Query psy12023
Match_columns 55
No_of_seqs 117 out of 1032
Neff 12.0
Searched_HMMs 46136
Date Fri Aug 16 16:40:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12023.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12023hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.8 1E-21 2.2E-26 89.2 2.6 53 1-54 187-239 (279)
2 KOG2462|consensus 99.7 5.4E-17 1.2E-21 74.1 2.2 50 1-51 215-264 (279)
3 KOG3623|consensus 99.6 9.5E-17 2.1E-21 80.8 0.9 49 2-51 282-330 (1007)
4 PHA02768 hypothetical protein; 99.6 2.9E-15 6.4E-20 54.6 2.0 43 2-47 6-48 (55)
5 KOG3623|consensus 99.5 1.5E-15 3.3E-20 76.7 1.2 50 1-51 922-971 (1007)
6 KOG3576|consensus 99.5 5.1E-15 1.1E-19 65.9 0.4 52 2-54 146-197 (267)
7 KOG1074|consensus 99.5 4.1E-15 9E-20 75.6 -0.3 52 2-54 354-405 (958)
8 KOG1074|consensus 99.4 3E-14 6.6E-19 72.6 1.5 51 3-54 881-931 (958)
9 PHA00733 hypothetical protein 99.4 5.5E-13 1.2E-17 56.2 4.0 51 1-54 73-123 (128)
10 PF13465 zf-H2C2_2: Zinc-finge 99.3 3.1E-12 6.8E-17 40.6 1.9 26 16-42 1-26 (26)
11 PHA00732 hypothetical protein 99.1 5.5E-11 1.2E-15 46.5 2.3 44 1-51 1-45 (79)
12 PHA00616 hypothetical protein 99.1 7E-11 1.5E-15 41.4 1.6 33 1-34 1-33 (44)
13 KOG3576|consensus 99.0 3.4E-11 7.4E-16 54.0 -0.3 52 2-54 118-169 (267)
14 PHA02768 hypothetical protein; 98.9 6E-10 1.3E-14 40.8 1.7 24 31-54 6-29 (55)
15 KOG3993|consensus 98.9 2.7E-10 5.8E-15 55.4 1.0 53 2-54 296-380 (500)
16 PHA00616 hypothetical protein 98.9 8.4E-10 1.8E-14 38.7 1.0 26 30-55 1-26 (44)
17 PF00096 zf-C2H2: Zinc finger, 98.9 1.5E-09 3.3E-14 33.3 1.4 22 31-52 1-22 (23)
18 PF05605 zf-Di19: Drought indu 98.8 1.4E-08 3E-13 37.2 3.9 50 2-54 3-53 (54)
19 PF13894 zf-C2H2_4: C2H2-type 98.8 2.9E-09 6.3E-14 32.7 1.7 24 31-54 1-24 (24)
20 KOG3608|consensus 98.8 1.5E-08 3.3E-13 48.8 3.6 51 2-53 264-315 (467)
21 PF13912 zf-C2H2_6: C2H2-type 98.8 4.3E-09 9.3E-14 33.4 1.2 25 30-54 1-25 (27)
22 KOG3608|consensus 98.6 2.3E-08 4.9E-13 48.3 1.7 51 1-54 237-287 (467)
23 PF00096 zf-C2H2: Zinc finger, 98.6 3.7E-08 8.1E-13 30.1 1.1 23 2-24 1-23 (23)
24 PHA00733 hypothetical protein 98.5 5.9E-08 1.3E-12 41.1 1.4 49 3-52 42-95 (128)
25 smart00355 ZnF_C2H2 zinc finge 98.4 2.2E-07 4.7E-12 28.7 1.9 23 31-53 1-23 (26)
26 KOG3993|consensus 98.4 1.5E-08 3.3E-13 49.6 -1.3 51 2-53 268-318 (500)
27 PF09237 GAGA: GAGA factor; I 98.4 1.2E-07 2.7E-12 34.1 1.0 31 25-55 19-49 (54)
28 PRK04860 hypothetical protein; 98.3 5.8E-07 1.3E-11 39.4 2.0 38 1-43 119-156 (160)
29 PF13912 zf-C2H2_6: C2H2-type 98.3 1.7E-07 3.6E-12 29.7 0.3 25 1-25 1-25 (27)
30 PHA00732 hypothetical protein 98.2 1.1E-06 2.4E-11 34.5 1.9 23 30-52 1-23 (79)
31 PF12756 zf-C2H2_2: C2H2 type 98.2 1.2E-06 2.7E-11 35.1 2.0 50 3-53 1-73 (100)
32 PLN03086 PRLI-interacting fact 98.2 4.2E-06 9E-11 42.8 3.7 36 2-40 479-514 (567)
33 PF13894 zf-C2H2_4: C2H2-type 98.2 1.4E-06 3.1E-11 26.4 1.4 23 2-24 1-23 (24)
34 PLN03086 PRLI-interacting fact 98.1 5.6E-06 1.2E-10 42.4 3.6 46 2-53 454-499 (567)
35 PF12874 zf-met: Zinc-finger o 98.1 1.9E-06 4.2E-11 26.6 1.1 22 31-52 1-22 (25)
36 PF13909 zf-H2C2_5: C2H2-type 98.1 2.5E-06 5.3E-11 26.2 1.2 23 31-54 1-23 (24)
37 smart00355 ZnF_C2H2 zinc finge 98.1 7.2E-06 1.6E-10 25.1 2.2 24 2-25 1-24 (26)
38 COG5189 SFP1 Putative transcri 98.0 2E-06 4.4E-11 41.4 0.3 50 1-51 349-419 (423)
39 PF09237 GAGA: GAGA factor; I 97.7 4E-05 8.7E-10 27.8 1.7 29 1-29 24-52 (54)
40 PF12171 zf-C2H2_jaz: Zinc-fin 97.6 1.5E-05 3.2E-10 25.2 -0.0 21 31-51 2-22 (27)
41 PF13913 zf-C2HC_2: zinc-finge 97.5 0.00014 2.9E-09 22.7 1.8 21 31-52 3-23 (25)
42 smart00451 ZnF_U1 U1-like zinc 97.2 0.00026 5.7E-09 23.3 1.4 21 31-51 4-24 (35)
43 KOG2893|consensus 96.4 0.00098 2.1E-08 31.5 0.1 41 4-49 13-53 (341)
44 COG5048 FOG: Zn-finger [Genera 96.3 0.00065 1.4E-08 33.1 -0.7 51 2-53 290-346 (467)
45 cd00350 rubredoxin_like Rubred 95.8 0.0074 1.6E-07 19.9 1.1 25 2-39 2-26 (33)
46 COG4049 Uncharacterized protei 95.7 0.0052 1.1E-07 22.8 0.7 26 26-52 14-39 (65)
47 cd00729 rubredoxin_SM Rubredox 95.6 0.01 2.2E-07 19.7 1.2 24 2-38 3-26 (34)
48 PF13719 zinc_ribbon_5: zinc-r 95.5 0.011 2.4E-07 20.0 1.2 33 3-41 4-36 (37)
49 PF13717 zinc_ribbon_4: zinc-r 95.1 0.015 3.2E-07 19.6 1.0 33 3-41 4-36 (36)
50 PRK00464 nrdR transcriptional 94.9 0.0047 1E-07 27.4 -0.6 40 2-43 1-41 (154)
51 PF04959 ARS2: Arsenite-resist 94.8 0.021 4.5E-07 26.7 1.3 26 28-54 76-101 (214)
52 TIGR02098 MJ0042_CXXC MJ0042 f 94.8 0.02 4.3E-07 19.2 1.0 34 2-41 3-36 (38)
53 PF02892 zf-BED: BED zinc fing 94.7 0.052 1.1E-06 18.8 2.0 23 31-53 17-43 (45)
54 TIGR00373 conserved hypothetic 94.6 0.028 6.2E-07 25.0 1.4 30 2-41 110-139 (158)
55 PRK06266 transcription initiat 94.5 0.028 6.1E-07 25.5 1.4 30 2-41 118-147 (178)
56 PF12013 DUF3505: Protein of u 94.2 0.06 1.3E-06 22.3 2.0 25 31-55 81-109 (109)
57 COG2888 Predicted Zn-ribbon RN 94.2 0.044 9.5E-07 20.6 1.3 8 31-38 51-58 (61)
58 KOG2186|consensus 94.0 0.039 8.5E-07 26.5 1.3 45 2-50 4-48 (276)
59 smart00659 RPOLCX RNA polymera 93.8 0.05 1.1E-06 19.2 1.1 26 2-39 3-28 (44)
60 PRK00398 rpoP DNA-directed RNA 93.6 0.031 6.8E-07 19.6 0.5 29 2-41 4-32 (46)
61 PF09538 FYDLN_acid: Protein o 93.5 0.068 1.5E-06 22.5 1.5 29 3-43 11-39 (108)
62 COG1592 Rubrerythrin [Energy p 93.5 0.059 1.3E-06 24.3 1.4 10 29-38 148-157 (166)
63 KOG1146|consensus 93.5 0.069 1.5E-06 31.0 1.8 49 2-51 466-539 (1406)
64 TIGR02605 CxxC_CxxC_SSSS putat 93.3 0.026 5.6E-07 20.3 0.1 29 2-38 6-34 (52)
65 PHA00626 hypothetical protein 93.3 0.029 6.3E-07 20.8 0.2 14 31-44 24-37 (59)
66 smart00531 TFIIE Transcription 93.3 0.061 1.3E-06 23.6 1.2 35 2-41 100-134 (147)
67 PF03604 DNA_RNApol_7kD: DNA d 92.9 0.079 1.7E-06 17.4 1.0 27 2-40 1-27 (32)
68 smart00734 ZnF_Rad18 Rad18-lik 92.4 0.17 3.8E-06 15.7 1.6 20 31-51 2-21 (26)
69 smart00614 ZnF_BED BED zinc fi 92.0 0.23 4.9E-06 17.7 1.9 21 31-51 19-44 (50)
70 PRK14890 putative Zn-ribbon RN 91.8 0.16 3.5E-06 19.1 1.3 7 31-37 49-55 (59)
71 PF05443 ROS_MUCR: ROS/MUCR tr 91.7 0.12 2.5E-06 22.6 1.1 21 31-54 73-93 (132)
72 PRK09678 DNA-binding transcrip 91.6 0.1 2.3E-06 20.4 0.8 39 2-43 2-42 (72)
73 COG3357 Predicted transcriptio 90.6 0.16 3.5E-06 20.8 0.9 11 31-41 59-69 (97)
74 COG5048 FOG: Zn-finger [Genera 90.1 0.28 6.1E-06 24.2 1.7 52 2-54 34-87 (467)
75 PF07754 DUF1610: Domain of un 89.9 0.17 3.7E-06 15.6 0.6 8 31-38 17-24 (24)
76 PF15269 zf-C2H2_7: Zinc-finge 89.7 0.31 6.7E-06 17.4 1.2 22 31-52 21-42 (54)
77 KOG4173|consensus 89.3 0.16 3.5E-06 23.9 0.5 51 3-54 108-170 (253)
78 COG1997 RPL43A Ribosomal prote 89.2 0.27 5.9E-06 20.0 1.0 11 31-41 54-64 (89)
79 TIGR02300 FYDLN_acid conserved 89.1 0.47 1E-05 20.7 1.8 29 3-43 11-39 (129)
80 PF09723 Zn-ribbon_8: Zinc rib 88.4 0.22 4.7E-06 17.2 0.5 12 31-42 6-17 (42)
81 PF14353 CpXC: CpXC protein 88.3 0.019 4.2E-07 24.4 -2.6 42 3-44 3-52 (128)
82 COG1996 RPC10 DNA-directed RNA 88.3 0.24 5.2E-06 18.0 0.6 27 2-39 7-33 (49)
83 PF07975 C1_4: TFIIH C1-like d 88.1 0.064 1.4E-06 19.6 -0.9 23 31-53 22-44 (51)
84 PTZ00255 60S ribosomal protein 87.5 0.24 5.1E-06 20.3 0.4 11 31-41 55-65 (90)
85 smart00834 CxxC_CXXC_SSSS Puta 87.4 0.3 6.4E-06 16.4 0.6 11 31-41 6-16 (41)
86 TIGR00622 ssl1 transcription f 87.3 0.62 1.4E-05 19.8 1.6 23 31-53 82-104 (112)
87 PF13878 zf-C2H2_3: zinc-finge 86.9 0.89 1.9E-05 15.7 1.9 23 31-53 14-38 (41)
88 PF09845 DUF2072: Zn-ribbon co 86.9 0.36 7.9E-06 21.1 0.8 15 1-15 1-15 (131)
89 KOG2593|consensus 86.4 0.58 1.3E-05 24.4 1.4 33 2-38 129-161 (436)
90 KOG4167|consensus 86.0 0.097 2.1E-06 28.8 -1.3 23 31-53 793-815 (907)
91 PF09986 DUF2225: Uncharacteri 85.9 0.45 9.7E-06 22.3 0.9 16 28-44 4-19 (214)
92 PF13451 zf-trcl: Probable zin 85.7 0.3 6.6E-06 17.7 0.3 15 2-16 5-19 (49)
93 KOG2071|consensus 85.7 0.75 1.6E-05 24.9 1.7 23 31-53 419-441 (579)
94 PF08790 zf-LYAR: LYAR-type C2 85.4 0.15 3.3E-06 16.3 -0.5 9 3-11 2-10 (28)
95 KOG2231|consensus 85.4 1.2 2.6E-05 24.7 2.3 48 3-55 184-237 (669)
96 KOG2071|consensus 85.0 0.77 1.7E-05 24.8 1.5 25 2-26 419-443 (579)
97 TIGR00280 L37a ribosomal prote 85.0 0.29 6.4E-06 20.0 0.1 10 31-40 54-63 (91)
98 PF10571 UPF0547: Uncharacteri 84.4 0.71 1.5E-05 14.4 0.9 11 31-41 15-25 (26)
99 PF12907 zf-met2: Zinc-binding 84.1 0.2 4.4E-06 17.4 -0.5 21 31-51 2-25 (40)
100 KOG0978|consensus 84.0 0.56 1.2E-05 25.9 0.8 19 31-49 679-697 (698)
101 PRK03824 hypA hydrogenase nick 83.6 0.36 7.9E-06 21.0 0.1 13 2-14 71-83 (135)
102 smart00154 ZnF_AN1 AN1-like Zi 83.0 0.78 1.7E-05 15.7 0.8 13 31-43 13-25 (39)
103 KOG2482|consensus 82.9 0.91 2E-05 23.2 1.2 23 31-53 196-218 (423)
104 PRK03976 rpl37ae 50S ribosomal 82.5 0.42 9E-06 19.6 0.0 10 31-40 55-64 (90)
105 COG4957 Predicted transcriptio 82.3 1.1 2.5E-05 19.8 1.3 21 31-54 77-97 (148)
106 COG1327 Predicted transcriptio 81.6 0.4 8.7E-06 21.5 -0.2 13 31-43 29-41 (156)
107 PF09963 DUF2197: Uncharacteri 81.2 0.63 1.4E-05 17.4 0.3 40 3-42 4-43 (56)
108 COG3364 Zn-ribbon containing p 80.9 1.2 2.6E-05 18.8 1.1 15 1-15 2-16 (112)
109 KOG1146|consensus 80.7 0.29 6.3E-06 28.8 -0.9 27 27-54 463-489 (1406)
110 PF01428 zf-AN1: AN1-like Zinc 80.5 0.56 1.2E-05 16.2 0.1 13 31-43 14-26 (43)
111 PF04780 DUF629: Protein of un 80.0 1.8 4E-05 23.0 1.7 24 31-54 58-81 (466)
112 PF01780 Ribosomal_L37ae: Ribo 79.4 0.29 6.3E-06 20.0 -0.9 10 31-40 54-63 (90)
113 PF01155 HypA: Hydrogenase exp 79.4 1.1 2.4E-05 18.9 0.8 11 3-13 72-82 (113)
114 COG5236 Uncharacterized conser 79.3 3.2 7E-05 21.5 2.4 19 4-22 223-241 (493)
115 PF10013 DUF2256: Uncharacteri 79.2 0.85 1.8E-05 16.0 0.4 14 31-44 9-22 (42)
116 COG3677 Transposase and inacti 79.1 1.3 2.9E-05 19.2 1.0 15 28-43 52-66 (129)
117 PF14446 Prok-RING_1: Prokaryo 79.1 1.1 2.3E-05 16.7 0.6 10 3-12 7-16 (54)
118 PF01363 FYVE: FYVE zinc finge 78.5 0.93 2E-05 17.1 0.4 27 3-42 11-37 (69)
119 TIGR00416 sms DNA repair prote 78.4 1.3 2.8E-05 23.2 1.0 11 2-12 8-18 (454)
120 PRK11823 DNA repair protein Ra 78.1 1.4 2.9E-05 23.1 1.0 11 2-12 8-18 (446)
121 cd00065 FYVE FYVE domain; Zinc 78.1 2.2 4.8E-05 15.3 1.4 26 3-41 4-29 (57)
122 COG1198 PriA Primosomal protei 78.1 0.57 1.2E-05 26.0 -0.3 22 17-39 463-484 (730)
123 PF04423 Rad50_zn_hook: Rad50 77.6 0.94 2E-05 16.4 0.3 12 32-43 22-33 (54)
124 cd01121 Sms Sms (bacterial rad 77.4 2 4.4E-05 22.0 1.5 11 2-12 1-11 (372)
125 KOG0717|consensus 77.2 1.5 3.2E-05 23.3 1.0 21 31-51 293-313 (508)
126 COG1773 Rubredoxin [Energy pro 76.8 1.2 2.6E-05 16.6 0.5 10 31-40 4-13 (55)
127 PRK12380 hydrogenase nickel in 76.6 1.6 3.6E-05 18.5 0.9 11 3-13 72-82 (113)
128 KOG2785|consensus 76.3 7.7 0.00017 20.3 3.2 49 3-52 168-242 (390)
129 PTZ00448 hypothetical protein; 75.6 2.3 5E-05 21.9 1.4 21 31-51 315-335 (373)
130 PF08209 Sgf11: Sgf11 (transcr 74.7 3.1 6.7E-05 13.8 1.5 19 31-50 5-23 (33)
131 smart00064 FYVE Protein presen 74.7 2.9 6.3E-05 15.7 1.3 11 31-41 27-37 (68)
132 PF01286 XPA_N: XPA protein N- 74.7 1.6 3.4E-05 14.6 0.5 12 32-43 5-16 (34)
133 TIGR00100 hypA hydrogenase nic 73.7 1.9 4.2E-05 18.3 0.8 11 3-13 72-82 (115)
134 PF07282 OrfB_Zn_ribbon: Putat 73.0 3.2 7E-05 15.6 1.3 12 31-42 47-58 (69)
135 PRK12496 hypothetical protein; 72.8 2.7 5.8E-05 19.0 1.1 11 32-42 145-155 (164)
136 PLN02294 cytochrome c oxidase 71.8 2.4 5.2E-05 19.6 0.9 18 23-42 136-153 (174)
137 COG4306 Uncharacterized protei 71.8 1.4 3E-05 19.3 0.1 12 31-42 69-80 (160)
138 PRK05978 hypothetical protein; 71.3 2.3 5.1E-05 19.1 0.8 12 31-42 53-64 (148)
139 KOG2636|consensus 71.2 4.2 9.1E-05 21.7 1.7 25 24-49 396-421 (497)
140 PRK00564 hypA hydrogenase nick 71.1 2.1 4.5E-05 18.3 0.6 11 3-13 73-83 (117)
141 KOG3408|consensus 70.8 2.7 5.8E-05 18.3 0.8 22 31-52 58-79 (129)
142 PF01927 Mut7-C: Mut7-C RNAse 70.3 5.1 0.00011 17.7 1.7 18 31-48 125-142 (147)
143 PRK00420 hypothetical protein; 69.6 4.9 0.00011 17.2 1.5 11 31-41 41-51 (112)
144 PF08274 PhnA_Zn_Ribbon: PhnA 68.9 2.9 6.4E-05 13.5 0.6 8 31-38 20-27 (30)
145 cd00924 Cyt_c_Oxidase_Vb Cytoc 67.8 3.4 7.4E-05 17.2 0.8 17 23-41 74-90 (97)
146 COG1571 Predicted DNA-binding 67.7 5.9 0.00013 21.0 1.8 29 3-43 352-380 (421)
147 PF02891 zf-MIZ: MIZ/SP-RING z 67.4 4.8 0.0001 14.5 1.1 8 31-38 42-49 (50)
148 PRK04351 hypothetical protein; 66.6 2 4.4E-05 19.2 0.1 11 31-41 133-143 (149)
149 PF06397 Desulfoferrod_N: Desu 66.3 2.7 6E-05 14.2 0.4 9 31-39 7-15 (36)
150 TIGR00244 transcriptional regu 65.7 3.4 7.4E-05 18.6 0.7 13 31-43 29-41 (147)
151 COG3091 SprT Zn-dependent meta 64.4 2.4 5.2E-05 19.2 0.1 9 31-39 141-149 (156)
152 KOG1842|consensus 64.0 3.8 8.3E-05 21.9 0.8 24 31-54 16-39 (505)
153 COG1675 TFA1 Transcription ini 62.5 5.8 0.00013 18.4 1.1 10 31-40 133-142 (176)
154 PF12773 DZR: Double zinc ribb 61.6 7.9 0.00017 13.5 1.3 11 31-41 30-40 (50)
155 PLN02748 tRNA dimethylallyltra 61.4 8.8 0.00019 20.6 1.8 21 31-51 419-440 (468)
156 COG4338 Uncharacterized protei 60.5 3.2 7E-05 15.1 0.1 13 32-44 14-26 (54)
157 cd00730 rubredoxin Rubredoxin; 60.2 4.8 0.0001 14.6 0.6 10 31-40 2-11 (50)
158 COG5151 SSL1 RNA polymerase II 59.9 6.2 0.00013 20.2 1.0 23 31-53 389-411 (421)
159 TIGR01206 lysW lysine biosynth 59.8 5.4 0.00012 14.8 0.7 11 31-41 3-13 (54)
160 smart00731 SprT SprT homologue 59.6 2.9 6.3E-05 18.4 -0.1 9 31-39 134-142 (146)
161 PF02176 zf-TRAF: TRAF-type zi 59.4 2.5 5.4E-05 15.3 -0.2 28 14-42 23-54 (60)
162 PF12230 PRP21_like_P: Pre-mRN 59.3 3.1 6.7E-05 19.7 0.0 21 31-52 169-189 (229)
163 PRK00432 30S ribosomal protein 58.5 8.3 0.00018 13.9 1.1 10 31-40 38-47 (50)
164 PRK08222 hydrogenase 4 subunit 58.1 16 0.00034 16.9 2.1 18 2-19 115-132 (181)
165 PF08271 TF_Zn_Ribbon: TFIIB z 57.4 7 0.00015 13.4 0.8 7 32-38 2-8 (43)
166 COG0675 Transposase and inacti 56.9 8.1 0.00017 18.9 1.2 12 31-42 323-334 (364)
167 smart00440 ZnF_C2C2 C2C2 Zinc 56.4 6.3 0.00014 13.4 0.6 11 31-41 29-39 (40)
168 PRK01343 zinc-binding protein; 55.5 11 0.00024 14.2 1.2 11 31-41 10-20 (57)
169 PF01096 TFIIS_C: Transcriptio 55.1 3.7 8.1E-05 13.9 -0.1 10 31-40 29-38 (39)
170 PF04606 Ogr_Delta: Ogr/Delta- 54.4 2.4 5.1E-05 15.0 -0.6 38 3-43 1-40 (47)
171 PF10164 DUF2367: Uncharacteri 54.3 8.7 0.00019 16.1 0.9 12 28-40 87-98 (98)
172 TIGR03831 YgiT_finger YgiT-typ 54.0 6.7 0.00015 13.2 0.5 14 28-41 30-43 (46)
173 PTZ00043 cytochrome c oxidase 53.8 8.1 0.00018 18.9 0.9 12 31-42 182-193 (268)
174 PF00301 Rubredoxin: Rubredoxi 53.8 5.8 0.00013 14.2 0.3 9 31-39 2-10 (47)
175 PF10083 DUF2321: Uncharacteri 53.5 7.8 0.00017 17.7 0.7 16 1-16 68-83 (158)
176 KOG4727|consensus 53.5 10 0.00022 17.7 1.1 21 30-50 75-95 (193)
177 COG5152 Uncharacterized conser 53.3 7.4 0.00016 18.6 0.7 18 26-43 192-209 (259)
178 PF10263 SprT-like: SprT-like 53.2 5.7 0.00012 17.4 0.3 10 31-40 144-153 (157)
179 PF14311 DUF4379: Domain of un 53.0 13 0.00029 13.4 1.3 13 31-43 29-41 (55)
180 TIGR00627 tfb4 transcription f 52.9 13 0.00029 18.5 1.5 12 31-42 256-267 (279)
181 cd01413 SIR2_Af2 SIR2_Af2: Arc 52.8 21 0.00046 17.0 2.1 30 3-38 115-144 (222)
182 TIGR00319 desulf_FeS4 desulfof 52.8 7.8 0.00017 12.5 0.6 10 31-40 8-17 (34)
183 COG0068 HypF Hydrogenase matur 52.7 1.3 2.8E-05 24.8 -1.9 13 3-15 125-137 (750)
184 PTZ00303 phosphatidylinositol 52.4 12 0.00026 22.0 1.5 10 4-13 463-472 (1374)
185 cd00974 DSRD Desulforedoxin (D 52.4 8 0.00017 12.5 0.6 10 31-40 5-14 (34)
186 PRK05580 primosome assembly pr 51.9 4.7 0.0001 22.4 -0.0 9 31-39 422-430 (679)
187 TIGR02159 PA_CoA_Oxy4 phenylac 51.5 4.1 8.8E-05 18.2 -0.3 8 31-38 106-113 (146)
188 PRK14138 NAD-dependent deacety 51.4 25 0.00055 17.1 2.3 31 3-38 121-151 (244)
189 PF03811 Zn_Tnp_IS1: InsA N-te 51.2 2 4.3E-05 14.5 -1.0 12 24-36 24-35 (36)
190 PF06524 NOA36: NOA36 protein; 51.1 3 6.5E-05 20.7 -0.7 23 28-51 208-230 (314)
191 COG1656 Uncharacterized conser 50.8 25 0.00054 16.3 2.1 18 31-48 131-148 (165)
192 PHA02998 RNA polymerase subuni 50.4 2.6 5.6E-05 19.6 -0.9 13 31-43 172-184 (195)
193 KOG3507|consensus 50.2 8 0.00017 14.7 0.5 10 31-40 38-47 (62)
194 PF13240 zinc_ribbon_2: zinc-r 50.1 10 0.00022 11.3 0.6 8 32-39 15-22 (23)
195 PRK12387 formate hydrogenlyase 49.8 22 0.00048 16.3 1.9 15 2-16 115-129 (180)
196 PF06170 DUF983: Protein of un 49.7 9.5 0.00021 15.5 0.7 12 31-42 9-20 (86)
197 COG1645 Uncharacterized Zn-fin 49.6 11 0.00023 16.7 0.9 10 31-40 45-54 (131)
198 PF03107 C1_2: C1 domain; Int 49.6 12 0.00025 11.8 1.1 6 33-38 3-8 (30)
199 PRK05452 anaerobic nitric oxid 49.4 5 0.00011 21.3 -0.1 12 2-13 426-437 (479)
200 PF10071 DUF2310: Zn-ribbon-co 49.4 9.3 0.0002 18.9 0.7 15 3-17 222-236 (258)
201 COG1326 Uncharacterized archae 49.1 17 0.00037 17.4 1.5 13 29-41 29-41 (201)
202 KOG2295|consensus 49.1 42 0.00091 19.0 2.9 28 26-54 506-535 (648)
203 PF10367 Vps39_2: Vacuolar sor 49.0 12 0.00025 15.2 0.9 12 31-42 79-90 (109)
204 COG2331 Uncharacterized protei 49.0 5.5 0.00012 16.0 -0.0 10 31-40 13-22 (82)
205 COG5188 PRP9 Splicing factor 3 48.8 13 0.00028 19.5 1.2 25 24-49 369-394 (470)
206 COG1066 Sms Predicted ATP-depe 48.1 11 0.00024 20.2 0.9 12 2-13 8-19 (456)
207 PLN03238 probable histone acet 48.0 23 0.0005 18.0 1.9 21 3-23 50-70 (290)
208 PRK06260 threonine synthase; V 47.9 12 0.00026 19.4 1.0 10 3-12 5-14 (397)
209 smart00132 LIM Zinc-binding do 47.2 12 0.00025 11.7 0.7 6 4-9 30-35 (39)
210 PF13248 zf-ribbon_3: zinc-rib 45.6 7.9 0.00017 11.7 0.1 7 3-9 4-10 (26)
211 PF08792 A2L_zn_ribbon: A2L zi 45.5 11 0.00024 12.4 0.5 10 31-40 22-31 (33)
212 cd01407 SIR2-fam SIR2 family o 45.5 35 0.00077 16.1 2.4 32 3-39 111-142 (218)
213 PF10537 WAC_Acf1_DNA_bd: ATP- 45.5 27 0.00058 14.7 2.2 36 2-39 4-39 (102)
214 PF05191 ADK_lid: Adenylate ki 44.9 7.9 0.00017 13.0 0.1 10 32-41 3-12 (36)
215 PF05741 zf-nanos: Nanos RNA b 44.8 10 0.00022 14.2 0.4 9 31-39 34-42 (55)
216 PF14787 zf-CCHC_5: GAG-polypr 44.4 14 0.0003 12.6 0.6 14 3-16 4-17 (36)
217 TIGR00595 priA primosomal prot 44.3 6.8 0.00015 21.0 -0.1 8 31-38 254-261 (505)
218 PRK08270 anaerobic ribonucleos 44.2 21 0.00045 20.2 1.5 9 31-39 640-648 (656)
219 PF09943 DUF2175: Uncharacteri 44.1 7.7 0.00017 16.4 0.0 9 31-39 3-11 (101)
220 COG1655 Uncharacterized protei 44.0 3.2 6.9E-05 20.2 -1.2 17 27-44 17-33 (267)
221 PF14447 Prok-RING_4: Prokaryo 43.8 18 0.00038 13.6 0.9 10 33-42 42-51 (55)
222 PF14375 Cys_rich_CWC: Cystein 43.0 16 0.00034 13.1 0.8 7 34-40 2-8 (50)
223 PRK08579 anaerobic ribonucleos 43.0 48 0.001 18.8 2.7 8 31-38 583-590 (625)
224 KOG0402|consensus 42.9 7.7 0.00017 15.8 -0.1 28 2-40 37-64 (92)
225 KOG4118|consensus 42.8 13 0.00029 14.5 0.6 22 31-52 39-60 (74)
226 PF03884 DUF329: Domain of unk 42.3 11 0.00024 14.2 0.3 12 31-42 3-14 (57)
227 COG2956 Predicted N-acetylgluc 42.0 40 0.00087 17.8 2.2 12 28-39 352-363 (389)
228 PF15135 UPF0515: Uncharacteri 41.9 12 0.00027 18.6 0.5 13 31-43 156-168 (278)
229 TIGR03829 YokU_near_AblA uncha 41.6 31 0.00066 14.3 1.6 18 3-20 37-54 (89)
230 KOG3014|consensus 41.2 26 0.00057 17.5 1.5 24 31-54 38-63 (257)
231 PF00412 LIM: LIM domain; Int 41.1 20 0.00043 12.6 0.9 13 31-43 27-39 (58)
232 PF02591 DUF164: Putative zinc 41.0 23 0.00051 12.8 2.2 13 25-38 42-54 (56)
233 TIGR00686 phnA alkylphosphonat 40.5 25 0.00055 15.1 1.2 11 31-41 20-30 (109)
234 PRK08271 anaerobic ribonucleos 40.2 41 0.00089 19.1 2.2 8 31-38 581-588 (623)
235 PRK14873 primosome assembly pr 39.8 6.2 0.00013 22.0 -0.7 10 30-39 422-431 (665)
236 KOG4477|consensus 39.7 11 0.00025 17.8 0.2 7 31-37 39-45 (228)
237 PF07295 DUF1451: Protein of u 38.7 14 0.0003 16.7 0.4 7 31-37 113-119 (146)
238 PF14690 zf-ISL3: zinc-finger 37.7 21 0.00047 12.1 0.8 9 2-10 3-11 (47)
239 KOG0317|consensus 37.5 42 0.00091 17.2 1.9 32 4-42 254-285 (293)
240 PF11931 DUF3449: Domain of un 37.4 11 0.00024 17.9 0.0 22 27-49 99-121 (196)
241 TIGR03830 CxxCG_CxxCG_HTH puta 37.4 37 0.0008 14.3 1.6 19 2-20 32-50 (127)
242 KOG2807|consensus 37.0 36 0.00077 17.9 1.6 23 31-53 346-368 (378)
243 PF06353 DUF1062: Protein of u 36.9 14 0.00029 16.6 0.2 11 2-12 14-24 (142)
244 TIGR00515 accD acetyl-CoA carb 36.6 35 0.00076 17.2 1.6 11 31-41 46-56 (285)
245 PF01215 COX5B: Cytochrome c o 36.4 8.6 0.00019 17.1 -0.4 19 23-43 107-125 (136)
246 KOG1280|consensus 36.4 45 0.00098 17.6 1.9 24 31-54 80-103 (381)
247 cd01675 RNR_III Class III ribo 35.9 37 0.0008 18.8 1.7 9 31-39 533-541 (555)
248 PF01844 HNH: HNH endonuclease 35.5 19 0.00041 12.1 0.5 10 33-42 1-10 (47)
249 PF13453 zf-TFIIB: Transcripti 35.3 27 0.00058 11.8 1.4 16 3-18 21-36 (41)
250 COG0846 SIR2 NAD-dependent pro 35.2 26 0.00055 17.3 1.0 31 3-38 124-154 (250)
251 KOG0801|consensus 35.2 7.1 0.00015 18.0 -0.8 10 31-40 139-148 (205)
252 COG4896 Uncharacterized protei 34.9 23 0.00049 13.6 0.7 10 31-40 32-41 (68)
253 PF04438 zf-HIT: HIT zinc fing 34.5 18 0.00038 11.6 0.3 11 31-41 14-24 (30)
254 KOG2907|consensus 34.4 21 0.00046 15.5 0.6 12 31-42 103-114 (116)
255 PRK00481 NAD-dependent deacety 34.4 51 0.0011 15.9 1.9 11 3-13 124-134 (242)
256 PF11494 Ta0938: Ta0938; Inte 34.3 22 0.00048 15.0 0.6 34 3-42 16-49 (105)
257 PF07649 C1_3: C1-like domain; 34.3 19 0.00042 11.1 0.4 10 31-40 16-25 (30)
258 KOG1409|consensus 34.1 14 0.0003 19.4 0.1 37 3-41 284-320 (404)
259 KOG1088|consensus 33.9 27 0.00059 15.3 0.9 14 31-44 99-112 (124)
260 TIGR03826 YvyF flagellar opero 33.8 15 0.00032 16.4 0.1 11 32-42 5-15 (137)
261 PLN03239 histone acetyltransfe 33.7 29 0.00062 18.2 1.0 21 31-51 107-127 (351)
262 PF13824 zf-Mss51: Zinc-finger 33.5 35 0.00075 12.8 1.0 13 28-41 13-25 (55)
263 PF11781 RRN7: RNA polymerase 33.3 26 0.00057 11.7 0.7 10 31-40 9-18 (36)
264 COG1631 RPL42A Ribosomal prote 33.1 15 0.00033 15.3 0.1 12 31-42 69-80 (94)
265 PF03563 Bunya_G2: Bunyavirus 33.0 33 0.00072 17.3 1.2 17 35-51 255-271 (285)
266 PF11023 DUF2614: Protein of u 32.9 24 0.00051 15.3 0.6 10 31-40 70-79 (114)
267 PRK10220 hypothetical protein; 32.9 51 0.0011 14.3 1.6 11 31-41 21-31 (111)
268 COG4847 Uncharacterized protei 32.7 16 0.00035 15.4 0.1 8 31-38 7-14 (103)
269 PF02146 SIR2: Sir2 family; I 32.4 58 0.0013 14.8 2.4 33 3-40 107-139 (178)
270 CHL00174 accD acetyl-CoA carbo 32.3 32 0.0007 17.5 1.1 12 31-42 58-69 (296)
