Query psy1181
Match_columns 82
No_of_seqs 110 out of 417
Neff 4.6
Searched_HMMs 46136
Date Fri Aug 16 19:35:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1181.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1181hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3456|consensus 100.0 2E-39 4.3E-44 220.8 2.3 78 1-78 41-118 (120)
2 PF10276 zf-CHCC: Zinc-finger 99.8 8E-21 1.7E-25 109.0 4.1 39 37-75 1-40 (40)
3 COG4391 Uncharacterized protei 99.7 1.3E-17 2.8E-22 103.5 5.3 46 32-77 16-61 (62)
4 PLN02294 cytochrome c oxidase 98.9 2.8E-09 6E-14 77.4 5.3 51 27-77 101-154 (174)
5 PF01215 COX5B: Cytochrome c o 98.6 3.6E-08 7.7E-13 69.1 3.8 52 26-78 72-126 (136)
6 cd00924 Cyt_c_Oxidase_Vb Cytoc 98.5 1.6E-07 3.5E-12 62.4 4.3 50 28-79 42-94 (97)
7 PTZ00043 cytochrome c oxidase 98.4 2.4E-07 5.3E-12 70.5 4.4 52 27-78 141-195 (268)
8 KOG3352|consensus 98.3 5.3E-07 1.1E-11 64.5 3.8 51 27-79 95-148 (153)
9 PF09538 FYDLN_acid: Protein o 96.2 0.0017 3.7E-08 43.8 0.9 21 56-77 19-39 (108)
10 TIGR02300 FYDLN_acid conserved 93.5 0.031 6.8E-07 39.2 0.9 21 56-77 19-39 (129)
11 PRK00398 rpoP DNA-directed RNA 93.5 0.083 1.8E-06 29.9 2.5 17 63-79 20-36 (46)
12 PF13465 zf-H2C2_2: Zinc-finge 90.0 0.19 4.1E-06 25.4 1.2 14 62-75 12-25 (26)
13 PF00096 zf-C2H2: Zinc finger, 89.4 0.15 3.2E-06 24.4 0.5 12 66-77 2-13 (23)
14 COG4530 Uncharacterized protei 88.6 0.17 3.8E-06 35.3 0.6 21 55-76 18-38 (129)
15 PF13913 zf-C2HC_2: zinc-finge 88.2 0.23 5E-06 25.2 0.7 13 65-77 3-15 (25)
16 smart00659 RPOLCX RNA polymera 86.4 0.75 1.6E-05 26.4 2.3 21 57-77 12-32 (44)
17 PF13894 zf-C2H2_4: C2H2-type 85.5 0.38 8.2E-06 22.2 0.7 13 66-78 2-14 (24)
18 PF13878 zf-C2H2_3: zinc-finge 85.4 0.74 1.6E-05 25.9 1.9 23 56-78 3-27 (41)
19 PF08792 A2L_zn_ribbon: A2L zi 85.0 1.3 2.8E-05 24.0 2.7 23 51-75 10-32 (33)
20 COG1996 RPC10 DNA-directed RNA 83.8 1 2.2E-05 26.8 2.1 18 61-78 21-38 (49)
21 TIGR02098 MJ0042_CXXC MJ0042 f 83.4 1.2 2.5E-05 23.9 2.1 13 63-75 24-36 (38)
22 PF14255 Cys_rich_CPXG: Cystei 81.5 0.78 1.7E-05 27.4 1.0 12 65-76 1-12 (52)
23 PF03604 DNA_RNApol_7kD: DNA d 80.7 1.1 2.3E-05 24.3 1.3 19 59-77 12-30 (32)
24 PF02892 zf-BED: BED zinc fing 79.6 0.82 1.8E-05 25.1 0.6 17 61-77 13-29 (45)
25 PF05605 zf-Di19: Drought indu 77.4 0.94 2E-05 26.2 0.4 10 65-74 3-12 (54)
26 COG1579 Zn-ribbon protein, pos 75.7 0.85 1.9E-05 34.6 -0.1 19 61-79 218-236 (239)
27 smart00614 ZnF_BED BED zinc fi 75.2 4.2 9.2E-05 23.1 2.8 16 63-78 17-32 (50)
28 PF13719 zinc_ribbon_5: zinc-r 74.9 2.1 4.5E-05 23.3 1.4 16 64-79 2-17 (37)
29 PF08271 TF_Zn_Ribbon: TFIIB z 74.6 5.1 0.00011 22.1 3.0 24 51-75 7-30 (43)
30 PF02748 PyrI_C: Aspartate car 73.5 4 8.7E-05 24.1 2.5 23 55-77 25-48 (52)
31 PF05129 Elf1: Transcription e 72.4 3.1 6.8E-05 26.5 1.9 36 38-77 20-59 (81)
32 PF13408 Zn_ribbon_recom: Reco 71.7 2.9 6.4E-05 23.5 1.6 15 63-77 4-18 (58)
33 PF14369 zf-RING_3: zinc-finge 71.7 3.9 8.4E-05 22.3 2.0 14 63-76 20-33 (35)
34 KOG1088|consensus 70.7 3.2 7E-05 29.0 1.8 18 62-79 96-113 (124)
35 PHA02768 hypothetical protein; 69.9 1.2 2.6E-05 27.0 -0.4 13 66-78 7-19 (55)
36 PF08685 GON: GON domain; Int 68.1 6.9 0.00015 29.2 3.2 33 40-74 30-76 (201)
37 PF01430 HSP33: Hsp33 protein; 67.9 3.2 6.9E-05 31.2 1.5 14 64-77 266-279 (280)
38 PF03966 Trm112p: Trm112p-like 67.1 5.1 0.00011 24.1 2.0 18 62-79 51-68 (68)
39 smart00647 IBR In Between Ring 66.0 9.3 0.0002 21.5 2.9 36 37-76 15-52 (64)
40 TIGR02605 CxxC_CxxC_SSSS putat 65.7 4.8 0.0001 22.7 1.6 18 55-72 17-34 (52)
41 PF14353 CpXC: CpXC protein 65.6 4.2 9E-05 26.9 1.5 15 64-78 38-52 (128)
42 TIGR03365 Bsubt_queE 7-cyano-7 64.9 6.3 0.00014 28.8 2.5 34 42-76 12-45 (238)
43 PF13240 zinc_ribbon_2: zinc-r 64.2 2.6 5.6E-05 21.0 0.2 12 62-73 11-22 (23)
44 PF14447 Prok-RING_4: Prokaryo 64.2 3.2 7E-05 25.2 0.7 28 51-78 26-53 (55)
45 PF06957 COPI_C: Coatomer (COP 63.0 4.9 0.00011 32.8 1.8 15 62-76 378-392 (422)
46 COG1281 Disulfide bond chapero 62.9 4.7 0.0001 31.5 1.6 16 63-78 265-280 (286)
47 PF02591 DUF164: Putative zinc 62.8 4.8 0.0001 23.4 1.3 41 30-73 14-55 (56)
48 PF13717 zinc_ribbon_4: zinc-r 61.8 5.8 0.00013 21.6 1.4 16 64-79 2-17 (36)
49 PF09237 GAGA: GAGA factor; I 60.8 3.6 7.9E-05 25.0 0.5 19 58-76 18-36 (54)
50 cd00498 Hsp33 Heat shock prote 60.3 5.3 0.00012 30.1 1.4 13 64-76 262-274 (275)
51 PF04423 Rad50_zn_hook: Rad50 60.2 5.5 0.00012 22.9 1.2 12 65-76 21-32 (54)
52 PF12660 zf-TFIIIC: Putative z 59.5 4.1 8.9E-05 26.6 0.6 43 36-78 27-69 (99)
53 PF13248 zf-ribbon_3: zinc-rib 58.0 3.7 8E-05 20.7 0.2 12 62-73 14-25 (26)
54 PRK00114 hslO Hsp33-like chape 58.0 6.5 0.00014 30.0 1.6 15 64-78 268-282 (293)
55 PF14446 Prok-RING_1: Prokaryo 57.8 7.9 0.00017 23.4 1.6 16 61-76 18-33 (54)
56 PF15616 TerY-C: TerY-C metal 57.5 6.8 0.00015 27.4 1.5 21 57-77 98-118 (131)
57 KOG2462|consensus 57.3 5.8 0.00013 31.1 1.2 21 58-78 155-175 (279)
58 PF09723 Zn-ribbon_8: Zinc rib 57.1 9.4 0.0002 21.2 1.8 18 55-72 17-34 (42)
59 smart00531 TFIIE Transcription 55.9 11 0.00023 25.8 2.3 45 34-79 93-138 (147)
60 smart00355 ZnF_C2H2 zinc finge 54.6 4.8 0.0001 18.3 0.2 12 66-77 2-13 (26)
61 TIGR00240 ATCase_reg aspartate 54.0 14 0.0003 26.5 2.6 40 38-77 101-145 (150)
62 smart00834 CxxC_CXXC_SSSS Puta 53.7 13 0.00029 19.5 2.0 13 62-74 24-36 (41)
63 PF12756 zf-C2H2_2: C2H2 type 52.8 9.2 0.0002 22.9 1.4 15 63-77 49-63 (100)
64 TIGR03829 YokU_near_AblA uncha 52.5 15 0.00032 24.2 2.4 37 41-77 3-48 (89)
65 PF13912 zf-C2H2_6: C2H2-type 50.9 9.3 0.0002 18.5 1.0 13 65-77 2-14 (27)
66 COG1645 Uncharacterized Zn-fin 50.0 18 0.0004 25.3 2.7 28 42-77 30-57 (131)
67 PF01428 zf-AN1: AN1-like Zinc 48.8 9.5 0.0002 21.2 0.9 16 63-78 12-27 (43)
68 PF14803 Nudix_N_2: Nudix N-te 48.4 21 0.00045 19.4 2.2 25 51-75 7-33 (34)
69 PF12171 zf-C2H2_jaz: Zinc-fin 47.6 9.5 0.00021 18.8 0.7 12 66-77 3-14 (27)
70 PHA00616 hypothetical protein 47.4 3.9 8.4E-05 23.8 -0.9 13 66-78 3-15 (44)
71 PRK13376 pyrB bifunctional asp 47.1 46 0.001 28.0 5.0 36 41-77 479-520 (525)
72 KOG1074|consensus 46.8 6.4 0.00014 35.3 -0.0 36 38-79 612-648 (958)
73 COG1781 PyrI Aspartate carbamo 46.5 18 0.00038 26.2 2.2 41 38-78 104-149 (153)
74 PRK11827 hypothetical protein; 45.6 34 0.00074 20.9 3.1 34 40-79 8-41 (60)
75 TIGR01206 lysW lysine biosynth 45.4 26 0.00056 20.9 2.5 14 63-76 21-34 (54)
76 PRK01402 hslO Hsp33-like chape 45.3 14 0.0003 29.0 1.7 15 64-78 308-322 (328)
77 PF10571 UPF0547: Uncharacteri 45.2 9.3 0.0002 19.6 0.4 13 63-75 13-25 (26)
78 PRK00893 aspartate carbamoyltr 45.0 21 0.00046 25.5 2.4 41 38-78 103-148 (152)
79 PF01485 IBR: IBR domain; Int 44.8 12 0.00027 21.0 1.0 12 64-75 40-51 (64)
80 PF06226 DUF1007: Protein of u 44.4 15 0.00032 26.6 1.6 15 46-60 13-27 (212)
81 PF14690 zf-ISL3: zinc-finger 43.8 13 0.00029 20.2 1.0 14 64-77 2-15 (47)
82 PRK03824 hypA hydrogenase nick 43.6 15 0.00033 25.1 1.4 27 53-79 96-123 (135)
83 COG1655 Uncharacterized protei 43.1 9.4 0.0002 29.7 0.4 17 62-78 17-33 (267)
84 PHA03296 envelope glycoprotein 42.5 26 0.00057 31.0 3.0 25 51-76 681-705 (814)
85 PF04475 DUF555: Protein of un 42.5 15 0.00032 24.9 1.2 19 55-74 39-57 (102)
86 cd03528 Rieske_RO_ferredoxin R 42.3 48 0.001 20.2 3.5 18 62-79 55-72 (98)
87 PF02489 Herpes_glycop_H: Herp 42.2 15 0.00032 30.8 1.4 33 41-76 538-573 (657)
88 PF01844 HNH: HNH endonuclease 42.0 11 0.00023 20.2 0.4 11 67-77 1-11 (47)
89 KOG1729|consensus 41.9 9.9 0.00021 29.6 0.3 31 50-82 156-187 (288)
90 PF08274 PhnA_Zn_Ribbon: PhnA 41.2 12 0.00025 20.0 0.5 15 65-79 3-17 (30)
91 COG2835 Uncharacterized conser 40.6 47 0.001 20.5 3.1 34 40-79 8-41 (60)
92 COG4888 Uncharacterized Zn rib 40.6 34 0.00074 23.3 2.7 36 38-77 20-59 (104)
93 PF00653 BIR: Inhibitor of Apo 40.5 35 0.00075 20.3 2.6 15 61-75 33-47 (70)
94 PRK03922 hypothetical protein; 40.4 17 0.00037 25.0 1.3 21 54-75 40-60 (113)
95 PF03119 DNA_ligase_ZBD: NAD-d 40.2 19 0.00042 18.6 1.2 14 66-79 1-14 (28)
96 PRK14892 putative transcriptio 40.0 52 0.0011 21.8 3.5 36 38-77 19-55 (99)
97 PF10013 DUF2256: Uncharacteri 39.7 13 0.00028 21.6 0.5 12 64-75 8-19 (42)
98 COG0602 NrdG Organic radical a 38.4 26 0.00056 25.5 2.1 32 44-76 14-45 (212)
99 TIGR02159 PA_CoA_Oxy4 phenylac 38.1 14 0.0003 25.9 0.6 13 64-76 105-117 (146)
100 COG1885 Uncharacterized protei 37.7 19 0.00041 24.8 1.2 23 52-75 38-60 (115)
101 smart00154 ZnF_AN1 AN1-like Zi 37.4 18 0.00039 19.9 0.9 16 64-79 12-27 (39)
102 smart00451 ZnF_U1 U1-like zinc 37.0 18 0.0004 18.2 0.8 14 63-76 2-15 (35)
103 cd00729 rubredoxin_SM Rubredox 35.8 20 0.00044 19.2 0.9 10 63-72 17-26 (34)
104 COG2093 DNA-directed RNA polym 35.8 21 0.00045 22.4 1.0 13 61-73 15-27 (64)
105 PF10601 zf-LITAF-like: LITAF- 35.6 26 0.00057 21.1 1.5 14 61-74 4-17 (73)
106 COG4049 Uncharacterized protei 34.8 15 0.00033 22.9 0.3 14 64-77 17-30 (65)
107 PF11793 FANCL_C: FANCL C-term 34.6 25 0.00055 21.4 1.3 14 64-77 55-68 (70)
108 COG1656 Uncharacterized conser 34.3 17 0.00038 26.4 0.6 22 53-76 121-142 (165)
109 COG5189 SFP1 Putative transcri 33.9 20 0.00043 29.3 0.9 19 61-79 395-413 (423)
110 KOG1391|consensus 33.6 14 0.0003 29.7 0.0 37 18-54 317-353 (396)
111 cd04487 RecJ_OBF2_like RecJ_OB 33.5 52 0.0011 20.1 2.6 30 35-69 2-32 (73)
112 PF05191 ADK_lid: Adenylate ki 33.4 25 0.00054 19.2 1.0 13 65-77 2-14 (36)
113 cd03469 Rieske_RO_Alpha_N Ries 32.9 80 0.0017 19.8 3.5 29 50-78 46-74 (118)
114 cd00022 BIR Baculoviral inhibi 32.7 36 0.00078 19.8 1.7 15 62-76 32-46 (69)
115 PHA00732 hypothetical protein 32.1 21 0.00045 22.5 0.6 13 66-78 29-41 (79)
116 PF03884 DUF329: Domain of unk 31.7 32 0.0007 20.8 1.4 14 64-77 2-15 (57)
117 KOG1522|consensus 31.7 30 0.00065 27.2 1.5 71 8-78 16-103 (285)
118 cd03529 Rieske_NirD Assimilato 31.0 97 0.0021 19.4 3.7 18 62-79 61-78 (103)
119 smart00729 Elp3 Elongator prot 31.0 33 0.00072 22.3 1.5 21 54-74 2-22 (216)
120 COG1571 Predicted DNA-binding 30.7 19 0.00042 29.6 0.4 14 66-79 352-365 (421)
121 cd00085 HNHc HNH nucleases; HN 30.4 22 0.00047 18.9 0.5 10 65-74 12-21 (57)
122 smart00064 FYVE Protein presen 30.4 33 0.00072 20.0 1.3 14 64-77 10-23 (68)
123 PF12760 Zn_Tnp_IS1595: Transp 30.3 25 0.00053 19.6 0.7 8 65-72 19-26 (46)
124 PF13005 zf-IS66: zinc-finger 30.3 34 0.00074 18.6 1.3 15 64-78 2-16 (47)
125 cd03531 Rieske_RO_Alpha_KSH Th 30.3 42 0.0009 21.8 1.9 17 62-78 57-73 (115)
126 COG5034 TNG2 Chromatin remodel 30.3 32 0.00069 26.9 1.5 31 38-72 232-269 (271)
127 TIGR02378 nirD_assim_sml nitri 30.2 41 0.00089 21.1 1.8 16 64-79 64-79 (105)
128 PRK09965 3-phenylpropionate di 30.0 1.5E+02 0.0032 18.7 4.7 20 60-79 55-74 (106)
129 cd03542 Rieske_RO_Alpha_HBDO R 29.9 50 0.0011 21.9 2.2 28 51-78 47-74 (123)
130 PF14569 zf-UDP: Zinc-binding 29.5 17 0.00038 23.7 -0.1 17 61-77 48-64 (80)
131 smart00746 TRASH metallochaper 29.5 25 0.00055 16.3 0.6 9 67-75 1-9 (39)
132 PF04606 Ogr_Delta: Ogr/Delta- 29.4 24 0.00052 19.9 0.5 10 66-75 1-10 (47)
133 PF06676 DUF1178: Protein of u 29.0 30 0.00066 24.5 1.1 17 61-77 29-45 (148)
134 PF07503 zf-HYPF: HypF finger; 29.0 25 0.00053 19.2 0.5 14 63-76 20-33 (35)
135 cd03474 Rieske_T4moC Toluene-4 28.9 90 0.0019 19.5 3.2 19 62-80 56-74 (108)
136 cd03028 GRX_PICOT_like Glutare 28.9 35 0.00077 21.0 1.3 22 51-72 7-28 (90)
137 cd03478 Rieske_AIFL_N AIFL (ap 28.8 1.4E+02 0.003 18.2 4.0 18 62-79 54-71 (95)
138 cd00350 rubredoxin_like Rubred 28.2 35 0.00076 17.9 1.0 10 63-72 16-25 (33)
139 KOG1280|consensus 27.7 26 0.00056 28.6 0.6 25 49-73 49-88 (381)
140 PF13824 zf-Mss51: Zinc-finger 27.5 27 0.00058 21.2 0.5 15 62-76 12-26 (55)
141 PRK00432 30S ribosomal protein 27.5 38 0.00082 19.7 1.2 12 63-74 36-47 (50)
142 PHA03294 envelope glycoprotein 27.4 46 0.001 29.6 2.2 33 41-76 701-733 (835)
143 smart00238 BIR Baculoviral inh 27.2 52 0.0011 19.2 1.8 15 62-76 34-48 (71)
144 cd03541 Rieske_RO_Alpha_CMO Ri 27.2 48 0.0011 21.9 1.8 17 62-78 58-74 (118)
145 PF07282 OrfB_Zn_ribbon: Putat 26.8 51 0.0011 19.2 1.7 23 51-75 35-57 (69)
146 PHA00733 hypothetical protein 26.5 34 0.00074 23.1 1.0 15 62-76 71-85 (128)
147 TIGR00510 lipA lipoate synthas 26.5 53 0.0011 25.4 2.1 49 26-75 36-85 (302)
148 smart00734 ZnF_Rad18 Rad18-lik 26.2 29 0.00064 17.5 0.5 11 65-75 2-12 (26)
149 KOG3623|consensus 26.0 16 0.00035 32.7 -0.8 16 64-79 281-296 (1007)
150 PF10080 DUF2318: Predicted me 26.0 40 0.00086 22.4 1.2 21 56-78 46-66 (102)
151 cd03467 Rieske Rieske domain; 25.8 1.6E+02 0.0035 17.8 4.0 40 39-79 34-73 (98)
152 PRK06366 acetyl-CoA acetyltran 25.8 23 0.00049 27.7 -0.0 37 18-54 309-345 (388)
153 PRK03681 hypA hydrogenase nick 25.8 43 0.00094 22.2 1.3 30 37-73 67-96 (114)
154 TIGR03655 anti_R_Lar restricti 25.6 30 0.00065 19.8 0.5 10 66-75 3-12 (53)
155 TIGR02646 conserved hypothetic 25.6 31 0.00066 23.5 0.6 14 64-77 24-37 (144)
156 PRK06245 cofG FO synthase subu 25.4 40 0.00086 25.5 1.2 21 52-72 11-31 (336)
157 PRK00420 hypothetical protein; 25.1 47 0.001 22.6 1.4 18 61-78 37-54 (112)
158 smart00507 HNHc HNH nucleases. 24.9 29 0.00063 18.0 0.3 11 65-75 11-21 (52)
159 PF03470 zf-XS: XS zinc finger 24.8 30 0.00065 20.0 0.4 7 67-73 1-7 (43)
160 TIGR03831 YgiT_finger YgiT-typ 24.7 66 0.0014 16.9 1.8 13 65-77 33-45 (46)
161 cd03532 Rieske_RO_Alpha_VanA_D 24.7 96 0.0021 19.9 2.8 17 62-78 60-76 (116)
162 PF04959 ARS2: Arsenite-resist 24.2 52 0.0011 24.6 1.6 15 62-76 75-89 (214)
163 PF09889 DUF2116: Uncharacteri 24.1 34 0.00074 20.8 0.5 11 65-75 4-14 (59)
164 PRK10824 glutaredoxin-4; Provi 24.1 48 0.001 22.2 1.3 23 51-73 14-36 (115)
165 PF13451 zf-trcl: Probable zin 24.0 60 0.0013 19.1 1.6 18 62-79 2-19 (49)
166 PF14952 zf-tcix: Putative tre 23.6 36 0.00077 19.9 0.5 11 63-73 10-20 (44)
167 PF10058 DUF2296: Predicted in 23.5 38 0.00082 20.0 0.7 9 64-72 44-52 (54)
168 PF03811 Zn_Tnp_IS1: InsA N-te 23.4 60 0.0013 17.7 1.4 16 64-79 5-21 (36)
169 PF14122 YokU: YokU-like prote 22.9 87 0.0019 20.7 2.3 36 42-77 4-48 (87)
170 PF01363 FYVE: FYVE zinc finge 22.9 19 0.00042 21.1 -0.7 12 65-76 10-21 (69)
171 KOG3993|consensus 22.5 22 0.00048 29.8 -0.6 17 61-77 353-369 (500)
172 PF14239 RRXRR: RRXRR protein 22.5 39 0.00086 24.7 0.7 40 5-44 107-159 (176)
173 PF14616 DUF4451: Domain of un 22.4 1.1E+02 0.0024 20.6 2.9 16 64-79 25-42 (124)
174 COG1592 Rubrerythrin [Energy p 22.3 39 0.00084 24.4 0.6 17 56-73 142-158 (166)
175 PF13821 DUF4187: Domain of un 21.8 33 0.00071 20.4 0.1 14 64-77 27-40 (55)
176 cd03530 Rieske_NirD_small_Baci 21.5 1.9E+02 0.0042 17.6 3.7 18 62-79 56-73 (98)
177 PF01927 Mut7-C: Mut7-C RNAse 21.4 66 0.0014 21.9 1.6 51 24-76 74-136 (147)
178 PRK02048 4-hydroxy-3-methylbut 21.4 51 0.0011 28.5 1.2 17 58-74 512-528 (611)
179 PTZ00255 60S ribosomal protein 21.3 18 0.00039 23.9 -1.2 10 63-72 35-44 (90)
180 cd01449 TST_Repeat_2 Thiosulfa 21.3 84 0.0018 19.4 2.0 32 26-57 68-108 (118)
181 PRK08116 hypothetical protein; 21.3 44 0.00095 24.9 0.8 15 61-75 13-27 (268)
182 PF09180 ProRS-C_1: Prolyl-tRN 20.9 42 0.00091 20.3 0.5 12 62-73 46-57 (68)
183 PRK00423 tfb transcription ini 20.3 57 0.0012 24.9 1.2 16 60-75 26-41 (310)
No 1
>KOG3456|consensus
Probab=100.00 E-value=2e-39 Score=220.79 Aligned_cols=78 Identities=58% Similarity=1.044 Sum_probs=75.8
Q ss_pred CCCcccCCcCcccccccccChhHHHhhhhcCCCeeecCceEeeCCCCCCCCCCeEEEEcCCCCeeecCCCCceeeecC
Q psy1181 1 KFEKDDYRPVRFVDKEKHVNTQFAIDLIAEVPPKPCKERVVWCDGGSGPTGHPKVYINLDKPGNHSCGYCGLRFFKED 78 (82)
Q Consensus 1 ~~~~~~~~~~rf~~~~~~~n~~~a~~li~e~P~i~v~~r~v~C~Gg~~~lgHP~Vyi~L~~~~~~~CpYCG~~y~~~~ 78 (82)
+||++|||++||++.+|.+|++|||+||+|+||+++++|+|.||||++|||||+||||||+++++.|+|||++|++++
T Consensus 41 ~~D~~Dyr~~rf~~~kk~vn~n~~m~LI~e~Pp~e~d~RVV~CdGg~~aLGHPkvyInLDk~~~~~CgYCGlrf~~dH 118 (120)
T KOG3456|consen 41 VTDQSDYRGNRFVKWKKDVNENSAMELISEVPPIEVDGRVVACDGGTPALGHPKVYINLDKPGPHICGYCGLRFVQDH 118 (120)
T ss_pred ccchHHHhHHHHHhhhhhcCccchhhhhhcCChhhccceEEEecCCCCCCCCCeEEEEcCCCCCcccccchhhhhhhh
Confidence 599999999999999999999999999999999999999999999999999999999999999999999999999843
No 2
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=99.82 E-value=8e-21 Score=109.01 Aligned_cols=39 Identities=54% Similarity=1.147 Sum_probs=34.8
Q ss_pred cCceEeeCCCCCCCCCCeEEEEcCCC-CeeecCCCCceee
Q psy1181 37 KERVVWCDGGSGPTGHPKVYINLDKP-GNHSCGYCGLRFF 75 (82)
Q Consensus 37 ~~r~v~C~Gg~~~lgHP~Vyi~L~~~-~~~~CpYCG~~y~ 75 (82)
++++|+|||+++++|||+|||+|+++ +.+.|||||++|+
T Consensus 1 ~~~~v~CdG~~~~lgHPrVyl~l~~~~~~~~CpYCg~~yv 40 (40)
T PF10276_consen 1 DGRRVSCDGGGGALGHPRVYLNLDDEPGPVVCPYCGTRYV 40 (40)
T ss_dssp -SSEEEEEESSTTSCCCCEEEE-TTTTCEEEETTTTEEEE
T ss_pred CCcEEEeCCCCCCCCCCeEEEecCCCCCeEECCCCCCEEC
Confidence 47899999999999999999999996 7799999999996
No 3
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.71 E-value=1.3e-17 Score=103.53 Aligned_cols=46 Identities=24% Similarity=0.637 Sum_probs=42.9
Q ss_pred CCeeecCceEeeCCCCCCCCCCeEEEEcCCCCeeecCCCCceeeec
Q psy1181 32 PPKPCKERVVWCDGGSGPTGHPKVYINLDKPGNHSCGYCGLRFFKE 77 (82)
Q Consensus 32 P~i~v~~r~v~C~Gg~~~lgHP~Vyi~L~~~~~~~CpYCG~~y~~~ 77 (82)
-.|.+.+..++|+|.+++.+||||||+|.+++++.|||||++|++.
