Query 033241
Match_columns 124
No_of_seqs 115 out of 600
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 11:32:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033241.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033241hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3048 Molecular chaperone Pr 100.0 8E-36 1.7E-40 210.2 15.4 120 3-122 4-123 (153)
2 PRK14011 prefoldin subunit alp 100.0 7.5E-30 1.6E-34 182.3 15.7 106 14-122 5-110 (144)
3 TIGR00293 prefoldin, archaeal 100.0 1.2E-29 2.5E-34 176.9 15.5 108 14-122 1-108 (126)
4 COG1730 GIM5 Predicted prefold 100.0 2.4E-29 5.2E-34 179.6 15.3 112 10-121 4-115 (145)
5 cd00584 Prefoldin_alpha Prefol 100.0 1.1E-28 2.4E-33 172.6 15.4 109 14-122 1-109 (129)
6 PRK03947 prefoldin subunit alp 100.0 1.3E-28 2.8E-33 174.6 15.6 110 13-122 7-116 (140)
7 PRK01203 prefoldin subunit alp 100.0 2E-27 4.4E-32 166.7 15.6 107 15-122 3-109 (130)
8 PF02996 Prefoldin: Prefoldin 100.0 1.3E-27 2.9E-32 164.6 11.0 98 25-122 2-99 (120)
9 cd00890 Prefoldin Prefoldin is 99.9 1.3E-25 2.9E-30 155.9 15.5 109 14-122 1-109 (129)
10 KOG3313 Molecular chaperone Pr 99.7 6.2E-16 1.3E-20 112.7 13.9 107 14-120 39-148 (187)
11 KOG3047 Predicted transcriptio 99.5 6.1E-13 1.3E-17 93.2 10.2 99 24-122 28-127 (157)
12 KOG3130 Uncharacterized conser 99.4 5.2E-13 1.1E-17 108.1 8.3 98 25-123 9-106 (514)
13 TIGR02338 gimC_beta prefoldin, 98.6 2.6E-07 5.5E-12 63.1 8.3 86 13-122 4-89 (110)
14 cd00632 Prefoldin_beta Prefold 98.6 3.3E-07 7.1E-12 62.1 7.3 83 15-121 2-84 (105)
15 PF01920 Prefoldin_2: Prefoldi 98.4 2E-05 4.4E-10 52.5 12.8 83 16-122 2-84 (106)
16 cd00890 Prefoldin Prefoldin is 98.3 4.7E-06 1E-10 57.4 8.6 96 14-122 8-116 (129)
17 cd00584 Prefoldin_alpha Prefol 98.0 6.8E-05 1.5E-09 52.1 9.2 96 14-122 8-116 (129)
18 PRK09343 prefoldin subunit bet 97.7 0.00031 6.7E-09 48.8 8.0 85 14-122 9-93 (121)
19 TIGR00293 prefoldin, archaeal 97.6 0.00024 5.3E-09 49.1 5.9 32 23-54 3-34 (126)
20 COG1382 GimC Prefoldin, chaper 97.5 0.00091 2E-08 46.5 7.5 84 15-122 9-92 (119)
21 PRK03947 prefoldin subunit alp 97.3 0.0025 5.5E-08 44.8 8.9 41 81-121 55-108 (140)
22 PF13758 Prefoldin_3: Prefoldi 97.0 0.00022 4.8E-09 48.0 0.9 86 35-122 4-90 (99)
23 KOG4098 Molecular chaperone Pr 97.0 0.0059 1.3E-07 43.1 7.6 86 12-121 15-100 (140)
24 COG1730 GIM5 Predicted prefold 96.9 0.014 2.9E-07 42.0 9.4 95 14-121 15-122 (145)
25 PRK14011 prefoldin subunit alp 96.9 0.0073 1.6E-07 43.3 7.6 68 14-81 12-89 (144)
26 PRK01203 prefoldin subunit alp 96.7 0.0072 1.6E-07 42.7 6.4 25 24-48 5-29 (130)
27 PF02996 Prefoldin: Prefoldin 96.4 0.015 3.2E-07 39.5 6.1 49 60-121 57-105 (120)
28 KOG3478 Prefoldin subunit 6, K 92.1 1.2 2.7E-05 30.7 7.1 83 15-121 8-90 (120)
29 PF06698 DUF1192: Protein of u 91.1 0.94 2E-05 27.7 5.2 31 7-37 16-46 (59)
30 PF08181 DegQ: DegQ (SacQ) fam 82.1 6.7 0.00015 22.3 4.9 35 13-47 5-39 (46)
31 PF05377 FlaC_arch: Flagella a 77.9 11 0.00023 22.8 5.1 28 24-51 5-32 (55)
32 PF09278 MerR-DNA-bind: MerR, 76.3 13 0.00029 21.9 6.7 44 12-55 15-65 (65)
33 PRK05771 V-type ATP synthase s 75.6 46 0.001 29.0 10.5 46 11-56 81-130 (646)
34 PF09006 Surfac_D-trimer: Lung 73.1 15 0.00032 21.4 4.6 26 23-48 3-28 (46)
35 PF14282 FlxA: FlxA-like prote 72.1 17 0.00037 24.4 5.6 37 10-46 42-78 (106)
36 PF04568 IATP: Mitochondrial A 71.6 14 0.00029 25.0 5.0 29 14-42 71-99 (100)
37 PF09278 MerR-DNA-bind: MerR, 71.2 7.3 0.00016 23.2 3.4 29 95-123 31-59 (65)
38 PF12757 DUF3812: Protein of u 71.2 19 0.00041 25.0 5.8 15 61-75 56-70 (126)
39 cd01106 HTH_TipAL-Mta Helix-Tu 70.9 24 0.00051 23.1 6.1 44 11-54 57-101 (103)
40 PTZ00454 26S protease regulato 69.3 49 0.0011 27.3 8.8 45 10-54 13-64 (398)
41 PRK10328 DNA binding protein, 67.4 36 0.00078 24.0 6.7 45 10-54 19-63 (134)
42 PF02388 FemAB: FemAB family; 67.2 14 0.00031 30.4 5.3 58 15-75 245-312 (406)
43 PRK10780 periplasmic chaperone 67.2 17 0.00037 26.0 5.2 36 47-83 124-159 (165)
44 PF01486 K-box: K-box region; 66.7 33 0.00072 22.4 6.8 27 8-34 42-68 (100)
45 PRK10947 global DNA-binding tr 65.3 41 0.0009 23.8 6.6 43 10-52 19-61 (135)
46 PF04977 DivIC: Septum formati 64.7 27 0.00058 21.3 5.1 41 14-54 19-59 (80)
47 PHA03155 hypothetical protein; 64.0 21 0.00045 24.7 4.7 33 1-37 1-33 (115)
48 TIGR02894 DNA_bind_RsfA transc 63.8 51 0.0011 24.1 7.0 16 10-25 78-93 (161)
49 cd04776 HTH_GnyR Helix-Turn-He 60.6 50 0.0011 22.4 6.6 29 22-50 83-111 (118)
50 PRK00888 ftsB cell division pr 60.2 40 0.00086 22.6 5.6 58 13-70 28-89 (105)
51 PRK14127 cell division protein 59.8 42 0.00091 22.9 5.7 44 11-54 22-65 (109)
52 PF11068 YlqD: YlqD protein; 59.3 59 0.0013 22.8 7.1 16 75-92 97-112 (131)
53 PF07889 DUF1664: Protein of u 58.9 56 0.0012 22.9 6.3 41 14-54 77-117 (126)
54 KOG0727 26S proteasome regulat 58.8 39 0.00085 27.2 6.1 81 8-96 21-105 (408)
55 PF06657 Cep57_MT_bd: Centroso 58.3 41 0.00089 21.4 5.2 42 5-46 3-44 (79)
56 PF14131 DUF4298: Domain of un 58.3 49 0.0011 21.5 6.2 36 14-49 2-37 (90)
57 CHL00154 rpl29 ribosomal prote 57.5 44 0.00095 20.7 5.1 32 1-32 1-32 (67)
58 COG4026 Uncharacterized protei 57.2 92 0.002 24.3 8.6 36 72-109 234-269 (290)
59 COG3074 Uncharacterized protei 55.8 11 0.00025 23.9 2.1 36 9-44 22-57 (79)
60 PF11629 Mst1_SARAH: C termina 55.8 40 0.00088 19.8 4.9 29 9-37 5-37 (49)
61 PF08946 Osmo_CC: Osmosensory 55.5 35 0.00076 19.8 4.0 29 17-45 10-38 (46)
62 PRK09343 prefoldin subunit bet 55.4 26 0.00056 24.1 4.1 84 14-121 16-99 (121)
63 PF12210 Hrs_helical: Hepatocy 55.1 61 0.0013 21.7 5.9 28 29-56 56-83 (96)
64 PF06013 WXG100: Proteins of 1 54.8 44 0.00095 19.9 5.9 34 12-45 4-37 (86)
65 PRK13922 rod shape-determining 53.5 84 0.0018 24.1 7.2 38 15-52 72-109 (276)
66 PF13118 DUF3972: Protein of u 53.5 13 0.00027 26.2 2.3 61 55-117 22-88 (126)
67 PF03980 Nnf1: Nnf1 ; InterPr 53.0 64 0.0014 21.3 7.5 46 6-51 58-105 (109)
68 PF12958 DUF3847: Protein of u 52.7 63 0.0014 21.1 5.5 34 13-46 2-35 (86)
69 PF04977 DivIC: Septum formati 52.5 51 0.0011 20.0 5.1 31 22-52 20-50 (80)
70 TIGR02047 CadR-PbrR Cd(II)/Pb( 52.1 74 0.0016 21.7 6.7 45 11-55 57-108 (127)
71 cd00894 PI3Kc_IB_gamma Phospho 51.7 71 0.0015 26.3 6.7 38 48-85 39-76 (365)
72 KOG3048 Molecular chaperone Pr 51.1 92 0.002 22.5 10.0 74 34-120 38-128 (153)
73 PF10046 BLOC1_2: Biogenesis o 50.9 69 0.0015 21.0 6.6 18 38-55 71-88 (99)
74 cd04770 HTH_HMRTR Helix-Turn-H 50.6 74 0.0016 21.3 6.7 45 11-55 57-108 (123)
75 PF13356 DUF4102: Domain of un 50.1 36 0.00079 21.6 4.0 31 86-116 48-78 (89)
76 PF12325 TMF_TATA_bd: TATA ele 49.9 80 0.0017 21.8 5.9 39 9-47 13-51 (120)
77 COG3879 Uncharacterized protei 49.9 1E+02 0.0023 24.0 7.1 31 16-46 54-84 (247)
78 cd01109 HTH_YyaN Helix-Turn-He 49.8 74 0.0016 21.1 6.9 44 11-54 57-107 (113)
79 PF05377 FlaC_arch: Flagella a 49.7 56 0.0012 19.6 6.3 38 15-52 3-40 (55)
80 cd04775 HTH_Cfa-like Helix-Tur 49.6 59 0.0013 21.3 5.1 44 11-55 57-100 (102)
81 PF09340 NuA4: Histone acetylt 49.4 55 0.0012 20.9 4.7 31 14-44 4-34 (80)
82 PF13815 Dzip-like_N: Iguana/D 49.2 50 0.0011 22.4 4.8 42 8-49 62-103 (118)
83 cd04782 HTH_BltR Helix-Turn-He 49.0 34 0.00074 22.2 3.8 27 97-123 71-97 (97)
84 PF02609 Exonuc_VII_S: Exonucl 49.0 52 0.0011 19.1 5.7 34 10-43 18-51 (53)
85 PRK14127 cell division protein 49.0 84 0.0018 21.4 6.8 37 14-50 32-68 (109)
86 PF06937 EURL: EURL protein; 47.8 80 0.0017 25.1 6.1 35 9-43 216-250 (285)
87 TIGR02047 CadR-PbrR Cd(II)/Pb( 47.2 36 0.00078 23.3 3.8 28 96-123 75-102 (127)
88 PF07106 TBPIP: Tat binding pr 47.1 52 0.0011 23.5 4.8 14 23-36 90-103 (169)
89 KOG3047 Predicted transcriptio 46.6 1.1E+02 0.0023 21.9 6.7 88 17-118 32-130 (157)
90 PF00384 Molybdopterin: Molybd 46.3 30 0.00066 27.7 3.8 28 88-115 12-39 (432)
91 PF08285 DPM3: Dolichol-phosph 46.1 23 0.0005 23.3 2.6 33 86-118 54-86 (91)
92 PF15397 DUF4618: Domain of un 45.3 99 0.0021 24.3 6.3 43 15-57 70-112 (258)
93 cd04786 HTH_MerR-like_sg7 Heli 45.0 1E+02 0.0022 21.3 6.2 25 30-54 82-106 (131)
94 PF10393 Matrilin_ccoil: Trime 44.5 63 0.0014 18.7 5.2 32 15-46 12-43 (47)
95 PF10400 Vir_act_alpha_C: Viru 44.5 48 0.001 20.7 3.9 29 95-123 16-44 (90)
96 PF08317 Spc7: Spc7 kinetochor 44.2 98 0.0021 24.6 6.4 30 17-46 235-264 (325)
97 PF04728 LPP: Lipoprotein leuc 43.8 72 0.0016 19.2 5.5 16 22-37 13-28 (56)
98 cd04789 HTH_Cfa Helix-Turn-Hel 43.8 83 0.0018 20.6 5.1 43 12-55 58-100 (102)
99 cd01107 HTH_BmrR Helix-Turn-He 43.7 93 0.002 20.5 5.4 45 11-55 58-104 (108)
100 PF09304 Cortex-I_coil: Cortex 43.7 1E+02 0.0023 21.0 6.4 33 13-45 31-63 (107)
101 PHA02047 phage lambda Rz1-like 43.6 92 0.002 21.0 5.1 25 17-41 39-63 (101)
102 TIGR03042 PS_II_psbQ_bact phot 43.1 1.1E+02 0.0025 21.8 5.9 39 4-43 22-60 (142)
103 PF11932 DUF3450: Protein of u 43.0 1.2E+02 0.0026 23.1 6.5 9 32-40 83-91 (251)
104 PF10148 SCHIP-1: Schwannomin- 43.0 66 0.0014 25.0 5.0 39 7-45 168-206 (238)
105 COG1862 YajC Preprotein transl 42.9 1E+02 0.0022 20.6 6.8 55 44-103 33-87 (97)
106 PRK09514 zntR zinc-responsive 42.8 45 0.00098 23.3 3.8 27 97-123 78-104 (140)
107 PF06120 Phage_HK97_TLTM: Tail 42.6 96 0.0021 24.9 6.0 45 9-53 64-108 (301)
108 PF09304 Cortex-I_coil: Cortex 42.4 1.1E+02 0.0024 20.9 6.1 34 15-48 40-73 (107)
109 PHA03162 hypothetical protein; 42.1 90 0.002 22.1 5.1 33 3-35 4-36 (135)
110 PF11932 DUF3450: Protein of u 42.0 1.3E+02 0.0028 22.9 6.5 16 24-39 82-97 (251)
111 cd04785 HTH_CadR-PbrR-like Hel 41.8 49 0.0011 22.5 3.8 28 96-123 75-102 (126)
112 PRK04863 mukB cell division pr 41.7 1.2E+02 0.0025 29.7 7.3 47 8-54 431-477 (1486)
113 PF14723 SSFA2_C: Sperm-specif 41.5 74 0.0016 23.6 4.8 25 13-37 146-170 (179)
114 cd04787 HTH_HMRTR_unk Helix-Tu 41.3 1.2E+02 0.0025 20.9 6.2 42 12-53 58-106 (133)
115 cd04784 HTH_CadR-PbrR Helix-Tu 41.3 50 0.0011 22.4 3.8 27 97-123 76-102 (127)
116 TIGR02043 ZntR Zn(II)-responsi 41.2 50 0.0011 22.7 3.8 27 97-123 78-104 (131)
117 PF08700 Vps51: Vps51/Vps67; 41.1 87 0.0019 19.4 6.0 30 10-39 17-46 (87)
118 PF07743 HSCB_C: HSCB C-termin 40.8 86 0.0019 19.2 5.2 42 13-55 25-66 (78)
119 TIGR01242 26Sp45 26S proteasom 40.7 65 0.0014 25.8 4.9 56 16-71 3-65 (364)
120 TIGR01280 xseB exodeoxyribonuc 40.6 87 0.0019 19.3 6.1 36 10-45 20-55 (67)
121 cd01282 HTH_MerR-like_sg3 Heli 40.6 49 0.0011 22.1 3.6 29 95-123 76-104 (112)
122 cd04770 HTH_HMRTR Helix-Turn-H 40.5 54 0.0012 22.0 3.8 27 97-123 76-102 (123)
123 KOG4603 TBP-1 interacting prot 40.5 56 0.0012 24.4 4.0 24 96-119 159-182 (201)
124 TIGR02051 MerR Hg(II)-responsi 40.3 54 0.0012 22.3 3.8 28 96-123 72-99 (124)
125 PF10438 Cyc-maltodext_C: Cycl 40.1 35 0.00076 21.8 2.7 20 69-88 8-27 (78)
126 PRK10803 tol-pal system protei 40.0 78 0.0017 24.5 5.1 29 16-44 58-86 (263)
127 TIGR00219 mreC rod shape-deter 40.0 1.8E+02 0.004 22.8 7.6 10 81-90 131-140 (283)
128 smart00338 BRLZ basic region l 40.0 82 0.0018 18.8 5.7 35 20-54 27-61 (65)
129 PF12795 MscS_porin: Mechanose 39.5 1.4E+02 0.003 22.5 6.4 40 7-46 73-112 (240)
130 PF11285 DUF3086: Protein of u 39.5 57 0.0012 25.8 4.2 31 11-41 3-33 (283)
131 cd04769 HTH_MerR2 Helix-Turn-H 39.4 1.2E+02 0.0025 20.3 6.4 43 12-54 57-107 (116)
132 cd04777 HTH_MerR-like_sg1 Heli 39.3 55 0.0012 21.5 3.7 26 98-123 79-104 (107)
133 cd04783 HTH_MerR1 Helix-Turn-H 39.2 57 0.0012 22.1 3.8 27 97-123 74-100 (126)
134 PF13093 FTA4: Kinetochore com 38.9 1.5E+02 0.0033 22.4 6.4 45 14-58 137-181 (213)
135 COG3879 Uncharacterized protei 38.8 1.4E+02 0.003 23.4 6.2 72 16-97 61-138 (247)
136 PRK00736 hypothetical protein; 38.8 69 0.0015 19.7 3.8 27 96-122 1-27 (68)
137 PF09789 DUF2353: Uncharacteri 38.7 1.4E+02 0.003 24.3 6.4 40 12-51 189-228 (319)
138 cd04783 HTH_MerR1 Helix-Turn-H 38.7 1.2E+02 0.0027 20.4 6.1 44 12-55 58-106 (126)
139 cd04786 HTH_MerR-like_sg7 Heli 38.6 59 0.0013 22.5 3.8 27 97-123 75-101 (131)
140 PRK15002 redox-sensitivie tran 38.5 1.5E+02 0.0032 21.2 6.8 46 11-56 67-120 (154)
141 KOG1760 Molecular chaperone Pr 38.3 1.4E+02 0.0031 21.0 10.3 31 91-121 72-102 (131)
142 cd02765 MopB_4 The MopB_4 CD i 38.2 25 0.00054 30.1 2.2 43 73-115 45-93 (567)
143 PRK10227 DNA-binding transcrip 37.9 60 0.0013 22.6 3.8 28 96-123 75-102 (135)
144 PF03938 OmpH: Outer membrane 37.6 25 0.00055 24.5 1.9 65 11-76 72-145 (158)
145 cd01282 HTH_MerR-like_sg3 Heli 37.6 1.2E+02 0.0027 20.1 6.8 44 11-54 56-109 (112)
146 cd04785 HTH_CadR-PbrR-like Hel 37.3 1.3E+02 0.0028 20.4 6.1 44 12-55 58-108 (126)
147 TIGR02449 conserved hypothetic 37.3 1E+02 0.0022 19.1 6.3 32 14-45 9-40 (65)
148 PTZ00361 26 proteosome regulat 36.9 2.5E+02 0.0055 23.5 8.4 83 14-97 60-161 (438)
149 PRK00977 exodeoxyribonuclease 36.9 1.1E+02 0.0024 19.4 6.1 36 10-45 29-64 (80)
150 PF00170 bZIP_1: bZIP transcri 36.8 93 0.002 18.5 5.8 32 21-52 28-59 (64)
151 cd02755 MopB_Thiosulfate-R-lik 36.7 55 0.0012 27.0 4.0 27 89-115 67-93 (454)
152 cd01109 HTH_YyaN Helix-Turn-He 36.6 68 0.0015 21.3 3.8 27 97-123 76-102 (113)
153 PRK09514 zntR zinc-responsive 36.4 1.5E+02 0.0032 20.6 6.3 28 28-55 83-110 (140)
154 PRK03578 hscB co-chaperone Hsc 36.4 1.1E+02 0.0024 22.3 5.2 9 45-53 147-155 (176)
155 KOG2264 Exostosin EXT1L [Signa 35.8 87 0.0019 27.9 5.1 31 14-44 95-125 (907)
156 cd04784 HTH_CadR-PbrR Helix-Tu 35.6 1.4E+02 0.003 20.1 6.4 46 11-56 57-109 (127)
157 cd04787 HTH_HMRTR_unk Helix-Tu 35.5 1.5E+02 0.0032 20.3 6.3 37 20-56 80-116 (133)
158 PF14197 Cep57_CLD_2: Centroso 35.3 1.1E+02 0.0024 19.0 4.5 30 24-53 3-32 (69)
159 cd02769 MopB_DMSOR-BSOR-TMAOR 35.0 52 0.0011 28.4 3.7 26 89-114 69-94 (609)
160 PRK13752 putative transcriptio 34.7 72 0.0016 22.5 3.8 26 98-123 82-107 (144)
161 PF05008 V-SNARE: Vesicle tran 34.4 1.1E+02 0.0024 18.7 4.7 35 16-50 36-71 (79)
162 PF15456 Uds1: Up-regulated Du 34.4 1.6E+02 0.0034 20.4 10.7 86 9-123 16-104 (124)
163 PRK15102 trimethylamine N-oxid 34.2 32 0.0007 30.8 2.4 42 74-115 81-139 (825)
164 cd04772 HTH_TioE_rpt1 First He 33.9 81 0.0018 20.5 3.8 25 97-121 73-97 (99)
165 TIGR02044 CueR Cu(I)-responsiv 33.4 1.5E+02 0.0033 20.0 6.7 45 11-55 57-108 (127)
166 PF01330 RuvA_N: RuvA N termin 33.1 60 0.0013 19.2 2.8 29 72-100 3-34 (61)
167 PF12269 zf-CpG_bind_C: CpG bi 33.1 1.1E+02 0.0023 23.8 4.7 39 18-56 28-66 (236)
168 PRK13752 putative transcriptio 33.1 1.7E+02 0.0038 20.5 6.1 44 12-55 65-113 (144)
169 PF03249 TSA: Type specific an 32.9 57 0.0012 27.4 3.4 39 60-98 423-483 (503)
170 cd02770 MopB_DmsA-EC This CD ( 32.8 60 0.0013 28.0 3.8 38 78-115 54-97 (617)
171 PRK13729 conjugal transfer pil 32.7 1.7E+02 0.0036 25.2 6.2 37 16-52 80-116 (475)
172 PRK14549 50S ribosomal protein 32.4 1.3E+02 0.0027 18.7 4.7 26 7-32 7-32 (69)
173 TIGR02043 ZntR Zn(II)-responsi 32.3 1.7E+02 0.0036 20.0 6.5 27 28-54 83-109 (131)
174 cd04776 HTH_GnyR Helix-Turn-He 32.3 1.6E+02 0.0035 19.8 5.7 44 12-55 56-109 (118)
175 cd04790 HTH_Cfa-like_unk Helix 32.3 1.9E+02 0.0042 20.8 6.7 45 11-55 58-103 (172)
176 PF05190 MutS_IV: MutS family 32.2 69 0.0015 19.8 3.1 26 82-108 61-86 (92)
177 PF07352 Phage_Mu_Gam: Bacteri 32.1 1E+02 0.0022 21.6 4.3 33 16-48 29-61 (149)
178 cd02772 MopB_NDH-1_NuoG2 MopB_ 32.0 45 0.00098 26.9 2.7 25 90-114 63-87 (414)
179 PRK05585 yajC preprotein trans 31.8 1.6E+02 0.0035 19.8 6.3 50 46-100 44-93 (106)
180 cd04788 HTH_NolA-AlbR Helix-Tu 31.8 76 0.0016 20.5 3.4 24 100-123 73-96 (96)
181 COG1382 GimC Prefoldin, chaper 31.7 1.8E+02 0.0039 20.2 6.0 84 14-121 12-98 (119)
182 PF13863 DUF4200: Domain of un 31.6 1.6E+02 0.0034 19.6 6.9 37 21-57 83-119 (126)
183 PRK14067 exodeoxyribonuclease 31.5 1.4E+02 0.0031 19.1 5.7 36 10-45 26-61 (80)
184 TIGR01950 SoxR redox-sensitive 31.5 1.8E+02 0.004 20.3 6.7 45 11-55 57-109 (142)
185 TIGR02051 MerR Hg(II)-responsi 31.4 1.7E+02 0.0036 19.8 6.2 44 12-55 57-105 (124)
186 cd05166 PI3Kc_II Phosphoinosit 31.2 1.8E+02 0.0038 23.8 6.0 58 26-84 12-69 (353)
187 PRK14063 exodeoxyribonuclease 31.2 1.4E+02 0.003 18.8 5.8 35 10-44 24-58 (76)
188 TIGR02420 dksA RNA polymerase- 31.0 1.6E+02 0.0035 19.5 5.2 26 12-37 1-26 (110)
189 cd04766 HTH_HspR Helix-Turn-He 30.7 1.4E+02 0.0031 18.8 4.6 28 12-40 59-86 (91)
190 PF10512 Borealin: Cell divisi 30.7 86 0.0019 21.6 3.6 37 3-39 74-112 (116)
191 PF14962 AIF-MLS: Mitochondria 30.3 17 0.00037 27.1 0.0 30 87-116 56-85 (180)
192 PRK00068 hypothetical protein; 30.3 98 0.0021 28.9 4.7 45 61-105 830-884 (970)
193 PF14588 YjgF_endoribonc: YjgF 30.2 56 0.0012 23.5 2.7 63 60-122 19-84 (148)
194 TIGR02164 torA trimethylamine- 30.1 64 0.0014 28.9 3.6 27 89-115 110-136 (822)
195 PF10398 DUF2443: Protein of u 30.1 1.3E+02 0.0028 19.3 4.0 19 38-56 55-73 (79)
196 PF12841 YvrJ: YvrJ protein fa 30.1 73 0.0016 17.6 2.6 18 105-122 20-37 (38)
197 TIGR02977 phageshock_pspA phag 30.0 2.4E+02 0.0051 21.1 6.5 34 17-50 104-137 (219)
198 TIGR02209 ftsL_broad cell divi 29.8 1.4E+02 0.003 18.4 5.5 39 16-55 28-66 (85)
199 TIGR02231 conserved hypothetic 29.8 2.7E+02 0.0059 23.5 7.1 46 9-54 121-166 (525)
200 cd01108 HTH_CueR Helix-Turn-He 29.4 1.8E+02 0.004 19.6 6.8 44 12-55 58-108 (127)
201 PF10392 COG5: Golgi transport 29.4 1.9E+02 0.0041 19.8 6.0 27 16-42 69-95 (132)
202 PF02388 FemAB: FemAB family; 29.4 98 0.0021 25.4 4.3 30 92-121 234-263 (406)
203 TIGR02395 rpoN_sigma RNA polym 29.4 3.4E+02 0.0073 22.7 8.1 80 41-123 195-291 (429)
204 PF10018 Med4: Vitamin-D-recep 29.3 2.3E+02 0.0049 20.7 6.3 26 20-45 23-48 (188)
205 TIGR01242 26Sp45 26S proteasom 29.3 2.9E+02 0.0064 22.0 9.4 34 14-47 8-41 (364)
206 PHA01750 hypothetical protein 29.1 1.5E+02 0.0033 18.6 5.6 33 21-53 37-69 (75)
207 cd02763 MopB_2 The MopB_2 CD i 29.0 75 0.0016 28.2 3.7 26 89-114 66-91 (679)
208 PF12718 Tropomyosin_1: Tropom 28.8 2.1E+02 0.0046 20.1 6.5 39 16-54 25-63 (143)
209 PRK00888 ftsB cell division pr 28.6 1.8E+02 0.004 19.4 5.3 25 16-40 38-62 (105)
210 PF08781 DP: Transcription fac 28.6 2.2E+02 0.0048 20.3 5.6 67 14-80 3-76 (142)
211 PF00429 TLV_coat: ENV polypro 28.5 2E+02 0.0044 25.0 6.2 44 13-56 422-469 (561)
212 PF00626 Gelsolin: Gelsolin re 28.5 1.3E+02 0.0029 17.7 4.1 13 79-91 24-36 (76)
213 PF11262 Tho2: Transcription f 28.4 1.2E+02 0.0027 23.9 4.6 27 11-37 16-42 (298)
214 cd01716 Hfq Hfq, an abundant, 28.4 85 0.0018 19.2 2.9 31 60-90 10-40 (61)
215 PF10779 XhlA: Haemolysin XhlA 28.3 1.5E+02 0.0032 18.2 5.9 33 16-48 3-35 (71)
216 PF10046 BLOC1_2: Biogenesis o 28.3 1.8E+02 0.0038 19.1 6.4 41 14-54 51-94 (99)
217 PRK00294 hscB co-chaperone Hsc 27.9 1.7E+02 0.0036 21.4 4.9 10 45-54 144-153 (173)
218 PF12443 AKNA: AT-hook-contain 27.8 81 0.0018 21.5 3.0 29 21-49 47-75 (106)
219 TIGR01706 NAPA periplasmic nit 27.6 52 0.0011 29.6 2.6 26 89-114 112-137 (830)
220 KOG2706 Predicted membrane pro 27.5 25 0.00054 28.8 0.5 32 64-95 12-43 (476)
221 KOG3905 Dynein light intermedi 27.5 1.6E+02 0.0035 24.6 5.1 49 61-120 205-253 (473)
222 COG1497 Predicted transcriptio 27.5 1.4E+02 0.003 23.5 4.5 49 29-92 71-119 (260)
223 PF11945 WASH_WAHD: WAHD domai 27.3 2.7E+02 0.0059 22.2 6.3 34 22-55 39-72 (297)
224 cd02759 MopB_Acetylene-hydrata 27.3 91 0.002 25.9 3.8 27 89-115 66-92 (477)
225 PRK02509 hypothetical protein; 27.2 1.1E+02 0.0023 28.6 4.4 45 61-105 902-955 (973)
226 TIGR01843 type_I_hlyD type I s 27.1 3.2E+02 0.007 21.7 8.8 8 92-99 310-317 (423)
227 COG1766 fliF Flagellar basal b 27.0 2.1E+02 0.0046 24.9 6.0 68 34-105 129-197 (545)
228 PHA03052 Hypothetical protein; 27.0 1.7E+02 0.0037 18.4 4.4 37 62-98 5-45 (69)
229 KOG2695 WD40 repeat protein [G 27.0 43 0.00094 27.8 1.8 28 68-95 344-371 (425)
230 TIGR02383 Hfq RNA chaperone Hf 26.8 93 0.002 19.0 2.9 30 60-89 14-43 (61)
231 PF12128 DUF3584: Protein of u 26.8 1.1E+02 0.0024 28.8 4.6 46 7-52 588-633 (1201)
232 cd02750 MopB_Nitrate-R-NarG-li 26.4 94 0.002 25.7 3.7 26 89-114 78-103 (461)
233 KOG2391 Vacuolar sorting prote 26.1 2.1E+02 0.0046 23.6 5.6 40 14-56 248-287 (365)
234 PRK09129 NADH dehydrogenase su 26.1 77 0.0017 28.2 3.4 38 77-114 266-305 (776)
235 KOG3366 Mitochondrial F1F0-ATP 26.0 1.1E+02 0.0025 22.5 3.7 28 96-123 101-128 (172)
236 PF05103 DivIVA: DivIVA protei 25.9 39 0.00085 22.7 1.2 34 13-46 19-52 (131)
237 cd02751 MopB_DMSOR-like The Mo 25.9 95 0.0021 26.7 3.8 27 89-115 69-95 (609)
238 PRK10227 DNA-binding transcrip 25.9 2.3E+02 0.005 19.6 6.7 44 11-54 57-107 (135)
239 PRK10869 recombination and rep 25.9 1.9E+02 0.004 25.0 5.5 21 13-33 318-338 (553)
240 TIGR00509 bisC_fam molybdopter 25.8 90 0.002 27.7 3.7 27 89-115 67-93 (770)
241 PRK14064 exodeoxyribonuclease 25.8 1.8E+02 0.0039 18.3 6.1 34 10-43 25-58 (75)
242 smart00502 BBC B-Box C-termina 25.5 1.9E+02 0.0041 18.5 4.7 30 26-55 72-101 (127)
243 cd02754 MopB_Nitrate-R-NapA-li 25.5 84 0.0018 26.6 3.4 38 77-114 48-88 (565)
244 PRK10093 primosomal replicatio 25.3 2.6E+02 0.0056 20.6 5.5 31 21-51 138-168 (171)
245 PF11853 DUF3373: Protein of u 25.3 80 0.0017 27.1 3.1 28 27-54 32-59 (489)
246 PRK13532 nitrate reductase cat 25.2 83 0.0018 28.3 3.4 25 90-114 113-137 (830)
247 PRK09973 putative outer membra 25.2 2E+02 0.0044 18.8 5.0 27 14-40 26-52 (85)
248 PF07716 bZIP_2: Basic region 25.2 1.5E+02 0.0032 17.1 4.6 15 25-39 31-45 (54)
249 PF08317 Spc7: Spc7 kinetochor 25.1 3.4E+02 0.0074 21.5 6.6 16 9-24 203-218 (325)
250 TIGR02166 dmsA_ynfE anaerobic 25.1 97 0.0021 27.5 3.8 27 89-115 116-142 (797)
251 PRK05771 V-type ATP synthase s 24.9 1.4E+02 0.003 26.1 4.7 24 17-40 220-243 (646)
252 cd00632 Prefoldin_beta Prefold 24.9 2.1E+02 0.0045 18.7 6.4 31 17-47 68-98 (105)
253 PF06156 DUF972: Protein of un 24.9 2.2E+02 0.0049 19.1 5.8 25 20-44 9-33 (107)
254 PRK07860 NADH dehydrogenase su 24.9 45 0.00097 30.0 1.6 36 79-114 274-312 (797)
255 PF08549 SWI-SNF_Ssr4: Fungal 24.8 3.2E+02 0.0068 24.6 6.7 50 6-55 351-400 (669)
256 PF11382 DUF3186: Protein of u 24.7 2.8E+02 0.0061 22.0 6.0 40 15-54 35-74 (308)
257 PF05384 DegS: Sensor protein 24.6 2.8E+02 0.006 20.1 6.4 43 13-55 14-56 (159)
258 cd04768 HTH_BmrR-like Helix-Tu 24.5 91 0.002 20.1 2.7 23 100-122 73-95 (96)
259 PRK06342 transcription elongat 24.5 2.7E+02 0.006 20.0 7.9 67 7-75 29-104 (160)
260 PF07445 priB_priC: Primosomal 24.4 2.6E+02 0.0056 20.3 5.4 25 30-54 142-166 (173)
261 PF10267 Tmemb_cc2: Predicted 24.3 4E+02 0.0087 22.2 7.0 60 12-71 41-101 (395)
262 TIGR03073 release_rtcB release 24.2 39 0.00083 27.7 1.0 36 66-102 43-78 (356)
263 cd02757 MopB_Arsenate-R This C 24.2 89 0.0019 26.4 3.3 38 77-114 50-97 (523)
264 PRK15488 thiosulfate reductase 24.2 1E+02 0.0023 27.2 3.8 27 89-115 110-136 (759)
265 PRK14069 exodeoxyribonuclease 24.2 2.2E+02 0.0049 18.9 6.1 34 10-43 27-60 (95)
266 cd00126 PAH Pancreatic Hormone 24.1 1.4E+02 0.003 16.4 3.1 22 11-32 11-32 (36)
267 PRK02793 phi X174 lysis protei 24.0 1.9E+02 0.0041 18.0 6.6 26 17-42 6-31 (72)
268 smart00787 Spc7 Spc7 kinetocho 24.0 3.2E+02 0.0069 21.9 6.2 9 13-21 202-210 (312)
269 PF10458 Val_tRNA-synt_C: Valy 23.9 1.7E+02 0.0038 17.5 3.9 18 100-117 39-56 (66)
270 PF13600 DUF4140: N-terminal d 23.9 2.1E+02 0.0045 18.4 5.0 25 22-46 73-97 (104)
271 PF14662 CCDC155: Coiled-coil 23.7 3E+02 0.0064 20.8 5.6 36 21-56 38-73 (193)
272 PRK10803 tol-pal system protei 23.7 3.5E+02 0.0075 20.9 6.3 29 23-51 58-86 (263)
273 cd04769 HTH_MerR2 Helix-Turn-H 23.7 1.7E+02 0.0038 19.4 4.1 34 20-53 80-113 (116)
274 smart00309 PAH Pancreatic horm 23.7 1.4E+02 0.003 16.3 3.1 23 10-32 10-32 (36)
275 PF04111 APG6: Autophagy prote 23.6 3.8E+02 0.0083 21.3 6.9 57 62-118 195-258 (314)
276 PF08581 Tup_N: Tup N-terminal 23.6 2.1E+02 0.0045 18.3 6.2 29 17-45 2-30 (79)
277 PF09932 DUF2164: Uncharacteri 23.6 1.5E+02 0.0033 18.8 3.5 25 97-121 51-75 (76)
278 COG1504 Uncharacterized conser 23.5 1.5E+02 0.0032 20.6 3.6 21 86-107 86-106 (121)
279 COG5509 Uncharacterized small 23.4 1.9E+02 0.0041 17.8 4.1 21 24-44 30-50 (65)
280 PF13094 CENP-Q: CENP-Q, a CEN 23.3 2.7E+02 0.0059 19.5 6.4 35 10-44 18-52 (160)
281 PF07412 Geminin: Geminin; In 23.2 2.5E+02 0.0055 21.2 5.2 31 26-56 139-169 (200)
282 PRK14066 exodeoxyribonuclease 23.2 2E+02 0.0044 18.1 6.1 35 10-44 23-57 (75)
283 PF01920 Prefoldin_2: Prefoldi 23.2 2.1E+02 0.0045 18.1 6.4 31 16-46 66-96 (106)
284 PRK14068 exodeoxyribonuclease 23.2 2.1E+02 0.0045 18.1 6.1 30 10-39 25-54 (76)
285 cd04781 HTH_MerR-like_sg6 Heli 23.0 2.4E+02 0.0052 18.8 6.1 45 11-55 56-103 (120)
286 PF04880 NUDE_C: NUDE protein, 23.0 1.7E+02 0.0037 21.4 4.2 10 14-23 2-11 (166)
287 PF07240 Turandot: Stress-indu 22.9 92 0.002 20.4 2.4 46 13-58 11-56 (85)
288 PRK14990 anaerobic dimethyl su 22.9 1.1E+02 0.0024 27.3 3.8 27 89-115 131-157 (814)
289 PF04124 Dor1: Dor1-like famil 22.8 1.6E+02 0.0036 23.4 4.4 33 8-40 3-35 (338)
290 PF04799 Fzo_mitofusin: fzo-li 22.6 3.2E+02 0.007 20.1 6.5 26 30-55 124-149 (171)
291 cd04454 S1_Rrp4_like S1_Rrp4_l 22.6 1.5E+02 0.0032 18.1 3.4 33 69-101 5-39 (82)
292 PRK10698 phage shock protein P 22.5 3.4E+02 0.0075 20.4 6.5 33 16-48 103-135 (222)
293 PRK01356 hscB co-chaperone Hsc 22.5 2.5E+02 0.0055 20.2 5.0 8 12-19 87-94 (166)
294 smart00262 GEL Gelsolin homolo 22.5 75 0.0016 19.8 2.0 13 81-93 34-46 (90)
295 PF04740 LXG: LXG domain of WX 22.4 2.5E+02 0.0053 20.3 5.0 36 12-47 3-38 (204)
296 PRK13182 racA polar chromosome 22.4 2.5E+02 0.0055 20.5 5.0 29 17-45 90-118 (175)
297 PF07763 FEZ: FEZ-like protein 22.4 3.5E+02 0.0076 21.1 5.9 39 8-46 167-205 (244)
298 cd04779 HTH_MerR-like_sg4 Heli 22.4 2.8E+02 0.006 19.3 5.5 31 24-54 79-109 (134)
299 PF10224 DUF2205: Predicted co 22.1 2.3E+02 0.0049 18.2 6.7 27 21-47 18-44 (80)
300 PRK00306 50S ribosomal protein 22.1 1.2E+02 0.0027 18.3 2.8 25 8-32 5-29 (66)
301 PF06295 DUF1043: Protein of u 22.0 2.7E+02 0.0059 19.1 5.4 17 36-52 57-73 (128)
302 COG1648 CysG Siroheme synthase 21.9 1.9E+02 0.004 21.8 4.3 51 69-120 108-173 (210)
303 KOG0652 26S proteasome regulat 21.9 2.8E+02 0.0061 22.6 5.4 40 9-48 17-56 (424)
304 PRK11118 putative monooxygenas 21.9 1.8E+02 0.004 19.6 3.8 29 87-115 48-76 (100)
305 PRK06007 fliF flagellar MS-rin 21.7 2.9E+02 0.0063 23.8 5.9 70 31-104 126-196 (542)
306 PRK13922 rod shape-determining 21.5 2.5E+02 0.0055 21.4 5.1 36 21-56 71-106 (276)
307 KOG2826 Actin-related protein 21.5 1.7E+02 0.0036 23.1 4.0 27 82-108 53-79 (301)
308 cd02766 MopB_3 The MopB_3 CD i 21.5 1.3E+02 0.0028 25.3 3.7 24 91-114 68-91 (501)
309 PRK14872 rod shape-determining 21.4 4.6E+02 0.0099 21.4 6.8 18 73-90 104-127 (337)
310 PF13814 Replic_Relax: Replica 21.4 1.9E+02 0.004 20.5 4.1 40 80-119 137-181 (191)
311 PF00159 Hormone_3: Pancreatic 21.3 1.6E+02 0.0034 16.1 3.2 22 10-31 10-31 (36)
312 COG4013 Uncharacterized protei 21.3 1.1E+02 0.0024 20.1 2.5 44 44-88 6-50 (91)
313 TIGR01950 SoxR redox-sensitive 21.3 1.8E+02 0.0038 20.4 3.9 27 97-123 77-103 (142)
314 TIGR01837 PHA_granule_1 poly(h 21.1 1.8E+02 0.0039 19.8 3.8 19 26-44 96-114 (118)
315 TIGR02544 III_secr_YscJ type I 21.0 3.5E+02 0.0076 20.0 6.2 59 33-95 100-159 (193)
316 PRK15396 murein lipoprotein; P 21.0 2.4E+02 0.0052 18.0 5.3 27 14-40 27-53 (78)
317 smart00150 SPEC Spectrin repea 21.0 2E+02 0.0044 17.2 5.0 30 15-44 34-63 (101)
318 PF02187 GAS2: Growth-Arrest-S 20.9 1.8E+02 0.0039 18.5 3.4 18 75-93 40-57 (73)
319 PRK15002 redox-sensitivie tran 20.9 1.8E+02 0.0039 20.8 3.9 27 97-123 87-113 (154)
320 TIGR03479 DMSO_red_II_alp DMSO 20.8 93 0.002 28.4 2.9 37 78-114 115-157 (912)
321 PF09177 Syntaxin-6_N: Syntaxi 20.8 2.5E+02 0.0053 18.1 5.2 23 32-54 45-67 (97)
322 PF11172 DUF2959: Protein of u 20.7 3.2E+02 0.007 20.7 5.3 39 14-52 59-97 (201)
323 PF07412 Geminin: Geminin; In 20.7 3.1E+02 0.0068 20.8 5.2 35 22-56 128-162 (200)
324 COG5570 Uncharacterized small 20.6 2E+02 0.0044 17.2 3.4 25 99-123 32-56 (57)
325 PF05681 Fumerase: Fumarate hy 20.5 3.4E+02 0.0074 21.4 5.7 70 10-103 14-85 (271)
326 PF10212 TTKRSYEDQ: Predicted 20.4 3.5E+02 0.0077 23.5 6.0 39 15-53 476-514 (518)
327 PF04120 Iron_permease: Low af 20.4 1.6E+02 0.0035 20.7 3.5 26 6-31 89-114 (132)
328 PF01455 HupF_HypC: HupF/HypC 20.3 2.2E+02 0.0047 17.5 3.7 27 78-106 38-65 (68)
329 PRK05886 yajC preprotein trans 20.2 2.9E+02 0.0064 18.8 6.4 47 47-98 31-77 (109)
330 cd02752 MopB_Formate-Dh-Na-lik 20.1 1.4E+02 0.0031 26.3 3.8 26 89-114 64-89 (649)
331 KOG4196 bZIP transcription fac 20.1 3.3E+02 0.0072 19.3 6.3 32 16-47 78-109 (135)
No 1
>KOG3048 consensus Molecular chaperone Prefoldin, subunit 5 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8e-36 Score=210.22 Aligned_cols=120 Identities=49% Similarity=0.787 Sum_probs=116.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCC
Q 033241 3 SSKGGGMEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDAR 82 (124)
Q Consensus 3 ~~~~i~~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~ 82 (124)
+++.|++|.||||||.++++++++|++.+++++++|.....+|.+|+++|+.+++..+|.++|||+++++||||++.|.+
T Consensus 4 ~s~~idltkLsleQL~~lk~q~dqEl~~lq~Sl~~L~~aq~k~~~~~~aln~~~~~~eGk~~LVPLTsSlYVPGkl~d~~ 83 (153)
T KOG3048|consen 4 ESKGIDLTKLSLEQLGALKKQFDQELNFLQDSLNALKGAQTKYEESIAALNDVQAANEGKKLLVPLTSSLYVPGKLSDNS 83 (153)
T ss_pred cccCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCeEEEecccceeccceecccc
Confidence 45789999999999999999999999999999999999999999999999999988899999999999999999999999
Q ss_pred eEEEEccCceeeecCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033241 83 KVLVDIGTGYFVEKTMDEGKDYCERKINLLKSNFDQLIEV 122 (124)
Q Consensus 83 ~VlV~lG~g~~vE~~~~eA~~~l~~r~~~l~~~i~~l~~~ 122 (124)
+++|+||+|||||+|.++|++|++||++.|.+++++++++
T Consensus 84 k~lVDIGTGYyVEK~~e~akdyfkRKve~l~kq~e~i~~i 123 (153)
T KOG3048|consen 84 KFLVDIGTGYYVEKDAEDAKDYFKRKVEYLTKQIEQIEGI 123 (153)
T ss_pred ceeEeccCceEEeechHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999865
No 2
>PRK14011 prefoldin subunit alpha; Provisional
Probab=99.97 E-value=7.5e-30 Score=182.31 Aligned_cols=106 Identities=17% Similarity=0.291 Sum_probs=99.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCcee
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYF 93 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~ 93 (124)
++++....+.+.++++.|++++..|+.++.+|..|+++|+.++ .+.++|||||+|+||||+|.++++|+|+||+|||
T Consensus 5 lq~~~~~l~~~~~qie~L~~si~~L~~a~~e~~~~ie~L~~l~---~~~eiLVPLg~s~yV~g~i~d~dkVlVdIGtGy~ 81 (144)
T PRK14011 5 LQNQFMALEVYNQQVQKLQEELSSIDMMKMELLKSIESMEGLK---TSEEILIPLGPGAFLKAKIVDPDKAILGVGSDIY 81 (144)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccC---CCCeEEEEcCCCcEEeEEecCCCeEEEEccCCeE
Confidence 6777888899999999999999999999999999999999886 3789999999999999999999999999999999
Q ss_pred eecCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033241 94 VEKTMDEGKDYCERKINLLKSNFDQLIEV 122 (124)
Q Consensus 94 vE~~~~eA~~~l~~r~~~l~~~i~~l~~~ 122 (124)
||+|.++|++||++|++.|++.++++.+.