271 PF14369 zf-RING_3: zinc-finge 32.2 29 0.00063 11.5 0.7 10 32-41 23-32 (35)
272 smart00661 RPOL9 RNA polymeras 32.1 29 0.00063 12.0 0.8 13 31-43 21-33 (52)
273 COG1594 RPB9 DNA-directed RNA 32.1 21 0.00045 15.3 0.4 11 31-41 101-111 (113)
274 KOG2169|consensus 31.9 44 0.00096 18.9 1.6 18 26-43 341-358 (636)
275 COG4830 RPS26B Ribosomal prote 31.9 30 0.00064 14.7 0.8 11 31-41 21-31 (108)
276 KOG2857|consensus 31.7 31 0.00066 15.7 0.9 21 2-22 18-38 (157)
277 PRK08197 threonine synthase; V 31.2 29 0.00063 18.1 0.9 11 2-12 8-18 (394)
278 KOG3352|consensus 30.9 30 0.00066 15.9 0.8 11 31-41 134-144 (153)
279 COG1579 Zn-ribbon protein, pos 30.8 54 0.0012 16.3 1.6 14 26-40 218-231 (239)
280 PF10276 zf-CHCC: Zinc-finger 30.6 16 0.00034 12.7 -0.1 10 31-40 30-39 (40)
281 PF09965 DUF2199: Uncharacteri 30.3 30 0.00065 15.7 0.8 9 2-10 1-9 (148)
282 COG4640 Predicted membrane pro 30.3 48 0.001 17.9 1.5 17 31-47 16-32 (465)
283 PRK11788 tetratricopeptide rep 30.0 33 0.00071 17.2 0.9 8 31-38 355-362 (389)
284 PLN00104 MYST -like histone ac 29.8 37 0.0008 18.5 1.1 20 3-22 200-219 (450)
285 PF13696 zf-CCHC_2: Zinc knuck 29.4 25 0.00055 11.6 0.3 9 31-39 9-17 (32)
286 CHL00112 rpl28 ribosomal prote 29.3 27 0.00059 13.4 0.5 10 31-40 3-12 (63)
287 KOG3183|consensus 29.3 24 0.00053 17.4 0.4 14 30-43 23-36 (250)
288 PRK12722 transcriptional activ 29.2 56 0.0012 15.6 1.5 27 3-38 136-162 (187)
289 PRK00415 rps27e 30S ribosomal 29.0 31 0.00068 13.1 0.6 13 31-43 31-43 (59)
290 PF09855 DUF2082: Nucleic-acid 29.0 31 0.00068 13.3 0.6 6 32-37 2-7 (64)
291 PF01722 BolA: BolA-like prote 29.0 29 0.00062 13.7 0.5 25 27-52 27-51 (76)
292 PTZ00064 histone acetyltransfe 29.0 47 0.001 18.6 1.3 20 3-22 282-301 (552)
293 PF06689 zf-C4_ClpX: ClpX C4-t 28.9 32 0.00069 11.8 0.6 10 32-41 3-12 (41)
294 PRK00418 DNA gyrase inhibitor; 28.9 37 0.00079 13.1 0.8 10 31-40 7-16 (62)
295 PF00935 Ribosomal_L44: Riboso 28.8 24 0.00051 14.2 0.3 11 31-41 54-64 (77)
296 PRK12860 transcriptional activ 28.8 53 0.0011 15.7 1.4 26 3-37 136-161 (189)
297 cd01412 SIRT5_Af1_CobB SIRT5_A 28.5 78 0.0017 15.1 2.2 11 3-13 111-121 (224)
298 COG1885 Uncharacterized protei 28.4 35 0.00076 14.7 0.8 10 3-12 51-60 (115)
299 COG1545 Predicted nucleic-acid 28.2 28 0.0006 15.5 0.5 11 31-41 30-40 (140)
300 TIGR00375 conserved hypothetic 27.5 44 0.00096 17.7 1.1 8 31-39 260-267 (374)
301 PF13695 zf-3CxxC: Zinc-bindin 27.4 29 0.00063 14.3 0.4 13 2-14 6-18 (98)
302 PF09889 DUF2116: Uncharacteri 27.2 51 0.0011 12.5 1.0 6 4-9 6-11 (59)
303 PF10058 DUF2296: Predicted in 27.2 33 0.00071 12.6 0.5 8 31-38 45-52 (54)
304 PF03119 DNA_ligase_ZBD: NAD-d 27.0 34 0.00073 10.7 0.5 8 33-40 2-9 (28)
305 PF13821 DUF4187: Domain of un 26.9 40 0.00087 12.5 0.7 14 4-17 30-43 (55)
306 PF01485 IBR: IBR domain; Int 26.9 36 0.00079 12.1 0.7 13 31-43 41-53 (64)
307 cd04476 RPA1_DBD_C RPA1_DBD_C: 26.9 43 0.00093 15.0 1.0 10 31-40 52-61 (166)
308 PF06220 zf-U1: U1 zinc finger 26.8 41 0.0009 11.3 1.3 11 31-41 4-14 (38)
309 PF09332 Mcm10: Mcm10 replicat 26.7 6.5 0.00014 20.2 -1.7 12 28-39 283-294 (344)
310 PF14803 Nudix_N_2: Nudix N-te 26.5 34 0.00074 11.3 0.5 8 33-40 3-10 (34)
311 COG4530 Uncharacterized protei 26.5 28 0.00062 15.1 0.3 13 30-42 26-38 (129)
312 PF11789 zf-Nse: Zinc-finger o 26.3 19 0.0004 13.4 -0.2 15 31-45 25-39 (57)
313 COG3024 Uncharacterized protei 26.3 41 0.0009 13.1 0.7 12 31-42 8-19 (65)
314 cd07153 Fur_like Ferric uptake 26.2 31 0.00068 14.2 0.5 12 31-42 74-85 (116)
315 PF13005 zf-IS66: zinc-finger 26.2 41 0.00088 11.5 0.7 10 3-12 4-13 (47)
316 smart00647 IBR In Between Ring 26.1 46 0.001 11.9 0.9 13 31-43 41-53 (64)
317 PF07503 zf-HYPF: HypF finger; 26.0 42 0.00092 11.2 0.9 11 31-41 22-32 (35)
318 PF05766 NinG: Bacteriophage L 25.4 44 0.00095 15.9 0.8 12 31-42 7-18 (189)
319 smart00507 HNHc HNH nucleases. 25.3 43 0.00093 11.0 0.7 11 31-41 11-21 (52)
320 PF05876 Terminase_GpA: Phage 25.3 21 0.00046 19.6 -0.2 38 3-41 202-240 (557)
321 PTZ00409 Sir2 (Silent Informat 25.3 1E+02 0.0023 15.5 2.4 11 3-13 139-149 (271)
322 COG5216 Uncharacterized conser 25.1 38 0.00082 12.9 0.5 10 31-41 23-32 (67)
323 smart00391 MBD Methyl-CpG bind 25.1 63 0.0014 12.8 1.3 18 34-51 34-51 (77)
324 TIGR00009 L28 ribosomal protei 25.0 30 0.00065 12.8 0.3 9 32-40 4-12 (56)
325 PF15616 TerY-C: TerY-C metal 24.1 12 0.00027 16.5 -0.9 8 31-38 106-113 (131)
326 PRK09335 30S ribosomal protein 24.0 55 0.0012 13.8 0.9 11 30-40 20-30 (95)
327 COG1379 PHP family phosphoeste 24.0 35 0.00076 18.0 0.4 10 31-40 266-275 (403)
328 PLN00186 ribosomal protein S26 24.0 56 0.0012 14.2 0.9 11 30-40 20-30 (109)
329 PF13408 Zn_ribbon_recom: Reco 23.8 34 0.00073 12.0 0.3 11 3-13 7-17 (58)
330 KOG4602|consensus 23.7 41 0.00088 17.0 0.6 9 31-39 269-277 (318)
331 KOG1818|consensus 23.7 41 0.00089 19.2 0.7 10 32-41 183-192 (634)
332 TIGR00598 rad14 DNA repair pro 23.7 25 0.00054 16.4 -0.1 10 4-13 1-10 (172)
333 PTZ00157 60S ribosomal protein 23.5 32 0.00069 14.1 0.2 10 31-40 70-79 (84)
334 COG4068 Uncharacterized protei 23.5 44 0.00095 12.8 0.5 11 31-41 9-19 (64)
335 PF01475 FUR: Ferric uptake re 23.4 33 0.00071 14.4 0.3 13 31-43 81-93 (120)
336 PF14255 Cys_rich_CPXG: Cystei 23.2 50 0.0011 12.1 0.7 9 32-40 2-10 (52)
337 KOG0782|consensus 23.1 28 0.0006 19.8 0.0 28 16-44 240-267 (1004)
338 PRK05654 acetyl-CoA carboxylas 23.1 55 0.0012 16.6 1.0 11 31-41 47-57 (292)
339 PF02148 zf-UBP: Zn-finger in 23.0 28 0.00061 12.9 0.0 19 31-49 12-33 (63)
340 COG0271 BolA Stress-induced mo 22.9 54 0.0012 13.6 0.8 26 26-52 37-62 (90)
341 PHA02942 putative transposase; 22.8 77 0.0017 16.8 1.5 14 28-42 341-354 (383)
342 KOG2747|consensus 22.8 49 0.0011 17.7 0.8 22 3-24 160-181 (396)
343 smart00746 TRASH metallochaper 22.7 40 0.00087 9.7 0.8 6 34-39 2-7 (39)
344 PRK11088 rrmA 23S rRNA methylt 22.6 47 0.001 16.2 0.7 11 31-41 3-13 (272)
345 PF03966 Trm112p: Trm112p-like 22.4 31 0.00068 13.1 0.1 11 31-41 54-64 (68)
346 cd02249 ZZ Zinc finger, ZZ typ 22.3 54 0.0012 11.3 0.7 6 33-38 3-8 (46)
347 PRK05767 rpl44e 50S ribosomal 22.1 33 0.00072 14.3 0.1 12 31-42 68-79 (92)
348 PLN02569 threonine synthase 22.0 68 0.0015 17.6 1.2 9 3-11 51-59 (484)
349 PF04988 AKAP95: A-kinase anch 22.0 73 0.0016 14.9 1.2 19 32-50 2-20 (165)
350 cd01410 SIRT7 SIRT7: Eukaryoti 21.8 1.1E+02 0.0024 14.5 2.9 33 3-39 97-129 (206)
351 PF07496 zf-CW: CW-type Zinc F 21.8 42 0.00092 11.9 0.4 8 31-38 4-11 (50)
352 PF11672 DUF3268: Protein of u 21.7 45 0.00096 14.2 0.5 8 31-38 32-39 (102)
353 COG4332 Uncharacterized protei 21.6 31 0.00067 16.4 0.0 11 2-12 50-60 (203)
354 PF12677 DUF3797: Domain of un 21.2 51 0.0011 12.1 0.5 9 31-39 14-22 (49)
355 PTZ00172 40S ribosomal protein 21.1 65 0.0014 14.0 0.9 11 30-40 20-30 (108)
356 COG4391 Uncharacterized protei 21.0 47 0.001 12.8 0.4 11 31-41 49-59 (62)
357 PF05290 Baculo_IE-1: Baculovi 21.0 65 0.0014 14.6 0.9 14 32-45 123-136 (140)
358 KOG0562|consensus 20.7 98 0.0021 14.7 1.4 8 44-51 167-174 (184)
359 PRK00359 rpmB 50S ribosomal pr 20.6 50 0.0011 13.1 0.5 10 31-40 3-12 (76)
360 PF03226 Yippee-Mis18: Yippee 20.6 80 0.0017 12.8 1.1 16 31-46 3-18 (96)
361 cd00122 MBD MeCP2, MBD1, MBD2, 20.5 72 0.0016 11.8 1.5 18 34-51 31-48 (62)
362 PF05129 Elf1: Transcription e 20.0 47 0.001 13.3 0.4 9 28-37 21-29 (81)
No 1
>KOG2462|consensus
Probab=99.84 E-value=1e-21 Score=89.18 Aligned_cols=53 Identities=25% Similarity=0.601 Sum_probs=50.5
Q ss_pred CCCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccchHHHHHHHhhc
Q psy12023 1 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 1 p~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
|++|..||+.|.+.+.|+.|+++|+|||| |.|..|+++|..+++|+-|+++|.
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiRTHTGEKP-F~C~hC~kAFADRSNLRAHmQTHS 239 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIRTHTGEKP-FSCPHCGKAFADRSNLRAHMQTHS 239 (279)
T ss_pred CcccccccccccchHHhhcccccccCCCC-ccCCcccchhcchHHHHHHHHhhc
Confidence 57899999999999999999999999998 999999999999999999999884
No 2
>KOG2462|consensus
Probab=99.66 E-value=5.4e-17 Score=74.13 Aligned_cols=50 Identities=24% Similarity=0.514 Sum_probs=47.8
Q ss_pred CCCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccchHHHHHHH
Q psy12023 1 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTHMA 51 (55)
Q Consensus 1 p~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~ 51 (55)
||.|..|++.|..+++|..|+.+|.+.++ |+|..|+|.|...+-|..|..
T Consensus 215 PF~C~hC~kAFADRSNLRAHmQTHS~~K~-~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 215 PFSCPHCGKAFADRSNLRAHMQTHSDVKK-HQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred CccCCcccchhcchHHHHHHHHhhcCCcc-ccCcchhhHHHHHHHHHHhhh
Confidence 79999999999999999999999999998 999999999999999999864
No 3
>KOG3623|consensus
Probab=99.62 E-value=9.5e-17 Score=80.82 Aligned_cols=49 Identities=33% Similarity=0.914 Sum_probs=46.7
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccchHHHHHHH
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTHMA 51 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~ 51 (55)
|+|.+||+.|..+..|+.|+++|.|++| |+|+.|+|.|+.+.+...|+.
T Consensus 282 FKCtECgKAFKfKHHLKEHlRIHSGEKP-feCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 282 FKCTECGKAFKFKHHLKEHLRIHSGEKP-FECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred ccccccchhhhhHHHHHhhheeecCCCC-cCCcccccccccCCccccccc
Confidence 7899999999999999999999999998 999999999999999988864
No 4
>PHA02768 hypothetical protein; Provisional
Probab=99.55 E-value=2.9e-15 Score=54.59 Aligned_cols=43 Identities=14% Similarity=0.396 Sum_probs=38.7
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccchHHH
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLT 47 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~ 47 (55)
|+|+.||+.|...+.|..|+++|+ ++ ++|..|++.|.+.+.|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~-~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TN-LKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--Cc-ccCCcccceecccceeE
Confidence 789999999999999999999999 45 99999999999877653
No 5
>KOG3623|consensus
Probab=99.54 E-value=1.5e-15 Score=76.65 Aligned_cols=50 Identities=30% Similarity=0.747 Sum_probs=41.5
Q ss_pred CCCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccchHHHHHHH
Q psy12023 1 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTHMA 51 (55)
Q Consensus 1 p~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~ 51 (55)
||+|..|.+.|..+..|..|.+.|.|++| |+|+.|+|.|+.+.+..+||.
T Consensus 922 PyqC~iCkKAFKHKHHLtEHkRLHSGEKP-fQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 922 PYQCIICKKAFKHKHHLTEHKRLHSGEKP-FQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred CcccchhhHhhhhhhhhhhhhhhccCCCc-chhhhhhhhcccccchHhhhc
Confidence 67888888888888888888888888887 888888888888888888864
No 6
>KOG3576|consensus
Probab=99.49 E-value=5.1e-15 Score=65.91 Aligned_cols=52 Identities=31% Similarity=0.721 Sum_probs=47.2
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccchHHHHHHHhhc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
+.|..||+.|...-+|++|+++|+|-+| |+|..|+++|.++-+|..|.+..|
T Consensus 146 ~lct~cgkgfndtfdlkrh~rthtgvrp-ykc~~c~kaftqrcsleshl~kvh 197 (267)
T KOG3576|consen 146 HLCTFCGKGFNDTFDLKRHTRTHTGVRP-YKCSLCEKAFTQRCSLESHLKKVH 197 (267)
T ss_pred HHHhhccCcccchhhhhhhhccccCccc-cchhhhhHHHHhhccHHHHHHHHc
Confidence 4588899999999999999999999777 999999999999999999987554
No 7
>KOG1074|consensus
Probab=99.48 E-value=4.1e-15 Score=75.63 Aligned_cols=52 Identities=23% Similarity=0.546 Sum_probs=48.0
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccchHHHHHHHhhc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
.+|..|.+.|...+.|+.|.+.|+|++| |+|.+||..|+.+.+|+.|...|+
T Consensus 354 hkCr~CakvfgS~SaLqiHlRSHTGERP-fqCnvCG~~FSTkGNLKvH~~rH~ 405 (958)
T KOG1074|consen 354 HKCRFCAKVFGSDSALQIHLRSHTGERP-FQCNVCGNRFSTKGNLKVHFQRHR 405 (958)
T ss_pred chhhhhHhhcCchhhhhhhhhccCCCCC-eeecccccccccccceeeeeeecc
Confidence 5799999999999999999999999998 999999999999999999866553
No 8
>KOG1074|consensus
Probab=99.45 E-value=3e-14 Score=72.63 Aligned_cols=51 Identities=25% Similarity=0.601 Sum_probs=49.0
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccchHHHHHHHhhc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
.|.+||+.|...+.|..|+++|+++++ |.|.+|++.|....+|+.||.+|+
T Consensus 881 ~C~vCgk~FsSSsALqiH~rTHtg~KP-F~C~fC~~aFttrgnLKvHMgtH~ 931 (958)
T KOG1074|consen 881 VCNVCGKQFSSSAALEIHMRTHTGPKP-FFCHFCEEAFTTRGNLKVHMGTHM 931 (958)
T ss_pred hhccchhcccchHHHHHhhhcCCCCCC-ccchhhhhhhhhhhhhhhhhcccc
Confidence 589999999999999999999999998 999999999999999999999886
No 9
>PHA00733 hypothetical protein
Probab=99.42 E-value=5.5e-13 Score=56.15 Aligned_cols=51 Identities=18% Similarity=0.490 Sum_probs=45.6
Q ss_pred CCCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccchHHHHHHHhhc
Q psy12023 1 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 1 p~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
||.|..|++.|.....|..|+..+ +.+ +.|.+|++.|.....|..|+...|
T Consensus 73 Py~C~~Cgk~Fss~s~L~~H~r~h--~~~-~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 73 PYVCPLCLMPFSSSVSLKQHIRYT--EHS-KVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CccCCCCCCcCCCHHHHHHHHhcC--CcC-ccCCCCCCccCCHHHHHHHHHHhc
Confidence 688999999999999999999875 345 999999999999999999998776
No 10
>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=99.28 E-value=3.1e-12 Score=40.64 Aligned_cols=26 Identities=31% Similarity=0.782 Sum_probs=23.2
Q ss_pred hHHhHHHHHhCCCCCccCCCCCccccc
Q psy12023 16 GIYRHKKFECGQEPKYQCPQCPYRAKQ 42 (55)
Q Consensus 16 ~~~~~~~~~~~~~~~~~c~~c~~~f~~ 42 (55)
+|..|+++|+++++ |.|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~-~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKP-YKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSS-EEESSSSEEESS
T ss_pred CHHHHhhhcCCCCC-CCCCCCcCeeCc
Confidence 47899999999998 999999999863
No 11
>PHA00732 hypothetical protein
Probab=99.13 E-value=5.5e-11 Score=46.53 Aligned_cols=44 Identities=25% Similarity=0.528 Sum_probs=36.5
Q ss_pred CCCCccccccccchhhHHhHHHH-HhCCCCCccCCCCCcccccchHHHHHHH
Q psy12023 1 MFMCDVCGKGYKYKNGIYRHKKF-ECGQEPKYQCPQCPYRAKQNAHLTTHMA 51 (55)
Q Consensus 1 p~~c~~c~~~~~~~~~~~~~~~~-~~~~~~~~~c~~c~~~f~~~~~l~~h~~ 51 (55)
||.|..|++.|.....|..|+.. |. + +.|+.|++.|.+ +..|.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~-~~C~~CgKsF~~---l~~H~~ 45 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---L-TKCPVCNKSYRR---LNQHFY 45 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---C-CccCCCCCEeCC---hhhhhc
Confidence 78999999999999999999884 54 3 689999999973 566654
No 12
>PHA00616 hypothetical protein
Probab=99.09 E-value=7e-11 Score=41.44 Aligned_cols=33 Identities=21% Similarity=0.343 Sum_probs=29.5
Q ss_pred CCCCccccccccchhhHHhHHHHHhCCCCCccCC
Q psy12023 1 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCP 34 (55)
Q Consensus 1 p~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~ 34 (55)
||+|..||+.|...+.+..|+..+.++++ +.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~-~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK-LTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc-ccee
Confidence 78999999999999999999999999887 7764
No 13
>KOG3576|consensus
Probab=99.02 E-value=3.4e-11 Score=54.03 Aligned_cols=52 Identities=25% Similarity=0.473 Sum_probs=48.2
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccchHHHHHHHhhc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
+.|..|++.|....-|.+|+..|..-+. +.|..||+.|...-.|++|+|+|.
T Consensus 118 ftCrvCgK~F~lQRmlnrh~kch~~vkr-~lct~cgkgfndtfdlkrh~rtht 169 (267)
T KOG3576|consen 118 FTCRVCGKKFGLQRMLNRHLKCHSDVKR-HLCTFCGKGFNDTFDLKRHTRTHT 169 (267)
T ss_pred eeeehhhhhhhHHHHHHHHhhhccHHHH-HHHhhccCcccchhhhhhhhcccc
Confidence 5799999999999999999999998788 999999999999999999999885
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.94 E-value=6e-10 Score=40.79 Aligned_cols=24 Identities=25% Similarity=0.570 Sum_probs=23.0
Q ss_pred ccCCCCCcccccchHHHHHHHhhc
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
|+|+.||+.|.+.++|..|+++|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC
Confidence 899999999999999999999985
No 15
>KOG3993|consensus
Probab=98.94 E-value=2.7e-10 Score=55.43 Aligned_cols=53 Identities=19% Similarity=0.520 Sum_probs=45.1
Q ss_pred CCCccccccccchhhHHhHHHHHhC--------CCC------------------------CccCCCCCcccccchHHHHH
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECG--------QEP------------------------KYQCPQCPYRAKQNAHLTTH 49 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~--------~~~------------------------~~~c~~c~~~f~~~~~l~~h 49 (55)
|.|.+|++.|....+|..|.++|-. ..+ .|.|..|++.|.+...|+.|
T Consensus 296 YrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKH 375 (500)
T KOG3993|consen 296 YRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKH 375 (500)
T ss_pred ecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHh
Confidence 7899999999999999999998731 111 17899999999999999999
Q ss_pred HHhhc
Q psy12023 50 MAIKH 54 (55)
Q Consensus 50 ~~~~~ 54 (55)
+..||
T Consensus 376 qlthq 380 (500)
T KOG3993|consen 376 QLTHQ 380 (500)
T ss_pred HHhhh
Confidence 88876
No 16
>PHA00616 hypothetical protein
Probab=98.87 E-value=8.4e-10 Score=38.74 Aligned_cols=26 Identities=23% Similarity=0.451 Sum_probs=24.0
Q ss_pred CccCCCCCcccccchHHHHHHHhhcC
Q psy12023 30 KYQCPQCPYRAKQNAHLTTHMAIKHY 55 (55)
Q Consensus 30 ~~~c~~c~~~f~~~~~l~~h~~~~~~ 55 (55)
||+|..||+.|.+.+.+..|++.+|.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg 26 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHK 26 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcC
Confidence 48999999999999999999998874
No 17
>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=98.86 E-value=1.5e-09 Score=33.28 Aligned_cols=22 Identities=32% Similarity=0.703 Sum_probs=17.2
Q ss_pred ccCCCCCcccccchHHHHHHHh
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAI 52 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~ 52 (55)
|.|+.|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 5677888888888888888776
No 18
>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=98.84 E-value=1.4e-08 Score=37.19 Aligned_cols=50 Identities=28% Similarity=0.672 Sum_probs=37.8
Q ss_pred CCCccccccccchhhHHhHHH-HHhCCCCCccCCCCCcccccchHHHHHHHhhc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKK-FECGQEPKYQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~-~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
|.|+.|++.| +...|..|.. .|..+...+.|++|...+. .+|..|+..+|
T Consensus 3 f~CP~C~~~~-~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGKGF-SESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCCcc-CHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 7899999954 5567888866 4555443389999998754 48999998887
No 19
>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=98.84 E-value=2.9e-09 Score=32.69 Aligned_cols=24 Identities=33% Similarity=0.764 Sum_probs=18.5
Q ss_pred ccCCCCCcccccchHHHHHHHhhc
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
|.|+.|++.|.....|..|++.+|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 578889999988888988888776
No 20
>KOG3608|consensus
Probab=98.77 E-value=1.5e-08 Score=48.85 Aligned_cols=51 Identities=18% Similarity=0.632 Sum_probs=38.3
Q ss_pred CCCccccccccchhhHHhHHHH-HhCCCCCccCCCCCcccccchHHHHHHHhh
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKF-ECGQEPKYQCPQCPYRAKQNAHLTTHMAIK 53 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~-~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~ 53 (55)
|+|..|+......+.|..|++. |..+++ |+|+.|+..+.+.+.|..|..+|
T Consensus 264 ykCplCdmtc~~~ssL~~H~r~rHs~dkp-fKCd~Cd~~c~~esdL~kH~~~H 315 (467)
T KOG3608|consen 264 YKCPLCDMTCSSASSLTTHIRYRHSKDKP-FKCDECDTRCVRESDLAKHVQVH 315 (467)
T ss_pred ccccccccCCCChHHHHHHHHhhhccCCC-ccccchhhhhccHHHHHHHHHhc
Confidence 5777788888888888888775 444444 88888888888888888887655
No 21
>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=98.76 E-value=4.3e-09 Score=33.43 Aligned_cols=25 Identities=16% Similarity=0.359 Sum_probs=20.9
Q ss_pred CccCCCCCcccccchHHHHHHHhhc
Q psy12023 30 KYQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 30 ~~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
||+|..|++.|.....|..|++.|+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 4788889999998888888887765
No 22
>KOG3608|consensus
Probab=98.61 E-value=2.3e-08 Score=48.29 Aligned_cols=51 Identities=27% Similarity=0.552 Sum_probs=44.3
Q ss_pred CCCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccchHHHHHHHhhc
Q psy12023 1 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 1 p~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
+|.|..|.+.|.....|..|+..|.. - |+|+.|+.+....++|..|++..|
T Consensus 237 ~fqC~~C~KrFaTeklL~~Hv~rHvn--~-ykCplCdmtc~~~ssL~~H~r~rH 287 (467)
T KOG3608|consen 237 SFQCAQCFKRFATEKLLKSHVVRHVN--C-YKCPLCDMTCSSASSLTTHIRYRH 287 (467)
T ss_pred chHHHHHHHHHhHHHHHHHHHHHhhh--c-ccccccccCCCChHHHHHHHHhhh
Confidence 47888899999999889999888876 3 899999999999999999998776
No 23
>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=98.55 E-value=3.7e-08 Score=30.07 Aligned_cols=23 Identities=30% Similarity=0.826 Sum_probs=20.7
Q ss_pred CCCccccccccchhhHHhHHHHH
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFE 24 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~ 24 (55)
|.|..|++.|..+..|..|+..|
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 57999999999999999998864
No 24
>PHA00733 hypothetical protein
Probab=98.50 E-value=5.9e-08 Score=41.11 Aligned_cols=49 Identities=16% Similarity=0.202 Sum_probs=34.1
Q ss_pred CCccccccccchhhHHhH--H---HHHhCCCCCccCCCCCcccccchHHHHHHHh
Q psy12023 3 MCDVCGKGYKYKNGIYRH--K---KFECGQEPKYQCPQCPYRAKQNAHLTTHMAI 52 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~--~---~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~ 52 (55)
.|..|.+.+.....+..+ . ..+.+.++ |.|..|++.|...+.|..|++.
