Query psy2414
Match_columns 114
No_of_seqs 111 out of 1119
Neff 10.0
Searched_HMMs 46136
Date Sat Aug 17 00:22:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2414.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2414hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 2.1E-23 4.6E-28 135.4 1.8 94 16-112 160-264 (279)
2 KOG2462|consensus 99.8 4.3E-20 9.4E-25 120.1 1.8 94 16-113 129-237 (279)
3 KOG3623|consensus 99.4 2.2E-14 4.7E-19 103.9 0.7 78 32-112 890-971 (1007)
4 KOG3623|consensus 99.3 1.6E-13 3.4E-18 99.6 -1.0 64 18-81 895-971 (1007)
5 KOG3608|consensus 99.2 8.3E-13 1.8E-17 89.2 -0.8 95 15-112 205-313 (467)
6 KOG3576|consensus 99.2 6.6E-13 1.4E-17 83.7 -2.6 75 34-111 115-193 (267)
7 KOG3576|consensus 99.2 1.1E-12 2.4E-17 82.7 -2.8 97 15-111 115-232 (267)
8 KOG1074|consensus 99.1 3.5E-11 7.5E-16 88.6 1.6 77 35-113 604-690 (958)
9 KOG3608|consensus 99.1 4.5E-11 9.7E-16 81.0 1.8 96 17-112 263-373 (467)
10 PHA02768 hypothetical protein; 98.9 7.3E-10 1.6E-14 56.2 2.8 44 60-108 5-48 (55)
11 PHA00733 hypothetical protein 98.9 8.6E-10 1.9E-14 66.0 3.4 73 34-112 38-120 (128)
12 PHA00733 hypothetical protein 98.8 1E-09 2.2E-14 65.7 -0.5 79 6-85 29-124 (128)
13 PLN03086 PRLI-interacting fact 98.7 4.3E-08 9.3E-13 71.0 5.1 95 3-103 440-553 (567)
14 PHA02768 hypothetical protein; 98.6 1.3E-08 2.8E-13 51.7 1.4 41 36-77 5-48 (55)
15 PHA00732 hypothetical protein 98.6 5.2E-08 1.1E-12 53.6 2.8 45 60-112 1-45 (79)
16 KOG1074|consensus 98.5 4.9E-08 1.1E-12 72.5 1.6 50 60-112 353-402 (958)
17 PLN03086 PRLI-interacting fact 98.4 2.9E-07 6.3E-12 66.8 3.7 88 18-112 434-535 (567)
18 PF13465 zf-H2C2_2: Zinc-finge 98.3 5.2E-07 1.1E-11 39.2 2.1 26 75-103 1-26 (26)
19 PF13465 zf-H2C2_2: Zinc-finge 98.1 1E-06 2.2E-11 38.3 1.0 21 52-72 5-26 (26)
20 PHA00616 hypothetical protein 98.0 3.1E-06 6.8E-11 41.0 1.8 29 60-89 1-29 (44)
21 PF00096 zf-C2H2: Zinc finger, 97.9 6.9E-06 1.5E-10 34.4 1.7 22 61-82 1-22 (23)
22 PF13894 zf-C2H2_4: C2H2-type 97.8 2.1E-05 4.6E-10 32.9 2.2 24 61-84 1-24 (24)
23 PHA00732 hypothetical protein 97.7 2.7E-05 5.9E-10 42.8 1.9 42 36-82 1-46 (79)
24 PHA00616 hypothetical protein 97.7 1.4E-05 3E-10 38.8 0.7 30 36-65 1-34 (44)
25 PF05605 zf-Di19: Drought indu 97.6 1.6E-05 3.4E-10 40.6 0.6 47 61-111 3-49 (54)
26 PF13912 zf-C2H2_6: C2H2-type 97.6 2E-05 4.4E-10 34.2 0.7 25 60-84 1-25 (27)
27 PF05605 zf-Di19: Drought indu 97.4 0.00032 6.9E-09 35.7 3.3 47 36-84 2-53 (54)
28 smart00355 ZnF_C2H2 zinc finge 97.1 0.00072 1.6E-08 28.3 2.7 22 61-82 1-22 (26)
29 KOG3993|consensus 97.1 0.00028 6.2E-09 49.6 1.8 28 60-87 356-383 (500)
30 PF13909 zf-H2C2_5: C2H2-type 96.9 0.0012 2.7E-08 27.6 2.2 24 61-85 1-24 (24)
31 PF00096 zf-C2H2: Zinc finger, 96.6 0.0016 3.4E-08 26.9 1.5 20 37-56 1-23 (23)
32 PF09237 GAGA: GAGA factor; I 96.5 0.0034 7.4E-08 31.3 2.4 26 60-85 24-49 (54)
33 PF12874 zf-met: Zinc-finger o 96.4 0.0015 3.2E-08 27.6 0.8 22 61-82 1-22 (25)
34 PF12756 zf-C2H2_2: C2H2 type 96.4 9.3E-05 2E-09 41.9 -4.1 68 38-112 1-71 (100)
35 PRK04860 hypothetical protein; 95.8 0.0071 1.5E-07 37.7 2.2 40 60-106 119-158 (160)
36 PRK04860 hypothetical protein; 95.8 0.0085 1.8E-07 37.3 2.4 38 35-73 118-156 (160)
37 COG5189 SFP1 Putative transcri 95.7 0.0072 1.6E-07 41.4 2.0 50 60-111 349-418 (423)
38 PF13913 zf-C2HC_2: zinc-finge 95.6 0.017 3.6E-07 24.5 2.2 20 61-81 3-22 (25)
39 PF12171 zf-C2H2_jaz: Zinc-fin 95.5 0.0034 7.3E-08 27.1 -0.1 21 61-81 2-22 (27)
40 KOG3993|consensus 95.5 0.0014 3E-08 46.3 -2.1 47 61-112 268-316 (500)
41 COG5189 SFP1 Putative transcri 95.2 0.0064 1.4E-07 41.6 0.4 49 33-81 346-419 (423)
42 smart00451 ZnF_U1 U1-like zinc 94.4 0.032 7E-07 25.3 1.6 22 60-81 3-24 (35)
43 PF12756 zf-C2H2_2: C2H2 type 92.3 0.14 3E-06 28.6 2.3 24 60-83 50-73 (100)
44 PF09538 FYDLN_acid: Protein o 92.0 0.11 2.5E-06 30.2 1.7 30 18-49 10-39 (108)
45 KOG2893|consensus 90.6 0.13 2.7E-06 34.2 1.0 11 60-70 34-44 (341)
46 PF09986 DUF2225: Uncharacteri 88.5 0.33 7.1E-06 31.7 1.8 16 16-31 4-19 (214)
47 PF13719 zinc_ribbon_5: zinc-r 88.4 0.39 8.4E-06 22.3 1.5 29 18-46 3-35 (37)
48 PRK00398 rpoP DNA-directed RNA 87.7 0.42 9.1E-06 23.2 1.5 28 18-46 4-31 (46)
49 cd00350 rubredoxin_like Rubred 87.3 0.43 9.3E-06 21.5 1.3 23 18-43 2-24 (33)
50 PF13717 zinc_ribbon_4: zinc-r 86.7 0.59 1.3E-05 21.5 1.6 11 19-29 4-14 (36)
51 COG1592 Rubrerythrin [Energy p 85.8 0.57 1.2E-05 29.4 1.7 8 60-67 149-156 (166)
52 TIGR02300 FYDLN_acid conserved 85.5 0.65 1.4E-05 27.8 1.7 29 19-49 11-39 (129)
53 COG4049 Uncharacterized protei 85.5 0.52 1.1E-05 24.0 1.1 29 57-85 13-42 (65)
54 COG5048 FOG: Zn-finger [Genera 84.6 0.53 1.1E-05 32.9 1.3 51 60-112 289-344 (467)
55 KOG2186|consensus 84.4 0.45 9.7E-06 31.8 0.8 44 37-81 4-49 (276)
56 COG2888 Predicted Zn-ribbon RN 83.8 2 4.4E-05 22.2 2.8 27 19-46 11-37 (61)
57 COG1997 RPL43A Ribosomal prote 83.5 0.88 1.9E-05 25.4 1.6 28 18-46 36-63 (89)
58 cd00729 rubredoxin_SM Rubredox 83.0 0.76 1.6E-05 20.9 1.0 10 18-27 3-12 (34)
59 TIGR02098 MJ0042_CXXC MJ0042 f 82.6 0.8 1.7E-05 21.1 1.1 9 19-27 4-12 (38)
60 COG1198 PriA Primosomal protei 81.4 0.92 2E-05 35.0 1.5 44 16-69 434-484 (730)
61 PF09723 Zn-ribbon_8: Zinc rib 80.5 0.61 1.3E-05 22.2 0.2 9 60-68 26-34 (42)
62 smart00659 RPOLCX RNA polymera 80.3 1.5 3.3E-05 21.2 1.6 24 18-43 3-26 (44)
63 smart00834 CxxC_CXXC_SSSS Puta 80.2 0.71 1.5E-05 21.5 0.4 10 19-28 7-16 (41)
64 PF14353 CpXC: CpXC protein 79.5 1.1 2.3E-05 26.7 1.1 14 18-31 2-15 (128)
65 smart00734 ZnF_Rad18 Rad18-lik 78.7 2.9 6.4E-05 17.7 2.1 20 61-81 2-21 (26)
66 PRK00464 nrdR transcriptional 78.5 1.2 2.5E-05 27.7 1.1 14 36-49 28-41 (154)
67 TIGR02605 CxxC_CxxC_SSSS putat 77.1 1 2.3E-05 22.2 0.5 10 37-46 6-15 (52)
68 PF04959 ARS2: Arsenite-resist 76.4 2.1 4.6E-05 28.1 1.9 26 60-85 77-102 (214)
69 smart00614 ZnF_BED BED zinc fi 76.1 3.2 6.9E-05 20.4 2.1 22 61-82 19-45 (50)
70 PF10571 UPF0547: Uncharacteri 76.0 2.4 5.1E-05 18.1 1.4 6 39-44 17-22 (26)
71 PHA00626 hypothetical protein 75.3 2.8 6E-05 21.4 1.7 12 61-72 24-35 (59)
72 KOG2186|consensus 75.1 2 4.4E-05 28.8 1.6 42 17-58 3-53 (276)
73 PF04810 zf-Sec23_Sec24: Sec23 75.1 3.6 7.9E-05 19.3 2.1 28 18-45 3-33 (40)
74 PF02892 zf-BED: BED zinc fing 73.5 2.5 5.4E-05 20.1 1.3 22 60-81 16-41 (45)
75 COG3357 Predicted transcriptio 73.4 2.6 5.6E-05 23.8 1.5 27 17-44 58-84 (97)
76 smart00661 RPOL9 RNA polymeras 72.5 4.9 0.00011 19.6 2.3 27 20-46 3-30 (52)
77 KOG1146|consensus 70.6 0.57 1.2E-05 38.1 -2.0 53 60-112 465-539 (1406)
78 PF12013 DUF3505: Protein of u 70.4 4.6 9.9E-05 23.3 2.2 25 61-85 81-109 (109)
79 COG1996 RPC10 DNA-directed RNA 69.5 2.9 6.3E-05 20.8 1.0 25 18-43 7-31 (49)
80 KOG1146|consensus 69.0 4.1 8.8E-05 33.6 2.2 48 34-81 463-539 (1406)
81 PF11781 RRN7: RNA polymerase 68.8 3.4 7.4E-05 19.0 1.1 27 16-44 7-33 (36)
82 PF03604 DNA_RNApol_7kD: DNA d 68.7 4 8.7E-05 18.3 1.3 8 60-67 17-24 (32)
83 TIGR00622 ssl1 transcription f 65.7 7.8 0.00017 22.8 2.4 18 92-109 82-99 (112)
84 PRK14890 putative Zn-ribbon RN 65.0 18 0.00039 18.7 3.7 10 36-45 25-34 (59)
85 smart00531 TFIIE Transcription 63.8 1.7 3.8E-05 26.6 -0.5 39 33-72 96-135 (147)
86 PF05191 ADK_lid: Adenylate ki 63.4 3 6.5E-05 19.2 0.4 25 20-44 4-29 (36)
87 PF01927 Mut7-C: Mut7-C RNAse 63.3 5.6 0.00012 24.3 1.7 13 61-73 125-137 (147)
88 PTZ00255 60S ribosomal protein 62.0 4.8 0.0001 22.7 1.1 29 17-46 36-64 (90)
89 PF11238 DUF3039: Protein of u 60.3 3.9 8.4E-05 21.0 0.5 27 20-46 28-54 (58)
90 TIGR00595 priA primosomal prot 59.8 11 0.00025 27.9 3.0 9 60-68 253-261 (505)
91 PF08274 PhnA_Zn_Ribbon: PhnA 59.2 4.3 9.3E-05 17.9 0.5 24 19-44 4-27 (30)
92 PF01286 XPA_N: XPA protein N- 58.9 6.3 0.00014 18.0 1.0 13 19-31 5-17 (34)
93 PF01363 FYVE: FYVE zinc finge 58.0 7 0.00015 20.4 1.3 29 17-48 9-37 (69)
94 TIGR00280 L37a ribosomal prote 57.7 4.9 0.00011 22.7 0.6 28 18-46 36-63 (91)
95 KOG3214|consensus 57.6 1.9 4.2E-05 24.7 -1.0 22 92-113 48-70 (109)
96 PRK09678 DNA-binding transcrip 57.3 4.2 9.2E-05 21.9 0.3 7 19-25 3-9 (72)
97 PF11494 Ta0938: Ta0938; Inte 56.5 9.8 0.00021 21.7 1.7 34 16-49 13-50 (105)
98 KOG4173|consensus 56.3 1.9 4E-05 28.2 -1.3 51 61-111 107-166 (253)
99 KOG4167|consensus 55.9 2.6 5.6E-05 32.6 -0.8 26 60-85 792-817 (907)
100 PF14803 Nudix_N_2: Nudix N-te 55.8 4.3 9.2E-05 18.5 0.2 25 20-44 3-30 (34)
101 PRK06266 transcription initiat 55.5 2.4 5.2E-05 27.0 -1.0 33 34-72 115-148 (178)
102 PRK14873 primosome assembly pr 55.1 12 0.00027 28.8 2.5 10 60-69 422-431 (665)
103 COG4530 Uncharacterized protei 55.0 8.1 0.00017 22.6 1.2 28 20-49 12-39 (129)
104 PF07754 DUF1610: Domain of un 54.5 17 0.00037 15.1 1.9 7 37-43 17-23 (24)
105 cd00065 FYVE FYVE domain; Zinc 53.6 11 0.00024 18.7 1.5 26 19-47 4-29 (57)
106 PRK00432 30S ribosomal protein 53.5 13 0.00029 18.4 1.7 25 19-45 22-46 (50)
107 COG1571 Predicted DNA-binding 53.4 9.9 0.00021 27.6 1.7 30 19-50 352-381 (421)
108 PF09845 DUF2072: Zn-ribbon co 52.7 7.3 0.00016 23.5 0.9 26 18-44 2-27 (131)
109 PF08271 TF_Zn_Ribbon: TFIIB z 52.6 5.3 0.00011 18.9 0.2 27 19-45 2-28 (43)
110 PRK00564 hypA hydrogenase nick 52.4 11 0.00023 22.3 1.5 26 16-44 70-96 (117)
111 PRK03976 rpl37ae 50S ribosomal 51.9 6.6 0.00014 22.2 0.5 28 18-46 37-64 (90)
112 COG0068 HypF Hydrogenase matur 51.5 7.8 0.00017 30.0 1.0 14 16-29 122-135 (750)
113 TIGR00373 conserved hypothetic 50.8 3 6.5E-05 25.9 -1.0 34 33-71 106-139 (158)
114 PRK03681 hypA hydrogenase nick 50.5 10 0.00022 22.3 1.2 25 18-44 71-95 (114)
115 cd00730 rubredoxin Rubredoxin; 49.6 13 0.00028 18.4 1.4 8 60-67 34-41 (50)
116 TIGR00686 phnA alkylphosphonat 49.2 12 0.00027 21.8 1.4 29 19-49 4-32 (109)
117 KOG2593|consensus 49.1 10 0.00023 27.5 1.3 14 36-49 128-141 (436)
118 CHL00174 accD acetyl-CoA carbo 48.7 5.9 0.00013 27.4 0.0 34 17-50 38-71 (296)
119 KOG2231|consensus 48.4 7.9 0.00017 29.8 0.7 12 18-29 100-111 (669)
120 KOG2041|consensus 48.2 11 0.00024 29.6 1.3 80 2-99 1102-1182(1189)
121 PF05443 ROS_MUCR: ROS/MUCR tr 48.2 12 0.00027 22.6 1.4 24 35-58 71-94 (132)
122 PF07282 OrfB_Zn_ribbon: Putat 48.0 17 0.00037 18.8 1.8 25 20-45 31-55 (69)
123 PF04780 DUF629: Protein of un 47.6 19 0.00041 26.6 2.4 30 60-89 57-86 (466)
124 PRK03564 formate dehydrogenase 47.4 19 0.00041 25.1 2.3 42 17-68 187-234 (309)
125 PF14446 Prok-RING_1: Prokaryo 47.1 18 0.00039 18.3 1.6 27 17-46 5-31 (54)
126 TIGR01562 FdhE formate dehydro 46.8 19 0.00041 25.0 2.3 43 17-69 184-233 (305)
127 PF15135 UPF0515: Uncharacteri 46.6 19 0.00041 24.4 2.1 32 16-47 131-166 (278)
128 PRK03824 hypA hydrogenase nick 46.5 11 0.00024 22.8 1.0 9 60-68 107-115 (135)
129 PF01780 Ribosomal_L37ae: Ribo 46.5 5.1 0.00011 22.6 -0.4 28 18-46 36-63 (90)
130 PRK10220 hypothetical protein; 46.5 19 0.0004 21.1 1.8 29 19-49 5-33 (111)
131 COG1656 Uncharacterized conser 46.4 16 0.00034 23.0 1.7 18 61-78 131-148 (165)
132 PF00301 Rubredoxin: Rubredoxi 45.7 9.6 0.00021 18.7 0.5 13 37-49 2-14 (47)
133 PRK12380 hydrogenase nickel in 45.3 12 0.00027 21.8 1.0 24 17-43 70-93 (113)
134 COG5236 Uncharacterized conser 45.1 17 0.00036 25.9 1.7 34 60-100 220-253 (493)
135 KOG2893|consensus 44.9 6.1 0.00013 26.5 -0.3 42 63-111 13-54 (341)
136 PRK05580 primosome assembly pr 44.5 28 0.00062 26.9 3.1 10 60-69 421-430 (679)
137 COG1773 Rubredoxin [Energy pro 44.4 17 0.00037 18.5 1.3 8 60-67 36-43 (55)
138 PF15269 zf-C2H2_7: Zinc-finge 44.4 25 0.00053 17.1 1.8 23 60-82 20-42 (54)
139 PRK01343 zinc-binding protein; 44.0 28 0.00061 17.8 2.1 17 13-29 5-21 (57)
140 TIGR01206 lysW lysine biosynth 43.9 23 0.00049 17.9 1.7 27 19-45 4-31 (54)
141 PRK12496 hypothetical protein; 43.7 22 0.00047 22.3 2.0 24 19-45 129-152 (164)
142 TIGR00100 hypA hydrogenase nic 42.3 15 0.00032 21.6 1.0 24 18-44 71-94 (115)
143 KOG2482|consensus 41.4 17 0.00036 25.8 1.3 23 60-82 195-217 (423)
144 PF13878 zf-C2H2_3: zinc-finge 41.1 18 0.00039 17.0 1.0 12 38-49 15-26 (41)
145 TIGR00515 accD acetyl-CoA carb 40.1 5.6 0.00012 27.3 -1.1 34 17-50 26-59 (285)
146 smart00154 ZnF_AN1 AN1-like Zi 40.1 15 0.00033 17.1 0.7 14 60-73 12-25 (39)
147 PF08394 Arc_trans_TRASH: Arch 39.8 9.1 0.0002 17.8 -0.1 10 20-29 1-10 (37)
148 PF04216 FdhE: Protein involve 39.0 6.4 0.00014 26.9 -1.0 42 18-69 173-220 (290)
149 COG1379 PHP family phosphoeste 38.6 15 0.00032 26.0 0.7 28 19-46 248-275 (403)
150 smart00064 FYVE Protein presen 38.4 24 0.00053 18.2 1.4 26 19-47 12-37 (68)
151 PF12907 zf-met2: Zinc-binding 37.8 21 0.00045 16.9 1.0 26 61-86 2-30 (40)
152 KOG1842|consensus 37.8 21 0.00046 26.2 1.4 14 36-49 15-28 (505)
153 PF07649 C1_3: C1-like domain; 37.7 24 0.00051 15.1 1.1 23 19-45 2-24 (30)
154 PF14369 zf-RING_3: zinc-finge 37.6 28 0.0006 15.8 1.4 8 39-46 24-31 (35)
155 PRK05654 acetyl-CoA carboxylas 37.5 6.3 0.00014 27.2 -1.2 32 18-49 28-59 (292)
156 PF07975 C1_4: TFIIH C1-like d 37.3 13 0.00029 18.5 0.3 14 35-48 20-33 (51)
157 PF01155 HypA: Hydrogenase exp 37.0 5.9 0.00013 23.2 -1.2 24 18-44 71-94 (113)
158 COG3091 SprT Zn-dependent meta 36.5 19 0.0004 22.5 0.9 33 60-100 117-149 (156)
159 COG5048 FOG: Zn-finger [Genera 36.1 24 0.00053 24.5 1.5 52 34-85 31-88 (467)
160 COG3677 Transposase and inacti 35.8 24 0.00052 21.2 1.3 32 18-49 31-66 (129)
161 PF12760 Zn_Tnp_IS1595: Transp 35.7 31 0.00067 16.5 1.5 10 34-43 35-44 (46)
162 PF00130 C1_1: Phorbol esters/ 35.7 44 0.00096 16.1 2.1 29 16-46 10-38 (53)
163 PF03811 Zn_Tnp_IS1: InsA N-te 35.6 39 0.00085 15.5 1.7 9 18-26 6-14 (36)
164 PF03107 C1_2: C1 domain; Int 34.8 39 0.00085 14.5 1.6 21 19-43 2-22 (30)
165 PF05290 Baculo_IE-1: Baculovi 34.3 29 0.00062 21.2 1.4 54 16-74 79-135 (140)
166 PF06689 zf-C4_ClpX: ClpX C4-t 34.0 13 0.00029 17.4 -0.0 25 19-43 3-31 (41)
167 cd02342 ZZ_UBA_plant Zinc fing 33.9 42 0.00092 16.1 1.7 20 19-42 2-21 (43)
168 cd02335 ZZ_ADA2 Zinc finger, Z 33.8 48 0.001 16.1 2.0 21 19-43 2-22 (49)
169 PF00628 PHD: PHD-finger; Int 33.3 58 0.0013 15.5 2.3 24 20-47 2-25 (51)
170 PRK00762 hypA hydrogenase nick 33.0 28 0.0006 20.7 1.2 11 18-29 71-81 (124)
171 PF13824 zf-Mss51: Zinc-finger 32.9 63 0.0014 16.5 2.3 17 33-49 11-27 (55)
172 PLN02294 cytochrome c oxidase 32.3 15 0.00033 23.3 0.0 21 52-72 133-153 (174)
173 COG4647 AcxC Acetone carboxyla 31.9 13 0.00028 22.5 -0.3 16 15-31 68-83 (165)
174 PF10263 SprT-like: SprT-like 31.8 26 0.00057 21.3 1.0 11 36-46 123-133 (157)
175 TIGR00416 sms DNA repair prote 30.9 43 0.00094 24.6 2.1 25 15-44 5-29 (454)
176 TIGR01053 LSD1 zinc finger dom 30.9 58 0.0013 14.4 1.9 24 19-43 3-26 (31)
177 KOG2907|consensus 30.7 42 0.00091 19.8 1.6 42 60-104 74-115 (116)
178 COG1327 Predicted transcriptio 30.7 29 0.00064 21.6 1.1 11 37-47 29-39 (156)
179 PRK12722 transcriptional activ 30.0 44 0.00096 21.6 1.8 8 60-67 154-161 (187)
180 PRK11823 DNA repair protein Ra 29.8 47 0.001 24.3 2.2 25 15-44 5-29 (446)
181 PF06170 DUF983: Protein of un 29.8 50 0.0011 18.4 1.8 23 14-36 5-27 (86)
182 COG4640 Predicted membrane pro 29.7 41 0.00089 24.5 1.8 13 61-73 16-28 (465)
183 TIGR00244 transcriptional regu 29.4 30 0.00066 21.4 1.0 12 37-48 29-40 (147)
184 PRK00420 hypothetical protein; 29.3 55 0.0012 19.3 2.0 28 18-47 24-51 (112)
185 PF04606 Ogr_Delta: Ogr/Delta- 29.2 13 0.00028 18.0 -0.5 6 97-102 33-38 (47)
186 cd00924 Cyt_c_Oxidase_Vb Cytoc 29.0 17 0.00037 20.8 -0.1 21 52-72 71-91 (97)
187 COG1779 C4-type Zn-finger prot 28.9 17 0.00037 23.6 -0.2 30 17-46 14-53 (201)
188 KOG2071|consensus 28.8 42 0.0009 25.6 1.7 23 60-82 418-440 (579)
189 KOG2785|consensus 28.5 20 0.00044 25.7 0.1 21 92-112 218-241 (390)
190 PRK12860 transcriptional activ 28.2 50 0.0011 21.4 1.8 10 19-28 136-145 (189)
191 cd02339 ZZ_Mind_bomb Zinc fing 27.3 74 0.0016 15.3 2.0 21 19-43 2-22 (45)
192 smart00290 ZnF_UBP Ubiquitin C 27.1 74 0.0016 15.1 2.0 13 36-48 11-23 (50)
193 PF00569 ZZ: Zinc finger, ZZ t 27.1 49 0.0011 15.8 1.3 24 16-43 3-26 (46)
194 COG4306 Uncharacterized protei 27.0 46 0.001 20.1 1.4 11 19-29 70-80 (160)
