Query psy3466
Match_columns 103
No_of_seqs 157 out of 1112
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 17:24:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3466.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3466hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10861 signal peptidase I; P 99.8 3.4E-20 7.4E-25 142.4 9.2 81 16-103 59-154 (324)
2 TIGR02227 sigpep_I_bact signal 99.8 2.8E-19 6.2E-24 125.1 7.9 77 20-103 1-80 (163)
3 TIGR02228 sigpep_I_arch signal 99.8 2.4E-18 5.2E-23 120.6 10.9 60 43-102 28-87 (158)
4 KOG3342|consensus 99.8 1.7E-18 3.7E-23 120.6 8.6 100 3-102 5-104 (180)
5 PF00717 Peptidase_S24: Peptid 99.5 5E-14 1.1E-18 84.9 5.9 51 50-102 1-51 (70)
6 cd06530 S26_SPase_I The S26 Ty 99.5 7.8E-14 1.7E-18 87.3 6.9 52 48-99 2-56 (85)
7 COG0681 LepB Signal peptidase 99.5 4.5E-14 9.7E-19 97.1 5.2 63 17-86 7-95 (166)
8 TIGR02754 sod_Ni_protease nick 99.5 2.4E-13 5.2E-18 86.2 7.0 53 50-102 2-57 (90)
9 KOG0171|consensus 99.4 2.2E-13 4.8E-18 95.9 6.3 69 28-103 22-94 (176)
10 KOG1568|consensus 99.3 1.3E-11 2.9E-16 86.8 6.0 55 48-102 33-96 (174)
11 cd06462 Peptidase_S24_S26 The 99.1 2.8E-10 6.1E-15 69.9 7.1 51 49-101 3-53 (84)
12 cd06529 S24_LexA-like Peptidas 99.1 7.9E-10 1.7E-14 67.8 6.8 49 49-101 3-51 (81)
13 COG2932 Predicted transcriptio 98.9 4.7E-09 1E-13 75.9 6.4 52 48-102 125-176 (214)
14 PRK00215 LexA repressor; Valid 98.5 5.8E-07 1.3E-11 64.4 6.7 49 48-100 120-169 (205)
15 PRK10276 DNA polymerase V subu 98.4 7E-07 1.5E-11 60.9 6.4 48 48-99 53-101 (139)
16 PRK13838 conjugal transfer pil 98.4 4.1E-06 8.9E-11 59.7 9.2 41 63-103 36-98 (176)
17 PRK12423 LexA repressor; Provi 98.3 1.8E-06 3.9E-11 62.2 6.6 49 48-100 116-165 (202)
18 TIGR00498 lexA SOS regulatory 98.2 5.3E-06 1.2E-10 59.1 6.9 49 48-100 113-162 (199)
19 TIGR02771 TraF_Ti conjugative 98.1 1.3E-05 2.8E-10 56.9 6.4 47 50-103 28-94 (171)
20 COG1974 LexA SOS-response tran 97.8 8.9E-05 1.9E-09 54.0 6.3 50 48-100 114-164 (201)
21 PRK13884 conjugal transfer pep 97.5 0.0012 2.6E-08 47.0 8.7 30 74-103 49-98 (178)
22 PF10502 Peptidase_S26: Signal 95.0 0.0065 1.4E-07 41.5 0.0 29 75-103 21-62 (138)
23 COG0361 InfA Translation initi 82.7 1.6 3.5E-05 27.1 2.7 23 59-82 46-68 (75)
24 TIGR00008 infA translation ini 81.4 1.8 3.9E-05 26.4 2.6 22 60-82 45-66 (68)
25 cd04456 S1_IF1A_like S1_IF1A_l 79.2 2.1 4.6E-05 26.6 2.4 24 60-83 39-62 (78)
26 PF10000 ACT_3: ACT domain; I 78.0 1.5 3.2E-05 26.9 1.4 36 54-89 12-49 (72)
27 PF05382 Amidase_5: Bacterioph 75.6 3.6 7.8E-05 28.5 3.0 39 50-88 50-88 (145)
28 TIGR00523 eIF-1A eukaryotic/ar 75.1 3.4 7.4E-05 26.8 2.7 24 60-83 58-81 (99)
29 COG3602 Uncharacterized protei 73.8 2.8 6.1E-05 28.4 2.0 17 54-70 12-28 (134)
30 KOG4146|consensus 71.2 6.7 0.00014 25.5 3.2 34 49-86 56-96 (101)
31 cd05793 S1_IF1A S1_IF1A: Trans 70.5 4.3 9.4E-05 25.1 2.2 21 61-82 40-60 (77)
32 PF01176 eIF-1a: Translation i 68.6 4.4 9.5E-05 24.0 1.9 12 75-86 41-52 (65)
33 PRK12442 translation initiatio 68.1 6.8 0.00015 25.0 2.8 22 60-82 47-68 (87)
34 PF15057 DUF4537: Domain of un 67.7 4.2 9E-05 27.3 1.9 19 52-70 48-66 (124)
35 PF10399 UCR_Fe-S_N: Ubiquitin 67.7 18 0.00038 19.8 4.1 27 12-38 9-35 (41)
36 COG5131 URM1 Ubiquitin-like pr 67.0 9.6 0.00021 24.6 3.3 34 49-86 51-91 (96)
37 PF09285 Elong-fact-P_C: Elong 64.6 14 0.0003 21.7 3.4 38 53-96 18-56 (56)
38 PF12273 RCR: Chitin synthesis 63.5 5.1 0.00011 26.7 1.7 15 20-34 2-16 (130)
39 PF04319 NifZ: NifZ domain; I 63.0 23 0.00051 21.9 4.4 30 56-85 1-35 (75)
40 PRK04012 translation initiatio 62.9 7.4 0.00016 25.3 2.3 21 61-82 61-81 (100)
41 PF13800 Sigma_reg_N: Sigma fa 62.7 27 0.00059 21.9 4.9 16 7-22 3-18 (96)
42 smart00652 eIF1a eukaryotic tr 62.0 8 0.00017 24.2 2.3 21 61-82 45-65 (83)
43 cd04720 BAH_Orc1p_Yeast BAH, o 58.7 26 0.00056 24.9 4.7 38 63-100 39-77 (179)
44 cd05792 S1_eIF1AD_like S1_eIF1 57.4 9.4 0.0002 23.8 2.0 22 61-82 40-61 (78)
45 COG0179 MhpD 2-keto-4-pentenoa 57.1 28 0.00061 26.4 4.9 31 59-89 224-255 (266)
46 cd06555 ASCH_PF0470_like ASC-1 57.1 39 0.00085 22.2 5.0 40 61-100 14-56 (109)
47 PF08802 CytB6-F_Fe-S: Cytochr 56.1 32 0.00069 18.7 4.8 31 10-40 4-34 (39)
48 TIGR02594 conserved hypothetic 53.9 31 0.00067 23.2 4.2 14 74-87 72-85 (129)
49 PF00278 Orn_DAP_Arg_deC: Pyri 53.6 16 0.00034 23.2 2.6 31 58-88 65-95 (116)
50 PF06890 Phage_Mu_Gp45: Bacter 52.2 23 0.0005 25.0 3.5 25 71-96 70-94 (162)
51 smart00841 Elong-fact-P_C Elon 51.7 25 0.00054 20.5 3.0 38 53-96 18-56 (56)
52 TIGR00038 efp translation elon 51.6 26 0.00057 24.9 3.8 37 55-97 147-184 (184)
53 COG1935 Uncharacterized conser 50.8 8 0.00017 26.1 0.9 21 59-79 38-58 (122)
54 PF07423 DUF1510: Protein of u 49.2 31 0.00068 25.5 3.9 13 20-32 14-26 (217)
55 cd04466 S1_YloQ_GTPase S1_YloQ 49.2 40 0.00086 19.2 3.7 25 74-98 36-60 (68)
56 PF09138 Urm1: Urm1 (Ubiquitin 48.3 15 0.00033 23.8 1.9 30 58-87 56-92 (96)
57 PF03908 Sec20: Sec20; InterP 47.8 67 0.0014 20.0 5.5 16 4-19 54-69 (92)
58 TIGR00998 8a0101 efflux pump m 47.2 96 0.0021 23.2 6.5 12 74-85 62-73 (334)
59 PRK14533 groES co-chaperonin G 45.8 10 0.00022 24.2 0.8 15 58-72 52-66 (91)
60 PF14118 YfzA: YfzA-like prote 45.7 23 0.00051 22.9 2.5 16 50-65 29-44 (94)
61 COG3655 Predicted transcriptio 45.4 16 0.00034 22.6 1.6 16 74-89 55-70 (73)
62 COG1188 Ribosome-associated he 45.2 69 0.0015 20.9 4.7 28 73-102 46-73 (100)
63 cd05794 S1_EF-P_repeat_2 S1_EF 45.2 31 0.00068 20.1 2.8 38 53-96 18-56 (56)
64 PRK05573 rplU 50S ribosomal pr 45.0 54 0.0012 21.3 4.2 34 49-85 3-36 (103)
65 PTZ00414 10 kDa heat shock pro 44.4 12 0.00026 24.4 1.0 15 58-72 61-75 (100)
66 TIGR00964 secE_bact preprotein 44.4 59 0.0013 18.4 4.3 20 2-21 5-27 (55)
67 PF13550 Phage-tail_3: Putativ 44.3 46 0.001 22.0 4.0 26 74-101 138-163 (164)
68 PRK15136 multidrug efflux syst 43.9 83 0.0018 24.7 5.8 12 74-85 81-92 (390)
69 PF04322 DUF473: Protein of un 43.4 14 0.0003 24.9 1.2 21 60-80 39-59 (119)
70 PF01878 EVE: EVE domain; Int 42.7 33 0.00072 22.8 3.0 15 74-88 38-52 (143)
71 TIGR01416 Rieske_proteo ubiqui 42.1 1.2E+02 0.0026 21.3 6.2 16 74-89 47-62 (174)
72 PF01616 Orbi_NS3: Orbivirus N 41.6 1E+02 0.0022 22.5 5.5 17 15-31 90-106 (195)
73 PLN00208 translation initiatio 40.2 27 0.00058 24.4 2.2 25 60-85 71-95 (145)
74 PF02362 B3: B3 DNA binding do 39.7 37 0.0008 20.7 2.7 16 73-88 71-86 (100)
75 PF05257 CHAP: CHAP domain; I 39.1 21 0.00045 23.1 1.5 13 73-85 60-72 (124)
76 PF09753 Use1: Membrane fusion 38.8 69 0.0015 23.6 4.4 19 20-38 228-246 (251)
77 PTZ00329 eukaryotic translatio 38.7 29 0.00063 24.4 2.3 23 60-83 71-93 (155)
78 TIGR02219 phage_NlpC_fam putat 37.6 24 0.00051 23.6 1.6 14 73-86 74-87 (134)
79 PF13856 Gifsy-2: ATP-binding 37.4 62 0.0013 20.2 3.5 26 72-100 62-87 (95)
80 PRK10691 hypothetical protein; 37.3 42 0.00092 24.4 3.0 30 59-88 181-211 (219)
81 KOG3251|consensus 37.2 1.1E+02 0.0023 22.8 5.1 30 7-36 178-207 (213)
82 PRK08564 5'-methylthioadenosin 36.9 23 0.0005 26.7 1.7 19 52-70 92-110 (267)
83 COG0234 GroS Co-chaperonin Gro 36.7 20 0.00043 23.3 1.1 11 75-85 58-68 (96)
84 PRK07597 secE preprotein trans 36.3 89 0.0019 18.1 4.3 21 2-22 14-37 (64)
85 COG4929 Uncharacterized membra 35.5 1.1E+02 0.0025 22.2 4.9 28 59-86 31-60 (190)
86 PF03904 DUF334: Domain of unk 35.1 1.6E+02 0.0034 22.2 5.7 25 17-41 146-170 (230)
87 PF07076 DUF1344: Protein of u 35.1 1E+02 0.0022 18.4 4.9 40 48-87 9-50 (61)
88 cd00320 cpn10 Chaperonin 10 Kd 34.7 1.2E+02 0.0025 19.1 4.5 14 74-87 56-69 (93)
89 PF00166 Cpn10: Chaperonin 10 34.6 1.2E+02 0.0025 19.0 4.6 14 74-87 56-69 (93)
90 PF12961 DUF3850: Domain of Un 34.3 1.1E+02 0.0025 18.7 4.5 36 62-98 15-50 (72)
91 PRK00364 groES co-chaperonin G 34.2 1.2E+02 0.0026 19.2 4.5 13 75-87 58-70 (95)
92 KOG3156|consensus 34.1 1.6E+02 0.0035 21.9 5.6 34 2-35 179-215 (220)
93 cd04497 hPOT1_OB1_like hPOT1_O 33.8 1.2E+02 0.0026 20.2 4.7 36 49-86 41-79 (138)
94 PF00584 SecE: SecE/Sec61-gamm 33.5 75 0.0016 17.8 3.2 20 3-22 7-29 (57)
95 KOG0557|consensus 33.4 82 0.0018 26.0 4.3 39 48-86 38-76 (470)
96 KOG1641|consensus 33.4 37 0.00079 22.4 1.9 30 50-79 56-86 (104)
97 TIGR01048 lysA diaminopimelate 33.0 66 0.0014 25.1 3.7 30 58-88 345-374 (417)
98 cd05790 S1_Rrp40 S1_Rrp40: Rrp 32.8 40 0.00086 21.2 2.0 18 53-70 43-60 (86)
99 PRK15203 4-hydroxyphenylacetat 32.6 50 0.0011 26.6 3.0 31 59-89 165-196 (429)
100 PRK08666 5'-methylthioadenosin 32.4 28 0.0006 25.9 1.5 19 52-70 84-102 (261)
101 TIGR01694 MTAP 5'-deoxy-5'-met 32.3 30 0.00066 25.3 1.6 19 52-70 84-102 (241)
102 CHL00075 rpl21 ribosomal prote 32.2 1.3E+02 0.0028 19.7 4.5 34 49-85 5-38 (108)
103 cd04713 BAH_plant_3 BAH, or Br 32.1 71 0.0015 21.8 3.4 25 75-99 20-44 (146)
104 PRK04542 elongation factor P; 32.0 80 0.0017 22.8 3.7 37 55-97 151-188 (189)
105 PF06940 DUF1287: Domain of un 31.8 32 0.0007 24.5 1.6 15 74-88 105-119 (164)
106 TIGR00061 L21 ribosomal protei 31.8 1.2E+02 0.0025 19.7 4.1 33 50-85 3-35 (101)
107 PRK09136 5'-methylthioadenosin 31.8 30 0.00064 25.8 1.5 22 49-70 81-102 (245)
108 PRK00276 infA translation init 31.7 52 0.0011 19.7 2.4 11 75-85 46-56 (72)
109 PRK14125 cell division suppres 31.4 1.5E+02 0.0032 19.2 4.8 15 73-87 77-91 (103)
110 PRK00529 elongation factor P; 31.0 81 0.0018 22.4 3.6 37 55-97 148-185 (186)
111 TIGR02303 HpaG-C-term 4-hydrox 30.8 63 0.0014 23.9 3.1 31 59-89 204-235 (245)
112 COG3008 PqiB Paraquat-inducibl 30.6 62 0.0013 27.3 3.3 55 17-82 21-77 (553)
113 PHA03164 hypothetical protein; 30.3 88 0.0019 19.7 3.2 13 22-34 66-78 (88)
114 KOG1535|consensus 29.8 68 0.0015 23.8 3.1 30 59-88 176-206 (217)
115 PRK14578 elongation factor P; 29.8 86 0.0019 22.6 3.6 37 55-97 150-187 (187)
116 PRK07432 5'-methylthioadenosin 29.4 51 0.0011 25.4 2.5 28 43-70 79-106 (290)
117 TIGR02178 yeiP elongation fact 28.9 70 0.0015 23.0 3.0 37 55-97 149-186 (186)
118 PF00877 NLPC_P60: NlpC/P60 fa 28.9 33 0.00071 21.4 1.2 13 74-86 50-62 (105)
119 PRK05740 secE preprotein trans 28.6 1.5E+02 0.0032 18.7 4.2 21 2-22 40-63 (92)
120 cd06829 PLPDE_III_CANSDC Type 28.5 78 0.0017 24.3 3.4 30 58-88 295-324 (346)
121 cd04451 S1_IF1 S1_IF1: Transla 28.3 54 0.0012 18.9 2.0 12 75-86 40-51 (64)
122 cd06836 PLPDE_III_ODC_DapDC_li 28.2 86 0.0019 24.4 3.6 29 59-88 328-356 (379)
123 COG4043 Preprotein translocase 28.0 43 0.00092 22.2 1.6 14 73-86 31-44 (111)
124 cd04092 mtEFG2_II_like mtEFG2_ 27.7 86 0.0019 18.7 2.9 12 74-85 59-70 (83)
125 cd06541 ASCH ASC-1 homology or 27.6 1.3E+02 0.0028 19.1 3.8 26 74-100 29-54 (105)
126 COG4959 TraF Type IV secretory 27.5 1E+02 0.0022 22.0 3.5 27 76-102 54-93 (173)
127 cd04088 EFG_mtEFG_II EFG_mtEFG 27.3 86 0.0019 18.5 2.8 12 74-85 59-70 (83)
128 PRK12278 50S ribosomal protein 27.1 1.4E+02 0.0029 22.2 4.3 34 49-85 3-36 (221)
129 PF09926 DUF2158: Uncharacteri 27.0 92 0.002 17.8 2.7 21 76-97 1-21 (53)
130 PHA02844 putative transmembran 26.9 1.3E+02 0.0029 18.6 3.6 16 20-35 51-66 (75)
131 PRK12426 elongation factor P; 26.8 94 0.002 22.4 3.3 38 54-97 147-185 (185)
132 PF07798 DUF1640: Protein of u 26.7 2.2E+02 0.0049 19.8 5.8 12 16-27 153-164 (177)
133 PRK00809 hypothetical protein; 26.6 72 0.0016 21.9 2.6 14 75-88 34-47 (144)
134 PRK11507 ribosome-associated p 26.2 40 0.00086 20.6 1.1 15 72-86 49-63 (70)
135 cd03703 aeIF5B_II aeIF5B_II: T 26.0 1.1E+02 0.0023 20.2 3.3 13 74-86 25-37 (110)
136 TIGR01697 PNPH-PUNA-XAPA inosi 25.9 48 0.001 24.4 1.7 19 52-70 91-109 (248)
137 PF00829 Ribosomal_L21p: Ribos 25.9 1.2E+02 0.0027 19.2 3.5 33 50-85 4-36 (96)
138 cd03695 CysN_NodQ_II CysN_NodQ 25.7 1.1E+02 0.0023 18.5 3.1 12 59-70 26-37 (81)
139 COG4079 Uncharacterized protei 25.5 1.1E+02 0.0023 23.5 3.5 27 61-87 247-273 (293)
140 COG0690 SecE Preprotein transl 25.5 1.6E+02 0.0035 17.7 4.5 13 2-14 24-36 (73)
141 TIGR01700 PNPH purine nucleosi 25.3 45 0.00098 24.6 1.5 19 52-70 91-109 (249)
142 CHL00010 infA translation init 25.3 83 0.0018 19.2 2.5 10 76-85 47-56 (78)
143 PHA02650 hypothetical protein; 25.2 1.1E+02 0.0025 19.2 3.1 12 26-37 58-69 (81)
144 PF07193 DUF1408: Protein of u 25.2 93 0.002 18.9 2.6 15 56-70 1-15 (75)
145 PF12666 PrgI: PrgI family pro 24.8 1.1E+02 0.0024 18.8 3.0 18 12-29 17-34 (93)
146 KOG1666|consensus 24.8 3E+02 0.0065 20.5 5.8 14 5-18 182-195 (220)
147 TIGR01698 PUNP purine nucleoti 24.8 1.2E+02 0.0027 22.5 3.8 23 48-70 87-109 (237)
148 COG4127 Uncharacterized conser 24.8 52 0.0011 25.6 1.8 26 74-99 71-96 (318)
149 PRK02268 hypothetical protein; 24.6 78 0.0017 21.8 2.5 13 75-87 35-47 (141)
150 cd03689 RF3_II RF3_II: this su 24.6 1.7E+02 0.0037 17.7 4.0 9 76-84 62-70 (85)
151 PRK08202 purine nucleoside pho 24.6 52 0.0011 24.7 1.8 21 50-70 111-131 (272)
152 PF08940 DUF1918: Domain of un 24.3 58 0.0013 19.2 1.5 36 61-96 4-40 (58)
153 cd06840 PLPDE_III_Bif_AspK_Dap 24.0 1.1E+02 0.0024 23.8 3.5 30 58-88 318-347 (368)
154 TIGR02896 spore_III_AF stage I 23.9 89 0.0019 20.4 2.5 12 18-29 4-15 (106)
155 KOG3208|consensus 23.7 1.7E+02 0.0037 21.9 4.2 24 12-35 203-227 (231)
156 PRK07823 5'-methylthioadenosin 23.5 71 0.0015 24.2 2.3 23 49-71 86-108 (264)
157 COG0019 LysA Diaminopimelate d 23.4 1.1E+02 0.0024 24.4 3.4 31 58-88 343-373 (394)
158 TIGR02305 HpaG-N-term 4-hydrox 23.2 1.3E+02 0.0027 21.5 3.5 30 59-88 167-197 (205)
159 cd03692 mtIF2_IVc mtIF2_IVc: t 23.2 1.2E+02 0.0027 18.3 3.0 9 74-82 74-82 (84)
160 COG0261 RplU Ribosomal protein 23.2 2.3E+02 0.005 18.6 4.4 33 50-85 4-36 (103)
161 TIGR01047 nspC carboxynorsperm 23.1 99 0.0022 24.2 3.1 30 58-88 309-338 (380)
162 PF07423 DUF1510: Protein of u 23.1 1.1E+02 0.0023 22.7 3.1 23 17-39 14-36 (217)
163 COG4698 Uncharacterized protei 22.8 1.1E+02 0.0023 22.4 2.9 25 16-40 9-33 (197)
164 PRK10838 spr outer membrane li 22.7 60 0.0013 23.4 1.7 13 74-86 127-139 (190)
165 cd06839 PLPDE_III_Btrk_like Ty 22.4 1.3E+02 0.0029 23.0 3.7 30 58-88 331-360 (382)
166 PF06071 YchF-GTPase_C: Protei 22.4 65 0.0014 20.4 1.6 14 74-87 71-84 (84)
167 PRK08931 5'-methylthioadenosin 22.3 75 0.0016 24.4 2.2 23 48-70 84-106 (289)
168 PF12791 RsgI_N: Anti-sigma fa 22.1 1.5E+02 0.0032 16.4 3.0 26 61-88 13-38 (56)
169 COG1209 RfbA dTDP-glucose pyro 22.1 1.5E+02 0.0032 23.0 3.7 33 62-103 127-159 (286)
170 PF11302 DUF3104: Protein of u 22.0 2.1E+02 0.0045 17.7 3.9 28 59-86 5-38 (75)
171 PRK07115 AMP nucleosidase; Pro 21.9 79 0.0017 23.7 2.2 19 52-70 94-112 (258)
172 TIGR03027 pepcterm_export puta 21.6 68 0.0015 22.0 1.7 16 55-70 147-162 (165)
173 TIGR03468 HpnG hopanoid-associ 21.4 61 0.0013 23.2 1.5 21 51-71 53-73 (212)
174 PRK12764 hypothetical protein; 21.3 1.2E+02 0.0026 25.0 3.3 30 59-88 181-211 (500)
175 smart00439 BAH Bromo adjacent 21.3 2.1E+02 0.0046 17.7 4.0 11 60-70 2-12 (120)
176 COG3944 Capsular polysaccharid 21.3 2.4E+02 0.0052 21.1 4.6 16 56-71 40-55 (226)
177 COG1097 RRP4 RNA-binding prote 21.1 72 0.0016 24.0 1.9 32 53-84 106-152 (239)
178 cd00622 PLPDE_III_ODC Type III 21.1 99 0.0021 23.6 2.7 30 59-88 312-341 (362)
179 PF09813 Coiled-coil_56: Coile 20.9 2.6E+02 0.0055 18.3 4.6 8 4-11 35-42 (100)
180 cd06828 PLPDE_III_DapDC Type I 20.9 1.5E+02 0.0033 22.6 3.7 30 58-88 323-352 (373)
181 cd03698 eRF3_II_like eRF3_II_l 20.5 87 0.0019 18.8 1.9 13 76-88 57-69 (83)
182 PF06107 DUF951: Bacterial pro 20.4 85 0.0018 18.5 1.7 14 76-89 2-15 (57)
183 PF14085 DUF4265: Domain of un 20.3 2.6E+02 0.0056 18.2 5.8 27 63-89 11-39 (117)
184 TIGR01718 Uridine-psphlse urid 20.2 76 0.0016 23.3 1.8 19 52-70 87-105 (245)
No 1
>PRK10861 signal peptidase I; Provisional
Probab=99.82 E-value=3.4e-20 Score=142.38 Aligned_cols=81 Identities=23% Similarity=0.352 Sum_probs=69.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCeEEEeCCCccccccCCCEEEEeecC--------------CCCCCCCcE
Q psy3466 16 QFLYQVLSFGMIVSSALMIWKGLMVLTGSESPIVVVLSGSMEPAFHRGDLLFLTNYQ--------------EEPVRVGEI 81 (103)
Q Consensus 16 ~~~~~i~~i~~~~~i~~li~~~~~~~~g~~~~~~~V~g~SM~Ptl~~gD~v~v~~~~--------------~~~~~~GDI 81 (103)
.+..|+..++.+++++++++.|++.. +.|+|+||+|||++||.++++|+. ..+|++|||
T Consensus 59 ~~~~~~~~~~~~l~i~~~ir~fv~~~-------~~Ips~SM~PTL~~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDI 131 (324)
T PRK10861 59 GWLETGASVFPVLAIVLIVRSFIYEP-------FQIPSGSMMPTLLIGDFILVEKFAYGIKDPITQTTLIETGHPKRGDI 131 (324)
T ss_pred hHHHHHHHHHHHHhHHHHHHhhEEEE-------EEECCCcCcCcccCCCEEEEEEeecCccCccccccccccCCCCCCCE
Confidence 36677777788888888899988886 999999999999999999999943 257999999
Q ss_pred EEEEeCCC-CcCEEEEEEEecCC
Q psy3466 82 VVFKVEGR-DIPIVHRVLKLHEK 103 (103)
Q Consensus 82 Vvf~~~~~-~~~~ikRVi~~~~~ 103 (103)
|+|+.|.+ +..|||||||+||.
