=71.08 E-value=8.8 Score=26.99 Aligned_cols=60 Identities=22% Similarity=0.165 Sum_probs=37.6
Q ss_pred CCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEe--ecCeeEEEEEeecCCccceEEE
Q psy3777 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKI--SYNEGIERTFQLYSPIISSIIV 88 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i--~~gvGVEr~fpl~SP~I~~I~V 88 (99)
..++.||.|.|-. |.-. -=+|.|+++....- .++|-.+ ....|+|.-+|+|.-.|.=+..
T Consensus 44 ~~IkkGD~V~Vis----G~~K---Gk~GkV~~V~~~~~--~V~VeGvn~~k~~G~~~e~pIh~SNV~l~~l 105 (120)
T PRK01191 44 LPVRKGDTVKVMR----GDFK---GEEGKVVEVDLKRG--RIYVEGVTVKKADGTEVPRPIHPSNVMITKL 105 (120)
T ss_pred ceEeCCCEEEEee----cCCC---CceEEEEEEEcCCC--EEEEeCcEEECCCCeEEEcccchhHeEEEeC
Confidence 3699999999964 3211 23499999864321 2333322 2235689999999887765443
No 12
>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=70.59 E-value=16 Score=24.28 Aligned_cols=47 Identities=17% Similarity=0.070 Sum_probs=34.2
Q ss_pred CCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCe
Q psy3777 18 NIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNE 70 (99)
Q Consensus 18 ~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gv 70 (99)
.-|-++-||.|.+.+.. |+ =...--..|..+..++.++.+||...|-
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 44679999999998864 22 1233444777788999999999976553
No 13
>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=68.85 E-value=5.1 Score=27.63 Aligned_cols=20 Identities=25% Similarity=0.356 Sum_probs=13.0
Q ss_pred CCCCCcCCCCEEEEEEEEec
Q psy3777 17 KNIPDFVTGDTIIVNLNVIE 36 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~~i~e 36 (99)
-.+|++++||+|...|.+..
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 57899999999999999864
No 14
>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=67.36 E-value=23 Score=27.58 Aligned_cols=51 Identities=31% Similarity=0.342 Sum_probs=36.8
Q ss_pred eeeceEEEEEEEEecCCCcceEEEEEeecCeeEEEEEeecCCccceEEEEEeee
Q psy3777 40 KRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQLYSPIISSIIVKRRGD 93 (99)
Q Consensus 40 ~r~q~f~GvvIa~r~~g~~stftlR~i~~gvGVEr~fpl~SP~I~~I~V~~~~k 93 (99)
-|.++|+|+.+-.++..+.+.=.+....+|.-.|+...|..|.- ||+|+|.
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 45689999999999877655444445567777999999999875 7888764
No 15
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=66.47 E-value=16 Score=25.49 Aligned_cols=57 Identities=7% Similarity=0.108 Sum_probs=35.5
Q ss_pred CCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCeeEEEEEeec
Q psy3777 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQLY 79 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gvGVEr~fpl~ 79 (99)
...|+|+.||+|... |.--.+..++-.--++++ +.--.+.+||+..|-=+|.+|+-.
T Consensus 6 ~~~~~lrkG~~i~~~-----g~p~~V~~~~~~kpGkhg-~a~vr~k~knL~tG~~~e~~~~s~ 62 (129)
T PRK03999 6 VEVGELKEGSYVVID-----GEPCKIVEISKSKPGKHG-SAKARIVAIGIFDGQKRSLVQPVD 62 (129)
T ss_pred ccHHHccCCCEEEEC-----CEEEEEEEEEeecCCCCC-cEEEEEEEEECCCCCEEEEEecCC
Confidence 356889999999652 432333333322222222 224667899999999999999743
No 16
>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=66.45 E-value=13 Score=23.95 Aligned_cols=32 Identities=28% Similarity=0.532 Sum_probs=22.2
Q ss_pred CcCCCCEEEEEEEEecCCceeeceEEEEEEEE
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISR 52 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~ 52 (99)
.|.|||.+.|++.+...++.+++...--++..
T Consensus 15 ~~~~Ge~i~v~v~i~n~s~~~i~~I~v~L~~~ 46 (136)
T PF02752_consen 15 AYVPGETIPVNVEIDNQSKKKIKKIKVSLVER 46 (136)
T ss_dssp EEETT--EEEEEEEEE-SSSEEEEEEEEEEEE
T ss_pred EECCCCEEEEEEEEEECCCCEEEEEEEEEEEE
Confidence 48999999999999877777776666555543
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=59.57 E-value=41 Score=21.89 Aligned_cols=52 Identities=21% Similarity=0.243 Sum_probs=36.1
Q ss_pred CCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecC----CCcceEEEEEeecCe
Q psy3777 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNK----GLNSNFIVRKISYNE 70 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~----g~~stftlR~i~~gv 70 (99)
+..++|||+|-|.-.-..+++..-.-..|-||...+. -..|=|.+=++-.|+
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 5678999999998654333445557789999987762 224558887776653
No 18
>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=59.37 E-value=26 Score=23.68 Aligned_cols=31 Identities=23% Similarity=0.513 Sum_probs=25.6
Q ss_pred CcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCC
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKG 56 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g 56 (99)
.+.||+.+.|++.-.+ . ..|.|..|.-|..+
T Consensus 29 ~y~pG~~~~Vtl~~~~---~--~~F~GF~lqAr~~~ 59 (135)
T cd08544 29 SYVPGETYTVTLSGSS---P--SPFRGFLLQARDAS 59 (135)
T ss_pred EECCCCEEEEEEECCC---C--CceeEEEEEEEcCC
Confidence 6899999999987432 2 79999999988865
No 19
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=57.48 E-value=13 Score=25.49 Aligned_cols=41 Identities=20% Similarity=0.511 Sum_probs=29.9
Q ss_pred CCCCCcCCCCEEEEEEEEe--cC-CceeeceEEEEEEEEecCCC
Q psy3777 17 KNIPDFVTGDTIIVNLNVI--EG-TRKRIQAYEGIVISRRNKGL 57 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~~i~--eg-~k~r~q~f~GvvIa~r~~g~ 57 (99)
+-+-+|.+||.|-+.+.=+ .| --.|.|=.+|+|+..+++..
T Consensus 28 r~l~ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay 71 (98)
T COG2139 28 RYLQEYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAY 71 (98)
T ss_pred hHHhhccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEE
Confidence 3466899999998876321 11 24789999999999997544
No 20
>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=57.42 E-value=9.3 Score=29.23 Aligned_cols=36 Identities=22% Similarity=0.328 Sum_probs=18.5
Q ss_pred CCCCcCCCCEEEEEEEEecCCceeeceE----EEEEEEEec
Q psy3777 18 NIPDFVTGDTIIVNLNVIEGTRKRIQAY----EGIVISRRN 54 (99)
Q Consensus 18 ~~p~f~~GD~v~V~~~i~eg~k~r~q~f----~GvvIa~r~ 54 (99)
.-|.|.+||.|+|.-.-.. .-+|+..| .|+|.+.++
T Consensus 131 ~~~~F~vGd~Vrv~~~~~~-~HtR~P~Y~rg~~G~I~~~~g 170 (222)
T PF02211_consen 131 APPRFAVGDRVRVRNLPPP-GHTRLPRYVRGKTGTIERVHG 170 (222)
T ss_dssp SS-SS-TT-EEEE-----S-S--SS-GGGTT-EEEEEEEEE
T ss_pred CCCCCCCCCEEEECCCCCC-CcccccHhhCCCeeEEEEEec
Confidence 4578999999999976654 36777766 677776654
No 21
>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=55.67 E-value=9.1 Score=24.99 Aligned_cols=14 Identities=21% Similarity=0.337 Sum_probs=9.1
Q ss_pred CCCcCCCCEEEEEE
Q psy3777 19 IPDFVTGDTIIVNL 32 (99)
Q Consensus 19 ~p~f~~GD~v~V~~ 32 (99)
.-.|+|||+|+=.+
T Consensus 66 ~~~FrpGDIVrA~V 79 (82)
T PF10447_consen 66 YDCFRPGDIVRARV 79 (82)
T ss_dssp GGT--SSSEEEEEE
T ss_pred HhccCCCCEEEEEE
Confidence 34699999998665
No 22
>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=54.88 E-value=11 Score=24.02 Aligned_cols=26 Identities=27% Similarity=0.386 Sum_probs=18.2
Q ss_pred cCCCCCcCCCCEEEEEEEEecCCcee
Q psy3777 16 KKNIPDFVTGDTIIVNLNVIEGTRKR 41 (99)
Q Consensus 16 ~~~~p~f~~GD~v~V~~~i~eg~k~r 41 (99)
+++.-.+.+||.|.|.++--+-+|-|
T Consensus 39 r~~rI~I~~GD~V~Ve~spyd~tkgr 64 (68)
T TIGR00008 39 RMHYIRILPGDKVKVELSPYDLTRGR 64 (68)
T ss_pred hhccEEECCCCEEEEEECcccCCcEe
Confidence 34455689999999998765444444
No 23
>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=54.53 E-value=19 Score=20.64 Aligned_cols=17 Identities=24% Similarity=0.266 Sum_probs=13.4
Q ss_pred CcCCCCEEEEEEEEecC
Q psy3777 21 DFVTGDTIIVNLNVIEG 37 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg 37 (99)
.|++||.|+|.+.-.+.
T Consensus 44 ~~~~Gd~v~v~i~~vd~ 60 (68)
T cd05688 44 VVNVGDEVEVKVLKIDK 60 (68)
T ss_pred EECCCCEEEEEEEEEEC
Confidence 38999999999765543
No 24
>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=53.57 E-value=36 Score=23.57 Aligned_cols=61 Identities=16% Similarity=0.138 Sum_probs=37.9
Q ss_pred CCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEee--cCeeEEEEEeecCCccceEEE
Q psy3777 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKIS--YNEGIERTFQLYSPIISSIIV 88 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~--~gvGVEr~fpl~SP~I~~I~V 88 (99)
-..++-||.|.|.- |.- .--+|.|+.+.++.. .+.|-.+- ...|+|.-.|+|.-+|+=+..
T Consensus 39 ~~~IkkGD~V~Vi~----Gk~---KGk~GkV~~V~~~~~--~V~Vegvn~~k~~G~~~e~pIh~SnV~l~~l 101 (114)
T TIGR01080 39 ALPVRKGDKVRIMR----GDF---KGHEGKVSKVDLKRY--RIYVEGVTKEKVNGTEVPVPIHPSNVMITKL 101 (114)
T ss_pred cceeecCCEEEEec----CCC---CCCEEEEEEEEcCCC--EEEEcCeEEECCCCeEEEeeechHHeEEEec
Confidence 34799999999964 421 235699999875443 23332221 123578888998777765443
No 25
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=53.33 E-value=9.7 Score=23.00 Aligned_cols=11 Identities=27% Similarity=0.537 Sum_probs=9.2
Q ss_pred cCCCCEEEEEE
Q psy3777 22 FVTGDTIIVNL 32 (99)
Q Consensus 22 f~~GD~v~V~~ 32 (99)
|++||+|+.+.
T Consensus 1 f~~GDvV~LKS 11 (53)
T PF09926_consen 1 FKIGDVVQLKS 11 (53)
T ss_pred CCCCCEEEEcc
Confidence 78999998864
No 26
>PF13144 SAF_2: SAF-like
Probab=53.00 E-value=61 Score=23.18 Aligned_cols=46 Identities=17% Similarity=0.151 Sum_probs=34.5
Q ss_pred CCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecC
Q psy3777 18 NIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYN 69 (99)
Q Consensus 18 ~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~g 69 (99)
..|.++-||.|.|.+.. |+ =..+--.+|..+..++.++.|||...|
T Consensus 136 ~~~~V~~G~~V~v~~~~--g~----i~i~~~g~Al~~G~~G~~I~V~N~~S~ 181 (196)
T PF13144_consen 136 PPPLVKRGDIVTVIARS--GG----ISISTEGKALEDGALGDTIRVKNLSSG 181 (196)
T ss_pred cceecCCCCEEEEEEEe--CC----EEEEEEEEEccCCCCCCEEEEEECCCC
Confidence 45789999999998864 22 123344478888899999999997655
No 27
>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=52.17 E-value=23 Score=19.56 Aligned_cols=15 Identities=27% Similarity=0.406 Sum_probs=12.6
Q ss_pred CcCCCCEEEEEEEEe
Q psy3777 21 DFVTGDTIIVNLNVI 35 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~ 35 (99)
.|++||+|++.+.-.
T Consensus 41 ~~~~G~~v~~~v~~~ 55 (65)
T cd00164 41 VFKVGDEVEVKVLEV 55 (65)
T ss_pred EeCCCCEEEEEEEEE
Confidence 499999999998654
No 28
>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=52.05 E-value=22 Score=21.05 Aligned_cols=16 Identities=25% Similarity=0.372 Sum_probs=12.8
Q ss_pred CcCCCCEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIE 36 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (99)
.|++||.|+|.+.-.+
T Consensus 47 ~~~~Gd~v~v~i~~vd 62 (77)
T cd05708 47 LFRVGDKVRAKVLKID 62 (77)
T ss_pred eecCCCEEEEEEEEEe
Confidence 3899999999876544
No 29
>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=51.80 E-value=22 Score=20.78 Aligned_cols=22 Identities=23% Similarity=0.303 Sum_probs=15.6
Q ss_pred CcCCCCEEEEEEEEecCCceee
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRI 42 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~ 42 (99)
.|++||.|+|.+.-.+.++.|+
T Consensus 45 ~~~~G~~v~v~v~~id~~~~~i 66 (69)
T cd05690 45 IYKKGQEVEAVVLNIDVERERI 66 (69)
T ss_pred EECCCCEEEEEEEEEECCcCEE
Confidence 4899999999976554444443
No 30
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=51.69 E-value=29 Score=16.88 Aligned_cols=27 Identities=30% Similarity=0.423 Sum_probs=18.4
Q ss_pred CcCCCCEEEEEEEEecCCceeeceEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~ 54 (99)
.|.+||.|+|.- |. ..-+.|.+.++.+
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 478999999964 32 2355788777653
No 31
>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=50.91 E-value=45 Score=19.74 Aligned_cols=43 Identities=19% Similarity=0.318 Sum_probs=28.2
Q ss_pred CCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCe
Q psy3777 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNE 70 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gv 70 (99)
.|.|..||+|-|.-... ..-.|=+++.+..| ...++|++....
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 47899999998874321 24445555555444 568888887665
No 32
>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=50.14 E-value=51 Score=19.32 Aligned_cols=35 Identities=26% Similarity=0.535 Sum_probs=24.3
Q ss_pred cCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEE
Q psy3777 22 FVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIV 63 (99)
Q Consensus 22 f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftl 63 (99)
|.+|+.|.+.. .+| +.+++-|+.++..+-...+.|
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 67899999887 223 699999999998654444444
No 33
>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=49.07 E-value=86 Score=22.98 Aligned_cols=49 Identities=22% Similarity=0.327 Sum_probs=32.2
Q ss_pred CCcCCCCEEEEEEEEecCCceeeceEEEEEEEEe----cCC-CcceEEEEEeecCeeEEEEEeecC
Q psy3777 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRR----NKG-LNSNFIVRKISYNEGIERTFQLYS 80 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r----~~g-~~stftlR~i~~gvGVEr~fpl~S 80 (99)
-++++||+|... |. .|+ |+... ++| .--.+.+|++..|.-+|++|+-..
T Consensus 4 ~~ik~G~~I~~~-----g~-----~~~--V~~~~~~kpGkg~A~~rvk~knL~tG~~~e~~f~~~~ 57 (184)
T TIGR00038 4 NDLRKGLVIELD-----GE-----PYV--VLEFEHVKPGKGQAFVRVKLKNLLTGKVLEKTFRSGE 57 (184)
T ss_pred hhccCCCEEEEC-----CE-----EEE--EEEEEEeeCCCCceEEEEEEEECCCCCEEEEEeCCCC
Confidence 478999999652 42 333 23321 232 234677999999999999998554
No 34
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=49.06 E-value=50 Score=24.87 Aligned_cols=48 Identities=8% Similarity=0.034 Sum_probs=34.1
Q ss_pred CCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCe
Q psy3777 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNE 70 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gv 70 (99)
..-|-++.||.|.|.+.. |+ = ...--..|..+.+.+..+.|||...|-
T Consensus 172 ~~~~~V~~G~~V~i~~~~--g~-~---~i~~~G~Al~~G~~Gd~IrVrN~~Sgk 219 (235)
T PRK07018 172 RQAWVVCKGQTVSIIARG--DG-F---SVKTEGEALNDGAVGQQIRVRNMASGQ 219 (235)
T ss_pred cCccEeCCCCEEEEEEec--CC-E---EEEEEEEEcCCCCCCCeEEEEECCCCC
Confidence 345679999999998863 21 1 222333677788999999999986653
No 35
>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=48.98 E-value=27 Score=21.59 Aligned_cols=22 Identities=5% Similarity=0.194 Sum_probs=16.7
Q ss_pred CcCCCCEEEEEEEEecCCceee
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRI 42 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~ 42 (99)
.|++||.|++.+.-.+.++.|+
T Consensus 50 ~~~~G~~v~~kVl~id~~~~~i 71 (74)
T cd05705 50 YLPEGKLLTAKVLSVNSEKNLV 71 (74)
T ss_pred ccCCCCEEEEEEEEEECCCCEE
Confidence 5899999999987665555554
No 36
>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=48.79 E-value=29 Score=19.71 Aligned_cols=16 Identities=25% Similarity=0.383 Sum_probs=12.9
Q ss_pred cCCCCEEEEEEEEecC
Q psy3777 22 FVTGDTIIVNLNVIEG 37 (99)
Q Consensus 22 f~~GD~v~V~~~i~eg 37 (99)
|++||.++|.+.-.+.