T Consensus 42 ~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kP-y~C~~Cgk~Fss~s~L~~H~r~ 95 (128)
T PHA00733 42 IRAVVKTLIYNPQLLDESSYLYKLLTSKAVSP-YVCPLCLMPFSSSVSLKQHIRY 95 (128)
T ss_pred HHHHHhhhccChhhhcchHHHHhhcccCCCCC-ccCCCCCCcCCCHHHHHHHHhc
Confidence 466677666655544444 1 12233455 9999999999999999999874
No 25
>smart00355 ZnF_C2H2 zinc finger.
Probab=98.44 E-value=2.2e-07 Score=28.68 Aligned_cols=23 Identities=35% Similarity=0.751 Sum_probs=18.3
Q ss_pred ccCCCCCcccccchHHHHHHHhh
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAIK 53 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~ 53 (55)
|.|..|++.|.....+..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 46788888888888888888754
No 26
>KOG3993|consensus
Probab=98.44 E-value=1.5e-08 Score=49.60 Aligned_cols=51 Identities=22% Similarity=0.511 Sum_probs=41.4
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccchHHHHHHHhh
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTHMAIK 53 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~ 53 (55)
|.|..|...+...-.|..|...-..-.- |+|+.|+|.|+-.++|..|.|.|
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vE-YrCPEC~KVFsCPANLASHRRWH 318 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVE-YRCPECDKVFSCPANLASHRRWH 318 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEee-ecCCcccccccCchhhhhhhccc
Confidence 4577788788777778888665554445 99999999999999999999987
No 27
>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=98.41 E-value=1.2e-07 Score=34.15 Aligned_cols=31 Identities=29% Similarity=0.636 Sum_probs=22.1
Q ss_pred hCCCCCccCCCCCcccccchHHHHHHHhhcC
Q psy12023 25 CGQEPKYQCPQCPYRAKQNAHLTTHMAIKHY 55 (55)
Q Consensus 25 ~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~ 55 (55)
....+|-.|++|+..+.+..+|++|+.+.|+
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhc
Confidence 3334448999999999999999999998885
No 28
>PRK04860 hypothetical protein; Provisional
Probab=98.30 E-value=5.8e-07 Score=39.43 Aligned_cols=38 Identities=21% Similarity=0.541 Sum_probs=31.6
Q ss_pred CCCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccc
Q psy12023 1 MFMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQN 43 (55)
Q Consensus 1 p~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~ 43 (55)
+|.|. |+. ....+..|.++++++++ |.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~-YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAV-YRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCcc-EECCCCCceeEEe
Confidence 47787 876 56678999999999888 9999999988654
No 29
>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=98.30 E-value=1.7e-07 Score=29.65 Aligned_cols=25 Identities=36% Similarity=0.828 Sum_probs=22.2
Q ss_pred CCCCccccccccchhhHHhHHHHHh
Q psy12023 1 MFMCDVCGKGYKYKNGIYRHKKFEC 25 (55)
Q Consensus 1 p~~c~~c~~~~~~~~~~~~~~~~~~ 25 (55)
||.|..|++.|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 6899999999999999999987654
No 30
>PHA00732 hypothetical protein
Probab=98.23 E-value=1.1e-06 Score=34.54 Aligned_cols=23 Identities=22% Similarity=0.528 Sum_probs=21.2
Q ss_pred CccCCCCCcccccchHHHHHHHh
Q psy12023 30 KYQCPQCPYRAKQNAHLTTHMAI 52 (55)
Q Consensus 30 ~~~c~~c~~~f~~~~~l~~h~~~ 52 (55)
||.|..|++.|.+.+.|..|++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~ 23 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARR 23 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhc
Confidence 48999999999999999999874
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=98.21 E-value=1.2e-06 Score=35.11 Aligned_cols=50 Identities=26% Similarity=0.613 Sum_probs=20.6
Q ss_pred CCccccccccchhhHHhHHHHHhC-----------------------CCCCccCCCCCcccccchHHHHHHHhh
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECG-----------------------QEPKYQCPQCPYRAKQNAHLTTHMAIK 53 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~-----------------------~~~~~~c~~c~~~f~~~~~l~~h~~~~ 53 (55)
+|..|+..|.....+..|+....+ ... +.|..|++.|.....|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~-~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKES-FRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ------------------------------------------------SS-EEBSSSS-EESSHHHHHHHHHHT
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCC-CCCCccCCCCcCHHHHHHHHcCc
Confidence 477788888777777777642211 123 78999999999999999999854
No 32
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.18 E-value=4.2e-06 Score=42.82 Aligned_cols=36 Identities=22% Similarity=0.479 Sum_probs=18.8
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCccc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRA 40 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f 40 (55)
+.|. |++.+ ....|..|+..+.+.++ +.|..|++.+
T Consensus 479 v~Cp-Cg~~~-~R~~L~~H~~thCp~Kp-i~C~fC~~~v 514 (567)
T PLN03086 479 LQCP-CGVVL-EKEQMVQHQASTCPLRL-ITCRFCGDMV 514 (567)
T ss_pred ccCC-CCCCc-chhHHHhhhhccCCCCc-eeCCCCCCcc
Confidence 3454 55433 33455555555555554 6666666655
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=98.17 E-value=1.4e-06 Score=26.38 Aligned_cols=23 Identities=30% Similarity=0.852 Sum_probs=18.8
Q ss_pred CCCccccccccchhhHHhHHHHH
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFE 24 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~ 24 (55)
|.|+.|++.|.....+..|+..+
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 57999999999999999998865
No 34
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.13 E-value=5.6e-06 Score=42.36 Aligned_cols=46 Identities=28% Similarity=0.689 Sum_probs=36.5
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccchHHHHHHHhh
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTHMAIK 53 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~ 53 (55)
+.|..|++.|. ...+..|+.++. ++ +.|+ |++.+ .+..|..|+..+
T Consensus 454 ~~C~~Cgk~f~-~s~LekH~~~~H--kp-v~Cp-Cg~~~-~R~~L~~H~~th 499 (567)
T PLN03086 454 VHCEKCGQAFQ-QGEMEKHMKVFH--EP-LQCP-CGVVL-EKEQMVQHQAST 499 (567)
T ss_pred ccCCCCCCccc-hHHHHHHHHhcC--CC-ccCC-CCCCc-chhHHHhhhhcc
Confidence 57999999996 577899999874 56 9999 99765 567888897654
No 35
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.09 E-value=1.9e-06 Score=26.63 Aligned_cols=22 Identities=18% Similarity=0.443 Sum_probs=17.2
Q ss_pred ccCCCCCcccccchHHHHHHHh
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAI 52 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~ 52 (55)
|.|.+|++.|.....+..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 4678888888888888888764
No 36
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=98.07 E-value=2.5e-06 Score=26.22 Aligned_cols=23 Identities=35% Similarity=1.005 Sum_probs=16.9
Q ss_pred ccCCCCCcccccchHHHHHHHhhc
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
|+|+.|+.... ...|..|++.+|
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 57888888777 778888888776
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=98.05 E-value=7.2e-06 Score=25.06 Aligned_cols=24 Identities=29% Similarity=0.663 Sum_probs=21.1
Q ss_pred CCCccccccccchhhHHhHHHHHh
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFEC 25 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~ 25 (55)
+.|..|++.|.....+..|+..|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999988654
No 38
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.96 E-value=2e-06 Score=41.36 Aligned_cols=50 Identities=34% Similarity=0.645 Sum_probs=37.9
Q ss_pred CCCCcc--ccccccchhhHHhHHHH-H-----------------h-CCCCCccCCCCCcccccchHHHHHHH
Q psy12023 1 MFMCDV--CGKGYKYKNGIYRHKKF-E-----------------C-GQEPKYQCPQCPYRAKQNAHLTTHMA 51 (55)
Q Consensus 1 p~~c~~--c~~~~~~~~~~~~~~~~-~-----------------~-~~~~~~~c~~c~~~f~~~~~l~~h~~ 51 (55)
||+|.+ |++.+.....|+-|+.- | . ..+| |+|.+|+|.++....|+-|..
T Consensus 349 pykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KP-YrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 349 PYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKP-YRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred eecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCc-eeccccchhhccCccceeccc
Confidence 678875 88888888888877651 1 0 1245 999999999999999987754
No 39
>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=97.69 E-value=4e-05 Score=27.77 Aligned_cols=29 Identities=21% Similarity=0.462 Sum_probs=21.3
Q ss_pred CCCCccccccccchhhHHhHHHHHhCCCC
Q psy12023 1 MFMCDVCGKGYKYKNGIYRHKKFECGQEP 29 (55)
Q Consensus 1 p~~c~~c~~~~~~~~~~~~~~~~~~~~~~ 29 (55)
|..|..|+.......+|.+|+++..+.++
T Consensus 24 PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 45799999999999999999998877654
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=97.58 E-value=1.5e-05 Score=25.16 Aligned_cols=21 Identities=24% Similarity=0.551 Sum_probs=15.2
Q ss_pred ccCCCCCcccccchHHHHHHH
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMA 51 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~ 51 (55)
|-|..|++.|.....+..|++
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 567777777777777777655
No 41
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=97.50 E-value=0.00014 Score=22.67 Aligned_cols=21 Identities=29% Similarity=0.574 Sum_probs=14.7
Q ss_pred ccCCCCCcccccchHHHHHHHh
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAI 52 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~ 52 (55)
..|+.|++.| ..+.|..|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4678888888 55567777653
No 42
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=97.25 E-value=0.00026 Score=23.34 Aligned_cols=21 Identities=14% Similarity=0.498 Sum_probs=17.9
Q ss_pred ccCCCCCcccccchHHHHHHH
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMA 51 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~ 51 (55)
|.|..|+..|.....+..|+.
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred eEccccCCccCCHHHHHHHHC
Confidence 789999999998888888865
No 43
>KOG2893|consensus
Probab=96.36 E-value=0.00098 Score=31.47 Aligned_cols=41 Identities=20% Similarity=0.516 Sum_probs=32.7
Q ss_pred CccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccchHHHHH
Q psy12023 4 CDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTH 49 (55)
Q Consensus 4 c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h 49 (55)
|..|++.|.....|..|+.. +. |+|.+|-+.+..-..|..|
T Consensus 13 cwycnrefddekiliqhqka----kh-fkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----KH-FKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhhh----cc-ceeeeehhhhccCCCceee
Confidence 77899999998888888763 67 9999998877666666666
No 44
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=96.29 E-value=0.00065 Score=33.09 Aligned_cols=51 Identities=22% Similarity=0.546 Sum_probs=42.9
Q ss_pred CCCccccccccchhhHHhHHH--HHhCC--CCCccCC--CCCcccccchHHHHHHHhh
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKK--FECGQ--EPKYQCP--QCPYRAKQNAHLTTHMAIK 53 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~--~~~~~--~~~~~c~--~c~~~f~~~~~l~~h~~~~ 53 (55)
+.|..|...+.....+..+.. .|.++ ++ +.|. .|++.|.+...+..|..++
T Consensus 290 ~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~-~~~p~~~~~~~~~~~~~~~~~~~~~ 346 (467)
T COG5048 290 IKSKQCNISFSRSSPLTRHLRSVNHSGESLKP-FSCPYSLCGKLFSRNDALKRHILLH 346 (467)
T ss_pred CCCccccCCccccccccccccccccccccCCc-eeeeccCCCccccccccccCCcccc
Confidence 467788888999999999999 89998 66 9998 7999999998888776654
No 45
>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=95.76 E-value=0.0074 Score=19.86 Aligned_cols=25 Identities=36% Similarity=0.978 Sum_probs=16.9
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYR 39 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~ 39 (55)
|.|..||....... .+ +.|++|+..
T Consensus 2 ~~C~~CGy~y~~~~------------~~-~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEE------------AP-WVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCc------------CC-CcCcCCCCc
Confidence 67888887654321 34 899999863
No 46
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=95.71 E-value=0.0052 Score=22.76 Aligned_cols=26 Identities=23% Similarity=0.571 Sum_probs=18.0
Q ss_pred CCCCCccCCCCCcccccchHHHHHHHh
Q psy12023 26 GQEPKYQCPQCPYRAKQNAHLTTHMAI 52 (55)
Q Consensus 26 ~~~~~~~c~~c~~~f~~~~~l~~h~~~ 52 (55)
|+.- +.|+-|+..|..+-+..+|...
T Consensus 14 GE~~-lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 14 GEEF-LRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred Ccee-eeCCchhHHHHHhHHHHHHhhH
Confidence 4444 6788888888877777777553
No 47
>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=95.56 E-value=0.01 Score=19.73 Aligned_cols=24 Identities=38% Similarity=0.905 Sum_probs=16.1
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPY 38 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~ 38 (55)
|.|..||.... ++.+|..|++|+.
T Consensus 3 ~~C~~CG~i~~-------------g~~~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGYIHE-------------GEEAPEKCPICGA 26 (34)
T ss_pred EECCCCCCEeE-------------CCcCCCcCcCCCC
Confidence 57888886643 2234478999986
No 48
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=95.53 E-value=0.011 Score=19.99 Aligned_cols=33 Identities=18% Similarity=0.590 Sum_probs=22.1
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAK 41 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~ 41 (55)
.|+.|+..|....+. +..+... .+|..|+..|.
T Consensus 4 ~CP~C~~~f~v~~~~-----l~~~~~~-vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDK-----LPAGGRK-VRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHH-----cccCCcE-EECCCCCcEee
Confidence 588888888765432 1233345 89999998774
No 49
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=95.12 E-value=0.015 Score=19.59 Aligned_cols=33 Identities=15% Similarity=0.346 Sum_probs=21.6
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAK 41 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~ 41 (55)
.|+.|+..|...... +-..... .+|..|+..|.
T Consensus 4 ~Cp~C~~~y~i~d~~-----ip~~g~~-v~C~~C~~~f~ 36 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEK-----IPPKGRK-VRCSKCGHVFF 36 (36)
T ss_pred ECCCCCCEEeCCHHH-----CCCCCcE-EECCCCCCEeC
Confidence 578888888765543 1122344 78999998763
No 50
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=94.87 E-value=0.0047 Score=27.35 Aligned_cols=40 Identities=15% Similarity=0.228 Sum_probs=21.2
Q ss_pred CCCccccccccc-hhhHHhHHHHHhCCCCCccCCCCCcccccc
Q psy12023 2 FMCDVCGKGYKY-KNGIYRHKKFECGQEPKYQCPQCPYRAKQN 43 (55)
Q Consensus 2 ~~c~~c~~~~~~-~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~ 43 (55)
.+|+.||..... .++...-.... -.+. ++|+.||.+|...
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~-~~~~-~~c~~c~~~f~~~ 41 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNA-IRRR-RECLACGKRFTTF 41 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCc-eeee-eeccccCCcceEe
Confidence 368899976521 11110000000 1134 8899999999654
No 51
>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=94.81 E-value=0.021 Score=26.67 Aligned_cols=26 Identities=27% Similarity=0.565 Sum_probs=20.0
Q ss_pred CCCccCCCCCcccccchHHHHHHHhhc
Q psy12023 28 EPKYQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 28 ~~~~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
.+ |.|.+|+|.|.-......|+...|
T Consensus 76 ~K-~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 76 DK-WRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp EE-EEE-SSS-EESSHHHHHHHHHHH-
T ss_pred CE-ECCCCCCcccCChHHHHHHHhhcC
Confidence 45 999999999999999999987665
No 52
>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=94.78 E-value=0.02 Score=19.23 Aligned_cols=34 Identities=12% Similarity=0.340 Sum_probs=22.0
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAK 41 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~ 41 (55)
..|..|+..|....+... ..... ..|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~-----~~~~~-v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG-----ANGGK-VRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcC-----CCCCE-EECCCCCCEEE
Confidence 358889988876553311 12234 78999998774
No 53
>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=94.68 E-value=0.052 Score=18.79 Aligned_cols=23 Identities=26% Similarity=0.453 Sum_probs=15.9
Q ss_pred ccCCCCCccccc----chHHHHHHHhh
Q psy12023 31 YQCPQCPYRAKQ----NAHLTTHMAIK 53 (55)
Q Consensus 31 ~~c~~c~~~f~~----~~~l~~h~~~~ 53 (55)
.+|..|++.+.. .+.|..|++..
T Consensus 17 a~C~~C~~~~~~~~~~ts~l~~HL~~~ 43 (45)
T PF02892_consen 17 AKCKYCGKVIKYSSGGTSNLKRHLKKK 43 (45)
T ss_dssp EEETTTTEE-----SSTHHHHHHHHHT
T ss_pred EEeCCCCeEEeeCCCcHHHHHHhhhhh
Confidence 789999987766 47888998543
No 54
>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=94.58 E-value=0.028 Score=24.95 Aligned_cols=30 Identities=17% Similarity=0.579 Sum_probs=20.8
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAK 41 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~ 41 (55)
|.|+.|+..|.....+. .. |.|+.||..+.
T Consensus 110 Y~Cp~c~~r~tf~eA~~---------~~-F~Cp~Cg~~L~ 139 (158)
T TIGR00373 110 FICPNMCVRFTFNEAME---------LN-FTCPRCGAMLD 139 (158)
T ss_pred EECCCCCcEeeHHHHHH---------cC-CcCCCCCCEee
Confidence 46888887777665542 24 89999987654
No 55
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=94.51 E-value=0.028 Score=25.48 Aligned_cols=30 Identities=23% Similarity=0.780 Sum_probs=21.1
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAK 41 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~ 41 (55)
|.|+.|+..|.....+ +.. |.|+.||..+-
T Consensus 118 Y~Cp~C~~rytf~eA~---------~~~-F~Cp~Cg~~L~ 147 (178)
T PRK06266 118 FFCPNCHIRFTFDEAM---------EYG-FRCPQCGEMLE 147 (178)
T ss_pred EECCCCCcEEeHHHHh---------hcC-CcCCCCCCCCe
Confidence 5688888887765543 124 99999997654
No 56
>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=94.19 E-value=0.06 Score=22.32 Aligned_cols=25 Identities=28% Similarity=0.756 Sum_probs=22.6
Q ss_pred ccC----CCCCcccccchHHHHHHHhhcC
Q psy12023 31 YQC----PQCPYRAKQNAHLTTHMAIKHY 55 (55)
Q Consensus 31 ~~c----~~c~~~f~~~~~l~~h~~~~~~ 55 (55)
|.| ..|+........+..|.+.+|.
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 8999999999999999998874
No 57
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=94.17 E-value=0.044 Score=20.62 Aligned_cols=8 Identities=50% Similarity=1.867 Sum_probs=5.4
Q ss_pred ccCCCCCc
Q psy12023 31 YQCPQCPY 38 (55)
Q Consensus 31 ~~c~~c~~ 38 (55)
|.|+.||.
T Consensus 51 Y~Cp~CGF 58 (61)
T COG2888 51 YRCPKCGF 58 (61)
T ss_pred eECCCcCc
Confidence 77777763
No 58
>KOG2186|consensus
Probab=94.03 E-value=0.039 Score=26.49 Aligned_cols=45 Identities=22% Similarity=0.499 Sum_probs=33.0
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccchHHHHHH
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQNAHLTTHM 50 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~ 50 (55)
|.|+.||....-. .+..|+....+ .- |.|.-|++.|.+ .+...|.
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn-~~-fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN-AY-FSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC-Ce-eEEeeccccccc-chhhhhh
Confidence 5799999876644 45668887777 45 899999999987 4455564
No 59
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=93.79 E-value=0.05 Score=19.19 Aligned_cols=26 Identities=31% Similarity=0.993 Sum_probs=17.9
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYR 39 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~ 39 (55)
|.|..||..+... ...+ .+|+.||..
T Consensus 3 Y~C~~Cg~~~~~~-----------~~~~-irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-----------SKDV-VRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-----------CCCc-eECCCCCce
Confidence 6788899876532 1234 899999864
No 60
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=93.58 E-value=0.031 Score=19.65 Aligned_cols=29 Identities=28% Similarity=0.707 Sum_probs=19.2
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAK 41 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~ 41 (55)
|.|..||..+...... .. ..|+.||..+-
T Consensus 4 y~C~~CG~~~~~~~~~----------~~-~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYG----------TG-VRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCC----------Cc-eECCCCCCeEE
Confidence 6788898877553211 14 78999987543
No 61
>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=93.52 E-value=0.068 Score=22.46 Aligned_cols=29 Identities=21% Similarity=0.561 Sum_probs=19.4
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQN 43 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~ 43 (55)
.|..||+.|=.. + +.|..|+.||..|.-.
T Consensus 11 ~Cp~CG~kFYDL-----------n-k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAKFYDL-----------N-KDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcchhccC-----------C-CCCccCCCCCCccCcc
Confidence 577888777331 2 3448899999877654
No 62
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=93.51 E-value=0.059 Score=24.30 Aligned_cols=10 Identities=30% Similarity=0.680 Sum_probs=6.6
Q ss_pred CCccCCCCCc
Q psy12023 29 PKYQCPQCPY 38 (55)
Q Consensus 29 ~~~~c~~c~~ 38 (55)
+|-.|++||.
T Consensus 148 ~P~~CPiCga 157 (166)
T COG1592 148 APEVCPICGA 157 (166)
T ss_pred CCCcCCCCCC
Confidence 3477888774
No 63
>KOG1146|consensus
Probab=93.46 E-value=0.069 Score=31.01 Aligned_cols=49 Identities=27% Similarity=0.614 Sum_probs=39.6
Q ss_pred CCCccccccccchhhHHhHHHHHh-------------------------CCCCCccCCCCCcccccchHHHHHHH
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFEC-------------------------GQEPKYQCPQCPYRAKQNAHLTTHMA 51 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~-------------------------~~~~~~~c~~c~~~f~~~~~l~~h~~ 51 (55)
+.|..|+..+.....|-.|++.-. +.++ |.|..|...++...+|.+|+.
T Consensus 466 ~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p-~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 466 LKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKP-YPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred ccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCc-ccceeeeeeeecchHHHHHHH
Confidence 578999999999999999988610 1134 889999999999999999965
No 64
>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=93.31 E-value=0.026 Score=20.25 Aligned_cols=29 Identities=21% Similarity=0.661 Sum_probs=18.6
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPY 38 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~ 38 (55)
|.|..||..|...... .. +.. ..|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~------~~-~~~-~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKM------SD-DPL-ATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEec------CC-CCC-CCCCCCCC
Confidence 6799999888654321 11 233 57999986
No 65
>PHA00626 hypothetical protein
Probab=93.30 E-value=0.029 Score=20.84 Aligned_cols=14 Identities=36% Similarity=0.940 Sum_probs=11.6
Q ss_pred ccCCCCCcccccch
Q psy12023 31 YQCPQCPYRAKQNA 44 (55)
Q Consensus 31 ~~c~~c~~~f~~~~ 44 (55)
|+|..|+..|+..+
T Consensus 24 YkCkdCGY~ft~~~ 37 (59)
T PHA00626 24 YVCCDCGYNDSKDA 37 (59)
T ss_pred eEcCCCCCeechhh
Confidence 99999999887553
No 66
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=93.26 E-value=0.061 Score=23.59 Aligned_cols=35 Identities=17% Similarity=0.579 Sum_probs=21.6
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAK 41 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~ 41 (55)
|.|+.|+..|.....+... .. ... |.|+.||....
T Consensus 100 Y~Cp~C~~~y~~~ea~~~~---d~-~~~-f~Cp~Cg~~l~ 134 (147)
T smart00531 100 YKCPNCQSKYTFLEANQLL---DM-DGT-FTCPRCGEELE 134 (147)
T ss_pred EECcCCCCEeeHHHHHHhc---CC-CCc-EECCCCCCEEE
Confidence 5688898888754432211 11 234 89999987653
No 67
>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=92.87 E-value=0.079 Score=17.44 Aligned_cols=27 Identities=37% Similarity=1.069 Sum_probs=15.7
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCccc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRA 40 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f 40 (55)
|.|..|+..+.... + .+ .+|..||...
T Consensus 1 Y~C~~Cg~~~~~~~----------~-~~-irC~~CG~RI 27 (32)
T PF03604_consen 1 YICGECGAEVELKP----------G-DP-IRCPECGHRI 27 (32)
T ss_dssp EBESSSSSSE-BST----------S-ST-SSBSSSS-SE
T ss_pred CCCCcCCCeeEcCC----------C-Cc-EECCcCCCeE
Confidence 46778887664221 2 33 7899998643
No 68
>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=92.43 E-value=0.17 Score=15.71 Aligned_cols=20 Identities=25% Similarity=0.624 Sum_probs=12.6
Q ss_pred ccCCCCCcccccchHHHHHHH
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMA 51 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~ 51 (55)
..|++|++.+ ....+..|.-
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3577888777 4455666643
No 69
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=92.01 E-value=0.23 Score=17.74 Aligned_cols=21 Identities=19% Similarity=0.547 Sum_probs=17.0
Q ss_pred ccCCCCCcccccc-----hHHHHHHH
Q psy12023 31 YQCPQCPYRAKQN-----AHLTTHMA 51 (55)
Q Consensus 31 ~~c~~c~~~f~~~-----~~l~~h~~ 51 (55)
..|..|++.+... ++|.+|+.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 6789999887654 68999987
No 70
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=91.79 E-value=0.16 Score=19.12 Aligned_cols=7 Identities=57% Similarity=1.820 Sum_probs=3.8
Q ss_pred ccCCCCC
Q psy12023 31 YQCPQCP 37 (55)
Q Consensus 31 ~~c~~c~ 37 (55)
|.|+.||
T Consensus 49 Y~CP~CG 55 (59)
T PRK14890 49 YTCPKCG 55 (59)
T ss_pred eECCCCC
Confidence 5555554
No 71
>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=91.72 E-value=0.12 Score=22.57 Aligned_cols=21 Identities=29% Similarity=0.600 Sum_probs=14.0
Q ss_pred ccCCCCCcccccchHHHHHHHhhc
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
..|-+||+.|.. |.+|.+.||
T Consensus 73 i~clecGk~~k~---LkrHL~~~~ 93 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHH 93 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT
T ss_pred eEEccCCcccch---HHHHHHHcc
Confidence 678899998865 488988886
No 72
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=91.59 E-value=0.1 Score=20.38 Aligned_cols=39 Identities=18% Similarity=0.398 Sum_probs=22.2
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCC--CCCcccccc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCP--QCPYRAKQN 43 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~--~c~~~f~~~ 43 (55)
+.|..||........-.... ...+.- ++|. .||.+|...
T Consensus 2 m~CP~Cg~~a~irtSr~~s~--~~~~~Y-~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITD--TTKERY-HQCQNVNCSATFITY 42 (72)
T ss_pred ccCCCCCCccEEEEChhcCh--hhheee-eecCCCCCCCEEEEE
Confidence 46888887664333222221 133344 7787 799988653
No 73
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=90.59 E-value=0.16 Score=20.77 Aligned_cols=11 Identities=18% Similarity=0.833 Sum_probs=5.2
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
-.|..||..|.
T Consensus 59 a~CkkCGfef~ 69 (97)
T COG3357 59 ARCKKCGFEFR 69 (97)
T ss_pred hhhcccCcccc
Confidence 44555554443
No 74
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.15 E-value=0.28 Score=24.23 Aligned_cols=52 Identities=23% Similarity=0.499 Sum_probs=39.1
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCC--CCcccccchHHHHHHHhhc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQ--CPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~--c~~~f~~~~~l~~h~~~~~ 54 (55)
+.|..|...+........+...+.++++ ..|.. |...+.....+..+...++
T Consensus 34 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 (467)
T COG5048 34 DSCPNCTDSFSRLEHLTRHIRSHTGEKP-SQCSYSGCDKSFSRPLELSRHLRTHH 87 (467)
T ss_pred hhcccccccccccchhhhhcccccccCC-ccccccccccccCCcchhhhhccccc
Confidence 3567788888888888999999999887 78754 5667777777777666554
No 75
>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=89.90 E-value=0.17 Score=15.59 Aligned_cols=8 Identities=38% Similarity=1.651 Sum_probs=6.7
Q ss_pred ccCCCCCc
Q psy12023 31 YQCPQCPY 38 (55)
Q Consensus 31 ~~c~~c~~ 38 (55)
|.|+.||+
T Consensus 17 f~CPnCG~ 24 (24)
T PF07754_consen 17 FPCPNCGF 24 (24)
T ss_pred EeCCCCCC
Confidence 89999884
No 76
>PF15269 zf-C2H2_7: Zinc-finger
Probab=89.65 E-value=0.31 Score=17.35 Aligned_cols=22 Identities=41% Similarity=1.000 Sum_probs=17.6
Q ss_pred ccCCCCCcccccchHHHHHHHh
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAI 52 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~ 52 (55)
|+|-+|..+....+.|-.|++.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 6677888888888888888763
No 77
>KOG4173|consensus
Probab=89.34 E-value=0.16 Score=23.88 Aligned_cols=51 Identities=24% Similarity=0.443 Sum_probs=35.8
Q ss_pred CCccccccccchhhHHhHHHH-H---------hCCCCCccC--CCCCcccccchHHHHHHHhhc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKF-E---------CGQEPKYQC--PQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~-~---------~~~~~~~~c--~~c~~~f~~~~~l~~h~~~~~ 54 (55)
.|.+|.+.|.....|..|+.- | .| ..-|+| ..|+..|...-....|+-..|
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG-~dMy~ClvEgCt~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERG-QDMYQCLVEGCTEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcC-ccHHHHHHHhhhhhhhhhhhhhhHHHHhc
Confidence 588899999988888777652 2 22 333777 458888888877778865443
No 78
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=89.17 E-value=0.27 Score=19.98 Aligned_cols=11 Identities=18% Similarity=0.769 Sum_probs=7.9
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
+.|..|+..|.