195 PRK04351 hypothetical protein; 26.9 47 0.001 20.5 1.5 32 36-71 112-143 (149)
196 PF02150 RNA_POL_M_15KD: RNA p 26.6 16 0.00035 16.6 -0.4 6 38-43 22-27 (35)
197 TIGR00270 conserved hypothetic 26.5 33 0.00071 21.3 0.8 25 19-43 2-31 (154)
198 PF13451 zf-trcl: Probable zin 26.4 35 0.00076 16.9 0.7 18 34-51 2-19 (49)
199 PF01428 zf-AN1: AN1-like Zinc 26.2 30 0.00066 16.3 0.5 14 35-48 12-25 (43)
200 KOG3408|consensus 25.9 39 0.00084 20.2 1.0 22 60-81 57-78 (129)
201 PF06827 zf-FPG_IleRS: Zinc fi 25.1 18 0.0004 15.5 -0.4 24 19-42 3-27 (30)
202 cd02344 ZZ_HERC2 Zinc finger, 25.0 87 0.0019 15.1 2.0 21 19-43 2-22 (45)
203 cd02337 ZZ_CBP Zinc finger, ZZ 25.0 80 0.0017 14.8 1.8 19 19-43 2-20 (41)
204 PF06397 Desulfoferrod_N: Desu 25.0 36 0.00077 15.7 0.6 12 35-46 5-16 (36)
205 KOG0717|consensus 24.9 44 0.00095 24.8 1.3 22 61-82 293-314 (508)
206 COG3024 Uncharacterized protei 24.8 63 0.0014 17.0 1.5 27 16-42 6-33 (65)
207 smart00731 SprT SprT homologue 24.7 67 0.0014 19.5 1.9 32 36-70 112-143 (146)
208 PF08790 zf-LYAR: LYAR-type C2 24.6 50 0.0011 14.3 0.9 9 38-46 2-10 (28)
209 PF04423 Rad50_zn_hook: Rad50 24.5 26 0.00057 17.3 0.1 10 93-102 22-31 (54)
210 PF13248 zf-ribbon_3: zinc-rib 24.3 61 0.0013 13.4 1.2 7 19-25 4-10 (26)
211 COG4332 Uncharacterized protei 24.1 59 0.0013 21.0 1.6 33 15-47 15-60 (203)
212 TIGR03831 YgiT_finger YgiT-typ 23.8 36 0.00078 15.7 0.5 13 16-28 31-43 (46)
213 PRK06424 transcription factor; 23.2 30 0.00064 21.3 0.2 25 19-43 2-30 (144)
214 KOG0782|consensus 23.2 20 0.00043 27.4 -0.7 32 19-50 255-290 (1004)
215 PF10013 DUF2256: Uncharacteri 22.4 48 0.001 15.9 0.7 12 18-29 9-20 (42)
216 PF06524 NOA36: NOA36 protein; 22.2 1.2E+02 0.0027 20.8 2.9 81 32-112 138-230 (314)
217 PF14311 DUF4379: Domain of un 22.0 50 0.0011 16.3 0.8 13 36-48 28-40 (55)
218 cd00029 C1 Protein kinase C co 21.9 74 0.0016 14.8 1.4 26 18-45 12-37 (50)
219 smart00249 PHD PHD zinc finger 21.7 97 0.0021 13.8 2.0 12 35-46 13-24 (47)
220 PF05180 zf-DNL: DNL zinc fing 21.5 18 0.00039 19.1 -0.9 33 37-69 5-38 (66)
221 smart00109 C1 Protein kinase C 21.4 80 0.0017 14.5 1.5 26 17-45 11-36 (49)
222 COG4888 Uncharacterized Zn rib 21.2 72 0.0016 18.4 1.4 13 15-27 20-32 (104)
223 cd02249 ZZ Zinc finger, ZZ typ 21.1 1.1E+02 0.0023 14.5 1.9 20 19-43 2-21 (46)
224 cd02341 ZZ_ZZZ3 Zinc finger, Z 21.0 1E+02 0.0022 15.0 1.8 7 19-25 2-8 (48)
225 smart00440 ZnF_C2C2 C2C2 Zinc 21.0 51 0.0011 15.3 0.7 15 13-27 24-38 (40)
226 PF08209 Sgf11: Sgf11 (transcr 20.4 72 0.0016 14.3 1.1 11 37-47 5-15 (33)
227 COG4957 Predicted transcriptio 20.1 49 0.0011 20.3 0.6 22 37-58 77-98 (148)
228 COG3364 Zn-ribbon containing p 20.0 52 0.0011 19.1 0.7 15 60-74 2-16 (112)
No 1
>KOG2462|consensus
Probab=99.87 E-value=2.1e-23 Score=135.44 Aligned_cols=94 Identities=17% Similarity=0.293 Sum_probs=82.0
Q ss_pred CccccCCCCCCCCCCC-------CCCCceecccccccccChhh---HHhhhcCC-CccCCCCcCcccChhHHHHHHHHHh
Q psy2414 16 PFITRNNTDSIFYPDP-------ASPGMYKCVICLKSVRSRWH---HLQTHFSR-NHKCPYCESVYSRVDTLKLHAKRVH 84 (114)
Q Consensus 16 ~~~~c~~c~~~f~~~~-------~~~~~~~C~~C~~~f~~~~~---h~~~h~~~-~~~c~~C~~~f~~~~~l~~H~~~~~ 84 (114)
+...|+.|||++.+.. +..-+++|..||+.|...|- |+|+|+|| ||.|..|+++|.+.+||+.||++ |
T Consensus 160 ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQT-H 238 (279)
T KOG2462|consen 160 KAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQT-H 238 (279)
T ss_pred ccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHh-h
Confidence 4456777777776654 56678999999999998886 99999999 99999999999999999999998 6
Q ss_pred CCCCCCccccCCCCCccCCCCCCCCCCC
Q psy2414 85 GLGISRYIHGLIPQLLFPTPHAKTSPVD 112 (114)
Q Consensus 85 ~~~~~~~~~c~~c~~~f~~~~~L~~h~~ 112 (114)
.+.++ |.|..|+|.|+..+-|.+|.+
T Consensus 239 S~~K~--~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 239 SDVKK--HQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred cCCcc--ccCcchhhHHHHHHHHHHhhh
Confidence 66666 899999999999999999875
No 2
>KOG2462|consensus
Probab=99.78 E-value=4.3e-20 Score=120.14 Aligned_cols=94 Identities=18% Similarity=0.198 Sum_probs=83.5
Q ss_pred CccccCCCCCCCCCCC------------CCCCceecccccccccChhh---HHhhhcCCCccCCCCcCcccChhHHHHHH
Q psy2414 16 PFITRNNTDSIFYPDP------------ASPGMYKCVICLKSVRSRWH---HLQTHFSRNHKCPYCESVYSRVDTLKLHA 80 (114)
Q Consensus 16 ~~~~c~~c~~~f~~~~------------~~~~~~~C~~C~~~f~~~~~---h~~~h~~~~~~c~~C~~~f~~~~~l~~H~ 80 (114)
+-++|++||+.+.+.+ ...+.+.|.+|++.+.+-.. |+++|+- +++|.+|||.|..++-|+-|+
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l-~c~C~iCGKaFSRPWLLQGHi 207 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTL-PCECGICGKAFSRPWLLQGHI 207 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCC-CcccccccccccchHHhhccc
Confidence 6678999999998876 23567899999999988776 8888853 799999999999999999999
Q ss_pred HHHhCCCCCCccccCCCCCccCCCCCCCCCCCC
Q psy2414 81 KRVHGLGISRYIHGLIPQLLFPTPHAKTSPVDR 113 (114)
Q Consensus 81 ~~~~~~~~~~~~~c~~c~~~f~~~~~L~~h~~~ 113 (114)
|+ |+||++ |.|..|+|.|...++|+-|+++
T Consensus 208 RT-HTGEKP--F~C~hC~kAFADRSNLRAHmQT 237 (279)
T KOG2462|consen 208 RT-HTGEKP--FSCPHCGKAFADRSNLRAHMQT 237 (279)
T ss_pred cc-ccCCCC--ccCCcccchhcchHHHHHHHHh
Confidence 98 899998 9999999999999999999875
No 3
>KOG3623|consensus
Probab=99.43 E-value=2.2e-14 Score=103.90 Aligned_cols=78 Identities=18% Similarity=0.296 Sum_probs=69.7
Q ss_pred CCCCceecccccccccChhh---HHhhhcCC-CccCCCCcCcccChhHHHHHHHHHhCCCCCCccccCCCCCccCCCCCC
Q psy2414 32 ASPGMYKCVICLKSVRSRWH---HLQTHFSR-NHKCPYCESVYSRVDTLKLHAKRVHGLGISRYIHGLIPQLLFPTPHAK 107 (114)
Q Consensus 32 ~~~~~~~C~~C~~~f~~~~~---h~~~h~~~-~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~c~~c~~~f~~~~~L 107 (114)
+.+.+|.|+.|+++|.-.+. |.--|+|+ ||+|.+|.|.|..+..|.-|+|. |.|+++ |.|+.|+|.|++....
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRL-HSGEKP--fQCdKClKRFSHSGSY 966 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRL-HSGEKP--FQCDKCLKRFSHSGSY 966 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhh-ccCCCc--chhhhhhhhcccccch
Confidence 44567999999999977665 88889999 99999999999999999999996 888988 9999999999999999
Q ss_pred CCCCC
Q psy2414 108 TSPVD 112 (114)
Q Consensus 108 ~~h~~ 112 (114)
.+|++
T Consensus 967 SQHMN 971 (1007)
T KOG3623|consen 967 SQHMN 971 (1007)
T ss_pred Hhhhc
Confidence 99986
No 4
>KOG3623|consensus
Probab=99.32 E-value=1.6e-13 Score=99.58 Aligned_cols=64 Identities=22% Similarity=0.508 Sum_probs=60.0
Q ss_pred cccCCCCCCCCCCC---------CCCCceecccccccccChhh---HHhhhcCC-CccCCCCcCcccChhHHHHHHH
Q psy2414 18 ITRNNTDSIFYPDP---------ASPGMYKCVICLKSVRSRWH---HLQTHFSR-NHKCPYCESVYSRVDTLKLHAK 81 (114)
Q Consensus 18 ~~c~~c~~~f~~~~---------~~~~~~~C~~C~~~f~~~~~---h~~~h~~~-~~~c~~C~~~f~~~~~l~~H~~ 81 (114)
+.|+.|+|+|...+ +|.+||+|.+|.++|+.+-+ |.|.|.|+ ||+|..|+|+|+...+..+||.
T Consensus 895 yaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 895 YACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred chHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 67999999998776 89999999999999988865 99999999 9999999999999999999986
No 5
>KOG3608|consensus
Probab=99.24 E-value=8.3e-13 Score=89.21 Aligned_cols=95 Identities=16% Similarity=0.288 Sum_probs=82.7
Q ss_pred CCccccCCCCCCCCCCC-----------CCCCceecccccccccChhh---HHhhhcCCCccCCCCcCcccChhHHHHHH
Q psy2414 15 QPFITRNNTDSIFYPDP-----------ASPGMYKCVICLKSVRSRWH---HLQTHFSRNHKCPYCESVYSRVDTLKLHA 80 (114)
Q Consensus 15 ~~~~~c~~c~~~f~~~~-----------~~~~~~~C~~C~~~f~~~~~---h~~~h~~~~~~c~~C~~~f~~~~~l~~H~ 80 (114)
.+.+.|..||.-|.++. ....+|.|..|.+.|..... |+..|.. -|+|+.|......++.|..|+
T Consensus 205 eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn-~ykCplCdmtc~~~ssL~~H~ 283 (467)
T KOG3608|consen 205 EKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN-CYKCPLCDMTCSSASSLTTHI 283 (467)
T ss_pred CeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh-cccccccccCCCChHHHHHHH
Confidence 45677999999998877 45568999999999987764 7777754 599999999999999999999
Q ss_pred HHHhCCCCCCccccCCCCCccCCCCCCCCCCC
Q psy2414 81 KRVHGLGISRYIHGLIPQLLFPTPHAKTSPVD 112 (114)
Q Consensus 81 ~~~~~~~~~~~~~c~~c~~~f~~~~~L~~h~~ 112 (114)
+..|..+++ ++|+.|++.|.+.++|.+|++
T Consensus 284 r~rHs~dkp--fKCd~Cd~~c~~esdL~kH~~ 313 (467)
T KOG3608|consen 284 RYRHSKDKP--FKCDECDTRCVRESDLAKHVQ 313 (467)
T ss_pred HhhhccCCC--ccccchhhhhccHHHHHHHHH
Confidence 999998888 999999999999999999986
No 6
>KOG3576|consensus
Probab=99.20 E-value=6.6e-13 Score=83.73 Aligned_cols=75 Identities=20% Similarity=0.332 Sum_probs=45.3
Q ss_pred CCceecccccccccChhh---HHhhhcCC-CccCCCCcCcccChhHHHHHHHHHhCCCCCCccccCCCCCccCCCCCCCC
Q psy2414 34 PGMYKCVICLKSVRSRWH---HLQTHFSR-NHKCPYCESVYSRVDTLKLHAKRVHGLGISRYIHGLIPQLLFPTPHAKTS 109 (114)
Q Consensus 34 ~~~~~C~~C~~~f~~~~~---h~~~h~~~-~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~c~~c~~~f~~~~~L~~ 109 (114)
...+.|..|++.|....- |++.|..- .+-|..||+.|.+.-+|.+|+++ |+|.++ |.|..|+|.|++...|..
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rt-htgvrp--ykc~~c~kaftqrcsles 191 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRT-HTGVRP--YKCSLCEKAFTQRCSLES 191 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhcc-ccCccc--cchhhhhHHHHhhccHHH
Confidence 344666666666654432 66666554 56666666666666666666665 555555 666666666666665554
Q ss_pred CC
Q psy2414 110 PV 111 (114)
Q Consensus 110 h~ 111 (114)
|+
T Consensus 192 hl 193 (267)
T KOG3576|consen 192 HL 193 (267)
T ss_pred HH
Confidence 43
No 7
>KOG3576|consensus
Probab=99.16 E-value=1.1e-12 Score=82.74 Aligned_cols=97 Identities=21% Similarity=0.259 Sum_probs=74.9
Q ss_pred CCccccCCCCCCCCCCC---------CCCCceecccccccccChhh---HHhhhcCC-CccCCCCcCcccChhHHHHHHH
Q psy2414 15 QPFITRNNTDSIFYPDP---------ASPGMYKCVICLKSVRSRWH---HLQTHFSR-NHKCPYCESVYSRVDTLKLHAK 81 (114)
Q Consensus 15 ~~~~~c~~c~~~f~~~~---------~~~~~~~C~~C~~~f~~~~~---h~~~h~~~-~~~c~~C~~~f~~~~~l~~H~~ 81 (114)
+....|.+|+|.|.-.. ...+.+.|..||+.|..... |+++|+|- ||+|..|+++|.+..+|..|.+
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~ 194 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLK 194 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHH
Confidence 34567999999998765 45677899999999977754 99999999 9999999999999999999998
Q ss_pred HHhCCCC--------CCccccCCCCCccCCCCCCCCCC
Q psy2414 82 RVHGLGI--------SRYIHGLIPQLLFPTPHAKTSPV 111 (114)
Q Consensus 82 ~~~~~~~--------~~~~~c~~c~~~f~~~~~L~~h~ 111 (114)
.+|+... ...|-|+.||.+-..+..+..|+
T Consensus 195 kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~ 232 (267)
T KOG3576|consen 195 KVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHL 232 (267)
T ss_pred HHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHH
Confidence 7666322 23356888886655544444443
No 8
>KOG1074|consensus
Probab=99.08 E-value=3.5e-11 Score=88.60 Aligned_cols=77 Identities=22% Similarity=0.351 Sum_probs=65.3
Q ss_pred CceecccccccccChhh---HHhhhcCC-CccCCCCcCcccChhHHHHHHHHHhCCCCC---CccccC---CCCCccCCC
Q psy2414 35 GMYKCVICLKSVRSRWH---HLQTHFSR-NHKCPYCESVYSRVDTLKLHAKRVHGLGIS---RYIHGL---IPQLLFPTP 104 (114)
Q Consensus 35 ~~~~C~~C~~~f~~~~~---h~~~h~~~-~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~---~~~~c~---~c~~~f~~~ 104 (114)
.|..|..|.+...-.+. |.+.|+|| ||+|.+||+.|.++.+|+.|+.+ |.. ++ --+.|+ +|.+.|+..
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~v-Hka-~p~~R~q~ScP~~~ic~~kftn~ 681 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSV-HKA-KPPARVQFSCPSTFICQKKFTNA 681 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccc-ccc-CccccccccCCchhhhccccccc
Confidence 46889999998877766 99999999 99999999999999999999986 442 12 125688 999999999
Q ss_pred CCCCCCCCC
Q psy2414 105 HAKTSPVDR 113 (114)
Q Consensus 105 ~~L~~h~~~ 113 (114)
..|.+||+.
T Consensus 682 V~lpQhIri 690 (958)
T KOG1074|consen 682 VTLPQHIRI 690 (958)
T ss_pred ccccceEEe
Confidence 999999964
No 9
>KOG3608|consensus
Probab=99.08 E-value=4.5e-11 Score=80.98 Aligned_cols=96 Identities=14% Similarity=0.125 Sum_probs=80.0
Q ss_pred ccccCCCCCCCCCCC----------CCCCceecccccccccChhh---HHhhhcCCCccCCC--CcCcccChhHHHHHHH
Q psy2414 17 FITRNNTDSIFYPDP----------ASPGMYKCVICLKSVRSRWH---HLQTHFSRNHKCPY--CESVYSRVDTLKLHAK 81 (114)
Q Consensus 17 ~~~c~~c~~~f~~~~----------~~~~~~~C~~C~~~f~~~~~---h~~~h~~~~~~c~~--C~~~f~~~~~l~~H~~ 81 (114)
.++|..|+-+.+..+ +..+|++|+.|.+.+...+. |...|++.-|+|.. |..++.+...+.+|++
T Consensus 263 ~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~ 342 (467)
T KOG3608|consen 263 CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRRHFL 342 (467)
T ss_pred cccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHHHHH
Confidence 356666666655544 56899999999999988875 88888733788877 9999999999999999
Q ss_pred HHhCCCCCCccccCCCCCccCCCCCCCCCCC
Q psy2414 82 RVHGLGISRYIHGLIPQLLFPTPHAKTSPVD 112 (114)
Q Consensus 82 ~~~~~~~~~~~~c~~c~~~f~~~~~L~~h~~ 112 (114)
.+|-|..++.|.|-+|++.|++-.+|.+|++
T Consensus 343 evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~ 373 (467)
T KOG3608|consen 343 EVHEGNNPILYACHCCDRFFTSGKSLSAHLM 373 (467)
T ss_pred HhccCCCCCceeeecchhhhccchhHHHHHH
Confidence 8888888888999999999999999999875
No 10
>PHA02768 hypothetical protein; Provisional
Probab=98.95 E-value=7.3e-10 Score=56.22 Aligned_cols=44 Identities=11% Similarity=0.255 Sum_probs=38.3
Q ss_pred CccCCCCcCcccChhHHHHHHHHHhCCCCCCccccCCCCCccCCCCCCC
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKRVHGLGISRYIHGLIPQLLFPTPHAKT 108 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~c~~c~~~f~~~~~L~ 108 (114)
.|+|+.||+.|...++|..|+++|. ++ +.|..|++.|.+.+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~---k~--~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN---TN--LKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC---Cc--ccCCcccceecccceeE
Confidence 4899999999999999999999854 23 68899999999988875
No 11
>PHA00733 hypothetical protein
Probab=98.94 E-value=8.6e-10 Score=66.02 Aligned_cols=73 Identities=15% Similarity=0.090 Sum_probs=51.1
Q ss_pred CCceecccccccccChhh---------HHhhhcCC-CccCCCCcCcccChhHHHHHHHHHhCCCCCCccccCCCCCccCC
Q psy2414 34 PGMYKCVICLKSVRSRWH---------HLQTHFSR-NHKCPYCESVYSRVDTLKLHAKRVHGLGISRYIHGLIPQLLFPT 103 (114)
Q Consensus 34 ~~~~~C~~C~~~f~~~~~---------h~~~h~~~-~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~c~~c~~~f~~ 103 (114)
.+++.|+.|...|..... |+..+ ++ ||.|..|++.|.....|..|+++ +. .+ +.|..|++.|..
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~-~~kPy~C~~Cgk~Fss~s~L~~H~r~-h~--~~--~~C~~CgK~F~~ 111 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSK-AVSPYVCPLCLMPFSSSVSLKQHIRY-TE--HS--KVCPVCGKEFRN 111 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccC-CCCCccCCCCCCcCCCHHHHHHHHhc-CC--cC--ccCCCCCCccCC
Confidence 455666666665554432 22222 34 89999999999999999988875 32 23 678889999999
Q ss_pred CCCCCCCCC
Q psy2414 104 PHAKTSPVD 112 (114)
Q Consensus 104 ~~~L~~h~~ 112 (114)
...|.+|+.
T Consensus 112 ~~sL~~H~~ 120 (128)
T PHA00733 112 TDSTLDHVC 120 (128)
T ss_pred HHHHHHHHH
Confidence 888888864
No 12
>PHA00733 hypothetical protein
Probab=98.76 E-value=1e-09 Score=65.72 Aligned_cols=79 Identities=23% Similarity=0.454 Sum_probs=63.3
Q ss_pred CCCCCCCCCCCccccCCCCCCCCCCC--------------CCCCceecccccccccChhh---HHhhhcCCCccCCCCcC
Q psy2414 6 SRYPPTSPIQPFITRNNTDSIFYPDP--------------ASPGMYKCVICLKSVRSRWH---HLQTHFSRNHKCPYCES 68 (114)
Q Consensus 6 ~~~~~~~~~~~~~~c~~c~~~f~~~~--------------~~~~~~~C~~C~~~f~~~~~---h~~~h~~~~~~c~~C~~ 68 (114)
.||....+=|+.+.|.+|.+.|.... .+++||.|+.|++.|..... |++.+. .++.|..|++
T Consensus 29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~-~~~~C~~CgK 107 (128)
T PHA00733 29 KRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTE-HSKVCPVCGK 107 (128)
T ss_pred hhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcCC-cCccCCCCCC
Confidence 35666666677788999998887765 34679999999999988875 776652 2899999999
Q ss_pred cccChhHHHHHHHHHhC
Q psy2414 69 VYSRVDTLKLHAKRVHG 85 (114)
Q Consensus 69 ~f~~~~~l~~H~~~~~~ 85 (114)
.|.....|..|+...|.