T Consensus 45 ~~~Gd~v~v~i~~vd~ 60 (68)
T cd05685 45 VSVGDIVEVKVISIDE 60 (68)
T ss_pred cCCCCEEEEEEEEEEC
Confidence 7999999999865543
No 37
>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=48.67 E-value=26 Score=20.83 Aligned_cols=15 Identities=13% Similarity=0.273 Sum_probs=12.3
Q ss_pred cCCCCEEEEEEEEec
Q psy3777 22 FVTGDTIIVNLNVIE 36 (99)
Q Consensus 22 f~~GD~v~V~~~i~e 36 (99)
|++||+|+|.+.-.+
T Consensus 50 ~~~Gd~v~vkv~~~d 64 (76)
T cd04452 50 VKVGRKEVVKVIRVD 64 (76)
T ss_pred eCCCCEEEEEEEEEE
Confidence 899999999976543
No 38
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=48.44 E-value=26 Score=22.55 Aligned_cols=31 Identities=32% Similarity=0.457 Sum_probs=22.3
Q ss_pred cCCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEe
Q psy3777 16 KKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRR 53 (99)
Q Consensus 16 ~~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r 53 (99)
+++=-+|++||++...-+.. | .|+|-.+..+
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 45555899999999987643 3 6777776654
No 39
>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=47.85 E-value=28 Score=21.32 Aligned_cols=23 Identities=13% Similarity=0.315 Sum_probs=16.6
Q ss_pred CcCCCCEEEEEEEEecCCceeec
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRIQ 43 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q 43 (99)
.|++||.|++.+.-.+.++.|+.
T Consensus 46 ~~~vG~~v~~kV~~id~~~~~i~ 68 (73)
T cd05703 46 KFPIGQALKAKVVGVDKEHKLLR 68 (73)
T ss_pred hCCCCCEEEEEEEEEeCCCCEEE
Confidence 49999999999776544455443
No 40
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=47.58 E-value=12 Score=30.64 Aligned_cols=15 Identities=40% Similarity=0.689 Sum_probs=13.0
Q ss_pred CCCCcCCCCEEEEEE
Q psy3777 18 NIPDFVTGDTIIVNL 32 (99)
Q Consensus 18 ~~p~f~~GD~v~V~~ 32 (99)
.+|+|+|||+|.+.-
T Consensus 243 rip~~~~gDiV~~~~ 257 (355)
T COG1499 243 RIPEFRPGDIVSVRG 257 (355)
T ss_pred ECCCCCCCCEEEECC
Confidence 479999999999864
No 41
>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=47.26 E-value=61 Score=19.33 Aligned_cols=49 Identities=18% Similarity=0.393 Sum_probs=28.9
Q ss_pred CcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCC-CcceEEEEEeecCeeEEEEEe
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKG-LNSNFIVRKISYNEGIERTFQ 77 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g-~~stftlR~i~~gvGVEr~fp 77 (99)
++++|.++.. +|+-=.+..++-+ .-++| .--.+.+||+..|.-+|.+|.
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 6889998866 3433333333221 12333 233456999999999999995
No 42
>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=47.13 E-value=24 Score=21.27 Aligned_cols=17 Identities=24% Similarity=0.387 Sum_probs=13.5
Q ss_pred CCcCCCCEEEEEEEEec
Q psy3777 20 PDFVTGDTIIVNLNVIE 36 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~e 36 (99)
..|++||.|+|.+.-.+
T Consensus 56 ~~~~~gd~v~v~v~~vd 72 (83)
T cd04471 56 KVFRLGDKVKVRVVRVD 72 (83)
T ss_pred CEEcCCCEEEEEEEEec
Confidence 35899999999986553
No 43
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=47.00 E-value=26 Score=24.86 Aligned_cols=21 Identities=33% Similarity=0.401 Sum_probs=13.3
Q ss_pred CcCCCCEEEEEEEEecCCceeeceEEEEEEEEe
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRR 53 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r 53 (99)
+|++||.|++. .+.|.|..+.
T Consensus 60 pf~vGD~I~i~------------~~~G~V~~I~ 80 (206)
T PF00924_consen 60 PFKVGDRIEIG------------GVEGRVEEIG 80 (206)
T ss_dssp SS-TT-EEESS------------S-EEEEEEE-
T ss_pred CccCCCEEEEE------------EeehHHHhcC
Confidence 79999999885 4567777765
No 44
>PRK15136 multidrug efflux system protein EmrA; Provisional
Probab=46.62 E-value=50 Score=26.54 Aligned_cols=33 Identities=12% Similarity=0.324 Sum_probs=24.7
Q ss_pred CCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEe
Q psy3777 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRR 53 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r 53 (99)
.+++.+++|+.|.|++..-.+. ..|.|.|..+.
T Consensus 261 ~~l~~v~~Gq~V~I~~da~p~~----~~~~G~V~~I~ 293 (390)
T PRK15136 261 TQLANMRIGQPATITSDIYGDD----VVYTGKVVGLD 293 (390)
T ss_pred HHHhcCCCCCEEEEEEecCCCC----ceEEEEEEEEC
Confidence 3567899999999987543221 37999999984
No 45
>PRK09455 rseB anti-sigma E factor; Provisional
Probab=46.31 E-value=1.3e+02 Score=24.03 Aligned_cols=52 Identities=19% Similarity=0.291 Sum_probs=39.4
Q ss_pred CceeeceEEEEEEEEecCCCcceEEEEEee-cCeeEEEEEeecCCccceEEEEEeee
Q psy3777 38 TRKRIQAYEGIVISRRNKGLNSNFIVRKIS-YNEGIERTFQLYSPIISSIIVKRRGD 93 (99)
Q Consensus 38 ~k~r~q~f~GvvIa~r~~g~~stftlR~i~-~gvGVEr~fpl~SP~I~~I~V~~~~k 93 (99)
+..+.++|+|+.+-.++..+ +|+.++-.. +|.=.|+.-.|.-|.- ||+|+|.
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 35677999999999997665 556666554 4555999999998874 7888875
No 46
>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=45.88 E-value=32 Score=20.43 Aligned_cols=16 Identities=13% Similarity=0.272 Sum_probs=12.8
Q ss_pred CcCCCCEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIE 36 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (99)
.|++||+|++.+.-..
T Consensus 47 ~~~~Gd~v~~~V~~~d 62 (73)
T cd05706 47 KFKKNDIVRACVLSVD 62 (73)
T ss_pred ccCCCCEEEEEEEEEe
Confidence 3999999999886543
No 47
>COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms]
Probab=45.51 E-value=44 Score=27.22 Aligned_cols=57 Identities=18% Similarity=0.203 Sum_probs=40.3
Q ss_pred cCCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecC-CC--------cceEEEEEeecCeeEEEEE
Q psy3777 16 KKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNK-GL--------NSNFIVRKISYNEGIERTF 76 (99)
Q Consensus 16 ~~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~-g~--------~stftlR~i~~gvGVEr~f 76 (99)
...++.++||+-++|++..-.++ ..|+|++-++-.. |. +.|...=++.+.+.|.-.|
T Consensus 253 ETqL~~~r~Gq~a~I~~da~~~~----~~~~G~v~~i~~~tg~~fsllp~~natgN~tkvvQRvPVrI~l 318 (352)
T COG1566 253 ETQLARVRPGQPAEITLDAYPGN----GVVEGIVEGIAPATGSAFSLLPAQNATGNWTKVVQRVPVRIEL 318 (352)
T ss_pred eeecCcccCCCeEEEEEEcCCCc----eEEEEEEEEecCCcccccccCCCccCCCCEEEEEEeeeEEEEe
Confidence 36789999999999999765332 7899999998752 21 3344444667777776555
No 48
>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=44.44 E-value=40 Score=23.34 Aligned_cols=37 Identities=19% Similarity=0.321 Sum_probs=27.4
Q ss_pred CCCCcCCCCEEEEEEEEe--cCCceeeceEEEEEEEEec
Q psy3777 18 NIPDFVTGDTIIVNLNVI--EGTRKRIQAYEGIVISRRN 54 (99)
Q Consensus 18 ~~p~f~~GD~v~V~~~i~--eg~k~r~q~f~GvvIa~r~ 54 (99)
..+....||+|.|.+.-. .+.-++-|.+.|+|+..+.
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 456788999999998765 3334556899999998775
No 49
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=44.33 E-value=26 Score=23.12 Aligned_cols=17 Identities=29% Similarity=0.638 Sum_probs=15.0
Q ss_pred CCCcCCCCEEEEEEEEe
Q psy3777 19 IPDFVTGDTIIVNLNVI 35 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~ 35 (99)
+..|.+||.|+|.+.+.
T Consensus 50 l~~~~~Gd~V~Vsf~i~ 66 (84)
T PF11325_consen 50 LDNFQVGDEVKVSFNIE 66 (84)
T ss_pred hccCCCCCEEEEEEEee
Confidence 37899999999999885
No 50
>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=44.08 E-value=37 Score=20.26 Aligned_cols=16 Identities=19% Similarity=0.331 Sum_probs=13.1
Q ss_pred CcCCCCEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIE 36 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (99)
.|++||.++|.+.-.+
T Consensus 40 ~~~~Gd~v~v~v~~v~ 55 (67)
T cd04455 40 SYRPGDRIKAYVLEVR 55 (67)
T ss_pred cCCCCCEEEEEEEEEe
Confidence 5899999999886544
No 51
>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=43.80 E-value=60 Score=18.31 Aligned_cols=46 Identities=22% Similarity=0.344 Sum_probs=32.2
Q ss_pred CCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCeeEEEEEe
Q psy3777 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQ 77 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gvGVEr~fp 77 (99)
+.+++|+.+.+.+ .+| +-|.|.|++..+. .++.|+ +-..|-+..++
T Consensus 1 ~~~~~G~~~~a~~--~d~-----~wyra~I~~~~~~---~~~~V~--f~D~G~~~~v~ 46 (57)
T smart00333 1 PTFKVGDKVAARW--EDG-----EWYRARIIKVDGE---QLYEVF--FIDYGNEEVVP 46 (57)
T ss_pred CCCCCCCEEEEEe--CCC-----CEEEEEEEEECCC---CEEEEE--EECCCccEEEe
Confidence 3689999999998 344 5999999999865 557774 33444444444
No 52
>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=43.48 E-value=38 Score=19.87 Aligned_cols=16 Identities=19% Similarity=0.324 Sum_probs=13.2
Q ss_pred cCCCCEEEEEEEEecC
Q psy3777 22 FVTGDTIIVNLNVIEG 37 (99)
Q Consensus 22 f~~GD~v~V~~~i~eg 37 (99)
|++||.+++.+.-.+.
T Consensus 45 ~~~G~~i~v~v~~~d~ 60 (70)
T cd05698 45 FRVGQVVKVKVLSCDP 60 (70)
T ss_pred ccCCCEEEEEEEEEcC
Confidence 9999999999876543
No 53
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=42.91 E-value=21 Score=23.17 Aligned_cols=20 Identities=30% Similarity=0.521 Sum_probs=15.2
Q ss_pred cCCCCCcCCCCEEEEEEEEe
Q psy3777 16 KKNIPDFVTGDTIIVNLNVI 35 (99)
Q Consensus 16 ~~~~p~f~~GD~v~V~~~i~ 35 (99)
++..-.+.|||.|.|..+--
T Consensus 41 r~~~i~I~~GD~V~Ve~~~~ 60 (75)
T COG0361 41 RKNRIRILPGDVVLVELSPY 60 (75)
T ss_pred hheeEEeCCCCEEEEEeccc
Confidence 34455789999999998753
No 54
>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=42.72 E-value=33 Score=20.79 Aligned_cols=16 Identities=19% Similarity=0.117 Sum_probs=12.9
Q ss_pred cCCCCEEEEEEEEecC
Q psy3777 22 FVTGDTIIVNLNVIEG 37 (99)
Q Consensus 22 f~~GD~v~V~~~i~eg 37 (99)
|++||.|+|.+.-.+.
T Consensus 49 ~~~Gd~v~vkv~~vd~ 64 (73)
T cd05686 49 VDVGEKVWVKVIGREM 64 (73)
T ss_pred ECCCCEEEEEEEEECC
Confidence 7999999999865543
No 55
>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=42.56 E-value=34 Score=20.41 Aligned_cols=16 Identities=19% Similarity=0.142 Sum_probs=13.1
Q ss_pred CcCCCCEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIE 36 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (99)
.|++||+|++.+.-..
T Consensus 46 ~~~~Gd~i~~kVl~~d 61 (70)
T cd05702 46 KFKIGQKIKARVIGGH 61 (70)
T ss_pred hCCCCCEEEEEEEEEe
Confidence 4999999999986543
No 56
>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=42.52 E-value=37 Score=20.09 Aligned_cols=21 Identities=29% Similarity=0.343 Sum_probs=15.0
Q ss_pred CcCCCCEEEEEEEEecCCcee
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKR 41 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r 41 (99)
.|+.||.|+|.+.-.+.++.+
T Consensus 48 ~~~~Gd~v~v~v~~id~~~~~ 68 (72)
T cd05689 48 VVSLGDEVEVMVLDIDEERRR 68 (72)
T ss_pred EeCCCCEEEEEEEEeeCCcCE
Confidence 489999999997655444444
No 57
>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=42.37 E-value=41 Score=19.76 Aligned_cols=16 Identities=19% Similarity=0.335 Sum_probs=12.9
Q ss_pred CcCCCCEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIE 36 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (99)
.|++||.|++.+.-..
T Consensus 44 ~~~~Gd~v~~~v~~~d 59 (68)
T cd05707 44 RFKVGQLVKGKIVSID 59 (68)
T ss_pred ccCCCCEEEEEEEEEe
Confidence 3999999999976543
No 58
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=41.86 E-value=98 Score=22.40 Aligned_cols=56 Identities=20% Similarity=0.186 Sum_probs=32.5
Q ss_pred CcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEe--ecCeeEEEEEeecCCccce
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKI--SYNEGIERTFQLYSPIISS 85 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i--~~gvGVEr~fpl~SP~I~~ 85 (99)
.++.||+|.|-- |.-. -=+|-|+++-.+.- .+.|-.+ ...-|-..-+|+|...+.=
T Consensus 46 ~IkkGD~V~Vi~----Gk~K---Gk~GkV~~V~~k~~--~ViVEgvn~~Kk~gk~~e~PIh~SNV~i 103 (143)
T PTZ00194 46 PVRKDDEVMVVR----GHHK---GREGKVTAVYRKKW--VIHIEKITREKANGEPVQIGIHPSNVII 103 (143)
T ss_pred eeecCCEEEEec----CCCC---CCceEEEEEEcCCC--EEEEeCeEEEecCCCEeecCcCchheEE
Confidence 699999999953 4321 12499999865432 3333222 1222333457888877643
No 59
>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=41.85 E-value=31 Score=21.60 Aligned_cols=22 Identities=14% Similarity=0.362 Sum_probs=18.3
Q ss_pred cCCCCCcCCCCEEEEEEEEecC
Q psy3777 16 KKNIPDFVTGDTIIVNLNVIEG 37 (99)
Q Consensus 16 ~~~~p~f~~GD~v~V~~~i~eg 37 (99)
..+++.++||.-|.|.|....|
T Consensus 32 ef~~~~L~~G~kV~V~yd~~~g 53 (61)
T PF07076_consen 32 EFDFDGLKPGMKVVVFYDEVDG 53 (61)
T ss_pred cccccccCCCCEEEEEEEccCC
Confidence 3578899999999999987654
No 60
>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=41.49 E-value=60 Score=20.87 Aligned_cols=29 Identities=17% Similarity=0.511 Sum_probs=19.9
Q ss_pred CcCCCCEEEEEEEEecCCceeeceEEEEEE
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVI 50 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI 50 (99)
...|||++.+.+.+.+- +...-.|.+.+.
T Consensus 88 ~v~pgd~l~i~~~i~~~-~~~~~~~~~~~~ 116 (131)
T cd00493 88 PVLPGDTLTLEVELLKV-RRGLGKFDGRAY 116 (131)
T ss_pred CcCCCCEEEEEEEEEEe-eCCEEEEEEEEE
Confidence 56799999999998742 334555555543
No 61
>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=41.38 E-value=56 Score=20.56 Aligned_cols=34 Identities=15% Similarity=0.327 Sum_probs=21.6
Q ss_pred CCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEE
Q psy3777 24 TGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRK 65 (99)
Q Consensus 24 ~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~ 65 (99)
.|+.|.++- .+.+-.|+|.+.++...- -|+.+|+
T Consensus 5 iGs~VSI~C------~~~lGVyQG~i~~V~~~~--qTI~l~~ 38 (62)
T cd01737 5 LGSIVSINC------GETLGVYQGLVSAVDQES--QTISLAF 38 (62)
T ss_pred cceEEEEec------CCceEEEEEEEEEeCccc--eEEEEee
Confidence 466666654 245679999999887532 3444444
No 62
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=41.29 E-value=34 Score=21.30 Aligned_cols=25 Identities=28% Similarity=0.476 Sum_probs=17.1
Q ss_pred cCCCCEEEEEEEEecCCceeeceEEEEEEEEe
Q psy3777 22 FVTGDTIIVNLNVIEGTRKRIQAYEGIVISRR 53 (99)
Q Consensus 22 f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r 53 (99)
..+||.|.|.....+.+ +|.++-+.
T Consensus 47 i~vGD~V~ve~~~~~~~-------~g~Iv~r~ 71 (72)
T PRK00276 47 ILPGDKVTVELSPYDLT-------KGRITYRH 71 (72)
T ss_pred cCCCCEEEEEEcccCCC-------eEEEEEEe
Confidence 68999999997654322 37766553
No 63
>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=40.95 E-value=91 Score=19.55 Aligned_cols=21 Identities=19% Similarity=0.245 Sum_probs=16.1
Q ss_pred CCCCCcCCCCEEEEEEEEecC
Q psy3777 17 KNIPDFVTGDTIIVNLNVIEG 37 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~~i~eg 37 (99)
.|-|-.+|||+|.+...+...