T Consensus 132 VVF~~P~~~~~~yIKRVIGlPGD 154 (324)
T PRK10861 132 VVFKYPEDPKLDYIKRVVGLPGD 154 (324)
T ss_pred EEEecCCCCCCcEEEEeeecCCc
Confidence 99998864 46799999999984
No 2
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=99.79 E-value=2.8e-19 Score=125.14 Aligned_cols=77 Identities=29% Similarity=0.420 Sum_probs=64.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCeEEEeCCCccccccCCCEEEEeec--CCCCCCCCcEEEEEeCCC-CcCEEEE
Q psy3466 20 QVLSFGMIVSSALMIWKGLMVLTGSESPIVVVLSGSMEPAFHRGDLLFLTNY--QEEPVRVGEIVVFKVEGR-DIPIVHR 96 (103)
Q Consensus 20 ~i~~i~~~~~i~~li~~~~~~~~g~~~~~~~V~g~SM~Ptl~~gD~v~v~~~--~~~~~~~GDIVvf~~~~~-~~~~ikR 96 (103)
|+..++++++++++++.+++.. +.|+|+||+|||++||+++++|. ...++++||+|+|+.|++ ++.++||
T Consensus 1 ~~~~~~~~~~~~~~i~~~~~~~-------~~v~g~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~~~~~~~~~iKR 73 (163)
T TIGR02227 1 LILSLLIAILLALLIRTFVFFP-------YKIPGGSMEPTLKEGDRILVNKFAYGTSDPKRGDIVVFKDPDDNKNIYVKR 73 (163)
T ss_pred CHHHHHHHHHHHHHHHhhEEEE-------EEECCcccccchhCCCEEEEEEeEcCCCCCCCCcEEEEecCCCCCceeEEE
Confidence 4556677777788888888776 99999999999999999999994 347899999999998753 4689999
Q ss_pred EEEecCC
Q psy3466 97 VLKLHEK 103 (103)
Q Consensus 97 Vi~~~~~ 103 (103)
|+|+|+.
T Consensus 74 Vig~pGd 80 (163)
T TIGR02227 74 VIGLPGD 80 (163)
T ss_pred EEecCCC
Confidence 9999873
No 3
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=99.78 E-value=2.4e-18 Score=120.61 Aligned_cols=60 Identities=40% Similarity=0.850 Sum_probs=52.3
Q ss_pred CCCCCeEEEeCCCccccccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEEEEEecC
Q psy3466 43 GSESPIVVVLSGSMEPAFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRVLKLHE 102 (103)
Q Consensus 43 g~~~~~~~V~g~SM~Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~~~ 102 (103)
++..|.+.|.|+||+||+++||++++++...+++++||||+|+.|++++.++|||+++.+
T Consensus 28 ~~~~p~v~V~g~SM~Ptl~~GD~vlv~~~~~~~~~~GDIVvf~~~~~~~~iihRVi~v~~ 87 (158)
T TIGR02228 28 SGPDPVVVVLSGSMEPTFNTGDLILVTGADPNDIQVGDVITYKSPGFNTPVTHRVIEINN 87 (158)
T ss_pred cCCCcEEEEcCCCCcCCccCCCEEEEEecccCCCCCCCEEEEEECCCCccEEEEEEEEEC
Confidence 444566779999999999999999999965689999999999998765789999999865
No 4
>KOG3342|consensus
Probab=99.77 E-value=1.7e-18 Score=120.61 Aligned_cols=100 Identities=80% Similarity=1.256 Sum_probs=91.6
Q ss_pred HHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCeEEEeCCCccccccCCCEEEEeecCCCCCCCCcEE
Q psy3466 3 QDAINDLKRLNKRQFLYQVLSFGMIVSSALMIWKGLMVLTGSESPIVVVLSGSMEPAFHRGDLLFLTNYQEEPVRVGEIV 82 (103)
Q Consensus 3 ~~~~~~~~~~~~r~~~~~i~~i~~~~~i~~li~~~~~~~~g~~~~~~~V~g~SM~Ptl~~gD~v~v~~~~~~~~~~GDIV 82 (103)
.+...++|+|+.|+.+.-++.+++++..++.+|..+....|.++|++.|-|+||||.++.||+++........++.||||
T Consensus 5 ~~~~~~~k~mn~Rq~l~Q~ln~~mivssA~MiwK~l~vvt~seSPiVVVLSgSMePaF~RGDlLfL~N~~~~p~~vGdiv 84 (180)
T KOG3342|consen 5 LEMFDDLKRMNIRQLLYQVLNFAMIVSSAYMIWKGLMVVTGSESPIVVVLSGSMEPAFHRGDLLFLTNRNEDPIRVGDIV 84 (180)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhheeeeCCCCCEEEEEcCCcCcccccccEEEEecCCCCcceeccEE
Confidence 34567899999999999999999999999999999999999999999999999999999999999997666788999999
Q ss_pred EEEeCCCCcCEEEEEEEecC
Q psy3466 83 VFKVEGRDIPIVHRVLKLHE 102 (103)
Q Consensus 83 vf~~~~~~~~~ikRVi~~~~ 102 (103)
||+.++.+-+.+|||+-+-+
T Consensus 85 Vf~vegR~IPiVHRviK~he 104 (180)
T KOG3342|consen 85 VFKVEGREIPIVHRVIKQHE 104 (180)
T ss_pred EEEECCccCchhHHHHHHhc
Confidence 99999887789999987655
No 5
>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=99.50 E-value=5e-14 Score=84.93 Aligned_cols=51 Identities=29% Similarity=0.482 Sum_probs=42.9
Q ss_pred EEeCCCccccccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEEEEEecC
Q psy3466 50 VVLSGSMEPAFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRVLKLHE 102 (103)
Q Consensus 50 ~V~g~SM~Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~~~ 102 (103)
+|.|+||+|+|++||++++++. .+++.||+|+|+.++....++||+++.++
T Consensus 1 ~V~GdSM~P~i~~Gd~v~v~~~--~~~~~gdivv~~~~~~~~~~iKrv~~~~~ 51 (70)
T PF00717_consen 1 RVEGDSMEPTIKDGDIVLVDPS--SEPKDGDIVVVKIDGDEELYIKRVVGEPG 51 (70)
T ss_dssp EEESSTTGGTSSTTEEEEEEET--S---TTSEEEEEETTEESEEEEEEEEETT
T ss_pred CeECcCcccCeeCCCEEEEEEc--CCCccCeEEEEEECCceeeEEEEEEEeCC
Confidence 5899999999999999999985 58999999999999763489999998876
No 6
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=99.50 E-value=7.8e-14 Score=87.29 Aligned_cols=52 Identities=40% Similarity=0.697 Sum_probs=45.3
Q ss_pred eEEEeCCCccccccCCCEEEEeecCC--CCCCCCcEEEEEeCCC-CcCEEEEEEE
Q psy3466 48 IVVVLSGSMEPAFHRGDLLFLTNYQE--EPVRVGEIVVFKVEGR-DIPIVHRVLK 99 (103)
Q Consensus 48 ~~~V~g~SM~Ptl~~gD~v~v~~~~~--~~~~~GDIVvf~~~~~-~~~~ikRVi~ 99 (103)
++.|+|+||+|++++||++++++... .++++||+|+|+.++. .+.++|||++
T Consensus 2 ~~~v~g~SM~P~i~~gd~v~v~~~~~~~~~~~~GDiv~~~~~~~~~~~~vkRv~~ 56 (85)
T cd06530 2 PVVVPGGSMEPTLQPGDLVLVNKLSYGFREPKRGDVVVFKSPGDPGKPIIKRVIG 56 (85)
T ss_pred eeEEcCCCCcCcccCCCEEEEEEeecccCCCCCCCEEEEeCCCCCCCEEEEEEEE
Confidence 48999999999999999999998532 3799999999999874 4689999986
No 7
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.48 E-value=4.5e-14 Score=97.15 Aligned_cols=63 Identities=37% Similarity=0.449 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHHHHHHHH--HHHHHHhhCCCCCeEEEeCCCccccccCCCEEEEeecCCC--------------------
Q psy3466 17 FLYQVLSFGMIVSSALMI--WKGLMVLTGSESPIVVVLSGSMEPAFHRGDLLFLTNYQEE-------------------- 74 (103)
Q Consensus 17 ~~~~i~~i~~~~~i~~li--~~~~~~~~g~~~~~~~V~g~SM~Ptl~~gD~v~v~~~~~~-------------------- 74 (103)
...|+..++.++++++++ ..+.+.. +.|+|+||+||++.||+++++|....
T Consensus 7 ~~~~~~~~~~~~~~~~~i~~~~~~~~~-------~~V~s~SM~Ptl~~GD~v~v~k~~~~~~~~~~~~~~~~~~~~~~~~ 79 (166)
T COG0681 7 FLELISSLLIAIILALIIGVRTFVFEP-------VVVPSGSMEPTLNVGDRVLVKKFSYGFGKLKVPDIIVLPAVVEGDL 79 (166)
T ss_pred HHHHHHHHHHHHHHhheeeeEEEEEEE-------EEECCCccccccccCCEEEEEeccccccCCccceeeecCCCCCcce
Confidence 445666677777777766 5555554 99999999999999999999994322
Q ss_pred ----CCCCCcEEEEEe
Q psy3466 75 ----PVRVGEIVVFKV 86 (103)
Q Consensus 75 ----~~~~GDIVvf~~ 86 (103)
-..+||+++|+.
T Consensus 80 ~kr~~~~~GD~i~~~~ 95 (166)
T COG0681 80 IKRVIGLRGDIVVFKD 95 (166)
T ss_pred EEEeccCCCCEEEEEC
Confidence 347788888886
No 8
>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=99.46 E-value=2.4e-13 Score=86.16 Aligned_cols=53 Identities=21% Similarity=0.292 Sum_probs=44.2
Q ss_pred EEeCCCccccccCCCEEEEeec--CCCCCCCCcEEEEEeCCC-CcCEEEEEEEecC
Q psy3466 50 VVLSGSMEPAFHRGDLLFLTNY--QEEPVRVGEIVVFKVEGR-DIPIVHRVLKLHE 102 (103)
Q Consensus 50 ~V~g~SM~Ptl~~gD~v~v~~~--~~~~~~~GDIVvf~~~~~-~~~~ikRVi~~~~ 102 (103)
.|+|+||+|||++||.+++++. ....+++||+|+|+.+++ .+.++||+++.++
T Consensus 2 ~V~g~SM~P~l~~GD~vlv~~~~~~~~~~~~Gdivv~~~~~~~~~~~vkRv~~~~~ 57 (90)
T TIGR02754 2 KVTGVSMSPTLPPGDRIIVVPWLKIFRVPPIGNVVVVRHPLQPYGLIIKRLAAVDD 57 (90)
T ss_pred EeeCCCccCccCCCCEEEEEEccccCCCCCCCeEEEEecCCCCcceEEEEeeEEcC
Confidence 6899999999999999999973 234557899999998763 3689999998864
No 9
>KOG0171|consensus
Probab=99.44 E-value=2.2e-13 Score=95.92 Aligned_cols=69 Identities=26% Similarity=0.390 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHHHhhCCCCCeEEEeCCCccccccCC-CEEEEee--cCCCCCCCCcEEEEEeCCC-CcCEEEEEEEecCC
Q psy3466 28 VSSALMIWKGLMVLTGSESPIVVVLSGSMEPAFHRG-DLLFLTN--YQEEPVRVGEIVVFKVEGR-DIPIVHRVLKLHEK 103 (103)
Q Consensus 28 ~~i~~li~~~~~~~~g~~~~~~~V~g~SM~Ptl~~g-D~v~v~~--~~~~~~~~GDIVvf~~~~~-~~~~ikRVi~~~~~ 103 (103)
.|++.....+++.+ ...+|.||+||++++ |+++++| +.++.+++||||++++|.. .+.++|||+|.++.
T Consensus 22 ~~f~h~t~~yl~e~-------~~~~gpSM~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~~~~~~~cKRIva~eGD 94 (176)
T KOG0171|consen 22 AAFTHVTHEYLGEF-------VMCSGPSMEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPPDPKEHICKRIVAMEGD 94 (176)
T ss_pred HHHHHHHHHHhcce-------eeccCCCcCceecCCCcEEehhhhhHhhcCCCCCCEEEEeCCCCchhhhhheeeccCCc
Confidence 34444455566654 889999999998866 5555577 5578899999999999865 47899999999873
No 10
>KOG1568|consensus
Probab=99.25 E-value=1.3e-11 Score=86.84 Aligned_cols=55 Identities=31% Similarity=0.496 Sum_probs=47.7
Q ss_pred eEEEeCCCccccccCC------CEEEEeecCC--CCCCCCcEEEEEeCCC-CcCEEEEEEEecC
Q psy3466 48 IVVVLSGSMEPAFHRG------DLLFLTNYQE--EPVRVGEIVVFKVEGR-DIPIVHRVLKLHE 102 (103)
Q Consensus 48 ~~~V~g~SM~Ptl~~g------D~v~v~~~~~--~~~~~GDIVvf~~~~~-~~~~ikRVi~~~~ 102 (103)
+..|.|.||+||++++ |.|++.|+.. +.+.+||||+|++|.+ ++++||||+|+++
T Consensus 33 va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~~p~~~~iKRv~aleg 96 (174)
T KOG1568|consen 33 VAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPNDPDKVIIKRVAALEG 96 (174)
T ss_pred EeEEecCcCCCccCCCcccccccEEEEEeeccccceeccCCEEEEeCCCChhheeeeeeecccc
Confidence 4789999999999876 8999999433 5589999999999965 5799999999987
No 11
>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=99.13 E-value=2.8e-10 Score=69.86 Aligned_cols=51 Identities=35% Similarity=0.546 Sum_probs=44.7
Q ss_pred EEEeCCCccccccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEEEEEec
Q psy3466 49 VVVLSGSMEPAFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRVLKLH 101 (103)
Q Consensus 49 ~~V~g~SM~Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~~ 101 (103)
+.+.|+||+|++.+||.+++++. ...++.||+++++.++ ...++||+...+
T Consensus 3 ~~v~g~SM~P~i~~gd~v~i~~~-~~~~~~G~iv~~~~~~-~~~~ikrl~~~~ 53 (84)
T cd06462 3 LRVEGDSMEPTIPDGDLVLVDKS-SYEPKRGDIVVFRLPG-GELTVKRVIGLP 53 (84)
T ss_pred eEEcCCCccCcccCCCEEEEEec-CCCCcCCEEEEEEcCC-CcEEEEEEEEEC
Confidence 78999999999999999999984 2358999999999887 367999999876
No 12
>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=99.06 E-value=7.9e-10 Score=67.83 Aligned_cols=49 Identities=33% Similarity=0.507 Sum_probs=44.0
Q ss_pred EEEeCCCccccccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEEEEEec
Q psy3466 49 VVVLSGSMEPAFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRVLKLH 101 (103)
Q Consensus 49 ~~V~g~SM~Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~~ 101 (103)
+.++|+||+|++++||.+++++. ..++.||++++..++ +.++||+...+
T Consensus 3 ~~v~g~sM~p~i~~gd~lii~~~--~~~~~g~i~~~~~~~--~~~ikr~~~~~ 51 (81)
T cd06529 3 LRVKGDSMEPTIPDGDLVLVDPS--DTPRDGDIVVARLDG--ELTVKRLQRRG 51 (81)
T ss_pred EEEECCCcCCccCCCCEEEEcCC--CCCCCCCEEEEEECC--EEEEEEEEECC
Confidence 78999999999999999999984 459999999999886 57999998776
No 13
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.89 E-value=4.7e-09 Score=75.92 Aligned_cols=52 Identities=25% Similarity=0.360 Sum_probs=42.6
Q ss_pred eEEEeCCCccccccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEEEEEecC
Q psy3466 48 IVVVLSGSMEPAFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRVLKLHE 102 (103)
Q Consensus 48 ~~~V~g~SM~Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~~~ 102 (103)
++.|.|+||+|++++||.++|+.- .+..+||.+++...+. +.||||+...++
T Consensus 125 ~i~V~GDSMeP~~~~Gd~ilVd~~--~~~~~gd~v~v~~~g~-~~~VK~l~~~~~ 176 (214)
T COG2932 125 ALRVTGDSMEPTYEDGDTLLVDPG--VNTRRGDRVYVETDGG-ELYVKKLQREPG 176 (214)
T ss_pred EEEEeCCcccccccCCCEEEECCC--CceeeCCEEEEEEeCC-eEEEEEEEEecC
Confidence 579999999999999999999973 5677888666655552 579999998876
No 14
>PRK00215 LexA repressor; Validated
Probab=98.47 E-value=5.8e-07 Score=64.41 Aligned_cols=49 Identities=27% Similarity=0.375 Sum_probs=41.7
Q ss_pred eEEEeCCCcc-ccccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEEEEEe
Q psy3466 48 IVVVLSGSME-PAFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRVLKL 100 (103)
Q Consensus 48 ~~~V~g~SM~-Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~ 100 (103)
.+.|.|+||. |++++||.+++++- .+++.||++++..++ +.++||+.-.
T Consensus 120 ~~~V~GdSM~~~~i~~Gd~v~v~~~--~~~~~G~ivv~~~~~--~~~vKrl~~~ 169 (205)
T PRK00215 120 LLRVRGDSMIDAGILDGDLVIVRKQ--QTARNGQIVVALIDD--EATVKRFRRE 169 (205)
T ss_pred EEEEccCCCCCCCcCCCCEEEEeCC--CCCCCCCEEEEEECC--EEEEEEEEEe
Confidence 5789999995 79999999999973 467899999998876 5799998754
No 15
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=98.44 E-value=7e-07 Score=60.91 Aligned_cols=48 Identities=27% Similarity=0.348 Sum_probs=40.3
Q ss_pred eEEEeCCCcc-ccccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEEEEE
Q psy3466 48 IVVVLSGSME-PAFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRVLK 99 (103)
Q Consensus 48 ~~~V~g~SM~-Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~ 99 (103)
...|+|+||. |++++||.+++++- .+++.||++++..++ ..++||..-
T Consensus 53 ~l~V~GdSM~~~~I~~GD~liVd~~--~~~~~Gdivv~~~~g--~~~vKrl~~ 101 (139)
T PRK10276 53 FVKASGDSMIDAGISDGDLLIVDSA--ITASHGDIVIAAVDG--EFTVKKLQL 101 (139)
T ss_pred EEEEecCCCCCCCCCCCCEEEEECC--CCCCCCCEEEEEECC--EEEEEEEEE
Confidence 4889999998 69999999999974 467899999998765 468999763
No 16
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=98.38 E-value=4.1e-06 Score=59.69 Aligned_cols=41 Identities=24% Similarity=0.359 Sum_probs=30.3
Q ss_pred CCEEEEeec--CCCCCCCCcEEEEEeCCCC--------------------cCEEEEEEEecCC
Q psy3466 63 GDLLFLTNY--QEEPVRVGEIVVFKVEGRD--------------------IPIVHRVLKLHEK 103 (103)
Q Consensus 63 gD~v~v~~~--~~~~~~~GDIVvf~~~~~~--------------------~~~ikRVi~~~~~ 103 (103)
.+-+.+.+. ...++++||+|+|+.|+.. ..++|||+|+|+.
T Consensus 36 S~pig~y~~~~~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD 98 (176)
T PRK13838 36 SEPLGLWRIEALDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQ 98 (176)
T ss_pred CCEEEEEEEeccCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCc
Confidence 355666663 3478999999999976431 2599999999973
No 17
>PRK12423 LexA repressor; Provisional
Probab=98.33 E-value=1.8e-06 Score=62.24 Aligned_cols=49 Identities=27% Similarity=0.369 Sum_probs=41.6
Q ss_pred eEEEeCCCcc-ccccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEEEEEe
Q psy3466 48 IVVVLSGSME-PAFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRVLKL 100 (103)
Q Consensus 48 ~~~V~g~SM~-Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~ 100 (103)
...|.|+||. |+|.+||.+++++- .+++.||++++..++ +.++||..-.
T Consensus 116 ~l~V~GdSM~~~~i~~Gd~viv~~~--~~~~~Gdivv~~~~~--~~~vKrl~~~ 165 (202)
T PRK12423 116 LLQVQGDSMIDDGILDGDLVGVHRS--PEARDGQIVVARLDG--EVTIKRLERS 165 (202)
T ss_pred EEEEecCcCCCCCcCCCCEEEEeCC--CcCCCCCEEEEEECC--EEEEEEEEEe
Confidence 5899999997 79999999999974 678899999998865 4689997643
No 18
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=98.22 E-value=5.3e-06 Score=59.15 Aligned_cols=49 Identities=33% Similarity=0.463 Sum_probs=41.4
Q ss_pred eEEEeCCCcc-ccccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEEEEEe
Q psy3466 48 IVVVLSGSME-PAFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRVLKL 100 (103)
Q Consensus 48 ~~~V~g~SM~-Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~ 100 (103)
++.|.|+||. |++++||.+++++. .+++.||++++..++ +.++||+.-.
T Consensus 113 ~~~V~GdSM~~~~i~~Gd~v~v~~~--~~~~~G~ivvv~~~~--~~~vKrl~~~ 162 (199)
T TIGR00498 113 LLKVMGDSMVDAGICDGDLLIVRSQ--KDARNGEIVAAMIDG--EVTVKRFYKD 162 (199)
T ss_pred EEEecCCCCCCCCCCCCCEEEEecC--CCCCCCCEEEEEECC--EEEEEEEEEE
Confidence 5899999996 68999999999974 588999999999854 5789997643
No 19
>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF. This protein is found in apparent operons encoding elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as lepB. This family is present in both Ti-type and I-type conjugative systems.
Probab=98.08 E-value=1.3e-05 Score=56.86 Aligned_cols=47 Identities=28% Similarity=0.395 Sum_probs=32.8
Q ss_pred EEeCCCccccccCCCEEEEeecCCCCCCCCcEEEEEeCCCCc--------------------CEEEEEEEecCC
Q psy3466 50 VVLSGSMEPAFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDI--------------------PIVHRVLKLHEK 103 (103)
Q Consensus 50 ~V~g~SM~Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~--------------------~~ikRVi~~~~~ 103 (103)
.-.++||-+.+- . .. ...++++||+|+|+.|+... .++|||+|+|+.