T Consensus 16 ~~I~~~~~~l~C~g~~~p~~HPrV~L~mg~~gev~CPYC~t~y~l~ 61 (62)
T COG4391 16 ETIEIGDLPLMCPGPEPPNDHPRVFLDMGDEGEVVCPYCSTRYRLN 61 (62)
T ss_pred eEEEeCCeeEEcCCCCCCCCCCEEEEEcCCCCcEecCccccEEEec
Confidence 3478899999999999999999999999999999999999999986
No 4
>PLN02294 cytochrome c oxidase subunit Vb
Probab=98.89 E-value=2.8e-09 Score=77.39 Aligned_cols=51 Identities=31% Similarity=0.500 Sum_probs=44.8
Q ss_pred hhhcCCCe---eecCceEeeCCCCCCCCCCeEEEEcCCCCeeecCCCCceeeec
Q psy1181 27 LIAEVPPK---PCKERVVWCDGGSGPTGHPKVYINLDKPGNHSCGYCGLRFFKE 77 (82)
Q Consensus 27 li~e~P~i---~v~~r~v~C~Gg~~~lgHP~Vyi~L~~~~~~~CpYCG~~y~~~ 77 (82)
-+.+-|++ ..+.|+|+|.|+.+...|-.+|++|.+..+.+||.||..|+++
T Consensus 101 GTke~P~lVpS~~d~RiVGCtg~~~eDsh~v~Wf~L~kGkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 101 GTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFELE 154 (174)
T ss_pred CCccCCcEeccCCCceEEeeCCCCCCCCceeEEEEecCCCceeCCCCCCEEEEE
Confidence 45666665 3479999999987888999999999999999999999999998
No 5
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=98.62 E-value=3.6e-08 Score=69.11 Aligned_cols=52 Identities=27% Similarity=0.344 Sum_probs=40.6
Q ss_pred hhhhcCCCe---eecCceEeeCCCCCCCCCCeEEEEcCCCCeeecCCCCceeeecC
Q psy1181 26 DLIAEVPPK---PCKERVVWCDGGSGPTGHPKVYINLDKPGNHSCGYCGLRFFKED 78 (82)
Q Consensus 26 ~li~e~P~i---~v~~r~v~C~Gg~~~lgHP~Vyi~L~~~~~~~CpYCG~~y~~~~ 78 (82)
.-+.+-|++ ..+.|+|+|.|.. ...|..+|++|.+..+.+||.||..|+++.
T Consensus 72 ~GT~e~P~lVpS~~~~RiVGC~g~~-~~sH~v~W~~l~~g~~~RCpeCG~~fkL~~ 126 (136)
T PF01215_consen 72 FGTKEDPILVPSYFDERIVGCTGEP-DDSHDVIWFWLHKGKPQRCPECGQVFKLKY 126 (136)
T ss_dssp --SSSS-CEEEESSSCEEEEESSST-T-SSS-EEEEEETTSEEEETTTEEEEEEEE
T ss_pred CCCccCCeEccCCCCceEEeeccCC-CCcceeEEEEEeCCCccCCCCCCeEEEEEE
Confidence 346677775 3379999999875 568999999999999999999999999976
No 6
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=98.50 E-value=1.6e-07 Score=62.43 Aligned_cols=50 Identities=26% Similarity=0.399 Sum_probs=41.5
Q ss_pred hhcCCCe---eecCceEeeCCCCCCCCCCeEEEEcCCCCeeecCCCCceeeecCC
Q psy1181 28 IAEVPPK---PCKERVVWCDGGSGPTGHPKVYINLDKPGNHSCGYCGLRFFKEDS 79 (82)
Q Consensus 28 i~e~P~i---~v~~r~v~C~Gg~~~lgHP~Vyi~L~~~~~~~CpYCG~~y~~~~~ 79 (82)
+.+-|++ ..+.|+|+|.|..+ .|-.+|++|.+..+.+|+.||..|+++..
T Consensus 42 T~e~P~lVpS~~~~RiVGC~g~~~--~h~v~W~~l~~g~~~rC~eCG~~fkL~~v 94 (97)
T cd00924 42 TKEDPNLVPSAFDKRIVGCICEPD--SHDVIWMWLEKGKPKRCPECGHVFKLVDV 94 (97)
T ss_pred CccCCeEecCCCCCeEEeeeCCCC--CceEEEEEEeCCCceeCCCCCcEEEEEEC
Confidence 4455554 23799999998754 99999999999999999999999999753
No 7
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=98.44 E-value=2.4e-07 Score=70.54 Aligned_cols=52 Identities=29% Similarity=0.406 Sum_probs=43.8
Q ss_pred hhhcCCCe---eecCceEeeCCCCCCCCCCeEEEEcCCCCeeecCCCCceeeecC
Q psy1181 27 LIAEVPPK---PCKERVVWCDGGSGPTGHPKVYINLDKPGNHSCGYCGLRFFKED 78 (82)
Q Consensus 27 li~e~P~i---~v~~r~v~C~Gg~~~lgHP~Vyi~L~~~~~~~CpYCG~~y~~~~ 78 (82)
-+.|-|++ ..+.|+|+|.|+.+...|-.+|+.+.+....+|+.||..|++..
T Consensus 141 GTkEdPiLVpSy~deRyVGCTGg~~EDeH~VvWFwLrEGkpqRCpECGqVFKLVr 195 (268)
T PTZ00043 141 GTIENPVLVPSVGTERVVGCTGGTGEHEHVPLWFRCREGFLYRCGECDQIFMLVR 195 (268)
T ss_pred CCccCCeEeccCCCceEEeccCCCccCCceeEEEEecCCCCccCCCCCcEEEEEE
Confidence 34556664 23699999999887889999999999999999999999999854
No 8
>KOG3352|consensus
Probab=98.33 E-value=5.3e-07 Score=64.47 Aligned_cols=51 Identities=27% Similarity=0.407 Sum_probs=42.9
Q ss_pred hhhcCCCe---eecCceEeeCCCCCCCCCCeEEEEcCCCCeeecCCCCceeeecCC
Q psy1181 27 LIAEVPPK---PCKERVVWCDGGSGPTGHPKVYINLDKPGNHSCGYCGLRFFKEDS 79 (82)
Q Consensus 27 li~e~P~i---~v~~r~v~C~Gg~~~lgHP~Vyi~L~~~~~~~CpYCG~~y~~~~~ 79 (82)
-+.+.|.+ ..+-|+|+| +.+...|+.+|+.|.|.+..+||.||.-|+++..
T Consensus 95 GTkedP~lV~S~~d~RiVGC--~c~eD~~~V~Wmwl~Kge~~rc~eCG~~fkL~~v 148 (153)
T KOG3352|consen 95 GTKEDPNLVPSYYDKRIVGC--GCEEDSHAVVWMWLEKGETQRCPECGHYFKLVPV 148 (153)
T ss_pred CcccCCccccccCCceEEee--cccCCCcceEEEEEEcCCcccCCcccceEEeeec
Confidence 35566765 347999999 5568899999999999999999999999999864
No 9
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=96.24 E-value=0.0017 Score=43.77 Aligned_cols=21 Identities=33% Similarity=0.686 Sum_probs=19.0
Q ss_pred EEEcCCCCeeecCCCCceeeec
Q psy1181 56 YINLDKPGNHSCGYCGLRFFKE 77 (82)
Q Consensus 56 yi~L~~~~~~~CpYCG~~y~~~ 77 (82)
|+.|++ .+++|||||+.|...
T Consensus 19 FYDLnk-~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 19 FYDLNK-DPIVCPKCGTEFPPE 39 (108)
T ss_pred hccCCC-CCccCCCCCCccCcc
Confidence 999998 789999999999776
No 10
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=93.54 E-value=0.031 Score=39.19 Aligned_cols=21 Identities=24% Similarity=0.463 Sum_probs=18.4
Q ss_pred EEEcCCCCeeecCCCCceeeec
Q psy1181 56 YINLDKPGNHSCGYCGLRFFKE 77 (82)
Q Consensus 56 yi~L~~~~~~~CpYCG~~y~~~ 77 (82)
|.+|++ .++.|||||..|...
T Consensus 19 FYDLnk-~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 19 FYDLNR-RPAVSPYTGEQFPPE 39 (129)
T ss_pred ccccCC-CCccCCCcCCccCcc
Confidence 899987 699999999998654
No 11
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=93.53 E-value=0.083 Score=29.88 Aligned_cols=17 Identities=29% Similarity=0.804 Sum_probs=13.8
Q ss_pred CeeecCCCCceeeecCC
Q psy1181 63 GNHSCGYCGLRFFKEDS 79 (82)
Q Consensus 63 ~~~~CpYCG~~y~~~~~ 79 (82)
+...|||||..+..++.
T Consensus 20 ~~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 20 TGVRCPYCGYRILFKER 36 (46)
T ss_pred CceECCCCCCeEEEccC
Confidence 37899999999887653
No 12
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=90.01 E-value=0.19 Score=25.41 Aligned_cols=14 Identities=36% Similarity=0.788 Sum_probs=11.9
Q ss_pred CCeeecCCCCceee
Q psy1181 62 PGNHSCGYCGLRFF 75 (82)
Q Consensus 62 ~~~~~CpYCG~~y~ 75 (82)
+.+..|++|+..|.
T Consensus 12 ~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 12 EKPYKCPYCGKSFS 25 (26)
T ss_dssp SSSEEESSSSEEES
T ss_pred CCCCCCCCCcCeeC
Confidence 45689999999996
No 13
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=89.40 E-value=0.15 Score=24.35 Aligned_cols=12 Identities=33% Similarity=0.850 Sum_probs=10.4
Q ss_pred ecCCCCceeeec
Q psy1181 66 SCGYCGLRFFKE 77 (82)
Q Consensus 66 ~CpYCG~~y~~~ 77 (82)
.|++||+.|...
T Consensus 2 ~C~~C~~~f~~~ 13 (23)
T PF00096_consen 2 KCPICGKSFSSK 13 (23)
T ss_dssp EETTTTEEESSH
T ss_pred CCCCCCCccCCH
Confidence 699999999764
No 14
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=88.58 E-value=0.17 Score=35.26 Aligned_cols=21 Identities=14% Similarity=0.381 Sum_probs=17.2
Q ss_pred EEEEcCCCCeeecCCCCceeee
Q psy1181 55 VYINLDKPGNHSCGYCGLRFFK 76 (82)
Q Consensus 55 Vyi~L~~~~~~~CpYCG~~y~~ 76 (82)
-|.+|+. .++.|||||..|.+
T Consensus 18 KFYDLNr-dPiVsPytG~s~P~ 38 (129)
T COG4530 18 KFYDLNR-DPIVSPYTGKSYPR 38 (129)
T ss_pred hhhccCC-CccccCcccccchH
Confidence 4788875 48999999999965
No 15
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=88.20 E-value=0.23 Score=25.23 Aligned_cols=13 Identities=31% Similarity=0.825 Sum_probs=10.8
Q ss_pred eecCCCCceeeec
Q psy1181 65 HSCGYCGLRFFKE 77 (82)
Q Consensus 65 ~~CpYCG~~y~~~ 77 (82)
..||+||+.|..+
T Consensus 3 ~~C~~CgR~F~~~ 15 (25)
T PF13913_consen 3 VPCPICGRKFNPD 15 (25)
T ss_pred CcCCCCCCEECHH
Confidence 5799999999654
No 16
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=86.43 E-value=0.75 Score=26.37 Aligned_cols=21 Identities=19% Similarity=0.466 Sum_probs=15.3
Q ss_pred EEcCCCCeeecCCCCceeeec
Q psy1181 57 INLDKPGNHSCGYCGLRFFKE 77 (82)
Q Consensus 57 i~L~~~~~~~CpYCG~~y~~~ 77 (82)
++++..+.+.||+||-+-..+
T Consensus 12 ~~~~~~~~irC~~CG~rIlyK 32 (44)
T smart00659 12 NEIKSKDVVRCRECGYRILYK 32 (44)
T ss_pred eecCCCCceECCCCCceEEEE
Confidence 345566789999999876544
No 17
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=85.54 E-value=0.38 Score=22.25 Aligned_cols=13 Identities=31% Similarity=0.789 Sum_probs=8.7
Q ss_pred ecCCCCceeeecC
Q psy1181 66 SCGYCGLRFFKED 78 (82)
Q Consensus 66 ~CpYCG~~y~~~~ 78 (82)
.|++||..|....
T Consensus 2 ~C~~C~~~~~~~~ 14 (24)
T PF13894_consen 2 QCPICGKSFRSKS 14 (24)
T ss_dssp E-SSTS-EESSHH
T ss_pred CCcCCCCcCCcHH
Confidence 6999999997643
No 18
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=85.35 E-value=0.74 Score=25.86 Aligned_cols=23 Identities=22% Similarity=0.651 Sum_probs=17.8
Q ss_pred EEEcCCC--CeeecCCCCceeeecC
Q psy1181 56 YINLDKP--GNHSCGYCGLRFFKED 78 (82)
Q Consensus 56 yi~L~~~--~~~~CpYCG~~y~~~~ 78 (82)
.|+++.. +..+|+-||..|....
T Consensus 3 ~Ld~gq~~~~~~~C~~CgM~Y~~~~ 27 (41)
T PF13878_consen 3 ILDLGQKSFGATTCPTCGMLYSPGS 27 (41)
T ss_pred EEeCCCCccCCcCCCCCCCEECCCC
Confidence 5777765 4789999999997643
No 19
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=85.03 E-value=1.3 Score=24.02 Aligned_cols=23 Identities=22% Similarity=0.478 Sum_probs=18.9
Q ss_pred CCCeEEEEcCCCCeeecCCCCceee
Q psy1181 51 GHPKVYINLDKPGNHSCGYCGLRFF 75 (82)
Q Consensus 51 gHP~Vyi~L~~~~~~~CpYCG~~y~ 75 (82)
+|+.|+.. +.+.-.|+-||..|.
T Consensus 10 ~~~~i~~~--~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 10 GGNGIVNK--EDDYEVCIFCGSSFP 32 (33)
T ss_pred CCCeEEEe--cCCeEEcccCCcEee
Confidence 78888873 567899999999986
No 20
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=83.83 E-value=1 Score=26.83 Aligned_cols=18 Identities=28% Similarity=0.776 Sum_probs=13.7
Q ss_pred CCCeeecCCCCceeeecC
Q psy1181 61 KPGNHSCGYCGLRFFKED 78 (82)
Q Consensus 61 ~~~~~~CpYCG~~y~~~~ 78 (82)
....++|||||-+-..+.
T Consensus 21 ~~~~irCp~Cg~rIl~K~ 38 (49)
T COG1996 21 ETRGIRCPYCGSRILVKE 38 (49)
T ss_pred ccCceeCCCCCcEEEEec
Confidence 456789999998866554
No 21
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=83.35 E-value=1.2 Score=23.86 Aligned_cols=13 Identities=38% Similarity=1.129 Sum_probs=11.0
Q ss_pred CeeecCCCCceee
Q psy1181 63 GNHSCGYCGLRFF 75 (82)
Q Consensus 63 ~~~~CpYCG~~y~ 75 (82)
..+.||.||..|.
T Consensus 24 ~~v~C~~C~~~~~ 36 (38)
T TIGR02098 24 GKVRCGKCGHVWY 36 (38)
T ss_pred CEEECCCCCCEEE
Confidence 4689999999885
No 22
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=81.55 E-value=0.78 Score=27.37 Aligned_cols=12 Identities=33% Similarity=0.697 Sum_probs=9.4
Q ss_pred eecCCCCceeee
Q psy1181 65 HSCGYCGLRFFK 76 (82)
Q Consensus 65 ~~CpYCG~~y~~ 76 (82)
..|||||..+..
