Query psy3492
Match_columns 85
No_of_seqs 139 out of 1087
Neff 11.1
Searched_HMMs 46136
Date Fri Aug 16 18:05:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3492.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3492hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 3.2E-25 6.9E-30 123.3 5.3 79 1-80 164-248 (279)
2 KOG2462|consensus 99.9 8.3E-23 1.8E-27 113.8 3.2 71 1-72 190-265 (279)
3 KOG3576|consensus 99.6 7.8E-17 1.7E-21 87.2 0.7 73 1-74 120-198 (267)
4 KOG3623|consensus 99.6 2.7E-16 5.9E-21 97.4 0.9 70 1-71 897-971 (1007)
5 KOG3576|consensus 99.6 3.6E-15 7.8E-20 80.8 3.5 75 1-75 148-237 (267)
6 KOG3623|consensus 99.5 6.8E-15 1.5E-19 91.4 3.2 79 1-80 213-314 (1007)
7 KOG3608|consensus 99.4 1.4E-13 3.1E-18 79.9 4.3 83 1-83 240-327 (467)
8 KOG1074|consensus 99.4 1.2E-14 2.7E-19 91.0 -0.2 73 1-74 608-692 (958)
9 PHA02768 hypothetical protein; 99.4 3.4E-13 7.5E-18 59.2 2.1 40 25-65 6-46 (55)
10 PHA00733 hypothetical protein 99.3 5.3E-12 1.1E-16 65.0 5.2 71 2-73 44-122 (128)
11 KOG3608|consensus 99.3 1.2E-11 2.6E-16 72.1 5.0 81 1-82 266-359 (467)
12 PHA02768 hypothetical protein; 99.2 1.8E-11 3.9E-16 53.8 1.9 40 1-40 8-47 (55)
13 KOG1074|consensus 99.0 1.1E-10 2.3E-15 74.0 2.2 49 1-50 882-932 (958)
14 PHA00732 hypothetical protein 99.0 9.2E-10 2E-14 52.3 3.2 47 24-73 1-47 (79)
15 PLN03086 PRLI-interacting fact 98.9 4.2E-09 9E-14 65.2 6.5 77 1-81 456-547 (567)
16 PHA00733 hypothetical protein 98.9 4.5E-09 9.8E-14 54.2 5.0 48 1-48 76-123 (128)
17 KOG3993|consensus 98.8 2.9E-09 6.2E-14 63.5 2.2 73 1-74 298-380 (500)
18 PF13465 zf-H2C2_2: Zinc-finge 98.8 4.5E-09 9.8E-14 39.8 2.0 23 13-35 1-25 (26)
19 PHA00732 hypothetical protein 98.6 6.3E-08 1.4E-12 46.0 3.3 46 1-50 4-49 (79)
20 PF00096 zf-C2H2: Zinc finger, 98.6 2.3E-08 5E-13 36.7 1.4 23 51-73 1-23 (23)
21 PHA00616 hypothetical protein 98.6 2.7E-08 5.9E-13 41.9 1.2 24 51-74 2-25 (44)
22 PLN03086 PRLI-interacting fact 98.5 3.6E-07 7.8E-12 57.0 5.0 67 1-71 481-561 (567)
23 PF13465 zf-H2C2_2: Zinc-finge 98.4 2E-07 4.3E-12 35.2 1.2 23 39-62 1-26 (26)
24 PF13894 zf-C2H2_4: C2H2-type 98.3 6.2E-07 1.3E-11 32.8 1.8 23 51-73 1-23 (24)
25 PF00096 zf-C2H2: Zinc finger, 98.3 5.5E-07 1.2E-11 32.9 1.6 21 1-21 3-23 (23)
26 PHA00616 hypothetical protein 98.3 4.6E-07 1E-11 38.2 1.3 26 24-50 1-26 (44)
27 PF05605 zf-Di19: Drought indu 98.2 5.2E-06 1.1E-10 36.7 4.2 46 24-72 2-51 (54)
28 PF05605 zf-Di19: Drought indu 98.1 1.9E-05 4.1E-10 34.9 4.4 43 1-46 5-51 (54)
29 PF12756 zf-C2H2_2: C2H2 type 98.1 3.1E-06 6.7E-11 41.5 2.1 71 1-74 2-74 (100)
30 smart00355 ZnF_C2H2 zinc finge 98.1 6E-06 1.3E-10 30.5 2.4 23 51-73 1-23 (26)
31 PF13912 zf-C2H2_6: C2H2-type 98.0 3.2E-06 6.9E-11 32.0 1.4 22 52-73 3-24 (27)
32 PF13912 zf-C2H2_6: C2H2-type 97.9 1.1E-05 2.3E-10 30.5 1.9 24 24-48 1-24 (27)
33 PF13894 zf-C2H2_4: C2H2-type 97.9 1.5E-05 3.4E-10 28.9 2.1 21 1-21 3-23 (24)
34 smart00355 ZnF_C2H2 zinc finge 97.6 8.9E-05 1.9E-09 27.1 2.3 21 1-21 3-23 (26)
35 KOG3993|consensus 97.5 1.9E-05 4E-10 47.8 -0.3 50 25-74 268-319 (500)
36 PF12874 zf-met: Zinc-finger o 97.5 7.8E-05 1.7E-09 27.5 1.3 21 51-71 1-21 (25)
37 PF13913 zf-C2HC_2: zinc-finge 97.3 0.00027 5.9E-09 26.3 2.1 20 52-72 4-23 (25)
38 COG5189 SFP1 Putative transcri 97.2 5.9E-05 1.3E-09 44.3 -0.3 49 23-71 348-419 (423)
39 PF13909 zf-H2C2_5: C2H2-type 97.1 0.0004 8.6E-09 25.3 1.6 22 51-73 1-22 (24)
40 PF12171 zf-C2H2_jaz: Zinc-fin 97.0 0.00023 5E-09 26.8 0.5 21 51-71 2-22 (27)
41 PF12874 zf-met: Zinc-finger o 97.0 0.00054 1.2E-08 25.1 1.5 20 25-44 1-20 (25)
42 PF09237 GAGA: GAGA factor; I 97.0 0.00089 1.9E-08 29.1 2.1 20 1-20 27-46 (54)
43 PF09237 GAGA: GAGA factor; I 96.4 0.004 8.7E-08 27.1 2.2 26 23-48 23-48 (54)
44 PRK04860 hypothetical protein; 96.3 0.0024 5.3E-08 34.4 1.6 34 24-62 119-155 (160)
45 PRK04860 hypothetical protein; 95.8 0.0075 1.6E-07 32.5 2.0 33 1-37 122-156 (160)
46 smart00451 ZnF_U1 U1-like zinc 95.7 0.011 2.4E-07 23.3 1.8 21 51-71 4-24 (35)
47 COG5189 SFP1 Putative transcri 95.4 0.0037 8E-08 37.1 -0.2 43 2-44 355-418 (423)
48 PF12756 zf-C2H2_2: C2H2 type 94.3 0.049 1.1E-06 26.4 2.2 21 1-21 53-73 (100)
49 KOG2186|consensus 94.1 0.031 6.8E-07 32.2 1.4 37 25-62 4-41 (276)
50 COG1997 RPL43A Ribosomal prote 93.8 0.026 5.6E-07 27.3 0.6 32 23-63 34-66 (89)
51 PF09986 DUF2225: Uncharacteri 93.7 0.0065 1.4E-07 34.2 -1.8 13 51-63 49-61 (214)
52 TIGR00622 ssl1 transcription f 93.5 0.11 2.3E-06 26.5 2.5 72 1-74 18-105 (112)
53 KOG2231|consensus 93.1 0.4 8.8E-06 31.6 5.1 72 8-80 124-214 (669)
54 smart00734 ZnF_Rad18 Rad18-lik 92.6 0.18 4E-06 18.7 2.0 19 52-71 3-21 (26)
55 KOG1146|consensus 92.2 0.11 2.4E-06 36.4 1.9 44 1-44 468-538 (1406)
56 COG2888 Predicted Zn-ribbon RN 92.0 0.15 3.3E-06 22.9 1.6 32 23-58 26-58 (61)
57 COG4049 Uncharacterized protei 91.4 0.11 2.4E-06 23.0 0.9 19 1-19 20-38 (65)
58 smart00531 TFIIE Transcription 91.1 0.12 2.6E-06 27.5 1.0 35 23-60 98-133 (147)
59 PF12013 DUF3505: Protein of u 91.0 0.28 6E-06 24.7 2.3 24 50-73 80-107 (109)
60 cd00350 rubredoxin_like Rubred 90.9 0.18 4E-06 19.7 1.3 11 25-35 2-12 (33)
61 TIGR02098 MJ0042_CXXC MJ0042 f 89.7 0.24 5.1E-06 19.9 1.1 33 25-61 3-36 (38)
62 PF13717 zinc_ribbon_4: zinc-r 89.6 0.41 8.8E-06 19.2 1.8 31 25-60 3-35 (36)
63 KOG1146|consensus 89.5 0.15 3.2E-06 35.9 0.6 65 8-72 446-540 (1406)
64 smart00614 ZnF_BED BED zinc fi 89.0 0.33 7.2E-06 20.8 1.4 21 51-71 19-44 (50)
65 PF10571 UPF0547: Uncharacteri 88.3 0.29 6.2E-06 18.2 0.8 10 52-61 16-25 (26)
66 COG5151 SSL1 RNA polymerase II 88.0 0.31 6.7E-06 29.3 1.2 53 27-80 365-418 (421)
67 PF04959 ARS2: Arsenite-resist 87.8 0.42 9E-06 27.2 1.6 22 51-72 78-99 (214)
68 cd00730 rubredoxin Rubredoxin; 87.7 0.2 4.4E-06 21.7 0.3 13 25-37 2-14 (50)
69 KOG4167|consensus 87.5 0.096 2.1E-06 34.7 -1.1 24 51-74 793-816 (907)
70 PF14353 CpXC: CpXC protein 87.2 0.63 1.4E-05 24.0 2.0 13 51-63 39-51 (128)
71 PTZ00255 60S ribosomal protein 87.1 0.16 3.5E-06 24.9 -0.2 31 23-62 35-66 (90)
72 TIGR00373 conserved hypothetic 86.8 1.5 3.2E-05 23.8 3.3 32 23-61 108-139 (158)
73 PF09538 FYDLN_acid: Protein o 86.7 0.48 1E-05 24.0 1.3 12 52-63 28-39 (108)
74 PF13719 zinc_ribbon_5: zinc-r 86.7 0.61 1.3E-05 18.8 1.4 33 25-61 3-36 (37)
75 PRK14890 putative Zn-ribbon RN 86.4 0.49 1.1E-05 21.3 1.1 9 25-33 26-34 (59)
76 TIGR00280 L37a ribosomal prote 86.3 0.17 3.8E-06 24.8 -0.3 32 23-63 34-66 (91)
77 KOG2482|consensus 86.1 2 4.3E-05 26.4 3.8 50 23-72 143-217 (423)
78 PRK06266 transcription initiat 85.8 0.71 1.5E-05 25.5 1.8 33 23-62 116-148 (178)
79 PF02892 zf-BED: BED zinc fing 85.2 0.79 1.7E-05 19.0 1.5 20 51-70 17-40 (45)
80 PF01780 Ribosomal_L37ae: Ribo 84.7 0.18 3.9E-06 24.7 -0.7 31 23-62 34-65 (90)
81 KOG2893|consensus 84.6 0.17 3.7E-06 29.3 -0.9 41 27-69 13-53 (341)
82 COG1773 Rubredoxin [Energy pro 84.6 0.29 6.4E-06 21.7 0.0 33 24-58 3-44 (55)
83 PF07754 DUF1610: Domain of un 84.4 0.47 1E-05 17.3 0.5 8 51-58 17-24 (24)
84 PF13878 zf-C2H2_3: zinc-finge 84.2 1.3 2.9E-05 18.3 1.9 21 1-21 16-38 (41)
85 PF00301 Rubredoxin: Rubredoxi 83.9 0.13 2.9E-06 22.0 -1.2 13 25-37 2-14 (47)
86 PRK03976 rpl37ae 50S ribosomal 83.8 0.23 5E-06 24.3 -0.5 31 23-62 35-66 (90)
87 KOG2907|consensus 81.6 0.78 1.7E-05 23.4 0.8 37 24-62 74-114 (116)
88 KOG4173|consensus 81.4 0.35 7.6E-06 27.4 -0.5 47 25-71 107-167 (253)
89 smart00834 CxxC_CXXC_SSSS Puta 80.8 0.64 1.4E-05 18.8 0.3 13 51-63 6-18 (41)
90 PRK00464 nrdR transcriptional 80.8 0.23 5E-06 26.8 -1.3 14 24-37 28-41 (154)
91 COG5236 Uncharacterized conser 80.3 2.2 4.7E-05 26.3 2.5 18 27-44 223-240 (493)
92 KOG2231|consensus 79.4 5.7 0.00012 26.7 4.2 20 1-20 185-204 (669)
93 COG1996 RPC10 DNA-directed RNA 79.1 0.98 2.1E-05 19.6 0.6 27 24-58 6-32 (49)
94 PF09723 Zn-ribbon_8: Zinc rib 78.9 0.73 1.6E-05 19.1 0.2 15 51-65 6-20 (42)
95 PF05443 ROS_MUCR: ROS/MUCR tr 78.4 1.6 3.4E-05 23.0 1.3 21 51-74 73-93 (132)
96 PF01927 Mut7-C: Mut7-C RNAse 76.1 1.2 2.6E-05 23.7 0.6 43 24-67 91-141 (147)
97 PF04959 ARS2: Arsenite-resist 75.7 2.8 6.1E-05 24.0 2.0 28 23-50 76-103 (214)
98 PHA00626 hypothetical protein 75.4 1.3 2.9E-05 19.7 0.5 14 51-64 24-37 (59)
99 TIGR02300 FYDLN_acid conserved 75.3 2.4 5.2E-05 22.2 1.5 10 52-61 28-37 (129)
100 COG5236 Uncharacterized conser 75.1 3 6.6E-05 25.7 2.1 71 10-81 165-253 (493)
101 PF15269 zf-C2H2_7: Zinc-finge 74.2 3.2 7E-05 17.6 1.5 21 51-71 21-41 (54)
102 COG1592 Rubrerythrin [Energy p 73.9 1.7 3.7E-05 23.8 0.8 9 51-59 135-143 (166)
103 TIGR02605 CxxC_CxxC_SSSS putat 72.6 1.4 3.1E-05 18.9 0.3 13 51-63 6-18 (52)
104 PF10013 DUF2256: Uncharacteri 72.6 3.2 6.9E-05 17.4 1.3 13 1-13 11-23 (42)
105 COG1571 Predicted DNA-binding 72.5 2.2 4.8E-05 26.8 1.2 32 25-65 351-382 (421)
106 COG5048 FOG: Zn-finger [Genera 72.5 0.53 1.2E-05 28.4 -1.5 50 24-74 289-347 (467)
107 PF04423 Rad50_zn_hook: Rad50 72.3 1.4 3.1E-05 19.2 0.2 12 1-12 23-34 (54)
108 PF08274 PhnA_Zn_Ribbon: PhnA 71.6 1.1 2.4E-05 17.3 -0.2 8 51-58 20-27 (30)
109 KOG2593|consensus 70.6 6.7 0.00015 24.9 2.8 34 23-58 127-161 (436)
110 KOG0717|consensus 70.3 2.8 6.1E-05 26.8 1.2 19 1-19 295-313 (508)
111 PRK09678 DNA-binding transcrip 69.2 1.2 2.6E-05 20.9 -0.4 11 51-61 28-40 (72)
112 COG1656 Uncharacterized conser 68.1 4.2 9.2E-05 22.3 1.5 41 25-66 98-146 (165)
113 KOG2785|consensus 67.7 19 0.0004 22.7 4.2 22 51-72 218-242 (390)
114 KOG4167|consensus 67.1 1.1 2.5E-05 30.1 -0.9 22 1-22 795-816 (907)
115 KOG1842|consensus 66.5 4.1 8.9E-05 26.0 1.4 22 51-72 16-37 (505)
116 COG4338 Uncharacterized protei 66.4 2.8 6.1E-05 18.1 0.5 13 1-13 15-27 (54)
117 PRK00432 30S ribosomal protein 65.9 5.1 0.00011 17.3 1.3 13 48-60 34-47 (50)
118 smart00440 ZnF_C2C2 C2C2 Zinc 63.9 0.82 1.8E-05 18.8 -1.3 11 51-61 29-39 (40)
119 PRK03824 hypA hydrogenase nick 62.9 2.7 5.8E-05 22.1 0.2 14 24-37 70-83 (135)
120 PF01363 FYVE: FYVE zinc finge 61.9 4.4 9.4E-05 18.4 0.8 8 27-34 12-19 (69)
121 PF01286 XPA_N: XPA protein N- 60.2 2.8 6E-05 16.7 -0.0 12 52-63 5-16 (34)
122 PF04780 DUF629: Protein of un 60.0 8.2 0.00018 24.8 1.9 22 51-72 58-79 (466)
123 COG0068 HypF Hydrogenase matur 59.7 1.3 2.9E-05 29.6 -1.5 38 26-65 125-166 (750)
124 PF10071 DUF2310: Zn-ribbon-co 59.7 4.1 9E-05 24.0 0.6 28 25-57 221-248 (258)
125 KOG2807|consensus 59.6 10 0.00022 23.4 2.1 29 51-79 346-374 (378)
126 PRK00398 rpoP DNA-directed RNA 58.7 4.1 8.9E-05 17.0 0.3 13 51-63 4-16 (46)
127 PF07975 C1_4: TFIIH C1-like d 58.6 1.7 3.7E-05 19.0 -0.9 24 51-74 22-45 (51)
128 PRK12380 hydrogenase nickel in 58.3 3.9 8.5E-05 20.8 0.3 24 25-58 71-94 (113)
129 smart00154 ZnF_AN1 AN1-like Zi 58.0 5.7 0.00012 16.2 0.7 15 24-38 12-26 (39)
130 PRK05978 hypothetical protein; 57.3 3.3 7.1E-05 22.3 -0.1 10 52-61 54-63 (148)
131 cd00065 FYVE FYVE domain; Zinc 56.6 10 0.00023 16.3 1.5 8 26-33 20-27 (57)
132 KOG2071|consensus 55.5 7.9 0.00017 25.5 1.3 24 51-74 419-442 (579)
133 KOG1280|consensus 54.7 14 0.00031 22.9 2.2 27 24-50 79-105 (381)
134 COG3677 Transposase and inacti 54.5 6.1 0.00013 20.7 0.6 13 51-63 54-66 (129)
135 cd00729 rubredoxin_SM Rubredox 54.4 5.6 0.00012 15.6 0.4 12 51-62 3-14 (34)
136 PF01155 HypA: Hydrogenase exp 54.4 3 6.6E-05 21.2 -0.5 13 25-37 71-83 (113)
137 COG1655 Uncharacterized protei 54.3 1.7 3.7E-05 25.2 -1.5 20 23-42 18-37 (267)
138 KOG3408|consensus 53.8 8.4 0.00018 20.1 1.0 23 51-73 58-80 (129)
139 PF09845 DUF2072: Zn-ribbon co 53.1 8.2 0.00018 20.4 0.9 26 24-57 1-26 (131)
140 PF09963 DUF2197: Uncharacteri 53.1 2.4 5.1E-05 18.9 -0.9 33 25-58 3-39 (56)
141 PRK05452 anaerobic nitric oxid 52.6 4.3 9.4E-05 26.0 -0.1 15 23-37 424-438 (479)
142 smart00659 RPOLCX RNA polymera 52.6 6.1 0.00013 16.6 0.4 13 51-63 3-15 (44)
143 TIGR00100 hypA hydrogenase nic 51.9 6 0.00013 20.2 0.3 24 25-58 71-94 (115)
144 PF10276 zf-CHCC: Zinc-finger 50.2 5.2 0.00011 16.5 -0.0 10 51-60 30-39 (40)
145 smart00064 FYVE Protein presen 50.2 13 0.00029 16.7 1.4 10 26-35 12-21 (68)
146 COG1779 C4-type Zn-finger prot 49.7 3.4 7.4E-05 23.3 -0.8 35 25-62 15-55 (201)
147 KOG0801|consensus 49.7 4.8 0.0001 22.1 -0.2 23 39-62 128-150 (205)
148 PF10537 WAC_Acf1_DNA_bd: ATP- 49.2 26 0.00056 17.6 2.3 33 1-33 6-39 (102)
149 COG3357 Predicted transcriptio 49.1 9 0.0002 18.9 0.7 14 23-36 57-70 (97)
150 PF13451 zf-trcl: Probable zin 49.0 5.9 0.00013 17.2 0.1 20 23-42 3-22 (49)
151 KOG2636|consensus 48.6 12 0.00026 24.0 1.3 21 51-71 402-423 (497)
152 PRK01343 zinc-binding protein; 48.3 9.8 0.00021 17.1 0.7 9 1-9 12-20 (57)
153 KOG0227|consensus 48.2 11 0.00024 21.4 1.0 25 46-70 48-73 (222)
154 PF01428 zf-AN1: AN1-like Zinc 48.1 5.3 0.00011 16.5 -0.2 16 23-38 12-27 (43)
155 COG4896 Uncharacterized protei 48.0 11 0.00024 17.2 0.8 8 51-58 32-39 (68)
156 smart00132 LIM Zinc-binding do 48.0 12 0.00027 14.2 1.0 10 51-60 28-37 (39)
157 PF05191 ADK_lid: Adenylate ki 47.2 5.7 0.00012 15.9 -0.1 10 52-61 3-12 (36)
158 cd00924 Cyt_c_Oxidase_Vb Cytoc 47.1 11 0.00023 18.9 0.8 14 23-36 78-91 (97)
159 PTZ00448 hypothetical protein; 46.8 20 0.00044 22.5 2.0 23 51-73 315-337 (373)
160 PF13240 zinc_ribbon_2: zinc-r 46.5 7.3 0.00016 13.8 0.1 6 53-58 16-21 (23)
161 TIGR01206 lysW lysine biosynth 45.9 11 0.00023 16.7 0.6 12 51-62 3-14 (54)
162 PRK00564 hypA hydrogenase nick 45.6 9 0.00019 19.7 0.4 12 25-36 72-83 (117)
163 PRK12722 transcriptional activ 44.8 21 0.00046 20.1 1.8 13 23-35 133-145 (187)
164 PF08790 zf-LYAR: LYAR-type C2 44.5 8.8 0.00019 14.6 0.2 9 26-34 2-10 (28)
165 PF03604 DNA_RNApol_7kD: DNA d 44.3 9.9 0.00021 14.8 0.3 11 51-61 1-11 (32)
166 PF10263 SprT-like: SprT-like 43.8 8.9 0.00019 20.3 0.2 8 51-58 144-151 (157)
167 PF14787 zf-CCHC_5: GAG-polypr 43.6 13 0.00027 15.0 0.6 9 1-9 5-13 (36)
168 PF08209 Sgf11: Sgf11 (transcr 43.5 7.3 0.00016 15.3 -0.1 20 51-71 5-24 (33)
169 PF07282 OrfB_Zn_ribbon: Putat 43.5 18 0.0004 16.3 1.3 13 51-63 47-59 (69)
170 KOG0978|consensus 42.8 6.8 0.00015 26.5 -0.3 19 51-69 679-697 (698)
171 PF09855 DUF2082: Nucleic-acid 42.6 13 0.00029 17.0 0.7 8 51-58 1-8 (64)
172 PF08271 TF_Zn_Ribbon: TFIIB z 42.5 13 0.00028 15.2 0.6 8 51-58 1-8 (43)
173 PLN02294 cytochrome c oxidase 41.6 14 0.0003 20.5 0.8 18 20-37 136-154 (174)
174 PRK12860 transcriptional activ 41.1 22 0.00048 20.1 1.5 13 23-35 133-145 (189)
175 COG4391 Uncharacterized protei 41.0 11 0.00023 17.2 0.2 36 23-61 23-59 (62)
176 COG4957 Predicted transcriptio 40.8 20 0.00044 19.2 1.2 17 3-22 81-97 (148)
177 PF06397 Desulfoferrod_N: Desu 40.8 9.9 0.00022 15.3 0.1 9 51-59 7-15 (36)
178 COG4530 Uncharacterized protei 40.3 24 0.00051 18.2 1.4 12 23-34 25-36 (129)
179 PF13248 zf-ribbon_3: zinc-rib 40.1 11 0.00024 13.7 0.2 6 53-58 19-24 (26)
180 PF03884 DUF329: Domain of unk 39.7 12 0.00025 16.8 0.2 9 1-9 5-13 (57)
181 PF11023 DUF2614: Protein of u 39.7 15 0.00033 18.9 0.7 33 23-65 68-100 (114)
182 PF11931 DUF3449: Domain of un 39.0 10 0.00022 21.5 0.0 21 51-71 102-123 (196)
183 COG3364 Zn-ribbon containing p 38.8 17 0.00038 18.4 0.8 17 23-39 1-17 (112)
184 KOG3002|consensus 38.4 34 0.00074 20.8 2.1 56 23-81 79-142 (299)
185 TIGR00515 accD acetyl-CoA carb 38.2 23 0.0005 21.3 1.4 31 25-62 27-57 (285)
186 PF07503 zf-HYPF: HypF finger; 37.9 3.3 7.1E-05 16.6 -1.5 6 52-57 23-28 (35)
187 PHA02998 RNA polymerase subuni 37.9 5.9 0.00013 22.1 -1.0 37 25-63 144-184 (195)
188 CHL00174 accD acetyl-CoA carbo 37.8 30 0.00064 21.0 1.8 13 51-63 58-70 (296)
189 COG1198 PriA Primosomal protei 37.8 6.9 0.00015 26.6 -0.8 8 51-58 476-483 (730)
190 PF14375 Cys_rich_CWC: Cystein 37.7 18 0.00039 15.5 0.7 11 1-11 1-11 (50)
191 KOG4602|consensus 37.1 11 0.00024 22.4 -0.0 36 24-59 233-277 (318)
192 COG3024 Uncharacterized protei 36.8 17 0.00038 16.7 0.6 8 1-8 10-17 (65)
193 PF14369 zf-RING_3: zinc-finge 36.0 19 0.00041 14.3 0.6 8 1-8 24-31 (35)
194 PRK08222 hydrogenase 4 subunit 35.8 34 0.00074 19.0 1.7 17 51-67 115-131 (181)
195 PF13453 zf-TFIIB: Transcripti 35.7 34 0.00074 13.8 1.4 18 51-68 20-37 (41)
196 COG3091 SprT Zn-dependent meta 35.3 16 0.00035 19.9 0.4 30 24-58 117-148 (156)
197 KOG0402|consensus 33.3 41 0.00089 16.4 1.5 31 23-62 35-66 (92)
198 PF08792 A2L_zn_ribbon: A2L zi 33.2 17 0.00037 14.2 0.2 11 51-61 22-32 (33)
199 PF12230 PRP21_like_P: Pre-mRN 32.9 14 0.00031 21.1 0.0 23 51-74 169-191 (229)
200 COG5188 PRP9 Splicing factor 3 32.6 21 0.00045 22.4 0.6 21 51-71 239-259 (470)
201 PF02891 zf-MIZ: MIZ/SP-RING z 32.4 20 0.00044 15.3 0.4 24 33-58 26-49 (50)
202 PF14446 Prok-RING_1: Prokaryo 32.3 19 0.0004 16.0 0.3 8 1-8 8-15 (54)
203 TIGR03829 YokU_near_AblA uncha 32.3 38 0.00083 16.7 1.4 17 1-17 38-54 (89)
204 smart00731 SprT SprT homologue 32.0 17 0.00037 19.3 0.2 9 51-59 134-142 (146)
205 PF11672 DUF3268: Protein of u 31.8 23 0.0005 17.9 0.6 9 24-32 2-10 (102)
206 TIGR03831 YgiT_finger YgiT-typ 31.8 22 0.00049 14.3 0.5 11 51-61 33-43 (46)
207 PF03107 C1_2: C1 domain; Int 31.4 38 0.00083 12.6 1.1 7 52-58 2-8 (30)
208 COG4888 Uncharacterized Zn rib 30.6 4.5 9.7E-05 20.3 -2.0 35 23-60 21-56 (104)
209 PF14255 Cys_rich_CPXG: Cystei 30.5 28 0.00061 15.2 0.7 9 52-60 2-10 (52)
210 PF09889 DUF2116: Uncharacteri 30.3 34 0.00074 15.4 1.0 9 1-9 6-14 (59)
211 cd00974 DSRD Desulforedoxin (D 29.9 23 0.00049 13.7 0.3 10 51-60 5-14 (34)
212 PF14311 DUF4379: Domain of un 29.7 21 0.00045 15.4 0.2 15 51-65 29-43 (55)
213 PRK05654 acetyl-CoA carboxylas 29.5 43 0.00094 20.3 1.6 11 51-61 47-57 (292)
214 PF00412 LIM: LIM domain; Int 29.5 37 0.0008 14.4 1.0 16 48-63 23-39 (58)
215 PF04438 zf-HIT: HIT zinc fing 29.2 18 0.00039 13.8 -0.0 11 51-61 14-24 (30)
216 TIGR00319 desulf_FeS4 desulfof 29.2 23 0.0005 13.6 0.3 10 51-60 8-17 (34)
217 KOG3816|consensus 29.1 27 0.00058 22.3 0.7 15 51-65 475-489 (526)
218 KOG2857|consensus 29.0 31 0.00068 18.6 0.8 21 51-71 18-38 (157)
219 PF13824 zf-Mss51: Zinc-finger 28.6 31 0.00067 15.4 0.7 11 51-61 15-25 (55)