T Consensus 54 W~C~kCg~~fA 64 (89)
T COG1997 54 WKCRKCGAKFA 64 (89)
T ss_pred EEcCCCCCeec
Confidence 67777777664
No 79
>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=89.08 E-value=0.47 Score=20.66 Aligned_cols=29 Identities=10% Similarity=0.122 Sum_probs=19.1
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQN 43 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~ 43 (55)
.|..||+.|=.. + +.|..|+.||..+.-.
T Consensus 11 ~Cp~cg~kFYDL-----------n-k~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 11 ICPNTGSKFYDL-----------N-RRPAVSPYTGEQFPPE 39 (129)
T ss_pred cCCCcCcccccc-----------C-CCCccCCCcCCccCcc
Confidence 577788776331 2 3448899999877544
No 80
>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=88.43 E-value=0.22 Score=17.23 Aligned_cols=12 Identities=25% Similarity=0.764 Sum_probs=8.9
Q ss_pred ccCCCCCccccc
Q psy12023 31 YQCPQCPYRAKQ 42 (55)
Q Consensus 31 ~~c~~c~~~f~~ 42 (55)
|+|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (42)
T PF09723_consen 6 YRCEECGHEFEV 17 (42)
T ss_pred EEeCCCCCEEEE
Confidence 778888877754
No 81
>PF14353 CpXC: CpXC protein
Probab=88.29 E-value=0.019 Score=24.42 Aligned_cols=42 Identities=19% Similarity=0.480 Sum_probs=23.5
Q ss_pred CCccccccccchhhHH--------hHHHHHhCCCCCccCCCCCcccccch
Q psy12023 3 MCDVCGKGYKYKNGIY--------RHKKFECGQEPKYQCPQCPYRAKQNA 44 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~--------~~~~~~~~~~~~~~c~~c~~~f~~~~ 44 (55)
.|..|+..|....... ....+-.|+--.+.|+.||..|.-..
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~ 52 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEY 52 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCC
Confidence 5778887765332111 12223344433388999999876443
No 82
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=88.28 E-value=0.24 Score=17.97 Aligned_cols=27 Identities=26% Similarity=0.741 Sum_probs=16.3
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYR 39 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~ 39 (55)
|.|..||+.+... ..... ..|+-||..
T Consensus 7 Y~C~~Cg~~~~~~----------~~~~~-irCp~Cg~r 33 (49)
T COG1996 7 YKCARCGREVELD----------QETRG-IRCPYCGSR 33 (49)
T ss_pred EEhhhcCCeeehh----------hccCc-eeCCCCCcE
Confidence 5688888877211 11233 788888853
No 83
>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=88.14 E-value=0.064 Score=19.59 Aligned_cols=23 Identities=22% Similarity=0.625 Sum_probs=13.4
Q ss_pred ccCCCCCcccccchHHHHHHHhh
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAIK 53 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~ 53 (55)
|+|+.|...|...-.+-.|+.+|
T Consensus 22 y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 22 YRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp E--TTTT--B-HHHHHTTTTTS-
T ss_pred EECCCCCCccccCcChhhhcccc
Confidence 99999999998777776676655
No 84
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=87.54 E-value=0.24 Score=20.27 Aligned_cols=11 Identities=18% Similarity=0.721 Sum_probs=6.7
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
+.|..|++.|.
T Consensus 55 W~C~~C~~~~A 65 (90)
T PTZ00255 55 WRCKGCKKTVA 65 (90)
T ss_pred EEcCCCCCEEe
Confidence 56666666553
No 85
>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=87.41 E-value=0.3 Score=16.39 Aligned_cols=11 Identities=27% Similarity=0.836 Sum_probs=8.4
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
|+|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 67888888764
No 86
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=87.31 E-value=0.62 Score=19.85 Aligned_cols=23 Identities=17% Similarity=0.417 Sum_probs=19.6
Q ss_pred ccCCCCCcccccchHHHHHHHhh
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAIK 53 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~ 53 (55)
|+|+.|...|...-+.-.|..+|
T Consensus 82 y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 82 YVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred eeCCCCCCccccccchhhhhhcc
Confidence 88999999999888888887765
No 87
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=86.93 E-value=0.89 Score=15.68 Aligned_cols=23 Identities=17% Similarity=0.320 Sum_probs=14.8
Q ss_pred ccCCCCCccccc--chHHHHHHHhh
Q psy12023 31 YQCPQCPYRAKQ--NAHLTTHMAIK 53 (55)
Q Consensus 31 ~~c~~c~~~f~~--~~~l~~h~~~~ 53 (55)
..|..||..+.. ...-..|.+.|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 578999987754 34445565544
No 88
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=86.93 E-value=0.36 Score=21.08 Aligned_cols=15 Identities=20% Similarity=0.603 Sum_probs=12.9
Q ss_pred CCCCccccccccchh
Q psy12023 1 MFMCDVCGKGYKYKN 15 (55)
Q Consensus 1 p~~c~~c~~~~~~~~ 15 (55)
|++|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 789999999998765
No 89
>KOG2593|consensus
Probab=86.44 E-value=0.58 Score=24.37 Aligned_cols=33 Identities=18% Similarity=0.607 Sum_probs=16.6
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPY 38 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~ 38 (55)
|.|+.|.+.|.....+ +......-. |.|..|+-
T Consensus 129 Y~Cp~C~kkyt~Lea~---~L~~~~~~~-F~C~~C~g 161 (436)
T KOG2593|consen 129 YVCPNCQKKYTSLEAL---QLLDNETGE-FHCENCGG 161 (436)
T ss_pred ccCCccccchhhhHHH---HhhcccCce-EEEecCCC
Confidence 5677777666544332 222222223 66766653
No 90
>KOG4167|consensus
Probab=86.04 E-value=0.097 Score=28.83 Aligned_cols=23 Identities=17% Similarity=0.353 Sum_probs=19.1
Q ss_pred ccCCCCCcccccchHHHHHHHhh
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAIK 53 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~ 53 (55)
|.|.+|++.|-.--++.-||+.|
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHH
Confidence 88999999998777777787765
No 91
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=85.95 E-value=0.45 Score=22.30 Aligned_cols=16 Identities=25% Similarity=0.563 Sum_probs=12.5
Q ss_pred CCCccCCCCCcccccch
Q psy12023 28 EPKYQCPQCPYRAKQNA 44 (55)
Q Consensus 28 ~~~~~c~~c~~~f~~~~ 44 (55)
+. +.|++|++.|....
T Consensus 4 k~-~~CPvC~~~F~~~~ 19 (214)
T PF09986_consen 4 KK-ITCPVCGKEFKTKK 19 (214)
T ss_pred Cc-eECCCCCCeeeeeE
Confidence 45 78999999887653
No 92
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=85.72 E-value=0.3 Score=17.70 Aligned_cols=15 Identities=27% Similarity=0.939 Sum_probs=10.5
Q ss_pred CCCccccccccchhh
Q psy12023 2 FMCDVCGKGYKYKNG 16 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~ 16 (55)
+.|..||..|.....
T Consensus 5 l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 5 LTCKDCGAEFVFTAG 19 (49)
T ss_pred EEcccCCCeEEEehh
Confidence 468888888776544
No 93
>KOG2071|consensus
Probab=85.71 E-value=0.75 Score=24.87 Aligned_cols=23 Identities=30% Similarity=0.600 Sum_probs=19.9
Q ss_pred ccCCCCCcccccchHHHHHHHhh
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAIK 53 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~ 53 (55)
-+|..||.+|.+......|+-+|
T Consensus 419 nqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 419 NQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred chhcccccccccchhhhhHhhhh
Confidence 78999999999988888887665
No 94
>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=85.44 E-value=0.15 Score=16.32 Aligned_cols=9 Identities=33% Similarity=0.877 Sum_probs=5.7
Q ss_pred CCccccccc
Q psy12023 3 MCDVCGKGY 11 (55)
Q Consensus 3 ~c~~c~~~~ 11 (55)
.|-.|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 456666666
No 95
>KOG2231|consensus
Probab=85.41 E-value=1.2 Score=24.66 Aligned_cols=48 Identities=23% Similarity=0.579 Sum_probs=27.3
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCC------CcccccchHHHHHHHhhcC
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQC------PYRAKQNAHLTTHMAIKHY 55 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c------~~~f~~~~~l~~h~~~~~~ 55 (55)
.|..|...|.....+..|+..+ . |.|..| ..-|.....|..|-+..||
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~----h-~~chfC~~~~~~neyy~~~~dLe~HfR~~Hf 237 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFD----H-EFCHFCDYKTGQNEYYNDYDDLEEHFRKGHF 237 (669)
T ss_pred cchhhhhhhccHHHHHHhhccc----e-eheeecCcccccchhcccchHHHHHhhhcCc
Confidence 3566666666666666665522 2 344444 2345566667777666665
No 96
>KOG2071|consensus
Probab=85.04 E-value=0.77 Score=24.84 Aligned_cols=25 Identities=16% Similarity=0.357 Sum_probs=20.7
Q ss_pred CCCccccccccchhhHHhHHHHHhC
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECG 26 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~ 26 (55)
-+|..||..|........++.+|..
T Consensus 419 nqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 419 NQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred chhcccccccccchhhhhHhhhhhh
Confidence 4799999999999888888877653
No 97
>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=84.99 E-value=0.29 Score=20.04 Aligned_cols=10 Identities=20% Similarity=0.810 Sum_probs=6.0
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
+.|..|++.|
T Consensus 54 W~C~~C~~~~ 63 (91)
T TIGR00280 54 WTCRKCGAKF 63 (91)
T ss_pred EEcCCCCCEE
Confidence 5666666655
No 98
>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=84.41 E-value=0.71 Score=14.38 Aligned_cols=11 Identities=36% Similarity=0.966 Sum_probs=8.1
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 36888888774
No 99
>PF12907 zf-met2: Zinc-binding
Probab=84.10 E-value=0.2 Score=17.35 Aligned_cols=21 Identities=24% Similarity=0.411 Sum_probs=11.1
Q ss_pred ccCCCCCccccc---chHHHHHHH
Q psy12023 31 YQCPQCPYRAKQ---NAHLTTHMA 51 (55)
Q Consensus 31 ~~c~~c~~~f~~---~~~l~~h~~ 51 (55)
+.|.+|..+|.. ...|..|-.
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 456666655432 344666643
No 100
>KOG0978|consensus
Probab=84.00 E-value=0.56 Score=25.91 Aligned_cols=19 Identities=26% Similarity=0.515 Sum_probs=14.8
Q ss_pred ccCCCCCcccccchHHHHH
Q psy12023 31 YQCPQCPYRAKQNAHLTTH 49 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h 49 (55)
-+|+.|+.+|.....+..|
T Consensus 679 RKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 679 RKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred CCCCCCCCCCCcccccccC
Confidence 5899999999887665543
No 101
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=83.63 E-value=0.36 Score=21.02 Aligned_cols=13 Identities=31% Similarity=0.899 Sum_probs=9.3
Q ss_pred CCCccccccccch
Q psy12023 2 FMCDVCGKGYKYK 14 (55)
Q Consensus 2 ~~c~~c~~~~~~~ 14 (55)
+.|..||..|...
T Consensus 71 ~~C~~CG~~~~~~ 83 (135)
T PRK03824 71 LKCRNCGNEWSLK 83 (135)
T ss_pred EECCCCCCEEecc
Confidence 4688898777653
No 102
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=82.99 E-value=0.78 Score=15.66 Aligned_cols=13 Identities=15% Similarity=0.501 Sum_probs=10.7
Q ss_pred ccCCCCCcccccc
Q psy12023 31 YQCPQCPYRAKQN 43 (55)
Q Consensus 31 ~~c~~c~~~f~~~ 43 (55)
+.|..|+..|...
T Consensus 13 f~C~~C~~~FC~~ 25 (39)
T smart00154 13 FKCRHCGNLFCGE 25 (39)
T ss_pred eECCccCCccccc
Confidence 8999999988654
No 103
>KOG2482|consensus
Probab=82.88 E-value=0.91 Score=23.19 Aligned_cols=23 Identities=26% Similarity=0.462 Sum_probs=20.6
Q ss_pred ccCCCCCcccccchHHHHHHHhh
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAIK 53 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~ 53 (55)
++|--|.+.|+.+..|+.|||..
T Consensus 196 ~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred heeeeeccccCCcHHHHHHHHhc
Confidence 78888999999999999999843
No 104
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=82.48 E-value=0.42 Score=19.58 Aligned_cols=10 Identities=20% Similarity=0.866 Sum_probs=5.5
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
+.|..|++.|
T Consensus 55 W~C~~C~~~~ 64 (90)
T PRK03976 55 WECRKCGAKF 64 (90)
T ss_pred EEcCCCCCEE
Confidence 5555555544
No 105
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=82.30 E-value=1.1 Score=19.78 Aligned_cols=21 Identities=19% Similarity=0.254 Sum_probs=15.3
Q ss_pred ccCCCCCcccccchHHHHHHHhhc
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
..|-++|+.|. +|++|+.+|+
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~ 97 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHY 97 (148)
T ss_pred EEEeccCcchH---HHHHHHhccc
Confidence 45777788774 5888988875
No 106
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=81.59 E-value=0.4 Score=21.49 Aligned_cols=13 Identities=23% Similarity=0.447 Sum_probs=10.0
Q ss_pred ccCCCCCcccccc
Q psy12023 31 YQCPQCPYRAKQN 43 (55)
Q Consensus 31 ~~c~~c~~~f~~~ 43 (55)
-+|..|+..|.+.
T Consensus 29 ReC~~C~~RFTTf 41 (156)
T COG1327 29 RECLECGERFTTF 41 (156)
T ss_pred hcccccccccchh
Confidence 5788999888653
No 107
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=81.22 E-value=0.63 Score=17.39 Aligned_cols=40 Identities=20% Similarity=0.454 Sum_probs=20.8
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCCccccc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQ 42 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~ 42 (55)
.|..|++...-........+.-......|.|+.|......
T Consensus 4 kC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~RI~~ 43 (56)
T PF09963_consen 4 KCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKERIRE 43 (56)
T ss_pred EEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHHHhH
Confidence 3666776655433322222222233445889988765443
No 108
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=80.90 E-value=1.2 Score=18.77 Aligned_cols=15 Identities=20% Similarity=0.547 Sum_probs=12.2
Q ss_pred CCCCccccccccchh
Q psy12023 1 MFMCDVCGKGYKYKN 15 (55)
Q Consensus 1 p~~c~~c~~~~~~~~ 15 (55)
|+.|..||..|..-+
T Consensus 2 pH~CtrCG~vf~~g~ 16 (112)
T COG3364 2 PHQCTRCGEVFDDGS 16 (112)
T ss_pred Cceeccccccccccc
Confidence 678999999998754
No 109
>KOG1146|consensus
Probab=80.67 E-value=0.29 Score=28.77 Aligned_cols=27 Identities=33% Similarity=0.675 Sum_probs=23.2
Q ss_pred CCCCccCCCCCcccccchHHHHHHHhhc
Q psy12023 27 QEPKYQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 27 ~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
.+. +.|+.|+..++....|-.|+|..|
T Consensus 463 ~kt-~~cpkc~~~yk~a~~L~vhmRskh 489 (1406)
T KOG1146|consen 463 FKT-LKCPKCNWHYKLAQTLGVHMRSKH 489 (1406)
T ss_pred ccc-ccCCccchhhhhHHHhhhcccccc
Confidence 345 899999999999999999999744
No 110
>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=80.50 E-value=0.56 Score=16.23 Aligned_cols=13 Identities=15% Similarity=0.524 Sum_probs=8.2
Q ss_pred ccCCCCCcccccc
Q psy12023 31 YQCPQCPYRAKQN 43 (55)
Q Consensus 31 ~~c~~c~~~f~~~ 43 (55)
+.|..|++.|...
T Consensus 14 ~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 14 FKCKHCGKSFCLK 26 (43)
T ss_dssp EE-TTTS-EE-TT
T ss_pred eECCCCCcccCcc
Confidence 8999999988654
No 111
>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=79.96 E-value=1.8 Score=22.96 Aligned_cols=24 Identities=25% Similarity=0.664 Sum_probs=19.8
Q ss_pred ccCCCCCcccccchHHHHHHHhhc
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
+.|+.|.+.|.....+..|+..-|
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH 81 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEH 81 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhh
Confidence 568999999999999999976444
No 112
>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=79.37 E-value=0.29 Score=20.01 Aligned_cols=10 Identities=20% Similarity=0.873 Sum_probs=5.4
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
+.|..|++.|
T Consensus 54 W~C~~C~~~~ 63 (90)
T PF01780_consen 54 WKCKKCGKKF 63 (90)
T ss_dssp EEETTTTEEE
T ss_pred eecCCCCCEE
Confidence 5555555544
No 113
>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=79.37 E-value=1.1 Score=18.88 Aligned_cols=11 Identities=27% Similarity=0.839 Sum_probs=5.9
Q ss_pred CCccccccccc
Q psy12023 3 MCDVCGKGYKY 13 (55)
Q Consensus 3 ~c~~c~~~~~~ 13 (55)
.|..||..|..
T Consensus 72 ~C~~Cg~~~~~ 82 (113)
T PF01155_consen 72 RCRDCGHEFEP 82 (113)
T ss_dssp EETTTS-EEEC
T ss_pred ECCCCCCEEec
Confidence 46666666643
No 114
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=79.34 E-value=3.2 Score=21.46 Aligned_cols=19 Identities=21% Similarity=0.454 Sum_probs=10.1
Q ss_pred CccccccccchhhHHhHHH
Q psy12023 4 CDVCGKGYKYKNGIYRHKK 22 (55)
Q Consensus 4 c~~c~~~~~~~~~~~~~~~ 22 (55)
|..|...|-....|..|++
T Consensus 223 C~FC~~~FYdDDEL~~HcR 241 (493)
T COG5236 223 CIFCKIYFYDDDELRRHCR 241 (493)
T ss_pred hhhccceecChHHHHHHHH
Confidence 4455555555555555555
No 115
>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=79.21 E-value=0.85 Score=16.02 Aligned_cols=14 Identities=21% Similarity=0.377 Sum_probs=10.6
Q ss_pred ccCCCCCcccccch
Q psy12023 31 YQCPQCPYRAKQNA 44 (55)
Q Consensus 31 ~~c~~c~~~f~~~~ 44 (55)
-.|.+|+..|...-
T Consensus 9 K~C~~C~rpf~WRK 22 (42)
T PF10013_consen 9 KICPVCGRPFTWRK 22 (42)
T ss_pred CcCcccCCcchHHH
Confidence 36889999987654
No 116
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=79.10 E-value=1.3 Score=19.24 Aligned_cols=15 Identities=20% Similarity=0.583 Sum_probs=11.9
Q ss_pred CCCccCCCCCcccccc
Q psy12023 28 EPKYQCPQCPYRAKQN 43 (55)
Q Consensus 28 ~~~~~c~~c~~~f~~~ 43 (55)
.. |.|..|++.|...
T Consensus 52 qR-yrC~~C~~tf~~~ 66 (129)
T COG3677 52 QR-YKCKSCGSTFTVE 66 (129)
T ss_pred cc-cccCCcCcceeee
Confidence 44 9999999988643
No 117
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=79.07 E-value=1.1 Score=16.67 Aligned_cols=10 Identities=60% Similarity=1.374 Sum_probs=6.1
Q ss_pred CCcccccccc
Q psy12023 3 MCDVCGKGYK 12 (55)
Q Consensus 3 ~c~~c~~~~~ 12 (55)
.|..|++.|.
T Consensus 7 ~C~~Cg~~~~ 16 (54)
T PF14446_consen 7 KCPVCGKKFK 16 (54)
T ss_pred cChhhCCccc
Confidence 4666666664
No 118
>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=78.55 E-value=0.93 Score=17.09 Aligned_cols=27 Identities=22% Similarity=0.550 Sum_probs=10.1
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCCccccc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQ 42 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~ 42 (55)
.|..|++.|.. ..++ ..|..||..|..
T Consensus 11 ~C~~C~~~F~~------------~~rr-hhCr~CG~~vC~ 37 (69)
T PF01363_consen 11 NCMICGKKFSL------------FRRR-HHCRNCGRVVCS 37 (69)
T ss_dssp B-TTT--B-BS------------SS-E-EE-TTT--EEEC
T ss_pred cCcCcCCcCCC------------ceee-EccCCCCCEECC
Confidence 36667777742 1233 667777766543
No 119
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=78.41 E-value=1.3 Score=23.19 Aligned_cols=11 Identities=36% Similarity=1.038 Sum_probs=6.6
Q ss_pred CCCcccccccc
Q psy12023 2 FMCDVCGKGYK 12 (55)
Q Consensus 2 ~~c~~c~~~~~ 12 (55)
|.|..||....
T Consensus 8 y~C~~Cg~~~~ 18 (454)
T TIGR00416 8 FVCQHCGADSP 18 (454)
T ss_pred EECCcCCCCCc
Confidence 56777765543
No 120
>PRK11823 DNA repair protein RadA; Provisional
Probab=78.13 E-value=1.4 Score=23.05 Aligned_cols=11 Identities=27% Similarity=0.957 Sum_probs=6.6
Q ss_pred CCCcccccccc
Q psy12023 2 FMCDVCGKGYK 12 (55)
Q Consensus 2 ~~c~~c~~~~~ 12 (55)
|.|..||....
T Consensus 8 y~C~~Cg~~~~ 18 (446)
T PRK11823 8 YVCQECGAESP 18 (446)
T ss_pred EECCcCCCCCc
Confidence 56777765543
No 121
>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=78.10 E-value=2.2 Score=15.30 Aligned_cols=26 Identities=23% Similarity=0.522 Sum_probs=14.8
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAK 41 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~ 41 (55)
.|..|++.|... .+. ..|..||..|.
T Consensus 4 ~C~~C~~~F~~~------------~rk-~~Cr~Cg~~~C 29 (57)
T cd00065 4 SCMGCGKPFTLT------------RRR-HHCRNCGRIFC 29 (57)
T ss_pred cCcccCccccCC------------ccc-cccCcCcCCcC
Confidence 466677666531 133 56667776654
No 122
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=78.06 E-value=0.57 Score=26.01 Aligned_cols=22 Identities=23% Similarity=0.323 Sum_probs=12.4
Q ss_pred HHhHHHHHhCCCCCccCCCCCcc
Q psy12023 17 IYRHKKFECGQEPKYQCPQCPYR 39 (55)
Q Consensus 17 ~~~~~~~~~~~~~~~~c~~c~~~ 39 (55)
|..|...+....| ..|+.||..
T Consensus 463 L~CH~Cg~~~~~p-~~Cp~Cgs~ 484 (730)
T COG1198 463 LRCHYCGYQEPIP-QSCPECGSE 484 (730)
T ss_pred eEeCCCCCCCCCC-CCCCCCCCC
Confidence 3334334443344 888888864
No 123
>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=77.63 E-value=0.94 Score=16.41 Aligned_cols=12 Identities=25% Similarity=0.672 Sum_probs=6.3
Q ss_pred cCCCCCcccccc
Q psy12023 32 QCPQCPYRAKQN 43 (55)
Q Consensus 32 ~c~~c~~~f~~~ 43 (55)
.|++|+..|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 899999988643
No 124
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=77.44 E-value=2 Score=21.95 Aligned_cols=11 Identities=27% Similarity=0.818 Sum_probs=6.3
Q ss_pred CCCcccccccc
Q psy12023 2 FMCDVCGKGYK 12 (55)
Q Consensus 2 ~~c~~c~~~~~ 12 (55)
|.|..||....
T Consensus 1 ~~c~~cg~~~~ 11 (372)
T cd01121 1 YVCSECGYVSP 11 (372)
T ss_pred CCCCCCCCCCC
Confidence 45666665543
No 125
>KOG0717|consensus
Probab=77.25 E-value=1.5 Score=23.34 Aligned_cols=21 Identities=24% Similarity=0.412 Sum_probs=18.4
Q ss_pred ccCCCCCcccccchHHHHHHH
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMA 51 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~ 51 (55)
+-|.+|.+.|...-.+..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 679999999999988988865
No 126
>COG1773 Rubredoxin [Energy production and conversion]
Probab=76.82 E-value=1.2 Score=16.60 Aligned_cols=10 Identities=30% Similarity=0.982 Sum_probs=6.5
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
|+|.+||..+
T Consensus 4 ~~C~~CG~vY 13 (55)
T COG1773 4 WRCSVCGYVY 13 (55)
T ss_pred eEecCCceEe
Confidence 6677776554
No 127
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=76.58 E-value=1.6 Score=18.45 Aligned_cols=11 Identities=18% Similarity=0.362 Sum_probs=6.6
Q ss_pred CCccccccccc
Q psy12023 3 MCDVCGKGYKY 13 (55)
Q Consensus 3 ~c~~c~~~~~~ 13 (55)
.|..|+..|..
T Consensus 72 ~C~~Cg~~~~~ 82 (113)
T PRK12380 72 WCWDCSQVVEI 82 (113)
T ss_pred EcccCCCEEec
Confidence 46777765543
No 128
>KOG2785|consensus
Probab=76.28 E-value=7.7 Score=20.32 Aligned_cols=49 Identities=22% Similarity=0.244 Sum_probs=33.7
Q ss_pred CCccccccccchhhHHhHHHHHhCC-----------------------CCCccCCCCC---cccccchHHHHHHHh
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQ-----------------------EPKYQCPQCP---YRAKQNAHLTTHMAI 52 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~-----------------------~~~~~c~~c~---~~f~~~~~l~~h~~~ 52 (55)
.|-.|++.+.....-..||..+.|- .. +.|-.|. +.|......+.||..
T Consensus 168 ~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~-~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 168 DCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIG-FICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred ceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccC-ceEEEeccccCcccccHHHHHHHhh
Confidence 4667777777777777777765542 22 5666666 888888888888764
No 129
>PTZ00448 hypothetical protein; Provisional
Probab=75.63 E-value=2.3 Score=21.94 Aligned_cols=21 Identities=14% Similarity=0.439 Sum_probs=17.2
Q ss_pred ccCCCCCcccccchHHHHHHH
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMA 51 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~ 51 (55)
|.|..|+..|......+.|.+
T Consensus 315 ~tC~~C~v~F~~~~~qR~H~K 335 (373)
T PTZ00448 315 LLCRKCNIQLMDHNAFKQHYR 335 (373)
T ss_pred ccccccccccCCHHHHHHHhh
Confidence 779999999977777777766
No 130
>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=74.72 E-value=3.1 Score=13.79 Aligned_cols=19 Identities=21% Similarity=0.704 Sum_probs=11.1
Q ss_pred ccCCCCCcccccchHHHHHH
Q psy12023 31 YQCPQCPYRAKQNAHLTTHM 50 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~ 50 (55)
+.|+.|++..... .+..|+
T Consensus 5 ~~C~nC~R~v~a~-RfA~HL 23 (33)
T PF08209_consen 5 VECPNCGRPVAAS-RFAPHL 23 (33)
T ss_dssp EE-TTTSSEEEGG-GHHHHH
T ss_pred EECCCCcCCcchh-hhHHHH
Confidence 6788888866433 355554
No 131
>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 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=74.66 E-value=1.6 Score=14.62 Aligned_cols=12 Identities=17% Similarity=0.528 Sum_probs=5.4
Q ss_pred cCCCCCcccccc
Q psy12023 32 QCPQCPYRAKQN 43 (55)
Q Consensus 32 ~c~~c~~~f~~~ 43 (55)
.|..|++.|..+
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 577788777544
No 133
>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=73.71 E-value=1.9 Score=18.30 Aligned_cols=11 Identities=18% Similarity=0.531 Sum_probs=6.7
Q ss_pred CCccccccccc
Q psy12023 3 MCDVCGKGYKY 13 (55)
Q Consensus 3 ~c~~c~~~~~~ 13 (55)
.|..|+..|..
T Consensus 72 ~C~~Cg~~~~~ 82 (115)
T TIGR00100 72 ECEDCSEEVSP 82 (115)
T ss_pred EcccCCCEEec
Confidence 46677766543
No 134
>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=72.96 E-value=3.2 Score=15.62 Aligned_cols=12 Identities=25% Similarity=1.154 Sum_probs=9.0
Q ss_pred ccCCCCCccccc
Q psy12023 31 YQCPQCPYRAKQ 42 (55)
Q Consensus 31 ~~c~~c~~~f~~ 42 (55)
+.|+.||.....
T Consensus 47 ~~C~~Cg~~~~r 58 (69)
T PF07282_consen 47 FTCPNCGFEMDR 58 (69)
T ss_pred EEcCCCCCEECc
Confidence 888888877543
No 135
>PRK12496 hypothetical protein; Provisional
Probab=72.79 E-value=2.7 Score=19.04 Aligned_cols=11 Identities=27% Similarity=0.591 Sum_probs=6.4
Q ss_pred cCCCCCccccc
Q psy12023 32 QCPQCPYRAKQ 42 (55)
Q Consensus 32 ~c~~c~~~f~~ 42 (55)
.|++||.....
T Consensus 145 ~C~~CG~~~~r 155 (164)
T PRK12496 145 VCEICGSPVKR 155 (164)
T ss_pred cCCCCCChhhh
Confidence 47777755443
No 136
>PLN02294 cytochrome c oxidase subunit Vb
Probab=71.83 E-value=2.4 Score=19.55 Aligned_cols=18 Identities=28% Similarity=0.755 Sum_probs=12.8
Q ss_pred HHhCCCCCccCCCCCccccc
Q psy12023 23 FECGQEPKYQCPQCPYRAKQ 42 (55)
Q Consensus 23 ~~~~~~~~~~c~~c~~~f~~ 42 (55)
.+.| ++ .+|.+||..|.-
T Consensus 136 L~kG-kp-~RCpeCG~~fkL 153 (174)
T PLN02294 136 LEKG-KS-FECPVCTQYFEL 153 (174)
T ss_pred ecCC-Cc-eeCCCCCCEEEE
Confidence 3344 55 899999988754
No 137
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.80 E-value=1.4 Score=19.28 Aligned_cols=12 Identities=25% Similarity=0.382 Sum_probs=7.7
Q ss_pred ccCCCCCccccc
Q psy12023 31 YQCPQCPYRAKQ 42 (55)
Q Consensus 31 ~~c~~c~~~f~~ 42 (55)
--|..||+.|.+
T Consensus 69 sfchncgs~fpw 80 (160)
T COG4306 69 SFCHNCGSRFPW 80 (160)
T ss_pred chhhcCCCCCCc
Confidence 556677777654
No 138
>PRK05978 hypothetical protein; Provisional
Probab=71.26 E-value=2.3 Score=19.07 Aligned_cols=12 Identities=17% Similarity=0.443 Sum_probs=7.7
Q ss_pred ccCCCCCccccc
Q psy12023 31 YQCPQCPYRAKQ 42 (55)
Q Consensus 31 ~~c~~c~~~f~~ 42 (55)
-.|+.||..|..