T Consensus 1 i~CPyCge~~~~ 12 (52)
T PF14255_consen 1 IQCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCCeeEE
Confidence 369999988754
No 23
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=80.71 E-value=1.1 Score=24.35 Aligned_cols=19 Identities=26% Similarity=0.515 Sum_probs=13.2
Q ss_pred cCCCCeeecCCCCceeeec
Q psy1181 59 LDKPGNHSCGYCGLRFFKE 77 (82)
Q Consensus 59 L~~~~~~~CpYCG~~y~~~ 77 (82)
|.....+.|++||-+-..+
T Consensus 12 ~~~~~~irC~~CG~RIlyK 30 (32)
T PF03604_consen 12 LKPGDPIRCPECGHRILYK 30 (32)
T ss_dssp BSTSSTSSBSSSS-SEEBE
T ss_pred cCCCCcEECCcCCCeEEEe
Confidence 5556778999999875543
No 24
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=79.63 E-value=0.82 Score=25.06 Aligned_cols=17 Identities=24% Similarity=0.528 Sum_probs=10.5
Q ss_pred CCCeeecCCCCceeeec
Q psy1181 61 KPGNHSCGYCGLRFFKE 77 (82)
Q Consensus 61 ~~~~~~CpYCG~~y~~~ 77 (82)
....+.|.||+..|...
T Consensus 13 ~~~~a~C~~C~~~~~~~ 29 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYS 29 (45)
T ss_dssp CSS-EEETTTTEE----
T ss_pred CcCeEEeCCCCeEEeeC
Confidence 35789999999999875
No 25
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=77.40 E-value=0.94 Score=26.17 Aligned_cols=10 Identities=50% Similarity=1.368 Sum_probs=8.0
Q ss_pred eecCCCCcee
Q psy1181 65 HSCGYCGLRF 74 (82)
Q Consensus 65 ~~CpYCG~~y 74 (82)
-+|||||.-|
T Consensus 3 f~CP~C~~~~ 12 (54)
T PF05605_consen 3 FTCPYCGKGF 12 (54)
T ss_pred cCCCCCCCcc
Confidence 5799999944
No 26
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=75.71 E-value=0.85 Score=34.65 Aligned_cols=19 Identities=32% Similarity=0.665 Sum_probs=14.3
Q ss_pred CCCeeecCCCCceeeecCC
Q psy1181 61 KPGNHSCGYCGLRFFKEDS 79 (82)
Q Consensus 61 ~~~~~~CpYCG~~y~~~~~ 79 (82)
++..+.|||||+.-+++.+
T Consensus 218 ~d~iv~CP~CgRILy~~e~ 236 (239)
T COG1579 218 KDEIVFCPYCGRILYYDES 236 (239)
T ss_pred CCCCccCCccchHHHhhhc
Confidence 3467899999997766554
No 27
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=75.16 E-value=4.2 Score=23.06 Aligned_cols=16 Identities=25% Similarity=0.794 Sum_probs=13.1
Q ss_pred CeeecCCCCceeeecC
Q psy1181 63 GNHSCGYCGLRFFKED 78 (82)
Q Consensus 63 ~~~~CpYCG~~y~~~~ 78 (82)
..+.|.||++.|....
T Consensus 17 ~~a~C~~C~~~l~~~~ 32 (50)
T smart00614 17 QRAKCKYCGKKLSRSS 32 (50)
T ss_pred eEEEecCCCCEeeeCC
Confidence 3589999999997653
No 28
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=74.93 E-value=2.1 Score=23.34 Aligned_cols=16 Identities=31% Similarity=0.536 Sum_probs=12.4
Q ss_pred eeecCCCCceeeecCC
Q psy1181 64 NHSCGYCGLRFFKEDS 79 (82)
Q Consensus 64 ~~~CpYCG~~y~~~~~ 79 (82)
..+||-|++.|...+.
T Consensus 2 ~i~CP~C~~~f~v~~~ 17 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDD 17 (37)
T ss_pred EEECCCCCceEEcCHH
Confidence 4689999999987653
No 29
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=74.58 E-value=5.1 Score=22.13 Aligned_cols=24 Identities=25% Similarity=0.599 Sum_probs=15.0
Q ss_pred CCCeEEEEcCCCCeeecCCCCceee
Q psy1181 51 GHPKVYINLDKPGNHSCGYCGLRFF 75 (82)
Q Consensus 51 gHP~Vyi~L~~~~~~~CpYCG~~y~ 75 (82)
|...+..+ ...|...|+.||..-.
T Consensus 7 g~~~~~~D-~~~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 7 GSKEIVFD-PERGELVCPNCGLVLE 30 (43)
T ss_dssp SSSEEEEE-TTTTEEEETTT-BBEE
T ss_pred cCCceEEc-CCCCeEECCCCCCEee
Confidence 33444444 3468899999998754
No 30
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=73.55 E-value=4 Score=24.13 Aligned_cols=23 Identities=26% Similarity=0.571 Sum_probs=14.1
Q ss_pred EEEEcCC-CCeeecCCCCceeeec
Q psy1181 55 VYINLDK-PGNHSCGYCGLRFFKE 77 (82)
Q Consensus 55 Vyi~L~~-~~~~~CpYCG~~y~~~ 77 (82)
.|.-+++ +..-+|-||++.|..+
T Consensus 25 ~F~v~~~~~~~~rC~YCe~~~~~~ 48 (52)
T PF02748_consen 25 RFYVIDKEPIKLRCHYCERIITED 48 (52)
T ss_dssp EEEEEETTTCEEEETTT--EEEHH
T ss_pred eEEEEeCCCCEEEeeCCCCEeccc
Confidence 3433443 5678999999998754
No 31
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=72.37 E-value=3.1 Score=26.49 Aligned_cols=36 Identities=31% Similarity=0.503 Sum_probs=19.8
Q ss_pred CceEeeCCCCCCCC-CCeEEEEcCCC---CeeecCCCCceeeec
Q psy1181 38 ERVVWCDGGSGPTG-HPKVYINLDKP---GNHSCGYCGLRFFKE 77 (82)
Q Consensus 38 ~r~v~C~Gg~~~lg-HP~Vyi~L~~~---~~~~CpYCG~~y~~~ 77 (82)
...+.|+== + .--|-+.|++. +...|..||..|...
T Consensus 20 ~~~F~CPfC----~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 20 PKVFDCPFC----NHEKSVSVKIDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp SS----TTT------SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred CceEcCCcC----CCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence 356777432 4 34578888875 568999999999764
No 32
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=71.69 E-value=2.9 Score=23.45 Aligned_cols=15 Identities=33% Similarity=0.857 Sum_probs=12.6
Q ss_pred CeeecCCCCceeeec
Q psy1181 63 GNHSCGYCGLRFFKE 77 (82)
Q Consensus 63 ~~~~CpYCG~~y~~~ 77 (82)
|...|++||..+...
T Consensus 4 g~l~C~~CG~~m~~~ 18 (58)
T PF13408_consen 4 GLLRCGHCGSKMTRR 18 (58)
T ss_pred CcEEcccCCcEeEEE
Confidence 678999999998764
No 33
>PF14369 zf-RING_3: zinc-finger
Probab=71.68 E-value=3.9 Score=22.30 Aligned_cols=14 Identities=21% Similarity=0.543 Sum_probs=11.0
Q ss_pred CeeecCCCCceeee
Q psy1181 63 GNHSCGYCGLRFFK 76 (82)
Q Consensus 63 ~~~~CpYCG~~y~~ 76 (82)
....||+|+..|+.
T Consensus 20 ~~~~CP~C~~gFvE 33 (35)
T PF14369_consen 20 SDVACPRCHGGFVE 33 (35)
T ss_pred CCcCCcCCCCcEeE
Confidence 34579999999975
No 34
>KOG1088|consensus
Probab=70.69 E-value=3.2 Score=28.99 Aligned_cols=18 Identities=28% Similarity=0.364 Sum_probs=15.3
Q ss_pred CCeeecCCCCceeeecCC
Q psy1181 62 PGNHSCGYCGLRFFKEDS 79 (82)
Q Consensus 62 ~~~~~CpYCG~~y~~~~~ 79 (82)
+|...||.||+.|.-..|
T Consensus 96 EG~l~CpetG~vfpI~~G 113 (124)
T KOG1088|consen 96 EGELVCPETGRVFPISDG 113 (124)
T ss_pred cceEecCCCCcEeecccC
Confidence 588999999999976654
No 35
>PHA02768 hypothetical protein; Provisional
Probab=69.95 E-value=1.2 Score=27.02 Aligned_cols=13 Identities=31% Similarity=0.833 Sum_probs=11.3
Q ss_pred ecCCCCceeeecC
Q psy1181 66 SCGYCGLRFFKED 78 (82)
Q Consensus 66 ~CpYCG~~y~~~~ 78 (82)
.|+.||++|....
T Consensus 7 ~C~~CGK~Fs~~~ 19 (55)
T PHA02768 7 ECPICGEIYIKRK 19 (55)
T ss_pred CcchhCCeeccHH
Confidence 7999999998765
No 36
>PF08685 GON: GON domain; InterPro: IPR012314 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. The ADAMTSs (a disintegrin and metalloproteinase domain with thrombospondin type-1 modules) are a family of zinc dependent metalloproteinases that play important roles in a variety of normal and pathological conditions. These enzymes show a complex domain organisation including signal sequence, propeptide, metalloproteinase domain (see PDOC50215 from PROSITEDOC), disintegrin-like domain (see PDOC00351 from PROSITEDOC), central TS-1 motif (see PDOC50092 from PROSITEDOC), cysteine-rich region, and a variable number of TS-like repeats at the C-terminal region. The GON domain is an approximately 200-residue module, whose presence is the hallmark of a subfamily of structurally and evolutionarily related ADAMTSs, called GON- ADAMTSs. The GON domain is characterised by the presence of several conserved cysteine residues and is likely to be globular [], []. Some proteins known to contain a GON domain are listed below: Mammalian ADAMTS-9 Mammalian ADAMTS-20 Caenorhabditis elegans gon-1, a protease required for gonadal morphogenesis Proteins containing the GON domain belong to MEROPS peptidase subfamily M12B (adamalysin, clan MA).; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding
Probab=68.08 E-value=6.9 Score=29.19 Aligned_cols=33 Identities=30% Similarity=0.663 Sum_probs=24.7
Q ss_pred eEeeCCCCCCCCCCeEEEEcCCC--------------CeeecCCCCcee
Q psy1181 40 VVWCDGGSGPTGHPKVYINLDKP--------------GNHSCGYCGLRF 74 (82)
Q Consensus 40 ~v~C~Gg~~~lgHP~Vyi~L~~~--------------~~~~CpYCG~~y 74 (82)
.|.|-| ++.+.|+.||+|.+. .+..|||=|.+.
T Consensus 30 ~IYCh~--M~s~~PkEYltL~~G~~eNyae~y~~Rl~~~~~Cp~ng~~~ 76 (201)
T PF08685_consen 30 KIYCHG--MASSTPKEYLTLPSGPQENYAEVYGKRLQNPSECPYNGSRR 76 (201)
T ss_pred EEEcCC--CCCCCCceeEEcCCCCccchheecchhccCCCcCCCCCCCC
Confidence 589964 789999999999832 134699777664
No 37
>PF01430 HSP33: Hsp33 protein; InterPro: IPR000397 Hsp33 is a molecular chaperone, distinguished from all other known chaperones by its mode of functional regulation. Its activity is redox regulated. Hsp33 is a cytoplasmically localized protein with highly reactive cysteines that respond quickly to changes in the redox environment. Oxidizing conditions like H2O2 cause disulphide bonds to form in Hsp33, a process that leads to the activation of its chaperone function [].; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0005737 cytoplasm; PDB: 1VZY_B 1VQ0_A 1I7F_A 3M7M_X 1XJH_A 1HW7_A.
Probab=67.91 E-value=3.2 Score=31.24 Aligned_cols=14 Identities=21% Similarity=0.795 Sum_probs=9.1
Q ss_pred eeecCCCCceeeec
Q psy1181 64 NHSCGYCGLRFFKE 77 (82)
Q Consensus 64 ~~~CpYCG~~y~~~ 77 (82)
+++|.|||++|..+
T Consensus 266 ev~C~fC~~~Y~f~ 279 (280)
T PF01430_consen 266 EVTCEFCGKKYRFT 279 (280)
T ss_dssp EEE-TTT--EEEEE
T ss_pred EEEeeCCCCEEEeC
Confidence 57999999999864
No 38
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=67.06 E-value=5.1 Score=24.13 Aligned_cols=18 Identities=28% Similarity=0.584 Sum_probs=15.0
Q ss_pred CCeeecCCCCceeeecCC
Q psy1181 62 PGNHSCGYCGLRFFKEDS 79 (82)
Q Consensus 62 ~~~~~CpYCG~~y~~~~~ 79 (82)
+|.-.||-||+.|.-++|
T Consensus 51 eg~L~Cp~c~r~YPI~dG 68 (68)
T PF03966_consen 51 EGELICPECGREYPIRDG 68 (68)
T ss_dssp TTEEEETTTTEEEEEETT
T ss_pred CCEEEcCCCCCEEeCCCC
Confidence 588999999999976654
No 39
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=66.04 E-value=9.3 Score=21.55 Aligned_cols=36 Identities=19% Similarity=0.480 Sum_probs=21.2
Q ss_pred cCceEeeCCCCCCCCCCeEEEEc--CCCCeeecCCCCceeee
Q psy1181 37 KERVVWCDGGSGPTGHPKVYINL--DKPGNHSCGYCGLRFFK 76 (82)
Q Consensus 37 ~~r~v~C~Gg~~~lgHP~Vyi~L--~~~~~~~CpYCG~~y~~ 76 (82)
+.....|++.+= ..+.+.. .....+.|+.||..|=.
T Consensus 15 ~~~~~~CP~~~C----~~~~~~~~~~~~~~v~C~~C~~~fC~ 52 (64)
T smart00647 15 NPDLKWCPAPDC----SAAIIVTEEEGCNRVTCPKCGFSFCF 52 (64)
T ss_pred CCCccCCCCCCC----cceEEecCCCCCCeeECCCCCCeECC
Confidence 345678985421 1112222 14567999999999854
No 40
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=65.67 E-value=4.8 Score=22.66 Aligned_cols=18 Identities=22% Similarity=0.416 Sum_probs=12.7
Q ss_pred EEEEcCCCCeeecCCCCc
Q psy1181 55 VYINLDKPGNHSCGYCGL 72 (82)
Q Consensus 55 Vyi~L~~~~~~~CpYCG~ 72 (82)
++..++.+....||.||.
T Consensus 17 ~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 17 VLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEecCCCCCCCCCCCCC
Confidence 344555556678999997
No 41
>PF14353 CpXC: CpXC protein
Probab=65.63 E-value=4.2 Score=26.88 Aligned_cols=15 Identities=33% Similarity=0.704 Sum_probs=12.2
Q ss_pred eeecCCCCceeeecC
Q psy1181 64 NHSCGYCGLRFFKED 78 (82)
Q Consensus 64 ~~~CpYCG~~y~~~~ 78 (82)
..+||.||..|....
T Consensus 38 ~~~CP~Cg~~~~~~~ 52 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEY 52 (128)
T ss_pred EEECCCCCCceecCC
Confidence 479999999997653
No 42
>TIGR03365 Bsubt_queE 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE. This uncharacterized enzyme, designated QueE, participates in the biosynthesis, from GTP, of 7-cyano-7-deazaguanosine, also called preQ0 because in many species it is a precursor of queuosine. In most Archaea, it is instead the precursor of a different tRNA modified base, archaeosine.
Probab=64.88 E-value=6.3 Score=28.85 Aligned_cols=34 Identities=15% Similarity=0.331 Sum_probs=26.8
Q ss_pred eeCCCCCCCCCCeEEEEcCCCCeeecCCCCceeee
Q psy1181 42 WCDGGSGPTGHPKVYINLDKPGNHSCGYCGLRFFK 76 (82)
Q Consensus 42 ~C~Gg~~~lgHP~Vyi~L~~~~~~~CpYCG~~y~~ 76 (82)
+-.|-|.-.|-|.|||.+. .-..+|+||.+.+..
T Consensus 12 SiQGEG~~~G~~~~FvR~~-gCNlrC~~Cdt~~~~ 45 (238)
T TIGR03365 12 TIQGEGMVIGQKTMFVRTG-GCDYRCSWCDSLFTW 45 (238)
T ss_pred ccccCccccCCeEEEEEeC-CcCCcCcCCCCcccc
Confidence 5566655679999999987 457899999988743
No 43
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=64.24 E-value=2.6 Score=21.04 Aligned_cols=12 Identities=25% Similarity=0.592 Sum_probs=8.7
Q ss_pred CCeeecCCCCce
Q psy1181 62 PGNHSCGYCGLR 73 (82)
Q Consensus 62 ~~~~~CpYCG~~ 73 (82)
++..-|++||..
T Consensus 11 ~~~~fC~~CG~~ 22 (23)
T PF13240_consen 11 DDAKFCPNCGTP 22 (23)
T ss_pred CcCcchhhhCCc
Confidence 345679999875
No 44
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=64.21 E-value=3.2 Score=25.24 Aligned_cols=28 Identities=25% Similarity=0.451 Sum_probs=18.8
Q ss_pred CCCeEEEEcCCCCeeecCCCCceeeecC
Q psy1181 51 GHPKVYINLDKPGNHSCGYCGLRFFKED 78 (82)
Q Consensus 51 gHP~Vyi~L~~~~~~~CpYCG~~y~~~~ 78 (82)
||=.=.-..+.+...-||.||++|...+
T Consensus 26 gH~I~~~~f~~~rYngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 26 GHLICDNCFPGERYNGCPFCGTPFEFDD 53 (55)
T ss_pred cceeeccccChhhccCCCCCCCcccCCC
Confidence 6644444444456688999999997653
No 45
>PF06957 COPI_C: Coatomer (COPI) alpha subunit C-terminus; InterPro: IPR010714 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit [, ]. This domain is found along with the IPR006692 from INTERPRO domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat; PDB: 3MKR_B 3MV2_E 3MKQ_B 3MV3_A.
Probab=63.02 E-value=4.9 Score=32.83 Aligned_cols=15 Identities=27% Similarity=0.877 Sum_probs=9.0
Q ss_pred CCeeecCCCCceeee
Q psy1181 62 PGNHSCGYCGLRFFK 76 (82)
Q Consensus 62 ~~~~~CpYCG~~y~~ 76 (82)
...+.|||||.+|.-
T Consensus 378 ~~~v~CP~cgA~y~~ 392 (422)
T PF06957_consen 378 SPSVKCPYCGAKYHP 392 (422)
T ss_dssp S-EEE-TTT--EEEG
T ss_pred CCCeeCCCCCCccCh
Confidence 356899999999974
No 46
>COG1281 Disulfide bond chaperones of the HSP33 family [Posttranslational modification, protein turnover, chaperones]
Probab=62.94 E-value=4.7 Score=31.48 Aligned_cols=16 Identities=19% Similarity=0.841 Sum_probs=13.5
Q ss_pred CeeecCCCCceeeecC
Q psy1181 63 GNHSCGYCGLRFFKED 78 (82)
Q Consensus 63 ~~~~CpYCG~~y~~~~ 78 (82)
-++.|.+||++|..+.
T Consensus 265 iev~C~FC~~~Y~f~~ 280 (286)
T COG1281 265 IEVTCEFCGTKYLFDE 280 (286)
T ss_pred eEEEeeccCCEEecCH
Confidence 3589999999998764
No 47
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=62.79 E-value=4.8 Score=23.36 Aligned_cols=41 Identities=20% Similarity=0.213 Sum_probs=26.9
Q ss_pred cCCCeeecCceEeeCCCCCCCCCCeEEEEcCCC-CeeecCCCCce
Q psy1181 30 EVPPKPCKERVVWCDGGSGPTGHPKVYINLDKP-GNHSCGYCGLR 73 (82)
Q Consensus 30 e~P~i~v~~r~v~C~Gg~~~lgHP~Vyi~L~~~-~~~~CpYCG~~ 73 (82)
..++..+.+. .|.|-.. .--|.++..|... +...||+||+.
T Consensus 14 g~~va~v~~~--~C~gC~~-~l~~~~~~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 14 GVAVARVEGG--TCSGCHM-ELPPQELNEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred CcEEEEeeCC--ccCCCCE-EcCHHHHHHHHcCCCeEECcCCCcc
Confidence 4455566665 7876532 2456667777554 67999999974
No 48
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=61.79 E-value=5.8 Score=21.56 Aligned_cols=16 Identities=19% Similarity=0.495 Sum_probs=11.9
Q ss_pred eeecCCCCceeeecCC
Q psy1181 64 NHSCGYCGLRFFKEDS 79 (82)
Q Consensus 64 ~~~CpYCG~~y~~~~~ 79 (82)
.++||-|+++|..++.
T Consensus 2 ~i~Cp~C~~~y~i~d~ 17 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDE 17 (36)
T ss_pred EEECCCCCCEEeCCHH
Confidence 4678888888877653
No 49
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=60.75 E-value=3.6 Score=25.03 Aligned_cols=19 Identities=16% Similarity=0.377 Sum_probs=10.1
Q ss_pred EcCCCCeeecCCCCceeee
Q psy1181 58 NLDKPGNHSCGYCGLRFFK 76 (82)
Q Consensus 58 ~L~~~~~~~CpYCG~~y~~ 76 (82)
.+....+.+||.|+..+.+
T Consensus 18 ~~~S~~PatCP~C~a~~~~ 36 (54)
T PF09237_consen 18 KSQSEQPATCPICGAVIRQ 36 (54)
T ss_dssp CCTTS--EE-TTT--EESS
T ss_pred hhccCCCCCCCcchhhccc
Confidence 3445678999999998764
No 50
>cd00498 Hsp33 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat shock), the Cys are reversibly oxidized to disulfide bonds, which causes the chaperone activity to be turned on. Hsp33 is homodimeric in its functional form.