T Consensus 6 TDr~iYrPGetV~~~~~~~~~ 26 (99)
T PF01835_consen 6 TDRPIYRPGETVHFRAIVRDL 26 (99)
T ss_dssp ESSSEE-TTSEEEEEEEEEEE
T ss_pred CCccCcCCCCEEEEEEEEecc
Confidence 467889999999999986543
No 64
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=40.95 E-value=18 Score=24.13 Aligned_cols=32 Identities=22% Similarity=0.352 Sum_probs=21.5
Q ss_pred cCCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEec
Q psy3777 16 KKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (99)
Q Consensus 16 ~~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~ 54 (99)
+++.-.+.+||.|.|.++--+-+ .|-++-+..
T Consensus 41 R~~rIrIl~GD~V~VE~spYDlt-------kGRIiyR~~ 72 (87)
T PRK12442 41 RKHRIRILAGDRVTLELSPYDLT-------KGRINFRHK 72 (87)
T ss_pred eeeeEEecCCCEEEEEECcccCC-------ceeEEEEec
Confidence 45556789999999998754333 366666553
No 65
>PRK04183 glutamyl-tRNA(Gln) amidotransferase subunit D; Validated
Probab=40.38 E-value=1e+02 Score=25.63 Aligned_cols=55 Identities=24% Similarity=0.492 Sum_probs=34.8
Q ss_pred CcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecC--eeEEEEEeecCCccceEEEEEeee
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYN--EGIERTFQLYSPIISSIIVKRRGD 93 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~g--vGVEr~fpl~SP~I~~I~V~~~~k 93 (99)
.+.+||.|+|... + ..|+|++|-... +..+++ |.-+| +|+.. -.|++|+++.++.
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 699999997655 233333 44444 56642 2456677776654
No 66
>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=40.12 E-value=22 Score=24.05 Aligned_cols=33 Identities=18% Similarity=0.410 Sum_probs=23.6
Q ss_pred CCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCC
Q psy3777 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGL 57 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~ 57 (99)
..+.||+.+.|++.. ...+.|.|..|.-+....
T Consensus 28 ~~y~pg~~~~Vtl~~-----~~~~~F~GFllqAr~~~~ 60 (132)
T PF02014_consen 28 SSYEPGQTYTVTLSS-----SGSSSFRGFLLQARDANN 60 (132)
T ss_dssp SSB-TTBEEEEEEEE-----TTTEEBSEEEEEEEETT-
T ss_pred CeEcCCCEEEEEEEC-----CCCCceeEEEEEEEeCCC
Confidence 358999999999932 233689999998886443
No 67
>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=39.99 E-value=50 Score=20.41 Aligned_cols=21 Identities=10% Similarity=0.317 Sum_probs=15.3
Q ss_pred CCCCCcCCCCEEEEEEEEecC
Q psy3777 17 KNIPDFVTGDTIIVNLNVIEG 37 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~~i~eg 37 (99)
.++..|++||.|...+...++
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 456789999999999987654
No 68
>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=39.81 E-value=57 Score=22.50 Aligned_cols=28 Identities=18% Similarity=0.402 Sum_probs=21.7
Q ss_pred CCcCCCCEEEEEEEEecCCceeeceEEEEEEEEec
Q psy3777 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~ 54 (99)
+.|.+||.|+|. +|. .+-|+|.+....+
T Consensus 107 ~~~~~G~~V~V~----~GP---f~g~~g~v~~~~~ 134 (159)
T TIGR01955 107 TLPYKGDKVRIT----DGA---FAGFEAIFLEPDG 134 (159)
T ss_pred cCCCCCCEEEEe----ccC---CCCcEEEEEEECC
Confidence 348999999885 353 5689999999874
No 69
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=39.81 E-value=46 Score=18.63 Aligned_cols=16 Identities=19% Similarity=0.364 Sum_probs=12.9
Q ss_pred CcCCCCEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIE 36 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (99)
.|++||.+++.+.-..
T Consensus 46 ~~~~G~~v~~~V~~~~ 61 (72)
T smart00316 46 VLKVGDEVKVKVLSVD 61 (72)
T ss_pred eecCCCEEEEEEEEEe
Confidence 3999999999886543
No 70
>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=39.69 E-value=60 Score=20.99 Aligned_cols=28 Identities=25% Similarity=0.568 Sum_probs=19.1
Q ss_pred CcCCCCEEEEEEEEecCCceeeceEEEEE
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIV 49 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~Gvv 49 (99)
...|||++.+...+.+- ..+.-.|++.+
T Consensus 87 pv~pgd~l~i~~~v~~~-~~~~~~~~~~~ 114 (131)
T cd01288 87 PVVPGDQLILEVELLKL-RRGIGKFKGKA 114 (131)
T ss_pred ccCCCCEEEEEEEEEEe-eCCEEEEEEEE
Confidence 46789999999998752 34445555544
No 71
>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=39.56 E-value=1.5e+02 Score=23.48 Aligned_cols=30 Identities=17% Similarity=0.309 Sum_probs=23.6
Q ss_pred CCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEec
Q psy3777 18 NIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (99)
Q Consensus 18 ~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~ 54 (99)
..++|.+||.|+|.- |. .+-|+|.+.....
T Consensus 202 ~~~~f~vGd~VrI~d----GP---F~GfeG~I~eid~ 231 (258)
T TIGR01956 202 NLSKFRVGNFVKIVD----GP---FKGIVGKIKKIDQ 231 (258)
T ss_pred cccCCCCCCEEEEEe----cC---CCCcEEEEEEEeC
Confidence 346799999999863 43 5789999999875
No 72
>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=39.24 E-value=48 Score=19.53 Aligned_cols=21 Identities=29% Similarity=0.403 Sum_probs=15.1
Q ss_pred CcCCCCEEEEEEEEecCCcee
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKR 41 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r 41 (99)
.|++||.+++.+.-.+..+.+
T Consensus 44 ~~~~Gd~i~~~V~~id~~~~~ 64 (69)
T cd05697 44 KFKPGLKVKCRVLSVEPERKR 64 (69)
T ss_pred cCCCCCEEEEEEEEEECCCCE
Confidence 499999999998765433333
No 73
>COG5636 Uncharacterized conserved protein, contains Zn-ribbon-like motif [Function unknown]
Probab=38.56 E-value=21 Score=28.07 Aligned_cols=16 Identities=31% Similarity=0.748 Sum_probs=13.4
Q ss_pred CCCCcCCCCEEEEEEE
Q psy3777 18 NIPDFVTGDTIIVNLN 33 (99)
Q Consensus 18 ~~p~f~~GD~v~V~~~ 33 (99)
-+|.|.|||+|.....
T Consensus 259 GlPaf~PGd~v~~~~n 274 (284)
T COG5636 259 GLPAFEPGDVVSFSMN 274 (284)
T ss_pred CCCCCCCCceeeeecc
Confidence 5799999999987654
No 74
>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=38.45 E-value=49 Score=19.31 Aligned_cols=15 Identities=20% Similarity=0.483 Sum_probs=12.3
Q ss_pred CcCCCCEEEEEEEEe
Q psy3777 21 DFVTGDTIIVNLNVI 35 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~ 35 (99)
.|++||.+++.+.-.
T Consensus 44 ~~~~Gd~v~~~v~~~ 58 (73)
T cd05691 44 RFKVGDEVEAKITNV 58 (73)
T ss_pred ccCCCCEEEEEEEEE
Confidence 389999999987654
No 75
>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=38.43 E-value=66 Score=21.51 Aligned_cols=28 Identities=25% Similarity=0.592 Sum_probs=18.8
Q ss_pred CcCCCCEEEEEEEEecCCceeeceEEEEE
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIV 49 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~Gvv 49 (99)
...|||++.+++.+.+- ..+.-.|.|.+
T Consensus 97 ~v~pGd~l~i~~~i~~~-~~~~~~~~~~~ 124 (140)
T TIGR01750 97 PVVPGDQLILHAEFLKK-RRKIGKFKGEA 124 (140)
T ss_pred ccCCCCEEEEEEEEEEc-cCCEEEEEEEE
Confidence 46789999999988742 33444555543
No 76
>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=38.35 E-value=15 Score=24.42 Aligned_cols=23 Identities=30% Similarity=0.517 Sum_probs=13.3
Q ss_pred CCCCcCCCCEEEEEEEEecCCcee
Q psy3777 18 NIPDFVTGDTIIVNLNVIEGTRKR 41 (99)
Q Consensus 18 ~~p~f~~GD~v~V~~~i~eg~k~r 41 (99)
...++.+|++|.|.|.+.+. ++|
T Consensus 62 ~w~~L~VG~~VMvNYN~d~P-~er 84 (85)
T PF12148_consen 62 KWDELKVGQVVMVNYNVDEP-KER 84 (85)
T ss_dssp -GGG--TT-EEEEEE-TTST-TS-
T ss_pred cHHhCCcccEEEEecCCCCc-ccC
Confidence 45579999999999988654 554
No 77
>COG2030 MaoC Acyl dehydratase [Lipid metabolism]
Probab=37.64 E-value=69 Score=22.52 Aligned_cols=17 Identities=24% Similarity=0.495 Sum_probs=14.5
Q ss_pred CCcCCCCEEEEEEEEec
Q psy3777 20 PDFVTGDTIIVNLNVIE 36 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~e 36 (99)
-.+.+||+|++...+.+
T Consensus 105 ~PV~~Gdtl~~~~~v~~ 121 (159)
T COG2030 105 KPVFPGDTLRARVEVLD 121 (159)
T ss_pred CCCCCCCEEEEEEEEEE
Confidence 35899999999999874
No 78
>KOG3409|consensus
Probab=37.62 E-value=73 Score=24.16 Aligned_cols=18 Identities=22% Similarity=0.386 Sum_probs=13.7
Q ss_pred CCCCCcCCCCEEEEEEEE
Q psy3777 17 KNIPDFVTGDTIIVNLNV 34 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~~i 34 (99)
+-+-.|+|||+|.-.+.-
T Consensus 118 ~v~ksFrPgDiVlAkVis 135 (193)
T KOG3409|consen 118 KVYKSFRPGDIVLAKVIS 135 (193)
T ss_pred hhhhccCCCcEEEEEEee
Confidence 345679999999887743
No 79
>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=36.37 E-value=58 Score=19.10 Aligned_cols=15 Identities=20% Similarity=0.326 Sum_probs=12.4
Q ss_pred CcCCCCEEEEEEEEe
Q psy3777 21 DFVTGDTIIVNLNVI 35 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~ 35 (99)
.|++||.+++.+.-.
T Consensus 44 ~~~~Gd~i~~~i~~~ 58 (70)
T cd05687 44 EVKVGDEVEVYVLRV 58 (70)
T ss_pred cCCCCCEEEEEEEEE
Confidence 399999999997654
No 80
>PRK00529 elongation factor P; Validated
Probab=36.07 E-value=1.7e+02 Score=21.36 Aligned_cols=55 Identities=18% Similarity=0.274 Sum_probs=33.0
Q ss_pred CCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCC-CcceEEEEEeecCeeEEEEEeecCC
Q psy3777 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKG-LNSNFIVRKISYNEGIERTFQLYSP 81 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g-~~stftlR~i~~gvGVEr~fpl~SP 81 (99)
.-+|++||+|.+. |.--++-.++-. +-++| .--.+.+|++..|--.|.+|+-...
T Consensus 4 a~~ik~G~~I~~~-----g~~~~V~~~~~~---kpGkg~A~vrvk~knL~tG~~~e~~f~~~e~ 59 (186)
T PRK00529 4 ANDLRKGLVIEID-----GEPYVVLEFEHV---KPGKGQAFVRTKLKNLLTGSVVEKTFKAGDK 59 (186)
T ss_pred hhhcCCCCEEEEC-----CEEEEEEEEEEe---eCCCCceEEEEEEEECCCCCeEEEEeCCCCE
Confidence 3579999999652 322222222111 11232 2345779999999999999976544
No 81
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=35.99 E-value=1.3e+02 Score=22.08 Aligned_cols=32 Identities=22% Similarity=0.314 Sum_probs=23.9
Q ss_pred CCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecC
Q psy3777 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNK 55 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~ 55 (99)
+...+|.+||.|+|.- |- ...|.|.|......
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 4456899999999853 42 34688899998864
No 82
>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=35.93 E-value=40 Score=22.00 Aligned_cols=17 Identities=18% Similarity=0.372 Sum_probs=14.2
Q ss_pred CCCCcCCCCEEEEEEEE
Q psy3777 18 NIPDFVTGDTIIVNLNV 34 (99)
Q Consensus 18 ~~p~f~~GD~v~V~~~i 34 (99)
++..+++||+|=|-++-
T Consensus 2 ~~~~~~~GD~VyViYrN 18 (75)
T PF11132_consen 2 DMKPYHAGDIVYVIYRN 18 (75)
T ss_pred CccccCCCCEEEEEEcC
Confidence 45789999999998874
No 83
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=35.73 E-value=78 Score=22.07 Aligned_cols=35 Identities=17% Similarity=0.235 Sum_probs=25.7
Q ss_pred CCcCCCCEEEEEEEEecC--CceeeceEEEEEEEEec
Q psy3777 20 PDFVTGDTIIVNLNVIEG--TRKRIQAYEGIVISRRN 54 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~eg--~k~r~q~f~GvvIa~r~ 54 (99)
+.-.+||++.|.+.-... .-.+-|.+.|+++.-+.
T Consensus 31 ~~a~iGD~I~vsVkk~~~~~~~kkg~v~~AvIVrtkk 67 (122)
T PRK05483 31 RYASIGDVIVVSVKEAIPRGKVKKGDVVKAVVVRTKK 67 (122)
T ss_pred CccccCCEEEEEEEEcCCCCcccCCCEeeEEEEEecc
Confidence 567899999999874221 23456899999998764
No 84
>KOG4020|consensus
Probab=35.33 E-value=25 Score=27.73 Aligned_cols=15 Identities=20% Similarity=0.658 Sum_probs=12.4
Q ss_pred CCCCcCCCCEEEEEE
Q psy3777 18 NIPDFVTGDTIIVNL 32 (99)
Q Consensus 18 ~~p~f~~GD~v~V~~ 32 (99)
-+|.|+|||+|....
T Consensus 237 G~PafkPGe~v~ls~ 251 (257)
T KOG4020|consen 237 GMPAFKPGEKVLLSD 251 (257)
T ss_pred CCCCCCCCCeEEecc
Confidence 469999999998754
No 85
>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=35.14 E-value=51 Score=22.82 Aligned_cols=21 Identities=19% Similarity=0.423 Sum_probs=13.7
Q ss_pred CcCCCCEEEEEEEEecCCcee
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKR 41 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r 41 (99)
.+.|||.|.+.+.+.+|.+-+
T Consensus 74 ni~p~D~v~I~VtvSDG~sl~ 94 (106)
T PF10610_consen 74 NISPGDKVKIIVTVSDGKSLH 94 (106)
T ss_dssp E--TT-EEEEEEEEE-SSS-E
T ss_pred EeCCCCeEEEEEEEcCCCeEE
Confidence 468999999999999986543
No 86
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=35.11 E-value=1.3e+02 Score=22.65 Aligned_cols=47 Identities=15% Similarity=0.038 Sum_probs=33.0
Q ss_pred CCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCe
Q psy3777 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNE 70 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gv 70 (99)
..-|-++-||.|.|.+.. |+ =+ =..+| .|..+...+.++.||| ..|-
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 345679999999998863 21 11 23455 6677888899999999 5553
No 87
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=35.10 E-value=1.2e+02 Score=21.75 Aligned_cols=50 Identities=12% Similarity=0.114 Sum_probs=34.5
Q ss_pred CCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCeeEE
Q psy3777 18 NIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIE 73 (99)
Q Consensus 18 ~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gvGVE 73 (99)
.-|-++-||.|.+.+... | =.+ ...| .|..+.+.+..+.+||...|-=|.
T Consensus 97 ~p~~V~rG~~V~i~~~~~-g--~~i-~~~G--~Al~~G~~Gd~IrVrN~~Sgkiv~ 146 (160)
T PRK06005 97 EPSLVTRGSPVKLVFSAG-G--LTI-TAAG--TPLQSGAAGDLIRVRNVDSGVIVS 146 (160)
T ss_pred CCcEEeCCCEEEEEEecC-C--EEE-EEEE--EEcccCCCCCEEEEEECCCCCEEE
Confidence 345699999999988642 2 111 2234 667788889999999987664443
No 88
>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=34.79 E-value=55 Score=19.84 Aligned_cols=16 Identities=13% Similarity=0.150 Sum_probs=13.1
Q ss_pred CCcCCCCEEEEEEEEe
Q psy3777 20 PDFVTGDTIIVNLNVI 35 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~ 35 (99)
..|++||.|++.+.-.