T Consensus 108 ~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 108 EFRNTDSTLDHVCKKHN 124 (128)
T ss_pred ccCCHHHHHHHHHHhcC
Confidence 99999999999986553
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.66 E-value=4.3e-08 Score=70.97 Aligned_cols=95 Identities=9% Similarity=0.063 Sum_probs=57.0
Q ss_pred CcCCCCCCCCCCCCccccCCCCCCCCCCC------CCCCceecccccccccChhh--HHhhhcCC-CccCCCCcCccc--
Q psy2414 3 GFKSRYPPTSPIQPFITRNNTDSIFYPDP------ASPGMYKCVICLKSVRSRWH--HLQTHFSR-NHKCPYCESVYS-- 71 (114)
Q Consensus 3 ~~~~~~~~~~~~~~~~~c~~c~~~f~~~~------~~~~~~~C~~C~~~f~~~~~--h~~~h~~~-~~~c~~C~~~f~-- 71 (114)
||+..+.. .-++.++.|+.|++.|.... .-.+++.|+ |+..+....- |+..|.++ ++.|+.|+..+.
T Consensus 440 ~Cg~v~~r-~el~~H~~C~~Cgk~f~~s~LekH~~~~Hkpv~Cp-Cg~~~~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g 517 (567)
T PLN03086 440 GCGIVLRV-EEAKNHVHCEKCGQAFQQGEMEKHMKVFHEPLQCP-CGVVLEKEQMVQHQASTCPLRLITCRFCGDMVQAG 517 (567)
T ss_pred cccceeec-cccccCccCCCCCCccchHHHHHHHHhcCCCccCC-CCCCcchhHHHhhhhccCCCCceeCCCCCCccccC
Confidence 45555543 33456677888877775322 113567777 7754422211 76667766 788888877774
Q ss_pred --------ChhHHHHHHHHHhCCCCCCccccCCCCCccCC
Q psy2414 72 --------RVDTLKLHAKRVHGLGISRYIHGLIPQLLFPT 103 (114)
Q Consensus 72 --------~~~~l~~H~~~~~~~~~~~~~~c~~c~~~f~~ 103 (114)
....|..|... . |.++ +.|..|++.+..
T Consensus 518 ~~~~d~~d~~s~Lt~HE~~-C-G~rt--~~C~~Cgk~Vrl 553 (567)
T PLN03086 518 GSAMDVRDRLRGMSEHESI-C-GSRT--APCDSCGRSVML 553 (567)
T ss_pred ccccchhhhhhhHHHHHHh-c-CCcc--eEccccCCeeee
Confidence 13467777765 2 4444 667778776654
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.64 E-value=1.3e-08 Score=51.68 Aligned_cols=41 Identities=29% Similarity=0.443 Sum_probs=34.5
Q ss_pred ceecccccccccChhh---HHhhhcCCCccCCCCcCcccChhHHH
Q psy2414 36 MYKCVICLKSVRSRWH---HLQTHFSRNHKCPYCESVYSRVDTLK 77 (114)
Q Consensus 36 ~~~C~~C~~~f~~~~~---h~~~h~~~~~~c~~C~~~f~~~~~l~ 77 (114)
-|+|+.|++.|....+ |+++|+ .+++|..|++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~-k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN-TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC-CcccCCcccceecccceeE
Confidence 3789999999988876 999998 4799999999999877663
No 15
>PHA00732 hypothetical protein
Probab=98.58 E-value=5.2e-08 Score=53.55 Aligned_cols=45 Identities=24% Similarity=0.303 Sum_probs=32.6
Q ss_pred CccCCCCcCcccChhHHHHHHHHHhCCCCCCccccCCCCCccCCCCCCCCCCC
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKRVHGLGISRYIHGLIPQLLFPTPHAKTSPVD 112 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~c~~c~~~f~~~~~L~~h~~ 112 (114)
||.|..|++.|....+|..|++.+|.+ +.|..|++.|. .|.+|++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~-----~~C~~CgKsF~---~l~~H~~ 45 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL-----TKCPVCNKSYR---RLNQHFY 45 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC-----CccCCCCCEeC---Chhhhhc
Confidence 577888888888888888887743442 35788888887 4667764
No 16
>KOG1074|consensus
Probab=98.49 E-value=4.9e-08 Score=72.48 Aligned_cols=50 Identities=20% Similarity=0.355 Sum_probs=34.7
Q ss_pred CccCCCCcCcccChhHHHHHHHHHhCCCCCCccccCCCCCccCCCCCCCCCCC
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKRVHGLGISRYIHGLIPQLLFPTPHAKTSPVD 112 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~c~~c~~~f~~~~~L~~h~~ 112 (114)
+.+|.+|.+.|...+.|+.|.|. |+|+++ |+|.+||..|+++.+|+-|+.
T Consensus 353 khkCr~CakvfgS~SaLqiHlRS-HTGERP--fqCnvCG~~FSTkGNLKvH~~ 402 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRS-HTGERP--FQCNVCGNRFSTKGNLKVHFQ 402 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhc-cCCCCC--eeecccccccccccceeeeee
Confidence 46677777777777777777775 666666 677777777777777766654
No 17
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.40 E-value=2.9e-07 Score=66.77 Aligned_cols=88 Identities=10% Similarity=0.154 Sum_probs=64.4
Q ss_pred cccC--CCCCCCCCCCCCCCceecccccccccChhh--HHhhhcCCCccCCCCcCcccChhHHHHHHHHHhCCCCCCccc
Q psy2414 18 ITRN--NTDSIFYPDPASPGMYKCVICLKSVRSRWH--HLQTHFSRNHKCPYCESVYSRVDTLKLHAKRVHGLGISRYIH 93 (114)
Q Consensus 18 ~~c~--~c~~~f~~~~~~~~~~~C~~C~~~f~~~~~--h~~~h~~~~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~ 93 (114)
+.|+ .|+..|... ..++.+.|+.|++.|....- |+..+. .++.|+ ||+.+ ....|..|+++ +-..++ +.
T Consensus 434 V~Cp~~~Cg~v~~r~-el~~H~~C~~Cgk~f~~s~LekH~~~~H-kpv~Cp-Cg~~~-~R~~L~~H~~t-hCp~Kp--i~ 506 (567)
T PLN03086 434 VVCPHDGCGIVLRVE-EAKNHVHCEKCGQAFQQGEMEKHMKVFH-EPLQCP-CGVVL-EKEQMVQHQAS-TCPLRL--IT 506 (567)
T ss_pred eeCCcccccceeecc-ccccCccCCCCCCccchHHHHHHHHhcC-CCccCC-CCCCc-chhHHHhhhhc-cCCCCc--ee
Confidence 4565 488888554 55778999999999864322 887763 489999 99755 66899999886 555666 78
Q ss_pred cCCCCCccCC----------CCCCCCCCC
Q psy2414 94 GLIPQLLFPT----------PHAKTSPVD 112 (114)
Q Consensus 94 c~~c~~~f~~----------~~~L~~h~~ 112 (114)
|..|++.|+. .+.|+.|.+
T Consensus 507 C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~ 535 (567)
T PLN03086 507 CRFCGDMVQAGGSAMDVRDRLRGMSEHES 535 (567)
T ss_pred CCCCCCccccCccccchhhhhhhHHHHHH
Confidence 9999999963 236777753
No 18
>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=98.32 E-value=5.2e-07 Score=39.18 Aligned_cols=26 Identities=15% Similarity=0.070 Sum_probs=17.9
Q ss_pred HHHHHHHHHhCCCCCCccccCCCCCccCC
Q psy2414 75 TLKLHAKRVHGLGISRYIHGLIPQLLFPT 103 (114)
Q Consensus 75 ~l~~H~~~~~~~~~~~~~~c~~c~~~f~~ 103 (114)
+|.+|+++ |+|+++ +.|+.|++.|.+
T Consensus 1 ~l~~H~~~-H~~~k~--~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRT-HTGEKP--YKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHH-HSSSSS--EEESSSSEEESS
T ss_pred CHHHHhhh-cCCCCC--CCCCCCcCeeCc
Confidence 46777775 666666 777777777753
No 19
>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=98.13 E-value=1e-06 Score=38.26 Aligned_cols=21 Identities=43% Similarity=0.980 Sum_probs=19.0
Q ss_pred HHhhhcCC-CccCCCCcCcccC
Q psy2414 52 HLQTHFSR-NHKCPYCESVYSR 72 (114)
Q Consensus 52 h~~~h~~~-~~~c~~C~~~f~~ 72 (114)
|++.|+++ ||.|+.|++.|..
T Consensus 5 H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 5 HMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHSSSSSEEESSSSEEESS
T ss_pred HhhhcCCCCCCCCCCCcCeeCc
Confidence 89999999 9999999998863
No 20
>PHA00616 hypothetical protein
Probab=98.04 E-value=3.1e-06 Score=41.03 Aligned_cols=29 Identities=17% Similarity=0.335 Sum_probs=24.5
Q ss_pred CccCCCCcCcccChhHHHHHHHHHhCCCCC
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKRVHGLGIS 89 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~ 89 (114)
||+|..||+.|...++|..|++.+|+ +++
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg-~~~ 29 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHK-QNK 29 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcC-CCc
Confidence 68999999999999999999997555 444
No 21
>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=97.93 E-value=6.9e-06 Score=34.36 Aligned_cols=22 Identities=41% Similarity=0.807 Sum_probs=19.9
Q ss_pred ccCCCCcCcccChhHHHHHHHH
Q psy2414 61 HKCPYCESVYSRVDTLKLHAKR 82 (114)
Q Consensus 61 ~~c~~C~~~f~~~~~l~~H~~~ 82 (114)
|.|+.|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 5789999999999999999986
No 22
>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=97.80 E-value=2.1e-05 Score=32.85 Aligned_cols=24 Identities=25% Similarity=0.693 Sum_probs=19.2
Q ss_pred ccCCCCcCcccChhHHHHHHHHHh
Q psy2414 61 HKCPYCESVYSRVDTLKLHAKRVH 84 (114)
Q Consensus 61 ~~c~~C~~~f~~~~~l~~H~~~~~ 84 (114)
|.|+.|++.|.....|..|+.++|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 579999999999999999998754
No 23
>PHA00732 hypothetical protein
Probab=97.68 E-value=2.7e-05 Score=42.81 Aligned_cols=42 Identities=33% Similarity=0.659 Sum_probs=30.1
Q ss_pred ceecccccccccChhh---HHhh-hcCCCccCCCCcCcccChhHHHHHHHH
Q psy2414 36 MYKCVICLKSVRSRWH---HLQT-HFSRNHKCPYCESVYSRVDTLKLHAKR 82 (114)
Q Consensus 36 ~~~C~~C~~~f~~~~~---h~~~-h~~~~~~c~~C~~~f~~~~~l~~H~~~ 82 (114)
||.|+.|++.|..... |++. |. ++.|+.|++.|. .+..|+++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~--~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT--LTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC--CCccCCCCCEeC---Chhhhhcc
Confidence 4678888888877664 6653 43 468889999887 47777754
No 24
>PHA00616 hypothetical protein
Probab=97.68 E-value=1.4e-05 Score=38.77 Aligned_cols=30 Identities=27% Similarity=0.527 Sum_probs=26.0
Q ss_pred ceecccccccccChhh---HHhhhcCC-CccCCC
Q psy2414 36 MYKCVICLKSVRSRWH---HLQTHFSR-NHKCPY 65 (114)
Q Consensus 36 ~~~C~~C~~~f~~~~~---h~~~h~~~-~~~c~~ 65 (114)
||.|..||+.|...+. |++.|+++ ++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899999999998876 99999998 887654
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=97.64 E-value=1.6e-05 Score=40.56 Aligned_cols=47 Identities=17% Similarity=0.187 Sum_probs=23.5
Q ss_pred ccCCCCcCcccChhHHHHHHHHHhCCCCCCccccCCCCCccCCCCCCCCCC
Q psy2414 61 HKCPYCESVYSRVDTLKLHAKRVHGLGISRYIHGLIPQLLFPTPHAKTSPV 111 (114)
Q Consensus 61 ~~c~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~c~~c~~~f~~~~~L~~h~ 111 (114)
|.|++|++ -.+...|..|+...|..+.. .+.|++|...++. +|.+|+
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~-~v~CPiC~~~~~~--~l~~Hl 49 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESK-NVVCPICSSRVTD--NLIRHL 49 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCC-CccCCCchhhhhh--HHHHHH
Confidence 55666666 33345566665555554322 2445666554332 454444
No 26
>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=97.62 E-value=2e-05 Score=34.21 Aligned_cols=25 Identities=20% Similarity=0.505 Sum_probs=21.1
Q ss_pred CccCCCCcCcccChhHHHHHHHHHh
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKRVH 84 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~~~ 84 (114)
||+|..|++.|....+|..|++.++
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 5789999999999999999987643
No 27
>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=97.36 E-value=0.00032 Score=35.69 Aligned_cols=47 Identities=32% Similarity=0.535 Sum_probs=33.5
Q ss_pred ceecccccccccChhh--HHh-hhcCC--CccCCCCcCcccChhHHHHHHHHHh
Q psy2414 36 MYKCVICLKSVRSRWH--HLQ-THFSR--NHKCPYCESVYSRVDTLKLHAKRVH 84 (114)
Q Consensus 36 ~~~C~~C~~~f~~~~~--h~~-~h~~~--~~~c~~C~~~f~~~~~l~~H~~~~~ 84 (114)
.|.|+.|++.|....- |.. .|..+ .+.|+.|...+. .+|..|+..+|
T Consensus 2 ~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 4789999995543322 644 46554 799999998654 48999998765
No 28
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.12 E-value=0.00072 Score=28.35 Aligned_cols=22 Identities=32% Similarity=0.723 Sum_probs=19.5
Q ss_pred ccCCCCcCcccChhHHHHHHHH
Q psy2414 61 HKCPYCESVYSRVDTLKLHAKR 82 (114)
Q Consensus 61 ~~c~~C~~~f~~~~~l~~H~~~ 82 (114)
++|..|++.|.....|..|++.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~ 22 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRT 22 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHH
Confidence 5788999999999999999885
No 29
>KOG3993|consensus
Probab=97.09 E-value=0.00028 Score=49.59 Aligned_cols=28 Identities=18% Similarity=0.290 Sum_probs=19.7
Q ss_pred CccCCCCcCcccChhHHHHHHHHHhCCC
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKRVHGLG 87 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~~~~~~ 87 (114)
-|.|..|++.|.....|+.|+-+|+..+
T Consensus 356 i~~C~~C~KkFrRqAYLrKHqlthq~~~ 383 (500)
T KOG3993|consen 356 IFSCHTCGKKFRRQAYLRKHQLTHQRAP 383 (500)
T ss_pred eeecHHhhhhhHHHHHHHHhHHhhhccc
Confidence 4677778888888878877766655543
No 30
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.88 E-value=0.0012 Score=27.62 Aligned_cols=24 Identities=46% Similarity=0.645 Sum_probs=18.5
Q ss_pred ccCCCCcCcccChhHHHHHHHHHhC
Q psy2414 61 HKCPYCESVYSRVDTLKLHAKRVHG 85 (114)
Q Consensus 61 ~~c~~C~~~f~~~~~l~~H~~~~~~ 85 (114)
|+|+.|..... ...|..|++.+|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 57899998888 8899999988663
No 31
>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=96.61 E-value=0.0016 Score=26.90 Aligned_cols=20 Identities=50% Similarity=0.932 Sum_probs=15.5
Q ss_pred eecccccccccChhh---HHhhh
Q psy2414 37 YKCVICLKSVRSRWH---HLQTH 56 (114)
Q Consensus 37 ~~C~~C~~~f~~~~~---h~~~h 56 (114)
|.|+.|++.|..... |++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 678999999988865 76653
No 32
>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=96.46 E-value=0.0034 Score=31.31 Aligned_cols=26 Identities=27% Similarity=0.497 Sum_probs=20.3
Q ss_pred CccCCCCcCcccChhHHHHHHHHHhC
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKRVHG 85 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~~~~ 85 (114)
|-.|+.|+..+....+|.+|+.+.|.
T Consensus 24 PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred CCCCCcchhhccchhhHHHHHHHHhc
Confidence 89999999999999999999988665
No 33
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.41 E-value=0.0015 Score=27.56 Aligned_cols=22 Identities=23% Similarity=0.617 Sum_probs=18.6
Q ss_pred ccCCCCcCcccChhHHHHHHHH
Q psy2414 61 HKCPYCESVYSRVDTLKLHAKR 82 (114)
Q Consensus 61 ~~c~~C~~~f~~~~~l~~H~~~ 82 (114)
|.|..|++.|.....|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 5688899999999999988764
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.37 E-value=9.3e-05 Score=41.88 Aligned_cols=68 Identities=15% Similarity=0.147 Sum_probs=16.2
Q ss_pred ecccccccccChhh---HHhhhcCCCccCCCCcCcccChhHHHHHHHHHhCCCCCCccccCCCCCccCCCCCCCCCCC
Q psy2414 38 KCVICLKSVRSRWH---HLQTHFSRNHKCPYCESVYSRVDTLKLHAKRVHGLGISRYIHGLIPQLLFPTPHAKTSPVD 112 (114)
Q Consensus 38 ~C~~C~~~f~~~~~---h~~~h~~~~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~c~~c~~~f~~~~~L~~h~~ 112 (114)
+|..|+..|.+... |+....+- ... ....+.....+..+++. .... . +.|..|++.|....+|..|++
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~--~~~-~~~~l~~~~~~~~~~~~-~~~~-~--~~C~~C~~~f~s~~~l~~Hm~ 71 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGF--DIP-DQKYLVDPNRLLNYLRK-KVKE-S--FRCPYCNKTFRSREALQEHMR 71 (100)
T ss_dssp ----------------------------------------------------S-S--EEBSSSS-EESSHHHHHHHHH
T ss_pred Ccccccccccccccccccccccccc--ccc-ccccccccccccccccc-ccCC-C--CCCCccCCCCcCHHHHHHHHc
Confidence 47788888766543 65432221 100 11112233333334332 1111 2 678888888888888877764
No 35
>PRK04860 hypothetical protein; Provisional
Probab=95.84 E-value=0.0071 Score=37.67 Aligned_cols=40 Identities=10% Similarity=0.013 Sum_probs=26.7
Q ss_pred CccCCCCcCcccChhHHHHHHHHHhCCCCCCccccCCCCCccCCCCC
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKRVHGLGISRYIHGLIPQLLFPTPHA 106 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~c~~c~~~f~~~~~ 106 (114)
+|.|. |+. ....+.+|.++ +.++++ +.|..|+..|....+
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri-~~g~~~--YrC~~C~~~l~~~~~ 158 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRV-VRGEAV--YRCRRCGETLVFKGE 158 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHH-hcCCcc--EECCCCCceeEEecc
Confidence 67776 776 55667777776 555555 677778777765443
No 36
>PRK04860 hypothetical protein; Provisional
Probab=95.78 E-value=0.0085 Score=37.33 Aligned_cols=38 Identities=16% Similarity=0.270 Sum_probs=29.6
Q ss_pred CceecccccccccChhhHHhhhcCC-CccCCCCcCcccCh
Q psy2414 35 GMYKCVICLKSVRSRWHHLQTHFSR-NHKCPYCESVYSRV 73 (114)
Q Consensus 35 ~~~~C~~C~~~f~~~~~h~~~h~~~-~~~c~~C~~~f~~~ 73 (114)
-+|.|. |+....+...|.++|+++ +|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQEHQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCCeeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 379998 988433333499999999 99999999887654
No 37
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=95.73 E-value=0.0072 Score=41.40 Aligned_cols=50 Identities=18% Similarity=0.244 Sum_probs=34.5
Q ss_pred CccCCC--CcCcccChhHHHHHHHHHh------------------CCCCCCccccCCCCCccCCCCCCCCCC
Q psy2414 60 NHKCPY--CESVYSRVDTLKLHAKRVH------------------GLGISRYIHGLIPQLLFPTPHAKTSPV 111 (114)
Q Consensus 60 ~~~c~~--C~~~f~~~~~l~~H~~~~~------------------~~~~~~~~~c~~c~~~f~~~~~L~~h~ 111 (114)
||+|++ |.|.+.....|.-|+---| ...++ |.|++|+|.|..-..|.=|+
T Consensus 349 pykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KP--YrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 349 PYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKP--YRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred eecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCc--eeccccchhhccCccceecc
Confidence 777766 7777777777776653111 11234 67999999999999998776
No 38
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.57 E-value=0.017 Score=24.53 Aligned_cols=20 Identities=35% Similarity=0.750 Sum_probs=15.1
Q ss_pred ccCCCCcCcccChhHHHHHHH
Q psy2414 61 HKCPYCESVYSRVDTLKLHAK 81 (114)
Q Consensus 61 ~~c~~C~~~f~~~~~l~~H~~ 81 (114)
..|+.||+.| .+..|..|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4688888888 5677777765
No 39
>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=95.52 E-value=0.0034 Score=27.09 Aligned_cols=21 Identities=33% Similarity=0.653 Sum_probs=15.5
Q ss_pred ccCCCCcCcccChhHHHHHHH
Q psy2414 61 HKCPYCESVYSRVDTLKLHAK 81 (114)
Q Consensus 61 ~~c~~C~~~f~~~~~l~~H~~ 81 (114)
|.|..|++.|.....+..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 567778888887777777654
No 40
>KOG3993|consensus
Probab=95.49 E-value=0.0014 Score=46.28 Aligned_cols=47 Identities=21% Similarity=0.265 Sum_probs=28.7
Q ss_pred ccCCCCcCcccChhHHHHHH--HHHhCCCCCCccccCCCCCccCCCCCCCCCCC
Q psy2414 61 HKCPYCESVYSRVDTLKLHA--KRVHGLGISRYIHGLIPQLLFPTPHAKTSPVD 112 (114)
Q Consensus 61 ~~c~~C~~~f~~~~~l~~H~--~~~~~~~~~~~~~c~~c~~~f~~~~~L~~h~~ 112 (114)
|.|++|.-.|.+.-.|.+|. +++|. . |+|..|+|.|.=+.+|-.|.+
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~v---E--YrCPEC~KVFsCPANLASHRR 316 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHV---E--YRCPECDKVFSCPANLASHRR 316 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEe---e--ecCCcccccccCchhhhhhhc
Confidence 66666666666666666664 33343 2 666666666666666666653
No 41
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=95.20 E-value=0.0064 Score=41.64 Aligned_cols=49 Identities=29% Similarity=0.600 Sum_probs=36.7
Q ss_pred CCCceeccc--ccccccChhh---HHh-------hh------------cCC-CccCCCCcCcccChhHHHHHHH
Q psy2414 33 SPGMYKCVI--CLKSVRSRWH---HLQ-------TH------------FSR-NHKCPYCESVYSRVDTLKLHAK 81 (114)
Q Consensus 33 ~~~~~~C~~--C~~~f~~~~~---h~~-------~h------------~~~-~~~c~~C~~~f~~~~~l~~H~~ 81 (114)
+++||+|+. |++.++.... |+. +| .+. ||.|++|+|.+.....|.-|..
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 469999997 9999887643 321 11 123 9999999999999999887754
No 42
>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=94.38 E-value=0.032 Score=25.26 Aligned_cols=22 Identities=18% Similarity=0.492 Sum_probs=18.6
Q ss_pred CccCCCCcCcccChhHHHHHHH
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAK 81 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~ 81 (114)
+|.|..|++.|.....+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 5789999999998888888875
No 43
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=92.27 E-value=0.14 Score=28.60 Aligned_cols=24 Identities=25% Similarity=0.801 Sum_probs=21.3
Q ss_pred CccCCCCcCcccChhHHHHHHHHH
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKRV 83 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~~ 83 (114)
.+.|..|++.|.....|..|++.+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 599999999999999999999864
No 44
>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=92.01 E-value=0.11 Score=30.22 Aligned_cols=30 Identities=17% Similarity=0.224 Sum_probs=19.8
Q ss_pred cccCCCCCCCCCCCCCCCceecccccccccCh
Q psy2414 18 ITRNNTDSIFYPDPASPGMYKCVICLKSVRSR 49 (114)
Q Consensus 18 ~~c~~c~~~f~~~~~~~~~~~C~~C~~~f~~~ 49 (114)
..|..||+.|-. .++.|-.|+.||..|...