220 COG1327 Predicted transcriptio 28.5 26 0.00057 19.1 0.5 13 1-13 31-43 (156)
221 PRK00418 DNA gyrase inhibitor; 28.3 30 0.00065 15.8 0.6 8 1-8 9-16 (62)
222 PF06170 DUF983: Protein of un 28.3 32 0.00069 16.7 0.7 13 51-63 9-21 (86)
223 PLN02748 tRNA dimethylallyltra 28.2 60 0.0013 21.2 2.1 22 23-44 417-439 (468)
224 COG1885 Uncharacterized protei 28.1 30 0.00066 17.6 0.7 9 1-9 52-60 (115)
225 COG5246 PRP11 Splicing factor 27.7 43 0.00094 19.0 1.2 24 46-69 48-72 (222)
226 PF14447 Prok-RING_4: Prokaryo 27.5 33 0.00071 15.3 0.7 12 52-63 41-52 (55)
227 PF11789 zf-Nse: Zinc-finger o 27.3 20 0.00044 15.9 -0.0 16 23-38 23-38 (57)
228 cd01410 SIRT7 SIRT7: Eukaryoti 27.2 1.3E+02 0.0028 17.1 3.2 15 23-37 94-108 (206)
229 smart00391 MBD Methyl-CpG bind 27.2 73 0.0016 15.1 1.8 21 54-74 34-54 (77)
230 PRK12387 formate hydrogenlyase 27.1 51 0.0011 18.1 1.5 16 51-66 115-130 (180)
231 smart00661 RPOL9 RNA polymeras 27.1 27 0.00059 14.6 0.4 11 51-61 21-31 (52)
232 COG1594 RPB9 DNA-directed RNA 26.9 17 0.00036 18.6 -0.4 11 51-61 101-111 (113)
233 TIGR00244 transcriptional regu 26.9 30 0.00065 18.8 0.6 14 1-14 31-44 (147)
234 PTZ00303 phosphatidylinositol 26.1 46 0.00099 23.6 1.4 10 1-10 463-472 (1374)
235 TIGR03830 CxxCG_CxxCG_HTH puta 25.9 73 0.0016 16.1 1.9 16 51-66 32-47 (127)
236 PF03966 Trm112p: Trm112p-like 25.8 24 0.00052 16.1 0.1 11 51-61 54-64 (68)
237 PF12760 Zn_Tnp_IS1595: Transp 25.7 66 0.0014 13.3 1.9 10 49-58 17-26 (46)
238 PF09332 Mcm10: Mcm10 replicat 25.7 37 0.0008 21.2 0.8 36 23-60 251-295 (344)
239 PF01096 TFIIS_C: Transcriptio 25.7 18 0.00038 14.6 -0.3 10 51-60 29-38 (39)
240 TIGR03826 YvyF flagellar opero 25.4 25 0.00054 18.8 0.1 12 51-62 82-93 (137)
241 PF02176 zf-TRAF: TRAF-type zi 25.4 14 0.00031 16.0 -0.7 21 23-44 8-30 (60)
242 PRK04351 hypothetical protein; 25.3 12 0.00026 20.2 -1.1 7 51-57 133-139 (149)
243 COG0675 Transposase and inacti 25.3 40 0.00088 20.0 1.0 13 51-63 323-335 (364)
244 PRK14559 putative protein seri 24.8 15 0.00033 24.7 -0.9 10 52-61 43-52 (645)
245 PF10367 Vps39_2: Vacuolar sor 24.7 40 0.00086 16.4 0.8 8 1-8 81-88 (109)
246 COG3478 Predicted nucleic-acid 24.7 37 0.00081 15.7 0.6 8 51-58 5-12 (68)
247 cd00122 MBD MeCP2, MBD1, MBD2, 24.0 85 0.0018 14.0 2.0 20 54-73 31-50 (62)
248 KOG1088|consensus 23.9 33 0.00071 17.9 0.4 15 51-65 99-113 (124)
249 PF13821 DUF4187: Domain of un 23.5 52 0.0011 14.5 0.9 17 51-67 28-44 (55)
250 COG4306 Uncharacterized protei 23.3 23 0.0005 18.7 -0.3 10 53-62 71-80 (160)
251 PF14952 zf-tcix: Putative tre 23.2 40 0.00088 14.2 0.5 8 51-58 12-19 (44)
252 COG5152 Uncharacterized conser 22.6 38 0.00082 19.5 0.5 15 23-37 195-209 (259)
253 PF12907 zf-met2: Zinc-binding 22.0 81 0.0018 13.0 1.4 21 25-45 2-25 (40)
254 PF02591 DUF164: Putative zinc 21.9 44 0.00096 14.5 0.5 32 25-59 23-55 (56)
255 PF06524 NOA36: NOA36 protein; 21.8 22 0.00048 21.3 -0.5 24 51-74 210-233 (314)
256 COG2331 Uncharacterized protei 21.6 27 0.00058 16.7 -0.2 10 51-60 13-22 (82)
257 PF10058 DUF2296: Predicted in 21.3 39 0.00084 14.9 0.3 8 51-58 45-52 (54)
258 PTZ00043 cytochrome c oxidase 21.3 50 0.0011 19.4 0.8 15 23-37 180-194 (268)
259 PF01215 COX5B: Cytochrome c o 21.2 29 0.00063 18.5 -0.1 15 23-37 111-125 (136)
260 PF01844 HNH: HNH endonuclease 21.2 43 0.00094 13.4 0.4 11 1-11 1-11 (47)
261 PLN03238 probable histone acet 21.1 99 0.0021 18.9 1.9 22 51-72 49-70 (290)
262 PF14205 Cys_rich_KTR: Cystein 20.6 50 0.0011 14.7 0.6 6 1-6 7-12 (55)
263 PRK03922 hypothetical protein; 20.5 57 0.0012 16.8 0.8 9 1-9 52-60 (113)
264 cd01396 MeCP2_MBD MeCP2, MBD1, 20.3 1.1E+02 0.0024 14.5 1.7 20 54-73 32-51 (77)
265 KOG4727|consensus 20.1 61 0.0013 18.2 0.9 19 1-19 78-96 (193)
No 1
>KOG2462|consensus
Probab=99.92 E-value=3.2e-25 Score=123.31 Aligned_cols=79 Identities=27% Similarity=0.444 Sum_probs=75.2
Q ss_pred CCCCcccccChHHHHHHHHhcCCCccCCCCccccCChHHHHHHHHhhCCC---ccCCcCccccCCHHHHHHHHhhcc---
Q psy3492 1 MPRLQVLISYNWCLKRHLNTHIKPFNCALCEYKAARPERLATHVIKVHNK---RICSKCSFLADDQETLNEHLQQHI--- 74 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h~~~~~c~~c~~~f~~~~~l~~h~~~~h~~---~~C~~c~~~f~~~~~l~~h~~~h~--- 74 (85)
|+.|+|+|.....|++|+++|+-+.+|.+||+.|..+.-|+-|+ +.|+| |.|+.|+|+|+.+++|+.|++||.
T Consensus 164 C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHi-RTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K 242 (279)
T KOG2462|consen 164 CKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHI-RTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVK 242 (279)
T ss_pred CCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhccc-ccccCCCCccCCcccchhcchHHHHHHHHhhcCCc
Confidence 78999999999999999999998999999999999999999999 79999 999999999999999999999999
Q ss_pred cccCcC
Q psy3492 75 FWECSF 80 (85)
Q Consensus 75 ~~~C~~ 80 (85)
.|+|+-
T Consensus 243 ~~qC~~ 248 (279)
T KOG2462|consen 243 KHQCPR 248 (279)
T ss_pred cccCcc
Confidence 888864
No 2
>KOG2462|consensus
Probab=99.87 E-value=8.3e-23 Score=113.76 Aligned_cols=71 Identities=28% Similarity=0.512 Sum_probs=68.2
Q ss_pred CCCCcccccChHHHHHHHHhcC--CCccCCCCccccCChHHHHHHHHhhCCC---ccCCcCccccCCHHHHHHHHhh
Q psy3492 1 MPRLQVLISYNWCLKRHLNTHI--KPFNCALCEYKAARPERLATHVIKVHNK---RICSKCSFLADDQETLNEHLQQ 72 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h~--~~~~c~~c~~~f~~~~~l~~h~~~~h~~---~~C~~c~~~f~~~~~l~~h~~~ 72 (85)
|.+|||.|...+.|+.|+++|+ |||.|..|+++|..+++|..|+ .+|.+ |+|+.|+|.|...+-|.+|...
T Consensus 190 C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHm-QTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 190 CGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHM-QTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred cccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHH-HhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 7899999999999999999999 9999999999999999999999 69998 9999999999999999999753
No 3
>KOG3576|consensus
Probab=99.62 E-value=7.8e-17 Score=87.21 Aligned_cols=73 Identities=25% Similarity=0.343 Sum_probs=65.4
Q ss_pred CCCCcccccChHHHHHHHHhcC--CCccCCCCccccCChHHHHHHHHhhCCC---ccCCcCccccCCHHHHHHHHh-hcc
Q psy3492 1 MPRLQVLISYNWCLKRHLNTHI--KPFNCALCEYKAARPERLATHVIKVHNK---RICSKCSFLADDQETLNEHLQ-QHI 74 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h~--~~~~c~~c~~~f~~~~~l~~h~~~~h~~---~~C~~c~~~f~~~~~l~~h~~-~h~ 74 (85)
|.+|+|.|....-|.+|++.|. +.+.|..||+.|...-.|++|+ +.|+| |+|..|+++|.+.-.|..|++ +|.
T Consensus 120 CrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~-rthtgvrpykc~~c~kaftqrcsleshl~kvhg 198 (267)
T KOG3576|consen 120 CRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHT-RTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHG 198 (267)
T ss_pred eehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhh-ccccCccccchhhhhHHHHhhccHHHHHHHHcC
Confidence 6789999999999999999998 8899999999999999999999 79999 999999999999999999977 554
No 4
>KOG3623|consensus
Probab=99.59 E-value=2.7e-16 Score=97.42 Aligned_cols=70 Identities=20% Similarity=0.433 Sum_probs=67.0
Q ss_pred CCCCcccccChHHHHHHHHhcC--CCccCCCCccccCChHHHHHHHHhhCCC---ccCCcCccccCCHHHHHHHHh
Q psy3492 1 MPRLQVLISYNWCLKRHLNTHI--KPFNCALCEYKAARPERLATHVIKVHNK---RICSKCSFLADDQETLNEHLQ 71 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h~--~~~~c~~c~~~f~~~~~l~~h~~~~h~~---~~C~~c~~~f~~~~~l~~h~~ 71 (85)
|..|+|+|...++|.+|..-|+ +||+|.+|.++|..+.-|..|. +.|.| |.|++|+|.|..+.....||-
T Consensus 897 CDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHk-RLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 897 CDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHK-RLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred HHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhh-hhccCCCcchhhhhhhhcccccchHhhhc
Confidence 6789999999999999999999 9999999999999999999999 79999 999999999999999999974
No 5
>KOG3576|consensus
Probab=99.56 E-value=3.6e-15 Score=80.84 Aligned_cols=75 Identities=29% Similarity=0.523 Sum_probs=68.3
Q ss_pred CCCCcccccChHHHHHHHHhcC--CCccCCCCccccCChHHHHHHHHhhCCC-------------ccCCcCccccCCHHH
Q psy3492 1 MPRLQVLISYNWCLKRHLNTHI--KPFNCALCEYKAARPERLATHVIKVHNK-------------RICSKCSFLADDQET 65 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h~--~~~~c~~c~~~f~~~~~l~~h~~~~h~~-------------~~C~~c~~~f~~~~~ 65 (85)
|..|||.|.....|++|+++|+ +||+|..|+++|.+.-+|..|+..+|.. |.|+.||..-..+..
T Consensus 148 ct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~ 227 (267)
T KOG3576|consen 148 CTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEV 227 (267)
T ss_pred HhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhH
Confidence 5679999999999999999999 9999999999999999999999767753 789999999999999
Q ss_pred HHHHHhhccc
Q psy3492 66 LNEHLQQHIF 75 (85)
Q Consensus 66 l~~h~~~h~~ 75 (85)
...|+..|.+
T Consensus 228 ~~~h~~~~hp 237 (267)
T KOG3576|consen 228 YYLHLKLHHP 237 (267)
T ss_pred HHHHHHhcCC
Confidence 9999988773
No 6
>KOG3623|consensus
Probab=99.52 E-value=6.8e-15 Score=91.41 Aligned_cols=79 Identities=29% Similarity=0.490 Sum_probs=57.1
Q ss_pred CCCCcccccChHHHHHHHH-hcC---CCccCCCCccccCChHHHHHHHHhhCCC----------------ccCCcCcccc
Q psy3492 1 MPRLQVLISYNWCLKRHLN-THI---KPFNCALCEYKAARPERLATHVIKVHNK----------------RICSKCSFLA 60 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~-~h~---~~~~c~~c~~~f~~~~~l~~h~~~~h~~----------------~~C~~c~~~f 60 (85)
|+.|.+.+.....|+.|++ .|. ..|.|..|..+|.+...|.+|+ ..|.. |+|.+|||+|
T Consensus 213 cpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm-~~hkpg~dqa~sltqsa~lRKFKCtECgKAF 291 (1007)
T KOG3623|consen 213 CPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHM-QLHKPGGDQAISLTQSALLRKFKCTECGKAF 291 (1007)
T ss_pred chhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHH-HhhcCCCcccccccchhhhccccccccchhh
Confidence 5667777777777777776 343 5577777877888877777777 55531 7777888888
Q ss_pred CCHHHHHHHHhhcc---cccCcC
Q psy3492 61 DDQETLNEHLQQHI---FWECSF 80 (85)
Q Consensus 61 ~~~~~l~~h~~~h~---~~~C~~ 80 (85)
...-.|+.|+|+|. ||+|+-
T Consensus 292 KfKHHLKEHlRIHSGEKPfeCpn 314 (1007)
T KOG3623|consen 292 KFKHHLKEHLRIHSGEKPFECPN 314 (1007)
T ss_pred hhHHHHHhhheeecCCCCcCCcc
Confidence 88877888888777 777753
No 7
>KOG3608|consensus
Probab=99.44 E-value=1.4e-13 Score=79.88 Aligned_cols=83 Identities=24% Similarity=0.486 Sum_probs=60.5
Q ss_pred CCCCcccccChHHHHHHHHhcCCCccCCCCccccCChHHHHHHHHhhCCC---ccCCcCccccCCHHHHHHHHhhcc--c
Q psy3492 1 MPRLQVLISYNWCLKRHLNTHIKPFNCALCEYKAARPERLATHVIKVHNK---RICSKCSFLADDQETLNEHLQQHI--F 75 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h~~~~~c~~c~~~f~~~~~l~~h~~~~h~~---~~C~~c~~~f~~~~~l~~h~~~h~--~ 75 (85)
|..|.|.|.....|..|+..|..-|+|..|+.+...+++|..|++..|.. |+|+.|.+.+.+.+.|.+|..+|+ .
T Consensus 240 C~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~ 319 (467)
T KOG3608|consen 240 CAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTV 319 (467)
T ss_pred HHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccccc
Confidence 44567777777777777777666677777777777777777777544554 778888888888888888887777 6
Q ss_pred ccCcCCCC
Q psy3492 76 WECSFQDA 83 (85)
Q Consensus 76 ~~C~~~~~ 83 (85)
|+|+++++
T Consensus 320 y~C~h~~C 327 (467)
T KOG3608|consen 320 YQCEHPDC 327 (467)
T ss_pred eecCCCCC
Confidence 77776543
No 8
>KOG1074|consensus
Probab=99.44 E-value=1.2e-14 Score=91.04 Aligned_cols=73 Identities=26% Similarity=0.467 Sum_probs=68.7
Q ss_pred CCCCcccccChHHHHHHHHhcC--CCccCCCCccccCChHHHHHHHHhhCCC-------ccCC---cCccccCCHHHHHH
Q psy3492 1 MPRLQVLISYNWCLKRHLNTHI--KPFNCALCEYKAARPERLATHVIKVHNK-------RICS---KCSFLADDQETLNE 68 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h~--~~~~c~~c~~~f~~~~~l~~h~~~~h~~-------~~C~---~c~~~f~~~~~l~~ 68 (85)
|-.|.++.+..+.|+.|.++|+ +||+|.+||++|..+.+|+.|+ .+|.. +.|+ +|-+.|.+.-.|..
T Consensus 608 CiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~-~vHka~p~~R~q~ScP~~~ic~~kftn~V~lpQ 686 (958)
T KOG1074|consen 608 CIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHM-SVHKAKPPARVQFSCPSTFICQKKFTNAVTLPQ 686 (958)
T ss_pred eeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcc-cccccCccccccccCCchhhhcccccccccccc
Confidence 5679999999999999999999 9999999999999999999999 78875 8899 99999999999999
Q ss_pred HHhhcc
Q psy3492 69 HLQQHI 74 (85)
Q Consensus 69 h~~~h~ 74 (85)
|+++|.
T Consensus 687 hIriH~ 692 (958)
T KOG1074|consen 687 HIRIHL 692 (958)
T ss_pred eEEeec
Confidence 999998
No 9
>PHA02768 hypothetical protein; Provisional
Probab=99.37 E-value=3.4e-13 Score=59.21 Aligned_cols=40 Identities=20% Similarity=0.449 Sum_probs=23.1
Q ss_pred ccCCCCccccCChHHHHHHHHhhCCC-ccCCcCccccCCHHH
Q psy3492 25 FNCALCEYKAARPERLATHVIKVHNK-RICSKCSFLADDQET 65 (85)
Q Consensus 25 ~~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~~f~~~~~ 65 (85)
|+|+.||+.|...+.|..|+ +.|.. ++|..|++.|...+.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~-r~H~k~~kc~~C~k~f~~~s~ 46 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHL-RKHNTNLKLSNCKRISLRTGE 46 (55)
T ss_pred cCcchhCCeeccHHHHHHHH-HhcCCcccCCcccceecccce
Confidence 45666666666666666665 45553 666666666555443
No 10
>PHA00733 hypothetical protein
Probab=99.32 E-value=5.3e-12 Score=65.00 Aligned_cols=71 Identities=18% Similarity=0.415 Sum_probs=55.5
Q ss_pred CCCcccccChHHHHH------HHHhcC-CCccCCCCccccCChHHHHHHHHhhCCC-ccCCcCccccCCHHHHHHHHhhc
Q psy3492 2 PRLQVLISYNWCLKR------HLNTHI-KPFNCALCEYKAARPERLATHVIKVHNK-RICSKCSFLADDQETLNEHLQQH 73 (85)
Q Consensus 2 ~~c~~~f~~~~~l~~------h~~~h~-~~~~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~~f~~~~~l~~h~~~h 73 (85)
.+|.+.|.....|.. ++..+. +||.|..|++.|.....|..|+ ..+.. |.|+.|++.|.....|..|+...
T Consensus 44 ~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~-r~h~~~~~C~~CgK~F~~~~sL~~H~~~~ 122 (128)
T PHA00733 44 AVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHI-RYTEHSKVCPVCGKEFRNTDSTLDHVCKK 122 (128)
T ss_pred HHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHH-hcCCcCccCCCCCCccCCHHHHHHHHHHh
Confidence 345555555544443 333444 8999999999999999999998 66655 99999999999999999998754
No 11
>KOG3608|consensus
Probab=99.26 E-value=1.2e-11 Score=72.07 Aligned_cols=81 Identities=28% Similarity=0.577 Sum_probs=70.9
Q ss_pred CCCCcccccChHHHHHHHHh-cC--CCccCCCCccccCChHHHHHHHHhhCCC--ccCCc--CccccCCHHHHHHHHhhc
Q psy3492 1 MPRLQVLISYNWCLKRHLNT-HI--KPFNCALCEYKAARPERLATHVIKVHNK--RICSK--CSFLADDQETLNEHLQQH 73 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~-h~--~~~~c~~c~~~f~~~~~l~~h~~~~h~~--~~C~~--c~~~f~~~~~l~~h~~~h 73 (85)
||.|..+....++|..|++. |+ +||+|+.|++.+...+.|.+|+ ..|+. |.|+. |..++.....+.+|.+.+
T Consensus 266 CplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~-~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~ev 344 (467)
T KOG3608|consen 266 CPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHV-QVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEV 344 (467)
T ss_pred ccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHH-HhccccceecCCCCCcHHHHHHHHHHHHHHHh
Confidence 78899999999999999994 66 9999999999999999999999 68988 99976 999999999999998854
Q ss_pred c------cccCcCCC
Q psy3492 74 I------FWECSFQD 82 (85)
Q Consensus 74 ~------~~~C~~~~ 82 (85)
. +|.|.+.+
T Consensus 345 hEg~np~~Y~CH~Cd 359 (467)
T KOG3608|consen 345 HEGNNPILYACHCCD 359 (467)
T ss_pred ccCCCCCceeeecch
Confidence 4 67776543
No 12
>PHA02768 hypothetical protein; Provisional
Probab=99.16 E-value=1.8e-11 Score=53.80 Aligned_cols=40 Identities=15% Similarity=0.175 Sum_probs=34.1
Q ss_pred CCCCcccccChHHHHHHHHhcCCCccCCCCccccCChHHH
Q psy3492 1 MPRLQVLISYNWCLKRHLNTHIKPFNCALCEYKAARPERL 40 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h~~~~~c~~c~~~f~~~~~l 40 (85)
|++||+.|....+|..|+++|.++++|..|++.|...+.|
T Consensus 8 C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 8 CPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cchhCCeeccHHHHHHHHHhcCCcccCCcccceeccccee
Confidence 7889999999999999998888888888888888877655
No 13
>KOG1074|consensus
Probab=99.04 E-value=1.1e-10 Score=73.97 Aligned_cols=49 Identities=29% Similarity=0.381 Sum_probs=37.1
Q ss_pred CCCCcccccChHHHHHHHHhcC--CCccCCCCccccCChHHHHHHHHhhCCC
Q psy3492 1 MPRLQVLISYNWCLKRHLNTHI--KPFNCALCEYKAARPERLATHVIKVHNK 50 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h~--~~~~c~~c~~~f~~~~~l~~h~~~~h~~ 50 (85)
|.+||+.|...+.|++|+++|+ |||.|.+|+++|..+.+|+.|+ ..|-.
T Consensus 882 C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHM-gtH~w 932 (958)
T KOG1074|consen 882 CNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHM-GTHMW 932 (958)
T ss_pred hccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhh-ccccc
Confidence 5677777777777777777777 7777777777777777777777 56653
No 14
>PHA00732 hypothetical protein
Probab=98.96 E-value=9.2e-10 Score=52.27 Aligned_cols=47 Identities=23% Similarity=0.505 Sum_probs=26.4
Q ss_pred CccCCCCccccCChHHHHHHHHhhCCCccCCcCccccCCHHHHHHHHhhc
Q psy3492 24 PFNCALCEYKAARPERLATHVIKVHNKRICSKCSFLADDQETLNEHLQQH 73 (85)
Q Consensus 24 ~~~c~~c~~~f~~~~~l~~h~~~~h~~~~C~~c~~~f~~~~~l~~h~~~h 73 (85)
||.|..|++.|.....|..|++..|.++.|+.||+.|.+ +..|.++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~~---l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYRR---LNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeCC---hhhhhccc
Confidence 455666666666666666665213444666666666652 44555443
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.95 E-value=4.2e-09 Score=65.25 Aligned_cols=77 Identities=14% Similarity=0.263 Sum_probs=60.5
Q ss_pred CCCCcccccChHHHHHHHHhcCCCccCCCCccccCChHHHHHHHHhhCCC---ccCCcCccccCC----------HHHHH
Q psy3492 1 MPRLQVLISYNWCLKRHLNTHIKPFNCALCEYKAARPERLATHVIKVHNK---RICSKCSFLADD----------QETLN 67 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h~~~~~c~~c~~~f~~~~~l~~h~~~~h~~---~~C~~c~~~f~~----------~~~l~ 67 (85)
|+.|++.|. ...|..|+.++.+|+.|. ||+.+ .+..|..|+ ..+-+ +.|+.|++.+.. .+.|.