T Consensus 82 VEk~~~eA~~~~~~ri~~l~~~~~~l~~~ 110 (144)
T PRK14011 82 LEKDVSEVIEDFKKSVEELDKTKKEGNKK 110 (144)
T ss_pred EEecHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999998888653
No 3
>TIGR00293 prefoldin, archaeal alpha subunit/eukaryotic subunit 5. This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and may hit large numbers of proteins that contain coiled coil regions.
Probab=99.97 E-value=1.2e-29 Score=176.88 Aligned_cols=108 Identities=33% Similarity=0.544 Sum_probs=103.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCcee
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYF 93 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~ 93 (124)
+++|.+.+++++++++.+++++..|...++++..++++|+.+++. .+.+++||||+|+|++|+|+++++|+||||+|||
T Consensus 1 ~qql~~q~~ql~~~i~~l~~~i~~l~~~i~e~~~~~~~L~~l~~~-~~~~~lv~lg~~~~v~~~v~~~~~v~v~iG~g~~ 79 (126)
T TIGR00293 1 LQQLAAELQILQQQVESLQAQIAALRALIAELETAIETLEDLKGA-EGKETLVPVGAGSFVKAKVKDTDKVLVSIGSGYY 79 (126)
T ss_pred CHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc-CCCeEEEEcCCCeEEEEEeCCCCEEEEEcCCCEE
Confidence 478999999999999999999999999999999999999999865 6899999999999999999999999999999999
Q ss_pred eecCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033241 94 VEKTMDEGKDYCERKINLLKSNFDQLIEV 122 (124)
Q Consensus 94 vE~~~~eA~~~l~~r~~~l~~~i~~l~~~ 122 (124)
||+|+++|++|+++|++.++++++++++.
T Consensus 80 vE~~~~eA~~~l~~~~~~l~~~~~~l~~~ 108 (126)
T TIGR00293 80 VEKDAEEAIEFLKKRIEELEKAIEKLQEA 108 (126)
T ss_pred EEecHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999998763
No 4
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=2.4e-29 Score=179.59 Aligned_cols=112 Identities=29% Similarity=0.524 Sum_probs=106.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEcc
Q 033241 10 EKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIG 89 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG 89 (124)
++.++++|.+.++.++.+++.|++++..|+.++.+++.|+++|+.++..++|.++|||+|+|+|++|+|.+.++|+|+||
T Consensus 4 ~~~~le~l~a~lq~l~~qie~L~~~i~~l~~~~~e~~~~~~tl~~lk~~~~g~E~LVpvGag~fv~~kv~~~~kviV~iG 83 (145)
T COG1730 4 TQQELEELAAQLQILQSQIESLQAQIAALNAAISELQTAIETLENLKGAGEGKEVLVPVGAGLFVKAKVKDMDKVIVSIG 83 (145)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEEEcCCCceEEEEeccCceEEEEcC
Confidence 56789999999999999999999999999999999999999999998655578999999999999999999999999999
Q ss_pred CceeeecCHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 90 TGYFVEKTMDEGKDYCERKINLLKSNFDQLIE 121 (124)
Q Consensus 90 ~g~~vE~~~~eA~~~l~~r~~~l~~~i~~l~~ 121 (124)
+|||||+++++|++|+++|++.|++.+.++++
T Consensus 84 sg~~ae~~~~eAie~l~k~~~~l~~~~~~l~~ 115 (145)
T COG1730 84 SGYYAEKSADEAIEFLKKRIEELEKAIEKLQQ 115 (145)
T ss_pred CceeeeecHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999998765
No 5
>cd00584 Prefoldin_alpha Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=99.96 E-value=1.1e-28 Score=172.60 Aligned_cols=109 Identities=35% Similarity=0.570 Sum_probs=104.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCcee
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYF 93 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~ 93 (124)
+++|...+++++++++.+++++..|+..+.+|..++++|+.|++.+.+.++|||||+|+|++|+|+++++|+||||+|||
T Consensus 1 ~~~l~~~~~~l~~~i~~l~~~~~~l~~~~~e~~~~~~~l~~l~~~~~~~~~lvplg~~~~~~~~i~~~~~v~v~iG~g~~ 80 (129)
T cd00584 1 LEQLAAQLQVLQQEIEELQQELARLNEAIAEYEQAKETLETLKKADEGKETLVPLGAGVFVKAKVKDTDKVLVDLGTGYY 80 (129)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCeEEeEEeCCCCEEEEEcCCCEE
Confidence 47899999999999999999999999999999999999999976567899999999999999999999999999999999
Q ss_pred eecCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033241 94 VEKTMDEGKDYCERKINLLKSNFDQLIEV 122 (124)
Q Consensus 94 vE~~~~eA~~~l~~r~~~l~~~i~~l~~~ 122 (124)
||+|+++|++|+++|++.+++.++++++.
T Consensus 81 vE~~~~eA~~~l~~r~~~l~~~~~~l~~~ 109 (129)
T cd00584 81 VEKDLEEAIEFLDKKIEELTKQIEKLQKE 109 (129)
T ss_pred EEecHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999998864
No 6
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=99.96 E-value=1.3e-28 Score=174.61 Aligned_cols=110 Identities=27% Similarity=0.511 Sum_probs=104.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCce
Q 033241 13 SVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGY 92 (124)
Q Consensus 13 ~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~ 92 (124)
.+++|...+++++++++.|++++..|+..++++..++++|+.|++...+.+++||||+|+|++|+|+++++|+||||+||
T Consensus 7 ~l~~l~~~~~~l~~~~~~l~~~~~~l~~~~~e~~~~~e~l~~l~~~~~~~e~lvplg~~~yv~~~v~~~~kV~v~lG~g~ 86 (140)
T PRK03947 7 ELEELAAQLQALQAQIEALQQQLEELQASINELDTAKETLEELKSKGEGKETLVPIGAGSFVKAKVKDKDKVIVSLGAGY 86 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCeEEEEcCCCcEEEEEecCCCeEEEEcCCCE
Confidence 57888999999999999999999999999999999999999998655789999999999999999999999999999999
Q ss_pred eeecCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033241 93 FVEKTMDEGKDYCERKINLLKSNFDQLIEV 122 (124)
Q Consensus 93 ~vE~~~~eA~~~l~~r~~~l~~~i~~l~~~ 122 (124)
|||+|+++|++|+++|++.+++.++++++.
T Consensus 87 ~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~ 116 (140)
T PRK03947 87 SAEKDLDEAIEILDKRKEELEKALEKLEEA 116 (140)
T ss_pred EEEecHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999988753
No 7
>PRK01203 prefoldin subunit alpha; Provisional
Probab=99.96 E-value=2e-27 Score=166.68 Aligned_cols=107 Identities=12% Similarity=0.328 Sum_probs=99.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCceee
Q 033241 15 EQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYFV 94 (124)
Q Consensus 15 e~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~v 94 (124)
+++....+.++++++.|+++++.|+.++.+|.+|+++|+.++ ...+.++|||||+|+||||+|.++++|+|+||+||||
T Consensus 3 ~~~~~~~~~~~~q~e~l~~ql~~L~~a~se~~~~ie~L~~~~-~~~~~eiLVPLg~slYV~gki~d~~kVlVdIGTGy~V 81 (130)
T PRK01203 3 RDVEAQLNYIESLISSVDSQIDSLNKTLSEVQQTISFLSDNE-LDNSKELLISIGSGIFADGNIKKDKDLIVPIGSGVYI 81 (130)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc-cCCCCeEEEEccCCceEeEEecCCCeEEEEcCCCeEE
Confidence 577788889999999999999999999999999999999976 3467999999999999999999999999999999999
Q ss_pred ecCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033241 95 EKTMDEGKDYCERKINLLKSNFDQLIEV 122 (124)
Q Consensus 95 E~~~~eA~~~l~~r~~~l~~~i~~l~~~ 122 (124)
|+|.++++++++++++.|++.+...++.
T Consensus 82 EK~~e~kie~L~~~ie~Le~~i~~K~~~ 109 (130)
T PRK01203 82 AEERERTIERLKENLEDLKDSIQKLNDQ 109 (130)
T ss_pred EecHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999998877654
No 8
>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits. Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal alpha subunit, eukaryotic prefoldin subunits 3 and 5 and the UXT (ubiquitously expressed transcript) family. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 1FXK_C 2ZDI_C.
Probab=99.95 E-value=1.3e-27 Score=164.60 Aligned_cols=98 Identities=29% Similarity=0.590 Sum_probs=89.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCceeeecCHHHHHHH
Q 033241 25 DLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYFVEKTMDEGKDY 104 (124)
Q Consensus 25 ~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~vE~~~~eA~~~ 104 (124)
+++++.+++++..|+..+.+|..++++|+.|++.+.+.+++||+|+|+|++|+|+++++|+|+||+|||||+|+++|++|
T Consensus 2 ~~~l~~l~~~~~~l~~~~~e~~~~~~~l~~l~~~~~~~~~lvplg~~~~v~g~i~~~~~vlV~lG~~~~vE~s~~eA~~~ 81 (120)
T PF02996_consen 2 QEELENLQQQIEQLEEQIEEYEEAKETLEELKKEKKEHEILVPLGSGVFVPGKIPDTDKVLVSLGAGYYVEMSLEEAIEF 81 (120)
T ss_dssp CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--TT-EEEEEECTTEEEEEE-SSTTEEEEEEETTEEEEEEHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCceeeecCCCCeEEEEEeCCCCEEEEEeeCCeEEEecHHHHHHH
Confidence 45678899999999999999999999999998656789999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhh
Q 033241 105 CERKINLLKSNFDQLIEV 122 (124)
Q Consensus 105 l~~r~~~l~~~i~~l~~~ 122 (124)
+++|++.+++.++++++.
T Consensus 82 l~~r~~~l~~~~~~l~~~ 99 (120)
T PF02996_consen 82 LKKRIKELEEQLEKLEKE 99 (120)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 999999999999998764
No 9
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=99.94 E-value=1.3e-25 Score=155.90 Aligned_cols=109 Identities=29% Similarity=0.533 Sum_probs=103.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCcee
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYF 93 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~ 93 (124)
+++|...+++++++++.+++++..+...+.+|..++++|+.+.....+.++++|+|+++|++|+|+++++|+|+||+|||
T Consensus 1 ~~~l~~~~~~l~~~i~~l~~~~~~l~~~~~e~~~~~~~l~~l~~~~~~~~~l~~~g~~~~~~~~i~~~~~v~v~iG~~~~ 80 (129)
T cd00890 1 LQELAAQLQQLQQQLEALQQQLQKLEAQLTEYEKAKETLETLKKAEEEKELLVPLGAGLFVKAEVKDDDKVLVDLGTGVY 80 (129)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCeEEEecCCceEEEEEECCCCEEEEEecCCEE
Confidence 47899999999999999999999999999999999999999987667889999999999999999999999999999999
Q ss_pred eecCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033241 94 VEKTMDEGKDYCERKINLLKSNFDQLIEV 122 (124)
Q Consensus 94 vE~~~~eA~~~l~~r~~~l~~~i~~l~~~ 122 (124)
||+|.++|++++++|++.+++.++++++.
T Consensus 81 ve~~~~eA~~~l~~r~~~l~~~~~~l~~~ 109 (129)
T cd00890 81 VEKSLEEAIEFLKKRLETLEKQIEKLEKQ 109 (129)
T ss_pred EEecHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999988764
No 10
>KOG3313 consensus Molecular chaperone Prefoldin, subunit 3 [Posttranslational modification, protein turnover, chaperones]
Probab=99.70 E-value=6.2e-16 Score=112.72 Aligned_cols=107 Identities=13% Similarity=0.218 Sum_probs=92.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCC---CCCceEEEecCCceeEeEEEcCCCeEEEEccC
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLR---PQGAKMLVPLTASLYVPGTLDDARKVLVDIGT 90 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~---~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~ 90 (124)
+.-+...+.++.---..+.++...|+..|++++.+++.+..|... +++.++.+-|+.|+|.+|.|+++++|.+|+||
T Consensus 39 l~~~~E~~~kYkfme~~l~a~~~~l~~kIPd~entLeiv~~l~~~~~~~~s~~t~f~lsd~vy~ka~V~~~~kV~LWLGA 118 (187)
T KOG3313|consen 39 LKKLQERYGKYKFMEASLLAQKRRLKTKIPDIENTLEIVQTLIAKKDEGESFETTFLLSDGVYTKASVPPTDKVYLWLGA 118 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHhCcccCcceeEEEEecccceeeeecCCcCeEEEEecc
Confidence 334444455555555678888999999999999999999998643 24489999999999999999999999999999
Q ss_pred ceeeecCHHHHHHHHHHHHHHHHHHHHHHh
Q 033241 91 GYFVEKTMDEGKDYCERKINLLKSNFDQLI 120 (124)
Q Consensus 91 g~~vE~~~~eA~~~l~~r~~~l~~~i~~l~ 120 (124)
++++|++++||.++|++++..+.++++.+.
T Consensus 119 nVMlEY~leEAeaLLkknl~sa~k~l~~~~ 148 (187)
T KOG3313|consen 119 NVMLEYDLEEAEALLKKNLTSAVKSLDVLE 148 (187)
T ss_pred eeEEEecHHHHHHHHHhhHHHHHHHHHHHH
Confidence 999999999999999999999999988765
No 11
>KOG3047 consensus Predicted transcriptional regulator UXT [Transcription]
Probab=99.47 E-value=6.1e-13 Score=93.15 Aligned_cols=99 Identities=14% Similarity=0.321 Sum_probs=84.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC-CCCCceEEEecCCceeEeEEEcCCCeEEEEccCceeeecCHHHHH
Q 033241 24 TDLEVNLLQDSLNNIRTATSRLESASTALHDLSL-RPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYFVEKTMDEGK 102 (124)
Q Consensus 24 l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~-~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~vE~~~~eA~ 102 (124)
+...+..-......++...++|.....+++.|.. .....+.-+.|||++|+.-.|+|+++|+|.+|.|||+|+++.+|+
T Consensus 28 ih~di~k~~d~~dKl~eQ~aeY~kLk~t~eRL~eaahkel~~ktdLGcnfFmdi~VpDTk~i~VaL~~~fflElkLadAi 107 (157)
T KOG3047|consen 28 IHPDIAKEEDEFDKLQEQCAEYAKLKFTCERLLEAAHKELEGKTDLGCNFFMDIEVPDTKHIVVALCDDFFLELKLADAI 107 (157)
T ss_pred hchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhhhhccccccceeeEeeecCCcceEEEEeecceeeeehHHHHH
Confidence 4455566666677778888888888888888642 234577889999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhh
Q 033241 103 DYCERKINLLKSNFDQLIEV 122 (124)
Q Consensus 103 ~~l~~r~~~l~~~i~~l~~~ 122 (124)
+|++|+.+.|.+..++|++.
T Consensus 108 Kf~DRK~dlLkel~ekLqKd 127 (157)
T KOG3047|consen 108 KFCDRKMDLLKELMEKLQKD 127 (157)
T ss_pred HHHHHhHHHHHHHHHHHHHh
Confidence 99999999999999998863
No 12
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.43 E-value=5.2e-13 Score=108.08 Aligned_cols=98 Identities=18% Similarity=0.322 Sum_probs=86.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCceeeecCHHHHHHH
Q 033241 25 DLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYFVEKTMDEGKDY 104 (124)
Q Consensus 25 ~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~vE~~~~eA~~~ 104 (124)
.+-.+.++.+..-.+.-...|...++.+..++ .+-+.+||||||.-.|++|++.++|.|+|.+|+|||.++|.-.|.++
T Consensus 9 ~~a~~~~~~ete~~~~v~~dye~~~erl~~~~-kkLs~~Imvpig~~a~mpG~lVhTNevtv~~g~nyf~~CS~h~A~~I 87 (514)
T KOG3130|consen 9 NAAKARLEVETECRKKVDNDYEALRERLSTLP-KKLSYNIMVPIGPFAFMPGKLVHTNEVTVLLGDNYFAKCSAHQAVGI 87 (514)
T ss_pred HHHHHHhHHHHHHHHHHhhhHHHHHHHHHHhh-hhcccceeeecccccccccceeeechhhhhhccchHhhhhHHHHHHH
Confidence 33345555666667777889999999999997 46789999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhh
Q 033241 105 CERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 105 l~~r~~~l~~~i~~l~~~~ 123 (124)
+++|++.++++++++.+++
T Consensus 88 ~~~R~~~~r~q~~~l~~~~ 106 (514)
T KOG3130|consen 88 VEHRKEHVRKQIDDLKKVM 106 (514)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 9999999999999997654
No 13
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=98.64 E-value=2.6e-07 Score=63.15 Aligned_cols=86 Identities=14% Similarity=0.127 Sum_probs=75.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCce
Q 033241 13 SVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGY 92 (124)
Q Consensus 13 ~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~ 92 (124)
.++++..-+++++++++.+..++..|...+.+...+++.|+.+++ +.+++-++|. +
T Consensus 4 ~~q~~~~~~q~~q~~~~~l~~q~~~le~~~~E~~~v~~eL~~l~~---d~~vyk~VG~---------------------v 59 (110)
T TIGR02338 4 QVQNQLAQLQQLQQQLQAVATQKQQVEAQLKEAEKALEELERLPD---DTPVYKSVGN---------------------L 59 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC---cchhHHHhch---------------------h
Confidence 467778889999999999999999999999999999999999974 4556666665 9
Q ss_pred eeecCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033241 93 FVEKTMDEGKDYCERKINLLKSNFDQLIEV 122 (124)
Q Consensus 93 ~vE~~~~eA~~~l~~r~~~l~~~i~~l~~~ 122 (124)
||+.|.++|+..+++|++.++..++.+.+.
T Consensus 60 lv~~~~~e~~~~l~~r~e~ie~~i~~lek~ 89 (110)
T TIGR02338 60 LVKTDKEEAIQELKEKKETLELRVKTLQRQ 89 (110)
T ss_pred hheecHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999988764
No 14
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=98.57 E-value=3.3e-07 Score=62.05 Aligned_cols=83 Identities=11% Similarity=0.133 Sum_probs=71.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCceee
Q 033241 15 EQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYFV 94 (124)
Q Consensus 15 e~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~v 94 (124)
+++...+++++++++.+.+++..|.....+...+.+.|..+++ +..++.++|. +||
T Consensus 2 q~~~~~~q~l~~~~~~l~~~~~~l~~~~~E~~~v~~EL~~l~~---d~~vy~~VG~---------------------vfv 57 (105)
T cd00632 2 QEQLAQLQQLQQQLQAYIVQRQKVEAQLNENKKALEELEKLAD---DAEVYKLVGN---------------------VLV 57 (105)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC---cchHHHHhhh---------------------HHh
Confidence 4566778899999999999999999999999999999999963 4556666665 999
Q ss_pred ecCHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 95 EKTMDEGKDYCERKINLLKSNFDQLIE 121 (124)
Q Consensus 95 E~~~~eA~~~l~~r~~~l~~~i~~l~~ 121 (124)
+.|.++|...++.|++.++..++.+.+
T Consensus 58 ~~~~~ea~~~Le~~~e~le~~i~~l~~ 84 (105)
T cd00632 58 KQEKEEARTELKERLETIELRIKRLER 84 (105)
T ss_pred hccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999888765
No 15
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=98.41 E-value=2e-05 Score=52.46 Aligned_cols=83 Identities=20% Similarity=0.329 Sum_probs=69.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCceeee
Q 033241 16 QLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYFVE 95 (124)
Q Consensus 16 ~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~vE 95 (124)
++..-.+.+..++..+..++..+.....++..+.+.|..+++ ..+|+..+| ++||+
T Consensus 2 e~~~~~~~l~~~l~~~~~q~~~l~~~~~~~~~~~~eL~~l~~-----------------------~~~~y~~vG-~~fv~ 57 (106)
T PF01920_consen 2 ELQNKFQELNQQLQQLEQQIQQLERQLRELELTLEELEKLDD-----------------------DRKVYKSVG-KMFVK 57 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSST-----------------------T-EEEEEET-TEEEE
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-----------------------cchhHHHHh-HHHHH
Confidence 455667788888889999999999999999999999998863 234556664 67999
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033241 96 KTMDEGKDYCERKINLLKSNFDQLIEV 122 (124)
Q Consensus 96 ~~~~eA~~~l~~r~~~l~~~i~~l~~~ 122 (124)
.|.+++++.++.+++.++..++++.+.
T Consensus 58 ~~~~~~~~~L~~~~~~~~~~i~~l~~~ 84 (106)
T PF01920_consen 58 QDKEEAIEELEERIEKLEKEIKKLEKQ 84 (106)
T ss_dssp EEHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999998764
No 16
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=98.34 E-value=4.7e-06 Score=57.40 Aligned_cols=96 Identities=23% Similarity=0.343 Sum_probs=75.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCC-------------CCCceEEEecCCceeEeEEEcC
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLR-------------PQGAKMLVPLTASLYVPGTLDD 80 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~-------------~~~~e~lVplg~~~yv~a~I~~ 80 (124)
..+|.+..+.+.+.+..+...+..++..+..+....++....... ..+.+++|+||+|+||+..+.+
T Consensus 8 ~~~l~~~i~~l~~~~~~l~~~~~e~~~~~~~l~~l~~~~~~~~~l~~~g~~~~~~~~i~~~~~v~v~iG~~~~ve~~~~e 87 (129)
T cd00890 8 LQQLQQQLEALQQQLQKLEAQLTEYEKAKETLETLKKAEEEKELLVPLGAGLFVKAEVKDDDKVLVDLGTGVYVEKSLEE 87 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCeEEEecCCceEEEEEECCCCEEEEEecCCEEEEecHHH
Confidence 456666777778888888888888887777777766555443210 1468899999999999999887
Q ss_pred CCeEEEEccCceeeecCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033241 81 ARKVLVDIGTGYFVEKTMDEGKDYCERKINLLKSNFDQLIEV 122 (124)
Q Consensus 81 ~~~VlV~lG~g~~vE~~~~eA~~~l~~r~~~l~~~i~~l~~~ 122 (124)
. ...+++.+++++++++.+++.+..+++.
T Consensus 88 A-------------~~~l~~r~~~l~~~~~~l~~~~~~~~~~ 116 (129)
T cd00890 88 A-------------IEFLKKRLETLEKQIEKLEKQLEKLQDQ 116 (129)
T ss_pred H-------------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5 5788999999999999999999888764
No 17
>cd00584 Prefoldin_alpha Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=98.02 E-value=6.8e-05 Score=52.06 Aligned_cols=96 Identities=22% Similarity=0.301 Sum_probs=72.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HhhccCC----------CCCceEEEecCCceeEeEEEcC
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTA---LHDLSLR----------PQGAKMLVPLTASLYVPGTLDD 80 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~---l~~L~~~----------~~~~e~lVplg~~~yv~a~I~~ 80 (124)
..+|....+.++++++.++..+..+...++.+...... .+.+-+- ..+.+++||||+|+|+...+.+
T Consensus 8 ~~~l~~~i~~l~~~~~~l~~~~~e~~~~~~~l~~l~~~~~~~~~lvplg~~~~~~~~i~~~~~v~v~iG~g~~vE~~~~e 87 (129)
T cd00584 8 LQVLQQEIEELQQELARLNEAIAEYEQAKETLETLKKADEGKETLVPLGAGVFVKAKVKDTDKVLVDLGTGYYVEKDLEE 87 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCeEEeEEeCCCCEEEEEcCCCEEEEecHHH
Confidence 45666777788888888888888888777777666441 1112111 2458899999999999999987
Q ss_pred CCeEEEEccCceeeecCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033241 81 ARKVLVDIGTGYFVEKTMDEGKDYCERKINLLKSNFDQLIEV 122 (124)
Q Consensus 81 ~~~VlV~lG~g~~vE~~~~eA~~~l~~r~~~l~~~i~~l~~~ 122 (124)
.. ..++.-++.+++.++.+++.+..+++.
T Consensus 88 A~-------------~~l~~r~~~l~~~~~~l~~~l~~l~~~ 116 (129)
T cd00584 88 AI-------------EFLDKKIEELTKQIEKLQKELAKLKDQ 116 (129)
T ss_pred HH-------------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55 678899999999999999999887753
No 18
>PRK09343 prefoldin subunit beta; Provisional
Probab=97.70 E-value=0.00031 Score=48.83 Aligned_cols=85 Identities=15% Similarity=0.126 Sum_probs=67.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCcee
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYF 93 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~ 93 (124)
++++...+++++++++.+..+...+.....+...+++-|+.|++ ..+|+-.+| .+|
T Consensus 9 ~q~~~~~~q~lq~~l~~~~~q~~~le~q~~e~~~~~~EL~~L~~-----------------------d~~VYk~VG-~vl 64 (121)
T PRK09343 9 VQAQLAQLQQLQQQLERLLQQKSQIDLELREINKALEELEKLPD-----------------------DTPIYKIVG-NLL 64 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC-----------------------cchhHHHhh-HHH
Confidence 45556667888889999999999999999999999999888863 233555555 577
Q ss_pred eecCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033241 94 VEKTMDEGKDYCERKINLLKSNFDQLIEV 122 (124)
Q Consensus 94 vE~~~~eA~~~l~~r~~~l~~~i~~l~~~ 122 (124)
|..|.++|+.-+++|++.++..|+.+.+.
T Consensus 65 v~qd~~e~~~~l~~r~E~ie~~ik~lekq 93 (121)
T PRK09343 65 VKVDKTKVEKELKERKELLELRSRTLEKQ 93 (121)
T ss_pred hhccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 88899999999999999888888887653
No 19
>TIGR00293 prefoldin, archaeal alpha subunit/eukaryotic subunit 5. This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and may hit large numbers of proteins that contain coiled coil regions.
Probab=97.57 E-value=0.00024 Score=49.07 Aligned_cols=32 Identities=19% Similarity=0.338 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 23 QTDLEVNLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 23 ~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
++.+.++.+++++..|+..+..+..++..+..
T Consensus 3 ql~~q~~ql~~~i~~l~~~i~~l~~~i~e~~~ 34 (126)
T TIGR00293 3 QLAAELQILQQQVESLQAQIAALRALIAELET 34 (126)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444445555555555555555544444444
No 20
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=97.45 E-value=0.00091 Score=46.50 Aligned_cols=84 Identities=17% Similarity=0.175 Sum_probs=65.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCceee
Q 033241 15 EQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYFV 94 (124)
Q Consensus 15 e~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~v 94 (124)
+++....++++++++.+-.+..++...+.+...|++-|+.+.++ ..|+-.+| +++|
T Consensus 9 q~~l~q~QqLq~ql~~~~~qk~~le~qL~E~~~al~Ele~l~eD-----------------------~~vYk~VG-~llv 64 (119)
T COG1382 9 QAQLAQLQQLQQQLQKVILQKQQLEAQLKEIEKALEELEKLDED-----------------------APVYKKVG-NLLV 64 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcc-----------------------cHHHHHhh-hHHh
Confidence 44445577888888888888888888888888888888887532 23444555 6788
Q ss_pred ecCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033241 95 EKTMDEGKDYCERKINLLKSNFDQLIEV 122 (124)
Q Consensus 95 E~~~~eA~~~l~~r~~~l~~~i~~l~~~ 122 (124)
..+.++|.+=++.|++.|+..++.|++.
T Consensus 65 k~~k~~~~~eL~er~E~Le~ri~tLekQ 92 (119)
T COG1382 65 KVSKEEAVDELEERKETLELRIKTLEKQ 92 (119)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 8899999999999999999988888754
No 21
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=97.34 E-value=0.0025 Score=44.80 Aligned_cols=41 Identities=24% Similarity=0.469 Sum_probs=23.0
Q ss_pred CCeEEEEccCceeeecCHHHHHH-------------HHHHHHHHHHHHHHHHhh
Q 033241 81 ARKVLVDIGTGYFVEKTMDEGKD-------------YCERKINLLKSNFDQLIE 121 (124)
Q Consensus 81 ~~~VlV~lG~g~~vE~~~~eA~~-------------~l~~r~~~l~~~i~~l~~ 121 (124)
..+++|++|+|+|+..++.+.-+ -++.-++.+++.++.+.+
T Consensus 55 ~~e~lvplg~~~yv~~~v~~~~kV~v~lG~g~~vE~~~~eA~~~l~~~~~~l~~ 108 (140)
T PRK03947 55 GKETLVPIGAGSFVKAKVKDKDKVIVSLGAGYSAEKDLDEAIEILDKRKEELEK 108 (140)
T ss_pred CCeEEEEcCCCcEEEEEecCCCeEEEEcCCCEEEEecHHHHHHHHHHHHHHHHH
Confidence 45566666666666665544333 445555566666555544
No 22
>PF13758 Prefoldin_3: Prefoldin subunit
Probab=97.04 E-value=0.00022 Score=48.03 Aligned_cols=86 Identities=17% Similarity=0.255 Sum_probs=61.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhccC-CCCCceEEEecCCceeEeEEEcCCCeEEEEccCceeeecCHHHHHHHHHHHHHHHH
Q 033241 35 LNNIRTATSRLESASTALHDLSL-RPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYFVEKTMDEGKDYCERKINLLK 113 (124)
Q Consensus 35 ~~~L~~~~~~~~~~~~~l~~L~~-~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~vE~~~~eA~~~l~~r~~~l~ 113 (124)
+...+.--.+|...++-|..++. .+.+.+=+..++.++ .|.+.+.+.|=.-+|.|-.+.+|.+++++++.||++.++
T Consensus 4 L~hWq~w~aEYe~LKEEi~~l~~~~~~~~e~l~~i~r~f--~g~lv~~kEi~~ilG~~~~i~Rt~~Qvv~~l~RRiDYV~ 81 (99)
T PF13758_consen 4 LYHWQTWEAEYEGLKEEIEALPEDDDATREDLLRIRRDF--GGSLVTEKEIKEILGEGQGITRTREQVVDVLSRRIDYVQ 81 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccCCCCHHHHHHHHHhc--CcccccHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHH
Confidence 33445555666666666766642 122233333344332 277778788888899999999999999999999999999
Q ss_pred HHHHHHhhh
Q 033241 114 SNFDQLIEV 122 (124)
Q Consensus 114 ~~i~~l~~~ 122 (124)
+++..+++.
T Consensus 82 ~Ni~tleKq 90 (99)
T PF13758_consen 82 QNIETLEKQ 90 (99)
T ss_pred HHHHHHHHH
Confidence 999999874
No 23
>KOG4098 consensus Molecular chaperone Prefoldin, subunit 2 [Posttranslational modification, protein turnover, chaperones]
Probab=96.98 E-value=0.0059 Score=43.13 Aligned_cols=86 Identities=15% Similarity=0.173 Sum_probs=70.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCc
Q 033241 12 MSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTG 91 (124)
Q Consensus 12 l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g 91 (124)
.+-+.+..-++++..+.+.|.+.+..|.....++.-.+++|+.+.+.. .+ + -+=.|
T Consensus 15 ~~q~~v~a~yn~~r~el~~ia~ki~~LE~d~~EH~lVi~tlk~~dp~R---KC--------------------f-RmIgG 70 (140)
T KOG4098|consen 15 SSQQAVVAKYNALRSELQQIASKITDLEMDLREHKLVIETLKDLDPTR---KC--------------------F-RMIGG 70 (140)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcChhh---HH--------------------H-HHhcc
Confidence 344566677889999999999999999999999999999999986421 11 1 11248
Q ss_pred eeeecCHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 92 YFVEKTMDEGKDYCERKINLLKSNFDQLIE 121 (124)
Q Consensus 92 ~~vE~~~~eA~~~l~~r~~~l~~~i~~l~~ 121 (124)
+.||+|+.+.+=.|..+.+.+++.+..|.+
T Consensus 71 vLVErTVkeVlP~L~~nke~i~~~i~~l~~ 100 (140)
T KOG4098|consen 71 VLVERTVKEVLPILQTNKENIEKVIKKLTD 100 (140)
T ss_pred chhhhhHHHHhHHHHhhHHHHHHHHHHHHH
Confidence 899999999999999999999999888765
No 24
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=96.94 E-value=0.014 Score=42.00 Aligned_cols=95 Identities=19% Similarity=0.266 Sum_probs=57.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---hhccCC----------CCCceEEEecCCceeEeEEEcC
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTAL---HDLSLR----------PQGAKMLVPLTASLYVPGTLDD 80 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l---~~L~~~----------~~~~e~lVplg~~~yv~a~I~~ 80 (124)
+..+.+..+.+++++..|...+..++..+..+......= +.|-|- ....+++||||+|+|+.=....
T Consensus 15 lq~l~~qie~L~~~i~~l~~~~~e~~~~~~tl~~lk~~~~g~E~LVpvGag~fv~~kv~~~~kviV~iGsg~~ae~~~~e 94 (145)
T COG1730 15 LQILQSQIESLQAQIAALNAAISELQTAIETLENLKGAGEGKEVLVPVGAGLFVKAKVKDMDKVIVSIGSGYYAEKSADE 94 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEEEcCCCceEEEEeccCceEEEEcCCceeeeecHHH
Confidence 344555666777888888888888887777765543222 112111 2347899999999998877654
Q ss_pred CCeEEEEccCceeeecCHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 81 ARKVLVDIGTGYFVEKTMDEGKDYCERKINLLKSNFDQLIE 121 (124)
Q Consensus 81 ~~~VlV~lG~g~~vE~~~~eA~~~l~~r~~~l~~~i~~l~~ 121 (124)
.= ..+++=++-+++.+..++..+.++.+
T Consensus 95 Ai-------------e~l~k~~~~l~~~~~~l~~~l~~l~~ 122 (145)
T COG1730 95 AI-------------EFLKKRIEELEKAIEKLQQALAELAQ 122 (145)
T ss_pred HH-------------HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 22 23444455555555555555555443
No 25
>PRK14011 prefoldin subunit alpha; Provisional
Probab=96.89 E-value=0.0073 Score=43.31 Aligned_cols=68 Identities=10% Similarity=0.119 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCC----------CCCceEEEecCCceeEeEEEcCC
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLR----------PQGAKMLVPLTASLYVPGTLDDA 81 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~----------~~~~e~lVplg~~~yv~a~I~~~ 81 (124)
++.+.+..+.+.+.++.|......+...+..+......-+.|-|- ....+++|++|.|+||.=.+.+.
T Consensus 12 l~~~~~qie~L~~si~~L~~a~~e~~~~ie~L~~l~~~~eiLVPLg~s~yV~g~i~d~dkVlVdIGtGy~VEk~~~eA 89 (144)
T PRK14011 12 LEVYNQQVQKLQEELSSIDMMKMELLKSIESMEGLKTSEEILIPLGPGAFLKAKIVDPDKAILGVGSDIYLEKDVSEV 89 (144)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCeEEEEcCCCcEEeEEecCCCeEEEEccCCeEEEecHHHH
Confidence 566667777788888888888888887777766443322223221 24578999999999998887763
No 26
>PRK01203 prefoldin subunit alpha; Provisional
Probab=96.71 E-value=0.0072 Score=42.69 Aligned_cols=25 Identities=8% Similarity=0.344 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 24 TDLEVNLLQDSLNNIRTATSRLESA 48 (124)
Q Consensus 24 l~~ei~~l~~~~~~L~~~~~~~~~~ 48 (124)
+.++++.++++++.|+..+..++.+
T Consensus 5 ~~~~~~~~~~q~e~l~~ql~~L~~a 29 (130)
T PRK01203 5 VEAQLNYIESLISSVDSQIDSLNKT 29 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444444444433
No 27
>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits. Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal alpha subunit, eukaryotic prefoldin subunits 3 and 5 and the UXT (ubiquitously expressed transcript) family. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 1FXK_C 2ZDI_C.
Probab=96.37 E-value=0.015 Score=39.50 Aligned_cols=49 Identities=24% Similarity=0.351 Sum_probs=35.0
Q ss_pred CCceEEEecCCceeEeEEEcCCCeEEEEccCceeeecCHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 60 QGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYFVEKTMDEGKDYCERKINLLKSNFDQLIE 121 (124)
Q Consensus 60 ~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~vE~~~~eA~~~l~~r~~~l~~~i~~l~~ 121 (124)
...+++|+||+|+|+.-.+.+..+ -++.=++.+++.++.+++.+..++.
T Consensus 57 ~~~~vlV~lG~~~~vE~s~~eA~~-------------~l~~r~~~l~~~~~~l~~~~~~~~~ 105 (120)
T PF02996_consen 57 DTDKVLVSLGAGYYVEMSLEEAIE-------------FLKKRIKELEEQLEKLEKELAELQA 105 (120)
T ss_dssp STTEEEEEEETTEEEEEEHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCEEEEEeeCCeEEEecHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 568899999999999999887443 3455566666666666666665543
No 28
>KOG3478 consensus Prefoldin subunit 6, KE2 family [Posttranslational modification, protein turnover, chaperones]
Probab=92.10 E-value=1.2 Score=30.65 Aligned_cols=83 Identities=14% Similarity=0.201 Sum_probs=52.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCceee
Q 033241 15 EQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYFV 94 (124)
Q Consensus 15 e~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~v 94 (124)
+++..-+++++.++...-.....|.....+=.-.++-++-|.+ .++|+=-+| .+.|
T Consensus 8 ee~~~kyq~LQk~l~k~~~~rqkle~qL~Enk~V~~Eldlle~-----------------------d~~VYKliG-pvLv 63 (120)
T KOG3478|consen 8 EEEANKYQNLQKELEKYVESRQKLETQLQENKIVLEELDLLEE-----------------------DSNVYKLIG-PVLV 63 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHhcc-----------------------cchHHHHhc-chhh
Confidence 4455556666666666666666666655555555555555542 223333344 4667
Q ss_pred ecCHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 95 EKTMDEGKDYCERKINLLKSNFDQLIE 121 (124)
Q Consensus 95 E~~~~eA~~~l~~r~~~l~~~i~~l~~ 121 (124)
.-+.+||+.-+.+|++.++..|..+++
T Consensus 64 kqel~EAr~nV~kRlefI~~Eikr~e~ 90 (120)
T KOG3478|consen 64 KQELEEARTNVGKRLEFISKEIKRLEN 90 (120)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 788999999999999988888876654
No 29
>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=91.08 E-value=0.94 Score=27.74 Aligned_cols=31 Identities=19% Similarity=0.294 Sum_probs=26.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 7 GGMEKMSVEQLKAIKEQTDLEVNLLQDSLNN 37 (124)
Q Consensus 7 i~~~~l~le~L~~~~~~l~~ei~~l~~~~~~ 37 (124)
-+|+.||+++|......|+.||..+.+.+..