T Consensus 28 ~N~T~S~P~g~Y----~-~~--~~~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRViglpGD 94 (171)
T TIGR02771 28 INTTKSLPLGLY----W-TT--SSKPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLPGD 94 (171)
T ss_pred EECCCCCcceEE----E-eC--CCCCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEeCCC
Confidence 444567665542 2 22 23689999999999875322 699999999973
No 20
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=97.76 E-value=8.9e-05 Score=53.99 Aligned_cols=50 Identities=28% Similarity=0.404 Sum_probs=43.3
Q ss_pred eEEEeCCCcc-ccccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEEEEEe
Q psy3466 48 IVVVLSGSME-PAFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRVLKL 100 (103)
Q Consensus 48 ~~~V~g~SM~-Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~ 100 (103)
...|.|+||. +.+.+||+|+|++- .+.+.||+|+-.-++ ++..+||..--
T Consensus 114 ~L~V~GdSM~~~gi~dGDlvvV~~~--~~a~~GdiVvA~i~g-~e~TvKrl~~~ 164 (201)
T COG1974 114 FLRVSGDSMIDAGILDGDLVVVDPT--EDAENGDIVVALIDG-EEATVKRLYRD 164 (201)
T ss_pred EEEecCCccccCcCCCCCEEEEcCC--CCCCCCCEEEEEcCC-CcEEEEEEEEe
Confidence 5889999998 78899999999974 789999999999888 56889997643
No 21
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=97.48 E-value=0.0012 Score=47.03 Aligned_cols=30 Identities=30% Similarity=0.351 Sum_probs=22.6
Q ss_pred CCCCCCcEEEEEeCCC--------------------CcCEEEEEEEecCC
Q psy3466 74 EPVRVGEIVVFKVEGR--------------------DIPIVHRVLKLHEK 103 (103)
Q Consensus 74 ~~~~~GDIVvf~~~~~--------------------~~~~ikRVi~~~~~ 103 (103)
.++++||+|+|..|.. ..+++|||+|+|+.
T Consensus 49 ~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pGD 98 (178)
T PRK13884 49 APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGD 98 (178)
T ss_pred CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCCc
Confidence 5688888888876541 13689999999973
No 22
>PF10502 Peptidase_S26: Signal peptidase, peptidase S26 ; InterPro: IPR019533 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents a conserved region found in the S26A family of serine endopeptidases, which function in the processing of newly-synthesised secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal signal peptides as proteins are translocated across membranes. ; PDB: 3S04_B 1KN9_C 1B12_D 3IIQ_B 1T7D_A.
Probab=95.00 E-value=0.0065 Score=41.48 Aligned_cols=29 Identities=24% Similarity=0.481 Sum_probs=0.0
Q ss_pred CCCCCcEEEEEeCCC-------------CcCEEEEEEEecCC
Q psy3466 75 PVRVGEIVVFKVEGR-------------DIPIVHRVLKLHEK 103 (103)
Q Consensus 75 ~~~~GDIVvf~~~~~-------------~~~~ikRVi~~~~~ 103 (103)
.+++||+|+|..|.. ...++|||+|+|+.
T Consensus 21 ~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD 62 (138)
T PF10502_consen 21 KIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGD 62 (138)
T ss_dssp ------------------------------------------
T ss_pred cccccccccccccccccccccccccccccccccccccccccc
Confidence 478888888887641 24789999999873
No 23
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=82.65 E-value=1.6 Score=27.14 Aligned_cols=23 Identities=22% Similarity=0.316 Sum_probs=18.0
Q ss_pred cccCCCEEEEeecCCCCCCCCcEE
Q psy3466 59 AFHRGDLLFLTNYQEEPVRVGEIV 82 (103)
Q Consensus 59 tl~~gD~v~v~~~~~~~~~~GDIV 82 (103)
-+.+||.|++... +.+.++|||+
T Consensus 46 ~I~~GD~V~Ve~~-~~d~~kg~I~ 68 (75)
T COG0361 46 RILPGDVVLVELS-PYDLTKGRIV 68 (75)
T ss_pred EeCCCCEEEEEec-ccccccccEE
Confidence 5679999999874 3568899976
No 24
>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=81.43 E-value=1.8 Score=26.39 Aligned_cols=22 Identities=18% Similarity=0.144 Sum_probs=12.8
Q ss_pred ccCCCEEEEeecCCCCCCCCcEE
Q psy3466 60 FHRGDLLFLTNYQEEPVRVGEIV 82 (103)
Q Consensus 60 l~~gD~v~v~~~~~~~~~~GDIV 82 (103)
+.+||.|.+... +.++.+|||+
T Consensus 45 I~~GD~V~Ve~s-pyd~tkgrIi 66 (68)
T TIGR00008 45 ILPGDKVKVELS-PYDLTRGRIT 66 (68)
T ss_pred ECCCCEEEEEEC-cccCCcEeEE
Confidence 346666666652 2456666664
No 25
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. 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=79.20 E-value=2.1 Score=26.59 Aligned_cols=24 Identities=25% Similarity=0.454 Sum_probs=14.9
Q ss_pred ccCCCEEEEeecCCCCCCCCcEEE
Q psy3466 60 FHRGDLLFLTNYQEEPVRVGEIVV 83 (103)
Q Consensus 60 l~~gD~v~v~~~~~~~~~~GDIVv 83 (103)
+..||.|++....+.+...|||+-
T Consensus 39 I~~GD~VlV~~~~~~~~~kg~Iv~ 62 (78)
T cd04456 39 IKRGDFLIVDPIEEGEDVKADIIF 62 (78)
T ss_pred EcCCCEEEEEecccCCCceEEEEE
Confidence 357777777764433566777663
No 26
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=77.97 E-value=1.5 Score=26.91 Aligned_cols=36 Identities=22% Similarity=0.290 Sum_probs=20.1
Q ss_pred CCccccccCCCEEEEeec-CCCCCCC-CcEEEEEeCCC
Q psy3466 54 GSMEPAFHRGDLLFLTNY-QEEPVRV-GEIVVFKVEGR 89 (103)
Q Consensus 54 ~SM~Ptl~~gD~v~v~~~-~~~~~~~-GDIVvf~~~~~ 89 (103)
.||+|.+++|+.||..-. ....+.. .=+-+|+.++.
T Consensus 12 ~~m~P~L~~~~yVF~t~~~~~~~~~~l~pi~~frE~EG 49 (72)
T PF10000_consen 12 ASMSPELNPGEYVFCTVPGDLADPPGLEPIATFREAEG 49 (72)
T ss_dssp ST-EEEE-SS-EEEEEE-S-GGGGGGG--SEEEEETTE
T ss_pred hhCCcEeCCCCEEEEEecCcccCccCCcceEEEEecCc
Confidence 589999999999999863 2222222 33467877653
No 27
>PF05382 Amidase_5: Bacteriophage peptidoglycan hydrolase ; InterPro: IPR008044 This entry is represented by Bacteriophage SFi21, lysin (Cell wall hydrolase; 3.5.1.28 from EC). At least one of proteins in this entry, the Pal protein from the pneumococcal bacteriophage Dp-1 (O03979 from SWISSPROT) has been shown to be an N-acetylmuramoyl-L-alanine amidase []. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside within this domain while a C-terminal domain binds to the choline residues of the cell wall teichoic acids [, ].
Probab=75.63 E-value=3.6 Score=28.53 Aligned_cols=39 Identities=8% Similarity=0.193 Sum_probs=27.1
Q ss_pred EEeCCCccccccCCCEEEEeecCCCCCCCCcEEEEEeCC
Q psy3466 50 VVLSGSMEPAFHRGDLLFLTNYQEEPVRVGEIVVFKVEG 88 (103)
Q Consensus 50 ~V~g~SM~Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~ 88 (103)
...+++|...|...=.-.+.+....++|+|||+++...+
T Consensus 50 ~~nT~tl~~~L~~~G~~~I~~~~~~~~q~GDI~I~g~~g 88 (145)
T PF05382_consen 50 AGNTETLHDWLKKNGFKKISENVDWNLQRGDIFIWGRRG 88 (145)
T ss_pred ccCHHHHHHHHhhCCcEEeccCCcccccCCCEEEEcCCC
Confidence 456789988776555555555323589999999986543
No 28
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=75.06 E-value=3.4 Score=26.85 Aligned_cols=24 Identities=17% Similarity=0.300 Sum_probs=14.5
Q ss_pred ccCCCEEEEeecCCCCCCCCcEEE
Q psy3466 60 FHRGDLLFLTNYQEEPVRVGEIVV 83 (103)
Q Consensus 60 l~~gD~v~v~~~~~~~~~~GDIVv 83 (103)
+..||.|++..++.+.-.+|||+-
T Consensus 58 I~~GD~VlVsp~d~~~~~kg~Iv~ 81 (99)
T TIGR00523 58 IREGDVVIVKPWEFQGDDKCDIVW 81 (99)
T ss_pred ecCCCEEEEEEccCCCCccEEEEE
Confidence 357777777665444344677653
No 29
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=73.80 E-value=2.8 Score=28.41 Aligned_cols=17 Identities=41% Similarity=0.651 Sum_probs=15.3
Q ss_pred CCccccccCCCEEEEee
Q psy3466 54 GSMEPAFHRGDLLFLTN 70 (103)
Q Consensus 54 ~SM~Ptl~~gD~v~v~~ 70 (103)
.||.|-+.+||.|+..-
T Consensus 12 ~smtPeL~~G~yVfcT~ 28 (134)
T COG3602 12 ASMTPELLDGDYVFCTV 28 (134)
T ss_pred HhcCccccCCceEEEEe
Confidence 48999999999999875
No 30
>KOG4146|consensus
Probab=71.21 E-value=6.7 Score=25.55 Aligned_cols=34 Identities=24% Similarity=0.601 Sum_probs=25.6
Q ss_pred EEEeCCCccccccCCCEEEEeecC-------CCCCCCCcEEEEEe
Q psy3466 49 VVVLSGSMEPAFHRGDLLFLTNYQ-------EEPVRVGEIVVFKV 86 (103)
Q Consensus 49 ~~V~g~SM~Ptl~~gD~v~v~~~~-------~~~~~~GDIVvf~~ 86 (103)
+.+.++|..| |-.+++|+.+ .++++.||.|+|-+
T Consensus 56 lFi~~gsvrp----Gii~lINd~DWEllekedy~ledgD~ivfiS 96 (101)
T KOG4146|consen 56 LFIHHGSVRP----GIIVLINDMDWELLEKEDYPLEDGDHIVFIS 96 (101)
T ss_pred eEeeCCcCcC----cEEEEEeccchhhhcccccCcccCCEEEEEE
Confidence 7788888655 5567777732 36899999999965
No 31
>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=70.49 E-value=4.3 Score=25.08 Aligned_cols=21 Identities=14% Similarity=0.434 Sum_probs=12.7
Q ss_pred cCCCEEEEeecCCCCCCCCcEE
Q psy3466 61 HRGDLLFLTNYQEEPVRVGEIV 82 (103)
Q Consensus 61 ~~gD~v~v~~~~~~~~~~GDIV 82 (103)
.+||.|++.... .+..+|||+
T Consensus 40 ~~GD~V~Ve~~~-~d~~kg~Iv 60 (77)
T cd05793 40 NEGDIVLVAPWD-FQDDKADII 60 (77)
T ss_pred cCCCEEEEEecc-ccCCEEEEE
Confidence 467777776532 356666665
No 32
>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=68.56 E-value=4.4 Score=24.00 Aligned_cols=12 Identities=17% Similarity=0.385 Sum_probs=5.4
Q ss_pred CCCCCcEEEEEe
Q psy3466 75 PVRVGEIVVFKV 86 (103)
Q Consensus 75 ~~~~GDIVvf~~ 86 (103)
-+++||.|....
T Consensus 41 wI~~GD~V~V~~ 52 (65)
T PF01176_consen 41 WIKRGDFVLVEP 52 (65)
T ss_dssp ---TTEEEEEEE
T ss_pred ecCCCCEEEEEe
Confidence 356666666653
No 33
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=68.12 E-value=6.8 Score=25.05 Aligned_cols=22 Identities=23% Similarity=0.169 Sum_probs=15.2
Q ss_pred ccCCCEEEEeecCCCCCCCCcEE
Q psy3466 60 FHRGDLLFLTNYQEEPVRVGEIV 82 (103)
Q Consensus 60 l~~gD~v~v~~~~~~~~~~GDIV 82 (103)
+.+||.|.+.-. +.++.+|+|+
T Consensus 47 Il~GD~V~VE~s-pYDltkGRIi 68 (87)
T PRK12442 47 ILAGDRVTLELS-PYDLTKGRIN 68 (87)
T ss_pred ecCCCEEEEEEC-cccCCceeEE
Confidence 457888888763 3567788765
No 34
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=67.70 E-value=4.2 Score=27.26 Aligned_cols=19 Identities=26% Similarity=0.380 Sum_probs=16.4
Q ss_pred eCCCccccccCCCEEEEee
Q psy3466 52 LSGSMEPAFHRGDLLFLTN 70 (103)
Q Consensus 52 ~g~SM~Ptl~~gD~v~v~~ 70 (103)
-+++|.|.|+.||.|++.-
T Consensus 48 ~~~~~~~~L~~GD~VLA~~ 66 (124)
T PF15057_consen 48 LSDAMRHSLQVGDKVLAPW 66 (124)
T ss_pred ccCcccCcCCCCCEEEEec
Confidence 3578999999999999974
No 35
>PF10399 UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; InterPro: IPR019470 This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex). This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with IPR017941 from INTERPRO, IPR004192 from INTERPRO and IPR015248 from INTERPRO. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1ZRT_R 2QJY_R 2FYN_L 2QJK_O 2QJP_I 2YIU_F.
Probab=67.65 E-value=18 Score=19.82 Aligned_cols=27 Identities=26% Similarity=0.244 Sum_probs=16.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3466 12 LNKRQFLYQVLSFGMIVSSALMIWKGL 38 (103)
Q Consensus 12 ~~~r~~~~~i~~i~~~~~i~~li~~~~ 38 (103)
-.+|+++......+.++..+..+|-|+
T Consensus 9 ~~RRdFL~~at~~~gavG~~~~a~Pfv 35 (41)
T PF10399_consen 9 PTRRDFLTIATSAVGAVGAAAAAWPFV 35 (41)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445666656555666666666666665
No 36
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=67.03 E-value=9.6 Score=24.63 Aligned_cols=34 Identities=21% Similarity=0.514 Sum_probs=24.1
Q ss_pred EEEeCCCccccccCCCEEEEeecC-------CCCCCCCcEEEEEe
Q psy3466 49 VVVLSGSMEPAFHRGDLLFLTNYQ-------EEPVRVGEIVVFKV 86 (103)
Q Consensus 49 ~~V~g~SM~Ptl~~gD~v~v~~~~-------~~~~~~GDIVvf~~ 86 (103)
+.+..++ +.+|-.+++|..+ ...++.||+|+|-+
T Consensus 51 ifie~g~----lrpGiI~LINd~DWeLleke~y~ledgDiIvfis 91 (96)
T COG5131 51 IFIEHGE----LRPGIICLINDMDWELLEKERYPLEDGDIIVFIS 91 (96)
T ss_pred eeecCCC----CcccEEEEEcCccHhhhhcccccCCCCCEEEEEe
Confidence 5556665 5667777887732 36789999999965
No 37
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=64.58 E-value=14 Score=21.65 Aligned_cols=38 Identities=21% Similarity=0.312 Sum_probs=22.6
Q ss_pred CCCcccc-ccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEE
Q psy3466 53 SGSMEPA-FHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHR 96 (103)
Q Consensus 53 g~SM~Pt-l~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikR 96 (103)
++++.|. |.+|-.+-+-. -++.||.|..+..+.. |+.|
T Consensus 18 ~~~~K~A~letG~~i~VP~----FI~~Gd~I~VdT~~g~--Yv~R 56 (56)
T PF09285_consen 18 SSSYKPATLETGAEIQVPL----FIEEGDKIKVDTRDGS--YVER 56 (56)
T ss_dssp STTEEEEEETTS-EEEEET----T--TT-EEEEETTTTE--EEEE
T ss_pred CCCccEEEEcCCCEEEccc----eecCCCEEEEECCCCe--EeCC
Confidence 3456654 46676666643 3899999999876544 8877
No 38
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=63.46 E-value=5.1 Score=26.72 Aligned_cols=15 Identities=33% Similarity=0.257 Sum_probs=6.5
Q ss_pred HHHHHHHHHHHHHHH
Q psy3466 20 QVLSFGMIVSSALMI 34 (103)
Q Consensus 20 ~i~~i~~~~~i~~li 34 (103)
|++.+++++++++++
T Consensus 2 W~l~~iii~~i~l~~ 16 (130)
T PF12273_consen 2 WVLFAIIIVAILLFL 16 (130)
T ss_pred eeeHHHHHHHHHHHH
Confidence 555444444333333
No 39
>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=63.03 E-value=23 Score=21.93 Aligned_cols=30 Identities=30% Similarity=0.413 Sum_probs=21.9
Q ss_pred ccccccCCCEEEEee-c----CCCCCCCCcEEEEE
Q psy3466 56 MEPAFHRGDLLFLTN-Y----QEEPVRVGEIVVFK 85 (103)
Q Consensus 56 M~Ptl~~gD~v~v~~-~----~~~~~~~GDIVvf~ 85 (103)
|+|.++.||.|.+.+ . .+.....|++++-+
T Consensus 1 ~~p~f~~G~~V~a~~~irNDGt~Pg~~~g~lLv~~ 35 (75)
T PF04319_consen 1 MPPRFEWGDKVRARKDIRNDGTFPGKEIGELLVRK 35 (75)
T ss_pred CCCccCCCCEEEEEEEeEcCCCCCCCCCCCEEEcC
Confidence 889999999999988 1 13345667777643
No 40
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=62.94 E-value=7.4 Score=25.34 Aligned_cols=21 Identities=14% Similarity=0.404 Sum_probs=12.6
Q ss_pred cCCCEEEEeecCCCCCCCCcEE
Q psy3466 61 HRGDLLFLTNYQEEPVRVGEIV 82 (103)
Q Consensus 61 ~~gD~v~v~~~~~~~~~~GDIV 82 (103)
..||.|++.... .+..+|||+
T Consensus 61 ~~GD~VlVe~~~-~~~~kg~Iv 81 (100)
T PRK04012 61 REGDVVIVAPWD-FQDEKADII 81 (100)
T ss_pred cCCCEEEEEecc-cCCCEEEEE
Confidence 467777776633 235666665
No 41
>PF13800 Sigma_reg_N: Sigma factor regulator N-terminal
Probab=62.70 E-value=27 Score=21.87 Aligned_cols=16 Identities=25% Similarity=0.341 Sum_probs=10.8
Q ss_pred HHHHhhhHHHHHHHHH
Q psy3466 7 NDLKRLNKRQFLYQVL 22 (103)
Q Consensus 7 ~~~~~~~~r~~~~~i~ 22 (103)
..+|+.++|..+++++
T Consensus 3 ~i~kK~K~k~~l~~~~ 18 (96)
T PF13800_consen 3 KILKKAKRKSRLRTVV 18 (96)
T ss_pred hHHHHHHHHHHHHHHH
Confidence 3477777777777653
No 42
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=62.03 E-value=8 Score=24.21 Aligned_cols=21 Identities=19% Similarity=0.457 Sum_probs=12.1
Q ss_pred cCCCEEEEeecCCCCCCCCcEE
Q psy3466 61 HRGDLLFLTNYQEEPVRVGEIV 82 (103)
Q Consensus 61 ~~gD~v~v~~~~~~~~~~GDIV 82 (103)
..||.|++.... .+..+|||+
T Consensus 45 ~~GD~VlVe~~~-~~~~kg~Iv 65 (83)
T smart00652 45 RRGDIVLVDPWD-FQDVKADII 65 (83)
T ss_pred cCCCEEEEEecC-CCCCEEEEE
Confidence 466777776532 335666654
No 43
>cd04720 BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology domain, as present in Orc1p, which again is part of the Saccharomyces cerevisiae Sir1-origin recognition complex, and as present in Sir3p. The Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=58.68 E-value=26 Score=24.89 Aligned_cols=38 Identities=18% Similarity=0.295 Sum_probs=26.5
Q ss_pred CCEEEEeec-CCCCCCCCcEEEEEeCCCCcCEEEEEEEe
Q psy3466 63 GDLLFLTNY-QEEPVRVGEIVVFKVEGRDIPIVHRVLKL 100 (103)
Q Consensus 63 gD~v~v~~~-~~~~~~~GDIVvf~~~~~~~~~ikRVi~~ 100 (103)
++.+...|. +...++.||.|+++.++...+++..|..+
T Consensus 39 ~~~i~l~R~~d~~~~~vGD~Vlik~~~~~~~~V~iI~ei 77 (179)
T cd04720 39 KRKIFLARDSDGLELSVGDTILVKDDVANSPSVYLIHEI 77 (179)
T ss_pred CCcEEEEEccCCeEEeCCCEEEEeCCCCCCCEEEEEEEE
Confidence 345556564 45678999999999876555677776544
No 44
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A 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.
Probab=57.36 E-value=9.4 Score=23.78 Aligned_cols=22 Identities=32% Similarity=0.492 Sum_probs=12.0
Q ss_pred cCCCEEEEeecCCCCCCCCcEE
Q psy3466 61 HRGDLLFLTNYQEEPVRVGEIV 82 (103)
Q Consensus 61 ~~gD~v~v~~~~~~~~~~GDIV 82 (103)
+.||.|++.+..+.+-..|||+
T Consensus 40 krGd~VlV~p~~~~~kvkgeIv 61 (78)
T cd05792 40 KRGDFVLVEPIEEGDKVKAEIV 61 (78)
T ss_pred EeCCEEEEEecccCCceEEEEE
Confidence 4666666666543333355555
No 45
>COG0179 MhpD 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=57.15 E-value=28 Score=26.38 Aligned_cols=31 Identities=19% Similarity=0.392 Sum_probs=24.8
Q ss_pred cccCCCEEEEeec-CCCCCCCCcEEEEEeCCC
Q psy3466 59 AFHRGDLLFLTNY-QEEPVRVGEIVVFKVEGR 89 (103)
Q Consensus 59 tl~~gD~v~v~~~-~~~~~~~GDIVvf~~~~~ 89 (103)
||++||+++.-.. ....++.||++...-++-
T Consensus 224 tL~pGDvI~TGTP~Gvg~l~~GD~v~~~iegi 255 (266)
T COG0179 224 TLEPGDVILTGTPSGVGFLKPGDVVEVEIEGI 255 (266)
T ss_pred ccCCCCEEEeCCCCCcccCCCCCEEEEEecce
Confidence 6999999998762 236789999999987764
No 46
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=57.08 E-value=39 Score=22.25 Aligned_cols=40 Identities=13% Similarity=0.334 Sum_probs=22.3
Q ss_pred cCCCEEEEeec-C--CCCCCCCcEEEEEeCCCCcCEEEEEEEe
Q psy3466 61 HRGDLLFLTNY-Q--EEPVRVGEIVVFKVEGRDIPIVHRVLKL 100 (103)
Q Consensus 61 ~~gD~v~v~~~-~--~~~~~~GDIVvf~~~~~~~~~ikRVi~~ 100 (103)
..|..-+=-|. + ..+++.||.++|+.-..+....-+|+.+
T Consensus 14 ~~G~KtiEiRlnD~kr~~ikvGD~I~f~~~~~~~~l~v~V~~i 56 (109)
T cd06555 14 KSGKKTIEIRLNDEKRQQIKVGDKILFNDLDTGQQLLVKVVDI 56 (109)
T ss_pred HcCCCEEEEEecccchhcCCCCCEEEEEEcCCCcEEEEEEEEE
Confidence 44544443342 2 2479999999997643223344555544
No 47
>PF08802 CytB6-F_Fe-S: Cytochrome B6-F complex Fe-S subunit ; InterPro: IPR014909 The cytochrome b6-f complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. The cytochrome b6-f complex has 4 large subunits, these are: cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are: PetG, PetL, PetM and PetN. The complex functions as a dimer. This protein corresponds to the alpha helical transmembrane domain of the cytochrome b6-f complex Rieske iron-sulphur subunit. ; GO: 0009496 plastoquinol-plastocyanin reductase activity, 0051537 2 iron, 2 sulfur cluster binding, 0055114 oxidation-reduction process, 0042651 thylakoid membrane; PDB: 1Q90_R 1VF5_D 2E75_D 2E74_D 2E76_D 2D2C_Q 2ZT9_D.