T Consensus 53 ~~C~~CG~~~~~ 64 (148)
T PRK05978 53 DHCAACGEDFTH 64 (148)
T ss_pred CCccccCCcccc
Confidence 467777766643
No 139
>KOG2636|consensus
Probab=71.22 E-value=4.2 Score=21.73 Aligned_cols=25 Identities=24% Similarity=0.426 Sum_probs=18.6
Q ss_pred HhCCCCCccCCCCC-cccccchHHHHH
Q psy12023 24 ECGQEPKYQCPQCP-YRAKQNAHLTTH 49 (55)
Q Consensus 24 ~~~~~~~~~c~~c~-~~f~~~~~l~~h 49 (55)
|..+.. |.|.+|| .+..-+-.+.+|
T Consensus 396 HGL~~e-y~CEICGNy~Y~GrkaF~RH 421 (497)
T KOG2636|consen 396 HGLDIE-YNCEICGNYVYKGRKAFDRH 421 (497)
T ss_pred cCCCcc-cceeeccCccccCcHHHHHH
Confidence 444555 9999999 677777777777
No 140
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=71.14 E-value=2.1 Score=18.26 Aligned_cols=11 Identities=27% Similarity=0.652 Sum_probs=6.6
Q ss_pred CCccccccccc
Q psy12023 3 MCDVCGKGYKY 13 (55)
Q Consensus 3 ~c~~c~~~~~~ 13 (55)
.|..|+..|..
T Consensus 73 ~C~~Cg~~~~~ 83 (117)
T PRK00564 73 ECKDCSHVFKP 83 (117)
T ss_pred EhhhCCCcccc
Confidence 46777765543
No 141
>KOG3408|consensus
Probab=70.78 E-value=2.7 Score=18.35 Aligned_cols=22 Identities=23% Similarity=0.461 Sum_probs=18.9
Q ss_pred ccCCCCCcccccchHHHHHHHh
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAI 52 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~ 52 (55)
|-|-.|.+-|.....|..|.+.
T Consensus 58 fyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 58 FYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred eehhhhhhhhcchHHHHHHHhc
Confidence 7788899999999999988663
No 142
>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=70.26 E-value=5.1 Score=17.69 Aligned_cols=18 Identities=22% Similarity=0.584 Sum_probs=13.9
Q ss_pred ccCCCCCcccccchHHHH
Q psy12023 31 YQCPQCPYRAKQNAHLTT 48 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~ 48 (55)
+.|+.|++.|..-++...
T Consensus 125 ~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 125 WRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred EECCCCCCEecccccHHH
Confidence 779999999877666543
No 143
>PRK00420 hypothetical protein; Validated
Probab=69.61 E-value=4.9 Score=17.24 Aligned_cols=11 Identities=18% Similarity=0.114 Sum_probs=7.6
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
..|+.||....
T Consensus 41 ~~Cp~Cg~~~~ 51 (112)
T PRK00420 41 VVCPVHGKVYI 51 (112)
T ss_pred eECCCCCCeee
Confidence 67888887543
No 144
>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=68.91 E-value=2.9 Score=13.51 Aligned_cols=8 Identities=38% Similarity=1.123 Sum_probs=5.7
Q ss_pred ccCCCCCc
Q psy12023 31 YQCPQCPY 38 (55)
Q Consensus 31 ~~c~~c~~ 38 (55)
+.|+.|+.
T Consensus 20 ~vCp~C~~ 27 (30)
T PF08274_consen 20 LVCPECGH 27 (30)
T ss_dssp EEETTTTE
T ss_pred EeCCcccc
Confidence 77777764
No 145
>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=67.76 E-value=3.4 Score=17.21 Aligned_cols=17 Identities=41% Similarity=0.882 Sum_probs=12.2
Q ss_pred HHhCCCCCccCCCCCcccc
Q psy12023 23 FECGQEPKYQCPQCPYRAK 41 (55)
Q Consensus 23 ~~~~~~~~~~c~~c~~~f~ 41 (55)
.+.+ ++ .+|..||.-|.
T Consensus 74 l~~g-~~-~rC~eCG~~fk 90 (97)
T cd00924 74 LEKG-KP-KRCPECGHVFK 90 (97)
T ss_pred EeCC-Cc-eeCCCCCcEEE
Confidence 3444 45 89999998775
No 146
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=67.66 E-value=5.9 Score=20.97 Aligned_cols=29 Identities=31% Similarity=0.855 Sum_probs=18.7
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccccc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQN 43 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~ 43 (55)
.|..||....+ .|..- |+|..|+..+...
T Consensus 352 ~Cp~Cg~~m~S-----------~G~~g-~rC~kCg~~~~~~ 380 (421)
T COG1571 352 VCPRCGGRMKS-----------AGRNG-FRCKKCGTRARET 380 (421)
T ss_pred CCCccCCchhh-----------cCCCC-cccccccccCCcc
Confidence 47777765433 23334 9999999877543
No 147
>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=67.38 E-value=4.8 Score=14.46 Aligned_cols=8 Identities=38% Similarity=1.302 Sum_probs=3.6
Q ss_pred ccCCCCCc
Q psy12023 31 YQCPQCPY 38 (55)
Q Consensus 31 ~~c~~c~~ 38 (55)
+.|++|++
T Consensus 42 W~CPiC~~ 49 (50)
T PF02891_consen 42 WKCPICNK 49 (50)
T ss_dssp -B-TTT--
T ss_pred eECcCCcC
Confidence 89999875
No 148
>PRK04351 hypothetical protein; Provisional
Probab=66.59 E-value=2 Score=19.18 Aligned_cols=11 Identities=36% Similarity=0.969 Sum_probs=7.2
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
|.|..|+..+.
T Consensus 133 yrCg~C~g~L~ 143 (149)
T PRK04351 133 YRCGKCRGKLK 143 (149)
T ss_pred EEeCCCCcEee
Confidence 77777776553
No 149
>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=66.34 E-value=2.7 Score=14.22 Aligned_cols=9 Identities=33% Similarity=1.021 Sum_probs=4.9
Q ss_pred ccCCCCCcc
Q psy12023 31 YQCPQCPYR 39 (55)
Q Consensus 31 ~~c~~c~~~ 39 (55)
|+|..||..
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 889999864
No 150
>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=65.65 E-value=3.4 Score=18.59 Aligned_cols=13 Identities=23% Similarity=0.460 Sum_probs=10.8
Q ss_pred ccCCCCCcccccc
Q psy12023 31 YQCPQCPYRAKQN 43 (55)
Q Consensus 31 ~~c~~c~~~f~~~ 43 (55)
-+|..|++.|++-
T Consensus 29 ReC~~C~~RFTTy 41 (147)
T TIGR00244 29 RECLECHERFTTF 41 (147)
T ss_pred ccCCccCCcccee
Confidence 5799999999764
No 151
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=64.40 E-value=2.4 Score=19.18 Aligned_cols=9 Identities=33% Similarity=1.084 Sum_probs=5.5
Q ss_pred ccCCCCCcc
Q psy12023 31 YQCPQCPYR 39 (55)
Q Consensus 31 ~~c~~c~~~ 39 (55)
|.|..|+..
T Consensus 141 YrC~~C~gk 149 (156)
T COG3091 141 YRCGKCGGK 149 (156)
T ss_pred EEeccCCce
Confidence 666666643
No 152
>KOG1842|consensus
Probab=64.03 E-value=3.8 Score=21.85 Aligned_cols=24 Identities=25% Similarity=0.682 Sum_probs=19.3
Q ss_pred ccCCCCCcccccchHHHHHHHhhc
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
|.|++|...|..-..|..|.-.-|
T Consensus 16 flCPiC~~dl~~~~~L~~H~d~eH 39 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLDVEH 39 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHhhhc
Confidence 889999998888888888865444
No 153
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=62.52 E-value=5.8 Score=18.41 Aligned_cols=10 Identities=30% Similarity=1.045 Sum_probs=7.2
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
|.|+.||...
T Consensus 133 F~Cp~Cg~~L 142 (176)
T COG1675 133 FTCPKCGEDL 142 (176)
T ss_pred CCCCCCCchh
Confidence 7788887644
No 154
>PF12773 DZR: Double zinc ribbon
Probab=61.65 E-value=7.9 Score=13.51 Aligned_cols=11 Identities=27% Similarity=0.697 Sum_probs=7.5
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
..|..|+....
T Consensus 30 ~~C~~Cg~~~~ 40 (50)
T PF12773_consen 30 KICPNCGAENP 40 (50)
T ss_pred CCCcCCcCCCc
Confidence 57888887543
No 155
>PLN02748 tRNA dimethylallyltransferase
Probab=61.44 E-value=8.8 Score=20.60 Aligned_cols=21 Identities=19% Similarity=0.430 Sum_probs=16.0
Q ss_pred ccCCCCCc-ccccchHHHHHHH
Q psy12023 31 YQCPQCPY-RAKQNAHLTTHMA 51 (55)
Q Consensus 31 ~~c~~c~~-~f~~~~~l~~h~~ 51 (55)
|.|++|+. .+........|.+
T Consensus 419 ~~Ce~C~~~~~~G~~eW~~Hlk 440 (468)
T PLN02748 419 YVCEACGNKVLRGAHEWEQHKQ 440 (468)
T ss_pred ccccCCCCcccCCHHHHHHHhc
Confidence 78999997 7877666666654
No 156
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.50 E-value=3.2 Score=15.07 Aligned_cols=13 Identities=23% Similarity=0.496 Sum_probs=9.5
Q ss_pred cCCCCCcccccch
Q psy12023 32 QCPQCPYRAKQNA 44 (55)
Q Consensus 32 ~c~~c~~~f~~~~ 44 (55)
.|++|+..|+..-
T Consensus 14 ICpvCqRPFsWRk 26 (54)
T COG4338 14 ICPVCQRPFSWRK 26 (54)
T ss_pred hhhhhcCchHHHH
Confidence 5788888887643
No 157
>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=60.21 E-value=4.8 Score=14.61 Aligned_cols=10 Identities=40% Similarity=1.042 Sum_probs=6.1
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
|+|..||..+
T Consensus 2 y~C~~CgyiY 11 (50)
T cd00730 2 YECRICGYIY 11 (50)
T ss_pred cCCCCCCeEE
Confidence 5666666544
No 158
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=59.92 E-value=6.2 Score=20.21 Aligned_cols=23 Identities=22% Similarity=0.492 Sum_probs=18.6
Q ss_pred ccCCCCCcccccchHHHHHHHhh
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAIK 53 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~ 53 (55)
|.|..|...|...-+.-.|..+|
T Consensus 389 Y~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 389 YQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred eechhhhhhhhhhhHHHHHHHHh
Confidence 89999999998887777776554
No 159
>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=59.79 E-value=5.4 Score=14.78 Aligned_cols=11 Identities=27% Similarity=1.069 Sum_probs=7.1
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
+.|+.|+..+.
T Consensus 3 ~~CP~CG~~ie 13 (54)
T TIGR01206 3 FECPDCGAEIE 13 (54)
T ss_pred cCCCCCCCEEe
Confidence 56777776553
No 160
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=59.64 E-value=2.9 Score=18.37 Aligned_cols=9 Identities=33% Similarity=1.084 Sum_probs=4.4
Q ss_pred ccCCCCCcc
Q psy12023 31 YQCPQCPYR 39 (55)
Q Consensus 31 ~~c~~c~~~ 39 (55)
|.|..|+..
T Consensus 134 y~C~~C~g~ 142 (146)
T smart00731 134 YRCGKCGGK 142 (146)
T ss_pred EEcCCCCCE
Confidence 555555443
No 161
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=59.36 E-value=2.5 Score=15.32 Aligned_cols=28 Identities=29% Similarity=0.683 Sum_probs=14.1
Q ss_pred hhhHHhHHHHHhCCCCCccCCC----CCccccc
Q psy12023 14 KNGIYRHKKFECGQEPKYQCPQ----CPYRAKQ 42 (55)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~c~~----c~~~f~~ 42 (55)
...|..|....-...+ ..|.. |+..+..
T Consensus 23 r~~l~~H~~~~C~~~~-v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 23 RKELDDHLENECPKRP-VPCPYSPYGCKERVPR 54 (60)
T ss_dssp CCCHHHHHHTTSTTSE-EE-SS----S--EEEH
T ss_pred HHHHHHHHHccCCCCc-EECCCCCCCCCCccch
Confidence 4456777664434344 67776 7666543
No 162
>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=59.26 E-value=3.1 Score=19.71 Aligned_cols=21 Identities=24% Similarity=0.406 Sum_probs=0.0
Q ss_pred ccCCCCCcccccchHHHHHHHh
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAI 52 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~ 52 (55)
..|++||....-. .+..|+|+
T Consensus 169 ~~cPitGe~IP~~-e~~eHmRi 189 (229)
T PF12230_consen 169 IICPITGEMIPAD-EMDEHMRI 189 (229)
T ss_dssp ----------------------
T ss_pred ccccccccccccc-cccccccc
Confidence 6799999887544 57888876
No 163
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=58.53 E-value=8.3 Score=13.95 Aligned_cols=10 Identities=30% Similarity=1.138 Sum_probs=6.6
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
+.|..|+..+
T Consensus 38 ~~C~~Cgyt~ 47 (50)
T PRK00432 38 WHCGKCGYTE 47 (50)
T ss_pred EECCCcCCEE
Confidence 6777777543
No 164
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=58.05 E-value=16 Score=16.90 Aligned_cols=18 Identities=11% Similarity=0.353 Sum_probs=12.9
Q ss_pred CCCccccccccchhhHHh
Q psy12023 2 FMCDVCGKGYKYKNGIYR 19 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~ 19 (55)
..|..||+.|.....+..
T Consensus 115 ~~C~~Cg~~f~~~k~i~~ 132 (181)
T PRK08222 115 QRCSRCERPFAPQKTVAL 132 (181)
T ss_pred CcCcccCCccCcHhHHHH
Confidence 468999999986655433
No 165
>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=57.37 E-value=7 Score=13.37 Aligned_cols=7 Identities=43% Similarity=1.393 Sum_probs=3.7
Q ss_pred cCCCCCc
Q psy12023 32 QCPQCPY 38 (55)
Q Consensus 32 ~c~~c~~ 38 (55)
.|+.|+.
T Consensus 2 ~Cp~Cg~ 8 (43)
T PF08271_consen 2 KCPNCGS 8 (43)
T ss_dssp SBTTTSS
T ss_pred CCcCCcC
Confidence 4555554
No 166
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=56.93 E-value=8.1 Score=18.91 Aligned_cols=12 Identities=25% Similarity=1.148 Sum_probs=8.7
Q ss_pred ccCCCCCccccc
Q psy12023 31 YQCPQCPYRAKQ 42 (55)
Q Consensus 31 ~~c~~c~~~f~~ 42 (55)
+.|+.||..+..
T Consensus 323 ~~C~~cg~~~~r 334 (364)
T COG0675 323 FKCPRCGFVHDR 334 (364)
T ss_pred EECCCCCCeehh
Confidence 788888876543
No 167
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=56.38 E-value=6.3 Score=13.45 Aligned_cols=11 Identities=36% Similarity=0.936 Sum_probs=8.4
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
|.|..|+..+.
T Consensus 29 y~C~~C~~~w~ 39 (40)
T smart00440 29 YVCTKCGHRWR 39 (40)
T ss_pred EEeCCCCCEeC
Confidence 78888887654
No 168
>PRK01343 zinc-binding protein; Provisional
Probab=55.54 E-value=11 Score=14.22 Aligned_cols=11 Identities=27% Similarity=0.815 Sum_probs=8.7
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
..|.+|++.+.
T Consensus 10 ~~CP~C~k~~~ 20 (57)
T PRK01343 10 RPCPECGKPST 20 (57)
T ss_pred CcCCCCCCcCc
Confidence 67999998764
No 169
>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=55.08 E-value=3.7 Score=13.90 Aligned_cols=10 Identities=40% Similarity=0.806 Sum_probs=7.4
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
|.|..|+..+
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 7788888765
No 170
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=54.44 E-value=2.4 Score=14.98 Aligned_cols=38 Identities=18% Similarity=0.296 Sum_probs=18.8
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCC--CCcccccc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQ--CPYRAKQN 43 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~--c~~~f~~~ 43 (55)
.|+.||............. ...+.= ++|.. ||..|...
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~--~~~~~Y-~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSP--LTRELY-CQCTNPECGHTFVAN 40 (47)
T ss_pred CcCCCCCeeEEEEchhhCc--ceEEEE-EEECCCcCCCEEEEE
Confidence 3777876655443222211 112222 56755 88877543
No 171
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=54.26 E-value=8.7 Score=16.14 Aligned_cols=12 Identities=17% Similarity=0.484 Sum_probs=8.7
Q ss_pred CCCccCCCCCccc
Q psy12023 28 EPKYQCPQCPYRA 40 (55)
Q Consensus 28 ~~~~~c~~c~~~f 40 (55)
+. .+|..||..|
T Consensus 87 r~-~rC~nCG~~f 98 (98)
T PF10164_consen 87 RE-RRCSNCGATF 98 (98)
T ss_pred Cc-cccCCCCccC
Confidence 44 6888888765
No 172
>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=54.00 E-value=6.7 Score=13.21 Aligned_cols=14 Identities=36% Similarity=0.688 Sum_probs=9.6
Q ss_pred CCCccCCCCCcccc
Q psy12023 28 EPKYQCPQCPYRAK 41 (55)
Q Consensus 28 ~~~~~c~~c~~~f~ 41 (55)
.|.+.|+.||..+-
T Consensus 30 vp~~~C~~CGE~~~ 43 (46)
T TIGR03831 30 VPALVCPQCGEEYL 43 (46)
T ss_pred CCccccccCCCEee
Confidence 34367999987654
No 173
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=53.84 E-value=8.1 Score=18.88 Aligned_cols=12 Identities=25% Similarity=0.620 Sum_probs=10.0
Q ss_pred ccCCCCCccccc
Q psy12023 31 YQCPQCPYRAKQ 42 (55)
Q Consensus 31 ~~c~~c~~~f~~ 42 (55)
.+|..||..|.-
T Consensus 182 qRCpECGqVFKL 193 (268)
T PTZ00043 182 YRCGECDQIFML 193 (268)
T ss_pred ccCCCCCcEEEE
Confidence 899999988753
No 174
>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=53.83 E-value=5.8 Score=14.20 Aligned_cols=9 Identities=67% Similarity=1.619 Sum_probs=5.2
Q ss_pred ccCCCCCcc
Q psy12023 31 YQCPQCPYR 39 (55)
Q Consensus 31 ~~c~~c~~~ 39 (55)
|+|.+|+..
T Consensus 2 y~C~~Cgyv 10 (47)
T PF00301_consen 2 YQCPVCGYV 10 (47)
T ss_dssp EEETTTSBE
T ss_pred cCCCCCCEE
Confidence 556666643
No 175
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=53.50 E-value=7.8 Score=17.72 Aligned_cols=16 Identities=31% Similarity=0.764 Sum_probs=11.7
Q ss_pred CCCCccccccccchhh
Q psy12023 1 MFMCDVCGKGYKYKNG 16 (55)
Q Consensus 1 p~~c~~c~~~~~~~~~ 16 (55)
|.=|..||+.|++...
T Consensus 68 PsYC~~CGkpyPWt~~ 83 (158)
T PF10083_consen 68 PSYCHNCGKPYPWTEN 83 (158)
T ss_pred ChhHHhCCCCCchHHH
Confidence 3448889999887654
No 176
>KOG4727|consensus
Probab=53.45 E-value=10 Score=17.69 Aligned_cols=21 Identities=24% Similarity=0.593 Sum_probs=17.5
Q ss_pred CccCCCCCcccccchHHHHHH
Q psy12023 30 KYQCPQCPYRAKQNAHLTTHM 50 (55)
Q Consensus 30 ~~~c~~c~~~f~~~~~l~~h~ 50 (55)
.|=|.+|.-.+..+.++-.|.
T Consensus 75 GyyCdVCdcvvKDSinflDHi 95 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHI 95 (193)
T ss_pred ceeeeecceeehhhHHHHHHh
Confidence 388999999999888887774
No 177
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=53.30 E-value=7.4 Score=18.62 Aligned_cols=18 Identities=17% Similarity=0.456 Sum_probs=12.3
Q ss_pred CCCCCccCCCCCcccccc
Q psy12023 26 GQEPKYQCPQCPYRAKQN 43 (55)
Q Consensus 26 ~~~~~~~c~~c~~~f~~~ 43 (55)
+++.||.|.+|.+.+..+
T Consensus 192 ~e~IPF~C~iCKkdy~sp 209 (259)
T COG5152 192 GEKIPFLCGICKKDYESP 209 (259)
T ss_pred CCCCceeehhchhhccch
Confidence 345459999888776543
No 178
>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=53.19 E-value=5.7 Score=17.42 Aligned_cols=10 Identities=30% Similarity=0.816 Sum_probs=4.9
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
|.|..|+..+
T Consensus 144 ~~C~~C~~~l 153 (157)
T PF10263_consen 144 YRCGRCGGPL 153 (157)
T ss_pred EECCCCCCEE
Confidence 4555555433
No 179
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=52.97 E-value=13 Score=13.38 Aligned_cols=13 Identities=31% Similarity=0.886 Sum_probs=8.6
Q ss_pred ccCCCCCcccccc
Q psy12023 31 YQCPQCPYRAKQN 43 (55)
Q Consensus 31 ~~c~~c~~~f~~~ 43 (55)
++|..|+..+...
T Consensus 29 W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 29 WKCPKCGHEWKAS 41 (55)
T ss_pred EECCCCCCeeEcc
Confidence 6788887665443
No 180
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=52.92 E-value=13 Score=18.55 Aligned_cols=12 Identities=25% Similarity=0.501 Sum_probs=7.5
Q ss_pred ccCCCCCccccc
Q psy12023 31 YQCPQCPYRAKQ 42 (55)
Q Consensus 31 ~~c~~c~~~f~~ 42 (55)
|.|++|...|..
T Consensus 256 yvCs~Clsi~C~ 267 (279)
T TIGR00627 256 FVCSVCLSVLCQ 267 (279)
T ss_pred EECCCccCCcCC
Confidence 677777665543
No 181
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, 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. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=52.84 E-value=21 Score=16.98 Aligned_cols=30 Identities=30% Similarity=0.588 Sum_probs=15.3
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCCc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPY 38 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~ 38 (55)
.|..|+..+..... ...... .. -.|+.|+.
T Consensus 115 ~C~~C~~~~~~~~~----~~~~~~-~~-p~C~~Cgg 144 (222)
T cd01413 115 YCVNCGSKYDLEEV----KYAKKH-EV-PRCPKCGG 144 (222)
T ss_pred eECCCCCCcchhHH----HHhccC-CC-CcCCCCCC
Confidence 47778776654322 111112 22 36888874
No 182
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=52.81 E-value=7.8 Score=12.51 Aligned_cols=10 Identities=30% Similarity=0.833 Sum_probs=7.6
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
|+|..|+...
T Consensus 8 ykC~~Cgniv 17 (34)
T TIGR00319 8 YKCEVCGNIV 17 (34)
T ss_pred EEcCCCCcEE
Confidence 8898888643
No 183
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=52.73 E-value=1.3 Score=24.76 Aligned_cols=13 Identities=23% Similarity=0.690 Sum_probs=7.7
Q ss_pred CCccccccccchh
Q psy12023 3 MCDVCGKGYKYKN 15 (55)
Q Consensus 3 ~c~~c~~~~~~~~ 15 (55)
.|..||..|..-.
T Consensus 125 ~CT~CGPRfTIi~ 137 (750)
T COG0068 125 NCTNCGPRFTIIE 137 (750)
T ss_pred ccCCCCcceeeec
Confidence 3666776665443
No 184
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=52.44 E-value=12 Score=21.98 Aligned_cols=10 Identities=30% Similarity=1.072 Sum_probs=6.8
Q ss_pred Cccccccccc
Q psy12023 4 CDVCGKGYKY 13 (55)
Q Consensus 4 c~~c~~~~~~ 13 (55)
|..|++.|..
T Consensus 463 C~~C~kkFfS 472 (1374)
T PTZ00303 463 CPSCGRAFIS 472 (1374)
T ss_pred ccCcCCcccc
Confidence 6777777754
No 185
>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=52.38 E-value=8 Score=12.50 Aligned_cols=10 Identities=30% Similarity=0.820 Sum_probs=7.2
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
|+|..|+...
T Consensus 5 ykC~~CGniv 14 (34)
T cd00974 5 YKCEICGNIV 14 (34)
T ss_pred EEcCCCCcEE
Confidence 7888887643
No 186
>PRK05580 primosome assembly protein PriA; Validated
Probab=51.89 E-value=4.7 Score=22.39 Aligned_cols=9 Identities=33% Similarity=0.973 Sum_probs=6.6
Q ss_pred ccCCCCCcc
Q psy12023 31 YQCPQCPYR 39 (55)
Q Consensus 31 ~~c~~c~~~ 39 (55)
..|+.|+..
T Consensus 422 ~~Cp~Cg~~ 430 (679)
T PRK05580 422 KACPECGST 430 (679)
T ss_pred CCCCCCcCC
Confidence 678888754
No 187
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=51.50 E-value=4.1 Score=18.20 Aligned_cols=8 Identities=50% Similarity=1.256 Sum_probs=4.0
Q ss_pred ccCCCCCc
Q psy12023 31 YQCPQCPY 38 (55)
Q Consensus 31 ~~c~~c~~ 38 (55)
..|+.||.
T Consensus 106 ~~cp~c~s 113 (146)
T TIGR02159 106 VQCPRCGS 113 (146)
T ss_pred CcCCCCCC
Confidence 34555554
No 188
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=51.40 E-value=25 Score=17.06 Aligned_cols=31 Identities=35% Similarity=0.742 Sum_probs=16.0
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCCc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPY 38 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~ 38 (55)
.|..|++.+....... .......| .|+.|+.
T Consensus 121 ~C~~C~~~~~~~~~~~---~~~~~~~p--~Cp~Cgg 151 (244)
T PRK14138 121 YCVRCGKRYTVEDVIE---KLEKSDVP--RCDDCSG 151 (244)
T ss_pred EECCCCCcccHHHHHH---HHhcCCCC--CCCCCCC
Confidence 4777887765433221 11112223 6888874
No 189
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=51.17 E-value=2 Score=14.48 Aligned_cols=12 Identities=33% Similarity=1.132 Sum_probs=6.6
Q ss_pred HhCCCCCccCCCC
Q psy12023 24 ECGQEPKYQCPQC 36 (55)
Q Consensus 24 ~~~~~~~~~c~~c 36 (55)
..|... |.|..|
T Consensus 24 ~~G~qr-yrC~~C 35 (36)
T PF03811_consen 24 PSGHQR-YRCKDC 35 (36)
T ss_pred CCCCEe-EecCcC
Confidence 334344 777665
No 190
>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=51.12 E-value=3 Score=20.67 Aligned_cols=23 Identities=26% Similarity=0.788 Sum_probs=13.9
Q ss_pred CCCccCCCCCcccccchHHHHHHH
Q psy12023 28 EPKYQCPQCPYRAKQNAHLTTHMA 51 (55)
Q Consensus 28 ~~~~~c~~c~~~f~~~~~l~~h~~ 51 (55)
++ +.|+.|+........|+.-.|
T Consensus 208 k~-~PCPKCg~et~eTkdLSmStR 230 (314)
T PF06524_consen 208 KP-IPCPKCGYETQETKDLSMSTR 230 (314)
T ss_pred CC-CCCCCCCCcccccccceeeee
Confidence 44 788888876655555543333
No 191
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=50.82 E-value=25 Score=16.34 Aligned_cols=18 Identities=28% Similarity=0.695 Sum_probs=13.8
Q ss_pred ccCCCCCcccccchHHHH
Q psy12023 31 YQCPQCPYRAKQNAHLTT 48 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~ 48 (55)
+.|..|++.+---++...
T Consensus 131 ~~C~~CgkiYW~GsHw~~ 148 (165)
T COG1656 131 YRCPKCGKIYWKGSHWRR 148 (165)
T ss_pred eECCCCcccccCchHHHH
Confidence 679999999876666543
No 192
>PHA02998 RNA polymerase subunit; Provisional
Probab=50.38 E-value=2.6 Score=19.65 Aligned_cols=13 Identities=23% Similarity=0.470 Sum_probs=10.0
Q ss_pred ccCCCCCcccccc
Q psy12023 31 YQCPQCPYRAKQN 43 (55)
Q Consensus 31 ~~c~~c~~~f~~~ 43 (55)
|.|..|+..|.-+
T Consensus 172 YkC~~CG~~wkpp 184 (195)
T PHA02998 172 HACRDCKKHFKPP 184 (195)
T ss_pred EEcCCCCCccCCc
Confidence 7899999887543
No 193
>KOG3507|consensus
Probab=50.16 E-value=8 Score=14.70 Aligned_cols=10 Identities=40% Similarity=1.155 Sum_probs=7.0
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
++|..||...
T Consensus 38 irCReCG~RI 47 (62)
T KOG3507|consen 38 IRCRECGYRI 47 (62)
T ss_pred EehhhcchHH
Confidence 7787787544
No 194
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=50.09 E-value=10 Score=11.28 Aligned_cols=8 Identities=38% Similarity=1.012 Sum_probs=4.3
Q ss_pred cCCCCCcc
Q psy12023 32 QCPQCPYR 39 (55)
Q Consensus 32 ~c~~c~~~ 39 (55)
-|+.||..
T Consensus 15 fC~~CG~~ 22 (23)
T PF13240_consen 15 FCPNCGTP 22 (23)
T ss_pred chhhhCCc
Confidence 36666543
No 195
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=49.75 E-value=22 Score=16.28 Aligned_cols=15 Identities=27% Similarity=0.798 Sum_probs=11.3
Q ss_pred CCCccccccccchhh
Q psy12023 2 FMCDVCGKGYKYKNG 16 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~ 16 (55)
..|..||+.|.....
T Consensus 115 ~~C~~CG~~f~~~~~ 129 (180)
T PRK12387 115 CNCRVCGRPFAVQKE 129 (180)
T ss_pred ccchhhCCccccHHH
Confidence 468899999876554
No 196
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=49.72 E-value=9.5 Score=15.51 Aligned_cols=12 Identities=25% Similarity=0.761 Sum_probs=8.6
Q ss_pred ccCCCCCccccc
Q psy12023 31 YQCPQCPYRAKQ 42 (55)
Q Consensus 31 ~~c~~c~~~f~~ 42 (55)
-+|+.||..+..