Probab=60.32 E-value=5.3 Score=30.13 Aligned_cols=13 Identities=23% Similarity=0.920 Sum_probs=11.5
Q ss_pred eeecCCCCceeee
Q psy1181 64 NHSCGYCGLRFFK 76 (82)
Q Consensus 64 ~~~CpYCG~~y~~ 76 (82)
+++|.|||+.|..
T Consensus 262 ev~C~FC~~~Y~f 274 (275)
T cd00498 262 EVTCEFCGEKYHF 274 (275)
T ss_pred EEEEeCCCCEEec
Confidence 5899999999975
No 51
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=60.24 E-value=5.5 Score=22.94 Aligned_cols=12 Identities=25% Similarity=0.620 Sum_probs=6.3
Q ss_pred eecCCCCceeee
Q psy1181 65 HSCGYCGLRFFK 76 (82)
Q Consensus 65 ~~CpYCG~~y~~ 76 (82)
..||-||+-|-.
T Consensus 21 ~~CPlC~r~l~~ 32 (54)
T PF04423_consen 21 GCCPLCGRPLDE 32 (54)
T ss_dssp EE-TTT--EE-H
T ss_pred CcCCCCCCCCCH
Confidence 399999998853
No 52
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=59.47 E-value=4.1 Score=26.63 Aligned_cols=43 Identities=19% Similarity=0.409 Sum_probs=18.7
Q ss_pred ecCceEeeCCCCCCCCCCeEEEEcCCCCeeecCCCCceeeecC
Q psy1181 36 CKERVVWCDGGSGPTGHPKVYINLDKPGNHSCGYCGLRFFKED 78 (82)
Q Consensus 36 v~~r~v~C~Gg~~~lgHP~Vyi~L~~~~~~~CpYCG~~y~~~~ 78 (82)
-+.+.+.|..|.--.-=-.-|+.|...+...|+.||+++....
T Consensus 27 ~~~~~~~C~~GH~w~RC~lT~l~i~~~~~r~C~~C~~~~l~~~ 69 (99)
T PF12660_consen 27 DDLDEAQCENGHVWPRCALTFLPIQTPGVRVCPVCGRRALDPE 69 (99)
T ss_dssp --SSEEE-TTS-EEEB-SSS-SBS-SS-EEE-TTT--EEE-GG
T ss_pred CCcCEeECCCCCEEeeeeeeeeeeccCCeeEcCCCCCEEecCc
Confidence 3445677865432000122367788888889999998886543
No 53
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=58.04 E-value=3.7 Score=20.70 Aligned_cols=12 Identities=33% Similarity=0.924 Sum_probs=8.6
Q ss_pred CCeeecCCCCce
Q psy1181 62 PGNHSCGYCGLR 73 (82)
Q Consensus 62 ~~~~~CpYCG~~ 73 (82)
.+...||+||..
T Consensus 14 ~~~~fC~~CG~~ 25 (26)
T PF13248_consen 14 PDAKFCPNCGAK 25 (26)
T ss_pred cccccChhhCCC
Confidence 356678888875
No 54
>PRK00114 hslO Hsp33-like chaperonin; Reviewed
Probab=57.96 E-value=6.5 Score=29.98 Aligned_cols=15 Identities=20% Similarity=0.915 Sum_probs=12.8
Q ss_pred eeecCCCCceeeecC
Q psy1181 64 NHSCGYCGLRFFKED 78 (82)
Q Consensus 64 ~~~CpYCG~~y~~~~ 78 (82)
+++|.||++.|....
T Consensus 268 ev~C~FC~~~Y~f~~ 282 (293)
T PRK00114 268 EMVCQFCGNKYLFDE 282 (293)
T ss_pred EEEEeCCCCEEEeCH
Confidence 589999999998753
No 55
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=57.82 E-value=7.9 Score=23.39 Aligned_cols=16 Identities=19% Similarity=0.488 Sum_probs=12.8
Q ss_pred CCCeeecCCCCceeee
Q psy1181 61 KPGNHSCGYCGLRFFK 76 (82)
Q Consensus 61 ~~~~~~CpYCG~~y~~ 76 (82)
++..+.||-||+.|-+
T Consensus 18 ~dDiVvCp~CgapyHR 33 (54)
T PF14446_consen 18 GDDIVVCPECGAPYHR 33 (54)
T ss_pred CCCEEECCCCCCcccH
Confidence 4568999999998854
No 56
>PF15616 TerY-C: TerY-C metal binding domain
Probab=57.54 E-value=6.8 Score=27.36 Aligned_cols=21 Identities=24% Similarity=0.469 Sum_probs=15.2
Q ss_pred EEcCCCCeeecCCCCceeeec
Q psy1181 57 INLDKPGNHSCGYCGLRFFKE 77 (82)
Q Consensus 57 i~L~~~~~~~CpYCG~~y~~~ 77 (82)
+=++.++.++||+||..=...
T Consensus 98 ~Ci~g~~~~~CPwCg~~g~~~ 118 (131)
T PF15616_consen 98 FCIDGEGEVTCPWCGNEGSFG 118 (131)
T ss_pred EEeCCCCCEECCCCCCeeeec
Confidence 345667789999999875443
No 57
>KOG2462|consensus
Probab=57.31 E-value=5.8 Score=31.05 Aligned_cols=21 Identities=33% Similarity=0.708 Sum_probs=13.9
Q ss_pred EcCCCCeeecCCCCceeeecC
Q psy1181 58 NLDKPGNHSCGYCGLRFFKED 78 (82)
Q Consensus 58 ~L~~~~~~~CpYCG~~y~~~~ 78 (82)
.|+......|+|||++|+.-+
T Consensus 155 ~~~s~ka~~C~~C~K~YvSmp 175 (279)
T KOG2462|consen 155 SLDSKKAFSCKYCGKVYVSMP 175 (279)
T ss_pred cccccccccCCCCCceeeehH
Confidence 344445567888888887543
No 58
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=57.12 E-value=9.4 Score=21.15 Aligned_cols=18 Identities=22% Similarity=0.501 Sum_probs=13.9
Q ss_pred EEEEcCCCCeeecCCCCc
Q psy1181 55 VYINLDKPGNHSCGYCGL 72 (82)
Q Consensus 55 Vyi~L~~~~~~~CpYCG~ 72 (82)
+...+..+....||-||.
T Consensus 17 ~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 17 VLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEEEcCCCCCCcCCCCCC
Confidence 455666667789999998
No 59
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=55.88 E-value=11 Score=25.85 Aligned_cols=45 Identities=18% Similarity=0.265 Sum_probs=25.6
Q ss_pred eeecCceEeeCCCCCCCCCCeEEEEc-CCCCeeecCCCCceeeecCC
Q psy1181 34 KPCKERVVWCDGGSGPTGHPKVYINL-DKPGNHSCGYCGLRFFKEDS 79 (82)
Q Consensus 34 i~v~~r~v~C~Gg~~~lgHP~Vyi~L-~~~~~~~CpYCG~~y~~~~~ 79 (82)
.+.+.....|+.-+.-.. -...+.+ +.++...||+||......+.
T Consensus 93 ~e~~~~~Y~Cp~C~~~y~-~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn 138 (147)
T smart00531 93 DETNNAYYKCPNCQSKYT-FLEANQLLDMDGTFTCPRCGEELEEDDN 138 (147)
T ss_pred cccCCcEEECcCCCCEee-HHHHHHhcCCCCcEECCCCCCEEEEcCc
Confidence 345666788975432111 0011122 34566999999998876653
No 60
>smart00355 ZnF_C2H2 zinc finger.
Probab=54.62 E-value=4.8 Score=18.28 Aligned_cols=12 Identities=33% Similarity=0.722 Sum_probs=9.8
Q ss_pred ecCCCCceeeec
Q psy1181 66 SCGYCGLRFFKE 77 (82)
Q Consensus 66 ~CpYCG~~y~~~ 77 (82)
.|+.|+..|...
T Consensus 2 ~C~~C~~~f~~~ 13 (26)
T smart00355 2 RCPECGKVFKSK 13 (26)
T ss_pred CCCCCcchhCCH
Confidence 599999998654
No 61
>TIGR00240 ATCase_reg aspartate carbamoyltransferase, regulatory subunit. The presence of this regulatory subunit allows feedback inhibition by CTP on aspartate carbamoyltransferase, the first step in the synthesis of CTP from aspartate. In many species, this regulatory subunit is not present. In Thermotoga maritima, the catalytic and regulatory subunits are encoded by a fused gene and the regulatory region has enough sequence differences to score below the trusted cutoff.
Probab=54.04 E-value=14 Score=26.45 Aligned_cols=40 Identities=15% Similarity=0.214 Sum_probs=25.3
Q ss_pred CceEeeCCCCC---CCCCCeEEEEcCCC--CeeecCCCCceeeec
Q psy1181 38 ERVVWCDGGSG---PTGHPKVYINLDKP--GNHSCGYCGLRFFKE 77 (82)
Q Consensus 38 ~r~v~C~Gg~~---~lgHP~Vyi~L~~~--~~~~CpYCG~~y~~~ 77 (82)
..++.|+.+.= .-.=+..|.-++++ ..-+|-||++.|..+
T Consensus 101 ~gi~kC~Np~CIT~~E~v~~~F~v~~~~~~~~lrC~YCe~~~~~~ 145 (150)
T TIGR00240 101 EGVLKCPNPNCISNAEPVSSKFYVRSEEPDIALRCYYCEKEIEHN 145 (150)
T ss_pred eeeEECCCCCCccCCCCCCcEEEEecCCCceEEEEECCCCEEecc
Confidence 34688876532 11234556555655 368999999999754
No 62
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=53.66 E-value=13 Score=19.54 Aligned_cols=13 Identities=23% Similarity=0.414 Sum_probs=9.9
Q ss_pred CCeeecCCCCcee
Q psy1181 62 PGNHSCGYCGLRF 74 (82)
Q Consensus 62 ~~~~~CpYCG~~y 74 (82)
.....||.||...
T Consensus 24 ~~~~~CP~Cg~~~ 36 (41)
T smart00834 24 DPLATCPECGGDV 36 (41)
T ss_pred CCCCCCCCCCCcc
Confidence 4567899999854
No 63
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=52.77 E-value=9.2 Score=22.88 Aligned_cols=15 Identities=27% Similarity=0.698 Sum_probs=11.0
Q ss_pred CeeecCCCCceeeec
Q psy1181 63 GNHSCGYCGLRFFKE 77 (82)
Q Consensus 63 ~~~~CpYCG~~y~~~ 77 (82)
....|.+|+..|...
T Consensus 49 ~~~~C~~C~~~f~s~ 63 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSR 63 (100)
T ss_dssp SSEEBSSSS-EESSH
T ss_pred CCCCCCccCCCCcCH
Confidence 358999999999643
No 64
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=52.54 E-value=15 Score=24.22 Aligned_cols=37 Identities=24% Similarity=0.638 Sum_probs=26.3
Q ss_pred EeeCCCCCCCCCCeEEEEcCCC---------CeeecCCCCceeeec
Q psy1181 41 VWCDGGSGPTGHPKVYINLDKP---------GNHSCGYCGLRFFKE 77 (82)
Q Consensus 41 v~C~Gg~~~lgHP~Vyi~L~~~---------~~~~CpYCG~~y~~~ 77 (82)
..|.|+....|-=.+++++.+. -...|+-||-.|..+
T Consensus 3 ~~C~~~~~~~~~tTv~~el~~G~~~IvIknVPa~~C~~CGe~y~~d 48 (89)
T TIGR03829 3 RWCEEEKAIARTTTVYWELPDGTKAIEIKETPSISCSHCGMEYQDD 48 (89)
T ss_pred cccCCCceecceEEEEEEecCCceEEEEecCCcccccCCCcEeecH
Confidence 3687766556777888888542 125799999999764
No 65
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=50.85 E-value=9.3 Score=18.47 Aligned_cols=13 Identities=31% Similarity=0.675 Sum_probs=10.6
Q ss_pred eecCCCCceeeec
Q psy1181 65 HSCGYCGLRFFKE 77 (82)
Q Consensus 65 ~~CpYCG~~y~~~ 77 (82)
..|..|+..|...
T Consensus 2 ~~C~~C~~~F~~~ 14 (27)
T PF13912_consen 2 FECDECGKTFSSL 14 (27)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCccCCccCCh
Confidence 4799999999653
No 66
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=50.02 E-value=18 Score=25.35 Aligned_cols=28 Identities=29% Similarity=0.564 Sum_probs=20.0
Q ss_pred eeCCCCCCCCCCeEEEEcCCCCeeecCCCCceeeec
Q psy1181 42 WCDGGSGPTGHPKVYINLDKPGNHSCGYCGLRFFKE 77 (82)
Q Consensus 42 ~C~Gg~~~lgHP~Vyi~L~~~~~~~CpYCG~~y~~~ 77 (82)
.|+--+.|| | . ++|.+.||-||.+++..
T Consensus 30 hCp~Cg~PL-----F-~--KdG~v~CPvC~~~~~~v 57 (131)
T COG1645 30 HCPKCGTPL-----F-R--KDGEVFCPVCGYREVVV 57 (131)
T ss_pred hCcccCCcc-----e-e--eCCeEECCCCCceEEEe
Confidence 576555566 2 2 89999999999776543
No 67
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=48.80 E-value=9.5 Score=21.16 Aligned_cols=16 Identities=25% Similarity=0.509 Sum_probs=10.3
Q ss_pred CeeecCCCCceeeecC
Q psy1181 63 GNHSCGYCGLRFFKED 78 (82)
Q Consensus 63 ~~~~CpYCG~~y~~~~ 78 (82)
-+..|++|+..|=.++
T Consensus 12 ~~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKH 27 (43)
T ss_dssp SHEE-TTTS-EE-TTT
T ss_pred CCeECCCCCcccCccc
Confidence 3678999999997655
No 68
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=48.40 E-value=21 Score=19.43 Aligned_cols=25 Identities=20% Similarity=0.385 Sum_probs=13.6
Q ss_pred CCCeEEEEcC--CCCeeecCCCCceee
Q psy1181 51 GHPKVYINLD--KPGNHSCGYCGLRFF 75 (82)
Q Consensus 51 gHP~Vyi~L~--~~~~~~CpYCG~~y~ 75 (82)
|+|..+.-++ ......|+=||....
T Consensus 7 G~~l~~~ip~gd~r~R~vC~~Cg~IhY 33 (34)
T PF14803_consen 7 GGPLERRIPEGDDRERLVCPACGFIHY 33 (34)
T ss_dssp --B-EEE--TT-SS-EEEETTTTEEE-
T ss_pred cChhhhhcCCCCCccceECCCCCCEEe
Confidence 7777777773 345689999997653
No 69
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=47.58 E-value=9.5 Score=18.83 Aligned_cols=12 Identities=33% Similarity=0.642 Sum_probs=10.1
Q ss_pred ecCCCCceeeec
Q psy1181 66 SCGYCGLRFFKE 77 (82)
Q Consensus 66 ~CpYCG~~y~~~ 77 (82)
.|.+|++.|...
T Consensus 3 ~C~~C~k~f~~~ 14 (27)
T PF12171_consen 3 YCDACDKYFSSE 14 (27)
T ss_dssp BBTTTTBBBSSH
T ss_pred CcccCCCCcCCH
Confidence 699999999754
No 70
>PHA00616 hypothetical protein
Probab=47.43 E-value=3.9 Score=23.75 Aligned_cols=13 Identities=38% Similarity=0.654 Sum_probs=10.9
Q ss_pred ecCCCCceeeecC
Q psy1181 66 SCGYCGLRFFKED 78 (82)
Q Consensus 66 ~CpYCG~~y~~~~ 78 (82)
.|+-||..|..+.
T Consensus 3 qC~~CG~~F~~~s 15 (44)
T PHA00616 3 QCLRCGGIFRKKK 15 (44)
T ss_pred ccchhhHHHhhHH
Confidence 6999999998654
No 71
>PRK13376 pyrB bifunctional aspartate carbamoyltransferase catalytic subunit/aspartate carbamoyltransferase regulatory subunit; Provisional
Probab=47.09 E-value=46 Score=27.95 Aligned_cols=36 Identities=22% Similarity=0.474 Sum_probs=23.6
Q ss_pred EeeCCCCCCC----C--CCeEEEEcCCCCeeecCCCCceeeec
Q psy1181 41 VWCDGGSGPT----G--HPKVYINLDKPGNHSCGYCGLRFFKE 77 (82)
Q Consensus 41 v~C~Gg~~~l----g--HP~Vyi~L~~~~~~~CpYCG~~y~~~ 77 (82)
+.|..+.=-. + =+..|.-. ..+.-+|.||++.|..+
T Consensus 479 ~~C~Np~CIt~~~~~e~~~~~F~~~-~~~~~~C~YCe~~~~~~ 520 (525)
T PRK13376 479 LRCKNENCITNPAHGENVSASFVRN-EKGRFVCEYCETPHTFE 520 (525)
T ss_pred EEeCCCCCcCCCCCCCcCCceEEEc-cCCEEEeeCCCCEeccc
Confidence 8997653211 1 24456555 45589999999999754
No 72
>KOG1074|consensus
Probab=46.76 E-value=6.4 Score=35.26 Aligned_cols=36 Identities=25% Similarity=0.455 Sum_probs=24.7
Q ss_pred CceEeeCCCCCCC-CCCeEEEEcCCCCeeecCCCCceeeecCC
Q psy1181 38 ERVVWCDGGSGPT-GHPKVYINLDKPGNHSCGYCGLRFFKEDS 79 (82)
Q Consensus 38 ~r~v~C~Gg~~~l-gHP~Vyi~L~~~~~~~CpYCG~~y~~~~~ 79 (82)
-|+++|.. +| .| |=+-..+.+.+|+.||+.|.-++-
T Consensus 612 ~rVlSC~s---aLqmH---yrtHtGERPFkCKiCgRAFtTkGN 648 (958)
T KOG1074|consen 612 LRVLSCPS---ALQMH---YRTHTGERPFKCKICGRAFTTKGN 648 (958)
T ss_pred eecccchh---hhhhh---hhcccCcCccccccccchhccccc
Confidence 46777753 44 44 444444567899999999988873
No 73
>COG1781 PyrI Aspartate carbamoyltransferase, regulatory subunit [Nucleotide transport and metabolism]
Probab=46.48 E-value=18 Score=26.15 Aligned_cols=41 Identities=27% Similarity=0.524 Sum_probs=24.6
Q ss_pred CceEeeCCCCCCC--C---CCeEEEEcCCCCeeecCCCCceeeecC
Q psy1181 38 ERVVWCDGGSGPT--G---HPKVYINLDKPGNHSCGYCGLRFFKED 78 (82)
Q Consensus 38 ~r~v~C~Gg~~~l--g---HP~Vyi~L~~~~~~~CpYCG~~y~~~~ 78 (82)
..++.|+..+=.. . -++-++.=+++...+|.||++.|..+.
T Consensus 104 ~gvlkCpN~nCITn~e~pv~s~F~~~~~~~~~lrC~YCe~~~~~~~ 149 (153)
T COG1781 104 EGVLRCPNPNCITNAEEPVESKFYVVSKEPLALRCKYCEKTFSEDE 149 (153)
T ss_pred ccEEEcCCCCcccCCCccCCccEEEEecCCcEEEEEecCcEechhh
Confidence 4568998764222 1 122333333455689999999987553
No 74
>PRK11827 hypothetical protein; Provisional
Probab=45.65 E-value=34 Score=20.90 Aligned_cols=34 Identities=24% Similarity=0.374 Sum_probs=23.3
Q ss_pred eEeeCCCCCCCCCCeEEEEcCCCCeeecCCCCceeeecCC
Q psy1181 40 VVWCDGGSGPTGHPKVYINLDKPGNHSCGYCGLRFFKEDS 79 (82)
Q Consensus 40 ~v~C~Gg~~~lgHP~Vyi~L~~~~~~~CpYCG~~y~~~~~ 79 (82)
+++|+.-.++| .| + .....-.|.-||+.|.-+++
T Consensus 8 ILaCP~ckg~L----~~-~-~~~~~Lic~~~~laYPI~dg 41 (60)
T PRK11827 8 IIACPVCNGKL----WY-N-QEKQELICKLDNLAFPLRDG 41 (60)
T ss_pred heECCCCCCcC----eE-c-CCCCeEECCccCeeccccCC
Confidence 57898765555 33 2 12456789999999976654
No 75
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=45.44 E-value=26 Score=20.90 Aligned_cols=14 Identities=21% Similarity=0.358 Sum_probs=11.3
Q ss_pred CeeecCCCCceeee
Q psy1181 63 GNHSCGYCGLRFFK 76 (82)
Q Consensus 63 ~~~~CpYCG~~y~~ 76 (82)
..+.||-||..|..
T Consensus 21 eiV~Cp~CGaeleV 34 (54)
T TIGR01206 21 ELVICDECGAELEV 34 (54)
T ss_pred CEEeCCCCCCEEEE
Confidence 46899999998854
No 76
>PRK01402 hslO Hsp33-like chaperonin; Reviewed
Probab=45.28 E-value=14 Score=28.99 Aligned_cols=15 Identities=13% Similarity=0.545 Sum_probs=12.8
Q ss_pred eeecCCCCceeeecC
Q psy1181 64 NHSCGYCGLRFFKED 78 (82)
Q Consensus 64 ~~~CpYCG~~y~~~~ 78 (82)
+++|.+||++|..+.