Probab=56.05 E-value=32 Score=18.71 Aligned_cols=31 Identities=16% Similarity=0.271 Sum_probs=21.8
Q ss_pred HhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3466 10 KRLNKRQFLYQVLSFGMIVSSALMIWKGLMV 40 (103)
Q Consensus 10 ~~~~~r~~~~~i~~i~~~~~i~~li~~~~~~ 40 (103)
..|.+|++..+++...+++.++.+++-++.+
T Consensus 4 Pdm~RR~lmN~ll~Gava~~a~~~lyP~~~f 34 (39)
T PF08802_consen 4 PDMSRRQLMNLLLGGAVAVPAGGMLYPYVKF 34 (39)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CChhHHHHHHHHHHhhHHHHHHHHhhhheeE
Confidence 4577899999988777777777777655544
No 48
>TIGR02594 conserved hypothetical protein TIGR02594. Members of this protein family known so far are restricted to the bacteria, and for the most to the proteobacteria. The function is unknown.
Probab=53.89 E-value=31 Score=23.15 Aligned_cols=14 Identities=21% Similarity=0.093 Sum_probs=8.9
Q ss_pred CCCCCCcEEEEEeC
Q psy3466 74 EPVRVGEIVVFKVE 87 (103)
Q Consensus 74 ~~~~~GDIVvf~~~ 87 (103)
.++++||+|+|+..
T Consensus 72 ~~p~~GDiv~f~~~ 85 (129)
T TIGR02594 72 SKPAYGCIAVKRRG 85 (129)
T ss_pred CCCCccEEEEEECC
Confidence 35677777777544
No 49
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR022643 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region []. This entry represents the C-terminal region of the Orn/DAP/Arg decarboxylases.; GO: 0003824 catalytic activity; PDB: 1TWI_B 1TUF_A 3MT1_A 3N2B_C 2O0T_A 1HKW_A 1HKV_A 3VAB_A 3N2O_A 7ODC_A ....
Probab=53.62 E-value=16 Score=23.17 Aligned_cols=31 Identities=26% Similarity=0.475 Sum_probs=21.4
Q ss_pred ccccCCCEEEEeecCCCCCCCCcEEEEEeCC
Q psy3466 58 PAFHRGDLLFLTNYQEEPVRVGEIVVFKVEG 88 (103)
Q Consensus 58 Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~ 88 (103)
||-..+|.+.-+..-+.+++.||.++|..-|
T Consensus 65 ptC~~~D~i~~~~~lP~~l~~GD~l~f~~~G 95 (116)
T PF00278_consen 65 PTCDSGDVIARDVMLPKELEVGDWLVFENMG 95 (116)
T ss_dssp SSSSTTSEEEEEEEEESTTTTT-EEEESS-S
T ss_pred CCcCCCceEeeeccCCCCCCCCCEEEEecCc
Confidence 6677889887554333489999999997654
No 50
>PF06890 Phage_Mu_Gp45: Bacteriophage Mu Gp45 protein; InterPro: IPR014462 This entry is represented by the Bacteriophage Mu, Gp45. The characteristics of the protein distribution suggest prophage matches.
Probab=52.16 E-value=23 Score=24.95 Aligned_cols=25 Identities=24% Similarity=0.546 Sum_probs=17.7
Q ss_pred cCCCCCCCCcEEEEEeCCCCcCEEEE
Q psy3466 71 YQEEPVRVGEIVVFKVEGRDIPIVHR 96 (103)
Q Consensus 71 ~~~~~~~~GDIVvf~~~~~~~~~ikR 96 (103)
|+...++.|++.+|...+. ..++||
T Consensus 70 yR~~~L~~GEvalY~~~G~-~I~L~~ 94 (162)
T PF06890_consen 70 YRPKGLKPGEVALYDDEGQ-KIHLKR 94 (162)
T ss_pred ccccCCCCCcEEEEcCCCC-EEEEEe
Confidence 4556788999999986664 455655
No 51
>smart00841 Elong-fact-P_C Elongation factor P, C-terminal. These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology PUBMED:15210970.
Probab=51.70 E-value=25 Score=20.55 Aligned_cols=38 Identities=18% Similarity=0.365 Sum_probs=25.1
Q ss_pred CCCccc-cccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEE
Q psy3466 53 SGSMEP-AFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHR 96 (103)
Q Consensus 53 g~SM~P-tl~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikR 96 (103)
++|+.| +|.+|-.+.+-. -++.||.|..+..... |+.|
T Consensus 18 ~~~~K~A~letG~~i~VP~----FI~~Gd~I~V~T~~g~--Y~~R 56 (56)
T smart00841 18 SGGTKPATLETGAVVQVPL----FINEGDKIKVDTRTGE--YVSR 56 (56)
T ss_pred CCCcceEEECCCCEEEcCC----cccCCCEEEEECCCCc--EEcC
Confidence 345554 566777766643 4899999988766543 7765
No 52
>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=51.65 E-value=26 Score=24.92 Aligned_cols=37 Identities=16% Similarity=0.313 Sum_probs=25.1
Q ss_pred Cccc-cccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEEE
Q psy3466 55 SMEP-AFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRV 97 (103)
Q Consensus 55 SM~P-tl~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikRV 97 (103)
|+.| +|.+|=.|-+- .-++.||.|..+..... |+.|+
T Consensus 147 ~~K~A~letG~~v~VP----~fi~~Gd~I~v~T~~g~--y~~R~ 184 (184)
T TIGR00038 147 GTKPATLETGAVVQVP----LFIEEGEKIKVDTRTGE--YVERA 184 (184)
T ss_pred CcccEEEcCCCEEEeC----CcccCCCEEEEECCCCc--EEecC
Confidence 5565 44566555543 34899999999877544 88885
No 53
>COG1935 Uncharacterized conserved protein [Function unknown]
Probab=50.79 E-value=8 Score=26.09 Aligned_cols=21 Identities=43% Similarity=0.702 Sum_probs=15.7
Q ss_pred cccCCCEEEEeecCCCCCCCC
Q psy3466 59 AFHRGDLLFLTNYQEEPVRVG 79 (103)
Q Consensus 59 tl~~gD~v~v~~~~~~~~~~G 79 (103)
.+++||+||+.....+++.+|
T Consensus 38 rl~~GDlVFlT~~~~~Dl~~G 58 (122)
T COG1935 38 RLHEGDLVFLTSTSLEDLTKG 58 (122)
T ss_pred cCCCCCEEEEehhHhhHhhcC
Confidence 468999999987555666666
No 54
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=49.23 E-value=31 Score=25.47 Aligned_cols=13 Identities=23% Similarity=0.414 Sum_probs=5.5
Q ss_pred HHHHHHHHHHHHH
Q psy3466 20 QVLSFGMIVSSAL 32 (103)
Q Consensus 20 ~i~~i~~~~~i~~ 32 (103)
.++.+++++++++
T Consensus 14 ~iLNiaI~IV~lL 26 (217)
T PF07423_consen 14 KILNIAIGIVSLL 26 (217)
T ss_pred hhHHHHHHHHHHH
Confidence 3444444444333
No 55
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=49.18 E-value=40 Score=19.20 Aligned_cols=25 Identities=28% Similarity=0.502 Sum_probs=16.2
Q ss_pred CCCCCCcEEEEEeCCCCcCEEEEEE
Q psy3466 74 EPVRVGEIVVFKVEGRDIPIVHRVL 98 (103)
Q Consensus 74 ~~~~~GDIVvf~~~~~~~~~ikRVi 98 (103)
..+-.||.|.+..++.+..+|.++.
T Consensus 36 ~~~~VGD~V~~~~~~~~~~~I~~vl 60 (68)
T cd04466 36 NPPAVGDRVEFEPEDDGEGVIEEIL 60 (68)
T ss_pred CCCCCCcEEEEEECCCCcEEEEEEe
Confidence 3478999999976544334565553
No 56
>PF09138 Urm1: Urm1 (Ubiquitin related modifier); InterPro: IPR015221 Ubiquitin related modifier 1 (Urm1) is a ubiquitin related protein that modifies proteins in the yeast ubiquitin-like urmylation pathway []. Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and sequence features of the common ancestor of the entire superfamily []. ; GO: 0034227 tRNA thio-modification, 0005737 cytoplasm; PDB: 2AX5_A 2QJL_A 2PKO_A 1WGK_A 1XO3_A 2K9X_A.
Probab=48.27 E-value=15 Score=23.77 Aligned_cols=30 Identities=13% Similarity=0.305 Sum_probs=20.5
Q ss_pred ccccCCCEEEEeecC-------CCCCCCCcEEEEEeC
Q psy3466 58 PAFHRGDLLFLTNYQ-------EEPVRVGEIVVFKVE 87 (103)
Q Consensus 58 Ptl~~gD~v~v~~~~-------~~~~~~GDIVvf~~~ 87 (103)
-++++|=+|++|..+ .+.++.||.|+|-+.
T Consensus 56 ~~vrPGILvLINd~DwEl~g~~~y~l~~~D~I~FiST 92 (96)
T PF09138_consen 56 GSVRPGILVLINDADWELLGEEDYVLKDGDNITFIST 92 (96)
T ss_dssp SSB-TTEEEEETTCEHHHHTCCCSB--TTEEEEEEET
T ss_pred CeEcCcEEEEEcCccceeecCcceEcCCCCEEEEEcc
Confidence 357777889999732 368999999999764
No 57
>PF03908 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membrane glycoprotein associated with secretory pathway.
Probab=47.85 E-value=67 Score=19.98 Aligned_cols=16 Identities=25% Similarity=0.245 Sum_probs=8.0
Q ss_pred HHHHHHHhhhHHHHHH
Q psy3466 4 DAINDLKRLNKRQFLY 19 (103)
Q Consensus 4 ~~~~~~~~~~~r~~~~ 19 (103)
.+..-+++++++...+
T Consensus 54 ~s~~ll~~l~r~~~~D 69 (92)
T PF03908_consen 54 KSRKLLKKLERRDKTD 69 (92)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 3444455565555543
No 58
>TIGR00998 8a0101 efflux pump membrane protein (multidrug resistance protein A).
Probab=47.23 E-value=96 Score=23.19 Aligned_cols=12 Identities=25% Similarity=0.459 Sum_probs=7.6
Q ss_pred CCCCCCcEEEEE
Q psy3466 74 EPVRVGEIVVFK 85 (103)
Q Consensus 74 ~~~~~GDIVvf~ 85 (103)
..++.||+++--
T Consensus 62 ~~V~kGq~L~~l 73 (334)
T TIGR00998 62 DYVKQGDVLVRL 73 (334)
T ss_pred CEEcCCCEEEEE
Confidence 456777776543
No 59
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=45.84 E-value=10 Score=24.20 Aligned_cols=15 Identities=20% Similarity=0.432 Sum_probs=8.8
Q ss_pred ccccCCCEEEEeecC
Q psy3466 58 PAFHRGDLLFLTNYQ 72 (103)
Q Consensus 58 Ptl~~gD~v~v~~~~ 72 (103)
+.++.||.|++.+|.
T Consensus 52 ~~Vk~GD~Vl~~~y~ 66 (91)
T PRK14533 52 FDIKVGDKVIFSKYA 66 (91)
T ss_pred ccccCCCEEEEccCC
Confidence 346666666666553
No 60
>PF14118 YfzA: YfzA-like protein
Probab=45.65 E-value=23 Score=22.90 Aligned_cols=16 Identities=25% Similarity=0.549 Sum_probs=12.7
Q ss_pred EEeCCCccccccCCCE
Q psy3466 50 VVLSGSMEPAFHRGDL 65 (103)
Q Consensus 50 ~V~g~SM~Ptl~~gD~ 65 (103)
.+.+.|+.|.+++||.
T Consensus 29 ~~d~t~w~pnf~~g~~ 44 (94)
T PF14118_consen 29 IFDGTGWGPNFNEGDF 44 (94)
T ss_pred HhhccccccccCCCch
Confidence 3457899999999874
No 61
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=45.43 E-value=16 Score=22.63 Aligned_cols=16 Identities=13% Similarity=0.293 Sum_probs=13.0
Q ss_pred CCCCCCcEEEEEeCCC
Q psy3466 74 EPVRVGEIVVFKVEGR 89 (103)
Q Consensus 74 ~~~~~GDIVvf~~~~~ 89 (103)
=+.++||++.|..+..
T Consensus 55 LeCqpgDiley~~d~~ 70 (73)
T COG3655 55 LECQPGDILEYVPDSD 70 (73)
T ss_pred cCCChhheeEEecCCc
Confidence 4789999999987654
No 62
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=45.23 E-value=69 Score=20.93 Aligned_cols=28 Identities=29% Similarity=0.548 Sum_probs=20.7
Q ss_pred CCCCCCCcEEEEEeCCCCcCEEEEEEEecC
Q psy3466 73 EEPVRVGEIVVFKVEGRDIPIVHRVLKLHE 102 (103)
Q Consensus 73 ~~~~~~GDIVvf~~~~~~~~~ikRVi~~~~ 102 (103)
..+++.||++.+..++. .+.=+|.++++
T Consensus 46 S~~VK~GD~l~i~~~~~--~~~v~Vl~~~~ 73 (100)
T COG1188 46 SKEVKVGDILTIRFGNK--EFTVKVLALGE 73 (100)
T ss_pred ccccCCCCEEEEEeCCc--EEEEEEEeccc
Confidence 36899999999988764 36667776654
No 63
>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=45.23 E-value=31 Score=20.11 Aligned_cols=38 Identities=21% Similarity=0.323 Sum_probs=23.3
Q ss_pred CCCcccc-ccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEE
Q psy3466 53 SGSMEPA-FHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHR 96 (103)
Q Consensus 53 g~SM~Pt-l~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikR 96 (103)
++++.|. |.+|-.+.+- .-++.||.|..+..... |+.|
T Consensus 18 ~~~~K~A~letG~~i~VP----~FI~~Gd~I~V~T~~g~--Y~~R 56 (56)
T cd05794 18 SSGTKPATLETGAEVQVP----LFIKEGEKIKVDTRTGE--YVER 56 (56)
T ss_pred CCCcceEEECCCCEEEcC----CeecCCCEEEEECCCCc--EecC
Confidence 4456654 4566444442 34788999988766543 7765
No 64
>PRK05573 rplU 50S ribosomal protein L21; Validated
Probab=45.02 E-value=54 Score=21.27 Aligned_cols=34 Identities=21% Similarity=0.456 Sum_probs=25.1
Q ss_pred EEEeCCCccccccCCCEEEEeecCCCCCCCCcEEEEE
Q psy3466 49 VVVLSGSMEPAFHRGDLLFLTNYQEEPVRVGEIVVFK 85 (103)
Q Consensus 49 ~~V~g~SM~Ptl~~gD~v~v~~~~~~~~~~GDIVvf~ 85 (103)
+.|..++.+=-..+||.+.+++. +.+.||.|.|+
T Consensus 3 AIi~~gGkQykV~~Gd~i~v~~l---~~~~G~~i~l~ 36 (103)
T PRK05573 3 AIIKTGGKQYKVEEGDVIKVEKL---DAEVGDTVEFD 36 (103)
T ss_pred EEEEECCEEEEEeCCCEEEEccc---CCCCCCEEEEe
Confidence 45667777777889999999985 35667776664
No 65
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=44.40 E-value=12 Score=24.39 Aligned_cols=15 Identities=27% Similarity=0.662 Sum_probs=7.8
Q ss_pred ccccCCCEEEEeecC
Q psy3466 58 PAFHRGDLLFLTNYQ 72 (103)
Q Consensus 58 Ptl~~gD~v~v~~~~ 72 (103)
+.++.||.|++.+|.
T Consensus 61 ~~Vk~GD~Vl~~~y~ 75 (100)
T PTZ00414 61 PTVKVGDTVLLPEFG 75 (100)
T ss_pred ceecCCCEEEEcCCC
Confidence 345555555555543
No 66
>TIGR00964 secE_bact preprotein translocase, SecE subunit, bacterial. This model represents exclusively the bacterial (and some organellar) SecE protein. SecE is part of the core heterotrimer, SecYEG, of the Sec preprotein translocase system. Other components are the ATPase SecA, a cytosolic chaperone SecB, and an accessory complex of SecDF and YajC.
Probab=44.35 E-value=59 Score=18.40 Aligned_cols=20 Identities=10% Similarity=0.288 Sum_probs=12.6
Q ss_pred hHHHHHHHHhhhH---HHHHHHH
Q psy3466 2 IQDAINDLKRLNK---RQFLYQV 21 (103)
Q Consensus 2 ~~~~~~~~~~~~~---r~~~~~i 21 (103)
+++..+++|+..+ ++..+..
T Consensus 5 ~~~~~~ElkkV~WPt~~e~~~~t 27 (55)
T TIGR00964 5 FKEVKAELKKVVWPSRKELITYT 27 (55)
T ss_pred HHHHHHHHhcCcCcCHHHHHhHH
Confidence 4677888988443 4555444
No 67
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=44.31 E-value=46 Score=21.99 Aligned_cols=26 Identities=15% Similarity=0.479 Sum_probs=19.4
Q ss_pred CCCCCCcEEEEEeCCCCcCEEEEEEEec
Q psy3466 74 EPVRVGEIVVFKVEGRDIPIVHRVLKLH 101 (103)
Q Consensus 74 ~~~~~GDIVvf~~~~~~~~~ikRVi~~~ 101 (103)
-.+++||+|...+++. -..=||.+++
T Consensus 138 ~~l~pGDvi~l~~~~~--~~~~RI~~i~ 163 (164)
T PF13550_consen 138 LALEPGDVIALSDDGR--DMRFRITEIE 163 (164)
T ss_pred ccCCCCCEEEEEeCCC--ceEEEEEEEe
Confidence 4588999999988854 4777877765
No 68
>PRK15136 multidrug efflux system protein EmrA; Provisional
Probab=43.86 E-value=83 Score=24.69 Aligned_cols=12 Identities=25% Similarity=0.457 Sum_probs=7.8
Q ss_pred CCCCCCcEEEEE
Q psy3466 74 EPVRVGEIVVFK 85 (103)
Q Consensus 74 ~~~~~GDIVvf~ 85 (103)
..++.||+++--
T Consensus 81 d~VkkGqvL~~L 92 (390)
T PRK15136 81 DFVKEGDVLVTL 92 (390)
T ss_pred CEECCCCEEEEE
Confidence 557777776543
No 69
>PF04322 DUF473: Protein of unknown function (DUF473); InterPro: IPR007417 This is a family of uncharacterised archaeal proteins.
Probab=43.38 E-value=14 Score=24.92 Aligned_cols=21 Identities=33% Similarity=0.513 Sum_probs=16.8
Q ss_pred ccCCCEEEEeecCCCCCCCCc
Q psy3466 60 FHRGDLLFLTNYQEEPVRVGE 80 (103)
Q Consensus 60 l~~gD~v~v~~~~~~~~~~GD 80 (103)
+++||.||+...+..++.+|+
T Consensus 39 ~~~Gd~VFlT~~~~~Dl~~Gt 59 (119)
T PF04322_consen 39 LDPGDRVFLTSVSLEDLTPGT 59 (119)
T ss_pred CCCCCEEEEecCCHHHCCCCC
Confidence 589999999886667777775
No 70
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=42.69 E-value=33 Score=22.82 Aligned_cols=15 Identities=27% Similarity=0.583 Sum_probs=8.6
Q ss_pred CCCCCCcEEEEEeCC
Q psy3466 74 EPVRVGEIVVFKVEG 88 (103)
Q Consensus 74 ~~~~~GDIVvf~~~~ 88 (103)
+.++.||-++|...+
T Consensus 38 ~~mk~GD~vifY~s~ 52 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSG 52 (143)
T ss_dssp HC--TT-EEEEEETS
T ss_pred hcCCCCCEEEEEEcC
Confidence 367777777777776
No 71
>TIGR01416 Rieske_proteo ubiquinol-cytochrome c reductase, iron-sulfur subunit. Most members of this family have a recognizable twin-arginine translocation (tat) signal sequence (DeltaPh-dependent translocation in chloroplast) for transport across the membrane with the 2Fe-2S group already bound. These signal sequences include a motif resembling RRxFLK before the transmembrane helix.
Probab=42.12 E-value=1.2e+02 Score=21.31 Aligned_cols=16 Identities=13% Similarity=0.397 Sum_probs=10.3
Q ss_pred CCCCCCcEEEEEeCCC
Q psy3466 74 EPVRVGEIVVFKVEGR 89 (103)
Q Consensus 74 ~~~~~GDIVvf~~~~~ 89 (103)
.+++.|.-..+..++.
T Consensus 47 ~eL~pG~~~~v~~~Gk 62 (174)
T TIGR01416 47 SKIQPGQQLTVEWRGK 62 (174)
T ss_pred HHCCCCCeEEEEECCe
Confidence 5666676666666654
No 72
>PF01616 Orbi_NS3: Orbivirus NS3; InterPro: IPR002565 This is a family of Orbivirus non structural protein of unknown function, but which may play a role in release of the virus from infected cells [].
Probab=41.64 E-value=1e+02 Score=22.50 Aligned_cols=17 Identities=29% Similarity=0.229 Sum_probs=8.4
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy3466 15 RQFLYQVLSFGMIVSSA 31 (103)
Q Consensus 15 r~~~~~i~~i~~~~~i~ 31 (103)
+.++.|+..+..++.++
T Consensus 90 ~~il~~~~li~a~v~l~ 106 (195)
T PF01616_consen 90 RRILHIVELIAAIVALL 106 (195)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45566655444444433
No 73
>PLN00208 translation initiation factor (eIF); Provisional
Probab=40.22 E-value=27 Score=24.36 Aligned_cols=25 Identities=8% Similarity=0.203 Sum_probs=15.9
Q ss_pred ccCCCEEEEeecCCCCCCCCcEEEEE
Q psy3466 60 FHRGDLLFLTNYQEEPVRVGEIVVFK 85 (103)
Q Consensus 60 l~~gD~v~v~~~~~~~~~~GDIVvf~ 85 (103)
+.+||.|++... ..+...|||+--.
T Consensus 71 I~~GD~VlVel~-~~d~~KgdIv~ry 95 (145)
T PLN00208 71 IAAGDIILVGLR-DYQDDKADVILKY 95 (145)
T ss_pred ecCCCEEEEEcc-CCCCCEEEEEEEc
Confidence 457888888753 3456777776433
No 74
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=39.75 E-value=37 Score=20.71 Aligned_cols=16 Identities=25% Similarity=0.715 Sum_probs=10.3
Q ss_pred CCCCCCCcEEEEEeCC
Q psy3466 73 EEPVRVGEIVVFKVEG 88 (103)
Q Consensus 73 ~~~~~~GDIVvf~~~~ 88 (103)
...++.||+++|+..+
T Consensus 71 ~n~L~~GD~~~F~~~~ 86 (100)
T PF02362_consen 71 DNGLKEGDVCVFELIG 86 (100)
T ss_dssp HCT--TT-EEEEEE-S
T ss_pred HcCCCCCCEEEEEEec
Confidence 4789999999999765
No 75
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=39.08 E-value=21 Score=23.11 Aligned_cols=13 Identities=31% Similarity=0.555 Sum_probs=8.6
Q ss_pred CCCCCCCcEEEEE
Q psy3466 73 EEPVRVGEIVVFK 85 (103)
Q Consensus 73 ~~~~~~GDIVvf~ 85 (103)
...|++|||++|+
T Consensus 60 ~~~P~~Gdivv~~ 72 (124)
T PF05257_consen 60 GSTPQPGDIVVWD 72 (124)
T ss_dssp CS---TTEEEEEE
T ss_pred CcccccceEEEec
Confidence 4789999999995
No 76
>PF09753 Use1: Membrane fusion protein Use1; InterPro: IPR019150 This entry represents a family of proteins, approximately 300 residues in length, involved in vesicle transport. They have a single C-terminal transmembrane domain and a SNARE [soluble NSF (N-ethylmaleimide-sensitive fusion protein) attachment protein receptor] domain of approximately 60 residues. The SNARE domains are essential for membrane fusion and are conserved from yeasts to humans. Use1 is one of the three protein subunits that make up the SNARE complex and it is specifically required for Golgi-endoplasmic reticulum retrograde transport [].