T Consensus 10 R~Cp~CG~kFYD--Lnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYD--LNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhcc--CCCCCccCCCCCCccCcc
Confidence 347777777755 555677777777666444
No 45
>KOG2893|consensus
Probab=90.59 E-value=0.13 Score=34.19 Aligned_cols=11 Identities=27% Similarity=0.736 Sum_probs=5.5
Q ss_pred CccCCCCcCcc
Q psy2414 60 NHKCPYCESVY 70 (114)
Q Consensus 60 ~~~c~~C~~~f 70 (114)
.|+|.+|.+.+
T Consensus 34 hfkchichkkl 44 (341)
T KOG2893|consen 34 HFKCHICHKKL 44 (341)
T ss_pred cceeeeehhhh
Confidence 45555554433
No 46
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=88.51 E-value=0.33 Score=31.73 Aligned_cols=16 Identities=19% Similarity=-0.014 Sum_probs=12.5
Q ss_pred CccccCCCCCCCCCCC
Q psy2414 16 PFITRNNTDSIFYPDP 31 (114)
Q Consensus 16 ~~~~c~~c~~~f~~~~ 31 (114)
..+.|++|++.|..+.
T Consensus 4 k~~~CPvC~~~F~~~~ 19 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKK 19 (214)
T ss_pred CceECCCCCCeeeeeE
Confidence 4577899998888764
No 47
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=88.39 E-value=0.39 Score=22.28 Aligned_cols=29 Identities=24% Similarity=0.272 Sum_probs=12.8
Q ss_pred cccCCCCCCCCCCC----CCCCceecccccccc
Q psy2414 18 ITRNNTDSIFYPDP----ASPGMYKCVICLKSV 46 (114)
Q Consensus 18 ~~c~~c~~~f~~~~----~~~~~~~C~~C~~~f 46 (114)
+.|+.|+..|.-.. .+.....|+.|+..|
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 34555555554332 122344455554443
No 48
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.74 E-value=0.42 Score=23.19 Aligned_cols=28 Identities=11% Similarity=0.065 Sum_probs=16.3
Q ss_pred cccCCCCCCCCCCCCCCCceecccccccc
Q psy2414 18 ITRNNTDSIFYPDPASPGMYKCVICLKSV 46 (114)
Q Consensus 18 ~~c~~c~~~f~~~~~~~~~~~C~~C~~~f 46 (114)
+.|..||..|.-.... ....|+.||..+
T Consensus 4 y~C~~CG~~~~~~~~~-~~~~Cp~CG~~~ 31 (46)
T PRK00398 4 YKCARCGREVELDEYG-TGVRCPYCGYRI 31 (46)
T ss_pred EECCCCCCEEEECCCC-CceECCCCCCeE
Confidence 5677777766554222 256777777543
No 49
>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=87.25 E-value=0.43 Score=21.48 Aligned_cols=23 Identities=13% Similarity=0.241 Sum_probs=11.2
Q ss_pred cccCCCCCCCCCCCCCCCceeccccc
Q psy2414 18 ITRNNTDSIFYPDPASPGMYKCVICL 43 (114)
Q Consensus 18 ~~c~~c~~~f~~~~~~~~~~~C~~C~ 43 (114)
+.|..||..+.. .+.++.|+.|+
T Consensus 2 ~~C~~CGy~y~~---~~~~~~CP~Cg 24 (33)
T cd00350 2 YVCPVCGYIYDG---EEAPWVCPVCG 24 (33)
T ss_pred EECCCCCCEECC---CcCCCcCcCCC
Confidence 345566554421 12455566655
No 50
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=86.73 E-value=0.59 Score=21.53 Aligned_cols=11 Identities=18% Similarity=0.075 Sum_probs=5.3
Q ss_pred ccCCCCCCCCC
Q psy2414 19 TRNNTDSIFYP 29 (114)
Q Consensus 19 ~c~~c~~~f~~ 29 (114)
.|+.|+..|.-
T Consensus 4 ~Cp~C~~~y~i 14 (36)
T PF13717_consen 4 TCPNCQAKYEI 14 (36)
T ss_pred ECCCCCCEEeC
Confidence 45555554443
No 51
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=85.82 E-value=0.57 Score=29.44 Aligned_cols=8 Identities=38% Similarity=1.119 Sum_probs=4.3
Q ss_pred CccCCCCc
Q psy2414 60 NHKCPYCE 67 (114)
Q Consensus 60 ~~~c~~C~ 67 (114)
|..|+.||
T Consensus 149 P~~CPiCg 156 (166)
T COG1592 149 PEVCPICG 156 (166)
T ss_pred CCcCCCCC
Confidence 55555554
No 52
>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=85.51 E-value=0.65 Score=27.79 Aligned_cols=29 Identities=17% Similarity=0.031 Sum_probs=18.5
Q ss_pred ccCCCCCCCCCCCCCCCceecccccccccCh
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICLKSVRSR 49 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~~~f~~~ 49 (114)
.|..||+.|.. .++.|-.|+.||..|...
T Consensus 11 ~Cp~cg~kFYD--Lnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 11 ICPNTGSKFYD--LNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cCCCcCccccc--cCCCCccCCCcCCccCcc
Confidence 47777777755 455667777777665433
No 53
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=85.46 E-value=0.52 Score=24.01 Aligned_cols=29 Identities=28% Similarity=0.576 Sum_probs=21.3
Q ss_pred cCC-CccCCCCcCcccChhHHHHHHHHHhC
Q psy2414 57 FSR-NHKCPYCESVYSRVDTLKLHAKRVHG 85 (114)
Q Consensus 57 ~~~-~~~c~~C~~~f~~~~~l~~H~~~~~~ 85 (114)
.|+ -+.|+-|+..|....+..+|+...|+
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 355 67888888888888888888765454
No 54
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=84.63 E-value=0.53 Score=32.87 Aligned_cols=51 Identities=20% Similarity=0.182 Sum_probs=38.8
Q ss_pred CccCCCCcCcccChhHHHHHHHH-HhCCC--CCCccccC--CCCCccCCCCCCCCCCC
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKR-VHGLG--ISRYIHGL--IPQLLFPTPHAKTSPVD 112 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~-~~~~~--~~~~~~c~--~c~~~f~~~~~L~~h~~ 112 (114)
++.|..|...|.....|..|.+. .|.++ ++ +.|. .|++.|.....|.+|..
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~--~~~p~~~~~~~~~~~~~~~~~~~ 344 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKP--FSCPYSLCGKLFSRNDALKRHIL 344 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCc--eeeeccCCCccccccccccCCcc
Confidence 46777788888888888888883 46666 55 6666 68888888888888874
No 55
>KOG2186|consensus
Probab=84.39 E-value=0.45 Score=31.82 Aligned_cols=44 Identities=25% Similarity=0.511 Sum_probs=25.8
Q ss_pred eecccccccccChhh--HHhhhcCCCccCCCCcCcccChhHHHHHHH
Q psy2414 37 YKCVICLKSVRSRWH--HLQTHFSRNHKCPYCESVYSRVDTLKLHAK 81 (114)
Q Consensus 37 ~~C~~C~~~f~~~~~--h~~~h~~~~~~c~~C~~~f~~~~~l~~H~~ 81 (114)
|.|..||....-..- |+..-.+.-|.|-.|++.|.. .....|..
T Consensus 4 FtCnvCgEsvKKp~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EehhhhhhhccccchHHHHHhccCCeeEEeeccccccc-chhhhhhh
Confidence 567777766544432 554444445777777777776 44555554
No 56
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=83.81 E-value=2 Score=22.18 Aligned_cols=27 Identities=11% Similarity=0.203 Sum_probs=12.8
Q ss_pred ccCCCCCCCCCCCCCCCceecccccccc
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICLKSV 46 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~~~f 46 (114)
.|..||...... .+--.|.|+.||+..
T Consensus 11 ~CtSCg~~i~p~-e~~v~F~CPnCGe~~ 37 (61)
T COG2888 11 VCTSCGREIAPG-ETAVKFPCPNCGEVE 37 (61)
T ss_pred eeccCCCEeccC-CceeEeeCCCCCcee
Confidence 455555544221 222346666666443
No 57
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=83.49 E-value=0.88 Score=25.38 Aligned_cols=28 Identities=14% Similarity=0.209 Sum_probs=13.3
Q ss_pred cccCCCCCCCCCCCCCCCceecccccccc
Q psy2414 18 ITRNNTDSIFYPDPASPGMYKCVICLKSV 46 (114)
Q Consensus 18 ~~c~~c~~~f~~~~~~~~~~~C~~C~~~f 46 (114)
+.|+.|++. .-+..+..-|.|..|+..|
T Consensus 36 ~~Cp~C~~~-~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 36 HVCPFCGRT-TVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CcCCCCCCc-ceeeeccCeEEcCCCCCee
Confidence 345555554 2222344445555555554
No 58
>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=82.99 E-value=0.76 Score=20.89 Aligned_cols=10 Identities=10% Similarity=-0.180 Sum_probs=5.1
Q ss_pred cccCCCCCCC
Q psy2414 18 ITRNNTDSIF 27 (114)
Q Consensus 18 ~~c~~c~~~f 27 (114)
+.|..||..+
T Consensus 3 ~~C~~CG~i~ 12 (34)
T cd00729 3 WVCPVCGYIH 12 (34)
T ss_pred EECCCCCCEe
Confidence 4455555443
No 59
>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=82.63 E-value=0.8 Score=21.09 Aligned_cols=9 Identities=22% Similarity=0.276 Sum_probs=4.2
Q ss_pred ccCCCCCCC
Q psy2414 19 TRNNTDSIF 27 (114)
Q Consensus 19 ~c~~c~~~f 27 (114)
.|+.|+..|
T Consensus 4 ~CP~C~~~~ 12 (38)
T TIGR02098 4 QCPNCKTSF 12 (38)
T ss_pred ECCCCCCEE
Confidence 344554444
No 60
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=81.35 E-value=0.92 Score=35.01 Aligned_cols=44 Identities=20% Similarity=0.357 Sum_probs=22.6
Q ss_pred CccccCCCCCCCCCCCCCCCceecccccccccChh--h----HHhhhcCC-CccCCCCcCc
Q psy2414 16 PFITRNNTDSIFYPDPASPGMYKCVICLKSVRSRW--H----HLQTHFSR-NHKCPYCESV 69 (114)
Q Consensus 16 ~~~~c~~c~~~f~~~~~~~~~~~C~~C~~~f~~~~--~----h~~~h~~~-~~~c~~C~~~ 69 (114)
+...|..||..+ +|+.|+-.+.... + |..-+... |..|+.||..
T Consensus 434 ~~l~C~~Cg~v~----------~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 434 PLLLCRDCGYIA----------ECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ceeecccCCCcc----------cCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 445677777755 3444443221111 1 33333344 7788888765
No 61
>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=80.45 E-value=0.61 Score=22.23 Aligned_cols=9 Identities=44% Similarity=0.955 Sum_probs=4.3
Q ss_pred CccCCCCcC
Q psy2414 60 NHKCPYCES 68 (114)
Q Consensus 60 ~~~c~~C~~ 68 (114)
+..|+.||.
T Consensus 26 ~~~CP~Cg~ 34 (42)
T PF09723_consen 26 PVPCPECGS 34 (42)
T ss_pred CCcCCCCCC
Confidence 444555543
No 62
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=80.33 E-value=1.5 Score=21.17 Aligned_cols=24 Identities=13% Similarity=0.077 Sum_probs=12.2
Q ss_pred cccCCCCCCCCCCCCCCCceeccccc
Q psy2414 18 ITRNNTDSIFYPDPASPGMYKCVICL 43 (114)
Q Consensus 18 ~~c~~c~~~f~~~~~~~~~~~C~~C~ 43 (114)
+.|..||..|.-. ...+..|+.||
T Consensus 3 Y~C~~Cg~~~~~~--~~~~irC~~CG 26 (44)
T smart00659 3 YICGECGRENEIK--SKDVVRCRECG 26 (44)
T ss_pred EECCCCCCEeecC--CCCceECCCCC
Confidence 4455666555443 22345555555
No 63
>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=80.15 E-value=0.71 Score=21.48 Aligned_cols=10 Identities=10% Similarity=0.129 Sum_probs=5.2
Q ss_pred ccCCCCCCCC
Q psy2414 19 TRNNTDSIFY 28 (114)
Q Consensus 19 ~c~~c~~~f~ 28 (114)
+|..||..|.
T Consensus 7 ~C~~Cg~~fe 16 (41)
T smart00834 7 RCEDCGHTFE 16 (41)
T ss_pred EcCCCCCEEE
Confidence 4555555543
No 64
>PF14353 CpXC: CpXC protein
Probab=79.46 E-value=1.1 Score=26.73 Aligned_cols=14 Identities=21% Similarity=0.067 Sum_probs=9.2
Q ss_pred cccCCCCCCCCCCC
Q psy2414 18 ITRNNTDSIFYPDP 31 (114)
Q Consensus 18 ~~c~~c~~~f~~~~ 31 (114)
+.|+.|+..|.-..
T Consensus 2 itCP~C~~~~~~~v 15 (128)
T PF14353_consen 2 ITCPHCGHEFEFEV 15 (128)
T ss_pred cCCCCCCCeeEEEE
Confidence 46777777776543
No 65
>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=78.66 E-value=2.9 Score=17.69 Aligned_cols=20 Identities=20% Similarity=0.448 Sum_probs=13.8
Q ss_pred ccCCCCcCcccChhHHHHHHH
Q psy2414 61 HKCPYCESVYSRVDTLKLHAK 81 (114)
Q Consensus 61 ~~c~~C~~~f~~~~~l~~H~~ 81 (114)
..|+.|++.+ ....++.|+.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3577888777 5567777765
No 66
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=78.46 E-value=1.2 Score=27.74 Aligned_cols=14 Identities=21% Similarity=0.441 Sum_probs=8.9
Q ss_pred ceecccccccccCh
Q psy2414 36 MYKCVICLKSVRSR 49 (114)
Q Consensus 36 ~~~C~~C~~~f~~~ 49 (114)
.+.|+.|+..|..-
T Consensus 28 ~~~c~~c~~~f~~~ 41 (154)
T PRK00464 28 RRECLACGKRFTTF 41 (154)
T ss_pred eeeccccCCcceEe
Confidence 36777777776543
No 67
>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=77.08 E-value=1 Score=22.23 Aligned_cols=10 Identities=30% Similarity=0.959 Sum_probs=4.8
Q ss_pred eecccccccc
Q psy2414 37 YKCVICLKSV 46 (114)
Q Consensus 37 ~~C~~C~~~f 46 (114)
|.|..|+..|
T Consensus 6 y~C~~Cg~~f 15 (52)
T TIGR02605 6 YRCTACGHRF 15 (52)
T ss_pred EEeCCCCCEe
Confidence 4455555444
No 68
>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=76.45 E-value=2.1 Score=28.06 Aligned_cols=26 Identities=19% Similarity=0.572 Sum_probs=20.6
Q ss_pred CccCCCCcCcccChhHHHHHHHHHhC
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKRVHG 85 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~~~~ 85 (114)
-|.|..|+|.|.-......||...|.
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred EECCCCCCcccCChHHHHHHHhhcCH
Confidence 79999999999999999999987665
No 69
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=76.14 E-value=3.2 Score=20.38 Aligned_cols=22 Identities=41% Similarity=0.815 Sum_probs=14.3
Q ss_pred ccCCCCcCcccCh-----hHHHHHHHH
Q psy2414 61 HKCPYCESVYSRV-----DTLKLHAKR 82 (114)
Q Consensus 61 ~~c~~C~~~f~~~-----~~l~~H~~~ 82 (114)
-.|..|++.+... ++|.+|+..
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 4566666666543 688888773
No 70
>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=75.98 E-value=2.4 Score=18.06 Aligned_cols=6 Identities=33% Similarity=0.695 Sum_probs=2.3
Q ss_pred cccccc
Q psy2414 39 CVICLK 44 (114)
Q Consensus 39 C~~C~~ 44 (114)
|+.||.
T Consensus 17 Cp~CG~ 22 (26)
T PF10571_consen 17 CPHCGY 22 (26)
T ss_pred CCCCCC
Confidence 333333
No 71
>PHA00626 hypothetical protein
Probab=75.35 E-value=2.8 Score=21.43 Aligned_cols=12 Identities=25% Similarity=0.290 Sum_probs=5.5
Q ss_pred ccCCCCcCcccC
Q psy2414 61 HKCPYCESVYSR 72 (114)
Q Consensus 61 ~~c~~C~~~f~~ 72 (114)
|.|..||..|+.
T Consensus 24 YkCkdCGY~ft~ 35 (59)
T PHA00626 24 YVCCDCGYNDSK 35 (59)
T ss_pred eEcCCCCCeech
Confidence 444444444443
No 72
>KOG2186|consensus
Probab=75.14 E-value=2 Score=28.81 Aligned_cols=42 Identities=17% Similarity=0.210 Sum_probs=26.3
Q ss_pred ccccCCCCCCCCCCC-------CCCCceecccccccccChhh--HHhhhcC
Q psy2414 17 FITRNNTDSIFYPDP-------ASPGMYKCVICLKSVRSRWH--HLQTHFS 58 (114)
Q Consensus 17 ~~~c~~c~~~f~~~~-------~~~~~~~C~~C~~~f~~~~~--h~~~h~~ 58 (114)
...|+.||.+..-+. -....|.|..|++.|-...- |..-.++
T Consensus 3 ~FtCnvCgEsvKKp~vekH~srCrn~~fSCIDC~k~F~~~sYknH~kCITE 53 (276)
T KOG2186|consen 3 FFTCNVCGESVKKPQVEKHMSRCRNAYFSCIDCGKTFERVSYKNHTKCITE 53 (276)
T ss_pred EEehhhhhhhccccchHHHHHhccCCeeEEeecccccccchhhhhhhhcch
Confidence 356888887766554 12256788889888865432 5554444
No 73
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=75.12 E-value=3.6 Score=19.28 Aligned_cols=28 Identities=11% Similarity=0.215 Sum_probs=13.2
Q ss_pred cccCCCCCCCCCCC---CCCCceeccccccc
Q psy2414 18 ITRNNTDSIFYPDP---ASPGMYKCVICLKS 45 (114)
Q Consensus 18 ~~c~~c~~~f~~~~---~~~~~~~C~~C~~~ 45 (114)
++|..|+.-++.-. .+.+.|.|..|+..
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEEEETTT--E
T ss_pred cccCCCCCEECCcceEcCCCCEEECcCCCCc
Confidence 46777766555443 45567788877743
No 74
>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=73.51 E-value=2.5 Score=20.06 Aligned_cols=22 Identities=41% Similarity=0.723 Sum_probs=12.2
Q ss_pred CccCCCCcCcccC----hhHHHHHHH
Q psy2414 60 NHKCPYCESVYSR----VDTLKLHAK 81 (114)
Q Consensus 60 ~~~c~~C~~~f~~----~~~l~~H~~ 81 (114)
-..|..|++.+.. .++|..|++
T Consensus 16 ~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 16 KAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp -EEETTTTEE-----SSTHHHHHHHH
T ss_pred eEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 4567777766654 367777774
No 75
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=73.43 E-value=2.6 Score=23.76 Aligned_cols=27 Identities=11% Similarity=0.053 Sum_probs=18.2
Q ss_pred ccccCCCCCCCCCCCCCCCceecccccc
Q psy2414 17 FITRNNTDSIFYPDPASPGMYKCVICLK 44 (114)
Q Consensus 17 ~~~c~~c~~~f~~~~~~~~~~~C~~C~~ 44 (114)
.-.|..||..|.. ..-.+|..|+.|..
T Consensus 58 Pa~CkkCGfef~~-~~ik~pSRCP~CKS 84 (97)
T COG3357 58 PARCKKCGFEFRD-DKIKKPSRCPKCKS 84 (97)
T ss_pred ChhhcccCccccc-cccCCcccCCcchh
Confidence 3468888888866 23455777887753
No 76
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=72.50 E-value=4.9 Score=19.61 Aligned_cols=27 Identities=11% Similarity=0.262 Sum_probs=15.6
Q ss_pred cCCCCCCCCCCCCCC-Cceecccccccc
Q psy2414 20 RNNTDSIFYPDPASP-GMYKCVICLKSV 46 (114)
Q Consensus 20 c~~c~~~f~~~~~~~-~~~~C~~C~~~f 46 (114)
|+.||.......... ..+.|+.|+..+
T Consensus 3 Cp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 3 CPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCccccccCCCCCEEECCcCCCeE
Confidence 667776554442222 367777777554
No 77
>KOG1146|consensus
Probab=70.63 E-value=0.57 Score=38.10 Aligned_cols=53 Identities=19% Similarity=0.201 Sum_probs=36.5
Q ss_pred CccCCCCcCcccChhHHHHHHHHHhCCCC----------------------CCccccCCCCCccCCCCCCCCCCC
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKRVHGLGI----------------------SRYIHGLIPQLLFPTPHAKTSPVD 112 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~~~~~~~----------------------~~~~~c~~c~~~f~~~~~L~~h~~ 112 (114)
.+.|+.|+..+.....|-.|+|..|...+ ..-+.|..|.-.+++..+|.+|++
T Consensus 465 t~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 465 TLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred cccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHH
Confidence 67777787777777777777775222111 011457889999999999988874
No 78
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=70.38 E-value=4.6 Score=23.28 Aligned_cols=25 Identities=28% Similarity=0.669 Sum_probs=22.1
Q ss_pred ccC----CCCcCcccChhHHHHHHHHHhC
Q psy2414 61 HKC----PYCESVYSRVDTLKLHAKRVHG 85 (114)
Q Consensus 61 ~~c----~~C~~~f~~~~~l~~H~~~~~~ 85 (114)
|.| ..|+..+.....+.+|.+.+|+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 8899999999999999987663
No 79
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=69.52 E-value=2.9 Score=20.75 Aligned_cols=25 Identities=12% Similarity=0.101 Sum_probs=11.0
Q ss_pred cccCCCCCCCCCCCCCCCceeccccc
Q psy2414 18 ITRNNTDSIFYPDPASPGMYKCVICL 43 (114)
Q Consensus 18 ~~c~~c~~~f~~~~~~~~~~~C~~C~ 43 (114)
+.|..||+.|... .......|+.|+
T Consensus 7 Y~C~~Cg~~~~~~-~~~~~irCp~Cg 31 (49)
T COG1996 7 YKCARCGREVELD-QETRGIRCPYCG 31 (49)
T ss_pred EEhhhcCCeeehh-hccCceeCCCCC
Confidence 4455555555211 222334455554
No 80
>KOG1146|consensus
Probab=68.98 E-value=4.1 Score=33.61 Aligned_cols=48 Identities=19% Similarity=0.315 Sum_probs=37.0
Q ss_pred CCceecccccccccChhh---HHhh---------------h----c------CC-CccCCCCcCcccChhHHHHHHH
Q psy2414 34 PGMYKCVICLKSVRSRWH---HLQT---------------H----F------SR-NHKCPYCESVYSRVDTLKLHAK 81 (114)
Q Consensus 34 ~~~~~C~~C~~~f~~~~~---h~~~---------------h----~------~~-~~~c~~C~~~f~~~~~l~~H~~ 81 (114)
.+.+.|+.|+..++.... |++. | . +. +|.|..|..++....+|.+|++
T Consensus 463 ~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 463 FKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred cccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHH
Confidence 467899999988876643 6655 1 1 12 7899999999999999999975
No 81
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=68.77 E-value=3.4 Score=19.01 Aligned_cols=27 Identities=22% Similarity=0.375 Sum_probs=18.0
Q ss_pred CccccCCCCCCCCCCCCCCCceecccccc
Q psy2414 16 PFITRNNTDSIFYPDPASPGMYKCVICLK 44 (114)
Q Consensus 16 ~~~~c~~c~~~f~~~~~~~~~~~C~~C~~ 44 (114)
+.+.|.+|+..+-. ..+..+.|..|+-
T Consensus 7 ~~~~C~~C~~~~~~--~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 7 PNEPCPVCGSRWFY--SDDGFYYCDRCGH 33 (36)
T ss_pred CCCcCCCCCCeEeE--ccCCEEEhhhCce
Confidence 44568888887444 4555677887763
No 82
>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=68.67 E-value=4 Score=18.29 Aligned_cols=8 Identities=38% Similarity=1.111 Sum_probs=3.6
Q ss_pred CccCCCCc
Q psy2414 60 NHKCPYCE 67 (114)
Q Consensus 60 ~~~c~~C~ 67 (114)
+..|+.||
T Consensus 17 ~irC~~CG 24 (32)
T PF03604_consen 17 PIRCPECG 24 (32)
T ss_dssp TSSBSSSS
T ss_pred cEECCcCC
Confidence 34444444
No 83
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=65.66 E-value=7.8 Score=22.78 Aligned_cols=18 Identities=6% Similarity=-0.162 Sum_probs=9.4
Q ss_pred cccCCCCCccCCCCCCCC
Q psy2414 92 IHGLIPQLLFPTPHAKTS 109 (114)
Q Consensus 92 ~~c~~c~~~f~~~~~L~~ 109 (114)
|.|..|...|-..-++.-
T Consensus 82 y~C~~C~~~FC~dCD~fi 99 (112)
T TIGR00622 82 YVCAVCKNVFCVDCDVFV 99 (112)
T ss_pred eeCCCCCCccccccchhh
Confidence 556666665554444333
No 84
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=64.99 E-value=18 Score=18.70 Aligned_cols=10 Identities=20% Similarity=0.527 Sum_probs=5.2
Q ss_pred ceeccccccc
Q psy2414 36 MYKCVICLKS 45 (114)
Q Consensus 36 ~~~C~~C~~~ 45 (114)
.|.|+.||..