T Consensus 16 ~dLs~lSv~EL~~RIa~L~aEI~R~~~~~~~ 46 (59)
T PF06698_consen 16 EDLSLLSVEELEERIALLEAEIARLEAAIAK 46 (59)
T ss_pred CCchhcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4799999999999999999999888876554
No 30
>PF08181 DegQ: DegQ (SacQ) family; InterPro: IPR012554 This family consists of the DegQ (formerly sacQ) regulatory peptides. The DegQ family of peptides control the rates of synthesis of a class of both secreted and intracellular degradative enzymes in Bacillus subtilis. DegQ is 46 amino acids long and activates the synthesis of degradative enzymes. The expression of this peptide was shown to be subjected both to catabolite repression and DegS-DegU-mediated control. Thus allowing an increase in the rate of synthesis of degQ under conditions of nitrogen starvation [].
Probab=82.15 E-value=6.7 Score=22.26 Aligned_cols=35 Identities=26% Similarity=0.377 Sum_probs=28.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 13 SVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLES 47 (124)
Q Consensus 13 ~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~ 47 (124)
.+|+|.++.=+++.++..-..++..++..+..|+.
T Consensus 5 ~ieelkqll~rle~eirett~sl~ninksidq~dk 39 (46)
T PF08181_consen 5 KIEELKQLLWRLENEIRETTDSLRNINKSIDQYDK 39 (46)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhc
Confidence 47888888889999988888888888888877754
No 31
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=77.90 E-value=11 Score=22.76 Aligned_cols=28 Identities=11% Similarity=0.297 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 24 TDLEVNLLQDSLNNIRTATSRLESASTA 51 (124)
Q Consensus 24 l~~ei~~l~~~~~~L~~~~~~~~~~~~~ 51 (124)
++.++..+...+..++....++.+.++.
T Consensus 5 lEn~~~~~~~~i~tvk~en~~i~~~ve~ 32 (55)
T PF05377_consen 5 LENELPRIESSINTVKKENEEISESVEK 32 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444444444444444433333
No 32
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=76.31 E-value=13 Score=21.94 Aligned_cols=44 Identities=20% Similarity=0.362 Sum_probs=29.0
Q ss_pred CCHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 12 MSVEQLKAIK-------EQTDLEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 12 l~le~L~~~~-------~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
+|++++..+. .....-.+.+..++..+...+.++..+.+.|..|
T Consensus 15 fsL~eI~~~l~l~~~~~~~~~~~~~~l~~~~~~i~~~i~~L~~~~~~L~~l 65 (65)
T PF09278_consen 15 FSLEEIRELLELYDQGDPPCADRRALLEEKLEEIEEQIAELQALRAQLEHL 65 (65)
T ss_dssp --HHHHHHHHHHCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 5677777766 2334445677777888888888888777776653
No 33
>PRK05771 V-type ATP synthase subunit I; Validated
Probab=75.56 E-value=46 Score=28.98 Aligned_cols=46 Identities=20% Similarity=0.305 Sum_probs=34.7
Q ss_pred CCCHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 033241 11 KMSVEQL----KAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLS 56 (124)
Q Consensus 11 ~l~le~L----~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~ 56 (124)
.++.+++ ....+.+.+++..+.+++.+|+..+.++++.++.|+-+.
T Consensus 81 ~~~~~e~~~~~~~~~~~~~~~i~~l~~~~~~L~~~~~~l~~~~~~l~~~~ 130 (646)
T PRK05771 81 VKSLEELIKDVEEELEKIEKEIKELEEEISELENEIKELEQEIERLEPWG 130 (646)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 3455544 345677788888888889999988888888888777764
No 34
>PF09006 Surfac_D-trimer: Lung surfactant protein D coiled-coil trimerisation; InterPro: IPR015097 This domain is found in the SFTPD family, which includes lung surfactant protein D (SFTPD), conglutinin, collectin-43 and collectin-46. It forms a triple-helical parallel coiled coil, and mediates trimerisation of the protein []. ; PDB: 4DN8_A 3G84_A 2RIE_C 3IKR_B 1B08_A 2GGX_B 2OS9_C 2ORK_B 1PWB_A 2RIA_C ....
Probab=73.08 E-value=15 Score=21.39 Aligned_cols=26 Identities=23% Similarity=0.305 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 23 QTDLEVNLLQDSLNNIRTATSRLESA 48 (124)
Q Consensus 23 ~l~~ei~~l~~~~~~L~~~~~~~~~~ 48 (124)
.|.+.++.|+.++..|+.+...|+.+
T Consensus 3 aLrqQv~aL~~qv~~Lq~~fs~yKKa 28 (46)
T PF09006_consen 3 ALRQQVEALQGQVQRLQAAFSQYKKA 28 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566678888888888888888876
No 35
>PF14282 FlxA: FlxA-like protein
Probab=72.12 E-value=17 Score=24.41 Aligned_cols=37 Identities=11% Similarity=0.227 Sum_probs=29.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 10 EKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLE 46 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~ 46 (124)
..|+.++-....+.|+.+|..|+.+|.+++....+-.
T Consensus 42 ~~~~~e~k~~q~q~Lq~QI~~LqaQI~qlq~q~~~~~ 78 (106)
T PF14282_consen 42 SDLDAEQKQQQIQLLQAQIQQLQAQIAQLQSQQAEQQ 78 (106)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4578888888888888999999988888887766643
No 36
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=71.62 E-value=14 Score=24.96 Aligned_cols=29 Identities=24% Similarity=0.377 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTAT 42 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~ 42 (124)
-|+|..+++++.+++..-++.+..|...+
T Consensus 71 kEqL~~Lk~kl~~e~~~~~k~i~~le~~I 99 (100)
T PF04568_consen 71 KEQLKKLKEKLKEEIEHHRKEIDELEKHI 99 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35666666666666666666666655443
No 37
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=71.23 E-value=7.3 Score=23.16 Aligned_cols=29 Identities=14% Similarity=0.319 Sum_probs=25.4
Q ss_pred ecCHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 95 EKTMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 95 E~~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
..+++++..++.++.+.+++++..++..|
T Consensus 31 ~~~~~~~~~~l~~~~~~i~~~i~~L~~~~ 59 (65)
T PF09278_consen 31 DPPCADRRALLEEKLEEIEEQIAELQALR 59 (65)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45778889999999999999999998765
No 38
>PF12757 DUF3812: Protein of unknown function (DUF3812); InterPro: IPR024527 This family of fungal proteins represents the eisosome 1 family. Eisosome protein 1 is required for normal formation of eisosomes, large cytoplasmic protein assemblies that localize to specialised domains on plasma membrane and mark the site of endocytosis [].
Probab=71.21 E-value=19 Score=25.04 Aligned_cols=15 Identities=20% Similarity=0.206 Sum_probs=9.7
Q ss_pred CceEEEecCCceeEe
Q 033241 61 GAKMLVPLTASLYVP 75 (124)
Q Consensus 61 ~~e~lVplg~~~yv~ 75 (124)
...-.|+||+|.|+.
T Consensus 56 ~~~gkV~lGGGl~m~ 70 (126)
T PF12757_consen 56 ENAGKVNLGGGLFMD 70 (126)
T ss_pred cCCCeeeCCCCcccC
Confidence 345567777777764
No 39
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=70.94 E-value=24 Score=23.12 Aligned_cols=44 Identities=11% Similarity=0.252 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 11 KMSVEQLKAIKEQT-DLEVNLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 11 ~l~le~L~~~~~~l-~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
-+|+.++..+.+.. ....+.+.++...|...+.++..+++.|+.
T Consensus 57 g~~l~~i~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~ 101 (103)
T cd01106 57 GFSLKEIKELLKDPSEDLLEALREQKELLEEKKERLDKLIKTIDR 101 (103)
T ss_pred CCCHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46778887777666 556678888888888888888888777764
No 40
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=69.25 E-value=49 Score=27.31 Aligned_cols=45 Identities=9% Similarity=0.195 Sum_probs=20.2
Q ss_pred CCCCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 10 EKMSVEQLKAIKEQTDLEV-------NLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei-------~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
+++....+......++.++ ..+......++..+..+++-++.+..
T Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 (398)
T PTZ00454 13 TTHTERDLYEKLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRIQS 64 (398)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 3444444444444444444 44444444444444444444444433
No 41
>PRK10328 DNA binding protein, nucleoid-associated; Provisional
Probab=67.44 E-value=36 Score=24.03 Aligned_cols=45 Identities=7% Similarity=0.114 Sum_probs=30.2
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 10 EKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
-.+|+++|....+.+..-++.-.......+....+..++++.+..
T Consensus 19 re~~~e~Lee~~ekl~~vv~er~~~~~~~~~~~~er~~~l~~i~~ 63 (134)
T PRK10328 19 REFSIDVLEEMLEKFRVVTKERREEEEQQQRELAERQEKINTWLE 63 (134)
T ss_pred HhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 368899999999988877776666555555555555544444443
No 42
>PF02388 FemAB: FemAB family; InterPro: IPR003447 The femAB operon codes for two nearly identical approximately 50kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan []. These proteins are also considered as a factor influencing the level of methicillin resistance [].; GO: 0016755 transferase activity, transferring amino-acyl groups; PDB: 1XE4_A 1NE9_A 3GKR_A 1XIX_A 1P4N_A 1XF8_A 1LRZ_A.
Probab=67.21 E-value=14 Score=30.35 Aligned_cols=58 Identities=22% Similarity=0.415 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEe
Q 033241 15 EQLKAIKEQTDLEVNLLQDS----------LNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVP 75 (124)
Q Consensus 15 e~L~~~~~~l~~ei~~l~~~----------~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~ 75 (124)
+.|.....+++.+++.+.+. +..++..+..+..-++-++.+... .+.+ +||++++|+.
T Consensus 245 ~~l~~~~~~~~~~i~~l~~~l~~~~k~~~k~~~~~~q~~~~~k~~~~~~~~~~~-~~~~--~~la~~l~~~ 312 (406)
T PF02388_consen 245 ESLQEKLEKLEKEIEKLEEKLEKNPKKKNKLKELEEQLASLEKRIEEAEELIAE-YGDE--IPLAGALFIY 312 (406)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH-THHHHHHHHHHHHHHHHHHHHHHHHHHHHH-H-SE--EEEEEEEEEE
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHHHHHHHHHHHh-cCCc--ceEEEEEEEE
Confidence 34444455555555555553 444444444444444444444211 1222 8999988765
No 43
>PRK10780 periplasmic chaperone; Provisional
Probab=67.21 E-value=17 Score=26.03 Aligned_cols=36 Identities=22% Similarity=0.277 Sum_probs=21.7
Q ss_pred HHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCe
Q 033241 47 SASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARK 83 (124)
Q Consensus 47 ~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~ 83 (124)
...++|+.+. ...|+...++-++.+|+...++=|+.
T Consensus 124 ki~~ai~~va-k~~gy~~Vld~~~v~Y~~~~~DIT~~ 159 (165)
T PRK10780 124 RIQTAVKSVA-NKQGYDLVVDANAVAYNSSDKDITAD 159 (165)
T ss_pred HHHHHHHHHH-HHcCCeEEEeCCceeeeCCCCCchHH
Confidence 4445555553 24578888887777777655443433
No 44
>PF01486 K-box: K-box region; InterPro: IPR002487 MADS genes in plants encode key developmental regulators of vegetative and reproductive development. The majority of the plant MADS proteins share a stereotypical MIKC structure. It comprises (from N- to C-terminal) an N-terminal domain, which is, however, present only in a minority of proteins; a MADS domain (see PDOC00302 from PROSITEDOC, IPR002100 from INTERPRO), which is the major determinant of DNA-binding but which also performs dimerisation and accessory factor binding functions; a weakly conserved intervening (I) domain, which constitutes a key molecular determinant for the selective formation of DNA-binding dimers; a keratin-like (K-box) domain, which promotes protein dimerisation; and a C-terminal (C) domain, which is involved in transcriptional activation or in the formation of ternary or quaternary protein complexes. The 80-amino acid K-box domain was originally identified as a region with low but significant similarity to a region of keratin, which is part of the coiled-coil sequence constituting the central rod-shaped domain of keratin [, , ]. The K-box protein-protein interaction domain which mediates heterodimerization of MIKC-type MADS proteins contains several heptad repeats in which the first and the fourth positions are occupied by hydrophobic amino acids suggesting that the K-box domain forms three amphipathic alpha-helices referred to as K1, K2, and K3 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=66.65 E-value=33 Score=22.41 Aligned_cols=27 Identities=15% Similarity=0.412 Sum_probs=21.3
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033241 8 GMEKMSVEQLKAIKEQTDLEVNLLQDS 34 (124)
Q Consensus 8 ~~~~l~le~L~~~~~~l~~ei~~l~~~ 34 (124)
++..||+++|..+-++++.=+..+..+
T Consensus 42 dL~~Ls~~eL~~LE~~Le~aL~~VR~r 68 (100)
T PF01486_consen 42 DLESLSLKELQQLEQQLESALKRVRSR 68 (100)
T ss_pred cccccchHHHHHHHHhhhhhHHHHHHH
Confidence 789999999999999988655544443
No 45
>PRK10947 global DNA-binding transcriptional dual regulator H-NS; Provisional
Probab=65.27 E-value=41 Score=23.76 Aligned_cols=43 Identities=12% Similarity=0.146 Sum_probs=29.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 10 EKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTAL 52 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l 52 (124)
-.||+++|....+.+..-++.-..........+.+..+.++.+
T Consensus 19 re~~~e~Lee~~ekl~~vv~er~ee~~~~~~~~~er~~kl~~~ 61 (135)
T PRK10947 19 RECTLETLEEMLEKLEVVVNERREEESAAAAEVEERTRKLQQY 61 (135)
T ss_pred HHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3689999999999988777766666555555555544444443
No 46
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=64.71 E-value=27 Score=21.31 Aligned_cols=41 Identities=15% Similarity=0.206 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
..++.+...+++.+++.++++...|+..+..+....+.|+.
T Consensus 19 ~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~~~~~ie~ 59 (80)
T PF04977_consen 19 YYQLNQEIAELQKEIEELKKENEELKEEIERLKNDPDYIEK 59 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHH
Confidence 34455555566666666666666666666666333444444
No 47
>PHA03155 hypothetical protein; Provisional
Probab=64.02 E-value=21 Score=24.69 Aligned_cols=33 Identities=27% Similarity=0.322 Sum_probs=26.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 1 MASSKGGGMEKMSVEQLKAIKEQTDLEVNLLQDSLNN 37 (124)
Q Consensus 1 m~~~~~i~~~~l~le~L~~~~~~l~~ei~~l~~~~~~ 37 (124)
||+++ ..++.|+|....++|+-|-..|.+.+.+
T Consensus 1 mas~~----~~~tvEeLaaeL~kL~~ENK~LKkkl~~ 33 (115)
T PHA03155 1 MASGR----ACADVEELEKELQKLKIENKALKKKLLQ 33 (115)
T ss_pred CCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 77755 3789999999999999888888776643
No 48
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=63.81 E-value=51 Score=24.14 Aligned_cols=16 Identities=0% Similarity=0.196 Sum_probs=12.5
Q ss_pred CCCCHHHHHHHHHHHH
Q 033241 10 EKMSVEQLKAIKEQTD 25 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~ 25 (124)
.+|++++...+.+.+.
T Consensus 78 ~~ltl~~vI~fLq~l~ 93 (161)
T TIGR02894 78 GSLTLQDVISFLQNLK 93 (161)
T ss_pred ccCCHHHHHHHHHHHH
Confidence 6788888888777765
No 49
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=60.64 E-value=50 Score=22.36 Aligned_cols=29 Identities=21% Similarity=0.286 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 22 EQTDLEVNLLQDSLNNIRTATSRLESAST 50 (124)
Q Consensus 22 ~~l~~ei~~l~~~~~~L~~~~~~~~~~~~ 50 (124)
+.+.+.++.+.+++..|+.....+...+.
T Consensus 83 ~~l~~~~~~l~~~~~~l~~~~~~L~~~~~ 111 (118)
T cd04776 83 EKIEKRRAELEQQRRDIDAALAELDAAEE 111 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444444444444444444433
No 50
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=60.20 E-value=40 Score=22.63 Aligned_cols=58 Identities=5% Similarity=0.050 Sum_probs=37.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCC----CCCceEEEecCC
Q 033241 13 SVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLR----PQGAKMLVPLTA 70 (124)
Q Consensus 13 ~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~----~~~~e~lVplg~ 70 (124)
...++.+...+++++++.++++-..|...+..++.-.+.++.+.-. ....|+.+.+..
T Consensus 28 ~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~~dyiEe~AR~~Lg~vk~gEivy~~~~ 89 (105)
T PRK00888 28 DYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGGQEAIEERARNELGMVKPGETFYRIVP 89 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcHHHHHHHHHHHcCCCCCCCEEEEeCC
Confidence 4566777777777888888888888888888877644566554210 123566665543
No 51
>PRK14127 cell division protein GpsB; Provisional
Probab=59.81 E-value=42 Score=22.92 Aligned_cols=44 Identities=9% Similarity=0.243 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 11 KMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 11 ~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
-.+.++.-.+.+++-.+++.+...+..|+..+.++...++.+..
T Consensus 22 GYd~~EVD~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~ 65 (109)
T PRK14127 22 GYDQDEVDKFLDDVIKDYEAFQKEIEELQQENARLKAQVDELTK 65 (109)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667777778888877777777777777777776666555554
No 52
>PF11068 YlqD: YlqD protein; InterPro: IPR021297 This bacterial family of proteins has no known function. ; PDB: 4DCI_C.
Probab=59.27 E-value=59 Score=22.81 Aligned_cols=16 Identities=25% Similarity=0.544 Sum_probs=7.1
Q ss_pred eEEEcCCCeEEEEccCce
Q 033241 75 PGTLDDARKVLVDIGTGY 92 (124)
Q Consensus 75 ~a~I~~~~~VlV~lG~g~ 92 (124)
.|.+. .-|-|.+|+++
T Consensus 97 qg~vE--~~v~V~vGD~~ 112 (131)
T PF11068_consen 97 QGQVE--SFVEVKVGDNW 112 (131)
T ss_dssp EEEEE--EEEEE-TTSBH
T ss_pred eeeeE--EEEEEecCCCh
Confidence 34444 23445555554
No 53
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=58.89 E-value=56 Score=22.86 Aligned_cols=41 Identities=17% Similarity=0.296 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
+++.....++...++..++..+.++...+..+..++..|+.
T Consensus 77 lDe~~ei~~~i~~eV~~v~~dv~~i~~dv~~v~~~V~~Le~ 117 (126)
T PF07889_consen 77 LDEQKEISKQIKDEVTEVREDVSQIGDDVDSVQQMVEGLEG 117 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Confidence 44455555555555555555555555555555555544443
No 54
>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]
Probab=58.83 E-value=39 Score=27.22 Aligned_cols=81 Identities=19% Similarity=0.283 Sum_probs=53.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCe
Q 033241 8 GMEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTAT----SRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARK 83 (124)
Q Consensus 8 ~~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~----~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~ 83 (124)
+++.+..++|--.+.+++.+++.++-+-.=++..+ .++..+.+-++.+++ |||--|-|..+.=.++.-
T Consensus 21 ~~~~~~~~dly~r~k~le~~le~l~vqe~yik~e~~~lkre~~~aqeevkriqs--------vplvigqfle~vdqnt~i 92 (408)
T KOG0727|consen 21 QLSGLDKEDLYVRYKKLERELELLEVQEDYIKDEQRNLKRELLHAQEEVKRIQS--------VPLVIGQFLEAVDQNTAI 92 (408)
T ss_pred CCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc--------cchHHHHHHHhhhccCce
Confidence 44556677788888888888887765544444333 344556666666653 788888888877444444
Q ss_pred EEEEccCceeeec
Q 033241 84 VLVDIGTGYFVEK 96 (124)
Q Consensus 84 VlV~lG~g~~vE~ 96 (124)
|--.-|.+|||-.
T Consensus 93 vgsttgsny~vri 105 (408)
T KOG0727|consen 93 VGSTTGSNYYVRI 105 (408)
T ss_pred eecccCCceEEee
Confidence 4445788999865
No 55
>PF06657 Cep57_MT_bd: Centrosome microtubule-binding domain of Cep57; InterPro: IPR010597 This entry is thought to represent a centrosomal protein of 57 kDa (Cep57-related protein). It is required for spindle microtubule attachment to both kinetochores and centrosomes and functions to tether minus-ends of spindle microtubules to centrosomes. It may act by forming ring-like structures around microtubules, or by serving as a cross-linker or scaffold at the attachment site [].
Probab=58.34 E-value=41 Score=21.45 Aligned_cols=42 Identities=7% Similarity=0.087 Sum_probs=31.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 5 KGGGMEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLE 46 (124)
Q Consensus 5 ~~i~~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~ 46 (124)
.+...++=+-..|..+...++-|+..++-.+..|+.....++
T Consensus 3 ~t~r~s~~p~~~Ls~vl~~LqDE~~hm~~e~~~L~~~~~~~d 44 (79)
T PF06657_consen 3 PTSRPSQSPGEALSEVLKALQDEFGHMKMEHQELQDEYKQMD 44 (79)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 345556666778888999999998888888877766555544
No 56
>PF14131 DUF4298: Domain of unknown function (DUF4298)
Probab=58.28 E-value=49 Score=21.51 Aligned_cols=36 Identities=11% Similarity=0.174 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESAS 49 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~ 49 (124)
++++++..++..+.+..+++.+..++...+.|.+..
T Consensus 2 I~eme~~y~~~~~~l~~le~~l~~~~~~~~~~~~L~ 37 (90)
T PF14131_consen 2 IQEMEKIYNEWCELLEELEEALEKWQEAQPDYRKLR 37 (90)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466777777777777777777777777777766553
No 57
>CHL00154 rpl29 ribosomal protein L29; Validated
Probab=57.54 E-value=44 Score=20.73 Aligned_cols=32 Identities=16% Similarity=0.071 Sum_probs=24.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 033241 1 MASSKGGGMEKMSVEQLKAIKEQTDLEVNLLQ 32 (124)
Q Consensus 1 m~~~~~i~~~~l~le~L~~~~~~l~~ei~~l~ 32 (124)
|+-.+.-.+-.||+++|......+..++-+|.
T Consensus 1 M~~mk~~elr~ls~~eL~~~l~elk~elf~LR 32 (67)
T CHL00154 1 MSLPKITDIIDLTDSEISEEIIKTKKELFDLR 32 (67)
T ss_pred CCCCCHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence 44334445678999999999999998887776
No 58
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=57.16 E-value=92 Score=24.34 Aligned_cols=36 Identities=17% Similarity=0.190 Sum_probs=26.4
Q ss_pred eeEeEEEcCCCeEEEEccCceeeecCHHHHHHHHHHHH
Q 033241 72 LYVPGTLDDARKVLVDIGTGYFVEKTMDEGKDYCERKI 109 (124)
Q Consensus 72 ~yv~a~I~~~~~VlV~lG~g~~vE~~~~eA~~~l~~r~ 109 (124)
.|+.+.... .|=+-+|++|..-.+.++|.+.++--.
T Consensus 234 ~~~~~~~e~--e~~i~lg~~~iaapsREdave~l~iik 269 (290)
T COG4026 234 GYIYAEDEK--EVEILLGTVYIAAPSREDAVEELEIIK 269 (290)
T ss_pred eeeeccccc--ccceeeeeeeeecCchHHHHHHHHHHH
Confidence 467666443 344668999999999999998776433
No 59
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.84 E-value=11 Score=23.90 Aligned_cols=36 Identities=19% Similarity=0.274 Sum_probs=19.0
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 9 MEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSR 44 (124)
Q Consensus 9 ~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~ 44 (124)
+-+|.+++|..-.+++.++.+..+.+...|...-..
T Consensus 22 LLQmEieELKEknn~l~~e~q~~q~~reaL~~eneq 57 (79)
T COG3074 22 LLQMEIEELKEKNNSLSQEVQNAQHQREALERENEQ 57 (79)
T ss_pred HHHHHHHHHHHHhhHhHHHHHHHHHHHHHHHHHHHH
Confidence 334555566555555555555555555554444333
No 60
>PF11629 Mst1_SARAH: C terminal SARAH domain of Mst1; InterPro: IPR024205 The SARAH (Sav/Rassf/Hpo) domain is found at the C terminus in three classes of eukaryotic tumour suppressors that give the domain its name. In the Sav (Salvador) and Hpo (Hippo) families, the SARAH domain mediates signal transduction from Hpo via the Sav scaffolding protein to the downstream component Wts (Warts); the phosphorylation of Wts by Hpo triggers cell cycle arrest and apoptosis by down-regulating cyclin E, Diap 1 and other targets []. The SARAH domain is also involved in dimerisation, as in the human Hpo orthologue, Mst1, which homodimerises via its C-terminal SARAH domain. The SARAH domain is found associated with other domains, such as protein kinase domains, WW/rsp5/WWP domain (IPR001202 from INTERPRO), C1 domain (IPR002219 from INTERPRO), LIM domain (IPR001781 from INTERPRO), or the Ras-associating (RA) domain (IPR000159 from INTERPRO).; GO: 0004674 protein serine/threonine kinase activity; PDB: 2JO8_A.
Probab=55.75 E-value=40 Score=19.80 Aligned_cols=29 Identities=21% Similarity=0.279 Sum_probs=19.2
Q ss_pred CCCCCHHHHHHHHHHHH----HHHHHHHHHHHH
Q 033241 9 MEKMSVEQLKAIKEQTD----LEVNLLQDSLNN 37 (124)
Q Consensus 9 ~~~l~le~L~~~~~~l~----~ei~~l~~~~~~ 37 (124)
+..+|.++|.+....++ +||+.|..+|..
T Consensus 5 Lk~ls~~eL~~rl~~LD~~ME~Eieelr~RY~~ 37 (49)
T PF11629_consen 5 LKFLSYEELQQRLASLDPEMEQEIEELRQRYQA 37 (49)
T ss_dssp GGGS-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhhCCHHHHHHHHHhCCHHHHHHHHHHHHHHHH
Confidence 46788999988766555 566666666554
No 61
>PF08946 Osmo_CC: Osmosensory transporter coiled coil; InterPro: IPR015041 The osmosensory transporter coiled coil is a C-terminal domain found in various bacterial osmoprotective transporters, such as ProP, Proline/betaine transporter, Proline permease 2 and the citrate proton symporters. It adopts an antiparallel coiled-coil structure, and is essential for osmosensory and osmoprotectant transporter function []. ; PDB: 1R48_B.
Probab=55.49 E-value=35 Score=19.77 Aligned_cols=29 Identities=10% Similarity=0.328 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 17 LKAIKEQTDLEVNLLQDSLNNIRTATSRL 45 (124)
Q Consensus 17 L~~~~~~l~~ei~~l~~~~~~L~~~~~~~ 45 (124)
|+..+.-+++.++.+.++|..|+.....+
T Consensus 10 Lqe~~d~IEqkiedid~qIaeLe~KR~~L 38 (46)
T PF08946_consen 10 LQEHYDNIEQKIEDIDEQIAELEAKRQRL 38 (46)
T ss_dssp -----THHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhHHHhHHHHHHHHHHHHHHHHHH
Confidence 44456666777777777777666665544
No 62
>PRK09343 prefoldin subunit beta; Provisional
Probab=55.37 E-value=26 Score=24.06 Aligned_cols=84 Identities=23% Similarity=0.222 Sum_probs=55.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCcee
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYF 93 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~ 93 (124)
+.++.+-.+.+....+.+..++.....+..++...-+.-.-++. + +.+||+-...+
T Consensus 16 ~q~lq~~l~~~~~q~~~le~q~~e~~~~~~EL~~L~~d~~VYk~----------V-G~vlv~qd~~e------------- 71 (121)
T PRK09343 16 LQQLQQQLERLLQQKSQIDLELREINKALEELEKLPDDTPIYKI----------V-GNLLVKVDKTK------------- 71 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcchhHHH----------h-hHHHhhccHHH-------------
Confidence 45556666677778888888888888888888776554444442 1 12555554443
Q ss_pred eecCHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 94 VEKTMDEGKDYCERKINLLKSNFDQLIE 121 (124)
Q Consensus 94 vE~~~~eA~~~l~~r~~~l~~~i~~l~~ 121 (124)
+..++++-++|++.+++.++++...+++
T Consensus 72 ~~~~l~~r~E~ie~~ik~lekq~~~l~~ 99 (121)
T PRK09343 72 VEKELKERKELLELRSRTLEKQEKKLRE 99 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456777778888777777777766654
No 63
>PF12210 Hrs_helical: Hepatocyte growth factor-regulated tyrosine kinase substrate; InterPro: IPR024641 This domain comprises the helical region of hepatocyte growth factor-regulated tyrosine kinase substrate (HRS). It is approximately 100 amino acids in length. Hrs, together with signal transducing adaptor molecule (STAM), forms the ESCRT-0 complex, which sorts ubiquitinated cell surface receptors to lysosomes for degradation []. ; PDB: 3F1I_H.
Probab=55.12 E-value=61 Score=21.70 Aligned_cols=28 Identities=14% Similarity=0.198 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 033241 29 NLLQDSLNNIRTATSRLESASTALHDLS 56 (124)
Q Consensus 29 ~~l~~~~~~L~~~~~~~~~~~~~l~~L~ 56 (124)
+.-...+..|+..+..+.+|..+|+.|.
T Consensus 56 ee~R~~~E~lQdkL~qi~eAR~AlDalR 83 (96)
T PF12210_consen 56 EEKRVYYEGLQDKLAQIKEARAALDALR 83 (96)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455567778888888888888888774
No 64
>PF06013 WXG100: Proteins of 100 residues with WXG; InterPro: IPR010310 ESAT-6 is a small protein appears to be of fundamental importance in virulence and protective immunity in Mycobacterium tuberculosis. Homologues have been detected in other Gram-positive bacterial species. It may represent a novel secretion system potentially driven by the PF01580 from PFAM domains in the YukA-like proteins []. Members of this protein family include secretion targets for type main variants of type VII secretion systems (T7SS), one found in the Actinobacteria, one found in the Firmicutes. This model was derived through iteration from PF06013 from PFAM. The best characterised member of this family is ESAT-6 from Mycobacterium tuberculosis. Members of this family usually are ~100 amino acids in length but occasionally have long C-terminal extension. ; PDB: 3FAV_A 1WA8_A 3Q4H_B 2KG7_A 2VRZ_B 2VS0_B 3OGI_A 3H6P_B 3GVM_B 3GWK_C ....
Probab=54.79 E-value=44 Score=19.93 Aligned_cols=34 Identities=26% Similarity=0.401 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 12 MSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRL 45 (124)
Q Consensus 12 l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~ 45 (124)
.++++|......+......+...+..|+..+..+
T Consensus 4 vd~~~l~~~a~~~~~~~~~l~~~~~~l~~~~~~l 37 (86)
T PF06013_consen 4 VDPEQLRAAAQQLQAQADELQSQLQQLESSIDSL 37 (86)
T ss_dssp SCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5688888888888877777777777776666554
No 65
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=53.52 E-value=84 Score=24.14 Aligned_cols=38 Identities=16% Similarity=0.150 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 15 EQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTAL 52 (124)
Q Consensus 15 e~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l 52 (124)
.++.+..++|.+|+..|+.+..+++....+.....+.+
T Consensus 72 ~~l~~en~~L~~e~~~l~~~~~~~~~l~~en~~L~~lL 109 (276)
T PRK13922 72 FDLREENEELKKELLELESRLQELEQLEAENARLRELL 109 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34444445555555555555554444444444443333
No 66
>PF13118 DUF3972: Protein of unknown function (DUF3972)
Probab=53.50 E-value=13 Score=26.20 Aligned_cols=61 Identities=18% Similarity=0.286 Sum_probs=31.9
Q ss_pred ccCCCCCceEEEecCCceeEeEEEcCCCeEEEEc--c----CceeeecCHHHHHHHHHHHHHHHHHHHH
Q 033241 55 LSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDI--G----TGYFVEKTMDEGKDYCERKINLLKSNFD 117 (124)
Q Consensus 55 L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~l--G----~g~~vE~~~~eA~~~l~~r~~~l~~~i~ 117 (124)
|....++..+++++++|.. +-|+....-++.. . ...|||+|+.--....++=+..-++.|.
T Consensus 22 l~~K~e~g~~~Ie~~~g~~--~~v~~~~~~~~~~~~~~~~~~~~fvEKTi~til~LheKvl~aKdETI~ 88 (126)
T PF13118_consen 22 LKSKNEDGKIYIEASSGTK--ALVPKAENELVSMNMSSHALDPMFVEKTIGTILNLHEKVLDAKDETIE 88 (126)
T ss_pred ccccccCCeEEEEcCcchH--HHhhHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHHhHHHHHH
Confidence 3334467889999999872 3333222211111 1 2259999955444444444444444333
No 67
>PF03980 Nnf1: Nnf1 ; InterPro: IPR007128 NNF1 is an essential yeast gene required for proper spindle orientation, nucleolar and nuclear envelope structure and mRNA export [].
Probab=53.00 E-value=64 Score=21.30 Aligned_cols=46 Identities=11% Similarity=0.046 Sum_probs=36.1
Q ss_pred CCCCCCCCHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 6 GGGMEKMSVEQLKA--IKEQTDLEVNLLQDSLNNIRTATSRLESASTA 51 (124)
Q Consensus 6 ~i~~~~l~le~L~~--~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~ 51 (124)
++...+++++++.. +........+.|...++.++.....+.+.+..
T Consensus 58 ~~~~~~l~P~~~i~a~l~~~~~~~~~~L~~~l~~l~~eN~~L~~~i~~ 105 (109)
T PF03980_consen 58 PVWRHSLTPEEDIRAHLAPYKKKEREQLNARLQELEEENEALAEEIQE 105 (109)
T ss_pred CCCCCCCChHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 78899999999877 45677778888888888888777777666544
No 68
>PF12958 DUF3847: Protein of unknown function (DUF3847); InterPro: IPR024215 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=52.70 E-value=63 Score=21.13 Aligned_cols=34 Identities=18% Similarity=0.386 Sum_probs=27.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 13 SVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLE 46 (124)
Q Consensus 13 ~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~ 46 (124)
++++|.+.....+.+++....++.+|+.....+.
T Consensus 2 ~Le~l~~e~e~~~~kl~q~e~~~k~L~nr~k~l~ 35 (86)
T PF12958_consen 2 TLEELQAEIEKAEKKLEQAEHKIKQLENRKKKLE 35 (86)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5788888888888888888888888888777664
No 69
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=52.45 E-value=51 Score=19.98 Aligned_cols=31 Identities=19% Similarity=0.308 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 22 EQTDLEVNLLQDSLNNIRTATSRLESASTAL 52 (124)
Q Consensus 22 ~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l 52 (124)
.++.++++.++.++..++....++..-++.+
T Consensus 20 ~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 20 YQLNQEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445555566666666665555555554444
No 70
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=52.11 E-value=74 Score=21.72 Aligned_cols=45 Identities=20% Similarity=0.341 Sum_probs=26.4
Q ss_pred CCCHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 11 KMSVEQLKAIKEQT-------DLEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 11 ~l~le~L~~~~~~l-------~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
-+|++++..+.... ....+.+..++..+...+.++....+.|+.+
T Consensus 57 G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~ 108 (127)
T TIGR02047 57 DMSLAEIRQLLRYQDKPEKSCSDVNALLDEHISHVRARIIKLQALIEQLVDL 108 (127)
T ss_pred CCCHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36677777654421 2234456666666666666666666666654
No 71
>cd00894 PI3Kc_IB_gamma Phosphoinositide 3-kinase (PI3K), class IB, gamma isoform, catalytic domain; The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. PI3Ks can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class I PI3Ks are the only enzymes capable of converting PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. Class I enzymes are heterodimers and exist in multiple isoforms consisting of one catalytic subunit (out of four isoforms) and one of several regulatory subunits. They are further classified into class IA (alpha, beta and
Probab=51.74 E-value=71 Score=26.28 Aligned_cols=38 Identities=18% Similarity=0.165 Sum_probs=24.5
Q ss_pred HHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEE
Q 033241 48 ASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVL 85 (124)
Q Consensus 48 ~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~Vl 85 (124)
..+.|+.++...-.....+|+..++.+.|-+.+.-+|+
T Consensus 39 l~~~l~~~~~~~~~~~~~lPl~P~~~~~~i~~~~~~v~ 76 (365)
T cd00894 39 LKQKLENLQNLNLPESFRVPYDPGLRAGALVIEKCKVM 76 (365)
T ss_pred HHHHHHHhhhccCCCCCCCCCCCceEEEEEEcCceEEE
Confidence 33444444322234578899999999999887765554
No 72
>KOG3048 consensus Molecular chaperone Prefoldin, subunit 5 [Posttranslational modification, protein turnover, chaperones]
Probab=51.11 E-value=92 Score=22.53 Aligned_cols=74 Identities=18% Similarity=0.309 Sum_probs=51.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccCC-----------------CCCceEEEecCCceeEeEEEcCCCeEEEEccCceeeec
Q 033241 34 SLNNIRTATSRLESASTALHDLSLR-----------------PQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYFVEK 96 (124)
Q Consensus 34 ~~~~L~~~~~~~~~~~~~l~~L~~~-----------------~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~vE~ 96 (124)
++...+....+-.++++.+.--..+ .+....||+||-|-||.=...+.. +|
T Consensus 38 ~L~~aq~k~~~~~~aln~~~~~~eGk~~LVPLTsSlYVPGkl~d~~k~lVDIGTGYyVEK~~e~ak--------dy---- 105 (153)
T KOG3048|consen 38 ALKGAQTKYEESIAALNDVQAANEGKKLLVPLTSSLYVPGKLSDNSKFLVDIGTGYYVEKDAEDAK--------DY---- 105 (153)
T ss_pred HHHHHHHHHHHHHHHHhhcccCCCCCeEEEecccceeccceeccccceeEeccCceEEeechHHHH--------HH----
Confidence 3666666667777777776653321 246789999999999987765533 33
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHh
Q 033241 97 TMDEGKDYCERKINLLKSNFDQLI 120 (124)
Q Consensus 97 ~~~eA~~~l~~r~~~l~~~i~~l~ 120 (124)
++.=++++++.++.++.-+.+-.
T Consensus 106 -fkRKve~l~kq~e~i~~i~~eK~ 128 (153)
T KOG3048|consen 106 -FKRKVEYLTKQIEQIEGILKEKT 128 (153)
T ss_pred -HHHHHHHHHHHHHHHHHHHHHHH
Confidence 35668899999988888776543
No 73
>PF10046 BLOC1_2: Biogenesis of lysosome-related organelles complex-1 subunit 2 ; InterPro: IPR019269 This entry represents a family of proteins that play a role in cellular proliferation, as well as in the biogenesis of specialised organelles of the endosomal-lysosomal system [].
Probab=50.88 E-value=69 Score=21.05 Aligned_cols=18 Identities=22% Similarity=0.346 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHHHHhhc
Q 033241 38 IRTATSRLESASTALHDL 55 (124)
Q Consensus 38 L~~~~~~~~~~~~~l~~L 55 (124)
+...+.++..+...|+.+
T Consensus 71 Ie~~V~~LE~~v~~LD~y 88 (99)
T PF10046_consen 71 IEEQVTELEQTVYELDEY 88 (99)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 333555555555544443
No 74
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=50.61 E-value=74 Score=21.29 Aligned_cols=45 Identities=18% Similarity=0.324 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 11 KMSVEQLKAIKEQTD-------LEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 11 ~l~le~L~~~~~~l~-------~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
-+|++++..+..... .-.+.+++++..+...+.++......|..+
T Consensus 57 G~sl~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~ 108 (123)
T cd04770 57 GFSLAEIRELLSLRDDGAAPCAEVRALLEEKLAEVEAKIAELQALRAELAGL 108 (123)
T ss_pred CCCHHHHHHHHHhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 366777776655332 334666777777777777777777666654
No 75
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=50.11 E-value=36 Score=21.58 Aligned_cols=31 Identities=16% Similarity=0.291 Sum_probs=22.6
Q ss_pred EEccCceeeecCHHHHHHHHHHHHHHHHHHH
Q 033241 86 VDIGTGYFVEKTMDEGKDYCERKINLLKSNF 116 (124)
Q Consensus 86 V~lG~g~~vE~~~~eA~~~l~~r~~~l~~~i 116 (124)
..+..|-|-++|+++|++...+-...+..-+
T Consensus 48 ~~~~lG~~p~~sl~~AR~~a~~~~~~~~~G~ 78 (89)
T PF13356_consen 48 RRITLGRYPELSLAEAREKARELRALVRQGI 78 (89)
T ss_dssp EEEEEEECTTS-HHHHHHHHHHHHHHHCTT-
T ss_pred EEeccCCCccCCHHHHHHHHHHHHHHHHcCC
Confidence 3456678999999999999887777665544
No 76
>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].
Probab=49.90 E-value=80 Score=21.83 Aligned_cols=39 Identities=21% Similarity=0.247 Sum_probs=30.2
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 9 MEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLES 47 (124)
Q Consensus 9 ~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~ 47 (124)
.+.--++.|.+...+++.|+..++.++..|........+
T Consensus 13 ~~~~~ve~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~ 51 (120)
T PF12325_consen 13 PSVQLVERLQSQLRRLEGELASLQEELARLEAERDELRE 51 (120)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344558889999999999999999888888776666543
No 77
>COG3879 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.90 E-value=1e+02 Score=24.04 Aligned_cols=31 Identities=13% Similarity=0.177 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 16 QLKAIKEQTDLEVNLLQDSLNNIRTATSRLE 46 (124)
Q Consensus 16 ~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~ 46 (124)
.|......+++..+.|++++..++..++.+.
T Consensus 54 ~L~~e~~s~Q~~~~~L~~ev~~~~~~~~s~~ 84 (247)
T COG3879 54 DLVKELRSLQKKVNTLAAEVEDLENKLDSVR 84 (247)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5666666777777777777777777777666
No 78
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=49.77 E-value=74 Score=21.06 Aligned_cols=44 Identities=18% Similarity=0.281 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 11 KMSVEQLKAIKEQT-------DLEVNLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 11 ~l~le~L~~~~~~l-------~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
-+|++++..+.... ....+.+.+++..|...+.++..+++.|+.