T Consensus 456 C~~Cgk~f~-~s~LekH~~~~Hkpv~Cp-Cg~~~-~R~~L~~H~-~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt 531 (567)
T PLN03086 456 CEKCGQAFQ-QGEMEKHMKVFHEPLQCP-CGVVL-EKEQMVQHQ-ASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMS 531 (567)
T ss_pred CCCCCCccc-hHHHHHHHHhcCCCccCC-CCCCc-chhHHHhhh-hccCCCCceeCCCCCCccccCccccchhhhhhhHH
Confidence 788999986 678999999877889999 99755 668899998 67766 889999998852 35788
Q ss_pred HHHhhcc--cccCcCC
Q psy3492 68 EHLQQHI--FWECSFQ 81 (85)
Q Consensus 68 ~h~~~h~--~~~C~~~ 81 (85)
.|..+.. ++.|...
T Consensus 532 ~HE~~CG~rt~~C~~C 547 (567)
T PLN03086 532 EHESICGSRTAPCDSC 547 (567)
T ss_pred HHHHhcCCcceEcccc
Confidence 8888766 6667543
No 16
>PHA00733 hypothetical protein
Probab=98.91 E-value=4.5e-09 Score=54.22 Aligned_cols=48 Identities=23% Similarity=0.317 Sum_probs=43.1
Q ss_pred CCCCcccccChHHHHHHHHhcCCCccCCCCccccCChHHHHHHHHhhC
Q psy3492 1 MPRLQVLISYNWCLKRHLNTHIKPFNCALCEYKAARPERLATHVIKVH 48 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h~~~~~c~~c~~~f~~~~~l~~h~~~~h 48 (85)
|++|++.|.....|..|++.+..++.|.+|+++|.....|..|+...|
T Consensus 76 C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 76 CPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 789999999999999999976677999999999999999999985444
No 17
>KOG3993|consensus
Probab=98.80 E-value=2.9e-09 Score=63.49 Aligned_cols=73 Identities=16% Similarity=0.154 Sum_probs=48.3
Q ss_pred CCCCcccccChHHHHHHHHhcC-CCccCCCCcc----ccCChHHHHHHHHhh----CCC-ccCCcCccccCCHHHHHHHH
Q psy3492 1 MPRLQVLISYNWCLKRHLNTHI-KPFNCALCEY----KAARPERLATHVIKV----HNK-RICSKCSFLADDQETLNEHL 70 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h~-~~~~c~~c~~----~f~~~~~l~~h~~~~----h~~-~~C~~c~~~f~~~~~l~~h~ 70 (85)
||+|+|.|+...+|.+|.++|. ++-.-.--+. ........+.-. +. -.| |.|..|+|.|.+..-|++|+
T Consensus 298 CPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~-rsg~dss~gi~~C~~C~KkFrRqAYLrKHq 376 (500)
T KOG3993|consen 298 CPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE-RSGDDSSSGIFSCHTCGKKFRRQAYLRKHQ 376 (500)
T ss_pred CCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhcc-ccCCcccCceeecHHhhhhhHHHHHHHHhH
Confidence 8999999999999999999997 4432210000 111111111111 11 112 99999999999999999999
Q ss_pred hhcc
Q psy3492 71 QQHI 74 (85)
Q Consensus 71 ~~h~ 74 (85)
-+|.
T Consensus 377 lthq 380 (500)
T KOG3993|consen 377 LTHQ 380 (500)
T ss_pred Hhhh
Confidence 8887
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=98.80 E-value=4.5e-09 Score=39.82 Aligned_cols=23 Identities=39% Similarity=0.907 Sum_probs=18.5
Q ss_pred HHHHHHHhcC--CCccCCCCccccC
Q psy3492 13 CLKRHLNTHI--KPFNCALCEYKAA 35 (85)
Q Consensus 13 ~l~~h~~~h~--~~~~c~~c~~~f~ 35 (85)
+|..|+++|+ +||.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 4778888888 8888888888875
No 19
>PHA00732 hypothetical protein
Probab=98.61 E-value=6.3e-08 Score=46.02 Aligned_cols=46 Identities=20% Similarity=0.292 Sum_probs=38.0
Q ss_pred CCCCcccccChHHHHHHHHhcCCCccCCCCccccCChHHHHHHHHhhCCC
Q psy3492 1 MPRLQVLISYNWCLKRHLNTHIKPFNCALCEYKAARPERLATHVIKVHNK 50 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h~~~~~c~~c~~~f~~~~~l~~h~~~~h~~ 50 (85)
|++|++.|.....|+.|++.+..++.|..|++.|.. +..|+ ....+
T Consensus 4 C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~~---l~~H~-~~~~~ 49 (79)
T PHA00732 4 CPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYRR---LNQHF-YSQYD 49 (79)
T ss_pred CCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeCC---hhhhh-cccCC
Confidence 789999999999999999853335689999999984 77787 56655
No 20
>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=98.61 E-value=2.3e-08 Score=36.67 Aligned_cols=23 Identities=22% Similarity=0.527 Sum_probs=16.3
Q ss_pred ccCCcCccccCCHHHHHHHHhhc
Q psy3492 51 RICSKCSFLADDQETLNEHLQQH 73 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h 73 (85)
|.|+.|++.|.....|..|++.|
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 46777777777777777777653
No 21
>PHA00616 hypothetical protein
Probab=98.57 E-value=2.7e-08 Score=41.87 Aligned_cols=24 Identities=21% Similarity=0.354 Sum_probs=14.1
Q ss_pred ccCCcCccccCCHHHHHHHHhhcc
Q psy3492 51 RICSKCSFLADDQETLNEHLQQHI 74 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~ 74 (85)
|+|+.||+.|.+.+.|..|++.|+
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~h 25 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVH 25 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhc
Confidence 455566666666666666665555
No 22
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.49 E-value=3.6e-07 Score=56.97 Aligned_cols=67 Identities=16% Similarity=0.311 Sum_probs=53.9
Q ss_pred CCCCcccccChHHHHHHHHhcC--CCccCCCCccccC----------ChHHHHHHHHhhCCC--ccCCcCccccCCHHHH
Q psy3492 1 MPRLQVLISYNWCLKRHLNTHI--KPFNCALCEYKAA----------RPERLATHVIKVHNK--RICSKCSFLADDQETL 66 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h~--~~~~c~~c~~~f~----------~~~~l~~h~~~~h~~--~~C~~c~~~f~~~~~l 66 (85)
|+ ||+.+ ....|..|+.+|. +++.|..|+..+. ....|..|+ ..... +.|..||+.+.... +
T Consensus 481 Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE-~~CG~rt~~C~~Cgk~Vrlrd-m 556 (567)
T PLN03086 481 CP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHE-SICGSRTAPCDSCGRSVMLKE-M 556 (567)
T ss_pred CC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHH-HhcCCcceEccccCCeeeehh-H
Confidence 77 99755 6789999998888 9999999999884 235789998 56544 89999999988874 6
Q ss_pred HHHHh
Q psy3492 67 NEHLQ 71 (85)
Q Consensus 67 ~~h~~ 71 (85)
..|+.
T Consensus 557 ~~H~~ 561 (567)
T PLN03086 557 DIHQI 561 (567)
T ss_pred HHHHH
Confidence 67765
No 23
>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=98.36 E-value=2e-07 Score=35.22 Aligned_cols=23 Identities=22% Similarity=0.465 Sum_probs=19.6
Q ss_pred HHHHHHHhhCCC---ccCCcCccccCC
Q psy3492 39 RLATHVIKVHNK---RICSKCSFLADD 62 (85)
Q Consensus 39 ~l~~h~~~~h~~---~~C~~c~~~f~~ 62 (85)
+|..|+ +.|+| |.|+.|++.|.+
T Consensus 1 ~l~~H~-~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHM-RTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHH-HHHSSSSSEEESSSSEEESS
T ss_pred CHHHHh-hhcCCCCCCCCCCCcCeeCc
Confidence 478899 68998 999999999864
No 24
>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=98.29 E-value=6.2e-07 Score=32.81 Aligned_cols=23 Identities=22% Similarity=0.479 Sum_probs=14.8
Q ss_pred ccCCcCccccCCHHHHHHHHhhc
Q psy3492 51 RICSKCSFLADDQETLNEHLQQH 73 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h 73 (85)
|.|+.|++.|.+...|..|++++
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 46777777777777777777654
No 25
>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=98.28 E-value=5.5e-07 Score=32.87 Aligned_cols=21 Identities=33% Similarity=0.347 Sum_probs=14.6
Q ss_pred CCCCcccccChHHHHHHHHhc
Q psy3492 1 MPRLQVLISYNWCLKRHLNTH 21 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h 21 (85)
|+.|++.|.....|..|++.|
T Consensus 3 C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 3 CPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp ETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCccCCHHHHHHHHhHC
Confidence 567777777777777776653
No 26
>PHA00616 hypothetical protein
Probab=98.27 E-value=4.6e-07 Score=38.18 Aligned_cols=26 Identities=15% Similarity=0.321 Sum_probs=15.9
Q ss_pred CccCCCCccccCChHHHHHHHHhhCCC
Q psy3492 24 PFNCALCEYKAARPERLATHVIKVHNK 50 (85)
Q Consensus 24 ~~~c~~c~~~f~~~~~l~~h~~~~h~~ 50 (85)
||.|..||+.|..++.|..|+ +.|.|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~-r~~hg 26 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHL-LSVHK 26 (44)
T ss_pred CCccchhhHHHhhHHHHHHHH-HHhcC
Confidence 456666666666666666666 34444
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=98.21 E-value=5.2e-06 Score=36.69 Aligned_cols=46 Identities=26% Similarity=0.533 Sum_probs=27.4
Q ss_pred CccCCCCccccCChHHHHHHHHhhCCC----ccCCcCccccCCHHHHHHHHhh
Q psy3492 24 PFNCALCEYKAARPERLATHVIKVHNK----RICSKCSFLADDQETLNEHLQQ 72 (85)
Q Consensus 24 ~~~c~~c~~~f~~~~~l~~h~~~~h~~----~~C~~c~~~f~~~~~l~~h~~~ 72 (85)
.|.|..|++ ......|..|....|.. +.||.|...+. ..|..|+..
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~ 51 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNS 51 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHH
Confidence 356777777 34455677776445554 66777766433 356666654
No 28
>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=98.06 E-value=1.9e-05 Score=34.89 Aligned_cols=43 Identities=21% Similarity=0.311 Sum_probs=33.7
Q ss_pred CCCCcccccChHHHHHHHH-hcC---CCccCCCCccccCChHHHHHHHHh
Q psy3492 1 MPRLQVLISYNWCLKRHLN-THI---KPFNCALCEYKAARPERLATHVIK 46 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~-~h~---~~~~c~~c~~~f~~~~~l~~h~~~ 46 (85)
||.|++ ..+...|..|.. .|. +.+.|.+|...+. .+|..|+..
T Consensus 5 CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~ 51 (54)
T PF05605_consen 5 CPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNS 51 (54)
T ss_pred CCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHH
Confidence 899999 566788999977 455 7799999998644 488888843
No 29
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=98.06 E-value=3.1e-06 Score=41.50 Aligned_cols=71 Identities=20% Similarity=0.149 Sum_probs=21.3
Q ss_pred CCCCcccccChHHHHHHHH-hcCCCccCCCCccccCChHHHHHHHHhhCCC-ccCCcCccccCCHHHHHHHHhhcc
Q psy3492 1 MPRLQVLISYNWCLKRHLN-THIKPFNCALCEYKAARPERLATHVIKVHNK-RICSKCSFLADDQETLNEHLQQHI 74 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~-~h~~~~~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~~f~~~~~l~~h~~~h~ 74 (85)
|..|+..|.....|..|+. .|..... ....+.....+..++...-.. +.|..|++.|.....|..|++.+.
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~~---~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDIP---DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp --------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred ccccccccccccccccccccccccccc---cccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 7789999999999999987 4541111 011122333333333111122 899999999999999999999653
No 30
>smart00355 ZnF_C2H2 zinc finger.
Probab=98.05 E-value=6e-06 Score=30.49 Aligned_cols=23 Identities=26% Similarity=0.652 Sum_probs=16.9
Q ss_pred ccCCcCccccCCHHHHHHHHhhc
Q psy3492 51 RICSKCSFLADDQETLNEHLQQH 73 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h 73 (85)
|.|+.|++.|...+.|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 46777777777777777777654
No 31
>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=98.03 E-value=3.2e-06 Score=32.00 Aligned_cols=22 Identities=27% Similarity=0.534 Sum_probs=11.9
Q ss_pred cCCcCccccCCHHHHHHHHhhc
Q psy3492 52 ICSKCSFLADDQETLNEHLQQH 73 (85)
Q Consensus 52 ~C~~c~~~f~~~~~l~~h~~~h 73 (85)
.|..|++.|.....|..|++.|
T Consensus 3 ~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 3 ECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EETTTTEEESSHHHHHHHHCTT
T ss_pred CCCccCCccCChhHHHHHhHHh
Confidence 4555555555555555555543
No 32
>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=97.91 E-value=1.1e-05 Score=30.51 Aligned_cols=24 Identities=29% Similarity=0.609 Sum_probs=20.5
Q ss_pred CccCCCCccccCChHHHHHHHHhhC
Q psy3492 24 PFNCALCEYKAARPERLATHVIKVH 48 (85)
Q Consensus 24 ~~~c~~c~~~f~~~~~l~~h~~~~h 48 (85)
||+|..|++.|.....|..|+ +.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~-~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHK-RSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHH-CTT
T ss_pred CCCCCccCCccCChhHHHHHh-HHh
Confidence 578999999999999999998 554
No 33
>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=97.87 E-value=1.5e-05 Score=28.89 Aligned_cols=21 Identities=24% Similarity=0.274 Sum_probs=13.3
Q ss_pred CCCCcccccChHHHHHHHHhc
Q psy3492 1 MPRLQVLISYNWCLKRHLNTH 21 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h 21 (85)
|+.|++.|.....|..|+..|
T Consensus 3 C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 3 CPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp -SSTS-EESSHHHHHHHHHHH
T ss_pred CcCCCCcCCcHHHHHHHHHhh
Confidence 567777777777777776654
No 34
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.59 E-value=8.9e-05 Score=27.14 Aligned_cols=21 Identities=29% Similarity=0.431 Sum_probs=13.5
Q ss_pred CCCCcccccChHHHHHHHHhc
Q psy3492 1 MPRLQVLISYNWCLKRHLNTH 21 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h 21 (85)
|+.|++.|.....|..|+..|
T Consensus 3 C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 3 CPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCcchhCCHHHHHHHHHHh
Confidence 556666666666666666544
No 35
>KOG3993|consensus
Probab=97.50 E-value=1.9e-05 Score=47.82 Aligned_cols=50 Identities=28% Similarity=0.433 Sum_probs=41.6
Q ss_pred ccCCCCccccCChHHHHHHHH--hhCCCccCCcCccccCCHHHHHHHHhhcc
Q psy3492 25 FNCALCEYKAARPERLATHVI--KVHNKRICSKCSFLADDQETLNEHLQQHI 74 (85)
Q Consensus 25 ~~c~~c~~~f~~~~~l~~h~~--~~h~~~~C~~c~~~f~~~~~l~~h~~~h~ 74 (85)
|.|..|...|...-.|.+|.. .+|..|+|++|+|.|+-+.+|..|.|.|-
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccC
Confidence 778889888888888888852 12223999999999999999999999987
No 36
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.46 E-value=7.8e-05 Score=27.51 Aligned_cols=21 Identities=24% Similarity=0.529 Sum_probs=12.4
Q ss_pred ccCCcCccccCCHHHHHHHHh
Q psy3492 51 RICSKCSFLADDQETLNEHLQ 71 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~ 71 (85)
|.|..|++.|.+...+..|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 345566666666666666654
No 37
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=97.35 E-value=0.00027 Score=26.27 Aligned_cols=20 Identities=20% Similarity=0.416 Sum_probs=13.7
Q ss_pred cCCcCccccCCHHHHHHHHhh
Q psy3492 52 ICSKCSFLADDQETLNEHLQQ 72 (85)
Q Consensus 52 ~C~~c~~~f~~~~~l~~h~~~ 72 (85)
.|+.||+.| .++.|..|+.+
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHHh
Confidence 577777777 55567777653
No 38
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.24 E-value=5.9e-05 Score=44.34 Aligned_cols=49 Identities=27% Similarity=0.537 Sum_probs=39.7
Q ss_pred CCccCCC--CccccCChHHHHHHHHhhCC--------------------C-ccCCcCccccCCHHHHHHHHh
Q psy3492 23 KPFNCAL--CEYKAARPERLATHVIKVHN--------------------K-RICSKCSFLADDQETLNEHLQ 71 (85)
Q Consensus 23 ~~~~c~~--c~~~f~~~~~l~~h~~~~h~--------------------~-~~C~~c~~~f~~~~~l~~h~~ 71 (85)
|||+|.+ |++.+.....|+-|+..-|. . |+|+.|+|.+.+...|+.|+.
T Consensus 348 KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred ceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 8999987 99999998888888743331 1 899999999999999988854
No 39
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.14 E-value=0.0004 Score=25.34 Aligned_cols=22 Identities=32% Similarity=0.800 Sum_probs=14.8
Q ss_pred ccCCcCccccCCHHHHHHHHhhc
Q psy3492 51 RICSKCSFLADDQETLNEHLQQH 73 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h 73 (85)
|+|+.|+.... ...|..|++.+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 56788887777 77788887764
No 40
>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=97.02 E-value=0.00023 Score=26.83 Aligned_cols=21 Identities=19% Similarity=0.548 Sum_probs=14.4
Q ss_pred ccCCcCccccCCHHHHHHHHh
Q psy3492 51 RICSKCSFLADDQETLNEHLQ 71 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~ 71 (85)
|-|..|++.|.+...+..|++
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 456777777777777766655
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.02 E-value=0.00054 Score=25.15 Aligned_cols=20 Identities=25% Similarity=0.667 Sum_probs=15.3
Q ss_pred ccCCCCccccCChHHHHHHH
Q psy3492 25 FNCALCEYKAARPERLATHV 44 (85)
Q Consensus 25 ~~c~~c~~~f~~~~~l~~h~ 44 (85)
|.|.+|+..|.....+..|+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~ 20 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHL 20 (25)
T ss_dssp EEETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCCCcCCHHHHHHHH
Confidence 45777888888888887776
No 42
>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=96.98 E-value=0.00089 Score=29.06 Aligned_cols=20 Identities=30% Similarity=0.418 Sum_probs=13.3
Q ss_pred CCCCcccccChHHHHHHHHh
Q psy3492 1 MPRLQVLISYNWCLKRHLNT 20 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~ 20 (85)
||+|+..+.+..+|.+|+..
T Consensus 27 CP~C~a~~~~srnLrRHle~ 46 (54)
T PF09237_consen 27 CPICGAVIRQSRNLRRHLEI 46 (54)
T ss_dssp -TTT--EESSHHHHHHHHHH
T ss_pred CCcchhhccchhhHHHHHHH
Confidence 77888888888888888764
No 43
>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=96.45 E-value=0.004 Score=27.07 Aligned_cols=26 Identities=23% Similarity=0.515 Sum_probs=15.3
Q ss_pred CCccCCCCccccCChHHHHHHHHhhC
Q psy3492 23 KPFNCALCEYKAARPERLATHVIKVH 48 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~h~~~~h 48 (85)
.|..|.+|+..+.+..+|.+|++..|
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~H 48 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIRH 48 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHHT
T ss_pred CCCCCCcchhhccchhhHHHHHHHHh
Confidence 67778888888888888887774444
No 44
>PRK04860 hypothetical protein; Provisional
Probab=96.34 E-value=0.0024 Score=34.36 Aligned_cols=34 Identities=21% Similarity=0.471 Sum_probs=20.7
Q ss_pred CccCCCCccccCChHHHHHHHHhhCCC---ccCCcCccccCC
Q psy3492 24 PFNCALCEYKAARPERLATHVIKVHNK---RICSKCSFLADD 62 (85)
Q Consensus 24 ~~~c~~c~~~f~~~~~l~~h~~~~h~~---~~C~~c~~~f~~ 62 (85)
+|.|. |+. ....+..|. +++++ |.|..|+..|..
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~-ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHN-RVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEcC-CCC---eeCHHHHHH-HHhcCCccEECCCCCceeEE
Confidence 36665 665 444566666 56665 777777766544
No 45
>PRK04860 hypothetical protein; Provisional
Probab=95.85 E-value=0.0075 Score=32.53 Aligned_cols=33 Identities=15% Similarity=0.187 Sum_probs=26.5
Q ss_pred CCCCcccccChHHHHHHHHhcC--CCccCCCCccccCCh
Q psy3492 1 MPRLQVLISYNWCLKRHLNTHI--KPFNCALCEYKAARP 37 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h~--~~~~c~~c~~~f~~~ 37 (85)
|. |++ ....+.+|.++|. ++|.|..|+..|...
T Consensus 122 C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 122 CK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred cC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 44 665 5677899999998 889999999887654
No 46
>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=95.73 E-value=0.011 Score=23.30 Aligned_cols=21 Identities=24% Similarity=0.539 Sum_probs=13.8
Q ss_pred ccCCcCccccCCHHHHHHHHh
Q psy3492 51 RICSKCSFLADDQETLNEHLQ 71 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~ 71 (85)
|.|+.|++.|.....+..|+.
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred eEccccCCccCCHHHHHHHHC
Confidence 556677777776666666654
No 47
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=95.38 E-value=0.0037 Score=37.13 Aligned_cols=43 Identities=23% Similarity=0.363 Sum_probs=35.7
Q ss_pred CCCcccccChHHHHHHHH-hc-----------------C---CCccCCCCccccCChHHHHHHH
Q psy3492 2 PRLQVLISYNWCLKRHLN-TH-----------------I---KPFNCALCEYKAARPERLATHV 44 (85)
Q Consensus 2 ~~c~~~f~~~~~l~~h~~-~h-----------------~---~~~~c~~c~~~f~~~~~l~~h~ 44 (85)
+.|.|+++..-.|+-|+. -| . |||+|.+|++.+.....|+-|.
T Consensus 355 ~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 355 EGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 358999999999998876 34 1 8999999999999988888774
No 48
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=94.28 E-value=0.049 Score=26.36 Aligned_cols=21 Identities=14% Similarity=0.218 Sum_probs=15.4
Q ss_pred CCCCcccccChHHHHHHHHhc
Q psy3492 1 MPRLQVLISYNWCLKRHLNTH 21 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h 21 (85)
|..|++.|.+...|..|+..+
T Consensus 53 C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 53 CPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp BSSSS-EESSHHHHHHHHHHT
T ss_pred CCccCCCCcCHHHHHHHHcCc
Confidence 677888888888888888754
No 49
>KOG2186|consensus
Probab=94.12 E-value=0.031 Score=32.23 Aligned_cols=37 Identities=22% Similarity=0.605 Sum_probs=16.1
Q ss_pred ccCCCCccccCChHHHHHHHHhhCCC-ccCCcCccccCC
Q psy3492 25 FNCALCEYKAARPERLATHVIKVHNK-RICSKCSFLADD 62 (85)
Q Consensus 25 ~~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~~f~~ 62 (85)
|.|.+||....-+ .+.+|+.+.+.. |.|..||+.|-.
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn~~fSCIDC~k~F~~ 41 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRNAYFSCIDCGKTFER 41 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccCCeeEEeeccccccc
Confidence 3455555443333 234454222222 555555555544
No 50
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=93.82 E-value=0.026 Score=27.31 Aligned_cols=32 Identities=19% Similarity=0.392 Sum_probs=24.8
Q ss_pred CCccCCCCccccCChHHHHHHHHhhCCC-ccCCcCccccCCH
Q psy3492 23 KPFNCALCEYKAARPERLATHVIKVHNK-RICSKCSFLADDQ 63 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~~f~~~ 63 (85)
.++.|..|++. .+. +..+| |.|..||..|+-.
T Consensus 34 ~~~~Cp~C~~~--------~Vk-R~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGRT--------TVK-RIATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCCc--------cee-eeccCeEEcCCCCCeeccc
Confidence 67899999865 233 67778 9999999988754
No 51
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=93.69 E-value=0.0065 Score=34.20 Aligned_cols=13 Identities=23% Similarity=0.823 Sum_probs=10.5
Q ss_pred ccCCcCccccCCH
Q psy3492 51 RICSKCSFLADDQ 63 (85)
Q Consensus 51 ~~C~~c~~~f~~~ 63 (85)
..||.||.++...
T Consensus 49 ~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 49 WVCPHCGYAAFEE 61 (214)
T ss_pred EECCCCCCccccc
Confidence 5799999887755
No 52
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.49 E-value=0.11 Score=26.47 Aligned_cols=72 Identities=18% Similarity=0.236 Sum_probs=44.8
Q ss_pred CCCCcccccChHHHHHHHHhcC---CCc------------cCCCCccccCChHHHHHHHHhhCCC-ccCCcCccccCCHH
Q psy3492 1 MPRLQVLISYNWCLKRHLNTHI---KPF------------NCALCEYKAARPERLATHVIKVHNK-RICSKCSFLADDQE 64 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h~---~~~------------~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~~f~~~~ 64 (85)
||+||-.......|.+.. -|. ++| .|-.|...|........-. ..-.+ |+|+.|...|-..-
T Consensus 18 CpiCgLtLVss~HLARSy-HHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~-~~~~~~y~C~~C~~~FC~dC 95 (112)
T TIGR00622 18 CPICGLTLILSTHLARSY-HHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDE-LKDSHRYVCAVCKNVFCVDC 95 (112)
T ss_pred CCcCCCEEeccchHHHhh-hccCCCcccccccccccCCCCcccCcCCCCCCcccccccc-cccccceeCCCCCCcccccc
Confidence 678887777777776542 122 333 2666777776543211111 11122 99999999999888
Q ss_pred HHHHHHhhcc
Q psy3492 65 TLNEHLQQHI 74 (85)
Q Consensus 65 ~l~~h~~~h~ 74 (85)
+.-.|-..|.