T Consensus 47 ~~~~~Gd~v~~kV~~~ 62 (72)
T cd05704 47 EGFKPGKIVRCCILSK 62 (72)
T ss_pred HhCCCCCEEEEEEEEe
Confidence 3499999999998654
No 89
>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=34.77 E-value=67 Score=23.50 Aligned_cols=33 Identities=21% Similarity=0.453 Sum_probs=23.3
Q ss_pred cCCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEE
Q psy3777 16 KKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVIS 51 (99)
Q Consensus 16 ~~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa 51 (99)
..+-|.|+-||.|.+.+.- +|.|.| ...|+..-
T Consensus 82 tv~kp~F~LGd~V~~~f~~-~~pkqR--lIlGv~lv 114 (150)
T PF07154_consen 82 TVQKPAFRLGDRVEFRFYS-DGPKQR--LILGVFLV 114 (150)
T ss_pred eccCCceecCCEEEEEecC-CCCceE--EEEEEEEe
Confidence 3567999999999999852 344544 56776554
No 90
>PRK00006 fabZ (3R)-hydroxymyristoyl-ACP dehydratase; Reviewed
Probab=34.72 E-value=76 Score=21.45 Aligned_cols=27 Identities=26% Similarity=0.683 Sum_probs=17.6
Q ss_pred cCCCCEEEEEEEEecCCceeeceEEEEE
Q psy3777 22 FVTGDTIIVNLNVIEGTRKRIQAYEGIV 49 (99)
Q Consensus 22 f~~GD~v~V~~~i~eg~k~r~q~f~Gvv 49 (99)
..|||++.+...+.+- +.+.-.|.+-+
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 33334444444
No 91
>KOG3416|consensus
Probab=34.69 E-value=24 Score=25.35 Aligned_cols=20 Identities=20% Similarity=0.275 Sum_probs=14.5
Q ss_pred CcCCCCEEEEEEEEecCCceeeceEEE
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRIQAYEG 47 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~G 47 (99)
.|.|||+|+.+== =...|+|
T Consensus 61 ~~~PGDIirLt~G-------y~Si~qg 80 (134)
T KOG3416|consen 61 LIQPGDIIRLTGG-------YASIFQG 80 (134)
T ss_pred ccCCccEEEeccc-------chhhhcC
Confidence 5999999998632 2357777
No 92
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=34.15 E-value=64 Score=22.50 Aligned_cols=27 Identities=22% Similarity=0.428 Sum_probs=21.5
Q ss_pred CcCCCCEEEEEEEEecCCceeeceEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~ 54 (99)
.|.+||.|+|. +|. .+-|+|++...++
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 48999999985 353 5789999998874
No 93
>PRK02268 hypothetical protein; Provisional
Probab=33.90 E-value=69 Score=22.99 Aligned_cols=34 Identities=24% Similarity=0.307 Sum_probs=24.2
Q ss_pred CCCCCcCCCCEEEEEE-EEecCCceeeceEEEEEE
Q psy3777 17 KNIPDFVTGDTIIVNL-NVIEGTRKRIQAYEGIVI 50 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~-~i~eg~k~r~q~f~GvvI 50 (99)
..+...+|||.|-.-+ ...-|++...|.|.|+=-
T Consensus 31 apl~RmkpGD~ivyYsp~~~~~~~~~~qaftAig~ 65 (141)
T PRK02268 31 APLRRMKPGDWIIYYSPKTTFGGKDKLQAFTAIGK 65 (141)
T ss_pred chhhcCCCCCEEEEEeceEecCCCcccceEEEEEE
Confidence 3556799999997643 223366788999999654
No 94
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=33.84 E-value=1.3e+02 Score=19.40 Aligned_cols=47 Identities=19% Similarity=0.278 Sum_probs=36.0
Q ss_pred CCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEE
Q psy3777 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIV 63 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftl 63 (99)
..-|.+..||+-.|++......-.-+..++|.|+=.-+...+.+.++
T Consensus 8 ~~~~PVeeGe~y~V~I~d~g~~GDGiarveGfvVFVp~a~~Gd~V~v 54 (73)
T COG3269 8 QRTPPVEEGETYEVEIEDVGDQGDGIARVEGFVVFVPGAEVGDEVKV 54 (73)
T ss_pred CCCCCcccCCEEEEEEEEeccCCCceEEEEEEEEEeCCCCCCCeeeE
Confidence 45678999999999998764344667888999999988666555554
No 95
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=33.80 E-value=1.2e+02 Score=21.58 Aligned_cols=35 Identities=23% Similarity=0.410 Sum_probs=26.9
Q ss_pred CCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEec
Q psy3777 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~ 54 (99)
+|.-.+||+|.|.+.-... -.|-|.+.++|+.-+.
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 3678899999999875433 3456999999998663
No 96
>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=33.68 E-value=34 Score=21.98 Aligned_cols=14 Identities=21% Similarity=0.579 Sum_probs=12.5
Q ss_pred CCCcCCCCEEEEEE
Q psy3777 19 IPDFVTGDTIIVNL 32 (99)
Q Consensus 19 ~p~f~~GD~v~V~~ 32 (99)
+|+..|||.|-||.
T Consensus 33 v~~~~vGD~VLVH~ 46 (76)
T TIGR00074 33 VGEVKVGDYVLVHV 46 (76)
T ss_pred eCCCCCCCEEEEec
Confidence 48899999999986
No 97
>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=33.63 E-value=33 Score=22.12 Aligned_cols=18 Identities=22% Similarity=0.409 Sum_probs=10.5
Q ss_pred cCCCCCcCCCCEEEEEEE
Q psy3777 16 KKNIPDFVTGDTIIVNLN 33 (99)
Q Consensus 16 ~~~~p~f~~GD~v~V~~~ 33 (99)
.+.+-.++|||.|.+.+.
T Consensus 37 ~k~L~~L~pGq~l~f~~d 54 (85)
T PF04225_consen 37 AKPLTRLKPGQTLEFQLD 54 (85)
T ss_dssp T--GGG--TT-EEEEEE-
T ss_pred cchHhhCCCCCEEEEEEC
Confidence 467888999999999875
No 98
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=33.38 E-value=64 Score=19.48 Aligned_cols=16 Identities=19% Similarity=0.140 Sum_probs=12.9
Q ss_pred CcCCCCEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIE 36 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (99)
.|++||.+++.+.-.+
T Consensus 46 ~~~vG~~v~~kV~~id 61 (71)
T cd05696 46 PFKAGTTHKARIIGYS 61 (71)
T ss_pred ccCCCCEEEEEEEEEe
Confidence 3999999999976543
No 99
>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=33.12 E-value=37 Score=22.04 Aligned_cols=15 Identities=20% Similarity=0.335 Sum_probs=12.3
Q ss_pred CcCCCCEEEEEEEEe
Q psy3777 21 DFVTGDTIIVNLNVI 35 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~ 35 (99)
.|+|||+|+-++.-.
T Consensus 60 ~f~~GDiV~AkVis~ 74 (92)
T cd05791 60 CFRPGDIVRAKVISL 74 (92)
T ss_pred hcCCCCEEEEEEEEc
Confidence 599999999988643
No 100
>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=33.04 E-value=57 Score=21.46 Aligned_cols=16 Identities=13% Similarity=0.289 Sum_probs=13.2
Q ss_pred CcCCCCEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIE 36 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (99)
.|++||+|++.+.-..
T Consensus 66 ~f~vGd~V~~kVi~~d 81 (100)
T cd05693 66 LFSVGQLVRCKVVSLD 81 (100)
T ss_pred hccCCCEEEEEEEEcc
Confidence 4999999999987654
No 101
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=32.53 E-value=1.2e+02 Score=18.37 Aligned_cols=32 Identities=25% Similarity=0.439 Sum_probs=22.8
Q ss_pred CCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecC
Q psy3777 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNK 55 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~ 55 (99)
..++.|+.|.|.+...++ .=.|+..|+++...
T Consensus 46 ~~l~~g~~v~v~~~~~~~----~y~F~s~V~~~~~~ 77 (87)
T PF12945_consen 46 IPLREGEEVIVRFISEDG----VYAFKSKVIGRISE 77 (87)
T ss_dssp CCS-TT-EEEEEEEE-SC----EEEEEEEEEEEE-S
T ss_pred EeecCCCEEEEEEEECCe----EEEEEEEEEEEEcC
Confidence 368899999999976432 78999999998743
No 102
>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=32.25 E-value=69 Score=19.65 Aligned_cols=15 Identities=13% Similarity=0.496 Sum_probs=12.2
Q ss_pred CcCCCCEEEEEEEEe
Q psy3777 21 DFVTGDTIIVNLNVI 35 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~ 35 (99)
.|++||.|+|.+.-.
T Consensus 58 ~~~~Gd~v~vkV~~i 72 (83)
T cd04461 58 GFKKGQSVTAKVTSV 72 (83)
T ss_pred hcCCCCEEEEEEEEE
Confidence 399999999997543
No 103
>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=32.17 E-value=1.1e+02 Score=18.88 Aligned_cols=45 Identities=24% Similarity=0.259 Sum_probs=24.2
Q ss_pred CCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEee
Q psy3777 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKIS 67 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~ 67 (99)
.|.|++||+|-|.-... ..+ ..-.|=++..+..+-...+.++++.
T Consensus 9 ~P~l~~GD~vlv~~~~~---~~~-~~~~Gdivv~~~~~~~~~~~vkRv~ 53 (90)
T TIGR02754 9 SPTLPPGDRIIVVPWLK---IFR-VPPIGNVVVVRHPLQPYGLIIKRLA 53 (90)
T ss_pred cCccCCCCEEEEEEccc---cCC-CCCCCeEEEEecCCCCcceEEEEee
Confidence 58899999998874211 011 1112544444433323457777764
No 104
>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=32.14 E-value=28 Score=21.97 Aligned_cols=13 Identities=38% Similarity=0.542 Sum_probs=8.6
Q ss_pred CCCCCcCCCCEEE
Q psy3777 17 KNIPDFVTGDTII 29 (99)
Q Consensus 17 ~~~p~f~~GD~v~ 29 (99)
+++.+|++||++.
T Consensus 71 ~~~~d~~~Gdvi~ 83 (84)
T cd03692 71 ENFNDIKVGDIIE 83 (84)
T ss_pred eCcccCCCCCEEE
Confidence 3455777788775
No 105
>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=31.98 E-value=68 Score=18.09 Aligned_cols=15 Identities=27% Similarity=0.350 Sum_probs=11.9
Q ss_pred CcCCCCEEEEEEEEe
Q psy3777 21 DFVTGDTIIVNLNVI 35 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~ 35 (99)
.|++||.++|.+.-.
T Consensus 44 ~~~~Gd~v~v~v~~~ 58 (69)
T cd05692 44 VLKEGDKVKVKVLSI 58 (69)
T ss_pred ccCCCCEEEEEEEEE
Confidence 389999999987443
No 106
>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=31.63 E-value=26 Score=24.73 Aligned_cols=14 Identities=36% Similarity=0.408 Sum_probs=11.6
Q ss_pred CCCcCCCCEEEEEE
Q psy3777 19 IPDFVTGDTIIVNL 32 (99)
Q Consensus 19 ~p~f~~GD~v~V~~ 32 (99)
.-++++||+|+|..
T Consensus 57 ~LDlRIGD~Vkv~~ 70 (131)
T PF08605_consen 57 YLDLRIGDTVKVDG 70 (131)
T ss_pred eeeeecCCEEEECC
Confidence 45899999999964
No 107
>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=31.52 E-value=34 Score=21.07 Aligned_cols=13 Identities=31% Similarity=0.478 Sum_probs=9.3
Q ss_pred CCcCCCCEEEEEE
Q psy3777 20 PDFVTGDTIIVNL 32 (99)
Q Consensus 20 p~f~~GD~v~V~~ 32 (99)
++|++||.|.|..
T Consensus 29 ~~f~~gd~V~i~~ 41 (74)
T PF01472_consen 29 GDFRKGDEVAIVD 41 (74)
T ss_dssp TT--TTSEEEEEE
T ss_pred CCcCCCCEEEEEc
Confidence 6799999999865
No 108
>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=31.21 E-value=1.3e+02 Score=21.30 Aligned_cols=35 Identities=23% Similarity=0.431 Sum_probs=26.6
Q ss_pred CCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEec
Q psy3777 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~ 54 (99)
+|.-.+||++.|.+.-... ..+-|.+.++++.-+.
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 3667899999999875433 3456899999998764
No 109
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=31.15 E-value=50 Score=21.05 Aligned_cols=15 Identities=20% Similarity=0.060 Sum_probs=12.2
Q ss_pred CCcCCCCEEEEEEEE
Q psy3777 20 PDFVTGDTIIVNLNV 34 (99)
Q Consensus 20 p~f~~GD~v~V~~~i 34 (99)
--+++||.|.|...-
T Consensus 37 iwI~~GD~V~Ve~~~ 51 (77)
T cd05793 37 VWINEGDIVLVAPWD 51 (77)
T ss_pred EEEcCCCEEEEEecc
Confidence 468999999998653
No 110
>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=31.04 E-value=43 Score=20.93 Aligned_cols=15 Identities=33% Similarity=0.656 Sum_probs=10.7
Q ss_pred CCCCcCCCCEEEEEE
Q psy3777 18 NIPDFVTGDTIIVNL 32 (99)
Q Consensus 18 ~~p~f~~GD~v~V~~ 32 (99)
=+|+..|||.|-||.
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 367899999999984
No 111
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=31.01 E-value=52 Score=20.62 Aligned_cols=38 Identities=8% Similarity=0.202 Sum_probs=23.6
Q ss_pred CCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEE
Q psy3777 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRK 65 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~ 65 (99)
|.++.||.|++.+..+.. -| =.|..+.-.| ..+...-|
T Consensus 1 ~~~~~Ge~v~~~~~~~~~------~Y-l~l~~~~~~G-~v~~L~Pn 38 (83)
T PF14326_consen 1 TVYRVGERVRFRVTSNRD------GY-LYLFYIDADG-KVTLLFPN 38 (83)
T ss_pred CcccCCCEEEEEEEeCCC------eE-EEEEEECCCC-CEEEEecC
Confidence 568999999999986421 22 4555665555 33444444
No 112
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=30.89 E-value=1.3e+02 Score=21.55 Aligned_cols=35 Identities=17% Similarity=0.386 Sum_probs=27.2
Q ss_pred CCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEec
Q psy3777 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~ 54 (99)
+|.-.+||++.|.+.-... -.+-|.+.++++.-+.
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 4678899999999876543 3466999999998663
No 113
>CHL00010 infA translation initiation factor 1
Probab=30.30 E-value=59 Score=20.65 Aligned_cols=26 Identities=27% Similarity=0.405 Sum_probs=18.3
Q ss_pred cCCCCEEEEEEEEecCCceeeceEEEEEEEEec
Q psy3777 22 FVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (99)
Q Consensus 22 f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~ 54 (99)
..+||.|.|..+..+. -+|.+|-+..
T Consensus 47 ~~vGD~V~ve~~~~~~-------~~g~Ii~r~~ 72 (78)
T CHL00010 47 ILPGDRVKVELSPYDL-------TKGRIIYRLR 72 (78)
T ss_pred cCCCCEEEEEEcccCC-------CeEEEEEEec
Confidence 5789999999754432 2488887664
No 114
>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=30.01 E-value=39 Score=21.14 Aligned_cols=14 Identities=14% Similarity=0.230 Sum_probs=8.8
Q ss_pred CcCCCCEEEEEEEE
Q psy3777 21 DFVTGDTIIVNLNV 34 (99)
Q Consensus 21 ~f~~GD~v~V~~~i 34 (99)
.+.|||.|.|.++-
T Consensus 12 ~l~pGD~l~i~v~~ 25 (82)
T PF02563_consen 12 RLGPGDVLRISVFG 25 (82)
T ss_dssp ---TT-EEEEEETT
T ss_pred EECCCCEEEEEEec
Confidence 58999999999863
No 115
>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=29.97 E-value=88 Score=20.62 Aligned_cols=30 Identities=23% Similarity=0.490 Sum_probs=16.0
Q ss_pred CcCCCCEEEEEEEEecC----CceeeceEEEEEE
Q psy3777 21 DFVTGDTIIVNLNVIEG----TRKRIQAYEGIVI 50 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg----~k~r~q~f~GvvI 50 (99)
.+..||.|.|.+.-..+ .-..-..|.|..|
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 47889999998874211 1123456666543
No 116
>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=29.92 E-value=1.1e+02 Score=20.01 Aligned_cols=32 Identities=6% Similarity=0.225 Sum_probs=24.3
Q ss_pred CCcCCCCEEEEEEEEecCCceeeceEEEEEEEEec
Q psy3777 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~ 54 (99)
-.|.+|.-++..+... ......|+|+|+++..
T Consensus 37 ~~~~~GmRfkM~fE~e---ds~~~~~~GtI~~v~~ 68 (83)
T PF06507_consen 37 HPWSVGMRFKMRFETE---DSSERRWQGTIVGVSD 68 (83)
T ss_pred CCCCCCcEEEEEeccC---CCccceeeeEEeEeec
Confidence 4799999999987543 3344567999999875
No 117
>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=29.83 E-value=61 Score=21.78 Aligned_cols=30 Identities=13% Similarity=0.323 Sum_probs=18.0
Q ss_pred CCcCCCC-EEEEEEEEecC--CceeeceEEEEE
Q psy3777 20 PDFVTGD-TIIVNLNVIEG--TRKRIQAYEGIV 49 (99)
Q Consensus 20 p~f~~GD-~v~V~~~i~eg--~k~r~q~f~Gvv 49 (99)
-.+.||| ++++++.+.+. .....-.|+|.+
T Consensus 95 ~~v~Pg~~~l~~~v~i~~~~~~~~~~~~~~~~~ 127 (138)
T PF07977_consen 95 GPVYPGDKTLRIEVEIKKIRRREGGMAIFDGTA 127 (138)
T ss_dssp S-B-TTE-EEEEEEEEEEEEEEETTEEEEEEEE
T ss_pred ccEeCCCcEEEEEEEEEEeecccCCEEEEEEEE
Confidence 4578999 99999888751 133344555544
No 118
>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=29.63 E-value=66 Score=18.96 Aligned_cols=22 Identities=18% Similarity=0.342 Sum_probs=16.1
Q ss_pred CCcCCCCEEEEEEEEecCCcee
Q psy3777 20 PDFVTGDTIIVNLNVIEGTRKR 41 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~eg~k~r 41 (99)
+.+++||.++|.+.-.+.++.+
T Consensus 47 ~~~~~G~~v~v~v~~vd~~~~~ 68 (74)
T PF00575_consen 47 EVYKIGQTVRVKVIKVDKEKGR 68 (74)
T ss_dssp GTCETTCEEEEEEEEEETTTTE
T ss_pred cccCCCCEEEEEEEEEECCCCe
Confidence 4699999999998765544433
No 119
>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=29.59 E-value=62 Score=21.54 Aligned_cols=16 Identities=25% Similarity=0.445 Sum_probs=13.6
Q ss_pred CcCCCCEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIE 36 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (99)
...|||+|.++..+.+
T Consensus 91 pv~~GDtl~~~~~v~~ 106 (146)
T cd03451 91 PVFHGDTLYAESEVLS 106 (146)
T ss_pred CCCCCCEEEEEEEEEE
Confidence 4789999999998864
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=29.27 E-value=33 Score=22.72 Aligned_cols=41 Identities=22% Similarity=0.306 Sum_probs=31.2
Q ss_pred HHHHHHHhhcCCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEE
Q psy3777 7 IEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVIS 51 (99)
Q Consensus 7 ~e~~~~~~~~~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa 51 (99)
+|++.+ .++-.+..|-+..+.+.-..+++-+-..|.|++-+
T Consensus 3 ~eqSyi----eNILRlN~GK~~T~y~Tfenn~ew~akvf~G~iE~ 43 (82)
T TIGR02728 3 VEQSYI----ENILRMNRGKTATVYMTFENSPEWAARVFRGQIEN 43 (82)
T ss_pred chHHHH----HHHHHhcCCceEEEEEEEcCChHhhhhheeeehhh
Confidence 466666 45667888999999887766666778899998755
No 121
>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=29.17 E-value=1.6e+02 Score=22.02 Aligned_cols=15 Identities=33% Similarity=0.437 Sum_probs=9.5
Q ss_pred CcCCCCEEEEEEEEe
Q psy3777 21 DFVTGDTIIVNLNVI 35 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~ 35 (99)
.+.|||.|++++.-.