T Consensus 57 G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~ 107 (113)
T cd01109 57 GMSIKDIKEYAELRREGDSTIPERLELLEEHREELEEQIAELQETLAYLDY 107 (113)
T ss_pred CCCHHHHHHHHHHHccCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36777777665432 344566777777777777777777776665
No 79
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=49.71 E-value=56 Score=19.64 Aligned_cols=38 Identities=13% Similarity=0.273 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 15 EQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTAL 52 (124)
Q Consensus 15 e~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l 52 (124)
.+|..-...++..+..++.+.+.+...+.++++.+.-|
T Consensus 3 ~elEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk~l 40 (55)
T PF05377_consen 3 DELENELPRIESSINTVKKENEEISESVEKIEENVKDL 40 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555556666666666666666666665554433
No 80
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=49.56 E-value=59 Score=21.28 Aligned_cols=44 Identities=16% Similarity=0.324 Sum_probs=26.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 11 KMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 11 ~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
-+|++++..+...-. ..+.+.+++..+...+.++......|..+
T Consensus 57 G~~l~ei~~~~~~~~-~~~~l~~~~~~l~~~i~~l~~~~~~l~~~ 100 (102)
T cd04775 57 GLPLEEIAGCLAQPH-VQAILEERLQSLNREIQRLRQQQQVLAAI 100 (102)
T ss_pred CCCHHHHHHHHcCCc-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 366777766543221 34566666777777777777776666553
No 81
>PF09340 NuA4: Histone acetyltransferase subunit NuA4; InterPro: IPR015418 The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast []. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control [].
Probab=49.41 E-value=55 Score=20.91 Aligned_cols=31 Identities=13% Similarity=0.225 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSR 44 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~ 44 (124)
|.+|.+.+++++.++..|+.+|-.+...-=+
T Consensus 4 L~~l~~~k~~Le~~L~~lE~qIy~~Et~YL~ 34 (80)
T PF09340_consen 4 LKELLQKKKKLEKDLAALEKQIYDKETSYLE 34 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677888888888888888877777654433
No 82
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=49.24 E-value=50 Score=22.37 Aligned_cols=42 Identities=17% Similarity=0.318 Sum_probs=28.4
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 8 GMEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESAS 49 (124)
Q Consensus 8 ~~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~ 49 (124)
.+.+|+++=|...++.+...+..+.+++..++....++....
T Consensus 62 rLaQl~ieYLl~~q~~L~~~~~~l~~~~~~~~~~~~~l~~~~ 103 (118)
T PF13815_consen 62 RLAQLSIEYLLHCQEYLSSQLEQLEERLQELQQEIEKLKQKL 103 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345666666666777777777777777777776666655444
No 83
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=49.02 E-value=34 Score=22.23 Aligned_cols=27 Identities=15% Similarity=0.290 Sum_probs=23.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 97 TMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 97 ~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
+.++..+++.++...++++++.++..+
T Consensus 71 ~~~~~~~~l~~~~~~l~~~i~~l~~~~ 97 (97)
T cd04782 71 NPDELIELLKKQEKEIKEEIEELQKIK 97 (97)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 457889999999999999999998753
No 84
>PF02609 Exonuc_VII_S: Exonuclease VII small subunit; InterPro: IPR003761 Exonuclease VII is composed of two non-identical subunits; one large subunit and 4 small ones []. This enzyme catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield nucleoside 5'-phosphates.; GO: 0008855 exodeoxyribonuclease VII activity, 0006308 DNA catabolic process, 0009318 exodeoxyribonuclease VII complex; PDB: 1VP7_F.
Probab=49.01 E-value=52 Score=19.06 Aligned_cols=34 Identities=12% Similarity=0.134 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 10 EKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATS 43 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~ 43 (124)
..+|+++...++++-..-+...++.+......+.
T Consensus 18 ~~~sLdes~~lyeeg~~l~~~c~~~L~~~e~~i~ 51 (53)
T PF02609_consen 18 GELSLDESLKLYEEGMELIKKCQERLEEAEQKIE 51 (53)
T ss_dssp T-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4567777777777776666666665555554443
No 85
>PRK14127 cell division protein GpsB; Provisional
Probab=48.98 E-value=84 Score=21.44 Aligned_cols=37 Identities=14% Similarity=0.178 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESAST 50 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~ 50 (124)
|+++..-++.+..++..|..++..|+..+.++..-+.
T Consensus 32 Ld~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~~ 68 (109)
T PRK14127 32 LDDVIKDYEAFQKEIEELQQENARLKAQVDELTKQVS 68 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 4566666777777777777777777777777766444
No 86
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation [].
Probab=47.78 E-value=80 Score=25.13 Aligned_cols=35 Identities=14% Similarity=0.288 Sum_probs=26.1
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 9 MEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATS 43 (124)
Q Consensus 9 ~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~ 43 (124)
++.|++++|.++...|...|+..-.++...-+...
T Consensus 216 L~~Mt~~EL~qL~~~L~~qIq~vfeeLt~~vQEKD 250 (285)
T PF06937_consen 216 LNSMTLDELKQLNEKLLQQIQDVFEELTQQVQEKD 250 (285)
T ss_pred hhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67899999999999888888776666555444333
No 87
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=47.21 E-value=36 Score=23.31 Aligned_cols=28 Identities=11% Similarity=0.186 Sum_probs=22.8
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 96 KTMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 96 ~~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
.+.++...++..++..++.++.+++..+
T Consensus 75 ~~~~~~~~~l~~~~~~l~~~i~~L~~~~ 102 (127)
T TIGR02047 75 KSCSDVNALLDEHISHVRARIIKLQALI 102 (127)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567788889999999999998887754
No 88
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=47.08 E-value=52 Score=23.47 Aligned_cols=14 Identities=29% Similarity=0.330 Sum_probs=5.6
Q ss_pred HHHHHHHHHHHHHH
Q 033241 23 QTDLEVNLLQDSLN 36 (124)
Q Consensus 23 ~l~~ei~~l~~~~~ 36 (124)
.+..++..++..+.
T Consensus 90 ~l~~~~k~l~~eL~ 103 (169)
T PF07106_consen 90 ELKKEVKSLEAELA 103 (169)
T ss_pred HHHHHHHHHHHHHH
Confidence 33334444444443
No 89
>KOG3047 consensus Predicted transcriptional regulator UXT [Transcription]
Probab=46.64 E-value=1.1e+02 Score=21.93 Aligned_cols=88 Identities=17% Similarity=0.201 Sum_probs=48.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHhhccC----------CCCCceEEEecCCceeEeEEEcCCCeEE
Q 033241 17 LKAIKEQTDLEVNLLQDSLNNIRTATSRLESAS-TALHDLSL----------RPQGAKMLVPLTASLYVPGTLDDARKVL 85 (124)
Q Consensus 17 L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~-~~l~~L~~----------~~~~~e~lVplg~~~yv~a~I~~~~~Vl 85 (124)
+.......+.-.+.+. .+.+|+....++.++. ..++.=.. -.....+.|-||.|+|+.-++.+.=
T Consensus 32 i~k~~d~~dKl~eQ~a-eY~kLk~t~eRL~eaahkel~~ktdLGcnfFmdi~VpDTk~i~VaL~~~fflElkLadAi--- 107 (157)
T KOG3047|consen 32 IAKEEDEFDKLQEQCA-EYAKLKFTCERLLEAAHKELEGKTDLGCNFFMDIEVPDTKHIVVALCDDFFLELKLADAI--- 107 (157)
T ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhchhhhhccccccceeeEeeecCCcceEEEEeecceeeeehHHHHH---
Confidence 3333333333333333 3667888888877654 22222111 1245788999999999998887632
Q ss_pred EEccCceeeecCHHHHHHHHHHHHHHHHHHHHH
Q 033241 86 VDIGTGYFVEKTMDEGKDYCERKINLLKSNFDQ 118 (124)
Q Consensus 86 V~lG~g~~vE~~~~eA~~~l~~r~~~l~~~i~~ 118 (124)
+.++.-.+.++.=.+.|.+...+
T Consensus 108 ----------Kf~DRK~dlLkel~ekLqKdsmk 130 (157)
T KOG3047|consen 108 ----------KFCDRKMDLLKELMEKLQKDSMK 130 (157)
T ss_pred ----------HHHHHhHHHHHHHHHHHHHhHHH
Confidence 23444445555555555444433
No 90
>PF00384 Molybdopterin: Molybdopterin oxidoreductase; InterPro: IPR006656 This domain is found in a number of molybdopterin-containing oxidoreductases, tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where a single domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor []. ; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E 3DMR_A 4DMR_A 1H5N_C 1E5V_A ....
Probab=46.30 E-value=30 Score=27.70 Aligned_cols=28 Identities=29% Similarity=0.381 Sum_probs=23.1
Q ss_pred ccCceeeecCHHHHHHHHHHHHHHHHHH
Q 033241 88 IGTGYFVEKTMDEGKDYCERKINLLKSN 115 (124)
Q Consensus 88 lG~g~~vE~~~~eA~~~l~~r~~~l~~~ 115 (124)
-|.|=|++.|-|||.+.+.++++.+.+.
T Consensus 12 rg~~~~~~isWdeAl~~ia~~l~~~~~~ 39 (432)
T PF00384_consen 12 RGDGKFVRISWDEALDEIAEKLKEIIDK 39 (432)
T ss_dssp TTSSSEEE--HHHHHHHHHHHHHHHHHH
T ss_pred CCCCCEEEccHHHHHHHhhhhccccccc
Confidence 5889999999999999999999987654
No 91
>PF08285 DPM3: Dolichol-phosphate mannosyltransferase subunit 3 (DPM3); InterPro: IPR013174 This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex [].
Probab=46.13 E-value=23 Score=23.33 Aligned_cols=33 Identities=15% Similarity=0.226 Sum_probs=28.8
Q ss_pred EEccCceeeecCHHHHHHHHHHHHHHHHHHHHH
Q 033241 86 VDIGTGYFVEKTMDEGKDYCERKINLLKSNFDQ 118 (124)
Q Consensus 86 V~lG~g~~vE~~~~eA~~~l~~r~~~l~~~i~~ 118 (124)
..+|-|++--.+++||-+-+.+.|++.++.+++
T Consensus 54 ~~lgy~v~tFnDcpeA~~eL~~eI~eAK~dLr~ 86 (91)
T PF08285_consen 54 FTLGYGVATFNDCPEAAKELQKEIKEAKADLRK 86 (91)
T ss_pred HHHHHhhhccCCCHHHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999999999998887654
No 92
>PF15397 DUF4618: Domain of unknown function (DUF4618)
Probab=45.26 E-value=99 Score=24.31 Aligned_cols=43 Identities=14% Similarity=0.227 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q 033241 15 EQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSL 57 (124)
Q Consensus 15 e~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~ 57 (124)
.+|+...+..+..+..|++++.+|+..+....+-+..|.+.++
T Consensus 70 ~eLqe~eek~e~~l~~Lq~ql~~l~akI~k~~~el~~L~TYkD 112 (258)
T PF15397_consen 70 AELQEWEEKEESKLSKLQQQLEQLDAKIQKTQEELNFLSTYKD 112 (258)
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 5677777888889999999999999999998888888888764
No 93
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=45.02 E-value=1e+02 Score=21.29 Aligned_cols=25 Identities=20% Similarity=0.283 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 30 LLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 30 ~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
.+++++..+...+.++....+.|..
T Consensus 82 ~l~~k~~~i~~~i~~L~~~~~~L~~ 106 (131)
T cd04786 82 ALERKVADIEALEARLAQNKAQLLV 106 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444444444433
No 94
>PF10393 Matrilin_ccoil: Trimeric coiled-coil oligomerisation domain of matrilin; InterPro: IPR019466 This entry represents a short domain found the matrilin (cartilage matrix) proteins. It forms a coiled coil structure and contains a single cysteine residue at its start which is likely to form a di-sulphide bridge with a corresponding cysteine in an upstream EGF domain (IPR006209 from INTERPRO), thereby spanning the VWA domain of the protein (IPR002035 from INTERPRO).This domain is likely to be responsible for protein trimerisation []. ; PDB: 1AQ5_C.
Probab=44.47 E-value=63 Score=18.74 Aligned_cols=32 Identities=22% Similarity=0.323 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 15 EQLKAIKEQTDLEVNLLQDSLNNIRTATSRLE 46 (124)
Q Consensus 15 e~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~ 46 (124)
|-+..++.+....++.|.+.+..+..++..++
T Consensus 12 Eslv~FQ~~v~~~lq~Lt~kL~~vs~RLe~LE 43 (47)
T PF10393_consen 12 ESLVAFQNKVTSALQSLTQKLDAVSKRLEALE 43 (47)
T ss_dssp THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34667777777788888877777666666554
No 95
>PF10400 Vir_act_alpha_C: Virulence activator alpha C-term; InterPro: IPR018309 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response []. This entry represents the C-terminal domain.; PDB: 1YG2_A.
Probab=44.47 E-value=48 Score=20.67 Aligned_cols=29 Identities=10% Similarity=0.151 Sum_probs=24.5
Q ss_pred ecCHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 95 EKTMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 95 E~~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
..+.++++..++++.+..++.+..+++++
T Consensus 16 ~~~~~~~~~~l~~~~~~~~~~l~~~~~~~ 44 (90)
T PF10400_consen 16 HLDPEEAIELLEERREQHEERLAEYEEIE 44 (90)
T ss_dssp TS-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999999988753
No 96
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=44.16 E-value=98 Score=24.64 Aligned_cols=30 Identities=13% Similarity=0.220 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 17 LKAIKEQTDLEVNLLQDSLNNIRTATSRLE 46 (124)
Q Consensus 17 L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~ 46 (124)
|....+++..+++.+.++...++..+.+.+
T Consensus 235 l~~el~~l~~~i~~~~~~k~~l~~eI~e~~ 264 (325)
T PF08317_consen 235 LQEELEELEEKIEELEEQKQELLAEIAEAE 264 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333333444444444444444444444433
No 97
>PF04728 LPP: Lipoprotein leucine-zipper; InterPro: IPR006817 This repeating sequence, NAKVDQLSNDV, is found in the enterobacterial outer membrane lipoprotein LPP. The outer membrane lipoprotein is the most abundant protein in an Escherichia coli cell. The messenger RNA for the lipoprotein of the E. coli outer membrane codes for a putative precursor, prolipoprotein, which has 20 additional amino acid residues extending from the amino terminus of the lipoprotein.; GO: 0019867 outer membrane; PDB: 1JCC_A 2GUV_C 2GUS_A 1JCD_A 1KFM_A 1T8Z_D 1KFN_A 1EQ7_A.
Probab=43.82 E-value=72 Score=19.23 Aligned_cols=16 Identities=19% Similarity=0.339 Sum_probs=6.0
Q ss_pred HHHHHHHHHHHHHHHH
Q 033241 22 EQTDLEVNLLQDSLNN 37 (124)
Q Consensus 22 ~~l~~ei~~l~~~~~~ 37 (124)
++|...+..|++.+..
T Consensus 13 q~L~~kvdqLs~dv~~ 28 (56)
T PF04728_consen 13 QTLNSKVDQLSSDVNA 28 (56)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3333333333333333
No 98
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=43.76 E-value=83 Score=20.60 Aligned_cols=43 Identities=23% Similarity=0.302 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 12 MSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 12 l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
+|++++..+... ....+.+.+++..+...+.++....+.|..+
T Consensus 58 ~~l~ei~~~l~~-~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~ 100 (102)
T cd04789 58 LSLKECLACLQG-KLTRSLLLERLSSLAEQIARKQQARDLLAAL 100 (102)
T ss_pred CCHHHHHHHHcC-CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566666654431 1234567777888888888888887777654
No 99
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=43.74 E-value=93 Score=20.49 Aligned_cols=45 Identities=20% Similarity=0.317 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 11 KMSVEQLKAIKEQTD--LEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 11 ~l~le~L~~~~~~l~--~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
-+|+.++..+..... .-...+.+++..|...+.++....+.|+.+
T Consensus 58 G~sl~~i~~l~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~ 104 (108)
T cd01107 58 GFPLEEIKEILDADNDDELRKLLREKLAELEAEIEELQRILRLLEDR 104 (108)
T ss_pred CCCHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 366777777655443 345567777777888888877777777653
No 100
>PF09304 Cortex-I_coil: Cortexillin I, coiled coil; InterPro: IPR015383 This domain is predominantly found in the actin-bundling protein cortexillin I from Dictyostelium discoideum (Slime mold). The domain has a structure consisting of an 18-heptad-repeat alpha-helical coiled-coil, and is a prerequisite for the assembly of Cortexillin I []. ; PDB: 1D7M_A.
Probab=43.72 E-value=1e+02 Score=21.02 Aligned_cols=33 Identities=21% Similarity=0.140 Sum_probs=15.9
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 13 SVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRL 45 (124)
Q Consensus 13 ~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~ 45 (124)
|.++|...+++|..-++.|+++-......+.++
T Consensus 31 S~~eL~kqkd~L~~~l~~L~~q~~s~~qr~~eL 63 (107)
T PF09304_consen 31 SQGELAKQKDQLRNALQSLQAQNASRNQRIAEL 63 (107)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555555555555544444444444443
No 101
>PHA02047 phage lambda Rz1-like protein
Probab=43.64 E-value=92 Score=20.97 Aligned_cols=25 Identities=16% Similarity=0.170 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 17 LKAIKEQTDLEVNLLQDSLNNIRTA 41 (124)
Q Consensus 17 L~~~~~~l~~ei~~l~~~~~~L~~~ 41 (124)
|.+..+.++..+..++++...|++.
T Consensus 39 la~qLE~a~~r~~~~Q~~V~~l~~k 63 (101)
T PHA02047 39 QTARLEALEVRYATLQRHVQAVEAR 63 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333444444444444444444443
No 102
>TIGR03042 PS_II_psbQ_bact photosystem II protein PsbQ. This protein through the member sll1638 from Synechocystis sp. PCC 6803, was shown to be part of the cyanobacteria photosystem II. It is homologous to (but quite diverged from) the chloroplast PsbQ protein, called oxygen-evolving enhancer protein 3 (OEE3). We designate this cyanobacteria protein PsbQ by homology.
Probab=43.06 E-value=1.1e+02 Score=21.81 Aligned_cols=39 Identities=18% Similarity=0.237 Sum_probs=24.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 4 SKGGGMEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATS 43 (124)
Q Consensus 4 ~~~i~~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~ 43 (124)
|......+-|+++|.+++.+.+ .++...+++..|+.-++
T Consensus 22 p~~~~p~tysp~~l~~i~~~~~-~i~~~~~r~~eLk~lI~ 60 (142)
T TIGR03042 22 PAAAVPPTYSPAQLAQIQRQAE-GIEAAKDRLPELASLVA 60 (142)
T ss_pred CcccCCCCCCHHHHHHHHHHHH-HHHHHHHhhHHHHHHHh
Confidence 3333367899999998877665 34555555555555443
No 103
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=43.04 E-value=1.2e+02 Score=23.07 Aligned_cols=9 Identities=11% Similarity=0.394 Sum_probs=3.2
Q ss_pred HHHHHHHHH
Q 033241 32 QDSLNNIRT 40 (124)
Q Consensus 32 ~~~~~~L~~ 40 (124)
++.+..|+.
T Consensus 83 ~~el~~L~~ 91 (251)
T PF11932_consen 83 EQELASLEQ 91 (251)
T ss_pred HHHHHHHHH
Confidence 333333333
No 104
>PF10148 SCHIP-1: Schwannomin-interacting protein 1; InterPro: IPR015649 SCHIP-1 is a coiled-coil protein that specifically associates with schwannomin in vitro and in vivo. The product of the neurofibromatosis type 2 (NF2) tumour suppressor gene, known as schwannomin or merlin, is involved in NF2-associated and sporadic schwannomas and meningiomas. It is closely related to the ezrin-radixin-moesin family members, which link membrane proteins to the cytoskeleton. Association with SCHIP-1 can be observed only with some naturally occurring mutants of schwannomin, or a schwannomin spliced isoform lacking exons 2 and 3, but not with the schwannomin isoform exhibiting growth-suppressive activity []. This entry consists of mammalian SCHIP-1 proteins from Mus musculus (Mouse) and Homo sapiens (Human).
Probab=42.98 E-value=66 Score=25.02 Aligned_cols=39 Identities=23% Similarity=0.341 Sum_probs=30.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 7 GGMEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRL 45 (124)
Q Consensus 7 i~~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~ 45 (124)
..++.+++++|+-+.+.++..|+.+...+-++.....++
T Consensus 168 ~~L~~~~~~qLq~i~~~l~~~i~~ln~~Lv~~L~~RD~L 206 (238)
T PF10148_consen 168 QDLTKMNVPQLQVIVNDLHEQIEALNEELVQLLLERDDL 206 (238)
T ss_pred HHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 457888999999999988888888887776666555544
No 105
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=42.93 E-value=1e+02 Score=20.61 Aligned_cols=55 Identities=16% Similarity=0.181 Sum_probs=36.2
Q ss_pred HHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCceeeecCHHHHHH
Q 033241 44 RLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYFVEKTMDEGKD 103 (124)
Q Consensus 44 ~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~vE~~~~eA~~ 103 (124)
+-++-.+-+++|++ |.+ |-.++|++-.-.-...+.+.|.+|.|+.+....+--.+
T Consensus 33 r~K~~~~ml~sL~k---GD~--VvT~gGi~G~V~~v~d~~v~I~l~~~~~i~~~k~aI~~ 87 (97)
T COG1862 33 RMKEHQELLNSLKK---GDE--VVTIGGIVGTVTKVGDDTVEIELGDGTKIKFEKEAIAT 87 (97)
T ss_pred HHHHHHHHHHhccC---CCE--EEEcCCeEEEEEEEecCcEEEEECCCeEEEEEHHHHHh
Confidence 44455666777775 333 55567777655544555699999999999887654433
No 106
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=42.85 E-value=45 Score=23.28 Aligned_cols=27 Identities=22% Similarity=0.341 Sum_probs=23.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 97 TMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 97 ~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
++++..++++++++.+++++.+|+..+
T Consensus 78 ~~~~~~~~l~~~~~~l~~~i~~L~~~~ 104 (140)
T PRK09514 78 TCQEVKGIVDEKLAEVEAKIAELQHMR 104 (140)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567889999999999999999988754
No 107
>PF06120 Phage_HK97_TLTM: Tail length tape measure protein; InterPro: IPR009302 This entry consists of the tail length tape measure protein from Bacteriophage HK97 and related sequences from Escherichia coli (strain K12).
Probab=42.63 E-value=96 Score=24.89 Aligned_cols=45 Identities=13% Similarity=0.271 Sum_probs=35.8
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033241 9 MEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALH 53 (124)
Q Consensus 9 ~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~ 53 (124)
+..||..+|.....++..-|......+..++..+.+++..++...
T Consensus 64 l~~Ms~~ql~~~~~k~~~si~~q~~~i~~l~~~i~~l~~~i~~y~ 108 (301)
T PF06120_consen 64 LKEMSSTQLRANIAKAEESIAAQKRAIEDLQKKIDSLKDQIKNYQ 108 (301)
T ss_pred HHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457899999999988888888888888888888877777765443
No 108
>PF09304 Cortex-I_coil: Cortexillin I, coiled coil; InterPro: IPR015383 This domain is predominantly found in the actin-bundling protein cortexillin I from Dictyostelium discoideum (Slime mold). The domain has a structure consisting of an 18-heptad-repeat alpha-helical coiled-coil, and is a prerequisite for the assembly of Cortexillin I []. ; PDB: 1D7M_A.
Probab=42.35 E-value=1.1e+02 Score=20.90 Aligned_cols=34 Identities=6% Similarity=0.124 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 15 EQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESA 48 (124)
Q Consensus 15 e~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~ 48 (124)
++|....+.++++.....+++..|+..+.+....
T Consensus 40 d~L~~~l~~L~~q~~s~~qr~~eLqaki~ea~~~ 73 (107)
T PF09304_consen 40 DQLRNALQSLQAQNASRNQRIAELQAKIDEARRN 73 (107)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455555555555555555555555555444433
No 109
>PHA03162 hypothetical protein; Provisional
Probab=42.15 E-value=90 Score=22.15 Aligned_cols=33 Identities=24% Similarity=0.230 Sum_probs=27.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 033241 3 SSKGGGMEKMSVEQLKAIKEQTDLEVNLLQDSL 35 (124)
Q Consensus 3 ~~~~i~~~~l~le~L~~~~~~l~~ei~~l~~~~ 35 (124)
+++.-+=.+++.|+|.+...+|+-|...|..++
T Consensus 4 ~~k~~pk~~~tmEeLaaeL~kLqmENK~LKkkl 36 (135)
T PHA03162 4 GSKKCPKAQPTMEDLAAEIAKLQLENKALKKKI 36 (135)
T ss_pred CcCCCCccCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 345566678999999999999998888887776
No 110
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=41.96 E-value=1.3e+02 Score=22.93 Aligned_cols=16 Identities=19% Similarity=0.412 Sum_probs=6.4
Q ss_pred HHHHHHHHHHHHHHHH
Q 033241 24 TDLEVNLLQDSLNNIR 39 (124)
Q Consensus 24 l~~ei~~l~~~~~~L~ 39 (124)
.++++..|++++..+.
T Consensus 82 q~~el~~L~~qi~~~~ 97 (251)
T PF11932_consen 82 QEQELASLEQQIEQIE 97 (251)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3333344444444333
No 111
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=41.79 E-value=49 Score=22.52 Aligned_cols=28 Identities=7% Similarity=0.213 Sum_probs=23.2
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 96 KTMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 96 ~~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
.+.+++..++..+...++.++..++..+
T Consensus 75 ~~~~~~~~~l~~~~~~l~~~i~~L~~~~ 102 (126)
T cd04785 75 RSCAEADAIARAHLADVRARIADLRRLE 102 (126)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3567888999999999999999988765
No 112
>PRK04863 mukB cell division protein MukB; Provisional
Probab=41.66 E-value=1.2e+02 Score=29.73 Aligned_cols=47 Identities=11% Similarity=0.191 Sum_probs=39.8
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 8 GMEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 8 ~~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
.+..||+++|......+++.++.++.++..++..........+.+..
T Consensus 431 ~~~~~SdEeLe~~LenF~aklee~e~qL~elE~kL~~lea~leql~~ 477 (1486)
T PRK04863 431 GLPDLTADNAEDWLEEFQAKEQEATEELLSLEQKLSVAQAAHSQFEQ 477 (1486)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999999999888888888887777666655
No 113
>PF14723 SSFA2_C: Sperm-specific antigen 2 C-terminus
Probab=41.47 E-value=74 Score=23.63 Aligned_cols=25 Identities=24% Similarity=0.383 Sum_probs=18.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 13 SVEQLKAIKEQTDLEVNLLQDSLNN 37 (124)
Q Consensus 13 ~le~L~~~~~~l~~ei~~l~~~~~~ 37 (124)
-.++|+.++..+.+|++.|..++..
T Consensus 146 EaeQLQsLR~avRqElqELE~QL~D 170 (179)
T PF14723_consen 146 EAEQLQSLRSAVRQELQELEFQLED 170 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3567888888888888888776554
No 114
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=41.35 E-value=1.2e+02 Score=20.85 Aligned_cols=42 Identities=17% Similarity=0.299 Sum_probs=19.3
Q ss_pred CCHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033241 12 MSVEQLKAIKEQTD-------LEVNLLQDSLNNIRTATSRLESASTALH 53 (124)
Q Consensus 12 l~le~L~~~~~~l~-------~ei~~l~~~~~~L~~~~~~~~~~~~~l~ 53 (124)
+|++++..+..... ...+.+..++..+...+.++....+.|+
T Consensus 58 ~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~ 106 (133)
T cd04787 58 FSLKDIKEILSHADQGESPCPMVRRLIEQRLAETERRIKELLKLRDRMQ 106 (133)
T ss_pred CCHHHHHHHHhhhccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55666555543221 1233444445555555555444444443
No 115
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=41.34 E-value=50 Score=22.38 Aligned_cols=27 Identities=7% Similarity=0.211 Sum_probs=22.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 97 TMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 97 ~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
+.++...++..++..+++++.+++..+
T Consensus 76 ~~~~~~~~l~~~~~~l~~~i~~L~~~~ 102 (127)
T cd04784 76 SCAEVNALIDEHLAHVRARIAELQALE 102 (127)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567788899999999999999887654
No 116
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=41.22 E-value=50 Score=22.69 Aligned_cols=27 Identities=22% Similarity=0.450 Sum_probs=22.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 97 TMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 97 ~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
+.++...+++.+++.+++++.+++..|
T Consensus 78 ~~~~~~~~l~~~~~~l~~~i~~L~~~~ 104 (131)
T TIGR02043 78 SCAEVKAIVDAKLELVDEKINELTKIR 104 (131)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567888999999999999999888765
No 117
>PF08700 Vps51: Vps51/Vps67; InterPro: IPR014812 The VFT tethering complex (also known as GARP complex, Golgi associated retrograde protein complex, Vps53 tethering complex) is a conserved eukaryotic docking complex which is involved in recycling of proteins from endosomes to the late Golgi. Vps51 (also known as Vps67) is a subunit of VFT and interacts with the SNARE Tlg1 [].
Probab=41.14 E-value=87 Score=19.41 Aligned_cols=30 Identities=10% Similarity=0.332 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 10 EKMSVEQLKAIKEQTDLEVNLLQDSLNNIR 39 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei~~l~~~~~~L~ 39 (124)
...++.++..+..++..++......+..+-
T Consensus 17 ~~~s~~~i~~~~~~L~~~i~~~~~eLr~~V 46 (87)
T PF08700_consen 17 KNSSIKEIRQLENKLRQEIEEKDEELRKLV 46 (87)
T ss_pred hhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467889999999999998888877766554
No 118
>PF07743 HSCB_C: HSCB C-terminal oligomerisation domain; InterPro: IPR009073 This entry represents the C-terminal oligomerisation domain found in HscB (heat shock cognate protein B), which is also known as HSC20 (20K heat shock cognate protein). HscB acts as a co-chaperone to regulate the ATPase activity and peptide-binding specificity of the molecular chaperone HscA, also known as HSC66 (HSP70 class). HscB proteins contain two domains, an N-terminal J-domain, which is involved in interactions with HscA, connected by a short loop to the C-terminal oligomerisation domain; the two domains make contact through a hydrophobic interface. The core of the oligomerisation domain is thought to bind and target proteins to HscA and consists of an open, three-helical bundle []. HscB, along with HscA, has been shown to play a role in the biogenesis of iron-sulphur proteins.; GO: 0006457 protein folding; PDB: 1FPO_C 3BVO_B 3HHO_A 3UO2_B 3UO3_B.
Probab=40.76 E-value=86 Score=19.24 Aligned_cols=42 Identities=21% Similarity=0.285 Sum_probs=27.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 13 SVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 13 ~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
+...|..+...++..+..+.+.+...- ...++..|.+.+..|
T Consensus 25 ~~~~L~~l~~~~~~~~~~~~~~l~~~f-~~~d~~~A~~~~~kL 66 (78)
T PF07743_consen 25 DEAELEELKKEIEERIKELIKELAEAF-DAKDWEEAKEALRKL 66 (78)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHHH-HTT-HHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH-ccCcHHHHHHHHHHH
Confidence 346777777777777777777666655 455666666666554
No 119
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=40.68 E-value=65 Score=25.76 Aligned_cols=56 Identities=16% Similarity=0.158 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCC-------CCCceEEEecCCc
Q 033241 16 QLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLR-------PQGAKMLVPLTAS 71 (124)
Q Consensus 16 ~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~-------~~~~e~lVplg~~ 71 (124)
.|....+++++++..++.++..++..+..+++-++.+...+.. -....++++-+.|
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 (364)
T TIGR01242 3 ELDVRIRKLEDEKRSLEKEKIRLERELERLRSEIERLRSPPLIVGTVLEVLDDNRVVVKSSTG 65 (364)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeEEEEEEEEecCCEEEEEeCCC
Confidence 4455666777777777777777777777766666655554311 1234556666554
No 120
>TIGR01280 xseB exodeoxyribonuclease VII, small subunit. This protein is the small subunit for exodeoxyribonuclease VII. Exodeoxyribonuclease VII is made of a complex of four small subunits to one large subunit. The complex degrades single-stranded DNA into large acid-insoluble oligonucleotides. These nucleotides are then degraded further into acid-soluble oligonucleotides.
Probab=40.63 E-value=87 Score=19.26 Aligned_cols=36 Identities=11% Similarity=0.118 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 10 EKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRL 45 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~ 45 (124)
..+|+++...++++--.-+...++.+...+..+..+
T Consensus 20 ~~l~Leesl~lyeeG~~L~k~c~~~L~~ae~kv~~l 55 (67)
T TIGR01280 20 GDLALEEALNLFERGMALARRCEKKLAQAEQRVRKL 55 (67)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567888888888888777777766555555555444
No 121
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=40.56 E-value=49 Score=22.06 Aligned_cols=29 Identities=10% Similarity=0.118 Sum_probs=24.3
Q ss_pred ecCHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 95 EKTMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 95 E~~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
+.+.++..++++.+...++.++..++..+
T Consensus 76 ~~~~~~~~~~l~~~~~~l~~~i~~L~~~~ 104 (112)
T cd01282 76 FRPCPDLLAVLRRELARIDRQIADLTRSR 104 (112)
T ss_pred CCccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667888999999999999999988764
No 122
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=40.52 E-value=54 Score=22.00 Aligned_cols=27 Identities=19% Similarity=0.284 Sum_probs=22.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 97 TMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 97 ~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
+.++...++++++..++++++.++..+
T Consensus 76 ~~~~~~~~l~~~~~~l~~~i~~l~~~~ 102 (123)
T cd04770 76 PCAEVRALLEEKLAEVEAKIAELQALR 102 (123)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457788999999999999999887764
No 123
>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]
Probab=40.50 E-value=56 Score=24.43 Aligned_cols=24 Identities=8% Similarity=0.205 Sum_probs=11.5
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHH
Q 033241 96 KTMDEGKDYCERKINLLKSNFDQL 119 (124)
Q Consensus 96 ~~~~eA~~~l~~r~~~l~~~i~~l 119 (124)
+....+..-..+|....++-++++
T Consensus 159 ~~y~~~~~~wrk~krmf~ei~d~~ 182 (201)
T KOG4603|consen 159 REYQKYCKEWRKRKRMFREIIDKL 182 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444555555555544444443
No 124
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=40.34 E-value=54 Score=22.30 Aligned_cols=28 Identities=14% Similarity=0.329 Sum_probs=23.1
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 96 KTMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 96 ~~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
.+.++..+++++++..++.++.+++..+
T Consensus 72 ~~~~~~~~~l~~~~~~l~~~i~~L~~~~ 99 (124)
T TIGR02051 72 THCREMYELASRKLKSVQAKMADLLRIE 99 (124)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3467888999999999999999887754
No 125
>PF10438 Cyc-maltodext_C: Cyclo-malto-dextrinase C-terminal domain; InterPro: IPR019492 This domain is at the very C terminus of cyclo-malto-dextrinase proteins and consists of 8 beta strands, is largely globular and appears to help stabilise the active sites created by upstream domains, IPR015171 from INTERPRO, and IPR006047 from INTERPRO. Cyclo-malto-dextrinases hydrolyse cyclodextrans to maltose and glucose and catalyse trans-glycosylation of oligosaccharides to the C3-, C4- or C6-hydroxyl groups of various acceptor sugar molecules. ; PDB: 3EDK_B 3EDD_A 3EDJ_B 3EDE_A 1H3G_B 3EDF_B.
Probab=40.15 E-value=35 Score=21.77 Aligned_cols=20 Identities=25% Similarity=0.308 Sum_probs=17.8
Q ss_pred CCceeEeEEEcCCCeEEEEc
Q 033241 69 TASLYVPGTLDDARKVLVDI 88 (124)
Q Consensus 69 g~~~yv~a~I~~~~~VlV~l 88 (124)
-.|+|+..+..+.++|+|-+
T Consensus 8 ~~gvYvYfR~~~~~tVmVil 27 (78)
T PF10438_consen 8 QDGVYVYFRYYDGKTVMVIL 27 (78)
T ss_dssp BTTEEEEEEEESSEEEEEEE
T ss_pred cCCEEEEEEEcCCCEEEEEE
Confidence 57999999999999998865
No 126
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=40.05 E-value=78 Score=24.52 Aligned_cols=29 Identities=10% Similarity=0.211 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 16 QLKAIKEQTDLEVNLLQDSLNNIRTATSR 44 (124)
Q Consensus 16 ~L~~~~~~l~~ei~~l~~~~~~L~~~~~~ 44 (124)
+|....+.+++|+..|+.+++.++..+.+
T Consensus 58 ~l~~ql~~lq~ev~~LrG~~E~~~~~l~~ 86 (263)
T PRK10803 58 QLQQQLSDNQSDIDSLRGQIQENQYQLNQ 86 (263)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence 34444444445554444444444443333
No 127
>TIGR00219 mreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.
Probab=40.05 E-value=1.8e+02 Score=22.79 Aligned_cols=10 Identities=20% Similarity=0.507 Sum_probs=7.1
Q ss_pred CCeEEEEccC
Q 033241 81 ARKVLVDIGT 90 (124)
Q Consensus 81 ~~~VlV~lG~ 90 (124)
.+.++++.|.
T Consensus 131 ~~~i~IdkGs 140 (283)
T TIGR00219 131 STQVVINKGF 140 (283)
T ss_pred ccEEEEcCcc
Confidence 3468888885
No 128
>smart00338 BRLZ basic region leucin zipper.
Probab=40.01 E-value=82 Score=18.76 Aligned_cols=35 Identities=17% Similarity=0.230 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 20 IKEQTDLEVNLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 20 ~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
..+.++.+++.|......|...+..+..-+..+..
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~ 61 (65)
T smart00338 27 EIEELERKVEQLEAENERLKKEIERLRRELEKLKS 61 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455555555555555555555555555444443
No 129
>PF12795 MscS_porin: Mechanosensitive ion channel porin domain
Probab=39.53 E-value=1.4e+02 Score=22.53 Aligned_cols=40 Identities=18% Similarity=0.256 Sum_probs=29.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 7 GGMEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLE 46 (124)
Q Consensus 7 i~~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~ 46 (124)
-.+..+|+++|.+........+...+.++..++..+..+.
T Consensus 73 ~~~~~~s~~eLeq~l~~~~~~L~~~q~~l~~~~~~l~~~~ 112 (240)
T PF12795_consen 73 EILANLSLEELEQRLSQEQAQLQELQEQLQQENSQLIEIQ 112 (240)
T ss_pred cCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3458899999999988888888777777776666554443
No 130
>PF11285 DUF3086: Protein of unknown function (DUF3086); InterPro: IPR021437 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=39.45 E-value=57 Score=25.82 Aligned_cols=31 Identities=16% Similarity=0.321 Sum_probs=25.4
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 11 KMSVEQLKAIKEQTDLEVNLLQDSLNNIRTA 41 (124)
Q Consensus 11 ~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~ 41 (124)
++.+-+|.+.++.++.+++.|+.+-.+++..
T Consensus 3 ~~~L~eL~qrk~~Lq~eIe~LerR~~ri~~E 33 (283)
T PF11285_consen 3 QEALKELEQRKQALQIEIEQLERRRERIEKE 33 (283)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567788888999999999998888888764
No 131
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=39.39 E-value=1.2e+02 Score=20.29 Aligned_cols=43 Identities=23% Similarity=0.302 Sum_probs=21.4
Q ss_pred CCHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 12 MSVEQLKAIKEQTD--------LEVNLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 12 l~le~L~~~~~~l~--------~ei~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
+|++++..+..... .-.+.++++...+...+.++......|+.
T Consensus 57 ~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~ 107 (116)
T cd04769 57 FTLAELKAIFAGHEGRAVLPWPHLQQALEDKKQEIRAQITELQQLLARLDA 107 (116)
T ss_pred CCHHHHHHHHhccccCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666665544322 11244555555555555555555555544
No 132
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=39.31 E-value=55 Score=21.47 Aligned_cols=26 Identities=19% Similarity=0.231 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 98 MDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 98 ~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
.++..+++.++++.++.++.+++..+
T Consensus 79 ~~~~~~~l~~~~~~l~~~i~~l~~~~ 104 (107)
T cd04777 79 QDYYKSFLKNKKDELEKEIEDLKKAI 104 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46678999999999999999998764
No 133
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=39.17 E-value=57 Score=22.10 Aligned_cols=27 Identities=19% Similarity=0.388 Sum_probs=22.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 97 TMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 97 ~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
+.++...++..+++.+++++..++..+
T Consensus 74 ~~~~~~~~l~~~~~~l~~~i~~L~~~~ 100 (126)
T cd04783 74 DCSEARELAEQKLAEVDEKIADLQRMR 100 (126)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467788999999999999999988765
No 134
>PF13093 FTA4: Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
Probab=38.85 E-value=1.5e+02 Score=22.38 Aligned_cols=45 Identities=7% Similarity=-0.014 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCC
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLR 58 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~ 58 (124)
-+++...+..+...+..+.+++..+....+.|......|+-+...
T Consensus 137 ~~e~~~rY~~l~~~L~~l~~~r~~~~~rl~~lr~L~~lLepf~~~ 181 (213)
T PF13093_consen 137 SPEEAERYAELRERLIELSEQRQYLQQRLEYLRRLRSLLEPFDSP 181 (213)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCC
Confidence 355666788888899999999999999999999999999888643
No 135
>COG3879 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.79 E-value=1.4e+02 Score=23.42 Aligned_cols=72 Identities=19% Similarity=0.306 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HhhccCC-----CCCceEEEecCCceeEeEEEcCCCeEEEEcc
Q 033241 16 QLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTA-LHDLSLR-----PQGAKMLVPLTASLYVPGTLDDARKVLVDIG 89 (124)
Q Consensus 16 ~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~-l~~L~~~-----~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG 89 (124)
.+++-..++..|++.+++.+........+...+++. ++.|+.. -.|.-+.|-|...-|.+.. +|
T Consensus 61 s~Q~~~~~L~~ev~~~~~~~~s~~~~~~t~~~~ie~~l~~l~~~aG~v~V~G~Gl~ITi~d~~~~~~~----------~~ 130 (247)
T COG3879 61 SLQKKVNTLAAEVEDLENKLDSVRRSVLTDDAALEDRLEKLRMLAGSVPVTGPGLVITIDDPGYSPNG----------VG 130 (247)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHHhccCCCcCCcEEEEecCCCCCccc----------CC
Confidence 444455566666667766666666444444444433 4444321 1233344444444443333 56
Q ss_pred CceeeecC
Q 033241 90 TGYFVEKT 97 (124)
Q Consensus 90 ~g~~vE~~ 97 (124)
.++++.-+
T Consensus 131 ~~~~vv~~ 138 (247)
T COG3879 131 PNSQVVHD 138 (247)
T ss_pred CCccccCH
Confidence 66666544
No 136
>PRK00736 hypothetical protein; Provisional
Probab=38.75 E-value=69 Score=19.75 Aligned_cols=27 Identities=11% Similarity=0.123 Sum_probs=18.4
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033241 96 KTMDEGKDYCERKINLLKSNFDQLIEV 122 (124)
Q Consensus 96 ~~~~eA~~~l~~r~~~l~~~i~~l~~~ 122 (124)
||.++-+.-|+-|+.+.+..|+.|+++
T Consensus 1 ~~~e~Ri~~LE~klafqe~tie~Ln~~ 27 (68)
T PRK00736 1 MDAEERLTELEIRVAEQEKTIEELSDQ 27 (68)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455666777777777777777777654
No 137
>PF09789 DUF2353: Uncharacterized coiled-coil protein (DUF2353); InterPro: IPR019179 Members of this family have been annotated as being coiled-coil domain-containing protein 149, however they currently have no known function.