T Consensus 96 D~fiHe~Lh~ 105 (112)
T TIGR00622 96 DVFVHESLHC 105 (112)
T ss_pred chhhhhhccC
Confidence 8888877776
No 53
>KOG2231|consensus
Probab=93.12 E-value=0.4 Score=31.62 Aligned_cols=72 Identities=25% Similarity=0.360 Sum_probs=43.0
Q ss_pred ccChHHHHHHHH-hcCCCccCCCCc---------cccCChHHHHHHHHhhCC------C-ccCCcCccccCCHHHHHHHH
Q psy3492 8 ISYNWCLKRHLN-THIKPFNCALCE---------YKAARPERLATHVIKVHN------K-RICSKCSFLADDQETLNEHL 70 (85)
Q Consensus 8 f~~~~~l~~h~~-~h~~~~~c~~c~---------~~f~~~~~l~~h~~~~h~------~-~~C~~c~~~f~~~~~l~~h~ 70 (85)
|.....|+.|+. .| +-+.|..|- ...-....|..|+..... | -.|+.|...|.....|..|+
T Consensus 124 ~~s~~~Lk~H~~~~H-~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~ 202 (669)
T KOG2231|consen 124 FKSVENLKNHMRDQH-KLHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHL 202 (669)
T ss_pred hhHHHHHHHHHHHhh-hhhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhh
Confidence 346788889985 44 333333332 122334566777622222 2 46788888899999999998
Q ss_pred hhcc--cccCcC
Q psy3492 71 QQHI--FWECSF 80 (85)
Q Consensus 71 ~~h~--~~~C~~ 80 (85)
+.+. ..-|+.
T Consensus 203 ~~~h~~chfC~~ 214 (669)
T KOG2231|consen 203 RFDHEFCHFCDY 214 (669)
T ss_pred ccceeheeecCc
Confidence 8654 444543
No 54
>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=92.63 E-value=0.18 Score=18.71 Aligned_cols=19 Identities=26% Similarity=0.517 Sum_probs=12.8
Q ss_pred cCCcCccccCCHHHHHHHHh
Q psy3492 52 ICSKCSFLADDQETLNEHLQ 71 (85)
Q Consensus 52 ~C~~c~~~f~~~~~l~~h~~ 71 (85)
.||.|++.+ ....++.|++
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577777776 4456677765
No 55
>KOG1146|consensus
Probab=92.19 E-value=0.11 Score=36.44 Aligned_cols=44 Identities=25% Similarity=0.545 Sum_probs=34.5
Q ss_pred CCCCcccccChHHHHHHHHh-cC--------------------------CCccCCCCccccCChHHHHHHH
Q psy3492 1 MPRLQVLISYNWCLKRHLNT-HI--------------------------KPFNCALCEYKAARPERLATHV 44 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~-h~--------------------------~~~~c~~c~~~f~~~~~l~~h~ 44 (85)
||.|+..|+....|..||+. |. +||.|..|...+..+.+|..|+
T Consensus 468 cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihl 538 (1406)
T KOG1146|consen 468 CPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHL 538 (1406)
T ss_pred CCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHH
Confidence 78999999999999999997 11 4567777777777777777666
No 56
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=91.97 E-value=0.15 Score=22.91 Aligned_cols=32 Identities=22% Similarity=0.421 Sum_probs=16.8
Q ss_pred CCccCCCCccccCChHHHHHHHHhhCCC-ccCCcCcc
Q psy3492 23 KPFNCALCEYKAARPERLATHVIKVHNK-RICSKCSF 58 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~ 58 (85)
..|.|..||+.....-.-- +.+.. |.|+.||.
T Consensus 26 v~F~CPnCGe~~I~Rc~~C----Rk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYRCAKC----RKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeehhhhH----HHcCCceECCCcCc
Confidence 3466777776555543321 12222 77777764
No 57
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=91.45 E-value=0.11 Score=23.03 Aligned_cols=19 Identities=26% Similarity=0.336 Sum_probs=15.8
Q ss_pred CCCCcccccChHHHHHHHH
Q psy3492 1 MPRLQVLISYNWCLKRHLN 19 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~ 19 (85)
||.||..|.....+.+|..
T Consensus 20 CPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 20 CPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred CCchhHHHHHhHHHHHHhh
Confidence 7888888888888888876
No 58
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=91.08 E-value=0.12 Score=27.49 Aligned_cols=35 Identities=17% Similarity=0.293 Sum_probs=23.4
Q ss_pred CCccCCCCccccCChHHHHHHHHhhCCC-ccCCcCcccc
Q psy3492 23 KPFNCALCEYKAARPERLATHVIKVHNK-RICSKCSFLA 60 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~~f 60 (85)
.-|.|+.|+..|.....+.. . ...+ |.|+.||...
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~-~--d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQL-L--DMDGTFTCPRCGEEL 133 (147)
T ss_pred cEEECcCCCCEeeHHHHHHh-c--CCCCcEECCCCCCEE
Confidence 56889999988886544321 1 2245 9999998755
No 59
>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=91.02 E-value=0.28 Score=24.65 Aligned_cols=24 Identities=17% Similarity=0.639 Sum_probs=21.6
Q ss_pred CccC----CcCccccCCHHHHHHHHhhc
Q psy3492 50 KRIC----SKCSFLADDQETLNEHLQQH 73 (85)
Q Consensus 50 ~~~C----~~c~~~f~~~~~l~~h~~~h 73 (85)
||.| ..|+....+...+.+|++.+
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~ 107 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKE 107 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHh
Confidence 4899 99999999999999999854
No 60
>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=90.89 E-value=0.18 Score=19.75 Aligned_cols=11 Identities=27% Similarity=0.920 Sum_probs=6.1
Q ss_pred ccCCCCccccC
Q psy3492 25 FNCALCEYKAA 35 (85)
Q Consensus 25 ~~c~~c~~~f~ 35 (85)
+.|.+||..+.
T Consensus 2 ~~C~~CGy~y~ 12 (33)
T cd00350 2 YVCPVCGYIYD 12 (33)
T ss_pred EECCCCCCEEC
Confidence 45666665543
No 61
>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=89.71 E-value=0.24 Score=19.91 Aligned_cols=33 Identities=15% Similarity=0.323 Sum_probs=18.6
Q ss_pred ccCCCCccccCChHHHHHHHHhhCCC-ccCCcCccccC
Q psy3492 25 FNCALCEYKAARPERLATHVIKVHNK-RICSKCSFLAD 61 (85)
Q Consensus 25 ~~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~~f~ 61 (85)
+.|..|+..|.-..... ....+ ..|+.||..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~----~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL----GANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHc----CCCCCEEECCCCCCEEE
Confidence 46777777766655421 11112 67777776653
No 62
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=89.64 E-value=0.41 Score=19.22 Aligned_cols=31 Identities=23% Similarity=0.417 Sum_probs=19.2
Q ss_pred ccCCCCccccCChHHHHHHHHhhCCC--ccCCcCcccc
Q psy3492 25 FNCALCEYKAARPERLATHVIKVHNK--RICSKCSFLA 60 (85)
Q Consensus 25 ~~c~~c~~~f~~~~~l~~h~~~~h~~--~~C~~c~~~f 60 (85)
..|..|+..|.-.... ....| .+|+.||..|
T Consensus 3 i~Cp~C~~~y~i~d~~-----ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK-----IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHH-----CCCCCcEEECCCCCCEe
Confidence 4577777777766542 12223 7788887765
No 63
>KOG1146|consensus
Probab=89.45 E-value=0.15 Score=35.89 Aligned_cols=65 Identities=22% Similarity=0.438 Sum_probs=46.9
Q ss_pred ccChHHHHHHHH-hcC--CCccCCCCccccCChHHHHHHHHhhCC------------------C---------ccCCcCc
Q psy3492 8 ISYNWCLKRHLN-THI--KPFNCALCEYKAARPERLATHVIKVHN------------------K---------RICSKCS 57 (85)
Q Consensus 8 f~~~~~l~~h~~-~h~--~~~~c~~c~~~f~~~~~l~~h~~~~h~------------------~---------~~C~~c~ 57 (85)
+.....+..++. .++ +.+.|..|+..|.+...|..|++..|- | |.|..|.
T Consensus 446 ~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~ 525 (1406)
T KOG1146|consen 446 LESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACN 525 (1406)
T ss_pred hhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeee
Confidence 333444444443 344 889999999999999999999943111 1 6788899
Q ss_pred cccCCHHHHHHHHhh
Q psy3492 58 FLADDQETLNEHLQQ 72 (85)
Q Consensus 58 ~~f~~~~~l~~h~~~ 72 (85)
.++.....|.+|+..
T Consensus 526 ~stttng~LsihlqS 540 (1406)
T KOG1146|consen 526 YSTTTNGNLSIHLQS 540 (1406)
T ss_pred eeeecchHHHHHHHH
Confidence 999998899999873
No 64
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=88.96 E-value=0.33 Score=20.83 Aligned_cols=21 Identities=24% Similarity=0.468 Sum_probs=13.1
Q ss_pred ccCCcCccccCCH-----HHHHHHHh
Q psy3492 51 RICSKCSFLADDQ-----ETLNEHLQ 71 (85)
Q Consensus 51 ~~C~~c~~~f~~~-----~~l~~h~~ 71 (85)
-.|..|++.+... +.|.+|++
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 3566777665444 56777766
No 65
>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=88.33 E-value=0.29 Score=18.24 Aligned_cols=10 Identities=20% Similarity=0.896 Sum_probs=6.5
Q ss_pred cCCcCccccC
Q psy3492 52 ICSKCSFLAD 61 (85)
Q Consensus 52 ~C~~c~~~f~ 61 (85)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 5677776664
No 66
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=88.04 E-value=0.31 Score=29.30 Aligned_cols=53 Identities=15% Similarity=0.258 Sum_probs=34.4
Q ss_pred CCCCccccCChHHHHHHHHhhCCC-ccCCcCccccCCHHHHHHHHhhcccccCcC
Q psy3492 27 CALCEYKAARPERLATHVIKVHNK-RICSKCSFLADDQETLNEHLQQHIFWECSF 80 (85)
Q Consensus 27 c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~~f~~~~~l~~h~~~h~~~~C~~ 80 (85)
|-.|-..|..+..-..-. ....+ |+|+.|...|-..-..-.|-..|..+-|+.
T Consensus 365 Cf~CQ~~fp~~~~~~~~~-~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~C~gCe~ 418 (421)
T COG5151 365 CFVCQGPFPKPPVSPFDE-STSSGRYQCELCKSTFCSDCDVFIHETLHFCIGCEL 418 (421)
T ss_pred ceeccCCCCCCCCCcccc-cccccceechhhhhhhhhhhHHHHHHHHhhCCCCcC
Confidence 555555555543322222 22233 999999999999988888888887666654
No 67
>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=87.82 E-value=0.42 Score=27.20 Aligned_cols=22 Identities=23% Similarity=0.427 Sum_probs=18.3
Q ss_pred ccCCcCccccCCHHHHHHHHhh
Q psy3492 51 RICSKCSFLADDQETLNEHLQQ 72 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~ 72 (85)
|.|+.|+|.|.......+|+..
T Consensus 78 ~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 78 WRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp EEE-SSS-EESSHHHHHHHHHH
T ss_pred ECCCCCCcccCChHHHHHHHhh
Confidence 8999999999999999999874
No 68
>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=87.66 E-value=0.2 Score=21.75 Aligned_cols=13 Identities=23% Similarity=0.846 Sum_probs=9.4
Q ss_pred ccCCCCccccCCh
Q psy3492 25 FNCALCEYKAARP 37 (85)
Q Consensus 25 ~~c~~c~~~f~~~ 37 (85)
|+|.+||..+...
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 6788888777643
No 69
>KOG4167|consensus
Probab=87.55 E-value=0.096 Score=34.69 Aligned_cols=24 Identities=21% Similarity=0.378 Sum_probs=22.6
Q ss_pred ccCCcCccccCCHHHHHHHHhhcc
Q psy3492 51 RICSKCSFLADDQETLNEHLQQHI 74 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~ 74 (85)
|-|.+|+|.|.-..+++.||++|.
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHH
Confidence 899999999999999999999986
No 70
>PF14353 CpXC: CpXC protein
Probab=87.21 E-value=0.63 Score=24.03 Aligned_cols=13 Identities=15% Similarity=0.335 Sum_probs=8.7
Q ss_pred ccCCcCccccCCH
Q psy3492 51 RICSKCSFLADDQ 63 (85)
Q Consensus 51 ~~C~~c~~~f~~~ 63 (85)
+.|+.||..|.-.
T Consensus 39 ~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 39 FTCPSCGHKFRLE 51 (128)
T ss_pred EECCCCCCceecC
Confidence 6788887766543
No 71
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=87.12 E-value=0.16 Score=24.85 Aligned_cols=31 Identities=13% Similarity=0.363 Sum_probs=22.8
Q ss_pred CCccCCCCccccCChHHHHHHHHhhCCC-ccCCcCccccCC
Q psy3492 23 KPFNCALCEYKAARPERLATHVIKVHNK-RICSKCSFLADD 62 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~~f~~ 62 (85)
..|.|..|++. .+ .+...| |.|..|++.|+-
T Consensus 35 a~y~CpfCgk~-----~v----kR~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGKH-----AV----KRQAVGIWRCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCCC-----ce----eeeeeEEEEcCCCCCEEeC
Confidence 67899999854 22 245567 999999988765
No 72
>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=86.77 E-value=1.5 Score=23.76 Aligned_cols=32 Identities=19% Similarity=0.314 Sum_probs=21.7
Q ss_pred CCccCCCCccccCChHHHHHHHHhhCCCccCCcCccccC
Q psy3492 23 KPFNCALCEYKAARPERLATHVIKVHNKRICSKCSFLAD 61 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~h~~~~h~~~~C~~c~~~f~ 61 (85)
.-|.|+.|+..|+....+. .+|.|+.||....
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~-------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME-------LNFTCPRCGAMLD 139 (158)
T ss_pred CeEECCCCCcEeeHHHHHH-------cCCcCCCCCCEee
Confidence 5577888887777665543 2388888886543
No 73
>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=86.68 E-value=0.48 Score=24.04 Aligned_cols=12 Identities=25% Similarity=0.642 Sum_probs=6.1
Q ss_pred cCCcCccccCCH
Q psy3492 52 ICSKCSFLADDQ 63 (85)
Q Consensus 52 ~C~~c~~~f~~~ 63 (85)
.|++||..|.-.
T Consensus 28 vCP~CG~~~~~~ 39 (108)
T PF09538_consen 28 VCPKCGTEFPPE 39 (108)
T ss_pred cCCCCCCccCcc
Confidence 455555554433
No 74
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=86.66 E-value=0.61 Score=18.77 Aligned_cols=33 Identities=18% Similarity=0.526 Sum_probs=18.2
Q ss_pred ccCCCCccccCChHHHHHHHHhhCCC-ccCCcCccccC
Q psy3492 25 FNCALCEYKAARPERLATHVIKVHNK-RICSKCSFLAD 61 (85)
Q Consensus 25 ~~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~~f~ 61 (85)
..|..|+..|.-...- + ....+ .+|+.|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~---l-~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK---L-PAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHH---c-ccCCcEEECCCCCcEee
Confidence 3566777776665541 1 22222 67777776653
No 75
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=86.36 E-value=0.49 Score=21.28 Aligned_cols=9 Identities=33% Similarity=0.707 Sum_probs=4.4
Q ss_pred ccCCCCccc
Q psy3492 25 FNCALCEYK 33 (85)
Q Consensus 25 ~~c~~c~~~ 33 (85)
|.|..||+.
T Consensus 26 F~CPnCG~~ 34 (59)
T PRK14890 26 FLCPNCGEV 34 (59)
T ss_pred eeCCCCCCe
Confidence 445555544
No 76
>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=86.30 E-value=0.17 Score=24.76 Aligned_cols=32 Identities=19% Similarity=0.437 Sum_probs=23.3
Q ss_pred CCccCCCCccccCChHHHHHHHHhhCCC-ccCCcCccccCCH
Q psy3492 23 KPFNCALCEYKAARPERLATHVIKVHNK-RICSKCSFLADDQ 63 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~~f~~~ 63 (85)
..|.|..|++. .+ .+...| |.|..|++.|.--
T Consensus 34 a~y~CpfCgk~-----~v----kR~a~GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 34 AKYVCPFCGKK-----TV----KRGSTGIWTCRKCGAKFAGG 66 (91)
T ss_pred cCccCCCCCCC-----ce----EEEeeEEEEcCCCCCEEeCC
Confidence 67899999854 22 256667 9999999877643
No 77
>KOG2482|consensus
Probab=86.13 E-value=2 Score=26.41 Aligned_cols=50 Identities=24% Similarity=0.563 Sum_probs=36.0
Q ss_pred CCccCCCCccccC-ChHHHHHHHHhhCC---C---------------------ccCCcCccccCCHHHHHHHHhh
Q psy3492 23 KPFNCALCEYKAA-RPERLATHVIKVHN---K---------------------RICSKCSFLADDQETLNEHLQQ 72 (85)
Q Consensus 23 ~~~~c~~c~~~f~-~~~~l~~h~~~~h~---~---------------------~~C~~c~~~f~~~~~l~~h~~~ 72 (85)
....|..|...+. ..+.+..|+-..|. | ++|-.|.+.|..+..|..||+-
T Consensus 143 fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 143 FSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred eeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHh
Confidence 5567888876443 55566666533332 1 6888999999999999999984
No 78
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=85.80 E-value=0.71 Score=25.49 Aligned_cols=33 Identities=18% Similarity=0.424 Sum_probs=22.3
Q ss_pred CCccCCCCccccCChHHHHHHHHhhCCCccCCcCccccCC
Q psy3492 23 KPFNCALCEYKAARPERLATHVIKVHNKRICSKCSFLADD 62 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~h~~~~h~~~~C~~c~~~f~~ 62 (85)
.-|.|..|+..|+....+. .+|.|+.||.....
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~-------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME-------YGFRCPQCGEMLEE 148 (178)
T ss_pred CEEECCCCCcEEeHHHHhh-------cCCcCCCCCCCCee
Confidence 4578888887777665432 23889999865443
No 79
>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=85.22 E-value=0.79 Score=18.96 Aligned_cols=20 Identities=25% Similarity=0.504 Sum_probs=9.3
Q ss_pred ccCCcCccccCCH----HHHHHHH
Q psy3492 51 RICSKCSFLADDQ----ETLNEHL 70 (85)
Q Consensus 51 ~~C~~c~~~f~~~----~~l~~h~ 70 (85)
..|..|++.+... +.|..|+
T Consensus 17 a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 17 AKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp EEETTTTEE-----SSTHHHHHHH
T ss_pred EEeCCCCeEEeeCCCcHHHHHHhh
Confidence 4566666555443 5566665
No 80
>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=84.67 E-value=0.18 Score=24.66 Aligned_cols=31 Identities=19% Similarity=0.514 Sum_probs=22.2
Q ss_pred CCccCCCCccccCChHHHHHHHHhhCCC-ccCCcCccccCC
Q psy3492 23 KPFNCALCEYKAARPERLATHVIKVHNK-RICSKCSFLADD 62 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~~f~~ 62 (85)
..|.|..|++.- + .+...| |.|..|++.|+-
T Consensus 34 ~ky~Cp~Cgk~~-----v----kR~a~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 34 AKYTCPFCGKTS-----V----KRVATGIWKCKKCGKKFAG 65 (90)
T ss_dssp S-BEESSSSSSE-----E----EEEETTEEEETTTTEEEE-
T ss_pred CCCcCCCCCCce-----e----EEeeeEEeecCCCCCEEeC
Confidence 789999998762 1 256777 999999887753
No 81
>KOG2893|consensus
Probab=84.64 E-value=0.17 Score=29.25 Aligned_cols=41 Identities=22% Similarity=0.284 Sum_probs=24.8
Q ss_pred CCCCccccCChHHHHHHHHhhCCCccCCcCccccCCHHHHHHH
Q psy3492 27 CALCEYKAARPERLATHVIKVHNKRICSKCSFLADDQETLNEH 69 (85)
Q Consensus 27 c~~c~~~f~~~~~l~~h~~~~h~~~~C~~c~~~f~~~~~l~~h 69 (85)
|=-|++.|....-|.+|+...| |+|.+|-|.+-.-..|..|
T Consensus 13 cwycnrefddekiliqhqkakh--fkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAKH--FKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhhhcc--ceeeeehhhhccCCCceee
Confidence 4447777887777777763333 7787776544443344444
No 82
>COG1773 Rubredoxin [Energy production and conversion]
Probab=84.61 E-value=0.29 Score=21.69 Aligned_cols=33 Identities=15% Similarity=0.517 Sum_probs=18.8
Q ss_pred CccCCCCccccCChHHHHHHHHhhCCC---------ccCCcCcc
Q psy3492 24 PFNCALCEYKAARPERLATHVIKVHNK---------RICSKCSF 58 (85)
Q Consensus 24 ~~~c~~c~~~f~~~~~l~~h~~~~h~~---------~~C~~c~~ 58 (85)
.++|.+||..|.-...-... .+-.| +.|+.||.
T Consensus 3 ~~~C~~CG~vYd~e~Gdp~~--gi~pgT~fedlPd~w~CP~Cg~ 44 (55)
T COG1773 3 RWRCSVCGYVYDPEKGDPRC--GIAPGTPFEDLPDDWVCPECGV 44 (55)
T ss_pred ceEecCCceEeccccCCccC--CCCCCCchhhCCCccCCCCCCC
Confidence 46788888776654322211 12222 78999873
No 83
>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=84.36 E-value=0.47 Score=17.35 Aligned_cols=8 Identities=38% Similarity=1.074 Sum_probs=5.5
Q ss_pred ccCCcCcc
Q psy3492 51 RICSKCSF 58 (85)
Q Consensus 51 ~~C~~c~~ 58 (85)
|.|+.||+
T Consensus 17 f~CPnCG~ 24 (24)
T PF07754_consen 17 FPCPNCGF 24 (24)
T ss_pred EeCCCCCC
Confidence 77777763
No 84
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=84.19 E-value=1.3 Score=18.26 Aligned_cols=21 Identities=29% Similarity=0.127 Sum_probs=11.0
Q ss_pred CCCCcccccCh--HHHHHHHHhc
Q psy3492 1 MPRLQVLISYN--WCLKRHLNTH 21 (85)
Q Consensus 1 c~~c~~~f~~~--~~l~~h~~~h 21 (85)
|++||..|... ..-..|.+.|
T Consensus 16 C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 16 CPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred CCCCCCEECCCCHHHHHHHHHHH
Confidence 66777665433 4444554443
No 85
>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=83.88 E-value=0.13 Score=22.02 Aligned_cols=13 Identities=23% Similarity=0.828 Sum_probs=8.6
Q ss_pred ccCCCCccccCCh
Q psy3492 25 FNCALCEYKAARP 37 (85)
Q Consensus 25 ~~c~~c~~~f~~~ 37 (85)
|+|.+|+..+...
T Consensus 2 y~C~~CgyvYd~~ 14 (47)
T PF00301_consen 2 YQCPVCGYVYDPE 14 (47)
T ss_dssp EEETTTSBEEETT
T ss_pred cCCCCCCEEEcCC
Confidence 5677777666544
No 86
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=83.82 E-value=0.23 Score=24.31 Aligned_cols=31 Identities=19% Similarity=0.434 Sum_probs=22.7
Q ss_pred CCccCCCCccccCChHHHHHHHHhhCCC-ccCCcCccccCC
Q psy3492 23 KPFNCALCEYKAARPERLATHVIKVHNK-RICSKCSFLADD 62 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~~f~~ 62 (85)
..|.|..|++. .+ .+...| |.|..|++.|+-
T Consensus 35 a~y~CpfCgk~-----~v----kR~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRP-----KV----KRVGTGIWECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCC-----ce----EEEEEEEEEcCCCCCEEeC
Confidence 67899999754 22 246667 999999987765
No 87
>KOG2907|consensus
Probab=81.59 E-value=0.78 Score=23.41 Aligned_cols=37 Identities=16% Similarity=0.424 Sum_probs=21.2
Q ss_pred CccCCCCccccCChHHHHHHHHhhCCC----ccCCcCccccCC
Q psy3492 24 PFNCALCEYKAARPERLATHVIKVHNK----RICSKCSFLADD 62 (85)
Q Consensus 24 ~~~c~~c~~~f~~~~~l~~h~~~~h~~----~~C~~c~~~f~~ 62 (85)
..+|..||..--.-+.++ +|....| |.|+.|++.|..
T Consensus 74 ~~kCpkCghe~m~Y~T~Q--lRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 74 KHKCPKCGHEEMSYHTLQ--LRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred hccCcccCCchhhhhhhh--cccccCCceEEEEcCccceeeec
Confidence 356777775433223332 2223444 889999887754
No 88
>KOG4173|consensus
Probab=81.41 E-value=0.35 Score=27.36 Aligned_cols=47 Identities=17% Similarity=0.427 Sum_probs=33.3
Q ss_pred ccCCCCccccCChHHHHHHHHhhCC---------C---ccC--CcCccccCCHHHHHHHHh
Q psy3492 25 FNCALCEYKAARPERLATHVIKVHN---------K---RIC--SKCSFLADDQETLNEHLQ 71 (85)
Q Consensus 25 ~~c~~c~~~f~~~~~l~~h~~~~h~---------~---~~C--~~c~~~f~~~~~l~~h~~ 71 (85)
-.|.+|.+.|....-|..|+.-.|. | |.| +.|+-.|.....-..|+-
T Consensus 107 ~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I 167 (253)
T KOG4173|consen 107 NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMI 167 (253)
T ss_pred chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHH
Confidence 4688888888888888887743343 2 666 458888888877777754
No 89
>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=80.81 E-value=0.64 Score=18.76 Aligned_cols=13 Identities=15% Similarity=0.370 Sum_probs=9.8
Q ss_pred ccCCcCccccCCH
Q psy3492 51 RICSKCSFLADDQ 63 (85)
Q Consensus 51 ~~C~~c~~~f~~~ 63 (85)
|.|+.||..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (41)
T smart00834 6 YRCEDCGHTFEVL 18 (41)
T ss_pred EEcCCCCCEEEEE
Confidence 7889999877544
No 90
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=80.78 E-value=0.23 Score=26.77 Aligned_cols=14 Identities=14% Similarity=0.275 Sum_probs=8.9
Q ss_pred CccCCCCccccCCh
Q psy3492 24 PFNCALCEYKAARP 37 (85)
Q Consensus 24 ~~~c~~c~~~f~~~ 37 (85)
-++|..||.+|...
T Consensus 28 ~~~c~~c~~~f~~~ 41 (154)
T PRK00464 28 RRECLACGKRFTTF 41 (154)
T ss_pred eeeccccCCcceEe
Confidence 36677777766654
No 91
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=80.32 E-value=2.2 Score=26.33 Aligned_cols=18 Identities=22% Similarity=0.545 Sum_probs=7.1
Q ss_pred CCCCccccCChHHHHHHH
Q psy3492 27 CALCEYKAARPERLATHV 44 (85)
Q Consensus 27 c~~c~~~f~~~~~l~~h~ 44 (85)
|..|...|-.-..|..|.