T Consensus 9 ~~C~~CG~d~~~ 20 (86)
T PF06170_consen 9 PRCPHCGLDYSH 20 (86)
T ss_pred CcccccCCcccc
Confidence 368888877654
No 197
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=49.63 E-value=11 Score=16.75 Aligned_cols=10 Identities=50% Similarity=1.208 Sum_probs=6.3
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
.-|++|+..+
T Consensus 45 v~CPvC~~~~ 54 (131)
T COG1645 45 VFCPVCGYRE 54 (131)
T ss_pred EECCCCCceE
Confidence 4677777533
No 198
>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=49.55 E-value=12 Score=11.76 Aligned_cols=6 Identities=33% Similarity=1.005 Sum_probs=2.5
Q ss_pred CCCCCc
Q psy12023 33 CPQCPY 38 (55)
Q Consensus 33 c~~c~~ 38 (55)
|.+|++
T Consensus 3 C~~C~~ 8 (30)
T PF03107_consen 3 CDVCRR 8 (30)
T ss_pred CCCCCC
Confidence 444443
No 199
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=49.43 E-value=5 Score=21.32 Aligned_cols=12 Identities=33% Similarity=0.659 Sum_probs=8.4
Q ss_pred CCCccccccccc
Q psy12023 2 FMCDVCGKGYKY 13 (55)
Q Consensus 2 ~~c~~c~~~~~~ 13 (55)
|.|..||..+..
T Consensus 426 ~~c~~c~~~yd~ 437 (479)
T PRK05452 426 MQCSVCQWIYDP 437 (479)
T ss_pred EEECCCCeEECC
Confidence 568888876654
No 200
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=49.36 E-value=9.3 Score=18.91 Aligned_cols=15 Identities=27% Similarity=0.835 Sum_probs=8.2
Q ss_pred CCccccccccchhhH
Q psy12023 3 MCDVCGKGYKYKNGI 17 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~ 17 (55)
.|+.||..+.....+
T Consensus 222 ~CP~Cg~~W~L~~pl 236 (258)
T PF10071_consen 222 KCPSCGGDWRLKEPL 236 (258)
T ss_pred CCCCCCCccccCCch
Confidence 366666665544433
No 201
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=49.08 E-value=17 Score=17.35 Aligned_cols=13 Identities=23% Similarity=0.595 Sum_probs=9.8
Q ss_pred CCccCCCCCcccc
Q psy12023 29 PKYQCPQCPYRAK 41 (55)
Q Consensus 29 ~~~~c~~c~~~f~ 41 (55)
+.++|..||..+.
T Consensus 29 ~lvrC~eCG~V~~ 41 (201)
T COG1326 29 PLVRCEECGTVHP 41 (201)
T ss_pred eEEEccCCCcEee
Confidence 3488999998763
No 202
>KOG2295|consensus
Probab=49.08 E-value=42 Score=18.98 Aligned_cols=28 Identities=25% Similarity=0.447 Sum_probs=21.6
Q ss_pred CCCCCccCCCCC--cccccchHHHHHHHhhc
Q psy12023 26 GQEPKYQCPQCP--YRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 26 ~~~~~~~c~~c~--~~f~~~~~l~~h~~~~~ 54 (55)
.+.+ |.|.+.| |.|.-......|....|
T Consensus 506 ~kdK-y~C~lsgc~KlF~gpEFvrKHi~~KH 535 (648)
T KOG2295|consen 506 DKDK-YLCPLSGCAKLFKGPEFVRKHINKKH 535 (648)
T ss_pred hccc-ccCCCcchHhhccCHHHHHHHHHHHH
Confidence 3445 9998755 99999988888877655
No 203
>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=49.03 E-value=12 Score=15.16 Aligned_cols=12 Identities=17% Similarity=0.426 Sum_probs=9.3
Q ss_pred ccCCCCCccccc
Q psy12023 31 YQCPQCPYRAKQ 42 (55)
Q Consensus 31 ~~c~~c~~~f~~ 42 (55)
-.|.+|++.+..
T Consensus 79 ~~C~vC~k~l~~ 90 (109)
T PF10367_consen 79 TKCSVCGKPLGN 90 (109)
T ss_pred CCccCcCCcCCC
Confidence 369999998765
No 204
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.96 E-value=5.5 Score=15.96 Aligned_cols=10 Identities=40% Similarity=1.122 Sum_probs=7.6
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
|+|.+|+..|
T Consensus 13 Y~c~~cg~~~ 22 (82)
T COG2331 13 YECTECGNRF 22 (82)
T ss_pred EeecccchHH
Confidence 7788888655
No 205
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=48.82 E-value=13 Score=19.51 Aligned_cols=25 Identities=16% Similarity=0.353 Sum_probs=16.4
Q ss_pred HhCCCCCccCCCCC-cccccchHHHHH
Q psy12023 24 ECGQEPKYQCPQCP-YRAKQNAHLTTH 49 (55)
Q Consensus 24 ~~~~~~~~~c~~c~-~~f~~~~~l~~h 49 (55)
|..++. |.|.+|| ....-+..+.+|
T Consensus 369 hgLd~e-f~CEICgNyvy~GR~~FdrH 394 (470)
T COG5188 369 HGLDIE-FECEICGNYVYYGRDRFDRH 394 (470)
T ss_pred cCCCcc-eeeeecccccccchHHHHhh
Confidence 444566 9999999 555555555555
No 206
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=48.11 E-value=11 Score=20.21 Aligned_cols=12 Identities=33% Similarity=0.755 Sum_probs=7.9
Q ss_pred CCCccccccccc
Q psy12023 2 FMCDVCGKGYKY 13 (55)
Q Consensus 2 ~~c~~c~~~~~~ 13 (55)
|.|..||..+..
T Consensus 8 f~C~~CG~~s~K 19 (456)
T COG1066 8 FVCQECGYVSPK 19 (456)
T ss_pred EEcccCCCCCcc
Confidence 567777766543
No 207
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=47.96 E-value=23 Score=17.99 Aligned_cols=21 Identities=29% Similarity=0.547 Sum_probs=12.1
Q ss_pred CCccccccccchhhHHhHHHH
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKF 23 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~ 23 (55)
-|+.|=+.|.....+..|+..
T Consensus 50 iCe~Clky~~~~~~l~~H~~~ 70 (290)
T PLN03238 50 ICEYCLKYMRKKKSLLRHLAK 70 (290)
T ss_pred EcCCCcchhCCHHHHHHHHHh
Confidence 355555666666666666553
No 208
>PRK06260 threonine synthase; Validated
Probab=47.90 E-value=12 Score=19.39 Aligned_cols=10 Identities=50% Similarity=1.105 Sum_probs=6.4
Q ss_pred CCcccccccc
Q psy12023 3 MCDVCGKGYK 12 (55)
Q Consensus 3 ~c~~c~~~~~ 12 (55)
.|..||..+.
T Consensus 5 ~C~~cg~~~~ 14 (397)
T PRK06260 5 KCIECGKEYD 14 (397)
T ss_pred EECCCCCCCC
Confidence 5667776654
No 209
>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=47.22 E-value=12 Score=11.75 Aligned_cols=6 Identities=67% Similarity=1.752 Sum_probs=2.3
Q ss_pred Cccccc
Q psy12023 4 CDVCGK 9 (55)
Q Consensus 4 c~~c~~ 9 (55)
|..|+.
T Consensus 30 C~~C~~ 35 (39)
T smart00132 30 CSKCGK 35 (39)
T ss_pred CcccCC
Confidence 333433
No 210
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=45.62 E-value=7.9 Score=11.74 Aligned_cols=7 Identities=43% Similarity=1.327 Sum_probs=4.2
Q ss_pred CCccccc
Q psy12023 3 MCDVCGK 9 (55)
Q Consensus 3 ~c~~c~~ 9 (55)
.|..||.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 4666665
No 211
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=45.53 E-value=11 Score=12.37 Aligned_cols=10 Identities=20% Similarity=0.255 Sum_probs=7.4
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
+.|..|+..|
T Consensus 22 ~~C~~Cg~~~ 31 (33)
T PF08792_consen 22 EVCIFCGSSF 31 (33)
T ss_pred EEcccCCcEe
Confidence 5688888765
No 212
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=45.53 E-value=35 Score=16.13 Aligned_cols=32 Identities=28% Similarity=0.644 Sum_probs=15.8
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCCcc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYR 39 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~ 39 (55)
.|..|+..+.... +. ...... .. -.|+.|+..
T Consensus 111 ~C~~C~~~~~~~~-~~--~~~~~~-~~-p~C~~Cg~~ 142 (218)
T cd01407 111 RCTKCGKEYPRDE-LQ--ADIDRE-EV-PRCPKCGGL 142 (218)
T ss_pred eeCCCcCCCcHHH-Hh--HhhccC-CC-CcCCCCCCc
Confidence 5777877665332 11 111122 22 378888754
No 213
>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=45.48 E-value=27 Score=14.74 Aligned_cols=36 Identities=8% Similarity=0.131 Sum_probs=24.1
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCcc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYR 39 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~ 39 (55)
|.|..-|..|.+=......+..... +. |.|...|+.
T Consensus 4 f~i~~T~EiF~dYe~Y~~R~~~y~~-~v-wtC~~TGk~ 39 (102)
T PF10537_consen 4 FYIPFTGEIFRDYEEYLKRMILYNQ-RV-WTCEITGKS 39 (102)
T ss_pred EEeCCCCcccCCHHHHHHHHHHHhC-Ce-eEEecCCCC
Confidence 4466677778777666666655544 44 889888763
No 214
>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=44.88 E-value=7.9 Score=12.96 Aligned_cols=10 Identities=30% Similarity=0.760 Sum_probs=5.6
Q ss_pred cCCCCCcccc
Q psy12023 32 QCPQCPYRAK 41 (55)
Q Consensus 32 ~c~~c~~~f~ 41 (55)
.|..||+.+.
T Consensus 3 ~C~~Cg~~Yh 12 (36)
T PF05191_consen 3 ICPKCGRIYH 12 (36)
T ss_dssp EETTTTEEEE
T ss_pred CcCCCCCccc
Confidence 4566666553
No 215
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=44.76 E-value=10 Score=14.17 Aligned_cols=9 Identities=44% Similarity=1.147 Sum_probs=2.7
Q ss_pred ccCCCCCcc
Q psy12023 31 YQCPQCPYR 39 (55)
Q Consensus 31 ~~c~~c~~~ 39 (55)
|.|+.||.+
T Consensus 34 y~Cp~CgAt 42 (55)
T PF05741_consen 34 YVCPICGAT 42 (55)
T ss_dssp ---TTT---
T ss_pred CcCCCCcCc
Confidence 788888875
No 216
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=44.44 E-value=14 Score=12.59 Aligned_cols=14 Identities=36% Similarity=1.165 Sum_probs=7.6
Q ss_pred CCccccccccchhh
Q psy12023 3 MCDVCGKGYKYKNG 16 (55)
Q Consensus 3 ~c~~c~~~~~~~~~ 16 (55)
.|..|++.+-..++
T Consensus 4 ~CprC~kg~Hwa~~ 17 (36)
T PF14787_consen 4 LCPRCGKGFHWASE 17 (36)
T ss_dssp C-TTTSSSCS-TTT
T ss_pred cCcccCCCcchhhh
Confidence 46777777765543
No 217
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=44.27 E-value=6.8 Score=21.02 Aligned_cols=8 Identities=50% Similarity=1.153 Sum_probs=5.7
Q ss_pred ccCCCCCc
Q psy12023 31 YQCPQCPY 38 (55)
Q Consensus 31 ~~c~~c~~ 38 (55)
..|+.|+.
T Consensus 254 ~~Cp~C~s 261 (505)
T TIGR00595 254 KTCPQCGS 261 (505)
T ss_pred CCCCCCCC
Confidence 67777775
No 218
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=44.18 E-value=21 Score=20.20 Aligned_cols=9 Identities=33% Similarity=0.848 Sum_probs=6.7
Q ss_pred ccCCCCCcc
Q psy12023 31 YQCPQCPYR 39 (55)
Q Consensus 31 ~~c~~c~~~ 39 (55)
+.|+.||..
T Consensus 640 ~~CP~CG~~ 648 (656)
T PRK08270 640 EFCPKCGEE 648 (656)
T ss_pred CCCcCCcCc
Confidence 788888854
No 219
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=44.11 E-value=7.7 Score=16.39 Aligned_cols=9 Identities=22% Similarity=0.704 Sum_probs=6.3
Q ss_pred ccCCCCCcc
Q psy12023 31 YQCPQCPYR 39 (55)
Q Consensus 31 ~~c~~c~~~ 39 (55)
|.|.+||+.
T Consensus 3 WkC~iCg~~ 11 (101)
T PF09943_consen 3 WKCYICGKP 11 (101)
T ss_pred eEEEecCCe
Confidence 677777763
No 220
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.96 E-value=3.2 Score=20.22 Aligned_cols=17 Identities=24% Similarity=0.708 Sum_probs=12.3
Q ss_pred CCCCccCCCCCcccccch
Q psy12023 27 QEPKYQCPQCPYRAKQNA 44 (55)
Q Consensus 27 ~~~~~~c~~c~~~f~~~~ 44 (55)
++. +.|++|+-.|....
T Consensus 17 kk~-ieCPvC~tkFkkee 33 (267)
T COG1655 17 KKT-IECPVCNTKFKKEE 33 (267)
T ss_pred hce-eccCcccchhhhhh
Confidence 455 88999988876543
No 221
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=43.83 E-value=18 Score=13.58 Aligned_cols=10 Identities=30% Similarity=0.664 Sum_probs=7.2
Q ss_pred CCCCCccccc
Q psy12023 33 CPQCPYRAKQ 42 (55)
Q Consensus 33 c~~c~~~f~~ 42 (55)
|+.|+..|..
T Consensus 42 CPfC~~~~~~ 51 (55)
T PF14447_consen 42 CPFCGTPFEF 51 (55)
T ss_pred CCCCCCcccC
Confidence 7788877754
No 222
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=43.00 E-value=16 Score=13.06 Aligned_cols=7 Identities=29% Similarity=0.648 Sum_probs=3.0
Q ss_pred CCCCccc
Q psy12023 34 PQCPYRA 40 (55)
Q Consensus 34 ~~c~~~f 40 (55)
+.|+..|
T Consensus 2 P~Cg~~f 8 (50)
T PF14375_consen 2 PRCGAPF 8 (50)
T ss_pred CCCCCcC
Confidence 3444444
No 223
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=42.96 E-value=48 Score=18.84 Aligned_cols=8 Identities=38% Similarity=1.173 Sum_probs=5.8
Q ss_pred ccCCCCCc
Q psy12023 31 YQCPQCPY 38 (55)
Q Consensus 31 ~~c~~c~~ 38 (55)
+.|+.||.
T Consensus 583 ~~CP~CGs 590 (625)
T PRK08579 583 TRCPRCGS 590 (625)
T ss_pred CcCcCCCC
Confidence 67888875
No 224
>KOG0402|consensus
Probab=42.89 E-value=7.7 Score=15.85 Aligned_cols=28 Identities=25% Similarity=0.729 Sum_probs=15.7
Q ss_pred CCCccccccccchhhHHhHHHHHhCCCCCccCCCCCccc
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRA 40 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f 40 (55)
|.|+.||+.-.-.. -.| . +.|..|.+.+
T Consensus 37 y~CsfCGK~~vKR~--------AvG--i-W~C~~C~kv~ 64 (92)
T KOG0402|consen 37 YTCSFCGKKTVKRK--------AVG--I-WKCGSCKKVV 64 (92)
T ss_pred hhhhhcchhhhhhh--------cee--E-EecCCcccee
Confidence 56888886432111 112 2 7787777765
No 225
>KOG4118|consensus
Probab=42.83 E-value=13 Score=14.46 Aligned_cols=22 Identities=14% Similarity=0.362 Sum_probs=14.6
Q ss_pred ccCCCCCcccccchHHHHHHHh
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAI 52 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~ 52 (55)
+.|.+|...-...-.+.+|...
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~ 60 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFEN 60 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhh
Confidence 6788887666666666666443
No 226
>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=42.30 E-value=11 Score=14.18 Aligned_cols=12 Identities=25% Similarity=0.642 Sum_probs=5.5
Q ss_pred ccCCCCCccccc
Q psy12023 31 YQCPQCPYRAKQ 42 (55)
Q Consensus 31 ~~c~~c~~~f~~ 42 (55)
..|++|++.+..
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 468888876544
No 227
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=41.96 E-value=40 Score=17.81 Aligned_cols=12 Identities=33% Similarity=1.320 Sum_probs=9.0
Q ss_pred CCCccCCCCCcc
Q psy12023 28 EPKYQCPQCPYR 39 (55)
Q Consensus 28 ~~~~~c~~c~~~ 39 (55)
++.|+|..||..
T Consensus 352 ~~~YRC~~CGF~ 363 (389)
T COG2956 352 KPRYRCQNCGFT 363 (389)
T ss_pred cCCceecccCCc
Confidence 455999999854
No 228
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=41.92 E-value=12 Score=18.56 Aligned_cols=13 Identities=23% Similarity=0.818 Sum_probs=10.7
Q ss_pred ccCCCCCcccccc
Q psy12023 31 YQCPQCPYRAKQN 43 (55)
Q Consensus 31 ~~c~~c~~~f~~~ 43 (55)
|.|..|+..|+-.
T Consensus 156 f~C~~C~h~F~G~ 168 (278)
T PF15135_consen 156 FHCPKCRHNFRGF 168 (278)
T ss_pred eecccccccchhh
Confidence 8899999988643
No 229
>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=41.65 E-value=31 Score=14.31 Aligned_cols=18 Identities=22% Similarity=0.558 Sum_probs=13.1
Q ss_pred CCccccccccchhhHHhH
Q psy12023 3 MCDVCGKGYKYKNGIYRH 20 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~ 20 (55)
.|+.||..+-..+.+..-
T Consensus 37 ~C~~CGe~y~~dev~~eI 54 (89)
T TIGR03829 37 SCSHCGMEYQDDTTVKEI 54 (89)
T ss_pred cccCCCcEeecHHHHHHH
Confidence 588999988776655444
No 230
>KOG3014|consensus
Probab=41.25 E-value=26 Score=17.45 Aligned_cols=24 Identities=13% Similarity=0.357 Sum_probs=16.2
Q ss_pred ccCCCCCcccccc--hHHHHHHHhhc
Q psy12023 31 YQCPQCPYRAKQN--AHLTTHMAIKH 54 (55)
Q Consensus 31 ~~c~~c~~~f~~~--~~l~~h~~~~~ 54 (55)
..|..|+..++.. ..-..|++.|.
T Consensus 38 ~~C~~Cgm~Yt~~s~EDe~~H~~fH~ 63 (257)
T KOG3014|consen 38 VKCKECGMKYTVTSPEDEALHEKFHN 63 (257)
T ss_pred eehhhcCceecCCCHHHHHHHHHHHH
Confidence 4799999877644 34466776664
No 231
>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=41.07 E-value=20 Score=12.65 Aligned_cols=13 Identities=15% Similarity=0.713 Sum_probs=9.5
Q ss_pred ccCCCCCcccccc
Q psy12023 31 YQCPQCPYRAKQN 43 (55)
Q Consensus 31 ~~c~~c~~~f~~~ 43 (55)
|.|..|++.+...
T Consensus 27 f~C~~C~~~l~~~ 39 (58)
T PF00412_consen 27 FKCSKCGKPLNDG 39 (58)
T ss_dssp SBETTTTCBTTTS
T ss_pred cccCCCCCccCCC
Confidence 7788888776544
No 232
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=41.05 E-value=23 Score=12.81 Aligned_cols=13 Identities=38% Similarity=0.767 Sum_probs=8.3
Q ss_pred hCCCCCccCCCCCc
Q psy12023 25 CGQEPKYQCPQCPY 38 (55)
Q Consensus 25 ~~~~~~~~c~~c~~ 38 (55)
.++.. ..|+.|++
T Consensus 42 ~~~~i-~~Cp~CgR 54 (56)
T PF02591_consen 42 KGDEI-VFCPNCGR 54 (56)
T ss_pred cCCCe-EECcCCCc
Confidence 34344 67888875
No 233
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=40.52 E-value=25 Score=15.14 Aligned_cols=11 Identities=36% Similarity=0.969 Sum_probs=7.5
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
+.|+.|+..+.
T Consensus 20 ~iCpeC~~EW~ 30 (109)
T TIGR00686 20 LICPSCLYEWN 30 (109)
T ss_pred eECcccccccc
Confidence 77777776554
No 234
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=40.19 E-value=41 Score=19.09 Aligned_cols=8 Identities=38% Similarity=1.024 Sum_probs=6.0
Q ss_pred ccCCCCCc
Q psy12023 31 YQCPQCPY 38 (55)
Q Consensus 31 ~~c~~c~~ 38 (55)
+.|+.||.
T Consensus 581 ~~CP~CGs 588 (623)
T PRK08271 581 KRCPICGS 588 (623)
T ss_pred cCCcCCCC
Confidence 67888875
No 235
>PRK14873 primosome assembly protein PriA; Provisional
Probab=39.79 E-value=6.2 Score=22.05 Aligned_cols=10 Identities=30% Similarity=1.145 Sum_probs=7.0
Q ss_pred CccCCCCCcc
Q psy12023 30 KYQCPQCPYR 39 (55)
Q Consensus 30 ~~~c~~c~~~ 39 (55)
|..|+.|+..
T Consensus 422 p~~Cp~Cgs~ 431 (665)
T PRK14873 422 DWRCPRCGSD 431 (665)
T ss_pred CccCCCCcCC
Confidence 3778888764
No 236
>KOG4477|consensus
Probab=39.65 E-value=11 Score=17.76 Aligned_cols=7 Identities=29% Similarity=1.122 Sum_probs=4.6
Q ss_pred ccCCCCC
Q psy12023 31 YQCPQCP 37 (55)
Q Consensus 31 ~~c~~c~ 37 (55)
|+|.+|+
T Consensus 39 fkC~vCd 45 (228)
T KOG4477|consen 39 FKCFVCD 45 (228)
T ss_pred hheeeec
Confidence 6666665
No 237
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=38.67 E-value=14 Score=16.66 Aligned_cols=7 Identities=29% Similarity=0.956 Sum_probs=3.1
Q ss_pred ccCCCCC
Q psy12023 31 YQCPQCP 37 (55)
Q Consensus 31 ~~c~~c~ 37 (55)
|.|..||
T Consensus 113 l~C~~Cg 119 (146)
T PF07295_consen 113 LVCENCG 119 (146)
T ss_pred EecccCC
Confidence 4444444
No 238
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=37.72 E-value=21 Score=12.11 Aligned_cols=9 Identities=33% Similarity=0.737 Sum_probs=5.1
Q ss_pred CCCcccccc
Q psy12023 2 FMCDVCGKG 10 (55)
Q Consensus 2 ~~c~~c~~~ 10 (55)
..|..||..
T Consensus 3 ~~Cp~Cg~~ 11 (47)
T PF14690_consen 3 PRCPHCGSP 11 (47)
T ss_pred ccCCCcCCC
Confidence 456666643
No 239
>KOG0317|consensus
Probab=37.50 E-value=42 Score=17.16 Aligned_cols=32 Identities=22% Similarity=0.595 Sum_probs=18.1
Q ss_pred CccccccccchhhHHhHHHHHhCCCCCccCCCCCccccc
Q psy12023 4 CDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQ 42 (55)
Q Consensus 4 c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~ 42 (55)
|..||-.|.+. .+. .+.+++. +|++|...|.-
T Consensus 254 aTpCGHiFCWs-CI~----~w~~ek~--eCPlCR~~~~p 285 (293)
T KOG0317|consen 254 ATPCGHIFCWS-CIL----EWCSEKA--ECPLCREKFQP 285 (293)
T ss_pred cCcCcchHHHH-HHH----HHHcccc--CCCcccccCCC
Confidence 45577666542 222 2344454 78888876643
No 240
>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=37.43 E-value=11 Score=17.88 Aligned_cols=22 Identities=23% Similarity=0.487 Sum_probs=0.0
Q ss_pred CCCCccCCCCCcc-cccchHHHHH
Q psy12023 27 QEPKYQCPQCPYR-AKQNAHLTTH 49 (55)
Q Consensus 27 ~~~~~~c~~c~~~-f~~~~~l~~h 49 (55)
.+. |.|.+||-. +.-+..+..|
T Consensus 99 ~~e-y~CEICGN~~Y~GrkaFekH 121 (196)
T PF11931_consen 99 GVE-YKCEICGNQSYKGRKAFEKH 121 (196)
T ss_dssp ------------------------
T ss_pred CCe-eeeEeCCCcceecHHHHHHh
Confidence 345 999999853 3233344444
No 241
>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=37.41 E-value=37 Score=14.25 Aligned_cols=19 Identities=21% Similarity=0.517 Sum_probs=11.6
Q ss_pred CCCccccccccchhhHHhH
Q psy12023 2 FMCDVCGKGYKYKNGIYRH 20 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~ 20 (55)
+.|+.||..+.........
T Consensus 32 ~~C~~CGe~~~~~e~~~~~ 50 (127)
T TIGR03830 32 WYCPACGEELLDPEESKRN 50 (127)
T ss_pred eECCCCCCEEEcHHHHHHH
Confidence 3577888776665544333
No 242
>KOG2807|consensus
Probab=36.96 E-value=36 Score=17.85 Aligned_cols=23 Identities=17% Similarity=0.463 Sum_probs=18.2
Q ss_pred ccCCCCCcccccchHHHHHHHhh
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAIK 53 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~ 53 (55)
|.|..|...|...-+.-.|...|
T Consensus 346 y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 346 YRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred EEchhccceeeccchHHHHhhhh
Confidence 88888888888887777776654
No 243
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=36.88 E-value=14 Score=16.62 Aligned_cols=11 Identities=18% Similarity=0.884 Sum_probs=6.7
Q ss_pred CCCcccccccc
Q psy12023 2 FMCDVCGKGYK 12 (55)
Q Consensus 2 ~~c~~c~~~~~ 12 (55)
|.|..|+..+.
T Consensus 14 YrC~~C~~TwN 24 (142)
T PF06353_consen 14 YRCEKCDYTWN 24 (142)
T ss_pred EEcccCcCccc
Confidence 45666766553
No 244
>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=36.64 E-value=35 Score=17.23 Aligned_cols=11 Identities=27% Similarity=0.836 Sum_probs=6.7
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
+.|+.|+.-|.
T Consensus 46 ~vc~~c~~h~r 56 (285)
T TIGR00515 46 EVCPKCDHHMR 56 (285)
T ss_pred CCCCCCCCcCc
Confidence 46666766554
No 245
>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=36.41 E-value=8.6 Score=17.14 Aligned_cols=19 Identities=32% Similarity=0.735 Sum_probs=12.9
Q ss_pred HHhCCCCCccCCCCCcccccc
Q psy12023 23 FECGQEPKYQCPQCPYRAKQN 43 (55)
Q Consensus 23 ~~~~~~~~~~c~~c~~~f~~~ 43 (55)
.+.+ ++ .+|..||.-|.-.
T Consensus 107 l~~g-~~-~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 107 LHKG-KP-QRCPECGQVFKLK 125 (136)
T ss_dssp EETT-SE-EEETTTEEEEEEE
T ss_pred EeCC-Cc-cCCCCCCeEEEEE
Confidence 3344 45 8999999887643
No 246
>KOG1280|consensus
Probab=36.36 E-value=45 Score=17.63 Aligned_cols=24 Identities=25% Similarity=0.614 Sum_probs=17.4
Q ss_pred ccCCCCCcccccchHHHHHHHhhc
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMAIKH 54 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~~~~ 54 (55)
|.|+.|+..-.....+..|....|
T Consensus 80 ftCPyC~~~Gfte~~f~~Hv~s~H 103 (381)
T KOG1280|consen 80 FTCPYCGIMGFTERQFGTHVLSQH 103 (381)
T ss_pred ccCCcccccccchhHHHHHhhhcC
Confidence 888888887667777777765444
No 247
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=35.86 E-value=37 Score=18.80 Aligned_cols=9 Identities=33% Similarity=1.316 Sum_probs=6.4
Q ss_pred ccCCCCCcc
Q psy12023 31 YQCPQCPYR 39 (55)
Q Consensus 31 ~~c~~c~~~ 39 (55)
+.|+.||..
T Consensus 533 ~~CP~CGs~ 541 (555)
T cd01675 533 FKCPKCGSE 541 (555)
T ss_pred CCCcCCCCc
Confidence 678888753
No 248
>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=35.47 E-value=19 Score=12.07 Aligned_cols=10 Identities=20% Similarity=0.600 Sum_probs=2.7
Q ss_pred CCCCCccccc
Q psy12023 33 CPQCPYRAKQ 42 (55)
Q Consensus 33 c~~c~~~f~~ 42 (55)
|..|++.+..
T Consensus 1 C~~C~~~~~~ 10 (47)
T PF01844_consen 1 CQYCGKPGSD 10 (47)
T ss_dssp -TTT--B--G
T ss_pred CCCCCCcCcc
Confidence 4556665543
No 249
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=35.32 E-value=27 Score=11.76 Aligned_cols=16 Identities=19% Similarity=0.443 Sum_probs=8.6
Q ss_pred CCccccccccchhhHH
Q psy12023 3 MCDVCGKGYKYKNGIY 18 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~ 18 (55)
.|..|+-.|-....+.
T Consensus 21 ~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 21 VCPSCGGIWFDAGELE 36 (41)
T ss_pred ECCCCCeEEccHHHHH
Confidence 3556665555555443
No 250
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=35.23 E-value=26 Score=17.33 Aligned_cols=31 Identities=32% Similarity=0.650 Sum_probs=15.1
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCCc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPY 38 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~ 38 (55)
.|..|+..+...... . ....+ .+ -.|..|+.
T Consensus 124 ~C~~C~~~~~~~~~~-~--~~~~~-~~-p~C~~Cg~ 154 (250)
T COG0846 124 RCSKCGNQYYDEDVI-K--FIEDG-LI-PRCPKCGG 154 (250)
T ss_pred EeCCCcCccchhhhh-h--hcccC-CC-CcCccCCC
Confidence 577777666533211 1 11112 22 37888876
No 251
>KOG0801|consensus
Probab=35.20 E-value=7.1 Score=18.05 Aligned_cols=10 Identities=30% Similarity=0.843 Sum_probs=8.1
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
++|++|.|..
T Consensus 139 ~KCPvC~K~V 148 (205)
T KOG0801|consen 139 MKCPVCHKVV 148 (205)
T ss_pred ccCCcccccc
Confidence 7899998754
No 252
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.93 E-value=23 Score=13.65 Aligned_cols=10 Identities=50% Similarity=1.371 Sum_probs=6.8
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
|.|+.|....
T Consensus 32 ymC~eC~~Rv 41 (68)
T COG4896 32 YMCPECEHRV 41 (68)
T ss_pred EechhhHhhh
Confidence 7788876544
No 253
>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=34.48 E-value=18 Score=11.56 Aligned_cols=11 Identities=45% Similarity=1.129 Sum_probs=5.4
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
|.|+.|+..+.