T Consensus 308 ev~CeFC~~~Y~f~~ 322 (328)
T PRK01402 308 SVTCEFCSRVYRFDP 322 (328)
T ss_pred EEEeeCCCCEEEeCH
Confidence 589999999998753
No 77
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=45.21 E-value=9.3 Score=19.63 Aligned_cols=13 Identities=31% Similarity=0.680 Sum_probs=9.9
Q ss_pred CeeecCCCCceee
Q psy1181 63 GNHSCGYCGLRFF 75 (82)
Q Consensus 63 ~~~~CpYCG~~y~ 75 (82)
....||.||-.|.
T Consensus 13 ~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 13 SAKFCPHCGYDFE 25 (26)
T ss_pred hcCcCCCCCCCCc
Confidence 3468999998874
No 78
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=45.02 E-value=21 Score=25.53 Aligned_cols=41 Identities=22% Similarity=0.336 Sum_probs=25.1
Q ss_pred CceEeeCCCCCC----CCCCeEEEEcCCC-CeeecCCCCceeeecC
Q psy1181 38 ERVVWCDGGSGP----TGHPKVYINLDKP-GNHSCGYCGLRFFKED 78 (82)
Q Consensus 38 ~r~v~C~Gg~~~----lgHP~Vyi~L~~~-~~~~CpYCG~~y~~~~ 78 (82)
..++.|+.+.=- -.=+..|.-+++. ..-+|-||++.|..+.
T Consensus 103 ~gi~kC~Np~CITn~~E~v~~~F~v~~~~~~~~rC~YCe~~~~~~~ 148 (152)
T PRK00893 103 EGVLKCPNPNCITNTNEPVESRFYVVDKEPIKLRCKYCEKEFSEDI 148 (152)
T ss_pred cceEECCCCCCcCCCCcCcCcEEEEEeCCCCEEEeeCCCCEechhh
Confidence 446889765311 1123345445543 5689999999997654
No 79
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=44.80 E-value=12 Score=20.96 Aligned_cols=12 Identities=33% Similarity=0.780 Sum_probs=9.6
Q ss_pred eeecCCCCceee
Q psy1181 64 NHSCGYCGLRFF 75 (82)
Q Consensus 64 ~~~CpYCG~~y~ 75 (82)
.+.|+.|+..|=
T Consensus 40 ~~~C~~C~~~fC 51 (64)
T PF01485_consen 40 IVTCPSCGTEFC 51 (64)
T ss_dssp -CCTTSCCSEEC
T ss_pred eeECCCCCCcCc
Confidence 389999999883
No 80
>PF06226 DUF1007: Protein of unknown function (DUF1007); InterPro: IPR010412 This is a family of conserved bacterial proteins with unknown function.
Probab=44.41 E-value=15 Score=26.65 Aligned_cols=15 Identities=33% Similarity=0.556 Sum_probs=12.1
Q ss_pred CCCCCCCCeEEEEcC
Q psy1181 46 GSGPTGHPKVYINLD 60 (82)
Q Consensus 46 g~~~lgHP~Vyi~L~ 60 (82)
...+..||.|||++.
T Consensus 13 ~~~a~AHPHvfId~~ 27 (212)
T PF06226_consen 13 PSPAFAHPHVFIDAR 27 (212)
T ss_pred ccccccCCcEEEEEE
Confidence 345789999999975
No 81
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=43.81 E-value=13 Score=20.19 Aligned_cols=14 Identities=21% Similarity=0.451 Sum_probs=9.8
Q ss_pred eeecCCCCceeeec
Q psy1181 64 NHSCGYCGLRFFKE 77 (82)
Q Consensus 64 ~~~CpYCG~~y~~~ 77 (82)
+..||+||..=...
T Consensus 2 ~~~Cp~Cg~~~~~~ 15 (47)
T PF14690_consen 2 PPRCPHCGSPSVHR 15 (47)
T ss_pred CccCCCcCCCceEC
Confidence 46899999664443
No 82
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=43.60 E-value=15 Score=25.12 Aligned_cols=27 Identities=22% Similarity=0.249 Sum_probs=15.0
Q ss_pred CeEEEEcCCCCeeecCCCCce-eeecCC
Q psy1181 53 PKVYINLDKPGNHSCGYCGLR-FFKEDS 79 (82)
Q Consensus 53 P~Vyi~L~~~~~~~CpYCG~~-y~~~~~ 79 (82)
|.-|++.-......||+||.. +....|
T Consensus 96 ~~~~~~~~~~~~~~CP~Cgs~~~~i~~G 123 (135)
T PRK03824 96 AIHFIPEVVHAFLKCPKCGSRDFEIVKG 123 (135)
T ss_pred cccccccccccCcCCcCCCCCCcEEecC
Confidence 334444333344679999975 444443
No 83
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.11 E-value=9.4 Score=29.68 Aligned_cols=17 Identities=29% Similarity=0.630 Sum_probs=14.1
Q ss_pred CCeeecCCCCceeeecC
Q psy1181 62 PGNHSCGYCGLRFFKED 78 (82)
Q Consensus 62 ~~~~~CpYCG~~y~~~~ 78 (82)
.+.+.||.|++.|+.+.
T Consensus 17 kk~ieCPvC~tkFkkee 33 (267)
T COG1655 17 KKTIECPVCNTKFKKEE 33 (267)
T ss_pred hceeccCcccchhhhhh
Confidence 35789999999998764
No 84
>PHA03296 envelope glycoprotein H; Provisional
Probab=42.55 E-value=26 Score=31.01 Aligned_cols=25 Identities=20% Similarity=0.365 Sum_probs=17.8
Q ss_pred CCCeEEEEcCCCCeeecCCCCceeee
Q psy1181 51 GHPKVYINLDKPGNHSCGYCGLRFFK 76 (82)
Q Consensus 51 gHP~Vyi~L~~~~~~~CpYCG~~y~~ 76 (82)
-=|.+++|+.. ....|+|||..|.+
T Consensus 681 kIp~v~LN~t~-~~k~C~yCGSVfLR 705 (814)
T PHA03296 681 KIEDGHLNLHG-AAIACILCGHAILQ 705 (814)
T ss_pred cccceeecCCC-CCCcCCcCCEEEEE
Confidence 34567777764 35789999998854
No 85
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=42.54 E-value=15 Score=24.94 Aligned_cols=19 Identities=26% Similarity=0.786 Sum_probs=14.1
Q ss_pred EEEEcCCCCeeecCCCCcee
Q psy1181 55 VYINLDKPGNHSCGYCGLRF 74 (82)
Q Consensus 55 Vyi~L~~~~~~~CpYCG~~y 74 (82)
-|..++ -|...||+||.-+
T Consensus 39 ~~VeIe-vG~~~cP~Cge~~ 57 (102)
T PF04475_consen 39 DYVEIE-VGDTICPKCGEEL 57 (102)
T ss_pred CeEEEe-cCcccCCCCCCcc
Confidence 366665 4778999999765
No 86
>cd03528 Rieske_RO_ferredoxin Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The ferredoxin component contains either a plant-type or Rieske-type [2Fe-2S] cluster. The Rieske ferredoxin component in this family carries an electron from the RO reductase component to the terminal RO oxygenase component. BPDO degrades biphenyls and polychlorinated biphenyls. BPDO ferredoxin (BphF) has structural features consistent with a minimal and perhaps archetypical Rieske protein in that the in
Probab=42.34 E-value=48 Score=20.20 Aligned_cols=18 Identities=28% Similarity=0.325 Sum_probs=15.2
Q ss_pred CCeeecCCCCceeeecCC
Q psy1181 62 PGNHSCGYCGLRFFKEDS 79 (82)
Q Consensus 62 ~~~~~CpYCG~~y~~~~~ 79 (82)
.+...|||-|.+|-++.|
T Consensus 55 ~~~i~Cp~Hg~~fd~~~G 72 (98)
T cd03528 55 GGVIECPLHGGRFDLRTG 72 (98)
T ss_pred CCEEEeCCcCCEEECCCC
Confidence 468999999999998554
No 87
>PF02489 Herpes_glycop_H: Herpesvirus glycoprotein H; InterPro: IPR003493 Herpesviruses are enveloped by a lipid bilayer that contains at least a dozen glycoproteins. The virion surface glycoproteins mediate recognition of susceptible cells and promote fusion of the viral envelope with the cell membrane, leading to virus entry. No single glycoprotein associated with the virion membrane has been identified as the fusogen []. Glycoprotein L (gL) forms a non-covalently linked heterodimer with glycoprotein H (gH). This heterodimer is essential for virus-cell and cell-cell fusion since the association of gH and gL is necessary for correct localisation of gH to the virion or cell surface. gH anchoring the heterodimer to the plasma membrane through its transmembrane domain. gL lacks a transmembrane domain and is secreted from cells when expressed in the absence of gH []. This entry represents Herpesvirus glycoprotein H (gH), which is a virion associated envelope glycoprotein []. Heterodimer formation between gH and gL has been demonstrated in both virions and infected cells []. Heterodimer formation between gL and gH is important for the proper folding of gH and its insertion into the membrane because the anti-gH conformation-dependent monoclonal antibodies (mAbs) 53S and LP11 bind gH only when gL is present [, ].; PDB: 3PHF_S 3M1C_A 2LQY_A 2XQY_A.
Probab=42.15 E-value=15 Score=30.78 Aligned_cols=33 Identities=30% Similarity=0.760 Sum_probs=13.8
Q ss_pred EeeCCCCCC---CCCCeEEEEcCCCCeeecCCCCceeee
Q psy1181 41 VWCDGGSGP---TGHPKVYINLDKPGNHSCGYCGLRFFK 76 (82)
Q Consensus 41 v~C~Gg~~~---lgHP~Vyi~L~~~~~~~CpYCG~~y~~ 76 (82)
-.|....+. .-=|++| |+. -...|+|||..|..
T Consensus 538 ~~C~~~~~~~~~~~i~~~~-Nit--~~~~C~~Cgsv~l~ 573 (657)
T PF02489_consen 538 STCSSSTGIIETRRIPVVY-NIT--PSKDCPFCGSVFLR 573 (657)
T ss_dssp T-S-CCEE-SEEEE--EE---SS--S-SS-STTT-EEEE
T ss_pred CCCcCCCCCCCccccCCCc-CCC--CCCCCCCCCcEEEE
Confidence 357654321 2335555 655 35689999998853
No 88
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=41.98 E-value=11 Score=20.21 Aligned_cols=11 Identities=36% Similarity=0.812 Sum_probs=4.7
Q ss_pred cCCCCceeeec
Q psy1181 67 CGYCGLRFFKE 77 (82)
Q Consensus 67 CpYCG~~y~~~ 77 (82)
|+|||..+...
T Consensus 1 C~~C~~~~~~~ 11 (47)
T PF01844_consen 1 CQYCGKPGSDN 11 (47)
T ss_dssp -TTT--B--GG
T ss_pred CCCCCCcCccC
Confidence 89999998554
No 89
>KOG1729|consensus
Probab=41.86 E-value=9.9 Score=29.58 Aligned_cols=31 Identities=23% Similarity=0.555 Sum_probs=24.3
Q ss_pred CCCCeEEEEcCCCCeeecCCCCc-eeeecCCCCC
Q psy1181 50 TGHPKVYINLDKPGNHSCGYCGL-RFFKEDSHHH 82 (82)
Q Consensus 50 lgHP~Vyi~L~~~~~~~CpYCG~-~y~~~~~~~h 82 (82)
..|..+||. .+....|.+|+. .|.+-.-.||
T Consensus 156 ~~~~~~W~P--D~ea~~C~~C~~~~Ftl~~RRHH 187 (288)
T KOG1729|consen 156 NNSAAVWLP--DSEATECMVCGCTEFTLSERRHH 187 (288)
T ss_pred CCcCCcccC--cccceecccCCCccccHHHHHHH
Confidence 478888987 456789999999 8887765554
No 90
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=41.22 E-value=12 Score=19.99 Aligned_cols=15 Identities=33% Similarity=0.773 Sum_probs=4.8
Q ss_pred eecCCCCceeeecCC
Q psy1181 65 HSCGYCGLRFFKEDS 79 (82)
Q Consensus 65 ~~CpYCG~~y~~~~~ 79 (82)
-.||.||..|.+.++
T Consensus 3 p~Cp~C~se~~y~D~ 17 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDG 17 (30)
T ss_dssp ---TTT-----EE-S
T ss_pred CCCCCCCCcceeccC
Confidence 369999999988654
No 91
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=40.59 E-value=47 Score=20.51 Aligned_cols=34 Identities=26% Similarity=0.498 Sum_probs=23.0
Q ss_pred eEeeCCCCCCCCCCeEEEEcCCCCeeecCCCCceeeecCC
Q psy1181 40 VVWCDGGSGPTGHPKVYINLDKPGNHSCGYCGLRFFKEDS 79 (82)
Q Consensus 40 ~v~C~Gg~~~lgHP~Vyi~L~~~~~~~CpYCG~~y~~~~~ 79 (82)
+++|+-..| |.+|.. ..+.-.|+-|++.|.-++|
T Consensus 8 iLaCP~~kg----~L~~~~--~~~~L~c~~~~~aYpI~dG 41 (60)
T COG2835 8 ILACPVCKG----PLVYDE--EKQELICPRCKLAYPIRDG 41 (60)
T ss_pred eeeccCcCC----cceEec--cCCEEEecccCceeecccC
Confidence 678865543 433332 2457899999999987765
No 92
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=40.56 E-value=34 Score=23.28 Aligned_cols=36 Identities=39% Similarity=0.692 Sum_probs=23.6
Q ss_pred CceEeeCCCCCCCCCCeEEEE-cCCC---CeeecCCCCceeeec
Q psy1181 38 ERVVWCDGGSGPTGHPKVYIN-LDKP---GNHSCGYCGLRFFKE 77 (82)
Q Consensus 38 ~r~v~C~Gg~~~lgHP~Vyi~-L~~~---~~~~CpYCG~~y~~~ 77 (82)
.+.+-|+- -||-+|-+. +++. +.+.|+-||++|..+
T Consensus 20 ~k~FtCp~----Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~e 59 (104)
T COG4888 20 PKTFTCPR----CGHEKVSSCTVKKTVNIGTAVCGNCGLSFECE 59 (104)
T ss_pred CceEecCc----cCCeeeeEEEEEecCceeEEEcccCcceEEEe
Confidence 45667743 267776633 2332 568999999999754
No 93
>PF00653 BIR: Inhibitor of Apoptosis domain; InterPro: IPR001370 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The baculovirus inhibitor of apoptosis protein repeat (BIR) is a domain of tandem repeats separated by a variable length linker that seems to confer cell death-preventing activity [, ]. The BIR domains characterise the Inhibitor of Apoptosis (IAP) family of proteins (MEROPS proteinase inhibitor family I32, clan IV) that suppress apoptosis by interacting with and inhibiting the enzymatic activity of both initiator and effector caspases (MEROPS peptidase family C14, IPR002398 from INTERPRO). Several distinct mammalian IAPs including XIAP, c-IAP1, c-IAP2, and ML-IAP, have been identified, and they all exhibit antiapoptotic activity in cell culture. The functional unit in each IAP protein is the baculoviral IAP repeat (BIR), which contains approximately 80 amino acids folded around a zinc atom. Most mammalian IAPs have more than one BIR domain, with the different BIR domains performing distinct functions. For example, in XIAP, the third BIR domain (BIR3) potently inhibits the catalytic activity of caspase-9, whereas the linker sequences immediately preceding the second BIR domain (BIR2) selectively targets caspase-3 or -7. The first-recognised members of family MEROPS inhibitor family I32 were viral proteins that inhibited the apoptosis of infected cells: Cp-IAP from Cydia pomonella granulosis virus (CpGV) [] and Op-IAP from Orgyia pseudotsugata multicapsid polyhedrosis virus(OpMNPV) []. The discovery of homologous proteins in mammals followed soon after with the recognition that mutations in the gene for neuronal apoptosis inhibitory protein (NIAP) underlie spinal muscular atrophy []. The inhibitors in family I32 all possess one or more 80-residue domains known as BIR (baculovirus inhibitor repeat) domains and have accordingly been termed 'BIR-containing' or 'BIRC' proteins as well as IAP proteins. The mechanism of inhibition of caspases by the IAP proteins is complex, and reactive site residues cannot yet be identified with any confidence. Despite the conservation of the BIR or IAP (inhibitor of apoptosis) domains throughout the family it seems clear that other parts of the molecules also make essential contributions to inhibitory activity. Homologs of most components in the mammalian apoptotic pathway have been identified in fruit flies. The Drosophila Apaf-1, known as Dapaf-1, HAC-1 or Dark, shares significant sequence similarity with its mammalian counterpart, and is critically important for the activation of the Drosophila initiator caspase Dronc. Dronc, in turn, cleaves and activates the effector caspase DrICE. The Drosophila IAP, DIAP1, binds to and in-activates both DrICE and Dronc through its BIR1 and BIR2 domains. During apoptosis, the anti-death function of DIAP1 is countered by at least four pro-apoptotic proteins, Reaper, Hid, Grim, and sickle, through direct physical interactions. These four proteins represent the functional homologs of the mammalian protein Smac, and they all share a conserved IAP-binding motif at their N termini. The three proteins Reaper, Hid, and Grim are collectively referred to as the RHG proteins [, ]. Both XIAP and DIAP1 contain a RING domain at their C termini, and can act as an E3 ubiquitin ligase. Indeed, both XIAP and DIAP1 have been shown to promote self-ubiquitination and degradation as well as to negatively regulate the target caspases. Nonetheless, important differences exist between XIAP and DIAP1. The primary function of XIAP is thought to inhibit the catalytic activities of caspases; to what extent the ubiquitinating activity of XIAP contributes to its function remains unclear. For DIAP1, however, the ubiquitinating activity appears to be essential for its function. Recently a Drosophila p53 protein has been identified that mediates apoptosis via a novel pathway involving the activation of the Reaper gene and subsequent inhibition of the inhibitors of apoptosis (IAPs). CIAP1, a major mammalian homologue of Drosophila IAPs, is irreversibly inhibited (cleaved) during p53-dependent apoptosis and this cleavage is mediated by a serine protease. Serine protease inhibitors that block CIAP1 cleavage inhibit p53-dependent apoptosis. Furthermore, activation of the p53 protein increases the transcription of the HTRA2 gene, which encodes a serine protease that interacts with CIAP1 and potentiates apoptosis. Therefore mammalian p53 protein activates apoptosis through a novel pathway functionally similar to that in Drosophila, which involves HTRA2 and subsequent inhibition of CIAP1 by cleavage [].; GO: 0005622 intracellular; PDB: 3HL5_B 3UW5_A 3CM7_A 1G3F_A 1G73_C 3G76_G 3CM2_C 2VSL_A 2OPZ_B 3CLX_A ....
Probab=40.52 E-value=35 Score=20.26 Aligned_cols=15 Identities=33% Similarity=0.684 Sum_probs=12.4
Q ss_pred CCCeeecCCCCceee
Q psy1181 61 KPGNHSCGYCGLRFF 75 (82)
Q Consensus 61 ~~~~~~CpYCG~~y~ 75 (82)
.+..+.|-|||....
T Consensus 33 ~~d~v~C~~C~~~l~ 47 (70)
T PF00653_consen 33 TGDRVRCFYCGLELD 47 (70)
T ss_dssp STTEEEETTTTEEEE
T ss_pred CCCEEEEeccCCEEe
Confidence 367899999999874
No 94
>PRK03922 hypothetical protein; Provisional
Probab=40.39 E-value=17 Score=25.05 Aligned_cols=21 Identities=29% Similarity=0.567 Sum_probs=15.4
Q ss_pred eEEEEcCCCCeeecCCCCceee
Q psy1181 54 KVYINLDKPGNHSCGYCGLRFF 75 (82)
Q Consensus 54 ~Vyi~L~~~~~~~CpYCG~~y~ 75 (82)
.-|..++ -|...||+||.-|.
T Consensus 40 l~yVeie-vG~~~cP~cge~~~ 60 (113)
T PRK03922 40 LDYVEVE-VGLTICPKCGEPFD 60 (113)
T ss_pred CCeEEEe-cCcccCCCCCCcCC
Confidence 4477765 46789999998663
No 95
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=40.23 E-value=19 Score=18.57 Aligned_cols=14 Identities=29% Similarity=0.963 Sum_probs=7.6
Q ss_pred ecCCCCceeeecCC
Q psy1181 66 SCGYCGLRFFKEDS 79 (82)
Q Consensus 66 ~CpYCG~~y~~~~~ 79 (82)
.||.||..-+++.+
T Consensus 1 ~CP~C~s~l~~~~~ 14 (28)
T PF03119_consen 1 TCPVCGSKLVREEG 14 (28)
T ss_dssp B-TTT--BEEE-CC
T ss_pred CcCCCCCEeEcCCC
Confidence 49999998876654
No 96
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=39.96 E-value=52 Score=21.84 Aligned_cols=36 Identities=25% Similarity=0.494 Sum_probs=26.7
Q ss_pred CceEeeCCCCCCCCCCeEEEEcCCC-CeeecCCCCceeeec
Q psy1181 38 ERVVWCDGGSGPTGHPKVYINLDKP-GNHSCGYCGLRFFKE 77 (82)
Q Consensus 38 ~r~v~C~Gg~~~lgHP~Vyi~L~~~-~~~~CpYCG~~y~~~ 77 (82)
...+.|+-= |++.|=+++++. ..+.|+-||..|...
T Consensus 19 pt~f~CP~C----ge~~v~v~~~k~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 19 PKIFECPRC----GKVSISVKIKKNIAIITCGNCGLYTEFE 55 (99)
T ss_pred CcEeECCCC----CCeEeeeecCCCcceEECCCCCCccCEE
Confidence 357889654 467888888874 457999999987543
No 97
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=39.65 E-value=13 Score=21.56 Aligned_cols=12 Identities=33% Similarity=0.786 Sum_probs=9.8
Q ss_pred eeecCCCCceee
Q psy1181 64 NHSCGYCGLRFF 75 (82)
Q Consensus 64 ~~~CpYCG~~y~ 75 (82)
.-.|+.||+.|.