T Consensus 223 C~FC~~~FYdDDEL~~Hc 240 (493)
T COG5236 223 CIFCKIYFYDDDELRRHC 240 (493)
T ss_pred hhhccceecChHHHHHHH
Confidence 333333333334444443
No 92
>KOG2231|consensus
Probab=79.43 E-value=5.7 Score=26.68 Aligned_cols=20 Identities=20% Similarity=-0.069 Sum_probs=10.2
Q ss_pred CCCCcccccChHHHHHHHHh
Q psy3492 1 MPRLQVLISYNWCLKRHLNT 20 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~ 20 (85)
|+.|...|.....|..|++.
T Consensus 185 C~~C~~~fld~~el~rH~~~ 204 (669)
T KOG2231|consen 185 CKFCHERFLDDDELYRHLRF 204 (669)
T ss_pred chhhhhhhccHHHHHHhhcc
Confidence 34455555555555555554
No 93
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=79.11 E-value=0.98 Score=19.56 Aligned_cols=27 Identities=19% Similarity=0.431 Sum_probs=15.3
Q ss_pred CccCCCCccccCChHHHHHHHHhhCCCccCCcCcc
Q psy3492 24 PFNCALCEYKAARPERLATHVIKVHNKRICSKCSF 58 (85)
Q Consensus 24 ~~~c~~c~~~f~~~~~l~~h~~~~h~~~~C~~c~~ 58 (85)
.|.|..||+.+.. + ....+..|+.||.
T Consensus 6 ~Y~C~~Cg~~~~~-------~-~~~~~irCp~Cg~ 32 (49)
T COG1996 6 EYKCARCGREVEL-------D-QETRGIRCPYCGS 32 (49)
T ss_pred EEEhhhcCCeeeh-------h-hccCceeCCCCCc
Confidence 3677778777611 1 1222267888874
No 94
>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=78.92 E-value=0.73 Score=19.09 Aligned_cols=15 Identities=13% Similarity=0.375 Sum_probs=10.7
Q ss_pred ccCCcCccccCCHHH
Q psy3492 51 RICSKCSFLADDQET 65 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~ 65 (85)
|.|..||..|.....
T Consensus 6 y~C~~Cg~~fe~~~~ 20 (42)
T PF09723_consen 6 YRCEECGHEFEVLQS 20 (42)
T ss_pred EEeCCCCCEEEEEEE
Confidence 788888877765543
No 95
>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=78.35 E-value=1.6 Score=23.03 Aligned_cols=21 Identities=29% Similarity=0.506 Sum_probs=14.8
Q ss_pred ccCCcCccccCCHHHHHHHHhhcc
Q psy3492 51 RICSKCSFLADDQETLNEHLQQHI 74 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~ 74 (85)
-.|-+||+.|... .+|++.|.
T Consensus 73 i~clecGk~~k~L---krHL~~~~ 93 (132)
T PF05443_consen 73 IICLECGKKFKTL---KRHLRTHH 93 (132)
T ss_dssp EE-TBT--EESBH---HHHHHHTT
T ss_pred eEEccCCcccchH---HHHHHHcc
Confidence 5789999999875 79999984
No 96
>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=76.11 E-value=1.2 Score=23.67 Aligned_cols=43 Identities=12% Similarity=0.171 Sum_probs=23.8
Q ss_pred CccCCCCccccCChHHHHHHHHhhCC-------C-ccCCcCccccCCHHHHH
Q psy3492 24 PFNCALCEYKAARPERLATHVIKVHN-------K-RICSKCSFLADDQETLN 67 (85)
Q Consensus 24 ~~~c~~c~~~f~~~~~l~~h~~~~h~-------~-~~C~~c~~~f~~~~~l~ 67 (85)
...|..|+..+..-+.-..-. .... . |.|+.||+.|=.-+...
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~-~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~ 141 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKD-RVPPYVYETYDEFWRCPGCGKIYWEGSHWR 141 (147)
T ss_pred CCccCCCCcEeeechhhcccc-ccCccccccCCeEEECCCCCCEecccccHH
Confidence 367999988654432211100 1111 1 78999999875554443
No 97
>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=75.70 E-value=2.8 Score=23.98 Aligned_cols=28 Identities=25% Similarity=0.562 Sum_probs=20.9
Q ss_pred CCccCCCCccccCChHHHHHHHHhhCCC
Q psy3492 23 KPFNCALCEYKAARPERLATHVIKVHNK 50 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~h~~~~h~~ 50 (85)
..|.|..|+|-|.-...+.+|+...|..
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred CEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 3488999999999999999999655654
No 98
>PHA00626 hypothetical protein
Probab=75.41 E-value=1.3 Score=19.69 Aligned_cols=14 Identities=14% Similarity=0.691 Sum_probs=11.5
Q ss_pred ccCCcCccccCCHH
Q psy3492 51 RICSKCSFLADDQE 64 (85)
Q Consensus 51 ~~C~~c~~~f~~~~ 64 (85)
|.|+.||..|+...
T Consensus 24 YkCkdCGY~ft~~~ 37 (59)
T PHA00626 24 YVCCDCGYNDSKDA 37 (59)
T ss_pred eEcCCCCCeechhh
Confidence 99999998887654
No 99
>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=75.31 E-value=2.4 Score=22.21 Aligned_cols=10 Identities=0% Similarity=-0.233 Sum_probs=4.8
Q ss_pred cCCcCccccC
Q psy3492 52 ICSKCSFLAD 61 (85)
Q Consensus 52 ~C~~c~~~f~ 61 (85)
.|++||..|.
T Consensus 28 vcP~cg~~~~ 37 (129)
T TIGR02300 28 VSPYTGEQFP 37 (129)
T ss_pred cCCCcCCccC
Confidence 4555554443
No 100
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=75.08 E-value=3 Score=25.73 Aligned_cols=71 Identities=20% Similarity=0.253 Sum_probs=43.7
Q ss_pred ChHHHHHHHHhcCCCccCCCCc---ccc------CChHHHHHHHHhhCC---C----ccCCcCccccCCHHHHHHHHhhc
Q psy3492 10 YNWCLKRHLNTHIKPFNCALCE---YKA------ARPERLATHVIKVHN---K----RICSKCSFLADDQETLNEHLQQH 73 (85)
Q Consensus 10 ~~~~l~~h~~~h~~~~~c~~c~---~~f------~~~~~l~~h~~~~h~---~----~~C~~c~~~f~~~~~l~~h~~~h 73 (85)
....|+.|...-...+-|.+|- +.| .....|..|. .... | -.|.-|..-|-..+.|..|.|..
T Consensus 165 ~~k~lk~H~K~~H~~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~-~~G~~e~GFKGHP~C~FC~~~FYdDDEL~~HcR~~ 243 (493)
T COG5236 165 SLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTLRDHK-NGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLR 243 (493)
T ss_pred hHHHHHHHHHhhcCcEEhHhhhcCcccCccceeeeecccccccc-cCCccccCcCCCchhhhccceecChHHHHHHHHhh
Confidence 3566777777533334455543 223 2334565665 2221 2 46888999999999999999954
Q ss_pred c--cccCcCC
Q psy3492 74 I--FWECSFQ 81 (85)
Q Consensus 74 ~--~~~C~~~ 81 (85)
+ .|-|+..
T Consensus 244 HE~ChICD~v 253 (493)
T COG5236 244 HEACHICDMV 253 (493)
T ss_pred hhhhhhhhcc
Confidence 4 6777654
No 101
>PF15269 zf-C2H2_7: Zinc-finger
Probab=74.15 E-value=3.2 Score=17.60 Aligned_cols=21 Identities=24% Similarity=0.679 Sum_probs=13.0
Q ss_pred ccCCcCccccCCHHHHHHHHh
Q psy3492 51 RICSKCSFLADDQETLNEHLQ 71 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~ 71 (85)
|+|-.|...-...+.|-+|++
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 556666666666666666665
No 102
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=73.85 E-value=1.7 Score=23.84 Aligned_cols=9 Identities=22% Similarity=1.014 Sum_probs=4.5
Q ss_pred ccCCcCccc
Q psy3492 51 RICSKCSFL 59 (85)
Q Consensus 51 ~~C~~c~~~ 59 (85)
|.|+.||..
T Consensus 135 ~vC~vCGy~ 143 (166)
T COG1592 135 WVCPVCGYT 143 (166)
T ss_pred EEcCCCCCc
Confidence 455555543
No 103
>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=72.62 E-value=1.4 Score=18.86 Aligned_cols=13 Identities=15% Similarity=0.358 Sum_probs=10.0
Q ss_pred ccCCcCccccCCH
Q psy3492 51 RICSKCSFLADDQ 63 (85)
Q Consensus 51 ~~C~~c~~~f~~~ 63 (85)
|.|..||..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (52)
T TIGR02605 6 YRCTACGHRFEVL 18 (52)
T ss_pred EEeCCCCCEeEEE
Confidence 7899999877654
No 104
>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=72.57 E-value=3.2 Score=17.36 Aligned_cols=13 Identities=8% Similarity=-0.036 Sum_probs=7.2
Q ss_pred CCCCcccccChHH
Q psy3492 1 MPRLQVLISYNWC 13 (85)
Q Consensus 1 c~~c~~~f~~~~~ 13 (85)
|++||..|+....
T Consensus 11 C~~C~rpf~WRKK 23 (42)
T PF10013_consen 11 CPVCGRPFTWRKK 23 (42)
T ss_pred CcccCCcchHHHH
Confidence 5566666655443
No 105
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=72.54 E-value=2.2 Score=26.83 Aligned_cols=32 Identities=19% Similarity=0.287 Sum_probs=20.6
Q ss_pred ccCCCCccccCChHHHHHHHHhhCCCccCCcCccccCCHHH
Q psy3492 25 FNCALCEYKAARPERLATHVIKVHNKRICSKCSFLADDQET 65 (85)
Q Consensus 25 ~~c~~c~~~f~~~~~l~~h~~~~h~~~~C~~c~~~f~~~~~ 65 (85)
-.|..||....++. .. ||+|+.||+.+.....
T Consensus 351 p~Cp~Cg~~m~S~G--------~~-g~rC~kCg~~~~~~~~ 382 (421)
T COG1571 351 PVCPRCGGRMKSAG--------RN-GFRCKKCGTRARETLI 382 (421)
T ss_pred CCCCccCCchhhcC--------CC-CcccccccccCCcccc
Confidence 36888887644332 11 5899999887766543
No 106
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=72.51 E-value=0.53 Score=28.43 Aligned_cols=50 Identities=24% Similarity=0.511 Sum_probs=33.8
Q ss_pred CccCCCCccccCChHHHHHHHHh--hCCC-----ccCC--cCccccCCHHHHHHHHhhcc
Q psy3492 24 PFNCALCEYKAARPERLATHVIK--VHNK-----RICS--KCSFLADDQETLNEHLQQHI 74 (85)
Q Consensus 24 ~~~c~~c~~~f~~~~~l~~h~~~--~h~~-----~~C~--~c~~~f~~~~~l~~h~~~h~ 74 (85)
++.|..|...|.....+..|. + .|.+ +.|+ .|++.|.+...+..|..+|+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~-~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~ 347 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHL-RSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHT 347 (467)
T ss_pred CCCCccccCCccccccccccc-cccccccccCCceeeeccCCCccccccccccCCccccc
Confidence 456666777777777777776 4 4443 4566 57777777777777777666
No 107
>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=72.26 E-value=1.4 Score=19.16 Aligned_cols=12 Identities=8% Similarity=-0.042 Sum_probs=5.2
Q ss_pred CCCCcccccChH
Q psy3492 1 MPRLQVLISYNW 12 (85)
Q Consensus 1 c~~c~~~f~~~~ 12 (85)
||+|+..|....
T Consensus 23 CPlC~r~l~~e~ 34 (54)
T PF04423_consen 23 CPLCGRPLDEEH 34 (54)
T ss_dssp -TTT--EE-HHH
T ss_pred CCCCCCCCCHHH
Confidence 677777776543
No 108
>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=71.59 E-value=1.1 Score=17.31 Aligned_cols=8 Identities=25% Similarity=1.074 Sum_probs=5.3
Q ss_pred ccCCcCcc
Q psy3492 51 RICSKCSF 58 (85)
Q Consensus 51 ~~C~~c~~ 58 (85)
+.|+.|+.
T Consensus 20 ~vCp~C~~ 27 (30)
T PF08274_consen 20 LVCPECGH 27 (30)
T ss_dssp EEETTTTE
T ss_pred EeCCcccc
Confidence 66777764
No 109
>KOG2593|consensus
Probab=70.64 E-value=6.7 Score=24.88 Aligned_cols=34 Identities=21% Similarity=0.348 Sum_probs=23.4
Q ss_pred CCccCCCCccccCChHHHHHHHHhhCCC-ccCCcCcc
Q psy3492 23 KPFNCALCEYKAARPERLATHVIKVHNK-RICSKCSF 58 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~ 58 (85)
.-|.|..|.+.|.....++.- ..-++ |.|..|+-
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~L~--~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQLL--DNETGEFHCENCGG 161 (436)
T ss_pred ccccCCccccchhhhHHHHhh--cccCceEEEecCCC
Confidence 568999999888877665421 22345 88888863
No 110
>KOG0717|consensus
Probab=70.30 E-value=2.8 Score=26.79 Aligned_cols=19 Identities=21% Similarity=-0.008 Sum_probs=11.7
Q ss_pred CCCCcccccChHHHHHHHH
Q psy3492 1 MPRLQVLISYNWCLKRHLN 19 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~ 19 (85)
|++|.|+|.+.-.+..|..
T Consensus 295 C~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 295 CVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred EeeccccccchHHHHhhHH
Confidence 5566666666666666644
No 111
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=69.21 E-value=1.2 Score=20.91 Aligned_cols=11 Identities=27% Similarity=0.461 Sum_probs=5.1
Q ss_pred ccCC--cCccccC
Q psy3492 51 RICS--KCSFLAD 61 (85)
Q Consensus 51 ~~C~--~c~~~f~ 61 (85)
+.|. +||..|.
T Consensus 28 ~qC~N~eCg~tF~ 40 (72)
T PRK09678 28 HQCQNVNCSATFI 40 (72)
T ss_pred eecCCCCCCCEEE
Confidence 4444 4554443
No 112
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=68.12 E-value=4.2 Score=22.30 Aligned_cols=41 Identities=12% Similarity=0.236 Sum_probs=23.5
Q ss_pred ccCCCCccccCChH--HHH-----HHHHhhCCC-ccCCcCccccCCHHHH
Q psy3492 25 FNCALCEYKAARPE--RLA-----THVIKVHNK-RICSKCSFLADDQETL 66 (85)
Q Consensus 25 ~~c~~c~~~f~~~~--~l~-----~h~~~~h~~-~~C~~c~~~f~~~~~l 66 (85)
-.|..|+......+ ... .+. ..+.. |.|+.||+.|=--++.
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~-~~~~~f~~C~~CgkiYW~GsHw 146 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVY-RNYEEFYRCPKCGKIYWKGSHW 146 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhh-hcccceeECCCCcccccCchHH
Confidence 46888887544332 222 122 23344 7899999877555444
No 113
>KOG2785|consensus
Probab=67.75 E-value=19 Score=22.68 Aligned_cols=22 Identities=23% Similarity=0.431 Sum_probs=18.1
Q ss_pred ccCCcCc---cccCCHHHHHHHHhh
Q psy3492 51 RICSKCS---FLADDQETLNEHLQQ 72 (85)
Q Consensus 51 ~~C~~c~---~~f~~~~~l~~h~~~ 72 (85)
+.|-.|. +.|........||..
T Consensus 218 ~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 218 FICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred ceEEEeccccCcccccHHHHHHHhh
Confidence 6777776 899999999999873
No 114
>KOG4167|consensus
Probab=67.11 E-value=1.1 Score=30.07 Aligned_cols=22 Identities=14% Similarity=-0.001 Sum_probs=19.8
Q ss_pred CCCCcccccChHHHHHHHHhcC
Q psy3492 1 MPRLQVLISYNWCLKRHLNTHI 22 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h~ 22 (85)
|.+|+|.|....++..||++|.
T Consensus 795 CreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 795 CRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred hHHHHHHHHHHhhhhHHHHHHH
Confidence 6789999999999999999987
No 115
>KOG1842|consensus
Probab=66.46 E-value=4.1 Score=25.97 Aligned_cols=22 Identities=27% Similarity=0.549 Sum_probs=15.8
Q ss_pred ccCCcCccccCCHHHHHHHHhh
Q psy3492 51 RICSKCSFLADDQETLNEHLQQ 72 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~ 72 (85)
|.||.|.+.|.+...|..|...
T Consensus 16 flCPiC~~dl~~~~~L~~H~d~ 37 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLDV 37 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHhh
Confidence 7777777777777777777663
No 116
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.36 E-value=2.8 Score=18.06 Aligned_cols=13 Identities=23% Similarity=0.077 Sum_probs=7.9
Q ss_pred CCCCcccccChHH
Q psy3492 1 MPRLQVLISYNWC 13 (85)
Q Consensus 1 c~~c~~~f~~~~~ 13 (85)
||+|+..|.....
T Consensus 15 CpvCqRPFsWRkK 27 (54)
T COG4338 15 CPVCQRPFSWRKK 27 (54)
T ss_pred hhhhcCchHHHHH
Confidence 5667776655443
No 117
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=65.87 E-value=5.1 Score=17.34 Aligned_cols=13 Identities=31% Similarity=0.782 Sum_probs=8.6
Q ss_pred CCC-ccCCcCcccc
Q psy3492 48 HNK-RICSKCSFLA 60 (85)
Q Consensus 48 h~~-~~C~~c~~~f 60 (85)
+.+ +.|..||..+
T Consensus 34 ~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 34 HLDRWHCGKCGYTE 47 (50)
T ss_pred cCCcEECCCcCCEE
Confidence 334 7888888643
No 118
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=63.85 E-value=0.82 Score=18.76 Aligned_cols=11 Identities=27% Similarity=0.703 Sum_probs=7.7
Q ss_pred ccCCcCccccC
Q psy3492 51 RICSKCSFLAD 61 (85)
Q Consensus 51 ~~C~~c~~~f~ 61 (85)
|.|..||..+.
T Consensus 29 y~C~~C~~~w~ 39 (40)
T smart00440 29 YVCTKCGHRWR 39 (40)
T ss_pred EEeCCCCCEeC
Confidence 77888876553
No 119
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=62.95 E-value=2.7 Score=22.15 Aligned_cols=14 Identities=14% Similarity=0.337 Sum_probs=10.5
Q ss_pred CccCCCCccccCCh
Q psy3492 24 PFNCALCEYKAARP 37 (85)
Q Consensus 24 ~~~c~~c~~~f~~~ 37 (85)
.+.|..||..|...
T Consensus 70 ~~~C~~CG~~~~~~ 83 (135)
T PRK03824 70 VLKCRNCGNEWSLK 83 (135)
T ss_pred EEECCCCCCEEecc
Confidence 47899999877654
No 120
>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=61.89 E-value=4.4 Score=18.37 Aligned_cols=8 Identities=38% Similarity=0.962 Sum_probs=2.0
Q ss_pred CCCCcccc
Q psy3492 27 CALCEYKA 34 (85)
Q Consensus 27 c~~c~~~f 34 (85)
|..|++.|
T Consensus 12 C~~C~~~F 19 (69)
T PF01363_consen 12 CMICGKKF 19 (69)
T ss_dssp -TTT--B-
T ss_pred CcCcCCcC
Confidence 44455555
No 121
>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=60.23 E-value=2.8 Score=16.69 Aligned_cols=12 Identities=25% Similarity=0.473 Sum_probs=5.2
Q ss_pred cCCcCccccCCH
Q psy3492 52 ICSKCSFLADDQ 63 (85)
Q Consensus 52 ~C~~c~~~f~~~ 63 (85)
.|.+||+.|..+
T Consensus 5 ~C~eC~~~f~dS 16 (34)
T PF01286_consen 5 KCDECGKPFMDS 16 (34)
T ss_dssp E-TTT--EES-S
T ss_pred hHhHhCCHHHHH
Confidence 467777776654
No 122
>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=59.97 E-value=8.2 Score=24.84 Aligned_cols=22 Identities=36% Similarity=0.637 Sum_probs=20.2
Q ss_pred ccCCcCccccCCHHHHHHHHhh
Q psy3492 51 RICSKCSFLADDQETLNEHLQQ 72 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~ 72 (85)
|.|+.|.+.|.....+..|+..
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~ 79 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQ 79 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHH
Confidence 7899999999999999999874
No 123
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=59.70 E-value=1.3 Score=29.64 Aligned_cols=38 Identities=21% Similarity=0.336 Sum_probs=19.4
Q ss_pred cCCCCccccCChHHHHHHHHhhCCC----ccCCcCccccCCHHH
Q psy3492 26 NCALCEYKAARPERLATHVIKVHNK----RICSKCSFLADDQET 65 (85)
Q Consensus 26 ~c~~c~~~f~~~~~l~~h~~~~h~~----~~C~~c~~~f~~~~~ 65 (85)
.|..||..|+--..|- .- +-++. -.|+.|.+.+..+-+
T Consensus 125 ~CT~CGPRfTIi~alP-YD-R~nTsM~~F~lC~~C~~EY~dP~n 166 (750)
T COG0068 125 NCTNCGPRFTIIEALP-YD-RENTSMADFPLCPFCDKEYKDPLN 166 (750)
T ss_pred ccCCCCcceeeeccCC-CC-cccCccccCcCCHHHHHHhcCccc
Confidence 4677777666543332 11 12222 346666666666644
No 124
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=59.67 E-value=4.1 Score=24.00 Aligned_cols=28 Identities=25% Similarity=0.395 Sum_probs=15.5
Q ss_pred ccCCCCccccCChHHHHHHHHhhCCCccCCcCc
Q psy3492 25 FNCALCEYKAARPERLATHVIKVHNKRICSKCS 57 (85)
Q Consensus 25 ~~c~~c~~~f~~~~~l~~h~~~~h~~~~C~~c~ 57 (85)
-.|..||+...-...| |- ..+ |+|+.|.
T Consensus 221 r~CP~Cg~~W~L~~pl--h~-iFd--FKCD~CR 248 (258)
T PF10071_consen 221 RKCPSCGGDWRLKEPL--HD-IFD--FKCDPCR 248 (258)
T ss_pred CCCCCCCCccccCCch--hh-cee--ccCCcce
Confidence 3577787755544443 11 112 7888774
No 125
>KOG2807|consensus
Probab=59.56 E-value=10 Score=23.37 Aligned_cols=29 Identities=17% Similarity=0.145 Sum_probs=22.6
Q ss_pred ccCCcCccccCCHHHHHHHHhhcccccCc
Q psy3492 51 RICSKCSFLADDQETLNEHLQQHIFWECS 79 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~~~~C~ 79 (85)
|.|..|...|-..-+.-.|-..|..+-|+
T Consensus 346 y~C~~Ck~~FCldCDv~iHesLh~CpgCe 374 (378)
T KOG2807|consen 346 YRCESCKNVFCLDCDVFIHESLHNCPGCE 374 (378)
T ss_pred EEchhccceeeccchHHHHhhhhcCCCcC
Confidence 88889998998888887887777644454
No 126
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=58.73 E-value=4.1 Score=17.03 Aligned_cols=13 Identities=15% Similarity=0.437 Sum_probs=8.6
Q ss_pred ccCCcCccccCCH
Q psy3492 51 RICSKCSFLADDQ 63 (85)
Q Consensus 51 ~~C~~c~~~f~~~ 63 (85)
|.|+.||..|...
T Consensus 4 y~C~~CG~~~~~~ 16 (46)
T PRK00398 4 YKCARCGREVELD 16 (46)
T ss_pred EECCCCCCEEEEC
Confidence 6788887765443
No 127
>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=58.60 E-value=1.7 Score=18.99 Aligned_cols=24 Identities=21% Similarity=0.098 Sum_probs=11.2
Q ss_pred ccCCcCccccCCHHHHHHHHhhcc
Q psy3492 51 RICSKCSFLADDQETLNEHLQQHI 74 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~ 74 (85)
|+|+.|+..|-..-++-.|..+|.
T Consensus 22 y~C~~C~~~FC~dCD~fiHE~LH~ 45 (51)
T PF07975_consen 22 YRCPKCKNHFCIDCDVFIHETLHN 45 (51)
T ss_dssp E--TTTT--B-HHHHHTTTTTS-S
T ss_pred EECCCCCCccccCcChhhhccccC
Confidence 777777777766665555544443
No 128
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=58.32 E-value=3.9 Score=20.84 Aligned_cols=24 Identities=17% Similarity=0.313 Sum_probs=14.0
Q ss_pred ccCCCCccccCChHHHHHHHHhhCCCccCCcCcc
Q psy3492 25 FNCALCEYKAARPERLATHVIKVHNKRICSKCSF 58 (85)
Q Consensus 25 ~~c~~c~~~f~~~~~l~~h~~~~h~~~~C~~c~~ 58 (85)
..|..|+..|.... ..+.||.||.
T Consensus 71 ~~C~~Cg~~~~~~~----------~~~~CP~Cgs 94 (113)
T PRK12380 71 AWCWDCSQVVEIHQ----------HDAQCPHCHG 94 (113)
T ss_pred EEcccCCCEEecCC----------cCccCcCCCC
Confidence 56777876554432 0156888873
No 129
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=58.01 E-value=5.7 Score=16.16 Aligned_cols=15 Identities=20% Similarity=0.434 Sum_probs=12.0
Q ss_pred CccCCCCccccCChH
Q psy3492 24 PFNCALCEYKAARPE 38 (85)
Q Consensus 24 ~~~c~~c~~~f~~~~ 38 (85)
|+.|..|++.|-...
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 788999988887654
No 130
>PRK05978 hypothetical protein; Provisional
Probab=57.30 E-value=3.3 Score=22.31 Aligned_cols=10 Identities=20% Similarity=0.391 Sum_probs=5.6
Q ss_pred cCCcCccccC
Q psy3492 52 ICSKCSFLAD 61 (85)
Q Consensus 52 ~C~~c~~~f~ 61 (85)
.|+.||..|.
T Consensus 54 ~C~~CG~~~~ 63 (148)
T PRK05978 54 HCAACGEDFT 63 (148)
T ss_pred CccccCCccc
Confidence 5666665444
No 131
>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=56.57 E-value=10 Score=16.27 Aligned_cols=8 Identities=25% Similarity=0.663 Sum_probs=3.1
Q ss_pred cCCCCccc
Q psy3492 26 NCALCEYK 33 (85)
Q Consensus 26 ~c~~c~~~ 33 (85)
.|..||+.