T Consensus 25 ~F~CPnCG~~ 34 (59)
T PRK14890 25 KFLCPNCGEV 34 (59)
T ss_pred EeeCCCCCCe
Confidence 3555555543
No 85
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=63.81 E-value=1.7 Score=26.57 Aligned_cols=39 Identities=21% Similarity=0.364 Sum_probs=22.7
Q ss_pred CCCceecccccccccChhh-HHhhhcCCCccCCCCcCcccC
Q psy2414 33 SPGMYKCVICLKSVRSRWH-HLQTHFSRNHKCPYCESVYSR 72 (114)
Q Consensus 33 ~~~~~~C~~C~~~f~~~~~-h~~~h~~~~~~c~~C~~~f~~ 72 (114)
+..-|.|+.|+..|..... .....++ .|.|+.||.....
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d~~~-~f~Cp~Cg~~l~~ 135 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLDMDG-TFTCPRCGEELEE 135 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcCCCC-cEECCCCCCEEEE
Confidence 3446788888877764432 1111111 4888888876543
No 86
>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=63.41 E-value=3 Score=19.21 Aligned_cols=25 Identities=12% Similarity=0.018 Sum_probs=10.5
Q ss_pred cCCCCCCCCCCC-CCCCceecccccc
Q psy2414 20 RNNTDSIFYPDP-ASPGMYKCVICLK 44 (114)
Q Consensus 20 c~~c~~~f~~~~-~~~~~~~C~~C~~ 44 (114)
|..||+.|.-.. .....-.|+.|+.
T Consensus 4 C~~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 4 CPKCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp ETTTTEEEETTTB--SSTTBCTTTTE
T ss_pred cCCCCCccccccCCCCCCCccCCCCC
Confidence 455555554433 2222334555543
No 87
>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=63.34 E-value=5.6 Score=24.31 Aligned_cols=13 Identities=31% Similarity=0.833 Sum_probs=7.0
Q ss_pred ccCCCCcCcccCh
Q psy2414 61 HKCPYCESVYSRV 73 (114)
Q Consensus 61 ~~c~~C~~~f~~~ 73 (114)
+.|+.||+.|..-
T Consensus 125 ~~C~~C~kiyW~G 137 (147)
T PF01927_consen 125 WRCPGCGKIYWEG 137 (147)
T ss_pred EECCCCCCEeccc
Confidence 4555555555443
No 88
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=62.00 E-value=4.8 Score=22.68 Aligned_cols=29 Identities=17% Similarity=0.209 Sum_probs=13.5
Q ss_pred ccccCCCCCCCCCCCCCCCceecccccccc
Q psy2414 17 FITRNNTDSIFYPDPASPGMYKCVICLKSV 46 (114)
Q Consensus 17 ~~~c~~c~~~f~~~~~~~~~~~C~~C~~~f 46 (114)
.+.|+.|++.-.. ..+...|.|..|++.|
T Consensus 36 ~y~CpfCgk~~vk-R~a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 36 KYFCPFCGKHAVK-RQAVGIWRCKGCKKTV 64 (90)
T ss_pred CccCCCCCCCcee-eeeeEEEEcCCCCCEE
Confidence 3456666542211 1233446666666554
No 89
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=60.32 E-value=3.9 Score=21.01 Aligned_cols=27 Identities=11% Similarity=0.201 Sum_probs=19.3
Q ss_pred cCCCCCCCCCCCCCCCceecccccccc
Q psy2414 20 RNNTDSIFYPDPASPGMYKCVICLKSV 46 (114)
Q Consensus 20 c~~c~~~f~~~~~~~~~~~C~~C~~~f 46 (114)
-..||+.|.-....++.-.|+.|.+.+
T Consensus 28 vALCGk~wvp~rdp~~~PVCP~Ck~iy 54 (58)
T PF11238_consen 28 VALCGKVWVPTRDPKPFPVCPECKEIY 54 (58)
T ss_pred EeeeCceeCCCCCCCCCCCCcCHHHHH
Confidence 357899998876555555788887654
No 90
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=59.78 E-value=11 Score=27.90 Aligned_cols=9 Identities=44% Similarity=1.113 Sum_probs=5.7
Q ss_pred CccCCCCcC
Q psy2414 60 NHKCPYCES 68 (114)
Q Consensus 60 ~~~c~~C~~ 68 (114)
|..|+.|+.
T Consensus 253 ~~~Cp~C~s 261 (505)
T TIGR00595 253 PKTCPQCGS 261 (505)
T ss_pred CCCCCCCCC
Confidence 566666654
No 91
>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=59.22 E-value=4.3 Score=17.93 Aligned_cols=24 Identities=13% Similarity=0.101 Sum_probs=9.8
Q ss_pred ccCCCCCCCCCCCCCCCceecccccc
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICLK 44 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~~ 44 (114)
+|..|+..+.- .....+.|++|+.
T Consensus 4 ~Cp~C~se~~y--~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTY--EDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----E--E-SSSEEETTTTE
T ss_pred CCCCCCCccee--ccCCEEeCCcccc
Confidence 46666665544 3444567777764
No 92
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=58.86 E-value=6.3 Score=17.96 Aligned_cols=13 Identities=8% Similarity=0.043 Sum_probs=5.4
Q ss_pred ccCCCCCCCCCCC
Q psy2414 19 TRNNTDSIFYPDP 31 (114)
Q Consensus 19 ~c~~c~~~f~~~~ 31 (114)
.|.+|++.|..+.
T Consensus 5 ~C~eC~~~f~dSy 17 (34)
T PF01286_consen 5 KCDECGKPFMDSY 17 (34)
T ss_dssp E-TTT--EES-SS
T ss_pred hHhHhCCHHHHHH
Confidence 4666666666654
No 93
>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=57.96 E-value=7 Score=20.35 Aligned_cols=29 Identities=17% Similarity=0.021 Sum_probs=12.7
Q ss_pred ccccCCCCCCCCCCCCCCCceecccccccccC
Q psy2414 17 FITRNNTDSIFYPDPASPGMYKCVICLKSVRS 48 (114)
Q Consensus 17 ~~~c~~c~~~f~~~~~~~~~~~C~~C~~~f~~ 48 (114)
...|..|++.|. ...+.+.|..||..|-.
T Consensus 9 ~~~C~~C~~~F~---~~~rrhhCr~CG~~vC~ 37 (69)
T PF01363_consen 9 ASNCMICGKKFS---LFRRRHHCRNCGRVVCS 37 (69)
T ss_dssp -SB-TTT--B-B---SSS-EEE-TTT--EEEC
T ss_pred CCcCcCcCCcCC---CceeeEccCCCCCEECC
Confidence 345788888883 23566778877776643
No 94
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=57.74 E-value=4.9 Score=22.69 Aligned_cols=28 Identities=14% Similarity=0.196 Sum_probs=12.8
Q ss_pred cccCCCCCCCCCCCCCCCceecccccccc
Q psy2414 18 ITRNNTDSIFYPDPASPGMYKCVICLKSV 46 (114)
Q Consensus 18 ~~c~~c~~~f~~~~~~~~~~~C~~C~~~f 46 (114)
+.|+.|++.-.. ..+...|.|..|++.|
T Consensus 36 y~CpfCgk~~vk-R~a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 36 YVCPFCGKKTVK-RGSTGIWTCRKCGAKF 63 (91)
T ss_pred ccCCCCCCCceE-EEeeEEEEcCCCCCEE
Confidence 455666542211 1233345566665554
No 95
>KOG3214|consensus
Probab=57.59 E-value=1.9 Score=24.67 Aligned_cols=22 Identities=27% Similarity=0.218 Sum_probs=13.1
Q ss_pred cccCCCCCccCC-CCCCCCCCCC
Q psy2414 92 IHGLIPQLLFPT-PHAKTSPVDR 113 (114)
Q Consensus 92 ~~c~~c~~~f~~-~~~L~~h~~~ 113 (114)
..|.+|+.+|++ ...|..+|++
T Consensus 48 ~sC~iC~esFqt~it~LsepIDV 70 (109)
T KOG3214|consen 48 ASCRICEESFQTTITALSEPIDV 70 (109)
T ss_pred eeeeehhhhhccchHhhccchHH
Confidence 456677777766 3455555543
No 96
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=57.25 E-value=4.2 Score=21.90 Aligned_cols=7 Identities=0% Similarity=-0.292 Sum_probs=3.3
Q ss_pred ccCCCCC
Q psy2414 19 TRNNTDS 25 (114)
Q Consensus 19 ~c~~c~~ 25 (114)
.|..||.
T Consensus 3 ~CP~Cg~ 9 (72)
T PRK09678 3 HCPLCQH 9 (72)
T ss_pred cCCCCCC
Confidence 3455543
No 97
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=56.53 E-value=9.8 Score=21.73 Aligned_cols=34 Identities=9% Similarity=0.088 Sum_probs=15.0
Q ss_pred CccccCCCCCCCCCCC---CCCCce-ecccccccccCh
Q psy2414 16 PFITRNNTDSIFYPDP---ASPGMY-KCVICLKSVRSR 49 (114)
Q Consensus 16 ~~~~c~~c~~~f~~~~---~~~~~~-~C~~C~~~f~~~ 49 (114)
+-..|..||+++..-. .|++.| -|+.|.+.|..-
T Consensus 13 ke~~CalCG~tWg~~y~Ev~G~rLfFCCd~ca~EF~nm 50 (105)
T PF11494_consen 13 KEMGCALCGATWGDYYEEVDGERLFFCCDDCAKEFKNM 50 (105)
T ss_dssp GGGS-SS---S---SS-B-TT--BSSS--SSSS-TTS-
T ss_pred ccccccccCCcHHHHHHhhcCCEEEEEcHHHHHHHHHH
Confidence 4567999999888665 677764 568898888665
No 98
>KOG4173|consensus
Probab=56.33 E-value=1.9 Score=28.17 Aligned_cols=51 Identities=16% Similarity=0.339 Sum_probs=31.8
Q ss_pred ccCCCCcCcccChhHHHHHHHHHhC------CCC-CCccccCC--CCCccCCCCCCCCCC
Q psy2414 61 HKCPYCESVYSRVDTLKLHAKRVHG------LGI-SRYIHGLI--PQLLFPTPHAKTSPV 111 (114)
Q Consensus 61 ~~c~~C~~~f~~~~~l~~H~~~~~~------~~~-~~~~~c~~--c~~~f~~~~~L~~h~ 111 (114)
-.|..|.+.|.+..-|..||...|. .++ ..-|.|.. |+..|.+..+-.+|+
T Consensus 107 ~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~ 166 (253)
T KOG4173|consen 107 NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHM 166 (253)
T ss_pred chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHH
Confidence 4677888888887777777632221 011 23356643 888888877766665
No 99
>KOG4167|consensus
Probab=55.87 E-value=2.6 Score=32.59 Aligned_cols=26 Identities=19% Similarity=0.411 Sum_probs=22.6
Q ss_pred CccCCCCcCcccChhHHHHHHHHHhC
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKRVHG 85 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~~~~ 85 (114)
-|.|+.|++.|-..-+++.||++|-.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 48999999999999999999987543
No 100
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=55.85 E-value=4.3 Score=18.47 Aligned_cols=25 Identities=8% Similarity=-0.020 Sum_probs=9.5
Q ss_pred cCCCCCCCCCCC---CCCCceecccccc
Q psy2414 20 RNNTDSIFYPDP---ASPGMYKCVICLK 44 (114)
Q Consensus 20 c~~c~~~f~~~~---~~~~~~~C~~C~~ 44 (114)
|..||......- .+...+.|+.|+.
T Consensus 3 C~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 3 CPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred cccccChhhhhcCCCCCccceECCCCCC
Confidence 566665544432 2223456666664
No 101
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=55.45 E-value=2.4 Score=26.96 Aligned_cols=33 Identities=15% Similarity=0.421 Sum_probs=20.1
Q ss_pred CCceecccccccccChhhHHhhhcCC-CccCCCCcCcccC
Q psy2414 34 PGMYKCVICLKSVRSRWHHLQTHFSR-NHKCPYCESVYSR 72 (114)
Q Consensus 34 ~~~~~C~~C~~~f~~~~~h~~~h~~~-~~~c~~C~~~f~~ 72 (114)
..-|.|+.|+..|..... + + .|.|+.||.....
T Consensus 115 ~~~Y~Cp~C~~rytf~eA-~-----~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEA-M-----EYGFRCPQCGEMLEE 148 (178)
T ss_pred CCEEECCCCCcEEeHHHH-h-----hcCCcCCCCCCCCee
Confidence 345778888766644321 1 2 4888888876543
No 102
>PRK14873 primosome assembly protein PriA; Provisional
Probab=55.05 E-value=12 Score=28.83 Aligned_cols=10 Identities=40% Similarity=1.046 Sum_probs=5.8
Q ss_pred CccCCCCcCc
Q psy2414 60 NHKCPYCESV 69 (114)
Q Consensus 60 ~~~c~~C~~~ 69 (114)
|+.|+.||..
T Consensus 422 p~~Cp~Cgs~ 431 (665)
T PRK14873 422 DWRCPRCGSD 431 (665)
T ss_pred CccCCCCcCC
Confidence 5666666543
No 103
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.03 E-value=8.1 Score=22.65 Aligned_cols=28 Identities=18% Similarity=0.052 Sum_probs=17.0
Q ss_pred cCCCCCCCCCCCCCCCceecccccccccCh
Q psy2414 20 RNNTDSIFYPDPASPGMYKCVICLKSVRSR 49 (114)
Q Consensus 20 c~~c~~~f~~~~~~~~~~~C~~C~~~f~~~ 49 (114)
|+.||+.|-. .++.|-.|+.||+.|..+
T Consensus 12 dPetg~KFYD--LNrdPiVsPytG~s~P~s 39 (129)
T COG4530 12 DPETGKKFYD--LNRDPIVSPYTGKSYPRS 39 (129)
T ss_pred Cccccchhhc--cCCCccccCcccccchHH
Confidence 5666666644 455666677777666433
No 104
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=54.45 E-value=17 Score=15.13 Aligned_cols=7 Identities=29% Similarity=0.880 Sum_probs=2.9
Q ss_pred eeccccc
Q psy2414 37 YKCVICL 43 (114)
Q Consensus 37 ~~C~~C~ 43 (114)
|.|+.||
T Consensus 17 f~CPnCG 23 (24)
T PF07754_consen 17 FPCPNCG 23 (24)
T ss_pred EeCCCCC
Confidence 4444443
No 105
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=53.58 E-value=11 Score=18.66 Aligned_cols=26 Identities=12% Similarity=0.083 Sum_probs=14.1
Q ss_pred ccCCCCCCCCCCCCCCCceeccccccccc
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICLKSVR 47 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~~~f~ 47 (114)
.|..|++.|.. ..+.+.|..|++.|-
T Consensus 4 ~C~~C~~~F~~---~~rk~~Cr~Cg~~~C 29 (57)
T cd00065 4 SCMGCGKPFTL---TRRRHHCRNCGRIFC 29 (57)
T ss_pred cCcccCccccC---CccccccCcCcCCcC
Confidence 35666666654 223455666665543
No 106
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=53.54 E-value=13 Score=18.40 Aligned_cols=25 Identities=16% Similarity=0.206 Sum_probs=13.0
Q ss_pred ccCCCCCCCCCCCCCCCceeccccccc
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICLKS 45 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~~~ 45 (114)
.|+.||..|... .+..+.|..|+..
T Consensus 22 fCP~Cg~~~m~~--~~~r~~C~~Cgyt 46 (50)
T PRK00432 22 FCPRCGSGFMAE--HLDRWHCGKCGYT 46 (50)
T ss_pred cCcCCCcchhec--cCCcEECCCcCCE
Confidence 466666543332 2245666666643
No 107
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=53.39 E-value=9.9 Score=27.61 Aligned_cols=30 Identities=10% Similarity=0.195 Sum_probs=22.7
Q ss_pred ccCCCCCCCCCCCCCCCceecccccccccChh
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICLKSVRSRW 50 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~~~f~~~~ 50 (114)
.|+.||.+-.+. |..-|.|..|+..+....
T Consensus 352 ~Cp~Cg~~m~S~--G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRMKSA--GRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCchhhc--CCCCcccccccccCCccc
Confidence 599999987764 555899999998775543
No 108
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=52.70 E-value=7.3 Score=23.53 Aligned_cols=26 Identities=12% Similarity=0.148 Sum_probs=17.9
Q ss_pred cccCCCCCCCCCCCCCCCceecccccc
Q psy2414 18 ITRNNTDSIFYPDPASPGMYKCVICLK 44 (114)
Q Consensus 18 ~~c~~c~~~f~~~~~~~~~~~C~~C~~ 44 (114)
.+|-.||+.|...+ .+-.-.|+.||.
T Consensus 2 H~Ct~Cg~~f~dgs-~eil~GCP~CGg 27 (131)
T PF09845_consen 2 HQCTKCGRVFEDGS-KEILSGCPECGG 27 (131)
T ss_pred cccCcCCCCcCCCc-HHHHccCcccCC
Confidence 46888999998653 234456888873
No 109
>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=52.57 E-value=5.3 Score=18.92 Aligned_cols=27 Identities=19% Similarity=0.031 Sum_probs=12.2
Q ss_pred ccCCCCCCCCCCCCCCCceeccccccc
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICLKS 45 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~~~ 45 (114)
.|+.|+....--.....-+.|..||..
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-BB
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCCE
Confidence 466666543111123334566666644
No 110
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=52.39 E-value=11 Score=22.26 Aligned_cols=26 Identities=19% Similarity=0.406 Sum_probs=15.0
Q ss_pred CccccCCCCCCCCCCCCCCCce-ecccccc
Q psy2414 16 PFITRNNTDSIFYPDPASPGMY-KCVICLK 44 (114)
Q Consensus 16 ~~~~c~~c~~~f~~~~~~~~~~-~C~~C~~ 44 (114)
....|..||..|.... ..+ .|+.|+.
T Consensus 70 ~~~~C~~Cg~~~~~~~---~~~~~CP~Cgs 96 (117)
T PRK00564 70 VELECKDCSHVFKPNA---LDYGVCEKCHS 96 (117)
T ss_pred CEEEhhhCCCccccCC---ccCCcCcCCCC
Confidence 3456888887664431 123 4777774
No 111
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=51.89 E-value=6.6 Score=22.15 Aligned_cols=28 Identities=11% Similarity=0.160 Sum_probs=12.2
Q ss_pred cccCCCCCCCCCCCCCCCceecccccccc
Q psy2414 18 ITRNNTDSIFYPDPASPGMYKCVICLKSV 46 (114)
Q Consensus 18 ~~c~~c~~~f~~~~~~~~~~~C~~C~~~f 46 (114)
+.|+.|++.-... .+...|.|..|++.|
T Consensus 37 y~CpfCgk~~vkR-~a~GIW~C~~C~~~~ 64 (90)
T PRK03976 37 HVCPVCGRPKVKR-VGTGIWECRKCGAKF 64 (90)
T ss_pred ccCCCCCCCceEE-EEEEEEEcCCCCCEE
Confidence 4455554321111 223345555555554
No 112
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=51.53 E-value=7.8 Score=30.04 Aligned_cols=14 Identities=36% Similarity=0.508 Sum_probs=7.5
Q ss_pred CccccCCCCCCCCC
Q psy2414 16 PFITRNNTDSIFYP 29 (114)
Q Consensus 16 ~~~~c~~c~~~f~~ 29 (114)
|++-|..||-+|+-
T Consensus 122 PF~~CT~CGPRfTI 135 (750)
T COG0068 122 PFINCTNCGPRFTI 135 (750)
T ss_pred cccccCCCCcceee
Confidence 44555555555544
No 113
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=50.79 E-value=3 Score=25.94 Aligned_cols=34 Identities=15% Similarity=0.328 Sum_probs=20.4
Q ss_pred CCCceecccccccccChhhHHhhhcCCCccCCCCcCccc
Q psy2414 33 SPGMYKCVICLKSVRSRWHHLQTHFSRNHKCPYCESVYS 71 (114)
Q Consensus 33 ~~~~~~C~~C~~~f~~~~~h~~~h~~~~~~c~~C~~~f~ 71 (114)
+..-|.|+.|+..|..... +. ..|.|+.||....
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA-~~----~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEA-ME----LNFTCPRCGAMLD 139 (158)
T ss_pred CCCeEECCCCCcEeeHHHH-HH----cCCcCCCCCCEee
Confidence 3445788888866644321 11 1488888887654
No 114
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=50.48 E-value=10 Score=22.26 Aligned_cols=25 Identities=8% Similarity=0.057 Sum_probs=13.7
Q ss_pred cccCCCCCCCCCCCCCCCceecccccc
Q psy2414 18 ITRNNTDSIFYPDPASPGMYKCVICLK 44 (114)
Q Consensus 18 ~~c~~c~~~f~~~~~~~~~~~C~~C~~ 44 (114)
..|..|+..|.... ...+.|+.|+.
T Consensus 71 ~~C~~Cg~~~~~~~--~~~~~CP~Cgs 95 (114)
T PRK03681 71 CWCETCQQYVTLLT--QRVRRCPQCHG 95 (114)
T ss_pred EEcccCCCeeecCC--ccCCcCcCcCC
Confidence 45777776664421 11245777763
No 115
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=49.59 E-value=13 Score=18.45 Aligned_cols=8 Identities=38% Similarity=1.182 Sum_probs=4.8
Q ss_pred CccCCCCc
Q psy2414 60 NHKCPYCE 67 (114)
Q Consensus 60 ~~~c~~C~ 67 (114)
.|.|+.|+
T Consensus 34 ~w~CP~C~ 41 (50)
T cd00730 34 DWVCPVCG 41 (50)
T ss_pred CCCCCCCC
Confidence 35666665
No 116
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=49.19 E-value=12 Score=21.80 Aligned_cols=29 Identities=14% Similarity=0.148 Sum_probs=18.7
Q ss_pred ccCCCCCCCCCCCCCCCceecccccccccCh
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICLKSVRSR 49 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~~~f~~~ 49 (114)
.|+.|+..|.. .....|.|++|+..+...
T Consensus 4 ~CP~C~seytY--~dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEYTY--HDGTQLICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcceE--ecCCeeECcccccccccc
Confidence 47777766655 333468888888766433
No 117
>KOG2593|consensus
Probab=49.10 E-value=10 Score=27.50 Aligned_cols=14 Identities=36% Similarity=0.510 Sum_probs=6.6
Q ss_pred ceecccccccccCh
Q psy2414 36 MYKCVICLKSVRSR 49 (114)
Q Consensus 36 ~~~C~~C~~~f~~~ 49 (114)
.|.|+.|.+.|...
T Consensus 128 ~Y~Cp~C~kkyt~L 141 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSL 141 (436)
T ss_pred cccCCccccchhhh
Confidence 34555555444333
No 118
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=48.70 E-value=5.9 Score=27.37 Aligned_cols=34 Identities=15% Similarity=0.208 Sum_probs=23.0
Q ss_pred ccccCCCCCCCCCCCCCCCceecccccccccChh
Q psy2414 17 FITRNNTDSIFYPDPASPGMYKCVICLKSVRSRW 50 (114)
Q Consensus 17 ~~~c~~c~~~f~~~~~~~~~~~C~~C~~~f~~~~ 50 (114)
-.+|+.|+.....+...+..+.|+.|+.-|....