T Consensus 8 ~K~C~~C~rpf~ 19 (42)
T PF10013_consen 8 SKICPVCGRPFT 19 (42)
T ss_pred CCcCcccCCcch
Confidence 358999999885
No 98
>COG0602 NrdG Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]
Probab=38.39 E-value=26 Score=25.53 Aligned_cols=32 Identities=22% Similarity=0.515 Sum_probs=24.2
Q ss_pred CCCCCCCCCCeEEEEcCCCCeeecCCCCceeee
Q psy1181 44 DGGSGPTGHPKVYINLDKPGNHSCGYCGLRFFK 76 (82)
Q Consensus 44 ~Gg~~~lgHP~Vyi~L~~~~~~~CpYCG~~y~~ 76 (82)
.|.|...|=|.||+.+. .-...|+||.+.+.-
T Consensus 14 QGEG~~~Gr~~vFVR~~-GC~l~C~~Cdt~~t~ 45 (212)
T COG0602 14 QGEGKNIGRPSVFVRFA-GCNLRCPGCDTKYTW 45 (212)
T ss_pred ecCcccccceeEEEEcC-CCCCCCCCCCChhhh
Confidence 44443569999999986 457899999987553
No 99
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=38.05 E-value=14 Score=25.86 Aligned_cols=13 Identities=23% Similarity=0.411 Sum_probs=10.8
Q ss_pred eeecCCCCceeee
Q psy1181 64 NHSCGYCGLRFFK 76 (82)
Q Consensus 64 ~~~CpYCG~~y~~ 76 (82)
.+.||+||.....
T Consensus 105 ~~~cp~c~s~~t~ 117 (146)
T TIGR02159 105 SVQCPRCGSADTT 117 (146)
T ss_pred CCcCCCCCCCCcE
Confidence 5899999988754
No 100
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=37.67 E-value=19 Score=24.82 Aligned_cols=23 Identities=30% Similarity=0.629 Sum_probs=17.3
Q ss_pred CCeEEEEcCCCCeeecCCCCceee
Q psy1181 52 HPKVYINLDKPGNHSCGYCGLRFF 75 (82)
Q Consensus 52 HP~Vyi~L~~~~~~~CpYCG~~y~ 75 (82)
+..-|..++ -|...||-||.-|.
T Consensus 38 ~~LdyV~ie-~G~t~CP~Cg~~~e 60 (115)
T COG1885 38 PDLDYVEIE-VGSTSCPKCGEPFE 60 (115)
T ss_pred CCCCeEEEe-cccccCCCCCCccc
Confidence 555677776 46789999998764
No 101
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=37.43 E-value=18 Score=19.94 Aligned_cols=16 Identities=31% Similarity=0.636 Sum_probs=13.0
Q ss_pred eeecCCCCceeeecCC
Q psy1181 64 NHSCGYCGLRFFKEDS 79 (82)
Q Consensus 64 ~~~CpYCG~~y~~~~~ 79 (82)
+..|.+|+..|=+++-
T Consensus 12 ~f~C~~C~~~FC~~HR 27 (39)
T smart00154 12 GFKCRHCGNLFCGEHR 27 (39)
T ss_pred CeECCccCCccccccC
Confidence 6789999999977653
No 102
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=37.04 E-value=18 Score=18.24 Aligned_cols=14 Identities=29% Similarity=0.814 Sum_probs=11.2
Q ss_pred CeeecCCCCceeee
Q psy1181 63 GNHSCGYCGLRFFK 76 (82)
Q Consensus 63 ~~~~CpYCG~~y~~ 76 (82)
+...|.+|+..|..
T Consensus 2 ~~~~C~~C~~~~~~ 15 (35)
T smart00451 2 GGFYCKLCNVTFTD 15 (35)
T ss_pred cCeEccccCCccCC
Confidence 35689999999873
No 103
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=35.84 E-value=20 Score=19.15 Aligned_cols=10 Identities=30% Similarity=0.873 Sum_probs=7.7
Q ss_pred CeeecCCCCc
Q psy1181 63 GNHSCGYCGL 72 (82)
Q Consensus 63 ~~~~CpYCG~ 72 (82)
-+..||.||.
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 3568999987
No 104
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=35.79 E-value=21 Score=22.42 Aligned_cols=13 Identities=23% Similarity=0.583 Sum_probs=9.7
Q ss_pred CCCeeecCCCCce
Q psy1181 61 KPGNHSCGYCGLR 73 (82)
Q Consensus 61 ~~~~~~CpYCG~~ 73 (82)
.++.-.||+||..
T Consensus 15 ~~d~e~CP~Cgs~ 27 (64)
T COG2093 15 PEDTEICPVCGST 27 (64)
T ss_pred CCCCccCCCCCCc
Confidence 3455679999986
No 105
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=35.63 E-value=26 Score=21.06 Aligned_cols=14 Identities=29% Similarity=0.712 Sum_probs=10.5
Q ss_pred CCCeeecCCCCcee
Q psy1181 61 KPGNHSCGYCGLRF 74 (82)
Q Consensus 61 ~~~~~~CpYCG~~y 74 (82)
.+....||+|+..=
T Consensus 4 ~p~~~~CP~C~~~~ 17 (73)
T PF10601_consen 4 EPVRIYCPYCQQQV 17 (73)
T ss_pred CceeeECCCCCCEE
Confidence 34568999999764
No 106
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=34.85 E-value=15 Score=22.89 Aligned_cols=14 Identities=29% Similarity=0.683 Sum_probs=11.3
Q ss_pred eeecCCCCceeeec
Q psy1181 64 NHSCGYCGLRFFKE 77 (82)
Q Consensus 64 ~~~CpYCG~~y~~~ 77 (82)
--.||-||..|...
T Consensus 17 ~lrCPRC~~~FR~~ 30 (65)
T COG4049 17 FLRCPRCGMVFRRR 30 (65)
T ss_pred eeeCCchhHHHHHh
Confidence 46899999999653
No 107
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=34.64 E-value=25 Score=21.37 Aligned_cols=14 Identities=21% Similarity=0.411 Sum_probs=8.7
Q ss_pred eeecCCCCceeeec
Q psy1181 64 NHSCGYCGLRFFKE 77 (82)
Q Consensus 64 ~~~CpYCG~~y~~~ 77 (82)
...||||.+....+
T Consensus 55 ~G~CP~C~~~i~~~ 68 (70)
T PF11793_consen 55 FGECPYCSSPISWS 68 (70)
T ss_dssp EEE-TTT-SEEEGG
T ss_pred ccCCcCCCCeeeEe
Confidence 46899999876543
No 108
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=34.25 E-value=17 Score=26.38 Aligned_cols=22 Identities=36% Similarity=0.634 Sum_probs=16.1
Q ss_pred CeEEEEcCCCCeeecCCCCceeee
Q psy1181 53 PKVYINLDKPGNHSCGYCGLRFFK 76 (82)
Q Consensus 53 P~Vyi~L~~~~~~~CpYCG~~y~~ 76 (82)
|+||.+- +.--.|+-||+.|=.
T Consensus 121 ~~~~~~~--~~f~~C~~CgkiYW~ 142 (165)
T COG1656 121 EKVYRNY--EEFYRCPKCGKIYWK 142 (165)
T ss_pred hhhhhcc--cceeECCCCcccccC
Confidence 4577774 356789999999854
No 109
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=33.88 E-value=20 Score=29.35 Aligned_cols=19 Identities=21% Similarity=0.427 Sum_probs=15.6
Q ss_pred CCCeeecCCCCceeeecCC
Q psy1181 61 KPGNHSCGYCGLRFFKEDS 79 (82)
Q Consensus 61 ~~~~~~CpYCG~~y~~~~~ 79 (82)
++++-+|+.|++||+.-.|
T Consensus 395 ~~KPYrCevC~KRYKNlNG 413 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNG 413 (423)
T ss_pred cCCceeccccchhhccCcc
Confidence 4577899999999987654
No 110
>KOG1391|consensus
Probab=33.58 E-value=14 Score=29.71 Aligned_cols=37 Identities=27% Similarity=0.315 Sum_probs=31.2
Q ss_pred ccChhHHHhhhhcCCCeeecCceEeeCCCCCCCCCCe
Q psy1181 18 HVNTQFAIDLIAEVPPKPCKERVVWCDGGSGPTGHPK 54 (82)
Q Consensus 18 ~~n~~~a~~li~e~P~i~v~~r~v~C~Gg~~~lgHP~ 54 (82)
++|.-+|...++-+....++...+.-.||.-+||||.
T Consensus 317 EvNEAFApQ~LAv~r~L~ld~sKlNVNGGAIALGHPL 353 (396)
T KOG1391|consen 317 EVNEAFAPQYLAVERSLDLDISKLNVNGGAIALGHPL 353 (396)
T ss_pred EechhhchHHHHHHHhhCCChhhccccCceeeccCcc
Confidence 6799999988888888788877888888877899995
No 111
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=33.52 E-value=52 Score=20.08 Aligned_cols=30 Identities=17% Similarity=0.150 Sum_probs=17.3
Q ss_pred eecCceEeeCCCCCCCCCCeEEEEcCCC-CeeecCC
Q psy1181 35 PCKERVVWCDGGSGPTGHPKVYINLDKP-GNHSCGY 69 (82)
Q Consensus 35 ~v~~r~v~C~Gg~~~lgHP~Vyi~L~~~-~~~~CpY 69 (82)
+|.+.+....- .-|| +|++|.++ ....|-.
T Consensus 2 ~v~GeVs~~~~---~~GH--vyfsLkD~~a~i~cv~ 32 (73)
T cd04487 2 HIEGEVVQIKQ---TSGP--TIFTLRDETGTVWAAA 32 (73)
T ss_pred EEEEEEecccc---CCCC--EEEEEEcCCEEEEEEE
Confidence 34444444432 3477 99999554 3567744
No 112
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=33.43 E-value=25 Score=19.17 Aligned_cols=13 Identities=31% Similarity=0.682 Sum_probs=10.2
Q ss_pred eecCCCCceeeec
Q psy1181 65 HSCGYCGLRFFKE 77 (82)
Q Consensus 65 ~~CpYCG~~y~~~ 77 (82)
..|+-||..|-..
T Consensus 2 r~C~~Cg~~Yh~~ 14 (36)
T PF05191_consen 2 RICPKCGRIYHIE 14 (36)
T ss_dssp EEETTTTEEEETT
T ss_pred cCcCCCCCccccc
Confidence 4799999999654
No 113
>cd03469 Rieske_RO_Alpha_N Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The oxygenase component may contain alpha and beta subunits, with the beta subunit having a purely structural function. Some oxygenase components contain only an alpha subunit. The oxygenase alpha subunit has two domains, an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from the reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Reduced pyridine nucleotide is used as the i
Probab=32.92 E-value=80 Score=19.80 Aligned_cols=29 Identities=17% Similarity=0.231 Sum_probs=21.0
Q ss_pred CCCCeEEEEcCCCCeeecCCCCceeeecC
Q psy1181 50 TGHPKVYINLDKPGNHSCGYCGLRFFKED 78 (82)
Q Consensus 50 lgHP~Vyi~L~~~~~~~CpYCG~~y~~~~ 78 (82)
.|-|..+-.+...+...|||-|.+|-+++
T Consensus 46 ~g~~L~~g~~~~~~~i~Cp~Hg~~Fd~~G 74 (118)
T cd03469 46 RGARLCEGRGGNAGRLVCPYHGWTYDLDG 74 (118)
T ss_pred CCCEeeeccCCCCCEEECCCCCCEECCCC
Confidence 35555555553457899999999998873
No 114
>cd00022 BIR Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
Probab=32.69 E-value=36 Score=19.80 Aligned_cols=15 Identities=27% Similarity=0.687 Sum_probs=12.2
Q ss_pred CCeeecCCCCceeee
Q psy1181 62 PGNHSCGYCGLRFFK 76 (82)
Q Consensus 62 ~~~~~CpYCG~~y~~ 76 (82)
...+.|.||+..+..
T Consensus 32 ~d~v~C~~C~~~~~~ 46 (69)
T cd00022 32 GDEVKCFFCGLELKN 46 (69)
T ss_pred CCEEEeCCCCCCccC
Confidence 457999999998854
No 115
>PHA00732 hypothetical protein
Probab=32.15 E-value=21 Score=22.55 Aligned_cols=13 Identities=15% Similarity=0.577 Sum_probs=10.8
Q ss_pred ecCCCCceeeecC
Q psy1181 66 SCGYCGLRFFKED 78 (82)
Q Consensus 66 ~CpYCG~~y~~~~ 78 (82)
.|+.||..|....
T Consensus 29 ~C~~CgKsF~~l~ 41 (79)
T PHA00732 29 KCPVCNKSYRRLN 41 (79)
T ss_pred ccCCCCCEeCChh
Confidence 7999999997543
No 116
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=31.73 E-value=32 Score=20.80 Aligned_cols=14 Identities=21% Similarity=0.378 Sum_probs=7.9
Q ss_pred eeecCCCCceeeec
Q psy1181 64 NHSCGYCGLRFFKE 77 (82)
Q Consensus 64 ~~~CpYCG~~y~~~ 77 (82)
.+.||.||+.....
T Consensus 2 ~v~CP~C~k~~~~~ 15 (57)
T PF03884_consen 2 TVKCPICGKPVEWS 15 (57)
T ss_dssp EEE-TTT--EEE-S
T ss_pred cccCCCCCCeeccc
Confidence 47899999998763
No 117
>KOG1522|consensus
Probab=31.69 E-value=30 Score=27.15 Aligned_cols=71 Identities=20% Similarity=0.200 Sum_probs=42.4
Q ss_pred CcCcccccccccChhH--HHhhhhcCCCeeecCceEeeCCCC---CCCCCCeEEEEcCCCC------------eeecCCC
Q psy1181 8 RPVRFVDKEKHVNTQF--AIDLIAEVPPKPCKERVVWCDGGS---GPTGHPKVYINLDKPG------------NHSCGYC 70 (82)
Q Consensus 8 ~~~rf~~~~~~~n~~~--a~~li~e~P~i~v~~r~v~C~Gg~---~~lgHP~Vyi~L~~~~------------~~~CpYC 70 (82)
.+++|+.+...+.--+ ..=||+|+|.|.++--.+-=...- .-+-|-.=-|.|..+. ..-|+.|
T Consensus 16 d~vkF~L~nTdlsvANsLRRV~iaEvPTiAID~VeIe~NssVL~DEFiAHRLGLIPl~S~~~~~l~ytrdC~C~~~C~eC 95 (285)
T KOG1522|consen 16 DNVKFVLSNTDLSVANSLRRVMIAEVPTIAIDLVEIEVNSSVLPDEFIAHRLGLIPLISDRIVELQYTRDCECDEFCPEC 95 (285)
T ss_pred CceEEEEecChHHHHHHHHHHHHhcCceeEEEEEEEecccccccHHHHHhhhcceeccchhhhhhhhcccCchhccCCcc
Confidence 3578888776552222 345899999986653333222111 1235555556665542 2359999
Q ss_pred CceeeecC
Q psy1181 71 GLRFFKED 78 (82)
Q Consensus 71 G~~y~~~~ 78 (82)
+..|.++-
T Consensus 96 SVef~L~~ 103 (285)
T KOG1522|consen 96 SVEFTLDV 103 (285)
T ss_pred eEEEEEee
Confidence 99998864
No 118
>cd03529 Rieske_NirD Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while fungal proteins have a C-terminal Rieske domain in addition to several other domains. The fungal NirD is involved in nutrient acquisition, functioning at the soil/fungus interface to control nutrient exchange between the fungus and the host plant. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The Rieske [2Fe-2S] cluster is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In this family, only a few members contain these residues. Other members may have lost the ability to bind the Rieske [2Fe-2S] cluster.
Probab=31.04 E-value=97 Score=19.35 Aligned_cols=18 Identities=6% Similarity=-0.101 Sum_probs=15.1
Q ss_pred CCeeecCCCCceeeecCC
Q psy1181 62 PGNHSCGYCGLRFFKEDS 79 (82)
Q Consensus 62 ~~~~~CpYCG~~y~~~~~ 79 (82)
.+..+|||-|.+|-++.+
T Consensus 61 ~~~i~Cp~Hg~~Fdl~tG 78 (103)
T cd03529 61 EPVVASPLYKQHFSLKTG 78 (103)
T ss_pred CeEEECCCCCCEEEcCCC
Confidence 347999999999987665
No 119
>smart00729 Elp3 Elongator protein 3, MiaB family, Radical SAM. This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.
Probab=30.95 E-value=33 Score=22.34 Aligned_cols=21 Identities=10% Similarity=0.344 Sum_probs=15.7
Q ss_pred eEEEEcCCCCeeecCCCCcee
Q psy1181 54 KVYINLDKPGNHSCGYCGLRF 74 (82)
Q Consensus 54 ~Vyi~L~~~~~~~CpYCG~~y 74 (82)
..+|.+...-...|.||....
T Consensus 2 ~~~i~~t~~C~~~C~yC~~~~ 22 (216)
T smart00729 2 LALYIITRGCPRRCTFCSFPS 22 (216)
T ss_pred ccEEEecCchhccCCcCCcCc
Confidence 457777766678899998754
No 120
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=30.67 E-value=19 Score=29.60 Aligned_cols=14 Identities=29% Similarity=0.567 Sum_probs=12.1
Q ss_pred ecCCCCceeeecCC
Q psy1181 66 SCGYCGLRFFKEDS 79 (82)
Q Consensus 66 ~CpYCG~~y~~~~~ 79 (82)
.||+||.+.++++.
T Consensus 352 ~Cp~Cg~~m~S~G~ 365 (421)
T COG1571 352 VCPRCGGRMKSAGR 365 (421)
T ss_pred CCCccCCchhhcCC
Confidence 69999999988764
No 121
>cd00085 HNHc HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.
Probab=30.44 E-value=22 Score=18.89 Aligned_cols=10 Identities=40% Similarity=0.803 Sum_probs=8.3
Q ss_pred eecCCCCcee
Q psy1181 65 HSCGYCGLRF 74 (82)
Q Consensus 65 ~~CpYCG~~y 74 (82)
..|+|||..+
T Consensus 12 ~~C~~c~~~~ 21 (57)
T cd00085 12 GLCPYCGKPG 21 (57)
T ss_pred CcCccCCCcC
Confidence 4799999875
No 122
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=30.31 E-value=25 Score=19.62 Aligned_cols=8 Identities=38% Similarity=0.941 Sum_probs=6.8
Q ss_pred eecCCCCc
Q psy1181 65 HSCGYCGL 72 (82)
Q Consensus 65 ~~CpYCG~ 72 (82)
..||.||.
T Consensus 19 ~~CP~Cg~ 26 (46)
T PF12760_consen 19 FVCPHCGS 26 (46)
T ss_pred CCCCCCCC
Confidence 56999996
No 124
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=30.30 E-value=34 Score=18.65 Aligned_cols=15 Identities=20% Similarity=0.430 Sum_probs=11.2
Q ss_pred eeecCCCCceeeecC
Q psy1181 64 NHSCGYCGLRFFKED 78 (82)
Q Consensus 64 ~~~CpYCG~~y~~~~ 78 (82)
+..||.||..+...+
T Consensus 2 ~~~C~~Cg~~l~~ig 16 (47)
T PF13005_consen 2 PRACPDCGGELKEIG 16 (47)
T ss_pred CCcCCCCCceeeECC
Confidence 357999999887544
No 125
>cd03531 Rieske_RO_Alpha_KSH The alignment model represents the N-terminal rieske iron-sulfur domain of KshA, the oxygenase component of 3-ketosteroid 9-alpha-hydroxylase (KSH). The terminal oxygenase component of KSH is a key enzyme in the microbial steroid degradation pathway, catalyzing the 9 alpha-hydroxylation of 4-androstene-3,17-dione (AD) and 1,4-androstadiene-3,17-dione (ADD). KSH is a two-component class IA monooxygenase, with terminal oxygenase (KshA) and oxygenase reductase (KshB) components. KSH activity has been found in many actino- and proteo- bacterial genera including Rhodococcus, Nocardia, Arthrobacter, Mycobacterium, and Burkholderia.
Probab=30.30 E-value=42 Score=21.78 Aligned_cols=17 Identities=12% Similarity=0.319 Sum_probs=14.3
Q ss_pred CCeeecCCCCceeeecC
Q psy1181 62 PGNHSCGYCGLRFFKED 78 (82)
Q Consensus 62 ~~~~~CpYCG~~y~~~~ 78 (82)
.+..+|||.|-+|-+++
T Consensus 57 ~~~i~CP~Hg~~fd~~G 73 (115)
T cd03531 57 GDEIACPFHDWRWGGDG 73 (115)
T ss_pred CCEEECCCCCCEECCCC
Confidence 46899999999998844
No 126
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=30.29 E-value=32 Score=26.93 Aligned_cols=31 Identities=23% Similarity=0.544 Sum_probs=22.4
Q ss_pred CceEeeCCCCCCCCCCeEEEEcC-------CCCeeecCCCCc
Q psy1181 38 ERVVWCDGGSGPTGHPKVYINLD-------KPGNHSCGYCGL 72 (82)
Q Consensus 38 ~r~v~C~Gg~~~lgHP~Vyi~L~-------~~~~~~CpYCG~ 72 (82)
+.+|+|||. .=++.|+.|+ ..|.-.||.|-.