Probab=38.73 E-value=1.4e+02 Score=24.25 Aligned_cols=40 Identities=13% Similarity=0.177 Sum_probs=36.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 12 MSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTA 51 (124)
Q Consensus 12 l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~ 51 (124)
++++.|...-.-+.+.+..++.....++..+.+|..++++
T Consensus 189 vDIDaLi~ENRyL~erl~q~qeE~~l~k~~i~KYK~~le~ 228 (319)
T PF09789_consen 189 VDIDALIMENRYLKERLKQLQEEKELLKQTINKYKSALER 228 (319)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4789999999999999999999999999999999998775
No 138
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=38.70 E-value=1.2e+02 Score=20.43 Aligned_cols=44 Identities=14% Similarity=0.318 Sum_probs=22.9
Q ss_pred CCHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 12 MSVEQLKAIKEQT-----DLEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 12 l~le~L~~~~~~l-----~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
+|++++..+.... ..-.+.+..++..+...+.++....+.|..+
T Consensus 58 ~sL~eI~~~l~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~l~~~ 106 (126)
T cd04783 58 FTLDEIAELLELDDGTDCSEARELAEQKLAEVDEKIADLQRMRASLQEL 106 (126)
T ss_pred CCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5566666554322 2223444555556666666666555555543
No 139
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=38.55 E-value=59 Score=22.52 Aligned_cols=27 Identities=22% Similarity=0.145 Sum_probs=23.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 97 TMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 97 ~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
+.++...+++++++.++..+.+|+..|
T Consensus 75 ~~~~~~~~l~~k~~~i~~~i~~L~~~~ 101 (131)
T cd04786 75 QHDELLAALERKVADIEALEARLAQNK 101 (131)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567888999999999999999998765
No 140
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=38.48 E-value=1.5e+02 Score=21.24 Aligned_cols=46 Identities=7% Similarity=-0.034 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 033241 11 KMSVEQLKAIKEQ--------TDLEVNLLQDSLNNIRTATSRLESASTALHDLS 56 (124)
Q Consensus 11 ~l~le~L~~~~~~--------l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~ 56 (124)
-+|++++..+... .+...+.+.+++..+...+.+++...+.|..+.
T Consensus 67 G~sL~eIk~ll~~~~~~~~~~~~~~~~ll~~k~~~l~~~I~~L~~~~~~L~~~i 120 (154)
T PRK15002 67 GIPLATIGEAFGVLPEGHTLSAKEWKQLSSQWREELDRRIHTLVALRDELDGCI 120 (154)
T ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3677777776542 234456666777777777777777777777653
No 141
>KOG1760 consensus Molecular chaperone Prefoldin, subunit 4 [Posttranslational modification, protein turnover, chaperones]
Probab=38.30 E-value=1.4e+02 Score=21.01 Aligned_cols=31 Identities=23% Similarity=0.356 Sum_probs=20.5
Q ss_pred ceeeecCHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 91 GYFVEKTMDEGKDYCERKINLLKSNFDQLIE 121 (124)
Q Consensus 91 g~~vE~~~~eA~~~l~~r~~~l~~~i~~l~~ 121 (124)
.+|+-++.+...+.|+...+.+.+.|+.++.
T Consensus 72 dvF~~~~~~~~~~~LEe~ke~l~k~i~~les 102 (131)
T KOG1760|consen 72 DVFIHVKLDKLQDQLEEKKETLEKEIEELES 102 (131)
T ss_pred hhheeccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566667777777777777777766666653
No 142
>cd02765 MopB_4 The MopB_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins
Probab=38.22 E-value=25 Score=30.08 Aligned_cols=43 Identities=21% Similarity=0.200 Sum_probs=33.2
Q ss_pred eEeEEEcCCCeEEEEc------cCceeeecCHHHHHHHHHHHHHHHHHH
Q 033241 73 YVPGTLDDARKVLVDI------GTGYFVEKTMDEGKDYCERKINLLKSN 115 (124)
Q Consensus 73 yv~a~I~~~~~VlV~l------G~g~~vE~~~~eA~~~l~~r~~~l~~~ 115 (124)
+..-.+.+++++.-++ |.|=|++.|-+||++++.+|++.+.+.
T Consensus 45 ~~~~~~y~pdRl~~Pl~R~g~rG~g~~~~iSWdEAl~~ia~kl~~~~~~ 93 (567)
T cd02765 45 SHLQRVYSPDRLKYPMKRVGERGEGKFERITWDEALDTIADKLTEAKRE 93 (567)
T ss_pred hhhhhhcChhhhcCCeeecCCCCCCcEEEecHHHHHHHHHHHHHHHHHH
Confidence 3344455666766665 678999999999999999999887653
No 143
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=37.92 E-value=60 Score=22.58 Aligned_cols=28 Identities=14% Similarity=0.246 Sum_probs=22.0
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 96 KTMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 96 ~~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
.+.++..+++..++..++.++.+|+..|
T Consensus 75 ~~~~~~~~~l~~~~~~l~~~i~~L~~~~ 102 (135)
T PRK10227 75 RHSADVKRRTLEKVAEIERHIEELQSMR 102 (135)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456677888888999999998888765
No 144
>PF03938 OmpH: Outer membrane protein (OmpH-like); InterPro: IPR005632 This entry includes outer membrane proteins such as OmpH (Skp) among others. OmpH (outer membrane protein H) is a major structural protein of the outer membrane. In Pasteurella multocida it acts as a channel-forming transmembrane porin []. Porins act as molecular sieves to allow the diffusion of small hydrophilic solutes through the outer membrane and also acts as a receptor for bacteriophages and bacteriocins. Porins are highly immunogenic and are conserved in bacterial families, making them attractive vaccine candidates []. The 17kDa protein (Skp, OmpH) of Escherichia coli is a homotrimeric periplasmic chaperone for newly synthesised outer-membrane proteins, the X-ray structure of which has been reported at resolutions of 2.35 A and 2.30 A [, ]. Three hairpin-shaped alpha-helical extensions reach out by approximately 60 A from a trimerisation domain, which is composed of three intersubunit beta-sheets that wind around a central axis. The alpha-helical extensions approach each other at their distal turns, resulting in a fold that resembles a 'three-pronged grasping forcep'. The overall shape of Skp is reminiscent of the cytosolic chaperone prefoldin (IPR009053 from INTERPRO), although it is based on a radically different topology. The peculiar architecture, with apparent plasticity of the prongs and distinct electrostatic and hydrophobic surface properties, supports the recently proposed biochemical mechanism of this chaperone: formation of a Skp(3)-Omp complex protects the outer membrane protein from aggregation during passage through the bacterial periplasm. The ability of Skp to prevent the aggregation of model substrates in vitro is independent of ATP. Skp can interact directly with membrane lipids and lipopolysaccharide. These interactions are needed for efficient Skp-assisted folding of membrane proteins [].; GO: 0051082 unfolded protein binding; PDB: 1SG2_C 1U2M_C.
Probab=37.59 E-value=25 Score=24.47 Aligned_cols=65 Identities=14% Similarity=0.216 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHhhccCCCCCceEEEecCCceeEeE
Q 033241 11 KMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSR---------LESASTALHDLSLRPQGAKMLVPLTASLYVPG 76 (124)
Q Consensus 11 ~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~---------~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a 76 (124)
+||.++.....++++...+.++.....++..+.. +.....+++.+- ...|..+.++-++-+|+..
T Consensus 72 ~ls~~~~~~~~~~l~~~~~~l~~~~~~~~~~l~~~~~~~~~~i~~~i~~~v~~~a-~~~g~~~Vl~~~~vly~~~ 145 (158)
T PF03938_consen 72 TLSEEERQKRQQELQQKEQELQQFQQQAQQQLQQEEQELLQPIQKKINKAVEEYA-KENGYDLVLDKNAVLYADP 145 (158)
T ss_dssp --SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHTT-SEEEEGGGEEEE-T
T ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHcCCeEEEeCCceEeeCC
Confidence 5666666666555555555554444433332222 112334444443 2357888888777666654
No 145
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=37.56 E-value=1.2e+02 Score=20.08 Aligned_cols=44 Identities=14% Similarity=0.209 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 11 KMSVEQLKAIKEQT----------DLEVNLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 11 ~l~le~L~~~~~~l----------~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
-+|++++..+.... .+..+.+..++..+...+.++....+.|..
T Consensus 56 G~sl~eI~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~ 109 (112)
T cd01282 56 GLTLEEIREFLPCLRGGEPTFRPCPDLLAVLRRELARIDRQIADLTRSRDRLDA 109 (112)
T ss_pred CCCHHHHHHHHHHhhCCCccCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36677777665432 234566777777777777777777776664
No 146
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=37.32 E-value=1.3e+02 Score=20.35 Aligned_cols=44 Identities=18% Similarity=0.346 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 12 MSVEQLKAIKEQTD-------LEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 12 l~le~L~~~~~~l~-------~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
+|++++..+..... .-.+.++.++..+...+.++......|..+
T Consensus 58 ~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~ 108 (126)
T cd04785 58 FSLEEIRALLALSDRPDRSCAEADAIARAHLADVRARIADLRRLEAELKRM 108 (126)
T ss_pred CCHHHHHHHHhhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56777776654321 234556666777777777777666666654
No 147
>TIGR02449 conserved hypothetical protein TIGR02449. Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.
Probab=37.32 E-value=1e+02 Score=19.09 Aligned_cols=32 Identities=28% Similarity=0.296 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRL 45 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~ 45 (124)
+++|....+++..+-..|.++...+......+
T Consensus 9 le~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L 40 (65)
T TIGR02449 9 VEHLLEYLERLKSENRLLRAQEKTWREERAQL 40 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57788888888888888888888777654443
No 148
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=36.91 E-value=2.5e+02 Score=23.54 Aligned_cols=83 Identities=20% Similarity=0.211 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCC----------CCCceEEEecC--CceeEe------
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLR----------PQGAKMLVPLT--ASLYVP------ 75 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~----------~~~~e~lVplg--~~~yv~------ 75 (124)
+-+|...++.+.-+.+.++.+.. ++....++....+-|+.|... -.+....|..+ ...||.
T Consensus 60 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~ 138 (438)
T PTZ00361 60 LLKLERIKDYLLLEEEFITNQEA-QKPAQEKNEAELKKVDDLRGSPLSVGTLEEIIDENHAIVSSSVGPEYYVNILSFVD 138 (438)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh-hhhHHHHHHHHHHHHHHhhCCCcEEEEEEEEeCCCeEEEEeCCCCEEEEeccCcCC
Confidence 34455556666666666665443 122233344444444444321 01223444433 234442
Q ss_pred -EEEcCCCeEEEEccCceeeecC
Q 033241 76 -GTLDDARKVLVDIGTGYFVEKT 97 (124)
Q Consensus 76 -a~I~~~~~VlV~lG~g~~vE~~ 97 (124)
..+.+...|.++--.+..++.=
T Consensus 139 ~~~l~~~~~v~l~~~~~~~~~~~ 161 (438)
T PTZ00361 139 KEQLEPGCSVLLHNKTHSVVGIL 161 (438)
T ss_pred HhhCCCCCEEEEcCCCCceEecC
Confidence 3345556666666555555543
No 149
>PRK00977 exodeoxyribonuclease VII small subunit; Provisional
Probab=36.88 E-value=1.1e+02 Score=19.45 Aligned_cols=36 Identities=17% Similarity=0.123 Sum_probs=21.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 10 EKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRL 45 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~ 45 (124)
..+||++...++++--.-+...++.+......+..+
T Consensus 29 ~~l~Lees~~lyeeg~~L~k~C~~~L~~ae~ki~~l 64 (80)
T PRK00977 29 GDLPLEESLAAFERGVALARQCQKKLQQAEQRVEKL 64 (80)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456677777766666666666655554444444443
No 150
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=36.84 E-value=93 Score=18.48 Aligned_cols=32 Identities=16% Similarity=0.255 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 21 KEQTDLEVNLLQDSLNNIRTATSRLESASTAL 52 (124)
Q Consensus 21 ~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l 52 (124)
.++++..+..|+.....|...+..+..-...|
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L 59 (64)
T PF00170_consen 28 IEELEEKVEELESENEELKKELEQLKKEIQSL 59 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444455555555554444444443333
No 151
>cd02755 MopB_Thiosulfate-R-like The MopB_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Members of the MopB_Thiosulfate-R-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=36.71 E-value=55 Score=26.98 Aligned_cols=27 Identities=33% Similarity=0.553 Sum_probs=24.2
Q ss_pred cCceeeecCHHHHHHHHHHHHHHHHHH
Q 033241 89 GTGYFVEKTMDEGKDYCERKINLLKSN 115 (124)
Q Consensus 89 G~g~~vE~~~~eA~~~l~~r~~~l~~~ 115 (124)
|.|=|.+.|-+||++++.++++.+.+.
T Consensus 67 G~g~~~~iSWdeAl~~ia~~l~~~~~~ 93 (454)
T cd02755 67 GEGKFREASWDEALQYIASKLKEIKEQ 93 (454)
T ss_pred CCCeEEEeCHHHHHHHHHHHHHHHHHh
Confidence 688999999999999999999887753
No 152
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=36.63 E-value=68 Score=21.26 Aligned_cols=27 Identities=22% Similarity=0.228 Sum_probs=22.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 97 TMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 97 ~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
++++..+++.+++..++.++..++..+
T Consensus 76 ~~~~~~~~l~~~~~~l~~~i~~l~~~~ 102 (113)
T cd01109 76 TIPERLELLEEHREELEEQIAELQETL 102 (113)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457788899999999999998887654
No 153
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=36.44 E-value=1.5e+02 Score=20.65 Aligned_cols=28 Identities=14% Similarity=0.366 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 28 VNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 28 i~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
.+.++.++..+...+.++......|..+
T Consensus 83 ~~~l~~~~~~l~~~i~~L~~~~~~L~~~ 110 (140)
T PRK09514 83 KGIVDEKLAEVEAKIAELQHMRRSLQRL 110 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555555555555555555554443
No 154
>PRK03578 hscB co-chaperone HscB; Provisional
Probab=36.40 E-value=1.1e+02 Score=22.34 Aligned_cols=9 Identities=22% Similarity=0.261 Sum_probs=3.7
Q ss_pred HHHHHHHHh
Q 033241 45 LESASTALH 53 (124)
Q Consensus 45 ~~~~~~~l~ 53 (124)
+..|...+.
T Consensus 147 ~~~A~~~~~ 155 (176)
T PRK03578 147 DQAAAEAVR 155 (176)
T ss_pred HHHHHHHHH
Confidence 444444433
No 155
>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]
Probab=35.80 E-value=87 Score=27.88 Aligned_cols=31 Identities=6% Similarity=0.323 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSR 44 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~ 44 (124)
+-+|+.-+|.++.+|+.+...++.|+..+..
T Consensus 95 L~ele~krqel~seI~~~n~kiEelk~~i~~ 125 (907)
T KOG2264|consen 95 LTELEVKRQELNSEIEEINTKIEELKRLIPQ 125 (907)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 4455556666666666666666665554443
No 156
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=35.59 E-value=1.4e+02 Score=20.14 Aligned_cols=46 Identities=17% Similarity=0.369 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 033241 11 KMSVEQLKAIKEQT-------DLEVNLLQDSLNNIRTATSRLESASTALHDLS 56 (124)
Q Consensus 11 ~l~le~L~~~~~~l-------~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~ 56 (124)
-+|++++..+.... ..-.+.+..++..+...+.++......|..+.
T Consensus 57 G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~ 109 (127)
T cd04784 57 DMSLDEIRTLLQLQDDPEASCAEVNALIDEHLAHVRARIAELQALEKQLQALR 109 (127)
T ss_pred CCCHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36777777765432 23345567777777777777777776666653
No 157
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=35.51 E-value=1.5e+02 Score=20.33 Aligned_cols=37 Identities=5% Similarity=0.228 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 033241 20 IKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLS 56 (124)
Q Consensus 20 ~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~ 56 (124)
...-+++.++.+.+++..|+.....+...+.......
T Consensus 80 ~~~~l~~~~~~l~~~i~~l~~~~~~l~~~~~~~~~~~ 116 (133)
T cd04787 80 VRRLIEQRLAETERRIKELLKLRDRMQQAVSQWQQMP 116 (133)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 3445566677777778888877777777766666654
No 158
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=35.33 E-value=1.1e+02 Score=18.96 Aligned_cols=30 Identities=20% Similarity=0.307 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033241 24 TDLEVNLLQDSLNNIRTATSRLESASTALH 53 (124)
Q Consensus 24 l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~ 53 (124)
++.++..|+.++..+...++.+....+.|.
T Consensus 3 Lea~~~~Lr~rLd~~~rk~~~~~~~~k~L~ 32 (69)
T PF14197_consen 3 LEAEIATLRNRLDSLTRKNSVHEIENKRLR 32 (69)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555555555555555555544444443
No 159
>cd02769 MopB_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=35.00 E-value=52 Score=28.39 Aligned_cols=26 Identities=23% Similarity=0.396 Sum_probs=24.0
Q ss_pred cCceeeecCHHHHHHHHHHHHHHHHH
Q 033241 89 GTGYFVEKTMDEGKDYCERKINLLKS 114 (124)
Q Consensus 89 G~g~~vE~~~~eA~~~l~~r~~~l~~ 114 (124)
|.|=|++.|-|||.+.+..|++.+.+
T Consensus 69 G~g~~~~ISWdEAld~IA~kl~~i~~ 94 (609)
T cd02769 69 GKEEFVRVSWDEALDLVAAELKRVRK 94 (609)
T ss_pred CCCCeEEecHHHHHHHHHHHHHHHHH
Confidence 57889999999999999999998876
No 160
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=34.72 E-value=72 Score=22.48 Aligned_cols=26 Identities=15% Similarity=0.351 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 98 MDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 98 ~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
.+++..++..+++.+++++++++..+
T Consensus 82 ~~~~~~ll~~k~~~l~~~i~~L~~~~ 107 (144)
T PRK13752 82 CEEASSLAEHKLKDVREKMADLARME 107 (144)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788999999999999999988754
No 161
>PF05008 V-SNARE: Vesicle transport v-SNARE protein N-terminus; InterPro: IPR007705 V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this []. This domain is the N-terminal half of the V-Snare proteins. ; GO: 0006886 intracellular protein transport, 0016020 membrane; PDB: 2V8S_V 1VCS_A 3ONL_C 3ONJ_A 2QYW_A.
Probab=34.41 E-value=1.1e+02 Score=18.68 Aligned_cols=35 Identities=20% Similarity=0.253 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Q 033241 16 QLKAIKEQTDLEVNLLQ-DSLNNIRTATSRLESAST 50 (124)
Q Consensus 16 ~L~~~~~~l~~ei~~l~-~~~~~L~~~~~~~~~~~~ 50 (124)
+...+.++++-|+..+. +....++..+..|+.-++
T Consensus 36 ea~~~l~qMe~E~~~~p~s~r~~~~~kl~~yr~~l~ 71 (79)
T PF05008_consen 36 EAEELLKQMELEVRSLPPSERNQYKSKLRSYRSELK 71 (79)
T ss_dssp HHHHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence 33344444444444443 223334444444443333
No 162
>PF15456 Uds1: Up-regulated During Septation
Probab=34.37 E-value=1.6e+02 Score=20.43 Aligned_cols=86 Identities=17% Similarity=0.182 Sum_probs=50.5
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEE
Q 033241 9 MEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATS---RLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVL 85 (124)
Q Consensus 9 ~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~---~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~Vl 85 (124)
-.-||.+++..+++++. .|..++..++..+. ++.+|...+..+...+...
T Consensus 16 feiLs~eEVe~LKkEl~----~L~~R~~~lr~kl~le~k~RdAa~sl~~l~~~~~~~----------------------- 68 (124)
T PF15456_consen 16 FEILSFEEVEELKKELR----SLDSRLEYLRRKLALESKIRDAAHSLSRLYSSSSRR----------------------- 68 (124)
T ss_pred CcccCHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccc-----------------------
Confidence 34577787777766543 55555555554443 4455555555553222111
Q ss_pred EEccCceeeecCHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 86 VDIGTGYFVEKTMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 86 V~lG~g~~vE~~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
-+.+-=.-...+++..-++++++.+...+.++++.+
T Consensus 69 --~~~~~~~~~~~eeel~~~~rk~ee~~~eL~~le~R~ 104 (124)
T PF15456_consen 69 --ARFSRESSLKAEEELAESDRKCEELAQELWKLENRL 104 (124)
T ss_pred --cCCCcchHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence 111111234567888999999999998888887643
No 163
>PRK15102 trimethylamine N-oxide reductase I catalytic subunit; Provisional
Probab=34.18 E-value=32 Score=30.79 Aligned_cols=42 Identities=17% Similarity=0.351 Sum_probs=33.2
Q ss_pred EeEEEcCCCeEEEEc-----------------cCceeeecCHHHHHHHHHHHHHHHHHH
Q 033241 74 VPGTLDDARKVLVDI-----------------GTGYFVEKTMDEGKDYCERKINLLKSN 115 (124)
Q Consensus 74 v~a~I~~~~~VlV~l-----------------G~g~~vE~~~~eA~~~l~~r~~~l~~~ 115 (124)
++..+.+++++.-++ |.|=|++.|-|||.+.+..|++.+.+.
T Consensus 81 ~~~~~y~pdRl~~PlkR~~~~~~~~~~~~g~RG~g~f~~ISWDEAld~IA~kl~~i~~~ 139 (825)
T PRK15102 81 IKGHVYNPSRIRYPMVRLDWLRKRHKSDTSQRGDNRFVRVSWDEALDLFYEELERVQKT 139 (825)
T ss_pred hhhhccChhhccCCceechhhhccCCCCcccCCCCcEEEecHHHHHHHHHHHHHHHHHh
Confidence 344555667765555 588999999999999999999988764
No 164
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=33.85 E-value=81 Score=20.55 Aligned_cols=25 Identities=16% Similarity=0.114 Sum_probs=22.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 97 TMDEGKDYCERKINLLKSNFDQLIE 121 (124)
Q Consensus 97 ~~~eA~~~l~~r~~~l~~~i~~l~~ 121 (124)
+.+++.++++.+...++.+++.+++
T Consensus 73 ~~~~~~~ll~~~~~~l~~~i~~L~~ 97 (99)
T cd04772 73 IVASALALVDAAHALLQRYRQQLDQ 97 (99)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4568999999999999999999875
No 165
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=33.37 E-value=1.5e+02 Score=19.99 Aligned_cols=45 Identities=20% Similarity=0.155 Sum_probs=27.5
Q ss_pred CCCHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 11 KMSVEQLKAIKEQT-------DLEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 11 ~l~le~L~~~~~~l-------~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
-+|++++..+.... ..-.+.+.+++..+...+.++....+.|+.+
T Consensus 57 G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~ 108 (127)
T TIGR02044 57 GFSLEECKELLNLWNDPNRTSADVKARTLEKVAEIERKISELQSMRDQLEAL 108 (127)
T ss_pred CCCHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35677776655421 2224456666777777777777777666654
No 166
>PF01330 RuvA_N: RuvA N terminal domain; InterPro: IPR013849 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. This entry represents domain I of RuvA, which has an OB-fold structure. This domain forms the RuvA tetramer contacts [].; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJP_A 1D8L_B 1CUK_A 1C7Y_A 1IXR_B 2ZTC_A 2ZTD_B 2H5X_A 2ZTE_A 1BVS_E ....
Probab=33.13 E-value=60 Score=19.19 Aligned_cols=29 Identities=24% Similarity=0.456 Sum_probs=19.3
Q ss_pred eeEeEEEcC--CCeEEEEcc-CceeeecCHHH
Q 033241 72 LYVPGTLDD--ARKVLVDIG-TGYFVEKTMDE 100 (124)
Q Consensus 72 ~yv~a~I~~--~~~VlV~lG-~g~~vE~~~~e 100 (124)
.|++|+|.+ .+.|++++| -||-+-.|...
T Consensus 3 ~~l~G~v~~~~~~~vvi~~~GvGy~v~v~~~~ 34 (61)
T PF01330_consen 3 AYLKGKVVEKNPDYVVIDVNGVGYEVFVPSNT 34 (61)
T ss_dssp EEEEEEEEEEESSEEEEEETTEEEEEEE-HHH
T ss_pred cEEEEEEEEEcCCEEEEEECCEEEEEEeCCch
Confidence 478888875 677888775 46666665543
No 167
>PF12269 zf-CpG_bind_C: CpG binding protein zinc finger C terminal domain; InterPro: IPR022056 This domain family is found in eukaryotes, and is approximately 240 amino acids in length. This domain is the zinc finger domain of a CpG binding DNA methyltransferase protein. It contains a CxxC motif which forms the zinc finger and binds to DNA.
Probab=33.09 E-value=1.1e+02 Score=23.85 Aligned_cols=39 Identities=10% Similarity=0.219 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 033241 18 KAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLS 56 (124)
Q Consensus 18 ~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~ 56 (124)
....++++.+....+..+..|.....++..-+...+..+
T Consensus 28 r~~Le~Ir~kq~~v~~~l~eLe~~~~el~~~i~~~k~~~ 66 (236)
T PF12269_consen 28 RKLLEEIRKKQQKVRNRLQELEKRFKELEAIIARAKQFT 66 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 344556666666777777777777777777666666543
No 168
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=33.08 E-value=1.7e+02 Score=20.49 Aligned_cols=44 Identities=16% Similarity=0.347 Sum_probs=25.1
Q ss_pred CCHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 12 MSVEQLKAIKEQT-----DLEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 12 l~le~L~~~~~~l-----~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
+|++++..+.... +...+.+.+++..+...+.++......|..+
T Consensus 65 ~sL~eI~~ll~~~~~~~~~~~~~ll~~k~~~l~~~i~~L~~~~~~L~~~ 113 (144)
T PRK13752 65 FSLDEIAELLRLEDGTHCEEASSLAEHKLKDVREKMADLARMEAVLSEL 113 (144)
T ss_pred CCHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5666666654311 2234455666666666666666666666553
No 169
>PF03249 TSA: Type specific antigen; InterPro: IPR004933 There are several antigenic variants in Rickettsia tsutsugamushi, and a type-specific antigen (TSA) of 56-kilodaltons located on the rickettsial surface is responsible for the variation [, ]. TSA proteins are probably integral membrane proteins. ; GO: 0016021 integral to membrane
Probab=32.95 E-value=57 Score=27.36 Aligned_cols=39 Identities=31% Similarity=0.455 Sum_probs=29.3
Q ss_pred CCceEEEecCCce-eEeEEEcCC---------------------CeEEEEccCceeeecCH
Q 033241 60 QGAKMLVPLTASL-YVPGTLDDA---------------------RKVLVDIGTGYFVEKTM 98 (124)
Q Consensus 60 ~~~e~lVplg~~~-yv~a~I~~~---------------------~~VlV~lG~g~~vE~~~ 98 (124)
+++.++.-+|+|+ |..|+|.+. +-|+|+|-.|||-.+|-
T Consensus 423 esfsiyag~gaglayt~gkid~~dik~~tgmvasgalgvainaaegv~vdieg~ym~sfsk 483 (503)
T PF03249_consen 423 ESFSIYAGLGAGLAYTYGKIDGKDIKGHTGMVASGALGVAINAAEGVYVDIEGGYMHSFSK 483 (503)
T ss_pred cceEEEeccccceeeecccccCcccccccceeeechhhhhhhhhceeEEeeecceEeeeee
Confidence 5677888889887 999999864 45777777777766654
No 170
>cd02770 MopB_DmsA-EC This CD (MopB_DmsA-EC) includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=32.81 E-value=60 Score=27.99 Aligned_cols=38 Identities=18% Similarity=0.326 Sum_probs=29.7
Q ss_pred EcCCCeEEEEc------cCceeeecCHHHHHHHHHHHHHHHHHH
Q 033241 78 LDDARKVLVDI------GTGYFVEKTMDEGKDYCERKINLLKSN 115 (124)
Q Consensus 78 I~~~~~VlV~l------G~g~~vE~~~~eA~~~l~~r~~~l~~~ 115 (124)
+.+++++.-++ |.|=|.+.|-|||++.+.+|++.+.+.
T Consensus 54 ~y~p~Rl~~Pl~R~g~rG~g~~~~isWDeAl~~ia~kl~~i~~~ 97 (617)
T cd02770 54 VYNPDRLKYPMKRVGKRGEGKFVRISWDEALDTIASELKRIIEK 97 (617)
T ss_pred hcChhHhcCCceecCcCCCCCeEEecHHHHHHHHHHHHHHHHHH
Confidence 44455554444 578999999999999999999988764
No 171
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=32.74 E-value=1.7e+02 Score=25.16 Aligned_cols=37 Identities=19% Similarity=0.274 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 16 QLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTAL 52 (124)
Q Consensus 16 ~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l 52 (124)
+|++....++++++.++.....++..+.+++.-+..|
T Consensus 80 ELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~L 116 (475)
T PRK13729 80 QMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAAL 116 (475)
T ss_pred HHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHH
Confidence 3333334444444433344444444444444444444
No 172
>PRK14549 50S ribosomal protein L29P; Provisional
Probab=32.40 E-value=1.3e+02 Score=18.65 Aligned_cols=26 Identities=23% Similarity=0.207 Sum_probs=22.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHH
Q 033241 7 GGMEKMSVEQLKAIKEQTDLEVNLLQ 32 (124)
Q Consensus 7 i~~~~l~le~L~~~~~~l~~ei~~l~ 32 (124)
-++..+|.++|......+..++-.|.
T Consensus 7 ~elr~ls~~eL~~~l~elk~eLf~LR 32 (69)
T PRK14549 7 SEIREMSPEEREEKLEELKLELLKER 32 (69)
T ss_pred HHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999998888877
No 173
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=32.34 E-value=1.7e+02 Score=20.05 Aligned_cols=27 Identities=11% Similarity=0.214 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 28 VNLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 28 i~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
.+.+.+++..++..+.++....+.|..
T Consensus 83 ~~~l~~~~~~l~~~i~~L~~~~~~L~~ 109 (131)
T TIGR02043 83 KAIVDAKLELVDEKINELTKIRRSLKK 109 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555555555555555555554
No 174
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=32.30 E-value=1.6e+02 Score=19.82 Aligned_cols=44 Identities=9% Similarity=0.244 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 12 MSVEQLKAIKEQ----------TDLEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 12 l~le~L~~~~~~----------l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
+|++++..+... +...++.+.+++..|...+.+++..++.|+..
T Consensus 56 ~~L~~I~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~L~~~ 109 (118)
T cd04776 56 FSLEEIRELLDLYDPPGGNRKQLEKMLEKIEKRRAELEQQRRDIDAALAELDAA 109 (118)
T ss_pred CCHHHHHHHHHhhccCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566666655442 23445677888888888888888888777764
No 175
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=32.28 E-value=1.9e+02 Score=20.80 Aligned_cols=45 Identities=22% Similarity=0.409 Sum_probs=25.5
Q ss_pred CCCHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 11 KMSVEQLKAIKEQT-DLEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 11 ~l~le~L~~~~~~l-~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
-+|++++..+.... ......+.+++..|...+.++......|..+
T Consensus 58 G~sL~eI~~ll~~~~~~~~~~L~~~~~~l~~ei~~L~~~~~~l~~l 103 (172)
T cd04790 58 GVSLEDIRSLLQQPGDDATDVLRRRLAELNREIQRLRQQQRAIATL 103 (172)
T ss_pred CCCHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35677777765421 1223445666666666666666666666554
No 176
>PF05190 MutS_IV: MutS family domain IV C-terminus.; InterPro: IPR007861 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the clamp domain (domain 4) found in proteins of the MutS family. The clamp domain is inserted within the core domain at the top of the lever helices. It has a beta-sheet structure [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B 1WBD_A 1WB9_A 3K0S_A 1OH6_A ....
Probab=32.24 E-value=69 Score=19.78 Aligned_cols=26 Identities=27% Similarity=0.074 Sum_probs=14.3
Q ss_pred CeEEEEccCceeeecCHHHHHHHHHHH
Q 033241 82 RKVLVDIGTGYFVEKTMDEGKDYCERK 108 (124)
Q Consensus 82 ~~VlV~lG~g~~vE~~~~eA~~~l~~r 108 (124)
+-+.+.- .+=++-++.++-.++..+-
T Consensus 61 ~~~~~~~-~k~~~rf~t~~l~~L~~~~ 86 (92)
T PF05190_consen 61 DFIIVSS-TKSGVRFTTPELKELNEEL 86 (92)
T ss_dssp TEEEEEE-ESSEEEEECHHHHHHHHHH
T ss_pred ceEEEEE-EcCcEEEECHHHHHHHHHH
Confidence 4444333 5555667777766655443
No 177
>PF07352 Phage_Mu_Gam: Bacteriophage Mu Gam like protein; InterPro: IPR009951 The Gam protein, originally characterised in Bacteriophage Mu, protects linear double stranded DNA from exonuclease degradation in vitro and in vivo []. This protein is also found in many bacterial species as part of a suspected prophage. Further studies have shown that Gam is a functional counterpart of the eukaryotic Ku protein, which has key roles in DNA repair and in certain transposition events. Gam displays DNA binding characteristics remarkably similar to those of human Ku []. In addition, Gam can interfere with Ty1 retrotransposition in Saccharomyces cerevisiae (Baker's yeast). These data reveal structural and functional parallels between bacteriophage Gam and eukaryotic Ku and suggest that their functions have been evolutionarily conserved [].; GO: 0003690 double-stranded DNA binding, 0042262 DNA protection; PDB: 2P2U_B.
Probab=32.12 E-value=1e+02 Score=21.62 Aligned_cols=33 Identities=21% Similarity=0.285 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 16 QLKAIKEQTDLEVNLLQDSLNNIRTATSRLESA 48 (124)
Q Consensus 16 ~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~ 48 (124)
++..+.+.++.++..+++++..|...+..|-++
T Consensus 29 ~I~~i~~~~~~~~~~l~~~i~~l~~~l~~y~e~ 61 (149)
T PF07352_consen 29 EIARIKEWYEAEIAPLQNRIEYLEGLLQAYAEA 61 (149)
T ss_dssp HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555666666666666666666666666554
No 178
>cd02772 MopB_NDH-1_NuoG2 MopB_NDH-1_NuoG2: The second domain of the NuoG subunit of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1), found in beta- and gammaproteobacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain (this CD), is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Although only vestigial sequence evidence remains of a molybdopterin binding site, this protein domain belongs to t
Probab=32.02 E-value=45 Score=26.90 Aligned_cols=25 Identities=12% Similarity=0.295 Sum_probs=22.4
Q ss_pred CceeeecCHHHHHHHHHHHHHHHHH
Q 033241 90 TGYFVEKTMDEGKDYCERKINLLKS 114 (124)
Q Consensus 90 ~g~~vE~~~~eA~~~l~~r~~~l~~ 114 (124)
.|-|.+.|-+||.+.+.+|++.+.+
T Consensus 63 ~g~~~~isWdeAl~~ia~~l~~i~~ 87 (414)
T cd02772 63 DGQWQEVDWETALEYVAEGLSAIIK 87 (414)
T ss_pred CCceEEecHHHHHHHHHHHHHHHHH
Confidence 4779999999999999999988765
No 179
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=31.83 E-value=1.6e+02 Score=19.75 Aligned_cols=50 Identities=12% Similarity=0.114 Sum_probs=34.0
Q ss_pred HHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCceeeecCHHH
Q 033241 46 ESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYFVEKTMDE 100 (124)
Q Consensus 46 ~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~vE~~~~e 100 (124)
++..+-++.|++ |.+ |=..+|+|-.-.=.+.+.|.+.++.|+.+.....-
T Consensus 44 k~~~~~~~~Lk~---Gd~--VvT~gGi~G~Vv~i~~~~v~lei~~g~~i~~~r~a 93 (106)
T PRK05585 44 KEHKKMLSSLAK---GDE--VVTNGGIIGKVTKVSEDFVIIELNDDTEIKIQKSA 93 (106)
T ss_pred HHHHHHHHhcCC---CCE--EEECCCeEEEEEEEeCCEEEEEECCCeEEEEEhHH
Confidence 344566677775 333 55678888764423458999999999888876553
No 180
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=31.82 E-value=76 Score=20.50 Aligned_cols=24 Identities=13% Similarity=0.299 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 100 EGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 100 eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
+..+++..+++.++++++.++..|
T Consensus 73 ~~~~~l~~~~~~l~~~i~~l~~~r 96 (96)
T cd04788 73 DPLELLRRQLARLEEQLELATRLR 96 (96)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhcC
Confidence 678899999999999999998765
No 181
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=31.70 E-value=1.8e+02 Score=20.20 Aligned_cols=84 Identities=23% Similarity=0.290 Sum_probs=50.2
Q ss_pred HHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccC
Q 033241 14 VEQLKAIKEQTD---LEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGT 90 (124)
Q Consensus 14 le~L~~~~~~l~---~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~ 90 (124)
+.++++++++++ .+.+.+..++.....+..++...-+-=.-.+. .+++||+.+- +.
T Consensus 12 l~q~QqLq~ql~~~~~qk~~le~qL~E~~~al~Ele~l~eD~~vYk~-----------VG~llvk~~k---~~------- 70 (119)
T COG1382 12 LAQLQQLQQQLQKVILQKQQLEAQLKEIEKALEELEKLDEDAPVYKK-----------VGNLLVKVSK---EE------- 70 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccHHHHH-----------hhhHHhhhhH---HH-------
Confidence 345555555554 45577778888888888887654332122221 1224444421 11
Q ss_pred ceeeecCHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 91 GYFVEKTMDEGKDYCERKINLLKSNFDQLIE 121 (124)
Q Consensus 91 g~~vE~~~~eA~~~l~~r~~~l~~~i~~l~~ 121 (124)
|--.+++=.++++.|++-|+++.+.+++
T Consensus 71 ---~~~eL~er~E~Le~ri~tLekQe~~l~e 98 (119)
T COG1382 71 ---AVDELEERKETLELRIKTLEKQEEKLQE 98 (119)
T ss_pred ---HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3346788888999998888888777654
No 182
>PF13863 DUF4200: Domain of unknown function (DUF4200)
Probab=31.64 E-value=1.6e+02 Score=19.60 Aligned_cols=37 Identities=8% Similarity=0.138 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q 033241 21 KEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSL 57 (124)
Q Consensus 21 ~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~ 57 (124)
..++..++..|...+..+...+.+|....+-|..+.+
T Consensus 83 i~~l~~~l~~l~~~~~k~e~~l~~~~~Y~~fL~~v~~ 119 (126)
T PF13863_consen 83 IKKLKAELEELKSEISKLEEKLEEYKKYEEFLEKVVP 119 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3444445555555555555555555555566665543
No 183
>PRK14067 exodeoxyribonuclease VII small subunit; Provisional
Probab=31.51 E-value=1.4e+02 Score=19.06 Aligned_cols=36 Identities=11% Similarity=0.094 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 10 EKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRL 45 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~ 45 (124)
..+||++...++++--.-+...++.+......+..+
T Consensus 26 ~~l~Lees~~lyeeG~~L~k~C~~~L~~ae~kI~~l 61 (80)
T PRK14067 26 GDLPLEESVALYKEGLGLARACREQLAKARNEIRLF 61 (80)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567788888777777776666666555555555444
No 184
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=31.50 E-value=1.8e+02 Score=20.31 Aligned_cols=45 Identities=9% Similarity=0.049 Sum_probs=26.1
Q ss_pred CCCHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 11 KMSVEQLKAIKEQT--------DLEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 11 ~l~le~L~~~~~~l--------~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
-+|++++..+...+ ....+.+.+++..+...+.++....+.|...
T Consensus 57 G~sL~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~ki~~L~~~~~~L~~~ 109 (142)
T TIGR01950 57 GIPLATIGEALAVLPEGRTPTADDWARLSSQWREELDERIDQLNALRDQLDGC 109 (142)
T ss_pred CCCHHHHHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35677777765432 2223445555666666666666666666654
No 185
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=31.39 E-value=1.7e+02 Score=19.79 Aligned_cols=44 Identities=16% Similarity=0.227 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 12 MSVEQLKAIKEQT-----DLEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 12 l~le~L~~~~~~l-----~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
+|++++..+.... ..-.+.++.++..++..+.++....+.|+.+
T Consensus 57 ~sl~eI~~~l~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~ 105 (124)
T TIGR02051 57 FSLEEIGGLLGLVDGTHCREMYELASRKLKSVQAKMADLLRIERLLEEL 105 (124)
T ss_pred CCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5666666655422 2334556666667777777766666666654
No 186
>cd05166 PI3Kc_II Phosphoinositide 3-kinase (PI3K), class II, catalytic domain; The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class II PI3Ks preferentially use PtdIns as a substrate to produce PtdIns(3)P, but can also phosphorylate PtdIns(4)P. They function as monomers and do not associate with any
Probab=31.23 E-value=1.8e+02 Score=23.78 Aligned_cols=58 Identities=16% Similarity=0.128 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeE
Q 033241 26 LEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKV 84 (124)
Q Consensus 26 ~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~V 84 (124)
+++..+...+...... .+.....+.++.++.......+.+|+...+.+.|-+.+.-+|
T Consensus 12 ~~l~~i~~~vk~~~~~-~~~~~l~~~l~~~~~~~~~~~~~lP~~p~~~~~~i~~~~~~v 69 (353)
T cd05166 12 NKLGSIAEDVKSASES-ARQHVLRTGLGRVDSFLLQNKCRLPLNPALDVKGIDVRECSY 69 (353)
T ss_pred HHHHHHHHHHhcCchH-HHHHHHHHHHHhhhhhccCCCCccCCCCceEEEeEEcCceEE
Confidence 3344444444443321 223333444444432222346889999988888877654333
No 187
>PRK14063 exodeoxyribonuclease VII small subunit; Provisional
Probab=31.15 E-value=1.4e+02 Score=18.84 Aligned_cols=35 Identities=11% Similarity=0.128 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 10 EKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSR 44 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~ 44 (124)
..+|+++...++++--.-+...++.+......+..
T Consensus 24 ~~l~Leesl~lyeeG~~L~k~C~~~L~~aE~ki~~ 58 (76)
T PRK14063 24 GDVPLEEAISYFKEGMELSKLCDEKLKNVQEQMAV 58 (76)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56788888888877776666666655555544443
No 188
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=31.04 E-value=1.6e+02 Score=19.54 Aligned_cols=26 Identities=19% Similarity=0.082 Sum_probs=17.9
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 12 MSVEQLKAIKEQTDLEVNLLQDSLNN 37 (124)
Q Consensus 12 l~le~L~~~~~~l~~ei~~l~~~~~~ 37 (124)
|+.+++..+++.|.+....|..++..