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rltA 71 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGYHLKMSS 71 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCCCcCCCH
Confidence 3568888877766655555677888887665443
No 119
>KOG2231|consensus
Probab=48.45 E-value=7.9 Score=29.77 Aligned_cols=12 Identities=17% Similarity=0.074 Sum_probs=8.9
Q ss_pred cccCCCCCCCCC
Q psy2414 18 ITRNNTDSIFYP 29 (114)
Q Consensus 18 ~~c~~c~~~f~~ 29 (114)
..|.+|+..|.-
T Consensus 100 ~~C~~C~~~~~~ 111 (669)
T KOG2231|consen 100 HSCHICDRRFRA 111 (669)
T ss_pred hhcCccccchhh
Confidence 468888888844
No 120
>KOG2041|consensus
Probab=48.17 E-value=11 Score=29.61 Aligned_cols=80 Identities=20% Similarity=0.299 Sum_probs=45.7
Q ss_pred CCcCCCCCCCCCCCCccccCCCCCCCCCCCCCCCceecccccccccChhhHHhhhcCC-CccCCCCcCcccChhHHHHHH
Q psy2414 2 FGFKSRYPPTSPIQPFITRNNTDSIFYPDPASPGMYKCVICLKSVRSRWHHLQTHFSR-NHKCPYCESVYSRVDTLKLHA 80 (114)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~~~~~~~C~~C~~~f~~~~~h~~~h~~~-~~~c~~C~~~f~~~~~l~~H~ 80 (114)
++.++.++...+..+-.-|..||..-... ...|++|.-.|..=-..-+.-+.. -|-|+.|. |
T Consensus 1102 ~~iFsk~~p~d~~~~~vdc~~cg~~i~~~-----~~~c~ec~~kfP~CiasG~pIt~~~fWlC~~Ck-----------H- 1164 (1189)
T KOG2041|consen 1102 FRIFSKNPPVDPNSAKVDCSVCGAKIDPY-----DLQCSECQTKFPVCIASGRPITDNIFWLCPRCK-----------H- 1164 (1189)
T ss_pred HHHhccCCCCCCCccceeeeecCCcCCcc-----CCCChhhcCcCceeeccCCccccceEEEccccc-----------c-
Confidence 34566777777777777888888644333 246888876663321111111122 36666662 2
Q ss_pred HHHhCCCCCCccccCCCCC
Q psy2414 81 KRVHGLGISRYIHGLIPQL 99 (114)
Q Consensus 81 ~~~~~~~~~~~~~c~~c~~ 99 (114)
+ .+..+.+.|.+|+.|-.
T Consensus 1165 ~-a~~~EIs~y~~CPLCHs 1182 (1189)
T KOG2041|consen 1165 R-AHQHEISKYNCCPLCHS 1182 (1189)
T ss_pred c-cccccccccccCccccC
Confidence 2 24446677888888865
No 121
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=48.16 E-value=12 Score=22.62 Aligned_cols=24 Identities=29% Similarity=0.523 Sum_probs=15.0
Q ss_pred CceecccccccccChhhHHhhhcC
Q psy2414 35 GMYKCVICLKSVRSRWHHLQTHFS 58 (114)
Q Consensus 35 ~~~~C~~C~~~f~~~~~h~~~h~~ 58 (114)
..-.|-+||+.|.....|++.|.|
T Consensus 71 d~i~clecGk~~k~LkrHL~~~~g 94 (132)
T PF05443_consen 71 DYIICLECGKKFKTLKRHLRTHHG 94 (132)
T ss_dssp S-EE-TBT--EESBHHHHHHHTT-
T ss_pred CeeEEccCCcccchHHHHHHHccC
Confidence 346799999999888668888854
No 122
>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=48.03 E-value=17 Score=18.84 Aligned_cols=25 Identities=12% Similarity=0.058 Sum_probs=9.9
Q ss_pred cCCCCCCCCCCCCCCCceeccccccc
Q psy2414 20 RNNTDSIFYPDPASPGMYKCVICLKS 45 (114)
Q Consensus 20 c~~c~~~f~~~~~~~~~~~C~~C~~~ 45 (114)
|..||..-.. ....+.+.|+.|+..
T Consensus 31 C~~CG~~~~~-~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 31 CPRCGHRNKK-RRSGRVFTCPNCGFE 55 (69)
T ss_pred ccCccccccc-ccccceEEcCCCCCE
Confidence 4444443333 122334444444433
No 123
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=47.59 E-value=19 Score=26.61 Aligned_cols=30 Identities=23% Similarity=0.510 Sum_probs=23.7
Q ss_pred CccCCCCcCcccChhHHHHHHHHHhCCCCC
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKRVHGLGIS 89 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~ 89 (114)
=+.|+.|.+.|.....+..|+...|.+.-.
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~~~l~ 86 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHPAGLK 86 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhhhhcC
Confidence 368888999999999999998766765543
No 124
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=47.43 E-value=19 Score=25.13 Aligned_cols=42 Identities=17% Similarity=0.213 Sum_probs=27.7
Q ss_pred ccccCCCCCCCCCCC------CCCCceecccccccccChhhHHhhhcCCCccCCCCcC
Q psy2414 17 FITRNNTDSIFYPDP------ASPGMYKCVICLKSVRSRWHHLQTHFSRNHKCPYCES 68 (114)
Q Consensus 17 ~~~c~~c~~~f~~~~------~~~~~~~C~~C~~~f~~~~~h~~~h~~~~~~c~~C~~ 68 (114)
...|++||....-.. .|.+...|..|+-.+... ..+|..||.
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~----------R~~C~~Cg~ 234 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVV----------RVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCccccc----------CccCCCCCC
Confidence 457999998764331 456677899998443111 377888885
No 125
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=47.06 E-value=18 Score=18.33 Aligned_cols=27 Identities=11% Similarity=0.033 Sum_probs=18.7
Q ss_pred ccccCCCCCCCCCCCCCCCceecccccccc
Q psy2414 17 FITRNNTDSIFYPDPASPGMYKCVICLKSV 46 (114)
Q Consensus 17 ~~~c~~c~~~f~~~~~~~~~~~C~~C~~~f 46 (114)
.-+|..||+.|... +--..|++|+..+
T Consensus 5 ~~~C~~Cg~~~~~~---dDiVvCp~Cgapy 31 (54)
T PF14446_consen 5 GCKCPVCGKKFKDG---DDIVVCPECGAPY 31 (54)
T ss_pred CccChhhCCcccCC---CCEEECCCCCCcc
Confidence 45688999888543 3346788888665
No 126
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=46.79 E-value=19 Score=25.04 Aligned_cols=43 Identities=16% Similarity=0.198 Sum_probs=27.9
Q ss_pred ccccCCCCCCCCCCC-------CCCCceecccccccccChhhHHhhhcCCCccCCCCcCc
Q psy2414 17 FITRNNTDSIFYPDP-------ASPGMYKCVICLKSVRSRWHHLQTHFSRNHKCPYCESV 69 (114)
Q Consensus 17 ~~~c~~c~~~f~~~~-------~~~~~~~C~~C~~~f~~~~~h~~~h~~~~~~c~~C~~~ 69 (114)
...|.+||....-.. .|.+...|..|+-.+... ..+|..||..
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~----------R~~C~~Cg~~ 233 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYV----------RVKCSHCEES 233 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCccccc----------CccCCCCCCC
Confidence 347999998764321 455677899998443111 3778888863
No 127
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=46.59 E-value=19 Score=24.37 Aligned_cols=32 Identities=16% Similarity=0.310 Sum_probs=15.8
Q ss_pred CccccCCCCCCCCCCC----CCCCceeccccccccc
Q psy2414 16 PFITRNNTDSIFYPDP----ASPGMYKCVICLKSVR 47 (114)
Q Consensus 16 ~~~~c~~c~~~f~~~~----~~~~~~~C~~C~~~f~ 47 (114)
+..+|..|.+.|.... .|..-|.|+.|+..|.
T Consensus 131 eVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~ 166 (278)
T PF15135_consen 131 EVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFR 166 (278)
T ss_pred ccccccccccccCCCccccccceeeeecccccccch
Confidence 3444555555443332 2333466666666554
No 128
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.54 E-value=11 Score=22.81 Aligned_cols=9 Identities=56% Similarity=1.040 Sum_probs=5.0
Q ss_pred CccCCCCcC
Q psy2414 60 NHKCPYCES 68 (114)
Q Consensus 60 ~~~c~~C~~ 68 (114)
.+.|+.||.
T Consensus 107 ~~~CP~Cgs 115 (135)
T PRK03824 107 FLKCPKCGS 115 (135)
T ss_pred CcCCcCCCC
Confidence 355666663
No 129
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=46.52 E-value=5.1 Score=22.59 Aligned_cols=28 Identities=21% Similarity=0.309 Sum_probs=12.3
Q ss_pred cccCCCCCCCCCCCCCCCceecccccccc
Q psy2414 18 ITRNNTDSIFYPDPASPGMYKCVICLKSV 46 (114)
Q Consensus 18 ~~c~~c~~~f~~~~~~~~~~~C~~C~~~f 46 (114)
+.|+.||+.-... ....-|.|..|++.|
T Consensus 36 y~Cp~Cgk~~vkR-~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 36 YTCPFCGKTSVKR-VATGIWKCKKCGKKF 63 (90)
T ss_dssp BEESSSSSSEEEE-EETTEEEETTTTEEE
T ss_pred CcCCCCCCceeEE-eeeEEeecCCCCCEE
Confidence 4455555432111 222235555555554
No 130
>PRK10220 hypothetical protein; Provisional
Probab=46.49 E-value=19 Score=21.10 Aligned_cols=29 Identities=21% Similarity=0.353 Sum_probs=19.1
Q ss_pred ccCCCCCCCCCCCCCCCceecccccccccCh
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICLKSVRSR 49 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~~~f~~~ 49 (114)
.|+.|+..|.. .....|.|++|+-.|...
T Consensus 5 ~CP~C~seytY--~d~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 5 HCPKCNSEYTY--EDNGMYICPECAHEWNDA 33 (111)
T ss_pred cCCCCCCcceE--cCCCeEECCcccCcCCcc
Confidence 47788776655 334468888888666443
No 131
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=46.43 E-value=16 Score=23.05 Aligned_cols=18 Identities=22% Similarity=0.654 Sum_probs=10.9
Q ss_pred ccCCCCcCcccChhHHHH
Q psy2414 61 HKCPYCESVYSRVDTLKL 78 (114)
Q Consensus 61 ~~c~~C~~~f~~~~~l~~ 78 (114)
+.|+.||+.|..-+.+..
T Consensus 131 ~~C~~CgkiYW~GsHw~~ 148 (165)
T COG1656 131 YRCPKCGKIYWKGSHWRR 148 (165)
T ss_pred eECCCCcccccCchHHHH
Confidence 457777776666555543
No 132
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=45.69 E-value=9.6 Score=18.68 Aligned_cols=13 Identities=23% Similarity=0.654 Sum_probs=7.7
Q ss_pred eecccccccccCh
Q psy2414 37 YKCVICLKSVRSR 49 (114)
Q Consensus 37 ~~C~~C~~~f~~~ 49 (114)
|.|..|+..+-..
T Consensus 2 y~C~~CgyvYd~~ 14 (47)
T PF00301_consen 2 YQCPVCGYVYDPE 14 (47)
T ss_dssp EEETTTSBEEETT
T ss_pred cCCCCCCEEEcCC
Confidence 5666777665443
No 133
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=45.33 E-value=12 Score=21.83 Aligned_cols=24 Identities=8% Similarity=-0.000 Sum_probs=13.8
Q ss_pred ccccCCCCCCCCCCCCCCCceeccccc
Q psy2414 17 FITRNNTDSIFYPDPASPGMYKCVICL 43 (114)
Q Consensus 17 ~~~c~~c~~~f~~~~~~~~~~~C~~C~ 43 (114)
...|..||..|... +..+.|+.|+
T Consensus 70 ~~~C~~Cg~~~~~~---~~~~~CP~Cg 93 (113)
T PRK12380 70 QAWCWDCSQVVEIH---QHDAQCPHCH 93 (113)
T ss_pred EEEcccCCCEEecC---CcCccCcCCC
Confidence 34677777666442 1234577776
No 134
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=45.12 E-value=17 Score=25.93 Aligned_cols=34 Identities=21% Similarity=0.402 Sum_probs=24.6
Q ss_pred CccCCCCcCcccChhHHHHHHHHHhCCCCCCccccCCCCCc
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKRVHGLGISRYIHGLIPQLL 100 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~c~~c~~~ 100 (114)
.-.|..|...|-+...|..|++..| ..|.+|++.
T Consensus 220 HP~C~FC~~~FYdDDEL~~HcR~~H-------E~ChICD~v 253 (493)
T COG5236 220 HPLCIFCKIYFYDDDELRRHCRLRH-------EACHICDMV 253 (493)
T ss_pred CchhhhccceecChHHHHHHHHhhh-------hhhhhhhcc
Confidence 3467778888888888888888644 346677664
No 135
>KOG2893|consensus
Probab=44.91 E-value=6.1 Score=26.50 Aligned_cols=42 Identities=17% Similarity=0.179 Sum_probs=26.1
Q ss_pred CCCCcCcccChhHHHHHHHHHhCCCCCCccccCCCCCccCCCCCCCCCC
Q psy2414 63 CPYCESVYSRVDTLKLHAKRVHGLGISRYIHGLIPQLLFPTPHAKTSPV 111 (114)
Q Consensus 63 c~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~c~~c~~~f~~~~~L~~h~ 111 (114)
|=+|++.|.+..-|.+|++.. +|+|.+|-|.+-+--.|..|-
T Consensus 13 cwycnrefddekiliqhqkak-------hfkchichkkl~sgpglsihc 54 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAK-------HFKCHICHKKLFSGPGLSIHC 54 (341)
T ss_pred eeecccccchhhhhhhhhhhc-------cceeeeehhhhccCCCceeeh
Confidence 555777777777777766532 277777766554444555554
No 136
>PRK05580 primosome assembly protein PriA; Validated
Probab=44.49 E-value=28 Score=26.91 Aligned_cols=10 Identities=40% Similarity=0.953 Sum_probs=5.7
Q ss_pred CccCCCCcCc
Q psy2414 60 NHKCPYCESV 69 (114)
Q Consensus 60 ~~~c~~C~~~ 69 (114)
|..|+.||..
T Consensus 421 ~~~Cp~Cg~~ 430 (679)
T PRK05580 421 PKACPECGST 430 (679)
T ss_pred CCCCCCCcCC
Confidence 5566666543
No 137
>COG1773 Rubredoxin [Energy production and conversion]
Probab=44.41 E-value=17 Score=18.50 Aligned_cols=8 Identities=38% Similarity=1.115 Sum_probs=4.9
Q ss_pred CccCCCCc
Q psy2414 60 NHKCPYCE 67 (114)
Q Consensus 60 ~~~c~~C~ 67 (114)
.+.|+.||
T Consensus 36 ~w~CP~Cg 43 (55)
T COG1773 36 DWVCPECG 43 (55)
T ss_pred ccCCCCCC
Confidence 36666665
No 138
>PF15269 zf-C2H2_7: Zinc-finger
Probab=44.38 E-value=25 Score=17.13 Aligned_cols=23 Identities=26% Similarity=0.287 Sum_probs=16.9
Q ss_pred CccCCCCcCcccChhHHHHHHHH
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKR 82 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~ 82 (114)
.|+|-+|.-.....+.|-.||+.
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred cceeecCCcccchHHHHHHHHHH
Confidence 46777787777777788777763
No 139
>PRK01343 zinc-binding protein; Provisional
Probab=43.97 E-value=28 Score=17.85 Aligned_cols=17 Identities=12% Similarity=0.087 Sum_probs=12.0
Q ss_pred CCCCccccCCCCCCCCC
Q psy2414 13 PIQPFITRNNTDSIFYP 29 (114)
Q Consensus 13 ~~~~~~~c~~c~~~f~~ 29 (114)
+..+...|.+|++.+..
T Consensus 5 ~~~p~~~CP~C~k~~~~ 21 (57)
T PRK01343 5 PLRPTRPCPECGKPSTR 21 (57)
T ss_pred cCCCCCcCCCCCCcCcC
Confidence 44567788888887753
No 140
>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=43.85 E-value=23 Score=17.93 Aligned_cols=27 Identities=7% Similarity=0.036 Sum_probs=13.2
Q ss_pred ccCCCCCCCCCCC-CCCCceeccccccc
Q psy2414 19 TRNNTDSIFYPDP-ASPGMYKCVICLKS 45 (114)
Q Consensus 19 ~c~~c~~~f~~~~-~~~~~~~C~~C~~~ 45 (114)
+|..||..+.-.. .......|+.|+..
T Consensus 4 ~CP~CG~~iev~~~~~GeiV~Cp~CGae 31 (54)
T TIGR01206 4 ECPDCGAEIELENPELGELVICDECGAE 31 (54)
T ss_pred CCCCCCCEEecCCCccCCEEeCCCCCCE
Confidence 5666666554332 11223456666644
No 141
>PRK12496 hypothetical protein; Provisional
Probab=43.74 E-value=22 Score=22.33 Aligned_cols=24 Identities=17% Similarity=0.246 Sum_probs=12.4
Q ss_pred ccCCCCCCCCCCCCCCCceeccccccc
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICLKS 45 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~~~ 45 (114)
.|..|++.|.....+ -.|+.||..
T Consensus 129 ~C~gC~~~~~~~~~~---~~C~~CG~~ 152 (164)
T PRK12496 129 VCKGCKKKYPEDYPD---DVCEICGSP 152 (164)
T ss_pred ECCCCCccccCCCCC---CcCCCCCCh
Confidence 466676666432211 246666643
No 142
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=42.33 E-value=15 Score=21.58 Aligned_cols=24 Identities=17% Similarity=0.454 Sum_probs=14.2
Q ss_pred cccCCCCCCCCCCCCCCCceecccccc
Q psy2414 18 ITRNNTDSIFYPDPASPGMYKCVICLK 44 (114)
Q Consensus 18 ~~c~~c~~~f~~~~~~~~~~~C~~C~~ 44 (114)
..|..|+..|.... ..+.|+.|+.
T Consensus 71 ~~C~~Cg~~~~~~~---~~~~CP~Cgs 94 (115)
T TIGR00100 71 CECEDCSEEVSPEI---DLYRCPKCHG 94 (115)
T ss_pred EEcccCCCEEecCC---cCccCcCCcC
Confidence 46777776664432 2356777763
No 143
>KOG2482|consensus
Probab=41.43 E-value=17 Score=25.82 Aligned_cols=23 Identities=35% Similarity=0.856 Sum_probs=21.2
Q ss_pred CccCCCCcCcccChhHHHHHHHH
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKR 82 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~ 82 (114)
.+.|-.|.+.|.....|..||+.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 57899999999999999999984
No 144
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=41.11 E-value=18 Score=17.04 Aligned_cols=12 Identities=17% Similarity=0.304 Sum_probs=6.9
Q ss_pred ecccccccccCh
Q psy2414 38 KCVICLKSVRSR 49 (114)
Q Consensus 38 ~C~~C~~~f~~~ 49 (114)
.|+.|+-.+...
T Consensus 15 ~C~~CgM~Y~~~ 26 (41)
T PF13878_consen 15 TCPTCGMLYSPG 26 (41)
T ss_pred CCCCCCCEECCC
Confidence 566666655433
No 145
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=40.15 E-value=5.6 Score=27.29 Aligned_cols=34 Identities=12% Similarity=0.266 Sum_probs=23.9
Q ss_pred ccccCCCCCCCCCCCCCCCceecccccccccChh
Q psy2414 17 FITRNNTDSIFYPDPASPGMYKCVICLKSVRSRW 50 (114)
Q Consensus 17 ~~~c~~c~~~f~~~~~~~~~~~C~~C~~~f~~~~ 50 (114)
-.+|+.|+.....+...+..+.|+.|+.-|....
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~a 59 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHMRMDA 59 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcCcCCH
Confidence 3578888887776655555678888887765443
No 146
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=40.13 E-value=15 Score=17.09 Aligned_cols=14 Identities=21% Similarity=0.657 Sum_probs=10.0
Q ss_pred CccCCCCcCcccCh
Q psy2414 60 NHKCPYCESVYSRV 73 (114)
Q Consensus 60 ~~~c~~C~~~f~~~ 73 (114)
|++|..|+..|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 67788887777653
No 147
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=39.80 E-value=9.1 Score=17.79 Aligned_cols=10 Identities=0% Similarity=-0.217 Sum_probs=5.3
Q ss_pred cCCCCCCCCC
Q psy2414 20 RNNTDSIFYP 29 (114)
Q Consensus 20 c~~c~~~f~~ 29 (114)
|+.||+.-..
T Consensus 1 Cd~CG~~I~~ 10 (37)
T PF08394_consen 1 CDYCGGEITG 10 (37)
T ss_pred CCccCCcccC
Confidence 5556655443
No 148
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=39.05 E-value=6.4 Score=26.90 Aligned_cols=42 Identities=21% Similarity=0.287 Sum_probs=18.2
Q ss_pred cccCCCCCCCCCCC----C--CCCceecccccccccChhhHHhhhcCCCccCCCCcCc
Q psy2414 18 ITRNNTDSIFYPDP----A--SPGMYKCVICLKSVRSRWHHLQTHFSRNHKCPYCESV 69 (114)
Q Consensus 18 ~~c~~c~~~f~~~~----~--~~~~~~C~~C~~~f~~~~~h~~~h~~~~~~c~~C~~~ 69 (114)
-.|++||....-.. . |.+...|..|+-.+... ...|+.||..
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~----------R~~Cp~Cg~~ 220 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFV----------RIKCPYCGNT 220 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE------------TTS-TTT---
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeec----------CCCCcCCCCC
Confidence 47999987554332 2 55677899998554221 2667777654
No 149
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=38.64 E-value=15 Score=26.02 Aligned_cols=28 Identities=11% Similarity=0.227 Sum_probs=14.3
Q ss_pred ccCCCCCCCCCCCCCCCceecccccccc
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICLKSV 46 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~~~f 46 (114)
.|..|...|.-.....-.|.|+.||..+
T Consensus 248 AC~rC~t~y~le~A~~~~wrCpkCGg~i 275 (403)
T COG1379 248 ACSRCYTRYSLEEAKSLRWRCPKCGGKI 275 (403)
T ss_pred HHHHhhhccCcchhhhhcccCcccccch
Confidence 3666665554432223346666666543
No 150
>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 PF12907 zf-met2: Zinc-binding
Probab=37.83 E-value=21 Score=16.89 Aligned_cols=26 Identities=27% Similarity=0.478 Sum_probs=18.1
Q ss_pred ccCCCCcCcc---cChhHHHHHHHHHhCC
Q psy2414 61 HKCPYCESVY---SRVDTLKLHAKRVHGL 86 (114)
Q Consensus 61 ~~c~~C~~~f---~~~~~l~~H~~~~~~~ 86 (114)
+.|..|...| .....|..|....|..
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK 30 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPK 30 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCC
Confidence 5688888544 4557788888766654
No 152
>KOG1842|consensus
Probab=37.80 E-value=21 Score=26.20 Aligned_cols=14 Identities=29% Similarity=0.636 Sum_probs=7.0
Q ss_pred ceecccccccccCh
Q psy2414 36 MYKCVICLKSVRSR 49 (114)
Q Consensus 36 ~~~C~~C~~~f~~~ 49 (114)
-+.|+.|..-|.+-
T Consensus 15 gflCPiC~~dl~~~ 28 (505)
T KOG1842|consen 15 GFLCPICLLDLPNL 28 (505)
T ss_pred cccCchHhhhhhhH
Confidence 34555555554443
No 153
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=37.73 E-value=24 Score=15.13 Aligned_cols=23 Identities=13% Similarity=0.208 Sum_probs=6.6
Q ss_pred ccCCCCCCCCCCCCCCCceeccccccc
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICLKS 45 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~~~ 45 (114)
.|+.|++... +...|.|..|+-.
T Consensus 2 ~C~~C~~~~~----~~~~Y~C~~Cdf~ 24 (30)
T PF07649_consen 2 RCDACGKPID----GGWFYRCSECDFD 24 (30)
T ss_dssp --TTTS--------S--EEE-TTT---
T ss_pred cCCcCCCcCC----CCceEECccCCCc
Confidence 3555655331 2245677776543
No 154
>PF14369 zf-RING_3: zinc-finger
Probab=37.62 E-value=28 Score=15.80 Aligned_cols=8 Identities=25% Similarity=0.679 Sum_probs=3.4
Q ss_pred cccccccc
Q psy2414 39 CVICLKSV 46 (114)
Q Consensus 39 C~~C~~~f 46 (114)
|+.|+..|
T Consensus 24 CP~C~~gF 31 (35)
T PF14369_consen 24 CPRCHGGF 31 (35)
T ss_pred CcCCCCcE
Confidence 44444333
No 155
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=37.47 E-value=6.3 Score=27.16 Aligned_cols=32 Identities=13% Similarity=0.292 Sum_probs=22.1
Q ss_pred cccCCCCCCCCCCCCCCCceecccccccccCh
Q psy2414 18 ITRNNTDSIFYPDPASPGMYKCVICLKSVRSR 49 (114)
Q Consensus 18 ~~c~~c~~~f~~~~~~~~~~~C~~C~~~f~~~ 49 (114)
.+|+.|+.....+...+..+.|+.|+.-|...