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 489999999999754
No 122
>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=29.04 E-value=1.3e+02 Score=24.61 Aligned_cols=70 Identities=10% Similarity=0.067 Sum_probs=42.1
Q ss_pred CCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCC----cceEEEEEeecCeeEEEEEeecCCccceEEEEE
Q psy3777 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGL----NSNFIVRKISYNEGIERTFQLYSPIISSIIVKR 90 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~----~stftlR~i~~gvGVEr~fpl~SP~I~~I~V~~ 90 (99)
.+++.+++|+.|.|++.- ...+...|.|.|..+..... +.+|+++=-+.-.. ....+|..-+-.++.+.-
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 567889999998888753 12222479999999875432 24566653331000 012356666777777753
No 123
>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=29.03 E-value=69 Score=20.73 Aligned_cols=17 Identities=24% Similarity=0.386 Sum_probs=15.0
Q ss_pred CCCcCCCCEEEEEEEEe
Q psy3777 19 IPDFVTGDTIIVNLNVI 35 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~ 35 (99)
-|.|.+||.|++.-.+.
T Consensus 2 ~p~f~~G~~V~a~~~ir 18 (75)
T PF04319_consen 2 PPRFEWGDKVRARKDIR 18 (75)
T ss_pred CCccCCCCEEEEEEEeE
Confidence 38899999999998885
No 124
>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=28.51 E-value=40 Score=22.55 Aligned_cols=15 Identities=27% Similarity=0.273 Sum_probs=7.7
Q ss_pred CCCCcCCCCEEEEEE
Q psy3777 18 NIPDFVTGDTIIVNL 32 (99)
Q Consensus 18 ~~p~f~~GD~v~V~~ 32 (99)
+.+.++|||.|.+.-
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 467899999999864
No 125
>PF13358 DDE_3: DDE superfamily endonuclease
Probab=28.26 E-value=26 Score=22.54 Aligned_cols=41 Identities=29% Similarity=0.359 Sum_probs=33.0
Q ss_pred EEEEEEecCCCcceEEEEEeecC--eeEEEEE-eecCCccceEE
Q psy3777 47 GIVISRRNKGLNSNFIVRKISYN--EGIERTF-QLYSPIISSII 87 (99)
Q Consensus 47 GvvIa~r~~g~~stftlR~i~~g--vGVEr~f-pl~SP~I~~I~ 87 (99)
++++--.|.....+=.++..+.. .|++..| |-|||.+.=||
T Consensus 81 ~~~li~DNa~~H~~~~~~~~l~~~~~~~~~~~~P~~sPdLNpiE 124 (146)
T PF13358_consen 81 RIVLIMDNASIHKSKKVQEWLEEHERGIELLFLPPYSPDLNPIE 124 (146)
T ss_pred EEEEecccccccccccccceeeccccccccccccCcCCccCHHH
Confidence 78888888888888888888877 7887776 99999876554
No 126
>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=27.95 E-value=57 Score=21.56 Aligned_cols=41 Identities=17% Similarity=0.300 Sum_probs=30.8
Q ss_pred HHHHHHHhhcCCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEE
Q psy3777 7 IEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVIS 51 (99)
Q Consensus 7 ~e~~~~~~~~~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa 51 (99)
+|++.+ .++-.+..|-...+.+.-..+++-+...|.|++-+
T Consensus 5 ~eqsYi----ENILRlN~GK~~T~Y~Tyenn~ewnakvf~GviE~ 45 (81)
T PF09671_consen 5 LEQSYI----ENILRLNRGKLATFYMTYENNSEWNAKVFRGVIEA 45 (81)
T ss_pred chHHHH----HHHHHhcCCceEEEEEEecCchhhhheeeEEEehh
Confidence 456666 46667888999998887765556678899999865
No 127
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=27.71 E-value=1.3e+02 Score=22.76 Aligned_cols=17 Identities=24% Similarity=0.272 Sum_probs=13.8
Q ss_pred CCCcCCCCEEEEEEEEe
Q psy3777 19 IPDFVTGDTIIVNLNVI 35 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~ 35 (99)
-|.|++||.|...+.-.
T Consensus 109 ~~~~~~GDlV~akV~~i 125 (235)
T PRK04163 109 RKYLDIGDYIIAKVKDV 125 (235)
T ss_pred HhhCCCCCEEEEEEEEE
Confidence 45699999999998654
No 128
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=27.40 E-value=87 Score=17.79 Aligned_cols=15 Identities=20% Similarity=0.313 Sum_probs=12.2
Q ss_pred CcCCCCEEEEEEEEe
Q psy3777 21 DFVTGDTIIVNLNVI 35 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~ 35 (99)
.|++||.|+|.+.-.
T Consensus 44 ~~~~Gd~v~v~v~~~ 58 (68)
T cd04472 44 VLKVGDEVKVKVIEV 58 (68)
T ss_pred ccCCCCEEEEEEEEE
Confidence 389999999997544
No 129
>PRK08059 general stress protein 13; Validated
Probab=27.32 E-value=84 Score=21.24 Aligned_cols=15 Identities=20% Similarity=0.308 Sum_probs=12.3
Q ss_pred CcCCCCEEEEEEEEe
Q psy3777 21 DFVTGDTIIVNLNVI 35 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~ 35 (99)
.|++||+|+|.+.-.
T Consensus 51 ~~~vGD~I~vkI~~i 65 (123)
T PRK08059 51 FLSVGDEVKVKVLSV 65 (123)
T ss_pred cCCCCCEEEEEEEEE
Confidence 489999999987654
No 130
>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=27.23 E-value=1.6e+02 Score=18.15 Aligned_cols=45 Identities=18% Similarity=0.270 Sum_probs=30.4
Q ss_pred CCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCeeEE
Q psy3777 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIE 73 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gvGVE 73 (99)
..+.+||.|.+.+....+ ...-...|.|...+..+-+. ..|.||+
T Consensus 35 ~~~~~g~~v~l~l~l~~~--~~~i~~~g~Vv~~~~~~~~~-------~~~~Gv~ 79 (96)
T TIGR02266 35 KPLAVGTRVELKLTLPGG--ERPVELKGVVAWVRPAADGG-------PPGMGVR 79 (96)
T ss_pred CCcCCCCEEEEEEEcCCC--CeEEEEEEEEEEeCCCCCCC-------CCeeEEE
Confidence 457999999999998743 22234679988877544322 3567776
No 131
>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=27.23 E-value=1.1e+02 Score=20.50 Aligned_cols=31 Identities=19% Similarity=0.254 Sum_probs=20.4
Q ss_pred CCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEe
Q psy3777 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRR 53 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r 53 (99)
-+...|||++.|.+.+...... +.|+-+...
T Consensus 7 ~~~a~~G~tv~V~V~v~~~~~~----i~~~~~~l~ 37 (141)
T PF00963_consen 7 SVSAKPGETVTVPVNVSNVSNS----IAGMQFTLS 37 (141)
T ss_dssp ECEE-TTSEEEEEEEEESCTTT----EEEEEEEEE
T ss_pred CceECCCCEEEEEEEEEcCCCc----EEEEEEEEE
Confidence 3457899999999999754322 555555544
No 132
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=27.17 E-value=1.2e+02 Score=21.98 Aligned_cols=17 Identities=12% Similarity=0.360 Sum_probs=14.4
Q ss_pred CCcCCCCEEEEEEEEec
Q psy3777 20 PDFVTGDTIIVNLNVIE 36 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~e 36 (99)
-+..|||++.++..+.+
T Consensus 137 kPV~pGD~L~~ea~v~~ 153 (185)
T PRK04424 137 RPVKLGERVVAKAEVVR 153 (185)
T ss_pred cCCCCCCEEEEEEEEEE
Confidence 35789999999999874
No 133
>COG3097 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.11 E-value=46 Score=22.86 Aligned_cols=14 Identities=29% Similarity=0.392 Sum_probs=11.9
Q ss_pred CCcCCCCEEEEEEE
Q psy3777 20 PDFVTGDTIIVNLN 33 (99)
Q Consensus 20 p~f~~GD~v~V~~~ 33 (99)
..|+|||+++|.-.
T Consensus 31 Shf~~g~vlrV~r~ 44 (106)
T COG3097 31 SHFKPGDVLRVGRF 44 (106)
T ss_pred hcCCCCCEEEEEEe
Confidence 46999999999764
No 134
>PRK07252 hypothetical protein; Provisional
Probab=26.86 E-value=83 Score=21.49 Aligned_cols=16 Identities=13% Similarity=0.333 Sum_probs=13.0
Q ss_pred CcCCCCEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIE 36 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (99)
.|++||.|+|.+.-..
T Consensus 47 ~~~vGD~V~VkI~~iD 62 (120)
T PRK07252 47 LLKVGEEVLVQVVDFD 62 (120)
T ss_pred ccCCCCEEEEEEEEEe
Confidence 4899999999986543
No 135
>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=26.55 E-value=1.7e+02 Score=20.32 Aligned_cols=35 Identities=17% Similarity=0.286 Sum_probs=25.6
Q ss_pred CCcCCCCEEEEEEEEec--CCceeeceEEEEEEEEec
Q psy3777 20 PDFVTGDTIIVNLNVIE--GTRKRIQAYEGIVISRRN 54 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~e--g~k~r~q~f~GvvIa~r~ 54 (99)
+.-.+||++.|.+.-.. +.-.+-|.+.++++.-+.
T Consensus 31 ~~a~iGD~I~vsVk~~~~~~~~kkg~v~~AvIVrtkk 67 (122)
T TIGR01067 31 RYATVGDVIVVVVKDAIPNGKVKKGDVVKAVIVRTKK 67 (122)
T ss_pred CccccCCEEEEEEEEcCCCCccccccEEEEEEEEeec
Confidence 56889999999987421 112456899999998763
No 136
>PRK13188 bifunctional UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase/(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase; Reviewed
Probab=26.46 E-value=98 Score=26.24 Aligned_cols=30 Identities=27% Similarity=0.491 Sum_probs=20.6
Q ss_pred CcCCCCEEEEEEEEecCCceeeceEEEEEE
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVI 50 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvI 50 (99)
...|||++.+++.+.+-....+-.|+|.+.
T Consensus 415 PV~PGDtL~I~veI~~~~~~giv~f~g~~~ 444 (464)
T PRK13188 415 KVVPGDTLIFKVELLSPIRRGICQMQGKAY 444 (464)
T ss_pred CCCCCCEEEEEEEEEEEecCCEEEEEEEEE
Confidence 467899999999876422344556666654
No 137
>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=26.37 E-value=1.5e+02 Score=17.64 Aligned_cols=32 Identities=16% Similarity=0.239 Sum_probs=22.9
Q ss_pred CcCCCCEEEEEEEEecCCceeeceEEEEEEEEecC
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNK 55 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~ 55 (99)
.+.+||.+.+.+.+..+.. .. +.|.|+..++.
T Consensus 44 ~~~~~~~v~l~~~~~~~~~--~~-~~~~V~~~~~~ 75 (102)
T PF07238_consen 44 PLEPGDRVRLSFSLPGGGF--PI-VTGRVVRIQKD 75 (102)
T ss_dssp G--TTSEEEEEEECTTTSC--EE-EEEEEEEEEEE
T ss_pred CCCCCCEEEEEEEeCCCCe--eE-EEEEEEEEECC
Confidence 7899999999998764432 11 99999998875
No 138
>PF03069 FmdA_AmdA: Acetamidase/Formamidase family; InterPro: IPR004304 This family includes amidohydrolases of formamide 3.5.1.49 from EC and acetamide 3.5.1 from EC. The formamidase from Methylophilus methylotrophus (Bacterium W3A1) forms a homotrimer suggesting that this may be a common property of other members of this family.; GO: 0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides, 0008152 metabolic process; PDB: 3TKK_D 3B9T_D 2II1_C 2F4L_C 2WKN_C.
Probab=26.29 E-value=92 Score=25.53 Aligned_cols=34 Identities=24% Similarity=0.352 Sum_probs=20.9
Q ss_pred cCCCCEEEEEEEEecCCceeec-eEEEEEEEEecCCC
Q psy3777 22 FVTGDTIIVNLNVIEGTRKRIQ-AYEGIVISRRNKGL 57 (99)
Q Consensus 22 f~~GD~v~V~~~i~eg~k~r~q-~f~GvvIa~r~~g~ 57 (99)
-.|||+|+|++...+- -..+ -|.|+.-...+.|.
T Consensus 79 AePGDvL~V~I~~i~p--i~~~~Gy~g~~~~~~g~G~ 113 (369)
T PF03069_consen 79 AEPGDVLEVEILDIRP--IPFRPGYTGVFDTRPGFGV 113 (369)
T ss_dssp --TT-EEEEEEEEEEE--EEE-SCCEEEEEEETTCST
T ss_pred CCCCCEEEEEEEeccc--cCCCCCceEEecCCCCccc
Confidence 4799999999976211 1112 57888877777775
No 139
>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=25.80 E-value=1.2e+02 Score=22.62 Aligned_cols=43 Identities=19% Similarity=0.325 Sum_probs=30.1
Q ss_pred CCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEE
Q psy3777 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVR 64 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR 64 (99)
.+++.+++|+.+.|++.... .-+.|.|.|..+.... +.++.++
T Consensus 205 ~~~~~i~~g~~~~v~~~~~~----~~~~~~g~v~~i~~~~-~~~~~v~ 247 (328)
T PF12700_consen 205 SDASKIKVGQKVEVTIDAPD----NGKSFTGKVSSISPSA-SRTFKVR 247 (328)
T ss_dssp CGTTTHTTTGEEEEEETTSS-----SSEEEEEEEEEESSE-TTEEEEE
T ss_pred HHHHhccCCcEEEEEEEeec----CCCceeeEEeecCCcc-ceeeEEE
Confidence 56788999999888776542 1258999998887655 4444444
No 140
>cd03452 MaoC_C MaoC_C The C-terminal hot dog fold of the MaoC (monoamine oxidase C) dehydratase regulatory protein. Orthologs of MaoC include PaaZ [Escherichia coli] and PaaN [Pseudomonas putida], which are putative ring-opening enzymes involved in phenylacetic acid degradation. The C-terminal domain of MaoC has sequence similarity to (R)-specific enoyl-CoA hydratase,Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. MaoC also has an N-terminal PutA domain like that found in the E. coli PutA proline dehydrogenase and other members of the aldehyde dehydrogenase family.
Probab=25.77 E-value=1.1e+02 Score=20.79 Aligned_cols=16 Identities=38% Similarity=0.434 Sum_probs=13.5
Q ss_pred CcCCCCEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIE 36 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (99)
+..|||+|.+...+.+
T Consensus 88 PV~~GDtl~~~~~V~~ 103 (142)
T cd03452 88 PVYPGDTIQVRLTCKR 103 (142)
T ss_pred CCCCCCEEEEEEEEEE
Confidence 4789999999998864
No 141
>TIGR03027 pepcterm_export putative polysaccharide export protein, PEP-CTERM sytem-associated. This protein family belongs to the larger set of polysaccharide biosynthesis/export proteins described by Pfam model pfam02563. Members of this family are variable in either containing of lacking a 78-residue insert, but appear to fall within a single clade, nevertheless, where the regions in which the gene is found encode components of the PEP-CTERM/EpsH proposed exosortase protein sorting system.
Probab=25.62 E-value=54 Score=23.10 Aligned_cols=13 Identities=23% Similarity=0.353 Sum_probs=11.3
Q ss_pred cCCCCEEEEEEEE
Q psy3777 22 FVTGDTIIVNLNV 34 (99)
Q Consensus 22 f~~GD~v~V~~~i 34 (99)
+.|||.|.|.++-
T Consensus 3 l~pGD~l~i~v~~ 15 (165)
T TIGR03027 3 IGPGDSLNINVWR 15 (165)
T ss_pred cCCCCEEEEEEcC
Confidence 6899999999874
No 142
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=25.61 E-value=86 Score=19.39 Aligned_cols=19 Identities=16% Similarity=0.489 Sum_probs=14.4
Q ss_pred CCCCC-cCCCCEEEE----EEEEe
Q psy3777 17 KNIPD-FVTGDTIIV----NLNVI 35 (99)
Q Consensus 17 ~~~p~-f~~GD~v~V----~~~i~ 35 (99)
..+|. .+.||++.+ .+.+.