T Consensus 1 M~~~~l~~~k~~L~~~~~~L~~~i~~ 26 (110)
T TIGR02420 1 MSEAQLEHFRKILLRWKQELLEEADK 26 (110)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45678888888887776666655443
No 189
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=30.70 E-value=1.4e+02 Score=18.83 Aligned_cols=28 Identities=25% Similarity=0.414 Sum_probs=13.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 12 MSVEQLKAIKEQTDLEVNLLQDSLNNIRT 40 (124)
Q Consensus 12 l~le~L~~~~~~l~~ei~~l~~~~~~L~~ 40 (124)
+|++++..+.. +..+++.+++++..|+.
T Consensus 59 ~~l~~i~~~l~-l~~~~~~l~~~l~~l~~ 86 (91)
T cd04766 59 VNLAGVKRILE-LEEELAELRAELDELRA 86 (91)
T ss_pred CCHHHHHHHHH-HHHHHHHHHHHHHHHHH
Confidence 44555554443 44444445544444443
No 190
>PF10512 Borealin: Cell division cycle-associated protein 8 ; InterPro: IPR018867 The chromosomal passenger complex of Aurora B kinase, INCENP, and Survivin has essential regulatory roles at centromeres and the central spindle in mitosis. Cell division cycle-associated protein 8, also known as Borealin, is also a member of the complex. Approximately half of Aurora B in mitotic cells is complexed with INCENP, Borealin, and Survivin. Depletion of Borealin by RNA interference delays mitotic progression and results in kinetochore-spindle mis-attachments and an increase in bipolar spindles associated with ectopic asters []. ; PDB: 2KDD_A.
Probab=30.69 E-value=86 Score=21.56 Aligned_cols=37 Identities=22% Similarity=0.277 Sum_probs=23.0
Q ss_pred CCCCCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 3 SSKGGGM--EKMSVEQLKAIKEQTDLEVNLLQDSLNNIR 39 (124)
Q Consensus 3 ~~~~i~~--~~l~le~L~~~~~~l~~ei~~l~~~~~~L~ 39 (124)
.|+.+.+ .+++-..|.++-+.--++|..|+.+++.+-
T Consensus 74 ~G~~~~l~~~dl~~~~l~~Ld~~tl~~ik~L~~~L~~i~ 112 (116)
T PF10512_consen 74 NGKPIRLLASDLDREDLEQLDPETLNQIKTLQANLQKIC 112 (116)
T ss_dssp SSS---EETTT--HHHHHTS-HHHHHHHHHHHHHHHHHH
T ss_pred CCeEEEcchhhcCHHHHHhcCHHHHHHHHHHHHHHHHHH
Confidence 4566777 788888888887777777777777776654
No 191
>PF14962 AIF-MLS: Mitochondria Localisation Sequence; PDB: 1M6I_A.
Probab=30.28 E-value=17 Score=27.06 Aligned_cols=30 Identities=27% Similarity=0.406 Sum_probs=0.0
Q ss_pred EccCceeeecCHHHHHHHHHHHHHHHHHHH
Q 033241 87 DIGTGYFVEKTMDEGKDYCERKINLLKSNF 116 (124)
Q Consensus 87 ~lG~g~~vE~~~~eA~~~l~~r~~~l~~~i 116 (124)
-+|+|||+=+|+.+=.+-++.|+..|...-
T Consensus 56 ~~gag~YaYkTv~~dq~Ry~eRi~~l~~r~ 85 (180)
T PF14962_consen 56 VSGAGYYAYKTVKSDQARYNERISELKERP 85 (180)
T ss_dssp ------------------------------
T ss_pred EEeeEEEEEEeecchhHHHHHHHHHHhhcC
Confidence 368999999999999999999999886543
No 192
>PRK00068 hypothetical protein; Validated
Probab=30.28 E-value=98 Score=28.88 Aligned_cols=45 Identities=22% Similarity=0.314 Sum_probs=36.7
Q ss_pred CceEEEecCCce------eEeEE----EcCCCeEEEEccCceeeecCHHHHHHHH
Q 033241 61 GAKMLVPLTASL------YVPGT----LDDARKVLVDIGTGYFVEKTMDEGKDYC 105 (124)
Q Consensus 61 ~~e~lVplg~~~------yv~a~----I~~~~~VlV~lG~g~~vE~~~~eA~~~l 105 (124)
|.-.-+|+|.|+ |++++ ++.-.+|+|.-|..+-.+-|++||.+-+
T Consensus 830 GNLLvlPi~~~lLYVePvYlqa~~~~~~P~L~rVivs~g~~v~~~~TL~eAL~~l 884 (970)
T PRK00068 830 GNLLTLPVGGSLLYVEPVYLRAGGQNSYPELKRVLVSYNDKVGYAPTIREALTQL 884 (970)
T ss_pred cceEEEEeCCeeEEEEeEEEecCCCCCCceeEEEEEEECCEeEeccCHHHHHHHH
Confidence 455667999886 66664 4556799999999999999999999876
No 193
>PF14588 YjgF_endoribonc: YjgF/chorismate_mutase-like, putative endoribonuclease; PDB: 2OTM_B 3D01_D.
Probab=30.20 E-value=56 Score=23.51 Aligned_cols=63 Identities=22% Similarity=0.248 Sum_probs=38.6
Q ss_pred CCceEEEecCCceeEeEEEcCCCeEEEE---ccCceeeecCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033241 60 QGAKMLVPLTASLYVPGTLDDARKVLVD---IGTGYFVEKTMDEGKDYCERKINLLKSNFDQLIEV 122 (124)
Q Consensus 60 ~~~e~lVplg~~~yv~a~I~~~~~VlV~---lG~g~~vE~~~~eA~~~l~~r~~~l~~~i~~l~~~ 122 (124)
..+.-.+-.|.-+|+.|.++..+..++. +|.++-+|--.+-|+--.-.=+..++..+..|.++
T Consensus 19 g~Y~p~~~~G~ll~vSGq~p~~~g~~~~~G~vG~~~s~e~g~~AAr~~~Ln~La~lk~~~G~LdrV 84 (148)
T PF14588_consen 19 GNYVPAVRVGNLLYVSGQLPRDDGKLLYTGKVGEDLSVEEGYEAARLCALNALAALKAALGDLDRV 84 (148)
T ss_dssp SSC-SEEEETTEEEEEEE--EETTEE-SBS-BTTTB-HHHHHHHHHHHHHHHHHHHHHHCTSGGGE
T ss_pred ceeeeEEEECCEEEEeccCcccCCEEeeecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHE
Confidence 3455566678999999999976665555 77776666655555555555666666666656554
No 194
>TIGR02164 torA trimethylamine-N-oxide reductase TorA. This very narrowly defined family represents TorA, part of a family of related molybdoenzymes that include biotin sulfoxide reductases, dimethyl sulfoxide reductases, and at least two different subfamilies of trimethylamine-N-oxide reductases. A single enzyme from the larger family may have more than one activity. TorA typically is located in the periplasm, has a Tat (twin-arginine translocation)-dependent signal sequence, and is encoded in a torCAD operon.
Probab=30.11 E-value=64 Score=28.94 Aligned_cols=27 Identities=26% Similarity=0.383 Sum_probs=24.4
Q ss_pred cCceeeecCHHHHHHHHHHHHHHHHHH
Q 033241 89 GTGYFVEKTMDEGKDYCERKINLLKSN 115 (124)
Q Consensus 89 G~g~~vE~~~~eA~~~l~~r~~~l~~~ 115 (124)
|.|=|.+.|-|||++.+..|++.+.+.
T Consensus 110 G~g~f~rISWDEAld~IA~kl~~i~~~ 136 (822)
T TIGR02164 110 GDNRFVRVTWDEALDLFYEELERVQKQ 136 (822)
T ss_pred CCCCEEEecHHHHHHHHHHHHHHHHHh
Confidence 688999999999999999999888654
No 195
>PF10398 DUF2443: Protein of unknown function (DUF2443); InterPro: IPR019469 This entry represents a small group of highly conserved proteins from bacteria, in particular Helicobacter species. The structure is a bundle of alpha helices. The function is not known. ; PDB: 1ZKE_F.
Probab=30.10 E-value=1.3e+02 Score=19.32 Aligned_cols=19 Identities=21% Similarity=0.358 Sum_probs=9.0
Q ss_pred HHHHHHHHHHHHHHHhhcc
Q 033241 38 IRTATSRLESASTALHDLS 56 (124)
Q Consensus 38 L~~~~~~~~~~~~~l~~L~ 56 (124)
+...+.++++++++|+.++
T Consensus 55 ideeV~~LKe~IdaLNK~K 73 (79)
T PF10398_consen 55 IDEEVEKLKEHIDALNKIK 73 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3334444445555555543
No 196
>PF12841 YvrJ: YvrJ protein family; InterPro: IPR024419 This entry is represents a family of uncharacterised protein. The function of the Bacillus subtilis YvrJ protein is not known, but its expression is regulated by the cell envelope stress-inducible sigma factor YvrI [].
Probab=30.07 E-value=73 Score=17.59 Aligned_cols=18 Identities=28% Similarity=0.494 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHhhh
Q 033241 105 CERKINLLKSNFDQLIEV 122 (124)
Q Consensus 105 l~~r~~~l~~~i~~l~~~ 122 (124)
+++|++.|.+.+.+|.+.
T Consensus 20 ~E~kld~L~~~i~~L~~~ 37 (38)
T PF12841_consen 20 IEKKLDELTESINELSEA 37 (38)
T ss_pred HHHHHHHHHHHHHHHHhh
Confidence 688999999999888753
No 197
>TIGR02977 phageshock_pspA phage shock protein A. Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by PFAM model pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects.
Probab=30.00 E-value=2.4e+02 Score=21.08 Aligned_cols=34 Identities=9% Similarity=0.166 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 17 LKAIKEQTDLEVNLLQDSLNNIRTATSRLESAST 50 (124)
Q Consensus 17 L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~ 50 (124)
|...+.++...++.+..++..|+..+.++..-.+
T Consensus 104 l~~~~~~~~~~v~~l~~~l~~L~~ki~~~k~k~~ 137 (219)
T TIGR02977 104 LERELAAVEETLAKLQEDIAKLQAKLAEARARQK 137 (219)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333444445555555555555555555544433
No 198
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=29.83 E-value=1.4e+02 Score=18.42 Aligned_cols=39 Identities=18% Similarity=0.337 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 16 QLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 16 ~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
++....+.++++++.++++...|+..+..+.. .+.|+.+
T Consensus 28 ~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~~-~~rIe~~ 66 (85)
T TIGR02209 28 QLNNELQKLQLEIDKLQKEWRDLQLEVAELSR-HERIEKI 66 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC-HHHHHHH
Confidence 44444555556666666666666666655543 3444443
No 199
>TIGR02231 conserved hypothetical protein. This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown.
Probab=29.77 E-value=2.7e+02 Score=23.53 Aligned_cols=46 Identities=11% Similarity=0.085 Sum_probs=35.0
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 9 MEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 9 ~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
.+..++.++.++...+.+++..+..++..+...+.++++.+..+..
T Consensus 121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~ 166 (525)
T TIGR02231 121 RNEPDLKEWFQAFDFNGSEIERLLTEDREAERRIRELEKQLSELQN 166 (525)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3467899999998888888888888888777777777666655543
No 200
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=29.44 E-value=1.8e+02 Score=19.64 Aligned_cols=44 Identities=14% Similarity=0.235 Sum_probs=25.4
Q ss_pred CCHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 12 MSVEQLKAIKEQT-------DLEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 12 l~le~L~~~~~~l-------~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
+|++++..+.... ..-.+.+.+++..+...+.++......|..+
T Consensus 58 ~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~l~~~ 108 (127)
T cd01108 58 FSLEEIRELLALWRDPSRASADVKALALEHIAELERKIAELQAMRRTLQQL 108 (127)
T ss_pred CCHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5666666654421 2233556666666666666666666666554
No 201
>PF10392 COG5: Golgi transport complex subunit 5; InterPro: IPR019465 The conserved oligomeric Golgi (COG) complex is a peripheral membrane complex involved in intra-Golgi protein trafficking. Subunit 5 is located in the smaller, B lobe, together with subunits 6-8, and has been shown to bind subunits 1 and 7 [].
Probab=29.42 E-value=1.9e+02 Score=19.81 Aligned_cols=27 Identities=22% Similarity=0.373 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 16 QLKAIKEQTDLEVNLLQDSLNNIRTAT 42 (124)
Q Consensus 16 ~L~~~~~~l~~ei~~l~~~~~~L~~~~ 42 (124)
++....+.+...++.|+..+..|+..+
T Consensus 69 ~~~~~l~~v~~~v~~L~~s~~RL~~eV 95 (132)
T PF10392_consen 69 ELESVLQAVRSSVESLQSSYERLRSEV 95 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444445555555444433
No 202
>PF02388 FemAB: FemAB family; InterPro: IPR003447 The femAB operon codes for two nearly identical approximately 50kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan []. These proteins are also considered as a factor influencing the level of methicillin resistance [].; GO: 0016755 transferase activity, transferring amino-acyl groups; PDB: 1XE4_A 1NE9_A 3GKR_A 1XIX_A 1P4N_A 1XF8_A 1LRZ_A.
Probab=29.38 E-value=98 Score=25.44 Aligned_cols=30 Identities=20% Similarity=0.293 Sum_probs=26.0
Q ss_pred eeeecCHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 92 YFVEKTMDEGKDYCERKINLLKSNFDQLIE 121 (124)
Q Consensus 92 ~~vE~~~~eA~~~l~~r~~~l~~~i~~l~~ 121 (124)
++++.+++++++.++.+++.+++.++++..
T Consensus 234 ~~A~l~~~~~~~~l~~~~~~~~~~i~~l~~ 263 (406)
T PF02388_consen 234 FLAELNGKEYLESLQEKLEKLEKEIEKLEE 263 (406)
T ss_dssp EEEEECCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred EEEEEcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999999998888765
No 203
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=29.38 E-value=3.4e+02 Score=22.69 Aligned_cols=80 Identities=14% Similarity=0.166 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHhhccCCCC-Cce---EEEecCCceeEeEEEcCCCeEEEEccCceeeec-------------CHHHHHH
Q 033241 41 ATSRLESASTALHDLSLRPQ-GAK---MLVPLTASLYVPGTLDDARKVLVDIGTGYFVEK-------------TMDEGKD 103 (124)
Q Consensus 41 ~~~~~~~~~~~l~~L~~~~~-~~e---~lVplg~~~yv~a~I~~~~~VlV~lG~g~~vE~-------------~~~eA~~ 103 (124)
...++.++++.|..|.|... .+. .-..+-..++|.-. .+.+.|.+-..++=+. ..+++.+
T Consensus 195 s~~~v~~~~~~I~~L~P~Pg~~~~~~~~~~yi~PDv~V~~~---~~~~~v~ln~~~~P~l~i~~~y~~~~~~~~~~~~~~ 271 (429)
T TIGR02395 195 SEEELKEALDLIKSLSPKPGKEFADPEEVEYVIPDVIVTKK---NGEWVVELNGRSLPELRINEEYFKLLKDAEKEAAAQ 271 (429)
T ss_pred CHHHHHHHHHHHhCCCCCCcccccCCCCCCccCCCEEEEEE---CCEEEEEEcCCCCceEEECHHHHHHHHhccchHHHH
Confidence 46788899999999976321 111 11123334443211 2223333322222111 1237779
Q ss_pred HHHHHHHHHHHHHHHHhhhh
Q 033241 104 YCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 104 ~l~~r~~~l~~~i~~l~~~~ 123 (124)
|++++++..+--++.+++.|
T Consensus 272 ylk~k~~~A~~li~~i~~R~ 291 (429)
T TIGR02395 272 YLKQKLKEARWLIKALEQRE 291 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 99999998888887776654
No 204
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=29.33 E-value=2.3e+02 Score=20.69 Aligned_cols=26 Identities=4% Similarity=0.233 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 20 IKEQTDLEVNLLQDSLNNIRTATSRL 45 (124)
Q Consensus 20 ~~~~l~~ei~~l~~~~~~L~~~~~~~ 45 (124)
.++.+...|..|.+.+..+...+.++
T Consensus 23 ~hq~~~~~I~~L~~e~~~ld~~i~~~ 48 (188)
T PF10018_consen 23 EHQENQARIQQLRAEIEELDEQIRDI 48 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555666666555555544443
No 205
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=29.28 E-value=2.9e+02 Score=21.96 Aligned_cols=34 Identities=26% Similarity=0.373 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLES 47 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~ 47 (124)
.++|....+.+..+...++..+..++..+.++..
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 41 (364)
T TIGR01242 8 IRKLEDEKRSLEKEKIRLERELERLRSEIERLRS 41 (364)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 5667777777777777888888888877777663
No 206
>PHA01750 hypothetical protein
Probab=29.11 E-value=1.5e+02 Score=18.59 Aligned_cols=33 Identities=15% Similarity=0.319 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033241 21 KEQTDLEVNLLQDSLNNIRTATSRLESASTALH 53 (124)
Q Consensus 21 ~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~ 53 (124)
.+=.++|+.+|..+++.++..+.++.+-++-|+
T Consensus 37 keIV~~ELdNL~~ei~~~kikqDnl~~qv~eik 69 (75)
T PHA01750 37 KEIVNSELDNLKTEIEELKIKQDELSRQVEEIK 69 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence 344557778888888888877777665544443
No 207
>cd02763 MopB_2 The MopB_2 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins
Probab=29.01 E-value=75 Score=28.21 Aligned_cols=26 Identities=19% Similarity=0.419 Sum_probs=23.5
Q ss_pred cCceeeecCHHHHHHHHHHHHHHHHH
Q 033241 89 GTGYFVEKTMDEGKDYCERKINLLKS 114 (124)
Q Consensus 89 G~g~~vE~~~~eA~~~l~~r~~~l~~ 114 (124)
|.|-|.+.|-+||++++.+|++.+.+
T Consensus 66 G~g~f~~ISWDEAld~IA~kL~~i~~ 91 (679)
T cd02763 66 GSGQFEEIEWEEAFSIATKRLKAARA 91 (679)
T ss_pred CCCceEEeCHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999988754
No 208
>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells. In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].
Probab=28.82 E-value=2.1e+02 Score=20.12 Aligned_cols=39 Identities=23% Similarity=0.316 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 16 QLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 16 ~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
+|.+...+.+.+|..|+..+..|...+..+...+..+..
T Consensus 25 ~le~~~~~~E~EI~sL~~K~~~lE~eld~~~~~l~~~k~ 63 (143)
T PF12718_consen 25 QLEQENEQKEQEITSLQKKNQQLEEELDKLEEQLKEAKE 63 (143)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444455566666777776666666666655544444433
No 209
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=28.60 E-value=1.8e+02 Score=19.35 Aligned_cols=25 Identities=4% Similarity=0.147 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 16 QLKAIKEQTDLEVNLLQDSLNNIRT 40 (124)
Q Consensus 16 ~L~~~~~~l~~ei~~l~~~~~~L~~ 40 (124)
++.+..++++++.+.|..++..|+.
T Consensus 38 ~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 38 AQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 3334444444555555555555543
No 210
>PF08781 DP: Transcription factor DP; InterPro: IPR014889 DP forms a heterodimer with E2F and regulates genes involved in cell cycle progression. The transcriptional activity of E2F is inhibited by the retinoblastoma protein which binds to the E2F-DP heterodimer [] and negatively regulates the G1-S transition. ; PDB: 2AZE_A.
Probab=28.58 E-value=2.2e+02 Score=20.32 Aligned_cols=67 Identities=10% Similarity=0.152 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCC-------ceEEEecCCceeEeEEEcC
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQG-------AKMLVPLTASLYVPGTLDD 80 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~-------~e~lVplg~~~yv~a~I~~ 80 (124)
.++|...+..+.+.|+.-.+.++.|.....-|+..+..=..+...+.. .-++|.-....-|...|.+
T Consensus 3 ~~~Le~ek~~~~~rI~~K~~~LqEL~~Q~va~knLv~RN~~~~~~~~~p~~~i~LPFIlV~T~~~a~I~ceiS~ 76 (142)
T PF08781_consen 3 CEELEEEKQRRRERIKKKKEQLQELILQQVAFKNLVQRNRQLEQSGNAPSSGIQLPFILVNTSKKAVIECEISE 76 (142)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSS--GEEESS-EEEEEESS--EEEEE-T
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCeeecCEEEEEecCCcEEEEEEcC
Confidence 467777888888888777777777777777777766554444321111 2244444555556666654
No 211
>PF00429 TLV_coat: ENV polyprotein (coat polyprotein); InterPro: IPR018154 Enveloped viruses such as Human immunodeficiency virus 1, influenza virus, and Ebola virus sp. express a surface glycoprotein that mediates both cell attachment and fusion of viral and cellular membranes. The ENV polyprotein (coat polyprotein) usually contains two coat proteins which differ depending on the source. The structure of a number of the ENV polyprotein domains have been determined: The crystal structure of an extraviral segment of the Moloney murine leukemia virus (MoMuLV) transmembrane (TM) subunit has been determined to 1.7-A resolution. This segment contains a trimeric coiled coil, with a hydrophobic cluster at its base and a strand that packs in an antiparallel orientation against the coiled coil. This structure serves as a model for a wide range of viral fusion proteins; key residues in this structure are conserved among C- and D-type retroviruses and the filovirus ebola []. An essential step in retrovirus infection is the binding of the virus to its receptor on a target cell. The structure of the receptor-binding domain of the envelope glycoprotein from Friend murine leukemia virus (F-MuLV) has been determined determined to 2.0-A resolution. The core of the domain is an antiparallel beta sandwich, with two interstrand loops forming a helical subdomain atop the sandwich. The residues in the helical region, but not in the beta sandwich, are highly variable among mammalian C-type retroviruses with distinct tropisms, indicating that the helical subdomain determines the receptor specificity of the virus []. ; PDB: 1LCS_B 1MOF_A 1XNL_A 2XZ3_A 1AOL_A 1Y4M_C.
Probab=28.50 E-value=2e+02 Score=24.97 Aligned_cols=44 Identities=20% Similarity=0.355 Sum_probs=36.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHhhcc
Q 033241 13 SVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESAS----TALHDLS 56 (124)
Q Consensus 13 ~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~----~~l~~L~ 56 (124)
+..++.++..+++..++.+++.++.|+..+..+.++. .+|+-|-
T Consensus 422 ~~~~~~~L~~~~~~d~~~~~~~i~~l~~~~~sl~~~v~qnr~~lD~l~ 469 (561)
T PF00429_consen 422 STQQYRQLSNALEEDLQALEDSISALQEQLTSLAEVVLQNRRALDLLT 469 (561)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCchhhhhhh
Confidence 4688889999999999999999999999998887643 5666654
No 212
>PF00626 Gelsolin: Gelsolin repeat; InterPro: IPR007123 Gelsolin is a cytoplasmic, calcium-regulated, actin-modulating protein that binds to the barbed ends of actin filaments, preventing monomer exchange (end-blocking or capping) []. It can promote nucleation (the assembly of monomers into filaments), as well as sever existing filaments. In addition, this protein binds with high affinity to fibronectin. Plasma gelsolin and cytoplasmic gelsolin are derived from a single gene by alternate initiation sites and differential splicing. Sequence comparisons indicate an evolutionary relationship between gelsolin, villin, fragmin and severin []. Six large repeating segments occur in gelsolin and villin, and 3 similar segments in severin and fragmin. While the multiple repeats have yet to be related to any known function of the actin-severing proteins, the superfamily appears to have evolved from an ancestral sequence of 120 to 130 amino acid residues [].; PDB: 3FG6_F 1RGI_G 2FGH_A 1D0N_B 3EGD_B 2NUP_B 2NUT_B 3EGX_B 1JHW_A 1J72_A ....
Probab=28.47 E-value=1.3e+02 Score=17.70 Aligned_cols=13 Identities=23% Similarity=0.345 Sum_probs=10.4
Q ss_pred cCCCeEEEEccCc
Q 033241 79 DDARKVLVDIGTG 91 (124)
Q Consensus 79 ~~~~~VlV~lG~g 91 (124)
....+|+||+|.+
T Consensus 24 d~~~~i~vW~G~~ 36 (76)
T PF00626_consen 24 DCGYEIFVWVGKK 36 (76)
T ss_dssp EESSEEEEEEHTT
T ss_pred EeCCCcEEEEecc
Confidence 3456899999988
No 213
>PF11262 Tho2: Transcription factor/nuclear export subunit protein 2; InterPro: IPR021418 THO and TREX form a eukaryotic complex which functions in messenger ribonucleoprotein metabolism and plays a role in preventing the transcription-associated genetic instability [],[]. Tho2, along with four other subunits forms THO []. This entry represents a conserved domain found towards the C terminus of these proteins.
Probab=28.45 E-value=1.2e+02 Score=23.89 Aligned_cols=27 Identities=22% Similarity=0.324 Sum_probs=17.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 11 KMSVEQLKAIKEQTDLEVNLLQDSLNN 37 (124)
Q Consensus 11 ~l~le~L~~~~~~l~~ei~~l~~~~~~ 37 (124)
+||+.++.-=.++++++++.|+.++.+
T Consensus 16 ~LsLyDI~vp~~~Y~~ei~~L~~~i~~ 42 (298)
T PF11262_consen 16 QLSLYDIYVPKELYDEEIERLEKEISQ 42 (298)
T ss_pred cCchhhcCCCHHHHHHHHHHHHHHHHH
Confidence 456666666666777777777766666
No 214
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=28.38 E-value=85 Score=19.20 Aligned_cols=31 Identities=10% Similarity=0.189 Sum_probs=25.5
Q ss_pred CCceEEEecCCceeEeEEEcCCCeEEEEccC
Q 033241 60 QGAKMLVPLTASLYVPGTLDDARKVLVDIGT 90 (124)
Q Consensus 60 ~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~ 90 (124)
+..++.|=|-.|+=++|+|.+-|+..|-+..
T Consensus 10 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~ 40 (61)
T cd01716 10 EKIPVTIYLVNGVQLKGQIESFDNFTVLLES 40 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEcceEEEEEE
Confidence 4578899999999999999998876666543
No 215
>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes [].
Probab=28.33 E-value=1.5e+02 Score=18.18 Aligned_cols=33 Identities=6% Similarity=0.202 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 16 QLKAIKEQTDLEVNLLQDSLNNIRTATSRLESA 48 (124)
Q Consensus 16 ~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~ 48 (124)
++..-..+.+..+++++..+..+.......+..
T Consensus 3 ~i~e~l~~ie~~l~~~~~~i~~lE~~~~~~e~~ 35 (71)
T PF10779_consen 3 DIKEKLNRIETKLDNHEERIDKLEKRDAANEKD 35 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344445555666666666666666666666555
No 216
>PF10046 BLOC1_2: Biogenesis of lysosome-related organelles complex-1 subunit 2 ; InterPro: IPR019269 This entry represents a family of proteins that play a role in cellular proliferation, as well as in the biogenesis of specialised organelles of the endosomal-lysosomal system [].
Probab=28.28 E-value=1.8e+02 Score=19.07 Aligned_cols=41 Identities=15% Similarity=0.276 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 14 VEQLKAIKEQTDLEV---NLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 14 le~L~~~~~~l~~ei---~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
+++|.+....++..+ ..+..++..|......++.....|+.
T Consensus 51 ~~~l~~k~~~l~~~l~~Id~Ie~~V~~LE~~v~~LD~ysk~LE~ 94 (99)
T PF10046_consen 51 LEDLNQKYEELQPYLQQIDQIEEQVTELEQTVYELDEYSKELES 94 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455444444333 33444777777777777766666554
No 217
>PRK00294 hscB co-chaperone HscB; Provisional
Probab=27.90 E-value=1.7e+02 Score=21.41 Aligned_cols=10 Identities=20% Similarity=0.199 Sum_probs=4.5
Q ss_pred HHHHHHHHhh
Q 033241 45 LESASTALHD 54 (124)
Q Consensus 45 ~~~~~~~l~~ 54 (124)
+..|.+.+..
T Consensus 144 ~~~A~~~v~k 153 (173)
T PRK00294 144 REEAERLMRR 153 (173)
T ss_pred HHHHHHHHHH
Confidence 4444444443
No 218
>PF12443 AKNA: AT-hook-containing transcription factor; InterPro: IPR022150 This domain family is found in eukaryotes, and is approximately 110 amino acids in length. This family contains a transcription factor which regulates the expression of the costimulatory molecules on lymphocytes.
Probab=27.76 E-value=81 Score=21.49 Aligned_cols=29 Identities=3% Similarity=0.137 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 21 KEQTDLEVNLLQDSLNNIRTATSRLESAS 49 (124)
Q Consensus 21 ~~~l~~ei~~l~~~~~~L~~~~~~~~~~~ 49 (124)
..+++++++.|-.+..+|++.+.++...+
T Consensus 47 ~~ege~~~qkL~eqteeLK~kvqe~sk~i 75 (106)
T PF12443_consen 47 IREGEQMIQKLGEQTEELKDKVQEFSKRI 75 (106)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 45788889999999999999988887653
No 219
>TIGR01706 NAPA periplasmic nitrate reductase, large subunit. The enzymes from Alicagenes eutrophus and Paracoccus pantotrophus have been characterized. In E. coli (as well as other organisms) this gene is part of a large nitrate reduction operon (napFDAGHBC).
Probab=27.58 E-value=52 Score=29.58 Aligned_cols=26 Identities=19% Similarity=0.190 Sum_probs=22.8
Q ss_pred cCceeeecCHHHHHHHHHHHHHHHHH
Q 033241 89 GTGYFVEKTMDEGKDYCERKINLLKS 114 (124)
Q Consensus 89 G~g~~vE~~~~eA~~~l~~r~~~l~~ 114 (124)
|.|=|.+.|-|||++.+.+|++.+.+
T Consensus 112 g~g~~~~iSWDeAl~~iA~kl~~i~~ 137 (830)
T TIGR01706 112 KDGEFTPVSWDQAFDEMEEQFKRALK 137 (830)
T ss_pred cCCCeeEcCHHHHHHHHHHHHHHHHH
Confidence 45889999999999999999987754
No 220
>KOG2706 consensus Predicted membrane protein [Function unknown]
Probab=27.49 E-value=25 Score=28.82 Aligned_cols=32 Identities=22% Similarity=0.411 Sum_probs=25.9
Q ss_pred EEEecCCceeEeEEEcCCCeEEEEccCceeee
Q 033241 64 MLVPLTASLYVPGTLDDARKVLVDIGTGYFVE 95 (124)
Q Consensus 64 ~lVplg~~~yv~a~I~~~~~VlV~lG~g~~vE 95 (124)
.+..+|+|+||+---....+++++-|.|+.+-
T Consensus 12 LL~c~GAg~YVkKIadegqr~LaS~~LG~~m~ 43 (476)
T KOG2706|consen 12 LLFCFGAGCYVKKIADEGQRILASGALGFAMS 43 (476)
T ss_pred HHhhcccchhhhhhccCCceEEeeccccceeh
Confidence 46789999999866555778999999998764
No 221
>KOG3905 consensus Dynein light intermediate chain [Cell motility]
Probab=27.47 E-value=1.6e+02 Score=24.58 Aligned_cols=49 Identities=18% Similarity=0.262 Sum_probs=35.6
Q ss_pred CceEEEecCCceeEeEEEcCCCeEEEEccCceeeecCHHHHHHHHHHHHHHHHHHHHHHh
Q 033241 61 GAKMLVPLTASLYVPGTLDDARKVLVDIGTGYFVEKTMDEGKDYCERKINLLKSNFDQLI 120 (124)
Q Consensus 61 ~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~vE~~~~eA~~~l~~r~~~l~~~i~~l~ 120 (124)
+-..++|||.+. ..-++|-.++|=+|--+|...|.+--+.-.++.+.++
T Consensus 205 de~~llPL~~dt-----------Lt~NlGi~vlVV~TK~D~~s~leke~eyrDehfdfiq 253 (473)
T KOG3905|consen 205 DEHVLLPLGQDT-----------LTHNLGIPVLVVCTKCDAVSVLEKEHEYRDEHFDFIQ 253 (473)
T ss_pred ccccccccCCcc-----------hhhcCCCcEEEEEeccchhhHhhhcchhhHHHHHHHH
Confidence 355788888754 3457888899999999998888777766666665554
No 222
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=27.46 E-value=1.4e+02 Score=23.51 Aligned_cols=49 Identities=14% Similarity=0.280 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCce
Q 033241 29 NLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGY 92 (124)
Q Consensus 29 ~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~ 92 (124)
+.+-+++..++.-..+....++....+.. -....|.+.++|.++++.||
T Consensus 71 e~l~~~~~dlr~f~~ev~~~l~~~~vw~A---------------IA~edI~~Gd~V~L~M~dG~ 119 (260)
T COG1497 71 EWLLEQLSDLRRFSEEVELVLDYVMVWTA---------------IAKEDIKEGDTVYLRMKDGY 119 (260)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhHHHHHH---------------hhHhhhccCCEEEEEecCcE
Confidence 45666666666666665444444444331 12245556666666666665
No 223
>PF11945 WASH_WAHD: WAHD domain of WASH complex; InterPro: IPR021854 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53. This entry represents the WASH subunit of the WASH complex. WASH genes duplicated to multiple chromosomal ends during primate evolution, with highest copy number reached in humans, whose WASH repertoires probably vary extensively among individuals []. It is therefore difficult to determine which gene is functional or not. The telomeric region of chromosome 9p is paralogous to the pericentromeric regions of chromosome 9 as well as to 2q. Paralogous regions contain 7 transcriptional units. Duplicated WASH genes are also present in the Xq/Yq pseudoautosomal region, as well as on chromosome 1 and 15. The chromosome 16 copy seems to be a pseudogene.
Probab=27.34 E-value=2.7e+02 Score=22.22 Aligned_cols=34 Identities=12% Similarity=0.129 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 22 EQTDLEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 22 ~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
.++.+.++...++++.++.++...+.-++.|.+.
T Consensus 39 ~rI~~Rv~~~~~~l~~i~~Ri~~~qaKi~~l~gs 72 (297)
T PF11945_consen 39 SRISARVERNRERLQAIQQRIEVAQAKIEKLQGS 72 (297)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 3445555555555555555555555555555443
No 224
>cd02759 MopB_Acetylene-hydratase The MopB_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=27.33 E-value=91 Score=25.85 Aligned_cols=27 Identities=22% Similarity=0.300 Sum_probs=23.9
Q ss_pred cCceeeecCHHHHHHHHHHHHHHHHHH
Q 033241 89 GTGYFVEKTMDEGKDYCERKINLLKSN 115 (124)
Q Consensus 89 G~g~~vE~~~~eA~~~l~~r~~~l~~~ 115 (124)
|.|=|.+.|-+||++++.++++.+.+.
T Consensus 66 G~g~~~~isWdeAl~~ia~~l~~~~~~ 92 (477)
T cd02759 66 GENKWERISWDEALDEIAEKLAEIKAE 92 (477)
T ss_pred CCCcEEEecHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999999887653
No 225
>PRK02509 hypothetical protein; Provisional
Probab=27.18 E-value=1.1e+02 Score=28.62 Aligned_cols=45 Identities=22% Similarity=0.437 Sum_probs=35.2
Q ss_pred CceEEEecCCce------eEeE---EEcCCCeEEEEccCceeeecCHHHHHHHH
Q 033241 61 GAKMLVPLTASL------YVPG---TLDDARKVLVDIGTGYFVEKTMDEGKDYC 105 (124)
Q Consensus 61 ~~e~lVplg~~~------yv~a---~I~~~~~VlV~lG~g~~vE~~~~eA~~~l 105 (124)
|.=.-+|+|.|+ |++| .++.-.+|+|.-|..+-.+-|++||.+-+
T Consensus 902 GNLLviPI~~sLLYVEPvYlqA~~~~lP~L~RVIVs~g~~vvm~~TL~eAL~~l 955 (973)
T PRK02509 902 GNLLVIPIEQSLLYVEPLYLEAEQNSLPTLARVIVAYENRIVMAPTLEEALQAI 955 (973)
T ss_pred cceEEEEeCCeeEEEeeEEEecCCCCCCeeEEEEEEECCEEEEccCHHHHHHHH
Confidence 445567999886 5665 23445699999999999999999998765
No 226
>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family. Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.
Probab=27.07 E-value=3.2e+02 Score=21.67 Aligned_cols=8 Identities=13% Similarity=0.243 Sum_probs=3.4
Q ss_pred eeeecCHH
Q 033241 92 YFVEKTMD 99 (124)
Q Consensus 92 ~~vE~~~~ 99 (124)
++|+..++
T Consensus 310 ~~v~~~v~ 317 (423)
T TIGR01843 310 LEIEAKLS 317 (423)
T ss_pred EEEEEEEC
Confidence 44444433
No 227
>COG1766 fliF Flagellar basal body M-ring protein [Cell motility and secretion]
Probab=27.04 E-value=2.1e+02 Score=24.90 Aligned_cols=68 Identities=16% Similarity=0.199 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecC-CceeEeEEEcCCCeEEEEccCceeeecCHHHHHHHH
Q 033241 34 SLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLT-ASLYVPGTLDDARKVLVDIGTGYFVEKTMDEGKDYC 105 (124)
Q Consensus 34 ~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg-~~~yv~a~I~~~~~VlV~lG~g~~vE~~~~eA~~~l 105 (124)
++.--.....++..++.+|...+. -.+++-+- .++|+...-+.+-.|+|.+..|.-+..+--.|+..|
T Consensus 129 ~v~~~RAlegELartI~~l~~V~~----ArVhl~lPk~s~Fv~~q~~psASV~l~l~pG~~l~~~qV~aI~~L 197 (545)
T COG1766 129 QVNYQRALEGELARTIVAIDGVKA----ARVHLVLPKDSLFVRDQQPPSASVVLKLKPGRNLSREQVRAIVHL 197 (545)
T ss_pred HHHHHHHHHHHHHHHHHHhhchhh----eeEEEecCCcchhhcccCCCceEEEEEccCCCCCCHHHHHHHHHH
Confidence 344444445567777777777642 34444444 478999988889999999999996665555555443
No 228
>PHA03052 Hypothetical protein; Provisional
Probab=26.97 E-value=1.7e+02 Score=18.42 Aligned_cols=37 Identities=14% Similarity=0.227 Sum_probs=29.5
Q ss_pred ceEEEecCCceeEeEEEc----CCCeEEEEccCceeeecCH
Q 033241 62 AKMLVPLTASLYVPGTLD----DARKVLVDIGTGYFVEKTM 98 (124)
Q Consensus 62 ~e~lVplg~~~yv~a~I~----~~~~VlV~lG~g~~vE~~~ 98 (124)
..+.+.||+.+-+++++. ..+.++.|+-.|-|+|.+-
T Consensus 5 ~~i~~slGs~ltI~Ckv~lg~g~~~a~V~W~~N~~~~e~~d 45 (69)
T PHA03052 5 EGIVTSLGSNLTITCKVSLRPPTTDADVFWISNGMYYEEDD 45 (69)
T ss_pred ccEEEEccCCceEeEEEEecCCCcceEEEEEeCCcEEeccc
Confidence 457789999999888875 3477899999999997653
No 229
>KOG2695 consensus WD40 repeat protein [General function prediction only]
Probab=26.96 E-value=43 Score=27.78 Aligned_cols=28 Identities=14% Similarity=0.489 Sum_probs=24.4
Q ss_pred cCCceeEeEEEcCCCeEEEEccCceeee
Q 033241 68 LTASLYVPGTLDDARKVLVDIGTGYFVE 95 (124)
Q Consensus 68 lg~~~yv~a~I~~~~~VlV~lG~g~~vE 95 (124)
+....|.++-|.+.+.+++.+|.+||.-
T Consensus 344 vN~~a~l~~~v~~eeg~I~s~GdDcytR 371 (425)
T KOG2695|consen 344 VNLSAYLPAHVKEEEGSIFSVGDDCYTR 371 (425)
T ss_pred cccccccccccccccceEEEccCeeEEE
Confidence 3456799999999999999999999964
No 230
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=26.84 E-value=93 Score=19.04 Aligned_cols=30 Identities=13% Similarity=0.175 Sum_probs=25.2
Q ss_pred CCceEEEecCCceeEeEEEcCCCeEEEEcc
Q 033241 60 QGAKMLVPLTASLYVPGTLDDARKVLVDIG 89 (124)
Q Consensus 60 ~~~e~lVplg~~~yv~a~I~~~~~VlV~lG 89 (124)
+..++-|=|-.|+=++|.|..-|+..|-+.
T Consensus 14 ~~~~Vti~L~nG~~l~G~I~~fD~ftVll~ 43 (61)
T TIGR02383 14 ERIPVTVFLVNGVQLKGVIESFDNFTVLLE 43 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEeeeEEEEE
Confidence 457888999999999999999887666654
No 231
>PF12128 DUF3584: Protein of unknown function (DUF3584); InterPro: IPR021979 This family consist of uncharacterised bacterial proteins.
Probab=26.80 E-value=1.1e+02 Score=28.85 Aligned_cols=46 Identities=15% Similarity=0.201 Sum_probs=31.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 7 GGMEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTAL 52 (124)
Q Consensus 7 i~~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l 52 (124)
+|++.++.|+..+-.++++++++.+...+........++.+.+...
T Consensus 588 LdL~~I~~pd~~~~ee~L~~~l~~~~~~l~~~~~~~~~~e~~l~~~ 633 (1201)
T PF12128_consen 588 LDLSAIDVPDYAASEEELRERLEQAEDQLQSAEERQEELEKQLKQI 633 (1201)
T ss_pred eehhhcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6778888887777777777777777777777766666655554333
No 232
>cd02750 MopB_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. Members of the MopB_Nitrate-R-NarG-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=26.36 E-value=94 Score=25.70 Aligned_cols=26 Identities=19% Similarity=0.171 Sum_probs=22.8
Q ss_pred cCceeeecCHHHHHHHHHHHHHHHHH
Q 033241 89 GTGYFVEKTMDEGKDYCERKINLLKS 114 (124)
Q Consensus 89 G~g~~vE~~~~eA~~~l~~r~~~l~~ 114 (124)
|.|=|.+.|-|||.+.+.++++.+.+
T Consensus 78 G~g~~~~isWdeAl~~ia~~l~~i~~ 103 (461)
T cd02750 78 GEGKWKRISWDEALELIADAIIDTIK 103 (461)
T ss_pred CCCceEEecHHHHHHHHHHHHHHHHH
Confidence 46889999999999999999887654
No 233
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=26.13 E-value=2.1e+02 Score=23.56 Aligned_cols=40 Identities=20% Similarity=0.334 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLS 56 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~ 56 (124)
..+|...++.|+++...|+.++.-|+....+ +++-.+.+.