Probab=38.75 E-value=69 Score=23.58 Aligned_cols=19 Identities=16% Similarity=-0.034 Sum_probs=7.6
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy3466 20 QVLSFGMIVSSALMIWKGL 38 (103)
Q Consensus 20 ~i~~i~~~~~i~~li~~~~ 38 (103)
|..++.++++++++++.++
T Consensus 228 ~~~~~~i~~v~~~Fi~mvl 246 (251)
T PF09753_consen 228 CWTWLMIFVVIIVFIMMVL 246 (251)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4444444433333333333
No 77
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=38.69 E-value=29 Score=24.44 Aligned_cols=23 Identities=9% Similarity=0.323 Sum_probs=14.5
Q ss_pred ccCCCEEEEeecCCCCCCCCcEEE
Q psy3466 60 FHRGDLLFLTNYQEEPVRVGEIVV 83 (103)
Q Consensus 60 l~~gD~v~v~~~~~~~~~~GDIVv 83 (103)
+.+||.|++... ..+..+|||+-
T Consensus 71 I~~GD~VlVel~-~yd~~KgdIi~ 93 (155)
T PTZ00329 71 INIGDIILVSLR-DFQDSKADVIL 93 (155)
T ss_pred ecCCCEEEEecc-CCCCCEEEEEE
Confidence 457777777652 34566677663
No 78
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by Pfam model pfam00877 and by Anantharaman and Aravind (PubMed:12620121). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes.
Probab=37.56 E-value=24 Score=23.59 Aligned_cols=14 Identities=21% Similarity=0.584 Sum_probs=11.5
Q ss_pred CCCCCCCcEEEEEe
Q psy3466 73 EEPVRVGEIVVFKV 86 (103)
Q Consensus 73 ~~~~~~GDIVvf~~ 86 (103)
.+++++||+|.|+.
T Consensus 74 ~~~~qpGDlvff~~ 87 (134)
T TIGR02219 74 CDAAQPGDVLVFRW 87 (134)
T ss_pred hhcCCCCCEEEEee
Confidence 36789999999975
No 79
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=37.39 E-value=62 Score=20.22 Aligned_cols=26 Identities=27% Similarity=0.250 Sum_probs=13.9
Q ss_pred CCCCCCCCcEEEEEeCCCCcCEEEEEEEe
Q psy3466 72 QEEPVRVGEIVVFKVEGRDIPIVHRVLKL 100 (103)
Q Consensus 72 ~~~~~~~GDIVvf~~~~~~~~~ikRVi~~ 100 (103)
+...|++||.|++. |+ .++|.|+---
T Consensus 62 d~~~P~~gd~v~~d--G~-~y~V~~~~~~ 87 (95)
T PF13856_consen 62 DYPKPRRGDRVVID--GE-SYTVTRFQEE 87 (95)
T ss_dssp S-----TT-EEEET--TE-EEEEEEEEEE
T ss_pred CCCCCCCCCEEEEC--Ce-EEEEeEEecC
Confidence 34559999999874 43 5788887543
No 80
>PRK10691 hypothetical protein; Provisional
Probab=37.27 E-value=42 Score=24.38 Aligned_cols=30 Identities=17% Similarity=0.411 Sum_probs=21.6
Q ss_pred cccCCCEEEEeec-CCCCCCCCcEEEEEeCC
Q psy3466 59 AFHRGDLLFLTNY-QEEPVRVGEIVVFKVEG 88 (103)
Q Consensus 59 tl~~gD~v~v~~~-~~~~~~~GDIVvf~~~~ 88 (103)
||++||+++.-.. ....++.||.+...-.+
T Consensus 181 tL~aGDvI~TGTp~g~~~l~~GD~v~~~i~g 211 (219)
T PRK10691 181 TLRAGDVVLTGTPEGVGPLQSGDELTVTFNG 211 (219)
T ss_pred ccCCCCEEEcCCCCCCEECCCCCEEEEEEeC
Confidence 7888888888763 23457888888776654
No 81
>KOG3251|consensus
Probab=37.24 E-value=1.1e+02 Score=22.76 Aligned_cols=30 Identities=7% Similarity=0.344 Sum_probs=17.6
Q ss_pred HHHHhhhHHHHHHHHHHHHHHHHHHHHHHH
Q psy3466 7 NDLKRLNKRQFLYQVLSFGMIVSSALMIWK 36 (103)
Q Consensus 7 ~~~~~~~~r~~~~~i~~i~~~~~i~~li~~ 36 (103)
.+++-+++|-.-+|++.++.++++.++++.
T Consensus 178 ~ti~lIeRR~~~Dk~iF~~G~i~~~v~~yl 207 (213)
T KOG3251|consen 178 QTIRLIERRVREDKIIFYGGVILTLVIMYL 207 (213)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 456667777777777655555444444433
No 82
>PRK08564 5'-methylthioadenosine phosphorylase II; Reviewed
Probab=36.93 E-value=23 Score=26.74 Aligned_cols=19 Identities=21% Similarity=0.497 Sum_probs=17.0
Q ss_pred eCCCccccccCCCEEEEee
Q psy3466 52 LSGSMEPAFHRGDLLFLTN 70 (103)
Q Consensus 52 ~g~SM~Ptl~~gD~v~v~~ 70 (103)
..+||.|.+++||+++.+.
T Consensus 92 avGsl~~~~~pGDlVv~~D 110 (267)
T PRK08564 92 AVGSLREDYKPGDFVIPDQ 110 (267)
T ss_pred cccccCCCCCCCCEEeehh
Confidence 4579999999999999887
No 83
>COG0234 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]
Probab=36.69 E-value=20 Score=23.32 Aligned_cols=11 Identities=45% Similarity=0.812 Sum_probs=6.7
Q ss_pred CCCCCcEEEEE
Q psy3466 75 PVRVGEIVVFK 85 (103)
Q Consensus 75 ~~~~GDIVvf~ 85 (103)
+++.||.|.|.
T Consensus 58 ~VkvGD~Vlf~ 68 (96)
T COG0234 58 DVKVGDRVLFG 68 (96)
T ss_pred ccccCCEEEEC
Confidence 35666666663
No 84
>PRK07597 secE preprotein translocase subunit SecE; Reviewed
Probab=36.28 E-value=89 Score=18.12 Aligned_cols=21 Identities=14% Similarity=0.409 Sum_probs=12.2
Q ss_pred hHHHHHHHHhhhH---HHHHHHHH
Q psy3466 2 IQDAINDLKRLNK---RQFLYQVL 22 (103)
Q Consensus 2 ~~~~~~~~~~~~~---r~~~~~i~ 22 (103)
.++..+++|+..+ ++..++..
T Consensus 14 ~~~~~~ElkkV~WPs~~e~~~~t~ 37 (64)
T PRK07597 14 FKDVKAELKKVTWPTRKELVRSTI 37 (64)
T ss_pred HHHHHHHHhhCcCcCHHHHHhHHH
Confidence 3566777888444 45555443
No 85
>COG4929 Uncharacterized membrane-anchored protein [Function unknown]
Probab=35.52 E-value=1.1e+02 Score=22.21 Aligned_cols=28 Identities=11% Similarity=0.271 Sum_probs=18.6
Q ss_pred cccCCCEEEEee--cCCCCCCCCcEEEEEe
Q psy3466 59 AFHRGDLLFLTN--YQEEPVRVGEIVVFKV 86 (103)
Q Consensus 59 tl~~gD~v~v~~--~~~~~~~~GDIVvf~~ 86 (103)
++..|+.++... .+++++=+||-++...
T Consensus 31 ~l~~G~~IiLqtaPVDPRslmrGDYmtLnY 60 (190)
T COG4929 31 ILTTGREIILQTAPVDPRSLMRGDYMTLNY 60 (190)
T ss_pred HhccCCEEEEEeCCCChHHhhccceEEeee
Confidence 345677777765 5667777788777654
No 86
>PF03904 DUF334: Domain of unknown function (DUF334); InterPro: IPR005602 This is a family of proteins found in Staphylococcus aureus plasmid with no characterised function.
Probab=35.13 E-value=1.6e+02 Score=22.15 Aligned_cols=25 Identities=8% Similarity=-0.069 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Q psy3466 17 FLYQVLSFGMIVSSALMIWKGLMVL 41 (103)
Q Consensus 17 ~~~~i~~i~~~~~i~~li~~~~~~~ 41 (103)
...+...-+.+.+++++++.++...
T Consensus 146 ~~k~~~~gi~aml~Vf~LF~lvmt~ 170 (230)
T PF03904_consen 146 RQKSMYKGIGAMLFVFMLFALVMTI 170 (230)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHh
Confidence 3445554555555555555555543
No 87
>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=35.12 E-value=1e+02 Score=18.39 Aligned_cols=40 Identities=23% Similarity=0.322 Sum_probs=28.9
Q ss_pred eEEEeCCCccccccCCCEEEEee-cCCCCCCCCc-EEEEEeC
Q psy3466 48 IVVVLSGSMEPAFHRGDLLFLTN-YQEEPVRVGE-IVVFKVE 87 (103)
Q Consensus 48 ~~~V~g~SM~Ptl~~gD~v~v~~-~~~~~~~~GD-IVvf~~~ 87 (103)
+..|...+|.=||..|.-.-+.. .+...++.|. |+++...
T Consensus 9 I~~id~~~~titLdDGksy~lp~ef~~~~L~~G~kV~V~yd~ 50 (61)
T PF07076_consen 9 IKSIDPETMTITLDDGKSYKLPEEFDFDGLKPGMKVVVFYDE 50 (61)
T ss_pred EEEEcCCceEEEecCCCEEECCCcccccccCCCCEEEEEEEc
Confidence 46778888999999997766655 5668899995 4455444
No 88
>cd00320 cpn10 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It forms heptameric rings with a dome-like structure, forming a lid to the large cavity of the tetradecameric cpn60 cylinder and thereby tightly regulating release and binding of proteins to the cpn60 surface.
Probab=34.71 E-value=1.2e+02 Score=19.13 Aligned_cols=14 Identities=36% Similarity=0.513 Sum_probs=9.6
Q ss_pred CCCCCCcEEEEEeC
Q psy3466 74 EPVRVGEIVVFKVE 87 (103)
Q Consensus 74 ~~~~~GDIVvf~~~ 87 (103)
.+++.||.|+|..-
T Consensus 56 ~~vk~GD~Vl~~~~ 69 (93)
T cd00320 56 LSVKVGDKVLFPKY 69 (93)
T ss_pred ccccCCCEEEECCC
Confidence 35778888887643
No 89
>PF00166 Cpn10: Chaperonin 10 Kd subunit; InterPro: IPR020818 The chaperonins are `helper' molecules required for correct folding and subsequent assembly of some proteins []. These are required for normal cell growth [], and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions. Type I chaperonins present in eubacteria, mitochondria and chloroplasts require the concerted action of 2 proteins, chaperonin 60 (cpn60) and chaperonin 10 (cpn10) []. The 10 kDa chaperonin (cpn10 - or groES in bacteria) exists as a ring-shaped oligomer of between six to eight identical subunits, while the 60 kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2 stacked rings, each ring containing 7 identical subunits []. These ring structures assemble by self-stimulation in the presence of Mg2+-ATP. The central cavity of the cylindrical cpn60 tetradecamer provides as isolated environment for protein folding whilst cpn-10 binds to cpn-60 and synchronizes the release of the folded protein in an Mg2+-ATP dependent manner []. The binding of cpn10 to cpn60 inhibits the weak ATPase activity of cpn60. Escherichia coli GroES has also been shown to bind ATP cooperatively, and with an affinity comparable to that of GroEL []. Each GroEL subunit contains three structurally distinct domains: an apical, an intermediate and an equatorial domain. The apical domain contains the binding sites for both GroES and the unfolded protein substrate. The equatorial domain contains the ATP-binding site and most of the oligomeric contacts. The intermediate domain links the apical and equatorial domains and transfers allosteric information between them. The GroEL oligomer is a tetradecamer, cylindrically shaped, that is organised in two heptameric rings stacked back to back. Each GroEL ring contains a central cavity, known as the `Anfinsen cage', that provides an isolated environment for protein folding. The identical 10 kDa subunits of GroES form a dome-like heptameric oligomer in solution. ATP binding to GroES may be important in charging the seven subunits of the interacting GroEL ring with ATP, to facilitate cooperative ATP binding and hydrolysis for substrate protein release.; GO: 0006457 protein folding, 0005737 cytoplasm; PDB: 1PF9_Q 1AON_P 1SX4_T 1SVT_R 2C7D_P 1PCQ_O 2C7C_Q 1GRU_Q 1WNR_F 1P3H_I ....
Probab=34.62 E-value=1.2e+02 Score=18.98 Aligned_cols=14 Identities=36% Similarity=0.506 Sum_probs=8.1
Q ss_pred CCCCCCcEEEEEeC
Q psy3466 74 EPVRVGEIVVFKVE 87 (103)
Q Consensus 74 ~~~~~GDIVvf~~~ 87 (103)
.+++.||.|.|...
T Consensus 56 ~~vk~GD~Vl~~~~ 69 (93)
T PF00166_consen 56 MDVKVGDKVLFPKY 69 (93)
T ss_dssp TSS-TTSEEEEETT
T ss_pred eeeeeccEEecccc
Confidence 45667777777543
No 90
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=34.34 E-value=1.1e+02 Score=18.72 Aligned_cols=36 Identities=19% Similarity=0.266 Sum_probs=21.7
Q ss_pred CCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEEEE
Q psy3466 62 RGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRVL 98 (103)
Q Consensus 62 ~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikRVi 98 (103)
+|..-+=-|.+.++.+.||++..+.=+. .-|+.|.+
T Consensus 15 ~G~KtfEiRkNDRdf~VGD~L~L~E~~~-~~YTGr~~ 50 (72)
T PF12961_consen 15 SGRKTFEIRKNDRDFQVGDILVLREWDN-GEYTGREI 50 (72)
T ss_pred CCCceEEEEecCCCCCCCCEEEEEEecC-CCccccEE
Confidence 4444444454558899999999865332 23554443
No 91
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=34.21 E-value=1.2e+02 Score=19.20 Aligned_cols=13 Identities=38% Similarity=0.583 Sum_probs=9.1
Q ss_pred CCCCCcEEEEEeC
Q psy3466 75 PVRVGEIVVFKVE 87 (103)
Q Consensus 75 ~~~~GDIVvf~~~ 87 (103)
+++.||.|+|...
T Consensus 58 ~vk~GD~Vlf~~~ 70 (95)
T PRK00364 58 DVKVGDKVLFGKY 70 (95)
T ss_pred ccCCCCEEEEcCC
Confidence 4777888887543
No 92
>KOG3156|consensus
Probab=34.09 E-value=1.6e+02 Score=21.88 Aligned_cols=34 Identities=18% Similarity=0.226 Sum_probs=19.7
Q ss_pred hHHHHHHHHh---hhHHHHHHHHHHHHHHHHHHHHHH
Q psy3466 2 IQDAINDLKR---LNKRQFLYQVLSFGMIVSSALMIW 35 (103)
Q Consensus 2 ~~~~~~~~~~---~~~r~~~~~i~~i~~~~~i~~li~ 35 (103)
|..|+.+||. -.+-+...|+..++.....+++.+
T Consensus 179 Id~Ev~~lk~qi~s~K~qt~qw~~g~v~~~~Al~La~ 215 (220)
T KOG3156|consen 179 IDQEVTNLKTQIESVKTQTIQWLIGVVTGTSALVLAY 215 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456677776 223467888876665544444443
No 93
>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=33.83 E-value=1.2e+02 Score=20.23 Aligned_cols=36 Identities=19% Similarity=0.276 Sum_probs=17.8
Q ss_pred EEEeCCCccccccCCCEEEEeec---CCCCCCCCcEEEEEe
Q psy3466 49 VVVLSGSMEPAFHRGDLLFLTNY---QEEPVRVGEIVVFKV 86 (103)
Q Consensus 49 ~~V~g~SM~Ptl~~gD~v~v~~~---~~~~~~~GDIVvf~~ 86 (103)
+.+..+|+.+ ..|=.+-+.+. ....++.||||.++.
T Consensus 41 l~i~D~S~~~--~~~l~v~~F~~~~~~LP~v~~GDVIll~~ 79 (138)
T cd04497 41 LTITDPSLAN--SDGLTVKLFRPNEESLPIVKVGDIILLRR 79 (138)
T ss_pred EEEECCCCCC--CCcEEEEEECCChhhCCCCCCCCEEEEEE
Confidence 4566667654 22222222221 122357788887754
No 94
>PF00584 SecE: SecE/Sec61-gamma subunits of protein translocation complex; InterPro: IPR001901 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. The chaperone protein SecB [] is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion []. SecE, part of the main SecYEG translocase complex, is ~106 residues in length, and spans the inner membrane of the Gram-negative bacterial envelope. Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. In eukaryotes, the evolutionary related protein sec61-gamma plays a role in protein translocation through the endoplasmic reticulum; it is part of a trimeric complex that also consist of sec61-alpha and beta []. Both secE and sec61-gamma are small proteins of about 60 to 90 amino acids that contain a single transmembrane region at their C-terminal extremity (Escherichia coli secE is an exception, in that it possess an extra N-terminal segment of 60 residues that contains two additional transmembrane domains) [].; GO: 0006605 protein targeting, 0006886 intracellular protein transport, 0016020 membrane; PDB: 3J01_B 2WW9_B 2WWA_B 3DL8_C 2WWB_B 3DIN_G 2ZJS_E 2ZQP_E.
Probab=33.49 E-value=75 Score=17.85 Aligned_cols=20 Identities=15% Similarity=0.429 Sum_probs=11.1
Q ss_pred HHHHHHHHhhhH---HHHHHHHH
Q psy3466 3 QDAINDLKRLNK---RQFLYQVL 22 (103)
Q Consensus 3 ~~~~~~~~~~~~---r~~~~~i~ 22 (103)
++..+++|+..+ ++..+...
T Consensus 7 ~~~~~Elkkv~WP~~~e~~~~t~ 29 (57)
T PF00584_consen 7 REVKKELKKVTWPSRKELLKSTI 29 (57)
T ss_dssp HCHHHHHHHHHCCCTHHHHHHHH
T ss_pred HHHHHHHHHhcCCCHHHHHHHHH
Confidence 456677887443 45554443
No 95
>KOG0557|consensus
Probab=33.43 E-value=82 Score=26.03 Aligned_cols=39 Identities=8% Similarity=0.239 Sum_probs=31.1
Q ss_pred eEEEeCCCccccccCCCEEEEeecCCCCCCCCcEEEEEe
Q psy3466 48 IVVVLSGSMEPAFHRGDLLFLTNYQEEPVRVGEIVVFKV 86 (103)
Q Consensus 48 ~~~V~g~SM~Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~ 86 (103)
...+.=.+|.||...|..+--.+.-...++.||++.=-.
T Consensus 38 h~~i~MPALSPTMeeGnIvsW~kKeGdkls~GDvl~EVE 76 (470)
T KOG0557|consen 38 HKTFSMPALSPTMEEGNIVSWKKKEGDKLSAGDVLLEVE 76 (470)
T ss_pred ceEeecCCCCccccCCceeeEeeccCCccCCCceEEEEe
Confidence 467777899999999999877664457899999986543
No 96
>KOG1641|consensus
Probab=33.36 E-value=37 Score=22.40 Aligned_cols=30 Identities=27% Similarity=0.511 Sum_probs=21.7
Q ss_pred EEeCCCccc-cccCCCEEEEeecCCCCCCCC
Q psy3466 50 VVLSGSMEP-AFHRGDLLFLTNYQEEPVRVG 79 (103)
Q Consensus 50 ~V~g~SM~P-tl~~gD~v~v~~~~~~~~~~G 79 (103)
...+++-.| ...+||+|+...|..++++-|
T Consensus 56 ~~~~G~~v~~~Vk~Gd~VLlpeygGt~V~l~ 86 (104)
T KOG1641|consen 56 RDKGGEIVPVSVKVGDRVLLPEYGGTKVKLG 86 (104)
T ss_pred ccCCCCCcCccccCCCEEEeeccCCcEEecc
Confidence 345566666 888999999988766666665
No 97
>TIGR01048 lysA diaminopimelate decarboxylase. This family consists of diaminopimelate decarboxylase, an enzyme which catalyzes the conversion of diaminopimelic acid into lysine during the last step of lysine biosynthesis.
Probab=33.00 E-value=66 Score=25.10 Aligned_cols=30 Identities=23% Similarity=0.369 Sum_probs=19.6
Q ss_pred ccccCCCEEEEeecCCCCCCCCcEEEEEeCC
Q psy3466 58 PAFHRGDLLFLTNYQEEPVRVGEIVVFKVEG 88 (103)
Q Consensus 58 Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~ 88 (103)
|+=.++|.+.-+. ...+++.||.++|.+-|
T Consensus 345 ~~C~~~D~l~~~~-~lp~l~~GD~l~~~~~G 374 (417)
T TIGR01048 345 PLCESGDVLARDR-ELPEVEPGDLLAVFDAG 374 (417)
T ss_pred CCcCCCCEEeecc-CCCCCCCCCEEEEeCCC
Confidence 3445677554333 23479999999997655
No 98
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 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 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=32.77 E-value=40 Score=21.24 Aligned_cols=18 Identities=22% Similarity=0.473 Sum_probs=14.4
Q ss_pred CCCccccccCCCEEEEee
Q psy3466 53 SGSMEPAFHRGDLLFLTN 70 (103)
Q Consensus 53 g~SM~Ptl~~gD~v~v~~ 70 (103)
+..|.|.|+.||+|...-
T Consensus 43 tk~~rp~L~~GDlV~ArV 60 (86)
T cd05790 43 TKRNRPNLNVGDLVYARV 60 (86)
T ss_pred cccccccCCCCCEEEEEE
Confidence 345789999999998864
No 99
>PRK15203 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase; Provisional
Probab=32.56 E-value=50 Score=26.60 Aligned_cols=31 Identities=23% Similarity=0.346 Sum_probs=22.6
Q ss_pred cccCCCEEEEeec-CCCCCCCCcEEEEEeCCC
Q psy3466 59 AFHRGDLLFLTNY-QEEPVRVGEIVVFKVEGR 89 (103)
Q Consensus 59 tl~~gD~v~v~~~-~~~~~~~GDIVvf~~~~~ 89 (103)
||.+||+++.-.. ....++.||.+...-++.
T Consensus 165 tL~pGDvI~TGTP~g~~~l~~GD~v~~~i~gi 196 (429)
T PRK15203 165 TLNPGDAILLGTPQARVEIQPGDRVRVLAEGF 196 (429)
T ss_pred CcCCCCEEEcCCCCCceECCCCCEEEEEEeCe
Confidence 6888998888763 224588899988877653
No 100
>PRK08666 5'-methylthioadenosine phosphorylase; Validated
Probab=32.37 E-value=28 Score=25.86 Aligned_cols=19 Identities=32% Similarity=0.697 Sum_probs=16.9
Q ss_pred eCCCccccccCCCEEEEee
Q psy3466 52 LSGSMEPAFHRGDLLFLTN 70 (103)
Q Consensus 52 ~g~SM~Ptl~~gD~v~v~~ 70 (103)
..+|+.|.+++||.|+.+.
T Consensus 84 saGsl~~~l~~GDiVi~~d 102 (261)
T PRK08666 84 AVGSLNPNMKPGDFVILDQ 102 (261)
T ss_pred cccccCCCCCCCCEEeehh
Confidence 3479999999999999987
No 101
>TIGR01694 MTAP 5'-deoxy-5'-methylthioadenosine phosphorylase. In between the trusted and noise cutoffs are: 1) several archaeal sequences which appear to contain several residues characteristic of phosphorylases which act on guanosine or inosine (according to the crystal structure of MTAP and alignments). In any case, these residues are not conserved. 2) sequences from Mycobacterium tuberculosis and Streptomyces coelicolor which have better, although not perfect retention of the active site residues, but considering the general observation that bacteria utilize the MTA/SAH nucleotidase enzyme and a kinase to do this reaction, these have been excluded pending stronger evidence of their function, and 3) a sequence from Drosophila which appears to be a recent divergence (long branch in neighbor-joining trees) and lacks some of the conserved active site residues.
Probab=32.28 E-value=30 Score=25.28 Aligned_cols=19 Identities=26% Similarity=0.492 Sum_probs=16.9
Q ss_pred eCCCccccccCCCEEEEee
Q psy3466 52 LSGSMEPAFHRGDLLFLTN 70 (103)
Q Consensus 52 ~g~SM~Ptl~~gD~v~v~~ 70 (103)
..+||.|.++.||+|+.+.