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 78888776543
No 254
>KOG2907|consensus
Probab=34.40 E-value=21 Score=15.49 Aligned_cols=12 Identities=42% Similarity=1.367 Sum_probs=8.3
Q ss_pred ccCCCCCccccc
Q psy12023 31 YQCPQCPYRAKQ 42 (55)
Q Consensus 31 ~~c~~c~~~f~~ 42 (55)
|.|..|+..|..
T Consensus 103 YTC~kC~~k~~e 114 (116)
T KOG2907|consen 103 YTCPKCKYKFTE 114 (116)
T ss_pred EEcCccceeeec
Confidence 677777777653
No 255
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=34.36 E-value=51 Score=15.94 Aligned_cols=11 Identities=36% Similarity=1.056 Sum_probs=7.1
Q ss_pred CCccccccccc
Q psy12023 3 MCDVCGKGYKY 13 (55)
Q Consensus 3 ~c~~c~~~~~~ 13 (55)
.|..|++.+..
T Consensus 124 ~C~~C~~~~~~ 134 (242)
T PRK00481 124 RCTKCGQTYDL 134 (242)
T ss_pred eeCCCCCCcCh
Confidence 57777766543
No 256
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=34.29 E-value=22 Score=15.02 Aligned_cols=34 Identities=21% Similarity=0.504 Sum_probs=11.6
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCCccccc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAKQ 42 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~ 42 (55)
.|..||..+.... +.+ .|++--|.|..|.+-|..
T Consensus 16 ~CalCG~tWg~~y-----~Ev-~G~rLfFCCd~ca~EF~n 49 (105)
T PF11494_consen 16 GCALCGATWGDYY-----EEV-DGERLFFCCDDCAKEFKN 49 (105)
T ss_dssp S-SS---S---SS------B--TT--BSSS--SSSS-TTS
T ss_pred cccccCCcHHHHH-----Hhh-cCCEEEEEcHHHHHHHHH
Confidence 4777887765321 222 244544778888887764
No 257
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=34.28 E-value=19 Score=11.14 Aligned_cols=10 Identities=30% Similarity=1.242 Sum_probs=4.2
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
|.|.+|+..+
T Consensus 16 Y~C~~Cdf~l 25 (30)
T PF07649_consen 16 YRCSECDFDL 25 (30)
T ss_dssp EE-TTT----
T ss_pred EECccCCCcc
Confidence 8888887543
No 258
>KOG1409|consensus
Probab=34.11 E-value=14 Score=19.37 Aligned_cols=37 Identities=14% Similarity=0.334 Sum_probs=21.1
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCCcccc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRAK 41 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~ 41 (55)
.|+.|...|-.. ....++....|-+. -.|..||+++.
T Consensus 284 ~cQ~c~qpffwn-~~~m~~~k~~glr~-h~crkcg~avc 320 (404)
T KOG1409|consen 284 SCQKCNQPFFWN-FRQMWDRKQLGLRQ-HHCRKCGKAVC 320 (404)
T ss_pred hhhhhCchHHHH-HHHHHhhhhhhhhh-hhhhhhhhhcC
Confidence 366666665433 34556665566555 56666666554
No 259
>KOG1088|consensus
Probab=33.93 E-value=27 Score=15.33 Aligned_cols=14 Identities=14% Similarity=0.221 Sum_probs=11.1
Q ss_pred ccCCCCCcccccch
Q psy12023 31 YQCPQCPYRAKQNA 44 (55)
Q Consensus 31 ~~c~~c~~~f~~~~ 44 (55)
..|+.||..|.-+.
T Consensus 99 l~CpetG~vfpI~~ 112 (124)
T KOG1088|consen 99 LVCPETGRVFPISD 112 (124)
T ss_pred EecCCCCcEeeccc
Confidence 78999999886543
No 260
>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=33.80 E-value=15 Score=16.41 Aligned_cols=11 Identities=27% Similarity=0.748 Sum_probs=8.5
Q ss_pred cCCCCCccccc
Q psy12023 32 QCPQCPYRAKQ 42 (55)
Q Consensus 32 ~c~~c~~~f~~ 42 (55)
.|+.||+.|..
T Consensus 5 nC~~CgklF~~ 15 (137)
T TIGR03826 5 NCPKCGRLFVK 15 (137)
T ss_pred cccccchhhhh
Confidence 58888888865
No 261
>PLN03239 histone acetyltransferase; Provisional
Probab=33.68 E-value=29 Score=18.19 Aligned_cols=21 Identities=19% Similarity=0.140 Sum_probs=18.0
Q ss_pred ccCCCCCcccccchHHHHHHH
Q psy12023 31 YQCPQCPYRAKQNAHLTTHMA 51 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~~h~~ 51 (55)
|.|..|-+-|.....+.+|+.
T Consensus 107 YiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 107 YVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred EEeccchhhhcCHHHHHHHHH
Confidence 889999998888888888864
No 262
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=33.46 E-value=35 Score=12.80 Aligned_cols=13 Identities=23% Similarity=0.858 Sum_probs=9.7
Q ss_pred CCCccCCCCCcccc
Q psy12023 28 EPKYQCPQCPYRAK 41 (55)
Q Consensus 28 ~~~~~c~~c~~~f~ 41 (55)
.. |.|+.||-..-
T Consensus 13 v~-~~Cp~cGipth 25 (55)
T PF13824_consen 13 VN-FECPDCGIPTH 25 (55)
T ss_pred cC-CcCCCCCCcCc
Confidence 45 89999997653
No 263
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=33.25 E-value=26 Score=11.69 Aligned_cols=10 Identities=40% Similarity=0.793 Sum_probs=7.3
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
..|.+|+..+
T Consensus 9 ~~C~~C~~~~ 18 (36)
T PF11781_consen 9 EPCPVCGSRW 18 (36)
T ss_pred CcCCCCCCeE
Confidence 5688888764
No 264
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=33.08 E-value=15 Score=15.28 Aligned_cols=12 Identities=17% Similarity=0.672 Sum_probs=8.9
Q ss_pred ccCCCCCccccc
Q psy12023 31 YQCPQCPYRAKQ 42 (55)
Q Consensus 31 ~~c~~c~~~f~~ 42 (55)
|+|.+|+++-..
T Consensus 69 ~~Ct~Cgkah~~ 80 (94)
T COG1631 69 LRCTECGKAHQR 80 (94)
T ss_pred EEehhhcccccc
Confidence 789999876443
No 265
>PF03563 Bunya_G2: Bunyavirus glycoprotein G2; InterPro: IPR005168 Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This entry represents the polyprotein region forming the G2 glycoprotein, which interacts with the IPR005167 from INTERPRO G1 glycoprotein [].
Probab=33.05 E-value=33 Score=17.34 Aligned_cols=17 Identities=12% Similarity=0.346 Sum_probs=13.9
Q ss_pred CCCcccccchHHHHHHH
Q psy12023 35 QCPYRAKQNAHLTTHMA 51 (55)
Q Consensus 35 ~c~~~f~~~~~l~~h~~ 51 (55)
+||..|.....++.|..
T Consensus 255 vCG~~f~~sd~mk~HR~ 271 (285)
T PF03563_consen 255 VCGMKFETSDRMKMHRE 271 (285)
T ss_pred eccccccchHHHHHHHh
Confidence 58889998888888854
No 266
>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=32.91 E-value=24 Score=15.35 Aligned_cols=10 Identities=30% Similarity=1.009 Sum_probs=8.3
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
.+|+.|++..
T Consensus 70 V~CP~C~K~T 79 (114)
T PF11023_consen 70 VECPNCGKQT 79 (114)
T ss_pred eECCCCCChH
Confidence 7899999865
No 267
>PRK10220 hypothetical protein; Provisional
Probab=32.91 E-value=51 Score=14.31 Aligned_cols=11 Identities=36% Similarity=1.026 Sum_probs=7.3
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
|.|+.|+.-+.
T Consensus 21 ~vCpeC~hEW~ 31 (111)
T PRK10220 21 YICPECAHEWN 31 (111)
T ss_pred EECCcccCcCC
Confidence 67777776544
No 268
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.68 E-value=16 Score=15.36 Aligned_cols=8 Identities=25% Similarity=0.766 Sum_probs=6.4
Q ss_pred ccCCCCCc
Q psy12023 31 YQCPQCPY 38 (55)
Q Consensus 31 ~~c~~c~~ 38 (55)
|+|.+|+.
T Consensus 7 wkC~VCg~ 14 (103)
T COG4847 7 WKCYVCGG 14 (103)
T ss_pred eeEeeeCC
Confidence 88888875
No 269
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=32.43 E-value=58 Score=14.81 Aligned_cols=33 Identities=30% Similarity=0.715 Sum_probs=17.8
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCCccc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYRA 40 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f 40 (55)
.|..|++.+...... ...... .. -.|+.|+...
T Consensus 107 ~C~~C~~~~~~~~~~---~~~~~~-~~-~~C~~C~~~l 139 (178)
T PF02146_consen 107 RCSKCGKEYDREDIV---DSIDEE-EP-PRCPKCGGLL 139 (178)
T ss_dssp EETTTSBEEEGHHHH---HHHHTT-SS-CBCTTTSCBE
T ss_pred eecCCCccccchhhc---cccccc-cc-ccccccCccC
Confidence 477788776543221 122223 23 3788888643
No 270
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=32.27 E-value=32 Score=17.54 Aligned_cols=12 Identities=42% Similarity=0.825 Sum_probs=7.5
Q ss_pred ccCCCCCccccc
Q psy12023 31 YQCPQCPYRAKQ 42 (55)
Q Consensus 31 ~~c~~c~~~f~~ 42 (55)
+.|+.|+.-|.-
T Consensus 58 ~vcp~c~~h~rl 69 (296)
T CHL00174 58 NICEQCGYHLKM 69 (296)
T ss_pred CCCCCCCCCcCC
Confidence 567777765543
No 271
>PF14369 zf-RING_3: zinc-finger
Probab=32.15 E-value=29 Score=11.48 Aligned_cols=10 Identities=30% Similarity=0.727 Sum_probs=7.2
Q ss_pred cCCCCCcccc
Q psy12023 32 QCPQCPYRAK 41 (55)
Q Consensus 32 ~c~~c~~~f~ 41 (55)
.|+.|+..|-
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 5888887663
No 272
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=32.14 E-value=29 Score=12.05 Aligned_cols=13 Identities=23% Similarity=0.825 Sum_probs=9.9
Q ss_pred ccCCCCCcccccc
Q psy12023 31 YQCPQCPYRAKQN 43 (55)
Q Consensus 31 ~~c~~c~~~f~~~ 43 (55)
+.|+.|+..+...
T Consensus 21 ~vC~~Cg~~~~~~ 33 (52)
T smart00661 21 FVCRKCGYEEPIE 33 (52)
T ss_pred EECCcCCCeEECC
Confidence 8899999766543
No 273
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=32.11 E-value=21 Score=15.31 Aligned_cols=11 Identities=45% Similarity=1.328 Sum_probs=7.5
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
|+|..||..++
T Consensus 101 y~C~~Cg~~wr 111 (113)
T COG1594 101 YKCTRCGYRWR 111 (113)
T ss_pred EEecccCCEee
Confidence 67777776654
No 274
>KOG2169|consensus
Probab=31.95 E-value=44 Score=18.94 Aligned_cols=18 Identities=33% Similarity=0.791 Sum_probs=12.7
Q ss_pred CCCCCccCCCCCcccccc
Q psy12023 26 GQEPKYQCPQCPYRAKQN 43 (55)
Q Consensus 26 ~~~~~~~c~~c~~~f~~~ 43 (55)
.+++.|.|.+|.+.+...
T Consensus 341 ~~~pTW~CPVC~~~~~~e 358 (636)
T KOG2169|consen 341 EQKPTWRCPVCQKAAPFE 358 (636)
T ss_pred cCCCeeeCccCCcccccc
Confidence 345669999999876543
No 275
>COG4830 RPS26B Ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=31.87 E-value=30 Score=14.70 Aligned_cols=11 Identities=18% Similarity=0.564 Sum_probs=8.5
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
..|+.||+...
T Consensus 21 v~CdnCg~~vP 31 (108)
T COG4830 21 VRCDNCGKAVP 31 (108)
T ss_pred eeeccccccCC
Confidence 77999997653
No 276
>KOG2857|consensus
Probab=31.68 E-value=31 Score=15.73 Aligned_cols=21 Identities=24% Similarity=0.403 Sum_probs=16.1
Q ss_pred CCCccccccccchhhHHhHHH
Q psy12023 2 FMCDVCGKGYKYKNGIYRHKK 22 (55)
Q Consensus 2 ~~c~~c~~~~~~~~~~~~~~~ 22 (55)
|+|..|...+.+...++.|..
T Consensus 18 YKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 18 YKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred ccCCCCCCccccchhhhhccC
Confidence 678888888777777777765
No 277
>PRK08197 threonine synthase; Validated
Probab=31.23 E-value=29 Score=18.06 Aligned_cols=11 Identities=36% Similarity=1.114 Sum_probs=6.9
Q ss_pred CCCcccccccc
Q psy12023 2 FMCDVCGKGYK 12 (55)
Q Consensus 2 ~~c~~c~~~~~ 12 (55)
+.|..||+.+.
T Consensus 8 ~~C~~Cg~~~~ 18 (394)
T PRK08197 8 LECSKCGETYD 18 (394)
T ss_pred EEECCCCCCCC
Confidence 35677776664
No 278
>KOG3352|consensus
Probab=30.93 E-value=30 Score=15.85 Aligned_cols=11 Identities=36% Similarity=0.830 Sum_probs=8.8
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
.+|.+||.-|.
T Consensus 134 ~rc~eCG~~fk 144 (153)
T KOG3352|consen 134 QRCPECGHYFK 144 (153)
T ss_pred ccCCcccceEE
Confidence 68899998775
No 279
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=30.78 E-value=54 Score=16.26 Aligned_cols=14 Identities=29% Similarity=0.453 Sum_probs=9.4
Q ss_pred CCCCCccCCCCCccc
Q psy12023 26 GQEPKYQCPQCPYRA 40 (55)
Q Consensus 26 ~~~~~~~c~~c~~~f 40 (55)
++.. ..|+.||.-.
T Consensus 218 ~d~i-v~CP~CgRIL 231 (239)
T COG1579 218 KDEI-VFCPYCGRIL 231 (239)
T ss_pred CCCC-ccCCccchHH
Confidence 4344 7899998754
No 280
>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=30.63 E-value=16 Score=12.68 Aligned_cols=10 Identities=40% Similarity=0.843 Sum_probs=7.6
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
..|+-|+..|
T Consensus 30 ~~CpYCg~~y 39 (40)
T PF10276_consen 30 VVCPYCGTRY 39 (40)
T ss_dssp EEETTTTEEE
T ss_pred EECCCCCCEE
Confidence 6788888765
No 281
>PF09965 DUF2199: Uncharacterized protein conserved in bacteria (DUF2199); InterPro: IPR018697 This domain has no known function.
Probab=30.35 E-value=30 Score=15.68 Aligned_cols=9 Identities=33% Similarity=1.294 Sum_probs=4.6
Q ss_pred CCCcccccc
Q psy12023 2 FMCDVCGKG 10 (55)
Q Consensus 2 ~~c~~c~~~ 10 (55)
|+|..||..
T Consensus 1 y~C~~Cg~~ 9 (148)
T PF09965_consen 1 YTCSCCGEE 9 (148)
T ss_pred CCCCcCCcc
Confidence 445555544
No 282
>COG4640 Predicted membrane protein [Function unknown]
Probab=30.29 E-value=48 Score=17.94 Aligned_cols=17 Identities=24% Similarity=0.456 Sum_probs=12.1
Q ss_pred ccCCCCCcccccchHHH
Q psy12023 31 YQCPQCPYRAKQNAHLT 47 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l~ 47 (55)
++|.+||..|.......
T Consensus 16 ~qC~qCG~~~t~~~sqa 32 (465)
T COG4640 16 VQCTQCGHKFTSRQSQA 32 (465)
T ss_pred ccccccCCcCCchhhhh
Confidence 56999998887655443
No 283
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=29.98 E-value=33 Score=17.24 Aligned_cols=8 Identities=38% Similarity=1.481 Sum_probs=5.1
Q ss_pred ccCCCCCc
Q psy12023 31 YQCPQCPY 38 (55)
Q Consensus 31 ~~c~~c~~ 38 (55)
+.|..||.
T Consensus 355 ~~c~~cg~ 362 (389)
T PRK11788 355 YRCRNCGF 362 (389)
T ss_pred EECCCCCC
Confidence 66666664
No 284
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=29.82 E-value=37 Score=18.49 Aligned_cols=20 Identities=40% Similarity=0.648 Sum_probs=11.4
Q ss_pred CCccccccccchhhHHhHHH
Q psy12023 3 MCDVCGKGYKYKNGIYRHKK 22 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~ 22 (55)
-|+.|=+.|.....+..|+.
T Consensus 200 iCe~Cl~y~~~~~~~~~H~~ 219 (450)
T PLN00104 200 FCEFCLKFMKRKEQLQRHMK 219 (450)
T ss_pred EchhhhhhhcCHHHHHHHHh
Confidence 45555555555555655554
No 285
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=29.44 E-value=25 Score=11.58 Aligned_cols=9 Identities=33% Similarity=1.076 Sum_probs=6.4
Q ss_pred ccCCCCCcc
Q psy12023 31 YQCPQCPYR 39 (55)
Q Consensus 31 ~~c~~c~~~ 39 (55)
|.|..|++.
T Consensus 9 Y~C~~C~~~ 17 (32)
T PF13696_consen 9 YVCHRCGQK 17 (32)
T ss_pred CEeecCCCC
Confidence 788877753
No 286
>CHL00112 rpl28 ribosomal protein L28; Provisional
Probab=29.35 E-value=27 Score=13.39 Aligned_cols=10 Identities=20% Similarity=0.335 Sum_probs=6.7
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
-.|++||+.-
T Consensus 3 r~C~i~GK~~ 12 (63)
T CHL00112 3 KKCQLTGKKA 12 (63)
T ss_pred CeeccCCCcC
Confidence 3688888743
No 287
>KOG3183|consensus
Probab=29.31 E-value=24 Score=17.45 Aligned_cols=14 Identities=14% Similarity=0.370 Sum_probs=10.9
Q ss_pred CccCCCCCcccccc
Q psy12023 30 KYQCPQCPYRAKQN 43 (55)
Q Consensus 30 ~~~c~~c~~~f~~~ 43 (55)
||.|+.|+..|...
T Consensus 23 Pf~Cd~C~~~FC~e 36 (250)
T KOG3183|consen 23 PFKCDGCSGIFCLE 36 (250)
T ss_pred ceeeCCccchhhhc
Confidence 49999999888643
No 288
>PRK12722 transcriptional activator FlhC; Provisional
Probab=29.25 E-value=56 Score=15.57 Aligned_cols=27 Identities=19% Similarity=0.538 Sum_probs=15.3
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCCc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPY 38 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~ 38 (55)
.|..||-.|.... +..... |.|+.|..
T Consensus 136 ~C~~Cgg~fv~~~--------~e~~~~-f~CplC~~ 162 (187)
T PRK12722 136 SCNCCGGHFVTHA--------HDPVGS-FVCGLCQP 162 (187)
T ss_pred cCCCCCCCeeccc--------cccCCC-CcCCCCCC
Confidence 4777777665322 112234 88888864
No 289
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=29.04 E-value=31 Score=13.13 Aligned_cols=13 Identities=15% Similarity=0.383 Sum_probs=9.8
Q ss_pred ccCCCCCcccccc
Q psy12023 31 YQCPQCPYRAKQN 43 (55)
Q Consensus 31 ~~c~~c~~~f~~~ 43 (55)
..|..|+.....+
T Consensus 31 V~C~~Cg~~L~~P 43 (59)
T PRK00415 31 VRCLVCGKTLAEP 43 (59)
T ss_pred EECcccCCCcccC
Confidence 7888898877554
No 290
>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=28.99 E-value=31 Score=13.27 Aligned_cols=6 Identities=50% Similarity=1.774 Sum_probs=2.8
Q ss_pred cCCCCC
Q psy12023 32 QCPQCP 37 (55)
Q Consensus 32 ~c~~c~ 37 (55)
.|+.|+
T Consensus 2 ~C~KCg 7 (64)
T PF09855_consen 2 KCPKCG 7 (64)
T ss_pred CCCCCC
Confidence 444444
No 291
>PF01722 BolA: BolA-like protein; InterPro: IPR002634 This family consist of the morpho-protein BolA from Escherichia coli and its various homologs. In E. coli, over-expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems during cell division []. The expression of BolA is growth rate regulated and is induced during the transition into the the stationary phase []. BolA is also induced by stress during early stages of growth [] and may have a general role in stress response. It has also been suggested that BolA can induce the transcription of penicillin binding proteins 6 and 5 [, ].; PDB: 1XS3_A 1V60_A 3O2E_A 1NY8_A 3TR3_A 2KZ0_A 2DHM_A 2KDN_A 1V9J_A.
Probab=28.98 E-value=29 Score=13.70 Aligned_cols=25 Identities=4% Similarity=0.088 Sum_probs=17.8
Q ss_pred CCCCccCCCCCcccccchHHHHHHHh
Q psy12023 27 QEPKYQCPQCPYRAKQNAHLTTHMAI 52 (55)
Q Consensus 27 ~~~~~~c~~c~~~f~~~~~l~~h~~~ 52 (55)
+.. |...+....|...+.+.+|+.+
T Consensus 27 ~sH-f~i~IvS~~F~g~s~i~rhr~V 51 (76)
T PF01722_consen 27 GSH-FKIIIVSDEFEGKSRIKRHRLV 51 (76)
T ss_dssp SSE-EEEEEECGGGTTS-HHHHHHHH
T ss_pred Cce-EEEEEEcHHhCCCCHHHHHHHH
Confidence 344 6666778888888888888764
No 292
>PTZ00064 histone acetyltransferase; Provisional
Probab=28.96 E-value=47 Score=18.57 Aligned_cols=20 Identities=20% Similarity=0.632 Sum_probs=11.1
Q ss_pred CCccccccccchhhHHhHHH
Q psy12023 3 MCDVCGKGYKYKNGIYRHKK 22 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~ 22 (55)
-|+.|=+.|.....+..|+.
T Consensus 282 ICEfCLkY~~s~~~l~rH~~ 301 (552)
T PTZ00064 282 FCEYCLDFFCFEDELIRHLS 301 (552)
T ss_pred EccchhhhhCCHHHHHHHHh
Confidence 35555555555555555554
No 293
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=28.95 E-value=32 Score=11.76 Aligned_cols=10 Identities=20% Similarity=0.604 Sum_probs=4.2
Q ss_pred cCCCCCcccc
Q psy12023 32 QCPQCPYRAK 41 (55)
Q Consensus 32 ~c~~c~~~f~ 41 (55)
.|+.||+.-.
T Consensus 3 ~CSFCgr~~~ 12 (41)
T PF06689_consen 3 RCSFCGRPES 12 (41)
T ss_dssp B-TTT--BTT
T ss_pred CccCCCCCHH
Confidence 5777776544
No 294
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=28.91 E-value=37 Score=13.08 Aligned_cols=10 Identities=30% Similarity=0.856 Sum_probs=8.1
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
..|+.|++..
T Consensus 7 v~CP~C~k~~ 16 (62)
T PRK00418 7 VNCPTCGKPV 16 (62)
T ss_pred ccCCCCCCcc
Confidence 6799999864
No 295
>PF00935 Ribosomal_L44: Ribosomal protein L44; InterPro: IPR000552 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of mammalian [], Trypanosoma brucei, Caenorhabditis elegans and fungal L44, and Haloarcula marismortui LA [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_r 1S1I_Z 3O5H_f 3O58_f 3IZR_r 1M1K_4 3CCQ_3 3CCL_3 3CME_3 1K73_4 ....
Probab=28.79 E-value=24 Score=14.19 Aligned_cols=11 Identities=18% Similarity=0.606 Sum_probs=7.5
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
++|..|++...
T Consensus 54 l~C~~C~~~~~ 64 (77)
T PF00935_consen 54 LECTECGKAHM 64 (77)
T ss_dssp EEETTTS-EEE
T ss_pred EEeCCCCcccc
Confidence 78989987643
No 296
>PRK12860 transcriptional activator FlhC; Provisional
Probab=28.76 E-value=53 Score=15.69 Aligned_cols=26 Identities=19% Similarity=0.505 Sum_probs=14.5
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCC
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCP 37 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~ 37 (55)
.|..||-.|.... +..... |.|+.|.
T Consensus 136 ~C~~Cgg~fv~~~--------~e~~~~-f~CplC~ 161 (189)
T PRK12860 136 RCCRCGGKFVTHA--------HDLRHN-FVCGLCQ 161 (189)
T ss_pred cCCCCCCCeeccc--------cccCCC-CcCCCCC
Confidence 4667776665321 112224 8888885
No 297
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; 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. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=28.52 E-value=78 Score=15.06 Aligned_cols=11 Identities=27% Similarity=0.540 Sum_probs=6.8
Q ss_pred CCccccccccc
Q psy12023 3 MCDVCGKGYKY 13 (55)
Q Consensus 3 ~c~~c~~~~~~ 13 (55)
.|..|+..+..
T Consensus 111 ~C~~C~~~~~~ 121 (224)
T cd01412 111 RCSSCGYVGEN 121 (224)
T ss_pred ccCCCCCCCCc
Confidence 46677766543
No 298
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.43 E-value=35 Score=14.66 Aligned_cols=10 Identities=30% Similarity=1.056 Sum_probs=6.1
Q ss_pred CCcccccccc
Q psy12023 3 MCDVCGKGYK 12 (55)
Q Consensus 3 ~c~~c~~~~~ 12 (55)
.|+.||..|.
T Consensus 51 ~CP~Cg~~~e 60 (115)
T COG1885 51 SCPKCGEPFE 60 (115)
T ss_pred cCCCCCCccc
Confidence 4666766553
No 299
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=28.19 E-value=28 Score=15.47 Aligned_cols=11 Identities=18% Similarity=0.383 Sum_probs=7.9
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
-+|..||..|-
T Consensus 30 ~kC~~CG~v~~ 40 (140)
T COG1545 30 TKCKKCGRVYF 40 (140)
T ss_pred EEcCCCCeEEc
Confidence 56888887653
No 300
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=27.48 E-value=44 Score=17.66 Aligned_cols=8 Identities=50% Similarity=1.173 Sum_probs=4.9
Q ss_pred ccCCCCCcc
Q psy12023 31 YQCPQCPYR 39 (55)
Q Consensus 31 ~~c~~c~~~ 39 (55)
..|+ ||+.
T Consensus 260 ~~Cp-CG~~ 267 (374)
T TIGR00375 260 ANCP-CGGR 267 (374)
T ss_pred CCCC-CCCc
Confidence 4566 6665
No 301
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=27.39 E-value=29 Score=14.31 Aligned_cols=13 Identities=31% Similarity=1.009 Sum_probs=7.4
Q ss_pred CCCccccccccch
Q psy12023 2 FMCDVCGKGYKYK 14 (55)
Q Consensus 2 ~~c~~c~~~~~~~ 14 (55)
|.|..|...+.+.
T Consensus 6 F~C~~C~~~W~S~ 18 (98)
T PF13695_consen 6 FQCSKCSRGWTSA 18 (98)
T ss_pred EECCCCCCCCccC
Confidence 4566666655544
No 302
>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=27.24 E-value=51 Score=12.51 Aligned_cols=6 Identities=83% Similarity=1.968 Sum_probs=2.7
Q ss_pred Cccccc
Q psy12023 4 CDVCGK 9 (55)
Q Consensus 4 c~~c~~ 9 (55)
|..||+
T Consensus 6 C~~CG~ 11 (59)
T PF09889_consen 6 CPVCGK 11 (59)
T ss_pred CCcCCC
Confidence 444443
No 303
>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=27.22 E-value=33 Score=12.64 Aligned_cols=8 Identities=50% Similarity=1.431 Sum_probs=6.5
Q ss_pred ccCCCCCc
Q psy12023 31 YQCPQCPY 38 (55)
Q Consensus 31 ~~c~~c~~ 38 (55)
|.|..|+.
T Consensus 45 y~C~~Cg~ 52 (54)
T PF10058_consen 45 YRCPYCGA 52 (54)
T ss_pred EEcCCCCC
Confidence 88888874
No 304
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=27.00 E-value=34 Score=10.66 Aligned_cols=8 Identities=38% Similarity=1.128 Sum_probs=3.0
Q ss_pred CCCCCccc
Q psy12023 33 CPQCPYRA 40 (55)
Q Consensus 33 c~~c~~~f 40 (55)
|++|+...
T Consensus 2 CP~C~s~l 9 (28)
T PF03119_consen 2 CPVCGSKL 9 (28)
T ss_dssp -TTT--BE
T ss_pred cCCCCCEe
Confidence 66776543
No 305
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=26.94 E-value=40 Score=12.48 Aligned_cols=14 Identities=29% Similarity=0.762 Sum_probs=9.1
Q ss_pred CccccccccchhhH
Q psy12023 4 CDVCGKGYKYKNGI 17 (55)
Q Consensus 4 c~~c~~~~~~~~~~ 17 (55)
|-.||..+.....|
T Consensus 30 C~~Cg~~Y~d~~dL 43 (55)
T PF13821_consen 30 CFWCGTKYDDEEDL 43 (55)
T ss_pred eeeeCCccCCHHHH
Confidence 55677777666555
No 306
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=26.91 E-value=36 Score=12.14 Aligned_cols=13 Identities=23% Similarity=0.506 Sum_probs=9.2
Q ss_pred ccCCCCCcccccc
Q psy12023 31 YQCPQCPYRAKQN 43 (55)
Q Consensus 31 ~~c~~c~~~f~~~ 43 (55)
..|..|+..|...
T Consensus 41 ~~C~~C~~~fC~~ 53 (64)
T PF01485_consen 41 VTCPSCGTEFCFK 53 (64)
T ss_dssp CCTTSCCSEECSS
T ss_pred eECCCCCCcCccc
Confidence 5788888777543
No 307
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=26.90 E-value=43 Score=15.02 Aligned_cols=10 Identities=30% Similarity=1.006 Sum_probs=7.8
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
|.|..|+...
T Consensus 52 ~~C~~C~~~~ 61 (166)
T cd04476 52 YRCEKCNKSV 61 (166)
T ss_pred EECCCCCCcC
Confidence 8888888764
No 308
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=26.82 E-value=41 Score=11.32 Aligned_cols=11 Identities=27% Similarity=0.639 Sum_probs=4.2
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
|=|+.|..-|.
T Consensus 4 yyCdyC~~~~~ 14 (38)
T PF06220_consen 4 YYCDYCKKYLT 14 (38)
T ss_dssp -B-TTT--B-S
T ss_pred eecccccceec
Confidence 66777777774
No 309
>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=26.74 E-value=6.5 Score=20.23 Aligned_cols=12 Identities=25% Similarity=0.794 Sum_probs=4.3
Q ss_pred CCCccCCCCCcc
Q psy12023 28 EPKYQCPQCPYR 39 (55)
Q Consensus 28 ~~~~~c~~c~~~ 39 (55)
+..|+|..|+..