T Consensus 232 GqMVaCDn~----nCkrEWFH~~CVGLk~pPKG~WYC~eCk~ 269 (271)
T COG5034 232 GQMVACDNA----NCKREWFHLECVGLKEPPKGKWYCPECKK 269 (271)
T ss_pred ccceecCCC----CCchhheeccccccCCCCCCcEeCHHhHh
Confidence 678888876 4567788776 236788999853
No 127
>TIGR02378 nirD_assim_sml nitrite reductase [NAD(P)H], small subunit. This model describes NirD, the small subunit of nitrite reductase [NAD(P)H] (the assimilatory nitrite reductase), which associates with NirB, the large subunit (TIGR02374). In a few bacteria such as Klebsiella pneumoniae and in Fungi, the two regions are fused.
Probab=30.18 E-value=41 Score=21.07 Aligned_cols=16 Identities=25% Similarity=0.241 Sum_probs=13.9
Q ss_pred eeecCCCCceeeecCC
Q psy1181 64 NHSCGYCGLRFFKEDS 79 (82)
Q Consensus 64 ~~~CpYCG~~y~~~~~ 79 (82)
..+|||.|-+|-++.+
T Consensus 64 ~i~Cp~Hg~~Fdl~tG 79 (105)
T TIGR02378 64 WVACPLHKRNFRLEDG 79 (105)
T ss_pred EEECCcCCCEEEcCCc
Confidence 3999999999998765
No 128
>PRK09965 3-phenylpropionate dioxygenase ferredoxin subunit; Provisional
Probab=30.03 E-value=1.5e+02 Score=18.72 Aligned_cols=20 Identities=10% Similarity=0.240 Sum_probs=15.9
Q ss_pred CCCCeeecCCCCceeeecCC
Q psy1181 60 DKPGNHSCGYCGLRFFKEDS 79 (82)
Q Consensus 60 ~~~~~~~CpYCG~~y~~~~~ 79 (82)
+..+...||+-|.+|-++.|
T Consensus 55 ~~~~~i~Cp~Hg~~Fd~~tG 74 (106)
T PRK09965 55 EDDATVECPLHAASFCLRTG 74 (106)
T ss_pred CCCCEEEcCCCCCEEEcCCC
Confidence 34468999999999988655
No 129
>cd03542 Rieske_RO_Alpha_HBDO Rieske non-heme iron oxygenase (RO) family, 2-Halobenzoate 1,2-dioxygenase (HBDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. HBDO catalyzes the double hydroxylation of 2-halobenzoates with concomitant release of halogenide and carbon dioxide, yielding catechol.
Probab=29.86 E-value=50 Score=21.89 Aligned_cols=28 Identities=18% Similarity=0.352 Sum_probs=18.9
Q ss_pred CCCeEEEEcCCCCeeecCCCCceeeecC
Q psy1181 51 GHPKVYINLDKPGNHSCGYCGLRFFKED 78 (82)
Q Consensus 51 gHP~Vyi~L~~~~~~~CpYCG~~y~~~~ 78 (82)
|.|...-.+...+..+|||-|-+|-.++
T Consensus 47 g~~L~~g~~~~~~~i~CP~Hg~~Fd~~G 74 (123)
T cd03542 47 GAMLCRRKQGNKGTFTCPFHGWTFSNTG 74 (123)
T ss_pred CCccccccccCCCEEECcCCCCEecCCc
Confidence 4444433344456899999999998544
No 130
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=29.54 E-value=17 Score=23.66 Aligned_cols=17 Identities=35% Similarity=0.788 Sum_probs=7.6
Q ss_pred CCCeeecCCCCceeeec
Q psy1181 61 KPGNHSCGYCGLRFFKE 77 (82)
Q Consensus 61 ~~~~~~CpYCG~~y~~~ 77 (82)
++|...||-|+++|..-
T Consensus 48 keg~q~CpqCkt~ykr~ 64 (80)
T PF14569_consen 48 KEGNQVCPQCKTRYKRH 64 (80)
T ss_dssp HTS-SB-TTT--B----
T ss_pred hcCcccccccCCCcccc
Confidence 46788999999999753
No 131
>smart00746 TRASH metallochaperone-like domain.
Probab=29.51 E-value=25 Score=16.28 Aligned_cols=9 Identities=33% Similarity=1.435 Sum_probs=7.2
Q ss_pred cCCCCceee
Q psy1181 67 CGYCGLRFF 75 (82)
Q Consensus 67 CpYCG~~y~ 75 (82)
|++||....
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 888988765
No 132
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=29.35 E-value=24 Score=19.91 Aligned_cols=10 Identities=30% Similarity=0.690 Sum_probs=7.0
Q ss_pred ecCCCCceee
Q psy1181 66 SCGYCGLRFF 75 (82)
Q Consensus 66 ~CpYCG~~y~ 75 (82)
.||.||.+-.
T Consensus 1 ~CP~Cg~~a~ 10 (47)
T PF04606_consen 1 RCPHCGSKAR 10 (47)
T ss_pred CcCCCCCeeE
Confidence 4888887654
No 133
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=29.04 E-value=30 Score=24.53 Aligned_cols=17 Identities=29% Similarity=0.483 Sum_probs=12.8
Q ss_pred CCCeeecCCCCceeeec
Q psy1181 61 KPGNHSCGYCGLRFFKE 77 (82)
Q Consensus 61 ~~~~~~CpYCG~~y~~~ 77 (82)
..|-..||+||..=+.+
T Consensus 29 ~~glv~CP~Cgs~~V~K 45 (148)
T PF06676_consen 29 ARGLVSCPVCGSTEVSK 45 (148)
T ss_pred HcCCccCCCCCCCeEee
Confidence 34778999999876544
No 134
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=28.99 E-value=25 Score=19.23 Aligned_cols=14 Identities=36% Similarity=0.610 Sum_probs=8.7
Q ss_pred CeeecCCCCceeee
Q psy1181 63 GNHSCGYCGLRFFK 76 (82)
Q Consensus 63 ~~~~CpYCG~~y~~ 76 (82)
....|+.||-+|.+
T Consensus 20 ~~isC~~CGPr~~i 33 (35)
T PF07503_consen 20 QFISCTNCGPRYSI 33 (35)
T ss_dssp TT--BTTCC-SCCC
T ss_pred cCccCCCCCCCEEE
Confidence 35789999999865
No 135
>cd03474 Rieske_T4moC Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent hydroxylation of toluene to form p-cresol. T4mo consists of an NADH oxidoreductase (T4moF), a diiron hydroxylase (T4moH), a catalytic effector protein (T4moD), and a Rieske ferredoxin (T4moC). T4moC contains a Rieske domain and functions as an obligate electron carrier between T4moF and T4moH. Rieske ferredoxins are found as subunits of membrane oxidase complexes, cis-dihydrodiol-forming aromatic dioxygenases, bacterial assimilatory nitrite reductases, and arsenite oxidase. Rieske ferredoxins are also found as soluble electron carriers in bacterial dioxygenase and monooxygenase complexes.
Probab=28.91 E-value=90 Score=19.53 Aligned_cols=19 Identities=16% Similarity=0.202 Sum_probs=15.9
Q ss_pred CCeeecCCCCceeeecCCC
Q psy1181 62 PGNHSCGYCGLRFFKEDSH 80 (82)
Q Consensus 62 ~~~~~CpYCG~~y~~~~~~ 80 (82)
.+...|||-|.+|-++++.
T Consensus 56 g~~i~CP~Hg~~Fdl~~G~ 74 (108)
T cd03474 56 GGVLTCRAHLWQFDADTGE 74 (108)
T ss_pred CCEEEeCCcCCEEECCCcc
Confidence 3589999999999988763
No 136
>cd03028 GRX_PICOT_like Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain followed by one to three GRX-like domains. It is interesting to note that PICOT from plants contain three repeats of the GRX-like domain, metazoan proteins (except for insect) have two repeats, while fungal sequences contain only one copy of the domain. PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli. Both GRX and TRX domains of PICOT are required for its activity. Characterized non-PICOT members of this family include CXIP1, a CAX-interacting protein
Probab=28.88 E-value=35 Score=20.99 Aligned_cols=22 Identities=23% Similarity=0.504 Sum_probs=14.8
Q ss_pred CCCeEEEEcCCCCeeecCCCCc
Q psy1181 51 GHPKVYINLDKPGNHSCGYCGL 72 (82)
Q Consensus 51 gHP~Vyi~L~~~~~~~CpYCG~ 72 (82)
.||.|-+.-..++.-.||||..
T Consensus 7 ~~~vvvf~k~~~~~~~Cp~C~~ 28 (90)
T cd03028 7 ENPVVLFMKGTPEEPRCGFSRK 28 (90)
T ss_pred cCCEEEEEcCCCCCCCCcHHHH
Confidence 5777766544345568999976
No 137
>cd03478 Rieske_AIFL_N AIFL (apoptosis-inducing factor like) family, N-terminal Rieske domain; members of this family show similarity to human AIFL, containing an N-terminal Rieske domain and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain (Pyr_redox). The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. AIFL shares 35% homology with human AIF (apoptosis-inducing factor), mainly in the Pyr_redox domain. AIFL is predominantly localized to the mitochondria. AIFL induces apoptosis in a caspase-dependent manner.
Probab=28.79 E-value=1.4e+02 Score=18.21 Aligned_cols=18 Identities=22% Similarity=0.414 Sum_probs=15.1
Q ss_pred CCeeecCCCCceeeecCC
Q psy1181 62 PGNHSCGYCGLRFFKEDS 79 (82)
Q Consensus 62 ~~~~~CpYCG~~y~~~~~ 79 (82)
.+...|||-|.+|-++.+
T Consensus 54 ~~~i~CP~Hg~~Fdl~tG 71 (95)
T cd03478 54 DGRIRCPWHGACFNLRTG 71 (95)
T ss_pred CCEEEcCCCCCEEECCCC
Confidence 468999999999998554
No 138
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=28.24 E-value=35 Score=17.87 Aligned_cols=10 Identities=30% Similarity=0.783 Sum_probs=7.9
Q ss_pred CeeecCCCCc
Q psy1181 63 GNHSCGYCGL 72 (82)
Q Consensus 63 ~~~~CpYCG~ 72 (82)
..-.||-||.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 4568999986
No 139
>KOG1280|consensus
Probab=27.75 E-value=26 Score=28.58 Aligned_cols=25 Identities=32% Similarity=0.725 Sum_probs=16.0
Q ss_pred CCCCCeEEEEcC---------------CCCeeecCCCCce
Q psy1181 49 PTGHPKVYINLD---------------KPGNHSCGYCGLR 73 (82)
Q Consensus 49 ~lgHP~Vyi~L~---------------~~~~~~CpYCG~~ 73 (82)
...||.+=|-+. .+..-+|||||..
T Consensus 49 ~~dHPmqcil~~~dfeL~f~Ge~i~~y~~qSftCPyC~~~ 88 (381)
T KOG1280|consen 49 DEDHPMQCILSRVDFELYFGGEPISHYDPQSFTCPYCGIM 88 (381)
T ss_pred CCCCceeEEeeccceeeEecCccccccccccccCCccccc
Confidence 347777655443 2334689999975
No 140
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=27.54 E-value=27 Score=21.16 Aligned_cols=15 Identities=27% Similarity=0.479 Sum_probs=11.1
Q ss_pred CCeeecCCCCceeee
Q psy1181 62 PGNHSCGYCGLRFFK 76 (82)
Q Consensus 62 ~~~~~CpYCG~~y~~ 76 (82)
.-...||+||..+.-
T Consensus 12 ~v~~~Cp~cGipthc 26 (55)
T PF13824_consen 12 HVNFECPDCGIPTHC 26 (55)
T ss_pred ccCCcCCCCCCcCcc
Confidence 345689999987654
No 141
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=27.50 E-value=38 Score=19.68 Aligned_cols=12 Identities=33% Similarity=0.816 Sum_probs=6.1
Q ss_pred CeeecCCCCcee
Q psy1181 63 GNHSCGYCGLRF 74 (82)
Q Consensus 63 ~~~~CpYCG~~y 74 (82)
+...|+-||..+
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 344555555544
No 142
>PHA03294 envelope glycoprotein H; Provisional
Probab=27.45 E-value=46 Score=29.59 Aligned_cols=33 Identities=27% Similarity=0.554 Sum_probs=19.5
Q ss_pred EeeCCCCCCCCCCeEEEEcCCCCeeecCCCCceeee
Q psy1181 41 VWCDGGSGPTGHPKVYINLDKPGNHSCGYCGLRFFK 76 (82)
Q Consensus 41 v~C~Gg~~~lgHP~Vyi~L~~~~~~~CpYCG~~y~~ 76 (82)
-.|....+ .+--+.|++.. ....|+|||..|..
T Consensus 701 ~~C~~~~~--~i~p~~l~~~~-~~~~C~yCgSV~mr 733 (835)
T PHA03294 701 ATCESTSG--NIEPVRLPRPG-NLKDCLYCGCVFMR 733 (835)
T ss_pred CCccCCCC--CCCceEecCCC-CcccCCcCCeEEEE
Confidence 45755422 23334555443 34789999998853
No 143
>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
Probab=27.18 E-value=52 Score=19.21 Aligned_cols=15 Identities=20% Similarity=0.474 Sum_probs=11.8
Q ss_pred CCeeecCCCCceeee
Q psy1181 62 PGNHSCGYCGLRFFK 76 (82)
Q Consensus 62 ~~~~~CpYCG~~y~~ 76 (82)
...+.|.||+..+..
T Consensus 34 ~d~v~C~~C~~~l~~ 48 (71)
T smart00238 34 GDEVKCFFCGGELDN 48 (71)
T ss_pred CCEEEeCCCCCCcCC
Confidence 347999999998754
No 144
>cd03541 Rieske_RO_Alpha_CMO Rieske non-heme iron oxygenase (RO) family, Choline monooxygenase (CMO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. CMO is a novel RO found in certain plants which catalyzes the first step in betaine synthesis. CMO is not found in animals or bacteria. In these organisms, the first step in betaine synthesis is catalyzed by either the membrane-bound choline dehydrogenase (CDH) or the soluble choline oxidase (COX).
Probab=27.16 E-value=48 Score=21.91 Aligned_cols=17 Identities=18% Similarity=0.350 Sum_probs=14.5
Q ss_pred CCeeecCCCCceeeecC
Q psy1181 62 PGNHSCGYCGLRFFKED 78 (82)
Q Consensus 62 ~~~~~CpYCG~~y~~~~ 78 (82)
.+..+|||-|-+|-+++
T Consensus 58 ~~~i~CP~Hgw~f~l~G 74 (118)
T cd03541 58 KSCFVCPYHGWVYGLDG 74 (118)
T ss_pred cCEEEeCCCCCEEcCCC
Confidence 35789999999998876
No 145
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=26.80 E-value=51 Score=19.23 Aligned_cols=23 Identities=22% Similarity=0.430 Sum_probs=14.6
Q ss_pred CCCeEEEEcCCCCeeecCCCCceee
Q psy1181 51 GHPKVYINLDKPGNHSCGYCGLRFF 75 (82)
Q Consensus 51 gHP~Vyi~L~~~~~~~CpYCG~~y~ 75 (82)
||...- ++ ......|+-||..+-
T Consensus 35 G~~~~~-~~-~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 35 GHRNKK-RR-SGRVFTCPNCGFEMD 57 (69)
T ss_pred cccccc-cc-ccceEEcCCCCCEEC
Confidence 666555 22 235678999988754
No 146
>PHA00733 hypothetical protein
Probab=26.50 E-value=34 Score=23.14 Aligned_cols=15 Identities=20% Similarity=0.394 Sum_probs=9.0
Q ss_pred CCeeecCCCCceeee
Q psy1181 62 PGNHSCGYCGLRFFK 76 (82)
Q Consensus 62 ~~~~~CpYCG~~y~~ 76 (82)
..+..|+.||+.|..
T Consensus 71 ~kPy~C~~Cgk~Fss 85 (128)
T PHA00733 71 VSPYVCPLCLMPFSS 85 (128)
T ss_pred CCCccCCCCCCcCCC
Confidence 345566666666654
No 147
>TIGR00510 lipA lipoate synthase. The family shows strong sequence conservation.
Probab=26.47 E-value=53 Score=25.36 Aligned_cols=49 Identities=10% Similarity=0.170 Sum_probs=30.7
Q ss_pred hhhhcCCCeeecCceEeeCCCCCC-CCCCeEEEEcCCCCeeecCCCCceee
Q psy1181 26 DLIAEVPPKPCKERVVWCDGGSGP-TGHPKVYINLDKPGNHSCGYCGLRFF 75 (82)
Q Consensus 26 ~li~e~P~i~v~~r~v~C~Gg~~~-lgHP~Vyi~L~~~~~~~CpYCG~~y~ 75 (82)
+++.+.-.-.|=+ .+.|+.-+.- .++=+.||.|...-...|.||+..+.
T Consensus 36 ~~~~~~~l~tvc~-~a~cpn~~ec~~~~tatfm~i~~gC~~~C~FC~v~~~ 85 (302)
T TIGR00510 36 NTMKNKGLHTVCE-EASCPNLTECWNHGTATFMILGDICTRRCPFCDVAHG 85 (302)
T ss_pred HHHHHCCCceeec-CCCCCCcccccCCCEEEEEecCcCcCCCCCcCCccCC
Confidence 4444444433311 1356544332 37788999998877899999998654
No 148
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=26.21 E-value=29 Score=17.53 Aligned_cols=11 Identities=18% Similarity=0.238 Sum_probs=9.0
Q ss_pred eecCCCCceee
Q psy1181 65 HSCGYCGLRFF 75 (82)
Q Consensus 65 ~~CpYCG~~y~ 75 (82)
+.||-|++.+.
T Consensus 2 v~CPiC~~~v~ 12 (26)
T smart00734 2 VQCPVCFREVP 12 (26)
T ss_pred CcCCCCcCccc
Confidence 57999999873
No 149
>KOG3623|consensus
Probab=26.03 E-value=16 Score=32.71 Aligned_cols=16 Identities=25% Similarity=0.536 Sum_probs=14.3
Q ss_pred eeecCCCCceeeecCC
Q psy1181 64 NHSCGYCGLRFFKEDS 79 (82)
Q Consensus 64 ~~~CpYCG~~y~~~~~ 79 (82)
...|+.||+.|++++|
T Consensus 281 KFKCtECgKAFKfKHH 296 (1007)
T KOG3623|consen 281 KFKCTECGKAFKFKHH 296 (1007)
T ss_pred cccccccchhhhhHHH
Confidence 5789999999999886
No 150
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=25.99 E-value=40 Score=22.44 Aligned_cols=21 Identities=29% Similarity=0.638 Sum_probs=16.4
Q ss_pred EEEcCCCCeeecCCCCceeeecC
Q psy1181 56 YINLDKPGNHSCGYCGLRFFKED 78 (82)
Q Consensus 56 yi~L~~~~~~~CpYCG~~y~~~~ 78 (82)
|.. +.+.+.|..||++|.+..
T Consensus 46 Y~q--~g~~lvC~~C~~~~~~~~ 66 (102)
T PF10080_consen 46 YYQ--EGDQLVCKNCGVRFNLPT 66 (102)
T ss_pred eEE--ECCEEEEecCCCEEehhh
Confidence 663 457899999999997653
No 151
>cd03467 Rieske Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis.
Probab=25.82 E-value=1.6e+02 Score=17.82 Aligned_cols=40 Identities=20% Similarity=0.165 Sum_probs=23.6
Q ss_pred ceEeeCCCCCCCCCCeEEEEcCCCCeeecCCCCceeeecCC
Q psy1181 39 RVVWCDGGSGPTGHPKVYINLDKPGNHSCGYCGLRFFKEDS 79 (82)
Q Consensus 39 r~v~C~Gg~~~lgHP~Vyi~L~~~~~~~CpYCG~~y~~~~~ 79 (82)
...+.++--+-.|-|...-. ...+...||+-|.+|-+++|
T Consensus 34 ~~~a~~~~CpH~g~~l~~~~-~~~~~i~Cp~H~~~f~~~~G 73 (98)
T cd03467 34 EVYALSNRCTHQGCPLSEGE-GEDGCIVCPCHGSRFDLRTG 73 (98)
T ss_pred EEEEEcCcCCCCCccCCcCc-cCCCEEEeCCCCCEEeCCCc
Confidence 45554443333333332222 23578999999999999654
No 152
>PRK06366 acetyl-CoA acetyltransferase; Provisional
Probab=25.79 E-value=23 Score=27.69 Aligned_cols=37 Identities=24% Similarity=0.303 Sum_probs=25.9
Q ss_pred ccChhHHHhhhhcCCCeeecCceEeeCCCCCCCCCCe
Q psy1181 18 HVNTQFAIDLIAEVPPKPCKERVVWCDGGSGPTGHPK 54 (82)
Q Consensus 18 ~~n~~~a~~li~e~P~i~v~~r~v~C~Gg~~~lgHP~ 54 (82)
++|..+|..-+....-..++..+|.-.||.-++|||.
T Consensus 309 Ei~daFa~~~l~~le~lgl~g~~vN~~GG~la~GHP~ 345 (388)
T PRK06366 309 EHNEAFSIASIIVRDQLKIDNERFNVNGGAVAIGHPI 345 (388)
T ss_pred eccchhHHHHHHHHHHhCCCCCccCCCCchhhhCCCc
Confidence 5566666655555555555666899998877889993
No 153
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.77 E-value=43 Score=22.21 Aligned_cols=30 Identities=23% Similarity=0.547 Sum_probs=16.6
Q ss_pred cCceEeeCCCCCCCCCCeEEEEcCCCCeeecCCCCce
Q psy1181 37 KERVVWCDGGSGPTGHPKVYINLDKPGNHSCGYCGLR 73 (82)
Q Consensus 37 ~~r~v~C~Gg~~~lgHP~Vyi~L~~~~~~~CpYCG~~ 73 (82)
-.-.+.|.-=+. ++.+.......||.||..