T Consensus 28 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 28 TKCPSCGQVLYRKELEANLNVCPKCGHHMRIS 59 (292)
T ss_pred eECCCccchhhHHHHHhcCCCCCCCCCCeeCC
Confidence 56888887776665545567888888776544
No 156
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=37.28 E-value=13 Score=18.55 Aligned_cols=14 Identities=21% Similarity=0.546 Sum_probs=5.8
Q ss_pred CceecccccccccC
Q psy2414 35 GMYKCVICLKSVRS 48 (114)
Q Consensus 35 ~~~~C~~C~~~f~~ 48 (114)
..|.|+.|.+.|-.
T Consensus 20 ~~y~C~~C~~~FC~ 33 (51)
T PF07975_consen 20 SRYRCPKCKNHFCI 33 (51)
T ss_dssp EEE--TTTT--B-H
T ss_pred CeEECCCCCCcccc
Confidence 45777777766643
No 157
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=36.99 E-value=5.9 Score=23.15 Aligned_cols=24 Identities=21% Similarity=0.329 Sum_probs=10.2
Q ss_pred cccCCCCCCCCCCCCCCCceecccccc
Q psy2414 18 ITRNNTDSIFYPDPASPGMYKCVICLK 44 (114)
Q Consensus 18 ~~c~~c~~~f~~~~~~~~~~~C~~C~~ 44 (114)
..|..||..|.-.. ..+.|+.|+.
T Consensus 71 ~~C~~Cg~~~~~~~---~~~~CP~Cgs 94 (113)
T PF01155_consen 71 ARCRDCGHEFEPDE---FDFSCPRCGS 94 (113)
T ss_dssp EEETTTS-EEECHH---CCHH-SSSSS
T ss_pred EECCCCCCEEecCC---CCCCCcCCcC
Confidence 34666666554321 1144555553
No 158
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=36.54 E-value=19 Score=22.46 Aligned_cols=33 Identities=18% Similarity=0.201 Sum_probs=18.4
Q ss_pred CccCCCCcCcccChhHHHHHHHHHhCCCCCCccccCCCCCc
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKRVHGLGISRYIHGLIPQLL 100 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~c~~c~~~ 100 (114)
+|.|. |+..+... ++|-. .-.|+ . |.|..|+-.
T Consensus 117 ~Y~C~-C~q~~l~~---RRhn~-~~~g~-~--YrC~~C~gk 149 (156)
T COG3091 117 PYRCQ-CQQHYLRI---RRHNT-VRRGE-V--YRCGKCGGK 149 (156)
T ss_pred eEEee-cCCccchh---hhccc-ccccc-e--EEeccCCce
Confidence 78888 88776553 22222 23333 2 666666643
No 159
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=36.14 E-value=24 Score=24.54 Aligned_cols=52 Identities=29% Similarity=0.577 Sum_probs=36.1
Q ss_pred CCceecccccccccChhh---HHhhhcCC-CccCCC--CcCcccChhHHHHHHHHHhC
Q psy2414 34 PGMYKCVICLKSVRSRWH---HLQTHFSR-NHKCPY--CESVYSRVDTLKLHAKRVHG 85 (114)
Q Consensus 34 ~~~~~C~~C~~~f~~~~~---h~~~h~~~-~~~c~~--C~~~f~~~~~l~~H~~~~~~ 85 (114)
..++.|+.|...|....+ |.+.+.++ +..|.. |...+.....+..|...++.
T Consensus 31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 (467)
T COG5048 31 PRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHN 88 (467)
T ss_pred CchhhcccccccccccchhhhhcccccccCCccccccccccccCCcchhhhhcccccc
Confidence 446778888777766654 77778877 777766 66677777777777665444
No 160
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=35.82 E-value=24 Score=21.22 Aligned_cols=32 Identities=16% Similarity=0.170 Sum_probs=18.8
Q ss_pred cccCCCCCCCCCCC----CCCCceecccccccccCh
Q psy2414 18 ITRNNTDSIFYPDP----ASPGMYKCVICLKSVRSR 49 (114)
Q Consensus 18 ~~c~~c~~~f~~~~----~~~~~~~C~~C~~~f~~~ 49 (114)
..|+.|+..-..+. .+...|.|..|++.|...
T Consensus 31 ~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 31 VNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred CcCCCCCccceeeECCccccccccccCCcCcceeee
Confidence 45777765441111 345667888888777554
No 161
>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=35.68 E-value=31 Score=16.48 Aligned_cols=10 Identities=40% Similarity=1.092 Sum_probs=4.9
Q ss_pred CCceeccccc
Q psy2414 34 PGMYKCVICL 43 (114)
Q Consensus 34 ~~~~~C~~C~ 43 (114)
...|.|..|.
T Consensus 35 ~~~~~C~~C~ 44 (46)
T PF12760_consen 35 RGRYRCKACR 44 (46)
T ss_pred CCeEECCCCC
Confidence 3445555554
No 162
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=35.67 E-value=44 Score=16.13 Aligned_cols=29 Identities=10% Similarity=0.145 Sum_probs=17.6
Q ss_pred CccccCCCCCCCCCCCCCCCceecccccccc
Q psy2414 16 PFITRNNTDSIFYPDPASPGMYKCVICLKSV 46 (114)
Q Consensus 16 ~~~~c~~c~~~f~~~~~~~~~~~C~~C~~~f 46 (114)
....|+.|++.... .+..-+.|..|+...
T Consensus 10 ~~~~C~~C~~~i~g--~~~~g~~C~~C~~~~ 38 (53)
T PF00130_consen 10 KPTYCDVCGKFIWG--LGKQGYRCSWCGLVC 38 (53)
T ss_dssp STEB-TTSSSBECS--SSSCEEEETTTT-EE
T ss_pred CCCCCcccCcccCC--CCCCeEEECCCCChH
Confidence 34568888877622 445568888887554
No 163
>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=35.57 E-value=39 Score=15.47 Aligned_cols=9 Identities=11% Similarity=0.076 Sum_probs=4.6
Q ss_pred cccCCCCCC
Q psy2414 18 ITRNNTDSI 26 (114)
Q Consensus 18 ~~c~~c~~~ 26 (114)
+.|+.|+.+
T Consensus 6 v~CP~C~s~ 14 (36)
T PF03811_consen 6 VHCPRCQST 14 (36)
T ss_pred eeCCCCCCC
Confidence 445555543
No 164
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=34.77 E-value=39 Score=14.51 Aligned_cols=21 Identities=14% Similarity=0.115 Sum_probs=12.6
Q ss_pred ccCCCCCCCCCCCCCCCceeccccc
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICL 43 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~ 43 (114)
.|+.|++..... .-|.|..|.
T Consensus 2 ~C~~C~~~~~~~----~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGF----YFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCC----EeEEeCCCC
Confidence 477777655332 157777776
No 165
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=34.32 E-value=29 Score=21.18 Aligned_cols=54 Identities=15% Similarity=0.318 Sum_probs=29.2
Q ss_pred CccccCCCCCCCCCCCCCCCceecc---cccccccChhhHHhhhcCCCccCCCCcCcccChh
Q psy2414 16 PFITRNNTDSIFYPDPASPGMYKCV---ICLKSVRSRWHHLQTHFSRNHKCPYCESVYSRVD 74 (114)
Q Consensus 16 ~~~~c~~c~~~f~~~~~~~~~~~C~---~C~~~f~~~~~h~~~h~~~~~~c~~C~~~f~~~~ 74 (114)
+.++|+.|..+..... --+|-+|- .|+-.+...|.|-.. --.|+.|.-+|..++
T Consensus 79 ~lYeCnIC~etS~ee~-FLKPneCCgY~iCn~Cya~LWK~~~~----ypvCPvCkTSFKss~ 135 (140)
T PF05290_consen 79 KLYECNICKETSAEER-FLKPNECCGYSICNACYANLWKFCNL----YPVCPVCKTSFKSSS 135 (140)
T ss_pred CceeccCcccccchhh-cCCcccccchHHHHHHHHHHHHHccc----CCCCCcccccccccc
Confidence 6789999987765443 22343331 233333333322222 246888888887654
No 166
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=34.01 E-value=13 Score=17.45 Aligned_cols=25 Identities=20% Similarity=0.286 Sum_probs=12.4
Q ss_pred ccCCCCCCCCCCC---CCC-Cceeccccc
Q psy2414 19 TRNNTDSIFYPDP---ASP-GMYKCVICL 43 (114)
Q Consensus 19 ~c~~c~~~f~~~~---~~~-~~~~C~~C~ 43 (114)
.|+.||+.-.... .|. ..+.|+.|-
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv 31 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECV 31 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHH
Confidence 4777777665544 222 456676654
No 167
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=33.90 E-value=42 Score=16.14 Aligned_cols=20 Identities=10% Similarity=0.039 Sum_probs=9.8
Q ss_pred ccCCCCCCCCCCCCCCCceecccc
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVIC 42 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C 42 (114)
.|+.||..... ...|+|..|
T Consensus 2 ~CDgCg~~PI~----G~RykC~~C 21 (43)
T cd02342 2 QCDGCGVLPIT----GPRYKSKVK 21 (43)
T ss_pred CCCCCCCCccc----ccceEeCCC
Confidence 46666654322 234555554
No 168
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=33.77 E-value=48 Score=16.09 Aligned_cols=21 Identities=14% Similarity=0.178 Sum_probs=11.9
Q ss_pred ccCCCCCCCCCCCCCCCceeccccc
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICL 43 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~ 43 (114)
.|+.|++.. .+...+.|..|.
T Consensus 2 ~Cd~C~~~~----~~g~r~~C~~C~ 22 (49)
T cd02335 2 HCDYCSKDI----TGTIRIKCAECP 22 (49)
T ss_pred CCCCcCCCC----CCCcEEECCCCC
Confidence 477776644 233456666654
No 169
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=33.30 E-value=58 Score=15.50 Aligned_cols=24 Identities=13% Similarity=0.173 Sum_probs=13.8
Q ss_pred cCCCCCCCCCCCCCCCceeccccccccc
Q psy2414 20 RNNTDSIFYPDPASPGMYKCVICLKSVR 47 (114)
Q Consensus 20 c~~c~~~f~~~~~~~~~~~C~~C~~~f~ 47 (114)
|.+|+. ...++....|+.|+..|.
T Consensus 2 C~vC~~----~~~~~~~i~C~~C~~~~H 25 (51)
T PF00628_consen 2 CPVCGQ----SDDDGDMIQCDSCNRWYH 25 (51)
T ss_dssp BTTTTS----SCTTSSEEEBSTTSCEEE
T ss_pred CcCCCC----cCCCCCeEEcCCCChhhC
Confidence 455665 123445667777776653
No 170
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.97 E-value=28 Score=20.75 Aligned_cols=11 Identities=9% Similarity=-0.315 Sum_probs=6.8
Q ss_pred cccCCCCCCCCC
Q psy2414 18 ITRNNTDSIFYP 29 (114)
Q Consensus 18 ~~c~~c~~~f~~ 29 (114)
..| .||..|..
T Consensus 71 ~~C-~Cg~~~~~ 81 (124)
T PRK00762 71 IEC-ECGYEGVV 81 (124)
T ss_pred EEe-eCcCcccc
Confidence 457 77766654
No 171
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=32.88 E-value=63 Score=16.46 Aligned_cols=17 Identities=12% Similarity=0.249 Sum_probs=10.2
Q ss_pred CCCceecccccccccCh
Q psy2414 33 SPGMYKCVICLKSVRSR 49 (114)
Q Consensus 33 ~~~~~~C~~C~~~f~~~ 49 (114)
+...|.|+.||-..--+
T Consensus 11 ~~v~~~Cp~cGipthcS 27 (55)
T PF13824_consen 11 AHVNFECPDCGIPTHCS 27 (55)
T ss_pred cccCCcCCCCCCcCccC
Confidence 34467788777654433
No 172
>PLN02294 cytochrome c oxidase subunit Vb
Probab=32.34 E-value=15 Score=23.26 Aligned_cols=21 Identities=14% Similarity=0.493 Sum_probs=15.8
Q ss_pred HHhhhcCCCccCCCCcCcccC
Q psy2414 52 HLQTHFSRNHKCPYCESVYSR 72 (114)
Q Consensus 52 h~~~h~~~~~~c~~C~~~f~~ 72 (114)
++..+.|+|..|..||..|..
T Consensus 133 Wf~L~kGkp~RCpeCG~~fkL 153 (174)
T PLN02294 133 WFWLEKGKSFECPVCTQYFEL 153 (174)
T ss_pred EEEecCCCceeCCCCCCEEEE
Confidence 455666668889999988765
No 173
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=31.95 E-value=13 Score=22.46 Aligned_cols=16 Identities=13% Similarity=-0.010 Sum_probs=10.8
Q ss_pred CCccccCCCCCCCCCCC
Q psy2414 15 QPFITRNNTDSIFYPDP 31 (114)
Q Consensus 15 ~~~~~c~~c~~~f~~~~ 31 (114)
++.++| +||.+|....
T Consensus 68 ~rv~rc-ecghsf~d~r 83 (165)
T COG4647 68 KRVIRC-ECGHSFGDYR 83 (165)
T ss_pred ccEEEE-eccccccChh
Confidence 345566 7888887765
No 174
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=31.81 E-value=26 Score=21.26 Aligned_cols=11 Identities=27% Similarity=0.875 Sum_probs=6.3
Q ss_pred ceecccccccc
Q psy2414 36 MYKCVICLKSV 46 (114)
Q Consensus 36 ~~~C~~C~~~f 46 (114)
.|.|..|+..+
T Consensus 123 ~~~C~~C~~~~ 133 (157)
T PF10263_consen 123 VYRCPSCGREY 133 (157)
T ss_pred EEEcCCCCCEe
Confidence 45666666544
No 175
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=30.89 E-value=43 Score=24.61 Aligned_cols=25 Identities=12% Similarity=0.029 Sum_probs=16.6
Q ss_pred CCccccCCCCCCCCCCCCCCCceecccccc
Q psy2414 15 QPFITRNNTDSIFYPDPASPGMYKCVICLK 44 (114)
Q Consensus 15 ~~~~~c~~c~~~f~~~~~~~~~~~C~~C~~ 44 (114)
+..+.|..||..+.. ..+.|+.|+.
T Consensus 5 ~~~y~C~~Cg~~~~~-----~~g~Cp~C~~ 29 (454)
T TIGR00416 5 KSKFVCQHCGADSPK-----WQGKCPACHA 29 (454)
T ss_pred CCeEECCcCCCCCcc-----ccEECcCCCC
Confidence 356788888876543 3467887763
No 176
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=30.87 E-value=58 Score=14.35 Aligned_cols=24 Identities=8% Similarity=0.350 Sum_probs=13.4
Q ss_pred ccCCCCCCCCCCCCCCCceeccccc
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICL 43 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~ 43 (114)
.|..|+..+.-. .|...+.|..|.
T Consensus 3 ~C~~C~t~L~yP-~gA~~vrCs~C~ 26 (31)
T TIGR01053 3 VCGGCRTLLMYP-RGASSVRCALCQ 26 (31)
T ss_pred CcCCCCcEeecC-CCCCeEECCCCC
Confidence 455555554443 455566666664
No 177
>KOG2907|consensus
Probab=30.73 E-value=42 Score=19.80 Aligned_cols=42 Identities=21% Similarity=0.322 Sum_probs=25.2
Q ss_pred CccCCCCcCcccChhHHHHHHHHHhCCCCCCccccCCCCCccCCC
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKRVHGLGISRYIHGLIPQLLFPTP 104 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~c~~c~~~f~~~ 104 (114)
..+|+.||-.=..-..| .+|. -.++..-||.|..|+..|+..
T Consensus 74 ~~kCpkCghe~m~Y~T~--QlRS-ADEGQTVFYTC~kC~~k~~e~ 115 (116)
T KOG2907|consen 74 KHKCPKCGHEEMSYHTL--QLRS-ADEGQTVFYTCPKCKYKFTEN 115 (116)
T ss_pred hccCcccCCchhhhhhh--hccc-ccCCceEEEEcCccceeeecc
Confidence 46888887532221222 1232 334557788999999988754
No 178
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=30.65 E-value=29 Score=21.59 Aligned_cols=11 Identities=18% Similarity=0.546 Sum_probs=5.2
Q ss_pred eeccccccccc
Q psy2414 37 YKCVICLKSVR 47 (114)
Q Consensus 37 ~~C~~C~~~f~ 47 (114)
-.|..|+..|.
T Consensus 29 ReC~~C~~RFT 39 (156)
T COG1327 29 RECLECGERFT 39 (156)
T ss_pred hcccccccccc
Confidence 34555554443
No 179
>PRK12722 transcriptional activator FlhC; Provisional
Probab=29.99 E-value=44 Score=21.56 Aligned_cols=8 Identities=25% Similarity=0.924 Sum_probs=4.1
Q ss_pred CccCCCCc
Q psy2414 60 NHKCPYCE 67 (114)
Q Consensus 60 ~~~c~~C~ 67 (114)
.|.|+.|.
T Consensus 154 ~f~CplC~ 161 (187)
T PRK12722 154 SFVCGLCQ 161 (187)
T ss_pred CCcCCCCC
Confidence 45555553
No 180
>PRK11823 DNA repair protein RadA; Provisional
Probab=29.84 E-value=47 Score=24.34 Aligned_cols=25 Identities=8% Similarity=0.012 Sum_probs=17.0
Q ss_pred CCccccCCCCCCCCCCCCCCCceecccccc
Q psy2414 15 QPFITRNNTDSIFYPDPASPGMYKCVICLK 44 (114)
Q Consensus 15 ~~~~~c~~c~~~f~~~~~~~~~~~C~~C~~ 44 (114)
+..+.|..||..+.. ..+.|+.|+.
T Consensus 5 ~~~y~C~~Cg~~~~~-----~~g~Cp~C~~ 29 (446)
T PRK11823 5 KTAYVCQECGAESPK-----WLGRCPECGA 29 (446)
T ss_pred CCeEECCcCCCCCcc-----cCeeCcCCCC
Confidence 456789898876544 3467877763
No 181
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=29.79 E-value=50 Score=18.38 Aligned_cols=23 Identities=9% Similarity=-0.048 Sum_probs=14.8
Q ss_pred CCCccccCCCCCCCCCCCCCCCc
Q psy2414 14 IQPFITRNNTDSIFYPDPASPGM 36 (114)
Q Consensus 14 ~~~~~~c~~c~~~f~~~~~~~~~ 36 (114)
++..-+|+.||..|.....++.|
T Consensus 5 Lk~~~~C~~CG~d~~~~~adDgP 27 (86)
T PF06170_consen 5 LKVAPRCPHCGLDYSHARADDGP 27 (86)
T ss_pred ccCCCcccccCCccccCCcCccc
Confidence 34455688888888776644433
No 182
>COG4640 Predicted membrane protein [Function unknown]
Probab=29.73 E-value=41 Score=24.46 Aligned_cols=13 Identities=15% Similarity=0.580 Sum_probs=6.5
Q ss_pred ccCCCCcCcccCh
Q psy2414 61 HKCPYCESVYSRV 73 (114)
Q Consensus 61 ~~c~~C~~~f~~~ 73 (114)
++|.+||..|...
T Consensus 16 ~qC~qCG~~~t~~ 28 (465)
T COG4640 16 VQCTQCGHKFTSR 28 (465)
T ss_pred ccccccCCcCCch
Confidence 4455555555443
No 183
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=29.38 E-value=30 Score=21.39 Aligned_cols=12 Identities=17% Similarity=0.611 Sum_probs=6.4
Q ss_pred eecccccccccC
Q psy2414 37 YKCVICLKSVRS 48 (114)
Q Consensus 37 ~~C~~C~~~f~~ 48 (114)
-+|..|++.|.+
T Consensus 29 ReC~~C~~RFTT 40 (147)
T TIGR00244 29 RECLECHERFTT 40 (147)
T ss_pred ccCCccCCccce
Confidence 445555555543
No 184
>PRK00420 hypothetical protein; Validated
Probab=29.28 E-value=55 Score=19.28 Aligned_cols=28 Identities=11% Similarity=-0.035 Sum_probs=18.0
Q ss_pred cccCCCCCCCCCCCCCCCceeccccccccc
Q psy2414 18 ITRNNTDSIFYPDPASPGMYKCVICLKSVR 47 (114)
Q Consensus 18 ~~c~~c~~~f~~~~~~~~~~~C~~C~~~f~ 47 (114)
-.|+.||..+-.- ......|+.|+....
T Consensus 24 ~~CP~Cg~pLf~l--k~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCGLPLFEL--KDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCCcceec--CCCceECCCCCCeee
Confidence 3588888665442 234577888887554
No 185
>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=29.25 E-value=13 Score=17.98 Aligned_cols=6 Identities=17% Similarity=-0.114 Sum_probs=2.7
Q ss_pred CCCccC
Q psy2414 97 PQLLFP 102 (114)
Q Consensus 97 c~~~f~ 102 (114)
||..|.
T Consensus 33 Cg~tfv 38 (47)
T PF04606_consen 33 CGHTFV 38 (47)
T ss_pred CCCEEE
Confidence 444443
No 186
>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=29.00 E-value=17 Score=20.77 Aligned_cols=21 Identities=19% Similarity=0.539 Sum_probs=14.8
Q ss_pred HHhhhcCCCccCCCCcCcccC
Q psy2414 52 HLQTHFSRNHKCPYCESVYSR 72 (114)
Q Consensus 52 h~~~h~~~~~~c~~C~~~f~~ 72 (114)
++..+.++|..|..||..|..
T Consensus 71 W~~l~~g~~~rC~eCG~~fkL 91 (97)
T cd00924 71 WMWLEKGKPKRCPECGHVFKL 91 (97)
T ss_pred EEEEeCCCceeCCCCCcEEEE
Confidence 455565568889889887753
No 187
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=28.90 E-value=17 Score=23.65 Aligned_cols=30 Identities=10% Similarity=-0.044 Sum_probs=16.5
Q ss_pred ccccCCCCCCCCCCC-------CCC---Cceecccccccc
Q psy2414 17 FITRNNTDSIFYPDP-------ASP---GMYKCVICLKSV 46 (114)
Q Consensus 17 ~~~c~~c~~~f~~~~-------~~~---~~~~C~~C~~~f 46 (114)
.+.|+.||.++.... .|+ ..+.|..||..+
T Consensus 14 ~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~ 53 (201)
T COG1779 14 RIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRS 53 (201)
T ss_pred eecCCcccceeeEEEeeecCCccceEEEEEEEccccCCcc
Confidence 456777777555443 222 235566666543
No 188
>KOG2071|consensus
Probab=28.76 E-value=42 Score=25.58 Aligned_cols=23 Identities=13% Similarity=0.342 Sum_probs=19.4
Q ss_pred CccCCCCcCcccChhHHHHHHHH
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAKR 82 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~~ 82 (114)
|-+|..||.+|........|+..
T Consensus 418 pnqC~~CG~R~~~~ee~sk~md~ 440 (579)
T KOG2071|consen 418 PNQCKSCGLRFDDSEERSKHMDI 440 (579)
T ss_pred cchhcccccccccchhhhhHhhh
Confidence 78999999999988777777654
No 189
>KOG2785|consensus
Probab=28.45 E-value=20 Score=25.66 Aligned_cols=21 Identities=14% Similarity=0.061 Sum_probs=16.2
Q ss_pred cccCCCC---CccCCCCCCCCCCC
Q psy2414 92 IHGLIPQ---LLFPTPHAKTSPVD 112 (114)
Q Consensus 92 ~~c~~c~---~~f~~~~~L~~h~~ 112 (114)
+.|..|. +.|.+-.+++.|++
T Consensus 218 ~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 218 FICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred ceEEEeccccCcccccHHHHHHHh
Confidence 6788888 77888777777764
No 190
>PRK12860 transcriptional activator FlhC; Provisional
Probab=28.17 E-value=50 Score=21.38 Aligned_cols=10 Identities=10% Similarity=-0.001 Sum_probs=4.9
Q ss_pred ccCCCCCCCC
Q psy2414 19 TRNNTDSIFY 28 (114)
Q Consensus 19 ~c~~c~~~f~ 28 (114)
.|..||..|.