T Consensus 20 ~Cr~Cg~~ 27 (57)
T cd00065 20 HCRNCGRI 27 (57)
T ss_pred ccCcCcCC
Confidence 34444433
No 132
>KOG2071|consensus
Probab=55.50 E-value=7.9 Score=25.55 Aligned_cols=24 Identities=29% Similarity=0.591 Sum_probs=20.3
Q ss_pred ccCCcCccccCCHHHHHHHHhhcc
Q psy3492 51 RICSKCSFLADDQETLNEHLQQHI 74 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~ 74 (85)
-.|..||..|.+......||..|.
T Consensus 419 nqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 419 NQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred chhcccccccccchhhhhHhhhhh
Confidence 468889999999988888888776
No 133
>KOG1280|consensus
Probab=54.74 E-value=14 Score=22.90 Aligned_cols=27 Identities=26% Similarity=0.615 Sum_probs=14.6
Q ss_pred CccCCCCccccCChHHHHHHHHhhCCC
Q psy3492 24 PFNCALCEYKAARPERLATHVIKVHNK 50 (85)
Q Consensus 24 ~~~c~~c~~~f~~~~~l~~h~~~~h~~ 50 (85)
.|.|..|+.+-.....+..|+...|..
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hpd 105 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHPE 105 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCcc
Confidence 355666665555555555555444443
No 134
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=54.53 E-value=6.1 Score=20.71 Aligned_cols=13 Identities=15% Similarity=0.312 Sum_probs=11.4
Q ss_pred ccCCcCccccCCH
Q psy3492 51 RICSKCSFLADDQ 63 (85)
Q Consensus 51 ~~C~~c~~~f~~~ 63 (85)
|.|+.|++.|...
T Consensus 54 yrC~~C~~tf~~~ 66 (129)
T COG3677 54 YKCKSCGSTFTVE 66 (129)
T ss_pred cccCCcCcceeee
Confidence 9999999988765
No 135
>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=54.40 E-value=5.6 Score=15.63 Aligned_cols=12 Identities=17% Similarity=0.930 Sum_probs=8.5
Q ss_pred ccCCcCccccCC
Q psy3492 51 RICSKCSFLADD 62 (85)
Q Consensus 51 ~~C~~c~~~f~~ 62 (85)
|+|..||..+..
T Consensus 3 ~~C~~CG~i~~g 14 (34)
T cd00729 3 WVCPVCGYIHEG 14 (34)
T ss_pred EECCCCCCEeEC
Confidence 678888876544
No 136
>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=54.39 E-value=3 Score=21.20 Aligned_cols=13 Identities=15% Similarity=0.276 Sum_probs=7.6
Q ss_pred ccCCCCccccCCh
Q psy3492 25 FNCALCEYKAARP 37 (85)
Q Consensus 25 ~~c~~c~~~f~~~ 37 (85)
+.|..||..|...
T Consensus 71 ~~C~~Cg~~~~~~ 83 (113)
T PF01155_consen 71 ARCRDCGHEFEPD 83 (113)
T ss_dssp EEETTTS-EEECH
T ss_pred EECCCCCCEEecC
Confidence 5677777766553
No 137
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.27 E-value=1.7 Score=25.16 Aligned_cols=20 Identities=25% Similarity=0.517 Sum_probs=14.3
Q ss_pred CCccCCCCccccCChHHHHH
Q psy3492 23 KPFNCALCEYKAARPERLAT 42 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~ 42 (85)
+.++|++|+-.|.....+..
T Consensus 18 k~ieCPvC~tkFkkeev~tg 37 (267)
T COG1655 18 KTIECPVCNTKFKKEEVKTG 37 (267)
T ss_pred ceeccCcccchhhhhheecc
Confidence 67889999888776654433
No 138
>KOG3408|consensus
Probab=53.81 E-value=8.4 Score=20.11 Aligned_cols=23 Identities=22% Similarity=0.456 Sum_probs=20.7
Q ss_pred ccCCcCccccCCHHHHHHHHhhc
Q psy3492 51 RICSKCSFLADDQETLNEHLQQH 73 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h 73 (85)
|-|-+|.+=|.....|..|.++-
T Consensus 58 fyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 58 FYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred eehhhhhhhhcchHHHHHHHhcc
Confidence 88999999999999999998853
No 139
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=53.14 E-value=8.2 Score=20.40 Aligned_cols=26 Identities=19% Similarity=0.609 Sum_probs=18.0
Q ss_pred CccCCCCccccCChHHHHHHHHhhCCCccCCcCc
Q psy3492 24 PFNCALCEYKAARPERLATHVIKVHNKRICSKCS 57 (85)
Q Consensus 24 ~~~c~~c~~~f~~~~~l~~h~~~~h~~~~C~~c~ 57 (85)
|++|..||+.|..-+.- +. -=|+.||
T Consensus 1 PH~Ct~Cg~~f~dgs~e---il-----~GCP~CG 26 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKE---IL-----SGCPECG 26 (131)
T ss_pred CcccCcCCCCcCCCcHH---HH-----ccCcccC
Confidence 67899999999876531 21 2477776
No 140
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=53.06 E-value=2.4 Score=18.93 Aligned_cols=33 Identities=21% Similarity=0.492 Sum_probs=16.8
Q ss_pred ccCCCCccccCCh--HHHHHHHHhhCCC--ccCCcCcc
Q psy3492 25 FNCALCEYKAARP--ERLATHVIKVHNK--RICSKCSF 58 (85)
Q Consensus 25 ~~c~~c~~~f~~~--~~l~~h~~~~h~~--~~C~~c~~ 58 (85)
..|..|++.+.-. +.....+ +...- |.|++|..
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrL-rnrPi~tYmC~eC~~ 39 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRL-RNRPIHTYMCDECKE 39 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHh-hcCCCcceeChhHHH
Confidence 4567777654322 2233333 22221 88888854
No 141
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=52.60 E-value=4.3 Score=25.96 Aligned_cols=15 Identities=13% Similarity=0.607 Sum_probs=11.1
Q ss_pred CCccCCCCccccCCh
Q psy3492 23 KPFNCALCEYKAARP 37 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~ 37 (85)
..|+|..||..+...
T Consensus 424 ~~~~c~~c~~~yd~~ 438 (479)
T PRK05452 424 PRMQCSVCQWIYDPA 438 (479)
T ss_pred CeEEECCCCeEECCC
Confidence 568888888777654
No 142
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=52.60 E-value=6.1 Score=16.59 Aligned_cols=13 Identities=23% Similarity=0.547 Sum_probs=9.2
Q ss_pred ccCCcCccccCCH
Q psy3492 51 RICSKCSFLADDQ 63 (85)
Q Consensus 51 ~~C~~c~~~f~~~ 63 (85)
|.|..||..|.-.
T Consensus 3 Y~C~~Cg~~~~~~ 15 (44)
T smart00659 3 YICGECGRENEIK 15 (44)
T ss_pred EECCCCCCEeecC
Confidence 6788888776643
No 143
>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=51.88 E-value=6 Score=20.23 Aligned_cols=24 Identities=21% Similarity=0.411 Sum_probs=14.2
Q ss_pred ccCCCCccccCChHHHHHHHHhhCCCccCCcCcc
Q psy3492 25 FNCALCEYKAARPERLATHVIKVHNKRICSKCSF 58 (85)
Q Consensus 25 ~~c~~c~~~f~~~~~l~~h~~~~h~~~~C~~c~~ 58 (85)
..|..|+..|..... .+.||.||.
T Consensus 71 ~~C~~Cg~~~~~~~~----------~~~CP~Cgs 94 (115)
T TIGR00100 71 CECEDCSEEVSPEID----------LYRCPKCHG 94 (115)
T ss_pred EEcccCCCEEecCCc----------CccCcCCcC
Confidence 567777766544321 156777774
No 144
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=50.22 E-value=5.2 Score=16.51 Aligned_cols=10 Identities=20% Similarity=0.541 Sum_probs=6.8
Q ss_pred ccCCcCcccc
Q psy3492 51 RICSKCSFLA 60 (85)
Q Consensus 51 ~~C~~c~~~f 60 (85)
-.|+.||..|
T Consensus 30 ~~CpYCg~~y 39 (40)
T PF10276_consen 30 VVCPYCGTRY 39 (40)
T ss_dssp EEETTTTEEE
T ss_pred EECCCCCCEE
Confidence 4677777665
No 145
>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 COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=49.73 E-value=3.4 Score=23.34 Aligned_cols=35 Identities=17% Similarity=0.403 Sum_probs=18.5
Q ss_pred ccCCCCccccCChHHHHHHHHhhCCC------ccCCcCccccCC
Q psy3492 25 FNCALCEYKAARPERLATHVIKVHNK------RICSKCSFLADD 62 (85)
Q Consensus 25 ~~c~~c~~~f~~~~~l~~h~~~~h~~------~~C~~c~~~f~~ 62 (85)
..|.+||..+.....+ .- .-|.| +.|..||+.++.
T Consensus 15 ~~CPvCg~~l~~~~~~--~~-IPyFG~V~i~t~~C~~CgYR~~D 55 (201)
T COG1779 15 IDCPVCGGTLKAHMYL--YD-IPYFGEVLISTGVCERCGYRSTD 55 (201)
T ss_pred ecCCcccceeeEEEee--ec-CCccceEEEEEEEccccCCcccc
Confidence 4677777643332221 11 23444 568888766543
No 147
>KOG0801|consensus
Probab=49.66 E-value=4.8 Score=22.12 Aligned_cols=23 Identities=22% Similarity=0.447 Sum_probs=14.5
Q ss_pred HHHHHHHhhCCCccCCcCccccCC
Q psy3492 39 RLATHVIKVHNKRICSKCSFLADD 62 (85)
Q Consensus 39 ~l~~h~~~~h~~~~C~~c~~~f~~ 62 (85)
+|-.|+ ..|.|++|+.|.|....
T Consensus 128 slP~hi-~~~~g~KCPvC~K~V~s 150 (205)
T KOG0801|consen 128 SLPVHI-MDHSGMKCPVCHKVVPS 150 (205)
T ss_pred ccceee-eccCCccCCccccccCC
Confidence 444555 55666888888775443
No 148
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=49.25 E-value=26 Score=17.65 Aligned_cols=33 Identities=6% Similarity=0.060 Sum_probs=23.8
Q ss_pred CCCCcccccChHHHHHHHHhcC-CCccCCCCccc
Q psy3492 1 MPRLQVLISYNWCLKRHLNTHI-KPFNCALCEYK 33 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~~h~-~~~~c~~c~~~ 33 (85)
|+.-|..|..-..+...+.... +.+.|...|+.
T Consensus 6 i~~T~EiF~dYe~Y~~R~~~y~~~vwtC~~TGk~ 39 (102)
T PF10537_consen 6 IPFTGEIFRDYEEYLKRMILYNQRVWTCEITGKS 39 (102)
T ss_pred eCCCCcccCCHHHHHHHHHHHhCCeeEEecCCCC
Confidence 4566777888777777766666 77888887764
No 149
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=49.05 E-value=9 Score=18.93 Aligned_cols=14 Identities=21% Similarity=0.740 Sum_probs=12.5
Q ss_pred CCccCCCCccccCC
Q psy3492 23 KPFNCALCEYKAAR 36 (85)
Q Consensus 23 ~~~~c~~c~~~f~~ 36 (85)
+|-.|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 88999999998876
No 150
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=49.01 E-value=5.9 Score=17.16 Aligned_cols=20 Identities=15% Similarity=0.225 Sum_probs=13.5
Q ss_pred CCccCCCCccccCChHHHHH
Q psy3492 23 KPFNCALCEYKAARPERLAT 42 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~ 42 (85)
+.+.|..||..|.....=+.
T Consensus 3 k~l~C~dCg~~FvfTa~EQ~ 22 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAGEQK 22 (49)
T ss_pred eeEEcccCCCeEEEehhHHH
Confidence 35678888888776654433
No 151
>KOG2636|consensus
Probab=48.58 E-value=12 Score=24.04 Aligned_cols=21 Identities=14% Similarity=0.616 Sum_probs=18.6
Q ss_pred ccCCcCc-cccCCHHHHHHHHh
Q psy3492 51 RICSKCS-FLADDQETLNEHLQ 71 (85)
Q Consensus 51 ~~C~~c~-~~f~~~~~l~~h~~ 71 (85)
|.|.+|| +.+..+..+.+|..
T Consensus 402 y~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 402 YNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred cceeeccCccccCcHHHHHHhH
Confidence 9999999 88999999988855
No 152
>PRK01343 zinc-binding protein; Provisional
Probab=48.29 E-value=9.8 Score=17.06 Aligned_cols=9 Identities=11% Similarity=0.013 Sum_probs=6.6
Q ss_pred CCCCccccc
Q psy3492 1 MPRLQVLIS 9 (85)
Q Consensus 1 c~~c~~~f~ 9 (85)
||+|++.+.
T Consensus 12 CP~C~k~~~ 20 (57)
T PRK01343 12 CPECGKPST 20 (57)
T ss_pred CCCCCCcCc
Confidence 788888764
No 153
>KOG0227|consensus
Probab=48.16 E-value=11 Score=21.38 Aligned_cols=25 Identities=24% Similarity=0.359 Sum_probs=16.2
Q ss_pred hhCCC-ccCCcCccccCCHHHHHHHH
Q psy3492 46 KVHNK-RICSKCSFLADDQETLNEHL 70 (85)
Q Consensus 46 ~~h~~-~~C~~c~~~f~~~~~l~~h~ 70 (85)
+.|+| |.|..|...-.+-.+...|.
T Consensus 48 kNh~G~yeCkLClT~H~ne~Syl~Ht 73 (222)
T KOG0227|consen 48 KNHLGKYECKLCLTLHNNEGSYLAHT 73 (222)
T ss_pred hccCcceeehhhhhhhcchhhhhhhh
Confidence 46667 88887766666665555553
No 154
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=48.08 E-value=5.3 Score=16.51 Aligned_cols=16 Identities=25% Similarity=0.563 Sum_probs=9.8
Q ss_pred CCccCCCCccccCChH
Q psy3492 23 KPFNCALCEYKAARPE 38 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~ 38 (85)
.|+.|..|++.|-...
T Consensus 12 ~~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKH 27 (43)
T ss_dssp SHEE-TTTS-EE-TTT
T ss_pred CCeECCCCCcccCccc
Confidence 4688888988887654
No 155
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.04 E-value=11 Score=17.16 Aligned_cols=8 Identities=25% Similarity=1.057 Sum_probs=5.4
Q ss_pred ccCCcCcc
Q psy3492 51 RICSKCSF 58 (85)
Q Consensus 51 ~~C~~c~~ 58 (85)
|.|++|..
T Consensus 32 ymC~eC~~ 39 (68)
T COG4896 32 YMCPECEH 39 (68)
T ss_pred EechhhHh
Confidence 77777753
No 156
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=48.02 E-value=12 Score=14.20 Aligned_cols=10 Identities=40% Similarity=0.557 Sum_probs=6.7
Q ss_pred ccCCcCcccc
Q psy3492 51 RICSKCSFLA 60 (85)
Q Consensus 51 ~~C~~c~~~f 60 (85)
|.|..|++.+
T Consensus 28 f~C~~C~~~L 37 (39)
T smart00132 28 FKCSKCGKPL 37 (39)
T ss_pred CCCcccCCcC
Confidence 6777777654
No 157
>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=47.15 E-value=5.7 Score=15.91 Aligned_cols=10 Identities=40% Similarity=0.959 Sum_probs=6.4
Q ss_pred cCCcCccccC
Q psy3492 52 ICSKCSFLAD 61 (85)
Q Consensus 52 ~C~~c~~~f~ 61 (85)
.|+.||+.|.
T Consensus 3 ~C~~Cg~~Yh 12 (36)
T PF05191_consen 3 ICPKCGRIYH 12 (36)
T ss_dssp EETTTTEEEE
T ss_pred CcCCCCCccc
Confidence 4677776654
No 158
>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=47.05 E-value=11 Score=18.88 Aligned_cols=14 Identities=29% Similarity=0.446 Sum_probs=11.4
Q ss_pred CCccCCCCccccCC
Q psy3492 23 KPFNCALCEYKAAR 36 (85)
Q Consensus 23 ~~~~c~~c~~~f~~ 36 (85)
+|.+|..||..|..
T Consensus 78 ~~~rC~eCG~~fkL 91 (97)
T cd00924 78 KPKRCPECGHVFKL 91 (97)
T ss_pred CceeCCCCCcEEEE
Confidence 78899999987753
No 159
>PTZ00448 hypothetical protein; Provisional
Probab=46.79 E-value=20 Score=22.45 Aligned_cols=23 Identities=22% Similarity=0.619 Sum_probs=20.2
Q ss_pred ccCCcCccccCCHHHHHHHHhhc
Q psy3492 51 RICSKCSFLADDQETLNEHLQQH 73 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h 73 (85)
|.|..|+-.|......+.|.++-
T Consensus 315 ~tC~~C~v~F~~~~~qR~H~KSD 337 (373)
T PTZ00448 315 LLCRKCNIQLMDHNAFKQHYRSE 337 (373)
T ss_pred ccccccccccCCHHHHHHHhhhh
Confidence 88999999999888999998853
No 160
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=46.52 E-value=7.3 Score=13.84 Aligned_cols=6 Identities=33% Similarity=1.243 Sum_probs=2.6
Q ss_pred CCcCcc
Q psy3492 53 CSKCSF 58 (85)
Q Consensus 53 C~~c~~ 58 (85)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 444443
No 161
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=45.95 E-value=11 Score=16.70 Aligned_cols=12 Identities=17% Similarity=0.313 Sum_probs=7.7
Q ss_pred ccCCcCccccCC
Q psy3492 51 RICSKCSFLADD 62 (85)
Q Consensus 51 ~~C~~c~~~f~~ 62 (85)
+.|+.||..+.-
T Consensus 3 ~~CP~CG~~iev 14 (54)
T TIGR01206 3 FECPDCGAEIEL 14 (54)
T ss_pred cCCCCCCCEEec
Confidence 467788765543
No 162
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=45.58 E-value=9 Score=19.67 Aligned_cols=12 Identities=17% Similarity=0.395 Sum_probs=7.5
Q ss_pred ccCCCCccccCC
Q psy3492 25 FNCALCEYKAAR 36 (85)
Q Consensus 25 ~~c~~c~~~f~~ 36 (85)
+.|..||..|..
T Consensus 72 ~~C~~Cg~~~~~ 83 (117)
T PRK00564 72 LECKDCSHVFKP 83 (117)
T ss_pred EEhhhCCCcccc
Confidence 567777755443
No 163
>PRK12722 transcriptional activator FlhC; Provisional
Probab=44.84 E-value=21 Score=20.11 Aligned_cols=13 Identities=15% Similarity=0.312 Sum_probs=6.9
Q ss_pred CCccCCCCccccC
Q psy3492 23 KPFNCALCEYKAA 35 (85)
Q Consensus 23 ~~~~c~~c~~~f~ 35 (85)
....|..||..|.
T Consensus 133 ~l~~C~~Cgg~fv 145 (187)
T PRK12722 133 QLSSCNCCGGHFV 145 (187)
T ss_pred eeccCCCCCCCee
Confidence 4445555655554
No 164
>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=44.51 E-value=8.8 Score=14.55 Aligned_cols=9 Identities=22% Similarity=0.571 Sum_probs=5.0
Q ss_pred cCCCCcccc
Q psy3492 26 NCALCEYKA 34 (85)
Q Consensus 26 ~c~~c~~~f 34 (85)
.|..|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 355566555
No 165
>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=44.29 E-value=9.9 Score=14.83 Aligned_cols=11 Identities=27% Similarity=0.754 Sum_probs=6.0
Q ss_pred ccCCcCccccC
Q psy3492 51 RICSKCSFLAD 61 (85)
Q Consensus 51 ~~C~~c~~~f~ 61 (85)
|.|..||..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 45666665544
No 166
>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=43.76 E-value=8.9 Score=20.31 Aligned_cols=8 Identities=25% Similarity=0.712 Sum_probs=4.0
Q ss_pred ccCCcCcc
Q psy3492 51 RICSKCSF 58 (85)
Q Consensus 51 ~~C~~c~~ 58 (85)
|.|..|+.
T Consensus 144 ~~C~~C~~ 151 (157)
T PF10263_consen 144 YRCGRCGG 151 (157)
T ss_pred EECCCCCC
Confidence 45555543
No 167
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=43.61 E-value=13 Score=15.03 Aligned_cols=9 Identities=22% Similarity=0.135 Sum_probs=4.0
Q ss_pred CCCCccccc
Q psy3492 1 MPRLQVLIS 9 (85)
Q Consensus 1 c~~c~~~f~ 9 (85)
|+.|++.|-
T Consensus 5 CprC~kg~H 13 (36)
T PF14787_consen 5 CPRCGKGFH 13 (36)
T ss_dssp -TTTSSSCS
T ss_pred CcccCCCcc
Confidence 455555543
No 168
>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=43.53 E-value=7.3 Score=15.35 Aligned_cols=20 Identities=20% Similarity=0.448 Sum_probs=12.0
Q ss_pred ccCCcCccccCCHHHHHHHHh
Q psy3492 51 RICSKCSFLADDQETLNEHLQ 71 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~ 71 (85)
+.|+.|++.+... -+..|+.
T Consensus 5 ~~C~nC~R~v~a~-RfA~HLe 24 (33)
T PF08209_consen 5 VECPNCGRPVAAS-RFAPHLE 24 (33)
T ss_dssp EE-TTTSSEEEGG-GHHHHHH
T ss_pred EECCCCcCCcchh-hhHHHHH
Confidence 6789998866544 3455553
No 169
>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=43.48 E-value=18 Score=16.28 Aligned_cols=13 Identities=31% Similarity=0.759 Sum_probs=10.1
Q ss_pred ccCCcCccccCCH
Q psy3492 51 RICSKCSFLADDQ 63 (85)
Q Consensus 51 ~~C~~c~~~f~~~ 63 (85)
|.|+.||......
T Consensus 47 ~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 47 FTCPNCGFEMDRD 59 (69)
T ss_pred EEcCCCCCEECcH
Confidence 8999999876554
No 170
>KOG0978|consensus
Probab=42.81 E-value=6.8 Score=26.46 Aligned_cols=19 Identities=26% Similarity=0.513 Sum_probs=14.9
Q ss_pred ccCCcCccccCCHHHHHHH
Q psy3492 51 RICSKCSFLADDQETLNEH 69 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h 69 (85)
.+||.|+.+|...+.+..|
T Consensus 679 RKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 679 RKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred CCCCCCCCCCCcccccccC
Confidence 6899999999887765443
No 171
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=42.59 E-value=13 Score=17.01 Aligned_cols=8 Identities=38% Similarity=0.833 Sum_probs=5.4
Q ss_pred ccCCcCcc
Q psy3492 51 RICSKCSF 58 (85)
Q Consensus 51 ~~C~~c~~ 58 (85)
|.|++||.
T Consensus 1 y~C~KCg~ 8 (64)
T PF09855_consen 1 YKCPKCGN 8 (64)
T ss_pred CCCCCCCC
Confidence 56777764
No 172
>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=42.50 E-value=13 Score=15.22 Aligned_cols=8 Identities=25% Similarity=0.750 Sum_probs=4.8
Q ss_pred ccCCcCcc
Q psy3492 51 RICSKCSF 58 (85)
Q Consensus 51 ~~C~~c~~ 58 (85)
|.|+.||.
T Consensus 1 m~Cp~Cg~ 8 (43)
T PF08271_consen 1 MKCPNCGS 8 (43)
T ss_dssp ESBTTTSS
T ss_pred CCCcCCcC
Confidence 35666664
No 173
>PLN02294 cytochrome c oxidase subunit Vb
Probab=41.58 E-value=14 Score=20.51 Aligned_cols=18 Identities=22% Similarity=0.458 Sum_probs=13.5
Q ss_pred hcC-CCccCCCCccccCCh
Q psy3492 20 THI-KPFNCALCEYKAARP 37 (85)
Q Consensus 20 ~h~-~~~~c~~c~~~f~~~ 37 (85)
.+. +|.+|..||..|...
T Consensus 136 L~kGkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 136 LEKGKSFECPVCTQYFELE 154 (174)
T ss_pred ecCCCceeCCCCCCEEEEE
Confidence 344 889999999887643
No 174
>PRK12860 transcriptional activator FlhC; Provisional
Probab=41.11 E-value=22 Score=20.09 Aligned_cols=13 Identities=23% Similarity=0.378 Sum_probs=6.3
Q ss_pred CCccCCCCccccC
Q psy3492 23 KPFNCALCEYKAA 35 (85)
Q Consensus 23 ~~~~c~~c~~~f~ 35 (85)
....|..||..|.
T Consensus 133 ~l~~C~~Cgg~fv 145 (189)
T PRK12860 133 QLARCCRCGGKFV 145 (189)
T ss_pred eeccCCCCCCCee
Confidence 3444555555444
No 175
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.96 E-value=11 Score=17.19 Aligned_cols=36 Identities=19% Similarity=0.267 Sum_probs=20.9
Q ss_pred CCccCCCCccccCChHHHHHHHHhhCCC-ccCCcCccccC
Q psy3492 23 KPFNCALCEYKAARPERLATHVIKVHNK-RICSKCSFLAD 61 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~~f~ 61 (85)
.++.|..-+..+..+..+ +..-..| -.|+.|++.|.
T Consensus 23 ~~l~C~g~~~p~~HPrV~---L~mg~~gev~CPYC~t~y~ 59 (62)
T COG4391 23 LPLMCPGPEPPNDHPRVF---LDMGDEGEVVCPYCSTRYR 59 (62)
T ss_pred eeEEcCCCCCCCCCCEEE---EEcCCCCcEecCccccEEE
Confidence 677787665555544322 1111222 67999998775
No 176
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=40.80 E-value=20 Score=19.15 Aligned_cols=17 Identities=41% Similarity=0.382 Sum_probs=8.8
Q ss_pred CCcccccChHHHHHHHHhcC
Q psy3492 3 RLQVLISYNWCLKRHLNTHI 22 (85)
Q Consensus 3 ~c~~~f~~~~~l~~h~~~h~ 22 (85)
++|+.| .+|++|..+|.
T Consensus 81 EDGkkf---KSLKRHL~t~~ 97 (148)
T COG4957 81 EDGKKF---KSLKRHLTTHY 97 (148)
T ss_pred ccCcch---HHHHHHHhccc
Confidence 455555 23556665543
No 177
>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=40.77 E-value=9.9 Score=15.32 Aligned_cols=9 Identities=22% Similarity=0.741 Sum_probs=4.4
Q ss_pred ccCCcCccc
Q psy3492 51 RICSKCSFL 59 (85)
Q Consensus 51 ~~C~~c~~~ 59 (85)
|+|..||..