T Consensus 67 ~p~~~~C~~Cg~-------~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 67 QEAECWCETCQQ-------YVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred eCcEEEcccCCC-------eeecCCccCCcCcCcCCC
Confidence 344567753221 444443333579999965
No 154
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=25.62 E-value=30 Score=19.82 Aligned_cols=10 Identities=30% Similarity=0.803 Sum_probs=7.2
Q ss_pred ecCCCCceee
Q psy1181 66 SCGYCGLRFF 75 (82)
Q Consensus 66 ~CpYCG~~y~ 75 (82)
.||.||-.=.
T Consensus 3 PCPfCGg~~~ 12 (53)
T TIGR03655 3 PCPFCGGADV 12 (53)
T ss_pred CCCCCCCcce
Confidence 5999996533
No 155
>TIGR02646 conserved hypothetical protein TIGR02646. Members of this uncharacterized protein family are found exclusively in bacteria. Neighboring genes in various genomes are also uncharacterized or may annotated as similar to restriction system proteins.
Probab=25.55 E-value=31 Score=23.46 Aligned_cols=14 Identities=21% Similarity=0.425 Sum_probs=10.2
Q ss_pred eeecCCCCceeeec
Q psy1181 64 NHSCGYCGLRFFKE 77 (82)
Q Consensus 64 ~~~CpYCG~~y~~~ 77 (82)
...|.||+..+...
T Consensus 24 ~~~C~YC~~~~~~~ 37 (144)
T TIGR02646 24 GGLCAYCEREIELL 37 (144)
T ss_pred CCCcCccCCCcCCC
Confidence 35799999966533
No 156
>PRK06245 cofG FO synthase subunit 1; Reviewed
Probab=25.44 E-value=40 Score=25.50 Aligned_cols=21 Identities=33% Similarity=0.798 Sum_probs=16.5
Q ss_pred CCeEEEEcCCCCeeecCCCCc
Q psy1181 52 HPKVYINLDKPGNHSCGYCGL 72 (82)
Q Consensus 52 HP~Vyi~L~~~~~~~CpYCG~ 72 (82)
=+..+|++...-...|.||+-
T Consensus 11 ~~~~~i~~Tn~C~~~C~fC~~ 31 (336)
T PRK06245 11 SRNVFIPLTYECRNRCGYCTF 31 (336)
T ss_pred ecceeeeccccccCCCccCCC
Confidence 356678887777889999984
No 157
>PRK00420 hypothetical protein; Validated
Probab=25.11 E-value=47 Score=22.58 Aligned_cols=18 Identities=22% Similarity=0.429 Sum_probs=14.6
Q ss_pred CCCeeecCCCCceeeecC
Q psy1181 61 KPGNHSCGYCGLRFFKED 78 (82)
Q Consensus 61 ~~~~~~CpYCG~~y~~~~ 78 (82)
+.|...||-||..+.-+.
T Consensus 37 k~g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 37 KDGEVVCPVHGKVYIVKS 54 (112)
T ss_pred CCCceECCCCCCeeeecc
Confidence 578999999999876544
No 158
>smart00507 HNHc HNH nucleases.
Probab=24.90 E-value=29 Score=18.01 Aligned_cols=11 Identities=36% Similarity=0.830 Sum_probs=9.2
Q ss_pred eecCCCCceee
Q psy1181 65 HSCGYCGLRFF 75 (82)
Q Consensus 65 ~~CpYCG~~y~ 75 (82)
..|.|||..+.
T Consensus 11 ~~C~~C~~~~~ 21 (52)
T smart00507 11 GVCAYCGKPAS 21 (52)
T ss_pred CCCcCCcCCCC
Confidence 58999999874
No 159
>PF03470 zf-XS: XS zinc finger domain; InterPro: IPR005381 This domain is a putative nucleic acid binding zinc finger and is found at the N terminus of proteins that also contain an adjacent XS domain IPR005380 from INTERPRO and in some proteins a C-terminal XH domain IPR005379 from INTERPRO.
Probab=24.82 E-value=30 Score=20.01 Aligned_cols=7 Identities=29% Similarity=1.103 Sum_probs=5.7
Q ss_pred cCCCCce
Q psy1181 67 CGYCGLR 73 (82)
Q Consensus 67 CpYCG~~ 73 (82)
||||...
T Consensus 1 CP~C~~k 7 (43)
T PF03470_consen 1 CPFCPGK 7 (43)
T ss_pred CCCCCCC
Confidence 9999764
No 160
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=24.74 E-value=66 Score=16.92 Aligned_cols=13 Identities=23% Similarity=0.733 Sum_probs=10.3
Q ss_pred eecCCCCceeeec
Q psy1181 65 HSCGYCGLRFFKE 77 (82)
Q Consensus 65 ~~CpYCG~~y~~~ 77 (82)
..|+-||..|...
T Consensus 33 ~~C~~CGE~~~~~ 45 (46)
T TIGR03831 33 LVCPQCGEEYLDA 45 (46)
T ss_pred cccccCCCEeeCC
Confidence 3699999998754
No 161
>cd03532 Rieske_RO_Alpha_VanA_DdmC Rieske non-heme iron oxygenase (RO) family, Vanillate-O-demethylase oxygenase (VanA) and dicamba O-demethylase oxygenase (DdmC) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Vanillate-O-demethylase is a heterodimeric enzyme consisting of a terminal oxygenase (VanA) and reductase (VanB) components. This enzyme reductively catalyzes the conversion of vanillate into protocatechuate and formaldehyde. Protocatechuate and vanillate are important intermediate metabolites in the degrad
Probab=24.74 E-value=96 Score=19.91 Aligned_cols=17 Identities=41% Similarity=0.853 Sum_probs=14.1
Q ss_pred CCeeecCCCCceeeecC
Q psy1181 62 PGNHSCGYCGLRFFKED 78 (82)
Q Consensus 62 ~~~~~CpYCG~~y~~~~ 78 (82)
.+...|||.|-+|-.++
T Consensus 60 ~~~i~Cp~Hg~~fd~~G 76 (116)
T cd03532 60 GGGLVCGYHGLEFDSDG 76 (116)
T ss_pred CCEEEeCCCCcEEcCCC
Confidence 46899999999998543
No 162
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=24.20 E-value=52 Score=24.58 Aligned_cols=15 Identities=27% Similarity=0.572 Sum_probs=10.4
Q ss_pred CCeeecCCCCceeee
Q psy1181 62 PGNHSCGYCGLRFFK 76 (82)
Q Consensus 62 ~~~~~CpYCG~~y~~ 76 (82)
+..-.|+.|++.|+-
T Consensus 75 ~~K~~C~lc~KlFkg 89 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKG 89 (214)
T ss_dssp SEEEEE-SSS-EESS
T ss_pred CCEECCCCCCcccCC
Confidence 456899999999964
No 163
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=24.09 E-value=34 Score=20.81 Aligned_cols=11 Identities=27% Similarity=0.652 Sum_probs=8.2
Q ss_pred eecCCCCceee
Q psy1181 65 HSCGYCGLRFF 75 (82)
Q Consensus 65 ~~CpYCG~~y~ 75 (82)
..|++||..-.
T Consensus 4 kHC~~CG~~Ip 14 (59)
T PF09889_consen 4 KHCPVCGKPIP 14 (59)
T ss_pred CcCCcCCCcCC
Confidence 46999997643
No 164
>PRK10824 glutaredoxin-4; Provisional
Probab=24.08 E-value=48 Score=22.23 Aligned_cols=23 Identities=22% Similarity=0.423 Sum_probs=13.7
Q ss_pred CCCeEEEEcCCCCeeecCCCCce
Q psy1181 51 GHPKVYINLDKPGNHSCGYCGLR 73 (82)
Q Consensus 51 gHP~Vyi~L~~~~~~~CpYCG~~ 73 (82)
.||.|-+.-..+..-.||||.+.
T Consensus 14 ~~~Vvvf~Kg~~~~p~Cpyc~~a 36 (115)
T PRK10824 14 ENPILLYMKGSPKLPSCGFSAQA 36 (115)
T ss_pred cCCEEEEECCCCCCCCCchHHHH
Confidence 45555553333445689999754
No 165
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=24.01 E-value=60 Score=19.13 Aligned_cols=18 Identities=22% Similarity=0.501 Sum_probs=13.8
Q ss_pred CCeeecCCCCceeeecCC
Q psy1181 62 PGNHSCGYCGLRFFKEDS 79 (82)
Q Consensus 62 ~~~~~CpYCG~~y~~~~~ 79 (82)
+....|.-||..|+...+
T Consensus 2 Dk~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAG 19 (49)
T ss_pred CeeEEcccCCCeEEEehh
Confidence 346789999999987543
No 166
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=23.60 E-value=36 Score=19.90 Aligned_cols=11 Identities=36% Similarity=0.827 Sum_probs=8.8
Q ss_pred CeeecCCCCce
Q psy1181 63 GNHSCGYCGLR 73 (82)
Q Consensus 63 ~~~~CpYCG~~ 73 (82)
|...||-||+-
T Consensus 10 GirkCp~CGt~ 20 (44)
T PF14952_consen 10 GIRKCPKCGTY 20 (44)
T ss_pred ccccCCcCcCc
Confidence 67789999863
No 167
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=23.54 E-value=38 Score=20.01 Aligned_cols=9 Identities=44% Similarity=1.217 Sum_probs=7.3
Q ss_pred eeecCCCCc
Q psy1181 64 NHSCGYCGL 72 (82)
Q Consensus 64 ~~~CpYCG~ 72 (82)
.-+|++||.
T Consensus 44 ~y~C~~Cg~ 52 (54)
T PF10058_consen 44 QYRCPYCGA 52 (54)
T ss_pred EEEcCCCCC
Confidence 458999995
No 168
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=23.36 E-value=60 Score=17.73 Aligned_cols=16 Identities=19% Similarity=0.407 Sum_probs=11.5
Q ss_pred eeecCCCCcee-eecCC
Q psy1181 64 NHSCGYCGLRF-FKEDS 79 (82)
Q Consensus 64 ~~~CpYCG~~y-~~~~~ 79 (82)
.+.||+|+..= +.+.|
T Consensus 5 ~v~CP~C~s~~~v~k~G 21 (36)
T PF03811_consen 5 DVHCPRCQSTEGVKKNG 21 (36)
T ss_pred eeeCCCCCCCCcceeCC
Confidence 47899999865 55554
No 169
>PF14122 YokU: YokU-like protein
Probab=22.95 E-value=87 Score=20.69 Aligned_cols=36 Identities=22% Similarity=0.659 Sum_probs=21.4
Q ss_pred eeCCCCCCCCCCeEEEEcC---------CCCeeecCCCCceeeec
Q psy1181 42 WCDGGSGPTGHPKVYINLD---------KPGNHSCGYCGLRFFKE 77 (82)
Q Consensus 42 ~C~Gg~~~lgHP~Vyi~L~---------~~~~~~CpYCG~~y~~~ 77 (82)
+|.+.....+--.||-.|. .+-...|.-||-.|.-+
T Consensus 4 wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~d 48 (87)
T PF14122_consen 4 WCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQDD 48 (87)
T ss_pred cccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEehh
Confidence 4544333334445555444 33456899999999754
No 170
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=22.93 E-value=19 Score=21.07 Aligned_cols=12 Identities=33% Similarity=0.800 Sum_probs=3.8
Q ss_pred eecCCCCceeee
Q psy1181 65 HSCGYCGLRFFK 76 (82)
Q Consensus 65 ~~CpYCG~~y~~ 76 (82)
..|..|++.|-+
T Consensus 10 ~~C~~C~~~F~~ 21 (69)
T PF01363_consen 10 SNCMICGKKFSL 21 (69)
T ss_dssp SB-TTT--B-BS
T ss_pred CcCcCcCCcCCC
Confidence 445555555533
No 171
>KOG3993|consensus
Probab=22.50 E-value=22 Score=29.83 Aligned_cols=17 Identities=35% Similarity=0.813 Sum_probs=13.9
Q ss_pred CCCeeecCCCCceeeec
Q psy1181 61 KPGNHSCGYCGLRFFKE 77 (82)
Q Consensus 61 ~~~~~~CpYCG~~y~~~ 77 (82)
.+|...|.+||+.|...
T Consensus 353 s~gi~~C~~C~KkFrRq 369 (500)
T KOG3993|consen 353 SSGIFSCHTCGKKFRRQ 369 (500)
T ss_pred cCceeecHHhhhhhHHH
Confidence 45788999999999754
No 172
>PF14239 RRXRR: RRXRR protein
Probab=22.49 E-value=39 Score=24.66 Aligned_cols=40 Identities=20% Similarity=0.313 Sum_probs=23.5
Q ss_pred ccCCcCccccccccc-------------ChhHHHhhhhcCCCeeecCceEeeC
Q psy1181 5 DDYRPVRFVDKEKHV-------------NTQFAIDLIAEVPPKPCKERVVWCD 44 (82)
Q Consensus 5 ~~~~~~rf~~~~~~~-------------n~~~a~~li~e~P~i~v~~r~v~C~ 44 (82)
--||..||.|+.+.. .-.|...|..=.|+..+.-..|.=|
T Consensus 107 ~RyR~~RF~NR~r~~gwL~PSl~~rv~~~l~~v~~L~~~~PIt~i~~E~v~FD 159 (176)
T PF14239_consen 107 TRYRKARFDNRKRPKGWLPPSLRHRVDTHLRWVKRLCKLLPITAIVVELVKFD 159 (176)
T ss_pred cccccccccccCCCCCCcCcCHHHHHHHHHHHHHHHHHhCCccceEEEEEEee
Confidence 369999999987542 1233344555566655554444443
No 173
>PF14616 DUF4451: Domain of unknown function (DUF4451)
Probab=22.38 E-value=1.1e+02 Score=20.64 Aligned_cols=16 Identities=25% Similarity=0.472 Sum_probs=12.5
Q ss_pred eeecCCCC--ceeeecCC
Q psy1181 64 NHSCGYCG--LRFFKEDS 79 (82)
Q Consensus 64 ~~~CpYCG--~~y~~~~~ 79 (82)
..-||||- .-|.++.+
T Consensus 25 eGlCp~C~~~~wl~lKnS 42 (124)
T PF14616_consen 25 EGLCPYCPGGNWLKLKNS 42 (124)
T ss_pred eeECCCCCCCcEeeeccc
Confidence 78999998 77777664
No 174
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=22.31 E-value=39 Score=24.44 Aligned_cols=17 Identities=24% Similarity=0.577 Sum_probs=13.1
Q ss_pred EEEcCCCCeeecCCCCce
Q psy1181 56 YINLDKPGNHSCGYCGLR 73 (82)
Q Consensus 56 yi~L~~~~~~~CpYCG~~ 73 (82)
|+-.+ +-+..||-||..
T Consensus 142 y~~~g-e~P~~CPiCga~ 158 (166)
T COG1592 142 YTHEG-EAPEVCPICGAP 158 (166)
T ss_pred CcccC-CCCCcCCCCCCh
Confidence 66666 678899999953
No 175
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=21.78 E-value=33 Score=20.37 Aligned_cols=14 Identities=29% Similarity=0.835 Sum_probs=11.2
Q ss_pred eeecCCCCceeeec
Q psy1181 64 NHSCGYCGLRFFKE 77 (82)
Q Consensus 64 ~~~CpYCG~~y~~~ 77 (82)
-.-|=|||..|...
T Consensus 27 ~~YC~~Cg~~Y~d~ 40 (55)
T PF13821_consen 27 HNYCFWCGTKYDDE 40 (55)
T ss_pred CceeeeeCCccCCH
Confidence 45799999999754
No 176
>cd03530 Rieske_NirD_small_Bacillus Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium.
Probab=21.47 E-value=1.9e+02 Score=17.56 Aligned_cols=18 Identities=11% Similarity=0.010 Sum_probs=15.5
Q ss_pred CCeeecCCCCceeeecCC
Q psy1181 62 PGNHSCGYCGLRFFKEDS 79 (82)
Q Consensus 62 ~~~~~CpYCG~~y~~~~~ 79 (82)
.+...|||=|.+|-++++
T Consensus 56 ~~~i~Cp~Hg~~Fdl~~G 73 (98)
T cd03530 56 GEYVTCPLHNWVIDLETG 73 (98)
T ss_pred CCEEECCCCCCEEECCCC
Confidence 468999999999998765
No 177
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=21.43 E-value=66 Score=21.89 Aligned_cols=51 Identities=22% Similarity=0.328 Sum_probs=29.2
Q ss_pred HHhhhhcCCCee-e---cCceEeeCCCCC--------CCCCCeEEEEcCCCCeeecCCCCceeee
Q psy1181 24 AIDLIAEVPPKP-C---KERVVWCDGGSG--------PTGHPKVYINLDKPGNHSCGYCGLRFFK 76 (82)
Q Consensus 24 a~~li~e~P~i~-v---~~r~v~C~Gg~~--------~lgHP~Vyi~L~~~~~~~CpYCG~~y~~ 76 (82)
..+++....+.. . -+|=..|.|.-- ..-.|.||-..+ ..-.||=||+.|=.
T Consensus 74 L~ev~~~~~l~~~~~~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~--~f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 74 LREVLERFGLKLRLDPIFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYD--EFWRCPGCGKIYWE 136 (147)
T ss_pred HHHHHHHcCCccccCCCCCccCCCCcEeeechhhccccccCccccccCC--eEEECCCCCCEecc
Confidence 344555555432 2 256666766321 124556665543 37899999999854
No 178
>PRK02048 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Provisional
Probab=21.37 E-value=51 Score=28.47 Aligned_cols=17 Identities=29% Similarity=0.475 Sum_probs=13.5
Q ss_pred EcCCCCeeecCCCCcee
Q psy1181 58 NLDKPGNHSCGYCGLRF 74 (82)
Q Consensus 58 ~L~~~~~~~CpYCG~~y 74 (82)
.+.|++.+.||=||+.+
T Consensus 512 R~sKTEyISCPsCGRTL 528 (611)
T PRK02048 512 RTSKTEYISCPGCGRTL 528 (611)
T ss_pred ccccceEEECCCCCcch
Confidence 34567789999999875
No 179
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=21.33 E-value=18 Score=23.89 Aligned_cols=10 Identities=30% Similarity=0.909 Sum_probs=5.8
Q ss_pred CeeecCCCCc
Q psy1181 63 GNHSCGYCGL 72 (82)
Q Consensus 63 ~~~~CpYCG~ 72 (82)
....||+||.
T Consensus 35 a~y~CpfCgk 44 (90)
T PTZ00255 35 AKYFCPFCGK 44 (90)
T ss_pred CCccCCCCCC
Confidence 3456666664
No 180
>cd01449 TST_Repeat_2 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue.
Probab=21.29 E-value=84 Score=19.40 Aligned_cols=32 Identities=28% Similarity=0.443 Sum_probs=19.1
Q ss_pred hhhhcCCCeeecCceEeeCCCCC---------CCCCCeEEE
Q psy1181 26 DLIAEVPPKPCKERVVWCDGGSG---------PTGHPKVYI 57 (82)
Q Consensus 26 ~li~e~P~i~v~~r~v~C~Gg~~---------~lgHP~Vyi 57 (82)
.++.+..+..-..-++.|.+|.. .+||+.|++
T Consensus 68 ~~~~~~~~~~~~~iv~yc~~g~~s~~~~~~l~~~G~~~v~~ 108 (118)
T cd01449 68 ALFAALGITPDKPVIVYCGSGVTACVLLLALELLGYKNVRL 108 (118)
T ss_pred HHHHHcCCCCCCCEEEECCcHHHHHHHHHHHHHcCCCCeee
Confidence 44444444344456788987532 259988764
No 181
>PRK08116 hypothetical protein; Validated
Probab=21.26 E-value=44 Score=24.89 Aligned_cols=15 Identities=33% Similarity=0.742 Sum_probs=11.1
Q ss_pred CCCeeecCCCCceee
Q psy1181 61 KPGNHSCGYCGLRFF 75 (82)
Q Consensus 61 ~~~~~~CpYCG~~y~ 75 (82)
.++...|++||....
T Consensus 13 ~~~~~~C~~Cg~~~~ 27 (268)
T PRK08116 13 EDGGEYCEVCGKRIE 27 (268)
T ss_pred cccCccCcCCCCcce
Confidence 446678999998654
No 182
>PF09180 ProRS-C_1: Prolyl-tRNA synthetase, C-terminal; InterPro: IPR016061 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. Prolyl tRNA synthetase (6.1.1.15 from EC) exists in two forms, which are loosely related. The first form is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota. Prolyl-tRNA synthetase belongs to class IIa. This domain is found at the C-terminal in archaeal and eukaryotic enzymes, as well as in certain bacterial ones.; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1NJ6_A 1NJ2_A 1NJ5_A 1NJ1_A 1H4T_C 1H4S_A 1HC7_C 1H4Q_B 3IAL_B.
Probab=20.87 E-value=42 Score=20.31 Aligned_cols=12 Identities=33% Similarity=0.747 Sum_probs=6.6
Q ss_pred CCeeecCCCCce
Q psy1181 62 PGNHSCGYCGLR 73 (82)
Q Consensus 62 ~~~~~CpYCG~~ 73 (82)
.....|.+||+.
T Consensus 46 ~~~~~Ci~cgk~ 57 (68)
T PF09180_consen 46 PEGGKCIVCGKP 57 (68)
T ss_dssp BTT-B-TTT-SB
T ss_pred CCCCeeecCCCh
Confidence 456899999963
No 183
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=20.31 E-value=57 Score=24.92 Aligned_cols=16 Identities=31% Similarity=0.588 Sum_probs=12.9
Q ss_pred CCCCeeecCCCCceee
Q psy1181 60 DKPGNHSCGYCGLRFF 75 (82)
Q Consensus 60 ~~~~~~~CpYCG~~y~ 75 (82)
...|...|..||+...
T Consensus 26 ~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 26 YERGEIVCADCGLVIE 41 (310)
T ss_pred CCCCeEeecccCCccc
Confidence 3579999999998763
Done!