T Consensus 84 saG~l~~~l~~GDlVI~~~ 102 (241)
T TIGR01694 84 AVGSLREEYPPGDLVVPDQ 102 (241)
T ss_pred cccccCCCCCCCCEEEEhh
Confidence 3479999999999999987
No 102
>CHL00075 rpl21 ribosomal protein L21
Probab=32.24 E-value=1.3e+02 Score=19.74 Aligned_cols=34 Identities=12% Similarity=0.384 Sum_probs=23.2
Q ss_pred EEEeCCCccccccCCCEEEEeecCCCCCCCCcEEEEE
Q psy3466 49 VVVLSGSMEPAFHRGDLLFLTNYQEEPVRVGEIVVFK 85 (103)
Q Consensus 49 ~~V~g~SM~Ptl~~gD~v~v~~~~~~~~~~GDIVvf~ 85 (103)
..|..++=+=-..+||.+.+++. +.+.||-|.|+
T Consensus 5 AIi~~gGkQykV~~Gd~i~vekl---~~~~G~~i~l~ 38 (108)
T CHL00075 5 AIIEAGGKQLWVEPGRFYDINHF---PLEPGTKILLN 38 (108)
T ss_pred EEEEECCEEEEEeCCCEEEEEEc---CCCCCCEEEEE
Confidence 45566666666788999999985 24566666553
No 103
>cd04713 BAH_plant_3 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=32.07 E-value=71 Score=21.76 Aligned_cols=25 Identities=16% Similarity=0.266 Sum_probs=13.3
Q ss_pred CCCCCcEEEEEeCCCCcCEEEEEEE
Q psy3466 75 PVRVGEIVVFKVEGRDIPIVHRVLK 99 (103)
Q Consensus 75 ~~~~GDIVvf~~~~~~~~~ikRVi~ 99 (103)
.++.||-|.++.++....||.+|..
T Consensus 20 ~y~vgD~Vlv~~~~~~~pyI~~I~~ 44 (146)
T cd04713 20 KYRLEDCVLLVPEDDQKPYIAIIKD 44 (146)
T ss_pred EEECCCEEEEeCCCCCCCEEEEEEE
Confidence 3555666666554333455555554
No 104
>PRK04542 elongation factor P; Provisional
Probab=31.97 E-value=80 Score=22.80 Aligned_cols=37 Identities=22% Similarity=0.407 Sum_probs=24.5
Q ss_pred Cccc-cccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEEE
Q psy3466 55 SMEP-AFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRV 97 (103)
Q Consensus 55 SM~P-tl~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikRV 97 (103)
+..| ||.+|=.|-+- .-++.||.|..+..... |+.|+
T Consensus 151 ~~KpAtLetG~~v~VP----~FI~~Gd~I~VdT~tge--Yv~R~ 188 (189)
T PRK04542 151 RTKPATLSTGLVIQVP----EYISTGEKIRINTEERK--FMGRA 188 (189)
T ss_pred CCccEEEcCCCEEEeC----CcccCCCEEEEECCCCc--EEeec
Confidence 3444 45566544442 34899999999877544 99886
No 105
>PF06940 DUF1287: Domain of unknown function (DUF1287); InterPro: IPR009706 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=31.84 E-value=32 Score=24.46 Aligned_cols=15 Identities=33% Similarity=0.687 Sum_probs=12.3
Q ss_pred CCCCCCcEEEEEeCC
Q psy3466 74 EPVRVGEIVVFKVEG 88 (103)
Q Consensus 74 ~~~~~GDIVvf~~~~ 88 (103)
++.+.||||+|+.++
T Consensus 105 ~~~q~GDIVtw~l~~ 119 (164)
T PF06940_consen 105 EDWQPGDIVTWRLPG 119 (164)
T ss_pred hhcCCCCEEEEeCCC
Confidence 578899999998665
No 106
>TIGR00061 L21 ribosomal protein L21. Eubacterial and chloroplast.
Probab=31.84 E-value=1.2e+02 Score=19.70 Aligned_cols=33 Identities=18% Similarity=0.301 Sum_probs=21.0
Q ss_pred EEeCCCccccccCCCEEEEeecCCCCCCCCcEEEEE
Q psy3466 50 VVLSGSMEPAFHRGDLLFLTNYQEEPVRVGEIVVFK 85 (103)
Q Consensus 50 ~V~g~SM~Ptl~~gD~v~v~~~~~~~~~~GDIVvf~ 85 (103)
.|..++=+=-..+||.+.+++. +.+.||.|.|+
T Consensus 3 Ii~~gGkQykV~~Gd~i~Ve~l---~~~~G~~i~l~ 35 (101)
T TIGR00061 3 IVEIGGKQYKVEEGQTVRIEKL---DAAPGDTVEFD 35 (101)
T ss_pred EEEECCEEEEEeCCCEEEEccc---CCCCCCEEEEE
Confidence 3444444555678899999885 24567666654
No 107
>PRK09136 5'-methylthioadenosine phosphorylase; Validated
Probab=31.84 E-value=30 Score=25.76 Aligned_cols=22 Identities=18% Similarity=0.291 Sum_probs=18.2
Q ss_pred EEEeCCCccccccCCCEEEEee
Q psy3466 49 VVVLSGSMEPAFHRGDLLFLTN 70 (103)
Q Consensus 49 ~~V~g~SM~Ptl~~gD~v~v~~ 70 (103)
.+-.-+|+.|.+++||+++.+.
T Consensus 81 ~t~aaG~l~~~l~~Gdlvi~~d 102 (245)
T PRK09136 81 AVNTVGGIHADMGPGTLVVPDQ 102 (245)
T ss_pred EecccccCCCCCCCCCEEEEHH
Confidence 3444569999999999999986
No 108
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=31.65 E-value=52 Score=19.66 Aligned_cols=11 Identities=18% Similarity=0.308 Sum_probs=9.3
Q ss_pred CCCCCcEEEEE
Q psy3466 75 PVRVGEIVVFK 85 (103)
Q Consensus 75 ~~~~GDIVvf~ 85 (103)
.+..||.|.|.
T Consensus 46 ~i~vGD~V~ve 56 (72)
T PRK00276 46 RILPGDKVTVE 56 (72)
T ss_pred ccCCCCEEEEE
Confidence 37889999998
No 109
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=31.38 E-value=1.5e+02 Score=19.15 Aligned_cols=15 Identities=20% Similarity=0.392 Sum_probs=10.0
Q ss_pred CCCCCCCcEEEEEeC
Q psy3466 73 EEPVRVGEIVVFKVE 87 (103)
Q Consensus 73 ~~~~~~GDIVvf~~~ 87 (103)
...++.|+.+..-..
T Consensus 77 ~~~I~~Gq~L~IP~~ 91 (103)
T PRK14125 77 SGHIKAGDKLVIPVL 91 (103)
T ss_pred CCcCCCCCEEEEecC
Confidence 346788888877433
No 110
>PRK00529 elongation factor P; Validated
Probab=31.02 E-value=81 Score=22.41 Aligned_cols=37 Identities=16% Similarity=0.312 Sum_probs=24.4
Q ss_pred Cccc-cccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEEE
Q psy3466 55 SMEP-AFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRV 97 (103)
Q Consensus 55 SM~P-tl~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikRV 97 (103)
+..| +|.+|=.+-+- .-++.||.|..+..... |+.|+
T Consensus 148 ~~K~A~letG~~v~VP----~fI~~Gd~I~v~T~~g~--y~~R~ 185 (186)
T PRK00529 148 GTKPATLETGAVVQVP----LFINEGEKIKVDTRTGE--YVERA 185 (186)
T ss_pred CcccEEEcCCCEEEeC----CeecCCCEEEEECCCCc--EEeec
Confidence 4444 34566544443 34899999998877544 99986
No 111
>TIGR02303 HpaG-C-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit. This model represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation. In E. coli and some other species this enzyme is encoded by a single polypeptide containing both this domain and the closely related N-terminal domain (TIGR02305). In other species such as Pasteurella multocida these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).
Probab=30.76 E-value=63 Score=23.94 Aligned_cols=31 Identities=23% Similarity=0.467 Sum_probs=24.0
Q ss_pred cccCCCEEEEeec-CCCCCCCCcEEEEEeCCC
Q psy3466 59 AFHRGDLLFLTNY-QEEPVRVGEIVVFKVEGR 89 (103)
Q Consensus 59 tl~~gD~v~v~~~-~~~~~~~GDIVvf~~~~~ 89 (103)
||++||+|+.-.. ....++.||.+...-.+-
T Consensus 204 tL~pGDvIlTGTp~g~~~l~~GD~v~~~i~gl 235 (245)
T TIGR02303 204 TLEPGDVILTGTPKGLSDVKPGDVVRLEIEGV 235 (245)
T ss_pred CcCCCCEEEcCCCCCCeEcCCCCEEEEEEcCc
Confidence 7999999998763 234689999998877654
No 112
>COG3008 PqiB Paraquat-inducible protein B [General function prediction only]
Probab=30.64 E-value=62 Score=27.27 Aligned_cols=55 Identities=11% Similarity=0.125 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCeEEEeCCCccccccCCCEEEEee--cCCCCCCCCcEE
Q psy3466 17 FLYQVLSFGMIVSSALMIWKGLMVLTGSESPIVVVLSGSMEPAFHRGDLLFLTN--YQEEPVRVGEIV 82 (103)
Q Consensus 17 ~~~~i~~i~~~~~i~~li~~~~~~~~g~~~~~~~V~g~SM~Ptl~~gD~v~v~~--~~~~~~~~GDIV 82 (103)
---|++.++.+++.++++|..+-.. |.+..=++.++|-+...| .+...++.|=|=
T Consensus 21 SpiWllPivAl~igawL~~~~~~~~-----------G~~Itl~f~saeGIeaGKT~Iry~gvdVG~V~ 77 (553)
T COG3008 21 SPIWLLPIVALLIGAWLLFQHVQDR-----------GPEITLTFESAEGIEAGKTPIRYQGVDVGVVT 77 (553)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHhc-----------CCeEEEEecCccccccCcceEEecceeeeEEE
Confidence 3458888887777777777665543 455555677788887777 233555555443
No 113
>PHA03164 hypothetical protein; Provisional
Probab=30.28 E-value=88 Score=19.68 Aligned_cols=13 Identities=23% Similarity=0.455 Sum_probs=5.2
Q ss_pred HHHHHHHHHHHHH
Q psy3466 22 LSFGMIVSSALMI 34 (103)
Q Consensus 22 ~~i~~~~~i~~li 34 (103)
+.+++++++++++
T Consensus 66 LaIamILfiifvl 78 (88)
T PHA03164 66 LAIAMILFIIFVL 78 (88)
T ss_pred HHHHHHHHHHHHH
Confidence 3344444444333
No 114
>KOG1535|consensus
Probab=29.82 E-value=68 Score=23.77 Aligned_cols=30 Identities=13% Similarity=0.314 Sum_probs=22.8
Q ss_pred cccCCCEEEEee-cCCCCCCCCcEEEEEeCC
Q psy3466 59 AFHRGDLLFLTN-YQEEPVRVGEIVVFKVEG 88 (103)
Q Consensus 59 tl~~gD~v~v~~-~~~~~~~~GDIVvf~~~~ 88 (103)
||.+||.++.-. ..-..++.||++-..-.+
T Consensus 176 tL~~GDvILTGTP~GVg~v~~Gd~i~~ei~~ 206 (217)
T KOG1535|consen 176 TLEPGDVILTGTPEGVGEVKPGDVIQCELLE 206 (217)
T ss_pred eecCCCEEEecCCCccccccCCCEEEecccc
Confidence 577899998876 234678899999887654
No 115
>PRK14578 elongation factor P; Provisional
Probab=29.76 E-value=86 Score=22.58 Aligned_cols=37 Identities=14% Similarity=0.199 Sum_probs=23.8
Q ss_pred Cccc-cccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEEE
Q psy3466 55 SMEP-AFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRV 97 (103)
Q Consensus 55 SM~P-tl~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikRV 97 (103)
+..| ++..|=.|-+- .-++.||.|..+..... |+.|+
T Consensus 150 ~~KpA~leTG~~v~VP----~FI~~Gd~I~VdT~~g~--Y~~R~ 187 (187)
T PRK14578 150 QTKEAVLETGLRLQVP----PYLESGEKIKVDTRDGR--FISRA 187 (187)
T ss_pred CcceEEEcCCCEEEeC----CcccCCCEEEEECCCCc--EEeeC
Confidence 3343 34556444442 34899999998877544 99885
No 116
>PRK07432 5'-methylthioadenosine phosphorylase; Provisional
Probab=29.44 E-value=51 Score=25.35 Aligned_cols=28 Identities=21% Similarity=0.216 Sum_probs=21.4
Q ss_pred CCCCCeEEEeCCCccccccCCCEEEEee
Q psy3466 43 GSESPIVVVLSGSMEPAFHRGDLLFLTN 70 (103)
Q Consensus 43 g~~~~~~~V~g~SM~Ptl~~gD~v~v~~ 70 (103)
|...-+.+-..+|+.|.+++||+++.+.
T Consensus 79 Gv~~ii~tna~Gsln~~~~pGdlvv~~D 106 (290)
T PRK07432 79 GVEYLISASAVGSLKEEAKPLDMVVPDQ 106 (290)
T ss_pred CCCEEEEEeccccccCCCCCCCEEeecc
Confidence 4333245566789999999999999887
No 117
>TIGR02178 yeiP elongation factor P-like protein YeiP. This model represents the family of Escherichia coli protein YeiP, a close homolog of elongation factor P (TIGR00038) and probably itself a translation factor. Member of this family are found only in some Gammaproteobacteria, including E. coli and Vibrio cholerae.
Probab=28.95 E-value=70 Score=23.03 Aligned_cols=37 Identities=19% Similarity=0.346 Sum_probs=24.4
Q ss_pred Cccc-cccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEEE
Q psy3466 55 SMEP-AFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRV 97 (103)
Q Consensus 55 SM~P-tl~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikRV 97 (103)
++.| +|.+|=.|-+- --++.||.|..+..... |+.|+
T Consensus 149 ~~KpA~LeTG~~v~VP----~FI~~Gd~IkVdTrtg~--Y~~R~ 186 (186)
T TIGR02178 149 RPKPAKLITGLVVQVP----EYITTGERILINTTERA--FMGRA 186 (186)
T ss_pred CcccEEEcCCCEEEeC----CeecCCCEEEEECCCCc--EEccC
Confidence 4454 45566555443 34899999999876544 88885
No 118
>PF00877 NLPC_P60: NlpC/P60 family; InterPro: IPR000064 The Escherichia coli NLPC/Listeria P60 domain occurs at the C terminus of a number of different bacterial and viral proteins. The viral proteins are either described as tail assembly proteins or Gp19. In bacteria, the proteins are variously described as being putative tail component of prophage, invasin, invasion associated protein, putative lipoprotein, cell wall hydrolase, or putative endopeptidase. The E. coli NLPC/Listeria P60 domain is contained within the boundaries of the cysteine peptidase domain that defines the MEROPS peptidase family C40 (clan C-). A type example being dipeptidyl-peptidase VI from Bacillus sphaericus and gamma-glutamyl-diamino acid-endopeptidase precursor from Lactococcus lactis 3.4.19.11 from EC. This group also contains proteins classified as non-peptidase homologues in that they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the C40 family. ; PDB: 3PVQ_B 3GT2_A 3NPF_B 2K1G_A 3I86_A 3S0Q_A 2XIV_A 3PBC_A 3NE0_A 3M1U_B ....
Probab=28.92 E-value=33 Score=21.41 Aligned_cols=13 Identities=23% Similarity=0.601 Sum_probs=11.0
Q ss_pred CCCCCCcEEEEEe
Q psy3466 74 EPVRVGEIVVFKV 86 (103)
Q Consensus 74 ~~~~~GDIVvf~~ 86 (103)
.++++||++.|+.
T Consensus 50 ~~~~pGDlif~~~ 62 (105)
T PF00877_consen 50 SELQPGDLIFFKG 62 (105)
T ss_dssp GG-TTTEEEEEEG
T ss_pred hcCCcccEEEEeC
Confidence 6899999999987
No 119
>PRK05740 secE preprotein translocase subunit SecE; Reviewed
Probab=28.62 E-value=1.5e+02 Score=18.73 Aligned_cols=21 Identities=10% Similarity=0.254 Sum_probs=12.8
Q ss_pred hHHHHHHHHhhhH---HHHHHHHH
Q psy3466 2 IQDAINDLKRLNK---RQFLYQVL 22 (103)
Q Consensus 2 ~~~~~~~~~~~~~---r~~~~~i~ 22 (103)
+++..+++|+..+ ++..+...
T Consensus 40 ~k~v~~ElkKV~WPtr~e~~~~t~ 63 (92)
T PRK05740 40 AKESRTEVRKVVWPTRQETLQTTL 63 (92)
T ss_pred HHHHHHHhhhccCcCHHHHHhHHH
Confidence 4677888888444 45554443
No 120
>cd06829 PLPDE_III_CANSDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase. Carboxynorspermidine decarboxylase (CANSDC) catalyzes the decarboxylation of carboxynorspermidine, the last step in the biosynthesis of norspermidine. It is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC), which are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. Based on this similarity, CANSDC may require homodimer formation and the presence of the PLP cofactor for its catalytic activity.
Probab=28.52 E-value=78 Score=24.25 Aligned_cols=30 Identities=27% Similarity=0.426 Sum_probs=20.4
Q ss_pred ccccCCCEEEEeecCCCCCCCCcEEEEEeCC
Q psy3466 58 PAFHRGDLLFLTNYQEEPVRVGEIVVFKVEG 88 (103)
Q Consensus 58 Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~ 88 (103)
|+=.++|.+. +.....+++.||.++|.+-|
T Consensus 295 p~C~s~D~l~-~~~~~~~l~~GD~l~~~~~G 324 (346)
T cd06829 295 NSCLAGDVIG-DYSFDEPLQVGDRLVFEDMA 324 (346)
T ss_pred CCCCcccEEe-ecccCCCCCCCCEEEEeCch
Confidence 4456778774 32223468999999998665
No 121
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=28.34 E-value=54 Score=18.86 Aligned_cols=12 Identities=17% Similarity=0.277 Sum_probs=10.0
Q ss_pred CCCCCcEEEEEe
Q psy3466 75 PVRVGEIVVFKV 86 (103)
Q Consensus 75 ~~~~GDIVvf~~ 86 (103)
.+..||.|.|+.
T Consensus 40 ~~~vGD~V~~~~ 51 (64)
T cd04451 40 RILPGDRVKVEL 51 (64)
T ss_pred ccCCCCEEEEEE
Confidence 478899999984
No 122
>cd06836 PLPDE_III_ODC_DapDC_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Uncharacterized Proteins with similarity to Ornithine and Diaminopimelate Decarboxylases. This subfamily contains uncharacterized proteins with similarity to ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Proteins in this subfamily may function as PLP-dependent decarbo
Probab=28.21 E-value=86 Score=24.38 Aligned_cols=29 Identities=24% Similarity=0.378 Sum_probs=19.4
Q ss_pred cccCCCEEEEeecCCCCCCCCcEEEEEeCC
Q psy3466 59 AFHRGDLLFLTNYQEEPVRVGEIVVFKVEG 88 (103)
Q Consensus 59 tl~~gD~v~v~~~~~~~~~~GDIVvf~~~~ 88 (103)
+=.++|.+.-+. ...+++.||+++|..-|
T Consensus 328 ~C~~~D~l~~~~-~lp~l~~GD~l~~~~~G 356 (379)
T cd06836 328 CCFAGDVLAKER-ALPPLEPGDYVAVHDTG 356 (379)
T ss_pred CCCCCCEEeecc-cCCCCCCCCEEEEeCCC
Confidence 334667655443 23469999999998655
No 123
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.02 E-value=43 Score=22.19 Aligned_cols=14 Identities=14% Similarity=0.536 Sum_probs=12.1
Q ss_pred CCCCCCCcEEEEEe
Q psy3466 73 EEPVRVGEIVVFKV 86 (103)
Q Consensus 73 ~~~~~~GDIVvf~~ 86 (103)
.+.+++||.|+|+.
T Consensus 31 rr~ik~GD~IiF~~ 44 (111)
T COG4043 31 RRQIKPGDKIIFNG 44 (111)
T ss_pred hcCCCCCCEEEEcC
Confidence 47899999999974
No 124
>cd04092 mtEFG2_II_like mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG1s are n
Probab=27.69 E-value=86 Score=18.67 Aligned_cols=12 Identities=25% Similarity=0.398 Sum_probs=8.0
Q ss_pred CCCCCCcEEEEE
Q psy3466 74 EPVRVGEIVVFK 85 (103)
Q Consensus 74 ~~~~~GDIVvf~ 85 (103)
++...|||+...
T Consensus 59 ~~~~aGdI~~i~ 70 (83)
T cd04092 59 PSLSAGNIGVIT 70 (83)
T ss_pred CeeCCCCEEEEE
Confidence 456778887653
No 125
>cd06541 ASCH ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery.
Probab=27.61 E-value=1.3e+02 Score=19.12 Aligned_cols=26 Identities=12% Similarity=0.210 Sum_probs=15.9
Q ss_pred CCCCCCcEEEEEeCCCCcCEEEEEEEe
Q psy3466 74 EPVRVGEIVVFKVEGRDIPIVHRVLKL 100 (103)
Q Consensus 74 ~~~~~GDIVvf~~~~~~~~~ikRVi~~ 100 (103)
..++.||.++|...+ ....+=|++++
T Consensus 29 ~~~k~Gd~~i~~~~~-~~~~~i~v~~V 54 (105)
T cd06541 29 QLPKAGDYLIILDGQ-QPLAIAEVVKV 54 (105)
T ss_pred cCCCCCCEEEEecCC-CcEEEEEEEEE
Confidence 568888888886544 33345555544
No 126
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=27.53 E-value=1e+02 Score=22.02 Aligned_cols=27 Identities=33% Similarity=0.556 Sum_probs=16.4
Q ss_pred CCCCcEEEEEeCCC-------------CcCEEEEEEEecC
Q psy3466 76 VRVGEIVVFKVEGR-------------DIPIVHRVLKLHE 102 (103)
Q Consensus 76 ~~~GDIVvf~~~~~-------------~~~~ikRVi~~~~ 102 (103)
++.||.|++..|+. ..+.+|||.|+++
T Consensus 54 vt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpg 93 (173)
T COG4959 54 VTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPG 93 (173)
T ss_pred cccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCC
Confidence 46666666665542 1346788877765
No 127
>cd04088 EFG_mtEFG_II EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more compl
Probab=27.26 E-value=86 Score=18.55 Aligned_cols=12 Identities=25% Similarity=0.338 Sum_probs=7.5
Q ss_pred CCCCCCcEEEEE
Q psy3466 74 EPVRVGEIVVFK 85 (103)
Q Consensus 74 ~~~~~GDIVvf~ 85 (103)
.+...|||+...