T Consensus 248 ~~kL~~~~etLEqq~~~L~~niDIL~~k~~e---al~~~~n~~ 287 (365)
T KOG2391|consen 248 KQKLVAMKETLEQQLQSLQKNIDILKSKVRE---ALEKAENLE 287 (365)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH---HHhhhccCc
No 234
>PRK09129 NADH dehydrogenase subunit G; Validated
Probab=26.12 E-value=77 Score=28.18 Aligned_cols=38 Identities=11% Similarity=0.222 Sum_probs=28.3
Q ss_pred EEcCCCeEEEEc--cCceeeecCHHHHHHHHHHHHHHHHH
Q 033241 77 TLDDARKVLVDI--GTGYFVEKTMDEGKDYCERKINLLKS 114 (124)
Q Consensus 77 ~I~~~~~VlV~l--G~g~~vE~~~~eA~~~l~~r~~~l~~ 114 (124)
.+.+++++.-++ +.|=|.+-|.+||++++.++++.+.+
T Consensus 266 ~l~~pdRl~~Pl~R~~g~~~~iSWdeAl~~ia~~L~~i~~ 305 (776)
T PRK09129 266 GLNSEDRLTKPMIKQGGQWKEVDWETALEYVAEGLKGIIE 305 (776)
T ss_pred ccccccccCCCeEecCCceEEcCHHHHHHHHHHHHHHHHh
Confidence 344555554444 35778999999999999999987764
No 235
>KOG3366 consensus Mitochondrial F1F0-ATP synthase, subunit d/ATP7 [Energy production and conversion]
Probab=26.00 E-value=1.1e+02 Score=22.55 Aligned_cols=28 Identities=18% Similarity=0.395 Sum_probs=24.0
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 96 KTMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 96 ~~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
..+.+......+|+..+++.++++++.|
T Consensus 101 ~~~ke~~~~s~~~iq~l~k~le~v~~~~ 128 (172)
T KOG3366|consen 101 KEIKEYESLSKKRIQELEKELEKVKSAR 128 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3567788889999999999999998876
No 236
>PF05103 DivIVA: DivIVA protein; InterPro: IPR007793 The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate minicells []. Inactivation of divIVA produces a minicell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype []. These proteins appear to contain coiled-coils.; PDB: 2WUK_C 2WUJ_A.
Probab=25.93 E-value=39 Score=22.69 Aligned_cols=34 Identities=12% Similarity=0.231 Sum_probs=18.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 13 SVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLE 46 (124)
Q Consensus 13 ~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~ 46 (124)
++.+.-.+...+..+++.|..++..|+..+.++.
T Consensus 19 d~~eVD~fl~~l~~~~~~l~~e~~~L~~~~~~l~ 52 (131)
T PF05103_consen 19 DPDEVDDFLDELAEELERLQRENAELKEEIEELQ 52 (131)
T ss_dssp EHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455555566666666666555555555444443
No 237
>cd02751 MopB_DMSOR-like The MopB_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. Members of the MopB_DMSOR-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=25.93 E-value=95 Score=26.71 Aligned_cols=27 Identities=26% Similarity=0.494 Sum_probs=23.9
Q ss_pred cCceeeecCHHHHHHHHHHHHHHHHHH
Q 033241 89 GTGYFVEKTMDEGKDYCERKINLLKSN 115 (124)
Q Consensus 89 G~g~~vE~~~~eA~~~l~~r~~~l~~~ 115 (124)
|.|=|.+.|-|||++.+.+|++.+.+.
T Consensus 69 g~g~~~~iSWDEAl~~iA~kl~~i~~~ 95 (609)
T cd02751 69 GEGEFVRISWDEALDLVASELKRIREK 95 (609)
T ss_pred CCCCEEEecHHHHHHHHHHHHHHHHHH
Confidence 378999999999999999999887653
No 238
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=25.85 E-value=2.3e+02 Score=19.60 Aligned_cols=44 Identities=11% Similarity=0.063 Sum_probs=23.3
Q ss_pred CCCHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 11 KMSVEQLKAIKEQT-------DLEVNLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 11 ~l~le~L~~~~~~l-------~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
-+|++++..+.... ..-.+.+.+++..+...+.++....+.|..
T Consensus 57 G~sl~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~ 107 (135)
T PRK10227 57 GFNLEESGELVNLFNDPQRHSADVKRRTLEKVAEIERHIEELQSMRDQLLA 107 (135)
T ss_pred CCCHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36677766654321 122344455555666666666665555554
No 239
>PRK10869 recombination and repair protein; Provisional
Probab=25.85 E-value=1.9e+02 Score=24.99 Aligned_cols=21 Identities=33% Similarity=0.230 Sum_probs=14.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHH
Q 033241 13 SVEQLKAIKEQTDLEVNLLQD 33 (124)
Q Consensus 13 ~le~L~~~~~~l~~ei~~l~~ 33 (124)
|++++..++++++++++.+.+
T Consensus 318 ~~~~~~~~~~~l~~eL~~L~~ 338 (553)
T PRK10869 318 SPEELPQHHQQLLEEQQQLDD 338 (553)
T ss_pred CHHHHHHHHHHHHHHHHHhhC
Confidence 677777777777777655444
No 240
>TIGR00509 bisC_fam molybdopterin guanine dinucleotide-containing S/N-oxide reductases. This enzyme family shares sequence similarity and a requirement for a molydenum cofactor as the only prosthetic group. The form of the cofactor is a single molybdenum atom coordinated by two molybdopterin guanine dinucleotide molecules. Members of the family include biotin sulfoxide reductase, dimethylsulfoxide reductase, and trimethylamine-N-oxide reductase, although a single member may show all those activities and related activities; it may not be possible to resolve the primary function for members of this family by sequence comparison alone. A number of similar molybdoproteins in which the N-terminal region contains a CXXXC motif and may bind an iron-sulfur cluster are excluded from this set, including formate dehydrogenases and nitrate reductases. Also excluded is the A chain of a heteromeric, anaerobic DMSO reductase, which also contains the CXXXC motif.
Probab=25.84 E-value=90 Score=27.71 Aligned_cols=27 Identities=22% Similarity=0.396 Sum_probs=24.0
Q ss_pred cCceeeecCHHHHHHHHHHHHHHHHHH
Q 033241 89 GTGYFVEKTMDEGKDYCERKINLLKSN 115 (124)
Q Consensus 89 G~g~~vE~~~~eA~~~l~~r~~~l~~~ 115 (124)
|.|=|++.|-|||.+.+..|+..+.+.
T Consensus 67 G~g~f~~iSWDEAl~~IA~kl~~i~~~ 93 (770)
T TIGR00509 67 GREEFVRVSWDEALDLVAEELKRVRKT 93 (770)
T ss_pred CCCCeEEecHHHHHHHHHHHHHHHHHh
Confidence 357899999999999999999988764
No 241
>PRK14064 exodeoxyribonuclease VII small subunit; Provisional
Probab=25.75 E-value=1.8e+02 Score=18.32 Aligned_cols=34 Identities=18% Similarity=0.117 Sum_probs=19.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 10 EKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATS 43 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~ 43 (124)
..+||++...++++--.-+...++.+..-...+.
T Consensus 25 ~~l~Leesl~~ye~G~~L~k~c~~~L~~ae~kv~ 58 (75)
T PRK14064 25 GSASLEDSLDMYQKGIELTKLCQDKLQSAEKRMA 58 (75)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566666666666666555555554444443333
No 242
>smart00502 BBC B-Box C-terminal domain. Coiled coil region C-terminal to (some) B-Box domains
Probab=25.50 E-value=1.9e+02 Score=18.54 Aligned_cols=30 Identities=13% Similarity=0.265 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 26 LEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 26 ~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
.....|..+...+......+..+++.++.+
T Consensus 72 ~~~~~l~~q~~~l~~~l~~l~~~~~~~e~~ 101 (127)
T smart00502 72 NKLKVLEQQLESLTQKQEKLSHAINFTEEA 101 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334566666677777777777777666664
No 243
>cd02754 MopB_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. Members of the MopB_Nitrate-R-NapA CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=25.46 E-value=84 Score=26.55 Aligned_cols=38 Identities=21% Similarity=0.382 Sum_probs=28.6
Q ss_pred EEcCCCeE---EEEccCceeeecCHHHHHHHHHHHHHHHHH
Q 033241 77 TLDDARKV---LVDIGTGYFVEKTMDEGKDYCERKINLLKS 114 (124)
Q Consensus 77 ~I~~~~~V---lV~lG~g~~vE~~~~eA~~~l~~r~~~l~~ 114 (124)
.+.+++++ ++-.|.|=|.+.|-+||++.+.+|++.+.+
T Consensus 48 ~~y~p~Rl~~Pl~R~~~~~~~~iSWdeAl~~ia~kl~~i~~ 88 (565)
T cd02754 48 TLNGPERLTRPLLRRNGGELVPVSWDEALDLIAERFKAIQA 88 (565)
T ss_pred ccCCcccccCCeEeCCCCCEEEccHHHHHHHHHHHHHHHHH
Confidence 34455554 344465589999999999999999987765
No 244
>PRK10093 primosomal replication protein N''; Provisional
Probab=25.34 E-value=2.6e+02 Score=20.65 Aligned_cols=31 Identities=19% Similarity=0.270 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 21 KEQTDLEVNLLQDSLNNIRTATSRLESASTA 51 (124)
Q Consensus 21 ~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~ 51 (124)
.++++.++..+..++...+.++.+++..++.
T Consensus 138 qq~lq~el~alegRL~RCrqAl~~IE~~Ier 168 (171)
T PRK10093 138 QQTLHREVEAYEGRLARCRHALEKIENVLAR 168 (171)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4455666666666666666666666655543
No 245
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=25.32 E-value=80 Score=27.12 Aligned_cols=28 Identities=11% Similarity=0.337 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 27 EVNLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 27 ei~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
+|+.|++++++|+..+.++.+-++.++.
T Consensus 32 kie~L~kql~~Lk~q~~~l~~~v~k~e~ 59 (489)
T PF11853_consen 32 KIEALKKQLEELKAQQDDLNDRVDKVEK 59 (489)
T ss_pred HHHHHHHHHHHHHHhhcccccccchhhH
Confidence 5556666666666655555444444433
No 246
>PRK13532 nitrate reductase catalytic subunit; Provisional
Probab=25.25 E-value=83 Score=28.27 Aligned_cols=25 Identities=20% Similarity=0.209 Sum_probs=22.3
Q ss_pred CceeeecCHHHHHHHHHHHHHHHHH
Q 033241 90 TGYFVEKTMDEGKDYCERKINLLKS 114 (124)
Q Consensus 90 ~g~~vE~~~~eA~~~l~~r~~~l~~ 114 (124)
.|=|.+.|-+||++++.++++.+.+
T Consensus 113 ~g~~~~isWdeAl~~iA~~l~~i~~ 137 (830)
T PRK13532 113 EGEFTPVSWDQAFDVMAEKFKKALK 137 (830)
T ss_pred CCCeEEecHHHHHHHHHHHHHHHHH
Confidence 6889999999999999999987754
No 247
>PRK09973 putative outer membrane lipoprotein; Provisional
Probab=25.19 E-value=2e+02 Score=18.75 Aligned_cols=27 Identities=19% Similarity=0.352 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRT 40 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~ 40 (124)
+++|..--+.+...++.+++.++.++.
T Consensus 26 vdqLss~V~~L~~kvdql~~dv~~a~a 52 (85)
T PRK09973 26 VNQLASNVQTLNAKIARLEQDMKALRP 52 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444444444444444444444443
No 248
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=25.18 E-value=1.5e+02 Score=17.07 Aligned_cols=15 Identities=27% Similarity=0.461 Sum_probs=5.6
Q ss_pred HHHHHHHHHHHHHHH
Q 033241 25 DLEVNLLQDSLNNIR 39 (124)
Q Consensus 25 ~~ei~~l~~~~~~L~ 39 (124)
+.++..|......|.
T Consensus 31 e~~~~~L~~en~~L~ 45 (54)
T PF07716_consen 31 EQEVQELEEENEQLR 45 (54)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 333333333333333
No 249
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=25.09 E-value=3.4e+02 Score=21.54 Aligned_cols=16 Identities=25% Similarity=0.517 Sum_probs=8.0
Q ss_pred CCCCCHHHHHHHHHHH
Q 033241 9 MEKMSVEQLKAIKEQT 24 (124)
Q Consensus 9 ~~~l~le~L~~~~~~l 24 (124)
++..+.++|..+++++
T Consensus 203 ~~~~D~~eL~~lr~eL 218 (325)
T PF08317_consen 203 IESCDQEELEALRQEL 218 (325)
T ss_pred hhhcCHHHHHHHHHHH
Confidence 3445555555554433
No 250
>TIGR02166 dmsA_ynfE anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family. Members of this family include known and probable dimethyl sulfoxide reductase (DMSO reductase) A chains. In E. coli, dmsA encodes the canonical anaerobic DMSO reductase A chain. The paralog ynfE, as part of ynfFGH expressed from a multicopy plasmid, could complement a dmsABC deletion, suggesting a similar function and some overlap in specificity, although YnfE could not substitute for DmsA in a mixed complex.
Probab=25.07 E-value=97 Score=27.51 Aligned_cols=27 Identities=22% Similarity=0.361 Sum_probs=23.8
Q ss_pred cCceeeecCHHHHHHHHHHHHHHHHHH
Q 033241 89 GTGYFVEKTMDEGKDYCERKINLLKSN 115 (124)
Q Consensus 89 G~g~~vE~~~~eA~~~l~~r~~~l~~~ 115 (124)
|.|=|++.|-|||++.+.+|++.+.+.
T Consensus 116 G~g~~~~iSWdeAl~~ia~kl~~i~~~ 142 (797)
T TIGR02166 116 GEGKFERISWDEATDTIADNLKRIIEK 142 (797)
T ss_pred CCCCeEEecHHHHHHHHHHHHHHHHHH
Confidence 468899999999999999999887653
No 251
>PRK05771 V-type ATP synthase subunit I; Validated
Probab=24.93 E-value=1.4e+02 Score=26.05 Aligned_cols=24 Identities=21% Similarity=0.282 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 17 LKAIKEQTDLEVNLLQDSLNNIRT 40 (124)
Q Consensus 17 L~~~~~~l~~ei~~l~~~~~~L~~ 40 (124)
+.+..++++.+++.+.+++..+..
T Consensus 220 l~~~l~~l~~~~~~~~~~l~~~~~ 243 (646)
T PRK05771 220 IKEELEEIEKERESLLEELKELAK 243 (646)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333344444444454444444444
No 252
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=24.93 E-value=2.1e+02 Score=18.72 Aligned_cols=31 Identities=19% Similarity=0.317 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 17 LKAIKEQTDLEVNLLQDSLNNIRTATSRLES 47 (124)
Q Consensus 17 L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~ 47 (124)
|....+.++.++..+..++..+.....++..
T Consensus 68 Le~~~e~le~~i~~l~~~~~~l~~~~~elk~ 98 (105)
T cd00632 68 LKERLETIELRIKRLERQEEDLQEKLKELQE 98 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334445555555555555555555444443
No 253
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=24.91 E-value=2.2e+02 Score=19.14 Aligned_cols=25 Identities=12% Similarity=0.252 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 20 IKEQTDLEVNLLQDSLNNIRTATSR 44 (124)
Q Consensus 20 ~~~~l~~ei~~l~~~~~~L~~~~~~ 44 (124)
...++++.+..+.+++..|+..+.+
T Consensus 9 ~l~~le~~l~~l~~~~~~LK~~~~~ 33 (107)
T PF06156_consen 9 RLDQLEQQLGQLLEELEELKKQLQE 33 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444444444444444333
No 254
>PRK07860 NADH dehydrogenase subunit G; Validated
Probab=24.87 E-value=45 Score=29.97 Aligned_cols=36 Identities=8% Similarity=0.175 Sum_probs=27.8
Q ss_pred cCCCeEEEEc---cCceeeecCHHHHHHHHHHHHHHHHH
Q 033241 79 DDARKVLVDI---GTGYFVEKTMDEGKDYCERKINLLKS 114 (124)
Q Consensus 79 ~~~~~VlV~l---G~g~~vE~~~~eA~~~l~~r~~~l~~ 114 (124)
.+.+++.-++ |.|=|.+.|-+||.+++.+|++.+.+
T Consensus 274 ~~~dRL~~PliR~~~g~f~~iSWdEAld~ia~kL~~i~~ 312 (797)
T PRK07860 274 TQPDRITTPLVRDEDGELEPASWSEALAVAARGLAAARG 312 (797)
T ss_pred ccccccCCceEEcCCCceEEcCHHHHHHHHHHHHHhhhc
Confidence 3445554444 78889999999999999999987653
No 255
>PF08549 SWI-SNF_Ssr4: Fungal domain of unknown function (DUF1750); InterPro: IPR013859 This is a fungal protein of unknown function.
Probab=24.75 E-value=3.2e+02 Score=24.55 Aligned_cols=50 Identities=4% Similarity=0.070 Sum_probs=39.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 6 GGGMEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 6 ~i~~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
.-.++.|.++....+.++..+.+...+.+|..++..-++-.+..+....|
T Consensus 351 ~~~~gkLdp~~aeeF~kRV~~~ia~~~AEIekmK~~Hak~m~k~k~~s~l 400 (669)
T PF08549_consen 351 KPYVGKLDPGKAEEFRKRVAKKIADMNAEIEKMKARHAKRMAKFKRNSLL 400 (669)
T ss_pred cccccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHH
Confidence 35578999999999999999999999999999998776654444444433
No 256
>PF11382 DUF3186: Protein of unknown function (DUF3186); InterPro: IPR021522 This bacterial family of proteins has no known function.
Probab=24.67 E-value=2.8e+02 Score=21.97 Aligned_cols=40 Identities=13% Similarity=0.150 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 15 EQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 15 e~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
..|.....++.++.+.++++++.++...+..+..++.+..
T Consensus 35 ~~l~~~~~~lr~e~~~l~~~~~~~~~~~~~~d~f~~~~~~ 74 (308)
T PF11382_consen 35 DSLEDQFDSLREENDELRAELDALQAQLNAADQFIAAVAP 74 (308)
T ss_pred hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555566677777778888888887777777766665554
No 257
>PF05384 DegS: Sensor protein DegS; InterPro: IPR008595 This is a group of Bacillus DegS proteins. The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterise the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon []. The entry also contains one sequence Q8R9D3 from SWISSPROT from Thermoanaerobacter tengcongensis which is described as a sensory transduction histidine kinase.; GO: 0016301 kinase activity, 0007165 signal transduction
Probab=24.62 E-value=2.8e+02 Score=20.11 Aligned_cols=43 Identities=26% Similarity=0.288 Sum_probs=34.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 13 SVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 13 ~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
|-+++-...+....+++.+...+..++..+.++-...+.|+..
T Consensus 14 sK~qIf~I~E~~R~E~~~l~~EL~evk~~v~~~I~evD~Le~~ 56 (159)
T PF05384_consen 14 SKEQIFEIAEQARQEYERLRKELEEVKEEVSEVIEEVDKLEKR 56 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567777888888999999999999988888877777777664
No 258
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=24.50 E-value=91 Score=20.11 Aligned_cols=23 Identities=17% Similarity=0.199 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhh
Q 033241 100 EGKDYCERKINLLKSNFDQLIEV 122 (124)
Q Consensus 100 eA~~~l~~r~~~l~~~i~~l~~~ 122 (124)
+..++++.+...+++.+++++..
T Consensus 73 ~~~~~l~~~~~~l~~~i~~l~~~ 95 (96)
T cd04768 73 ELTAMLLEKKQAIQQKIDRLQQL 95 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 78899999999999999998865
No 259
>PRK06342 transcription elongation factor regulatory protein; Validated
Probab=24.45 E-value=2.7e+02 Score=19.99 Aligned_cols=67 Identities=9% Similarity=0.070 Sum_probs=30.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEe
Q 033241 7 GGMEKMSVEQLKAIKEQTDLEVNLLQ---------DSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVP 75 (124)
Q Consensus 7 i~~~~l~le~L~~~~~~l~~ei~~l~---------~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~ 75 (124)
+.+|.-..+.|....+.|..++..-. .+...+...+..+..-++...-+.+ . ...--|.+|+.+-+.
T Consensus 29 ~~lT~~G~~~L~~El~~L~~~i~~Ar~~GDlsEak~~~~~~e~rI~~L~~~L~~A~Ii~~-~-~~~d~V~~Gs~V~l~ 104 (160)
T PRK06342 29 NLVTEAGLKALEDQLAQARAAYEAAQAIEDVNERRRQMARPLRDLRYLAARRRTAQLMPD-P-ASTDVVAFGSTVTFS 104 (160)
T ss_pred ceECHHHHHHHHHHHHHHHHHHHHHHHCCChhHHHHHHHHHHHHHHHHHHHHccCEEECC-C-CCCCEEEeCcEEEEE
Confidence 34444444445444445544443332 2233344444444444433333332 1 123457777776654
No 260
>PF07445 priB_priC: Primosomal replication protein priB and priC; InterPro: IPR010890 This family contains the bacterial primosomal replication proteins priB and priC (approximately 180 residues long). In Escherichia coli, these function in the assembly of the primosome [].
Probab=24.35 E-value=2.6e+02 Score=20.31 Aligned_cols=25 Identities=16% Similarity=0.228 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 30 LLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 30 ~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
.++..+..+.....+...|++.|+.
T Consensus 142 ~lq~ei~a~e~RL~RCr~Ai~~iE~ 166 (173)
T PF07445_consen 142 QLQQEILALEQRLQRCRQAIEKIEE 166 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444555555555555555443
No 261
>PF10267 Tmemb_cc2: Predicted transmembrane and coiled-coil 2 protein; InterPro: IPR019394 This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.
Probab=24.30 E-value=4e+02 Score=22.24 Aligned_cols=60 Identities=10% Similarity=0.081 Sum_probs=43.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc-CCCCCceEEEecCCc
Q 033241 12 MSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLS-LRPQGAKMLVPLTAS 71 (124)
Q Consensus 12 l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~-~~~~~~e~lVplg~~ 71 (124)
-+-+|+...++.++..-+...+.|.+|+.+...|..-+.-++.-. ......+++-..+.|
T Consensus 41 aDk~Q~~rIkq~FekkNqksa~~i~~lqkkL~~y~~~l~ele~~~~~~~~p~~~~~~~~~~ 101 (395)
T PF10267_consen 41 ADKQQAARIKQVFEKKNQKSAQTIAQLQKKLEQYHKRLKELEQGGSSSRQPKEVLRDMGQG 101 (395)
T ss_pred ccHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCchhhhccccc
Confidence 456788889999999999999999999999999887766666543 111234444444443
No 262
>TIGR03073 release_rtcB release factor H-coupled RctB family protein. Members of this family are related to RctB. RctB a protein of known structure but unknown function that often is encoded near RNA cyclase and therefore is suggested to be a tRNA or mRNA processing enzyme. This family of RctB-like proteins in encoded upstream of, and apparently is translationally coupled to, the putative peptide chain release factor RF-H (TIGR03072), product of the prfH gene. Note that a large deletion at the junction between this gene and the prfH gene in Escherichia coli K-12 marks both as probable pseudogenes.
Probab=24.23 E-value=39 Score=27.65 Aligned_cols=36 Identities=25% Similarity=0.273 Sum_probs=28.1
Q ss_pred EecCCceeEeEEEcCCCeEEEEccCceeeecCHHHHH
Q 033241 66 VPLTASLYVPGTLDDARKVLVDIGTGYFVEKTMDEGK 102 (124)
Q Consensus 66 Vplg~~~yv~a~I~~~~~VlV~lG~g~~vE~~~~eA~ 102 (124)
+|+|+.++..+.|. +.-|=+|||+|..+=.+--.+.
T Consensus 43 ~pIG~v~~~~~~I~-P~~VG~DIgCGm~l~~t~l~~~ 78 (356)
T TIGR03073 43 YPIGAAFFSVGRFY-PALVGNDIGCGMALWQTGLLAR 78 (356)
T ss_pred cceEEEEecCCEEe-ccccccCcCCeEEEEecCCChH
Confidence 89999888777877 5679999999999966543333
No 263
>cd02757 MopB_Arsenate-R This CD includes the respiratory arsenate reductase, As(V), catalytic subunit (ArrA) and other related proteins. These members belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=24.22 E-value=89 Score=26.44 Aligned_cols=38 Identities=26% Similarity=0.343 Sum_probs=29.5
Q ss_pred EEcCCCeEEEEc------c----CceeeecCHHHHHHHHHHHHHHHHH
Q 033241 77 TLDDARKVLVDI------G----TGYFVEKTMDEGKDYCERKINLLKS 114 (124)
Q Consensus 77 ~I~~~~~VlV~l------G----~g~~vE~~~~eA~~~l~~r~~~l~~ 114 (124)
.+.+++++.-++ | .|=|.+.|-+||.+.+.++++.+.+
T Consensus 50 ~~y~pdRi~~Pl~R~~~rg~~~~~g~~~~isWdeAl~~ia~~l~~~~~ 97 (523)
T cd02757 50 QVYDPDRILYPMKRTNPRKGRDVDPKFVPISWDEALDTIADKIRALRK 97 (523)
T ss_pred hhcCccccccCeeecCCCCCCCCCCCeeEecHHHHHHHHHHHHHHHHH
Confidence 344566655544 4 7889999999999999999987765
No 264
>PRK15488 thiosulfate reductase PhsA; Provisional
Probab=24.18 E-value=1e+02 Score=27.20 Aligned_cols=27 Identities=30% Similarity=0.419 Sum_probs=23.6
Q ss_pred cCceeeecCHHHHHHHHHHHHHHHHHH
Q 033241 89 GTGYFVEKTMDEGKDYCERKINLLKSN 115 (124)
Q Consensus 89 G~g~~vE~~~~eA~~~l~~r~~~l~~~ 115 (124)
|.|=|.+.|-+||.+.+.+|+..+.+.
T Consensus 110 g~g~~~~iSWdEAl~~ia~~l~~i~~~ 136 (759)
T PRK15488 110 GEGKWQEISWDEAYQEIAAKLNAIKQQ 136 (759)
T ss_pred CCCCeEEeCHHHHHHHHHHHHHHHHHH
Confidence 368899999999999999999887653
No 265
>PRK14069 exodeoxyribonuclease VII small subunit; Provisional
Probab=24.17 E-value=2.2e+02 Score=18.89 Aligned_cols=34 Identities=12% Similarity=0.061 Sum_probs=18.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 10 EKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATS 43 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~ 43 (124)
..+||++...++++--.-+...+..+......+.
T Consensus 27 gdl~LEesl~lyeeGv~L~k~C~~~L~~AE~kV~ 60 (95)
T PRK14069 27 QDFSLEESLKAYERGMELKKICSGILDDAEGKIE 60 (95)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566666666666665555555554444443333
No 266
>cd00126 PAH Pancreatic Hormone domain, a regulator of pancreatic and gastrointestinal functions; neuropeptide Y (NPY)b, peptide YY (PYY), and pancreatic polypetide (PP) are closely related; propeptide is enzymatically cleaved to yield the mature active peptide with amidated C-terminal ends; receptor binding and activation functions may reside in the N- and C-termini respectively; occurs in neurons, intestinal endocrine cells, and pancreas; exist as monomers and dimers
Probab=24.06 E-value=1.4e+02 Score=16.37 Aligned_cols=22 Identities=23% Similarity=0.238 Sum_probs=17.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHH
Q 033241 11 KMSVEQLKAIKEQTDLEVNLLQ 32 (124)
Q Consensus 11 ~l~le~L~~~~~~l~~ei~~l~ 32 (124)
.-|.|+|.....++.+-++.+.
T Consensus 11 ~a~~eel~~Y~~~L~~Yinlit 32 (36)
T cd00126 11 DASPEELRQYLAALREYINLIT 32 (36)
T ss_pred CCCHHHHHHHHHHHHHHHHHHc
Confidence 3568999999999888776653
No 267
>PRK02793 phi X174 lysis protein; Provisional
Probab=24.01 E-value=1.9e+02 Score=17.97 Aligned_cols=26 Identities=8% Similarity=0.183 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 17 LKAIKEQTDLEVNLLQDSLNNIRTAT 42 (124)
Q Consensus 17 L~~~~~~l~~ei~~l~~~~~~L~~~~ 42 (124)
+.+....|+..+......+..|+..+
T Consensus 6 ~e~Ri~~LE~~lafQe~tIe~Ln~~v 31 (72)
T PRK02793 6 LEARLAELESRLAFQEITIEELNVTV 31 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33334444444444444444444433
No 268
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=23.98 E-value=3.2e+02 Score=21.89 Aligned_cols=9 Identities=22% Similarity=0.246 Sum_probs=3.7
Q ss_pred CHHHHHHHH
Q 033241 13 SVEQLKAIK 21 (124)
Q Consensus 13 ~le~L~~~~ 21 (124)
++++|..++
T Consensus 202 d~~eL~~lk 210 (312)
T smart00787 202 DPTELDRAK 210 (312)
T ss_pred CHHHHHHHH
Confidence 344444443
No 269
>PF10458 Val_tRNA-synt_C: Valyl tRNA synthetase tRNA binding arm; InterPro: IPR019499 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the C-terminal domain of Valyl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IVS_B 1GAX_B.
Probab=23.93 E-value=1.7e+02 Score=17.53 Aligned_cols=18 Identities=17% Similarity=0.226 Sum_probs=6.7
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 033241 100 EGKDYCERKINLLKSNFD 117 (124)
Q Consensus 100 eA~~~l~~r~~~l~~~i~ 117 (124)
+-++--..++..+...+.
T Consensus 39 eVve~er~kl~~~~~~~~ 56 (66)
T PF10458_consen 39 EVVEKEREKLEELEEELE 56 (66)
T ss_dssp CHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 333333333333333333
No 270
>PF13600 DUF4140: N-terminal domain of unknown function (DUF4140)
Probab=23.87 E-value=2.1e+02 Score=18.43 Aligned_cols=25 Identities=24% Similarity=0.421 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 22 EQTDLEVNLLQDSLNNIRTATSRLE 46 (124)
Q Consensus 22 ~~l~~ei~~l~~~~~~L~~~~~~~~ 46 (124)
.+++++++.++.++..++..+.-+.
T Consensus 73 ~~l~~~l~~l~~~~~~~~~~~~~~~ 97 (104)
T PF13600_consen 73 KELEEELEALEDELAALQDEIQALE 97 (104)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444444444433
No 271
>PF14662 CCDC155: Coiled-coil region of CCDC155
Probab=23.74 E-value=3e+02 Score=20.76 Aligned_cols=36 Identities=22% Similarity=0.332 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 033241 21 KEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLS 56 (124)
Q Consensus 21 ~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~ 56 (124)
-.++.+++..|..++..++.+...++...+-++.|+
T Consensus 38 na~L~~e~~~L~~q~~s~Qqal~~aK~l~eEledLk 73 (193)
T PF14662_consen 38 NAQLAEEITDLRKQLKSLQQALQKAKALEEELEDLK 73 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455555666666666655555544444444443
No 272
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=23.73 E-value=3.5e+02 Score=20.92 Aligned_cols=29 Identities=10% Similarity=0.102 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 23 QTDLEVNLLQDSLNNIRTATSRLESASTA 51 (124)
Q Consensus 23 ~l~~ei~~l~~~~~~L~~~~~~~~~~~~~ 51 (124)
++...++.+++.+..|+..+++..--++.
T Consensus 58 ~l~~ql~~lq~ev~~LrG~~E~~~~~l~~ 86 (263)
T PRK10803 58 QLQQQLSDNQSDIDSLRGQIQENQYQLNQ 86 (263)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence 44455555555555555555554444433
No 273
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.67 E-value=1.7e+02 Score=19.40 Aligned_cols=34 Identities=9% Similarity=0.282 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033241 20 IKEQTDLEVNLLQDSLNNIRTATSRLESASTALH 53 (124)
Q Consensus 20 ~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~ 53 (124)
+..-+++..+.+.+++..++...+.+...++.+.
T Consensus 80 ~~~~l~~~~~~l~~~i~~l~~~~~~l~~~~~~~~ 113 (116)
T cd04769 80 LQQALEDKKQEIRAQITELQQLLARLDAFEASLK 113 (116)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3445555556666666666666666665555443
No 274
>smart00309 PAH Pancreatic hormones / neuropeptide F / peptide YY family. Pancreatic hormone is a regulator of pancreatic and gastrointestinal functions.
Probab=23.67 E-value=1.4e+02 Score=16.35 Aligned_cols=23 Identities=22% Similarity=0.255 Sum_probs=17.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHH
Q 033241 10 EKMSVEQLKAIKEQTDLEVNLLQ 32 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei~~l~ 32 (124)
..-|+|||.+...++.+-++.+.
T Consensus 10 ~~a~~e~l~~Y~~~L~~Yinlit 32 (36)
T smart00309 10 DDASPEDLRQYLAALREYINLIT 32 (36)
T ss_pred CCCCHHHHHHHHHHHHHHHHHhc
Confidence 35688999999999888776553
No 275
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=23.65 E-value=3.8e+02 Score=21.35 Aligned_cols=57 Identities=14% Similarity=0.141 Sum_probs=31.8
Q ss_pred ceEEEecCCceeEeEEEcCC-CeEEEEccCc------eeeecCHHHHHHHHHHHHHHHHHHHHH
Q 033241 62 AKMLVPLTASLYVPGTLDDA-RKVLVDIGTG------YFVEKTMDEGKDYCERKINLLKSNFDQ 118 (124)
Q Consensus 62 ~e~lVplg~~~yv~a~I~~~-~~VlV~lG~g------~~vE~~~~eA~~~l~~r~~~l~~~i~~ 118 (124)
.-.+||+|+-.+|.-...+. ..++=--|.| +|-...++.|...+=.=+..+-..+..
T Consensus 195 ~y~l~P~Gs~S~I~~~~~~~~~~~~~ly~~~~~~~~~~f~~~~Fd~am~~~L~~~~q~~~~~~~ 258 (314)
T PF04111_consen 195 RYRLVPMGSFSKIEKLEGDKDKTTYPLYSSGSFSLGRLFSSRKFDKAMVAFLDCLQQLAEFVEK 258 (314)
T ss_dssp SEEEE--GGG-EEEECS---TCEEEESS--SS----GGG--SHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cceeEecCCCCEEEEeccCCCCeEEecccCCCchhhhhhhhcchHHHHHHHHHHHHHHHHHHHh
Confidence 47899999988887765543 3444444444 467899999988776666666555543
No 276
>PF08581 Tup_N: Tup N-terminal; InterPro: IPR013890 The N-terminal region of the Tup protein has been shown to interact with the Ssn6 transcriptional co-repressor []. ; PDB: 3VP9_B 3VP8_B.
Probab=23.60 E-value=2.1e+02 Score=18.29 Aligned_cols=29 Identities=14% Similarity=0.213 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 17 LKAIKEQTDLEVNLLQDSLNNIRTATSRL 45 (124)
Q Consensus 17 L~~~~~~l~~ei~~l~~~~~~L~~~~~~~ 45 (124)
|..+.+++..|.+.+.+.+..++....+|
T Consensus 2 l~elLd~ir~Ef~~~~~e~~~~k~~~~e~ 30 (79)
T PF08581_consen 2 LNELLDAIRQEFENLSQEANSYKHQKDEY 30 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHHHH
Confidence 44455556666666665554444443333
No 277
>PF09932 DUF2164: Uncharacterized conserved protein (DUF2164); InterPro: IPR018680 This family of various hypothetical prokaryotic proteins has no known function.
Probab=23.56 E-value=1.5e+02 Score=18.78 Aligned_cols=25 Identities=12% Similarity=0.255 Sum_probs=20.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 97 TMDEGKDYCERKINLLKSNFDQLIE 121 (124)
Q Consensus 97 ~~~eA~~~l~~r~~~l~~~i~~l~~ 121 (124)
.+.+|..++.+|.+.++..+-.+++
T Consensus 51 gv~DA~~~~~~r~~~l~~~ly~lEk 75 (76)
T PF09932_consen 51 GVQDAQAVLEERMEDLEEELYELEK 75 (76)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHhhC
Confidence 4688999999999999988876654
No 278
>COG1504 Uncharacterized conserved protein [Function unknown]
Probab=23.46 E-value=1.5e+02 Score=20.59 Aligned_cols=21 Identities=14% Similarity=0.090 Sum_probs=9.6
Q ss_pred EEccCceeeecCHHHHHHHHHH
Q 033241 86 VDIGTGYFVEKTMDEGKDYCER 107 (124)
Q Consensus 86 V~lG~g~~vE~~~~eA~~~l~~ 107 (124)
-+-|+++ ++.|.+||++.+++
T Consensus 86 r~k~~~v-i~~pT~EAikr~ne 106 (121)
T COG1504 86 RKKGCEV-IELPTPEAIKRYNE 106 (121)
T ss_pred HhcCCeE-EEeCCHHHHHHHHH
Confidence 3344443 33445555555443
No 279
>COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown]
Probab=23.39 E-value=1.9e+02 Score=17.79 Aligned_cols=21 Identities=14% Similarity=0.398 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 033241 24 TDLEVNLLQDSLNNIRTATSR 44 (124)
Q Consensus 24 l~~ei~~l~~~~~~L~~~~~~ 44 (124)
+++.|..|+..|..|+.....
T Consensus 30 l~eRIalLq~EIeRlkAe~~k 50 (65)
T COG5509 30 LEERIALLQAEIERLKAELAK 50 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 344444444444444444443
No 280
>PF13094 CENP-Q: CENP-Q, a CENPA-CAD centromere complex subunit
Probab=23.34 E-value=2.7e+02 Score=19.54 Aligned_cols=35 Identities=14% Similarity=0.176 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 10 EKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSR 44 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~ 44 (124)
..++.+.|.....+++..+.....++..|+..+.+
T Consensus 18 ~~~~~e~ll~~~~~LE~qL~~~~~~l~lLq~e~~~ 52 (160)
T PF13094_consen 18 DSFDYEQLLDRKRALERQLAANLHQLELLQEEIEK 52 (160)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35667777777777777666444444444444333
No 281
>PF07412 Geminin: Geminin; InterPro: IPR022786 This family contains the eukaryotic protein geminin (approximately 200 residues long). Geminin inhibits DNA replication by preventing the incorporation of MCM complex into prereplication complex, and is degraded during the mitotic phase of the cell cycle. It has been proposed that geminin inhibits DNA replication during S, G2, and M phases and that geminin destruction at the metaphase-anaphase transition permits replication in the succeeding cell cycle []. ; GO: 0008156 negative regulation of DNA replication; PDB: 1T6F_B 2LP0_B 1UII_B 2WVR_B 2ZXX_B.
Probab=23.24 E-value=2.5e+02 Score=21.23 Aligned_cols=31 Identities=10% Similarity=0.262 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 033241 26 LEVNLLQDSLNNIRTATSRLESASTALHDLS 56 (124)
Q Consensus 26 ~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~ 56 (124)
.++..|......|.......+-..+.|+.|.
T Consensus 139 eEi~~lk~en~~L~elae~~~~la~~ie~l~ 169 (200)
T PF07412_consen 139 EEIAKLKEENEELKELAEHVQYLAEVIERLT 169 (200)
T ss_dssp HHHHHHHHHHHCCHHHHHHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3333344333334444444444445555553
No 282
>PRK14066 exodeoxyribonuclease VII small subunit; Provisional
Probab=23.23 E-value=2e+02 Score=18.08 Aligned_cols=35 Identities=9% Similarity=0.068 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 10 EKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSR 44 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~ 44 (124)
..+||++...++++--.-+...++.+......+..
T Consensus 23 g~l~Leesl~lyeeG~~L~k~C~~~L~~ae~kv~~ 57 (75)
T PRK14066 23 GELSLDDSLKAFEEGVKHAAFCSKKLDEAERRVEV 57 (75)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56778887777777766666665544444444433
No 283
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=23.21 E-value=2.1e+02 Score=18.15 Aligned_cols=31 Identities=19% Similarity=0.317 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 16 QLKAIKEQTDLEVNLLQDSLNNIRTATSRLE 46 (124)
Q Consensus 16 ~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~ 46 (124)
.|..-...++.++..+..++..+...+.++.
T Consensus 66 ~L~~~~~~~~~~i~~l~~~~~~l~~~l~~~~ 96 (106)
T PF01920_consen 66 ELEERIEKLEKEIKKLEKQLKYLEKKLKELK 96 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444555555555555555544444443
No 284
>PRK14068 exodeoxyribonuclease VII small subunit; Provisional
Probab=23.20 E-value=2.1e+02 Score=18.13 Aligned_cols=30 Identities=17% Similarity=0.131 Sum_probs=15.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 10 EKMSVEQLKAIKEQTDLEVNLLQDSLNNIR 39 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei~~l~~~~~~L~ 39 (124)
..+||++...++++--.-+...+..+..-.
T Consensus 25 gdl~Leesl~lyeeG~~L~k~C~~~L~~ae 54 (76)
T PRK14068 25 ETVSLEESLDLYQRGMKLSAACDTTLKNAE 54 (76)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455666666666655555555544333333
No 285
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=23.04 E-value=2.4e+02 Score=18.81 Aligned_cols=45 Identities=16% Similarity=0.354 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 11 KMSVEQLKAIKEQT---DLEVNLLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 11 ~l~le~L~~~~~~l---~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
-+|++++..+.... ....+.+.+++..+...+.++....+.|...
T Consensus 56 G~~L~eI~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~L~~~ 103 (120)
T cd04781 56 GFSLDEIQAMLSHDGKPPIDRQLLKAKAAELDQQIQRLQAMRELLRHV 103 (120)
T ss_pred CCCHHHHHHHHhccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35677777665432 2223556666667777777777666666654
No 286
>PF04880 NUDE_C: NUDE protein, C-terminal conserved region; InterPro: IPR006964 This domain represents the C-terminal conserved region of NUDE proteins. Emericella nidulans (Aspergillus nidulans) NUDE, acts in the cytoplasmic dynein/dynactin pathway and is required for distribution of nuclei []. It is a homologue of the nuclear distribution protein RO11 of Neurospora crassa. NUDE interacts with the NUDF via an N-terminal coiled coil domain; this is the only domain which is absolutely required for NUDE function.; PDB: 2V66_B 2V71_B.
Probab=22.97 E-value=1.7e+02 Score=21.40 Aligned_cols=10 Identities=20% Similarity=0.335 Sum_probs=4.7
Q ss_pred HHHHHHHHHH
Q 033241 14 VEQLKAIKEQ 23 (124)
Q Consensus 14 le~L~~~~~~ 23 (124)
|+++.+-+++
T Consensus 2 LeD~EsklN~ 11 (166)
T PF04880_consen 2 LEDFESKLNQ 11 (166)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
Confidence 4555554433
No 287
>PF07240 Turandot: Stress-inducible humoral factor Turandot; InterPro: IPR010825 This family consists of several Drosophila species specific Turandot proteins. The Turandot A (TotA) gene encodes a humoral factor, which is secreted from the fat body and accumulates in the body fluids. TotA is strongly induced upon bacterial challenge, as well as by other types of stress such as high temperature, mechanical pressure, dehydration, UV irradiation, and oxidative agents. It is also upregulated during metamorphosis and at high age. Flies that overexpress TotA show prolonged survival and retain normal activity at otherwise lethal temperatures. Although TotA is only induced by severe stress, it responds to a much wider range of stimuli than heat shock genes such as hsp70 or immune genes such as Cecropin A1 [].
Probab=22.92 E-value=92 Score=20.37 Aligned_cols=46 Identities=13% Similarity=0.201 Sum_probs=34.1
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCC
Q 033241 13 SVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLR 58 (124)
Q Consensus 13 ~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~ 58 (124)
++++|..+++.+-..+..--+.-.++...+.+|.+....|+.+++.