T Consensus 28 ~~LP~~~keGDvl~i~~~~~~~~d 51 (71)
T PF11213_consen 28 SRLPEGAKEGDVLEIGEDGSIEID 51 (71)
T ss_pred HHCCCCCCcccEEEECCCceEEEC
Confidence 35665 999999999 66653
No 143
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=25.05 E-value=1e+02 Score=21.26 Aligned_cols=19 Identities=32% Similarity=0.616 Sum_probs=14.9
Q ss_pred ceEEEEEEEEecCCCcceEEEE
Q psy3777 43 QAYEGIVISRRNKGLNSNFIVR 64 (99)
Q Consensus 43 q~f~GvvIa~r~~g~~stftlR 64 (99)
+.|+|+|++.+ ++.|++|+
T Consensus 30 k~l~G~VvS~K---m~KTvvV~ 48 (108)
T PRK08572 30 QVLEGTVVSDK---MHKTVVVE 48 (108)
T ss_pred EEEEEEEEecC---CCceEEEE
Confidence 78999999975 57777754
No 144
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=25.01 E-value=96 Score=19.53 Aligned_cols=18 Identities=33% Similarity=0.331 Sum_probs=14.6
Q ss_pred CCCcCCCCEEEEEEEEec
Q psy3777 19 IPDFVTGDTIIVNLNVIE 36 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~e 36 (99)
.+.+.+||.|+|+=.+.|
T Consensus 42 ~~~~~~Gd~V~vtG~v~e 59 (78)
T cd04486 42 GADVAVGDLVRVTGTVTE 59 (78)
T ss_pred CCCCCCCCEEEEEEEEEe
Confidence 567899999999877654
No 145
>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=24.98 E-value=2.3e+02 Score=19.33 Aligned_cols=43 Identities=14% Similarity=0.120 Sum_probs=27.8
Q ss_pred CCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCee
Q psy3777 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEG 71 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gvG 71 (99)
+.|.+||.|+|.- |. .+-|+|.++...+... -.+|.=...+.-
T Consensus 85 ~~~~~Gd~V~I~~----GP---f~G~~g~v~~~d~~k~--~v~v~l~~~~~~ 127 (145)
T TIGR00405 85 ESIKKGDIVEIIS----GP---FKGERAKVIRVDESKE--EVTLELIEAAVP 127 (145)
T ss_pred cccCCCCEEEEee----cC---CCCCeEEEEEEcCCCC--EEEEEEEEcCcc
Confidence 4699999999853 43 4678899999876433 344433334433
No 146
>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=24.90 E-value=1.4e+02 Score=18.39 Aligned_cols=28 Identities=18% Similarity=0.210 Sum_probs=22.6
Q ss_pred CcCCCCEEEEEEEEecCCceeeceEEEEEEEEecC
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNK 55 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~ 55 (99)
-|.+|+.|.++..- | +.|+|=|.+-...
T Consensus 2 ~f~iGs~V~~kTc~--g-----~~ieGEV~afD~~ 29 (61)
T cd01735 2 CFSVGSQVSCRTCF--E-----QRLQGEVVAFDYP 29 (61)
T ss_pred ccccccEEEEEecC--C-----ceEEEEEEEecCC
Confidence 48899999998764 4 4899999987753
No 147
>PF13437 HlyD_3: HlyD family secretion protein
Probab=24.89 E-value=1.8e+02 Score=18.14 Aligned_cols=33 Identities=30% Similarity=0.466 Sum_probs=25.7
Q ss_pred CCCCCcC-CCCEEEEEEEEecCCceeeceEEEEEEEEec
Q psy3777 17 KNIPDFV-TGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (99)
Q Consensus 17 ~~~p~f~-~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~ 54 (99)
+++..++ +||-+.+++. .+. + +.|.|.|..+..
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 5677887 9999999986 222 2 399999999887
No 148
>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=24.85 E-value=96 Score=21.53 Aligned_cols=34 Identities=18% Similarity=0.280 Sum_probs=25.9
Q ss_pred hHHHHHHHHHHhhcCCCCCcCCCCEEEEEEEEecC
Q psy3777 3 LIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEG 37 (99)
Q Consensus 3 li~~~e~~~~~~~~~~~p~f~~GD~v~V~~~i~eg 37 (99)
++..+..+.+.. ++.+.+++.||++.=.++..++
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 455666666654 6788999999999988887754
No 149
>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=24.84 E-value=1.1e+02 Score=17.78 Aligned_cols=31 Identities=19% Similarity=0.277 Sum_probs=20.2
Q ss_pred CCCCcCCCCEEEEEEEEecCCceeeceEEEEEEE
Q psy3777 18 NIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVIS 51 (99)
Q Consensus 18 ~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa 51 (99)
+-....|||+|..++.+..... ..-.++++.
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 4456899999999998864221 334455554
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=24.66 E-value=1.3e+02 Score=17.65 Aligned_cols=27 Identities=26% Similarity=0.412 Sum_probs=16.8
Q ss_pred CcCCCCEEEEEEEEecCCceeeceEEEEEEE
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKRIQAYEGIVIS 51 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa 51 (99)
..-.||.|.|.+.- .++-..-+|-|+.
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 45679999999874 2333566777664
No 151
>cd04328 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of eukaryotic RNA polymerase (RNAP) I that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNP III, and RpoE of archaeal RNAP. Rpa43 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Rpa43 heterodimerizes with Rpa14 and this heterodimer has genetic and biochemical characteristics similar to those of the Rpb7/Rpb4 heterodimer of RNAP II. In addition, the Rpa43/Rpa14 heterodimer binds single-stranded RNA, as is the case for the Rpb7/Rpb4 and the archaeal E/F complexes. The position of Rpa43/Rpa14 in the three-dimensional structure of RNAP I is similar to that of Rpb4/Rpb7, which forms an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Rpb43 binds Rrn3, an rDNA-specific transcription factor, functionally equivalent to TFIIB, invo
Probab=24.39 E-value=1.1e+02 Score=19.47 Aligned_cols=41 Identities=22% Similarity=0.217 Sum_probs=22.5
Q ss_pred ceEEEEEEEEecCCC--cceEEEEEeec--CeeEEEEEeecCCcc
Q psy3777 43 QAYEGIVISRRNKGL--NSNFIVRKISY--NEGIERTFQLYSPII 83 (99)
Q Consensus 43 q~f~GvvIa~r~~g~--~stftlR~i~~--gvGVEr~fpl~SP~I 83 (99)
+.++|+|++..+--. +.+=.+..-.. .+.|+-.+-++.|.+
T Consensus 45 ~~l~Gv~l~~~di~~~~~~~~~i~~~~~~~~~~V~~~~lVFrP~~ 89 (89)
T cd04328 45 PKLKGVVLAYSNIKLLEGELAKIVDDSPFIFVWISADFLVFRPKI 89 (89)
T ss_pred ccCCeEEEEecceEeccccceeeeCCCcEEEEEEEEEEEEEecCC
Confidence 467899999876222 22122222111 123677777888853
No 152
>cd03454 YdeM YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
Probab=24.24 E-value=89 Score=20.76 Aligned_cols=16 Identities=31% Similarity=0.588 Sum_probs=13.5
Q ss_pred CcCCCCEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIE 36 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (99)
.+.|||+|.++..+.+
T Consensus 88 pv~~Gd~l~~~~~v~~ 103 (140)
T cd03454 88 PVRPGDTLSVEVEVLD 103 (140)
T ss_pred CCCCCCEEEEEEEEEE
Confidence 4789999999998863
No 153
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=24.14 E-value=61 Score=21.82 Aligned_cols=16 Identities=19% Similarity=0.225 Sum_probs=13.1
Q ss_pred CCCCcCCCCEEEEEEE
Q psy3777 18 NIPDFVTGDTIIVNLN 33 (99)
Q Consensus 18 ~~p~f~~GD~v~V~~~ 33 (99)
+...+.|||+|.|...
T Consensus 136 ~~~~l~pGDvi~l~~~ 151 (164)
T PF13550_consen 136 DGLALEPGDVIALSDD 151 (164)
T ss_pred hhccCCCCCEEEEEeC
Confidence 4457999999999875
No 154
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=23.95 E-value=79 Score=21.30 Aligned_cols=16 Identities=25% Similarity=0.107 Sum_probs=12.8
Q ss_pred CCcCCCCEEEEEEEEe
Q psy3777 20 PDFVTGDTIIVNLNVI 35 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~ 35 (99)
--+.+||.|.|..+.-
T Consensus 58 IwI~~GD~VlVe~~~~ 73 (100)
T PRK04012 58 MWIREGDVVIVAPWDF 73 (100)
T ss_pred EEecCCCEEEEEeccc
Confidence 4689999999997643
No 155
>PF02107 FlgH: Flagellar L-ring protein; InterPro: IPR000527 The flgH, flgI and fliF genes of Salmonella typhimurium encode the major proteins for the L, P and M rings of the flagellar basal body []. In fact, the basal body consists of four rings (L,P,S and M) surrounding the flagellar rod, which is believed to transmit motor rotation to the filament []. The M ring is integral to the inner membrane of the cell, and may be connected to the rod via the S (supramembrane) ring, which lies just distal to it. The L and P rings reside in the outer membrane and periplasmic space, respectively. FlgH and FlgI, which are exported across the cell membrane to their destinations in the outer membrane and periplasmic space, have typical N-terminal cleaved signal-peptide sequences. FlgH is predicted to have an extensive beta-sheet structure, in keeping with other outer membrane proteins [].; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0009427 bacterial-type flagellum basal body, distal rod, L ring
Probab=23.95 E-value=76 Score=23.16 Aligned_cols=18 Identities=22% Similarity=0.180 Sum_probs=14.4
Q ss_pred CCCCCcCCCCEEEEEEEE
Q psy3777 17 KNIPDFVTGDTIIVNLNV 34 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~~i 34 (99)
.|.-..++||+|.|.+.-
T Consensus 20 ~D~rA~~VGDiiTV~v~E 37 (179)
T PF02107_consen 20 SDRRARRVGDIITVVVSE 37 (179)
T ss_pred ccccccCCCCEEEEEEEE
Confidence 355678999999998764
No 156
>cd03446 MaoC_like MoaC_like Similar to the MaoC (monoamine oxidase C) dehydratase regulatory protein but without the N-terminal PutA domain. This protein family has a hot-dog fold similar to that of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
Probab=23.94 E-value=91 Score=20.53 Aligned_cols=16 Identities=38% Similarity=0.524 Sum_probs=13.5
Q ss_pred CcCCCCEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIE 36 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (99)
.+.+||+|.++..+.+
T Consensus 90 pv~~GD~l~~~~~v~~ 105 (140)
T cd03446 90 PVFIGDTIRAEAEVVE 105 (140)
T ss_pred CCCCCCEEEEEEEEEE
Confidence 4799999999998863
No 157
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=23.85 E-value=1e+02 Score=21.08 Aligned_cols=14 Identities=7% Similarity=0.304 Sum_probs=10.8
Q ss_pred CCCCcCCCCEEEEE
Q psy3777 18 NIPDFVTGDTIIVN 31 (99)
Q Consensus 18 ~~p~f~~GD~v~V~ 31 (99)
..+.|.+||+|+|.
T Consensus 61 ~a~~l~~GdvV~I~ 74 (129)
T PRK06461 61 QAGSLKEGEVVEIE 74 (129)
T ss_pred ccccCCCCCEEEEE
Confidence 34568889998887
No 158
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: 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 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=23.85 E-value=1.3e+02 Score=17.79 Aligned_cols=16 Identities=6% Similarity=0.345 Sum_probs=12.5
Q ss_pred CcCCCCEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIE 36 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (99)
.|++||.+.+.+.-..
T Consensus 42 ~~~~G~~i~~kVi~id 57 (66)
T cd05695 42 TYKEGQKVRARILYVD 57 (66)
T ss_pred CcCCCCEEEEEEEEEe
Confidence 4999999999865443
No 159
>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=23.82 E-value=2.6e+02 Score=19.48 Aligned_cols=28 Identities=29% Similarity=0.507 Sum_probs=21.6
Q ss_pred CCcCCCCEEEEEEEEecCCceeeceEEEEEEEEec
Q psy3777 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~ 54 (99)
+.|.+||.|+|. +|. .+-|+|++....+
T Consensus 118 ~~~~~G~~V~I~----~Gp---f~G~~g~v~~~~~ 145 (172)
T TIGR00922 118 IDFEVGEQVRVN----DGP---FANFTGTVEEVDY 145 (172)
T ss_pred cCCCCCCEEEEe----ecC---CCCcEEEEEEEcC
Confidence 348999999986 343 5688999999864
No 160
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits 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 Saccharomyces 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=23.80 E-value=77 Score=19.38 Aligned_cols=17 Identities=18% Similarity=0.327 Sum_probs=13.6
Q ss_pred CCCcCCCCEEEEEEEEe
Q psy3777 19 IPDFVTGDTIIVNLNVI 35 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~ 35 (99)
-+.|++||.+.+.+.-.
T Consensus 48 ~~~~~~GD~i~~~V~~~ 64 (82)
T cd04454 48 RKSLQPGDLILAKVISL 64 (82)
T ss_pred HhcCCCCCEEEEEEEEe
Confidence 34599999999998654
No 161
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=23.75 E-value=1.8e+02 Score=19.43 Aligned_cols=59 Identities=20% Similarity=0.311 Sum_probs=37.8
Q ss_pred CCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEe-ecCe-e-------------EEEEEeecCCccceEEE
Q psy3777 24 TGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKI-SYNE-G-------------IERTFQLYSPIISSIIV 88 (99)
Q Consensus 24 ~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i-~~gv-G-------------VEr~fpl~SP~I~~I~V 88 (99)
.|..|.+... +. -.|+|++..+.. -++|++|+|+ .+|+ | .+ ..-+..--|++++|
T Consensus 7 IGs~ISlisk----~~---iRYeG~L~~Id~--~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~-~I~Fr~sDIkdL~v 76 (96)
T PF12701_consen 7 IGSKISLISK----SD---IRYEGILYSIDT--EDSTITLKNVRSFGTEGRPTDREIPPSDEVYD-YIVFRGSDIKDLKV 76 (96)
T ss_dssp TTCEEEEEET----TT---EEEEEEEEEEET--TTTEEEEEEEEETTETTSS-SS---C-CSSSS-EEEEETTTEEEEEE
T ss_pred cCCEEEEEEC----CC---cEEEEEEEEEcC--CCCEEEeeeeeecCcCCCCcCcccCCCCceee-EEEEEccccceEEE
Confidence 5777777542 11 479999999885 4799999998 4565 1 11 11234566777777
Q ss_pred EEee
Q psy3777 89 KRRG 92 (99)
Q Consensus 89 ~~~~ 92 (99)
+...
T Consensus 77 ~e~~ 80 (96)
T PF12701_consen 77 IEPP 80 (96)
T ss_dssp CE-S
T ss_pred EcCC
Confidence 7643
No 162
>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=23.37 E-value=52 Score=19.16 Aligned_cols=44 Identities=16% Similarity=0.397 Sum_probs=23.8
Q ss_pred CCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCee
Q psy3777 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEG 71 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gvG 71 (99)
.|.|.+||+|-|.-.. ....|=++..+..|-. ..+++++....|
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 4889999999887321 2222322333322211 478888774443
No 163
>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=23.35 E-value=1.4e+02 Score=20.70 Aligned_cols=32 Identities=13% Similarity=0.170 Sum_probs=21.2
Q ss_pred CCcCCCCEEEEEEEEe----cCCceeeceEEEEEEE
Q psy3777 20 PDFVTGDTIIVNLNVI----EGTRKRIQAYEGIVIS 51 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~----eg~k~r~q~f~GvvIa 51 (99)
-.+.+||.|-|.+... .++.++-.+|.|..|-
T Consensus 98 L~L~~GD~Vwl~l~~~~~~i~~~~~~~stFSGfLl~ 133 (135)
T smart00110 98 LQLRQGDQVWLELPDEKNGLYAGEYVDSTFSGFLLF 133 (135)
T ss_pred EEECCCCEEEEEEeCCCCceecCCCCcEEEEEEEEe
Confidence 3578999999887531 1233566778887763
No 164
>PF01575 MaoC_dehydratas: MaoC like domain; InterPro: IPR002539 The C terminus of the MaoC protein is found to share similarity with a wide variety of enzymes. All these enzymes contain multiple domains. This domain is found in parts of two enzymes that have been assigned dehydratase activities. A deletion mutant of the C-terminal 271 amino acids in Q02207 from SWISSPROT abolished its 2-enoyl-CoA hydratase activity, suggesting that this region may be a hydratase enzyme []. The maoC gene is part of a operon with maoA which is involved in the synthesis of monoamine oxidase [].; GO: 0016491 oxidoreductase activity, 0008152 metabolic process; PDB: 3HMJ_H 2UV8_I 2VKZ_G 1PN4_C 1PN2_B 1S9C_K 3OML_A 1Q6W_B 2B3M_A 3K67_B ....
Probab=23.32 E-value=1.2e+02 Score=19.93 Aligned_cols=17 Identities=29% Similarity=0.511 Sum_probs=13.1
Q ss_pred CCcCCCCEEEEEEEEec
Q psy3777 20 PDFVTGDTIIVNLNVIE 36 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~e 36 (99)
-...+||+|.+...+.+
T Consensus 87 ~PV~~gdtl~~~~~v~~ 103 (122)
T PF01575_consen 87 APVFPGDTLTAEVEVTE 103 (122)
T ss_dssp S--BTTEEEEEEEEEEE
T ss_pred ccccCCCEEEEEEEEEE
Confidence 35889999999999875
No 165
>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=23.32 E-value=1.4e+02 Score=20.43 Aligned_cols=30 Identities=13% Similarity=0.283 Sum_probs=18.5
Q ss_pred CCcCCCCEEEEEEEEecCCceeeceEEEEE
Q psy3777 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIV 49 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~eg~k~r~q~f~Gvv 49 (99)
|.+.+||++.+++....-..+..-.|.|.+
T Consensus 91 ~v~p~Gd~l~i~~~~~~~~~~~~~~~~~~~ 120 (138)
T cd01289 91 DRFDLGSTLLIVVAELLQGDSGLGVFECTI 120 (138)
T ss_pred ceeCCCCeeEEEeeeeeeCCCcEEEEEEEE
Confidence 445559999998876532113566666653
No 166
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=23.10 E-value=65 Score=21.01 Aligned_cols=13 Identities=23% Similarity=0.503 Sum_probs=11.5
Q ss_pred CCcCCCCEEEEEE
Q psy3777 20 PDFVTGDTIIVNL 32 (99)
Q Consensus 20 p~f~~GD~v~V~~ 32 (99)
|+..+||.|-||.