T Consensus 59 ~~~~aGdI~~i~ 70 (83)
T cd04088 59 EEAGAGDIGAVA 70 (83)
T ss_pred CEeCCCCEEEEE
Confidence 345667777663
No 128
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=27.12 E-value=1.4e+02 Score=22.19 Aligned_cols=34 Identities=29% Similarity=0.461 Sum_probs=24.0
Q ss_pred EEEeCCCccccccCCCEEEEeecCCCCCCCCcEEEEE
Q psy3466 49 VVVLSGSMEPAFHRGDLLFLTNYQEEPVRVGEIVVFK 85 (103)
Q Consensus 49 ~~V~g~SM~Ptl~~gD~v~v~~~~~~~~~~GDIVvf~ 85 (103)
..|..++-+=-..+||.+.++++. .+.||-|.|+
T Consensus 3 AVI~~gGKQykV~~Gd~i~Vekl~---~~~G~~i~~~ 36 (221)
T PRK12278 3 AVIKTGGKQYKVQAGDLLRVEKLA---AEAGETVQFG 36 (221)
T ss_pred EEEEeCCEEEEEeCCCEEEEeccC---CCCCCEEEEe
Confidence 456666777677899999999862 3557766664
No 129
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=26.99 E-value=92 Score=17.82 Aligned_cols=21 Identities=29% Similarity=0.490 Sum_probs=13.7
Q ss_pred CCCCcEEEEEeCCCCcCEEEEE
Q psy3466 76 VRVGEIVVFKVEGRDIPIVHRV 97 (103)
Q Consensus 76 ~~~GDIVvf~~~~~~~~~ikRV 97 (103)
++.||+|..++.+. ...|..+
T Consensus 1 f~~GDvV~LKSGGp-~MTV~~v 21 (53)
T PF09926_consen 1 FKIGDVVQLKSGGP-RMTVTEV 21 (53)
T ss_pred CCCCCEEEEccCCC-CeEEEEc
Confidence 36788888887764 4555544
No 130
>PHA02844 putative transmembrane protein; Provisional
Probab=26.86 E-value=1.3e+02 Score=18.60 Aligned_cols=16 Identities=13% Similarity=0.360 Sum_probs=6.2
Q ss_pred HHHHHHHHHHHHHHHH
Q psy3466 20 QVLSFGMIVSSALMIW 35 (103)
Q Consensus 20 ~i~~i~~~~~i~~li~ 35 (103)
|++.++.+++++++.+
T Consensus 51 ~ii~i~~v~~~~~~~f 66 (75)
T PHA02844 51 WILTIIFVVFATFLTF 66 (75)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3333333344443333
No 131
>PRK12426 elongation factor P; Provisional
Probab=26.80 E-value=94 Score=22.38 Aligned_cols=38 Identities=16% Similarity=0.378 Sum_probs=25.2
Q ss_pred CCccc-cccCCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEEE
Q psy3466 54 GSMEP-AFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRV 97 (103)
Q Consensus 54 ~SM~P-tl~~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikRV 97 (103)
++..| ||..|=.|-|- --++.||.|..+..... |+.|+
T Consensus 147 ~~~KpAtLeTG~~V~VP----~FI~~Gd~IkVdT~~ge--Y~~R~ 185 (185)
T PRK12426 147 GGAKKALLETGVEVLVP----PFVEIGDVIKVDTRTCE--YIQRV 185 (185)
T ss_pred CCcccEEEcCCCEEEeC----CcccCCCEEEEECCCCe--EEeeC
Confidence 44555 45667555553 34899999988776544 88885
No 132
>PF07798 DUF1640: Protein of unknown function (DUF1640); InterPro: IPR024461 This family consists of uncharacterised proteins.
Probab=26.73 E-value=2.2e+02 Score=19.76 Aligned_cols=12 Identities=8% Similarity=-0.139 Sum_probs=6.9
Q ss_pred HHHHHHHHHHHH
Q psy3466 16 QFLYQVLSFGMI 27 (103)
Q Consensus 16 ~~~~~i~~i~~~ 27 (103)
..++|+..++++
T Consensus 153 ~~lr~~~g~i~~ 164 (177)
T PF07798_consen 153 DTLRWLVGVIFG 164 (177)
T ss_pred HHHHHHHHHHHH
Confidence 466777654443
No 133
>PRK00809 hypothetical protein; Provisional
Probab=26.58 E-value=72 Score=21.86 Aligned_cols=14 Identities=21% Similarity=0.413 Sum_probs=7.6
Q ss_pred CCCCCcEEEEEeCC
Q psy3466 75 PVRVGEIVVFKVEG 88 (103)
Q Consensus 75 ~~~~GDIVvf~~~~ 88 (103)
..+.||-++|++++
T Consensus 34 ~Mk~GD~v~fYhs~ 47 (144)
T PRK00809 34 KVKPGDKLIIYVSQ 47 (144)
T ss_pred hCCCCCEEEEEECC
Confidence 35556666655554
No 134
>PRK11507 ribosome-associated protein; Provisional
Probab=26.23 E-value=40 Score=20.63 Aligned_cols=15 Identities=20% Similarity=0.288 Sum_probs=12.0
Q ss_pred CCCCCCCCcEEEEEe
Q psy3466 72 QEEPVRVGEIVVFKV 86 (103)
Q Consensus 72 ~~~~~~~GDIVvf~~ 86 (103)
+.+.+.+||+|.|..
T Consensus 49 RgkKl~~GD~V~~~g 63 (70)
T PRK11507 49 KRCKIVAGQTVSFAG 63 (70)
T ss_pred cCCCCCCCCEEEECC
Confidence 347899999999953
No 135
>cd03703 aeIF5B_II aeIF5B_II: This family represents the domain II of archeal and eukaryotic aeIF5B. aeIF5B is a homologue of prokaryotic Initiation Factor 2 (IF2). Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of joining of 60S subunits. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains of EF1A, eEF1A and aeIF2gamma.
Probab=25.98 E-value=1.1e+02 Score=20.24 Aligned_cols=13 Identities=23% Similarity=0.337 Sum_probs=7.6
Q ss_pred CCCCCCcEEEEEe
Q psy3466 74 EPVRVGEIVVFKV 86 (103)
Q Consensus 74 ~~~~~GDIVvf~~ 86 (103)
..++.||.|++-.
T Consensus 25 GtL~~GD~Iv~g~ 37 (110)
T cd03703 25 GTLREGDTIVVCG 37 (110)
T ss_pred CeEecCCEEEEcc
Confidence 4466666666643
No 136
>TIGR01697 PNPH-PUNA-XAPA inosine guanosine and xanthosine phosphorylase family. Sequences from Clostridium and Thermotoga fall between these last two clades and are uncharacterized with respect to substrate range and operon.
Probab=25.93 E-value=48 Score=24.41 Aligned_cols=19 Identities=32% Similarity=0.856 Sum_probs=16.8
Q ss_pred eCCCccccccCCCEEEEee
Q psy3466 52 LSGSMEPAFHRGDLLFLTN 70 (103)
Q Consensus 52 ~g~SM~Ptl~~gD~v~v~~ 70 (103)
..+|+.|.++.||.|+.+.
T Consensus 91 saGsl~~~l~~GDiVI~~~ 109 (248)
T TIGR01697 91 AAGGLNPDFKPGDLMIIKD 109 (248)
T ss_pred ccccCCCCCCCCCEEEEhh
Confidence 3469999999999999987
No 137
>PF00829 Ribosomal_L21p: Ribosomal prokaryotic L21 protein; InterPro: IPR001787 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 L21 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L21 is known to bind to the 23S rRNA in the presence of L20. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups: Bacterial L21. Marchantia polymorpha chloroplast L21. Cyanelle L21. Plant chloroplast L21 (nuclear-encoded). Bacterial L21 is a protein of about 100 amino-acid residues, the mature form of the spinach chloroplast L21 has 200 residues.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XG0_V 2X9S_V 2XG2_V 3UZ1_2 2Y19_V 2WDL_V 3V23_V 2WRO_V 2WRL_V 2Y11_V ....
Probab=25.89 E-value=1.2e+02 Score=19.23 Aligned_cols=33 Identities=15% Similarity=0.343 Sum_probs=21.7
Q ss_pred EEeCCCccccccCCCEEEEeecCCCCCCCCcEEEEE
Q psy3466 50 VVLSGSMEPAFHRGDLLFLTNYQEEPVRVGEIVVFK 85 (103)
Q Consensus 50 ~V~g~SM~Ptl~~gD~v~v~~~~~~~~~~GDIVvf~ 85 (103)
.|..++=+=-..+||.+.+++. +.+.||-+.|+
T Consensus 4 Ii~~ggkQykV~~gd~i~v~~l---~~~~G~~i~l~ 36 (96)
T PF00829_consen 4 IIEIGGKQYKVEEGDVIDVERL---DAEVGDKIELD 36 (96)
T ss_dssp EEESSSEEEEESSSEEEEEEST---SSSTTSEEEET
T ss_pred EEEECCEEEEEeCCCEEEECCc---CcCCCCEEEEE
Confidence 3444444445678899999875 55678777664
No 138
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=25.74 E-value=1.1e+02 Score=18.45 Aligned_cols=12 Identities=17% Similarity=0.299 Sum_probs=6.0
Q ss_pred cccCCCEEEEee
Q psy3466 59 AFHRGDLLFLTN 70 (103)
Q Consensus 59 tl~~gD~v~v~~ 70 (103)
+++.||.+.+.+
T Consensus 26 ~v~~Gd~v~~~P 37 (81)
T cd03695 26 SIRVGDEVVVLP 37 (81)
T ss_pred eEECCCEEEEcC
Confidence 344556554443
No 139
>COG4079 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.53 E-value=1.1e+02 Score=23.51 Aligned_cols=27 Identities=22% Similarity=0.230 Sum_probs=17.4
Q ss_pred cCCCEEEEeecCCCCCCCCcEEEEEeC
Q psy3466 61 HRGDLLFLTNYQEEPVRVGEIVVFKVE 87 (103)
Q Consensus 61 ~~gD~v~v~~~~~~~~~~GDIVvf~~~ 87 (103)
-|||.|+-.--...++++||.|+.++.
T Consensus 247 gPg~~v~m~v~~~g~~~pGd~vvv~dg 273 (293)
T COG4079 247 GPGEEVVMAVEGNGEVEPGDRVVVKDG 273 (293)
T ss_pred CCCceEEEEEccCCccCCCCEEEEecC
Confidence 366666654433456888888888754
No 140
>COG0690 SecE Preprotein translocase subunit SecE [Intracellular trafficking and secretion]
Probab=25.52 E-value=1.6e+02 Score=17.74 Aligned_cols=13 Identities=15% Similarity=0.320 Sum_probs=8.1
Q ss_pred hHHHHHHHHhhhH
Q psy3466 2 IQDAINDLKRLNK 14 (103)
Q Consensus 2 ~~~~~~~~~~~~~ 14 (103)
+++...++++..|
T Consensus 24 ~~~~~~E~~KV~W 36 (73)
T COG0690 24 FKEVRKELKKVVW 36 (73)
T ss_pred HHHHHHHHHhccC
Confidence 3566777888433
No 141
>TIGR01700 PNPH purine nucleoside phosphorylase I, inosine and guanosine-specific. Several metazoan enzymes (PNPH) are well characterized including the human and bovine enzymes which have been crystallized.
Probab=25.30 E-value=45 Score=24.64 Aligned_cols=19 Identities=32% Similarity=0.849 Sum_probs=16.9
Q ss_pred eCCCccccccCCCEEEEee
Q psy3466 52 LSGSMEPAFHRGDLLFLTN 70 (103)
Q Consensus 52 ~g~SM~Ptl~~gD~v~v~~ 70 (103)
..+|+.|.+++||.|+.+.
T Consensus 91 saGsl~~~l~~GDiVi~~d 109 (249)
T TIGR01700 91 AAGGINPEFKVGDLMLIRD 109 (249)
T ss_pred ccccCCCCCCCCCEEEEhh
Confidence 3469999999999999987
No 142
>CHL00010 infA translation initiation factor 1
Probab=25.29 E-value=83 Score=19.20 Aligned_cols=10 Identities=20% Similarity=0.302 Sum_probs=7.9
Q ss_pred CCCCcEEEEE
Q psy3466 76 VRVGEIVVFK 85 (103)
Q Consensus 76 ~~~GDIVvf~ 85 (103)
|..||.|.|.
T Consensus 47 ~~vGD~V~ve 56 (78)
T CHL00010 47 ILPGDRVKVE 56 (78)
T ss_pred cCCCCEEEEE
Confidence 5678888887
No 143
>PHA02650 hypothetical protein; Provisional
Probab=25.24 E-value=1.1e+02 Score=19.17 Aligned_cols=12 Identities=17% Similarity=0.138 Sum_probs=4.5
Q ss_pred HHHHHHHHHHHH
Q psy3466 26 MIVSSALMIWKG 37 (103)
Q Consensus 26 ~~~~i~~li~~~ 37 (103)
.+++++++.+.+
T Consensus 58 ~v~i~~l~~flY 69 (81)
T PHA02650 58 SLIIVALFSFFV 69 (81)
T ss_pred HHHHHHHHHHHH
Confidence 333333333333
No 144
>PF07193 DUF1408: Protein of unknown function (DUF1408); InterPro: IPR009848 This entry is represented by Bacteriophage bIL285, Orf11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Lactococcus lactis and related phage proteins of around 75 residues in length. The function of this family is unknown.
Probab=25.20 E-value=93 Score=18.91 Aligned_cols=15 Identities=27% Similarity=0.290 Sum_probs=12.1
Q ss_pred ccccccCCCEEEEee
Q psy3466 56 MEPAFHRGDLLFLTN 70 (103)
Q Consensus 56 M~Ptl~~gD~v~v~~ 70 (103)
|+.++.+|-.|..-+
T Consensus 1 m~t~i~ngr~v~~ip 15 (75)
T PF07193_consen 1 METTIINGRKVRLIP 15 (75)
T ss_pred CceEEEcCcEEEEec
Confidence 778889998887766
No 145
>PF12666 PrgI: PrgI family protein; InterPro: IPR024414 This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 116 and 146 amino acids in length. PrgI is found encoded on plasmids of Enterococcus faecalis, its function is not known.
Probab=24.85 E-value=1.1e+02 Score=18.79 Aligned_cols=18 Identities=22% Similarity=0.187 Sum_probs=9.2
Q ss_pred hhHHHHHHHHHHHHHHHH
Q psy3466 12 LNKRQFLYQVLSFGMIVS 29 (103)
Q Consensus 12 ~~~r~~~~~i~~i~~~~~ 29 (103)
+.+|++.-.+...++++.
T Consensus 17 lT~RQl~~l~~~~~~~~~ 34 (93)
T PF12666_consen 17 LTLRQLICLAIGALVGVG 34 (93)
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 556776554444444433
No 146
>KOG1666|consensus
Probab=24.81 E-value=3e+02 Score=20.53 Aligned_cols=14 Identities=14% Similarity=0.181 Sum_probs=7.5
Q ss_pred HHHHHHhhhHHHHH
Q psy3466 5 AINDLKRLNKRQFL 18 (103)
Q Consensus 5 ~~~~~~~~~~r~~~ 18 (103)
+..+++.|..|-..
T Consensus 182 S~kiL~tM~RR~~~ 195 (220)
T KOG1666|consen 182 SRKILTTMTRRLIR 195 (220)
T ss_pred HHHHHHHHHHHHHH
Confidence 44556667555443
No 147
>TIGR01698 PUNP purine nucleotide phosphorylase. methylthioadenosine.
Probab=24.78 E-value=1.2e+02 Score=22.49 Aligned_cols=23 Identities=13% Similarity=0.423 Sum_probs=19.3
Q ss_pred eEEEeCCCccccccCCCEEEEee
Q psy3466 48 IVVVLSGSMEPAFHRGDLLFLTN 70 (103)
Q Consensus 48 ~~~V~g~SM~Ptl~~gD~v~v~~ 70 (103)
+.+-..+|+.|.+++||+++++.
T Consensus 87 i~tna~Gsl~~~~~pGdlv~~~D 109 (237)
T TIGR01698 87 ILTNAAGGLRQDWGPGTPVLISD 109 (237)
T ss_pred EEEcccccCCCCCCCCCEEeech
Confidence 35555679999999999999987
No 148
>COG4127 Uncharacterized conserved protein [Function unknown]
Probab=24.78 E-value=52 Score=25.62 Aligned_cols=26 Identities=12% Similarity=0.308 Sum_probs=17.7
Q ss_pred CCCCCCcEEEEEeCCCCcCEEEEEEE
Q psy3466 74 EPVRVGEIVVFKVEGRDIPIVHRVLK 99 (103)
Q Consensus 74 ~~~~~GDIVvf~~~~~~~~~ikRVi~ 99 (103)
.+++.||.|+-..+...+++|.||-+
T Consensus 71 neI~KGDlvi~y~k~~r~y~IGkVts 96 (318)
T COG4127 71 NEIQKGDLVITYSKSNRTYLIGKVTS 96 (318)
T ss_pred HHhccCcEEEeecccCceEEEEEecC
Confidence 45777777776666555677877754
No 149
>PRK02268 hypothetical protein; Provisional
Probab=24.65 E-value=78 Score=21.84 Aligned_cols=13 Identities=8% Similarity=0.432 Sum_probs=7.6
Q ss_pred CCCCCcEEEEEeC
Q psy3466 75 PVRVGEIVVFKVE 87 (103)
Q Consensus 75 ~~~~GDIVvf~~~ 87 (103)
..++||-++|++|
T Consensus 35 RmkpGD~ivyYsp 47 (141)
T PRK02268 35 RMKPGDWIIYYSP 47 (141)
T ss_pred cCCCCCEEEEEec
Confidence 3466666666554
No 150
>cd03689 RF3_II RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the ribosome after release of the nascent polypeptide. RF3 in the GDP state binds to the ribosomal class I RF complex, followed by an exchange of GDP for GTP and release of the class I RF. Sequence comparison of class II release factors with elongation factors shows that prokaryotic RF3 is more similar to EF-G whereas eukaryotic eRF3 is more similar to eEF1A, implying that their precise function may differ.
Probab=24.57 E-value=1.7e+02 Score=17.72 Aligned_cols=9 Identities=22% Similarity=0.431 Sum_probs=4.9
Q ss_pred CCCCcEEEE
Q psy3466 76 VRVGEIVVF 84 (103)
Q Consensus 76 ~~~GDIVvf 84 (103)
...|||++.
T Consensus 62 a~aGdIv~v 70 (85)
T cd03689 62 AYPGDIIGL 70 (85)
T ss_pred ECCCCEEEE
Confidence 445566555
No 151
>PRK08202 purine nucleoside phosphorylase; Provisional
Probab=24.56 E-value=52 Score=24.67 Aligned_cols=21 Identities=29% Similarity=0.746 Sum_probs=17.7
Q ss_pred EEeCCCccccccCCCEEEEee
Q psy3466 50 VVLSGSMEPAFHRGDLLFLTN 70 (103)
Q Consensus 50 ~V~g~SM~Ptl~~gD~v~v~~ 70 (103)
+=..+|+.|.+++||+|+.+.
T Consensus 111 tgaaGsL~~~l~~GDiVi~~d 131 (272)
T PRK08202 111 TNAAGGLNPDFGPGDLMLISD 131 (272)
T ss_pred ecccccCCCCCCCCCEEEEch
Confidence 334569999999999999987
No 152
>PF08940 DUF1918: Domain of unknown function (DUF1918); InterPro: IPR015035 This domain is found in various hypothetical bacterial proteins, and has no known function. ; PDB: 2A7Y_A.
Probab=24.31 E-value=58 Score=19.24 Aligned_cols=36 Identities=31% Similarity=0.395 Sum_probs=19.6
Q ss_pred cCCCEEEEeecC-CCCCCCCcEEEEEeCCCCcCEEEE
Q psy3466 61 HRGDLLFLTNYQ-EEPVRVGEIVVFKVEGRDIPIVHR 96 (103)
Q Consensus 61 ~~gD~v~v~~~~-~~~~~~GDIVvf~~~~~~~~~ikR 96 (103)
+.||++.+.... -..-+.|.|+-.+.++..-.|.=|
T Consensus 4 ~vGD~lvv~g~~vg~~~r~GeIveV~g~dG~PPY~VR 40 (58)
T PF08940_consen 4 SVGDRLVVHGRTVGQPDRHGEIVEVRGPDGSPPYLVR 40 (58)
T ss_dssp -TTEEEEES-TTTS--EEEEEEEE-S-SSS-S-EEEE
T ss_pred CCCCEEEEcCCcCCCCCcEeEEEEEECCCCCCCEEEE
Confidence 578999998632 244567899988777554456544
No 153
>cd06840 PLPDE_III_Bif_AspK_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bifunctional Aspartate Kinase/Diaminopimelate Decarboxylase. Bifunctional aspartate kinase/diaminopimelate decarboxylase (AspK/DapDC, EC 4.1.1.20/EC 2.7.2.4) typically exists in bacteria. These proteins contain an N-terminal AspK region and a C-terminal DapDC region, which contains a PLP-binding TIM-barrel domain followed by beta-sandwich domain, characteristic of fold type III PLP-dependent enzymes. Members of this subfamily have not been fully characterized. Based on their sequence, these proteins may catalyze both reactions catalyzed by AspK and DapDC. AspK catalyzes the phosphorylation of L-aspartate to produce 4-phospho-L-aspartate while DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine.
Probab=24.00 E-value=1.1e+02 Score=23.76 Aligned_cols=30 Identities=20% Similarity=0.370 Sum_probs=20.8
Q ss_pred ccccCCCEEEEeecCCCCCCCCcEEEEEeCC
Q psy3466 58 PAFHRGDLLFLTNYQEEPVRVGEIVVFKVEG 88 (103)
Q Consensus 58 Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~ 88 (103)
|+=.++|.+--+.. ..++++||.++|.+-|
T Consensus 318 p~C~~~D~l~~~~~-lp~l~~GD~l~~~~~G 347 (368)
T cd06840 318 PICESGDVLGRDRL-LPETEEGDVILIANAG 347 (368)
T ss_pred CCcCCCCEEeeccc-CCCCCCCCEEEEecCC
Confidence 44557786655443 3459999999998665
No 154
>TIGR02896 spore_III_AF stage III sporulation protein AF. This family represents the stage III sporulation protein AF of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of this protein is poorly conserved, so only the N-terminal region, which includes two predicted transmembrane domains, is included in the seed alignment.
Probab=23.87 E-value=89 Score=20.44 Aligned_cols=12 Identities=8% Similarity=-0.069 Sum_probs=5.6
Q ss_pred HHHHHHHHHHHH
Q psy3466 18 LYQVLSFGMIVS 29 (103)
Q Consensus 18 ~~~i~~i~~~~~ 29 (103)
..|+..+++.++
T Consensus 4 ~~Wv~~i~~~~i 15 (106)
T TIGR02896 4 KEWVTNIIVLIL 15 (106)
T ss_pred HHHHHHHHHHHH
Confidence 345555444443
No 155
>KOG3208|consensus
Probab=23.69 E-value=1.7e+02 Score=21.91 Aligned_cols=24 Identities=13% Similarity=0.227 Sum_probs=11.3
Q ss_pred hhHHHHHH-HHHHHHHHHHHHHHHH
Q psy3466 12 LNKRQFLY-QVLSFGMIVSSALMIW 35 (103)
Q Consensus 12 ~~~r~~~~-~i~~i~~~~~i~~li~ 35 (103)
++.|+-.+ .++..++.+|+.++++
T Consensus 203 Ik~kkrrdslILa~Vis~C~llllf 227 (231)
T KOG3208|consen 203 IKIKKRRDSLILAAVISVCTLLLLF 227 (231)
T ss_pred HHHHhhhhhHHHHHHHHHHHHHHHH
Confidence 44444333 3445555566555443
No 156
>PRK07823 5'-methylthioadenosine phosphorylase; Validated
Probab=23.48 E-value=71 Score=24.16 Aligned_cols=23 Identities=17% Similarity=0.351 Sum_probs=17.9
Q ss_pred EEEeCCCccccccCCCEEEEeec
Q psy3466 49 VVVLSGSMEPAFHRGDLLFLTNY 71 (103)
Q Consensus 49 ~~V~g~SM~Ptl~~gD~v~v~~~ 71 (103)
.+-..+||.|.+++||+++.+-+
T Consensus 86 ~tnA~Gsln~~~~pGdlvi~dd~ 108 (264)
T PRK07823 86 APCAVGSLRPELGPGTVVVPDQL 108 (264)
T ss_pred EecccccCCCCCCCCCEEEcchh
Confidence 34445799999999999996553
No 157
>COG0019 LysA Diaminopimelate decarboxylase [Amino acid transport and metabolism]
Probab=23.44 E-value=1.1e+02 Score=24.41 Aligned_cols=31 Identities=32% Similarity=0.594 Sum_probs=22.8
Q ss_pred ccccCCCEEEEeecCCCCCCCCcEEEEEeCC
Q psy3466 58 PAFHRGDLLFLTNYQEEPVRVGEIVVFKVEG 88 (103)
Q Consensus 58 Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~ 88 (103)
|+-..||.+.-++.-+...+.||.++|..-+
T Consensus 343 ~~CesgD~~~~d~~lp~~~~~GD~l~i~~aG 373 (394)
T COG0019 343 PTCESGDVLARDRALPEPLKVGDLLVILDAG 373 (394)
T ss_pred CCcCCCCeeeeeeeCCCCCCCCCEEEEcccc
Confidence 5677889888555434566799999997654
No 158
>TIGR02305 HpaG-N-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, N-terminal subunit. This model represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation. In E. coli and some other species this enzyme is encoded by a single polypeptide containing both this domain and the closely related C-terminal domain (TIGR02303). In other species such as Pasteurella multocida these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).