T Consensus 136 ~C~~Cgg~fv 145 (189)
T PRK12860 136 RCCRCGGKFV 145 (189)
T ss_pred cCCCCCCCee
Confidence 4555554444
No 191
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=27.29 E-value=74 Score=15.29 Aligned_cols=21 Identities=14% Similarity=0.115 Sum_probs=10.9
Q ss_pred ccCCCCCCCCCCCCCCCceeccccc
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICL 43 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~ 43 (114)
.|+.|++.. .....|+|..|.
T Consensus 2 ~Cd~C~~~~----i~G~RykC~~C~ 22 (45)
T cd02339 2 ICDTCRKQG----IIGIRWKCAECP 22 (45)
T ss_pred CCCCCCCCC----cccCeEECCCCC
Confidence 466776532 222346666654
No 192
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=27.12 E-value=74 Score=15.09 Aligned_cols=13 Identities=15% Similarity=0.514 Sum_probs=8.3
Q ss_pred ceecccccccccC
Q psy2414 36 MYKCVICLKSVRS 48 (114)
Q Consensus 36 ~~~C~~C~~~f~~ 48 (114)
.|.|..|+..+..
T Consensus 11 l~~CL~C~~~~c~ 23 (50)
T smart00290 11 LWLCLTCGQVGCG 23 (50)
T ss_pred eEEecCCCCcccC
Confidence 6777777765543
No 193
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=27.12 E-value=49 Score=15.80 Aligned_cols=24 Identities=17% Similarity=0.200 Sum_probs=12.2
Q ss_pred CccccCCCCCCCCCCCCCCCceeccccc
Q psy2414 16 PFITRNNTDSIFYPDPASPGMYKCVICL 43 (114)
Q Consensus 16 ~~~~c~~c~~~f~~~~~~~~~~~C~~C~ 43 (114)
..+.|+.|+.... ....|.|..|.
T Consensus 3 ~~~~C~~C~~~~i----~g~Ry~C~~C~ 26 (46)
T PF00569_consen 3 HGYTCDGCGTDPI----IGVRYHCLVCP 26 (46)
T ss_dssp SSCE-SSS-SSSE----ESSEEEESSSS
T ss_pred CCeECcCCCCCcC----cCCeEECCCCC
Confidence 4567888876321 12357777664
No 194
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.99 E-value=46 Score=20.09 Aligned_cols=11 Identities=27% Similarity=-0.031 Sum_probs=6.4
Q ss_pred ccCCCCCCCCC
Q psy2414 19 TRNNTDSIFYP 29 (114)
Q Consensus 19 ~c~~c~~~f~~ 29 (114)
-|..||+.|+.
T Consensus 70 fchncgs~fpw 80 (160)
T COG4306 70 FCHNCGSRFPW 80 (160)
T ss_pred hhhcCCCCCCc
Confidence 46666666654
No 195
>PRK04351 hypothetical protein; Provisional
Probab=26.94 E-value=47 Score=20.52 Aligned_cols=32 Identities=16% Similarity=0.496 Sum_probs=17.2
Q ss_pred ceecccccccccChhhHHhhhcCCCccCCCCcCccc
Q psy2414 36 MYKCVICLKSVRSRWHHLQTHFSRNHKCPYCESVYS 71 (114)
Q Consensus 36 ~~~C~~C~~~f~~~~~h~~~h~~~~~~c~~C~~~f~ 71 (114)
.|.|..|+..+... +.+....|.|..|+-.+.
T Consensus 112 ~Y~C~~Cg~~~~r~----Rr~n~~~yrCg~C~g~L~ 143 (149)
T PRK04351 112 LYECQSCGQQYLRK----RRINTKRYRCGKCRGKLK 143 (149)
T ss_pred EEECCCCCCEeeee----eecCCCcEEeCCCCcEee
Confidence 47787777554332 112112577777765543
No 196
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=26.63 E-value=16 Score=16.55 Aligned_cols=6 Identities=33% Similarity=0.866 Sum_probs=2.5
Q ss_pred eccccc
Q psy2414 38 KCVICL 43 (114)
Q Consensus 38 ~C~~C~ 43 (114)
.|..|+
T Consensus 22 ~C~~C~ 27 (35)
T PF02150_consen 22 ACRTCG 27 (35)
T ss_dssp EESSSS
T ss_pred CCCCCC
Confidence 344444
No 197
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=26.54 E-value=33 Score=21.33 Aligned_cols=25 Identities=12% Similarity=0.074 Sum_probs=17.7
Q ss_pred ccCCCCCCCCCCC-----CCCCceeccccc
Q psy2414 19 TRNNTDSIFYPDP-----ASPGMYKCVICL 43 (114)
Q Consensus 19 ~c~~c~~~f~~~~-----~~~~~~~C~~C~ 43 (114)
.|..||+...... .|.....|..|.
T Consensus 2 ~CEiCG~~i~~~~~~v~iega~l~vC~~C~ 31 (154)
T TIGR00270 2 NCEICGRKIKGKGFKIVIEGSEMTVCGECR 31 (154)
T ss_pred ccccCCCccCCCCeEEEEcCeEEehhhhHH
Confidence 4888888776653 556667788776
No 198
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=26.41 E-value=35 Score=16.91 Aligned_cols=18 Identities=11% Similarity=0.015 Sum_probs=12.0
Q ss_pred CCceecccccccccChhh
Q psy2414 34 PGMYKCVICLKSVRSRWH 51 (114)
Q Consensus 34 ~~~~~C~~C~~~f~~~~~ 51 (114)
++.+.|..||..|.....
T Consensus 2 Dk~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAG 19 (49)
T ss_pred CeeEEcccCCCeEEEehh
Confidence 356778888887755443
No 199
>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=26.20 E-value=30 Score=16.27 Aligned_cols=14 Identities=36% Similarity=0.415 Sum_probs=8.5
Q ss_pred CceecccccccccC
Q psy2414 35 GMYKCVICLKSVRS 48 (114)
Q Consensus 35 ~~~~C~~C~~~f~~ 48 (114)
-|+.|..|+..|-.
T Consensus 12 ~~~~C~~C~~~FC~ 25 (43)
T PF01428_consen 12 LPFKCKHCGKSFCL 25 (43)
T ss_dssp SHEE-TTTS-EE-T
T ss_pred CCeECCCCCcccCc
Confidence 47888888888754
No 200
>KOG3408|consensus
Probab=25.88 E-value=39 Score=20.25 Aligned_cols=22 Identities=27% Similarity=0.484 Sum_probs=16.2
Q ss_pred CccCCCCcCcccChhHHHHHHH
Q psy2414 60 NHKCPYCESVYSRVDTLKLHAK 81 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~~l~~H~~ 81 (114)
.|.|-.|.+-|.+...|..|.+
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHh
Confidence 4777777777777777777764
No 201
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=25.07 E-value=18 Score=15.47 Aligned_cols=24 Identities=13% Similarity=0.106 Sum_probs=8.9
Q ss_pred ccCCCCCCCCCCC-CCCCceecccc
Q psy2414 19 TRNNTDSIFYPDP-ASPGMYKCVIC 42 (114)
Q Consensus 19 ~c~~c~~~f~~~~-~~~~~~~C~~C 42 (114)
+|..|+....... .++.++-|+.|
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rC 27 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRC 27 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTT
T ss_pred cCccCCCcceEeEecCCCCeECcCC
Confidence 3555555443332 23334555555
No 202
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=25.04 E-value=87 Score=15.13 Aligned_cols=21 Identities=19% Similarity=0.270 Sum_probs=10.6
Q ss_pred ccCCCCCCCCCCCCCCCceeccccc
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICL 43 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~ 43 (114)
.|+.|+.... ....|+|..|.
T Consensus 2 ~Cd~C~~~pI----~G~RykC~~C~ 22 (45)
T cd02344 2 TCDGCQMFPI----NGPRFKCRNCD 22 (45)
T ss_pred CCCCCCCCCC----ccCeEECCCCC
Confidence 4666654321 12356666654
No 203
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=25.00 E-value=80 Score=14.80 Aligned_cols=19 Identities=21% Similarity=0.462 Sum_probs=10.6
Q ss_pred ccCCCCCCCCCCCCCCCceeccccc
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICL 43 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~ 43 (114)
.|+.|+.. .+..|.|..|.
T Consensus 2 ~C~~C~~~------~~~r~~C~~C~ 20 (41)
T cd02337 2 TCNECKHH------VETRWHCTVCE 20 (41)
T ss_pred cCCCCCCc------CCCceECCCCc
Confidence 46667551 12556777664
No 204
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=24.95 E-value=36 Score=15.70 Aligned_cols=12 Identities=42% Similarity=0.797 Sum_probs=5.6
Q ss_pred Cceecccccccc
Q psy2414 35 GMYKCVICLKSV 46 (114)
Q Consensus 35 ~~~~C~~C~~~f 46 (114)
+-|+|..|++..
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 347777777653
No 205
>KOG0717|consensus
Probab=24.94 E-value=44 Score=24.84 Aligned_cols=22 Identities=23% Similarity=0.463 Sum_probs=18.5
Q ss_pred ccCCCCcCcccChhHHHHHHHH
Q psy2414 61 HKCPYCESVYSRVDTLKLHAKR 82 (114)
Q Consensus 61 ~~c~~C~~~f~~~~~l~~H~~~ 82 (114)
+.|..|.+.|....+|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7888999999998888888753
No 206
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.81 E-value=63 Score=17.00 Aligned_cols=27 Identities=4% Similarity=-0.113 Sum_probs=14.7
Q ss_pred CccccCCCCCCCCCCC-CCCCceecccc
Q psy2414 16 PFITRNNTDSIFYPDP-ASPGMYKCVIC 42 (114)
Q Consensus 16 ~~~~c~~c~~~f~~~~-~~~~~~~C~~C 42 (114)
...+|.+||+.-.... +.-+||-+.-|
T Consensus 6 ~~v~CP~Cgkpv~w~~~s~frPFCSkRC 33 (65)
T COG3024 6 ITVPCPTCGKPVVWGEESPFRPFCSKRC 33 (65)
T ss_pred ccccCCCCCCcccccccCCcCcchhHhh
Confidence 4567888888665533 22334433334
No 207
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=24.66 E-value=67 Score=19.48 Aligned_cols=32 Identities=16% Similarity=0.338 Sum_probs=15.0
Q ss_pred ceecccccccccChhhHHhhhcCCCccCCCCcCcc
Q psy2414 36 MYKCVICLKSVRSRWHHLQTHFSRNHKCPYCESVY 70 (114)
Q Consensus 36 ~~~C~~C~~~f~~~~~h~~~h~~~~~~c~~C~~~f 70 (114)
.|.|..|+..+.....+... ..+.|..|+-.+
T Consensus 112 ~y~C~~C~~~~~~~rr~~~~---~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYLRVRRSNNV---SRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCceEccccCc---ceEEcCCCCCEE
Confidence 56676676554321111111 136666666543
No 208
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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 C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=24.55 E-value=50 Score=14.31 Aligned_cols=9 Identities=33% Similarity=0.892 Sum_probs=4.5
Q ss_pred ecccccccc
Q psy2414 38 KCVICLKSV 46 (114)
Q Consensus 38 ~C~~C~~~f 46 (114)
.|..|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 344555555
No 209
>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=24.49 E-value=26 Score=17.32 Aligned_cols=10 Identities=0% Similarity=-0.333 Sum_probs=4.7
Q ss_pred ccCCCCCccC
Q psy2414 93 HGLIPQLLFP 102 (114)
Q Consensus 93 ~c~~c~~~f~ 102 (114)
+|+.|+..|.
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp E-TTT--EE-
T ss_pred cCCCCCCCCC
Confidence 7888887765
No 210
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=24.30 E-value=61 Score=13.37 Aligned_cols=7 Identities=14% Similarity=-0.035 Sum_probs=4.1
Q ss_pred ccCCCCC
Q psy2414 19 TRNNTDS 25 (114)
Q Consensus 19 ~c~~c~~ 25 (114)
.|..||+
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 4566665
No 211
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.10 E-value=59 Score=20.99 Aligned_cols=33 Identities=24% Similarity=0.319 Sum_probs=20.4
Q ss_pred CCccccCCCC--CCCCCCC------CCCC-----ceeccccccccc
Q psy2414 15 QPFITRNNTD--SIFYPDP------ASPG-----MYKCVICLKSVR 47 (114)
Q Consensus 15 ~~~~~c~~c~--~~f~~~~------~~~~-----~~~C~~C~~~f~ 47 (114)
++...|+.|| +.|..+. .++. -|+|..|++++.
T Consensus 15 q~~k~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWlIYkC~~Cd~tWN 60 (203)
T COG4332 15 QPAKRCNSCGVKRAFTCSGKFRVNAQGKVLDVWLIYKCTHCDYTWN 60 (203)
T ss_pred hhhhhCcccCCcceeeecCcEEEcCCCcEEEEEEEEEeeccCCccc
Confidence 3556799998 4555544 1221 288999987753
No 212
>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=23.76 E-value=36 Score=15.75 Aligned_cols=13 Identities=8% Similarity=0.204 Sum_probs=8.9
Q ss_pred CccccCCCCCCCC
Q psy2414 16 PFITRNNTDSIFY 28 (114)
Q Consensus 16 ~~~~c~~c~~~f~ 28 (114)
|.+.|+.||..+-
T Consensus 31 p~~~C~~CGE~~~ 43 (46)
T TIGR03831 31 PALVCPQCGEEYL 43 (46)
T ss_pred CccccccCCCEee
Confidence 5566888886653
No 213
>PRK06424 transcription factor; Provisional
Probab=23.24 E-value=30 Score=21.28 Aligned_cols=25 Identities=8% Similarity=0.024 Sum_probs=17.5
Q ss_pred ccCCCCCCCCCCC----CCCCceeccccc
Q psy2414 19 TRNNTDSIFYPDP----ASPGMYKCVICL 43 (114)
Q Consensus 19 ~c~~c~~~f~~~~----~~~~~~~C~~C~ 43 (114)
.|+.||+.-.... .|.....|+.|.
T Consensus 2 ~CE~CG~~~~~~~~v~ieg~~l~vC~~Ca 30 (144)
T PRK06424 2 ECEMCGKKVPQTTKVMIDGAILNVCDDCA 30 (144)
T ss_pred cccccCcccCCceEEEEcCeeeehhHHHH
Confidence 4888988776554 566667777775
No 214
>KOG0782|consensus
Probab=23.19 E-value=20 Score=27.42 Aligned_cols=32 Identities=13% Similarity=0.130 Sum_probs=22.9
Q ss_pred ccCCCCCCCCCCC---CCCC-ceecccccccccChh
Q psy2414 19 TRNNTDSIFYPDP---ASPG-MYKCVICLKSVRSRW 50 (114)
Q Consensus 19 ~c~~c~~~f~~~~---~~~~-~~~C~~C~~~f~~~~ 50 (114)
+|+.|||.|.++. ..+. .-.|..|..+|..+-
T Consensus 255 kC~~CgKgFQQKf~FhsKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 255 KCNTCGKGFQQKFFFHSKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred ccchhhhhhhhheeeccccEEEEEehHHHHHhhcch
Confidence 6999999998886 2221 346888888876664
No 215
>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=22.39 E-value=48 Score=15.87 Aligned_cols=12 Identities=8% Similarity=-0.305 Sum_probs=8.1
Q ss_pred cccCCCCCCCCC
Q psy2414 18 ITRNNTDSIFYP 29 (114)
Q Consensus 18 ~~c~~c~~~f~~ 29 (114)
=.|..|++.|.-
T Consensus 9 K~C~~C~rpf~W 20 (42)
T PF10013_consen 9 KICPVCGRPFTW 20 (42)
T ss_pred CcCcccCCcchH
Confidence 347778777754
No 216
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=22.24 E-value=1.2e+02 Score=20.81 Aligned_cols=81 Identities=12% Similarity=0.115 Sum_probs=43.0
Q ss_pred CCCCceecccccccccChhh--HHhhh-c-C-CCccCCCCcCcccC------hhHHHHHHHHHhC-CCCCCccccCCCCC
Q psy2414 32 ASPGMYKCVICLKSVRSRWH--HLQTH-F-S-RNHKCPYCESVYSR------VDTLKLHAKRVHG-LGISRYIHGLIPQL 99 (114)
Q Consensus 32 ~~~~~~~C~~C~~~f~~~~~--h~~~h-~-~-~~~~c~~C~~~f~~------~~~l~~H~~~~~~-~~~~~~~~c~~c~~ 99 (114)
.|.+.|.|..|....-.... ||..- . + +.|+|..|++.=.. ......|++.... .++...+-|+.|+.
T Consensus 138 hGGrif~CsfC~~flCEDDQFEHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKCg~ 217 (314)
T PF06524_consen 138 HGGRIFKCSFCDNFLCEDDQFEHQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKCGY 217 (314)
T ss_pred CCCeEEEeecCCCeeeccchhhhhhhhhhhhcccccccccccccchhhhheeeeehhhhhhhcccccccCCCCCCCCCCC
Confidence 35667888888754433322 66532 2 2 27888887653221 1223356653211 12222256888887
Q ss_pred ccCCCCCCCCCCC
Q psy2414 100 LFPTPHAKTSPVD 112 (114)
Q Consensus 100 ~f~~~~~L~~h~~ 112 (114)
-.+....|...++
T Consensus 218 et~eTkdLSmStR 230 (314)
T PF06524_consen 218 ETQETKDLSMSTR 230 (314)
T ss_pred cccccccceeeee
Confidence 7776666655443
No 217
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=21.97 E-value=50 Score=16.33 Aligned_cols=13 Identities=23% Similarity=0.590 Sum_probs=7.6
Q ss_pred ceecccccccccC
Q psy2414 36 MYKCVICLKSVRS 48 (114)
Q Consensus 36 ~~~C~~C~~~f~~ 48 (114)
-|.|..|+-.+..
T Consensus 28 ~W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 28 WWKCPKCGHEWKA 40 (55)
T ss_pred EEECCCCCCeeEc
Confidence 3677777655533
No 218
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=21.89 E-value=74 Score=14.83 Aligned_cols=26 Identities=8% Similarity=0.045 Sum_probs=14.8
Q ss_pred cccCCCCCCCCCCCCCCCceeccccccc
Q psy2414 18 ITRNNTDSIFYPDPASPGMYKCVICLKS 45 (114)
Q Consensus 18 ~~c~~c~~~f~~~~~~~~~~~C~~C~~~ 45 (114)
..|+.|++.+... ...-+.|..|+..
T Consensus 12 ~~C~~C~~~i~~~--~~~~~~C~~C~~~ 37 (50)
T cd00029 12 TFCDVCRKSIWGL--FKQGLRCSWCKVK 37 (50)
T ss_pred CChhhcchhhhcc--ccceeEcCCCCCc
Confidence 3477777665431 2345667777544
No 219
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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 DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=21.49 E-value=18 Score=19.14 Aligned_cols=33 Identities=18% Similarity=0.415 Sum_probs=15.2
Q ss_pred eecccccccccChhhHHhhhcCC-CccCCCCcCc
Q psy2414 37 YKCVICLKSVRSRWHHLQTHFSR-NHKCPYCESV 69 (114)
Q Consensus 37 ~~C~~C~~~f~~~~~h~~~h~~~-~~~c~~C~~~ 69 (114)
|.|..|+..-...-..+..+.|- -.+|+-|...
T Consensus 5 FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~ 38 (66)
T PF05180_consen 5 FTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNR 38 (66)
T ss_dssp EEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--E
T ss_pred EEcCCCCCccceeeCHHHHhCCeEEEECCCCcce
Confidence 66777763321111134455555 6777777543
No 221
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=21.42 E-value=80 Score=14.51 Aligned_cols=26 Identities=8% Similarity=0.027 Sum_probs=15.2
Q ss_pred ccccCCCCCCCCCCCCCCCceeccccccc
Q psy2414 17 FITRNNTDSIFYPDPASPGMYKCVICLKS 45 (114)
Q Consensus 17 ~~~c~~c~~~f~~~~~~~~~~~C~~C~~~ 45 (114)
...|+.|++.+.... ..+.|..|+..
T Consensus 11 ~~~C~~C~~~i~~~~---~~~~C~~C~~~ 36 (49)
T smart00109 11 PTKCCVCRKSIWGSF---QGLRCSWCKVK 36 (49)
T ss_pred CCCccccccccCcCC---CCcCCCCCCch
Confidence 345777777664421 35667777543
No 222
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=21.22 E-value=72 Score=18.45 Aligned_cols=13 Identities=8% Similarity=-0.225 Sum_probs=6.3
Q ss_pred CCccccCCCCCCC
Q psy2414 15 QPFITRNNTDSIF 27 (114)
Q Consensus 15 ~~~~~c~~c~~~f 27 (114)
.....|..|+..-
T Consensus 20 ~k~FtCp~Cghe~ 32 (104)
T COG4888 20 PKTFTCPRCGHEK 32 (104)
T ss_pred CceEecCccCCee
Confidence 3344555555443
No 223
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=21.08 E-value=1.1e+02 Score=14.50 Aligned_cols=20 Identities=15% Similarity=0.416 Sum_probs=11.4
Q ss_pred ccCCCCCCCCCCCCCCCceeccccc
Q psy2414 19 TRNNTDSIFYPDPASPGMYKCVICL 43 (114)
Q Consensus 19 ~c~~c~~~f~~~~~~~~~~~C~~C~ 43 (114)
.|+.|++.. .| ..|.|..|.
T Consensus 2 ~C~~C~~~i----~g-~r~~C~~C~ 21 (46)
T cd02249 2 SCDGCLKPI----VG-VRYHCLVCE 21 (46)
T ss_pred CCcCCCCCC----cC-CEEECCCCC
Confidence 477777622 22 456676664
No 224
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=21.01 E-value=1e+02 Score=15.03 Aligned_cols=7 Identities=0% Similarity=-0.054 Sum_probs=3.8
Q ss_pred ccCCCCC
Q psy2414 19 TRNNTDS 25 (114)
Q Consensus 19 ~c~~c~~ 25 (114)
.|+.|+.
T Consensus 2 ~Cd~C~~ 8 (48)
T cd02341 2 KCDSCGI 8 (48)
T ss_pred CCCCCCC
Confidence 4555554
No 225
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=20.96 E-value=51 Score=15.31 Aligned_cols=15 Identities=13% Similarity=0.319 Sum_probs=7.3
Q ss_pred CCCCccccCCCCCCC
Q psy2414 13 PIQPFITRNNTDSIF 27 (114)
Q Consensus 13 ~~~~~~~c~~c~~~f 27 (114)
++...+.|..|+..|
T Consensus 24 ~mT~fy~C~~C~~~w 38 (40)
T smart00440 24 PMTVFYVCTKCGHRW 38 (40)
T ss_pred CCeEEEEeCCCCCEe
Confidence 333445555555443
No 226
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=20.36 E-value=72 Score=14.32 Aligned_cols=11 Identities=27% Similarity=0.606 Sum_probs=4.9
Q ss_pred eeccccccccc
Q psy2414 37 YKCVICLKSVR 47 (114)
Q Consensus 37 ~~C~~C~~~f~ 47 (114)
+.|+.|++.+.
T Consensus 5 ~~C~nC~R~v~ 15 (33)
T PF08209_consen 5 VECPNCGRPVA 15 (33)
T ss_dssp EE-TTTSSEEE
T ss_pred EECCCCcCCcc
Confidence 44555555443
No 227
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=20.10 E-value=49 Score=20.26 Aligned_cols=22 Identities=32% Similarity=0.416 Sum_probs=18.1
Q ss_pred eecccccccccChhhHHhhhcC
Q psy2414 37 YKCVICLKSVRSRWHHLQTHFS 58 (114)
Q Consensus 37 ~~C~~C~~~f~~~~~h~~~h~~ 58 (114)
-.|.++|+.|++...|+..|-+
T Consensus 77 IicLEDGkkfKSLKRHL~t~~g 98 (148)
T COG4957 77 IICLEDGKKFKSLKRHLTTHYG 98 (148)
T ss_pred EEEeccCcchHHHHHHHhcccC
Confidence 5799999999888778888755
No 228
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=20.01 E-value=52 Score=19.09 Aligned_cols=15 Identities=27% Similarity=0.738 Sum_probs=12.2
Q ss_pred CccCCCCcCcccChh
Q psy2414 60 NHKCPYCESVYSRVD 74 (114)
Q Consensus 60 ~~~c~~C~~~f~~~~ 74 (114)
|++|.-||..|.+-+
T Consensus 2 pH~CtrCG~vf~~g~ 16 (112)
T COG3364 2 PHQCTRCGEVFDDGS 16 (112)
T ss_pred Cceeccccccccccc
Confidence 578999999998853
Done!