T Consensus 283 KRFFkC~~C~~R 294 (344)
T PF09332_consen 283 KRFFKCKDCGNR 294 (344)
T ss_dssp -EEEE-T-TS-E
T ss_pred eeeEECCCCCCe
Confidence 444556666653
No 310
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=26.53 E-value=34 Score=11.31 Aligned_cols=8 Identities=50% Similarity=1.065 Sum_probs=2.4
Q ss_pred CCCCCccc
Q psy12023 33 CPQCPYRA 40 (55)
Q Consensus 33 c~~c~~~f 40 (55)
|+.||...
T Consensus 3 C~~CG~~l 10 (34)
T PF14803_consen 3 CPQCGGPL 10 (34)
T ss_dssp -TTT--B-
T ss_pred cccccChh
Confidence 56666543
No 311
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.50 E-value=28 Score=15.10 Aligned_cols=13 Identities=8% Similarity=-0.062 Sum_probs=10.0
Q ss_pred CccCCCCCccccc
Q psy12023 30 KYQCPQCPYRAKQ 42 (55)
Q Consensus 30 ~~~c~~c~~~f~~ 42 (55)
|..|+.||++|..
T Consensus 26 PiVsPytG~s~P~ 38 (129)
T COG4530 26 PIVSPYTGKSYPR 38 (129)
T ss_pred ccccCcccccchH
Confidence 4888889998843
No 312
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=26.31 E-value=19 Score=13.38 Aligned_cols=15 Identities=13% Similarity=0.233 Sum_probs=8.3
Q ss_pred ccCCCCCcccccchH
Q psy12023 31 YQCPQCPYRAKQNAH 45 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~ 45 (55)
+....|+..|...+-
T Consensus 25 V~s~~C~H~fek~aI 39 (57)
T PF11789_consen 25 VKSKKCGHTFEKEAI 39 (57)
T ss_dssp EEESSS--EEEHHHH
T ss_pred cCcCCCCCeecHHHH
Confidence 666677777765543
No 313
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.27 E-value=41 Score=13.08 Aligned_cols=12 Identities=25% Similarity=0.567 Sum_probs=8.5
Q ss_pred ccCCCCCccccc
Q psy12023 31 YQCPQCPYRAKQ 42 (55)
Q Consensus 31 ~~c~~c~~~f~~ 42 (55)
..|+.||+..-+
T Consensus 8 v~CP~Cgkpv~w 19 (65)
T COG3024 8 VPCPTCGKPVVW 19 (65)
T ss_pred ccCCCCCCcccc
Confidence 678889885543
No 314
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=26.20 E-value=31 Score=14.22 Aligned_cols=12 Identities=17% Similarity=0.393 Sum_probs=9.4
Q ss_pred ccCCCCCccccc
Q psy12023 31 YQCPQCPYRAKQ 42 (55)
Q Consensus 31 ~~c~~c~~~f~~ 42 (55)
+.|..||+.+.-
T Consensus 74 ~~C~~Cg~i~~~ 85 (116)
T cd07153 74 LICTKCGKVIDF 85 (116)
T ss_pred eEeCCCCCEEEe
Confidence 779999987653
No 315
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=26.16 E-value=41 Score=11.47 Aligned_cols=10 Identities=40% Similarity=0.886 Sum_probs=6.1
Q ss_pred CCcccccccc
Q psy12023 3 MCDVCGKGYK 12 (55)
Q Consensus 3 ~c~~c~~~~~ 12 (55)
.|..||..+.
T Consensus 4 ~C~~Cg~~l~ 13 (47)
T PF13005_consen 4 ACPDCGGELK 13 (47)
T ss_pred cCCCCCceee
Confidence 4666766555
No 316
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=26.07 E-value=46 Score=11.89 Aligned_cols=13 Identities=23% Similarity=0.690 Sum_probs=9.4
Q ss_pred ccCCCCCcccccc
Q psy12023 31 YQCPQCPYRAKQN 43 (55)
Q Consensus 31 ~~c~~c~~~f~~~ 43 (55)
..|+.|+..|...
T Consensus 41 v~C~~C~~~fC~~ 53 (64)
T smart00647 41 VTCPKCGFSFCFR 53 (64)
T ss_pred eECCCCCCeECCC
Confidence 7787788877653
No 317
>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=25.99 E-value=42 Score=11.17 Aligned_cols=11 Identities=27% Similarity=0.643 Sum_probs=5.6
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
..|..||-.++
T Consensus 22 isC~~CGPr~~ 32 (35)
T PF07503_consen 22 ISCTNCGPRYS 32 (35)
T ss_dssp --BTTCC-SCC
T ss_pred ccCCCCCCCEE
Confidence 55778886654
No 318
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=25.40 E-value=44 Score=15.91 Aligned_cols=12 Identities=17% Similarity=0.293 Sum_probs=9.1
Q ss_pred ccCCCCCccccc
Q psy12023 31 YQCPQCPYRAKQ 42 (55)
Q Consensus 31 ~~c~~c~~~f~~ 42 (55)
-+|.+|+..|.-
T Consensus 7 rKCKvCg~~F~P 18 (189)
T PF05766_consen 7 RKCKVCGEWFVP 18 (189)
T ss_pred CcCcccCCcccc
Confidence 678888887754
No 319
>smart00507 HNHc HNH nucleases.
Probab=25.34 E-value=43 Score=11.01 Aligned_cols=11 Identities=27% Similarity=0.425 Sum_probs=7.3
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
+.|..|+..+.
T Consensus 11 ~~C~~C~~~~~ 21 (52)
T smart00507 11 GVCAYCGKPAS 21 (52)
T ss_pred CCCcCCcCCCC
Confidence 46777877653
No 320
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=25.32 E-value=21 Score=19.64 Aligned_cols=38 Identities=21% Similarity=0.421 Sum_probs=19.2
Q ss_pred CCccccccccchhhHHhHHHH-HhCCCCCccCCCCCcccc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKF-ECGQEPKYQCPQCPYRAK 41 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~-~~~~~~~~~c~~c~~~f~ 41 (55)
.|..||..+.-...-...... ...... |.|+.||....
T Consensus 202 pCPhCg~~~~l~~~~l~w~~~~~~~~a~-y~C~~Cg~~i~ 240 (557)
T PF05876_consen 202 PCPHCGEEQVLEWENLKWDKGEAPETAR-YVCPHCGCEIE 240 (557)
T ss_pred cCCCCCCCccccccceeecCCCCccceE-EECCCCcCCCC
Confidence 588888766543211111000 111123 88988887654
No 321
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=25.29 E-value=1e+02 Score=15.46 Aligned_cols=11 Identities=27% Similarity=0.606 Sum_probs=7.0
Q ss_pred CCccccccccc
Q psy12023 3 MCDVCGKGYKY 13 (55)
Q Consensus 3 ~c~~c~~~~~~ 13 (55)
.|..|+..+..
T Consensus 139 ~C~~C~~~~~~ 149 (271)
T PTZ00409 139 RCCTCRKTIQL 149 (271)
T ss_pred eeCCCCCCccc
Confidence 47777766553
No 322
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=25.14 E-value=38 Score=12.95 Aligned_cols=10 Identities=50% Similarity=1.245 Sum_probs=6.0
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
|.|+ ||-.|-
T Consensus 23 yPCP-CGDRFe 32 (67)
T COG5216 23 YPCP-CGDRFE 32 (67)
T ss_pred ecCC-CCCEeE
Confidence 4455 777664
No 323
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=25.09 E-value=63 Score=12.81 Aligned_cols=18 Identities=11% Similarity=0.351 Sum_probs=14.1
Q ss_pred CCCCcccccchHHHHHHH
Q psy12023 34 PQCPYRAKQNAHLTTHMA 51 (55)
Q Consensus 34 ~~c~~~f~~~~~l~~h~~ 51 (55)
.-||+.|+....+..++.
T Consensus 34 sP~GkklRs~~ev~~YL~ 51 (77)
T smart00391 34 SPCGKKLRSKSELARYLH 51 (77)
T ss_pred CCCCCeeeCHHHHHHHHH
Confidence 459999998888887754
No 324
>TIGR00009 L28 ribosomal protein L28. This model describes bacterial and chloroplast forms of the 50S ribosomal protein L28, a polypeptide about 60 amino acids in length. Mitochondrial homologs differ substantially in architecture and are not included.
Probab=25.04 E-value=30 Score=12.82 Aligned_cols=9 Identities=11% Similarity=0.235 Sum_probs=6.3
Q ss_pred cCCCCCccc
Q psy12023 32 QCPQCPYRA 40 (55)
Q Consensus 32 ~c~~c~~~f 40 (55)
.|++||+.-
T Consensus 4 ~C~i~GK~~ 12 (56)
T TIGR00009 4 KCQLTGKGP 12 (56)
T ss_pred EeeeCCCcC
Confidence 588888743
No 325
>PF15616 TerY-C: TerY-C metal binding domain
Probab=24.12 E-value=12 Score=16.55 Aligned_cols=8 Identities=38% Similarity=0.991 Sum_probs=4.2
Q ss_pred ccCCCCCc
Q psy12023 31 YQCPQCPY 38 (55)
Q Consensus 31 ~~c~~c~~ 38 (55)
..|+.|++
T Consensus 106 ~~CPwCg~ 113 (131)
T PF15616_consen 106 VTCPWCGN 113 (131)
T ss_pred EECCCCCC
Confidence 45555554
No 326
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=24.01 E-value=55 Score=13.81 Aligned_cols=11 Identities=36% Similarity=0.724 Sum_probs=8.2
Q ss_pred CccCCCCCccc
Q psy12023 30 KYQCPQCPYRA 40 (55)
Q Consensus 30 ~~~c~~c~~~f 40 (55)
+..|..||...
T Consensus 20 ~V~C~nCgr~v 30 (95)
T PRK09335 20 YVQCDNCGRRV 30 (95)
T ss_pred cEEeCCCCCcC
Confidence 37899998643
No 327
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=24.00 E-value=35 Score=17.96 Aligned_cols=10 Identities=30% Similarity=1.132 Sum_probs=6.2
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
+.|+.||..+
T Consensus 266 wrCpkCGg~i 275 (403)
T COG1379 266 WRCPKCGGKI 275 (403)
T ss_pred ccCcccccch
Confidence 5666676644
No 328
>PLN00186 ribosomal protein S26; Provisional
Probab=23.99 E-value=56 Score=14.16 Aligned_cols=11 Identities=18% Similarity=0.661 Sum_probs=8.3
Q ss_pred CccCCCCCccc
Q psy12023 30 KYQCPQCPYRA 40 (55)
Q Consensus 30 ~~~c~~c~~~f 40 (55)
+..|..||+..
T Consensus 20 ~V~C~nCgr~v 30 (109)
T PLN00186 20 RIRCSNCGKCV 30 (109)
T ss_pred ceeeCCCcccc
Confidence 48899998644
No 329
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=23.84 E-value=34 Score=12.05 Aligned_cols=11 Identities=27% Similarity=0.700 Sum_probs=7.6
Q ss_pred CCccccccccc
Q psy12023 3 MCDVCGKGYKY 13 (55)
Q Consensus 3 ~c~~c~~~~~~ 13 (55)
.|..||..+..
T Consensus 7 ~C~~CG~~m~~ 17 (58)
T PF13408_consen 7 RCGHCGSKMTR 17 (58)
T ss_pred EcccCCcEeEE
Confidence 47788877654
No 330
>KOG4602|consensus
Probab=23.73 E-value=41 Score=17.01 Aligned_cols=9 Identities=44% Similarity=1.147 Sum_probs=7.5
Q ss_pred ccCCCCCcc
Q psy12023 31 YQCPQCPYR 39 (55)
Q Consensus 31 ~~c~~c~~~ 39 (55)
|.|++||.+
T Consensus 269 YVCPiCGAT 277 (318)
T KOG4602|consen 269 YVCPICGAT 277 (318)
T ss_pred hcCcccccc
Confidence 889999865
No 331
>KOG1818|consensus
Probab=23.72 E-value=41 Score=19.21 Aligned_cols=10 Identities=20% Similarity=0.454 Sum_probs=4.3
Q ss_pred cCCCCCcccc
Q psy12023 32 QCPQCPYRAK 41 (55)
Q Consensus 32 ~c~~c~~~f~ 41 (55)
.|..||..|.
T Consensus 183 HCr~CG~vFC 192 (634)
T KOG1818|consen 183 HCRNCGQVFC 192 (634)
T ss_pred cccccchhhc
Confidence 4444444443
No 332
>TIGR00598 rad14 DNA repair protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.70 E-value=25 Score=16.43 Aligned_cols=10 Identities=40% Similarity=0.999 Sum_probs=5.7
Q ss_pred Cccccccccc
Q psy12023 4 CDVCGKGYKY 13 (55)
Q Consensus 4 c~~c~~~~~~ 13 (55)
|..||..|..
T Consensus 1 C~eCg~~~~D 10 (172)
T TIGR00598 1 CEECGKIFMD 10 (172)
T ss_pred Cccccchhhh
Confidence 5567765543
No 333
>PTZ00157 60S ribosomal protein L36a; Provisional
Probab=23.49 E-value=32 Score=14.12 Aligned_cols=10 Identities=20% Similarity=0.863 Sum_probs=7.3
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
++|..|++..
T Consensus 70 l~C~~C~~~~ 79 (84)
T PTZ00157 70 LECTKCKSKR 79 (84)
T ss_pred EEecccCcee
Confidence 7788887653
No 334
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=23.46 E-value=44 Score=12.79 Aligned_cols=11 Identities=18% Similarity=0.407 Sum_probs=7.8
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
-.|.+||++..
T Consensus 9 ~HC~VCg~aIp 19 (64)
T COG4068 9 RHCVVCGKAIP 19 (64)
T ss_pred ccccccCCcCC
Confidence 35888988653
No 335
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=23.43 E-value=33 Score=14.38 Aligned_cols=13 Identities=23% Similarity=0.606 Sum_probs=8.2
Q ss_pred ccCCCCCcccccc
Q psy12023 31 YQCPQCPYRAKQN 43 (55)
Q Consensus 31 ~~c~~c~~~f~~~ 43 (55)
+.|..||+.+.-.
T Consensus 81 ~iC~~Cg~v~~~~ 93 (120)
T PF01475_consen 81 FICTQCGKVIDLD 93 (120)
T ss_dssp EEETTTS-EEEE-
T ss_pred EEECCCCCEEEec
Confidence 6788999876543
No 336
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=23.20 E-value=50 Score=12.14 Aligned_cols=9 Identities=44% Similarity=0.947 Sum_probs=4.1
Q ss_pred cCCCCCccc
Q psy12023 32 QCPQCPYRA 40 (55)
Q Consensus 32 ~c~~c~~~f 40 (55)
.|+-||..+
T Consensus 2 ~CPyCge~~ 10 (52)
T PF14255_consen 2 QCPYCGEPI 10 (52)
T ss_pred CCCCCCCee
Confidence 344555433
No 337
>KOG0782|consensus
Probab=23.14 E-value=28 Score=19.83 Aligned_cols=28 Identities=21% Similarity=0.354 Sum_probs=14.8
Q ss_pred hHHhHHHHHhCCCCCccCCCCCcccccch
Q psy12023 16 GIYRHKKFECGQEPKYQCPQCPYRAKQNA 44 (55)
Q Consensus 16 ~~~~~~~~~~~~~~~~~c~~c~~~f~~~~ 44 (55)
.+.+|.=+|..... -+|..|++.|.+.-
T Consensus 240 ~fvrHHWVHrrRqe-GkC~~CgKgFQQKf 267 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQE-GKCNTCGKGFQQKF 267 (1004)
T ss_pred cchHHhHhhHhhhc-cccchhhhhhhhhe
Confidence 44444444443222 36777777776553
No 338
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=23.13 E-value=55 Score=16.64 Aligned_cols=11 Identities=27% Similarity=0.848 Sum_probs=6.6
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
+.|+.|+.-|.
T Consensus 47 ~vc~~c~~h~r 57 (292)
T PRK05654 47 NVCPKCGHHMR 57 (292)
T ss_pred CCCCCCCCCee
Confidence 46666666554
No 339
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=23.00 E-value=28 Score=12.93 Aligned_cols=19 Identities=26% Similarity=0.606 Sum_probs=12.1
Q ss_pred ccCCCCCcccccc---hHHHHH
Q psy12023 31 YQCPQCPYRAKQN---AHLTTH 49 (55)
Q Consensus 31 ~~c~~c~~~f~~~---~~l~~h 49 (55)
+.|-.|+..+... .....|
T Consensus 12 w~CL~Cg~~~C~~~~~~Ha~~H 33 (63)
T PF02148_consen 12 WLCLTCGYVGCGRYSNGHALKH 33 (63)
T ss_dssp EEETTTS-EEETTTSTSHHHHH
T ss_pred EEeCCCCcccccCCcCcHHHHh
Confidence 8888898877654 344444
No 340
>COG0271 BolA Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]
Probab=22.86 E-value=54 Score=13.59 Aligned_cols=26 Identities=8% Similarity=0.147 Sum_probs=19.8
Q ss_pred CCCCCccCCCCCcccccchHHHHHHHh
Q psy12023 26 GQEPKYQCPQCPYRAKQNAHLTTHMAI 52 (55)
Q Consensus 26 ~~~~~~~c~~c~~~f~~~~~l~~h~~~ 52 (55)
++.. |...+....|.-.+-+.+|+.+
T Consensus 37 ~~~H-f~i~IVS~~F~G~s~v~rHr~V 62 (90)
T COG0271 37 GGSH-FKVVIVSEAFQGKSLVARHRLV 62 (90)
T ss_pred CCCe-EEEEEEchhhCCccHHHHHHHH
Confidence 3445 7777788899999999998764
No 341
>PHA02942 putative transposase; Provisional
Probab=22.85 E-value=77 Score=16.77 Aligned_cols=14 Identities=29% Similarity=1.016 Sum_probs=10.2
Q ss_pred CCCccCCCCCccccc
Q psy12023 28 EPKYQCPQCPYRAKQ 42 (55)
Q Consensus 28 ~~~~~c~~c~~~f~~ 42 (55)
+. |.|..||.....
T Consensus 341 r~-f~C~~CG~~~dr 354 (383)
T PHA02942 341 RY-FHCPSCGYENDR 354 (383)
T ss_pred CE-EECCCCCCEeCc
Confidence 44 999999976543
No 342
>KOG2747|consensus
Probab=22.80 E-value=49 Score=17.74 Aligned_cols=22 Identities=32% Similarity=0.522 Sum_probs=10.7
Q ss_pred CCccccccccchhhHHhHHHHH
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFE 24 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~ 24 (55)
.|+.|=+-+.....+..|+...
T Consensus 160 iCEfCLkY~~s~~~l~rH~~kC 181 (396)
T KOG2747|consen 160 ICEFCLKYMKSRTSLQRHLKKC 181 (396)
T ss_pred EehHHHhHhchHHHHHHHHHhc
Confidence 3444444444555555555443
No 343
>smart00746 TRASH metallochaperone-like domain.
Probab=22.71 E-value=40 Score=9.71 Aligned_cols=6 Identities=17% Similarity=0.296 Sum_probs=2.6
Q ss_pred CCCCcc
Q psy12023 34 PQCPYR 39 (55)
Q Consensus 34 ~~c~~~ 39 (55)
..|+..
T Consensus 2 ~~C~~~ 7 (39)
T smart00746 2 SFCGKD 7 (39)
T ss_pred CCCCCC
Confidence 344443
No 344
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=22.59 E-value=47 Score=16.22 Aligned_cols=11 Identities=45% Similarity=1.050 Sum_probs=7.9
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
+.|++|+..+.
T Consensus 3 ~~CP~C~~~l~ 13 (272)
T PRK11088 3 YQCPLCHQPLT 13 (272)
T ss_pred ccCCCCCcchh
Confidence 67888887663
No 345
>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=22.42 E-value=31 Score=13.06 Aligned_cols=11 Identities=27% Similarity=0.745 Sum_probs=8.7
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
..|+.|+..|.
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 67888988764
No 346
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=22.26 E-value=54 Score=11.30 Aligned_cols=6 Identities=33% Similarity=0.938 Sum_probs=2.5
Q ss_pred CCCCCc
Q psy12023 33 CPQCPY 38 (55)
Q Consensus 33 c~~c~~ 38 (55)
|+.|++
T Consensus 3 C~~C~~ 8 (46)
T cd02249 3 CDGCLK 8 (46)
T ss_pred CcCCCC
Confidence 444443
No 347
>PRK05767 rpl44e 50S ribosomal protein L44e; Validated
Probab=22.14 E-value=33 Score=14.33 Aligned_cols=12 Identities=25% Similarity=0.850 Sum_probs=8.7
Q ss_pred ccCCCCCccccc
Q psy12023 31 YQCPQCPYRAKQ 42 (55)
Q Consensus 31 ~~c~~c~~~f~~ 42 (55)
++|..|++....
T Consensus 68 ~~C~~C~~~~~~ 79 (92)
T PRK05767 68 YRCTECGKAHTR 79 (92)
T ss_pred EEecccChhhcc
Confidence 789889876543
No 348
>PLN02569 threonine synthase
Probab=22.01 E-value=68 Score=17.59 Aligned_cols=9 Identities=33% Similarity=0.911 Sum_probs=4.5
Q ss_pred CCccccccc
Q psy12023 3 MCDVCGKGY 11 (55)
Q Consensus 3 ~c~~c~~~~ 11 (55)
.|..||+.+
T Consensus 51 ~C~~Cg~~y 59 (484)
T PLN02569 51 ECPLTGEKY 59 (484)
T ss_pred EeCCCCCcC
Confidence 355555544
No 349
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=21.99 E-value=73 Score=14.91 Aligned_cols=19 Identities=21% Similarity=0.728 Sum_probs=8.8
Q ss_pred cCCCCCcccccchHHHHHH
Q psy12023 32 QCPQCPYRAKQNAHLTTHM 50 (55)
Q Consensus 32 ~c~~c~~~f~~~~~l~~h~ 50 (55)
.|..|....-....+..|.
T Consensus 2 ~Cs~CKfrtf~~~ei~~Hl 20 (165)
T PF04988_consen 2 TCSFCKFRTFEEKEIEKHL 20 (165)
T ss_pred ccceeeeecccHHHHHHHH
Confidence 3555554433444444443
No 350
>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=21.84 E-value=1.1e+02 Score=14.54 Aligned_cols=33 Identities=18% Similarity=0.391 Sum_probs=15.9
Q ss_pred CCccccccccchhhHHhHHHHHhCCCCCccCCCCCcc
Q psy12023 3 MCDVCGKGYKYKNGIYRHKKFECGQEPKYQCPQCPYR 39 (55)
Q Consensus 3 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~ 39 (55)
.|..|+..+....... .....+.. -.|+.|+..
T Consensus 97 ~C~~C~~~~~~~~~~~---~~~~~~~~-p~C~~Cgg~ 129 (206)
T cd01410 97 VCKSCGPEYVRDDVVE---TRGDKETG-RRCHACGGI 129 (206)
T ss_pred cCCCCCCccchHHHHH---HhhcCCCC-CcCCCCcCc
Confidence 4777776654332211 11112222 468888753
No 351
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 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 CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=21.81 E-value=42 Score=11.94 Aligned_cols=8 Identities=38% Similarity=0.820 Sum_probs=2.6
Q ss_pred ccCCCCCc
Q psy12023 31 YQCPQCPY 38 (55)
Q Consensus 31 ~~c~~c~~ 38 (55)
.+|..|+|
T Consensus 4 VQCd~C~K 11 (50)
T PF07496_consen 4 VQCDSCLK 11 (50)
T ss_dssp EE-TTT--
T ss_pred EECCCCCc
Confidence 34555554
No 352
>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=21.71 E-value=45 Score=14.20 Aligned_cols=8 Identities=38% Similarity=1.095 Sum_probs=6.1
Q ss_pred ccCCCCCc
Q psy12023 31 YQCPQCPY 38 (55)
Q Consensus 31 ~~c~~c~~ 38 (55)
|.|..|+.
T Consensus 32 y~C~~C~A 39 (102)
T PF11672_consen 32 YVCTPCDA 39 (102)
T ss_pred EECCCCCc
Confidence 78888864
No 353
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.65 E-value=31 Score=16.42 Aligned_cols=11 Identities=18% Similarity=0.803 Sum_probs=6.9
Q ss_pred CCCcccccccc
Q psy12023 2 FMCDVCGKGYK 12 (55)
Q Consensus 2 ~~c~~c~~~~~ 12 (55)
|+|..|++.+.
T Consensus 50 YkC~~Cd~tWN 60 (203)
T COG4332 50 YKCTHCDYTWN 60 (203)
T ss_pred EEeeccCCccc
Confidence 56777776654
No 354
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=21.20 E-value=51 Score=12.08 Aligned_cols=9 Identities=33% Similarity=1.102 Sum_probs=5.9
Q ss_pred ccCCCCCcc
Q psy12023 31 YQCPQCPYR 39 (55)
Q Consensus 31 ~~c~~c~~~ 39 (55)
-.|+.||..
T Consensus 14 ~~Cp~CGN~ 22 (49)
T PF12677_consen 14 CKCPKCGND 22 (49)
T ss_pred ccCcccCCc
Confidence 358888753
No 355
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=21.15 E-value=65 Score=13.95 Aligned_cols=11 Identities=18% Similarity=0.558 Sum_probs=8.3
Q ss_pred CccCCCCCccc
Q psy12023 30 KYQCPQCPYRA 40 (55)
Q Consensus 30 ~~~c~~c~~~f 40 (55)
+..|..||...
T Consensus 20 ~V~C~nCgr~v 30 (108)
T PTZ00172 20 PVRCSNCGRCV 30 (108)
T ss_pred cEEeCCccccc
Confidence 48899998644
No 356
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.03 E-value=47 Score=12.82 Aligned_cols=11 Identities=36% Similarity=0.908 Sum_probs=8.2
Q ss_pred ccCCCCCcccc
Q psy12023 31 YQCPQCPYRAK 41 (55)
Q Consensus 31 ~~c~~c~~~f~ 41 (55)
..|+-|+..|.
T Consensus 49 v~CPYC~t~y~ 59 (62)
T COG4391 49 VVCPYCSTRYR 59 (62)
T ss_pred EecCccccEEE
Confidence 56888887775
No 357
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=21.00 E-value=65 Score=14.60 Aligned_cols=14 Identities=29% Similarity=0.662 Sum_probs=10.4
Q ss_pred cCCCCCcccccchH
Q psy12023 32 QCPQCPYRAKQNAH 45 (55)
Q Consensus 32 ~c~~c~~~f~~~~~ 45 (55)
.|++|.-+|+.++.
T Consensus 123 vCPvCkTSFKss~~ 136 (140)
T PF05290_consen 123 VCPVCKTSFKSSSS 136 (140)
T ss_pred CCCccccccccccc
Confidence 68888888876643
No 358
>KOG0562|consensus
Probab=20.71 E-value=98 Score=14.68 Aligned_cols=8 Identities=25% Similarity=0.576 Sum_probs=3.7
Q ss_pred hHHHHHHH
Q psy12023 44 AHLTTHMA 51 (55)
Q Consensus 44 ~~l~~h~~ 51 (55)
+-|+.|.+
T Consensus 167 ~kLK~Hl~ 174 (184)
T KOG0562|consen 167 PKLKAHLR 174 (184)
T ss_pred HHHHHHHH
Confidence 34444444
No 359
>PRK00359 rpmB 50S ribosomal protein L28; Reviewed
Probab=20.59 E-value=50 Score=13.13 Aligned_cols=10 Identities=10% Similarity=0.032 Sum_probs=6.6
Q ss_pred ccCCCCCccc
Q psy12023 31 YQCPQCPYRA 40 (55)
Q Consensus 31 ~~c~~c~~~f 40 (55)
-.|++||+.-
T Consensus 3 r~C~i~GK~~ 12 (76)
T PRK00359 3 RVCEITGKGP 12 (76)
T ss_pred CccccCCCCC
Confidence 3678888743
No 360
>PF03226 Yippee-Mis18: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; InterPro: IPR004910 This entry represents the Yippee-like (YPEL) family of putative zinc-binding proteins which is highly conserved among eukaryotes. The first protein in this family to be characterised, the Yippee protein from Drosophila, was identified by yeast interaction trap screen as a protein that physically interacts with moth hemolin []. It was subsequently found to be a member of a highly conserved family of proteins found in diverse eukaryotes including plants, animals and fungi []. Mammals contain five members of this family, YPEL1 to YPEL5, while other organisms tend to contain only two or three members. The mammalian proteins all appear to localise in the nucleus. YPEL1-4 are located in an unknown structure located on or close to the mitotic apparatus in the mitotic phase, whereas in the interphase they are located in the nuclei and nucleoli. In contrast, YPEL5 is localised to the centrosome and nucleus during interphase and at the mitotic spindle during mitosis, suggesting a function distinct from that of YPEL1-4. The localisation of the YPEL proteins suggests a novel, thopugh still unknown, function involved in cell division.
Probab=20.59 E-value=80 Score=12.77 Aligned_cols=16 Identities=25% Similarity=0.632 Sum_probs=8.0
Q ss_pred ccCCCCCcccccchHH
Q psy12023 31 YQCPQCPYRAKQNAHL 46 (55)
Q Consensus 31 ~~c~~c~~~f~~~~~l 46 (55)
|.|..|...+..+..+
T Consensus 3 f~C~~C~t~l~ds~~l 18 (96)
T PF03226_consen 3 FQCKNCKTILADSNEL 18 (96)
T ss_pred EECCCCCCCcCCHHHh
Confidence 4555555554444433
No 361
>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=20.46 E-value=72 Score=11.84 Aligned_cols=18 Identities=6% Similarity=0.311 Sum_probs=13.4
Q ss_pred CCCCcccccchHHHHHHH
Q psy12023 34 PQCPYRAKQNAHLTTHMA 51 (55)
Q Consensus 34 ~~c~~~f~~~~~l~~h~~ 51 (55)
.-||+.|+....+..++.
T Consensus 31 sP~Gk~~Rs~~ev~~yL~ 48 (62)
T cd00122 31 SPCGKKLRSKPEVARYLE 48 (62)
T ss_pred CCCCceecCHHHHHHHHH
Confidence 447888888888777654
No 362
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=20.01 E-value=47 Score=13.33 Aligned_cols=9 Identities=33% Similarity=1.202 Sum_probs=3.2
Q ss_pred CCCccCCCCC
Q psy12023 28 EPKYQCPQCP 37 (55)
Q Consensus 28 ~~~~~c~~c~ 37 (55)
+. |.|+.|+
T Consensus 21 ~~-F~CPfC~ 29 (81)
T PF05129_consen 21 KV-FDCPFCN 29 (81)
T ss_dssp S-----TTT-
T ss_pred ce-EcCCcCC
Confidence 44 8899998
Done!