T Consensus 11 ni~eLi~fY~ky~~~~~L~~~~r~~~d~~i~~y~~~~~lVDGvPaQ 56 (85)
T PF07240_consen 11 NIQELIAFYEKYSPRLPLTPQDRQRIDRFIRRYKEENNLVDGVPAQ 56 (85)
T ss_pred hHHHHHHHHHHcCccCCCCHHHHHHHHHHHHHHHHHhhcccCcCCC
Confidence 4678888888877665555556677888888888887778887754
No 288
>PRK14990 anaerobic dimethyl sulfoxide reductase subunit A; Provisional
Probab=22.91 E-value=1.1e+02 Score=27.27 Aligned_cols=27 Identities=22% Similarity=0.335 Sum_probs=23.8
Q ss_pred cCceeeecCHHHHHHHHHHHHHHHHHH
Q 033241 89 GTGYFVEKTMDEGKDYCERKINLLKSN 115 (124)
Q Consensus 89 G~g~~vE~~~~eA~~~l~~r~~~l~~~ 115 (124)
|.|=|++.|-|||.+++.+|++.+.+.
T Consensus 131 G~g~~~~iSWdEAl~~Ia~kl~~i~~~ 157 (814)
T PRK14990 131 GEGKFERISWEEAYDIIATNMQRLIKE 157 (814)
T ss_pred CCCCeEEeCHHHHHHHHHHHHHHHHHh
Confidence 468899999999999999999887653
No 289
>PF04124 Dor1: Dor1-like family ; InterPro: IPR007255 Dor1 is involved in vesicle targeting to the yeast Golgi apparatus and complexes with a number of other trafficking proteins, which include Sec34 and Sec35 [].
Probab=22.80 E-value=1.6e+02 Score=23.40 Aligned_cols=33 Identities=18% Similarity=0.245 Sum_probs=25.9
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 8 GMEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRT 40 (124)
Q Consensus 8 ~~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~ 40 (124)
.++++++++|...-+.+.+++..+.++++.|-.
T Consensus 3 ~l~s~~l~~L~~Ep~~L~~~~~~l~~ql~~La~ 35 (338)
T PF04124_consen 3 ELTSLSLESLFSEPQSLSEEIASLDAQLQSLAF 35 (338)
T ss_pred ccccCCHHHHHhhHHHHHHHHHHHHHHHHHHHH
Confidence 367888899988888888888888777776654
No 290
>PF04799 Fzo_mitofusin: fzo-like conserved region; InterPro: IPR006884 This entry represents the heptad repeat domain which is conserved at the C terminus of Fzo/mitofusion family of GTPases. Fzo is a mediator of mitochondrial fusion during spermatogenesis []. This conserved region is also found in the human mitofusin protein []. This domain forms a dimeric antiparallel coiled coil structure, which has been proposed to act as a mitochodrial tether before vesicle fusion [].; GO: 0003924 GTPase activity, 0006184 GTP catabolic process, 0008053 mitochondrial fusion, 0005741 mitochondrial outer membrane, 0016021 integral to membrane; PDB: 1T3J_A.
Probab=22.60 E-value=3.2e+02 Score=20.14 Aligned_cols=26 Identities=23% Similarity=0.392 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033241 30 LLQDSLNNIRTATSRLESASTALHDL 55 (124)
Q Consensus 30 ~l~~~~~~L~~~~~~~~~~~~~l~~L 55 (124)
.|..++.+|...+..++.+....+.|
T Consensus 124 eL~~eI~~L~~~i~~le~~~~~~k~L 149 (171)
T PF04799_consen 124 ELEDEIKQLEKEIQRLEEIQSKSKTL 149 (171)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444444444444444333333
No 291
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=22.59 E-value=1.5e+02 Score=18.15 Aligned_cols=33 Identities=18% Similarity=0.037 Sum_probs=24.2
Q ss_pred CCceeEeEEEcC--CCeEEEEccCceeeecCHHHH
Q 033241 69 TASLYVPGTLDD--ARKVLVDIGTGYFVEKTMDEG 101 (124)
Q Consensus 69 g~~~yv~a~I~~--~~~VlV~lG~g~~vE~~~~eA 101 (124)
..|-.|.|+|.. .+.++|++|.++..-.+..+.
T Consensus 5 ~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~ 39 (82)
T cd04454 5 DVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSA 39 (82)
T ss_pred CCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhc
Confidence 345667788775 678999999987777776654
No 292
>PRK10698 phage shock protein PspA; Provisional
Probab=22.55 E-value=3.4e+02 Score=20.44 Aligned_cols=33 Identities=9% Similarity=0.130 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 16 QLKAIKEQTDLEVNLLQDSLNNIRTATSRLESA 48 (124)
Q Consensus 16 ~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~ 48 (124)
.|...+.+.+..++.|..++..|+..+.+.+.=
T Consensus 103 ~l~~~~~~~~~~~~~L~~~l~~L~~ki~eak~k 135 (222)
T PRK10698 103 TLEHEVTLVDETLARMKKEIGELENKLSETRAR 135 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444444555555555555555555554433
No 293
>PRK01356 hscB co-chaperone HscB; Provisional
Probab=22.52 E-value=2.5e+02 Score=20.21 Aligned_cols=8 Identities=25% Similarity=0.227 Sum_probs=3.4
Q ss_pred CCHHHHHH
Q 033241 12 MSVEQLKA 19 (124)
Q Consensus 12 l~le~L~~ 19 (124)
++++=|.+
T Consensus 87 ~d~~fLme 94 (166)
T PRK01356 87 LSPLELSI 94 (166)
T ss_pred CCHHHHHH
Confidence 34444433
No 294
>smart00262 GEL Gelsolin homology domain. Gelsolin/severin/villin homology domain. Calcium-binding and actin-binding. Both intra- and extracellular domains.
Probab=22.49 E-value=75 Score=19.79 Aligned_cols=13 Identities=15% Similarity=0.176 Sum_probs=9.2
Q ss_pred CCeEEEEccCcee
Q 033241 81 ARKVLVDIGTGYF 93 (124)
Q Consensus 81 ~~~VlV~lG~g~~ 93 (124)
.+.|+||+|.+.-
T Consensus 34 ~~~iyvW~G~~as 46 (90)
T smart00262 34 GSEIYVWVGKKSS 46 (90)
T ss_pred CCEEEEEECCCCC
Confidence 4678888887643
No 295
>PF04740 LXG: LXG domain of WXG superfamily; InterPro: IPR006829 This group of putative transposases is found in Gram-positive bacteria, mostly Bacillus members and is thought to be a Cytosolic protein. However, we have also found a Bacillus subtilis bacteriophage SPbetac2 homologue (O64023 from SWISSPROT), possibly arising as a result of horizontal transfer. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=22.43 E-value=2.5e+02 Score=20.26 Aligned_cols=36 Identities=22% Similarity=0.397 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 12 MSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLES 47 (124)
Q Consensus 12 l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~ 47 (124)
++..+|....+.+...++.+.+++..+..++..+..
T Consensus 3 ~d~~el~~~~~~~~~~~~~~~~~l~~l~~ai~~~~~ 38 (204)
T PF04740_consen 3 LDVSELHSQAESTNSSLKELKEQLESLQKAINQFIS 38 (204)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 566777777777777777777777777776666553
No 296
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=22.42 E-value=2.5e+02 Score=20.54 Aligned_cols=29 Identities=14% Similarity=0.118 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 17 LKAIKEQTDLEVNLLQDSLNNIRTATSRL 45 (124)
Q Consensus 17 L~~~~~~l~~ei~~l~~~~~~L~~~~~~~ 45 (124)
|....+.+.+.++.|+..+..+-..+..|
T Consensus 90 Le~~~~~l~~ri~eLe~~l~~kad~vvsY 118 (175)
T PRK13182 90 LEAQLNTITRRLDELERQLQQKADDVVSY 118 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhhH
Confidence 34444555555666665555544444333
No 297
>PF07763 FEZ: FEZ-like protein; InterPro: IPR011680 This is a family of eukaryotic proteins thought to be involved in axonal outgrowth and fasciculation []. The N-terminal regions of these sequences are less conserved than the C-terminal regions, and are highly acidic []. The Caenorhabditis elegans homolog, UNC-76 (Q7JNU9 from SWISSPROT), may play structural and signalling roles in the control of axonal extension and adhesion (particularly in the presence of adjacent neuronal cells []) and these roles have also been postulated for other FEZ family proteins []. Certain homologs have been definitively found to interact with the N-terminal variable region (V1) of PKC-zeta, and this interaction causes cytoplasmic translocation of the FEZ family protein in mammalian neuronal cells []. The C-terminal region probably participates in the association with the regulatory domain of PKC-zeta []. The members of this family are predicted to form coiled-coil structures [, ], which may interact with members of the RhoA family of signalling proteins [], but are not thought to contain other characteristic protein motifs []. Certain members of this family are expressed almost exclusively in the brain, whereas others (such as FEZ2, Q76LN0 from SWISSPROT) are expressed in other tissues, and are thought to perform similar but unknown functions in these tissues [].
Probab=22.36 E-value=3.5e+02 Score=21.12 Aligned_cols=39 Identities=18% Similarity=0.355 Sum_probs=31.2
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 8 GMEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLE 46 (124)
Q Consensus 8 ~~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~ 46 (124)
.+..||+-+|..+..+++..|..++..+-+-.+...++.
T Consensus 167 ~L~~LS~seL~~ll~e~E~~Ir~ySEeLV~qLA~RDELe 205 (244)
T PF07763_consen 167 GLRQLSLSELNELLEEMETAIREYSEELVQQLALRDELE 205 (244)
T ss_pred HHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466799999999999999999998888776666555543
No 298
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.36 E-value=2.8e+02 Score=19.28 Aligned_cols=31 Identities=16% Similarity=0.304 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033241 24 TDLEVNLLQDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 24 l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
+.++++.+..++..+...+..+.+..+.++.
T Consensus 79 ~~~~~~~l~~~i~~Le~~l~~L~~~~~~l~~ 109 (134)
T cd04779 79 VAQEVQLVCDQIDGLEHRLKQLKPIASQTDR 109 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555555555555555555555533
No 299
>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure. The exact function is unknown.
Probab=22.12 E-value=2.3e+02 Score=18.22 Aligned_cols=27 Identities=30% Similarity=0.331 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 21 KEQTDLEVNLLQDSLNNIRTATSRLES 47 (124)
Q Consensus 21 ~~~l~~ei~~l~~~~~~L~~~~~~~~~ 47 (124)
++.+.+++..||..+..|-..+...++
T Consensus 18 k~~Li~ei~~LQ~sL~~L~~Rve~Vk~ 44 (80)
T PF10224_consen 18 KEELIQEILELQDSLEALSDRVEEVKE 44 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456666666666666666555555443
No 300
>PRK00306 50S ribosomal protein L29; Reviewed
Probab=22.12 E-value=1.2e+02 Score=18.33 Aligned_cols=25 Identities=24% Similarity=0.251 Sum_probs=20.8
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHH
Q 033241 8 GMEKMSVEQLKAIKEQTDLEVNLLQ 32 (124)
Q Consensus 8 ~~~~l~le~L~~~~~~l~~ei~~l~ 32 (124)
.+-.+|.++|......+..++-.+.
T Consensus 5 elr~ls~~eL~~~l~~lkkeL~~lR 29 (66)
T PRK00306 5 ELRELSVEELNEKLLELKKELFNLR 29 (66)
T ss_pred HHhhCCHHHHHHHHHHHHHHHHHHH
Confidence 4668999999999998888887776
No 301
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=22.00 E-value=2.7e+02 Score=19.08 Aligned_cols=17 Identities=12% Similarity=0.081 Sum_probs=7.3
Q ss_pred HHHHHHHHHHHHHHHHH
Q 033241 36 NNIRTATSRLESASTAL 52 (124)
Q Consensus 36 ~~L~~~~~~~~~~~~~l 52 (124)
..+.....+|++.-.-+
T Consensus 57 ~Ll~~l~~~Y~~l~~Hl 73 (128)
T PF06295_consen 57 ELLDNLTQDYQKLYQHL 73 (128)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33444444454444333
No 302
>COG1648 CysG Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]
Probab=21.94 E-value=1.9e+02 Score=21.76 Aligned_cols=51 Identities=16% Similarity=0.254 Sum_probs=33.0
Q ss_pred CCceeEeEEEcCCCeEEEEccCce---------------eeecCHHHHHHHHHHHHHHHHHHHHHHh
Q 033241 69 TASLYVPGTLDDARKVLVDIGTGY---------------FVEKTMDEGKDYCERKINLLKSNFDQLI 120 (124)
Q Consensus 69 g~~~yv~a~I~~~~~VlV~lG~g~---------------~vE~~~~eA~~~l~~r~~~l~~~i~~l~ 120 (124)
-|.+++|+.+.... +.|.|++|- ++.-+..++..+..+..+.++....+..
T Consensus 108 ~~~f~~Pa~~~r~~-l~iaIsT~G~sP~la~~ir~~Ie~~l~~~~~~~~~~~~~~R~~v~~~~~~~~ 173 (210)
T COG1648 108 LCDFIFPAIVDRGP-LQIAISTGGKSPVLARLLREKIEALLPPSLGEVAELAARLRERVKGSLPKGK 173 (210)
T ss_pred cCceecceeeccCC-eEEEEECCCCChHHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHhccccHH
Confidence 37889999887644 999999987 4455555555555555555554444433
No 303
>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]
Probab=21.92 E-value=2.8e+02 Score=22.58 Aligned_cols=40 Identities=15% Similarity=0.285 Sum_probs=32.9
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 9 MEKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESA 48 (124)
Q Consensus 9 ~~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~ 48 (124)
+-.+|.+++.....-++.|+..+++..+.++..+..+.+.
T Consensus 17 ~~~mste~i~~rtrlldnEirI~~sev~ri~he~~~~~ek 56 (424)
T KOG0652|consen 17 ILSMSTEEIISRTRLLDNEIRIMKSEVQRINHELQAMKEK 56 (424)
T ss_pred hhhccHHHHHHHHHHhhhHHHHHHHHHHHhhhHHHHHHHH
Confidence 4578899999999999999999999998888776665543
No 304
>PRK11118 putative monooxygenase; Provisional
Probab=21.90 E-value=1.8e+02 Score=19.59 Aligned_cols=29 Identities=17% Similarity=0.205 Sum_probs=24.8
Q ss_pred EccCceeeecCHHHHHHHHHHHHHHHHHH
Q 033241 87 DIGTGYFVEKTMDEGKDYCERKINLLKSN 115 (124)
Q Consensus 87 ~lG~g~~vE~~~~eA~~~l~~r~~~l~~~ 115 (124)
..+.|+|+--+.+.|..|++.....|+..
T Consensus 48 ~eaGGiYlF~~e~~a~aYl~mH~aRL~~~ 76 (100)
T PRK11118 48 QEAGGIYLFEDEASAEAYLEMHTARLKNF 76 (100)
T ss_pred cccceEEEECCHHHHHHHHHHHHHHHHhc
Confidence 45789999999999999999888777654
No 305
>PRK06007 fliF flagellar MS-ring protein; Reviewed
Probab=21.69 E-value=2.9e+02 Score=23.84 Aligned_cols=70 Identities=14% Similarity=0.228 Sum_probs=44.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecC-CceeEeEEEcCCCeEEEEccCceeeecCHHHHHHH
Q 033241 31 LQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLT-ASLYVPGTLDDARKVLVDIGTGYFVEKTMDEGKDY 104 (124)
Q Consensus 31 l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg-~~~yv~a~I~~~~~VlV~lG~g~~vE~~~~eA~~~ 104 (124)
+.+++.-......++..++.+++..+. -.+++-+- .++|+.-.-+.+-.|+|.+-.|.-+...--+|+..
T Consensus 126 f~q~v~y~rAlegELartI~~i~~V~~----ArVhl~lP~~s~F~~~~~~~tASV~l~l~~g~~L~~~qV~aI~~ 196 (542)
T PRK06007 126 FEEQVNYQRALEGELARTIESLDGVKA----ARVHLALPKESVFVREQQPPSASVVLTLKPGRALDPEQVKAIVH 196 (542)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCcce----eEEEEECCCCccccccCCCCcEEEEEeccCCCCCCHHHHHHHHH
Confidence 344555566666778888877777652 33433333 47888877777888999988877654444444433
No 306
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=21.51 E-value=2.5e+02 Score=21.44 Aligned_cols=36 Identities=17% Similarity=0.082 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 033241 21 KEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLS 56 (124)
Q Consensus 21 ~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~ 56 (124)
+.++.+|.+.|.++...|+....+++++.+-.+.|+
T Consensus 71 ~~~l~~en~~L~~e~~~l~~~~~~~~~l~~en~~L~ 106 (276)
T PRK13922 71 LFDLREENEELKKELLELESRLQELEQLEAENARLR 106 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567788889999999999999998877766666654
No 307
>KOG2826 consensus Actin-related protein Arp2/3 complex, subunit ARPC2 [Cytoskeleton]
Probab=21.50 E-value=1.7e+02 Score=23.12 Aligned_cols=27 Identities=22% Similarity=0.436 Sum_probs=23.4
Q ss_pred CeEEEEccCceeeecCHHHHHHHHHHH
Q 033241 82 RKVLVDIGTGYFVEKTMDEGKDYCERK 108 (124)
Q Consensus 82 ~~VlV~lG~g~~vE~~~~eA~~~l~~r 108 (124)
.+|+++|-..+|.|.-..-|.++|++-
T Consensus 53 tkillSislK~y~elq~~Ga~~LLk~~ 79 (301)
T KOG2826|consen 53 TKILLSISLKFYKELQLHGADDLLKRV 79 (301)
T ss_pred eEEEEEEehhhHHHHHHcCHHHHHHHH
Confidence 479999999999999988888888763
No 308
>cd02766 MopB_3 The MopB_3 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins
Probab=21.45 E-value=1.3e+02 Score=25.30 Aligned_cols=24 Identities=25% Similarity=0.339 Sum_probs=22.0
Q ss_pred ceeeecCHHHHHHHHHHHHHHHHH
Q 033241 91 GYFVEKTMDEGKDYCERKINLLKS 114 (124)
Q Consensus 91 g~~vE~~~~eA~~~l~~r~~~l~~ 114 (124)
|=|.+.|-+||.+++..|++.+.+
T Consensus 68 g~~~~isWdeAl~~ia~~l~~i~~ 91 (501)
T cd02766 68 GQWERISWDEALDTIAAKLKEIKA 91 (501)
T ss_pred CceEEecHHHHHHHHHHHHHHHHH
Confidence 689999999999999999988775
No 309
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=21.36 E-value=4.6e+02 Score=21.43 Aligned_cols=18 Identities=11% Similarity=0.287 Sum_probs=11.9
Q ss_pred eEeEEEcC------CCeEEEEccC
Q 033241 73 YVPGTLDD------ARKVLVDIGT 90 (124)
Q Consensus 73 yv~a~I~~------~~~VlV~lG~ 90 (124)
|+.|+|.. .+.++++.|.
T Consensus 104 ~i~ArVI~r~ps~~~~~ltInkGs 127 (337)
T PRK14872 104 LIMGRVIFRDPAHWGSSCWINVGK 127 (337)
T ss_pred eEEEEEEEeCCCccceEEEEcccc
Confidence 67777764 3467777774
No 310
>PF13814 Replic_Relax: Replication-relaxation
Probab=21.36 E-value=1.9e+02 Score=20.46 Aligned_cols=40 Identities=15% Similarity=0.150 Sum_probs=33.7
Q ss_pred CCCeEEEEccCc----eeeecCH-HHHHHHHHHHHHHHHHHHHHH
Q 033241 80 DARKVLVDIGTG----YFVEKTM-DEGKDYCERKINLLKSNFDQL 119 (124)
Q Consensus 80 ~~~~VlV~lG~g----~~vE~~~-~eA~~~l~~r~~~l~~~i~~l 119 (124)
-+|-++.+-..+ ||+|.+. .|....+.+|++....-+...
T Consensus 137 ~PDa~~~~~~~~~~~~~fiEvD~~te~~~~l~~Kl~~Y~~~~~~~ 181 (191)
T PF13814_consen 137 RPDAVFRWRDGDREVRFFIEVDRGTESPARLRRKLERYRRYLRSG 181 (191)
T ss_pred eCCEEEEEecCCeEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHH
Confidence 467788888888 9999999 888999999999888777665
No 311
>PF00159 Hormone_3: Pancreatic hormone peptide; InterPro: IPR001955 Pancreatic hormone (PP) [] is a peptide synthesized in pancreatic islets of Langherhans, which acts as a regulator of pancreatic and gastrointestinal functions. The hormone is produced as a larger propeptide, which is enzymatically cleaved to yield the mature active peptide: this is 36 amino acids in length [] and has an amidated C terminus []. The hormone has a globular structure, residues 2-8 forming a left-handed poly-proline-II-like helix, residues 9-13 a beta turn, and 14-32 an alpha-helix,held close to the first helix by hydrophobic interactions []. Unlike glucagon, another peptide hormone, the structure of pancreatic peptide is preserved in aqueous solution []. Both N and C termini are required for activity: receptor binding and activation functions may reside in the N and C termini respectively []. Pancreatic hormone is part of a wider family of active peptides that includes: Neuropeptide Y (NPY) [], one of the most abundant peptides in the mammalian nervous system. NPY is implicated in the control of feeding and the secretion of the gonadotrophin-releasing hormone. Peptide YY (PYY) []. PPY is a gut peptide that inhibits exocrine pancreatic secretion, has a vasoconstrictory action and inhibits jejunal and colonic mobility. Various NPY and PYY-like polypeptides from fish and amphibians [, ]. Neuropeptide F (NPF) from invertebrates such as worms and snail. Skin peptide Tyr-Tyr (SPYY) from the frog Phyllomedusa bicolor. SPYY shows a large spectra of antibacterial and antifungal activity. All these peptides are 36 to 39 amino acids long. Like most active peptides, their C-terminal is amidated and they are synthesized as larger protein precursors.; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 1LJV_A 1BBA_A 1V1D_A 1PPT_A 2H3T_A 2H4B_A 2BF9_A 2H3S_B 1K8V_A 2DF0_A ....
Probab=21.30 E-value=1.6e+02 Score=16.09 Aligned_cols=22 Identities=23% Similarity=0.173 Sum_probs=16.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHH
Q 033241 10 EKMSVEQLKAIKEQTDLEVNLL 31 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei~~l 31 (124)
..-|+|+|.+...++.+-++.+
T Consensus 10 ~~aspeel~~Y~~~L~~Y~~lv 31 (36)
T PF00159_consen 10 DFASPEELAQYYAALRHYINLV 31 (36)
T ss_dssp TTSSHHHHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHH
Confidence 3457899999999888766654
No 312
>COG4013 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.28 E-value=1.1e+02 Score=20.12 Aligned_cols=44 Identities=11% Similarity=0.195 Sum_probs=25.8
Q ss_pred HHHHHHHHHhhccCC-CCCceEEEecCCceeEeEEEcCCCeEEEEc
Q 033241 44 RLESASTALHDLSLR-PQGAKMLVPLTASLYVPGTLDDARKVLVDI 88 (124)
Q Consensus 44 ~~~~~~~~l~~L~~~-~~~~e~lVplg~~~yv~a~I~~~~~VlV~l 88 (124)
......+.|+.++.. +.|..+-..+| .+|+||++.+.+.=++.+
T Consensus 6 ~~~~peEl~eY~~eeV~~gd~vel~~g-rVhIpG~vv~~n~g~l~l 50 (91)
T COG4013 6 DVKNPEELIEYLNEEVDVGDYVELYFG-RVHIPGRVVHYNDGLLRL 50 (91)
T ss_pred hhcCHHHHHHHHHhcCCCCCEEEEEEE-EEEeccEEEEeeccEEEE
Confidence 344555667777532 23333334443 489999999877655443
No 313
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=21.27 E-value=1.8e+02 Score=20.41 Aligned_cols=27 Identities=26% Similarity=0.244 Sum_probs=20.1
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 97 TMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 97 ~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
+.++...++..+...+++++.+|+..|
T Consensus 77 ~~~~~~~~l~~~~~~l~~ki~~L~~~~ 103 (142)
T TIGR01950 77 TADDWARLSSQWREELDERIDQLNALR 103 (142)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356667788888888888888877654
No 314
>TIGR01837 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein. This model describes a domain found in some proteins associated with polyhydroxyalkanoate (PHA) granules in a subset of species that have PHA inclusion granules. Included are two tandem proteins of Pseudomonas oleovorans, PhaI and PhaF, and their homologs in related species. PhaF proteins have a low-complexity C-terminal region with repeats similar to AAAKP.
Probab=21.13 E-value=1.8e+02 Score=19.78 Aligned_cols=19 Identities=11% Similarity=0.258 Sum_probs=7.9
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 033241 26 LEVNLLQDSLNNIRTATSR 44 (124)
Q Consensus 26 ~ei~~l~~~~~~L~~~~~~ 44 (124)
.+++.|..++..|...+.+
T Consensus 96 ~ev~~L~~RI~~Le~~l~~ 114 (118)
T TIGR01837 96 EEIEALSAKIEQLAVQVEE 114 (118)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444333
No 315
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF.
Probab=21.04 E-value=3.5e+02 Score=19.97 Aligned_cols=59 Identities=14% Similarity=0.167 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCC-ceeEeEEEcCCCeEEEEccCceeee
Q 033241 33 DSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTA-SLYVPGTLDDARKVLVDIGTGYFVE 95 (124)
Q Consensus 33 ~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~-~~yv~a~I~~~~~VlV~lG~g~~vE 95 (124)
++..-......++..++.++..... -.+.+-+.. +.|..-.-+.+-.|+|.+..|.-.+
T Consensus 100 e~~~~~~ale~EL~rtI~~i~~V~~----ArVhl~~P~~~~f~~~~~~~sASV~l~~~~g~~l~ 159 (193)
T TIGR02544 100 ERARYLYAIEQRLEQTLSQIDGVIS----ARVHVVLPENDNNGRPKKPSSASVFIKYRPGLNLD 159 (193)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCeee----eEEEEECCCCCcccccCCCCcEEEEEEeCCCCCcH
Confidence 3344445555677777777777652 334443333 3777766666778999998887554
No 316
>PRK15396 murein lipoprotein; Provisional
Probab=21.04 E-value=2.4e+02 Score=18.03 Aligned_cols=27 Identities=22% Similarity=0.442 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRT 40 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~ 40 (124)
+++|..--+.+..+++.+.+..+.++.
T Consensus 27 vd~LssqV~~L~~kvdql~~dv~~~~~ 53 (78)
T PRK15396 27 IDQLSSDVQTLNAKVDQLSNDVNAMRS 53 (78)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444444444444443333
No 317
>smart00150 SPEC Spectrin repeats.
Probab=21.01 E-value=2e+02 Score=17.23 Aligned_cols=30 Identities=13% Similarity=0.215 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 15 EQLKAIKEQTDLEVNLLQDSLNNIRTATSR 44 (124)
Q Consensus 15 e~L~~~~~~l~~ei~~l~~~~~~L~~~~~~ 44 (124)
+.+...++.+..+++..+..+..+......
T Consensus 34 ~~~~~~~~~~~~e~~~~~~~v~~~~~~~~~ 63 (101)
T smart00150 34 EALLKKHEALEAELEAHEERVEALNELGEQ 63 (101)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence 333334445555555555544444444333
No 318
>PF02187 GAS2: Growth-Arrest-Specific Protein 2 Domain; InterPro: IPR003108 The growth-arrest-specific protein 2 domain is found associated with the spectrin repeat, calponin homology domain and EF hand in many proteins. It is found among others in the growth arrest-specific protein 2 [].; GO: 0007050 cell cycle arrest; PDB: 1V5R_A.
Probab=20.91 E-value=1.8e+02 Score=18.47 Aligned_cols=18 Identities=22% Similarity=0.287 Sum_probs=13.2
Q ss_pred eEEEcCCCeEEEEccCcee
Q 033241 75 PGTLDDARKVLVDIGTGYF 93 (124)
Q Consensus 75 ~a~I~~~~~VlV~lG~g~~ 93 (124)
-.+|- .+.|+|-+|.||-
T Consensus 40 ~~ril-~~~vMVRVGGGW~ 57 (73)
T PF02187_consen 40 FVRIL-RSHVMVRVGGGWD 57 (73)
T ss_dssp EEEET-TTEEEEEETTEEE
T ss_pred EEEEe-CCEEEEEeCCcHH
Confidence 34444 3689999999984
No 319
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=20.87 E-value=1.8e+02 Score=20.79 Aligned_cols=27 Identities=19% Similarity=0.231 Sum_probs=21.2
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 97 TMDEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 97 ~~~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
+.++...++..++..++.+|.+++..+
T Consensus 87 ~~~~~~~ll~~k~~~l~~~I~~L~~~~ 113 (154)
T PRK15002 87 SAKEWKQLSSQWREELDRRIHTLVALR 113 (154)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456677888888888888888887754
No 320
>TIGR03479 DMSO_red_II_alp DMSO reductase family type II enzyme, molybdopterin subunit. This model represents the molybdopterin subunit, typically called the alpha subunit, of various proteins that also contain an iron-sulfur subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase, ethylbenzene dehydrogenase, and an archaeal respiratory nitrate reductase. This alpha subunit has a twin-arginine translocation (TAT) signal for Sec-independent translocation across the plasma membrane.
Probab=20.78 E-value=93 Score=28.39 Aligned_cols=37 Identities=16% Similarity=0.121 Sum_probs=28.3
Q ss_pred EcCCCeEEEEc------cCceeeecCHHHHHHHHHHHHHHHHH
Q 033241 78 LDDARKVLVDI------GTGYFVEKTMDEGKDYCERKINLLKS 114 (124)
Q Consensus 78 I~~~~~VlV~l------G~g~~vE~~~~eA~~~l~~r~~~l~~ 114 (124)
+.+++++.-++ |.|=|++.|-+||.+++..++..+.+
T Consensus 115 ~y~p~Rl~~Pl~R~g~RG~G~~~~iSWdEAld~IA~kl~~i~~ 157 (912)
T TIGR03479 115 MYGDDRLKYPLKRVGERGEGKWKRISWDEALTEIADKIIDTFE 157 (912)
T ss_pred hcCcccccCceeecCCCCCCceEEeCHHHHHHHHHHHHHHHHH
Confidence 44555554443 58999999999999999999877654
No 321
>PF09177 Syntaxin-6_N: Syntaxin 6, N-terminal; InterPro: IPR015260 Members of this entry, which are found in the amino terminus of various SNARE proteins, adopt a structure consisting of an antiparallel three-helix bundle. Their exact function has not been determined, though it is known that they regulate the SNARE motif, as well as mediate various protein-protein interactions involved in membrane-transport []. ; GO: 0048193 Golgi vesicle transport, 0016020 membrane; PDB: 1LVF_B 2C5I_T 2C5J_A 2C5K_T 4DND_A.
Probab=20.75 E-value=2.5e+02 Score=18.09 Aligned_cols=23 Identities=22% Similarity=0.299 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhh
Q 033241 32 QDSLNNIRTATSRLESASTALHD 54 (124)
Q Consensus 32 ~~~~~~L~~~~~~~~~~~~~l~~ 54 (124)
...+..+...+.++.+++..++.
T Consensus 45 ~~~l~~ie~~L~DL~~aV~ive~ 67 (97)
T PF09177_consen 45 RNALQSIEWDLEDLEEAVRIVEK 67 (97)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 33444444455555555555443
No 322
>PF11172 DUF2959: Protein of unknown function (DUF2959); InterPro: IPR021342 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=20.69 E-value=3.2e+02 Score=20.72 Aligned_cols=39 Identities=15% Similarity=0.152 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 14 VEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTAL 52 (124)
Q Consensus 14 le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l 52 (124)
-.+|...++++..+.+.....-..+...|..+++.-+++
T Consensus 59 ggdLe~~Y~~ln~~ye~s~~~A~~V~~RI~~vE~Va~AL 97 (201)
T PF11172_consen 59 GGDLEDKYNALNDEYESSEDAAEEVSDRIDAVEDVADAL 97 (201)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345566666666666666666666666666655555444
No 323
>PF07412 Geminin: Geminin; InterPro: IPR022786 This family contains the eukaryotic protein geminin (approximately 200 residues long). Geminin inhibits DNA replication by preventing the incorporation of MCM complex into prereplication complex, and is degraded during the mitotic phase of the cell cycle. It has been proposed that geminin inhibits DNA replication during S, G2, and M phases and that geminin destruction at the metaphase-anaphase transition permits replication in the succeeding cell cycle []. ; GO: 0008156 negative regulation of DNA replication; PDB: 1T6F_B 2LP0_B 1UII_B 2WVR_B 2ZXX_B.
Probab=20.67 E-value=3.1e+02 Score=20.75 Aligned_cols=35 Identities=11% Similarity=0.281 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 033241 22 EQTDLEVNLLQDSLNNIRTATSRLESASTALHDLS 56 (124)
Q Consensus 22 ~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~ 56 (124)
.+|..+++.+...+..|+....++.+..+.+.+|.
T Consensus 128 e~Lh~~ie~~~eEi~~lk~en~~L~elae~~~~la 162 (200)
T PF07412_consen 128 EKLHKEIEQKDEEIAKLKEENEELKELAEHVQYLA 162 (200)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445566666666667766666666777666654
No 324
>COG5570 Uncharacterized small protein [Function unknown]
Probab=20.62 E-value=2e+02 Score=17.18 Aligned_cols=25 Identities=20% Similarity=0.126 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhh
Q 033241 99 DEGKDYCERKINLLKSNFDQLIEVR 123 (124)
Q Consensus 99 ~eA~~~l~~r~~~l~~~i~~l~~~~ 123 (124)
+.++.-++||.-.|++.|+.|...+
T Consensus 32 d~~i~eLKRrKL~lKeeIEkLka~~ 56 (57)
T COG5570 32 DLAIRELKRRKLRLKEEIEKLKAQM 56 (57)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhccC
Confidence 5678889999999999999887653
No 325
>PF05681 Fumerase: Fumarate hydratase (Fumerase); InterPro: IPR004646 This entry represents various Fe-S type hydro-lyases, including the alpha subunit from both L-tartrate dehydratase (TtdA; 4.2.1.32 from EC) and class 1 fumarate hydratases (4.2.1.2 from EC), which includes both aerobic (FumA) and anaerobic (FumB) types []. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase (see IPR000362 from INTERPRO). Proteins in this group represent a subset of closely related proteins or modules, including the Escherichia coli tartrate dehydratase alpha chain and the N-terminal region of the class I fumarase (where the C-terminal region is homologous to the tartrate dehydratase beta chain). The activity of archaeal proteins in this group is unknown. Fumarate hydratase (also known as fumarase) is a component of the citric acid cycle. In facultative anaerobes such as E. coli, fumarase also engages in the reductive pathway from oxaloacetate to succinate during anaerobic growth. Three fumarases, FumA, FumB, and FumC, have been reported in E. coli. fumA and fumB genes are homologous and encode products of identical sizes which form thermolabile dimers of Mr 120,000. FumA and FumB are class I enzymes and are members of the iron-dependent hydrolases, which include aconitase and malate hydratase. The active FumA contains a 4Fe-4S centre, and it can be inactivated upon oxidation to give a 3Fe-4S centre [].; GO: 0016829 lyase activity
Probab=20.51 E-value=3.4e+02 Score=21.37 Aligned_cols=70 Identities=24% Similarity=0.294 Sum_probs=41.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCC--eEEEE
Q 033241 10 EKMSVEQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDAR--KVLVD 87 (124)
Q Consensus 10 ~~l~le~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~--~VlV~ 87 (124)
+.|+.+-+.++++.++.|-.... -..|+.-+..++-| .+-..|+.. ||. .|+|+
T Consensus 14 ~~lp~Dv~~al~~a~~~E~~~~a--k~vl~~ileN~~iA-------------~~~~~PlCQ---------DTG~~~~fv~ 69 (271)
T PF05681_consen 14 TYLPDDVLEALKKAYERETSPLA--KWVLEQILENAEIA-------------AKEKLPLCQ---------DTGIPVFFVE 69 (271)
T ss_pred hhCCHHHHHHHHHHHHccCCHHH--HHHHHHHHHHHHHH-------------hhcCccccc---------CCCeEEEEEE
Confidence 45777777777777776655442 22333333333322 122245543 444 48888
Q ss_pred ccCceeeecCHHHHHH
Q 033241 88 IGTGYFVEKTMDEGKD 103 (124)
Q Consensus 88 lG~g~~vE~~~~eA~~ 103 (124)
+|.++.+.-++.+|+.
T Consensus 70 ~G~~~~~~g~l~~ai~ 85 (271)
T PF05681_consen 70 IGQDVPIEGDLEEAIN 85 (271)
T ss_pred ECCCCCcChhHHHHHH
Confidence 8999998887777765
No 326
>PF10212 TTKRSYEDQ: Predicted coiled-coil domain-containing protein; InterPro: IPR019348 This entry represents a C-terminal 500 residue region, which contains a conserved TTKRSYEDQ motif. It is found in a family of coiled-coil domain-containing proteins that are conserved from nematodes to humans. These proteins also contain an N-terminal domain with a KLRAQ motif (IPR019343 from INTERPRO). The function of these proteins is not known.
Probab=20.42 E-value=3.5e+02 Score=23.49 Aligned_cols=39 Identities=8% Similarity=0.310 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033241 15 EQLKAIKEQTDLEVNLLQDSLNNIRTATSRLESASTALH 53 (124)
Q Consensus 15 e~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~~~~~l~ 53 (124)
++|.-.+.-++.++..+++++..++..+..-.+-|++|+
T Consensus 476 DEL~TTr~NYE~QLs~MSEHLasmNeqL~~Q~eeI~~LK 514 (518)
T PF10212_consen 476 DELETTRRNYEEQLSMMSEHLASMNEQLAKQREEIQTLK 514 (518)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 344455556667777777777777777776666666655
No 327
>PF04120 Iron_permease: Low affinity iron permease ; InterPro: IPR007251 Although originally identified as a low-affinity iron(II) permease [, ], Fet4 has since been shown to import several other transition metal ions, including copper [, ] and zinc []. Copper, cobalt, and cadmium inhibit Fet4 [, ]. Fet4 is an integral protein of the plasma membrane [, ]. FET4 is not essential, not even in fet3 fet4 double mutants []. Over expression of FET4 improves growth under alkaline conditions []. Transcription of FET4 is induced by Aft1 in response to low levels of iron [, , ] or by Zap1 in response to low zinc [, ], but not in response to low copper []. When the high-affinity iron permease component Fet3 is deleted, FET4 is induced by the addition of copper, zinc, cobalt, or manganese []. It is also induced under anaerobic conditions [, , ] and repressed by Rox1 in aerobic conditions [, ]. Rox1 attenuates the activation of FET4 by Aft1 or Zap1 []. ; GO: 0055085 transmembrane transport
Probab=20.41 E-value=1.6e+02 Score=20.68 Aligned_cols=26 Identities=15% Similarity=0.183 Sum_probs=20.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHH
Q 033241 6 GGGMEKMSVEQLKAIKEQTDLEVNLL 31 (124)
Q Consensus 6 ~i~~~~l~le~L~~~~~~l~~ei~~l 31 (124)
-|++..|+.++|..+++.+++....-
T Consensus 89 li~iE~l~~~el~~~~~~~~~~~~~~ 114 (132)
T PF04120_consen 89 LIDIEDLTEEELEEIRKRYERLAEQA 114 (132)
T ss_pred hCCcccCCHHHHHHHHHHHHHHHHHh
Confidence 48899999999999998888655443
No 328
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=20.31 E-value=2.2e+02 Score=17.50 Aligned_cols=27 Identities=19% Similarity=0.341 Sum_probs=16.7
Q ss_pred EcCCCeEEEEccCceee-ecCHHHHHHHHH
Q 033241 78 LDDARKVLVDIGTGYFV-EKTMDEGKDYCE 106 (124)
Q Consensus 78 I~~~~~VlV~lG~g~~v-E~~~~eA~~~l~ 106 (124)
+...+.|+|+.| |-+ ..+-++|.+.++
T Consensus 38 v~~Gd~VLVHaG--~Ai~~ideeeA~e~l~ 65 (68)
T PF01455_consen 38 VKVGDYVLVHAG--FAIEKIDEEEAEETLD 65 (68)
T ss_dssp B-TT-EEEEETT--EEEEEE-HHHHHHHHH
T ss_pred CCCCCEEEEecC--hhheeCCHHHHHHHHH
Confidence 456789999977 444 457777877654
No 329
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=20.23 E-value=2.9e+02 Score=18.75 Aligned_cols=47 Identities=17% Similarity=0.083 Sum_probs=30.8
Q ss_pred HHHHHHhhccCCCCCceEEEecCCceeEeEEEcCCCeEEEEccCceeeecCH
Q 033241 47 SASTALHDLSLRPQGAKMLVPLTASLYVPGTLDDARKVLVDIGTGYFVEKTM 98 (124)
Q Consensus 47 ~~~~~l~~L~~~~~~~e~lVplg~~~yv~a~I~~~~~VlV~lG~g~~vE~~~ 98 (124)
+-.+-+++|++ |.+ |=.++|+|-.-.=.+.+.|.|.++.|+.+....
T Consensus 31 ~~~~m~~~Lk~---GD~--VvT~gGi~G~V~~I~d~~v~leia~gv~i~~~r 77 (109)
T PRK05886 31 ATIDLHESLQP---GDR--VHTTSGLQATIVGITDDTVDLEIAPGVVTTWMK 77 (109)
T ss_pred HHHHHHHhcCC---CCE--EEECCCeEEEEEEEeCCEEEEEECCCeEEEEEh
Confidence 34456677775 334 555778886533223578999999998887654
No 330
>cd02752 MopB_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. Members of the MopB_Formate-Dh-Na-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=20.13 E-value=1.4e+02 Score=26.32 Aligned_cols=26 Identities=31% Similarity=0.477 Sum_probs=23.6
Q ss_pred cCceeeecCHHHHHHHHHHHHHHHHH
Q 033241 89 GTGYFVEKTMDEGKDYCERKINLLKS 114 (124)
Q Consensus 89 G~g~~vE~~~~eA~~~l~~r~~~l~~ 114 (124)
|.|=|.+.|-+||++.+.++++.+.+
T Consensus 64 g~g~~~~iSWdeAld~iA~klk~i~~ 89 (649)
T cd02752 64 GSGKWEEISWDEALDEIARKMKDIRD 89 (649)
T ss_pred CCCCEEEeCHHHHHHHHHHHHHHHHH
Confidence 66889999999999999999988765
No 331
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=20.10 E-value=3.3e+02 Score=19.31 Aligned_cols=32 Identities=19% Similarity=0.278 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033241 16 QLKAIKEQTDLEVNLLQDSLNNIRTATSRLES 47 (124)
Q Consensus 16 ~L~~~~~~l~~ei~~l~~~~~~L~~~~~~~~~ 47 (124)
+|...+-.+.++++.|...+..+.....-|..
T Consensus 78 eLE~~k~~L~qqv~~L~~e~s~~~~E~da~k~ 109 (135)
T KOG4196|consen 78 ELEKEKAELQQQVEKLKEENSRLRRELDAYKS 109 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444555555555555544444444433
Done!