T Consensus 41 ~~~~vGDyVLVHa 53 (82)
T PRK10413 41 PADLLGQWVLVHV 53 (82)
T ss_pred cccccCCEEEEec
Confidence 6789999999986
No 167
>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=23.06 E-value=1.2e+02 Score=18.52 Aligned_cols=18 Identities=28% Similarity=0.397 Sum_probs=14.2
Q ss_pred CCCcCCCCEEEEE-EEEec
Q psy3777 19 IPDFVTGDTIIVN-LNVIE 36 (99)
Q Consensus 19 ~p~f~~GD~v~V~-~~i~e 36 (99)
.+.+.+||++.+. -++.+
T Consensus 46 ~~~~~~G~vv~i~~~~v~~ 64 (82)
T cd04491 46 ADDLEPGDVVRIENAYVRE 64 (82)
T ss_pred cccCCCCCEEEEEeEEEEe
Confidence 6789999999988 66554
No 168
>cd03453 SAV4209_like SAV4209_like. Similar in sequence to the Streptomyces avermitilis SAV4209 protein, with a hot dog fold that is similar to those of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
Probab=23.02 E-value=96 Score=20.45 Aligned_cols=16 Identities=25% Similarity=0.185 Sum_probs=13.6
Q ss_pred CcCCCCEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIE 36 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (99)
...+||++.++..+.+
T Consensus 80 Pv~~Gdtl~~~~~v~~ 95 (127)
T cd03453 80 PVPVPDTLTCTGIVVE 95 (127)
T ss_pred cCcCCCEEEEEEEEEE
Confidence 4799999999998864
No 169
>COG0668 MscS Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=22.92 E-value=1.7e+02 Score=21.69 Aligned_cols=38 Identities=24% Similarity=0.288 Sum_probs=24.4
Q ss_pred CCcCCCCEEEEEE-EE-----ecCCceeeceEEEEEEEEecCCC
Q psy3777 20 PDFVTGDTIIVNL-NV-----IEGTRKRIQAYEGIVISRRNKGL 57 (99)
Q Consensus 20 p~f~~GD~v~V~~-~i-----~eg~k~r~q~f~GvvIa~r~~g~ 57 (99)
-.|++||.|++.- .. .+-.-+++..+.|-++.+-|+-+
T Consensus 146 ~~f~vGD~I~i~~~~~G~V~~i~~~~T~ir~~dg~~v~iPNs~i 189 (316)
T COG0668 146 RPFKVGDWIEIGSGVEGTVEDIGLRSTTIRTLDGRIVTIPNSKL 189 (316)
T ss_pred cCcCcCCEEEECCCceEEEEEEEEEEEEEEcCCCCEEEccchhh
Confidence 4699999999962 10 11124556777787777777544
No 170
>PRK11507 ribosome-associated protein; Provisional
Probab=22.77 E-value=62 Score=20.66 Aligned_cols=12 Identities=25% Similarity=0.376 Sum_probs=9.8
Q ss_pred CCcCCCCEEEEE
Q psy3777 20 PDFVTGDTIIVN 31 (99)
Q Consensus 20 p~f~~GD~v~V~ 31 (99)
-.++|||+|.+.
T Consensus 51 kKl~~GD~V~~~ 62 (70)
T PRK11507 51 CKIVAGQTVSFA 62 (70)
T ss_pred CCCCCCCEEEEC
Confidence 468999999873
No 171
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=22.59 E-value=1.1e+02 Score=18.42 Aligned_cols=13 Identities=15% Similarity=0.233 Sum_probs=11.0
Q ss_pred cCCCCEEEEEEEE
Q psy3777 22 FVTGDTIIVNLNV 34 (99)
Q Consensus 22 f~~GD~v~V~~~i 34 (99)
|++||.|+|.+.-
T Consensus 49 ~~~Gd~v~v~v~~ 61 (79)
T cd05684 49 VKRGQKVKVKVIS 61 (79)
T ss_pred eCCCCEEEEEEEE
Confidence 7999999998754
No 172
>PRK12786 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=22.54 E-value=2.6e+02 Score=22.56 Aligned_cols=47 Identities=6% Similarity=-0.030 Sum_probs=33.1
Q ss_pred CCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCeeE
Q psy3777 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGI 72 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gvGV 72 (99)
+-++-||.|.+.+... | =....-..|..+.+.+.++.|||...|-=|
T Consensus 257 ~lV~rGd~V~i~~~~g-g-----l~v~~~G~ALe~G~~Gd~IrV~N~~S~kiv 303 (338)
T PRK12786 257 DLVQRGQLVTLIYQTP-G-----IYLTARGKALEDGAEGDVVRVLNLQSKRTV 303 (338)
T ss_pred cEEcCCCEEEEEEEcC-C-----EEEEEEEEEccccCCCCEEEEEECCCCCEE
Confidence 4589999999998642 1 123344467778888999999998655433
No 173
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: 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 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=22.43 E-value=1.3e+02 Score=18.46 Aligned_cols=16 Identities=6% Similarity=0.312 Sum_probs=12.4
Q ss_pred CCcCCCCEEEEEEEEe
Q psy3777 20 PDFVTGDTIIVNLNVI 35 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~ 35 (99)
..|++||.+.+.+.-.
T Consensus 42 ~~~~~Gq~v~~~V~~v 57 (74)
T cd05694 42 SKLKVGQLLLCVVEKV 57 (74)
T ss_pred cccCCCCEEEEEEEEE
Confidence 4589999999987533
No 174
>cd03441 R_hydratase_like (R)-hydratase [(R)-specific enoyl-CoA hydratase]. Catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. The structure of the monomer includes a five-strand antiparallel beta-sheet wrapped around a central alpha helix, referred to as a hot dog fold. The active site lies within a substrate-binding tunnel formed by the homodimer. Other enzymes with this fold include MaoC dehydratase, Hydratase-Dehydrogenase-Epimerase protein (HDE), and the fatty acid synthase beta subunit.
Probab=22.42 E-value=1e+02 Score=19.49 Aligned_cols=17 Identities=29% Similarity=0.520 Sum_probs=14.3
Q ss_pred CCcCCCCEEEEEEEEec
Q psy3777 20 PDFVTGDTIIVNLNVIE 36 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~e 36 (99)
-.+.+||+|.+...+.+
T Consensus 79 ~Pv~~Gd~l~~~~~v~~ 95 (127)
T cd03441 79 APVFPGDTLRVEVEVLG 95 (127)
T ss_pred CCcCCCCEEEEEEEEEE
Confidence 35889999999999864
No 175
>cd08548 Type_I_cohesin_like Type I cohesin domain, interaction partner of dockerin. Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. The cellulosome consists of scaffoldin, a noncatalytic scaffolding polypeptide, that comprises repeating cohesion modules and a single carbohydrate-binding module (CBM). Specific calcium-dependent interactions between cohesins and dockerins appear to be essential for cellulosome assembly. This subfamily represents type I cohesins; their interactions with dockerin mediate assembly of a range of dockerin-borne enzymes to the complex.
Probab=22.37 E-value=1.3e+02 Score=20.70 Aligned_cols=47 Identities=19% Similarity=0.190 Sum_probs=26.6
Q ss_pred cCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCc-ceEEEEEeecCeeEEE
Q psy3777 22 FVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLN-SNFIVRKISYNEGIER 74 (99)
Q Consensus 22 f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~-stftlR~i~~gvGVEr 74 (99)
-+|||+|.|-+.+..-.+.-+..++ .... .+ +-+.+=.+-.|--+..
T Consensus 10 ~~~G~tv~VpV~~~~v~~~~i~~~~---f~l~---yD~s~Lev~~v~~G~i~~~ 57 (135)
T cd08548 10 GKPGDTVTVPVTLSNVPSKGIGACD---FVLS---YDPSVLEVVSVEAGDIVKN 57 (135)
T ss_pred ecCCCEEEEEEEEecCCccCEEEEE---EEEE---eCCceeEEEecccCceecC
Confidence 5799999999999754333344333 3222 23 3355555555544443
No 176
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=22.20 E-value=79 Score=16.85 Aligned_cols=13 Identities=38% Similarity=0.473 Sum_probs=11.0
Q ss_pred CcCCCCEEEEEEE
Q psy3777 21 DFVTGDTIIVNLN 33 (99)
Q Consensus 21 ~f~~GD~v~V~~~ 33 (99)
.|++||.|.|.-.
T Consensus 20 ~~~~Gd~v~v~~~ 32 (58)
T smart00326 20 SFKKGDIITVLEK 32 (58)
T ss_pred CCCCCCEEEEEEc
Confidence 6999999999754
No 177
>cd05794 S1_EF-P_repeat_2 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=22.16 E-value=78 Score=19.28 Aligned_cols=16 Identities=31% Similarity=0.594 Sum_probs=11.4
Q ss_pred CCCCc-CCCCEEEEEEE
Q psy3777 18 NIPDF-VTGDTIIVNLN 33 (99)
Q Consensus 18 ~~p~f-~~GD~v~V~~~ 33 (99)
..|.| ..||.|+|...
T Consensus 33 ~VP~FI~~Gd~I~V~T~ 49 (56)
T cd05794 33 QVPLFIKEGEKIKVDTR 49 (56)
T ss_pred EcCCeecCCCEEEEECC
Confidence 45765 88888888654
No 178
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=22.11 E-value=2.9e+02 Score=19.40 Aligned_cols=48 Identities=15% Similarity=0.135 Sum_probs=32.7
Q ss_pred CCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCeeE
Q psy3777 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGI 72 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gvGV 72 (99)
-+-++-||.|.+.+... | =++ .-+| .|..+.+.+.++.|||...|-=|
T Consensus 79 p~lV~rG~~V~i~~~~g-g--l~i-~~~G--~AL~~G~~Gd~IrV~N~~S~riV 126 (141)
T PRK12618 79 PAIVDRNQLVPLAYRLG-G--LEI-RTEG--RALSRGGVGDEIRVMNLSSRTTV 126 (141)
T ss_pred ccEEeCCCEEEEEEecC-C--EEE-EEEE--EEcccCCCCCEEEEEECCCCCEE
Confidence 34689999999988642 1 111 2335 55667888999999997666433
No 179
>PRK14578 elongation factor P; Provisional
Probab=22.08 E-value=3.4e+02 Score=20.19 Aligned_cols=63 Identities=16% Similarity=0.147 Sum_probs=35.3
Q ss_pred CCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceE---EEEEeecCeeEEEEEeecCCccceEEEEE
Q psy3777 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNF---IVRKISYNEGIERTFQLYSPIISSIIVKR 90 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stf---tlR~i~~gvGVEr~fpl~SP~I~~I~V~~ 90 (99)
.-+|++|.++... |.--++..|+= .+-++|-..+| .+||+..|--+|++|.-- -.++...+-+
T Consensus 4 ~~dik~G~~i~~d-----g~~~~V~~~~~---~kpg~~g~~a~vr~klknl~tG~~~e~tf~s~-d~ve~a~ve~ 69 (187)
T PRK14578 4 TSDFKKGLVIQLD-----GAPCLLLDVTF---QSPSARGANTMVKTKYRNLLTGQVLEKTFRSG-DKVEEADFER 69 (187)
T ss_pred hhhcCCCCEEEEC-----CEEEEEEEEEE---EcCCCCCCceEEEEEEEECCCCCEEEEEECCC-CEEEEeEEEE
Confidence 3478889888763 32222222211 11222223334 799999999999999643 3355444443
No 180
>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=22.03 E-value=67 Score=18.89 Aligned_cols=16 Identities=31% Similarity=0.621 Sum_probs=12.3
Q ss_pred cCCCCCc-CCCCEEEEE
Q psy3777 16 KKNIPDF-VTGDTIIVN 31 (99)
Q Consensus 16 ~~~~p~f-~~GD~v~V~ 31 (99)
.+|+|.+ +.||+|.|.
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 5788885 899999984
No 181
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=21.99 E-value=49 Score=20.14 Aligned_cols=16 Identities=19% Similarity=0.106 Sum_probs=10.3
Q ss_pred CCCcCCCCEEEEEEEE
Q psy3777 19 IPDFVTGDTIIVNLNV 34 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i 34 (99)
.--+++||.|.|....
T Consensus 39 ~iwI~~GD~V~V~~~~ 54 (65)
T PF01176_consen 39 RIWIKRGDFVLVEPSP 54 (65)
T ss_dssp CC---TTEEEEEEEST
T ss_pred eEecCCCCEEEEEecc
Confidence 3468999999998854
No 182
>TIGR00998 8a0101 efflux pump membrane protein (multidrug resistance protein A).
Probab=21.86 E-value=1.4e+02 Score=22.72 Aligned_cols=36 Identities=14% Similarity=0.309 Sum_probs=26.8
Q ss_pred CCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCC
Q psy3777 17 KNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKG 56 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g 56 (99)
.+++.+++|+.+.|++... +.. +.|+|.|..+....
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 4677899999999997532 211 37999999998753
No 183
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=21.63 E-value=97 Score=21.31 Aligned_cols=19 Identities=21% Similarity=0.377 Sum_probs=15.6
Q ss_pred CCCCcCCCCEEEEEEEEec
Q psy3777 18 NIPDFVTGDTIIVNLNVIE 36 (99)
Q Consensus 18 ~~p~f~~GD~v~V~~~i~e 36 (99)
++..+++||.|...+...+
T Consensus 85 ~l~~lk~G~~V~F~~~~~~ 103 (115)
T PRK09838 85 KMSEIKTGDKVAFNFVQQG 103 (115)
T ss_pred hhccCCCCCEEEEEEEEcC
Confidence 4567999999999998654
No 184
>PRK13692 (3R)-hydroxyacyl-ACP dehydratase subunit HadA; Provisional
Probab=21.61 E-value=1e+02 Score=21.85 Aligned_cols=16 Identities=25% Similarity=0.422 Sum_probs=13.8
Q ss_pred CcCCCCEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIE 36 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (99)
+++|||+|.+...+.+
T Consensus 96 PV~~GDtL~~~~eV~~ 111 (159)
T PRK13692 96 PIVAGDKLYCDVYVDS 111 (159)
T ss_pred CccCCCEEEEEEEEEE
Confidence 4899999999998864
No 185
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=21.58 E-value=2.2e+02 Score=26.09 Aligned_cols=37 Identities=22% Similarity=0.231 Sum_probs=28.1
Q ss_pred CcCCCCEEEEEEEEecCCcee----------------------eceEEEEEEEEecCCC
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKR----------------------IQAYEGIVISRRNKGL 57 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r----------------------~q~f~GvvIa~r~~g~ 57 (99)
.|++||.|+|.+.-.+.++.| -+.|+|.|..+...|+
T Consensus 710 ~~kvGq~VkvkVl~ID~e~rrI~LS~K~l~~dpw~~~~~~~~vG~iV~GkV~~v~~~Gv 768 (863)
T PRK12269 710 ELEVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVSSVTDFGI 768 (863)
T ss_pred ccCCCCEEEEEEEEEeccCCEEEEEecccccChHHHHHhhCCCCCEEEEEEEEEecCeE
Confidence 499999999988765444333 3578999999988774
No 186
>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=21.56 E-value=93 Score=21.35 Aligned_cols=33 Identities=36% Similarity=0.714 Sum_probs=25.2
Q ss_pred cCCCCC-----cCCCCEEEEEEEEecCCceeeceEEEEE
Q psy3777 16 KKNIPD-----FVTGDTIIVNLNVIEGTRKRIQAYEGIV 49 (99)
Q Consensus 16 ~~~~p~-----f~~GD~v~V~~~i~eg~k~r~q~f~Gvv 49 (99)
+-|+|. |.|||+-.|++.--.| +.++.=|.|.+
T Consensus 60 RLdIpaGTavRFEPG~~k~V~LV~~gG-~r~v~G~~gl~ 97 (101)
T TIGR00192 60 RLDIPSGTAVRFEPGEEKSVELVAIGG-NRRIYGFNGLV 97 (101)
T ss_pred ccccCCCCeEeECCCCeEEEEEEEccC-ceEEEccCccc
Confidence 567874 9999999999876544 66777777665
No 187
>COG2100 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=21.53 E-value=2.6e+02 Score=23.51 Aligned_cols=32 Identities=16% Similarity=0.434 Sum_probs=24.2
Q ss_pred cCCCC-CcCCCCEEEEEEEEecCCceeeceEEEEEEEEec
Q psy3777 16 KKNIP-DFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (99)
Q Consensus 16 ~~~~p-~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~ 54 (99)
+..+| +|+.||+|++.+... | .++|=.+++-+
T Consensus 345 Rp~lp~PF~rGevv~aevV~~-G------r~kGEmlavAr 377 (414)
T COG2100 345 RPRLPKPFKRGEVVKAEVVLP-G------RLKGEMLAVAR 377 (414)
T ss_pred CCCCCCccccCcEEEEEEEec-c------eecceEEEEec
Confidence 35667 499999999998653 5 67787777665
No 188
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=21.53 E-value=96 Score=21.06 Aligned_cols=17 Identities=24% Similarity=0.233 Sum_probs=13.8
Q ss_pred CCCCCcCCCCEEEEEEE
Q psy3777 17 KNIPDFVTGDTIIVNLN 33 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~~ 33 (99)
.+-.+.++||.|.|.+.