T Consensus 7 YkC~~CGni 15 (36)
T PF06397_consen 7 YKCEHCGNI 15 (36)
T ss_dssp EE-TTT--E
T ss_pred EEccCCCCE
Confidence 788888753
No 178
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.30 E-value=24 Score=18.18 Aligned_cols=12 Identities=8% Similarity=0.052 Sum_probs=6.2
Q ss_pred CCccCCCCcccc
Q psy3492 23 KPFNCALCEYKA 34 (85)
Q Consensus 23 ~~~~c~~c~~~f 34 (85)
.|..|..||+.|
T Consensus 25 dPiVsPytG~s~ 36 (129)
T COG4530 25 DPIVSPYTGKSY 36 (129)
T ss_pred CccccCcccccc
Confidence 345555555555
No 179
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=40.09 E-value=11 Score=13.68 Aligned_cols=6 Identities=33% Similarity=1.237 Sum_probs=3.0
Q ss_pred CCcCcc
Q psy3492 53 CSKCSF 58 (85)
Q Consensus 53 C~~c~~ 58 (85)
|+.||.
T Consensus 19 C~~CG~ 24 (26)
T PF13248_consen 19 CPNCGA 24 (26)
T ss_pred ChhhCC
Confidence 555554
No 180
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=39.74 E-value=12 Score=16.82 Aligned_cols=9 Identities=11% Similarity=0.043 Sum_probs=3.6
Q ss_pred CCCCccccc
Q psy3492 1 MPRLQVLIS 9 (85)
Q Consensus 1 c~~c~~~f~ 9 (85)
||+|++.+.
T Consensus 5 CP~C~k~~~ 13 (57)
T PF03884_consen 5 CPICGKPVE 13 (57)
T ss_dssp -TTT--EEE
T ss_pred CCCCCCeec
Confidence 667776543
No 181
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=39.69 E-value=15 Score=18.91 Aligned_cols=33 Identities=18% Similarity=0.337 Sum_probs=17.9
Q ss_pred CCccCCCCccccCChHHHHHHHHhhCCCccCCcCccccCCHHH
Q psy3492 23 KPFNCALCEYKAARPERLATHVIKVHNKRICSKCSFLADDQET 65 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~h~~~~h~~~~C~~c~~~f~~~~~ 65 (85)
...+|+.|++...-... . ..|..|+....-..+
T Consensus 68 v~V~CP~C~K~TKmLGr----~------D~CM~C~~pLTLd~~ 100 (114)
T PF11023_consen 68 VQVECPNCGKQTKMLGR----V------DACMHCKEPLTLDPS 100 (114)
T ss_pred eeeECCCCCChHhhhch----h------hccCcCCCcCccCch
Confidence 66788888765322111 0 467777655444433
No 182
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=39.04 E-value=10 Score=21.52 Aligned_cols=21 Identities=19% Similarity=0.468 Sum_probs=0.0
Q ss_pred ccCCcCc-cccCCHHHHHHHHh
Q psy3492 51 RICSKCS-FLADDQETLNEHLQ 71 (85)
Q Consensus 51 ~~C~~c~-~~f~~~~~l~~h~~ 71 (85)
|.|.+|| ..+..+..+.+|..
T Consensus 102 y~CEICGN~~Y~GrkaFekHF~ 123 (196)
T PF11931_consen 102 YKCEICGNQSYKGRKAFEKHFQ 123 (196)
T ss_dssp ----------------------
T ss_pred eeeEeCCCcceecHHHHHHhcC
Confidence 9999998 46667777777754
No 183
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=38.79 E-value=17 Score=18.38 Aligned_cols=17 Identities=18% Similarity=0.376 Sum_probs=13.3
Q ss_pred CCccCCCCccccCChHH
Q psy3492 23 KPFNCALCEYKAARPER 39 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~ 39 (85)
.|+.|..||..|..-+.
T Consensus 1 MpH~CtrCG~vf~~g~~ 17 (112)
T COG3364 1 MPHQCTRCGEVFDDGSE 17 (112)
T ss_pred CCceecccccccccccH
Confidence 37889999999987543
No 184
>KOG3002|consensus
Probab=38.41 E-value=34 Score=20.81 Aligned_cols=56 Identities=18% Similarity=0.229 Sum_probs=27.7
Q ss_pred CCccCCCCccccCChHHHHHHHHhhCCC--ccCC----cCccccCCHHHHHHHHhhcc--cccCcCC
Q psy3492 23 KPFNCALCEYKAARPERLATHVIKVHNK--RICS----KCSFLADDQETLNEHLQQHI--FWECSFQ 81 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~h~~~~h~~--~~C~----~c~~~f~~~~~l~~h~~~h~--~~~C~~~ 81 (85)
+..+|..|...+.....+. ++.+-.. ..|+ .|.+.|..... ..|.+.-. ++.||.+
T Consensus 79 ~~~~CP~Cr~~~g~~R~~a--mEkV~e~~~vpC~~~~~GC~~~~~Y~~~-~~HE~~C~f~~~~CP~p 142 (299)
T KOG3002|consen 79 VSNKCPTCRLPIGNIRCRA--MEKVAEAVLVPCKNAKLGCTKSFPYGEK-SKHEKVCEFRPCSCPVP 142 (299)
T ss_pred hcccCCccccccccHHHHH--HHHHHHhceecccccccCCceeeccccc-cccccccccCCcCCCCC
Confidence 3455666665555433322 2222222 4454 36666666655 45555333 6667665
No 185
>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=38.16 E-value=23 Score=21.31 Aligned_cols=31 Identities=19% Similarity=0.465 Sum_probs=15.5
Q ss_pred ccCCCCccccCChHHHHHHHHhhCCCccCCcCccccCC
Q psy3492 25 FNCALCEYKAARPERLATHVIKVHNKRICSKCSFLADD 62 (85)
Q Consensus 25 ~~c~~c~~~f~~~~~l~~h~~~~h~~~~C~~c~~~f~~ 62 (85)
.+|..|+.....+ .|.... +.|++||.-|.-
T Consensus 27 ~~c~~c~~~~~~~-~l~~~~------~vc~~c~~h~rl 57 (285)
T TIGR00515 27 TKCPKCGQVLYTK-ELERNL------EVCPKCDHHMRM 57 (285)
T ss_pred eECCCCcchhhHH-HHHhhC------CCCCCCCCcCcC
Confidence 3566666543322 232222 577777765543
No 186
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=37.91 E-value=3.3 Score=16.56 Aligned_cols=6 Identities=33% Similarity=1.326 Sum_probs=2.3
Q ss_pred cCCcCc
Q psy3492 52 ICSKCS 57 (85)
Q Consensus 52 ~C~~c~ 57 (85)
.|..||
T Consensus 23 sC~~CG 28 (35)
T PF07503_consen 23 SCTNCG 28 (35)
T ss_dssp -BTTCC
T ss_pred cCCCCC
Confidence 344444
No 187
>PHA02998 RNA polymerase subunit; Provisional
Probab=37.90 E-value=5.9 Score=22.12 Aligned_cols=37 Identities=16% Similarity=0.358 Sum_probs=20.6
Q ss_pred ccCCCCccccCChHHHHHHHHhhCCC----ccCCcCccccCCH
Q psy3492 25 FNCALCEYKAARPERLATHVIKVHNK----RICSKCSFLADDQ 63 (85)
Q Consensus 25 ~~c~~c~~~f~~~~~l~~h~~~~h~~----~~C~~c~~~f~~~ 63 (85)
..|..|+..-.....++ .|....+ |.|..||+.|.-+
T Consensus 144 v~CPkCg~~~A~f~qlQ--TRSADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 144 TPCPNCKSKNTTPMMIQ--TRAADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCCceEEEEEe--eccCCCCceEEEEcCCCCCccCCc
Confidence 56777875433322222 2122223 8999999877655
No 188
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=37.81 E-value=30 Score=21.05 Aligned_cols=13 Identities=23% Similarity=0.746 Sum_probs=7.9
Q ss_pred ccCCcCccccCCH
Q psy3492 51 RICSKCSFLADDQ 63 (85)
Q Consensus 51 ~~C~~c~~~f~~~ 63 (85)
+.|+.||.-|.-.
T Consensus 58 ~vcp~c~~h~rlt 70 (296)
T CHL00174 58 NICEQCGYHLKMS 70 (296)
T ss_pred CCCCCCCCCcCCC
Confidence 5677777655433
No 189
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=37.76 E-value=6.9 Score=26.62 Aligned_cols=8 Identities=25% Similarity=0.912 Sum_probs=4.3
Q ss_pred ccCCcCcc
Q psy3492 51 RICSKCSF 58 (85)
Q Consensus 51 ~~C~~c~~ 58 (85)
..|+.||.
T Consensus 476 ~~Cp~Cgs 483 (730)
T COG1198 476 QSCPECGS 483 (730)
T ss_pred CCCCCCCC
Confidence 45666653
No 190
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=37.67 E-value=18 Score=15.48 Aligned_cols=11 Identities=18% Similarity=0.238 Sum_probs=5.8
Q ss_pred CCCCcccccCh
Q psy3492 1 MPRLQVLISYN 11 (85)
Q Consensus 1 c~~c~~~f~~~ 11 (85)
||.||..|.-.
T Consensus 1 CP~Cg~~f~C~ 11 (50)
T PF14375_consen 1 CPRCGAPFECG 11 (50)
T ss_pred CCCCCCcCCCC
Confidence 45566555443
No 191
>KOG4602|consensus
Probab=37.14 E-value=11 Score=22.39 Aligned_cols=36 Identities=28% Similarity=0.576 Sum_probs=18.1
Q ss_pred CccCCCCccccCChHHHHHHHHhhCCC---------ccCCcCccc
Q psy3492 24 PFNCALCEYKAARPERLATHVIKVHNK---------RICSKCSFL 59 (85)
Q Consensus 24 ~~~c~~c~~~f~~~~~l~~h~~~~h~~---------~~C~~c~~~ 59 (85)
+.-|..|...-.....+..|..+...| |.|++||..
T Consensus 233 ~l~CvFC~nN~E~~A~y~tH~lkd~dgRVLCPkLR~YVCPiCGAT 277 (318)
T KOG4602|consen 233 PLCCVFCFNNAEEFARYHTHPLKDKDGRVLCPKLRSYVCPICGAT 277 (318)
T ss_pred ceeEEeecCCCchhhheecccccCCCCcEechhHhhhcCcccccc
Confidence 345666654433334444443222222 888888854
No 192
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.82 E-value=17 Score=16.69 Aligned_cols=8 Identities=13% Similarity=0.131 Sum_probs=5.5
Q ss_pred CCCCcccc
Q psy3492 1 MPRLQVLI 8 (85)
Q Consensus 1 c~~c~~~f 8 (85)
||.||+..
T Consensus 10 CP~Cgkpv 17 (65)
T COG3024 10 CPTCGKPV 17 (65)
T ss_pred CCCCCCcc
Confidence 67777754
No 193
>PF14369 zf-RING_3: zinc-finger
Probab=35.97 E-value=19 Score=14.26 Aligned_cols=8 Identities=25% Similarity=0.185 Sum_probs=4.2
Q ss_pred CCCCcccc
Q psy3492 1 MPRLQVLI 8 (85)
Q Consensus 1 c~~c~~~f 8 (85)
||.|+..|
T Consensus 24 CP~C~~gF 31 (35)
T PF14369_consen 24 CPRCHGGF 31 (35)
T ss_pred CcCCCCcE
Confidence 45555544
No 194
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=35.77 E-value=34 Score=18.96 Aligned_cols=17 Identities=29% Similarity=0.516 Sum_probs=13.4
Q ss_pred ccCCcCccccCCHHHHH
Q psy3492 51 RICSKCSFLADDQETLN 67 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~ 67 (85)
..|..||+.|.....+.
T Consensus 115 ~~C~~Cg~~f~~~k~i~ 131 (181)
T PRK08222 115 QRCSRCERPFAPQKTVA 131 (181)
T ss_pred CcCcccCCccCcHhHHH
Confidence 78999999998665543
No 195
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=35.66 E-value=34 Score=13.78 Aligned_cols=18 Identities=22% Similarity=0.481 Sum_probs=12.0
Q ss_pred ccCCcCccccCCHHHHHH
Q psy3492 51 RICSKCSFLADDQETLNE 68 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~ 68 (85)
+.|+.|+-.+.....|.+
T Consensus 20 d~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 20 DVCPSCGGIWFDAGELEK 37 (41)
T ss_pred EECCCCCeEEccHHHHHH
Confidence 667777776666666544
No 196
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=35.32 E-value=16 Score=19.89 Aligned_cols=30 Identities=30% Similarity=0.667 Sum_probs=14.0
Q ss_pred CccCCCCccccCChHHHHHHHHhhCCC--ccCCcCcc
Q psy3492 24 PFNCALCEYKAARPERLATHVIKVHNK--RICSKCSF 58 (85)
Q Consensus 24 ~~~c~~c~~~f~~~~~l~~h~~~~h~~--~~C~~c~~ 58 (85)
+|.|. |+.-+.... +|- .+-.| |.|..|+-
T Consensus 117 ~Y~C~-C~q~~l~~R---Rhn-~~~~g~~YrC~~C~g 148 (156)
T COG3091 117 PYRCQ-CQQHYLRIR---RHN-TVRRGEVYRCGKCGG 148 (156)
T ss_pred eEEee-cCCccchhh---hcc-cccccceEEeccCCc
Confidence 46666 665544322 221 22223 66666653
No 197
>KOG0402|consensus
Probab=33.27 E-value=41 Score=16.41 Aligned_cols=31 Identities=16% Similarity=0.510 Sum_probs=20.2
Q ss_pred CCccCCCCccccCChHHHHHHHHhhCCC-ccCCcCccccCC
Q psy3492 23 KPFNCALCEYKAARPERLATHVIKVHNK-RICSKCSFLADD 62 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~~f~~ 62 (85)
-.|.|..||+. .++ +...| |.|..|.+.+..
T Consensus 35 aky~CsfCGK~-----~vK----R~AvGiW~C~~C~kv~ag 66 (92)
T KOG0402|consen 35 AKYTCSFCGKK-----TVK----RKAVGIWKCGSCKKVVAG 66 (92)
T ss_pred hhhhhhhcchh-----hhh----hhceeEEecCCccceecc
Confidence 56888888864 221 34556 888888776543
No 198
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=33.21 E-value=17 Score=14.21 Aligned_cols=11 Identities=18% Similarity=0.422 Sum_probs=7.8
Q ss_pred ccCCcCccccC
Q psy3492 51 RICSKCSFLAD 61 (85)
Q Consensus 51 ~~C~~c~~~f~ 61 (85)
+.|..||..|.
T Consensus 22 ~~C~~Cg~~~~ 32 (33)
T PF08792_consen 22 EVCIFCGSSFP 32 (33)
T ss_pred EEcccCCcEee
Confidence 67888887653
No 199
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=32.94 E-value=14 Score=21.12 Aligned_cols=23 Identities=17% Similarity=0.427 Sum_probs=0.0
Q ss_pred ccCCcCccccCCHHHHHHHHhhcc
Q psy3492 51 RICSKCSFLADDQETLNEHLQQHI 74 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~ 74 (85)
..|+.||...... .+..|+|+..
T Consensus 169 ~~cPitGe~IP~~-e~~eHmRi~L 191 (229)
T PF12230_consen 169 IICPITGEMIPAD-EMDEHMRIEL 191 (229)
T ss_dssp ------------------------
T ss_pred ccccccccccccc-cccccccccc
Confidence 6899999876665 6899999876
No 200
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=32.61 E-value=21 Score=22.40 Aligned_cols=21 Identities=24% Similarity=0.447 Sum_probs=18.3
Q ss_pred ccCCcCccccCCHHHHHHHHh
Q psy3492 51 RICSKCSFLADDQETLNEHLQ 71 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~ 71 (85)
+=|+.|++.|..+..+..|+.
T Consensus 239 ~YC~~C~r~f~~~~VFe~Hl~ 259 (470)
T COG5188 239 VYCVKCGREFSRSKVFEYHLE 259 (470)
T ss_pred eeeHhhhhHhhhhHHHHHHHh
Confidence 458999999999999999875
No 201
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=32.43 E-value=20 Score=15.35 Aligned_cols=24 Identities=17% Similarity=0.196 Sum_probs=10.3
Q ss_pred ccCChHHHHHHHHhhCCCccCCcCcc
Q psy3492 33 KAARPERLATHVIKVHNKRICSKCSF 58 (85)
Q Consensus 33 ~f~~~~~l~~h~~~~h~~~~C~~c~~ 58 (85)
.|...+.|.... . ...|.|+.|++
T Consensus 26 CFDl~~fl~~~~-~-~~~W~CPiC~~ 49 (50)
T PF02891_consen 26 CFDLESFLESNQ-R-TPKWKCPICNK 49 (50)
T ss_dssp -EEHHHHHHHHH-H-S---B-TTT--
T ss_pred eECHHHHHHHhh-c-cCCeECcCCcC
Confidence 366666665444 2 22289999875
No 202
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=32.34 E-value=19 Score=15.99 Aligned_cols=8 Identities=13% Similarity=-0.023 Sum_probs=3.5
Q ss_pred CCCCcccc
Q psy3492 1 MPRLQVLI 8 (85)
Q Consensus 1 c~~c~~~f 8 (85)
|++||+.|
T Consensus 8 C~~Cg~~~ 15 (54)
T PF14446_consen 8 CPVCGKKF 15 (54)
T ss_pred ChhhCCcc
Confidence 34444444
No 203
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=32.30 E-value=38 Score=16.69 Aligned_cols=17 Identities=6% Similarity=-0.105 Sum_probs=11.1
Q ss_pred CCCCcccccChHHHHHH
Q psy3492 1 MPRLQVLISYNWCLKRH 17 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h 17 (85)
|+.||..|-....+..-
T Consensus 38 C~~CGe~y~~dev~~eI 54 (89)
T TIGR03829 38 CSHCGMEYQDDTTVKEI 54 (89)
T ss_pred ccCCCcEeecHHHHHHH
Confidence 67778777766655433
No 204
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=31.98 E-value=17 Score=19.25 Aligned_cols=9 Identities=33% Similarity=0.574 Sum_probs=4.5
Q ss_pred ccCCcCccc
Q psy3492 51 RICSKCSFL 59 (85)
Q Consensus 51 ~~C~~c~~~ 59 (85)
|.|..|+..
T Consensus 134 y~C~~C~g~ 142 (146)
T smart00731 134 YRCGKCGGK 142 (146)
T ss_pred EEcCCCCCE
Confidence 555555543
No 205
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=31.83 E-value=23 Score=17.91 Aligned_cols=9 Identities=33% Similarity=0.899 Sum_probs=4.7
Q ss_pred CccCCCCcc
Q psy3492 24 PFNCALCEY 32 (85)
Q Consensus 24 ~~~c~~c~~ 32 (85)
|..|.-||.
T Consensus 2 p~~CpYCg~ 10 (102)
T PF11672_consen 2 PIICPYCGG 10 (102)
T ss_pred CcccCCCCC
Confidence 445555554
No 206
>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=31.76 E-value=22 Score=14.30 Aligned_cols=11 Identities=18% Similarity=0.404 Sum_probs=7.2
Q ss_pred ccCCcCccccC
Q psy3492 51 RICSKCSFLAD 61 (85)
Q Consensus 51 ~~C~~c~~~f~ 61 (85)
+.|+.||..+-
T Consensus 33 ~~C~~CGE~~~ 43 (46)
T TIGR03831 33 LVCPQCGEEYL 43 (46)
T ss_pred cccccCCCEee
Confidence 66777776543
No 207
>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=31.41 E-value=38 Score=12.63 Aligned_cols=7 Identities=29% Similarity=0.790 Sum_probs=3.2
Q ss_pred cCCcCcc
Q psy3492 52 ICSKCSF 58 (85)
Q Consensus 52 ~C~~c~~ 58 (85)
.|..|++
T Consensus 2 ~C~~C~~ 8 (30)
T PF03107_consen 2 WCDVCRR 8 (30)
T ss_pred CCCCCCC
Confidence 3444444
No 208
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=30.63 E-value=4.5 Score=20.33 Aligned_cols=35 Identities=20% Similarity=0.513 Sum_probs=18.6
Q ss_pred CCccCCCCccccCChHHHHHHHHhhCCC-ccCCcCcccc
Q psy3492 23 KPFNCALCEYKAARPERLATHVIKVHNK-RICSKCSFLA 60 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~~f 60 (85)
+.|.|..|+..-...-.++. ....+ ..|..||..|
T Consensus 21 k~FtCp~Cghe~vs~ctvkk---~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTVKK---TVNIGTAVCGNCGLSF 56 (104)
T ss_pred ceEecCccCCeeeeEEEEEe---cCceeEEEcccCcceE
Confidence 56888888865333222211 11222 5677777554
No 209
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=30.54 E-value=28 Score=15.23 Aligned_cols=9 Identities=22% Similarity=0.475 Sum_probs=5.4
Q ss_pred cCCcCcccc
Q psy3492 52 ICSKCSFLA 60 (85)
Q Consensus 52 ~C~~c~~~f 60 (85)
.||.||..+
T Consensus 2 ~CPyCge~~ 10 (52)
T PF14255_consen 2 QCPYCGEPI 10 (52)
T ss_pred CCCCCCCee
Confidence 577776543
No 210
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=30.32 E-value=34 Score=15.43 Aligned_cols=9 Identities=22% Similarity=0.098 Sum_probs=5.0
Q ss_pred CCCCccccc
Q psy3492 1 MPRLQVLIS 9 (85)
Q Consensus 1 c~~c~~~f~ 9 (85)
|+.||+.-.
T Consensus 6 C~~CG~~Ip 14 (59)
T PF09889_consen 6 CPVCGKPIP 14 (59)
T ss_pred CCcCCCcCC
Confidence 556665543
No 211
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=29.94 E-value=23 Score=13.68 Aligned_cols=10 Identities=20% Similarity=0.580 Sum_probs=6.6
Q ss_pred ccCCcCcccc
Q psy3492 51 RICSKCSFLA 60 (85)
Q Consensus 51 ~~C~~c~~~f 60 (85)
|+|..||...
T Consensus 5 ykC~~CGniv 14 (34)
T cd00974 5 YKCEICGNIV 14 (34)
T ss_pred EEcCCCCcEE
Confidence 6777777543
No 212
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=29.71 E-value=21 Score=15.44 Aligned_cols=15 Identities=20% Similarity=0.353 Sum_probs=11.8
Q ss_pred ccCCcCccccCCHHH
Q psy3492 51 RICSKCSFLADDQET 65 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~ 65 (85)
++|+.||..+...-.
T Consensus 29 W~C~~Cgh~w~~~v~ 43 (55)
T PF14311_consen 29 WKCPKCGHEWKASVN 43 (55)
T ss_pred EECCCCCCeeEccHh
Confidence 899999988776643
No 213
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=29.51 E-value=43 Score=20.26 Aligned_cols=11 Identities=27% Similarity=0.830 Sum_probs=7.1
Q ss_pred ccCCcCccccC
Q psy3492 51 RICSKCSFLAD 61 (85)
Q Consensus 51 ~~C~~c~~~f~ 61 (85)
+.|++||.-|.
T Consensus 47 ~vc~~c~~h~r 57 (292)
T PRK05654 47 NVCPKCGHHMR 57 (292)
T ss_pred CCCCCCCCCee
Confidence 56777776554
No 214
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=29.48 E-value=37 Score=14.39 Aligned_cols=16 Identities=38% Similarity=0.602 Sum_probs=10.1
Q ss_pred CCC-ccCCcCccccCCH
Q psy3492 48 HNK-RICSKCSFLADDQ 63 (85)
Q Consensus 48 h~~-~~C~~c~~~f~~~ 63 (85)
|.. |.|..|++.+...
T Consensus 23 H~~Cf~C~~C~~~l~~~ 39 (58)
T PF00412_consen 23 HPECFKCSKCGKPLNDG 39 (58)
T ss_dssp ETTTSBETTTTCBTTTS
T ss_pred EccccccCCCCCccCCC
Confidence 444 7788887765543
No 215
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=29.23 E-value=18 Score=13.77 Aligned_cols=11 Identities=18% Similarity=0.377 Sum_probs=4.9
Q ss_pred ccCCcCccccC
Q psy3492 51 RICSKCSFLAD 61 (85)
Q Consensus 51 ~~C~~c~~~f~ 61 (85)
|.|+.|+..+-
T Consensus 14 Y~Cp~C~~~~C 24 (30)
T PF04438_consen 14 YRCPRCGARYC 24 (30)
T ss_dssp EE-TTT--EES
T ss_pred EECCCcCCcee
Confidence 67777765543
No 216
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=29.18 E-value=23 Score=13.62 Aligned_cols=10 Identities=20% Similarity=0.594 Sum_probs=7.0
Q ss_pred ccCCcCcccc
Q psy3492 51 RICSKCSFLA 60 (85)
Q Consensus 51 ~~C~~c~~~f 60 (85)
|+|..||...
T Consensus 8 ykC~~Cgniv 17 (34)
T TIGR00319 8 YKCEVCGNIV 17 (34)
T ss_pred EEcCCCCcEE
Confidence 7888887543
No 217
>KOG3816|consensus
Probab=29.10 E-value=27 Score=22.26 Aligned_cols=15 Identities=13% Similarity=0.419 Sum_probs=7.1
Q ss_pred ccCCcCccccCCHHH
Q psy3492 51 RICSKCSFLADDQET 65 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~ 65 (85)
+.|..|++.......
T Consensus 475 ~~C~~C~k~l~~~~q 489 (526)
T KOG3816|consen 475 LVCQSCRKSLGVRDQ 489 (526)
T ss_pred hhhhhhccccccHHH
Confidence 344555555444443
No 218
>KOG2857|consensus
Probab=29.03 E-value=31 Score=18.62 Aligned_cols=21 Identities=24% Similarity=0.309 Sum_probs=15.9
Q ss_pred ccCCcCccccCCHHHHHHHHh
Q psy3492 51 RICSKCSFLADDQETLNEHLQ 71 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~ 71 (85)
|+|+.|...+-+-.-++.|+.
T Consensus 18 YKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 18 YKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred ccCCCCCCccccchhhhhccC
Confidence 788888777777777777765
No 219
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=28.58 E-value=31 Score=15.37 Aligned_cols=11 Identities=18% Similarity=0.549 Sum_probs=8.6
Q ss_pred ccCCcCccccC
Q psy3492 51 RICSKCSFLAD 61 (85)
Q Consensus 51 ~~C~~c~~~f~ 61 (85)
|.|+.||-.+-
T Consensus 15 ~~Cp~cGipth 25 (55)
T PF13824_consen 15 FECPDCGIPTH 25 (55)
T ss_pred CcCCCCCCcCc
Confidence 99999996543
No 220
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=28.53 E-value=26 Score=19.10 Aligned_cols=13 Identities=0% Similarity=-0.468 Sum_probs=8.8
Q ss_pred CCCCcccccChHH
Q psy3492 1 MPRLQVLISYNWC 13 (85)
Q Consensus 1 c~~c~~~f~~~~~ 13 (85)
|+.|++.|+.-..