Probab=23.25 E-value=1.3e+02 Score=21.47 Aligned_cols=30 Identities=30% Similarity=0.452 Sum_probs=20.8
Q ss_pred cccCCCEEEEeec-CCCCCCCCcEEEEEeCC
Q psy3466 59 AFHRGDLLFLTNY-QEEPVRVGEIVVFKVEG 88 (103)
Q Consensus 59 tl~~gD~v~v~~~-~~~~~~~GDIVvf~~~~ 88 (103)
+|++||+|+.-.. ....++.||.+...-++
T Consensus 167 ~L~aGdvI~TGT~~g~~~l~~Gd~v~~~i~g 197 (205)
T TIGR02305 167 TLNPGDVLLLGTPEARVEVGPGDRVRVEAEG 197 (205)
T ss_pred CcCCCCEEEeCCCCCCeecCCCCEEEEEEcC
Confidence 4888888877663 23467888888776654
No 159
>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=23.24 E-value=1.2e+02 Score=18.33 Aligned_cols=9 Identities=33% Similarity=0.955 Sum_probs=5.5
Q ss_pred CCCCCCcEE
Q psy3466 74 EPVRVGEIV 82 (103)
Q Consensus 74 ~~~~~GDIV 82 (103)
.++++||++
T Consensus 74 ~d~~~Gdvi 82 (84)
T cd03692 74 NDIKVGDII 82 (84)
T ss_pred ccCCCCCEE
Confidence 366666665
No 160
>COG0261 RplU Ribosomal protein L21 [Translation, ribosomal structure and biogenesis]
Probab=23.17 E-value=2.3e+02 Score=18.63 Aligned_cols=33 Identities=18% Similarity=0.401 Sum_probs=23.0
Q ss_pred EEeCCCccccccCCCEEEEeecCCCCCCCCcEEEEE
Q psy3466 50 VVLSGSMEPAFHRGDLLFLTNYQEEPVRVGEIVVFK 85 (103)
Q Consensus 50 ~V~g~SM~Ptl~~gD~v~v~~~~~~~~~~GDIVvf~ 85 (103)
.+.++.=+=-..+||.+.+++. +...||-|.|.
T Consensus 4 ii~tGGKQykV~~G~~i~vEkl---~~e~g~~v~f~ 36 (103)
T COG0261 4 IIKTGGKQYKVEEGDVIKVEKL---DAEPGDKVEFD 36 (103)
T ss_pred EEEECCEEEEEecCCEEEEEEc---CCCCCCEEEEE
Confidence 4455555555678999999985 45677777774
No 161
>TIGR01047 nspC carboxynorspermidine decarboxylase. This protein is related to diaminopimelate decarboxylase. It is the last enzyme in norspermidine biosynthesis by an unusual pathway shown in Vibrio alginolyticus.
Probab=23.12 E-value=99 Score=24.16 Aligned_cols=30 Identities=27% Similarity=0.316 Sum_probs=19.0
Q ss_pred ccccCCCEEEEeecCCCCCCCCcEEEEEeCC
Q psy3466 58 PAFHRGDLLFLTNYQEEPVRVGEIVVFKVEG 88 (103)
Q Consensus 58 Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~ 88 (103)
|+=.++|.+. +.....+++.||.++|.+-|
T Consensus 309 ~~C~s~D~l~-~~~~lp~l~~GD~l~~~~~G 338 (380)
T TIGR01047 309 CTCLAGDVMG-EYAFDEPLKVGDKLVFLDMI 338 (380)
T ss_pred CCCCcccEEe-ecccCCCCCCCCEEEEcCcC
Confidence 3445667664 32223478899999997654
No 162
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=23.10 E-value=1.1e+02 Score=22.70 Aligned_cols=23 Identities=0% Similarity=-0.057 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q psy3466 17 FLYQVLSFGMIVSSALMIWKGLM 39 (103)
Q Consensus 17 ~~~~i~~i~~~~~i~~li~~~~~ 39 (103)
.+..++.++++++|+++.+.+||
T Consensus 14 ~iLNiaI~IV~lLIiiva~~lf~ 36 (217)
T PF07423_consen 14 KILNIAIGIVSLLIIIVAYQLFF 36 (217)
T ss_pred hhHHHHHHHHHHHHHHHhhhhee
Confidence 44444445555666666655444
No 163
>COG4698 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.84 E-value=1.1e+02 Score=22.39 Aligned_cols=25 Identities=12% Similarity=0.215 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3466 16 QFLYQVLSFGMIVSSALMIWKGLMV 40 (103)
Q Consensus 16 ~~~~~i~~i~~~~~i~~li~~~~~~ 40 (103)
..|+|+..+++++.+++++..+++.
T Consensus 9 n~WKw~f~iLLAln~l~~~~i~~~v 33 (197)
T COG4698 9 NYWKWLFFILLALNTLLAVLIALFV 33 (197)
T ss_pred cHHHHHHHHHHHHHHHHHHHhheee
Confidence 4677877777776666554444443
No 164
>PRK10838 spr outer membrane lipoprotein; Provisional
Probab=22.74 E-value=60 Score=23.37 Aligned_cols=13 Identities=31% Similarity=0.851 Sum_probs=8.6
Q ss_pred CCCCCCcEEEEEe
Q psy3466 74 EPVRVGEIVVFKV 86 (103)
Q Consensus 74 ~~~~~GDIVvf~~ 86 (103)
.++++||+|.|+.
T Consensus 127 ~~lqpGDLVfF~~ 139 (190)
T PRK10838 127 SKLRTGDLVLFRA 139 (190)
T ss_pred CCCCCCcEEEECC
Confidence 4567777777753
No 165
>cd06839 PLPDE_III_Btrk_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Btrk Decarboxylase. This subfamily is composed of Bacillus circulans BtrK decarboxylase and similar proteins. These proteins are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases, eukaryotic ornithine decarboxylases and diaminopimelate decarboxylases. BtrK is presumed to function as a PLP-dependent decarboxylase involved in the biosynthesis of the aminoglycoside antibiotic butirosin. Homodimer formation and the presence of the PLP cofactor may be required for catalytic activity.
Probab=22.41 E-value=1.3e+02 Score=22.97 Aligned_cols=30 Identities=27% Similarity=0.274 Sum_probs=20.8
Q ss_pred ccccCCCEEEEeecCCCCCCCCcEEEEEeCC
Q psy3466 58 PAFHRGDLLFLTNYQEEPVRVGEIVVFKVEG 88 (103)
Q Consensus 58 Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~ 88 (103)
|+-..+|.+.-+.. ..+++.||.++|.+-|
T Consensus 331 ~~C~~~D~~~~~~~-lp~l~~GD~l~~~~~G 360 (382)
T cd06839 331 PLCTPLDLLGRNVE-LPPLEPGDLVAVLQSG 360 (382)
T ss_pred CCCCCCCEEeeccc-CCCCCCCCEEEEecCC
Confidence 44556787764442 3468999999998665
No 166
>PF06071 YchF-GTPase_C: Protein of unknown function (DUF933); InterPro: IPR013029 This domain is found at the C terminus of family of conserved hypothetical proteins found in both prokaryotes and eukaryotes. While the function of these proteins is not known, the crystal structure of P44681 from SWISSPROT from Haemophilus influenzae has been determined []. This protein consists of three domains: an N-terminal domain which has a mononucleotide binding fold typical for the P-loop NTPases, a central domain which forms an alpha-helical coiled coil, and this C-terminal domain which is composed of a six-stranded half-barrel curved around an alpha helix. The central domain and this domain are topologically similar to RNA-binding proteins, while the N-terminal region contains the features typical of GTP-dependent molecular switches. The purified protein was capable of binding both double-stranded nucleic acid and GTP. It was suggested, therefore, that this protein might be part of a nucleoprotein complex and could function as a GTP-dependent translation factor.; PDB: 1NI3_A 1JAL_A 2DWQ_B 2DBY_A 2OHF_A.
Probab=22.41 E-value=65 Score=20.38 Aligned_cols=14 Identities=29% Similarity=0.520 Sum_probs=8.5
Q ss_pred CCCCCCcEEEEEeC
Q psy3466 74 EPVRVGEIVVFKVE 87 (103)
Q Consensus 74 ~~~~~GDIVvf~~~ 87 (103)
.-++.|||+.|+.+
T Consensus 71 YivqDGDIi~f~fN 84 (84)
T PF06071_consen 71 YIVQDGDIIHFRFN 84 (84)
T ss_dssp -B--TTEEEEEEE-
T ss_pred eeEeCCCEEEEEcC
Confidence 46799999999753
No 167
>PRK08931 5'-methylthioadenosine phosphorylase; Provisional
Probab=22.30 E-value=75 Score=24.39 Aligned_cols=23 Identities=13% Similarity=0.378 Sum_probs=19.0
Q ss_pred eEEEeCCCccccccCCCEEEEee
Q psy3466 48 IVVVLSGSMEPAFHRGDLLFLTN 70 (103)
Q Consensus 48 ~~~V~g~SM~Ptl~~gD~v~v~~ 70 (103)
+.+-..+|+.|.+++||+++.+.
T Consensus 84 i~tnA~Gsln~~~~pGd~vi~~D 106 (289)
T PRK08931 84 VSLSACGSFREELPPGTFVIVDQ 106 (289)
T ss_pred EEecccccCCCCCCCCCEEeehh
Confidence 34455679999999999999986
No 168
>PF12791 RsgI_N: Anti-sigma factor N-terminus; InterPro: IPR024449 The heat shock genes in Bacillus subtilis can be classified into several groups according to their regulation [], and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes []. Regulation of sigma factor I is carried out by RsgI from the same operon. This entry represents the N-terminal cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) which has been shown to interact directly with Sigma-I [].
Probab=22.07 E-value=1.5e+02 Score=16.44 Aligned_cols=26 Identities=15% Similarity=0.354 Sum_probs=19.5
Q ss_pred cCCCEEEEeecCCCCCCCCcEEEEEeCC
Q psy3466 61 HRGDLLFLTNYQEEPVRVGEIVVFKVEG 88 (103)
Q Consensus 61 ~~gD~v~v~~~~~~~~~~GDIVvf~~~~ 88 (103)
.+|+.+-+.+. .+++.||.|.|...+
T Consensus 13 ~dGeF~~ik~~--~~~~vG~eI~~~~~~ 38 (56)
T PF12791_consen 13 PDGEFIKIKRK--PGMEVGQEIEFDEKD 38 (56)
T ss_pred CCCcEEEEeCC--CCCcccCEEEEechh
Confidence 46777777663 459999999997654
No 169
>COG1209 RfbA dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]
Probab=22.07 E-value=1.5e+02 Score=22.98 Aligned_cols=33 Identities=27% Similarity=0.437 Sum_probs=23.8
Q ss_pred CCCEEEEeecCCCCCCCCcEEEEEeCCCCcCEEEEEEEecCC
Q psy3466 62 RGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRVLKLHEK 103 (103)
Q Consensus 62 ~gD~v~v~~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~~~~ 103 (103)
.|-.+++.+. .+|+|.-|+.|+.++ ||+++.||
T Consensus 127 ~ga~i~~~~V--~dP~rfGV~e~d~~~-------~v~~l~EK 159 (286)
T COG1209 127 SGATILLYEV--DDPSRYGVVEFDEDG-------KVIGLEEK 159 (286)
T ss_pred CCcEEEEEEc--CCcccceEEEEcCCC-------cEEEeEEC
Confidence 4677787776 689999999997553 56666554
No 170
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=22.03 E-value=2.1e+02 Score=17.74 Aligned_cols=28 Identities=14% Similarity=0.334 Sum_probs=16.6
Q ss_pred cccCCCEEEEeecC------CCCCCCCcEEEEEe
Q psy3466 59 AFHRGDLLFLTNYQ------EEPVRVGEIVVFKV 86 (103)
Q Consensus 59 tl~~gD~v~v~~~~------~~~~~~GDIVvf~~ 86 (103)
..++||.|++.... .++--.|+|+-+..
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~g 38 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEG 38 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEec
Confidence 35788888887631 12233577776643
No 171
>PRK07115 AMP nucleosidase; Provisional
Probab=21.89 E-value=79 Score=23.71 Aligned_cols=19 Identities=16% Similarity=0.447 Sum_probs=16.8
Q ss_pred eCCCccccccCCCEEEEee
Q psy3466 52 LSGSMEPAFHRGDLLFLTN 70 (103)
Q Consensus 52 ~g~SM~Ptl~~gD~v~v~~ 70 (103)
..+++.|.++.||+|+...
T Consensus 94 taGaL~~~l~~GDiVI~t~ 112 (258)
T PRK07115 94 KCGGLKSKYQVGDYFLPIA 112 (258)
T ss_pred cccCcCCCCCCCCEEEEEE
Confidence 3569999999999999987
No 172
>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=21.57 E-value=68 Score=21.98 Aligned_cols=16 Identities=19% Similarity=0.490 Sum_probs=9.0
Q ss_pred CccccccCCCEEEEee
Q psy3466 55 SMEPAFHRGDLLFLTN 70 (103)
Q Consensus 55 SM~Ptl~~gD~v~v~~ 70 (103)
+..+.|++||.+++.+
T Consensus 147 ~~n~~L~~gD~I~Vp~ 162 (165)
T TIGR03027 147 TANVELKPGDVLIIPE 162 (165)
T ss_pred cCCceeCCCCEEEEec
Confidence 3445566666666643
No 173
>TIGR03468 HpnG hopanoid-associated phosphorylase. The sequences in this family are members of the pfam01048 family of phosphorylases typically acting on nucleotide-sugar substrates. The genes of the family modeled here are generally in the same locus with genes involved in the biosynthesis and elaboration of hopene, the cyclization product of the polyisoprenoid squalene. This gene is adjacent to the genes PhnA-E and squalene-hopene cyclase (which would be HpnF) in Zymomonas mobilis and their association with hopene biosynthesis has been noted in the literature. Extending the gene symbol sequence, we suggest the symbol HpnG for the product of this gene. Hopanoids are known to be components of the plasma membrane and to have polar sugar head groups in Z. mobilis and other species.
Probab=21.43 E-value=61 Score=23.21 Aligned_cols=21 Identities=29% Similarity=0.582 Sum_probs=17.5
Q ss_pred EeCCCccccccCCCEEEEeec
Q psy3466 51 VLSGSMEPAFHRGDLLFLTNY 71 (103)
Q Consensus 51 V~g~SM~Ptl~~gD~v~v~~~ 71 (103)
=..+++.|.+++||.++.+..
T Consensus 53 G~aG~l~~~l~~Gdvvi~~~~ 73 (212)
T TIGR03468 53 GTAGALDPALQPGDLVVPEEV 73 (212)
T ss_pred EecccCCCCCCCCCEEeehhh
Confidence 345699999999999998763
No 174
>PRK12764 hypothetical protein; Provisional
Probab=21.33 E-value=1.2e+02 Score=25.01 Aligned_cols=30 Identities=17% Similarity=0.372 Sum_probs=23.4
Q ss_pred cccCCCEEEEeec-CCCCCCCCcEEEEEeCC
Q psy3466 59 AFHRGDLLFLTNY-QEEPVRVGEIVVFKVEG 88 (103)
Q Consensus 59 tl~~gD~v~v~~~-~~~~~~~GDIVvf~~~~ 88 (103)
||++||+++.-.. ....++.||.+...-.+
T Consensus 181 tL~pGDvIlTGTp~g~~~l~pGD~v~~~i~g 211 (500)
T PRK12764 181 TLEEGDVILTGTPAGSSVAAPGDVVEVEVDA 211 (500)
T ss_pred CcCCCCEEEeCCCCCCeecCCCCEEEEEEcC
Confidence 7999999998763 33568999999887765
No 175
>smart00439 BAH Bromo adjacent homology domain.
Probab=21.33 E-value=2.1e+02 Score=17.67 Aligned_cols=11 Identities=18% Similarity=0.531 Sum_probs=6.1
Q ss_pred ccCCCEEEEee
Q psy3466 60 FHRGDLLFLTN 70 (103)
Q Consensus 60 l~~gD~v~v~~ 70 (103)
++.||.|++..
T Consensus 2 ~~vgd~V~v~~ 12 (120)
T smart00439 2 IRVGDFVLVEP 12 (120)
T ss_pred cccCCEEEEeC
Confidence 45556666554
No 176
>COG3944 Capsular polysaccharide biosynthesis protein [Cell envelope biogenesis, outer membrane]
Probab=21.31 E-value=2.4e+02 Score=21.09 Aligned_cols=16 Identities=6% Similarity=0.474 Sum_probs=12.8
Q ss_pred ccccccCCCEEEEeec
Q psy3466 56 MEPAFHRGDLLFLTNY 71 (103)
Q Consensus 56 M~Ptl~~gD~v~v~~~ 71 (103)
+.|+++....++++..
T Consensus 40 i~P~YqssTqilV~~~ 55 (226)
T COG3944 40 IKPTYQSSTQILVNQS 55 (226)
T ss_pred cCcccccceEEEEecc
Confidence 3489999999999873
No 177
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=21.15 E-value=72 Score=24.02 Aligned_cols=32 Identities=22% Similarity=0.409 Sum_probs=23.5
Q ss_pred CCCccccccCCCEEEEeec---------------CCCCCCCCcEEEE
Q psy3466 53 SGSMEPAFHRGDLLFLTNY---------------QEEPVRVGEIVVF 84 (103)
Q Consensus 53 g~SM~Ptl~~gD~v~v~~~---------------~~~~~~~GDIVvf 84 (103)
+..|+|.|+.||.+.+.-. ....++.|-+|-.
T Consensus 106 ~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i 152 (239)
T COG1097 106 EKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKI 152 (239)
T ss_pred ccccccccccCCEEEEEEEEccCCCceEEEeecCCCccccCCEEEEE
Confidence 6799999999999987641 1345677776655
No 178
>cd00622 PLPDE_III_ODC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase. This subfamily is composed mainly of eukaryotic ornithine decarboxylases (ODC, EC 4.1.1.17) and ODC-like enzymes from prokaryotes represented by Vibrio vulnificus LysineOrnithine decarboxylase. These are fold type III PLP-dependent enzymes that differ from most bacterial ODCs which are fold type I PLP-dependent enzymes. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. Members of this subfamily contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity. Also members of this su
Probab=21.06 E-value=99 Score=23.57 Aligned_cols=30 Identities=20% Similarity=0.358 Sum_probs=17.9
Q ss_pred cccCCCEEEEeecCCCCCCCCcEEEEEeCC
Q psy3466 59 AFHRGDLLFLTNYQEEPVRVGEIVVFKVEG 88 (103)
Q Consensus 59 tl~~gD~v~v~~~~~~~~~~GDIVvf~~~~ 88 (103)
+=.++|.+--+..-+.++++||.++|..-|
T Consensus 312 ~C~~~D~l~~~~~lp~~l~~GD~l~~~~~G 341 (362)
T cd00622 312 TCDSLDVIYEDVLLPEDLAVGDWLLFENMG 341 (362)
T ss_pred CCCcccEecccCcCcccCCCCCEEEEcCCC
Confidence 344556544333212348999999997655
No 179
>PF09813 Coiled-coil_56: Coiled-coil domain-containing protein 56; InterPro: IPR018628 Members of this family of proteins have no known function.
Probab=20.92 E-value=2.6e+02 Score=18.32 Aligned_cols=8 Identities=38% Similarity=0.559 Sum_probs=4.1
Q ss_pred HHHHHHHh
Q psy3466 4 DAINDLKR 11 (103)
Q Consensus 4 ~~~~~~~~ 11 (103)
-+++.+++
T Consensus 35 vE~~~~kr 42 (100)
T PF09813_consen 35 VELQQLKR 42 (100)
T ss_pred HHHHHHHH
Confidence 34555555
No 180
>cd06828 PLPDE_III_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase. Diaminopimelate decarboxylase (DapDC, EC 4.1.1.20) participates in the last step of lysine biosynthesis. It converts meso-2,6-diaminoheptanedioate to L-lysine. It is a fold type III PLP-dependent enzyme that contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. DapDC exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.
Probab=20.89 E-value=1.5e+02 Score=22.55 Aligned_cols=30 Identities=20% Similarity=0.404 Sum_probs=19.6
Q ss_pred ccccCCCEEEEeecCCCCCCCCcEEEEEeCC
Q psy3466 58 PAFHRGDLLFLTNYQEEPVRVGEIVVFKVEG 88 (103)
Q Consensus 58 Ptl~~gD~v~v~~~~~~~~~~GDIVvf~~~~ 88 (103)
||=.++|.+.-+. ...+++.||.++|.+-|
T Consensus 323 ~~C~~~D~l~~~~-~lp~l~~GD~l~~~~~G 352 (373)
T cd06828 323 PICESGDVFAKDR-ELPEVEEGDLLAIHDAG 352 (373)
T ss_pred CCCCCCCEEeecc-cCCCCCCCCEEEEeCCC
Confidence 3444567554333 23479999999998665
No 181
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=20.48 E-value=87 Score=18.77 Aligned_cols=13 Identities=38% Similarity=0.560 Sum_probs=8.0
Q ss_pred CCCCcEEEEEeCC
Q psy3466 76 VRVGEIVVFKVEG 88 (103)
Q Consensus 76 ~~~GDIVvf~~~~ 88 (103)
-..||.|.+.-.+
T Consensus 57 a~aGd~v~~~l~~ 69 (83)
T cd03698 57 AVAGENVRLKLKG 69 (83)
T ss_pred ECCCCEEEEEECC
Confidence 4567777765543
No 182
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=20.38 E-value=85 Score=18.47 Aligned_cols=14 Identities=36% Similarity=0.425 Sum_probs=10.6
Q ss_pred CCCCcEEEEEeCCC
Q psy3466 76 VRVGEIVVFKVEGR 89 (103)
Q Consensus 76 ~~~GDIVvf~~~~~ 89 (103)
++.||||..+.+..
T Consensus 2 ~~vgDiV~mKK~HP 15 (57)
T PF06107_consen 2 YEVGDIVEMKKPHP 15 (57)
T ss_pred ccCCCEEEEcCCCC
Confidence 57789998887753
No 183
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=20.30 E-value=2.6e+02 Score=18.18 Aligned_cols=27 Identities=19% Similarity=0.273 Sum_probs=17.7
Q ss_pred CCEEEEee--cCCCCCCCCcEEEEEeCCC
Q psy3466 63 GDLLFLTN--YQEEPVRVGEIVVFKVEGR 89 (103)
Q Consensus 63 gD~v~v~~--~~~~~~~~GDIVvf~~~~~ 89 (103)
+|..-+.. ....++..||+|..+.++.
T Consensus 11 ~~~y~l~n~Pf~a~glA~gDvV~~~~~~g 39 (117)
T PF14085_consen 11 DDTYRLDNIPFFAYGLALGDVVRAEPDDG 39 (117)
T ss_pred CCEEEEEecccccCCCCCCCEEEEEeCCC
Confidence 34444443 2347889999999988763
No 184
>TIGR01718 Uridine-psphlse uridine phosphorylase. Sequences from Clostridium, Streptomyces, Treponema, Halobacterium and Pyrobaculum were included above trusted on the basis of sequence homology and a PAM-based neighbor-joining tree. A clade including second sequences from Halobacterium and Vibrio was somewhat more distantly related and may represent a slightly different substrate specificity - these were placed below the noise cutoff. More distantly related is a clade of archaeal sequences which as related to the DeoD family of inosine phosphorylases (TIGR00107) as they are to these uridine phosphorylases. This clade includes a characterized protein from Sulfolobus solfataricus which has been mis-named as a methylthioadenosine phosphorylase, but which acts on inosine and guanosine - it is unclear whether uridine has been evaluated as a substrate.
Probab=20.18 E-value=76 Score=23.29 Aligned_cols=19 Identities=32% Similarity=0.669 Sum_probs=16.7
Q ss_pred eCCCccccccCCCEEEEee
Q psy3466 52 LSGSMEPAFHRGDLLFLTN 70 (103)
Q Consensus 52 ~g~SM~Ptl~~gD~v~v~~ 70 (103)
..+++.|.++.||.|+.+.
T Consensus 87 taG~l~~~~~~GDiVI~~~ 105 (245)
T TIGR01718 87 TTGAIQPHINVGDVLITTA 105 (245)
T ss_pred ccccCCCCCCCCCEEEeCc
Confidence 3569999999999999987
Done!