T Consensus 47 ~~~~~~~~GD~V~v~i~ 63 (135)
T PF04246_consen 47 PNPIGAKVGDRVEVEIP 63 (135)
T ss_pred cCCCCCCCCCEEEEEec
Confidence 35567999999999875
No 189
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=21.49 E-value=1.3e+02 Score=20.45 Aligned_cols=44 Identities=18% Similarity=0.447 Sum_probs=28.2
Q ss_pred CCCCcCCCCEEEEEEEEe--cC-CceeeceEEEEEEEEecCCCcceE
Q psy3777 18 NIPDFVTGDTIIVNLNVI--EG-TRKRIQAYEGIVISRRNKGLNSNF 61 (99)
Q Consensus 18 ~~p~f~~GD~v~V~~~i~--eg-~k~r~q~f~GvvIa~r~~g~~stf 61 (99)
.+-.|++||.|.+...=. .| --.+.+--.|.|...+++...--+
T Consensus 31 ~l~~y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A~~V~v 77 (98)
T PRK04306 31 ALQEFEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRAYIVEV 77 (98)
T ss_pred HHHhccCCCEEEEEecCceecCCccccccCCCEEEEeecCeEEEEEE
Confidence 345799999999876321 11 124556668999998876544333
No 190
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=21.46 E-value=1.2e+02 Score=19.05 Aligned_cols=19 Identities=21% Similarity=0.623 Sum_probs=13.7
Q ss_pred ceEEEEEEEEecCCCcceEEEE
Q psy3777 43 QAYEGIVISRRNKGLNSNFIVR 64 (99)
Q Consensus 43 q~f~GvvIa~r~~g~~stftlR 64 (99)
+.|.|+|++.+ .+.|.+++
T Consensus 2 ~~l~G~Vvs~k---m~KTvvV~ 20 (71)
T TIGR03635 2 KTLQGVVVSDK---MDKTIVVL 20 (71)
T ss_pred eEEEEEEEccc---CCceEEEE
Confidence 57999999964 35666654
No 191
>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=21.45 E-value=96 Score=19.23 Aligned_cols=16 Identities=19% Similarity=0.526 Sum_probs=13.8
Q ss_pred EEeecCCccceEEEEE
Q psy3777 75 TFQLYSPIISSIIVKR 90 (99)
Q Consensus 75 ~fpl~SP~I~~I~V~~ 90 (99)
+|.++||.-++++|+=
T Consensus 11 ~F~vwAP~A~~V~l~l 26 (85)
T cd02853 11 RFRLWAPDAKRVTLRL 26 (85)
T ss_pred EEEEeCCCCCEEEEEe
Confidence 6899999999998874
No 192
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=21.39 E-value=71 Score=20.52 Aligned_cols=14 Identities=14% Similarity=0.154 Sum_probs=9.7
Q ss_pred CcCCCCEEEEEEEE
Q psy3777 21 DFVTGDTIIVNLNV 34 (99)
Q Consensus 21 ~f~~GD~v~V~~~i 34 (99)
.+++||+|++.-..
T Consensus 48 g~k~GdVvkI~R~S 61 (74)
T PF01191_consen 48 GAKPGDVVKIIRKS 61 (74)
T ss_dssp T--TTSEEEEEEEE
T ss_pred CCCCCCEEEEEecC
Confidence 56899999997653
No 193
>PRK13691 (3R)-hydroxyacyl-ACP dehydratase subunit HadC; Provisional
Probab=21.29 E-value=1e+02 Score=22.04 Aligned_cols=16 Identities=13% Similarity=0.432 Sum_probs=13.8
Q ss_pred CcCCCCEEEEEEEEec
Q psy3777 21 DFVTGDTIIVNLNVIE 36 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~e 36 (99)
++++||+|.++..+.+
T Consensus 96 PV~~GDtL~~~~~V~~ 111 (166)
T PRK13691 96 PVLAGDKLWARMDIHS 111 (166)
T ss_pred CcCCCCEEEEEEEEEE
Confidence 4899999999999863
No 194
>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family. Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.
Probab=21.21 E-value=1.1e+02 Score=23.91 Aligned_cols=38 Identities=18% Similarity=0.194 Sum_probs=27.9
Q ss_pred cCCCCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecC
Q psy3777 16 KKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNK 55 (99)
Q Consensus 16 ~~~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~ 55 (99)
..+++.+++|+.|.|++.-- ..++...|.|.|..+...
T Consensus 318 ~~~~~~i~~G~~v~v~~~~~--~~~~~~~~~g~V~~i~~~ 355 (423)
T TIGR01843 318 PKDIGFVHVGQPAEIKFSAF--PYRRYGILNGKVKSISPD 355 (423)
T ss_pred hhhhhhhCCCCceEEEEecC--CCcccCCccEEEEEECCC
Confidence 35788899999999876532 234455789999999753
No 195
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=21.20 E-value=1.2e+02 Score=18.08 Aligned_cols=20 Identities=20% Similarity=0.381 Sum_probs=11.7
Q ss_pred CCCC-CcCCCCEEEEEEEEec
Q psy3777 17 KNIP-DFVTGDTIIVNLNVIE 36 (99)
Q Consensus 17 ~~~p-~f~~GD~v~V~~~i~e 36 (99)
.+.| ++.+||.|.|-++...
T Consensus 32 ~e~~~~~~~Gd~v~VFvY~D~ 52 (61)
T PF13509_consen 32 SEVPEPLKVGDEVEVFVYLDK 52 (61)
T ss_dssp GG------TTSEEEEEEEE-T
T ss_pred HHcCCCCCCCCEEEEEEEECC
Confidence 3444 5999999999999753
No 196
>TIGR00849 gutA PTS system, glucitol/sorbitol-specific IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. This family consists only of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria.The system in E.Coli consists of a IIA protein, and a IIBC protein. This family is specific for the IIA component.
Probab=21.03 E-value=82 Score=21.93 Aligned_cols=15 Identities=20% Similarity=0.364 Sum_probs=12.9
Q ss_pred CCCCCcCCCCEEEEE
Q psy3777 17 KNIPDFVTGDTIIVN 31 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~ 31 (99)
..+|++++||++.+.
T Consensus 105 ~~~p~i~~G~~I~i~ 119 (121)
T TIGR00849 105 KEPPKIKPGSKFSIV 119 (121)
T ss_pred CCCCcCCCCCEEEEE
Confidence 468999999999874
No 197
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=20.91 E-value=3e+02 Score=19.20 Aligned_cols=47 Identities=19% Similarity=0.223 Sum_probs=29.2
Q ss_pred CCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCCcceEEEEEeecCeeEEEE
Q psy3777 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERT 75 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~~stftlR~i~~gvGVEr~ 75 (99)
..|.+||.|+|.- |. .+-|+|.+....... ...+|.=-+-|-.+.-.
T Consensus 125 ~~~~~Gd~VrI~~----GP---f~G~~g~v~~i~~~~--~r~~v~l~~~G~~~~v~ 171 (181)
T PRK05609 125 VDFEVGEMVRVID----GP---FADFNGTVEEVDYEK--SKLKVLVSIFGRETPVE 171 (181)
T ss_pred cCCCCCCEEEEec----cC---CCCCEEEEEEEeCCC--CEEEEEEEECCCceEEE
Confidence 4589999999962 43 467899999986422 23444334445444333
No 198
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=20.90 E-value=56 Score=21.56 Aligned_cols=14 Identities=14% Similarity=0.442 Sum_probs=7.0
Q ss_pred CCCCCcCCCCEEEE
Q psy3777 17 KNIPDFVTGDTIIV 30 (99)
Q Consensus 17 ~~~p~f~~GD~v~V 30 (99)
.++|.+++-|-|..
T Consensus 38 ~qLPkI~~~DPva~ 51 (80)
T COG2012 38 EQLPKIKASDPVAK 51 (80)
T ss_pred HHCCcccccChhHH
Confidence 45665554444433
No 199
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=20.87 E-value=2e+02 Score=22.56 Aligned_cols=31 Identities=29% Similarity=0.475 Sum_probs=26.0
Q ss_pred eEEEEEEEEecCCCcceEEEEEeecCee-EEEEEe
Q psy3777 44 AYEGIVISRRNKGLNSNFIVRKISYNEG-IERTFQ 77 (99)
Q Consensus 44 ~f~GvvIa~r~~g~~stftlR~i~~gvG-VEr~fp 77 (99)
.|.|+|-.++-.-.++.|++ -+|.| +|-+|-
T Consensus 70 ~fVGvvrni~~~ttn~~~~i---EDGTG~Ievr~W 101 (258)
T COG5235 70 QFVGVVRNIKTSTTNSMFVI---EDGTGSIEVRFW 101 (258)
T ss_pred EEEEEEEeeeecccceEEEE---ecCCceEEEEec
Confidence 69999999998888888887 67998 887763
No 200
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=20.76 E-value=2.5e+02 Score=23.52 Aligned_cols=37 Identities=22% Similarity=0.231 Sum_probs=24.6
Q ss_pred CcCCCCEEEEEEEEecCCcee----------------------eceEEEEEEEEecCCC
Q psy3777 21 DFVTGDTIIVNLNVIEGTRKR----------------------IQAYEGIVISRRNKGL 57 (99)
Q Consensus 21 ~f~~GD~v~V~~~i~eg~k~r----------------------~q~f~GvvIa~r~~g~ 57 (99)
.|++||.|.|.+.-...++.+ -+.+.|.|..+...|+
T Consensus 331 ~~~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~ 389 (565)
T PRK06299 331 VVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGA 389 (565)
T ss_pred hcCCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHhCCCCCEEEEEEEEEecceE
Confidence 389999999986433222222 2578888888877664
No 201
>COG1945 Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) [Amino acid transport and metabolism]
Probab=20.76 E-value=2e+02 Score=21.32 Aligned_cols=38 Identities=18% Similarity=0.378 Sum_probs=24.3
Q ss_pred CCCCCcCCCCEEEEEEE--EecCCceeeceEEEEEEEEec
Q psy3777 17 KNIPDFVTGDTIIVNLN--VIEGTRKRIQAYEGIVISRRN 54 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~~--i~eg~k~r~q~f~GvvIa~r~ 54 (99)
..+|+|.||.+|-+-+- .+++.-+.+..--|+++.+.+
T Consensus 57 ~gl~kl~pG~iv~~V~Ar~~S~~~G~~isaaig~a~p~D~ 96 (163)
T COG1945 57 DGLPKLPPGAILFCVMARGTSNEPGRTISAAIGVAIPRDK 96 (163)
T ss_pred hcCCcCCCCcEEeEEEeecccCCCCceeeeeeeEEecCCC
Confidence 34899999999998765 222223445555566666554
No 202
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=20.55 E-value=2.2e+02 Score=19.83 Aligned_cols=52 Identities=15% Similarity=0.257 Sum_probs=30.7
Q ss_pred CCCcCCCCEEEEEEEEecCCceeeceEEEEEEEEecCCC-cceEEEEEeecCeeEEEEEee
Q psy3777 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGL-NSNFIVRKISYNEGIERTFQL 78 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~~g~-~stftlR~i~~gvGVEr~fpl 78 (99)
.-+|++|-+|.+. |.--++..++ -.+-++|- -..+.++|++.|.-+|.+|+-
T Consensus 6 ~~~lr~G~~i~~d-----g~~~~V~~~~---~~KpGKg~a~vrvk~k~l~tG~~~e~~f~~ 58 (131)
T COG0231 6 ASELRKGLYIVID-----GEPYVVVEIS---HVKPGKGGAFVRVKLKNLFTGKKVEKTFKA 58 (131)
T ss_pred HHHccCCCEEEEC-----CeEEEEEEEE---EccCCCCCcEEEEEEEEccCCCEEEEEEcC
Confidence 3468899888742 3222222221 12223332 344559999999999999964
No 203
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=20.52 E-value=2.6e+02 Score=23.02 Aligned_cols=35 Identities=23% Similarity=0.272 Sum_probs=22.9
Q ss_pred cCCCCEEEEEEEEecCCcee----------------------eceEEEEEEEEecCC
Q psy3777 22 FVTGDTIIVNLNVIEGTRKR----------------------IQAYEGIVISRRNKG 56 (99)
Q Consensus 22 f~~GD~v~V~~~i~eg~k~r----------------------~q~f~GvvIa~r~~g 56 (99)
|.+||.|+|.+.-...++.| -+.+.|.|..+...|
T Consensus 318 ~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G 374 (516)
T TIGR00717 318 VKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFG 374 (516)
T ss_pred ccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEecce
Confidence 89999999997522222222 246778887776655
No 204
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=20.46 E-value=1.5e+02 Score=23.09 Aligned_cols=12 Identities=17% Similarity=0.360 Sum_probs=10.3
Q ss_pred CCcCCCCEEEEE
Q psy3777 20 PDFVTGDTIIVN 31 (99)
Q Consensus 20 p~f~~GD~v~V~ 31 (99)
.+|++||.|++.
T Consensus 128 rpf~vGD~I~i~ 139 (286)
T PRK10334 128 RPFRAGEYVDLG 139 (286)
T ss_pred CCCCCCCEEEEC
Confidence 479999999984
No 205
>PF13538 UvrD_C_2: UvrD-like helicase C-terminal domain; PDB: 1W36_G 3K70_G 3DMN_A 3UPU_B 3GPL_A 3E1S_A 3GP8_A.
Probab=20.41 E-value=60 Score=20.19 Aligned_cols=11 Identities=27% Similarity=0.730 Sum_probs=5.5
Q ss_pred cCCCCEEEEEE
Q psy3777 22 FVTGDTIIVNL 32 (99)
Q Consensus 22 f~~GD~v~V~~ 32 (99)
|++||.+.++.
T Consensus 1 ~~~gD~vv~~~ 11 (104)
T PF13538_consen 1 FRPGDKVVITR 11 (104)
T ss_dssp --TT-EEEE-C
T ss_pred CcCcCEEEEEe
Confidence 78888887765
No 206
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=20.35 E-value=56 Score=20.79 Aligned_cols=49 Identities=20% Similarity=0.367 Sum_probs=28.8
Q ss_pred cCCCCCcCCCCEEEEEEEEecCCceeeceE---EE--EEEEEecCCCcceEEEEE
Q psy3777 16 KKNIPDFVTGDTIIVNLNVIEGTRKRIQAY---EG--IVISRRNKGLNSNFIVRK 65 (99)
Q Consensus 16 ~~~~p~f~~GD~v~V~~~i~eg~k~r~q~f---~G--vvIa~r~~g~~stftlR~ 65 (99)
++.+....+|++++|..... ++.+.+..| +| -+....-.|--..|++|+
T Consensus 23 kk~l~~m~~Ge~LeV~~ddp-~~~~dIp~~~~~~~~~~ll~~e~~~~~~~~~Ikk 76 (78)
T COG0425 23 KKALAKLKPGEILEVIADDP-AAKEDIPAWAKKEGGHELLEVEQEGGVYRILIKK 76 (78)
T ss_pred HHHHHcCCCCCEEEEEecCc-chHHHHHHHHHHcCCcEEEEEEecCCcEEEEEEe
Confidence 35567889999999988764 455444443 22 444444433344555554
No 207
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=20.33 E-value=82 Score=21.89 Aligned_cols=16 Identities=25% Similarity=0.345 Sum_probs=13.8
Q ss_pred CCCCCcCCCCEEEEEE
Q psy3777 17 KNIPDFVTGDTIIVNL 32 (99)
Q Consensus 17 ~~~p~f~~GD~v~V~~ 32 (99)
.++.++++||.|.|+.
T Consensus 68 ~~L~~l~~GD~I~v~~ 83 (144)
T cd05829 68 FRLGDLRKGDKVEVTR 83 (144)
T ss_pred cchhcCCCCCEEEEEE
Confidence 3678999999999986
No 208
>PF08755 YccV-like: Hemimethylated DNA-binding protein YccV like; InterPro: IPR011722 This entry describes the small protein from Escherichia coli YccV and its homologs in other Proteobacteria. YccV is now described as a hemimethylated DNA binding protein []. The model entry describes a domain in longer eukaryotic proteins.; PDB: 1VBV_A.
Probab=20.29 E-value=96 Score=20.43 Aligned_cols=25 Identities=20% Similarity=0.472 Sum_probs=13.5
Q ss_pred CCcCCCCEEEEEEEEecCCceeeceEEEEEEEEec
Q psy3777 20 PDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54 (99)
Q Consensus 20 p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa~r~ 54 (99)
+.|++|++|+ -|.-.|.|||++-.-
T Consensus 2 ~~f~vGqvv~----------Hr~~~y~GVIvgwD~ 26 (100)
T PF08755_consen 2 VKFRVGQVVR----------HRRYGYRGVIVGWDP 26 (100)
T ss_dssp -SS-TT-EEE----------ETTT--EEEEEEEE-
T ss_pred cccccCCEEE----------EeeeCccEEEECccc
Confidence 4689999884 223478899987554
No 209
>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=20.15 E-value=1.5e+02 Score=17.83 Aligned_cols=31 Identities=19% Similarity=0.282 Sum_probs=20.4
Q ss_pred CCCCcCCCCEEEEEEEEecCCceeeceEEEEEEE
Q psy3777 18 NIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVIS 51 (99)
Q Consensus 18 ~~p~f~~GD~v~V~~~i~eg~k~r~q~f~GvvIa 51 (99)
+-+...+||++..++.+..... ....++.+.
T Consensus 33 ~~~~~~~Gd~v~ytitvtN~G~---~~a~nv~v~ 63 (76)
T PF01345_consen 33 NPSTANPGDTVTYTITVTNTGP---APATNVVVT 63 (76)
T ss_pred CCCcccCCCEEEEEEEEEECCC---CeeEeEEEE
Confidence 4567999999999998864221 234555543
No 210
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: 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 LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=20.13 E-value=1.6e+02 Score=17.30 Aligned_cols=40 Identities=25% Similarity=0.555 Sum_probs=24.7
Q ss_pred CCCcCCCCEEEEEEEEecCCceeeceEEE-EEEEEecCCCcceEEEEEeecCe
Q psy3777 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEG-IVISRRNKGLNSNFIVRKISYNE 70 (99)
Q Consensus 19 ~p~f~~GD~v~V~~~i~eg~k~r~q~f~G-vvIa~r~~g~~stftlR~i~~gv 70 (99)
.|.|..||+|-+... .+ .-.| +|+...+ + ...+|++....
T Consensus 11 ~p~i~~gd~lii~~~-----~~---~~~g~i~~~~~~-~---~~~ikr~~~~~ 51 (81)
T cd06529 11 EPTIPDGDLVLVDPS-----DT---PRDGDIVVARLD-G---ELTVKRLQRRG 51 (81)
T ss_pred CCccCCCCEEEEcCC-----CC---CCCCCEEEEEEC-C---EEEEEEEEECC
Confidence 477999999977531 11 2334 4444443 3 56788887666
Done!