T Consensus 31 C~~C~~RFTTfE~ 43 (156)
T COG1327 31 CLECGERFTTFER 43 (156)
T ss_pred ccccccccchhhe
Confidence 6778877766543
No 221
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=28.33 E-value=30 Score=15.81 Aligned_cols=8 Identities=13% Similarity=0.131 Sum_probs=5.5
Q ss_pred CCCCcccc
Q psy3492 1 MPRLQVLI 8 (85)
Q Consensus 1 c~~c~~~f 8 (85)
||+|++..
T Consensus 9 CP~C~k~~ 16 (62)
T PRK00418 9 CPTCGKPV 16 (62)
T ss_pred CCCCCCcc
Confidence 67787753
No 222
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=28.26 E-value=32 Score=16.75 Aligned_cols=13 Identities=15% Similarity=0.452 Sum_probs=8.2
Q ss_pred ccCCcCccccCCH
Q psy3492 51 RICSKCSFLADDQ 63 (85)
Q Consensus 51 ~~C~~c~~~f~~~ 63 (85)
-+|+.||..|...
T Consensus 9 ~~C~~CG~d~~~~ 21 (86)
T PF06170_consen 9 PRCPHCGLDYSHA 21 (86)
T ss_pred CcccccCCccccC
Confidence 3677787666543
No 223
>PLN02748 tRNA dimethylallyltransferase
Probab=28.19 E-value=60 Score=21.16 Aligned_cols=22 Identities=14% Similarity=0.344 Sum_probs=14.2
Q ss_pred CCccCCCCcc-ccCChHHHHHHH
Q psy3492 23 KPFNCALCEY-KAARPERLATHV 44 (85)
Q Consensus 23 ~~~~c~~c~~-~f~~~~~l~~h~ 44 (85)
+.|.|++|+. .+.....+..|+
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hl 439 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHK 439 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHh
Confidence 4556777775 566666666665
No 224
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.05 E-value=30 Score=17.59 Aligned_cols=9 Identities=11% Similarity=0.146 Sum_probs=5.1
Q ss_pred CCCCccccc
Q psy3492 1 MPRLQVLIS 9 (85)
Q Consensus 1 c~~c~~~f~ 9 (85)
||.||..|.
T Consensus 52 CP~Cg~~~e 60 (115)
T COG1885 52 CPKCGEPFE 60 (115)
T ss_pred CCCCCCccc
Confidence 566665543
No 225
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=27.69 E-value=43 Score=18.96 Aligned_cols=24 Identities=21% Similarity=0.331 Sum_probs=13.2
Q ss_pred hhCCC-ccCCcCccccCCHHHHHHH
Q psy3492 46 KVHNK-RICSKCSFLADDQETLNEH 69 (85)
Q Consensus 46 ~~h~~-~~C~~c~~~f~~~~~l~~h 69 (85)
..|+| |.|..|...-.+-.+...|
T Consensus 48 knh~Gk~vC~LC~T~H~~e~Sy~~H 72 (222)
T COG5246 48 KNHTGKYVCLLCKTKHLTEMSYVKH 72 (222)
T ss_pred hcCCCcEEeeeeccccccHHHHHHh
Confidence 35556 6666665555554444444
No 226
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=27.50 E-value=33 Score=15.29 Aligned_cols=12 Identities=17% Similarity=0.232 Sum_probs=8.6
Q ss_pred cCCcCccccCCH
Q psy3492 52 ICSKCSFLADDQ 63 (85)
Q Consensus 52 ~C~~c~~~f~~~ 63 (85)
-|+.||+.|...
T Consensus 41 gCPfC~~~~~~~ 52 (55)
T PF14447_consen 41 GCPFCGTPFEFD 52 (55)
T ss_pred CCCCCCCcccCC
Confidence 488898877543
No 227
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=27.31 E-value=20 Score=15.88 Aligned_cols=16 Identities=13% Similarity=0.316 Sum_probs=7.2
Q ss_pred CCccCCCCccccCChH
Q psy3492 23 KPFNCALCEYKAARPE 38 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~ 38 (85)
.|+....|+..|...+
T Consensus 23 ~PV~s~~C~H~fek~a 38 (57)
T PF11789_consen 23 DPVKSKKCGHTFEKEA 38 (57)
T ss_dssp SEEEESSS--EEEHHH
T ss_pred CCcCcCCCCCeecHHH
Confidence 3455555665555443
No 228
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=27.24 E-value=1.3e+02 Score=17.12 Aligned_cols=15 Identities=20% Similarity=0.173 Sum_probs=8.3
Q ss_pred CCccCCCCccccCCh
Q psy3492 23 KPFNCALCEYKAARP 37 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~ 37 (85)
....|..|+..+...
T Consensus 94 ~~~~C~~C~~~~~~~ 108 (206)
T cd01410 94 FIEVCKSCGPEYVRD 108 (206)
T ss_pred CcccCCCCCCccchH
Confidence 345566676555433
No 229
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=27.18 E-value=73 Score=15.08 Aligned_cols=21 Identities=19% Similarity=0.224 Sum_probs=17.1
Q ss_pred CcCccccCCHHHHHHHHhhcc
Q psy3492 54 SKCSFLADDQETLNEHLQQHI 74 (85)
Q Consensus 54 ~~c~~~f~~~~~l~~h~~~h~ 74 (85)
.-||+.|.+...+...+..+.
T Consensus 34 sP~GkklRs~~ev~~YL~~~~ 54 (77)
T smart00391 34 SPCGKKLRSKSELARYLHKNG 54 (77)
T ss_pred CCCCCeeeCHHHHHHHHHhCC
Confidence 349999999999999987543
No 230
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=27.10 E-value=51 Score=18.15 Aligned_cols=16 Identities=19% Similarity=0.254 Sum_probs=13.0
Q ss_pred ccCCcCccccCCHHHH
Q psy3492 51 RICSKCSFLADDQETL 66 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l 66 (85)
+.|..||+.|.....+
T Consensus 115 ~~C~~CG~~f~~~~~i 130 (180)
T PRK12387 115 CNCRVCGRPFAVQKEI 130 (180)
T ss_pred ccchhhCCccccHHHH
Confidence 7899999999866543
No 231
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=27.06 E-value=27 Score=14.63 Aligned_cols=11 Identities=27% Similarity=0.845 Sum_probs=8.1
Q ss_pred ccCCcCccccC
Q psy3492 51 RICSKCSFLAD 61 (85)
Q Consensus 51 ~~C~~c~~~f~ 61 (85)
+.|+.||..+.
T Consensus 21 ~vC~~Cg~~~~ 31 (52)
T smart00661 21 FVCRKCGYEEP 31 (52)
T ss_pred EECCcCCCeEE
Confidence 78888886544
No 232
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=26.95 E-value=17 Score=18.65 Aligned_cols=11 Identities=18% Similarity=0.688 Sum_probs=8.8
Q ss_pred ccCCcCccccC
Q psy3492 51 RICSKCSFLAD 61 (85)
Q Consensus 51 ~~C~~c~~~f~ 61 (85)
|.|..||..+.
T Consensus 101 y~C~~Cg~~wr 111 (113)
T COG1594 101 YKCTRCGYRWR 111 (113)
T ss_pred EEecccCCEee
Confidence 88999987664
No 233
>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=26.93 E-value=30 Score=18.75 Aligned_cols=14 Identities=0% Similarity=-0.410 Sum_probs=9.1
Q ss_pred CCCCcccccChHHH
Q psy3492 1 MPRLQVLISYNWCL 14 (85)
Q Consensus 1 c~~c~~~f~~~~~l 14 (85)
|+.||+.|++-..+
T Consensus 31 C~~C~~RFTTyErv 44 (147)
T TIGR00244 31 CLECHERFTTFERA 44 (147)
T ss_pred CCccCCccceeeec
Confidence 66777777665433
No 234
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=26.07 E-value=46 Score=23.58 Aligned_cols=10 Identities=10% Similarity=-0.061 Sum_probs=5.0
Q ss_pred CCCCcccccC
Q psy3492 1 MPRLQVLISY 10 (85)
Q Consensus 1 c~~c~~~f~~ 10 (85)
|..|++.|..
T Consensus 463 C~~C~kkFfS 472 (1374)
T PTZ00303 463 CPSCGRAFIS 472 (1374)
T ss_pred ccCcCCcccc
Confidence 4455555543
No 235
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=25.92 E-value=73 Score=16.07 Aligned_cols=16 Identities=25% Similarity=0.316 Sum_probs=9.3
Q ss_pred ccCCcCccccCCHHHH
Q psy3492 51 RICSKCSFLADDQETL 66 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l 66 (85)
+.|+.||..+......
T Consensus 32 ~~C~~CGe~~~~~e~~ 47 (127)
T TIGR03830 32 WYCPACGEELLDPEES 47 (127)
T ss_pred eECCCCCCEEEcHHHH
Confidence 5666666655555443
No 236
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=25.76 E-value=24 Score=16.06 Aligned_cols=11 Identities=27% Similarity=0.543 Sum_probs=9.0
Q ss_pred ccCCcCccccC
Q psy3492 51 RICSKCSFLAD 61 (85)
Q Consensus 51 ~~C~~c~~~f~ 61 (85)
..|+.||+.|.
T Consensus 54 L~Cp~c~r~YP 64 (68)
T PF03966_consen 54 LICPECGREYP 64 (68)
T ss_dssp EEETTTTEEEE
T ss_pred EEcCCCCCEEe
Confidence 78999998774
No 237
>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=25.73 E-value=66 Score=13.30 Aligned_cols=10 Identities=20% Similarity=0.753 Sum_probs=7.0
Q ss_pred CCccCCcCcc
Q psy3492 49 NKRICSKCSF 58 (85)
Q Consensus 49 ~~~~C~~c~~ 58 (85)
.|+.|+.||.
T Consensus 17 ~g~~CP~Cg~ 26 (46)
T PF12760_consen 17 DGFVCPHCGS 26 (46)
T ss_pred CCCCCCCCCC
Confidence 3477888875
No 238
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=25.69 E-value=37 Score=21.15 Aligned_cols=36 Identities=25% Similarity=0.511 Sum_probs=16.3
Q ss_pred CCccCCCCccccCChHHHHHHHHhhCCC---------ccCCcCcccc
Q psy3492 23 KPFNCALCEYKAARPERLATHVIKVHNK---------RICSKCSFLA 60 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~~~l~~h~~~~h~~---------~~C~~c~~~f 60 (85)
+.+.|..|.++....+..-.-. .|.. |.|..|++..
T Consensus 251 kav~C~~C~yt~~~~~~~C~~~--~H~l~~~~a~KRFFkC~~C~~Rt 295 (344)
T PF09332_consen 251 KAVTCKQCKYTAFKPSDRCKEE--GHPLKWHDAVKRFFKCKDCGNRT 295 (344)
T ss_dssp EEEEETTT--EESS--HHHHHT--T--EEEEEEE-EEEE-T-TS-EE
T ss_pred EEEEcCCCCCcccCcchhHHhc--CCceEEeeeeeeeEECCCCCCee
Confidence 5577888887766665543221 2322 7888888643
No 239
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (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 eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=25.68 E-value=18 Score=14.62 Aligned_cols=10 Identities=20% Similarity=0.657 Sum_probs=6.8
Q ss_pred ccCCcCcccc
Q psy3492 51 RICSKCSFLA 60 (85)
Q Consensus 51 ~~C~~c~~~f 60 (85)
|.|..||..+
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 7777777654
No 240
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=25.43 E-value=25 Score=18.78 Aligned_cols=12 Identities=17% Similarity=0.534 Sum_probs=8.7
Q ss_pred ccCCcCccccCC
Q psy3492 51 RICSKCSFLADD 62 (85)
Q Consensus 51 ~~C~~c~~~f~~ 62 (85)
+.|+.||.....
T Consensus 82 ~~CE~CG~~I~~ 93 (137)
T TIGR03826 82 YPCERCGTSIRE 93 (137)
T ss_pred CcccccCCcCCC
Confidence 788888875544
No 241
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=25.36 E-value=14 Score=16.01 Aligned_cols=21 Identities=24% Similarity=0.608 Sum_probs=9.7
Q ss_pred CCccCCC--CccccCChHHHHHHH
Q psy3492 23 KPFNCAL--CEYKAARPERLATHV 44 (85)
Q Consensus 23 ~~~~c~~--c~~~f~~~~~l~~h~ 44 (85)
.+..|.. |...+. +..|..|+
T Consensus 8 ~~v~C~~~cc~~~i~-r~~l~~H~ 30 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-RKELDDHL 30 (60)
T ss_dssp SEEE-TT--S-BEEE-CCCHHHHH
T ss_pred CEeeCCCCCccccee-HHHHHHHH
Confidence 3455655 333333 34577776
No 242
>PRK04351 hypothetical protein; Provisional
Probab=25.26 E-value=12 Score=20.16 Aligned_cols=7 Identities=43% Similarity=1.056 Sum_probs=3.3
Q ss_pred ccCCcCc
Q psy3492 51 RICSKCS 57 (85)
Q Consensus 51 ~~C~~c~ 57 (85)
|.|..|+
T Consensus 133 yrCg~C~ 139 (149)
T PRK04351 133 YRCGKCR 139 (149)
T ss_pred EEeCCCC
Confidence 4444444
No 243
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.25 E-value=40 Score=19.98 Aligned_cols=13 Identities=31% Similarity=0.884 Sum_probs=9.8
Q ss_pred ccCCcCccccCCH
Q psy3492 51 RICSKCSFLADDQ 63 (85)
Q Consensus 51 ~~C~~c~~~f~~~ 63 (85)
|.|+.||..+...
T Consensus 323 ~~C~~cg~~~~rD 335 (364)
T COG0675 323 FKCPRCGFVHDRD 335 (364)
T ss_pred EECCCCCCeehhh
Confidence 8899998765554
No 244
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=24.81 E-value=15 Score=24.73 Aligned_cols=10 Identities=20% Similarity=0.601 Sum_probs=5.7
Q ss_pred cCCcCccccC
Q psy3492 52 ICSKCSFLAD 61 (85)
Q Consensus 52 ~C~~c~~~f~ 61 (85)
-|+.||....
T Consensus 43 fC~~CG~~~~ 52 (645)
T PRK14559 43 HCPNCGAETG 52 (645)
T ss_pred cccccCCccc
Confidence 4666765443
No 245
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=24.72 E-value=40 Score=16.39 Aligned_cols=8 Identities=0% Similarity=-0.255 Sum_probs=3.8
Q ss_pred CCCCcccc
Q psy3492 1 MPRLQVLI 8 (85)
Q Consensus 1 c~~c~~~f 8 (85)
|++|++.+
T Consensus 81 C~vC~k~l 88 (109)
T PF10367_consen 81 CSVCGKPL 88 (109)
T ss_pred ccCcCCcC
Confidence 44455444
No 246
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=24.72 E-value=37 Score=15.69 Aligned_cols=8 Identities=38% Similarity=0.775 Sum_probs=5.5
Q ss_pred ccCCcCcc
Q psy3492 51 RICSKCSF 58 (85)
Q Consensus 51 ~~C~~c~~ 58 (85)
++|++||-
T Consensus 5 ~kCpKCgn 12 (68)
T COG3478 5 FKCPKCGN 12 (68)
T ss_pred ccCCCcCC
Confidence 56888863
No 247
>cd00122 MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.
Probab=24.03 E-value=85 Score=13.96 Aligned_cols=20 Identities=15% Similarity=0.245 Sum_probs=15.7
Q ss_pred CcCccccCCHHHHHHHHhhc
Q psy3492 54 SKCSFLADDQETLNEHLQQH 73 (85)
Q Consensus 54 ~~c~~~f~~~~~l~~h~~~h 73 (85)
.-||+.|.+...+...+..+
T Consensus 31 sP~Gk~~Rs~~ev~~yL~~~ 50 (62)
T cd00122 31 SPCGKKLRSKPEVARYLEKT 50 (62)
T ss_pred CCCCceecCHHHHHHHHHhC
Confidence 34789999999888887754
No 248
>KOG1088|consensus
Probab=23.95 E-value=33 Score=17.89 Aligned_cols=15 Identities=7% Similarity=0.169 Sum_probs=12.2
Q ss_pred ccCCcCccccCCHHH
Q psy3492 51 RICSKCSFLADDQET 65 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~ 65 (85)
..|++||+.|.-+..
T Consensus 99 l~CpetG~vfpI~~G 113 (124)
T KOG1088|consen 99 LVCPETGRVFPISDG 113 (124)
T ss_pred EecCCCCcEeecccC
Confidence 889999999876544
No 249
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=23.49 E-value=52 Score=14.51 Aligned_cols=17 Identities=35% Similarity=0.585 Sum_probs=12.0
Q ss_pred ccCCcCccccCCHHHHH
Q psy3492 51 RICSKCSFLADDQETLN 67 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~ 67 (85)
+=|-.||..|.....|.
T Consensus 28 ~YC~~Cg~~Y~d~~dL~ 44 (55)
T PF13821_consen 28 NYCFWCGTKYDDEEDLE 44 (55)
T ss_pred ceeeeeCCccCCHHHHH
Confidence 34677888888877764
No 250
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.27 E-value=23 Score=18.70 Aligned_cols=10 Identities=20% Similarity=0.361 Sum_probs=4.7
Q ss_pred CCcCccccCC
Q psy3492 53 CSKCSFLADD 62 (85)
Q Consensus 53 C~~c~~~f~~ 62 (85)
|..||+.|.+
T Consensus 71 chncgs~fpw 80 (160)
T COG4306 71 CHNCGSRFPW 80 (160)
T ss_pred hhcCCCCCCc
Confidence 3445555444
No 251
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=23.22 E-value=40 Score=14.25 Aligned_cols=8 Identities=50% Similarity=1.140 Sum_probs=6.2
Q ss_pred ccCCcCcc
Q psy3492 51 RICSKCSF 58 (85)
Q Consensus 51 ~~C~~c~~ 58 (85)
-+|+.||.
T Consensus 12 rkCp~CGt 19 (44)
T PF14952_consen 12 RKCPKCGT 19 (44)
T ss_pred ccCCcCcC
Confidence 67999874
No 252
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=22.58 E-value=38 Score=19.49 Aligned_cols=15 Identities=33% Similarity=0.902 Sum_probs=13.0
Q ss_pred CCccCCCCccccCCh
Q psy3492 23 KPFNCALCEYKAARP 37 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~ 37 (85)
.||.|.+|.+.|..+
T Consensus 195 IPF~C~iCKkdy~sp 209 (259)
T COG5152 195 IPFLCGICKKDYESP 209 (259)
T ss_pred Cceeehhchhhccch
Confidence 789999999888776
No 253
>PF12907 zf-met2: Zinc-binding
Probab=22.05 E-value=81 Score=13.00 Aligned_cols=21 Identities=19% Similarity=0.431 Sum_probs=9.9
Q ss_pred ccCCCCccccC---ChHHHHHHHH
Q psy3492 25 FNCALCEYKAA---RPERLATHVI 45 (85)
Q Consensus 25 ~~c~~c~~~f~---~~~~l~~h~~ 45 (85)
+.|.+|..+|. ....|..|..
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~e 25 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAE 25 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHH
Confidence 34556654433 2244555553
No 254
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=21.87 E-value=44 Score=14.48 Aligned_cols=32 Identities=13% Similarity=0.424 Sum_probs=16.9
Q ss_pred ccCCCCccccCChHHHHHHHHhhCCC-ccCCcCccc
Q psy3492 25 FNCALCEYKAARPERLATHVIKVHNK-RICSKCSFL 59 (85)
Q Consensus 25 ~~c~~c~~~f~~~~~l~~h~~~~h~~-~~C~~c~~~ 59 (85)
-.|.-|.-..... ...-+ ..-.+ ..|+.||+.
T Consensus 23 ~~C~gC~~~l~~~--~~~~i-~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 23 GTCSGCHMELPPQ--ELNEI-RKGDEIVFCPNCGRI 55 (56)
T ss_pred CccCCCCEEcCHH--HHHHH-HcCCCeEECcCCCcc
Confidence 4566665443332 22223 22234 789999874
No 255
>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=21.84 E-value=22 Score=21.28 Aligned_cols=24 Identities=21% Similarity=0.511 Sum_probs=16.8
Q ss_pred ccCCcCccccCCHHHHHHHHhhcc
Q psy3492 51 RICSKCSFLADDQETLNEHLQQHI 74 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~ 74 (85)
+.||+||........|..--|+|.
T Consensus 210 ~PCPKCg~et~eTkdLSmStR~hk 233 (314)
T PF06524_consen 210 IPCPKCGYETQETKDLSMSTRSHK 233 (314)
T ss_pred CCCCCCCCcccccccceeeeecch
Confidence 678888877777776666555554
No 256
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.57 E-value=27 Score=16.72 Aligned_cols=10 Identities=20% Similarity=0.468 Sum_probs=7.5
Q ss_pred ccCCcCcccc
Q psy3492 51 RICSKCSFLA 60 (85)
Q Consensus 51 ~~C~~c~~~f 60 (85)
|+|.+||..|
T Consensus 13 Y~c~~cg~~~ 22 (82)
T COG2331 13 YECTECGNRF 22 (82)
T ss_pred EeecccchHH
Confidence 7888888654
No 257
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=21.30 E-value=39 Score=14.85 Aligned_cols=8 Identities=25% Similarity=0.633 Sum_probs=6.8
Q ss_pred ccCCcCcc
Q psy3492 51 RICSKCSF 58 (85)
Q Consensus 51 ~~C~~c~~ 58 (85)
|.|+.||.
T Consensus 45 y~C~~Cg~ 52 (54)
T PF10058_consen 45 YRCPYCGA 52 (54)
T ss_pred EEcCCCCC
Confidence 89999974
No 258
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=21.27 E-value=50 Score=19.43 Aligned_cols=15 Identities=13% Similarity=0.277 Sum_probs=12.6
Q ss_pred CCccCCCCccccCCh
Q psy3492 23 KPFNCALCEYKAARP 37 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~ 37 (85)
++.+|..||..|...
T Consensus 180 kpqRCpECGqVFKLV 194 (268)
T PTZ00043 180 FLYRCGECDQIFMLV 194 (268)
T ss_pred CCccCCCCCcEEEEE
Confidence 889999999887653
No 259
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=21.21 E-value=29 Score=18.53 Aligned_cols=15 Identities=27% Similarity=0.430 Sum_probs=11.7
Q ss_pred CCccCCCCccccCCh
Q psy3492 23 KPFNCALCEYKAARP 37 (85)
Q Consensus 23 ~~~~c~~c~~~f~~~ 37 (85)
+|.+|..||..|...
T Consensus 111 ~~~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 111 KPQRCPECGQVFKLK 125 (136)
T ss_dssp SEEEETTTEEEEEEE
T ss_pred CccCCCCCCeEEEEE
Confidence 788899999887643
No 260
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=21.17 E-value=43 Score=13.44 Aligned_cols=11 Identities=18% Similarity=-0.321 Sum_probs=3.3
Q ss_pred CCCCcccccCh
Q psy3492 1 MPRLQVLISYN 11 (85)
Q Consensus 1 c~~c~~~f~~~ 11 (85)
|+.|++.+...
T Consensus 1 C~~C~~~~~~~ 11 (47)
T PF01844_consen 1 CQYCGKPGSDN 11 (47)
T ss_dssp -TTT--B--GG
T ss_pred CCCCCCcCccC
Confidence 55666655444
No 261
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=21.06 E-value=99 Score=18.91 Aligned_cols=22 Identities=27% Similarity=0.520 Sum_probs=19.9
Q ss_pred ccCCcCccccCCHHHHHHHHhh
Q psy3492 51 RICSKCSFLADDQETLNEHLQQ 72 (85)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~ 72 (85)
|.|+.|-+-|.....+.+|+..
T Consensus 49 yiCe~Clky~~~~~~l~~H~~~ 70 (290)
T PLN03238 49 YICEYCLKYMRKKKSLLRHLAK 70 (290)
T ss_pred EEcCCCcchhCCHHHHHHHHHh
Confidence 9999999999999999999874
No 262
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=20.62 E-value=50 Score=14.70 Aligned_cols=6 Identities=17% Similarity=-0.020 Sum_probs=3.4
Q ss_pred CCCCcc
Q psy3492 1 MPRLQV 6 (85)
Q Consensus 1 c~~c~~ 6 (85)
||.||.
T Consensus 7 CP~Cgn 12 (55)
T PF14205_consen 7 CPICGN 12 (55)
T ss_pred CCCCCC
Confidence 566663
No 263
>PRK03922 hypothetical protein; Provisional
Probab=20.51 E-value=57 Score=16.80 Aligned_cols=9 Identities=11% Similarity=0.157 Sum_probs=4.6
Q ss_pred CCCCccccc
Q psy3492 1 MPRLQVLIS 9 (85)
Q Consensus 1 c~~c~~~f~ 9 (85)
||.||..|.
T Consensus 52 cP~cge~~~ 60 (113)
T PRK03922 52 CPKCGEPFD 60 (113)
T ss_pred CCCCCCcCC
Confidence 455555543
No 264
>cd01396 MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
Probab=20.29 E-value=1.1e+02 Score=14.48 Aligned_cols=20 Identities=15% Similarity=0.066 Sum_probs=16.8
Q ss_pred CcCccccCCHHHHHHHHhhc
Q psy3492 54 SKCSFLADDQETLNEHLQQH 73 (85)
Q Consensus 54 ~~c~~~f~~~~~l~~h~~~h 73 (85)
.-+|+.|.+...+.+.+..+
T Consensus 32 sP~Gkk~RS~~ev~~yL~~~ 51 (77)
T cd01396 32 SPTGKKFRSKVELARYLEKN 51 (77)
T ss_pred CCCCCEEECHHHHHHHHHhC
Confidence 34789999999999998876
No 265
>KOG4727|consensus
Probab=20.08 E-value=61 Score=18.18 Aligned_cols=19 Identities=11% Similarity=0.134 Sum_probs=14.5
Q ss_pred CCCCcccccChHHHHHHHH
Q psy3492 1 MPRLQVLISYNWCLKRHLN 19 (85)
Q Consensus 1 c~~c~~~f~~~~~l~~h~~ 19 (85)
|.+|.-++...-++..|+.
T Consensus 78 CdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 78 CDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred eeecceeehhhHHHHHHhc
Confidence 6778888888877777765
Done!